Psyllid ID: psy986

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70-
Protein Sequence
MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFMVLTKTVYRLK
Secondary Structure (PSIPRED)
ccccccccccccHHHHHHHHccccHHHHHHHHHccEEEEEEccccccccccccccccccEEEEEEcccccc
Secondary Structure Prediction (SSPRO)
cccEEHHHEEcccHcccEEEcccccEEEEEEccccEEEEEEEccccccccccccccccEEEEEcccEEEcc
Coil and Loop (DISEMBL)
mleyseeslqvprnlvgkvigknGRIIQEIVDKSGVVrvkiegdnepqptlpreegqvpFMVLTKTVYRLK
Flexible Loop (DISEMBL)
mleyseeslqvprnlvgkvigkngriiqeivdksgvvrvkiegdnepqptlpreegqvpfmvltktvyrlk
Low Complexity Region (SEG)
MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFMVLTKTVYRLK
Disordered region (IsUnstruct)
*************NLVGKVIGKNGRIIQEIVDKSGVVRVKI******************FMVLTKTV****
Disordered Region (DISOPRED)
*LEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRV******************VPFMVLTKTV****
Disordered Region (DISEMBL)
MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFMVLTKTVYRLK
Disordered Region (DISPRO)
MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFMVLTKTVYRLK
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFMVLTKTVYRLK
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	71	2.2.26 [Sep-21-2011]
P51114	621	Fragile X mental retardat	no	N/A	0.859	0.098	0.714	6e-19
Q5XI81	568	Fragile X mental retardat	yes	N/A	0.859	0.107	0.714	6e-19
Q2TBT7	621	Fragile X mental retardat	yes	N/A	0.859	0.098	0.714	6e-19
P51116	673	Fragile X mental retardat	no	N/A	0.845	0.089	0.725	7e-19
P51115	676	Fragile X mental retardat	N/A	N/A	0.845	0.088	0.725	8e-19
Q61584	677	Fragile X mental retardat	no	N/A	0.859	0.090	0.714	8e-19
Q5BJ56	674	Fragile X mental retardat	yes	N/A	0.845	0.089	0.725	8e-19
Q7ZTQ5	675	Fragile X mental retardat	N/A	N/A	0.845	0.088	0.725	9e-19
O70523	621	Fragile X mental retardat	no	N/A	0.859	0.098	0.698	1e-18
Q9NFU0	684	Fragile X mental retardat	yes	N/A	0.887	0.092	0.666	2e-17

>sp|P51114|FXR1_HUMAN Fragile X mental retardation syndrome-related protein 1 OS=Homo sapiens GN=FXR1 PE=1 SV=3

 Score = 92.8 bits (229), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 55/63 (87%), Gaps = 2/63 (3%)

Query: 1   MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPF 60
            LE+ E+ +QVPRNLVGKVIGKNG++IQEIVDKSGVVRV+IEGDNE +  LPRE+G VPF
Sbjct: 278 FLEFVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENK--LPREDGMVPF 335

Query: 61  MVL 63
           + +
Sbjct: 336 VFV 338

RNA-binding protein required for embryonic and postnatal development of muscle tissue. May regulate intracellular transport and local translation of certain mRNAs.
Homo sapiens (taxid: 9606)

>sp|Q5XI81|FXR1_RAT Fragile X mental retardation syndrome-related protein 1 OS=Rattus norvegicus GN=Fxr1 PE=2 SV=1

 Score = 92.4 bits (228), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 55/63 (87%), Gaps = 2/63 (3%)

Query: 1   MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPF 60
            LE+ E+ +QVPRNLVGKVIGKNG++IQEIVDKSGVVRV+IEGDNE +  LPRE+G VPF
Sbjct: 278 FLEFVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENK--LPREDGMVPF 335

Query: 61  MVL 63
           + +
Sbjct: 336 VFV 338

RNA-binding protein required for embryonic and postnatal development of muscle tissue. May regulate intracellular transport and local translation of certain mRNAs.

Rattus norvegicus (taxid: 10116)

>sp|Q2TBT7|FXR1_BOVIN Fragile X mental retardation syndrome-related protein 1 OS=Bos taurus GN=FXR1 PE=2 SV=1

 Score = 92.4 bits (228), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 55/63 (87%), Gaps = 2/63 (3%)

Query: 1   MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPF 60
            LE+ E+ +QVPRNLVGKVIGKNG++IQEIVDKSGVVRV+IEGDNE +  LPRE+G VPF
Sbjct: 278 FLEFVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENK--LPREDGMVPF 335

Query: 61  MVL 63
           + +
Sbjct: 336 VFV 338

RNA-binding protein required for embryonic and postnatal development of muscle tissue. May regulate intracellular transport and local translation of certain mRNAs.

Bos taurus (taxid: 9913)

>sp|P51116|FXR2_HUMAN Fragile X mental retardation syndrome-related protein 2 OS=Homo sapiens GN=FXR2 PE=1 SV=2

 Score = 92.4 bits (228), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 45/62 (72%), Positives = 56/62 (90%), Gaps = 2/62 (3%)

Query: 2   LEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFM 61
           LE+SE+S+QVPRNLVGKVIGKNG++IQEIVDKSGVVRV++EGDN+ +   PREEG VPF+
Sbjct: 289 LEFSEDSVQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRVEGDNDKKN--PREEGMVPFI 346

Query: 62  VL 63
            +
Sbjct: 347 FV 348

RNA-binding protein.

Homo sapiens (taxid: 9606)

>sp|P51115|FXR1A_XENLA Fragile X mental retardation syndrome-related protein 1 homolog A OS=Xenopus laevis GN=fxr1-a PE=1 SV=2

 Score = 92.4 bits (228), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 45/62 (72%), Positives = 55/62 (88%), Gaps = 2/62 (3%)

Query: 2   LEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFM 61
           LE+ E+ +QVPRNLVGKVIGKNG++IQEIVDKSGVVRV+IEGDNE +  LPRE+G VPF+
Sbjct: 279 LEFVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNETK--LPREDGMVPFV 336

Query: 62  VL 63
            +
Sbjct: 337 FV 338

RNA-binding protein. Binds poly(G) and poly(U) but not poly(A) or poly(C). Regulates somite formation, probably by regulating gene expression.

Xenopus laevis (taxid: 8355)

>sp|Q61584|FXR1_MOUSE Fragile X mental retardation syndrome-related protein 1 OS=Mus musculus GN=Fxr1 PE=1 SV=2

 Score = 92.4 bits (228), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 55/63 (87%), Gaps = 2/63 (3%)

Query: 1   MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPF 60
            LE+ E+ +QVPRNLVGKVIGKNG++IQEIVDKSGVVRV+IEGDNE +  LPRE+G VPF
Sbjct: 278 FLEFVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENK--LPREDGMVPF 335

Query: 61  MVL 63
           + +
Sbjct: 336 VFV 338

RNA-binding protein required for embryonic and postnatal development of muscle tissue. May regulate intracellular transport and local translation of certain mRNAs.

Mus musculus (taxid: 10090)

>sp|Q5BJ56|FXR1_XENTR Fragile X mental retardation syndrome-related protein 1 homolog OS=Xenopus tropicalis GN=fxr1 PE=2 SV=2

 Score = 92.0 bits (227), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 45/62 (72%), Positives = 55/62 (88%), Gaps = 2/62 (3%)

Query: 2   LEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFM 61
           LE+ E+ +QVPRNLVGKVIGKNG++IQEIVDKSGVVRV+IEGDNE +  LPRE+G VPF+
Sbjct: 279 LEFVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNETK--LPREDGMVPFV 336

Query: 62  VL 63
            +
Sbjct: 337 FV 338

RNA-binding protein. Binds poly(G) and poly(U) but not poly(A) or poly(C). Regulates somite formation, probably by regulating gene expression.

Xenopus tropicalis (taxid: 8364)

>sp|Q7ZTQ5|FXR1B_XENLA Fragile X mental retardation syndrome-related protein 1 homolog B OS=Xenopus laevis GN=fxr1-b PE=2 SV=1

 Score = 92.0 bits (227), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 45/62 (72%), Positives = 55/62 (88%), Gaps = 2/62 (3%)

Query: 2   LEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFM 61
           LE+ E+ +QVPRNLVGKVIGKNG++IQEIVDKSGVVRV+IEGDNE +  LPRE+G VPF+
Sbjct: 279 LEFVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNETK--LPREDGMVPFV 336

Query: 62  VL 63
            +
Sbjct: 337 FV 338

RNA-binding protein. Binds poly(G) and poly(U) but not poly(A) or poly(C). Regulates somite formation, probably by regulating gene expression.

Xenopus laevis (taxid: 8355)

>sp|O70523|FXR1_CRIGR Fragile X mental retardation syndrome-related protein 1 OS=Cricetulus griseus GN=FXR1 PE=2 SV=1

 Score = 91.7 bits (226), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 2/63 (3%)

Query: 1   MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPF 60
            +E+ E+ +QVPRNLVGKVIGKNG++IQEIVDKSGVVRV+IEGDNE +  LPRE+G VPF
Sbjct: 278 FMEFVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENK--LPREDGMVPF 335

Query: 61  MVL 63
           + +
Sbjct: 336 VFV 338

RNA-binding protein required for embryonic and postnatal development of muscle tissue. May regulate intracellular transport and local translation of certain mRNAs.

Cricetulus griseus (taxid: 10029)

>sp|Q9NFU0|FMR1_DROME Fragile X mental retardation syndrome-related protein 1 OS=Drosophila melanogaster GN=Fmr1 PE=1 SV=1

 Score = 87.8 bits (216), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 44/66 (66%), Positives = 50/66 (75%), Gaps = 3/66 (4%)

Query: 1   MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVK---IEGDNEPQPTLPREEGQ 57
           MLEY+EE  QVPR LVGKVIGKNGRIIQEIVDKSGV R+K   I GD+E    +PRE   
Sbjct: 281 MLEYAEEFFQVPRELVGKVIGKNGRIIQEIVDKSGVFRIKVSAIAGDDEQDQNIPRELAH 340

Query: 58  VPFMVL 63
           VPF+ +
Sbjct: 341 VPFVFI 346

RNA-binding protein that associates with translating ribosomes and acts as a negative translational regulator of specific mRNAs. Represses translation of futsch to regulate microtubule-dependent synaptic growth and function. Part of the RNA interference (RNAi)-related apparatus; double-stranded RNA induces potent and specific gene silencing. Regulates photoreceptor structure and neurotransmission in the eye. Required for stability of the central pair of microtubules in the spermatid axoneme.

Drosophila melanogaster (taxid: 7227)

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	71
157122825	717	fragile X mental retardation syndrome-re	0.887	0.087	0.904	6e-26
189235654	660	PREDICTED: similar to fragile X mental r	0.887	0.095	0.920	2e-25
270004423	677	hypothetical protein TcasGA2_TC003774 [T	0.887	0.093	0.920	2e-25
312374565	282	hypothetical protein AND_15781 [Anophele	0.887	0.223	0.888	2e-25
332023074	599	Fragile X mental retardation syndrome-re	0.887	0.105	0.904	1e-24
307203416	603	Fragile X mental retardation syndrome-re	0.887	0.104	0.904	1e-24
345493180	613	PREDICTED: fragile X mental retardation	0.887	0.102	0.904	1e-24
345493184	605	PREDICTED: fragile X mental retardation	0.887	0.104	0.904	2e-24
383859712	597	PREDICTED: fragile X mental retardation	0.887	0.105	0.888	2e-24
242018237	492	conserved hypothetical protein [Pediculu	0.887	0.128	0.888	2e-24

>gi|157122825|ref|XP_001659932.1| fragile X mental retardation syndrome-related protein 1, putative [Aedes aegypti] gi|108874593|gb|EAT38818.1| AAEL009326-PA [Aedes aegypti]

 Score =  121 bits (303), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 57/63 (90%), Positives = 62/63 (98%)

Query: 1   MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPF 60
           MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEP+P++PREEGQVPF
Sbjct: 273 MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPEPSIPREEGQVPF 332

Query: 61  MVL 63
           + +
Sbjct: 333 VFV 335

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189235654|ref|XP_969396.2| PREDICTED: similar to fragile X mental retardation syndrome-related protein 1, putative [Tribolium castaneum]

 Score =  120 bits (300), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 58/63 (92%), Positives = 61/63 (96%)

Query: 1   MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPF 60
           MLEYSEESLQVPR LVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT+PREEGQVPF
Sbjct: 279 MLEYSEESLQVPRALVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTIPREEGQVPF 338

Query: 61  MVL 63
           + +
Sbjct: 339 VFV 341

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270004423|gb|EFA00871.1| hypothetical protein TcasGA2_TC003774 [Tribolium castaneum]

 Score =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 58/63 (92%), Positives = 61/63 (96%)

Query: 1   MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPF 60
           MLEYSEESLQVPR LVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT+PREEGQVPF
Sbjct: 296 MLEYSEESLQVPRALVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTIPREEGQVPF 355

Query: 61  MVL 63
           + +
Sbjct: 356 VFV 358

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312374565|gb|EFR22095.1| hypothetical protein AND_15781 [Anopheles darlingi]

 Score =  119 bits (298), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 56/63 (88%), Positives = 62/63 (98%)

Query: 1   MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPF 60
           MLEY+EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEP+P++PREEGQVPF
Sbjct: 187 MLEYNEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPEPSIPREEGQVPF 246

Query: 61  MVL 63
           + +
Sbjct: 247 VFV 249

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332023074|gb|EGI63339.1| Fragile X mental retardation syndrome-related protein 1 [Acromyrmex echinatior]

 Score =  117 bits (293), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 57/63 (90%), Positives = 61/63 (96%)

Query: 1   MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPF 60
           MLEYSEES+QVPR LVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT+PREEGQVPF
Sbjct: 279 MLEYSEESIQVPRVLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTIPREEGQVPF 338

Query: 61  MVL 63
           + +
Sbjct: 339 VFV 341

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307203416|gb|EFN82491.1| Fragile X mental retardation syndrome-related protein 1 [Harpegnathos saltator]

 Score =  117 bits (293), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 57/63 (90%), Positives = 61/63 (96%)

Query: 1   MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPF 60
           MLEYSEES+QVPR LVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT+PREEGQVPF
Sbjct: 317 MLEYSEESIQVPRVLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTIPREEGQVPF 376

Query: 61  MVL 63
           + +
Sbjct: 377 VFV 379

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345493180|ref|XP_003427019.1| PREDICTED: fragile X mental retardation syndrome-related protein 1-like isoform 2 [Nasonia vitripennis]

 Score =  116 bits (291), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 57/63 (90%), Positives = 61/63 (96%)

Query: 1   MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPF 60
           MLEYSEES+QVPR LVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT+PREEGQVPF
Sbjct: 279 MLEYSEESIQVPRILVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTIPREEGQVPF 338

Query: 61  MVL 63
           + +
Sbjct: 339 VFV 341

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345493184|ref|XP_003427020.1| PREDICTED: fragile X mental retardation syndrome-related protein 1-like isoform 3 [Nasonia vitripennis]

 Score =  116 bits (291), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 57/63 (90%), Positives = 61/63 (96%)

Query: 1   MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPF 60
           MLEYSEES+QVPR LVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT+PREEGQVPF
Sbjct: 303 MLEYSEESIQVPRILVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTIPREEGQVPF 362

Query: 61  MVL 63
           + +
Sbjct: 363 VFV 365

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383859712|ref|XP_003705336.1| PREDICTED: fragile X mental retardation syndrome-related protein 1-like [Megachile rotundata]

 Score =  116 bits (291), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 56/63 (88%), Positives = 61/63 (96%)

Query: 1   MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPF 60
           MLEYSEES+QVPR LVGKVIGKNGR+IQEIVDKSGVVRVKIEGDNEPQPT+PREEGQVPF
Sbjct: 279 MLEYSEESIQVPRVLVGKVIGKNGRVIQEIVDKSGVVRVKIEGDNEPQPTIPREEGQVPF 338

Query: 61  MVL 63
           + +
Sbjct: 339 VFV 341

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242018237|ref|XP_002429585.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212514552|gb|EEB16847.1| conserved hypothetical protein [Pediculus humanus corporis]

 Score =  116 bits (290), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 56/63 (88%), Positives = 61/63 (96%)

Query: 1   MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPF 60
           MLEYSEES++VPR LVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT+PREEGQVPF
Sbjct: 280 MLEYSEESIKVPRVLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTIPREEGQVPF 339

Query: 61  MVL 63
           + +
Sbjct: 340 VFV 342

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	71
UNIPROTKB|E1B9L5	646	FXR2 "Uncharacterized protein"	0.816	0.089	0.75	1.5e-18
UNIPROTKB|F1M3Y6	654	Fxr2 "Protein Fxr2" [Rattus no	0.816	0.088	0.75	1.5e-18
UNIPROTKB|E2R2H9	672	FXR2 "Uncharacterized protein"	0.816	0.086	0.75	1.6e-18
UNIPROTKB|P51116	673	FXR2 "Fragile X mental retarda	0.816	0.086	0.75	1.6e-18
UNIPROTKB|F1ST39	673	FXR2 "Uncharacterized protein"	0.816	0.086	0.75	1.6e-18
UNIPROTKB|E7EU85	454	FXR1 "Fragile X mental retarda	0.873	0.136	0.723	1.7e-18
UNIPROTKB|E9PFF5	490	FXR1 "Fragile X mental retarda	0.873	0.126	0.723	2.1e-18
UNIPROTKB|A6QLG6	539	FXR1 "Fragile X mental retarda	0.873	0.115	0.723	2.7e-18
UNIPROTKB|F6XQE7	539	FXR1 "Uncharacterized protein"	0.873	0.115	0.723	2.7e-18
UNIPROTKB|F1SGB0	540	FXR1 "Uncharacterized protein"	0.873	0.114	0.723	2.7e-18

UNIPROTKB|E1B9L5 FXR2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 233 (87.1 bits), Expect = 1.5e-18, P = 1.5e-18
 Identities = 45/60 (75%), Positives = 55/60 (91%)

Query:     2 LEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFM 61
             LE+SE+S+QVPRNLVGKVIGKNG++IQEIVDKSGVVRV++EGDN+ +   PREEG VPF+
Sbjct:   262 LEFSEDSVQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRVEGDNDKKN--PREEGMVPFI 319

GO:0005737 "cytoplasm" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F1M3Y6 Fxr2 "Protein Fxr2" [Rattus norvegicus (taxid:10116)]

 Score = 233 (87.1 bits), Expect = 1.5e-18, P = 1.5e-18
 Identities = 45/60 (75%), Positives = 55/60 (91%)

Query:     2 LEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFM 61
             LE+SE+S+QVPRNLVGKVIGKNG++IQEIVDKSGVVRV++EGDN+ +   PREEG VPF+
Sbjct:   408 LEFSEDSVQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRVEGDNDKKN--PREEGMVPFI 465

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|E2R2H9 FXR2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 233 (87.1 bits), Expect = 1.6e-18, P = 1.6e-18
 Identities = 45/60 (75%), Positives = 55/60 (91%)

Query:     2 LEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFM 61
             LE+SE+S+QVPRNLVGKVIGKNG++IQEIVDKSGVVRV++EGDN+ +   PREEG VPF+
Sbjct:   289 LEFSEDSVQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRVEGDNDKKN--PREEGMVPFI 346

GO:0005737 "cytoplasm" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|P51116 FXR2 "Fragile X mental retardation syndrome-related protein 2" [Homo sapiens (taxid:9606)]

 Score = 233 (87.1 bits), Expect = 1.6e-18, P = 1.6e-18
 Identities = 45/60 (75%), Positives = 55/60 (91%)

Query:     2 LEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFM 61
             LE+SE+S+QVPRNLVGKVIGKNG++IQEIVDKSGVVRV++EGDN+ +   PREEG VPF+
Sbjct:   289 LEFSEDSVQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRVEGDNDKKN--PREEGMVPFI 346

GO:0003723 "RNA binding" evidence=IEA

GO:0022625 "cytosolic large ribosomal subunit" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|F1ST39 FXR2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 233 (87.1 bits), Expect = 1.6e-18, P = 1.6e-18
 Identities = 45/60 (75%), Positives = 55/60 (91%)

Query:     2 LEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFM 61
             LE+SE+S+QVPRNLVGKVIGKNG++IQEIVDKSGVVRV++EGDN+ +   PREEG VPF+
Sbjct:   289 LEFSEDSVQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRVEGDNDKKN--PREEGMVPFI 346

GO:0005737 "cytoplasm" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|E7EU85 FXR1 "Fragile X mental retardation syndrome-related protein 1" [Homo sapiens (taxid:9606)]

 Score = 229 (85.7 bits), Expect = 1.7e-18, P = 1.7e-18
 Identities = 47/65 (72%), Positives = 57/65 (87%)

Query:     2 LEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFM 61
             LE+ E+ +QVPRNLVGKVIGKNG++IQEIVDKSGVVRV+IEGDNE +  LPRE+G VPF+
Sbjct:   194 LEFVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENK--LPREDGMVPFV 251

Query:    62 VL-TK 65
              + TK
Sbjct:   252 FVGTK 256

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|E9PFF5 FXR1 "Fragile X mental retardation syndrome-related protein 1" [Homo sapiens (taxid:9606)]

 Score = 229 (85.7 bits), Expect = 2.1e-18, P = 2.1e-18
 Identities = 47/65 (72%), Positives = 57/65 (87%)

Query:     2 LEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFM 61
             LE+ E+ +QVPRNLVGKVIGKNG++IQEIVDKSGVVRV+IEGDNE +  LPRE+G VPF+
Sbjct:   230 LEFVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENK--LPREDGMVPFV 287

Query:    62 VL-TK 65
              + TK
Sbjct:   288 FVGTK 292

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|A6QLG6 FXR1 "Fragile X mental retardation syndrome-related protein 1" [Bos taurus (taxid:9913)]

 Score = 229 (85.7 bits), Expect = 2.7e-18, P = 2.7e-18
 Identities = 47/65 (72%), Positives = 57/65 (87%)

Query:     2 LEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFM 61
             LE+ E+ +QVPRNLVGKVIGKNG++IQEIVDKSGVVRV+IEGDNE +  LPRE+G VPF+
Sbjct:   279 LEFVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENK--LPREDGMVPFV 336

Query:    62 VL-TK 65
              + TK
Sbjct:   337 FVGTK 341

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F6XQE7 FXR1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 229 (85.7 bits), Expect = 2.7e-18, P = 2.7e-18
 Identities = 47/65 (72%), Positives = 57/65 (87%)

Query:     2 LEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFM 61
             LE+ E+ +QVPRNLVGKVIGKNG++IQEIVDKSGVVRV+IEGDNE +  LPRE+G VPF+
Sbjct:   279 LEFVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENK--LPREDGMVPFV 336

Query:    62 VL-TK 65
              + TK
Sbjct:   337 FVGTK 341

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F1SGB0 FXR1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 229 (85.7 bits), Expect = 2.7e-18, P = 2.7e-18
 Identities = 47/65 (72%), Positives = 57/65 (87%)

Query:     2 LEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFM 61
             LE+ E+ +QVPRNLVGKVIGKNG++IQEIVDKSGVVRV+IEGDNE +  LPRE+G VPF+
Sbjct:   279 LEFVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENK--LPREDGMVPFV 336

Query:    62 VL-TK 65
              + TK
Sbjct:   337 FVGTK 341

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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5XI81	FXR1_RAT	No assigned EC number	0.7142	0.8591	0.1073	yes	N/A
Q5BJ56	FXR1_XENTR	No assigned EC number	0.7258	0.8450	0.0890	yes	N/A
Q2TBT7	FXR1_BOVIN	No assigned EC number	0.7142	0.8591	0.0982	yes	N/A
Q9NFU0	FMR1_DROME	No assigned EC number	0.6666	0.8873	0.0921	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	71
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	3e-07
pfam00013	59	pfam00013, KH_1, KH domain	3e-06
smart00322	68	smart00322, KH, K homology RNA-binding domain	1e-05
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	3e-05
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	2e-04
PRK13764	602	PRK13764, PRK13764, ATPase; Provisional	2e-04
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	5e-04
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	0.001
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	0.001
pfam13014	42	pfam13014, KH_3, KH domain	0.002
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	0.004

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

 Score = 42.5 bits (101), Expect = 3e-07
 Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 1/44 (2%)

Query: 6  EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
           E + VP +LVG++IGK G  I+EI +++G  ++KI        
Sbjct: 1  TERVLVPSSLVGRIIGKGGSTIKEIREETG-AKIKIPDSGSGSE 43

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

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

 Score = 39.9 bits (94), Expect = 3e-06
 Identities = 15/41 (36%), Positives = 28/41 (68%), Gaps = 1/41 (2%)

Query: 6  EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE 46
           E + +P + VG++IGK G  I+EI +++G V+++I  D +
Sbjct: 1  TERILIPPDKVGRIIGKGGSNIKEIREETG-VKIRIPDDRD 40

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

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

 Score = 38.0 bits (89), Expect = 1e-05
 Identities = 13/46 (28%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 6  EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTL 51
             + +P + VG +IGK G  I++I +++G V++ I G    +  +
Sbjct: 4  TIEVLIPADKVGLIIGKGGSTIKKIEEETG-VKIDIPGPGSEERVV 48

Length = 68

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

 Score = 37.1 bits (87), Expect = 3e-05
 Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 1/40 (2%)

Query: 11 VPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT 50
          VP +  G +IGK G  I+EI +++G  ++++     P  T
Sbjct: 6  VPSSQAGSIIGKGGSTIKEIREETG-AKIRVSKSVLPGST 44

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

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

 Score = 37.3 bits (88), Expect = 2e-04
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 7/49 (14%)

Query: 7   ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVV-------RVKIEGDNEPQ 48
           E++++P + +  VIG  G+ I+EI +++G          VKI   +   
Sbjct: 556 ETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDDGTVKIAATDGEA 604

Length = 693

>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional

 Score = 36.7 bits (86), Expect = 2e-04
 Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 11  VPRNLVGKVIGKNGRIIQEIVDKSGV-VRVKIEGDNEPQPTLPREEGQV 58
           VP   + KVIGK G+ I++I  K G+ + V+   +   +     EE  V
Sbjct: 487 VPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEPGEEAEEGEEVTV 535

Length = 602

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

 Score = 34.0 bits (79), Expect = 5e-04
 Identities = 11/31 (35%), Positives = 22/31 (70%)

Query: 6  EESLQVPRNLVGKVIGKNGRIIQEIVDKSGV 36
           E +++P+ L   +IGK G  I++I++++GV
Sbjct: 1  TEEVEIPKKLHRFIIGKKGSNIRKIMEETGV 31

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

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

 Score = 34.8 bits (81), Expect = 0.001
 Identities = 12/38 (31%), Positives = 26/38 (68%), Gaps = 1/38 (2%)

Query: 7   ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD 44
           E++++  + +  VIG  G++I+EI +++G  ++ IE D
Sbjct: 553 ETIKINPDKIRDVIGPGGKVIREITEETG-AKIDIEDD 589

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

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

 Score = 34.5 bits (80), Expect = 0.001
 Identities = 13/46 (28%), Positives = 28/46 (60%), Gaps = 3/46 (6%)

Query: 1   MLEYSE--ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD 44
           +  Y+   E++++  + +  VIG  G+ I+ I +++G V++ IE D
Sbjct: 546 LSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETG-VKIDIEDD 590

Length = 692

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

 Score = 31.8 bits (73), Expect = 0.002
 Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 1/35 (2%)

Query: 15 LVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
          LVG +IGK G  I+EI +++G  +++I        
Sbjct: 1  LVGAIIGKGGETIKEIREETG-AKIQIPKPEPGSG 34

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

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

 Score = 31.7 bits (73), Expect = 0.004
 Identities = 13/38 (34%), Positives = 28/38 (73%), Gaps = 1/38 (2%)

Query: 7  ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD 44
          E++++P + +  VIG  G+ I++I++++G V++ IE D
Sbjct: 4  ETMKIPPDKIRDVIGPGGKTIKKIIEETG-VKIDIEDD 40

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	71
COG1837	76	Predicted RNA-binding protein (contains KH domain)	99.39
PRK00468	75	hypothetical protein; Provisional	99.38
PRK02821	77	hypothetical protein; Provisional	99.29
PRK01064	78	hypothetical protein; Provisional	98.91
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	98.4
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	98.35
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	98.23
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	98.07
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	98.0
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	97.99
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	97.94
smart00322	69	KH K homology RNA-binding domain.	97.92
PF13014	43	KH_3: KH domain	97.63
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	97.38
PRK08406	140	transcription elongation factor NusA-like protein;	97.34
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	96.82
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	96.79
PRK13763	180	putative RNA-processing protein; Provisional	96.7
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	95.98
PRK13764	602	ATPase; Provisional	95.95
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	95.93
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	95.89
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	95.81
PRK12704	520	phosphodiesterase; Provisional	95.7
KOG1676|consensus	600		95.69
PRK00106	535	hypothetical protein; Provisional	95.64
KOG2190|consensus	485		95.61
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	95.38
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	95.2
PRK12705	508	hypothetical protein; Provisional	95.03
PRK08406	140	transcription elongation factor NusA-like protein;	94.92
KOG2193|consensus	584		94.86
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	94.4
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	94.4
COG1855	604	ATPase (PilT family) [General function prediction	94.22
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	94.04
PRK13763	180	putative RNA-processing protein; Provisional	94.02
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	93.72
KOG2192|consensus	390		93.43
COG0195	190	NusA Transcription elongation factor [Transcriptio	92.87
KOG2190|consensus	485		91.45
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	90.84
KOG1676|consensus	600		90.41
COG0195	190	NusA Transcription elongation factor [Transcriptio	89.97
COG1094	194	Predicted RNA-binding protein (contains KH domains	89.77
KOG2191|consensus	402		89.67
PRK06418	166	transcription elongation factor NusA-like protein;	89.49
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	88.08
cd02412	109	30S_S3_KH K homology RNA-binding (KH) domain of th	87.38
PRK12328	374	nusA transcription elongation factor NusA; Provisi	86.88
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	86.71
cd02411	85	archeal_30S_S3_KH K homology RNA-binding domain (K	86.13
KOG2193|consensus	584		85.84
PRK12327	362	nusA transcription elongation factor NusA; Provisi	85.77
KOG2192|consensus	390		85.6
TIGR01953	341	NusA transcription termination factor NusA. This m	84.39
PRK09202	470	nusA transcription elongation factor NusA; Validat	83.54
COG1847	208	Jag Predicted RNA-binding protein [General functio	81.92
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	81.28
PRK00089	292	era GTPase Era; Reviewed	80.59
PRK12329	449	nusA transcription elongation factor NusA; Provisi	80.02

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

Probab=99.39  E-value=1.9e-13  Score=86.29  Aligned_cols=37  Identities=38%  Similarity=0.427  Sum_probs=34.4

Q ss_pred             ceeeeeeeeCCCccCcccccCchhHHHHHhhhceeEE
Q psy986            3 EYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRV   39 (71)
Q Consensus         3 Ef~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~i   39 (71)
                      .+..++|.|+++|+||+|||+||+||||||++.+++.
T Consensus        28 ~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll~a~~~   64 (76)
T COG1837          28 KTVTIELRVAPEDMGKVIGKQGRTIQAIRTLLSAVGS   64 (76)
T ss_pred             CeEEEEEEECcccccceecCCChhHHHHHHHHHHhcc
Confidence            3678999999999999999999999999999999876

>PRK00468 hypothetical protein; Provisional

Probab=99.38  E-value=1.7e-13  Score=85.58  Aligned_cols=37  Identities=35%  Similarity=0.419  Sum_probs=34.1

Q ss_pred             eeeeeeeeCCCccCcccccCchhHHHHHhhhceeEEe
Q psy986            4 YSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVK   40 (71)
Q Consensus         4 f~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~ik   40 (71)
                      +..+.|.|+++|+||||||+||+|+||||++++++.+
T Consensus        29 ~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~aaa~k   65 (75)
T PRK00468         29 SVILELKVAPEDMGKVIGKQGRIAKAIRTVVKAAAIK   65 (75)
T ss_pred             eEEEEEEEChhhCcceecCCChhHHHHHHHHHHHHhc
Confidence            5678999999999999999999999999999988655

>PRK02821 hypothetical protein; Provisional

Probab=99.29  E-value=1.3e-12  Score=82.20  Aligned_cols=34  Identities=24%  Similarity=0.358  Sum_probs=32.0

Q ss_pred             eeeeeeeeCCCccCcccccCchhHHHHHhhhcee
Q psy986            4 YSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVV   37 (71)
Q Consensus         4 f~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~   37 (71)
                      .....|.|+++|+||+|||+||+|+|||++++++
T Consensus        30 ~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a~   63 (77)
T PRK02821         30 GRTLEVRVHPDDLGKVIGRGGRTATALRTVVAAI   63 (77)
T ss_pred             cEEEEEEEChhhCcceeCCCCchHHHHHHHHHHh
Confidence            5678999999999999999999999999999987

>PRK01064 hypothetical protein; Provisional

Probab=98.91  E-value=5.6e-10  Score=70.34  Aligned_cols=37  Identities=32%  Similarity=0.375  Sum_probs=33.2

Q ss_pred             eeeeeeeeCCCccCcccccCchhHHHHHhhhceeEEe
Q psy986            4 YSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVK   40 (71)
Q Consensus         4 f~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~ik   40 (71)
                      +..+.+.|+++|+|++|||+|++|+|||+++++++.+
T Consensus        29 ~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~~~~~~   65 (78)
T PRK01064         29 TIIYELTVAKPDIGKIIGKEGRTIKAIRTLLVSVASR   65 (78)
T ss_pred             EEEEEEEECcccceEEECCCCccHHHHHHHHHHHHhh
Confidence            5678899999999999999999999999999887543

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

Probab=98.40  E-value=8.5e-07  Score=50.29  Aligned_cols=36  Identities=44%  Similarity=0.841  Sum_probs=31.6

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      ..+.||++.+|++||++|+++++|+..+++ .+.+..
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~-~I~i~~   37 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGA-KIKIPD   37 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCC-EEEEcC
Confidence            578999999999999999999999999975 566663

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.

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=98.35  E-value=1.2e-07  Score=56.87  Aligned_cols=35  Identities=14%  Similarity=0.279  Sum_probs=31.3

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEE
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRV   39 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~i   39 (71)
                      ....+.++.+|.|++|||+|++++||+++++++.-
T Consensus        29 ~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~~   63 (73)
T PF13083_consen   29 DTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAAN   63 (73)
T ss_dssp             TEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEECCCccceEECCCCeeHHHHHHHHHHHHH
Confidence            45678999999999999999999999999988753

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=98.23  E-value=2.9e-06  Score=49.85  Aligned_cols=38  Identities=32%  Similarity=0.629  Sum_probs=33.2

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCC
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDN   45 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~   45 (71)
                      ..+.||.+.+|++|||+|.+++.|++.+|+ .+++..++
T Consensus         2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga-~I~i~~~~   39 (65)
T cd02396           2 LRLLVPSSQAGSIIGKGGSTIKEIREETGA-KIRVSKSV   39 (65)
T ss_pred             EEEEECHHHcCeeECCCcHHHHHHHHHHCC-EEEEcCCC
Confidence            468899999999999999999999999987 68887443

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

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

Probab=98.07  E-value=4.9e-06  Score=49.08  Aligned_cols=36  Identities=33%  Similarity=0.744  Sum_probs=31.8

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      -..+.||++.+|++|||+|.+|+.|++.+++- ++++
T Consensus         3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~-I~i~   38 (61)
T cd02393           3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVK-IDIE   38 (61)
T ss_pred             EEEEEeChhheeeeECCCchHHHHHHHHHCCE-EEeC
Confidence            35789999999999999999999999999865 6665

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=98.00  E-value=2.3e-06  Score=48.95  Aligned_cols=37  Identities=46%  Similarity=0.859  Sum_probs=32.9

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD   44 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~   44 (71)
                      ..+.||++++|++||++|++++.|+..+++. +.++.+
T Consensus         2 ~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~-I~i~~~   38 (60)
T PF00013_consen    2 ERIEVPSSLVGRIIGKKGSNIKEIEEETGVK-IQIPDD   38 (60)
T ss_dssp             EEEEEEHHHHHHHHTGGGHHHHHHHHHHTSE-EEEEST
T ss_pred             EEEEECHHHcCEEECCCCCcHHHhhhhcCeE-EEEcCC
Confidence            5789999999999999999999999999865 888643

; 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 ....

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

Probab=97.99  E-value=6.3e-06  Score=48.67  Aligned_cols=30  Identities=27%  Similarity=0.452  Sum_probs=27.6

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhc
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSG   35 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~   35 (71)
                      ...+.|+++++|++|||+|++|+.++.+++
T Consensus        26 ~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~   55 (61)
T cd02134          26 RARVVVPDDQLGLAIGKGGQNVRLASKLLG   55 (61)
T ss_pred             EEEEEECcccceeeECCCCHHHHHHHHHHC
Confidence            456889999999999999999999999887

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

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=97.94  E-value=1.4e-05  Score=45.86  Aligned_cols=36  Identities=31%  Similarity=0.716  Sum_probs=31.1

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      ..+.||++.+|.+||++|.+|+.|++..+ +.+.+..
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g-~~I~i~~   37 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETG-VKIRFPD   37 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhC-CEEEcCC
Confidence            57899999999999999999999999886 4466653

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.

>smart00322 KH K homology RNA-binding domain

Probab=97.92  E-value=1.2e-05  Score=44.38  Aligned_cols=38  Identities=32%  Similarity=0.603  Sum_probs=32.5

Q ss_pred             eeeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            4 YSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         4 f~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      .....+.||.+.+|.+||++|.++++|+..++ +.+.+.
T Consensus         2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~-~~i~~~   39 (69)
T smart00322        2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETG-VKIDIP   39 (69)
T ss_pred             ceEEEEEEcchhcceeECCCchHHHHHHHHHC-CEEEEC
Confidence            35678999999999999999999999999986 445554

>PF13014 KH_3: KH domain

Probab=97.63  E-value=9.2e-05  Score=40.46  Aligned_cols=28  Identities=39%  Similarity=0.835  Sum_probs=24.7

Q ss_pred             ccCcccccCchhHHHHHhhhceeEEeecC
Q psy986           15 LVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus        15 dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      .+|.+||++|.+|+.|++.++ +.|+|..
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg-~~I~i~~   28 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETG-AKIQIPP   28 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhC-cEEEECC
Confidence            479999999999999999988 5688875

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=97.38  E-value=0.00011  Score=44.74  Aligned_cols=32  Identities=19%  Similarity=0.400  Sum_probs=28.5

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeE
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVR   38 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~   38 (71)
                      ..+.+..++.|++|||+|+++.||..++..+.
T Consensus        26 i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~   57 (77)
T cd02414          26 VEVNISGDDIGLLIGKRGKTLDALQYLANLVL   57 (77)
T ss_pred             EEEEEecCCCCeEECCCCccHHHHHHHHHHHH
Confidence            36889999999999999999999999888653

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

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=97.34  E-value=0.00016  Score=49.20  Aligned_cols=30  Identities=30%  Similarity=0.362  Sum_probs=27.0

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhce
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGV   36 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a   36 (71)
                      ..+.|+++++|+.|||+|+++++++.+++-
T Consensus       101 ~~V~V~~~d~g~aIGK~G~ni~la~~L~~~  130 (140)
T PRK08406        101 AYVEVAPEDKGIAIGKNGKNIERAKDLAKR  130 (140)
T ss_pred             EEEEECccccchhhCCCCHHHHHHHHHhCC
Confidence            457899999999999999999999988763

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=96.82  E-value=0.00063  Score=47.14  Aligned_cols=34  Identities=32%  Similarity=0.753  Sum_probs=30.1

Q ss_pred             eeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            9 LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         9 l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      +.||++-+|.+||++|++|+.|...+++- ++++.
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~-I~Id~   35 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVK-LDIDS   35 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcE-EEEEc
Confidence            68999999999999999999999999854 77763

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.

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

Probab=96.79  E-value=0.0018  Score=36.27  Aligned_cols=33  Identities=30%  Similarity=0.345  Sum_probs=27.5

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhcee
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVV   37 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~   37 (71)
                      ....+.+++.+.|.+|||+|++++++..+++..
T Consensus        25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~   57 (68)
T cd02409          25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKL   57 (68)
T ss_pred             EEEEEEECCCCCceEECCCCccHHHHHHHHHHH
Confidence            344677777799999999999999999888743

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

>PRK13763 putative RNA-processing protein; Provisional

Probab=96.70  E-value=0.0014  Score=45.73  Aligned_cols=38  Identities=32%  Similarity=0.702  Sum_probs=33.2

Q ss_pred             eeeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            4 YSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         4 f~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      +....+.||++-+|.+||++|.+|++|.+..++ .++++
T Consensus         2 ~~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~-~I~i~   39 (180)
T PRK13763          2 MMMEYVKIPKDRIGVLIGKKGETKKEIEERTGV-KLEID   39 (180)
T ss_pred             CceEEEEcCHHHhhhHhccchhHHHHHHHHHCc-EEEEE
Confidence            356789999999999999999999999999974 47776

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=95.98  E-value=0.0064  Score=51.06  Aligned_cols=36  Identities=33%  Similarity=0.713  Sum_probs=31.8

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      .+.+++|++.+|.+||.+|++|++|.+..|+- |+|+
T Consensus       579 ~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~-Idi~  614 (719)
T TIGR02696       579 IITVKIPVDKIGEVIGPKGKMINQIQDETGAE-ISIE  614 (719)
T ss_pred             eEEEEeChHHhhheeCCCcHhHHHHHHHHCCE-EEEe
Confidence            36789999999999999999999999999854 6666

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.

>PRK13764 ATPase; Provisional

Probab=95.95  E-value=0.01  Score=48.81  Aligned_cols=40  Identities=33%  Similarity=0.541  Sum_probs=33.3

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCC
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE   46 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e   46 (71)
                      .-.+.||+.+++++|||+|+.|..|...+| +.++|...+|
T Consensus       482 ~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~-~~i~v~~~~~  521 (602)
T PRK13764        482 KAVVYVPEKDIPKVIGKGGKRIKKIEKKLG-IDIDVRPLDE  521 (602)
T ss_pred             eEEEEEChhhhhHHhccCcchHHHHHHHhC-CceEEEEccc
Confidence            456899999999999999999999999998 4566654444

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=95.93  E-value=0.0049  Score=50.75  Aligned_cols=35  Identities=31%  Similarity=0.708  Sum_probs=31.2

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      +.++||++.+|++||++|++|++|.+..|+- |+|+
T Consensus       553 ~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~-I~i~  587 (684)
T TIGR03591       553 ETIKINPDKIRDVIGPGGKVIREITEETGAK-IDIE  587 (684)
T ss_pred             EEEecCHHHHHhhcCCCcHHHHHHHHHHCCE-EEEe
Confidence            5789999999999999999999999988854 6665

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

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

Probab=95.89  E-value=0.007  Score=40.35  Aligned_cols=30  Identities=27%  Similarity=0.689  Sum_probs=26.1

Q ss_pred             CccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986           14 NLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD   44 (71)
Q Consensus        14 ~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~   44 (71)
                      +.+|++||.+|+++|.|.+..++- |.|.++
T Consensus        15 N~IG~IIGPgG~tiK~i~~eTg~k-I~Irg~   44 (120)
T cd02395          15 NFVGLILGPRGNTLKQLEKETGAK-ISIRGK   44 (120)
T ss_pred             CeeEEEECCCChHHHHHHHHHCCE-EEEecC
Confidence            679999999999999999999954 777754

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.

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=95.81  E-value=0.01  Score=47.56  Aligned_cols=33  Identities=27%  Similarity=0.642  Sum_probs=27.0

Q ss_pred             ceeeeeeeeCCC-ccCcccccCchhHHHHHhhhc
Q psy986            3 EYSEESLQVPRN-LVGKVIGKNGRIIQEIVDKSG   35 (71)
Q Consensus         3 Ef~e~~l~V~~~-dvGKVIGk~Gr~ikaIr~~~~   35 (71)
                      |.+...|.+|.+ ..||+|||.||+|+++-+..|
T Consensus       202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tg  235 (514)
T TIGR03319       202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTG  235 (514)
T ss_pred             hheeeeEEcCChhhhccccCCCcchHHHHHHHhC
Confidence            456677888884 569999999999999976666

>PRK12704 phosphodiesterase; Provisional

Probab=95.70  E-value=0.012  Score=47.25  Aligned_cols=33  Identities=27%  Similarity=0.629  Sum_probs=26.7

Q ss_pred             ceeeeeeeeCC-CccCcccccCchhHHHHHhhhc
Q psy986            3 EYSEESLQVPR-NLVGKVIGKNGRIIQEIVDKSG   35 (71)
Q Consensus         3 Ef~e~~l~V~~-~dvGKVIGk~Gr~ikaIr~~~~   35 (71)
                      |.+...+.+|. +..||+|||.||+|+++-...|
T Consensus       208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tg  241 (520)
T PRK12704        208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTG  241 (520)
T ss_pred             hhceeeeecCCchhhcceeCCCcchHHHHHHHhC
Confidence            45667788888 4569999999999999976665

>KOG1676|consensus

Probab=95.69  E-value=0.01  Score=49.26  Aligned_cols=41  Identities=32%  Similarity=0.794  Sum_probs=36.4

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCCC
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEP   47 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e~   47 (71)
                      ...+.||+.-||-||||+|.+||.|-...| ++|.|..|+++
T Consensus       231 ~~~V~VPr~~VG~IIGkgGE~IKklq~etG-~KIQfkpDd~p  271 (600)
T KOG1676|consen  231 TREVKVPRSKVGIIIGKGGEMIKKLQNETG-AKIQFKPDDDP  271 (600)
T ss_pred             eeEEeccccceeeEEecCchHHHHHhhccC-ceeEeecCCCC
Confidence            457899999999999999999999988877 68888888885

>PRK00106 hypothetical protein; Provisional

Probab=95.64  E-value=0.012  Score=47.79  Aligned_cols=33  Identities=30%  Similarity=0.677  Sum_probs=27.5

Q ss_pred             ceeeeeeeeCC-CccCcccccCchhHHHHHhhhc
Q psy986            3 EYSEESLQVPR-NLVGKVIGKNGRIIQEIVDKSG   35 (71)
Q Consensus         3 Ef~e~~l~V~~-~dvGKVIGk~Gr~ikaIr~~~~   35 (71)
                      |.+...+.+|. +..||+|||.||+|+++-+..|
T Consensus       223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tG  256 (535)
T PRK00106        223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTG  256 (535)
T ss_pred             hheeeeEEcCChHhhcceeCCCcchHHHHHHHhC
Confidence            45667788888 4569999999999999987776

>KOG2190|consensus

Probab=95.61  E-value=0.011  Score=47.45  Aligned_cols=38  Identities=37%  Similarity=0.742  Sum_probs=33.4

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD   44 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~   44 (71)
                      .-.|-||.+.+|=+|||+|..||.||+..+ +.+++.+|
T Consensus       139 ~~RLlVp~sq~GslIGK~G~~Ik~Ire~Tg-A~I~v~~~  176 (485)
T KOG2190|consen  139 TCRLLVPSSQVGSLIGKGGSLIKEIREETG-AKIRVSSD  176 (485)
T ss_pred             EEEEEechhheeeeeccCcHHHHHHHHhcC-ceEEecCC
Confidence            356889999999999999999999999955 68888876

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=95.38  E-value=0.0099  Score=41.17  Aligned_cols=22  Identities=32%  Similarity=0.682  Sum_probs=20.5

Q ss_pred             ccCcccccCchhHHHHHhhhce
Q psy986           15 LVGKVIGKNGRIIQEIVDKSGV   36 (71)
Q Consensus        15 dvGKVIGk~Gr~ikaIr~~~~a   36 (71)
                      ..|++||++|+++++|-+.+++
T Consensus        99 ~~griIG~~G~t~~~ie~~t~~  120 (172)
T TIGR03665        99 IKGRIIGEGGKTRRIIEELTGV  120 (172)
T ss_pred             HHhhhcCCCcHHHHHHHHHHCC
Confidence            6999999999999999998885

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.

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=95.20  E-value=0.016  Score=39.81  Aligned_cols=30  Identities=23%  Similarity=0.282  Sum_probs=26.4

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhc
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSG   35 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~   35 (71)
                      ...+.||+++.|..|||+|+.++-.+.+++
T Consensus       101 ~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~  130 (141)
T TIGR01952       101 VAYVEVHPRDKGIAIGKGGKNIERAKELAK  130 (141)
T ss_pred             EEEEEEChhhhhhhhCCCchhHHHHHHHhc
Confidence            456889999999999999999998887765

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

>PRK12705 hypothetical protein; Provisional

Probab=95.03  E-value=0.014  Score=47.12  Aligned_cols=39  Identities=28%  Similarity=0.624  Sum_probs=28.9

Q ss_pred             ceeeeeeeeCCC-ccCcccccCchhHHHHHhhhceeEEeec
Q psy986            3 EYSEESLQVPRN-LVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         3 Ef~e~~l~V~~~-dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      |.+...+..|.+ ..||+|||.||.|+++-...|+ .+-|+
T Consensus       196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGv-dliid  235 (508)
T PRK12705        196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGV-DLIID  235 (508)
T ss_pred             hheeeeeecCChHhhccccCccchhHHHHHHhhCC-ceEec
Confidence            445566777774 5699999999999999877774 33343

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=94.92  E-value=0.023  Score=38.62  Aligned_cols=34  Identities=24%  Similarity=0.417  Sum_probs=28.2

Q ss_pred             eeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            8 SLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         8 ~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      .+-|++.++|..||++|..||+|.++++- .+++-
T Consensus        35 i~vV~~~~vG~~IG~~G~rI~~i~e~lge-kIdVv   68 (140)
T PRK08406         35 IFVVKEGDMGLAIGKGGENVKRLEEKLGK-DIELV   68 (140)
T ss_pred             EEEEeCCCccccCCcCchHHHHHHHHhCC-ceEEE
Confidence            45678999999999999999999888763 56653

>KOG2193|consensus

Probab=94.86  E-value=0.017  Score=47.27  Aligned_cols=37  Identities=30%  Similarity=0.606  Sum_probs=31.2

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      +|-+++||..-.||||||+|++.+.+-.+.+| .+.|-
T Consensus       493 lethirVPs~~aGRvIGKGGktVnELQnlt~A-eV~vP  529 (584)
T KOG2193|consen  493 LETHIRVPSSAAGRVIGKGGKTVNELQNLTSA-EVVVP  529 (584)
T ss_pred             eeeeeeccchhhhhhhccccccHHHHhccccc-eEEcc
Confidence            56789999999999999999999999887775 34443

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=94.40  E-value=0.014  Score=50.12  Aligned_cols=37  Identities=22%  Similarity=0.489  Sum_probs=32.9

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      ...++||++.+|.+||.+|++|++|.+-.++-.++++
T Consensus       686 i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~  722 (891)
T PLN00207        686 IHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ  722 (891)
T ss_pred             eEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC
Confidence            3578999999999999999999999999987766665

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=94.40  E-value=0.049  Score=37.40  Aligned_cols=36  Identities=19%  Similarity=0.362  Sum_probs=29.4

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      .-.+-|.+.++|..||++|..||+++++.|- .+++-
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~ge-kIdVV   69 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGK-SIELI   69 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCC-eeEEE
Confidence            3456789999999999999999999887773 55553

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

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

Probab=94.22  E-value=0.034  Score=46.03  Aligned_cols=39  Identities=36%  Similarity=0.647  Sum_probs=31.9

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCC
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE   46 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e   46 (71)
                      ..+.||+.+++++|||+|+.|+.|...+| ..+++..-++
T Consensus       488 avv~vpe~~i~~vigk~g~~i~~ie~klg-i~I~v~~~e~  526 (604)
T COG1855         488 AVVKVPEKYIPKVIGKGGKRIKEIEKKLG-IKIDVKPLEE  526 (604)
T ss_pred             EEEEeCHHHhhHHhhcccchHHHHHHHhC-CceEEEEccc
Confidence            56899999999999999999999999988 4555543333

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=94.04  E-value=0.025  Score=33.82  Aligned_cols=29  Identities=28%  Similarity=0.367  Sum_probs=24.6

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhc
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSG   35 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~   35 (71)
                      -.+.+..+..|.+||++|+.++.|++.++
T Consensus        27 ~~i~i~~~~~~ivIGk~G~~ik~i~~~~~   55 (78)
T PF07650_consen   27 IIIVIKASQPGIVIGKKGSNIKKIREELR   55 (78)
T ss_dssp             EEEEEEESSHHHHHTGGGHHHHHHHHHHH
T ss_pred             EEEEEeCCCccHhHHhhhHHHHHHHHHHH
Confidence            45667788999999999999999987665

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

>PRK13763 putative RNA-processing protein; Provisional

Probab=94.02  E-value=0.03  Score=39.08  Aligned_cols=22  Identities=32%  Similarity=0.682  Sum_probs=20.3

Q ss_pred             ccCcccccCchhHHHHHhhhce
Q psy986           15 LVGKVIGKNGRIIQEIVDKSGV   36 (71)
Q Consensus        15 dvGKVIGk~Gr~ikaIr~~~~a   36 (71)
                      -.|++||++|+++++|-+.+++
T Consensus       105 ~~griIG~~G~~~k~ie~~t~~  126 (180)
T PRK13763        105 IKGRIIGEGGKTRRIIEELTGV  126 (180)
T ss_pred             HhhheeCCCcHHHHHHHHHHCc
Confidence            5899999999999999988885

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=93.72  E-value=0.022  Score=47.02  Aligned_cols=35  Identities=34%  Similarity=0.795  Sum_probs=30.9

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      ..+++|++.+|.+||.+|++|++|.+..++ .++++
T Consensus       556 ~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~-~idi~  590 (693)
T PRK11824        556 ETIKIPPDKIRDVIGPGGKTIREITEETGA-KIDIE  590 (693)
T ss_pred             eeecCCHHHHHHHhcCCchhHHHHHHHHCC-ccccC
Confidence            467889999999999999999999999988 56654

>KOG2192|consensus

Probab=93.43  E-value=0.11  Score=40.82  Aligned_cols=40  Identities=35%  Similarity=0.663  Sum_probs=33.5

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCC
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE   46 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e   46 (71)
                      .-.+.+|.++-|-+|||+|..|+.||.-+|| .|+++-.-|
T Consensus       316 TaQvtip~dlggsiigkggqri~~ir~esGA-~Ikideple  355 (390)
T KOG2192|consen  316 TAQVTIPKDLGGSIIGKGGQRIKQIRHESGA-SIKIDEPLE  355 (390)
T ss_pred             eeeEecccccCcceecccchhhhhhhhccCc-eEEecCcCC
Confidence            4578899999999999999999999999885 677764333

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=92.87  E-value=0.069  Score=38.33  Aligned_cols=36  Identities=25%  Similarity=0.399  Sum_probs=29.9

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      ...+.||+++.+++|||+|+.++.+..+.| ..++|.
T Consensus       143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg-~~i~I~  178 (190)
T COG0195         143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTG-WEIDIE  178 (190)
T ss_pred             EEEEEECHHHHhhccCcccHHHHHHHHHhC-CEEEEE
Confidence            467889999999999999999999988877 344444

>KOG2190|consensus

Probab=91.45  E-value=0.19  Score=40.43  Aligned_cols=41  Identities=37%  Similarity=0.644  Sum_probs=34.0

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCC
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE   46 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e   46 (71)
                      ....+.||.+++|-+|||+|+.|..||...| +.|+|...++
T Consensus       338 v~~~l~vps~~igciiGk~G~~iseir~~tg-A~I~I~~~~~  378 (485)
T KOG2190|consen  338 VTQRLLVPSDLIGCIIGKGGAKISEIRQRTG-ASISILNKEE  378 (485)
T ss_pred             eeeeeccCccccceeecccccchHHHHHhcC-CceEEccccc
Confidence            3467899999999999999999999998887 4667764444

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

Probab=90.84  E-value=0.15  Score=31.08  Aligned_cols=39  Identities=23%  Similarity=0.359  Sum_probs=28.4

Q ss_pred             eeeeCCCc-----cCcccccCchhHHHHHhhhceeEEeecCCCC
Q psy986            8 SLQVPRNL-----VGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE   46 (71)
Q Consensus         8 ~l~V~~~d-----vGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e   46 (71)
                      .+-|...+     +|..||++|..|++|...++--.+++-..++
T Consensus         6 kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~s~   49 (69)
T PF13184_consen    6 KVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEYSD   49 (69)
T ss_dssp             EEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE--S
T ss_pred             EEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEcCC
Confidence            34566677     9999999999999999999767787754333

>KOG1676|consensus

Probab=90.41  E-value=0.14  Score=42.65  Aligned_cols=38  Identities=32%  Similarity=0.595  Sum_probs=32.2

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD   44 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~   44 (71)
                      +..+.||.+-+|=||||+|.+||.|-+.+|| .|-...+
T Consensus       319 ~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA-~~el~r~  356 (600)
T KOG1676|consen  319 QFYMKVPADKCGLVIGRGGETIKQINQQSGA-RCELSRQ  356 (600)
T ss_pred             eEEEeccccccccccCCCccchhhhcccCCc-cccccCC
Confidence            6678999999999999999999999999995 4444444

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=89.97  E-value=0.37  Score=34.61  Aligned_cols=36  Identities=25%  Similarity=0.396  Sum_probs=30.4

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      .....+..+.||..||++|..++++...++ =.|+|-
T Consensus        77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLg-ekIdVV  112 (190)
T COG0195          77 VVSNVVKIDPVGACIGKRGSRVKAVSEELG-EKIDVV  112 (190)
T ss_pred             eEEeecCcCchhhhccCCChHHHHHHHHhC-CceEEE
Confidence            345667778899999999999999999999 777774

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

Probab=89.77  E-value=0.2  Score=36.54  Aligned_cols=22  Identities=32%  Similarity=0.753  Sum_probs=19.7

Q ss_pred             ccCcccccCchhHHHHHhhhce
Q psy986           15 LVGKVIGKNGRIIQEIVDKSGV   36 (71)
Q Consensus        15 dvGKVIGk~Gr~ikaIr~~~~a   36 (71)
                      -.||+||++|+|-++|-.+.++
T Consensus       112 ~kgRIIG~~GkTr~~IE~lt~~  133 (194)
T COG1094         112 IKGRIIGREGKTRRAIEELTGV  133 (194)
T ss_pred             hhceeeCCCchHHHHHHHHhCC
Confidence            3799999999999999988875

>KOG2191|consensus

Probab=89.67  E-value=0.3  Score=38.93  Aligned_cols=37  Identities=32%  Similarity=0.595  Sum_probs=31.9

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      +-.+-||..-.|-+|||+|-+||+|++.+++ .|+|++
T Consensus       133 qikivvPNstag~iigkggAtiK~~~Eqsga-~iqisP  169 (402)
T KOG2191|consen  133 QIKIVVPNSTAGMIIGKGGATIKAIQEQSGA-WIQISP  169 (402)
T ss_pred             eeEEeccCCcccceecCCcchHHHHHHhhCc-ceEecc
Confidence            3567899999999999999999999999985 566664

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=89.49  E-value=0.37  Score=34.14  Aligned_cols=33  Identities=30%  Similarity=0.433  Sum_probs=27.2

Q ss_pred             eeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            8 SLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         8 ~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      .+-|.+.+ |..|||+|.+++++...+|- .+++-
T Consensus        64 IfvV~~gd-g~aIGk~G~~ik~l~~~lgk-~VevV   96 (166)
T PRK06418         64 ILLVTSGP-RIPIGKGGKIAKALSRKLGK-KVRVV   96 (166)
T ss_pred             EEEEeCCC-cccccccchHHHHHHHHhCC-cEEEE
Confidence            35577889 99999999999999999985 55553

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=88.08  E-value=0.24  Score=35.83  Aligned_cols=29  Identities=28%  Similarity=0.531  Sum_probs=25.4

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhc
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSG   35 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~   35 (71)
                      ..++||++.++++||++|.+++.|-...+
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~  175 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETG  175 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhC
Confidence            35899999999999999999999986654

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

Probab=87.38  E-value=0.6  Score=30.12  Aligned_cols=29  Identities=21%  Similarity=0.321  Sum_probs=23.0

Q ss_pred             eeeeCCCccCcccccCchhHHHHHhhhce
Q psy986            8 SLQVPRNLVGKVIGKNGRIIQEIVDKSGV   36 (71)
Q Consensus         8 ~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a   36 (71)
                      .+.+.-+..|.+||++|+.+++++..+..
T Consensus        64 ~I~I~t~rPg~vIG~~G~~i~~L~~~l~~   92 (109)
T cd02412          64 EVTIHTARPGIIIGKKGAGIEKLRKELQK   92 (109)
T ss_pred             EEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence            34455556899999999999999987764

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

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=86.88  E-value=1.1  Score=35.41  Aligned_cols=41  Identities=24%  Similarity=0.329  Sum_probs=32.4

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEee--cCCCCC
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKI--EGDNEP   47 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki--~~~~e~   47 (71)
                      .-.+.||+++.+..|||+|+.++-.+.+.|- .++|  -++.|+
T Consensus       309 ~~~V~V~~~qlslAIGk~GqNvrLA~~LtGw-kIDI~s~~~~~~  351 (374)
T PRK12328        309 KAIVTLLSDQKSKAIGKNGINIRLASMLTGY-EIELNEIGSKEN  351 (374)
T ss_pred             EEEEEEChHHhhhhhcCCChhHHHHHHHhCC-EEEEEECCCCcc
Confidence            3468899999999999999999999888884 4444  445554

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

Probab=86.71  E-value=0.48  Score=40.18  Aligned_cols=36  Identities=31%  Similarity=0.669  Sum_probs=30.6

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      .+.++++++-++-+||++|++|++|.+..|+ .|.|+
T Consensus       553 i~t~~i~~dKI~dvIG~gGk~I~~I~eetg~-~Idie  588 (692)
T COG1185         553 IETIKIDPDKIRDVIGPGGKTIKAITEETGV-KIDIE  588 (692)
T ss_pred             eEEEccCHHHHhhccCCcccchhhhhhhhCc-EEEec
Confidence            4678999999999999999999999988874 45555

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

Probab=86.13  E-value=0.78  Score=28.26  Aligned_cols=28  Identities=25%  Similarity=0.447  Sum_probs=22.3

Q ss_pred             eeeCCCccCcccccCchhHHHHHhhhce
Q psy986            9 LQVPRNLVGKVIGKNGRIIQEIVDKSGV   36 (71)
Q Consensus         9 l~V~~~dvGKVIGk~Gr~ikaIr~~~~a   36 (71)
                      +.+.-..-|.+||++|+.++.++..+..
T Consensus        42 V~I~t~~pg~iIGk~G~~I~~l~~~l~k   69 (85)
T cd02411          42 ITIYAERPGMVIGRGGKNIRELTEILET   69 (85)
T ss_pred             EEEEECCCCceECCCchhHHHHHHHHHH
Confidence            3344478899999999999999987753

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

>KOG2193|consensus

Probab=85.84  E-value=0.45  Score=39.29  Aligned_cols=36  Identities=31%  Similarity=0.591  Sum_probs=29.7

Q ss_pred             eeeeCCCccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986            8 SLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD   44 (71)
Q Consensus         8 ~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~   44 (71)
                      .+-||...+|-+|||+|..||.|..-.| +.|||...
T Consensus       414 ~~fiP~~~vGAiIGkkG~hIKql~Rfag-ASiKIapp  449 (584)
T KOG2193|consen  414 RMFIPAQAVGAIIGKKGQHIKQLSRFAG-ASIKIAPP  449 (584)
T ss_pred             eeeccHHHHHHHHhhcchhHHHHHHhcc-ceeeecCC
Confidence            5678999999999999999999876666 57788743

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=85.77  E-value=0.62  Score=36.27  Aligned_cols=37  Identities=22%  Similarity=0.364  Sum_probs=30.2

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      .-.+.||+++.+..|||+|+.++--..+.|- .++|..
T Consensus       304 ~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~-~idi~s  340 (362)
T PRK12327        304 AARVVVPDYQLSLAIGKEGQNARLAARLTGW-KIDIKS  340 (362)
T ss_pred             EEEEEEChhhcchhhcCCChhHHHHHHHHCC-eeeEEE
Confidence            3568899999999999999999998888774 355543

>KOG2192|consensus

Probab=85.60  E-value=0.33  Score=38.20  Aligned_cols=35  Identities=40%  Similarity=0.682  Sum_probs=28.7

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEee
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKI   41 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki   41 (71)
                      |-.+-|+++..|-+||+||.-||.+|++-.| +.||
T Consensus       124 e~rllihqs~ag~iigrngskikelrekcsa-rlki  158 (390)
T KOG2192|consen  124 ELRLLIHQSLAGGIIGRNGSKIKELREKCSA-RLKI  158 (390)
T ss_pred             hhhhhhhhhhccceecccchhHHHHHHhhhh-hhhh
Confidence            4456789999999999999999999998763 4444

>TIGR01953 NusA transcription termination factor NusA

Probab=84.39  E-value=0.73  Score=35.53  Aligned_cols=36  Identities=19%  Similarity=0.407  Sum_probs=29.6

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      .-.+.||+++.+..|||+|+.++-.+.+.| ..++|-
T Consensus       302 ~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g-~~IdI~  337 (341)
T TIGR01953       302 SAEVVVPDDQLSLAIGKGGQNVRLASKLTG-WNIDVK  337 (341)
T ss_pred             EEEEEEChHHcchhhcCCChhHHHHHHHhC-CEEEEE
Confidence            356889999999999999999998887777 345554

This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=83.54  E-value=0.7  Score=37.05  Aligned_cols=36  Identities=25%  Similarity=0.442  Sum_probs=30.0

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      ...+-||+++++..|||+|++++-.+.+.|- .++|-
T Consensus       303 ~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~-~idi~  338 (470)
T PRK09202        303 SADVVVPDDQLSLAIGKNGQNVRLASKLTGW-KIDIM  338 (470)
T ss_pred             EEEEEECcchHHHhhCCCCeeHHHHHHHHCC-eEEEE
Confidence            4568899999999999999999999888874 35554

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

Probab=81.92  E-value=0.78  Score=33.83  Aligned_cols=34  Identities=18%  Similarity=0.331  Sum_probs=27.7

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEe
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVK   40 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~ik   40 (71)
                      ..+++.-++.|++||++|++.+|+--+..++.-+
T Consensus        93 v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~  126 (208)
T COG1847          93 VVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK  126 (208)
T ss_pred             EEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence            3566777889999999999999999887776444

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

Probab=81.28  E-value=1.7  Score=27.07  Aligned_cols=28  Identities=21%  Similarity=0.369  Sum_probs=21.9

Q ss_pred             eeeCCCccCcccccCchhHHHHHhhhce
Q psy986            9 LQVPRNLVGKVIGKNGRIIQEIVDKSGV   36 (71)
Q Consensus         9 l~V~~~dvGKVIGk~Gr~ikaIr~~~~a   36 (71)
                      +.+.-..-|-+||++|+.++.++..+..
T Consensus        34 I~I~tarPg~vIG~~G~~i~~L~~~L~k   61 (81)
T cd02413          34 IIIRATRTQNVLGEKGRRIRELTSLVQK   61 (81)
T ss_pred             EEEEeCCCceEECCCchhHHHHHHHHHH
Confidence            3444455699999999999999987653

S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>PRK00089 era GTPase Era; Reviewed

Probab=80.59  E-value=1.1  Score=32.01  Aligned_cols=30  Identities=27%  Similarity=0.492  Sum_probs=22.2

Q ss_pred             eeeeeeC-CCccCcccccCchhHHHHHhhhc
Q psy986            6 EESLQVP-RNLVGKVIGKNGRIIQEIVDKSG   35 (71)
Q Consensus         6 e~~l~V~-~~dvGKVIGk~Gr~ikaIr~~~~   35 (71)
                      +-.|.|. ++..+=||||+|+.|++|.+.+.
T Consensus       227 ~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar  257 (292)
T PRK00089        227 EATIYVERDSQKGIIIGKGGAMLKKIGTEAR  257 (292)
T ss_pred             EEEEEEccCCceeEEEeCCcHHHHHHHHHHH
Confidence            3445554 45678899999999999986554

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=80.02  E-value=1.3  Score=35.86  Aligned_cols=29  Identities=24%  Similarity=0.434  Sum_probs=25.5

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhc
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSG   35 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~   35 (71)
                      -.+.||+++.+..|||+|++++--..+.|
T Consensus       337 a~V~V~~~qlslAIGK~GqNvrLAs~Ltg  365 (449)
T PRK12329        337 AHVLVPPDQLSLAIGKEGQNVRLAARLTG  365 (449)
T ss_pred             EEEEEChHhcchhhcCCChhHHHHHHHHC
Confidence            46899999999999999999988776665

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	71
2qnd_A	144	Crystal Structure Of The Kh1-Kh2 Domains From Human		2e-18

>pdb|2QND|A Chain A, Crystal Structure Of The Kh1-Kh2 Domains From Human Fragile X Mental Retardation Protein Length = 144

Iteration: 1
 Score = 87.4 bits (215), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 42/63 (66%), Positives = 54/63 (85%), Gaps = 2/63 (3%)
Query: 1   MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPF 60
            LE++E+ +QVPRNLVGKVIGKNG++IQEIVDKSGVVRV+IE +NE    +P+EEG VPF
Sbjct: 63  FLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENE--KNVPQEEGXVPF 120
Query: 61  MVL 63
           + +
Sbjct: 121 VFV 123

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	71
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	1e-12
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	4e-05
1we8_A	104	Tudor and KH domain containing protein; structural	2e-08
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	9e-08
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-07
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	3e-07
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	5e-07
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	7e-07
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	8e-07
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	1e-06
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	1e-06
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	2e-06
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-06
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	1e-05
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	2e-06
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-06
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	3e-06
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	1e-04
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	3e-06
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	1e-05
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-05
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	4e-05
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	3e-05
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	3e-05
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	6e-05
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	6e-05
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	1e-04
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	1e-04
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	3e-04
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	4e-04
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	6e-04
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	6e-04
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	9e-04

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Length = 144

 Score = 57.3 bits (138), Expect = 1e-12
 Identities = 42/62 (67%), Positives = 52/62 (83%), Gaps = 2/62 (3%)

Query: 1   MLEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPF 60
            LE++E+ +QVPRNLVGKVIGKNG++IQEIVDKSGVVRV+IE +NE     P+EEG VPF
Sbjct: 63  FLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNV--PQEEGMVPF 120

Query: 61  MV 62
           + 
Sbjct: 121 VF 122

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Length = 144

 Score = 37.7 bits (87), Expect = 4e-05
 Identities = 12/41 (29%), Positives = 19/41 (46%)

Query: 7  ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEP 47
          E   V  +L+G  IG +G  IQ+     GV  + ++ D   
Sbjct: 6  EQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCT 46

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Length = 104

 Score = 46.0 bits (109), Expect = 2e-08
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 7  ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPR 53
          E L VP+  VG++IG+ G  I+ I   SG  ++  + ++E    L R
Sbjct: 17 EQLSVPQRSVGRIIGRGGETIRSICKASG-AKITCDKESEGTLLLSR 62

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

 Score = 43.4 bits (103), Expect = 9e-08
 Identities = 15/41 (36%), Positives = 24/41 (58%), Gaps = 1/41 (2%)

Query: 9  LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
          + VP NLVG ++GK G+ + E  + +G  R++I    E  P
Sbjct: 7  MAVPENLVGAILGKGGKTLVEYQELTG-ARIQISKKGEFLP 46

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

 Score = 42.7 bits (101), Expect = 2e-07
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 5  SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPR 53
          + + + +P    G VIGK G  I+++ +++G V++ +  D      + +
Sbjct: 14 TVQEIMIPAGKAGLVIGKGGETIKQLQERAG-VKMILIQDGSQNTNVDK 61

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

 Score = 42.3 bits (100), Expect = 3e-07
 Identities = 15/41 (36%), Positives = 24/41 (58%), Gaps = 1/41 (2%)

Query: 9  LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
          + VP NLVG ++GK G+ + E  + +G  R++I    E  P
Sbjct: 7  IAVPENLVGAILGKGGKTLVEYQELTG-ARIQISKKGEFLP 46

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

 Score = 42.0 bits (99), Expect = 5e-07
 Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 5  SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPR 53
          + + + +P +  G VIGK G  I+++ +++G V++ +  D        +
Sbjct: 15 AVQEIMIPASKAGLVIGKGGETIKQLQERAG-VKMVMIQDGPQNTGADK 62

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

 Score = 41.6 bits (98), Expect = 7e-07
 Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 1/43 (2%)

Query: 7  ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
          E  +VP  +VG +IG+ G  I  I  +SG  +++I  D+   P
Sbjct: 17 EEYKVPDGMVGFIIGRGGEQISRIQQESG-CKIQIAPDSGGLP 58

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

 Score = 41.7 bits (98), Expect = 8e-07
 Identities = 16/41 (39%), Positives = 29/41 (70%), Gaps = 1/41 (2%)

Query: 9  LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
          + VPR+ VG VIG++G +I++I + +G VR++ + D+   P
Sbjct: 15 VPVPRHSVGVVIGRSGEMIKKIQNDAG-VRIQFKQDDGTGP 54

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

 Score = 41.4 bits (97), Expect = 1e-06
 Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 1/46 (2%)

Query: 5  SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT 50
           E +  +P +  G VIG+ G  ++ I  ++G   V+I     P   
Sbjct: 7  GEMTFSIPTHKCGLVIGRGGENVKAINQQTG-AFVEISRQLPPNGD 51

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

 Score = 40.7 bits (96), Expect = 1e-06
 Identities = 14/41 (34%), Positives = 25/41 (60%), Gaps = 1/41 (2%)

Query: 9  LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
          + +P++L G +IGK G+ I++I  +SG   +KI+   E   
Sbjct: 11 VTIPKDLAGSIIGKGGQRIKQIRHESG-ASIKIDEPLEGSE 50

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A Length = 89

 Score = 40.4 bits (95), Expect = 2e-06
 Identities = 14/38 (36%), Positives = 25/38 (65%), Gaps = 1/38 (2%)

Query: 9  LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE 46
          + +P++L G +IGK G+ I++I  +SG   +KI+   E
Sbjct: 18 VTIPKDLAGSIIGKGGQRIKQIRHESG-ASIKIDEPLE 54

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

 Score = 41.7 bits (98), Expect = 2e-06
 Identities = 16/44 (36%), Positives = 29/44 (65%), Gaps = 1/44 (2%)

Query: 6   EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
              + VPR+ VG VIG++G +I++I + +G VR++ + D+   P
Sbjct: 92  GIDVPVPRHSVGVVIGRSGEMIKKIQNDAG-VRIQFKQDDGTGP 134

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

 Score = 39.4 bits (92), Expect = 1e-05
 Identities = 11/45 (24%), Positives = 24/45 (53%), Gaps = 1/45 (2%)

Query: 9  LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPR 53
          + +P    G VIGK G  I+++ +++G V++ +  D      + +
Sbjct: 6  IMIPAGKAGLVIGKGGETIKQLQERAG-VKMILIQDGSQNTNVDK 49

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1 Length = 82

 Score = 40.3 bits (95), Expect = 2e-06
 Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 7  ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
            L +P NL+G +IG+ G  I EI   SG  ++KI    E   
Sbjct: 8  HELTIPNNLIGCIIGRQGANINEIRQMSG-AQIKIANPVEGSS 49

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

 Score = 41.3 bits (97), Expect = 2e-06
 Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 1/42 (2%)

Query: 9   LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT 50
           L VP +  G +IGK G  I+EI + +G  +V++ GD  P  T
Sbjct: 93  LVVPASQCGSLIGKGGCKIKEIRESTG-AQVQVAGDMLPNST 133

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163

 Score = 40.9 bits (96), Expect = 3e-06
 Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 1/42 (2%)

Query: 9   LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT 50
           ++VP +  G+VIGK G+ + E+ + +    V +  D  P   
Sbjct: 89  IRVPASAAGRVIGKGGKTVNELQNLTA-AEVVVPRDQTPDEN 129

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163

 Score = 36.7 bits (85), Expect = 1e-04
 Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 1/42 (2%)

Query: 9  LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT 50
          + +P   VG +IGK G+ I+++   +    +KI     P   
Sbjct: 7  VFIPAQAVGAIIGKKGQHIKQLSRFAS-ASIKIAPPETPDSK 47

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

 Score = 39.2 bits (92), Expect = 3e-06
 Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 1/41 (2%)

Query: 9  LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
          L +P +L+G +IG+ G  I EI   SG  ++KI    E   
Sbjct: 9  LTIPNDLIGCIIGRQGAKINEIRQMSG-AQIKIANPVEGST 48

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

 Score = 38.6 bits (90), Expect = 1e-05
 Identities = 11/46 (23%), Positives = 22/46 (47%)

Query: 3  EYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQ 48
            +E  + +P  L   +IG  GR+I+ I+++ G V +    +    
Sbjct: 15 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGS 60

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

 Score = 38.7 bits (90), Expect = 2e-05
 Identities = 11/39 (28%), Positives = 22/39 (56%), Gaps = 1/39 (2%)

Query: 9   LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEP 47
           + VP +  G +IGK G  ++ I+++SG   V++    + 
Sbjct: 108 IIVPNSTAGLIIGKGGATVKAIMEQSG-AWVQLSQKPDG 145

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

 Score = 38.3 bits (89), Expect = 4e-05
 Identities = 10/44 (22%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 9  LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLP 52
          + +P    G +IGK G+ I ++  ++G   +K+    +  P   
Sbjct: 10 VLIPSYAAGSIIGKGGQTIVQLQKETG-ATIKLSKSKDFYPGTT 52

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94

 Score = 37.4 bits (87), Expect = 3e-05
 Identities = 11/44 (25%), Positives = 24/44 (54%), Gaps = 1/44 (2%)

Query: 7  ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT 50
           ++ +P+     VIGKNG  +Q++  K+   +++I   ++P   
Sbjct: 19 ATVAIPKEHHRFVIGKNGEKLQDLELKTA-TKIQIPRPDDPSNQ 61

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

 Score = 38.3 bits (89), Expect = 3e-05
 Identities = 16/41 (39%), Positives = 28/41 (68%), Gaps = 1/41 (2%)

Query: 9  LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
          + +PR  VG VIG+NG +I++I + +G VR++ + D+   P
Sbjct: 7  VPIPRFAVGIVIGRNGEMIKKIQNDAG-VRIQFKPDDGTTP 46

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

 Score = 37.5 bits (87), Expect = 6e-05
 Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 1/41 (2%)

Query: 9   LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
             VP    G +IGK G  I+ I  +SG  R++++ +  P  
Sbjct: 108 FIVPTGKTGLIIGKGGETIKSISQQSG-ARIELQRNPPPNA 147

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

 Score = 36.1 bits (84), Expect = 6e-05
 Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 1/39 (2%)

Query: 9  LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEP 47
          L +    VG +IGK G  ++++ ++SG  R+ I   N P
Sbjct: 9  LLMHGKEVGSIIGKKGESVKKMREESG-ARINISEGNCP 46

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

 Score = 35.4 bits (82), Expect = 1e-04
 Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 1/46 (2%)

Query: 3  EYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQ 48
                + +       +IGK+G  I  I D+   V V+I  D+E  
Sbjct: 3  RMDYVEINIDHKFHRHLIGKSGANINRIKDQYK-VSVRIPPDSEKS 47

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

 Score = 35.9 bits (83), Expect = 1e-04
 Identities = 10/43 (23%), Positives = 21/43 (48%), Gaps = 1/43 (2%)

Query: 6  EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQ 48
             ++VP +L   VIG+ G  I++++D+   V + +       
Sbjct: 18 TIEVEVPFDLHRYVIGQKGSGIRKMMDEFE-VNIHVPAPELQS 59

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 97

 Score = 34.8 bits (80), Expect = 3e-04
 Identities = 9/45 (20%), Positives = 20/45 (44%), Gaps = 1/45 (2%)

Query: 6  EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT 50
          + S+ V      K+IG+ G +I +I  +   V ++    ++    
Sbjct: 18 KLSVTVDPKYHPKIIGRKGAVITQIRLEHD-VNIQFPDKDDGNQP 61

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

 Score = 35.6 bits (83), Expect = 4e-04
 Identities = 9/38 (23%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

Query: 7   ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD 44
           E++QVP +   K +G  G  ++++  ++G V +    +
Sbjct: 569 ETVQVPLSKRAKFVGPGGYNLKKLQAETG-VTISQVDE 605

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

 Score = 34.0 bits (78), Expect = 6e-04
 Identities = 10/45 (22%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 7  ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTL 51
          E + +   +  ++IG  G+ I++I+D+   V ++      P P  
Sbjct: 19 EDVPLDHRVHARIIGARGKAIRKIMDEFK-VDIRFPQSGAPDPNC 62

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

 Score = 35.2 bits (82), Expect = 6e-04
 Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 7/47 (14%)

Query: 7   ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVV-------RVKIEGDNE 46
           E++ +P + + +VIG  G++I+EIV  +G          VK+   + 
Sbjct: 572 ETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVKVSASDG 618

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

 Score = 34.4 bits (80), Expect = 9e-04
 Identities = 10/38 (26%), Positives = 24/38 (63%), Gaps = 1/38 (2%)

Query: 7   ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD 44
            ++++  + +  VIGK G +I+ + +++G   ++IE D
Sbjct: 562 HTIKINPDKIKDVIGKGGSVIRALTEETG-TTIEIEDD 598

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	71
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.12
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	98.61
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	98.4
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	98.37
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	98.37
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	98.29
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	98.27
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	98.26
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	98.24
1we8_A	104	Tudor and KH domain containing protein; structural	98.22
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	98.21
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	98.2
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	98.15
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	98.14
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.13
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	98.12
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	98.1
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	98.07
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	98.02
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	98.01
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	97.96
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	97.93
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	97.92
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	97.91
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	97.89
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	97.89
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	97.87
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	97.85
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	97.74
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	97.73
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	97.69
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	97.68
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	97.26
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	97.13
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	96.53
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	96.42
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	96.2
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	95.96
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	95.55
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	95.53
1tua_A	191	Hypothetical protein APE0754; structural genomics,	95.01
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	94.6
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	92.77
1tua_A	191	Hypothetical protein APE0754; structural genomics,	91.18
2cxc_A	144	NUSA; transcription termination, RNA binding prote	90.88
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	90.54
2pt7_G	152	HP1451, hypothetical protein; ATPase, protein-prot	90.31
2cxc_A	144	NUSA; transcription termination, RNA binding prote	89.9
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	88.5
3gku_A	225	Probable RNA-binding protein; APC21302, clostridiu	88.48
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	88.43
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	88.35
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	85.62
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	82.15
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	81.15

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

Probab=99.12  E-value=2.8e-11  Score=80.21  Aligned_cols=63  Identities=67%  Similarity=1.105  Sum_probs=54.7

Q ss_pred             cceeeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCCCCCCCCCCCCccceEEeeeE
Q psy986            2 LEYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFMVLTKT   66 (71)
Q Consensus         2 LEf~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e~~~~~~~~~~~vpF~~vGt~   66 (71)
                      |++.+..+.||++.+|.+|||+|++|+.|++.+|+..++|..+++..  .+.+++.+||.++||.
T Consensus        64 l~~~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~--~~~~~~~~~vtI~G~~  126 (144)
T 2qnd_A           64 LEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKN--VPQEEGMVPFVFVGTK  126 (144)
T ss_dssp             HCEEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTC--CCCCTTEEEEEEEEEH
T ss_pred             hhcceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCC--ccccCCeeEEEEEeCH
Confidence            56778899999999999999999999999999999999998765542  3567788999999984

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

Probab=98.61  E-value=5.5e-08  Score=57.28  Aligned_cols=41  Identities=34%  Similarity=0.653  Sum_probs=35.6

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCC
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE   46 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e   46 (71)
                      ....+.||++.+|.+|||+|++|+.|+..+|+ .++|+.+++
T Consensus         3 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga-~I~i~~~~~   43 (76)
T 1dtj_A            3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGA-RIQISKKGE   43 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCC-EEEECCTTC
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCC-EEEECcCCC
Confidence            34678999999999999999999999999996 788886544

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

Probab=98.40  E-value=4.3e-07  Score=54.67  Aligned_cols=38  Identities=34%  Similarity=0.712  Sum_probs=34.1

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      ....+.||++.+|.+|||+|++|+.|++.+++ .|+|+.
T Consensus         7 ~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga-~I~i~~   44 (82)
T 1zzk_A            7 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGA-SIKIDE   44 (82)
T ss_dssp             EEEEEEEETTTGGGGTCGGGHHHHHHHHHHCC-EEEECC
T ss_pred             EEEEEEEChHhcCeeECCCchHHHHHHHHHCC-EEEEcC
Confidence            45689999999999999999999999999996 688863

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

Probab=98.37  E-value=4.6e-07  Score=57.35  Aligned_cols=40  Identities=28%  Similarity=0.498  Sum_probs=35.2

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCC
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE   46 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e   46 (71)
                      ...+.||.+.+|.||||+|++|+.|++.+++ .|+|+.+.+
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa-~I~I~~~~~   47 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGA-FVEISRQLP   47 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSS-EEEECCCCC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCC-EEEEcCccC
Confidence            5689999999999999999999999999986 688875443

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

Probab=98.37  E-value=1.4e-07  Score=57.22  Aligned_cols=40  Identities=35%  Similarity=0.668  Sum_probs=35.1

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCC
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE   46 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e   46 (71)
                      ...+.||++.+|.||||+|.+|+.|++.+|+ .|+|+.+++
T Consensus         4 t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga-~I~I~~~~~   43 (87)
T 1ec6_A            4 LVEIAVPENLVGAILGKGGKTLVEYQELTGA-RIQISKKGE   43 (87)
T ss_dssp             EEEEEEEHHHHHHHHCGGGHHHHHHHHHHCC-EEEECCTTC
T ss_pred             EEEEEEChHHcCeeECCCcHhHHHHHHHhCC-EEEEccCCC
Confidence            4678999999999999999999999999996 688885443

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

Probab=98.29  E-value=5.3e-07  Score=53.33  Aligned_cols=41  Identities=27%  Similarity=0.403  Sum_probs=35.6

Q ss_pred             ceeeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986            3 EYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD   44 (71)
Q Consensus         3 Ef~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~   44 (71)
                      +++...+.||++.+|.+||++|++|+.|++..+ +.++|+.+
T Consensus         3 ~~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg-~~I~i~~~   43 (71)
T 1vig_A            3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYK-VSVRIPPD   43 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTC-CEEECCCC
T ss_pred             ceEEEEEEECHHHhhhhcCCCCccHHHHHHHHC-CEEEECCC
Confidence            567889999999999999999999999999987 45777643

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

Probab=98.27  E-value=7.3e-07  Score=53.96  Aligned_cols=37  Identities=27%  Similarity=0.587  Sum_probs=33.5

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      ...+.||++.+|+||||+|.+|+.|++.+++ .++|+.
T Consensus        15 ~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga-~I~i~~   51 (85)
T 2opv_A           15 VQEIMIPAGKAGLVIGKGGETIKQLQERAGV-KMILIQ   51 (85)
T ss_dssp             EEEEEECTTTHHHHHTTTTHHHHHHHHHHTC-EEEECS
T ss_pred             EEEEEeChhheeeeECCCCHHHHHHHHHHCC-EEEEcC
Confidence            5689999999999999999999999999996 678874

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

Probab=98.26  E-value=3.5e-07  Score=54.15  Aligned_cols=38  Identities=37%  Similarity=0.722  Sum_probs=34.0

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      ....+.||++.+|.+|||+|.+|+.|++.+| +.++|+.
T Consensus         5 ~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tg-a~I~i~~   42 (76)
T 2p2r_A            5 TSHELTIPNDLIGCIIGRQGAKINEIRQMSG-AQIKIAN   42 (76)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHC-CEEEECC
T ss_pred             eEEEEEEChHHcceEECCCChHHHHHHHHHC-CEEEEcC
Confidence            4568999999999999999999999999999 4688874

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

Probab=98.24  E-value=3.8e-07  Score=56.19  Aligned_cols=39  Identities=36%  Similarity=0.673  Sum_probs=34.8

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD   44 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~   44 (71)
                      ....+.||++.+|.||||+|++|+.|++.+++ .|+|+.+
T Consensus        15 ~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga-~I~I~~~   53 (92)
T 1x4n_A           15 MTEEYKVPDGMVGFIIGRGGEQISRIQQESGC-KIQIAPD   53 (92)
T ss_dssp             EEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCC-EEEECSC
T ss_pred             EEEEEEEChHHcceeECCCchHHHHHHHHhCC-EEEEcCC
Confidence            45789999999999999999999999999996 6888754

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1

Probab=98.22  E-value=9.2e-07  Score=55.48  Aligned_cols=39  Identities=33%  Similarity=0.679  Sum_probs=34.2

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCC
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDN   45 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~   45 (71)
                      ...+.||++.+|.||||+|.+|+.|++.+++ .|+|+.++
T Consensus        16 ~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga-~I~I~~~~   54 (104)
T 1we8_A           16 FEQLSVPQRSVGRIIGRGGETIRSICKASGA-KITCDKES   54 (104)
T ss_dssp             EEEEEEETTTHHHHHTTTSHHHHHHHHHHCC-EEEECCSS
T ss_pred             EEEEEEChhheeeeECCCCHHHHHHHHHHCC-EEEEecCC
Confidence            4678999999999999999999999999986 68887443

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1

Probab=98.21  E-value=9.1e-07  Score=53.11  Aligned_cols=39  Identities=38%  Similarity=0.694  Sum_probs=34.5

Q ss_pred             eeeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            4 YSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         4 f~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      .....+.||++.+|.||||+|.+|+.|++.+|+ .|+|+.
T Consensus         5 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga-~I~i~~   43 (82)
T 1wvn_A            5 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGA-QIKIAN   43 (82)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCC-EEEECC
T ss_pred             cEEEEEEEchHhccceeCCCchhHHHHHHHhCC-EEEEec
Confidence            356789999999999999999999999999995 588874

>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=98.20  E-value=1.2e-06  Score=57.13  Aligned_cols=53  Identities=28%  Similarity=0.562  Sum_probs=40.4

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCCCCCCCCCCCCccceEEeee
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFMVLTK   65 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e~~~~~~~~~~~vpF~~vGt   65 (71)
                      ..+.||++.+|.+|||+|.+|+.|++.+|+ .+++..+..     +......++.+.|+
T Consensus        87 ~~i~vp~~~~g~iIGkgG~~I~~i~~~tga-~I~i~~~~~-----~~~~~~~~v~I~G~  139 (163)
T 3krm_A           87 THIRVPASAAGRVIGKGGKTVNELQNLTAA-EVVVPRDQT-----PDENDQVIVKIIGH  139 (163)
T ss_dssp             EEEEEETTTHHHHHCGGGHHHHHHHHHHCC-EEECCTTCC-----CCTTSEEEEEEEEC
T ss_pred             EEEEcChhheeeEEcCCChHHHHHHHHhCC-eEEECCCCC-----CCCCCceEEEEEeC
Confidence            379999999999999999999999999985 778864332     22333445666665

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A

Probab=98.15  E-value=7.6e-07  Score=54.39  Aligned_cols=38  Identities=34%  Similarity=0.712  Sum_probs=33.9

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      ....+.||++.+|.||||+|++|+.|++.+++ .|+|+.
T Consensus        14 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga-~I~I~~   51 (89)
T 1j5k_A           14 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGA-SIKIDE   51 (89)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCC-EEEECS
T ss_pred             EEEEEEEChhhcceeECCCCHhHHHHHHHhCC-eEEecC
Confidence            45679999999999999999999999999986 688863

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

Probab=98.14  E-value=6.6e-07  Score=53.05  Aligned_cols=39  Identities=28%  Similarity=0.505  Sum_probs=34.3

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD   44 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~   44 (71)
                      ....+.||++.+|.+|||+|.+|+.|++.+|+ .++|+.+
T Consensus         5 ~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga-~I~i~~~   43 (73)
T 2axy_A            5 LTIRLLMHGKEVGSIIGKKGESVKKMREESGA-RINISEG   43 (73)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCC-EEEECSS
T ss_pred             EEEEEEEChhHeeeEECCCCHHHHHHHHHHCC-EEEEecC
Confidence            45678999999999999999999999999985 6888743

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

Probab=98.13  E-value=8.7e-07  Score=56.24  Aligned_cols=39  Identities=28%  Similarity=0.467  Sum_probs=35.2

Q ss_pred             eeeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            4 YSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         4 f~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      .....++||++.+|.+||++|++|++|++..|+-+|+|+
T Consensus        14 ~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~   52 (91)
T 2cpq_A           14 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELD   52 (91)
T ss_dssp             SEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEE
T ss_pred             ceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEE
Confidence            345789999999999999999999999999998678887

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

Probab=98.12  E-value=1.9e-06  Score=54.92  Aligned_cols=39  Identities=38%  Similarity=0.762  Sum_probs=34.3

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCC
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDN   45 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~   45 (71)
                      ...+.||++.+|.||||+|.+|+.|++.+++ .|+|+.++
T Consensus        12 ~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGa-kI~I~~~~   50 (106)
T 2hh3_A           12 GIDVPVPRHSVGVVIGRSGEMIKKIQNDAGV-RIQFKQDD   50 (106)
T ss_dssp             CEEEEEETTTHHHHHTTTTHHHHHHHHHHTC-EEEECSSC
T ss_pred             EEEEEECHHHcCccCCCCcHHHHHHHHHHCc-EEEEecCC
Confidence            4689999999999999999999999999985 78887443

>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=98.10  E-value=3e-06  Score=55.93  Aligned_cols=39  Identities=33%  Similarity=0.624  Sum_probs=34.8

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD   44 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~   44 (71)
                      ....+.||++.+|.+|||+|++|+.|++.+++ .|+|..+
T Consensus       104 ~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga-~I~i~~~  142 (174)
T 1j4w_A          104 QEFNFIVPTGKTGLIIGKGGETIKSISQQSGA-RIELQRN  142 (174)
T ss_dssp             CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCC-EEEEECC
T ss_pred             EEEEEEEChHHcCeeECCCchHHHHHHHHHCC-EEEECCC
Confidence            36689999999999999999999999999996 6888754

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

Probab=98.07  E-value=1.5e-06  Score=53.62  Aligned_cols=39  Identities=28%  Similarity=0.612  Sum_probs=34.2

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD   44 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~   44 (71)
                      ....+.||++.+|.||||+|.+|+.|++.+++ .|+|+.+
T Consensus        15 ~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga-~I~I~~~   53 (94)
T 1x4m_A           15 AVQEIMIPASKAGLVIGKGGETIKQLQERAGV-KMVMIQD   53 (94)
T ss_dssp             EEEEEEECHHHHHHHSCSSSSHHHHHHHHHTS-EEEECCS
T ss_pred             EEEEEEEChhhcceEECCCCHHHHHHHHHHCC-eEEecCC
Confidence            45689999999999999999999999999995 6888743

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

Probab=98.02  E-value=3.4e-06  Score=52.67  Aligned_cols=38  Identities=24%  Similarity=0.368  Sum_probs=33.2

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      ....+.||++.+|+|||++|.+|+.|++..+ +.|+|..
T Consensus        17 ~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg-~~I~i~~   54 (97)
T 2ctl_A           17 FKLSVTVDPKYHPKIIGRKGAVITQIRLEHD-VNIQFPD   54 (97)
T ss_dssp             CEEEEECCTTTHHHHSCSSSCHHHHHHHHHT-CEEECCC
T ss_pred             eeEEEEECHHHhhhcCCCCchhHHHHHHHHC-CEEEecC
Confidence            3568999999999999999999999999988 4577763

>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=98.01  E-value=3.1e-06  Score=54.74  Aligned_cols=37  Identities=41%  Similarity=0.791  Sum_probs=33.4

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD   44 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~   44 (71)
                      ..+.||++.+|++|||+|++|+.|++.+++ .++|..+
T Consensus        93 ~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~-~I~i~~~  129 (164)
T 2jvz_A           93 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGV-RIQFKQD  129 (164)
T ss_dssp             BCCEEETTTHHHHHCSSSHHHHHHHHHTCC-EEEECCC
T ss_pred             EEEEEChhhccccCCCCcHhHHHHHHHHCC-eEEEeCC
Confidence            678999999999999999999999999986 7888744

>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=97.96  E-value=2.5e-06  Score=55.43  Aligned_cols=38  Identities=37%  Similarity=0.626  Sum_probs=34.1

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      ....+.||++.+|.+|||+|++|+.|++.+|+ .+++..
T Consensus        89 ~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga-~I~i~~  126 (160)
T 2jzx_A           89 VTLRLVVPASQCGSLIGKGGCKIKEIRESTGA-QVQVAG  126 (160)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSS-EECCCC
T ss_pred             EEEEEEEChhheeeEECCCCHHHHHHHHHhCC-eEEECC
Confidence            35688999999999999999999999999996 788874

>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=97.93  E-value=3.4e-06  Score=55.69  Aligned_cols=39  Identities=38%  Similarity=0.716  Sum_probs=34.5

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD   44 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~   44 (71)
                      ....+.||++.+|.+|||+|.+|+.|++.++ +.|+|+.+
T Consensus         3 ~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg-~~I~i~~~   41 (174)
T 1j4w_A            3 HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAG-VRIQFKPD   41 (174)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHC-CEEEEECC
T ss_pred             eEEEEEEChhheeeeecCCchHHHHHHHHhC-CEEEEecC
Confidence            3568999999999999999999999999999 57888743

>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=97.92  E-value=7.7e-06  Score=52.85  Aligned_cols=38  Identities=29%  Similarity=0.613  Sum_probs=33.0

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD   44 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~   44 (71)
                      ...+.||++.+|.+|||+|.+|+.|++.++ +.+++..+
T Consensus         3 ~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg-~~I~i~~~   40 (164)
T 2jvz_A            3 VQEIMIPAGKAGLVIGKGGETIKQLQERAG-VKMILIQD   40 (164)
T ss_dssp             EEEEEECTTCHHHHTCTTTHHHHHHHHTSC-SEEEECCC
T ss_pred             EEEEEechhheeEEECCChHHHHHHHHHhC-CeEEEecC
Confidence            467899999999999999999999999998 45777643

>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=97.91  E-value=7.7e-06  Score=50.50  Aligned_cols=37  Identities=27%  Similarity=0.519  Sum_probs=32.2

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      ....+.||++.+|.+||++|.+|+.|++..+ +.|+|+
T Consensus        17 ~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg-~~I~i~   53 (94)
T 2cte_A           17 ASATVAIPKEHHRFVIGKNGEKLQDLELKTA-TKIQIP   53 (94)
T ss_dssp             EEEEEECCTTTHHHHHCSSSCHHHHHHHHTT-CCCBCC
T ss_pred             eEEEEEEChHHeeeeECCCChhHHHHHHHHC-CEEEeC
Confidence            4578999999999999999999999999987 456665

>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=97.89  E-value=3.3e-06  Score=55.82  Aligned_cols=39  Identities=28%  Similarity=0.590  Sum_probs=34.6

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD   44 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~   44 (71)
                      ....+.||++.+|.+|||+|++|+.|++.+|+ .|+|..+
T Consensus       104 ~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga-~I~i~~~  142 (178)
T 2anr_A          104 NQVKIIVPNSTAGLIIGKGGATVKAIMEQSGA-WVQLSQK  142 (178)
T ss_dssp             GEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSC-EEEECCC
T ss_pred             eEEEEEEchhheeeeECCCcHHHHHHHHHHCC-EEEEeCC
Confidence            35689999999999999999999999999996 7888744

>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=97.89  E-value=9.2e-06  Score=50.63  Aligned_cols=39  Identities=21%  Similarity=0.467  Sum_probs=34.2

Q ss_pred             eeeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            4 YSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         4 f~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      .....+.||++.+|.+||++|++|+.|++..+ +.|+|..
T Consensus        16 ~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg-~~I~i~~   54 (95)
T 2ctm_A           16 MVSEDVPLDHRVHARIIGARGKAIRKIMDEFK-VDIRFPQ   54 (95)
T ss_dssp             CCCEEEECCTTTHHHHHCSSSCHHHHHHHHHT-CEEECCC
T ss_pred             cEEEEEEECHHHccccCCCCcchHHHHHHHHC-CeEEecC
Confidence            35678999999999999999999999999987 6777763

>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=97.87  E-value=9.7e-06  Score=52.74  Aligned_cols=39  Identities=26%  Similarity=0.457  Sum_probs=34.2

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD   44 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~   44 (71)
                      -...+.||++.+|.+|||+|.+|+.|++.+++ .++++.+
T Consensus         3 ~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~-~I~i~~~   41 (163)
T 3krm_A            3 EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASA-SIKIAPP   41 (163)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTC-EEEECCC
T ss_pred             eEEEEEechhhcceeECCCcHHHHHHHHHHCC-eEEEcCC
Confidence            35678999999999999999999999999995 7888743

>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=97.85  E-value=6.6e-06  Score=50.45  Aligned_cols=38  Identities=26%  Similarity=0.503  Sum_probs=33.2

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      ....+.||.+.+|-||||+|.+|++|++.+++ .|+|..
T Consensus        10 ~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga-~I~I~~   47 (83)
T 2dgr_A           10 TTIQVRVPYRVVGLVVGPKGATIKRIQQRTHT-YIVTPG   47 (83)
T ss_dssp             EEEEEECCHHHHHHHHTTTTSSHHHHHHHTTC-EEECCC
T ss_pred             eEEEEEeChHHeeeeECCCchHHHHHHHHhCC-eEEecC
Confidence            35678999999999999999999999999885 577764

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

Probab=97.74  E-value=8.3e-06  Score=51.11  Aligned_cols=41  Identities=27%  Similarity=0.566  Sum_probs=36.5

Q ss_pred             ceeeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            3 EYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         3 Ef~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      ++.+..+.||++..+.+||++|++|++|.+..+-+.|+|..
T Consensus        15 ~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~   55 (95)
T 2ctj_A           15 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPV   55 (95)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCC
T ss_pred             hcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCC
Confidence            47789999999999999999999999999999657788863

>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=97.73  E-value=1e-05  Score=51.09  Aligned_cols=37  Identities=27%  Similarity=0.466  Sum_probs=32.3

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      ...+.||++.+|.|||++|++|+.|++..++ .|+|+.
T Consensus        18 ~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~-~I~I~~   54 (104)
T 2ctk_A           18 TIEVEVPFDLHRYVIGQKGSGIRKMMDEFEV-NIHVPA   54 (104)
T ss_dssp             EEEEECCHHHHHHHHCSSSHHHHHHHHHTCC-EEECCC
T ss_pred             EEEEEEChHHccceeCCCchHHHHHHHHHCC-EEEecC
Confidence            4678999999999999999999999999874 577763

>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=97.69  E-value=1.6e-05  Score=52.47  Aligned_cols=40  Identities=23%  Similarity=0.446  Sum_probs=34.7

Q ss_pred             eeeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986            4 YSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD   44 (71)
Q Consensus         4 f~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~   44 (71)
                      .....+.||.+.+|.+|||+|.+|+.|++.+++ .|+|+.+
T Consensus         5 ~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~-~I~i~~~   44 (178)
T 2anr_A            5 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGA-TIKLSKS   44 (178)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCC-EEEECCT
T ss_pred             CEEEEEEEChhHeeeeECCCcHHHHHHHHHhCC-eEEEecC
Confidence            356789999999999999999999999999984 5888643

>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=97.68  E-value=1.2e-05  Score=52.21  Aligned_cols=38  Identities=29%  Similarity=0.518  Sum_probs=33.7

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      ....+.||++.+|.+|||+|.+|+.|++.+++ .++++.
T Consensus         5 ~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~-~I~i~~   42 (160)
T 2jzx_A            5 LTIRLLMHGKEVGSIIGKKGESVKKMREESGA-RINISE   42 (160)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCS-EEEEEC
T ss_pred             EEEEEEEchhheeeeECCCcHHHHHHHHHHCC-EEEEcC
Confidence            35689999999999999999999999999995 688873

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

Probab=97.26  E-value=0.0002  Score=45.13  Aligned_cols=40  Identities=23%  Similarity=0.395  Sum_probs=35.3

Q ss_pred             eeeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            4 YSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         4 f~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      +....|.||+.+-+.+||++|.+|+.||+....+.|++..
T Consensus        26 ~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~   65 (102)
T 2ctf_A           26 FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE   65 (102)
T ss_dssp             CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS
T ss_pred             eEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC
Confidence            4568899999999999999999999999988667887763

>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=97.13  E-value=0.00024  Score=46.68  Aligned_cols=30  Identities=33%  Similarity=0.513  Sum_probs=28.4

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhc
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSG   35 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~   35 (71)
                      .+++.||.+.+|-+||++|.+|++|++.++
T Consensus         5 ~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~g   34 (144)
T 2qnd_A            5 HEQFIVREDLMGLAIGTHGANIQQARKVPG   34 (144)
T ss_dssp             EEEEECCGGGHHHHHCGGGHHHHHHHTSTT
T ss_pred             EEEEEECCcceeeEECCChhHHHHHHHHHC
Confidence            467899999999999999999999999999

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

Probab=96.53  E-value=0.0026  Score=41.49  Aligned_cols=39  Identities=28%  Similarity=0.399  Sum_probs=31.0

Q ss_pred             eeeeeeeeCCC-------ccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            4 YSEESLQVPRN-------LVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         4 f~e~~l~V~~~-------dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      +.++.|.||-+       .+|+|||.+|.+||.|....| +.|.|.+
T Consensus        11 ~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG-~kI~I~G   56 (119)
T 2yqr_A           11 YVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETG-AKVFLRG   56 (119)
T ss_dssp             CEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHC-CEEEEES
T ss_pred             EEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHC-CEEEEec
Confidence            45666777654       789999999999999999988 4566654

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

Probab=96.42  E-value=0.001  Score=47.03  Aligned_cols=36  Identities=25%  Similarity=0.611  Sum_probs=32.1

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      ..+.||++-+|.+||++|.+|++|.+.+| +.|+++.
T Consensus        36 ~~i~IP~~kig~lIG~gGk~Ik~I~e~tg-vkI~I~~   71 (219)
T 2e3u_A           36 EYVKIPKDRIAVLIGKKGQTKKEIEKRTK-TKITIDS   71 (219)
T ss_dssp             EEEECCHHHHHHHHCGGGHHHHHHHHHHT-EEEEECT
T ss_pred             EEEEeCHHHhhhhhcccHHHHHHHHHHHC-cEEEEEc
Confidence            47999999999999999999999999988 5677763

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

Probab=96.20  E-value=0.0018  Score=42.56  Aligned_cols=38  Identities=24%  Similarity=0.619  Sum_probs=31.9

Q ss_pred             eeeeeeeCCC------ccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            5 SEESLQVPRN------LVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         5 ~e~~l~V~~~------dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      ..+.|.||.+      .+|++||.+|+++|.|-.-.|+ .|.|.+
T Consensus         7 ~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~-kI~Irg   50 (131)
T 1k1g_A            7 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNA-KIMIRG   50 (131)
T ss_dssp             EEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCC-EEEEEE
T ss_pred             EEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCC-eEEecC
Confidence            4577899988      8999999999999999999885 466643

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

Probab=95.96  E-value=0.002  Score=51.60  Aligned_cols=36  Identities=25%  Similarity=0.436  Sum_probs=31.8

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      ...++||++.+|.+||++|++|+.|.+..|+ .|+|+
T Consensus       568 ~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~-~I~I~  603 (630)
T 3u1k_A          568 VETVQVPLSKRAKFVGPGGYNLKKLQAETGV-TISQV  603 (630)
T ss_dssp             EEEEECCHHHHHHHHCGGGHHHHHHHHHHCC-EEEEC
T ss_pred             EEEEEeChhHhheeECCCChhHHHHHHHHCC-EEEEc
Confidence            3578999999999999999999999998886 57776

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

Probab=95.55  E-value=0.0028  Score=44.77  Aligned_cols=27  Identities=37%  Similarity=0.625  Sum_probs=23.3

Q ss_pred             ccCcccccCchhHHHHHhhhceeEEeec
Q psy986           15 LVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus        15 dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      .+|++|||+|+++++|...+|+ .+.|.
T Consensus       139 ~~GriIGk~G~tik~ie~~Tg~-~I~v~  165 (219)
T 2e3u_A          139 VRGRIIGRKGRTRQIIEEMSGA-SVSVY  165 (219)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHCC-EEEEE
T ss_pred             hhheeECCCchHHHHHHHHhCc-eEEEC
Confidence            5899999999999999999985 56664

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

Probab=95.53  E-value=0.011  Score=39.67  Aligned_cols=37  Identities=27%  Similarity=0.633  Sum_probs=30.0

Q ss_pred             eeeeeeCCCc------cCcccccCchhHHHHHhhhceeEEeecC
Q psy986            6 EESLQVPRNL------VGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         6 e~~l~V~~~d------vGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      .+.|.||-+.      +|++||.+|+++|.|-...|+ .|.|.|
T Consensus         3 ~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~-kI~IrG   45 (140)
T 2bl5_A            3 QEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGC-KIMVRG   45 (140)
T ss_dssp             EEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSE-EEEEES
T ss_pred             eeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCC-eEEEec
Confidence            4567777665      999999999999999999885 466654

>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=95.01  E-value=0.0052  Score=42.82  Aligned_cols=27  Identities=22%  Similarity=0.551  Sum_probs=22.4

Q ss_pred             ccCcccccCchhHHHHHhhhceeEEeec
Q psy986           15 LVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus        15 dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      .+||+|||+|+++++|....|+ .+.|.
T Consensus       108 ~~GrIIGk~G~tik~iE~~Tg~-~I~v~  134 (191)
T 1tua_A          108 IKGRIIGEGGRARRTIEEMTDT-YINVG  134 (191)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTC-EEEEC
T ss_pred             HhhheeCCCccHHHHHHHHHCc-eEEEc
Confidence            5899999999999999988884 44454

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

Probab=94.60  E-value=0.006  Score=49.78  Aligned_cols=35  Identities=37%  Similarity=0.813  Sum_probs=0.0

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      ..+++|++.+|.|||++|++|++|.+..|+ .|+|+
T Consensus       572 ~~~~i~~~ki~~vig~gg~~i~~i~~~tg~-~idi~  606 (726)
T 4aid_A          572 ETINIPTDKIREVIGSGGKVIREIVATTGA-KVDIN  606 (726)
T ss_dssp             ------------------------------------
T ss_pred             EEEeCCHHHHHhhcCCCchhHHHHHHHHCC-ceeEE
Confidence            578999999999999999999999988876 45555

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

Probab=92.77  E-value=0.02  Score=46.53  Aligned_cols=35  Identities=26%  Similarity=0.659  Sum_probs=0.0

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      ..+++|++.+|.+||++|++|++|.+..|+ .++|+
T Consensus       562 ~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~-~IdI~  596 (723)
T 3cdi_A          562 HTIKINPDKIKDVIGKGGSVIRALTEETGT-TIEIE  596 (723)
T ss_dssp             ------------------------------------
T ss_pred             EEEEECHHHhcccccccceeeeeeehhhCc-eEEec
Confidence            568899999999999999999999998884 46665

>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=91.18  E-value=0.13  Score=35.68  Aligned_cols=36  Identities=25%  Similarity=0.518  Sum_probs=31.4

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      ...+.||++-+|-+||+.|.+++.|.+.++ +.++++
T Consensus         5 ~~~i~VP~~rvg~liGk~g~~~k~i~e~~g-~~i~id   40 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTG-TVITVD   40 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHT-EEEEEE
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHC-cEEEEE
Confidence            368999999999999999999999999887 456665

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

Probab=90.88  E-value=0.11  Score=34.68  Aligned_cols=31  Identities=19%  Similarity=0.278  Sum_probs=26.9

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhc
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSG   35 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~   35 (71)
                      ....+.||+++.+..|||+|+.++-...+.+
T Consensus       103 ~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg  133 (144)
T 2cxc_A          103 KQVVIKVSEDDKGAAIGKGGKNVKRARLVLS  133 (144)
T ss_dssp             EEEEEEECTTTHHHHHCGGGHHHHHHHHHHH
T ss_pred             EEEEEEEChHHhhhccCCCCHHHHHHHHHhC
Confidence            3457899999999999999999998887766

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

Probab=90.54  E-value=0.022  Score=46.56  Aligned_cols=35  Identities=29%  Similarity=0.650  Sum_probs=10.8

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      ..+++|++.+|.+||++|++|+.|++..|+. |+|+
T Consensus       600 ~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~-IdI~  634 (757)
T 1e3p_A          600 ITVKIPVDKIGEVIGPKRQMINQIQEDTGAE-ITIE  634 (757)
T ss_dssp             CCC------------------CTTCCCCCSC-C---
T ss_pred             EEEEEChHHeehcccccceeeehhhHhhCCE-EEec
Confidence            4689999999999999999999999888864 4444

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

Probab=90.31  E-value=0.1  Score=35.20  Aligned_cols=28  Identities=11%  Similarity=0.084  Sum_probs=23.8

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhh
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKS   34 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~   34 (71)
                      ..+.+.-+++|-+|||.|.|.+|+--++
T Consensus        35 i~i~i~ged~glLIGK~G~TL~ALQyL~   62 (152)
T 2pt7_G           35 LLIDIDGEDSALLIGEKGYRYKALSYLL   62 (152)
T ss_dssp             EEEEEEEGGGTTTTCGGGHHHHHHHHHH
T ss_pred             EEEEEecCCcceEECCCCcchHHHHHHH
Confidence            3567788999999999999999987655

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

Probab=89.90  E-value=0.22  Score=33.32  Aligned_cols=39  Identities=18%  Similarity=0.317  Sum_probs=31.3

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCC
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE   46 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e   46 (71)
                      -.+-|++.++|..||++|..+|+|...+ --.|+|-..++
T Consensus        38 ~i~vVk~g~vGa~IG~~G~ri~~i~~el-gekIdIV~~s~   76 (144)
T 2cxc_A           38 LIFLVSEGEAGRAIGRGGRLIKLLREAL-GKNIEVVEYSS   76 (144)
T ss_dssp             EEEEECTTCHHHHHCGGGHHHHHHHHHH-SSEEEEEECCS
T ss_pred             EEEEEeCCCccccCccCchHHHHHHHHh-CCeeEEEEcCC
Confidence            3577889999999999999999999888 45677643333

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

Probab=88.50  E-value=0.13  Score=39.22  Aligned_cols=36  Identities=8%  Similarity=0.237  Sum_probs=31.0

Q ss_pred             eeeeeeeCCCccCcccccCc--hhHHHHHhhhceeEEee
Q psy986            5 SEESLQVPRNLVGKVIGKNG--RIIQEIVDKSGVVRVKI   41 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~G--r~ikaIr~~~~a~~iki   41 (71)
                      ...++.||+.+.+.+|||+|  ..|+.|++..+ +.|++
T Consensus        30 VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtg-v~I~f   67 (376)
T 3n89_A           30 VTLNMEFESQYYSLMTSDNGDHENVASIMAETN-TLIQL   67 (376)
T ss_dssp             EEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHT-CEEEC
T ss_pred             EEEEEEEchhhhhhhccCCChHHHHHHHHHHhC-CeEEC
Confidence            34578899999999999999  99999999886 56666

>3gku_A Probable RNA-binding protein; APC21302, clostridium symbiosum ATCC 14 structural genomics, PSI-2, protein structure initiative; 2.95A {Clostridium symbiosum atcc 14940}

Probab=88.48  E-value=0.07  Score=38.09  Aligned_cols=31  Identities=19%  Similarity=0.369  Sum_probs=26.3

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhcee
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVV   37 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~   37 (71)
                      ..+.+..+|.|.+|||+|.+.+|+..++..+
T Consensus        94 i~i~i~g~d~g~LIGk~G~tLdALQyL~~~~  124 (225)
T 3gku_A           94 MNVNLKGDDMGILIGKRGQTLDSLQYLVSLV  124 (225)
T ss_dssp             EEEEEECHHHHHCSTTHHHHHHHHHHHHHHH
T ss_pred             EEEEEcCCccceeecCCCeEhHHHHHHHHHH
Confidence            3567788899999999999999998877654

>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1

Probab=88.43  E-value=0.91  Score=29.96  Aligned_cols=27  Identities=22%  Similarity=0.437  Sum_probs=23.5

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHH-Hhhh
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEI-VDKS   34 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaI-r~~~   34 (71)
                      .++.+++||+..|++||   .+|+++ .+..
T Consensus         7 l~~~i~I~P~~~~~~i~---~~I~~~L~~~~   34 (187)
T 1go3_E            7 IADVVKVPPEEFGKDLK---ETVKKILMEKY   34 (187)
T ss_dssp             EEEEEEECGGGTTSCHH---HHHHHHHHHHH
T ss_pred             EEEEEEECHHHhCccHH---HHHHHHHHHHh
Confidence            57889999999999999   688885 7766

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

Probab=88.35  E-value=0.32  Score=35.39  Aligned_cols=40  Identities=30%  Similarity=0.479  Sum_probs=32.0

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCCC
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEP   47 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e~   47 (71)
                      ..+.||+++.+..|||+|++++--..+.+- .++|....+.
T Consensus       186 a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~-~idI~~~~~~  225 (251)
T 2asb_A          186 ARVVVPDFQLSLAIGKEGQNARLAARLTGW-RIDIRGDAPP  225 (251)
T ss_dssp             EEEEECGGGHHHHHCGGGHHHHHHHHHHSC-EEEEEESSCC
T ss_pred             EEEEEChHHhhhhhcCCcCcHHHHHHHHCC-EecceEHHHh
Confidence            568899999999999999999988888773 5666544443

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

Probab=85.62  E-value=0.37  Score=36.64  Aligned_cols=36  Identities=11%  Similarity=0.246  Sum_probs=30.7

Q ss_pred             eeeeeeCCCccCcccccCc--hhHHHHHhhhceeEEeec
Q psy986            6 EESLQVPRNLVGKVIGKNG--RIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~G--r~ikaIr~~~~a~~iki~   42 (71)
                      ...+.|++.....+|||+|  ..|+.||+..|+ .|.+-
T Consensus       187 s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv-~I~FP  224 (376)
T 3n89_A          187 TLHFTLSTYYVDQVLGSSSTAQLMPVIERETTT-IISYP  224 (376)
T ss_dssp             EEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTC-EEECC
T ss_pred             EEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCC-EEECC
Confidence            3478999999999999999  678999999985 77763

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

Probab=82.15  E-value=0.85  Score=34.68  Aligned_cols=40  Identities=28%  Similarity=0.416  Sum_probs=32.0

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCC
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE   46 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e   46 (71)
                      ...+.||+++.+..|||+|+.++-...+.|- .++|..+.+
T Consensus       308 ~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~-~idI~~~~~  347 (366)
T 1k0r_A          308 AARVVVPDFQLSLAIGKEGQNARLAARLTGW-RIDIRGDAP  347 (366)
T ss_dssp             EEEEEECGGGHHHHHCGGGHHHHHHHHHHCC-EEEEEESSC
T ss_pred             EEEEEEChHHhhhccCCCcHHHHHHHHHHCC-eeeeeEHHH
Confidence            3568899999999999999999988888774 566654443

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

Probab=81.15  E-value=0.65  Score=34.85  Aligned_cols=36  Identities=22%  Similarity=0.384  Sum_probs=29.3

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      .-.+.||+++.+..|||+|++++--..+.|- .++|.
T Consensus       304 ~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~-~idi~  339 (344)
T 1hh2_P          304 AARVLVPPTQLSLAIGKGGQNARLAAKLTGW-KIDIK  339 (344)
T ss_dssp             EEEEEECTTSHHHHHCGGGHHHHHHHHHHSC-EEEEE
T ss_pred             EEEEEEChHHcchhhcCCCccHHHHHHHHCC-Eecee
Confidence            3568899999999999999999988877773 45554

---

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	71
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	7e-07
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	1e-06
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	2e-06
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	2e-06
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	3e-06
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	5e-06
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	6e-06
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	2e-05
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	2e-05
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-05
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	3e-05
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	3e-05
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	5e-05
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	9e-05
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	1e-04
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	1e-04
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	1e-04
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	2e-04
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	2e-04
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	6e-04
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	0.001
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	0.003

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.2 bits (94), Expect = 7e-07
 Identities = 15/41 (36%), Positives = 24/41 (58%), Gaps = 1/41 (2%)

Query: 9  LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
          + VP NLVG ++GK G+ + E  + +G  R++I    E  P
Sbjct: 7  MAVPENLVGAILGKGGKTLVEYQELTG-ARIQISKKGEFLP 46

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

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

 Score = 40.0 bits (93), Expect = 1e-06
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 7  ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPR 53
          E L VP+  VG++IG+ G  I+ I   SG  ++  + ++E    L R
Sbjct: 17 EQLSVPQRSVGRIIGRGGETIRSICKASG-AKITCDKESEGTLLLSR 62

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

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

 Score = 39.1 bits (91), Expect = 2e-06
 Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 6  EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT 50
          E +  VP    G +IGK G  I+ I  +SG  R++++ +  P   
Sbjct: 2  EFNFIVPTGKTGLIIGKGGETIKSISQQSG-ARIELQRNPPPNAD 45

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

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

 Score = 38.6 bits (90), Expect = 2e-06
 Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 1/43 (2%)

Query: 7  ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
          E  +VP  +VG +IG+ G  I  I  +SG  +++I  D+   P
Sbjct: 10 EEYKVPDGMVGFIIGRGGEQISRIQQESG-CKIQIAPDSGGLP 51

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 82

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

 Score = 38.7 bits (90), Expect = 3e-06
 Identities = 11/42 (26%), Positives = 21/42 (50%)

Query: 6  EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEP 47
          E  + +P  L   +IG  GR+I+ I+++ G V +    +   
Sbjct: 11 EVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSG 52

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

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

 Score = 37.9 bits (88), Expect = 5e-06
 Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 7  ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
            L +P NL+G +IG+ G  I EI   SG  ++KI    E   
Sbjct: 4  HELTIPNNLIGCIIGRQGANINEIRQMSG-AQIKIANPVEGSS 45

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.4 bits (87), Expect = 6e-06
 Identities = 13/43 (30%), Positives = 24/43 (55%), Gaps = 1/43 (2%)

Query: 9  LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTL 51
          L +    VG +IGK G  ++++ ++SG  R+ I   N P+  +
Sbjct: 8  LLMHGKEVGSIIGKKGESVKKMREESG-ARINISEGNCPERII 49

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

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

 Score = 36.7 bits (85), Expect = 2e-05
 Identities = 10/42 (23%), Positives = 21/42 (50%), Gaps = 1/42 (2%)

Query: 6  EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEP 47
             ++VP +L   VIG+ G  I++++D+   V + +      
Sbjct: 11 TIEVEVPFDLHRYVIGQKGSGIRKMMDEFE-VNIHVPAPELQ 51

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 35.8 bits (83), Expect = 2e-05
 Identities = 11/38 (28%), Positives = 24/38 (63%), Gaps = 1/38 (2%)

Query: 7  ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD 44
           ++++P + +G+VIG   ++I +I + +G   + IE D
Sbjct: 5  ITVKIPVDKIGEVIGPKRQMINQIQEDTG-AEITIEDD 41

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

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

 Score = 36.2 bits (84), Expect = 2e-05
 Identities = 11/45 (24%), Positives = 25/45 (55%), Gaps = 1/45 (2%)

Query: 7  ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTL 51
           ++ +P+     VIGKNG  +Q++  K+   +++I   ++P   +
Sbjct: 12 ATVAIPKEHHRFVIGKNGEKLQDLELKTA-TKIQIPRPDDPSNQI 55

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

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

 Score = 36.0 bits (83), Expect = 3e-05
 Identities = 9/45 (20%), Positives = 20/45 (44%), Gaps = 1/45 (2%)

Query: 6  EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT 50
          + S+ V      K+IG+ G +I +I  +   V ++    ++    
Sbjct: 11 KLSVTVDPKYHPKIIGRKGAVITQIRLEHD-VNIQFPDKDDGNQP 54

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

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

 Score = 36.1 bits (83), Expect = 3e-05
 Identities = 11/48 (22%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 7  ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPRE 54
          + + +P +  G VIGK G  I+++ +++G V++ +  D        + 
Sbjct: 10 QEIMIPASKAGLVIGKGGETIKQLQERAG-VKMVMIQDGPQNTGADKP 56

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

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

 Score = 35.2 bits (81), Expect = 5e-05
 Identities = 16/41 (39%), Positives = 28/41 (68%), Gaps = 1/41 (2%)

Query: 9  LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
          + +PR  VG VIG+NG +I++I + +G VR++ + D+   P
Sbjct: 7  VPIPRFAVGIVIGRNGEMIKKIQNDAG-VRIQFKPDDGTTP 46

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.5 bits (79), Expect = 9e-05
 Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 1/43 (2%)

Query: 7  ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQP 49
            + +P++L G +IGK G+ I++I  +SG   +KI+   E   
Sbjct: 6  TQVTIPKDLAGSIIGKGGQRIKQIRHESG-ASIKIDEPLEGSE 47

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

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

 Score = 34.8 bits (80), Expect = 1e-04
 Identities = 10/37 (27%), Positives = 21/37 (56%), Gaps = 1/37 (2%)

Query: 9  LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDN 45
          ++V    +G VIG  G +  EI+ ++G   + ++ +N
Sbjct: 7  VKVKPERLGAVIGPRGEVKAEIMRRTG-TVITVDTEN 42

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

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

 Score = 34.3 bits (79), Expect = 1e-04
 Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 1/42 (2%)

Query: 6  EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEP 47
             + +       +IGK+G  I  I D+   V V+I  D+E 
Sbjct: 6  YVEINIDHKFHRHLIGKSGANINRIKDQYK-VSVRIPPDSEK 46

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

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

 Score = 34.0 bits (78), Expect = 1e-04
 Identities = 10/45 (22%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 6  EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPT 50
           E + +   +  ++IG  G+ I++I+D+   V ++      P P 
Sbjct: 11 SEDVPLDHRVHARIIGARGKAIRKIMDEFK-VDIRFPQSGAPDPN 54

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

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

 Score = 34.1 bits (78), Expect = 2e-04
 Identities = 9/42 (21%), Positives = 18/42 (42%)

Query: 6  EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEP 47
            S+  P  L   +IGK G+ + +I  +   V ++     + 
Sbjct: 22 VSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGEDK 63

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 33.9 bits (78), Expect = 2e-04
 Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 7/47 (14%)

Query: 7  ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVV-------RVKIEGDNE 46
            + +    V +VIGK G +I+ +  +  V         + + GD  
Sbjct: 3  RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQNGLIWVNGDRR 49

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 32.4 bits (74), Expect = 6e-04
 Identities = 10/45 (22%), Positives = 18/45 (40%), Gaps = 7/45 (15%)

Query: 9  LQVPRNLVGKVIGKNGRIIQEIVDKSGVV-------RVKIEGDNE 46
          + +    V +VIGKN  + + +  KSG         R+     + 
Sbjct: 5  IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSR 49

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

 Score = 32.0 bits (73), Expect = 0.001
 Identities = 9/47 (19%), Positives = 23/47 (48%), Gaps = 7/47 (14%)

Query: 7  ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVV-------RVKIEGDNE 46
          + +++    V +VIG+   +++ + +K+          R+ +E  NE
Sbjct: 3  KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARNGRIHLECPNE 49

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 30.6 bits (69), Expect = 0.003
 Identities = 11/30 (36%), Positives = 15/30 (50%)

Query: 7  ESLQVPRNLVGKVIGKNGRIIQEIVDKSGV 36
          E   V  +L+G  IG +G  IQ+     GV
Sbjct: 10 EEFVVREDLMGLAIGTHGSNIQQARKVPGV 39

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	71
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	98.73
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	98.7
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	98.57
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	98.54
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.4
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	98.4
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	98.35
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	98.33
d2cpqa1	78	Fragile X mental retardation syndrome related prot	98.3
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.21
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	98.21
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.2
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.12
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.1
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	98.07
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	98.06
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.06
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	97.97
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	97.94
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	97.88
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	97.71
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	97.68
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	96.65
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	94.27
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	93.82
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	90.36
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	87.97
d1egaa2	113	GTPase Era C-terminal domain {Escherichia coli [Ta	83.48
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	80.23

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

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

Probab=98.73  E-value=5.5e-09  Score=60.33  Aligned_cols=40  Identities=33%  Similarity=0.595  Sum_probs=35.3

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCC
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE   46 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e   46 (71)
                      ++++.||.+.+|++|||+|.+|+.|++.+|+ .++|+.+.+
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga-~I~i~~~~~   41 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGA-RIELQRNPP   41 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCC-EEEEECCCT
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCc-EEEEeecCC
Confidence            5789999999999999999999999999984 788875544

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.70  E-value=8.1e-09  Score=60.01  Aligned_cols=54  Identities=28%  Similarity=0.503  Sum_probs=41.6

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCCCCCCCCCCCCccceEEeee
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFMVLTK   65 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e~~~~~~~~~~~vpF~~vGt   65 (71)
                      .++.||.+.+|.+|||+|++|+.|++.+| +.++|..+++..+    ....-.+.+.|+
T Consensus         5 i~i~VP~~~vg~iIGk~G~~Ik~I~~~sg-a~I~i~~~~~~~~----~~~~r~v~I~G~   58 (74)
T d1dtja_           5 VEMAVPENLVGAILGKGGKTLVEYQELTG-ARIQISKKGEFLP----GTRNRRVTITGS   58 (74)
T ss_dssp             EEEEEETTTHHHHHCSTTHHHHHHHHHHC-CEEEECCTTCCST----TCCEEEEEEEES
T ss_pred             EEEEeCHHHcceeECCCChhHHHHHHHcC-CEEEEccCCCCCC----CCCceEEEEEeC
Confidence            46889999999999999999999999998 6688876555322    112346777776

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.57  E-value=2.6e-08  Score=57.48  Aligned_cols=53  Identities=30%  Similarity=0.502  Sum_probs=40.2

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCCCCCCCCCCCCccceEEeee
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFMVLTK   65 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e~~~~~~~~~~~vpF~~vGt   65 (71)
                      +.+++.||.+.+|.+|||+|++|+.|++.++ +.+.|+.+++..       ..-.+.+.|+
T Consensus         2 ~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tg-a~I~i~~~~~~~-------~~r~v~I~G~   54 (70)
T d1wvna1           2 TTHELTIPNNLIGCIIGRQGANINEIRQMSG-AQIKIANPVEGS-------SGRQVTITGS   54 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHC-CEEEECCCCTTC-------SEEEEEEEEC
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcC-cEEEEcCCCCCC-------CcEEEEEEeC
Confidence            4567999999999999999999999999999 467786433221       1234667775

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.54  E-value=7.6e-08  Score=55.37  Aligned_cols=38  Identities=34%  Similarity=0.721  Sum_probs=33.8

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD   44 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~   44 (71)
                      ...+.||.+.+|.+|||+|.+|+.|+..+++ .+++..+
T Consensus         5 t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga-~I~i~~~   42 (75)
T d1zzka1           5 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGA-SIKIDEP   42 (75)
T ss_dssp             EEEEEEETTTGGGGTCGGGHHHHHHHHHHCC-EEEECCT
T ss_pred             EEEEEEChHhcCeeECCCCchHHHHHhhcCC-eEEEccC
Confidence            4578999999999999999999999999996 7888643

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.40  E-value=6.2e-08  Score=56.96  Aligned_cols=43  Identities=26%  Similarity=0.563  Sum_probs=37.1

Q ss_pred             ceeeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCC
Q psy986            3 EYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDN   45 (71)
Q Consensus         3 Ef~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~   45 (71)
                      ++....+.||+..+|.+|||+|.+|+.|+..++.+.+++..++
T Consensus         8 ~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~   50 (82)
T d2ctja1           8 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG   50 (82)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT
T ss_pred             CcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCCC
Confidence            4677899999999999999999999999999877888876433

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.40  E-value=7.1e-08  Score=55.63  Aligned_cols=40  Identities=38%  Similarity=0.712  Sum_probs=34.5

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCC
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE   46 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e   46 (71)
                      ...+.||.+.+|.||||+|.+|+.|+..+++ .++|..+++
T Consensus         4 ~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga-~I~i~~~~~   43 (74)
T d1j4wa1           4 MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGV-RIQFKPDDG   43 (74)
T ss_dssp             EEEEEEEHHHHHHHHCGGGHHHHHHHHHHCC-EEEEECCTT
T ss_pred             EEEEEeCHHHCCeeECCCCcHHHHHHHHcCC-EEEeccCCC
Confidence            4578899999999999999999999999986 588875443

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

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

Probab=98.35  E-value=1.5e-07  Score=55.28  Aligned_cols=39  Identities=28%  Similarity=0.612  Sum_probs=34.1

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD   44 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~   44 (71)
                      ..+.+.||++.+|.+|||+|.+|++|++.++ +.++|..+
T Consensus         8 ~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tg-a~I~i~~~   46 (81)
T d1x4ma1           8 AVQEIMIPASKAGLVIGKGGETIKQLQERAG-VKMVMIQD   46 (81)
T ss_dssp             EEEEEEECHHHHHHHSCSSSSHHHHHHHHHT-SEEEECCS
T ss_pred             EEEEEEECHHHcCeeECCCCchHHHHHHHhC-CeEEEccC
Confidence            4567889999999999999999999999998 57888643

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

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

Probab=98.33  E-value=4.1e-07  Score=55.47  Aligned_cols=56  Identities=25%  Similarity=0.393  Sum_probs=41.7

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCCCCCCCCCCCCccceEEeeeE
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEPQPTLPREEGQVPFMVLTKT   66 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e~~~~~~~~~~~vpF~~vGt~   66 (71)
                      ..+.|.||.+.+|+||||+|.+|+.|++..++ .|.|..+++..     ....-.+.+.|+.
T Consensus        15 v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga-~I~i~~~~~~~-----~~~~r~v~I~G~~   70 (104)
T d1we8a_          15 VFEQLSVPQRSVGRIIGRGGETIRSICKASGA-KITCDKESEGT-----LLLSRLIKISGTQ   70 (104)
T ss_dssp             EEEEEEEETTTHHHHHTTTSHHHHHHHHHHCC-EEEECCSSCCS-----SSSEEEEEEEEEH
T ss_pred             EEEEEEECHHHhcceECCCCcchHHHHHHcCC-EEEECCCCCCC-----CCCccEEEEEeCH
Confidence            34779999999999999999999999999995 68886443321     1122356677763

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.30  E-value=1.4e-07  Score=56.21  Aligned_cols=33  Identities=33%  Similarity=0.503  Sum_probs=30.1

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeE
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVR   38 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~   38 (71)
                      .+++.||++.+|.|||++|++|++|+..+|+-.
T Consensus         9 t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i   41 (78)
T d2cpqa1           9 HEEFVVREDLMGLAIGTHGSNIQQARKVPGVTA   41 (78)
T ss_dssp             EEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEE
T ss_pred             eEEEEECHHHHHHHcCCChHHHHHHHHhcCcEE
Confidence            457999999999999999999999999999753

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

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

Probab=98.21  E-value=2.7e-07  Score=55.99  Aligned_cols=37  Identities=27%  Similarity=0.574  Sum_probs=33.1

Q ss_pred             eeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCC
Q psy986            8 SLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDN   45 (71)
Q Consensus         8 ~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~   45 (71)
                      +++||++.+|.|||++|.+|++|++.+++ .+.|+.++
T Consensus         6 ~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~-~I~Id~d~   42 (84)
T d1tuaa1           6 YVKVKPERLGAVIGPRGEVKAEIMRRTGT-VITVDTEN   42 (84)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHHHHTE-EEEEETTT
T ss_pred             EEEeCHHHcCeeecCCchhHHHHHHHHCC-EEEEEcCC
Confidence            58999999999999999999999999997 68886443

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.21  E-value=2.1e-07  Score=53.53  Aligned_cols=37  Identities=30%  Similarity=0.550  Sum_probs=32.7

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      ...+.||.+.+|.+|||+|.+|+.|++.+++ .++++.
T Consensus         5 t~~i~vp~~~~g~IIGk~G~~I~~I~~~tga-~I~i~~   41 (71)
T d2axya1           5 TIRLLMHGKEVGSIIGKKGESVKKMREESGA-RINISE   41 (71)
T ss_dssp             EEEEEEEHHHHHHHHCGGGHHHHHHHHHHCC-EEEECS
T ss_pred             EEEEEECHHHcCeEECCCChhHHHHHHHhCC-EEEEcC
Confidence            4578999999999999999999999999985 588863

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

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

Probab=98.20  E-value=5.3e-07  Score=51.89  Aligned_cols=38  Identities=26%  Similarity=0.392  Sum_probs=33.4

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      ..-++.||+...|.+||++|.+|+.|++..++ .+++..
T Consensus         5 ~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~-~I~i~~   42 (71)
T d1viga_           5 DYVEINIDHKFHRHLIGKSGANINRIKDQYKV-SVRIPP   42 (71)
T ss_dssp             EEEEEEECSSHHHHHTCSSCCHHHHHHHHTCC-EEECCC
T ss_pred             EEEEEEECHHHhcccCCCCCchHHHHHHHhCC-EEEeCC
Confidence            45579999999999999999999999999985 788853

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

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

Probab=98.12  E-value=1.2e-06  Score=51.41  Aligned_cols=39  Identities=21%  Similarity=0.467  Sum_probs=34.3

Q ss_pred             eeeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            4 YSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         4 f~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      +..+.+.||+..+|.+||++|.+|+.|+...++ .+++..
T Consensus         9 ~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~-~I~~p~   47 (81)
T d2ctma1           9 MVSEDVPLDHRVHARIIGARGKAIRKIMDEFKV-DIRFPQ   47 (81)
T ss_dssp             CCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTC-EEECCC
T ss_pred             CEEEEEEECHHHHhhccCCCCccHHHHHHHhCC-EEEeCC
Confidence            566889999999999999999999999999874 677753

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.10  E-value=8.6e-07  Score=52.86  Aligned_cols=41  Identities=24%  Similarity=0.391  Sum_probs=35.3

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCC
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE   46 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e   46 (71)
                      ...++.||++.+|.+||++|++|+.|+...| +.|++..+++
T Consensus        10 vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg-~~I~~p~~~~   50 (91)
T d2ctka1          10 VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFE-VNIHVPAPEL   50 (91)
T ss_dssp             EEEEEECCHHHHHHHHCSSSHHHHHHHHHTC-CEEECCCTTT
T ss_pred             EEEEEEECHHHHhHhcCCCchhHHHHHHHhC-CEEEECCCCC
Confidence            4678999999999999999999999999998 4788864433

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=98.07  E-value=1.1e-06  Score=51.03  Aligned_cols=38  Identities=34%  Similarity=0.649  Sum_probs=33.3

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      ....+.||.+.+|.+||++|.+|+.|+..++ +.+.|..
T Consensus         8 ~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg-~~I~i~~   45 (79)
T d1x4na1           8 MTEEYKVPDGMVGFIIGRGGEQISRIQQESG-CKIQIAP   45 (79)
T ss_dssp             EEEEEEEEHHHHHHHHCSSSHHHHHHHHHSC-CEEEECS
T ss_pred             EEEEEEEChHhhcceECCCchhHHHHHHHhC-CEEEEcC
Confidence            4578999999999999999999999999998 5677764

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=98.06  E-value=8e-07  Score=53.50  Aligned_cols=35  Identities=23%  Similarity=0.406  Sum_probs=31.3

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      +.+.||++.+|+|||++|++|++|++..+ +.|.|+
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg-~~I~i~   37 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELD-VQIVVG   37 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHT-CEEEEC
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHC-CEEEEC
Confidence            46899999999999999999999999998 557775

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.06  E-value=4e-07  Score=53.03  Aligned_cols=34  Identities=26%  Similarity=0.430  Sum_probs=28.4

Q ss_pred             eeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            8 SLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         8 ~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      .++||++.+|++|||+|.++++|....++ .+.|+
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~-~I~i~   37 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGC-SIFVA   37 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC----CEEC
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCC-EEEEc
Confidence            47899999999999999999999999986 57764

>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=97.97  E-value=2.6e-06  Score=49.82  Aligned_cols=38  Identities=26%  Similarity=0.496  Sum_probs=33.0

Q ss_pred             eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986            5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG   43 (71)
Q Consensus         5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~   43 (71)
                      ...++.||++.+|.+||++|.+|+.|+...| +.+++..
T Consensus        10 ~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg-~~I~~p~   47 (81)
T d2ctea1          10 ASATVAIPKEHHRFVIGKNGEKLQDLELKTA-TKIQIPR   47 (81)
T ss_dssp             EEEEEECCTTTHHHHHCSSSCHHHHHHHHTT-CCCBCCC
T ss_pred             eEEEEEECHHHHhhccCCCChhHHHHHHHhC-CEEEECC
Confidence            4578999999999999999999999999997 5666643

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

Probab=97.94  E-value=5.1e-07  Score=51.24  Aligned_cols=35  Identities=29%  Similarity=0.650  Sum_probs=8.9

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      ..++||++.+|.|||++|.+||.|+...|+- ++++
T Consensus         5 ~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~-I~i~   39 (54)
T d1e3ha4           5 ITVKIPVDKIGEVIGPKRQMINQIQEDTGAE-ITIE   39 (54)
T ss_dssp             C---------------------CHHHHSCCC-C---
T ss_pred             EEEEeCHHHeeEEECCccHHHHHHHHHHCCE-EEEe
Confidence            5789999999999999999999999999854 7775

>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=97.88  E-value=5.2e-06  Score=48.60  Aligned_cols=35  Identities=26%  Similarity=0.414  Sum_probs=32.0

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      ..+.||+..+|.+||++|.+|+.|++..+ +.+++.
T Consensus        12 ~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~-~~I~~~   46 (84)
T d2ctla1          12 LSVTVDPKYHPKIIGRKGAVITQIRLEHD-VNIQFP   46 (84)
T ss_dssp             EEEECCTTTHHHHSCSSSCHHHHHHHHHT-CEEECC
T ss_pred             EEEEECHHHHhhhcCCCchhHHHHHHHhC-CEEEEC
Confidence            47889999999999999999999999998 588885

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

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

Probab=97.71  E-value=1.7e-05  Score=47.49  Aligned_cols=39  Identities=23%  Similarity=0.411  Sum_probs=34.8

Q ss_pred             eeeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            4 YSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         4 f~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      +....+.||+...+.+||++|.+|+.|+...+.+.|.+.
T Consensus        20 ~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~   58 (90)
T d2ctfa1          20 FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFT   58 (90)
T ss_dssp             CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEEC
T ss_pred             cEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeC
Confidence            567899999999999999999999999998776777775

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=97.68  E-value=1.6e-05  Score=48.47  Aligned_cols=35  Identities=14%  Similarity=0.394  Sum_probs=31.1

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      ..++||++.+|+|||++|.+|+.|.+..++ .+.|+
T Consensus         3 ~vi~I~~~ki~~vIG~gG~~ik~i~~~t~~-~I~I~   37 (87)
T d2z0sa2           3 KIVEISPAKVPRVIGRKMSMLKTLEEKTEC-KIFVA   37 (87)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCC-EEEEE
T ss_pred             EEEEEChhhcceeECCCCcHHHHHHHHHCC-EEEEC
Confidence            458999999999999999999999999986 47775

>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=96.65  E-value=0.00033  Score=43.61  Aligned_cols=27  Identities=22%  Similarity=0.560  Sum_probs=23.3

Q ss_pred             ccCcccccCchhHHHHHhhhceeEEeec
Q psy986           15 LVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus        15 dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      ..|+|||++|++|++|....|+- +.|+
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~-I~I~   49 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTY-INVG   49 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCE-EEEC
T ss_pred             HhcceeCCCcHHHHHHHHHHCCe-EEEe
Confidence            37999999999999999999864 6665

>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.27  E-value=0.013  Score=33.71  Aligned_cols=40  Identities=28%  Similarity=0.416  Sum_probs=31.4

Q ss_pred             eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCC
Q psy986            6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE   46 (71)
Q Consensus         6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e   46 (71)
                      ...+.||+++....|||+|..++=.-.+.| ..++|-.+.|
T Consensus        27 ~~~v~V~~~qls~AIGk~G~NvrLas~Ltg-~~IdI~~ese   66 (67)
T d2asba3          27 AARVVVPDFQLSLAIGKEGQNARLAARLTG-WRIDIRGDAP   66 (67)
T ss_dssp             EEEEEECGGGHHHHHCGGGHHHHHHHHHHS-CEEEEEESSC
T ss_pred             EEEEEECcccccchhcCCceeHHHHHHHHC-CEEEEEeCCC
Confidence            356789999999999999999987777777 4666654433

>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Thermotoga maritima [TaxId: 2336]

Probab=93.82  E-value=0.022  Score=32.73  Aligned_cols=35  Identities=23%  Similarity=0.395  Sum_probs=28.9

Q ss_pred             eeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986            7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE   42 (71)
Q Consensus         7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~   42 (71)
                      -.+.||+++.+..|||+|..++=...+.| ..++|.
T Consensus        29 ~~v~V~~~qls~AIGk~G~NvrLas~Ltg-~~idI~   63 (68)
T d1hh2p3          29 ARVLVPPTQLSLAIGKGGQNARLAAKLTG-WKIDIK   63 (68)
T ss_dssp             EEEEECTTSHHHHHCGGGHHHHHHHHHHS-CEEEEE
T ss_pred             EEEEECcccccccccCCcchHHHHHHHHC-CEEeeE
Confidence            46889999999999999999987777776 366654

>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=90.36  E-value=0.069  Score=33.20  Aligned_cols=35  Identities=23%  Similarity=0.569  Sum_probs=28.4

Q ss_pred             eeeeeeCCCc------cCcccccCchhHHHHHhhhceeEEee
Q psy986            6 EESLQVPRNL------VGKVIGKNGRIIQEIVDKSGVVRVKI   41 (71)
Q Consensus         6 e~~l~V~~~d------vGKVIGk~Gr~ikaIr~~~~a~~iki   41 (71)
                      .+.|.||.+.      +|++||.+|.+.|.|-.-.|+ .|.|
T Consensus         4 ~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgc-kI~I   44 (122)
T d1k1ga_           4 SDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNA-KIMI   44 (122)
T ss_dssp             EEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCC-EEEE
T ss_pred             eEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCC-EEEE
Confidence            4667788765      999999999999999988884 4444

>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=87.97  E-value=0.061  Score=34.26  Aligned_cols=35  Identities=29%  Similarity=0.676  Sum_probs=27.6

Q ss_pred             eeeeeeCC------CccCcccccCchhHHHHHhhhceeEEee
Q psy986            6 EESLQVPR------NLVGKVIGKNGRIIQEIVDKSGVVRVKI   41 (71)
Q Consensus         6 e~~l~V~~------~dvGKVIGk~Gr~ikaIr~~~~a~~iki   41 (71)
                      ++.|.||.      +++|++||.+|.+.|.|-.-.|+ .|.|
T Consensus         3 ~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~-kI~I   43 (134)
T d2bl5a1           3 QEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGC-KIMV   43 (134)
T ss_dssp             EEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSE-EEEE
T ss_pred             ceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCC-EEEE
Confidence            45666664      47999999999999999999884 4444

>d1egaa2 d.52.3.1 (A:183-295) GTPase Era C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: GTPase Era C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=83.48  E-value=0.18  Score=30.73  Aligned_cols=28  Identities=29%  Similarity=0.292  Sum_probs=20.1

Q ss_pred             eeeeCC-CccCcccccCchhHHHHHhhhc
Q psy986            8 SLQVPR-NLVGKVIGKNGRIIQEIVDKSG   35 (71)
Q Consensus         8 ~l~V~~-~dvGKVIGk~Gr~ikaIr~~~~   35 (71)
                      .+.|++ +..+=+||++|+.|++|...+.
T Consensus        52 ~I~V~~~sqk~IiIGk~G~~ik~I~~~ar   80 (113)
T d1egaa2          52 LILVEREGQKKMVIGNKGAKIKTIGIEAR   80 (113)
T ss_dssp             EEEESSHHHHHHHHCGGGHHHHHHHHHHH
T ss_pred             EEEECCcchhhhhhcccchHHHHHHHHHH
Confidence            344543 3456689999999999986554

>d1wh9a_ d.52.3.1 (A:) Ribosomal protein S3 N-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Ribosomal protein S3 N-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=80.23  E-value=0.28  Score=29.22  Aligned_cols=29  Identities=21%  Similarity=0.338  Sum_probs=22.9

Q ss_pred             eeeeCCCccCcccccCchhHHHHHhhhce
Q psy986            8 SLQVPRNLVGKVIGKNGRIIQEIVDKSGV   36 (71)
Q Consensus         8 ~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a   36 (71)
                      .|.+.-.--|-||||+|..|+.++..+..
T Consensus        38 ~I~I~tarPGivIGrkG~~I~~L~~~l~k   66 (92)
T d1wh9a_          38 EIIILATRTQNVLGEKGRRIRELTAVVQK   66 (92)
T ss_dssp             EEEEEESCHHHHHCGGGHHHHHHHHHHHH
T ss_pred             EEEEEeCCCceeeccCchhHHHHHHHHHH
Confidence            34555566799999999999999977653