Psyllid ID: psy2768

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90------
Protein Sequence
MAQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQPSID
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHccccccccccEEEEEEEccccccEEEccccHHHHHHHHHHccEEEcccccccccEEEEEEccHHHHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHccccccccccEEEEEEEEccHHccEEEccccHHHHHHHHHcccEEEEEccccccccEEEEEccHHHHHHHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
MAQYLIFEKMREeglfagadEVRLTIELVvpssqvgriigkggqNVRELQRSTgsmiklpnsfneeetnvHIVGSFFSVqetlkgcpnivdqpsid
Flexible Loop (DISEMBL)
MAQYLIFEKMREEGLFAGADEVRLTIELvvpssqvgriigkggqnvRELQRSTGSMIKLPNSFNEEETNVHIVGSFFsvqetlkgcpnivdqpsid
Low Complexity Region (SEG)
MAQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQPSID
Disordered region (IsUnstruct)
***YLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKG*************************TNVHIVGSFFSVQETLKGCPNI*******
Disordered Region (DISOPRED)
MAQYLIF*******************ELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL******EETNVHIVGSFFSVQETLKGCPNIVD*****
Disordered Region (DISEMBL)
MAQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQPSID
Disordered Region (DISPRO)
MAQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQPSID
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	96	2.2.26 [Sep-21-2011]
Q5SF07	592	Insulin-like growth facto	yes	N/A	0.947	0.153	0.414	5e-11
Q9NZI8	577	Insulin-like growth facto	yes	N/A	0.947	0.157	0.361	2e-10
Q8CGX0	577	Insulin-like growth facto	yes	N/A	0.947	0.157	0.361	2e-10
O88477	577	Insulin-like growth facto	no	N/A	0.947	0.157	0.361	2e-10
Q5RB68	556	Insulin-like growth facto	no	N/A	0.822	0.142	0.439	2e-10
Q9Y6M1	599	Insulin-like growth facto	no	N/A	0.822	0.131	0.439	3e-10
O42254	576	Insulin-like growth facto	yes	N/A	0.947	0.157	0.361	4e-10
Q9PW80	582	Insulin-like growth facto	no	N/A	0.947	0.156	0.372	8e-10
Q5ZLP8	584	Insulin-like growth facto	no	N/A	0.822	0.135	0.390	2e-09
O57526	593	Insulin-like growth facto	N/A	N/A	0.822	0.133	0.390	2e-09

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

 Score = 66.6 bits (161), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 39/94 (41%), Positives = 52/94 (55%), Gaps = 3/94 (3%)

Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
           AQ  IF K++EE  F   +EV+L   + VPSS  GR+IGKGG+ V ELQ  T + + +P 
Sbjct: 481 AQGRIFGKLKEENFFNPKEEVKLEAHIRVPSSTAGRVIGKGGKTVNELQNLTSAEVIVPR 540

Query: 62  SFN---EEETNVHIVGSFFSVQETLKGCPNIVDQ 92
                  EE  V I+G FF+ Q   +    IV Q
Sbjct: 541 DQTPDENEEVIVRIIGHFFASQTAQRKIREIVQQ 574

Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNAs. Binding is isoform-specific. May regulate translation of target mRNAs.
Mus musculus (taxid: 10090)

>sp|Q9NZI8|IF2B1_HUMAN Insulin-like growth factor 2 mRNA-binding protein 1 OS=Homo sapiens GN=IGF2BP1 PE=1 SV=2

 Score = 64.3 bits (155), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 34/94 (36%), Positives = 54/94 (57%), Gaps = 3/94 (3%)

Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
           AQ  I+ K++EE  F   +EV+L   + VP+S  GR+IGKGG+ V ELQ  T + + +P 
Sbjct: 466 AQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPR 525

Query: 62  SFNEEETN---VHIVGSFFSVQETLKGCPNIVDQ 92
               +E +   V I+G F++ Q   +   +I+ Q
Sbjct: 526 DQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQ 559

RNA-binding factor that affects mRNA nuclear export, localization, stability and translation. Component of the CRD-mediated complex that promotes MYC mRNA stabilization. Regulates mRNA stability during the integrated cellular stress response (ISR) in stress granules (SGs). Stabilizes the BTRC/FBW1A mRNA from degradation by disrupting miRNA-dependent interaction with AGO2. Identified in a HCV IRES-mediated translation complex, that enhances translation at the Hepatitis C virus (HCV) RNA-replicon via the internal ribosome entry site (IRES), but does not affect 5'cap-dependent translation. Acts as a HIV-1 retrovirus restriction factor that reduces HIV-1 assembly by inhibiting viral RNA packaging, assembly and processing of HIV-1 GAG protein on cellular membranes. Binds to mRNAs in stress granules (SGs). Binds to the stem-loop IV of the 5'-UTR and to the variable region and the poly(U-C) motif of the 3'-UTR of the HCV RNA-replicon. Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulates its subcellular localization and translation. Binds both to the coding region mRNA stability determinant (CRD) and to AU-rich sequences in the 3'-UTR of the MYC and CD44 mRNAs and stabilizes these mRNAs. Binds to the fourth and fifth exons of the oncofetal H19 and neuron-specific TAU mRNAs and regulates their localizations. Binds to the adenine-rich autoregulatory sequence (ARS) 5'-UTR of the PABPC1 mRNA and is involved in its translational repression. The RNA-binding activity to ARS is stimulated by PABPC1. Binds to the coding sequence region of BTRC/FBW1A mRNA and mediates stabilization of BTRC/FBW1A and MYC mRNAs in response to beta-catenin signaling. Binding to RNA employs a cooperative, sequential mechanism of homo- or heterodimerisation. Also involved in growth or survival of lung-cancer cells. Protects the MYC and MDR-1 mRNAs from cleavage by a endoribonuclease, thus prolonging their stabilities (By similarity). Binds to the 3'-UTR axonal localization signal (ALS) of TAU mRNA (By similarity). Binds to a conserved 54-nucleotide element in the 3'-UTR of the beta actin mRNA known as the 'zipcode' (By similarity). Promotes translocation of the beta-actin mRNA to dendrites (By similarity). May act as a regulator of mRNA transport to activated synapses in response to synaptic activity.

Homo sapiens (taxid: 9606)

>sp|Q8CGX0|IF2B1_RAT Insulin-like growth factor 2 mRNA-binding protein 1 OS=Rattus norvegicus GN=Igf2bp1 PE=1 SV=1

 Score = 64.3 bits (155), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 34/94 (36%), Positives = 54/94 (57%), Gaps = 3/94 (3%)

Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
           AQ  I+ K++EE  F   +EV+L   + VP+S  GR+IGKGG+ V ELQ  T + + +P 
Sbjct: 466 AQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPR 525

Query: 62  SFNEEETN---VHIVGSFFSVQETLKGCPNIVDQ 92
               +E +   V I+G F++ Q   +   +I+ Q
Sbjct: 526 DQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQ 559

RNA-binding factor that affects mRNA nuclear export, localization, stability and translation. Component of the CRD-mediated complex that promotes MYC mRNA stabilization (By similarity). Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulates its subcellular localization and translation (By similarity). Binds both to the coding region mRNA stability determinant (CRD) in the coding region and to AU-rich sequences in the 3'-UTR of the MYC mRNA. Protects the MYC mRNA from cleavage by a endoribonuclease, thus prolonging its stability. Protects the MDR-1 mRNA from cleavage by a endoribonuclease, thus prolonging its stability (By similarity). Binds to the 3'-UTR axonal localization signal (ALS) of TAU mRNA (By similarity). Binds both to the coding region mRNA stability determinant (CRD) and to AU-rich sequences in the 3'-UTR of the CD44 mRNA (By similarity). Plays a role in regulating the stability of MYC and CD44 mRNAs (By similarity). Binds to the fourth and fifth exons of the oncofetal H19 and neuron-specific TAU mRNAs and regulates their localizations (By similarity). Binds to the adenine-rich autoregulatory sequence (ARS) 5'-UTR of the PABPC1 mRNA and is involved in its translational repression. The RNA-binding activity to ARS is stimulated by PABPC1 (By similarity). Binds to the coding sequence region of BTRC/FBW1A mRNA and mediates stabilization of BTRC/FBW1A and MYC mRNAs in response to beta-catenin signaling (By similarity). Binding to RNA employs a cooperative, sequential mechanism of homo- or heterodimerisation (By similarity). Also involved in growth or survival of lung-cancer cells (By similarity). Binds to a conserved 54-nucleotide element in the 3'-UTR of the beta actin mRNA known as the 'zipcode'. Promotes translocation of the beta-actin mRNA to dendrites. May act as a regulator of mRNA transport to activated synapses in response to synaptic activity.

Rattus norvegicus (taxid: 10116)

>sp|O88477|IF2B1_MOUSE Insulin-like growth factor 2 mRNA-binding protein 1 OS=Mus musculus GN=Igf2bp1 PE=1 SV=1

 Score = 63.9 bits (154), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 34/94 (36%), Positives = 54/94 (57%), Gaps = 3/94 (3%)

Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
           AQ  I+ K++EE  F   +EV+L   + VP+S  GR+IGKGG+ V ELQ  T + + +P 
Sbjct: 466 AQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPR 525

Query: 62  SFNEEETN---VHIVGSFFSVQETLKGCPNIVDQ 92
               +E +   V I+G F++ Q   +   +I+ Q
Sbjct: 526 DQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQ 559

RNA-binding factor that affects mRNA nuclear export, localization, stability and translation. Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulates its subcellular localization and translation. Binds both to the coding region mRNA stability determinant (CRD) and to AU-rich sequences in the 3'-UTR of the MYC mRNA. Protects the MYC and MDR-1 mRNAs from cleavage by a endoribonuclease, thus prolonging their stabilities. Binds to the 3'-UTR axonal localization signal (ALS) of TAU mRNA. Component of the CRD-mediated complex that promotes MYC mRNA stabilization (By similarity). Binds both to the coding region mRNA stability determinant (CRD) and to AU-rich sequences in the 3'-UTR of the CD44 mRNA (By similarity). Plays a role in regulating the stability of MYC and CD44 mRNAs (By similarity). Binds to the fourth and fifth exons of the oncofetal H19 and neuron-specific TAU mRNAs and regulates their localizations (By similarity). Binds to the adenine-rich autoregulatory sequence (ARS) 5'-UTR of the PABPC1 mRNA and is involved in its translational repression. The RNA-binding activity to ARS is stimulated by PABPC1 (By similarity). Binds to the coding sequence region of BTRC/FBW1A mRNA and mediates stabilization of BTRC/FBW1A and MYC mRNAs in response to beta-catenin signaling (By similarity). Binding to RNA employs a cooperative, sequential mechanism of homo- or heterodimerisation (By similarity). Also involved in growth or survival of lung-cancer cells (By similarity). Binds to a conserved 54-nucleotide element in the 3'-UTR of the beta actin mRNA known as the 'zipcode' (By similarity). Promotes translocation of the beta-actin mRNA to dendrites (By similarity). May act as a regulator of mRNA transport to activated synapses in response to synaptic activity.

Mus musculus (taxid: 10090)

>sp|Q5RB68|IF2B2_PONAB Insulin-like growth factor 2 mRNA-binding protein 2 OS=Pongo abelii GN=IGF2BP2 PE=2 SV=1

 Score = 63.9 bits (154), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 36/82 (43%), Positives = 48/82 (58%), Gaps = 3/82 (3%)

Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
           AQ  IF K++EE  F   +EV+L   + VPSS  GR+IGKGG+ V ELQ  T + + +P 
Sbjct: 445 AQGRIFGKLKEENFFNPKEEVKLEAHIRVPSSTAGRVIGKGGKTVNELQNLTSAEVIVPR 504

Query: 62  SFN---EEETNVHIVGSFFSVQ 80
                  EE  V I+G FF+ Q
Sbjct: 505 DQTPDENEEVIVRIIGHFFASQ 526

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

Pongo abelii (taxid: 9601)

>sp|Q9Y6M1|IF2B2_HUMAN Insulin-like growth factor 2 mRNA-binding protein 2 OS=Homo sapiens GN=IGF2BP2 PE=1 SV=2

 Score = 63.9 bits (154), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 36/82 (43%), Positives = 48/82 (58%), Gaps = 3/82 (3%)

Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
           AQ  IF K++EE  F   +EV+L   + VPSS  GR+IGKGG+ V ELQ  T + + +P 
Sbjct: 488 AQGRIFGKLKEENFFNPKEEVKLEAHIRVPSSTAGRVIGKGGKTVNELQNLTSAEVIVPR 547

Query: 62  SFN---EEETNVHIVGSFFSVQ 80
                  EE  V I+G FF+ Q
Sbjct: 548 DQTPDENEEVIVRIIGHFFASQ 569

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

Homo sapiens (taxid: 9606)

>sp|O42254|IF2B1_CHICK Insulin-like growth factor 2 mRNA-binding protein 1 OS=Gallus gallus GN=IGF2BP1 PE=1 SV=1

 Score = 63.2 bits (152), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 34/94 (36%), Positives = 53/94 (56%), Gaps = 3/94 (3%)

Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
           AQ  I+ K++EE  F   +EV+L   + VP+S  GR+IGKGG+ V ELQ  T + + +P 
Sbjct: 465 AQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPR 524

Query: 62  SFNEEETN---VHIVGSFFSVQETLKGCPNIVDQ 92
               +E     V I+G F++ Q   +   +I+ Q
Sbjct: 525 DQTPDENEQVIVKIIGHFYASQMAQRKIRDILAQ 558

RNA-binding factor that affects mRNA nuclear export, localization, stability and translation. Component of the coding region determinant (CRD)-mediated complex that promotes mRNA stability. May regulate mRNA stability in stress granules during the cellular stress response (By similarity). Acts as translational regulator that represses translation by blocking translation initiation. Promotes transport and localization of the beta-actin mRNA to actin-rich protrusions in primary fibroblasts and neurons. Binds to a conserved 54-nucleotide element in the 3'-UTR of the beta actin mRNA known as the 'zipcode'. Binds to the minimal 5'-ACACCC-3'sequence that is sufficient for localization of beta actin mRNA.

Gallus gallus (taxid: 9031)

>sp|Q9PW80|IF2B3_DANRE Insulin-like growth factor 2 mRNA-binding protein 3 OS=Danio rerio GN=igf2bp3 PE=1 SV=1

 Score = 62.4 bits (150), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 35/94 (37%), Positives = 51/94 (54%), Gaps = 3/94 (3%)

Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
           AQ  IF K++EE  F   +EV+L   + VPS   GR+IGKGG+ V ELQ  T + + +P 
Sbjct: 469 AQGRIFGKLKEENFFGPKEEVKLEAHIKVPSFAAGRVIGKGGKTVNELQNLTSAEVVVPR 528

Query: 62  SFNEEETN---VHIVGSFFSVQETLKGCPNIVDQ 92
               +E +   V I G F++ Q   +    I+ Q
Sbjct: 529 DQTPDENDQVVVKITGHFYASQLAQRKIQEIISQ 562

RNA-binding protein that may regulate mRNA translation and stability (By similarity). Involved in the correct neuronal crest migration.

Danio rerio (taxid: 7955)

>sp|Q5ZLP8|IF2B3_CHICK Insulin-like growth factor 2 mRNA-binding protein 3 OS=Gallus gallus GN=IGF2BP3 PE=2 SV=1

 Score = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 32/82 (39%), Positives = 47/82 (57%), Gaps = 3/82 (3%)

Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
           AQ  I+ K++EE  F   +EV+L   + VPS   GR+IGKGG+ V ELQ  T + + +P 
Sbjct: 470 AQGRIYGKLKEENFFGPKEEVKLEAHIKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPR 529

Query: 62  SFNEEETN---VHIVGSFFSVQ 80
               +E +   V I G F++ Q
Sbjct: 530 DQTPDENDQVVVKITGHFYACQ 551

RNA-binding protein that may regulate mRNA translation and stability.

Gallus gallus (taxid: 9031)

>sp|O57526|IF23B_XENLA Insulin-like growth factor 2 mRNA-binding protein 3-B OS=Xenopus laevis GN=igf2bp3-b PE=1 SV=1

 Score = 60.8 bits (146), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 32/82 (39%), Positives = 47/82 (57%), Gaps = 3/82 (3%)

Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
           AQ  I+ K++EE  F   +EV+L   + VPS   GR+IGKGG+ V ELQ  T + + +P 
Sbjct: 478 AQGRIYGKLKEENFFGPKEEVKLEAHIKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPR 537

Query: 62  SFNEEETN---VHIVGSFFSVQ 80
               +E +   V I G F++ Q
Sbjct: 538 DQTPDENDQVVVKITGHFYASQ 559

RNA-binding protein that acts as a regulator of mRNA transport and localization. Mediates the specific association of Vg1 RNA to microtubules. May regulate mRNA translation (By similarity). Binds specifically to the vegetal localization elements (VLE or VgLE) in the 3'-UTR of Vg1 and VegT mRNAs. Binds to the Vg1 and VegT mRNAs in both the nucleus and the cytoplasm. Binds to the RNA sequence motif 5'-UUCAC-3'. May regulate mRNA translation (By similarity). Acts as a transcription regulator. Binds to the 5'-[TA]GGTTACT-3' motif within element 3 of the TFIIIA gene promoter. Binds DNA.

Xenopus laevis (taxid: 8355)

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	96
189237154	1116	PREDICTED: similar to igf2 mRNA binding	0.843	0.072	0.75	1e-27
270007202	710	hypothetical protein TcasGA2_TC013744 [T	0.822	0.111	0.768	2e-27
170036665	520	igf2 mRNA binding protein [Culex quinque	0.885	0.163	0.685	2e-27
157114471	541	igf2 mRNA binding protein, putative [Aed	0.822	0.146	0.734	5e-27
118792630	494	AGAP012103-PA [Anopheles gambiae str. PE	0.822	0.159	0.722	4e-26
357615456	599	putative igf2 mRNA binding protein [Dana	0.833	0.133	0.701	5e-26
195439130	587	GK16164 [Drosophila willistoni] gi|19416	0.822	0.134	0.717	1e-25
332025247	568	Insulin-like growth factor 2 mRNA-bindin	0.812	0.137	0.741	2e-25
195131533	596	GI15803 [Drosophila mojavensis] gi|19390	0.822	0.132	0.705	2e-25
307189125	587	Insulin-like growth factor 2 mRNA-bindin	0.812	0.132	0.741	2e-25

>gi|189237154|ref|XP_973939.2| PREDICTED: similar to igf2 mRNA binding protein, putative [Tribolium castaneum]

 Score =  127 bits (318), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 63/84 (75%), Positives = 71/84 (84%), Gaps = 3/84 (3%)

Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
           AQYLIFEKMREEG  AG+D+VRLT+E++VPSSQVGRIIGKGGQNVRELQR TGS+IKLP 
Sbjct: 414 AQYLIFEKMREEGFVAGSDDVRLTVEIMVPSSQVGRIIGKGGQNVRELQRVTGSVIKLPE 473

Query: 62  ---SFNEEETNVHIVGSFFSVQET 82
              S  E+ET VHI+G FFSVQ  
Sbjct: 474 QGASPQEDETTVHIIGPFFSVQSA 497

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270007202|gb|EFA03650.1| hypothetical protein TcasGA2_TC013744 [Tribolium castaneum]

 Score =  126 bits (316), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 63/82 (76%), Positives = 71/82 (86%), Gaps = 3/82 (3%)

Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
           AQYLIFEKMREEG  AG+D+VRLT+E++VPSSQVGRIIGKGGQNVRELQR TGS+IKLP 
Sbjct: 565 AQYLIFEKMREEGFVAGSDDVRLTVEIMVPSSQVGRIIGKGGQNVRELQRVTGSVIKLPE 624

Query: 62  ---SFNEEETNVHIVGSFFSVQ 80
              S  E+ET VHI+G FFSVQ
Sbjct: 625 QGASPQEDETTVHIIGPFFSVQ 646

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170036665|ref|XP_001846183.1| igf2 mRNA binding protein [Culex quinquefasciatus] gi|167879496|gb|EDS42879.1| igf2 mRNA binding protein [Culex quinquefasciatus]

 Score =  126 bits (316), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 61/89 (68%), Positives = 73/89 (82%), Gaps = 4/89 (4%)

Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
           AQYLIFEKMREEG  +G D+VRLT+E++VPS+QVGRIIGKGGQNVRELQR TGS+IKLP 
Sbjct: 408 AQYLIFEKMREEGFVSGTDDVRLTVEILVPSAQVGRIIGKGGQNVRELQRVTGSIIKLPE 467

Query: 62  SFN----EEETNVHIVGSFFSVQETLKGC 86
                  +EET VHI+G FFSVQ +++ C
Sbjct: 468 HTAATPVDEETTVHIIGPFFSVQVSVENC 496

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157114471|ref|XP_001652287.1| igf2 mRNA binding protein, putative [Aedes aegypti] gi|108877277|gb|EAT41502.1| AAEL006876-PA [Aedes aegypti]

 Score =  124 bits (312), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 61/83 (73%), Positives = 71/83 (85%), Gaps = 4/83 (4%)

Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLP- 60
           AQYLIFEKMREEG  +G D+VRLT+E++VPS+QVGRIIGKGGQNVRELQR TGS+IKLP 
Sbjct: 409 AQYLIFEKMREEGFVSGTDDVRLTVEILVPSAQVGRIIGKGGQNVRELQRVTGSIIKLPE 468

Query: 61  ---NSFNEEETNVHIVGSFFSVQ 80
              N+  +EET VHI+G FFSVQ
Sbjct: 469 HTTNTPVDEETTVHIIGPFFSVQ 491

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|118792630|ref|XP_320427.3| AGAP012103-PA [Anopheles gambiae str. PEST] gi|116116989|gb|EAA00333.3| AGAP012103-PA [Anopheles gambiae str. PEST]

 Score =  122 bits (305), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 60/83 (72%), Positives = 68/83 (81%), Gaps = 4/83 (4%)

Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
           AQYLIFEKMREEG  +G D+VRLT+E+ VPS+QVGRIIGKGGQNVRELQR TGS+IKLP 
Sbjct: 346 AQYLIFEKMREEGFVSGTDDVRLTVEIFVPSAQVGRIIGKGGQNVRELQRVTGSIIKLPE 405

Query: 62  SFN----EEETNVHIVGSFFSVQ 80
                  +EET VHI+G FFSVQ
Sbjct: 406 HTASAPVDEETTVHIIGPFFSVQ 428

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357615456|gb|EHJ69667.1| putative igf2 mRNA binding protein [Danaus plexippus]

 Score =  121 bits (304), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 61/87 (70%), Positives = 70/87 (80%), Gaps = 7/87 (8%)

Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
           AQYLIFEKMREEG  +G+D+VRLT+ +VV SSQVGRIIGKGGQNVRELQR TGS+IKLP 
Sbjct: 420 AQYLIFEKMREEGFMSGSDDVRLTVAIVVASSQVGRIIGKGGQNVRELQRVTGSLIKLPE 479

Query: 62  -------SFNEEETNVHIVGSFFSVQE 81
                  + N+ ET VHIVG F+SVQE
Sbjct: 480 QPQPPTAAGNDHETTVHIVGHFYSVQE 506

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195439130|ref|XP_002067484.1| GK16164 [Drosophila willistoni] gi|194163569|gb|EDW78470.1| GK16164 [Drosophila willistoni]

 Score =  120 bits (300), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 61/85 (71%), Positives = 68/85 (80%), Gaps = 6/85 (7%)

Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
           AQY+IFEKMREEG   G D+VRLTIEL+V SSQVGRIIGKGGQNVRELQR TGS+IKLP 
Sbjct: 367 AQYMIFEKMREEGFMCGTDDVRLTIELLVASSQVGRIIGKGGQNVRELQRVTGSVIKLPE 426

Query: 62  ------SFNEEETNVHIVGSFFSVQ 80
                 S  +EET VHI+G F+SVQ
Sbjct: 427 HALAPPSGGDEETPVHIIGPFYSVQ 451

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332025247|gb|EGI65421.1| Insulin-like growth factor 2 mRNA-binding protein 1 [Acromyrmex echinatior]

 Score =  120 bits (300), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 63/85 (74%), Positives = 70/85 (82%), Gaps = 7/85 (8%)

Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL-- 59
           AQYLIFEKMREEG  AG ++VRLTIE++VPS+QVGRIIGKGGQNVRELQR TGS+IKL  
Sbjct: 403 AQYLIFEKMREEGYVAGTEDVRLTIEILVPSTQVGRIIGKGGQNVRELQRVTGSVIKLSE 462

Query: 60  ----PNSFNEEETNVHIVGSFFSVQ 80
               P S  EEET VHI+G FFSVQ
Sbjct: 463 QQATPPSA-EEETTVHIIGPFFSVQ 486

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195131533|ref|XP_002010205.1| GI15803 [Drosophila mojavensis] gi|193908655|gb|EDW07522.1| GI15803 [Drosophila mojavensis]

 Score =  120 bits (300), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 60/85 (70%), Positives = 68/85 (80%), Gaps = 6/85 (7%)

Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
           AQY+IFEKMREEG   G D+VRLT+EL+V SSQVGRIIGKGGQNVRELQR TGS+IKLP 
Sbjct: 358 AQYMIFEKMREEGFMCGTDDVRLTVELLVASSQVGRIIGKGGQNVRELQRVTGSVIKLPE 417

Query: 62  ------SFNEEETNVHIVGSFFSVQ 80
                 S  +EET VHI+G F+SVQ
Sbjct: 418 HALAPPSGGDEETPVHIIGPFYSVQ 442

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307189125|gb|EFN73581.1| Insulin-like growth factor 2 mRNA-binding protein 1 [Camponotus floridanus]

 Score =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 63/85 (74%), Positives = 70/85 (82%), Gaps = 7/85 (8%)

Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL-- 59
           AQYLIFEKMREEG  AG ++VRLTIE++VPS+QVGRIIGKGGQNVRELQR TGS+IKL  
Sbjct: 429 AQYLIFEKMREEGYVAGTEDVRLTIEILVPSTQVGRIIGKGGQNVRELQRVTGSVIKLSE 488

Query: 60  ----PNSFNEEETNVHIVGSFFSVQ 80
               P S  EEET VHI+G FFSVQ
Sbjct: 489 QQATPPSA-EEETTVHIIGPFFSVQ 512

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	96
FB|FBgn0262735	588	Imp "IGF-II mRNA-binding prote	0.822	0.134	0.705	2.2e-24
UNIPROTKB|K7GM69	202	RFC4 "Uncharacterized protein"	0.822	0.391	0.439	1.7e-11
UNIPROTKB|K7GQW0	477	RFC4 "Uncharacterized protein"	0.947	0.190	0.414	2.3e-11
UNIPROTKB|K7GQ87	498	RFC4 "Uncharacterized protein"	0.947	0.182	0.414	2.5e-11
UNIPROTKB|K7GKD3	520	RFC4 "Uncharacterized protein"	0.947	0.175	0.414	2.7e-11
UNIPROTKB|F1SFK0	524	RFC4 "Uncharacterized protein"	0.947	0.173	0.414	2.8e-11
UNIPROTKB|F1PDI8	531	IGF2BP2 "Uncharacterized prote	0.947	0.171	0.414	2.8e-11
UNIPROTKB|Q5RB68	556	IGF2BP2 "Insulin-like growth f	0.947	0.163	0.414	3.1e-11
ZFIN|ZDB-GENE-060503-536	446	igf2bp2b "insulin-like growth	0.947	0.204	0.382	3.4e-11
MGI|MGI:1890358	592	Igf2bp2 "insulin-like growth f	0.947	0.153	0.414	3.4e-11

FB|FBgn0262735 Imp "IGF-II mRNA-binding protein" [Drosophila melanogaster (taxid:7227)]

 Score = 286 (105.7 bits), Expect = 2.2e-24, P = 2.2e-24
 Identities = 60/85 (70%), Positives = 68/85 (80%)

Query:     2 AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
             AQY+IFEKMREEG   G D+VRLT+EL+V SSQVGRIIGKGGQNVRELQR TGS+IKLP 
Sbjct:   382 AQYMIFEKMREEGFMCGTDDVRLTVELLVASSQVGRIIGKGGQNVRELQRVTGSVIKLPE 441

Query:    62 ------SFNEEETNVHIVGSFFSVQ 80
                   S  +EET VHI+G F+SVQ
Sbjct:   442 HALAPPSGGDEETPVHIIGLFYSVQ 466

GO:0003729 "mRNA binding" evidence=ISS

GO:0000166 "nucleotide binding" evidence=IEA

GO:0007399 "nervous system development" evidence=IMP

GO:0051124 "synaptic growth at neuromuscular junction" evidence=IMP

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

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

GO:0071011 "precatalytic spliceosome" evidence=IDA

GO:0007283 "spermatogenesis" evidence=IEP

UNIPROTKB|K7GM69 RFC4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 157 (60.3 bits), Expect = 1.7e-11, P = 1.7e-11
 Identities = 36/82 (43%), Positives = 48/82 (58%)

Query:     2 AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
             AQ  IF K++EE  F   +EV+L   + VPSS  GR+IGKGG+ V ELQ  T + + +P 
Sbjct:    83 AQGRIFGKLKEENFFNPKEEVKLEAHIRVPSSTAGRVIGKGGKTVNELQNLTSAEVIVPR 142

Query:    62 SFN---EEETNVHIVGSFFSVQ 80
                    EE  V I+G FF+ Q
Sbjct:   143 DQTPDENEEVIVRIIGHFFASQ 164

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|K7GQW0 RFC4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 164 (62.8 bits), Expect = 2.3e-11, P = 2.3e-11
 Identities = 39/94 (41%), Positives = 52/94 (55%)

Query:     2 AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
             AQ  IF K++EE  F   +EV+L   + VPSS  GR+IGKGG+ V ELQ  T + + +P 
Sbjct:   366 AQGRIFGKLKEENFFNPKEEVKLEAHIRVPSSTAGRVIGKGGKTVNELQNLTSAEVIVPR 425

Query:    62 SFN---EEETNVHIVGSFFSVQETLKGCPNIVDQ 92
                    EE  V I+G FF+ Q   +    IV Q
Sbjct:   426 DQTPDENEEVIVRIIGHFFASQTAQRKIREIVQQ 459

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|K7GQ87 RFC4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 164 (62.8 bits), Expect = 2.5e-11, P = 2.5e-11
 Identities = 39/94 (41%), Positives = 52/94 (55%)

Query:     2 AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
             AQ  IF K++EE  F   +EV+L   + VPSS  GR+IGKGG+ V ELQ  T + + +P 
Sbjct:   387 AQGRIFGKLKEENFFNPKEEVKLEAHIRVPSSTAGRVIGKGGKTVNELQNLTSAEVIVPR 446

Query:    62 SFN---EEETNVHIVGSFFSVQETLKGCPNIVDQ 92
                    EE  V I+G FF+ Q   +    IV Q
Sbjct:   447 DQTPDENEEVIVRIIGHFFASQTAQRKIREIVQQ 480

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|K7GKD3 RFC4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 164 (62.8 bits), Expect = 2.7e-11, P = 2.7e-11
 Identities = 39/94 (41%), Positives = 52/94 (55%)

Query:     2 AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
             AQ  IF K++EE  F   +EV+L   + VPSS  GR+IGKGG+ V ELQ  T + + +P 
Sbjct:   409 AQGRIFGKLKEENFFNPKEEVKLEAHIRVPSSTAGRVIGKGGKTVNELQNLTSAEVIVPR 468

Query:    62 SFN---EEETNVHIVGSFFSVQETLKGCPNIVDQ 92
                    EE  V I+G FF+ Q   +    IV Q
Sbjct:   469 DQTPDENEEVIVRIIGHFFASQTAQRKIREIVQQ 502

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1SFK0 RFC4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 164 (62.8 bits), Expect = 2.8e-11, P = 2.8e-11
 Identities = 39/94 (41%), Positives = 52/94 (55%)

Query:     2 AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
             AQ  IF K++EE  F   +EV+L   + VPSS  GR+IGKGG+ V ELQ  T + + +P 
Sbjct:   413 AQGRIFGKLKEENFFNPKEEVKLEAHIRVPSSTAGRVIGKGGKTVNELQNLTSAEVIVPR 472

Query:    62 SFN---EEETNVHIVGSFFSVQETLKGCPNIVDQ 92
                    EE  V I+G FF+ Q   +    IV Q
Sbjct:   473 DQTPDENEEVIVRIIGHFFASQTAQRKIREIVQQ 506

GO:0048027 "mRNA 5'-UTR binding" evidence=IEA

GO:0044430 "cytoskeletal part" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003730 "mRNA 3'-UTR binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1PDI8 IGF2BP2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 164 (62.8 bits), Expect = 2.8e-11, P = 2.8e-11
 Identities = 39/94 (41%), Positives = 52/94 (55%)

Query:     2 AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
             AQ  IF K++EE  F   +EV+L   + VPSS  GR+IGKGG+ V ELQ  T + + +P 
Sbjct:   420 AQGRIFGKLKEENFFNPKEEVKLEAHIRVPSSTAGRVIGKGGKTVNELQNLTSAEVIVPR 479

Query:    62 SFN---EEETNVHIVGSFFSVQETLKGCPNIVDQ 92
                    EE  V I+G FF+ Q   +    IV Q
Sbjct:   480 DQTPDENEEVIVRIIGHFFASQTAQRKIREIVQQ 513

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q5RB68 IGF2BP2 "Insulin-like growth factor 2 mRNA-binding protein 2" [Pongo abelii (taxid:9601)]

 Score = 164 (62.8 bits), Expect = 3.1e-11, P = 3.1e-11
 Identities = 39/94 (41%), Positives = 52/94 (55%)

Query:     2 AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
             AQ  IF K++EE  F   +EV+L   + VPSS  GR+IGKGG+ V ELQ  T + + +P 
Sbjct:   445 AQGRIFGKLKEENFFNPKEEVKLEAHIRVPSSTAGRVIGKGGKTVNELQNLTSAEVIVPR 504

Query:    62 SFN---EEETNVHIVGSFFSVQETLKGCPNIVDQ 92
                    EE  V I+G FF+ Q   +    IV Q
Sbjct:   505 DQTPDENEEVIVRIIGHFFASQTAQRKIREIVQQ 538

GO:0003730 "mRNA 3'-UTR binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0005856 "cytoskeleton" evidence=ISS

GO:0048027 "mRNA 5'-UTR binding" evidence=ISS

ZFIN|ZDB-GENE-060503-536 igf2bp2b "insulin-like growth factor 2 mRNA binding protein 2b" [Danio rerio (taxid:7955)]

 Score = 162 (62.1 bits), Expect = 3.4e-11, P = 3.4e-11
 Identities = 36/94 (38%), Positives = 53/94 (56%)

Query:     2 AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
             AQ  I+ K++EE  F   +EV+L   + VPS+  GR+IGKGG+ V ELQ  T + + +P 
Sbjct:   333 AQGRIYGKLKEENFFTAKEEVKLEAHIKVPSTAAGRVIGKGGKTVNELQNLTSAEVIVPR 392

Query:    62 SFNEEETN---VHIVGSFFSVQETLKGCPNIVDQ 92
                 +E +   V I+G FF+ Q   +    IV Q
Sbjct:   393 DQTPDENDDVFVKIIGHFFASQTAQRKIREIVQQ 426

GO:0003723 "RNA binding" evidence=IEA

MGI|MGI:1890358 Igf2bp2 "insulin-like growth factor 2 mRNA binding protein 2" [Mus musculus (taxid:10090)]

 Score = 164 (62.8 bits), Expect = 3.4e-11, P = 3.4e-11
 Identities = 39/94 (41%), Positives = 52/94 (55%)

Query:     2 AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
             AQ  IF K++EE  F   +EV+L   + VPSS  GR+IGKGG+ V ELQ  T + + +P 
Sbjct:   481 AQGRIFGKLKEENFFNPKEEVKLEAHIRVPSSTAGRVIGKGGKTVNELQNLTSAEVIVPR 540

Query:    62 SFN---EEETNVHIVGSFFSVQETLKGCPNIVDQ 92
                    EE  V I+G FF+ Q   +    IV Q
Sbjct:   541 DQTPDENEEVIVRIIGHFFASQTAQRKIREIVQQ 574

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003730 "mRNA 3'-UTR binding" evidence=ISO

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0005856 "cytoskeleton" evidence=ISO

GO:0006417 "regulation of translation" evidence=IEA

GO:0048027 "mRNA 5'-UTR binding" evidence=ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	96
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	4e-13
pfam00013	59	pfam00013, KH_1, KH domain	8e-13
smart00322	68	smart00322, KH, K homology RNA-binding domain	2e-11
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	5e-10
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	1e-07
pfam13014	42	pfam13014, KH_3, KH domain	8e-07
cd02409	68	cd02409, KH-II, KH-II (K homology RNA-binding doma	4e-06
cd02134	61	cd02134, NusA_KH, NusA_K homology RNA-binding doma	8e-05
pfam07650	77	pfam07650, KH_2, KH domain	2e-04
PRK09202	470	PRK09202, nusA, transcription elongation factor Nu	7e-04
TIGR01953	341	TIGR01953, NusA, transcription termination factor	0.003
PRK12329	449	PRK12329, nusA, transcription elongation factor Nu	0.004

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

 Score = 58.3 bits (142), Expect = 4e-13
 Identities = 27/58 (46%), Positives = 41/58 (70%), Gaps = 1/58 (1%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFN-EEETNVHIVGSFFSVQE 81
          T  ++VPSS VGRIIGKGG  ++E++  TG+ IK+P+S +  EE  V I G+  +V++
Sbjct: 1  TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEK 58

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 = 57.2 bits (139), Expect = 8e-13
 Identities = 21/60 (35%), Positives = 38/60 (63%), Gaps = 3/60 (5%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLK 84
          T  +++P  +VGRIIGKGG N++E++  TG  I++P   ++ +  V I G+   V++  +
Sbjct: 1  TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIP---DDRDDTVTISGTPEQVEKAKE 57

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 = 53.8 bits (130), Expect = 2e-11
 Identities = 22/57 (38%), Positives = 37/57 (64%), Gaps = 1/57 (1%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQE 81
          TIE+++P+ +VG IIGKGG  +++++  TG  I +P   +EE   V I G   +V++
Sbjct: 4  TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERV-VEITGPPENVEK 59

Length = 68

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

 Score = 50.6 bits (122), Expect = 5e-10
 Identities = 26/62 (41%), Positives = 37/62 (59%), Gaps = 2/62 (3%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETN--VHIVGSFFSVQET 82
          T+ L+VPSSQ G IIGKGG  ++E++  TG+ I++  S     T   V I G   +VQ+ 
Sbjct: 1  TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKA 60

Query: 83 LK 84
          L 
Sbjct: 61 LL 62

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

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

 Score = 44.4 bits (106), Expect = 1e-07
 Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGS 75
          T E+ +P      IIGK G N+R++   TG  I+ P+    +   + I G 
Sbjct: 1  TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDP-GSKSDTITITGP 50

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

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

 Score = 41.4 bits (98), Expect = 8e-07
 Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 1/42 (2%)

Query: 34 QVGRIIGKGGQNVRELQRSTGSMIKLPNSF-NEEETNVHIVG 74
           VG IIGKGG+ ++E++  TG+ I++P       E  V I G
Sbjct: 1  LVGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTITG 42

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

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

 Score = 40.3 bits (95), Expect = 4e-06
 Identities = 15/39 (38%), Positives = 23/39 (58%)

Query: 23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
          R+ I +VV   Q G +IGK GQN+R LQ+    +++   
Sbjct: 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLLRKKR 62

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension. Length = 68

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

 Score = 36.8 bits (86), Expect = 8e-05
 Identities = 16/35 (45%), Positives = 20/35 (57%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL 59
             +VVP  Q+G  IGKGGQNVR   +  G  I +
Sbjct: 26 RARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60

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

>gnl|CDD|203707 pfam07650, KH_2, KH domain

 Score = 36.0 bits (84), Expect = 2e-04
 Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 5/62 (8%)

Query: 4  YLIFEKMREEGLFAGADEVRLT---IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLP 60
            +  ++++ G      E+  T   + +V+ +SQ G +IGKGG N+++L +    +I+L 
Sbjct: 4  EFLAVELKKAG--ISDIEIERTPNRVIVVIRTSQPGIVIGKGGSNIKKLGKELRKLIELE 61

Query: 61 NS 62
            
Sbjct: 62 GK 63

Length = 77

>gnl|CDD|236410 PRK09202, nusA, transcription elongation factor NusA; Validated

 Score = 36.4 bits (85), Expect = 7e-04
 Identities = 14/28 (50%), Positives = 18/28 (64%)

Query: 20  DEVRLTIELVVPSSQVGRIIGKGGQNVR 47
           DE   + ++VVP  Q+   IGK GQNVR
Sbjct: 298 DEDEHSADVVVPDDQLSLAIGKNGQNVR 325

Length = 470

>gnl|CDD|233654 TIGR01953, NusA, transcription termination factor NusA

 Score = 34.5 bits (80), Expect = 0.003
 Identities = 19/38 (50%), Positives = 24/38 (63%)

Query: 20  DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMI 57
           DE + + E+VVP  Q+   IGKGGQNVR   + TG  I
Sbjct: 297 DEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNI 334

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 [Transcription, Transcription factors]. Length = 341

>gnl|CDD|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional

 Score = 34.4 bits (79), Expect = 0.004
 Identities = 22/52 (42%), Positives = 27/52 (51%), Gaps = 6/52 (11%)

Query: 17  AGADEVRLT------IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS 62
           A  DEVRL         ++VP  Q+   IGK GQNVR   R TG  I + +S
Sbjct: 322 ARVDEVRLVDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKDS 373

Length = 449

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	96
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.76
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.69
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.69
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.69
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.63
KOG1676|consensus	600		99.62
KOG2190|consensus	485		99.59
KOG2191|consensus	402		99.53
KOG2193|consensus	584		99.52
KOG2191|consensus	402		99.5
smart00322	69	KH K homology RNA-binding domain.	99.49
PF13014	43	KH_3: KH domain	99.45
KOG2192|consensus	390		99.39
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	99.26
KOG2192|consensus	390		99.24
KOG1676|consensus	600		99.23
KOG2193|consensus	584		99.2
PRK13763	180	putative RNA-processing protein; Provisional	99.18
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.18
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	99.15
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.13
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	99.11
PRK13763	180	putative RNA-processing protein; Provisional	99.07
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.07
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	99.0
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	98.82
KOG2190|consensus	485		98.81
KOG0336|consensus	629		98.75
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.45
KOG0119|consensus	554		98.42
KOG2814|consensus	345		98.39
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	98.26
KOG1067|consensus	760		98.25
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	98.13
PRK00106	535	hypothetical protein; Provisional	98.07
PRK12704	520	phosphodiesterase; Provisional	98.05
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	98.01
KOG1588|consensus	259		97.97
PRK12705	508	hypothetical protein; Provisional	97.9
KOG2279|consensus	608		97.86
COG5176	269	MSL5 Splicing factor (branch point binding protein	97.7
KOG3273|consensus	252		97.66
PRK00468	75	hypothetical protein; Provisional	97.64
KOG2113|consensus	394		97.63
PRK02821	77	hypothetical protein; Provisional	97.52
COG1837	76	Predicted RNA-binding protein (contains KH domain)	97.49
PRK01064	78	hypothetical protein; Provisional	97.38
KOG4369|consensus	2131		97.34
KOG2279|consensus	608		97.27
COG1094	194	Predicted RNA-binding protein (contains KH domains	97.04
PRK08406	140	transcription elongation factor NusA-like protein;	97.01
PRK08406	140	transcription elongation factor NusA-like protein;	96.82
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	96.71
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	96.71
KOG2208|consensus	753		96.58
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	96.51
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	96.34
KOG2874|consensus	356		96.19
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	96.14
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	96.11
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	96.06
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	95.71
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	95.54
TIGR01953	341	NusA transcription termination factor NusA. This m	95.31
COG0195	190	NusA Transcription elongation factor [Transcriptio	95.25
PRK13764	602	ATPase; Provisional	95.1
PRK12328	374	nusA transcription elongation factor NusA; Provisi	95.07
COG1855	604	ATPase (PilT family) [General function prediction	95.06
PRK06418	166	transcription elongation factor NusA-like protein;	94.9
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	94.66
PRK09202	470	nusA transcription elongation factor NusA; Validat	94.41
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	94.33
PRK12327	362	nusA transcription elongation factor NusA; Provisi	94.3
KOG2208|consensus	753		94.2
TIGR00436	270	era GTP-binding protein Era. Era is an essential G	93.82
cd02412	109	30S_S3_KH K homology RNA-binding (KH) domain of th	93.43
cd02411	85	archeal_30S_S3_KH K homology RNA-binding domain (K	93.42
PRK12329	449	nusA transcription elongation factor NusA; Provisi	93.39
PRK15494	339	era GTPase Era; Provisional	93.04
COG0195	190	NusA Transcription elongation factor [Transcriptio	92.97
COG0092	233	RpsC Ribosomal protein S3 [Translation, ribosomal	91.43
COG1159	298	Era GTPase [General function prediction only]	91.29
KOG1423|consensus	379		89.3
PRK00089	292	era GTPase Era; Reviewed	89.0
COG5166	657	Uncharacterized conserved protein [Function unknow	87.2
PRK12327	362	nusA transcription elongation factor NusA; Provisi	86.96
TIGR03675	630	arCOG00543 arCOG00543 universal archaeal KH-domain	86.86
COG1782	637	Predicted metal-dependent RNase, consists of a met	86.47
TIGR01953	341	NusA transcription termination factor NusA. This m	85.76
KOG2113|consensus	394		85.57
TIGR01008	195	rpsC_E_A ribosomal protein S3, eukaryotic/archaeal	84.41
COG1847	208	Jag Predicted RNA-binding protein [General functio	84.29
PRK04191	207	rps3p 30S ribosomal protein S3P; Reviewed	84.14
PRK12329	449	nusA transcription elongation factor NusA; Provisi	84.09
PTZ00084	220	40S ribosomal protein S3; Provisional	83.65
PRK12328	374	nusA transcription elongation factor NusA; Provisi	83.53
CHL00048	214	rps3 ribosomal protein S3	82.7
PRK09202	470	nusA transcription elongation factor NusA; Validat	82.31
COG1702	348	PhoH Phosphate starvation-inducible protein PhoH,	81.34

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.76  E-value=3.5e-18  Score=98.06  Aligned_cols=63  Identities=41%  Similarity=0.603  Sum_probs=58.4

Q ss_pred             EEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCC--CCCceEEEEEcCHHHHHHHHHHHh
Q psy2768          25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF--NEEETNVHIVGSFFSVQETLKGCP   87 (96)
Q Consensus        25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~--~~~~~~v~I~G~~~~v~~A~~~I~   87 (96)
                      +++|.||.+.+|+|||++|++|++|+++|||+|.+.+..  +..++.|+|.|+++++..|+.+|.
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~   65 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLIL   65 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhhC
Confidence            468999999999999999999999999999999999854  578899999999999999999874

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

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.69  E-value=5.4e-17  Score=91.42  Aligned_cols=60  Identities=43%  Similarity=0.617  Sum_probs=55.5

Q ss_pred             EEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHH
Q psy2768          25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGC   86 (96)
Q Consensus        25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I   86 (96)
                      |.++.||.+++|+|||++|++|++|+++|||+|++++. + .+..|+|.|+++++..|+++|
T Consensus         1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~-~-~~~~v~I~G~~~~v~~A~~~I   60 (60)
T PF00013_consen    1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD-D-ERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST-T-EEEEEEEEESHHHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC-C-CcEEEEEEeCHHHHHHHHhhC
Confidence            67899999999999999999999999999999999976 3 456999999999999999886

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

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.69  E-value=5.5e-17  Score=91.95  Aligned_cols=61  Identities=26%  Similarity=0.408  Sum_probs=56.4

Q ss_pred             EEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHh
Q psy2768          26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCP   87 (96)
Q Consensus        26 ~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~   87 (96)
                      .++.||.+++|+|||++|++|++|+++|||+|.+++.. ..++.|+|+|+++++..|+.+|.
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-~~~~~v~I~G~~~~v~~A~~~i~   62 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-SKSDTITITGPKENVEKAKEEIL   62 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-CCCCEEEEEcCHHHHHHHHHHhC
Confidence            57899999999999999999999999999999999865 56799999999999999998873

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

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

Probab=99.69  E-value=1.3e-16  Score=90.75  Aligned_cols=60  Identities=20%  Similarity=0.366  Sum_probs=55.0

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcC-HHHHHHHHHHHh
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGS-FFSVQETLKGCP   87 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~-~~~v~~A~~~I~   87 (96)
                      +.+..+.||.+++|+||||||++|++|+++|||+|++++     ++.|.|+|+ +++++.|+.+|.
T Consensus         1 P~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----~g~v~I~G~~~~~v~~A~~~I~   61 (61)
T cd02393           1 PRIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-----DGTVYIAASDKEAAEKAKKMIE   61 (61)
T ss_pred             CeEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-----CCEEEEEeCCHHHHHHHHHHhC
Confidence            356789999999999999999999999999999999997     468999998 899999998874

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

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

Probab=99.63  E-value=2.6e-15  Score=84.94  Aligned_cols=62  Identities=42%  Similarity=0.608  Sum_probs=56.5

Q ss_pred             EEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCC-CCCceEEEEEcCHHHHHHHHHHHh
Q psy2768          26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF-NEEETNVHIVGSFFSVQETLKGCP   87 (96)
Q Consensus        26 ~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~-~~~~~~v~I~G~~~~v~~A~~~I~   87 (96)
                      .++.||.+++|.|||++|++|++|+++|||+|.|+... +..++.|.|.|+.+++..|+.+|.
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i~   64 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELIL   64 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHhC
Confidence            57899999999999999999999999999999999853 356899999999999999998873

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.

>KOG1676|consensus

Probab=99.62  E-value=2.8e-15  Score=114.55  Aligned_cols=92  Identities=29%  Similarity=0.407  Sum_probs=79.2

Q ss_pred             hHHHHHHHHHHhcccC--------CCCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC--CCCCceEEE
Q psy2768           2 AQYLIFEKMREEGLFA--------GADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS--FNEEETNVH   71 (96)
Q Consensus         2 A~~~I~~k~~e~~~~~--------~~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~~~~v~   71 (96)
                      |..|+.|-|+|+.-..        +......+.++.||.+.||.||||+|++||.|+.+||+||+|..+  +.+.||.+.
T Consensus       200 a~~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~  279 (600)
T KOG1676|consen  200 AKQLVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQ  279 (600)
T ss_pred             HHHHHHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceee
Confidence            6788999999764211        144556699999999999999999999999999999999999774  457899999


Q ss_pred             EEcCHHHHHHHHHHHhHHhcCC
Q psy2768          72 IVGSFFSVQETLKGCPNIVDQP   93 (96)
Q Consensus        72 I~G~~~~v~~A~~~I~~~i~~~   93 (96)
                      |.|+++.|+.|.++|.++|+..
T Consensus       280 IiG~~d~ie~Aa~lI~eii~~~  301 (600)
T KOG1676|consen  280 IIGTVDQIEHAAELINEIIAEA  301 (600)
T ss_pred             eecCHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999998753

>KOG2190|consensus

Probab=99.59  E-value=6.7e-15  Score=111.80  Aligned_cols=90  Identities=33%  Similarity=0.435  Sum_probs=73.4

Q ss_pred             hHHHHHHHHHHhcc--cCC---CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC--CCCCceEEEEEc
Q psy2768           2 AQYLIFEKMREEGL--FAG---ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS--FNEEETNVHIVG   74 (96)
Q Consensus         2 A~~~I~~k~~e~~~--~~~---~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~~~~v~I~G   74 (96)
                      |+.+|..+.+++..  ..+   .....++++|.||.+++|.||||+|+.||+|+++|||+|.+...  |.+++|.|+|.|
T Consensus       111 a~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG  190 (485)
T KOG2190|consen  111 AFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISG  190 (485)
T ss_pred             HHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcC
Confidence            45556665553332  111   22235899999999999999999999999999999999999885  888999999999


Q ss_pred             CHHHHHHHHHHHhHHhc
Q psy2768          75 SFFSVQETLKGCPNIVD   91 (96)
Q Consensus        75 ~~~~v~~A~~~I~~~i~   91 (96)
                      .+++|.+|+..|...|.
T Consensus       191 ~~~av~~al~~Is~~L~  207 (485)
T KOG2190|consen  191 EPDAVKKALVQISSRLL  207 (485)
T ss_pred             chHHHHHHHHHHHHHHH
Confidence            99999999999999443

>KOG2191|consensus

Probab=99.53  E-value=8.6e-14  Score=100.81  Aligned_cols=90  Identities=24%  Similarity=0.357  Sum_probs=73.3

Q ss_pred             HHHHHHHHHHhcccC---C------CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC-CC---CCCceE
Q psy2768           3 QYLIFEKMREEGLFA---G------ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN-SF---NEEETN   69 (96)
Q Consensus         3 ~~~I~~k~~e~~~~~---~------~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~-~~---~~~~~~   69 (96)
                      ..+|+||++|..-..   .      ..+....+++.+|++.+|.||||||++||.+++++||+|+|.. .|   +..+|+
T Consensus       102 ~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqerv  181 (402)
T KOG2191|consen  102 HEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERV  181 (402)
T ss_pred             HHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEE
Confidence            568999999975311   1      1122245899999999999999999999999999999999984 33   358999


Q ss_pred             EEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          70 VHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        70 v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      |++.|.+++..+|..+|.+.+.+
T Consensus       182 vt~sge~e~~~~A~~~IL~Ki~e  204 (402)
T KOG2191|consen  182 VTVSGEPEQNMKAVSLILQKIQE  204 (402)
T ss_pred             EEecCCHHHHHHHHHHHHHHhhc
Confidence            99999999999999999985443

>KOG2193|consensus

Probab=99.52  E-value=1.4e-14  Score=107.70  Aligned_cols=91  Identities=41%  Similarity=0.672  Sum_probs=82.9

Q ss_pred             hHHHHHHHHHHhcccCCCCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC--CCC-CceEEEEEcCHHH
Q psy2768           2 AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS--FNE-EETNVHIVGSFFS   78 (96)
Q Consensus         2 A~~~I~~k~~e~~~~~~~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~-~~~~v~I~G~~~~   78 (96)
                      ||.+||.|+.|+++..+++...+...+.||.+.+|++|||||.++++|+.-|++.+.||++  |++ +...|.|.|+..+
T Consensus       471 AQgrifgKikEenf~~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhfya  550 (584)
T KOG2193|consen  471 AQGRIFGKIKEENFFLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHFYA  550 (584)
T ss_pred             hhhhhhhhhhhhccCCchhhheeeeeeeccchhhhhhhccccccHHHHhccccceEEccccCCCCccceeeeeeechhhc
Confidence            7899999999999988888899999999999999999999999999999999999999994  444 4466889999999


Q ss_pred             HHHHHHHHhHHhcC
Q psy2768          79 VQETLKGCPNIVDQ   92 (96)
Q Consensus        79 v~~A~~~I~~~i~~   92 (96)
                      ...|...|.+++.+
T Consensus       551 tq~aQrki~~iv~q  564 (584)
T KOG2193|consen  551 TQNAQRKIAHIVNQ  564 (584)
T ss_pred             chHHHHHHHHHHHH
Confidence            99999999998764

>KOG2191|consensus

Probab=99.50  E-value=1e-13  Score=100.38  Aligned_cols=72  Identities=29%  Similarity=0.452  Sum_probs=67.0

Q ss_pred             CceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC----CCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS----FNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        21 ~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~----~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      +..+.++++||+..+|.||||||++|.++|++|||+|++.+.    |+++||+|.|.|+.+.+......|.+.|++
T Consensus        36 ~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire  111 (402)
T KOG2191|consen   36 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIRE  111 (402)
T ss_pred             CCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHH
Confidence            345999999999999999999999999999999999999983    889999999999999999999999997765

>smart00322 KH K homology RNA-binding domain

Probab=99.49  E-value=4.6e-13  Score=75.35  Aligned_cols=67  Identities=34%  Similarity=0.584  Sum_probs=60.5

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHh
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIV   90 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i   90 (96)
                      ..+.++.||.+.+|.+||++|++|++|++.||++|.++.... ....+.|.|+++++..|..+|.+.+
T Consensus         2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~-~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS-EERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC-CccEEEEEcCHHHHHHHHHHHHHHh
Confidence            467899999999999999999999999999999999987433 4688999999999999999998865

>PF13014 KH_3: KH domain

Probab=99.45  E-value=2.4e-13  Score=71.99  Aligned_cols=41  Identities=44%  Similarity=0.770  Sum_probs=37.5

Q ss_pred             ccceeeccchhHHHHHHHHhCCeEEecC--CCCCCceEEEEEc
Q psy2768          34 QVGRIIGKGGQNVRELQRSTGSMIKLPN--SFNEEETNVHIVG   74 (96)
Q Consensus        34 ~vg~iIGkgG~~Ik~i~~~tg~~I~i~~--~~~~~~~~v~I~G   74 (96)
                      ++|+|||++|++|++|+++|||+|+|++  .++..++.|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence            5899999999999999999999999999  4566889999987

>KOG2192|consensus

Probab=99.39  E-value=1.7e-12  Score=92.36  Aligned_cols=73  Identities=27%  Similarity=0.405  Sum_probs=67.3

Q ss_pred             CCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC-CCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN-SFNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        20 ~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~-~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      +.+..+..+.||++.-|.||||||..|++|+.++|+.|+++. ..++.+|.++|+|+.++++.|+.+++..+++
T Consensus       311 GGPitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vkq  384 (390)
T KOG2192|consen  311 GGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ  384 (390)
T ss_pred             CCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHHh
Confidence            456778899999999999999999999999999999999999 5677899999999999999999999987764

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=99.26  E-value=3.9e-11  Score=94.64  Aligned_cols=85  Identities=21%  Similarity=0.266  Sum_probs=75.0

Q ss_pred             hHHHHHHHHHHhcccC--CCCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcC-HHH
Q psy2768           2 AQYLIFEKMREEGLFA--GADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGS-FFS   78 (96)
Q Consensus         2 A~~~I~~k~~e~~~~~--~~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~-~~~   78 (96)
                      |...|++.|++....+  .+...+....+.||.+.+|.+||+||.+||+|+++||++|+|.+     +..|.|.+. .++
T Consensus       554 g~~~Il~~m~~al~~p~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-----~G~V~I~a~d~~~  628 (719)
T TIGR02696       554 ARLAILDVMAEAIDTPDEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED-----DGTVYIGAADGPS  628 (719)
T ss_pred             HHHHHHHHHHHHHhCccccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec-----CcEEEEEeCCHHH
Confidence            4567899999875433  36778999999999999999999999999999999999999997     688999884 599


Q ss_pred             HHHHHHHHhHHhc
Q psy2768          79 VQETLKGCPNIVD   91 (96)
Q Consensus        79 v~~A~~~I~~~i~   91 (96)
                      .++|+.+|..++.
T Consensus       629 ~~~A~~~I~~i~~  641 (719)
T TIGR02696       629 AEAARAMINAIAN  641 (719)
T ss_pred             HHHHHHHHHHhhC
Confidence            9999999999887

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.

>KOG2192|consensus

Probab=99.24  E-value=8.2e-12  Score=88.90  Aligned_cols=77  Identities=22%  Similarity=0.315  Sum_probs=70.7

Q ss_pred             CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC--CCCCCceEEEEEcCHHHHHHHHHHHhHHhcCCCC
Q psy2768          19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN--SFNEEETNVHIVGSFFSVQETLKGCPNIVDQPSI   95 (96)
Q Consensus        19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~--~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~~   95 (96)
                      ....+..+++.|.++.+|.||||.|++||+|++++.++++|..  +|..++|+|.+.|.+..|..+++.|.+++.+.++
T Consensus       118 ~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pi  196 (390)
T KOG2192|consen  118 QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISESPI  196 (390)
T ss_pred             CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCc
Confidence            4456789999999999999999999999999999999999987  6889999999999999999999999998887654

>KOG1676|consensus

Probab=99.23  E-value=2.9e-11  Score=92.84  Aligned_cols=74  Identities=26%  Similarity=0.457  Sum_probs=66.1

Q ss_pred             CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCC---CCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF---NEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      ......+.++.||.+.+|.||||||.+||.|++.|||++.+-++.   ....+.+.|+|++++|+.|+.++.++|++
T Consensus       134 q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e  210 (600)
T KOG1676|consen  134 QGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILRE  210 (600)
T ss_pred             CCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHh
Confidence            335678999999999999999999999999999999999987742   23678999999999999999999999985

>KOG2193|consensus

Probab=99.20  E-value=1e-11  Score=92.72  Aligned_cols=75  Identities=21%  Similarity=0.334  Sum_probs=67.9

Q ss_pred             CceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC--CCCCceEEEEEcCHHHHHHHHHHHhHHhcCCCC
Q psy2768          21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS--FNEEETNVHIVGSFFSVQETLKGCPNIVDQPSI   95 (96)
Q Consensus        21 ~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~~   95 (96)
                      ...+.+++.||..++|.||||.|++||+|-+.|.|+|+|-+.  .+..|+.++|-|++++..+|+++|.+++.+..+
T Consensus       196 ~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~  272 (584)
T KOG2193|consen  196 LKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGTSKACKMILEIMQKEAV  272 (584)
T ss_pred             ccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccchHHHHHHHHHHHHHhhh
Confidence            347889999999999999999999999999999999999883  466899999999999999999999998876544

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.18  E-value=6.1e-11  Score=80.20  Aligned_cols=65  Identities=20%  Similarity=0.320  Sum_probs=58.7

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEE----cCHHHHHHHHHHHhHHhc
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIV----GSFFSVQETLKGCPNIVD   91 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~----G~~~~v~~A~~~I~~~i~   91 (96)
                      .....+.||.+.+|.|||++|.+|+.|+++||++|++...    +..|.|.    ++++++.+|+.+|..+..
T Consensus         2 ~~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~----~g~V~I~~~~~~d~~~i~kA~~~I~ai~~   70 (180)
T PRK13763          2 MMMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE----TGEVIIEPTDGEDPLAVLKARDIVKAIGR   70 (180)
T ss_pred             CceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC----CCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence            3567899999999999999999999999999999999973    3778885    899999999999999876

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.18  E-value=3.1e-11  Score=81.07  Aligned_cols=61  Identities=23%  Similarity=0.424  Sum_probs=55.0

Q ss_pred             EEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEE---EcCHHHHHHHHHHHhHHhcC
Q psy2768          28 LVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHI---VGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        28 ~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I---~G~~~~v~~A~~~I~~~i~~   92 (96)
                      +.||.+.+|.+||+||++|+.|+++||++|++.+.    +..|.|   .++++++.+|+.+|..+...
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~----~g~V~I~~~t~d~~~i~kA~~~I~~i~~g   65 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE----TGEVKIEEEDEDPLAVMKAREVVKAIGRG   65 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC----CceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence            57999999999999999999999999999999973    367888   78999999999999997763

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.

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=99.15  E-value=1.6e-10  Score=91.17  Aligned_cols=88  Identities=18%  Similarity=0.278  Sum_probs=74.8

Q ss_pred             hHHHHHHHHHHhcccC---CCCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEc-CHH
Q psy2768           2 AQYLIFEKMREEGLFA---GADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVG-SFF   77 (96)
Q Consensus         2 A~~~I~~k~~e~~~~~---~~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G-~~~   77 (96)
                      +...|++.|++....+   .+...+...++.||.+.+|.|||+||++||.|+++|||+|+|.+     +..|.|.+ +.+
T Consensus       526 ~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-----dG~V~i~~~~~~  600 (684)
T TIGR03591       526 GRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-----DGTVKIAASDGE  600 (684)
T ss_pred             HHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-----CeEEEEEECcHH
Confidence            3467888888875433   37788999999999999999999999999999999999999987     57888877 459


Q ss_pred             HHHHHHHHHhHHhcCCC
Q psy2768          78 SVQETLKGCPNIVDQPS   94 (96)
Q Consensus        78 ~v~~A~~~I~~~i~~~~   94 (96)
                      .+.+|+.+|..+...+.
T Consensus       601 ~~~~a~~~I~~~~~~~~  617 (684)
T TIGR03591       601 AAEAAIKMIEGITAEPE  617 (684)
T ss_pred             HHHHHHHHHHhhhcccc
Confidence            99999999999876544

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).

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.13  E-value=1.6e-10  Score=77.58  Aligned_cols=55  Identities=29%  Similarity=0.414  Sum_probs=50.5

Q ss_pred             CccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcCC
Q psy2768          33 SQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQP   93 (96)
Q Consensus        33 ~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   93 (96)
                      ..+|+|||++|++++.|+..|||+|.|++      ..|.|.|++++++.|+..|+++++..
T Consensus        98 ~~~griIG~~G~t~~~ie~~t~~~i~i~~------~~v~i~G~~~~~~~A~~~i~~li~~~  152 (172)
T TIGR03665        98 RIKGRIIGEGGKTRRIIEELTGVSISVYG------KTVGIIGDPEQVQIAREAIEMLIEGA  152 (172)
T ss_pred             HHHhhhcCCCcHHHHHHHHHHCCeEEEcC------CEEEEECCHHHHHHHHHHHHHHHcCC
Confidence            36899999999999999999999999984      67999999999999999999988653

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

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

Probab=99.11  E-value=4.3e-10  Score=71.73  Aligned_cols=62  Identities=19%  Similarity=0.348  Sum_probs=51.2

Q ss_pred             cCccceeeccchhHHHHHHHHhCCeEEecCCCC------------------CCceEEEEEcC---HHHHHHHHHHHhHHh
Q psy2768          32 SSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFN------------------EEETNVHIVGS---FFSVQETLKGCPNIV   90 (96)
Q Consensus        32 ~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~------------------~~~~~v~I~G~---~~~v~~A~~~I~~~i   90 (96)
                      -+++|.|||++|+++|+|+++|||+|.|.....                  ...--|.|+++   .+++.+|+.+|..++
T Consensus        14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll   93 (120)
T cd02395          14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL   93 (120)
T ss_pred             CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence            367899999999999999999999999987410                  11256888885   499999999999988


Q ss_pred             cCC
Q psy2768          91 DQP   93 (96)
Q Consensus        91 ~~~   93 (96)
                      ...
T Consensus        94 ~~~   96 (120)
T cd02395          94 KPA   96 (120)
T ss_pred             ccC
Confidence            754

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

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.07  E-value=4.8e-10  Score=75.86  Aligned_cols=55  Identities=27%  Similarity=0.402  Sum_probs=49.8

Q ss_pred             CccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcCC
Q psy2768          33 SQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQP   93 (96)
Q Consensus        33 ~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   93 (96)
                      ..+|+|||++|++++.|++.|||+|.|++      ..|.|.|+++++..|...|+.+++..
T Consensus       104 r~~griIG~~G~~~k~ie~~t~~~i~i~~------~~v~i~G~~~~~~~A~~~I~~li~g~  158 (180)
T PRK13763        104 RIKGRIIGEGGKTRRIIEELTGVDISVYG------KTVAIIGDPEQVEIAREAIEMLIEGA  158 (180)
T ss_pred             HHhhheeCCCcHHHHHHHHHHCcEEEEcC------CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence            36899999999999999999999999985      34889999999999999999988653

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=99.07  E-value=3.5e-10  Score=90.95  Aligned_cols=89  Identities=20%  Similarity=0.296  Sum_probs=78.2

Q ss_pred             hHHHHHHHHHHhcccCC---CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCe-EEecCCCCCCceEEEEEcC-H
Q psy2768           2 AQYLIFEKMREEGLFAG---ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSM-IKLPNSFNEEETNVHIVGS-F   76 (96)
Q Consensus         2 A~~~I~~k~~e~~~~~~---~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~-I~i~~~~~~~~~~v~I~G~-~   76 (96)
                      |...|++.|++.+..+.   +...+....+.||.+.+|.|||.||.+||+|+++||++ |++.+     +..|.|.+. .
T Consensus       660 g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d-----dg~V~I~a~d~  734 (891)
T PLN00207        660 GRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD-----DGTVKITAKDL  734 (891)
T ss_pred             HHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC-----CeeEEEEeCCH
Confidence            45679999999876543   78889999999999999999999999999999999999 99987     688999984 5


Q ss_pred             HHHHHHHHHHhHHhcCCCC
Q psy2768          77 FSVQETLKGCPNIVDQPSI   95 (96)
Q Consensus        77 ~~v~~A~~~I~~~i~~~~~   95 (96)
                      +++++|+.+|..+...+.+
T Consensus       735 ~~i~~A~~~I~~l~~~~~v  753 (891)
T PLN00207        735 SSLEKSKAIISSLTMVPTV  753 (891)
T ss_pred             HHHHHHHHHHHHHhcCcCC
Confidence            9999999999998776543

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

Probab=99.00  E-value=1e-09  Score=85.75  Aligned_cols=89  Identities=18%  Similarity=0.249  Sum_probs=79.5

Q ss_pred             hHHHHHHHHHHhcccCC---CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCH-H
Q psy2768           2 AQYLIFEKMREEGLFAG---ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSF-F   77 (96)
Q Consensus         2 A~~~I~~k~~e~~~~~~---~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~-~   77 (96)
                      |..+|++.|.+.+..+.   +...+...++.|+.+.++-+||+||++|++|.++||++|++.+     +..|.|.++. +
T Consensus       527 aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied-----dGtv~i~~s~~~  601 (692)
T COG1185         527 ARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED-----DGTVKIAASDGE  601 (692)
T ss_pred             HHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC-----CCcEEEEecchH
Confidence            56789999999876543   6777889999999999999999999999999999999999995     5789999876 9


Q ss_pred             HHHHHHHHHhHHhcCCCC
Q psy2768          78 SVQETLKGCPNIVDQPSI   95 (96)
Q Consensus        78 ~v~~A~~~I~~~i~~~~~   95 (96)
                      .+..|+..|..+++++++
T Consensus       602 ~~~~ak~~I~~i~~e~ev  619 (692)
T COG1185         602 SAKKAKERIEAITREVEV  619 (692)
T ss_pred             HHHHHHHHHHHHHhhccc
Confidence            999999999999988765

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=98.82  E-value=7e-09  Score=82.12  Aligned_cols=88  Identities=20%  Similarity=0.344  Sum_probs=74.9

Q ss_pred             hHHHHHHHHHHhcccCC---CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcC-HH
Q psy2768           2 AQYLIFEKMREEGLFAG---ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGS-FF   77 (96)
Q Consensus         2 A~~~I~~k~~e~~~~~~---~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~-~~   77 (96)
                      |...|+++|.+....+.   +...+....+.||.+.++.+||+||.+||+|.++||++|++.+     +..|.|++. .+
T Consensus       529 g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d-----~G~v~i~~~~~~  603 (693)
T PRK11824        529 GRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED-----DGTVKIAATDGE  603 (693)
T ss_pred             HHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC-----CceEEEEcccHH
Confidence            45789999999865443   5667888899999999999999999999999999999999875     588999885 59


Q ss_pred             HHHHHHHHHhHHhcCCC
Q psy2768          78 SVQETLKGCPNIVDQPS   94 (96)
Q Consensus        78 ~v~~A~~~I~~~i~~~~   94 (96)
                      .+++|+.+|..+...+.
T Consensus       604 ~~~~a~~~I~~~~~~~~  620 (693)
T PRK11824        604 AAEAAKERIEGITAEPE  620 (693)
T ss_pred             HHHHHHHHHHHhcccCc
Confidence            99999999999876643

>KOG2190|consensus

Probab=98.81  E-value=7.7e-09  Score=79.03  Aligned_cols=72  Identities=29%  Similarity=0.367  Sum_probs=65.0

Q ss_pred             CceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCC---CCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF---NEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        21 ~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      ...++.++.||++++|++|||+|++|.+|++.|||.|.|.+.+   ...++.++|+|...+...+..++...+..
T Consensus       335 ~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~  409 (485)
T KOG2190|consen  335 TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEVSGVREALVQITGMLREDLLAQYLIRARLSA  409 (485)
T ss_pred             cceeeeeeccCccccceeecccccchHHHHHhcCCceEEccccccCCcceeEEEecchhHHHHhhhhhccccccc
Confidence            6678999999999999999999999999999999999999854   66899999999999999999988665544

>KOG0336|consensus

Probab=98.75  E-value=7.8e-09  Score=77.84  Aligned_cols=72  Identities=22%  Similarity=0.340  Sum_probs=64.1

Q ss_pred             CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      .+...+++.|.+.+++||.+||+||++|+.||..|+++|++.++.  .+..|+|.|....-.+|+..|...++.
T Consensus        42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~--~e~kv~ifg~~~m~~kaka~id~~~~k  113 (629)
T KOG0336|consen   42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD--LEVKVTIFGINHMRKKAKASIDRGQDK  113 (629)
T ss_pred             cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC--ceeEEEEechHHHHHHHHhhHhhhhhh
Confidence            566788999999999999999999999999999999999999853  478899999999999999988876543

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

Probab=98.45  E-value=7.3e-07  Score=60.88  Aligned_cols=54  Identities=28%  Similarity=0.477  Sum_probs=50.0

Q ss_pred             ccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcCC
Q psy2768          34 QVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQP   93 (96)
Q Consensus        34 ~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   93 (96)
                      ..|+|||++|.+-+-|++-|||.|.|..      ..|.|.|.++++..|+..|..+++..
T Consensus       112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g------~tVaiiG~~~~v~iAr~AVemli~G~  165 (194)
T COG1094         112 IKGRIIGREGKTRRAIEELTGVYISVYG------KTVAIIGGFEQVEIAREAVEMLINGA  165 (194)
T ss_pred             hhceeeCCCchHHHHHHHHhCCeEEEeC------cEEEEecChhhhHHHHHHHHHHHcCC
Confidence            4699999999999999999999999995      78999999999999999999988764

>KOG0119|consensus

Probab=98.42  E-value=6.7e-07  Score=68.10  Aligned_cols=71  Identities=24%  Similarity=0.389  Sum_probs=57.4

Q ss_pred             ceeEEEEEeec------CccceeeccchhHHHHHHHHhCCeEEecCC----------------CCC-CceEEEEEcCH-H
Q psy2768          22 VRLTIELVVPS------SQVGRIIGKGGQNVRELQRSTGSMIKLPNS----------------FNE-EETNVHIVGSF-F   77 (96)
Q Consensus        22 ~~~~~~~~ip~------~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~----------------~~~-~~~~v~I~G~~-~   77 (96)
                      ..++-++.||.      ++||.|||..|.+.|+|+++|||+|.|...                ++. .+--|.|+++. +
T Consensus       136 ~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~e  215 (554)
T KOG0119|consen  136 AKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQE  215 (554)
T ss_pred             cccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHH
Confidence            36777888885      689999999999999999999999999651                111 22347788755 9


Q ss_pred             HHHHHHHHHhHHhcC
Q psy2768          78 SVQETLKGCPNIVDQ   92 (96)
Q Consensus        78 ~v~~A~~~I~~~i~~   92 (96)
                      .|++|+++|+.+|.+
T Consensus       216 ki~~Ai~vienli~~  230 (554)
T KOG0119|consen  216 KIKKAIAVIENLIQS  230 (554)
T ss_pred             HHHHHHHHHHHHHHh
Confidence            999999999998876

>KOG2814|consensus

Probab=98.39  E-value=4e-07  Score=66.39  Aligned_cols=70  Identities=27%  Similarity=0.345  Sum_probs=59.2

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      .++..+.++++..|.|||+.|.+-+.|+++|+|+|.+|.+....+.+..+.+..++|.+|...|..++.+
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids  125 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLIDS  125 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHHHh
Confidence            5788899999999999999999999999999999999985544344444445779999999999998765

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=98.26  E-value=1.9e-06  Score=60.47  Aligned_cols=64  Identities=20%  Similarity=0.273  Sum_probs=56.7

Q ss_pred             EEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCH-HHHHHHHHHHhHHhcCCC
Q psy2768          26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSF-FSVQETLKGCPNIVDQPS   94 (96)
Q Consensus        26 ~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~-~~v~~A~~~I~~~i~~~~   94 (96)
                      ..+.||.++++++||++|.+|+.|.+.|+++|.+..     +..|.|.++. +++..|+.+|+.+-++++
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-----NG~VwI~~~~~~~~~~a~~~I~~~e~~~~  211 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-----NGRIWIKGPDEEDEEIAIEAIKKIEREAH  211 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-----CcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence            458999999999999999999999999999999986     5889999865 799999999998876654

>KOG1067|consensus

Probab=98.25  E-value=2.7e-06  Score=66.11  Aligned_cols=87  Identities=18%  Similarity=0.238  Sum_probs=74.1

Q ss_pred             hHHHHHHHHHHhcccCC---CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEc-CHH
Q psy2768           2 AQYLIFEKMREEGLFAG---ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVG-SFF   77 (96)
Q Consensus         2 A~~~I~~k~~e~~~~~~---~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G-~~~   77 (96)
                      |...|++.|.+.+..+.   +...++...+.++.+.+..+||++|-..|+|+.+||+.-.++      +..++|.. ++.
T Consensus       572 ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD------e~t~~i~A~~~~  645 (760)
T KOG1067|consen  572 ARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD------EGTFSIFAPTQA  645 (760)
T ss_pred             HHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec------CceEEEEecCHH
Confidence            56789999999876443   677899999999999999999999999999999999766666      46777776 569


Q ss_pred             HHHHHHHHHhHHhcCCC
Q psy2768          78 SVQETLKGCPNIVDQPS   94 (96)
Q Consensus        78 ~v~~A~~~I~~~i~~~~   94 (96)
                      +.++|+..|..++..+.
T Consensus       646 am~~Ak~~I~~i~~~~~  662 (760)
T KOG1067|consen  646 AMEEAKEFIDGIIKDDQ  662 (760)
T ss_pred             HHHHHHHHHHHHhcCcc
Confidence            99999999999876654

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=98.13  E-value=1.9e-05  Score=60.98  Aligned_cols=69  Identities=22%  Similarity=0.341  Sum_probs=56.7

Q ss_pred             eeEEEEEeecC-ccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEc-CHHHHHHHHHHHhHHhcCCCC
Q psy2768          23 RLTIELVVPSS-QVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVG-SFFSVQETLKGCPNIVDQPSI   95 (96)
Q Consensus        23 ~~~~~~~ip~~-~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i~~~~~   95 (96)
                      ..+-.+.+|++ +-|+||||.|.+||-++.-||+.+-|++.|    ..|+++| +|---+-|...+..++.+.-|
T Consensus       203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp----~~v~ls~fdp~rreia~~~l~~li~dgri  273 (514)
T TIGR03319       203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP----EAVILSGFDPVRREIARMALEKLIQDGRI  273 (514)
T ss_pred             heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCC----CeEEecCCchHHHHHHHHHHHHHHHcCCC
Confidence            45556889985 559999999999999999999999999854    5677888 677778888888888876543

>PRK00106 hypothetical protein; Provisional

Probab=98.07  E-value=3.6e-05  Score=59.74  Aligned_cols=70  Identities=21%  Similarity=0.331  Sum_probs=57.6

Q ss_pred             ceeEEEEEeec-CccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEc-CHHHHHHHHHHHhHHhcCCCC
Q psy2768          22 VRLTIELVVPS-SQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVG-SFFSVQETLKGCPNIVDQPSI   95 (96)
Q Consensus        22 ~~~~~~~~ip~-~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i~~~~~   95 (96)
                      ...+-.+.+|+ ++-|+||||.|.+|+-++.-||+.+-|++.|    ..|.++| +|---+-|...+..++.+.-|
T Consensus       223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp----~~v~lS~fdpvRReiAr~~le~Li~dgrI  294 (535)
T PRK00106        223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP----EVVVLSGFDPIRREIARMTLESLIKDGRI  294 (535)
T ss_pred             hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC----CeEEEeCCChHHHHHHHHHHHHHHHcCCc
Confidence            35556688998 4559999999999999999999999999855    5677888 678888888888888876543

>PRK12704 phosphodiesterase; Provisional

Probab=98.05  E-value=3.5e-05  Score=59.69  Aligned_cols=66  Identities=23%  Similarity=0.347  Sum_probs=52.9

Q ss_pred             eeEEEEEeecC-ccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEc-CHHHHHHHHHHHhHHhcC
Q psy2768          23 RLTIELVVPSS-QVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVG-SFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        23 ~~~~~~~ip~~-~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i~~   92 (96)
                      ..+-.+.+|++ +-|+||||.|.+||-++.-||+.|-|++.|    ..|.++| +|-.-+.|...+..++.+
T Consensus       209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp----~~v~ls~~~~~rre~a~~~l~~l~~d  276 (520)
T PRK12704        209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP----EAVILSGFDPIRREIARLALEKLVQD  276 (520)
T ss_pred             hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCC----CeEEEecCChhhHHHHHHHHHHHHhc
Confidence            45556889984 559999999999999999999999999854    5677888 566666777777776654

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

Probab=98.01  E-value=1.3e-05  Score=45.24  Aligned_cols=37  Identities=43%  Similarity=0.656  Sum_probs=34.4

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEe
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL   59 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i   59 (96)
                      .....+.||.+..|..|||+|.+|+.+++.+|-+|.|
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            4688899999999999999999999999999988876

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.

>KOG1588|consensus

Probab=97.97  E-value=1.4e-05  Score=56.75  Aligned_cols=73  Identities=22%  Similarity=0.332  Sum_probs=53.3

Q ss_pred             CCCceeEEEEEeecC------ccceeeccchhHHHHHHHHhCCeEEecCC---------------CC------CCceEEE
Q psy2768          19 ADEVRLTIELVVPSS------QVGRIIGKGGQNVRELQRSTGSMIKLPNS---------------FN------EEETNVH   71 (96)
Q Consensus        19 ~~~~~~~~~~~ip~~------~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~---------------~~------~~~~~v~   71 (96)
                      ......+.++.||-.      +||+|+|+.|.++|+|+++|||+|.|...               |+      .=.-.|.
T Consensus        87 ~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe  166 (259)
T KOG1588|consen   87 GKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIE  166 (259)
T ss_pred             CCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEE
Confidence            455678888999965      89999999999999999999999999541               11      1123355


Q ss_pred             EEcCHHH----HHHHHHHHhHHhc
Q psy2768          72 IVGSFFS----VQETLKGCPNIVD   91 (96)
Q Consensus        72 I~G~~~~----v~~A~~~I~~~i~   91 (96)
                      ..+++.-    +..|+..|..+|.
T Consensus       167 ~~~p~~ea~~rl~~AleeI~klL~  190 (259)
T KOG1588|consen  167 TEAPPAEAYARLAYALEEIKKLLV  190 (259)
T ss_pred             EeCCHHHHHHHHHHHHHHHHHhcC
Confidence            5666633    4467888887653

>PRK12705 hypothetical protein; Provisional

Probab=97.90  E-value=4.2e-05  Score=59.08  Aligned_cols=70  Identities=21%  Similarity=0.305  Sum_probs=56.1

Q ss_pred             eeEEEEEeecCcc-ceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEc-CHHHHHHHHHHHhHHhcCCCCC
Q psy2768          23 RLTIELVVPSSQV-GRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVG-SFFSVQETLKGCPNIVDQPSID   96 (96)
Q Consensus        23 ~~~~~~~ip~~~v-g~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i~~~~~~   96 (96)
                      ...-.+.+|++-+ |+||||.|.+||.++..||+.+.|++.|    ..|.+.+ +|.--+.|...+..++..+.++
T Consensus       197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp----~~V~ls~fdp~rreia~~~l~~Li~dgri~  268 (508)
T PRK12705        197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP----EAVVISSFNPIRREIARLTLEKLLADGRIH  268 (508)
T ss_pred             heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc----cchhhcccCccchHHHHHHHHHHHhcCCCC
Confidence            4455678887555 9999999999999999999999999865    4466766 5677788888888888777653

>KOG2279|consensus

Probab=97.86  E-value=1.1e-05  Score=62.19  Aligned_cols=72  Identities=29%  Similarity=0.423  Sum_probs=62.5

Q ss_pred             CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHh
Q psy2768          19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIV   90 (96)
Q Consensus        19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i   90 (96)
                      +....+..++.+|...+-.++||+|++|+.++..|+++|.+.+..-..++.-.+.|.+.++..|...+..++
T Consensus        63 e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g~e~~~~~~~~p~~v~~a~a~~~~~~  134 (608)
T KOG2279|consen   63 KPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPVQVCKAKAAIHQIL  134 (608)
T ss_pred             CchhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCCcccchhhccCCCCCChHHHHHHHHH
Confidence            445678899999999999999999999999999999999999865555677777778999999999888843

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

Probab=97.70  E-value=5.3e-05  Score=52.62  Aligned_cols=72  Identities=18%  Similarity=0.257  Sum_probs=48.2

Q ss_pred             CCCceeEEEEEee------cCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEc-CHHHHHHHHHHHhHHhc
Q psy2768          19 ADEVRLTIELVVP------SSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVG-SFFSVQETLKGCPNIVD   91 (96)
Q Consensus        19 ~~~~~~~~~~~ip------~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i~   91 (96)
                      .....++-.+.||      .+++|.|||+.|++.|++++.|+|+|.|.....  .....+.. ++++...|-.-+.-++.
T Consensus       143 ~rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gs--vKegk~ssd~p~~~~N~e~~lhcLI~  220 (269)
T COG5176         143 IRPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGS--VKEGKISSDTPESLKNAEAVLHCLIE  220 (269)
T ss_pred             cCcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccc--cccCcccccCchhhhhhHHhHHHHhh
Confidence            3445666777777      468999999999999999999999999976321  12233333 24455555554544444


Q ss_pred             C
Q psy2768          92 Q   92 (96)
Q Consensus        92 ~   92 (96)
                      .
T Consensus       221 a  221 (269)
T COG5176         221 A  221 (269)
T ss_pred             c
Confidence            3

>KOG3273|consensus

Probab=97.66  E-value=1.9e-05  Score=54.54  Aligned_cols=56  Identities=29%  Similarity=0.567  Sum_probs=50.2

Q ss_pred             cCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHH-hcCC
Q psy2768          32 SSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNI-VDQP   93 (96)
Q Consensus        32 ~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~-i~~~   93 (96)
                      +..+|+|+||+|.+---|++.|.++|.+.+      ..++|-|..+++..|...|+.+ +-+|
T Consensus       177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad------~kIHiLG~~~niriAR~avcsLIlGsp  233 (252)
T KOG3273|consen  177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD------SKIHILGAFQNIRIARDAVCSLILGSP  233 (252)
T ss_pred             HHHHHHhhcCCCcceeeeeccceeEEEecC------ceEEEeecchhhHHHHHhhHhhhccCC
Confidence            457899999999999999999999999994      7899999999999999999994 5444

>PRK00468 hypothetical protein; Provisional

Probab=97.64  E-value=6.8e-05  Score=44.13  Aligned_cols=35  Identities=26%  Similarity=0.526  Sum_probs=30.1

Q ss_pred             CCCceeEEEEEeecCccceeeccchhHHHHHHHHh
Q psy2768          19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRST   53 (96)
Q Consensus        19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~t   53 (96)
                      ..+....+++.+..+-+|++|||+|.+++.|+.--
T Consensus        25 ~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         25 EGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             eCCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            34556889999999999999999999999998643

>KOG2113|consensus

Probab=97.63  E-value=4.2e-05  Score=55.85  Aligned_cols=68  Identities=25%  Similarity=0.387  Sum_probs=59.6

Q ss_pred             CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhH
Q psy2768          19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPN   88 (96)
Q Consensus        19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~   88 (96)
                      +....++..+.+|..+++.+.|++|.+||.++.+|.++|+-|..+.  +-.+.++|.++.|..|++.|..
T Consensus        21 ~~p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~e--ePiF~vTg~~edv~~aRrei~s   88 (394)
T KOG2113|consen   21 SIGQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGE--EPIFPVTGRHEDVRRARREIPS   88 (394)
T ss_pred             CCCCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCC--CCcceeccCchhHHHHhhcCcc
Confidence            3347889999999999999999999999999999999999887543  4778899999999999988765

>PRK02821 hypothetical protein; Provisional

Probab=97.52  E-value=0.00011  Score=43.48  Aligned_cols=36  Identities=25%  Similarity=0.544  Sum_probs=30.3

Q ss_pred             CCceeEEEEEeecCccceeeccchhHHHHHHHHhCC
Q psy2768          20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGS   55 (96)
Q Consensus        20 ~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~   55 (96)
                      ......+.+.+.++-+|++|||+|.+++.|+.--.+
T Consensus        27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence            344578999999999999999999999999876543

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

Probab=97.49  E-value=0.00015  Score=42.79  Aligned_cols=34  Identities=32%  Similarity=0.617  Sum_probs=30.2

Q ss_pred             CCCceeEEEEEeecCccceeeccchhHHHHHHHH
Q psy2768          19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRS   52 (96)
Q Consensus        19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~   52 (96)
                      ..+....+++.+.++-+|.+|||+|.+++-|+.-
T Consensus        25 ~~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          25 EGEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             ecCCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            3467889999999999999999999999999853

>PRK01064 hypothetical protein; Provisional

Probab=97.38  E-value=0.00027  Score=41.91  Aligned_cols=35  Identities=26%  Similarity=0.537  Sum_probs=30.8

Q ss_pred             CCCceeEEEEEeecCccceeeccchhHHHHHHHHh
Q psy2768          19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRST   53 (96)
Q Consensus        19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~t   53 (96)
                      .+...+.+++.+..+..|++|||+|++++.|+.-.
T Consensus        25 ~~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~   59 (78)
T PRK01064         25 QGTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL   59 (78)
T ss_pred             eCCCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence            44667889999999999999999999999998753

>KOG4369|consensus

Probab=97.34  E-value=6e-05  Score=62.87  Aligned_cols=73  Identities=23%  Similarity=0.215  Sum_probs=63.4

Q ss_pred             eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC-CC-CCCceEEEEEcCHHHHHHHHHHHhHHhcCCCCC
Q psy2768          24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN-SF-NEEETNVHIVGSFFSVQETLKGCPNIVDQPSID   96 (96)
Q Consensus        24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~-~~-~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~~~   96 (96)
                      -...+.+|.....++||+||.+++.++.-||+-|.+.+ .+ +..||.+.+.|.++++..|-..|.-.+-+|.+|
T Consensus      1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i~Dpdv~ 1414 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPIIDPDVS 1414 (2131)
T ss_pred             cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccceeecCCcC
Confidence            34567889999999999999999999999999999988 33 357899999999999999999998877777654

>KOG2279|consensus

Probab=97.27  E-value=0.00018  Score=55.70  Aligned_cols=71  Identities=27%  Similarity=0.371  Sum_probs=58.8

Q ss_pred             CceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCC-CCCceEEEEEcCHHHHHHHHHHHhHHhc
Q psy2768          21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF-NEEETNVHIVGSFFSVQETLKGCPNIVD   91 (96)
Q Consensus        21 ~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~-~~~~~~v~I~G~~~~v~~A~~~I~~~i~   91 (96)
                      ..++...+.+|...+++++||+|.++++++..++++|.++.+. ....+...|.|...-...|+.++.+.++
T Consensus       137 ~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~  208 (608)
T KOG2279|consen  137 NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVS  208 (608)
T ss_pred             CCcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhcccc
Confidence            3578888999999999999999999999999999999999863 2345667777777777788888877544

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

Probab=97.04  E-value=0.0033  Score=43.15  Aligned_cols=65  Identities=17%  Similarity=0.301  Sum_probs=54.2

Q ss_pred             ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEc-----CHHHHHHHHHHHhHHh
Q psy2768          22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVG-----SFFSVQETLKGCPNIV   90 (96)
Q Consensus        22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G-----~~~~v~~A~~~I~~~i   90 (96)
                      ...+..+.||....+.+||+.|...+.|.+.+++++.++..    +..|.|..     +|-.+.+|...|+.+=
T Consensus         6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~----~~~V~i~~~~~t~Dp~~~~ka~d~VkAIg   75 (194)
T COG1094           6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK----TGSVTIRTTRKTEDPLALLKARDVVKAIG   75 (194)
T ss_pred             ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC----CCeEEEEecCCCCChHHHHHHHHHHHHHh
Confidence            34566789999999999999999999999999999999974    45566643     5788999999888763

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=97.01  E-value=0.0012  Score=43.02  Aligned_cols=37  Identities=41%  Similarity=0.604  Sum_probs=33.5

Q ss_pred             eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEec
Q psy2768          24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLP   60 (96)
Q Consensus        24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~   60 (96)
                      -.+-|.|+...+|+.||++|++|+.|++..|-+|.|-
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVv   68 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELV   68 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEE
Confidence            4567888999999999999999999999999999983

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=96.82  E-value=0.0013  Score=43.01  Aligned_cols=39  Identities=18%  Similarity=0.280  Sum_probs=34.5

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN   61 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~   61 (96)
                      .....+.||.+..|..|||+|++++.++.-++-.+.|.+
T Consensus        98 ~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~~  136 (140)
T PRK08406         98 DKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDIDD  136 (140)
T ss_pred             cEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCeE
Confidence            456778899999999999999999999999999887753

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

Probab=96.71  E-value=0.0039  Score=44.05  Aligned_cols=58  Identities=24%  Similarity=0.349  Sum_probs=45.4

Q ss_pred             EEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHH-HHHHHHHHHhHH
Q psy2768          27 ELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFF-SVQETLKGCPNI   89 (96)
Q Consensus        27 ~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~-~v~~A~~~I~~~   89 (96)
                      -+.||...+.++||++|+.++-+.+.|+|+|-|-.     +..|-+.|..+ ....|...|..+
T Consensus       149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-----NG~IWV~~~~~~~e~~~~~aI~~i  207 (239)
T COG1097         149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-----NGRIWVDGENESLEELAIEAIRKI  207 (239)
T ss_pred             EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-----CCEEEecCCCcchHHHHHHHHHHH
Confidence            46899999999999999999999999999999987     45666666654 344444444444

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=96.71  E-value=0.0011  Score=38.22  Aligned_cols=35  Identities=31%  Similarity=0.433  Sum_probs=29.2

Q ss_pred             CceeEEEEEeecCccceeeccchhHHHHHHHHhCC
Q psy2768          21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGS   55 (96)
Q Consensus        21 ~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~   55 (96)
                      .....+.+.+..+..|.+|||.|.+++.||--.+.
T Consensus        26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~   60 (73)
T PF13083_consen   26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA   60 (73)
T ss_dssp             TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence            44567778889999999999999999999976543

>KOG2208|consensus

Probab=96.58  E-value=0.0034  Score=50.79  Aligned_cols=69  Identities=19%  Similarity=0.315  Sum_probs=60.2

Q ss_pred             ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhc
Q psy2768          22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVD   91 (96)
Q Consensus        22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~   91 (96)
                      +.....+.+-......++||+|.++.+|++++.|.+.++. .++.+..+.++|....+.+|...++....
T Consensus       345 nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~-~~~~~~~v~~~~~~~~~~ka~~~v~~~~~  413 (753)
T KOG2208|consen  345 NNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK-QGSNNKKVVITGVSANDEKAVEDVEKIIA  413 (753)
T ss_pred             cceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc-ccCCCCCeEEeccccchhHHHHHHHHHHH
Confidence            3477888899999999999999999999999999999998 34557889999999999999988887543

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

Probab=96.51  E-value=0.006  Score=33.75  Aligned_cols=35  Identities=43%  Similarity=0.681  Sum_probs=28.4

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhCCeE
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMI   57 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I   57 (96)
                      .....+.+.....|.+||++|.+++.++..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            45556666666789999999999999999988554

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.

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=96.34  E-value=0.0048  Score=40.39  Aligned_cols=35  Identities=40%  Similarity=0.716  Sum_probs=33.1

Q ss_pred             EEEEEeecCccceeeccchhHHHHHHHHhCCeEEe
Q psy2768          25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL   59 (96)
Q Consensus        25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i   59 (96)
                      .+-|.|....+|+.||++|++|+.+++..|-+|.+
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdV   68 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIEL   68 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEE
Confidence            77789999999999999999999999999999988

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.

>KOG2874|consensus

Probab=96.19  E-value=0.012  Score=42.76  Aligned_cols=51  Identities=24%  Similarity=0.401  Sum_probs=45.5

Q ss_pred             ceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          36 GRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        36 g~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      -++||..|++++.|+--|.|.|-|..      ..|.+.|...++..+...+.+.+.+
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVqG------~TVsaiGpfkGlkevr~IV~DcM~N  211 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQG------NTVSAIGPFKGLKEVRKIVEDCMKN  211 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEeeC------cEEEeecCcchHHHHHHHHHHHHhc
Confidence            57999999999999999999999995      5688889999999999888886654

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=96.14  E-value=0.11  Score=35.50  Aligned_cols=65  Identities=14%  Similarity=0.239  Sum_probs=55.2

Q ss_pred             eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      -.+.+..+....-.+...+|..++++-...||+|.+...    +..+.|+|+...+..+...|.+++.+
T Consensus        26 g~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~----~~~i~I~g~k~~~~~i~~~i~~~l~~   90 (210)
T PF14611_consen   26 GDLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS----ENRIRITGTKSTAEYIEASINEILSN   90 (210)
T ss_pred             ceeEEEecchheeeeecCCchHHHHHHHhcCceEEEecC----CcEEEEEccHHHHHHHHHHHHHHHhh
Confidence            344555568888999999999999998888999999873    57899999999999999999988754

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=96.11  E-value=0.0044  Score=36.04  Aligned_cols=35  Identities=29%  Similarity=0.501  Sum_probs=29.6

Q ss_pred             eEEEEEeecCccceeeccchhHHHHHHHHhCCeEE
Q psy2768          24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIK   58 (96)
Q Consensus        24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~   58 (96)
                      ....+.+..+.-|.+||++|++|++|....+-.+.
T Consensus        25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~   59 (78)
T PF07650_consen   25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE   59 (78)
T ss_dssp             SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence            45678889999999999999999999887766554

; 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 ....

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

Probab=96.06  E-value=0.0055  Score=35.38  Aligned_cols=36  Identities=28%  Similarity=0.517  Sum_probs=28.3

Q ss_pred             EEEEeecCc-----cceeeccchhHHHHHHHHh-CCeEEecC
Q psy2768          26 IELVVPSSQ-----VGRIIGKGGQNVRELQRST-GSMIKLPN   61 (96)
Q Consensus        26 ~~~~ip~~~-----vg~iIGkgG~~Ik~i~~~t-g~~I~i~~   61 (96)
                      ..+.|.+..     +|..||++|.+|+.|.++. |-+|++-.
T Consensus         5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~   46 (69)
T PF13184_consen    5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE   46 (69)
T ss_dssp             EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred             EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence            345566666     8999999999999999999 99998865

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=95.71  E-value=0.014  Score=34.07  Aligned_cols=34  Identities=26%  Similarity=0.532  Sum_probs=27.2

Q ss_pred             EEEEEeecCccceeeccchhHHHHHHHHhCCeEE
Q psy2768          25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIK   58 (96)
Q Consensus        25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~   58 (96)
                      .+.+.+..+..|.+|||.|.++..||--++.-++
T Consensus        25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~   58 (77)
T cd02414          25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN   58 (77)
T ss_pred             EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence            3556677788999999999999999987764443

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.

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=95.54  E-value=0.012  Score=38.58  Aligned_cols=39  Identities=21%  Similarity=0.322  Sum_probs=34.5

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN   61 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~   61 (96)
                      .....+.||.+..|..|||+|.+++-..+-++-+++|.+
T Consensus        99 ~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~~  137 (141)
T TIGR01952        99 KKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDIDD  137 (141)
T ss_pred             CEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCeE
Confidence            456778899999999999999999999999998887763

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.

>TIGR01953 NusA transcription termination factor NusA

Probab=95.31  E-value=0.019  Score=42.51  Aligned_cols=38  Identities=45%  Similarity=0.612  Sum_probs=35.6

Q ss_pred             eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768          24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN   61 (96)
Q Consensus        24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~   61 (96)
                      ....+.||.+..+..|||+|.+++--.+-||.+|+|..
T Consensus       301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            56889999999999999999999999999999999975

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.

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=95.25  E-value=0.02  Score=39.20  Aligned_cols=37  Identities=43%  Similarity=0.575  Sum_probs=35.0

Q ss_pred             EEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768          25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN   61 (96)
Q Consensus        25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~   61 (96)
                      ...+.||.+..+..|||+|.+++-..+-||-+++|..
T Consensus       143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            6778899999999999999999999999999999976

>PRK13764 ATPase; Provisional

Probab=95.10  E-value=0.018  Score=45.68  Aligned_cols=39  Identities=23%  Similarity=0.534  Sum_probs=35.6

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN   61 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~   61 (96)
                      .-...+.||...++.+|||+|.+|++|.+..|..|.|..
T Consensus       480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~  518 (602)
T PRK13764        480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP  518 (602)
T ss_pred             CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence            445678999999999999999999999999999999976

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=95.07  E-value=0.025  Score=42.42  Aligned_cols=38  Identities=32%  Similarity=0.344  Sum_probs=35.7

Q ss_pred             eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768          24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN   61 (96)
Q Consensus        24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~   61 (96)
                      ....+.||.+..+..|||+|.+++--.+-||.+|+|..
T Consensus       308 ~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s  345 (374)
T PRK12328        308 KKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNE  345 (374)
T ss_pred             cEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEE
Confidence            46788999999999999999999999999999999977

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

Probab=95.06  E-value=0.016  Score=44.95  Aligned_cols=38  Identities=26%  Similarity=0.545  Sum_probs=34.7

Q ss_pred             eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768          24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN   61 (96)
Q Consensus        24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~   61 (96)
                      -...+.+|...++.+|||+|.+|++|++..|-+|.|..
T Consensus       486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~  523 (604)
T COG1855         486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKP  523 (604)
T ss_pred             CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEE
Confidence            34668899999999999999999999999999999976

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=94.90  E-value=0.038  Score=37.11  Aligned_cols=36  Identities=31%  Similarity=0.492  Sum_probs=30.3

Q ss_pred             EEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768          25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN   61 (96)
Q Consensus        25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~   61 (96)
                      .+-|.|.... |.-|||+|.+++.+++..|-+|.+-.
T Consensus        62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE   97 (166)
T PRK06418         62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE   97 (166)
T ss_pred             EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence            3446666667 99999999999999999999998843

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

Probab=94.66  E-value=0.053  Score=32.16  Aligned_cols=37  Identities=19%  Similarity=0.504  Sum_probs=29.7

Q ss_pred             eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEec
Q psy2768          24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLP   60 (96)
Q Consensus        24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~   60 (96)
                      ...++.|-...-|.+||++|+.|++|++.-.....++
T Consensus        30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~   66 (81)
T cd02413          30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP   66 (81)
T ss_pred             CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence            3467788888889999999999999988766555554

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.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=94.41  E-value=0.038  Score=42.62  Aligned_cols=38  Identities=39%  Similarity=0.550  Sum_probs=35.7

Q ss_pred             eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768          24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN   61 (96)
Q Consensus        24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~   61 (96)
                      -...+.||....+.-|||+|.+++-..+-||.+|.|-.
T Consensus       302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~  339 (470)
T PRK09202        302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT  339 (470)
T ss_pred             CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence            47789999999999999999999999999999999976

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

Probab=94.33  E-value=0.07  Score=35.11  Aligned_cols=39  Identities=36%  Similarity=0.572  Sum_probs=32.8

Q ss_pred             EEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCC
Q psy2768          25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF   63 (96)
Q Consensus        25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~   63 (96)
                      +-++.|-.+.-|.+||++|.++++|..+||-+-.|-+.|
T Consensus        77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtp  115 (145)
T cd02410          77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTP  115 (145)
T ss_pred             CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecC
Confidence            345667777889999999999999999999888887643

The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=94.30  E-value=0.052  Score=40.59  Aligned_cols=40  Identities=38%  Similarity=0.473  Sum_probs=36.5

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS   62 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~   62 (96)
                      .....+.||.+..+..|||+|.+++--.+-||.+|+|...
T Consensus       302 ~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~  341 (362)
T PRK12327        302 EKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE  341 (362)
T ss_pred             CcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence            3568899999999999999999999999999999999763

>KOG2208|consensus

Probab=94.20  E-value=0.11  Score=42.38  Aligned_cols=65  Identities=25%  Similarity=0.315  Sum_probs=47.9

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhC-CeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhH
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTG-SMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPN   88 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg-~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~   88 (96)
                      .....+.+|...+.++||.+|+.|+.|..++| ..|..++. ......+++.|....+..++.+...
T Consensus       419 ~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~-~~~~~~~~~~~~~~dv~~~~~~~~~  484 (753)
T KOG2208|consen  419 IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN-NNSSDMVTIRGISKDVEKSVSLLKA  484 (753)
T ss_pred             cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC-CcccccceEeccccccchhHHHHHh
Confidence            56777999999999999999999999999999 55555543 2334556777766666655544443

>TIGR00436 era GTP-binding protein Era

Probab=93.82  E-value=0.16  Score=35.86  Aligned_cols=30  Identities=27%  Similarity=0.393  Sum_probs=23.3

Q ss_pred             eeEEEEEee-cCccceeeccchhHHHHHHHH
Q psy2768          23 RLTIELVVP-SSQVGRIIGKGGQNVRELQRS   52 (96)
Q Consensus        23 ~~~~~~~ip-~~~vg~iIGkgG~~Ik~i~~~   52 (96)
                      .+...+.|+ .++-+.|||++|+.||+|...
T Consensus       220 ~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~  250 (270)
T TIGR00436       220 KIHALISVERESQKKIIIGKNGSMIKAIGIA  250 (270)
T ss_pred             EEEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence            466777787 455599999999999887644

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

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

Probab=93.43  E-value=0.1  Score=32.48  Aligned_cols=30  Identities=27%  Similarity=0.572  Sum_probs=24.5

Q ss_pred             EEEEeecCccceeeccchhHHHHHHHHhCC
Q psy2768          26 IELVVPSSQVGRIIGKGGQNVRELQRSTGS   55 (96)
Q Consensus        26 ~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~   55 (96)
                      +++.+-...-|.+||+.|++|++|++....
T Consensus        63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~   92 (109)
T cd02412          63 VEVTIHTARPGIIIGKKGAGIEKLRKELQK   92 (109)
T ss_pred             EEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence            566777777899999999999999876543

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.

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

Probab=93.42  E-value=0.12  Score=30.70  Aligned_cols=28  Identities=32%  Similarity=0.684  Sum_probs=22.1

Q ss_pred             EEEEeecCccceeeccchhHHHHHHHHh
Q psy2768          26 IELVVPSSQVGRIIGKGGQNVRELQRST   53 (96)
Q Consensus        26 ~~~~ip~~~vg~iIGkgG~~Ik~i~~~t   53 (96)
                      .++.+-...-|.+||++|++|+++++.-
T Consensus        40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l   67 (85)
T cd02411          40 TQITIYAERPGMVIGRGGKNIRELTEIL   67 (85)
T ss_pred             EEEEEEECCCCceECCCchhHHHHHHHH
Confidence            4455555778999999999999887754

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.

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=93.39  E-value=0.078  Score=40.68  Aligned_cols=38  Identities=39%  Similarity=0.531  Sum_probs=35.5

Q ss_pred             eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768          24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN   61 (96)
Q Consensus        24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~   61 (96)
                      ....+.||.+..+..|||+|.+++--..-||.+|.|..
T Consensus       335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            45689999999999999999999999999999999976

>PRK15494 era GTPase Era; Provisional

Probab=93.04  E-value=0.22  Score=36.61  Aligned_cols=37  Identities=30%  Similarity=0.468  Sum_probs=26.6

Q ss_pred             eeEEEEEeec-CccceeeccchhHHHHHH--------HHhCCeEEe
Q psy2768          23 RLTIELVVPS-SQVGRIIGKGGQNVRELQ--------RSTGSMIKL   59 (96)
Q Consensus        23 ~~~~~~~ip~-~~vg~iIGkgG~~Ik~i~--------~~tg~~I~i   59 (96)
                      .+...+.|+. ++-+.|||++|+.||+|.        +-.|++|.+
T Consensus       272 ~i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l  317 (339)
T PRK15494        272 KINQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHL  317 (339)
T ss_pred             EEEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEE
Confidence            3567778874 455999999999998764        445665554

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=92.97  E-value=0.13  Score=35.31  Aligned_cols=37  Identities=30%  Similarity=0.464  Sum_probs=30.9

Q ss_pred             EEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768          25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN   61 (96)
Q Consensus        25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~   61 (96)
                      ...+.+-...+|..||++|++++.+.++.|-+|.|-.
T Consensus        77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe  113 (190)
T COG0195          77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVE  113 (190)
T ss_pred             eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEE
Confidence            3455556777899999999999999999999998833

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

Probab=91.43  E-value=0.21  Score=35.28  Aligned_cols=30  Identities=23%  Similarity=0.504  Sum_probs=25.4

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHH
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRS   52 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~   52 (96)
                      +...++.|....-|.+||++|+.|++|++.
T Consensus        50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~   79 (233)
T COG0092          50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKE   79 (233)
T ss_pred             CCceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence            566778888888999999999999887654

>COG1159 Era GTPase [General function prediction only]

Probab=91.29  E-value=0.54  Score=34.41  Aligned_cols=31  Identities=29%  Similarity=0.497  Sum_probs=22.8

Q ss_pred             CceeEEEEEeec-CccceeeccchhHHHHHHH
Q psy2768          21 EVRLTIELVVPS-SQVGRIIGKGGQNVRELQR   51 (96)
Q Consensus        21 ~~~~~~~~~ip~-~~vg~iIGkgG~~Ik~i~~   51 (96)
                      .-.+...+.|+. ++=|.||||+|++||+|-.
T Consensus       226 ~~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~  257 (298)
T COG1159         226 LLKIHATIYVERESQKGIIIGKNGAMIKKIGT  257 (298)
T ss_pred             eEEEEEEEEEecCCccceEECCCcHHHHHHHH
Confidence            335555677774 5559999999999987643

>KOG1423|consensus

Probab=89.30  E-value=0.65  Score=34.60  Aligned_cols=35  Identities=29%  Similarity=0.562  Sum_probs=26.9

Q ss_pred             CCCceeEEEEEeecC-ccceeeccchhHHHHHHHHh
Q psy2768          19 ADEVRLTIELVVPSS-QVGRIIGKGGQNVRELQRST   53 (96)
Q Consensus        19 ~~~~~~~~~~~ip~~-~vg~iIGkgG~~Ik~i~~~t   53 (96)
                      .+.-.+..++.+|.. ....||||||..|++|-.+-
T Consensus       323 ~g~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a  358 (379)
T KOG1423|consen  323 AGVLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRA  358 (379)
T ss_pred             CcEEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHH
Confidence            334567788999954 55778999999999986654

>PRK00089 era GTPase Era; Reviewed

Probab=89.00  E-value=0.68  Score=32.86  Aligned_cols=36  Identities=33%  Similarity=0.545  Sum_probs=25.8

Q ss_pred             eEEEEEee-cCccceeeccchhHHHHHH--------HHhCCeEEe
Q psy2768          24 LTIELVVP-SSQVGRIIGKGGQNVRELQ--------RSTGSMIKL   59 (96)
Q Consensus        24 ~~~~~~ip-~~~vg~iIGkgG~~Ik~i~--------~~tg~~I~i   59 (96)
                      +...+.|. .++-+.|||++|+.||+|.        +-+|++|.+
T Consensus       226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l  270 (292)
T PRK00089        226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL  270 (292)
T ss_pred             EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence            55667776 4556999999999998765        445665554

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=87.20  E-value=0.44  Score=37.50  Aligned_cols=70  Identities=20%  Similarity=0.143  Sum_probs=49.0

Q ss_pred             ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC---CCC-CceEEEEEcCH---HHHHHHHHHHhHHhc
Q psy2768          22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS---FNE-EETNVHIVGSF---FSVQETLKGCPNIVD   91 (96)
Q Consensus        22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~---~~~-~~~~v~I~G~~---~~v~~A~~~I~~~i~   91 (96)
                      =+....|.||.+.+-.|||.||..|++.....++.|++...   +.+ -...|.|..+.   +++.-++.-..+++.
T Consensus       447 Fpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~  523 (657)
T COG5166         447 FPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVK  523 (657)
T ss_pred             CchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHh
Confidence            35667899999999999999999999999999999998762   211 22336665543   344445444444443

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=86.96  E-value=0.63  Score=34.90  Aligned_cols=28  Identities=25%  Similarity=0.442  Sum_probs=24.9

Q ss_pred             CccceeeccchhHHHHHHHHh-CCeEEec
Q psy2768          33 SQVGRIIGKGGQNVRELQRST-GSMIKLP   60 (96)
Q Consensus        33 ~~vg~iIGkgG~~Ik~i~~~t-g~~I~i~   60 (96)
                      +-+|+.||++|++|+.|.++. |-+|+|-
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv  273 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDII  273 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEE
Confidence            457999999999999998888 8999883

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

Probab=86.86  E-value=0.84  Score=36.52  Aligned_cols=40  Identities=33%  Similarity=0.529  Sum_probs=33.9

Q ss_pred             eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCC
Q psy2768          24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF   63 (96)
Q Consensus        24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~   63 (96)
                      .+-++.|-...-|.+|||+|.+.++|-.+||-+-.|-+.|
T Consensus        93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~  132 (630)
T TIGR03675        93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTP  132 (630)
T ss_pred             CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecC
Confidence            3446677888899999999999999999999888887643

This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.

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

Probab=86.47  E-value=0.91  Score=35.84  Aligned_cols=38  Identities=34%  Similarity=0.581  Sum_probs=32.2

Q ss_pred             EEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC
Q psy2768          25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS   62 (96)
Q Consensus        25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~   62 (96)
                      +-++.|-...-|.+|||+|++.++|..+||-.-.|-+.
T Consensus       100 tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~  137 (637)
T COG1782         100 TGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT  137 (637)
T ss_pred             CceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence            34567888888999999999999999999987777663

>TIGR01953 NusA transcription termination factor NusA

Probab=85.76  E-value=0.82  Score=34.01  Aligned_cols=29  Identities=21%  Similarity=0.505  Sum_probs=25.3

Q ss_pred             CccceeeccchhHHHHHHHHh-CCeEEecC
Q psy2768          33 SQVGRIIGKGGQNVRELQRST-GSMIKLPN   61 (96)
Q Consensus        33 ~~vg~iIGkgG~~Ik~i~~~t-g~~I~i~~   61 (96)
                      +-+|+.||++|++|+.|.++. |-+|+|-.
T Consensus       243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~  272 (341)
T TIGR01953       243 DPVGACVGPKGSRIQAISKELNGEKIDIIE  272 (341)
T ss_pred             CcceeeECCCCchHHHHHHHhCCCeEEEEE
Confidence            457999999999999999888 89998833

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.

>KOG2113|consensus

Probab=85.57  E-value=0.6  Score=34.65  Aligned_cols=67  Identities=21%  Similarity=0.255  Sum_probs=52.7

Q ss_pred             CCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHH-HHHHH-HHHhH
Q psy2768          20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFS-VQETL-KGCPN   88 (96)
Q Consensus        20 ~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~-v~~A~-~~I~~   88 (96)
                      .....+....+|-..+|.+.|..|++|+.+|+.++..|.-+-.  ..+-+..++|.+.. +++|. ..|+.
T Consensus       111 ~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~--~~~~Vf~Vtg~~~nC~kra~s~eie~  179 (394)
T KOG2113|consen  111 ASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR--CGEPVFCVTGAPKNCVKRARSCEIEQ  179 (394)
T ss_pred             ccCCCceeeeccceeeeeccccccCccchheecccceEeeecc--CCCceEEEecCCcchhhhccccchhh
Confidence            3556778889999999999999999999999999999877653  23577888898866 66665 44443

>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type

Probab=84.41  E-value=1.5  Score=30.24  Aligned_cols=30  Identities=30%  Similarity=0.657  Sum_probs=24.1

Q ss_pred             eEEEEEeecCccceeeccchhHHHHHHHHh
Q psy2768          24 LTIELVVPSSQVGRIIGKGGQNVRELQRST   53 (96)
Q Consensus        24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~t   53 (96)
                      ...++.|....-|.+||++|+.|++|++.-
T Consensus        38 ~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l   67 (195)
T TIGR01008        38 LGTKVIIFAERPGLVIGRGGRRIRELTEKL   67 (195)
T ss_pred             CcEEEEEEECCCceEECCCchHHHHHHHHH
Confidence            346677777778999999999999887654

This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.

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

Probab=84.29  E-value=0.86  Score=31.72  Aligned_cols=38  Identities=21%  Similarity=0.357  Sum_probs=31.3

Q ss_pred             ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEe
Q psy2768          22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL   59 (96)
Q Consensus        22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i   59 (96)
                      ....+.+.+-.+..|.+||+.|.++..||--+...++-
T Consensus        89 ~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~  126 (208)
T COG1847          89 EGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK  126 (208)
T ss_pred             cCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence            45566778888889999999999999999888765554

>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed

Probab=84.14  E-value=1.5  Score=30.38  Aligned_cols=30  Identities=30%  Similarity=0.616  Sum_probs=23.0

Q ss_pred             EEEEeecCccceeeccchhHHHHHHHHhCC
Q psy2768          26 IELVVPSSQVGRIIGKGGQNVRELQRSTGS   55 (96)
Q Consensus        26 ~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~   55 (96)
                      .++.|-...-|.+||++|++|+++++.-.-
T Consensus        42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk   71 (207)
T PRK04191         42 TRITIYAERPGMVIGRGGKNIRELTEILEK   71 (207)
T ss_pred             EEEEEEECCCCeEECCCchhHHHHHHHHHH
Confidence            445555577899999999999988776543

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=84.09  E-value=0.87  Score=35.11  Aligned_cols=28  Identities=25%  Similarity=0.455  Sum_probs=24.9

Q ss_pred             CccceeeccchhHHHHHHHHh-CCeEEec
Q psy2768          33 SQVGRIIGKGGQNVRELQRST-GSMIKLP   60 (96)
Q Consensus        33 ~~vg~iIGkgG~~Ik~i~~~t-g~~I~i~   60 (96)
                      +-+|+.||++|++|+.|.++. |-+|+|-
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI  305 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVI  305 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEE
Confidence            457999999999999998888 8999983

>PTZ00084 40S ribosomal protein S3; Provisional

Probab=83.65  E-value=1.6  Score=30.70  Aligned_cols=30  Identities=20%  Similarity=0.506  Sum_probs=23.8

Q ss_pred             EEEEEeecCccceeeccchhHHHHHHHHhC
Q psy2768          25 TIELVVPSSQVGRIIGKGGQNVRELQRSTG   54 (96)
Q Consensus        25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg   54 (96)
                      ..++.|-...-|.+||++|..|++|++.-.
T Consensus        45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L~   74 (220)
T PTZ00084         45 RTEIIIRATRTREVLGDKGRRIRELTSLLQ   74 (220)
T ss_pred             cEEEEEEECCCccEEcCCchHHHHHHHHHH
Confidence            366677777789999999999998876543

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=83.53  E-value=0.82  Score=34.47  Aligned_cols=28  Identities=18%  Similarity=0.395  Sum_probs=24.9

Q ss_pred             CccceeeccchhHHHHHHHHh-CCeEEec
Q psy2768          33 SQVGRIIGKGGQNVRELQRST-GSMIKLP   60 (96)
Q Consensus        33 ~~vg~iIGkgG~~Ik~i~~~t-g~~I~i~   60 (96)
                      +-+|+.||++|++|+.|.++- |-+|+|-
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI  279 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCI  279 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEE
Confidence            457999999999999998888 8999983

>CHL00048 rps3 ribosomal protein S3

Probab=82.70  E-value=1.9  Score=30.04  Aligned_cols=30  Identities=20%  Similarity=0.297  Sum_probs=24.2

Q ss_pred             eEEEEEeecCccceeeccchhHHHHHHHHh
Q psy2768          24 LTIELVVPSSQVGRIIGKGGQNVRELQRST   53 (96)
Q Consensus        24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~t   53 (96)
                      ...++.|-...-|.+||++|.+|++|++.-
T Consensus        66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L   95 (214)
T CHL00048         66 DLIQVIIYTGFPKLLIERKGRGIEELQINL   95 (214)
T ss_pred             CeEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence            346667777778999999999999987765

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=82.31  E-value=1.1  Score=34.75  Aligned_cols=28  Identities=21%  Similarity=0.476  Sum_probs=24.7

Q ss_pred             CccceeeccchhHHHHHHHHh-CCeEEec
Q psy2768          33 SQVGRIIGKGGQNVRELQRST-GSMIKLP   60 (96)
Q Consensus        33 ~~vg~iIGkgG~~Ik~i~~~t-g~~I~i~   60 (96)
                      +-+|+.||++|++|+.|.++. |-+|.|-
T Consensus       245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv  273 (470)
T PRK09202        245 DPVGACVGMRGSRIQAISNELGGEKIDII  273 (470)
T ss_pred             ChhHccCCCCCchHHHHHHHhCCCeEEEE
Confidence            347999999999999999888 8999983

>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]

Probab=81.34  E-value=5  Score=30.06  Aligned_cols=50  Identities=18%  Similarity=0.181  Sum_probs=43.5

Q ss_pred             cCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHh
Q psy2768          32 SSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCP   87 (96)
Q Consensus        32 ~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~   87 (96)
                      .+.+-.+.|..|.+++.+.+..|+.|....      ..++|.|+...+..|...+.
T Consensus        23 ~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG------~~~~i~g~~~~v~~A~~~l~   72 (348)
T COG1702          23 DNELVALFGPTDTNLSLLEIALGVSIVARG------EAVRIIGARPLVDVATRVLL   72 (348)
T ss_pred             chhhhhhcCCCCccHHHHHHHhCcEEEeCC------ceEEEEechHHHHHHHHHHh
Confidence            556678889999999999999999998874      77899999778888888777

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	96
3krm_A	163	Imp1 Kh34 Length = 163		2e-11
2jzx_A	160	Pcbp2 Kh1-Kh2 Domains Length = 160		4e-06
2ann_A	178	Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDE		1e-04
2anr_A	178	Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TAND		1e-04
2opu_A	89	Solution Nmr Structure Of The First Domain Of Ksrp		5e-04

>pdb|3KRM|A Chain A, Imp1 Kh34 Length = 163

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/94 (36%), Positives = 54/94 (57%), Gaps = 3/94 (3%)
Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
           AQ  I+ K++EE  F   +EV+L   + VP+S  GR+IGKGG+ V ELQ  T + + +P 
Sbjct: 63  AQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPR 122
Query: 62  SFNEEETN---VHIVGSFFSVQETLKGCPNIVDQ 92
               +E +   V I+G F++ Q   +   +I+ Q
Sbjct: 123 DQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQ 156

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 24/63 (38%), Positives = 39/63 (61%), Gaps = 2/63 (3%)
Query: 24  LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF--NEEETNVHIVGSFFSVQE 81
           +T+ LVVP+SQ G +IGKGG  ++E++ STG+ +++      N  E  + I G   S+ E
Sbjct: 89  VTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIE 148
Query: 82  TLK 84
            +K
Sbjct: 149 CVK 151

>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH 25 NT RNA Hairpin Length = 178

Iteration: 1
 Score = 41.2 bits (95), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/37 (48%), Positives = 27/37 (72%)
Query: 26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS 62
          +++++PS   G IIGKGGQ + +LQ+ TG+ IKL  S
Sbjct: 8  LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKS 44

>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH 25NT RNA Hairpin Length = 178

Iteration: 1
 Score = 41.2 bits (95), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/37 (48%), Positives = 27/37 (72%)
Query: 26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS 62
          +++++PS   G IIGKGGQ + +LQ+ TG+ IKL  S
Sbjct: 8  LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKS 44

>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp Length = 89

Iteration: 1
 Score = 39.3 bits (90), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 37/60 (61%), Gaps = 1/60 (1%)
Query: 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL-PNSFNEEETNVHIVGSFFSVQET 82
          +T E  VP   VG IIG+GG+ + ++Q+ +G  +++ P+S    E +V + G+  SVQ+ 
Sbjct: 16 MTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKA 75

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	96
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	7e-19
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	2e-09
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	8e-16
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	6e-14
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	1e-13
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-10
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	3e-13
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	3e-13
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	6e-13
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	5e-10
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	8e-13
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	9e-13
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	1e-12
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	2e-12
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	3e-12
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	3e-12
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	9e-12
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	1e-11
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	3e-11
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	5e-11
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	3e-09
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	1e-10
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	1e-10
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	3e-10
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	1e-09
1we8_A	104	Tudor and KH domain containing protein; structural	6e-10
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	2e-09
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	5e-09
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	6e-08
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	2e-06
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	2e-06
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	2e-04
2cxc_A	144	NUSA; transcription termination, RNA binding prote	4e-05
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	2e-04
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	3e-04
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	6e-04
1tua_A	191	Hypothetical protein APE0754; structural genomics,	9e-04

>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 = 75.2 bits (185), Expect = 7e-19
 Identities = 32/83 (38%), Positives = 49/83 (59%), Gaps = 3/83 (3%)

Query: 2   AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
           AQ  I+ K++EE  F   +EV+L   + VP+S  GR+IGKGG+ V ELQ  T + + +P 
Sbjct: 63  AQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPR 122

Query: 62  SFNEEETN---VHIVGSFFSVQE 81
               +E +   V I+G F++ Q 
Sbjct: 123 DQTPDENDQVIVKIIGHFYASQM 145

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

 Score = 50.5 bits (121), Expect = 2e-09
 Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 2/54 (3%)

Query: 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNE--EETNVHIVGS 75
            +++ +P+  VG IIGK GQ++++L R   + IK+        +   V I G 
Sbjct: 3  EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGP 56

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

 Score = 65.6 bits (160), Expect = 8e-16
 Identities = 17/82 (20%), Positives = 35/82 (42%), Gaps = 1/82 (1%)

Query: 14 GLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL-PNSFNEEETNVHI 72
          G  A    +   I++ VP   VG +IG+ G+ ++++Q   G  I+   +     E   HI
Sbjct: 1  GAMATGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHI 60

Query: 73 VGSFFSVQETLKGCPNIVDQPS 94
          +G     +   +   +++    
Sbjct: 61 MGPPDRCEHAARIINDLLQSLR 82

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

 Score = 60.4 bits (147), Expect = 6e-14
 Identities = 17/67 (25%), Positives = 35/67 (52%), Gaps = 3/67 (4%)

Query: 17 AGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNE---EETNVHIV 73
          A   +     E+++P+ + G +IGKGG+ +++LQ   G  + L    ++    +  + I+
Sbjct: 7  ANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRII 66

Query: 74 GSFFSVQ 80
          G  + VQ
Sbjct: 67 GDPYKVQ 73

>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 = 61.3 bits (149), Expect = 1e-13
 Identities = 27/90 (30%), Positives = 48/90 (53%), Gaps = 7/90 (7%)

Query: 2   AQYLIFEKMREEGLFAGADEVR-----LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSM 56
           A  +I +K+ E+   +  +        +T+ LVVP+SQ G +IGKGG  ++E++ STG+ 
Sbjct: 62  AFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQ 121

Query: 57  IKLPNSFNEEETN--VHIVGSFFSVQETLK 84
           +++        T   + I G   S+ E +K
Sbjct: 122 VQVAGDMLPNSTERAITIAGIPQSIIECVK 151

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

 Score = 53.2 bits (128), Expect = 2e-10
 Identities = 17/64 (26%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQ 80
           V LTI L++   +VG IIGK G++V++++  +G+ I +      E   + + G   ++ 
Sbjct: 2  NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERI-ITLAGPTNAIF 60

Query: 81 ETLK 84
          +   
Sbjct: 61 KAFA 64

>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 = 58.4 bits (142), Expect = 3e-13
 Identities = 20/59 (33%), Positives = 34/59 (57%), Gaps = 1/59 (1%)

Query: 23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF-NEEETNVHIVGSFFSVQ 80
          + T EL +P++ +G IIG+ G N+ E+++ +G+ IK+ N         V I GS  S+ 
Sbjct: 5  QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASIS 63

>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 = 58.6 bits (142), Expect = 3e-13
 Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 3/66 (4%)

Query: 18 GADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL---PNSFNEEETNVHIVG 74
          G        E+++P+S+ G +IGKGG+ +++LQ   G  + +          +  + I G
Sbjct: 9  GDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITG 68

Query: 75 SFFSVQ 80
            + VQ
Sbjct: 69 DPYKVQ 74

>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 = 59.8 bits (145), Expect = 6e-13
 Identities = 19/87 (21%), Positives = 35/87 (40%), Gaps = 7/87 (8%)

Query: 2   AQYLIFEKMREEGLFAGADEVR------LTIELVVPSSQVGRIIGKGGQNVRELQRSTGS 55
           A  ++ + +RE       D           I++ VP   VG +IG+ G+ ++++Q   G 
Sbjct: 63  ACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGV 122

Query: 56  MIKLPNSF-NEEETNVHIVGSFFSVQE 81
            I+         E   HI+G     + 
Sbjct: 123 RIQFKQDDGTGPEKIAHIMGPPDRCEH 149

>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 = 52.1 bits (125), Expect = 5e-10
 Identities = 16/60 (26%), Positives = 32/60 (53%), Gaps = 3/60 (5%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF---NEEETNVHIVGSFFSVQE 81
            E+++P+ + G +IGKGG+ +++LQ   G  + L          +  + I+G  + VQ+
Sbjct: 3  VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQ 62

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

 Score = 57.7 bits (140), Expect = 8e-13
 Identities = 17/58 (29%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF-NEEETNVHIVGSFFSVQ 80
          +T ++ +P    G IIGKGGQ +++++  +G+ IK+       E+  + I G+   +Q
Sbjct: 14 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQ 71

>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 = 57.4 bits (139), Expect = 9e-13
 Identities = 21/58 (36%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL-PNSFNEEETNVHIVGSFFSVQ 80
          +T E  VP   VG IIG+GG+ +  +Q+ +G  I++ P+S    E +  + G+  SVQ
Sbjct: 15 MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQ 72

>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 = 57.3 bits (139), Expect = 1e-12
 Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 4/63 (6%)

Query: 22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF----NEEETNVHIVGSFF 77
          ++  +E+ VP + VG I+GKGG+ + E Q  TG+ I++              V I GS  
Sbjct: 1  MKELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPA 60

Query: 78 SVQ 80
          + Q
Sbjct: 61 ATQ 63

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

 Score = 56.5 bits (137), Expect = 2e-12
 Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 1/64 (1%)

Query: 18 GADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL-PNSFNEEETNVHIVGSF 76
          GA    +T ++ +P    G IIGKGGQ +++++  +G+ IK+       E+  + I G+ 
Sbjct: 1  GAMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ 60

Query: 77 FSVQ 80
            +Q
Sbjct: 61 DQIQ 64

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

 Score = 56.8 bits (137), Expect = 3e-12
 Identities = 16/67 (23%), Positives = 33/67 (49%), Gaps = 4/67 (5%)

Query: 18 GADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL----PNSFNEEETNVHIV 73
          GA      +   +P+ + G +IG+GG+NV+ + + TG+ +++    P + +       I 
Sbjct: 1  GAMAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIR 60

Query: 74 GSFFSVQ 80
          GS   + 
Sbjct: 61 GSPQQID 67

>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 = 56.1 bits (136), Expect = 3e-12
 Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 4/63 (6%)

Query: 22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF----NEEETNVHIVGSFF 77
          ++  +E+ VP + VG I+GKGG+ + E Q  TG+ I++              V I GS  
Sbjct: 1  MKELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPA 60

Query: 78 SVQ 80
          + Q
Sbjct: 61 ATQ 63

>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 = 54.6 bits (132), Expect = 9e-12
 Identities = 17/65 (26%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSV 79
            V LTI L++   +VG IIGK G++V++++  +G+ I +      E   + + G   ++
Sbjct: 1  KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERI-ITLAGPTNAI 59

Query: 80 QETLK 84
           +   
Sbjct: 60 FKAFA 64

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

 Score = 54.2 bits (131), Expect = 1e-11
 Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF-NEEETNVHIVGSFFSVQ 80
          + EL +P+  +G IIG+ G  + E+++ +G+ IK+ N      +  V I GS  S+ 
Sbjct: 6  SHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASIS 62

>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 = 54.0 bits (130), Expect = 3e-11
 Identities = 11/60 (18%), Positives = 31/60 (51%), Gaps = 1/60 (1%)

Query: 21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQ 80
          + + +  + +P      +IGK G+ +++L+  T + I++P   ++    + I G+   ++
Sbjct: 14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-DDPSNQIKITGTKEGIE 72

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

 Score = 54.9 bits (132), Expect = 5e-11
 Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 3/68 (4%)

Query: 17  AGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL---PNSFNEEETNVHIV 73
               +    ++++VP+S  G IIGKGG  V+ +   +G+ ++L   P+  N +   V + 
Sbjct: 97  TVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVS 156

Query: 74  GSFFSVQE 81
           G     ++
Sbjct: 157 GEPEQNRK 164

>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 = 50.2 bits (120), Expect = 3e-09
 Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 4/62 (6%)

Query: 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNE----EETNVHIVGSFFSV 79
            +++++PS   G IIGKGGQ + +LQ+ TG+ IKL  S +      E    I G+  ++
Sbjct: 6  YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEAL 65

Query: 80 QE 81
            
Sbjct: 66 NA 67

>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 = 52.5 bits (126), Expect = 1e-10
 Identities = 14/61 (22%), Positives = 28/61 (45%)

Query: 21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQ 80
          E  ++ ++ +      RIIG  G+ +R++       I+ P S   +   V + G   +V+
Sbjct: 14 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVE 73

Query: 81 E 81
          E
Sbjct: 74 E 74

>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 = 52.5 bits (126), Expect = 1e-10
 Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 1/70 (1%)

Query: 12 EEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVH 71
            G  A    V +TIE+ VP      +IG+ G  +R++       I +P     +   + 
Sbjct: 5  SSGKEALEALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP-ELQSDIIA 63

Query: 72 IVGSFFSVQE 81
          I G   ++  
Sbjct: 64 ITGLAANLDR 73

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

 Score = 52.9 bits (127), Expect = 3e-10
 Identities = 15/68 (22%), Positives = 30/68 (44%), Gaps = 4/68 (5%)

Query: 18  GADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF----NEEETNVHIV 73
           G          +VP+ + G IIGKGG+ ++ + + +G+ I+L  +     +       I 
Sbjct: 98  GPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIR 157

Query: 74  GSFFSVQE 81
           G+   +  
Sbjct: 158 GTPQQIDY 165

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

 Score = 51.4 bits (123), Expect = 1e-09
 Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL-PNSFNEEETNVHIVGS 75
           I++ +P   VG +IG+ G+ ++++Q   G  I+  P+     E    I G 
Sbjct: 4  MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGP 55

>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 = 50.6 bits (121), Expect = 6e-10
 Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 3/60 (5%)

Query: 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL---PNSFNEEETNVHIVGSFFSVQ 80
          +  +L VP   VGRIIG+GG+ +R + +++G+ I               + I G+   V 
Sbjct: 15 VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVA 74

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

 Score = 48.5 bits (116), Expect = 2e-09
 Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQE 81
           +E+ +       +IGK G N+  ++      +++P   +E+   + I G    VQ+
Sbjct: 6  YVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD-SEKSNLIRIEGDPQGVQQ 61

>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 = 47.9 bits (114), Expect = 5e-09
 Identities = 10/63 (15%), Positives = 25/63 (39%), Gaps = 2/63 (3%)

Query: 21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLP--NSFNEEETNVHIVGSFFS 78
               + + V      +IIG+ G  + +++      I+ P  +  N+ +  + I G   +
Sbjct: 14 LRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKN 73

Query: 79 VQE 81
           + 
Sbjct: 74 TEA 76

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 83

 Score = 44.9 bits (106), Expect = 6e-08
 Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 2/58 (3%)

Query: 23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQ 80
          + TI++ VP   VG ++G  G  ++ +Q+ T + I  P    ++E    + G   +V 
Sbjct: 9  QTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR--DKEPVFAVTGMPENVD 64

>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 = 41.7 bits (98), Expect = 2e-06
 Identities = 14/69 (20%), Positives = 28/69 (40%), Gaps = 2/69 (2%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQ-RSTGSMIKLPNSFNEEETNVHIVGSFFSVQETL 83
           +E+ +P+     +IG  G+ +R +     G  I  P         V I G    V++  
Sbjct: 18 EVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-GSGSDTVVIRGPSSDVEKAK 76

Query: 84 KGCPNIVDQ 92
          K   ++ ++
Sbjct: 77 KQLLHLAEE 85

>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 = 42.3 bits (99), Expect = 2e-06
 Identities = 11/51 (21%), Positives = 21/51 (41%), Gaps = 3/51 (5%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGS 75
            + +V    +G  IG  G N+++ ++  G         +E+    HI G 
Sbjct: 5  HEQFIVREDLMGLAIGTHGANIQQARKVPGVTA---IDLDEDTCTFHIYGE 52

>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 = 37.3 bits (86), Expect = 2e-04
 Identities = 15/83 (18%), Positives = 35/83 (42%), Gaps = 7/83 (8%)

Query: 6   IFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTG-SMIKLPNSFN 64
           I+ + ++    A +        + VP + VG++IGK G+ ++E+   +G   +++     
Sbjct: 49  IYGEDQDAVKKARSFLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENE 108

Query: 65  E------EETNVHIVGSFFSVQE 81
           +             VG+  S+  
Sbjct: 109 KNVPQEEGMVPFVFVGTKDSIAN 131

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

 Score = 38.5 bits (90), Expect = 4e-05
 Identities = 9/35 (25%), Positives = 14/35 (40%)

Query: 20  DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTG 54
                 + + V     G  IGKGG+NV+  +    
Sbjct: 99  RNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLS 133

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B Length = 219

 Score = 37.0 bits (85), Expect = 2e-04
 Identities = 11/61 (18%), Positives = 27/61 (44%), Gaps = 6/61 (9%)

Query: 21  EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQ 80
           ++ +  E        GRIIG+ G+  + ++  +G+ + +          V I+G+   ++
Sbjct: 126 DIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSV------YGKTVAIIGNPIQIE 179

Query: 81  E 81
            
Sbjct: 180 I 180

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

 Score = 37.2 bits (85), Expect = 3e-04
 Identities = 16/70 (22%), Positives = 26/70 (37%), Gaps = 8/70 (11%)

Query: 23 RLTIELVVPSSQVGRIIGKGG--QNVRELQRSTGSMIKLPNSFNEEETN------VHIVG 74
          R+T+ +   S     +    G  +NV  +   T ++I+LP+      T       V I G
Sbjct: 29 RVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITG 88

Query: 75 SFFSVQETLK 84
           F  V     
Sbjct: 89 YFGDVDRARM 98

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

 Score = 34.9 bits (80), Expect = 6e-04
 Identities = 16/68 (23%), Positives = 25/68 (36%), Gaps = 14/68 (20%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLK 84
             +  PS     IIGK GQN+ ++               ++   VHI  +    + TL+
Sbjct: 28 VSSVAAPSWLHRFIIGKKGQNLAKIT--------------QQMPKVHIEFTEGEDKITLE 73

Query: 85 GCPNIVDQ 92
          G    V  
Sbjct: 74 GPTEDVSV 81

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

 Score = 35.4 bits (81), Expect = 9e-04
 Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 6/51 (11%)

Query: 31  PSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQE 81
                GRIIG+GG+  R ++  T + I +       E  V I+G +     
Sbjct: 105 LKRIKGRIIGEGGRARRTIEEMTDTYINV------GEYEVAIIGDYERAMA 149

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	96
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.84
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.84
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.84
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.83
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.83
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.81
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.81
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.8
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.8
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.8
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.78
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.78
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.78
1we8_A	104	Tudor and KH domain containing protein; structural	99.78
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.77
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.77
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.77
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.76
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.75
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.74
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.72
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.72
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.72
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.71
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.68
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.67
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.67
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.66
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.65
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.63
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.58
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.54
2cpq_A	91	FragIle X mental retardation syndrome related prot	99.5
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.42
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.36
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.35
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	99.33
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	99.27
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	99.26
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.21
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	99.09
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	99.05
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.01
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.0
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	99.0
1tua_A	191	Hypothetical protein APE0754; structural genomics,	98.88
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	98.41
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	98.06
2cxc_A	144	NUSA; transcription termination, RNA binding prote	96.58
2cxc_A	144	NUSA; transcription termination, RNA binding prote	95.51
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	95.37
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	94.49
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	94.45
2pt7_G	152	HP1451, hypothetical protein; ATPase, protein-prot	92.15
1wh9_A	92	40S ribosomal protein S3; KH domain, structural ge	91.72
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	91.05
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	87.06
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	85.41
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	84.23
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	82.95
3gku_A	225	Probable RNA-binding protein; APC21302, clostridiu	81.27

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

Probab=99.84  E-value=5.8e-21  Score=111.20  Aligned_cols=71  Identities=25%  Similarity=0.473  Sum_probs=65.8

Q ss_pred             CceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        21 ~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      ..+++++|.||.+.+|.||||||++|++|+++|||+|+|++. +..+|.|+|+|+++++.+|+.+|.+++.+
T Consensus         2 ~~~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~-~~~er~v~I~G~~~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A            2 NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-NCPERIITLAGPTNAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             CceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC-CCCcEEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            357899999999999999999999999999999999999985 56789999999999999999999998764

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

Probab=99.84  E-value=1.4e-20  Score=111.65  Aligned_cols=73  Identities=27%  Similarity=0.437  Sum_probs=67.3

Q ss_pred             CCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC-CCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS-FNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        20 ~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~-~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      ..+.++.++.||.+.+|.||||+|++|++|+++|||+|+|++. ++..++.|+|+|+++++..|+.+|.+++.+
T Consensus         3 ~g~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   76 (82)
T 1zzk_A            3 MGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ   76 (82)
T ss_dssp             CCCCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            3568999999999999999999999999999999999999984 566789999999999999999999998765

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

Probab=99.84  E-value=8.4e-21  Score=111.09  Aligned_cols=72  Identities=25%  Similarity=0.371  Sum_probs=66.8

Q ss_pred             ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC-CCCCCceEEEEEcCHHHHHHHHHHHhHHhcCC
Q psy2768          22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN-SFNEEETNVHIVGSFFSVQETLKGCPNIVDQP   93 (96)
Q Consensus        22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~-~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   93 (96)
                      ..++.++.||.+.+|.||||||++|++|+++|||+|+|++ .++..++.|+|+|+++++..|+.+|.+++.+.
T Consensus         3 ~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCCCCCCCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            5788999999999999999999999999999999999998 45678999999999999999999999988753

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

Probab=99.83  E-value=1.8e-20  Score=111.14  Aligned_cols=72  Identities=28%  Similarity=0.402  Sum_probs=65.7

Q ss_pred             ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC-CCCCceEEEEEcCHHHHHHHHHHHhHHhcCC
Q psy2768          22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS-FNEEETNVHIVGSFFSVQETLKGCPNIVDQP   93 (96)
Q Consensus        22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~-~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   93 (96)
                      ..++.++.||.+.+|.||||||++|++|+++|||+|+|++. ++..++.|+|+|+++++.+|+.+|.+++.+.
T Consensus         4 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            4 SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            57899999999999999999999999999999999999984 5677999999999999999999999988754

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

Probab=99.83  E-value=2.2e-20  Score=109.10  Aligned_cols=70  Identities=30%  Similarity=0.409  Sum_probs=64.0

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC----CCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS----FNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~----~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      ..+.++.||.+.+|+||||||++|++|++.|||+|+|++.    +++.++.|+|+|+++++..|+.+|.+++.+
T Consensus         2 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            2 KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             CEEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             ceEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            4678999999999999999999999999999999999984    456789999999999999999999998764

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

Probab=99.81  E-value=3e-20  Score=111.83  Aligned_cols=75  Identities=27%  Similarity=0.420  Sum_probs=68.2

Q ss_pred             CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC-CCCCceEEEEEcCHHHHHHHHHHHhHHhcCC
Q psy2768          19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS-FNEEETNVHIVGSFFSVQETLKGCPNIVDQP   93 (96)
Q Consensus        19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~-~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   93 (96)
                      .....++.++.||.+.+|.||||+|++|++|+++|||+|+|++. ++.+++.|+|+|+++++++|+.+|.+++.+.
T Consensus         9 ~~~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A            9 LGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             -CCCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            35678999999999999999999999999999999999999984 5667899999999999999999999988654

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

Probab=99.81  E-value=2.1e-19  Score=117.73  Aligned_cols=92  Identities=37%  Similarity=0.626  Sum_probs=79.2

Q ss_pred             hHHHHHHHHHHhcccCCCCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC--CCC-CceEEEEEcCHHH
Q psy2768           2 AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS--FNE-EETNVHIVGSFFS   78 (96)
Q Consensus         2 A~~~I~~k~~e~~~~~~~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~-~~~~v~I~G~~~~   78 (96)
                      |+.+|++.|.+.....+......+.++.||.+++|+||||||++|++|++.|||+|+|++.  |+. .++.|+|+|++++
T Consensus        63 A~~~I~~~~~e~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~  142 (163)
T 3krm_A           63 AQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYA  142 (163)
T ss_dssp             HHHHHHHHHHHTTSSCSSCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCCCCTTSEEEEEEEECHHH
T ss_pred             HHHHHHHHHhcccccccccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCCCCCCCCceEEEEEeCHHH
Confidence            6788999999885544555667889999999999999999999999999999999999874  343 3458999999999


Q ss_pred             HHHHHHHHhHHhcCC
Q psy2768          79 VQETLKGCPNIVDQP   93 (96)
Q Consensus        79 v~~A~~~I~~~i~~~   93 (96)
                      +..|+.+|.+++++.
T Consensus       143 v~~A~~~I~~~i~~~  157 (163)
T 3krm_A          143 SQMAQRKIRDILAQV  157 (163)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999988653

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

Probab=99.80  E-value=5.8e-20  Score=110.03  Aligned_cols=70  Identities=30%  Similarity=0.409  Sum_probs=64.3

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC----CCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS----FNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~----~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      ..+.++.||.+.+|+||||||++|++|+++|||+|+|++.    +++.++.|+|+|+++++..|+.+|.+++.+
T Consensus         2 k~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~   75 (87)
T 1ec6_A            2 KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (87)
T ss_dssp             CSEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Confidence            3578999999999999999999999999999999999984    466789999999999999999999998764

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

Probab=99.80  E-value=4e-19  Score=105.98  Aligned_cols=74  Identities=23%  Similarity=0.472  Sum_probs=66.2

Q ss_pred             CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC---CCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS---FNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~---~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      .+....+.++.||.+.+|+||||||++||+|+++|||+|+|++.   +...++.|+|+|+++++..|+.+|.+++.+
T Consensus         9 ~g~~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A            9 GGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             CSCSSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            34557889999999999999999999999999999999999984   245789999999999999999999998753

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

Probab=99.80  E-value=1.4e-19  Score=109.45  Aligned_cols=74  Identities=28%  Similarity=0.410  Sum_probs=67.5

Q ss_pred             CCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC-CCCCceEEEEEcCHHHHHHHHHHHhHHhcCC
Q psy2768          20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS-FNEEETNVHIVGSFFSVQETLKGCPNIVDQP   93 (96)
Q Consensus        20 ~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~-~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   93 (96)
                      ....++.+|.||.+++|+||||+|++|++|+++|||+|+|++. ++..++.|+|+|+++++.+|+.+|.+++++.
T Consensus        11 ~~~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~   85 (92)
T 1x4n_A           11 QRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKG   85 (92)
T ss_dssp             CCCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            3467899999999999999999999999999999999999985 4567899999999999999999999987654

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

Probab=99.78  E-value=7.3e-19  Score=109.02  Aligned_cols=70  Identities=20%  Similarity=0.454  Sum_probs=64.1

Q ss_pred             EEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCC----CCCceEEEEEcCHHHHHHHHHHHhHHhcCCC
Q psy2768          25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF----NEEETNVHIVGSFFSVQETLKGCPNIVDQPS   94 (96)
Q Consensus        25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~----~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~   94 (96)
                      +.+|.||.+++|+||||+|++||+|+++|||+|+|++..    +..++.|+|+|+++++.+|+.+|.+++.+..
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~~   81 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPL   81 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCSCC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhccc
Confidence            789999999999999999999999999999999999852    3467999999999999999999999987753

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

Probab=99.78  E-value=4.8e-19  Score=107.52  Aligned_cols=77  Identities=21%  Similarity=0.407  Sum_probs=69.0

Q ss_pred             CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCC---CCCceEEEEEcCHHHHHHHHHHHhHHhcCCCC
Q psy2768          19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF---NEEETNVHIVGSFFSVQETLKGCPNIVDQPSI   95 (96)
Q Consensus        19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~~   95 (96)
                      .....++.+|.||.+++|+||||+|++||+|+++|||+|+|++..   ...++.|+|+|+++++..|+.+|.+++.++..
T Consensus        10 ~~p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~   89 (94)
T 1x4m_A           10 DGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRDQGS   89 (94)
T ss_dssp             CCCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCCCSS
T ss_pred             CCCCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHhccCC
Confidence            345678999999999999999999999999999999999999842   34689999999999999999999999988653

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

Probab=99.78  E-value=3.6e-19  Score=110.39  Aligned_cols=73  Identities=21%  Similarity=0.365  Sum_probs=63.7

Q ss_pred             CceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC-CCCCceEEEEEcCHHHHHHHHHHHhHHhcCC
Q psy2768          21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS-FNEEETNVHIVGSFFSVQETLKGCPNIVDQP   93 (96)
Q Consensus        21 ~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~-~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   93 (96)
                      ....++++.||.+++|+||||+|++||+|+++|||+|+|+++ ++..++.|+|+|+++++++|+.+|++++.+.
T Consensus         8 ~~~~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~~er~V~I~G~~e~v~~A~~~I~~ii~~~   81 (106)
T 2hh3_A            8 RIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSL   81 (106)
T ss_dssp             ----CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            345688999999999999999999999999999999999864 4557899999999999999999999988654

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

Probab=99.78  E-value=1e-18  Score=107.78  Aligned_cols=73  Identities=25%  Similarity=0.377  Sum_probs=66.7

Q ss_pred             CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCC---CCceEEEEEcCHHHHHHHHHHHhHHhc
Q psy2768          19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFN---EEETNVHIVGSFFSVQETLKGCPNIVD   91 (96)
Q Consensus        19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~---~~~~~v~I~G~~~~v~~A~~~I~~~i~   91 (96)
                      +...+.+.+|.||.+++|.||||||++|++|+++|||+|+|++...   ..++.|+|+|+++++.+|+.+|.+++.
T Consensus        10 s~~ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~~v~~A~~~I~~~i~   85 (104)
T 1we8_A           10 TENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVS   85 (104)
T ss_dssp             SSSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred             CCCCCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHHHHHHHHHHHHHHHh
Confidence            5678999999999999999999999999999999999999998432   258999999999999999999999875

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=3e-19  Score=106.39  Aligned_cols=72  Identities=21%  Similarity=0.293  Sum_probs=64.2

Q ss_pred             CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      ......+.++.||.+++|.||||+|++||+|+++|||+|+|++..  .++.++|+|+++++++|+.+|.+++..
T Consensus         5 ~~~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~--~~~~v~ItG~~e~v~~A~~~I~~~i~~   76 (83)
T 2dgr_A            5 SSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD--KEPVFAVTGMPENVDRAREEIEAHITL   76 (83)
T ss_dssp             CSCCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS--SCCEEEEEECTTTHHHHHHHHHHHHHS
T ss_pred             CCCCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC--CCCeEEEEcCHHHHHHHHHHHHHHHhc
Confidence            344678999999999999999999999999999999999999633  268899999999999999999997653

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

Probab=99.77  E-value=1e-18  Score=114.18  Aligned_cols=91  Identities=32%  Similarity=0.446  Sum_probs=78.1

Q ss_pred             hHHHHHHHHHHhcccCC-----CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC--CCCCCceEEEEEc
Q psy2768           2 AQYLIFEKMREEGLFAG-----ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN--SFNEEETNVHIVG   74 (96)
Q Consensus         2 A~~~I~~k~~e~~~~~~-----~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~--~~~~~~~~v~I~G   74 (96)
                      |+.+|.++|.++...+.     ....+.+.++.||.+++|+||||||++|++|++.|||+|+|++  .|+..++.|+|+|
T Consensus        62 A~~~I~~~i~e~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~v~I~G  141 (160)
T 2jzx_A           62 AFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAG  141 (160)
T ss_dssp             HHHHHHHHHHHHHTSCCCSSSCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCCCSTTCCEEEEEEEE
T ss_pred             HHHHHHHHHHhhccccCCCCccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCCCCCCCCceEEEEEc
Confidence            67889999988743211     2345789999999999999999999999999999999999987  3567789999999


Q ss_pred             CHHHHHHHHHHHhHHhcC
Q psy2768          75 SFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        75 ~~~~v~~A~~~I~~~i~~   92 (96)
                      +++++..|+.+|.+++.+
T Consensus       142 ~~~~v~~A~~~I~~~i~e  159 (160)
T 2jzx_A          142 IPQSIIECVKQICVVMLE  159 (160)
T ss_dssp             CHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhc
Confidence            999999999999997643

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

Probab=99.77  E-value=9.4e-19  Score=101.31  Aligned_cols=68  Identities=18%  Similarity=0.273  Sum_probs=62.1

Q ss_pred             ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHh
Q psy2768          22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIV   90 (96)
Q Consensus        22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i   90 (96)
                      ...+.++.||.+++|.|||+||++|++|+++|||+|+|+++. ..++.|+|+|+++++++|+.+|.+++
T Consensus         3 ~~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g-~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             ceEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC-CcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            457889999999999999999999999999999999999854 35789999999999999999999875

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

Probab=99.76  E-value=6.2e-19  Score=107.37  Aligned_cols=75  Identities=20%  Similarity=0.261  Sum_probs=67.2

Q ss_pred             CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcCC
Q psy2768          19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQP   93 (96)
Q Consensus        19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   93 (96)
                      .....++.++.||.+++|.|||+||++|++|+++|||+|+|++..+.+++.|+|+|++++++.|+.+|..+++++
T Consensus        12 ~l~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~~~~~~V~I~G~~e~v~~A~~~I~~i~~e~   86 (95)
T 2ctm_A           12 ELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAIDHILNLEEEY   86 (95)
T ss_dssp             CTTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCSCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             hhcccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHHH
Confidence            345678999999999999999999999999999999999999865445679999999999999999999987653

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

Probab=99.75  E-value=2.4e-18  Score=105.10  Aligned_cols=71  Identities=17%  Similarity=0.292  Sum_probs=64.3

Q ss_pred             ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCC--CCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF--NEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~--~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      ..++.+|.||.+++|.||||||++|++|+++|||+|+|++..  +..++.|+|+|+++++..|+.+|..++.+
T Consensus        15 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e   87 (97)
T 2ctl_A           15 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGE   87 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            368999999999999999999999999999999999999853  33678999999999999999999998754

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

Probab=99.74  E-value=3.3e-18  Score=103.84  Aligned_cols=71  Identities=17%  Similarity=0.366  Sum_probs=64.1

Q ss_pred             CceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        21 ~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      ...++.++.||.+.+|.|||+||++||+|+++|||+|+|++.. ..++.|+|+|+++++.+|+.+|..++.+
T Consensus        14 ~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~-~~~~~V~I~G~~e~v~~A~~~I~~i~~~   84 (94)
T 2cte_A           14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-DPSNQIKITGTKEGIEKARHEVLLISAE   84 (94)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-SSCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC-CCCCeEEEEECHHHHHHHHHHHHHHhhc
Confidence            4578999999999999999999999999999999999999743 2357999999999999999999998764

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

Probab=99.72  E-value=5.8e-18  Score=104.58  Aligned_cols=73  Identities=22%  Similarity=0.279  Sum_probs=65.8

Q ss_pred             CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      +...+.+.+|.||.+++|.|||+||++|++|+++|||+|+|++... ..+.|+|+|++++++.|+.+|..++++
T Consensus        12 ~~~ap~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g~-~~~~V~I~G~~e~v~~A~~~I~~i~~e   84 (104)
T 2ctk_A           12 EALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL-QSDIIAITGLAANLDRAKAGLLERVKE   84 (104)
T ss_dssp             CCSSCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTT-TCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             HhhCCEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCCC-CcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            4566899999999999999999999999999999999999998533 346999999999999999999998765

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

Probab=99.72  E-value=8.7e-18  Score=109.80  Aligned_cols=92  Identities=20%  Similarity=0.329  Sum_probs=74.6

Q ss_pred             hHHHHHHHHHHhcccC---C---CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC-CCCCceEEEEEc
Q psy2768           2 AQYLIFEKMREEGLFA---G---ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS-FNEEETNVHIVG   74 (96)
Q Consensus         2 A~~~I~~k~~e~~~~~---~---~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~-~~~~~~~v~I~G   74 (96)
                      |+.+|.+.+.+.....   .   ......+.++.||.+++|+||||+|++|++|+++|||+|+|++. ++..++.|+|+|
T Consensus        63 A~~~I~~ii~e~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~~~~~~~~v~I~G  142 (164)
T 2jvz_A           63 ACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMG  142 (164)
T ss_dssp             HHHHHHHHTTCSSSCCCSSCSSCTTSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCCTTSSEEEEEEES
T ss_pred             HHHHHHHHHHhccCCCCCCccccCCCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCCCCCCcEEEEEEc
Confidence            6778888887653211   1   11113568899999999999999999999999999999999874 344579999999


Q ss_pred             CHHHHHHHHHHHhHHhcCC
Q psy2768          75 SFFSVQETLKGCPNIVDQP   93 (96)
Q Consensus        75 ~~~~v~~A~~~I~~~i~~~   93 (96)
                      +++++..|+.+|.++++++
T Consensus       143 ~~~~v~~A~~~I~~~i~~~  161 (164)
T 2jvz_A          143 PPDRCEHAARIINDLLQSL  161 (164)
T ss_dssp             CHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhhh
Confidence            9999999999999988754

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

Probab=99.72  E-value=1.9e-17  Score=109.81  Aligned_cols=92  Identities=23%  Similarity=0.332  Sum_probs=74.1

Q ss_pred             hHHHHHHHHHHhcccC--------------CCCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCC---C
Q psy2768           2 AQYLIFEKMREEGLFA--------------GADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF---N   64 (96)
Q Consensus         2 A~~~I~~k~~e~~~~~--------------~~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~---~   64 (96)
                      |..+|.+++.+.....              .......+.++.||.+++|+||||+|++|++|++.|||+|+|++.+   +
T Consensus        68 A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~  147 (178)
T 2anr_A           68 VHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGIN  147 (178)
T ss_dssp             HHHHHHHHHTCCCCC-----------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC----
T ss_pred             HHHHHHHHHhccCCccccCCcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCCCCC
Confidence            5677777776642110              0122357899999999999999999999999999999999998753   4


Q ss_pred             CCceEEEEEcCHHHHHHHHHHHhHHhcCC
Q psy2768          65 EEETNVHIVGSFFSVQETLKGCPNIVDQP   93 (96)
Q Consensus        65 ~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   93 (96)
                      ..++.|+|+|+++++..|+.+|.+++.+.
T Consensus       148 ~~~~~v~I~G~~~~v~~A~~~I~~~i~e~  176 (178)
T 2anr_A          148 LQNRVVTVSGEPEQNRKAVELIIQKIQED  176 (178)
T ss_dssp             CCEEEEEEESSHHHHHHHHHHHHHHHHSC
T ss_pred             CCceEEEEEcCHHHHHHHHHHHHHHHHhC
Confidence            56899999999999999999999977654

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

Probab=99.71  E-value=7.3e-17  Score=106.72  Aligned_cols=68  Identities=21%  Similarity=0.385  Sum_probs=61.6

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCC----CCCceEEEEEcCHHHHHHHHHHHhHHh
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF----NEEETNVHIVGSFFSVQETLKGCPNIV   90 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~----~~~~~~v~I~G~~~~v~~A~~~I~~~i   90 (96)
                      ..+.++.||.+++|+||||+|++|++|++.|||+|+|++..    +..++.|+|+|+++++..|+.+|.++|
T Consensus       103 ~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          103 LQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             -CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             cEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCCCCCCCCCceEEEEECCHHHHHHHHHHHHHhC
Confidence            46889999999999999999999999999999999998742    356899999999999999999999864

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

Probab=99.68  E-value=1.2e-16  Score=104.48  Aligned_cols=70  Identities=23%  Similarity=0.337  Sum_probs=64.4

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC--CCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS--FNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      +-+++|.||.+.+|.||||+|++|++|+++|||+|+|++.  ++..++.|+|+|+++++..|+.+|.+++.+
T Consensus         2 ~~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~e~v~~A~~~I~~~~~e   73 (163)
T 3krm_A            2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKE   73 (163)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Confidence            4588999999999999999999999999999999999983  577899999999999999999999986653

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

Probab=99.67  E-value=1.9e-16  Score=103.40  Aligned_cols=70  Identities=24%  Similarity=0.498  Sum_probs=63.8

Q ss_pred             eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC---CCCCceEEEEEcCHHHHHHHHHHHhHHhcCC
Q psy2768          24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS---FNEEETNVHIVGSFFSVQETLKGCPNIVDQP   93 (96)
Q Consensus        24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~---~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   93 (96)
                      .+.+|.||.+.+|.||||+|++|++|+++|||+|++++.   ++..++.|+|+|+++++..|+.+|.+++.+.
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~ii~e~   74 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRER   74 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHHHHHHHHHHHHHHTTCS
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Confidence            578999999999999999999999999999999999763   3456899999999999999999999988754

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

Probab=99.67  E-value=1.8e-16  Score=105.05  Aligned_cols=72  Identities=29%  Similarity=0.431  Sum_probs=65.8

Q ss_pred             ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC----CCCCceEEEEEcCHHHHHHHHHHHhHHhcCC
Q psy2768          22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS----FNEEETNVHIVGSFFSVQETLKGCPNIVDQP   93 (96)
Q Consensus        22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~----~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   93 (96)
                      ..++++|.||.+.+|.||||+|++|++|+++|||+|+|++.    ++..+|.|+|+|+++++.+|+.+|.+++.+.
T Consensus         4 ~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~~~~~   79 (178)
T 2anr_A            4 SQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREM   79 (178)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHHHHHHHHHHHHHHTCC
T ss_pred             CCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            46899999999999999999999999999999999999873    4578899999999999999999999987653

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

Probab=99.66  E-value=1.7e-16  Score=104.95  Aligned_cols=70  Identities=20%  Similarity=0.337  Sum_probs=64.0

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC-CCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN-SFNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~-~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      ..+++|.||.+.+|.||||+|++|++|+++|||+|+|++ .++..++.|+|+|+++++.+|+.+|.+++.+
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~~~~   72 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRS   72 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            467899999999999999999999999999999999986 4566789999999999999999999997754

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

Probab=99.65  E-value=2.5e-16  Score=102.70  Aligned_cols=70  Identities=26%  Similarity=0.472  Sum_probs=64.0

Q ss_pred             CceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhc
Q psy2768          21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVD   91 (96)
Q Consensus        21 ~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~   91 (96)
                      ..+++++|.||.+.+|.||||||++|++|+++|||+|+|++. +..++.|+|+|+++++.+|+.+|.+++.
T Consensus         2 ~~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~-~~~~r~v~I~G~~~~v~~A~~~I~~~i~   71 (160)
T 2jzx_A            2 NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-NCPERIITLAGPTNAIFKAFAMIIDKLE   71 (160)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC-TTTEEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred             CccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC-CCCceEEEEEeCHHHHHHHHHHHHHHHH
Confidence            357899999999999999999999999999999999999985 4568999999999999999999988654

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

Probab=99.63  E-value=1.9e-16  Score=96.32  Aligned_cols=75  Identities=19%  Similarity=0.298  Sum_probs=66.3

Q ss_pred             CCCceeEEEEEeecCccceeeccchhHHHHHHHHh-CCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcCCC
Q psy2768          19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRST-GSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQPS   94 (96)
Q Consensus        19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~t-g~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~   94 (96)
                      .-...++..|.||.++++.|||+||++|++|+++| ||+|+|++. +...+.|+|+|+.+++++|+.+|..++.++.
T Consensus        12 e~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~-g~~~~~V~I~G~~~~v~~A~~~I~~iv~e~e   87 (95)
T 2ctj_A           12 DLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-GSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQ   87 (95)
T ss_dssp             CCCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-TTTCCEEEEESCHHHHHHHHHHHHHHHHHHS
T ss_pred             HHhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCC-CCCcceEEEEcCHHHHHHHHHHHHHHHhhhh
Confidence            34567889999999999999999999999999999 999999974 3446789999999999999999999887543

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

Probab=99.58  E-value=3.7e-15  Score=91.67  Aligned_cols=66  Identities=21%  Similarity=0.264  Sum_probs=60.4

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHH-hCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRS-TGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~-tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      ..+.++.||..+++.|||++|++|++|+++ ++++|++|+    .++.|+|.|+++.|.+|+..|..++++
T Consensus        26 ~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~----~~~~ItI~G~~~~V~~a~~~I~~~v~e   92 (102)
T 2ctf_A           26 FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE----GEDKITLEGPTEDVSVAQEQIEGMVKD   92 (102)
T ss_dssp             CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS----SSCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC----CCCEEEEECCHHHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999997 599999997    357999999999999999999988753

>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=99.54  E-value=9.7e-15  Score=94.54  Aligned_cols=68  Identities=22%  Similarity=0.331  Sum_probs=59.1

Q ss_pred             EEEEEeecCccceeeccchhHHHHHHHHhCC-eEEecCCCCC----Cc--eEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGS-MIKLPNSFNE----EE--TNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~-~I~i~~~~~~----~~--~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      ..++.||.+++|.+|||+|.+|+.+++.||+ +|+|+..++.    .+  ..|+|+|++++++.|+.+|...+++
T Consensus        68 e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~v~~Ak~li~~~l~~  142 (144)
T 2qnd_A           68 EDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLNY  142 (144)
T ss_dssp             EEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHHHHHHHHHHHHHHHT
T ss_pred             eEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            4889999999999999999999999999997 9999873221    22  3589999999999999999998865

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

Probab=99.50  E-value=1.6e-14  Score=87.12  Aligned_cols=69  Identities=23%  Similarity=0.272  Sum_probs=61.8

Q ss_pred             CCceeEEEEEeecCccceeeccchhHHHHHHHHhCCe-EEecCCCCCCceEEEEEc-CHHHHHHHHHHHhHHhcC
Q psy2768          20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSM-IKLPNSFNEEETNVHIVG-SFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        20 ~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~-I~i~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i~~   92 (96)
                      -..++...|.||.+.+|.+||+||++|++|+++||++ |+|.+.    ++.|+|+| +.+++++|+.+|..+.+.
T Consensus        11 ~~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~ed----dG~V~I~g~~~ea~~~A~~~I~~ie~~   81 (91)
T 2cpq_A           11 LAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDED----TGTFRIYGESADAVKKARGFLEFVEDF   81 (91)
T ss_dssp             SSCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEETT----TTEEEEEESSHHHHHHHHHHHSCCCCC
T ss_pred             ccCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEcC----CCEEEEEECCHHHHHHHHHHHHhhheE
Confidence            3467899999999999999999999999999999998 999852    48999999 789999999999887554

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

Probab=99.42  E-value=1.9e-13  Score=100.12  Aligned_cols=71  Identities=21%  Similarity=0.278  Sum_probs=63.5

Q ss_pred             CCCceeEEEEEeecCccceeeccch--hHHHHHHHHhCCeEEecCCC--C----CCceEEEEEcCHHHHHHHHHHHhHH
Q psy2768          19 ADEVRLTIELVVPSSQVGRIIGKGG--QNVRELQRSTGSMIKLPNSF--N----EEETNVHIVGSFFSVQETLKGCPNI   89 (96)
Q Consensus        19 ~~~~~~~~~~~ip~~~vg~iIGkgG--~~Ik~i~~~tg~~I~i~~~~--~----~~~~~v~I~G~~~~v~~A~~~I~~~   89 (96)
                      .....+|+++.||..+++.||||||  ++|++|+++|||+|++|+..  .    .....|+|+|.+++|++|+.+|.++
T Consensus        25 ~~~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l  103 (376)
T 3n89_A           25 INPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRN  103 (376)
T ss_dssp             CCTTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHS
T ss_pred             ecCCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhc
Confidence            4567999999999999999999999  99999999999999999843  1    3446799999999999999999875

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

Probab=99.36  E-value=9.4e-13  Score=90.48  Aligned_cols=85  Identities=16%  Similarity=0.206  Sum_probs=59.0

Q ss_pred             HHHHHHHHHHhcc-----cCC---CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEc
Q psy2768           3 QYLIFEKMREEGL-----FAG---ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVG   74 (96)
Q Consensus         3 ~~~I~~k~~e~~~-----~~~---~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G   74 (96)
                      +.+|+.|++.+.-     .+.   +...+.+.++.||.+.+|.|||+||.+|+.|+++|||+|+++..    ++.|+|.|
T Consensus         5 ~~~~~~k~~~~~~~~~~~~pr~e~s~~aP~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~~----~g~V~I~~   80 (219)
T 2e3u_A            5 FEKLMKKFENVNKDGEIVEDEDEWEEFFKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSE----TGEVWITS   80 (219)
T ss_dssp             ----------------------------CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECTT----TCEEEEEE
T ss_pred             HHHHHHHHHhhcccCCCCCCccccCCCCCEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEcC----CCEEEEec
Confidence            5678888887421     111   45677888999999999999999999999999999999999843    56788887


Q ss_pred             C-----HHHHHHHHHHHhHHhc
Q psy2768          75 S-----FFSVQETLKGCPNIVD   91 (96)
Q Consensus        75 ~-----~~~v~~A~~~I~~~i~   91 (96)
                      +     ++++.+|+.+|..+..
T Consensus        81 ~~~t~d~~~i~kA~~~I~~i~r  102 (219)
T 2e3u_A           81 TKETEDPLAVWKARDIVLAIGR  102 (219)
T ss_dssp             CTTCCSHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCHHHHHHHHHHHHHHhc
Confidence            5     6999999999999873

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

Probab=99.35  E-value=3.1e-12  Score=93.71  Aligned_cols=84  Identities=19%  Similarity=0.273  Sum_probs=65.2

Q ss_pred             HHHHHHHHHhcccCCCCCceeEEEEEeecCccceeeccch--hHHHHHHHHhCCeEEecCCCC-----CCceEEEEEcCH
Q psy2768           4 YLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGG--QNVRELQRSTGSMIKLPNSFN-----EEETNVHIVGSF   76 (96)
Q Consensus         4 ~~I~~k~~e~~~~~~~~~~~~~~~~~ip~~~vg~iIGkgG--~~Ik~i~~~tg~~I~i~~~~~-----~~~~~v~I~G~~   76 (96)
                      ..+++++.++   .......++.++.||..+++.|||++|  ..|++|+++|||+|.+|+..+     .....|+|+|+.
T Consensus       169 ~~Ll~~l~~~---e~~~~~~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~~ItItGs~  245 (376)
T 3n89_A          169 KRLNEILFRE---SPAPENNFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNI  245 (376)
T ss_dssp             HHHHHHHCC-----CCCSSCEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC---------CCEEEEEEESCH
T ss_pred             HHHHHHHHhh---hcccccceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCCceEEEEEeCH
Confidence            3455555443   123456899999999999999999999  566999999999999997432     235689999999


Q ss_pred             HHHHHHHHHHhHHh
Q psy2768          77 FSVQETLKGCPNIV   90 (96)
Q Consensus        77 ~~v~~A~~~I~~~i   90 (96)
                      ++|..|+..|.++|
T Consensus       246 e~V~~Ark~I~~lL  259 (376)
T 3n89_A          246 DNVLKARRYIMDLL  259 (376)
T ss_dssp             HHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHhhC
Confidence            99999999999875

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

Probab=99.33  E-value=2.9e-12  Score=81.90  Aligned_cols=71  Identities=18%  Similarity=0.401  Sum_probs=60.7

Q ss_pred             ceeEEEEEeecC------ccceeeccchhHHHHHHHHhCCeEEecCCC-----------------CCCceEEEEEc-CHH
Q psy2768          22 VRLTIELVVPSS------QVGRIIGKGGQNVRELQRSTGSMIKLPNSF-----------------NEEETNVHIVG-SFF   77 (96)
Q Consensus        22 ~~~~~~~~ip~~------~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~-----------------~~~~~~v~I~G-~~~   77 (96)
                      ..++.++.||.+      ++|.|||++|.+||+|+++|||+|.|....                 ...+-.|.|++ +.+
T Consensus         5 ~k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e   84 (131)
T 1k1g_A            5 TRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTME   84 (131)
T ss_dssp             CCEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHH
T ss_pred             ceEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHH
Confidence            468899999988      889999999999999999999999997521                 11256788988 569


Q ss_pred             HHHHHHHHHhHHhcC
Q psy2768          78 SVQETLKGCPNIVDQ   92 (96)
Q Consensus        78 ~v~~A~~~I~~~i~~   92 (96)
                      .+.+|+.+|..++..
T Consensus        85 ~~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999999875

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

Probab=99.27  E-value=6.3e-12  Score=97.21  Aligned_cols=83  Identities=20%  Similarity=0.258  Sum_probs=71.2

Q ss_pred             HHHHHHHHHHhcccCC---CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcC-HHH
Q psy2768           3 QYLIFEKMREEGLFAG---ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGS-FFS   78 (96)
Q Consensus         3 ~~~I~~k~~e~~~~~~---~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~-~~~   78 (96)
                      ...|++.|++....+.   +...+....+.||.+.+|.+||+||++||.|+++|||+|+|.+     +..|.|.|+ +++
T Consensus       543 ~~~I~~~m~~al~~~~~~~~~~ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d-----~G~V~I~~~~~~~  617 (630)
T 3u1k_A          543 KKEILQIMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD-----EETFSVFAPTPSA  617 (630)
T ss_dssp             HHHHHHHHHHHCSSCCSSCCTTCCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS-----SSEEEEEESSHHH
T ss_pred             HHHHHHHHHHHHHHHHhhhcccCCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC-----CcEEEEEeCCHHH
Confidence            4568888888765443   6777999999999999999999999999999999999999985     588999986 589


Q ss_pred             HHHHHHHHhHHh
Q psy2768          79 VQETLKGCPNIV   90 (96)
Q Consensus        79 v~~A~~~I~~~i   90 (96)
                      ..+|+.+|..++
T Consensus       618 ~~~A~~~I~~i~  629 (630)
T 3u1k_A          618 MHEARDFITEIC  629 (630)
T ss_dssp             HHHHHHHTTC--
T ss_pred             HHHHHHHHHHHh
Confidence            999999998875

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

Probab=99.26  E-value=2.6e-11  Score=76.30  Aligned_cols=73  Identities=18%  Similarity=0.145  Sum_probs=58.7

Q ss_pred             CCceeEEEEEeecC-------ccceeeccchhHHHHHHHHhCCeEEecCCC-----------CCCceEEEEEc-CHHHHH
Q psy2768          20 DEVRLTIELVVPSS-------QVGRIIGKGGQNVRELQRSTGSMIKLPNSF-----------NEEETNVHIVG-SFFSVQ   80 (96)
Q Consensus        20 ~~~~~~~~~~ip~~-------~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~-----------~~~~~~v~I~G-~~~~v~   80 (96)
                      .-..++.++.||.+       ++|.|||++|.+||+|+++|||+|.|....           ...+-.|.|++ ++++++
T Consensus         8 ~~~~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~   87 (119)
T 2yqr_A            8 GMHYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLA   87 (119)
T ss_dssp             CCSCEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHH
T ss_pred             CeeEEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHH
Confidence            33467788888875       789999999999999999999999997421           11345677776 579999


Q ss_pred             HHHHHHhHHhcC
Q psy2768          81 ETLKGCPNIVDQ   92 (96)
Q Consensus        81 ~A~~~I~~~i~~   92 (96)
                      +|+.+|.+++..
T Consensus        88 ~A~~~Ie~Ll~~   99 (119)
T 2yqr_A           88 AAKKLCENLLQT   99 (119)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhc
Confidence            999999998764

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

Probab=99.21  E-value=2.6e-11  Score=83.26  Aligned_cols=53  Identities=19%  Similarity=0.380  Sum_probs=49.4

Q ss_pred             ccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          34 QVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        34 ~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      .+|+||||+|++|+.|++.|||+|.|++      +.|+|.|++++++.|+.+|.+++..
T Consensus       139 ~~GriIGk~G~tik~ie~~Tg~~I~v~~------~~v~i~G~~~~i~~A~~~i~~li~g  191 (219)
T 2e3u_A          139 VRGRIIGRKGRTRQIIEEMSGASVSVYG------KTVAIIGNPIQIEIAKTAIEKLARG  191 (219)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHCCEEEEET------TEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             hhheeECCCchHHHHHHHHhCceEEECC------eEEEEEeCHHHHHHHHHHHHHHHcC
Confidence            6899999999999999999999999984      5699999999999999999998855

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

Probab=99.09  E-value=2.1e-10  Score=73.96  Aligned_cols=69  Identities=25%  Similarity=0.385  Sum_probs=54.3

Q ss_pred             eEEEEEeecCc------cceeeccchhHHHHHHHHhCCeEEecCCCC-------------------CCceEEEEEcC-HH
Q psy2768          24 LTIELVVPSSQ------VGRIIGKGGQNVRELQRSTGSMIKLPNSFN-------------------EEETNVHIVGS-FF   77 (96)
Q Consensus        24 ~~~~~~ip~~~------vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~-------------------~~~~~v~I~G~-~~   77 (96)
                      ++.++.||.+.      +|.|||++|.++|+|+++|||+|.|.....                   ..+--|.|++. ++
T Consensus         2 ~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~   81 (140)
T 2bl5_A            2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (140)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             ceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCch
Confidence            46678888655      899999999999999999999999986321                   01126778884 33


Q ss_pred             -----HHHHHHHHHhHHhcC
Q psy2768          78 -----SVQETLKGCPNIVDQ   92 (96)
Q Consensus        78 -----~v~~A~~~I~~~i~~   92 (96)
                           .+..|+.+|..++..
T Consensus        82 ~~~~~~l~~A~~~I~~lL~p  101 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLVP  101 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSSC
T ss_pred             hhHHHHHHHHHHHHHHHCCC
Confidence                 799999999998764

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

Probab=99.05  E-value=6e-10  Score=71.25  Aligned_cols=69  Identities=14%  Similarity=0.163  Sum_probs=62.2

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhc
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVD   91 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~   91 (96)
                      .-.+.|.+....++.|+|++|+.|+.|+..|++.|++.....+.+..|+|+|++..-..|+.+|..+.+
T Consensus        55 ~dPlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s~g~tEVtIfG~~~~Q~rak~MI~sLA~  123 (140)
T 3v69_A           55 EDPKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGPERRAEIWIFGPPPFRRDVDRMLTDLAH  123 (140)
T ss_dssp             SSCEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCTTSCEEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCCCCcEEEEEECCHHHHHHHHHHHHHHHH
Confidence            345678999999999999999999999999999999999655678999999999999999999988753

>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=99.01  E-value=2.8e-10  Score=73.43  Aligned_cols=63  Identities=16%  Similarity=0.156  Sum_probs=48.8

Q ss_pred             ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHH
Q psy2768          22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGC   86 (96)
Q Consensus        22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I   86 (96)
                      ..++.+|.||.+.+|++||++|++|+.|++++|  |++....+..+..+...++|+.+..|+.++
T Consensus         2 ~~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~g--I~ii~~~~~~~~~i~~~~~p~~v~~~~~~l   64 (144)
T 2qnd_A            2 SRFHEQFIVREDLMGLAIGTHGANIQQARKVPG--VTAIDLDEDTCTFHIYGEDQDAVKKARSFL   64 (144)
T ss_dssp             --CEEEEECCGGGHHHHHCGGGHHHHHHHTSTT--EEEEEEETTTTEEEEEESSHHHHHHHHHHH
T ss_pred             CceEEEEEECCcceeeEECCChhHHHHHHHHHC--CeEeccCCCchheeeccCCHHHHHHHHHhh
Confidence            367899999999999999999999999999999  555443233455555566899999987643

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

Probab=99.00  E-value=2.5e-10  Score=76.96  Aligned_cols=53  Identities=25%  Similarity=0.448  Sum_probs=49.3

Q ss_pred             ccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          34 QVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        34 ~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      ..|+||||+|++++.|+..|||+|.|++      ..|.|.|++++++.|...|++++..
T Consensus       108 ~~GrIIGk~G~tik~iE~~Tg~~I~v~~------~~v~i~G~~~~i~~Ar~~i~~li~g  160 (191)
T 1tua_A          108 IKGRIIGEGGRARRTIEEMTDTYINVGE------YEVAIIGDYERAMAAKQAIEMLAEG  160 (191)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECS------SEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             HhhheeCCCccHHHHHHHHHCceEEEcC------CEEEEEeChHHHHHHHHHHHHHHcC
Confidence            5899999999999999999999999985      4899999999999999999998764

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

Probab=99.00  E-value=1.1e-10  Score=91.34  Aligned_cols=88  Identities=18%  Similarity=0.328  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHhcccCC---CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcC-HHH
Q psy2768           3 QYLIFEKMREEGLFAG---ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGS-FFS   78 (96)
Q Consensus         3 ~~~I~~k~~e~~~~~~---~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~-~~~   78 (96)
                      ...|++.|++....+.   +...+....+.||.+.++.+||+||.+||+|+++||++|+|.+     +..|.|.+. .++
T Consensus       546 ~~~I~~~m~~al~~~r~~~~~~ap~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~d-----dG~v~I~~~~~~~  620 (726)
T 4aid_A          546 RAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIND-----DGVVKVSASDGAK  620 (726)
T ss_dssp             HHHHHHHHHTTCSSCCSSCCSSCCC------------------------------------------------CCSCHHH
T ss_pred             HHHHHHHHHHHHHhhhhhhcccCCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC-----CceEEEEeCCHHH
Confidence            4568888888765332   5677889999999999999999999999999999999999985     577888875 699


Q ss_pred             HHHHHHHHhHHhcCCCC
Q psy2768          79 VQETLKGCPNIVDQPSI   95 (96)
Q Consensus        79 v~~A~~~I~~~i~~~~~   95 (96)
                      .++|+.+|..++.++.+
T Consensus       621 ~~~A~~~i~~i~~~~~v  637 (726)
T 4aid_A          621 IKAAIDWIKSITDEAEV  637 (726)
T ss_dssp             HHHHHHC----------
T ss_pred             HHHHHHHHHHHhhhhcC
Confidence            99999999998876543

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

Probab=98.88  E-value=3.4e-09  Score=71.42  Aligned_cols=63  Identities=21%  Similarity=0.267  Sum_probs=56.9

Q ss_pred             EEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEE-----cCHHHHHHHHHHHhHHhcC
Q psy2768          26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIV-----GSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        26 ~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~-----G~~~~v~~A~~~I~~~i~~   92 (96)
                      ..+.||.+.+|.|||++|++++.|++.+|++|.++..    ++.++|.     |++.++.+|..+|..+...
T Consensus         6 ~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~~----~~~V~i~t~~~t~dp~~i~KA~dlI~ai~rg   73 (191)
T 1tua_A            6 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE----NSMVIVEPEAEGIPPVNLMKAAEVVKAISLG   73 (191)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT----TTEEEEEESSTTSCHHHHHHHHHHHHHHHHT
T ss_pred             eEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEcC----CCeEEEEeCCCCCCHHHHHHHHHHHHHHHcC
Confidence            6899999999999999999999999999999999853    6778888     9999999999999876653

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

Probab=98.41  E-value=7e-08  Score=75.72  Aligned_cols=87  Identities=17%  Similarity=0.285  Sum_probs=8.8

Q ss_pred             HHHHHHHHHHhcccCC---CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCH-HH
Q psy2768           3 QYLIFEKMREEGLFAG---ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSF-FS   78 (96)
Q Consensus         3 ~~~I~~k~~e~~~~~~---~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~-~~   78 (96)
                      ...|++.|++....+.   +...+....+.||.+.++.+||+||.+|++|.++||+.|+|..     +..+.|.+.. ..
T Consensus       536 ~~~I~~~m~~al~~~~~~~~~~ap~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~-----dg~v~I~~~~~~~  610 (723)
T 3cdi_A          536 RLHILGVMEQAINAPRGDISEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED-----DGTVKIAATDGEK  610 (723)
T ss_dssp             HHHHHHHHHHHCC-------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHhhhcchhccccCceEEEEEECHHHhcccccccceeeeeeehhhCceEEecC-----CccEEEecCCHHH
Confidence            3467888888654332   5677889999999999999999999999999999999999985     5678887754 78


Q ss_pred             HHHHHHHHhHHhcCCC
Q psy2768          79 VQETLKGCPNIVDQPS   94 (96)
Q Consensus        79 v~~A~~~I~~~i~~~~   94 (96)
                      ..+|..+|..+..++.
T Consensus       611 ~~~a~~~i~~i~~~~~  626 (723)
T 3cdi_A          611 AKHAIRRIEEITAEIE  626 (723)
T ss_dssp             ----------------
T ss_pred             HHHHHHHHHHHhhhhh
Confidence            8888888887765543

>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=98.06  E-value=1.5e-07  Score=74.20  Aligned_cols=83  Identities=18%  Similarity=0.246  Sum_probs=35.9

Q ss_pred             HHHHHHHHHHhcccC--CCCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcC-HHHH
Q psy2768           3 QYLIFEKMREEGLFA--GADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGS-FFSV   79 (96)
Q Consensus         3 ~~~I~~k~~e~~~~~--~~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~-~~~v   79 (96)
                      ...|++.|++....+  .+...+....+.||.+.+|.+||+||.+||+|+++||+.|+|.+     +..|.|++. ....
T Consensus       575 ~~~I~~~m~~al~~~~~~~~~ap~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~-----dG~v~Is~~~~~~~  649 (757)
T 1e3p_A          575 RLHILDVMMEAIDTPDEMSPNAPRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED-----DGTIYIGAADGPAA  649 (757)
T ss_dssp             HHHHHHHHHHHCSSCCCCCTTSCBCCCC------------------CTTCCCCCSCC-------------CCCBSSHHHH
T ss_pred             HHHHHHHHHHHhcccccccccCceeEEEEEChHHeehcccccceeeehhhHhhCCEEEecC-----CceEEEecCCHHHH
Confidence            456788888765322  25566778889999999999999999999999999999999985     567788764 4777


Q ss_pred             HHHHHHHhHHh
Q psy2768          80 QETLKGCPNIV   90 (96)
Q Consensus        80 ~~A~~~I~~~i   90 (96)
                      +.|..+|..+.
T Consensus       650 ~~a~~~i~~i~  660 (757)
T 1e3p_A          650 EAARATINGIA  660 (757)
T ss_dssp             CC---------
T ss_pred             HHHHHHHHHhc
Confidence            78877777765

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

Probab=96.58  E-value=0.0018  Score=41.56  Aligned_cols=40  Identities=25%  Similarity=0.502  Sum_probs=35.5

Q ss_pred             ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768          22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN   61 (96)
Q Consensus        22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~   61 (96)
                      ..-.+.+.|+...+|+.||++|++++.++++.|-+|+|-.
T Consensus        34 ~~dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~   73 (144)
T 2cxc_A           34 ENNRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVE   73 (144)
T ss_dssp             GGTEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEE
T ss_pred             CCCEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEE
Confidence            3456788999999999999999999999999999998843

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

Probab=95.51  E-value=0.0027  Score=40.77  Aligned_cols=39  Identities=23%  Similarity=0.368  Sum_probs=35.2

Q ss_pred             ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEec
Q psy2768          22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLP   60 (96)
Q Consensus        22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~   60 (96)
                      ......+.||.+..+..|||+|.+++-..+-||.+|+|.
T Consensus       101 ~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A          101 GVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             TEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             CcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence            456778899999999999999999999999999988775

>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=95.37  E-value=0.013  Score=40.76  Aligned_cols=39  Identities=38%  Similarity=0.467  Sum_probs=36.0

Q ss_pred             eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC
Q psy2768          24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS   62 (96)
Q Consensus        24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~   62 (96)
                      ....+.||.++.+.-|||+|.+++--.+-||.+|+|...
T Consensus       184 ~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  222 (251)
T 2asb_A          184 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  222 (251)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             cEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEH
Confidence            467899999999999999999999999999999999763

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

Probab=94.49  E-value=0.028  Score=41.03  Aligned_cols=39  Identities=38%  Similarity=0.467  Sum_probs=36.0

Q ss_pred             eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC
Q psy2768          24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS   62 (96)
Q Consensus        24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~   62 (96)
                      ....+.||.+..+..|||+|.+++-..+-||.+|+|...
T Consensus       307 ~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  345 (366)
T 1k0r_A          307 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  345 (366)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEES
T ss_pred             cEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEH
Confidence            467899999999999999999999999999999999764

>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=94.45  E-value=0.03  Score=40.54  Aligned_cols=39  Identities=36%  Similarity=0.528  Sum_probs=35.9

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN   61 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~   61 (96)
                      .....+.||.++.+.-|||+|.+++--.+-||.+|+|..
T Consensus       302 ~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s  340 (344)
T 1hh2_P          302 NKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP  340 (344)
T ss_dssp             TTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceee
Confidence            456889999999999999999999999999999999864

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

Probab=92.15  E-value=0.086  Score=33.97  Aligned_cols=29  Identities=14%  Similarity=0.236  Sum_probs=25.1

Q ss_pred             EEEEEeecCccceeeccchhHHHHHHHHh
Q psy2768          25 TIELVVPSSQVGRIIGKGGQNVRELQRST   53 (96)
Q Consensus        25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~t   53 (96)
                      ++.+.+-.+..|.+|||.|.+++.||--+
T Consensus        34 ~i~i~i~ged~glLIGK~G~TL~ALQyL~   62 (152)
T 2pt7_G           34 VLLIDIDGEDSALLIGEKGYRYKALSYLL   62 (152)
T ss_dssp             EEEEEEEEGGGTTTTCGGGHHHHHHHHHH
T ss_pred             EEEEEEecCCcceEECCCCcchHHHHHHH
Confidence            46677788899999999999999998766

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

Probab=91.72  E-value=0.089  Score=31.09  Aligned_cols=28  Identities=21%  Similarity=0.568  Sum_probs=22.3

Q ss_pred             EEEEEeecCccceeeccchhHHHHHHHH
Q psy2768          25 TIELVVPSSQVGRIIGKGGQNVRELQRS   52 (96)
Q Consensus        25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~   52 (96)
                      ..++.|....-|.+||++|+.|++|+..
T Consensus        36 ~i~I~I~tarPg~vIGkkG~~Ie~L~~~   63 (92)
T 1wh9_A           36 RTEIIILATRTQNVLGEKGRRIRELTAV   63 (92)
T ss_dssp             CEEEEEEESCHHHHHCGGGHHHHHHHHH
T ss_pred             eEEEEEEeCCCceEEcCCcHHHHHHHHH
Confidence            4567777778899999999999877553

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

Probab=91.05  E-value=0.63  Score=31.56  Aligned_cols=59  Identities=19%  Similarity=0.202  Sum_probs=46.0

Q ss_pred             EEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHH
Q psy2768          26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNI   89 (96)
Q Consensus        26 ~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~   89 (96)
                      .-+.++...+.+++|+++..+..|.+.+++.|-+-.     +..|-|.++......+...|..+
T Consensus       138 ~v~~vs~~~v~rl~~~~~~~l~~l~~~~~~ei~vG~-----NG~IWi~~~~~~~~~~~~ai~~~  196 (229)
T 2ba0_A          138 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ-----NGLIWVNGDRRKVSIAEEAIYLI  196 (229)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT-----TSEEEEESCHHHHHHHHHHHHHH
T ss_pred             EEEEECHHHhHHHhcCCchHHHHhcccCCeEEEEEC-----CcEEEEeCCchhHHHHHHHHHHH
Confidence            345788888889999999999999999999999976     46777888876555555555443

>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=87.06  E-value=0.23  Score=34.51  Aligned_cols=29  Identities=31%  Similarity=0.496  Sum_probs=25.5

Q ss_pred             CccceeeccchhHHHHH-HHHhCCeEEecC
Q psy2768          33 SQVGRIIGKGGQNVREL-QRSTGSMIKLPN   61 (96)
Q Consensus        33 ~~vg~iIGkgG~~Ik~i-~~~tg~~I~i~~   61 (96)
                      +-+|+.||++|++|+.+ ++..|-+|+|-.
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~  155 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIID  155 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEE
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEE
Confidence            45799999999999999 888899999943

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

Probab=85.41  E-value=4.1  Score=27.51  Aligned_cols=59  Identities=15%  Similarity=0.153  Sum_probs=46.1

Q ss_pred             EEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEc-CHHHHHHHHHHHhHH
Q psy2768          26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVG-SFFSVQETLKGCPNI   89 (96)
Q Consensus        26 ~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~   89 (96)
                      +-+.++...+.+++|++|..+..|.+.+++.|-+-.     +..|-|.+ +++....+...|..+
T Consensus       150 ~vv~vs~~~~~rl~~~~~~~l~~l~~~~~~~i~vG~-----NG~IWi~~~~~~~~~~~~~ai~~~  209 (235)
T 2z0s_A          150 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR-----NGRIHLECPNEDLEAIAVMAIKII  209 (235)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET-----TTEEEEECSCHHHHHHHHHHHHHH
T ss_pred             EEEEECHHHhHHHhcCcchHHHHhcccCCeEEEEeC-----CCEEEEecCCHHHHHHHHHHHHHH
Confidence            456788889999999999999999989999999986     46677775 556666555555554

>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=84.23  E-value=0.4  Score=34.96  Aligned_cols=29  Identities=31%  Similarity=0.470  Sum_probs=25.9

Q ss_pred             CccceeeccchhHHHHHHHHh-CCeEEecC
Q psy2768          33 SQVGRIIGKGGQNVRELQRST-GSMIKLPN   61 (96)
Q Consensus        33 ~~vg~iIGkgG~~Ik~i~~~t-g~~I~i~~   61 (96)
                      +-+|+.||++|++|+.|.++. |-+|+|-.
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~  278 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIID  278 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEE
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEE
Confidence            567999999999999999998 99999843

>3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA, 30S ribosome ASSE GTP-binding, nucleotide-binding; HET: GNP; 1.90A {Aquifex aeolicus} PDB: 3r9w_A* 3r9x_A*

Probab=82.95  E-value=0.93  Score=31.47  Aligned_cols=39  Identities=28%  Similarity=0.393  Sum_probs=28.2

Q ss_pred             ceeEEEEEeec-CccceeeccchhHHHHH--------HHHhCCeEEec
Q psy2768          22 VRLTIELVVPS-SQVGRIIGKGGQNVREL--------QRSTGSMIKLP   60 (96)
Q Consensus        22 ~~~~~~~~ip~-~~vg~iIGkgG~~Ik~i--------~~~tg~~I~i~   60 (96)
                      ..+...+.|.. ++-+.|||++|+.||+|        ++.+|++|.+.
T Consensus       238 ~~i~a~i~ve~~~~k~i~ig~~g~~ik~i~~~ar~~~~~~~~~~v~l~  285 (308)
T 3iev_A          238 LVIKGEIIVDRENLKPIIIGKKGQRLKEIGKRARQELELILGRPVYLE  285 (308)
T ss_dssp             EEEEEEEEESSGGGHHHHHCGGGHHHHHHHHHHHHHHHHHHTSCEEEE
T ss_pred             EEEEEEEEEccCCcceEEEcCCcHHHHHHHHHHHHHHHHHhCCceEEE
Confidence            35666777775 46699999999999865        44567776653

>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=81.27  E-value=0.67  Score=31.59  Aligned_cols=59  Identities=19%  Similarity=0.248  Sum_probs=36.1

Q ss_pred             EEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCC-CceEEEEEcCHHHHHHHHHH
Q psy2768          25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNE-EETNVHIVGSFFSVQETLKG   85 (96)
Q Consensus        25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~-~~~~v~I~G~~~~v~~A~~~   85 (96)
                      .+.+.+..+..|.+|||.|.+++.||--+..-++-.  .+. ..-.+-+.|-.+.-...+..
T Consensus        93 ~i~i~i~g~d~g~LIGk~G~tLdALQyL~~~~vn~~--~~~~~rv~LDi~~YR~rR~e~L~~  152 (225)
T 3gku_A           93 EMNVNLKGDDMGILIGKRGQTLDSLQYLVSLVVNKS--SSDYIRVKLDTENYRERRKETLET  152 (225)
T ss_dssp             EEEEEEECHHHHHCSTTHHHHHHHHHHHHHHHHHHT--CSSCCEEEEESTTHHHHHHHHHHH
T ss_pred             EEEEEEcCCccceeecCCCeEhHHHHHHHHHHHHhc--CCCceEEEEecchHHHHHHHHHHH
Confidence            345556677899999999999999998876444322  211 12334444544554444433

---

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	96
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	5e-13
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	1e-11
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	3e-11
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	3e-11
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	5e-11
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	5e-11
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	6e-11
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	1e-10
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	1e-10
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	2e-10
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	3e-10
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	7e-10
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	3e-09
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	9e-09
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	4e-07
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	3e-06
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	7e-06
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	3e-05
d2asba3	67	d.52.3.1 (A:263-329) Transcription factor NusA, C-	5e-05
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	8e-05
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	1e-04
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	2e-04
d1hh2p3	68	d.52.3.1 (P:277-344) Transcription factor NusA, C-	2e-04
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	3e-04
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	8e-04

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

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

 Score = 56.7 bits (137), Expect = 5e-13
 Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQE 81
          V LTI L++   +VG IIGK G++V++++  +G+ I +    N  E  + + G   ++ +
Sbjct: 2  VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-NCPERIITLAGPTNAIFK 60

Query: 82 TLK 84
             
Sbjct: 61 AFA 63

>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 = 53.2 bits (128), Expect = 1e-11
 Identities = 12/72 (16%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQ 80
          + + +  + +P      +IGK G+ +++L+  T + I++P   ++    + I G+   ++
Sbjct: 7  QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-DDPSNQIKITGTKEGIE 65

Query: 81 ETLKGCPNIVDQ 92
          +       I  +
Sbjct: 66 KARHEVLLISAE 77

>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 = 52.1 bits (125), Expect = 3e-11
 Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 4/64 (6%)

Query: 22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS----FNEEETNVHIVGSFF 77
          ++  +E+ VP + VG I+GKGG+ + E Q  TG+ I++              V I GS  
Sbjct: 1  MKELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPA 60

Query: 78 SVQE 81
          + Q 
Sbjct: 61 ATQA 64

>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 = 51.8 bits (124), Expect = 3e-11
 Identities = 20/60 (33%), Positives = 34/60 (56%), Gaps = 1/60 (1%)

Query: 23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF-NEEETNVHIVGSFFSVQE 81
          + T EL +P++ +G IIG+ G N+ E+++ +G+ IK+ N         V I GS  S+  
Sbjct: 1  QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISL 60

>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 = 51.8 bits (124), Expect = 5e-11
 Identities = 14/69 (20%), Positives = 29/69 (42%), Gaps = 1/69 (1%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNE-EETNVHIVGSFFSVQETL 83
           I++ +P   VG +IG+ G+ ++++Q   G  I+         E    I G     Q   
Sbjct: 4  MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAA 63

Query: 84 KGCPNIVDQ 92
          +   +++  
Sbjct: 64 EIITDLLRS 72

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

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

 Score = 51.4 bits (123), Expect = 5e-11
 Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF-NEEETNVHIVGSFFSVQETL 83
          T E  VP   VG IIG+GG+ +  +Q+ +G  I++        E +  + G+  SVQ   
Sbjct: 9  TEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAK 68

Query: 84 KGCPNIVDQ 92
          +    IV++
Sbjct: 69 RLLDQIVEK 77

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

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

 Score = 51.4 bits (123), Expect = 6e-11
 Identities = 14/68 (20%), Positives = 31/68 (45%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLK 84
          + ++ +      RIIG  G+ +R++       I+ P S   +   V + G   +V+E + 
Sbjct: 11 SEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAID 70

Query: 85 GCPNIVDQ 92
             N+ ++
Sbjct: 71 HILNLEEE 78

>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 = 51.0 bits (122), Expect = 1e-10
 Identities = 15/69 (21%), Positives = 27/69 (39%), Gaps = 1/69 (1%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLK 84
          TIE+ VP      +IG+ G  +R++       I +P     +   + I G   ++     
Sbjct: 11 TIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP-ELQSDIIAITGLAANLDRAKA 69

Query: 85 GCPNIVDQP 93
          G    V + 
Sbjct: 70 GLLERVKEL 78

>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 = 50.3 bits (120), Expect = 1e-10
 Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF-NEEETNVHIVGSFFSVQE 81
           +T ++ +P    G IIGKGGQ +++++  +G+ IK+       E+  + I G+   +Q 
Sbjct: 3  IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQN 62

Query: 82 TLKGCPNIVDQPS 94
                N V Q S
Sbjct: 63 AQYLLQNSVKQYS 75

>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 = 50.1 bits (120), Expect = 2e-10
 Identities = 11/57 (19%), Positives = 24/57 (42%), Gaps = 1/57 (1%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQE 81
           +E+ +       +IGK G N+  ++      +++P    +    + I G    VQ+
Sbjct: 6  YVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNL-IRIEGDPQGVQQ 61

>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 = 49.8 bits (119), Expect = 3e-10
 Identities = 12/71 (16%), Positives = 28/71 (39%), Gaps = 2/71 (2%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLP--NSFNEEETNVHIVGSFFSVQET 82
           + + V      +IIG+ G  + +++      I+ P  +  N+ +  + I G   + +  
Sbjct: 11 KLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAA 70

Query: 83 LKGCPNIVDQP 93
                IV + 
Sbjct: 71 RDAILRIVGEL 81

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

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

 Score = 48.4 bits (115), Expect = 7e-10
 Identities = 14/61 (22%), Positives = 28/61 (45%), Gaps = 4/61 (6%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFN----EEETNVHIVGSFFSVQ 80
              +VP+ + G IIGKGG+ ++ + + +G+ I+L  +             I G+   + 
Sbjct: 2  EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQID 61

Query: 81 E 81
           
Sbjct: 62 Y 62

>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 = 47.3 bits (112), Expect = 3e-09
 Identities = 17/67 (25%), Positives = 33/67 (49%), Gaps = 3/67 (4%)

Query: 18 GADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF---NEEETNVHIVG 74
          G        E+++P+S+ G +IGKGG+ +++LQ   G  + +          +  + I G
Sbjct: 2  GDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITG 61

Query: 75 SFFSVQE 81
            + VQ+
Sbjct: 62 DPYKVQQ 68

>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 = 46.5 bits (110), Expect = 9e-09
 Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 3/63 (4%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF---NEEETNVHIVGSFFSVQE 81
            +L VP   VGRIIG+GG+ +R + +++G+ I               + I G+   V  
Sbjct: 16 FEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAA 75

Query: 82 TLK 84
             
Sbjct: 76 AKH 78

>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 = 41.8 bits (98), Expect = 4e-07
 Identities = 12/69 (17%), Positives = 27/69 (39%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLK 84
           +E+ +P+     +IG  G+ +R +    G +             V I G    V++  K
Sbjct: 11 EVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEKAKK 70

Query: 85 GCPNIVDQP 93
             ++ ++ 
Sbjct: 71 QLLHLAEEK 79

>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 = 38.9 bits (91), Expect = 3e-06
 Identities = 12/51 (23%), Positives = 27/51 (52%), Gaps = 5/51 (9%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGS 75
           I + +P  ++G +IG   Q + ++Q  TG+ I +     E++  ++I  +
Sbjct: 4  IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITI-----EDDGTIYIGAA 49

>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 = 38.6 bits (90), Expect = 7e-06
 Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 4/47 (8%)

Query: 26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHI 72
          I + V   ++G +IG  G+   E+ R TG++I      + E + V +
Sbjct: 5  IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVIT----VDTENSMVIV 47

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 104

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

 Score = 37.4 bits (87), Expect = 3e-05
 Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 6/59 (10%)

Query: 35 VGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQP 93
           GRIIG+GG+  R ++  T + I +       E  V I+G +       +    + +  
Sbjct: 24 KGRIIGEGGRARRTIEEMTDTYINV------GEYEVAIIGDYERAMAAKQAIEMLAEGR 76

>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]} Length = 67

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]

 Score = 35.8 bits (83), Expect = 5e-05
 Identities = 16/38 (42%), Positives = 19/38 (50%)

Query: 20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMI 57
          D+      +VVP  Q+   IGK GQN R   R TG  I
Sbjct: 22 DQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRI 59

>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 = 35.9 bits (83), Expect = 8e-05
 Identities = 10/55 (18%), Positives = 22/55 (40%), Gaps = 5/55 (9%)

Query: 30 VPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLK 84
          +  ++V R+IGK G  ++ L+      I +      +   + + G    V    +
Sbjct: 7  INPARVPRVIGKKGSMIKLLKSELDVQIVV-----GQNGLIWVNGDRRKVSIAEE 56

>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 = 34.9 bits (80), Expect = 1e-04
 Identities = 9/35 (25%), Positives = 15/35 (42%)

Query: 23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMI 57
              E VV    +G  IG  G N+++ ++  G   
Sbjct: 7  AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTA 41

>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 = 34.3 bits (79), Expect = 2e-04
 Identities = 8/46 (17%), Positives = 14/46 (30%), Gaps = 5/46 (10%)

Query: 30 VPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGS 75
          +   +V R+IGK       L   +G  I +          +     
Sbjct: 7  IMPVKVPRVIGKNKSMYETLTSKSGCSIFV-----ANNGRIWATCP 47

>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]} Length = 68

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]

 Score = 34.3 bits (79), Expect = 2e-04
 Identities = 15/38 (39%), Positives = 21/38 (55%)

Query: 20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMI 57
          D+      ++VP +Q+   IGKGGQN R   + TG  I
Sbjct: 23 DKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKI 60

>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 = 34.4 bits (79), Expect = 3e-04
 Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 1/38 (2%)

Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQ-RSTGSMIKLPN 61
             +  PS     IIGK GQN+ ++  +     I+   
Sbjct: 22 VSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE 59

>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 = 33.1 bits (76), Expect = 8e-04
 Identities = 7/28 (25%), Positives = 15/28 (53%)

Query: 30 VPSSQVGRIIGKGGQNVRELQRSTGSMI 57
          +  ++V R+IG+    ++ L+  T   I
Sbjct: 7  ISPAKVPRVIGRKMSMLKTLEEKTECKI 34

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	96
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.85
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.84
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.84
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.84
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.83
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.82
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.82
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.81
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.79
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.78
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.78
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.76
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.75
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.72
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.72
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.72
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.71
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.65
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	99.57
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	99.54
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	99.48
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	99.36
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	99.33
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.9
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	98.64
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	97.31
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	97.24
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	96.67
d1egaa2	113	GTPase Era C-terminal domain {Escherichia coli [Ta	96.24
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	94.43
d1wf3a2	118	GTPase Era C-terminal domain {Thermus thermophilus	92.26
d2uubc1	105	Ribosomal protein S3 N-terminal domain {Thermus th	91.99
d2asba2	79	Transcription factor NusA, C-terminal domains {Myc	90.15
d1hh2p2	78	Transcription factor NusA, C-terminal domains {The	86.77
d2qalc1	105	Ribosomal protein S3 N-terminal domain {Escherichi	86.75

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

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

Probab=99.85  E-value=2.7e-21  Score=111.47  Aligned_cols=71  Identities=28%  Similarity=0.467  Sum_probs=65.7

Q ss_pred             ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC-CCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS-FNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~-~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      +.+|.++.||.+++|+|||++|++|++|+++|||+|+|+++ ++.+++.|+|+|+++++..|+.+|.+++++
T Consensus         2 p~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e   73 (75)
T d1zzka1           2 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ   73 (75)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            46789999999999999999999999999999999999874 556789999999999999999999998865

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

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

Probab=99.84  E-value=1.3e-21  Score=112.70  Aligned_cols=70  Identities=20%  Similarity=0.337  Sum_probs=64.9

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC-CCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS-FNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~-~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      ..++++.||.+++|+||||+|++|++|+++|||+|+|++. ++..++.|+|+|+++++..|+.+|.+++++
T Consensus         2 ~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   72 (74)
T d1j4wa1           2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRS   72 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            5689999999999999999999999999999999999874 456789999999999999999999998875

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

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

Probab=99.84  E-value=4.1e-21  Score=109.67  Aligned_cols=67  Identities=30%  Similarity=0.421  Sum_probs=62.4

Q ss_pred             eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC-CCCCCceEEEEEcCHHHHHHHHHHHhHHh
Q psy2768          24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN-SFNEEETNVHIVGSFFSVQETLKGCPNIV   90 (96)
Q Consensus        24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~-~~~~~~~~v~I~G~~~~v~~A~~~I~~~i   90 (96)
                      .|.+|.||.+++|+||||+|++|++|+++|||+|.|++ .++..++.|+|+|+++++..|+.+|.+.|
T Consensus         2 ~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   69 (70)
T d1wvna1           2 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            58899999999999999999999999999999999987 45667899999999999999999999865

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

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

Probab=99.84  E-value=3.2e-21  Score=110.37  Aligned_cols=70  Identities=26%  Similarity=0.476  Sum_probs=64.6

Q ss_pred             ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      .++++++.||.+.+|+||||+|++|++|+++|||+|++++. +.+++.|+|+|+++++.+|+.+|.+++++
T Consensus         2 ~~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~-~~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           2 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-NCPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             ccEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC-CCCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            46899999999999999999999999999999999999874 45589999999999999999999998764

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

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

Probab=99.83  E-value=7.3e-21  Score=108.79  Aligned_cols=66  Identities=21%  Similarity=0.423  Sum_probs=59.9

Q ss_pred             EEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC----CCCCceEEEEEcCHHHHHHHHHHHhHHh
Q psy2768          25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS----FNEEETNVHIVGSFFSVQETLKGCPNIV   90 (96)
Q Consensus        25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~----~~~~~~~v~I~G~~~~v~~A~~~I~~~i   90 (96)
                      ..+|.||.+.+|+||||+|++|++|++.|||+|+|++.    +++.+|.|+|+|+++++..|+.+|.++|
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~e~i   71 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            46899999999999999999999999999999999863    3457899999999999999999999864

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

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

Probab=99.82  E-value=1.9e-20  Score=107.81  Aligned_cols=67  Identities=31%  Similarity=0.423  Sum_probs=61.4

Q ss_pred             eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC----CCCCceEEEEEcCHHHHHHHHHHHhHHh
Q psy2768          24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS----FNEEETNVHIVGSFFSVQETLKGCPNIV   90 (96)
Q Consensus        24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~----~~~~~~~v~I~G~~~~v~~A~~~I~~~i   90 (96)
                      .++++.||.+++|+||||+|++|++|+++|||+|+|++.    ++.+++.|+|+|++++++.|+.+|.+++
T Consensus         3 ~~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            357899999999999999999999999999999999873    4457899999999999999999999876

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

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

Probab=99.82  E-value=1.6e-20  Score=109.82  Aligned_cols=75  Identities=21%  Similarity=0.433  Sum_probs=67.6

Q ss_pred             CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC---CCCCceEEEEEcCHHHHHHHHHHHhHHhcCC
Q psy2768          19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS---FNEEETNVHIVGSFFSVQETLKGCPNIVDQP   93 (96)
Q Consensus        19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~---~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   93 (96)
                      +.....+.++.||.+++|+||||+|++|++|+++|||+|.|++.   ++..++.|+|+|++++|..|+.+|.+++++.
T Consensus         3 ~~~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   80 (81)
T d1x4ma1           3 DGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRDQ   80 (81)
T ss_dssp             CCCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CCCccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            45568999999999999999999999999999999999999762   3457899999999999999999999988763

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

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

Probab=99.81  E-value=3.4e-20  Score=107.84  Aligned_cols=73  Identities=29%  Similarity=0.423  Sum_probs=66.9

Q ss_pred             CCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC-CCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS-FNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        20 ~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~-~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      ....++.++.||.+++|.|||++|++|++|++.|||+|.|++. ++..++.|+|+|+++++..|+.+|.+++++
T Consensus         4 ~~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   77 (79)
T d1x4na1           4 QRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEK   77 (79)
T ss_dssp             CCCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             cCCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            4467899999999999999999999999999999999999884 556789999999999999999999998864

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

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

Probab=99.79  E-value=9e-20  Score=106.61  Aligned_cols=72  Identities=21%  Similarity=0.304  Sum_probs=65.2

Q ss_pred             CceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        21 ~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      ...++.++.||..++|+|||++|++|++|+++|||+|+|++..+.+.+.|+|+|++++|.+|+.+|.+++++
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~~v~I~G~~~~V~~A~~~I~~i~~e   78 (81)
T d2ctma1           7 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAIDHILNLEEE   78 (81)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCSCTTEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccCCCCCEEEEeCCHHHHHHHHHHHHHHHHH
Confidence            456788999999999999999999999999999999999986555567899999999999999999998764

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

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

Probab=99.78  E-value=2.1e-19  Score=109.40  Aligned_cols=74  Identities=24%  Similarity=0.362  Sum_probs=66.3

Q ss_pred             CCCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCC---CCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          19 ADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF---NEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        19 ~~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      ++..+++.+|.||.+++|+||||+|.+|++|+++|||+|.|++.+   ...++.|+|+|++++|.+|+.+|.+++++
T Consensus        10 ~~~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   86 (104)
T d1we8a_          10 TENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSE   86 (104)
T ss_dssp             SSSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhC
Confidence            456689999999999999999999999999999999999998742   34679999999999999999999998753

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

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

Probab=99.78  E-value=2.3e-19  Score=105.42  Aligned_cols=70  Identities=17%  Similarity=0.302  Sum_probs=64.0

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCC--CCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS--FNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      .+++++.||..++|+|||++|++|++|+++|||+|+|++.  ++.+++.|+|.|++++|..|+.+|.+++++
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e   80 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGE   80 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCCCCCcceEEEECCHHHHHHHHHHHHHHHHh
Confidence            6789999999999999999999999999999999999873  455678999999999999999999998754

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

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

Probab=99.76  E-value=3.7e-19  Score=103.95  Aligned_cols=72  Identities=17%  Similarity=0.373  Sum_probs=65.1

Q ss_pred             CCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        20 ~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      ....++.++.||.+++|+|||++|++|++|+++|||+|++|+. ++.++.|+|+|+++++.+|+.+|.+++++
T Consensus         6 ~~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-~~~~~~v~I~G~~~~v~~A~~~I~~iv~e   77 (81)
T d2ctea1           6 LQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-DDPSNQIKITGTKEGIEKARHEVLLISAE   77 (81)
T ss_dssp             CCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT-TSSCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             hcCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCC-CCCCCEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            3456899999999999999999999999999999999999874 34578899999999999999999998865

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

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

Probab=99.75  E-value=1.3e-18  Score=99.30  Aligned_cols=68  Identities=18%  Similarity=0.291  Sum_probs=61.5

Q ss_pred             ceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHh
Q psy2768          22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIV   90 (96)
Q Consensus        22 ~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i   90 (96)
                      .....++.||.+++|.|||++|++|++|+++|||+|++++. +..++.|+|.|++++|..|+.+|.+++
T Consensus         3 ~~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~-~~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD-SEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC-CSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             ceEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCC-CCCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            35678899999999999999999999999999999999874 345688999999999999999999875

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

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

Probab=99.72  E-value=4.2e-18  Score=101.27  Aligned_cols=72  Identities=22%  Similarity=0.306  Sum_probs=64.9

Q ss_pred             CCceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        20 ~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      ...+++.++.||.+++|.|||++|++|++|+++|||+|.+|+. ++.+..|+|+|++++|+.|+.+|.+++.+
T Consensus         6 ~~~~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-~~~~~~v~I~G~~~~V~~A~~~I~~~v~e   77 (91)
T d2ctka1           6 ALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP-ELQSDIIAITGLAANLDRAKAGLLERVKE   77 (91)
T ss_dssp             CSSCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT-TTTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             hhCCEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCC-CCCcceEEEECCHHHHHHHHHHHHHHHHH
Confidence            3458999999999999999999999999999999999999874 34467899999999999999999998753

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

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

Probab=99.72  E-value=3.3e-18  Score=99.96  Aligned_cols=72  Identities=19%  Similarity=0.311  Sum_probs=63.8

Q ss_pred             CCceeEEEEEeecCccceeeccchhHHHHHHHH-hCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRS-TGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        20 ~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~-tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      .....+.++.||..++|+||||+|++|++|+++ ++++|++++. +..++.|+|+|++++|.+|+.+|.+++++
T Consensus         6 ~~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~-~~~~~~v~I~G~~~~v~~A~~~I~~~v~e   78 (82)
T d2ctja1           6 LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-GSGSDTVVIRGPSSDVEKAKKQLLHLAEE   78 (82)
T ss_dssp             CCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-TTTCCEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hcCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCC-CCCCceEEEeCCHHHHHHHHHHHHHHHhh
Confidence            345678999999999999999999999999977 5999999874 34578999999999999999999998875

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

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

Probab=99.72  E-value=5.2e-18  Score=99.80  Aligned_cols=64  Identities=17%  Similarity=0.190  Sum_probs=59.3

Q ss_pred             EEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcCCC
Q psy2768          26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQPS   94 (96)
Q Consensus        26 ~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~   94 (96)
                      ..+.||.+.+|+|||+||++|++|+++|||+|+|++     ++.|+|+|+++++..|+.+|+.+++++.
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~-----~g~v~I~G~~e~v~~A~~~I~~i~~ea~   66 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ-----NGLIWVNGDRRKVSIAEEAIYLIEQEAH   66 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT-----TSEEEEESCHHHHHHHHHHHHHHHHCSC
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC-----CCEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            457899999999999999999999999999999986     4689999999999999999999988765

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

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

Probab=99.71  E-value=2.5e-18  Score=99.95  Aligned_cols=72  Identities=19%  Similarity=0.223  Sum_probs=63.6

Q ss_pred             CceeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEc-CHHHHHHHHHHHhHHhcCCCC
Q psy2768          21 EVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVG-SFFSVQETLKGCPNIVDQPSI   95 (96)
Q Consensus        21 ~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i~~~~~   95 (96)
                      ...++.+|.||.+++|.|||+||++|++|++.|||+|.+.+.   .++.|+|+| +++++++|+.+|+.+.+...+
T Consensus         5 ~~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~---~~g~v~I~g~~~eav~~A~~~Ie~~~~~~eV   77 (78)
T d2cpqa1           5 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE---DTGTFRIYGESADAVKKARGFLEFVEDFIQV   77 (78)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET---TTTEEEEEESSHHHHHHHHHHHSCCCCCCCC
T ss_pred             cCCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC---CCceEEEEECCHHHHHHHHHHHHHhheeecC
Confidence            457899999999999999999999999999999999998763   357899999 699999999999988776553

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

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

Probab=99.65  E-value=1.6e-16  Score=94.30  Aligned_cols=69  Identities=20%  Similarity=0.253  Sum_probs=62.1

Q ss_pred             CCceeEEEEEeecCccceeeccchhHHHHHHHHh-CCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcC
Q psy2768          20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRST-GSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQ   92 (96)
Q Consensus        20 ~~~~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~t-g~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   92 (96)
                      ....++.++.||..+++.|||+||++|++|++++ |++|.+++.    +..|+|+|++++|+.|+.+|.+++++
T Consensus        17 ~~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~~----~~~v~i~G~~~~ve~Ak~~I~~iv~e   86 (90)
T d2ctfa1          17 ANSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG----EDKITLEGPTEDVSVAQEQIEGMVKD   86 (90)
T ss_dssp             CCCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS----SCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             cCCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCCC----CceEEEeCCHHHHHHHHHHHHHHHHH
Confidence            3457899999999999999999999999999995 899999863    47899999999999999999998763

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

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

Probab=99.57  E-value=8.4e-17  Score=91.36  Aligned_cols=64  Identities=20%  Similarity=0.273  Sum_probs=51.3

Q ss_pred             EEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcC-HHHHHHHHHHHhHHhcCCCC
Q psy2768          27 ELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGS-FFSVQETLKGCPNIVDQPSI   95 (96)
Q Consensus        27 ~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~i~~~~~   95 (96)
                      -+.||.+.+|+||||+|++||.|+++|||+|+|++     +..|+|+|. ++++..|..+|..+.++..+
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~-----~g~v~I~g~~~~~v~~A~~~I~~i~~ea~~   68 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN-----NGRIWATCPSRFSEEILIEAIRKIENESHI   68 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECT-----TSEEEC-----CTTCCTHHHHTTTTTTTTC
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcC-----CCEEEEEeCCHHHHHHHHHHHHHHHHhhcc
Confidence            47899999999999999999999999999999975     467999995 68999999999998887653

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

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

Probab=99.54  E-value=9.4e-15  Score=86.07  Aligned_cols=64  Identities=14%  Similarity=0.146  Sum_probs=57.9

Q ss_pred             EEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcC-HHHHHHHHHHHhHHhcCCCC
Q psy2768          27 ELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGS-FFSVQETLKGCPNIVDQPSI   95 (96)
Q Consensus        27 ~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~i~~~~~   95 (96)
                      .+.||.+.+|.|||+||++|+.|+++|||+|.|.+     +..|.|.|+ .+.+..|+.+|..+.+++.+
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d-----~G~V~I~g~~~~~~~~A~~~I~~I~~ea~v   68 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR-----NGRIHLECPNEDLEAIAVMAIKIIDEEAYT   68 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET-----TTEEEEECSCHHHHHHHHHHHHHHHHCSCC
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC-----CcEEEEEeCCHHHHHHHHHHHHHHHHhchh
Confidence            47899999999999999999999999999999986     468999995 79999999999999887653

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

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

Probab=99.48  E-value=7.3e-15  Score=86.09  Aligned_cols=62  Identities=21%  Similarity=0.247  Sum_probs=52.1

Q ss_pred             EEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEE-----EcCHHHHHHHHHHHhHHhc
Q psy2768          26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHI-----VGSFFSVQETLKGCPNIVD   91 (96)
Q Consensus        26 ~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I-----~G~~~~v~~A~~~I~~~i~   91 (96)
                      +.+.||.+.+|.|||+||++||+|+++|||+|+|++..    ..+.+     .|.+.++.+|..+|.++..
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~----g~v~i~~~~~~~~~~a~~~a~~iI~aI~r   71 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTEN----SMVIVEPEAEGIPPVNLMKAAEVVKAISL   71 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTT----TEEEEEESSTTSCHHHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCC----CeEEEecCCccccHHHHHHHHHHHHHHhC
Confidence            46899999999999999999999999999999998643    33333     4678899999999988754

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

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

Probab=99.36  E-value=4.8e-13  Score=80.95  Aligned_cols=55  Identities=24%  Similarity=0.418  Sum_probs=49.4

Q ss_pred             ccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCHHHHHHHHHHHhHHhcCCC
Q psy2768          34 QVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSFFSVQETLKGCPNIVDQPS   94 (96)
Q Consensus        34 ~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~   94 (96)
                      ..|+|||+||++|+.|++.|||+|.|.+      ..+.+.|+++++..|+.+|..++..++
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~d------~~v~iig~~e~i~~A~~~Ie~li~~~e   77 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVGE------YEVAIIGDYERAMAAKQAIEMLAEGRM   77 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECS------SEEEEEEEHHHHHHHHHHHHHHHTTCC
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEeC------CeEEEEECchhHHHHHHHHHHHHcCCC
Confidence            4799999999999999999999999975      347778999999999999999998764

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

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

Probab=99.33  E-value=2.2e-14  Score=77.53  Aligned_cols=49  Identities=22%  Similarity=0.428  Sum_probs=16.1

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecCCCCCCceEEEEEcCH
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSF   76 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~~   76 (96)
                      +...++.||.+.+|.|||+||++||+|+++|||+|++.+     ++.|.|+|+.
T Consensus         2 P~~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d-----dg~v~I~a~~   50 (54)
T d1e3ha4           2 PRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED-----DGTIYIGAAD   50 (54)
T ss_dssp             CBCC---------------------CHHHHSCCCC-------------CCCCBS
T ss_pred             CeEEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC-----CeEEEEEecC
Confidence            445678999999999999999999999999999999985     5778887753

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

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

Probab=98.90  E-value=2e-09  Score=66.36  Aligned_cols=70  Identities=19%  Similarity=0.431  Sum_probs=55.1

Q ss_pred             eeEEEEEeecCc------cceeeccchhHHHHHHHHhCCeEEecCC----------C------C-CCceEEEEEcC-HHH
Q psy2768          23 RLTIELVVPSSQ------VGRIIGKGGQNVRELQRSTGSMIKLPNS----------F------N-EEETNVHIVGS-FFS   78 (96)
Q Consensus        23 ~~~~~~~ip~~~------vg~iIGkgG~~Ik~i~~~tg~~I~i~~~----------~------~-~~~~~v~I~G~-~~~   78 (96)
                      .++.++.||.+.      +|.|||++|++.|+|+++|||+|.|...          .      . ...--|.|+++ ++.
T Consensus         2 k~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~   81 (122)
T d1k1ga_           2 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN   81 (122)
T ss_dssp             CEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHH
T ss_pred             ceeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhh
Confidence            467788888765      8999999999999999999999999541          0      0 11234667774 589


Q ss_pred             HHHHHHHHhHHhcC
Q psy2768          79 VQETLKGCPNIVDQ   92 (96)
Q Consensus        79 v~~A~~~I~~~i~~   92 (96)
                      +..|+.+|..++..
T Consensus        82 ~~~A~~~i~~ll~~   95 (122)
T d1k1ga_          82 VKKAVEQIRNILKQ   95 (122)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999998853

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

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

Probab=98.64  E-value=4.4e-08  Score=61.11  Aligned_cols=69  Identities=25%  Similarity=0.380  Sum_probs=52.0

Q ss_pred             eEEEEEeec------CccceeeccchhHHHHHHHHhCCeEEecCCCC-------------------CCceEEEEEcCH--
Q psy2768          24 LTIELVVPS------SQVGRIIGKGGQNVRELQRSTGSMIKLPNSFN-------------------EEETNVHIVGSF--   76 (96)
Q Consensus        24 ~~~~~~ip~------~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~-------------------~~~~~v~I~G~~--   76 (96)
                      ++.++.||.      +++|.|||++|.++|+|+++|||+|.|.....                   ..+=-|.|+++.  
T Consensus         2 l~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~   81 (134)
T d2bl5a1           2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (134)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             cceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcH
Confidence            456777774      47899999999999999999999999966210                   123346777742  


Q ss_pred             ----HHHHHHHHHHhHHhcC
Q psy2768          77 ----FSVQETLKGCPNIVDQ   92 (96)
Q Consensus        77 ----~~v~~A~~~I~~~i~~   92 (96)
                          ..+..|+.+|..++..
T Consensus        82 ~~a~~kl~~A~~~I~~lL~p  101 (134)
T d2bl5a1          82 NRAELKLKRAVEEVKKLLVP  101 (134)
T ss_dssp             HHHHHHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHHHHHHHHHcCC
Confidence                3588999999997743

>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=97.31  E-value=0.0001  Score=40.40  Aligned_cols=38  Identities=37%  Similarity=0.539  Sum_probs=35.3

Q ss_pred             eEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768          24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN   61 (96)
Q Consensus        24 ~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~   61 (96)
                      -...+.||.+..+..|||+|.+++-..+-||.+|+|..
T Consensus        27 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          27 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             TEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            45788999999999999999999999999999999975

>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=97.24  E-value=8.7e-05  Score=40.61  Aligned_cols=39  Identities=38%  Similarity=0.457  Sum_probs=35.8

Q ss_pred             eeEEEEEeecCccceeeccchhHHHHHHHHhCCeEEecC
Q psy2768          23 RLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN   61 (96)
Q Consensus        23 ~~~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~   61 (96)
                      .-...+.||.+..+..|||+|.+++-..+-||.+|+|..
T Consensus        25 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~   63 (67)
T d2asba3          25 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG   63 (67)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEe
Confidence            446788999999999999999999999999999999975

>d2ja9a2 d.51.1.1 (A:152-236) Ribosomal RNA-processing protein 40, RRP40 {Saccharomyces cerevisiae [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Ribosomal RNA-processing protein 40, RRP40
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=96.67  E-value=0.0007  Score=38.43  Aligned_cols=59  Identities=5%  Similarity=-0.031  Sum_probs=48.0

Q ss_pred             EEEeecCccceeeccchh-HHHHHHHHhCCeEEecCCCCCCceEEEEEcC-HHHHHHHHHHHhHHh
Q psy2768          27 ELVVPSSQVGRIIGKGGQ-NVRELQRSTGSMIKLPNSFNEEETNVHIVGS-FFSVQETLKGCPNIV   90 (96)
Q Consensus        27 ~~~ip~~~vg~iIGkgG~-~Ik~i~~~tg~~I~i~~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~i   90 (96)
                      -+.||.+++.+++|++++ .++.|.+.+++.|-|-.     +..|-|.|. ++....+...|..+-
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~-----NGrIWi~~~~~~~~i~i~~aI~~~e   64 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGL-----NGKIWVKCEELSNTLACYRTIMECC   64 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEET-----TTEEEEECSSHHHHHHHHHHHHHHH
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEec-----CcEEEEECCCHHHHHHHHHHHHHHH
Confidence            467999999999999998 79999999999999997     578888884 566666666565543

>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=96.24  E-value=0.0028  Score=37.56  Aligned_cols=51  Identities=12%  Similarity=0.191  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHhcccC----------C-CCCceeEEEEEeecC-ccceeeccchhHHHHHHHHh
Q psy2768           3 QYLIFEKMREEGLFA----------G-ADEVRLTIELVVPSS-QVGRIIGKGGQNVRELQRST   53 (96)
Q Consensus         3 ~~~I~~k~~e~~~~~----------~-~~~~~~~~~~~ip~~-~vg~iIGkgG~~Ik~i~~~t   53 (96)
                      +..+|..+.+|.+.+          . ++.-.+...+.|+.+ +-+.|||++|++|++|...+
T Consensus        17 RE~il~~l~~EiPY~~~v~i~~~~~~~~~~~~I~a~I~V~~~sqk~IiIGk~G~~ik~I~~~a   79 (113)
T d1egaa2          17 REKLMRFLGAELPYSVTVEIERFVSNERGGYDINGLILVEREGQKKMVIGNKGAKIKTIGIEA   79 (113)
T ss_dssp             HHHHHHHHGGGCCTTEEEEEEEEECCSSCSEEEEEEEEESSHHHHHHHHCGGGHHHHHHHHHH
T ss_pred             HHHHHHhcccccCeEEEEEEEEEeecccceEEEEEEEEECCcchhhhhhcccchHHHHHHHHH
Confidence            456788888876422          1 223457788888854 45999999999998876543

>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=94.43  E-value=0.0091  Score=34.11  Aligned_cols=31  Identities=19%  Similarity=0.504  Sum_probs=25.8

Q ss_pred             EEEEEeecCccceeeccchhHHHHHHHHhCC
Q psy2768          25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGS   55 (96)
Q Consensus        25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~tg~   55 (96)
                      .+++.|....-|.|||++|+.|++|++.-.-
T Consensus        36 ~i~I~I~tarPGivIGrkG~~I~~L~~~l~k   66 (92)
T d1wh9a_          36 RTEIIILATRTQNVLGEKGRRIRELTAVVQK   66 (92)
T ss_dssp             CEEEEEEESCHHHHHCGGGHHHHHHHHHHHH
T ss_pred             eEEEEEEeCCCceeeccCchhHHHHHHHHHH
Confidence            4667888889999999999999999765543

>d1wf3a2 d.52.3.1 (A:181-298) GTPase Era C-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: GTPase Era C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=92.26  E-value=0.028  Score=33.33  Aligned_cols=38  Identities=26%  Similarity=0.484  Sum_probs=27.5

Q ss_pred             ceeEEEEEeecC-ccceeeccchhHHHHH--------HHHhCCeEEe
Q psy2768          22 VRLTIELVVPSS-QVGRIIGKGGQNVREL--------QRSTGSMIKL   59 (96)
Q Consensus        22 ~~~~~~~~ip~~-~vg~iIGkgG~~Ik~i--------~~~tg~~I~i   59 (96)
                      -.+...+.|+.+ +-+.|||++|++|++|        ++-+++++.+
T Consensus        48 l~I~~~I~V~~~sqK~IiIGk~G~~ik~Ig~~aR~~le~~~~~kV~L   94 (118)
T d1wf3a2          48 LYIKAILYVERPSQKAIVIGEGGRKIKEIGQATRKQLEALLGKKVYL   94 (118)
T ss_dssp             EEEEEEEEESSHHHHHHHHCGGGHHHHHHHHHHHHHHHHHHTSEEEE
T ss_pred             EEEEEEEEeCccchhhhhhccCchhHHHHHHHHHHHHHHHhCCCeEE
Confidence            356777888854 5589999999999865        4455666654

>d2uubc1 d.52.3.1 (C:2-106) Ribosomal protein S3 N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Ribosomal protein S3 N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=91.99  E-value=0.019  Score=33.38  Aligned_cols=29  Identities=28%  Similarity=0.626  Sum_probs=24.1

Q ss_pred             EEEEEeecCccceeeccchhHHHHHHHHh
Q psy2768          25 TIELVVPSSQVGRIIGKGGQNVRELQRST   53 (96)
Q Consensus        25 ~~~~~ip~~~vg~iIGkgG~~Ik~i~~~t   53 (96)
                      .+++.|....-|.|||++|+.|+.|+++-
T Consensus        62 ~i~I~I~tarPG~iIGkkG~~i~~L~~~l   90 (105)
T d2uubc1          62 NVAVTVHVAKPGVVIGRGGERIRVLREEL   90 (105)
T ss_dssp             CEECCEEESCHHHHHCSTTSHHHHHHHHH
T ss_pred             cEEEEEEECCCceEEcCCchhHHHHHHHH
Confidence            46677778889999999999998887653

>d2asba2 d.52.3.1 (A:184-262) 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=90.15  E-value=0.063  Score=29.62  Aligned_cols=28  Identities=32%  Similarity=0.461  Sum_probs=22.7

Q ss_pred             CccceeeccchhHHHHHHHHh-CCeEEec
Q psy2768          33 SQVGRIIGKGGQNVRELQRST-GSMIKLP   60 (96)
Q Consensus        33 ~~vg~iIGkgG~~Ik~i~~~t-g~~I~i~   60 (96)
                      +-+|+.+|.+|++|+.|.++. |-+|+|-
T Consensus        47 DpvGacvG~~GsRI~~I~~eL~gEkIDii   75 (79)
T d2asba2          47 NAKGACIGPMGQRVRNVMSELSGEKIDII   75 (79)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEE
T ss_pred             CceeEEECCCccHHHHHHHHhCCceEEEE
Confidence            457999999999999997776 5677663

>d1hh2p2 d.52.3.1 (P:199-276) 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=86.77  E-value=0.12  Score=28.36  Aligned_cols=27  Identities=22%  Similarity=0.613  Sum_probs=22.2

Q ss_pred             CccceeeccchhHHHHHHHHh-CCeEEe
Q psy2768          33 SQVGRIIGKGGQNVRELQRST-GSMIKL   59 (96)
Q Consensus        33 ~~vg~iIGkgG~~Ik~i~~~t-g~~I~i   59 (96)
                      +-+|+.+|.+|++|+.|.++. |-+|+|
T Consensus        47 DpvGacVG~~G~RI~~I~~eL~gEkIDi   74 (78)
T d1hh2p2          47 DPIGACIGEGGSRIAAILKELKGEKLDV   74 (78)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEE
T ss_pred             CeeEEEECCCchHHHHHHHHhCCceeEE
Confidence            457999999999999997776 566665

>d2qalc1 d.52.3.1 (C:1-105) Ribosomal protein S3 N-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: Ribosomal protein S3 N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=86.75  E-value=0.068  Score=30.91  Aligned_cols=27  Identities=30%  Similarity=0.657  Sum_probs=22.2

Q ss_pred             EEEEeecCccceeeccchhHHHHHHHH
Q psy2768          26 IELVVPSSQVGRIIGKGGQNVRELQRS   52 (96)
Q Consensus        26 ~~~~ip~~~vg~iIGkgG~~Ik~i~~~   52 (96)
                      +++.|-...-|.|||++|+.|.+|+..
T Consensus        63 i~V~I~tarPGviIG~~G~~i~~L~~~   89 (105)
T d2qalc1          63 IRVTIHTARPGIVIGKKGEDVEKLRKV   89 (105)
T ss_dssp             BCCEEEESCHHHHHCTTSHHHHHHHHH
T ss_pred             EEEEEEeCCCccEeccCcccHHHHHHH
Confidence            556777788899999999999887654