Psyllid ID: psy14680

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------
Protein Sequence
MRLKSPFIRADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGFEPSTSD
Secondary Structure (PSIPRED)
cccccccccccccEEEEEEEcccccEEEEccccHHHHHHHHHHccEEEEccccccccccccEEEEEEccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccEEEEEEEccHHHHHEEccccHHHHHHHHHcccEEEEccccccccccEEEEEEEEccccccccccc
Coil and Loop (DISEMBL)
mrlkspfiradgvcqikilvpsyaagaiigkggETIAQIQKDTgskikmskandfypVYQVITLFLlsrpgfepstsd
Flexible Loop (DISEMBL)
mrlkspfiradgvcqIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFllsrpgfepstsd
Low Complexity Region (SEG)
MRLKSPFIRADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGFEPSTSD
Disordered region (IsUnstruct)
******FIRADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLS**********
Disordered Region (DISOPRED)
****************KILVPSYAAGAIIGKGGETIAQIQKDTGS*IKMSKANDFYPVYQVITLFLLSR*********
Disordered Region (DISEMBL)
MRLKSPFIRADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGFEPSTSD
Disordered Region (DISPRO)
*********ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG*******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MRLKSPFIRADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGFEPSTSD
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	78	2.2.26 [Sep-21-2011]
Q9JKN6	507	RNA-binding protein Nova-	yes	N/A	0.602	0.092	0.659	3e-12
Q2PFW9	483	RNA-binding protein Nova-	N/A	N/A	0.602	0.097	0.659	3e-12
Q80WA4	474	RNA-binding protein Nova-	no	N/A	0.602	0.099	0.659	3e-12
Q9UNW9	492	RNA-binding protein Nova-	no	N/A	0.538	0.085	0.690	6e-12
P51513	510	RNA-binding protein Nova-	no	N/A	0.602	0.092	0.62	1e-10

>sp|Q9JKN6|NOVA1_MOUSE RNA-binding protein Nova-1 OS=Mus musculus GN=Nova1 PE=1 SV=2

 Score = 70.5 bits (171), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 31/47 (65%), Positives = 41/47 (87%)

Query: 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          DG   +K+L+PSYAAG+IIGKGG+TI Q+QK+TG+ IK+SK+ DFYP
Sbjct: 47 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP 93

Functions to regulate alternative splicing in neurons by binding pre-mRNA in a sequence-specific manner to activate exon inclusion. It binds specifically to the sequence UCAUY. Most likely acts to activate the inclusion of exon E3A in the glycine receptor alpha-2 chain and of exon E9 in gamma-aminobutyric-acid receptor gamma-2 subunit via a distal downstream UCAU-rich intronic splicing enhancer.
Mus musculus (taxid: 10090)

>sp|Q2PFW9|NOVA1_MACFA RNA-binding protein Nova-1 OS=Macaca fascicularis GN=NOVA1 PE=2 SV=1

 Score = 70.5 bits (171), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 31/47 (65%), Positives = 41/47 (87%)

Query: 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          DG   +K+L+PSYAAG+IIGKGG+TI Q+QK+TG+ IK+SK+ DFYP
Sbjct: 47 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP 93

May regulate RNA splicing or metabolism in a specific subset of developing neurons.

Macaca fascicularis (taxid: 9541)

>sp|Q80WA4|NOVA1_RAT RNA-binding protein Nova-1 (Fragment) OS=Rattus norvegicus GN=Nova1 PE=2 SV=1

 Score = 70.5 bits (171), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 31/47 (65%), Positives = 41/47 (87%)

Query: 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          DG   +K+L+PSYAAG+IIGKGG+TI Q+QK+TG+ IK+SK+ DFYP
Sbjct: 46 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP 92

Functions to regulate alternative splicing in neurons by binding pre-mRNA in a sequence-specific manner to activate exon inclusion. It binds specifically to the sequence UCAUY (By similarity). Acts to regulate a novel glycine receptor alpha-2 chain splice variant (alpha-2N) in developing spinal cord.

Rattus norvegicus (taxid: 10116)

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

 Score = 69.7 bits (169), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 29/42 (69%), Positives = 39/42 (92%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          +K+L+PSYAAG+IIGKGG+TI Q+QK+TG+ IK+SK+ DFYP
Sbjct: 35 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP 76

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

Homo sapiens (taxid: 9606)

>sp|P51513|NOVA1_HUMAN RNA-binding protein Nova-1 OS=Homo sapiens GN=NOVA1 PE=1 SV=1

 Score = 65.1 bits (157), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 31/50 (62%), Positives = 41/50 (82%), Gaps = 3/50 (6%)

Query: 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKI---KMSKANDFYP 57
          DG   +K+L+PSYAAG+IIGKGG+TI Q+QK+TG+ I   K+SK+ DFYP
Sbjct: 47 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKLSKSKDFYP 96

May regulate RNA splicing or metabolism in a specific subset of developing neurons.

Homo sapiens (taxid: 9606)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	78
242019024	319	polyrC binding protein, putative [Pedicu	0.653	0.159	0.730	1e-13
322780737	483	hypothetical protein SINV_05815 [Solenop	0.641	0.103	0.666	2e-13
345495410	533	PREDICTED: hypothetical protein LOC10011	0.602	0.088	0.708	6e-13
321468687	573	hypothetical protein DAPPUDRAFT_225024 [	0.705	0.095	0.696	6e-13
189239335	535	PREDICTED: similar to pasilla CG16765-PK	0.589	0.085	0.723	1e-12
270009705	564	hypothetical protein TcasGA2_TC008998 [T	0.589	0.081	0.723	1e-12
307213191	514	RNA-binding protein Nova-1 [Harpegnathos	0.589	0.089	0.702	1e-12
332026626	514	RNA-binding protein Nova-1 [Acromyrmex e	0.589	0.089	0.702	1e-12
307181420	514	RNA-binding protein Nova-1 [Camponotus f	0.589	0.089	0.702	2e-12
328784994	514	PREDICTED: RNA-binding protein Nova-2-li	0.589	0.089	0.702	2e-12

>gi|242019024|ref|XP_002429966.1| polyrC binding protein, putative [Pediculus humanus corporis] gi|212515021|gb|EEB17228.1| polyrC binding protein, putative [Pediculus humanus corporis]

 Score = 80.5 bits (197), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 38/52 (73%), Positives = 45/52 (86%), Gaps = 1/52 (1%)

Query: 7   FIRADGVC-QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
           F+  DG+   +KILVP  AAGAIIGKGGETIAQ+QKDTG+++KMSKANDFYP
Sbjct: 60  FLGGDGIVYHLKILVPCIAAGAIIGKGGETIAQLQKDTGARMKMSKANDFYP 111

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322780737|gb|EFZ09994.1| hypothetical protein SINV_05815 [Solenopsis invicta]

 Score = 79.7 bits (195), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 34/51 (66%), Positives = 44/51 (86%)

Query: 7  FIRADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          F+  DG   +K+LVP  AAGAIIGKGG+TIAQ+QKDTG+++KMSK++DFYP
Sbjct: 7  FVGGDGTYHLKVLVPGVAAGAIIGKGGDTIAQLQKDTGARVKMSKSHDFYP 57

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345495410|ref|XP_001602171.2| PREDICTED: hypothetical protein LOC100118119 [Nasonia vitripennis]

 Score = 78.2 bits (191), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 34/48 (70%), Positives = 42/48 (87%)

Query: 10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
           DG   +K+LVP  AAGAIIGKGGETIAQ+QKDTG+++KMSK++DFYP
Sbjct: 41 GDGTYHLKVLVPGVAAGAIIGKGGETIAQLQKDTGARVKMSKSHDFYP 88

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321468687|gb|EFX79671.1| hypothetical protein DAPPUDRAFT_225024 [Daphnia pulex]

 Score = 78.2 bits (191), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 39/56 (69%), Positives = 45/56 (80%), Gaps = 1/56 (1%)

Query: 2  RLKSPFIRADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          R KS F   DG   +K+LVPS AAGAIIGKGGETIAQ+QK+  ++IKMSKANDFYP
Sbjct: 45 RKKSHFT-GDGSIYLKVLVPSVAAGAIIGKGGETIAQVQKEVNARIKMSKANDFYP 99

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189239335|ref|XP_973573.2| PREDICTED: similar to pasilla CG16765-PK [Tribolium castaneum]

 Score = 77.0 bits (188), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 42/47 (89%)

Query: 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          DG    K+LVPS AAGAIIGKGGETIAQ+QK+TG+++KMSK++DFYP
Sbjct: 42 DGTYHFKVLVPSVAAGAIIGKGGETIAQLQKETGARVKMSKSHDFYP 88

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270009705|gb|EFA06153.1| hypothetical protein TcasGA2_TC008998 [Tribolium castaneum]

 Score = 77.0 bits (188), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 42/47 (89%)

Query: 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          DG    K+LVPS AAGAIIGKGGETIAQ+QK+TG+++KMSK++DFYP
Sbjct: 42 DGTYHFKVLVPSVAAGAIIGKGGETIAQLQKETGARVKMSKSHDFYP 88

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307213191|gb|EFN88688.1| RNA-binding protein Nova-1 [Harpegnathos saltator]

 Score = 77.0 bits (188), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 33/47 (70%), Positives = 42/47 (89%)

Query: 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          DG   +K+LVP  AAGAIIGKGG+TIAQ+QKDTG+++KMSK++DFYP
Sbjct: 42 DGTYHLKVLVPGVAAGAIIGKGGDTIAQLQKDTGARVKMSKSHDFYP 88

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332026626|gb|EGI66735.1| RNA-binding protein Nova-1 [Acromyrmex echinatior]

 Score = 77.0 bits (188), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 33/47 (70%), Positives = 42/47 (89%)

Query: 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          DG   +K+LVP  AAGAIIGKGG+TIAQ+QKDTG+++KMSK++DFYP
Sbjct: 42 DGTYHLKVLVPGVAAGAIIGKGGDTIAQLQKDTGARVKMSKSHDFYP 88

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307181420|gb|EFN69015.1| RNA-binding protein Nova-1 [Camponotus floridanus]

 Score = 76.6 bits (187), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 33/47 (70%), Positives = 42/47 (89%)

Query: 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          DG   +K+LVP  AAGAIIGKGG+TIAQ+QKDTG+++KMSK++DFYP
Sbjct: 42 DGTYHLKVLVPGVAAGAIIGKGGDTIAQLQKDTGARVKMSKSHDFYP 88

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328784994|ref|XP_003250531.1| PREDICTED: RNA-binding protein Nova-2-like [Apis mellifera]

 Score = 76.6 bits (187), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 33/47 (70%), Positives = 42/47 (89%)

Query: 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          DG   +K+LVP  AAGAIIGKGG+TIAQ+QKDTG+++KMSK++DFYP
Sbjct: 42 DGTYHLKVLVPGVAAGAIIGKGGDTIAQLQKDTGARVKMSKSHDFYP 88

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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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	78
UNIPROTKB|F8VWX1	173	NOVA1 "RNA-binding protein Nov	0.628	0.283	0.653	1e-13
UNIPROTKB|F8VYI3	121	NOVA1 "RNA-binding protein Nov	0.602	0.388	0.659	2.7e-13
UNIPROTKB|F8W659	211	NOVA1 "RNA-binding protein Nov	0.602	0.222	0.659	2.7e-13
UNIPROTKB|I3L2B5	152	NOVA1 "RNA-binding protein Nov	0.602	0.309	0.659	2.7e-13
UNIPROTKB|D4A6P7	155	Nova1 "RNA-binding protein Nov	0.602	0.303	0.659	2.7e-13
UNIPROTKB|J3KQU3	277	NOVA1 "RNA-binding protein Nov	0.602	0.169	0.659	3.3e-13
UNIPROTKB|F1NP95	345	NOVA1 "Uncharacterized protein	0.602	0.136	0.659	8.8e-13
RGD|621345	474	Nova1 "neuro-oncological ventr	0.602	0.099	0.659	1.9e-12
UNIPROTKB|F1LMZ7	474	Nova1 "RNA-binding protein Nov	0.602	0.099	0.659	1.9e-12
UNIPROTKB|D3DS81	483	NOVA1 "Neuro-oncological ventr	0.602	0.097	0.659	2e-12

UNIPROTKB|F8VWX1 NOVA1 "RNA-binding protein Nova-1" [Homo sapiens (taxid:9606)]

 Score = 178 (67.7 bits), Expect = 1.0e-13, P = 1.0e-13
 Identities = 32/49 (65%), Positives = 42/49 (85%)

Query:     9 RADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
             R DG   +K+L+PSYAAG+IIGKGG+TI Q+QK+TG+ IK+SK+ DFYP
Sbjct:     8 REDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP 56

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F8VYI3 NOVA1 "RNA-binding protein Nova-1" [Homo sapiens (taxid:9606)]

 Score = 174 (66.3 bits), Expect = 2.7e-13, P = 2.7e-13
 Identities = 31/47 (65%), Positives = 41/47 (87%)

Query:    11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
             DG   +K+L+PSYAAG+IIGKGG+TI Q+QK+TG+ IK+SK+ DFYP
Sbjct:    47 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP 93

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F8W659 NOVA1 "RNA-binding protein Nova-1" [Homo sapiens (taxid:9606)]

 Score = 174 (66.3 bits), Expect = 2.7e-13, P = 2.7e-13
 Identities = 31/47 (65%), Positives = 41/47 (87%)

Query:    11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
             DG   +K+L+PSYAAG+IIGKGG+TI Q+QK+TG+ IK+SK+ DFYP
Sbjct:    47 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP 93

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|I3L2B5 NOVA1 "RNA-binding protein Nova-1" [Homo sapiens (taxid:9606)]

 Score = 174 (66.3 bits), Expect = 2.7e-13, P = 2.7e-13
 Identities = 31/47 (65%), Positives = 41/47 (87%)

Query:    11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
             DG   +K+L+PSYAAG+IIGKGG+TI Q+QK+TG+ IK+SK+ DFYP
Sbjct:    47 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP 93

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|D4A6P7 Nova1 "RNA-binding protein Nova-1" [Rattus norvegicus (taxid:10116)]

 Score = 174 (66.3 bits), Expect = 2.7e-13, P = 2.7e-13
 Identities = 31/47 (65%), Positives = 41/47 (87%)

Query:    11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
             DG   +K+L+PSYAAG+IIGKGG+TI Q+QK+TG+ IK+SK+ DFYP
Sbjct:    46 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP 92

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|J3KQU3 NOVA1 "RNA-binding protein Nova-1" [Homo sapiens (taxid:9606)]

 Score = 174 (66.3 bits), Expect = 3.3e-13, P = 3.3e-13
 Identities = 31/47 (65%), Positives = 41/47 (87%)

Query:    11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
             DG   +K+L+PSYAAG+IIGKGG+TI Q+QK+TG+ IK+SK+ DFYP
Sbjct:     6 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP 52

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F1NP95 NOVA1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 174 (66.3 bits), Expect = 8.8e-13, P = 8.8e-13
 Identities = 31/47 (65%), Positives = 41/47 (87%)

Query:    11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
             DG   +K+L+PSYAAG+IIGKGG+TI Q+QK+TG+ IK+SK+ DFYP
Sbjct:    30 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP 76

GO:0003723 "RNA binding" evidence=IEA

RGD|621345 Nova1 "neuro-oncological ventral antigen 1" [Rattus norvegicus (taxid:10116)]

 Score = 174 (66.3 bits), Expect = 1.9e-12, P = 1.9e-12
 Identities = 31/47 (65%), Positives = 41/47 (87%)

Query:    11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
             DG   +K+L+PSYAAG+IIGKGG+TI Q+QK+TG+ IK+SK+ DFYP
Sbjct:    46 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP 92

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

GO:0003723 "RNA binding" evidence=IEA

GO:0003729 "mRNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=IEA

GO:0007399 "nervous system development" evidence=IDA

UNIPROTKB|F1LMZ7 Nova1 "RNA-binding protein Nova-1" [Rattus norvegicus (taxid:10116)]

 Score = 174 (66.3 bits), Expect = 1.9e-12, P = 1.9e-12
 Identities = 31/47 (65%), Positives = 41/47 (87%)

Query:    11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
             DG   +K+L+PSYAAG+IIGKGG+TI Q+QK+TG+ IK+SK+ DFYP
Sbjct:    46 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP 92

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|D3DS81 NOVA1 "Neuro-oncological ventral antigen 1, isoform CRA_a" [Homo sapiens (taxid:9606)]

 Score = 174 (66.3 bits), Expect = 2.0e-12, P = 2.0e-12
 Identities = 31/47 (65%), Positives = 41/47 (87%)

Query:    11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
             DG   +K+L+PSYAAG+IIGKGG+TI Q+QK+TG+ IK+SK+ DFYP
Sbjct:    47 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP 93

GO:0003723 "RNA binding" evidence=IEA

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9JKN6	NOVA1_MOUSE	No assigned EC number	0.6595	0.6025	0.0927	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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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	78
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	5e-13
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	6e-10
pfam00013	59	pfam00013, KH_1, KH domain	4e-09
smart00322	68	smart00322, KH, K homology RNA-binding domain	5e-08
pfam13014	42	pfam13014, KH_3, KH domain	4e-07
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	8e-05
cd02409	68	cd02409, KH-II, KH-II (K homology RNA-binding doma	5e-04
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	0.001
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	0.002
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	0.002

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

 Score = 57.1 bits (139), Expect = 5e-13
 Identities = 21/37 (56%), Positives = 32/37 (86%)

Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK 51
           +++LVPS  AG+IIGKGG TI +I+++TG+KI++SK
Sbjct: 1  TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSK 37

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

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

 Score = 49.5 bits (119), Expect = 6e-10
 Identities = 19/39 (48%), Positives = 28/39 (71%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
           ++LVPS   G IIGKGG TI +I+++TG+KIK+  +  
Sbjct: 2  ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS 40

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 = 47.2 bits (113), Expect = 4e-09
 Identities = 16/36 (44%), Positives = 24/36 (66%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK 51
           +IL+P    G IIGKGG  I +I+++TG KI++  
Sbjct: 2  ERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPD 37

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 = 44.6 bits (106), Expect = 5e-08
 Identities = 17/40 (42%), Positives = 26/40 (65%)

Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
           I++L+P+   G IIGKGG TI +I+++TG KI +     
Sbjct: 4  TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS 43

Length = 68

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

 Score = 41.8 bits (99), Expect = 4e-07
 Identities = 17/30 (56%), Positives = 24/30 (80%)

Query: 25 AGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
           GAIIGKGGETI +I+++TG+KI++ K   
Sbjct: 2  VGAIIGKGGETIKEIREETGAKIQIPKPEP 31

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

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

 Score = 38.5 bits (91), Expect = 8e-05
 Identities = 11/22 (50%), Positives = 17/22 (77%)

Query: 26  GAIIGKGGETIAQIQKDTGSKI 47
             +IG GG+TI +I ++TG+KI
Sbjct: 566 RDVIGPGGKTIREITEETGAKI 587

Length = 693

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

 Score = 34.5 bits (80), Expect = 5e-04
 Identities = 12/45 (26%), Positives = 20/45 (44%)

Query: 7  FIRADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK 51
            R     +I I+V     G +IGK G+ I  +QK     ++  +
Sbjct: 18 IERTPDRIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLLRKKR 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|239087 cd02394, vigilin_like_KH, K homology RNA-binding domain_vigilin_like

 Score = 33.3 bits (77), Expect = 0.001
 Identities = 11/27 (40%), Positives = 15/27 (55%)

Query: 28 IIGKGGETIAQIQKDTGSKIKMSKAND 54
          IIGK G  I +I ++TG KI+      
Sbjct: 14 IIGKKGSNIRKIMEETGVKIRFPDPGS 40

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

 Score = 32.5 bits (75), Expect = 0.002
 Identities = 11/22 (50%), Positives = 16/22 (72%)

Query: 26 GAIIGKGGETIAQIQKDTGSKI 47
            +IG GG+TI +I ++TG KI
Sbjct: 14 RDVIGPGGKTIKKIIEETGVKI 35

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

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

 Score = 34.4 bits (80), Expect = 0.002
 Identities = 10/22 (45%), Positives = 16/22 (72%)

Query: 26  GAIIGKGGETIAQIQKDTGSKI 47
             +IG GG+ I +I ++TG+KI
Sbjct: 563 RDVIGPGGKVIREITEETGAKI 584

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	78
KOG2191|consensus	402		99.66
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.65
PF13014	43	KH_3: KH domain	99.53
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.46
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.44
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.4
KOG2190|consensus	485		99.38
KOG1676|consensus	600		99.37
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.36
KOG2191|consensus	402		99.23
KOG2193|consensus	584		99.19
smart00322	69	KH K homology RNA-binding domain.	99.16
KOG1676|consensus	600		99.15
KOG2192|consensus	390		99.13
KOG2193|consensus	584		99.02
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.91
KOG2190|consensus	485		98.78
KOG2192|consensus	390		98.76
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	98.57
PRK13763	180	putative RNA-processing protein; Provisional	98.5
KOG1588|consensus	259		98.42
KOG0336|consensus	629		98.37
PRK13763	180	putative RNA-processing protein; Provisional	98.34
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	98.3
KOG0119|consensus	554		98.23
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	98.16
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.08
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.03
COG5176	269	MSL5 Splicing factor (branch point binding protein	97.95
PRK00468	75	hypothetical protein; Provisional	97.7
PRK02821	77	hypothetical protein; Provisional	97.57
PRK01064	78	hypothetical protein; Provisional	97.5
COG1837	76	Predicted RNA-binding protein (contains KH domain)	97.43
KOG2113|consensus	394		97.39
KOG2279|consensus	608		97.38
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	97.24
PRK12704	520	phosphodiesterase; Provisional	97.2
PRK08406	140	transcription elongation factor NusA-like protein;	97.15
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	97.13
KOG2814|consensus	345		97.12
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.11
COG1094	194	Predicted RNA-binding protein (contains KH domains	97.02
PRK00106	535	hypothetical protein; Provisional	97.0
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	96.93
PRK08406	140	transcription elongation factor NusA-like protein;	96.91
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	96.67
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	96.49
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	96.48
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	96.47
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.43
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	96.38
PRK12705	508	hypothetical protein; Provisional	96.35
KOG4369|consensus	2131		96.31
COG1094	194	Predicted RNA-binding protein (contains KH domains	96.18
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	96.17
PRK12328	374	nusA transcription elongation factor NusA; Provisi	95.91
TIGR01953	341	NusA transcription termination factor NusA. This m	95.82
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	95.81
PRK13764	602	ATPase; Provisional	95.75
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	95.73
COG1855	604	ATPase (PilT family) [General function prediction	95.61
COG0195	190	NusA Transcription elongation factor [Transcriptio	95.5
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.2
PRK09202	470	nusA transcription elongation factor NusA; Validat	95.19
KOG2279|consensus	608		95.1
PRK06418	166	transcription elongation factor NusA-like protein;	94.85
KOG2208|consensus	753		94.69
cd02412	109	30S_S3_KH K homology RNA-binding (KH) domain of th	94.67
cd02411	85	archeal_30S_S3_KH K homology RNA-binding domain (K	94.66
PRK12329	449	nusA transcription elongation factor NusA; Provisi	94.43
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	94.36
COG0092	233	RpsC Ribosomal protein S3 [Translation, ribosomal	93.95
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	93.92
KOG2113|consensus	394		93.82
COG0195	190	NusA Transcription elongation factor [Transcriptio	93.44
TIGR00436	270	era GTP-binding protein Era. Era is an essential G	93.03
PRK15494	339	era GTPase Era; Provisional	92.15
PRK00089	292	era GTPase Era; Reviewed	91.78
COG1159	298	Era GTPase [General function prediction only]	90.36
TIGR01008	195	rpsC_E_A ribosomal protein S3, eukaryotic/archaeal	89.52
PRK04191	207	rps3p 30S ribosomal protein S3P; Reviewed	89.45
KOG3273|consensus	252		89.11
CHL00048	214	rps3 ribosomal protein S3	89.04
PRK12327	362	nusA transcription elongation factor NusA; Provisi	88.46
KOG1423|consensus	379		88.41
PTZ00084	220	40S ribosomal protein S3; Provisional	88.39
KOG2208|consensus	753		88.37
TIGR01953	341	NusA transcription termination factor NusA. This m	87.9
TIGR03675	630	arCOG00543 arCOG00543 universal archaeal KH-domain	86.88
COG1847	208	Jag Predicted RNA-binding protein [General functio	86.3
PRK12329	449	nusA transcription elongation factor NusA; Provisi	86.07
PRK12328	374	nusA transcription elongation factor NusA; Provisi	84.92
PRK09202	470	nusA transcription elongation factor NusA; Validat	83.81
TIGR01009	211	rpsC_bact ribosomal protein S3, bacterial type. TI	83.46
COG1782	637	Predicted metal-dependent RNase, consists of a met	82.13

>KOG2191|consensus

Probab=99.66  E-value=2e-16  Score=114.39  Aligned_cols=66  Identities=47%  Similarity=0.752  Sum_probs=60.2

Q ss_pred             CcccCCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680          6 PFIRADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus         6 ~~~~~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ++.-.++...++++||+..+|.||||||++|.+|+++|||+|++++..||+||++||+|.|+|+-+
T Consensus        31 ~n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~e   96 (402)
T KOG2191|consen   31 TNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVE   96 (402)
T ss_pred             ccCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHH
Confidence            443345569999999999999999999999999999999999999999999999999999999854

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.65  E-value=1.6e-16  Score=90.47  Aligned_cols=56  Identities=41%  Similarity=0.662  Sum_probs=50.8

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      +++|+||.+.+|.||||+|++|++|+++|||+|++.+..+  ++..+|.|+|.|++++
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~--~~~~~r~v~I~G~~~~   56 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL--PGSTERVVTISGKPSA   56 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC--CCCCceEEEEEeCHHH
Confidence            3789999999999999999999999999999999997653  5789999999999764

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

>PF13014 KH_3: KH domain

Probab=99.53  E-value=2.3e-14  Score=75.73  Aligned_cols=43  Identities=35%  Similarity=0.548  Sum_probs=39.1

Q ss_pred             ceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEec
Q psy14680         24 AAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLS   68 (78)
Q Consensus        24 ~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G   68 (78)
                      ++|+||||+|++|++|+++|||+|+|++  +..++..+|.|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~--~~~~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPP--ENEPGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECC--ccCCCCCceEEEEEC
Confidence            5899999999999999999999999998  335788999999997

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.46  E-value=3.1e-14  Score=79.85  Aligned_cols=52  Identities=25%  Similarity=0.345  Sum_probs=47.0

Q ss_pred             EEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        16 ~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      .++.||.+++|.|||++|++|++|+++|||+|++++..     ..++.|+|+|++++
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-----~~~~~v~I~G~~~~   53 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-----SKSDTITITGPKEN   53 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-----CCCCEEEEEcCHHH
Confidence            57899999999999999999999999999999999754     57899999999653

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

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

Probab=99.44  E-value=1.8e-13  Score=76.28  Aligned_cols=53  Identities=38%  Similarity=0.613  Sum_probs=47.7

Q ss_pred             EEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        16 ~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      .++.||..++|.|||++|++|++|+++|||+|.|++..+   +..++.|.|.|+++
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~---~~~~~~v~i~G~~~   54 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS---GSEERIVTITGTPE   54 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC---CCCceEEEEEcCHH
Confidence            689999999999999999999999999999999997542   56899999999854

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.

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.40  E-value=8.2e-14  Score=77.64  Aligned_cols=51  Identities=33%  Similarity=0.497  Sum_probs=45.3

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      +.+|.||.+++|+|||++|++|++|+++|||+|+++++     + .+..|+|+|+++
T Consensus         1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~-----~-~~~~v~I~G~~~   51 (60)
T PF00013_consen    1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD-----D-ERDIVTISGSPE   51 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST-----T-EEEEEEEEESHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC-----C-CcEEEEEEeCHH
Confidence            57899999999999999999999999999999999854     2 455999999654

; 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 ....

>KOG2190|consensus

Probab=99.38  E-value=7.1e-13  Score=99.87  Aligned_cols=58  Identities=33%  Similarity=0.578  Sum_probs=54.4

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      ..+++|+||.+++|.||||+|+.||+|+++|||+|+|..+  ++|..++|.|+|.|.|+.
T Consensus       137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~--~lP~ster~V~IsG~~~a  194 (485)
T KOG2190|consen  137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD--MLPNSTERAVTISGEPDA  194 (485)
T ss_pred             ceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC--CCCcccceeEEEcCchHH
Confidence            4789999999999999999999999999999999999986  589999999999999864

>KOG1676|consensus

Probab=99.37  E-value=6.2e-13  Score=101.36  Aligned_cols=58  Identities=31%  Similarity=0.497  Sum_probs=53.3

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      ..++++.||.+.||.||||+|++||+|+.+||+||+|.++.+  +.+.||.+.|.|+++.
T Consensus       229 ~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~--p~speR~~~IiG~~d~  286 (600)
T KOG1676|consen  229 SATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD--PSSPERPAQIIGTVDQ  286 (600)
T ss_pred             cceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCC--CCCccceeeeecCHHH
Confidence            458999999999999999999999999999999999999775  5789999999999763

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

Probab=99.36  E-value=2e-12  Score=73.12  Aligned_cols=46  Identities=28%  Similarity=0.481  Sum_probs=41.9

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEecc
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSR   69 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~   69 (78)
                      ...+.||.+++|+||||+|++|++|+++|||+|.|++         ++.|.|+|+
T Consensus         3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~---------~g~v~I~G~   48 (61)
T cd02393           3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED---------DGTVYIAAS   48 (61)
T ss_pred             EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC---------CCEEEEEeC
Confidence            5678999999999999999999999999999999984         346999996

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.

>KOG2191|consensus

Probab=99.23  E-value=1.3e-11  Score=89.68  Aligned_cols=59  Identities=39%  Similarity=0.485  Sum_probs=53.3

Q ss_pred             eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      .++++++|++.+|.||||+|.+||.+++++||.|+|++.....-+..||++++.|.|++
T Consensus       132 kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~  190 (402)
T KOG2191|consen  132 KQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQ  190 (402)
T ss_pred             ceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHH
Confidence            56999999999999999999999999999999999996544456789999999999864

>KOG2193|consensus

Probab=99.19  E-value=6.3e-12  Score=93.77  Aligned_cols=61  Identities=28%  Similarity=0.475  Sum_probs=55.7

Q ss_pred             CCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        10 ~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      .++...++|+||...||+|||++|.+||+|.+.+||.|+|.+++  .+...+|+|+|+|.|+.
T Consensus       407 ~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE--~pdvseRMViItGppea  467 (584)
T KOG2193|consen  407 NPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPE--IPDVSERMVIITGPPEA  467 (584)
T ss_pred             CcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCC--CCCcceeEEEecCChHH
Confidence            35678899999999999999999999999999999999999875  57789999999999863

>smart00322 KH K homology RNA-binding domain

Probab=99.16  E-value=8.5e-11  Score=64.74  Aligned_cols=54  Identities=33%  Similarity=0.582  Sum_probs=47.2

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ....++.||...+|.+||++|++|++|++.|||+|.+....     .....+.|.|.++
T Consensus         2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-----~~~~~v~i~g~~~   55 (69)
T smart00322        2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-----SEERVVEITGPPE   55 (69)
T ss_pred             ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-----CCccEEEEEcCHH
Confidence            35789999999999999999999999999999999998543     2678899999853

>KOG1676|consensus

Probab=99.15  E-value=5.9e-11  Score=90.72  Aligned_cols=62  Identities=31%  Similarity=0.439  Sum_probs=55.9

Q ss_pred             CCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        10 ~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      +...++.++.||++.+|+||||+|++||+|+++|||++++.++++..++ .++.+.|+|+|+.
T Consensus       135 ~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~-~~KplritGdp~~  196 (600)
T KOG1676|consen  135 GSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG-ADKPLRITGDPDK  196 (600)
T ss_pred             CccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC-CCCceeecCCHHH
Confidence            4567899999999999999999999999999999999999998865444 8899999999975

>KOG2192|consensus

Probab=99.13  E-value=7.1e-11  Score=84.37  Aligned_cols=61  Identities=23%  Similarity=0.406  Sum_probs=54.4

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCCCC
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGFEP   74 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~~~   74 (78)
                      ....+..+.||.+.-|.||||+|.+|++|++++||.|.+..+   ..|+.||+++|+|+-++-+
T Consensus       312 GPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikidep---leGsedrIitItGTqdQIq  372 (390)
T KOG2192|consen  312 GPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITITGTQDQIQ  372 (390)
T ss_pred             CceeeeeEecccccCcceecccchhhhhhhhccCceEEecCc---CCCCCceEEEEeccHHHHh
Confidence            446788999999999999999999999999999999999854   4689999999999976544

>KOG2193|consensus

Probab=99.02  E-value=2.1e-10  Score=85.78  Aligned_cols=63  Identities=30%  Similarity=0.378  Sum_probs=57.1

Q ss_pred             CCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCCCC
Q psy14680         10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGFEP   74 (78)
Q Consensus        10 ~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~~~   74 (78)
                      ..-..++|++||..++|+||||.|++||.|.+.|.|+|.|.+...  .|..||.++|.|+|+..+
T Consensus       195 q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken--~Gaaek~itvh~tpEg~s  257 (584)
T KOG2193|consen  195 QLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKEN--AGAAEKIITVHSTPEGTS  257 (584)
T ss_pred             cccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeeccc--CCcccCceEEecCccchH
Confidence            345688999999999999999999999999999999999998763  699999999999998754

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

Probab=98.91  E-value=4.8e-09  Score=66.56  Aligned_cols=38  Identities=34%  Similarity=0.652  Sum_probs=33.3

Q ss_pred             EEEecC------CceeeEEecCCchHHHHHHHhCCeEEEecCCC
Q psy14680         17 KILVPS------YAAGAIIGKGGETIAQIQKDTGSKIKMSKAND   54 (78)
Q Consensus        17 ~l~vP~------~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~   54 (78)
                      +++||.      .++|.|||++|++||+|+++|||+|.|..++.
T Consensus         3 ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs   46 (120)
T cd02395           3 KVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGS   46 (120)
T ss_pred             EEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcc
Confidence            455655      78999999999999999999999999998754

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

>KOG2190|consensus

Probab=98.78  E-value=1.7e-08  Score=76.41  Aligned_cols=56  Identities=27%  Similarity=0.453  Sum_probs=50.3

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEecc
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSR   69 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~   69 (78)
                      +...++|++++...+|.||||+|..||+||++|.++|.|...   .++..||+++|+|.
T Consensus        40 ~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~---~~~c~eRIiti~g~   95 (485)
T KOG2190|consen   40 DETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNES---LPGCPERIITITGN   95 (485)
T ss_pred             CCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecC---CCCCCcceEEEecc
Confidence            444558999999999999999999999999999999999854   47899999999994

>KOG2192|consensus

Probab=98.76  E-value=1.6e-08  Score=72.46  Aligned_cols=54  Identities=26%  Similarity=0.434  Sum_probs=48.8

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEecc
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSR   69 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~   69 (78)
                      ...+.+++++.+..+|+||||+|+|||.|+.+.+|.|+|++.     +.++|+++|+.+
T Consensus        45 ~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds-----~~peri~tisad   98 (390)
T KOG2192|consen   45 RSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS-----SGPERILTISAD   98 (390)
T ss_pred             hcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC-----CCCceeEEEecc
Confidence            456899999999999999999999999999999999999964     468999999764

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=98.57  E-value=2.1e-08  Score=66.68  Aligned_cols=34  Identities=38%  Similarity=0.723  Sum_probs=32.5

Q ss_pred             EEecCCceeeEEecCCchHHHHHHHhCCeEEEec
Q psy14680         18 ILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK   51 (78)
Q Consensus        18 l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~   51 (78)
                      +.||.+.+|.|||++|++|+.|+++|||+|++.+
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~   35 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS   35 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc
Confidence            5789999999999999999999999999999995

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

>PRK13763 putative RNA-processing protein; Provisional

Probab=98.50  E-value=8.1e-08  Score=64.34  Aligned_cols=46  Identities=26%  Similarity=0.423  Sum_probs=40.2

Q ss_pred             eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEe
Q psy14680         14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLL   67 (78)
Q Consensus        14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~   67 (78)
                      ....+.||.+.+|.|||++|++|+.|+++|||+|++..+        +..|.|.
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~--------~g~V~I~   48 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE--------TGEVIIE   48 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC--------CCeEEEE
Confidence            467899999999999999999999999999999999853        2456675

>KOG1588|consensus

Probab=98.42  E-value=5.2e-07  Score=63.72  Aligned_cols=46  Identities=26%  Similarity=0.462  Sum_probs=41.0

Q ss_pred             CCCeeEEEEEecC------CceeeEEecCCchHHHHHHHhCCeEEEecCCCC
Q psy14680         10 ADGVCQIKILVPS------YAAGAIIGKGGETIAQIQKDTGSKIKMSKANDF   55 (78)
Q Consensus        10 ~~~~~~~~l~vP~------~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~   55 (78)
                      .....+.+++||.      ++||.|+|..|.++|+|+++|||+|-|.-.++.
T Consensus        88 ~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSm  139 (259)
T KOG1588|consen   88 KPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSM  139 (259)
T ss_pred             CceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcc
Confidence            4567889999987      599999999999999999999999999987753

>KOG0336|consensus

Probab=98.37  E-value=2.5e-07  Score=69.83  Aligned_cols=57  Identities=25%  Similarity=0.443  Sum_probs=49.9

Q ss_pred             cccCCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEecc
Q psy14680          7 FIRADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSR   69 (78)
Q Consensus         7 ~~~~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~   69 (78)
                      ...|.+.+++.+.|-+.+||.+||++|++||.||..|+++|+|.+..      .+-.|+|.|.
T Consensus        40 ~aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~------~e~kv~ifg~   96 (629)
T KOG0336|consen   40 AAAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD------LEVKVTIFGI   96 (629)
T ss_pred             cccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC------ceeEEEEech
Confidence            34567889999999999999999999999999999999999999754      5777888774

>PRK13763 putative RNA-processing protein; Provisional

Probab=98.34  E-value=2.6e-07  Score=61.89  Aligned_cols=40  Identities=33%  Similarity=0.458  Sum_probs=34.3

Q ss_pred             CceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         23 YAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        23 ~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      ...|+|||++|++++.|+..|||+|+|..          +.+.|.|+|+.
T Consensus       104 r~~griIG~~G~~~k~ie~~t~~~i~i~~----------~~v~i~G~~~~  143 (180)
T PRK13763        104 RIKGRIIGEGGKTRRIIEELTGVDISVYG----------KTVAIIGDPEQ  143 (180)
T ss_pred             HHhhheeCCCcHHHHHHHHHHCcEEEEcC----------CEEEEEeCHHH
Confidence            46899999999999999999999999973          23888897753

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=98.30  E-value=3e-07  Score=61.20  Aligned_cols=40  Identities=33%  Similarity=0.430  Sum_probs=35.2

Q ss_pred             CceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         23 YAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        23 ~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      ..+|+|||++|++++.|+..|||+|.|..          +.|.|.|+|++
T Consensus        98 ~~~griIG~~G~t~~~ie~~t~~~i~i~~----------~~v~i~G~~~~  137 (172)
T TIGR03665        98 RIKGRIIGEGGKTRRIIEELTGVSISVYG----------KTVGIIGDPEQ  137 (172)
T ss_pred             HHHhhhcCCCcHHHHHHHHHHCCeEEEcC----------CEEEEECCHHH
Confidence            36899999999999999999999999972          56999998754

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

>KOG0119|consensus

Probab=98.23  E-value=1.7e-06  Score=65.70  Aligned_cols=42  Identities=29%  Similarity=0.499  Sum_probs=38.1

Q ss_pred             eeEEEEEecC------CceeeEEecCCchHHHHHHHhCCeEEEecCCC
Q psy14680         13 VCQIKILVPS------YAAGAIIGKGGETIAQIQKDTGSKIKMSKAND   54 (78)
Q Consensus        13 ~~~~~l~vP~------~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~   54 (78)
                      .++-+++||.      ++||+|||.+|.|.|+|+++|||||.|.-.+.
T Consensus       137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgS  184 (554)
T KOG0119|consen  137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGS  184 (554)
T ss_pred             ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEecccc
Confidence            7888999986      79999999999999999999999999987553

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

Probab=98.16  E-value=4.7e-06  Score=46.89  Aligned_cols=37  Identities=32%  Similarity=0.540  Sum_probs=34.5

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEE
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKM   49 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i   49 (78)
                      .....+.||.+..|..|||+|.+|+.+++.+|.+|.|
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            4688999999999999999999999999999998876

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.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.08  E-value=7.2e-06  Score=64.74  Aligned_cols=42  Identities=31%  Similarity=0.527  Sum_probs=37.6

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN   53 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~   53 (78)
                      -.....+.||.+.+|.|||+||.+||.|+++||++|.|.+++
T Consensus       576 aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~G  617 (719)
T TIGR02696       576 APRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDDG  617 (719)
T ss_pred             CCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecCc
Confidence            345678899999999999999999999999999999998543

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

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.03  E-value=2.9e-06  Score=66.48  Aligned_cols=41  Identities=27%  Similarity=0.427  Sum_probs=37.2

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN   53 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~   53 (78)
                      ....++.||.+.+|.|||+||++||.|+++|||+|.|.+++
T Consensus       550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~ddG  590 (684)
T TIGR03591       550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDDG  590 (684)
T ss_pred             CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecCe
Confidence            45678899999999999999999999999999999998644

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).

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

Probab=97.95  E-value=1.7e-05  Score=55.24  Aligned_cols=43  Identities=28%  Similarity=0.441  Sum_probs=38.0

Q ss_pred             CCeeEEEEEecC------CceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680         11 DGVCQIKILVPS------YAAGAIIGKGGETIAQIQKDTGSKIKMSKAN   53 (78)
Q Consensus        11 ~~~~~~~l~vP~------~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~   53 (78)
                      +...+-+++||.      .+||+|||..|.++|+|+..|+|+|.|...+
T Consensus       145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g  193 (269)
T COG5176         145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSG  193 (269)
T ss_pred             cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence            456778888885      7899999999999999999999999998665

>PRK00468 hypothetical protein; Provisional

Probab=97.70  E-value=5.6e-05  Score=44.46  Aligned_cols=34  Identities=21%  Similarity=0.337  Sum_probs=30.2

Q ss_pred             CCCeeEEEEEecCCceeeEEecCCchHHHHHHHh
Q psy14680         10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDT   43 (78)
Q Consensus        10 ~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~T   43 (78)
                      ++....+++.+..+-+|.||||+|.+|+.||.--
T Consensus        26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            4566889999999999999999999999999754

>PRK02821 hypothetical protein; Provisional

Probab=97.57  E-value=9.7e-05  Score=43.71  Aligned_cols=36  Identities=19%  Similarity=0.350  Sum_probs=30.9

Q ss_pred             CCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCC
Q psy14680         10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGS   45 (78)
Q Consensus        10 ~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga   45 (78)
                      +.....+++.+..+-+|.||||+|.+|+.||.--.+
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            345578999999999999999999999999986544

>PRK01064 hypothetical protein; Provisional

Probab=97.50  E-value=0.00021  Score=42.31  Aligned_cols=34  Identities=29%  Similarity=0.336  Sum_probs=30.2

Q ss_pred             CCCeeEEEEEecCCceeeEEecCCchHHHHHHHh
Q psy14680         10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDT   43 (78)
Q Consensus        10 ~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~T   43 (78)
                      +...+.+++.+...-.|.+|||+|.+|+.||.-.
T Consensus        26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~   59 (78)
T PRK01064         26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL   59 (78)
T ss_pred             CCCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence            4667889999999999999999999999999753

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

Probab=97.43  E-value=0.00022  Score=42.11  Aligned_cols=33  Identities=30%  Similarity=0.457  Sum_probs=29.9

Q ss_pred             CCCeeEEEEEecCCceeeEEecCCchHHHHHHH
Q psy14680         10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKD   42 (78)
Q Consensus        10 ~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~   42 (78)
                      ++....+++.+..+-+|.||||+|.+|+.||.-
T Consensus        26 ~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             cCCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            466788999999999999999999999999964

>KOG2113|consensus

Probab=97.39  E-value=0.00017  Score=52.75  Aligned_cols=56  Identities=20%  Similarity=0.208  Sum_probs=47.2

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      +..++..+.||..+++.|.|++|..||.|+.+|.++|.-+..++      |-++.++|.++.
T Consensus        23 p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~e------ePiF~vTg~~ed   78 (394)
T KOG2113|consen   23 GQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGE------EPIFPVTGRHED   78 (394)
T ss_pred             CCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCC------CCcceeccCchh
Confidence            47788999999999999999999999999999999999987653      455666766653

>KOG2279|consensus

Probab=97.38  E-value=0.00017  Score=55.72  Aligned_cols=59  Identities=31%  Similarity=0.437  Sum_probs=47.9

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCCC
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGFE   73 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~~   73 (78)
                      ...+.++++||...|-+|+||+|++|++|+..|++||.+..+.    -..++...+.|.|...
T Consensus        65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed----~g~e~~~~~~~~p~~v  123 (608)
T KOG2279|consen   65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED----VGDERVLLISGFPVQV  123 (608)
T ss_pred             hhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc----CCcccchhhccCCCCC
Confidence            3568899999999999999999999999999999999998653    2355666666555543

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

Probab=97.24  E-value=0.00023  Score=56.07  Aligned_cols=40  Identities=30%  Similarity=0.444  Sum_probs=36.3

Q ss_pred             eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680         14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN   53 (78)
Q Consensus        14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~   53 (78)
                      -...+.|+.+.++.+||++|.+|++|.++||++|+|.+++
T Consensus       552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~IdieddG  591 (692)
T COG1185         552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDDG  591 (692)
T ss_pred             ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCCC
Confidence            4567889999999999999999999999999999999554

>PRK12704 phosphodiesterase; Provisional

Probab=97.20  E-value=0.00059  Score=52.27  Aligned_cols=39  Identities=23%  Similarity=0.409  Sum_probs=33.4

Q ss_pred             eeEEEEEecC-CceeeEEecCCchHHHHHHHhCCeEEEec
Q psy14680         13 VCQIKILVPS-YAAGAIIGKGGETIAQIQKDTGSKIKMSK   51 (78)
Q Consensus        13 ~~~~~l~vP~-~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~   51 (78)
                      ...-.+.+|+ ++-|.||||.|.||+.++.-||+-|.|++
T Consensus       209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd  248 (520)
T PRK12704        209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD  248 (520)
T ss_pred             hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC
Confidence            4455667888 55599999999999999999999999984

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=97.15  E-value=0.00062  Score=44.14  Aligned_cols=39  Identities=28%  Similarity=0.505  Sum_probs=35.8

Q ss_pred             eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecC
Q psy14680         14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKA   52 (78)
Q Consensus        14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~   52 (78)
                      ..+.++|+...+|+.||++|++|+.|++..|-+|.|-.-
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~   70 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY   70 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc
Confidence            467788899999999999999999999999999999874

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=97.13  E-value=0.00068  Score=51.88  Aligned_cols=40  Identities=23%  Similarity=0.392  Sum_probs=34.0

Q ss_pred             CeeEEEEEecC-CceeeEEecCCchHHHHHHHhCCeEEEec
Q psy14680         12 GVCQIKILVPS-YAAGAIIGKGGETIAQIQKDTGSKIKMSK   51 (78)
Q Consensus        12 ~~~~~~l~vP~-~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~   51 (78)
                      ....-.+.+|+ ++-|.||||.|.||+.++..||+-|.|++
T Consensus       202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd  242 (514)
T TIGR03319       202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD  242 (514)
T ss_pred             hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC
Confidence            34555678888 45599999999999999999999999985

>KOG2814|consensus

Probab=97.12  E-value=0.00027  Score=51.70  Aligned_cols=51  Identities=25%  Similarity=0.346  Sum_probs=41.9

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEec
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLS   68 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G   68 (78)
                      .....+.++....|.|||++|.+.++|+++|+|+|.++++.     ...-.++|.|
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~-----~n~~~i~i~~  106 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN-----TNKEEIKIIG  106 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC-----CCcceEEEee
Confidence            35667889999999999999999999999999999999765     2344455544

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.11  E-value=0.00022  Score=57.69  Aligned_cols=42  Identities=24%  Similarity=0.346  Sum_probs=37.2

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCe-EEEecCC
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSK-IKMSKAN   53 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~-I~i~~~~   53 (78)
                      -.....+.||.+++|.|||.||.+|+.|.++||++ |.+.+++
T Consensus       683 aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~ddg  725 (891)
T PLN00207        683 APLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDDG  725 (891)
T ss_pred             CCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCCe
Confidence            34577889999999999999999999999999999 9888543

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

Probab=97.02  E-value=0.00097  Score=45.58  Aligned_cols=39  Identities=28%  Similarity=0.324  Sum_probs=33.7

Q ss_pred             ceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         24 AAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        24 ~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      ..|+|||++|.+-+.|+.-|+|.|.|..          ..|.|.|.+.+
T Consensus       112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g----------~tVaiiG~~~~  150 (194)
T COG1094         112 IKGRIIGREGKTRRAIEELTGVYISVYG----------KTVAIIGGFEQ  150 (194)
T ss_pred             hhceeeCCCchHHHHHHHHhCCeEEEeC----------cEEEEecChhh
Confidence            4699999999999999999999999983          33888888765

>PRK00106 hypothetical protein; Provisional

Probab=97.00  E-value=0.0012  Score=51.01  Aligned_cols=40  Identities=23%  Similarity=0.415  Sum_probs=34.2

Q ss_pred             CeeEEEEEecC-CceeeEEecCCchHHHHHHHhCCeEEEec
Q psy14680         12 GVCQIKILVPS-YAAGAIIGKGGETIAQIQKDTGSKIKMSK   51 (78)
Q Consensus        12 ~~~~~~l~vP~-~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~   51 (78)
                      ....-.+.+|+ ++-|.||||.|.||+.++.-||+-|.|++
T Consensus       223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd  263 (535)
T PRK00106        223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD  263 (535)
T ss_pred             hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC
Confidence            34556678888 55599999999999999999999999985

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

Probab=96.93  E-value=0.0023  Score=34.97  Aligned_cols=35  Identities=31%  Similarity=0.404  Sum_probs=28.3

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeE
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKI   47 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I   47 (78)
                      ...+.+.+.....|.+||++|.+++.|+..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            35556666666789999999999999999988554

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.

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=96.91  E-value=0.00093  Score=43.32  Aligned_cols=40  Identities=20%  Similarity=0.287  Sum_probs=35.2

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEe
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMS   50 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~   50 (78)
                      ++...+.+.|+....|..|||+|.|++.+++-++-++.|.
T Consensus        96 ~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         96 NGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             CCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence            3346777889999999999999999999999999988775

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=96.67  E-value=0.0005  Score=54.18  Aligned_cols=40  Identities=33%  Similarity=0.544  Sum_probs=34.8

Q ss_pred             eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680         14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN   53 (78)
Q Consensus        14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~   53 (78)
                      ....+.||.+.++.+||.||.+||.|.++||++|.+.+++
T Consensus       554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~G  593 (693)
T PRK11824        554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDDG  593 (693)
T ss_pred             hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCCc
Confidence            4456677999999999999999999999999999987544

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=96.49  E-value=0.0034  Score=36.48  Aligned_cols=35  Identities=20%  Similarity=0.335  Sum_probs=28.1

Q ss_pred             eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEE
Q psy14680         14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIK   48 (78)
Q Consensus        14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~   48 (78)
                      ..+.+.|.....|.+|||.|.++..||--++.-++
T Consensus        24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~   58 (77)
T cd02414          24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN   58 (77)
T ss_pred             CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence            34667777888999999999999999987665444

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

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=96.48  E-value=0.00077  Score=38.66  Aligned_cols=35  Identities=26%  Similarity=0.340  Sum_probs=29.4

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCC
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGS   45 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga   45 (78)
                      .....+.+.+..+..|.+|||+|.+++.||.-.+.
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            45567778889999999999999999999976644

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

Probab=96.47  E-value=0.0018  Score=37.34  Aligned_cols=38  Identities=37%  Similarity=0.507  Sum_probs=29.5

Q ss_pred             EEEEecCCc-----eeeEEecCCchHHHHHHHh-CCeEEEecCC
Q psy14680         16 IKILVPSYA-----AGAIIGKGGETIAQIQKDT-GSKIKMSKAN   53 (78)
Q Consensus        16 ~~l~vP~~~-----vG~IIGk~G~~Ik~i~~~T-ga~I~i~~~~   53 (78)
                      .++.|-...     +|..||++|.+|+.|.++. |-+|.|-...
T Consensus         5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~s   48 (69)
T PF13184_consen    5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEYS   48 (69)
T ss_dssp             EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE--
T ss_pred             EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEcC
Confidence            456666666     8999999999999999999 9999998643

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.43  E-value=0.0021  Score=44.67  Aligned_cols=37  Identities=22%  Similarity=0.403  Sum_probs=33.7

Q ss_pred             EEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecC
Q psy14680         16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKA   52 (78)
Q Consensus        16 ~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~   52 (78)
                      +.+.||...++.+||++|.+|+.|.+.|+++|.|-.+
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N  183 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN  183 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC
Confidence            5578899999999999999999999999999999754

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=96.38  E-value=0.004  Score=40.57  Aligned_cols=38  Identities=29%  Similarity=0.532  Sum_probs=34.9

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecC
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKA   52 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~   52 (78)
                      .+-++|....+|+.||++|++|+.|++..|-+|.|-.-
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVey   71 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEY   71 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEc
Confidence            66778899999999999999999999999999999874

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

>PRK12705 hypothetical protein; Provisional

Probab=96.35  E-value=0.0035  Score=48.13  Aligned_cols=41  Identities=27%  Similarity=0.438  Sum_probs=33.8

Q ss_pred             CeeEEEEEecCCce-eeEEecCCchHHHHHHHhCCeEEEecC
Q psy14680         12 GVCQIKILVPSYAA-GAIIGKGGETIAQIQKDTGSKIKMSKA   52 (78)
Q Consensus        12 ~~~~~~l~vP~~~v-G~IIGk~G~~Ik~i~~~Tga~I~i~~~   52 (78)
                      ....-.+.+|++-+ |.||||.|.||+.++..||+-|.|++.
T Consensus       196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt  237 (508)
T PRK12705        196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT  237 (508)
T ss_pred             hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC
Confidence            34455567787554 999999999999999999999999853

>KOG4369|consensus

Probab=96.31  E-value=0.0014  Score=55.00  Aligned_cols=58  Identities=26%  Similarity=0.247  Sum_probs=49.5

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEec-CCCCCCCCceeEEEEeccCCC
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK-ANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~-~~~~~~g~~er~v~I~G~p~~   72 (78)
                      +...-++-+|.....+|||++|.||..++.-||+.|.|.+ .+   .+..||.+.+.|.|+.
T Consensus      1338 ~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~---~Nqaers~~~kg~p~~ 1396 (2131)
T KOG4369|consen 1338 PANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQP---DNQAERSKAPKGRPPS 1396 (2131)
T ss_pred             cccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCC---ccchhhhcccCCCChh
Confidence            3445567889999999999999999999999999999987 43   3568999999999874

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

Probab=96.18  E-value=0.014  Score=40.00  Aligned_cols=54  Identities=22%  Similarity=0.383  Sum_probs=44.4

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEecc-CCCCC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSR-PGFEP   74 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~-p~~~~   74 (78)
                      .....+.||...+|.+||+.|+.-+.|.+.+++++.++.        .++.|.|..+ +..||
T Consensus         7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~--------~~~~V~i~~~~~t~Dp   61 (194)
T COG1094           7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS--------KTGSVTIRTTRKTEDP   61 (194)
T ss_pred             cceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC--------CCCeEEEEecCCCCCh
Confidence            345668999999999999999999999999999999983        4667787766 33444

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=96.17  E-value=0.0017  Score=37.44  Aligned_cols=35  Identities=29%  Similarity=0.528  Sum_probs=29.3

Q ss_pred             eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEE
Q psy14680         14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIK   48 (78)
Q Consensus        14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~   48 (78)
                      ..+.+.+..+..|.+||++|++|++|++..+-.+.
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            45677889999999999999999999887765553

; 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 ....

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=95.91  E-value=0.014  Score=43.51  Aligned_cols=43  Identities=21%  Similarity=0.199  Sum_probs=38.6

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCC
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND   54 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~   54 (78)
                      ......+.||.+..++.|||+|.|++-..+-||.+|.|-.-++
T Consensus       306 ~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~  348 (374)
T PRK12328        306 EEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS  348 (374)
T ss_pred             CCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence            3457889999999999999999999999999999999987553

>TIGR01953 NusA transcription termination factor NusA

Probab=95.82  E-value=0.01  Score=43.51  Aligned_cols=40  Identities=28%  Similarity=0.417  Sum_probs=36.8

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEec
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK   51 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~   51 (78)
                      ......+.||.+..++.|||+|.|++-..+-||.+|.|-.
T Consensus       299 ~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       299 DKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             CCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            3467889999999999999999999999999999999975

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.

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=95.81  E-value=0.0072  Score=39.36  Aligned_cols=39  Identities=23%  Similarity=0.314  Sum_probs=34.7

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEe
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMS   50 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~   50 (78)
                      +.....+.||.+..++.|||+|.|++...+-++-++.|.
T Consensus        98 ~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952        98 GKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             CCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence            456678899999999999999999999999999888775

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.

>PRK13764 ATPase; Provisional

Probab=95.75  E-value=0.0085  Score=46.90  Aligned_cols=43  Identities=28%  Similarity=0.485  Sum_probs=38.1

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCC
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND   54 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~   54 (78)
                      ......++||...++.+|||+|.+|++|++..|..|.|.+..+
T Consensus       479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~  521 (602)
T PRK13764        479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDE  521 (602)
T ss_pred             cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccc
Confidence            3445678999999999999999999999999999999988654

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

Probab=95.73  E-value=0.014  Score=34.61  Aligned_cols=36  Identities=11%  Similarity=0.345  Sum_probs=28.8

Q ss_pred             eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEE
Q psy14680         14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKM   49 (78)
Q Consensus        14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i   49 (78)
                      ..+++.|-...-|.+||++|++|++|++.-.....+
T Consensus        30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~   65 (81)
T cd02413          30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF   65 (81)
T ss_pred             CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence            347788888899999999999999998876544444

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.

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

Probab=95.61  E-value=0.011  Score=45.65  Aligned_cols=40  Identities=33%  Similarity=0.539  Sum_probs=36.0

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCC
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND   54 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~   54 (78)
                      ...+.||...++.+|||+|.+|++|++..|-+|.|...++
T Consensus       487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~  526 (604)
T COG1855         487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE  526 (604)
T ss_pred             eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence            4567899999999999999999999999999999987653

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=95.50  E-value=0.012  Score=40.00  Aligned_cols=38  Identities=26%  Similarity=0.410  Sum_probs=35.5

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecC
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKA   52 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~   52 (78)
                      ...+.||.+..+..|||+|.|++-..+-||-++.|...
T Consensus       143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~  180 (190)
T COG0195         143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI  180 (190)
T ss_pred             EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence            77888999999999999999999999999999999753

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.20  E-value=0.024  Score=41.95  Aligned_cols=43  Identities=26%  Similarity=0.417  Sum_probs=38.5

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN   53 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~   53 (78)
                      +......+.||.+..++-|||+|.|++--.+-||.+|.|-...
T Consensus       300 ~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~~  342 (362)
T PRK12327        300 EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSES  342 (362)
T ss_pred             CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEHH
Confidence            3446788999999999999999999999999999999998754

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=95.19  E-value=0.018  Score=43.86  Aligned_cols=40  Identities=28%  Similarity=0.372  Sum_probs=37.0

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKA   52 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~   52 (78)
                      ...+.+.||....+.-|||+|.|++-..+-||.+|.|-..
T Consensus       301 ~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        301 EHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             CCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence            3588899999999999999999999999999999999864

>KOG2279|consensus

Probab=95.10  E-value=0.0081  Score=46.69  Aligned_cols=57  Identities=30%  Similarity=0.431  Sum_probs=46.6

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccC
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRP   70 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p   70 (78)
                      +..+...+-+|...+++|+||+|.++..|+..++|+|.+..++.   ..-.|...|.+.-
T Consensus       137 ~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr---~g~~~~~~i~~qq  193 (608)
T KOG2279|consen  137 NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGR---LGLSRLIKISGQQ  193 (608)
T ss_pred             CCcccccccchhhhcccccccchhhhcchhcccccccccccccc---cccccceeccccc
Confidence            44567778899999999999999999999999999999998763   3456666666543

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=94.85  E-value=0.044  Score=36.68  Aligned_cols=38  Identities=26%  Similarity=0.462  Sum_probs=32.4

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN   53 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~   53 (78)
                      .+-++|.... |.-|||+|.+++.+++..|-+|.|-...
T Consensus        62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~s   99 (166)
T PRK06418         62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEKT   99 (166)
T ss_pred             EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEcC
Confidence            4456666666 9999999999999999999999998754

>KOG2208|consensus

Probab=94.69  E-value=0.018  Score=46.14  Aligned_cols=61  Identities=18%  Similarity=0.230  Sum_probs=52.2

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCCCCCC
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGFEPST   76 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~~~~~   76 (78)
                      .+...+.+.+-......++||+|.++.+|++++.|.|.+...+     ..+..+.++|.-.++++.
T Consensus       344 ~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~-----~~~~~v~~~~~~~~~~ka  404 (753)
T KOG2208|consen  344 ENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQG-----SNNKKVVITGVSANDEKA  404 (753)
T ss_pred             ccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccccc-----CCCCCeEEeccccchhHH
Confidence            3447788888999999999999999999999999999999743     578889999988777654

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

Probab=94.67  E-value=0.029  Score=34.72  Aligned_cols=30  Identities=27%  Similarity=0.556  Sum_probs=24.9

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHHHhC
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQKDTG   44 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tg   44 (78)
                      .+++.|-...-|.|||++|++|++|++.-.
T Consensus        62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~   91 (109)
T cd02412          62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQ   91 (109)
T ss_pred             CEEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence            466777778899999999999999887643

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=94.66  E-value=0.039  Score=32.58  Aligned_cols=28  Identities=25%  Similarity=0.512  Sum_probs=22.5

Q ss_pred             EEEEecCCceeeEEecCCchHHHHHHHh
Q psy14680         16 IKILVPSYAAGAIIGKGGETIAQIQKDT   43 (78)
Q Consensus        16 ~~l~vP~~~vG~IIGk~G~~Ik~i~~~T   43 (78)
                      +++.|-...-|.+||++|++|++|++.-
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            5555555888999999999999887753

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=94.43  E-value=0.036  Score=42.14  Aligned_cols=41  Identities=27%  Similarity=0.371  Sum_probs=36.9

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecC
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKA   52 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~   52 (78)
                      ......+.||.+..++-|||+|.|++--.+-||.+|.|...
T Consensus       333 ~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s~  373 (449)
T PRK12329        333 EGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKDS  373 (449)
T ss_pred             CCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccccH
Confidence            34567899999999999999999999999999999999753

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

Probab=94.36  E-value=0.06  Score=37.96  Aligned_cols=37  Identities=22%  Similarity=0.460  Sum_probs=33.8

Q ss_pred             EEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680         17 KILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN   53 (78)
Q Consensus        17 ~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~   53 (78)
                      =+.||...|-++||++|+.++-|.+.|+|.|.|-.++
T Consensus       149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG  185 (239)
T COG1097         149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNG  185 (239)
T ss_pred             EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecCC
Confidence            3678999999999999999999999999999998765

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

Probab=93.95  E-value=0.059  Score=37.87  Aligned_cols=30  Identities=23%  Similarity=0.480  Sum_probs=25.0

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHH
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKD   42 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~   42 (78)
                      ...+++.|-...-|.||||+|++|.+|++.
T Consensus        50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~   79 (233)
T COG0092          50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKE   79 (233)
T ss_pred             CCceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence            346778888899999999999999887654

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

Probab=93.92  E-value=0.11  Score=34.05  Aligned_cols=37  Identities=30%  Similarity=0.618  Sum_probs=32.2

Q ss_pred             EEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680         17 KILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN   53 (78)
Q Consensus        17 ~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~   53 (78)
                      ++.|=...-|++|||+|.++++|..+||-+-.|-+..
T Consensus        79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtp  115 (145)
T cd02410          79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTP  115 (145)
T ss_pred             EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecC
Confidence            4566678889999999999999999999999887643

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.

>KOG2113|consensus

Probab=93.82  E-value=0.078  Score=39.14  Aligned_cols=56  Identities=23%  Similarity=0.277  Sum_probs=48.5

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      +........+|...+|++.|..|.+|+.+++.+...|.-.-+      ..+-++.++|.|.+
T Consensus       112 s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~------~~~~Vf~Vtg~~~n  167 (394)
T KOG2113|consen  112 SGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR------CGEPVFCVTGAPKN  167 (394)
T ss_pred             cCCCceeeeccceeeeeccccccCccchheecccceEeeecc------CCCceEEEecCCcc
Confidence            566778889999999999999999999999999999988743      36778889998776

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=93.44  E-value=0.096  Score=35.67  Aligned_cols=37  Identities=27%  Similarity=0.425  Sum_probs=31.3

Q ss_pred             EEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680         17 KILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN   53 (78)
Q Consensus        17 ~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~   53 (78)
                      -+.+-.+.+|+.||++|++|+.|.++-|-+|.|-.-.
T Consensus        79 ~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s  115 (190)
T COG0195          79 SNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS  115 (190)
T ss_pred             EeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeC
Confidence            3444557889999999999999999999999998644

>TIGR00436 era GTP-binding protein Era

Probab=93.03  E-value=0.18  Score=35.00  Aligned_cols=30  Identities=30%  Similarity=0.295  Sum_probs=23.1

Q ss_pred             eEEEEEecC-CceeeEEecCCchHHHHHHHh
Q psy14680         14 CQIKILVPS-YAAGAIIGKGGETIAQIQKDT   43 (78)
Q Consensus        14 ~~~~l~vP~-~~vG~IIGk~G~~Ik~i~~~T   43 (78)
                      +...++|.. ++-+.|||++|+.||+|...+
T Consensus       221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a  251 (270)
T TIGR00436       221 IHALISVERESQKKIIIGKNGSMIKAIGIAA  251 (270)
T ss_pred             EEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence            556667764 566999999999999876543

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

>PRK15494 era GTPase Era; Provisional

Probab=92.15  E-value=0.26  Score=35.63  Aligned_cols=29  Identities=28%  Similarity=0.361  Sum_probs=22.5

Q ss_pred             eEEEEEecC-CceeeEEecCCchHHHHHHH
Q psy14680         14 CQIKILVPS-YAAGAIIGKGGETIAQIQKD   42 (78)
Q Consensus        14 ~~~~l~vP~-~~vG~IIGk~G~~Ik~i~~~   42 (78)
                      +...++|.. ++-+.|||++|+.||+|...
T Consensus       273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~  302 (339)
T PRK15494        273 INQVIVVSRESYKTIILGKNGSKIKEIGAK  302 (339)
T ss_pred             EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence            556677765 56699999999999987543

>PRK00089 era GTPase Era; Reviewed

Probab=91.78  E-value=0.33  Score=33.80  Aligned_cols=29  Identities=34%  Similarity=0.575  Sum_probs=21.8

Q ss_pred             eEEEEEecC-CceeeEEecCCchHHHHHHH
Q psy14680         14 CQIKILVPS-YAAGAIIGKGGETIAQIQKD   42 (78)
Q Consensus        14 ~~~~l~vP~-~~vG~IIGk~G~~Ik~i~~~   42 (78)
                      +...++|.. ++-+.|||++|+.||+|...
T Consensus       226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~  255 (292)
T PRK00089        226 IEATIYVERDSQKGIIIGKGGAMLKKIGTE  255 (292)
T ss_pred             EEEEEEEccCCceeEEEeCCcHHHHHHHHH
Confidence            455566654 56699999999999987644

>COG1159 Era GTPase [General function prediction only]

Probab=90.36  E-value=0.45  Score=34.59  Aligned_cols=31  Identities=32%  Similarity=0.435  Sum_probs=22.8

Q ss_pred             eeEEEEEecC-CceeeEEecCCchHHHHHHHh
Q psy14680         13 VCQIKILVPS-YAAGAIIGKGGETIAQIQKDT   43 (78)
Q Consensus        13 ~~~~~l~vP~-~~vG~IIGk~G~~Ik~i~~~T   43 (78)
                      .+...++|+. ++=|.||||+|+.||+|-..+
T Consensus       228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~A  259 (298)
T COG1159         228 KIHATIYVERESQKGIIIGKNGAMIKKIGTAA  259 (298)
T ss_pred             EEEEEEEEecCCccceEECCCcHHHHHHHHHH
Confidence            3455567765 556999999999999876543

>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type

Probab=89.52  E-value=0.42  Score=32.66  Aligned_cols=30  Identities=23%  Similarity=0.522  Sum_probs=24.6

Q ss_pred             eEEEEEecCCceeeEEecCCchHHHHHHHh
Q psy14680         14 CQIKILVPSYAAGAIIGKGGETIAQIQKDT   43 (78)
Q Consensus        14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~T   43 (78)
                      ..+++.|-...-|.+||++|.+|++|++.-
T Consensus        38 ~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l   67 (195)
T TIGR01008        38 LGTKVIIFAERPGLVIGRGGRRIRELTEKL   67 (195)
T ss_pred             CcEEEEEEECCCceEECCCchHHHHHHHHH
Confidence            346777888888999999999999877653

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.

>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed

Probab=89.45  E-value=0.42  Score=32.77  Aligned_cols=29  Identities=24%  Similarity=0.499  Sum_probs=22.9

Q ss_pred             EEEEecCCceeeEEecCCchHHHHHHHhC
Q psy14680         16 IKILVPSYAAGAIIGKGGETIAQIQKDTG   44 (78)
Q Consensus        16 ~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tg   44 (78)
                      +++.|-...-|.+||++|++|++|++.-.
T Consensus        42 i~I~I~ta~PGivIGk~G~~I~klk~~Lk   70 (207)
T PRK04191         42 TRITIYAERPGMVIGRGGKNIRELTEILE   70 (207)
T ss_pred             EEEEEEECCCCeEECCCchhHHHHHHHHH
Confidence            45555558889999999999999877653

>KOG3273|consensus

Probab=89.11  E-value=0.093  Score=36.61  Aligned_cols=30  Identities=40%  Similarity=0.548  Sum_probs=27.3

Q ss_pred             CCceeeEEecCCchHHHHHHHhCCeEEEec
Q psy14680         22 SYAAGAIIGKGGETIAQIQKDTGSKIKMSK   51 (78)
Q Consensus        22 ~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~   51 (78)
                      +..+|+|+||+|.+--.|+..|.++|.+..
T Consensus       177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad  206 (252)
T KOG3273|consen  177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD  206 (252)
T ss_pred             HHHHHHhhcCCCcceeeeeccceeEEEecC
Confidence            467899999999999999999999999974

>CHL00048 rps3 ribosomal protein S3

Probab=89.04  E-value=0.47  Score=32.77  Aligned_cols=29  Identities=17%  Similarity=0.306  Sum_probs=23.6

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHHHh
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQKDT   43 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~T   43 (78)
                      .+++.|-...-|.|||++|.+|++|++.-
T Consensus        67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L   95 (214)
T CHL00048         67 LIQVIIYTGFPKLLIERKGRGIEELQINL   95 (214)
T ss_pred             eEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence            45666667788999999999999988754

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=88.46  E-value=0.5  Score=35.06  Aligned_cols=31  Identities=29%  Similarity=0.472  Sum_probs=27.7

Q ss_pred             CceeeEEecCCchHHHHHHHh-CCeEEEecCC
Q psy14680         23 YAAGAIIGKGGETIAQIQKDT-GSKIKMSKAN   53 (78)
Q Consensus        23 ~~vG~IIGk~G~~Ik~i~~~T-ga~I~i~~~~   53 (78)
                      +-+|+.||++|++|+.|.++. |-+|.|-.-.
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s  276 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWS  276 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEcC
Confidence            568999999999999999888 9999998743

>KOG1423|consensus

Probab=88.41  E-value=0.71  Score=34.32  Aligned_cols=32  Identities=31%  Similarity=0.589  Sum_probs=26.2

Q ss_pred             eeEEEEEecC-CceeeEEecCCchHHHHHHHhC
Q psy14680         13 VCQIKILVPS-YAAGAIIGKGGETIAQIQKDTG   44 (78)
Q Consensus        13 ~~~~~l~vP~-~~vG~IIGk~G~~Ik~i~~~Tg   44 (78)
                      .++.++.+|. +..-.||||||..|++|-++.+
T Consensus       327 ~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~  359 (379)
T KOG1423|consen  327 FIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN  359 (379)
T ss_pred             EEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence            5788899987 4557899999999999877643

>PTZ00084 40S ribosomal protein S3; Provisional

Probab=88.39  E-value=0.52  Score=32.84  Aligned_cols=29  Identities=14%  Similarity=0.354  Sum_probs=23.8

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHHHh
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQKDT   43 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~T   43 (78)
                      .+++.|-...-|.|||++|..|++|++.-
T Consensus        45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L   73 (220)
T PTZ00084         45 RTEIIIRATRTREVLGDKGRRIRELTSLL   73 (220)
T ss_pred             cEEEEEEECCCccEEcCCchHHHHHHHHH
Confidence            46677777888999999999999877654

>KOG2208|consensus

Probab=88.37  E-value=0.4  Score=38.61  Aligned_cols=42  Identities=21%  Similarity=0.368  Sum_probs=38.9

Q ss_pred             CCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEec
Q psy14680         10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK   51 (78)
Q Consensus        10 ~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~   51 (78)
                      ....++..+.+|.++...+||++|++.+++.+++++.+.+..
T Consensus       705 ~~~~~~~~~~~p~~~~~~~ig~~g~~~r~~~~~~~~~~~~~~  746 (753)
T KOG2208|consen  705 AKNLVTKEIEIPRSLHRYLIGPKGSNLRQLEKEFNVNIVVPN  746 (753)
T ss_pred             cccceeeEEeccHHHhhhccCCCCccHHHHHHHhccceecCC
Confidence            466788999999999999999999999999999999999986

>TIGR01953 NusA transcription termination factor NusA

Probab=87.90  E-value=0.61  Score=34.29  Aligned_cols=31  Identities=32%  Similarity=0.513  Sum_probs=27.7

Q ss_pred             CceeeEEecCCchHHHHHHHh-CCeEEEecCC
Q psy14680         23 YAAGAIIGKGGETIAQIQKDT-GSKIKMSKAN   53 (78)
Q Consensus        23 ~~vG~IIGk~G~~Ik~i~~~T-ga~I~i~~~~   53 (78)
                      +-+|+.||++|++|+.|.++- |-+|.|-.-.
T Consensus       243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s  274 (341)
T TIGR01953       243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYS  274 (341)
T ss_pred             CcceeeECCCCchHHHHHHHhCCCeEEEEEcC
Confidence            567999999999999999998 9999998743

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.

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

Probab=86.88  E-value=1  Score=35.54  Aligned_cols=38  Identities=29%  Similarity=0.539  Sum_probs=32.9

Q ss_pred             EEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680         16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN   53 (78)
Q Consensus        16 ~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~   53 (78)
                      =+++|=+..-|.+|||+|.++++|-++||-+-.|-+..
T Consensus        95 ~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~  132 (630)
T TIGR03675        95 GEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTP  132 (630)
T ss_pred             ceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecC
Confidence            35667778889999999999999999999999987643

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.

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

Probab=86.30  E-value=0.55  Score=32.55  Aligned_cols=37  Identities=22%  Similarity=0.304  Sum_probs=29.0

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEE
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIK   48 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~   48 (78)
                      ....+.+-+-.+..|.+||+.|.++..||--+.+-+.
T Consensus        89 ~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~  125 (208)
T COG1847          89 EGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLN  125 (208)
T ss_pred             cCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhh
Confidence            4456667777777999999999999999977655443

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=86.07  E-value=0.59  Score=35.74  Aligned_cols=31  Identities=29%  Similarity=0.463  Sum_probs=27.7

Q ss_pred             CceeeEEecCCchHHHHHHHh-CCeEEEecCC
Q psy14680         23 YAAGAIIGKGGETIAQIQKDT-GSKIKMSKAN   53 (78)
Q Consensus        23 ~~vG~IIGk~G~~Ik~i~~~T-ga~I~i~~~~   53 (78)
                      +-+|+.||++|++|+.|.++- |-+|.|-.-.
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys  308 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWS  308 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEcC
Confidence            567999999999999999998 9999998743

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=84.92  E-value=0.62  Score=34.83  Aligned_cols=31  Identities=26%  Similarity=0.401  Sum_probs=27.6

Q ss_pred             CceeeEEecCCchHHHHHHHh-CCeEEEecCC
Q psy14680         23 YAAGAIIGKGGETIAQIQKDT-GSKIKMSKAN   53 (78)
Q Consensus        23 ~~vG~IIGk~G~~Ik~i~~~T-ga~I~i~~~~   53 (78)
                      +-+|+.||++|++|+.|.++- |-+|.|-.-.
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s  282 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYS  282 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcC
Confidence            567999999999999999988 9999998743

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=83.81  E-value=0.84  Score=34.96  Aligned_cols=31  Identities=29%  Similarity=0.429  Sum_probs=27.5

Q ss_pred             CceeeEEecCCchHHHHHHHh-CCeEEEecCC
Q psy14680         23 YAAGAIIGKGGETIAQIQKDT-GSKIKMSKAN   53 (78)
Q Consensus        23 ~~vG~IIGk~G~~Ik~i~~~T-ga~I~i~~~~   53 (78)
                      +-+|+.||++|++|+.|.++- |-+|.|-.-.
T Consensus       245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s  276 (470)
T PRK09202        245 DPVGACVGMRGSRIQAISNELGGEKIDIILWS  276 (470)
T ss_pred             ChhHccCCCCCchHHHHHHHhCCCeEEEEEcC
Confidence            567999999999999999988 9999998743

>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type

Probab=83.46  E-value=1.2  Score=30.61  Aligned_cols=28  Identities=32%  Similarity=0.646  Sum_probs=23.1

Q ss_pred             EEEEecCCceeeEEecCCchHHHHHHHh
Q psy14680         16 IKILVPSYAAGAIIGKGGETIAQIQKDT   43 (78)
Q Consensus        16 ~~l~vP~~~vG~IIGk~G~~Ik~i~~~T   43 (78)
                      +++.|-...-|.|||++|.++++|++.-
T Consensus        64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l   91 (211)
T TIGR01009        64 IRVTIHTARPGIVIGKKGSEIEKLRKDL   91 (211)
T ss_pred             eEEEEEeCCCcceeCCCchHHHHHHHHH
Confidence            6677777778999999999999987543

TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.

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

Probab=82.13  E-value=1.9  Score=34.01  Aligned_cols=38  Identities=29%  Similarity=0.548  Sum_probs=32.5

Q ss_pred             EEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680         16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN   53 (78)
Q Consensus        16 ~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~   53 (78)
                      =+++|=+..-|++|||+|++.+.|-++||-.-.|-+..
T Consensus       101 GEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~P  138 (637)
T COG1782         101 GEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTP  138 (637)
T ss_pred             ceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecC
Confidence            35677788889999999999999999999988877643

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	78
2ann_A	178	Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDE		6e-13
2anr_A	178	Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TAND		7e-13
1ec6_A	87	Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Bind		1e-05
1dt4_A	73	Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Bind		2e-05
1dtj_A	76	Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Bind		2e-05
1ztg_A	74	Human Alpha Polyc Binding Protein Kh1 Length = 74		7e-04

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 29/42 (69%), Positives = 39/42 (92%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          +K+L+PSYAAG+IIGKGG+TI Q+QK+TG+ IK+SK+ DFYP
Sbjct: 8  LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP 49

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 29/42 (69%), Positives = 39/42 (92%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          +K+L+PSYAAG+IIGKGG+TI Q+QK+TG+ IK+SK+ DFYP
Sbjct: 8  LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP 49

>pdb|1EC6|A Chain A, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding Domain Bound To 20-Mer Rna Hairpin Length = 87

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 31/42 (73%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          ++I VP    GAI+GKGG+T+ + Q+ TG++I++SK  +F P
Sbjct: 5  VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP 46

>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding Domain Length = 73

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 30/42 (71%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          ++I VP    GAI+GKGG+T+ + Q+ TG +I++SK  +F P
Sbjct: 5  VEIAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLP 46

>pdb|1DTJ|A Chain A, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding Domain Length = 76

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 18/42 (42%), Positives = 31/42 (73%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          +++ VP    GAI+GKGG+T+ + Q+ TG++I++SK  +F P
Sbjct: 5  VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP 46

>pdb|1ZTG|A Chain A, Human Alpha Polyc Binding Protein Kh1 Length = 74

Iteration: 1
 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 15/42 (35%), Positives = 31/42 (73%)
Query: 12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN 53
          G+  I++L+     G+IIGK GE++ +I++++G++I +S+ N
Sbjct: 1  GILTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGN 42

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	78
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	7e-15
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	7e-15
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	6e-11
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	1e-14
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-14
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	5e-10
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	2e-13
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	2e-13
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	4e-13
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	1e-10
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	6e-13
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	6e-13
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	3e-10
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	1e-12
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	3e-10
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-12
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	3e-12
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	4e-12
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	5e-12
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	1e-11
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	2e-11
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	5e-11
1we8_A	104	Tudor and KH domain containing protein; structural	4e-10
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	7e-09
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	8e-09
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	1e-08
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	5e-08
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	4e-07
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	6e-07
1tua_A	191	Hypothetical protein APE0754; structural genomics,	2e-06
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	3e-06
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	2e-05
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	4e-05
2cxc_A	144	NUSA; transcription termination, RNA binding prote	6e-05
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	6e-05
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	8e-05
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	2e-04

>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 = 61.9 bits (151), Expect = 7e-15
 Identities = 18/43 (41%), Positives = 31/43 (72%)

Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
           +++ VP    GAI+GKGG+T+ + Q+ TG++I++SK  +F P
Sbjct: 4  LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP 46

>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 = 64.1 bits (156), Expect = 7e-15
 Identities = 29/42 (69%), Positives = 39/42 (92%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          +K+L+PSYAAG+IIGKGG+TI Q+QK+TG+ IK+SK+ DFYP
Sbjct: 8  LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP 49

>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 = 54.1 bits (130), Expect = 6e-11
 Identities = 18/41 (43%), Positives = 29/41 (70%)

Query: 11  DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK 51
           D   Q+KI+VP+  AG IIGKGG T+  I + +G+ +++S+
Sbjct: 101 DRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQ 141

>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 = 61.6 bits (150), Expect = 1e-14
 Identities = 19/43 (44%), Positives = 31/43 (72%)

Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
           ++I VP    GAI+GKGG+T+ + Q+ TG++I++SK  +F P
Sbjct: 4  LVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP 46

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

 Score = 63.0 bits (153), Expect = 2e-14
 Identities = 16/46 (34%), Positives = 25/46 (54%)

Query: 12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          G   I + +P +A G +IG+ GE I +IQ D G +I+    +   P
Sbjct: 1  GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTP 46

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

 Score = 51.4 bits (123), Expect = 5e-10
 Identities = 16/47 (34%), Positives = 27/47 (57%)

Query: 11  DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
            G+ +   +VP+   G IIGKGGETI  I + +G++I++ +      
Sbjct: 101 GGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNA 147

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

 Score = 58.1 bits (141), Expect = 2e-13
 Identities = 13/43 (30%), Positives = 30/43 (69%)

Query: 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN 53
          +    I++L+     G+IIGK GE++ ++++++G++I +S+ N
Sbjct: 2  NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN 44

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

 Score = 59.0 bits (143), Expect = 2e-13
 Identities = 15/43 (34%), Positives = 25/43 (58%)

Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
           I + VP ++ G +IG+ GE I +IQ D G +I+  + +   P
Sbjct: 12 GIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGP 54

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

 Score = 59.4 bits (144), Expect = 4e-13
 Identities = 16/42 (38%), Positives = 26/42 (61%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
           +I++P+  AG +IGKGGETI Q+Q+  G K+ + +      
Sbjct: 4  QEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNT 45

>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 = 53.3 bits (128), Expect = 1e-10
 Identities = 14/45 (31%), Positives = 25/45 (55%)

Query: 10  ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
           +     I + VP ++ G +IG+ GE I +IQ D G +I+  + + 
Sbjct: 87  SRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDG 131

>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 = 57.4 bits (139), Expect = 6e-13
 Identities = 18/48 (37%), Positives = 27/48 (56%)

Query: 10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
            G    +I++P+  AG +IGKGGETI Q+Q+  G K+ M +      
Sbjct: 11 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNT 58

>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 = 59.0 bits (143), Expect = 6e-13
 Identities = 13/43 (30%), Positives = 30/43 (69%)

Query: 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN 53
          +    I++L+     G+IIGK GE++ ++++++G++I +S+ N
Sbjct: 2  NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN 44

>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 = 52.1 bits (125), Expect = 3e-10
 Identities = 14/54 (25%), Positives = 32/54 (59%)

Query: 11  DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITL 64
                ++++VP+   G++IGKGG  I +I++ TG++++++         + IT+
Sbjct: 86  RPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITI 139

>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 = 58.2 bits (141), Expect = 1e-12
 Identities = 13/39 (33%), Positives = 24/39 (61%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
          +++ +P+ A GAIIGK G+ I Q+ +   + IK++    
Sbjct: 5  VQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPET 43

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

 Score = 52.1 bits (125), Expect = 3e-10
 Identities = 14/43 (32%), Positives = 28/43 (65%)

Query: 9   RADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK 51
           + +   +  I VP+ AAG +IGKGG+T+ ++Q  T +++ + +
Sbjct: 80  KEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPR 122

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

 Score = 55.8 bits (135), Expect = 2e-12
 Identities = 16/40 (40%), Positives = 26/40 (65%)

Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
            +I++P+  AG +IGKGGETI Q+Q+  G K+ + +   
Sbjct: 15 VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGS 54

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

 Score = 55.6 bits (134), Expect = 3e-12
 Identities = 11/43 (25%), Positives = 25/43 (58%)

Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          ++   +P++  G +IG+GGE +  I + TG+ +++S+      
Sbjct: 8  EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNG 50

>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 = 55.0 bits (133), Expect = 4e-12
 Identities = 15/39 (38%), Positives = 27/39 (69%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
           ++ +P   AG+IIGKGG+ I QI+ ++G+ IK+ +  +
Sbjct: 9  TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE 47

>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 = 54.6 bits (132), Expect = 5e-12
 Identities = 15/39 (38%), Positives = 27/39 (69%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
           ++ +P   AG+IIGKGG+ I QI+ ++G+ IK+ +  +
Sbjct: 16 TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE 54

>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 = 53.8 bits (130), Expect = 1e-11
 Identities = 11/39 (28%), Positives = 25/39 (64%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
           ++ +P+   G IIG+ G  I +I++ +G++IK++   +
Sbjct: 8  HELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVE 46

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

 Score = 52.7 bits (127), Expect = 2e-11
 Identities = 11/40 (27%), Positives = 25/40 (62%)

Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
            ++ +P+   G IIG+ G  I +I++ +G++IK++   +
Sbjct: 6  SHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVE 45

>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 = 52.4 bits (126), Expect = 5e-11
 Identities = 15/39 (38%), Positives = 26/39 (66%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
           +  VP    G IIG+GGE I++IQ+++G KI+++  + 
Sbjct: 17 EEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG 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 = 4e-10
 Identities = 17/40 (42%), Positives = 25/40 (62%)

Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
            ++ VP  + G IIG+GGETI  I K +G+KI   K ++
Sbjct: 16 FEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE 55

>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 = 46.9 bits (111), Expect = 7e-09
 Identities = 13/49 (26%), Positives = 22/49 (44%)

Query: 6  PFIRADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
              + G   I++ VP    G ++G  G TI +IQ+ T + I     + 
Sbjct: 2  SSGSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDK 50

>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 = 46.6 bits (111), Expect = 8e-09
 Identities = 10/39 (25%), Positives = 21/39 (53%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
            + +P      +IGK GE +  ++  T +KI++ + +D
Sbjct: 19 ATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDD 57

>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 = 46.4 bits (110), Expect = 1e-08
 Identities = 12/50 (24%), Positives = 21/50 (42%)

Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITL 64
          ++ + V       IIG+ G  I QI+ +    I+    +D       IT+
Sbjct: 18 KLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITI 67

>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 = 46.6 bits (110), Expect = 5e-08
 Identities = 11/42 (26%), Positives = 20/42 (47%)

Query: 17 KILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPV 58
           + +P      +IGK G+T  +I+K T +KI +        +
Sbjct: 37 YVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSETGEVWI 78

>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 = 42.5 bits (100), Expect = 4e-07
 Identities = 8/39 (20%), Positives = 16/39 (41%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
          I++ VP      +IG+ G  I ++  +    I +     
Sbjct: 19 IEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL 57

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

 Score = 41.6 bits (98), Expect = 6e-07
 Identities = 7/39 (17%), Positives = 18/39 (46%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
          ++I +       +IGK G  I +I+      +++   ++
Sbjct: 7  VEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSE 45

>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 = 41.9 bits (98), Expect = 2e-06
 Identities = 13/35 (37%), Positives = 20/35 (57%)

Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKM 49
          +I + V     GA+IG  GE  A+I + TG+ I +
Sbjct: 5  RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITV 39

>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 = 40.1 bits (94), Expect = 3e-06
 Identities = 7/46 (15%), Positives = 17/46 (36%)

Query: 9  RADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
            + +    + +       IIG  G+ I +I  +    I+  ++  
Sbjct: 12 ELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA 57

>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 = 39.2 bits (91), Expect = 2e-05
 Identities = 9/33 (27%), Positives = 12/33 (36%)

Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKI 47
            + +V     G  IG  G  I Q +K  G   
Sbjct: 5  HEQFIVREDLMGLAIGTHGANIQQARKVPGVTA 37

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

 Score = 38.6 bits (91), Expect = 4e-05
 Identities = 9/22 (40%), Positives = 14/22 (63%)

Query: 26  GAIIGKGGETIAQIQKDTGSKI 47
             +IG GG+ I +I   TG+K+
Sbjct: 582 REVIGSGGKVIREIVATTGAKV 603

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

 Score = 37.7 bits (88), Expect = 6e-05
 Identities = 11/33 (33%), Positives = 17/33 (51%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIK 48
          +  LV    AG  IG+GG  I  +++  G  I+
Sbjct: 38 LIFLVSEGEAGRAIGRGGRLIKLLREALGKNIE 70

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

 Score = 38.3 bits (90), Expect = 6e-05
 Identities = 7/22 (31%), Positives = 12/22 (54%)

Query: 26  GAIIGKGGETIAQIQKDTGSKI 47
              +G GG  + ++Q +TG  I
Sbjct: 579 AKFVGPGGYNLKKLQAETGVTI 600

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

 Score = 37.9 bits (89), Expect = 8e-05
 Identities = 9/22 (40%), Positives = 14/22 (63%)

Query: 26  GAIIGKGGETIAQIQKDTGSKI 47
             +IGKGG  I  + ++TG+ I
Sbjct: 572 KDVIGKGGSVIRALTEETGTTI 593

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A Length = 757

 Score = 37.2 bits (87), Expect = 2e-04
 Identities = 11/22 (50%), Positives = 16/22 (72%)

Query: 26  GAIIGKGGETIAQIQKDTGSKI 47
           G +IG   + I QIQ+DTG++I
Sbjct: 610 GEVIGPKRQMINQIQEDTGAEI 631

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	78
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.73
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.69
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.68
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.67
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.67
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.67
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.66
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.66
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.65
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.63
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.63
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.62
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.59
1we8_A	104	Tudor and KH domain containing protein; structural	99.59
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.57
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.54
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.53
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.53
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.48
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.48
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.46
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.45
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.42
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.42
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.41
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.39
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.38
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.37
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.36
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.18
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.15
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	99.06
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.05
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.02
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.89
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.81
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.78
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	98.61
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	98.49
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	98.36
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	98.34
1tua_A	191	Hypothetical protein APE0754; structural genomics,	98.29
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	98.23
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	98.21
1tua_A	191	Hypothetical protein APE0754; structural genomics,	98.12
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.73
2cxc_A	144	NUSA; transcription termination, RNA binding prote	96.59
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	96.47
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	96.28
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	95.63
2cxc_A	144	NUSA; transcription termination, RNA binding prote	95.54
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	94.99
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	94.69
1wh9_A	92	40S ribosomal protein S3; KH domain, structural ge	92.91
2pt7_G	152	HP1451, hypothetical protein; ATPase, protein-prot	91.58
3u5c_D	240	RP13, YS3, 40S ribosomal protein S3; translation,	85.99
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	85.47
3j20_C	210	30S ribosomal protein S3P; archaea, archaeal, KINK	85.13
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	84.86
3iz6_B	227	40S ribosomal protein S3 (S3P); eukaryotic ribosom	84.2
2xzm_C	243	KH domain containing protein; ribosome, translatio	83.73
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	82.49
3r8n_C	206	30S ribosomal protein S3; protein biosynthesis, RN	80.63

>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=99.73  E-value=1.7e-18  Score=99.98  Aligned_cols=59  Identities=32%  Similarity=0.559  Sum_probs=54.6

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ..++++.||.+++|+||||+|++|++|+++|||+|+|++++++.++..+|.|+|+|+|+
T Consensus         2 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~   60 (76)
T 1dtj_A            2 KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPA   60 (76)
T ss_dssp             CEEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHH
T ss_pred             ceEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeCHH
Confidence            46789999999999999999999999999999999999877677889999999999864

>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=99.69  E-value=3.4e-18  Score=101.34  Aligned_cols=59  Identities=34%  Similarity=0.567  Sum_probs=54.4

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ..+++|.||.+.+|+||||+|++|++|+++|||+|+|+++.++.++..+|.|+|+|+++
T Consensus         2 k~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~   60 (87)
T 1ec6_A            2 KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPA   60 (87)
T ss_dssp             CSEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHH
T ss_pred             ceEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHH
Confidence            35789999999999999999999999999999999999876667889999999999864

>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=99.68  E-value=2.1e-17  Score=96.95  Aligned_cols=59  Identities=19%  Similarity=0.331  Sum_probs=53.3

Q ss_pred             CCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        10 ~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      .....+++|.||.+++|.||||+|++|++|+++|||+|+|.++   .++..+|.|+|+|+++
T Consensus         2 ~g~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~---~~~~~~r~v~I~G~~~   60 (82)
T 1wvn_A            2 LGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP---VEGSSGRQVTITGSAA   60 (82)
T ss_dssp             CTTCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC---CTTCSEEEEEEEECHH
T ss_pred             CCCcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecC---CCCCCceEEEEEcCHH
Confidence            3557899999999999999999999999999999999999864   3678999999999874

>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=99.67  E-value=4.1e-17  Score=95.80  Aligned_cols=58  Identities=26%  Similarity=0.467  Sum_probs=52.4

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ...++.++.||.+++|.||||+|++|++|+++|||+|+|+++   .++..+|.|+|+|+++
T Consensus         4 g~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~---~~~~~~~~v~I~G~~~   61 (82)
T 1zzk_A            4 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITITGTQD   61 (82)
T ss_dssp             CCCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT---TSCSSEEEEEEEECHH
T ss_pred             CCeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCC---CCCCCceEEEEEeCHH
Confidence            456899999999999999999999999999999999999864   3678899999999864

>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=99.67  E-value=7.3e-17  Score=97.01  Aligned_cols=64  Identities=31%  Similarity=0.386  Sum_probs=56.0

Q ss_pred             ccCCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680          8 IRADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus         8 ~~~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      ..++...+.+|.||.+++|+||||+|++|++|+++|||+|+|.+++... ...+|.|+|+|+++.
T Consensus         9 ~~~p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~-~~~~r~v~I~G~~~~   72 (94)
T 1x4m_A            9 GDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN-TGADKPLRITGDPYK   72 (94)
T ss_dssp             CCCCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCS-SCSCEEEEEEECTTT
T ss_pred             CCCCCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCC-CCCceEEEEEeCHHH
Confidence            3567889999999999999999999999999999999999999865422 347999999998764

>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=99.67  E-value=1.5e-17  Score=96.03  Aligned_cols=55  Identities=24%  Similarity=0.453  Sum_probs=50.4

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ..+.++|+||.+.+|.||||+|++|++|+++|||+|+|+++     +.++|.|+|+|+++
T Consensus         3 ~~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~-----~~~er~v~I~G~~~   57 (73)
T 2axy_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-----NCPERIITLAGPTN   57 (73)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-----CCSEEEEEEEECHH
T ss_pred             ceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC-----CCCcEEEEEEeCHH
Confidence            45789999999999999999999999999999999999975     36899999999864

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

Probab=99.66  E-value=8.8e-17  Score=94.95  Aligned_cols=67  Identities=27%  Similarity=0.366  Sum_probs=57.2

Q ss_pred             CCCcccCCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680          4 KSPFIRADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus         4 ~~~~~~~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ++.+..++.....+|.||.+++|+||||+|++|++|+++|||+|+|.+++. .+...+|.|+|+|+|+
T Consensus         4 ~~~~~~g~~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~-~~~~~er~v~I~G~~~   70 (85)
T 2opv_A            4 HDNANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGS-QNTNVDKPLRIIGDPY   70 (85)
T ss_dssp             CSSCCCSCSSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSC-SSTTSCEEEEEEECHH
T ss_pred             cccCCCCCCCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCC-CCCCCceEEEEEeCHH
Confidence            444555667788999999999999999999999999999999999998653 2467899999999764

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

Probab=99.66  E-value=2e-17  Score=95.79  Aligned_cols=57  Identities=19%  Similarity=0.341  Sum_probs=52.0

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ...+++|.||.+++|.||||+|++|++|+++|||+|+|.++   .++..+|.|+|+|+|+
T Consensus         3 ~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~---~~~~~~~~v~I~G~~~   59 (76)
T 2p2r_A            3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANP---VEGSTDRQVTITGSAA   59 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCC---CTTCSEEEEEEEECHH
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCC---CCCCCeEEEEEEeCHH
Confidence            45789999999999999999999999999999999999963   4678999999999865

>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=99.65  E-value=5.9e-17  Score=96.00  Aligned_cols=58  Identities=24%  Similarity=0.351  Sum_probs=51.9

Q ss_pred             cCCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680          9 RADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus         9 ~~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      +.++..+++|.||.+++|+||||+|++||+|+++|||+|+|++.+      .++.++|+|+++.
T Consensus         5 ~~~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~------~~~~v~ItG~~e~   62 (83)
T 2dgr_A            5 SSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD------KEPVFAVTGMPEN   62 (83)
T ss_dssp             CSCCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS------SCCEEEEEECTTT
T ss_pred             CCCCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC------CCCeEEEEcCHHH
Confidence            346678999999999999999999999999999999999998644      3689999999965

>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=99.63  E-value=1.3e-16  Score=95.62  Aligned_cols=59  Identities=31%  Similarity=0.472  Sum_probs=53.2

Q ss_pred             CCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        10 ~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ....++++|.||.+++|+||||+|++|++|+++|||+|+|.++.   ++..+|.|+|+|+++
T Consensus        11 ~~~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~---~g~~~r~v~I~G~~e   69 (92)
T 1x4n_A           11 QRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS---GGLPERSCMLTGTPE   69 (92)
T ss_dssp             CCCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC---TTCSEEEEEEEECHH
T ss_pred             CCCCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCC---CCCCccEEEEEeCHH
Confidence            35568999999999999999999999999999999999999754   467899999999864

>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=99.63  E-value=8.1e-17  Score=95.88  Aligned_cols=59  Identities=25%  Similarity=0.461  Sum_probs=53.3

Q ss_pred             CCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        10 ~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      +...+++++.||.+++|.||||+|++|++|+++|||+|+|++.   .++..+|.|+|+|+++
T Consensus        10 ~~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~---~~~~~~~~v~I~G~~e   68 (89)
T 1j5k_A           10 GGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITITGTQD   68 (89)
T ss_dssp             CCCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSC---CSSSSEEEEEEEEEHH
T ss_pred             CCCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCC---CCCCCccEEEEEcCHH
Confidence            3568899999999999999999999999999999999999864   3678899999999865

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

Probab=99.62  E-value=1.9e-16  Score=97.31  Aligned_cols=57  Identities=21%  Similarity=0.420  Sum_probs=51.1

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      +++|.||.+++|+||||+|++|++|+++|||+|+|.++.+...+..+|.|+|+|+++
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e   64 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQ   64 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHH
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHH
Confidence            789999999999999999999999999999999999865434556899999999765

>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=99.59  E-value=3.2e-16  Score=102.19  Aligned_cols=61  Identities=48%  Similarity=0.761  Sum_probs=56.3

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ++.++++|+||.+++|.||||+|++|++|+++|||+|+|++.+++.++..+|.|+|+|+++
T Consensus         3 ~~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~   63 (178)
T 2anr_A            3 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIE   63 (178)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHH
T ss_pred             CCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHH
Confidence            5678999999999999999999999999999999999999877777899999999999864

>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=99.59  E-value=1.5e-15  Score=92.74  Aligned_cols=64  Identities=27%  Similarity=0.384  Sum_probs=53.9

Q ss_pred             cccCCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680          7 FIRADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus         7 ~~~~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      .+......+++|.||.+++|.||||+|++|++|+++|||+|+|.+..+. ....+|.|+|+|+++
T Consensus         8 ~~s~~ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~-~~~~~~~V~I~G~~~   71 (104)
T 1we8_A            8 ILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG-TLLLSRLIKISGTQK   71 (104)
T ss_dssp             CCSSSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC-SSSSEEEEEEEEEHH
T ss_pred             ccCCCCCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCC-CCCCcceEEEEcCHH
Confidence            3445567889999999999999999999999999999999999975431 134699999999875

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

Probab=99.57  E-value=8.2e-16  Score=94.59  Aligned_cols=55  Identities=27%  Similarity=0.504  Sum_probs=49.4

Q ss_pred             eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      .+++|.||.+++|+||||+|++||+|+++|||+|+|.++.   ++..+|.|+|+|+++
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~---~~~~er~V~I~G~~e   65 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD---GTGPEKIAHIMGPPD   65 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSC---SSSSEEEEEEESSHH
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCC---CCCceeEEEEEeCHH
Confidence            4789999999999999999999999999999999998754   457899999999864

>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=99.54  E-value=2.6e-15  Score=96.58  Aligned_cols=57  Identities=28%  Similarity=0.498  Sum_probs=51.9

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ..+++|+||.+.+|.||||+|++|++|+++|||+|+|++++  .++..+|.|+|+|+|+
T Consensus         2 ~~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~--~~~~~~r~v~I~G~~e   58 (163)
T 3krm_A            2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPE--TPDSKVRMVIITGPPE   58 (163)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCS--STTCSEEEEEEEECHH
T ss_pred             ceEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCC--CCCCCceEEEEEcCHH
Confidence            35789999999999999999999999999999999999754  4788999999999764

>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=99.53  E-value=6.4e-15  Score=89.15  Aligned_cols=58  Identities=17%  Similarity=0.219  Sum_probs=51.6

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ..++++|.||.+++|.||||+|++|++|+++|||+|+|+++++  ++..+|.|+|+|+++
T Consensus        15 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~--~~~~~~~V~I~G~~e   72 (97)
T 2ctl_A           15 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD--GNQPQDQITITGYEK   72 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT--CSSCSSEEEEESCHH
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC--CCCCccEEEEEeCHH
Confidence            3578999999999999999999999999999999999998764  455789999999743

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

Probab=99.53  E-value=1.1e-14  Score=83.57  Aligned_cols=55  Identities=15%  Similarity=0.227  Sum_probs=49.3

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ...+.++.||.+++|.|||++|++|++|+++|||+|+|++++     ..+|.|+|+|.++
T Consensus         3 ~~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g-----~~~~~V~I~G~~~   57 (71)
T 1vig_A            3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-----EKSNLIRIEGDPQ   57 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-----SSSEEEEEEESSH
T ss_pred             ceEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC-----CcccEEEEEcCHH
Confidence            456889999999999999999999999999999999999755     3679999999853

>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=99.48  E-value=9.3e-15  Score=87.81  Aligned_cols=56  Identities=16%  Similarity=0.309  Sum_probs=49.5

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ...++.+|.||.+++|.|||++|++|++|+++|||+|+|++.+     ..++.|+|+|+++
T Consensus        14 ~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~-----~~~~~V~I~G~~e   69 (94)
T 2cte_A           14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-----DPSNQIKITGTKE   69 (94)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-----SSCCEEEEEECHH
T ss_pred             CCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC-----CCCCeEEEEECHH
Confidence            5578999999999999999999999999999999999998643     3468899999853

>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=99.48  E-value=1.9e-14  Score=92.16  Aligned_cols=57  Identities=32%  Similarity=0.473  Sum_probs=50.7

Q ss_pred             eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ++++|+||.+++|.||||+|++|++|+++|||+|++.++.. .++..+|.|+|+|+++
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~-~~~~~~r~v~I~G~~~   58 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGS-QNTNVDKPLRIIGDPY   58 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTT-SSSSSCEEEEEEECHH
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCC-CCCCCceEEEEEcCHH
Confidence            57899999999999999999999999999999999987542 3567899999999764

>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=99.46  E-value=3e-14  Score=92.65  Aligned_cols=59  Identities=27%  Similarity=0.478  Sum_probs=51.7

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ...++|.||.+++|+||||+|++|++|+++|||+|+|.++....++..+|.|+|+|+++
T Consensus       103 ~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~  161 (174)
T 1j4w_A          103 LQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQ  161 (174)
T ss_dssp             -CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHH
T ss_pred             cEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCCCCCCCCCceEEEEECCHH
Confidence            46889999999999999999999999999999999999765434457899999999764

>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=99.45  E-value=2.2e-14  Score=93.22  Aligned_cols=56  Identities=27%  Similarity=0.497  Sum_probs=50.3

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ..+++|+||.+++|.||||+|++|++|+++|||+|+|.++.   ++..+|.|+|+|+++
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~---~~~~~r~v~I~G~~~   57 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD---GTTPERIAQITGPPD   57 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCT---TSCSEEEEEEEECHH
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCC---CCCCccEEEEEeCHH
Confidence            46789999999999999999999999999999999998642   467899999999864

>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=99.42  E-value=6e-14  Score=84.63  Aligned_cols=57  Identities=14%  Similarity=0.227  Sum_probs=50.8

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ...++.++.||.+++|.|||++|++|++|+++|||+|+|+++++    ..+|.|+|+|.++
T Consensus        14 ~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~----~~~~~V~I~G~~e   70 (95)
T 2ctm_A           14 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA----PDPNCVTVTGLPE   70 (95)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC----SCTTEEEEESCHH
T ss_pred             cccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCC----CCCcEEEEEcCHH
Confidence            56789999999999999999999999999999999999987653    3578999999863

>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=99.42  E-value=3.3e-14  Score=91.10  Aligned_cols=58  Identities=24%  Similarity=0.519  Sum_probs=52.4

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ....+++.||.+++|+||||+|++|++|+++|||+|+|.++  ..++..+|.|+|+|+++
T Consensus        87 ~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~--~~~~~~~~~v~I~G~~~  144 (160)
T 2jzx_A           87 PPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGD--MLPNSTERAITIAGIPQ  144 (160)
T ss_dssp             CSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCC--CSTTCCEEEEEEEECHH
T ss_pred             CCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCC--CCCCCCceEEEEEcCHH
Confidence            35899999999999999999999999999999999999864  35778999999999765

>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=99.41  E-value=4.6e-14  Score=90.46  Aligned_cols=55  Identities=24%  Similarity=0.453  Sum_probs=49.9

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ..+.++|+||.+.+|.||||+|++|++|+++|||+|+|+++     +..+|.|+|+|+++
T Consensus         3 ~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~-----~~~~r~v~I~G~~~   57 (160)
T 2jzx_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-----NCPERIITLAGPTN   57 (160)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC-----TTTEEEEEEEEEHH
T ss_pred             ccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC-----CCCceEEEEEeCHH
Confidence            46789999999999999999999999999999999999964     35799999999853

>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=99.39  E-value=1.7e-13  Score=88.00  Aligned_cols=59  Identities=25%  Similarity=0.421  Sum_probs=49.9

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCC-ceeEEEEeccCC
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVY-QVITLFLLSRPG   71 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~-~er~v~I~G~p~   71 (78)
                      ....+.+|.||.+++|.||||+|++|++|+++|||+|+|++++.  ++. .++.|+|+|+++
T Consensus        82 ~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~--~~~~~~~~v~I~G~~~  141 (163)
T 3krm_A           82 EVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQT--PDENDQVIVKIIGHFY  141 (163)
T ss_dssp             CCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCC--CCTTSEEEEEEEECHH
T ss_pred             CCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCCC--CCCCCceEEEEEeCHH
Confidence            34567899999999999999999999999999999999987542  334 445899999864

>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=99.38  E-value=7.7e-14  Score=90.83  Aligned_cols=59  Identities=34%  Similarity=0.504  Sum_probs=50.4

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ....++|.||.+++|+||||+|++|++|+++|||+|+|.+..+ .++..+|.|+|+|+++
T Consensus       102 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~-~~~~~~~~v~I~G~~~  160 (178)
T 2anr_A          102 RANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPD-GINLQNRVVTVSGEPE  160 (178)
T ss_dssp             GGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC-----CCEEEEEEESSHH
T ss_pred             CceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCC-CCCCCceEEEEEcCHH
Confidence            3478999999999999999999999999999999999987542 3567899999999874

>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=99.37  E-value=1.3e-13  Score=88.34  Aligned_cols=55  Identities=27%  Similarity=0.504  Sum_probs=49.4

Q ss_pred             eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      .++++.||.+++|.||||+|++|++|+++|||+|+|.+..   +...+|.|+|+|+++
T Consensus        91 ~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~---~~~~~~~v~I~G~~~  145 (164)
T 2jvz_A           91 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD---GTGPEKIAHIMGPPD  145 (164)
T ss_dssp             SSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCC---TTSSEEEEEEESCHH
T ss_pred             ceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCC---CCCCcEEEEEEcCHH
Confidence            4588999999999999999999999999999999998754   456799999999865

>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=99.36  E-value=1.6e-13  Score=83.88  Aligned_cols=53  Identities=17%  Similarity=0.199  Sum_probs=47.8

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRP   70 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p   70 (78)
                      ....+|.||.+++|.|||++|++|++|+++|||+|+|+++++     ..+.|+|+|++
T Consensus        16 p~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g~-----~~~~V~I~G~~   68 (104)
T 2ctk_A           16 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL-----QSDIIAITGLA   68 (104)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTT-----TCCEEEEEECH
T ss_pred             CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCCC-----CcceEEEEcCH
Confidence            478999999999999999999999999999999999997652     45689999986

>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=99.18  E-value=5.1e-12  Score=80.82  Aligned_cols=58  Identities=21%  Similarity=0.381  Sum_probs=47.3

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHHHhCC-eEEEecCCCCCCCCce--eEEEEeccCCC
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGS-KIKMSKANDFYPVYQV--ITLFLLSRPGF   72 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga-~I~i~~~~~~~~g~~e--r~v~I~G~p~~   72 (78)
                      ..++.||.+.+|++|||+|.||+.+++.||| +|+|.+..+......+  +.|+|+|++++
T Consensus        68 e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~  128 (144)
T 2qnd_A           68 EDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDS  128 (144)
T ss_dssp             EEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHH
T ss_pred             eEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHH
Confidence            4889999999999999999999999999997 9999986543212233  46999998753

>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=99.15  E-value=1.1e-11  Score=74.71  Aligned_cols=57  Identities=16%  Similarity=0.328  Sum_probs=50.1

Q ss_pred             CCCeeEEEEEecCCceeeEEecCCchHHHHHHHh-CCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDT-GSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        10 ~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~T-ga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ..+..+..|.||.++++.|||++|.+|++|+++| ||+|+|++++     ...+.|+|+|...
T Consensus        13 ~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g-----~~~~~V~I~G~~~   70 (95)
T 2ctj_A           13 LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG-----SGSDTVVIRGPSS   70 (95)
T ss_dssp             CCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT-----TTCCEEEEESCHH
T ss_pred             HhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCCC-----CCcceEEEEcCHH
Confidence            3567889999999999999999999999999999 9999998654     4677899999753

>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=99.06  E-value=1.5e-10  Score=73.41  Aligned_cols=44  Identities=25%  Similarity=0.443  Sum_probs=39.4

Q ss_pred             CCeeEEEEEecCC------ceeeEEecCCchHHHHHHHhCCeEEEecCCC
Q psy14680         11 DGVCQIKILVPSY------AAGAIIGKGGETIAQIQKDTGSKIKMSKAND   54 (78)
Q Consensus        11 ~~~~~~~l~vP~~------~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~   54 (78)
                      ...++.+++||.+      ++|.|||++|++||+|+++|||+|.|...+.
T Consensus         4 ~~k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS   53 (131)
T 1k1g_A            4 ATRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGS   53 (131)
T ss_dssp             -CCEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTT
T ss_pred             CceEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcc
Confidence            3568999999988      9999999999999999999999999987553

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

Probab=99.05  E-value=6.4e-11  Score=86.07  Aligned_cols=62  Identities=15%  Similarity=0.122  Sum_probs=52.1

Q ss_pred             CCeeEEEEEecCCceeeEEecCC--chHHHHHHHhCCeEEEecCC--CCCCCCceeEEEEeccCCC
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGG--ETIAQIQKDTGSKIKMSKAN--DFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G--~~Ik~i~~~Tga~I~i~~~~--~~~~g~~er~v~I~G~p~~   72 (78)
                      .+.+++++.||..+++.||||+|  ++|++|+++|||+|++++.+  ...+......|+|+|.+++
T Consensus        27 ~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~en   92 (376)
T 3n89_A           27 PTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGD   92 (376)
T ss_dssp             TTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHH
T ss_pred             CCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHH
Confidence            67899999999999999999999  99999999999999998654  1112245568999998753

>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=99.02  E-value=1.2e-10  Score=71.00  Aligned_cols=53  Identities=21%  Similarity=0.276  Sum_probs=46.3

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHH-hCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKD-TGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~-Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      ...+.++.||..+.+.|||++|++|++|+++ ++++|++++        .++.|+|+|.++.
T Consensus        25 ~~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~--------~~~~ItI~G~~~~   78 (102)
T 2ctf_A           25 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE--------GEDKITLEGPTED   78 (102)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS--------SSCEEEEEECHHH
T ss_pred             CeEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC--------CCCEEEEECCHHH
Confidence            3478999999999999999999999999997 599999985        3568999998753

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

Probab=98.89  E-value=3.7e-10  Score=67.87  Aligned_cols=51  Identities=22%  Similarity=0.299  Sum_probs=44.8

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCe-EEEecCCCCCCCCceeEEEEecc
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSK-IKMSKANDFYPVYQVITLFLLSR   69 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~-I~i~~~~~~~~g~~er~v~I~G~   69 (78)
                      ...+...|.||.+++|.+||++|++|++|+++||++ |.|.+        .+..|+|.|.
T Consensus        12 ~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e--------ddG~V~I~g~   63 (91)
T 2cpq_A           12 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE--------DTGTFRIYGE   63 (91)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET--------TTTEEEEEES
T ss_pred             cCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc--------CCCEEEEEEC
Confidence            456889999999999999999999999999999998 99973        2467889884

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

Probab=98.81  E-value=4.2e-09  Score=65.88  Aligned_cols=42  Identities=24%  Similarity=0.279  Sum_probs=37.2

Q ss_pred             CeeEEEEEecCC-------ceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680         12 GVCQIKILVPSY-------AAGAIIGKGGETIAQIQKDTGSKIKMSKAN   53 (78)
Q Consensus        12 ~~~~~~l~vP~~-------~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~   53 (78)
                      ..++.+++||..       ++|.|||++|.+||+|+++|||+|.|..++
T Consensus        10 ~~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~g   58 (119)
T 2yqr_A           10 HYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKG   58 (119)
T ss_dssp             SCEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBT
T ss_pred             eEEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCC
Confidence            357889999875       789999999999999999999999998554

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

Probab=98.78  E-value=1.9e-09  Score=69.12  Aligned_cols=41  Identities=34%  Similarity=0.494  Sum_probs=36.8

Q ss_pred             eEEEEEecCCc------eeeEEecCCchHHHHHHHhCCeEEEecCCC
Q psy14680         14 CQIKILVPSYA------AGAIIGKGGETIAQIQKDTGSKIKMSKAND   54 (78)
Q Consensus        14 ~~~~l~vP~~~------vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~   54 (78)
                      ++.+++||...      +|.|||++|+++|+|+++|||+|.|...++
T Consensus         2 ~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS   48 (140)
T 2bl5_A            2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGS   48 (140)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTS
T ss_pred             ceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCC
Confidence            57789998744      999999999999999999999999998764

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

Probab=98.61  E-value=7e-09  Score=66.15  Aligned_cols=53  Identities=17%  Similarity=0.149  Sum_probs=40.2

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      .++.++.||.+.+|++||++|++|++|++++|  |++....    ..+++.+...++|+
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~g--I~ii~~~----~~~~~~i~~~~~p~   55 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPG--VTAIDLD----EDTCTFHIYGEDQD   55 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTT--EEEEEEE----TTTTEEEEEESSHH
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHC--CeEeccC----CCchheeeccCCHH
Confidence            56899999999999999999999999999999  6554322    13455555555554

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

Probab=98.49  E-value=3.2e-08  Score=67.24  Aligned_cols=49  Identities=24%  Similarity=0.379  Sum_probs=42.9

Q ss_pred             eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccC
Q psy14680         14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRP   70 (78)
Q Consensus        14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p   70 (78)
                      ...++.||.+.+|.|||++|++|+.|+++|||+|++..        .++.|+|.++.
T Consensus        34 ~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~--------~~g~V~I~~~~   82 (219)
T 2e3u_A           34 QEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS--------ETGEVWITSTK   82 (219)
T ss_dssp             CEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT--------TTCEEEEEECT
T ss_pred             EEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc--------CCCEEEEecCC
Confidence            45689999999999999999999999999999999973        24568888764

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

Probab=98.36  E-value=5.1e-08  Score=66.25  Aligned_cols=38  Identities=26%  Similarity=0.448  Sum_probs=34.0

Q ss_pred             ceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         24 AAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        24 ~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      .+|+||||+|++|+.|++.|||+|.|..          +.|.|.|+++
T Consensus       139 ~~GriIGk~G~tik~ie~~Tg~~I~v~~----------~~v~i~G~~~  176 (219)
T 2e3u_A          139 VRGRIIGRKGRTRQIIEEMSGASVSVYG----------KTVAIIGNPI  176 (219)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHCCEEEEET----------TEEEEEECHH
T ss_pred             hhheeECCCchHHHHHHHHhCceEEECC----------eEEEEEeCHH
Confidence            6899999999999999999999999972          4599999864

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

Probab=98.34  E-value=1.7e-07  Score=68.09  Aligned_cols=61  Identities=10%  Similarity=0.178  Sum_probs=45.8

Q ss_pred             CeeEEEEEecCCceeeEEecCC--chHHHHHHHhCCeEEEecCCCCCC-CCceeEEEEeccCCC
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGG--ETIAQIQKDTGSKIKMSKANDFYP-VYQVITLFLLSRPGF   72 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G--~~Ik~i~~~Tga~I~i~~~~~~~~-g~~er~v~I~G~p~~   72 (78)
                      ..+++.+.|+..++..||||+|  ..|++|+++|||+|++++.++... ......|+|+|++++
T Consensus       184 ~~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~~ItItGs~e~  247 (376)
T 3n89_A          184 NNFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDN  247 (376)
T ss_dssp             SCEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC---------CCEEEEEEESCHHH
T ss_pred             cceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCCceEEEEEeCHHH
Confidence            4689999999999999999999  456999999999999987653111 123567999998753

>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=98.29  E-value=1.6e-07  Score=62.72  Aligned_cols=48  Identities=27%  Similarity=0.373  Sum_probs=41.9

Q ss_pred             eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEecc
Q psy14680         14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSR   69 (78)
Q Consensus        14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~   69 (78)
                      ..+++.||...+|.|||++|++++.|++.+|++|++..        .++.++|..+
T Consensus         4 ~~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~--------~~~~V~i~t~   51 (191)
T 1tua_A            4 PRIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT--------ENSMVIVEPE   51 (191)
T ss_dssp             CCEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET--------TTTEEEEEES
T ss_pred             cceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc--------CCCeEEEEeC
Confidence            34789999999999999999999999999999999973        4667788743

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

Probab=98.23  E-value=6.5e-07  Score=68.51  Aligned_cols=49  Identities=22%  Similarity=0.375  Sum_probs=42.2

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEecc
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSR   69 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~   69 (78)
                      -.....+.||.+++|.|||+||++||.|+++|||+|.|.++         -.|.|.+.
T Consensus       565 ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d~---------G~V~I~~~  613 (630)
T 3u1k_A          565 GPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVDE---------ETFSVFAP  613 (630)
T ss_dssp             CCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS---------SEEEEEES
T ss_pred             CCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcCC---------cEEEEEeC
Confidence            34578899999999999999999999999999999999843         35777774

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

Probab=98.21  E-value=7.8e-07  Score=56.91  Aligned_cols=55  Identities=16%  Similarity=0.275  Sum_probs=47.7

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ..++.+.+.+..++.|+|++|+.|+.|+..|++.|+|.+-.   + +.+-.|+|.|+|.
T Consensus        55 ~dPlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~---s-~g~tEVtIfG~~~  109 (140)
T 3v69_A           55 EDPKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWG---P-ERRAEIWIFGPPP  109 (140)
T ss_dssp             SSCEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCC---T-TSCEEEEEESCHH
T ss_pred             CCCeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccC---C-CCcEEEEEECCHH
Confidence            45678899999999999999999999999999999999753   2 4677899999874

>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=98.12  E-value=2.1e-07  Score=62.16  Aligned_cols=39  Identities=23%  Similarity=0.381  Sum_probs=33.7

Q ss_pred             CceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         23 YAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        23 ~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ...|+||||+|.+++.|+..|||+|.|..          +.+.|.|+++
T Consensus       107 r~~GrIIGk~G~tik~iE~~Tg~~I~v~~----------~~v~i~G~~~  145 (191)
T 1tua_A          107 RIKGRIIGEGGRARRTIEEMTDTYINVGE----------YEVAIIGDYE  145 (191)
T ss_dssp             HHHHHHHCGGGHHHHHHHHHHTCEEEECS----------SEEEEEEEHH
T ss_pred             HHhhheeCCCccHHHHHHHHHCceEEEcC----------CEEEEEeChH
Confidence            35899999999999999999999999972          2688888764

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

Probab=97.73  E-value=7.4e-06  Score=63.62  Aligned_cols=41  Identities=27%  Similarity=0.452  Sum_probs=0.8

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN   53 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~   53 (78)
                      .....+.||.+++|.|||+||.+|++|+++||++|.|.+++
T Consensus       569 p~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~ddG  609 (726)
T 4aid_A          569 PKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDG  609 (726)
T ss_dssp             CC---------------------------------------
T ss_pred             CeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEECCc
Confidence            34678899999999999999999999999999999998654

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

Probab=96.59  E-value=0.00087  Score=42.84  Aligned_cols=41  Identities=27%  Similarity=0.452  Sum_probs=36.9

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN   53 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~   53 (78)
                      .-.+.++|+...+|+.||++|++|+.|+++.|-+|.|-...
T Consensus        35 ~dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s   75 (144)
T 2cxc_A           35 NNRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYS   75 (144)
T ss_dssp             GTEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECC
T ss_pred             CCEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcC
Confidence            35678899999999999999999999999999999998744

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

Probab=96.47  E-value=0.00045  Score=53.64  Aligned_cols=41  Identities=24%  Similarity=0.412  Sum_probs=0.0

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN   53 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~   53 (78)
                      .....+.||.++++.+||++|.+|+.|.++||+.|.|..++
T Consensus       559 p~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~dg  599 (723)
T 3cdi_A          559 PRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIEDDG  599 (723)
T ss_dssp             -----------------------------------------
T ss_pred             ceEEEEEECHHHhcccccccceeeeeeehhhCceEEecCCc
Confidence            34567789999999999999999999999999999998654

>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=96.28  E-value=0.00025  Score=55.32  Aligned_cols=40  Identities=33%  Similarity=0.546  Sum_probs=13.1

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCC
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND   54 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~   54 (78)
                      ...+.||.+.+|.+||++|.+|++|+++||+.|.|..++.
T Consensus       599 ~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~dG~  638 (757)
T 1e3p_A          599 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIEDDGT  638 (757)
T ss_dssp             CCCC------------------CTTCCCCCSCC-------
T ss_pred             eEEEEEChHHeehcccccceeeehhhHhhCCEEEecCCce
Confidence            3467899999999999999999999999999999986543

>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=95.63  E-value=0.0081  Score=41.53  Aligned_cols=42  Identities=21%  Similarity=0.378  Sum_probs=38.0

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND   54 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~   54 (78)
                      .....+.||....++-|||+|.|++--.+-||.+|.|....+
T Consensus       183 ~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~~  224 (251)
T 2asb_A          183 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAP  224 (251)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESSC
T ss_pred             CcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHHH
Confidence            357889999999999999999999999999999999987544

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

Probab=95.54  E-value=0.0017  Score=41.43  Aligned_cols=40  Identities=30%  Similarity=0.430  Sum_probs=36.1

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEe
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMS   50 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~   50 (78)
                      ++.....+.||.+..++.|||+|.|++-..+-||.+|.|.
T Consensus       100 ~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A          100 NGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             TTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             CCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence            3567788999999999999999999999999999998775

>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=94.99  E-value=0.014  Score=41.84  Aligned_cols=42  Identities=31%  Similarity=0.391  Sum_probs=37.6

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecC
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKA   52 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~   52 (78)
                      +......+.||....++-|||+|.|++--.+-||.+|.|...
T Consensus       300 ~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s~  341 (344)
T 1hh2_P          300 KENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI  341 (344)
T ss_dssp             TTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             CCCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceeec
Confidence            344578899999999999999999999999999999999753

>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=94.69  E-value=0.018  Score=41.74  Aligned_cols=43  Identities=21%  Similarity=0.361  Sum_probs=38.7

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCC
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND   54 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~   54 (78)
                      ......+.||....++.|||+|.|++-..+-||.+|.|....+
T Consensus       305 ~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~~  347 (366)
T 1k0r_A          305 TARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAP  347 (366)
T ss_dssp             TTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEESSC
T ss_pred             CCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEHHH
Confidence            3557889999999999999999999999999999999987543

>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=92.91  E-value=0.022  Score=33.59  Aligned_cols=27  Identities=15%  Similarity=0.427  Sum_probs=22.2

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHH
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQK   41 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~   41 (78)
                      .+++.|-...-|.|||++|..|.+|++
T Consensus        36 ~i~I~I~tarPg~vIGkkG~~Ie~L~~   62 (92)
T 1wh9_A           36 RTEIIILATRTQNVLGEKGRRIRELTA   62 (92)
T ss_dssp             CEEEEEEESCHHHHHCGGGHHHHHHHH
T ss_pred             eEEEEEEeCCCceEEcCCcHHHHHHHH
Confidence            466777788899999999998887655

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

Probab=91.58  E-value=0.045  Score=35.10  Aligned_cols=29  Identities=14%  Similarity=0.127  Sum_probs=23.8

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHHHh
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQKDT   43 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~T   43 (78)
                      ++.+-+-.+..|.+|||.|.+++.||--+
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            45666778899999999999999987543

>3u5c_D RP13, YS3, 40S ribosomal protein S3; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_B 3o30_C 3o2z_C 3u5g_D 1s1h_C 3jyv_C*

Probab=85.99  E-value=0.2  Score=34.34  Aligned_cols=27  Identities=11%  Similarity=0.434  Sum_probs=22.2

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHH
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQK   41 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~   41 (78)
                      .+++.|-...-|.|||++|..|++|++
T Consensus        45 ~i~I~I~t~rPg~VIGkkG~~I~~L~~   71 (240)
T 3u5c_D           45 KTEVIIRATRTQDVLGENGRRINELTL   71 (240)
T ss_dssp             CEEEEEEESCHHHHHTTTTCTHHHHHH
T ss_pred             eEEEEEEeCCCceEEcCCchhHHHHHH
Confidence            356777788899999999999987654

>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=85.47  E-value=0.31  Score=33.30  Aligned_cols=37  Identities=30%  Similarity=0.398  Sum_probs=27.0

Q ss_pred             eeEEEEEecC-CceeeEEecCCchHHHHHH--------HhCCeEEE
Q psy14680         13 VCQIKILVPS-YAAGAIIGKGGETIAQIQK--------DTGSKIKM   49 (78)
Q Consensus        13 ~~~~~l~vP~-~~vG~IIGk~G~~Ik~i~~--------~Tga~I~i   49 (78)
                      .+...++|.. ++-|.||||+|+.||+|..        ..|++|.+
T Consensus       239 ~i~a~i~ve~~~~k~i~ig~~g~~ik~i~~~ar~~~~~~~~~~v~l  284 (308)
T 3iev_A          239 VIKGEIIVDRENLKPIIIGKKGQRLKEIGKRARQELELILGRPVYL  284 (308)
T ss_dssp             EEEEEEEESSGGGHHHHHCGGGHHHHHHHHHHHHHHHHHHTSCEEE
T ss_pred             EEEEEEEEccCCcceEEEcCCcHHHHHHHHHHHHHHHHHhCCceEE
Confidence            4666677765 4669999999999997754        45666554

>3j20_C 30S ribosomal protein S3P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=85.13  E-value=0.19  Score=33.82  Aligned_cols=36  Identities=28%  Similarity=0.604  Sum_probs=26.3

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHH----HHhC---CeEEEe
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQ----KDTG---SKIKMS   50 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~----~~Tg---a~I~i~   50 (78)
                      .+++.|-...-|.|||++|..|++|+    +.++   .+|.|.
T Consensus        41 ~~~I~I~t~rPg~vIG~~G~~I~~L~~~l~k~~~~~~v~I~i~   83 (210)
T 3j20_C           41 GTKVIIFAANPGYVIGRGGRRIRELTRILEKQFGLENPQIEVE   83 (210)
T ss_dssp             CCEEEEEESCHHHHHCSSSHHHHHHHHHHHHHSSCSSCEEEEE
T ss_pred             eEEEEEEeCCCceEEcCCchhHHHHHHHHHHHhCCCceEEEEE
Confidence            35666777788999999999998865    4555   455554

>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=84.86  E-value=0.2  Score=34.55  Aligned_cols=32  Identities=31%  Similarity=0.508  Sum_probs=27.9

Q ss_pred             CceeeEEecCCchHHHH-HHHhCCeEEEecCCC
Q psy14680         23 YAAGAIIGKGGETIAQI-QKDTGSKIKMSKAND   54 (78)
Q Consensus        23 ~~vG~IIGk~G~~Ik~i-~~~Tga~I~i~~~~~   54 (78)
                      +-+|+-||++|++|+.| ++-.|-+|.|-.-.+
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~  158 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDD  158 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCS
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEecC
Confidence            56799999999999999 888899999987543

>3iz6_B 40S ribosomal protein S3 (S3P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=84.20  E-value=0.2  Score=34.02  Aligned_cols=27  Identities=15%  Similarity=0.450  Sum_probs=22.7

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHH
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQK   41 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~   41 (78)
                      .+++.|-...-|.|||++|..|++|++
T Consensus        45 ~i~I~I~tarPg~vIGkkG~~I~~L~~   71 (227)
T 3iz6_B           45 RTEIIIRATRTQNVLGEKGRRIRELTS   71 (227)
T ss_dssp             EECCEEECTTHHHHHCSSSSHHHHHHH
T ss_pred             cEEEEEEeCCCceEEcCCchhHHHHHH
Confidence            466778888899999999999988654

>2xzm_C KH domain containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_C

Probab=83.73  E-value=0.31  Score=33.47  Aligned_cols=29  Identities=14%  Similarity=0.252  Sum_probs=23.5

Q ss_pred             eEEEEEecCCceeeEEecCCchHHHHHHH
Q psy14680         14 CQIKILVPSYAAGAIIGKGGETIAQIQKD   42 (78)
Q Consensus        14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~   42 (78)
                      ..+++.|-...-|.|||++|..|++|++.
T Consensus        47 ~~i~I~I~tarPg~vIGkkG~~I~~L~~~   75 (243)
T 2xzm_C           47 TKTEIRIKATKPQQVIGVEGKKHKELTQF   75 (243)
T ss_dssp             SCEEEEEEESCHHHHHCSSSHHHHHHHHH
T ss_pred             CeEEEEEEcCCCceEECCCchHHHHHHHH
Confidence            34677777888999999999999887653

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

Probab=82.49  E-value=0.31  Score=35.21  Aligned_cols=31  Identities=29%  Similarity=0.491  Sum_probs=28.1

Q ss_pred             CceeeEEecCCchHHHHHHHh-CCeEEEecCC
Q psy14680         23 YAAGAIIGKGGETIAQIQKDT-GSKIKMSKAN   53 (78)
Q Consensus        23 ~~vG~IIGk~G~~Ik~i~~~T-ga~I~i~~~~   53 (78)
                      +-+|+.||++|++|+.|.++- |-+|.|-...
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s  280 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYD  280 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECC
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEEcC
Confidence            568999999999999999999 9999998754

---

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	78
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	5e-11
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	2e-10
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	2e-10
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	1e-09
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	5e-09
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	8e-09
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	1e-08
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	1e-08
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	2e-08
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	2e-08
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	4e-08
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	3e-07
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	4e-07
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	7e-07
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	2e-06
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	6e-06
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	4e-05
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	1e-04
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	2e-04
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	2e-04
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	4e-04
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	5e-04
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	6e-04
d2bl5a1	134	d.51.1.1 (A:1-134) Quaking protein A (Xqua) {Afric	0.004

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

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

 Score = 50.5 bits (121), Expect = 5e-11
 Identities = 13/39 (33%), Positives = 29/39 (74%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
          I++L+     G+IIGK GE++ ++++++G++I +S+ N 
Sbjct: 6  IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC 44

>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 = 49.5 bits (118), Expect = 2e-10
 Identities = 15/43 (34%), Positives = 24/43 (55%)

Query: 12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
          G   I + +P +A G +IG+ GE I +IQ D G +I+    + 
Sbjct: 1  GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDG 43

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

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

 Score = 49.4 bits (118), Expect = 2e-10
 Identities = 18/42 (42%), Positives = 31/42 (73%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          +++ VP    GAI+GKGG+T+ + Q+ TG++I++SK  +F P
Sbjct: 5  VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP 46

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

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

 Score = 47.5 bits (113), Expect = 1e-09
 Identities = 16/42 (38%), Positives = 27/42 (64%)

Query: 13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
          V   +  VP    G IIG+GGE I++IQ+++G KI+++  + 
Sbjct: 7  VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG 48

>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 = 45.9 bits (109), Expect = 5e-09
 Identities = 10/39 (25%), Positives = 21/39 (53%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
            + +P      +IGK GE +  ++  T +KI++ + +D
Sbjct: 12 ATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDD 50

>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 = 45.6 bits (108), Expect = 8e-09
 Identities = 12/50 (24%), Positives = 21/50 (42%)

Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITL 64
          ++ + V       IIG+ G  I QI+ +    I+    +D       IT+
Sbjct: 11 KLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITI 60

>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 = 44.9 bits (106), Expect = 1e-08
 Identities = 15/43 (34%), Positives = 25/43 (58%)

Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
          +   +VP+   G IIGKGGETI  I + +G++I++ +      
Sbjct: 2  EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNA 44

>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 = 44.9 bits (106), Expect = 1e-08
 Identities = 18/45 (40%), Positives = 27/45 (60%)

Query: 10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
            G    +I++P+  AG +IGKGGETI Q+Q+  G K+ M +   
Sbjct: 4  GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGP 48

>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 = 44.1 bits (104), Expect = 2e-08
 Identities = 11/39 (28%), Positives = 25/39 (64%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
           ++ +P+   G IIG+ G  I +I++ +G++IK++   +
Sbjct: 4  HELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVE 42

>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 = 44.4 bits (105), Expect = 2e-08
 Identities = 8/39 (20%), Positives = 16/39 (41%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
          I++ VP      +IG+ G  I ++  +    I +     
Sbjct: 12 IEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL 50

>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 = 43.7 bits (103), Expect = 4e-08
 Identities = 15/47 (31%), Positives = 28/47 (59%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVI 62
           ++ +P   AG+IIGKGG+ I QI+ ++G+ IK+ +  +      + 
Sbjct: 6  TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIIT 52

>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 = 40.9 bits (96), Expect = 3e-07
 Identities = 7/39 (17%), Positives = 18/39 (46%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
          ++I +       +IGK G  I +I+      +++   ++
Sbjct: 7  VEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSE 45

>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 = 41.5 bits (97), Expect = 4e-07
 Identities = 17/42 (40%), Positives = 25/42 (59%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
           ++ VP  + G IIG+GGETI  I K +G+KI   K ++   
Sbjct: 17 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTL 58

>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 = 40.2 bits (94), Expect = 7e-07
 Identities = 7/46 (15%), Positives = 17/46 (36%)

Query: 9  RADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
            + +    + +       IIG  G+ I +I  +    I+  ++  
Sbjct: 5  ELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA 50

>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 = 39.4 bits (92), Expect = 2e-06
 Identities = 13/37 (35%), Positives = 20/37 (54%)

Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK 51
          +I + V     GA+IG  GE  A+I + TG+ I +  
Sbjct: 4  RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT 40

>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 = 37.3 bits (87), Expect = 6e-06
 Identities = 13/33 (39%), Positives = 20/33 (60%)

Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIK 48
          I + +P    G +IG   + I QIQ+DTG++I 
Sbjct: 5  ITVKIPVDKIGEVIGPKRQMINQIQEDTGAEIT 37

>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 = 4e-05
 Identities = 6/34 (17%), Positives = 15/34 (44%)

Query: 18 ILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK 51
          + +       +IGK G  I  ++ +   +I + +
Sbjct: 5  VAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ 38

>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 = 34.8 bits (80), Expect = 1e-04
 Identities = 8/40 (20%), Positives = 18/40 (45%), Gaps = 1/40 (2%)

Query: 15 QIKILVPSYAAGAIIGKGGETIAQI-QKDTGSKIKMSKAN 53
          ++++ +P+    ++IG  G  I  I ++  G  I      
Sbjct: 11 EVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG 50

>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 = 34.1 bits (78), Expect = 2e-04
 Identities = 9/38 (23%), Positives = 13/38 (34%)

Query: 17 KILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
          + +V     G  IG  G  I Q +K  G        + 
Sbjct: 11 EFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDT 48

>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 = 33.6 bits (77), Expect = 2e-04
 Identities = 6/34 (17%), Positives = 12/34 (35%)

Query: 18 ILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK 51
          I +       +IGK       +   +G  I ++ 
Sbjct: 5  IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN 38

>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 = 33.3 bits (76), Expect = 4e-04
 Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 9  RADGVCQIKILVPSYAAGAIIGKGGETIAQIQKD-TGSKIKMSKANDFY 56
          +A+      +  PS+    IIGK G+ +A+I +      I+ ++  D  
Sbjct: 16 KANSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGEDKI 64

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

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

 Score = 33.5 bits (77), Expect = 5e-04
 Identities = 9/22 (40%), Positives = 13/22 (59%)

Query: 26 GAIIGKGGETIAQIQKDTGSKI 47
          G IIG+GG     I++ T + I
Sbjct: 25 GRIIGEGGRARRTIEEMTDTYI 46

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

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

 Score = 32.8 bits (75), Expect = 6e-04
 Identities = 5/30 (16%), Positives = 13/30 (43%)

Query: 18 ILVPSYAAGAIIGKGGETIAQIQKDTGSKI 47
          + +       +IG+    +  +++ T  KI
Sbjct: 5  VEISPAKVPRVIGRKMSMLKTLEEKTECKI 34

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

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

 Score = 31.3 bits (71), Expect = 0.004
 Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 6/39 (15%)

Query: 17 KILVPSYAA------GAIIGKGGETIAQIQKDTGSKIKM 49
          K+ VP          G I+G  G T  Q++ +TG KI +
Sbjct: 5  KLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMV 43

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	78
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.75
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.75
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.72
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.7
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.69
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.69
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.68
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.63
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.62
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.54
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.5
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.5
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.46
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.4
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.38
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.32
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	99.26
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.26
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	99.17
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.14
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	99.1
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.96
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.76
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	98.66
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.5
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	97.39
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	97.36
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	95.45
d1egaa2	113	GTPase Era C-terminal domain {Escherichia coli [Ta	94.42
d2uubc1	105	Ribosomal protein S3 N-terminal domain {Thermus th	94.11
d1wf3a2	118	GTPase Era C-terminal domain {Thermus thermophilus	93.06
d2qalc1	105	Ribosomal protein S3 N-terminal domain {Escherichi	90.43
d2asba2	79	Transcription factor NusA, C-terminal domains {Myc	90.11
d1hh2p2	78	Transcription factor NusA, C-terminal domains {The	88.66
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	84.45

>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=99.75  E-value=2.6e-19  Score=102.20  Aligned_cols=59  Identities=32%  Similarity=0.555  Sum_probs=54.5

Q ss_pred             eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      ..+++.||.+++|.||||+|++|++|+++|||+|+|+++.+..++..+|.|+|+|++++
T Consensus         3 ~~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~   61 (74)
T d1dtja_           3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA   61 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHH
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEeCHHH
Confidence            46899999999999999999999999999999999998877778899999999998753

>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=99.75  E-value=2.7e-19  Score=101.46  Aligned_cols=58  Identities=28%  Similarity=0.474  Sum_probs=53.0

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      +++|.||++.+|+||||+|++|++|+++|||+|+|+++.+..++..+|.|+|+|+|++
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~   59 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQ   59 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHH
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEeCHHH
Confidence            4689999999999999999999999999999999998766667789999999999864

>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=99.72  E-value=3.6e-18  Score=98.83  Aligned_cols=64  Identities=31%  Similarity=0.393  Sum_probs=56.8

Q ss_pred             ccCCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680          8 IRADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus         8 ~~~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      ..++...+.+|.||..++|+||||+|++|++|+++|||+|+|+++.+ .++..+|.|+|+|+|++
T Consensus         2 g~~~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~-~~~~~~r~v~I~G~~~~   65 (81)
T d1x4ma1           2 GDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGP-QNTGADKPLRITGDPYK   65 (81)
T ss_dssp             CCCCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCC-CSSCSCEEEEEEECTTT
T ss_pred             CCCCccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCC-CCCCCceEEEEEeCHHH
Confidence            35678899999999999999999999999999999999999987543 35678999999999975

>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=99.70  E-value=2e-18  Score=97.65  Aligned_cols=57  Identities=19%  Similarity=0.324  Sum_probs=51.5

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      +.+.+|.||.+++|+||||+|++|++|+++|||+|+|+++.   ++..+|.|+|+|+|++
T Consensus         1 q~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~---~~~~~r~v~I~G~~~~   57 (70)
T d1wvna1           1 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPV---EGSSGRQVTITGSAAS   57 (70)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCC---TTCSEEEEEEEECHHH
T ss_pred             CeEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCC---CCCCcEEEEEEeCHHH
Confidence            36889999999999999999999999999999999998654   5788999999999764

>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=99.69  E-value=5.5e-18  Score=96.44  Aligned_cols=58  Identities=26%  Similarity=0.434  Sum_probs=52.2

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      ..++.++.||.+++|.||||+|++|++|+++|||+|+|.++.   ++..+|.|+|+|++++
T Consensus         2 p~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~---~~~~~r~i~I~G~~~~   59 (75)
T d1zzka1           2 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL---EGSEDRIITITGTQDQ   59 (75)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTT---SCSSEEEEEEEECHHH
T ss_pred             CcEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCC---CCCCceEEEEEeCHHH
Confidence            357889999999999999999999999999999999998654   5789999999998753

>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=99.69  E-value=3.1e-18  Score=97.45  Aligned_cols=57  Identities=26%  Similarity=0.469  Sum_probs=51.7

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      ...+++.||.+++|+||||+|++|++|+++|||+|+|.++.   ++..+|.|+|+|++++
T Consensus         2 ~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~---~~~~~r~v~I~G~~~~   58 (74)
T d1j4wa1           2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD---GTTPERIAQITGPPDR   58 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCT---TSCSEEEEEEEECHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCC---CCCCeeEEEEEeCHHH
Confidence            46899999999999999999999999999999999998764   5678999999998753

>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=99.68  E-value=2.8e-18  Score=97.23  Aligned_cols=55  Identities=25%  Similarity=0.495  Sum_probs=50.1

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      .++++|+||.+.+|.||||+|++|++|+++|||+|++++++     .+||.|+|+|+|++
T Consensus         3 ~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~-----~~er~v~I~G~~~~   57 (71)
T d2axya1           3 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN-----CPERIITLAGPTNA   57 (71)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSC-----CSEEEEEEEECHHH
T ss_pred             cEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCCC-----CCcceEEEEECHHH
Confidence            57899999999999999999999999999999999998643     57999999998763

>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=99.63  E-value=8.9e-17  Score=96.63  Aligned_cols=64  Identities=27%  Similarity=0.359  Sum_probs=55.2

Q ss_pred             ccCCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680          8 IRADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus         8 ~~~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      ......++.+|.||..++|+||||+|.+|++|+++|||+|+|+++.+. ....+|.|+|+|++++
T Consensus         9 ~~~~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~-~~~~~r~v~I~G~~~~   72 (104)
T d1we8a_           9 LTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG-TLLLSRLIKISGTQKE   72 (104)
T ss_dssp             CSSSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC-SSSSEEEEEEEEEHHH
T ss_pred             cCCCCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCC-CCCCccEEEEEeCHHH
Confidence            345667889999999999999999999999999999999999876542 3457899999998764

>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=99.62  E-value=4.6e-17  Score=93.54  Aligned_cols=59  Identities=31%  Similarity=0.457  Sum_probs=53.3

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      ...++.++.||..++|.|||++|.+|++|+++|||+|+|+++.   ++..+|.|+|+|+|++
T Consensus         5 ~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~---~~~~~r~v~I~G~~~~   63 (79)
T d1x4na1           5 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS---GGLPERSCMLTGTPES   63 (79)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC---TTCSEEEEEEEECHHH
T ss_pred             CCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCC---CCCCceEEEEEeCHHH
Confidence            4568899999999999999999999999999999999998754   5788999999998754

>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=99.54  E-value=8.9e-16  Score=88.99  Aligned_cols=58  Identities=17%  Similarity=0.207  Sum_probs=51.6

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      .+++++.||..++|.|||++|++|++|+++|||+|++++.+.  ++..++.|+|+|++++
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~--~~~~~~~i~I~G~~e~   66 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD--GNQPQDQITITGYEKN   66 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT--CSSCSSEEEEESCHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCC--CCCCcceEEEECCHHH
Confidence            467899999999999999999999999999999999987653  5678899999998653

>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=99.50  E-value=5.1e-15  Score=83.56  Aligned_cols=56  Identities=14%  Similarity=0.192  Sum_probs=49.8

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      ....+++.||..++|.|||++|++|++|+++|||+|++++++     ..++.|+|+|++++
T Consensus         3 ~~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~-----~~~~~v~I~G~~~~   58 (71)
T d1viga_           3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-----EKSNLIRIEGDPQG   58 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-----SSSEEEEEEESSHH
T ss_pred             ceEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCCC-----CCCCEEEEECCHHH
Confidence            346789999999999999999999999999999999998643     57889999998764

>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=99.50  E-value=1.9e-15  Score=87.19  Aligned_cols=57  Identities=16%  Similarity=0.274  Sum_probs=51.0

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      ....+.++.||..++|+|||++|++|++|+++|||+|++++.+     ..++.|+|+|++++
T Consensus         7 ~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~-----~~~~~v~I~G~~~~   63 (81)
T d2ctea1           7 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-----DPSNQIKITGTKEG   63 (81)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-----SSCCEEEEEECHHH
T ss_pred             cCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCCC-----CCCCEEEEEeCHHH
Confidence            4567899999999999999999999999999999999998654     57889999998764

>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=99.46  E-value=8.8e-15  Score=84.32  Aligned_cols=58  Identities=14%  Similarity=0.205  Sum_probs=50.2

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      ...++.++.||..++|.|||++|++|++|+++|||+|+++++++    ..++.|+|+|++++
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~----~~~~~v~I~G~~~~   64 (81)
T d2ctma1           7 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA----PDPNCVTVTGLPEN   64 (81)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC----SCTTEEEEESCHHH
T ss_pred             hcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC----CCCCEEEEeCCHHH
Confidence            45677899999999999999999999999999999999987653    23578999998754

>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=99.40  E-value=1.7e-14  Score=83.07  Aligned_cols=57  Identities=16%  Similarity=0.306  Sum_probs=49.7

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHH-hCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKD-TGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~-Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      .+..+.++.||..++|+||||+|++|++|+++ ++|+|++++.+     ..++.|+|+|++++
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~-----~~~~~v~I~G~~~~   64 (82)
T d2ctja1           7 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG-----SGSDTVVIRGPSSD   64 (82)
T ss_dssp             CSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT-----TTCCEEEEESCHHH
T ss_pred             cCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCCC-----CCCceEEEeCCHHH
Confidence            45678999999999999999999999999987 59999998644     57899999998753

>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=99.38  E-value=3.1e-14  Score=83.48  Aligned_cols=55  Identities=16%  Similarity=0.200  Sum_probs=49.4

Q ss_pred             eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      .++.++.||..++|.|||++|++|++|+++|||+|.+++.+     ..++.|+|+|++++
T Consensus         9 ~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~-----~~~~~v~I~G~~~~   63 (91)
T d2ctka1           9 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-----LQSDIIAITGLAAN   63 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT-----TTCCEEEEEECHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCCC-----CCcceEEEECCHHH
Confidence            57899999999999999999999999999999999998654     56789999998753

>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=99.32  E-value=7.6e-14  Score=80.33  Aligned_cols=52  Identities=19%  Similarity=0.190  Sum_probs=45.3

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEecc
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSR   69 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~   69 (78)
                      ...++.++.||.+++|+|||++|++|++|+++|||+|.+.++       .++.|.|.|.
T Consensus         5 ~~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~-------~~g~v~I~g~   56 (78)
T d2cpqa1           5 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-------DTGTFRIYGE   56 (78)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-------TTTEEEEEES
T ss_pred             cCCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC-------CCceEEEEEC
Confidence            345788999999999999999999999999999999998753       3467899984

>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=99.26  E-value=2.1e-13  Score=73.83  Aligned_cols=48  Identities=31%  Similarity=0.508  Sum_probs=15.2

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ..++.||.+++|.|||+||.+||+|+++|||+|+|.+         +..|+|.|.-.
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d---------dg~v~I~a~~~   51 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED---------DGTIYIGAADG   51 (54)
T ss_dssp             CC---------------------CHHHHSCCCC-----------------CCCCBSS
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC---------CeEEEEEecCc
Confidence            3568899999999999999999999999999999974         45677777543

>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=99.26  E-value=3.9e-13  Score=78.29  Aligned_cols=47  Identities=13%  Similarity=0.191  Sum_probs=41.6

Q ss_pred             EEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        16 ~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      .-+.||.+.+|.||||+|++|++|+++|||+|+|.+         ++.|+|+|+++
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~---------~g~v~I~G~~e   49 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ---------NGLIWVNGDRR   49 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT---------TSEEEEESCHH
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC---------CCEEEEEeCHH
Confidence            357899999999999999999999999999999974         34689999874

>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=99.17  E-value=2.7e-12  Score=74.77  Aligned_cols=37  Identities=35%  Similarity=0.501  Sum_probs=34.3

Q ss_pred             EEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecC
Q psy14680         16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKA   52 (78)
Q Consensus        16 ~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~   52 (78)
                      +.+.||.+.+|.||||+|++|++|+++|||+|+|..+
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d   41 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE   41 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcC
Confidence            4589999999999999999999999999999999753

>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=99.14  E-value=1.6e-11  Score=71.83  Aligned_cols=54  Identities=20%  Similarity=0.294  Sum_probs=47.0

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHH-hCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKD-TGSKIKMSKANDFYPVYQVITLFLLSRPGF   72 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~-Tga~I~i~~~~~~~~g~~er~v~I~G~p~~   72 (78)
                      +...+.++.||..+++.|||++|++|++|+++ ++++|+++++        +..|+|+|+++.
T Consensus        18 ~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~~--------~~~v~i~G~~~~   72 (90)
T d2ctfa1          18 NSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG--------EDKITLEGPTED   72 (90)
T ss_dssp             CCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS--------SCEEEEEECHHH
T ss_pred             CCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCCC--------CceEEEeCCHHH
Confidence            55789999999999999999999999999999 4899999742        456999998753

>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=99.10  E-value=3.8e-12  Score=71.52  Aligned_cols=44  Identities=14%  Similarity=0.190  Sum_probs=33.4

Q ss_pred             EEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEecc
Q psy14680         17 KILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSR   69 (78)
Q Consensus        17 ~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~   69 (78)
                      -+.||.+.+|.||||+|++|++|+++|||+|+|.++         ..|+|+|.
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~---------g~v~I~g~   47 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANN---------GRIWATCP   47 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECTT---------SEEEC---
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcCC---------CEEEEEeC
Confidence            367899999999999999999999999999999742         24889885

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

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

Probab=98.96  E-value=1.6e-10  Score=67.55  Aligned_cols=45  Identities=13%  Similarity=0.228  Sum_probs=39.6

Q ss_pred             EEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccC
Q psy14680         17 KILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRP   70 (78)
Q Consensus        17 ~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p   70 (78)
                      -+.||.+.+|.|||++|++|+.|+++|||+|.|.+++         .|.|.|..
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d~G---------~V~I~g~~   48 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARNG---------RIHLECPN   48 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEETTT---------EEEEECSC
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECCCc---------EEEEEeCC
Confidence            4689999999999999999999999999999998543         48888864

>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=98.76  E-value=1.3e-09  Score=66.94  Aligned_cols=42  Identities=26%  Similarity=0.494  Sum_probs=37.8

Q ss_pred             eeEEEEEecCCc------eeeEEecCCchHHHHHHHhCCeEEEecCCC
Q psy14680         13 VCQIKILVPSYA------AGAIIGKGGETIAQIQKDTGSKIKMSKAND   54 (78)
Q Consensus        13 ~~~~~l~vP~~~------vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~   54 (78)
                      +++.+++||...      +|.|||.+|+++|+|+++|||+|.|.-.++
T Consensus         2 k~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS   49 (122)
T d1k1ga_           2 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGS   49 (122)
T ss_dssp             CEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTT
T ss_pred             ceeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCC
Confidence            568899999864      999999999999999999999999987664

>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=98.66  E-value=2.9e-09  Score=66.40  Aligned_cols=41  Identities=34%  Similarity=0.481  Sum_probs=37.4

Q ss_pred             eEEEEEecC------CceeeEEecCCchHHHHHHHhCCeEEEecCCC
Q psy14680         14 CQIKILVPS------YAAGAIIGKGGETIAQIQKDTGSKIKMSKAND   54 (78)
Q Consensus        14 ~~~~l~vP~------~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~   54 (78)
                      ++.+++||.      .++|.|||.+|+++|+|+++|||+|.|.-.++
T Consensus         2 l~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS   48 (134)
T d2bl5a1           2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGS   48 (134)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTS
T ss_pred             cceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCC
Confidence            577899986      58899999999999999999999999998775

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

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

Probab=98.50  E-value=7.4e-09  Score=62.02  Aligned_cols=38  Identities=24%  Similarity=0.393  Sum_probs=31.2

Q ss_pred             ceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680         24 AAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG   71 (78)
Q Consensus        24 ~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~   71 (78)
                      ..|+|||++|.+|+.|++.|||+|.|..+          .+.|.|+++
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~d~----------~v~iig~~e   60 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVGEY----------EVAIIGDYE   60 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECSS----------EEEEEEEHH
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEeCC----------eEEEEECch
Confidence            47999999999999999999999999631          266667653

>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=97.39  E-value=4e-05  Score=42.07  Aligned_cols=43  Identities=21%  Similarity=0.373  Sum_probs=38.4

Q ss_pred             CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680         11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN   53 (78)
Q Consensus        11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~   53 (78)
                      .......+.||.+..+..|||+|.|++-..+-||.+|.|-.+.
T Consensus        23 e~~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~es   65 (67)
T d2asba3          23 QTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA   65 (67)
T ss_dssp             TTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESS
T ss_pred             CCCcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeCC
Confidence            3445788999999999999999999999999999999998654

>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=97.36  E-value=5.9e-05  Score=41.47  Aligned_cols=41  Identities=32%  Similarity=0.396  Sum_probs=36.9

Q ss_pred             CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecC
Q psy14680         12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKA   52 (78)
Q Consensus        12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~   52 (78)
                      ..-...+.||.+..+..|||+|.|++-..+-||.+|.|...
T Consensus        25 ~~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s~   65 (68)
T d1hh2p3          25 ENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI   65 (68)
T ss_dssp             TTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             CCCEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEEc
Confidence            34468899999999999999999999999999999999753

>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=95.45  E-value=0.0014  Score=37.62  Aligned_cols=29  Identities=14%  Similarity=0.365  Sum_probs=25.2

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHHHh
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQKDT   43 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~T   43 (78)
                      .+++.|-...-|.||||+|++|++|++.-
T Consensus        36 ~i~I~I~tarPGivIGrkG~~I~~L~~~l   64 (92)
T d1wh9a_          36 RTEIIILATRTQNVLGEKGRRIRELTAVV   64 (92)
T ss_dssp             CEEEEEEESCHHHHHCGGGHHHHHHHHHH
T ss_pred             eEEEEEEeCCCceeeccCchhHHHHHHHH
Confidence            46788889999999999999999987654

>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=94.42  E-value=0.0043  Score=36.52  Aligned_cols=31  Identities=26%  Similarity=0.242  Sum_probs=24.8

Q ss_pred             eeEEEEEecC-CceeeEEecCCchHHHHHHHh
Q psy14680         13 VCQIKILVPS-YAAGAIIGKGGETIAQIQKDT   43 (78)
Q Consensus        13 ~~~~~l~vP~-~~vG~IIGk~G~~Ik~i~~~T   43 (78)
                      .+...++|+. ++-+.|||++|++||+|...+
T Consensus        48 ~I~a~I~V~~~sqk~IiIGk~G~~ik~I~~~a   79 (113)
T d1egaa2          48 DINGLILVEREGQKKMVIGNKGAKIKTIGIEA   79 (113)
T ss_dssp             EEEEEEEESSHHHHHHHHCGGGHHHHHHHHHH
T ss_pred             EEEEEEEECCcchhhhhhcccchHHHHHHHHH
Confidence            4777788877 555999999999999886543

>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=94.11  E-value=0.0037  Score=36.40  Aligned_cols=29  Identities=28%  Similarity=0.606  Sum_probs=24.1

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHHHh
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQKDT   43 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~T   43 (78)
                      .+++.|-...-|.|||++|+.|++|+++-
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            36677777899999999999998887753

>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=93.06  E-value=0.01  Score=35.10  Aligned_cols=37  Identities=24%  Similarity=0.398  Sum_probs=27.0

Q ss_pred             eeEEEEEecC-CceeeEEecCCchHHHHH--------HHhCCeEEE
Q psy14680         13 VCQIKILVPS-YAAGAIIGKGGETIAQIQ--------KDTGSKIKM   49 (78)
Q Consensus        13 ~~~~~l~vP~-~~vG~IIGk~G~~Ik~i~--------~~Tga~I~i   49 (78)
                      .+...++|+. ++-+.|||++|++||+|.        +.++++|.+
T Consensus        49 ~I~~~I~V~~~sqK~IiIGk~G~~ik~Ig~~aR~~le~~~~~kV~L   94 (118)
T d1wf3a2          49 YIKAILYVERPSQKAIVIGEGGRKIKEIGQATRKQLEALLGKKVYL   94 (118)
T ss_dssp             EEEEEEEESSHHHHHHHHCGGGHHHHHHHHHHHHHHHHHHTSEEEE
T ss_pred             EEEEEEEeCccchhhhhhccCchhHHHHHHHHHHHHHHHhCCCeEE
Confidence            4566778877 555999999999999765        445666644

>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=90.43  E-value=0.015  Score=33.75  Aligned_cols=28  Identities=29%  Similarity=0.604  Sum_probs=23.0

Q ss_pred             EEEEEecCCceeeEEecCCchHHHHHHH
Q psy14680         15 QIKILVPSYAAGAIIGKGGETIAQIQKD   42 (78)
Q Consensus        15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~   42 (78)
                      .+++.|-...-|.|||++|+.|.+|+++
T Consensus        62 ~i~V~I~tarPGviIG~~G~~i~~L~~~   89 (105)
T d2qalc1          62 SIRVTIHTARPGIVIGKKGEDVEKLRKV   89 (105)
T ss_dssp             CBCCEEEESCHHHHHCTTSHHHHHHHHH
T ss_pred             cEEEEEEeCCCccEeccCcccHHHHHHH
Confidence            3566777789999999999999887754

>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=90.11  E-value=0.034  Score=30.86  Aligned_cols=29  Identities=31%  Similarity=0.525  Sum_probs=24.2

Q ss_pred             CceeeEEecCCchHHHHHHHh-CCeEEEec
Q psy14680         23 YAAGAIIGKGGETIAQIQKDT-GSKIKMSK   51 (78)
Q Consensus        23 ~~vG~IIGk~G~~Ik~i~~~T-ga~I~i~~   51 (78)
                      +-+|+.||.+|++|+.|.++- |-+|.|-.
T Consensus        47 DpvGacvG~~GsRI~~I~~eL~gEkIDii~   76 (79)
T d2asba2          47 NAKGACIGPMGQRVRNVMSELSGEKIDIID   76 (79)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEE
T ss_pred             CceeEEECCCccHHHHHHHHhCCceEEEEE
Confidence            567999999999999987776 77787764

>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=88.66  E-value=0.066  Score=29.55  Aligned_cols=28  Identities=43%  Similarity=0.662  Sum_probs=23.4

Q ss_pred             CceeeEEecCCchHHHHHHHh-CCeEEEe
Q psy14680         23 YAAGAIIGKGGETIAQIQKDT-GSKIKMS   50 (78)
Q Consensus        23 ~~vG~IIGk~G~~Ik~i~~~T-ga~I~i~   50 (78)
                      +-+|+.+|.+|++|+.|.++- |-+|.|-
T Consensus        47 DpvGacVG~~G~RI~~I~~eL~gEkIDii   75 (78)
T d1hh2p2          47 DPIGACIGEGGSRIAAILKELKGEKLDVL   75 (78)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEE
T ss_pred             CeeEEEECCCchHHHHHHHHhCCceeEEE
Confidence            567999999999999988776 6777765

>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=84.45  E-value=0.097  Score=29.03  Aligned_cols=36  Identities=11%  Similarity=0.015  Sum_probs=31.7

Q ss_pred             EEecCCceeeEEecCCc-hHHHHHHHhCCeEEEecCC
Q psy14680         18 ILVPSYAAGAIIGKGGE-TIAQIQKDTGSKIKMSKAN   53 (78)
Q Consensus        18 l~vP~~~vG~IIGk~G~-~Ik~i~~~Tga~I~i~~~~   53 (78)
                      +-||..++-.+||++++ -++.|.+.++|.|.|-.++
T Consensus         5 ~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~NG   41 (85)
T d2ja9a2           5 IDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNG   41 (85)
T ss_dssp             EECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEETTT
T ss_pred             EEecHHHHHHHHcCCCChHHHHHHhhcCceEEEecCc
Confidence            56888899999999998 6888999999999998655