Citrus Sinensis ID: 029038

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
Protein Sequence
MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLSIIEEARKRQALATSAAAQ
Secondary Structure (PSIPRED)
cccEEEEccEEEcccccccccEEEEEEccccccEEEEEcccccEEEEEcccccccEEEEEEEEEEEEEcccEEEEEEccEEEEEcccccccccEEEEEccccEEEEEEEEEcccEEEEEccccEEEEEEEEEEEEEcccccEEEEEcccccEEEEEEcEEEEEEcccccEEEccccccEEEEHHHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cccEEEEccEEccccccccccEEEEEEccccccEEEEEccccEEEEEEccHHHHcEEEEEEEEEEEcccccEEEEEccccEEEcccccEEEccEEEEEcccccEEEEEEEccccEEEEEccccccEEEEEEEEEccccccEEEEEEEccccEEEEEcccEEEEEcccccEEEccccccEEEHHHHHHHHHHHHHHHcccc
Coil and Loop (DISEMBL)
mqrhvlvdakvrtdktypagfmdvvsipktnenFRLLYDtkgrfrlhsIRDEEAKFKLCKvrsvqfgqkgipyintydgrtirypdplikandtikldlETNKITEFIKFDVGNVVMVTggrnrgrvgiiknrekhkgsfeTIHIQDALGHEFATRLGNvftigkgtkpwvslpkgkgikLSIIEEARKRQALATSAAAQ
Flexible Loop (DISEMBL)
mqrhvlvdakvrtdktypagfmdvvsipktnenFRLLYDTKGRFRLHSIRDEEakfklckvrsvqfgqkgipyintydgrtirYPDPLIKANDTIKLDLETNKItefikfdvgnvvmvtggrnrgrvgiiknrekhkgsFETIHIQDALGHEFATRLGNVFTigkgtkpwvslpkgkGIKLSIIEEARKRQALATSAAAQ
Low Complexity Region (SEG)
MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLSIIEEARKRQALATSAAAQ
Disordered region (IsUnstruct)
*****LVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLSII****************
Disordered Region (DISOPRED)
*QRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLSII****************
Disordered Region (DISEMBL)
MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLSIIEEAR************
Disordered Region (DISPRO)
*QRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLSIIEEARKRQALA******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLSIIEEARKRQALATSAAAQ
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	200	2.2.26 [Sep-21-2011]
Q8VYK6	262	40S ribosomal protein S4-	yes	no	0.985	0.751	0.904	1e-104
P49204	262	40S ribosomal protein S4-	yes	no	0.985	0.751	0.904	1e-103
P46300	264	40S ribosomal protein S4	N/A	no	0.995	0.753	0.884	1e-103
Q93VH9	261	40S ribosomal protein S4-	yes	no	0.95	0.727	0.926	1e-103
O22424	265	40S ribosomal protein S4	N/A	no	0.95	0.716	0.905	1e-101
P46299	262	40S ribosomal protein S4	N/A	no	0.985	0.751	0.888	1e-101
P49398	265	40S ribosomal protein S4	yes	no	0.95	0.716	0.894	1e-100
O81363	261	40S ribosomal protein S4	N/A	no	0.93	0.712	0.884	2e-95
P47961	263	40S ribosomal protein S4	yes	no	0.99	0.752	0.666	2e-76
P79103	263	40S ribosomal protein S4	yes	no	0.99	0.752	0.666	2e-76

>sp|Q8VYK6|RS43_ARATH 40S ribosomal protein S4-3 OS=Arabidopsis thaliana GN=RPS4D PE=2 SV=2

 Score =  375 bits (964), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 180/199 (90%), Positives = 189/199 (94%), Gaps = 2/199 (1%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRH+ VD KVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSI+DEEAKFKLCK
Sbjct: 66  MQRHIQVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIKDEEAKFKLCK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VRS+QFGQKGIPY+NTYDGRTIRYPDPLIK NDTIKLDLE NKI EFIKFDVGNVVMVTG
Sbjct: 126 VRSIQFGQKGIPYLNTYDGRTIRYPDPLIKPNDTIKLDLEANKIVEFIKFDVGNVVMVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRNRGRVG+IKNREKHKGSFETIHIQD+ GHEFATRLGNV+TIGKGTKPWVSLPKGKGIK
Sbjct: 186 GRNRGRVGVIKNREKHKGSFETIHIQDSTGHEFATRLGNVYTIGKGTKPWVSLPKGKGIK 245

Query: 181 LSIIEEARKRQALATSAAA 199
           L+IIEEARKR  LA+  AA
Sbjct: 246 LTIIEEARKR--LASQQAA 262

Arabidopsis thaliana (taxid: 3702)

>sp|P49204|RS42_ARATH 40S ribosomal protein S4-2 OS=Arabidopsis thaliana GN=RPS4B PE=2 SV=4

 Score =  375 bits (962), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 180/199 (90%), Positives = 189/199 (94%), Gaps = 2/199 (1%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRH+ VD KVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSI+DEEAKFKLCK
Sbjct: 66  MQRHIQVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIKDEEAKFKLCK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VRS+QFGQKGIPY+NTYDGRTIRYPDPLIK NDTIKLDLE NKI EFIKFDVGNVVMVTG
Sbjct: 126 VRSIQFGQKGIPYLNTYDGRTIRYPDPLIKPNDTIKLDLEENKIVEFIKFDVGNVVMVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRNRGRVG+IKNREKHKGSFETIHIQD+ GHEFATRLGNV+TIGKGTKPWVSLPKGKGIK
Sbjct: 186 GRNRGRVGVIKNREKHKGSFETIHIQDSTGHEFATRLGNVYTIGKGTKPWVSLPKGKGIK 245

Query: 181 LSIIEEARKRQALATSAAA 199
           L+IIEEARKR  LA+  AA
Sbjct: 246 LTIIEEARKR--LASQQAA 262

Arabidopsis thaliana (taxid: 3702)

>sp|P46300|RS4_SOLTU 40S ribosomal protein S4 OS=Solanum tuberosum GN=RPS4 PE=2 SV=1

 Score =  375 bits (962), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 176/199 (88%), Positives = 190/199 (95%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQR V+VD KVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHS+RDEE+KFKLCK
Sbjct: 66  MQRQVMVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEESKFKLCK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VRSVQFGQKGIPY+NTYDGRTIRYPDPLIKANDTIKLDLE+NKI +FIKFDVGNVVMVTG
Sbjct: 126 VRSVQFGQKGIPYLNTYDGRTIRYPDPLIKANDTIKLDLESNKIVDFIKFDVGNVVMVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRNRGRVG+IKNREKHKGSFET+HIQD+ GHEFATRLGNVFT+GKGTKPWVSLPKGKGIK
Sbjct: 186 GRNRGRVGVIKNREKHKGSFETLHIQDSQGHEFATRLGNVFTLGKGTKPWVSLPKGKGIK 245

Query: 181 LSIIEEARKRQALATSAAA 199
           L+IIE+ARKR A  ++  A
Sbjct: 246 LTIIEDARKRLAAQSATPA 264

Solanum tuberosum (taxid: 4113)

>sp|Q93VH9|RS41_ARATH 40S ribosomal protein S4-1 OS=Arabidopsis thaliana GN=RPS4A PE=2 SV=1

 Score =  372 bits (956), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 176/190 (92%), Positives = 184/190 (96%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRH+ VD KVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSI+DEEAKFKLCK
Sbjct: 66  MQRHIQVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIKDEEAKFKLCK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VRS+QFGQKGIPY+NTYDGRTIRYPDPLIK NDTIKLDLE NKI EFIKFDVGNVVMVTG
Sbjct: 126 VRSIQFGQKGIPYLNTYDGRTIRYPDPLIKPNDTIKLDLEENKIVEFIKFDVGNVVMVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRNRGRVG+IKNREKHKGSFETIHIQD+ GHEFATRLGNV+TIGKGTKPWVSLPKGKGIK
Sbjct: 186 GRNRGRVGVIKNREKHKGSFETIHIQDSTGHEFATRLGNVYTIGKGTKPWVSLPKGKGIK 245

Query: 181 LSIIEEARKR 190
           L+IIEEARKR
Sbjct: 246 LTIIEEARKR 255

Arabidopsis thaliana (taxid: 3702)

>sp|O22424|RS4_MAIZE 40S ribosomal protein S4 OS=Zea mays GN=RPS4 PE=2 SV=1

 Score =  366 bits (940), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 172/190 (90%), Positives = 184/190 (96%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRHVLVD KVRTDKTYPAGFMDV+SIPKTNEN+RLLYDTKGRFRLH IRDE+AKFKLCK
Sbjct: 66  MQRHVLVDGKVRTDKTYPAGFMDVISIPKTNENYRLLYDTKGRFRLHPIRDEDAKFKLCK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VRSVQFGQKGIPY+NTYDGRTIRYPDPLIKANDTIK+DLETNKI +FIKFDVGNVVMVTG
Sbjct: 126 VRSVQFGQKGIPYLNTYDGRTIRYPDPLIKANDTIKIDLETNKIVDFIKFDVGNVVMVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRN GRVG+IKNREKHKGSFETIH++D+LGH+FATR+GNVFTIGKG KPWVSLPKGKGIK
Sbjct: 186 GRNTGRVGVIKNREKHKGSFETIHVEDSLGHQFATRMGNVFTIGKGNKPWVSLPKGKGIK 245

Query: 181 LSIIEEARKR 190
           LSIIEE RKR
Sbjct: 246 LSIIEEQRKR 255

Zea mays (taxid: 4577)

>sp|P46299|RS4_GOSHI 40S ribosomal protein S4 OS=Gossypium hirsutum GN=RPS4 PE=2 SV=1

 Score =  365 bits (938), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 175/197 (88%), Positives = 185/197 (93%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRHV+VD KVRTDKTYPAGFMDVVSIPKTNE+FRLLYDTKGRF LH+I  +E KFKLCK
Sbjct: 66  MQRHVMVDGKVRTDKTYPAGFMDVVSIPKTNEDFRLLYDTKGRFCLHAITGDETKFKLCK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VRSVQFGQKGIPY+NTYDGRTIRYPDPLIKANDTIKLDLE+NKI +FIKFDVGNVVMVTG
Sbjct: 126 VRSVQFGQKGIPYLNTYDGRTIRYPDPLIKANDTIKLDLESNKIVDFIKFDVGNVVMVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRNRGRVG+IKNREKHKGSFETIH+QDA GHEFATRLGNVFTIGKGTKPWVSLPK KGIK
Sbjct: 186 GRNRGRVGVIKNREKHKGSFETIHVQDAAGHEFATRLGNVFTIGKGTKPWVSLPKRKGIK 245

Query: 181 LSIIEEARKRQALATSA 197
           LSIIEEARKR A   +A
Sbjct: 246 LSIIEEARKRLAAQNAA 262

Gossypium hirsutum (taxid: 3635)

>sp|P49398|RS4_ORYSJ 40S ribosomal protein S4 OS=Oryza sativa subsp. japonica GN=RPS4 PE=2 SV=3

 Score =  363 bits (931), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 170/190 (89%), Positives = 183/190 (96%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRHVLVD KVRTDKTYPAGFMDV+SIPKT EN+RLLYDTKGRFRL S++DE+AKFKLCK
Sbjct: 66  MQRHVLVDGKVRTDKTYPAGFMDVISIPKTGENYRLLYDTKGRFRLQSVKDEDAKFKLCK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VRSVQFGQKGIPY+NTYDGRTIRYPDP+IKANDTIK+DLETNKI +FIKFDVGNVVMVTG
Sbjct: 126 VRSVQFGQKGIPYLNTYDGRTIRYPDPIIKANDTIKIDLETNKIVDFIKFDVGNVVMVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRN GRVG+IKNREKHKGSFETIH++DALGH+FATRLGNVFTIGKG KPWVSLPKGKGIK
Sbjct: 186 GRNTGRVGVIKNREKHKGSFETIHVEDALGHQFATRLGNVFTIGKGNKPWVSLPKGKGIK 245

Query: 181 LSIIEEARKR 190
           LSIIEE RKR
Sbjct: 246 LSIIEEQRKR 255

Oryza sativa subsp. japonica (taxid: 39947)

>sp|O81363|RS4_PRUAR 40S ribosomal protein S4 OS=Prunus armeniaca GN=RPS4 PE=2 SV=1

 Score =  347 bits (891), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 168/190 (88%), Positives = 178/190 (93%), Gaps = 4/190 (2%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRH+LVD K+     +     DVVSIPKTNENFRLLYDTKGRFRLHSIRDEE+KFKLCK
Sbjct: 66  MQRHILVDGKIH----FCIRLSDVVSIPKTNENFRLLYDTKGRFRLHSIRDEESKFKLCK 121

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKIT+FIKFDVGNVVMVTG
Sbjct: 122 VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITDFIKFDVGNVVMVTG 181

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRNRGRVG+IKNREKHKGSFETIH+QDA GHEFATRLGNVFTIGKGTKPWVSLPKGKGIK
Sbjct: 182 GRNRGRVGVIKNREKHKGSFETIHVQDATGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 241

Query: 181 LSIIEEARKR 190
           L+I+EEA+KR
Sbjct: 242 LTILEEAKKR 251

Prunus armeniaca (taxid: 36596)

>sp|P47961|RS4_CRIGR 40S ribosomal protein S4 OS=Cricetulus griseus GN=RPS4 PE=2 SV=2

 Score =  285 bits (729), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 132/198 (66%), Positives = 160/198 (80%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQR + +D KVRTD TYPAGFMDV+SI KT ENFRL+YDTKGRF +H I  EEAK+KLCK
Sbjct: 66  MQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITSEEAKYKLCK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VR +  G KGIP++ T+D RTIRYPDPLIK NDTI++DLET KIT+FIKFD GN+ MVTG
Sbjct: 126 VRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           G N GR+G+I NRE+H GSF+ +H++DA G+ FATRL N+F IGKG KPW+SLP+GKGI+
Sbjct: 186 GANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIR 245

Query: 181 LSIIEEARKRQALATSAA 198
           L+I EE  KR A   S+ 
Sbjct: 246 LTIAEERDKRLAAKQSSG 263

Cricetulus griseus (taxid: 10029)

>sp|P79103|RS4_BOVIN 40S ribosomal protein S4 OS=Bos taurus GN=RPS4 PE=2 SV=3

 Score =  284 bits (727), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 132/198 (66%), Positives = 160/198 (80%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQR + +D KVRTD TYPAGFMDV+SI KT ENFRL+YDTKGRF +H I  EEAK+KLCK
Sbjct: 66  MQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VR +  G KGIP++ T+D RTIRYPDPLIK NDTI++DLET KIT+FIKFD GN+ MVTG
Sbjct: 126 VRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           G N GR+G+I NRE+H GSF+ +H++DA G+ FATRL N+F IGKG KPW+SLP+GKGI+
Sbjct: 186 GANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIR 245

Query: 181 LSIIEEARKRQALATSAA 198
           L+I EE  KR A   S+ 
Sbjct: 246 LTIAEERDKRLAAKQSSG 263

Bos taurus (taxid: 9913)

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	200
255543308	263	40S ribosomal protein S4, putative [Rici	0.99	0.752	0.939	1e-106
255549228	263	40S ribosomal protein S4, putative [Rici	0.99	0.752	0.934	1e-106
449509213	264	PREDICTED: 40S ribosomal protein S4-like	0.995	0.753	0.924	1e-105
357468567	264	40S ribosomal protein S4 [Medicago trunc	0.995	0.753	0.914	1e-104
192912988	265	40S ribosomal protein S4 [Elaeis guineen	0.99	0.747	0.919	1e-104
224087813	263	predicted protein [Populus trichocarpa]	0.99	0.752	0.904	1e-104
192912992	265	40S ribosomal protein S4 [Elaeis guineen	0.99	0.747	0.929	1e-104
449465358	264	PREDICTED: 40S ribosomal protein S4-like	0.995	0.753	0.914	1e-104
73759787	264	ribosomal protein S4 [Panax ginseng]	0.995	0.753	0.909	1e-104
356496247	264	PREDICTED: 40S ribosomal protein S4-like	0.995	0.753	0.909	1e-103

>gi|255543308|ref|XP_002512717.1| 40S ribosomal protein S4, putative [Ricinus communis] gi|223548678|gb|EEF50169.1| 40S ribosomal protein S4, putative [Ricinus communis]

 Score =  389 bits (1000), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 186/198 (93%), Positives = 194/198 (97%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRD+EAKFKLCK
Sbjct: 66  MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDDEAKFKLCK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VRSVQFGQKGIPY+NTYDGRTIRYPDPLIKANDTIKLDLE+NKITEFIKFDVGNVVMVTG
Sbjct: 126 VRSVQFGQKGIPYLNTYDGRTIRYPDPLIKANDTIKLDLESNKITEFIKFDVGNVVMVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRNRGRVG+IKNREKHKGSFETIHIQD+ GHEFATR+GNVFTIGKGTKPWVSLPKGKGIK
Sbjct: 186 GRNRGRVGVIKNREKHKGSFETIHIQDSTGHEFATRMGNVFTIGKGTKPWVSLPKGKGIK 245

Query: 181 LSIIEEARKRQALATSAA 198
           LSIIEEARKR A + +AA
Sbjct: 246 LSIIEEARKRLAASQTAA 263

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255549228|ref|XP_002515668.1| 40S ribosomal protein S4, putative [Ricinus communis] gi|223545211|gb|EEF46720.1| 40S ribosomal protein S4, putative [Ricinus communis]

 Score =  388 bits (996), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 185/198 (93%), Positives = 193/198 (97%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRD+EAKFKLCK
Sbjct: 66  MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDDEAKFKLCK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VRSVQFGQKGIPY+NTYDGRTIRYPDPLIKANDTIKLDLE+NKIT+FIKFDVGNVVMVTG
Sbjct: 126 VRSVQFGQKGIPYLNTYDGRTIRYPDPLIKANDTIKLDLESNKITDFIKFDVGNVVMVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRNRGRVG+IKNREKHKGSFETIH+QDA GHEFATR+GNVFTIGKGTKPWVSLPKGKGIK
Sbjct: 186 GRNRGRVGVIKNREKHKGSFETIHVQDATGHEFATRMGNVFTIGKGTKPWVSLPKGKGIK 245

Query: 181 LSIIEEARKRQALATSAA 198
           LSIIEEARKR A A + A
Sbjct: 246 LSIIEEARKRLAAAQAVA 263

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449509213|ref|XP_004163526.1| PREDICTED: 40S ribosomal protein S4-like [Cucumis sativus]

 Score =  384 bits (987), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 184/199 (92%), Positives = 192/199 (96%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRHVLVDAKVRTDKTYPAGFMDVVSIPKT+ENFRLLYDTKGRFRLHSIRDEEAKFKLCK
Sbjct: 66  MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTSENFRLLYDTKGRFRLHSIRDEEAKFKLCK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VRSVQFGQKGIPY+NTYDGRTIRYPDPLIKANDTIKLDLE+NKI +FIKFDVGNVVMVTG
Sbjct: 126 VRSVQFGQKGIPYLNTYDGRTIRYPDPLIKANDTIKLDLESNKIADFIKFDVGNVVMVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRNRGRVG+IKNREKHKGSFETIHIQDA GHEFATRLGNVFTIGKGTKPWVSLPKGKGIK
Sbjct: 186 GRNRGRVGVIKNREKHKGSFETIHIQDATGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 245

Query: 181 LSIIEEARKRQALATSAAA 199
           L+IIEEARKR A  ++  A
Sbjct: 246 LTIIEEARKRLASQSAVTA 264

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357468567|ref|XP_003604568.1| 40S ribosomal protein S4 [Medicago truncatula] gi|355505623|gb|AES86765.1| 40S ribosomal protein S4 [Medicago truncatula]

 Score =  384 bits (986), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 182/199 (91%), Positives = 191/199 (95%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRHVLVD KVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHS+RD+EAKFKLCK
Sbjct: 66  MQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSVRDDEAKFKLCK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VRSVQFGQKGIPY+NTYDGRTIRYPDPLIKANDTIKLDLE NKIT+FIKFDVGNVVMVTG
Sbjct: 126 VRSVQFGQKGIPYLNTYDGRTIRYPDPLIKANDTIKLDLENNKITDFIKFDVGNVVMVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRNRGRVG+IKNREKHKG+FETIH+QDA GHEFATRLGNVFTIGKGTKPWVSLPKGKGIK
Sbjct: 186 GRNRGRVGVIKNREKHKGTFETIHVQDASGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 245

Query: 181 LSIIEEARKRQALATSAAA 199
           L++IEEARKRQA     AA
Sbjct: 246 LTVIEEARKRQAAQNVTAA 264

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|192912988|gb|ACF06602.1| 40S ribosomal protein S4 [Elaeis guineensis]

 Score =  383 bits (984), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 182/198 (91%), Positives = 192/198 (96%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRHV+VD KVRTDKTYP+GFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK
Sbjct: 66  MQRHVMVDGKVRTDKTYPSGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VRSVQFGQKGIPY+NT+DGRTIRYPDPLIKANDTIKLDLE NKI +FIKFDVGNVVMVTG
Sbjct: 126 VRSVQFGQKGIPYLNTFDGRTIRYPDPLIKANDTIKLDLEANKIVDFIKFDVGNVVMVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRNRGRVG+IKNREKHKGSFETIH+QDALGHEFATR+GNVFTIGKGTKPWVSLPKGKGIK
Sbjct: 186 GRNRGRVGVIKNREKHKGSFETIHLQDALGHEFATRIGNVFTIGKGTKPWVSLPKGKGIK 245

Query: 181 LSIIEEARKRQALATSAA 198
           LSIIEEARKR A + +AA
Sbjct: 246 LSIIEEARKRLAASGAAA 263

Source: Elaeis guineensis

Species: Elaeis guineensis

Genus: Elaeis

Family: Arecaceae

Order: Arecales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224087813|ref|XP_002308235.1| predicted protein [Populus trichocarpa] gi|222854211|gb|EEE91758.1| predicted protein [Populus trichocarpa]

 Score =  382 bits (982), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 179/198 (90%), Positives = 193/198 (97%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRHVLVD KVRTDKTYP+GFMDVVSIPKTNE+FRLLYDTKGRFRLHS+RD+EAKFKLCK
Sbjct: 66  MQRHVLVDGKVRTDKTYPSGFMDVVSIPKTNESFRLLYDTKGRFRLHSLRDDEAKFKLCK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VRS+QFGQKGIPY+NTYDGRTIRYPDPLIKANDTIKLDLE+NKI +FIKFDVGNVVMVTG
Sbjct: 126 VRSIQFGQKGIPYLNTYDGRTIRYPDPLIKANDTIKLDLESNKIVDFIKFDVGNVVMVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRNRGRVG+IKNREKHKGSFETIH+QDA GHEFATRLGNVFTIGKG+KPW+SLPKGKGIK
Sbjct: 186 GRNRGRVGVIKNREKHKGSFETIHVQDATGHEFATRLGNVFTIGKGSKPWISLPKGKGIK 245

Query: 181 LSIIEEARKRQALATSAA 198
           LSIIEEARKRQA + +AA
Sbjct: 246 LSIIEEARKRQAASQTAA 263

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|192912992|gb|ACF06604.1| 40S ribosomal protein S4 [Elaeis guineensis]

 Score =  382 bits (982), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 184/198 (92%), Positives = 190/198 (95%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRHVLVD KVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK
Sbjct: 66  MQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VRSVQFG KGIPY+NTYDGRTIRYPDPLIKANDTIKLDLET KI +FIKFDVGNVVMVTG
Sbjct: 126 VRSVQFGHKGIPYLNTYDGRTIRYPDPLIKANDTIKLDLETYKIVDFIKFDVGNVVMVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRNRGRVG+IKNREKHKGSFETIH+QDA GHEFATRLGNVFTIGKGTKPWVSLPKGKGIK
Sbjct: 186 GRNRGRVGVIKNREKHKGSFETIHLQDATGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 245

Query: 181 LSIIEEARKRQALATSAA 198
           LSIIEEARKR A + +AA
Sbjct: 246 LSIIEEARKRLAASGAAA 263

Source: Elaeis guineensis

Species: Elaeis guineensis

Genus: Elaeis

Family: Arecaceae

Order: Arecales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449465358|ref|XP_004150395.1| PREDICTED: 40S ribosomal protein S4-like [Cucumis sativus] gi|449496881|ref|XP_004160252.1| PREDICTED: 40S ribosomal protein S4-like [Cucumis sativus]

 Score =  382 bits (980), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 182/199 (91%), Positives = 190/199 (95%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRHVLVD KVRTDKT+PAGFMDVVSIPKTNENFRLLYDTKGRFRLHS+RDEEAK+KLCK
Sbjct: 66  MQRHVLVDGKVRTDKTFPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSVRDEEAKYKLCK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VRSVQFGQKGIPY+NTYDGRTIRYPDPLIKANDTIKLDLE+NKI +FIKFDVGNVVMVTG
Sbjct: 126 VRSVQFGQKGIPYLNTYDGRTIRYPDPLIKANDTIKLDLESNKIADFIKFDVGNVVMVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRNRGRVG+IKNREKHKGSFETIHIQDA GHEFATRLGNVFTIGKGTKPWVSLPKGKGIK
Sbjct: 186 GRNRGRVGVIKNREKHKGSFETIHIQDATGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 245

Query: 181 LSIIEEARKRQALATSAAA 199
           LSIIEEARKR A   +  A
Sbjct: 246 LSIIEEARKRLASQATVTA 264

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|73759787|dbj|BAE20168.1| ribosomal protein S4 [Panax ginseng]

 Score =  382 bits (980), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 181/199 (90%), Positives = 189/199 (94%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRHVLVD KVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHS+RDEEAKFKLCK
Sbjct: 66  MQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSVRDEEAKFKLCK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLE NKI +FIKFDVGNVVMVTG
Sbjct: 126 VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEANKIADFIKFDVGNVVMVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRN GRVG+IKNREKHKGSFET+HIQD+LGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK
Sbjct: 186 GRNTGRVGVIKNREKHKGSFETVHIQDSLGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 245

Query: 181 LSIIEEARKRQALATSAAA 199
           L+IIEEARKR    ++  A
Sbjct: 246 LTIIEEARKRNVAQSATTA 264

Source: Panax ginseng

Species: Panax ginseng

Genus: Panax

Family: Araliaceae

Order: Apiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356496247|ref|XP_003516980.1| PREDICTED: 40S ribosomal protein S4-like [Glycine max]

 Score =  381 bits (978), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 181/199 (90%), Positives = 189/199 (94%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRHVLVD KVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHS+RDEE+KFKLCK
Sbjct: 66  MQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSVRDEESKFKLCK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VRSVQFGQKGIPY+NTYDGRTIRYPDPLIKANDTIKLDLE+NKIT+FIKFDVGNVVMVTG
Sbjct: 126 VRSVQFGQKGIPYLNTYDGRTIRYPDPLIKANDTIKLDLESNKITDFIKFDVGNVVMVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRNRGRVG+IKNREKHKGSFETIH+QDA GHEFATR+GNVF IGKGTKPWVSLPKGKGIK
Sbjct: 186 GRNRGRVGVIKNREKHKGSFETIHVQDATGHEFATRMGNVFIIGKGTKPWVSLPKGKGIK 245

Query: 181 LSIIEEARKRQALATSAAA 199
           LSIIEEARKR A      A
Sbjct: 246 LSIIEEARKRLAAQNETVA 264

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	200
TAIR|locus:2171198	262	AT5G58420 [Arabidopsis thalian	0.985	0.751	0.904	2.6e-95
TAIR|locus:2169339	262	AT5G07090 [Arabidopsis thalian	0.985	0.751	0.904	3.3e-95
TAIR|locus:2827612	261	AT2G17360 [Arabidopsis thalian	0.95	0.727	0.926	1.1e-94
UNIPROTKB|J9P5V0	267	J9P5V0 "Uncharacterized protei	0.985	0.737	0.675	3.2e-72
UNIPROTKB|P79103	263	RPS4 "40S ribosomal protein S4	0.985	0.749	0.670	6.7e-72
UNIPROTKB|F2Z4Q1	263	RPS4X "Uncharacterized protein	0.985	0.749	0.670	6.7e-72
UNIPROTKB|P62701	263	RPS4X "40S ribosomal protein S	0.985	0.749	0.670	6.7e-72
UNIPROTKB|F1RQ91	263	RPS4X "Uncharacterized protein	0.985	0.749	0.670	6.7e-72
UNIPROTKB|P62704	263	RPS4X "40S ribosomal protein S	0.985	0.749	0.670	6.7e-72
UNIPROTKB|P62705	263	RPS4X "40S ribosomal protein S	0.985	0.749	0.670	6.7e-72

TAIR|locus:2171198 AT5G58420 [Arabidopsis thaliana (taxid:3702)]

 Score = 948 (338.8 bits), Expect = 2.6e-95, P = 2.6e-95
 Identities = 180/199 (90%), Positives = 189/199 (94%)

Query:     1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
             MQRH+ VD KVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSI+DEEAKFKLCK
Sbjct:    66 MQRHIQVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIKDEEAKFKLCK 125

Query:    61 VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
             VRS+QFGQKGIPY+NTYDGRTIRYPDPLIK NDTIKLDLE NKI EFIKFDVGNVVMVTG
Sbjct:   126 VRSIQFGQKGIPYLNTYDGRTIRYPDPLIKPNDTIKLDLEANKIVEFIKFDVGNVVMVTG 185

Query:   121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
             GRNRGRVG+IKNREKHKGSFETIHIQD+ GHEFATRLGNV+TIGKGTKPWVSLPKGKGIK
Sbjct:   186 GRNRGRVGVIKNREKHKGSFETIHIQDSTGHEFATRLGNVYTIGKGTKPWVSLPKGKGIK 245

Query:   181 LSIIEEARKRQALATSAAA 199
             L+IIEEARKR  LA+  AA
Sbjct:   246 LTIIEEARKR--LASQQAA 262

GO:0003723 "RNA binding" evidence=IEA

GO:0003735 "structural constituent of ribosome" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA;ISS

GO:0022627 "cytosolic small ribosomal subunit" evidence=ISS;IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

GO:0001510 "RNA methylation" evidence=RCA

TAIR|locus:2169339 AT5G07090 [Arabidopsis thaliana (taxid:3702)]

 Score = 947 (338.4 bits), Expect = 3.3e-95, P = 3.3e-95
 Identities = 180/199 (90%), Positives = 189/199 (94%)

Query:     1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
             MQRH+ VD KVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSI+DEEAKFKLCK
Sbjct:    66 MQRHIQVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIKDEEAKFKLCK 125

Query:    61 VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
             VRS+QFGQKGIPY+NTYDGRTIRYPDPLIK NDTIKLDLE NKI EFIKFDVGNVVMVTG
Sbjct:   126 VRSIQFGQKGIPYLNTYDGRTIRYPDPLIKPNDTIKLDLEENKIVEFIKFDVGNVVMVTG 185

Query:   121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
             GRNRGRVG+IKNREKHKGSFETIHIQD+ GHEFATRLGNV+TIGKGTKPWVSLPKGKGIK
Sbjct:   186 GRNRGRVGVIKNREKHKGSFETIHIQDSTGHEFATRLGNVYTIGKGTKPWVSLPKGKGIK 245

Query:   181 LSIIEEARKRQALATSAAA 199
             L+IIEEARKR  LA+  AA
Sbjct:   246 LTIIEEARKR--LASQQAA 262

GO:0003723 "RNA binding" evidence=IEA

GO:0003735 "structural constituent of ribosome" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA;ISS

GO:0022627 "cytosolic small ribosomal subunit" evidence=ISS

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0005774 "vacuolar membrane" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005829 "cytosol" evidence=RCA

GO:0005794 "Golgi apparatus" evidence=RCA

GO:0009220 "pyrimidine ribonucleotide biosynthetic process" evidence=RCA

TAIR|locus:2827612 AT2G17360 [Arabidopsis thaliana (taxid:3702)]

 Score = 942 (336.7 bits), Expect = 1.1e-94, P = 1.1e-94
 Identities = 176/190 (92%), Positives = 184/190 (96%)

Query:     1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
             MQRH+ VD KVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSI+DEEAKFKLCK
Sbjct:    66 MQRHIQVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIKDEEAKFKLCK 125

Query:    61 VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
             VRS+QFGQKGIPY+NTYDGRTIRYPDPLIK NDTIKLDLE NKI EFIKFDVGNVVMVTG
Sbjct:   126 VRSIQFGQKGIPYLNTYDGRTIRYPDPLIKPNDTIKLDLEENKIVEFIKFDVGNVVMVTG 185

Query:   121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
             GRNRGRVG+IKNREKHKGSFETIHIQD+ GHEFATRLGNV+TIGKGTKPWVSLPKGKGIK
Sbjct:   186 GRNRGRVGVIKNREKHKGSFETIHIQDSTGHEFATRLGNVYTIGKGTKPWVSLPKGKGIK 245

Query:   181 LSIIEEARKR 190
             L+IIEEARKR
Sbjct:   246 LTIIEEARKR 255

GO:0003723 "RNA binding" evidence=IEA

GO:0003735 "structural constituent of ribosome" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA;ISS

GO:0022627 "cytosolic small ribosomal subunit" evidence=ISS;IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0005774 "vacuolar membrane" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

GO:0001510 "RNA methylation" evidence=RCA

UNIPROTKB|J9P5V0 J9P5V0 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 730 (262.0 bits), Expect = 3.2e-72, P = 3.2e-72
 Identities = 133/197 (67%), Positives = 160/197 (81%)

Query:     1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
             MQR + +D KVRTD TYPAGFMDV+SI KT ENFRL+YDTKGRF +H I  EEAK+KLCK
Sbjct:    66 MQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCK 125

Query:    61 VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
             VR +  G KGIP++ T+D RTIRYPDPLIK NDTI++DLET KIT+FIKFD GN+ MVTG
Sbjct:   126 VRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTG 185

Query:   121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
             G N GR+G+I NREKH GSF+ +H++DA G+ FATRL N+F IGKG KPW+SLP+GKGI+
Sbjct:   186 GANLGRIGVITNREKHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIR 245

Query:   181 LSIIEEARKRQALATSA 197
             L+I EE  KR A   S+
Sbjct:   246 LTIAEERDKRLAAKQSS 262

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0003735 "structural constituent of ribosome" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|P79103 RPS4 "40S ribosomal protein S4" [Bos taurus (taxid:9913)]

 Score = 727 (261.0 bits), Expect = 6.7e-72, P = 6.7e-72
 Identities = 132/197 (67%), Positives = 160/197 (81%)

Query:     1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
             MQR + +D KVRTD TYPAGFMDV+SI KT ENFRL+YDTKGRF +H I  EEAK+KLCK
Sbjct:    66 MQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCK 125

Query:    61 VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
             VR +  G KGIP++ T+D RTIRYPDPLIK NDTI++DLET KIT+FIKFD GN+ MVTG
Sbjct:   126 VRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTG 185

Query:   121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
             G N GR+G+I NRE+H GSF+ +H++DA G+ FATRL N+F IGKG KPW+SLP+GKGI+
Sbjct:   186 GANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIR 245

Query:   181 LSIIEEARKRQALATSA 197
             L+I EE  KR A   S+
Sbjct:   246 LTIAEERDKRLAAKQSS 262

GO:0019843 "rRNA binding" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0003735 "structural constituent of ribosome" evidence=IEA

UNIPROTKB|F2Z4Q1 RPS4X "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 727 (261.0 bits), Expect = 6.7e-72, P = 6.7e-72
 Identities = 132/197 (67%), Positives = 160/197 (81%)

Query:     1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
             MQR + +D KVRTD TYPAGFMDV+SI KT ENFRL+YDTKGRF +H I  EEAK+KLCK
Sbjct:    66 MQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCK 125

Query:    61 VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
             VR +  G KGIP++ T+D RTIRYPDPLIK NDTI++DLET KIT+FIKFD GN+ MVTG
Sbjct:   126 VRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTG 185

Query:   121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
             G N GR+G+I NRE+H GSF+ +H++DA G+ FATRL N+F IGKG KPW+SLP+GKGI+
Sbjct:   186 GANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIR 245

Query:   181 LSIIEEARKRQALATSA 197
             L+I EE  KR A   S+
Sbjct:   246 LTIAEERDKRLAAKQSS 262

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0003735 "structural constituent of ribosome" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|P62701 RPS4X "40S ribosomal protein S4, X isoform" [Homo sapiens (taxid:9606)]

 Score = 727 (261.0 bits), Expect = 6.7e-72, P = 6.7e-72
 Identities = 132/197 (67%), Positives = 160/197 (81%)

Query:     1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
             MQR + +D KVRTD TYPAGFMDV+SI KT ENFRL+YDTKGRF +H I  EEAK+KLCK
Sbjct:    66 MQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCK 125

Query:    61 VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
             VR +  G KGIP++ T+D RTIRYPDPLIK NDTI++DLET KIT+FIKFD GN+ MVTG
Sbjct:   126 VRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTG 185

Query:   121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
             G N GR+G+I NRE+H GSF+ +H++DA G+ FATRL N+F IGKG KPW+SLP+GKGI+
Sbjct:   186 GANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIR 245

Query:   181 LSIIEEARKRQALATSA 197
             L+I EE  KR A   S+
Sbjct:   246 LTIAEERDKRLAAKQSS 262

GO:0019843 "rRNA binding" evidence=IEA

GO:0005840 "ribosome" evidence=IDA

GO:0006412 "translation" evidence=IC;IMP;TAS

GO:0008284 "positive regulation of cell proliferation" evidence=IMP

GO:0045727 "positive regulation of translation" evidence=IMP

GO:0022627 "cytosolic small ribosomal subunit" evidence=NAS;IDA

GO:0007275 "multicellular organismal development" evidence=IMP

GO:0003735 "structural constituent of ribosome" evidence=IMP

GO:0030529 "ribonucleoprotein complex" evidence=IDA

GO:0005844 "polysome" evidence=IDA

GO:0015935 "small ribosomal subunit" evidence=IDA

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006413 "translational initiation" evidence=TAS

GO:0006414 "translational elongation" evidence=TAS

GO:0006415 "translational termination" evidence=TAS

GO:0006614 "SRP-dependent cotranslational protein targeting to membrane" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0019058 "viral infectious cycle" evidence=TAS

GO:0019083 "viral transcription" evidence=TAS

GO:0044267 "cellular protein metabolic process" evidence=TAS

UNIPROTKB|F1RQ91 RPS4X "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 727 (261.0 bits), Expect = 6.7e-72, P = 6.7e-72
 Identities = 132/197 (67%), Positives = 160/197 (81%)

Query:     1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
             MQR + +D KVRTD TYPAGFMDV+SI KT ENFRL+YDTKGRF +H I  EEAK+KLCK
Sbjct:    66 MQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCK 125

Query:    61 VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
             VR +  G KGIP++ T+D RTIRYPDPLIK NDTI++DLET KIT+FIKFD GN+ MVTG
Sbjct:   126 VRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTG 185

Query:   121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
             G N GR+G+I NRE+H GSF+ +H++DA G+ FATRL N+F IGKG KPW+SLP+GKGI+
Sbjct:   186 GANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIR 245

Query:   181 LSIIEEARKRQALATSA 197
             L+I EE  KR A   S+
Sbjct:   246 LTIAEERDKRLAAKQSS 262

GO:0045727 "positive regulation of translation" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005844 "polysome" evidence=IEA

GO:0003735 "structural constituent of ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|P62704 RPS4X "40S ribosomal protein S4, X isoform" [Mesocricetus auratus (taxid:10036)]

 Score = 727 (261.0 bits), Expect = 6.7e-72, P = 6.7e-72
 Identities = 132/197 (67%), Positives = 160/197 (81%)

Query:     1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
             MQR + +D KVRTD TYPAGFMDV+SI KT ENFRL+YDTKGRF +H I  EEAK+KLCK
Sbjct:    66 MQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCK 125

Query:    61 VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
             VR +  G KGIP++ T+D RTIRYPDPLIK NDTI++DLET KIT+FIKFD GN+ MVTG
Sbjct:   126 VRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTG 185

Query:   121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
             G N GR+G+I NRE+H GSF+ +H++DA G+ FATRL N+F IGKG KPW+SLP+GKGI+
Sbjct:   186 GANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIR 245

Query:   181 LSIIEEARKRQALATSA 197
             L+I EE  KR A   S+
Sbjct:   246 LTIAEERDKRLAAKQSS 262

GO:0005840 "ribosome" evidence=ISS

GO:0030529 "ribonucleoprotein complex" evidence=ISS

UNIPROTKB|P62705 RPS4X "40S ribosomal protein S4, X isoform" [Felis catus (taxid:9685)]

 Score = 727 (261.0 bits), Expect = 6.7e-72, P = 6.7e-72
 Identities = 132/197 (67%), Positives = 160/197 (81%)

Query:     1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
             MQR + +D KVRTD TYPAGFMDV+SI KT ENFRL+YDTKGRF +H I  EEAK+KLCK
Sbjct:    66 MQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCK 125

Query:    61 VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
             VR +  G KGIP++ T+D RTIRYPDPLIK NDTI++DLET KIT+FIKFD GN+ MVTG
Sbjct:   126 VRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTG 185

Query:   121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
             G N GR+G+I NRE+H GSF+ +H++DA G+ FATRL N+F IGKG KPW+SLP+GKGI+
Sbjct:   186 GANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIR 245

Query:   181 LSIIEEARKRQALATSA 197
             L+I EE  KR A   S+
Sbjct:   246 LTIAEERDKRLAAKQSS 262

GO:0005840 "ribosome" evidence=ISS

GO:0030529 "ribonucleoprotein complex" evidence=ISS

---

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)
O81363	RS4_PRUAR	No assigned EC number	0.8842	0.93	0.7126	N/A	no
Q9N3X2	RS4_CAEEL	No assigned EC number	0.6073	0.955	0.7374	yes	no
P47836	RS4_CHICK	No assigned EC number	0.6616	0.99	0.7528	yes	no
O59950	RS4_YARLI	No assigned EC number	0.6666	0.96	0.7384	yes	no
Q8VYK6	RS43_ARATH	No assigned EC number	0.9045	0.985	0.7519	yes	no
P49204	RS42_ARATH	No assigned EC number	0.9045	0.985	0.7519	yes	no
Q9P4W9	RS4C_SCHPO	No assigned EC number	0.6839	0.965	0.7366	yes	no
P0CX36	RS4B_YEAST	No assigned EC number	0.6510	0.96	0.7356	yes	no
P79103	RS4_BOVIN	No assigned EC number	0.6666	0.99	0.7528	yes	no
O22424	RS4_MAIZE	No assigned EC number	0.9052	0.95	0.7169	N/A	no
P47961	RS4_CRIGR	No assigned EC number	0.6666	0.99	0.7528	yes	no
P46300	RS4_SOLTU	No assigned EC number	0.8844	0.995	0.7537	N/A	no
O62739	RS4Y1_MONDO	No assigned EC number	0.6515	0.99	0.7528	yes	no
O62738	RS4X_MONDO	No assigned EC number	0.6718	0.96	0.7300	yes	no
P49398	RS4_ORYSJ	No assigned EC number	0.8947	0.95	0.7169	yes	no
Q93VH9	RS41_ARATH	No assigned EC number	0.9263	0.95	0.7279	yes	no
P41042	RS4_DROME	No assigned EC number	0.6461	0.975	0.7471	yes	no
Q6PBC4	RS4_XENTR	No assigned EC number	0.6616	0.99	0.7528	yes	no
P62703	RS4X_RAT	No assigned EC number	0.6666	0.99	0.7528	yes	no
P62702	RS4X_MOUSE	No assigned EC number	0.6666	0.99	0.7528	yes	no
P51405	RS4_DICDI	No assigned EC number	0.6182	0.93	0.6966	yes	no
Q9USW5	RS4B_SCHPO	No assigned EC number	0.6839	0.965	0.7366	yes	no
P62701	RS4X_HUMAN	No assigned EC number	0.6666	0.99	0.7528	yes	no
P0CX35	RS4A_YEAST	No assigned EC number	0.6510	0.96	0.7356	yes	no
P46299	RS4_GOSHI	No assigned EC number	0.8883	0.985	0.7519	N/A	no
Q642H9	RS4X_DANRE	No assigned EC number	0.6515	0.99	0.7528	yes	no
P87158	RS4A_SCHPO	No assigned EC number	0.6839	0.965	0.7366	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_fgenesh4_pm.C_LG_VI0361	40S ribosomal protein S4 (RPS4A) (263 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	fgenesh4_pg.C_LG_VI001257	SubName- Full=Putative uncharacterized protein; (180 aa)	•		•	•			•		0.755
	grail3.0071003601	SubName- Full=Putative uncharacterized protein; (181 aa)	•		•	•			•		0.755
	estExt_fgenesh4_pg.C_LG_VI1248	SubName- Full=Putative uncharacterized protein; (181 aa)	•		•	•			•		0.755
	estExt_Genewise1_v1.C_LG_XI3222	SubName- Full=Putative uncharacterized protein; (181 aa)	•		•	•			•		0.755
	estExt_fgenesh4_pg.C_LG_VII0552	SubName- Full=Putative uncharacterized protein; (146 aa)	•		•	•					0.741
	estExt_fgenesh4_pm.C_LG_III0216	SubName- Full=Putative uncharacterized protein; (146 aa)	•		•	•					0.728
	estExt_fgenesh4_pg.C_LG_V0222	SubName- Full=Putative uncharacterized protein; (147 aa)	•		•	•					0.711
	gw1.57.264.1	SubName- Full=Putative uncharacterized protein; (258 aa)	•		•	•	•		•		0.677
	estExt_Genewise1_v1.C_LG_VII3915	SubName- Full=Putative uncharacterized protein; (260 aa)	•		•	•	•		•		0.675
	estExt_fgenesh4_kg.C_LG_XVII0009	SubName- Full=Putative uncharacterized protein; (144 aa)			•	•		•	•		0.664

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	200
PLN00036	261	PLN00036, PLN00036, 40S ribosomal protein S4; Prov	1e-133
PTZ00118	262	PTZ00118, PTZ00118, 40S ribosomal protein S4; Prov	2e-84
COG1471	241	COG1471, RPS4A, Ribosomal protein S4E [Translation	9e-78
PTZ00223	273	PTZ00223, PTZ00223, 40S ribosomal protein S4; Prov	2e-57
PRK04313	237	PRK04313, PRK04313, 30S ribosomal protein S4e; Val	3e-50
pfam00900	77	pfam00900, Ribosomal_S4e, Ribosomal family S4e	4e-37
cd06087	55	cd06087, KOW_RPS4, KOW motif of Ribosomal Protein	7e-29
pfam00467	32	pfam00467, KOW, KOW motif	0.003

>gnl|CDD|177670 PLN00036, PLN00036, 40S ribosomal protein S4; Provisional

 Score =  373 bits (960), Expect = e-133
 Identities = 171/192 (89%), Positives = 182/192 (94%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRHV VD KVRTDKTYPAGFMDV+SIPKTNENFRLLYDTKGRFRLH I DEEAKFKLCK
Sbjct: 66  MQRHVKVDGKVRTDKTYPAGFMDVISIPKTNENFRLLYDTKGRFRLHRINDEEAKFKLCK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VR +QFGQKGIPY+NT+DGRTIRYPDPLIKANDTIK+DLETNKI +FIKFDVGN+VMVTG
Sbjct: 126 VRKIQFGQKGIPYLNTHDGRTIRYPDPLIKANDTIKIDLETNKIVDFIKFDVGNLVMVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRNRGRVG+IKNREKHKGSFE IH++DA GHEFATRLGNVF IGKGTKPW+SLPKGKGIK
Sbjct: 186 GRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPKGKGIK 245

Query: 181 LSIIEEARKRQA 192
           LSIIEEARKR A
Sbjct: 246 LSIIEEARKRLA 257

Length = 261

>gnl|CDD|240277 PTZ00118, PTZ00118, 40S ribosomal protein S4; Provisional

 Score =  250 bits (639), Expect = 2e-84
 Identities = 120/194 (61%), Positives = 147/194 (75%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           +Q+ V VD KVRTD TYP GFMDVVS+ KTNE FRLLYDTKGRF  H I +EEAK+KLC+
Sbjct: 66  IQKIVKVDGKVRTDCTYPVGFMDVVSLTKTNEYFRLLYDTKGRFVPHKITNEEAKYKLCR 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           V+    G K +    T+DGRTIRY  P +K  D+++LDLET K+ EF+KF+VGN+VM+TG
Sbjct: 126 VKKTFLGPKEVSIAVTHDGRTIRYVHPDVKVGDSLRLDLETGKVLEFLKFEVGNLVMITG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           G N GRVG I ++EKH GSF+ IH++D+ G  FATRL NVF IG GTKP+VSLP+ +GIK
Sbjct: 186 GHNVGRVGTIVSKEKHPGSFDLIHVKDSRGKTFATRLSNVFVIGVGTKPYVSLPRERGIK 245

Query: 181 LSIIEEARKRQALA 194
             IIEE R R A A
Sbjct: 246 KDIIEERRNRLAKA 259

Length = 262

>gnl|CDD|224388 COG1471, RPS4A, Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]

 Score =  232 bits (594), Expect = 9e-78
 Identities = 84/178 (47%), Positives = 108/178 (60%), Gaps = 2/178 (1%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
            +  VLVD KVR D  +P G MDV+SIPKT E++R+L D KGR  LH I  EEA +KLCK
Sbjct: 65  SEGKVLVDGKVRKDYKFPVGLMDVISIPKTGEHYRVLPDEKGRLVLHPISAEEASYKLCK 124

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           V++    + G   +N +DGR IR  D   K  DT+K+ L   KI E IKF+ G +V VTG
Sbjct: 125 VKNKTTVKGGRIQLNLHDGRNIRLEDDNYKTGDTVKISLPEQKIVEHIKFEEGALVYVTG 184

Query: 121 GRNRGRVGIIKNREKHKGS-FETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGK 177
           GR+ GRVG I   E  + S    + ++D  G+ F T    VF IG+  KP +SLPK K
Sbjct: 185 GRHVGRVGTIVEIEIQESSKPNLVTVEDEEGNTFQTIKDYVFVIGED-KPVISLPKEK 241

Length = 241

>gnl|CDD|140250 PTZ00223, PTZ00223, 40S ribosomal protein S4; Provisional

 Score =  181 bits (461), Expect = 2e-57
 Identities = 92/190 (48%), Positives = 123/190 (64%), Gaps = 1/190 (0%)

Query: 2   QRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKV 61
           Q  V VD K R D  YPAGFMDVV IPKT + FR+LYD KGRF L  + + EA+ KL KV
Sbjct: 64  QGLVCVDGKPRKDGKYPAGFMDVVEIPKTGDRFRILYDVKGRFALVKVSEAEAQIKLMKV 123

Query: 62  RSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGG 121
            +V      IP   T+DG  IRYPDP     DT+  +++  K+ + IK   G VVMVTGG
Sbjct: 124 VNVYTATGRIPVAVTHDGHRIRYPDPRTSRGDTLVYNVKEKKVVDLIKNRNGKVVMVTGG 183

Query: 122 RNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPW-VSLPKGKGIK 180
            NRGR+G I + E+H G+F+   ++DA GHEFATR  N+F IGK      V+LPK +G++
Sbjct: 184 ANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRAANIFVIGKDMNSVPVTLPKQQGLR 243

Query: 181 LSIIEEARKR 190
           +++I+E  ++
Sbjct: 244 INVIQEREEK 253

Length = 273

>gnl|CDD|179820 PRK04313, PRK04313, 30S ribosomal protein S4e; Validated

 Score =  161 bits (411), Expect = 3e-50
 Identities = 71/175 (40%), Positives = 101/175 (57%), Gaps = 3/175 (1%)

Query: 2   QRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKV 61
           +  VLVD +VR D  +P G MDV+SIP+T E +R+L D KGR  L  I +EEAK KLCK+
Sbjct: 63  EGKVLVDGRVRKDYKFPVGLMDVISIPETGEYYRVLPDEKGRLVLIPISEEEAKLKLCKI 122

Query: 62  RSVQFGQKGIPYINTYDGRTIRYPDPL-IKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
            +    + G   +N +DGR I        K  D++ + L   +I + I F+ GN+ ++TG
Sbjct: 123 ENKTTVKGGKIQLNLHDGRNILVDVEDDYKTGDSLLISLPEQEIVDHIPFEEGNLAIITG 182

Query: 121 GRNRGRVGIIKNREKHKGSFE-TIHIQDALGHEFATRLGNVFTIGKGTKPWVSLP 174
           G++ G +G IK  E  K S    + ++D  G +F T L  VF IGK  KP + LP
Sbjct: 183 GKHVGEIGKIKEIEVTKSSKPNIVTLEDKDGEKFETILDYVFVIGKE-KPVIKLP 236

Length = 237

>gnl|CDD|189761 pfam00900, Ribosomal_S4e, Ribosomal family S4e

 Score =  123 bits (311), Expect = 4e-37
 Identities = 42/77 (54%), Positives = 53/77 (68%)

Query: 29  KTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPL 88
           KT E++R+LYD KGR  LH I  EEAK+KLCKV++    + G P +N +DGR IRYPDP 
Sbjct: 1   KTGEHYRVLYDVKGRLVLHRISAEEAKYKLCKVKNKTTVKGGKPQLNLHDGRNIRYPDPD 60

Query: 89  IKANDTIKLDLETNKIT 105
            K  DT+ +DL T KI 
Sbjct: 61  YKTGDTLVIDLPTQKIV 77

Length = 77

>gnl|CDD|240511 cd06087, KOW_RPS4, KOW motif of Ribosomal Protein S4 (RPS4)

 Score =  101 bits (255), Expect = 7e-29
 Identities = 37/55 (67%), Positives = 46/55 (83%)

Query: 110 FDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIG 164
           F+ GN+ MVTGGRN GRVG+IK  E+HKGSF+ +H++DA G+EFATRL NVF IG
Sbjct: 1   FEEGNLAMVTGGRNVGRVGVIKEIERHKGSFDIVHVKDAAGNEFATRLSNVFVIG 55

RPS4 plays a critical role in the core assembly of the small ribosomal subunit with a KOW motif at its C-terminal. RPS4 also acts as a general transcription antiterminator factor and regulates ribosomal RNA expression level. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. RPS4 deficiency in human has been associated with Turner syndrome. Archeae RPS4 (RPS4e) showed substantial identity to the eukaryotic equivalents RPS4, but the archaeal proteins formed a different complex from the eukaryotic proteins. Length = 55

>gnl|CDD|144165 pfam00467, KOW, KOW motif

 Score = 33.9 bits (79), Expect = 0.003
 Identities = 8/27 (29%), Positives = 13/27 (48%)

Query: 112 VGNVVMVTGGRNRGRVGIIKNREKHKG 138
            G+VV V  G  +G+ G +   +  K 
Sbjct: 1   KGDVVRVISGPFKGKKGKVVEVDDSKA 27

This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and NusG. Length = 32

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	200
PLN00036	261	40S ribosomal protein S4; Provisional	100.0
PTZ00118	262	40S ribosomal protein S4; Provisional	100.0
PTZ00223	273	40S ribosomal protein S4; Provisional	100.0
PRK04313	237	30S ribosomal protein S4e; Validated	100.0
COG1471	241	RPS4A Ribosomal protein S4E [Translation, ribosoma	100.0
KOG0378	263	consensus 40S ribosomal protein S4 [Translation, r	100.0
PF00900	77	Ribosomal_S4e: Ribosomal family S4e; InterPro: IPR	100.0
PF00467	32	KOW: KOW motif; InterPro: IPR005824 Ribosomes are	96.96
smart00739	28	KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif i	96.93
PF01479	48	S4: S4 domain; InterPro: IPR002942 Ribosomes are t	96.57
TIGR01080	114	rplX_A_E ribosomal protein L24p/L26e, archaeal/euk	94.24
cd00165	70	S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The	93.59
smart00363	60	S4 S4 RNA-binding domain.	92.78
PRK01191	120	rpl24p 50S ribosomal protein L24P; Validated	92.26
PRK12281	76	rplX 50S ribosomal protein L24; Reviewed	91.15
CHL00141	83	rpl24 ribosomal protein L24; Validated	90.53
PRK00004	105	rplX 50S ribosomal protein L24; Reviewed	89.53
TIGR02988	59	YaaA_near_RecF S4 domain protein YaaA. This small	86.36
TIGR01079	104	rplX_bact ribosomal protein L24, bacterial/organel	84.79
PTZ00194	143	60S ribosomal protein L26; Provisional	82.48

>PLN00036 40S ribosomal protein S4; Provisional

Probab=100.00  E-value=3.1e-84  Score=566.87  Aligned_cols=195  Identities=86%  Similarity=1.345  Sum_probs=191.6

Q ss_pred             CCccEEECCEEeccCCCCceeeEEEEecCCCceEEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCce
Q 029038            1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGR   80 (200)
Q Consensus         1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGr   80 (200)
                      +||+|+|||+||+|++||||||||||||++||||||+||++|||++|+|++|||+||||||++|++++||+|||+|||||
T Consensus        66 ~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt~e~yRvl~D~kGrf~l~~I~~eeA~~KLcKV~~k~~~~gG~~ql~~hDGr  145 (261)
T PLN00036         66 MQRHVKVDGKVRTDKTYPAGFMDVISIPKTNENFRLLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHDGR  145 (261)
T ss_pred             hCCeEEECCEEeccCCCCCceeEEEEEcCCCCeEEEEECCCceEEEEEcChHHccceEEEEEEEEEecCCeEEEEecCCc
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeCCCCccCCCeEEEecCCCceeEEEEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEeEeeccE
Q 029038           81 TIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNV  160 (200)
Q Consensus        81 ni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d~~g~~F~T~~~~v  160 (200)
                      ||+|+||.||+||||+|+||+++|++|+||++||+||||||+|+|++|+|.+|+++++++++||++|++|++|+|+++||
T Consensus       146 ni~~~d~~~k~~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d~~g~~F~T~~~~v  225 (261)
T PLN00036        146 TIRYPDPLIKANDTIKIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNV  225 (261)
T ss_pred             eeccCCCccccCCEEEEeCCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEccCCCceEeCcCCCceeeehhHHHHHHHHhhhh
Q 029038          161 FTIGKGTKPWVSLPKGKGIKLSIIEEARKRQALATS  196 (200)
Q Consensus       161 fvIG~~~~p~isLp~~~gi~~~~~e~~~~~~~~~~~  196 (200)
                      ||||++++||||||+++|||++++|| |++||.+-+
T Consensus       226 fvIG~~~kp~isLp~~~gi~~~~~e~-r~~~~~~~~  260 (261)
T PLN00036        226 FVIGKGTKPWISLPKGKGIKLSIIEE-ARKRLAAGQ  260 (261)
T ss_pred             EEEccCCCeeEeCcCCCCcccchHHH-HHHhhhhhc
Confidence            99999899999999999999999999 999997654

>PTZ00118 40S ribosomal protein S4; Provisional

Probab=100.00  E-value=1.2e-83  Score=563.37  Aligned_cols=194  Identities=60%  Similarity=0.978  Sum_probs=191.0

Q ss_pred             CCccEEECCEEeccCCCCceeeEEEEecCCCceEEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCce
Q 029038            1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGR   80 (200)
Q Consensus         1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGr   80 (200)
                      +||+|+||||||+|++||||||||||||++||||||+||++|||++|+|++|||+||||||++|++++||+|||+|||||
T Consensus        66 ~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt~e~yRvl~D~kGr~~l~~I~~eeA~~KLcKV~~k~~~~gg~~~l~~hDGr  145 (262)
T PTZ00118         66 IQKIVKVDGKVRTDCTYPVGFMDVVSLTKTNEYFRLLYDTKGRFVPHKITNEEAKYKLCRVKKTFLGPKEVSIAVTHDGR  145 (262)
T ss_pred             HCCcEEECCEEEccCCCCCceeEEEEEcCCCCeEEEEECCCccEEEEEcCHHHhcceEEEEeEEEECCCCeEEEEecCcc
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeCCCCccCCCeEEEecCCCceeEEEEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEeEeeccE
Q 029038           81 TIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNV  160 (200)
Q Consensus        81 ni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d~~g~~F~T~~~~v  160 (200)
                      ||+|+||.||+||||+|+||+++|++|+||++||+||||||+|+|++|+|.+++++++|+++|||+|++|++|+|+++||
T Consensus       146 ni~~~d~~ik~~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~d~~g~~F~T~~~~v  225 (262)
T PTZ00118        146 TIRYVHPDVKVGDSLRLDLETGKVLEFLKFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKDSRGKTFATRLSNV  225 (262)
T ss_pred             eeccCCCcccCCCEEEEECCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEEeCCCCeEEEEeeeE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEccCCCceEeCcCCCceeeehhHHHHHHHHhhh
Q 029038          161 FTIGKGTKPWVSLPKGKGIKLSIIEEARKRQALAT  195 (200)
Q Consensus       161 fvIG~~~~p~isLp~~~gi~~~~~e~~~~~~~~~~  195 (200)
                      ||||++++||||||++||||||++|| |+++|.+.
T Consensus       226 fvIG~~~kp~islp~~kgi~~~~~e~-~~~~~~~~  259 (262)
T PTZ00118        226 FVIGVGTKPYVSLPRERGIKKDIIEE-RRNRLAKA  259 (262)
T ss_pred             EEEccCCCeeEeCcCCCCccccHHHH-HHHHHHHH
Confidence            99999899999999999999999999 99998764

>PTZ00223 40S ribosomal protein S4; Provisional

Probab=100.00  E-value=2.7e-83  Score=563.66  Aligned_cols=196  Identities=48%  Similarity=0.788  Sum_probs=191.7

Q ss_pred             CCccEEECCEEeccCCCCceeeEEEEecCCCceEEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCce
Q 029038            1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGR   80 (200)
Q Consensus         1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGr   80 (200)
                      +||+|+||||||+|++||||||||||||++||||||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||
T Consensus        63 ~~~~V~VDGkvr~D~~~PvGlMDVIsI~kt~e~yRvl~D~kGrf~l~~I~~eeA~~KLcKV~~k~~~~gG~~ql~~hDGr  142 (273)
T PTZ00223         63 RQGLVCVDGKPRKDGKYPAGFMDVVEIPKTGDRFRILYDVKGRFALVKVSEAEAQIKLMKVVNVYTATGRIPVAVTHDGH  142 (273)
T ss_pred             hCCeEEECCEEEccCCCCCceeEEEEEcCCCCeEEEEECCCCcEEEEEcChHHccceEEEEEEEEEecCCeeEEEecCCc
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeCCCCccCCCeEEEecCCCceeEEEEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEeEeeccE
Q 029038           81 TIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNV  160 (200)
Q Consensus        81 ni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d~~g~~F~T~~~~v  160 (200)
                      ||+|+||.||+||||+|+||+++|++|+||++||+||||||+|+|++|+|.+|+++++++++||++|++|++|+|+++||
T Consensus       143 nI~~~d~~~k~~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d~~g~~F~T~~~~V  222 (273)
T PTZ00223        143 RIRYPDPRTSRGDTLVYNVKEKKVVDLIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRAANI  222 (273)
T ss_pred             eeccCCccccCCCEEEEECCCCeeeEEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEccC-CCceEeCcCCCceeeehhHHHHHHHHhhhhh
Q 029038          161 FTIGKG-TKPWVSLPKGKGIKLSIIEEARKRQALATSA  197 (200)
Q Consensus       161 fvIG~~-~~p~isLp~~~gi~~~~~e~~~~~~~~~~~~  197 (200)
                      ||||++ ++||||||++||||||++|| |+++|.+..+
T Consensus       223 fvIG~~~~kp~IsLp~~kgi~~~~~e~-~~~~~~~~~~  259 (273)
T PTZ00223        223 FVIGKDMNSVPVTLPKQQGLRINVIQE-REEKLIAAEA  259 (273)
T ss_pred             EEEeCCCCCcceECcCCCCccccHHHH-HHHHHHHHHh
Confidence            999996 69999999999999999999 9999877654

>PRK04313 30S ribosomal protein S4e; Validated

Probab=100.00  E-value=2.1e-76  Score=511.99  Aligned_cols=174  Identities=40%  Similarity=0.653  Sum_probs=170.9

Q ss_pred             CCccEEECCEEeccCCCCceeeEEEEecCCCceEEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCce
Q 029038            1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGR   80 (200)
Q Consensus         1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGr   80 (200)
                      +||+|+||||||+|++||||||||||||++||||||+||++|||++|+|++|||+||||||++|++++||+|||+|||||
T Consensus        62 ~~~~V~VDGkvr~D~~~PvGlmDVIsI~~~~e~yRvl~d~kgr~~l~~I~~eea~~KL~KV~~k~~~~gG~~ql~~hDGr  141 (237)
T PRK04313         62 NEGKVLVDGRVRKDYKFPVGLMDVISIPETGEYYRVLPDEKGRLVLIPISEEEAKLKLCKIENKTTVKGGKIQLNLHDGR  141 (237)
T ss_pred             hCCcEEECCEEEcccccCcCceeEEEEccCCCeEEEEECCCCcEEEEECChHHccceEEEEEeEEEecCCEEEEEecCCc
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeCC-CCccCCCeEEEecCCCceeEEEEeeCCcEEEEECCCcceeEEEEEEEEEec-CCccEEEEEcCCCCeEeEeec
Q 029038           81 TIRYPD-PLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLG  158 (200)
Q Consensus        81 ni~~~d-~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~-~s~~iV~v~d~~g~~F~T~~~  158 (200)
                      ||+++| |.||+||||+|+||+++|++|+||++||+||||||+|+||+|+|.+|++++ +++++||++|++|++|+|+++
T Consensus       142 ni~~~~~~~~k~~Dtv~i~l~~~kI~~~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~~G~~F~T~~~  221 (237)
T PRK04313        142 NILVDVEDDYKTGDSLLISLPEQEIVDHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKDGEKFETILD  221 (237)
T ss_pred             eEEccCccccccCCEEEEECCCCceeEEEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcCCCCEEEEEee
Confidence            999998 999999999999999999999999999999999999999999999999999 678999999999999999999


Q ss_pred             cEEEEccCCCceEeCcC
Q 029038          159 NVFTIGKGTKPWVSLPK  175 (200)
Q Consensus       159 ~vfvIG~~~~p~isLp~  175 (200)
                      ||||||+ ++|||+||.
T Consensus       222 ~vfvIG~-~kp~isl~~  237 (237)
T PRK04313        222 YVFVIGK-EKPVIKLPE  237 (237)
T ss_pred             eEEEEcC-CCcceeCCC
Confidence            9999999 999999984

>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=4.5e-74  Score=494.53  Aligned_cols=176  Identities=47%  Similarity=0.724  Sum_probs=172.4

Q ss_pred             CCccEEECCEEeccCCCCceeeEEEEecCCCceEEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCce
Q 029038            1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGR   80 (200)
Q Consensus         1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGr   80 (200)
                      ++|+|+|||+||+|++||||||||||||+|||+||||||.+|||.||+|++|||.||||||++|++++||++||||||||
T Consensus        65 ~~g~v~VDG~vRkd~kfPVGlmDVisip~tgE~yRvl~d~~grl~l~~is~EeA~~Kl~kV~nKt~vkgG~~QLn~hDGr  144 (241)
T COG1471          65 SEGKVLVDGKVRKDYKFPVGLMDVISIPKTGEHYRVLPDEKGRLVLHPISAEEASYKLCKVKNKTTVKGGRIQLNLHDGR  144 (241)
T ss_pred             hcCcEEECCEEeccccCCcceEEEEEECCCCceEEEEecCCccEEEEecChhhccceEEEEEeEEEecCCEEEEEecCCc
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeCCCCccCCCeEEEecCCCceeEEEEeeCCcEEEEECCCcceeEEEEEEEEEec-CCccEEEEEcCCCCeEeEeecc
Q 029038           81 TIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGN  159 (200)
Q Consensus        81 ni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~-~s~~iV~v~d~~g~~F~T~~~~  159 (200)
                      |++++|+.|+++|||++++|+++|++||||++|++|||+||+|+|++|+|.+|+.++ +++++||++|.+|+.|+|+++|
T Consensus       145 ni~~~d~~~k~~Dtv~i~lp~~~I~~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~~~g~~F~T~~~y  224 (241)
T COG1471         145 NIRLEDDNYKTGDTVKISLPEQKIVEHIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDEEGNTFQTIKDY  224 (241)
T ss_pred             eeeccCCccccccEEEEeCCChhheeEeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEecCCCCceEEeeeE
Confidence            999999999999999999999999999999999999999999999999999999999 5578999999999999999999


Q ss_pred             EEEEccCCCceEeCcCCC
Q 029038          160 VFTIGKGTKPWVSLPKGK  177 (200)
Q Consensus       160 vfvIG~~~~p~isLp~~~  177 (200)
                      |||||+ ++|||+||.|+
T Consensus       225 VfvIG~-~k~~i~l~~e~  241 (241)
T COG1471         225 VFVIGE-DKPVISLPKEK  241 (241)
T ss_pred             EEEEcC-CCceEeCCCCC
Confidence            999999 99999999874

>KOG0378 consensus 40S ribosomal protein S4 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=6.2e-73  Score=489.80  Aligned_cols=195  Identities=68%  Similarity=1.131  Sum_probs=192.4

Q ss_pred             CCccEEECCEEeccCCCCceeeEEEEecCCCceEEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCce
Q 029038            1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGR   80 (200)
Q Consensus         1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGr   80 (200)
                      ||+.|+|||+||+|.+||+|||||++|++|||+||++||++|||.+|+|++|||+||||||++++.+.+|+|+|++||||
T Consensus        66 ~qr~i~v~gkvrt~~~yp~g~mDvisiekTge~fr~iyd~k~~F~~hrI~~eeakyKLcKVrk~f~~tkGiP~lvthDg~  145 (263)
T KOG0378|consen   66 MQREIKVDGKVRTDSTYPAGFMDVISIEKTGEHFRLIYDQKGRFAVHRITSEEAKYKLCKVRKIFLGTKGIPHLVTHDGR  145 (263)
T ss_pred             HHhhhhccceeecccccccceeEEEEecccchhhhhhhhcccceEEEEeccccccceeeeeEEEEeeccCcceEEccCCc
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeCCCCccCCCeEEEecCCCceeEEEEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEeEeeccE
Q 029038           81 TIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNV  160 (200)
Q Consensus        81 ni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d~~g~~F~T~~~~v  160 (200)
                      +||||||.+|+|||+++++++++|.++++|++|++||++||+|+||+|+|.+.|+|+|+|++||++|++|++|+|+++|+
T Consensus       146 tIrypDplIk~~dtI~~~~~t~kit~~ikf~~~~~~~vtgg~n~gRig~i~~rerh~G~f~vvhvkdt~gnsFatrLsNi  225 (263)
T KOG0378|consen  146 TIRYPDPLIKVNDTIKIDLETSKITDFIKFDTGNLCMVTGGANLGRIGVIKNRERHPGSFDVVHVKDTNGNSFATRLSNI  225 (263)
T ss_pred             eEecCCcccCccceeeccCCCceeeeeeccCccceeeeeccccccccccccccccCCCceEEEEEEecCCcEeeeeeccE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEccCCCceEeCcCCCceeeehhHHHHHHHHhhhh
Q 029038          161 FTIGKGTKPWVSLPKGKGIKLSIIEEARKRQALATS  196 (200)
Q Consensus       161 fvIG~~~~p~isLp~~~gi~~~~~e~~~~~~~~~~~  196 (200)
                      |+||+|++||||||+++||+++++|| |++||+|--
T Consensus       226 fvIgkgnKpwisLPkgkgi~~siaEe-~dkrl~~k~  260 (263)
T KOG0378|consen  226 FVIGEGNKPWISLPKGKGIALSIAEE-RDKRLAAKI  260 (263)
T ss_pred             EEEecCCCccccCccccCccchhhHH-HHHHHhhhc
Confidence            99999999999999999999999999 999998754

>PF00900 Ribosomal_S4e: Ribosomal family S4e; InterPro: IPR013845 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=100.00  E-value=2.7e-36  Score=222.17  Aligned_cols=77  Identities=64%  Similarity=1.028  Sum_probs=69.8

Q ss_pred             CCCceEEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCceEEeeCCCCccCCCeEEEecCCCcee
Q 029038           29 KTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKIT  105 (200)
Q Consensus        29 kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGrni~~~d~~ik~~DTv~i~l~~~kI~  105 (200)
                      ||||+|||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+||||+++||++||+
T Consensus         1 kt~e~yRvl~d~kgr~~l~~I~~eea~~KLckV~~k~~~~gG~~ql~~hDGrni~~~~~~~k~~Dtv~i~l~~~kI~   77 (77)
T PF00900_consen    1 KTGEHYRVLYDTKGRFVLHPISEEEAKYKLCKVRNKTTGKGGKPQLNTHDGRNIRYPDPDIKTNDTVVIDLPTQKIV   77 (77)
T ss_dssp             CTTEEEEEEE-TTS-EEEEEE-TTGGGEEEEEEEEEEEEGGGEEEEEETTTEEEES-SST--TTEEEEEETTTTEEE
T ss_pred             CCCcEEEEEECCCCcEEEEECCHHHccCeEEEEeEEEEecCCcEEEEecCceEEEcCcCCccCCCEEEEECCCCcCC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999986

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes yeast S7 (YS6); archaeal S4e; and mammalian and plant cytoplasmic S4 []. Two highly similar isoforms of mammalian S4 exist, one coded by a gene on chromosome Y, and the other on chromosome X. These proteins have 233 to 264 amino acids. This entry represents the central region of these proteins.; PDB: 2XZM_W 2XZN_W 3IZ6_D 3KBG_A 3U5G_E 3U5C_E 3IZB_D.

>PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=96.96  E-value=0.001  Score=40.96  Aligned_cols=31  Identities=29%  Similarity=0.566  Sum_probs=25.9

Q ss_pred             CCcEEEEECCCcceeEEEEEEEEEecCCccEEEE
Q 029038          112 VGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHI  145 (200)
Q Consensus       112 ~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v  145 (200)
                      +|+.|+|+.|++.|+.|+|.++..+.   ..|++
T Consensus         1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~---~~V~v   31 (32)
T PF00467_consen    1 VGDTVKVISGPFKGKIGKIVEIDRSK---VRVTV   31 (32)
T ss_dssp             TTSEEEESSSTTTTEEEEEEEEETTT---TEEEE
T ss_pred             CCCEEEEeEcCCCCceEEEEEEECCC---CEEEE
Confidence            58999999999999999999997543   44554

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....

>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif

Probab=96.93  E-value=0.00089  Score=38.96  Aligned_cols=27  Identities=37%  Similarity=0.668  Sum_probs=24.6

Q ss_pred             EeeCCcEEEEECCCcceeEEEEEEEEE
Q 029038          109 KFDVGNVVMVTGGRNRGRVGIIKNREK  135 (200)
Q Consensus       109 ~fe~G~~~~v~gG~n~G~vG~I~~i~~  135 (200)
                      +|++|+.++|++|.+.|..|+|.++..
T Consensus         1 ~~~~G~~V~I~~G~~~g~~g~i~~i~~   27 (28)
T smart00739        1 KFEVGDTVRVIAGPFKGKVGKVLEVDG   27 (28)
T ss_pred             CCCCCCEEEEeECCCCCcEEEEEEEcC
Confidence            478999999999999999999999863

Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.

>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=96.57  E-value=0.0015  Score=42.75  Aligned_cols=25  Identities=36%  Similarity=0.357  Sum_probs=23.4

Q ss_pred             CCccEEECCEEeccCCCCceeeEEE
Q 029038            1 MQRHVLVDAKVRTDKTYPAGFMDVV   25 (200)
Q Consensus         1 ~q~~V~VDGkvr~D~k~PvG~MDVI   25 (200)
                      ++|.|+|||++++|+.|++...|+|
T Consensus        24 ~~g~V~VNg~~v~~~~~~v~~~d~I   48 (48)
T PF01479_consen   24 KQGRVKVNGKVVKDPSYIVKPGDVI   48 (48)
T ss_dssp             HTTTEEETTEEESSTTSBESTTEEE
T ss_pred             CCCEEEECCEEEcCCCCCCCCcCCC
Confidence            4799999999999999999999987

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....

>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic

Probab=94.24  E-value=0.12  Score=41.05  Aligned_cols=40  Identities=15%  Similarity=0.287  Sum_probs=32.2

Q ss_pred             EEEEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcC
Q 029038          106 EFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDA  148 (200)
Q Consensus       106 ~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d~  148 (200)
                      +.+++..|+.+.|++|++-|..|+|.++....   ..|.|+.-
T Consensus        38 r~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~---~~V~Vegv   77 (114)
T TIGR01080        38 RALPVRKGDKVRIMRGDFKGHEGKVSKVDLKR---YRIYVEGV   77 (114)
T ss_pred             ccceeecCCEEEEecCCCCCCEEEEEEEEcCC---CEEEEcCe
Confidence            55688999999999999999999999997333   35666653

This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.

>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes

Probab=93.59  E-value=0.12  Score=33.88  Aligned_cols=39  Identities=28%  Similarity=0.416  Sum_probs=29.5

Q ss_pred             CCccEEECCEEeccCCCCceeeEEEEecCCCceEEEEEc
Q 029038            1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYD   39 (200)
Q Consensus         1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d   39 (200)
                      ++|.|+|||+..++..+++-..|+|++........++|.
T Consensus        24 ~~g~V~vn~~~~~~~~~~v~~~d~i~i~~~~~~~~i~~e   62 (70)
T cd00165          24 KHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYE   62 (70)
T ss_pred             HcCCEEECCEEccCCccCcCCCCEEEEcCCCcccceeec
Confidence            368999999999999999988899999764322234443

>smart00363 S4 S4 RNA-binding domain

Probab=92.78  E-value=0.1  Score=33.32  Aligned_cols=28  Identities=32%  Similarity=0.293  Sum_probs=25.3

Q ss_pred             CccEEECCEEeccCCCCceeeEEEEecC
Q 029038            2 QRHVLVDAKVRTDKTYPAGFMDVVSIPK   29 (200)
Q Consensus         2 q~~V~VDGkvr~D~k~PvG~MDVIsI~k   29 (200)
                      +|.|+|||++.++..+++--.|.|+++.
T Consensus        25 ~g~i~vng~~~~~~~~~l~~gd~i~~~~   52 (60)
T smart00363       25 QGRVKVNGKKVTKPSYIVKPGDVISVRG   52 (60)
T ss_pred             cCCEEECCEEecCCCeEeCCCCEEEEcc
Confidence            6889999999999999998889999975

>PRK01191 rpl24p 50S ribosomal protein L24P; Validated

Probab=92.26  E-value=0.42  Score=38.33  Aligned_cols=38  Identities=21%  Similarity=0.378  Sum_probs=30.7

Q ss_pred             EEEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEc
Q 029038          107 FIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD  147 (200)
Q Consensus       107 ~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d  147 (200)
                      .+++..|+.+.|+.|+.-|..|+|.++....+   .|+|+.
T Consensus        43 ~~~IkkGD~V~VisG~~KGk~GkV~~V~~~~~---~V~VeG   80 (120)
T PRK01191         43 SLPVRKGDTVKVMRGDFKGEEGKVVEVDLKRG---RIYVEG   80 (120)
T ss_pred             cceEeCCCEEEEeecCCCCceEEEEEEEcCCC---EEEEeC
Confidence            45788999999999999999999999965433   465654

>PRK12281 rplX 50S ribosomal protein L24; Reviewed

Probab=91.15  E-value=0.34  Score=35.69  Aligned_cols=38  Identities=21%  Similarity=0.451  Sum_probs=31.7

Q ss_pred             EEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcC
Q 029038          108 IKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDA  148 (200)
Q Consensus       108 i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d~  148 (200)
                      +++..|+.+.|+.|+.-|++|+|.++.+..   ..|.||+-
T Consensus         5 ~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~---~~V~Vegv   42 (76)
T PRK12281          5 LKVKKGDMVKVIAGDDKGKTGKVLAVLPKK---NRVIVEGV   42 (76)
T ss_pred             ccccCCCEEEEeEcCCCCcEEEEEEEEcCC---CEEEEcCc
Confidence            478899999999999999999999997544   35777653

>CHL00141 rpl24 ribosomal protein L24; Validated

Probab=90.53  E-value=0.42  Score=35.73  Aligned_cols=38  Identities=16%  Similarity=0.457  Sum_probs=31.4

Q ss_pred             EEEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEc
Q 029038          107 FIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD  147 (200)
Q Consensus       107 ~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d  147 (200)
                      .+++..|+.+.|+.|+.-|+.|+|.++.+..   ..|+|++
T Consensus         6 ~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~---~~V~Veg   43 (83)
T CHL00141          6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKKS---NKVIVKG   43 (83)
T ss_pred             eCcccCCCEEEEeEcCCCCcEEEEEEEEcCC---CEEEEcC
Confidence            3578899999999999999999999997543   3577765

>PRK00004 rplX 50S ribosomal protein L24; Reviewed

Probab=89.53  E-value=0.49  Score=36.75  Aligned_cols=37  Identities=22%  Similarity=0.505  Sum_probs=29.8

Q ss_pred             EEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEc
Q 029038          108 IKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD  147 (200)
Q Consensus       108 i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d  147 (200)
                      +++..|+.+.|+.|++-|++|+|.++.....   .|+|++
T Consensus         3 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~---~V~Veg   39 (105)
T PRK00004          3 MKIKKGDTVIVIAGKDKGKRGKVLKVLPKKN---KVIVEG   39 (105)
T ss_pred             CcccCCCEEEEeEcCCCCcEEEEEEEEcCCC---EEEEcC
Confidence            4788999999999999999999999975432   355554

>TIGR02988 YaaA_near_RecF S4 domain protein YaaA

Probab=86.36  E-value=0.77  Score=31.29  Aligned_cols=27  Identities=26%  Similarity=0.358  Sum_probs=23.7

Q ss_pred             CccEEECCEEeccCCCCceeeEEEEec
Q 029038            2 QRHVLVDAKVRTDKTYPAGFMDVVSIP   28 (200)
Q Consensus         2 q~~V~VDGkvr~D~k~PvG~MDVIsI~   28 (200)
                      +|.|+|||++++.+.|.+--=|+|+|+
T Consensus        33 ~G~V~VNg~~~~~~~~~l~~Gd~v~i~   59 (59)
T TIGR02988        33 ENEVLVNGELENRRGKKLYPGDVIEIP   59 (59)
T ss_pred             cCCEEECCEEccCCCCCCCCCCEEEeC
Confidence            689999999999888988888888874

This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.

>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle

Probab=84.79  E-value=1.3  Score=34.34  Aligned_cols=29  Identities=24%  Similarity=0.462  Sum_probs=25.7

Q ss_pred             EeeCCcEEEEECCCcceeEEEEEEEEEec
Q 029038          109 KFDVGNVVMVTGGRNRGRVGIIKNREKHK  137 (200)
Q Consensus       109 ~fe~G~~~~v~gG~n~G~vG~I~~i~~~~  137 (200)
                      ++..|+.+.|+.|+.-|..|+|.++.+..
T Consensus         3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~   31 (104)
T TIGR01079         3 KIKKGDTVKVISGKDKGKRGKVLKVLPKT   31 (104)
T ss_pred             cccCCCEEEEeEcCCCCcEEEEEEEEcCC
Confidence            67789999999999999999999996543

This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.

>PTZ00194 60S ribosomal protein L26; Provisional

Probab=82.48  E-value=2.3  Score=35.14  Aligned_cols=55  Identities=27%  Similarity=0.361  Sum_probs=38.6

Q ss_pred             EEEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEE-----cCCCCeEe--EeeccEEEEc
Q 029038          107 FIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQ-----DALGHEFA--TRLGNVFTIG  164 (200)
Q Consensus       107 ~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~-----d~~g~~F~--T~~~~vfvIG  164 (200)
                      .+++..|+.+.|+.|++-|..|+|.++....+   .|.|+     ..+|..++  --.|||+++-
T Consensus        44 s~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~---~ViVEgvn~~Kk~gk~~e~PIh~SNV~iv~  105 (143)
T PTZ00194         44 SMPVRKDDEVMVVRGHHKGREGKVTAVYRKKW---VIHIEKITREKANGEPVQIGIHPSNVIITK  105 (143)
T ss_pred             cceeecCCEEEEecCCCCCCceEEEEEEcCCC---EEEEeCeEEEecCCCEeecCcCchheEEEc
Confidence            34788899999999999999999999975443   34443     35554433  3346676664

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	200
3iz6_D	265	Localization Of The Small Subunit Ribosomal Protein		1e-101
3izb_D	261	Localization Of The Small Subunit Ribosomal Protein		2e-72
2xzm_W	260	Crystal Structure Of The Eukaryotic 40s Ribosomal S		9e-57
3zey_1	273	High-resolution Cryo-electron Microscopy Structure		6e-46
3j20_E	243	Promiscuous Behavior Of Proteins In Archaeal Riboso		2e-16
3kbg_A	213	Crystal Structure Of The 30s Ribosomal Protein S4e		5e-15

>pdb|3IZ6|D Chain D, Localization Of The Small Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 265

Iteration: 1
 Score =  363 bits (931), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 170/190 (89%), Positives = 183/190 (96%)
Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRHVLVD KVRTDKTYPAGFMDV+SIPKT EN+RLLYDTKGRFRL S++DE+AKFKLCK
Sbjct: 66  MQRHVLVDGKVRTDKTYPAGFMDVISIPKTGENYRLLYDTKGRFRLQSVKDEDAKFKLCK 125
Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VRSVQFGQKGIPY+NTYDGRTIRYPDP+IKANDTIK+DLETNKI +FIKFDVGNVVMVTG
Sbjct: 126 VRSVQFGQKGIPYLNTYDGRTIRYPDPIIKANDTIKIDLETNKIVDFIKFDVGNVVMVTG 185
Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRN GRVG+IKNREKHKGSFETIH++DALGH+FATRLGNVFTIGKG KPWVSLPKGKGIK
Sbjct: 186 GRNTGRVGVIKNREKHKGSFETIHVEDALGHQFATRLGNVFTIGKGNKPWVSLPKGKGIK 245
Query: 181 LSIIEEARKR 190
           LSIIEE RKR
Sbjct: 246 LSIIEEQRKR 255

>pdb|3IZB|D Chain D, Localization Of The Small Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 261

Iteration: 1
 Score =  268 bits (684), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 125/192 (65%), Positives = 155/192 (80%)
Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRHV VD KVRTD TYPAGFMDV+++  TNENFRL+YD KGRF +H I DEEA +KL K
Sbjct: 66  MQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASYKLGK 125
Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           V+ VQ G+KG+PY+ T+DGRTIRYPDP IK NDT+K+DL + KIT+FIKFD G +V VTG
Sbjct: 126 VKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLVYVTG 185
Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRN GR+G I ++E+H G F+ +HI+D+L + F TRL NVF IG+  KP++SLPKGKGIK
Sbjct: 186 GRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKGKGIK 245
Query: 181 LSIIEEARKRQA 192
           LSI EE  +R+A
Sbjct: 246 LSIAEERDRRRA 257

>pdb|2XZM|W Chain W, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit In Complex With Initiation Factor 1. This File Contains The 40s Subunit And Initiation Factor For Molecule 1 Length = 260

Iteration: 1
 Score =  216 bits (549), Expect = 9e-57,   Method: Compositional matrix adjust.
 Identities = 105/190 (55%), Positives = 137/190 (72%), Gaps = 1/190 (0%)
Query: 2   QRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKV 61
           +++V VD KVR DK YP G MDVV I KT+++FR+LYDTKGRF L S+  EEAK+KL KV
Sbjct: 69  EQNVFVDGKVRRDKGYPTGLMDVVRIEKTDQSFRILYDTKGRFVLKSLSKEEAKYKLLKV 128
Query: 62  RSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGG 121
            +   G   IPYI T+D RTIR+P+P IK  DT+K DL  NKI  F   + GNV  +  G
Sbjct: 129 TAKAIGPNQIPYIVTHDSRTIRFPNPEIKIGDTLKYDLVNNKIENFAHLESGNVCYIQQG 188
Query: 122 RNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKL 181
            N GRVGII++ EKH+GSF+  H++DA G+ FATRLGN+F +G+G K W+ LP G G++ 
Sbjct: 189 NNIGRVGIIQHIEKHQGSFDICHVKDAKGNAFATRLGNIFVLGQGKKSWIELPSGDGVRE 248
Query: 182 SIIEEARKRQ 191
           +I+EE RKR+
Sbjct: 249 TILEE-RKRK 257

>pdb|3ZEY|1 Chain 1, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 273

Iteration: 1
 Score =  180 bits (456), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 91/183 (49%), Positives = 120/183 (65%), Gaps = 1/183 (0%)
Query: 5   VLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSV 64
           V VD K R D  YPAGFMDVV IPKT + FR+LYD KGRF L  + + E+  K+ KV +V
Sbjct: 67  VCVDGKPRKDGKYPAGFMDVVEIPKTGDRFRILYDVKGRFALVRVSEAESSIKMMKVVNV 126
Query: 65  QFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNR 124
             G   IP   T+DG  IRYPDP     DT+  D++  K+ + IK   G VVMVTGG NR
Sbjct: 127 YTGTGRIPVAVTHDGHRIRYPDPRTSRGDTLVYDVKEKKVLDLIKIGNGKVVMVTGGANR 186
Query: 125 GRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPW-VSLPKGKGIKLSI 183
           GR+G I + E+H G+F+   ++DA GHEFATR  N+F IGK      V+LPK +G+++++
Sbjct: 187 GRIGEIVSIERHPGAFDIARLKDASGHEFATRATNIFVIGKDMSSVPVTLPKQQGLRINV 246
Query: 184 IEE 186
           I+E
Sbjct: 247 IQE 249

>pdb|3J20|E Chain E, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (30s Ribosomal Subunit) Length = 243

Iteration: 1
 Score = 82.4 bits (202), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 58/174 (33%), Positives = 92/174 (52%), Gaps = 7/174 (4%)
Query: 6   LVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQ 65
           LVD +VR D  +P G MDVVSIP+T E++R+L +  G+  LH I ++EA  K  ++R+ +
Sbjct: 72  LVDGRVRKDYKFPVGIMDVVSIPETGEHYRVLPNRIGKLILHPISEDEAFIKPLRIRNKR 131
Query: 66  FGQKGIPYINTYDGR----TIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGG 121
             +     +N +DG     +I   D    +  T+ + +   +I E + F+ G  V VT G
Sbjct: 132 MIKGARVQLNFHDGTNHIVSIAEKDNYFTSY-TVLMKVPEREILEVLPFEKGAYVFVTQG 190
Query: 122 RNRGRVG-IIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLP 174
           +N  R G I++ +    G  + + I+D  G  F T     F +G   KP +SLP
Sbjct: 191 KNVARKGRIVEIKRFPMGWPDVVTIEDEEGELFDTLKEYAFVVGT-DKPKISLP 243

>pdb|3KBG|A Chain A, Crystal Structure Of The 30s Ribosomal Protein S4e From Thermoplasma Acidophilum. Northeast Structural Genomics Consortium Target Tar28 Length = 213

Iteration: 1
 Score = 77.4 bits (189), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 56/172 (32%), Positives = 81/172 (47%), Gaps = 7/172 (4%)
Query: 5   VLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSV 64
           V VD K   +K +  GF DV+ I    E++R++Y+ +G   L     E A  KL KVRS 
Sbjct: 36  VKVDGKTVREKKFAVGFXDVIEI--NGESYRVVYNDQGALVLXKETKERASXKLLKVRSK 93
Query: 65  QFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNR 124
                    + T+DGRT    D  IK  D + + +   KI+E IK   GN   +T G + 
Sbjct: 94  VIAPGNRIQLGTHDGRTFITDDKSIKVGDVLAVSVPDXKISEIIKXQPGNKAYITAGSHV 153
Query: 125 GRVGIIKNREKHKGSFET-IHIQDALGHEFATRLGNVFTIGKGTKPWVSLPK 175
            + G I   E  +GS    +H Q+     F+T   +VF IG     +V  P+
Sbjct: 154 NQTGTISKIEAKEGSSANLVHFQEG----FSTIKDHVFXIGSSKFSFVLSPE 201

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	200
3iz6_D	265	40S ribosomal protein S4 (S4E); eukaryotic ribosom	2e-89
3u5c_E	261	RP5, S7, YS6, 40S ribosomal protein S4-A; translat	1e-88
2xzm_W	260	40S ribosomal protein S4; ribosome, translation; 3	8e-86
3kbg_A	213	30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2	2e-69

>3iz6_D 40S ribosomal protein S4 (S4E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Length = 265

 Score =  262 bits (670), Expect = 2e-89
 Identities = 174/198 (87%), Positives = 188/198 (94%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRHVLVD KVRTDKTYPAGFMDV+SIPKT EN+RLLYDTKGRFRL S++DE+AKFKLCK
Sbjct: 66  MQRHVLVDGKVRTDKTYPAGFMDVISIPKTGENYRLLYDTKGRFRLQSVKDEDAKFKLCK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VRSVQFGQKGIPY+NTYDGRTIRYPDP+IKANDTIK+DLETNKI +FIKFDVGNVVMVTG
Sbjct: 126 VRSVQFGQKGIPYLNTYDGRTIRYPDPIIKANDTIKIDLETNKIVDFIKFDVGNVVMVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRN GRVG+IKNREKHKGSFETIH++DALGH+FATRLGNVFTIGKG KPWVSLPKGKGIK
Sbjct: 186 GRNTGRVGVIKNREKHKGSFETIHVEDALGHQFATRLGNVFTIGKGNKPWVSLPKGKGIK 245

Query: 181 LSIIEEARKRQALATSAA 198
           LSIIEE RKR A A +AA
Sbjct: 246 LSIIEEQRKRDAAAQAAA 263

>3u5c_E RP5, S7, YS6, 40S ribosomal protein S4-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_D 3u5g_E Length = 261

 Score =  260 bits (665), Expect = 1e-88
 Identities = 125/192 (65%), Positives = 155/192 (80%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
           MQRHV VD KVRTD TYPAGFMDV+++  TNENFRL+YD KGRF +H I DEEA +KL K
Sbjct: 66  MQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASYKLGK 125

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           V+ VQ G+KG+PY+ T+DGRTIRYPDP IK NDT+K+DL + KIT+FIKFD G +V VTG
Sbjct: 126 VKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLVYVTG 185

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           GRN GR+G I ++E+H G F+ +HI+D+L + F TRL NVF IG+  KP++SLPKGKGIK
Sbjct: 186 GRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKGKGIK 245

Query: 181 LSIIEEARKRQA 192
           LSI EE  +R+A
Sbjct: 246 LSIAEERDRRRA 257

>2xzm_W 40S ribosomal protein S4; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_W Length = 260

 Score =  253 bits (646), Expect = 8e-86
 Identities = 102/192 (53%), Positives = 137/192 (71%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
            +++V VD KVR DK YP G MDVV I KT+++FR+LYDTKGRF L S+  EEAK+KL K
Sbjct: 68  KEQNVFVDGKVRRDKGYPTGLMDVVRIEKTDQSFRILYDTKGRFVLKSLSKEEAKYKLLK 127

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           V +   G   IPYI T+D RTIR+P+P IK  DT+K DL  NKI  F   + GNV  +  
Sbjct: 128 VTAKAIGPNQIPYIVTHDSRTIRFPNPEIKIGDTLKYDLVNNKIENFAHLESGNVCYIQQ 187

Query: 121 GRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPKGKGIK 180
           G N GRVGII++ EKH+GSF+  H++DA G+ FATRLGN+F +G+G K W+ LP G G++
Sbjct: 188 GNNIGRVGIIQHIEKHQGSFDICHVKDAKGNAFATRLGNIFVLGQGKKSWIELPSGDGVR 247

Query: 181 LSIIEEARKRQA 192
            +I+EE +++ +
Sbjct: 248 ETILEERKRKFS 259

>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum} Length = 213

 Score =  209 bits (533), Expect = 2e-69
 Identities = 57/176 (32%), Positives = 82/176 (46%), Gaps = 7/176 (3%)

Query: 1   MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCK 60
               V VD K   +K +  GFMDV+ I    E++R++Y+ +G   L     E A  KL K
Sbjct: 32  ANGLVKVDGKTVREKKFAVGFMDVIEIN--GESYRVVYNDQGALVLMKETKERASMKLLK 89

Query: 61  VRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTG 120
           VRS          + T+DGRT    D  IK  D + + +   KI+E IK   GN   +T 
Sbjct: 90  VRSKVIAPGNRIQLGTHDGRTFITDDKSIKVGDVLAVSVPDMKISEIIKMQPGNKAYITA 149

Query: 121 GRNRGRVGIIKNREKHKGS-FETIHIQDALGHEFATRLGNVFTIGKGTKPWVSLPK 175
           G +  + G I   E  +GS    +H Q+     F+T   +VF IG     +V  P+
Sbjct: 150 GSHVNQTGTISKIEAKEGSSANLVHFQEG----FSTIKDHVFMIGSSKFSFVLSPE 201

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	200
3iz6_D	265	40S ribosomal protein S4 (S4E); eukaryotic ribosom	100.0
3u5c_E	261	RP5, S7, YS6, 40S ribosomal protein S4-A; translat	100.0
2xzm_W	260	40S ribosomal protein S4; ribosome, translation; 3	100.0
3j20_E	243	30S ribosomal protein S4E; archaea, archaeal, KINK	100.0
3kbg_A	213	30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2	100.0
2ckk_A	127	KIN17; beta barrel, ribosomal protein, ribonucleop	95.69
2do3_A	69	Transcription elongation factor SPT5; KOW motif, s	95.21
1vq8_T	120	50S ribosomal protein L24P; ribosome 50S, protein-	87.18
3j21_U	121	50S ribosomal protein L24P; archaea, archaeal, KIN	83.05
1nz9_A	58	Transcription antitermination protein NUSG; transc	82.07
1p9k_A	79	ORF, hypothetical protein; alfal motif, RNA-bindin	80.81

>3iz6_D 40S ribosomal protein S4 (S4E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=100.00  E-value=1.9e-88  Score=593.29  Aligned_cols=198  Identities=86%  Similarity=1.369  Sum_probs=175.7

Q ss_pred             CCccEEECCEEeccCCCCceeeEEEEecCCCceEEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCce
Q 029038            1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGR   80 (200)
Q Consensus         1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGr   80 (200)
                      |||+|+||||||||++||+|||||||||+|||||||+||++|||.+|+|++|||+||||||++|+++++|+|||+|||||
T Consensus        66 ~q~~VkVDGkvrtD~~~PvG~MDVIsI~kt~e~fRll~D~kGrf~l~~I~~eEA~~KLcKV~~k~~~~~G~pql~tHDGr  145 (265)
T 3iz6_D           66 MQRHVLVDGKVRTDKTYPAGFMDVISIPKTGENYRLLYDTKGRFRLQSVKDEDAKFKLCKVRSVQFGQKGIPYLNTYDGR  145 (265)
T ss_dssp             HTTCCEETTEECCCTTCCCCTTCEEECCSSCCEEEEEECTTSCEEEEEECHHHHTCEEEEEEEEECCSSSCCEEEETTSC
T ss_pred             HCCcEEECCEEeccCCCCCcEEEEEEEcCCCCEEEEEECCCCcEEEEECChHHcceEEEEEEEEEEccCCceEEEeecce
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeCCCCccCCCeEEEecCCCceeEEEEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEeEeeccE
Q 029038           81 TIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNV  160 (200)
Q Consensus        81 ni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d~~g~~F~T~~~~v  160 (200)
                      ||+||||.||+||||+||||++||++||||++||+||||||+|+|++|+|++|++|+||+++|||+|++|++|+|+++||
T Consensus       146 ti~~~dp~ik~~DTv~idl~~~kI~d~ikfe~Gnl~mvtgG~n~GriG~I~~ie~~~gs~~iV~vkd~~g~~F~T~~~nv  225 (265)
T 3iz6_D          146 TIRYPDPIIKANDTIKIDLETNKIVDFIKFDVGNVVMVTGGRNTGRVGVIKNREKHKGSFETIHVEDALGHQFATRLGNV  225 (265)
T ss_dssp             CCBSCSSCCCTTCEEEECSSSCCEEEEECCSTTCEEEECSSSSCSCEEEEEEEECCSSSCCEEEECCCSSCCEEEEGGGE
T ss_pred             EEecCCCCcccCCEEEEECCCCceeeEEEccCCCEEEEEcCCcceEEEEEEEEEEecCCCcEEEEEECCCCeEEEEeCeE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEccCCCceEeCcCCCceeeehhHHHHHHHHhhhhhcc
Q 029038          161 FTIGKGTKPWVSLPKGKGIKLSIIEEARKRQALATSAAA  199 (200)
Q Consensus       161 fvIG~~~~p~isLp~~~gi~~~~~e~~~~~~~~~~~~~~  199 (200)
                      ||||++++||||||++|||||+++|| |++||+|..++|
T Consensus       226 fvIGk~~kp~IsLp~~kg~~~~~~ee-r~~~~~~~~~~~  263 (265)
T 3iz6_D          226 FTIGKGNKPWVSLPKGKGIKLSIIEE-QRKRDAAAQAAA  263 (265)
T ss_dssp             EEEECSSCCCCCCCCCC----------------------
T ss_pred             EEEccCCCeeEeCCCCCceeeehHHh-HHHHHHHhhhhc
Confidence            99999889999999999999999999 999998876654

>3u5c_E RP5, S7, YS6, 40S ribosomal protein S4-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_D 3u5g_E

Probab=100.00  E-value=5.4e-88  Score=589.36  Aligned_cols=194  Identities=64%  Similarity=1.078  Sum_probs=191.4

Q ss_pred             CCccEEECCEEeccCCCCceeeEEEEecCCCceEEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCce
Q 029038            1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGR   80 (200)
Q Consensus         1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGr   80 (200)
                      |||+|+||||||||++||+|||||||||+|||||||+||++|||.+|+|++|||+||||||++|+++++|+|||+|||||
T Consensus        66 ~q~~VkVDGkvrtD~~~PvG~MDVIsI~kt~e~fRll~D~kGrf~l~~I~~eEA~~KLcKV~~k~~~~~G~pql~tHDGr  145 (261)
T 3u5c_E           66 MQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASYKLGKVKKVQLGKKGVPYVVTHDGR  145 (261)
T ss_dssp             TTTCEEETTBCCCCTTCEEETTCEEEETTTTEEEECCBCSSSCBCCEECCTTGGGCEECCEEEEEECGGGCEEEEETTTE
T ss_pred             HCCcEEECCEEeccCCCCCceEEEEEEcCCCCEEEEEECCCCcEEEEECChHHcceEEEEEEEEEEecCCceEEEEecce
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeCCCCccCCCeEEEecCCCceeEEEEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEeEeeccE
Q 029038           81 TIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNV  160 (200)
Q Consensus        81 ni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d~~g~~F~T~~~~v  160 (200)
                      ||+||||.||+||||+||||++||++||||++||+||||||+|+|++|+|++|++|+||+++|||+|++|++|+|+++||
T Consensus       146 ti~~~dp~ik~~Dtv~idl~~~kI~d~ikfe~Gnl~mvtgG~n~GriG~I~~ie~~~gs~~iV~vkd~~g~~F~T~~~nv  225 (261)
T 3u5c_E          146 TIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLVYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNV  225 (261)
T ss_dssp             EEESCCSSCCTTCEEEECSSSSCEEEEECCCSSCCEEECSSTTTTCBCCCCEEECCTTSCCEEEEECTTSCEEEEEGGGE
T ss_pred             EEecCCCCcccCCEEEEECCCCceeeEEEccCCCEEEEEcCCcceEEEEEEEEEEecCCCcEEEEEECCCCeEEEEeCeE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEccCCCceEeCcCCCceeeehhHHHHHHHHhhh
Q 029038          161 FTIGKGTKPWVSLPKGKGIKLSIIEEARKRQALAT  195 (200)
Q Consensus       161 fvIG~~~~p~isLp~~~gi~~~~~e~~~~~~~~~~  195 (200)
                      ||||++++||||||++|||||+++|| |++||+|.
T Consensus       226 fvIGk~~kp~IsLp~~kg~~~~~~ee-r~~~~~~~  259 (261)
T 3u5c_E          226 FVIGEQGKPYISLPKGKGIKLSIAEE-RDRRRAQQ  259 (261)
T ss_dssp             EECCSSSCCSSCCCTTTTCCCCHHHH-HHHHTTTT
T ss_pred             EEEccCCCeeEeCCCCCceeeehHHh-HHHHHHhc
Confidence            99999889999999999999999999 99998664

>2xzm_W 40S ribosomal protein S4; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_W

Probab=100.00  E-value=1.1e-85  Score=574.51  Aligned_cols=192  Identities=55%  Similarity=0.937  Sum_probs=189.0

Q ss_pred             CC--ccEEECCEEeccCCCCceeeEEEEecCCCceEEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccC
Q 029038            1 MQ--RHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYD   78 (200)
Q Consensus         1 ~q--~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hD   78 (200)
                      +|  |+|+||||||+|++||||||||||||+|||||||+||++|||.+|+|++|||+||||||++|++++||+|||+|||
T Consensus        66 ~q~~~~VkVDGkvr~D~~~PvG~MDVIsI~kt~e~fRll~D~kGrf~l~~I~~eEA~~KLcKV~~k~~~k~G~~ql~~HD  145 (260)
T 2xzm_W           66 NDKEQNVFVDGKVRRDKGYPTGLMDVVRIEKTDQSFRILYDTKGRFVLKSLSKEEAKYKLLKVTAKAIGPNQIPYIVTHD  145 (260)
T ss_dssp             TSTTCCEEETTEECCCTTCEECTTCEEEEGGGTEEEEEEECSSSCEEEEECCTTGGGEEEEEEEEEEEETTTEEEEEETT
T ss_pred             hccCCeEEECCEEeccCCCCCcEEEEEeEcCCCCEEEEEEcCCccEEEEEcChHHcccEEEEEEEEEEccCCceEEEecC
Confidence            46  9999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceEEeeCCCCccCCCeEEEecCCCceeEEEEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEeEeec
Q 029038           79 GRTIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLG  158 (200)
Q Consensus        79 Grni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d~~g~~F~T~~~  158 (200)
                      ||||+|+||.||+||||+||||++||++||||++||+||||||+|+||+|+|++++++++|+++|||+|++|++|+|+++
T Consensus       146 Grti~~~d~~ik~~Dtv~idl~~~kI~d~ikfe~G~l~mvtgG~n~GriG~I~~~e~~~gs~~iV~vkd~~g~~F~T~~~  225 (260)
T 2xzm_W          146 SRTIRFPNPEIKIGDTLKYDLVNNKIENFAHLESGNVCYIQQGNNIGRVGIIQHIEKHQGSFDICHVKDAKGNAFATRLG  225 (260)
T ss_dssp             TEEEESCCSSCCTTBEEEEETTTTEEECCCBCCSSCEEEECSSTTTTCEEEEEEEECCCSSCCEEEEECTTCCCEEEEGG
T ss_pred             CceEeccCCcCccCCeEEEeCCCCceeeEEEecCCCEEEEECCccceeEEEEEEEEecCCCCcEEEEEeCCCCeEEEEEe
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEccCCCceEeCcCCCceeeehhHHHHHHHHh
Q 029038          159 NVFTIGKGTKPWVSLPKGKGIKLSIIEEARKRQAL  193 (200)
Q Consensus       159 ~vfvIG~~~~p~isLp~~~gi~~~~~e~~~~~~~~  193 (200)
                      ||||||++++||||||+++|||||++|| |++||+
T Consensus       226 ~vfvIG~~~kp~Islp~~kgi~l~i~ee-r~~~~~  259 (260)
T 2xzm_W          226 NIFVLGQGKKSWIELPSGDGVRETILEE-RKRKFS  259 (260)
T ss_dssp             GEEEEESTTCCSSCCSSSSSCCCCHHHH-HHHHTC
T ss_pred             eEEEECCCCceeEecCCCCCeecchhhh-hhhhhc
Confidence            9999999779999999999999999999 999874

>3j20_E 30S ribosomal protein S4E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=100.00  E-value=4.3e-76  Score=510.51  Aligned_cols=173  Identities=32%  Similarity=0.482  Sum_probs=170.8

Q ss_pred             CCccEEECCEEeccCCCCceeeEEEEecCCCceEEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCce
Q 029038            1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGR   80 (200)
Q Consensus         1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGr   80 (200)
                      +||+|+||||+|+|++|||||||||||++++|+||++||++|||.+|+|++|||+||||||++|++++||+|||+|||||
T Consensus        67 ~~~~I~VdGKvr~d~~ypvG~mDVIsI~kt~e~fr~i~d~kGr~~~~~I~~eea~~KLcKV~~k~~~~~G~~~l~~hDgr  146 (243)
T 3j20_E           67 NEGKFLVDGRVRKDYKFPVGIMDVVSIPETGEHYRVLPNRIGKLILHPISEDEAFIKPLRIRNKRMIKGARVQLNFHDGT  146 (243)
T ss_dssp             HHCSCEETTEECCCSSCEECTTCEEEETTTTEEEEEEECSSSCEEEEEECTTTTTEEEECCSCEEEETTTEEEECCSSCC
T ss_pred             HCCcEEECCEEeccccCCcccceEEEecccCceeEEEecCCCceEEEEeChhhccceEEEEeeeEEccCCeeEEEecCCc
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeC---CCCccCCCeEEEecCCCceeEEEEeeCCcEEEEECCCcceeEEEEEEEEEecCC-ccEEEEEcCCCCeEeEe
Q 029038           81 TIRYP---DPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGS-FETIHIQDALGHEFATR  156 (200)
Q Consensus        81 ni~~~---d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s-~~iV~v~d~~g~~F~T~  156 (200)
                      ||+||   ||.||+||||+||||++||+|||||++||+||||||+|+||+|+|++|++|++| +++|||+|++|++|+|+
T Consensus       147 ~i~~p~~~d~~ik~~Dtv~idl~~~kI~d~ikf~~G~l~mvtgG~n~GriG~I~~ie~~~gs~~~~V~v~d~~g~~F~T~  226 (243)
T 3j20_E          147 NHIVSIAEKDNYFTSYTVLMKVPEREILEVLPFEKGAYVFVTQGKNVARKGRIVEIKRFPMGWPDVVTIEDEEGELFDTL  226 (243)
T ss_dssp             CEECSSSSCSSCSSCEEEEEETTTTEEEEEEECCTTCEEEECSSSSTTCEEEEEECCCCCSSSCCEEEEEESSCCCEEEE
T ss_pred             eEEcccccCCCcccCCEEEEECCCCCeeeEEeccCCCEEEEECCccceEEEEEEEEEEecCCCceEEEEEcCCCCEEEEE
Confidence            99999   999999999999999999999999999999999999999999999999999988 99999999999999999


Q ss_pred             eccEEEEccCCCceEeCc
Q 029038          157 LGNVFTIGKGTKPWVSLP  174 (200)
Q Consensus       157 ~~~vfvIG~~~~p~isLp  174 (200)
                      ++||||||+ ++||||||
T Consensus       227 ~~~vfvIGk-~kp~islp  243 (243)
T 3j20_E          227 KEYAFVVGT-DKPKISLP  243 (243)
T ss_dssp             TTTEEEEES-SCSCCSCC
T ss_pred             eceEEEECC-CCccccCC
Confidence            999999999 99999998

>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum}

Probab=100.00  E-value=5.2e-73  Score=483.20  Aligned_cols=173  Identities=34%  Similarity=0.479  Sum_probs=161.4

Q ss_pred             CCccEEECCEEeccCCCCceeeEEEEecCCCceEEEEEcCCCceEEEEcCccccceeeEEEEEEEEeeCCeeEEEccCce
Q 029038            1 MQRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYINTYDGR   80 (200)
Q Consensus         1 ~q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl~d~kgrf~l~~I~~eEa~~KLcKV~~k~~~~gG~~ql~~hDGr   80 (200)
                      +||+|+||||+|+|++|||||||||||  ++|+||++||++|||.+|+|++|||+||||||++|++++||+|||+|||||
T Consensus        32 ~~~~I~VDGKvr~d~~ypvG~mDVIsI--t~e~fRli~d~kGrf~~~~I~~eea~~KLcKV~~k~~~~~G~~~l~~HDGr  109 (213)
T 3kbg_A           32 ANGLVKVDGKTVREKKFAVGFMDVIEI--NGESYRVVYNDQGALVLMKETKERASMKLLKVRSKVIAPGNRIQLGTHDGR  109 (213)
T ss_dssp             HTTCEEETTEECCCTTCEECTTCEEEE--TTEEEEEEECTTSCEEEEECCTTGGGEEEEEEEEEEEEGGGEEEEEETTSC
T ss_pred             HCCCEEECCEEecccCCCccceeEEEe--cCceeEEEecCCCcEEEEEeChhHccceEEEEEEEEEecCCeeEEEecCcc
Confidence            589999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeCCCCccCCCeEEEecCCCceeEEEEeeCCcEEEEECCCcceeEEEEEEEEEecCC-ccEEEEEcCCCCeEeEeecc
Q 029038           81 TIRYPDPLIKANDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGS-FETIHIQDALGHEFATRLGN  159 (200)
Q Consensus        81 ni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s-~~iV~v~d~~g~~F~T~~~~  159 (200)
                      ||+||||.||+||||++|||++||+|||||++||+||||||+|+||+|+|++|++++|| +++||++    ++|+|+++|
T Consensus       110 ti~~pd~~ik~~Dtv~idl~~~kI~d~ikf~~G~l~mvtgG~n~GriG~I~~ie~~~gs~~~iV~v~----~~F~T~~~~  185 (213)
T 3kbg_A          110 TFITDDKSIKVGDVLAVSVPDMKISEIIKMQPGNKAYITAGSHVNQTGTISKIEAKEGSSANLVHFQ----EGFSTIKDH  185 (213)
T ss_dssp             EEEECCTTCCTTCEEEEETTTCCEEEEECCSTTCEEEECSSTTTTCEEEEEEECCCSCC--CEEEET----TTEEEEGGG
T ss_pred             EEEcCCCCcccCCEEEEECCCCceeeEEEcCCCCEEEEECCCcceEEEEEEEEEEccCCCCCEEEEE----EEEEeeece
Confidence            99999999999999999999999999999999999999999999999999999999999 5899997    689999999


Q ss_pred             EEEEccCCCceEeCcCCCcee
Q 029038          160 VFTIGKGTKPWVSLPKGKGIK  180 (200)
Q Consensus       160 vfvIG~~~~p~isLp~~~gi~  180 (200)
                      |||||+ ++|||.+|++.=|-
T Consensus       186 vfvIGk-~~p~i~~~p~~~~~  205 (213)
T 3kbg_A          186 VFMIGS-SKFSFVLSPEEVIP  205 (213)
T ss_dssp             EEEEEC-SSCBCC--------
T ss_pred             EEEEcC-CCccEEeChHHccc
Confidence            999999 79999877665443

>2ckk_A KIN17; beta barrel, ribosomal protein, ribonucleoprotein, nuclear protein; 1.45A {Homo sapiens}

Probab=95.69  E-value=0.031  Score=43.59  Aligned_cols=41  Identities=22%  Similarity=0.477  Sum_probs=32.6

Q ss_pred             CCeEEEecCCCceeEEEEeeCCcEEEEECCCcceeEEEEEEEEE
Q 029038           92 NDTIKLDLETNKITEFIKFDVGNVVMVTGGRNRGRVGIIKNREK  135 (200)
Q Consensus        92 ~DTv~i~l~~~kI~~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~  135 (200)
                      ++.|  .+....+-..+| ..|..+||..|.|.|..|++.++..
T Consensus        56 g~~v--~v~q~~LETViP-~~g~~V~Iv~G~~rG~~g~L~~id~   96 (127)
T 2ckk_A           56 GDKL--KLDQTHLETVIP-APGKRILVLNGGYRGNEGTLESINE   96 (127)
T ss_dssp             CCEE--EEEGGGEEECCC-CTTCEEEECSSTTTTCEEEEEEEEG
T ss_pred             CCEE--EEchHHcEEecC-CCCCEEEEEecccCCcEEEEEEEeC
Confidence            4544  555545656677 8999999999999999999999953

>2do3_A Transcription elongation factor SPT5; KOW motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: b.34.5.5

Probab=95.21  E-value=0.034  Score=39.60  Aligned_cols=44  Identities=32%  Similarity=0.413  Sum_probs=34.5

Q ss_pred             eeCCcEEEEECCCcceeEEEEEEEEEecCCcc-EEEEEcCCCCeEeEeec
Q 029038          110 FDVGNVVMVTGGRNRGRVGIIKNREKHKGSFE-TIHIQDALGHEFATRLG  158 (200)
Q Consensus       110 fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~-iV~v~d~~g~~F~T~~~  158 (200)
                      |++|+.+-|++|+|.|+.|.|..++     .+ ++.+-|...+++.-...
T Consensus        18 F~~GDHVkVi~G~~~getGlVV~v~-----~d~v~v~SD~t~~Ei~V~~~   62 (69)
T 2do3_A           18 FKMGDHVKVIAGRFEGDTGLIVRVE-----ENFVILFSDLTMHELKVLPR   62 (69)
T ss_dssp             CCTTCEEEESSSTTTTCEEEEEEEC-----SSCEEEEESSSCSEEEECTT
T ss_pred             ccCCCeEEEeccEEcCceEEEEEEe-----CCEEEEEeCCCCCEEEEEhH
Confidence            7899999999999999999999986     23 55566766666654433

>1vq8_T 50S ribosomal protein L24P; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: b.34.5.1 PDB: 1vq4_T* 1vq5_T* 1vq6_T* 1vq7_T* 1s72_T* 1vq9_T* 1vqk_T* 1vql_T* 1vqm_T* 1vqn_T* 1vqo_T* 1vqp_T* 1yhq_T* 1yi2_T* 1yij_T* 1yit_T* 1yj9_T* 1yjn_T* 1yjw_T* 2otj_T* ...

Probab=87.18  E-value=1.3  Score=34.42  Aligned_cols=56  Identities=25%  Similarity=0.345  Sum_probs=40.0

Q ss_pred             EEEEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcC-----CCCeEeE--eeccEEEEc
Q 029038          106 EFIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDA-----LGHEFAT--RLGNVFTIG  164 (200)
Q Consensus       106 ~~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d~-----~g~~F~T--~~~~vfvIG  164 (200)
                      ..+++..|+.+.|+.|+.-|..|+|..+..   ....|+||.-     +|.+++-  -.+||+++-
T Consensus        39 r~~~IkkGD~V~Vi~G~dKGk~GkV~~V~~---k~~~V~VEgvn~kK~~Gg~~e~pIh~SNV~i~~  101 (120)
T 1vq8_T           39 RNVRVNAGDTVEVLRGDFAGEEGEVINVDL---DKAVIHVEDVTLEKTDGEEVPRPLDTSNVRVTD  101 (120)
T ss_dssp             SEEECCTTCEEEECSSTTTTCEEEEEEEET---TTTEEEETTCEEECSSSCEEECCBCGGGEEEEE
T ss_pred             ccccccCCCEEEEEecCCCCCEEEEEEEEC---CCCEEEEeCeEeEcCCCCEEEeeechHHEEEEe
Confidence            457889999999999999999999999863   2345777654     3444432  245666554

>3j21_U 50S ribosomal protein L24P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=83.05  E-value=1.8  Score=33.58  Aligned_cols=38  Identities=18%  Similarity=0.283  Sum_probs=30.8

Q ss_pred             EEEeeCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEc
Q 029038          107 FIKFDVGNVVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD  147 (200)
Q Consensus       107 ~i~fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~iV~v~d  147 (200)
                      .+++..|+.+.|+.|+.-|..|+|..+...   ...|+||.
T Consensus        43 ~~~IkkGD~V~Vi~GkdKGk~GkV~~V~~k---~~~V~VEg   80 (121)
T 3j21_U           43 NLPVRVGDKVRIMRGDYKGHEGKVVEVDLK---RYRIYVEG   80 (121)
T ss_dssp             EEECCSSSEEEECSSSCSSEEEEEEEEETT---TTEEEETT
T ss_pred             ccccccCCEEEEeecCCCCcEeEEEEEEec---CCEEEEeC
Confidence            578899999999999999999999998633   23566653

>1nz9_A Transcription antitermination protein NUSG; transcription elongation, riken structural genomics/proteomics initiative, RSGI; NMR {Thermus thermophilus} SCOP: b.34.5.4

Probab=82.07  E-value=4.2  Score=26.64  Aligned_cols=27  Identities=22%  Similarity=0.345  Sum_probs=25.2

Q ss_pred             EEeeCCcEEEEECCCcceeEEEEEEEE
Q 029038          108 IKFDVGNVVMVTGGRNRGRVGIIKNRE  134 (200)
Q Consensus       108 i~fe~G~~~~v~gG~n~G~vG~I~~i~  134 (200)
                      ++|++|+.+.|+.|.-.|..|+|.++.
T Consensus         3 ~~~~~Gd~V~V~~Gpf~g~~g~v~~v~   29 (58)
T 1nz9_A            3 VAFREGDQVRVVSGPFADFTGTVTEIN   29 (58)
T ss_dssp             CSCCTTCEEEECSGGGTTCEEEEEEEE
T ss_pred             cccCCCCEEEEeecCCCCcEEEEEEEc
Confidence            568999999999999999999999986

>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston structural genomics initiative, BSGI; NMR {Escherichia coli} SCOP: d.66.1.6

Probab=80.81  E-value=0.83  Score=31.78  Aligned_cols=33  Identities=24%  Similarity=0.227  Sum_probs=26.2

Q ss_pred             CccEEECCEEeccCCCCceeeEEEEecCCCceEEE
Q 029038            2 QRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRL   36 (200)
Q Consensus         2 q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRv   36 (200)
                      +|.|+|||++.++..+.+---|+|++.  ++.+.+
T Consensus        45 ~G~V~VNG~~v~~~~~~v~~gd~I~v~--~~~~~~   77 (79)
T 1p9k_A           45 EGQVKVDGAVETRKRCKIVAGQTVSFA--GHSVQV   77 (79)
T ss_dssp             HHHHEETTBCCCCSSCCCCSSEEEEET--TEEEEE
T ss_pred             CCEEEECCEEecCCCCCCCCCCEEEEC--CEEEEE
Confidence            688999999999988888777999985  444443

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	200
d2do3a1	62	Transcription elongation factor SPT5 {Human (Homo	95.38
d1p9ka_	79	Hypothetical protein YbcJ {Escherichia coli [TaxId	92.33
d1vioa2	58	Pseudouridine synthase RsuA N-terminal domain {Hae	90.96
d1nz9a_	58	N-utilization substance G protein NusG, C-terminal	88.12
d1kska3	59	Pseudouridine synthase RsuA N-terminal domain {Esc	87.2
d1dm9a_	104	Heat shock protein 15 kD {Escherichia coli [TaxId:	86.49
d1nppa2	58	N-utilization substance G protein NusG, C-terminal	84.63

>d2do3a1 b.34.5.5 (A:462-523) Transcription elongation factor SPT5 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: SPT5 KOW domain-like
domain: Transcription elongation factor SPT5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.38  E-value=0.014  Score=39.08  Aligned_cols=45  Identities=31%  Similarity=0.420  Sum_probs=35.6

Q ss_pred             eeCCcEEEEECCCcceeEEEEEEEEEecCCcc-EEEEEcCCCCeEeEeecc
Q 029038          110 FDVGNVVMVTGGRNRGRVGIIKNREKHKGSFE-TIHIQDALGHEFATRLGN  159 (200)
Q Consensus       110 fe~G~~~~v~gG~n~G~vG~I~~i~~~~~s~~-iV~v~d~~g~~F~T~~~~  159 (200)
                      |++|+.+-|++|+|.|..|.|..++     .+ ++.+.|...+++.-...+
T Consensus        11 F~~GDhVkVi~G~~~g~tGlVV~v~-----~~~v~~~SD~t~~Ei~V~~~d   56 (62)
T d2do3a1          11 FKMGDHVKVIAGRFEGDTGLIVRVE-----ENFVILFSDLTMHELKVLPRD   56 (62)
T ss_dssp             CCTTCEEEESSSTTTTCEEEEEEEC-----SSCEEEEESSSCSEEEECTTS
T ss_pred             cCCCCeEEEeccEEcCccEEEEEEe-----CCEEEEEeCCCCCEEEEehHH
Confidence            8899999999999999999999884     23 556677777777654443

>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: YbcJ-like
domain: Hypothetical protein YbcJ
species: Escherichia coli [TaxId: 562]

Probab=92.33  E-value=0.029  Score=38.50  Aligned_cols=34  Identities=24%  Similarity=0.238  Sum_probs=30.4

Q ss_pred             CccEEECCEEeccCCCCceeeEEEEecCCCceEEEE
Q 029038            2 QRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRLL   37 (200)
Q Consensus         2 q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRvl   37 (200)
                      +|.|+|||++.+++.|.+--=|+|+++  |+.++++
T Consensus        45 ~G~V~VNG~~~~~p~~~V~~~d~I~vd--G~~i~iv   78 (79)
T d1p9ka_          45 EGQVKVDGAVETRKRCKIVAGQTVSFA--GHSVQVV   78 (79)
T ss_dssp             HHHHEETTBCCCCSSCCCCSSEEEEET--TEEEEEE
T ss_pred             hCCcccCCEEeccccccCCCCCEEEEC--CEEEEEE
Confidence            689999999999999999989999996  7877765

>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Pseudouridine synthase RsuA N-terminal domain
domain: Pseudouridine synthase RsuA N-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=90.96  E-value=0.042  Score=35.25  Aligned_cols=27  Identities=11%  Similarity=0.129  Sum_probs=25.3

Q ss_pred             CccEEECCEEeccCCCCceeeEEEEec
Q 029038            2 QRHVLVDAKVRTDKTYPAGFMDVVSIP   28 (200)
Q Consensus         2 q~~V~VDGkvr~D~k~PvG~MDVIsI~   28 (200)
                      +|.|+|||++++++.|-+--.|.|++.
T Consensus        25 ~g~V~Vng~~v~~~~~~v~~~d~I~~~   51 (58)
T d1vioa2          25 QSAVKINGEIVKSGSVQISQEDEIYFE   51 (58)
T ss_dssp             TTCEEETTEECCCTTCEECTTSCEEET
T ss_pred             cCeEEECCEEeCCCCCCCCCCCEEEEC
Confidence            689999999999999999999999985

>d1nz9a_ b.34.5.4 (A:) N-utilization substance G protein NusG, C-terminal domain {Thermus thermophilus [TaxId: 274]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: N-utilization substance G protein NusG, C-terminal domain
domain: N-utilization substance G protein NusG, C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=88.12  E-value=0.14  Score=33.07  Aligned_cols=27  Identities=22%  Similarity=0.345  Sum_probs=25.3

Q ss_pred             EEeeCCcEEEEECCCcceeEEEEEEEE
Q 029038          108 IKFDVGNVVMVTGGRNRGRVGIIKNRE  134 (200)
Q Consensus       108 i~fe~G~~~~v~gG~n~G~vG~I~~i~  134 (200)
                      +.|++|+.+.|+.|.-.|..|+|.++.
T Consensus         3 v~F~~Gd~V~I~~GpF~g~~g~V~~i~   29 (58)
T d1nz9a_           3 VAFREGDQVRVVSGPFADFTGTVTEIN   29 (58)
T ss_dssp             CSCCTTCEEEECSGGGTTCEEEEEEEE
T ss_pred             ccccCCCEEEEeccCCCCCEEEEEEEc
Confidence            579999999999999999999999984

>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Pseudouridine synthase RsuA N-terminal domain
domain: Pseudouridine synthase RsuA N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=87.20  E-value=0.12  Score=33.00  Aligned_cols=27  Identities=15%  Similarity=0.111  Sum_probs=24.7

Q ss_pred             CccEEECCEEeccCCCCceeeEEEEec
Q 029038            2 QRHVLVDAKVRTDKTYPAGFMDVVSIP   28 (200)
Q Consensus         2 q~~V~VDGkvr~D~k~PvG~MDVIsI~   28 (200)
                      +|.|.|||++++++.|-|---|.|++.
T Consensus        24 ~g~V~Vng~~v~~~~~~V~~~d~I~~d   50 (59)
T d1kska3          24 GNRVTVDGEIVRNAAFKLLPEHDVAYD   50 (59)
T ss_dssp             TTCEEETTEECCCTTCEECTTCCEEET
T ss_pred             cCcEEECCEEeecCCcCcCCCCEEEEC
Confidence            689999999999999988888999985

>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Heat shock protein 15 kD
domain: Heat shock protein 15 kD
species: Escherichia coli [TaxId: 562]

Probab=86.49  E-value=0.23  Score=35.50  Aligned_cols=34  Identities=6%  Similarity=0.076  Sum_probs=29.2

Q ss_pred             CccEEECCEEeccCCCCceeeEEEEecCCCceEEE
Q 029038            2 QRHVLVDAKVRTDKTYPAGFMDVVSIPKTNENFRL   36 (200)
Q Consensus         2 q~~V~VDGkvr~D~k~PvG~MDVIsI~kt~e~yRv   36 (200)
                      +|.|+|||++.+ +.|.+-.-|+|+|...+..+.+
T Consensus        29 ~G~V~vNg~~vK-ps~~vk~GDvI~i~~~~~~~~i   62 (104)
T d1dm9a_          29 GGKVHYNGQRSK-PSKIVELNATLTLRQGNDERTV   62 (104)
T ss_dssp             TTCEEETTEECC-TTCBCCTTCEEEEEETTEEEEE
T ss_pred             cCCeeeCCeecc-ccccCCCCCEEEEEeCCeEEEE
Confidence            689999999875 8999999999999887666554

>d1nppa2 b.34.5.4 (A:191-248) N-utilization substance G protein NusG, C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: N-utilization substance G protein NusG, C-terminal domain
domain: N-utilization substance G protein NusG, C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=84.63  E-value=0.32  Score=31.26  Aligned_cols=27  Identities=22%  Similarity=0.384  Sum_probs=25.0

Q ss_pred             EEeeCCcEEEEECCCcceeEEEEEEEE
Q 029038          108 IKFDVGNVVMVTGGRNRGRVGIIKNRE  134 (200)
Q Consensus       108 i~fe~G~~~~v~gG~n~G~vG~I~~i~  134 (200)
                      +.|++|+.+.|+.|.-.|..|+|.++.
T Consensus         3 vdf~~Gd~V~I~~GpF~g~~g~V~~i~   29 (58)
T d1nppa2           3 VEFEKGDQVRVIEGPFMNFTGTVEEVH   29 (58)
T ss_dssp             CSCCTTCEEEECSSTTTTCEEEEEEEE
T ss_pred             ccccCCCEEEEcccCCCCCEEEEEEEc
Confidence            358999999999999999999999985