Citrus Sinensis ID: 029796

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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-------
Protein Sequence
MSFFFSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQAAA
Secondary Structure (PSIPRED)
ccEEEEEccEEEEEEEEcccccEEEEEEEccccEEEEEccHHHccEEEEEEEEEEEEEcccEEEEEEccEEEEEcccccccccEEEEEcccccEEEEEEEEcccEEEEEccccEEEEEEEEEEEEEcccccEEEEEcccccEEEEEEcEEEEEEcccccEEEccccccEEEEHHHHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
cEEEEEcccccEEEEEEccccccEEEEEccccEEEEEEccHHHHcEEEEEEEEEEEcccccEEEEEccccEEEcccccEEEccEEEEEcccccEEEEEEEccccEEEEEccccccEEEEEEEEEccccccEEEEEEEccccEEEEEcccEEEEEcccccEEEccccccEEEcHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
msfffsfgtlltdvvsipktnenFRLLYDtkgrfrlhsLRDEEAKFKLCKvrsvqfgqkgipyintydgrtirypdplikandtikldleenkitdfikfdvGNIVMVTggrnrgrvgiiknrekhkgsfeTIHIQDALGHEFATRLGNvftigkgskpwvslpkgkgikLSIIEEARKRQAAQAAA
Flexible Loop (DISEMBL)
msfffsfgtlltdvvsipktnenfrLLYDTKGRFRLHSLRDEEAkfklckvrsvqfgqkgipyintydgrtirypdplIKANDTIKLDLEENKitdfikfdvgnivmvtggrnrgrvgiiknrekhkgsFETIHIQDALGHEFATRLGNVFTigkgskpwvslpkgkGIKLSIIEEARKRQAAQAAA
Low Complexity Region (SEG)
MSFFFSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEarkrqaaqaaa
Disordered region (IsUnstruct)
**FFFSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSII*************
Disordered Region (DISOPRED)
*SFFFSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE***********
Disordered Region (DISEMBL)
MSFFFSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEA**********
Disordered Region (DISPRO)
MSFFFSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQA*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSFFFSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQAAA
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	187	2.2.26 [Sep-21-2011]
P46300	264	40S ribosomal protein S4	N/A	no	0.935	0.662	0.908	1e-92
P49204	262	40S ribosomal protein S4-	yes	no	0.935	0.667	0.902	5e-92
O81363	261	40S ribosomal protein S4	N/A	no	0.930	0.666	0.913	1e-91
Q93VH9	261	40S ribosomal protein S4-	yes	no	0.930	0.666	0.902	2e-91
Q8VYK6	262	40S ribosomal protein S4-	yes	no	0.935	0.667	0.897	2e-91
P46299	262	40S ribosomal protein S4	N/A	no	0.935	0.667	0.891	8e-89
O22424	265	40S ribosomal protein S4	N/A	no	0.898	0.633	0.886	3e-87
P49398	265	40S ribosomal protein S4	yes	no	0.898	0.633	0.880	4e-86
Q642H9	263	40S ribosomal protein S4,	yes	no	0.978	0.695	0.622	5e-67
P47961	263	40S ribosomal protein S4	yes	no	0.935	0.665	0.657	1e-66

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

 Score =  338 bits (866), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 159/175 (90%), Positives = 170/175 (97%)

Query: 13  DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
           DVVSIPKTNENFRLLYDTKGRFRLHSLRDEE+KFKLCKVRSVQFGQKGIPY+NTYDGRTI
Sbjct: 88  DVVSIPKTNENFRLLYDTKGRFRLHSLRDEESKFKLCKVRSVQFGQKGIPYLNTYDGRTI 147

Query: 73  RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
           RYPDPLIKANDTIKLDLE NKI DFIKFDVGN+VMVTGGRNRGRVG+IKNREKHKGSFET
Sbjct: 148 RYPDPLIKANDTIKLDLESNKIVDFIKFDVGNVVMVTGGRNRGRVGVIKNREKHKGSFET 207

Query: 133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQAAA 187
           +HIQD+ GHEFATRLGNVFT+GKG+KPWVSLPKGKGIKL+IIE+ARKR AAQ+A 
Sbjct: 208 LHIQDSQGHEFATRLGNVFTLGKGTKPWVSLPKGKGIKLTIIEDARKRLAAQSAT 262

Solanum tuberosum (taxid: 4113)

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

 Score =  336 bits (862), Expect = 5e-92,   Method: Compositional matrix adjust.
 Identities = 158/175 (90%), Positives = 170/175 (97%)

Query: 13  DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
           DVVSIPKTNENFRLLYDTKGRFRLHS++DEEAKFKLCKVRS+QFGQKGIPY+NTYDGRTI
Sbjct: 88  DVVSIPKTNENFRLLYDTKGRFRLHSIKDEEAKFKLCKVRSIQFGQKGIPYLNTYDGRTI 147

Query: 73  RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
           RYPDPLIK NDTIKLDLEENKI +FIKFDVGN+VMVTGGRNRGRVG+IKNREKHKGSFET
Sbjct: 148 RYPDPLIKPNDTIKLDLEENKIVEFIKFDVGNVVMVTGGRNRGRVGVIKNREKHKGSFET 207

Query: 133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQAAA 187
           IHIQD+ GHEFATRLGNV+TIGKG+KPWVSLPKGKGIKL+IIEEARKR A+Q AA
Sbjct: 208 IHIQDSTGHEFATRLGNVYTIGKGTKPWVSLPKGKGIKLTIIEEARKRLASQQAA 262

Arabidopsis thaliana (taxid: 3702)

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

 Score =  335 bits (859), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 159/174 (91%), Positives = 169/174 (97%)

Query: 7   FGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINT 66
           F   L+DVVSIPKTNENFRLLYDTKGRFRLHS+RDEE+KFKLCKVRSVQFGQKGIPYINT
Sbjct: 78  FCIRLSDVVSIPKTNENFRLLYDTKGRFRLHSIRDEESKFKLCKVRSVQFGQKGIPYINT 137

Query: 67  YDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKH 126
           YDGRTIRYPDPLIKANDTIKLDLE NKITDFIKFDVGN+VMVTGGRNRGRVG+IKNREKH
Sbjct: 138 YDGRTIRYPDPLIKANDTIKLDLETNKITDFIKFDVGNVVMVTGGRNRGRVGVIKNREKH 197

Query: 127 KGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKR 180
           KGSFETIH+QDA GHEFATRLGNVFTIGKG+KPWVSLPKGKGIKL+I+EEA+KR
Sbjct: 198 KGSFETIHVQDATGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLTILEEAKKR 251

Prunus armeniaca (taxid: 36596)

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

 Score =  334 bits (857), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 157/174 (90%), Positives = 169/174 (97%)

Query: 13  DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
           DVVSIPKTNENFRLLYDTKGRFRLHS++DEEAKFKLCKVRS+QFGQKGIPY+NTYDGRTI
Sbjct: 88  DVVSIPKTNENFRLLYDTKGRFRLHSIKDEEAKFKLCKVRSIQFGQKGIPYLNTYDGRTI 147

Query: 73  RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
           RYPDPLIK NDTIKLDLEENKI +FIKFDVGN+VMVTGGRNRGRVG+IKNREKHKGSFET
Sbjct: 148 RYPDPLIKPNDTIKLDLEENKIVEFIKFDVGNVVMVTGGRNRGRVGVIKNREKHKGSFET 207

Query: 133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQAA 186
           IHIQD+ GHEFATRLGNV+TIGKG+KPWVSLPKGKGIKL+IIEEARKR +AQ A
Sbjct: 208 IHIQDSTGHEFATRLGNVYTIGKGTKPWVSLPKGKGIKLTIIEEARKRLSAQQA 261

Arabidopsis thaliana (taxid: 3702)

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

 Score =  334 bits (856), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 157/175 (89%), Positives = 169/175 (96%)

Query: 13  DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
           DVVSIPKTNENFRLLYDTKGRFRLHS++DEEAKFKLCKVRS+QFGQKGIPY+NTYDGRTI
Sbjct: 88  DVVSIPKTNENFRLLYDTKGRFRLHSIKDEEAKFKLCKVRSIQFGQKGIPYLNTYDGRTI 147

Query: 73  RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
           RYPDPLIK NDTIKLDLE NKI +FIKFDVGN+VMVTGGRNRGRVG+IKNREKHKGSFET
Sbjct: 148 RYPDPLIKPNDTIKLDLEANKIVEFIKFDVGNVVMVTGGRNRGRVGVIKNREKHKGSFET 207

Query: 133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQAAA 187
           IHIQD+ GHEFATRLGNV+TIGKG+KPWVSLPKGKGIKL+IIEEARKR A+Q AA
Sbjct: 208 IHIQDSTGHEFATRLGNVYTIGKGTKPWVSLPKGKGIKLTIIEEARKRLASQQAA 262

Arabidopsis thaliana (taxid: 3702)

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

 Score =  325 bits (834), Expect = 8e-89,   Method: Compositional matrix adjust.
 Identities = 156/175 (89%), Positives = 165/175 (94%)

Query: 13  DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
           DVVSIPKTNE+FRLLYDTKGRF LH++  +E KFKLCKVRSVQFGQKGIPY+NTYDGRTI
Sbjct: 88  DVVSIPKTNEDFRLLYDTKGRFCLHAITGDETKFKLCKVRSVQFGQKGIPYLNTYDGRTI 147

Query: 73  RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
           RYPDPLIKANDTIKLDLE NKI DFIKFDVGN+VMVTGGRNRGRVG+IKNREKHKGSFET
Sbjct: 148 RYPDPLIKANDTIKLDLESNKIVDFIKFDVGNVVMVTGGRNRGRVGVIKNREKHKGSFET 207

Query: 133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQAAA 187
           IH+QDA GHEFATRLGNVFTIGKG+KPWVSLPK KGIKLSIIEEARKR AAQ AA
Sbjct: 208 IHVQDAAGHEFATRLGNVFTIGKGTKPWVSLPKRKGIKLSIIEEARKRLAAQNAA 262

Gossypium hirsutum (taxid: 3635)

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

 Score =  320 bits (821), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 149/168 (88%), Positives = 163/168 (97%)

Query: 13  DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
           DV+SIPKTNEN+RLLYDTKGRFRLH +RDE+AKFKLCKVRSVQFGQKGIPY+NTYDGRTI
Sbjct: 88  DVISIPKTNENYRLLYDTKGRFRLHPIRDEDAKFKLCKVRSVQFGQKGIPYLNTYDGRTI 147

Query: 73  RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
           RYPDPLIKANDTIK+DLE NKI DFIKFDVGN+VMVTGGRN GRVG+IKNREKHKGSFET
Sbjct: 148 RYPDPLIKANDTIKIDLETNKIVDFIKFDVGNVVMVTGGRNTGRVGVIKNREKHKGSFET 207

Query: 133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKR 180
           IH++D+LGH+FATR+GNVFTIGKG+KPWVSLPKGKGIKLSIIEE RKR
Sbjct: 208 IHVEDSLGHQFATRMGNVFTIGKGNKPWVSLPKGKGIKLSIIEEQRKR 255

Zea mays (taxid: 4577)

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

 Score =  317 bits (811), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 148/168 (88%), Positives = 162/168 (96%)

Query: 13  DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
           DV+SIPKT EN+RLLYDTKGRFRL S++DE+AKFKLCKVRSVQFGQKGIPY+NTYDGRTI
Sbjct: 88  DVISIPKTGENYRLLYDTKGRFRLQSVKDEDAKFKLCKVRSVQFGQKGIPYLNTYDGRTI 147

Query: 73  RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
           RYPDP+IKANDTIK+DLE NKI DFIKFDVGN+VMVTGGRN GRVG+IKNREKHKGSFET
Sbjct: 148 RYPDPIIKANDTIKIDLETNKIVDFIKFDVGNVVMVTGGRNTGRVGVIKNREKHKGSFET 207

Query: 133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKR 180
           IH++DALGH+FATRLGNVFTIGKG+KPWVSLPKGKGIKLSIIEE RKR
Sbjct: 208 IHVEDALGHQFATRLGNVFTIGKGNKPWVSLPKGKGIKLSIIEEQRKR 255

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q642H9|RS4X_DANRE 40S ribosomal protein S4, X isoform OS=Danio rerio GN=rps4x PE=2 SV=3

 Score =  253 bits (646), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 114/183 (62%), Positives = 148/183 (80%)

Query: 5   FSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYI 64
            ++ T   DVVSI KT ENFRL+YD KGRF +H + +EEAK+KLCKVR +  G KGIP++
Sbjct: 80  ITYPTGFMDVVSIEKTGENFRLIYDVKGRFTVHRITNEEAKYKLCKVRKILIGTKGIPHL 139

Query: 65  NTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNRE 124
            T+D RTIRYPDPLIK NDTI++DL+  KITDFIKF+ GN+ MVTGG N GR+G+I NRE
Sbjct: 140 VTHDARTIRYPDPLIKVNDTIRIDLDTGKITDFIKFETGNMCMVTGGANLGRIGVITNRE 199

Query: 125 KHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQ 184
           KH GSF+ +H++D++G+ FATRL N+F IGKG+KPWVSLP+GKG++L+I EE  KR AA+
Sbjct: 200 KHPGSFDVVHVKDSIGNSFATRLSNIFVIGKGNKPWVSLPRGKGVRLTIAEERDKRLAAK 259

Query: 185 AAA 187
            ++
Sbjct: 260 QSS 262

Danio rerio (taxid: 7955)

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

 Score =  252 bits (643), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 115/175 (65%), Positives = 144/175 (82%)

Query: 13  DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
           DV+SI KT ENFRL+YDTKGRF +H +  EEAK+KLCKVR +  G KGIP++ T+D RTI
Sbjct: 88  DVISIDKTGENFRLIYDTKGRFAVHRITSEEAKYKLCKVRKIFVGTKGIPHLVTHDARTI 147

Query: 73  RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
           RYPDPLIK NDTI++DLE  KITDFIKFD GN+ MVTGG N GR+G+I NRE+H GSF+ 
Sbjct: 148 RYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDV 207

Query: 133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQAAA 187
           +H++DA G+ FATRL N+F IGKG+KPW+SLP+GKGI+L+I EE  KR AA+ ++
Sbjct: 208 VHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIRLTIAEERDKRLAAKQSS 262

Cricetulus griseus (taxid: 10029)

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	187
225448546	264	PREDICTED: 40S ribosomal protein S4-like	0.973	0.689	0.895	3e-92
297736557	246	unnamed protein product [Vitis vinifera]	0.973	0.739	0.895	4e-92
449465358	264	PREDICTED: 40S ribosomal protein S4-like	0.973	0.689	0.895	6e-92
449460918	216	PREDICTED: 40S ribosomal protein S4-like	0.989	0.856	0.881	7e-92
192912988	265	40S ribosomal protein S4 [Elaeis guineen	0.973	0.686	0.890	8e-92
449465362	264	PREDICTED: 40S ribosomal protein S4-like	0.967	0.685	0.895	1e-91
224087813	263	predicted protein [Populus trichocarpa]	0.973	0.692	0.884	1e-91
357468567	264	40S ribosomal protein S4 [Medicago trunc	0.919	0.651	0.930	1e-91
73759787	264	ribosomal protein S4 [Panax ginseng]	0.935	0.662	0.92	2e-91
255549228	263	40S ribosomal protein S4, putative [Rici	0.935	0.665	0.926	2e-91

>gi|225448546|ref|XP_002276986.1| PREDICTED: 40S ribosomal protein S4-like [Vitis vinifera]

 Score =  342 bits (878), Expect = 3e-92,   Method: Compositional matrix adjust.
 Identities = 163/182 (89%), Positives = 174/182 (95%)

Query: 6   SFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYIN 65
           ++ +   DVVSIPKTNENFRLLYDTKGRFRLHS+RDEEAKFKLCKVRSVQFGQKGIPY+N
Sbjct: 81  TYPSGFMDVVSIPKTNENFRLLYDTKGRFRLHSVRDEEAKFKLCKVRSVQFGQKGIPYLN 140

Query: 66  TYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREK 125
           TYDGRTIRYPDPLIKANDTIKLDLE NKITDFIKFDVGN+VMVTGGRNRGRVG+IKNREK
Sbjct: 141 TYDGRTIRYPDPLIKANDTIKLDLESNKITDFIKFDVGNVVMVTGGRNRGRVGVIKNREK 200

Query: 126 HKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQA 185
           HKG+FETIHIQDA GHEFATRLGNVF IGKG+KPWVSLPKGKGIKLSIIEEA+KR AAQA
Sbjct: 201 HKGTFETIHIQDATGHEFATRLGNVFIIGKGTKPWVSLPKGKGIKLSIIEEAKKRLAAQA 260

Query: 186 AA 187
           A+
Sbjct: 261 AS 262

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297736557|emb|CBI25428.3| unnamed protein product [Vitis vinifera]

 Score =  342 bits (877), Expect = 4e-92,   Method: Compositional matrix adjust.
 Identities = 163/182 (89%), Positives = 174/182 (95%)

Query: 6   SFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYIN 65
           ++ +   DVVSIPKTNENFRLLYDTKGRFRLHS+RDEEAKFKLCKVRSVQFGQKGIPY+N
Sbjct: 63  TYPSGFMDVVSIPKTNENFRLLYDTKGRFRLHSVRDEEAKFKLCKVRSVQFGQKGIPYLN 122

Query: 66  TYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREK 125
           TYDGRTIRYPDPLIKANDTIKLDLE NKITDFIKFDVGN+VMVTGGRNRGRVG+IKNREK
Sbjct: 123 TYDGRTIRYPDPLIKANDTIKLDLESNKITDFIKFDVGNVVMVTGGRNRGRVGVIKNREK 182

Query: 126 HKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQA 185
           HKG+FETIHIQDA GHEFATRLGNVF IGKG+KPWVSLPKGKGIKLSIIEEA+KR AAQA
Sbjct: 183 HKGTFETIHIQDATGHEFATRLGNVFIIGKGTKPWVSLPKGKGIKLSIIEEAKKRLAAQA 242

Query: 186 AA 187
           A+
Sbjct: 243 AS 244

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  342 bits (876), Expect = 6e-92,   Method: Compositional matrix adjust.
 Identities = 163/182 (89%), Positives = 171/182 (93%)

Query: 6   SFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYIN 65
           +F     DVVSIPKTNENFRLLYDTKGRFRLHS+RDEEAK+KLCKVRSVQFGQKGIPY+N
Sbjct: 81  TFPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSVRDEEAKYKLCKVRSVQFGQKGIPYLN 140

Query: 66  TYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREK 125
           TYDGRTIRYPDPLIKANDTIKLDLE NKI DFIKFDVGN+VMVTGGRNRGRVG+IKNREK
Sbjct: 141 TYDGRTIRYPDPLIKANDTIKLDLESNKIADFIKFDVGNVVMVTGGRNRGRVGVIKNREK 200

Query: 126 HKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQA 185
           HKGSFETIHIQDA GHEFATRLGNVFTIGKG+KPWVSLPKGKGIKLSIIEEARKR A+QA
Sbjct: 201 HKGSFETIHIQDATGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLSIIEEARKRLASQA 260

Query: 186 AA 187
             
Sbjct: 261 TV 262

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449460918|ref|XP_004148191.1| PREDICTED: 40S ribosomal protein S4-like [Cucumis sativus]

 Score =  341 bits (875), Expect = 7e-92,   Method: Compositional matrix adjust.
 Identities = 164/186 (88%), Positives = 173/186 (93%), Gaps = 1/186 (0%)

Query: 3   FFFSFGTLLT-DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGI 61
           FF     L   DVVSIPKT+ENFRLLYDTKGRFRLHS+RDEEAKFKLCKVRSVQFGQKGI
Sbjct: 29  FFIGLTILFVLDVVSIPKTSENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGI 88

Query: 62  PYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIK 121
           PY+NTYDGRTIRYPDPLIKANDTIKLDLE NKI DFIKFDVGN+VMVTGGRNRGRVG+IK
Sbjct: 89  PYLNTYDGRTIRYPDPLIKANDTIKLDLESNKIADFIKFDVGNVVMVTGGRNRGRVGVIK 148

Query: 122 NREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQ 181
           NREKHKGSFETIHIQDA GHEFATRLGNVFTIGKG+KPWVSLPKGKGIKL+IIEEARKR 
Sbjct: 149 NREKHKGSFETIHIQDATGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLTIIEEARKRL 208

Query: 182 AAQAAA 187
           A+Q+A 
Sbjct: 209 ASQSAV 214

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  341 bits (874), Expect = 8e-92,   Method: Compositional matrix adjust.
 Identities = 162/182 (89%), Positives = 173/182 (95%)

Query: 6   SFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYIN 65
           ++ +   DVVSIPKTNENFRLLYDTKGRFRLHS+RDEEAKFKLCKVRSVQFGQKGIPY+N
Sbjct: 81  TYPSGFMDVVSIPKTNENFRLLYDTKGRFRLHSIRDEEAKFKLCKVRSVQFGQKGIPYLN 140

Query: 66  TYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREK 125
           T+DGRTIRYPDPLIKANDTIKLDLE NKI DFIKFDVGN+VMVTGGRNRGRVG+IKNREK
Sbjct: 141 TFDGRTIRYPDPLIKANDTIKLDLEANKIVDFIKFDVGNVVMVTGGRNRGRVGVIKNREK 200

Query: 126 HKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQA 185
           HKGSFETIH+QDALGHEFATR+GNVFTIGKG+KPWVSLPKGKGIKLSIIEEARKR AA  
Sbjct: 201 HKGSFETIHLQDALGHEFATRIGNVFTIGKGTKPWVSLPKGKGIKLSIIEEARKRLAASG 260

Query: 186 AA 187
           AA
Sbjct: 261 AA 262

Source: Elaeis guineensis

Species: Elaeis guineensis

Genus: Elaeis

Family: Arecaceae

Order: Arecales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449465362|ref|XP_004150397.1| PREDICTED: 40S ribosomal protein S4-like [Cucumis sativus] gi|449496878|ref|XP_004160251.1| PREDICTED: 40S ribosomal protein S4-like [Cucumis sativus]

 Score =  341 bits (874), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 162/181 (89%), Positives = 172/181 (95%)

Query: 6   SFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYIN 65
           +F     DVVSIPKT+ENFRLLYDTKGRFRLHS+RDEEAK+KLCKVRSVQFGQKGIPY+N
Sbjct: 81  TFPAGFMDVVSIPKTSENFRLLYDTKGRFRLHSVRDEEAKYKLCKVRSVQFGQKGIPYLN 140

Query: 66  TYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREK 125
           TYDGRTIRYPDPLIKANDTIKLDLE NKI DFIKFDVGN+VMVTGGRNRGRVG+IKNREK
Sbjct: 141 TYDGRTIRYPDPLIKANDTIKLDLESNKIADFIKFDVGNVVMVTGGRNRGRVGVIKNREK 200

Query: 126 HKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQA 185
           HKGSFETIHIQDA GHEFATRLGNVFT+GKG+KPWVSLPKGKGIKLSIIEEARKR A+QA
Sbjct: 201 HKGSFETIHIQDATGHEFATRLGNVFTVGKGTKPWVSLPKGKGIKLSIIEEARKRLASQA 260

Query: 186 A 186
           A
Sbjct: 261 A 261

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  340 bits (873), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 161/182 (88%), Positives = 172/182 (94%)

Query: 6   SFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYIN 65
           ++ +   DVVSIPKTNE+FRLLYDTKGRFRLHSLRD+EAKFKLCKVRS+QFGQKGIPY+N
Sbjct: 81  TYPSGFMDVVSIPKTNESFRLLYDTKGRFRLHSLRDDEAKFKLCKVRSIQFGQKGIPYLN 140

Query: 66  TYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREK 125
           TYDGRTIRYPDPLIKANDTIKLDLE NKI DFIKFDVGN+VMVTGGRNRGRVG+IKNREK
Sbjct: 141 TYDGRTIRYPDPLIKANDTIKLDLESNKIVDFIKFDVGNVVMVTGGRNRGRVGVIKNREK 200

Query: 126 HKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQA 185
           HKGSFETIH+QDA GHEFATRLGNVFTIGKGSKPW+SLPKGKGIKLSIIEEARKRQAA  
Sbjct: 201 HKGSFETIHVQDATGHEFATRLGNVFTIGKGSKPWISLPKGKGIKLSIIEEARKRQAASQ 260

Query: 186 AA 187
            A
Sbjct: 261 TA 262

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  340 bits (873), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 160/172 (93%), Positives = 170/172 (98%)

Query: 13  DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
           DVVSIPKTNENFRLLYDTKGRFRLHS+RD+EAKFKLCKVRSVQFGQKGIPY+NTYDGRTI
Sbjct: 88  DVVSIPKTNENFRLLYDTKGRFRLHSVRDDEAKFKLCKVRSVQFGQKGIPYLNTYDGRTI 147

Query: 73  RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
           RYPDPLIKANDTIKLDLE NKITDFIKFDVGN+VMVTGGRNRGRVG+IKNREKHKG+FET
Sbjct: 148 RYPDPLIKANDTIKLDLENNKITDFIKFDVGNVVMVTGGRNRGRVGVIKNREKHKGTFET 207

Query: 133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQ 184
           IH+QDA GHEFATRLGNVFTIGKG+KPWVSLPKGKGIKL++IEEARKRQAAQ
Sbjct: 208 IHVQDASGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLTVIEEARKRQAAQ 259

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  340 bits (872), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 161/175 (92%), Positives = 169/175 (96%)

Query: 13  DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
           DVVSIPKTNENFRLLYDTKGRFRLHS+RDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI
Sbjct: 88  DVVSIPKTNENFRLLYDTKGRFRLHSVRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 147

Query: 73  RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
           RYPDPLIKANDTIKLDLE NKI DFIKFDVGN+VMVTGGRN GRVG+IKNREKHKGSFET
Sbjct: 148 RYPDPLIKANDTIKLDLEANKIADFIKFDVGNVVMVTGGRNTGRVGVIKNREKHKGSFET 207

Query: 133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQAAA 187
           +HIQD+LGHEFATRLGNVFTIGKG+KPWVSLPKGKGIKL+IIEEARKR  AQ+A 
Sbjct: 208 VHIQDSLGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLTIIEEARKRNVAQSAT 262

Source: Panax ginseng

Species: Panax ginseng

Genus: Panax

Family: Araliaceae

Order: Apiales

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 =  340 bits (872), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 163/176 (92%), Positives = 171/176 (97%), Gaps = 1/176 (0%)

Query: 13  DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
           DVVSIPKTNENFRLLYDTKGRFRLHS+RD+EAKFKLCKVRSVQFGQKGIPY+NTYDGRTI
Sbjct: 88  DVVSIPKTNENFRLLYDTKGRFRLHSIRDDEAKFKLCKVRSVQFGQKGIPYLNTYDGRTI 147

Query: 73  RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
           RYPDPLIKANDTIKLDLE NKITDFIKFDVGN+VMVTGGRNRGRVG+IKNREKHKGSFET
Sbjct: 148 RYPDPLIKANDTIKLDLESNKITDFIKFDVGNVVMVTGGRNRGRVGVIKNREKHKGSFET 207

Query: 133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKR-QAAQAAA 187
           IH+QDA GHEFATR+GNVFTIGKG+KPWVSLPKGKGIKLSIIEEARKR  AAQA A
Sbjct: 208 IHVQDATGHEFATRMGNVFTIGKGTKPWVSLPKGKGIKLSIIEEARKRLAAAQAVA 263

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	187
TAIR|locus:2827612	261	AT2G17360 [Arabidopsis thalian	0.877	0.628	0.914	3.2e-81
TAIR|locus:2169339	262	AT5G07090 [Arabidopsis thalian	0.877	0.625	0.914	3.2e-81
TAIR|locus:2171198	262	AT5G58420 [Arabidopsis thalian	0.877	0.625	0.908	1.4e-80
UNIPROTKB|J9P5V0	267	J9P5V0 "Uncharacterized protei	0.877	0.614	0.682	1e-61
UNIPROTKB|P79103	263	RPS4 "40S ribosomal protein S4	0.877	0.623	0.676	2.1e-61
UNIPROTKB|F2Z4Q1	263	RPS4X "Uncharacterized protein	0.877	0.623	0.676	2.1e-61
UNIPROTKB|P62701	263	RPS4X "40S ribosomal protein S	0.877	0.623	0.676	2.1e-61
UNIPROTKB|F1RQ91	263	RPS4X "Uncharacterized protein	0.877	0.623	0.676	2.1e-61
UNIPROTKB|P62704	263	RPS4X "40S ribosomal protein S	0.877	0.623	0.676	2.1e-61
UNIPROTKB|P62705	263	RPS4X "40S ribosomal protein S	0.877	0.623	0.676	2.1e-61

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

 Score = 815 (292.0 bits), Expect = 3.2e-81, P = 3.2e-81
 Identities = 150/164 (91%), Positives = 161/164 (98%)

Query:    13 DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
             DVVSIPKTNENFRLLYDTKGRFRLHS++DEEAKFKLCKVRS+QFGQKGIPY+NTYDGRTI
Sbjct:    88 DVVSIPKTNENFRLLYDTKGRFRLHSIKDEEAKFKLCKVRSIQFGQKGIPYLNTYDGRTI 147

Query:    73 RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
             RYPDPLIK NDTIKLDLEENKI +FIKFDVGN+VMVTGGRNRGRVG+IKNREKHKGSFET
Sbjct:   148 RYPDPLIKPNDTIKLDLEENKIVEFIKFDVGNVVMVTGGRNRGRVGVIKNREKHKGSFET 207

Query:   133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 176
             IHIQD+ GHEFATRLGNV+TIGKG+KPWVSLPKGKGIKL+IIEE
Sbjct:   208 IHIQDSTGHEFATRLGNVYTIGKGTKPWVSLPKGKGIKLTIIEE 251

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

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

 Score = 815 (292.0 bits), Expect = 3.2e-81, P = 3.2e-81
 Identities = 150/164 (91%), Positives = 161/164 (98%)

Query:    13 DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
             DVVSIPKTNENFRLLYDTKGRFRLHS++DEEAKFKLCKVRS+QFGQKGIPY+NTYDGRTI
Sbjct:    88 DVVSIPKTNENFRLLYDTKGRFRLHSIKDEEAKFKLCKVRSIQFGQKGIPYLNTYDGRTI 147

Query:    73 RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
             RYPDPLIK NDTIKLDLEENKI +FIKFDVGN+VMVTGGRNRGRVG+IKNREKHKGSFET
Sbjct:   148 RYPDPLIKPNDTIKLDLEENKIVEFIKFDVGNVVMVTGGRNRGRVGVIKNREKHKGSFET 207

Query:   133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 176
             IHIQD+ GHEFATRLGNV+TIGKG+KPWVSLPKGKGIKL+IIEE
Sbjct:   208 IHIQDSTGHEFATRLGNVYTIGKGTKPWVSLPKGKGIKLTIIEE 251

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:2171198 AT5G58420 [Arabidopsis thaliana (taxid:3702)]

 Score = 809 (289.8 bits), Expect = 1.4e-80, P = 1.4e-80
 Identities = 149/164 (90%), Positives = 160/164 (97%)

Query:    13 DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
             DVVSIPKTNENFRLLYDTKGRFRLHS++DEEAKFKLCKVRS+QFGQKGIPY+NTYDGRTI
Sbjct:    88 DVVSIPKTNENFRLLYDTKGRFRLHSIKDEEAKFKLCKVRSIQFGQKGIPYLNTYDGRTI 147

Query:    73 RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
             RYPDPLIK NDTIKLDLE NKI +FIKFDVGN+VMVTGGRNRGRVG+IKNREKHKGSFET
Sbjct:   148 RYPDPLIKPNDTIKLDLEANKIVEFIKFDVGNVVMVTGGRNRGRVGVIKNREKHKGSFET 207

Query:   133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 176
             IHIQD+ GHEFATRLGNV+TIGKG+KPWVSLPKGKGIKL+IIEE
Sbjct:   208 IHIQDSTGHEFATRLGNVYTIGKGTKPWVSLPKGKGIKLTIIEE 251

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

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

 Score = 631 (227.2 bits), Expect = 1.0e-61, P = 1.0e-61
 Identities = 112/164 (68%), Positives = 137/164 (83%)

Query:    13 DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
             DV+SI KT ENFRL+YDTKGRF +H +  EEAK+KLCKVR +  G KGIP++ T+D RTI
Sbjct:    88 DVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHLVTHDARTI 147

Query:    73 RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
             RYPDPLIK NDTI++DLE  KITDFIKFD GN+ MVTGG N GR+G+I NREKH GSF+ 
Sbjct:   148 RYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNREKHPGSFDV 207

Query:   133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 176
             +H++DA G+ FATRL N+F IGKG+KPW+SLP+GKGI+L+I EE
Sbjct:   208 VHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIRLTIAEE 251

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 = 628 (226.1 bits), Expect = 2.1e-61, P = 2.1e-61
 Identities = 111/164 (67%), Positives = 137/164 (83%)

Query:    13 DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
             DV+SI KT ENFRL+YDTKGRF +H +  EEAK+KLCKVR +  G KGIP++ T+D RTI
Sbjct:    88 DVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHLVTHDARTI 147

Query:    73 RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
             RYPDPLIK NDTI++DLE  KITDFIKFD GN+ MVTGG N GR+G+I NRE+H GSF+ 
Sbjct:   148 RYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDV 207

Query:   133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 176
             +H++DA G+ FATRL N+F IGKG+KPW+SLP+GKGI+L+I EE
Sbjct:   208 VHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIRLTIAEE 251

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 = 628 (226.1 bits), Expect = 2.1e-61, P = 2.1e-61
 Identities = 111/164 (67%), Positives = 137/164 (83%)

Query:    13 DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
             DV+SI KT ENFRL+YDTKGRF +H +  EEAK+KLCKVR +  G KGIP++ T+D RTI
Sbjct:    88 DVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHLVTHDARTI 147

Query:    73 RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
             RYPDPLIK NDTI++DLE  KITDFIKFD GN+ MVTGG N GR+G+I NRE+H GSF+ 
Sbjct:   148 RYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDV 207

Query:   133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 176
             +H++DA G+ FATRL N+F IGKG+KPW+SLP+GKGI+L+I EE
Sbjct:   208 VHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIRLTIAEE 251

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 = 628 (226.1 bits), Expect = 2.1e-61, P = 2.1e-61
 Identities = 111/164 (67%), Positives = 137/164 (83%)

Query:    13 DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
             DV+SI KT ENFRL+YDTKGRF +H +  EEAK+KLCKVR +  G KGIP++ T+D RTI
Sbjct:    88 DVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHLVTHDARTI 147

Query:    73 RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
             RYPDPLIK NDTI++DLE  KITDFIKFD GN+ MVTGG N GR+G+I NRE+H GSF+ 
Sbjct:   148 RYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDV 207

Query:   133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 176
             +H++DA G+ FATRL N+F IGKG+KPW+SLP+GKGI+L+I EE
Sbjct:   208 VHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIRLTIAEE 251

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 = 628 (226.1 bits), Expect = 2.1e-61, P = 2.1e-61
 Identities = 111/164 (67%), Positives = 137/164 (83%)

Query:    13 DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
             DV+SI KT ENFRL+YDTKGRF +H +  EEAK+KLCKVR +  G KGIP++ T+D RTI
Sbjct:    88 DVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHLVTHDARTI 147

Query:    73 RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
             RYPDPLIK NDTI++DLE  KITDFIKFD GN+ MVTGG N GR+G+I NRE+H GSF+ 
Sbjct:   148 RYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDV 207

Query:   133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 176
             +H++DA G+ FATRL N+F IGKG+KPW+SLP+GKGI+L+I EE
Sbjct:   208 VHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIRLTIAEE 251

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 = 628 (226.1 bits), Expect = 2.1e-61, P = 2.1e-61
 Identities = 111/164 (67%), Positives = 137/164 (83%)

Query:    13 DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
             DV+SI KT ENFRL+YDTKGRF +H +  EEAK+KLCKVR +  G KGIP++ T+D RTI
Sbjct:    88 DVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHLVTHDARTI 147

Query:    73 RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
             RYPDPLIK NDTI++DLE  KITDFIKFD GN+ MVTGG N GR+G+I NRE+H GSF+ 
Sbjct:   148 RYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDV 207

Query:   133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 176
             +H++DA G+ FATRL N+F IGKG+KPW+SLP+GKGI+L+I EE
Sbjct:   208 VHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIRLTIAEE 251

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 = 628 (226.1 bits), Expect = 2.1e-61, P = 2.1e-61
 Identities = 111/164 (67%), Positives = 137/164 (83%)

Query:    13 DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
             DV+SI KT ENFRL+YDTKGRF +H +  EEAK+KLCKVR +  G KGIP++ T+D RTI
Sbjct:    88 DVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHLVTHDARTI 147

Query:    73 RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
             RYPDPLIK NDTI++DLE  KITDFIKFD GN+ MVTGG N GR+G+I NRE+H GSF+ 
Sbjct:   148 RYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDV 207

Query:   133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 176
             +H++DA G+ FATRL N+F IGKG+KPW+SLP+GKGI+L+I EE
Sbjct:   208 VHVKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIRLTIAEE 251

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	0.9137	0.9304	0.6666	N/A	no
Q9N3X2	RS4_CAEEL	No assigned EC number	0.5842	0.9518	0.6872	yes	no
P47836	RS4_CHICK	No assigned EC number	0.6514	0.9358	0.6653	yes	no
O59950	RS4_YARLI	No assigned EC number	0.6256	0.9572	0.6884	yes	no
Q8VYK6	RS43_ARATH	No assigned EC number	0.8971	0.9358	0.6679	yes	no
P49204	RS42_ARATH	No assigned EC number	0.9028	0.9358	0.6679	yes	no
Q9P4W9	RS4C_SCHPO	No assigned EC number	0.6428	0.9732	0.6946	yes	no
P0CX36	RS4B_YEAST	No assigned EC number	0.6184	0.9251	0.6628	yes	no
P79103	RS4_BOVIN	No assigned EC number	0.6571	0.9358	0.6653	yes	no
O22424	RS4_MAIZE	No assigned EC number	0.8869	0.8983	0.6339	N/A	no
P47961	RS4_CRIGR	No assigned EC number	0.6571	0.9358	0.6653	yes	no
P46300	RS4_SOLTU	No assigned EC number	0.9085	0.9358	0.6628	N/A	no
O62739	RS4Y1_MONDO	No assigned EC number	0.64	0.9358	0.6653	yes	no
O62738	RS4X_MONDO	No assigned EC number	0.6627	0.9197	0.6539	yes	no
P49398	RS4_ORYSJ	No assigned EC number	0.8809	0.8983	0.6339	yes	no
Q93VH9	RS41_ARATH	No assigned EC number	0.9022	0.9304	0.6666	yes	no
P41042	RS4_DROME	No assigned EC number	0.6337	0.9197	0.6590	yes	no
Q6PBC4	RS4_XENTR	No assigned EC number	0.6514	0.9358	0.6653	yes	no
P62703	RS4X_RAT	No assigned EC number	0.6571	0.9358	0.6653	yes	no
P62702	RS4X_MOUSE	No assigned EC number	0.6571	0.9358	0.6653	yes	no
P51405	RS4_DICDI	No assigned EC number	0.5975	0.8770	0.6142	yes	no
Q9USW5	RS4B_SCHPO	No assigned EC number	0.6428	0.9732	0.6946	yes	no
P62701	RS4X_HUMAN	No assigned EC number	0.6571	0.9358	0.6653	yes	no
P0CX35	RS4A_YEAST	No assigned EC number	0.6184	0.9251	0.6628	yes	no
P46299	RS4_GOSHI	No assigned EC number	0.8914	0.9358	0.6679	N/A	no
Q642H9	RS4X_DANRE	No assigned EC number	0.6229	0.9786	0.6958	yes	no
P87158	RS4A_SCHPO	No assigned EC number	0.6428	0.9732	0.6946	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	187
PLN00036	261	PLN00036, PLN00036, 40S ribosomal protein S4; Prov	1e-117
PTZ00118	262	PTZ00118, PTZ00118, 40S ribosomal protein S4; Prov	1e-70
COG1471	241	COG1471, RPS4A, Ribosomal protein S4E [Translation	2e-65
PTZ00223	273	PTZ00223, PTZ00223, 40S ribosomal protein S4; Prov	1e-51
PRK04313	237	PRK04313, PRK04313, 30S ribosomal protein S4e; Val	5e-40
pfam00900	77	pfam00900, Ribosomal_S4e, Ribosomal family S4e	6e-37
cd06087	55	cd06087, KOW_RPS4, KOW motif of Ribosomal Protein	6e-29
pfam00467	32	pfam00467, KOW, KOW motif	0.002

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

 Score =  331 bits (851), Expect = e-117
 Identities = 151/176 (85%), Positives = 163/176 (92%)

Query: 11  LTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGR 70
             DV+SIPKTNENFRLLYDTKGRFRLH + DEEAKFKLCKVR +QFGQKGIPY+NT+DGR
Sbjct: 86  FMDVISIPKTNENFRLLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHDGR 145

Query: 71  TIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSF 130
           TIRYPDPLIKANDTIK+DLE NKI DFIKFDVGN+VMVTGGRNRGRVG+IKNREKHKGSF
Sbjct: 146 TIRYPDPLIKANDTIKIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSF 205

Query: 131 ETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQAA 186
           E IH++DA GHEFATRLGNVF IGKG+KPW+SLPKGKGIKLSIIEEARKR AA  A
Sbjct: 206 EIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPKGKGIKLSIIEEARKRLAAGQA 261

Length = 261

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

 Score =  214 bits (547), Expect = 1e-70
 Identities = 100/177 (56%), Positives = 130/177 (73%)

Query: 6   SFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYIN 65
           ++     DVVS+ KTNE FRLLYDTKGRF  H + +EEAK+KLC+V+    G K +    
Sbjct: 81  TYPVGFMDVVSLTKTNEYFRLLYDTKGRFVPHKITNEEAKYKLCRVKKTFLGPKEVSIAV 140

Query: 66  TYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREK 125
           T+DGRTIRY  P +K  D+++LDLE  K+ +F+KF+VGN+VM+TGG N GRVG I ++EK
Sbjct: 141 THDGRTIRYVHPDVKVGDSLRLDLETGKVLEFLKFEVGNLVMITGGHNVGRVGTIVSKEK 200

Query: 126 HKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQA 182
           H GSF+ IH++D+ G  FATRL NVF IG G+KP+VSLP+ +GIK  IIEE R R A
Sbjct: 201 HPGSFDLIHVKDSRGKTFATRLSNVFVIGVGTKPYVSLPRERGIKKDIIEERRNRLA 257

Length = 262

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

 Score =  200 bits (510), Expect = 2e-65
 Identities = 74/162 (45%), Positives = 98/162 (60%), Gaps = 2/162 (1%)

Query: 7   FGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINT 66
           F   L DV+SIPKT E++R+L D KGR  LH +  EEA +KLCKV++    + G   +N 
Sbjct: 81  FPVGLMDVISIPKTGEHYRVLPDEKGRLVLHPISAEEASYKLCKVKNKTTVKGGRIQLNL 140

Query: 67  YDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKH 126
           +DGR IR  D   K  DT+K+ L E KI + IKF+ G +V VTGGR+ GRVG I   E  
Sbjct: 141 HDGRNIRLEDDNYKTGDTVKISLPEQKIVEHIKFEEGALVYVTGGRHVGRVGTIVEIEIQ 200

Query: 127 KGS-FETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGK 167
           + S    + ++D  G+ F T    VF IG+  KP +SLPK K
Sbjct: 201 ESSKPNLVTVEDEEGNTFQTIKDYVFVIGED-KPVISLPKEK 241

Length = 241

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

 Score =  166 bits (422), Expect = 1e-51
 Identities = 82/175 (46%), Positives = 114/175 (65%), Gaps = 1/175 (0%)

Query: 13  DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
           DVV IPKT + FR+LYD KGRF L  + + EA+ KL KV +V      IP   T+DG  I
Sbjct: 85  DVVEIPKTGDRFRILYDVKGRFALVKVSEAEAQIKLMKVVNVYTATGRIPVAVTHDGHRI 144

Query: 73  RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
           RYPDP     DT+  +++E K+ D IK   G +VMVTGG NRGR+G I + E+H G+F+ 
Sbjct: 145 RYPDPRTSRGDTLVYNVKEKKVVDLIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDI 204

Query: 133 IHIQDALGHEFATRLGNVFTIGKG-SKPWVSLPKGKGIKLSIIEEARKRQAAQAA 186
             ++DA GHEFATR  N+F IGK  +   V+LPK +G+++++I+E  ++  A  A
Sbjct: 205 ARLKDASGHEFATRAANIFVIGKDMNSVPVTLPKQQGLRINVIQEREEKLIAAEA 259

Length = 273

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

 Score =  135 bits (342), Expect = 5e-40
 Identities = 64/160 (40%), Positives = 91/160 (56%), Gaps = 3/160 (1%)

Query: 7   FGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINT 66
           F   L DV+SIP+T E +R+L D KGR  L  + +EEAK KLCK+ +    + G   +N 
Sbjct: 78  FPVGLMDVISIPETGEYYRVLPDEKGRLVLIPISEEEAKLKLCKIENKTTVKGGKIQLNL 137

Query: 67  YDGRTIRYPDPL-IKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREK 125
           +DGR I        K  D++ + L E +I D I F+ GN+ ++TGG++ G +G IK  E 
Sbjct: 138 HDGRNILVDVEDDYKTGDSLLISLPEQEIVDHIPFEEGNLAIITGGKHVGEIGKIKEIEV 197

Query: 126 HKGSFE-TIHIQDALGHEFATRLGNVFTIGKGSKPWVSLP 164
            K S    + ++D  G +F T L  VF IGK  KP + LP
Sbjct: 198 TKSSKPNIVTLEDKDGEKFETILDYVFVIGK-EKPVIKLP 236

Length = 237

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

 Score =  122 bits (309), Expect = 6e-37
 Identities = 40/77 (51%), Positives = 52/77 (67%)

Query: 19 KTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPL 78
          KT E++R+LYD KGR  LH +  EEAK+KLCKV++    + G P +N +DGR IRYPDP 
Sbjct: 1  KTGEHYRVLYDVKGRLVLHRISAEEAKYKLCKVKNKTTVKGGKPQLNLHDGRNIRYPDPD 60

Query: 79 IKANDTIKLDLEENKIT 95
           K  DT+ +DL   KI 
Sbjct: 61 YKTGDTLVIDLPTQKIV 77

Length = 77

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

 Score =  101 bits (254), Expect = 6e-29
 Identities = 37/55 (67%), Positives = 46/55 (83%)

Query: 100 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIG 154
           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 = 34.3 bits (80), Expect = 0.002
 Identities = 7/27 (25%), Positives = 13/27 (48%)

Query: 102 VGNIVMVTGGRNRGRVGIIKNREKHKG 128
            G++V 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	187
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	97.14
smart00739	28	KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif i	97.04
TIGR01080	114	rplX_A_E ribosomal protein L24p/L26e, archaeal/euk	94.99
PRK01191	120	rpl24p 50S ribosomal protein L24P; Validated	93.21
PRK12281	76	rplX 50S ribosomal protein L24; Reviewed	91.88
CHL00141	83	rpl24 ribosomal protein L24; Validated	91.11
PRK00004	105	rplX 50S ribosomal protein L24; Reviewed	90.37
PTZ00194	143	60S ribosomal protein L26; Provisional	89.42
TIGR01079	104	rplX_bact ribosomal protein L24, bacterial/organel	86.61
PF13051	68	DUF3912: Protein of unknown function (DUF3912)	81.18

>PLN00036 40S ribosomal protein S4; Provisional

Probab=100.00  E-value=2.4e-77  Score=517.86  Aligned_cols=182  Identities=80%  Similarity=1.285  Sum_probs=178.9

Q ss_pred             eecccceeEEEEecCCCceEEEEEcCCCceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCCCcccCCe
Q 029796            5 FSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDT   84 (187)
Q Consensus         5 ~kfPvGlMDVIsI~kt~e~yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~DT   84 (187)
                      ++||||||||||||++||||||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+|||
T Consensus        80 ~~fPvG~mDVIsI~kt~e~yRvl~D~kGrf~l~~I~~eeA~~KLcKV~~k~~~~gG~~ql~~hDGrni~~~d~~~k~~Dt  159 (261)
T PLN00036         80 KTYPAGFMDVISIPKTNENFRLLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHDGRTIRYPDPLIKANDT  159 (261)
T ss_pred             CCCCCceeEEEEEcCCCCeEEEEECCCceEEEEEcChHHccceEEEEEEEEEecCCeEEEEecCCceeccCCCccccCCE
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEEEeeceEEEEccCCCceEEcc
Q 029796           85 IKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLP  164 (187)
Q Consensus        85 v~i~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIG~~~~p~IsLp  164 (187)
                      |+|+||+++|++|+||++||+||||||+|+|++|+|.+|+++++++++||++|++|++|+|+++||||||++++|||+||
T Consensus       160 v~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d~~g~~F~T~~~~vfvIG~~~kp~isLp  239 (261)
T PLN00036        160 IKIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLP  239 (261)
T ss_pred             EEEeCCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999998899999999


Q ss_pred             CCceeeeehhHHHHHHHHHHHhC
Q 029796          165 KGKGIKLSIIEEARKRQAAQAAA  187 (187)
Q Consensus       165 ~~~Gi~~~~~e~~~~~~~~~~~~  187 (187)
                      +++|||++++|| |++++++.++
T Consensus       240 ~~~gi~~~~~e~-r~~~~~~~~~  261 (261)
T PLN00036        240 KGKGIKLSIIEE-ARKRLAAGQA  261 (261)
T ss_pred             CCCCcccchHHH-HHHhhhhhcC
Confidence            999999999999 9999988764

>PTZ00118 40S ribosomal protein S4; Provisional

Probab=100.00  E-value=6.8e-77  Score=515.33  Aligned_cols=181  Identities=55%  Similarity=0.929  Sum_probs=178.0

Q ss_pred             eecccceeEEEEecCCCceEEEEEcCCCceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCCCcccCCe
Q 029796            5 FSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDT   84 (187)
Q Consensus         5 ~kfPvGlMDVIsI~kt~e~yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~DT   84 (187)
                      ++||||||||||||+||||||||||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+|||
T Consensus        80 ~~fPvG~mDVIsI~kt~e~yRvl~D~kGr~~l~~I~~eeA~~KLcKV~~k~~~~gg~~~l~~hDGrni~~~d~~ik~~Dt  159 (262)
T PTZ00118         80 CTYPVGFMDVVSLTKTNEYFRLLYDTKGRFVPHKITNEEAKYKLCRVKKTFLGPKEVSIAVTHDGRTIRYVHPDVKVGDS  159 (262)
T ss_pred             CCCCCceeEEEEEcCCCCeEEEEECCCccEEEEEcCHHHhcceEEEEeEEEECCCCeEEEEecCcceeccCCCcccCCCE
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEEEeeceEEEEccCCCceEEcc
Q 029796           85 IKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLP  164 (187)
Q Consensus        85 v~i~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIG~~~~p~IsLp  164 (187)
                      |+|+||+++|++|+||++||+||||||+|+|++|+|.+++++++++++|||+|++|++|+|+++||||||++++|||+||
T Consensus       160 v~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~d~~g~~F~T~~~~vfvIG~~~kp~islp  239 (262)
T PTZ00118        160 LRLDLETGKVLEFLKFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKDSRGKTFATRLSNVFVIGVGTKPYVSLP  239 (262)
T ss_pred             EEEECCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999998899999999


Q ss_pred             CCceeeeehhHHHHHHHHHHHh
Q 029796          165 KGKGIKLSIIEEARKRQAAQAA  186 (187)
Q Consensus       165 ~~~Gi~~~~~e~~~~~~~~~~~  186 (187)
                      ++||||+|++|| |++++++++
T Consensus       240 ~~kgi~~~~~e~-~~~~~~~~~  260 (262)
T PTZ00118        240 RERGIKKDIIEE-RRNRLAKAL  260 (262)
T ss_pred             CCCCccccHHHH-HHHHHHHHh
Confidence            999999999999 999998865

>PTZ00223 40S ribosomal protein S4; Provisional

Probab=100.00  E-value=1.3e-76  Score=515.89  Aligned_cols=181  Identities=45%  Similarity=0.742  Sum_probs=177.4

Q ss_pred             eecccceeEEEEecCCCceEEEEEcCCCceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCCCcccCCe
Q 029796            5 FSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDT   84 (187)
Q Consensus         5 ~kfPvGlMDVIsI~kt~e~yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~DT   84 (187)
                      ++||||||||||||++|||||||||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+|||
T Consensus        77 ~~~PvGlMDVIsI~kt~e~yRvl~D~kGrf~l~~I~~eeA~~KLcKV~~k~~~~gG~~ql~~hDGrnI~~~d~~~k~~Dt  156 (273)
T PTZ00223         77 GKYPAGFMDVVEIPKTGDRFRILYDVKGRFALVKVSEAEAQIKLMKVVNVYTATGRIPVAVTHDGHRIRYPDPRTSRGDT  156 (273)
T ss_pred             CCCCCceeEEEEEcCCCCeEEEEECCCCcEEEEEcChHHccceEEEEEEEEEecCCeeEEEecCCceeccCCccccCCCE
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEEEeeceEEEEccC-CCceEEc
Q 029796           85 IKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKG-SKPWVSL  163 (187)
Q Consensus        85 v~i~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIG~~-~~p~IsL  163 (187)
                      |+|+||+++|++|+||++||+||||||+|+|++|+|.+|+.+++++++||++|++|++|+|+++||||||++ ++|||+|
T Consensus       157 v~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d~~g~~F~T~~~~VfvIG~~~~kp~IsL  236 (273)
T PTZ00223        157 LVYNVKEKKVVDLIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRAANIFVIGKDMNSVPVTL  236 (273)
T ss_pred             EEEECCCCeeeEEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEeCCCCCcceEC
Confidence            999999999999999999999999999999999999999999999999999999999999999999999985 6999999


Q ss_pred             cCCceeeeehhHHHHHHHHHHHh
Q 029796          164 PKGKGIKLSIIEEARKRQAAQAA  186 (187)
Q Consensus       164 p~~~Gi~~~~~e~~~~~~~~~~~  186 (187)
                      |++||||||++|| |++++++++
T Consensus       237 p~~kgi~~~~~e~-~~~~~~~~~  258 (273)
T PTZ00223        237 PKQQGLRINVIQE-REEKLIAAE  258 (273)
T ss_pred             cCCCCccccHHHH-HHHHHHHHH
Confidence            9999999999999 999997765

>PRK04313 30S ribosomal protein S4e; Validated

Probab=100.00  E-value=1.9e-69  Score=463.62  Aligned_cols=160  Identities=39%  Similarity=0.629  Sum_probs=157.1

Q ss_pred             eecccceeEEEEecCCCceEEEEEcCCCceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCC-CCcccCC
Q 029796            5 FSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPD-PLIKAND   83 (187)
Q Consensus         5 ~kfPvGlMDVIsI~kt~e~yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d-~~ik~~D   83 (187)
                      ++||||||||||||++||+|||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+++| |.||+||
T Consensus        76 ~~~PvGlmDVIsI~~~~e~yRvl~d~kgr~~l~~I~~eea~~KL~KV~~k~~~~gG~~ql~~hDGrni~~~~~~~~k~~D  155 (237)
T PRK04313         76 YKFPVGLMDVISIPETGEYYRVLPDEKGRLVLIPISEEEAKLKLCKIENKTTVKGGKIQLNLHDGRNILVDVEDDYKTGD  155 (237)
T ss_pred             cccCcCceeEEEEccCCCeEEEEECCCCcEEEEECChHHccceEEEEEeEEEecCCEEEEEecCCceEEccCccccccCC
Confidence            789999999999999999999999999999999999999999999999999999999999999999999988 9999999


Q ss_pred             eEEEecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEEec-CCccEEEEEcCCCCeEEEeeceEEEEccCCCceEE
Q 029796           84 TIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVS  162 (187)
Q Consensus        84 Tv~i~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~-~s~~~V~i~d~~g~~F~T~~~~vfvIG~~~~p~Is  162 (187)
                      ||+|+||+|+|++|+||++||+||||||+|+|++|+|.+|++++ +++++||++|++|++|+|+++||||||+ ++|+|+
T Consensus       156 tv~i~l~~~kI~~~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~~G~~F~T~~~~vfvIG~-~kp~is  234 (237)
T PRK04313        156 SLLISLPEQEIVDHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKDGEKFETILDYVFVIGK-EKPVIK  234 (237)
T ss_pred             EEEEECCCCceeEEEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcCCCCEEEEEeeeEEEEcC-CCccee
Confidence            99999999999999999999999999999999999999999999 6779999999999999999999999997 999999


Q ss_pred             ccC
Q 029796          163 LPK  165 (187)
Q Consensus       163 Lp~  165 (187)
                      ||.
T Consensus       235 l~~  237 (237)
T PRK04313        235 LPE  237 (237)
T ss_pred             CCC
Confidence            984

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

Probab=100.00  E-value=1.9e-67  Score=448.77  Aligned_cols=162  Identities=45%  Similarity=0.698  Sum_probs=158.9

Q ss_pred             eecccceeEEEEecCCCceEEEEEcCCCceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCCCcccCCe
Q 029796            5 FSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDT   84 (187)
Q Consensus         5 ~kfPvGlMDVIsI~kt~e~yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~DT   84 (187)
                      |+||||||||||||+|||+||||||.+|+|.||+|++|||.||||||++|++++||++|||||||||++++|+.|++|||
T Consensus        79 ~kfPVGlmDVisip~tgE~yRvl~d~~grl~l~~is~EeA~~Kl~kV~nKt~vkgG~~QLn~hDGrni~~~d~~~k~~Dt  158 (241)
T COG1471          79 YKFPVGLMDVISIPKTGEHYRVLPDEKGRLVLHPISAEEASYKLCKVKNKTTVKGGRIQLNLHDGRNIRLEDDNYKTGDT  158 (241)
T ss_pred             ccCCcceEEEEEECCCCceEEEEecCCccEEEEecChhhccceEEEEEeEEEecCCEEEEEecCCceeeccCCccccccE
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEEec-CCccEEEEEcCCCCeEEEeeceEEEEccCCCceEEc
Q 029796           85 IKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSL  163 (187)
Q Consensus        85 v~i~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~-~s~~~V~i~d~~g~~F~T~~~~vfvIG~~~~p~IsL  163 (187)
                      |++++|+++|++||||++|++||||||+|+|++|+|.+|+.++ +++|+|+++|.+|+.|+|+++||||||+ ++|||+|
T Consensus       159 v~i~lp~~~I~~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~~~g~~F~T~~~yVfvIG~-~k~~i~l  237 (241)
T COG1471         159 VKISLPEQKIVEHIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDEEGNTFQTIKDYVFVIGE-DKPVISL  237 (241)
T ss_pred             EEEeCCChhheeEeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEecCCCCceEEeeeEEEEEcC-CCceEeC
Confidence            9999999999999999999999999999999999999999998 6669999999999999999999999997 9999999


Q ss_pred             cCCc
Q 029796          164 PKGK  167 (187)
Q Consensus       164 p~~~  167 (187)
                      |+++
T Consensus       238 ~~e~  241 (241)
T COG1471         238 PKEK  241 (241)
T ss_pred             CCCC
Confidence            9874

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

Probab=100.00  E-value=9.5e-66  Score=440.43  Aligned_cols=181  Identities=63%  Similarity=1.076  Sum_probs=178.5

Q ss_pred             eecccceeEEEEecCCCceEEEEEcCCCceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCCCcccCCe
Q 029796            5 FSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDT   84 (187)
Q Consensus         5 ~kfPvGlMDVIsI~kt~e~yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~DT   84 (187)
                      .+||+|||||++|++|||+||++||++|+|.+|+|++|||+||||||++++.+.+|+|+|++||||+||||||.+|++||
T Consensus        80 ~~yp~g~mDvisiekTge~fr~iyd~k~~F~~hrI~~eeakyKLcKVrk~f~~tkGiP~lvthDg~tIrypDplIk~~dt  159 (263)
T KOG0378|consen   80 STYPAGFMDVISIEKTGEHFRLIYDQKGRFAVHRITSEEAKYKLCKVRKIFLGTKGIPHLVTHDGRTIRYPDPLIKVNDT  159 (263)
T ss_pred             cccccceeEEEEecccchhhhhhhhcccceEEEEeccccccceeeeeEEEEeeccCcceEEccCCceEecCCcccCccce
Confidence            36999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEEEeeceEEEEccCCCceEEcc
Q 029796           85 IKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLP  164 (187)
Q Consensus        85 v~i~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIG~~~~p~IsLp  164 (187)
                      +++++++++|.++++|+.|++||++||+|+||+|+|.+.++|+|++++||++|++|++|+|+++|+|+||++++||||||
T Consensus       160 I~~~~~t~kit~~ikf~~~~~~~vtgg~n~gRig~i~~rerh~G~f~vvhvkdt~gnsFatrLsNifvIgkgnKpwisLP  239 (263)
T KOG0378|consen  160 IKIDLETSKITDFIKFDTGNLCMVTGGANLGRIGVIKNRERHPGSFDVVHVKDTNGNSFATRLSNIFVIGEGNKPWISLP  239 (263)
T ss_pred             eeccCCCceeeeeeccCccceeeeeccccccccccccccccCCCceEEEEEEecCCcEeeeeeccEEEEecCCCccccCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCceeeeehhHHHHHHHHHHHh
Q 029796          165 KGKGIKLSIIEEARKRQAAQAA  186 (187)
Q Consensus       165 ~~~Gi~~~~~e~~~~~~~~~~~  186 (187)
                      +++||+++++|| ||+|++++.
T Consensus       240 kgkgi~~siaEe-~dkrl~~k~  260 (263)
T KOG0378|consen  240 KGKGIALSIAEE-RDKRLAAKI  260 (263)
T ss_pred             cccCccchhhHH-HHHHHhhhc
Confidence            999999999999 999999875

>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=1e-36  Score=222.05  Aligned_cols=77  Identities=61%  Similarity=1.011  Sum_probs=69.8

Q ss_pred             CCCceEEEEEcCCCceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCCCcccCCeEEEecCCCeee
Q 029796           19 KTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKIT   95 (187)
Q Consensus        19 kt~e~yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~DTv~i~l~~~kI~   95 (187)
                      +|||+|||+||++|+|.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+||||+++||++||+
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            68999999999999999999999999999999999999999999999999999999999999999999999999985

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=97.14  E-value=0.00053  Score=41.81  Aligned_cols=31  Identities=29%  Similarity=0.560  Sum_probs=26.2

Q ss_pred             CCcEEEEECCCcceeEEEEEEEEEecCCccEEEE
Q 029796          102 VGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHI  135 (187)
Q Consensus       102 ~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i  135 (187)
                      +|+.|+|+.|++.|+.|+|.++..+.   +.|++
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            59999999999999999999997643   55655

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=97.04  E-value=0.00064  Score=39.14  Aligned_cols=27  Identities=37%  Similarity=0.661  Sum_probs=24.6

Q ss_pred             EecCCcEEEEECCCcceeEEEEEEEEE
Q 029796           99 KFDVGNIVMVTGGRNRGRVGIIKNREK  125 (187)
Q Consensus        99 ~fe~G~~~~vtgG~n~G~vG~I~~i~~  125 (187)
                      +|++|+.++|++|.+.|.+|+|.++..
T Consensus         1 ~~~~G~~V~I~~G~~~g~~g~i~~i~~   27 (28)
T smart00739        1 KFEVGDTVRVIAGPFKGKVGKVLEVDG   27 (28)
T ss_pred             CCCCCCEEEEeECCCCCcEEEEEEEcC
Confidence            478999999999999999999999853

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

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

Probab=94.99  E-value=0.06  Score=42.23  Aligned_cols=40  Identities=15%  Similarity=0.228  Sum_probs=32.5

Q ss_pred             eEEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcC
Q 029796           96 DFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDA  138 (187)
Q Consensus        96 ~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~  138 (187)
                      +.+++..|+.+.|++|++-|..|+|.++...   .+.|.|+.-
T Consensus        38 r~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~---~~~V~Vegv   77 (114)
T TIGR01080        38 RALPVRKGDKVRIMRGDFKGHEGKVSKVDLK---RYRIYVEGV   77 (114)
T ss_pred             ccceeecCCEEEEecCCCCCCEEEEEEEEcC---CCEEEEcCe
Confidence            5568899999999999999999999999743   245667653

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.

>PRK01191 rpl24p 50S ribosomal protein L24P; Validated

Probab=93.21  E-value=0.25  Score=39.19  Aligned_cols=38  Identities=18%  Similarity=0.308  Sum_probs=30.8

Q ss_pred             EEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEc
Q 029796           97 FIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD  137 (187)
Q Consensus        97 ~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d  137 (187)
                      .+++..|+.+.|+.|+.-|..|+|.++....   +.|+|+.
T Consensus        43 ~~~IkkGD~V~VisG~~KGk~GkV~~V~~~~---~~V~VeG   80 (120)
T PRK01191         43 SLPVRKGDTVKVMRGDFKGEEGKVVEVDLKR---GRIYVEG   80 (120)
T ss_pred             cceEeCCCEEEEeecCCCCceEEEEEEEcCC---CEEEEeC
Confidence            4578899999999999999999999996543   3466654

>PRK12281 rplX 50S ribosomal protein L24; Reviewed

Probab=91.88  E-value=0.26  Score=35.88  Aligned_cols=38  Identities=21%  Similarity=0.459  Sum_probs=31.8

Q ss_pred             EEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcC
Q 029796           98 IKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDA  138 (187)
Q Consensus        98 i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~  138 (187)
                      +++..|+.+.|+.|+.-|++|+|.++.+..   +.|.+++-
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            478899999999999999999999997643   45777654

>CHL00141 rpl24 ribosomal protein L24; Validated

Probab=91.11  E-value=0.35  Score=35.74  Aligned_cols=39  Identities=15%  Similarity=0.434  Sum_probs=32.0

Q ss_pred             EEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcC
Q 029796           97 FIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDA  138 (187)
Q Consensus        97 ~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~  138 (187)
                      .+++..|+.+.|+.|+.-|+.|+|.++.+..   +.|++++-
T Consensus         6 ~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~---~~V~Vegv   44 (83)
T CHL00141          6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKKS---NKVIVKGI   44 (83)
T ss_pred             eCcccCCCEEEEeEcCCCCcEEEEEEEEcCC---CEEEEcCc
Confidence            3478899999999999999999999997543   46777643

>PRK00004 rplX 50S ribosomal protein L24; Reviewed

Probab=90.37  E-value=0.39  Score=36.89  Aligned_cols=37  Identities=22%  Similarity=0.504  Sum_probs=30.0

Q ss_pred             EEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEc
Q 029796           98 IKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD  137 (187)
Q Consensus        98 i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d  137 (187)
                      .++..|+.+.|+.|++-|.+|+|.++....   +.|+|++
T Consensus         3 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~---~~V~Veg   39 (105)
T PRK00004          3 MKIKKGDTVIVIAGKDKGKRGKVLKVLPKK---NKVIVEG   39 (105)
T ss_pred             CcccCCCEEEEeEcCCCCcEEEEEEEEcCC---CEEEEcC
Confidence            378899999999999999999999996543   3455554

>PTZ00194 60S ribosomal protein L26; Provisional

Probab=89.42  E-value=0.82  Score=37.30  Aligned_cols=57  Identities=25%  Similarity=0.308  Sum_probs=38.2

Q ss_pred             EEecCCcEEEEECCCcceeEEEEEEEEEecCCc--cEEEEEcCCCCeEE--EeeceEEEEc
Q 029796           98 IKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSF--ETIHIQDALGHEFA--TRLGNVFTIG  154 (187)
Q Consensus        98 i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~--~~V~i~d~~g~~F~--T~~~~vfvIG  154 (187)
                      +++..|+.+.|+.|++-|..|+|.++....+..  +=|.+.-..|..++  --.+||+++-
T Consensus        45 ~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~Kk~gk~~e~PIh~SNV~iv~  105 (143)
T PTZ00194         45 MPVRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITREKANGEPVQIGIHPSNVIITK  105 (143)
T ss_pred             ceeecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEEecCCCEeecCcCchheEEEc
Confidence            478889999999999999999999997644321  22233335554433  2346666654

>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle

Probab=86.61  E-value=1.2  Score=34.32  Aligned_cols=28  Identities=25%  Similarity=0.470  Sum_probs=25.4

Q ss_pred             EecCCcEEEEECCCcceeEEEEEEEEEe
Q 029796           99 KFDVGNIVMVTGGRNRGRVGIIKNREKH  126 (187)
Q Consensus        99 ~fe~G~~~~vtgG~n~G~vG~I~~i~~~  126 (187)
                      ++..|+.+.|+.|+.-|.+|+|.++.+.
T Consensus         3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~   30 (104)
T TIGR01079         3 KIKKGDTVKVISGKDKGKRGKVLKVLPK   30 (104)
T ss_pred             cccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence            6788999999999999999999999654

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

>PF13051 DUF3912: Protein of unknown function (DUF3912)

Probab=81.18  E-value=4.5  Score=28.70  Aligned_cols=49  Identities=27%  Similarity=0.507  Sum_probs=37.0

Q ss_pred             CCcEEEEECCCcceeEEEEEEEEEec-CCccEEEEEcCCCCeEEEeeceEEEEc
Q 029796          102 VGNIVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIG  154 (187)
Q Consensus       102 ~G~~~~vtgG~n~G~vG~I~~i~~~~-~s~~~V~i~d~~g~~F~T~~~~vfvIG  154 (187)
                      +|..|+|-.|.+.-|+|.++.-+... ++|.+|.    ++...+--+..+..+|
T Consensus         5 ~gqkayikdgp~rnrigivk~~e~q~~~~f~ivi----~~q~i~velkdivlvg   54 (68)
T PF13051_consen    5 VGQKAYIKDGPYRNRIGIVKKNEKQLESHFAIVI----GEQSIDVELKDIVLVG   54 (68)
T ss_pred             cccEeeeccCCccceeEEEecchhhcCCcEEEEE----CCeEEEEEeeeEEEEE
Confidence            48899999999999999999888766 4445542    3345666677777777

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	187
3iz6_D	265	Localization Of The Small Subunit Ribosomal Protein		7e-85
3izb_D	261	Localization Of The Small Subunit Ribosomal Protein		2e-59
2xzm_W	260	Crystal Structure Of The Eukaryotic 40s Ribosomal S		2e-49
3zey_1	273	High-resolution Cryo-electron Microscopy Structure		6e-40
3kbg_A	213	Crystal Structure Of The 30s Ribosomal Protein S4e		6e-12
3j20_E	243	Promiscuous Behavior Of Proteins In Archaeal Riboso		3e-11

>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 =  309 bits (791), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 145/164 (88%), Positives = 159/164 (96%)
Query: 13  DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
           DV+SIPKT EN+RLLYDTKGRFRL S++DE+AKFKLCKVRSVQFGQKGIPY+NTYDGRTI
Sbjct: 88  DVISIPKTGENYRLLYDTKGRFRLQSVKDEDAKFKLCKVRSVQFGQKGIPYLNTYDGRTI 147
Query: 73  RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
           RYPDP+IKANDTIK+DLE NKI DFIKFDVGN+VMVTGGRN GRVG+IKNREKHKGSFET
Sbjct: 148 RYPDPIIKANDTIKIDLETNKIVDFIKFDVGNVVMVTGGRNTGRVGVIKNREKHKGSFET 207
Query: 133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 176
           IH++DALGH+FATRLGNVFTIGKG+KPWVSLPKGKGIKLSIIEE
Sbjct: 208 IHVEDALGHQFATRLGNVFTIGKGNKPWVSLPKGKGIKLSIIEE 251

>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 =  224 bits (572), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 104/164 (63%), Positives = 131/164 (79%)
Query: 13  DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
           DV+++  TNENFRL+YD KGRF +H + DEEA +KL KV+ VQ G+KG+PY+ T+DGRTI
Sbjct: 88  DVITLDATNENFRLVYDVKGRFAVHRITDEEASYKLGKVKKVQLGKKGVPYVVTHDGRTI 147
Query: 73  RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
           RYPDP IK NDT+K+DL   KITDFIKFD G +V VTGGRN GR+G I ++E+H G F+ 
Sbjct: 148 RYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLVYVTGGRNLGRIGTIVHKERHDGGFDL 207
Query: 133 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 176
           +HI+D+L + F TRL NVF IG+  KP++SLPKGKGIKLSI EE
Sbjct: 208 VHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKGKGIKLSIAEE 251

>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 =  191 bits (485), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 92/170 (54%), Positives = 122/170 (71%)
Query: 7   FGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINT 66
           + T L DVV I KT+++FR+LYDTKGRF L SL  EEAK+KL KV +   G   IPYI T
Sbjct: 84  YPTGLMDVVRIEKTDQSFRILYDTKGRFVLKSLSKEEAKYKLLKVTAKAIGPNQIPYIVT 143
Query: 67  YDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKH 126
           +D RTIR+P+P IK  DT+K DL  NKI +F   + GN+  +  G N GRVGII++ EKH
Sbjct: 144 HDSRTIRFPNPEIKIGDTLKYDLVNNKIENFAHLESGNVCYIQQGNNIGRVGIIQHIEKH 203
Query: 127 KGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 176
           +GSF+  H++DA G+ FATRLGN+F +G+G K W+ LP G G++ +I+EE
Sbjct: 204 QGSFDICHVKDAKGNAFATRLGNIFVLGQGKKSWIELPSGDGVRETILEE 253

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

Iteration: 1
 Score =  159 bits (403), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 81/165 (49%), Positives = 110/165 (66%), Gaps = 1/165 (0%)
Query: 13  DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 72
           DVV IPKT + FR+LYD KGRF L  + + E+  K+ KV +V  G   IP   T+DG  I
Sbjct: 85  DVVEIPKTGDRFRILYDVKGRFALVRVSEAESSIKMMKVVNVYTGTGRIPVAVTHDGHRI 144
Query: 73  RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 132
           RYPDP     DT+  D++E K+ D IK   G +VMVTGG NRGR+G I + E+H G+F+ 
Sbjct: 145 RYPDPRTSRGDTLVYDVKEKKVLDLIKIGNGKVVMVTGGANRGRIGEIVSIERHPGAFDI 204
Query: 133 IHIQDALGHEFATRLGNVFTIGKG-SKPWVSLPKGKGIKLSIIEE 176
             ++DA GHEFATR  N+F IGK  S   V+LPK +G+++++I+E
Sbjct: 205 ARLKDASGHEFATRATNIFVIGKDMSSVPVTLPKQQGLRINVIQE 249

>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 = 67.0 bits (162), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 49/160 (30%), Positives = 74/160 (46%), Gaps = 7/160 (4%)
Query: 7   FGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINT 66
           F     DV+ I    E++R++Y+ +G   L     E A  KL KVRS          + T
Sbjct: 48  FAVGFXDVIEI--NGESYRVVYNDQGALVLXKETKERASXKLLKVRSKVIAPGNRIQLGT 105
Query: 67  YDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKH 126
           +DGRT    D  IK  D + + + + KI++ IK   GN   +T G +  + G I   E  
Sbjct: 106 HDGRTFITDDKSIKVGDVLAVSVPDXKISEIIKXQPGNKAYITAGSHVNQTGTISKIEAK 165
Query: 127 KGSFET-IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPK 165
           +GS    +H Q+     F+T   +VF IG     +V  P+
Sbjct: 166 EGSSANLVHFQEG----FSTIKDHVFXIGSSKFSFVLSPE 201

>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 = 64.7 bits (156), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 49/165 (29%), Positives = 85/165 (51%), Gaps = 7/165 (4%)
Query: 5   FSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYI 64
           + F   + DVVSIP+T E++R+L +  G+  LH + ++EA  K  ++R+ +  +     +
Sbjct: 81  YKFPVGIMDVVSIPETGEHYRVLPNRIGKLILHPISEDEAFIKPLRIRNKRMIKGARVQL 140
Query: 65  NTYDGR----TIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVG-I 119
           N +DG     +I   D    +  T+ + + E +I + + F+ G  V VT G+N  R G I
Sbjct: 141 NFHDGTNHIVSIAEKDNYFTSY-TVLMKVPEREILEVLPFEKGAYVFVTQGKNVARKGRI 199
Query: 120 IKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLP 164
           ++ +    G  + + I+D  G  F T     F +G   KP +SLP
Sbjct: 200 VEIKRFPMGWPDVVTIEDEEGELFDTLKEYAFVVGT-DKPKISLP 243

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	187
3iz6_D	265	40S ribosomal protein S4 (S4E); eukaryotic ribosom	6e-81
3u5c_E	261	RP5, S7, YS6, 40S ribosomal protein S4-A; translat	2e-80
2xzm_W	260	40S ribosomal protein S4; ribosome, translation; 3	9e-77
3kbg_A	213	30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2	3e-60

>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 =  240 bits (613), Expect = 6e-81
 Identities = 152/181 (83%), Positives = 167/181 (92%)

Query: 7   FGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINT 66
           +     DV+SIPKT EN+RLLYDTKGRFRL S++DE+AKFKLCKVRSVQFGQKGIPY+NT
Sbjct: 82  YPAGFMDVISIPKTGENYRLLYDTKGRFRLQSVKDEDAKFKLCKVRSVQFGQKGIPYLNT 141

Query: 67  YDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKH 126
           YDGRTIRYPDP+IKANDTIK+DLE NKI DFIKFDVGN+VMVTGGRN GRVG+IKNREKH
Sbjct: 142 YDGRTIRYPDPIIKANDTIKIDLETNKIVDFIKFDVGNVVMVTGGRNTGRVGVIKNREKH 201

Query: 127 KGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQAA 186
           KGSFETIH++DALGH+FATRLGNVFTIGKG+KPWVSLPKGKGIKLSIIEE RKR AA  A
Sbjct: 202 KGSFETIHVEDALGHQFATRLGNVFTIGKGNKPWVSLPKGKGIKLSIIEEQRKRDAAAQA 261

Query: 187 A 187
           A
Sbjct: 262 A 262

>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 =  239 bits (610), Expect = 2e-80
 Identities = 107/179 (59%), Positives = 137/179 (76%)

Query: 7   FGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINT 66
           +     DV+++  TNENFRL+YD KGRF +H + DEEA +KL KV+ VQ G+KG+PY+ T
Sbjct: 82  YPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASYKLGKVKKVQLGKKGVPYVVT 141

Query: 67  YDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKH 126
           +DGRTIRYPDP IK NDT+K+DL   KITDFIKFD G +V VTGGRN GR+G I ++E+H
Sbjct: 142 HDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLVYVTGGRNLGRIGTIVHKERH 201

Query: 127 KGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQA 185
            G F+ +HI+D+L + F TRL NVF IG+  KP++SLPKGKGIKLSI EE  +R+A Q 
Sbjct: 202 DGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKGKGIKLSIAEERDRRRAQQG 260

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

 Score =  229 bits (585), Expect = 9e-77
 Identities = 92/176 (52%), Positives = 126/176 (71%)

Query: 7   FGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINT 66
           + T L DVV I KT+++FR+LYDTKGRF L SL  EEAK+KL KV +   G   IPYI T
Sbjct: 84  YPTGLMDVVRIEKTDQSFRILYDTKGRFVLKSLSKEEAKYKLLKVTAKAIGPNQIPYIVT 143

Query: 67  YDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKH 126
           +D RTIR+P+P IK  DT+K DL  NKI +F   + GN+  +  G N GRVGII++ EKH
Sbjct: 144 HDSRTIRFPNPEIKIGDTLKYDLVNNKIENFAHLESGNVCYIQQGNNIGRVGIIQHIEKH 203

Query: 127 KGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQA 182
           +GSF+  H++DA G+ FATRLGN+F +G+G K W+ LP G G++ +I+EE +++ +
Sbjct: 204 QGSFDICHVKDAKGNAFATRLGNIFVLGQGKKSWIELPSGDGVRETILEERKRKFS 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 =  186 bits (472), Expect = 3e-60
 Identities = 49/161 (30%), Positives = 74/161 (45%), Gaps = 7/161 (4%)

Query: 6   SFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYIN 65
            F     DV+ I    E++R++Y+ +G   L     E A  KL KVRS          + 
Sbjct: 47  KFAVGFMDVIEIN--GESYRVVYNDQGALVLMKETKERASMKLLKVRSKVIAPGNRIQLG 104

Query: 66  TYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREK 125
           T+DGRT    D  IK  D + + + + KI++ IK   GN   +T G +  + G I   E 
Sbjct: 105 THDGRTFITDDKSIKVGDVLAVSVPDMKISEIIKMQPGNKAYITAGSHVNQTGTISKIEA 164

Query: 126 HKGS-FETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPK 165
            +GS    +H Q+     F+T   +VF IG     +V  P+
Sbjct: 165 KEGSSANLVHFQEG----FSTIKDHVFMIGSSKFSFVLSPE 201

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	187
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	95.77
2do3_A	69	Transcription elongation factor SPT5; KOW motif, s	95.52
1vq8_T	120	50S ribosomal protein L24P; ribosome 50S, protein-	88.24
3u5e_Y	127	L33, YL33, 60S ribosomal protein L26-A; translatio	85.75
3j21_U	121	50S ribosomal protein L24P; archaea, archaeal, KIN	84.91
1nz9_A	58	Transcription antitermination protein NUSG; transc	84.58
3iz5_Y	150	60S ribosomal protein L26 (L24P); eukaryotic ribos	80.1

>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-80  Score=536.99  Aligned_cols=182  Identities=81%  Similarity=1.309  Sum_probs=161.7

Q ss_pred             eecccceeEEEEecCCCceEEEEEcCCCceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCCCcccCCe
Q 029796            5 FSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDT   84 (187)
Q Consensus         5 ~kfPvGlMDVIsI~kt~e~yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~DT   84 (187)
                      ++||||||||||||+|||||||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+||||.||+|||
T Consensus        80 ~~~PvG~MDVIsI~kt~e~fRll~D~kGrf~l~~I~~eEA~~KLcKV~~k~~~~~G~pql~tHDGrti~~~dp~ik~~DT  159 (265)
T 3iz6_D           80 KTYPAGFMDVISIPKTGENYRLLYDTKGRFRLQSVKDEDAKFKLCKVRSVQFGQKGIPYLNTYDGRTIRYPDPIIKANDT  159 (265)
T ss_dssp             TTCCCCTTCEEECCSSCCEEEEEECTTSCEEEEEECHHHHTCEEEEEEEEECCSSSCCEEEETTSCCCBSCSSCCCTTCE
T ss_pred             CCCCCcEEEEEEEcCCCCEEEEEECCCCcEEEEECChHHcceEEEEEEEEEEccCCceEEEeecceEEecCCCCcccCCE
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEEEeeceEEEEccCCCceEEcc
Q 029796           85 IKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLP  164 (187)
Q Consensus        85 v~i~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIG~~~~p~IsLp  164 (187)
                      |+||||++||+|||||++||+||||||+|+|++|+|++|++|+||+++|||+|++|++|+|+++||||||++++||||||
T Consensus       160 v~idl~~~kI~d~ikfe~Gnl~mvtgG~n~GriG~I~~ie~~~gs~~iV~vkd~~g~~F~T~~~nvfvIGk~~kp~IsLp  239 (265)
T 3iz6_D          160 IKIDLETNKIVDFIKFDVGNVVMVTGGRNTGRVGVIKNREKHKGSFETIHVEDALGHQFATRLGNVFTIGKGNKPWVSLP  239 (265)
T ss_dssp             EEECSSSCCEEEEECCSTTCEEEECSSSSCSCEEEEEEEECCSSSCCEEEECCCSSCCEEEEGGGEEEEECSSCCCCCCC
T ss_pred             EEEECCCCceeeEEEccCCCEEEEEcCCcceEEEEEEEEEEecCCCcEEEEEECCCCeEEEEeCeEEEEccCCCeeEeCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999889999999


Q ss_pred             CCceeeeehhHHHHHHHHHHHhC
Q 029796          165 KGKGIKLSIIEEARKRQAAQAAA  187 (187)
Q Consensus       165 ~~~Gi~~~~~e~~~~~~~~~~~~  187 (187)
                      ++|||||+++|| |++|++++++
T Consensus       240 ~~kg~~~~~~ee-r~~~~~~~~~  261 (265)
T 3iz6_D          240 KGKGIKLSIIEE-QRKRDAAAQA  261 (265)
T ss_dssp             CCC--------------------
T ss_pred             CCCceeeehHHh-HHHHHHHhhh
Confidence            999999999999 9999988753

>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=2.7e-80  Score=535.06  Aligned_cols=181  Identities=60%  Similarity=1.018  Sum_probs=178.0

Q ss_pred             eecccceeEEEEecCCCceEEEEEcCCCceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCCCcccCCe
Q 029796            5 FSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDT   84 (187)
Q Consensus         5 ~kfPvGlMDVIsI~kt~e~yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~DT   84 (187)
                      ++||||||||||||+|||||||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+||||.||+|||
T Consensus        80 ~~~PvG~MDVIsI~kt~e~fRll~D~kGrf~l~~I~~eEA~~KLcKV~~k~~~~~G~pql~tHDGrti~~~dp~ik~~Dt  159 (261)
T 3u5c_E           80 TTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASYKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDT  159 (261)
T ss_dssp             TTCEEETTCEEEETTTTEEEECCBCSSSCBCCEECCTTGGGCEECCEEEEEECGGGCEEEEETTTEEEESCCSSCCTTCE
T ss_pred             CCCCCceEEEEEEcCCCCEEEEEECCCCcEEEEECChHHcceEEEEEEEEEEecCCceEEEEecceEEecCCCCcccCCE
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEEEeeceEEEEccCCCceEEcc
Q 029796           85 IKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLP  164 (187)
Q Consensus        85 v~i~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIG~~~~p~IsLp  164 (187)
                      |+||||++||+|||||++||+||||||+|+|++|+|++|++|++|+++|||+|++|++|+|+++||||||++++||||||
T Consensus       160 v~idl~~~kI~d~ikfe~Gnl~mvtgG~n~GriG~I~~ie~~~gs~~iV~vkd~~g~~F~T~~~nvfvIGk~~kp~IsLp  239 (261)
T 3u5c_E          160 VKIDLASGKITDFIKFDAGKLVYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLP  239 (261)
T ss_dssp             EEECSSSSCEEEEECCCSSCCEEECSSTTTTCBCCCCEEECCTTSCCEEEEECTTSCEEEEEGGGEEECCSSSCCSSCCC
T ss_pred             EEEECCCCceeeEEEccCCCEEEEEcCCcceEEEEEEEEEEecCCCcEEEEEECCCCeEEEEeCeEEEEccCCCeeEeCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999889999999


Q ss_pred             CCceeeeehhHHHHHHHHHHHh
Q 029796          165 KGKGIKLSIIEEARKRQAAQAA  186 (187)
Q Consensus       165 ~~~Gi~~~~~e~~~~~~~~~~~  186 (187)
                      ++|||||+++|| |++|++++.
T Consensus       240 ~~kg~~~~~~ee-r~~~~~~~~  260 (261)
T 3u5c_E          240 KGKGIKLSIAEE-RDRRRAQQG  260 (261)
T ss_dssp             TTTTCCCCHHHH-HHHHTTTTC
T ss_pred             CCCceeeehHHh-HHHHHHhcc
Confidence            999999999999 999997764

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

Probab=100.00  E-value=2.1e-78  Score=523.02  Aligned_cols=178  Identities=53%  Similarity=0.909  Sum_probs=174.9

Q ss_pred             eecccceeEEEEecCCCceEEEEEcCCCceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCCCcccCCe
Q 029796            5 FSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDT   84 (187)
Q Consensus         5 ~kfPvGlMDVIsI~kt~e~yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~DT   84 (187)
                      ++||||||||||||+|||||||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+|||
T Consensus        82 ~~~PvG~MDVIsI~kt~e~fRll~D~kGrf~l~~I~~eEA~~KLcKV~~k~~~k~G~~ql~~HDGrti~~~d~~ik~~Dt  161 (260)
T 2xzm_W           82 KGYPTGLMDVVRIEKTDQSFRILYDTKGRFVLKSLSKEEAKYKLLKVTAKAIGPNQIPYIVTHDSRTIRFPNPEIKIGDT  161 (260)
T ss_dssp             TTCEECTTCEEEEGGGTEEEEEEECSSSCEEEEECCTTGGGEEEEEEEEEEEETTTEEEEEETTTEEEESCCSSCCTTBE
T ss_pred             CCCCCcEEEEEeEcCCCCEEEEEEcCCccEEEEEcChHHcccEEEEEEEEEEccCCceEEEecCCceEeccCCcCccCCe
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEEEeeceEEEEccCCCceEEcc
Q 029796           85 IKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLP  164 (187)
Q Consensus        85 v~i~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIG~~~~p~IsLp  164 (187)
                      |+||||++||+|||||++||+||||||+|+||+|+|++++++++|+|+|||+|++|++|+|+++||||||++++||||||
T Consensus       162 v~idl~~~kI~d~ikfe~G~l~mvtgG~n~GriG~I~~~e~~~gs~~iV~vkd~~g~~F~T~~~~vfvIG~~~kp~Islp  241 (260)
T 2xzm_W          162 LKYDLVNNKIENFAHLESGNVCYIQQGNNIGRVGIIQHIEKHQGSFDICHVKDAKGNAFATRLGNIFVLGQGKKSWIELP  241 (260)
T ss_dssp             EEEETTTTEEECCCBCCSSCEEEECSSTTTTCEEEEEEEECCCSSCCEEEEECTTCCCEEEEGGGEEEEESTTCCSSCCS
T ss_pred             EEEeCCCCceeeEEEecCCCEEEEECCccceeEEEEEEEEecCCCCcEEEEEeCCCCeEEEEEeeEEEECCCCceeEecC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999998679999999


Q ss_pred             CCceeeeehhHHHHHHHHH
Q 029796          165 KGKGIKLSIIEEARKRQAA  183 (187)
Q Consensus       165 ~~~Gi~~~~~e~~~~~~~~  183 (187)
                      +++|||||++|| |++|++
T Consensus       242 ~~kgi~l~i~ee-r~~~~~  259 (260)
T 2xzm_W          242 SGDGVRETILEE-RKRKFS  259 (260)
T ss_dssp             SSSSCCCCHHHH-HHHHTC
T ss_pred             CCCCeecchhhh-hhhhhc
Confidence            999999999999 998864

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

Probab=100.00  E-value=6.6e-69  Score=460.58  Aligned_cols=159  Identities=29%  Similarity=0.443  Sum_probs=156.9

Q ss_pred             eecccceeEEEEecCCCceEEEEEcCCCceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeC---CCCccc
Q 029796            5 FSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYP---DPLIKA   81 (187)
Q Consensus         5 ~kfPvGlMDVIsI~kt~e~yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~---d~~ik~   81 (187)
                      ++|||||||||||++++|+||++||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+||   ||.||+
T Consensus        81 ~~ypvG~mDVIsI~kt~e~fr~i~d~kGr~~~~~I~~eea~~KLcKV~~k~~~~~G~~~l~~hDgr~i~~p~~~d~~ik~  160 (243)
T 3j20_E           81 YKFPVGIMDVVSIPETGEHYRVLPNRIGKLILHPISEDEAFIKPLRIRNKRMIKGARVQLNFHDGTNHIVSIAEKDNYFT  160 (243)
T ss_dssp             SSCEECTTCEEEETTTTEEEEEEECSSSCEEEEEECTTTTTEEEECCSCEEEETTTEEEECCSSCCCEECSSSSCSSCSS
T ss_pred             ccCCcccceEEEecccCceeEEEecCCCceEEEEeChhhccceEEEEeeeEEccCCeeEEEecCCceEEcccccCCCccc
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999   999999


Q ss_pred             CCeEEEecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEEecCC-ccEEEEEcCCCCeEEEeeceEEEEccCCCce
Q 029796           82 NDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGS-FETIHIQDALGHEFATRLGNVFTIGKGSKPW  160 (187)
Q Consensus        82 ~DTv~i~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s-~~~V~i~d~~g~~F~T~~~~vfvIG~~~~p~  160 (187)
                      ||||+||||++||+|||||++||+||||||+|+|++|+|++|+++++| +++|||+|++|++|+|+++||||||+ ++||
T Consensus       161 ~Dtv~idl~~~kI~d~ikf~~G~l~mvtgG~n~GriG~I~~ie~~~gs~~~~V~v~d~~g~~F~T~~~~vfvIGk-~kp~  239 (243)
T 3j20_E          161 SYTVLMKVPEREILEVLPFEKGAYVFVTQGKNVARKGRIVEIKRFPMGWPDVVTIEDEEGELFDTLKEYAFVVGT-DKPK  239 (243)
T ss_dssp             CEEEEEETTTTEEEEEEECCTTCEEEECSSSSTTCEEEEEECCCCCSSSCCEEEEEESSCCCEEEETTTEEEEES-SCSC
T ss_pred             CCEEEEECCCCCeeeEEeccCCCEEEEECCccceEEEEEEEEEEecCCCceEEEEEcCCCCEEEEEeceEEEECC-CCcc
Confidence            999999999999999999999999999999999999999999999988 89999999999999999999999998 9999


Q ss_pred             EEcc
Q 029796          161 VSLP  164 (187)
Q Consensus       161 IsLp  164 (187)
                      ||||
T Consensus       240 islp  243 (243)
T 3j20_E          240 ISLP  243 (243)
T ss_dssp             CSCC
T ss_pred             ccCC
Confidence            9998

>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=9.4e-66  Score=433.87  Aligned_cols=159  Identities=32%  Similarity=0.449  Sum_probs=147.3

Q ss_pred             eecccceeEEEEecCCCceEEEEEcCCCceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCCCcccCCe
Q 029796            5 FSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDT   84 (187)
Q Consensus         5 ~kfPvGlMDVIsI~kt~e~yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~DT   84 (187)
                      ++|||||||||||  ++|+||++||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+||||.||+|||
T Consensus        46 ~~ypvG~mDVIsI--t~e~fRli~d~kGrf~~~~I~~eea~~KLcKV~~k~~~~~G~~~l~~HDGrti~~pd~~ik~~Dt  123 (213)
T 3kbg_A           46 KKFAVGFMDVIEI--NGESYRVVYNDQGALVLMKETKERASMKLLKVRSKVIAPGNRIQLGTHDGRTFITDDKSIKVGDV  123 (213)
T ss_dssp             TTCEECTTCEEEE--TTEEEEEEECTTSCEEEEECCTTGGGEEEEEEEEEEEEGGGEEEEEETTSCEEEECCTTCCTTCE
T ss_pred             cCCCccceeEEEe--cCceeEEEecCCCcEEEEEeChhHccceEEEEEEEEEecCCeeEEEecCccEEEcCCCCcccCCE
Confidence            5899999999999  99999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEEecCC-ccEEEEEcCCCCeEEEeeceEEEEccCCCceEEc
Q 029796           85 IKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGS-FETIHIQDALGHEFATRLGNVFTIGKGSKPWVSL  163 (187)
Q Consensus        85 v~i~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s-~~~V~i~d~~g~~F~T~~~~vfvIG~~~~p~IsL  163 (187)
                      |++|||++||+||+||++||+||||||+|+||+|+|++|+++++| +++||++    ++|+|+++||||||+ ++|||.+
T Consensus       124 v~idl~~~kI~d~ikf~~G~l~mvtgG~n~GriG~I~~ie~~~gs~~~iV~v~----~~F~T~~~~vfvIGk-~~p~i~~  198 (213)
T 3kbg_A          124 LAVSVPDMKISEIIKMQPGNKAYITAGSHVNQTGTISKIEAKEGSSANLVHFQ----EGFSTIKDHVFMIGS-SKFSFVL  198 (213)
T ss_dssp             EEEETTTCCEEEEECCSTTCEEEECSSTTTTCEEEEEEECCCSCC--CEEEET----TTEEEEGGGEEEEEC-SSCBCC-
T ss_pred             EEEECCCCceeeEEEcCCCCEEEEECCCcceEEEEEEEEEEccCCCCCEEEEE----EEEEeeeceEEEEcC-CCccEEe
Confidence            999999999999999999999999999999999999999999999 5999997    679999999999998 7999977


Q ss_pred             cCCceee
Q 029796          164 PKGKGIK  170 (187)
Q Consensus       164 p~~~Gi~  170 (187)
                      |++.=|.
T Consensus       199 ~p~~~~~  205 (213)
T 3kbg_A          199 SPEEVIP  205 (213)
T ss_dssp             -------
T ss_pred             ChHHccc
Confidence            6664443

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

Probab=95.77  E-value=0.022  Score=44.01  Aligned_cols=42  Identities=21%  Similarity=0.486  Sum_probs=32.8

Q ss_pred             cCCeEEEecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEE
Q 029796           81 ANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREK  125 (187)
Q Consensus        81 ~~DTv~i~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~  125 (187)
                      .++.|  .+....+--.+| +.|+.+||..|.|.|..|++.++..
T Consensus        55 ~g~~v--~v~q~~LETViP-~~g~~V~Iv~G~~rG~~g~L~~id~   96 (127)
T 2ckk_A           55 SGDKL--KLDQTHLETVIP-APGKRILVLNGGYRGNEGTLESINE   96 (127)
T ss_dssp             TCCEE--EEEGGGEEECCC-CTTCEEEECSSTTTTCEEEEEEEEG
T ss_pred             CCCEE--EEchHHcEEecC-CCCCEEEEEecccCCcEEEEEEEeC
Confidence            34555  444444556667 9999999999999999999999954

>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=95.52  E-value=0.025  Score=39.81  Aligned_cols=46  Identities=30%  Similarity=0.390  Sum_probs=35.3

Q ss_pred             ecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEEEeece
Q 029796          100 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGN  149 (187)
Q Consensus       100 fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~  149 (187)
                      |++|+.+-|++|+|.|..|.|..++.    .-++.+.|...+++.-...+
T Consensus        18 F~~GDHVkVi~G~~~getGlVV~v~~----d~v~v~SD~t~~Ei~V~~~d   63 (69)
T 2do3_A           18 FKMGDHVKVIAGRFEGDTGLIVRVEE----NFVILFSDLTMHELKVLPRD   63 (69)
T ss_dssp             CCTTCEEEESSSTTTTCEEEEEEECS----SCEEEEESSSCSEEEECTTS
T ss_pred             ccCCCeEEEeccEEcCceEEEEEEeC----CEEEEEeCCCCCEEEEEhHH
Confidence            78999999999999999999999862    24455667777666544433

>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=88.24  E-value=0.82  Score=35.07  Aligned_cols=56  Identities=25%  Similarity=0.334  Sum_probs=40.6

Q ss_pred             eEEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcC-----CCCeEEEe--eceEEEEc
Q 029796           96 DFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDA-----LGHEFATR--LGNVFTIG  154 (187)
Q Consensus        96 ~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~-----~g~~F~T~--~~~vfvIG  154 (187)
                      ..+++..|+.+.|+.|+.-|..|+|..+..   ..+.|+||.-     +|.+++-.  .+||+++-
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            457889999999999999999999999853   3356777655     34344432  46776664

>3u5e_Y L33, YL33, 60S ribosomal protein L26-A; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 2wwa_L 2ww9_L 2wwb_L 3o5h_X 3o58_X 3u5i_Y 4b6a_Y 1s1i_U 3izc_Y 3izs_Y 3jyw_U

Probab=85.75  E-value=1.2  Score=34.60  Aligned_cols=39  Identities=18%  Similarity=0.324  Sum_probs=31.4

Q ss_pred             eEEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEc
Q 029796           96 DFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD  137 (187)
Q Consensus        96 ~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d  137 (187)
                      -.++...|+.+.|+.|+.-|..|+|..+....   +.|+||.
T Consensus        46 rs~~IkkgD~V~Vi~GkdKGk~GkV~~V~~kk---~~V~VEg   84 (127)
T 3u5e_Y           46 KALPIRRDDEVLVVRGSKKGQEGKISSVYRLK---FAVQVDK   84 (127)
T ss_dssp             CEEECCTTCEEEECSSTTTTCEEEEEEEEGGG---TEEEEET
T ss_pred             CcccccCCCEEEEeecCCCCccceEEEEECCC---CEEEEeC
Confidence            35788899999999999999999999985432   4566654

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

Probab=84.91  E-value=1.2  Score=34.11  Aligned_cols=37  Identities=19%  Similarity=0.286  Sum_probs=30.6

Q ss_pred             EEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEE
Q 029796           97 FIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQ  136 (187)
Q Consensus        97 ~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~  136 (187)
                      .+++..|+.+.|+.|+.-|..|+|.++...   .+.|+||
T Consensus        43 ~~~IkkGD~V~Vi~GkdKGk~GkV~~V~~k---~~~V~VE   79 (121)
T 3j21_U           43 NLPVRVGDKVRIMRGDYKGHEGKVVEVDLK---RYRIYVE   79 (121)
T ss_dssp             EEECCSSSEEEECSSSCSSEEEEEEEEETT---TTEEEET
T ss_pred             ccccccCCEEEEeecCCCCcEeEEEEEEec---CCEEEEe
Confidence            578899999999999999999999998543   2456665

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

Probab=84.58  E-value=2.7  Score=27.24  Aligned_cols=43  Identities=19%  Similarity=0.299  Sum_probs=31.7

Q ss_pred             EEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCe
Q 029796           98 IKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHE  142 (187)
Q Consensus        98 i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~  142 (187)
                      ++|++|+.+.|+.|.-.|..|+|.++... ...-.|.++ .-|.+
T Consensus         3 ~~~~~Gd~V~V~~Gpf~g~~g~v~~v~~~-k~~v~V~v~-~~Gr~   45 (58)
T 1nz9_A            3 VAFREGDQVRVVSGPFADFTGTVTEINPE-RGKVKVMVT-IFGRE   45 (58)
T ss_dssp             CSCCTTCEEEECSGGGTTCEEEEEEEETT-TTEEEEEEE-SSSSE
T ss_pred             cccCCCCEEEEeecCCCCcEEEEEEEcCC-CCEEEEEEE-eCCCE
Confidence            56899999999999999999999998642 123444453 44443

---

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	187
d2do3a1	62	Transcription elongation factor SPT5 {Human (Homo	95.88
d1nz9a_	58	N-utilization substance G protein NusG, C-terminal	90.46
d1vqot1	119	Ribosomal proteins L24 (L24p) {Archaeon Haloarcula	88.64
d1nppa2	58	N-utilization substance G protein NusG, C-terminal	87.93

>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=95.88  E-value=0.0093  Score=39.60  Aligned_cols=46  Identities=30%  Similarity=0.390  Sum_probs=36.1

Q ss_pred             ecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEEEeece
Q 029796          100 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGN  149 (187)
Q Consensus       100 fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~  149 (187)
                      |++|+.+-|++|+|.|..|.|..++.    .-++.+.|...+++.-...+
T Consensus        11 F~~GDhVkVi~G~~~g~tGlVV~v~~----~~v~~~SD~t~~Ei~V~~~d   56 (62)
T d2do3a1          11 FKMGDHVKVIAGRFEGDTGLIVRVEE----NFVILFSDLTMHELKVLPRD   56 (62)
T ss_dssp             CCTTCEEEESSSTTTTCEEEEEEECS----SCEEEEESSSCSEEEECTTS
T ss_pred             cCCCCeEEEeccEEcCccEEEEEEeC----CEEEEEeCCCCCEEEEehHH
Confidence            78999999999999999999998842    24555677777777655444

>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=90.46  E-value=0.076  Score=34.07  Aligned_cols=27  Identities=22%  Similarity=0.340  Sum_probs=25.3

Q ss_pred             EEecCCcEEEEECCCcceeEEEEEEEE
Q 029796           98 IKFDVGNIVMVTGGRNRGRVGIIKNRE  124 (187)
Q Consensus        98 i~fe~G~~~~vtgG~n~G~vG~I~~i~  124 (187)
                      +.|++|+.+.|+.|.-.|..|+|.++.
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

>d1vqot1 b.34.5.1 (T:1-119) Ribosomal proteins L24 (L24p) {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: Ribosomal proteins L24p and L21e
domain: Ribosomal proteins L24 (L24p)
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=88.64  E-value=0.31  Score=35.54  Aligned_cols=56  Identities=23%  Similarity=0.311  Sum_probs=39.5

Q ss_pred             eEEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEE-----cCCCCeEEEe--eceEEEEc
Q 029796           96 DFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQ-----DALGHEFATR--LGNVFTIG  154 (187)
Q Consensus        96 ~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~-----d~~g~~F~T~--~~~vfvIG  154 (187)
                      ..++...|+.+.|+.|++-|..|+|.++...   .+.|.|+     -..|...+..  .+||+++.
T Consensus        38 r~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k---~~~V~Vegin~~k~~~k~~~~pIh~SNv~i~~  100 (119)
T d1vqot1          38 RNVRVNAGDTVEVLRGDFAGEEGEVINVDLD---KAVIHVEDVTLEKTDGEEVPRPLDTSNVRVTD  100 (119)
T ss_dssp             SEEECCTTCEEEECSSTTTTCEEEEEEEETT---TTEEEETTCEEECTTSCEEECCBCGGGEEEEE
T ss_pred             cccceeCCCEEEEeecCCCCCcceEEEEECC---CCEEEEeCcEEEecCCceeeccCchHHEEEEe
Confidence            4578889999999999999999999998543   2445554     3455544433  46666665

>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=87.93  E-value=0.17  Score=32.25  Aligned_cols=28  Identities=21%  Similarity=0.359  Sum_probs=25.4

Q ss_pred             EEecCCcEEEEECCCcceeEEEEEEEEE
Q 029796           98 IKFDVGNIVMVTGGRNRGRVGIIKNREK  125 (187)
Q Consensus        98 i~fe~G~~~~vtgG~n~G~vG~I~~i~~  125 (187)
                      +.|++|+.+-|+.|.-+|..|+|.++..
T Consensus         3 vdf~~Gd~V~I~~GpF~g~~g~V~~i~~   30 (58)
T d1nppa2           3 VEFEKGDQVRVIEGPFMNFTGTVEEVHP   30 (58)
T ss_dssp             CSCCTTCEEEECSSTTTTCEEEEEEEEG
T ss_pred             ccccCCCEEEEcccCCCCCEEEEEEEcC
Confidence            4689999999999999999999999854