Citrus Sinensis ID: 046473

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120
Protein Sequence
SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQASSIFCGYVKI
Secondary Structure (PSIPRED)
cccccccccccccEEEEEEEcccccccHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHcccEEEEEEEcccHHHHHHcEEEcccEEEccccHHHHHHHHEEEEEccccccEEEEEEEEc
Secondary Structure Prediction (SSPRO)
ccEEEEccccccccEEEEEEcccccccHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHcccccEEEEEEcEEEcHHHHHHHHccccEEcccccHHHHHHHHHHHHHHHcccEEEEEEEEc
Coil and Loop (DISEMBL)
savqkrfkfpenSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRAtsmkfkdgymissgypvkeYIDSAVRHVLXRQASSIFCGYVKI
Flexible Loop (DISEMBL)
savqkrfkfpensvELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQASSIFCGYVKI
Low Complexity Region (SEG)
SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLxRQASSIFCGYVKI
Disordered region (IsUnstruct)
*************VELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQASSIFCGYV**
Disordered Region (DISOPRED)
SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVL*RQASSIFCGYVKI
Disordered Region (DISEMBL)
SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQASSIFCGYVKI
Disordered Region (DISPRO)
SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQASSIFCGYVKI
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQASSIFCGYVKI
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	120	2.2.26 [Sep-21-2011]
Q9M339	249	40S ribosomal protein S3-	yes	no	0.916	0.441	0.809	5e-46
Q9SIP7	250	40S ribosomal protein S3-	no	no	0.908	0.436	0.807	6e-46
Q9FJA6	248	40S ribosomal protein S3-	no	no	0.908	0.439	0.798	2e-45
P62909	243	40S ribosomal protein S3	yes	no	0.916	0.452	0.736	9e-41
P62908	243	40S ribosomal protein S3	yes	no	0.916	0.452	0.736	9e-41
E2RH47	243	40S ribosomal protein S3	yes	no	0.916	0.452	0.736	9e-41
Q0Z8U2	243	40S ribosomal protein S3	yes	no	0.916	0.452	0.736	9e-41
P23396	243	40S ribosomal protein S3	yes	no	0.916	0.452	0.736	9e-41
Q3T169	243	40S ribosomal protein S3	yes	no	0.916	0.452	0.736	9e-41
P47835	246	40S ribosomal protein S3-	N/A	no	0.916	0.447	0.736	1e-40

>sp|Q9M339|RS32_ARATH 40S ribosomal protein S3-2 OS=Arabidopsis thaliana GN=RPS3B PE=1 SV=1

 Score =  182 bits (463), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 89/110 (80%), Positives = 95/110 (86%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           S VQKRFKFP +SVELYAEKVNNRGLCAIAQAESLR + L  +  + ACYGVLRF+MESG
Sbjct: 71  SLVQKRFKFPVDSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQA 110
           AKGCEVIVSGKLRA RA SMKFKDGYM+SSG P KEYIDSAVRHVL RQ 
Sbjct: 131 AKGCEVIVSGKLRAARAKSMKFKDGYMVSSGQPTKEYIDSAVRHVLLRQG 180

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SIP7|RS31_ARATH 40S ribosomal protein S3-1 OS=Arabidopsis thaliana GN=RPS3A PE=1 SV=1

 Score =  182 bits (461), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 88/109 (80%), Positives = 95/109 (87%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           S VQKRFKFP +SVELYAEKVNNRGLCAIAQAESLR + L  +  + ACYGVLRF+MESG
Sbjct: 71  SLVQKRFKFPVDSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
           AKGCEVIVSGKLRA RA SMKFKDGYM+SSG P KEYID+AVRHVL RQ
Sbjct: 131 AKGCEVIVSGKLRAARAKSMKFKDGYMVSSGQPTKEYIDAAVRHVLLRQ 179

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FJA6|RS33_ARATH 40S ribosomal protein S3-3 OS=Arabidopsis thaliana GN=RPS3C PE=1 SV=1

 Score =  180 bits (457), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 87/109 (79%), Positives = 95/109 (87%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           S VQKRFKFP++SVELYAEKV NRGLCAIAQAESLR + L  +  + ACYGVLRF+MESG
Sbjct: 71  SLVQKRFKFPQDSVELYAEKVANRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
           AKGCEVIVSGKLRA RA SMKFKDGYM+SSG P KEYID+AVRHVL RQ
Sbjct: 131 AKGCEVIVSGKLRAARAKSMKFKDGYMVSSGQPTKEYIDAAVRHVLLRQ 179

Arabidopsis thaliana (taxid: 3702)

>sp|P62909|RS3_RAT 40S ribosomal protein S3 OS=Rattus norvegicus GN=Rps3 PE=1 SV=1

 Score =  165 bits (417), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 81/110 (73%), Positives = 88/110 (80%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           + VQKRF FPE SVELYAEKV  RGLCAIAQAESLR + L  +  + ACYGVLRFIMESG
Sbjct: 71  AVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQA 110
           AKGCEV+VSGKLR QRA SMKF DG MI SG PV  Y+D+AVRHVL RQ 
Sbjct: 131 AKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG 180

Rattus norvegicus (taxid: 10116)

>sp|P62908|RS3_MOUSE 40S ribosomal protein S3 OS=Mus musculus GN=Rps3 PE=1 SV=1

 Score =  165 bits (417), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 81/110 (73%), Positives = 88/110 (80%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           + VQKRF FPE SVELYAEKV  RGLCAIAQAESLR + L  +  + ACYGVLRFIMESG
Sbjct: 71  AVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQA 110
           AKGCEV+VSGKLR QRA SMKF DG MI SG PV  Y+D+AVRHVL RQ 
Sbjct: 131 AKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG 180

Mus musculus (taxid: 10090)

>sp|E2RH47|RS3_CANFA 40S ribosomal protein S3 OS=Canis familiaris GN=RPS3 PE=1 SV=1

 Score =  165 bits (417), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 81/110 (73%), Positives = 88/110 (80%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           + VQKRF FPE SVELYAEKV  RGLCAIAQAESLR + L  +  + ACYGVLRFIMESG
Sbjct: 71  AVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQA 110
           AKGCEV+VSGKLR QRA SMKF DG MI SG PV  Y+D+AVRHVL RQ 
Sbjct: 131 AKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG 180

Canis familiaris (taxid: 9615)

>sp|Q0Z8U2|RS3_PIG 40S ribosomal protein S3 OS=Sus scrofa GN=RPS3 PE=2 SV=1

 Score =  165 bits (417), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 81/110 (73%), Positives = 88/110 (80%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           + VQKRF FPE SVELYAEKV  RGLCAIAQAESLR + L  +  + ACYGVLRFIMESG
Sbjct: 71  AVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQA 110
           AKGCEV+VSGKLR QRA SMKF DG MI SG PV  Y+D+AVRHVL RQ 
Sbjct: 131 AKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG 180

Sus scrofa (taxid: 9823)

>sp|P23396|RS3_HUMAN 40S ribosomal protein S3 OS=Homo sapiens GN=RPS3 PE=1 SV=2

 Score =  165 bits (417), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 81/110 (73%), Positives = 88/110 (80%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           + VQKRF FPE SVELYAEKV  RGLCAIAQAESLR + L  +  + ACYGVLRFIMESG
Sbjct: 71  AVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQA 110
           AKGCEV+VSGKLR QRA SMKF DG MI SG PV  Y+D+AVRHVL RQ 
Sbjct: 131 AKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG 180

Homo sapiens (taxid: 9606)

>sp|Q3T169|RS3_BOVIN 40S ribosomal protein S3 OS=Bos taurus GN=RPS3 PE=2 SV=1

 Score =  165 bits (417), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 81/110 (73%), Positives = 88/110 (80%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           + VQKRF FPE SVELYAEKV  RGLCAIAQAESLR + L  +  + ACYGVLRFIMESG
Sbjct: 71  AVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQA 110
           AKGCEV+VSGKLR QRA SMKF DG MI SG PV  Y+D+AVRHVL RQ 
Sbjct: 131 AKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG 180

Bos taurus (taxid: 9913)

>sp|P47835|RS32_XENLA 40S ribosomal protein S3-B OS=Xenopus laevis GN=rps3-b PE=2 SV=1

 Score =  164 bits (416), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 81/110 (73%), Positives = 88/110 (80%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           + VQKRF FPE SVELYAEKV  RGLCAIAQAESLR + L  +  + ACYGVLRFIMESG
Sbjct: 71  AVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQA 110
           AKGCEV+VSGKLR QRA SMKF DG MI SG PV  Y+D+AVRHVL RQ 
Sbjct: 131 AKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG 180

Xenopus laevis (taxid: 8355)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	120
343887316	184	40S ribosomal protein S3 [Citrus unshiu]	0.975	0.635	0.881	2e-51
225444782	234	PREDICTED: 40S ribosomal protein S3-3 [V	0.916	0.470	0.854	2e-47
449447888	236	PREDICTED: 40S ribosomal protein S3-3-li	0.916	0.466	0.854	2e-47
359476269	235	PREDICTED: 40S ribosomal protein S3-3-li	0.916	0.468	0.845	3e-47
225442156	234	PREDICTED: 40S ribosomal protein S3-3 [V	0.916	0.470	0.845	3e-47
388494596	237	unknown [Lotus japonicus] gi|388504726|g	0.908	0.459	0.853	4e-47
357438107	239	40S ribosomal protein S3 [Medicago trunc	0.916	0.460	0.845	4e-47
356559951	236	PREDICTED: 40S ribosomal protein S3-3-li	0.908	0.461	0.853	4e-47
356534900	239	PREDICTED: 40S ribosomal protein S3-3-li	0.916	0.460	0.845	4e-47
358348478	239	40S ribosomal protein S3 [Medicago trunc	0.916	0.460	0.845	4e-47

>gi|343887316|dbj|BAK61862.1| 40S ribosomal protein S3 [Citrus unshiu]

 Score =  206 bits (523), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 104/118 (88%), Positives = 108/118 (91%), Gaps = 1/118 (0%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFI-MES 59
           SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLR + L  +  + AC GVLRFI +ES
Sbjct: 14  SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACCGVLRFIILES 73

Query: 60  GAKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQASSIFCGY 117
           GAKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVL RQASSIFCGY
Sbjct: 74  GAKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLLRQASSIFCGY 131

Source: Citrus unshiu

Species: Citrus unshiu

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225444782|ref|XP_002279950.1| PREDICTED: 40S ribosomal protein S3-3 [Vitis vinifera] gi|297738588|emb|CBI27833.3| unnamed protein product [Vitis vinifera]

 Score =  192 bits (489), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 94/110 (85%), Positives = 98/110 (89%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           S VQKRFKFPENSVELYAEKVNNRGLCA+AQAESLR + L  +  + ACYGVLRFIMESG
Sbjct: 71  SVVQKRFKFPENSVELYAEKVNNRGLCAVAQAESLRYKLLGGLAVRRACYGVLRFIMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQA 110
           AKGCEVIVSGKLRAQRA SMKFKDGYMISSG PVKEYIDSAVRHVL RQ 
Sbjct: 131 AKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVKEYIDSAVRHVLLRQG 180

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449447888|ref|XP_004141698.1| PREDICTED: 40S ribosomal protein S3-3-like [Cucumis sativus] gi|449521735|ref|XP_004167885.1| PREDICTED: 40S ribosomal protein S3-3-like [Cucumis sativus]

 Score =  192 bits (489), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 94/110 (85%), Positives = 98/110 (89%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           S VQKRFKFPENSVELYAEKVNNRGLCAIAQAESLR + L  +  + ACYGVLRF+MESG
Sbjct: 71  SVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQA 110
           AKGCEVIVSGKLRAQRA SMKFKDGYMISSG PVKEYIDSAVRHVL RQ 
Sbjct: 131 AKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVKEYIDSAVRHVLLRQG 180

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359476269|ref|XP_002281141.2| PREDICTED: 40S ribosomal protein S3-3-like [Vitis vinifera] gi|296081703|emb|CBI20708.3| unnamed protein product [Vitis vinifera]

 Score =  191 bits (486), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 93/110 (84%), Positives = 98/110 (89%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           S VQKRFKFPENSVELYAEKVNNRGLCAIAQAESLR + L  +  + ACYGVLRF+MESG
Sbjct: 71  SVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQA 110
           AKGCEVIVSGKLRAQRA SMKFKDGYMISSG PVK+YIDSAVRHVL RQ 
Sbjct: 131 AKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVKDYIDSAVRHVLLRQG 180

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225442156|ref|XP_002275541.1| PREDICTED: 40S ribosomal protein S3-3 [Vitis vinifera] gi|297743020|emb|CBI35887.3| unnamed protein product [Vitis vinifera]

 Score =  191 bits (486), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 93/110 (84%), Positives = 98/110 (89%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           S VQKRFKFPEN+VELYAEKVNNRGLCAIAQAESLR + L  +  + ACYGVLRF+MESG
Sbjct: 71  SVVQKRFKFPENTVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQA 110
           AKGCEVIVSGKLRAQRA SMKFKDGYMISSG PVKEYIDSAVRHVL RQ 
Sbjct: 131 AKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVKEYIDSAVRHVLLRQG 180

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388494596|gb|AFK35364.1| unknown [Lotus japonicus] gi|388504726|gb|AFK40429.1| unknown [Lotus japonicus]

 Score =  191 bits (486), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 93/109 (85%), Positives = 98/109 (89%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           S VQKRFKFPENSVELYAEKVNNRGLCAIAQAESLR + L  +  + ACYGVLRF+MESG
Sbjct: 71  SVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
           AKGCEVIVSGKLRAQRA SMKFKDGYMISSG PVK+YIDSAVRHVL RQ
Sbjct: 131 AKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVKDYIDSAVRHVLLRQ 179

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357438107|ref|XP_003589329.1| 40S ribosomal protein S3 [Medicago truncatula] gi|355478377|gb|AES59580.1| 40S ribosomal protein S3 [Medicago truncatula]

 Score =  191 bits (486), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 93/110 (84%), Positives = 98/110 (89%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           S VQKRFKFPENSVELYAEKVNNRGLCAIAQAESLR + L  +  + ACYGVLRF+MESG
Sbjct: 71  SVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKVLGGLAVRRACYGVLRFVMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQA 110
           AKGCEVIVSGKLRAQRA SMKFKDGYMISSG PVK+YIDSAVRHVL RQ 
Sbjct: 131 AKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVKDYIDSAVRHVLLRQG 180

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356559951|ref|XP_003548259.1| PREDICTED: 40S ribosomal protein S3-3-like [Glycine max]

 Score =  191 bits (486), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 93/109 (85%), Positives = 98/109 (89%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           S VQKRFKFPENSVELYAEKVNNRGLCAIAQAESLR + L  +  + ACYGVLRF+MESG
Sbjct: 71  SVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
           AKGCEVIVSGKLRAQRA SMKFKDGYMISSG PVK+YIDSAVRHVL RQ
Sbjct: 131 AKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVKDYIDSAVRHVLLRQ 179

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356534900|ref|XP_003535989.1| PREDICTED: 40S ribosomal protein S3-3-like [Glycine max]

 Score =  191 bits (486), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 93/110 (84%), Positives = 98/110 (89%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           S VQKRFKFPENSVELYAEKVNNRGLCAIAQAESLR + L  +  + ACYGVLRF+MESG
Sbjct: 71  SVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQA 110
           AKGCEVIVSGKLRAQRA SMKFKDGYMISSG PVK+YIDSAVRHVL RQ 
Sbjct: 131 AKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVKDYIDSAVRHVLLRQG 180

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358348478|ref|XP_003638273.1| 40S ribosomal protein S3 [Medicago truncatula] gi|355504208|gb|AES85411.1| 40S ribosomal protein S3 [Medicago truncatula]

 Score =  191 bits (486), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 93/110 (84%), Positives = 98/110 (89%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           S VQKRFKFPENSVELYAEKVNNRGLCAIAQAESLR + L  +  + ACYGVLRF+MESG
Sbjct: 71  SVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQA 110
           AKGCEVIVSGKLRAQRA SMKFKDGYMISSG PVK+YIDSAVRHVL RQ 
Sbjct: 131 AKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVKDYIDSAVRHVLLRQG 180

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	120
TAIR|locus:2084490	249	AT3G53870 [Arabidopsis thalian	0.908	0.437	0.816	5.2e-42
TAIR|locus:2065863	250	AT2G31610 [Arabidopsis thalian	0.908	0.436	0.807	1.1e-41
TAIR|locus:2169518	248	AT5G35530 [Arabidopsis thalian	0.908	0.439	0.798	2.8e-41
ASPGD|ASPL0000016707	264	AN4087 [Emericella nidulans (t	0.908	0.412	0.733	3e-37
UNIPROTKB|F1N9X5	243	RPS3 "Uncharacterized protein"	0.908	0.448	0.743	6.3e-37
UNIPROTKB|F1NPA9	211	RPS3 "Uncharacterized protein"	0.908	0.516	0.743	6.3e-37
UNIPROTKB|Q3T169	243	RPS3 "40S ribosomal protein S3	0.908	0.448	0.743	6.3e-37
UNIPROTKB|E2RH47	243	RPS3 "40S ribosomal protein S3	0.908	0.448	0.743	6.3e-37
UNIPROTKB|P23396	243	RPS3 "40S ribosomal protein S3	0.908	0.448	0.743	6.3e-37
UNIPROTKB|F1SUM7	195	RPS3 "40S ribosomal protein S3	0.908	0.558	0.743	6.3e-37

TAIR|locus:2084490 AT3G53870 [Arabidopsis thaliana (taxid:3702)]

 Score = 445 (161.7 bits), Expect = 5.2e-42, P = 5.2e-42
 Identities = 89/109 (81%), Positives = 95/109 (87%)

Query:     1 SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
             S VQKRFKFP +SVELYAEKVNNRGLCAIAQAESLR + L  +  + ACYGVLRF+MESG
Sbjct:    71 SLVQKRFKFPVDSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESG 130

Query:    61 AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
             AKGCEVIVSGKLRA RA SMKFKDGYM+SSG P KEYIDSAVRHVL RQ
Sbjct:   131 AKGCEVIVSGKLRAARAKSMKFKDGYMVSSGQPTKEYIDSAVRHVLLRQ 179

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:0015935 "small ribosomal subunit" evidence=IEA

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

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0009651 "response to salt stress" evidence=IEP

GO:0009506 "plasmodesma" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

TAIR|locus:2065863 AT2G31610 [Arabidopsis thaliana (taxid:3702)]

 Score = 442 (160.7 bits), Expect = 1.1e-41, P = 1.1e-41
 Identities = 88/109 (80%), Positives = 95/109 (87%)

Query:     1 SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
             S VQKRFKFP +SVELYAEKVNNRGLCAIAQAESLR + L  +  + ACYGVLRF+MESG
Sbjct:    71 SLVQKRFKFPVDSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESG 130

Query:    61 AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
             AKGCEVIVSGKLRA RA SMKFKDGYM+SSG P KEYID+AVRHVL RQ
Sbjct:   131 AKGCEVIVSGKLRAARAKSMKFKDGYMVSSGQPTKEYIDAAVRHVLLRQ 179

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:0015935 "small ribosomal subunit" evidence=IEA

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

GO:0009507 "chloroplast" evidence=IDA

GO:0005773 "vacuole" evidence=IDA

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0005774 "vacuolar membrane" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0009651 "response to salt stress" evidence=IEP

GO:0005829 "cytosol" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

TAIR|locus:2169518 AT5G35530 [Arabidopsis thaliana (taxid:3702)]

 Score = 438 (159.2 bits), Expect = 2.8e-41, P = 2.8e-41
 Identities = 87/109 (79%), Positives = 95/109 (87%)

Query:     1 SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
             S VQKRFKFP++SVELYAEKV NRGLCAIAQAESLR + L  +  + ACYGVLRF+MESG
Sbjct:    71 SLVQKRFKFPQDSVELYAEKVANRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESG 130

Query:    61 AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
             AKGCEVIVSGKLRA RA SMKFKDGYM+SSG P KEYID+AVRHVL RQ
Sbjct:   131 AKGCEVIVSGKLRAARAKSMKFKDGYMVSSGQPTKEYIDAAVRHVLLRQ 179

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:0015935 "small ribosomal subunit" evidence=IEA

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:0009651 "response to salt stress" evidence=IEP

GO:0005829 "cytosol" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

GO:0001510 "RNA methylation" evidence=RCA

ASPGD|ASPL0000016707 AN4087 [Emericella nidulans (taxid:162425)]

 Score = 400 (145.9 bits), Expect = 3.0e-37, P = 3.0e-37
 Identities = 80/109 (73%), Positives = 88/109 (80%)

Query:     1 SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
             S +QKRFKFPENSV LYA KV NRGL A+AQ ESLR + L  +  + ACYGVLRFIMESG
Sbjct:    72 SLIQKRFKFPENSVSLYAAKVQNRGLSAVAQCESLRYKLLNGLAVRRACYGVLRFIMESG 131

Query:    61 AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
             AKGCEV+VSGKLRA RA SMKF DG+MI SG P KE+IDSA RHVL RQ
Sbjct:   132 AKGCEVVVSGKLRAARAKSMKFTDGFMIHSGQPAKEFIDSATRHVLLRQ 180

GO:0006407 "rRNA export from nucleus" evidence=IEA

GO:0000056 "ribosomal small subunit export from nucleus" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005576 "extracellular region" evidence=IDA

GO:0030686 "90S preribosome" evidence=IEA

GO:0030688 "preribosome, small subunit precursor" evidence=IEA

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

GO:0003906 "DNA-(apurinic or apyrimidinic site) lyase activity" evidence=IEA

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

UNIPROTKB|F1N9X5 RPS3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 397 (144.8 bits), Expect = 6.3e-37, P = 6.3e-37
 Identities = 81/109 (74%), Positives = 88/109 (80%)

Query:     1 SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
             + VQKRF FPE SVELYAEKV  RGLCAIAQAESLR + L  +  + ACYGVLRFIMESG
Sbjct:    71 AVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESG 130

Query:    61 AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
             AKGCEV+VSGKLR QRA SMKF DG MI SG PV  Y+D+AVRHVL RQ
Sbjct:   131 AKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQ 179

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

GO:0006412 "translation" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0003729 "mRNA binding" evidence=IEA

GO:0003906 "DNA-(apurinic or apyrimidinic site) lyase activity" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006917 "induction of apoptosis" evidence=IEA

GO:0006919 "activation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

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

GO:0032088 "negative regulation of NF-kappaB transcription factor activity" evidence=IEA

GO:0032587 "ruffle membrane" evidence=IEA

GO:0045738 "negative regulation of DNA repair" evidence=IEA

GO:0051059 "NF-kappaB binding" evidence=IEA

UNIPROTKB|F1NPA9 RPS3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 397 (144.8 bits), Expect = 6.3e-37, P = 6.3e-37
 Identities = 81/109 (74%), Positives = 88/109 (80%)

Query:     1 SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
             + VQKRF FPE SVELYAEKV  RGLCAIAQAESLR + L  +  + ACYGVLRFIMESG
Sbjct:    61 AVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESG 120

Query:    61 AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
             AKGCEV+VSGKLR QRA SMKF DG MI SG PV  Y+D+AVRHVL RQ
Sbjct:   121 AKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQ 169

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

GO:0006412 "translation" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0003729 "mRNA binding" evidence=IEA

GO:0003906 "DNA-(apurinic or apyrimidinic site) lyase activity" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006917 "induction of apoptosis" evidence=IEA

GO:0006919 "activation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

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

GO:0032088 "negative regulation of NF-kappaB transcription factor activity" evidence=IEA

GO:0032587 "ruffle membrane" evidence=IEA

GO:0045738 "negative regulation of DNA repair" evidence=IEA

GO:0051059 "NF-kappaB binding" evidence=IEA

UNIPROTKB|Q3T169 RPS3 "40S ribosomal protein S3" [Bos taurus (taxid:9913)]

 Score = 397 (144.8 bits), Expect = 6.3e-37, P = 6.3e-37
 Identities = 81/109 (74%), Positives = 88/109 (80%)

Query:     1 SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
             + VQKRF FPE SVELYAEKV  RGLCAIAQAESLR + L  +  + ACYGVLRFIMESG
Sbjct:    71 AVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESG 130

Query:    61 AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
             AKGCEV+VSGKLR QRA SMKF DG MI SG PV  Y+D+AVRHVL RQ
Sbjct:   131 AKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQ 179

GO:0030529 "ribonucleoprotein complex" evidence=ISS

GO:0051059 "NF-kappaB binding" evidence=IEA

GO:0045738 "negative regulation of DNA repair" evidence=IEA

GO:0032587 "ruffle membrane" evidence=IEA

GO:0032088 "negative regulation of NF-kappaB transcription factor activity" evidence=IEA

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

GO:0019901 "protein kinase binding" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0006919 "activation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0006917 "induction of apoptosis" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0003906 "DNA-(apurinic or apyrimidinic site) lyase activity" evidence=IEA

GO:0003729 "mRNA binding" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|E2RH47 RPS3 "40S ribosomal protein S3" [Canis lupus familiaris (taxid:9615)]

 Score = 397 (144.8 bits), Expect = 6.3e-37, P = 6.3e-37
 Identities = 81/109 (74%), Positives = 88/109 (80%)

Query:     1 SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
             + VQKRF FPE SVELYAEKV  RGLCAIAQAESLR + L  +  + ACYGVLRFIMESG
Sbjct:    71 AVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESG 130

Query:    61 AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
             AKGCEV+VSGKLR QRA SMKF DG MI SG PV  Y+D+AVRHVL RQ
Sbjct:   131 AKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQ 179

GO:0051059 "NF-kappaB binding" evidence=IEA

GO:0045738 "negative regulation of DNA repair" evidence=IEA

GO:0032587 "ruffle membrane" evidence=IEA

GO:0032088 "negative regulation of NF-kappaB transcription factor activity" evidence=IEA

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

GO:0019901 "protein kinase binding" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0006919 "activation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0006917 "induction of apoptosis" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0003906 "DNA-(apurinic or apyrimidinic site) lyase activity" evidence=IEA

GO:0003729 "mRNA binding" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|P23396 RPS3 "40S ribosomal protein S3" [Homo sapiens (taxid:9606)]

 Score = 397 (144.8 bits), Expect = 6.3e-37, P = 6.3e-37
 Identities = 81/109 (74%), Positives = 88/109 (80%)

Query:     1 SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
             + VQKRF FPE SVELYAEKV  RGLCAIAQAESLR + L  +  + ACYGVLRFIMESG
Sbjct:    71 AVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESG 130

Query:    61 AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
             AKGCEV+VSGKLR QRA SMKF DG MI SG PV  Y+D+AVRHVL RQ
Sbjct:   131 AKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQ 179

GO:0003735 "structural constituent of ribosome" evidence=NAS;IDA

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

GO:0045738 "negative regulation of DNA repair" evidence=IMP

GO:0032088 "negative regulation of NF-kappaB transcription factor activity" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

GO:0004519 "endonuclease activity" evidence=IMP

GO:0019901 "protein kinase binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IDA

GO:0006917 "induction of apoptosis" evidence=IDA

GO:0006919 "activation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IDA

GO:0051536 "iron-sulfur cluster binding" evidence=NAS

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

GO:0006413 "translational initiation" evidence=NAS;TAS

GO:0003729 "mRNA binding" evidence=IDA

GO:0051059 "NF-kappaB binding" evidence=IPI

GO:0006974 "response to DNA damage stimulus" evidence=IEP

GO:0003684 "damaged DNA binding" evidence=IDA

GO:0003906 "DNA-(apurinic or apyrimidinic site) lyase activity" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005829 "cytosol" evidence=IDA;TAS

GO:0032587 "ruffle membrane" evidence=IDA

GO:0030529 "ribonucleoprotein complex" evidence=IDA

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" 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|F1SUM7 RPS3 "40S ribosomal protein S3" [Sus scrofa (taxid:9823)]

 Score = 397 (144.8 bits), Expect = 6.3e-37, P = 6.3e-37
 Identities = 81/109 (74%), Positives = 88/109 (80%)

Query:     1 SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
             + VQKRF FPE SVELYAEKV  RGLCAIAQAESLR + L  +  + ACYGVLRFIMESG
Sbjct:    23 AVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESG 82

Query:    61 AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
             AKGCEV+VSGKLR QRA SMKF DG MI SG PV  Y+D+AVRHVL RQ
Sbjct:    83 AKGCEVVVSGKLRGQRAKSMKFVDGVMIHSGDPVNYYVDTAVRHVLLRQ 131

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5R465	RS3_PONAB	No assigned EC number	0.7272	0.9166	0.4526	yes	no
O60128	RS3_SCHPO	No assigned EC number	0.7009	0.8916	0.4297	yes	no
E2RH47	RS3_CANFA	No assigned EC number	0.7363	0.9166	0.4526	yes	no
Q0Z8U2	RS3_PIG	No assigned EC number	0.7363	0.9166	0.4526	yes	no
P23396	RS3_HUMAN	No assigned EC number	0.7363	0.9166	0.4526	yes	no
Q3T169	RS3_BOVIN	No assigned EC number	0.7363	0.9166	0.4526	yes	no
P62909	RS3_RAT	No assigned EC number	0.7363	0.9166	0.4526	yes	no
P62908	RS3_MOUSE	No assigned EC number	0.7363	0.9166	0.4526	yes	no
Q9M339	RS32_ARATH	No assigned EC number	0.8090	0.9166	0.4417	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

Fail to connect to STRING server

---

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	120
PTZ00084	220	PTZ00084, PTZ00084, 40S ribosomal protein S3; Prov	9e-59
TIGR01008	195	TIGR01008, rpsC_E_A, ribosomal protein S3, eukaryo	1e-27
COG0092	233	COG0092, RpsC, Ribosomal protein S3 [Translation,	7e-19
PRK04191	207	PRK04191, rps3p, 30S ribosomal protein S3P; Review	3e-18
pfam00189	85	pfam00189, Ribosomal_S3_C, Ribosomal protein S3, C	3e-12
cd02413	81	cd02413, 40S_S3_KH, K homology RNA-binding (KH) do	9e-09

>gnl|CDD|240260 PTZ00084, PTZ00084, 40S ribosomal protein S3; Provisional

 Score =  179 bits (457), Expect = 9e-59
 Identities = 78/109 (71%), Positives = 91/109 (83%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           S +QKRF FPE  VEL+AE+V NRGLCA+AQAESLR + L  +  + A YGVLR +MESG
Sbjct: 71  SLLQKRFGFPEGKVELFAERVENRGLCAMAQAESLRYKLLEGLPVRRAAYGVLRHVMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
           AKGCEVIVSGKLRAQRA SMKF+DGYMIS+G P K+++DSAVRHVL RQ
Sbjct: 131 AKGCEVIVSGKLRAQRAKSMKFRDGYMISTGQPKKDFVDSAVRHVLMRQ 179

Length = 220

>gnl|CDD|130081 TIGR01008, rpsC_E_A, ribosomal protein S3, eukaryotic/archaeal type

 Score =  100 bits (250), Expect = 1e-27
 Identities = 42/107 (39%), Positives = 59/107 (55%), Gaps = 2/107 (1%)

Query: 3   VQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAK 62
           +QK+F   EN   +  E+V N  L A  QAE + +     +  + A Y  +R IME+GAK
Sbjct: 67  LQKKFG-LENPQ-IDVEEVENPELNAQVQAERIARSLERGLHFRRAAYTAVRRIMEAGAK 124

Query: 63  GCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
           G EV +SGKL  +RA + KF  GY+  SG PV+E +D      L + 
Sbjct: 125 GVEVTISGKLTGERARTEKFAAGYLKHSGEPVEELVDKGFAIALLKL 171

This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 195

>gnl|CDD|223170 COG0092, RpsC, Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]

 Score = 78.1 bits (193), Expect = 7e-19
 Identities = 25/109 (22%), Positives = 46/109 (42%), Gaps = 5/109 (4%)

Query: 2   AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGA 61
            ++K F      V++  E+V    L A   AES+ ++    +  + A    ++  M +GA
Sbjct: 79  ELEKLFGKEN--VQINIEEVKKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGA 136

Query: 62  KGCEVIVSGKLRAQR-ATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
           KG ++ VSG+L     A + K+++G +          ID          
Sbjct: 137 KGIKIQVSGRLGGAEIARTEKYREGRVPLHTLRAD--IDYGTAEAHTTY 183

Length = 233

>gnl|CDD|235247 PRK04191, rps3p, 30S ribosomal protein S3P; Reviewed

 Score = 75.7 bits (187), Expect = 3e-18
 Identities = 25/59 (42%), Positives = 36/59 (61%)

Query: 48  ACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVL 106
           A +  +R IME+GA G E+I+SGKL  +RA + KF +GY+  SG P +E +D       
Sbjct: 112 AAHSAIRRIMEAGALGVEIIISGKLTGERARTEKFTEGYIKKSGEPAEELVDRGFAIAK 170

Length = 207

>gnl|CDD|215779 pfam00189, Ribosomal_S3_C, Ribosomal protein S3, C-terminal domain

 Score = 57.1 bits (139), Expect = 3e-12
 Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 4/64 (6%)

Query: 48  ACYGVLRFI-MESGAKGCEVIVSGKLR-AQRATSMKFKDGYMISSGYPVKEYIDSAVRHV 105
           A    +R I  + GAKG ++ +SG+L  A+RA + K+K+G +    + ++  ID A    
Sbjct: 15  AIKQAIRRIMKKGGAKGIKIQISGRLNGAERARTEKYKEGRV--PLHTLRADIDYAFAEA 72

Query: 106 LXRQ 109
             + 
Sbjct: 73  KTKY 76

This family contains a central domain pfam00013, hence the amino and carboxyl terminal domains are stored separately. This is a minimal carboxyl-terminal domain. Some are much longer. Length = 85

>gnl|CDD|239096 cd02413, 40S_S3_KH, K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3

 Score = 48.4 bits (116), Expect = 9e-09
 Identities = 21/25 (84%), Positives = 21/25 (84%)

Query: 1  SAVQKRFKFPENSVELYAEKVNNRG 25
          S VQKRF FPE SVELYAEKV NRG
Sbjct: 57 SLVQKRFNFPEGSVELYAEKVANRG 81

S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 81

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	120
PTZ00084	220	40S ribosomal protein S3; Provisional	100.0
COG0092	233	RpsC Ribosomal protein S3 [Translation, ribosomal	100.0
TIGR01008	195	rpsC_E_A ribosomal protein S3, eukaryotic/archaeal	100.0
PRK04191	207	rps3p 30S ribosomal protein S3P; Reviewed	100.0
CHL00048	214	rps3 ribosomal protein S3	100.0
TIGR01009	211	rpsC_bact ribosomal protein S3, bacterial type. TI	100.0
PRK00310	232	rpsC 30S ribosomal protein S3; Reviewed	100.0
KOG3181	244	consensus 40S ribosomal protein S3 [Translation, r	100.0
PF00189	85	Ribosomal_S3_C: Ribosomal protein S3, C-terminal d	99.91

>PTZ00084 40S ribosomal protein S3; Provisional

Probab=100.00  E-value=7e-45  Score=286.42  Aligned_cols=114  Identities=68%  Similarity=1.028  Sum_probs=109.3

Q ss_pred             ccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccchhhhhhcc
Q 046473            2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMK   81 (120)
Q Consensus         2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~GerAR~e~   81 (120)
                      .|++.|++++++|+|+|.||++|++||.++|++||+|||+|++|||||+++|+++|++||+||||+|||||+|||||+||
T Consensus        72 ~L~k~~~~~~~~i~i~v~ev~~P~l~A~lvA~~IA~qLe~rv~FRRa~k~ai~~~m~aGakGikI~iSGRL~~EiARtE~  151 (220)
T PTZ00084         72 LLQKRFGFPEGKVELFAERVENRGLCAMAQAESLRYKLLEGLPVRRAAYGVLRHVMESGAKGCEVIVSGKLRAQRAKSMK  151 (220)
T ss_pred             HHHHHhCCCCceEEEEEEEecCCCcCHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHcCCceEEEEEccchhhHHHHhhH
Confidence            47889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccceeeeccchhhhhhhheeeeEeCcCCe---eEEec
Q 046473           82 FKDGYMISSGYPVKEYIDSAVRHVLXRQA---SSIFC  115 (120)
Q Consensus        82 ~~eG~vp~sG~~~~~~idy~~~~a~tk~G---v~~~~  115 (120)
                      |+||+|.|||+++++||||++.||+|+||   |+||-
T Consensus       152 ~~eGrVl~Tg~~~~~~idy~~~~a~t~yGviGVKVwI  188 (220)
T PTZ00084        152 FRDGYMISTGQPKKDFVDSAVRHVLMRQGVIGVKVKI  188 (220)
T ss_pred             hhccEEEecCchHHHheehheEEEcccCceeeEEEEE
Confidence            99999999999999999999999999886   56663

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

Probab=100.00  E-value=1.1e-44  Score=287.04  Aligned_cols=107  Identities=23%  Similarity=0.277  Sum_probs=100.5

Q ss_pred             ccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccch-hhhhhc
Q 046473            2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRA-QRATSM   80 (120)
Q Consensus         2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~G-erAR~e   80 (120)
                      .|++.|+.+  +++|+|+||++|+|||+++|++||.|||+|++|||||++||+++|++||+||||+|||||+| +|||+|
T Consensus        79 ~l~k~~g~~--~v~I~i~EV~~peL~A~lvA~~IA~qLErrv~FRRA~k~ai~~~M~aGAkGiki~vSGRL~GaeiAR~E  156 (233)
T COG0092          79 ELEKLFGKE--NVQINIEEVKKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLGGAEIARTE  156 (233)
T ss_pred             HHHHHhCCC--CceEEEEEcCCCCcCHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHcCCceeEEEEecccchHHHHhHH
Confidence            477889875  67777999999999999999999999999999999999999999999999999999999999 779999


Q ss_pred             cccceeeeccchhhhhhhheeeeEeCcCCeeE
Q 046473           81 KFKDGYMISSGYPVKEYIDSAVRHVLXRQASS  112 (120)
Q Consensus        81 ~~~eG~vp~sG~~~~~~idy~~~~a~tk~Gv~  112 (120)
                      ||+||+||||  |++++|||++++|+|+||++
T Consensus       157 ~y~eG~vplh--tlrAdIDyg~a~A~ttyGii  186 (233)
T COG0092         157 KYREGRVPLH--TLRADIDYGTAEAHTTYGVI  186 (233)
T ss_pred             HHhcceeEcc--ccceeeeeeeEEEEecCceE
Confidence            9999999996  68999999999999999764

>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type

Probab=100.00  E-value=2.8e-44  Score=278.66  Aligned_cols=112  Identities=35%  Similarity=0.498  Sum_probs=105.0

Q ss_pred             ccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccchhhhhhcc
Q 046473            2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMK   81 (120)
Q Consensus         2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~GerAR~e~   81 (120)
                      .|+++|+..  +++|+|.||++|++||.++|++||+|||+|++|||||+++|+++|++||+||||+|||||+|||||+||
T Consensus        66 ~l~k~~~~~--~~~I~v~ev~~p~l~A~lvA~~Ia~qLe~rv~fRra~k~ai~~~m~aGakGikI~iSGRL~GeiARtE~  143 (195)
T TIGR01008        66 KLQKKFGLE--NPQIDVEEVENPELNAQVQAERIARSLERGLHFRRAAYTAVRRIMEAGAKGVEVTISGKLTGERARTEK  143 (195)
T ss_pred             HHHHHhCCC--ceEEEEEEEeCCCcCHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCceEEEEEcccccchhhhhhh
Confidence            467778763  578889999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccceeeeccchhhhhhhheeeeEeCcCCe---eEEec
Q 046473           82 FKDGYMISSGYPVKEYIDSAVRHVLXRQA---SSIFC  115 (120)
Q Consensus        82 ~~eG~vp~sG~~~~~~idy~~~~a~tk~G---v~~~~  115 (120)
                      |+||+||+||||+..+||||+++|+|+||   |+||-
T Consensus       144 ~~eG~v~~sG~Pl~t~IDya~~~a~t~yGviGIKVwI  180 (195)
T TIGR01008       144 FAAGYLKHSGEPAEELVDKGFAIALLKLGVLGVKVKI  180 (195)
T ss_pred             eeccEEecCCCcchheeeeEEEEEecCCceEEEEEEE
Confidence            99999999999999999999999999997   56774

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

>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed

Probab=100.00  E-value=3.2e-44  Score=279.72  Aligned_cols=112  Identities=29%  Similarity=0.401  Sum_probs=104.4

Q ss_pred             ccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccchhhhhhcc
Q 046473            2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMK   81 (120)
Q Consensus         2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~GerAR~e~   81 (120)
                      +|++.|+..  ++.|+|.||++|++||.++|++||+|||+|++|||||+++|+++|++||+||||+|||||+|||||+||
T Consensus        68 ~Lkk~~~~~--~v~I~v~ev~~p~~~a~~vA~~ia~qLe~r~~fRra~k~~i~~~~~agakGiki~iSGrL~Ge~AR~e~  145 (207)
T PRK04191         68 ILEKKFGLE--NPQIDVKEVENPELNARVVAFRLANALERGWHFRRAAHSAIRRIMEAGALGVEIIISGKLTGERARTEK  145 (207)
T ss_pred             HHHHHhCCC--ceeEEEEEEeCCCcCHHHHHHHHHHHHHccchHHHHHHHHHHHHHHcCCeeEEEEEccccchHHHHhhh
Confidence            466677654  467779999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccceeeeccchhhhhhhheeeeEeCcCCe---eEEec
Q 046473           82 FKDGYMISSGYPVKEYIDSAVRHVLXRQA---SSIFC  115 (120)
Q Consensus        82 ~~eG~vp~sG~~~~~~idy~~~~a~tk~G---v~~~~  115 (120)
                      |+||+||+||||+..+||||+++|+|+||   |+||-
T Consensus       146 ~~eG~v~~~G~pl~tlIdya~~~a~t~~GviGIKVwI  182 (207)
T PRK04191        146 FTEGYIKKSGEPAEELVDRGFAIAKLKLGIIGVEVRI  182 (207)
T ss_pred             hhcceEeccCCcchheeeeEEEEEecCCeeEEEEEEE
Confidence            99999999999999999999999999997   56774

>CHL00048 rps3 ribosomal protein S3

Probab=100.00  E-value=7.1e-39  Score=251.00  Aligned_cols=112  Identities=14%  Similarity=0.118  Sum_probs=105.8

Q ss_pred             ccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccch-hhhhhc
Q 046473            2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRA-QRATSM   80 (120)
Q Consensus         2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~G-erAR~e   80 (120)
                      .|++.|+++++++.|+|.||++|++||.++|++||+|||+|++||||++++++++|++||+||||+|||||+| ||||+|
T Consensus        94 ~L~k~~~~~~~~i~I~v~ev~~p~~~A~~iA~~ia~~Le~r~~fRra~~~~i~~~~~~ga~GikI~iSGRL~Gae~AR~e  173 (214)
T CHL00048         94 NLQKELNSVNRKLNINITEVKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADIKGIKIQISGRLNGAEIARVE  173 (214)
T ss_pred             HHHHHhCCCCceEEEEEEEecCCCcCHHHHHHHHHHHHhcChhHHHHHHHHHHHHHHhCCcEEEEEEecccCccchheEE
Confidence            3677888888899999999999999999999999999999999999999999999999999999999999999 999999


Q ss_pred             cccceeeeccchhhhhhhheeeeEeCcCCe---eEEec
Q 046473           81 KFKDGYMISSGYPVKEYIDSAVRHVLXRQA---SSIFC  115 (120)
Q Consensus        81 ~~~eG~vp~sG~~~~~~idy~~~~a~tk~G---v~~~~  115 (120)
                      ||++|+||+  ||++++|||++++|+|+||   |+||-
T Consensus       174 ~~~~G~vpl--~tl~a~Idy~~~~a~t~~G~~GVKVwI  209 (214)
T CHL00048        174 WIREGRVPL--QTLRAKIDYCSYPARTIYGVLGIKIWI  209 (214)
T ss_pred             EEecceeEC--CcchhheEEEEEEEecCCceEEEEEEE
Confidence            999999998  4899999999999999986   56774

>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type

Probab=100.00  E-value=4.6e-37  Score=240.22  Aligned_cols=109  Identities=22%  Similarity=0.257  Sum_probs=101.1

Q ss_pred             ccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccch-hhhhhc
Q 046473            2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRA-QRATSM   80 (120)
Q Consensus         2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~G-erAR~e   80 (120)
                      .|+++|+   +++.|+|.+|++|++||.++|++||+|||+|++|||+++++++++|++||+||||+|||||+| ||||+|
T Consensus        90 ~l~~~~~---~~~~i~v~~v~~p~~~a~~iA~~ia~~Le~~~~fRr~~~~~i~~~~~~g~~GikI~isGRl~g~e~Ar~e  166 (211)
T TIGR01009        90 DLQKLTG---KEVQINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGAKGIKVQVSGRLGGAEIARTE  166 (211)
T ss_pred             HHHHHhC---CceEEEEEEecCCCcCHHHHHHHHHHHHHccccHHHHHHHHHHHHHhcCCcEEEEEEecccCchhhhhee
Confidence            3566775   468888999999999999999999999999999999999999999999999999999999999 999999


Q ss_pred             cccceeeeccchhhhhhhheeeeEeCcCCe---eEEec
Q 046473           81 KFKDGYMISSGYPVKEYIDSAVRHVLXRQA---SSIFC  115 (120)
Q Consensus        81 ~~~eG~vp~sG~~~~~~idy~~~~a~tk~G---v~~~~  115 (120)
                      ||++|+||++  |++++|||++++|+|+||   |+||-
T Consensus       167 ~~~~G~vpl~--t~~~~Idy~~~~a~T~~G~~GvKVwI  202 (211)
T TIGR01009       167 WYKEGRVPLH--TLRADIDYATAEAHTTYGIIGVKVWI  202 (211)
T ss_pred             eeeeCccCcc--cchhhcEEEEEEEEcCCceEEEEEEE
Confidence            9999999984  799999999999999987   56664

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

>PRK00310 rpsC 30S ribosomal protein S3; Reviewed

Probab=100.00  E-value=1.6e-36  Score=240.17  Aligned_cols=109  Identities=21%  Similarity=0.243  Sum_probs=101.0

Q ss_pred             ccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccch-hhhhhc
Q 046473            2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRA-QRATSM   80 (120)
Q Consensus         2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~G-erAR~e   80 (120)
                      .|++.|+   ++++|+|.||++|++||.++|++||+|||+|++|||+++++|+++|++||+||+|+|||||+| ||||+|
T Consensus        90 ~L~~~~~---~~~~i~v~ev~~p~~~a~~iA~~ia~~Le~r~~fRr~~~~~i~~~~~~g~~GikI~isGRl~g~e~Ar~e  166 (232)
T PRK00310         90 ELEKLTG---KPVQINIVEVKKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKVQVSGRLGGAEIARTE  166 (232)
T ss_pred             HHHHHhC---CceEEEEEEecCCCcCHHHHHHHHHHHHHccchHHHHHHHHHHHHHHcCCcEEEEEEcCCCCcceeeeEE
Confidence            3566665   478888999999999999999999999999999999999999999999999999999999999 999999


Q ss_pred             cccceeeeccchhhhhhhheeeeEeCcCCe---eEEec
Q 046473           81 KFKDGYMISSGYPVKEYIDSAVRHVLXRQA---SSIFC  115 (120)
Q Consensus        81 ~~~eG~vp~sG~~~~~~idy~~~~a~tk~G---v~~~~  115 (120)
                      ||++|+||++  |++++|||++++|+|+||   |+||-
T Consensus       167 ~~~~G~vpl~--t~~~~Idy~~~~a~T~~Gv~GVKVwI  202 (232)
T PRK00310        167 WYREGRVPLH--TLRADIDYGTAEAHTTYGIIGVKVWI  202 (232)
T ss_pred             Eeeecccccc--eeeeeeEEEEEEEecCCceEEEEEEE
Confidence            9999999984  799999999999999986   56663

>KOG3181 consensus 40S ribosomal protein S3 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=9.8e-34  Score=221.25  Aligned_cols=112  Identities=77%  Similarity=1.123  Sum_probs=110.0

Q ss_pred             CccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccchhhhhhc
Q 046473            1 SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSM   80 (120)
Q Consensus         1 ~~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~GerAR~e   80 (120)
                      +++||||++++..|++++++|.+.+|||..+||+|+++|..+.++|||++.+++.+|++|||||+|++||||+|+||+++
T Consensus        71 ~lvqkRf~f~~~svelyaEkV~~rGLcAiaQaeslryKllgGlavRRA~ygvlr~vmesgAkGceviVSGKLrgqRAKsm  150 (244)
T KOG3181|consen   71 SLVQKRFKFPEGSVELYAEKVANRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESGAKGCEVIVSGKLRGQRAKSM  150 (244)
T ss_pred             HHHHHhcCCCCCcEEEehhhhhccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHccCCccEEEEeccchhhhhhcc
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccceeeeccchhhhhhhheeeeEeCcCCeeE
Q 046473           81 KFKDGYMISSGYPVKEYIDSAVRHVLXRQASS  112 (120)
Q Consensus        81 ~~~eG~vp~sG~~~~~~idy~~~~a~tk~Gv~  112 (120)
                      ||.+|.|.|||||..+|||.|++|++++|||+
T Consensus       151 KF~DG~mIhSG~pv~dyi~ta~rhVllrQGVl  182 (244)
T KOG3181|consen  151 KFVDGLMIHSGQPVKDYIDTAVRHVLLRQGVL  182 (244)
T ss_pred             ccccceEEecCCcHHHHHHHHHHhhhhhccee
Confidence            99999999999999999999999999999986

>PF00189 Ribosomal_S3_C: Ribosomal protein S3, C-terminal domain; InterPro: IPR001351 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.91  E-value=7.9e-25  Score=149.16  Aligned_cols=77  Identities=27%  Similarity=0.348  Sum_probs=72.8

Q ss_pred             HHHHHhhhhhHHHHHHHHHHHHH-HHhCCceeEEEEecccch-hhhhhccccceeeeccchhhhhhhheeeeEeCcCCee
Q 046473           34 SLRKEGLAVIVCKMACYGVLRFI-MESGAKGCEVIVSGKLRA-QRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQAS  111 (120)
Q Consensus        34 ~ia~qLe~r~~fRra~~~ai~~~-m~aGAkGikI~ISGrL~G-erAR~e~~~eG~vp~sG~~~~~~idy~~~~a~tk~Gv  111 (120)
                      +|+++||++.+|||+++.+++.+ |++|++||+|++||||+| +|||+|+|.+|.+|+  +++.++|||++.+++|++|+
T Consensus         1 ~i~~~l~k~~~~r~~i~~~~~~i~~~~~~~GikI~isGRl~g~~rar~~~~~~G~i~~--~~~~~~Idy~~~~~~tk~G~   78 (85)
T PF00189_consen    1 FIAQKLEKRISFRRIIKKIIRRIMMNKGIKGIKIQISGRLNGAERARTEKFKKGKISL--QTFKSNIDYASSHAKTKYGV   78 (85)
T ss_dssp             HHHHHHHTTSTHHHHHHHHHHHHHHCTTSSEEEEEEESSGGGTSSSEEEEEEEESSSS--SSSTTEEEEEEEEEEESSSE
T ss_pred             ChHHHHhcCcHHHHHHHHHHHHHHhhcccceEEEEEeecCCCCccceEEEEECCCCcc--ccceeeeeEEEEEEEcCCee
Confidence            58999999999999999999999 788999999999999999 999999999999976  68999999999999999875


Q ss_pred             E
Q 046473          112 S  112 (120)
Q Consensus       112 ~  112 (120)
                      .
T Consensus        79 ~   79 (85)
T PF00189_consen   79 I   79 (85)
T ss_dssp             E
T ss_pred             E
Confidence            3

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 [, ]. Ribosomal protein S3 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S3 is known to be involved in the binding of initiator Met-tRNA. This family of ribosomal proteins includes S3 from bacteria, algae and plant chloroplast, cyanelle, archaebacteria, plant mitochondria, vertebrates, insects, Caenorhabditis elegans and yeast []. This entry is the C-terminal domain.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_C 2XZM_C 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	120
3iz6_B	227	Localization Of The Small Subunit Ribosomal Protein		1e-45
2zkq_c	243	Structure Of A Mammalian Ribosomal 40s Subunit With		7e-42
3izb_B	240	Localization Of The Small Subunit Ribosomal Protein		2e-34
1s1h_C	192	Structure Of The Ribosomal 80s-Eef2-Sordarin Comple		2e-34
3jyv_C	188	Structure Of The 40s Rrna And Proteins And PE TRNA		2e-34
3zey_X	214	High-resolution Cryo-electron Microscopy Structure		6e-28
2xzm_C	243	Crystal Structure Of The Eukaryotic 40s Ribosomal S		5e-26
3j20_C	210	Promiscuous Behavior Of Proteins In Archaeal Riboso		5e-05
1wh9_A	92	Solution Structure Of The Kh Domain Of Human Riboso		6e-05

>pdb|3IZ6|B Chain B, Localization Of The Small Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 227

Iteration: 1
 Score =  177 bits (449), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 88/110 (80%), Positives = 93/110 (84%)
Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           S VQKRF F EN VELYAEKV NRGLCAIAQAESLR + L  +  + ACYGVLRF+MESG
Sbjct: 71  SVVQKRFNFLENGVELYAEKVVNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESG 130
Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQA 110
           AKGCEVIVSGKLRAQRA SMKFKDGYMISSG PV EYID+AVRHVL RQ 
Sbjct: 131 AKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDAAVRHVLLRQG 180

>pdb|2ZKQ|CC Chain c, Structure Of A Mammalian Ribosomal 40s Subunit Within An 80s Complex Obtained By Docking Homology Models Of The Rna And Proteins Into An 8.7 A Cryo-Em Map Length = 243

Iteration: 1
 Score =  165 bits (417), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 81/110 (73%), Positives = 88/110 (80%)
Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           + VQKRF FPE SVELYAEKV  RGLCAIAQAESLR + L  +  + ACYGVLRFIMESG
Sbjct: 71  AVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESG 130
Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQA 110
           AKGCEV+VSGKLR QRA SMKF DG MI SG PV  Y+D+AVRHVL RQ 
Sbjct: 131 AKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG 180

>pdb|3IZB|B Chain B, Localization Of The Small Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 240

Iteration: 1
 Score =  140 bits (353), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 64/107 (59%), Positives = 85/107 (79%)
Query: 3   VQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAK 62
           VQKRFK+   ++ LYAE+V +RGL A+AQAES++ + L  +  + A YGV+R++MESGAK
Sbjct: 73  VQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVVRYVMESGAK 132
Query: 63  GCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
           GCEV+VSGKLRA RA +MKF DG++I SG PV ++ID+A RHVL RQ
Sbjct: 133 GCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQ 179

>pdb|1S1H|C Chain C, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From Yeast Obtained By Docking Atomic Models For Rna And Protein Components Into A 11.7 A Cryo-Em Map. This File, 1s1h, Contains 40s Subunit. The 60s Ribosomal Subunit Is In File 1s1i Length = 192

Iteration: 1
 Score =  140 bits (353), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 64/107 (59%), Positives = 85/107 (79%)
Query: 3   VQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAK 62
           VQKRFK+   ++ LYAE+V +RGL A+AQAES++ + L  +  + A YGV+R++MESGAK
Sbjct: 72  VQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVVRYVMESGAK 131
Query: 63  GCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
           GCEV+VSGKLRA RA +MKF DG++I SG PV ++ID+A RHVL RQ
Sbjct: 132 GCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQ 178

>pdb|3JYV|C Chain C, Structure Of The 40s Rrna And Proteins And PE TRNA FOR EUKARYOTIC Ribosome Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome At 8.9a Resolution Length = 188

Iteration: 1
 Score =  140 bits (353), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 64/107 (59%), Positives = 85/107 (79%)
Query: 3   VQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAK 62
           VQKRFK+   ++ LYAE+V +RGL A+AQAES++ + L  +  + A YGV+R++MESGAK
Sbjct: 68  VQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVVRYVMESGAK 127
Query: 63  GCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
           GCEV+VSGKLRA RA +MKF DG++I SG PV ++ID+A RHVL RQ
Sbjct: 128 GCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQ 174

>pdb|3ZEY|X Chain X, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 214

Iteration: 1
 Score =  119 bits (297), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 53/102 (51%), Positives = 76/102 (74%)
Query: 3   VQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAK 62
           +Q+RF + E  ++L+AE+V  RGL A+AQAESLR + L+ +  + A  G++R++MESGAK
Sbjct: 72  LQQRFNYKEGKLQLFAERVEVRGLSAMAQAESLRFKLLSNLQVRRAAMGIIRYVMESGAK 131
Query: 63  GCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRH 104
           GCEV + GK++ QRA SM F+DGYMI SG   K ++D+A RH
Sbjct: 132 GCEVTIGGKIKGQRAKSMTFRDGYMIKSGTAHKHFVDTATRH 173

>pdb|2XZM|C Chain C, 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 = 243

Iteration: 1
 Score =  112 bits (280), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 48/108 (44%), Positives = 77/108 (71%)
Query: 3   VQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAK 62
           +QKRF + ++ ++++AE +  +GLCA AQ E++  + L  +  ++A   +++ +++ GAK
Sbjct: 76  LQKRFGYSDDQIQIWAEPIKFKGLCASAQVEAMNYKLLKDVPVRLAANYIIKSVIQDGAK 135
Query: 63  GCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQA 110
           GCE+I+SGKL+ QRA +MKFK GYMI +G P  +YID AVRHV  +Q 
Sbjct: 136 GCEIIISGKLKQQRAKTMKFKQGYMICTGQPKNDYIDVAVRHVFFKQG 183

>pdb|3J20|C Chain C, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (30s Ribosomal Subunit) Length = 210

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 19/53 (35%), Positives = 30/53 (56%)
Query: 56  IMESGAKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXR 108
           IM +GA+G E+ +SGKL  +RA S++F  GY+   G P +  +       L +
Sbjct: 120 IMNNGARGVEIRLSGKLTGERAKSIRFYQGYLAKVGNPAETLVSKGYAQALLK 172

>pdb|1WH9|A Chain A, Solution Structure Of The Kh Domain Of Human Ribosomal Protein S3 Length = 92

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 19/23 (82%), Positives = 19/23 (82%)
Query: 3  VQKRFKFPENSVELYAEKVNNRG 25
          VQKRF FPE SVELYAEKV  RG
Sbjct: 64 VQKRFGFPEGSVELYAEKVATRG 86

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	120
2xzm_C	243	KH domain containing protein; ribosome, translatio	4e-40
3u5c_D	240	RP13, YS3, 40S ribosomal protein S3; translation,	2e-35
2zkq_c	243	40S ribosomal protein S3E; protein-RNA complex, 40	2e-34
3iz6_B	227	40S ribosomal protein S3 (S3P); eukaryotic ribosom	4e-34
1wh9_A	92	40S ribosomal protein S3; KH domain, structural ge	7e-09

>2xzm_C KH domain containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_C Length = 243

 Score =  132 bits (335), Expect = 4e-40
 Identities = 48/109 (44%), Positives = 77/109 (70%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
             +QKRF + ++ ++++AE +  +GLCA AQ E++  + L  +  ++A   +++ +++ G
Sbjct: 74  QFLQKRFGYSDDQIQIWAEPIKFKGLCASAQVEAMNYKLLKDVPVRLAANYIIKSVIQDG 133

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
           AKGCE+I+SGKL+ QRA +MKFK GYMI +G P  +YID AVRHV  +Q
Sbjct: 134 AKGCEIIISGKLKQQRAKTMKFKQGYMICTGQPKNDYIDVAVRHVFFKQ 182

>3u5c_D RP13, YS3, 40S ribosomal protein S3; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_B 3o30_C 3o2z_C 3u5g_D 1s1h_C 3jyv_C* Length = 240

 Score =  120 bits (303), Expect = 2e-35
 Identities = 64/109 (58%), Positives = 85/109 (77%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
             VQKRFK+   ++ LYAE+V +RGL A+AQAES++ + L  +  + A YGV+R++MESG
Sbjct: 71  LLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVVRYVMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
           AKGCEV+VSGKLRA RA +MKF DG++I SG PV ++ID+A RHVL RQ
Sbjct: 131 AKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQ 179

>2zkq_c 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 243

 Score =  117 bits (296), Expect = 2e-34
 Identities = 81/109 (74%), Positives = 88/109 (80%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           + VQKRF FPE SVELYAEKV  RGLCAIAQAESLR + L  +  + ACYGVLRFIMESG
Sbjct: 71  AVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
           AKGCEV+VSGKLR QRA SMKF DG MI SG PV  Y+D+AVRHVL RQ
Sbjct: 131 AKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQ 179

>3iz6_B 40S ribosomal protein S3 (S3P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} PDB: 1s1h_C 3jyv_C* Length = 227

 Score =  117 bits (294), Expect = 4e-34
 Identities = 88/109 (80%), Positives = 93/109 (85%)

Query: 1   SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
           S VQKRF F EN VELYAEKV NRGLCAIAQAESLR + L  +  + ACYGVLRF+MESG
Sbjct: 71  SVVQKRFNFLENGVELYAEKVVNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESG 130

Query: 61  AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
           AKGCEVIVSGKLRAQRA SMKFKDGYMISSG PV EYID+AVRHVL RQ
Sbjct: 131 AKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDAAVRHVLLRQ 179

>1wh9_A 40S ribosomal protein S3; KH domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, ribosome; NMR {Homo sapiens} SCOP: d.52.3.1 Length = 92

 Score = 48.3 bits (115), Expect = 7e-09
 Identities = 19/30 (63%), Positives = 21/30 (70%)

Query: 1  SAVQKRFKFPENSVELYAEKVNNRGLCAIA 30
          + VQKRF FPE SVELYAEKV  RG    +
Sbjct: 62 AVVQKRFGFPEGSVELYAEKVATRGSGPSS 91

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	120
3u5c_D	240	RP13, YS3, 40S ribosomal protein S3; translation,	100.0
3iz6_B	227	40S ribosomal protein S3 (S3P); eukaryotic ribosom	100.0
3j20_C	210	30S ribosomal protein S3P; archaea, archaeal, KINK	100.0
2zkq_c	243	40S ribosomal protein S3E; protein-RNA complex, 40	100.0
2xzm_C	243	KH domain containing protein; ribosome, translatio	100.0
3bbn_C	218	Ribosomal protein S3; small ribosomal subunit, spi	100.0
3r8n_C	206	30S ribosomal protein S3; protein biosynthesis, RN	100.0
3i1m_C	233	30S ribosomal protein S3; ribosome structure, prot	100.0
2vqe_C	239	30S ribosomal protein S3; tRNA-binding, rRNA-bindi	100.0
1wh9_A	92	40S ribosomal protein S3; KH domain, structural ge	97.27

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

Probab=100.00  E-value=1.5e-45  Score=292.15  Aligned_cols=114  Identities=56%  Similarity=0.920  Sum_probs=110.0

Q ss_pred             ccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccchhhhhhcc
Q 046473            2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMK   81 (120)
Q Consensus         2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~GerAR~e~   81 (120)
                      .|+++|++++++|+|+++||++|++||+++|++||+|||+|++|||||+++|+++|++||+||||+|||||+|+|||+||
T Consensus        72 ~l~k~~~~~~~~v~I~i~eV~~p~l~A~lvAe~IA~qLe~rv~FRRA~k~ai~~am~aGakGikI~iSGRL~Ga~ARtE~  151 (240)
T 3u5c_D           72 LVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVVRYVMESGAKGCEVVVSGKLRAARAKAMK  151 (240)
T ss_dssp             HHHHHHTCCTTSSEEEEECCSCGGGCHHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHTTCSEEEEEEEECSSSSSCEEEE
T ss_pred             HHHHHhCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCCceeEEEEecccCCceeeEEe
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccceeeeccchhhhhhhheeeeEeCcCCee---EEec
Q 046473           82 FKDGYMISSGYPVKEYIDSAVRHVLXRQAS---SIFC  115 (120)
Q Consensus        82 ~~eG~vp~sG~~~~~~idy~~~~a~tk~Gv---~~~~  115 (120)
                      |++|+|+|||||++++||||+++|+|+||+   +||-
T Consensus       152 ~~eG~vlhTgqtlra~IDYa~~~a~T~yGviGVKVWI  188 (240)
T 3u5c_D          152 FADGFLIHSGQPVNDFIDTATRHVLMRQGVLGIKVKI  188 (240)
T ss_dssp             EEEECCCCSSHHHHHHEEEEEEEEECSSCEEEEEEEE
T ss_pred             eecCeeccCCChhhheeeEEEEEEEcCCeeEEEEEEE
Confidence            999999999999999999999999999985   4774

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

Probab=100.00  E-value=7.7e-46  Score=291.88  Aligned_cols=110  Identities=79%  Similarity=1.154  Sum_probs=107.5

Q ss_pred             ccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccchhhhhhcc
Q 046473            2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMK   81 (120)
Q Consensus         2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~GerAR~e~   81 (120)
                      .|+++|++++++++|+++||++|++||+++|++||+|||+|++|||||+++++++|++||+||||+|||||+|+|||+||
T Consensus        72 ~l~k~~~~~~~~v~I~i~eV~~p~l~A~lvAe~Ia~qLe~rv~fRrA~k~ai~~~m~aGakGikI~iSGRL~GaiARtE~  151 (227)
T 3iz6_B           72 VVQKRFNFLENGVELYAEKVVNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESGAKGCEVIVSGKLRAQRAKSMK  151 (227)
T ss_dssp             HHHHHHCCCSCCCCCEEECCSSSTTSCSHHHHHHHTTTTTCCCHHHHHHHHHHTTTTTCCSEEECCBCSCGGGSSCCCBC
T ss_pred             HHHHHhCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHcCCceEEEEEecccCCceeeEee
Confidence            47889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccceeeeccchhhhhhhheeeeEeCcCCee
Q 046473           82 FKDGYMISSGYPVKEYIDSAVRHVLXRQAS  111 (120)
Q Consensus        82 ~~eG~vp~sG~~~~~~idy~~~~a~tk~Gv  111 (120)
                      |+||+|||||||++++||||+++|+|+||+
T Consensus       152 ~~eG~vlhTlqtlra~IDya~~~a~T~yGv  181 (227)
T 3iz6_B          152 FKDGYMISSGQPVNEYIDAAVRHVLLRQGV  181 (227)
T ss_dssp             CEEECCCSSSSCTTSCEEECCCCCBCSSSB
T ss_pred             eeCCeecccCChhhheeeEEEEEEEcCCee
Confidence            999999999999999999999999999885

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

Probab=100.00  E-value=8.7e-44  Score=277.49  Aligned_cols=112  Identities=29%  Similarity=0.458  Sum_probs=103.4

Q ss_pred             ccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccchhhhhhcc
Q 046473            2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMK   81 (120)
Q Consensus         2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~GerAR~e~   81 (120)
                      .|+++|++++  ++|+++||++|++||+++|++||+|||+|++|||||+++++++|++||+||+|+|||||+|||||+||
T Consensus        68 ~l~k~~~~~~--v~I~i~eV~~p~l~A~lvAe~Ia~qLe~rv~fRra~k~ai~~~m~~GakGikI~iSGRL~GeiARtE~  145 (210)
T 3j20_C           68 ILEKQFGLEN--PQIEVEEIKNPYLNAKVQAVRLAQALERGIHFRRAAYAALRAIMNNGARGVEIRLSGKLTGERAKSIR  145 (210)
T ss_dssp             HHHHHSSCSS--CEEEEEECSCTTTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSEEEEEEEECTTTTSCEEEE
T ss_pred             HHHHHhCCCc--eEEEEEEecCCccCHHHHHHHHHHHHhhcccHHHHHHHHHHHHHhcCCceEEEEEecccCcceeeEEe
Confidence            4788898744  66778999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccceeeeccchhhhhhhheeeeEeCcCCe---eEEec
Q 046473           82 FKDGYMISSGYPVKEYIDSAVRHVLXRQA---SSIFC  115 (120)
Q Consensus        82 ~~eG~vp~sG~~~~~~idy~~~~a~tk~G---v~~~~  115 (120)
                      |++|+||++|.+.+++||||+++|+|+||   |+||-
T Consensus       146 ~~eG~vpl~tl~a~~~IDya~~~a~T~yGviGVKVwI  182 (210)
T 3j20_C          146 FYQGYLAKVGNPAETLVSKGYAQALLKLGVIGVKVAI  182 (210)
T ss_dssp             EEEECCCCSSSHHHHHSEEEEEEEECSSCEEEEEEEE
T ss_pred             eecceeeccCCcchhcEEEEEEEEEcCCcEEEEEEEE
Confidence            99999999876677799999999999998   56763

>2zkq_c 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}

Probab=100.00  E-value=1e-43  Score=282.06  Aligned_cols=114  Identities=71%  Similarity=1.052  Sum_probs=108.6

Q ss_pred             ccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccchhhhhhcc
Q 046473            2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMK   81 (120)
Q Consensus         2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~GerAR~e~   81 (120)
                      .|+++|++.+++++|+++||++|++||+++|++||+|||+|++|||||+++|+++|++||+||||+|||||+|+|||+||
T Consensus        72 ~L~k~~~~~~~~v~I~i~eV~~p~l~A~lvAe~IA~qLe~rv~FRRa~k~ai~~am~aGakGikI~iSGRL~GaiARtE~  151 (243)
T 2zkq_c           72 VVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKLRGQRAKSMK  151 (243)
T ss_dssp             HHHHHSCTTTCCCCCEEEECSCGGGCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHSSCSEEEEEECSSGGGSSCCCBC
T ss_pred             HHHHHhCcCCceEEEEEEEecCcccCHHHHHHHHHHHHHcchhHHHHHHHHHHHHHhcCCceEEEEEecchhhHhhhhhh
Confidence            47889999899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccceeeeccchhhhhhhheeeeEeCcCCee---EEec
Q 046473           82 FKDGYMISSGYPVKEYIDSAVRHVLXRQAS---SIFC  115 (120)
Q Consensus        82 ~~eG~vp~sG~~~~~~idy~~~~a~tk~Gv---~~~~  115 (120)
                      |+||+|.|||+|++++||||+++|+|+||+   +||-
T Consensus       152 ~~eG~vLhTg~plra~IDYa~~~a~T~yGvlGVKVWI  188 (243)
T 2zkq_c          152 FVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKI  188 (243)
T ss_dssp             CEEESSHHHHSSTTCCEEEEEECCCCSSCCCCEEEEE
T ss_pred             hcCcEEeecCchhhhceeEEEEEEEcCCceEEEEEEE
Confidence            999999888888999999999999998864   6664

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

Probab=100.00  E-value=3.9e-43  Score=278.74  Aligned_cols=114  Identities=42%  Similarity=0.783  Sum_probs=108.8

Q ss_pred             ccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccchhhhhhcc
Q 046473            2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMK   81 (120)
Q Consensus         2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~GerAR~e~   81 (120)
                      .|+++|++.+++++|+++||++|++||+++|++||+|||+|++|||||+++|+++|++||+||||+|||||+|+|||+||
T Consensus        75 ~L~k~~~~~~~~v~I~i~eV~~p~l~A~lvAe~IA~qLe~Rv~FRRA~k~ai~~am~aGakGIkI~iSGRL~GaiARtE~  154 (243)
T 2xzm_C           75 FLQKRFGYSDDQIQIWAEPIKFKGLCASAQVEAMNYKLLKDVPVRLAANYIIKSVIQDGAKGCEIIISGKLKQQRAKTMK  154 (243)
T ss_dssp             HHHHHHCCTTTTSEEEEEECSCGGGCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTCSEEEEEEEECTTSSSCEEEE
T ss_pred             HHHHHhCcCCceEEEEEEEecCcccCHHHHHHHHHHHHHccchHHHHHHHHHHHHHhcCCceEEEEEeCCccchhheeee
Confidence            47889999899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccceeeeccchhhhhhhheeeeEeCcCCee---EEec
Q 046473           82 FKDGYMISSGYPVKEYIDSAVRHVLXRQAS---SIFC  115 (120)
Q Consensus        82 ~~eG~vp~sG~~~~~~idy~~~~a~tk~Gv---~~~~  115 (120)
                      |+||+|.|||+|++++||||+++|+|+||+   +||-
T Consensus       155 ~~eG~vL~T~rplra~IDYa~~~a~T~yGvlGVKVWI  191 (243)
T 2xzm_C          155 FKQGYMICTGQPKNDYIDVAVRHVFFKQGIMGVKVKI  191 (243)
T ss_dssp             EEEECCCCSSSHHHHSEEEEEEEEECSSSEEEEEEEE
T ss_pred             eeCCeEeecCcchhhheEEEEEEEEcCCceEEEEEEE
Confidence            999999999999999999999999999875   5664

>3bbn_C Ribosomal protein S3; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=100.00  E-value=6.8e-43  Score=273.30  Aligned_cols=112  Identities=13%  Similarity=0.146  Sum_probs=105.8

Q ss_pred             ccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccch-hhhhhc
Q 046473            2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRA-QRATSM   80 (120)
Q Consensus         2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~G-erAR~e   80 (120)
                      .|++.|++.+++++|+++||++|++||+++|++||+|||+|++|||||+++++++|++||+||||+|||||+| ||||+|
T Consensus        98 ~l~k~~~~~~~~v~i~i~ev~~p~l~A~lvAe~Ia~qLe~r~~fRra~k~ai~~~m~~gakGikI~iSGRL~Gae~AR~e  177 (218)
T 3bbn_C           98 NVQKELNCVNRKLNIAITRIAKPYGDPNILAEFIAGQLKSRVSFRKAMKKAIELTEQADTKGIQIQIAGRIDGKEIARIE  177 (218)
T ss_dssp             HHHHHSCSSCCCCCCCEEECSCTTTSHHHHHHHSTTTTTTTCCHHHHHTHHHHHHHTTCCSEEEEECCSCCTTCSSCCCC
T ss_pred             HHHHHhccCCceEEEEEEEecCCCcCHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHhCCCeEEEEEccCcchhhheeEE
Confidence            3677888778889999999999999999999999999999999999999999999999999999999999999 999999


Q ss_pred             cccceeeeccchhhhhhhheeeeEeCcCCe---eEEec
Q 046473           81 KFKDGYMISSGYPVKEYIDSAVRHVLXRQA---SSIFC  115 (120)
Q Consensus        81 ~~~eG~vp~sG~~~~~~idy~~~~a~tk~G---v~~~~  115 (120)
                      ||+||+||+  ||++++||||+++|+|+||   |+||-
T Consensus       178 ~~~eG~vpl--~tlra~IDy~~~~a~T~yGviGVKVWI  213 (218)
T 3bbn_C          178 WIREGRVPL--QTIRAKIDYCAYTVRTIYGVLGIKIWI  213 (218)
T ss_dssp             EEEEECCCS--SCSTTCCBCCEEECCCSSCCCEEEEEE
T ss_pred             eEecccccC--CccccceEEEEEEEEcCCeeEEEEEEE
Confidence            999999999  5999999999999999887   56774

>3i1m_C 30S ribosomal protein S3; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_C* 3e1a_O 3e1c_O 1vs5_C 3i1o_C 3i1q_C 3i1s_C 3i1z_C 3i21_C 3izv_G* 3izw_G* 3kc4_C 3or9_C 3ora_C 3sfs_C* 3uoq_C* 4gaq_C* 4gas_C* 2qal_C* 1p6g_C ...

Probab=100.00  E-value=8.7e-42  Score=269.64  Aligned_cols=109  Identities=19%  Similarity=0.211  Sum_probs=101.6

Q ss_pred             ccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccch-hhhhhc
Q 046473            2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRA-QRATSM   80 (120)
Q Consensus         2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~G-erAR~e   80 (120)
                      .|+++|+.   +++|+|+||++|++||+++|++||+|||+|++|||||+++|+++|++||+||||+|||||+| ||||+|
T Consensus        90 ~L~k~~~~---~v~I~i~eV~~p~l~A~lvAe~IA~qLe~rv~FRramk~ai~~am~aGakGikI~iSGRL~GaeiARtE  166 (233)
T 3i1m_C           90 VVADIAGV---PAQINIAEVRKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTE  166 (233)
T ss_dssp             HHHHHHTS---CBCCEEEECSSGGGCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHTTCCSEEEEEEESSTTSCSSCCCC
T ss_pred             HHHHHHCC---ceEEEEEeecCCCcCHHHHHHHHHHHHHccccHHHHHHHHHHhhhhcCCceEEEEEccccCCCcceeEE
Confidence            46778875   37888999999999999999999999999999999999999999999999999999999999 899999


Q ss_pred             cccceeeeccchhhhhhhheeeeEeCcCCe---eEEec
Q 046473           81 KFKDGYMISSGYPVKEYIDSAVRHVLXRQA---SSIFC  115 (120)
Q Consensus        81 ~~~eG~vp~sG~~~~~~idy~~~~a~tk~G---v~~~~  115 (120)
                      ||++|+||++  |++++||||+++|+|+||   |+||-
T Consensus       167 ~~~eG~vPL~--Tlra~IDY~~~~a~T~yGviGVKVWI  202 (233)
T 3i1m_C          167 WYREGRVPLH--TLRADIDYNTSEAHTTYGVIGVKVWI  202 (233)
T ss_dssp             BCCEECCCTT--CSSSEEEEEEECCEETTEECEEEEEE
T ss_pred             EEecCeeecc--ccccccEEEEEEEEcCCeeEEEEEEE
Confidence            9999999984  799999999999999987   56773

>2vqe_C 30S ribosomal protein S3; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} PDB: 1gix_F* 1hnw_C* 1hnx_C* 1hnz_C* 1hr0_C 1ibk_C* 1ibl_C* 1ibm_C 1j5e_C 1jgo_F* 1jgp_F* 1jgq_F* 1ml5_F* 1n32_C* 1n33_C* 1n34_C 1n36_C 1xmo_C* 1xmq_C* 1xnq_C* ...

Probab=100.00  E-value=7.4e-41  Score=265.09  Aligned_cols=108  Identities=23%  Similarity=0.260  Sum_probs=100.7

Q ss_pred             cccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccch-hhhhhcc
Q 046473            3 VQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRA-QRATSMK   81 (120)
Q Consensus         3 l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~G-erAR~e~   81 (120)
                      |++.|+   .+++|++.||++|++||+++|++||+|||+|++|||||+++++++|++||+||||+|||||+| ||||+||
T Consensus        91 L~k~~~---~~v~I~i~eVk~p~l~A~lvAe~Ia~qLe~rv~FRra~k~ai~~am~~gakGIkI~iSGRL~GaeiARtE~  167 (239)
T 2vqe_C           91 LAKLTG---KNVALNVQEVQNPNLSAPLVAQRVAEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEW  167 (239)
T ss_dssp             HHHHST---TCCCCEEEECSCTTSCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHSSCSEEEEEECSCTTTCSSCCCBC
T ss_pred             HHHHhC---CeeEEEEEEecCCCcCHHHHHHHHHHHHHccchHHHHHHHHHHHHHHcCCCceEEEEcCCcchhhhhhhhh
Confidence            566665   468888999999999999999999999999999999999999999999999999999999999 8999999


Q ss_pred             ccceeeeccchhhhhhhheeeeEeCcCCe---eEEec
Q 046473           82 FKDGYMISSGYPVKEYIDSAVRHVLXRQA---SSIFC  115 (120)
Q Consensus        82 ~~eG~vp~sG~~~~~~idy~~~~a~tk~G---v~~~~  115 (120)
                      |++|+||++  |++++||||+++|+|+||   |+||-
T Consensus       168 ~~eG~vpL~--Tlra~IDYa~~~a~T~yGviGVKVWI  202 (239)
T 2vqe_C          168 AAQGRVPLH--TLRANIDYGFALARTTYGVLGVKAYI  202 (239)
T ss_dssp             CEEECCCTT--CGGGCEEEEEECCBCSSCBCCEEEEE
T ss_pred             hhcCccccC--CccceeEEEEEEEEcCCeeEEEEEEE
Confidence            999999984  799999999999999987   56774

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

Probab=97.27  E-value=8.7e-05  Score=50.57  Aligned_cols=28  Identities=68%  Similarity=0.929  Sum_probs=25.6

Q ss_pred             ccccccCCCCCeEEEEEEEecCCCcCHH
Q 046473            2 AVQKRFKFPENSVELYAEKVNNRGLCAI   29 (120)
Q Consensus         2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~   29 (120)
                      .|++.|++.+++|+|+|+||++|++||+
T Consensus        63 ~l~k~~~~~~~~v~I~I~eV~~P~ldA~   90 (92)
T 1wh9_A           63 VVQKRFGFPEGSVELYAEKVATRGSGPS   90 (92)
T ss_dssp             HHHHHHCCCTTSEEEEEEECCCSCCCSC
T ss_pred             HHHHHhCCCCCeEEEEEEEecCCCcCCC
Confidence            4788999989999999999999999985

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	120
d1wh9a_	92	d.52.3.1 (A:) Ribosomal protein S3 N-terminal doma	9e-09

>d1wh9a_ d.52.3.1 (A:) Ribosomal protein S3 N-terminal domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 92

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

 Score = 47.0 bits (112), Expect = 9e-09
 Identities = 19/30 (63%), Positives = 21/30 (70%)

Query: 1  SAVQKRFKFPENSVELYAEKVNNRGLCAIA 30
          + VQKRF FPE SVELYAEKV  RG    +
Sbjct: 62 AVVQKRFGFPEGSVELYAEKVATRGSGPSS 91

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	120
d2qalc2	101	Ribosomal protein S3 C-terminal domain {Escherichi	100.0
d2uubc2	101	Ribosomal protein S3 C-terminal domain {Thermus th	100.0
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	96.37

>d2qalc2 d.53.1.1 (C:106-206) Ribosomal protein S3 C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S3 C-terminal domain
superfamily: Ribosomal protein S3 C-terminal domain
family: Ribosomal protein S3 C-terminal domain
domain: Ribosomal protein S3 C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=6.7e-38  Score=218.66  Aligned_cols=92  Identities=21%  Similarity=0.229  Sum_probs=87.5

Q ss_pred             cCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccch-hhhhhccccceeeeccchhhhhhhhe
Q 046473           22 NNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRA-QRATSMKFKDGYMISSGYPVKEYIDS  100 (120)
Q Consensus        22 ~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~G-erAR~e~~~eG~vp~sG~~~~~~idy  100 (120)
                      ++|+|||+++|++||+|||+|++|||+++++++++|++||+||+|+|||||+| ||||+|||++|++|++  |++++|||
T Consensus         1 k~P~l~A~~vA~~IA~~LErr~~fRr~~~~~i~~~m~~ga~GikI~isGRl~gae~Ar~e~~~~G~ipl~--t~~~~Idy   78 (101)
T d2qalc2           1 RKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLH--TLRADIDY   78 (101)
T ss_dssp             SCGGGCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHSSCSEEEEEECSCGGGCSSCCCCCCEEECCCTT--CGGGCEEE
T ss_pred             CCCCcCHHHHHHHHHHHHHcchHHHHHHHHHHHHHhhcchheEEEEEeccccchhhheeEEEEEeccccc--ccceeEEE
Confidence            58999999999999999999999999999999999999999999999999999 9999999999999995  79999999


Q ss_pred             eeeEeCcCCe---eEEec
Q 046473          101 AVRHVLXRQA---SSIFC  115 (120)
Q Consensus       101 ~~~~a~tk~G---v~~~~  115 (120)
                      ++++|+|+||   |+||-
T Consensus        79 ~~~~a~t~~Gv~GVKVwI   96 (101)
T d2qalc2          79 NTSEAHTTYGVIGVKVWI   96 (101)
T ss_dssp             EECCCCBTTBCCCEEEEE
T ss_pred             EEEEEEcCceeEEEEEEE
Confidence            9999999876   56774

>d2uubc2 d.53.1.1 (C:107-207) Ribosomal protein S3 C-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S3 C-terminal domain
superfamily: Ribosomal protein S3 C-terminal domain
family: Ribosomal protein S3 C-terminal domain
domain: Ribosomal protein S3 C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=9.9e-37  Score=212.69  Aligned_cols=89  Identities=24%  Similarity=0.237  Sum_probs=86.0

Q ss_pred             cCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccch-hhhhhccccceeeeccchhhhhhhhe
Q 046473           22 NNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRA-QRATSMKFKDGYMISSGYPVKEYIDS  100 (120)
Q Consensus        22 ~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~G-erAR~e~~~eG~vp~sG~~~~~~idy  100 (120)
                      +||+|||+++|++||.|||+|++|||+++++++++|++||+||+|+|||||+| +|||+||+.+|.+|+  ||++++|||
T Consensus         1 ~nP~l~A~~vA~~Ia~~Ler~~~fRra~~~~l~~~m~~ga~GikI~isGrl~g~~~ar~~~~~~G~~~~--~t~~~~Idy   78 (101)
T d2uubc2           1 QNPNLSAPLVAQRVAEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPL--HTLRANIDY   78 (101)
T ss_dssp             SSTTSCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTCSEEEEEEEESGGGCSSCEEEEEEEECCCT--TCTTSCEEE
T ss_pred             CCCccCHHHHHHHHHHHHHccchHHHHHHHHHHHhhhcCccEEEEEEecccCCccceeEEEEEeeeecC--cceecceeE
Confidence            58999999999999999999999999999999999999999999999999999 999999999999998  589999999


Q ss_pred             eeeEeCcCCeeE
Q 046473          101 AVRHVLXRQASS  112 (120)
Q Consensus       101 ~~~~a~tk~Gv~  112 (120)
                      ++++|+|+||++
T Consensus        79 ~~~~a~tk~Gvi   90 (101)
T d2uubc2          79 GFALARTTYGVL   90 (101)
T ss_dssp             EEEEEECSSCEE
T ss_pred             EEEEEEcCCccE
Confidence            999999998754

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

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

Probab=96.37  E-value=0.00072  Score=44.58  Aligned_cols=28  Identities=68%  Similarity=0.929  Sum_probs=26.0

Q ss_pred             ccccccCCCCCeEEEEEEEecCCCcCHH
Q 046473            2 AVQKRFKFPENSVELYAEKVNNRGLCAI   29 (120)
Q Consensus         2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~   29 (120)
                      .|+++|++++++++|++++|.+.+|||.
T Consensus        63 ~l~k~~~~~~~~i~lnae~Ia~r~l~~~   90 (92)
T d1wh9a_          63 VVQKRFGFPEGSVELYAEKVATRGSGPS   90 (92)
T ss_dssp             HHHHHHCCCTTSEEEEEEECCCSCCCSC
T ss_pred             HHHHHHCCCCCcEEEEEEeecccCCCcc
Confidence            4789999999999999999999999984