Psyllid ID: psy17945

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210----
Protein Sequence
MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGEIPVASVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPAFPQKKLPFKTASLYLAGMLIAIWMSVQSLMGANKNPEDKPYLFRIKSTPGQNQTHNLYH
Secondary Structure (PSIPRED)
ccccccEEEEEEEccccHHHHccccccccEEEcccccHHHHEEEEEEEEEEEcEEEEEEEEEEcccccccccccccccccEEEEEccccccccccccccccccccccccccccccccccEEEEEcccccccccccccccccEEEEEccccccccccccccccccccHHHHcHHHHHHHHccccccccccccccccEEEEEEccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccEEEEEEEccEEHHHHHHEEccccEEEEcccccHHHHHHHHHEEEHHccEEEEEEEEEcccccccccccccccccEEEEEccccccccccccHHcccccccccccccccEEEEEEEEEEcccccccccccccccccEEEEEccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccccEEEEEEccccccccccccc
Coil and Loop (DISEMBL)
mesgakgceVVVSgklrgqraksmkfvdglmihsgdpcndyvntATRHVLLRQGVLGikvkimlpwdstgktgpkkplpdnvnvlepkeevnptipssqvldkplaklgeipvasVLGIKVKimlpwdstgktgpkkplpdnvnvlepkeevnpafpqkklpfkTASLYLAGMLIAIWMSVQSLmganknpedkpylfrikstpgqnqthnlyh
Flexible Loop (DISEMBL)
mesgakgcevvvsgklrgqrakSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLpwdstgktgpkkplpdNVNVLEpkeevnptipssqvldkPLAKLGEIPVASVLGIKVKIMLpwdstgktgpkkplPDNVNVLEPKEevnpafpqkklpFKTASLYLAGMLIAIWMSVQSLMGANKNPEDKPYLFrikstpgqnqthnlyh
Low Complexity Region (SEG)
MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGEIPVASVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPAFPQKKLPFKTASLYLAGMLIAIWMSVQSLMGANKNPEDKPYLFRIKSTPGQNQTHNLYH
Disordered region (IsUnstruct)
*********VVVS********KSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLPWD************************************PLAKLGEIPVASVLGIKVKIMLPWD*******************************KLPFKTASLYLAGMLIAIWMSVQSLM*****************************
Disordered Region (DISOPRED)
**SGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLPWDS*********LPDNVNVLEPK****************************LGIKVKIMLPW***********LPDNVNVLEPKEEVNP******************MLIAIW***************KPYLFRIKSTP**********
Disordered Region (DISEMBL)
MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGEIPVASVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPAFPQKKLPFKTASLYLAGMLIAIWMSVQSLMGANKNPEDKPYLFRIKSTPG*********
Disordered Region (DISPRO)
****AKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGEIPVASVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPAFPQKKLPFKTASLYLAGMLIAIWMSVQSLMGANKNPEDKPYLFRIKSTPG*********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGEIPVASVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPAFPQKKLPFKTASLYLAGMLIAIWMSVQSLMGANKNPEDKPYLFRIKSTPGQNQTHNLYH
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	214	2.2.26 [Sep-21-2011]
P48153	243	40S ribosomal protein S3	N/A	N/A	0.537	0.473	0.767	3e-44
Q90YS2	245	40S ribosomal protein S3	N/A	N/A	0.462	0.404	0.838	5e-44
P02350	246	40S ribosomal protein S3-	N/A	N/A	0.462	0.402	0.828	6e-44
P47835	246	40S ribosomal protein S3-	N/A	N/A	0.462	0.402	0.828	8e-44
Q0Z8U2	243	40S ribosomal protein S3	yes	N/A	0.462	0.407	0.838	9e-44
P23396	243	40S ribosomal protein S3	yes	N/A	0.462	0.407	0.838	9e-44
Q3T169	243	40S ribosomal protein S3	yes	N/A	0.462	0.407	0.838	9e-44
Q5R465	243	40S ribosomal protein S3	yes	N/A	0.462	0.407	0.838	1e-43
Q06559	246	40S ribosomal protein S3	yes	N/A	0.528	0.459	0.752	2e-43
P62909	243	40S ribosomal protein S3	yes	N/A	0.462	0.407	0.828	2e-43

>sp|P48153|RS3_MANSE 40S ribosomal protein S3 OS=Manduca sexta GN=RpS3 PE=2 SV=1

 Score =  178 bits (451), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 89/116 (76%), Positives = 97/116 (83%), Gaps = 1/116 (0%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGA+GCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV
Sbjct: 128 MESGARGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 187

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGEIPVASV 116
           KIMLPWD  GK GPKKP PD++ V EPK+E  P  P+S +     A L + PVA+V
Sbjct: 188 KIMLPWDQQGKNGPKKPQPDHILVTEPKDEPAPLEPTSDIRSLAPAPLPQ-PVAAV 242

Manduca sexta (taxid: 7130)

>sp|Q90YS2|RS3_ICTPU 40S ribosomal protein S3 OS=Ictalurus punctatus GN=rps3 PE=2 SV=1

 Score =  177 bits (449), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 83/99 (83%), Positives = 91/99 (91%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDP N YV+TA RHVLLRQGVLGIKV
Sbjct: 127 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKV 186

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQ 99
           KIMLPWD +GK GPKKPLPD+V+++EPKEE+ PT P S+
Sbjct: 187 KIMLPWDPSGKIGPKKPLPDHVSIVEPKEEILPTTPVSE 225

Ictalurus punctatus (taxid: 7998)

>sp|P02350|RS31_XENLA 40S ribosomal protein S3-A OS=Xenopus laevis GN=rps3-a PE=2 SV=2

 Score =  177 bits (448), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 82/99 (82%), Positives = 91/99 (91%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDP N YV+TA RHVLLRQGVLGIKV
Sbjct: 127 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKV 186

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQ 99
           KIMLPWD +GK GPKKPLPD+V+++EPK+E+ PT P S+
Sbjct: 187 KIMLPWDPSGKIGPKKPLPDHVSIVEPKDEIVPTTPISE 225

Xenopus laevis (taxid: 8355)

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

 Score =  176 bits (447), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 82/99 (82%), Positives = 91/99 (91%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDP N YV+TA RHVLLRQGVLGIKV
Sbjct: 127 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKV 186

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQ 99
           KIMLPWD +GK GPKKPLPD+V+++EPK+E+ PT P S+
Sbjct: 187 KIMLPWDPSGKIGPKKPLPDHVSIVEPKDEIVPTTPISE 225

Xenopus laevis (taxid: 8355)

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

 Score =  176 bits (446), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 83/99 (83%), Positives = 91/99 (91%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDP N YV+TA RHVLLRQGVLGIKV
Sbjct: 127 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKV 186

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQ 99
           KIMLPWD TGK GPKKPLPD+V+++EPK+E+ PT P S+
Sbjct: 187 KIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISE 225

Sus scrofa (taxid: 9823)

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

 Score =  176 bits (446), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 83/99 (83%), Positives = 91/99 (91%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDP N YV+TA RHVLLRQGVLGIKV
Sbjct: 127 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKV 186

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQ 99
           KIMLPWD TGK GPKKPLPD+V+++EPK+E+ PT P S+
Sbjct: 187 KIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISE 225

Homo sapiens (taxid: 9606)

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

 Score =  176 bits (446), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 83/99 (83%), Positives = 91/99 (91%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDP N YV+TA RHVLLRQGVLGIKV
Sbjct: 127 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKV 186

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQ 99
           KIMLPWD TGK GPKKPLPD+V+++EPK+E+ PT P S+
Sbjct: 187 KIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISE 225

Bos taurus (taxid: 9913)

>sp|Q5R465|RS3_PONAB 40S ribosomal protein S3 OS=Pongo abelii GN=RPS3 PE=2 SV=1

 Score =  176 bits (446), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 83/99 (83%), Positives = 91/99 (91%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDP N YV+TA RHVLLRQGVLGIKV
Sbjct: 127 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKV 186

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQ 99
           KIMLPWD TGK GPKKPLPD+V+++EPK+E+ PT P S+
Sbjct: 187 KIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISE 225

Pongo abelii (taxid: 9601)

>sp|Q06559|RS3_DROME 40S ribosomal protein S3 OS=Drosophila melanogaster GN=RpS3 PE=1 SV=1

 Score =  175 bits (444), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 88/117 (75%), Positives = 94/117 (80%), Gaps = 4/117 (3%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYV TATRHVLLRQGVLGIKV
Sbjct: 129 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVETATRHVLLRQGVLGIKV 188

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVL----DKPLAKLGEIPV 113
           K+MLP+D   K GPKKPLPDNV+V+EPKEE     P ++       KPL  L E  V
Sbjct: 189 KVMLPYDPKNKIGPKKPLPDNVSVVEPKEEKIYETPETEYKIPPPSKPLDDLSEAKV 245

Has DNA repair activity directed towards the mutagenic lesions 8-oxoguanine and abasic sites in DNA. It can cleave DNA containing 8-oxoguanine residues efficiently. Also acts as an ap lyase, cleaving phosphodiester bonds via a beta,delta elimination reaction.

Drosophila melanogaster (taxid: 7227)

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

 Score =  175 bits (443), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 82/99 (82%), Positives = 91/99 (91%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDP N YV+TA RHVLLRQGVLGIKV
Sbjct: 127 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKV 186

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQ 99
           KIMLPWD +GK GPKKPLPD+V+++EPK+E+ PT P S+
Sbjct: 187 KIMLPWDPSGKIGPKKPLPDHVSIVEPKDEILPTTPISE 225

Rattus norvegicus (taxid: 10116)

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	214
110456370	220	putative ribosomal protein S3 [Diaphorin	0.537	0.522	1.0	5e-61
264667327	240	ribosomal protein S3 [Chrysomela tremula	0.514	0.458	0.813	2e-47
449885323	240	ribosomal protein S3 [Phaedon cochlearia	0.514	0.458	0.813	4e-47
209693449	245	ribosomal protein S3 [Acyrthosiphon pisu	0.485	0.424	0.865	6e-47
157118129	243	40S ribosomal protein S3 [Aedes aegypti]	0.537	0.473	0.794	1e-46
157118131	256	40S ribosomal protein S3 [Aedes aegypti]	0.537	0.449	0.794	2e-46
332375642	232	unknown [Dendroctonus ponderosae]	0.467	0.431	0.88	4e-46
288869512	241	ribosomal protein S3 [Tribolium castaneu	0.467	0.414	0.88	5e-46
70906311	243	ribosomal protein S3 [Aedes albopictus]	0.537	0.473	0.786	5e-46
70909549	158	ribosomal protein S3e [Mycetophagus quad	0.467	0.632	0.88	8e-46

>gi|110456370|gb|ABG74703.1| putative ribosomal protein S3 [Diaphorina citri]

 Score =  239 bits (610), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 115/115 (100%), Positives = 115/115 (100%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV
Sbjct: 106 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 165

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGEIPVAS 115
           KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGEIPVAS
Sbjct: 166 KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGEIPVAS 220

Source: Diaphorina citri

Species: Diaphorina citri

Genus: Diaphorina

Family: Psyllidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|264667327|gb|ACY71249.1| ribosomal protein S3 [Chrysomela tremula]

 Score =  194 bits (492), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 96/118 (81%), Positives = 103/118 (87%), Gaps = 8/118 (6%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           ME GAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYV+TATRHVLLRQGVLGIKV
Sbjct: 127 MECGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVDTATRHVLLRQGVLGIKV 186

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQV----LDKPLAKLGEIPVA 114
           KIMLPWD+TGKTGPKKPLPDNV V EPK+E+ P  PSS++    +D PLA    IPVA
Sbjct: 187 KIMLPWDATGKTGPKKPLPDNVAVAEPKDEILPLYPSSEIKPIKVDAPLA----IPVA 240

Source: Chrysomela tremula

Species: Chrysomela tremula

Genus: Chrysomela

Family: Chrysomelidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|449885323|gb|AGF29412.1| ribosomal protein S3 [Phaedon cochleariae]

 Score =  193 bits (490), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 96/118 (81%), Positives = 103/118 (87%), Gaps = 8/118 (6%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           ME GAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYV+TATRHVLLRQGVLGIKV
Sbjct: 127 MECGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVDTATRHVLLRQGVLGIKV 186

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQV----LDKPLAKLGEIPVA 114
           KIMLPWD +GKTGPKKPLPDNV+V+EPKEE+ P  PSS++     D PLA    IPVA
Sbjct: 187 KIMLPWDPSGKTGPKKPLPDNVSVVEPKEEILPLFPSSEIKPVKSDAPLA----IPVA 240

Source: Phaedon cochleariae

Species: Phaedon cochleariae

Genus: Phaedon

Family: Chrysomelidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|209693449|ref|NP_001129413.1| ribosomal protein S3 [Acyrthosiphon pisum] gi|239790667|dbj|BAH71881.1| ACYPI005949 [Acyrthosiphon pisum]

 Score =  192 bits (489), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 90/104 (86%), Positives = 94/104 (90%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVN ATRHVLLRQGVLGIKV
Sbjct: 128 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNVATRHVLLRQGVLGIKV 187

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKP 104
           KIMLPWD TGK GPKKPLPDNV+V EPKEE+ P  P+S +  KP
Sbjct: 188 KIMLPWDQTGKLGPKKPLPDNVSVAEPKEEILPIAPTSDIKSKP 231

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157118129|ref|XP_001659022.1| 40S ribosomal protein S3 [Aedes aegypti] gi|70906313|gb|AAZ14892.1| ribosomal protein S3 [Aedes aegypti] gi|108875827|gb|EAT40052.1| AAEL008192-PA [Aedes aegypti]

 Score =  191 bits (486), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 93/117 (79%), Positives = 104/117 (88%), Gaps = 2/117 (1%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCN+YV+TATRHVLLRQGVLGIKV
Sbjct: 127 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNEYVDTATRHVLLRQGVLGIKV 186

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGEI--PVAS 115
           KIMLPWD  GK GPKKPLPDNV+V+EPK+E+  + P S+  +KP  +LGE+  PVAS
Sbjct: 187 KIMLPWDPNGKIGPKKPLPDNVSVVEPKDEIMYSTPRSEPKNKPTLELGEVVEPVAS 243

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157118131|ref|XP_001659023.1| 40S ribosomal protein S3 [Aedes aegypti] gi|403182936|gb|EJY57732.1| AAEL008192-PB [Aedes aegypti]

 Score =  191 bits (485), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 93/117 (79%), Positives = 104/117 (88%), Gaps = 2/117 (1%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCN+YV+TATRHVLLRQGVLGIKV
Sbjct: 140 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNEYVDTATRHVLLRQGVLGIKV 199

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGEI--PVAS 115
           KIMLPWD  GK GPKKPLPDNV+V+EPK+E+  + P S+  +KP  +LGE+  PVAS
Sbjct: 200 KIMLPWDPNGKIGPKKPLPDNVSVVEPKDEIMYSTPRSEPKNKPTLELGEVVEPVAS 256

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332375642|gb|AEE62962.1| unknown [Dendroctonus ponderosae]

 Score =  190 bits (482), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 88/100 (88%), Positives = 96/100 (96%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           ME GAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYV+TATRHVLLRQGVLGIKV
Sbjct: 127 MECGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVDTATRHVLLRQGVLGIKV 186

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQV 100
           KIMLP+D TGK GPKKPLPDNV+V+EPK+EV PT+PSS++
Sbjct: 187 KIMLPYDPTGKIGPKKPLPDNVSVVEPKDEVVPTVPSSEI 226

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|288869512|ref|NP_001165863.1| ribosomal protein S3 [Tribolium castaneum] gi|270006106|gb|EFA02554.1| hypothetical protein TcasGA2_TC008261 [Tribolium castaneum]

 Score =  189 bits (481), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 88/100 (88%), Positives = 95/100 (95%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           ME GAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYV+TATRHVLLRQGVLGIKV
Sbjct: 127 MECGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVDTATRHVLLRQGVLGIKV 186

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQV 100
           KIMLPWD +GKTGPKKPLPDNV+V+EPKEE+ P  PSS++
Sbjct: 187 KIMLPWDPSGKTGPKKPLPDNVSVVEPKEEILPAYPSSEI 226

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|70906311|gb|AAZ14891.1| ribosomal protein S3 [Aedes albopictus]

 Score =  189 bits (481), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 92/117 (78%), Positives = 103/117 (88%), Gaps = 2/117 (1%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCN+YV+TATRHVLLRQGVLGIKV
Sbjct: 127 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNEYVDTATRHVLLRQGVLGIKV 186

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGEI--PVAS 115
           KIMLPWD  GK GPKKPLPDNV+V+EPK+E+  + P S+  +KP  +L E+  PVAS
Sbjct: 187 KIMLPWDPNGKIGPKKPLPDNVSVVEPKDEIMYSTPRSEPKNKPTMELAEVVEPVAS 243

Source: Aedes albopictus

Species: Aedes albopictus

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|70909549|emb|CAJ17196.1| ribosomal protein S3e [Mycetophagus quadripustulatus]

 Score =  189 bits (479), Expect = 8e-46,   Method: Compositional matrix adjust.
 Identities = 88/100 (88%), Positives = 95/100 (95%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           ME GAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYV+TATRHVLLRQGVLGIKV
Sbjct: 43  MECGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVDTATRHVLLRQGVLGIKV 102

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQV 100
           KIMLPWD TGKTGPK+PLPDNV+V+EPKEE+ P  PSS++
Sbjct: 103 KIMLPWDPTGKTGPKRPLPDNVSVVEPKEEILPKAPSSEI 142

Source: Mycetophagus quadripustulatus

Species: Mycetophagus quadripustulatus

Genus: Mycetophagus

Family: Mycetophagidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	214
UNIPROTKB|Q3T169	243	RPS3 "40S ribosomal protein S3	0.485	0.427	0.819	1.4e-41
UNIPROTKB|E9PL09	231	RPS3 "40S ribosomal protein S3	0.485	0.450	0.819	1.4e-41
UNIPROTKB|H0YEU2	171	RPS3 "40S ribosomal protein S3	0.485	0.608	0.819	1.4e-41
UNIPROTKB|J3KN86	259	RPS3 "40S ribosomal protein S3	0.485	0.401	0.819	1.4e-41
UNIPROTKB|P23396	243	RPS3 "40S ribosomal protein S3	0.485	0.427	0.819	1.4e-41
UNIPROTKB|Q0Z8U2	243	RPS3 "40S ribosomal protein S3	0.485	0.427	0.819	1.4e-41
UNIPROTKB|Q5R465	243	RPS3 "40S ribosomal protein S3	0.485	0.427	0.819	1.4e-41
UNIPROTKB|E9PSF4	103	RPS3 "40S ribosomal protein S3	0.462	0.961	0.838	1.7e-41
UNIPROTKB|F1N9X5	243	RPS3 "Uncharacterized protein"	0.485	0.427	0.819	1.7e-41
UNIPROTKB|F1SUM7	195	RPS3 "40S ribosomal protein S3	0.485	0.533	0.809	2.8e-41

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

 Score = 441 (160.3 bits), Expect = 1.4e-41, P = 1.4e-41
 Identities = 86/105 (81%), Positives = 93/105 (88%)

Query:     1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
             MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDP N YV+TA RHVLLRQGVLGIKV
Sbjct:   127 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKV 186

Query:    61 KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIP-SSQVLDKP 104
             KIMLPWD TGK GPKKPLPD+V+++EPK+E+ PT P S Q   KP
Sbjct:   187 KIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKP 231

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|E9PL09 RPS3 "40S ribosomal protein S3" [Homo sapiens (taxid:9606)]

 Score = 441 (160.3 bits), Expect = 1.4e-41, P = 1.4e-41
 Identities = 86/105 (81%), Positives = 93/105 (88%)

Query:     1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
             MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDP N YV+TA RHVLLRQGVLGIKV
Sbjct:   115 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKV 174

Query:    61 KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIP-SSQVLDKP 104
             KIMLPWD TGK GPKKPLPD+V+++EPK+E+ PT P S Q   KP
Sbjct:   175 KIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKP 219

GO:0003723 "RNA binding" evidence=IEA

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

GO:0006412 "translation" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

UNIPROTKB|H0YEU2 RPS3 "40S ribosomal protein S3" [Homo sapiens (taxid:9606)]

 Score = 441 (160.3 bits), Expect = 1.4e-41, P = 1.4e-41
 Identities = 86/105 (81%), Positives = 93/105 (88%)

Query:     1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
             MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDP N YV+TA RHVLLRQGVLGIKV
Sbjct:    55 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKV 114

Query:    61 KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIP-SSQVLDKP 104
             KIMLPWD TGK GPKKPLPD+V+++EPK+E+ PT P S Q   KP
Sbjct:   115 KIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKP 159

GO:0003723 "RNA binding" evidence=IEA

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

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

UNIPROTKB|J3KN86 RPS3 "40S ribosomal protein S3" [Homo sapiens (taxid:9606)]

 Score = 441 (160.3 bits), Expect = 1.4e-41, P = 1.4e-41
 Identities = 86/105 (81%), Positives = 93/105 (88%)

Query:     1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
             MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDP N YV+TA RHVLLRQGVLGIKV
Sbjct:   143 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKV 202

Query:    61 KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIP-SSQVLDKP 104
             KIMLPWD TGK GPKKPLPD+V+++EPK+E+ PT P S Q   KP
Sbjct:   203 KIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKP 247

GO:0003723 "RNA binding" evidence=IEA

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

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

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

 Score = 441 (160.3 bits), Expect = 1.4e-41, P = 1.4e-41
 Identities = 86/105 (81%), Positives = 93/105 (88%)

Query:     1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
             MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDP N YV+TA RHVLLRQGVLGIKV
Sbjct:   127 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKV 186

Query:    61 KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIP-SSQVLDKP 104
             KIMLPWD TGK GPKKPLPD+V+++EPK+E+ PT P S Q   KP
Sbjct:   187 KIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKP 231

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|Q0Z8U2 RPS3 "40S ribosomal protein S3" [Sus scrofa (taxid:9823)]

 Score = 441 (160.3 bits), Expect = 1.4e-41, P = 1.4e-41
 Identities = 86/105 (81%), Positives = 93/105 (88%)

Query:     1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
             MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDP N YV+TA RHVLLRQGVLGIKV
Sbjct:   127 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKV 186

Query:    61 KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIP-SSQVLDKP 104
             KIMLPWD TGK GPKKPLPD+V+++EPK+E+ PT P S Q   KP
Sbjct:   187 KIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKP 231

GO:0030529 "ribonucleoprotein complex" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|Q5R465 RPS3 "40S ribosomal protein S3" [Pongo abelii (taxid:9601)]

 Score = 441 (160.3 bits), Expect = 1.4e-41, P = 1.4e-41
 Identities = 86/105 (81%), Positives = 93/105 (88%)

Query:     1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
             MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDP N YV+TA RHVLLRQGVLGIKV
Sbjct:   127 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKV 186

Query:    61 KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIP-SSQVLDKP 104
             KIMLPWD TGK GPKKPLPD+V+++EPK+E+ PT P S Q   KP
Sbjct:   187 KIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKP 231

GO:0030529 "ribonucleoprotein complex" evidence=ISS

UNIPROTKB|E9PSF4 RPS3 "40S ribosomal protein S3" [Homo sapiens (taxid:9606)]

 Score = 440 (159.9 bits), Expect = 1.7e-41, P = 1.7e-41
 Identities = 83/99 (83%), Positives = 91/99 (91%)

Query:     1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
             MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDP N YV+TA RHVLLRQGVLGIKV
Sbjct:     1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKV 60

Query:    61 KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQ 99
             KIMLPWD TGK GPKKPLPD+V+++EPK+E+ PT P S+
Sbjct:    61 KIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISE 99

GO:0003723 "RNA binding" evidence=IEA

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

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

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

 Score = 440 (159.9 bits), Expect = 1.7e-41, P = 1.7e-41
 Identities = 86/105 (81%), Positives = 93/105 (88%)

Query:     1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
             MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDP N YV+TA RHVLLRQGVLGIKV
Sbjct:   127 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKV 186

Query:    61 KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIP-SSQVLDKP 104
             KIMLPWD +GK GPKKPLPD+V+++EPKEE+ PT P S Q   KP
Sbjct:   187 KIMLPWDPSGKIGPKKPLPDHVSIVEPKEEILPTTPISEQKGGKP 231

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|F1SUM7 RPS3 "40S ribosomal protein S3" [Sus scrofa (taxid:9823)]

 Score = 438 (159.2 bits), Expect = 2.8e-41, P = 2.8e-41
 Identities = 85/105 (80%), Positives = 93/105 (88%)

Query:     1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
             MESGAKGCEVVVSGKLRGQRAKSMKFVDG+MIHSGDP N YV+TA RHVLLRQGVLGIKV
Sbjct:    79 MESGAKGCEVVVSGKLRGQRAKSMKFVDGVMIHSGDPVNYYVDTAVRHVLLRQGVLGIKV 138

Query:    61 KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIP-SSQVLDKP 104
             KIMLPWD TGK GPKKPLPD+V+++EPK+E+ PT P S Q   KP
Sbjct:   139 KIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKP 183

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	0.8383	0.4626	0.4074	yes	N/A
P05750	RS3_YEAST	No assigned EC number	0.7252	0.4065	0.3625	yes	N/A
P48152	RS3_CAEEL	No assigned EC number	0.7070	0.4626	0.4008	yes	N/A
O60128	RS3_SCHPO	No assigned EC number	0.6571	0.4719	0.4056	yes	N/A
E2RH47	RS3_CANFA	No assigned EC number	0.8282	0.4626	0.4074	yes	N/A
Q0Z8U2	RS3_PIG	No assigned EC number	0.8383	0.4626	0.4074	yes	N/A
P23396	RS3_HUMAN	No assigned EC number	0.8383	0.4626	0.4074	yes	N/A
Q3T169	RS3_BOVIN	No assigned EC number	0.8383	0.4626	0.4074	yes	N/A
P62909	RS3_RAT	No assigned EC number	0.8282	0.4626	0.4074	yes	N/A
P62908	RS3_MOUSE	No assigned EC number	0.8282	0.4626	0.4074	yes	N/A
Q06559	RS3_DROME	No assigned EC number	0.7521	0.5280	0.4593	yes	N/A
Q9SIP7	RS31_ARATH	No assigned EC number	0.6034	0.5327	0.456	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	214
PTZ00084	220	PTZ00084, PTZ00084, 40S ribosomal protein S3; Prov	4e-53
TIGR01008	195	TIGR01008, rpsC_E_A, ribosomal protein S3, eukaryo	7e-31
PRK04191	207	PRK04191, rps3p, 30S ribosomal protein S3P; Review	5e-24
COG0092	233	COG0092, RpsC, Ribosomal protein S3 [Translation,	1e-23
pfam00189	85	pfam00189, Ribosomal_S3_C, Ribosomal protein S3, C	3e-18
PTZ00084	220	PTZ00084, PTZ00084, 40S ribosomal protein S3; Prov	1e-13

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

 Score =  169 bits (430), Expect = 4e-53
 Identities = 65/90 (72%), Positives = 76/90 (84%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEV+VSGKLR QRAKSMKF DG MI +G P  D+V++A RHVL+RQGV+G+KV
Sbjct: 127 MESGAKGCEVIVSGKLRAQRAKSMKFRDGYMISTGQPKKDFVDSAVRHVLMRQGVIGVKV 186

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEE 90
           KIMLP+D +GK GP  PLPD + VLEPKEE
Sbjct: 187 KIMLPYDPSGKNGPSAPLPDVITVLEPKEE 216

Length = 220

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

 Score =  111 bits (280), Expect = 7e-31
 Identities = 40/86 (46%), Positives = 52/86 (60%), Gaps = 9/86 (10%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           ME+GAKG EV +SGKL G+RA++ KF  G + HSG+P  + V+      LL+ GVLG+KV
Sbjct: 119 MEAGAKGVEVTISGKLTGERARTEKFAAGYLKHSGEPVEELVDKGFAIALLKLGVLGVKV 178

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLE 86
           KIM          P   LPD V + E
Sbjct: 179 KIM---------PPDVKLPDEVEIKE 195

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

 Score = 94.2 bits (235), Expect = 5e-24
 Identities = 34/90 (37%), Positives = 55/90 (61%), Gaps = 9/90 (10%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           ME+GA G E+++SGKL G+RA++ KF +G +  SG+P  + V+       L+ G++G++V
Sbjct: 121 MEAGALGVEIIISGKLTGERARTEKFTEGYIKKSGEPAEELVDRGFAIAKLKLGIIGVEV 180

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEE 90
           +IM P D+         LPD + + EP E 
Sbjct: 181 RIMPP-DAK--------LPDEIEIKEPVEV 201

Length = 207

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

 Score = 93.9 bits (234), Expect = 1e-23
 Identities = 26/91 (28%), Positives = 42/91 (46%), Gaps = 7/91 (7%)

Query: 1   MESGAKGCEVVVSGKLRGQR-AKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIK 59
           M +GAKG ++ VSG+L G   A++ K+ +G +       +  ++  T       GV+G+K
Sbjct: 132 MRAGAKGIKIQVSGRLGGAEIARTEKYREGRVPLHTLRAD--IDYGTAEAHTTYGVIGVK 189

Query: 60  VKIMLPWDSTGKTGPKKPLPDNVNVLEPKEE 90
           V I            K  + +   V EP EE
Sbjct: 190 VWIYKG----EVLPDKVEIKEPAEVEEPAEE 216

Length = 233

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

 Score = 75.6 bits (187), Expect = 3e-18
 Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 3/63 (4%)

Query: 1  MESGAKGCEVVVSGKLRG-QRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIK 59
           + GAKG ++ +SG+L G +RA++ K+ +G +          ++ A      + GV+G+K
Sbjct: 25 KKGGAKGIKIQISGRLNGAERARTEKYKEGRV--PLHTLRADIDYAFAEAKTKYGVIGVK 82

Query: 60 VKI 62
          V I
Sbjct: 83 VWI 85

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|240260 PTZ00084, PTZ00084, 40S ribosomal protein S3; Provisional

 Score = 67.0 bits (164), Expect = 1e-13
 Identities = 25/36 (69%), Positives = 30/36 (83%)

Query: 116 VLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEE 151
           V+G+KVKIMLP+D +GK GP  PLPD + VLEPKEE
Sbjct: 181 VIGVKVKIMLPYDPSGKNGPSAPLPDVITVLEPKEE 216

Length = 220

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	214
KOG3181|consensus	244		100.0
PTZ00084	220	40S ribosomal protein S3; Provisional	100.0
PRK04191	207	rps3p 30S ribosomal protein S3P; Reviewed	99.97
TIGR01008	195	rpsC_E_A ribosomal protein S3, eukaryotic/archaeal	99.96
COG0092	233	RpsC Ribosomal protein S3 [Translation, ribosomal	99.94
TIGR01009	211	rpsC_bact ribosomal protein S3, bacterial type. TI	99.84
CHL00048	214	rps3 ribosomal protein S3	99.84
PRK00310	232	rpsC 30S ribosomal protein S3; Reviewed	99.83
PF00189	85	Ribosomal_S3_C: Ribosomal protein S3, C-terminal d	99.81
KOG3181|consensus	244		99.78
PTZ00084	220	40S ribosomal protein S3; Provisional	98.94
PRK04191	207	rps3p 30S ribosomal protein S3P; Reviewed	97.47
COG0092	233	RpsC Ribosomal protein S3 [Translation, ribosomal	95.49
TIGR01008	195	rpsC_E_A ribosomal protein S3, eukaryotic/archaeal	95.49
PRK00310	232	rpsC 30S ribosomal protein S3; Reviewed	86.66
TIGR01009	211	rpsC_bact ribosomal protein S3, bacterial type. TI	83.99
CHL00048	214	rps3 ribosomal protein S3	82.96

>KOG3181|consensus

Probab=100.00  E-value=2.7e-42  Score=298.96  Aligned_cols=101  Identities=77%  Similarity=1.204  Sum_probs=99.5

Q ss_pred             CCCCCceeEEEEcccchhhhhceecccceEEeccCcchhhheeeEEEEEeccCeeeeEEEEEECCCCCCCCCCCCCCCCC
Q psy17945          1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLPWDSTGKTGPKKPLPD   80 (214)
Q Consensus         1 MeaGAkG~EIvISGKL~GeRARseKF~dG~m~~sG~p~r~~VD~a~~ha~lkqGvIGIKV~Im~p~Dp~Gk~Gp~~~LPD   80 (214)
                      |+|||+||||+|||||+||||++|||.||+|+|||||+++|||+|++|++|+||+|||||+||+||||+|++||+.+|||
T Consensus       127 mesgAkGceviVSGKLrgqRAKsmKF~DG~mIhSG~pv~dyi~ta~rhVllrQGVlGIkVkIMlpydp~g~~GP~~pLPD  206 (244)
T KOG3181|consen  127 MESGAKGCEVIVSGKLRGQRAKSMKFVDGLMIHSGQPVKDYIDTAVRHVLLRQGVLGIKVKIMLPYDPKGKLGPKKPLPD  206 (244)
T ss_pred             HHccCCccEEEEeccchhhhhhccccccceEEecCCcHHHHHHHHHHhhhhhcceeeeEEEEeccCCcccCcCCCCCCCC
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEeCCcccCCCCCCccccc
Q psy17945         81 NVNVLEPKEEVNPTIPSSQVL  101 (214)
Q Consensus        81 ~v~I~epkee~~~~~p~s~~~  101 (214)
                      +|+|.||+||+++++|.++.+
T Consensus       207 ~v~i~ePkee~~~~~p~~~~~  227 (244)
T KOG3181|consen  207 RVTILEPKEEEPITAPAQVAK  227 (244)
T ss_pred             eeEEeCccccccccCchhhhc
Confidence            999999999999999999865

>PTZ00084 40S ribosomal protein S3; Provisional

Probab=100.00  E-value=2.6e-34  Score=248.56  Aligned_cols=92  Identities=71%  Similarity=1.178  Sum_probs=89.9

Q ss_pred             CCCCCceeEEEEcccchhhhhceecccceEEeccCcchhhheeeEEEEEeccCeeeeEEEEEECCCCCCCCCCCCCCCCC
Q psy17945          1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLPWDSTGKTGPKKPLPD   80 (214)
Q Consensus         1 MeaGAkG~EIvISGKL~GeRARseKF~dG~m~~sG~p~r~~VD~a~~ha~lkqGvIGIKV~Im~p~Dp~Gk~Gp~~~LPD   80 (214)
                      |+|||+||+|+|||||+|||||+|||++|+|.|||++++++||||++||+|+||+||||||||+||||+|.+||+++|||
T Consensus       127 m~aGakGikI~iSGRL~~EiARtE~~~eGrVl~Tg~~~~~~idy~~~~a~t~yGviGVKVwI~~~~~~~~~~~~~~~~pD  206 (220)
T PTZ00084        127 MESGAKGCEVIVSGKLRAQRAKSMKFRDGYMISTGQPKKDFVDSAVRHVLMRQGVIGVKVKIMLPYDPSGKNGPSAPLPD  206 (220)
T ss_pred             HHcCCceEEEEEccchhhHHHHhhHhhccEEEecCchHHHheehheEEEcccCceeeEEEEEECCCCcccccCCCCCCCC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEeCCcccCC
Q psy17945         81 NVNVLEPKEEVN   92 (214)
Q Consensus        81 ~v~I~epkee~~   92 (214)
                      .|+|+||+++..
T Consensus       207 ~~~i~~~~~~~~  218 (220)
T PTZ00084        207 VITVLEPKEETA  218 (220)
T ss_pred             cEEEeCCccccc
Confidence            999999999843

>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed

Probab=99.97  E-value=1.3e-31  Score=228.21  Aligned_cols=83  Identities=40%  Similarity=0.769  Sum_probs=80.1

Q ss_pred             CCCCCceeEEEEcccchhhhhceecccceEEeccCcchhhheeeEEEEEeccCeeeeEEEEEECCCCCCCCCCCCCCCCC
Q psy17945          1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLPWDSTGKTGPKKPLPD   80 (214)
Q Consensus         1 MeaGAkG~EIvISGKL~GeRARseKF~dG~m~~sG~p~r~~VD~a~~ha~lkqGvIGIKV~Im~p~Dp~Gk~Gp~~~LPD   80 (214)
                      |++||+||+|+|||||+|||||+|||++|+|++||+|+..+||||++||+|+||+||||||||+|         +.+|||
T Consensus       121 ~~agakGiki~iSGrL~Ge~AR~e~~~eG~v~~~G~pl~tlIdya~~~a~t~~GviGIKVwI~~~---------~~~~pd  191 (207)
T PRK04191        121 MEAGALGVEIIISGKLTGERARTEKFTEGYIKKSGEPAEELVDRGFAIAKLKLGIIGVEVRIMPP---------DAKLPD  191 (207)
T ss_pred             HHcCCeeEEEEEccccchHHHHhhhhhcceEeccCCcchheeeeEEEEEecCCeeEEEEEEEECC---------CCCCCC
Confidence            78999999999999999999999999999999999999999999999999999999999999997         689999


Q ss_pred             eEEEeCCcccCC
Q psy17945         81 NVNVLEPKEEVN   92 (214)
Q Consensus        81 ~v~I~epkee~~   92 (214)
                      .|+|++|++++.
T Consensus       192 ~~~i~~~~~~~~  203 (207)
T PRK04191        192 EIEIKEPVEVEE  203 (207)
T ss_pred             EEEEeCCCCccc
Confidence            999999988754

>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type

Probab=99.96  E-value=6.7e-30  Score=217.60  Aligned_cols=77  Identities=52%  Similarity=0.864  Sum_probs=74.5

Q ss_pred             CCCCCceeEEEEcccchhhhhceecccceEEeccCcchhhheeeEEEEEeccCeeeeEEEEEECCCCCCCCCCCCCCCCC
Q psy17945          1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLPWDSTGKTGPKKPLPD   80 (214)
Q Consensus         1 MeaGAkG~EIvISGKL~GeRARseKF~dG~m~~sG~p~r~~VD~a~~ha~lkqGvIGIKV~Im~p~Dp~Gk~Gp~~~LPD   80 (214)
                      |++||+||+|+|||||+|||||+|||++|+|++||+|+..+||||++||+|+||+||||||||+|         +.+|||
T Consensus       119 m~aGakGikI~iSGRL~GeiARtE~~~eG~v~~sG~Pl~t~IDya~~~a~t~yGviGIKVwI~~~---------~~~~pD  189 (195)
T TIGR01008       119 MEAGAKGVEVTISGKLTGERARTEKFAAGYLKHSGEPAEELVDKGFAIALLKLGVLGVKVKIMPP---------DVKLPD  189 (195)
T ss_pred             HHcCCceEEEEEcccccchhhhhhheeccEEecCCCcchheeeeEEEEEecCCceEEEEEEEECC---------CCCCCC
Confidence            78999999999999999999999999999999999999999999999999999999999999997         578999


Q ss_pred             eEEEeC
Q psy17945         81 NVNVLE   86 (214)
Q Consensus        81 ~v~I~e   86 (214)
                      .|+|+|
T Consensus       190 ~~~i~~  195 (195)
T TIGR01008       190 EVEIKE  195 (195)
T ss_pred             EEEecC
Confidence            999975

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.

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

Probab=99.94  E-value=4.4e-27  Score=205.89  Aligned_cols=82  Identities=34%  Similarity=0.503  Sum_probs=73.9

Q ss_pred             CCCCCceeEEEEcccchhhh-hceecccceEEeccCcchhhheeeEEEEEeccCeeeeEEEEEECCCCCCCCCCCCCCCC
Q psy17945          1 MESGAKGCEVVVSGKLRGQR-AKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLPWDSTGKTGPKKPLP   79 (214)
Q Consensus         1 MeaGAkG~EIvISGKL~GeR-ARseKF~dG~m~~sG~p~r~~VD~a~~ha~lkqGvIGIKV~Im~p~Dp~Gk~Gp~~~LP   79 (214)
                      |++||+||+|+|||||+|+| ||+|||++|+|+|||  ++++||||+++|+|+||+||||||||+|.          .||
T Consensus       132 M~aGAkGiki~vSGRL~GaeiAR~E~y~eG~vplht--lrAdIDyg~a~A~ttyGiiGVKVwI~~ge----------~l~  199 (233)
T COG0092         132 MRAGAKGIKIQVSGRLGGAEIARTEKYREGRVPLHT--LRADIDYGTAEAHTTYGVIGVKVWIYKGE----------VLP  199 (233)
T ss_pred             HHcCCceeEEEEecccchHHHHhHHHHhcceeEccc--cceeeeeeeEEEEecCceEEEEEEEecCC----------cCC
Confidence            89999999999999999977 999999999999999  66679999999999999999999999983          899


Q ss_pred             CeEEEeCCcccCCCC
Q psy17945         80 DNVNVLEPKEEVNPT   94 (214)
Q Consensus        80 D~v~I~epkee~~~~   94 (214)
                      |.+.+.++.++..+.
T Consensus       200 ~~~~~~~~~~~~~~~  214 (233)
T COG0092         200 DKVEIKEPAEVEEPA  214 (233)
T ss_pred             CcccccCcccccccc
Confidence            999887766654433

>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type

Probab=99.84  E-value=1.5e-21  Score=167.33  Aligned_cols=63  Identities=32%  Similarity=0.449  Sum_probs=61.3

Q ss_pred             CCCCCceeEEEEcccchh-hhhceecccceEEeccCcchhhheeeEEEEEeccCeeeeEEEEEECC
Q psy17945          1 MESGAKGCEVVVSGKLRG-QRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLP   65 (214)
Q Consensus         1 MeaGAkG~EIvISGKL~G-eRARseKF~dG~m~~sG~p~r~~VD~a~~ha~lkqGvIGIKV~Im~p   65 (214)
                      |++||+||+|+|||||+| ||||+|+|.+|+|++++  ++++||||+++|.|++|++|||||||++
T Consensus       142 ~~~g~~GikI~isGRl~g~e~Ar~e~~~~G~vpl~t--~~~~Idy~~~~a~T~~G~~GvKVwI~~~  205 (211)
T TIGR01009       142 MKAGAKGIKVQVSGRLGGAEIARTEWYKEGRVPLHT--LRADIDYATAEAHTTYGIIGVKVWIFKG  205 (211)
T ss_pred             HhcCCcEEEEEEecccCchhhhheeeeeeCccCccc--chhhcEEEEEEEEcCCceEEEEEEEEcC
Confidence            689999999999999999 89999999999999998  9999999999999999999999999997

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

>CHL00048 rps3 ribosomal protein S3

Probab=99.84  E-value=2.2e-21  Score=166.69  Aligned_cols=63  Identities=24%  Similarity=0.311  Sum_probs=61.0

Q ss_pred             CCCCCceeEEEEcccchh-hhhceecccceEEeccCcchhhheeeEEEEEeccCeeeeEEEEEECC
Q psy17945          1 MESGAKGCEVVVSGKLRG-QRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLP   65 (214)
Q Consensus         1 MeaGAkG~EIvISGKL~G-eRARseKF~dG~m~~sG~p~r~~VD~a~~ha~lkqGvIGIKV~Im~p   65 (214)
                      |++||+||+|+|||||+| ||||+|+|.+|+|++++  ++++||||+++|.|++|++|||||||++
T Consensus       149 ~~~ga~GikI~iSGRL~Gae~AR~e~~~~G~vpl~t--l~a~Idy~~~~a~t~~G~~GVKVwI~~~  212 (214)
T CHL00048        149 EKADIKGIKIQISGRLNGAEIARVEWIREGRVPLQT--LRAKIDYCSYPARTIYGVLGIKIWIFKD  212 (214)
T ss_pred             HHhCCcEEEEEEecccCccchheEEEEecceeECCc--chhheEEEEEEEecCCceEEEEEEEEcC
Confidence            689999999999999999 89999999999999988  9999999999999999999999999986

>PRK00310 rpsC 30S ribosomal protein S3; Reviewed

Probab=99.83  E-value=2e-21  Score=168.66  Aligned_cols=63  Identities=30%  Similarity=0.423  Sum_probs=61.0

Q ss_pred             CCCCCceeEEEEcccchh-hhhceecccceEEeccCcchhhheeeEEEEEeccCeeeeEEEEEECC
Q psy17945          1 MESGAKGCEVVVSGKLRG-QRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLP   65 (214)
Q Consensus         1 MeaGAkG~EIvISGKL~G-eRARseKF~dG~m~~sG~p~r~~VD~a~~ha~lkqGvIGIKV~Im~p   65 (214)
                      |++||+||+|+|||||+| +|||+|+|.+|+|++++  ++++||||+++|+|++|+||||||||++
T Consensus       142 ~~~g~~GikI~isGRl~g~e~Ar~e~~~~G~vpl~t--~~~~Idy~~~~a~T~~Gv~GVKVwI~~~  205 (232)
T PRK00310        142 MRAGAKGIKVQVSGRLGGAEIARTEWYREGRVPLHT--LRADIDYGTAEAHTTYGIIGVKVWIYKG  205 (232)
T ss_pred             HHcCCcEEEEEEcCCCCcceeeeEEEeeecccccce--eeeeeEEEEEEEecCCceEEEEEEEECC
Confidence            689999999999999999 89999999999999887  9999999999999999999999999997

>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=99.81  E-value=2.2e-20  Score=138.88  Aligned_cols=60  Identities=38%  Similarity=0.635  Sum_probs=57.2

Q ss_pred             CCCCCceeEEEEcccchh-hhhceecccceEEeccCcchhhheeeEEEEEeccCeeeeEEEEE
Q psy17945          1 MESGAKGCEVVVSGKLRG-QRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKI   62 (214)
Q Consensus         1 MeaGAkG~EIvISGKL~G-eRARseKF~dG~m~~sG~p~r~~VD~a~~ha~lkqGvIGIKV~I   62 (214)
                      |++||+||+|+|||||+| +|||+++|..|.|  ++++++++||||++++.|++|++||||||
T Consensus        25 ~~~~~~GikI~isGRl~g~~rar~~~~~~G~i--~~~~~~~~Idy~~~~~~tk~G~~GIKVwI   85 (85)
T PF00189_consen   25 MNKGIKGIKIQISGRLNGAERARTEKFKKGKI--SLQTFKSNIDYASSHAKTKYGVIGIKVWI   85 (85)
T ss_dssp             HCTTSSEEEEEEESSGGGTSSSEEEEEEEESS--SSSSSTTEEEEEEEEEEESSSEEEEEEEE
T ss_pred             hhcccceEEEEEeecCCCCccceEEEEECCCC--ccccceeeeeEEEEEEEcCCeeEEEEEEC
Confidence            568999999999999999 9999999999999  66679999999999999999999999998

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 ....

>KOG3181|consensus

Probab=99.78  E-value=7.6e-20  Score=159.47  Aligned_cols=95  Identities=40%  Similarity=0.607  Sum_probs=78.9

Q ss_pred             ccCeeeeEEEEEECCCCCCCCCCC----CCCCCCeEEEeC--CcccCCCCCCcccccCCcccccCCCCcccccceEEEEe
Q psy17945         51 LRQGVLGIKVKIMLPWDSTGKTGP----KKPLPDNVNVLE--PKEEVNPTIPSSQVLDKPLAKLGEIPVASVLGIKVKIM  124 (214)
Q Consensus        51 lkqGvIGIKV~Im~p~Dp~Gk~Gp----~~~LPD~v~I~e--pkee~~~~~p~s~~~~~p~~~~~~~~~~GvLGIKVkIM  124 (214)
                      +..|.-|++|.+      +||...    ...+-|.+.|++  |..+.+.+.-++..   .++        ||||||||||
T Consensus       127 mesgAkGceviV------SGKLrgqRAKsmKF~DG~mIhSG~pv~dyi~ta~rhVl---lrQ--------GVlGIkVkIM  189 (244)
T KOG3181|consen  127 MESGAKGCEVIV------SGKLRGQRAKSMKFVDGLMIHSGQPVKDYIDTAVRHVL---LRQ--------GVLGIKVKIM  189 (244)
T ss_pred             HHccCCccEEEE------eccchhhhhhccccccceEEecCCcHHHHHHHHHHhhh---hhc--------ceeeeEEEEe
Confidence            455788999988      566543    456899999984  66666767666654   445        9999999999


Q ss_pred             cCCCCCCCCCCCCCCCCeeEEeCCCCCCCCCCCcccCC
Q psy17945        125 LPWDSTGKTGPKKPLPDNVNVLEPKEEVNPAFPQKKLP  162 (214)
Q Consensus       125 lp~Dp~Gk~Gp~~plPD~V~i~epk~e~~~~~p~~~~~  162 (214)
                      |||||+|+.||++||||+|+|+|||||+++++|.+...
T Consensus       190 lpydp~g~~GP~~pLPD~v~i~ePkee~~~~~p~~~~~  227 (244)
T KOG3181|consen  190 LPYDPKGKLGPKKPLPDRVTILEPKEEEPITAPAQVAK  227 (244)
T ss_pred             ccCCcccCcCCCCCCCCeeEEeCccccccccCchhhhc
Confidence            99999999999999999999999999999999988654

>PTZ00084 40S ribosomal protein S3; Provisional

Probab=98.94  E-value=7.7e-10  Score=96.61  Aligned_cols=41  Identities=61%  Similarity=1.078  Sum_probs=38.8

Q ss_pred             cccccceEEEEecCCCCCCCCCCCCCCCCeeEEeCCCCCCC
Q psy17945        113 VASVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVN  153 (214)
Q Consensus       113 ~~GvLGIKVkIMlp~Dp~Gk~Gp~~plPD~V~i~epk~e~~  153 (214)
                      ..|+|||||.||+||||+|..||+.+|||.|.|.||+++..
T Consensus       178 ~yGviGVKVwI~~~~~~~~~~~~~~~~pD~~~i~~~~~~~~  218 (220)
T PTZ00084        178 RQGVIGVKVKIMLPYDPSGKNGPSAPLPDVITVLEPKEETA  218 (220)
T ss_pred             cCceeeEEEEEECCCCcccccCCCCCCCCcEEEeCCccccc
Confidence            56999999999999999999999999999999999999854

>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed

Probab=97.47  E-value=0.00013  Score=63.06  Aligned_cols=36  Identities=31%  Similarity=0.538  Sum_probs=30.6

Q ss_pred             CcccccceEEEEecCCCCCCCCCCCCCCCCeeEEeCCCCCCCCCC
Q psy17945        112 PVASVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPAF  156 (214)
Q Consensus       112 ~~~GvLGIKVkIMlp~Dp~Gk~Gp~~plPD~V~i~epk~e~~~~~  156 (214)
                      ...|+|||||.||+|         ..+|||.|+|.||++++..+.
T Consensus       171 t~~GviGIKVwI~~~---------~~~~pd~~~i~~~~~~~~~~~  206 (207)
T PRK04191        171 LKLGIIGVEVRIMPP---------DAKLPDEIEIKEPVEVEEVVE  206 (207)
T ss_pred             cCCeeEEEEEEEECC---------CCCCCCEEEEeCCCCcccccC
Confidence            356999999999995         378999999999999876553

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

Probab=95.49  E-value=0.013  Score=52.56  Aligned_cols=78  Identities=28%  Similarity=0.474  Sum_probs=45.2

Q ss_pred             ccCeeeeEEEEEECCCCCCCCCCCCC-----CCCCe-EEEeCCcccCCCCCCcccccCCcccccCCCCcccccceEEEEe
Q psy17945         51 LRQGVLGIKVKIMLPWDSTGKTGPKK-----PLPDN-VNVLEPKEEVNPTIPSSQVLDKPLAKLGEIPVASVLGIKVKIM  124 (214)
Q Consensus        51 lkqGvIGIKV~Im~p~Dp~Gk~Gp~~-----~LPD~-v~I~epkee~~~~~p~s~~~~~p~~~~~~~~~~GvLGIKVkIM  124 (214)
                      ++.|..||||.|      +|+.|-..     .+-+- |-.+--..++.+..  ++  +.        --.|+|||||.||
T Consensus       132 M~aGAkGiki~v------SGRL~GaeiAR~E~y~eG~vplhtlrAdIDyg~--a~--A~--------ttyGiiGVKVwI~  193 (233)
T COG0092         132 MRAGAKGIKIQV------SGRLGGAEIARTEKYREGRVPLHTLRADIDYGT--AE--AH--------TTYGVIGVKVWIY  193 (233)
T ss_pred             HHcCCceeEEEE------ecccchHHHHhHHHHhcceeEccccceeeeeee--EE--EE--------ecCceEEEEEEEe
Confidence            788999999999      78887443     11121 11111111111110  00  01        2349999999999


Q ss_pred             cCCCCCCCCCCCCCCCCeeEEeCCCCCCCCCC
Q psy17945        125 LPWDSTGKTGPKKPLPDNVNVLEPKEEVNPAF  156 (214)
Q Consensus       125 lp~Dp~Gk~Gp~~plPD~V~i~epk~e~~~~~  156 (214)
                      .|-          -|||.+.+.++.++..+..
T Consensus       194 ~ge----------~l~~~~~~~~~~~~~~~~~  215 (233)
T COG0092         194 KGE----------VLPDKVEIKEPAEVEEPAE  215 (233)
T ss_pred             cCC----------cCCCcccccCccccccccc
Confidence            973          5777777766666655543

>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type

Probab=95.49  E-value=0.012  Score=50.97  Aligned_cols=27  Identities=52%  Similarity=0.741  Sum_probs=22.6

Q ss_pred             CcccccceEEEEecCCCCCCCCCCCCCCCCeeEEeC
Q psy17945        112 PVASVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLE  147 (214)
Q Consensus       112 ~~~GvLGIKVkIMlp~Dp~Gk~Gp~~plPD~V~i~e  147 (214)
                      ...|+|||||.||.|         ..+|||.|+|.|
T Consensus       169 t~yGviGIKVwI~~~---------~~~~pD~~~i~~  195 (195)
T TIGR01008       169 LKLGVLGVKVKIMPP---------DVKLPDEVEIKE  195 (195)
T ss_pred             cCCceEEEEEEEECC---------CCCCCCEEEecC
Confidence            356999999999985         257999999965

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.

>PRK00310 rpsC 30S ribosomal protein S3; Reviewed

Probab=86.66  E-value=0.69  Score=40.92  Aligned_cols=63  Identities=24%  Similarity=0.244  Sum_probs=33.7

Q ss_pred             ccCeeeeEEEEEECCCCCCCCCCCCCCCCCeEEEeCCcccCCCCCCcccccCCcccccCC-CCcccccceEEEEecC
Q psy17945         51 LRQGVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGE-IPVASVLGIKVKIMLP  126 (214)
Q Consensus        51 lkqGvIGIKV~Im~p~Dp~Gk~Gp~~~LPD~v~I~epkee~~~~~p~s~~~~~p~~~~~~-~~~~GvLGIKVkIMlp  126 (214)
                      ++.|+.||||.|      +|+++-.    +.-....-++-.++.......   -.-...+ ....|+|||||.||++
T Consensus       142 ~~~g~~GikI~i------sGRl~g~----e~Ar~e~~~~G~vpl~t~~~~---Idy~~~~a~T~~Gv~GVKVwI~~~  205 (232)
T PRK00310        142 MRAGAKGIKVQV------SGRLGGA----EIARTEWYREGRVPLHTLRAD---IDYGTAEAHTTYGIIGVKVWIYKG  205 (232)
T ss_pred             HHcCCcEEEEEE------cCCCCcc----eeeeEEEeeecccccceeeee---eEEEEEEEecCCceEEEEEEEECC
Confidence            567999999999      7877642    111222222222321111110   0000111 2466999999999996

>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type

Probab=83.99  E-value=1.1  Score=39.18  Aligned_cols=63  Identities=24%  Similarity=0.328  Sum_probs=32.4

Q ss_pred             ccCeeeeEEEEEECCCCCCCCCCCCCCCCCeEEEeCCcccCCCCCCcccccCCcccccCC-CCcccccceEEEEecC
Q psy17945         51 LRQGVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGE-IPVASVLGIKVKIMLP  126 (214)
Q Consensus        51 lkqGvIGIKV~Im~p~Dp~Gk~Gp~~~LPD~v~I~epkee~~~~~p~s~~~~~p~~~~~~-~~~~GvLGIKVkIMlp  126 (214)
                      ++.|+.||||.|      +|+.+-.+ ..-....   .+-.+|.   +.....-.-...+ .-..|+|||||.||+.
T Consensus       142 ~~~g~~GikI~i------sGRl~g~e-~Ar~e~~---~~G~vpl---~t~~~~Idy~~~~a~T~~G~~GvKVwI~~~  205 (211)
T TIGR01009       142 MKAGAKGIKVQV------SGRLGGAE-IARTEWY---KEGRVPL---HTLRADIDYATAEAHTTYGIIGVKVWIFKG  205 (211)
T ss_pred             HhcCCcEEEEEE------ecccCchh-hhheeee---eeCccCc---ccchhhcEEEEEEEEcCCceEEEEEEEEcC
Confidence            577999999999      67766321 1111111   1111211   1111000000111 2466999999999985

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

>CHL00048 rps3 ribosomal protein S3

Probab=82.96  E-value=1.2  Score=38.96  Aligned_cols=74  Identities=20%  Similarity=0.179  Sum_probs=37.3

Q ss_pred             hhheeeEEEEEeccCeeeeEEEEEECCCCCCCCCCCCCCCCCeEEEeCCcccCCCCCCcccccCCcccccCC-CCccccc
Q psy17945         39 NDYVNTATRHVLLRQGVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGE-IPVASVL  117 (214)
Q Consensus        39 r~~VD~a~~ha~lkqGvIGIKV~Im~p~Dp~Gk~Gp~~~LPD~v~I~epkee~~~~~p~s~~~~~p~~~~~~-~~~~GvL  117 (214)
                      |..+..+.+.+ ++.|+.||||.|      +|+.+-. ...-.-...   +-.+   |-+.....-.-...+ .-..|++
T Consensus       138 Rra~~~~i~~~-~~~ga~GikI~i------SGRL~Ga-e~AR~e~~~---~G~v---pl~tl~a~Idy~~~~a~t~~G~~  203 (214)
T CHL00048        138 RKAMKKAIELA-EKADIKGIKIQI------SGRLNGA-EIARVEWIR---EGRV---PLQTLRAKIDYCSYPARTIYGVL  203 (214)
T ss_pred             HHHHHHHHHHH-HHhCCcEEEEEE------ecccCcc-chheEEEEe---ccee---ECCcchhheEEEEEEEecCCceE
Confidence            33333333333 566999999999      7887743 222222222   2222   222211000001111 2456999


Q ss_pred             ceEEEEecC
Q psy17945        118 GIKVKIMLP  126 (214)
Q Consensus       118 GIKVkIMlp  126 (214)
                      ||||.||+-
T Consensus       204 GVKVwI~~~  212 (214)
T CHL00048        204 GIKIWIFKD  212 (214)
T ss_pred             EEEEEEEcC
Confidence            999999973

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	214
2zkq_c	243	Structure Of A Mammalian Ribosomal 40s Subunit With		8e-45
2zkq_c	243	Structure Of A Mammalian Ribosomal 40s Subunit With		1e-12
3iz6_B	227	Localization Of The Small Subunit Ribosomal Protein		5e-34
3iz6_B	227	Localization Of The Small Subunit Ribosomal Protein		5e-07
3izb_B	240	Localization Of The Small Subunit Ribosomal Protein		3e-32
1s1h_C	192	Structure Of The Ribosomal 80s-Eef2-Sordarin Comple		8e-27
3jyv_C	188	Structure Of The 40s Rrna And Proteins And PE TRNA		9e-27
2xzm_C	243	Crystal Structure Of The Eukaryotic 40s Ribosomal S		6e-25
3zey_X	214	High-resolution Cryo-electron Microscopy Structure		4e-21
3j20_C	210	Promiscuous Behavior Of Proteins In Archaeal Riboso		2e-11

>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 =  176 bits (446), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 83/99 (83%), Positives = 91/99 (91%)
Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDP N YV+TA RHVLLRQGVLGIKV
Sbjct: 127 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKV 186
Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQ 99
           KIMLPWD TGK GPKKPLPD+V+++EPK+E+ PT P S+
Sbjct: 187 KIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISE 225

>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 = 69.7 bits (169), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 31/42 (73%), Positives = 37/42 (88%)
Query: 116 VLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPAFP 157
           VLGIKVKIMLPWD TGK GPKKPLPD+V+++EPK+E+ P  P
Sbjct: 181 VLGIKVKIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTP 222

>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 =  140 bits (353), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 67/90 (74%), Positives = 72/90 (80%)
Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEV+VSGKLR QRAKSMKF DG MI SG P N+Y++ A RHVLLRQGVLGIKV
Sbjct: 127 MESGAKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDAAVRHVLLRQGVLGIKV 186
Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEE 90
           KIML WD  GK GP  PLPD V +  PKEE
Sbjct: 187 KIMLDWDPKGKLGPTTPLPDLVTIHPPKEE 216

>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 = 51.2 bits (121), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 25/36 (69%), Positives = 26/36 (72%)
Query: 116 VLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEE 151
           VLGIKVKIML WD  GK GP  PLPD V +  PKEE
Sbjct: 181 VLGIKVKIMLDWDPKGKLGPTTPLPDLVTIHPPKEE 216

>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 =  134 bits (338), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 66/91 (72%), Positives = 75/91 (82%), Gaps = 4/91 (4%)
Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEVVVSGKLR  RAK+MKF DG +IHSG P ND+++TATRHVL+RQGVLGIKV
Sbjct: 127 MESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQGVLGIKV 186
Query: 61  KIML-PWDSTGKTGPKKPLPDNVNVLEPKEE 90
           KIM  P  S  +TGP K LPD V ++EPKEE
Sbjct: 187 KIMRDPAKS--RTGP-KALPDAVTIIEPKEE 214

>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 =  116 bits (291), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 51/63 (80%), Positives = 57/63 (90%)
Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEVVVSGKLR  RAK+MKF DG +IHSG P ND+++TATRHVL+RQGVLGIKV
Sbjct: 126 MESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQGVLGIKV 185
Query: 61  KIM 63
           KIM
Sbjct: 186 KIM 188

>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 =  116 bits (290), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 51/63 (80%), Positives = 57/63 (90%)
Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEVVVSGKLR  RAK+MKF DG +IHSG P ND+++TATRHVL+RQGVLGIKV
Sbjct: 122 MESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQGVLGIKV 181
Query: 61  KIM 63
           KIM
Sbjct: 182 KIM 184

>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 =  110 bits (275), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 49/91 (53%), Positives = 68/91 (74%), Gaps = 2/91 (2%)
Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           ++ GAKGCE+++SGKL+ QRAK+MKF  G MI +G P NDY++ A RHV  +QG++G+KV
Sbjct: 130 IQDGAKGCEIIISGKLKQQRAKTMKFKQGYMICTGQPKNDYIDVAVRHVFFKQGIMGVKV 189
Query: 61  KIMLPWD--STGKTGPKKPLPDNVNVLEPKE 89
           KIMLP++     K G K P+PDNV +  PK+
Sbjct: 190 KIMLPYEPNPAKKFGVKTPIPDNVIIHPPKQ 220

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

Iteration: 1
 Score = 97.8 bits (242), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 48/88 (54%), Positives = 59/88 (67%), Gaps = 3/88 (3%)
Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEV + GK++GQRAKSM F DG MI SG     +V+TATRH  LR G +G+ V
Sbjct: 126 MESGAKGCEVTIGGKIKGQRAKSMTFRDGYMIKSGTAHKHFVDTATRHCHLRAGTIGVNV 185
Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPK 88
           KIM P     +    + LPD + V+EPK
Sbjct: 186 KIMRPQSMIEE---DEVLPDVITVIEPK 210

>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 = 65.9 bits (159), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 36/91 (39%), Positives = 52/91 (57%), Gaps = 10/91 (10%)
Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           M +GA+G E+ +SGKL G+RAKS++F  G +   G+P    V+      LL+ GV+G+KV
Sbjct: 121 MNNGARGVEIRLSGKLTGERAKSIRFYQGYLAKVGNPAETLVSKGYAQALLKLGVIGVKV 180
Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLE-PKEE 90
            IM P            LPD + ++E P EE
Sbjct: 181 AIMPPGAR---------LPDEIEIIEKPVEE 202

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	214
2xzm_C	243	KH domain containing protein; ribosome, translatio	1e-45
2xzm_C	243	KH domain containing protein; ribosome, translatio	1e-10
2zkq_c	243	40S ribosomal protein S3E; protein-RNA complex, 40	7e-43
2zkq_c	243	40S ribosomal protein S3E; protein-RNA complex, 40	1e-13
3iz6_B	227	40S ribosomal protein S3 (S3P); eukaryotic ribosom	2e-41
3iz6_B	227	40S ribosomal protein S3 (S3P); eukaryotic ribosom	1e-12
3u5c_D	240	RP13, YS3, 40S ribosomal protein S3; translation,	3e-37
3u5c_D	240	RP13, YS3, 40S ribosomal protein S3; translation,	2e-08

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

 Score =  150 bits (381), Expect = 1e-45
 Identities = 51/112 (45%), Positives = 75/112 (66%), Gaps = 2/112 (1%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           ++ GAKGCE+++SGKL+ QRAK+MKF  G MI +G P NDY++ A RHV  +QG++G+KV
Sbjct: 130 IQDGAKGCEIIISGKLKQQRAKTMKFKQGYMICTGQPKNDYIDVAVRHVFFKQGIMGVKV 189

Query: 61  KIMLPWD--STGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGE 110
           KIMLP++     K G K P+PDNV +  PK+  +     + V  +  A+  +
Sbjct: 190 KIMLPYEPNPAKKFGVKTPIPDNVIIHPPKQITDDKEIRTAVEQQQPAQPEQ 241

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

 Score = 58.2 bits (141), Expect = 1e-10
 Identities = 18/46 (39%), Positives = 28/46 (60%), Gaps = 2/46 (4%)

Query: 116 VLGIKVKIMLPWD--STGKTGPKKPLPDNVNVLEPKEEVNPAFPQK 159
           ++G+KVKIMLP++     K G K P+PDNV +  PK+  +    + 
Sbjct: 184 IMGVKVKIMLPYEPNPAKKFGVKTPIPDNVIIHPPKQITDDKEIRT 229

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

 Score =  143 bits (362), Expect = 7e-43
 Identities = 87/114 (76%), Positives = 95/114 (83%), Gaps = 1/114 (0%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDP N YV+TA RHVLLRQGVLGIKV
Sbjct: 127 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKV 186

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQV-LDKPLAKLGEIPV 113
           KIMLPWD TGK GPKKPLPD+V+++EPK+E+ PT P S+    KP       PV
Sbjct: 187 KIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPV 240

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

 Score = 66.3 bits (162), Expect = 1e-13
 Identities = 31/45 (68%), Positives = 38/45 (84%)

Query: 116 VLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPAFPQKK 160
           VLGIKVKIMLPWD TGK GPKKPLPD+V+++EPK+E+ P  P  +
Sbjct: 181 VLGIKVKIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISE 225

>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 =  139 bits (351), Expect = 2e-41
 Identities = 68/99 (68%), Positives = 74/99 (74%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEV+VSGKLR QRAKSMKF DG MI SG P N+Y++ A RHVLLRQGVLGIKV
Sbjct: 127 MESGAKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDAAVRHVLLRQGVLGIKV 186

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQ 99
           KIML WD  GK GP  PLPD V +  PKEE     P+  
Sbjct: 187 KIMLDWDPKGKLGPTTPLPDLVTIHPPKEENELRPPALV 225

>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 = 63.6 bits (155), Expect = 1e-12
 Identities = 26/42 (61%), Positives = 27/42 (64%)

Query: 116 VLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPAFP 157
           VLGIKVKIML WD  GK GP  PLPD V +  PKEE     P
Sbjct: 181 VLGIKVKIMLDWDPKGKLGPTTPLPDLVTIHPPKEENELRPP 222

>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 =  128 bits (324), Expect = 3e-37
 Identities = 64/99 (64%), Positives = 73/99 (73%), Gaps = 2/99 (2%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEVVVSGKLR  RAK+MKF DG +IHSG P ND+++TATRHVL+RQGVLGIKV
Sbjct: 127 MESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQGVLGIKV 186

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQ 99
           KIM   D        K LPD V ++EPKEE     PS +
Sbjct: 187 KIM--RDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVK 223

>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 = 52.1 bits (125), Expect = 2e-08
 Identities = 22/45 (48%), Positives = 24/45 (53%), Gaps = 2/45 (4%)

Query: 116 VLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPAFPQKK 160
           VLGIKVKIM   D        K LPD V ++EPKEE     P  K
Sbjct: 181 VLGIKVKIM--RDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVK 223

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	214
3iz6_B	227	40S ribosomal protein S3 (S3P); eukaryotic ribosom	100.0
2zkq_c	243	40S ribosomal protein S3E; protein-RNA complex, 40	100.0
3u5c_D	240	RP13, YS3, 40S ribosomal protein S3; translation,	100.0
2xzm_C	243	KH domain containing protein; ribosome, translatio	100.0
3j20_C	210	30S ribosomal protein S3P; archaea, archaeal, KINK	99.96
2vqe_C	239	30S ribosomal protein S3; tRNA-binding, rRNA-bindi	99.89
3r8n_C	206	30S ribosomal protein S3; protein biosynthesis, RN	99.88
3bbn_C	218	Ribosomal protein S3; small ribosomal subunit, spi	99.88
3i1m_C	233	30S ribosomal protein S3; ribosome structure, prot	99.88
3iz6_B	227	40S ribosomal protein S3 (S3P); eukaryotic ribosom	99.42
2zkq_c	243	40S ribosomal protein S3E; protein-RNA complex, 40	99.39
2xzm_C	243	KH domain containing protein; ribosome, translatio	99.24
3u5c_D	240	RP13, YS3, 40S ribosomal protein S3; translation,	99.22
3j20_C	210	30S ribosomal protein S3P; archaea, archaeal, KINK	97.1
2vqe_C	239	30S ribosomal protein S3; tRNA-binding, rRNA-bindi	95.02
3bbn_C	218	Ribosomal protein S3; small ribosomal subunit, spi	90.79
3i1m_C	233	30S ribosomal protein S3; ribosome structure, prot	86.11
3r8n_C	206	30S ribosomal protein S3; protein biosynthesis, RN	84.76

>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=3.1e-38  Score=273.07  Aligned_cols=98  Identities=69%  Similarity=1.101  Sum_probs=91.5

Q ss_pred             CCCCCceeEEEEcccchhhhhceecccceEEeccCcchhhheeeEEEEEeccCeeeeEEEEEECCCCCCCCCCCCCCCCC
Q psy17945          1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLPWDSTGKTGPKKPLPD   80 (214)
Q Consensus         1 MeaGAkG~EIvISGKL~GeRARseKF~dG~m~~sG~p~r~~VD~a~~ha~lkqGvIGIKV~Im~p~Dp~Gk~Gp~~~LPD   80 (214)
                      |++||+||+|+|||||+|+|||+|||++|+|+||+|+++++||||++||+|+||+||||||||+||||+|++||+++|||
T Consensus       127 m~aGakGikI~iSGRL~GaiARtE~~~eG~vlhTlqtlra~IDya~~~a~T~yGviGVKVWI~~~~dp~g~~g~~~~lpD  206 (227)
T 3iz6_B          127 MESGAKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDAAVRHVLLRQGVLGIKVKIMLDWDPKGKLGPTTPLPD  206 (227)
T ss_dssp             TTTCCSEEECCBCSCGGGSSCCCBCCEEECCCSSSSCTTSCEEECCCCCBCSSSBCCCCCEEECSCTTSCCCCCSSCCCC
T ss_pred             HHcCCceEEEEEecccCCceeeEeeeeCCeecccCChhhheeeEEEEEEEcCCeeEEEEEEEECCCCcccccCCCCCCCC
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEeCCcccCCCCCCcc
Q psy17945         81 NVNVLEPKEEVNPTIPSS   98 (214)
Q Consensus        81 ~v~I~epkee~~~~~p~s   98 (214)
                      +|+|+||++|..+.+|..
T Consensus       207 ~v~i~~pk~~~~~~~~~~  224 (227)
T 3iz6_B          207 LVTIHPPKEENELRPPAL  224 (227)
T ss_dssp             CCSCCCCSSCCCC-----
T ss_pred             eEEEeCCCcccCCCCCcc
Confidence            999999999976666643

>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=3.6e-38  Score=275.01  Aligned_cols=101  Identities=82%  Similarity=1.288  Sum_probs=66.1

Q ss_pred             CCCCCceeEEEEcccchhhhhceecccceEEeccCcchhhheeeEEEEEeccCeeeeEEEEEECCCCCCCCCCCCCCCCC
Q psy17945          1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLPWDSTGKTGPKKPLPD   80 (214)
Q Consensus         1 MeaGAkG~EIvISGKL~GeRARseKF~dG~m~~sG~p~r~~VD~a~~ha~lkqGvIGIKV~Im~p~Dp~Gk~Gp~~~LPD   80 (214)
                      |++||+||+|+|||||+|+|||+|||++|+|.|+|+|++++||||++||+|+||+||||||||+||||+|++||+++|||
T Consensus       127 m~aGakGikI~iSGRL~GaiARtE~~~eG~vLhTg~plra~IDYa~~~a~T~yGvlGVKVWI~~~~dp~g~~gp~~~lpD  206 (243)
T 2zkq_c          127 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPTGKIGPKKPLPD  206 (243)
T ss_dssp             HHSSCSEEEEEECSSGGGSSCCCBCCEEESSHHHHSSTTCCEEEEEECCCCSSCCCCEEEEEECCCC-------------
T ss_pred             HhcCCceEEEEEecchhhHhhhhhhhcCcEEeecCchhhhceeEEEEEEEcCCceEEEEEEEecCCCcCCcCCCCCCCCC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEeCCcccCCCCCCccccc
Q psy17945         81 NVNVLEPKEEVNPTIPSSQVL  101 (214)
Q Consensus        81 ~v~I~epkee~~~~~p~s~~~  101 (214)
                      +|+|+||++|..+++|.|+.+
T Consensus       207 ~v~i~e~k~~~~~~~~~~~~~  227 (243)
T 2zkq_c          207 HVSIVEPKDEILPTTPISEQK  227 (243)
T ss_dssp             ---------------------
T ss_pred             eEEEeCCccccccCCCccccc
Confidence            999999999999999999764

>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=6.6e-37  Score=266.88  Aligned_cols=98  Identities=68%  Similarity=1.074  Sum_probs=96.2

Q ss_pred             CCCCCceeEEEEcccchhhhhceecccceEEeccCcchhhheeeEEEEEeccCeeeeEEEEEECCCCCC-CCCCCCCCCC
Q psy17945          1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLPWDST-GKTGPKKPLP   79 (214)
Q Consensus         1 MeaGAkG~EIvISGKL~GeRARseKF~dG~m~~sG~p~r~~VD~a~~ha~lkqGvIGIKV~Im~p~Dp~-Gk~Gp~~~LP   79 (214)
                      |++||+||+|+|||||+|+|||+|||++|+|+||||+++++||||++||+|+||+||||||||+  ||+ |++|| ++||
T Consensus       127 m~aGakGikI~iSGRL~Ga~ARtE~~~eG~vlhTgqtlra~IDYa~~~a~T~yGviGVKVWI~~--dp~~g~~g~-~~lp  203 (240)
T 3u5c_D          127 MESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQGVLGIKVKIMR--DPAKSRTGP-KALP  203 (240)
T ss_dssp             HHTTCSEEEEEEEECSSSSSCEEEEEEEECCCCSSHHHHHHEEEEEEEEECSSCEEEEEEEEEC--CGGGCSSSC-SSCT
T ss_pred             HhcCCceeEEEEecccCCceeeEEeeecCeeccCCChhhheeeEEEEEEEcCCeeEEEEEEEEe--CcccccCCC-CCCC
Confidence            7899999999999999999999999999999999999999999999999999999999999999  999 99999 9999


Q ss_pred             CeEEEeCCcccCCCCCCccccc
Q psy17945         80 DNVNVLEPKEEVNPTIPSSQVL  101 (214)
Q Consensus        80 D~v~I~epkee~~~~~p~s~~~  101 (214)
                      |+|+|+||++|..+++|.|+++
T Consensus       204 D~v~i~epk~~~~~~~~~~~~~  225 (240)
T 3u5c_D          204 DAVTIIEPKEEEPILAPSVKDY  225 (240)
T ss_dssp             TCCEECCCCCCCCCCCCCEEEC
T ss_pred             CeEEEECCccccCCCCCccccc
Confidence            9999999999999999999975

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

Probab=100.00  E-value=5.2e-36  Score=261.31  Aligned_cols=99  Identities=48%  Similarity=0.907  Sum_probs=95.8

Q ss_pred             CCCCCceeEEEEcccchhhhhceecccceEEeccCcchhhheeeEEEEEeccCeeeeEEEEEECCCCCCCCC--CCCCCC
Q psy17945          1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLPWDSTGKT--GPKKPL   78 (214)
Q Consensus         1 MeaGAkG~EIvISGKL~GeRARseKF~dG~m~~sG~p~r~~VD~a~~ha~lkqGvIGIKV~Im~p~Dp~Gk~--Gp~~~L   78 (214)
                      |++||+||+|+|||||+|+|||+|||++|+|.|+++|++++||||+++|+|+||+||||||||+||||+|++  ||+++|
T Consensus       130 m~aGakGIkI~iSGRL~GaiARtE~~~eG~vL~T~rplra~IDYa~~~a~T~yGvlGVKVWI~~~~~~~g~~~~gp~~~l  209 (243)
T 2xzm_C          130 IQDGAKGCEIIISGKLKQQRAKTMKFKQGYMICTGQPKNDYIDVAVRHVFFKQGIMGVKVKIMLPYEPNPAKKFGVKTPI  209 (243)
T ss_dssp             HHTTCSEEEEEEEECTTSSSCEEEEEEEECCCCSSSHHHHSEEEEEEEEECSSSEEEEEEEEECCCCCCTTCCSSCCSCC
T ss_pred             HhcCCceEEEEEeCCccchhheeeeeeCCeEeecCcchhhheEEEEEEEEcCCceEEEEEEEecCCCcCCcccCCCCCCC
Confidence            789999999999999999999999999999999999999999999999999999999999999999999999  999999


Q ss_pred             CCeEEEeCCcccCCCCCCccc
Q psy17945         79 PDNVNVLEPKEEVNPTIPSSQ   99 (214)
Q Consensus        79 PD~v~I~epkee~~~~~p~s~   99 (214)
                      ||.|+|+||++|+.++++++.
T Consensus       210 pD~v~i~e~k~~~~~~~~~~~  230 (243)
T 2xzm_C          210 PDNVIIHPPKQITDDKEIRTA  230 (243)
T ss_dssp             SSCCBCCCCCCCCCCCCCCCC
T ss_pred             CCeEEEeCCCccccccccccc
Confidence            999999999999888888864

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

Probab=99.96  E-value=6.5e-30  Score=218.78  Aligned_cols=82  Identities=41%  Similarity=0.762  Sum_probs=63.9

Q ss_pred             CCCCCceeEEEEcccchhhhhceecccceEEeccCcchhhheeeEEEEEeccCeeeeEEEEEECCCCCCCCCCCCCCCCC
Q psy17945          1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLPWDSTGKTGPKKPLPD   80 (214)
Q Consensus         1 MeaGAkG~EIvISGKL~GeRARseKF~dG~m~~sG~p~r~~VD~a~~ha~lkqGvIGIKV~Im~p~Dp~Gk~Gp~~~LPD   80 (214)
                      |++||+||+|+|||||+|||||+|||++|+||++|.+++++||||++||+|+||+||||||||+|         +.+|||
T Consensus       121 m~~GakGikI~iSGRL~GeiARtE~~~eG~vpl~tl~a~~~IDya~~~a~T~yGviGVKVwI~~~---------e~~lpd  191 (210)
T 3j20_C          121 MNNGARGVEIRLSGKLTGERAKSIRFYQGYLAKVGNPAETLVSKGYAQALLKLGVIGVKVAIMPP---------GARLPD  191 (210)
T ss_dssp             HHHHCSEEEEEEEECTTTTSCEEEEEEEECCCCSSSHHHHHSEEEEEEEECSSCEEEEEEEEECC---------C-----
T ss_pred             HhcCCceEEEEEecccCcceeeEEeeecceeeccCCcchhcEEEEEEEEEcCCcEEEEEEEEECC---------CCCCCC
Confidence            68999999999999999999999999999999999888889999999999999999999999997         567999


Q ss_pred             eEEEeCCcccC
Q psy17945         81 NVNVLEPKEEV   91 (214)
Q Consensus        81 ~v~I~epkee~   91 (214)
                      +|+|++|+.++
T Consensus       192 ~~~i~~~~~~~  202 (210)
T 3j20_C          192 EIEIIEKPVEE  202 (210)
T ss_dssp             -----------
T ss_pred             cEEEeCcchhh
Confidence            99999988774

>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=99.89  E-value=2.1e-24  Score=187.61  Aligned_cols=64  Identities=33%  Similarity=0.435  Sum_probs=61.8

Q ss_pred             CCCCCceeEEEEcccchh-hhhceecccceEEeccCcchhhheeeEEEEEeccCeeeeEEEEEECCC
Q psy17945          1 MESGAKGCEVVVSGKLRG-QRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLPW   66 (214)
Q Consensus         1 MeaGAkG~EIvISGKL~G-eRARseKF~dG~m~~sG~p~r~~VD~a~~ha~lkqGvIGIKV~Im~p~   66 (214)
                      |++||+||+|+|||||+| ||||+|||.+|+|++++  ++++||||+++|+|+||+||||||||++.
T Consensus       142 m~~gakGIkI~iSGRL~GaeiARtE~~~eG~vpL~T--lra~IDYa~~~a~T~yGviGVKVWI~~ge  206 (239)
T 2vqe_C          142 MESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHT--LRANIDYGFALARTTYGVLGVKAYIFLGE  206 (239)
T ss_dssp             HHSSCSEEEEEECSCTTTCSSCCCBCCEEECCCTTC--GGGCEEEEEECCBCSSCBCCEEEEEECCC
T ss_pred             HHcCCCceEEEEcCCcchhhhhhhhhhhcCccccCC--ccceeEEEEEEEEcCCeeEEEEEEEEcCC
Confidence            689999999999999999 69999999999999998  99999999999999999999999999983

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

Probab=99.88  E-value=6.8e-24  Score=181.59  Aligned_cols=63  Identities=22%  Similarity=0.344  Sum_probs=61.4

Q ss_pred             CCCCCceeEEEEcccchh-hhhceecccceEEeccCcchhhheeeEEEEEeccCeeeeEEEEEECC
Q psy17945          1 MESGAKGCEVVVSGKLRG-QRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLP   65 (214)
Q Consensus         1 MeaGAkG~EIvISGKL~G-eRARseKF~dG~m~~sG~p~r~~VD~a~~ha~lkqGvIGIKV~Im~p   65 (214)
                      |++||+||+|+|||||+| ||||+|+|.+|+||+++  ++++||||+++|+|+||+||||||||+|
T Consensus       153 m~~gakGikI~iSGRL~Gae~AR~e~~~eG~vpl~t--lra~IDy~~~~a~T~yGviGVKVWI~~~  216 (218)
T 3bbn_C          153 EQADTKGIQIQIAGRIDGKEIARIEWIREGRVPLQT--IRAKIDYCAYTVRTIYGVLGIKIWIFMG  216 (218)
T ss_dssp             HTTCCSEEEEECCSCCTTCSSCCCCEEEEECCCSSC--STTCCBCCEEECCCSSCCCEEEEEEECC
T ss_pred             HHhCCCeEEEEEccCcchhhheeEEeEecccccCCc--cccceEEEEEEEEcCCeeEEEEEEEecC
Confidence            789999999999999999 99999999999999976  9999999999999999999999999997

>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=99.88  E-value=1.1e-23  Score=182.70  Aligned_cols=63  Identities=32%  Similarity=0.413  Sum_probs=61.3

Q ss_pred             CCCCCceeEEEEcccchh-hhhceecccceEEeccCcchhhheeeEEEEEeccCeeeeEEEEEECC
Q psy17945          1 MESGAKGCEVVVSGKLRG-QRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLP   65 (214)
Q Consensus         1 MeaGAkG~EIvISGKL~G-eRARseKF~dG~m~~sG~p~r~~VD~a~~ha~lkqGvIGIKV~Im~p   65 (214)
                      |++||+||+|+|||||+| ||||+|||.+|+||+++  ++++||||+++|+|+||+||||||||++
T Consensus       142 m~aGakGikI~iSGRL~GaeiARtE~~~eG~vPL~T--lra~IDY~~~~a~T~yGviGVKVWI~~g  205 (233)
T 3i1m_C          142 MRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHT--LRADIDYNTSEAHTTYGVIGVKVWIFKG  205 (233)
T ss_dssp             HTTCCSEEEEEEESSTTSCSSCCCCBCCEECCCTTC--SSSEEEEEEECCEETTEECEEEEEEEEE
T ss_pred             hhcCCceEEEEEccccCCCcceeEEEEecCeeeccc--cccccEEEEEEEEcCCeeEEEEEEEECC
Confidence            789999999999999999 79999999999999998  8999999999999999999999999997

>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=99.42  E-value=3.5e-14  Score=122.98  Aligned_cols=94  Identities=35%  Similarity=0.539  Sum_probs=61.3

Q ss_pred             ccCeeeeEEEEEECCCCCCCCCCCCCCCCCeEEEeCCcccCCCC--CCcccccCCcccccCCC-CcccccceEEEEecCC
Q psy17945         51 LRQGVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPT--IPSSQVLDKPLAKLGEI-PVASVLGIKVKIMLPW  127 (214)
Q Consensus        51 lkqGvIGIKV~Im~p~Dp~Gk~Gp~~~LPD~v~I~epkee~~~~--~p~s~~~~~p~~~~~~~-~~~GvLGIKVkIMlp~  127 (214)
                      ++.|+.||||.|      +|+++-.  ..-.-...+-.   ++.  .|....   ---...+. -..|+|||||.||+||
T Consensus       127 m~aGakGikI~i------SGRL~Ga--iARtE~~~eG~---vlhTlqtlra~---IDya~~~a~T~yGviGVKVWI~~~~  192 (227)
T 3iz6_B          127 MESGAKGCEVIV------SGKLRAQ--RAKSMKFKDGY---MISSGQPVNEY---IDAAVRHVLLRQGVLGIKVKIMLDW  192 (227)
T ss_dssp             TTTCCSEEECCB------CSCGGGS--SCCCBCCEEEC---CCSSSSCTTSC---EEECCCCCBCSSSBCCCCCEEECSC
T ss_pred             HHcCCceEEEEE------ecccCCc--eeeEeeeeCCe---ecccCChhhhe---eeEEEEEEEcCCeeEEEEEEEECCC
Confidence            788999999998      7887742  22221111111   111  111100   00011122 4679999999999999


Q ss_pred             CCCCCCCCCCCCCCeeEEeCCCCCCCCCCCc
Q psy17945        128 DSTGKTGPKKPLPDNVNVLEPKEEVNPAFPQ  158 (214)
Q Consensus       128 Dp~Gk~Gp~~plPD~V~i~epk~e~~~~~p~  158 (214)
                      ||+|++||+++|||+|+|+|||+|+.+.+|.
T Consensus       193 dp~g~~g~~~~lpD~v~i~~pk~~~~~~~~~  223 (227)
T 3iz6_B          193 DPKGKLGPTTPLPDLVTIHPPKEENELRPPA  223 (227)
T ss_dssp             TTSCCCCCSSCCCCCCSCCCCSSCCCC----
T ss_pred             CcccccCCCCCCCCeEEEeCCCcccCCCCCc
Confidence            9999999999999999999999998888775

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

Probab=99.39  E-value=6.5e-14  Score=122.39  Aligned_cols=97  Identities=38%  Similarity=0.651  Sum_probs=35.3

Q ss_pred             ccCeeeeEEEEEECCCCCCCCCCCCCCCCCeEEEeCCcccCCCC-CCcccccCCcccccCC-CCcccccceEEEEecCCC
Q psy17945         51 LRQGVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPT-IPSSQVLDKPLAKLGE-IPVASVLGIKVKIMLPWD  128 (214)
Q Consensus        51 lkqGvIGIKV~Im~p~Dp~Gk~Gp~~~LPD~v~I~epkee~~~~-~p~s~~~~~p~~~~~~-~~~~GvLGIKVkIMlp~D  128 (214)
                      ++.|+.||||.|      +|+++-.  ..-.-...+-.-  +.+ .|....   ---...+ .-..|+|||||.||+|||
T Consensus       127 m~aGakGikI~i------SGRL~Ga--iARtE~~~eG~v--LhTg~plra~---IDYa~~~a~T~yGvlGVKVWI~~~~d  193 (243)
T 2zkq_c          127 MESGAKGCEVVV------SGKLRGQ--RAKSMKFVDGLM--IHSGDPVNYY---VDTAVRHVLLRQGVLGIKVKIMLPWD  193 (243)
T ss_dssp             HHSSCSEEEEEE------CSSGGGS--SCCCBCCEEESS--HHHHSSTTCC---EEEEEECCCCSSCCCCEEEEEECCCC
T ss_pred             HhcCCceEEEEE------ecchhhH--hhhhhhhcCcEE--eecCchhhhc---eeEEEEEEEcCCceEEEEEEEecCCC
Confidence            678999999999      7887633  222211111111  100 000000   0000111 236799999999999999


Q ss_pred             CCCCCCCCCCCCCeeEEeCCCCCCCCCCCccc
Q psy17945        129 STGKTGPKKPLPDNVNVLEPKEEVNPAFPQKK  160 (214)
Q Consensus       129 p~Gk~Gp~~plPD~V~i~epk~e~~~~~p~~~  160 (214)
                      |+|+.||+++|||.|+|+|||||+.+++|.|.
T Consensus       194 p~g~~gp~~~lpD~v~i~e~k~~~~~~~~~~~  225 (243)
T 2zkq_c          194 PTGKIGPKKPLPDHVSIVEPKDEILPTTPISE  225 (243)
T ss_dssp             --------------------------------
T ss_pred             cCCcCCCCCCCCCeEEEeCCccccccCCCccc
Confidence            99999999999999999999999998888775

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

Probab=99.24  E-value=4.1e-12  Score=110.98  Aligned_cols=97  Identities=26%  Similarity=0.434  Sum_probs=66.8

Q ss_pred             ccCeeeeEEEEEECCCCCCCCCCCCCCCCCeEEEeCCcccCCCCC-CcccccCCcccccCC-CCcccccceEEEEecCCC
Q psy17945         51 LRQGVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTI-PSSQVLDKPLAKLGE-IPVASVLGIKVKIMLPWD  128 (214)
Q Consensus        51 lkqGvIGIKV~Im~p~Dp~Gk~Gp~~~LPD~v~I~epkee~~~~~-p~s~~~~~p~~~~~~-~~~~GvLGIKVkIMlp~D  128 (214)
                      ++.|+.||||.|      +|+++-.  ..-.-...+-.-  +.+- |....-.  - ...+ .-..|+|||||.||+|||
T Consensus       130 m~aGakGIkI~i------SGRL~Ga--iARtE~~~eG~v--L~T~rplra~ID--Y-a~~~a~T~yGvlGVKVWI~~~~~  196 (243)
T 2xzm_C          130 IQDGAKGCEIII------SGKLKQQ--RAKTMKFKQGYM--ICTGQPKNDYID--V-AVRHVFFKQGIMGVKVKIMLPYE  196 (243)
T ss_dssp             HHTTCSEEEEEE------EECTTSS--SCEEEEEEEECC--CCSSSHHHHSEE--E-EEEEEECSSSEEEEEEEEECCCC
T ss_pred             HhcCCceEEEEE------eCCccch--hheeeeeeCCeE--eecCcchhhheE--E-EEEEEEcCCceEEEEEEEecCCC
Confidence            678999999999      7888744  444444433332  2110 0010000  0 0011 135699999999999999


Q ss_pred             CCCCC--CCCCCCCCeeEEeCCCCCCCCCCCccc
Q psy17945        129 STGKT--GPKKPLPDNVNVLEPKEEVNPAFPQKK  160 (214)
Q Consensus       129 p~Gk~--Gp~~plPD~V~i~epk~e~~~~~p~~~  160 (214)
                      |+|+.  ||+++|||.|+|+|||||++..++.+.
T Consensus       197 ~~g~~~~gp~~~lpD~v~i~e~k~~~~~~~~~~~  230 (243)
T 2xzm_C          197 PNPAKKFGVKTPIPDNVIIHPPKQITDDKEIRTA  230 (243)
T ss_dssp             CCTTCCSSCCSCCSSCCBCCCCCCCCCCCCCCCC
T ss_pred             cCCcccCCCCCCCCCeEEEeCCCccccccccccc
Confidence            99999  999999999999999999887766653

>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=99.22  E-value=4.5e-12  Score=110.78  Aligned_cols=94  Identities=32%  Similarity=0.401  Sum_probs=66.1

Q ss_pred             ccCeeeeEEEEEECCCCCCCCCCCCCCCCCeEEEeCCcccCCCCC---CcccccCCcccccCC-CCcccccceEEEEecC
Q psy17945         51 LRQGVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTI---PSSQVLDKPLAKLGE-IPVASVLGIKVKIMLP  126 (214)
Q Consensus        51 lkqGvIGIKV~Im~p~Dp~Gk~Gp~~~LPD~v~I~epkee~~~~~---p~s~~~~~p~~~~~~-~~~~GvLGIKVkIMlp  126 (214)
                      ++.|+.||||.|      +|+++-.  ..-.-...+-.   +..+   -+..-.   - ...+ .-..|+|||||.||+ 
T Consensus       127 m~aGakGikI~i------SGRL~Ga--~ARtE~~~eG~---vlhTgqtlra~ID---Y-a~~~a~T~yGviGVKVWI~~-  190 (240)
T 3u5c_D          127 MESGAKGCEVVV------SGKLRAA--RAKAMKFADGF---LIHSGQPVNDFID---T-ATRHVLMRQGVLGIKVKIMR-  190 (240)
T ss_dssp             HHTTCSEEEEEE------EECSSSS--SCEEEEEEEEC---CCCSSHHHHHHEE---E-EEEEEECSSCEEEEEEEEEC-
T ss_pred             HhcCCceeEEEE------ecccCCc--eeeEEeeecCe---eccCCChhhheee---E-EEEEEEcCCeeEEEEEEEEe-
Confidence            678999999999      7888744  33333333322   1111   111000   0 0111 135699999999999 


Q ss_pred             CCCC-CCCCCCCCCCCeeEEeCCCCCCCCCCCcccCC
Q psy17945        127 WDST-GKTGPKKPLPDNVNVLEPKEEVNPAFPQKKLP  162 (214)
Q Consensus       127 ~Dp~-Gk~Gp~~plPD~V~i~epk~e~~~~~p~~~~~  162 (214)
                       ||+ |++|| +||||+|+|+|||+|+.+++|.|..-
T Consensus       191 -dp~~g~~g~-~~lpD~v~i~epk~~~~~~~~~~~~~  225 (240)
T 3u5c_D          191 -DPAKSRTGP-KALPDAVTIIEPKEEEPILAPSVKDY  225 (240)
T ss_dssp             -CGGGCSSSC-SSCTTCCEECCCCCCCCCCCCCEEEC
T ss_pred             -CcccccCCC-CCCCCeEEEECCccccCCCCCccccc
Confidence             999 99999 99999999999999999999998754

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

Probab=97.10  E-value=0.00014  Score=62.39  Aligned_cols=81  Identities=20%  Similarity=0.380  Sum_probs=34.1

Q ss_pred             ccCeeeeEEEEEECCCCCCCCCCCCCCCCCeEEEeCCcccCCCCCC-cccccCCcccccCCC-CcccccceEEEEecCCC
Q psy17945         51 LRQGVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIP-SSQVLDKPLAKLGEI-PVASVLGIKVKIMLPWD  128 (214)
Q Consensus        51 lkqGvIGIKV~Im~p~Dp~Gk~Gp~~~LPD~v~I~epkee~~~~~p-~s~~~~~p~~~~~~~-~~~GvLGIKVkIMlp~D  128 (214)
                      ++.|+.||||.|      +|+.+-  ...-.-...+   -.+|... +...  .---...+. -..|+|||||.||+|  
T Consensus       121 m~~GakGikI~i------SGRL~G--eiARtE~~~e---G~vpl~tl~a~~--~IDya~~~a~T~yGviGVKVwI~~~--  185 (210)
T 3j20_C          121 MNNGARGVEIRL------SGKLTG--ERAKSIRFYQ---GYLAKVGNPAET--LVSKGYAQALLKLGVIGVKVAIMPP--  185 (210)
T ss_dssp             HHHHCSEEEEEE------EECTTT--TSCEEEEEEE---ECCCCSSSHHHH--HSEEEEEEEECSSCEEEEEEEEECC--
T ss_pred             HhcCCceEEEEE------ecccCc--ceeeEEeeec---ceeeccCCcchh--cEEEEEEEEEcCCcEEEEEEEEECC--
Confidence            578999999999      788874  2332222222   1121111 1100  000001111 356999999999995  


Q ss_pred             CCCCCCCCCCCCCeeEEeCCCCCCC
Q psy17945        129 STGKTGPKKPLPDNVNVLEPKEEVN  153 (214)
Q Consensus       129 p~Gk~Gp~~plPD~V~i~epk~e~~  153 (214)
                             ..+|||.|+|.||+.++.
T Consensus       186 -------e~~lpd~~~i~~~~~~~~  203 (210)
T 3j20_C          186 -------GARLPDEIEIIEKPVEEE  203 (210)
T ss_dssp             -------C-----------------
T ss_pred             -------CCCCCCcEEEeCcchhhh
Confidence                   457999999999998853

>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=95.02  E-value=0.018  Score=50.18  Aligned_cols=78  Identities=21%  Similarity=0.214  Sum_probs=34.3

Q ss_pred             ccCeeeeEEEEEECCCCCCCCCCCCCCCCCeEEEeCCcccCCCCCCcccccCCcccccCCC-CcccccceEEEEecCC-C
Q psy17945         51 LRQGVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGEI-PVASVLGIKVKIMLPW-D  128 (214)
Q Consensus        51 lkqGvIGIKV~Im~p~Dp~Gk~Gp~~~LPD~v~I~epkee~~~~~p~s~~~~~p~~~~~~~-~~~GvLGIKVkIMlp~-D  128 (214)
                      ++.|+.||||.|      +|+++-.+ ..-   ..--.+-.++...   ..+.---...+. -..|+|||||.||++. .
T Consensus       142 m~~gakGIkI~i------SGRL~Gae-iAR---tE~~~eG~vpL~T---lra~IDYa~~~a~T~yGviGVKVWI~~ge~l  208 (239)
T 2vqe_C          142 MESGAKGAKVIV------SGRIGGAE-QAR---TEWAAQGRVPLHT---LRANIDYGFALARTTYGVLGVKAYIFLGEVI  208 (239)
T ss_dssp             HHSSCSEEEEEE------CSCTTTCS-SCC---CBCCEEECCCTTC---GGGCEEEEEECCBCSSCBCCEEEEEECCCC-
T ss_pred             HHcCCCceEEEE------cCCcchhh-hhh---hhhhhcCccccCC---ccceeEEEEEEEEcCCeeEEEEEEEEcCCcC
Confidence            678999999999      78887432 111   1111111121111   110000011122 4679999999999984 4


Q ss_pred             CCCCCCCCCCCCC
Q psy17945        129 STGKTGPKKPLPD  141 (214)
Q Consensus       129 p~Gk~Gp~~plPD  141 (214)
                      |.++.+|..++|-
T Consensus       209 ~~~~~~~~~~~~~  221 (239)
T 2vqe_C          209 GGQKPKARPELPK  221 (239)
T ss_dssp             -------------
T ss_pred             CCcCCCCCCCCcc
Confidence            7888887666553

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

Probab=90.79  E-value=0.32  Score=41.50  Aligned_cols=63  Identities=21%  Similarity=0.171  Sum_probs=34.3

Q ss_pred             ccCeeeeEEEEEECCCCCCCCCCCCCCCCCeEEEeCCcccCCCCCCcccccCCcccccCC-CCcccccceEEEEecC
Q psy17945         51 LRQGVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGE-IPVASVLGIKVKIMLP  126 (214)
Q Consensus        51 lkqGvIGIKV~Im~p~Dp~Gk~Gp~~~LPD~v~I~epkee~~~~~p~s~~~~~p~~~~~~-~~~~GvLGIKVkIMlp  126 (214)
                      ++.|+.||||.|      +|+.+-. ...-.-...   +-.+|..+....   ---...+ .-..|+|||||.||++
T Consensus       153 m~~gakGikI~i------SGRL~Ga-e~AR~e~~~---eG~vpl~tlra~---IDy~~~~a~T~yGviGVKVWI~~~  216 (218)
T 3bbn_C          153 EQADTKGIQIQI------AGRIDGK-EIARIEWIR---EGRVPLQTIRAK---IDYCAYTVRTIYGVLGIKIWIFMG  216 (218)
T ss_dssp             HTTCCSEEEEEC------CSCCTTC-SSCCCCEEE---EECCCSSCSTTC---CBCCEEECCCSSCCCEEEEEEECC
T ss_pred             HHhCCCeEEEEE------ccCcchh-hheeEEeEe---cccccCCccccc---eEEEEEEEEcCCeeEEEEEEEecC
Confidence            678999999999      7888742 222222221   112222221110   0000111 2367999999999986

>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=86.11  E-value=0.37  Score=41.85  Aligned_cols=63  Identities=25%  Similarity=0.316  Sum_probs=33.3

Q ss_pred             ccCeeeeEEEEEECCCCCCCCCCCCCCCCCeEEEeCCcccCCCCCCcccccCCcccccCCC-CcccccceEEEEecC
Q psy17945         51 LRQGVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGEI-PVASVLGIKVKIMLP  126 (214)
Q Consensus        51 lkqGvIGIKV~Im~p~Dp~Gk~Gp~~~LPD~v~I~epkee~~~~~p~s~~~~~p~~~~~~~-~~~GvLGIKVkIMlp  126 (214)
                      ++.|+.||||.|      +|+.+-.+ ..-   ..--.+-.+   |.+...+.---...+. -..|+|||||.||.+
T Consensus       142 m~aGakGikI~i------SGRL~Gae-iAR---tE~~~eG~v---PL~Tlra~IDY~~~~a~T~yGviGVKVWI~~g  205 (233)
T 3i1m_C          142 MRLGAKGIKVEV------SGRLGGAE-IAR---TEWYREGRV---PLHTLRADIDYNTSEAHTTYGVIGVKVWIFKG  205 (233)
T ss_dssp             HTTCCSEEEEEE------ESSTTSCS-SCC---CCBCCEECC---CTTCSSSEEEEEEECCEETTEECEEEEEEEEE
T ss_pred             hhcCCceEEEEE------ccccCCCc-cee---EEEEecCee---eccccccccEEEEEEEEcCCeeEEEEEEEECC
Confidence            678999999999      78876321 111   111111112   1111111000011222 467999999999996

---

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	214
d2uubc2	101	d.53.1.1 (C:107-207) Ribosomal protein S3 C-termin	2e-11
d2qalc2	101	d.53.1.1 (C:106-206) Ribosomal protein S3 C-termin	2e-08

>d2uubc2 d.53.1.1 (C:107-207) Ribosomal protein S3 C-terminal domain {Thermus thermophilus [TaxId: 274]} Length = 101

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]

 Score = 56.4 bits (136), Expect = 2e-11
 Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 3/66 (4%)

Query: 1  MESGAKGCEVVVSGKLRGQRAKSMKFV-DGLMIHSGDPCNDYVNTATRHVLLRQGVLGIK 59
          MESGAKG +V+VSG++ G      ++   G +          ++          GVLG+K
Sbjct: 36 MESGAKGAKVIVSGRIGGAEQARTEWAAQGRV--PLHTLRANIDYGFALARTTYGVLGVK 93

Query: 60 VKIMLP 65
            I L 
Sbjct: 94 AYIFLG 99

>d2qalc2 d.53.1.1 (C:106-206) Ribosomal protein S3 C-terminal domain {Escherichia coli [TaxId: 562]} Length = 101

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]

 Score = 48.7 bits (116), Expect = 2e-08
 Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 3/66 (4%)

Query: 1  MESGAKGCEVVVSGKLRG-QRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIK 59
          M  GAKG +V VSG+L G + A++  + +G +       +  ++  T       GV+G+K
Sbjct: 36 MRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRAD--IDYNTSEAHTTYGVIGVK 93

Query: 60 VKIMLP 65
          V I   
Sbjct: 94 VWIFKG 99

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	214
d2qalc2	101	Ribosomal protein S3 C-terminal domain {Escherichi	99.89
d2uubc2	101	Ribosomal protein S3 C-terminal domain {Thermus th	99.88
d2qalc2	101	Ribosomal protein S3 C-terminal domain {Escherichi	93.24
d2uubc2	101	Ribosomal protein S3 C-terminal domain {Thermus th	83.03

>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=99.89  E-value=1.7e-24  Score=165.13  Aligned_cols=63  Identities=32%  Similarity=0.413  Sum_probs=61.1

Q ss_pred             CCCCCceeEEEEcccchh-hhhceecccceEEeccCcchhhheeeEEEEEeccCeeeeEEEEEECC
Q psy17945          1 MESGAKGCEVVVSGKLRG-QRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLP   65 (214)
Q Consensus         1 MeaGAkG~EIvISGKL~G-eRARseKF~dG~m~~sG~p~r~~VD~a~~ha~lkqGvIGIKV~Im~p   65 (214)
                      |++||+||+|+|||||+| +|||+|+|.+|++++++  ++.+||||+++|+|++|+||||||||+|
T Consensus        36 m~~ga~GikI~isGRl~gae~Ar~e~~~~G~ipl~t--~~~~Idy~~~~a~t~~Gv~GVKVwI~~~   99 (101)
T d2qalc2          36 MRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHT--LRADIDYNTSEAHTTYGVIGVKVWIFKG   99 (101)
T ss_dssp             HHSSCSEEEEEECSCGGGCSSCCCCCCEEECCCTTC--GGGCEEEEECCCCBTTBCCCEEEEEECC
T ss_pred             hhcchheEEEEEeccccchhhheeEEEEEecccccc--cceeEEEEEEEEEcCceeEEEEEEEECC
Confidence            689999999999999999 89999999999999998  8889999999999999999999999997

>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=99.88  E-value=1.5e-23  Score=159.75  Aligned_cols=63  Identities=33%  Similarity=0.464  Sum_probs=60.6

Q ss_pred             CCCCCceeEEEEcccchh-hhhceecccceEEeccCcchhhheeeEEEEEeccCeeeeEEEEEECC
Q psy17945          1 MESGAKGCEVVVSGKLRG-QRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKVKIMLP   65 (214)
Q Consensus         1 MeaGAkG~EIvISGKL~G-eRARseKF~dG~m~~sG~p~r~~VD~a~~ha~lkqGvIGIKV~Im~p   65 (214)
                      |++||+||+|+|||||+| +|||+++|..|.+++++  ++++||||+++|.|++|+||||||||+|
T Consensus        36 m~~ga~GikI~isGrl~g~~~ar~~~~~~G~~~~~t--~~~~Idy~~~~a~tk~GviGVKVwI~~~   99 (101)
T d2uubc2          36 MESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHT--LRANIDYGFALARTTYGVLGVKAYIFLG   99 (101)
T ss_dssp             HHTTCSEEEEEEEESGGGCSSCEEEEEEEECCCTTC--TTSCEEEEEEEEECSSCEEEEEEEEECC
T ss_pred             hhcCccEEEEEEecccCCccceeEEEEEeeeecCcc--eecceeEEEEEEEcCCccEEEEEEEECC
Confidence            789999999999999988 89999999999999865  9999999999999999999999999997

>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=93.24  E-value=0.033  Score=40.75  Aligned_cols=64  Identities=25%  Similarity=0.246  Sum_probs=33.1

Q ss_pred             eccCeeeeEEEEEECCCCCCCCCCCCCCCCCeEEEeCCcccCCCCCCcccccCCcccccCCC-CcccccceEEEEecC
Q psy17945         50 LLRQGVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGEI-PVASVLGIKVKIMLP  126 (214)
Q Consensus        50 ~lkqGvIGIKV~Im~p~Dp~Gk~Gp~~~LPD~v~I~epkee~~~~~p~s~~~~~p~~~~~~~-~~~GvLGIKVkIMlp  126 (214)
                      .++.|+.||||.|      +|+++..+.    -....-++-.++....+..   ---...+. -..|+|||||.||.|
T Consensus        35 ~m~~ga~GikI~i------sGRl~gae~----Ar~e~~~~G~ipl~t~~~~---Idy~~~~a~t~~Gv~GVKVwI~~~   99 (101)
T d2qalc2          35 AMRLGAKGIKVEV------SGRLGGAEI----ARTEWYREGRVPLHTLRAD---IDYNTSEAHTTYGVIGVKVWIFKG   99 (101)
T ss_dssp             HHHSSCSEEEEEE------CSCGGGCSS----CCCCCCEEECCCTTCGGGC---EEEEECCCCBTTBCCCEEEEEECC
T ss_pred             HhhcchheEEEEE------eccccchhh----heeEEEEEeccccccccee---EEEEEEEEEcCceeEEEEEEEECC
Confidence            4788999999999      788843221    1111111112222221110   00001111 345999999999986

>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=83.03  E-value=0.2  Score=36.33  Aligned_cols=63  Identities=22%  Similarity=0.283  Sum_probs=32.6

Q ss_pred             ccCeeeeEEEEEECCCCCCCCCCCCCCCCCeEEEeCCcccCCCCCCcccccCCcccccCC-CCcccccceEEEEecC
Q psy17945         51 LRQGVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGE-IPVASVLGIKVKIMLP  126 (214)
Q Consensus        51 lkqGvIGIKV~Im~p~Dp~Gk~Gp~~~LPD~v~I~epkee~~~~~p~s~~~~~p~~~~~~-~~~~GvLGIKVkIMlp  126 (214)
                      ++.|+.||+|.|      +|+++-..    .-...--..-.++..+....-..-   ..+ .--.|+|||||.||+|
T Consensus        36 m~~ga~GikI~i------sGrl~g~~----~ar~~~~~~G~~~~~t~~~~Idy~---~~~a~tk~GviGVKVwI~~~   99 (101)
T d2uubc2          36 MESGAKGAKVIV------SGRIGGAE----QARTEWAAQGRVPLHTLRANIDYG---FALARTTYGVLGVKAYIFLG   99 (101)
T ss_dssp             HHTTCSEEEEEE------EESGGGCS----SCEEEEEEEECCCTTCTTSCEEEE---EEEEECSSCEEEEEEEEECC
T ss_pred             hhcCccEEEEEE------ecccCCcc----ceeEEEEEeeeecCcceecceeEE---EEEEEcCCccEEEEEEEECC
Confidence            688999999999      67774211    111111111122232222110000   001 1245999999999997