Psyllid ID: psy8115

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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-------22
Protein Sequence
MFGLWKMETTRSGQHANKGQEWPISTRYITTPWRPGPGVPTTPLTQTISNGATVRDSPLGFSVLFRVLVNTIGVSNSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTYADAPSTLPVDA
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccEEEccccccccccccccEEEEccccEEcccccEEEEEEEEEEEccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEcccEEEEEEEEccccEEcccccHHHHHHHHHHHHHHccccccEEEEEEEEccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccEEEEEcccccccccccccccccEEEEccccccccccccccccEEEccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHcccccEEEEEccccEEEEEEEEccccEccccccHHHHHHHHHHHHcccccccEEEEEEEcccccccHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHccccccccccccc
Coil and Loop (DISEMBL)
mfglwkmettrsgqhankgqewpistryittpwrpgpgvpttpltqtisngatvrdsplgFSVLFRVLVNTIGVSNSLSICVSLQFVADGVFRAELDEFLTRElaedgysgveirftpaRTEIIIMATRTqnvlgdkgrRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLavrrynsdvslyclncytyadapstlpvda
Flexible Loop (DISEMBL)
mfglwkmettrsgqhankgqewpisTRYITTPWRPGPGVPTTPLTQTISNGATVRDSPLGFSVLFRVLVNTIGVSNSLSICVSLQFVADGVFRAELDEFLTrelaedgysgveirftparteIIIMAtrtqnvlgdkgrrIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCytyadapstlpvda
Low Complexity Region (SEG)
MFGLWKMETTRSGQHANKGQEWPISTRYITTPWRPGPGVPTTPLTQTISNGATVRDSPLGFSVLFRVLVNTIGVSNSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTYADAPSTLPVDA
Disordered region (IsUnstruct)
*********************WPISTRYITTPWRPGPGVPTTPLTQTISNGATVRDSPLGFSVLFRVLVNTIGVSNSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTYAD*********
Disordered Region (DISOPRED)
************************STRYITTPWRPGPGVPTTPLTQTISNGATVRDSPLGFSVLFRVLVNTIGVSNSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTYADAPSTLP***
Disordered Region (DISEMBL)
******************GQEWPISTRYITTPWRPGPGVPTTPLTQTISNGATVRDSPLGFSVLFRVLVNTIGVSNSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTYADAPSTLPVDA
Disordered Region (DISPRO)
*FGLWKMETTRSG******QEWPISTRYITTPWRPGPGVPTTPLTQTISNGATVRDSPLGFSVLFRVLVNTIGVSNSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTYADAPSTL****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MFGLWKMETTRSGQHANKGQEWPISTRYITTPWRPGPGVPTTPLTQTISNGATVRDSPLGFSVLFRVLVNTIGVSNSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTYADAPSTLPVDA
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	218	2.2.26 [Sep-21-2011]
P62909	243	40S ribosomal protein S3	yes	N/A	0.532	0.477	0.801	4e-49
P62908	243	40S ribosomal protein S3	yes	N/A	0.532	0.477	0.801	4e-49
E2RH47	243	40S ribosomal protein S3	yes	N/A	0.532	0.477	0.801	4e-49
Q0Z8U2	243	40S ribosomal protein S3	yes	N/A	0.532	0.477	0.801	4e-49
P23396	243	40S ribosomal protein S3	yes	N/A	0.532	0.477	0.801	4e-49
Q3T169	243	40S ribosomal protein S3	yes	N/A	0.532	0.477	0.801	4e-49
P02350	246	40S ribosomal protein S3-	N/A	N/A	0.532	0.471	0.801	4e-49
P79891	253	40S ribosomal protein S3	N/A	N/A	0.532	0.458	0.801	6e-49
Q5R465	243	40S ribosomal protein S3	yes	N/A	0.532	0.477	0.793	1e-48
Q90YS2	245	40S ribosomal protein S3	N/A	N/A	0.532	0.473	0.793	2e-48

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

 Score =  194 bits (493), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 93/116 (80%), Positives = 107/116 (92%)

Query: 77  SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
           ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct: 2   AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query: 137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct: 62  KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

Rattus norvegicus (taxid: 10116)

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

 Score =  194 bits (493), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 93/116 (80%), Positives = 107/116 (92%)

Query: 77  SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
           ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct: 2   AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query: 137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct: 62  KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

Mus musculus (taxid: 10090)

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

 Score =  194 bits (493), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 93/116 (80%), Positives = 107/116 (92%)

Query: 77  SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
           ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct: 2   AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query: 137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct: 62  KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

Canis familiaris (taxid: 9615)

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

 Score =  194 bits (493), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 93/116 (80%), Positives = 107/116 (92%)

Query: 77  SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
           ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct: 2   AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query: 137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct: 62  KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

Sus scrofa (taxid: 9823)

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

 Score =  194 bits (493), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 93/116 (80%), Positives = 107/116 (92%)

Query: 77  SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
           ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct: 2   AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query: 137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct: 62  KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

Homo sapiens (taxid: 9606)

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

 Score =  194 bits (493), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 93/116 (80%), Positives = 107/116 (92%)

Query: 77  SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
           ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct: 2   AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query: 137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct: 62  KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

Bos taurus (taxid: 9913)

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

 Score =  194 bits (492), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 93/116 (80%), Positives = 107/116 (92%)

Query: 77  SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
           ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct: 2   AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query: 137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct: 62  KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

Xenopus laevis (taxid: 8355)

>sp|P79891|RS3_AMBME 40S ribosomal protein S3 OS=Ambystoma mexicanum GN=RPS3 PE=2 SV=1

 Score =  194 bits (492), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 93/116 (80%), Positives = 107/116 (92%)

Query: 77  SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
           ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct: 2   AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query: 137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct: 62  KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

Ambystoma mexicanum (taxid: 8296)

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

 Score =  192 bits (489), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 92/116 (79%), Positives = 107/116 (92%)

Query: 77  SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
           ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct: 2   AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query: 137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           KGRRIRELT+VVQKRF F +G++ELYAE+VATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct: 62  KGRRIRELTAVVQKRFGFPEGSVELYAEEVATRGLCAIAQAESLRYKLLGGLAVRR 117

Pongo abelii (taxid: 9601)

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

 Score =  192 bits (487), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 92/116 (79%), Positives = 106/116 (91%)

Query: 77  SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
           ++ I    +FV+DG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct: 2   AVQISKKRKFVSDGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query: 137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           KGRRIRELT+VVQKRF F  G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct: 62  KGRRIRELTAVVQKRFGFPRGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

Ictalurus punctatus (taxid: 7998)

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	218
121543809	248	putative ribosomal protein S3 [Maconelli	0.495	0.435	0.907	4e-49
121511934	243	40S ribosomal protein S3 [Xenopsylla che	0.522	0.469	0.842	2e-48
149068846	151	rCG40478, isoform CRA_h [Rattus norvegic	0.582	0.841	0.755	4e-48
157118131	256	40S ribosomal protein S3 [Aedes aegypti]	0.495	0.421	0.888	8e-48
395521196	245	PREDICTED: 40S ribosomal protein S3 [Sar	0.5	0.444	0.853	9e-48
417409029	251	Putative 40s ribosomal protein s3, parti	0.545	0.474	0.789	1e-47
312380148	278	hypothetical protein AND_07881 [Anophele	0.490	0.384	0.897	1e-47
260833516	226	hypothetical protein BRAFLDRAFT_56803 [B	0.495	0.477	0.870	1e-47
148684443	243	ribosomal protein S3, isoform CRA_e [Mus	0.532	0.477	0.801	1e-47
348522975	245	PREDICTED: 40S ribosomal protein S3-like	0.532	0.473	0.801	1e-47

>gi|121543809|gb|ABM55569.1| putative ribosomal protein S3 [Maconellicoccus hirsutus]

 Score =  200 bits (508), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 98/108 (90%), Positives = 104/108 (96%)

Query: 85  QFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 144
           +FVADGVF+AEL+EFL RELAEDGYSGV+IR TP RTEIIIMATRTQNVLG+KGRRIREL
Sbjct: 10  KFVADGVFKAELNEFLMRELAEDGYSGVQIRVTPTRTEIIIMATRTQNVLGEKGRRIREL 69

Query: 145 TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           TSVVQKRFKF DG+IELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR
Sbjct: 70  TSVVQKRFKFPDGSIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 117

Source: Maconellicoccus hirsutus

Species: Maconellicoccus hirsutus

Genus: Maconellicoccus

Family: Pseudococcidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|121511934|gb|ABM55418.1| 40S ribosomal protein S3 [Xenopsylla cheopis]

 Score =  197 bits (501), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 96/114 (84%), Positives = 105/114 (92%)

Query: 79  SICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKG 138
           +I    +FVADGVF+AEL+EFLTRELAEDGYSGVE+R TP RTEIIIMATRTQNVLG+KG
Sbjct: 4   AISKKRKFVADGVFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIIMATRTQNVLGEKG 63

Query: 139 RRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           RRIRELT+VVQKRF F D ++ELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR
Sbjct: 64  RRIRELTAVVQKRFNFIDNSVELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 117

Source: Xenopsylla cheopis

Species: Xenopsylla cheopis

Genus: Xenopsylla

Family: Pulicidae

Order: Siphonaptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|149068846|gb|EDM18398.1| rCG40478, isoform CRA_h [Rattus norvegicus]

 Score =  196 bits (499), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 96/127 (75%), Positives = 111/127 (87%)

Query: 77  SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
           ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct: 2   AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query: 137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSD 196
           KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR  S 
Sbjct: 62  KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRVGSQ 121

Query: 197 VSLYCLN 203
               CL+
Sbjct: 122 SHPPCLS 128

Source: Rattus norvegicus

Species: Rattus norvegicus

Genus: Rattus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

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

 Score =  195 bits (496), Expect = 8e-48,   Method: Compositional matrix adjust.
 Identities = 96/108 (88%), Positives = 103/108 (95%)

Query: 85  QFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 144
           QFVA+G+FRAEL+EFLTRELAEDGYSGVE+R TP RTEIIIMATRTQNVLG+KGRRIREL
Sbjct: 23  QFVANGMFRAELNEFLTRELAEDGYSGVEVRVTPTRTEIIIMATRTQNVLGEKGRRIREL 82

Query: 145 TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           T+VVQKRF FA G +ELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR
Sbjct: 83  TAVVQKRFGFAPGTVELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 130

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|395521196|ref|XP_003764704.1| PREDICTED: 40S ribosomal protein S3 [Sarcophilus harrisii]

 Score =  195 bits (496), Expect = 9e-48,   Method: Compositional matrix adjust.
 Identities = 93/109 (85%), Positives = 105/109 (96%)

Query: 84  LQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRE 143
           +QFVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+KGRRIRE
Sbjct: 11  VQFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRE 70

Query: 144 LTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           LT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct: 71  LTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 119

Source: Sarcophilus harrisii

Species: Sarcophilus harrisii

Genus: Sarcophilus

Family: Dasyuridae

Order: Dasyuromorphia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|417409029|gb|JAA51041.1| Putative 40s ribosomal protein s3, partial [Desmodus rotundus]

 Score =  195 bits (496), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 94/119 (78%), Positives = 108/119 (90%)

Query: 74  VSNSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNV 133
           V  ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNV
Sbjct: 7   VKMAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNV 66

Query: 134 LGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           LG+KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct: 67  LGEKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 125

Source: Desmodus rotundus

Species: Desmodus rotundus

Genus: Desmodus

Family: Phyllostomidae

Order: Chiroptera

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|312380148|gb|EFR26232.1| hypothetical protein AND_07881 [Anopheles darlingi]

 Score =  195 bits (496), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 96/107 (89%), Positives = 103/107 (96%)

Query: 86  FVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELT 145
           FVA+G+FRAEL+EFLTRELAEDGYSGVE+R TP RTEIIIMATRTQNVLG+KGRRIRELT
Sbjct: 46  FVANGMFRAELNEFLTRELAEDGYSGVEVRVTPTRTEIIIMATRTQNVLGEKGRRIRELT 105

Query: 146 SVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           SVVQKRF FA G++ELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR
Sbjct: 106 SVVQKRFGFAPGSVELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 152

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|260833516|ref|XP_002611703.1| hypothetical protein BRAFLDRAFT_56803 [Branchiostoma floridae] gi|229297074|gb|EEN67713.1| hypothetical protein BRAFLDRAFT_56803 [Branchiostoma floridae]

 Score =  195 bits (495), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 94/108 (87%), Positives = 103/108 (95%)

Query: 85  QFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 144
           +FVADGVF+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+KGRRIREL
Sbjct: 10  KFVADGVFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIREL 69

Query: 145 TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           TSVVQKRF FA+G +ELYAEKVA RGLCAIAQAESLRYKL+GGLAVRR
Sbjct: 70  TSVVQKRFGFAEGTVELYAEKVAQRGLCAIAQAESLRYKLLGGLAVRR 117

Source: Branchiostoma floridae

Species: Branchiostoma floridae

Genus: Branchiostoma

Family: Branchiostomidae

Phylum: Chordata

Superkingdom: Eukaryota

>gi|148684443|gb|EDL16390.1| ribosomal protein S3, isoform CRA_e [Mus musculus]

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 93/116 (80%), Positives = 107/116 (92%)

Query: 77  SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
           ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct: 2   AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query: 137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct: 62  KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

Source: Mus musculus

Species: Mus musculus

Genus: Mus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|348522975|ref|XP_003448999.1| PREDICTED: 40S ribosomal protein S3-like [Oreochromis niloticus]

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 93/116 (80%), Positives = 107/116 (92%)

Query: 77  SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
           ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct: 2   AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query: 137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct: 62  KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

Source: Oreochromis niloticus

Species: Oreochromis niloticus

Genus: Oreochromis

Family: Cichlidae

Order: Perciformes

Class: Actinopterygii

Phylum: Chordata

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	218
UNIPROTKB|H0YCJ7	135	RPS3 "40S ribosomal protein S3	0.541	0.874	0.798	6.2e-46
UNIPROTKB|F1N9X5	243	RPS3 "Uncharacterized protein"	0.532	0.477	0.801	3.4e-45
UNIPROTKB|Q3T169	243	RPS3 "40S ribosomal protein S3	0.532	0.477	0.801	3.4e-45
UNIPROTKB|E2RH47	243	RPS3 "40S ribosomal protein S3	0.532	0.477	0.801	3.4e-45
UNIPROTKB|E9PL45	164	RPS3 "40S ribosomal protein S3	0.532	0.707	0.801	3.4e-45
UNIPROTKB|F2Z2S8	117	RPS3 "40S ribosomal protein S3	0.532	0.991	0.801	3.4e-45
UNIPROTKB|P23396	243	RPS3 "40S ribosomal protein S3	0.532	0.477	0.801	3.4e-45
UNIPROTKB|Q0Z8U2	243	RPS3 "40S ribosomal protein S3	0.532	0.477	0.801	3.4e-45
MGI|MGI:1350917	243	Rps3 "ribosomal protein S3" [M	0.532	0.477	0.801	3.4e-45
RGD|619888	243	Rps3 "ribosomal protein S3" [R	0.532	0.477	0.801	3.4e-45

UNIPROTKB|H0YCJ7 RPS3 "40S ribosomal protein S3" [Homo sapiens (taxid:9606)]

 Score = 482 (174.7 bits), Expect = 6.2e-46, P = 6.2e-46
 Identities = 95/119 (79%), Positives = 109/119 (91%)

Query:    85 QFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 144
             +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+KGRRIREL
Sbjct:     7 KFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIREL 66

Query:   145 TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVS-LYCL 202
             T+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR     + L+CL
Sbjct:    67 TAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRVGPKAARLWCL 125

GO:0003723 "RNA binding" evidence=IEA

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

 Score = 475 (172.3 bits), Expect = 3.4e-45, P = 3.4e-45
 Identities = 93/116 (80%), Positives = 107/116 (92%)

Query:    77 SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
             ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct:     2 AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query:   137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
             KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct:    62 KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

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

GO:0006412 "translation" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0003729 "mRNA binding" evidence=IEA

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

GO:0004519 "endonuclease activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006917 "induction of apoptosis" evidence=IEA

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

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

GO:0019901 "protein kinase binding" evidence=IEA

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

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

GO:0032587 "ruffle membrane" evidence=IEA

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

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

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

 Score = 475 (172.3 bits), Expect = 3.4e-45, P = 3.4e-45
 Identities = 93/116 (80%), Positives = 107/116 (92%)

Query:    77 SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
             ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct:     2 AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query:   137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
             KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct:    62 KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

GO:0030529 "ribonucleoprotein complex" evidence=ISS

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

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

GO:0032587 "ruffle membrane" evidence=IEA

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

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

GO:0019901 "protein kinase binding" evidence=IEA

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

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

GO:0006917 "induction of apoptosis" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

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

GO:0003729 "mRNA binding" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

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

 Score = 475 (172.3 bits), Expect = 3.4e-45, P = 3.4e-45
 Identities = 93/116 (80%), Positives = 107/116 (92%)

Query:    77 SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
             ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct:     2 AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query:   137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
             KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct:    62 KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

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|E9PL45 RPS3 "40S ribosomal protein S3" [Homo sapiens (taxid:9606)]

 Score = 475 (172.3 bits), Expect = 3.4e-45, P = 3.4e-45
 Identities = 93/116 (80%), Positives = 107/116 (92%)

Query:    77 SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
             ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct:     2 AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query:   137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
             KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct:    62 KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

GO:0003723 "RNA binding" evidence=IEA

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

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

UNIPROTKB|F2Z2S8 RPS3 "40S ribosomal protein S3" [Homo sapiens (taxid:9606)]

 Score = 475 (172.3 bits), Expect = 3.4e-45, P = 3.4e-45
 Identities = 93/116 (80%), Positives = 107/116 (92%)

Query:    77 SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
             ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct:     2 AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query:   137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
             KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct:    62 KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

 Score = 475 (172.3 bits), Expect = 3.4e-45, P = 3.4e-45
 Identities = 93/116 (80%), Positives = 107/116 (92%)

Query:    77 SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
             ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct:     2 AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query:   137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
             KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct:    62 KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

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 = 475 (172.3 bits), Expect = 3.4e-45, P = 3.4e-45
 Identities = 93/116 (80%), Positives = 107/116 (92%)

Query:    77 SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
             ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct:     2 AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query:   137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
             KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct:    62 KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

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

MGI|MGI:1350917 Rps3 "ribosomal protein S3" [Mus musculus (taxid:10090)]

 Score = 475 (172.3 bits), Expect = 3.4e-45, P = 3.4e-45
 Identities = 93/116 (80%), Positives = 107/116 (92%)

Query:    77 SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
             ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct:     2 AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query:   137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
             KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct:    62 KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

GO:0003684 "damaged DNA binding" evidence=ISO

GO:0003723 "RNA binding" evidence=IEA

GO:0003729 "mRNA binding" evidence=ISO

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

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

GO:0004519 "endonuclease activity" evidence=ISO

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO;IDA

GO:0005829 "cytosol" evidence=ISO

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0006917 "induction of apoptosis" evidence=ISO

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

GO:0012505 "endomembrane system" evidence=ISO

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0019901 "protein kinase binding" evidence=ISO

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

GO:0030425 "dendrite" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=ISO

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

GO:0032587 "ruffle membrane" evidence=ISO

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

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

RGD|619888 Rps3 "ribosomal protein S3" [Rattus norvegicus (taxid:10116)]

 Score = 475 (172.3 bits), Expect = 3.4e-45, P = 3.4e-45
 Identities = 93/116 (80%), Positives = 107/116 (92%)

Query:    77 SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
             ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct:     2 AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61

Query:   137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
             KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct:    62 KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

GO:0003684 "damaged DNA binding" evidence=ISO

GO:0003723 "RNA binding" evidence=IEA

GO:0003729 "mRNA binding" evidence=ISO

GO:0003735 "structural constituent of ribosome" evidence=IC;ISO

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

GO:0004519 "endonuclease activity" evidence=ISO

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0005829 "cytosol" evidence=ISO

GO:0006412 "translation" evidence=IC

GO:0006917 "induction of apoptosis" evidence=ISO

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

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

GO:0012505 "endomembrane system" evidence=IDA

GO:0019901 "protein kinase binding" evidence=ISO

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

GO:0030425 "dendrite" evidence=IDA

GO:0030529 "ribonucleoprotein complex" evidence=ISO;ISS

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

GO:0032587 "ruffle membrane" evidence=ISO

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

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

---

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	0.7931	0.5321	0.4773	yes	N/A
P05750	RS3_YEAST	No assigned EC number	0.624	0.5733	0.5208	yes	N/A
P48152	RS3_CAEEL	No assigned EC number	0.7641	0.4862	0.4291	yes	N/A
O60128	RS3_SCHPO	No assigned EC number	0.6538	0.5963	0.5220	yes	N/A
E2RH47	RS3_CANFA	No assigned EC number	0.8017	0.5321	0.4773	yes	N/A
Q0Z8U2	RS3_PIG	No assigned EC number	0.8017	0.5321	0.4773	yes	N/A
P23396	RS3_HUMAN	No assigned EC number	0.8017	0.5321	0.4773	yes	N/A
Q3T169	RS3_BOVIN	No assigned EC number	0.8017	0.5321	0.4773	yes	N/A
P62909	RS3_RAT	No assigned EC number	0.8017	0.5321	0.4773	yes	N/A
P62908	RS3_MOUSE	No assigned EC number	0.8017	0.5321	0.4773	yes	N/A
Q9FJA6	RS33_ARATH	No assigned EC number	0.8425	0.4954	0.4354	yes	N/A
Q06559	RS3_DROME	No assigned EC number	0.7153	0.5963	0.5284	yes	N/A
P90526	RS3_DICDI	No assigned EC number	0.575	0.5458	0.5458	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	218
PTZ00084	220	PTZ00084, PTZ00084, 40S ribosomal protein S3; Prov	8e-65
cd02413	81	cd02413, 40S_S3_KH, K homology RNA-binding (KH) do	8e-51
TIGR01008	195	TIGR01008, rpsC_E_A, ribosomal protein S3, eukaryo	7e-34
COG0092	233	COG0092, RpsC, Ribosomal protein S3 [Translation,	2e-24
cd02411	85	cd02411, archeal_30S_S3_KH, K homology RNA-binding	8e-18
PRK04191	207	PRK04191, rps3p, 30S ribosomal protein S3P; Review	5e-17
pfam07650	77	pfam07650, KH_2, KH domain	4e-16
cd02409	68	cd02409, KH-II, KH-II (K homology RNA-binding doma	2e-11

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

 Score =  199 bits (508), Expect = 8e-65
 Identities = 83/107 (77%), Positives = 95/107 (88%)

Query: 86  FVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELT 145
           FVADGVF AEL+EFL+RELAEDGYSGVE+R TP RTEIII ATRT+ VLGDKGRRIRELT
Sbjct: 11  FVADGVFYAELNEFLSRELAEDGYSGVEVRVTPIRTEIIIRATRTREVLGDKGRRIRELT 70

Query: 146 SVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           S++QKRF F +G +EL+AE+V  RGLCA+AQAESLRYKL+ GL VRR
Sbjct: 71  SLLQKRFGFPEGKVELFAERVENRGLCAMAQAESLRYKLLEGLPVRR 117

Length = 220

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

 Score =  158 bits (403), Expect = 8e-51
 Identities = 67/81 (82%), Positives = 74/81 (91%)

Query: 90  GVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQ 149
           GVF AEL+EFLTRELAEDGYSGVE+R TP RTEIII ATRTQNVLG+KGRRIRELTS+VQ
Sbjct: 1   GVFYAELNEFLTRELAEDGYSGVEVRVTPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQ 60

Query: 150 KRFKFADGAIELYAEKVATRG 170
           KRF F +G++ELYAEKVA RG
Sbjct: 61  KRFNFPEGSVELYAEKVANRG 81

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

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

 Score =  119 bits (300), Expect = 7e-34
 Identities = 52/107 (48%), Positives = 65/107 (60%), Gaps = 2/107 (1%)

Query: 86  FVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELT 145
           FVA+GV R  +DEFL +EL E GYSGV++R TP  T++II A R   V+G  GRRIRELT
Sbjct: 5   FVAEGVKRTLIDEFLKKELREAGYSGVDVRVTPLGTKVIIFAERPGLVIGRGGRRIRELT 64

Query: 146 SVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
             +QK  KF     ++  E+V    L A  QAE +   L  GL  RR
Sbjct: 65  EKLQK--KFGLENPQIDVEEVENPELNAQVQAERIARSLERGLHFRR 109

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

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

 Score = 95.8 bits (239), Expect = 2e-24
 Identities = 36/108 (33%), Positives = 56/108 (51%), Gaps = 2/108 (1%)

Query: 85  QFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 144
           ++    V   ++ EFL +EL+  G SGVEI  TP  T + I A R   V+G KG  I +L
Sbjct: 17  EYAKLLVEDLKIREFLEKELSNAGISGVEIERTPKGTRVTIHAARPGLVIGKKGSNIEKL 76

Query: 145 TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
              ++K F   +  +++  E+V    L A   AES+  +L   ++ RR
Sbjct: 77  RKELEKLFGKEN--VQINIEEVKKPELDAQLVAESIAQQLERRVSFRR 122

Length = 233

>gnl|CDD|239094 cd02411, archeal_30S_S3_KH, K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein

 Score = 74.6 bits (184), Expect = 8e-18
 Identities = 33/79 (41%), Positives = 48/79 (60%)

Query: 82  VSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRI 141
           V  +FV +GV R  +DE+L +EL   GY G+EI  TP  T+I I A R   V+G  G+ I
Sbjct: 1   VERKFVNEGVKRTMIDEYLEKELERAGYGGMEILRTPLGTQITIYAERPGMVIGRGGKNI 60

Query: 142 RELTSVVQKRFKFADGAIE 160
           RELT +++ +F   +  I+
Sbjct: 61  RELTEILETKFGLENPQID 79

S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 85

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

 Score = 75.7 bits (187), Expect = 5e-17
 Identities = 39/101 (38%), Positives = 56/101 (55%), Gaps = 12/101 (11%)

Query: 85  QFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 144
           +FV +G+ +  +DE+L +EL   GY G+EI+ TP  T I I A R   V+G  G+ IREL
Sbjct: 6   KFVEEGLKKVMIDEYLAKELYRAGYGGMEIKKTPLGTRITIYAERPGMVIGRGGKNIREL 65

Query: 145 TSVVQKRFKFADGAI--------ELYAEKVATRGLCAIAQA 177
           T +++K+F   +  I        EL A  VA R    +A A
Sbjct: 66  TEILEKKFGLENPQIDVKEVENPELNARVVAFR----LANA 102

Length = 207

>gnl|CDD|203707 pfam07650, KH_2, KH domain

 Score = 69.9 bits (172), Expect = 4e-16
 Identities = 22/72 (30%), Positives = 37/72 (51%)

Query: 95  ELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKF 154
           E+ EFL  EL + G S +EI  TP R  ++I  ++   V+G  G  I++L   ++K  + 
Sbjct: 1   EIREFLAVELKKAGISDIEIERTPNRVIVVIRTSQPGIVIGKGGSNIKKLGKELRKLIEL 60

Query: 155 ADGAIELYAEKV 166
               + L   +V
Sbjct: 61  EGKKVYLNIVEV 72

Length = 77

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

 Score = 57.3 bits (139), Expect = 2e-11
 Identities = 29/60 (48%), Positives = 36/60 (60%), Gaps = 2/60 (3%)

Query: 97  DEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQ--NVLGDKGRRIRELTSVVQKRFKF 154
            EFL + LA  G SGVEI  TP R EIII+  R Q   V+G KG+ IR L  ++QK  + 
Sbjct: 1   REFLKKLLAPAGISGVEIERTPDRIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLLRK 60

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension. Length = 68

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	218
PTZ00084	220	40S ribosomal protein S3; Provisional	100.0
COG0092	233	RpsC Ribosomal protein S3 [Translation, ribosomal	100.0
TIGR01008	195	rpsC_E_A ribosomal protein S3, eukaryotic/archaeal	100.0
PRK04191	207	rps3p 30S ribosomal protein S3P; Reviewed	100.0
CHL00048	214	rps3 ribosomal protein S3	100.0
TIGR01009	211	rpsC_bact ribosomal protein S3, bacterial type. TI	99.97
PRK00310	232	rpsC 30S ribosomal protein S3; Reviewed	99.97
KOG3181|consensus	244		99.95
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	99.87
cd02412	109	30S_S3_KH K homology RNA-binding (KH) domain of th	99.84
cd02411	85	archeal_30S_S3_KH K homology RNA-binding domain (K	99.82
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	99.6
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	98.91
smart00322	69	KH K homology RNA-binding domain.	97.77
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	96.96
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	96.96
PRK01064	78	hypothetical protein; Provisional	95.88
PF00189	85	Ribosomal_S3_C: Ribosomal protein S3, C-terminal d	95.75
COG1847	208	Jag Predicted RNA-binding protein [General functio	94.96
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	94.84
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	94.72
PRK02821	77	hypothetical protein; Provisional	94.55
PRK08406	140	transcription elongation factor NusA-like protein;	94.1
PRK00468	75	hypothetical protein; Provisional	93.33
TIGR00436	270	era GTP-binding protein Era. Era is an essential G	92.77
PRK15494	339	era GTPase Era; Provisional	92.65
COG1159	298	Era GTPase [General function prediction only]	92.46
COG1837	76	Predicted RNA-binding protein (contains KH domain)	91.65
COG1782	637	Predicted metal-dependent RNase, consists of a met	91.15
PRK00089	292	era GTPase Era; Reviewed	89.81
TIGR03675	630	arCOG00543 arCOG00543 universal archaeal KH-domain	88.25
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	86.84

>PTZ00084 40S ribosomal protein S3; Provisional

Probab=100.00  E-value=1.9e-37  Score=270.35  Aligned_cols=129  Identities=66%  Similarity=0.970  Sum_probs=126.5

Q ss_pred             cchhhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCC
Q psy8115          78 LSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADG  157 (218)
Q Consensus        78 ~~~~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~k  157 (218)
                      .|++.+++||+|++++++|||||.++|.++|||+|+|+|+++.++|+||+++||+|||++|+++++|++.|+++|+++++
T Consensus         3 ~~~~~~k~fi~~~~~~~~~re~l~k~~~~agis~ieI~Rt~~~i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~~~~~~   82 (220)
T PTZ00084          3 GQISKKRKFVADGVFYAELNEFLSRELAEDGYSGVEVRVTPIRTEIIIRATRTREVLGDKGRRIRELTSLLQKRFGFPEG   82 (220)
T ss_pred             cccchhhHHHHcchhhHHHHHHHHHHHHHCCcceEEEEEcCCcEEEEEEECCCccEEcCCchHHHHHHHHHHHHhCCCCc
Confidence            56889999999999999999999999999999999999999999999999999999999999999999999999998889


Q ss_pred             cEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCC
Q psy8115         158 AIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYT  206 (218)
Q Consensus       158 kI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA  206 (218)
                      +|+|++.||++|++||.++|++||+|||+|++||||||+||+++|++||
T Consensus        83 ~i~i~v~ev~~P~l~A~lvA~~IA~qLe~rv~FRRa~k~ai~~~m~aGa  131 (220)
T PTZ00084         83 KVELFAERVENRGLCAMAQAESLRYKLLEGLPVRRAAYGVLRHVMESGA  131 (220)
T ss_pred             eEEEEEEEecCCCcCHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHcCC
Confidence            9999999999999999999999999999999999999999999999998

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

Probab=100.00  E-value=2e-36  Score=265.26  Aligned_cols=122  Identities=29%  Similarity=0.369  Sum_probs=117.0

Q ss_pred             hhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEE
Q psy8115          81 CVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIE  160 (218)
Q Consensus        81 ~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~  160 (218)
                      .+|.+++.+|.   +|||||.++|.+||||+|+|+|++++++|+||++|||+|||++|++|++|+..|+++|+.+  ++.
T Consensus        16 ~~~~~~l~ed~---kIre~l~k~l~~Ag~s~veIeR~~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~--~v~   90 (233)
T COG0092          16 KEYAKLLVEDL---KIREFLEKELSNAGISGVEIERTPKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKE--NVQ   90 (233)
T ss_pred             ccchHHHHHHH---HHHHHHHHHHHhCCcceEEEEecCCceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCC--Cce
Confidence            57888888887   9999999999999999999999999999999999999999999999999999999999963  788


Q ss_pred             EEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCCc
Q psy8115         161 LYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTY  207 (218)
Q Consensus       161 I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA~  207 (218)
                      |+|.||++|++||+++|++||.|||+|++||||||+||+++|++||-
T Consensus        91 I~i~EV~~peL~A~lvA~~IA~qLErrv~FRRA~k~ai~~~M~aGAk  137 (233)
T COG0092          91 INIEEVKKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGAK  137 (233)
T ss_pred             EEEEEcCCCCcCHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHcCCc
Confidence            99999999999999999999999999999999999999999999984

>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type

Probab=100.00  E-value=2.6e-35  Score=252.95  Aligned_cols=122  Identities=41%  Similarity=0.581  Sum_probs=118.4

Q ss_pred             hhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEE
Q psy8115          83 SLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELY  162 (218)
Q Consensus        83 ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~  162 (218)
                      +++|++|++++.+|||||.++|.++|||+|+|+|+++.++|+||+++||++||++|+++++|++.|+++++.  .+++|+
T Consensus         2 ~kkfi~~~~~~~~ire~l~k~~~~agis~ieI~r~~~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k~~~~--~~~~I~   79 (195)
T TIGR01008         2 ERKFVAEGLKRTLIDEFLKKELREAGYSGVDVRVTPLGTKVIIFAERPGLVIGRGGRRIRELTEKLQKKFGL--ENPQID   79 (195)
T ss_pred             cEehHhcchHHHHHHHHHHHHHHhCCeeEEEEEEcCCcEEEEEEECCCceEECCCchHHHHHHHHHHHHhCC--CceEEE
Confidence            689999999999999999999999999999999999999999999999999999999999999999999975  368999


Q ss_pred             EEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCC
Q psy8115         163 AEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYT  206 (218)
Q Consensus       163 I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA  206 (218)
                      +.||++|++||.++|++||+|||+|++||||||+||+++|++||
T Consensus        80 v~ev~~p~l~A~lvA~~Ia~qLe~rv~fRra~k~ai~~~m~aGa  123 (195)
T TIGR01008        80 VEEVENPELNAQVQAERIARSLERGLHFRRAAYTAVRRIMEAGA  123 (195)
T ss_pred             EEEEeCCCcCHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCC
Confidence            99999999999999999999999999999999999999999997

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

>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed

Probab=100.00  E-value=4.9e-34  Score=246.40  Aligned_cols=124  Identities=31%  Similarity=0.468  Sum_probs=119.7

Q ss_pred             hhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEE
Q psy8115          81 CVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIE  160 (218)
Q Consensus        81 ~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~  160 (218)
                      ..+++|++|++++.+||+||.+.|.+|||++|+|+|++++++|+||+++||++||++|+++++|+..|++.++.  .++.
T Consensus         2 ~~~~~fi~~~~~~~~irefi~~~~~~AgIs~IeI~Rt~~~i~I~I~ta~PGivIGk~G~~I~klk~~Lkk~~~~--~~v~   79 (207)
T PRK04191          2 AIEKKFVEEGLKKVMIDEYLAKELYRAGYGGMEIKKTPLGTRITIYAERPGMVIGRGGKNIRELTEILEKKFGL--ENPQ   79 (207)
T ss_pred             chhhHHHHcchHHHHHHHHHHhhhhhcceeEEEEEEcCCcEEEEEEECCCCeEECCCchhHHHHHHHHHHHhCC--Ccee
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999975  3588


Q ss_pred             EEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCC
Q psy8115         161 LYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYT  206 (218)
Q Consensus       161 I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA  206 (218)
                      |++.||++|++||.++|++||+|||+|++||||||+||+++|++||
T Consensus        80 I~v~ev~~p~~~a~~vA~~ia~qLe~r~~fRra~k~~i~~~~~aga  125 (207)
T PRK04191         80 IDVKEVENPELNARVVAFRLANALERGWHFRRAAHSAIRRIMEAGA  125 (207)
T ss_pred             EEEEEEeCCCcCHHHHHHHHHHHHHccchHHHHHHHHHHHHHHcCC
Confidence            8899999999999999999999999999999999999999999997

>CHL00048 rps3 ribosomal protein S3

Probab=100.00  E-value=4.8e-32  Score=235.29  Aligned_cols=137  Identities=15%  Similarity=0.109  Sum_probs=124.0

Q ss_pred             hhhhcc-cccchhhhhhHHh-hhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHH
Q psy8115          70 NTIGVS-NSLSICVSLQFVA-DGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSV  147 (218)
Q Consensus        70 ~~~~~~-m~~~~~~ykkfV~-d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~  147 (218)
                      ..|.+. .+.. ++|+++|. |.+++.+|++||.+++.+|||++|+|+|+++.++|+||+++||.|||++|+++++|++.
T Consensus        16 ~~~~S~W~a~~-~~y~~~l~eD~~ir~~i~~~l~~~~~~agis~i~I~r~~~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~   94 (214)
T CHL00048         16 QKHHSLWFAQP-KNYSEGLQEDKKIRDCIKNYVQKNIKYEGIARIEIQRKIDLIQVIIYTGFPKLLIERKGRGIEELQIN   94 (214)
T ss_pred             CCCceEEecCh-hhhHHHHHHHHHHHHHHHHHHHhhhhhCCeeEEEEEEcCCeEEEEEEECCCceEECCCcHhHHHHHHH
Confidence            455433 5543 79999998 66677777777777789999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCCc
Q psy8115         148 VQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTY  207 (218)
Q Consensus       148 LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA~  207 (218)
                      |++.|++.++++.|++.||++|++||.++|++||+|||+|++|||||+++++++|++||-
T Consensus        95 L~k~~~~~~~~i~I~v~ev~~p~~~A~~iA~~ia~~Le~r~~fRra~~~~i~~~~~~ga~  154 (214)
T CHL00048         95 LQKELNSVNRKLNINITEVKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADIK  154 (214)
T ss_pred             HHHHhCCCCceEEEEEEEecCCCcCHHHHHHHHHHHHhcChhHHHHHHHHHHHHHHhCCc
Confidence            999998777789999999999999999999999999999999999999999999999873

>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type

Probab=99.97  E-value=1.1e-31  Score=232.54  Aligned_cols=135  Identities=19%  Similarity=0.280  Sum_probs=124.6

Q ss_pred             HHH-Hhhhhhcc-cccchhhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHH
Q psy8115          65 FRV-LVNTIGVS-NSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIR  142 (218)
Q Consensus        65 ~~~-~~~~~~~~-m~~~~~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik  142 (218)
                      ||. +...|.|. .++. ++|+++|.||.   +|||||.++|.++||++|+|+|+++.++|+||+++|++|||++|++++
T Consensus        10 fRLGi~~~w~S~Wfa~~-k~Y~~~l~eD~---~IR~~i~k~~~~agis~IeI~rt~~~i~I~I~~~~pg~vIG~~g~~i~   85 (211)
T TIGR01009        10 FRLGITKDWKSRWYANP-KEYAKLLHEDL---KIRNYIKKELSNAGISDVEIERPADKIRVTIHTARPGIVIGKKGSEIE   85 (211)
T ss_pred             cccccccCCceEEccCc-chhHHHHHHHH---HHHHHHHHHhhhCCcceEEEEEcCCceEEEEEeCCCcceeCCCchHHH
Confidence            344 33456444 6665 79999999999   999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCC
Q psy8115         143 ELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYT  206 (218)
Q Consensus       143 ~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA  206 (218)
                      +|++.|++.|+   .++.|++.+|++|+++|.++|++||+|||+|++||||++++|+++|++||
T Consensus        86 ~l~~~l~~~~~---~~~~i~v~~v~~p~~~a~~iA~~ia~~Le~~~~fRr~~~~~i~~~~~~g~  146 (211)
T TIGR01009        86 KLRKDLQKLTG---KEVQINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGA  146 (211)
T ss_pred             HHHHHHHHHhC---CceEEEEEEecCCCcCHHHHHHHHHHHHHccccHHHHHHHHHHHHHhcCC
Confidence            99999999996   46899999999999999999999999999999999999999999999986

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

>PRK00310 rpsC 30S ribosomal protein S3; Reviewed

Probab=99.97  E-value=5e-31  Score=231.30  Aligned_cols=131  Identities=20%  Similarity=0.247  Sum_probs=122.5

Q ss_pred             hhhhhcc-cccchhhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHH
Q psy8115          69 VNTIGVS-NSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSV  147 (218)
Q Consensus        69 ~~~~~~~-m~~~~~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~  147 (218)
                      ...|.|. .+.. ++|+++|.||.   +||+||.++|.++||++|+|+|+++.++|+||+++|++|||++|+++++|++.
T Consensus        15 ~k~w~S~Wya~~-k~Y~~~L~eD~---~IRe~i~k~~~~agis~IeI~R~~~~i~I~I~~~rP~~iiG~~g~~i~~l~~~   90 (232)
T PRK00310         15 IKDWDSRWYADK-KDYADLLHEDL---KIRKFLKKKLKKAGVSRIEIERPAKRVRVTIHTARPGIVIGKKGAEIEKLRKE   90 (232)
T ss_pred             cCCCCCeEeCCc-chhHHHHHHHH---HHHHHHHHhHhhCceeEEEEEEcCCeEEEEEEECCCccccCCCcHHHHHHHHH
Confidence            3456544 6643 79999999999   99999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCC
Q psy8115         148 VQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYT  206 (218)
Q Consensus       148 LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA  206 (218)
                      |++.|+   +++.|++.||++|+++|.++|++||+|||+|++||||++++|+++|++||
T Consensus        91 L~~~~~---~~~~i~v~ev~~p~~~a~~iA~~ia~~Le~r~~fRr~~~~~i~~~~~~g~  146 (232)
T PRK00310         91 LEKLTG---KPVQINIVEVKKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGA  146 (232)
T ss_pred             HHHHhC---CceEEEEEEecCCCcCHHHHHHHHHHHHHccchHHHHHHHHHHHHHHcCC
Confidence            999996   57899999999999999999999999999999999999999999999986

>KOG3181|consensus

Probab=99.95  E-value=3e-28  Score=210.02  Aligned_cols=132  Identities=73%  Similarity=1.047  Sum_probs=128.9

Q ss_pred             cccchhhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCC
Q psy8115          76 NSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFA  155 (218)
Q Consensus        76 m~~~~~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~  155 (218)
                      |+.+|+..++|+.||+++++++|||.++|.+.|||++|++.||.+++|+|.+++|+.++|.+|.+|++|+..+||+|++.
T Consensus         1 ~a~~iSkkrkfv~dGvf~AELnef~treLaedGySgvEvRvtptr~eiIi~atrtq~vlGEkgrRirelt~lvqkRf~f~   80 (244)
T KOG3181|consen    1 MALQISKKRKFVADGVFYAELNEFLTRELAEDGYSGVEVRVTPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFKFP   80 (244)
T ss_pred             CccccchhhhhhhcchhHHHHHHHHHHHHHhcCcCceEEEeeccceeEEEEecchhhhhhhcchhHHHHHHHHHHhcCCC
Confidence            46678899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCCc
Q psy8115         156 DGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTY  207 (218)
Q Consensus       156 ~kkI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA~  207 (218)
                      +..|++++++|.+.+|||..+|++|+++|-.++++||||+.+++.+|++||-
T Consensus        81 ~~svelyaEkV~~rGLcAiaQaeslryKllgGlavRRA~ygvlr~vmesgAk  132 (244)
T KOG3181|consen   81 EGSVELYAEKVANRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESGAK  132 (244)
T ss_pred             CCcEEEehhhhhccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHccCC
Confidence            9999999999999999999999999999999999999999999999999985

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

Probab=99.87  E-value=1.3e-21  Score=147.08  Aligned_cols=80  Identities=83%  Similarity=1.219  Sum_probs=76.9

Q ss_pred             hhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecCC
Q psy8115          90 GVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATR  169 (218)
Q Consensus        90 ~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP  169 (218)
                      ++++++||+||.+++.+||||+|||+|++++++|+|||++||++||++|+++++|++.|++.|++++++|+|++++|.+.
T Consensus         1 ~~~~~~Ire~l~k~~~~agis~IeI~Rt~~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~~~i~v~~~~v~~~   80 (81)
T cd02413           1 GVFYAELNEFLTRELAEDGYSGVEVRVTPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPEGSVELYAEKVANR   80 (81)
T ss_pred             CchhHHHHHHHHHHHHhCCeeeEEEEEcCCeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCCCeEEEEEEEcccC
Confidence            35788999999999999999999999999999999999999999999999999999999999999999999999999875

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

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

Probab=99.84  E-value=6.2e-21  Score=149.61  Aligned_cols=94  Identities=19%  Similarity=0.301  Sum_probs=85.9

Q ss_pred             hhhhcc-cccchhhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHH
Q psy8115          70 NTIGVS-NSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVV  148 (218)
Q Consensus        70 ~~~~~~-m~~~~~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~L  148 (218)
                      ..|.+. +|.. ++|++++.+|.   +||+||.+.+.+|||++|+|+|+++.++|+||+++||+|||++|+++++|++.|
T Consensus        15 ~~~~s~W~~~~-~~y~~~l~ed~---~IR~yL~k~~~~agis~I~I~R~~~~i~I~I~t~rPg~vIG~~G~~i~~L~~~l   90 (109)
T cd02412          15 KDWDSRWYADK-KDYAELLHEDL---KIRKFIKKKLKKAGISRIEIERKADRVEVTIHTARPGIIIGKKGAGIEKLRKEL   90 (109)
T ss_pred             CCCcceEcCCc-hhhHHHHHhHH---HHHHHHHHHHhhCCccEEEEEEcCCCEEEEEEeCCCCcccCCchHHHHHHHHHH
Confidence            456444 7764 69999999999   999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhCCCCCcEEEEEEEecCC
Q psy8115         149 QKRFKFADGAIELYAEKVATR  169 (218)
Q Consensus       149 qK~~~~~~kkI~I~I~EV~nP  169 (218)
                      ++.+++  +++.|+|.||.+|
T Consensus        91 ~~~~~~--~~~~I~V~ev~~P  109 (109)
T cd02412          91 QKLLGN--KKVRINIVEVKKP  109 (109)
T ss_pred             HHHhCC--CceEEEEEEecCC
Confidence            999864  5789999999998

S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein

Probab=99.82  E-value=5.9e-20  Score=138.09  Aligned_cols=84  Identities=38%  Similarity=0.649  Sum_probs=79.4

Q ss_pred             hhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEE
Q psy8115          83 SLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELY  162 (218)
Q Consensus        83 ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~  162 (218)
                      +++|++|++++.+||+||.+.+..||||+|+|+|+++.++|+||+++||.+||++|+++++|+..|++.++.  .++.|+
T Consensus         2 ~~~~~~~~~~~~~Ir~fl~~~~~~agIs~IeI~r~~~~i~V~I~t~~pg~iIGk~G~~I~~l~~~l~k~~~~--~~v~I~   79 (85)
T cd02411           2 ERKFVNEGVKRTMIDEYLEKELERAGYGGMEILRTPLGTQITIYAERPGMVIGRGGKNIRELTEILETKFGL--ENPQID   79 (85)
T ss_pred             eEeHHhcchHHHHHHHHHHhhhhhCcccEEEEEEcCCcEEEEEEECCCCceECCCchhHHHHHHHHHHHhCC--CCceEE
Confidence            688999999999999999999999999999999999999999999999999999999999999999999974  478888


Q ss_pred             EEEecC
Q psy8115         163 AEKVAT  168 (218)
Q Consensus       163 I~EV~n  168 (218)
                      |.||++
T Consensus        80 v~ev~~   85 (85)
T cd02411          80 VQEVEN   85 (85)
T ss_pred             EEEecC
Confidence            899875

S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=99.60  E-value=2e-15  Score=110.48  Aligned_cols=77  Identities=29%  Similarity=0.434  Sum_probs=72.5

Q ss_pred             HHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhC-CCCCcEEEEEEEecCCCc
Q psy8115          95 ELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFK-FADGAIELYAEKVATRGL  171 (218)
Q Consensus        95 ~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~-~~~kkI~I~I~EV~nP~l  171 (218)
                      +|++||.+++..+|+++|+|+|+++.+.|++|+++|+++||++|+.+++|+..+++.+. +.+++|.+++.+|++|++
T Consensus         1 eI~~~l~~~~~~~~~~~i~I~r~~~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~~~~~~~V~l~v~~V~~~~~   78 (78)
T PF07650_consen    1 EIRYFLFKEIKKAGISDIEIERTPDQIIIVIKASQPGIVIGKKGSNIKKIREELRKELEKLLNKKVFLNVVKVKKPWR   78 (78)
T ss_dssp             HHHHHHHHHTTTTTEEEEEEEESSSEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHHHHCSSSEEEEEEEESSCGG
T ss_pred             ChhhhHHhhhhhccCceEEEEEcCCeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHhhcCCCcEEEEEEEecCCCC
Confidence            68999999999999999999999999999999999999999999999999999999995 457889999999999974

; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....

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

Probab=98.91  E-value=7.6e-09  Score=71.38  Aligned_cols=65  Identities=43%  Similarity=0.641  Sum_probs=57.6

Q ss_pred             HHHHHhhhccCCeeeeEEEecCCeEEEEEEecc--cceEeccCcccHHHHHHHHHHHhCCCCCcEEEEE
Q psy8115          97 DEFLTRELAEDGYSGVEIRFTPARTEIIIMATR--TQNVLGDKGRRIRELTSVVQKRFKFADGAIELYA  163 (218)
Q Consensus        97 Refl~K~l~~AGIs~IEI~Rt~~~I~IiI~aar--PgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I  163 (218)
                      |+||.+.+..+|+++|+|+++++...+.+++.+  ||.+||++|+.++.|+..+++.+  .++++.|++
T Consensus         1 r~~l~~~~~~~~i~~i~i~~~~~~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~--~~~~~~i~v   67 (68)
T cd02409           1 REFLKKLLAPAGISGVEIERTPDRIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL--RKKRVKIDV   67 (68)
T ss_pred             ChHHHHHHHHCCCCeEEEEEcCCcEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc--CCCceEEEE
Confidence            478888888899999999999888999999999  99999999999999999999988  356666654

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.

>smart00322 KH K homology RNA-binding domain

Probab=97.77  E-value=2.5e-05  Score=52.69  Aligned_cols=67  Identities=15%  Similarity=0.174  Sum_probs=52.9

Q ss_pred             CeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHH
Q psy8115         119 ARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLI  185 (218)
Q Consensus       119 ~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLE  185 (218)
                      ..++|.|+...++.+||++|+.+++|++.....+...+..-...+..|..+..++...++.|..+++
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~~v~~a~~~i~~~~~   69 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELILEILE   69 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHHHHHHHHHHHHHHhC
Confidence            4578889999999999999999999999887666543322134557788888999999999988764

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=96.96  E-value=0.0011  Score=47.91  Aligned_cols=68  Identities=15%  Similarity=0.175  Sum_probs=46.0

Q ss_pred             HHHHHHHhhhccCCeeeeEEE--ecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEE
Q psy8115          95 ELDEFLTRELAEDGYSGVEIR--FTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELY  162 (218)
Q Consensus        95 ~IRefl~K~l~~AGIs~IEI~--Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~  162 (218)
                      .+++|+..-+...+=-.|++.  .....+.+.+.....|.+||++|+.++.|+..++...+-...++.|.
T Consensus         3 ~l~~~l~~l~~~~~~v~v~~~~~~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~~~~~~~~~v~   72 (73)
T PF13083_consen    3 FLEDFLKNLVDKPMDVEVTIEIEEDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAANKHGKRVRVE   72 (73)
T ss_dssp             --HHHHHHHHHHTT--EEEEEEETTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHHHHT-SS-EEE
T ss_pred             hHHHHHHHHhCCcCeEEEEEEEcCCceEEEEEECCCccceEECCCCeeHHHHHHHHHHHHHhCCCEEEEe
Confidence            456666665533222224443  45779999999999999999999999999999988776545556553

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=96.96  E-value=0.0058  Score=44.89  Aligned_cols=56  Identities=20%  Similarity=0.319  Sum_probs=46.6

Q ss_pred             HHHHhhhccCCe-eeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhC
Q psy8115          98 EFLTRELAEDGY-SGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFK  153 (218)
Q Consensus        98 efl~K~l~~AGI-s~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~  153 (218)
                      +||.+-+...|+ +.|++....+.+.+.|....+|.+||++|+.++.|+..+...++
T Consensus         2 ~~L~~il~~mg~~~~v~~~~~~~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~   58 (77)
T cd02414           2 EFLEEVLELMGIEADVDVEEEGDTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN   58 (77)
T ss_pred             hHHHHHHHHcCCCcEEEEEecCCEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence            466666666666 34777777889999999999999999999999999999888776

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

>PRK01064 hypothetical protein; Provisional

Probab=95.88  E-value=0.13  Score=38.80  Aligned_cols=54  Identities=9%  Similarity=0.162  Sum_probs=41.6

Q ss_pred             eEEEecCCeEEEEEEeccc--ceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEE
Q psy8115         112 VEIRFTPARTEIIIMATRT--QNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEK  165 (218)
Q Consensus       112 IEI~Rt~~~I~IiI~aarP--giVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~E  165 (218)
                      |+.......+.+.+++...  |.+||++|+.++.++..+.......++++.+.|.+
T Consensus        21 V~~~~~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~~~~~~~~~rv~leI~~   76 (78)
T PRK01064         21 IKEVQGTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLVSVASRNNVKVSLEIME   76 (78)
T ss_pred             EEEEeCCCEEEEEEEECcccceEEECCCCccHHHHHHHHHHHHhhCCCEEEEEEec
Confidence            4444445677777887766  78999999999999999988776656777776654

>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=95.75  E-value=0.012  Score=44.29  Aligned_cols=28  Identities=18%  Similarity=0.074  Sum_probs=25.1

Q ss_pred             HHHHHHHcChhHHHHHHHHHHHH-HHcCC
Q psy8115         179 SLRYKLIGGLAVRRYNSDVSLYC-LNCYT  206 (218)
Q Consensus       179 ~IA~QLEkRv~FRRAmK~AIr~a-mkaGA  206 (218)
                      +|+++||++.+|||+++++++.+ |++|+
T Consensus         1 ~i~~~l~k~~~~r~~i~~~~~~i~~~~~~   29 (85)
T PF00189_consen    1 FIAQKLEKRISFRRIIKKIIRRIMMNKGI   29 (85)
T ss_dssp             HHHHHHHTTSTHHHHHHHHHHHHHHCTTS
T ss_pred             ChHHHHhcCcHHHHHHHHHHHHHHhhccc
Confidence            58999999999999999999999 65555

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 ....

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

Probab=94.96  E-value=0.13  Score=45.44  Aligned_cols=110  Identities=14%  Similarity=0.151  Sum_probs=76.0

Q ss_pred             hhHHHHHHHHHHhhhccCCee-eeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCC---CcEEEEEEE
Q psy8115          90 GVFRAELDEFLTRELAEDGYS-GVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFAD---GAIELYAEK  165 (218)
Q Consensus        90 ~iir~~IRefl~K~l~~AGIs-~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~---kkI~I~I~E  165 (218)
                      ..+..++.+||..-+..-|++ .|.+......+.+.|....++.+||++|+.++.|+...+-.++...   .+|.|++..
T Consensus        61 ~~~~~~~~~~L~ell~~m~~~~~i~v~~~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~~~g~~~~v~ldv~~  140 (208)
T COG1847          61 EKIAQEAKDYLEELLELMDFEVTITVSEEGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNKIGGKFKRVTLDVGD  140 (208)
T ss_pred             hHHHHHHHHHHHHHHHHhCCceEEEEeecCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhhhcCcceEEEEEhhh
Confidence            345568899999888877765 4888888899999999999999999999999999988887665322   345555542


Q ss_pred             ecC-CCcCHHHHHHHHHHHH-HcChh---------HHHHHHHHHH
Q psy8115         166 VAT-RGLCAIAQAESLRYKL-IGGLA---------VRRYNSDVSL  199 (218)
Q Consensus       166 V~n-P~l~A~llAe~IA~QL-EkRv~---------FRRAmK~AIr  199 (218)
                      =.. ..-.=..+|+.+|.|. +.+-+         =||.++.++.
T Consensus       141 yRerR~e~L~~LA~~~A~rV~~tg~~v~L~pM~~~ERkIVH~~l~  185 (208)
T COG1847         141 YRERRKETLIKLAERAAERVLETGRSVELEPMPPFERKIVHTALS  185 (208)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCeeecCCCCHHHHHHHHHHHH
Confidence            221 1122244666666655 22221         3667777665

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

Probab=94.84  E-value=0.25  Score=41.43  Aligned_cols=86  Identities=24%  Similarity=0.280  Sum_probs=58.4

Q ss_pred             HHHHHhhh-ccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHH
Q psy8115          97 DEFLTREL-AEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIA  175 (218)
Q Consensus        97 Refl~K~l-~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~l  175 (218)
                      ++.+.+-. .+||+.+  |...++.=+|+|++.+||.+||++|..++++..    ..|.   .-.|    +..|=+.+..
T Consensus        55 ~~~I~~ivP~ea~i~d--i~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~----~tgW---~p~v----vRtpPi~S~t  121 (145)
T cd02410          55 IKIILEIVPEEAGITD--IYFDDDTGEVIIEAEKPGLVIGKGGSTLREITR----ETGW---APKV----VRTPPIQSRT  121 (145)
T ss_pred             HHHHHHhCCCccCcee--eEecCCCcEEEEEEcCCeEEEecCchhHHHHHH----HhCC---eeEE----EecCCCCcHH
Confidence            34444433 2578865  455677789999999999999999988877665    4443   2333    6667677776


Q ss_pred             HHHHHHHHHHcChhHHHHHHH
Q psy8115         176 QAESLRYKLIGGLAVRRYNSD  196 (218)
Q Consensus       176 lAe~IA~QLEkRv~FRRAmK~  196 (218)
                      + +.|++-|-+--.+|+-+-+
T Consensus       122 i-~~ir~~l~~~~~eR~~~L~  141 (145)
T cd02410         122 V-KSIRRFLRREREERKEILK  141 (145)
T ss_pred             H-HHHHHHHHHhHHHHHHHHH
Confidence            5 5666777666667765433

The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

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

Probab=94.72  E-value=0.073  Score=37.62  Aligned_cols=53  Identities=15%  Similarity=0.315  Sum_probs=43.0

Q ss_pred             HHHHHhhhccCCeeeeEEEec-CCeEEEEEEecccceEeccCcccHHHHHHHHH
Q psy8115          97 DEFLTRELAEDGYSGVEIRFT-PARTEIIIMATRTQNVLGDKGRRIRELTSVVQ  149 (218)
Q Consensus        97 Refl~K~l~~AGIs~IEI~Rt-~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~Lq  149 (218)
                      .+|+..-+.-+.+.+|++... .+...|.+....-+..||++|++++.+++.+.
T Consensus         2 ~~~i~n~~~p~~i~~V~~~~~~~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~   55 (61)
T cd02134           2 AEFIRNALSPAKVTSVTVLDDEEKRARVVVPDDQLGLAIGKGGQNVRLASKLLG   55 (61)
T ss_pred             HHHHHHhcCcccceEEEEecCCCcEEEEEECcccceeeECCCCHHHHHHHHHHC
Confidence            357777777778888888655 47888888888889999999999999887665

NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.

>PRK02821 hypothetical protein; Provisional

Probab=94.55  E-value=0.62  Score=35.07  Aligned_cols=65  Identities=17%  Similarity=0.228  Sum_probs=44.4

Q ss_pred             HHHHhhhcc-CCeeeeEEEecCCeEEEEEEeccc--ceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEE
Q psy8115          98 EFLTRELAE-DGYSGVEIRFTPARTEIIIMATRT--QNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEK  165 (218)
Q Consensus        98 efl~K~l~~-AGIs~IEI~Rt~~~I~IiI~aarP--giVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~E  165 (218)
                      +|+-+.|-+ -.=-.|+.+.....+.+.|+++.-  |.|||++|+.++.|+..+.-.   .++++.+.|.+
T Consensus         7 ~~ivk~LVd~Pe~V~V~~~~~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a~---~~~~v~leI~~   74 (77)
T PRK02821          7 EHLVRGIVDNPDDVRVDSHTNRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAAI---GGRGVRVDVVD   74 (77)
T ss_pred             HHHHHHhCCCCCeEEEEEEECCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHHh---cCCeEEEEEEe
Confidence            445454432 112225555556677778887654  569999999999999999876   46788877665

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=94.10  E-value=0.085  Score=43.45  Aligned_cols=60  Identities=15%  Similarity=0.321  Sum_probs=48.4

Q ss_pred             HHHHHHHhhhccCCeeeeEEEecC--CeEEEEEEecccceEeccCcccHHHHHHHHHHHhCC
Q psy8115          95 ELDEFLTRELAEDGYSGVEIRFTP--ARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKF  154 (218)
Q Consensus        95 ~IRefl~K~l~~AGIs~IEI~Rt~--~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~  154 (218)
                      ...+|+.+-+..+++.+|+|....  ..+.|.+.-..-+..||++|+.++.++..+.+.|+.
T Consensus        73 d~~~fI~n~l~Pa~V~~v~I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di  134 (140)
T PRK08406         73 DPEEFIKNIFAPAAVRSVTIKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI  134 (140)
T ss_pred             CHHHHHHHHcCCCEEEEEEEEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence            567889888999999999885443  345566666777889999999999999999887764

>PRK00468 hypothetical protein; Provisional

Probab=93.33  E-value=1.1  Score=33.48  Aligned_cols=52  Identities=13%  Similarity=0.136  Sum_probs=37.3

Q ss_pred             eEEEecCCeEEEEEEeccc--ceEeccCcccHHHHHHHHHHHhCCCCCcEEEEE
Q psy8115         112 VEIRFTPARTEIIIMATRT--QNVLGDKGRRIRELTSVVQKRFKFADGAIELYA  163 (218)
Q Consensus       112 IEI~Rt~~~I~IiI~aarP--giVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I  163 (218)
                      |+.+.....+.+.|+++.-  |.|||++|+.++.|+..+.-.-...++++.+.|
T Consensus        21 V~~~~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~aaa~k~~~rv~leI   74 (75)
T PRK00468         21 VNEIEGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVKAAAIKENKRVVVEI   74 (75)
T ss_pred             EEEEeCCCeEEEEEEEChhhCcceecCCChhHHHHHHHHHHHHhcCCCEEEEEE
Confidence            4444555677777777654  569999999999999999865444456666543

>TIGR00436 era GTP-binding protein Era

Probab=92.77  E-value=0.86  Score=40.06  Aligned_cols=74  Identities=18%  Similarity=0.311  Sum_probs=46.9

Q ss_pred             hHHhhhhHHHHHHHHHHhhhccCCeeeeEEEe---cC---CeEEEEEEecccc---eEeccCcccHHHH----HHHHHHH
Q psy8115          85 QFVADGVFRAELDEFLTRELAEDGYSGVEIRF---TP---ARTEIIIMATRTQ---NVLGDKGRRIREL----TSVVQKR  151 (218)
Q Consensus        85 kfV~d~iir~~IRefl~K~l~~AGIs~IEI~R---t~---~~I~IiI~aarPg---iVIGrkG~~Ik~L----~~~LqK~  151 (218)
                      +|....++|.++-+++..++..+=  .|+|+.   .+   ..|...|++.|+.   +|||++|+.|+++    +..|++.
T Consensus       181 ~~~~~e~ire~~~~~~~~e~p~~~--~~~~~~~~~~~~~~~~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ar~~l~~~  258 (270)
T TIGR00436       181 RFKISEIIREKIIRYTKEEIPHSV--RVEIERKSFNEKGLLKIHALISVERESQKKIIIGKNGSMIKAIGIAARKDILEL  258 (270)
T ss_pred             HHHHHHHHHHHHHHhcccccCceE--EEEEEEEEECCCCeEEEEEEEEECcCCceeEEEcCCcHHHHHHHHHHHHHHHHH
Confidence            444555666666666666654432  233332   22   2577889998874   7999999999776    5667777


Q ss_pred             hCCCCCcEEEEE
Q psy8115         152 FKFADGAIELYA  163 (218)
Q Consensus       152 ~~~~~kkI~I~I  163 (218)
                      |+   .+|.+.+
T Consensus       259 ~~---~~v~l~l  267 (270)
T TIGR00436       259 FD---CDVFLEL  267 (270)
T ss_pred             hC---CCEEEEE
Confidence            76   5565543

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

>PRK15494 era GTPase Era; Provisional

Probab=92.65  E-value=0.9  Score=41.80  Aligned_cols=99  Identities=19%  Similarity=0.307  Sum_probs=60.1

Q ss_pred             cchhhHHHHhhhh--h--cccccchhh-hhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEec---C---CeEEEEEEec
Q psy8115          60 GFSVLFRVLVNTI--G--VSNSLSICV-SLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFT---P---ARTEIIIMAT  128 (218)
Q Consensus        60 ~~~~~~~~~~~~~--~--~~m~~~~~~-ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt---~---~~I~IiI~aa  128 (218)
                      |...+|..+.+..  +  .+...++.+ -.+|+...++|.+|-+++..++..+  ..|+|+.-   .   ..|...||+.
T Consensus       203 gv~eL~~~L~~~l~~~~~~~~~~~~td~~~~~~~~eiiRe~~~~~~~~EiP~~--~~v~i~~~~~~~~~~~~i~~~i~v~  280 (339)
T PRK15494        203 NIDGLLEYITSKAKISPWLYAEDDITDLPMRFIAAEITREQLFLNLQKELPYK--LTVQTEKWEDLKDKSVKINQVIVVS  280 (339)
T ss_pred             CHHHHHHHHHHhCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHhhCCcccCce--EEEEEEEEEEcCCCeEEEEEEEEEC
Confidence            4556666665543  1  222222222 2355566677777777777776554  22444332   2   2477899998


Q ss_pred             ccc---eEeccCcccHHHH----HHHHHHHhCCCCCcEEEEE
Q psy8115         129 RTQ---NVLGDKGRRIREL----TSVVQKRFKFADGAIELYA  163 (218)
Q Consensus       129 rPg---iVIGrkG~~Ik~L----~~~LqK~~~~~~kkI~I~I  163 (218)
                      |++   +|||++|+.|+++    +..|++.|+   .+|.+.+
T Consensus       281 ~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~---~~v~l~l  319 (339)
T PRK15494        281 RESYKTIILGKNGSKIKEIGAKSRMQMERFFG---FPVHLFL  319 (339)
T ss_pred             CCCceeEEEcCCcHHHHHHHHHHHHHHHHHhC---CCeEEEE
Confidence            886   7999999999776    566777776   4554443

>COG1159 Era GTPase [General function prediction only]

Probab=92.46  E-value=1.2  Score=41.44  Aligned_cols=69  Identities=23%  Similarity=0.347  Sum_probs=48.6

Q ss_pred             hhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecC------CeEEEEEEeccc---ceEeccCcccHHHH----HHHHHH
Q psy8115          84 LQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTP------ARTEIIIMATRT---QNVLGDKGRRIREL----TSVVQK  150 (218)
Q Consensus        84 kkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~------~~I~IiI~aarP---giVIGrkG~~Ik~L----~~~LqK  150 (218)
                      -+|+.-.++|.++=.|+..++..+  ..|+|++..      ..|.-.|++.|-   ++|||++|+.|+++    +.++++
T Consensus       188 ~rf~~aEiiREk~~~~l~eElPhs--v~VeIe~~~~~~~~~~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~  265 (298)
T COG1159         188 ERFLAAEIIREKLLLLLREELPHS--VAVEIEEFEEREKGLLKIHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEK  265 (298)
T ss_pred             HHHHHHHHHHHHHHHhcccccCce--EEEEEEEEEecCCCeEEEEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHH
Confidence            345666667777777777777654  447776642      256667888665   58999999999776    667888


Q ss_pred             HhCC
Q psy8115         151 RFKF  154 (218)
Q Consensus       151 ~~~~  154 (218)
                      .|+.
T Consensus       266 l~~~  269 (298)
T COG1159         266 LLGC  269 (298)
T ss_pred             HhCC
Confidence            8863

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

Probab=91.65  E-value=2.2  Score=32.15  Aligned_cols=47  Identities=13%  Similarity=0.187  Sum_probs=33.5

Q ss_pred             cCCeEEEEEEeccc--ceEeccCcccHHHHHHHHHHHhCCCCCcEEEEE
Q psy8115         117 TPARTEIIIMATRT--QNVLGDKGRRIRELTSVVQKRFKFADGAIELYA  163 (218)
Q Consensus       117 t~~~I~IiI~aarP--giVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I  163 (218)
                      ....+.+.|+++..  |-|||++|+.++.|+..|.-.-.-.++++.|.+
T Consensus        26 ~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll~a~~~~~~~~v~i~i   74 (76)
T COG1837          26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLLSAVGSKDSKRVVVEI   74 (76)
T ss_pred             cCCeEEEEEEECcccccceecCCChhHHHHHHHHHHhcccCceEEEEEe
Confidence            35576666666654  569999999999999999865543345555544

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

Probab=91.15  E-value=1.3  Score=44.25  Aligned_cols=78  Identities=27%  Similarity=0.335  Sum_probs=52.3

Q ss_pred             HHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHH
Q psy8115          95 ELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAI  174 (218)
Q Consensus        95 ~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~  174 (218)
                      .|+|.+.+   +|||++  |....+.=+|+|.+.+||++||+.|+..+++...    .+..   -.|    +..|-+...
T Consensus        80 ~I~eivP~---ea~i~~--i~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~----tgW~---p~i----vR~PPi~S~  143 (637)
T COG1782          80 IILEIVPE---EAGITD--IYFDDDTGEVIIEAKKPGLVIGKGGSTLREITAE----TGWA---PKI----VRTPPIQSR  143 (637)
T ss_pred             HHHHhCcc---ccCcee--EEecCCCceEEEEecCCceEEecCchHHHHHHHH----hCCc---cee----eecCCCchh
Confidence            44554443   688987  6667888899999999999999999887776653    3332   223    566767666


Q ss_pred             HHHHHHHHHHHcChh
Q psy8115         175 AQAESLRYKLIGGLA  189 (218)
Q Consensus       175 llAe~IA~QLEkRv~  189 (218)
                      .+ ++|+.-|.+-..
T Consensus       144 ti-~~ir~~l~~~~~  157 (637)
T COG1782         144 TI-KSIREILRSERK  157 (637)
T ss_pred             hH-HHHHHHHHHhHH
Confidence            65 344444444333

>PRK00089 era GTPase Era; Reviewed

Probab=89.81  E-value=2.7  Score=37.03  Aligned_cols=73  Identities=25%  Similarity=0.342  Sum_probs=44.2

Q ss_pred             HHhhhhHHHHHHHHHHhhhccCCeeeeEEEe----cCCeEEEEEEecccc---eEeccCcccHHHH----HHHHHHHhCC
Q psy8115          86 FVADGVFRAELDEFLTRELAEDGYSGVEIRF----TPARTEIIIMATRTQ---NVLGDKGRRIREL----TSVVQKRFKF  154 (218)
Q Consensus        86 fV~d~iir~~IRefl~K~l~~AGIs~IEI~R----t~~~I~IiI~aarPg---iVIGrkG~~Ik~L----~~~LqK~~~~  154 (218)
                      |....++|.++-+++.+++..+  ..|+|+.    ....|...|++.++.   +|||++|+.|+++    +..|++.|+ 
T Consensus       189 ~~~~EiiRe~~~~~l~~e~p~~--~~v~~~~~~~~~~~~i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~-  265 (292)
T PRK00089        189 FLAAEIIREKLLRLLGDELPYS--VAVEIEKFEERGLVRIEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLG-  265 (292)
T ss_pred             HHHHHHHHHHHHhhCCccCCce--EEEEEEEEEECCeEEEEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhC-
Confidence            4444455555555555555433  1133321    223577789998885   7999999999776    456777776 


Q ss_pred             CCCcEEEEE
Q psy8115         155 ADGAIELYA  163 (218)
Q Consensus       155 ~~kkI~I~I  163 (218)
                        .+|.+.+
T Consensus       266 --~~v~l~l  272 (292)
T PRK00089        266 --KKVFLEL  272 (292)
T ss_pred             --CCEEEEE
Confidence              4554443

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

Probab=88.25  E-value=3.7  Score=41.42  Aligned_cols=77  Identities=25%  Similarity=0.309  Sum_probs=53.2

Q ss_pred             cCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHH
Q psy8115         106 EDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLI  185 (218)
Q Consensus       106 ~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLE  185 (218)
                      +||+.+  |...++.=+|+|.+.+||.|||+.|..++++..    ..+.   .-.|    +..|-+....+ +.|+.-|-
T Consensus        82 ~~~~~~--~~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~----~~~w---~~~~----~~~~~~~~~~~-~~~~~~~~  147 (630)
T TIGR03675        82 EAGITD--IYFDDVTGEVIIEAEKPGLVIGKGGSTLREITA----ETGW---TPKV----VRTPPIESKTI-KNIREYLR  147 (630)
T ss_pred             cCCcee--EEecCCCceEEEEEcCCeEEEecCcchHHHHHH----HhCC---eeeE----EecCCCCcHHH-HHHHHHHH
Confidence            588865  555777889999999999999999988877665    3443   2233    66777777765 45666665


Q ss_pred             cChhHHHHHHH
Q psy8115         186 GGLAVRRYNSD  196 (218)
Q Consensus       186 kRv~FRRAmK~  196 (218)
                      +--..|+-+-+
T Consensus       148 ~~~~~r~~~l~  158 (630)
T TIGR03675       148 SESEERKEFLR  158 (630)
T ss_pred             HhHHHHHHHHH
Confidence            55555554433

This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=86.84  E-value=1.1  Score=37.20  Aligned_cols=60  Identities=15%  Similarity=0.283  Sum_probs=44.8

Q ss_pred             HHHHHHHhhhccCCeeeeEEEecCC--eEEEEEEecccceEeccCcccHHHHHHHHHHHhCC
Q psy8115          95 ELDEFLTRELAEDGYSGVEIRFTPA--RTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKF  154 (218)
Q Consensus        95 ~IRefl~K~l~~AGIs~IEI~Rt~~--~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~  154 (218)
                      -+.+|+.+.|.-|.+.+|.+.-...  ...|.+.-..-+..||++|++++.....+...++.
T Consensus        74 D~~~fI~N~l~PA~V~~V~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI  135 (141)
T TIGR01952        74 NLEEFVANKLAPAEVKNVTVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI  135 (141)
T ss_pred             CHHHHHHHcCCCceEEEEEEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence            5678888889999999998865322  34455555556789999999998888877766653

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	218
2zkq_c	243	Structure Of A Mammalian Ribosomal 40s Subunit With		3e-50
3iz6_B	227	Localization Of The Small Subunit Ribosomal Protein		1e-46
3izb_B	240	Localization Of The Small Subunit Ribosomal Protein		1e-39
1s1h_C	192	Structure Of The Ribosomal 80s-Eef2-Sordarin Comple		2e-39
3jyv_C	188	Structure Of The 40s Rrna And Proteins And PE TRNA		2e-39
3zey_X	214	High-resolution Cryo-electron Microscopy Structure		2e-34
1wh9_A	92	Solution Structure Of The Kh Domain Of Human Riboso		7e-34
2xzm_C	243	Crystal Structure Of The Eukaryotic 40s Ribosomal S		7e-27
3j20_C	210	Promiscuous Behavior Of Proteins In Archaeal Riboso		3e-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 =  194 bits (493), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 93/116 (80%), Positives = 107/116 (92%)
Query: 77  SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
           ++ I    +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct: 2   AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61
Query: 137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct: 62  KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

>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 =  182 bits (462), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 89/108 (82%), Positives = 97/108 (89%)
Query: 85  QFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 144
           +FV+DGVF AEL+E LTRELAEDGYSGVE+R TP RTEIII ATRTQNVLG+KGRRIREL
Sbjct: 10  KFVSDGVFYAELNEMLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIREL 69
Query: 145 TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           TSVVQKRF F +  +ELYAEKV  RGLCAIAQAESLRYKL+GGLAVRR
Sbjct: 70  TSVVQKRFNFLENGVELYAEKVVNRGLCAIAQAESLRYKLLGGLAVRR 117

>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 =  159 bits (402), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 78/125 (62%), Positives = 96/125 (76%)
Query: 80  ICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGR 139
           I    + VADGVF AEL+EF TRELAE+GYSGVE+R TP +TE+II ATRTQ+VLG+ GR
Sbjct: 5   ISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENGR 64
Query: 140 RIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSL 199
           RI ELT +VQKRFK+A G I LYAE+V  RGL A+AQAES+++KL+ GLA+RR    V  
Sbjct: 65  RINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVVR 124
Query: 200 YCLNC 204
           Y +  
Sbjct: 125 YVMES 129

>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 =  158 bits (400), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 77/120 (64%), Positives = 95/120 (79%)
Query: 85  QFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 144
           + VADGVF AEL+EF TRELAE+GYSGVE+R TP +TE+II ATRTQ+VLG+ GRRI EL
Sbjct: 9   KLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENGRRINEL 68
Query: 145 TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNC 204
           T +VQKRFK+A G I LYAE+V  RGL A+AQAES+++KL+ GLA+RR    V  Y +  
Sbjct: 69  TLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVVRYVMES 128

>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 =  158 bits (400), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 77/120 (64%), Positives = 95/120 (79%)
Query: 85  QFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 144
           + VADGVF AEL+EF TRELAE+GYSGVE+R TP +TE+II ATRTQ+VLG+ GRRI EL
Sbjct: 5   KLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENGRRINEL 64
Query: 145 TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNC 204
           T +VQKRFK+A G I LYAE+V  RGL A+AQAES+++KL+ GLA+RR    V  Y +  
Sbjct: 65  TLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVVRYVMES 124

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

Iteration: 1
 Score =  142 bits (357), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 68/118 (57%), Positives = 90/118 (76%)
Query: 86  FVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELT 145
            V DGVF AEL EFL RELA+DG++GVE R TP RTEI+I +T+T+ VLG+KGRRIRELT
Sbjct: 10  MVRDGVFYAELFEFLKRELADDGFAGVEHRVTPTRTEIVIRSTKTREVLGEKGRRIRELT 69
Query: 146 SVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLN 203
           + +Q+RF + +G ++L+AE+V  RGL A+AQAESLR+KL+  L VRR    +  Y + 
Sbjct: 70  ACLQQRFNYKEGKLQLFAERVEVRGLSAMAQAESLRFKLLSNLQVRRAAMGIIRYVME 127

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

Iteration: 1
 Score =  140 bits (352), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 66/79 (83%), Positives = 75/79 (94%)
Query: 92  FRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKR 151
           F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+KGRRIRELT+VVQKR
Sbjct: 8   FKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKR 67
Query: 152 FKFADGAIELYAEKVATRG 170
           F F +G++ELYAEKVATRG
Sbjct: 68  FGFPEGSVELYAEKVATRG 86

>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 =  116 bits (291), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 52/107 (48%), Positives = 78/107 (72%)
Query: 85  QFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 144
           +FVADGVF AEL  F ++ L + GY+G+E+R TP +TEI I AT+ Q V+G +G++ +EL
Sbjct: 13  KFVADGVFNAELHSFFSKSLQDAGYAGIEVRRTPTKTEIRIKATKPQQVIGVEGKKHKEL 72
Query: 145 TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVR 191
           T  +QKRF ++D  I+++AE +  +GLCA AQ E++ YKL+  + VR
Sbjct: 73  TQFLQKRFGYSDDQIQIWAEPIKFKGLCASAQVEAMNYKLLKDVPVR 119

>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 = 65.1 bits (157), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 40/109 (36%), Positives = 61/109 (55%), Gaps = 2/109 (1%)
Query: 80  ICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGR 139
           + +   F+ + V    +DEFL +EL   GY G++I+ TP  T++II A     V+G  GR
Sbjct: 1   MAIERYFIREAVREMLIDEFLEKELRRAGYGGLDIKKTPLGTKVIIFAANPGYVIGRGGR 60
Query: 140 RIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGL 188
           RIRELT +++K+F   +  IE+  E++    L A  QA  L   L  G+
Sbjct: 61  RIRELTRILEKQFGLENPQIEV--EEIKNPYLNAKVQAVRLAQALERGI 107

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	218
3u5c_D	240	RP13, YS3, 40S ribosomal protein S3; translation,	1e-49
3iz6_B	227	40S ribosomal protein S3 (S3P); eukaryotic ribosom	4e-49
2zkq_c	243	40S ribosomal protein S3E; protein-RNA complex, 40	6e-49
2xzm_C	243	KH domain containing protein; ribosome, translatio	5e-46
1wh9_A	92	40S ribosomal protein S3; KH domain, structural ge	2e-44

>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 =  160 bits (407), Expect = 1e-49
 Identities = 75/108 (69%), Positives = 92/108 (85%)

Query: 85  QFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 144
           + VADGVF AEL+EF TRELAE+GYSGVE+R TP +TE+II ATRTQ+VLG+ GRRI EL
Sbjct: 10  KLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENGRRINEL 69

Query: 145 TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           T +VQKRFK+A G I LYAE+V  RGL A+AQAES+++KL+ GLA+RR
Sbjct: 70  TLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRR 117

>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 =  159 bits (403), Expect = 4e-49
 Identities = 89/109 (81%), Positives = 97/109 (88%)

Query: 85  QFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 144
           +FV+DGVF AEL+E LTRELAEDGYSGVE+R TP RTEIII ATRTQNVLG+KGRRIREL
Sbjct: 10  KFVSDGVFYAELNEMLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIREL 69

Query: 145 TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRY 193
           TSVVQKRF F +  +ELYAEKV  RGLCAIAQAESLRYKL+GGLAVRR 
Sbjct: 70  TSVVQKRFNFLENGVELYAEKVVNRGLCAIAQAESLRYKLLGGLAVRRA 118

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

 Score =  159 bits (403), Expect = 6e-49
 Identities = 92/109 (84%), Positives = 104/109 (95%)

Query: 85  QFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 144
           +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+KGRRIREL
Sbjct: 10  KFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIREL 69

Query: 145 TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRY 193
           T+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR 
Sbjct: 70  TAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRA 118

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

 Score =  151 bits (384), Expect = 5e-46
 Identities = 52/108 (48%), Positives = 78/108 (72%)

Query: 85  QFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 144
           +FVADGVF AEL  F ++ L + GY+G+E+R TP +TEI I AT+ Q V+G +G++ +EL
Sbjct: 13  KFVADGVFNAELHSFFSKSLQDAGYAGIEVRRTPTKTEIRIKATKPQQVIGVEGKKHKEL 72

Query: 145 TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
           T  +QKRF ++D  I+++AE +  +GLCA AQ E++ YKL+  + VR 
Sbjct: 73  TQFLQKRFGYSDDQIQIWAEPIKFKGLCASAQVEAMNYKLLKDVPVRL 120

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

 Score =  142 bits (359), Expect = 2e-44
 Identities = 66/89 (74%), Positives = 76/89 (85%)

Query: 87  VADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTS 146
                F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+KGRRIRELT+
Sbjct: 3   SGSSGFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTA 62

Query: 147 VVQKRFKFADGAIELYAEKVATRGLCAIA 175
           VVQKRF F +G++ELYAEKVATRG    +
Sbjct: 63  VVQKRFGFPEGSVELYAEKVATRGSGPSS 91

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	218
3u5c_D	240	RP13, YS3, 40S ribosomal protein S3; translation,	100.0
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
3j20_C	210	30S ribosomal protein S3P; archaea, archaeal, KINK	100.0
2xzm_C	243	KH domain containing protein; ribosome, translatio	100.0
3r8n_C	206	30S ribosomal protein S3; protein biosynthesis, RN	100.0
3i1m_C	233	30S ribosomal protein S3; ribosome structure, prot	100.0
3bbn_C	218	Ribosomal protein S3; small ribosomal subunit, spi	100.0
2vqe_C	239	30S ribosomal protein S3; tRNA-binding, rRNA-bindi	100.0
1wh9_A	92	40S ribosomal protein S3; KH domain, structural ge	99.92
2pt7_G	152	HP1451, hypothetical protein; ATPase, protein-prot	96.14
3gku_A	225	Probable RNA-binding protein; APC21302, clostridiu	94.05
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	87.57
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	84.18
1ega_A	301	Protein (GTP-binding protein ERA); GTPase, RNA-bin	84.15

>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=8.5e-39  Score=280.48  Aligned_cols=132  Identities=59%  Similarity=0.882  Sum_probs=127.6

Q ss_pred             cccchhhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCC
Q psy8115          76 NSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFA  155 (218)
Q Consensus        76 m~~~~~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~  155 (218)
                      |+.+|+.+++|++|+.++++||+||.++|.++|||+|||+|++++++|+||+++||+|||++|++|++|++.|+|+|++.
T Consensus         1 ~~~~~~~~~k~vadg~~~~~ire~l~k~l~~agis~IeI~Rt~~~i~I~I~t~rPg~VIGkkG~~I~~L~~~l~k~~~~~   80 (240)
T 3u5c_D            1 MVALISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENGRRINELTLLVQKRFKYA   80 (240)
T ss_dssp             --CCCCHHHHHHHHHHHHHHHHHHHHHHTGGGTEEEEEEEECSSCEEEEEEESCHHHHHTTTTCTHHHHHHHHHHHHTCC
T ss_pred             CcccccccceEeecCchHHHHHHHHHHHHHhCCcceEEEEEcCCeEEEEEEeCCCceEEcCCchhHHHHHHHHHHHhCCC
Confidence            67889999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             CCcEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCCc
Q psy8115         156 DGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTY  207 (218)
Q Consensus       156 ~kkI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA~  207 (218)
                      +++|+|+++||++|++||+++|++||+|||+|++||||||++|+++|++||-
T Consensus        81 ~~~v~I~i~eV~~p~l~A~lvAe~IA~qLe~rv~FRRA~k~ai~~am~aGak  132 (240)
T 3u5c_D           81 PGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVVRYVMESGAK  132 (240)
T ss_dssp             TTSSEEEEECCSCGGGCHHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHTTCS
T ss_pred             CCeEEEEEEEecCCCcCHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCCc
Confidence            8999999999999999999999999999999999999999999999999973

>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=1.2e-39  Score=284.13  Aligned_cols=132  Identities=69%  Similarity=0.985  Sum_probs=119.0

Q ss_pred             cccchhhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCC
Q psy8115          76 NSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFA  155 (218)
Q Consensus        76 m~~~~~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~  155 (218)
                      |+.+|+.+++||+||+++++||+||.++|.+||||+|||+|++++++|+||+++||+|||++|+++++|++.|+|+|++.
T Consensus         1 ~~~~~~~~rkfv~dg~~~a~Ire~l~k~l~~agis~IeI~R~~~~i~I~I~tarPg~vIGkkG~~I~~L~~~l~k~~~~~   80 (227)
T 3iz6_B            1 MATQISKKKKFVSDGVFYAELNEMLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFNFL   80 (227)
T ss_dssp             -----------CHHHHHHHHHHHHHHHHTSSCSSCCEECCEETTEECCEEECTTHHHHHCSSSSHHHHHHHHHHHHHCCC
T ss_pred             CccchhhhhhhhhcCeehHHHHHHHHHHHHhCCcceEEEEEcCCcEEEEEEeCCCceEEcCCchhHHHHHHHHHHHhCCC
Confidence            67889999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             CCcEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCCc
Q psy8115         156 DGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTY  207 (218)
Q Consensus       156 ~kkI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA~  207 (218)
                      +++++|+++||++|++||+++||+||+|||+|++||||||+||+++|++||-
T Consensus        81 ~~~v~I~i~eV~~p~l~A~lvAe~Ia~qLe~rv~fRrA~k~ai~~~m~aGak  132 (227)
T 3iz6_B           81 ENGVELYAEKVVNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESGAK  132 (227)
T ss_dssp             SCCCCCEEECCSSSTTSCSHHHHHHHTTTTTCCCHHHHHHHHHHTTTTTCCS
T ss_pred             CCeEEEEEEEecCCCcCHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHcCCc
Confidence            8999999999999999999999999999999999999999999999999973

>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=9.5e-39  Score=280.70  Aligned_cols=132  Identities=71%  Similarity=1.056  Sum_probs=127.4

Q ss_pred             cccchhhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCC
Q psy8115          76 NSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFA  155 (218)
Q Consensus        76 m~~~~~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~  155 (218)
                      |+.+++.+++||+||+++.+||+||.++|.++|||+|||+|++++++|+||+++||+|||++|+++++|++.|+|+|++.
T Consensus         1 ~~~~~~~~rkfv~dgv~~~~IR~~l~k~l~~agis~IeIeRt~~~i~I~I~tarPg~vIGkkG~~I~~L~~~L~k~~~~~   80 (243)
T 2zkq_c            1 MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGFP   80 (243)
T ss_dssp             -CBCCCCTTTHHHHHHHHHHHHHHHHHHTCTTTEEEEECBEETTEECCEEEESCHHHHHCGGGHHHHHHHHHHHHHSCTT
T ss_pred             CCcchhhhhHHHhcChHHHHHHHHHHHHHHHCCcceEEEEEcCCcEEEEEEeCCCceEEcCCchHHHHHHHHHHHHhCcC
Confidence            56678899999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             CCcEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCCc
Q psy8115         156 DGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTY  207 (218)
Q Consensus       156 ~kkI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA~  207 (218)
                      +++++|++.||++|++||+++||+||+|||+|++||||||+||+++|++||-
T Consensus        81 ~~~v~I~i~eV~~p~l~A~lvAe~IA~qLe~rv~FRRa~k~ai~~am~aGak  132 (243)
T 2zkq_c           81 EGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAK  132 (243)
T ss_dssp             TCCCCCEEEECSCGGGCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHSSCS
T ss_pred             CceEEEEEEEecCcccCHHHHHHHHHHHHHcchhHHHHHHHHHHHHHhcCCc
Confidence            8899999999999999999999999999999999999999999999999973

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

Probab=100.00  E-value=5.3e-37  Score=264.78  Aligned_cols=126  Identities=33%  Similarity=0.471  Sum_probs=120.8

Q ss_pred             hhhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcE
Q psy8115          80 ICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAI  159 (218)
Q Consensus        80 ~~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI  159 (218)
                      |..+++|++|++++.+||+||.++|.++|||+|||+|++++++|+||+++||+|||++|+++++|++.|+|+|++  +++
T Consensus         1 m~~~k~fv~~~~~d~~Ir~~l~k~l~~agis~ieI~r~~~~~~I~I~t~rPg~vIG~~G~~I~~L~~~l~k~~~~--~~v   78 (210)
T 3j20_C            1 MAIERYFIREAVREMLIDEFLEKELRRAGYGGLDIKKTPLGTKVIIFAANPGYVIGRGGRRIRELTRILEKQFGL--ENP   78 (210)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHGGGTCEEEEEEECCSSCCEEEEEESCHHHHHCSSSHHHHHHHHHHHHHSSC--SSC
T ss_pred             CcchHHHHHhhhHHHHHHHHHHHHHHHCCcceEEEEECCCeEEEEEEeCCCceEEcCCchhHHHHHHHHHHHhCC--Cce
Confidence            357889999999999999999999999999999999999999999999999999999999999999999999986  458


Q ss_pred             EEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCCc
Q psy8115         160 ELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTY  207 (218)
Q Consensus       160 ~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA~  207 (218)
                      .|++.||++|++||+++|++||+|||+|++||||||++|+++|++||-
T Consensus        79 ~I~i~eV~~p~l~A~lvAe~Ia~qLe~rv~fRra~k~ai~~~m~~Gak  126 (210)
T 3j20_C           79 QIEVEEIKNPYLNAKVQAVRLAQALERGIHFRRAAYAALRAIMNNGAR  126 (210)
T ss_dssp             EEEEEECSCTTTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEEEecCCccCHHHHHHHHHHHHhhcccHHHHHHHHHHHHHhcCCc
Confidence            888999999999999999999999999999999999999999999873

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

Probab=100.00  E-value=1.2e-36  Score=267.36  Aligned_cols=129  Identities=41%  Similarity=0.689  Sum_probs=125.5

Q ss_pred             cchhhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCC
Q psy8115          78 LSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADG  157 (218)
Q Consensus        78 ~~~~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~k  157 (218)
                      .+++.+++|+.|++++.+||+||.++|.+||||+|||+|++++++|+||+++||+|||++|+++++|++.|+++|++.++
T Consensus         6 ~~~~~~kkfv~~~l~ed~Ir~~l~~~l~~agis~IeI~r~~~~i~I~I~tarPg~vIGkkG~~I~~L~~~L~k~~~~~~~   85 (243)
T 2xzm_C            6 RAINKKKKFVADGVFNAELHSFFSKSLQDAGYAGIEVRRTPTKTEIRIKATKPQQVIGVEGKKHKELTQFLQKRFGYSDD   85 (243)
T ss_dssp             SCCCHHHHHHHHHHHHHHHHHHHHHHCCSSCEEEECCEECSSCEEEEEEESCHHHHHCSSSHHHHHHHHHHHHHHCCTTT
T ss_pred             hhhhhHHHHHHhHhHHHHHHHHHHHHHHHCCcceEEEEECCCeEEEEEEcCCCceEECCCchHHHHHHHHHHHHhCcCCc
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999998888


Q ss_pred             cEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCC
Q psy8115         158 AIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYT  206 (218)
Q Consensus       158 kI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA  206 (218)
                      +++|++.||++|++||+++|++||+|||+|++||||||+||+++|++||
T Consensus        86 ~v~I~i~eV~~p~l~A~lvAe~IA~qLe~Rv~FRRA~k~ai~~am~aGa  134 (243)
T 2xzm_C           86 QIQIWAEPIKFKGLCASAQVEAMNYKLLKDVPVRLAANYIIKSVIQDGA  134 (243)
T ss_dssp             TSEEEEEECSCGGGCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTC
T ss_pred             eEEEEEEEecCcccCHHHHHHHHHHHHHccchHHHHHHHHHHHHHhcCC
Confidence            9999999999999999999999999999999999999999999999997

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

Probab=100.00  E-value=2.6e-35  Score=257.64  Aligned_cols=136  Identities=18%  Similarity=0.190  Sum_probs=124.2

Q ss_pred             HHHHh-hhhhcc-cccchhhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHH
Q psy8115          65 FRVLV-NTIGVS-NSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIR  142 (218)
Q Consensus        65 ~~~~~-~~~~~~-m~~~~~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik  142 (218)
                      ||..+ ..|.|. +|.. ++|++++.+|.   +||+||.++|.++|||+|||+|+++.++|+||+++||+|||++|++++
T Consensus        10 fRlGi~~~w~S~W~a~~-k~y~~~l~eD~---kIr~~l~k~l~~agis~IeI~R~~~~i~I~I~t~rPg~vIGkkG~~I~   85 (233)
T 3i1m_C           10 IRLGIVKPWNSTWFANT-KEFADNLDSDF---KVRQYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKKGEDVE   85 (233)
T ss_dssp             TTTTSSCCCSBCCCCCH-HHHHHHHHHHH---HHHHHHHHHTGGGTEEEEEBCCCSSCBCCEEEESCHHHHHCSTTHHHH
T ss_pred             EeecccCCceeEEecCc-chhHHHHHHHH---HHHHHHHHHHHhcCCCcEEEEEcCCeEEEEEEECCCCccccCcchHHH
Confidence            34444 346444 6654 69999999999   999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCCc
Q psy8115         143 ELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTY  207 (218)
Q Consensus       143 ~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA~  207 (218)
                      +|+..|+++|+.   ++.|+++||++|++||+++||+||+|||+|++||||||+||+++|++||-
T Consensus        86 ~L~~~L~k~~~~---~v~I~i~eV~~p~l~A~lvAe~IA~qLe~rv~FRramk~ai~~am~aGak  147 (233)
T 3i1m_C           86 KLRKVVADIAGV---PAQINIAEVRKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAK  147 (233)
T ss_dssp             HHHHHHHHHHTS---CBCCEEEECSSGGGCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHTTCCS
T ss_pred             HHHHHHHHHHCC---ceEEEEEeecCCCcCHHHHHHHHHHHHHccccHHHHHHHHHHhhhhcCCc
Confidence            999999999984   48899999999999999999999999999999999999999999999973

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

Probab=100.00  E-value=3e-35  Score=254.74  Aligned_cols=139  Identities=13%  Similarity=0.091  Sum_probs=127.0

Q ss_pred             HHHHhh-hhhcc-cccchhhhhhHHhhhhHHHHHHHHHHhhhcc-----C---CeeeeEEEecCCeEEEEEEecccceEe
Q psy8115          65 FRVLVN-TIGVS-NSLSICVSLQFVADGVFRAELDEFLTRELAE-----D---GYSGVEIRFTPARTEIIIMATRTQNVL  134 (218)
Q Consensus        65 ~~~~~~-~~~~~-m~~~~~~ykkfV~d~iir~~IRefl~K~l~~-----A---GIs~IEI~Rt~~~I~IiI~aarPgiVI  134 (218)
                      ||..++ .|.+. +|.. ++|++++.+|.   +||+||.++|.+     |   |||+|||+|+++.++|+||+++||+||
T Consensus        10 fRlgi~~~w~S~W~a~~-k~y~~~l~eD~---~IR~~i~~~l~~~~~~~a~~~gis~ieI~r~~~~i~I~I~~~rPg~vI   85 (218)
T 3bbn_C           10 FRLGTTQSHYSLWFSQP-KNYAEGLQEDQ---KIRDCIKNYVQKNTKTSSGVEGIARIEIQKRIDLIQVIIHMGFPKLLI   85 (218)
T ss_dssp             SSTTTTSCCSBCCCCCT-TSSHHHHHHHH---HHHHHHHSCCSSSSCCTTTTTCEEEEEBCBSSSCBCCEEEESCTTTTS
T ss_pred             eecCccCCcceEEeCCh-hHHHHHHHHHH---HHHHHHHHHHhhhcccccccCccceEEEEEcCCeEEEEEEecCCCcEe
Confidence            444444 56444 6643 69999999999   999999999997     8   999999999999999999999999999


Q ss_pred             ccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCCc
Q psy8115         135 GDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTY  207 (218)
Q Consensus       135 GrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA~  207 (218)
                      |++|+++++|+..|++.|++.++++.|++.||++|++||.++||+||+|||+|++||||||+||+++|++||-
T Consensus        86 Gk~g~~i~~L~~~l~k~~~~~~~~v~i~i~ev~~p~l~A~lvAe~Ia~qLe~r~~fRra~k~ai~~~m~~gak  158 (218)
T 3bbn_C           86 ENRPQGVEDLKINVQKELNCVNRKLNIAITRIAKPYGDPNILAEFIAGQLKSRVSFRKAMKKAIELTEQADTK  158 (218)
T ss_dssp             CSSSCTTHHHHHHHHHHSCSSCCCCCCCEEECSCTTTSHHHHHHHSTTTTTTTCCHHHHHTHHHHHHHTTCCS
T ss_pred             cCCcHHHHHHHHHHHHHhccCCceEEEEEEEecCCCcCHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHhCCC
Confidence            9999999999999999997666889999999999999999999999999999999999999999999999973

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

Probab=100.00  E-value=1.5e-34  Score=253.48  Aligned_cols=136  Identities=18%  Similarity=0.219  Sum_probs=124.5

Q ss_pred             HHHHhh-hhhcc-cccchhhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHH
Q psy8115          65 FRVLVN-TIGVS-NSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIR  142 (218)
Q Consensus        65 ~~~~~~-~~~~~-m~~~~~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik  142 (218)
                      ||..+| .|.+. +|.. ++|.+++.+|.   +||+||.++|.++|||+|+|+|+++.++|+||+++||+|||++|++++
T Consensus        10 fRLgi~~~w~S~W~a~~-k~y~~~l~eD~---~IR~~l~k~l~~agis~IeIeR~~~~i~I~I~tarPg~vIGkkG~~I~   85 (239)
T 2vqe_C           10 FRLGITRDWESRWYAGK-KQYRHLLLEDQ---RIRGLLEKELYSAGLARVDIERAADNVAVTVHVAKPGVVIGRGGERIR   85 (239)
T ss_dssp             TTTTSSCCCSBCCCCCT-TTHHHHHHHHH---HHHHHHHTTTTTTCEEEECBCBSSSCBCCEEEESCGGGTSCSSSSHHH
T ss_pred             EecCccCCcceEEeCCH-hHHHHHHHHHH---HHHHHHHHHHHhcCCceEEEEECCCeEEEEEEeCCCcceecCCchHHH
Confidence            455444 46544 6654 69999999999   999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhCCCCCcEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCCc
Q psy8115         143 ELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTY  207 (218)
Q Consensus       143 ~L~~~LqK~~~~~~kkI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA~  207 (218)
                      +|+..|+++++   +++.|++.||++|++||+++|++||+|||+|++||||||++|+++|++||-
T Consensus        86 ~L~~~L~k~~~---~~v~I~i~eVk~p~l~A~lvAe~Ia~qLe~rv~FRra~k~ai~~am~~gak  147 (239)
T 2vqe_C           86 VLREELAKLTG---KNVALNVQEVQNPNLSAPLVAQRVAEQIERRFAVRRAIKQAVQRVMESGAK  147 (239)
T ss_dssp             HHHHHHHHHST---TCCCCEEEECSCTTSCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHSSCS
T ss_pred             HHHHHHHHHhC---CeeEEEEEEecCCCcCHHHHHHHHHHHHHccchHHHHHHHHHHHHHHcCCC
Confidence            99999999996   578899999999999999999999999999999999999999999999973

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

Probab=99.92  E-value=6.5e-26  Score=173.00  Aligned_cols=87  Identities=76%  Similarity=1.116  Sum_probs=84.5

Q ss_pred             hhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEec
Q psy8115          88 ADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVA  167 (218)
Q Consensus        88 ~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~  167 (218)
                      +||+++++||+||.++|.+||||+|||+|++++++|+|||+|||+|||++|++|++|+..|+|+|++.+++|+|+++||+
T Consensus         4 ~~gv~~~~IR~~i~k~l~~aGis~IeIeR~~~~i~I~I~tarPg~vIGkkG~~Ie~L~~~l~k~~~~~~~~v~I~I~eV~   83 (92)
T 1wh9_A            4 GSSGFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGFPEGSVELYAEKVA   83 (92)
T ss_dssp             SSCSHHHHHHHHHHHHTTTTTEEEEEEEECSSCEEEEEEESCHHHHHCGGGHHHHHHHHHHHHHHCCCTTSEEEEEEECC
T ss_pred             hhhhHHHHHHHHHHHHHHHCceeeEEEEECCCeEEEEEEeCCCceEEcCCcHHHHHHHHHHHHHhCCCCCeEEEEEEEec
Confidence            58999999999999999999999999999999999999999999999999999999999999999987899999999999


Q ss_pred             CCCcCHH
Q psy8115         168 TRGLCAI  174 (218)
Q Consensus       168 nP~l~A~  174 (218)
                      +|++||+
T Consensus        84 ~P~ldA~   90 (92)
T 1wh9_A           84 TRGSGPS   90 (92)
T ss_dssp             CSCCCSC
T ss_pred             CCCcCCC
Confidence            9999985

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

Probab=96.14  E-value=0.0079  Score=49.20  Aligned_cols=60  Identities=22%  Similarity=0.324  Sum_probs=51.3

Q ss_pred             HHHHHHHHhhhccCCee--eeEE-EecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhC
Q psy8115          94 AELDEFLTRELAEDGYS--GVEI-RFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFK  153 (218)
Q Consensus        94 ~~IRefl~K~l~~AGIs--~IEI-~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~  153 (218)
                      .++.+||..-+...|+.  .|++ ....+.+.|.|.....|++||+.|+.++.|+..++...+
T Consensus         5 ~~~~~~L~~il~~m~~~~~~i~v~~~~~~~i~i~i~ged~glLIGK~G~TL~ALQyL~~~~vn   67 (152)
T 2pt7_G            5 HEIKQELKDLFSHLPYKINKVEVSLYEPGVLLIDIDGEDSALLIGEKGYRYKALSYLLFNWIH   67 (152)
T ss_dssp             HHHHHHHHHHTTTTTCCEEEEEEEEEETTEEEEEEEEGGGTTTTCGGGHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCceEEEEEEecCCEEEEEEecCCcceEECCCCcchHHHHHHHHHHhh
Confidence            36788999999999985  4677 345778999999999999999999999999999987665

>3gku_A Probable RNA-binding protein; APC21302, clostridium symbiosum ATCC 14 structural genomics, PSI-2, protein structure initiative; 2.95A {Clostridium symbiosum atcc 14940}

Probab=94.05  E-value=0.12  Score=44.63  Aligned_cols=59  Identities=12%  Similarity=0.281  Sum_probs=48.1

Q ss_pred             HHHHHHHhhhccCCee-eeEEEec--CCeEEEEEEecccceEeccCcccHHHHHHHHHHHhC
Q psy8115          95 ELDEFLTRELAEDGYS-GVEIRFT--PARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFK  153 (218)
Q Consensus        95 ~IRefl~K~l~~AGIs-~IEI~Rt--~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~  153 (218)
                      ...+||..-|...|+. .|++.-.  .+.+.|.|.....+++||++|+.++.|+..+...++
T Consensus        65 ~a~~~L~~ll~~m~~~~~i~~~~~~~~~~i~i~i~g~d~g~LIGk~G~tLdALQyL~~~~vn  126 (225)
T 3gku_A           65 KAIEFLEQVFDAMNMAVDISVEYNETEKEMNVNLKGDDMGILIGKRGQTLDSLQYLVSLVVN  126 (225)
T ss_dssp             HHHHHHHHHHHHTTCCCEEEEEEETTTTEEEEEEECHHHHHCSTTHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCeEEEEEEecCCCEEEEEEcCCccceeecCCCeEhHHHHHHHHHHHH
Confidence            5668888888888884 3555432  478999999999999999999999999999888775

>3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA, 30S ribosome ASSE GTP-binding, nucleotide-binding; HET: GNP; 1.90A {Aquifex aeolicus} PDB: 3r9w_A* 3r9x_A*

Probab=87.57  E-value=1.2  Score=38.39  Aligned_cols=99  Identities=16%  Similarity=0.234  Sum_probs=55.3

Q ss_pred             cchhhHHHHhhhhhc----ccccchh-hhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEE---ecC-----CeEEEEEE
Q psy8115          60 GFSVLFRVLVNTIGV----SNSLSIC-VSLQFVADGVFRAELDEFLTRELAEDGYSGVEIR---FTP-----ARTEIIIM  126 (218)
Q Consensus        60 ~~~~~~~~~~~~~~~----~m~~~~~-~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~---Rt~-----~~I~IiI~  126 (218)
                      |...+|..+++.+..    +...++. .-.++....+++.++.+.+..++..+ + .|+|+   ...     ..|.-+|+
T Consensus       168 gv~~L~~~l~~~l~~~~~~~~~~~~td~~~~~~~~e~irek~~~~~~~eiP~~-~-~v~i~~~~~~~~~~~~~~i~a~i~  245 (308)
T 3iev_A          168 NLDELVKTILKYLPEGEPLFPEDMITDLPLRLLAAEIVREKAMMLTREEVPTS-I-AVKINEIKPGDANPNMLVIKGEII  245 (308)
T ss_dssp             SHHHHHHHHHHHSCBCCCSSCTTCCBCCCHHHHHHHHHHHHHHHTCCTTHHHH-C-EEEEEEEEECSSCTTSEEEEEEEE
T ss_pred             CHHHHHHHHHHhCccCCCCCCcccccCCCHHHHHHHHHHHHHHhhhhhhcCCe-e-EEEeEEEEEccCCCCeEEEEEEEE
Confidence            556677777665521    1111111 12233334445555555555555443 2 24442   222     36777999


Q ss_pred             ecccc---eEeccCcccHHHH----HHHHHHHhCCCCCcEEEEE
Q psy8115         127 ATRTQ---NVLGDKGRRIREL----TSVVQKRFKFADGAIELYA  163 (218)
Q Consensus       127 aarPg---iVIGrkG~~Ik~L----~~~LqK~~~~~~kkI~I~I  163 (218)
                      +.|++   +|||++|+.|+++    +..|++.|+   .+|.+.+
T Consensus       246 ve~~~~k~i~ig~~g~~ik~i~~~ar~~~~~~~~---~~v~l~l  286 (308)
T 3iev_A          246 VDRENLKPIIIGKKGQRLKEIGKRARQELELILG---RPVYLEL  286 (308)
T ss_dssp             ESSGGGHHHHHCGGGHHHHHHHHHHHHHHHHHHT---SCEEEEE
T ss_pred             EccCCcceEEEcCCcHHHHHHHHHHHHHHHHHhC---CceEEEE
Confidence            98886   6999999999776    557777886   4554443

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1

Probab=84.18  E-value=1.1  Score=32.09  Aligned_cols=74  Identities=15%  Similarity=0.126  Sum_probs=43.1

Q ss_pred             eEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCC-----cEEEEEEEecCCCcCHHHHHHHHHHHHHcChhHHHHH
Q psy8115         120 RTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADG-----AIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYN  194 (218)
Q Consensus       120 ~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~k-----kI~I~I~EV~nP~l~A~llAe~IA~QLEkRv~FRRAm  194 (218)
                      .+++.|-...-|.|||++|+.|++|++.=.-.....+.     .-.-....|.-+ .++.-.|..+...+-.....||+-
T Consensus         4 t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~-~~~v~~A~~~I~~~i~~~~~~r~~   82 (87)
T 1ec6_A            4 LVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS-PAATQAAQYLISQRVTYEQGVRAS   82 (87)
T ss_dssp             EEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESS-HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhcccccccc
Confidence            45677777888999999999999887743211111110     000001223332 356777887777776666666653

>1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like, hydrolase; 2.40A {Escherichia coli} SCOP: c.37.1.8 d.52.3.1 PDB: 1x1l_X 3ieu_A* 1x18_X

Probab=84.15  E-value=3.4  Score=35.49  Aligned_cols=62  Identities=29%  Similarity=0.413  Sum_probs=41.3

Q ss_pred             hhHHHHHHHHHHhhhccCCeeeeEEEec------CCeEEEEEEecccc---eEeccCcccHHHHH----HHHHHHhC
Q psy8115          90 GVFRAELDEFLTRELAEDGYSGVEIRFT------PARTEIIIMATRTQ---NVLGDKGRRIRELT----SVVQKRFK  153 (218)
Q Consensus        90 ~iir~~IRefl~K~l~~AGIs~IEI~Rt------~~~I~IiI~aarPg---iVIGrkG~~Ik~L~----~~LqK~~~  153 (218)
                      ..+|.++-+.+..++..+  ..|+|+.-      ..++...|++.+.+   ++||++|+.++++.    ..|++.|+
T Consensus       196 e~~re~l~~~l~~e~p~~--~~v~i~~~~~~~~~~~~i~~~i~v~~~~~k~i~ig~~G~~~k~ig~~ar~~i~~~~~  270 (301)
T 1ega_A          196 EIIREKLMRFLGAELPYS--VTVEIERFVSNERGGYDINGLILVEREGQKKMVIGNKGAKIKTIGIEARKDMQEMFE  270 (301)
T ss_dssp             HHHHHHHHHHHGGGCCTT--EEEEEEEEECCSSCSEEEEEEEEESSHHHHHHHHCGGGHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhCCCCCeE--EEEEEEEEEecCCCeEEEEEEEEEEECCceEEEECCCcHHHHHHHHHHHHHHHHHHC
Confidence            344555556655555444  44667622      34677888886654   69999999997774    56777776

---

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	218
d1wh9a_	92	d.52.3.1 (A:) Ribosomal protein S3 N-terminal doma	2e-39
d2uubc1	105	d.52.3.1 (C:2-106) Ribosomal protein S3 N-terminal	2e-05
d2qalc1	105	d.52.3.1 (C:1-105) Ribosomal protein S3 N-terminal	5e-05

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

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

 Score =  128 bits (324), Expect = 2e-39
 Identities = 66/87 (75%), Positives = 76/87 (87%)

Query: 89  DGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVV 148
              F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+KGRRIRELT+VV
Sbjct: 5   SSGFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVV 64

Query: 149 QKRFKFADGAIELYAEKVATRGLCAIA 175
           QKRF F +G++ELYAEKVATRG    +
Sbjct: 65  QKRFGFPEGSVELYAEKVATRGSGPSS 91

>d2uubc1 d.52.3.1 (C:2-106) Ribosomal protein S3 N-terminal domain {Thermus thermophilus [TaxId: 274]} Length = 105

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Ribosomal protein S3 N-terminal domain
species: Thermus thermophilus [TaxId: 274]

 Score = 40.2 bits (94), Expect = 2e-05
 Identities = 14/56 (25%), Positives = 22/56 (39%)

Query: 98  EFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFK 153
             L +EL   G + V+I        + +   +   V+G  G RIR L   + K   
Sbjct: 40  GLLEKELYSAGLARVDIERAADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTG 95

>d2qalc1 d.52.3.1 (C:1-105) Ribosomal protein S3 N-terminal domain {Escherichia coli [TaxId: 562]} Length = 105

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Ribosomal protein S3 N-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 39.1 bits (91), Expect = 5e-05
 Identities = 16/56 (28%), Positives = 25/56 (44%)

Query: 98  EFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFK 153
           ++LT+ELA+   S + I        + I   R   V+G KG  + +L  VV     
Sbjct: 40  QYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAG 95

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	218
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	99.9
d2uubc1	105	Ribosomal protein S3 N-terminal domain {Thermus th	99.83
d2qalc1	105	Ribosomal protein S3 N-terminal domain {Escherichi	99.83
d2uubc2	101	Ribosomal protein S3 C-terminal domain {Thermus th	99.27
d2qalc2	101	Ribosomal protein S3 C-terminal domain {Escherichi	99.19
d1egaa2	113	GTPase Era C-terminal domain {Escherichia coli [Ta	93.93
d1wf3a2	118	GTPase Era C-terminal domain {Thermus thermophilus	92.28
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	90.37
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	80.96

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

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

Probab=99.90  E-value=3e-24  Score=162.53  Aligned_cols=83  Identities=80%  Similarity=1.177  Sum_probs=80.7

Q ss_pred             HHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecCCCc
Q psy8115          92 FRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGL  171 (218)
Q Consensus        92 ir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~nP~l  171 (218)
                      |+++|||||.++|.+||||+|+|+|++++++|+|||+|||+|||++|+++++|++.|+|+|++.+++|+|++++|++.+|
T Consensus         8 f~a~Ire~l~k~l~~Agis~ieI~Rt~~~i~I~I~tarPGivIGrkG~~I~~L~~~l~k~~~~~~~~i~lnae~Ia~r~l   87 (92)
T d1wh9a_           8 FKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGS   87 (92)
T ss_dssp             HHHHHHHHHHHHTTTTTEEEEEEEECSSCEEEEEEESCHHHHHCGGGHHHHHHHHHHHHHHCCCTTSEEEEEEECCCSCC
T ss_pred             HHHHHHHHHHHHHHhCCcceEEEEECCCeEEEEEEeCCCceeeccCchhHHHHHHHHHHHHCCCCCcEEEEEEeecccCC
Confidence            38899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHH
Q psy8115         172 CAI  174 (218)
Q Consensus       172 ~A~  174 (218)
                      ||.
T Consensus        88 ~~~   90 (92)
T d1wh9a_          88 GPS   90 (92)
T ss_dssp             CSC
T ss_pred             Ccc
Confidence            984

>d2uubc1 d.52.3.1 (C:2-106) Ribosomal protein S3 N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Ribosomal protein S3 N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=99.83  E-value=3.2e-22  Score=153.99  Aligned_cols=95  Identities=19%  Similarity=0.277  Sum_probs=83.0

Q ss_pred             HHHHhh-hhhcc-cccchhhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCcccHH
Q psy8115          65 FRVLVN-TIGVS-NSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIR  142 (218)
Q Consensus        65 ~~~~~~-~~~~~-m~~~~~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~Ik  142 (218)
                      ||..++ .|.|. .|.. ++|+++|.+|.   +||+||.+++.+||||+|+|+|+++.++|+|||+|||+|||++|++++
T Consensus         9 fRlGi~k~w~S~W~a~~-~~y~~~l~eD~---~IR~~i~k~~~~agIs~IeIeR~~~~i~I~I~tarPG~iIGkkG~~i~   84 (105)
T d2uubc1           9 FRLGITRDWESRWYAGK-KQYRHLLLEDQ---RIRGLLEKELYSAGLARVDIERAADNVAVTVHVAKPGVVIGRGGERIR   84 (105)
T ss_dssp             TTTTTTSCCSCBCCCCT-TTTTHHHHHHH---HHHHHHHHSTTTTTEEEECCEESSSCEECCEEESCHHHHHCSTTSHHH
T ss_pred             eeecccCCCCceEcCCh-hhhHHHHHHHH---HHHHHHHhhccccCcceEEEEEccCcEEEEEEECCCceEEcCCchhHH
Confidence            444444 46444 6654 79999999999   999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhCCCCCcEEEEEEEe
Q psy8115         143 ELTSVVQKRFKFADGAIELYAEKV  166 (218)
Q Consensus       143 ~L~~~LqK~~~~~~kkI~I~I~EV  166 (218)
                      +|++.|++.++   +++.|+|.||
T Consensus        85 ~L~~~l~k~~~---k~v~inI~EV  105 (105)
T d2uubc1          85 VLREELAKLTG---KNVALNVQEV  105 (105)
T ss_dssp             HHHHHHHHHSS---CCCCCCCCBC
T ss_pred             HHHHHHHHHhC---CCceEEEEEC
Confidence            99999999887   4566777775

>d2qalc1 d.52.3.1 (C:1-105) Ribosomal protein S3 N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Ribosomal protein S3 N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.83  E-value=6.9e-22  Score=152.37  Aligned_cols=97  Identities=19%  Similarity=0.208  Sum_probs=85.1

Q ss_pred             hhHHHHhh-hhhcc-cccchhhhhhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEecCCeEEEEEEecccceEeccCccc
Q psy8115          63 VLFRVLVN-TIGVS-NSLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRR  140 (218)
Q Consensus        63 ~~~~~~~~-~~~~~-m~~~~~~ykkfV~d~iir~~IRefl~K~l~~AGIs~IEI~Rt~~~I~IiI~aarPgiVIGrkG~~  140 (218)
                      ..||..++ .|.|. .|.. ++|+++|+||.   +||+|+.+++.+||||+|+|+|+.+.++|+|||+|||+|||++|++
T Consensus         7 ~GfRlGi~~~~~S~Wfa~~-~~Y~~~l~eD~---~IR~~i~k~~~~a~Is~IeIeR~~~~i~V~I~tarPGviIG~~G~~   82 (105)
T d2qalc1           7 NGIRLGIVKPWNSTWFANT-KEFADNLDSDF---KVRQYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKKGED   82 (105)
T ss_dssp             HHHTTTTTSCCSCCCCCCH-HHHHHHHHHHH---HHHHHHHHTTSTTCEEEEECCCCSSCBCCEEEESCHHHHHCTTSHH
T ss_pred             cceeecccCCCCCEEcCCc-cchHHHHHHHH---HHHHHHHHHHHhcccceEEEEecCCcEEEEEEeCCCccEeccCccc
Confidence            34566655 45444 6654 79999999999   9999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhCCCCCcEEEEEEEe
Q psy8115         141 IRELTSVVQKRFKFADGAIELYAEKV  166 (218)
Q Consensus       141 Ik~L~~~LqK~~~~~~kkI~I~I~EV  166 (218)
                      +++|+..|+|.++   +++.|+|.||
T Consensus        83 i~~L~~~l~k~~~---~~v~inI~EV  105 (105)
T d2qalc1          83 VEKLRKVVADIAG---VPAQINIAEV  105 (105)
T ss_dssp             HHHHHHHHHHHHT---SCBCCEEECC
T ss_pred             HHHHHHHHHHHhC---CCceEEEEEC
Confidence            9999999999997   4577777876

>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=99.27  E-value=1.7e-12  Score=98.65  Aligned_cols=41  Identities=17%  Similarity=0.085  Sum_probs=39.4

Q ss_pred             cCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCCc
Q psy8115         167 ATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTY  207 (218)
Q Consensus       167 ~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA~  207 (218)
                      +||++||+++|++||.|||+|++||||++++++++|++||-
T Consensus         1 ~nP~l~A~~vA~~Ia~~Ler~~~fRra~~~~l~~~m~~ga~   41 (101)
T d2uubc2           1 QNPNLSAPLVAQRVAEQIERRFAVRRAIKQAVQRVMESGAK   41 (101)
T ss_dssp             SSTTSCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHTTCS
T ss_pred             CCCccCHHHHHHHHHHHHHccchHHHHHHHHHHHhhhcCcc
Confidence            58999999999999999999999999999999999999973

>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=99.19  E-value=6.5e-12  Score=95.34  Aligned_cols=41  Identities=17%  Similarity=0.033  Sum_probs=39.4

Q ss_pred             cCCCcCHHHHHHHHHHHHHcChhHHHHHHHHHHHHHHcCCc
Q psy8115         167 ATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNCYTY  207 (218)
Q Consensus       167 ~nP~l~A~llAe~IA~QLEkRv~FRRAmK~AIr~amkaGA~  207 (218)
                      ++|++||+++|++||+|||+|++|||+++++++++|++||-
T Consensus         1 k~P~l~A~~vA~~IA~~LErr~~fRr~~~~~i~~~m~~ga~   41 (101)
T d2qalc2           1 RKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAK   41 (101)
T ss_dssp             SCGGGCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHSSCS
T ss_pred             CCCCcCHHHHHHHHHHHHHcchHHHHHHHHHHHHHhhcchh
Confidence            58999999999999999999999999999999999999974

>d1egaa2 d.52.3.1 (A:183-295) GTPase Era C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: GTPase Era C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.93  E-value=0.15  Score=37.61  Aligned_cols=76  Identities=28%  Similarity=0.394  Sum_probs=51.2

Q ss_pred             hhHHhhhhHHHHHHHHHHhhhccCCeeeeEEEe---cC---CeEEEEEEecccc---eEeccCcccHHHHH----HHHHH
Q psy8115          84 LQFVADGVFRAELDEFLTRELAEDGYSGVEIRF---TP---ARTEIIIMATRTQ---NVLGDKGRRIRELT----SVVQK  150 (218)
Q Consensus        84 kkfV~d~iir~~IRefl~K~l~~AGIs~IEI~R---t~---~~I~IiI~aarPg---iVIGrkG~~Ik~L~----~~LqK  150 (218)
                      .+|+-..++|.++-+++.+++...=  .|+|..   ..   ..|...|++.+.+   +|||++|+.|+++.    ..|++
T Consensus         8 ~~~~i~EiIRE~il~~l~~EiPY~~--~v~i~~~~~~~~~~~~I~a~I~V~~~sqk~IiIGk~G~~ik~I~~~ar~~le~   85 (113)
T d1egaa2           8 QRFMASEIIREKLMRFLGAELPYSV--TVEIERFVSNERGGYDINGLILVEREGQKKMVIGNKGAKIKTIGIEARKDMQE   85 (113)
T ss_dssp             HHHHHHHHHHHHHHHHHGGGCCTTE--EEEEEEEECCSSCSEEEEEEEEESSHHHHHHHHCGGGHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcccccCeEE--EEEEEEEeecccceEEEEEEEEECCcchhhhhhcccchHHHHHHHHHHHHHHH
Confidence            3455566778888888888876542  233332   22   2588889998886   69999999997765    55666


Q ss_pred             HhCCCCCcEEEEEE
Q psy8115         151 RFKFADGAIELYAE  164 (218)
Q Consensus       151 ~~~~~~kkI~I~I~  164 (218)
                      .|+   .+|.+.+.
T Consensus        86 ~~~---~kV~L~L~   96 (113)
T d1egaa2          86 MFE---APVHLELW   96 (113)
T ss_dssp             HTT---SCEEEEEE
T ss_pred             HhC---CCeEEEEE
Confidence            775   55655443

>d1wf3a2 d.52.3.1 (A:181-298) GTPase Era C-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: GTPase Era C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=92.28  E-value=0.14  Score=38.17  Aligned_cols=72  Identities=22%  Similarity=0.280  Sum_probs=45.1

Q ss_pred             hhHHHHHHHHHHhhhccCCeeeeE-EE-ecC--CeEEEEEEecccc---eEeccCcccHHHH----HHHHHHHhCCCCCc
Q psy8115          90 GVFRAELDEFLTRELAEDGYSGVE-IR-FTP--ARTEIIIMATRTQ---NVLGDKGRRIREL----TSVVQKRFKFADGA  158 (218)
Q Consensus        90 ~iir~~IRefl~K~l~~AGIs~IE-I~-Rt~--~~I~IiI~aarPg---iVIGrkG~~Ik~L----~~~LqK~~~~~~kk  158 (218)
                      .++|.+|-+++..++...=.-.|+ .+ +..  ..|...|++.+..   +|||++|+.|+++    +..|++.|+   .+
T Consensus        15 EiIREkil~~l~~EiPY~~~v~ie~~~e~~~~~l~I~~~I~V~~~sqK~IiIGk~G~~ik~Ig~~aR~~le~~~~---~k   91 (118)
T d1wf3a2          15 EILREEAMKRLWHEVPYAVATKVEEVAERENGVLYIKAILYVERPSQKAIVIGEGGRKIKEIGQATRKQLEALLG---KK   91 (118)
T ss_dssp             HHHHHHHHHTCCTTHHHHCEEEEEEEEEETTTEEEEEEEEEESSHHHHHHHHCGGGHHHHHHHHHHHHHHHHHHT---SE
T ss_pred             HHHHHHHHHhcccccCceEEEEEEEeeecCCceEEEEEEEEeCccchhhhhhccCchhHHHHHHHHHHHHHHHhC---CC
Confidence            344555555566665543222233 32 333  3677789998876   6999999999754    667777886   56


Q ss_pred             EEEEEE
Q psy8115         159 IELYAE  164 (218)
Q Consensus       159 I~I~I~  164 (218)
                      |.+.+.
T Consensus        92 V~L~L~   97 (118)
T d1wf3a2          92 VYLDLE   97 (118)
T ss_dssp             EEEEEE
T ss_pred             eEEEEE
Confidence            655443

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

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

Probab=90.37  E-value=0.037  Score=39.13  Aligned_cols=75  Identities=12%  Similarity=0.084  Sum_probs=46.2

Q ss_pred             EEEEEEecccceEeccCcccHHHHHHHHHHHhCCCCCcEEEEEEEecC-CCcCHHHHHHHHHHHHHcChhHHHHHH
Q psy8115         121 TEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVAT-RGLCAIAQAESLRYKLIGGLAVRRYNS  195 (218)
Q Consensus       121 I~IiI~aarPgiVIGrkG~~Ik~L~~~LqK~~~~~~kkI~I~I~EV~n-P~l~A~llAe~IA~QLEkRv~FRRAmK  195 (218)
                      +.|.|-..+-|.|||++|+.|++|++.=--........-.+.+..... -.-.|.-.|+.+..+++++.+--+|++
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~g~v~i~~~~~~~~~~a~~~a~~iI~aI~rGf~Pe~a~~   80 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFPPEKAFR   80 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTTTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCCHHHHGG
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCCCeEEEecCCccccHHHHHHHHHHHHHHhCCCChHHHHH
Confidence            567777788899999999999887764332222111111111222221 223456678999999998888777763

>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Thermotoga maritima [TaxId: 2336]

Probab=80.96  E-value=0.65  Score=31.43  Aligned_cols=47  Identities=19%  Similarity=0.274  Sum_probs=36.5

Q ss_pred             HHHHHhhhccCCeeeeEEE-ecCCeEEEEEEecccceEeccCcccHHH
Q psy8115          97 DEFLTRELAEDGYSGVEIR-FTPARTEIIIMATRTQNVLGDKGRRIRE  143 (218)
Q Consensus        97 Refl~K~l~~AGIs~IEI~-Rt~~~I~IiI~aarPgiVIGrkG~~Ik~  143 (218)
                      .+|+.+.|.-|.+.+|+|. .......|++--..-+..||++|++++-
T Consensus         4 ~~fI~nAL~PA~v~~V~i~de~~~~~~v~V~~~qls~AIGk~G~NvrL   51 (68)
T d1hh2p3           4 KQLIANALAPATVIEVEILDKENKAARVLVPPTQLSLAIGKGGQNARL   51 (68)
T ss_dssp             HHHHHHHTCSSCCSEEEEEETTTTEEEEEECTTSHHHHHCGGGHHHHH
T ss_pred             HHHHHHhCCCCeeeEEEEEcCCCCEEEEEECcccccccccCCcchHHH
Confidence            5789999999999999983 3345666666666667899999999943