Psyllid ID: psy7992

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-
Protein Sequence
MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHRNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI
Secondary Structure (PSIPRED)
cccccccccccccccccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHcccccccccHHHHHHccHHHHHHHHHHHHHHHHcccccHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cccccccccccEEccccccccHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHccccccccccHHHHHcccHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHcccc
Coil and Loop (DISEMBL)
mvnnrvpsvhsktyvtprrpyekARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHRNALLRRLVRIGvldeskmklDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI
Flexible Loop (DISEMBL)
mvnnrvpsvhsktyvtprrpyekarLDQELKIigeyglrnkrevWRVKYALAKIRKAARelltldekehrnallrrlvrigvldeskmklDYVWGLKIEDFLERRLQTQVFKlglaksihharVLIRQRHI
Low Complexity Region (SEG)
MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHRNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI
Disordered region (IsUnstruct)
************************RLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHRNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLI*****
Disordered Region (DISOPRED)
************TYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRK***************ALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI
Disordered Region (DISEMBL)
*****************RRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHRNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI
Disordered Region (DISPRO)
****RVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHRNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQR**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHRNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI
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	131	2.2.26 [Sep-21-2011]
P55935	195	40S ribosomal protein S9	yes	N/A	1.0	0.671	0.904	1e-63
P29314	194	40S ribosomal protein S9	yes	N/A	0.938	0.634	0.867	5e-56
A9L913	194	40S ribosomal protein S9	N/A	N/A	0.938	0.634	0.867	5e-56
Q6ZWN5	194	40S ribosomal protein S9	yes	N/A	0.938	0.634	0.867	5e-56
P46781	194	40S ribosomal protein S9	yes	N/A	0.938	0.634	0.867	5e-56
A6QLG5	194	40S ribosomal protein S9	yes	N/A	0.938	0.634	0.867	5e-56
Q29197	130	40S ribosomal protein S9	yes	N/A	0.916	0.923	0.848	8e-53
Q20228	189	40S ribosomal protein S9	yes	N/A	0.969	0.671	0.75	5e-51
P52810	190	40S ribosomal protein S9	yes	N/A	0.961	0.663	0.748	5e-49
O59675	192	40S ribosomal protein S9-	yes	N/A	0.961	0.656	0.732	9e-49

>sp|P55935|RS9_DROME 40S ribosomal protein S9 OS=Drosophila melanogaster GN=RpS9 PE=2 SV=2

 Score =  241 bits (614), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 123/136 (90%), Positives = 127/136 (93%), Gaps = 5/136 (3%)

Query: 1   MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60
           MVN R+PSV SKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE
Sbjct: 1   MVNGRIPSVFSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60

Query: 61  LLTLDEKEHR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGL 115
           LLTLDEK+ +     NALLRRLVRIGVLDES+MKLDYV GLKIEDFLERRLQTQVFKLGL
Sbjct: 61  LLTLDEKDEKRLFQGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGL 120

Query: 116 AKSIHHARVLIRQRHI 131
           AKSIHHARVLIRQRHI
Sbjct: 121 AKSIHHARVLIRQRHI 136

Drosophila melanogaster (taxid: 7227)

>sp|P29314|RS9_RAT 40S ribosomal protein S9 OS=Rattus norvegicus GN=Rps9 PE=1 SV=4

 Score =  215 bits (548), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 111/128 (86%), Positives = 117/128 (91%), Gaps = 5/128 (3%)

Query: 9   VHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKE 68
           V  KTYVTPRRP+EK+RLDQELK+IGEYGLRNKREVWRVK+ LAKIRKAARELLTLDEK+
Sbjct: 8   VCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKD 67

Query: 69  HR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHAR 123
            R     NALLRRLVRIGVLDE KMKLDY+ GLKIEDFLERRLQTQVFKLGLAKSIHHAR
Sbjct: 68  PRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHAR 127

Query: 124 VLIRQRHI 131
           VLIRQRHI
Sbjct: 128 VLIRQRHI 135

Rattus norvegicus (taxid: 10116)

>sp|A9L913|RS9_PAPAN 40S ribosomal protein S9 OS=Papio anubis GN=RPS9 PE=3 SV=1

 Score =  215 bits (548), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 111/128 (86%), Positives = 117/128 (91%), Gaps = 5/128 (3%)

Query: 9   VHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKE 68
           V  KTYVTPRRP+EK+RLDQELK+IGEYGLRNKREVWRVK+ LAKIRKAARELLTLDEK+
Sbjct: 8   VCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKD 67

Query: 69  HR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHAR 123
            R     NALLRRLVRIGVLDE KMKLDY+ GLKIEDFLERRLQTQVFKLGLAKSIHHAR
Sbjct: 68  PRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHAR 127

Query: 124 VLIRQRHI 131
           VLIRQRHI
Sbjct: 128 VLIRQRHI 135

Papio anubis (taxid: 9555)

>sp|Q6ZWN5|RS9_MOUSE 40S ribosomal protein S9 OS=Mus musculus GN=Rps9 PE=2 SV=3

 Score =  215 bits (548), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 111/128 (86%), Positives = 117/128 (91%), Gaps = 5/128 (3%)

Query: 9   VHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKE 68
           V  KTYVTPRRP+EK+RLDQELK+IGEYGLRNKREVWRVK+ LAKIRKAARELLTLDEK+
Sbjct: 8   VCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKD 67

Query: 69  HR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHAR 123
            R     NALLRRLVRIGVLDE KMKLDY+ GLKIEDFLERRLQTQVFKLGLAKSIHHAR
Sbjct: 68  PRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHAR 127

Query: 124 VLIRQRHI 131
           VLIRQRHI
Sbjct: 128 VLIRQRHI 135

Mus musculus (taxid: 10090)

>sp|P46781|RS9_HUMAN 40S ribosomal protein S9 OS=Homo sapiens GN=RPS9 PE=1 SV=3

 Score =  215 bits (548), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 111/128 (86%), Positives = 117/128 (91%), Gaps = 5/128 (3%)

Query: 9   VHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKE 68
           V  KTYVTPRRP+EK+RLDQELK+IGEYGLRNKREVWRVK+ LAKIRKAARELLTLDEK+
Sbjct: 8   VCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKD 67

Query: 69  HR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHAR 123
            R     NALLRRLVRIGVLDE KMKLDY+ GLKIEDFLERRLQTQVFKLGLAKSIHHAR
Sbjct: 68  PRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHAR 127

Query: 124 VLIRQRHI 131
           VLIRQRHI
Sbjct: 128 VLIRQRHI 135

Homo sapiens (taxid: 9606)

>sp|A6QLG5|RS9_BOVIN 40S ribosomal protein S9 OS=Bos taurus GN=RPS9 PE=2 SV=1

 Score =  215 bits (548), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 111/128 (86%), Positives = 117/128 (91%), Gaps = 5/128 (3%)

Query: 9   VHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKE 68
           V  KTYVTPRRP+EK+RLDQELK+IGEYGLRNKREVWRVK+ LAKIRKAARELLTLDEK+
Sbjct: 8   VCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKD 67

Query: 69  HR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHAR 123
            R     NALLRRLVRIGVLDE KMKLDY+ GLKIEDFLERRLQTQVFKLGLAKSIHHAR
Sbjct: 68  PRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHAR 127

Query: 124 VLIRQRHI 131
           VLIRQRHI
Sbjct: 128 VLIRQRHI 135

Bos taurus (taxid: 9913)

>sp|Q29197|RS9_PIG 40S ribosomal protein S9 (Fragment) OS=Sus scrofa GN=RPS9 PE=2 SV=1

 Score =  205 bits (521), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 106/125 (84%), Positives = 112/125 (89%), Gaps = 5/125 (4%)

Query: 9   VHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKE 68
           V  KTYVTPRRP+EK+RLDQELK+IGEYGLRNKREVWRVK+ LAKIRKAARELLTLDEK+
Sbjct: 6   VCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKD 65

Query: 69  HR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHAR 123
            R     NALLRRLVRIGVLDE KMKLDY+ GLKIEDFLERRLQTQVFKLGLA SIHH R
Sbjct: 66  PRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAXSIHHXR 125

Query: 124 VLIRQ 128
           VLIRQ
Sbjct: 126 VLIRQ 130

Sus scrofa (taxid: 9823)

>sp|Q20228|RS9_CAEEL 40S ribosomal protein S9 OS=Caenorhabditis elegans GN=rps-9 PE=3 SV=1

 Score =  199 bits (505), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 99/132 (75%), Positives = 116/132 (87%), Gaps = 5/132 (3%)

Query: 5   RVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTL 64
           R+ +V SK   +PRRP+EK RLDQELK+IG +GL+NKREVWRVKY LAK+RKAARELLTL
Sbjct: 3   RLKTVQSKVTKSPRRPFEKERLDQELKLIGTFGLKNKREVWRVKYTLAKVRKAARELLTL 62

Query: 65  DEKEHR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSI 119
           ++K+ +     NALLRRLV+IGVLDE+KMKLDYV GLK+EDFLERRLQTQVFKLGLAKSI
Sbjct: 63  EDKDPKRLFEGNALLRRLVKIGVLDETKMKLDYVLGLKVEDFLERRLQTQVFKLGLAKSI 122

Query: 120 HHARVLIRQRHI 131
           HHAR+LI+Q HI
Sbjct: 123 HHARILIKQHHI 134

Caenorhabditis elegans (taxid: 6239)

>sp|P52810|RS9_PODAS 40S ribosomal protein S9 OS=Podospora anserina GN=RPS9 PE=3 SV=1

 Score =  192 bits (488), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 98/131 (74%), Positives = 110/131 (83%), Gaps = 5/131 (3%)

Query: 6   VPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLD 65
            P  +SKT   PRRP+E ARLD ELK++GEYGLRNKREVWRV   L+KIR+AARELLTLD
Sbjct: 2   APRSYSKTAKVPRRPFEAARLDSELKLVGEYGLRNKREVWRVLLTLSKIRRAARELLTLD 61

Query: 66  EKEHR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIH 120
           EK+ +     NAL+RRLVR+GVLDES+MKLDYV  LK EDFLERRLQT V+KLGLAKSIH
Sbjct: 62  EKDPKRLFEGNALIRRLVRVGVLDESRMKLDYVLALKAEDFLERRLQTLVYKLGLAKSIH 121

Query: 121 HARVLIRQRHI 131
           HARVLIRQRHI
Sbjct: 122 HARVLIRQRHI 132

Podospora anserina (taxid: 5145)

>sp|O59675|RS9B_SCHPO 40S ribosomal protein S9-B OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rps9b PE=1 SV=3

 Score =  191 bits (486), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 96/131 (73%), Positives = 109/131 (83%), Gaps = 5/131 (3%)

Query: 6   VPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLD 65
            P   SKTY  PRRP+E ARLD ELK+ GEYGLRNK E+WRV   L+KIR+AARELLTLD
Sbjct: 4   APRKQSKTYKVPRRPFESARLDAELKLAGEYGLRNKHEIWRVALTLSKIRRAARELLTLD 63

Query: 66  EKEHR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIH 120
           EK+ +     NA++RRLVR+G+LDES+MKLDYV  L+IEDFLERRLQTQVFKLGLAKSIH
Sbjct: 64  EKDPKRLFEGNAIIRRLVRLGILDESRMKLDYVLALRIEDFLERRLQTQVFKLGLAKSIH 123

Query: 121 HARVLIRQRHI 131
           HARVLI QRHI
Sbjct: 124 HARVLIFQRHI 134

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

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	131
110671456	195	putative ribosomal protein S9 [Diaphorin	1.0	0.671	0.941	3e-64
38047837	191	similar to Drosophila melanogaster RpS9,	1.0	0.685	0.904	7e-62
38048283	163	similar to Drosophila melanogaster RpS9,	1.0	0.803	0.904	8e-62
194747739	195	GF24655 [Drosophila ananassae] gi|195428	1.0	0.671	0.904	8e-62
24661707	195	ribosomal protein S9, isoform A [Drosoph	1.0	0.671	0.904	1e-61
195377017	195	GJ13353 [Drosophila virilis] gi|19415444	1.0	0.671	0.904	1e-61
195015334	195	GH15146 [Drosophila grimshawi] gi|193897	1.0	0.671	0.904	1e-61
125977176	195	GA28351 [Drosophila pseudoobscura pseudo	1.0	0.671	0.904	1e-61
90819966	193	putative S9e ribosomal protein [Graphoce	1.0	0.678	0.897	1e-61
24661715	137	ribosomal protein S9, isoform B [Drosoph	1.0	0.956	0.904	1e-61

>gi|110671456|gb|ABG81979.1| putative ribosomal protein S9 [Diaphorina citri]

 Score =  249 bits (636), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 128/136 (94%), Positives = 129/136 (94%), Gaps = 5/136 (3%)

Query: 1   MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60
           MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE
Sbjct: 1   MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60

Query: 61  LLTLDEKEHR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGL 115
           LLTLDEKE R     NALLRRLVRIGVLDES+MKLDYV GLKIEDFLERRLQTQVFKLGL
Sbjct: 61  LLTLDEKEQRRLFEGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGL 120

Query: 116 AKSIHHARVLIRQRHI 131
           AKSIHHARVLIRQRHI
Sbjct: 121 AKSIHHARVLIRQRHI 136

Source: Diaphorina citri

Species: Diaphorina citri

Genus: Diaphorina

Family: Psyllidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|38047837|gb|AAR09821.1| similar to Drosophila melanogaster RpS9, partial [Drosophila yakuba]

 Score =  241 bits (615), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 123/136 (90%), Positives = 127/136 (93%), Gaps = 5/136 (3%)

Query: 1   MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60
           MVN R+PSV SKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE
Sbjct: 1   MVNGRIPSVFSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60

Query: 61  LLTLDEKEHR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGL 115
           LLTLDEK+ +     NALLRRLVRIGVLDES+MKLDYV GLKIEDFLERRLQTQVFKLGL
Sbjct: 61  LLTLDEKDEKRLFQGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGL 120

Query: 116 AKSIHHARVLIRQRHI 131
           AKSIHHARVLIRQRHI
Sbjct: 121 AKSIHHARVLIRQRHI 136

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|38048283|gb|AAR10044.1| similar to Drosophila melanogaster RpS9, partial [Drosophila yakuba]

 Score =  241 bits (614), Expect = 8e-62,   Method: Compositional matrix adjust.
 Identities = 123/136 (90%), Positives = 127/136 (93%), Gaps = 5/136 (3%)

Query: 1   MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60
           MVN R+PSV SKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE
Sbjct: 1   MVNGRIPSVFSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60

Query: 61  LLTLDEKEHR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGL 115
           LLTLDEK+ +     NALLRRLVRIGVLDES+MKLDYV GLKIEDFLERRLQTQVFKLGL
Sbjct: 61  LLTLDEKDEKRLFQGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGL 120

Query: 116 AKSIHHARVLIRQRHI 131
           AKSIHHARVLIRQRHI
Sbjct: 121 AKSIHHARVLIRQRHI 136

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194747739|ref|XP_001956309.1| GF24655 [Drosophila ananassae] gi|195428917|ref|XP_002062512.1| GK17575 [Drosophila willistoni] gi|190623591|gb|EDV39115.1| GF24655 [Drosophila ananassae] gi|194158597|gb|EDW73498.1| GK17575 [Drosophila willistoni]

 Score =  241 bits (614), Expect = 8e-62,   Method: Compositional matrix adjust.
 Identities = 123/136 (90%), Positives = 127/136 (93%), Gaps = 5/136 (3%)

Query: 1   MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60
           MVN R+PSV SKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE
Sbjct: 1   MVNGRIPSVFSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60

Query: 61  LLTLDEKEHR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGL 115
           LLTLDEK+ +     NALLRRLVRIGVLDES+MKLDYV GLKIEDFLERRLQTQVFKLGL
Sbjct: 61  LLTLDEKDEKRLFQGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGL 120

Query: 116 AKSIHHARVLIRQRHI 131
           AKSIHHARVLIRQRHI
Sbjct: 121 AKSIHHARVLIRQRHI 136

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|24661707|ref|NP_524004.2| ribosomal protein S9, isoform A [Drosophila melanogaster] gi|24661711|ref|NP_729506.1| ribosomal protein S9, isoform D [Drosophila melanogaster] gi|194867971|ref|XP_001972186.1| GG14025 [Drosophila erecta] gi|195326350|ref|XP_002029892.1| GM24860 [Drosophila sechellia] gi|195490797|ref|XP_002093291.1| RpS9 [Drosophila yakuba] gi|195589072|ref|XP_002084280.1| GD12912 [Drosophila simulans] gi|60416385|sp|P55935.2|RS9_DROME RecName: Full=40S ribosomal protein S9 gi|7294919|gb|AAF50249.1| ribosomal protein S9, isoform A [Drosophila melanogaster] gi|23093773|gb|AAN11946.1| ribosomal protein S9, isoform D [Drosophila melanogaster] gi|190653969|gb|EDV51212.1| GG14025 [Drosophila erecta] gi|194118835|gb|EDW40878.1| GM24860 [Drosophila sechellia] gi|194179392|gb|EDW93003.1| RpS9 [Drosophila yakuba] gi|194196289|gb|EDX09865.1| GD12912 [Drosophila simulans] gi|254750749|gb|ACT80127.1| LD13662p [Drosophila melanogaster]

 Score =  241 bits (614), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 123/136 (90%), Positives = 127/136 (93%), Gaps = 5/136 (3%)

Query: 1   MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60
           MVN R+PSV SKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE
Sbjct: 1   MVNGRIPSVFSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60

Query: 61  LLTLDEKEHR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGL 115
           LLTLDEK+ +     NALLRRLVRIGVLDES+MKLDYV GLKIEDFLERRLQTQVFKLGL
Sbjct: 61  LLTLDEKDEKRLFQGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGL 120

Query: 116 AKSIHHARVLIRQRHI 131
           AKSIHHARVLIRQRHI
Sbjct: 121 AKSIHHARVLIRQRHI 136

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195377017|ref|XP_002047289.1| GJ13353 [Drosophila virilis] gi|194154447|gb|EDW69631.1| GJ13353 [Drosophila virilis]

 Score =  241 bits (614), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 123/136 (90%), Positives = 127/136 (93%), Gaps = 5/136 (3%)

Query: 1   MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60
           MVN R+PSV SKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE
Sbjct: 1   MVNGRIPSVFSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60

Query: 61  LLTLDEKEHR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGL 115
           LLTLDEK+ +     NALLRRLVRIGVLDES+MKLDYV GLKIEDFLERRLQTQVFKLGL
Sbjct: 61  LLTLDEKDEKRLFQGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGL 120

Query: 116 AKSIHHARVLIRQRHI 131
           AKSIHHARVLIRQRHI
Sbjct: 121 AKSIHHARVLIRQRHI 136

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195015334|ref|XP_001984182.1| GH15146 [Drosophila grimshawi] gi|193897664|gb|EDV96530.1| GH15146 [Drosophila grimshawi]

 Score =  240 bits (613), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 123/136 (90%), Positives = 127/136 (93%), Gaps = 5/136 (3%)

Query: 1   MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60
           MVN R+PSV SKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE
Sbjct: 1   MVNGRIPSVFSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60

Query: 61  LLTLDEKEHR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGL 115
           LLTLDEK+ +     NALLRRLVRIGVLDES+MKLDYV GLKIEDFLERRLQTQVFKLGL
Sbjct: 61  LLTLDEKDEKRLFQGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGL 120

Query: 116 AKSIHHARVLIRQRHI 131
           AKSIHHARVLIRQRHI
Sbjct: 121 AKSIHHARVLIRQRHI 136

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|125977176|ref|XP_001352621.1| GA28351 [Drosophila pseudoobscura pseudoobscura] gi|195168054|ref|XP_002024847.1| GL17960 [Drosophila persimilis] gi|195178296|ref|XP_002029028.1| GL20135 [Drosophila persimilis] gi|195191346|ref|XP_002029552.1| GL21280 [Drosophila persimilis] gi|54641369|gb|EAL30119.1| GA28351 [Drosophila pseudoobscura pseudoobscura] gi|194103695|gb|EDW25738.1| GL21280 [Drosophila persimilis] gi|194108277|gb|EDW30320.1| GL17960 [Drosophila persimilis] gi|194117383|gb|EDW39426.1| GL20135 [Drosophila persimilis]

 Score =  240 bits (613), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 123/136 (90%), Positives = 127/136 (93%), Gaps = 5/136 (3%)

Query: 1   MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60
           MVN R+PSV SKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE
Sbjct: 1   MVNGRIPSVFSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60

Query: 61  LLTLDEKEHR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGL 115
           LLTLDEK+ +     NALLRRLVRIGVLDES+MKLDYV GLKIEDFLERRLQTQVFKLGL
Sbjct: 61  LLTLDEKDEKRLFQGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGL 120

Query: 116 AKSIHHARVLIRQRHI 131
           AKSIHHARVLIRQRHI
Sbjct: 121 AKSIHHARVLIRQRHI 136

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|90819966|gb|ABD98740.1| putative S9e ribosomal protein [Graphocephala atropunctata]

 Score =  240 bits (612), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 122/136 (89%), Positives = 127/136 (93%), Gaps = 5/136 (3%)

Query: 1   MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60
           MVN R+PSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKY LAKIRKAARE
Sbjct: 1   MVNGRIPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYTLAKIRKAARE 60

Query: 61  LLTLDEKEHR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGL 115
           LLTL+EK+ R     NALLRRLVRIGVLDE++MKLDYV GLKIEDFLERRLQTQVFKLGL
Sbjct: 61  LLTLEEKDQRRLFNGNALLRRLVRIGVLDENRMKLDYVLGLKIEDFLERRLQTQVFKLGL 120

Query: 116 AKSIHHARVLIRQRHI 131
           AKSIHHARVLIRQRHI
Sbjct: 121 AKSIHHARVLIRQRHI 136

Source: Graphocephala atropunctata

Species: Graphocephala atropunctata

Genus: Graphocephala

Family: Cicadellidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|24661715|ref|NP_729507.1| ribosomal protein S9, isoform B [Drosophila melanogaster] gi|7294920|gb|AAF50250.1| ribosomal protein S9, isoform B [Drosophila melanogaster] gi|16769450|gb|AAL28944.1| LD32106p [Drosophila melanogaster] gi|220954208|gb|ACL89647.1| RpS9-PB [synthetic construct]

 Score =  240 bits (612), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 123/136 (90%), Positives = 127/136 (93%), Gaps = 5/136 (3%)

Query: 1   MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60
           MVN R+PSV SKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE
Sbjct: 1   MVNGRIPSVFSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60

Query: 61  LLTLDEKEHR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGL 115
           LLTLDEK+ +     NALLRRLVRIGVLDES+MKLDYV GLKIEDFLERRLQTQVFKLGL
Sbjct: 61  LLTLDEKDEKRLFQGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGL 120

Query: 116 AKSIHHARVLIRQRHI 131
           AKSIHHARVLIRQRHI
Sbjct: 121 AKSIHHARVLIRQRHI 136

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	131
FB|FBgn0010408	195	RpS9 "Ribosomal protein S9" [D	1.0	0.671	0.904	1.2e-58
UNIPROTKB|A6QLG5	194	RPS9 "40S ribosomal protein S9	0.916	0.618	0.88	2.1e-52
UNIPROTKB|E2R8R8	194	RPS9 "Uncharacterized protein"	0.916	0.618	0.88	2.1e-52
UNIPROTKB|B5MCT8	139	RPS9 "40S ribosomal protein S9	0.916	0.863	0.88	2.1e-52
UNIPROTKB|C9JM19	156	RPS9 "Ribosomal protein S9, is	0.916	0.769	0.88	2.1e-52
UNIPROTKB|P46781	194	RPS9 "40S ribosomal protein S9	0.916	0.618	0.88	2.1e-52
UNIPROTKB|A9L913	194	RPS9 "40S ribosomal protein S9	0.916	0.618	0.88	2.1e-52
MGI|MGI:1924096	194	Rps9 "ribosomal protein S9" [M	0.916	0.618	0.88	2.1e-52
RGD|2320851	139	LOC100364509 "ribosomal protei	0.916	0.863	0.88	2.1e-52
RGD|619889	194	Rps9 "ribosomal protein S9" [R	0.916	0.618	0.88	2.1e-52

FB|FBgn0010408 RpS9 "Ribosomal protein S9" [Drosophila melanogaster (taxid:7227)]

 Score = 602 (217.0 bits), Expect = 1.2e-58, P = 1.2e-58
 Identities = 123/136 (90%), Positives = 127/136 (93%)

Query:     1 MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60
             MVN R+PSV SKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE
Sbjct:     1 MVNGRIPSVFSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60

Query:    61 LLTLDEKEHR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGL 115
             LLTLDEK+ +     NALLRRLVRIGVLDES+MKLDYV GLKIEDFLERRLQTQVFKLGL
Sbjct:    61 LLTLDEKDEKRLFQGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGL 120

Query:   116 AKSIHHARVLIRQRHI 131
             AKSIHHARVLIRQRHI
Sbjct:   121 AKSIHHARVLIRQRHI 136

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

GO:0006412 "translation" evidence=ISS;NAS

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

GO:0005840 "ribosome" evidence=IDA;NAS

GO:0019843 "rRNA binding" evidence=IEA

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0000022 "mitotic spindle elongation" evidence=IMP

UNIPROTKB|A6QLG5 RPS9 "40S ribosomal protein S9" [Bos taurus (taxid:9913)]

 Score = 543 (196.2 bits), Expect = 2.1e-52, P = 2.1e-52
 Identities = 110/125 (88%), Positives = 116/125 (92%)

Query:    12 KTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR- 70
             KTYVTPRRP+EK+RLDQELK+IGEYGLRNKREVWRVK+ LAKIRKAARELLTLDEK+ R 
Sbjct:    11 KTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRR 70

Query:    71 ----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLI 126
                 NALLRRLVRIGVLDE KMKLDY+ GLKIEDFLERRLQTQVFKLGLAKSIHHARVLI
Sbjct:    71 LFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLI 130

Query:   127 RQRHI 131
             RQRHI
Sbjct:   131 RQRHI 135

GO:0030529 "ribonucleoprotein complex" evidence=ISS

GO:0045182 "translation regulator activity" evidence=IEA

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

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

GO:0005730 "nucleolus" evidence=IEA

GO:0019843 "rRNA binding" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|E2R8R8 RPS9 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 543 (196.2 bits), Expect = 2.1e-52, P = 2.1e-52
 Identities = 110/125 (88%), Positives = 116/125 (92%)

Query:    12 KTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR- 70
             KTYVTPRRP+EK+RLDQELK+IGEYGLRNKREVWRVK+ LAKIRKAARELLTLDEK+ R 
Sbjct:    11 KTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRR 70

Query:    71 ----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLI 126
                 NALLRRLVRIGVLDE KMKLDY+ GLKIEDFLERRLQTQVFKLGLAKSIHHARVLI
Sbjct:    71 LFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLI 130

Query:   127 RQRHI 131
             RQRHI
Sbjct:   131 RQRHI 135

GO:0045182 "translation regulator activity" evidence=IEA

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

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

GO:0005730 "nucleolus" evidence=IEA

GO:0019843 "rRNA binding" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|B5MCT8 RPS9 "40S ribosomal protein S9" [Homo sapiens (taxid:9606)]

 Score = 543 (196.2 bits), Expect = 2.1e-52, P = 2.1e-52
 Identities = 110/125 (88%), Positives = 116/125 (92%)

Query:    12 KTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR- 70
             KTYVTPRRP+EK+RLDQELK+IGEYGLRNKREVWRVK+ LAKIRKAARELLTLDEK+ R 
Sbjct:    11 KTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRR 70

Query:    71 ----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLI 126
                 NALLRRLVRIGVLDE KMKLDY+ GLKIEDFLERRLQTQVFKLGLAKSIHHARVLI
Sbjct:    71 LFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLI 130

Query:   127 RQRHI 131
             RQRHI
Sbjct:   131 RQRHI 135

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

GO:0006412 "translation" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0019843 "rRNA binding" evidence=IEA

UNIPROTKB|C9JM19 RPS9 "Ribosomal protein S9, isoform CRA_e" [Homo sapiens (taxid:9606)]

 Score = 543 (196.2 bits), Expect = 2.1e-52, P = 2.1e-52
 Identities = 110/125 (88%), Positives = 116/125 (92%)

Query:    12 KTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR- 70
             KTYVTPRRP+EK+RLDQELK+IGEYGLRNKREVWRVK+ LAKIRKAARELLTLDEK+ R 
Sbjct:    11 KTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRR 70

Query:    71 ----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLI 126
                 NALLRRLVRIGVLDE KMKLDY+ GLKIEDFLERRLQTQVFKLGLAKSIHHARVLI
Sbjct:    71 LFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLI 130

Query:   127 RQRHI 131
             RQRHI
Sbjct:   131 RQRHI 135

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

GO:0006412 "translation" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0019843 "rRNA binding" evidence=IEA

UNIPROTKB|P46781 RPS9 "40S ribosomal protein S9" [Homo sapiens (taxid:9606)]

 Score = 543 (196.2 bits), Expect = 2.1e-52, P = 2.1e-52
 Identities = 110/125 (88%), Positives = 116/125 (92%)

Query:    12 KTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR- 70
             KTYVTPRRP+EK+RLDQELK+IGEYGLRNKREVWRVK+ LAKIRKAARELLTLDEK+ R 
Sbjct:    11 KTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRR 70

Query:    71 ----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLI 126
                 NALLRRLVRIGVLDE KMKLDY+ GLKIEDFLERRLQTQVFKLGLAKSIHHARVLI
Sbjct:    71 LFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLI 130

Query:   127 RQRHI 131
             RQRHI
Sbjct:   131 RQRHI 135

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

GO:0019843 "rRNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

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

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

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

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0045182 "translation regulator activity" evidence=IMP

GO:0005840 "ribosome" evidence=NAS

GO:0030529 "ribonucleoprotein complex" evidence=IDA

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

GO:0005829 "cytosol" evidence=TAS

GO:0006413 "translational initiation" evidence=TAS

GO:0006414 "translational elongation" evidence=TAS

GO:0006415 "translational termination" evidence=TAS

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

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0019058 "viral infectious cycle" evidence=TAS

GO:0019083 "viral transcription" evidence=TAS

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

GO:0006417 "regulation of translation" evidence=IMP

UNIPROTKB|A9L913 RPS9 "40S ribosomal protein S9" [Papio anubis (taxid:9555)]

 Score = 543 (196.2 bits), Expect = 2.1e-52, P = 2.1e-52
 Identities = 110/125 (88%), Positives = 116/125 (92%)

Query:    12 KTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR- 70
             KTYVTPRRP+EK+RLDQELK+IGEYGLRNKREVWRVK+ LAKIRKAARELLTLDEK+ R 
Sbjct:    11 KTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRR 70

Query:    71 ----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLI 126
                 NALLRRLVRIGVLDE KMKLDY+ GLKIEDFLERRLQTQVFKLGLAKSIHHARVLI
Sbjct:    71 LFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLI 130

Query:   127 RQRHI 131
             RQRHI
Sbjct:   131 RQRHI 135

GO:0030529 "ribonucleoprotein complex" evidence=ISS

MGI|MGI:1924096 Rps9 "ribosomal protein S9" [Mus musculus (taxid:10090)]

 Score = 543 (196.2 bits), Expect = 2.1e-52, P = 2.1e-52
 Identities = 110/125 (88%), Positives = 116/125 (92%)

Query:    12 KTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR- 70
             KTYVTPRRP+EK+RLDQELK+IGEYGLRNKREVWRVK+ LAKIRKAARELLTLDEK+ R 
Sbjct:    11 KTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRR 70

Query:    71 ----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLI 126
                 NALLRRLVRIGVLDE KMKLDY+ GLKIEDFLERRLQTQVFKLGLAKSIHHARVLI
Sbjct:    71 LFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLI 130

Query:   127 RQRHI 131
             RQRHI
Sbjct:   131 RQRHI 135

GO:0003723 "RNA binding" evidence=IEA

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

GO:0005622 "intracellular" evidence=IEA

GO:0005730 "nucleolus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=ISO

GO:0006417 "regulation of translation" evidence=ISO

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

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0019843 "rRNA binding" evidence=IEA

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

GO:0030529 "ribonucleoprotein complex" evidence=ISO

GO:0045182 "translation regulator activity" evidence=ISO

RGD|2320851 LOC100364509 "ribosomal protein S9-like" [Rattus norvegicus (taxid:10116)]

 Score = 543 (196.2 bits), Expect = 2.1e-52, P = 2.1e-52
 Identities = 110/125 (88%), Positives = 116/125 (92%)

Query:    12 KTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR- 70
             KTYVTPRRP+EK+RLDQELK+IGEYGLRNKREVWRVK+ LAKIRKAARELLTLDEK+ R 
Sbjct:    11 KTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRR 70

Query:    71 ----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLI 126
                 NALLRRLVRIGVLDE KMKLDY+ GLKIEDFLERRLQTQVFKLGLAKSIHHARVLI
Sbjct:    71 LFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLI 130

Query:   127 RQRHI 131
             RQRHI
Sbjct:   131 RQRHI 135

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

GO:0006412 "translation" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0019843 "rRNA binding" evidence=IEA

RGD|619889 Rps9 "ribosomal protein S9" [Rattus norvegicus (taxid:10116)]

 Score = 543 (196.2 bits), Expect = 2.1e-52, P = 2.1e-52
 Identities = 110/125 (88%), Positives = 116/125 (92%)

Query:    12 KTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR- 70
             KTYVTPRRP+EK+RLDQELK+IGEYGLRNKREVWRVK+ LAKIRKAARELLTLDEK+ R 
Sbjct:    11 KTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRR 70

Query:    71 ----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLI 126
                 NALLRRLVRIGVLDE KMKLDY+ GLKIEDFLERRLQTQVFKLGLAKSIHHARVLI
Sbjct:    71 LFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLI 130

Query:   127 RQRHI 131
             RQRHI
Sbjct:   131 RQRHI 135

GO:0003674 "molecular_function" evidence=ND

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

GO:0005730 "nucleolus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0006412 "translation" evidence=IEA;ISO

GO:0006417 "regulation of translation" evidence=ISO

GO:0008150 "biological_process" evidence=ND

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

GO:0019843 "rRNA binding" evidence=IEA

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

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

GO:0045182 "translation regulator activity" 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)
B8GEG7	RS4_METPE	No assigned EC number	0.4586	0.9465	0.6850	yes	N/A
Q97B95	RS4_THEVO	No assigned EC number	0.4580	0.9465	0.62	yes	N/A
A2BK77	RS4_HYPBU	No assigned EC number	0.4806	0.9389	0.6988	yes	N/A
P55935	RS9_DROME	No assigned EC number	0.9044	1.0	0.6717	yes	N/A
P05755	RS9B_YEAST	No assigned EC number	0.6818	0.9694	0.6512	yes	N/A
Q09757	RS9A_SCHPO	No assigned EC number	0.7251	0.9618	0.6596	yes	N/A
O26142	RS4_METTH	No assigned EC number	0.4108	0.9389	0.7192	yes	N/A
P14132	RS9_DICDI	No assigned EC number	0.6793	0.9618	0.6810	yes	N/A
Q29197	RS9_PIG	No assigned EC number	0.848	0.9160	0.9230	yes	N/A
Q8SRW6	RS9_ENCCU	No assigned EC number	0.4511	0.9236	0.6576	yes	N/A
P29314	RS9_RAT	No assigned EC number	0.8671	0.9389	0.6340	yes	N/A
Q20228	RS9_CAEEL	No assigned EC number	0.75	0.9694	0.6719	yes	N/A
Q9FLF0	RS92_ARATH	No assigned EC number	0.6764	1.0	0.6649	yes	N/A
Q9HQJ6	RS4_HALSA	No assigned EC number	0.3888	0.9541	0.7352	yes	N/A
A6QLG5	RS9_BOVIN	No assigned EC number	0.8671	0.9389	0.6340	yes	N/A
P46781	RS9_HUMAN	No assigned EC number	0.8671	0.9389	0.6340	yes	N/A
A9L913	RS9_PAPAN	No assigned EC number	0.8671	0.9389	0.6340	N/A	N/A
A2SSV9	RS4_METLZ	No assigned EC number	0.4135	0.9465	0.6850	yes	N/A
Q12ZR5	RS4_METBU	No assigned EC number	0.3984	0.9465	0.6739	yes	N/A
A3DMQ4	RS4_STAMF	No assigned EC number	0.4921	0.9465	0.7380	yes	N/A
C3NMQ2	RS4_SULIN	No assigned EC number	0.3906	0.9541	0.6906	yes	N/A
A3CWH7	RS4_METMJ	No assigned EC number	0.4210	0.9465	0.6813	yes	N/A
O28000	RS4_ARCFU	No assigned EC number	0.4477	0.9465	0.7209	yes	N/A
Q96YV8	RS4_SULTO	No assigned EC number	0.4062	0.9541	0.7062	yes	N/A
Q00862	RS4_HALMA	No assigned EC number	0.4193	0.9236	0.7076	yes	N/A
Q2FT97	RS4_METHJ	No assigned EC number	0.4511	0.9465	0.6850	yes	N/A
C3MZ03	RS4_SULIM	No assigned EC number	0.3906	0.9541	0.6906	yes	N/A
O13516	RS9A_YEAST	No assigned EC number	0.6742	0.9694	0.6446	yes	N/A
P39467	RS4_SULAC	No assigned EC number	0.4186	0.9465	0.7045	yes	N/A
A1RWT8	RS4_THEPD	No assigned EC number	0.4453	0.9541	0.7267	yes	N/A
P52810	RS9_PODAS	No assigned EC number	0.7480	0.9618	0.6631	yes	N/A
Q9HJD7	RS4_THEAC	No assigned EC number	0.4427	0.9465	0.6231	yes	N/A
Q6ZWN5	RS9_MOUSE	No assigned EC number	0.8671	0.9389	0.6340	yes	N/A
B0R4Y0	RS4_HALS3	No assigned EC number	0.3888	0.9541	0.7352	yes	N/A
A7IAH7	RS4_METB6	No assigned EC number	0.4360	0.9465	0.6702	yes	N/A
Q9YB58	RS4_AERPE	No assigned EC number	0.4140	0.9541	0.7309	yes	N/A
C3N8R6	RS4_SULIY	No assigned EC number	0.3906	0.9541	0.6906	yes	N/A
Q0W1V5	RS4_UNCMA	No assigned EC number	0.4148	0.9465	0.6048	yes	N/A
A8A8W3	RS4_IGNH4	No assigned EC number	0.5038	0.9389	0.7409	yes	N/A
A8MDS5	RS4_CALMQ	No assigned EC number	0.4318	0.9389	0.6795	yes	N/A
O59675	RS9B_SCHPO	No assigned EC number	0.7328	0.9618	0.6562	yes	N/A
Q8TVC0	RS4_METKA	No assigned EC number	0.4384	0.9541	0.6720	yes	N/A
A0B9L2	RS4_METTP	No assigned EC number	0.4427	0.9465	0.6775	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	131
PTZ00155	181	PTZ00155, PTZ00155, 40S ribosomal protein S9; Prov	2e-68
PLN00189	194	PLN00189, PLN00189, 40S ribosomal protein S9; Prov	2e-62
TIGR01018	162	TIGR01018, rpsD_arch, ribosomal protein S4(archaea	5e-53
PRK04051	177	PRK04051, rps4p, 30S ribosomal protein S4P; Valida	7e-43
COG0522	205	COG0522, RpsD, Ribosomal protein S4 and related pr	4e-21
pfam00163	93	pfam00163, Ribosomal_S4, Ribosomal protein S4/S9 N	5e-17
pfam01479	48	pfam01479, S4, S4 domain	4e-04
PRK05327	203	PRK05327, rpsD, 30S ribosomal protein S4; Validate	0.003

>gnl|CDD|185484 PTZ00155, PTZ00155, 40S ribosomal protein S9; Provisional

 Score =  203 bits (518), Expect = 2e-68
 Identities = 96/133 (72%), Positives = 109/133 (81%), Gaps = 5/133 (3%)

Query: 4   NRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLT 63
            R    HSKTY TPRRP+EK RLD ELK+ GEYGL+NKRE+WRV+Y LAKIRKAARELLT
Sbjct: 2   GRNYRNHSKTYKTPRRPFEKERLDAELKLCGEYGLKNKREIWRVQYTLAKIRKAARELLT 61

Query: 64  LDEKEHR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKS 118
           LDEK+ +      ALLRR+ R+G+LDE + KLDYV GL +E  LERRLQT+VFKLGLAKS
Sbjct: 62  LDEKDPKRLFEGEALLRRMHRLGLLDEDERKLDYVLGLTVEKLLERRLQTKVFKLGLAKS 121

Query: 119 IHHARVLIRQRHI 131
           IHHARVLIRQRHI
Sbjct: 122 IHHARVLIRQRHI 134

Length = 181

>gnl|CDD|177783 PLN00189, PLN00189, 40S ribosomal protein S9; Provisional

 Score =  188 bits (480), Expect = 2e-62
 Identities = 92/136 (67%), Positives = 107/136 (78%), Gaps = 5/136 (3%)

Query: 1   MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARE 60
           MV+      + KT+  PRRPYEK RLD ELK++GEYGLRNKRE+WRV+YAL++IR AAR 
Sbjct: 1   MVHVSFYRNYGKTFKKPRRPYEKERLDAELKLVGEYGLRNKRELWRVQYALSRIRNAARM 60

Query: 61  LLTLDEKEHR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGL 115
           LLTLDEK  R      ALLRR+ R G+LDES+ KLDYV  L +E+FLERRLQT VFK G+
Sbjct: 61  LLTLDEKNPRRIFEGEALLRRMNRYGLLDESQNKLDYVLALTVENFLERRLQTLVFKSGM 120

Query: 116 AKSIHHARVLIRQRHI 131
           AKSIHHARVLIRQRHI
Sbjct: 121 AKSIHHARVLIRQRHI 136

Length = 194

>gnl|CDD|213577 TIGR01018, rpsD_arch, ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type)

 Score =  164 bits (416), Expect = 5e-53
 Identities = 78/129 (60%), Positives = 94/129 (72%), Gaps = 3/129 (2%)

Query: 6   VPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLD 65
            P    K Y TPR P+ K RLD+ELK++G+YGLRNK+EVW+ +  L K R+AARELL LD
Sbjct: 3   DPRKPRKKYETPRHPWIKERLDRELKLVGKYGLRNKKEVWKAETTLRKYRRAARELLGLD 62

Query: 66  EK---EHRNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHA 122
           ++      N LLRRLVR+G+LDE   KLD V GL +EDFLERRLQTQVFK GLA++IH A
Sbjct: 63  DEQRLFEGNQLLRRLVRLGILDEENAKLDDVLGLTVEDFLERRLQTQVFKKGLARTIHQA 122

Query: 123 RVLIRQRHI 131
           R LI   HI
Sbjct: 123 RQLIVHGHI 131

This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4 [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 162

>gnl|CDD|179730 PRK04051, rps4p, 30S ribosomal protein S4P; Validated

 Score =  138 bits (350), Expect = 7e-43
 Identities = 57/128 (44%), Positives = 77/128 (60%), Gaps = 4/128 (3%)

Query: 7   PSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDE 66
           P    K Y TP  P++K R+ +E +++G+YGLRNKRE+W+ +  L K R+ AR LL L  
Sbjct: 4   PKKPRKKYETPNHPWQKERIAEERELLGKYGLRNKRELWKAQSILRKYRRQARSLLALPP 63

Query: 67  KEH---RNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHAR 123
           +E       LL +L R G+L E    LD V  L +ED LERRLQT V++ GLA++   AR
Sbjct: 64  EERAKEEEQLLGKLKRYGILKE-NATLDDVLSLTVEDILERRLQTIVYRKGLARTPKQAR 122

Query: 124 VLIRQRHI 131
             I   HI
Sbjct: 123 QFIVHGHI 130

Length = 177

>gnl|CDD|223596 COG0522, RpsD, Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]

 Score = 83.9 bits (208), Expect = 4e-21
 Identities = 32/116 (27%), Positives = 48/116 (41%), Gaps = 9/116 (7%)

Query: 16  TPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHRNALLR 75
               P+ K RL +E K+  + G ++ +E W+         +  ++L             R
Sbjct: 15  LGFNPWLKERLCKERKLPYKPG-QHGQERWKKLSDYGLQLREKQKLRAFYGV-LEKQFRR 72

Query: 76  RLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 131
            L   G L         V GL +   LERRL   V++LG AK+   AR L+   HI
Sbjct: 73  YLKEAGRLKG-------VTGLNLLALLERRLDNVVYRLGFAKTRRQARQLVSHGHI 121

Length = 205

>gnl|CDD|215762 pfam00163, Ribosomal_S4, Ribosomal protein S4/S9 N-terminal domain

 Score = 70.4 bits (173), Expect = 5e-17
 Identities = 40/97 (41%), Positives = 48/97 (49%), Gaps = 12/97 (12%)

Query: 11  SKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKE-- 68
             T   PRR  E  RL  + K+ GEYGLR  +  WRVK       + +R LL LDEK+  
Sbjct: 5   GPTLKLPRRLGELPRLTAKTKLAGEYGLRPGQHGWRVKKG-----RLSRYLLRLDEKQKL 59

Query: 69  --HRNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLE 103
                 L R+L R GVL     KLD   GL + D LE
Sbjct: 60  RFFYGLLERQLRRYGVLA---KKLDGSLGLNLLDLLE 93

This family includes small ribosomal subunit S9 from prokaryotes and S16 from metazoans. This domain is predicted to bind to ribosomal RNA. This domain is composed of four helices in the known structure. However the domain is discontinuous in sequence and the alignment for this family contains only the first three helices. Length = 93

>gnl|CDD|201819 pfam01479, S4, S4 domain

 Score = 35.5 bits (83), Expect = 4e-04
 Identities = 13/28 (46%), Positives = 16/28 (57%)

Query: 104 RRLQTQVFKLGLAKSIHHARVLIRQRHI 131
            RL   + +LGLA S   AR LIR  H+
Sbjct: 1   MRLDKVLARLGLASSRSEARQLIRHGHV 28

The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA. Length = 48

>gnl|CDD|235411 PRK05327, rpsD, 30S ribosomal protein S4; Validated

 Score = 35.5 bits (83), Expect = 0.003
 Identities = 13/30 (43%), Positives = 17/30 (56%)

Query: 102 LERRLQTQVFKLGLAKSIHHARVLIRQRHI 131
           LE RL   V++LG A +   AR L+   HI
Sbjct: 91  LESRLDNVVYRLGFAPTRRQARQLVSHGHI 120

Length = 203

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	131
TIGR01018	162	rpsD_arch ribosomal protein S4(archaeal type)/S9(e	100.0
PLN00189	194	40S ribosomal protein S9; Provisional	100.0
PTZ00155	181	40S ribosomal protein S9; Provisional	100.0
PRK04051	177	rps4p 30S ribosomal protein S4P; Validated	100.0
KOG3301|consensus	183		100.0
KOG4655|consensus	181		100.0
COG0522	205	RpsD Ribosomal protein S4 and related proteins [Tr	99.94
PF00163	94	Ribosomal_S4: Ribosomal protein S4/S9 N-terminal d	98.63
CHL00113	201	rps4 ribosomal protein S4; Reviewed	97.65
TIGR01017	200	rpsD_bact ribosomal protein S4, bacterial/organell	97.44
PRK05327	203	rpsD 30S ribosomal protein S4; Validated	97.42
PF01479	48	S4: S4 domain; InterPro: IPR002942 Ribosomes are t	97.35
cd00165	70	S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The	88.36
smart00363	60	S4 S4 RNA-binding domain.	83.59

>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type)

Probab=100.00  E-value=2e-52  Score=321.11  Aligned_cols=123  Identities=63%  Similarity=1.012  Sum_probs=119.4

Q ss_pred             CCCCCccccCCCCchhhhhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH-----HHHHHHHHHcc
Q psy7992           7 PSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR-----NALLRRLVRIG   81 (131)
Q Consensus         7 ~~~~~k~~~~P~~pw~~~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~-----~~LL~kL~~~G   81 (131)
                      |++++|+|+||++||++|++++|+++|++|||+||+|||+||++|++||++|+.|++++  ||+     ++||+|||+||
T Consensus         4 p~~~~k~~~~P~~pw~ker~~~E~~l~~kYgLknk~E~wk~~~~~~kiR~~Ar~L~~l~--d~~r~~~~~~LL~kL~~~G   81 (162)
T TIGR01018         4 PRKPRKKYETPRHPWIKERLDRELKLVGKYGLRNKKEVWKAETTLRKYRRAARELLGLD--DEQRLFEGNQLLRRLVRLG   81 (162)
T ss_pred             CCCCCcccCCCCCChhhhhCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHcCC--cHHHHHHHHHHHHHHHHcC
Confidence            68999999999999999999999999999999999999999999999999999999999  665     89999999999


Q ss_pred             ccCcCccchhhhhhhhhhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992          82 VLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus        82 ll~e~~~~L~~vl~ltv~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      ||+|++.+||+|++|||++|||||||+|||++|||+|++||||||+||||
T Consensus        82 ll~e~~~~Ld~vl~Ltv~~~leRRL~~vv~r~g~a~s~~~ArqlI~hgHI  131 (162)
T TIGR01018        82 ILDEENAKLDDVLGLTVEDFLERRLQTQVFKKGLARTIHQARQLIVHGHI  131 (162)
T ss_pred             CCccccCCHHHHHhccHHHHHHHhHhhHhhhccCcCCHHHHHHHhhCCCe
Confidence            99876789999999999999999999999999999999999999999998

This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.

>PLN00189 40S ribosomal protein S9; Provisional

Probab=100.00  E-value=2.3e-52  Score=328.31  Aligned_cols=131  Identities=70%  Similarity=1.062  Sum_probs=126.9

Q ss_pred             CCCCCCCCCCCccccCCCCchhhhhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH-----HHHHH
Q psy7992           1 MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR-----NALLR   75 (131)
Q Consensus         1 ~~~~~~~~~~~k~~~~P~~pw~~~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~-----~~LL~   75 (131)
                      |+-+.++++++|+|+||++||+++|+++|+++|++|||+||+|||+|+++|++||++|+.|++++++||+     .+||+
T Consensus         1 ~~~~~~~~~~~K~y~tP~~P~ek~Rl~~E~kli~kYgLknK~E~wky~~ll~kiRk~Ar~Ll~l~~~d~~r~~~~~~LL~   80 (194)
T PLN00189          1 MVHVSFYRNYGKTFKKPRRPYEKERLDAELKLVGEYGLRNKRELWRVQYALSRIRNAARMLLTLDEKNPRRIFEGEALLR   80 (194)
T ss_pred             CCcccCCCCCCcccCCCCCchhhHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHccCCCccHhHHHHHHHHH
Confidence            6777789999999999999999999999999999999999999999999999999999999999999996     89999


Q ss_pred             HHHHccccCcCccchhhhhhhhhhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992          76 RLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus        76 kL~~~Gll~e~~~~L~~vl~ltv~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      |||+||||++++.+||+|++|+|++|||||||+|||++|||+|+++|||||+||||
T Consensus        81 kL~~~GlL~~~~~~Ld~vl~Ltvs~~leRRL~~vv~r~g~a~si~~ARqlI~hgHI  136 (194)
T PLN00189         81 RMNRYGLLDESQNKLDYVLALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHI  136 (194)
T ss_pred             HHHHhCCccccccCHHHHhhccHHHHHHhhhceeeeecCCcCCHHHHHHheeCCCE
Confidence            99999999767889999999999999999999999999999999999999999998

>PTZ00155 40S ribosomal protein S9; Provisional

Probab=100.00  E-value=1.2e-50  Score=315.97  Aligned_cols=128  Identities=75%  Similarity=1.148  Sum_probs=123.9

Q ss_pred             CCCCCCCCccccCCCCchhhhhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH-----HHHHHHHH
Q psy7992           4 NRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR-----NALLRRLV   78 (131)
Q Consensus         4 ~~~~~~~~k~~~~P~~pw~~~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~-----~~LL~kL~   78 (131)
                      .++|++++|+|+||++||+++|+++|+++|++|||+||+|||+|+++|++||++|+.|++++++||+     ++||+||+
T Consensus         2 ~~~~~~~~k~y~~P~~P~~k~rl~~E~~li~kYgLknk~E~wk~~~~~~kiR~~Ar~L~~l~~~d~~r~~~~~~LL~kL~   81 (181)
T PTZ00155          2 GRNYRNHSKTYKTPRRPFEKERLDAELKLCGEYGLKNKREIWRVQYTLAKIRKAARELLTLDEKDPKRLFEGEALLRRMH   81 (181)
T ss_pred             CCCCCCCCcccCCCCCchhHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHH
Confidence            3568999999999999999999999999999999999999999999999999999999999999996     89999999


Q ss_pred             HccccCcCccchhhhhhhhhhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992          79 RIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus        79 ~~Gll~e~~~~L~~vl~ltv~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      +||++.+++++|++|++|++++|||||||+|||++|||+|+++|||||+||||
T Consensus        82 ~~Gi~~~~k~~l~~~~~l~~~~~leRRL~~iv~r~g~A~ti~~ARqlI~HGHI  134 (181)
T PTZ00155         82 RLGLLDEDERKLDYVLGLTVEKLLERRLQTKVFKLGLAKSIHHARVLIRQRHI  134 (181)
T ss_pred             HhCCcchhhccHHHHHCccHHHHHHHhhhhHHHhccCcCCHHHhhhheeCCCE
Confidence            99999766789999999999999999999999999999999999999999998

>PRK04051 rps4p 30S ribosomal protein S4P; Validated

Probab=100.00  E-value=1.3e-48  Score=303.58  Aligned_cols=124  Identities=45%  Similarity=0.767  Sum_probs=117.3

Q ss_pred             CCCCCccccCCCCchhhhhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH---HHHHHHHHHcccc
Q psy7992           7 PSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR---NALLRRLVRIGVL   83 (131)
Q Consensus         7 ~~~~~k~~~~P~~pw~~~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~---~~LL~kL~~~Gll   83 (131)
                      |++++|+|+||++||++||+++|+++|++|||+||+|||+||++|++||++|+.|++.++....   ++||+|||+||||
T Consensus         4 p~~~~k~~~~P~~pw~~~r~~~E~~l~~~YgLknk~E~wk~~~~~~~iR~~Ar~Ll~~~~~~r~~~~~~Ll~kL~~~Gil   83 (177)
T PRK04051          4 PKKPRKKYETPNHPWQKERIAEERELLGKYGLRNKRELWKAQSILRKYRRQARSLLALPPEERAKEEEQLLGKLKRYGIL   83 (177)
T ss_pred             CCCCCcCcCCCCCchhhhhcHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHcCCC
Confidence            7999999999999999999999999999999999999999999999999999999995432211   8999999999999


Q ss_pred             CcCccchhhhhhhhhhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992          84 DESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus        84 ~e~~~~L~~vl~ltv~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      + ++.+||+|++|||++|||||||++|++.|||+|+++|+|||.||||
T Consensus        84 ~-~~~~L~~vl~L~v~~~lerRLd~il~r~gla~S~~~Ar~lI~hGhV  130 (177)
T PRK04051         84 K-ENATLDDVLSLTVEDILERRLQTIVYRKGLARTPKQARQFIVHGHI  130 (177)
T ss_pred             C-CCCCHHHHHhccHHHHHHhHHHHHHHHccCcCCHHHHHHHHHcCCE
Confidence            8 4889999999999999999999999999999999999999999997

>KOG3301|consensus

Probab=100.00  E-value=4.6e-37  Score=236.39  Aligned_cols=119  Identities=80%  Similarity=1.190  Sum_probs=114.8

Q ss_pred             CccccCCCCchhhhhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH-----HHHHHHHHHccccCc
Q psy7992          11 SKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR-----NALLRRLVRIGVLDE   85 (131)
Q Consensus        11 ~k~~~~P~~pw~~~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~-----~~LL~kL~~~Gll~e   85 (131)
                      +|+|++|+.|||++|++.|+++++.|||+|++|+|+....+.++|+.||.|  |+++||.     .+|+++|.+.|+++|
T Consensus         1 ~k~y~~PRrpfek~Rld~elkl~g~yglknk~elwr~~~~l~K~r~aaR~l--l~~k~p~rlf~g~allrrLvr~g~l~e   78 (183)
T KOG3301|consen    1 SKTYKTPRRPFEKERLDAELKLVGEYGLKNKRELWRVSRSLSKIRYAAREL--LDEKDPKRLFEGNALLRRLVRYGVLDE   78 (183)
T ss_pred             CCccCCCCChHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHHHHH--hccccHHHHhcchHHHHHHHHHhhhhc
Confidence            589999999999999999999999999999999999999999999999999  6677774     899999999999999


Q ss_pred             CccchhhhhhhhhhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992          86 SKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus        86 ~~~~L~~vl~ltv~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      ++.+||+|+.+++++||||||||+||++|||.||+|||++|.|+||
T Consensus        79 ~~~Kldyvl~l~ie~fLErRLqt~vFklGlAkSIhhARvLi~~rhI  124 (183)
T KOG3301|consen   79 RKNKLDYVLALTVEDFLERRLQTIVFKLGLAKSIHHARVLIRQRHI  124 (183)
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHhcCccE
Confidence            9999999999999999999999999999999999999999999998

>KOG4655|consensus

Probab=100.00  E-value=1.8e-35  Score=227.73  Aligned_cols=116  Identities=24%  Similarity=0.370  Sum_probs=113.7

Q ss_pred             cCCCCchhhhhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH-----HHHHHHHHHccccCcCccc
Q psy7992          15 VTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR-----NALLRRLVRIGVLDESKMK   89 (131)
Q Consensus        15 ~~P~~pw~~~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~-----~~LL~kL~~~Gll~e~~~~   89 (131)
                      ++.|.+|+.+..++|..++++|||+++|||.+||.+++++|++|+.|..+++.|||     ..||+|||.||+++ +.++
T Consensus        14 kVdFLnWkv~d~~re~~v~rrY~l~~REdY~kyn~l~~~~r~la~~l~~l~~sDpfR~~~t~~LL~kly~~Gvip-Tr~~   92 (181)
T KOG4655|consen   14 KVDFLNWKVTDHHRELCVLRRYHLKKREDYTKYNRLAGKVRKLANRLALLDESDPFRLQYTLLLLEKLYAMGVIP-TRKS   92 (181)
T ss_pred             hcccceeeecCchhhHHHHHHHhcccHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHHHHHhhccccccceec-chhh
Confidence            67899999999999999999999999999999999999999999999999999998     79999999999999 8999


Q ss_pred             hhhhhhhhhhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992          90 LDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus        90 L~~vl~ltv~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      ++++.++|+|+||+||||+|+.+++||+|+++|..||+||||
T Consensus        93 l~~~~kvtvssfCrRRLP~Vm~~l~m~~~~k~A~~~vEqGHV  134 (181)
T KOG4655|consen   93 LELTEKVTVSSFCRRRLPVVMGRLRMAESVKEAVRFVEQGHV  134 (181)
T ss_pred             hhhcccchhHHHhhhccceeeeechhhhhHHHHHHHHHcCce
Confidence            999999999999999999999999999999999999999997

>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]

Probab=99.94  E-value=1.6e-26  Score=183.34  Aligned_cols=113  Identities=29%  Similarity=0.385  Sum_probs=105.5

Q ss_pred             CCcc--ccCCCCchhhhhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHccccCcCc
Q psy7992          10 HSKT--YVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHRNALLRRLVRIGVLDESK   87 (131)
Q Consensus        10 ~~k~--~~~P~~pw~~~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~~~LL~kL~~~Gll~e~~   87 (131)
                      ++++  |++|++||.+++...|.+.+..|| +++.+.|+-.+.++..++.+++|..... ....+|+++|+++|++++  
T Consensus         7 ~~~K~~rr~g~~~~~~~~~~~~~~~~~~pG-qhk~~~~~k~s~yg~qL~ekqkl~~~yg-~~ekqf~~~l~~a~~l~g--   82 (205)
T COG0522           7 PKKKLSRRLGFNPWLKERLCKERKLPYKPG-QHGQERWKKLSDYGLQLREKQKLRAFYG-VLEKQFRRYLKEAGRLKG--   82 (205)
T ss_pred             cccceeeecCCChHHHHHHHHHhhcCCCcc-ccchhHHHHHHHHHHHHHHHHHhhhhcc-HHHHHHHHHHHHHhccCC--
Confidence            6666  999999999999999999999999 9999999999999999999999998766 223899999999999983  


Q ss_pred             cchhhhhhhhhhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992          88 MKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus        88 ~~L~~vl~ltv~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                           ++++|+++||||||||||||+|||.|++||||||+||||
T Consensus        83 -----~~~~~~~~~LErRLd~vVyR~GfA~T~~qARQlV~HGHI  121 (205)
T COG0522          83 -----VTGLNLLALLERRLDNVVYRLGFAKTRRQARQLVSHGHI  121 (205)
T ss_pred             -----hHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHhhcceE
Confidence                 779999999999999999999999999999999999998

>PF00163 Ribosomal_S4: Ribosomal protein S4/S9 N-terminal domain; InterPro: IPR001912 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=98.63  E-value=2.8e-10  Score=79.36  Aligned_cols=89  Identities=36%  Similarity=0.448  Sum_probs=80.9

Q ss_pred             CCCCccccCCCCchhhhhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH----HHHHHHHHHcccc
Q psy7992           8 SVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR----NALLRRLVRIGVL   83 (131)
Q Consensus         8 ~~~~k~~~~P~~pw~~~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~----~~LL~kL~~~Gll   83 (131)
                      +...++|+.|++||..+.+..|..++++||+.+..+.|+.+..    |++++.+..|++++++    ..++++|+++|++
T Consensus         2 R~~~~~~k~~Rr~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----rk~s~y~~qL~eKqk~r~~yg~lekql~~~~~~   77 (94)
T PF00163_consen    2 RYRGPKCKLPRRLGEKLWLTEKAKLIRRYGLRPGQHGWRRKSR----RKLSRYGLQLREKQKLRFYYGILEKQLRRYGKI   77 (94)
T ss_dssp             CSHSCCCHHHHHCTSHCTCSCCCSHCCSSSSSSSSSTTSHHHH----HCCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred             CcCCCccccCCCCCCCccCCCcccccccccccccccccccccc----ccchhhhcccccCCchhhhhhhHHHHHHHHHHH
Confidence            4567889999999999999999999999999999999888765    9999999999999996    6899999999999


Q ss_pred             CcCccchhhhhhhhhhhHhh
Q psy7992          84 DESKMKLDYVWGLKIEDFLE  103 (131)
Q Consensus        84 ~e~~~~L~~vl~ltv~~fle  103 (131)
                      .   ..++.+.+.++++|||
T Consensus        78 a---~k~~g~tg~~l~~lLE   94 (94)
T PF00163_consen   78 A---AKLKGVTGENLLQLLE   94 (94)
T ss_dssp             H---HHSSSHHHHHHHHHHH
T ss_pred             H---HhcCCCHHHHHHHHhC
Confidence            6   5688899999999997

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 S4 is one of the proteins from the small ribosomal subunit. S4 is known to bind directly to 16S ribosomal RNA. The crystal structure of a bacterial S4 protein revealed a two domain molecule. The first domain is composed of four helices in the known structure. The second domain is an insertion within domain 1 and displays some structural homology with the ETS DNA binding domain []. This entry represents the domain found at the N terminus of small ribosomal subunits S4 and S9. ; GO: 0019843 rRNA binding, 0005622 intracellular; PDB: 3BBN_D 2WWL_D 3OR9_D 3OFA_D 2QBB_D 3OFP_D 4A2I_D 2QB9_D 3OFO_D 2QBF_D ....

>CHL00113 rps4 ribosomal protein S4; Reviewed

Probab=97.65  E-value=3.5e-05  Score=61.25  Aligned_cols=34  Identities=41%  Similarity=0.691  Sum_probs=31.9

Q ss_pred             hhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992          98 IEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus        98 v~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      .-.+||.|||.++++.|++.|..+|+|+|.||||
T Consensus        83 ll~~LE~RLD~~L~r~g~~~SR~~ArqlI~~G~V  116 (201)
T CHL00113         83 LLQLLEMRLDNILFRLGMAPTIPAARQLVNHGHI  116 (201)
T ss_pred             HHHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCcE
Confidence            4478999999999999999999999999999997

>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type

Probab=97.44  E-value=0.00011  Score=58.12  Aligned_cols=33  Identities=39%  Similarity=0.621  Sum_probs=31.1

Q ss_pred             hhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992          99 EDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus        99 ~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      -.++|.|||.++++.|++.|..+|+++|.||||
T Consensus        85 l~~le~RLD~~L~~~g~~~SR~~ArqlI~~G~V  117 (200)
T TIGR01017        85 LRLLESRLDNVVYRLGFAPTRFAARQLVSHGHI  117 (200)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCCE
Confidence            367889999999999999999999999999997

This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.

>PRK05327 rpsD 30S ribosomal protein S4; Validated

Probab=97.42  E-value=0.00012  Score=58.05  Aligned_cols=33  Identities=39%  Similarity=0.660  Sum_probs=31.2

Q ss_pred             hhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992          99 EDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus        99 ~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      -.++|.|||+++++.||+.|..+|+++|.||||
T Consensus        88 l~~lE~RLD~iL~~~g~~~SR~~arqlI~~G~V  120 (203)
T PRK05327         88 LQLLESRLDNVVYRLGFAPTRRQARQLVSHGHI  120 (203)
T ss_pred             HHHHHHHHHHHHHHcCccCCHHHHHHHHHCCcE
Confidence            468899999999999999999999999999997

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

Probab=97.35  E-value=0.00012  Score=44.51  Aligned_cols=28  Identities=43%  Similarity=0.541  Sum_probs=26.7

Q ss_pred             hhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992         104 RRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus       104 rRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      +||+.++.+.|++.|..+|+++|.||+|
T Consensus         1 ~RLd~~L~~~~~~~sr~~a~~~I~~g~V   28 (48)
T PF01479_consen    1 MRLDKFLSRLGLASSRSEARRLIKQGRV   28 (48)
T ss_dssp             EBHHHHHHHTTSSSSHHHHHHHHHTTTE
T ss_pred             CCHHHHHHHcCCcCCHHHHHHhcCCCEE
Confidence            4899999999999999999999999986

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

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

Probab=88.36  E-value=0.38  Score=29.11  Aligned_cols=27  Identities=44%  Similarity=0.642  Sum_probs=23.9

Q ss_pred             hhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992         105 RLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus       105 RL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      ||+.++.+.++..|..+|+++|.+|+|
T Consensus         2 rl~~~l~~~~~~~sr~~~~~~i~~g~V   28 (70)
T cd00165           2 RLDKILARLGLAPSRSEARQLIKHGHV   28 (70)
T ss_pred             cHHHHHHHhccccCHHHHHHHHHcCCE
Confidence            677888888888999999999999986

>smart00363 S4 S4 RNA-binding domain

Probab=83.59  E-value=0.98  Score=26.46  Aligned_cols=27  Identities=44%  Similarity=0.565  Sum_probs=23.2

Q ss_pred             hhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992         105 RLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus       105 RL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      ||+.++...++..|..+|+.+|.+|+|
T Consensus         2 rl~~~l~~~~~~~s~~~~~~~i~~g~i   28 (60)
T smart00363        2 RLDKFLARLGLAPSRSQARKLIEQGRV   28 (60)
T ss_pred             cHHHHHHHcCcccCHHHHHHHHHcCCE
Confidence            677788777788899999999999975

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	131
3izb_C	197	Localization Of The Small Subunit Ribosomal Protein		3e-48
3jyv_D	158	Structure Of The 40s Rrna And Proteins And PE TRNA		7e-47
3iz6_C	195	Localization Of The Small Subunit Ribosomal Protein		2e-43
2xzm_D	181	Crystal Structure Of The Eukaryotic 40s Ribosomal S		4e-43
1s1h_D	179	Structure Of The Ribosomal 80s-Eef2-Sordarin Comple		8e-41
3zey_6	190	High-resolution Cryo-electron Microscopy Structure		3e-35
3j20_D	180	Promiscuous Behavior Of Proteins In Archaeal Riboso		3e-16

>pdb|3IZB|C Chain C, Localization Of The Small Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 197

Iteration: 1
 Score =  186 bits (472), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 89/132 (67%), Positives = 110/132 (83%), Gaps = 5/132 (3%)
Query: 5   RVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTL 64
           R P  +SKTY TP+RPYE +RLD ELK+ GE+GL+NK+E++R+ + L+KIR+AAR+LLT 
Sbjct: 3   RAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLTR 62
Query: 65  DEKEHR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSI 119
           DEK+ +     NAL+RRLVR+GVL E K KLDYV  LK+EDFLERRLQTQV+KLGLAKS+
Sbjct: 63  DEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKSV 122
Query: 120 HHARVLIRQRHI 131
           HHARVLI QRHI
Sbjct: 123 HHARVLITQRHI 134

>pdb|3JYV|D Chain D, 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 = 158

Iteration: 1
 Score =  181 bits (460), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 87/128 (67%), Positives = 108/128 (84%), Gaps = 5/128 (3%)
Query: 9   VHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKE 68
            +SKTY TP+RPYE +RLD ELK+ GE+GL+NK+E++R+ + L+KIR+AAR+LLT DEK+
Sbjct: 2   TYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLTRDEKD 61
Query: 69  HR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHAR 123
            +     NAL+RRLVR+GVL E K KLDYV  LK+EDFLERRLQTQV+KLGLAKS+HHAR
Sbjct: 62  PKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKSVHHAR 121
Query: 124 VLIRQRHI 131
           VLI QRHI
Sbjct: 122 VLITQRHI 129

>pdb|3IZ6|C Chain C, Localization Of The Small Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 195

Iteration: 1
 Score =  170 bits (431), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 89/134 (66%), Positives = 103/134 (76%), Gaps = 7/134 (5%)
Query: 5   RVPSVHSKTYVT--PRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELL 62
           R P  +SKTY T  PRRPYEK RLD ELK++GEYGLR KRE+WRV+YAL++IR  AR LL
Sbjct: 3   RAPRTYSKTYSTKKPRRPYEKERLDAELKLVGEYGLRCKRELWRVQYALSRIRNNARHLL 62
Query: 63  TLDEKEHR-----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAK 117
           TLDEK  R      ALLRR+ R G+L + + KLDYV  L +E+FL RRLQT VFK G+AK
Sbjct: 63  TLDEKNPRRIFEGEALLRRMNRYGLLADGQNKLDYVLALTVENFLARRLQTLVFKAGMAK 122
Query: 118 SIHHARVLIRQRHI 131
           SIHHARVLIRQRHI
Sbjct: 123 SIHHARVLIRQRHI 136

>pdb|2XZM|D Chain D, 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 = 181

Iteration: 1
 Score =  169 bits (428), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 86/126 (68%), Positives = 100/126 (79%), Gaps = 5/126 (3%)
Query: 11  SKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR 70
           SKTY TPRRPYEK RLD E+K+IG +GL+NKREVWRV+  LAK RKAARELLTLD K+ R
Sbjct: 9   SKTYSTPRRPYEKERLDNEMKLIGTFGLKNKREVWRVQMILAKFRKAARELLTLDPKDPR 68
Query: 71  -----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVL 125
                +ALLRR+ + G+L E + KLDYV GL I   +ERRLQT+VFKL LA SIHH+RVL
Sbjct: 69  RLFEGSALLRRMFKYGLLSEQERKLDYVLGLTIHKLMERRLQTRVFKLNLANSIHHSRVL 128
Query: 126 IRQRHI 131
           IRQRHI
Sbjct: 129 IRQRHI 134

>pdb|1S1H|D Chain D, 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 = 179

Iteration: 1
 Score =  161 bits (408), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 79/116 (68%), Positives = 98/116 (84%), Gaps = 5/116 (4%)
Query: 21  YEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR-----NALLR 75
           YE +RLD ELK+ GE+GL+NK+E++R+ + L+KIR+AAR+LLT DEK+ +     NAL+R
Sbjct: 1   YESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLTRDEKDPKRLFEGNALIR 60
Query: 76  RLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 131
           RLVR+GVL E K KLDYV  LK+EDFLERRLQTQV+KLGLAKS+HHARVLI QRHI
Sbjct: 61  RLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKSVHHARVLITQRHI 116

>pdb|3ZEY|6 Chain 6, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 190

Iteration: 1
 Score =  143 bits (361), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 73/126 (57%), Positives = 92/126 (73%), Gaps = 5/126 (3%)
Query: 11  SKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR 70
           ++ +  PRRP+EK RLD+E+K+ G+YGLR KRE+WRV   L+K+R+ AR LLTL E   R
Sbjct: 8   NRVWKAPRRPFEKERLDREMKLCGQYGLRCKREIWRVNMTLSKMRRTARLLLTLPENHPR 67
Query: 71  -----NALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVL 125
                +A++RR    G LDE K KLDYV  L + D LERRLQT VFK GLAKS+HH+RVL
Sbjct: 68  RLLEGSAIMRRCHGYGFLDEDKDKLDYVLSLTVPDILERRLQTVVFKHGLAKSVHHSRVL 127
Query: 126 IRQRHI 131
           I+QRHI
Sbjct: 128 IQQRHI 133

>pdb|3J20|D Chain D, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (30s Ribosomal Subunit) Length = 180

Iteration: 1
 Score = 80.1 bits (196), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 58/128 (45%), Positives = 77/128 (60%), Gaps = 4/128 (3%)
Query: 7   PSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDE 66
           P    K Y TP  P+ K RLD+E  ++ +Y L+NK+E+W+ +  L   R+ AR LL    
Sbjct: 4   PKRQRKKYETPPHPWIKERLDRERVLMDKYELKNKKELWKHETQLKNFRRRARRLLAARG 63
Query: 67  KE---HRNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHAR 123
           K+    R  LL RL R+G+L E  + LD V  L IED LERRLQT V+K GLA+++  AR
Sbjct: 64  KQAEIEREQLLARLKRLGLLPEDAV-LDDVLSLTIEDILERRLQTIVYKKGLARTMRQAR 122
Query: 124 VLIRQRHI 131
            LI   HI
Sbjct: 123 QLIVHGHI 130

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	131
2xzm_D	181	Ribosomal protein S4 containing protein; ribosome,	3e-39
3u5c_J	197	40S ribosomal protein S9-A; translation, ribosome,	3e-39
3iz6_C	195	40S ribosomal protein S9 (S4P); eukaryotic ribosom	7e-37
2cqj_A	71	BRMS2, U3 small nucleolar ribonucleoprotein protei	9e-13

>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_D Length = 181

 Score =  129 bits (325), Expect = 3e-39
 Identities = 85/132 (64%), Positives = 100/132 (75%), Gaps = 5/132 (3%)

Query: 5   RVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTL 64
           +     SKTY TPRRPYEK RLD E+K+IG +GL+NKREVWRV+  LAK RKAARELLTL
Sbjct: 3   KTYINTSKTYSTPRRPYEKERLDNEMKLIGTFGLKNKREVWRVQMILAKFRKAARELLTL 62

Query: 65  DEKE-----HRNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSI 119
           D K+       +ALLRR+ + G+L E + KLDYV GL I   +ERRLQT+VFKL LA SI
Sbjct: 63  DPKDPRRLFEGSALLRRMFKYGLLSEQERKLDYVLGLTIHKLMERRLQTRVFKLNLANSI 122

Query: 120 HHARVLIRQRHI 131
           HH+RVLIRQRHI
Sbjct: 123 HHSRVLIRQRHI 134

>3u5c_J 40S ribosomal protein S9-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_C 3o30_E 3o2z_E 3u5g_J 1s1h_D 3jyv_D* Length = 197

 Score =  129 bits (326), Expect = 3e-39
 Identities = 89/132 (67%), Positives = 109/132 (82%), Gaps = 5/132 (3%)

Query: 5   RVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTL 64
           R P  +SKTY TP+RPYE +RLD ELK+ GE+GL+NK+E++R+ + L+KIR+AAR+LLT 
Sbjct: 3   RAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLTR 62

Query: 65  DEKE-----HRNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSI 119
           DEK+       NAL+RRLVR+GVL E K KLDYV  LK+EDFLERRLQTQV+KLGLAKS+
Sbjct: 63  DEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKSV 122

Query: 120 HHARVLIRQRHI 131
           HHARVLI QRHI
Sbjct: 123 HHARVLITQRHI 134

>3iz6_C 40S ribosomal protein S9 (S4P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Length = 195

 Score =  123 bits (310), Expect = 7e-37
 Identities = 88/134 (65%), Positives = 102/134 (76%), Gaps = 7/134 (5%)

Query: 5   RVPSVHSKTYVT--PRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELL 62
           R P  +SKTY T  PRRPYEK RLD ELK++GEYGLR KRE+WRV+YAL++IR  AR LL
Sbjct: 3   RAPRTYSKTYSTKKPRRPYEKERLDAELKLVGEYGLRCKRELWRVQYALSRIRNNARHLL 62

Query: 63  TLDEKE-----HRNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAK 117
           TLDEK         ALLRR+ R G+L + + KLDYV  L +E+FL RRLQT VFK G+AK
Sbjct: 63  TLDEKNPRRIFEGEALLRRMNRYGLLADGQNKLDYVLALTVENFLARRLQTLVFKAGMAK 122

Query: 118 SIHHARVLIRQRHI 131
           SIHHARVLIRQRHI
Sbjct: 123 SIHHARVLIRQRHI 136

>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 71

 Score = 58.1 bits (141), Expect = 9e-13
 Identities = 10/34 (29%), Positives = 16/34 (47%)

Query: 98  IEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI 131
                 RRL T + KL +A+ +  A   + Q H+
Sbjct: 2   SSGSSGRRLPTVLLKLRMAQHLQAAVAFVEQGHV 35

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	131
3u5c_J	197	40S ribosomal protein S9-A; translation, ribosome,	100.0
3j20_D	180	30S ribosomal protein S4P; archaea, archaeal, KINK	100.0
2xzm_D	181	Ribosomal protein S4 containing protein; ribosome,	100.0
3iz6_C	195	40S ribosomal protein S9 (S4P); eukaryotic ribosom	100.0
2cqj_A	71	BRMS2, U3 small nucleolar ribonucleoprotein protei	99.01
3bbn_D	201	Ribosomal protein S4; small ribosomal subunit, spi	98.58
1c05_A	159	Ribosomal protein S4 delta 41; two subdomains, uni	98.33
2vqe_D	209	30S ribosomal protein S4; tRNA-binding, rRNA-bindi	97.79
3r8n_D	205	30S ribosomal protein S4; protein biosynthesis, RN	97.61
3j20_E	243	30S ribosomal protein S4E; archaea, archaeal, KINK	86.51
1p9k_A	79	ORF, hypothetical protein; alfal motif, RNA-bindin	83.61

>3u5c_J 40S ribosomal protein S9-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_C 3o30_E 3o2z_E 3u5g_J 1s1h_D 3jyv_D*

Probab=100.00  E-value=2.2e-48  Score=305.36  Aligned_cols=129  Identities=69%  Similarity=1.095  Sum_probs=124.0

Q ss_pred             CCCCCCCCCCCccccCCCCchhhhhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH-----HHHHH
Q psy7992           1 MVNNRVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR-----NALLR   75 (131)
Q Consensus         1 ~~~~~~~~~~~k~~~~P~~pw~~~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~-----~~LL~   75 (131)
                      ||.+  |++++|+|+||++||+++|+++|+++|++|||+||+|||+|+++|++||++|+.|++|+++||+     ++||+
T Consensus         1 ~~~~--~~~~~k~~~tP~~p~~~~r~~~E~~l~~~YgL~nKrE~wr~~~~l~~iR~~Ar~Ll~l~~~dp~r~~~~~~LL~   78 (197)
T 3u5c_J            1 MPRA--PRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLTRDEKDPKRLFEGNALIR   78 (197)
T ss_dssp             -CCC--CCCCCCSCCCCSSSCCHHHHHHHHHHHHHHTCSCHHHHHHHHHHHHHHHHHHHHHHTSCTTCHHHHHHHHHHHH
T ss_pred             CCCC--CCCCCcccCCCCCchhHHhhHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHH
Confidence            4444  8999999999999999999999999999999999999999999999999999999999999987     89999


Q ss_pred             HHHHccccCcCccchhhhhhhhhhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992          76 RLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus        76 kL~~~Gll~e~~~~L~~vl~ltv~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      |||+||||++++.+|++|++||+++|||+|||++|+++|||+|+.+|+|||.||||
T Consensus        79 kL~~~Gil~~~~~~L~~v~~l~~~~~le~RLD~~L~r~G~a~Sr~~ArqLI~~GhV  134 (197)
T 3u5c_J           79 RLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKSVHHARVLITQRHI  134 (197)
T ss_dssp             HHHHHTSSCGGGCSSHHHHHCCHHHHHTTSHHHHHHHSSTTSSHHHHHHHHHTSCC
T ss_pred             HHHHcCCCCCcccChhhhhcccHHHHHHHHHHHHHHHccccCCHHHHHHHHHcCCE
Confidence            99999999867899999999999999999999999999999999999999999998

>3j20_D 30S ribosomal protein S4P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=100.00  E-value=2.4e-46  Score=290.31  Aligned_cols=124  Identities=46%  Similarity=0.731  Sum_probs=116.3

Q ss_pred             CCCCCccccCCCCchhhhhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH---HHHHHHHHHcccc
Q psy7992           7 PSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR---NALLRRLVRIGVL   83 (131)
Q Consensus         7 ~~~~~k~~~~P~~pw~~~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~---~~LL~kL~~~Gll   83 (131)
                      |++++|+|+||++||++||+++|++++++|||+||+|||+||++|++||++|+.|++++++|+.   ++||+|||+||||
T Consensus         4 p~~~~k~~~~p~~pw~~~r~~~E~kl~~~YgL~nk~e~wk~~~~l~~~r~~Ar~L~~l~~~d~~~~~~~LL~kL~~~Gll   83 (180)
T 3j20_D            4 PKRQRKKYETPPHPWIKERLDRERVLMDKYELKNKKELWKHETQLKNFRRRARRLLAARGKQAEIEREQLLARLKRLGLL   83 (180)
T ss_dssp             -----CCCCCCSSSSCHHHHHHHHHHHHHHTCSCTHHHHHHHHHHHHHHHHHHHHHHSCTTSCTHHHHHHHHHHHHHTSS
T ss_pred             CCCCCCCCCCCCCchhhhhhHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHcCCC
Confidence            6999999999999999999999999999999999999999999999999999999999999953   8999999999999


Q ss_pred             CcCccchhhhhhhhhhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992          84 DESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus        84 ~e~~~~L~~vl~ltv~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      ++ +.+||+|++|++++|||+|||++|++.|||+|+.+|++||.||||
T Consensus        84 ~~-~~~L~~vl~l~~~~~le~RLD~~L~~~G~a~SR~~Ar~LI~~G~V  130 (180)
T 3j20_D           84 PE-DAVLDDVLSLTIEDILERRLQTIVYKKGLARTMRQARQLIVHGHI  130 (180)
T ss_dssp             SS-CCCSHHHHTCCHHHHHHTSHHHHHHHHTSSSSHHHHHHHHHHTCC
T ss_pred             CC-CCCHHHHhccchHhhhhhhhhheeecCcccCcHHHHHHHHHcCCe
Confidence            94 899999999999999999999999999999999999999999998

>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_D

Probab=100.00  E-value=2.6e-44  Score=278.76  Aligned_cols=127  Identities=68%  Similarity=1.047  Sum_probs=123.4

Q ss_pred             CCCCCCCccccCCCCchhhhhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH-----HHHHHHHHH
Q psy7992           5 RVPSVHSKTYVTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR-----NALLRRLVR   79 (131)
Q Consensus         5 ~~~~~~~k~~~~P~~pw~~~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~-----~~LL~kL~~   79 (131)
                      +.|++++|+|+||++||++|++++|+++|++|||+||+|||+|+++|++||++|+.|++||++||+     .+||+||++
T Consensus         3 ~~~~~~~k~~~~p~~~w~~~~~~~E~~l~~~YgL~nk~e~w~~~~~~~~iR~~ar~L~~l~~~d~~r~~~~~~ll~kl~~   82 (181)
T 2xzm_D            3 KTYINTSKTYSTPRRPYEKERLDNEMKLIGTFGLKNKREVWRVQMILAKFRKAARELLTLDPKDPRRLFEGSALLRRMFK   82 (181)
T ss_dssp             CCCSCCCCCCCCCSSTTCHHHHHHHHHHHHHTTCCSHHHHHHHHHHHHHHHHHHHHHHTSCTTCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcccCCCCCCccccccHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHcCCccccHHHHHHHHHHHHHHH
Confidence            458999999999999999999999999999999999999999999999999999999999999995     899999999


Q ss_pred             ccccCcCccchhhhhhhhhhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992          80 IGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus        80 ~Gll~e~~~~L~~vl~ltv~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      +|++.+.+++|+.+.+|++++||++|||++|++.||+.|..+|+++|.||||
T Consensus        83 ~g~~~~~kqkl~~~~gl~~~~~le~RLD~vL~~~G~a~SR~~Ar~LI~~G~V  134 (181)
T 2xzm_D           83 YGLLSEQERKLDYVLGLTIHKLMERRLQTRVFKLNLANSIHHSRVLIRQRHI  134 (181)
T ss_dssp             TTSSCTTCCSTHHHHSCCHHHHHTTBHHHHHHHTTCSSSTTHHHHHTTTTCC
T ss_pred             hccccchhhhHHHHhCcCcchhhccchhHHHHhccccCCHHHHHHHHHCCEE
Confidence            9999866899999999999999999999999999999999999999999998

>3iz6_C 40S ribosomal protein S9 (S4P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=100.00  E-value=1.4e-47  Score=300.35  Aligned_cols=129  Identities=68%  Similarity=1.070  Sum_probs=123.4

Q ss_pred             CCCCCCCCCCCccc--cCCCCchhhhhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHH-----HHH
Q psy7992           1 MVNNRVPSVHSKTY--VTPRRPYEKARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHR-----NAL   73 (131)
Q Consensus         1 ~~~~~~~~~~~k~~--~~P~~pw~~~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~-----~~L   73 (131)
                      ||++  |++++|+|  +||++||+++|+++|+++|++|||+||+|||+|+++|++||++|+.|++++++||+     ++|
T Consensus         1 ~~~~--~~~~~k~~~~~~P~~p~~~~r~~~E~~l~~~YgL~nKrE~wr~~~~l~~iR~~Ar~L~~l~e~d~~r~~~~~~l   78 (195)
T 3iz6_C            1 MPRA--PRTYSKTYSTKKPRRPYEKERLDAELKLVGEYGLRCKRELWRVQYALSRIRNNARHLLTLDEKNPRRIFEGEAL   78 (195)
T ss_dssp             CCHH--HHHHHHHHHSCCSSCCCCCSHHHHHHHHHHHHHHHTCCSTTHHHHHHHHHHSSSCHHHHHHHTCCCHHHHHHHH
T ss_pred             CCCC--cCCCCceeCCCCCCCchhHHhhHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHcCCccchHHHHHHHHH
Confidence            4544  79999999  99999999999999999999999999999999999999999999999999999975     899


Q ss_pred             HHHHHHccccCcCccchhhhhhhhhhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992          74 LRRLVRIGVLDESKMKLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus        74 L~kL~~~Gll~e~~~~L~~vl~ltv~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      |+|||+||+|+++..+||+|++||+++|||+|||++|+++|||+|+.+|+|||.||||
T Consensus        79 L~kL~~~Gll~e~~~~Ld~vl~l~~~~~le~RLD~~L~r~G~a~SR~~ArqlI~~GhV  136 (195)
T 3iz6_C           79 LRRMNRYGLLADGQNKLDYVLALTVENFLARRLQTLVFKAGMAKSIHHARVLIRQRHI  136 (195)
T ss_dssp             TCSSSTTSHHHHHHHTTCCEETTEECCCTTSCCCSSCCCCCCHHHHSCTTSHHHHHST
T ss_pred             HHHHHHcCCCCccccCHHHHHhhhHHHHHHhhhhHHHHhccccCCHHHHHHHHHcCCE
Confidence            9999999999866789999999999999999999999999999999999999999998

>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.01  E-value=4.5e-11  Score=79.39  Aligned_cols=34  Identities=29%  Similarity=0.428  Sum_probs=32.9

Q ss_pred             hhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992          98 IEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus        98 v~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      +++||++|||+++++.|||+|..+|+++|.||||
T Consensus         2 ~~~~l~~RLD~~l~~~gla~SR~~A~~lI~~G~V   35 (71)
T 2cqj_A            2 SSGSSGRRLPTVLLKLRMAQHLQAAVAFVEQGHV   35 (71)
T ss_dssp             CSSCCEEEHHHHHHHTTCSSSHHHHHHHHHTTCE
T ss_pred             HHHHHHHHHHHHHHHhCCcCCHHHHHHHHHCCcE
Confidence            6799999999999999999999999999999997

>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=98.58  E-value=9.9e-08  Score=74.64  Aligned_cols=71  Identities=35%  Similarity=0.536  Sum_probs=54.6

Q ss_pred             hhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHccccCcCccchhhhhhhhhhhHhh
Q psy7992          24 ARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHRNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLE  103 (131)
Q Consensus        24 ~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~~~LL~kL~~~Gll~e~~~~L~~vl~ltv~~fle  103 (131)
                      .++.++.++...|||..        +.+.++.+.|+.+.                  |...   .        +.-++||
T Consensus        46 ~~l~ekqkl~~~yGl~e--------~q~~~~~~~a~~~~------------------g~tg---~--------~ll~~Le   88 (201)
T 3bbn_D           46 IRLEEKQKLRFHYGITE--------RQLLKYVRIARKAK------------------GSTG---Q--------VLLQLLE   88 (201)
T ss_dssp             HHHTTHHHHHHHHTCCH--------HHHHHHHHHHHHSS------------------SCTT---T--------TTTHHHH
T ss_pred             HHHHHHHHHHHHhCChH--------HHHHHHHHHHHhcc------------------CCcH---H--------HHHHHHH
Confidence            56778888889999872        34455566666543                  3222   1        1338999


Q ss_pred             hhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992         104 RRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus       104 rRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      +|||++|+++||+.|..+|+|+|.||||
T Consensus        89 ~RLD~~L~r~g~a~SR~~ArqLI~~G~V  116 (201)
T 3bbn_D           89 MRLDNILFRLGMAPTIPGARQLVNHRHI  116 (201)
T ss_dssp             SBTTTTTTTTTSSSSSHHHHHHHHTTCE
T ss_pred             HHHHHHHHHcCCcCCHHHHHHHHhCCcE
Confidence            9999999999999999999999999997

>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif, ribosome; NMR {Geobacillus stearothermophilus} SCOP: d.66.1.2 PDB: 1c06_A 1eg0_A 1qd7_C

Probab=98.33  E-value=6.1e-07  Score=67.31  Aligned_cols=71  Identities=30%  Similarity=0.456  Sum_probs=56.3

Q ss_pred             hhhhHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHccccCcCccchhhhhhhhhhhHhh
Q psy7992          24 ARLDQELKIIGEYGLRNKREVWRVKYALAKIRKAARELLTLDEKEHRNALLRRLVRIGVLDESKMKLDYVWGLKIEDFLE  103 (131)
Q Consensus        24 ~r~~~E~~i~~~YgLknk~E~~ky~~l~~~iRk~ar~L~~l~~~d~~~~LL~kL~~~Gll~e~~~~L~~vl~ltv~~fle  103 (131)
                      .++.++.++...|||.        ++.+.++.+.|+++....                             +-++.++|+
T Consensus         8 ~~l~~kqk~~~~yg~~--------e~q~~~~~~~a~~~~g~~-----------------------------~~~~~~~le   50 (159)
T 1c05_A            8 LQLQEKQKLRHMYGVN--------ERQFRKTFEEAGKMPGKH-----------------------------GENFMILLE   50 (159)
T ss_dssp             HHHHHHHHHHHTTTCC--------HHHHHHHHHHHTTSSSTH-----------------------------HHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCC--------HHHHHHHHHHHHhccCCh-----------------------------hHHHHHHHH
Confidence            5788899999999998        345666666666544321                             112457899


Q ss_pred             hhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992         104 RRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus       104 rRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      .|||.++++.|++.|..+|+++|.||||
T Consensus        51 ~RLD~~L~~~g~~~SR~~ar~lI~~G~V   78 (159)
T 1c05_A           51 SRLDNLVYRLGLARTRRQARQLVTHGHI   78 (159)
T ss_dssp             HBHHHHHHHTTSCSSHHHHHHHHHTTCE
T ss_pred             HHHHHHHHHcCCcCCHHHHHHHHHCCCE
Confidence            9999999999999999999999999997

>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D* 1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D* 1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G 2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ...

Probab=97.79  E-value=4.4e-05  Score=59.57  Aligned_cols=33  Identities=45%  Similarity=0.697  Sum_probs=31.1

Q ss_pred             hhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992          99 EDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus        99 ~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      ...++.|||.++++.|++.|..+|+++|.||||
T Consensus        94 ~~~le~RLD~~L~~~g~~~SR~~arqLI~~G~V  126 (209)
T 2vqe_D           94 LGLLESRLDNVVYRLGFAVSRRQARQLVRHGHI  126 (209)
T ss_dssp             HHHHHTBHHHHHHHTTSSSSHHHHHHHHHTTCE
T ss_pred             HHhHHHHHHHHHHHhcCcCCHHHHHHHHHCCCE
Confidence            467889999999999999999999999999997

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

Probab=86.51  E-value=0.25  Score=39.49  Aligned_cols=34  Identities=18%  Similarity=0.271  Sum_probs=25.6

Q ss_pred             chhhhhhhhhhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992          89 KLDYVWGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus        89 ~L~~vl~ltv~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      +++.|+  ...-||+-       ++|+|.|.++|+|++.||||
T Consensus        38 ~~~~~l--PL~i~LRd-------rLgyA~t~rEar~Iv~~~~I   71 (243)
T 3j20_E           38 NMRTSI--PLLYIVRD-------YLGYAKTAREARKILNEGKF   71 (243)
T ss_dssp             CSTTCE--EHHHHHHT-------TSCCCSSHHHHHHHHHHCSC
T ss_pred             ccccce--eehhhhhh-------hhccccCHHHHHHHHHCCcE
Confidence            355553  33345554       57999999999999999997

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

Probab=83.61  E-value=0.11  Score=33.77  Aligned_cols=28  Identities=18%  Similarity=0.165  Sum_probs=25.4

Q ss_pred             hhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992         104 RRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus       104 rRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      .||+..+...|++.|..+|+.+|.+|.|
T Consensus        21 ~RLdk~L~~~g~~~SR~~a~~lI~~G~V   48 (79)
T 1p9k_A           21 VELCDLLKLEGWSESGAQAKIAIAEGQV   48 (79)
T ss_dssp             CCHHHHHHHHTSCSSSSTTSHHHHHHHH
T ss_pred             chHHHHHHHCCCCCCHHHHHHHHHCCEE
Confidence            5999999999999999999999998864

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	131
d2gy9d1	204	Ribosomal protein S4 {Escherichia coli [TaxId: 562	99.24
d1c06a_	159	Ribosomal protein S4 {Bacillus stearothermophilus	99.21
d2uubd1	208	Ribosomal protein S4 {Thermus thermophilus [TaxId:	99.13
d1vioa2	58	Pseudouridine synthase RsuA N-terminal domain {Hae	93.75
d1kska3	59	Pseudouridine synthase RsuA N-terminal domain {Esc	93.09
d1p9ka_	79	Hypothetical protein YbcJ {Escherichia coli [TaxId	90.72
d1h3fa2	81	Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain	83.27

>d2gy9d1 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Escherichia coli [TaxId: 562]

Probab=99.24  E-value=6e-12  Score=97.08  Aligned_cols=34  Identities=29%  Similarity=0.568  Sum_probs=32.4

Q ss_pred             hhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992          98 IEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus        98 v~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      .-.+||+|||+||||+|||.|+.+|||+|+||||
T Consensus        88 l~~~LE~RLDnvv~R~gfa~t~~~ARQ~v~Hghi  121 (204)
T d2gy9d1          88 LLALLEGRLDNVVYRMGFGATRAEARQLVSHKAI  121 (204)
T ss_dssp             HHHHHTTBHHHHHHHHTSSSSHHHHHHHHHTTCE
T ss_pred             HHHHHHHHHHHHHhhccccccHHHHHHHHHhcce
Confidence            4489999999999999999999999999999997

>d1c06a_ d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.21  E-value=3e-12  Score=95.48  Aligned_cols=34  Identities=41%  Similarity=0.663  Sum_probs=32.2

Q ss_pred             hhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992          98 IEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus        98 v~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      .-.+||+|||+||||+|||.|+.+|||+|+||||
T Consensus        45 ll~llE~RlD~vv~r~gfa~t~~~arQ~v~Hghi   78 (159)
T d1c06a_          45 FMILLESRLDNLVYRLGLARTRRQARQLVTHGHI   78 (159)
T ss_dssp             HHHHHHHCHHHHHHHHTSSSSHHHHHHHHHTSCE
T ss_pred             HHHHHHHHhhhhhccCcccCCHHHHHHHHHhcce
Confidence            3489999999999999999999999999999997

>d2uubd1 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Thermus thermophilus [TaxId: 274]

Probab=99.13  E-value=4.6e-12  Score=98.05  Aligned_cols=34  Identities=44%  Similarity=0.686  Sum_probs=32.3

Q ss_pred             hhhHhhhhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992          98 IEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus        98 v~~flerRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      .-.+||+|||+||||+|||.|+.+|||||+||||
T Consensus        92 ll~lLE~Rld~vv~r~g~a~t~~~ARQ~v~Hg~i  125 (208)
T d2uubd1          92 FLGLLESRLDNVVYRLGFAVSRRQARQLVRHGHI  125 (208)
T ss_dssp             HHHHHHTBHHHHHHHTTSSSSHHHHHHHHHTTCE
T ss_pred             HHHHHHHHHHHHHHhccccccHHHHHHHHHhcCe
Confidence            4489999999999999999999999999999997

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

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

Probab=93.75  E-value=0.011  Score=35.45  Aligned_cols=26  Identities=23%  Similarity=0.132  Sum_probs=24.3

Q ss_pred             hhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992         105 RLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus       105 RL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      ||+.++...+++ |..+|+++|.+|+|
T Consensus         3 RLD~~Ls~~~~~-SR~~a~~lI~~g~V   28 (58)
T d1vioa2           3 RLDKFIAENVGL-TRSQATKAIRQSAV   28 (58)
T ss_dssp             EHHHHHHHHHTC-CHHHHHHHHHTTCE
T ss_pred             HHHHHHHHcCCC-CHHHHHHHHHcCeE
Confidence            899999999988 99999999999986

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

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

Probab=93.09  E-value=0.016  Score=34.71  Aligned_cols=26  Identities=23%  Similarity=0.056  Sum_probs=24.3

Q ss_pred             hhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992         105 RLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus       105 RL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      ||+.++...+++ |..+|.++|.+|+|
T Consensus         2 RLdk~l~~~~~~-SR~~a~~lI~~g~V   27 (59)
T d1kska3           2 RLDKFIAQQLGV-SRAIAGREIRGNRV   27 (59)
T ss_dssp             EHHHHHHHHHTC-CHHHHHHHHHTTCE
T ss_pred             cHHHHHHHcCCC-CHHHHHHHHHcCcE
Confidence            899999999988 99999999999986

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

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

Probab=90.72  E-value=0.011  Score=37.82  Aligned_cols=28  Identities=18%  Similarity=0.165  Sum_probs=25.8

Q ss_pred             hhhhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992         104 RRLQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus       104 rRL~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      -||+-++...|++.|..+|.++|.+|+|
T Consensus        21 irL~k~L~~~gl~~Sr~eAk~lI~~G~V   48 (79)
T d1p9ka_          21 VELCDLLKLEGWSESGAQAKIAIAEGQV   48 (79)
T ss_dssp             CCHHHHHHHHTSCSSSSTTSHHHHHHHH
T ss_pred             EEHHHHHHHCCCccCHHHHHHHHHhCCc
Confidence            4889999999999999999999999875

>d1h3fa2 d.66.1.4 (A:352-432) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
domain: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=83.27  E-value=0.3  Score=30.57  Aligned_cols=26  Identities=31%  Similarity=0.327  Sum_probs=22.4

Q ss_pred             hhhhhhhcccCCCHHHHHhhhccCCC
Q psy7992         106 LQTQVFKLGLAKSIHHARVLIRQRHI  131 (131)
Q Consensus       106 L~~vv~r~~~a~si~~Arq~I~hgHI  131 (131)
                      |..++...|++.|-.+||.+|.+|-|
T Consensus        20 l~~ll~~~gl~~S~searRlI~~g~V   45 (81)
T d1h3fa2          20 VARLFTLAGLTPSNAEARRLIQNRGL   45 (81)
T ss_dssp             HHHHHHHTTSSSSHHHHHHHHHTTCE
T ss_pred             HHHHHHHcCCCcCHHHHHHHHHcCCE
Confidence            45567899999999999999999854