Psyllid ID: psy16455

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--
Protein Sequence
MHMKGPHYKKRPPRQPLLGKPFAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQLTPGK
Secondary Structure (PSIPRED)
cccccccccccccccccEEEEcccccEEEEEEccccccccccEEEEEEcccccccccccEEEEEEccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccEEEEccccccccEEEEcccEEEEEEEccccccccccEEEEEEccccccccccEEEEEEcccccccccccccccccc
Coil and Loop (DISEMBL)
mhmkgphykkrpprqpllgkpfakgkemvayipgeghnlqehNIVLckvgrvkdlpgvkikcvrgvydlphvvkktqltpgk
Flexible Loop (DISEMBL)
mhmkgphykkrpprqpllGKPFAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIkcvrgvydlphvvkktqltpgk
Low Complexity Region (SEG)
MHMKGPHYKKRPPRQPLLGKPFAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQLTPGK
Disordered region (IsUnstruct)
*************************KEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVK********
Disordered Region (DISOPRED)
*****************LGKPFAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPH***********
Disordered Region (DISEMBL)
***********PPRQPLLGKPFAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQLTPGK
Disordered Region (DISPRO)
****GPHYKKRPPRQPLLGKPFAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLP************
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MHMKGPHYKKRPPRQPLLGKPFAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQLTPGK
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	82	2.2.26 [Sep-21-2011]
P10735	140	40S ribosomal protein S12	yes	N/A	0.939	0.55	0.6	5e-27
Q29RU1	139	28S ribosomal protein S12	yes	N/A	0.658	0.388	0.629	3e-13
B0RB33	124	30S ribosomal protein S12	yes	N/A	0.682	0.451	0.589	6e-13
A5CUB9	124	30S ribosomal protein S12	yes	N/A	0.682	0.451	0.589	6e-13
C5CGR9	124	30S ribosomal protein S12	yes	N/A	0.682	0.451	0.571	6e-13
A0M5A2	124	30S ribosomal protein S12	yes	N/A	0.682	0.451	0.625	7e-13
Q6ACY7	124	30S ribosomal protein S12	yes	N/A	0.682	0.451	0.589	8e-13
O35680	139	28S ribosomal protein S12	yes	N/A	0.658	0.388	0.629	8e-13
A5FMY5	127	30S ribosomal protein S12	yes	N/A	0.682	0.440	0.607	9e-13
A6GZA3	127	30S ribosomal protein S12	yes	N/A	0.682	0.440	0.607	9e-13

>sp|P10735|RT12_DROME 40S ribosomal protein S12, mitochondrial OS=Drosophila melanogaster GN=tko PE=1 SV=1

 Score =  119 bits (298), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 63/105 (60%), Positives = 69/105 (65%), Gaps = 28/105 (26%)

Query: 1   MHMKGPHYKKRPPRQPLLGKPFAKG----------------------------KEMVAYI 32
           MH  GPH K RPPRQPL GKPFAKG                            KEMVAYI
Sbjct: 36  MHRSGPHIKTRPPRQPLDGKPFAKGVVLKTLIKKPKKPNSANRKCVLVRLSTGKEMVAYI 95

Query: 33  PGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
           PG GHNLQEHNIVLC+VGR++D+PGVK+K VRGVYDL HVVKK+Q
Sbjct: 96  PGIGHNLQEHNIVLCRVGRLQDVPGVKLKAVRGVYDLAHVVKKSQ 140

Drosophila melanogaster (taxid: 7227)

>sp|Q29RU1|RT12_BOVIN 28S ribosomal protein S12, mitochondrial OS=Bos taurus GN=MRPS12 PE=2 SV=1

 Score = 73.6 bits (179), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 34/54 (62%), Positives = 42/54 (77%)

Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKK 75
            + G+E V +IPGEGHNLQEH++VL + GR +DLPGVK+K VRG YD  HV KK
Sbjct: 85  LSTGREAVCFIPGEGHNLQEHHVVLVQGGRTQDLPGVKLKVVRGKYDCGHVQKK 138

Bos taurus (taxid: 9913)

>sp|B0RB33|RS12_CLAMS 30S ribosomal protein S12 OS=Clavibacter michiganensis subsp. sepedonicus (strain ATCC 33113 / JCM 9667) GN=rpsL PE=3 SV=1

 Score = 72.8 bits (177), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 33/56 (58%), Positives = 41/56 (73%)

Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
            + G+E+ AYIPGEGHNLQEH++VL + GRVKDLPGV+ K VRG  D   V  + Q
Sbjct: 57  LSNGQEVTAYIPGEGHNLQEHSMVLVRGGRVKDLPGVRYKIVRGALDTQAVKNRKQ 112

Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.

Clavibacter michiganensis subsp. sepedonicus (strain ATCC 33113 / JCM 9667) (taxid: 31964)

>sp|A5CUB9|RS12_CLAM3 30S ribosomal protein S12 OS=Clavibacter michiganensis subsp. michiganensis (strain NCPPB 382) GN=rpsL PE=3 SV=1

 Score = 72.8 bits (177), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 33/56 (58%), Positives = 41/56 (73%)

Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
            + G+E+ AYIPGEGHNLQEH++VL + GRVKDLPGV+ K VRG  D   V  + Q
Sbjct: 57  LSNGQEVTAYIPGEGHNLQEHSMVLVRGGRVKDLPGVRYKIVRGALDTQAVKNRKQ 112

Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.

Clavibacter michiganensis subsp. michiganensis (strain NCPPB 382) (taxid: 443906)

>sp|C5CGR9|RS12_KOSOT 30S ribosomal protein S12 OS=Kosmotoga olearia (strain TBF 19.5.1) GN=rpsL PE=3 SV=1

 Score = 72.8 bits (177), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 32/56 (57%), Positives = 40/56 (71%)

Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
            + G E+ AYIPGEGHNLQEH++VL + GRVKDLPGV+ K +RG  D   V  + Q
Sbjct: 57  LSNGTEVTAYIPGEGHNLQEHSVVLVRGGRVKDLPGVRYKIIRGALDAEGVANRRQ 112

Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.

Kosmotoga olearia (strain TBF 19.5.1) (taxid: 521045)

>sp|A0M5A2|RS12_GRAFK 30S ribosomal protein S12 OS=Gramella forsetii (strain KT0803) GN=rpsL PE=3 SV=1

 Score = 72.4 bits (176), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 35/56 (62%), Positives = 40/56 (71%)

Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
              GKE+ AYIPGEGHNLQEH+IVL + GRVKDLPGV+   VRG  D   V  +TQ
Sbjct: 57  LTNGKEVNAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYHIVRGALDTAGVEGRTQ 112

Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.

Gramella forsetii (strain KT0803) (taxid: 411154)

>sp|Q6ACY7|RS12_LEIXX 30S ribosomal protein S12 OS=Leifsonia xyli subsp. xyli (strain CTCB07) GN=rpsL PE=3 SV=1

 Score = 72.4 bits (176), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 33/56 (58%), Positives = 40/56 (71%)

Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
            + G E+ AYIPGEGHNLQEH++VL + GRVKDLPGV+ K VRG  D   V  + Q
Sbjct: 57  LSNGTEVTAYIPGEGHNLQEHSMVLVRGGRVKDLPGVRYKIVRGALDTQAVKNRKQ 112

Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.

Leifsonia xyli subsp. xyli (strain CTCB07) (taxid: 281090)

>sp|O35680|RT12_MOUSE 28S ribosomal protein S12, mitochondrial OS=Mus musculus GN=Mrps12 PE=2 SV=1

 Score = 72.4 bits (176), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 34/54 (62%), Positives = 41/54 (75%)

Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKK 75
            + GKE V +IPGEGH LQEH++VL + GR +DLPGVK+K VRG YD  HV KK
Sbjct: 85  LSTGKEAVCFIPGEGHTLQEHHVVLVEGGRTQDLPGVKLKVVRGKYDCGHVQKK 138

Mus musculus (taxid: 10090)

>sp|A5FMY5|RS12_FLAJ1 30S ribosomal protein S12 OS=Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / UW101) GN=rpsL PE=3 SV=1

 Score = 72.0 bits (175), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 34/56 (60%), Positives = 39/56 (69%)

Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
              G E+ AYIPGEGHNLQEH+IVL + GRVKDLPGV+   VRG  D   V  +TQ
Sbjct: 57  LTNGNEVNAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYHIVRGALDTSGVAGRTQ 112

Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.

Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / UW101) (taxid: 376686)

>sp|A6GZA3|RS12_FLAPJ 30S ribosomal protein S12 OS=Flavobacterium psychrophilum (strain JIP02/86 / ATCC 49511) GN=rpsL PE=3 SV=1

 Score = 72.0 bits (175), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 34/56 (60%), Positives = 39/56 (69%)

Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
              G E+ AYIPGEGHNLQEH+IVL + GRVKDLPGV+   VRG  D   V  +TQ
Sbjct: 57  LTNGNEVNAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYHIVRGALDTSGVAGRTQ 112

Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.

Flavobacterium psychrophilum (strain JIP02/86 / ATCC 49511) (taxid: 402612)

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	82
195060244	143	GH17581 [Drosophila grimshawi] gi|193896	0.939	0.538	0.6	7e-26
386763685	154	technical knockout, isoform C [Drosophil	0.939	0.5	0.6	1e-25
194913252	140	GG12613 [Drosophila erecta] gi|190648333	0.939	0.55	0.590	2e-25
17933526	140	technical knockout, isoform B [Drosophil	0.939	0.55	0.6	2e-25
125983242	140	GA20693 [Drosophila pseudoobscura pseudo	0.939	0.55	0.590	2e-25
6691839	140	technical knockout protein [Drosophila m	0.939	0.55	0.6	2e-25
195347956	140	GM18879 [Drosophila sechellia] gi|195564	0.939	0.55	0.590	3e-25
195397549	141	GJ17060 [Drosophila virilis] gi|19414715	0.939	0.546	0.6	4e-25
194768829	140	GF21950 [Drosophila ananassae] gi|190617	0.939	0.55	0.580	5e-25
195457094	111	GK17857 [Drosophila willistoni] gi|19417	0.939	0.693	0.6	5e-25

>gi|195060244|ref|XP_001995772.1| GH17581 [Drosophila grimshawi] gi|193896558|gb|EDV95424.1| GH17581 [Drosophila grimshawi]

 Score =  121 bits (303), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 63/105 (60%), Positives = 69/105 (65%), Gaps = 28/105 (26%)

Query: 1   MHMKGPHYKKRPPRQPLLGKPFAKG----------------------------KEMVAYI 32
           MH  GPH K RPPRQPL GKPFAKG                            KEMVAYI
Sbjct: 39  MHRTGPHIKTRPPRQPLDGKPFAKGVVLKTLIKKPKKPNSANRKCALVRLSTGKEMVAYI 98

Query: 33  PGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
           PG GHNLQEHNIVLC+VGR++D+PGVK+K VRGVYDL HV+KKTQ
Sbjct: 99  PGIGHNLQEHNIVLCRVGRLQDVPGVKLKAVRGVYDLAHVIKKTQ 143

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|386763685|ref|NP_001245490.1| technical knockout, isoform C [Drosophila melanogaster] gi|6594153|emb|CAB63528.1| EG:BACH59J11.1 [Drosophila melanogaster] gi|284793740|gb|ADB93360.1| MIP16231p [Drosophila melanogaster] gi|383293163|gb|AFH07204.1| technical knockout, isoform C [Drosophila melanogaster]

 Score =  120 bits (300), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 63/105 (60%), Positives = 69/105 (65%), Gaps = 28/105 (26%)

Query: 1   MHMKGPHYKKRPPRQPLLGKPFAKG----------------------------KEMVAYI 32
           MH  GPH K RPPRQPL GKPFAKG                            KEMVAYI
Sbjct: 50  MHRSGPHIKTRPPRQPLDGKPFAKGVVLKTLIKKPKKPNSANRKCVLVRLSTGKEMVAYI 109

Query: 33  PGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
           PG GHNLQEHNIVLC+VGR++D+PGVK+K VRGVYDL HVVKK+Q
Sbjct: 110 PGIGHNLQEHNIVLCRVGRLQDVPGVKLKAVRGVYDLAHVVKKSQ 154

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194913252|ref|XP_001982657.1| GG12613 [Drosophila erecta] gi|190648333|gb|EDV45626.1| GG12613 [Drosophila erecta]

 Score =  119 bits (298), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 62/105 (59%), Positives = 69/105 (65%), Gaps = 28/105 (26%)

Query: 1   MHMKGPHYKKRPPRQPLLGKPFAKG----------------------------KEMVAYI 32
           MH  GPH K RPPRQPL GKPFAKG                            KEMVAYI
Sbjct: 36  MHRSGPHVKTRPPRQPLDGKPFAKGVVLKTLIKKPKKPNSANRKCVLVRLSTGKEMVAYI 95

Query: 33  PGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
           PG GHNLQEHNIVLC+VGR++D+PGVK+K VRGVYDL HV+KK+Q
Sbjct: 96  PGIGHNLQEHNIVLCRVGRLQDVPGVKLKAVRGVYDLAHVIKKSQ 140

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|17933526|ref|NP_525050.1| technical knockout, isoform B [Drosophila melanogaster] gi|134053|sp|P10735.1|RT12_DROME RecName: Full=40S ribosomal protein S12, mitochondrial; Short=MRP-S12; Short=S12mt; AltName: Full=MT-RPS12; AltName: Full=Protein technical knockout locus; Flags: Precursor gi|158602|gb|AAA28935.1| tko gene product (pot.); putative [Drosophila melanogaster] gi|6691818|emb|CAB65841.1| EG:BACH59J11.1 [Drosophila melanogaster] gi|7290321|gb|AAF45781.1| technical knockout, isoform B [Drosophila melanogaster] gi|54650528|gb|AAV36843.1| RH56553p [Drosophila melanogaster]

 Score =  119 bits (298), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 63/105 (60%), Positives = 69/105 (65%), Gaps = 28/105 (26%)

Query: 1   MHMKGPHYKKRPPRQPLLGKPFAKG----------------------------KEMVAYI 32
           MH  GPH K RPPRQPL GKPFAKG                            KEMVAYI
Sbjct: 36  MHRSGPHIKTRPPRQPLDGKPFAKGVVLKTLIKKPKKPNSANRKCVLVRLSTGKEMVAYI 95

Query: 33  PGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
           PG GHNLQEHNIVLC+VGR++D+PGVK+K VRGVYDL HVVKK+Q
Sbjct: 96  PGIGHNLQEHNIVLCRVGRLQDVPGVKLKAVRGVYDLAHVVKKSQ 140

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|125983242|ref|XP_001355386.1| GA20693 [Drosophila pseudoobscura pseudoobscura] gi|54643701|gb|EAL32444.1| GA20693 [Drosophila pseudoobscura pseudoobscura]

 Score =  119 bits (298), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 62/105 (59%), Positives = 69/105 (65%), Gaps = 28/105 (26%)

Query: 1   MHMKGPHYKKRPPRQPLLGKPFAKG----------------------------KEMVAYI 32
           MH  GPH K RPPRQPL GKPFAKG                            KEMVAYI
Sbjct: 36  MHRTGPHIKTRPPRQPLDGKPFAKGVVLKTLIKKPKKPNSANRKCVLVRLSTGKEMVAYI 95

Query: 33  PGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
           PG GHNLQEHNIVLC+VGR++D+PGVK+K VRGVYDL HV+KK+Q
Sbjct: 96  PGIGHNLQEHNIVLCRVGRLQDVPGVKLKAVRGVYDLAHVIKKSQ 140

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|6691839|emb|CAB65721.1| technical knockout protein [Drosophila melanogaster]

 Score =  119 bits (298), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 63/105 (60%), Positives = 69/105 (65%), Gaps = 28/105 (26%)

Query: 1   MHMKGPHYKKRPPRQPLLGKPFAKG----------------------------KEMVAYI 32
           MH  GPH K RPPRQPL GKPFAKG                            KEMVAYI
Sbjct: 36  MHRSGPHIKTRPPRQPLDGKPFAKGVVLKTLIKKPKKPNSANRKCVLVRHSTGKEMVAYI 95

Query: 33  PGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
           PG GHNLQEHNIVLC+VGR++D+PGVK+K VRGVYDL HVVKK+Q
Sbjct: 96  PGIGHNLQEHNIVLCRVGRLQDVPGVKLKAVRGVYDLAHVVKKSQ 140

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195347956|ref|XP_002040517.1| GM18879 [Drosophila sechellia] gi|195564791|ref|XP_002105996.1| GD16364 [Drosophila simulans] gi|194121945|gb|EDW43988.1| GM18879 [Drosophila sechellia] gi|194203362|gb|EDX16938.1| GD16364 [Drosophila simulans]

 Score =  119 bits (297), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 62/105 (59%), Positives = 69/105 (65%), Gaps = 28/105 (26%)

Query: 1   MHMKGPHYKKRPPRQPLLGKPFAKG----------------------------KEMVAYI 32
           MH  GPH K RPPRQPL GKPFAKG                            KEMVAYI
Sbjct: 36  MHRSGPHIKTRPPRQPLDGKPFAKGVVLKTLIKKPKKPNSANRKCVLVRLSTGKEMVAYI 95

Query: 33  PGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
           PG GHNLQEHNIVLC+VGR++D+PGVK+K VRGVYDL HV+KK+Q
Sbjct: 96  PGIGHNLQEHNIVLCRVGRLQDVPGVKLKAVRGVYDLAHVIKKSQ 140

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195397549|ref|XP_002057391.1| GJ17060 [Drosophila virilis] gi|194147158|gb|EDW62877.1| GJ17060 [Drosophila virilis]

 Score =  118 bits (296), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 63/105 (60%), Positives = 69/105 (65%), Gaps = 28/105 (26%)

Query: 1   MHMKGPHYKKRPPRQPLLGKPFAKG----------------------------KEMVAYI 32
           MH  GPH KKRPPRQPL GKPFAKG                            KEMVAYI
Sbjct: 37  MHRTGPHIKKRPPRQPLDGKPFAKGVVLKTLIKKPKKPNSANRKCALVRLSTGKEMVAYI 96

Query: 33  PGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
           PG GHNLQEHNIVLC+VGR++D+PGVK+K VRGVYDL HV+KK Q
Sbjct: 97  PGIGHNLQEHNIVLCRVGRLQDVPGVKLKAVRGVYDLAHVIKKGQ 141

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194768829|ref|XP_001966514.1| GF21950 [Drosophila ananassae] gi|190617278|gb|EDV32802.1| GF21950 [Drosophila ananassae]

 Score =  118 bits (295), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 61/105 (58%), Positives = 69/105 (65%), Gaps = 28/105 (26%)

Query: 1   MHMKGPHYKKRPPRQPLLGKPFAKG----------------------------KEMVAYI 32
           MH  GPH K RPPRQPL GKPFAKG                            KEMVAY+
Sbjct: 36  MHRTGPHIKTRPPRQPLDGKPFAKGVVLKTFIKKPKKPNSANRKCVLVRLSTGKEMVAYV 95

Query: 33  PGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
           PG GHNLQEHNIVLC+VGR++D+PGVK+K VRGVYDL HV+KK+Q
Sbjct: 96  PGIGHNLQEHNIVLCRVGRLQDVPGVKLKAVRGVYDLAHVIKKSQ 140

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195457094|ref|XP_002075423.1| GK17857 [Drosophila willistoni] gi|194171508|gb|EDW86409.1| GK17857 [Drosophila willistoni]

 Score =  118 bits (295), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 63/105 (60%), Positives = 69/105 (65%), Gaps = 28/105 (26%)

Query: 1   MHMKGPHYKKRPPRQPLLGKPFAKG----------------------------KEMVAYI 32
           MH  GPH KKRPPRQPL GKPFAKG                            KEMVAYI
Sbjct: 7   MHRSGPHIKKRPPRQPLDGKPFAKGVVLKTLIKKPKKPNSANRKCVLVRLSTGKEMVAYI 66

Query: 33  PGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
           PG GHNLQEHNIVLC+VGR++D+PGVK+K VRGVYDL HV+KKT 
Sbjct: 67  PGIGHNLQEHNIVLCRVGRLQDVPGVKLKAVRGVYDLAHVIKKTN 111

Source: Drosophila willistoni

Species: Drosophila willistoni

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	82
FB|FBgn0003714	140	tko "technical knockout" [Dros	0.902	0.528	0.64	1.7e-20
UNIPROTKB|O15235	138	MRPS12 "28S ribosomal protein	0.621	0.369	0.647	1.4e-17
UNIPROTKB|H9L236	110	MRPS12 "Uncharacterized protei	0.646	0.481	0.603	2.9e-17
ZFIN|ZDB-GENE-091204-48	143	si:dkey-17e16.10 "si:dkey-17e1	0.670	0.384	0.654	7.7e-16
UNIPROTKB|Q29RU1	139	MRPS12 "28S ribosomal protein	0.621	0.366	0.666	1.8e-14
MGI|MGI:1346333	139	Mrps12 "mitochondrial ribosoma	0.621	0.366	0.666	3.8e-14
RGD|1306221	139	Mrps12 "mitochondrial ribosoma	0.621	0.366	0.666	3.8e-14
UNIPROTKB|E2RE10	139	MRPS12 "Uncharacterized protei	0.621	0.366	0.627	2.7e-13
TIGR_CMR|NSE_0689	122	NSE_0689 "ribosomal protein S1	0.536	0.360	0.681	1.2e-12
TIGR_CMR|CJE_0540	128	CJE_0540 "ribosomal protein S1	0.634	0.406	0.634	1.5e-12

FB|FBgn0003714 tko "technical knockout" [Drosophila melanogaster (taxid:7227)]

 Score = 242 (90.2 bits), Expect = 1.7e-20, P = 1.7e-20
 Identities = 48/75 (64%), Positives = 59/75 (78%)

Query:     3 MKGPHYKKRPPRQPLLGKPFAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKC 62
             +K P       R+ +L +  + GKEMVAYIPG GHNLQEHNIVLC+VGR++D+PGVK+K 
Sbjct:    67 IKKPKKPNSANRKCVLVR-LSTGKEMVAYIPGIGHNLQEHNIVLCRVGRLQDVPGVKLKA 125

Query:    63 VRGVYDLPHVVKKTQ 77
             VRGVYDL HVVKK+Q
Sbjct:   126 VRGVYDLAHVVKKSQ 140

GO:0007638 "mechanosensory behavior" evidence=IMP

GO:0009612 "response to mechanical stimulus" evidence=IMP

GO:0006412 "translation" evidence=ISS

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

GO:0005763 "mitochondrial small ribosomal subunit" evidence=ISS

GO:0007605 "sensory perception of sound" evidence=IMP

GO:0008049 "male courtship behavior" evidence=IMP

GO:0007619 "courtship behavior" evidence=TAS

GO:0001666 "response to hypoxia" evidence=IDA

UNIPROTKB|O15235 MRPS12 "28S ribosomal protein S12, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 173 (66.0 bits), Expect = 1.4e-17, Sum P(2) = 1.4e-17
 Identities = 33/51 (64%), Positives = 38/51 (74%)

Query:    25 GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKK 75
             G+E V +IPGEGH LQEH IVL + GR +DLPGVK+  VRG YD  HV KK
Sbjct:    88 GREAVCFIPGEGHTLQEHQIVLVEGGRTQDLPGVKLTVVRGKYDCGHVQKK 138

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

GO:0006412 "translation" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0005761 "mitochondrial ribosome" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|H9L236 MRPS12 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 182 (69.1 bits), Expect = 2.9e-17, Sum P(2) = 2.9e-17
 Identities = 32/53 (60%), Positives = 42/53 (79%)

Query:    23 AKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKK 75
             + G+E+V ++PGEGHNLQEH++VL + GR +DLPGVK+  VRG YD  HV KK
Sbjct:    57 SNGREVVCFVPGEGHNLQEHHVVLVQGGRTQDLPGVKLTVVRGKYDCAHVQKK 109

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

GO:0006412 "translation" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

ZFIN|ZDB-GENE-091204-48 si:dkey-17e16.10 "si:dkey-17e16.10" [Danio rerio (taxid:7955)]

 Score = 198 (74.8 bits), Expect = 7.7e-16, P = 7.7e-16
 Identities = 36/55 (65%), Positives = 43/55 (78%)

Query:    23 AKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
             + G+E V YIPGEGHNLQEHN+VL + GR +DLPGVK+  +RG YD  HVVKK Q
Sbjct:    89 SNGQEAVVYIPGEGHNLQEHNVVLVQGGRTQDLPGVKLAVIRGKYDCAHVVKKKQ 143

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

GO:0005840 "ribosome" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

UNIPROTKB|Q29RU1 MRPS12 "28S ribosomal protein S12, mitochondrial" [Bos taurus (taxid:9913)]

 Score = 185 (70.2 bits), Expect = 1.8e-14, P = 1.8e-14
 Identities = 34/51 (66%), Positives = 41/51 (80%)

Query:    25 GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKK 75
             G+E V +IPGEGHNLQEH++VL + GR +DLPGVK+K VRG YD  HV KK
Sbjct:    88 GREAVCFIPGEGHNLQEHHVVLVQGGRTQDLPGVKLKVVRGKYDCGHVQKK 138

GO:0005739 "mitochondrion" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

MGI|MGI:1346333 Mrps12 "mitochondrial ribosomal protein S12" [Mus musculus (taxid:10090)]

 Score = 182 (69.1 bits), Expect = 3.8e-14, P = 3.8e-14
 Identities = 34/51 (66%), Positives = 40/51 (78%)

Query:    25 GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKK 75
             GKE V +IPGEGH LQEH++VL + GR +DLPGVK+K VRG YD  HV KK
Sbjct:    88 GKEAVCFIPGEGHTLQEHHVVLVEGGRTQDLPGVKLKVVRGKYDCGHVQKK 138

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

GO:0005622 "intracellular" evidence=IEA

GO:0005739 "mitochondrion" evidence=IDA

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

RGD|1306221 Mrps12 "mitochondrial ribosomal protein S12" [Rattus norvegicus (taxid:10116)]

 Score = 182 (69.1 bits), Expect = 3.8e-14, P = 3.8e-14
 Identities = 34/51 (66%), Positives = 40/51 (78%)

Query:    25 GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKK 75
             GKE V +IPGEGH LQEH++VL + GR +DLPGVK+K VRG YD  HV KK
Sbjct:    88 GKEAVCFIPGEGHTLQEHHVVLVEGGRTQDLPGVKLKVVRGKYDCGHVQKK 138

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

GO:0005739 "mitochondrion" evidence=IEA;ISO

GO:0006412 "translation" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

UNIPROTKB|E2RE10 MRPS12 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 174 (66.3 bits), Expect = 2.7e-13, P = 2.7e-13
 Identities = 32/51 (62%), Positives = 40/51 (78%)

Query:    25 GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKK 75
             G+E V +IPGEGH+LQEH++VL + GR +DLPGVK+  VRG YD  HV KK
Sbjct:    88 GREAVCFIPGEGHSLQEHHVVLVQGGRTQDLPGVKLTVVRGKYDCGHVQKK 138

GO:0005739 "mitochondrion" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

TIGR_CMR|NSE_0689 NSE_0689 "ribosomal protein S12" [Neorickettsia sennetsu str. Miyayama (taxid:222891)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 30/44 (68%), Positives = 37/44 (84%)

Query:    25 GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYD 68
             G E++AYIPGEGHNLQEH++V  + GRVKDLPGV+   VRGV+D
Sbjct:    60 GAEVIAYIPGEGHNLQEHSVVCIRGGRVKDLPGVRYHIVRGVFD 103

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

GO:0006412 "translation" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

TIGR_CMR|CJE_0540 CJE_0540 "ribosomal protein S12" [Campylobacter jejuni RM1221 (taxid:195099)]

 Score = 167 (63.8 bits), Expect = 1.5e-12, P = 1.5e-12
 Identities = 33/52 (63%), Positives = 39/52 (75%)

Query:    25 GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKT 76
             G E+++YI GEGHNLQEH+IVL + GRVKDLPGVK   VRG  D   V K+T
Sbjct:    60 GFEVISYIGGEGHNLQEHSIVLVRGGRVKDLPGVKYHIVRGALDTAGVAKRT 111

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

GO:0006412 "translation" evidence=ISS

GO:0006450 "regulation of translational fidelity" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
B3PMF1	RS12_MYCA5	No assigned EC number	0.5714	0.6829	0.4057	yes	N/A
B2RLZ6	RS12_PORG3	No assigned EC number	0.6071	0.6829	0.4179	yes	N/A
C5CC69	RS12_MICLC	No assigned EC number	0.6415	0.6463	0.4274	yes	N/A
O70089	RS12_AQUAE	No assigned EC number	0.5892	0.6829	0.4375	yes	N/A
A6GZA3	RS12_FLAPJ	No assigned EC number	0.6071	0.6829	0.4409	yes	N/A
Q7MTK9	RS12_PORGI	No assigned EC number	0.6071	0.6829	0.4179	yes	N/A
P10735	RT12_DROME	No assigned EC number	0.6	0.9390	0.55	yes	N/A
P0A4A3	RS12_STRCO	No assigned EC number	0.5892	0.6829	0.4552	yes	N/A
Q83HC7	RS12_TROW8	No assigned EC number	0.5892	0.6829	0.4516	yes	N/A
A5FMY5	RS12_FLAJ1	No assigned EC number	0.6071	0.6829	0.4409	yes	N/A
P0A4A4	RS12_STRAW	No assigned EC number	0.5892	0.6829	0.4552	yes	N/A
A5CUB9	RS12_CLAM3	No assigned EC number	0.5892	0.6829	0.4516	yes	N/A
B4U739	RS12_HYDS0	No assigned EC number	0.5714	0.6829	0.4148	yes	N/A
Q83FN9	RS12_TROWT	No assigned EC number	0.5892	0.6829	0.4516	yes	N/A
Q6KHS3	RS12_MYCMO	No assigned EC number	0.5535	0.6829	0.4028	yes	N/A
O35680	RT12_MOUSE	No assigned EC number	0.6296	0.6585	0.3884	yes	N/A
Q2S3R9	RS12_SALRD	No assigned EC number	0.6071	0.6829	0.4516	yes	N/A
A7NR68	RS12_ROSCS	No assigned EC number	0.5714	0.6829	0.3888	yes	N/A
O15235	RT12_HUMAN	No assigned EC number	0.6111	0.6585	0.3913	yes	N/A
Q5SHN3	RS12_THET8	No assigned EC number	0.6470	0.6219	0.3863	yes	N/A
B0RB33	RS12_CLAMS	No assigned EC number	0.5892	0.6829	0.4516	yes	N/A
Q8EX21	RS12_MYCPE	No assigned EC number	0.5666	0.7317	0.4285	yes	N/A
A6LEJ5	RS12_PARD8	No assigned EC number	0.6071	0.6829	0.4117	yes	N/A
A5USJ4	RS12_ROSS1	No assigned EC number	0.5714	0.6829	0.3888	yes	N/A
Q8RIL9	RS12_FUSNN	No assigned EC number	0.5714	0.6829	0.4590	yes	N/A
A9H3R9	RS12_GLUDA	No assigned EC number	0.5714	0.6829	0.4552	yes	N/A
B3E073	RS12_METI4	No assigned EC number	0.6153	0.6341	0.3687	yes	N/A
Q29RU1	RT12_BOVIN	No assigned EC number	0.6296	0.6585	0.3884	yes	N/A
Q6ACY7	RS12_LEIXX	No assigned EC number	0.5892	0.6829	0.4516	yes	N/A
A4FPN0	RS12_SACEN	No assigned EC number	0.5892	0.6829	0.4516	yes	N/A
B1W419	RS12_STRGG	No assigned EC number	0.5892	0.6829	0.4552	yes	N/A
A5FZW9	RS12_ACICJ	No assigned EC number	0.5714	0.6829	0.4552	yes	N/A
A6KYJ9	RS12_BACV8	No assigned EC number	0.5892	0.6829	0.4087	yes	N/A
C5CGR9	RS12_KOSOT	No assigned EC number	0.5714	0.6829	0.4516	yes	N/A
Q2SSX1	RS12_MYCCT	No assigned EC number	0.5714	0.6829	0.4028	yes	N/A
Q5RB32	RT12_PONAB	No assigned EC number	0.6111	0.6585	0.3884	yes	N/A
P17293	RS12_THETH	No assigned EC number	0.6470	0.6219	0.3863	yes	N/A
A9KRZ1	RS12_CLOPH	No assigned EC number	0.5535	0.6829	0.4	yes	N/A
Q8VMU2	RS12_MYCMS	No assigned EC number	0.5714	0.6829	0.4028	yes	N/A
A0M5A2	RS12_GRAFK	No assigned EC number	0.625	0.6829	0.4516	yes	N/A
P61941	RS12_THET2	No assigned EC number	0.6470	0.6219	0.3863	yes	N/A
Q7NAV1	RS12_MYCGA	No assigned EC number	0.5892	0.6829	0.3971	yes	N/A
Q0BUQ4	RS12_GRABC	No assigned EC number	0.5714	0.6829	0.4552	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	82
cd03368	108	cd03368, Ribosomal_S12, S12-like family, 30S ribos	1e-26
PRK05163	124	PRK05163, rpsL, 30S ribosomal protein S12; Validat	4e-20
TIGR00981	124	TIGR00981, rpsL_bact, ribosomal protein S12, bacte	1e-17
CHL00051	123	CHL00051, rps12, ribosomal protein S12	5e-17
COG0048	129	COG0048, RpsL, Ribosomal protein S12 [Translation,	8e-17
pfam00164	122	pfam00164, Ribosomal_S12, Ribosomal protein S12	1e-15
PTZ00115	290	PTZ00115, PTZ00115, 40S ribosomal protein S12; Pro	9e-13
cd00319	95	cd00319, Ribosomal_S12_like, Ribosomal protein S12	2e-06

>gnl|CDD|239466 cd03368, Ribosomal_S12, S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit interactions

 Score = 93.0 bits (232), Expect = 1e-26
 Identities = 43/104 (41%), Positives = 52/104 (50%), Gaps = 29/104 (27%)

Query: 1   MHMKGPHYKKRPPRQP-LLGKPFAKG----------------------------KEMVAY 31
           +  KG   KK+  + P L G P  KG                            KE+ AY
Sbjct: 5   LIRKGRKKKKKKSKSPALEGCPQKKGVCLKVYTTTPKKPNSALRKVARVRLSNGKEVTAY 64

Query: 32  IPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKK 75
           IPGEGHNLQEH++VL + GRVKDLPGV+   VRGV DL  V  +
Sbjct: 65  IPGEGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGVLDLAGVKNR 108

S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. Antibiotics such as streptomycin bind S12 and cause the ribosome to misread the genetic code. Length = 108

>gnl|CDD|235355 PRK05163, rpsL, 30S ribosomal protein S12; Validated

 Score = 76.9 bits (190), Expect = 4e-20
 Identities = 32/53 (60%), Positives = 38/53 (71%)

Query: 25  GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
           G E+ AYIPGEGHNLQEH++VL + GRVKDLPGV+   VRG  D   V  + Q
Sbjct: 60  GFEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGVKDRKQ 112

Length = 124

>gnl|CDD|130054 TIGR00981, rpsL_bact, ribosomal protein S12, bacterial/organelle

 Score = 71.0 bits (174), Expect = 1e-17
 Identities = 32/53 (60%), Positives = 38/53 (71%)

Query: 25  GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
           G E+ AYIPGEGHNLQEH++VL + GRVKDLPGV+   VRG  D   V  + Q
Sbjct: 60  GFEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGVKNRKQ 112

This model recognizes ribosomal protein S12 of Bacteria, mitochondria, and chloroplasts. The homologous ribosomal proteins of Archaea and Eukarya, termed S23 in Eukarya and S12 or S23 in Archaea, score below the trusted cutoff [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 124

>gnl|CDD|176992 CHL00051, rps12, ribosomal protein S12

 Score = 69.3 bits (170), Expect = 5e-17
 Identities = 29/44 (65%), Positives = 34/44 (77%)

Query: 25  GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYD 68
           G E+ AYIPG GHNLQEH++VL + GRVKDLPGV+   VRG  D
Sbjct: 60  GFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGTLD 103

Length = 123

>gnl|CDD|223126 COG0048, RpsL, Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]

 Score = 68.8 bits (169), Expect = 8e-17
 Identities = 34/53 (64%), Positives = 40/53 (75%)

Query: 25  GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
           GKE+ AYIPGEGHNLQEH+ VL + GRVKDLPGV+ K VRG  D   V+ + Q
Sbjct: 66  GKEVTAYIPGEGHNLQEHSEVLIRGGRVKDLPGVRYKVVRGALDSLGVLDRGQ 118

Length = 129

>gnl|CDD|201049 pfam00164, Ribosomal_S12, Ribosomal protein S12

 Score = 65.4 bits (160), Expect = 1e-15
 Identities = 33/53 (62%), Positives = 40/53 (75%)

Query: 25  GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
           GKE+ AYIPG+GHNLQEH+ VL + GRVKDLPGV+ K VRG  D+  V  + Q
Sbjct: 59  GKEVTAYIPGDGHNLQEHSEVLIRGGRVKDLPGVRYKVVRGALDVAGVSDRKQ 111

Length = 122

>gnl|CDD|240276 PTZ00115, PTZ00115, 40S ribosomal protein S12; Provisional

 Score = 61.0 bits (148), Expect = 9e-13
 Identities = 26/45 (57%), Positives = 32/45 (71%)

Query: 25  GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDL 69
           G+ +  YIPG GHNL  H++VL + GR KD+PG   K VRGVYDL
Sbjct: 156 GRTVTVYIPGIGHNLNTHSVVLVRGGRCKDVPGCNYKAVRGVYDL 200

Length = 290

>gnl|CDD|238196 cd00319, Ribosomal_S12_like, Ribosomal protein S12-like family; composed of prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins

 Score = 41.6 bits (97), Expect = 2e-06
 Identities = 30/42 (71%), Positives = 35/42 (83%)

Query: 25 GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGV 66
          G E+ AYIPGEGHNLQEH++VL + GRVKDLPGV+   VRGV
Sbjct: 45 GYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGV 86

S12 and S23 are located at the interface of the large and small ribosomal subunits, adjacent to the decoding center. They play an important role in translocation during the peptide elongation step of protein synthesis. They are also involved in important RNA and protein interactions. Ribosomal protein S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. S23 interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes translocation. Mutations in S12 and S23 have been found to affect translational accuracy. Antibiotics such as streptomycin may also bind S12/S23 and cause the ribosome to misread the genetic code. Length = 95

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	82
CHL00051	123	rps12 ribosomal protein S12	100.0
PRK05163	124	rpsL 30S ribosomal protein S12; Validated	100.0
TIGR00981	124	rpsL_bact ribosomal protein S12, bacterial/organel	100.0
cd03368	108	Ribosomal_S12 S12-like family, 30S ribosomal prote	100.0
PF00164	122	Ribosom_S12_S23: Ribosomal protein S12/S23; InterP	100.0
cd00319	95	Ribosomal_S12_like Ribosomal protein S12-like fami	100.0
PTZ00115	290	40S ribosomal protein S12; Provisional	100.0
COG0048	129	RpsL Ribosomal protein S12 [Translation, ribosomal	99.98
KOG1750|consensus	139		99.96
cd03367	115	Ribosomal_S23 S12-like family, 40S ribosomal prote	99.92
TIGR00982	139	S23_S12_E_A ribosomal protein S23 (S12). This mode	99.91
PTZ00067	143	40S ribosomal S23; Provisional	99.9
PRK04211	145	rps12P 30S ribosomal protein S12P; Reviewed	99.9
KOG1749|consensus	143		99.38

>CHL00051 rps12 ribosomal protein S12

Probab=100.00  E-value=7.2e-38  Score=219.54  Aligned_cols=79  Identities=43%  Similarity=0.648  Sum_probs=69.9

Q ss_pred             CCCCCCCCCC-CCCCCCCCCCCccC----------------------------CCEEEEEecCCCCCCCcccEEEEecCC
Q psy16455          1 MHMKGPHYKK-RPPRQPLLGKPFAK----------------------------GKEMVAYIPGEGHNLQEHNIVLCKVGR   51 (82)
Q Consensus         1 l~~~g~~~~~-~~~~~~L~~~Pq~k----------------------------gk~v~AyIPG~Ghnlqehs~VLVrGGr   51 (82)
                      |.+.++.++. +.++++|++|||+|                            |++||||||||||||||||+|||||||
T Consensus         7 l~~~~r~~k~~~~k~~~L~g~Pq~kGv~lkv~~~~pKKPNSA~RKvarVrLsngk~v~AyIPGeGhnlqehs~VLvrGGr   86 (123)
T CHL00051          7 LIRNTRQPIRNKTKSPALRGCPQRRGTCTRVYTITPKKPNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVLVRGGR   86 (123)
T ss_pred             hhhcCCCCccccccCcccccCcccCeEEEEEEeccccCCChhheeEEEEEccCCCEEEEEcCCCCccccccCEEEEeCCc
Confidence            3455554443 34557999999999                            999999999999999999999999999


Q ss_pred             cCCCCCceEEEeeeecCCcccccccccC
Q psy16455         52 VKDLPGVKIKCVRGVYDLPHVVKKTQLT   79 (82)
Q Consensus        52 ~~DLPGVkykvVrG~~D~~~v~~R~~~~   79 (82)
                      ++|||||+|++|||+|||++|.+|+++.
T Consensus        87 v~DlPGVrykvVRG~~D~~gv~~R~~~R  114 (123)
T CHL00051         87 VKDLPGVRYHIVRGTLDAVGVKDRQQGR  114 (123)
T ss_pred             cCCCCCeeEEEEeeeecccccccccccc
Confidence            9999999999999999999999998874

>PRK05163 rpsL 30S ribosomal protein S12; Validated

Probab=100.00  E-value=1.2e-37  Score=218.60  Aligned_cols=79  Identities=47%  Similarity=0.694  Sum_probs=70.3

Q ss_pred             CCCCCCCCCCCC-CCCCCCCCCccC----------------------------CCEEEEEecCCCCCCCcccEEEEecCC
Q psy16455          1 MHMKGPHYKKRP-PRQPLLGKPFAK----------------------------GKEMVAYIPGEGHNLQEHNIVLCKVGR   51 (82)
Q Consensus         1 l~~~g~~~~~~~-~~~~L~~~Pq~k----------------------------gk~v~AyIPG~Ghnlqehs~VLVrGGr   51 (82)
                      |++.+++++.++ ++++|++|||++                            |++||||||||||||||||+||||||+
T Consensus         7 l~~~~r~~k~~~~k~~~l~~~Pq~kGv~l~v~~~~pKKPNSA~RKvarVrL~ngk~v~AyIPGeGhnlqehs~VLvrGGr   86 (124)
T PRK05163          7 LVRKGRKSKVKKSKSPALNACPQKRGVCTRVYTTTPKKPNSALRKVARVRLTNGFEVTAYIPGEGHNLQEHSVVLIRGGR   86 (124)
T ss_pred             HhhcCCCCCcccccCcccccCcccCcEEEEEEecCccCCCchhheEEEEEeCCCCEEEEEcCCCCCCccccCEEEEeCCc
Confidence            345665555444 456899999999                            999999999999999999999999999


Q ss_pred             cCCCCCceEEEeeeecCCcccccccccC
Q psy16455         52 VKDLPGVKIKCVRGVYDLPHVVKKTQLT   79 (82)
Q Consensus        52 ~~DLPGVkykvVrG~~D~~~v~~R~~~~   79 (82)
                      ++|||||+|++|||+|||++|.+|+++.
T Consensus        87 v~DlPGVrykvVrG~~D~~gv~~R~~~R  114 (124)
T PRK05163         87 VKDLPGVRYHIVRGALDTAGVKDRKQGR  114 (124)
T ss_pred             cCCCCCcEEEEeeeeecccccccccccc
Confidence            9999999999999999999999998874

>TIGR00981 rpsL_bact ribosomal protein S12, bacterial/organelle

Probab=100.00  E-value=1.5e-37  Score=218.09  Aligned_cols=79  Identities=48%  Similarity=0.715  Sum_probs=70.5

Q ss_pred             CCCCCCCCCCCC-CCCCCCCCCccC----------------------------CCEEEEEecCCCCCCCcccEEEEecCC
Q psy16455          1 MHMKGPHYKKRP-PRQPLLGKPFAK----------------------------GKEMVAYIPGEGHNLQEHNIVLCKVGR   51 (82)
Q Consensus         1 l~~~g~~~~~~~-~~~~L~~~Pq~k----------------------------gk~v~AyIPG~Ghnlqehs~VLVrGGr   51 (82)
                      |++.+++++.++ ++++|++|||++                            |++||||||||||||||||+||||||+
T Consensus         7 l~~~~r~kk~~~~k~~~l~g~Pq~kGi~l~~~~~~pKKPNSA~RKvarVrL~ngk~v~AyIPG~Ghnlqehs~VLvrGGr   86 (124)
T TIGR00981         7 LIRKGRKKKKKKSKSPALEACPQKRGVCTRVYTTTPKKPNSALRKVARVRLTNGFEVTAYIPGEGHNLQEHSVVLIRGGR   86 (124)
T ss_pred             hhhcCCCCccccccCcccccCCccCcEEEEEEeccccCCCchhheeEEEEeCCCCEEEEEcCCCCCCccccCEEEEeCCc
Confidence            345666555444 457899999999                            999999999999999999999999999


Q ss_pred             cCCCCCceEEEeeeecCCcccccccccC
Q psy16455         52 VKDLPGVKIKCVRGVYDLPHVVKKTQLT   79 (82)
Q Consensus        52 ~~DLPGVkykvVrG~~D~~~v~~R~~~~   79 (82)
                      ++|||||+|++|||+|||++|.+|+++.
T Consensus        87 v~DlPGVkykvVrG~~D~~gv~~R~~~R  114 (124)
T TIGR00981        87 VKDLPGVRYHIVRGALDTAGVKNRKQGR  114 (124)
T ss_pred             cCCCCCeEEEEEeEeecccccccccccc
Confidence            9999999999999999999999998874

This model recognizes ribosomal protein S12 of Bacteria, mitochondria, and chloroplasts. The homologous ribosomal proteins of Archaea and Eukarya, termed S23 in Eukarya and S12 or S23 in Archaea, score below the trusted cutoff.

>cd03368 Ribosomal_S12 S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit interactions

Probab=100.00  E-value=1.9e-37  Score=213.46  Aligned_cols=75  Identities=56%  Similarity=0.862  Sum_probs=66.3

Q ss_pred             CCCCCCCCCCCC-CCCCCCCCCccC----------------------------CCEEEEEecCCCCCCCcccEEEEecCC
Q psy16455          1 MHMKGPHYKKRP-PRQPLLGKPFAK----------------------------GKEMVAYIPGEGHNLQEHNIVLCKVGR   51 (82)
Q Consensus         1 l~~~g~~~~~~~-~~~~L~~~Pq~k----------------------------gk~v~AyIPG~Ghnlqehs~VLVrGGr   51 (82)
                      |.++++++++++ ++++|++|||+|                            |++|+||||||||||||||+|||||||
T Consensus         5 l~~~~r~~k~~~~k~~~l~g~Pq~kGi~l~v~~~~pKKPNSA~RKvarV~L~ngk~v~AyIPG~Ghnlqehs~VLvrGGr   84 (108)
T cd03368           5 LIRKGRKKKKKKSKSPALEGCPQKKGVCLKVYTTTPKKPNSALRKVARVRLSNGKEVTAYIPGEGHNLQEHSVVLVRGGR   84 (108)
T ss_pred             eeecCCCCccccccCCcccCCcccCcEEEEEEeccccCCChhheeeEEEEecCCCEEEEEcCCCCCCccccCEEEEeCCc
Confidence            345555444444 457999999999                            999999999999999999999999999


Q ss_pred             cCCCCCceEEEeeeecCCcccccc
Q psy16455         52 VKDLPGVKIKCVRGVYDLPHVVKK   75 (82)
Q Consensus        52 ~~DLPGVkykvVrG~~D~~~v~~R   75 (82)
                      ++|||||+|++|||+|||++|.+|
T Consensus        85 v~DlPGVkykvvRG~~D~~gv~~R  108 (108)
T cd03368          85 VKDLPGVRYHIVRGVLDLAGVKNR  108 (108)
T ss_pred             cCCCCCeEEEEEeeecccccccCC
Confidence            999999999999999999999886

S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. Antibiotics such as streptomycin bind S12 and cause the ribosome to misread the genetic code.

>PF00164 Ribosom_S12_S23: Ribosomal protein S12/S23; InterPro: IPR006032 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=100.00  E-value=2.7e-35  Score=205.74  Aligned_cols=71  Identities=55%  Similarity=0.894  Sum_probs=63.9

Q ss_pred             CCCCCCCCCCCCCccC----------------------------CCEEEEEecCCCCCCCcccEEEEecCCcCCCCCceE
Q psy16455          9 KKRPPRQPLLGKPFAK----------------------------GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKI   60 (82)
Q Consensus         9 ~~~~~~~~L~~~Pq~k----------------------------gk~v~AyIPG~Ghnlqehs~VLVrGGr~~DLPGVky   60 (82)
                      .++.++++|+++||+|                            |++|+||||||||||||||+||||||+++|||||+|
T Consensus        15 ~~~~k~~~l~~~Pq~kGi~l~~~~~~pKKPNSA~RK~arVrL~n~k~v~AyIPg~Ghnlqehs~VLVrGgrv~DlPGVky   94 (122)
T PF00164_consen   15 KRKSKSPALGGCPQKKGICLKVVTVKPKKPNSAIRKVARVRLSNGKKVTAYIPGEGHNLQEHSVVLVRGGRVGDLPGVKY   94 (122)
T ss_dssp             TCSHSSSSSTTSSEEEEEEEEEEEEEESTTTCSEEEEEEEEETTSEEEEEEC-SSSCCSTTTSEEEEEEESBTTSTTECE
T ss_pred             CccccCCccCCCCccCcEEeecccccccCccchhhhcceeeeccCceEEEEecCCcccccccceEEEeccccCCCCceEE
Confidence            3345567999999999                            999999999999999999999999999999999999


Q ss_pred             EEeeeecCCcccccccccC
Q psy16455         61 KCVRGVYDLPHVVKKTQLT   79 (82)
Q Consensus        61 kvVrG~~D~~~v~~R~~~~   79 (82)
                      ++|||+|||++|.+|+++-
T Consensus        95 kvVRG~~D~~gV~~r~~~r  113 (122)
T PF00164_consen   95 KVVRGVYDVAGVSNRKKAR  113 (122)
T ss_dssp             EBETTSTTCSSSTT-SSSC
T ss_pred             EEEeeccccccccHHHHhh
Confidence            9999999999999988764

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 S12 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S12 is known to be involved in the translation initiation step. It is a very basic protein of 120 to 150 amino-acid residues. S12 belongs to a family of ribosomal proteins which are grouped on the basis of sequence similarities. This protein is known typically as S12 in bacteria, S23 in eukaryotes and as either S12 or S23 in the Archaea []. Bacterial S12 molecules contain a conserved aspartic acid residue which undergoes a novel post-translational modification, beta-methylthiolation, to form the corresponding 3-methylthioaspartic acid.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZKQ_l 3BBN_L 3PYU_L 3D5A_L 3MS0_L 3MR8_L 3F1G_L 2OW8_m 3PYS_L 2QNH_m ....

>cd00319 Ribosomal_S12_like Ribosomal protein S12-like family; composed of prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins

Probab=100.00  E-value=7.8e-35  Score=196.79  Aligned_cols=65  Identities=57%  Similarity=0.965  Sum_probs=61.7

Q ss_pred             CCCCCCCCCCCccC----------------------------CCEEEEEecCCCCCCCcccEEEEecCCcCCCCCceEEE
Q psy16455         11 RPPRQPLLGKPFAK----------------------------GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKC   62 (82)
Q Consensus        11 ~~~~~~L~~~Pq~k----------------------------gk~v~AyIPG~Ghnlqehs~VLVrGGr~~DLPGVkykv   62 (82)
                      +.++++|++|||+|                            |++||||||||||||||||+|||||||++|||||+|++
T Consensus         3 ~~k~~~l~~~Pq~kGi~l~~~~~~pKkPNSA~RK~arV~L~ngk~v~ayIPg~Gh~lqeh~~VLvrGGr~~DlPGVrykv   82 (95)
T cd00319           3 KSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHI   82 (95)
T ss_pred             ccccCcccCCcccCeEEEEEEeccccCCChhhceEEEEEccCCCEEEEECCCCCcccccccEEEEeCCCcCCCCCcEEEE
Confidence            34568999999999                            99999999999999999999999999999999999999


Q ss_pred             eeeecCCcccccc
Q psy16455         63 VRGVYDLPHVVKK   75 (82)
Q Consensus        63 VrG~~D~~~v~~R   75 (82)
                      |||+|||+++.+|
T Consensus        83 VrG~~d~~~v~~R   95 (95)
T cd00319          83 VRGVYDAAGVKDR   95 (95)
T ss_pred             EcccchhhhccCC
Confidence            9999999999876

S12 and S23 are located at the interface of the large and small ribosomal subunits, adjacent to the decoding center. They play an important role in translocation during the peptide elongation step of protein synthesis. They are also involved in important RNA and protein interactions. Ribosomal protein S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. S23 interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes translocation. Mutations in S12 and S23 have been found to affect translational accuracy. Antibiotics such as streptomycin may also bind S12/S23 and cause the ribosome to misread the genetic code.

>PTZ00115 40S ribosomal protein S12; Provisional

Probab=100.00  E-value=2.6e-33  Score=217.08  Aligned_cols=71  Identities=45%  Similarity=0.750  Sum_probs=65.8

Q ss_pred             CCCCCCCCCCCCCccC----------------------------CCEEEEEecCCCCCCCcccEEEEecCCcCCCCCceE
Q psy16455          9 KKRPPRQPLLGKPFAK----------------------------GKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKI   60 (82)
Q Consensus         9 ~~~~~~~~L~~~Pq~k----------------------------gk~v~AyIPG~Ghnlqehs~VLVrGGr~~DLPGVky   60 (82)
                      .+.+++++|+||||+|                            |++||||||||||||||||+||||||+++|||||+|
T Consensus       112 ~~~~k~paL~g~PQkKGIclkv~~~tPKKPNSA~RKvarVrLsNGk~VtAyIPGeGHnLQEHs~VLVRGGrvkDLPGVrY  191 (290)
T PTZ00115        112 PKNRRSKWLEGAPQKKGICVKVRVQTPRKPNSGLRKVARVRLSTGRTVTVYIPGIGHNLNTHSVVLVRGGRCKDVPGCNY  191 (290)
T ss_pred             CCCCcCccccCCcccCeEEEEeeecCCCCCCccccceEEEEecCCCEEEEEcCCCCcccccCCEEEEeCCCcCCCCCceE
Confidence            3444556899999999                            999999999999999999999999999999999999


Q ss_pred             EEeeeecCCcccccccccC
Q psy16455         61 KCVRGVYDLPHVVKKTQLT   79 (82)
Q Consensus        61 kvVrG~~D~~~v~~R~~~~   79 (82)
                      ++|||+|||++|.+|+++.
T Consensus       192 kvVRG~~D~~gV~~Rk~~R  210 (290)
T PTZ00115        192 KAVRGVYDLLPVKNRARSR  210 (290)
T ss_pred             EEeeeeccccccccccccc
Confidence            9999999999999998864

>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]

Probab=99.98  E-value=4e-33  Score=196.95  Aligned_cols=77  Identities=51%  Similarity=0.712  Sum_probs=67.4

Q ss_pred             CCCCCCCCC-CCCCCCCCCCccC----------------------------CCEEEEEecCCCCCCCcccEEEEecCCcC
Q psy16455          3 MKGPHYKKR-PPRQPLLGKPFAK----------------------------GKEMVAYIPGEGHNLQEHNIVLCKVGRVK   53 (82)
Q Consensus         3 ~~g~~~~~~-~~~~~L~~~Pq~k----------------------------gk~v~AyIPG~Ghnlqehs~VLVrGGr~~   53 (82)
                      |.++..... .+++||++|||++                            |++||||||||||||||||+||||||+++
T Consensus        15 R~~rr~~~~k~Ks~~L~g~Pq~RGv~~~v~~~~pKkPNSAlRK~~RVrL~NG~~VtAyiPg~Gh~lqEH~~Vli~G~~v~   94 (129)
T COG0048          15 RKKRRSLGLKSKSPALEGAPQARGVCTRVYTVTPKKPNSALRKVARVRLINGKEVTAYIPGEGHNLQEHSEVLIRGGRVK   94 (129)
T ss_pred             hcccccccccccCCcccCCCccceEEEEEEecccCCCChhhheeEEEEeeCCcEEEEEcCCCCccccccCEEEEecCccC
Confidence            444333333 3456999999999                            99999999999999999999999999999


Q ss_pred             CCCCceEEEeeeecCCcccccccccC
Q psy16455         54 DLPGVKIKCVRGVYDLPHVVKKTQLT   79 (82)
Q Consensus        54 DLPGVkykvVrG~~D~~~v~~R~~~~   79 (82)
                      |||||+||||||.+|.+++..|.++.
T Consensus        95 DlPGVRy~vvrg~~ds~~v~~r~~~r  120 (129)
T COG0048          95 DLPGVRYKVVRGALDSLGVLDRGQKR  120 (129)
T ss_pred             CCCCceEEEEEEcchhhhhhhhcccc
Confidence            99999999999999999999887754

>KOG1750|consensus

Probab=99.96  E-value=1.6e-30  Score=185.46  Aligned_cols=76  Identities=54%  Similarity=0.861  Sum_probs=67.7

Q ss_pred             CCCC-C-CCCCCCCCCCCCCCCCccC----------------------------CCEEEEEecCCCCCCCcccEEEEecC
Q psy16455          1 MHMK-G-PHYKKRPPRQPLLGKPFAK----------------------------GKEMVAYIPGEGHNLQEHNIVLCKVG   50 (82)
Q Consensus         1 l~~~-g-~~~~~~~~~~~L~~~Pq~k----------------------------gk~v~AyIPG~Ghnlqehs~VLVrGG   50 (82)
                      |+|. | +++|+..++.+|++|||.+                            |.+|+|||||+|||+|||++||||||
T Consensus        34 liR~~~r~~kRr~~~~~~L~g~p~~kgvvl~v~t~~pkkPnsa~rK~~~vrlstg~~i~ayipg~ghnlqehs~Vlvrgg  113 (139)
T KOG1750|consen   34 LIRNGGRPPKRRPRKSPALDGCPQRKGVVLRVFTRKPKKPNSANRKCARVRLSTGREVTAYIPGIGHNLQEHSIVLVRGG  113 (139)
T ss_pred             HHhcCCCCCccCCcccccccCCcccccEEEEEEEecCCCCCccceeeEEEEecCchheeeeCCCccccceeEEEEEEecc
Confidence            3555 3 4555555567999999999                            99999999999999999999999999


Q ss_pred             CcCCCCCceEEEeeeecCCccccccc
Q psy16455         51 RVKDLPGVKIKCVRGVYDLPHVVKKT   76 (82)
Q Consensus        51 r~~DLPGVkykvVrG~~D~~~v~~R~   76 (82)
                      |++|||||+|++|||+|||++|.+|.
T Consensus       114 r~qdlpgvk~~~vRg~~d~~~V~~r~  139 (139)
T KOG1750|consen  114 RVQDLPGVKYHVVRGVYDLAGVVGRI  139 (139)
T ss_pred             eeccCcchhhhhhhhhhhhccccCCC
Confidence            99999999999999999999999873

>cd03367 Ribosomal_S23 S12-like family, 40S ribosomal protein S23 subfamily; S23 is located at the interface of the large and small ribosomal subunits of eukaryotes, adjacent to the decoding center

Probab=99.92  E-value=1.5e-25  Score=155.94  Aligned_cols=56  Identities=39%  Similarity=0.707  Sum_probs=51.6

Q ss_pred             CCCCCCCCCCCCccC-----------------------------CCEEEEEecCCC--CCCCcccEEEEec-----CCcC
Q psy16455         10 KRPPRQPLLGKPFAK-----------------------------GKEMVAYIPGEG--HNLQEHNIVLCKV-----GRVK   53 (82)
Q Consensus        10 ~~~~~~~L~~~Pq~k-----------------------------gk~v~AyIPG~G--hnlqehs~VLVrG-----Gr~~   53 (82)
                      .+.+.++|++|||+|                             |++|||||||||  |||||||+|||||     |+++
T Consensus         9 ~~~k~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~~ngk~itAyIPG~G~~~~lqeh~~VLV~G~G~~Gg~v~   88 (115)
T cd03367           9 TKYKADPLGGAPHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPGDGCLNFIDENDEVLVAGFGRKGRAVG   88 (115)
T ss_pred             ccccCCcccCCCccCeEEEEEeecCCCCCChhhceEEEEEEccCCeEEEEEeCCCCcccccccCCEEEEEecccCCCccC
Confidence            445678999999999                             999999999999  6999999999999     7899


Q ss_pred             CCCCceEEEeee
Q psy16455         54 DLPGVKIKCVRG   65 (82)
Q Consensus        54 DLPGVkykvVrG   65 (82)
                      |||||+|++|+-
T Consensus        89 DlPGVrykvVkV  100 (115)
T cd03367          89 DIPGVRFKVVKV  100 (115)
T ss_pred             CCCceEEEEEEE
Confidence            999999999984

It interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes the translocation of the growing peptidyl-tRNA to the P site to make room for the next aminoacyl-tRNA at the A (acceptor) site. Through its interaction with eEF2, S23 may play an important role in translocation. Also members of this subfamily are the archaeal 30S ribosomal S12 proteins. Prokaryotic S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as control element for the rRNA- and tRNA-driven movements of translocation. S12 and S23 are also implicated in translation accuracy. Antibiotics such as streptomycin bind S12/S23 and cause the ribosome to misread the genetic code.

>TIGR00982 S23_S12_E_A ribosomal protein S23 (S12)

Probab=99.91  E-value=1.8e-24  Score=154.44  Aligned_cols=55  Identities=36%  Similarity=0.694  Sum_probs=50.8

Q ss_pred             CCCCCCCCCCCccC-----------------------------CCEEEEEecCCCC--CCCcccEEEEec------CCcC
Q psy16455         11 RPPRQPLLGKPFAK-----------------------------GKEMVAYIPGEGH--NLQEHNIVLCKV------GRVK   53 (82)
Q Consensus        11 ~~~~~~L~~~Pq~k-----------------------------gk~v~AyIPG~Gh--nlqehs~VLVrG------Gr~~   53 (82)
                      ..+.++|+++||+|                             |++||||||||||  ||||||+|||+|      |+++
T Consensus        30 ~~K~~~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~~ngk~vtAyiPg~G~~~~lqeh~~VLV~G~gg~~gg~v~  109 (139)
T TIGR00982        30 KRKADPLEGAPMARGIVLEKVGVEARQPNSAIRKCVRVQLIKNGKVVTAFCPGDGAINFIDEHDEVIIEGIGGPRGRSMG  109 (139)
T ss_pred             ccccCcccCCCccCeEEEEEEeecCCCCCcccceEEEEEEccCCeEEEEEeCCCccccccccCCEEEEEecCccCCCCcC
Confidence            44568999999999                             9999999999997  799999999999      7999


Q ss_pred             CCCCceEEEeee
Q psy16455         54 DLPGVKIKCVRG   65 (82)
Q Consensus        54 DLPGVkykvVrG   65 (82)
                      |||||+|+||+-
T Consensus       110 DlPGVrykvVkV  121 (139)
T TIGR00982       110 DIPGVRYKVVKV  121 (139)
T ss_pred             CCCceEEEEEEE
Confidence            999999999983

This model represents the eukaryotic and archaeal homologs of bacterial ribosomal protein S12. This protein is known typically as S23 in eukaryotes and as either S12 or S23 in the Archaea.

>PTZ00067 40S ribosomal S23; Provisional

Probab=99.90  E-value=3e-24  Score=153.91  Aligned_cols=55  Identities=38%  Similarity=0.685  Sum_probs=50.9

Q ss_pred             CCCCCCCCCCCccC-----------------------------CCEEEEEecCCC--CCCCcccEEEEec-C----CcCC
Q psy16455         11 RPPRQPLLGKPFAK-----------------------------GKEMVAYIPGEG--HNLQEHNIVLCKV-G----RVKD   54 (82)
Q Consensus        11 ~~~~~~L~~~Pq~k-----------------------------gk~v~AyIPG~G--hnlqehs~VLVrG-G----r~~D   54 (82)
                      ..+.+||++|||+|                             |++|||||||||  |||||||+|||+| |    +++|
T Consensus        35 ~~k~~pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtAyiPg~G~lh~lqEh~~VLV~G~Gr~g~~v~D  114 (143)
T PTZ00067         35 RYKANPFGGASHAKGIVVEKIGIEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFINENDEVLVSGFGRSGHAVGD  114 (143)
T ss_pred             ccccCcccCCCccceEEEEEEeecCCCCChhhceEEEEEEccCCcEEEEEeCCCCcccccccCCEEEEEecCcCCCccCC
Confidence            34568999999999                             999999999999  9999999999999 7    6999


Q ss_pred             CCCceEEEeee
Q psy16455         55 LPGVKIKCVRG   65 (82)
Q Consensus        55 LPGVkykvVrG   65 (82)
                      ||||+|+|||-
T Consensus       115 lPGVrykvVrV  125 (143)
T PTZ00067        115 IPGVRFKVVKV  125 (143)
T ss_pred             CCceEEEEEEE
Confidence            99999999984

>PRK04211 rps12P 30S ribosomal protein S12P; Reviewed

Probab=99.90  E-value=3.5e-24  Score=153.85  Aligned_cols=54  Identities=35%  Similarity=0.707  Sum_probs=50.2

Q ss_pred             CCCCCCCCCCccC-----------------------------CCEEEEEecCCCC--CCCcccEEEEec------CCcCC
Q psy16455         12 PPRQPLLGKPFAK-----------------------------GKEMVAYIPGEGH--NLQEHNIVLCKV------GRVKD   54 (82)
Q Consensus        12 ~~~~~L~~~Pq~k-----------------------------gk~v~AyIPG~Gh--nlqehs~VLVrG------Gr~~D   54 (82)
                      .+.++|++|||+|                             |++||||||||||  ||||||+|||+|      |+++|
T Consensus        37 ~K~~~l~g~Pq~kGivl~~~~v~pKKPNSA~RK~arV~L~~Ngk~vtAyIPg~G~~~~lqEh~~VLV~G~gg~~gg~v~D  116 (145)
T PRK04211         37 EKADPLEGAPMARGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKQVTAFCPGDGAINFIDEHDEVVIEGIGGPKGRSMGD  116 (145)
T ss_pred             cccCcccCCCccCeEEEEEeeecCCCCchhhceeEEEEEccCCeEEEEEeCCCccccccccCCEEEEeecCccCCCCcCC
Confidence            4568999999999                             9999999999997  899999999999      68999


Q ss_pred             CCCceEEEeee
Q psy16455         55 LPGVKIKCVRG   65 (82)
Q Consensus        55 LPGVkykvVrG   65 (82)
                      ||||+|+||.-
T Consensus       117 lPGVrykvVkV  127 (145)
T PRK04211        117 IPGVRYKVIKV  127 (145)
T ss_pred             CCceEEEEEEE
Confidence            99999999973

>KOG1749|consensus

Probab=99.38  E-value=8e-13  Score=94.78  Aligned_cols=41  Identities=39%  Similarity=0.783  Sum_probs=38.2

Q ss_pred             CCEEEEEecCCC--CCCCcccEEEEec----CC-cCCCCCceEEEeee
Q psy16455         25 GKEMVAYIPGEG--HNLQEHNIVLCKV----GR-VKDLPGVKIKCVRG   65 (82)
Q Consensus        25 gk~v~AyIPG~G--hnlqehs~VLVrG----Gr-~~DLPGVkykvVrG   65 (82)
                      |++||||+|-+|  ++++|+|+|||.|    |+ ++|+|||+|+||.-
T Consensus        78 gKKITafVp~dgcln~ieendevlv~gfgrkg~avgdipgvrfkvvkv  125 (143)
T KOG1749|consen   78 GKKITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKV  125 (143)
T ss_pred             CceEEEEecCCCceeeeccCCeeeeeccCccCccccCCCceEEEEEEE
Confidence            999999999999  9999999999999    44 89999999999873

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	82
4g5k_O	128	Crystal Structure Of The 70s Ribosome With Tetracyc		9e-14
3d5a_L	134	Structural Basis For Translation Termination On The		1e-13
3fic_L	125	T. Thermophilus 70s Ribosome In Complex With Mrna,		1e-13
1fjg_L	135	Structure Of The Thermus Thermophilus 30s Ribosomal		1e-13
1pn7_O	124	Coordinates Of S12, L11 Proteins And P-Trna, From T		1e-13
2f4v_L	132	30s Ribosome + Designer Antibiotic Length = 132		1e-13
1i94_L	131	Crystal Structures Of The Small Ribosomal Subunit W		1e-13
4dr1_L	135	Crystal Structure Of The Apo 30s Ribosomal Subunit		9e-13
3bbn_L	123	Homology Model For The Spinach Chloroplast 30s Subu		2e-11
1zn1_L	97	Coordinates Of Rrf Fitted Into Cryo-Em Map Of The 7		5e-11
1p6g_L	123	Real Space Refined Coordinates Of The 30s Subunit F		6e-11
2gy9_L	101	Structure Of The 30s Subunit Of A Pre-Translocation		6e-11
1vs5_L	124	Crystal Structure Of The Bacterial Ribosome From Es		6e-11

>pdb|4G5K|O Chain O, Crystal Structure Of The 70s Ribosome With Tetracycline. This Entry Contains The 30s Subunit Of Molecule A. Length = 128

Iteration: 1
 Score = 71.6 bits (174), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 33/51 (64%), Positives = 38/51 (74%)
Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHV 72
              G E+ AYIPGEGHNLQEH++VL + GRVKDLPGV+   VRGVYD   V
Sbjct: 57  LTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGV 107

>pdb|3D5A|L Chain L, Structural Basis For Translation Termination On The 70s Ribosome. This File Contains The 30s Subunit, Release Factor 1 (Rf1), Two Trna, And Mrna Molecules Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes As Described In Remark 400. Length = 134

Iteration: 1
 Score = 71.6 bits (174), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 33/51 (64%), Positives = 38/51 (74%)
Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHV 72
              G E+ AYIPGEGHNLQEH++VL + GRVKDLPGV+   VRGVYD   V
Sbjct: 59  LTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGV 109

>pdb|3FIC|L Chain L, T. Thermophilus 70s Ribosome In Complex With Mrna, Trnas And Ef- Tu.Gdp.Kirromycin Ternary Complex, Fitted To A 6.4 A Cryo-Em Map. This File Contains The 30s Subunit And The Ligands Length = 125

Iteration: 1
 Score = 71.6 bits (174), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 33/51 (64%), Positives = 38/51 (74%)
Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHV 72
              G E+ AYIPGEGHNLQEH++VL + GRVKDLPGV+   VRGVYD   V
Sbjct: 56  LTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGV 106

>pdb|1FJG|L Chain L, Structure Of The Thermus Thermophilus 30s Ribosomal Subunit In Complex With The Antibiotics Streptomycin, Spectinomycin, And Paromomycin Length = 135

Iteration: 1
 Score = 71.6 bits (174), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 33/51 (64%), Positives = 38/51 (74%)
Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHV 72
              G E+ AYIPGEGHNLQEH++VL + GRVKDLPGV+   VRGVYD   V
Sbjct: 60  LTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGV 110

>pdb|1PN7|O Chain O, Coordinates Of S12, L11 Proteins And P-Trna, From The 70s X- Ray Structure Aligned To The 70s Cryo-Em Map Of E.Coli Ribosome Length = 124

Iteration: 1
 Score = 71.6 bits (174), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 33/51 (64%), Positives = 38/51 (74%)
Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHV 72
              G E+ AYIPGEGHNLQEH++VL + GRVKDLPGV+   VRGVYD   V
Sbjct: 56  LTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGV 106

>pdb|2F4V|L Chain L, 30s Ribosome + Designer Antibiotic Length = 132

Iteration: 1
 Score = 71.6 bits (174), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 33/51 (64%), Positives = 38/51 (74%)
Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHV 72
              G E+ AYIPGEGHNLQEH++VL + GRVKDLPGV+   VRGVYD   V
Sbjct: 57  LTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGV 107

>pdb|1I94|L Chain L, Crystal Structures Of The Small Ribosomal Subunit With Tetracycline, Edeine And If3 Length = 131

Iteration: 1
 Score = 71.6 bits (174), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 33/51 (64%), Positives = 38/51 (74%)
Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHV 72
              G E+ AYIPGEGHNLQEH++VL + GRVKDLPGV+   VRGVYD   V
Sbjct: 56  LTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGV 106

>pdb|4DR1|L Chain L, Crystal Structure Of The Apo 30s Ribosomal Subunit From Thermus Thermophilus (hb8) Length = 135

Iteration: 1
 Score = 68.6 bits (166), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 32/51 (62%), Positives = 37/51 (72%)
Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHV 72
              G E+ AYIPGEGHNLQEH++VL + GRVK LPGV+   VRGVYD   V
Sbjct: 60  LTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKXLPGVRYHIVRGVYDAAGV 110

>pdb|3BBN|L Chain L, Homology Model For The Spinach Chloroplast 30s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 123

Iteration: 1
 Score = 63.9 bits (154), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/56 (55%), Positives = 37/56 (66%)
Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
              G E+ AYIPG GHNLQEH++VL + GRVKDLPGV+   VRG  D   V  + Q
Sbjct: 57  LTSGFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGTLDAVGVKDRQQ 112

>pdb|1ZN1|L Chain L, Coordinates Of Rrf Fitted Into Cryo-Em Map Of The 70s Post- Termination Complex Length = 97

Iteration: 1
 Score = 62.8 bits (151), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 29/56 (51%), Positives = 37/56 (66%)
Query: 22 FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
             G E+ +YI GEGHNLQEH+++L + GRVKDLPGV+   VRG  D   V  + Q
Sbjct: 30 LTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQ 85

>pdb|1P6G|L Chain L, Real Space Refined Coordinates Of The 30s Subunit Fitted Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp State Of E. Coli 70s Ribosome Length = 123

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 29/56 (51%), Positives = 37/56 (66%)
Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
              G E+ +YI GEGHNLQEH+++L + GRVKDLPGV+   VRG  D   V  + Q
Sbjct: 56  LTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQ 111

>pdb|2GY9|L Chain L, Structure Of The 30s Subunit Of A Pre-Translocational E. Coli Ribosome Obtained By Fitting Atomic Models For Rna And Protein Components Into Cryo-Em Map Emd-1056 Length = 101

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 29/56 (51%), Positives = 37/56 (66%)
Query: 22 FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
             G E+ +YI GEGHNLQEH+++L + GRVKDLPGV+   VRG  D   V  + Q
Sbjct: 35 LTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQ 90

>pdb|1VS5|L Chain L, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With The Antibiotic Kasugamyin At 3.5a Resolution. This File Contains The 30s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. Length = 124

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 29/56 (51%), Positives = 37/56 (66%)
Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
              G E+ +YI GEGHNLQEH+++L + GRVKDLPGV+   VRG  D   V  + Q
Sbjct: 57  LTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQ 112

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	82
2vqe_L	135	30S ribosomal protein S12, 30S ribosomal protein S	4e-13
2xzm_L	142	40S ribosomal protein S12; ribosome, translation;	2e-11
3u5c_X	145	RP37, S28, YS14, 40S ribosomal protein S23-A; tran	1e-08

>2vqe_L 30S ribosomal protein S12, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: i.1.1.1 PDB: 1gix_O* 1hnw_L* 1hnx_L* 1hnz_L* 1hr0_L 1ibk_L* 1ibl_L* 1ibm_L 1j5e_L 1jgo_O* 1jgp_O* 1jgq_O* 1mj1_O* 1ml5_O* 1mvr_O 1n32_L* 1n33_L* 1n34_L 1n36_L 1xmo_L* ... Length = 135

 Score = 59.3 bits (143), Expect = 4e-13
 Identities = 33/56 (58%), Positives = 40/56 (71%)

Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
              G E+ AYIPGEGHNLQEH++VL + GRVKDLPGV+   VRGVYD   V  + +
Sbjct: 60  LTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKK 115

>2xzm_L 40S ribosomal protein S12; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_L 3j0o_L 3j0l_L 3j0p_L 3j0q_L 3iz6_L 3jyv_L* 1s1h_L* Length = 142

 Score = 54.7 bits (131), Expect = 2e-11
 Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 9/65 (13%)

Query: 22  FAKGKEMVAYIPGEG--HNLQEHNIVLC-----KVGRVKDLPGVKIK--CVRGVYDLPHV 72
               K++ A++P +G  + L E++ VL      +   V D+PGV+ K  CV+G+  L   
Sbjct: 76  RKNSKKIAAFVPMDGCLNFLAENDEVLVAGLGRQGHAVGDIPGVRFKVVCVKGISLLALF 135

Query: 73  VKKTQ 77
             K +
Sbjct: 136 KGKKE 140

>3u5c_X RP37, S28, YS14, 40S ribosomal protein S23-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_L 3o30_P 3o2z_P 3u5g_X 3jyv_L* 1s1h_L* 2zkq_l 3iz6_L Length = 145

 Score = 47.4 bits (112), Expect = 1e-08
 Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 7/73 (9%)

Query: 2   HMKGPHYKKRPPRQPLLGKPFAKGKEMVAYIPGEG--HNLQEHNIVL----CKVGRVK-D 54
                       R+ +  +    GK++ A++P +G  + + E++ VL     + G+ K D
Sbjct: 57  LGIESKQPNSAIRKCVRVQLIKNGKKVTAFVPNDGCLNFVDENDEVLLAGFGRKGKAKGD 116

Query: 55  LPGVKIKCVRGVY 67
           +PGV+ K V+   
Sbjct: 117 IPGVRFKVVKVSG 129

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	82
2vqe_L	135	30S ribosomal protein S12, 30S ribosomal protein S	100.0
2xzm_L	142	40S ribosomal protein S12; ribosome, translation;	99.91
3u5c_X	145	RP37, S28, YS14, 40S ribosomal protein S23-A; tran	99.91
3j20_N	147	30S ribosomal protein S12P; archaea, archaeal, KIN	99.9

>2vqe_L 30S ribosomal protein S12, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: i.1.1.1 PDB: 1gix_O* 1hnw_L* 1hnx_L* 1hnz_L* 1hr0_L 1ibk_L* 1ibl_L* 1ibm_L 1j5e_L 1jgo_O* 1jgp_O* 1jgq_O* 1mj1_O* 1ml5_O* 1mvr_O 1n32_L* 1n33_L* 1n34_L 1n36_L 1xmo_L* ...

Probab=100.00  E-value=2.3e-37  Score=218.78  Aligned_cols=78  Identities=50%  Similarity=0.821  Sum_probs=69.8

Q ss_pred             CCCCCCCCCCCC-CCCCCCCCccC----------------------------CCEEEEEecCCCCCCCcccEEEEecCCc
Q psy16455          2 HMKGPHYKKRPP-RQPLLGKPFAK----------------------------GKEMVAYIPGEGHNLQEHNIVLCKVGRV   52 (82)
Q Consensus         2 ~~~g~~~~~~~~-~~~L~~~Pq~k----------------------------gk~v~AyIPG~Ghnlqehs~VLVrGGr~   52 (82)
                      +|.++.++++++ .++|++|||++                            |++||||||||||||||||+|||||||+
T Consensus        11 ~r~~r~~~~~k~k~~~l~g~Pq~kGv~l~v~~~~pKKPNSA~RK~arVrL~ngk~VtAyIPG~GhnlqEhs~VLVrGgrv   90 (135)
T 2vqe_L           11 VRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRV   90 (135)
T ss_dssp             HHTCCCCCCCCCSCCCSSSCSEEEEEESCCCEECCCTTCCCCEECCEEEETTSCEEEEECCSSCCCCCTTCEEEEEECCC
T ss_pred             hccCCCCCCccCcCCcccCCCCcCeEEEEEEecCCCCCchhheeEEEEEcCCCCEEEEEcCCCCCccCcCCEEEEcCCCc
Confidence            456655554444 46999999999                            9999999999999999999999999999


Q ss_pred             CCCCCceEEEeeeecCCcccccccccC
Q psy16455         53 KDLPGVKIKCVRGVYDLPHVVKKTQLT   79 (82)
Q Consensus        53 ~DLPGVkykvVrG~~D~~~v~~R~~~~   79 (82)
                      +|||||+|+||||+|||++|.+|+++.
T Consensus        91 ~DlPGVrykvVrG~lD~~gv~~R~~~R  117 (135)
T 2vqe_L           91 KDLPGVRYHIVRGVYDAAGVKDRKKSR  117 (135)
T ss_dssp             TTSTTCCEEECTTSTTSCCCTTCCSSG
T ss_pred             CCCCCeeEEEEeEeecCcccccccccc
Confidence            999999999999999999999998864

>2xzm_L 40S ribosomal protein S12; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_L 3j0o_L 3j0l_L 3j0p_L 3j0q_L 3iz6_L 3jyv_L* 1s1h_L*

Probab=99.91  E-value=2.8e-25  Score=158.08  Aligned_cols=52  Identities=37%  Similarity=0.593  Sum_probs=49.6

Q ss_pred             CCCCCCCccC-----------------------------CCEEEEEecCCCC--CCCcccEEEEec-----CCcCCCCCc
Q psy16455         15 QPLLGKPFAK-----------------------------GKEMVAYIPGEGH--NLQEHNIVLCKV-----GRVKDLPGV   58 (82)
Q Consensus        15 ~~L~~~Pq~k-----------------------------gk~v~AyIPG~Gh--nlqehs~VLVrG-----Gr~~DLPGV   58 (82)
                      +||+|+||+|                             |++||||||||||  ||||||+|||+|     |+++|||||
T Consensus        40 ~pl~g~pq~kGIvl~~~~~~pKkPNSA~RK~arVqL~kNgk~vtAyIPg~G~l~~lqEh~~VLVrG~G~~ggrv~DlPGV  119 (142)
T 2xzm_L           40 NPFMGASHAKGLVTEKIGIESKQPNSAVRKCVRVLLRKNSKKIAAFVPMDGCLNFLAENDEVLVAGLGRQGHAVGDIPGV  119 (142)
T ss_dssp             STTTTCSEEEEEEEEEEEEECCTTCCCEEEEEEEEETTTCCEEEEECCSSSGGGTCCTTCEEEEEESSSSSSCCTTCSSC
T ss_pred             CcccCCCccceEEEEEEecccCCCCcccccEEEEEEecCCeEEEEEeCCCCcccccccCCEEEEEecccCCCccCCCCCc
Confidence            8999999999                             9999999999996  999999999999     899999999


Q ss_pred             eEEEeeee
Q psy16455         59 KIKCVRGV   66 (82)
Q Consensus        59 kykvVrG~   66 (82)
                      +|+|||+.
T Consensus       120 rykvVrv~  127 (142)
T 2xzm_L          120 RFKVVCVK  127 (142)
T ss_dssp             CEEEEEES
T ss_pred             eEEEEEEC
Confidence            99999963

>3u5c_X RP37, S28, YS14, 40S ribosomal protein S23-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_L 3o30_P 3o2z_P 3u5g_X 3j2k_X 3jyv_L* 1s1h_L* 2zkq_l 3iz6_L

Probab=99.91  E-value=2.9e-25  Score=158.42  Aligned_cols=54  Identities=33%  Similarity=0.567  Sum_probs=50.4

Q ss_pred             CCCCCCCCCccC-----------------------------CCEEEEEecCCCC--CCCcccEEEEec-----CCcCCCC
Q psy16455         13 PRQPLLGKPFAK-----------------------------GKEMVAYIPGEGH--NLQEHNIVLCKV-----GRVKDLP   56 (82)
Q Consensus        13 ~~~~L~~~Pq~k-----------------------------gk~v~AyIPG~Gh--nlqehs~VLVrG-----Gr~~DLP   56 (82)
                      +++||+++||+|                             |++||||||||||  ||||||+|||+|     |+++|||
T Consensus        39 K~~~l~g~pq~kGivl~~~~~~pKkPNSA~RK~arV~L~kngk~vtAyIPg~G~l~~lqEh~~VLV~G~G~~Gg~v~DlP  118 (145)
T 3u5c_X           39 KSSPFGGSSHAKGIVLEKLGIESKQPNSAIRKCVRVQLIKNGKKVTAFVPNDGCLNFVDENDEVLLAGFGRKGKAKGDIP  118 (145)
T ss_dssp             HSSSSCSSSEEEEEEEEEEBCBCCTTCCCBCCEEEEEETTTCCEEEEECCSSSCGGGCCTTCEEEEECCSSSSSCCSSST
T ss_pred             ccCccCCCCccCeEEEEEeecccCCCCccceeEEEEEEccCCCEEEEEeCCCCccccCCcCCEEEEEeccccCCccCCCC
Confidence            357899999998                             9999999999997  999999999999     7899999


Q ss_pred             CceEEEeeee
Q psy16455         57 GVKIKCVRGV   66 (82)
Q Consensus        57 GVkykvVrG~   66 (82)
                      ||+|+|||+.
T Consensus       119 GVrykvVrv~  128 (145)
T 3u5c_X          119 GVRFKVVKVS  128 (145)
T ss_dssp             TCCEEEEEST
T ss_pred             ceeEEEEEEC
Confidence            9999999975

>3j20_N 30S ribosomal protein S12P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=99.90  E-value=5.9e-25  Score=157.10  Aligned_cols=54  Identities=37%  Similarity=0.704  Sum_probs=50.2

Q ss_pred             CCCCCCCCCccC-----------------------------CCEEEEEecCCCC--CCCcccEEEEec------CCcCCC
Q psy16455         13 PRQPLLGKPFAK-----------------------------GKEMVAYIPGEGH--NLQEHNIVLCKV------GRVKDL   55 (82)
Q Consensus        13 ~~~~L~~~Pq~k-----------------------------gk~v~AyIPG~Gh--nlqehs~VLVrG------Gr~~DL   55 (82)
                      +++||+++||++                             |++||||||||||  ||||||+|||+|      |+++||
T Consensus        40 K~~~l~g~pq~kGIvl~~~~~~pKkPNSA~RK~arV~L~kngk~vtAyIPg~Ghln~lqEh~~VLV~G~gg~~gg~v~Dl  119 (147)
T 3j20_N           40 KSDPLEGAPQARGIVLEKIAVEAKQPNSGMRKAVRVQLIKNGKVVTAFCPGDGAIKFIDEHDEVIIEGIGGPKGGSMGDI  119 (147)
T ss_dssp             HHSSSTTCSCEEEEEEEEEEEECCSSCCCEEEEEEEEETTTCCEEEEECCSSSGGGTCCTTCEEEEEECSCTTSCCCSSC
T ss_pred             ccchhhcCCccceEEEEEeecCCCCCCceeeeEEEEEEccCCcEEEEEcCCchhhcccccCCEEEEeeccCcCCCccCCC
Confidence            357999999999                             9999999999998  999999999999      669999


Q ss_pred             CCceEEEeeee
Q psy16455         56 PGVKIKCVRGV   66 (82)
Q Consensus        56 PGVkykvVrG~   66 (82)
                      |||+|+||+..
T Consensus       120 PGVrykvVkv~  130 (147)
T 3j20_N          120 PGIRYKVVKVN  130 (147)
T ss_dssp             SSCCEEEEEET
T ss_pred             CceeEEEEEEC
Confidence            99999999975

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	82
d2uubl1	118	b.40.4.5 (L:5-122) Ribosomal protein S12 {Thermus	3e-22

>d2uubl1 b.40.4.5 (L:5-122) Ribosomal protein S12 {Thermus thermophilus [TaxId: 274]} Length = 118

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S12
species: Thermus thermophilus [TaxId: 274]

 Score = 80.9 bits (200), Expect = 3e-22
 Identities = 33/56 (58%), Positives = 40/56 (71%)

Query: 22  FAKGKEMVAYIPGEGHNLQEHNIVLCKVGRVKDLPGVKIKCVRGVYDLPHVVKKTQ 77
              G E+ AYIPGEGHNLQEH++VL + GRVKDLPGV+   VRGVYD   V  + +
Sbjct: 56  LTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKK 111

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	82
d2uubl1	118	Ribosomal protein S12 {Thermus thermophilus [TaxId	100.0

>d2uubl1 b.40.4.5 (L:5-122) Ribosomal protein S12 {Thermus thermophilus [TaxId: 274]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S12
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=1.5e-39  Score=224.11  Aligned_cols=78  Identities=50%  Similarity=0.821  Sum_probs=69.6

Q ss_pred             CCCCCCCCCCCC-CCCCCCCCccC----------------------------CCEEEEEecCCCCCCCcccEEEEecCCc
Q psy16455          2 HMKGPHYKKRPP-RQPLLGKPFAK----------------------------GKEMVAYIPGEGHNLQEHNIVLCKVGRV   52 (82)
Q Consensus         2 ~~~g~~~~~~~~-~~~L~~~Pq~k----------------------------gk~v~AyIPG~Ghnlqehs~VLVrGGr~   52 (82)
                      +|.++.++++++ .++|++|||+|                            |++||||||||||||||||+|||||||+
T Consensus         7 ~rk~R~kk~~k~k~~aL~~~PqkkGvc~kv~~~~PKKPNSA~RKvarVrLsng~~v~AyIPG~GhnlqEHs~VLvrGGrv   86 (118)
T d2uubl1           7 VRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRV   86 (118)
T ss_dssp             HHHCCCCCCCCCSCCCTTTCSCEEEEEEEEEEECCCTTCCSCEEEEEEEETTSCEEEEECCSSCCCCCTTCEEEECCCCC
T ss_pred             cccCCCCCccCCCCcccccCCccceEEEEEEEeccCCCcceeeeEEEEEecCCeEEEEEcCCCCcCcccCCEEEEeCCcc
Confidence            455655444444 45899999999                            9999999999999999999999999999


Q ss_pred             CCCCCceEEEeeeecCCcccccccccC
Q psy16455         53 KDLPGVKIKCVRGVYDLPHVVKKTQLT   79 (82)
Q Consensus        53 ~DLPGVkykvVrG~~D~~~v~~R~~~~   79 (82)
                      +|||||+|+||||+|||++|.+|+++.
T Consensus        87 ~DlPGVry~vvrG~~D~~~v~~Rk~~R  113 (118)
T d2uubl1          87 KDLPGVRYHIVRGVYDAAGVKDRKKSR  113 (118)
T ss_dssp             TTSTTCCEEBCTTSTTCCCCTTCCSST
T ss_pred             ccCCCcEEEEEeeeecccccccccccc
Confidence            999999999999999999999999875