Citrus Sinensis ID: 042342

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80-------
Protein Sequence
PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPIISLKGCMR
Secondary Structure (PSIPRED)
cccccccccEEEEEEEEEEEcccccccccEEEEEEEccccEEEEEEcccccccccccccEEEEEEcccccccccccccEEEcccccc
Secondary Structure Prediction (SSPRO)
cccccccccEEEEEEEEEcccccccHHHHHEEEEEEEcccEEEEEEcccccEEEcccccEEEEEEcccccccccccccEEEEEcccc
Coil and Loop (DISEMBL)
pfagpshakgiVLEKIGieakqpnfairKCSRVQLIKNGKKIvtfvpsdgclnyiEENDKVLIAGfgrkghavatsppiislkgcmr
Flexible Loop (DISEMBL)
pfagpshakgiVLEKigieakqpnfaiRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGrkghavatsppiislkgcmr
Low Complexity Region (SEG)
PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPIISLKGCMR
Disordered region (IsUnstruct)
*********GIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII*******
Disordered Region (DISOPRED)
*****SHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPIISLKGCMR
Disordered Region (DISEMBL)
PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPIISLKGCMR
Disordered Region (DISPRO)
*****SHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPIISLKGCMR
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPIISLKGCMR
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	87	2.2.26 [Sep-21-2011]
Q9M5Z9	142	40S ribosomal protein S23	N/A	no	0.908	0.556	0.848	2e-33
P46297	142	40S ribosomal protein S23	N/A	no	0.908	0.556	0.848	2e-33
P49201	142	40S ribosomal protein S23	yes	no	0.908	0.556	0.848	3e-33
Q9SF35	142	40S ribosomal protein S23	yes	no	0.908	0.556	0.835	4e-32
Q86FP7	143	40S ribosomal protein S23	N/A	no	0.908	0.552	0.797	9e-32
P62268	143	40S ribosomal protein S23	yes	no	0.908	0.552	0.784	2e-31
P62267	143	40S ribosomal protein S23	yes	no	0.908	0.552	0.784	2e-31
P62266	143	40S ribosomal protein S23	yes	no	0.908	0.552	0.784	2e-31
P62298	143	40S ribosomal protein S23	N/A	no	0.908	0.552	0.784	2e-31
Q3T199	143	40S ribosomal protein S23	yes	no	0.908	0.552	0.784	2e-31

>sp|Q9M5Z9|RS23_EUPES 40S ribosomal protein S23 OS=Euphorbia esula GN=RPS23 PE=2 SV=1

 Score =  140 bits (353), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 67/79 (84%), Positives = 71/79 (89%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PFAG SHAKGIVLEKIGIEAKQPN AIRKC+RVQLIKNGKKI  FVP+DGCLNYIEEND+
Sbjct: 39  PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDE 98

Query: 61  VLIAGFGRKGHAVATSPPI 79
           VLIAGFGRKGHAV   P +
Sbjct: 99  VLIAGFGRKGHAVGDIPGV 117

Euphorbia esula (taxid: 3993)

>sp|P46297|RS23_FRAAN 40S ribosomal protein S23 OS=Fragaria ananassa GN=RPS23 PE=2 SV=1

 Score =  140 bits (353), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 67/79 (84%), Positives = 71/79 (89%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PFAG SHAKGIVLEKIGIEAKQPN AIRKC+RVQLIKNGKKI  FVP+DGCLNYIEEND+
Sbjct: 39  PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDE 98

Query: 61  VLIAGFGRKGHAVATSPPI 79
           VLIAGFGRKGHAV   P +
Sbjct: 99  VLIAGFGRKGHAVGDIPGV 117

Fragaria ananassa (taxid: 3747)

>sp|P49201|RS232_ARATH 40S ribosomal protein S23-2 OS=Arabidopsis thaliana GN=RPS23B PE=2 SV=2

 Score =  140 bits (352), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 67/79 (84%), Positives = 71/79 (89%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PFAG SHAKGIVLEKIGIEAKQPN AIRKC+RVQLIKNGKKI  FVP+DGCLNYIEEND+
Sbjct: 39  PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDE 98

Query: 61  VLIAGFGRKGHAVATSPPI 79
           VLIAGFGRKGHAV   P +
Sbjct: 99  VLIAGFGRKGHAVGDIPGV 117

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SF35|RS231_ARATH 40S ribosomal protein S23-1 OS=Arabidopsis thaliana GN=RPS23A PE=2 SV=2

 Score =  136 bits (343), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 66/79 (83%), Positives = 70/79 (88%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PFA  SHAKGIVLEKIGIEAKQPN AIRKC+RVQLIKNGKKI  FVP+DGCLNYIEEND+
Sbjct: 39  PFACSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDE 98

Query: 61  VLIAGFGRKGHAVATSPPI 79
           VLIAGFGRKGHAV   P +
Sbjct: 99  VLIAGFGRKGHAVGDIPGV 117

Arabidopsis thaliana (taxid: 3702)

>sp|Q86FP7|RS23_DERVA 40S ribosomal protein S23 OS=Dermacentor variabilis GN=RpS23 PE=2 SV=1

 Score =  135 bits (339), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 63/79 (79%), Positives = 68/79 (86%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PF G SHAKGIVLEK+G+EAKQPN AIRKC RVQLIKNGKKI  FVP DGCLNYIEEND+
Sbjct: 40  PFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDE 99

Query: 61  VLIAGFGRKGHAVATSPPI 79
           VL+AGFGRKGHAV   P +
Sbjct: 100 VLVAGFGRKGHAVGDIPGV 118

Dermacentor variabilis (taxid: 34621)

>sp|P62268|RS23_RAT 40S ribosomal protein S23 OS=Rattus norvegicus GN=Rps23 PE=1 SV=3

 Score =  134 bits (336), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 62/79 (78%), Positives = 69/79 (87%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PF G SHAKGIVLEK+G+EAKQPN AIRKC RVQLIKNGKKI  FVP+DGCLN+IEEND+
Sbjct: 40  PFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDE 99

Query: 61  VLIAGFGRKGHAVATSPPI 79
           VL+AGFGRKGHAV   P +
Sbjct: 100 VLVAGFGRKGHAVGDIPGV 118

Rattus norvegicus (taxid: 10116)

>sp|P62267|RS23_MOUSE 40S ribosomal protein S23 OS=Mus musculus GN=Rps23 PE=2 SV=3

 Score =  134 bits (336), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 62/79 (78%), Positives = 69/79 (87%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PF G SHAKGIVLEK+G+EAKQPN AIRKC RVQLIKNGKKI  FVP+DGCLN+IEEND+
Sbjct: 40  PFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDE 99

Query: 61  VLIAGFGRKGHAVATSPPI 79
           VL+AGFGRKGHAV   P +
Sbjct: 100 VLVAGFGRKGHAVGDIPGV 118

Mus musculus (taxid: 10090)

>sp|P62266|RS23_HUMAN 40S ribosomal protein S23 OS=Homo sapiens GN=RPS23 PE=1 SV=3

 Score =  134 bits (336), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 62/79 (78%), Positives = 69/79 (87%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PF G SHAKGIVLEK+G+EAKQPN AIRKC RVQLIKNGKKI  FVP+DGCLN+IEEND+
Sbjct: 40  PFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDE 99

Query: 61  VLIAGFGRKGHAVATSPPI 79
           VL+AGFGRKGHAV   P +
Sbjct: 100 VLVAGFGRKGHAVGDIPGV 118

Homo sapiens (taxid: 9606)

>sp|P62298|RS23_CHILA 40S ribosomal protein S23 OS=Chinchilla lanigera GN=RPS23 PE=2 SV=1

 Score =  134 bits (336), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 62/79 (78%), Positives = 69/79 (87%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PF G SHAKGIVLEK+G+EAKQPN AIRKC RVQLIKNGKKI  FVP+DGCLN+IEEND+
Sbjct: 40  PFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDE 99

Query: 61  VLIAGFGRKGHAVATSPPI 79
           VL+AGFGRKGHAV   P +
Sbjct: 100 VLVAGFGRKGHAVGDIPGV 118

Chinchilla lanigera (taxid: 34839)

>sp|Q3T199|RS23_BOVIN 40S ribosomal protein S23 OS=Bos taurus GN=RPS23 PE=2 SV=1

 Score =  134 bits (336), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 62/79 (78%), Positives = 69/79 (87%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PF G SHAKGIVLEK+G+EAKQPN AIRKC RVQLIKNGKKI  FVP+DGCLN+IEEND+
Sbjct: 40  PFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDE 99

Query: 61  VLIAGFGRKGHAVATSPPI 79
           VL+AGFGRKGHAV   P +
Sbjct: 100 VLVAGFGRKGHAVGDIPGV 118

Bos taurus (taxid: 9913)

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	87
413932621	1166	PHD finger protein [Zea mays]	0.908	0.067	0.835	1e-32
296086075	198	unnamed protein product [Vitis vinifera]	0.908	0.398	0.848	6e-32
405977517	698	40S ribosomal protein S23 [Crassostrea g	0.908	0.113	0.784	8e-32
388510820	142	unknown [Lotus japonicus]	0.908	0.556	0.848	9e-32
255565826	142	40S ribosomal protein S23, putative [Ric	0.908	0.556	0.848	9e-32
388521427	142	unknown [Lotus japonicus]	0.908	0.556	0.848	9e-32
225439888	142	PREDICTED: 40S ribosomal protein S23-lik	0.908	0.556	0.848	9e-32
192910822	142	40S ribosomal protein S23 [Elaeis guinee	0.908	0.556	0.848	9e-32
224069336	142	predicted protein [Populus trichocarpa]	0.908	0.556	0.848	1e-31
62287478	142	RecName: Full=40S ribosomal protein S23	0.908	0.556	0.848	1e-31

>gi|413932621|gb|AFW67172.1| PHD finger protein [Zea mays]

 Score =  143 bits (360), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 66/79 (83%), Positives = 71/79 (89%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PFAG SHAKGIVLEKIGIEAKQPN AIRKC+RVQL+KNGKKI  FVP+DGCLNYIEEND+
Sbjct: 39  PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLVKNGKKIAAFVPNDGCLNYIEENDE 98

Query: 61  VLIAGFGRKGHAVATSPPI 79
           VLIAGFGRKGHAV   P +
Sbjct: 99  VLIAGFGRKGHAVGDIPGV 117

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296086075|emb|CBI31516.3| unnamed protein product [Vitis vinifera]

 Score =  141 bits (355), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 67/79 (84%), Positives = 71/79 (89%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PFAG SHAKGIVLEKIGIEAKQPN AIRKC+RVQLIKNGKKI  FVP+DGCLNYIEEND+
Sbjct: 95  PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDE 154

Query: 61  VLIAGFGRKGHAVATSPPI 79
           VLIAGFGRKGHAV   P +
Sbjct: 155 VLIAGFGRKGHAVGDIPGV 173

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|405977517|gb|EKC41960.1| 40S ribosomal protein S23 [Crassostrea gigas]

 Score =  140 bits (354), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 62/79 (78%), Positives = 69/79 (87%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PF G SHAKGIVLEK+G+EAKQPN AIRKC RVQLIKNGKKI  FVP+DGCLNY+EEND+
Sbjct: 39  PFQGSSHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNYVEENDE 98

Query: 61  VLIAGFGRKGHAVATSPPI 79
           VL+AGFGRKGHAV   P +
Sbjct: 99  VLVAGFGRKGHAVGDIPGV 117

Source: Crassostrea gigas

Species: Crassostrea gigas

Genus: Crassostrea

Family: Ostreidae

Order: Ostreoida

Class: Bivalvia

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|388510820|gb|AFK43476.1| unknown [Lotus japonicus]

 Score =  140 bits (353), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 67/79 (84%), Positives = 71/79 (89%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PFAG SHAKGIVLEKIGIEAKQPN AIRKC+RVQLIKNGKKI  FVP+DGCLNYIEEND+
Sbjct: 39  PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDE 98

Query: 61  VLIAGFGRKGHAVATSPPI 79
           VLIAGFGRKGHAV   P +
Sbjct: 99  VLIAGFGRKGHAVGDIPGV 117

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255565826|ref|XP_002523902.1| 40S ribosomal protein S23, putative [Ricinus communis] gi|255568414|ref|XP_002525181.1| 40S ribosomal protein S23, putative [Ricinus communis] gi|223535478|gb|EEF37147.1| 40S ribosomal protein S23, putative [Ricinus communis] gi|223536832|gb|EEF38471.1| 40S ribosomal protein S23, putative [Ricinus communis]

 Score =  140 bits (353), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 67/79 (84%), Positives = 71/79 (89%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PFAG SHAKGIVLEKIGIEAKQPN AIRKC+RVQLIKNGKKI  FVP+DGCLNYIEEND+
Sbjct: 39  PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDE 98

Query: 61  VLIAGFGRKGHAVATSPPI 79
           VLIAGFGRKGHAV   P +
Sbjct: 99  VLIAGFGRKGHAVGDIPGV 117

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388521427|gb|AFK48775.1| unknown [Lotus japonicus]

 Score =  140 bits (353), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 67/79 (84%), Positives = 71/79 (89%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PFAG SHAKGIVLEKIGIEAKQPN AIRKC+RVQLIKNGKKI  FVP+DGCLNYIEEND+
Sbjct: 39  PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDE 98

Query: 61  VLIAGFGRKGHAVATSPPI 79
           VLIAGFGRKGHAV   P +
Sbjct: 99  VLIAGFGRKGHAVGDIPGV 117

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225439888|ref|XP_002279025.1| PREDICTED: 40S ribosomal protein S23-like [Vitis vinifera]

 Score =  140 bits (353), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 67/79 (84%), Positives = 71/79 (89%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PFAG SHAKGIVLEKIGIEAKQPN AIRKC+RVQLIKNGKKI  FVP+DGCLNYIEEND+
Sbjct: 39  PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDE 98

Query: 61  VLIAGFGRKGHAVATSPPI 79
           VLIAGFGRKGHAV   P +
Sbjct: 99  VLIAGFGRKGHAVGDIPGV 117

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|192910822|gb|ACF06519.1| 40S ribosomal protein S23 [Elaeis guineensis]

 Score =  140 bits (353), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 67/79 (84%), Positives = 71/79 (89%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PFAG SHAKGIVLEKIGIEAKQPN AIRKC+RVQLIKNGKKI  FVP+DGCLNYIEEND+
Sbjct: 39  PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDE 98

Query: 61  VLIAGFGRKGHAVATSPPI 79
           VLIAGFGRKGHAV   P +
Sbjct: 99  VLIAGFGRKGHAVGDIPGV 117

Source: Elaeis guineensis

Species: Elaeis guineensis

Genus: Elaeis

Family: Arecaceae

Order: Arecales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224069336|ref|XP_002326333.1| predicted protein [Populus trichocarpa] gi|224098071|ref|XP_002311115.1| predicted protein [Populus trichocarpa] gi|224112945|ref|XP_002316341.1| predicted protein [Populus trichocarpa] gi|224140159|ref|XP_002323452.1| predicted protein [Populus trichocarpa] gi|118483731|gb|ABK93759.1| unknown [Populus trichocarpa] gi|118484067|gb|ABK93919.1| unknown [Populus trichocarpa] gi|118487579|gb|ABK95615.1| unknown [Populus trichocarpa] gi|222833526|gb|EEE72003.1| predicted protein [Populus trichocarpa] gi|222850935|gb|EEE88482.1| predicted protein [Populus trichocarpa] gi|222865381|gb|EEF02512.1| predicted protein [Populus trichocarpa] gi|222868082|gb|EEF05213.1| predicted protein [Populus trichocarpa]

 Score =  140 bits (353), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 67/79 (84%), Positives = 71/79 (89%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PFAG SHAKGIVLEKIGIEAKQPN AIRKC+RVQLIKNGKKI  FVP+DGCLNYIEEND+
Sbjct: 39  PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDE 98

Query: 61  VLIAGFGRKGHAVATSPPI 79
           VLIAGFGRKGHAV   P +
Sbjct: 99  VLIAGFGRKGHAVGDIPGV 117

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|62287478|sp|Q9M5Z9.1|RS23_EUPES RecName: Full=40S ribosomal protein S23 gi|6716785|gb|AAF26742.1|AF220539_1 40s ribosomal protein S23 [Euphorbia esula]

 Score =  140 bits (353), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 67/79 (84%), Positives = 71/79 (89%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PFAG SHAKGIVLEKIGIEAKQPN AIRKC+RVQLIKNGKKI  FVP+DGCLNYIEEND+
Sbjct: 39  PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDE 98

Query: 61  VLIAGFGRKGHAVATSPPI 79
           VLIAGFGRKGHAV   P +
Sbjct: 99  VLIAGFGRKGHAVGDIPGV 117

Source: Euphorbia esula

Species: Euphorbia esula

Genus: Euphorbia

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	87
TAIR|locus:2151301	142	AT5G02960 [Arabidopsis thalian	0.908	0.556	0.848	6e-32
TAIR|locus:2074954	142	AT3G09680 [Arabidopsis thalian	0.908	0.556	0.835	5.4e-31
UNIPROTKB|F1NDC2	145	RPS23 "Uncharacterized protein	0.908	0.544	0.784	1.8e-30
UNIPROTKB|E1BEQ3	143	E1BEQ3 "Uncharacterized protei	0.908	0.552	0.784	1.8e-30
UNIPROTKB|Q3T199	143	RPS23 "40S ribosomal protein S	0.908	0.552	0.784	1.8e-30
UNIPROTKB|J9NZX6	143	RPS23 "Uncharacterized protein	0.908	0.552	0.784	1.8e-30
UNIPROTKB|D6RD47	134	RPS23 "40S ribosomal protein S	0.908	0.589	0.784	1.8e-30
UNIPROTKB|P62266	143	RPS23 "40S ribosomal protein S	0.908	0.552	0.784	1.8e-30
UNIPROTKB|F2Z512	143	RPS23 "40S ribosomal protein S	0.908	0.552	0.784	1.8e-30
UNIPROTKB|Q6SA96	143	RPS23 "40S ribosomal protein S	0.908	0.552	0.784	1.8e-30

TAIR|locus:2151301 AT5G02960 [Arabidopsis thaliana (taxid:3702)]

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 67/79 (84%), Positives = 71/79 (89%)

Query:     1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
             PFAG SHAKGIVLEKIGIEAKQPN AIRKC+RVQLIKNGKKI  FVP+DGCLNYIEEND+
Sbjct:    39 PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDE 98

Query:    61 VLIAGFGRKGHAVATSPPI 79
             VLIAGFGRKGHAV   P +
Sbjct:    99 VLIAGFGRKGHAVGDIPGV 117

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

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0022626 "cytosolic ribosome" evidence=IDA

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

GO:0005794 "Golgi apparatus" evidence=RCA

TAIR|locus:2074954 AT3G09680 [Arabidopsis thaliana (taxid:3702)]

 Score = 341 (125.1 bits), Expect = 5.4e-31, P = 5.4e-31
 Identities = 66/79 (83%), Positives = 70/79 (88%)

Query:     1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
             PFA  SHAKGIVLEKIGIEAKQPN AIRKC+RVQLIKNGKKI  FVP+DGCLNYIEEND+
Sbjct:    39 PFACSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDE 98

Query:    61 VLIAGFGRKGHAVATSPPI 79
             VLIAGFGRKGHAV   P +
Sbjct:    99 VLIAGFGRKGHAVGDIPGV 117

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

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0005730 "nucleolus" evidence=IDA

GO:0022626 "cytosolic ribosome" evidence=IDA

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

GO:0005794 "Golgi apparatus" evidence=RCA

UNIPROTKB|F1NDC2 RPS23 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 336 (123.3 bits), Expect = 1.8e-30, P = 1.8e-30
 Identities = 62/79 (78%), Positives = 69/79 (87%)

Query:     1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
             PF G SHAKGIVLEK+G+EAKQPN AIRKC RVQLIKNGKKI  FVP+DGCLN+IEEND+
Sbjct:    42 PFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDE 101

Query:    61 VLIAGFGRKGHAVATSPPI 79
             VL+AGFGRKGHAV   P +
Sbjct:   102 VLVAGFGRKGHAVGDIPGV 120

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

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|E1BEQ3 E1BEQ3 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 336 (123.3 bits), Expect = 1.8e-30, P = 1.8e-30
 Identities = 62/79 (78%), Positives = 69/79 (87%)

Query:     1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
             PF G SHAKGIVLEK+G+EAKQPN AIRKC RVQLIKNGKKI  FVP+DGCLN+IEEND+
Sbjct:    40 PFGGTSHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDE 99

Query:    61 VLIAGFGRKGHAVATSPPI 79
             VL+AGFGRKGHAV   P +
Sbjct:   100 VLVAGFGRKGHAVGDIPGV 118

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|Q3T199 RPS23 "40S ribosomal protein S23" [Bos taurus (taxid:9913)]

 Score = 336 (123.3 bits), Expect = 1.8e-30, P = 1.8e-30
 Identities = 62/79 (78%), Positives = 69/79 (87%)

Query:     1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
             PF G SHAKGIVLEK+G+EAKQPN AIRKC RVQLIKNGKKI  FVP+DGCLN+IEEND+
Sbjct:    40 PFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDE 99

Query:    61 VLIAGFGRKGHAVATSPPI 79
             VL+AGFGRKGHAV   P +
Sbjct:   100 VLVAGFGRKGHAVGDIPGV 118

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|J9NZX6 RPS23 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 336 (123.3 bits), Expect = 1.8e-30, P = 1.8e-30
 Identities = 62/79 (78%), Positives = 69/79 (87%)

Query:     1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
             PF G SHAKGIVLEK+G+EAKQPN AIRKC RVQLIKNGKKI  FVP+DGCLN+IEEND+
Sbjct:    40 PFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDE 99

Query:    61 VLIAGFGRKGHAVATSPPI 79
             VL+AGFGRKGHAV   P +
Sbjct:   100 VLVAGFGRKGHAVGDIPGV 118

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|D6RD47 RPS23 "40S ribosomal protein S23" [Homo sapiens (taxid:9606)]

 Score = 336 (123.3 bits), Expect = 1.8e-30, P = 1.8e-30
 Identities = 62/79 (78%), Positives = 69/79 (87%)

Query:     1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
             PF G SHAKGIVLEK+G+EAKQPN AIRKC RVQLIKNGKKI  FVP+DGCLN+IEEND+
Sbjct:    40 PFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDE 99

Query:    61 VLIAGFGRKGHAVATSPPI 79
             VL+AGFGRKGHAV   P +
Sbjct:   100 VLVAGFGRKGHAVGDIPGV 118

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

GO:0006412 "translation" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=IEA

UNIPROTKB|P62266 RPS23 "40S ribosomal protein S23" [Homo sapiens (taxid:9606)]

 Score = 336 (123.3 bits), Expect = 1.8e-30, P = 1.8e-30
 Identities = 62/79 (78%), Positives = 69/79 (87%)

Query:     1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
             PF G SHAKGIVLEK+G+EAKQPN AIRKC RVQLIKNGKKI  FVP+DGCLN+IEEND+
Sbjct:    40 PFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDE 99

Query:    61 VLIAGFGRKGHAVATSPPI 79
             VL+AGFGRKGHAV   P +
Sbjct:   100 VLVAGFGRKGHAVGDIPGV 118

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

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

GO:0006412 "translation" evidence=IC;TAS

GO:0003674 "molecular_function" evidence=ND

GO:0005840 "ribosome" evidence=NAS

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:0005515 "protein binding" evidence=IPI

UNIPROTKB|F2Z512 RPS23 "40S ribosomal protein S23" [Sus scrofa (taxid:9823)]

 Score = 336 (123.3 bits), Expect = 1.8e-30, P = 1.8e-30
 Identities = 62/79 (78%), Positives = 69/79 (87%)

Query:     1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
             PF G SHAKGIVLEK+G+EAKQPN AIRKC RVQLIKNGKKI  FVP+DGCLN+IEEND+
Sbjct:    40 PFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDE 99

Query:    61 VLIAGFGRKGHAVATSPPI 79
             VL+AGFGRKGHAV   P +
Sbjct:   100 VLVAGFGRKGHAVGDIPGV 118

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

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|Q6SA96 RPS23 "40S ribosomal protein S23" [Sus scrofa (taxid:9823)]

 Score = 336 (123.3 bits), Expect = 1.8e-30, P = 1.8e-30
 Identities = 62/79 (78%), Positives = 69/79 (87%)

Query:     1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
             PF G SHAKGIVLEK+G+EAKQPN AIRKC RVQLIKNGKKI  FVP+DGCLN+IEEND+
Sbjct:    40 PFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDE 99

Query:    61 VLIAGFGRKGHAVATSPPI 79
             VL+AGFGRKGHAV   P +
Sbjct:   100 VLVAGFGRKGHAVGDIPGV 118

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P79057	RS23_SCHPO	No assigned EC number	0.7088	0.9080	0.5524	yes	no
P49201	RS232_ARATH	No assigned EC number	0.8481	0.9080	0.5563	yes	no
Q19877	RS23_CAEEL	No assigned EC number	0.7594	0.9080	0.5524	yes	no
P62266	RS23_HUMAN	No assigned EC number	0.7848	0.9080	0.5524	yes	no
P62267	RS23_MOUSE	No assigned EC number	0.7848	0.9080	0.5524	yes	no
Q873W8	RS23_ASPFU	No assigned EC number	0.7215	0.9080	0.5448	yes	no
Q55A19	RS23_DICDI	No assigned EC number	0.7088	0.9080	0.5524	yes	no
P0CX29	RS23A_YEAST	No assigned EC number	0.7215	0.9080	0.5448	yes	no
P62268	RS23_RAT	No assigned EC number	0.7848	0.9080	0.5524	yes	no
Q9SF35	RS231_ARATH	No assigned EC number	0.8354	0.9080	0.5563	yes	no
Q8T3U2	RS23_DROME	No assigned EC number	0.7848	0.9080	0.5524	yes	no
Q8I7D5	RS23_CIOIN	No assigned EC number	0.7974	0.9080	0.5524	yes	no
P0CX30	RS23B_YEAST	No assigned EC number	0.7215	0.9080	0.5448	yes	no
P0CY40	RS23B_NAUCC	No assigned EC number	0.7215	0.9080	0.5448	yes	no
Q6SA96	RS23_PIG	No assigned EC number	0.7848	0.9080	0.5524	yes	no
Q3T199	RS23_BOVIN	No assigned EC number	0.7848	0.9080	0.5524	yes	no
P0CY39	RS23A_NAUCC	No assigned EC number	0.7215	0.9080	0.5448	yes	no
Q6FLA8	RS23_CANGA	No assigned EC number	0.7215	0.9080	0.5448	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_Genewise1_v1.C_95480002	annotation not avaliable (136 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.XVI.1998.1	SubName- Full=Putative uncharacterized protein; (204 aa)	•			•	•	•	•		0.782
	eugene3.00061162	SubName- Full=Putative uncharacterized protein; (208 aa)	•			•	•	•	•		0.774
	eugene3.00091453	SubName- Full=Putative uncharacterized protein; (151 aa)			•	•			•		0.528
	estExt_fgenesh4_pg.C_LG_XI0480	SubName- Full=Putative uncharacterized protein; (151 aa)			•	•			•		0.528
	estExt_fgenesh4_kg.C_LG_IV0037	SubName- Full=Putative uncharacterized protein; (152 aa)			•	•			•		0.526
	gw1.57.264.1	SubName- Full=Putative uncharacterized protein; (258 aa)			•	•			•		0.515
	estExt_Genewise1_v1.C_LG_VII3915	SubName- Full=Putative uncharacterized protein; (260 aa)			•	•			•		0.514
	estExt_Genewise1_v1.C_LG_III1727	RecName- Full=Ribosomal protein L37;; Binds to the 23S rRNA (By similarity) (96 aa)			•	•			•		0.479
	estExt_Genewise1_v1.C_LG_I0199	RecName- Full=Ribosomal protein L37;; Binds to the 23S rRNA (By similarity) (96 aa)			•	•			•		0.479
	estExt_fgenesh4_pm.C_LG_VIII0253	RecName- Full=60S acidic ribosomal protein P0; (323 aa)			•	•		•			0.471

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	87
PTZ00067	143	PTZ00067, PTZ00067, 40S ribosomal S23; Provisional	1e-45
cd03367	115	cd03367, Ribosomal_S23, S12-like family, 40S ribos	5e-45
PRK04211	145	PRK04211, rps12P, 30S ribosomal protein S12P; Revi	7e-31
TIGR00982	139	TIGR00982, S23_S12_E_A, ribosomal protein S23 (S12	2e-27
cd00319	95	cd00319, Ribosomal_S12_like, Ribosomal protein S12	1e-25
pfam00164	122	pfam00164, Ribosomal_S12, Ribosomal protein S12	9e-24
COG0048	129	COG0048, RpsL, Ribosomal protein S12 [Translation,	2e-22
cd03368	108	cd03368, Ribosomal_S12, S12-like family, 30S ribos	3e-04
CHL00051	123	CHL00051, rps12, ribosomal protein S12	5e-04
TIGR00981	124	TIGR00981, rpsL_bact, ribosomal protein S12, bacte	0.004

>gnl|CDD|185422 PTZ00067, PTZ00067, 40S ribosomal S23; Provisional

 Score =  142 bits (361), Expect = 1e-45
 Identities = 60/77 (77%), Positives = 66/77 (85%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PF G SHAKGIV+EKIGIEAKQPN AIRKC RVQLIKNGKKI  FVP+DGCLN+I END+
Sbjct: 40  PFGGASHAKGIVVEKIGIEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFINENDE 99

Query: 61  VLIAGFGRKGHAVATSP 77
           VL++GFGR GHAV   P
Sbjct: 100 VLVSGFGRSGHAVGDIP 116

Length = 143

>gnl|CDD|239465 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

 Score =  140 bits (354), Expect = 5e-45
 Identities = 58/77 (75%), Positives = 64/77 (83%)

Query: 1  PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
          P  G  HAKGIVLEK+G+EAKQPN AIRKC RVQLIKNGKKI  FVP DGCLN+I+END+
Sbjct: 15 PLGGAPHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPGDGCLNFIDENDE 74

Query: 61 VLIAGFGRKGHAVATSP 77
          VL+AGFGRKG AV   P
Sbjct: 75 VLVAGFGRKGRAVGDIP 91

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. Length = 115

>gnl|CDD|235257 PRK04211, rps12P, 30S ribosomal protein S12P; Reviewed

 Score =  105 bits (264), Expect = 7e-31
 Identities = 44/73 (60%), Positives = 56/73 (76%), Gaps = 1/73 (1%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           P  G   A+GIVLEK+G+EAKQPN AIRKC RVQLIKNGK++  F P DG +N+I+E+D+
Sbjct: 41  PLEGAPMARGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKQVTAFCPGDGAINFIDEHDE 100

Query: 61  VLIAGF-GRKGHA 72
           V+I G  G KG +
Sbjct: 101 VVIEGIGGPKGRS 113

Length = 145

>gnl|CDD|130055 TIGR00982, S23_S12_E_A, ribosomal protein S23 (S12)

 Score = 96.5 bits (240), Expect = 2e-27
 Identities = 43/80 (53%), Positives = 58/80 (72%), Gaps = 1/80 (1%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           P  G   A+GIVLEK+G+EA+QPN AIRKC RVQLIKNGK +  F P DG +N+I+E+D+
Sbjct: 35  PLEGAPMARGIVLEKVGVEARQPNSAIRKCVRVQLIKNGKVVTAFCPGDGAINFIDEHDE 94

Query: 61  VLIAGF-GRKGHAVATSPPI 79
           V+I G  G +G ++   P +
Sbjct: 95  VIIEGIGGPRGRSMGDIPGV 114

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 [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 139

>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 = 90.9 bits (225), Expect = 1e-25
 Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 3/65 (4%)

Query: 1  PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
             G    +G+      +  K+PN A+RK ++V+L  +G ++  ++P +G  + ++E+  
Sbjct: 8  ALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLT-SGYEVTAYIPGEG--HNLQEHSV 64

Query: 61 VLIAG 65
          VLI G
Sbjct: 65 VLIRG 69

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

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

 Score = 86.6 bits (215), Expect = 9e-24
 Identities = 28/69 (40%), Positives = 42/69 (60%), Gaps = 3/69 (4%)

Query: 1  PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
             G    +GI LE   I  K+PN A+RK +RV+LI NGK++  ++P DG  + ++E+ +
Sbjct: 22 ALEGCPQKRGICLEVYTITPKKPNSALRKVARVRLI-NGKEVTAYIPGDG--HNLQEHSE 78

Query: 61 VLIAGFGRK 69
          VLI G   K
Sbjct: 79 VLIRGGRVK 87

Length = 122

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

 Score = 83.4 bits (207), Expect = 2e-22
 Identities = 24/69 (34%), Positives = 40/69 (57%), Gaps = 3/69 (4%)

Query: 1  PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
             G   A+G+      +  K+PN A+RK +RV+LI NGK++  ++P +G    ++E+ +
Sbjct: 29 ALEGAPQARGVCTRVYTVTPKKPNSALRKVARVRLI-NGKEVTAYIPGEGHN--LQEHSE 85

Query: 61 VLIAGFGRK 69
          VLI G   K
Sbjct: 86 VLIRGGRVK 94

Length = 129

>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 = 36.3 bits (85), Expect = 3e-04
 Identities = 23/60 (38%), Positives = 39/60 (65%), Gaps = 4/60 (6%)

Query: 9  KGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGR 68
          KG+ L+      K+PN A+RK +RV+L  NGK++  ++P +G  + ++E+  VL+ G GR
Sbjct: 29 KGVCLKVYTTTPKKPNSALRKVARVRL-SNGKEVTAYIPGEG--HNLQEHSVVLVRG-GR 84

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|176992 CHL00051, rps12, ribosomal protein S12

 Score = 35.8 bits (83), Expect = 5e-04
 Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 4/60 (6%)

Query: 9  KGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGR 68
          +G       I  K+PN A+RK +RV+L  +G +I  ++P  G  + ++E+  VL+ G GR
Sbjct: 31 RGTCTRVYTITPKKPNSALRKVARVRL-TSGFEITAYIPGIG--HNLQEHSVVLVRG-GR 86

Length = 123

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

 Score = 33.2 bits (76), Expect = 0.004
 Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 4/60 (6%)

Query: 9  KGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGR 68
          +G+         K+PN A+RK +RV+L  NG ++  ++P +G  + ++E+  VLI G GR
Sbjct: 31 RGVCTRVYTTTPKKPNSALRKVARVRL-TNGFEVTAYIPGEG--HNLQEHSVVLIRG-GR 86

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	87
cd03367	115	Ribosomal_S23 S12-like family, 40S ribosomal prote	100.0
PTZ00067	143	40S ribosomal S23; Provisional	100.0
TIGR00982	139	S23_S12_E_A ribosomal protein S23 (S12). This mode	100.0
PRK04211	145	rps12P 30S ribosomal protein S12P; Reviewed	100.0
KOG1749	143	consensus 40S ribosomal protein S23 [Translation,	100.0
cd00319	95	Ribosomal_S12_like Ribosomal protein S12-like fami	100.0
COG0048	129	RpsL Ribosomal protein S12 [Translation, ribosomal	100.0
cd03368	108	Ribosomal_S12 S12-like family, 30S ribosomal prote	100.0
PRK05163	124	rpsL 30S ribosomal protein S12; Validated	100.0
CHL00051	123	rps12 ribosomal protein S12	100.0
TIGR00981	124	rpsL_bact ribosomal protein S12, bacterial/organel	100.0
PF00164	122	Ribosom_S12_S23: Ribosomal protein S12/S23; InterP	100.0
PTZ00115	290	40S ribosomal protein S12; Provisional	100.0
KOG1750	139	consensus Mitochondrial/chloroplast ribosomal prot	99.97
TIGR00008	68	infA translation initiation factor IF-1. This fami	95.21
COG0361	75	InfA Translation initiation factor 1 (IF-1) [Trans	93.57
PRK12442	87	translation initiation factor IF-1; Reviewed	90.25
smart00652	83	eIF1a eukaryotic translation initiation factor 1A.	88.34
cd04456	78	S1_IF1A_like S1_IF1A_like: Translation initiation	86.57
TIGR00523	99	eIF-1A eukaryotic/archaeal initiation factor 1A. R	81.48

>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=100.00  E-value=5.3e-49  Score=275.72  Aligned_cols=81  Identities=72%  Similarity=1.175  Sum_probs=80.0

Q ss_pred             CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342            1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII   80 (87)
Q Consensus         1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~   80 (87)
                      ||+++||+||||++++++||||||||+||||||||++||++|||||||||||+||||||+|||+|||++|++++|||||+
T Consensus        15 ~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~~ngk~itAyIPG~G~~~~lqeh~~VLV~G~G~~Gg~v~DlPGVr   94 (115)
T cd03367          15 PLGGAPHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPGDGCLNFIDENDEVLVAGFGRKGRAVGDIPGVR   94 (115)
T ss_pred             cccCCCccCeEEEEEeecCCCCCChhhceEEEEEEccCCeEEEEEeCCCCcccccccCCEEEEEecccCCCccCCCCceE
Confidence            79999999999999999999999999999999999899999999999999999999999999999999999999999999


Q ss_pred             e
Q 042342           81 S   81 (87)
Q Consensus        81 y   81 (87)
                      |
T Consensus        95 y   95 (115)
T cd03367          95 F   95 (115)
T ss_pred             E
Confidence            8

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.

>PTZ00067 40S ribosomal S23; Provisional

Probab=100.00  E-value=1e-47  Score=277.17  Aligned_cols=81  Identities=74%  Similarity=1.200  Sum_probs=79.9

Q ss_pred             CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342            1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII   80 (87)
Q Consensus         1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~   80 (87)
                      ||+++||++|||++++++||||||||+||||||||++||++|||||||||+|+||||||+|||+||||+|++++|||||+
T Consensus        40 pl~g~pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~kngk~vtAyiPg~G~lh~lqEh~~VLV~G~Gr~g~~v~DlPGVr  119 (143)
T PTZ00067         40 PFGGASHAKGIVVEKIGIEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFINENDEVLVSGFGRSGHAVGDIPGVR  119 (143)
T ss_pred             cccCCCccceEEEEEEeecCCCCChhhceEEEEEEccCCcEEEEEeCCCCcccccccCCEEEEEecCcCCCccCCCCceE
Confidence            89999999999999999999999999999999999889999999999999888999999999999999999999999999


Q ss_pred             e
Q 042342           81 S   81 (87)
Q Consensus        81 y   81 (87)
                      |
T Consensus       120 y  120 (143)
T PTZ00067        120 F  120 (143)
T ss_pred             E
Confidence            8

>TIGR00982 S23_S12_E_A ribosomal protein S23 (S12)

Probab=100.00  E-value=2.1e-47  Score=274.50  Aligned_cols=81  Identities=53%  Similarity=0.971  Sum_probs=79.9

Q ss_pred             CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecC-CCCCCCCCCCCc
Q 042342            1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFG-RKGHAVATSPPI   79 (87)
Q Consensus         1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfG-r~g~~v~DlPGV   79 (87)
                      ||+++||+||||++++++||||||||+||||||||++||++||||||||||+|||||||+|||+||| ++|++++|||||
T Consensus        35 ~l~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~~ngk~vtAyiPg~G~~~~lqeh~~VLV~G~gg~~gg~v~DlPGV  114 (139)
T TIGR00982        35 PLEGAPMARGIVLEKVGVEARQPNSAIRKCVRVQLIKNGKVVTAFCPGDGAINFIDEHDEVIIEGIGGPRGRSMGDIPGV  114 (139)
T ss_pred             cccCCCccCeEEEEEEeecCCCCCcccceEEEEEEccCCeEEEEEeCCCccccccccCCEEEEEecCccCCCCcCCCCce
Confidence            7999999999999999999999999999999999999999999999999999999999999999998 999999999999


Q ss_pred             ee
Q 042342           80 IS   81 (87)
Q Consensus        80 ~y   81 (87)
                      +|
T Consensus       115 ry  116 (139)
T TIGR00982       115 RY  116 (139)
T ss_pred             EE
Confidence            99

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.

>PRK04211 rps12P 30S ribosomal protein S12P; Reviewed

Probab=100.00  E-value=2e-47  Score=276.07  Aligned_cols=81  Identities=56%  Similarity=0.984  Sum_probs=79.9

Q ss_pred             CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecC-CCCCCCCCCCCc
Q 042342            1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFG-RKGHAVATSPPI   79 (87)
Q Consensus         1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfG-r~g~~v~DlPGV   79 (87)
                      ||+++||++|||++++++||||||||+||||||||++||++||||||||||+|||||||+|||+||| ++|++++|||||
T Consensus        41 ~l~g~Pq~kGivl~~~~v~pKKPNSA~RK~arV~L~~Ngk~vtAyIPg~G~~~~lqEh~~VLV~G~gg~~gg~v~DlPGV  120 (145)
T PRK04211         41 PLEGAPMARGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKQVTAFCPGDGAINFIDEHDEVVIEGIGGPKGRSMGDIPGV  120 (145)
T ss_pred             cccCCCccCeEEEEEeeecCCCCchhhceeEEEEEccCCeEEEEEeCCCccccccccCCEEEEeecCccCCCCcCCCCce
Confidence            7999999999999999999999999999999999999999999999999999999999999999998 999999999999


Q ss_pred             ee
Q 042342           80 IS   81 (87)
Q Consensus        80 ~y   81 (87)
                      +|
T Consensus       121 ry  122 (145)
T PRK04211        121 RY  122 (145)
T ss_pred             EE
Confidence            98

>KOG1749 consensus 40S ribosomal protein S23 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=3.5e-46  Score=267.79  Aligned_cols=81  Identities=78%  Similarity=1.235  Sum_probs=80.3

Q ss_pred             CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342            1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII   80 (87)
Q Consensus         1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~   80 (87)
                      ||+|+||+||||||++++|+||||||+|||+|||||+|||+||||+|.||||||++|||+|||.||||+||+++||||||
T Consensus        40 pfggashAKgIvLEKigVEAKQPNSAiRKcvRvQLIkngKKITafVp~dgcln~ieendevlv~gfgrkg~avgdipgvr  119 (143)
T KOG1749|consen   40 PFGGASHAKGIVLEKIGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVR  119 (143)
T ss_pred             CCCCccccceeEEEeeeeeccCCcHHHhhheeeeeeeCCceEEEEecCCCceeeeccCCeeeeeccCccCccccCCCceE
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             e
Q 042342           81 S   81 (87)
Q Consensus        81 y   81 (87)
                      +
T Consensus       120 f  120 (143)
T KOG1749|consen  120 F  120 (143)
T ss_pred             E
Confidence            7

>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=1.1e-44  Score=246.87  Aligned_cols=73  Identities=30%  Similarity=0.597  Sum_probs=71.5

Q ss_pred             CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342            1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII   80 (87)
Q Consensus         1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~   80 (87)
                      ||+++||+||||+++++++|||||||+|||||||| +||++|+||||||||  ||||||+|||+| ||    ++|||||+
T Consensus         8 ~l~~~Pq~kGi~l~~~~~~pKkPNSA~RK~arV~L-~ngk~v~ayIPg~Gh--~lqeh~~VLvrG-Gr----~~DlPGVr   79 (95)
T cd00319           8 ALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRL-TSGYEVTAYIPGEGH--NLQEHSVVLIRG-GR----VKDLPGVR   79 (95)
T ss_pred             cccCCcccCeEEEEEEeccccCCChhhceEEEEEc-cCCCEEEEECCCCCc--ccccccEEEEeC-CC----cCCCCCcE
Confidence            79999999999999999999999999999999999 699999999999999  999999999999 99    99999999


Q ss_pred             e
Q 042342           81 S   81 (87)
Q Consensus        81 y   81 (87)
                      |
T Consensus        80 y   80 (95)
T cd00319          80 Y   80 (95)
T ss_pred             E
Confidence            9

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.

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

Probab=100.00  E-value=1.9e-44  Score=256.64  Aligned_cols=73  Identities=37%  Similarity=0.714  Sum_probs=71.4

Q ss_pred             CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342            1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII   80 (87)
Q Consensus         1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~   80 (87)
                      ||+++||++|||+|++++||||||||+||||||||+ ||++||||||||||  +|||||+||||| |+    ++||||||
T Consensus        29 ~L~g~Pq~RGv~~~v~~~~pKkPNSAlRK~~RVrL~-NG~~VtAyiPg~Gh--~lqEH~~Vli~G-~~----v~DlPGVR  100 (129)
T COG0048          29 ALEGAPQARGVCTRVYTVTPKKPNSALRKVARVRLI-NGKEVTAYIPGEGH--NLQEHSEVLIRG-GR----VKDLPGVR  100 (129)
T ss_pred             cccCCCccceEEEEEEecccCCCChhhheeEEEEee-CCcEEEEEcCCCCc--cccccCEEEEec-Cc----cCCCCCce
Confidence            799999999999999999999999999999999995 99999999999999  899999999999 78    99999999


Q ss_pred             e
Q 042342           81 S   81 (87)
Q Consensus        81 y   81 (87)
                      |
T Consensus       101 y  101 (129)
T COG0048         101 Y  101 (129)
T ss_pred             E
Confidence            9

>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=7.5e-44  Score=247.46  Aligned_cols=73  Identities=36%  Similarity=0.664  Sum_probs=71.7

Q ss_pred             CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342            1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII   80 (87)
Q Consensus         1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~   80 (87)
                      ||+++||+||||+++++++|||||||+|||||||| +||++|+||||||||  ||||||+|||+| ||    ++|||||+
T Consensus        21 ~l~g~Pq~kGi~l~v~~~~pKKPNSA~RKvarV~L-~ngk~v~AyIPG~Gh--nlqehs~VLvrG-Gr----v~DlPGVk   92 (108)
T cd03368          21 ALEGCPQKKGVCLKVYTTTPKKPNSALRKVARVRL-SNGKEVTAYIPGEGH--NLQEHSVVLVRG-GR----VKDLPGVR   92 (108)
T ss_pred             cccCCcccCcEEEEEEeccccCCChhheeeEEEEe-cCCCEEEEEcCCCCC--CccccCEEEEeC-Cc----cCCCCCeE
Confidence            68999999999999999999999999999999999 699999999999999  999999999999 99    99999999


Q ss_pred             e
Q 042342           81 S   81 (87)
Q Consensus        81 y   81 (87)
                      |
T Consensus        93 y   93 (108)
T cd03368          93 Y   93 (108)
T ss_pred             E
Confidence            9

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.

>PRK05163 rpsL 30S ribosomal protein S12; Validated

Probab=100.00  E-value=2.6e-43  Score=249.46  Aligned_cols=73  Identities=32%  Similarity=0.579  Sum_probs=71.9

Q ss_pred             CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342            1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII   80 (87)
Q Consensus         1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~   80 (87)
                      ||+++||++|||+++++++|||||||+|||||||| +||++|+||||||||  ||||||+|||+| |+    ++|||||+
T Consensus        23 ~l~~~Pq~kGv~l~v~~~~pKKPNSA~RKvarVrL-~ngk~v~AyIPGeGh--nlqehs~VLvrG-Gr----v~DlPGVr   94 (124)
T PRK05163         23 ALNACPQKRGVCTRVYTTTPKKPNSALRKVARVRL-TNGFEVTAYIPGEGH--NLQEHSVVLIRG-GR----VKDLPGVR   94 (124)
T ss_pred             ccccCcccCcEEEEEEecCccCCCchhheEEEEEe-CCCCEEEEEcCCCCC--CccccCEEEEeC-Cc----cCCCCCcE
Confidence            68999999999999999999999999999999999 999999999999999  999999999999 99    99999999


Q ss_pred             e
Q 042342           81 S   81 (87)
Q Consensus        81 y   81 (87)
                      |
T Consensus        95 y   95 (124)
T PRK05163         95 Y   95 (124)
T ss_pred             E
Confidence            9

>CHL00051 rps12 ribosomal protein S12

Probab=100.00  E-value=2.6e-43  Score=249.19  Aligned_cols=73  Identities=33%  Similarity=0.566  Sum_probs=72.0

Q ss_pred             CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342            1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII   80 (87)
Q Consensus         1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~   80 (87)
                      ||+++||++|||+++++++|||||||+|||||||| +||++|+||||||||  ||||||+||||| ||    ++|||||+
T Consensus        23 ~L~g~Pq~kGv~lkv~~~~pKKPNSA~RKvarVrL-sngk~v~AyIPGeGh--nlqehs~VLvrG-Gr----v~DlPGVr   94 (123)
T CHL00051         23 ALRGCPQRRGTCTRVYTITPKKPNSALRKVARVRL-TSGFEITAYIPGIGH--NLQEHSVVLVRG-GR----VKDLPGVR   94 (123)
T ss_pred             ccccCcccCeEEEEEEeccccCCChhheeEEEEEc-cCCCEEEEEcCCCCc--cccccCEEEEeC-Cc----cCCCCCee
Confidence            68999999999999999999999999999999999 999999999999999  999999999999 99    99999999


Q ss_pred             e
Q 042342           81 S   81 (87)
Q Consensus        81 y   81 (87)
                      |
T Consensus        95 y   95 (123)
T CHL00051         95 Y   95 (123)
T ss_pred             E
Confidence            9

>TIGR00981 rpsL_bact ribosomal protein S12, bacterial/organelle

Probab=100.00  E-value=3.2e-43  Score=249.05  Aligned_cols=73  Identities=32%  Similarity=0.580  Sum_probs=71.9

Q ss_pred             CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342            1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII   80 (87)
Q Consensus         1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~   80 (87)
                      ||+++||++|||+++++++|||||||+|||||||| +||++|+||||||||  ||||||+||||| ||    ++|||||+
T Consensus        23 ~l~g~Pq~kGi~l~~~~~~pKKPNSA~RKvarVrL-~ngk~v~AyIPG~Gh--nlqehs~VLvrG-Gr----v~DlPGVk   94 (124)
T TIGR00981        23 ALEACPQKRGVCTRVYTTTPKKPNSALRKVARVRL-TNGFEVTAYIPGEGH--NLQEHSVVLIRG-GR----VKDLPGVR   94 (124)
T ss_pred             ccccCCccCcEEEEEEeccccCCCchhheeEEEEe-CCCCEEEEEcCCCCC--CccccCEEEEeC-Cc----cCCCCCeE
Confidence            68999999999999999999999999999999999 999999999999999  999999999999 99    99999999


Q ss_pred             e
Q 042342           81 S   81 (87)
Q Consensus        81 y   81 (87)
                      |
T Consensus        95 y   95 (124)
T TIGR00981        95 Y   95 (124)
T ss_pred             E
Confidence            9

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.

>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=8.6e-43  Score=245.73  Aligned_cols=73  Identities=40%  Similarity=0.730  Sum_probs=70.5

Q ss_pred             CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342            1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII   80 (87)
Q Consensus         1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~   80 (87)
                      ||+++||+||||+++++++|||||||+|||||||| +|+++|+||||||||  ||||||+|||+| |+    ++|||||+
T Consensus        22 ~l~~~Pq~kGi~l~~~~~~pKKPNSA~RK~arVrL-~n~k~v~AyIPg~Gh--nlqehs~VLVrG-gr----v~DlPGVk   93 (122)
T PF00164_consen   22 ALGGCPQKKGICLKVVTVKPKKPNSAIRKVARVRL-SNGKKVTAYIPGEGH--NLQEHSVVLVRG-GR----VGDLPGVK   93 (122)
T ss_dssp             SSTTSSEEEEEEEEEEEEEESTTTCSEEEEEEEEE-TTSEEEEEEC-SSSC--CSTTTSEEEEEE-ES----BTTSTTEC
T ss_pred             ccCCCCccCcEEeecccccccCccchhhhcceeee-ccCceEEEEecCCcc--cccccceEEEec-cc----cCCCCceE
Confidence            68999999999999999999999999999999999 699999999999999  999999999999 88    99999999


Q ss_pred             e
Q 042342           81 S   81 (87)
Q Consensus        81 y   81 (87)
                      |
T Consensus        94 y   94 (122)
T PF00164_consen   94 Y   94 (122)
T ss_dssp             E
T ss_pred             E
Confidence            8

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 ....

>PTZ00115 40S ribosomal protein S12; Provisional

Probab=100.00  E-value=1.2e-38  Score=249.04  Aligned_cols=73  Identities=27%  Similarity=0.508  Sum_probs=71.4

Q ss_pred             CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342            1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII   80 (87)
Q Consensus         1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~   80 (87)
                      .|+++||+||||+++++++|||||||+|||||||| +||++|+||||||||  ||||||+|||+| |+    ++|||||+
T Consensus       119 aL~g~PQkKGIclkv~~~tPKKPNSA~RKvarVrL-sNGk~VtAyIPGeGH--nLQEHs~VLVRG-Gr----vkDLPGVr  190 (290)
T PTZ00115        119 WLEGAPQKKGICVKVRVQTPRKPNSGLRKVARVRL-STGRTVTVYIPGIGH--NLNTHSVVLVRG-GR----CKDVPGCN  190 (290)
T ss_pred             cccCCcccCeEEEEeeecCCCCCCccccceEEEEe-cCCCEEEEEcCCCCc--ccccCCEEEEeC-CC----cCCCCCce
Confidence            37899999999999999999999999999999999 899999999999999  999999999999 99    99999999


Q ss_pred             e
Q 042342           81 S   81 (87)
Q Consensus        81 y   81 (87)
                      |
T Consensus       191 Y  191 (290)
T PTZ00115        191 Y  191 (290)
T ss_pred             E
Confidence            9

>KOG1750 consensus Mitochondrial/chloroplast ribosomal protein S12 [Translation, ribosomal structure and biogenesis]

Probab=99.97  E-value=1.6e-32  Score=197.38  Aligned_cols=73  Identities=36%  Similarity=0.659  Sum_probs=71.7

Q ss_pred             CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342            1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII   80 (87)
Q Consensus         1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~   80 (87)
                      +|+++||.+|||+++++++|||||||.|||++|+| +||.+|+|||||+||  |+|||+.||++| ||    ++|+|||+
T Consensus        51 ~L~g~p~~kgvvl~v~t~~pkkPnsa~rK~~~vrl-stg~~i~ayipg~gh--nlqehs~Vlvrg-gr----~qdlpgvk  122 (139)
T KOG1750|consen   51 ALDGCPQRKGVVLRVFTRKPKKPNSANRKCARVRL-STGREVTAYIPGIGH--NLQEHSIVLVRG-GR----VQDLPGVK  122 (139)
T ss_pred             cccCCcccccEEEEEEEecCCCCCccceeeEEEEe-cCchheeeeCCCccc--cceeEEEEEEec-ce----eccCcchh
Confidence            58899999999999999999999999999999999 999999999999999  999999999999 99    99999999


Q ss_pred             e
Q 042342           81 S   81 (87)
Q Consensus        81 y   81 (87)
                      |
T Consensus       123 ~  123 (139)
T KOG1750|consen  123 Y  123 (139)
T ss_pred             h
Confidence            7

>TIGR00008 infA translation initiation factor IF-1

Probab=95.21  E-value=0.045  Score=35.43  Aligned_cols=34  Identities=26%  Similarity=0.415  Sum_probs=27.7

Q ss_pred             EEEEEEecCCcEEEEEeCCCCccc--ccccCCeEEEe
Q 042342           30 CSRVQLIKNGKKIVTFVPSDGCLN--YIEENDKVLIA   64 (87)
Q Consensus        30 ~~rV~Likngk~v~A~IPg~G~ln--~lqeh~~VLV~   64 (87)
                      -.+|+| -||+++.|||||-=-.|  -+.+.|.|+|+
T Consensus        19 ~f~V~l-~ng~~vla~i~GKmr~~rI~I~~GD~V~Ve   54 (68)
T TIGR00008        19 MFRVEL-ENGHEVLAHISGKIRMHYIRILPGDKVKVE   54 (68)
T ss_pred             EEEEEE-CCCCEEEEEecCcchhccEEECCCCEEEEE
Confidence            467899 89999999999954422  37899999998

This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).

>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]

Probab=93.57  E-value=0.16  Score=33.56  Aligned_cols=34  Identities=29%  Similarity=0.326  Sum_probs=29.4

Q ss_pred             EEEEEecCCcEEEEEeCCCCcccc--cccCCeEEEee
Q 042342           31 SRVQLIKNGKKIVTFVPSDGCLNY--IEENDKVLIAG   65 (87)
Q Consensus        31 ~rV~Likngk~v~A~IPg~G~ln~--lqeh~~VLV~G   65 (87)
                      .+|+| -||+++.|+|||-.-.|+  |-+-|.|+|+=
T Consensus        22 f~v~~-edg~~~~ahI~GKmr~~~i~I~~GD~V~Ve~   57 (75)
T COG0361          22 FRVEL-ENGHERLAHISGKMRKNRIRILPGDVVLVEL   57 (75)
T ss_pred             EEEEe-cCCcEEEEEccCcchheeEEeCCCCEEEEEe
Confidence            67999 999999999999997544  67999999984

>PRK12442 translation initiation factor IF-1; Reviewed

Probab=90.25  E-value=0.64  Score=31.64  Aligned_cols=35  Identities=23%  Similarity=0.244  Sum_probs=28.6

Q ss_pred             EEEEEEecCCcEEEEEeCCCCcccc--cccCCeEEEee
Q 042342           30 CSRVQLIKNGKKIVTFVPSDGCLNY--IEENDKVLIAG   65 (87)
Q Consensus        30 ~~rV~Likngk~v~A~IPg~G~ln~--lqeh~~VLV~G   65 (87)
                      -.+|+| -||..|.|||+|-=-.|+  |.+.|.|+|+=
T Consensus        21 ~frV~L-enG~~vla~isGKmR~~rIrIl~GD~V~VE~   57 (87)
T PRK12442         21 RFRVTL-ENGVEVGAYASGRMRKHRIRILAGDRVTLEL   57 (87)
T ss_pred             EEEEEe-CCCCEEEEEeccceeeeeEEecCCCEEEEEE
Confidence            467999 899999999999765443  57889999983

>smart00652 eIF1a eukaryotic translation initiation factor 1A

Probab=88.34  E-value=1.1  Score=29.40  Aligned_cols=34  Identities=24%  Similarity=0.304  Sum_probs=27.0

Q ss_pred             EEEEEecCCcEEEEEeCCCCc-ccccccCCeEEEee
Q 042342           31 SRVQLIKNGKKIVTFVPSDGC-LNYIEENDKVLIAG   65 (87)
Q Consensus        31 ~rV~Likngk~v~A~IPg~G~-ln~lqeh~~VLV~G   65 (87)
                      .+|++ .||+++.|+|||-=. --.+.+.|.|+|+=
T Consensus        20 ~~V~~-~dG~~~la~ipgK~Rk~iwI~~GD~VlVe~   54 (83)
T smart00652       20 LEVMC-ADGKERLARIPGKMRKKVWIRRGDIVLVDP   54 (83)
T ss_pred             EEEEE-CCCCEEEEEEchhhcccEEEcCCCEEEEEe
Confidence            57888 899999999999421 12588999999984

>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain

Probab=86.57  E-value=1.7  Score=28.30  Aligned_cols=35  Identities=14%  Similarity=0.262  Sum_probs=27.4

Q ss_pred             EEEEEEecCCcEEEEEeCCCCc-ccccccCCeEEEee
Q 042342           30 CSRVQLIKNGKKIVTFVPSDGC-LNYIEENDKVLIAG   65 (87)
Q Consensus        30 ~~rV~Likngk~v~A~IPg~G~-ln~lqeh~~VLV~G   65 (87)
                      -.+|++ .||+++.|.|||-=. ---+.+.|.|+|+=
T Consensus        14 ~~~V~~-~dg~~~l~~i~gK~Rk~iwI~~GD~VlV~~   49 (78)
T cd04456          14 RHEVEC-ADGQRRLVSIPGKLRKNIWIKRGDFLIVDP   49 (78)
T ss_pred             EEEEEE-CCCCEEEEEEchhhccCEEEcCCCEEEEEe
Confidence            467888 899999999999421 02688999999973

IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.

>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A

Probab=81.48  E-value=3.1  Score=28.33  Aligned_cols=34  Identities=24%  Similarity=0.313  Sum_probs=26.8

Q ss_pred             EEEEEEecCCcEEEEEeCCCC-cccccccCCeEEEe
Q 042342           30 CSRVQLIKNGKKIVTFVPSDG-CLNYIEENDKVLIA   64 (87)
Q Consensus        30 ~~rV~Likngk~v~A~IPg~G-~ln~lqeh~~VLV~   64 (87)
                      -.+|++ -||+++.|+|||-= .--.+.+.|.|+|.
T Consensus        33 ~~~V~~-~dG~~~la~i~GK~Rk~iwI~~GD~VlVs   67 (99)
T TIGR00523        33 RVKVRC-LDGKTRLGRIPGKLKKRIWIREGDVVIVK   67 (99)
T ss_pred             EEEEEe-CCCCEEEEEEchhhcccEEecCCCEEEEE
Confidence            467888 89999999999942 12258899999994

Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	87
3iz6_L	142	Localization Of The Small Subunit Ribosomal Protein		1e-33
2zkq_l	143	Structure Of A Mammalian Ribosomal 40s Subunit With		2e-32
3izb_L	145	Localization Of The Small Subunit Ribosomal Protein		8e-30
3zey_S	143	High-resolution Cryo-electron Microscopy Structure		8e-30
3j2k_X	144	Cryo-Em Structure Of The Mammalian Erf1-Erf3-Associ		8e-30
1s1h_L	118	Structure Of The Ribosomal 80s-Eef2-Sordarin Comple		1e-29
2xzm_L	142	Crystal Structure Of The Eukaryotic 40s Ribosomal S		1e-26
3j0l_L	141	Core Of Mammalian 80s Pre-Ribosome In Complex With		1e-26
3j20_N	147	Promiscuous Behavior Of Proteins In Archaeal Riboso		4e-17

>pdb|3IZ6|L Chain L, Localization Of The Small Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 142

Iteration: 1
 Score =  138 bits (347), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 65/79 (82%), Positives = 71/79 (89%)
Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PFAG SHAKGIVLEKIGIEAKQPN AIRKC+RVQL+KNGKKI  FVP+DGCLN+IEEND+
Sbjct: 39  PFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLVKNGKKIAAFVPNDGCLNFIEENDE 98
Query: 61  VLIAGFGRKGHAVATSPPI 79
           VLIAGFGRKGHAV   P +
Sbjct: 99  VLIAGFGRKGHAVGDIPGV 117

>pdb|2ZKQ|LL Chain l, Structure Of A Mammalian Ribosomal 40s Subunit Within An 80s Complex Obtained By Docking Homology Models Of The Rna And Proteins Into An 8.7 A Cryo-Em Map Length = 143

Iteration: 1
 Score =  134 bits (336), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 62/79 (78%), Positives = 69/79 (87%)
Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PF G SHAKGIVLEK+G+EAKQPN AIRKC RVQLIKNGKKI  FVP+DGCLN+IEEND+
Sbjct: 40  PFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDE 99
Query: 61  VLIAGFGRKGHAVATSPPI 79
           VL+AGFGRKGHAV   P +
Sbjct: 100 VLVAGFGRKGHAVGDIPGV 118

>pdb|3IZB|L Chain L, Localization Of The Small Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 145

Iteration: 1
 Score =  125 bits (313), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 57/79 (72%), Positives = 67/79 (84%)
Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PF G SHAKGIVLEK+GIE+KQPN AIRKC RVQLIKNGKK+  FVP+DGCLN+++END+
Sbjct: 42  PFGGSSHAKGIVLEKLGIESKQPNSAIRKCVRVQLIKNGKKVTAFVPNDGCLNFVDENDE 101
Query: 61  VLIAGFGRKGHAVATSPPI 79
           VL+AGFGRKG A    P +
Sbjct: 102 VLLAGFGRKGKAKGDIPGV 120

>pdb|3ZEY|S Chain S, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 143

Iteration: 1
 Score =  125 bits (313), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 58/79 (73%), Positives = 67/79 (84%)
Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PF G SHAKGIVLEKIG+ AKQPN AIRKC RVQLIKN KKI+ FVP+DGCL++IEEND+
Sbjct: 40  PFGGSSHAKGIVLEKIGVGAKQPNSAIRKCVRVQLIKNDKKIIAFVPNDGCLHFIEENDE 99
Query: 61  VLIAGFGRKGHAVATSPPI 79
           VL++GFGR GHAV   P +
Sbjct: 100 VLVSGFGRSGHAVGDIPGV 118

>pdb|3J2K|X Chain X, Cryo-Em Structure Of The Mammalian Erf1-Erf3-Associated Termination Complex Length = 144

Iteration: 1
 Score =  125 bits (313), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 57/79 (72%), Positives = 67/79 (84%)
Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PF G SHAKGIVLEK+GIE+KQPN AIRKC RVQLIKNGKK+  FVP+DGCLN+++END+
Sbjct: 41  PFGGSSHAKGIVLEKLGIESKQPNSAIRKCVRVQLIKNGKKVTAFVPNDGCLNFVDENDE 100
Query: 61  VLIAGFGRKGHAVATSPPI 79
           VL+AGFGRKG A    P +
Sbjct: 101 VLLAGFGRKGKAKGDIPGV 119

>pdb|1S1H|L Chain L, 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 = 118

Iteration: 1
 Score =  124 bits (312), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 57/79 (72%), Positives = 67/79 (84%)
Query: 1  PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
          PF G SHAKGIVLEK+GIE+KQPN AIRKC RVQLIKNGKK+  FVP+DGCLN+++END+
Sbjct: 15 PFGGSSHAKGIVLEKLGIESKQPNSAIRKCVRVQLIKNGKKVTAFVPNDGCLNFVDENDE 74
Query: 61 VLIAGFGRKGHAVATSPPI 79
          VL+AGFGRKG A    P +
Sbjct: 75 VLLAGFGRKGKAKGDIPGV 93

>pdb|2XZM|L Chain L, 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 = 142

Iteration: 1
 Score =  114 bits (286), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 53/79 (67%), Positives = 62/79 (78%)
Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PF G SHAKG+V EKIGIE+KQPN A+RKC RV L KN KKI  FVP DGCLN++ END+
Sbjct: 41  PFMGASHAKGLVTEKIGIESKQPNSAVRKCVRVLLRKNSKKIAAFVPMDGCLNFLAENDE 100
Query: 61  VLIAGFGRKGHAVATSPPI 79
           VL+AG GR+GHAV   P +
Sbjct: 101 VLVAGLGRQGHAVGDIPGV 119

>pdb|3J0L|L Chain L, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas Fitted To A 9.8a Cryo-Em Map: Classic Pre State 1 Length = 141

Iteration: 1
 Score =  114 bits (286), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 53/79 (67%), Positives = 62/79 (78%)
Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PF G SHAKG+V EKIGIE+KQPN A+RKC RV L KN KKI  FVP DGCLN++ END+
Sbjct: 40  PFMGASHAKGLVTEKIGIESKQPNSAVRKCVRVLLRKNSKKIAAFVPMDGCLNFLAENDE 99
Query: 61  VLIAGFGRKGHAVATSPPI 79
           VL+AG GR+GHAV   P +
Sbjct: 100 VLVAGLGRQGHAVGDIPGV 118

>pdb|3J20|N Chain N, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (30s Ribosomal Subunit) Length = 147

Iteration: 1
 Score = 83.2 bits (204), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 42/80 (52%), Positives = 54/80 (67%), Gaps = 1/80 (1%)
Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           P  G   A+GIVLEKI +EAKQPN  +RK  RVQLIKNGK +  F P DG + +I+E+D+
Sbjct: 43  PLEGAPQARGIVLEKIAVEAKQPNSGMRKAVRVQLIKNGKVVTAFCPGDGAIKFIDEHDE 102
Query: 61  VLIAGFGR-KGHAVATSPPI 79
           V+I G G  KG ++   P I
Sbjct: 103 VIIEGIGGPKGGSMGDIPGI 122

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	87
2xzm_L	142	40S ribosomal protein S12; ribosome, translation;	3e-21
3u5c_X	145	RP37, S28, YS14, 40S ribosomal protein S23-A; tran	2e-18
2vqe_L	135	30S ribosomal protein S12, 30S ribosomal protein S	1e-04

>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 = 80.5 bits (198), Expect = 3e-21
 Identities = 53/77 (68%), Positives = 61/77 (79%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PF G SHAKG+V EKIGIE+KQPN A+RKC RV L KN KKI  FVP DGCLN++ END+
Sbjct: 41  PFMGASHAKGLVTEKIGIESKQPNSAVRKCVRVLLRKNSKKIAAFVPMDGCLNFLAENDE 100

Query: 61  VLIAGFGRKGHAVATSP 77
           VL+AG GR+GHAV   P
Sbjct: 101 VLVAGLGRQGHAVGDIP 117

>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 = 73.2 bits (179), Expect = 2e-18
 Identities = 57/77 (74%), Positives = 66/77 (85%)

Query: 1   PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
           PF G SHAKGIVLEK+GIE+KQPN AIRKC RVQLIKNGKK+  FVP+DGCLN+++END+
Sbjct: 42  PFGGSSHAKGIVLEKLGIESKQPNSAIRKCVRVQLIKNGKKVTAFVPNDGCLNFVDENDE 101

Query: 61  VLIAGFGRKGHAVATSP 77
           VL+AGFGRKG A    P
Sbjct: 102 VLLAGFGRKGKAKGDIP 118

>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 = 36.9 bits (85), Expect = 1e-04
 Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 4/71 (5%)

Query: 1  PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
             G    +G+      +  K+PN A+RK ++V+L  +G ++  ++P +G  + ++E+  
Sbjct: 26 ALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRL-TSGYEVTAYIPGEG--HNLQEHSV 82

Query: 61 VLIAGFGRKGH 71
          VLI G GR   
Sbjct: 83 VLIRG-GRVKD 92

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	87
2xzm_L	142	40S ribosomal protein S12; ribosome, translation;	100.0
3u5c_X	145	RP37, S28, YS14, 40S ribosomal protein S23-A; tran	100.0
3j20_N	147	30S ribosomal protein S12P; archaea, archaeal, KIN	100.0
2vqe_L	135	30S ribosomal protein S12, 30S ribosomal protein S	100.0

>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=100.00  E-value=8.8e-50  Score=286.56  Aligned_cols=81  Identities=65%  Similarity=1.073  Sum_probs=80.2

Q ss_pred             CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342            1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII   80 (87)
Q Consensus         1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~   80 (87)
                      ||+++||++|||+|++++||||||||+||||||||++||++||||||||||||||||||+|||+|||++|++++|||||+
T Consensus        41 pl~g~pq~kGIvl~~~~~~pKkPNSA~RK~arVqL~kNgk~vtAyIPg~G~l~~lqEh~~VLVrG~G~~ggrv~DlPGVr  120 (142)
T 2xzm_L           41 PFMGASHAKGLVTEKIGIESKQPNSAVRKCVRVLLRKNSKKIAAFVPMDGCLNFLAENDEVLVAGLGRQGHAVGDIPGVR  120 (142)
T ss_dssp             TTTTCSEEEEEEEEEEEEECCTTCCCEEEEEEEEETTTCCEEEEECCSSSGGGTCCTTCEEEEEESSSSSSCCTTCSSCC
T ss_pred             cccCCCccceEEEEEEecccCCCCcccccEEEEEEecCCeEEEEEeCCCCcccccccCCEEEEEecccCCCccCCCCCce
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             e
Q 042342           81 S   81 (87)
Q Consensus        81 y   81 (87)
                      |
T Consensus       121 y  121 (142)
T 2xzm_L          121 F  121 (142)
T ss_dssp             E
T ss_pred             E
Confidence            8

>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=100.00  E-value=1.4e-49  Score=286.32  Aligned_cols=81  Identities=70%  Similarity=1.173  Sum_probs=80.2

Q ss_pred             CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342            1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII   80 (87)
Q Consensus         1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~   80 (87)
                      ||+++||++|||++++++||||||||+||||||||++||++||||||||||||||||||+|||+|||++|++++|||||+
T Consensus        42 ~l~g~pq~kGivl~~~~~~pKkPNSA~RK~arV~L~kngk~vtAyIPg~G~l~~lqEh~~VLV~G~G~~Gg~v~DlPGVr  121 (145)
T 3u5c_X           42 PFGGSSHAKGIVLEKLGIESKQPNSAIRKCVRVQLIKNGKKVTAFVPNDGCLNFVDENDEVLLAGFGRKGKAKGDIPGVR  121 (145)
T ss_dssp             SSCSSSEEEEEEEEEEBCBCCTTCCCBCCEEEEEETTTCCEEEEECCSSSCGGGCCTTCEEEEECCSSSSSCCSSSTTCC
T ss_pred             ccCCCCccCeEEEEEeecccCCCCccceeEEEEEEccCCCEEEEEeCCCCccccCCcCCEEEEEeccccCCccCCCCcee
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             e
Q 042342           81 S   81 (87)
Q Consensus        81 y   81 (87)
                      |
T Consensus       122 y  122 (145)
T 3u5c_X          122 F  122 (145)
T ss_dssp             E
T ss_pred             E
Confidence            8

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

Probab=100.00  E-value=1.1e-48  Score=282.10  Aligned_cols=81  Identities=52%  Similarity=0.888  Sum_probs=80.0

Q ss_pred             CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecC-CCCCCCCCCCCc
Q 042342            1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFG-RKGHAVATSPPI   79 (87)
Q Consensus         1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfG-r~g~~v~DlPGV   79 (87)
                      ||+++||++|||++++++||||||||+||||||||++||++||||||||||||||||||+|||+||| ++|++++|||||
T Consensus        43 ~l~g~pq~kGIvl~~~~~~pKkPNSA~RK~arV~L~kngk~vtAyIPg~Ghln~lqEh~~VLV~G~gg~~gg~v~DlPGV  122 (147)
T 3j20_N           43 PLEGAPQARGIVLEKIAVEAKQPNSGMRKAVRVQLIKNGKVVTAFCPGDGAIKFIDEHDEVIIEGIGGPKGGSMGDIPGI  122 (147)
T ss_dssp             SSTTCSCEEEEEEEEEEEECCSSCCCEEEEEEEEETTTCCEEEEECCSSSGGGTCCTTCEEEEEECSCTTSCCCSSCSSC
T ss_pred             hhhcCCccceEEEEEeecCCCCCCceeeeEEEEEEccCCcEEEEEcCCchhhcccccCCEEEEeeccCcCCCccCCCCce
Confidence            7999999999999999999999999999999999999999999999999999999999999999999 999999999999


Q ss_pred             ee
Q 042342           80 IS   81 (87)
Q Consensus        80 ~y   81 (87)
                      +|
T Consensus       123 ry  124 (147)
T 3j20_N          123 RY  124 (147)
T ss_dssp             CE
T ss_pred             eE
Confidence            98

>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=1.4e-43  Score=252.81  Aligned_cols=73  Identities=30%  Similarity=0.597  Sum_probs=71.9

Q ss_pred             CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342            1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII   80 (87)
Q Consensus         1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~   80 (87)
                      ||+++||++|||+++++++|||||||+|||||||| +||++||||||||||  ||||||+||||| ||    ++|||||+
T Consensus        26 ~l~g~Pq~kGv~l~v~~~~pKKPNSA~RK~arVrL-~ngk~VtAyIPG~Gh--nlqEhs~VLVrG-gr----v~DlPGVr   97 (135)
T 2vqe_L           26 ALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRL-TSGYEVTAYIPGEGH--NLQEHSVVLIRG-GR----VKDLPGVR   97 (135)
T ss_dssp             CSSSCSEEEEEESCCCEECCCTTCCCCEECCEEEE-TTSCEEEEECCSSCC--CCCTTCEEEEEE-CC----CTTSTTCC
T ss_pred             cccCCCCcCeEEEEEEecCCCCCchhheeEEEEEc-CCCCEEEEEcCCCCC--ccCcCCEEEEcC-CC----cCCCCCee
Confidence            68999999999999999999999999999999999 999999999999999  999999999999 99    99999999


Q ss_pred             e
Q 042342           81 S   81 (87)
Q Consensus        81 y   81 (87)
                      |
T Consensus        98 y   98 (135)
T 2vqe_L           98 Y   98 (135)
T ss_dssp             E
T ss_pred             E
Confidence            8

---

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	87
d2uubl1	118	b.40.4.5 (L:5-122) Ribosomal protein S12 {Thermus	4e-12

>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 = 55.1 bits (133), Expect = 4e-12
 Identities = 19/70 (27%), Positives = 38/70 (54%), Gaps = 4/70 (5%)

Query: 1  PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDK 60
             G    +G+      +  K+PN A+RK ++V+ + +G ++  ++P +G  + ++E+  
Sbjct: 22 ALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVR-LTSGYEVTAYIPGEG--HNLQEHSV 78

Query: 61 VLIAGFGRKG 70
          VLI G GR  
Sbjct: 79 VLIRG-GRVK 87

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	87
d2uubl1	118	Ribosomal protein S12 {Thermus thermophilus [TaxId	100.0
d1ah9a_	71	Translational initiation factor 1, IF1 {Escherichi	91.22

>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=1.2e-43  Score=246.84  Aligned_cols=73  Identities=30%  Similarity=0.597  Sum_probs=71.8

Q ss_pred             CCCCCCccceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCcccccccCCeEEEeecCCCCCCCCCCCCce
Q 042342            1 PFAGPSHAKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLNYIEENDKVLIAGFGRKGHAVATSPPII   80 (87)
Q Consensus         1 pl~~~pq~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln~lqeh~~VLV~GfGr~g~~v~DlPGV~   80 (87)
                      +|+++||+||||+++++++|||||||+|||||||| +||++|+||||||||  ||||||+||||| ||    ++|||||+
T Consensus        22 aL~~~PqkkGvc~kv~~~~PKKPNSA~RKvarVrL-sng~~v~AyIPG~Gh--nlqEHs~VLvrG-Gr----v~DlPGVr   93 (118)
T d2uubl1          22 ALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRL-TSGYEVTAYIPGEGH--NLQEHSVVLIRG-GR----VKDLPGVR   93 (118)
T ss_dssp             CTTTCSCEEEEEEEEEEECCCTTCCSCEEEEEEEE-TTSCEEEEECCSSCC--CCCTTCEEEECC-CC----CTTSTTCC
T ss_pred             ccccCCccceEEEEEEEeccCCCcceeeeEEEEEe-cCCeEEEEEcCCCCc--CcccCCEEEEeC-Cc----cccCCCcE
Confidence            58999999999999999999999999999999999 899999999999999  999999999999 99    99999999


Q ss_pred             e
Q 042342           81 S   81 (87)
Q Consensus        81 y   81 (87)
                      |
T Consensus        94 y   94 (118)
T d2uubl1          94 Y   94 (118)
T ss_dssp             E
T ss_pred             E
Confidence            9

>d1ah9a_ b.40.4.5 (A:) Translational initiation factor 1, IF1 {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Translational initiation factor 1, IF1
species: Escherichia coli [TaxId: 562]

Probab=91.22  E-value=0.11  Score=31.02  Aligned_cols=46  Identities=35%  Similarity=0.490  Sum_probs=34.0

Q ss_pred             cceeEEeeeeeeecCCCcccccEEEEEEecCCcEEEEEeCCCCccc--ccccCCeEEEe
Q 042342            8 AKGIVLEKIGIEAKQPNFAIRKCSRVQLIKNGKKIVTFVPSDGCLN--YIEENDKVLIA   64 (87)
Q Consensus         8 ~kGivl~~~~~~pKkPNSA~RK~~rV~Likngk~v~A~IPg~G~ln--~lqeh~~VLV~   64 (87)
                      ..|+|++.+      ||.-    .+|+| -||+++.|+|||-=--+  .+.+.|.|+|+
T Consensus         8 ~~G~V~e~l------g~~~----f~V~l-~ng~~~~a~i~Gkmrk~ri~i~~GD~V~Ve   55 (71)
T d1ah9a_           8 MQGTVLETL------PNTM----FRVEL-ENGHVVTAHISGKMRKNYIRILTGDKVTVE   55 (71)
T ss_dssp             CCEEEEEEC------SSSE----EEEEE-TTSCEEEEEECSSGGGTTCCCCTTCEECCE
T ss_pred             EEEEEEEEc------CCCE----EEEEe-CCCCEEEEEccchhheeEEEecCCCEEEEE
Confidence            345555554      4443    67899 99999999999965322  58899999987