Citrus Sinensis ID: 035463

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60-----
Protein Sequence
MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESEREARRLR
Secondary Structure (PSIPRED)
cccccEEEEEEEEcccccccccEEEEEEEEEcccccEEEEccccccccccEEEEEHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccEEEEEEEEEcccccccEEEEEEEEEEcccccEEEEccccccccccEEEHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MDSQIKHAVVVKVMgrtgsrgqVTQVRVKFLddqnrfimrnvkgpvregdILTLLESEREARRLR
Flexible Loop (DISEMBL)
MDSQIKHAVVVkvmgrtgsrgqvtqvrvkflddqnrfimrnvkgpvregdiltlleserearrlr
Low Complexity Region (SEG)
MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDIltlleserearrlr
Disordered region (IsUnstruct)
******HAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTL***********
Disordered Region (DISOPRED)
****IKH*VVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESERE*****
Disordered Region (DISEMBL)
MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESEREARRLR
Disordered Region (DISPRO)
**SQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESEREA****
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESEREARRLR
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	65	2.2.26 [Sep-21-2011]
P46302	65	40S ribosomal protein S28	N/A	no	1.0	1.0	0.923	4e-27
P34789	64	40S ribosomal protein S28	yes	no	0.984	1.0	0.923	3e-26
Q9SR73	64	40S ribosomal protein S28	yes	no	0.984	1.0	0.923	3e-26
Q90YP3	69	40S ribosomal protein S28	N/A	no	0.938	0.884	0.803	5e-21
Q6PBK3	69	40S ribosomal protein S28	yes	no	0.938	0.884	0.803	5e-21
Q9W334	65	40S ribosomal protein S28	yes	no	1.0	1.0	0.753	1e-20
P62859	69	40S ribosomal protein S28	yes	no	0.938	0.884	0.786	2e-20
Q6QAT1	69	40S ribosomal protein S28	yes	no	0.938	0.884	0.786	2e-20
P62858	69	40S ribosomal protein S28	yes	no	0.938	0.884	0.786	2e-20
P62857	69	40S ribosomal protein S28	yes	no	0.938	0.884	0.786	2e-20

>sp|P46302|RS28_MAIZE 40S ribosomal protein S28 OS=Zea mays GN=RPS28 PE=3 SV=1

 Score =  119 bits (299), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 60/65 (92%), Positives = 62/65 (95%)

Query: 1  MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESERE 60
          MD+Q+K AVVVKVMGRTGSRGQVTQVRVKFLDDQNR IMRNVKGPV EGDILTLLESERE
Sbjct: 1  MDTQVKLAVVVKVMGRTGSRGQVTQVRVKFLDDQNRLIMRNVKGPVCEGDILTLLESERE 60

Query: 61 ARRLR 65
          ARRLR
Sbjct: 61 ARRLR 65

Zea mays (taxid: 4577)

>sp|P34789|RS282_ARATH 40S ribosomal protein S28-2 OS=Arabidopsis thaliana GN=RPS28C PE=3 SV=1

 Score =  116 bits (291), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 60/65 (92%), Positives = 62/65 (95%), Gaps = 1/65 (1%)

Query: 1  MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESERE 60
          MDSQIKHAVVVKVMGRTGSRGQVTQVRVKF D  +RFIMRNVKGPVREGD+LTLLESERE
Sbjct: 1  MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFTD-SDRFIMRNVKGPVREGDVLTLLESERE 59

Query: 61 ARRLR 65
          ARRLR
Sbjct: 60 ARRLR 64

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SR73|RS281_ARATH 40S ribosomal protein S28-1 OS=Arabidopsis thaliana GN=RPS28A PE=3 SV=1

 Score =  116 bits (291), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 60/65 (92%), Positives = 62/65 (95%), Gaps = 1/65 (1%)

Query: 1  MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESERE 60
          MDSQIKHAVVVKVMGRTGSRGQVTQVRVKF  D +R+IMRNVKGPVREGDILTLLESERE
Sbjct: 1  MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFT-DSDRYIMRNVKGPVREGDILTLLESERE 59

Query: 61 ARRLR 65
          ARRLR
Sbjct: 60 ARRLR 64

Arabidopsis thaliana (taxid: 3702)

>sp|Q90YP3|RS28_ICTPU 40S ribosomal protein S28 OS=Ictalurus punctatus GN=rps28 PE=3 SV=1

 Score = 99.8 bits (247), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 49/61 (80%), Positives = 55/61 (90%)

Query: 5  IKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESEREARRL 64
          IK A V KV+GRTGS+GQ TQVRV+F+DD NR I+RNVKGPVREGD+LTLLESEREARRL
Sbjct: 9  IKLARVTKVLGRTGSQGQCTQVRVEFMDDSNRSIIRNVKGPVREGDVLTLLESEREARRL 68

Query: 65 R 65
          R
Sbjct: 69 R 69

Ictalurus punctatus (taxid: 7998)

>sp|Q6PBK3|RS28_DANRE 40S ribosomal protein S28 OS=Danio rerio GN=rps28 PE=3 SV=1

 Score = 99.8 bits (247), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 49/61 (80%), Positives = 55/61 (90%)

Query: 5  IKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESEREARRL 64
          IK A V KV+GRTGS+GQ TQVRV+F+DD NR I+RNVKGPVREGD+LTLLESEREARRL
Sbjct: 9  IKLARVTKVLGRTGSQGQCTQVRVEFMDDSNRSIIRNVKGPVREGDVLTLLESEREARRL 68

Query: 65 R 65
          R
Sbjct: 69 R 69

Danio rerio (taxid: 7955)

>sp|Q9W334|RS28_DROME 40S ribosomal protein S28 OS=Drosophila melanogaster GN=RpS28b PE=3 SV=2

 Score = 98.2 bits (243), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 49/65 (75%), Positives = 57/65 (87%)

Query: 1  MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESERE 60
          MD  +  A V+KV+GRTGS+GQ TQV+V+FL +QNR I+RNVKGPVREGDILTLLESERE
Sbjct: 1  MDKPVVWARVMKVLGRTGSQGQCTQVKVEFLGEQNRQIIRNVKGPVREGDILTLLESERE 60

Query: 61 ARRLR 65
          ARRLR
Sbjct: 61 ARRLR 65

Drosophila melanogaster (taxid: 7227)

>sp|P62859|RS28_RAT 40S ribosomal protein S28 OS=Rattus norvegicus GN=Rps28 PE=1 SV=1

 Score = 97.4 bits (241), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 55/61 (90%)

Query: 5  IKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESEREARRL 64
          IK A V KV+GRTGS+GQ TQVRV+F+DD +R I+RNVKGPVREGD+LTLLESEREARRL
Sbjct: 9  IKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRL 68

Query: 65 R 65
          R
Sbjct: 69 R 69

Rattus norvegicus (taxid: 10116)

>sp|Q6QAT1|RS28_PIG 40S ribosomal protein S28 OS=Sus scrofa GN=RPS28 PE=3 SV=2

 Score = 97.4 bits (241), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 55/61 (90%)

Query: 5  IKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESEREARRL 64
          IK A V KV+GRTGS+GQ TQVRV+F+DD +R I+RNVKGPVREGD+LTLLESEREARRL
Sbjct: 9  IKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRL 68

Query: 65 R 65
          R
Sbjct: 69 R 69

Sus scrofa (taxid: 9823)

>sp|P62858|RS28_MOUSE 40S ribosomal protein S28 OS=Mus musculus GN=Rps28 PE=2 SV=1

 Score = 97.4 bits (241), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 55/61 (90%)

Query: 5  IKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESEREARRL 64
          IK A V KV+GRTGS+GQ TQVRV+F+DD +R I+RNVKGPVREGD+LTLLESEREARRL
Sbjct: 9  IKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRL 68

Query: 65 R 65
          R
Sbjct: 69 R 69

Mus musculus (taxid: 10090)

>sp|P62857|RS28_HUMAN 40S ribosomal protein S28 OS=Homo sapiens GN=RPS28 PE=1 SV=1

 Score = 97.4 bits (241), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 55/61 (90%)

Query: 5  IKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESEREARRL 64
          IK A V KV+GRTGS+GQ TQVRV+F+DD +R I+RNVKGPVREGD+LTLLESEREARRL
Sbjct: 9  IKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRL 68

Query: 65 R 65
          R
Sbjct: 69 R 69

Homo sapiens (taxid: 9606)

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	65
255559537	65	ribosomal protein S28, putative [Ricinus	1.0	1.0	0.984	2e-28
224100565	65	predicted protein [Populus trichocarpa]	1.0	1.0	0.969	4e-28
449440915	65	PREDICTED: 40S ribosomal protein S28-lik	1.0	1.0	0.969	6e-28
449477088	68	PREDICTED: 40S ribosomal protein S28-lik	1.0	0.955	0.969	7e-28
3947719	65	ribosomal protein S28 [Prunus persica] g	1.0	1.0	0.969	9e-28
21902507	65	ribosomal protein small subunit 28 [Heli	1.0	1.0	0.953	2e-27
330318585	65	ribosomal protein s28 [Camellia sinensis	1.0	1.0	0.938	2e-27
297739775	111	unnamed protein product [Vitis vinifera]	1.0	0.585	0.953	2e-27
357496579	75	30S ribosomal protein S28e [Medicago tru	1.0	0.866	0.969	2e-27
124359133	65	Ribosomal protein S28e [Medicago truncat	1.0	1.0	0.969	3e-27

>gi|255559537|ref|XP_002520788.1| ribosomal protein S28, putative [Ricinus communis] gi|255581574|ref|XP_002531592.1| ribosomal protein S28, putative [Ricinus communis] gi|223528788|gb|EEF30795.1| ribosomal protein S28, putative [Ricinus communis] gi|223539919|gb|EEF41497.1| ribosomal protein S28, putative [Ricinus communis] gi|313586485|gb|ADR71253.1| 40S ribosomal protein S28A [Hevea brasiliensis] gi|313586487|gb|ADR71254.1| 40S ribosomal protein S28B [Hevea brasiliensis]

 Score =  129 bits (324), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 64/65 (98%), Positives = 65/65 (100%)

Query: 1  MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESERE 60
          MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGD+LTLLESERE
Sbjct: 1  MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDVLTLLESERE 60

Query: 61 ARRLR 65
          ARRLR
Sbjct: 61 ARRLR 65

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224100565|ref|XP_002311925.1| predicted protein [Populus trichocarpa] gi|224110082|ref|XP_002315409.1| predicted protein [Populus trichocarpa] gi|118481584|gb|ABK92734.1| unknown [Populus trichocarpa] gi|118481768|gb|ABK92823.1| unknown [Populus trichocarpa] gi|118482102|gb|ABK92982.1| unknown [Populus trichocarpa] gi|118482699|gb|ABK93268.1| unknown [Populus trichocarpa] gi|222851745|gb|EEE89292.1| predicted protein [Populus trichocarpa] gi|222864449|gb|EEF01580.1| predicted protein [Populus trichocarpa]

 Score =  128 bits (322), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 63/65 (96%), Positives = 65/65 (100%)

Query: 1  MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESERE 60
          MDSQIKHAVVVK+MGRTGSRGQVTQVRVKF+DDQNRFIMRNVKGPVREGDILTLLESERE
Sbjct: 1  MDSQIKHAVVVKIMGRTGSRGQVTQVRVKFIDDQNRFIMRNVKGPVREGDILTLLESERE 60

Query: 61 ARRLR 65
          ARRLR
Sbjct: 61 ARRLR 65

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449440915|ref|XP_004138229.1| PREDICTED: 40S ribosomal protein S28-like [Cucumis sativus] gi|449440917|ref|XP_004138230.1| PREDICTED: 40S ribosomal protein S28-like [Cucumis sativus] gi|449440919|ref|XP_004138231.1| PREDICTED: 40S ribosomal protein S28-like [Cucumis sativus] gi|449440921|ref|XP_004138232.1| PREDICTED: 40S ribosomal protein S28-like [Cucumis sativus] gi|449463340|ref|XP_004149392.1| PREDICTED: 40S ribosomal protein S28-like [Cucumis sativus] gi|449463342|ref|XP_004149393.1| PREDICTED: 40S ribosomal protein S28-like [Cucumis sativus] gi|449477091|ref|XP_004154926.1| PREDICTED: 40S ribosomal protein S28-like [Cucumis sativus] gi|449477094|ref|XP_004154927.1| PREDICTED: 40S ribosomal protein S28-like [Cucumis sativus] gi|449477096|ref|XP_004154928.1| PREDICTED: 40S ribosomal protein S28-like [Cucumis sativus] gi|449477100|ref|XP_004154929.1| PREDICTED: 40S ribosomal protein S28-like [Cucumis sativus] gi|449503792|ref|XP_004162179.1| PREDICTED: 40S ribosomal protein S28-like [Cucumis sativus] gi|449503794|ref|XP_004162180.1| PREDICTED: 40S ribosomal protein S28-like [Cucumis sativus] gi|449503796|ref|XP_004162181.1| PREDICTED: 40S ribosomal protein S28-like [Cucumis sativus]

 Score =  127 bits (320), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 63/65 (96%), Positives = 65/65 (100%)

Query: 1  MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESERE 60
          M+SQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNR+IMRNVKGPVREGDILTLLESERE
Sbjct: 1  MESQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRYIMRNVKGPVREGDILTLLESERE 60

Query: 61 ARRLR 65
          ARRLR
Sbjct: 61 ARRLR 65

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449477088|ref|XP_004154925.1| PREDICTED: 40S ribosomal protein S28-like [Cucumis sativus]

 Score =  127 bits (320), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 63/65 (96%), Positives = 65/65 (100%)

Query: 1  MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESERE 60
          M+SQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNR+IMRNVKGPVREGDILTLLESERE
Sbjct: 4  MESQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRYIMRNVKGPVREGDILTLLESERE 63

Query: 61 ARRLR 65
          ARRLR
Sbjct: 64 ARRLR 68

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|3947719|emb|CAA10101.1| ribosomal protein S28 [Prunus persica] gi|3947721|emb|CAA10102.1| ribosomal protein S28 [Prunus persica] gi|3947723|emb|CAA10103.1| ribosomal protein S28 [Prunus persica]

 Score =  127 bits (319), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 63/65 (96%), Positives = 64/65 (98%)

Query: 1  MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESERE 60
          MDS +KHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESERE
Sbjct: 1  MDSTVKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESERE 60

Query: 61 ARRLR 65
          ARRLR
Sbjct: 61 ARRLR 65

Source: Prunus persica

Species: Prunus persica

Genus: Prunus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|21902507|gb|AAM78552.1|AF522185_1 ribosomal protein small subunit 28 [Helianthus annuus]

 Score =  126 bits (317), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 62/65 (95%), Positives = 65/65 (100%)

Query: 1  MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESERE 60
          M+SQIKHAVVVKVMGR+GSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGD+LTLLESERE
Sbjct: 1  MESQIKHAVVVKVMGRSGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDVLTLLESERE 60

Query: 61 ARRLR 65
          ARRLR
Sbjct: 61 ARRLR 65

Source: Helianthus annuus

Species: Helianthus annuus

Genus: Helianthus

Family: Asteraceae

Order: Asterales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|330318585|gb|AEC10961.1| ribosomal protein s28 [Camellia sinensis]

 Score =  126 bits (317), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 61/65 (93%), Positives = 65/65 (100%)

Query: 1  MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESERE 60
          M+SQIKHA+VVKVMGRTGSRGQVTQVRVKF+DDQNRFIMRNVKGPVREGD+LTLLESERE
Sbjct: 1  MESQIKHAIVVKVMGRTGSRGQVTQVRVKFIDDQNRFIMRNVKGPVREGDVLTLLESERE 60

Query: 61 ARRLR 65
          ARRLR
Sbjct: 61 ARRLR 65

Source: Camellia sinensis

Species: Camellia sinensis

Genus: Camellia

Family: Theaceae

Order: Ericales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297739775|emb|CBI29957.3| unnamed protein product [Vitis vinifera]

 Score =  126 bits (316), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 62/65 (95%), Positives = 64/65 (98%)

Query: 1   MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESERE 60
           M+S +KHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESERE
Sbjct: 47  MESGVKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESERE 106

Query: 61  ARRLR 65
           ARRLR
Sbjct: 107 ARRLR 111

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357496579|ref|XP_003618578.1| 30S ribosomal protein S28e [Medicago truncatula] gi|355493593|gb|AES74796.1| 30S ribosomal protein S28e [Medicago truncatula]

 Score =  126 bits (316), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 63/65 (96%), Positives = 64/65 (98%)

Query: 1  MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESERE 60
          M+SQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNR IMRNVKGPVREGDILTLLESERE
Sbjct: 11 MESQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRHIMRNVKGPVREGDILTLLESERE 70

Query: 61 ARRLR 65
          ARRLR
Sbjct: 71 ARRLR 75

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|124359133|gb|ABD32492.2| Ribosomal protein S28e [Medicago truncatula] gi|388522463|gb|AFK49293.1| unknown [Medicago truncatula]

 Score =  125 bits (315), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 63/65 (96%), Positives = 64/65 (98%)

Query: 1  MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESERE 60
          M+SQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNR IMRNVKGPVREGDILTLLESERE
Sbjct: 1  MESQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRHIMRNVKGPVREGDILTLLESERE 60

Query: 61 ARRLR 65
          ARRLR
Sbjct: 61 ARRLR 65

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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	65
UNIPROTKB|Q0IXR7	65	Os10g0411700 "Os10g0411700 pro	0.784	0.784	0.921	7.2e-20
TAIR|locus:2164386	64	RPS28 "AT5G64140" [Arabidopsis	0.769	0.781	0.901	8.3e-19
TAIR|locus:2100118	64	AT3G10090 "AT3G10090" [Arabido	0.769	0.781	0.901	1.4e-18
TAIR|locus:2150610	64	AT5G03850 "AT5G03850" [Arabido	0.769	0.781	0.901	1.4e-18
UNIPROTKB|A8IKP1	65	RPS28 "Ribosomal protein S28"	0.784	0.784	0.843	5.8e-18
ZFIN|ZDB-GENE-030131-2022	69	rps28 "ribosomal protein S28"	0.723	0.681	0.744	7.9e-14
FB|FBgn0030136	65	RpS28b "Ribosomal protein S28b	0.784	0.784	0.686	1.6e-13
UNIPROTKB|Q74ZD8	67	RPS28A "40S ribosomal protein	0.784	0.761	0.698	2.7e-13
POMBASE|SPAC25G10.06	68	rps2801 "40S ribosomal protein	0.784	0.75	0.685	2.7e-13
POMBASE|SPCC285.15c	68	rps2802 "40S ribosomal protein	0.784	0.75	0.685	2.7e-13

UNIPROTKB|Q0IXR7 Os10g0411700 "Os10g0411700 protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 236 (88.1 bits), Expect = 7.2e-20, P = 7.2e-20
 Identities = 47/51 (92%), Positives = 49/51 (96%)

Query:     1 MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDI 51
             MD+Q+K AVVVKVMGRTGSRGQVTQVRVKFLDDQNR IMRNVKGPVREGDI
Sbjct:     1 MDTQVKLAVVVKVMGRTGSRGQVTQVRVKFLDDQNRLIMRNVKGPVREGDI 51

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

GO:0006407 "rRNA export from nucleus" evidence=ISS

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

TAIR|locus:2164386 RPS28 "AT5G64140" [Arabidopsis thaliana (taxid:3702)]

 Score = 226 (84.6 bits), Expect = 8.3e-19, P = 8.3e-19
 Identities = 46/51 (90%), Positives = 48/51 (94%)

Query:     1 MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDI 51
             MDSQIKHAVVVKVMGRTGSRGQVTQVRVKF D  +RFIMRNVKGPVREGD+
Sbjct:     1 MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFTDS-DRFIMRNVKGPVREGDV 50

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

GO:0005622 "intracellular" evidence=IEA;IBA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006407 "rRNA export from nucleus" evidence=IBA

GO:0006412 "translation" evidence=IEA;ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

GO:0022626 "cytosolic ribosome" evidence=IDA

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

TAIR|locus:2100118 AT3G10090 "AT3G10090" [Arabidopsis thaliana (taxid:3702)]

 Score = 224 (83.9 bits), Expect = 1.4e-18, P = 1.4e-18
 Identities = 46/51 (90%), Positives = 48/51 (94%)

Query:     1 MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDI 51
             MDSQIKHAVVVKVMGRTGSRGQVTQVRVKF D  +R+IMRNVKGPVREGDI
Sbjct:     1 MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFTDS-DRYIMRNVKGPVREGDI 50

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

GO:0005622 "intracellular" evidence=IEA;IBA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006407 "rRNA export from nucleus" evidence=IBA

GO:0006412 "translation" evidence=IEA;ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0005618 "cell wall" evidence=IDA

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

GO:0005829 "cytosol" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

TAIR|locus:2150610 AT5G03850 "AT5G03850" [Arabidopsis thaliana (taxid:3702)]

 Score = 224 (83.9 bits), Expect = 1.4e-18, P = 1.4e-18
 Identities = 46/51 (90%), Positives = 48/51 (94%)

Query:     1 MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDI 51
             MDSQIKHAVVVKVMGRTGSRGQVTQVRVKF D  +R+IMRNVKGPVREGDI
Sbjct:     1 MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFTDS-DRYIMRNVKGPVREGDI 50

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

GO:0005622 "intracellular" evidence=IEA;IBA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006407 "rRNA export from nucleus" evidence=IBA

GO:0006412 "translation" evidence=IEA;ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

GO:0005886 "plasma membrane" evidence=IDA

GO:0005618 "cell wall" evidence=IDA

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

GO:0005829 "cytosol" evidence=RCA

GO:0005794 "Golgi apparatus" evidence=RCA

UNIPROTKB|A8IKP1 RPS28 "Ribosomal protein S28" [Chlamydomonas reinhardtii (taxid:3055)]

 Score = 218 (81.8 bits), Expect = 5.8e-18, P = 5.8e-18
 Identities = 43/51 (84%), Positives = 47/51 (92%)

Query:     1 MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDI 51
             MD+  K A+V+KV+GRTGSRGQVTQVRVKFLDDQNR IMRNVKGPVREGDI
Sbjct:     1 MDAPAKLAIVMKVIGRTGSRGQVTQVRVKFLDDQNRLIMRNVKGPVREGDI 51

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

GO:0006407 "rRNA export from nucleus" evidence=ISS

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

ZFIN|ZDB-GENE-030131-2022 rps28 "ribosomal protein S28" [Danio rerio (taxid:7955)]

 Score = 179 (68.1 bits), Expect = 7.9e-14, P = 7.9e-14
 Identities = 35/47 (74%), Positives = 41/47 (87%)

Query:     5 IKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDI 51
             IK A V KV+GRTGS+GQ TQVRV+F+DD NR I+RNVKGPVREGD+
Sbjct:     9 IKLARVTKVLGRTGSQGQCTQVRVEFMDDSNRSIIRNVKGPVREGDV 55

GO:0005840 "ribosome" evidence=IEA

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

GO:0006412 "translation" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0006407 "rRNA export from nucleus" evidence=IBA

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

GO:0030529 "ribonucleoprotein complex" evidence=IEA

FB|FBgn0030136 RpS28b "Ribosomal protein S28b" [Drosophila melanogaster (taxid:7227)]

 Score = 176 (67.0 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 35/51 (68%), Positives = 43/51 (84%)

Query:     1 MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDI 51
             MD  +  A V+KV+GRTGS+GQ TQV+V+FL +QNR I+RNVKGPVREGDI
Sbjct:     1 MDKPVVWARVMKVLGRTGSQGQCTQVKVEFLGEQNRQIIRNVKGPVREGDI 51

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

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

GO:0006412 "translation" evidence=IEA

GO:0005811 "lipid particle" evidence=IDA

GO:0006407 "rRNA export from nucleus" evidence=IBA

UNIPROTKB|Q74ZD8 RPS28A "40S ribosomal protein S28" [Ashbya gossypii ATCC 10895 (taxid:284811)]

 Score = 174 (66.3 bits), Expect = 2.7e-13, P = 2.7e-13
 Identities = 37/53 (69%), Positives = 44/53 (83%)

Query:     1 MDSQ--IKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDI 51
             MDS+  +  A V+KV+GRTGSRG VTQVRV+FLDD +R I+RNVKGPVRE DI
Sbjct:     1 MDSKTPVTLAKVIKVLGRTGSRGGVTQVRVEFLDDTSRTIVRNVKGPVRENDI 53

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

GO:0006407 "rRNA export from nucleus" evidence=ISS

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

POMBASE|SPAC25G10.06 rps2801 "40S ribosomal protein S28 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 174 (66.3 bits), Expect = 2.7e-13, P = 2.7e-13
 Identities = 37/54 (68%), Positives = 44/54 (81%)

Query:     1 MDSQ---IKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDI 51
             MDS    +K A V+KV+GRTGSRG VTQVRV+F+DD +R I+RNVKGPVRE DI
Sbjct:     1 MDSSKVPVKLAKVIKVLGRTGSRGGVTQVRVEFMDDTSRSIIRNVKGPVREDDI 54

GO:0002181 "cytoplasmic translation" evidence=NAS

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

GO:0005829 "cytosol" evidence=IDA

GO:0006412 "translation" evidence=ISO

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

GO:0042254 "ribosome biogenesis" evidence=ISO

POMBASE|SPCC285.15c rps2802 "40S ribosomal protein S28, Rps2802" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 174 (66.3 bits), Expect = 2.7e-13, P = 2.7e-13
 Identities = 37/54 (68%), Positives = 44/54 (81%)

Query:     1 MDSQ---IKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDI 51
             MDS    +K A V+KV+GRTGSRG VTQVRV+F+DD +R I+RNVKGPVRE DI
Sbjct:     1 MDSSKVPVKLAKVIKVLGRTGSRGGVTQVRVEFMDDTSRSIIRNVKGPVREDDI 54

GO:0000028 "ribosomal small subunit assembly" evidence=IMP

GO:0000056 "ribosomal small subunit export from nucleus" evidence=IMP

GO:0000469 "cleavage involved in rRNA processing" evidence=IDA

GO:0002181 "cytoplasmic translation" evidence=ISO

GO:0003674 "molecular_function" evidence=ND

GO:0005730 "nucleolus" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

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

GO:0030490 "maturation of SSU-rRNA" evidence=IMP

---

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)
Q6PS50	RS28_BOMMO	No assigned EC number	0.7076	1.0	1.0	N/A	no
P57711	RS28_THEAC	No assigned EC number	0.5151	0.9846	0.9275	yes	no
P62857	RS28_HUMAN	No assigned EC number	0.7868	0.9384	0.8840	yes	no
P62859	RS28_RAT	No assigned EC number	0.7868	0.9384	0.8840	yes	no
P62858	RS28_MOUSE	No assigned EC number	0.7868	0.9384	0.8840	yes	no
Q97BK7	RS28_THEVO	No assigned EC number	0.5151	0.9846	0.9275	yes	no
Q9W334	RS28_DROME	No assigned EC number	0.7538	1.0	1.0	yes	no
P61029	RS28_PYRAB	No assigned EC number	0.5666	0.8923	0.8169	yes	no
O26356	RS28_METTH	No assigned EC number	0.5166	0.8923	0.8529	yes	no
Q9Y9A6	RS28_AERPE	No assigned EC number	0.5932	0.8769	0.6951	yes	no
A4YCQ2	RS28_METS5	No assigned EC number	0.5593	0.8769	0.7125	yes	no
O61590	RS28_OSTOS	No assigned EC number	0.7424	1.0	0.9848	N/A	no
Q54MZ5	RS28_DICDI	No assigned EC number	0.625	0.9384	0.8472	yes	no
B1Y9V2	RS28_PYRNV	No assigned EC number	0.5762	0.8769	0.7402	yes	no
A4WLP1	RS28_PYRAR	No assigned EC number	0.5593	0.8769	0.7402	yes	no
Q6LZI8	RS28_METMP	No assigned EC number	0.5254	0.8769	0.75	yes	no
P0C0X0	RS28B_YEAST	No assigned EC number	0.7164	1.0	0.9701	yes	no
Q7S6W5	RS28_NEUCR	No assigned EC number	0.7205	1.0	0.9558	N/A	no
Q8TVE7	RS28_METKA	No assigned EC number	0.6271	0.8769	0.7702	yes	no
A6USH4	RS28_METVS	No assigned EC number	0.5254	0.8769	0.75	yes	no
Q6EV21	RS28_PAPDA	No assigned EC number	0.7076	1.0	1.0	N/A	no
Q6QAT1	RS28_PIG	No assigned EC number	0.7868	0.9384	0.8840	yes	no
B1L5N5	RS28_KORCO	No assigned EC number	0.5833	0.8923	0.8169	yes	no
A1RS33	RS28_PYRIL	No assigned EC number	0.5	0.9846	0.8311	yes	no
P46302	RS28_MAIZE	No assigned EC number	0.9230	1.0	1.0	N/A	no
P33285	RS28_KLULA	No assigned EC number	0.7164	1.0	0.9701	yes	no
Q9SR73	RS281_ARATH	No assigned EC number	0.9230	0.9846	1.0	yes	no
Q90YP3	RS28_ICTPU	No assigned EC number	0.8032	0.9384	0.8840	N/A	no
Q56JX6	RS28_BOVIN	No assigned EC number	0.7868	0.9384	0.8840	yes	no
P34789	RS282_ARATH	No assigned EC number	0.9230	0.9846	1.0	yes	no
Q962Q2	RS28_SPOFR	No assigned EC number	0.7076	1.0	1.0	N/A	no
Q95Y04	RS28_CAEEL	No assigned EC number	0.8135	0.8923	0.8923	yes	no
P61030	RS28_PYRHO	No assigned EC number	0.5666	0.8923	0.8169	yes	no
P61031	RS28_NANEQ	No assigned EC number	0.5781	0.9538	0.7045	yes	no
A4FYI6	RS28_METM5	No assigned EC number	0.5084	0.8769	0.75	yes	no
O29493	RS28_ARCFU	No assigned EC number	0.5076	0.9692	0.8873	yes	no
Q74ZD8	RS28_ASHGO	No assigned EC number	0.7313	1.0	0.9701	yes	no
Q6FLC3	RS28_CANGA	No assigned EC number	0.7142	0.9692	0.9402	yes	no
A1RXH2	RS28_THEPD	No assigned EC number	0.5762	0.8769	0.7402	yes	no
Q8U159	RS28_PYRFU	No assigned EC number	0.5666	0.8923	0.8169	yes	no
Q10421	RS28_SCHPO	No assigned EC number	0.7352	1.0	0.9558	yes	no
P54065	RS28_METJA	No assigned EC number	0.5593	0.8769	0.76	yes	no
Q975Z8	RS28_SULTO	No assigned EC number	0.5932	0.8769	0.6867	yes	no
Q3E7X9	RS28A_YEAST	No assigned EC number	0.7142	0.9692	0.9402	yes	no
Q4JAV1	RS28_SULAC	No assigned EC number	0.5932	0.8769	0.6785	yes	no
P33286	RS28_KLUMA	No assigned EC number	0.7313	1.0	0.9701	N/A	no
Q6PBK3	RS28_DANRE	No assigned EC number	0.8032	0.9384	0.8840	yes	no
Q6KZI6	RS28_PICTO	No assigned EC number	0.5151	0.9846	0.9275	yes	no
Q8ZTA7	RS28_PYRAE	No assigned EC number	0.5762	0.8769	0.7402	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_fgenesh4_pg.C_LG_VIII0110	SubName- Full=Putative uncharacterized protein; (65 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	grail3.0066003101	hypothetical protein (168 aa)	•		•	•			•		0.873
	estExt_Genewise1_v1.C_LG_IX0690	SubName- Full=Putative uncharacterized protein; (168 aa)	•		•	•			•		0.871
	estExt_fgenesh4_pg.C_410046	SubName- Full=Putative uncharacterized protein; (128 aa)	•			•			•		0.848
	estExt_Genewise1_v1.C_LG_XIX2192	SubName- Full=Putative uncharacterized protein; (128 aa)	•			•			•		0.845
	gw1.120.71.1	hypothetical protein (874 aa)	•					•	•		0.762
	eugene3.34750001	Predicted protein (55 aa)	•						•		0.742
	eugene3.00081030	SubName- Full=Putative uncharacterized protein; (155 aa)	•		•	•			•		0.725
	estExt_fgenesh4_kg.C_LG_XVII0009	SubName- Full=Putative uncharacterized protein; (144 aa)				•	•	•	•		0.691
	eugene3.00041113	hypothetical protein (144 aa)				•	•	•	•		0.680
	estExt_fgenesh4_pm.C_LG_I0760	hypothetical protein (122 aa)			•	•			•		0.621

---

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	65
cd04457	60	cd04457, S1_S28E, S1_S28E: S28E, S1-like RNA-bindi	1e-29
pfam01200	69	pfam01200, Ribosomal_S28e, Ribosomal protein S28e	4e-26
PTZ00085	73	PTZ00085, PTZ00085, 40S ribosomal protein S28; Pro	8e-25
COG2053	69	COG2053, RPS28A, Ribosomal protein S28E/S33 [Trans	3e-20
PRK04007	70	PRK04007, rps28e, 30S ribosomal protein S28e; Vali	2e-19

>gnl|CDD|239904 cd04457, S1_S28E, S1_S28E: S28E, S1-like RNA-binding domain

 Score = 98.5 bits (246), Expect = 1e-29
 Identities = 47/60 (78%), Positives = 55/60 (91%)

Query: 6  KHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESEREARRLR 65
          K A V+KV+GRTGSRG+VTQVRV+F+DD+ R I+RNVKGPVREGDIL LLE+EREARRLR
Sbjct: 1  KLAEVIKVLGRTGSRGEVTQVRVEFMDDKGRSIIRNVKGPVREGDILMLLETEREARRLR 60

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. S28E protein is a component of the 30S ribosomal subunit. S28E is highly conserved among archaea and eukaryotes. S28E may control precursor RNA splicing and turnover in mRNA maturation process but its function in the ribosome is largely unknown. The structure contains an OB-fold found in many oligosaccharide and nucleic acid binding proteins. This implies that S28E might be involved in protein synthesis. Length = 60

>gnl|CDD|216359 pfam01200, Ribosomal_S28e, Ribosomal protein S28e

 Score = 90.1 bits (224), Expect = 4e-26
 Identities = 44/66 (66%), Positives = 54/66 (81%), Gaps = 2/66 (3%)

Query: 2  DSQIKHAVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDILTLLESER 59
          + + K A V++V+GRTGSRG+VTQVRV+ L+  D+ R I RNVKGPVR GDIL LLE+ER
Sbjct: 4  EQEAKLAEVIEVLGRTGSRGEVTQVRVRILEGRDKGRIITRNVKGPVRVGDILMLLETER 63

Query: 60 EARRLR 65
          EARRLR
Sbjct: 64 EARRLR 69

Length = 69

>gnl|CDD|240261 PTZ00085, PTZ00085, 40S ribosomal protein S28; Provisional

 Score = 86.7 bits (215), Expect = 8e-25
 Identities = 43/68 (63%), Positives = 54/68 (79%), Gaps = 3/68 (4%)

Query: 1  MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQ---NRFIMRNVKGPVREGDILTLLES 57
             Q K A V+KV+GRTGSRG VTQVRV+ + ++    R ++RNVKGPVREGDIL+L+E+
Sbjct: 6  DTEQPKLAKVIKVLGRTGSRGGVTQVRVQLMGEEGDAGRTLIRNVKGPVREGDILSLMET 65

Query: 58 EREARRLR 65
          EREARRLR
Sbjct: 66 EREARRLR 73

Length = 73

>gnl|CDD|224964 COG2053, RPS28A, Ribosomal protein S28E/S33 [Translation, ribosomal structure and biogenesis]

 Score = 75.1 bits (185), Expect = 3e-20
 Identities = 41/67 (61%), Positives = 51/67 (76%), Gaps = 2/67 (2%)

Query: 1  MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDILTLLESE 58
          M  +   A V++V+GRTG  G+VTQV+V+ L+  D+ R I RNVKGPVR GDIL LLE+E
Sbjct: 1  MMEEATPAEVIEVLGRTGMTGEVTQVKVRILEGRDKGRIITRNVKGPVRVGDILMLLETE 60

Query: 59 REARRLR 65
          REARRLR
Sbjct: 61 REARRLR 67

Length = 69

>gnl|CDD|235197 PRK04007, rps28e, 30S ribosomal protein S28e; Validated

 Score = 73.1 bits (180), Expect = 2e-19
 Identities = 35/67 (52%), Positives = 48/67 (71%), Gaps = 2/67 (2%)

Query: 1  MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDILTLLESE 58
           + +   A V++++GRTG  G+VTQV+ + L+  D+ R I RNVKGPVR GDIL L E+E
Sbjct: 2  AEEEGTPAEVIEIIGRTGMTGEVTQVKCRILEGRDKGRIITRNVKGPVRVGDILMLRETE 61

Query: 59 REARRLR 65
          REAR+L 
Sbjct: 62 REARKLG 68

Length = 70

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	65
PF01200	69	Ribosomal_S28e: Ribosomal protein S28e; InterPro:	100.0
cd04457	60	S1_S28E S1_S28E: S28E, S1-like RNA-binding domain.	100.0
PRK04007	70	rps28e 30S ribosomal protein S28e; Validated	100.0
PTZ00085	73	40S ribosomal protein S28; Provisional	100.0
KOG3502	66	consensus 40S ribosomal protein S28 [Translation,	100.0
COG2053	69	RPS28A Ribosomal protein S28E/S33 [Translation, ri	100.0

>PF01200 Ribosomal_S28e: Ribosomal protein S28e; InterPro: IPR000289 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=100.00  E-value=1.2e-41  Score=210.70  Aligned_cols=65  Identities=80%  Similarity=1.147  Sum_probs=52.0

Q ss_pred             CCc---cceeEEEEEEccccCCcccEEEEEEEEcCCCC-ceEEeeecCccccCcEEeeehhHHHHhhcC
Q 035463            1 MDS---QIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQN-RFIMRNVKGPVREGDILTLLESEREARRLR   65 (65)
Q Consensus         1 md~---~~~~A~V~kVlGRtGs~G~~tqVrve~l~~~~-r~i~RnVkGPVr~GDil~LlEserEarrlr   65 (65)
                      ||+   ++++|+|+||||||||+|+||||||+||++++ |+|+||||||||+||||+|+||||||||||
T Consensus         1 m~~~~~~~~~A~V~kVlgRtGs~G~~tQVrv~~l~~~~gR~i~RNVkGPVr~GDil~LlEtEREArrlr   69 (69)
T PF01200_consen    1 MDTSVQPIKLARVIKVLGRTGSRGQVTQVRVEFLDGDKGRSIIRNVKGPVREGDILTLLETEREARRLR   69 (69)
T ss_dssp             --S---SSEEEEEEEEECCCTSSSSEEEEEEEESSSSSS-EEEEEECSTTSTT-EEEESSSS-------
T ss_pred             CCcccCCceeEEEEEEcccccCcccEEEEEEEEecCCcceEEeecccCCcccCcEEEEeehhhhhhhcC
Confidence            664   68999999999999999999999999999876 999999999999999999999999999997

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 [, ]. A number of eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. Examples are: Mammalian S28 [] Plant S28 [] Fungi S33 [] Archaebacterial S28e. These proteins have from 64 to 78 amino acids and a highly conserved C-terminal region.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_Y 2XZN_1 2XZM_1 1NY4_A 1NE3_A 3U5C_c 3U5G_c 3O30_R 3O2Z_R 3IZB_Y.

>cd04457 S1_S28E S1_S28E: S28E, S1-like RNA-binding domain

Probab=100.00  E-value=1.3e-40  Score=201.89  Aligned_cols=60  Identities=78%  Similarity=1.161  Sum_probs=58.7

Q ss_pred             eeEEEEEEccccCCcccEEEEEEEEcCCCCceEEeeecCccccCcEEeeehhHHHHhhcC
Q 035463            6 KHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESEREARRLR   65 (65)
Q Consensus         6 ~~A~V~kVlGRtGs~G~~tqVrve~l~~~~r~i~RnVkGPVr~GDil~LlEserEarrlr   65 (65)
                      ++|+|+||+|||||+|+||||||+||+|++|+|+||||||||+||||+|+|||||||+||
T Consensus         1 ~~A~V~kvlGRtG~~G~~tQVrv~~l~d~~r~i~RNVKGPVr~GDIl~L~EteREArrlr   60 (60)
T cd04457           1 KLAEVIKVLGRTGSRGEVTQVRVEFMDDKGRSIIRNVKGPVREGDILMLLETEREARRLR   60 (60)
T ss_pred             CceEEEEEeccccCcCcEEEEEEEEeeCCCcEEEEeccCCcccCcEEeehhhhhhhhhcC
Confidence            479999999999999999999999999999999999999999999999999999999996

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. S28E protein is a component of the 30S ribosomal subunit. S28E is highly conserved among archaea and eukaryotes. S28E may control precursor RNA splicing and turnover in mRNA maturation process but its function in the ribosome is largely unknown. The structure contains an OB-fold found in many oligosaccharide and nucleic acid binding proteins. This implies that S28E might be involved in protein synthesis.

>PRK04007 rps28e 30S ribosomal protein S28e; Validated

Probab=100.00  E-value=3.3e-39  Score=200.47  Aligned_cols=63  Identities=54%  Similarity=0.843  Sum_probs=59.9

Q ss_pred             ccceeEEEEEEccccCCcccEEEEEEEEcCCC--CceEEeeecCccccCcEEeeehhHHHHhhcC
Q 035463            3 SQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQ--NRFIMRNVKGPVREGDILTLLESEREARRLR   65 (65)
Q Consensus         3 ~~~~~A~V~kVlGRtGs~G~~tqVrve~l~~~--~r~i~RnVkGPVr~GDil~LlEserEarrlr   65 (65)
                      ...++|+|+||||||||+|++|||||+||+++  +|+|+||||||||+||||+|+|||||||+|+
T Consensus         4 ~~~~~A~VikVlGRTG~~G~~tQVrv~~l~~~~~~R~i~RNVkGPVR~GDIl~L~EteREAr~l~   68 (70)
T PRK04007          4 EEGTPAEVIEIIGRTGMTGEVTQVKCRILEGRDKGRIITRNVKGPVRVGDILMLRETEREARKLG   68 (70)
T ss_pred             ccCceEEEEEEeccccccccEEEEEEEEecCCCcCcEEEEeccCCcccCcEEEEhhhhhHHHhhc
Confidence            45789999999999999999999999999955  9999999999999999999999999999985

>PTZ00085 40S ribosomal protein S28; Provisional

Probab=100.00  E-value=3.5e-39  Score=201.69  Aligned_cols=63  Identities=68%  Similarity=1.038  Sum_probs=60.4

Q ss_pred             ccceeEEEEEEccccCCcccEEEEEEEEcCCC---CceEEeeecCccccCcEEeeehhHHHHhhcC
Q 035463            3 SQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQ---NRFIMRNVKGPVREGDILTLLESEREARRLR   65 (65)
Q Consensus         3 ~~~~~A~V~kVlGRtGs~G~~tqVrve~l~~~---~r~i~RnVkGPVr~GDil~LlEserEarrlr   65 (65)
                      .++++|+|+||||||||+|+||||||+||+++   +|+|+||||||||+||||+|+|||||||+||
T Consensus         8 ~~~~~A~VikVlGRTG~~G~~tQVrv~~l~~~~d~~r~i~RNVkGPVr~GDIl~L~EteREAr~lr   73 (73)
T PTZ00085          8 EQPKLAKVIKVLGRTGSRGGVTQVRVQLMGEEGDAGRTLIRNVKGPVREGDILSLMETEREARRLR   73 (73)
T ss_pred             cCceeEEEEEEeccccCcccEEEEEEEEccCCcccCcEEEEeccCCcccCcEEeehhhhhhhhhcC
Confidence            47899999999999999999999999999965   6999999999999999999999999999997

>KOG3502 consensus 40S ribosomal protein S28 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=4.2e-40  Score=202.50  Aligned_cols=64  Identities=80%  Similarity=1.111  Sum_probs=61.9

Q ss_pred             CCc--cceeEEEEEEccccCCcccEEEEEEEEcCCCCceEEeeecCccccCcEEeeehhHHHHhhcC
Q 035463            1 MDS--QIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESEREARRLR   65 (65)
Q Consensus         1 md~--~~~~A~V~kVlGRtGs~G~~tqVrve~l~~~~r~i~RnVkGPVr~GDil~LlEserEarrlr   65 (65)
                      ||+  |+++|+|+||||||||+|+|||||||||+ .+|+|+||||||||+||||.|+||||||||||
T Consensus         1 m~~~~~~~larVtkVlGRTgsqGq~tqvrvef~~-~~RsIirnVKgPvr~gdil~lleserEarrlr   66 (66)
T KOG3502|consen    1 MDSKQPIKLARVTKVLGRTGSQGQCTQVRVEFMD-TSRSIIRNVKGPVREGDILTLLESEREARRLR   66 (66)
T ss_pred             CCccchhhHhhhhhhhcccCCCCcEEEEEEEecc-ccHHHHHhccCCccccchhhhhhchhhHhhcC
Confidence            787  79999999999999999999999999998 68999999999999999999999999999997

>COG2053 RPS28A Ribosomal protein S28E/S33 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=2.9e-35  Score=182.38  Aligned_cols=61  Identities=66%  Similarity=1.002  Sum_probs=59.0

Q ss_pred             ceeEEEEEEccccCCcccEEEEEEEEcC--CCCceEEeeecCccccCcEEeeehhHHHHhhcC
Q 035463            5 IKHAVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDILTLLESEREARRLR   65 (65)
Q Consensus         5 ~~~A~V~kVlGRtGs~G~~tqVrve~l~--~~~r~i~RnVkGPVr~GDil~LlEserEarrlr   65 (65)
                      .++|+|++||||||++|++|||+|+||+  |++|+|+||||||||+||||+|+|||||||+|+
T Consensus         5 ~~~aeVi~vlgRTG~~GevtQVk~ril~grdkgRiitRNV~GPVrvgDIl~L~EteREAr~l~   67 (69)
T COG2053           5 ATPAEVIEVLGRTGMTGEVTQVKVRILEGRDKGRIITRNVKGPVRVGDILMLLETEREARRLR   67 (69)
T ss_pred             ccchheeeeecccCccCcEEEEEEEEeecCCcCcEEeeeccCCcccccEEeehhhhhhhhhhc
Confidence            5679999999999999999999999999  899999999999999999999999999999985

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	65
3iz6_Y	65	Localization Of The Small Subunit Ribosomal Protein		3e-21
3izb_Y	67	Localization Of The Small Subunit Ribosomal Protein		9e-13
3zey_Z	103	High-resolution Cryo-electron Microscopy Structure		2e-10
1ny4_A	82	Solution Structure Of The 30s Ribosomal Protein S28		1e-07
3j20_X	71	Promiscuous Behavior Of Proteins In Archaeal Riboso		2e-07
1ne3_A	68	Solution Structure Of Ribosomal Protein S28e From M		5e-07
2xzm_1	68	Crystal Structure Of The Eukaryotic 40s Ribosomal S		2e-05

>pdb|3IZ6|Y Chain Y, Localization Of The Small Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 65

Iteration: 1
 Score = 96.7 bits (239), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 47/51 (92%), Positives = 49/51 (96%)
Query: 1  MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDI 51
          MD+Q+K AVVVKVMGRTGSRGQVTQVRVKFLDDQNR IMRNVKGPVREGDI
Sbjct: 1  MDTQVKLAVVVKVMGRTGSRGQVTQVRVKFLDDQNRLIMRNVKGPVREGDI 51

>pdb|3IZB|Y Chain Y, Localization Of The Small Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 67

Iteration: 1
 Score = 68.6 bits (166), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 33/49 (67%), Positives = 41/49 (83%)
Query: 3  SQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDI 51
          + +  A V+KV+GRTGSRG VTQVRV+FL+D +R I+RNVKGPVRE DI
Sbjct: 5  TPVTLAKVIKVLGRTGSRGGVTQVRVEFLEDTSRTIVRNVKGPVRENDI 53

>pdb|3ZEY|Z Chain Z, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 103

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 29/53 (54%), Positives = 40/53 (75%), Gaps = 5/53 (9%)
Query: 4  QIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQ-----NRFIMRNVKGPVREGDI 51
          Q +  V++KV+GRTGSRG VTQVRV+ + ++     NR I+RNVKGP +EGD+
Sbjct: 37 QAQVGVIIKVLGRTGSRGNVTQVRVRLMAEEGSPEANRTIVRNVKGPCKEGDM 89

>pdb|1NY4|A Chain A, Solution Structure Of The 30s Ribosomal Protein S28e From Pyrococcus Horikoshii. Northeast Structural Genomics Consortium Target Jr19 Length = 82

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/46 (56%), Positives = 36/46 (78%), Gaps = 2/46 (4%)
Query: 8  AVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDI 51
          A V++++GRTG+ G VTQV+V+ L+  D+ R I RNV+GPVR GDI
Sbjct: 9  AEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRVGDI 54

>pdb|3J20|X Chain X, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (30s Ribosomal Subunit) Length = 71

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/46 (56%), Positives = 36/46 (78%), Gaps = 2/46 (4%)
Query: 8  AVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDI 51
          A V++++GRTG+ G VTQV+V+ L+  D+ R I RNV+GPVR GDI
Sbjct: 9  AEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRIGDI 54

>pdb|1NE3|A Chain A, Solution Structure Of Ribosomal Protein S28e From Methanobacterium Thermoautotrophicum. Ontario Centre For Structural Proteomics Target Mth0256_1_68; Northeast Structural Genomics Target Tt744 Length = 68

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 24/46 (52%), Positives = 33/46 (71%), Gaps = 2/46 (4%)
Query: 8  AVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDI 51
          A V++V+ RTG  G+V QV+ + LD  D+ R + RNV GP+REGDI
Sbjct: 7  AEVIEVLKRTGMTGEVMQVKCRILDGRDKGRILTRNVMGPIREGDI 52

>pdb|2XZM|1 Chain 1, 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 = 68

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/51 (43%), Positives = 34/51 (66%), Gaps = 2/51 (3%)
Query: 3  SQIKHAVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDI 51
           +   A ++ V+G+TGSRG +TQVRV  +   ++ R ++RNVKG  R GD+
Sbjct: 4  EETTKARIMDVLGKTGSRGGITQVRVVLISGKEEGRQLIRNVKGACRVGDV 54
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	65
3u5c_C	254	Guanine nucleotide-binding protein subunit beta-L	4e-29
2xzm_1	68	Ribosomal protein S28E containing protein; ribosom	4e-27
1ny4_A	82	30S ribosomal protein S28E; JR19, structure, autos	5e-26
1ne3_A	68	30S ribosomal protein S28E; beta protein, structur	4e-25

>3u5c_C Guanine nucleotide-binding protein subunit beta-L protein (ASC1, RACK1); translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_E 3o30_B 3o2z_B 3u5g_C 3jyv_E* 1s1h_E Length = 254

 Score = 96.7 bits (241), Expect = 4e-29
 Identities = 2/64 (3%), Positives = 11/64 (17%)

Query: 2  DSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESEREA 61
              +           G   +      +         +  +    +   I  +       
Sbjct: 4  PEAQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVTKLGRLVKAGKITTIEEIFLHSLPV 63

Query: 62 RRLR 65
          +  +
Sbjct: 64 KEFQ 67

>2xzm_1 Ribosomal protein S28E containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_1 Length = 68

 Score = 92.1 bits (229), Expect = 4e-27
 Identities = 33/66 (50%), Positives = 46/66 (69%), Gaps = 2/66 (3%)

Query: 2  DSQIKHAVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDILTLLESER 59
            +   A ++ V+G+TGSRG +TQVRV  +   ++ R ++RNVKG  R GD+L L+E ER
Sbjct: 3  TEETTKARIMDVLGKTGSRGGITQVRVVLISGKEEGRQLIRNVKGACRVGDVLELMECER 62

Query: 60 EARRLR 65
          EARRLR
Sbjct: 63 EARRLR 68

>1ny4_A 30S ribosomal protein S28E; JR19, structure, autostructure, northeast structural genomics consortium, PSI, protein structure initiative; NMR {Pyrococcus horikoshii} SCOP: b.40.4.5 Length = 82

 Score = 89.5 bits (222), Expect = 5e-26
 Identities = 34/66 (51%), Positives = 49/66 (74%), Gaps = 2/66 (3%)

Query: 2  DSQIKHAVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDILTLLESER 59
          + +   A V++++GRTG+ G VTQV+V+ L+  D+ R I RNV+GPVR GDIL L E+ER
Sbjct: 3  EDEGYPAEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRVGDILILRETER 62

Query: 60 EARRLR 65
          EAR ++
Sbjct: 63 EAREIK 68

>1ne3_A 30S ribosomal protein S28E; beta protein, structural genomics, OCSP, NESG, protein structure initiative, PSI; NMR {Methanothermococcusthermolithotrophicus} SCOP: b.40.4.5 Length = 68

 Score = 87.1 bits (216), Expect = 4e-25
 Identities = 31/64 (48%), Positives = 44/64 (68%), Gaps = 2/64 (3%)

Query: 4  QIKHAVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDILTLLESEREA 61
              A V++V+ RTG  G+V QV+ + LD  D+ R + RNV GP+REGDIL LL++ REA
Sbjct: 3  DATPAEVIEVLKRTGMTGEVMQVKCRILDGRDKGRILTRNVMGPIREGDILMLLDTIREA 62

Query: 62 RRLR 65
          + +R
Sbjct: 63 KEIR 66

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	65
3u5c_c	67	S33, YS27, 40S ribosomal protein S28-A; translatio	100.0
2xzm_1	68	Ribosomal protein S28E containing protein; ribosom	100.0
1ne3_A	68	30S ribosomal protein S28E; beta protein, structur	100.0
3j20_X	71	30S ribosomal protein S28E; archaea, archaeal, KIN	100.0
1ny4_A	82	30S ribosomal protein S28E; JR19, structure, autos	100.0

>3u5c_c S33, YS27, 40S ribosomal protein S28-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_Y 3o30_R 3o2z_R 3u5g_c 3iz6_Y

Probab=100.00  E-value=7.8e-43  Score=214.31  Aligned_cols=65  Identities=72%  Similarity=1.067  Sum_probs=61.0

Q ss_pred             CCc--cceeEEEEEEccccCCcccEEEEEEEEcCCCCceEEeeecCccccCcEEeeehhHHHHhhcC
Q 035463            1 MDS--QIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESEREARRLR   65 (65)
Q Consensus         1 md~--~~~~A~V~kVlGRtGs~G~~tqVrve~l~~~~r~i~RnVkGPVr~GDil~LlEserEarrlr   65 (65)
                      ||+  |+++|+|+||||||||+|+||||||+||+|++|+|+||||||||+||||+|+|||||||+||
T Consensus         1 m~~~~p~~~A~VikVlGRtGs~G~~tQVrv~~l~d~~r~i~RnVkGPVR~GDIl~L~EtEREarrlr   67 (67)
T 3u5c_c            1 MDNKTPVTLAKVIKVLGRTGSRGGVTQVRVEFLEDTSRTIVRNVKGPVRENDILVLMESEREARRLR   67 (67)
T ss_dssp             ----CCCEEEEEEEEEEEESSSCCEEEEEEEESSSCSCEEEEECSSCCCTTCEEEESSSSCCCCCCC
T ss_pred             CCCCCCcEEEEEEEEecCCcCcccEEEEEEEEecCCCcEEEecccCCcccCCEEEEehhhhhhhhcC
Confidence            664  68999999999999999999999999999999999999999999999999999999999997

>2xzm_1 Ribosomal protein S28E containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_1

Probab=100.00  E-value=6.2e-41  Score=206.33  Aligned_cols=65  Identities=52%  Similarity=0.878  Sum_probs=61.3

Q ss_pred             CCc-cceeEEEEEEccccCCcccEEEEEEEEcCCC--CceEEeeecCccccCcEEeeehhHHHHhhcC
Q 035463            1 MDS-QIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQ--NRFIMRNVKGPVREGDILTLLESEREARRLR   65 (65)
Q Consensus         1 md~-~~~~A~V~kVlGRtGs~G~~tqVrve~l~~~--~r~i~RnVkGPVr~GDil~LlEserEarrlr   65 (65)
                      |++ ++++|+|+||+|||||+|+||||||+||+++  +|+|+||||||||+||||+|+|||||||+||
T Consensus         1 ~~~~~~~~A~VikVlGRTGs~G~~tQVrv~~l~~~~~~R~i~RnVkGPVr~GDil~L~EteREArrlr   68 (68)
T 2xzm_1            1 MNTEETTKARIMDVLGKTGSRGGITQVRVVLISGKEEGRQLIRNVKGACRVGDVLELMECEREARRLR   68 (68)
T ss_dssp             -CCCCCEEEEEEEEEEEECCCCCEEEEEEEECSSSCCSCEEEEEEESCCCTTCEEEESCSSCCCCCCC
T ss_pred             CCcCcceEEEEEEEeccccCCCcEEEEEEEECcCCCCCcEEEeeccCCcccCcEEeehhhhhhhhhcC
Confidence            665 6899999999999999999999999999966  9999999999999999999999999999996

>1ne3_A 30S ribosomal protein S28E; beta protein, structural genomics, OCSP, NESG, protein structure initiative, PSI; NMR {Methanothermococcusthermolithotrophicus} SCOP: b.40.4.5

Probab=100.00  E-value=5.5e-40  Score=202.11  Aligned_cols=64  Identities=52%  Similarity=0.862  Sum_probs=60.0

Q ss_pred             CCccceeEEEEEEccccCCcccEEEEEEEEcC--CCCceEEeeecCccccCcEEeeehhHHHHhhcC
Q 035463            1 MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDILTLLESEREARRLR   65 (65)
Q Consensus         1 md~~~~~A~V~kVlGRtGs~G~~tqVrve~l~--~~~r~i~RnVkGPVr~GDil~LlEserEarrlr   65 (65)
                      |+. .++|+|+||||||||+|+||||||+||+  |++|+|+||||||||+||||+|+|||||||+|+
T Consensus         1 ~~~-~~~A~V~kVlGRTGs~G~~tQVrv~~l~~~~~~R~i~RnVkGPVR~GDil~L~EtEREArrl~   66 (68)
T 1ne3_A            1 MDD-ATPAEVIEVLKRTGMTGEVMQVKCRILDGRDKGRILTRNVMGPIREGDILMLLDTIREAKEIR   66 (68)
T ss_dssp             CCC-SEEEEEEEEECCSSSSSSSEEEEEEESSSSSCSCEEEEEECSCCCTTCEEEECCCCCCCCCCC
T ss_pred             CCC-ceEEEEEEEeCcccCcCcEEEEEEEEccCCCCCcEEEeeccCCcccCcEEEehhhhHHHhhcc
Confidence            554 5799999999999999999999999997  469999999999999999999999999999986

>3j20_X 30S ribosomal protein S28E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=100.00  E-value=6.9e-40  Score=203.07  Aligned_cols=62  Identities=55%  Similarity=0.865  Sum_probs=59.9

Q ss_pred             cceeEEEEEEccccCCcccEEEEEEEEc--CCCCceEEeeecCccccCcEEeeehhHHHHhhcC
Q 035463            4 QIKHAVVVKVMGRTGSRGQVTQVRVKFL--DDQNRFIMRNVKGPVREGDILTLLESEREARRLR   65 (65)
Q Consensus         4 ~~~~A~V~kVlGRtGs~G~~tqVrve~l--~~~~r~i~RnVkGPVr~GDil~LlEserEarrlr   65 (65)
                      ..++|+|+||||||||+|+||||||+||  +|++|+|+||||||||+||||+|+|||||||+|+
T Consensus         5 ~~~~A~VikVlGRTGs~G~~tQVrve~l~g~d~~R~i~RNVKGPVR~GDIl~L~EtEREArrl~   68 (71)
T 3j20_X            5 EGYPAEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRIGDILILRETEREAREIK   68 (71)
T ss_dssp             CCEEEEEEEEEEECCSSCCEEEEEEEECSSSSCSCEEEEEEESCCCTTCEEEESCSSCCCCCCC
T ss_pred             cCceEEEEEEecCCcCCccEEEEEEEEeecCCCCCEEEeeccCCcccCcEEEeehhhHHHHhhc
Confidence            4789999999999999999999999999  7999999999999999999999999999999985

>1ny4_A 30S ribosomal protein S28E; JR19, structure, autostructure, northeast structural genomics consortium, PSI, protein structure initiative; NMR {Pyrococcus horikoshii} SCOP: b.40.4.5

Probab=100.00  E-value=6.5e-39  Score=203.09  Aligned_cols=62  Identities=55%  Similarity=0.885  Sum_probs=59.2

Q ss_pred             cceeEEEEEEccccCCcccEEEEEEEEcC--CCCceEEeeecCccccCcEEeeehhHHHHhhcC
Q 035463            4 QIKHAVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDILTLLESEREARRLR   65 (65)
Q Consensus         4 ~~~~A~V~kVlGRtGs~G~~tqVrve~l~--~~~r~i~RnVkGPVr~GDil~LlEserEarrlr   65 (65)
                      .+++|+|+||||||||+|+||||||+||+  |++|+|+||||||||+||||+|+|||||||+|+
T Consensus         5 ~~~~A~VikVlGRTGs~G~~TQVrVe~l~~~~~~R~i~RNVKGPVR~GDIL~LlEtEREArrl~   68 (82)
T 1ny4_A            5 EGYPAEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRVGDILILRETEREAREIK   68 (82)
T ss_dssp             SSCEEEEEEECCCCCSSSSEEEEEEEESSSSSCSCEEEEEEESCCCTTCEEECSCCCCCCCCCS
T ss_pred             cceeEEEEEEeCcccCcCcEEEEEEEEccCCCCCcEEEeeccCCcccCcEEeehhhHHHHHHHh
Confidence            47899999999999999999999999997  458999999999999999999999999999985

---

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	65
d1ne3a_	68	b.40.4.5 (A:) Ribosomal protein S28e {Archaeon Met	1e-27
d1ny4a_	71	b.40.4.5 (A:) Ribosomal protein S28e {Archaeon Pyr	2e-26

>d1ne3a_ b.40.4.5 (A:) Ribosomal protein S28e {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 68

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S28e
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

 Score = 92.0 bits (229), Expect = 1e-27
 Identities = 31/60 (51%), Positives = 44/60 (73%), Gaps = 2/60 (3%)

Query: 8  AVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDILTLLESEREARRLR 65
          A V++V+ RTG  G+V QV+ + LD  D+ R + RNV GP+REGDIL LL++ REA+ +R
Sbjct: 7  AEVIEVLKRTGMTGEVMQVKCRILDGRDKGRILTRNVMGPIREGDILMLLDTIREAKEIR 66

>d1ny4a_ b.40.4.5 (A:) Ribosomal protein S28e {Archaeon Pyrococcus horikoshii [TaxId: 53953]} Length = 71

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S28e
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

 Score = 89.3 bits (222), Expect = 2e-26
 Identities = 34/60 (56%), Positives = 47/60 (78%), Gaps = 2/60 (3%)

Query: 8  AVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDILTLLESEREARRLR 65
          A V++++GRTG+ G VTQV+V+ L+  D+ R I RNV+GPVR GDIL L E+EREAR ++
Sbjct: 9  AEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRVGDILILRETEREAREIK 68

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	65
d1ne3a_	68	Ribosomal protein S28e {Archaeon Methanobacterium	100.0
d1ny4a_	71	Ribosomal protein S28e {Archaeon Pyrococcus horiko	100.0

>d1ne3a_ b.40.4.5 (A:) Ribosomal protein S28e {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S28e
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=100.00  E-value=4.9e-40  Score=200.98  Aligned_cols=64  Identities=52%  Similarity=0.865  Sum_probs=61.0

Q ss_pred             CCccceeEEEEEEccccCCcccEEEEEEEEcC--CCCceEEeeecCccccCcEEeeehhHHHHhhcC
Q 035463            1 MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDILTLLESEREARRLR   65 (65)
Q Consensus         1 md~~~~~A~V~kVlGRtGs~G~~tqVrve~l~--~~~r~i~RnVkGPVr~GDil~LlEserEarrlr   65 (65)
                      ||.. ++|+|+||||||||+|+||||||+||+  |.+|+|+||||||||+||||+|+|||||||+||
T Consensus         1 m~~~-~~A~V~~vlGRTG~~G~~tQVrv~~l~g~d~~r~i~RNVkGPVr~GDIl~L~EtErEArrlr   66 (68)
T d1ne3a_           1 MDDA-TPAEVIEVLKRTGMTGEVMQVKCRILDGRDKGRILTRNVMGPIREGDILMLLDTIREAKEIR   66 (68)
T ss_dssp             CCCS-EEEEEEEEECCSSSSSSSEEEEEEESSSSSCSCEEEEEECSCCCTTCEEEECCCCCCCCCCC
T ss_pred             CCCC-cceEEEEEeccccCcCcEEEEEEEEeeCCCcCCEEEeeccCCcccCcEEEEeehhhHHhhhc
Confidence            6664 789999999999999999999999999  789999999999999999999999999999997

>d1ny4a_ b.40.4.5 (A:) Ribosomal protein S28e {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S28e
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=100.00  E-value=4.2e-39  Score=198.14  Aligned_cols=62  Identities=55%  Similarity=0.885  Sum_probs=59.6

Q ss_pred             cceeEEEEEEccccCCcccEEEEEEEEcC--CCCceEEeeecCccccCcEEeeehhHHHHhhcC
Q 035463            4 QIKHAVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDILTLLESEREARRLR   65 (65)
Q Consensus         4 ~~~~A~V~kVlGRtGs~G~~tqVrve~l~--~~~r~i~RnVkGPVr~GDil~LlEserEarrlr   65 (65)
                      ..++|+|+||||||||+|+||||||+||+  |.+|+|+||||||||+||||+|+|||||||+||
T Consensus         5 ~~~pA~V~~vlGRTG~~G~~tQVrv~~l~g~d~~r~i~RNVkGPVr~GDIl~L~EtErEArrlr   68 (71)
T d1ny4a_           5 EGYPAEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRVGDILILRETEREAREIK   68 (71)
T ss_dssp             SSCEEEEEEECCCCCSSSSEEEEEEEESSSSSCSCEEEEEEESCCCTTCEEECSCCCCCCCCCS
T ss_pred             CccceEEEEEeccccCcCcEEEEEEEEeeCCCcCCEEEecccCCcccCcEEEeehhhHHHHhhc
Confidence            46799999999999999999999999999  789999999999999999999999999999995