Citrus Sinensis ID: 037546

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60------
Protein Sequence
MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR
Secondary Structure (PSIPRED)
ccccccEEEEEEEEcccccccccEEEEEEEEccccccEEEEccccccccccEEEEEHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccEEEEEEEEEEcccccccEEEEEEEEEcccccEEEEccccccccccEEEHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MDTGGPKKATVIKVIgrtgsrgqVTQVRVQFMDDtkrqitrnvkgpvrvGDILTLLESEREARRLR
Flexible Loop (DISEMBL)
mdtggpkkatvikvigrtgsrgqvtqvrvqfmddtkrqitrnvkgpvrvgdiltlleserearrlr
Low Complexity Region (SEG)
MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDIltlleserearrlr
Disordered region (IsUnstruct)
**********VIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLL**********
Disordered Region (DISOPRED)
******K**TVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESERE*****
Disordered Region (DISEMBL)
********ATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR
Disordered Region (DISPRO)
***GGPKKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREA****
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR
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	66	2.2.26 [Sep-21-2011]
P62859	69	40S ribosomal protein S28	yes	no	0.909	0.869	0.8	1e-19
Q6QAT1	69	40S ribosomal protein S28	yes	no	0.909	0.869	0.8	1e-19
P62858	69	40S ribosomal protein S28	yes	no	0.909	0.869	0.8	1e-19
P62857	69	40S ribosomal protein S28	yes	no	0.909	0.869	0.8	1e-19
Q56JX6	69	40S ribosomal protein S28	yes	no	0.909	0.869	0.8	1e-19
Q90YP3	69	40S ribosomal protein S28	N/A	no	0.909	0.869	0.783	2e-19
Q6PBK3	69	40S ribosomal protein S28	yes	no	0.909	0.869	0.783	2e-19
P46302	65	40S ribosomal protein S28	N/A	no	0.984	1.0	0.772	3e-19
Q10421	68	40S ribosomal protein S28	yes	no	0.909	0.882	0.816	3e-19
P33285	67	40S ribosomal protein S28	yes	no	1.0	0.985	0.746	5e-19

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

 Score = 94.7 bits (234), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 48/60 (80%), Positives = 52/60 (86%)

Query: 7  KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR 66
          K A V KV+GRTGS+GQ TQVRV+FMDDT R I RNVKGPVR GD+LTLLESEREARRLR
Sbjct: 10 KLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRLR 69

Rattus norvegicus (taxid: 10116)

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

 Score = 94.7 bits (234), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 48/60 (80%), Positives = 52/60 (86%)

Query: 7  KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR 66
          K A V KV+GRTGS+GQ TQVRV+FMDDT R I RNVKGPVR GD+LTLLESEREARRLR
Sbjct: 10 KLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRLR 69

Sus scrofa (taxid: 9823)

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

 Score = 94.7 bits (234), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 48/60 (80%), Positives = 52/60 (86%)

Query: 7  KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR 66
          K A V KV+GRTGS+GQ TQVRV+FMDDT R I RNVKGPVR GD+LTLLESEREARRLR
Sbjct: 10 KLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRLR 69

Mus musculus (taxid: 10090)

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

 Score = 94.7 bits (234), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 48/60 (80%), Positives = 52/60 (86%)

Query: 7  KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR 66
          K A V KV+GRTGS+GQ TQVRV+FMDDT R I RNVKGPVR GD+LTLLESEREARRLR
Sbjct: 10 KLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRLR 69

Homo sapiens (taxid: 9606)

>sp|Q56JX6|RS28_BOVIN 40S ribosomal protein S28 OS=Bos taurus GN=RPS28 PE=3 SV=1

 Score = 94.7 bits (234), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 48/60 (80%), Positives = 52/60 (86%)

Query: 7  KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR 66
          K A V KV+GRTGS+GQ TQVRV+FMDDT R I RNVKGPVR GD+LTLLESEREARRLR
Sbjct: 10 KLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRLR 69

Bos taurus (taxid: 9913)

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

 Score = 94.0 bits (232), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 47/60 (78%), Positives = 52/60 (86%)

Query: 7  KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR 66
          K A V KV+GRTGS+GQ TQVRV+FMDD+ R I RNVKGPVR GD+LTLLESEREARRLR
Sbjct: 10 KLARVTKVLGRTGSQGQCTQVRVEFMDDSNRSIIRNVKGPVREGDVLTLLESEREARRLR 69

Ictalurus punctatus (taxid: 7998)

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

 Score = 94.0 bits (232), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 47/60 (78%), Positives = 52/60 (86%)

Query: 7  KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR 66
          K A V KV+GRTGS+GQ TQVRV+FMDD+ R I RNVKGPVR GD+LTLLESEREARRLR
Sbjct: 10 KLARVTKVLGRTGSQGQCTQVRVEFMDDSNRSIIRNVKGPVREGDVLTLLESEREARRLR 69

Danio rerio (taxid: 7955)

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

 Score = 94.0 bits (232), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 51/66 (77%), Positives = 55/66 (83%), Gaps = 1/66 (1%)

Query: 1  MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESER 60
          MDT   K A V+KV+GRTGSRGQVTQVRV+F+DD  R I RNVKGPV  GDILTLLESER
Sbjct: 1  MDTQ-VKLAVVVKVMGRTGSRGQVTQVRVKFLDDQNRLIMRNVKGPVCEGDILTLLESER 59

Query: 61 EARRLR 66
          EARRLR
Sbjct: 60 EARRLR 65

Zea mays (taxid: 4577)

>sp|Q10421|RS28_SCHPO 40S ribosomal protein S28 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rps28a PE=3 SV=1

 Score = 93.6 bits (231), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 49/60 (81%), Positives = 51/60 (85%)

Query: 7  KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR 66
          K A VIKV+GRTGSRG VTQVRV+FMDDT R I RNVKGPVR  DIL LLESEREARRLR
Sbjct: 9  KLAKVIKVLGRTGSRGGVTQVRVEFMDDTSRSIIRNVKGPVREDDILVLLESEREARRLR 68

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

>sp|P33285|RS28_KLULA 40S ribosomal protein S28 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) GN=RPS28 PE=3 SV=1

 Score = 92.8 bits (229), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 50/67 (74%), Positives = 55/67 (82%), Gaps = 1/67 (1%)

Query: 1  MDTGGP-KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESE 59
          MDT  P   A VIKV+GRTGSRG VTQVRV+F++DT R I RNVKGPVR GDIL L+ESE
Sbjct: 1  MDTKTPVTLAKVIKVLGRTGSRGGVTQVRVEFLEDTTRTIVRNVKGPVREGDILVLMESE 60

Query: 60 REARRLR 66
          REARRLR
Sbjct: 61 REARRLR 67

Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid: 284590)

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	66
145343552	64	Ribosomal protein S28e [Ostreococcus luc	0.909	0.937	0.85	8e-20
218184502	400	hypothetical protein OsI_33537 [Oryza sa	1.0	0.165	0.712	1e-19
356503875	105	PREDICTED: 40S ribosomal protein S28-lik	0.909	0.571	0.816	1e-19
297739775	111	unnamed protein product [Vitis vinifera]	0.939	0.558	0.806	2e-19
116778536	65	unknown [Picea sitchensis] gi|116778837|	0.984	1.0	0.803	2e-19
357496579	75	30S ribosomal protein S28e [Medicago tru	0.909	0.8	0.816	3e-19
328353488	769	Probable urea active transporter 2 [Koma	1.0	0.085	0.731	3e-19
124359133	65	Ribosomal protein S28e [Medicago truncat	0.909	0.923	0.816	4e-19
356505487	65	PREDICTED: 40S ribosomal protein S28-lik	0.909	0.923	0.816	4e-19
357474797	221	40S ribosomal protein S28 [Medicago trun	0.909	0.271	0.816	4e-19

>gi|145343552|ref|XP_001416383.1| Ribosomal protein S28e [Ostreococcus lucimarinus CCE9901] gi|144576608|gb|ABO94676.1| Ribosomal protein S28e [Ostreococcus lucimarinus CCE9901]

 Score =  100 bits (250), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 51/60 (85%), Positives = 55/60 (91%)

Query: 7  KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR 66
          KKA V+KVIGRTGSRGQVTQVRV+F+DD  RQI RNVKGPVR GDILTL+ESEREARRLR
Sbjct: 5  KKAIVMKVIGRTGSRGQVTQVRVKFLDDQNRQIMRNVKGPVREGDILTLMESEREARRLR 64

Source: Ostreococcus lucimarinus CCE9901

Species: Ostreococcus 'lucimarinus'

Genus: Ostreococcus

Order: Mamiellales

Class: Mamiellophyceae

Phylum: Chlorophyta

Superkingdom: Eukaryota

>gi|218184502|gb|EEC66929.1| hypothetical protein OsI_33537 [Oryza sativa Indica Group]

 Score =  100 bits (249), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 52/73 (71%), Positives = 56/73 (76%), Gaps = 7/73 (9%)

Query: 1   MDTGGP-------KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDIL 53
           MD   P       K A V+KV+GRTGSRGQVTQVRV+F+DD  R I RNVKGPVR GDIL
Sbjct: 328 MDNSSPGRMDTQVKLAVVVKVMGRTGSRGQVTQVRVKFLDDQNRLIMRNVKGPVREGDIL 387

Query: 54  TLLESEREARRLR 66
           TLLESEREARRLR
Sbjct: 388 TLLESEREARRLR 400

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356503875|ref|XP_003520726.1| PREDICTED: 40S ribosomal protein S28-like [Glycine max]

 Score =  100 bits (248), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 49/60 (81%), Positives = 53/60 (88%)

Query: 7   KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR 66
           K A V+KV+GRTGSRGQVTQVRV+F+DD  R I RNVKGPVR GDILTLLESEREARRLR
Sbjct: 46  KHALVVKVMGRTGSRGQVTQVRVKFLDDQNRHIMRNVKGPVREGDILTLLESEREARRLR 105

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  100 bits (248), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 50/62 (80%), Positives = 54/62 (87%)

Query: 5   GPKKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARR 64
           G K A V+KV+GRTGSRGQVTQVRV+F+DD  R I RNVKGPVR GDILTLLESEREARR
Sbjct: 50  GVKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDILTLLESEREARR 109

Query: 65  LR 66
           LR
Sbjct: 110 LR 111

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116778536|gb|ABK20899.1| unknown [Picea sitchensis] gi|116778837|gb|ABK21020.1| unknown [Picea sitchensis] gi|116779805|gb|ABK21436.1| unknown [Picea sitchensis] gi|116779938|gb|ABK21486.1| unknown [Picea sitchensis] gi|116779954|gb|ABK21493.1| unknown [Picea sitchensis] gi|116779984|gb|ABK21504.1| unknown [Picea sitchensis] gi|116780339|gb|ABK21639.1| unknown [Picea sitchensis] gi|116780954|gb|ABK21897.1| unknown [Picea sitchensis] gi|116788726|gb|ABK24977.1| unknown [Picea sitchensis] gi|116790627|gb|ABK25683.1| unknown [Picea sitchensis] gi|148906383|gb|ABR16346.1| unknown [Picea sitchensis] gi|148907364|gb|ABR16816.1| unknown [Picea sitchensis] gi|148907622|gb|ABR16940.1| unknown [Picea sitchensis] gi|148908891|gb|ABR17550.1| unknown [Picea sitchensis] gi|148908941|gb|ABR17575.1| unknown [Picea sitchensis] gi|148909740|gb|ABR17961.1| unknown [Picea sitchensis] gi|148910472|gb|ABR18311.1| unknown [Picea sitchensis] gi|148910818|gb|ABR18475.1| unknown [Picea sitchensis] gi|224285480|gb|ACN40462.1| unknown [Picea sitchensis] gi|224286119|gb|ACN40770.1| unknown [Picea sitchensis]

 Score = 99.4 bits (246), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 53/66 (80%), Positives = 57/66 (86%), Gaps = 1/66 (1%)

Query: 1  MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESER 60
          MDTG  K A V+KVIGRTGSRGQVTQVRV+F+DD  R I RNVKGPVR GD+LTLLESER
Sbjct: 1  MDTG-VKLAVVVKVIGRTGSRGQVTQVRVKFLDDQNRLIMRNVKGPVREGDVLTLLESER 59

Query: 61 EARRLR 66
          EARRLR
Sbjct: 60 EARRLR 65

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

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 = 99.0 bits (245), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 49/60 (81%), Positives = 53/60 (88%)

Query: 7  KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR 66
          K A V+KV+GRTGSRGQVTQVRV+F+DD  R I RNVKGPVR GDILTLLESEREARRLR
Sbjct: 16 KHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRHIMRNVKGPVREGDILTLLESEREARRLR 75

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|328353488|emb|CCA39886.1| Probable urea active transporter 2 [Komagataella pastoris CBS 7435]

 Score = 99.0 bits (245), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 49/67 (73%), Positives = 54/67 (80%), Gaps = 1/67 (1%)

Query: 1   MDTGGPKK-ATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESE 59
           MDT  P   A VIKV+GRTGSRG VTQVRV+F+DD+ R I RNVKGPVR  DIL L+ESE
Sbjct: 703 MDTKTPVTLAKVIKVLGRTGSRGGVTQVRVEFLDDSSRTIVRNVKGPVRENDILCLMESE 762

Query: 60  REARRLR 66
           REARRLR
Sbjct: 763 REARRLR 769

Source: Komagataella pastoris CBS 7435

Species: Komagataella pastoris

Genus: Komagataella

Family: Saccharomycetaceae

Order: Saccharomycetales

Class: Saccharomycetes

Phylum: Ascomycota

Superkingdom: Eukaryota

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

 Score = 98.6 bits (244), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 49/60 (81%), Positives = 53/60 (88%)

Query: 7  KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR 66
          K A V+KV+GRTGSRGQVTQVRV+F+DD  R I RNVKGPVR GDILTLLESEREARRLR
Sbjct: 6  KHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRHIMRNVKGPVREGDILTLLESEREARRLR 65

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356505487|ref|XP_003521522.1| PREDICTED: 40S ribosomal protein S28-like [Glycine max] gi|356549946|ref|XP_003543351.1| PREDICTED: 40S ribosomal protein S28 [Glycine max] gi|356572706|ref|XP_003554507.1| PREDICTED: 40S ribosomal protein S28-like isoform 1 [Glycine max] gi|356572708|ref|XP_003554508.1| PREDICTED: 40S ribosomal protein S28-like isoform 2 [Glycine max] gi|356572714|ref|XP_003554511.1| PREDICTED: 40S ribosomal protein S28-like [Glycine max] gi|255628293|gb|ACU14491.1| unknown [Glycine max]

 Score = 98.6 bits (244), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 49/60 (81%), Positives = 53/60 (88%)

Query: 7  KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR 66
          K A V+KV+GRTGSRGQVTQVRV+F+DD  R I RNVKGPVR GDILTLLESEREARRLR
Sbjct: 6  KHALVVKVMGRTGSRGQVTQVRVKFLDDQNRHIMRNVKGPVREGDILTLLESEREARRLR 65

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357474797|ref|XP_003607684.1| 40S ribosomal protein S28 [Medicago truncatula] gi|355508739|gb|AES89881.1| 40S ribosomal protein S28 [Medicago truncatula]

 Score = 98.6 bits (244), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 49/60 (81%), Positives = 52/60 (86%)

Query: 7   KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR 66
           K A V+KVIGRTGSRGQVTQVRV+F DD+ R I RNVKGPVR GD LTLLESEREARRLR
Sbjct: 162 KNAVVVKVIGRTGSRGQVTQVRVKFNDDSNRHIMRNVKGPVREGDTLTLLESEREARRLR 221

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	66
UNIPROTKB|Q0IXR7	65	Os10g0411700 "Os10g0411700 pro	0.772	0.784	0.730	1e-13
UNIPROTKB|A8IKP1	65	RPS28 "Ribosomal protein S28"	0.696	0.707	0.782	2.1e-13
UNIPROTKB|Q56JX6	69	RPS28 "40S ribosomal protein S	0.787	0.753	0.690	2.7e-13
UNIPROTKB|P62857	69	RPS28 "40S ribosomal protein S	0.787	0.753	0.690	2.7e-13
UNIPROTKB|Q6QAT1	69	RPS28 "40S ribosomal protein S	0.787	0.753	0.690	2.7e-13
MGI|MGI:1859516	69	Rps28 "ribosomal protein S28"	0.787	0.753	0.690	2.7e-13
POMBASE|SPAC25G10.06	68	rps2801 "40S ribosomal protein	0.696	0.676	0.782	2.7e-13
POMBASE|SPCC285.15c	68	rps2802 "40S ribosomal protein	0.696	0.676	0.782	2.7e-13
RGD|621046	69	Rps28 "ribosomal protein S28"	0.787	0.753	0.690	2.7e-13
UNIPROTKB|F1NTT2	68	RPS28 "Uncharacterized protein	0.696	0.676	0.739	3.4e-13

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

 Score = 178 (67.7 bits), Expect = 1.0e-13, P = 1.0e-13
 Identities = 38/52 (73%), Positives = 42/52 (80%)

Query:     1 MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDI 52
             MDT   K A V+KV+GRTGSRGQVTQVRV+F+DD  R I RNVKGPVR GDI
Sbjct:     1 MDTQ-VKLAVVVKVMGRTGSRGQVTQVRVKFLDDQNRLIMRNVKGPVREGDI 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

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

 Score = 175 (66.7 bits), Expect = 2.1e-13, P = 2.1e-13
 Identities = 36/46 (78%), Positives = 39/46 (84%)

Query:     7 KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDI 52
             K A V+KVIGRTGSRGQVTQVRV+F+DD  R I RNVKGPVR GDI
Sbjct:     6 KLAIVMKVIGRTGSRGQVTQVRVKFLDDQNRLIMRNVKGPVREGDI 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

UNIPROTKB|Q56JX6 RPS28 "40S ribosomal protein S28" [Bos taurus (taxid:9913)]

 Score = 174 (66.3 bits), Expect = 2.7e-13, P = 2.7e-13
 Identities = 38/55 (69%), Positives = 42/55 (76%)

Query:     1 MDTGG--P-KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDI 52
             MDT    P K A V KV+GRTGS+GQ TQVRV+FMDDT R I RNVKGPVR GD+
Sbjct:     1 MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDV 55

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

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

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

GO:0042274 "ribosomal small subunit biogenesis" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0006412 "translation" evidence=IEA

UNIPROTKB|P62857 RPS28 "40S ribosomal protein S28" [Homo sapiens (taxid:9606)]

 Score = 174 (66.3 bits), Expect = 2.7e-13, P = 2.7e-13
 Identities = 38/55 (69%), Positives = 42/55 (76%)

Query:     1 MDTGG--P-KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDI 52
             MDT    P K A V KV+GRTGS+GQ TQVRV+FMDDT R I RNVKGPVR GD+
Sbjct:     1 MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDV 55

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

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

GO:0015935 "small ribosomal subunit" evidence=IDA

GO:0006412 "translation" evidence=IC;TAS

GO:0006364 "rRNA processing" evidence=IMP

GO:0042274 "ribosomal small subunit biogenesis" evidence=IMP

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

UNIPROTKB|Q6QAT1 RPS28 "40S ribosomal protein S28" [Sus scrofa (taxid:9823)]

 Score = 174 (66.3 bits), Expect = 2.7e-13, P = 2.7e-13
 Identities = 38/55 (69%), Positives = 42/55 (76%)

Query:     1 MDTGG--P-KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDI 52
             MDT    P K A V KV+GRTGS+GQ TQVRV+FMDDT R I RNVKGPVR GD+
Sbjct:     1 MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDV 55

GO:0042274 "ribosomal small subunit biogenesis" evidence=IEA

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

GO:0006364 "rRNA processing" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

MGI|MGI:1859516 Rps28 "ribosomal protein S28" [Mus musculus (taxid:10090)]

 Score = 174 (66.3 bits), Expect = 2.7e-13, P = 2.7e-13
 Identities = 38/55 (69%), Positives = 42/55 (76%)

Query:     1 MDTGG--P-KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDI 52
             MDT    P K A V KV+GRTGS+GQ TQVRV+FMDDT R I RNVKGPVR GD+
Sbjct:     1 MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDV 55

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

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006364 "rRNA processing" evidence=ISO

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

GO:0006412 "translation" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=ISO

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

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0042274 "ribosomal small subunit biogenesis" evidence=ISO

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 = 36/46 (78%), Positives = 38/46 (82%)

Query:     7 KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDI 52
             K A VIKV+GRTGSRG VTQVRV+FMDDT R I RNVKGPVR  DI
Sbjct:     9 KLAKVIKVLGRTGSRGGVTQVRVEFMDDTSRSIIRNVKGPVREDDI 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 = 36/46 (78%), Positives = 38/46 (82%)

Query:     7 KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDI 52
             K A VIKV+GRTGSRG VTQVRV+FMDDT R I RNVKGPVR  DI
Sbjct:     9 KLAKVIKVLGRTGSRGGVTQVRVEFMDDTSRSIIRNVKGPVREDDI 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

RGD|621046 Rps28 "ribosomal protein S28" [Rattus norvegicus (taxid:10116)]

 Score = 174 (66.3 bits), Expect = 2.7e-13, P = 2.7e-13
 Identities = 38/55 (69%), Positives = 42/55 (76%)

Query:     1 MDTGG--P-KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDI 52
             MDT    P K A V KV+GRTGS+GQ TQVRV+FMDDT R I RNVKGPVR GD+
Sbjct:     1 MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDV 55

GO:0003723 "RNA binding" evidence=TAS

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

GO:0006364 "rRNA processing" evidence=ISO

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

GO:0006412 "translation" evidence=IEA

GO:0015935 "small ribosomal subunit" evidence=ISO

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

GO:0042274 "ribosomal small subunit biogenesis" evidence=ISO

UNIPROTKB|F1NTT2 RPS28 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 173 (66.0 bits), Expect = 3.4e-13, P = 3.4e-13
 Identities = 34/46 (73%), Positives = 38/46 (82%)

Query:     7 KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDI 52
             K A V KV+GRTGS+GQ TQVRV+FMDDT R I RNVKGPVR GD+
Sbjct:     9 KLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDV 54

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

GO:0006412 "translation" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

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

GO:0042274 "ribosomal small subunit biogenesis" 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)
Q8TVE7	RS28_METKA	No assigned EC number	0.5932	0.8636	0.7702	yes	no
P62857	RS28_HUMAN	No assigned EC number	0.8	0.9090	0.8695	yes	no
P62859	RS28_RAT	No assigned EC number	0.8	0.9090	0.8695	yes	no
Q6EV21	RS28_PAPDA	No assigned EC number	0.7758	0.8787	0.8923	N/A	no
Q8TQL8	RS28_METAC	No assigned EC number	0.5	0.9696	0.8421	yes	no
B1Y9V2	RS28_PYRNV	No assigned EC number	0.5614	0.8333	0.7142	yes	no
Q97BK7	RS28_THEVO	No assigned EC number	0.5230	0.9090	0.8695	yes	no
Q9W334	RS28_DROME	No assigned EC number	0.7586	0.8787	0.8923	no	no
P61029	RS28_PYRAB	No assigned EC number	0.5820	0.9545	0.8873	yes	no
Q8PU75	RS28_METMA	No assigned EC number	0.5	0.9696	0.8767	yes	no
Q10421	RS28_SCHPO	No assigned EC number	0.8166	0.9090	0.8823	yes	no
A4YCQ2	RS28_METS5	No assigned EC number	0.5762	0.8636	0.7125	yes	no
O61590	RS28_OSTOS	No assigned EC number	0.7704	0.9090	0.9090	N/A	no
Q54MZ5	RS28_DICDI	No assigned EC number	0.6393	0.8787	0.8055	yes	no
Q7S6W5	RS28_NEUCR	No assigned EC number	0.75	0.9090	0.8823	N/A	no
A4WLP1	RS28_PYRAR	No assigned EC number	0.5789	0.8333	0.7142	yes	no
Q6LZI8	RS28_METMP	No assigned EC number	0.5423	0.8636	0.75	yes	no
P0C0X0	RS28B_YEAST	No assigned EC number	0.7164	1.0	0.9850	yes	no
Q74ZD8	RS28_ASHGO	No assigned EC number	0.7313	1.0	0.9850	yes	no
P57711	RS28_THEAC	No assigned EC number	0.5230	0.9090	0.8695	yes	no
A6USH4	RS28_METVS	No assigned EC number	0.5593	0.8636	0.75	yes	no
P62858	RS28_MOUSE	No assigned EC number	0.8	0.9090	0.8695	yes	no
Q6QAT1	RS28_PIG	No assigned EC number	0.8	0.9090	0.8695	yes	no
P61031	RS28_NANEQ	No assigned EC number	0.5932	0.8636	0.6477	yes	no
Q9Y9A6	RS28_AERPE	No assigned EC number	0.6271	0.8636	0.6951	yes	no
P46302	RS28_MAIZE	No assigned EC number	0.7727	0.9848	1.0	N/A	no
A6UT50	RS28_META3	No assigned EC number	0.5254	0.8636	0.76	yes	no
Q6PBK3	RS28_DANRE	No assigned EC number	0.7833	0.9090	0.8695	yes	no
Q9SR73	RS281_ARATH	No assigned EC number	0.8	0.8939	0.9218	yes	no
Q90YP3	RS28_ICTPU	No assigned EC number	0.7833	0.9090	0.8695	N/A	no
Q56JX6	RS28_BOVIN	No assigned EC number	0.8	0.9090	0.8695	yes	no
P34789	RS282_ARATH	No assigned EC number	0.7833	0.8939	0.9218	yes	no
Q962Q2	RS28_SPOFR	No assigned EC number	0.7758	0.8787	0.8923	N/A	no
Q95Y04	RS28_CAEEL	No assigned EC number	0.7796	0.8787	0.8923	yes	no
P61030	RS28_PYRHO	No assigned EC number	0.5820	0.9545	0.8873	yes	no
B1L5N5	RS28_KORCO	No assigned EC number	0.5671	0.9545	0.8873	yes	no
Q8ZTA7	RS28_PYRAE	No assigned EC number	0.5614	0.8333	0.7142	yes	no
O29493	RS28_ARCFU	No assigned EC number	0.5254	0.8636	0.8028	yes	no
Q6FLC3	RS28_CANGA	No assigned EC number	0.7164	1.0	0.9850	yes	no
A1RXH2	RS28_THEPD	No assigned EC number	0.5932	0.8636	0.7402	yes	no
Q8U159	RS28_PYRFU	No assigned EC number	0.5671	0.9545	0.8873	yes	no
Q6PS50	RS28_BOMMO	No assigned EC number	0.7758	0.8787	0.8923	N/A	no
P54065	RS28_METJA	No assigned EC number	0.5932	0.8636	0.76	yes	no
Q975Z8	RS28_SULTO	No assigned EC number	0.6101	0.8636	0.6867	yes	no
Q3E7X9	RS28A_YEAST	No assigned EC number	0.7164	1.0	0.9850	yes	no
Q4JAV1	RS28_SULAC	No assigned EC number	0.6101	0.8636	0.6785	yes	no
P33286	RS28_KLUMA	No assigned EC number	0.7313	1.0	0.9850	N/A	no
P33285	RS28_KLULA	No assigned EC number	0.7462	1.0	0.9850	yes	no
A1RS33	RS28_PYRIL	No assigned EC number	0.5762	0.8636	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

Fail to connect to STRING server

---

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	66
cd04457	60	cd04457, S1_S28E, S1_S28E: S28E, S1-like RNA-bindi	8e-29
PTZ00085	73	PTZ00085, PTZ00085, 40S ribosomal protein S28; Pro	4e-26
pfam01200	69	pfam01200, Ribosomal_S28e, Ribosomal protein S28e	4e-25
COG2053	69	COG2053, RPS28A, Ribosomal protein S28E/S33 [Trans	2e-20
PRK04007	70	PRK04007, rps28e, 30S ribosomal protein S28e; Vali	5e-18

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

 Score = 96.6 bits (241), Expect = 8e-29
 Identities = 48/60 (80%), Positives = 52/60 (86%)

Query: 7  KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR 66
          K A VIKV+GRTGSRG+VTQVRV+FMDD  R I RNVKGPVR GDIL 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|240261 PTZ00085, PTZ00085, 40S ribosomal protein S28; Provisional

 Score = 90.2 bits (224), Expect = 4e-26
 Identities = 47/69 (68%), Positives = 53/69 (76%), Gaps = 3/69 (4%)

Query: 1  MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFMDDTK---RQITRNVKGPVRVGDILTLLE 57
           DT  PK A VIKV+GRTGSRG VTQVRVQ M +     R + RNVKGPVR GDIL+L+E
Sbjct: 5  QDTEQPKLAKVIKVLGRTGSRGGVTQVRVQLMGEEGDAGRTLIRNVKGPVREGDILSLME 64

Query: 58 SEREARRLR 66
          +EREARRLR
Sbjct: 65 TEREARRLR 73

Length = 73

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

 Score = 87.4 bits (217), Expect = 4e-25
 Identities = 46/62 (74%), Positives = 53/62 (85%), Gaps = 2/62 (3%)

Query: 7  KKATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDILTLLESEREARR 64
          K A VI+V+GRTGSRG+VTQVRV+ ++  D  R ITRNVKGPVRVGDIL LLE+EREARR
Sbjct: 8  KLAEVIEVLGRTGSRGEVTQVRVRILEGRDKGRIITRNVKGPVRVGDILMLLETEREARR 67

Query: 65 LR 66
          LR
Sbjct: 68 LR 69

Length = 69

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

 Score = 75.9 bits (187), Expect = 2e-20
 Identities = 42/62 (67%), Positives = 50/62 (80%), Gaps = 2/62 (3%)

Query: 7  KKATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDILTLLESEREARR 64
            A VI+V+GRTG  G+VTQV+V+ ++  D  R ITRNVKGPVRVGDIL LLE+EREARR
Sbjct: 6  TPAEVIEVLGRTGMTGEVTQVKVRILEGRDKGRIITRNVKGPVRVGDILMLLETEREARR 65

Query: 65 LR 66
          LR
Sbjct: 66 LR 67

Length = 69

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

 Score = 69.6 bits (171), Expect = 5e-18
 Identities = 38/60 (63%), Positives = 47/60 (78%), Gaps = 2/60 (3%)

Query: 9  ATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDILTLLESEREARRLR 66
          A VI++IGRTG  G+VTQV+ + ++  D  R ITRNVKGPVRVGDIL L E+EREAR+L 
Sbjct: 9  AEVIEIIGRTGMTGEVTQVKCRILEGRDKGRIITRNVKGPVRVGDILMLRETEREARKLG 68

Length = 70

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	66
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=7.7e-42  Score=212.06  Aligned_cols=66  Identities=79%  Similarity=1.085  Sum_probs=51.7

Q ss_pred             CCCC--CCeeEEEEEeccccCCcCcEEEEEEEEecCCC-cEEEeeecCccccCcEEEeehhHHHHhhcC
Q 037546            1 MDTG--GPKKATVIKVIGRTGSRGQVTQVRVQFMDDTK-RQITRNVKGPVRVGDILTLLESEREARRLR   66 (66)
Q Consensus         1 md~~--~~~~A~V~kVlGRtGs~G~~tqVrve~l~d~~-r~i~RnVkGPVr~GDil~LlEsErEarrlr   66 (66)
                      ||+.  .+++|+|+||||||||+|+||||||+||++++ |+|+||||||||+||||+|+||||||||||
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            7763  29999999999999999999999999999766 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=202.32  Aligned_cols=60  Identities=80%  Similarity=1.139  Sum_probs=58.6

Q ss_pred             eeEEEEEeccccCCcCcEEEEEEEEecCCCcEEEeeecCccccCcEEEeehhHHHHhhcC
Q 037546            7 KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR   66 (66)
Q Consensus         7 ~~A~V~kVlGRtGs~G~~tqVrve~l~d~~r~i~RnVkGPVr~GDil~LlEsErEarrlr   66 (66)
                      ++|+|+||+|||||+|+||||||+||+|++|+|+||||||||+||||+|+|||||||+||
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=7.8e-39  Score=199.33  Aligned_cols=61  Identities=61%  Similarity=0.902  Sum_probs=58.8

Q ss_pred             CeeEEEEEeccccCCcCcEEEEEEEEecC--CCcEEEeeecCccccCcEEEeehhHHHHhhcC
Q 037546            6 PKKATVIKVIGRTGSRGQVTQVRVQFMDD--TKRQITRNVKGPVRVGDILTLLESEREARRLR   66 (66)
Q Consensus         6 ~~~A~V~kVlGRtGs~G~~tqVrve~l~d--~~r~i~RnVkGPVr~GDil~LlEsErEarrlr   66 (66)
                      .++|+|+||||||||+|++|||||+||++  .+|+|+||||||||+||||+|+|||||||+|+
T Consensus         6 ~~~A~VikVlGRTG~~G~~tQVrv~~l~~~~~~R~i~RNVkGPVR~GDIl~L~EteREAr~l~   68 (70)
T PRK04007          6 GTPAEVIEIIGRTGMTGEVTQVKCRILEGRDKGRIITRNVKGPVRVGDILMLRETEREARKLG   68 (70)
T ss_pred             CceEEEEEEeccccccccEEEEEEEEecCCCcCcEEEEeccCCcccCcEEEEhhhhhHHHhhc
Confidence            78999999999999999999999999994  59999999999999999999999999999985

>PTZ00085 40S ribosomal protein S28; Provisional

Probab=100.00  E-value=9.5e-39  Score=200.20  Aligned_cols=61  Identities=74%  Similarity=1.087  Sum_probs=59.0

Q ss_pred             CeeEEEEEeccccCCcCcEEEEEEEEecCC---CcEEEeeecCccccCcEEEeehhHHHHhhcC
Q 037546            6 PKKATVIKVIGRTGSRGQVTQVRVQFMDDT---KRQITRNVKGPVRVGDILTLLESEREARRLR   66 (66)
Q Consensus         6 ~~~A~V~kVlGRtGs~G~~tqVrve~l~d~---~r~i~RnVkGPVr~GDil~LlEsErEarrlr   66 (66)
                      +++|+|+||||||||+|+||||||+||+++   +|+|+||||||||+||||+|+|||||||+||
T Consensus        10 ~~~A~VikVlGRTG~~G~~tQVrv~~l~~~~d~~r~i~RNVkGPVr~GDIl~L~EteREAr~lr   73 (73)
T PTZ00085         10 PKLAKVIKVLGRTGSRGGVTQVRVQLMGEEGDAGRTLIRNVKGPVREGDILSLMETEREARRLR   73 (73)
T ss_pred             ceeEEEEEEeccccCcccEEEEEEEEccCCcccCcEEEEeccCCcccCcEEeehhhhhhhhhcC
Confidence            899999999999999999999999999955   6999999999999999999999999999997

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

Probab=100.00  E-value=5.1e-40  Score=202.63  Aligned_cols=65  Identities=77%  Similarity=1.040  Sum_probs=61.6

Q ss_pred             CCCC-CCeeEEEEEeccccCCcCcEEEEEEEEecCCCcEEEeeecCccccCcEEEeehhHHHHhhcC
Q 037546            1 MDTG-GPKKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR   66 (66)
Q Consensus         1 md~~-~~~~A~V~kVlGRtGs~G~~tqVrve~l~d~~r~i~RnVkGPVr~GDil~LlEsErEarrlr   66 (66)
                      ||+. .+++|+|+||||||||+|+|||||||||+ .+|+|+||||||||+||||.|+||||||||||
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            7872 28999999999999999999999999998 79999999999999999999999999999997

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

Probab=100.00  E-value=3e-35  Score=182.71  Aligned_cols=61  Identities=69%  Similarity=1.027  Sum_probs=59.0

Q ss_pred             CeeEEEEEeccccCCcCcEEEEEEEEec--CCCcEEEeeecCccccCcEEEeehhHHHHhhcC
Q 037546            6 PKKATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDILTLLESEREARRLR   66 (66)
Q Consensus         6 ~~~A~V~kVlGRtGs~G~~tqVrve~l~--d~~r~i~RnVkGPVr~GDil~LlEsErEarrlr   66 (66)
                      .++|+|++||||||++|++|||+|+||+  |++|+|+||||||||+||||+|+|||||||+|+
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            4779999999999999999999999999  999999999999999999999999999999985

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	66
3iz6_Y	65	Localization Of The Small Subunit Ribosomal Protein		2e-13
3izb_Y	67	Localization Of The Small Subunit Ribosomal Protein		2e-12
1ny4_A	82	Solution Structure Of The 30s Ribosomal Protein S28		3e-08
3zey_Z	103	High-resolution Cryo-electron Microscopy Structure		5e-08
3j20_X	71	Promiscuous Behavior Of Proteins In Archaeal Riboso		6e-08
2xzm_1	68	Crystal Structure Of The Eukaryotic 40s Ribosomal S		1e-07
1ne3_A	68	Solution Structure Of Ribosomal Protein S28e From M		4e-06

>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 = 70.5 bits (171), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 38/52 (73%), Positives = 42/52 (80%), Gaps = 1/52 (1%)
Query: 1  MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDI 52
          MDT   K A V+KV+GRTGSRGQVTQVRV+F+DD  R I RNVKGPVR GDI
Sbjct: 1  MDTQ-VKLAVVVKVMGRTGSRGQVTQVRVKFLDDQNRLIMRNVKGPVREGDI 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 = 67.4 bits (163), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 36/53 (67%), Positives = 40/53 (75%), Gaps = 1/53 (1%)
Query: 1  MDTGGP-KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDI 52
          MD   P   A VIKV+GRTGSRG VTQVRV+F++DT R I RNVKGPVR  DI
Sbjct: 1  MDNKTPVTLAKVIKVLGRTGSRGGVTQVRVEFLEDTSRTIVRNVKGPVRENDI 53

>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 = 53.1 bits (126), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 31/53 (58%), Positives = 39/53 (73%), Gaps = 4/53 (7%)
Query: 2  DTGGPKKATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDI 52
          D G P  A VI++IGRTG+ G VTQV+V+ ++  D  R I RNV+GPVRVGDI
Sbjct: 4  DEGYP--AEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRVGDI 54

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 27/47 (57%), Positives = 33/47 (70%), Gaps = 5/47 (10%)
Query: 11 VIKVIGRTGSRGQVTQVRVQFMD-----DTKRQITRNVKGPVRVGDI 52
          +IKV+GRTGSRG VTQVRV+ M      +  R I RNVKGP + GD+
Sbjct: 43 IIKVLGRTGSRGNVTQVRVRLMAEEGSPEANRTIVRNVKGPCKEGDM 89

>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 = 52.4 bits (124), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 30/53 (56%), Positives = 39/53 (73%), Gaps = 4/53 (7%)
Query: 2  DTGGPKKATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDI 52
          D G P  A VI++IGRTG+ G VTQV+V+ ++  D  R I RNV+GPVR+GDI
Sbjct: 4  DEGYP--AEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRIGDI 54

>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 = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/54 (50%), Positives = 37/54 (68%), Gaps = 2/54 (3%)
Query: 1  MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDI 52
          M+T    KA ++ V+G+TGSRG +TQVRV  +   +  RQ+ RNVKG  RVGD+
Sbjct: 1  MNTEETTKARIMDVLGKTGSRGGITQVRVVLISGKEEGRQLIRNVKGACRVGDV 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 = 46.6 bits (109), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 27/54 (50%), Positives = 35/54 (64%), Gaps = 4/54 (7%)
Query: 1  MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDI 52
          MD   P  A VI+V+ RTG  G+V QV+ + +D  D  R +TRNV GP+R GDI
Sbjct: 1  MDDATP--AEVIEVLKRTGMTGEVMQVKCRILDGRDKGRILTRNVMGPIREGDI 52
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	66
3u5c_C	254	Guanine nucleotide-binding protein subunit beta-L	9e-29
2xzm_1	68	Ribosomal protein S28E containing protein; ribosom	4e-28
1ny4_A	82	30S ribosomal protein S28E; JR19, structure, autos	3e-27
1ne3_A	68	30S ribosomal protein S28E; beta protein, structur	7e-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 = 95.9 bits (239), Expect = 9e-29
 Identities = 3/67 (4%), Positives = 13/67 (19%), Gaps = 1/67 (1%)

Query: 1  MDTGGP-KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESE 59
          M      ++          G   +      +            +    ++  I  +    
Sbjct: 1  MSAPEAQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVTKLGRLVKAGKITTIEEIFLHS 60

Query: 60 REARRLR 66
             +  +
Sbjct: 61 LPVKEFQ 67

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

 Score = 94.4 bits (235), Expect = 4e-28
 Identities = 38/68 (55%), Positives = 49/68 (72%), Gaps = 2/68 (2%)

Query: 1  MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDILTLLES 58
          M+T    KA ++ V+G+TGSRG +TQVRV  +   +  RQ+ RNVKG  RVGD+L L+E 
Sbjct: 1  MNTEETTKARIMDVLGKTGSRGGITQVRVVLISGKEEGRQLIRNVKGACRVGDVLELMEC 60

Query: 59 EREARRLR 66
          EREARRLR
Sbjct: 61 EREARRLR 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 = 93.0 bits (231), Expect = 3e-27
 Identities = 37/68 (54%), Positives = 48/68 (70%), Gaps = 2/68 (2%)

Query: 1  MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDILTLLES 58
          M       A VI++IGRTG+ G VTQV+V+ ++  D  R I RNV+GPVRVGDIL L E+
Sbjct: 1  MAEDEGYPAEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRVGDILILRET 60

Query: 59 EREARRLR 66
          EREAR ++
Sbjct: 61 EREAREIK 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 = 86.4 bits (214), Expect = 7e-25
 Identities = 31/63 (49%), Positives = 43/63 (68%), Gaps = 2/63 (3%)

Query: 6  PKKATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDILTLLESEREAR 63
             A VI+V+ RTG  G+V QV+ + +D  D  R +TRNV GP+R GDIL LL++ REA+
Sbjct: 4  ATPAEVIEVLKRTGMTGEVMQVKCRILDGRDKGRILTRNVMGPIREGDILMLLDTIREAK 63

Query: 64 RLR 66
           +R
Sbjct: 64 EIR 66

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	66
3u5c_c	67	S33, YS27, 40S ribosomal protein S28-A; translatio	100.0
2xzm_1	68	Ribosomal protein S28E containing protein; ribosom	100.0
3j20_X	71	30S ribosomal protein S28E; archaea, archaeal, KIN	100.0
1ne3_A	68	30S ribosomal protein S28E; beta protein, structur	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=7.9e-43  Score=214.81  Aligned_cols=66  Identities=71%  Similarity=1.007  Sum_probs=60.6

Q ss_pred             CCCCC-CeeEEEEEeccccCCcCcEEEEEEEEecCCCcEEEeeecCccccCcEEEeehhHHHHhhcC
Q 037546            1 MDTGG-PKKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDILTLLESEREARRLR   66 (66)
Q Consensus         1 md~~~-~~~A~V~kVlGRtGs~G~~tqVrve~l~d~~r~i~RnVkGPVr~GDil~LlEsErEarrlr   66 (66)
                      ||+.. +++|+|+||||||||+|+||||||+||+|++|+|+||||||||+||||+|+|||||||+||
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            77633 8999999999999999999999999999999999999999999999999999999999997

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

Probab=100.00  E-value=5.8e-41  Score=206.97  Aligned_cols=66  Identities=58%  Similarity=0.906  Sum_probs=61.8

Q ss_pred             CCCCCCeeEEEEEeccccCCcCcEEEEEEEEecCC--CcEEEeeecCccccCcEEEeehhHHHHhhcC
Q 037546            1 MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFMDDT--KRQITRNVKGPVRVGDILTLLESEREARRLR   66 (66)
Q Consensus         1 md~~~~~~A~V~kVlGRtGs~G~~tqVrve~l~d~--~r~i~RnVkGPVr~GDil~LlEsErEarrlr   66 (66)
                      |+++.+++|+|+||||||||+|+||||||+||+++  +|+|+||||||||+||||+|+|||||||+||
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            67755899999999999999999999999999855  9999999999999999999999999999997

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

Probab=100.00  E-value=4.2e-40  Score=204.54  Aligned_cols=66  Identities=55%  Similarity=0.860  Sum_probs=61.6

Q ss_pred             CCCCCCeeEEEEEeccccCCcCcEEEEEEEEe--cCCCcEEEeeecCccccCcEEEeehhHHHHhhcC
Q 037546            1 MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFM--DDTKRQITRNVKGPVRVGDILTLLESEREARRLR   66 (66)
Q Consensus         1 md~~~~~~A~V~kVlGRtGs~G~~tqVrve~l--~d~~r~i~RnVkGPVr~GDil~LlEsErEarrlr   66 (66)
                      |..+..++|+|+||||||||+|+||||||+||  +|++|+|+||||||||+||||+|+|||||||+|+
T Consensus         1 ~~~~~~~~A~VikVlGRTGs~G~~tQVrve~l~g~d~~R~i~RNVKGPVR~GDIl~L~EtEREArrl~   68 (71)
T 3j20_X            1 MAEDEGYPAEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRIGDILILRETEREAREIK   68 (71)
T ss_dssp             CCCCCCEEEEEEEEEEECCSSCCEEEEEEEECSSSSCSCEEEEEEESCCCTTCEEEESCSSCCCCCCC
T ss_pred             CCcccCceEEEEEEecCCcCCccEEEEEEEEeecCCCCCEEEeeccCCcccCcEEEeehhhHHHHhhc
Confidence            44434789999999999999999999999999  7999999999999999999999999999999985

>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=4e-40  Score=203.24  Aligned_cols=64  Identities=52%  Similarity=0.827  Sum_probs=60.1

Q ss_pred             CCCCCCeeEEEEEeccccCCcCcEEEEEEEEec--CCCcEEEeeecCccccCcEEEeehhHHHHhhcC
Q 037546            1 MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDILTLLESEREARRLR   66 (66)
Q Consensus         1 md~~~~~~A~V~kVlGRtGs~G~~tqVrve~l~--d~~r~i~RnVkGPVr~GDil~LlEsErEarrlr   66 (66)
                      |+.  .++|+|+||||||||+|+||||||+||+  |++|+|+||||||||+||||+|+|||||||+|+
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            454  5899999999999999999999999997  569999999999999999999999999999986

>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=1.6e-39  Score=206.35  Aligned_cols=66  Identities=56%  Similarity=0.877  Sum_probs=60.8

Q ss_pred             CCCCCCeeEEEEEeccccCCcCcEEEEEEEEec--CCCcEEEeeecCccccCcEEEeehhHHHHhhcC
Q 037546            1 MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDILTLLESEREARRLR   66 (66)
Q Consensus         1 md~~~~~~A~V~kVlGRtGs~G~~tqVrve~l~--d~~r~i~RnVkGPVr~GDil~LlEsErEarrlr   66 (66)
                      |....+++|+|+||||||||+|+||||||+||+  |++|+|+||||||||+||||+|+|||||||+|+
T Consensus         1 m~~~~~~~A~VikVlGRTGs~G~~TQVrVe~l~~~~~~R~i~RNVKGPVR~GDIL~LlEtEREArrl~   68 (82)
T 1ny4_A            1 MAEDEGYPAEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRVGDILILRETEREAREIK   68 (82)
T ss_dssp             CCCCSSCEEEEEEECCCCCSSSSEEEEEEEESSSSSCSCEEEEEEESCCCTTCEEECSCCCCCCCCCS
T ss_pred             CCcccceeEEEEEEeCcccCcCcEEEEEEEEccCCCCCcEEEeeccCCcccCcEEeehhhHHHHHHHh
Confidence            443338999999999999999999999999997  569999999999999999999999999999985

---

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	66
d1ne3a_	68	b.40.4.5 (A:) Ribosomal protein S28e {Archaeon Met	2e-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 = 91.6 bits (228), Expect = 2e-27
 Identities = 31/63 (49%), Positives = 43/63 (68%), Gaps = 2/63 (3%)

Query: 6  PKKATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDILTLLESEREAR 63
             A VI+V+ RTG  G+V QV+ + +D  D  R +TRNV GP+R GDIL LL++ REA+
Sbjct: 4  ATPAEVIEVLKRTGMTGEVMQVKCRILDGRDKGRILTRNVMGPIREGDILMLLDTIREAK 63

Query: 64 RLR 66
           +R
Sbjct: 64 EIR 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 = 37/68 (54%), Positives = 48/68 (70%), Gaps = 2/68 (2%)

Query: 1  MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDILTLLES 58
          M       A VI++IGRTG+ G VTQV+V+ ++  D  R I RNV+GPVRVGDIL L E+
Sbjct: 1  MAEDEGYPAEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRVGDILILRET 60

Query: 59 EREARRLR 66
          EREAR ++
Sbjct: 61 EREAREIK 68

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	66
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=4e-40  Score=201.89  Aligned_cols=64  Identities=52%  Similarity=0.827  Sum_probs=61.1

Q ss_pred             CCCCCCeeEEEEEeccccCCcCcEEEEEEEEec--CCCcEEEeeecCccccCcEEEeehhHHHHhhcC
Q 037546            1 MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDILTLLESEREARRLR   66 (66)
Q Consensus         1 md~~~~~~A~V~kVlGRtGs~G~~tqVrve~l~--d~~r~i~RnVkGPVr~GDil~LlEsErEarrlr   66 (66)
                      ||.  .++|+|+||||||||+|+||||||+||+  |.+|+|+||||||||+||||+|+|||||||+||
T Consensus         1 m~~--~~~A~V~~vlGRTG~~G~~tQVrv~~l~g~d~~r~i~RNVkGPVr~GDIl~L~EtErEArrlr   66 (68)
T d1ne3a_           1 MDD--ATPAEVIEVLKRTGMTGEVMQVKCRILDGRDKGRILTRNVMGPIREGDILMLLDTIREAKEIR   66 (68)
T ss_dssp             CCC--SEEEEEEEEECCSSSSSSSEEEEEEESSSSSCSCEEEEEECSCCCTTCEEEECCCCCCCCCCC
T ss_pred             CCC--CcceEEEEEeccccCcCcEEEEEEEEeeCCCcCCEEEeeccCCcccCcEEEEeehhhHHhhhc
Confidence            665  4899999999999999999999999999  889999999999999999999999999999997

>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=1.6e-39  Score=200.56  Aligned_cols=66  Identities=56%  Similarity=0.877  Sum_probs=61.4

Q ss_pred             CCCCCCeeEEEEEeccccCCcCcEEEEEEEEec--CCCcEEEeeecCccccCcEEEeehhHHHHhhcC
Q 037546            1 MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDILTLLESEREARRLR   66 (66)
Q Consensus         1 md~~~~~~A~V~kVlGRtGs~G~~tqVrve~l~--d~~r~i~RnVkGPVr~GDil~LlEsErEarrlr   66 (66)
                      |......+|+|+||||||||+|+||||||+||+  |.+|+|+||||||||+||||+|+|||||||+||
T Consensus         1 m~~~~~~pA~V~~vlGRTG~~G~~tQVrv~~l~g~d~~r~i~RNVkGPVr~GDIl~L~EtErEArrlr   68 (71)
T d1ny4a_           1 MAEDEGYPAEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRVGDILILRETEREAREIK   68 (71)
T ss_dssp             CCCCSSCEEEEEEECCCCCSSSSEEEEEEEESSSSSCSCEEEEEEESCCCTTCEEECSCCCCCCCCCS
T ss_pred             CCccCccceEEEEEeccccCcCcEEEEEEEEeeCCCcCCEEEecccCCcccCcEEEeehhhHHHHhhc
Confidence            444336899999999999999999999999999  889999999999999999999999999999995