Psyllid ID: psy5287

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60-----
Protein Sequence
MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESEREARRLR
Secondary Structure (PSIPRED)
cccccEEEEEEEEcccccccccEEEEEEEEEcccccEEEEccccccccccEEEEEHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccEEEEEEEEEcccccccEEEEEEEEEEcccccEEEEccccccccccEEEHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MDKQVVLARVIKTlgrtgsqgqctQVKVEFigdqnrtiirnvkgpvregdILTLLESEREARRLR
Flexible Loop (DISEMBL)
MDKQVVLARViktlgrtgsqgqctqvkvefigdqnrtiirnvkgpvregdiltlleserearrlr
Low Complexity Region (SEG)
MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDIltlleserearrlr
Disordered region (IsUnstruct)
****VVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTL***********
Disordered Region (DISOPRED)
****VVL*RVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESERE*****
Disordered Region (DISEMBL)
MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESEREARRLR
Disordered Region (DISPRO)
**KQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESEREA****
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESEREARRLR
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]
Q9W334	65	40S ribosomal protein S28	yes	N/A	1.0	1.0	0.892	3e-26
Q962Q2	65	40S ribosomal protein S28	N/A	N/A	1.0	1.0	0.861	1e-24
Q6EV21	65	40S ribosomal protein S28	N/A	N/A	1.0	1.0	0.861	1e-24
Q6PS50	65	40S ribosomal protein S28	N/A	N/A	1.0	1.0	0.861	1e-24
Q95Y04	65	40S ribosomal protein S28	yes	N/A	0.984	0.984	0.848	7e-23
Q90YP3	69	40S ribosomal protein S28	N/A	N/A	0.907	0.855	0.864	7e-23
Q6PBK3	69	40S ribosomal protein S28	yes	N/A	0.907	0.855	0.864	7e-23
P62859	69	40S ribosomal protein S28	yes	N/A	0.907	0.855	0.847	4e-22
Q6QAT1	69	40S ribosomal protein S28	yes	N/A	0.907	0.855	0.847	4e-22
P62858	69	40S ribosomal protein S28	yes	N/A	0.907	0.855	0.847	4e-22

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

 Score =  117 bits (292), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 58/65 (89%), Positives = 61/65 (93%)

Query: 1  MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESERE 60
          MDK VV ARV+K LGRTGSQGQCTQVKVEF+G+QNR IIRNVKGPVREGDILTLLESERE
Sbjct: 1  MDKPVVWARVMKVLGRTGSQGQCTQVKVEFLGEQNRQIIRNVKGPVREGDILTLLESERE 60

Query: 61 ARRLR 65
          ARRLR
Sbjct: 61 ARRLR 65

Drosophila melanogaster (taxid: 7227)

>sp|Q962Q2|RS28_SPOFR 40S ribosomal protein S28 OS=Spodoptera frugiperda GN=RpS28 PE=3 SV=1

 Score =  111 bits (278), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 56/65 (86%), Positives = 60/65 (92%)

Query: 1  MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESERE 60
          MDK  VLARV+K LGRTGSQGQCTQVKVEFIG+ +R IIRNVKGPVR+GDILTLLESERE
Sbjct: 1  MDKPNVLARVVKVLGRTGSQGQCTQVKVEFIGETSRQIIRNVKGPVRDGDILTLLESERE 60

Query: 61 ARRLR 65
          ARRLR
Sbjct: 61 ARRLR 65

Spodoptera frugiperda (taxid: 7108)

>sp|Q6EV21|RS28_PAPDA 40S ribosomal protein S28 OS=Papilio dardanus GN=RpS28 PE=3 SV=1

 Score =  111 bits (278), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 56/65 (86%), Positives = 60/65 (92%)

Query: 1  MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESERE 60
          MDK  VLARV+K LGRTGSQGQCTQVKVEFIG+ +R IIRNVKGPVR+GDILTLLESERE
Sbjct: 1  MDKPNVLARVVKVLGRTGSQGQCTQVKVEFIGETSRQIIRNVKGPVRDGDILTLLESERE 60

Query: 61 ARRLR 65
          ARRLR
Sbjct: 61 ARRLR 65

Papilio dardanus (taxid: 77259)

>sp|Q6PS50|RS28_BOMMO 40S ribosomal protein S28 OS=Bombyx mori GN=RpS28 PE=3 SV=1

 Score =  111 bits (278), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 56/65 (86%), Positives = 60/65 (92%)

Query: 1  MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESERE 60
          MDK  VLARV+K LGRTGSQGQCTQVKVEFIG+ +R IIRNVKGPVR+GDILTLLESERE
Sbjct: 1  MDKPNVLARVVKVLGRTGSQGQCTQVKVEFIGETSRQIIRNVKGPVRDGDILTLLESERE 60

Query: 61 ARRLR 65
          ARRLR
Sbjct: 61 ARRLR 65

Bombyx mori (taxid: 7091)

>sp|Q95Y04|RS28_CAEEL 40S ribosomal protein S28 OS=Caenorhabditis elegans GN=rps-28 PE=3 SV=1

 Score =  105 bits (263), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 56/66 (84%), Positives = 60/66 (90%), Gaps = 2/66 (3%)

Query: 1  MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQN-RTIIRNVKGPVREGDILTLLESER 59
          MDK + LARV K +GRTGSQGQCTQV+VEFI DQN R+IIRNVKGPVREGDILTLLESER
Sbjct: 1  MDK-LTLARVTKVIGRTGSQGQCTQVRVEFINDQNNRSIIRNVKGPVREGDILTLLESER 59

Query: 60 EARRLR 65
          EARRLR
Sbjct: 60 EARRLR 65

Caenorhabditis elegans (taxid: 6239)

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

 Score =  105 bits (263), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 51/59 (86%), Positives = 55/59 (93%)

Query: 7  LARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESEREARRLR 65
          LARV K LGRTGSQGQCTQV+VEF+ D NR+IIRNVKGPVREGD+LTLLESEREARRLR
Sbjct: 11 LARVTKVLGRTGSQGQCTQVRVEFMDDSNRSIIRNVKGPVREGDVLTLLESEREARRLR 69

Ictalurus punctatus (taxid: 7998)

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

 Score =  105 bits (263), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 51/59 (86%), Positives = 55/59 (93%)

Query: 7  LARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESEREARRLR 65
          LARV K LGRTGSQGQCTQV+VEF+ D NR+IIRNVKGPVREGD+LTLLESEREARRLR
Sbjct: 11 LARVTKVLGRTGSQGQCTQVRVEFMDDSNRSIIRNVKGPVREGDVLTLLESEREARRLR 69

Danio rerio (taxid: 7955)

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

 Score =  103 bits (256), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 50/59 (84%), Positives = 55/59 (93%)

Query: 7  LARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESEREARRLR 65
          LARV K LGRTGSQGQCTQV+VEF+ D +R+IIRNVKGPVREGD+LTLLESEREARRLR
Sbjct: 11 LARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRLR 69

Rattus norvegicus (taxid: 10116)

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

 Score =  103 bits (256), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 50/59 (84%), Positives = 55/59 (93%)

Query: 7  LARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESEREARRLR 65
          LARV K LGRTGSQGQCTQV+VEF+ D +R+IIRNVKGPVREGD+LTLLESEREARRLR
Sbjct: 11 LARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRLR 69

Sus scrofa (taxid: 9823)

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

 Score =  103 bits (256), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 50/59 (84%), Positives = 55/59 (93%)

Query: 7  LARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESEREARRLR 65
          LARV K LGRTGSQGQCTQV+VEF+ D +R+IIRNVKGPVREGD+LTLLESEREARRLR
Sbjct: 11 LARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRLR 69

Mus musculus (taxid: 10090)

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
383850448	113	PREDICTED: 40S ribosomal protein S28-lik	1.0	0.575	0.907	5e-26
91094381	65	PREDICTED: similar to ribosomal protein	1.0	1.0	0.938	1e-25
242021748	67	40S ribosomal protein S28, putative [Ped	0.984	0.955	0.937	2e-25
170060838	65	ribosomal protein S28 [Culex quinquefasc	1.0	1.0	0.923	2e-25
328779779	65	PREDICTED: 40S ribosomal protein S28-lik	1.0	1.0	0.907	3e-25
157114485	65	ribosomal protein S28, putative [Aedes a	1.0	1.0	0.907	4e-25
187175305	65	ribosomal protein S28e-like [Acyrthosiph	1.0	1.0	0.907	5e-25
121543975	65	ribosomal protein S28e-like protein [Mac	1.0	1.0	0.907	6e-25
18858095	65	ribosomal protein S28b [Drosophila melan	1.0	1.0	0.892	1e-24
69608596	65	ribosomal protein S28e [Biphyllus lunatu	1.0	1.0	0.907	2e-24

>gi|383850448|ref|XP_003700807.1| PREDICTED: 40S ribosomal protein S28-like [Megachile rotundata]

 Score =  121 bits (303), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 59/65 (90%), Positives = 62/65 (95%)

Query: 1   MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESERE 60
           MDK VVLARVIK LGRTGSQGQCTQVKVEF+G+QNR IIRNVKGPVREGD+LTLLESERE
Sbjct: 49  MDKPVVLARVIKVLGRTGSQGQCTQVKVEFLGEQNRQIIRNVKGPVREGDLLTLLESERE 108

Query: 61  ARRLR 65
           ARRLR
Sbjct: 109 ARRLR 113

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91094381|ref|XP_971000.1| PREDICTED: similar to ribosomal protein S28e [Tribolium castaneum] gi|69608600|emb|CAJ01883.1| ribosomal protein S28e [Micromalthus debilis] gi|69608604|emb|CAJ01884.1| ribosomal protein S28e [Mycetophagus quadripustulatus] gi|264667435|gb|ACY71303.1| ribosomal protein S28 [Chrysomela tremula] gi|270014912|gb|EFA11360.1| hypothetical protein TcasGA2_TC011517 [Tribolium castaneum]

 Score =  120 bits (301), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 61/65 (93%), Positives = 62/65 (95%)

Query: 1  MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESERE 60
          MDK VVLARVIK LGRTGSQGQCTQVKVEFIG+QNR IIRNVKGPVREGDILTLLESERE
Sbjct: 1  MDKPVVLARVIKVLGRTGSQGQCTQVKVEFIGEQNRQIIRNVKGPVREGDILTLLESERE 60

Query: 61 ARRLR 65
          ARRLR
Sbjct: 61 ARRLR 65

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242021748|ref|XP_002431305.1| 40S ribosomal protein S28, putative [Pediculus humanus corporis] gi|212516573|gb|EEB18567.1| 40S ribosomal protein S28, putative [Pediculus humanus corporis]

 Score =  119 bits (298), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 60/64 (93%), Positives = 60/64 (93%)

Query: 1  MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESERE 60
          MDK VVLARVIK LGRTGSQGQCTQVKVEFIGDQNR IIRNVKGPVREGDILTLLESERE
Sbjct: 1  MDKPVVLARVIKVLGRTGSQGQCTQVKVEFIGDQNRQIIRNVKGPVREGDILTLLESERE 60

Query: 61 ARRL 64
          ARR 
Sbjct: 61 ARRF 64

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170060838|ref|XP_001865978.1| ribosomal protein S28 [Culex quinquefasciatus] gi|170060842|ref|XP_001865980.1| 40S ribosomal protein S28 [Culex quinquefasciatus] gi|167879215|gb|EDS42598.1| ribosomal protein S28 [Culex quinquefasciatus] gi|167879217|gb|EDS42600.1| 40S ribosomal protein S28 [Culex quinquefasciatus]

 Score =  119 bits (298), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 60/65 (92%), Positives = 61/65 (93%)

Query: 1  MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESERE 60
          MDK VVLARVIK LGRTGSQGQCTQVKVEFI +QNR IIRNVKGPVREGDILTLLESERE
Sbjct: 1  MDKSVVLARVIKVLGRTGSQGQCTQVKVEFISEQNRQIIRNVKGPVREGDILTLLESERE 60

Query: 61 ARRLR 65
          ARRLR
Sbjct: 61 ARRLR 65

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328779779|ref|XP_003249702.1| PREDICTED: 40S ribosomal protein S28-like [Apis mellifera] gi|350422767|ref|XP_003493276.1| PREDICTED: 40S ribosomal protein S28-like [Bombus impatiens] gi|350422770|ref|XP_003493277.1| PREDICTED: 40S ribosomal protein S28-like [Bombus impatiens] gi|380011140|ref|XP_003689670.1| PREDICTED: 40S ribosomal protein S28-like [Apis florea] gi|285027703|gb|ADC34225.1| ribosomal protein S28e [Solenopsis invicta] gi|307166370|gb|EFN60507.1| 40S ribosomal protein S28 [Camponotus floridanus] gi|307195301|gb|EFN77249.1| 40S ribosomal protein S28 [Harpegnathos saltator] gi|332022410|gb|EGI62718.1| 40S ribosomal protein S28 [Acromyrmex echinatior]

 Score =  119 bits (297), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 59/65 (90%), Positives = 62/65 (95%)

Query: 1  MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESERE 60
          MDK VVLARVIK LGRTGSQGQCTQVKVEF+G+QNR IIRNVKGPVREGD+LTLLESERE
Sbjct: 1  MDKPVVLARVIKVLGRTGSQGQCTQVKVEFLGEQNRQIIRNVKGPVREGDLLTLLESERE 60

Query: 61 ARRLR 65
          ARRLR
Sbjct: 61 ARRLR 65

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157114485|ref|XP_001652294.1| ribosomal protein S28, putative [Aedes aegypti] gi|94468900|gb|ABF18299.1| ribosomal protein S28E [Aedes aegypti] gi|108877284|gb|EAT41509.1| AAEL006860-PA [Aedes aegypti]

 Score =  118 bits (296), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 59/65 (90%), Positives = 61/65 (93%)

Query: 1  MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESERE 60
          MDK VVLARV+K LGRTGSQGQCTQVKVEFI +QNR IIRNVKGPVREGDILTLLESERE
Sbjct: 1  MDKSVVLARVVKVLGRTGSQGQCTQVKVEFISEQNRQIIRNVKGPVREGDILTLLESERE 60

Query: 61 ARRLR 65
          ARRLR
Sbjct: 61 ARRLR 65

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|187175305|ref|NP_001119669.1| ribosomal protein S28e-like [Acyrthosiphon pisum] gi|187175307|ref|NP_001119670.1| ribosomal protein S28e-like [Acyrthosiphon pisum] gi|193582610|ref|XP_001943747.1| PREDICTED: 40S ribosomal protein S28-like [Acyrthosiphon pisum] gi|89473734|gb|ABD72679.1| ribosomal protein S28e-like [Acyrthosiphon pisum] gi|89473788|gb|ABD72706.1| ribosomal protein S28e-like [Acyrthosiphon pisum]

 Score =  118 bits (295), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 59/65 (90%), Positives = 62/65 (95%)

Query: 1  MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESERE 60
          MDK VVL+RV+K LGRTGSQGQCTQVKVEFIG+QNR IIRNVKGPVREGDILTLLESERE
Sbjct: 1  MDKPVVLSRVLKVLGRTGSQGQCTQVKVEFIGEQNRQIIRNVKGPVREGDILTLLESERE 60

Query: 61 ARRLR 65
          ARRLR
Sbjct: 61 ARRLR 65

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|121543975|gb|ABM55652.1| ribosomal protein S28e-like protein [Maconellicoccus hirsutus]

 Score =  117 bits (294), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 59/65 (90%), Positives = 62/65 (95%)

Query: 1  MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESERE 60
          M+K VVLARV+K LGRTGSQGQCTQVKVEFIG+QNR IIRNVKGPVREGDILTLLESERE
Sbjct: 1  MEKPVVLARVMKVLGRTGSQGQCTQVKVEFIGEQNRQIIRNVKGPVREGDILTLLESERE 60

Query: 61 ARRLR 65
          ARRLR
Sbjct: 61 ARRLR 65

Source: Maconellicoccus hirsutus

Species: Maconellicoccus hirsutus

Genus: Maconellicoccus

Family: Pseudococcidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|18858095|ref|NP_572568.1| ribosomal protein S28b [Drosophila melanogaster] gi|125983790|ref|XP_001355660.1| GA15566 [Drosophila pseudoobscura pseudoobscura] gi|194890478|ref|XP_001977317.1| GG18316 [Drosophila erecta] gi|195044778|ref|XP_001991871.1| GH12901 [Drosophila grimshawi] gi|195134759|ref|XP_002011804.1| GI14378 [Drosophila mojavensis] gi|195350506|ref|XP_002041781.1| GM11375 [Drosophila sechellia] gi|195393766|ref|XP_002055524.1| GJ19416 [Drosophila virilis] gi|195446918|ref|XP_002070981.1| GK25380 [Drosophila willistoni] gi|195481706|ref|XP_002101747.1| GE17798 [Drosophila yakuba] gi|195565977|ref|XP_002106570.1| GD16052 [Drosophila simulans] gi|51316939|sp|Q9W334.2|RS28_DROME RecName: Full=40S ribosomal protein S28 gi|10728547|gb|AAF46503.2| ribosomal protein S28b [Drosophila melanogaster] gi|16769298|gb|AAL28868.1| LD23674p [Drosophila melanogaster] gi|54643976|gb|EAL32719.1| GA15566 [Drosophila pseudoobscura pseudoobscura] gi|190648966|gb|EDV46244.1| GG18316 [Drosophila erecta] gi|193901629|gb|EDW00496.1| GH12901 [Drosophila grimshawi] gi|193909058|gb|EDW07925.1| GI14378 [Drosophila mojavensis] gi|194123586|gb|EDW45629.1| GM11375 [Drosophila sechellia] gi|194150034|gb|EDW65725.1| GJ19416 [Drosophila virilis] gi|194167066|gb|EDW81967.1| GK25380 [Drosophila willistoni] gi|194189271|gb|EDX02855.1| GE17798 [Drosophila yakuba] gi|194203950|gb|EDX17526.1| GD16052 [Drosophila simulans] gi|220947628|gb|ACL86357.1| RpS28b-PA [synthetic construct] gi|220956992|gb|ACL91039.1| RpS28b-PA [synthetic construct]

 Score =  117 bits (292), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 58/65 (89%), Positives = 61/65 (93%)

Query: 1  MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESERE 60
          MDK VV ARV+K LGRTGSQGQCTQVKVEF+G+QNR IIRNVKGPVREGDILTLLESERE
Sbjct: 1  MDKPVVWARVMKVLGRTGSQGQCTQVKVEFLGEQNRQIIRNVKGPVREGDILTLLESERE 60

Query: 61 ARRLR 65
          ARRLR
Sbjct: 61 ARRLR 65

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|69608596|emb|CAJ01882.1| ribosomal protein S28e [Biphyllus lunatus]

 Score =  116 bits (291), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 59/65 (90%), Positives = 61/65 (93%)

Query: 1  MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESERE 60
          MDK VVLARV+K LGRTGSQGQCTQVKVEFIG+QNR IIRNVKGPVREGDILTLL SERE
Sbjct: 1  MDKPVVLARVMKVLGRTGSQGQCTQVKVEFIGEQNRQIIRNVKGPVREGDILTLLGSERE 60

Query: 61 ARRLR 65
          ARRLR
Sbjct: 61 ARRLR 65

Source: Biphyllus lunatus

Species: Biphyllus lunatus

Genus: Biphyllus

Family: Biphyllidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	65
FB|FBgn0030136	65	RpS28b "Ribosomal protein S28b	0.784	0.784	0.862	1.1e-18
WB|WBGene00004497	65	rps-28 [Caenorhabditis elegans	0.769	0.769	0.807	2.9e-16
UNIPROTKB|Q95Y04	65	rps-28 "40S ribosomal protein	0.769	0.769	0.807	2.9e-16
ZFIN|ZDB-GENE-030131-2022	69	rps28 "ribosomal protein S28"	0.723	0.681	0.787	1.3e-15
FB|FBgn0039739	64	RpS28a "Ribosomal protein S28a	0.769	0.781	0.764	2.6e-15
UNIPROTKB|F1NTT2	68	RPS28 "Uncharacterized protein	0.723	0.691	0.765	5.4e-15
UNIPROTKB|Q56JX6	69	RPS28 "40S ribosomal protein S	0.723	0.681	0.765	5.4e-15
UNIPROTKB|P62857	69	RPS28 "40S ribosomal protein S	0.723	0.681	0.765	5.4e-15
UNIPROTKB|Q6QAT1	69	RPS28 "40S ribosomal protein S	0.723	0.681	0.765	5.4e-15
UNIPROTKB|Q0IXR7	65	Os10g0411700 "Os10g0411700 pro	0.784	0.784	0.725	5.4e-15

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

 Score = 225 (84.3 bits), Expect = 1.1e-18, P = 1.1e-18
 Identities = 44/51 (86%), Positives = 47/51 (92%)

Query:     1 MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDI 51
             MDK VV ARV+K LGRTGSQGQCTQVKVEF+G+QNR IIRNVKGPVREGDI
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

WB|WBGene00004497 rps-28 [Caenorhabditis elegans (taxid:6239)]

 Score = 202 (76.2 bits), Expect = 2.9e-16, P = 2.9e-16
 Identities = 42/52 (80%), Positives = 46/52 (88%)

Query:     1 MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQN-RTIIRNVKGPVREGDI 51
             MDK + LARV K +GRTGSQGQCTQV+VEFI DQN R+IIRNVKGPVREGDI
Sbjct:     1 MDK-LTLARVTKVIGRTGSQGQCTQVRVEFINDQNNRSIIRNVKGPVREGDI 51

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

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0018996 "molting cycle, collagen and cuticulin-based cuticle" evidence=IMP

GO:0006915 "apoptotic process" evidence=IMP

UNIPROTKB|Q95Y04 rps-28 "40S ribosomal protein S28" [Caenorhabditis elegans (taxid:6239)]

 Score = 202 (76.2 bits), Expect = 2.9e-16, P = 2.9e-16
 Identities = 42/52 (80%), Positives = 46/52 (88%)

Query:     1 MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQN-RTIIRNVKGPVREGDI 51
             MDK + LARV K +GRTGSQGQCTQV+VEFI DQN R+IIRNVKGPVREGDI
Sbjct:     1 MDK-LTLARVTKVIGRTGSQGQCTQVRVEFINDQNNRSIIRNVKGPVREGDI 51

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

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

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

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

 Score = 196 (74.1 bits), Expect = 1.3e-15, P = 1.3e-15
 Identities = 37/47 (78%), Positives = 42/47 (89%)

Query:     5 VVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDI 51
             + LARV K LGRTGSQGQCTQV+VEF+ D NR+IIRNVKGPVREGD+
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|FBgn0039739 RpS28a "Ribosomal protein S28a" [Drosophila melanogaster (taxid:7227)]

 Score = 193 (73.0 bits), Expect = 2.6e-15, P = 2.6e-15
 Identities = 39/51 (76%), Positives = 44/51 (86%)

Query:     1 MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDI 51
             MDK    ARV++ LGRTGSQGQCTQV+VEF+GDQ+R IIRNVKGPVR GDI
Sbjct:     1 MDKPQY-ARVVEILGRTGSQGQCTQVRVEFLGDQSRQIIRNVKGPVRVGDI 50

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

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

GO:0006412 "translation" evidence=IEA

GO:0035220 "wing disc development" evidence=IMP

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

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

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 36/47 (76%), Positives = 42/47 (89%)

Query:     5 VVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDI 51
             + LARV K LGRTGSQGQCTQV+VEF+ D +R+IIRNVKGPVREGD+
Sbjct:     8 IKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDV 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

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

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 36/47 (76%), Positives = 42/47 (89%)

Query:     5 VVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDI 51
             + LARV K LGRTGSQGQCTQV+VEF+ D +R+IIRNVKGPVREGD+
Sbjct:     9 IKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDV 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 = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 36/47 (76%), Positives = 42/47 (89%)

Query:     5 VVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDI 51
             + LARV K LGRTGSQGQCTQV+VEF+ D +R+IIRNVKGPVREGD+
Sbjct:     9 IKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDV 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 = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 36/47 (76%), Positives = 42/47 (89%)

Query:     5 VVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDI 51
             + LARV K LGRTGSQGQCTQV+VEF+ D +R+IIRNVKGPVREGD+
Sbjct:     9 IKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDV 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

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

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 37/51 (72%), Positives = 44/51 (86%)

Query:     1 MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDI 51
             MD QV LA V+K +GRTGS+GQ TQV+V+F+ DQNR I+RNVKGPVREGDI
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

---

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	0.6101	0.8769	0.7702	yes	N/A
P62857	RS28_HUMAN	No assigned EC number	0.8474	0.9076	0.8550	yes	N/A
P62859	RS28_RAT	No assigned EC number	0.8474	0.9076	0.8550	yes	N/A
Q6EV21	RS28_PAPDA	No assigned EC number	0.8615	1.0	1.0	N/A	N/A
B1Y9V2	RS28_PYRNV	No assigned EC number	0.5614	0.8461	0.7142	yes	N/A
Q97BK7	RS28_THEVO	No assigned EC number	0.5	0.9846	0.9275	yes	N/A
Q9W334	RS28_DROME	No assigned EC number	0.8923	1.0	1.0	yes	N/A
P61029	RS28_PYRAB	No assigned EC number	0.5666	0.8923	0.8169	yes	N/A
O26356	RS28_METTH	No assigned EC number	0.5	0.8923	0.8529	yes	N/A
Q9Y9A6	RS28_AERPE	No assigned EC number	0.5593	0.8769	0.6951	yes	N/A
Q10421	RS28_SCHPO	No assigned EC number	0.7704	0.9384	0.8970	yes	N/A
A4YCQ2	RS28_METS5	No assigned EC number	0.5423	0.8769	0.7125	yes	N/A
O61590	RS28_OSTOS	No assigned EC number	0.7878	1.0	0.9848	N/A	N/A
Q54MZ5	RS28_DICDI	No assigned EC number	0.6406	0.9384	0.8472	yes	N/A
Q7S6W5	RS28_NEUCR	No assigned EC number	0.7377	0.9384	0.8970	N/A	N/A
A4WLP1	RS28_PYRAR	No assigned EC number	0.5789	0.8461	0.7142	yes	N/A
Q6LZI8	RS28_METMP	No assigned EC number	0.4687	0.9538	0.8157	yes	N/A
P0C0X0	RS28B_YEAST	No assigned EC number	0.7164	1.0	0.9701	yes	N/A
Q74ZD8	RS28_ASHGO	No assigned EC number	0.7164	1.0	0.9701	yes	N/A
P57711	RS28_THEAC	No assigned EC number	0.5	0.9846	0.9275	yes	N/A
A6USH4	RS28_METVS	No assigned EC number	0.4687	0.9538	0.8157	yes	N/A
P62858	RS28_MOUSE	No assigned EC number	0.8474	0.9076	0.8550	yes	N/A
Q6QAT1	RS28_PIG	No assigned EC number	0.8474	0.9076	0.8550	yes	N/A
B1L5N5	RS28_KORCO	No assigned EC number	0.5	0.8923	0.8169	yes	N/A
A1RS33	RS28_PYRIL	No assigned EC number	0.5737	0.9076	0.7662	yes	N/A
P46302	RS28_MAIZE	No assigned EC number	0.7692	1.0	1.0	N/A	N/A
A6UT50	RS28_META3	No assigned EC number	0.4375	0.9538	0.8266	yes	N/A
P33285	RS28_KLULA	No assigned EC number	0.7704	0.9384	0.9104	yes	N/A
Q9SR73	RS281_ARATH	No assigned EC number	0.7230	0.9846	1.0	yes	N/A
Q90YP3	RS28_ICTPU	No assigned EC number	0.8644	0.9076	0.8550	N/A	N/A
Q56JX6	RS28_BOVIN	No assigned EC number	0.8474	0.9076	0.8550	yes	N/A
P34789	RS282_ARATH	No assigned EC number	0.7076	0.9846	1.0	yes	N/A
Q962Q2	RS28_SPOFR	No assigned EC number	0.8615	1.0	1.0	N/A	N/A
Q95Y04	RS28_CAEEL	No assigned EC number	0.8484	0.9846	0.9846	yes	N/A
P61030	RS28_PYRHO	No assigned EC number	0.5666	0.8923	0.8169	yes	N/A
P61031	RS28_NANEQ	No assigned EC number	0.5932	0.8769	0.6477	yes	N/A
O29493	RS28_ARCFU	No assigned EC number	0.5084	0.8769	0.8028	yes	N/A
Q6FLC3	RS28_CANGA	No assigned EC number	0.7313	1.0	0.9701	yes	N/A
A1RXH2	RS28_THEPD	No assigned EC number	0.5081	0.9076	0.7662	yes	N/A
Q8U159	RS28_PYRFU	No assigned EC number	0.5666	0.8923	0.8169	yes	N/A
Q6PS50	RS28_BOMMO	No assigned EC number	0.8615	1.0	1.0	N/A	N/A
P54065	RS28_METJA	No assigned EC number	0.5156	0.9538	0.8266	yes	N/A
Q975Z8	RS28_SULTO	No assigned EC number	0.5762	0.8769	0.6867	yes	N/A
Q3E7X9	RS28A_YEAST	No assigned EC number	0.7164	1.0	0.9701	yes	N/A
Q4JAV1	RS28_SULAC	No assigned EC number	0.5762	0.8769	0.6785	yes	N/A
P33286	RS28_KLUMA	No assigned EC number	0.7313	1.0	0.9701	N/A	N/A
Q6PBK3	RS28_DANRE	No assigned EC number	0.8644	0.9076	0.8550	yes	N/A
Q6KZI6	RS28_PICTO	No assigned EC number	0.4848	0.9846	0.9275	yes	N/A
Q8ZTA7	RS28_PYRAE	No assigned EC number	0.5614	0.8461	0.7142	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	65
cd04457	60	cd04457, S1_S28E, S1_S28E: S28E, S1-like RNA-bindi	4e-29
PTZ00085	73	PTZ00085, PTZ00085, 40S ribosomal protein S28; Pro	2e-25
pfam01200	69	pfam01200, Ribosomal_S28e, Ribosomal protein S28e	4e-25
COG2053	69	COG2053, RPS28A, Ribosomal protein S28E/S33 [Trans	5e-19
PRK04007	70	PRK04007, rps28e, 30S ribosomal protein S28e; Vali	3e-17

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

 Score = 97.3 bits (243), Expect = 4e-29
 Identities = 46/59 (77%), Positives = 53/59 (89%)

Query: 7  LARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESEREARRLR 65
          LA VIK LGRTGS+G+ TQV+VEF+ D+ R+IIRNVKGPVREGDIL LLE+EREARRLR
Sbjct: 2  LAEVIKVLGRTGSRGEVTQVRVEFMDDKGRSIIRNVKGPVREGDILMLLETEREARRLR 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 = 88.7 bits (220), Expect = 2e-25
 Identities = 44/68 (64%), Positives = 56/68 (82%), Gaps = 3/68 (4%)

Query: 1  MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQ---NRTIIRNVKGPVREGDILTLLES 57
            +Q  LA+VIK LGRTGS+G  TQV+V+ +G++    RT+IRNVKGPVREGDIL+L+E+
Sbjct: 6  DTEQPKLAKVIKVLGRTGSRGGVTQVRVQLMGEEGDAGRTLIRNVKGPVREGDILSLMET 65

Query: 58 EREARRLR 65
          EREARRLR
Sbjct: 66 EREARRLR 73

Length = 73

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

 Score = 87.4 bits (217), Expect = 4e-25
 Identities = 41/66 (62%), Positives = 51/66 (77%), Gaps = 2/66 (3%)

Query: 2  DKQVVLARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDILTLLESER 59
          +++  LA VI+ LGRTGS+G+ TQV+V  +   D+ R I RNVKGPVR GDIL LLE+ER
Sbjct: 4  EQEAKLAEVIEVLGRTGSRGEVTQVRVRILEGRDKGRIITRNVKGPVRVGDILMLLETER 63

Query: 60 EARRLR 65
          EARRLR
Sbjct: 64 EARRLR 69

Length = 69

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

 Score = 72.1 bits (177), Expect = 5e-19
 Identities = 41/67 (61%), Positives = 48/67 (71%), Gaps = 2/67 (2%)

Query: 1  MDKQVVLARVIKTLGRTGSQGQCTQVKVEFI--GDQNRTIIRNVKGPVREGDILTLLESE 58
          M ++   A VI+ LGRTG  G+ TQVKV  +   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 = 67.3 bits (165), Expect = 3e-17
 Identities = 35/67 (52%), Positives = 45/67 (67%), Gaps = 2/67 (2%)

Query: 1  MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDILTLLESE 58
           +++   A VI+ +GRTG  G+ TQVK   +   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
PTZ00085	73	40S ribosomal protein S28; Provisional	100.0
PRK04007	70	rps28e 30S ribosomal protein S28e; Validated	100.0
KOG3502|consensus	66		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=5.3e-42  Score=212.12  Aligned_cols=65  Identities=77%  Similarity=1.137  Sum_probs=52.2

Q ss_pred             CCc---cceEEEEEEeccccCCcCcEEEEEEEEcCCCC-cEEEecccCccccCcEEeeehhHHHHhhcC
Q psy5287           1 MDK---QVVLARVIKTLGRTGSQGQCTQVKVEFIGDQN-RTIIRNVKGPVREGDILTLLESEREARRLR   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   69999999999999999999999999999876 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=1e-40  Score=202.22  Aligned_cols=60  Identities=77%  Similarity=1.143  Sum_probs=58.6

Q ss_pred             eEEEEEEeccccCCcCcEEEEEEEEcCCCCcEEEecccCccccCcEEeeehhHHHHhhcC
Q psy5287           6 VLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESEREARRLR   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.

>PTZ00085 40S ribosomal protein S28; Provisional

Probab=100.00  E-value=2.2e-39  Score=202.47  Aligned_cols=63  Identities=70%  Similarity=1.090  Sum_probs=60.4

Q ss_pred             ccceEEEEEEeccccCCcCcEEEEEEEEcCCC---CcEEEecccCccccCcEEeeehhHHHHhhcC
Q psy5287           3 KQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQ---NRTIIRNVKGPVREGDILTLLESEREARRLR   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            36899999999999999999999999999976   6999999999999999999999999999997

>PRK04007 rps28e 30S ribosomal protein S28e; Validated

Probab=100.00  E-value=2.3e-39  Score=201.10  Aligned_cols=62  Identities=55%  Similarity=0.793  Sum_probs=59.6

Q ss_pred             cceEEEEEEeccccCCcCcEEEEEEEEcCCC--CcEEEecccCccccCcEEeeehhHHHHhhcC
Q psy5287           4 QVVLARVIKTLGRTGSQGQCTQVKVEFIGDQ--NRTIIRNVKGPVREGDILTLLESEREARRLR   65 (65)
Q Consensus         4 ~~~~A~V~kVlGRtGs~G~~tqVrve~l~~~--~r~i~RnVkGPVr~GDil~LlEseREarrlr   65 (65)
                      ..++|+|+||||||||+|++|||||+||+++  +|+|+||||||||+||||+|+|||||||+|+
T Consensus         5 ~~~~A~VikVlGRTG~~G~~tQVrv~~l~~~~~~R~i~RNVkGPVR~GDIl~L~EteREAr~l~   68 (70)
T PRK04007          5 EGTPAEVIEIIGRTGMTGEVTQVKCRILEGRDKGRIITRNVKGPVRVGDILMLRETEREARKLG   68 (70)
T ss_pred             cCceEEEEEEeccccccccEEEEEEEEecCCCcCcEEEEeccCCcccCcEEEEhhhhhHHHhhc
Confidence            5789999999999999999999999999965  8999999999999999999999999999985

>KOG3502|consensus

Probab=100.00  E-value=2.7e-40  Score=203.25  Aligned_cols=64  Identities=81%  Similarity=1.194  Sum_probs=61.9

Q ss_pred             CCc--cceEEEEEEeccccCCcCcEEEEEEEEcCCCCcEEEecccCccccCcEEeeehhHHHHhhcC
Q psy5287           1 MDK--QVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESEREARRLR   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 78999999999999999999999999999997

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

Probab=100.00  E-value=4.4e-35  Score=181.43  Aligned_cols=61  Identities=66%  Similarity=0.944  Sum_probs=58.7

Q ss_pred             ceEEEEEEeccccCCcCcEEEEEEEEcC--CCCcEEEecccCccccCcEEeeehhHHHHhhcC
Q psy5287           5 VVLARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDILTLLESEREARRLR   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            4679999999999999999999999999  789999999999999999999999999999985

---

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		1e-15
3izb_Y	67	Localization Of The Small Subunit Ribosomal Protein		2e-13
3zey_Z	103	High-resolution Cryo-electron Microscopy Structure		1e-08
1ny4_A	82	Solution Structure Of The 30s Ribosomal Protein S28		3e-06
3j20_X	71	Promiscuous Behavior Of Proteins In Archaeal Riboso		4e-06
1ne3_A	68	Solution Structure Of Ribosomal Protein S28e From M		3e-05
2xzm_1	68	Crystal Structure Of The Eukaryotic 40s Ribosomal S		3e-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 = 77.8 bits (190), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 37/51 (72%), Positives = 44/51 (86%)
Query: 1  MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDI 51
          MD QV LA V+K +GRTGS+GQ TQV+V+F+ DQNR I+RNVKGPVREGDI
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 = 70.9 bits (172), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 36/53 (67%), Positives = 43/53 (81%), Gaps = 2/53 (3%)
Query: 1  MDKQ--VVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDI 51
          MD +  V LA+VIK LGRTGS+G  TQV+VEF+ D +RTI+RNVKGPVRE DI
Sbjct: 1  MDNKTPVTLAKVIKVLGRTGSRGGVTQVRVEFLEDTSRTIVRNVKGPVRENDI 53

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 26/47 (55%), Positives = 35/47 (74%), Gaps = 5/47 (10%)
Query: 10 VIKTLGRTGSQGQCTQVKVEFIGDQ-----NRTIIRNVKGPVREGDI 51
          +IK LGRTGS+G  TQV+V  + ++     NRTI+RNVKGP +EGD+
Sbjct: 43 IIKVLGRTGSRGNVTQVRVRLMAEEGSPEANRTIVRNVKGPCKEGDM 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 = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/46 (56%), Positives = 32/46 (69%), Gaps = 2/46 (4%)
Query: 8  ARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDI 51
          A VI+ +GRTG+ G  TQVKV  +   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 = 46.2 bits (108), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/46 (56%), Positives = 32/46 (69%), Gaps = 2/46 (4%)
Query: 8  ARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDI 51
          A VI+ +GRTG+ G  TQVKV  +   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 = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/46 (50%), Positives = 29/46 (63%), Gaps = 2/46 (4%)
Query: 8  ARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDI 51
          A VI+ L RTG  G+  QVK   +   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 = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/46 (50%), Positives = 32/46 (69%), Gaps = 2/46 (4%)
Query: 8  ARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDI 51
          AR++  LG+TGS+G  TQV+V  I   ++ R +IRNVKG  R GD+
Sbjct: 9  ARIMDVLGKTGSRGGITQVRVVLISGKEEGRQLIRNVKGACRVGDV 54

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	1e-29
2xzm_1	68	Ribosomal protein S28E containing protein; ribosom	2e-28
1ny4_A	82	30S ribosomal protein S28E; JR19, structure, autos	2e-28
1ne3_A	68	30S ribosomal protein S28E; beta protein, structur	2e-26

>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 = 98.6 bits (246), Expect = 1e-29
 Identities = 6/62 (9%), Positives = 13/62 (20%)

Query: 4  QVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESEREARR 63
               R        G   +      E  G    T +  +    +   I  +       + 
Sbjct: 6  AQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVTKLGRLVKAGKITTIEEIFLHSLPVKE 65

Query: 64 LR 65
           +
Sbjct: 66 FQ 67

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

 Score = 95.2 bits (237), Expect = 2e-28
 Identities = 34/66 (51%), Positives = 46/66 (69%), Gaps = 2/66 (3%)

Query: 2  DKQVVLARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDILTLLESER 59
           ++   AR++  LG+TGS+G  TQV+V  I   ++ R +IRNVKG  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 = 95.7 bits (238), Expect = 2e-28
 Identities = 34/66 (51%), Positives = 45/66 (68%), Gaps = 2/66 (3%)

Query: 2  DKQVVLARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDILTLLESER 59
          + +   A VI+ +GRTG+ G  TQVKV  +   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 = 90.6 bits (225), Expect = 2e-26
 Identities = 30/64 (46%), Positives = 40/64 (62%), Gaps = 2/64 (3%)

Query: 4  QVVLARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDILTLLESEREA 61
              A VI+ L RTG  G+  QVK   +   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=4.6e-43  Score=215.22  Aligned_cols=65  Identities=74%  Similarity=1.090  Sum_probs=61.0

Q ss_pred             CCc--cceEEEEEEeccccCCcCcEEEEEEEEcCCCCcEEEecccCccccCcEEeeehhHHHHhhcC
Q psy5287           1 MDK--QVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESEREARRLR   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=2.8e-41  Score=207.73  Aligned_cols=65  Identities=54%  Similarity=0.865  Sum_probs=61.5

Q ss_pred             CCc-cceEEEEEEeccccCCcCcEEEEEEEEcCCC--CcEEEecccCccccCcEEeeehhHHHHhhcC
Q psy5287           1 MDK-QVVLARVIKTLGRTGSQGQCTQVKVEFIGDQ--NRTIIRNVKGPVREGDILTLLESEREARRLR   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            666 6899999999999999999999999999976  8999999999999999999999999999997

>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=3.8e-40  Score=202.73  Aligned_cols=64  Identities=48%  Similarity=0.777  Sum_probs=60.0

Q ss_pred             CCccceEEEEEEeccccCCcCcEEEEEEEEcCC--CCcEEEecccCccccCcEEeeehhHHHHhhcC
Q psy5287           1 MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGD--QNRTIIRNVKGPVREGDILTLLESEREARRLR   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 58999999999999999999999999985  59999999999999999999999999999986

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

Probab=100.00  E-value=4.7e-40  Score=203.71  Aligned_cols=65  Identities=54%  Similarity=0.816  Sum_probs=61.1

Q ss_pred             CCc-cceEEEEEEeccccCCcCcEEEEEEEEc--CCCCcEEEecccCccccCcEEeeehhHHHHhhcC
Q psy5287           1 MDK-QVVLARVIKTLGRTGSQGQCTQVKVEFI--GDQNRTIIRNVKGPVREGDILTLLESEREARRLR   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~~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            444 3789999999999999999999999999  7899999999999999999999999999999985

>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=3.3e-39  Score=204.32  Aligned_cols=62  Identities=53%  Similarity=0.808  Sum_probs=59.2

Q ss_pred             cceEEEEEEeccccCCcCcEEEEEEEEcCC--CCcEEEecccCccccCcEEeeehhHHHHhhcC
Q psy5287           4 QVVLARVIKTLGRTGSQGQCTQVKVEFIGD--QNRTIIRNVKGPVREGDILTLLESEREARRLR   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            478999999999999999999999999985  58999999999999999999999999999985

---

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	4e-28
d1ny4a_	71	b.40.4.5 (A:) Ribosomal protein S28e {Archaeon Pyr	5e-27

>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 = 93.5 bits (233), Expect = 4e-28
 Identities = 30/64 (46%), Positives = 40/64 (62%), Gaps = 2/64 (3%)

Query: 4  QVVLARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDILTLLESEREA 61
              A VI+ L RTG  G+  QVK   +   D+ R + RNV GP+REGDIL LL++ REA
Sbjct: 3  DATPAEVIEVLKRTGMTGEVMQVKCRILDGRDKGRILTRNVMGPIREGDILMLLDTIREA 62

Query: 62 RRLR 65
          + +R
Sbjct: 63 KEIR 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 = 90.5 bits (225), Expect = 5e-27
 Identities = 34/67 (50%), Positives = 45/67 (67%), Gaps = 2/67 (2%)

Query: 1  MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDILTLLESE 58
           + +   A VI+ +GRTG+ G  TQVKV  +   D+ R I RNV+GPVR GDIL L E+E
Sbjct: 2  AEDEGYPAEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRVGDILILRETE 61

Query: 59 REARRLR 65
          REAR ++
Sbjct: 62 REAREIK 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=3.9e-40  Score=201.31  Aligned_cols=64  Identities=50%  Similarity=0.801  Sum_probs=60.8

Q ss_pred             CCccceEEEEEEeccccCCcCcEEEEEEEEcC--CCCcEEEecccCccccCcEEeeehhHHHHhhcC
Q psy5287           1 MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDILTLLESEREARRLR   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 MDD-ATPAEVIEVLKRTGMTGEVMQVKCRILDGRDKGRILTRNVMGPIREGDILMLLDTIREAKEIR   66 (68)
T ss_dssp             CCC-SEEEEEEEEECCSSSSSSSEEEEEEESSSSSCSCEEEEEECSCCCTTCEEEECCCCCCCCCCC
T ss_pred             CCC-CcceEEEEEeccccCcCcEEEEEEEEeeCCCcCCEEEeeccCCcccCcEEEEeehhhHHhhhc
Confidence            665 4799999999999999999999999999  678999999999999999999999999999997

>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=2.4e-39  Score=199.11  Aligned_cols=62  Identities=55%  Similarity=0.833  Sum_probs=59.4

Q ss_pred             cceEEEEEEeccccCCcCcEEEEEEEEcC--CCCcEEEecccCccccCcEEeeehhHHHHhhcC
Q psy5287           4 QVVLARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDILTLLESEREARRLR   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  678999999999999999999999999999995