Citrus Sinensis ID: 030110

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180---
Protein Sequence
MATPLSNFFSFILPSNALPKNSTPLAQPNHLSLSSQQKPKNASFSKVAPAQPQESHDSSSASSSSTELASVICPSLAYANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRRRSQFRGPVQNRQEATPTKKDDDDEDNWELPEGDIPY
Secondary Structure (PSIPRED)
cccccccccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcHHcccccccEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccHHHccEEEEccccEEEEEEcccccHHHHHHHHHHHHHHcccHHHHHHHHHcccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
matplsnffsfilpsnalpknstplaqpnhlslssqqkpknasfskvapaqpqeshdsssasssstelasvicpslayantlffkSAYNVQvvvdenepeERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRrrsqfrgpvqnrqeatptkkddddednwelpegdipy
Flexible Loop (DISEMBL)
MATPLSNFFSFILPSNALPKNSTPLAQPNHLSLSSQQKPKNASFSKVAPAQPQESHDSSSASSSSTELASVICPSLAYANTLFFKSAYNVQVVVDENEPEErllnrfrrevmragviqeckrrrffetkqdekkrktreaakrnrrrrsqfrgpvqnrqeatptkkddddednwelpegdipy
Low Complexity Region (SEG)
MATPLSNFFSFILPSNALPKNSTPLAQPNHLSLSSQQKPKNASFSKVAPAQPQEshdsssassssTELASVICPSLAYANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDekkrktreaakrnrrrrSQFRGPVQNRQEATPTKKDDDDEDNWELPEGDIPY
Disordered region (IsUnstruct)
*******FFSFIL*******************************************************ASVICPSLAYANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRF**********************************************************
Disordered Region (DISOPRED)
*****SNFFSFIL************************************************************PSLAYANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFE**********************************************WELPEGDIPY
Disordered Region (DISEMBL)
MATPLSNFFSFILPSNALPKNSTPLAQP*****************************************SVICPSLAYANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFE*********************************************NWELPEGDIPY
Disordered Region (DISPRO)
*****SNFFSFILPSN*****************************************************SVICPSLAYANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQ*EKKRK**********************************EDNWELPEGDIPY
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MATPLSNFFSFILPSNALPKNSTPLAQPNHLSLSSQQKPKNASFSKVAPAQPQESHDSSSASSSSTELASVICPSLAYANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRRRSQFRGPVQNRQEATPTKKDDDDEDNWELPEGDIPY
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	183	2.2.26 [Sep-21-2011]
P82024	35	30S ribosomal protein S21	N/A	no	0.191	1.0	0.885	5e-09
P48949	60	30S ribosomal protein S21	N/A	no	0.251	0.766	0.521	3e-06
B0CE36	59	30S ribosomal protein S21	yes	no	0.316	0.983	0.525	1e-05
P0A4B7	62	30S ribosomal protein S21	yes	no	0.311	0.919	0.456	2e-05
P0A4B8	62	30S ribosomal protein S21	yes	no	0.311	0.919	0.456	2e-05
Q3M446	62	30S ribosomal protein S21	yes	no	0.311	0.919	0.456	2e-05
B2UNE2	83	30S ribosomal protein S21	yes	no	0.300	0.662	0.436	2e-05
Q602S0	77	30S ribosomal protein S21	yes	no	0.393	0.935	0.375	4e-05
Q2JM43	61	30S ribosomal protein S21	yes	no	0.306	0.918	0.438	5e-05
Q2JXR2	61	30S ribosomal protein S21	yes	no	0.306	0.918	0.438	6e-05

>sp|P82024|RR21_SPIOL 30S ribosomal protein S21, chloroplastic (Fragment) OS=Spinacia oleracea GN=rps21 PE=1 SV=1

 Score = 60.5 bits (145), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 31/35 (88%), Positives = 34/35 (97%)

Query: 84  FKSAYNVQVVVDENEPEERLLNRFRREVMRAGVIQ 118
           F+SAYNVQV+VD+NE EERLLNRFRREVMRAGVIQ
Sbjct: 1   FRSAYNVQVLVDDNENEERLLNRFRREVMRAGVIQ 35

Binds directly to 16S ribosomal RNA.
Spinacia oleracea (taxid: 3562)

>sp|P48949|RS21_SYNY3 30S ribosomal protein S21 OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=rpsU PE=3 SV=1

 Score = 51.2 bits (121), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/46 (52%), Positives = 34/46 (73%)

Query: 91  QVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRK 136
           QVVV +NEP E  L RF+R+V +AG+  + K+ +FFET Q++ KRK
Sbjct: 3   QVVVGQNEPIESALRRFKRQVAKAGIYTDFKKHQFFETPQEKHKRK 48

Synechocystis sp. (strain PCC 6803 / Kazusa) (taxid: 1111708)

>sp|B0CE36|RS21_ACAM1 30S ribosomal protein S21 OS=Acaryochloris marina (strain MBIC 11017) GN=rpsU PE=3 SV=1

 Score = 49.7 bits (117), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 31/59 (52%), Positives = 42/59 (71%), Gaps = 1/59 (1%)

Query: 90  VQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRRR 148
           VQVV+ E+E  E  L RF+R+V +AG++ + KRRR FET  ++KKRK R A +R RR R
Sbjct: 2   VQVVLGEDEGIESALRRFKRQVSKAGILADVKRRRHFETPLEKKKRK-RIATRRKRRFR 59

Acaryochloris marina (strain MBIC 11017) (taxid: 329726)

>sp|P0A4B7|RS21A_NOSS1 30S ribosomal protein S21 A OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=rpsU1 PE=3 SV=1

 Score = 48.5 bits (114), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 38/57 (66%)

Query: 91  QVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRR 147
           Q+VV ENE  E  L RF+REV +AG+ Q+ ++ R FET  ++ KRK     K+++RR
Sbjct: 3   QIVVGENEHIESALRRFKREVSKAGIFQDMRKHRHFETPIEKSKRKKLALHKQSKRR 59

Nostoc sp. (strain PCC 7120 / UTEX 2576) (taxid: 103690)

>sp|P0A4B8|RS21A_ANAVA 30S ribosomal protein S21 A OS=Anabaena variabilis GN=rpsU1 PE=1 SV=3

 Score = 48.5 bits (114), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 38/57 (66%)

Query: 91  QVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRR 147
           Q+VV ENE  E  L RF+REV +AG+ Q+ ++ R FET  ++ KRK     K+++RR
Sbjct: 3   QIVVGENEHIESALRRFKREVSKAGIFQDMRKHRHFETPIEKSKRKKLALHKQSKRR 59

Anabaena variabilis (taxid: 1172)

>sp|Q3M446|RS213_ANAVT 30S ribosomal protein S21 3 OS=Anabaena variabilis (strain ATCC 29413 / PCC 7937) GN=rpsU3 PE=3 SV=1

 Score = 48.5 bits (114), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 38/57 (66%)

Query: 91  QVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRR 147
           Q+VV ENE  E  L RF+REV +AG+ Q+ ++ R FET  ++ KRK     K+++RR
Sbjct: 3   QIVVGENEHIESALRRFKREVSKAGIFQDMRKHRHFETPIEKSKRKKLALHKQSKRR 59

Anabaena variabilis (strain ATCC 29413 / PCC 7937) (taxid: 240292)

>sp|B2UNE2|RS21_AKKM8 30S ribosomal protein S21 OS=Akkermansia muciniphila (strain ATCC BAA-835) GN=rpsU PE=3 SV=1

 Score = 48.5 bits (114), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 37/55 (67%)

Query: 91  QVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNR 145
           +V V + EP +R L R + ++   G++ E +RRR FET  DE++RK R A+KRN+
Sbjct: 3   EVTVRKGEPIDRALKRLKTKLDVEGILDEMRRRRAFETPMDERRRKARSASKRNK 57

Akkermansia muciniphila (strain ATCC BAA-835) (taxid: 349741)

>sp|Q602S0|RS21_METCA 30S ribosomal protein S21 OS=Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath) GN=rpsU PE=3 SV=1

 Score = 47.8 bits (112), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/72 (37%), Positives = 45/72 (62%)

Query: 92  VVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRRRSQF 151
           + + ENEP E  + RF+R   +AGV+ E +RR ++E   +E+KRK   A KR+ ++ S+ 
Sbjct: 4   IKIRENEPFEIAIRRFKRACEKAGVLSEVRRREYYEKPTEERKRKAAAAIKRHLKKLSRE 63

Query: 152 RGPVQNRQEATP 163
           R  +QN ++  P
Sbjct: 64  RFALQNLRKGRP 75

Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath) (taxid: 243233)

>sp|Q2JM43|RS21_SYNJB 30S ribosomal protein S21 OS=Synechococcus sp. (strain JA-2-3B'a(2-13)) GN=rpsU PE=3 SV=1

 Score = 47.4 bits (111), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 39/57 (68%), Gaps = 1/57 (1%)

Query: 91  QVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRR 147
           QV + ENE  E  L RF+R+V +AG++++ +  R FET  +++KRK   A +RNRR+
Sbjct: 3   QVTIGENEGIESALRRFKRQVSKAGILRDLRNHRHFETNLEKRKRKA-VAVRRNRRK 58

Synechococcus sp. (strain JA-2-3B'a(2-13)) (taxid: 321332)

>sp|Q2JXR2|RS21_SYNJA 30S ribosomal protein S21 OS=Synechococcus sp. (strain JA-3-3Ab) GN=rpsU PE=3 SV=1

 Score = 47.0 bits (110), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 39/57 (68%), Gaps = 1/57 (1%)

Query: 91  QVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRR 147
           QV + ENE  E  L RF+R+V +AG++++ +  R FET  +++KRK   A +RNRR+
Sbjct: 3   QVTIGENEGIESALRRFKRQVSKAGILRDLRNHRHFETNLEKRKRKA-VAMRRNRRK 58

Synechococcus sp. (strain JA-3-3Ab) (taxid: 321327)

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	183
255536923	175	structural constituent of ribosome, puta	0.945	0.988	0.659	3e-53
224060243	176	predicted protein [Populus trichocarpa]	0.939	0.977	0.652	6e-46
225451423	188	PREDICTED: uncharacterized protein LOC10	0.950	0.925	0.618	4e-45
147845835	188	hypothetical protein VITISV_031115 [Viti	0.661	0.643	0.770	5e-45
188036222	190	Chain U, Homology Model For The Spinach	0.639	0.615	0.789	4e-41
449455866	183	PREDICTED: uncharacterized protein LOC10	0.639	0.639	0.789	6e-41
297814952	184	hypothetical protein ARALYDRAFT_484499 [	0.945	0.940	0.554	2e-40
18405254	183	ribosomal protein S21 family protein [Ar	0.945	0.945	0.563	2e-38
356511811	176	PREDICTED: uncharacterized protein LOC10	0.945	0.982	0.516	1e-37
356570139	202	PREDICTED: uncharacterized protein LOC10	0.699	0.633	0.664	6e-37

>gi|255536923|ref|XP_002509528.1| structural constituent of ribosome, putative [Ricinus communis] gi|223549427|gb|EEF50915.1| structural constituent of ribosome, putative [Ricinus communis]

 Score =  213 bits (541), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 122/185 (65%), Positives = 142/185 (76%), Gaps = 12/185 (6%)

Query: 1   MAT--PLSNFFSFILPSNALPKNSTPLAQPNHLSLSSQQKPKNASFSKVAPAQPQESHDS 58
           MAT  PL+NF SF+LP+N  P+ ++ L+  + L+ S  Q  K    SK+ P     +HDS
Sbjct: 1   MATSLPLTNFLSFLLPTNPPPRPTSQLSFSSPLTRSLPQNSK----SKLIPLA---AHDS 53

Query: 59  SSASSSSTELASVICPSLAYANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGVIQ 118
            S S   TEL+S I PSLA AN LFF+SAYNVQV+VD+NEPEERLLNRFRREVMRAGVIQ
Sbjct: 54  GSLS---TELSSAINPSLANANILFFRSAYNVQVIVDDNEPEERLLNRFRREVMRAGVIQ 110

Query: 119 ECKRRRFFETKQDEKKRKTREAAKRNRRRRSQFRGPVQNRQEATPTKKDDDDEDNWELPE 178
           ECKRRRFFE KQDEKKRKTREAAKRN++RR Q R   QN+QE + TKKDDDD DNWELPE
Sbjct: 111 ECKRRRFFENKQDEKKRKTREAAKRNKKRRPQSRFTTQNKQETSTTKKDDDDGDNWELPE 170

Query: 179 GDIPY 183
           GD+PY
Sbjct: 171 GDLPY 175

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224060243|ref|XP_002300102.1| predicted protein [Populus trichocarpa] gi|118487561|gb|ABK95607.1| unknown [Populus trichocarpa] gi|222847360|gb|EEE84907.1| predicted protein [Populus trichocarpa]

 Score =  189 bits (479), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 122/187 (65%), Positives = 139/187 (74%), Gaps = 15/187 (8%)

Query: 1   MATPLS--NFFSFILPSNALPKNSTPLAQPNHLSLSS--QQKPKNASFSKVAPAQPQESH 56
           MAT LS  NF SF  PSN  PK   P  Q   LS S+   QK K+  FS        + +
Sbjct: 1   MATSLSLPNFLSFFSPSNPPPKTPVPPPQ---LSFSTPQAQKYKSLLFS--------QEN 49

Query: 57  DSSSASSSSTELASVICPSLAYANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGV 116
           D     S STEL+SV+CPSLAY+NTLFFKSAYNVQVVV++NEPEERLLNRFRREVMRAGV
Sbjct: 50  DGGHCGSLSTELSSVVCPSLAYSNTLFFKSAYNVQVVVEDNEPEERLLNRFRREVMRAGV 109

Query: 117 IQECKRRRFFETKQDEKKRKTREAAKRNRRRRSQFRGPVQNRQEATPTKKDDDDEDNWEL 176
           IQECKRRRF E KQ+EKKRK REA KRNRRRR Q RGP QN+ EA+P+KK+DDD+DNWE+
Sbjct: 110 IQECKRRRFHENKQEEKKRKVREAHKRNRRRRPQMRGPFQNKPEASPSKKNDDDDDNWEM 169

Query: 177 PEGDIPY 183
           PEGD  +
Sbjct: 170 PEGDASF 176

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225451423|ref|XP_002268728.1| PREDICTED: uncharacterized protein LOC100241260 [Vitis vinifera]

 Score =  186 bits (472), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 112/181 (61%), Positives = 132/181 (72%), Gaps = 7/181 (3%)

Query: 7   NFFSFILPSNALPKNSTPLAQPNHLSLSSQQKP-KNASFSKVAPAQ--PQESHDSSSASS 63
           NF SFILPS            PN +S S    P    S S   P+Q   +   D     S
Sbjct: 11  NFLSFILPSKP---PLPKTPPPNFISPSPHADPLPTLSVSAPPPSQFDARTPRDGLLQHS 67

Query: 64  SSTELASVICPSLAYANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGVIQECKRR 123
           SS++L +V+CPSLAY+NTLFFKSAYNVQV+V++NEPEE+LLNRFRREVMRAGVIQECKRR
Sbjct: 68  SSSDLMAVVCPSLAYSNTLFFKSAYNVQVIVEDNEPEEKLLNRFRREVMRAGVIQECKRR 127

Query: 124 RFFETKQDEKKRKTREAAKRNRRRRSQFRGPVQN-RQEATPTKKDDDDEDNWELPEGDIP 182
           RFFE KQDEKKRKTREAAKRNRRRR Q R   Q+ +QE +  KKDDD+EDNWE+PEG++P
Sbjct: 128 RFFENKQDEKKRKTREAAKRNRRRRPQSRFSTQDSKQEGSKNKKDDDEEDNWEVPEGELP 187

Query: 183 Y 183
           +
Sbjct: 188 F 188

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147845835|emb|CAN82190.1| hypothetical protein VITISV_031115 [Vitis vinifera]

 Score =  186 bits (471), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 94/122 (77%), Positives = 111/122 (90%), Gaps = 1/122 (0%)

Query: 63  SSSTELASVICPSLAYANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGVIQECKR 122
           SSS++L +V+CPSLAY+NTLFFKSAYNVQV+V++NEPEE+LLNRFRREVMRAGVIQECKR
Sbjct: 67  SSSSDLMAVVCPSLAYSNTLFFKSAYNVQVIVEDNEPEEKLLNRFRREVMRAGVIQECKR 126

Query: 123 RRFFETKQDEKKRKTREAAKRNRRRRSQFRGPVQN-RQEATPTKKDDDDEDNWELPEGDI 181
           RRFFE KQDEKKRKTREAAKRNRRRR Q R   Q+ +QE +  KKDDD+EDNWE+PEG++
Sbjct: 127 RRFFENKQDEKKRKTREAAKRNRRRRPQSRFSTQDSKQEGSKNKKDDDEEDNWEVPEGEL 186

Query: 182 PY 183
           P+
Sbjct: 187 PF 188

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|188036222|pdb|3BBN|U Chain U, Homology Model For The Spinach Chloroplast 30s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome. gi|17154781|gb|AAL35983.1|AF104396_1 ribosome-like protein [Cucumis sativus]

 Score =  172 bits (437), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 94/119 (78%), Positives = 103/119 (86%), Gaps = 2/119 (1%)

Query: 65  STELASVICPSLAYANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGVIQECKRRR 124
           S ELASVICPSLAYANT+FF+SAYNVQVVVD+NEPEERLLNRFRREVMRAGVIQECKRRR
Sbjct: 72  SAELASVICPSLAYANTMFFRSAYNVQVVVDDNEPEERLLNRFRREVMRAGVIQECKRRR 131

Query: 125 FFETKQDEKKRKTREAAKRNRRRRSQFRGPVQNRQEATPTKKDDDDEDNWELPEG-DIP 182
           FFE  QD +KRKTREAAKRNRRRR Q R   QN+Q+   TK++ DD DNW+LPE  DIP
Sbjct: 132 FFENTQDVRKRKTREAAKRNRRRRPQARFTPQNKQDVPATKQEADD-DNWDLPEDEDIP 189

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449455866|ref|XP_004145671.1| PREDICTED: uncharacterized protein LOC101216973 [Cucumis sativus] gi|449523367|ref|XP_004168695.1| PREDICTED: uncharacterized protein LOC101228071 [Cucumis sativus]

 Score =  172 bits (436), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 94/119 (78%), Positives = 103/119 (86%), Gaps = 2/119 (1%)

Query: 65  STELASVICPSLAYANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGVIQECKRRR 124
           S ELASVICPSLAYANT+FF+SAYNVQVVVD+NEPEERLLNRFRREVMRAGVIQECKRRR
Sbjct: 65  SAELASVICPSLAYANTMFFRSAYNVQVVVDDNEPEERLLNRFRREVMRAGVIQECKRRR 124

Query: 125 FFETKQDEKKRKTREAAKRNRRRRSQFRGPVQNRQEATPTKKDDDDEDNWELPEG-DIP 182
           FFE  QD +KRKTREAAKRNRRRR Q R   QN+Q+   TK++ DD DNW+LPE  DIP
Sbjct: 125 FFENTQDVRKRKTREAAKRNRRRRPQARFTPQNKQDVPATKQEADD-DNWDLPEDEDIP 182

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297814952|ref|XP_002875359.1| hypothetical protein ARALYDRAFT_484499 [Arabidopsis lyrata subsp. lyrata] gi|297321197|gb|EFH51618.1| hypothetical protein ARALYDRAFT_484499 [Arabidopsis lyrata subsp. lyrata]

 Score =  170 bits (431), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 101/182 (55%), Positives = 129/182 (70%), Gaps = 9/182 (4%)

Query: 5   LSNFFSFILPSNALPKNSTPLAQPNHLSLSSQQKPKNASFSKVAPAQPQESHDSSSASSS 64
           L++F SFI P  +  K + P          SQ++  + +   ++         SS+ASS 
Sbjct: 7   LTSFISFISPFKSQTKPTPPPNLTLPSPTISQRRRNDLAIESMSV-----DESSSTASSI 61

Query: 65  STELASVICPSLAYANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGVIQECKRRR 124
           S+ELASVICPSLAY+NTLFF S YNVQV V++NE EERL+NRFRREVMR GVIQECKRRR
Sbjct: 62  SSELASVICPSLAYSNTLFFSSGYNVQVFVEDNESEERLVNRFRREVMRTGVIQECKRRR 121

Query: 125 FFETKQDEKKRKTREAAKRNRRRRSQFRGPVQNRQE----ATPTKKDDDDEDNWELPEGD 180
           +FE KQDEKKR+TR+AAKRN++RR Q R   + R+E    AT +KK D++EDNWE+P GD
Sbjct: 122 YFENKQDEKKRRTRDAAKRNKKRRPQARFTQETREEAAAAATKSKKKDEEEDNWEMPGGD 181

Query: 181 IP 182
           +P
Sbjct: 182 VP 183

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18405254|ref|NP_566809.1| ribosomal protein S21 family protein [Arabidopsis thaliana] gi|9294081|dbj|BAB01933.1| unnamed protein product [Arabidopsis thaliana] gi|332643753|gb|AEE77274.1| ribosomal protein S21 family protein [Arabidopsis thaliana]

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 102/181 (56%), Positives = 129/181 (71%), Gaps = 8/181 (4%)

Query: 5   LSNFFSFILPSNALPKNSTPLAQPNHLSLSSQQKPKNASFSKVAPAQPQESHDSSSASSS 64
           L++F SFI P  +  K + P          SQ++  + +   +A         SS+ASS 
Sbjct: 7   LTSFISFISPFKSQTKPTPPPNLTLPSPTISQRRRNDLAIESMAV-----EETSSTASSL 61

Query: 65  STELASVICPSLAYANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGVIQECKRRR 124
           S+ELASVICPSLAY+NTLFF S YNVQV V++NE EERL+NRFRREVMR GVIQECKRRR
Sbjct: 62  SSELASVICPSLAYSNTLFFSSGYNVQVFVEDNESEERLVNRFRREVMRTGVIQECKRRR 121

Query: 125 FFETKQDEKKRKTREAAKRNRRRRSQFRGPVQNRQE---ATPTKKDDDDEDNWELPEGDI 181
           +FE KQDEKKR+TR+AAKRN++RR Q R   + R+E   AT +KK D++EDNWE+P GD+
Sbjct: 122 YFENKQDEKKRRTRDAAKRNKKRRPQARFTQETREEAAAATKSKKKDEEEDNWEMPGGDV 181

Query: 182 P 182
           P
Sbjct: 182 P 182

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356511811|ref|XP_003524616.1| PREDICTED: uncharacterized protein LOC100777605 [Glycine max]

 Score =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 94/182 (51%), Positives = 127/182 (69%), Gaps = 9/182 (4%)

Query: 2   ATPLSNFFSFILPSNALPKNSTPLAQPNHLSLSSQQKPKNASFSKVAPAQPQESHDSSSA 61
           ++ ++NF SF L +   P  S P   P   + S  QKP     S   P   Q +   S +
Sbjct: 4   SSTINNFLSFFLRTKPPPPPSPPQFNP---TTSQNQKP-----SSSQPLIAQYNPPPSPS 55

Query: 62  SSSSTELASVICPSLAYANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGVIQECK 121
            +SS+EL+SVICPS+AY+NTLFF+S YNVQVVV E+E EE+LL RFRREV++AG++QEC+
Sbjct: 56  CASSSELSSVICPSMAYSNTLFFRSPYNVQVVVAEDESEEKLLGRFRREVIKAGIVQECR 115

Query: 122 RRRFFETKQDEKKRKTREAAKRNRRRRSQFRGPVQNRQEATPTKKDDDDEDNWELPEGDI 181
           RRR+FE K +EKKRK+REAA+ NR+RR   +   Q +Q+ + TK+ +DDEDNW+LPEGD 
Sbjct: 116 RRRYFENKHEEKKRKSREAARCNRKRRPMSKTVGQKKQDVSATKR-EDDEDNWDLPEGDT 174

Query: 182 PY 183
            Y
Sbjct: 175 LY 176

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356570139|ref|XP_003553248.1| PREDICTED: uncharacterized protein LOC100780245 [Glycine max]

 Score =  159 bits (401), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 91/137 (66%), Positives = 102/137 (74%), Gaps = 9/137 (6%)

Query: 48  APAQPQESHDSSSASSSSTELASVICPSLAYANTLFFKSAYNVQVVVDENEPEERLLNRF 107
           A  Q Q+ H       SS EL++V  PS A+ANTLFF+SAYNVQVVVDENEPEERLLNRF
Sbjct: 70  AKHQDQDHH-------SSAELSAVANPSHAHANTLFFRSAYNVQVVVDENEPEERLLNRF 122

Query: 108 RREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRRRSQFRG-PVQNRQEATPTKK 166
           RREVMRAGVIQECKRRRFFE KQ+EKKRK REAAKR  R R        QN+ +   TKK
Sbjct: 123 RREVMRAGVIQECKRRRFFENKQEEKKRKNREAAKRKSRSRRSQSRFQPQNKPDVAATKK 182

Query: 167 DDDDEDNWELPEGDIPY 183
           ++DD DNW+LPE D PY
Sbjct: 183 EEDD-DNWDLPEVDAPY 198

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

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	183
TAIR|locus:2095143	183	GHS1 "GLUCOSE HYPERSENSITIVE 1	0.945	0.945	0.475	3.1e-35
TAIR|locus:2161912	217	AT5G63300 [Arabidopsis thalian	0.316	0.267	0.593	1.2e-12
UNIPROTKB|P68679	71	rpsU [Escherichia coli K-12 (t	0.196	0.507	0.472	0.00049

TAIR|locus:2095143 GHS1 "GLUCOSE HYPERSENSITIVE 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 381 (139.2 bits), Expect = 3.1e-35, P = 3.1e-35
 Identities = 86/181 (47%), Positives = 106/181 (58%)

Query:     5 LSNFFSFILPSNALPKNSTPLAQPNHLSLSSQQKPKNASFSKVAPAQPQEXXXXXXXXXX 64
             L++F SFI P  +  K + P   PN L+L S    +         +   E          
Sbjct:     7 LTSFISFISPFKSQTKPTPP---PN-LTLPSPTISQRRRNDLAIESMAVEETSSTASSLS 62

Query:    65 XTELASVICPSLAYANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGVIQECKRRR 124
              +ELASVICPSLAY+NTLFF S YNVQV V++NE EERL+NRFRREVMR GVIQECKRRR
Sbjct:    63 -SELASVICPSLAYSNTLFFSSGYNVQVFVEDNESEERLVNRFRREVMRTGVIQECKRRR 121

Query:   125 FFETKQDXXXXXXXXXXXXXXXXXSQFRGPVQNRQEA---TPTKKDDDDEDNWELPEGDI 181
             +FE KQD                  Q R   + R+EA   T +KK D++EDNWE+P GD+
Sbjct:   122 YFENKQDEKKRRTRDAAKRNKKRRPQARFTQETREEAAAATKSKKKDEEEDNWEMPGGDV 181

Query:   182 P 182
             P
Sbjct:   182 P 182

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

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0042254 "ribosome biogenesis" evidence=ISS

GO:0009534 "chloroplast thylakoid" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

TAIR|locus:2161912 AT5G63300 [Arabidopsis thaliana (taxid:3702)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 35/59 (59%), Positives = 45/59 (76%)

Query:    71 VICPSLAYANTLFFKSAY-NVQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFET 128
             V  PSLA AN +FFKS+Y NV+VV  + E EE+L+N F+R   RAGV+QE +RRRFFE+
Sbjct:    62 VAYPSLANANLVFFKSSYYNVEVVPKDGESEEQLVNDFKRSCFRAGVLQESRRRRFFES 120

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

GO:0005622 "intracellular" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM

GO:0042254 "ribosome biogenesis" evidence=ISS

UNIPROTKB|P68679 rpsU [Escherichia coli K-12 (taxid:83333)]

 Score = 87 (35.7 bits), Expect = 0.00049, P = 0.00049
 Identities = 17/36 (47%), Positives = 24/36 (66%)

Query:    92 VVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFE 127
             + V ENEP +  L RF+R   +AGV+ E +RR F+E
Sbjct:     4 IKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYE 39


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.314   0.129   0.375    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      183       155   0.00096  105 3  11 23  0.39    32
                                                     30  0.41    34


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  3
  No. of states in DFA:  585 (62 KB)
  Total size of DFA:  142 KB (2087 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  14.82u 0.11s 14.93t   Elapsed:  00:00:00
  Total cpu time:  14.82u 0.11s 14.93t   Elapsed:  00:00:00
  Start:  Fri May 10 08:36:06 2013   End:  Fri May 10 08:36:06 2013

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

GO:0006412 "translation" evidence=IEA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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	183
pfam01165	53	pfam01165, Ribosomal_S21, Ribosomal protein S21	9e-16
PRK00270	64	PRK00270, rpsU, 30S ribosomal protein S21; Reviewe	1e-14
COG0828	67	COG0828, RpsU, Ribosomal protein S21 [Translation,	5e-13
TIGR00030	58	TIGR00030, S21p, ribosomal protein S21	3e-12

>gnl|CDD|201634 pfam01165, Ribosomal_S21, Ribosomal protein S21

 Score = 67.6 bits (166), Expect = 9e-16
 Identities = 26/53 (49%), Positives = 39/53 (73%)

Query: 90  VQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAK 142
           V+V V ENE  ER L RF+R+V + G+++E +RRRF+E   +++KRK REA +
Sbjct: 1   VEVKVKENENIERALRRFKRKVEKNGILRELRRRRFYEKPSEKRKRKKREARR 53

Length = 53

>gnl|CDD|234707 PRK00270, rpsU, 30S ribosomal protein S21; Reviewed

 Score = 64.9 bits (159), Expect = 1e-14
 Identities = 25/63 (39%), Positives = 42/63 (66%)

Query: 90  VQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRRRS 149
            QV V ENE  ++ L RF+R+V +AG+++E +RR F+E   +++KRK   A KR R++ +
Sbjct: 2   PQVKVRENESIDKALRRFKRKVEKAGILRELRRREFYEKPSEKRKRKKAAARKRRRKKLA 61

Query: 150 QFR 152
           +  
Sbjct: 62  REE 64

Length = 64

>gnl|CDD|223898 COG0828, RpsU, Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]

 Score = 60.8 bits (148), Expect = 5e-13
 Identities = 25/59 (42%), Positives = 38/59 (64%)

Query: 90  VQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRRR 148
            QV V ENEP ++ L RF+R+V + G+++E K R F+E   +++KRK   A KR  +R 
Sbjct: 2   PQVKVRENEPLDKALRRFKRKVEKEGILREMKEREFYEKPSEKRKRKKAAARKRKFKRL 60

Length = 67

>gnl|CDD|129141 TIGR00030, S21p, ribosomal protein S21

 Score = 58.4 bits (142), Expect = 3e-12
 Identities = 21/58 (36%), Positives = 38/58 (65%)

Query: 90  VQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRR 147
             V V E E  +  L RF+R++ + G+++E K+RR++E   + ++RK + AAKR R++
Sbjct: 1   PTVKVKEGESIDSALRRFKRKLEKEGILRELKKRRYYEKPSERRRRKEKAAAKRIRKK 58

This model describes bacterial ribosomal protein S21 and most mitochondrial and chloroplast equivalents [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 58

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	183
PRK00270	64	rpsU 30S ribosomal protein S21; Reviewed	99.87
TIGR00030	58	S21p ribosomal protein S21. This model describes b	99.87
COG0828	67	RpsU Ribosomal protein S21 [Translation, ribosomal	99.85
PF01165	57	Ribosomal_S21: Ribosomal protein S21; InterPro: IP	99.63

>PRK00270 rpsU 30S ribosomal protein S21; Reviewed

Probab=99.87  E-value=1.4e-22  Score=143.92  Aligned_cols=61  Identities=41%  Similarity=0.698  Sum_probs=58.2

Q ss_pred             ceEEEecCCCcHHHHHHHHHHHHHhhhhHHHHhhhcccCCchHHHHHHHHHHHHHHHHhhh
Q 030110           89 NVQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRRRS  149 (183)
Q Consensus        89 mv~V~V~enE~iE~ALRRFKRkv~keGIL~E~KrRRyYEKPSeKRKRK~~eA~rR~rKrr~  149 (183)
                      |++|.|++||+||.|||+|||+|+++|||+|+|+|+||||||++|+|+..+|.+|++++.+
T Consensus         1 M~~V~V~~~e~ie~Alrrfkr~~~k~gil~e~r~r~~yekPs~krkrk~~~a~rr~~k~~~   61 (64)
T PRK00270          1 MPQVKVRENESIDKALRRFKRKVEKAGILRELRRREFYEKPSEKRKRKKAAARKRRRKKLA   61 (64)
T ss_pred             CCeeEeCCCChHHHHHHHHHHHHHHcchHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHh
Confidence            7899999999999999999999999999999999999999999999999999999987543

>TIGR00030 S21p ribosomal protein S21

Probab=99.87  E-value=1.8e-22  Score=140.98  Aligned_cols=57  Identities=37%  Similarity=0.694  Sum_probs=54.7

Q ss_pred             eEEEecCCCcHHHHHHHHHHHHHhhhhHHHHhhhcccCCchHHHHHHHHHHHHHHHH
Q 030110           90 VQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRR  146 (183)
Q Consensus        90 v~V~V~enE~iE~ALRRFKRkv~keGIL~E~KrRRyYEKPSeKRKRK~~eA~rR~rK  146 (183)
                      ++|.|++||+||+|||+|||+|+++|||+|||+|+||||||++|+|+.++|++|+++
T Consensus         1 ~~V~V~~~e~ie~alrrfkr~~~~~gil~e~r~r~~yeKPs~krkrk~~~a~rr~~k   57 (58)
T TIGR00030         1 PTVKVKEGESIDSALRRFKRKLEKEGILRELKKRRYYEKPSERRRRKEKAAAKRIRK   57 (58)
T ss_pred             CeeEeCCCCcHHHHHHHHHHHHHHcchHHHHHHHHhhcCHHHHHHHHHHHHHHHHhc
Confidence            579999999999999999999999999999999999999999999999999998865

This model describes bacterial ribosomal protein S21 and most mitochondrial and chloroplast equivalents.

>COG0828 RpsU Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]

Probab=99.85  E-value=2.8e-21  Score=139.45  Aligned_cols=62  Identities=40%  Similarity=0.667  Sum_probs=58.5

Q ss_pred             ceEEEecCCCcHHHHHHHHHHHHHhhhhHHHHhhhcccCCchHHHHHHHHHHHHHHHHhhhc
Q 030110           89 NVQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRRRSQ  150 (183)
Q Consensus        89 mv~V~V~enE~iE~ALRRFKRkv~keGIL~E~KrRRyYEKPSeKRKRK~~eA~rR~rKrr~~  150 (183)
                      |++|.|++||+||.|||+|||+|+++|||+|+|+|+|||+|+++++||..+|.+|..|+..+
T Consensus         1 M~~v~V~ene~~d~ALrrFKr~~~k~gil~e~k~r~~yEkPs~krkrK~a~a~kr~~k~~~k   62 (67)
T COG0828           1 MPQVKVRENEPLDKALRRFKRKVEKEGILREMKEREFYEKPSEKRKRKKAAARKRKFKRLRK   62 (67)
T ss_pred             CCeeeecCCChHHHHHHHHHHHHHHHHHHHHHHHHHhccCchHHHHHHHHHHHHHHHHHHHH
Confidence            78999999999999999999999999999999999999999999999999999998776543

>PF01165 Ribosomal_S21: Ribosomal protein S21; InterPro: IPR001911 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.63  E-value=3.4e-19  Score=122.30  Aligned_cols=57  Identities=40%  Similarity=0.704  Sum_probs=50.9

Q ss_pred             eEEEecCCCcHHHHHHHHHHHHHhhhhHHHHhhhcccCCchHHHHHHHHHHHHHHHH
Q 030110           90 VQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRR  146 (183)
Q Consensus        90 v~V~V~enE~iE~ALRRFKRkv~keGIL~E~KrRRyYEKPSeKRKRK~~eA~rR~rK  146 (183)
                      |+|.|++||++|.||++|+++|+++||++|+|+++|||||+++|+++..++.+|..|
T Consensus         1 v~V~V~~~~~~e~Alrr~~r~~~~~gi~~~~r~r~~yekps~kRkrk~~~~~rr~~k   57 (57)
T PF01165_consen    1 VTVKVRDGEDVERALRRFKRKVRRNGILKELRKRRFYEKPSEKRKRKRSERWRRRFK   57 (57)
T ss_dssp             ---EEESSSSSSSSSGTTCCTSSTTHHHTTTSSSB-SSSCCCCTTHCCCCCTHHHHH
T ss_pred             CeeecCCCCCHHHHHHHHHHHHHHcChHHHHHHHHhcCCHHHHHHHHHHHHHHHHhC
Confidence            589999999999999999999999999999999999999999999999999888764

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 [, ]. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryote ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S21 contains 55-70 amino acid residues, and has only been found in eubacteria to date, though it has been reported that plant chloroplasts and mammalian mitochondria contain ribosomal subunit protein S21. Experimental evidence has revealed that S21 is well exposed on the surface of the Escherichia coli ribosome [], and is one of the 'split proteins': these are a discrete group that are selectively removed from 30S subunits under low salt conditions and are required for the formation of activated 30S reconstitution intermediate (RI*) particles.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2VHO_U 3J18_U 2AVY_U 3OFO_U 3OFP_U 2WWL_U 3J0X_X 3IZV_Y 3ORA_U 3IZW_Y ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	183
3bbn_U	190	Homology Model For The Spinach Chloroplast 30s Subu		3e-37

>pdb|3BBN|U Chain U, Homology Model For The Spinach Chloroplast 30s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 190

Iteration: 1
 Score =  150 bits (380), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 78/118 (66%), Positives = 86/118 (72%), Gaps = 2/118 (1%)
Query: 66  TELASVICPSLAYANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRF 125
            ELASVICPSLAYANT+FF+SAYNVQVVVD+NEPEERLLNRFRREVMRAGVIQECKRRRF
Sbjct: 73  AELASVICPSLAYANTMFFRSAYNVQVVVDDNEPEERLLNRFRREVMRAGVIQECKRRRF 132
Query: 126 FETKQDXXXXXXXXXXXXXXXXXSQFRGPVQNRQEATPTKKDDDDEDNWELPEG-DIP 182
           FE  QD                  Q R   QN+Q+   TK++ DD DNW+LPE  DIP
Sbjct: 133 FENTQDVRKRKTREAAKRNRRRRPQARFTPQNKQDVPATKQEADD-DNWDLPEDEDIP 189

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	183
3bbn_U	190	Ribosomal protein S21; small ribosomal subunit, sp	2e-39
3i1m_U	71	30S ribosomal protein S21; ribosome structure, pro	7e-18
3r8n_U	51	30S ribosomal protein S21; protein biosynthesis, R	8e-13

>3bbn_U Ribosomal protein S21; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 190

 Score =  131 bits (331), Expect = 2e-39
 Identities = 105/180 (58%), Positives = 123/180 (68%), Gaps = 2/180 (1%)

Query: 5   LSNFFSFILPSNALPKNSTPLAQPNHLSLSSQQKPKNASFSKVAPAQPQESHDSSSASSS 64
           LS+FFSF+LPS   P         +  S S+   P+  +      +         + S  
Sbjct: 11  LSSFFSFLLPSKPPPPKPHQPFIASSPSPSNHAAPQFQTLKSRDGSVALNPQQGPNHSEP 70

Query: 65  -STELASVICPSLAYANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGVIQECKRR 123
            S ELASVICPSLAYANT+FF+SAYNVQVVVD+NEPEERLLNRFRREVMRAGVIQECKRR
Sbjct: 71  LSAELASVICPSLAYANTMFFRSAYNVQVVVDDNEPEERLLNRFRREVMRAGVIQECKRR 130

Query: 124 RFFETKQDEKKRKTREAAKRNRRRRSQFRGPVQNRQEATPTKKDDDDEDNWELPEGDIPY 183
           RFFE  QD +KRKTREAAKRNRRRR Q R   QN+Q+   TK++ DD DNW+LPE +   
Sbjct: 131 RFFENTQDVRKRKTREAAKRNRRRRPQARFTPQNKQDVPATKQEADD-DNWDLPEDEDIP 189

>3i1m_U 30S ribosomal protein S21; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_U* 2avy_U 2aw7_U 2vho_U 2vhp_U 3df1_U* 3df3_U* 3e1a_Q 3e1c_Q 1vs5_U 3i1o_U 3i1q_U 3i1s_U 3i1z_U 3i21_U 3izv_Y* 3izw_Y* 3kc4_U 3or9_U 3ora_U ... Length = 71

 Score = 72.9 bits (179), Expect = 7e-18
 Identities = 23/64 (35%), Positives = 36/64 (56%)

Query: 91  QVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRRRSQ 150
            + V ENEP +  L RF+R   +AGV+ E +RR F+E    E+KR    A KR+ ++ ++
Sbjct: 3   VIKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVKRHAKKLAR 62

Query: 151 FRGP 154
               
Sbjct: 63  ENAR 66

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	183
3bbn_U	190	Ribosomal protein S21; small ribosomal subunit, sp	100.0
3i1m_U	71	30S ribosomal protein S21; ribosome structure, pro	99.83
3r8n_U	51	30S ribosomal protein S21; protein biosynthesis, R	99.78

>3bbn_U Ribosomal protein S21; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=100.00  E-value=2.6e-59  Score=388.82  Aligned_cols=175  Identities=61%  Similarity=0.940  Sum_probs=52.8

Q ss_pred             CCcccccccccCCCCCC-CCCCCCC--CCCccccCC---CCCCCCccccccCCCCCCCCCCCCCCCCcccchhhhhccch
Q 030110            3 TPLSNFFSFILPSNALP-KNSTPLA--QPNHLSLSS---QQKPKNASFSKVAPAQPQESHDSSSASSSSTELASVICPSL   76 (183)
Q Consensus         3 ~~~~~f~sf~~p~~~~~-~~~~~~~--~p~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~sv~~p~l   76 (183)
                      +||+||||||||+|||+ ++++|..  .|+++++++   |+++++ +.......    ..++++++|+|+++++|+||++
T Consensus         9 ~s~~~f~sf~~~sk~~~~~~~~p~~~~~p~~~~~~~~~~~~~~~~-~~~~~~~~----~~~~~~~~~~s~~~~~~~~P~~   83 (190)
T 3bbn_U            9 ASLSSFFSFLLPSKPPPPKPHQPFIASSPSPSNHAAPQFQTLKSR-DGSVALNP----QQGPNHSEPLSAELASVICPSL   83 (190)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhHHHHHHHhccCCCCCCCCCCCcccCCCccccccCcchhhccCc-ccceeccc----cccCCcccccchhhHhhhCchh
Confidence            68999999999999996 3332211  266776554   667755 33333222    4789999999999999999999


Q ss_pred             hhhhhhcccCccceEEEecCCCcHHHHHHHHHHHHHhhhhHHHHhhhcccCCchHHHHHHHHHHHHHHHHhhhcCCCCCC
Q 030110           77 AYANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRRRSQFRGPVQ  156 (183)
Q Consensus        77 a~sn~l~fk~~~mv~V~V~enE~iE~ALRRFKRkv~keGIL~E~KrRRyYEKPSeKRKRK~~eA~rR~rKrr~~~r~~~~  156 (183)
                      +|+|+++|+|.||++|.|+|||+||+|||||||+|+++|||+|||+|+|||||+++||||.++|+||++||+.+.+++++
T Consensus        84 ~~an~~~~kg~~M~~V~VkeNE~iE~ALRRFKRkveKeGIlrElRrRr~YEKPSeKRKRK~~eA~rR~rKrR~~~~~~~~  163 (190)
T 3bbn_U           84 AYANTMFFRSAYNVQVVVDDNEPEERLLNRFRREVMRAGVIQECKRRRFFENTQDVRKRKTREAAKRNRRRRPQARFTPQ  163 (190)
T ss_dssp             -------------CCCCCCCCSSCCCCCCSSSTTTTTTHHHHSSSSCCCTTTTTTHHHHHHHHTTC--------------
T ss_pred             hhcchhhccCCcccEEEecCCCCHHHHHHHHHHHHHHccHHHHHHHHHhccCHHHHHHHHHHHHHHHHHHhhhccCCCcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcCCCCCCCCCCCCCCCCCCCCCC-CCC
Q 030110          157 NRQEATPTKKDDDDEDNWELPEGD-IPY  183 (183)
Q Consensus       157 ~k~e~~~~~~~ddd~DnWelp~~d-~p~  183 (183)
                      ++++. +.+++||||||||||+|| |||
T Consensus       164 ~~~~~-~~~~~de~dDnWe~p~~~~~p~  190 (190)
T 3bbn_U          164 NKQDV-PATKQEADDDNWDLPEDEDIPS  190 (190)
T ss_dssp             ----------------------------
T ss_pred             ccccc-ccccccccccCcCCCCcCcCCC
Confidence            98874 778999999999999998 997

>3i1m_U 30S ribosomal protein S21; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_U* 2avy_U 2aw7_U 2vho_U 2vhp_U 3df1_U* 3df3_U* 3e1a_Q 3e1c_Q 1vs5_U 3i1o_U 3i1q_U 3i1s_U 3i1z_U 3i21_U 3izv_Y* 3izw_Y* 3kc4_U 3or9_U 3ora_U ...

Probab=99.83  E-value=1.9e-23  Score=150.56  Aligned_cols=62  Identities=37%  Similarity=0.614  Sum_probs=50.8

Q ss_pred             ceEEEecCCCcHHHHHHHHHHHHHhhhhHHHHhhhcccCCchHHHHHHHHHHHHHHHHhhhc
Q 030110           89 NVQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRRRSQ  150 (183)
Q Consensus        89 mv~V~V~enE~iE~ALRRFKRkv~keGIL~E~KrRRyYEKPSeKRKRK~~eA~rR~rKrr~~  150 (183)
                      |++|.|+|||+||.|||+|||+|+++|||+|+|+|+||||||++|+||..+|++|.+|+..+
T Consensus         1 M~~V~V~enE~ie~ALRrfKR~~~k~Gil~e~Rrr~~yEKPs~kRkrk~~~a~kR~~k~~~~   62 (71)
T 3i1m_U            1 MPVIKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVKRHAKKLAR   62 (71)
T ss_dssp             ---CEEECCSSCCSCCCTTTTSSSTHHHHTTSSSCCCSSSHHHHHHHHHHTSCC--------
T ss_pred             CCeeEeCCCCCHHHHHHHHHHHHHHccHHHHHHHHHhccCHHHHHHHHHHHHHHHHHHHHHH
Confidence            78999999999999999999999999999999999999999999999999999998886544

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Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

No hit with probability above 80.00