Citrus Sinensis ID: 030403

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------18
Protein Sequence
MAHRRCLHVLSRHAAALLSLKTPPTLPFSTSISLKGLTPFQHRSLISSTLGPTNWSHYRHFSSNKNDDEGEDVDEDEDEDEETADESYEGEEIGDTVPDLGREYTLEEKEAEAAEIGYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPCWF
Secondary Structure (PSIPRED)
ccccHHHHHHHHcccHHHcccccccccccccccccccccccccccccccccccccccccEEccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHccEEEEEccccccccccccccEEEEEEccEEEEEEcccEEEEEEEcccccccEEEEcccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHccHHHHcccccccccccccccccccccccccccccccccccccccccEcccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccEEEcccccccccccccccEEEEEEEcccEEEEccccEEEEEEEEEEEcccEEEEcccccc
Coil and Loop (DISEMBL)
MAHRRCLHVLSRHAAALlslktpptlpfstsislkgltpfqhrslisstlgptnwshyrhfssnknddegedvdedededeetadesyegeeigdtvpdlgreytlEEKEAEAAEIGYkvlgplrksdrvfkkyEPAFAVVQIGShqfkvsngdsiFTERLKFCevndklsferpcwf
Flexible Loop (DISEMBL)
MAHRRCLHVLSRHAAALLSLKTPPTLPFSTSISLKGLTPFQHRSLISSTLGPTNWSHYRHfssnknddegedvdEDEDEDeetadesyegeeigdtvpdlGREYTLEEKEAEaaeigykvlgpLRKSDRVFKKYEPAFAVVqigshqfkvsnGDSIFTERLKFcevndklsferpcwf
Low Complexity Region (SEG)
MAHRRCLHVLSRHAAALLSLKTPPTLPFSTSISLKGLTPFQHRSLISSTLGPTNWSHYRHFSSNKNddegedvdedededeetadesyegeeIGDTVPDLGREYTLEEKEAEAAEIGYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPCWF
Disordered region (IsUnstruct)
*****CLHVLSRHAAALLSLKTPPTLPFSTSISLKGLTPFQHRSLISSTLGPTNWSHY******************************************************AAEIGYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPCW*
Disordered Region (DISOPRED)
***R*C**VLSRHAAALLSLKTPPTL*******************ISSTLGPTNWS***********************************************************IGYKVLG**********KYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPCWF
Disordered Region (DISEMBL)
MAHRRCLHVLSRHAAALLSLKTPPTLPFSTSISLKGLTPFQHRSLISSTLGPTNWSHYRHFSS****************************EIGDTVPDLGREYTLEEKEAEAAEIGYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPCWF
Disordered Region (DISPRO)
*****CLHVLSRHAAALLSLKTP*TLPFSTSISLKGLTPFQHRSLISSTLGPTNWSHYRH*******************************************YTLEEKEAEAAEIGYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPCWF
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAHRRCLHVLSRHAAALLSLKTPPTLPFSTSISLKGLTPFQHRSLISSTLGPTNWSHYRHFSSNKNDDEGEDVDEDEDEDEETADESYEGEEIGDTVPDLGREYTLEEKEAEAAEIGYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPCWF
Positional Conservation
no confident homologs detected

---

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	178	2.2.26 [Sep-21-2011]
Q8L9A0	270	50S ribosomal protein L21	yes	no	0.943	0.622	0.459	6e-28

>sp|Q8L9A0|RM21_ARATH 50S ribosomal protein L21, mitochondrial OS=Arabidopsis thaliana GN=RPL21M PE=2 SV=1

 Score =  123 bits (309), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 84/183 (45%), Positives = 113/183 (61%), Gaps = 15/183 (8%)

Query: 1   MAHRRCLHVLSRHAAALLSLKTPPTLP------FS-TSISLKGLTPFQHRSLISSTLGPT 53
           MA  RC   LSR A  + S+    ++       FS TSIS   + P  +RSL  +    +
Sbjct: 1   MASLRCFRELSRRATTVFSINQTRSISSFHGIEFSGTSISHGTVIP--NRSLTRNLPWYS 58

Query: 54  NW--SHYRHFSSNKNDDEGEDVDEDEDEDEETADESYEGEEIGDTVPDLGREYTLEEKEA 111
           +W  S  R FSSN  D + ++   + ++D+E   E +E     D   ++ REY+  EK  
Sbjct: 59  HWYRSQDRCFSSNTKDTDEDEESSEGEDDDEEEGEDFEDS--ADM--EVEREYSPAEKVE 114

Query: 112 EAAEIGYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLS 171
           EA EIGYKV+GPL+ S+R+FK YEP FA+VQIGSHQFKVSNGDSIFTE+LKFC++NDKL 
Sbjct: 115 EAEEIGYKVMGPLKPSERLFKPYEPVFAIVQIGSHQFKVSNGDSIFTEKLKFCDINDKLE 174

Query: 172 FER 174
             +
Sbjct: 175 LTK 177

This protein binds to 23S ribosomal RNA in the presence of protein L20.
Arabidopsis thaliana (taxid: 3702)

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	178
255556067	268	50S ribosomal protein L21, mitochondrial	0.904	0.600	0.505	9e-36
313585316	271	mitochondrial 50S ribosomal protein L21	0.932	0.612	0.548	4e-32
449452985	270	PREDICTED: 50S ribosomal protein L21, mi	0.971	0.640	0.544	2e-31
449489339	270	PREDICTED: LOW QUALITY PROTEIN: 50S ribo	0.971	0.640	0.544	2e-31
307136145	279	50S ribosomal protein l21 mitochondrial	0.949	0.605	0.527	2e-31
297798872	770	hypothetical protein ARALYDRAFT_328625 [	0.960	0.222	0.434	2e-28
18417696	270	50S ribosomal protein L21 [Arabidopsis t	0.943	0.622	0.459	3e-26
357511751	290	50S ribosomal protein L21 [Medicago trun	0.949	0.582	0.479	1e-25
357511749	300	50S ribosomal protein L21 [Medicago trun	0.949	0.563	0.479	2e-25
388506582	300	unknown [Medicago truncatula]	0.949	0.563	0.479	2e-25

>gi|255556067|ref|XP_002519068.1| 50S ribosomal protein L21, mitochondrial precursor, putative [Ricinus communis] gi|223541731|gb|EEF43279.1| 50S ribosomal protein L21, mitochondrial precursor, putative [Ricinus communis]

 Score =  155 bits (391), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 95/188 (50%), Positives = 116/188 (61%), Gaps = 27/188 (14%)

Query: 1   MAHRRCLHVLSRHAAALLS-----LKTPPTLP-FSTSISLKGLTPFQHRSLISSTLGPTN 54
           MA RR LH L+R   A++S     L     LP F +S+S+K L      SLI +    T 
Sbjct: 1   MAQRRRLHSLTRQVIAIISSNPTQLHHTVKLPSFPSSLSIKTL----RSSLIFTNTNATC 56

Query: 55  ---WSHY-----RHFSSNKNDDEGEDVDEDEDEDEETADESYEGEEIGDTVPDLGREYTL 106
              WSH+     R+FSS+  D    D  ED+  D +       GEE+ ++  DL REYTL
Sbjct: 57  HSLWSHHHHRNHRYFSSDYGDKSENDETEDDGSDSD-------GEEVTES--DLKREYTL 107

Query: 107 EEKEAEAAEIGYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCEV 166
           +EKE EAA IGYKV+GPL  S+RV K YEP FAV+QIGSHQFKVSNGD IFTERLKFC+V
Sbjct: 108 QEKEEEAAAIGYKVIGPLGDSERVIKAYEPVFAVIQIGSHQFKVSNGDCIFTERLKFCDV 167

Query: 167 NDKLSFER 174
           NDKL   +
Sbjct: 168 NDKLILNK 175

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|313585316|gb|ADR70863.1| mitochondrial 50S ribosomal protein L21 [Hevea brasiliensis]

 Score =  142 bits (359), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 102/186 (54%), Positives = 118/186 (63%), Gaps = 20/186 (10%)

Query: 1   MAHRRCLHVLSRHAAALLSLKTPPTL--PFSTSISLKGLTPFQHRSLISS----TLGPTN 54
           MA RRCLH L+R A ALLS   P TL  P   + S   L   +   +  S    T   + 
Sbjct: 1   MAQRRCLHTLTRQAIALLS-SNPTTLYHPCKVAASFPNLNSVKALLICKSSHVFTKADSI 59

Query: 55  WS------HYRHFSSNKNDDEGEDVDEDEDEDEETADESYEGEEIGDTVPDLGREYTLEE 108
           W       H R+FSS     +  D  E++DEDEETA E  +GEE+  +  DL REYT EE
Sbjct: 60  WCSFWPYHHRRYFSS-----DSRDESENDDEDEETAGEDSDGEEVKGS--DLKREYTAEE 112

Query: 109 KEAEAAEIGYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCEVND 168
           KE EAA IGYKV+GPL+KSD VFK YEP FAVVQIGSHQFKVSNGD IFTE+LKFCEVND
Sbjct: 113 KEEEAAAIGYKVVGPLQKSDLVFKPYEPVFAVVQIGSHQFKVSNGDCIFTEKLKFCEVND 172

Query: 169 KLSFER 174
           KL   +
Sbjct: 173 KLILNK 178

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449452985|ref|XP_004144239.1| PREDICTED: 50S ribosomal protein L21, mitochondrial-like [Cucumis sativus]

 Score =  140 bits (353), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 98/180 (54%), Positives = 118/180 (65%), Gaps = 7/180 (3%)

Query: 1   MAHRRCLHVLSRHAAALLSLKTPPTLPFSTSISLKGLTPFQHRSL---ISSTLGP---TN 54
           MA+RRCL VL+RHA+A+ S K P   P  T+ S        H SL   +S+   P   T 
Sbjct: 1   MANRRCLQVLTRHASAIFSTK-PYIHPLKTAPSFLSQNFRTHASLSNCLSAKTDPSLCTY 59

Query: 55  WSHYRHFSSNKNDDEGEDVDEDEDEDEETADESYEGEEIGDTVPDLGREYTLEEKEAEAA 114
           W H R+ SS+  +   +D  EDEDEDE+      E + I  +   + +EYT EE EAEAA
Sbjct: 60  WPHTRYLSSDSRNGSEDDFTEDEDEDEDDEAYDSEDDGISTSSRVMKKEYTKEEMEAEAA 119

Query: 115 EIGYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFER 174
            IGYKVLGPL +S+ VFK YEPAFAVVQIGSHQFKVSNGDSIFTERLKFC+VNDKL   +
Sbjct: 120 AIGYKVLGPLDQSEGVFKPYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCDVNDKLILNK 179

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449489339|ref|XP_004158283.1| PREDICTED: LOW QUALITY PROTEIN: 50S ribosomal protein L21, mitochondrial-like [Cucumis sativus]

 Score =  140 bits (353), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 98/180 (54%), Positives = 118/180 (65%), Gaps = 7/180 (3%)

Query: 1   MAHRRCLHVLSRHAAALLSLKTPPTLPFSTSISLKGLTPFQHRSL---ISSTLGP---TN 54
           MA+RRCL VL+RHA+A+ S K P   P  T+ S        H SL   +S+   P   T 
Sbjct: 1   MANRRCLQVLTRHASAIFSTK-PYIHPLKTAPSFLSQNFRTHASLSNCLSAKTDPSLCTY 59

Query: 55  WSHYRHFSSNKNDDEGEDVDEDEDEDEETADESYEGEEIGDTVPDLGREYTLEEKEAEAA 114
           W H R+ SS+  +   +D  EDEDEDE+      E + I  +   + +EYT EE EAEAA
Sbjct: 60  WPHTRYLSSDSRNGSEDDFTEDEDEDEDDEAYDSEDDGISTSSRVMKKEYTKEEMEAEAA 119

Query: 115 EIGYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFER 174
            IGYKVLGPL +S+ VFK YEPAFAVVQIGSHQFKVSNGDSIFTERLKFC+VNDKL   +
Sbjct: 120 AIGYKVLGPLDQSEGVFKPYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCDVNDKLILNK 179

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|307136145|gb|ADN33989.1| 50S ribosomal protein l21 mitochondrial precursor [Cucumis melo subsp. melo]

 Score =  140 bits (353), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 97/184 (52%), Positives = 121/184 (65%), Gaps = 15/184 (8%)

Query: 1   MAHRRCLHVLSRHAAALLS-------LKTPPTLPFSTSISLKGLTPFQHRSLISSTLGP- 52
           MA+RRCL VL+RHA+A+LS       LK  P+L F    +   L+     + +S+   P 
Sbjct: 10  MANRRCLQVLTRHASAILSTKPYIHTLKIAPSLLFENFHTHASLS-----NCLSAKTDPS 64

Query: 53  --TNWSHYRHFSSNKNDDEGEDVDEDEDEDEETADESYEGEEIGDTVPDLGREYTLEEKE 110
             T WSH R+ SS+  +   +D  EDEDEDE+      E + I  +   + +EYT EE E
Sbjct: 65  LCTYWSHTRYLSSDSRNGNEDDFTEDEDEDEDDEAYDSEDDGISTSSRVMKKEYTKEEME 124

Query: 111 AEAAEIGYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKL 170
           AEAA IGYKVLGPL +S+ +FK YEPAFAVVQIGSHQFKVSNGDSIFTERLKFC+VNDKL
Sbjct: 125 AEAAAIGYKVLGPLDQSEGIFKPYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCDVNDKL 184

Query: 171 SFER 174
              +
Sbjct: 185 ILNK 188

Source: Cucumis melo subsp. melo

Species: Cucumis melo

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297798872|ref|XP_002867320.1| hypothetical protein ARALYDRAFT_328625 [Arabidopsis lyrata subsp. lyrata] gi|297313156|gb|EFH43579.1| hypothetical protein ARALYDRAFT_328625 [Arabidopsis lyrata subsp. lyrata]

 Score =  130 bits (328), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 79/182 (43%), Positives = 111/182 (60%), Gaps = 11/182 (6%)

Query: 1   MAHRRCLHVLSRHAAALLSLKTPPTLPFSTSISLKGLTPFQHRSLISSTLGPTNWSHY-- 58
           MA  RC   LSR A  + S+    ++     I L G T   H ++I +     N + Y  
Sbjct: 499 MASLRCFRELSRRATTVYSIIQTRSISSFPGIELSG-TSISHGTVIPNRSLSRNLTWYSL 557

Query: 59  ------RHFSSNKNDDEGEDVDEDEDEDEETADESYEGEEIGDTVPDLGREYTLEEKEAE 112
                 R FSSN ND   ++   + +++++  +E  + E+  +   ++ REY+  EK  E
Sbjct: 558 WYRSQDRRFSSNTNDTAEDEESSEGEDEDDDDEEGEDFEDSAEM--EVEREYSPAEKVEE 615

Query: 113 AAEIGYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSF 172
           AAEIGYKV+GPL+ S+R+FK YEP FA+VQIGSHQFKVSNGDSIFTE+LKFC++NDKL  
Sbjct: 616 AAEIGYKVMGPLKPSERLFKPYEPVFAIVQIGSHQFKVSNGDSIFTEKLKFCDINDKLEL 675

Query: 173 ER 174
            +
Sbjct: 676 TK 677

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18417696|ref|NP_567861.1| 50S ribosomal protein L21 [Arabidopsis thaliana] gi|29839556|sp|Q8L9A0.1|RM21_ARATH RecName: Full=50S ribosomal protein L21, mitochondrial; Flags: Precursor gi|12641613|emb|CAC27453.1| putative ribosomal protein L21 [Arabidopsis thaliana] gi|21595368|gb|AAM66095.1| unknown [Arabidopsis thaliana] gi|29028852|gb|AAO64805.1| At4g30930 [Arabidopsis thaliana] gi|110736393|dbj|BAF00165.1| hypothetical protein [Arabidopsis thaliana] gi|225898835|dbj|BAH30548.1| hypothetical protein [Arabidopsis thaliana] gi|332660431|gb|AEE85831.1| 50S ribosomal protein L21 [Arabidopsis thaliana]

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 84/183 (45%), Positives = 113/183 (61%), Gaps = 15/183 (8%)

Query: 1   MAHRRCLHVLSRHAAALLSLKTPPTLP------FS-TSISLKGLTPFQHRSLISSTLGPT 53
           MA  RC   LSR A  + S+    ++       FS TSIS   + P  +RSL  +    +
Sbjct: 1   MASLRCFRELSRRATTVFSINQTRSISSFHGIEFSGTSISHGTVIP--NRSLTRNLPWYS 58

Query: 54  NW--SHYRHFSSNKNDDEGEDVDEDEDEDEETADESYEGEEIGDTVPDLGREYTLEEKEA 111
           +W  S  R FSSN  D + ++   + ++D+E   E +E     D   ++ REY+  EK  
Sbjct: 59  HWYRSQDRCFSSNTKDTDEDEESSEGEDDDEEEGEDFEDS--ADM--EVEREYSPAEKVE 114

Query: 112 EAAEIGYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLS 171
           EA EIGYKV+GPL+ S+R+FK YEP FA+VQIGSHQFKVSNGDSIFTE+LKFC++NDKL 
Sbjct: 115 EAEEIGYKVMGPLKPSERLFKPYEPVFAIVQIGSHQFKVSNGDSIFTEKLKFCDINDKLE 174

Query: 172 FER 174
             +
Sbjct: 175 LTK 177

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357511751|ref|XP_003626164.1| 50S ribosomal protein L21 [Medicago truncatula] gi|355501179|gb|AES82382.1| 50S ribosomal protein L21 [Medicago truncatula]

 Score =  121 bits (303), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 93/194 (47%), Positives = 110/194 (56%), Gaps = 25/194 (12%)

Query: 4   RRCLHVLSRHAAALLSLKTPPTLPFSTSISLKG-------LTPFQHRSLISSTLGPTNWS 56
           RRCL  L+R +   LSL   P      S +          L P    S  +S  G   W 
Sbjct: 6   RRCLQALTRQSQPTLSLFKDPLSLRLLSSAALLNHNISSPLLPIFTNSKPTSAFG--QWH 63

Query: 57  HYRHFSSNKNDDEGEDVDEDE--------------DEDEETADESYEGEEIGDTVPDLGR 102
           H R+FSS+K DD  ++    E              D+D+   +E    +E  DTV    R
Sbjct: 64  HGRYFSSSKQDDHIKEGGTHEIEDEDDDSDGDDDDDDDDYDEEEGDYEDEDDDTVAVSSR 123

Query: 103 E--YTLEEKEAEAAEIGYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTER 160
           +  YT EEKEAEA  IGYKV+GPL+K+D VFK YEPAFAVVQIGSHQFKVSNGDSIFTER
Sbjct: 124 KKVYTEEEKEAEAEAIGYKVVGPLQKNDNVFKPYEPAFAVVQIGSHQFKVSNGDSIFTER 183

Query: 161 LKFCEVNDKLSFER 174
           LKFCEVNDKL   +
Sbjct: 184 LKFCEVNDKLILNK 197

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357511749|ref|XP_003626163.1| 50S ribosomal protein L21 [Medicago truncatula] gi|355501178|gb|AES82381.1| 50S ribosomal protein L21 [Medicago truncatula]

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 93/194 (47%), Positives = 110/194 (56%), Gaps = 25/194 (12%)

Query: 4   RRCLHVLSRHAAALLSLKTPPTLPFSTSISLKG-------LTPFQHRSLISSTLGPTNWS 56
           RRCL  L+R +   LSL   P      S +          L P    S  +S  G   W 
Sbjct: 16  RRCLQALTRQSQPTLSLFKDPLSLRLLSSAALLNHNISSPLLPIFTNSKPTSAFG--QWH 73

Query: 57  HYRHFSSNKNDDEGEDVDEDE--------------DEDEETADESYEGEEIGDTVPDLGR 102
           H R+FSS+K DD  ++    E              D+D+   +E    +E  DTV    R
Sbjct: 74  HGRYFSSSKQDDHIKEGGTHEIEDEDDDSDGDDDDDDDDYDEEEGDYEDEDDDTVAVSSR 133

Query: 103 E--YTLEEKEAEAAEIGYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTER 160
           +  YT EEKEAEA  IGYKV+GPL+K+D VFK YEPAFAVVQIGSHQFKVSNGDSIFTER
Sbjct: 134 KKVYTEEEKEAEAEAIGYKVVGPLQKNDNVFKPYEPAFAVVQIGSHQFKVSNGDSIFTER 193

Query: 161 LKFCEVNDKLSFER 174
           LKFCEVNDKL   +
Sbjct: 194 LKFCEVNDKLILNK 207

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388506582|gb|AFK41357.1| unknown [Medicago truncatula]

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 93/194 (47%), Positives = 110/194 (56%), Gaps = 25/194 (12%)

Query: 4   RRCLHVLSRHAAALLSLKTPPTLPFSTSISLKG-------LTPFQHRSLISSTLGPTNWS 56
           RRCL  L+R +   LSL   P      S +          L P    S  +S  G   W 
Sbjct: 16  RRCLQALTRQSQPTLSLFKDPLSLRLLSSAALLNHNISSPLLPIFTNSKPTSAFG--QWH 73

Query: 57  HYRHFSSNKNDDEGEDVDEDE--------------DEDEETADESYEGEEIGDTVPDLGR 102
           H R+FSS+K DD  ++    E              D+D+   +E    +E  DTV    R
Sbjct: 74  HGRYFSSSKQDDHIKEGGTHEIGDEDDDSDGDDDDDDDDYDEEEGDYEDEDDDTVAVSSR 133

Query: 103 E--YTLEEKEAEAAEIGYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTER 160
           +  YT EEKEAEA  IGYKV+GPL+K+D VFK YEPAFAVVQIGSHQFKVSNGDSIFTER
Sbjct: 134 KKVYTEEEKEAEAEAIGYKVVGPLQKNDNVFKPYEPAFAVVQIGSHQFKVSNGDSIFTER 193

Query: 161 LKFCEVNDKLSFER 174
           LKFCEVNDKL   +
Sbjct: 194 LKFCEVNDKLILNK 207

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

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	178
TAIR|locus:2126699	270	NFD1 "NUCLEAR FUSION DEFECTIVE	0.966	0.637	0.396	3.5e-27

TAIR|locus:2126699 NFD1 "NUCLEAR FUSION DEFECTIVE 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 305 (112.4 bits), Expect = 3.5e-27, P = 3.5e-27
 Identities = 71/179 (39%), Positives = 94/179 (52%)

Query:     1 MAHRRCLHVLSRHAAALLSLKTPPTLPFSTSISLKGLTPFQHRSLISSTLGPTNWSHYRH 60
             MA  RC   LSR A  + S+    ++     I   G T   H ++I +     N   Y H
Sbjct:     1 MASLRCFRELSRRATTVFSINQTRSISSFHGIEFSG-TSISHGTVIPNRSLTRNLPWYSH 59

Query:    61 FSSNKNXXXXXXXXXXXXXXXXXXXXXXXXXXIGDTVPD-----LGREYTLEEKEAEAAE 115
             +  +++                           G+   D     + REY+  EK  EA E
Sbjct:    60 WYRSQDRCFSSNTKDTDEDEESSEGEDDDEEE-GEDFEDSADMEVEREYSPAEKVEEAEE 118

Query:   116 IGYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFER 174
             IGYKV+GPL+ S+R+FK YEP FA+VQIGSHQFKVSNGDSIFTE+LKFC++NDKL   +
Sbjct:   119 IGYKVMGPLKPSERLFKPYEPVFAIVQIGSHQFKVSNGDSIFTEKLKFCDINDKLELTK 177


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        0.320   0.134   0.411    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      178       152   0.00073  105 3  11 22  0.47    31
                                                     30  0.40    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:  1
  No. of states in DFA:  590 (63 KB)
  Total size of DFA:  148 KB (2090 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:  13.90u 0.17s 14.07t   Elapsed:  00:00:01
  Total cpu time:  13.90u 0.17s 14.07t   Elapsed:  00:00:01
  Start:  Mon May 20 17:39:51 2013   End:  Mon May 20 17:39:52 2013

GO:0003723 "RNA binding" evidence=IEA

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

GO:0005840 "ribosome" evidence=ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM

GO:0000741 "karyogamy" evidence=RCA;IMP

GO:0005739 "mitochondrion" evidence=IDA

GO:0009553 "embryo sac development" evidence=IMP

GO:0009555 "pollen development" evidence=IMP

GO:0009567 "double fertilization forming a zygote and endosperm" evidence=IMP

GO:0001510 "RNA methylation" evidence=RCA

GO:0006342 "chromatin silencing" evidence=RCA

GO:0006606 "protein import into nucleus" evidence=RCA

GO:0009560 "embryo sac egg cell differentiation" evidence=RCA

GO:0016572 "histone phosphorylation" evidence=RCA

GO:0051567 "histone H3-K9 methylation" evidence=RCA

---

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	178
pfam00829	96	pfam00829, Ribosomal_L21p, Ribosomal prokaryotic L	8e-08
PRK05573	103	PRK05573, rplU, 50S ribosomal protein L21; Validat	2e-06
COG0261	103	COG0261, RplU, Ribosomal protein L21 [Translation,	0.002

>gnl|CDD|201461 pfam00829, Ribosomal_L21p, Ribosomal prokaryotic L21 protein

 Score = 47.5 bits (114), Expect = 8e-08
 Identities = 16/37 (43%), Positives = 25/37 (67%), Gaps = 1/37 (2%)

Query: 138 FAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFER 174
           +A+++ G  Q+KV  GD IF E+L   EV DK+ F++
Sbjct: 2   YAIIETGGKQYKVEEGDVIFVEKLD-AEVGDKIEFDK 37

Length = 96

>gnl|CDD|235510 PRK05573, rplU, 50S ribosomal protein L21; Validated

 Score = 44.3 bits (106), Expect = 2e-06
 Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 1/36 (2%)

Query: 138 FAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFE 173
           +A+++ G  Q+KV  GD I  E+L   EV D + F+
Sbjct: 2   YAIIKTGGKQYKVEEGDVIKVEKLD-AEVGDTVEFD 36

Length = 103

>gnl|CDD|223339 COG0261, RplU, Ribosomal protein L21 [Translation, ribosomal structure and biogenesis]

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 1/35 (2%)

Query: 138 FAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSF 172
           +A+++ G  Q+KV  GD I  E+L   E  DK+ F
Sbjct: 2   YAIIKTGGKQYKVEEGDVIKVEKLDA-EPGDKVEF 35

Length = 103

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	178
CHL00075	108	rpl21 ribosomal protein L21	99.55
PF00829	96	Ribosomal_L21p: Ribosomal prokaryotic L21 protein;	99.54
COG0261	103	RplU Ribosomal protein L21 [Translation, ribosomal	99.54
PRK05573	103	rplU 50S ribosomal protein L21; Validated	99.52
KOG1686	151	consensus Mitochondrial/chloroplast ribosomal L21	99.51
TIGR00061	101	L21 ribosomal protein L21. Eubacterial and chlorop	99.42
PF11356	87	Pilus_PilP: Type IV pilus biogenesis; InterPro: IP	91.61
PF04931	784	DNA_pol_phi: DNA polymerase phi; InterPro: IPR0070	87.26
PF04351	149	PilP: Pilus assembly protein, PilP; InterPro: IPR0	83.39
PF10446	458	DUF2457: Protein of unknown function (DUF2457); In	81.55
COG0662	127	{ManC} Mannose-6-phosphate isomerase [Carbohydrate	80.94

>CHL00075 rpl21 ribosomal protein L21

Probab=99.55  E-value=5e-15  Score=113.98  Aligned_cols=42  Identities=19%  Similarity=0.272  Sum_probs=40.5

Q ss_pred             ceEEEEeeCCeEEEEeCCCEEEecccCCCCCCCeEEecccccC
Q 030403          136 PAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPCWF  178 (178)
Q Consensus       136 ~MYAIVeiGGKQYKV~eGD~I~VErL~~aEvGdkI~LdkVLLv  178 (178)
                      .|||||++|||||||++||+|.||+|+ +++|++|+|++|||+
T Consensus         2 ~myAIi~~gGkQykV~~Gd~i~vekl~-~~~G~~i~l~~VL~~   43 (108)
T CHL00075          2 MTYAIIEAGGKQLWVEPGRFYDINHFP-LEPGTKILLNRVLLI   43 (108)
T ss_pred             cEEEEEEECCEEEEEeCCCEEEEEEcC-CCCCCEEEEEEEEEE
Confidence            699999999999999999999999997 899999999999985

>PF00829 Ribosomal_L21p: Ribosomal prokaryotic L21 protein; InterPro: IPR001787 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.54  E-value=4.6e-15  Score=111.13  Aligned_cols=41  Identities=39%  Similarity=0.712  Sum_probs=38.7

Q ss_pred             eEEEEeeCCeEEEEeCCCEEEecccCCCCCCCeEEecccccC
Q 030403          137 AFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPCWF  178 (178)
Q Consensus       137 MYAIVeiGGKQYKV~eGD~I~VErL~~aEvGdkI~LdkVLLv  178 (178)
                      |||||++|||||||++||+|.|++|. +++|++|+|++|||+
T Consensus         1 myAIi~~ggkQykV~~gd~i~v~~l~-~~~G~~i~l~~VL~~   41 (96)
T PF00829_consen    1 MYAIIEIGGKQYKVEEGDVIDVERLD-AEVGDKIELDKVLLI   41 (96)
T ss_dssp             -EEEEESSSEEEEESSSEEEEEESTS-SSTTSEEEETTEEEE
T ss_pred             CEEEEEECCEEEEEeCCCEEEECCcC-cCCCCEEEEEEEEEE
Confidence            99999999999999999999999995 999999999999985

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L21 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L21 is known to bind to the 23S rRNA in the presence of L20. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups: Bacterial L21. Marchantia polymorpha chloroplast L21. Cyanelle L21. Plant chloroplast L21 (nuclear-encoded). Bacterial L21 is a protein of about 100 amino-acid residues, the mature form of the spinach chloroplast L21 has 200 residues.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XG0_V 2X9S_V 2XG2_V 3UZ1_2 2Y19_V 2WDL_V 3V23_V 2WRO_V 2WRL_V 2Y11_V ....

>COG0261 RplU Ribosomal protein L21 [Translation, ribosomal structure and biogenesis]

Probab=99.54  E-value=5.3e-15  Score=114.04  Aligned_cols=41  Identities=34%  Similarity=0.629  Sum_probs=40.0

Q ss_pred             eEEEEeeCCeEEEEeCCCEEEecccCCCCCCCeEEecccccC
Q 030403          137 AFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPCWF  178 (178)
Q Consensus       137 MYAIVeiGGKQYKV~eGD~I~VErL~~aEvGdkI~LdkVLLv  178 (178)
                      |||||++|||||||++||+|+||+|. +++|++|+|++|||+
T Consensus         1 mYAii~tGGKQykV~~G~~i~vEkl~-~e~g~~v~f~~VL~v   41 (103)
T COG0261           1 MYAIIKTGGKQYKVEEGDVIKVEKLD-AEPGDKVEFDEVLMV   41 (103)
T ss_pred             CeEEEEECCEEEEEecCCEEEEEEcC-CCCCCEEEEEEEEEE
Confidence            99999999999999999999999997 899999999999986

>PRK05573 rplU 50S ribosomal protein L21; Validated

Probab=99.52  E-value=1.1e-14  Score=110.66  Aligned_cols=41  Identities=34%  Similarity=0.648  Sum_probs=39.8

Q ss_pred             eEEEEeeCCeEEEEeCCCEEEecccCCCCCCCeEEecccccC
Q 030403          137 AFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPCWF  178 (178)
Q Consensus       137 MYAIVeiGGKQYKV~eGD~I~VErL~~aEvGdkI~LdkVLLv  178 (178)
                      |||||++|||||||++||+|.|++|+ +++|++|.|++|||+
T Consensus         1 MyAIi~~gGkQykV~~Gd~i~v~~l~-~~~G~~i~l~~VL~~   41 (103)
T PRK05573          1 MYAIIKTGGKQYKVEEGDVIKVEKLD-AEVGDTVEFDEVLLV   41 (103)
T ss_pred             CEEEEEECCEEEEEeCCCEEEEcccC-CCCCCEEEEeEEEEE
Confidence            99999999999999999999999997 999999999999985

>KOG1686 consensus Mitochondrial/chloroplast ribosomal L21 protein [Translation, ribosomal structure and biogenesis]

Probab=99.51  E-value=8.9e-15  Score=118.93  Aligned_cols=67  Identities=36%  Similarity=0.378  Sum_probs=65.0

Q ss_pred             HHHHhCcEEecccccCccccccCCceEEEEeeCCeEEEEeCCCEEEecccCCCCCCCeEEecccccC
Q 030403          112 EAAEIGYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPCWF  178 (178)
Q Consensus       112 ea~~igykvvg~~~~~~~~~k~~~~MYAIVeiGGKQYKV~eGD~I~VErL~~aEvGdkI~LdkVLLv  178 (178)
                      ||+.|+|+|||++.++.+-+.+|++.||||.+||+||||+.||+||.++++.++++|+|.+++|||+
T Consensus         1 ea~~~e~v~vg~l~s~~~~~~kr~~~favv~v~srq~kvs~gd~iy~eg~~p~nv~d~i~l~kVlLv   67 (151)
T KOG1686|consen    1 MAASSETVTVGRLASACSHSIKRPSGFAVVSVGSRQRKVSSGDTIYTEGLKPKNVLDSIPLPKVLLV   67 (151)
T ss_pred             CcccceeEEEeccchhhhhccccCCccEEEEEcceeEEecCCCeeeecCccccccccccccceEEEe
Confidence            5788999999999999999999999999999999999999999999999999999999999999985

>TIGR00061 L21 ribosomal protein L21

Probab=99.42  E-value=1.6e-13  Score=104.44  Aligned_cols=40  Identities=30%  Similarity=0.634  Sum_probs=38.7

Q ss_pred             EEEEeeCCeEEEEeCCCEEEecccCCCCCCCeEEecccccC
Q 030403          138 FAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPCWF  178 (178)
Q Consensus       138 YAIVeiGGKQYKV~eGD~I~VErL~~aEvGdkI~LdkVLLv  178 (178)
                      ||||++|||||||++||+|.||+|+ +++|+.|+|++|||+
T Consensus         1 yAIi~~gGkQykV~~Gd~i~Ve~l~-~~~G~~i~l~~VLlv   40 (101)
T TIGR00061         1 YAIVEIGGKQYKVEEGQTVRIEKLD-AAPGDTVEFDKVLMV   40 (101)
T ss_pred             CEEEEECCEEEEEeCCCEEEEcccC-CCCCCEEEEEEEEEE
Confidence            8999999999999999999999997 899999999999985

Eubacterial and chloroplast.

>PF11356 Pilus_PilP: Type IV pilus biogenesis; InterPro: IPR022753 Type IV pili are required for auto-agglutination, twitching motility, biofilm formation, adherence and DNA uptake during transformation []

Probab=91.61  E-value=0.18  Score=35.62  Aligned_cols=42  Identities=21%  Similarity=0.284  Sum_probs=28.8

Q ss_pred             HHHHHHhCcEEecccccCccccccCCceEEEEe-eCCeEEEEeCCCEEE
Q 030403          110 EAEAAEIGYKVLGPLRKSDRVFKKYEPAFAVVQ-IGSHQFKVSNGDSIF  157 (178)
Q Consensus       110 ~~ea~~igykvvg~~~~~~~~~k~~~~MYAIVe-iGGKQYKV~eGD~I~  157 (178)
                      ...+...+++++|-+...      ....+|||+ .+|+|..+..||.|-
T Consensus        20 ~~~~~~~~l~L~Gvi~~~------~~~~~Aii~~~~~~~~~~~~Gd~i~   62 (87)
T PF11356_consen   20 PAPATSLNLTLVGVISGG------GGRSSAIIRPSGGEQRTYRVGDTIP   62 (87)
T ss_dssp             -S--S-SSSEEEEEE-SC------SSS-EEEEE-CTTEEEEE-TTEE-S
T ss_pred             CCCCCCCCcEEEEEEEcC------CCceEEEEEeCCCcEEEEECcCEeC
Confidence            345566789999988322      267899999 999999999999987

PilP is an inner membrane protein, required for pilus expression and transformation []. PilP interacts with PilQ which suggests that the two proteins may have coordinated activity in functions such as pilus extrusion/retraction []. ; PDB: 3OSS_C 2LNV_A.

>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar

Probab=87.26  E-value=0.47  Score=46.32  Aligned_cols=11  Identities=27%  Similarity=0.220  Sum_probs=5.8

Q ss_pred             HHHHHHHHhCc
Q 030403          108 EKEAEAAEIGY  118 (178)
Q Consensus       108 e~~~ea~~igy  118 (178)
                      -..+.++++|.
T Consensus       704 ~~~~l~~aL~~  714 (784)
T PF04931_consen  704 FRSALAKALGD  714 (784)
T ss_pred             HHHHHHHHhcc
Confidence            33444666664

The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent

>PF04351 PilP: Pilus assembly protein, PilP; InterPro: IPR007446 The PilP family are periplasmic proteins involved in the biogenesis of type IV pili []

Probab=83.39  E-value=1.4  Score=34.91  Aligned_cols=35  Identities=29%  Similarity=0.443  Sum_probs=28.8

Q ss_pred             cEEecccccCccccccCCceEEEEee-CCeEEEEeCCCEEEec
Q 030403          118 YKVLGPLRKSDRVFKKYEPAFAVVQI-GSHQFKVSNGDSIFTE  159 (178)
Q Consensus       118 ykvvg~~~~~~~~~k~~~~MYAIVei-GGKQYKV~eGD~I~VE  159 (178)
                      .|.||-|...       ..++|+|+. .|+=|+|..|++|=-+
T Consensus        79 LklvG~l~~~-------~~~~ALv~~pdg~v~~V~~G~yiG~n  114 (149)
T PF04351_consen   79 LKLVGTLSQG-------GQPWALVQDPDGKVYRVKVGDYIGQN  114 (149)
T ss_dssp             EEEEEEEEET-------TEEEEEEEE-TTEEEEEETTEEETTT
T ss_pred             eEEEEEEeeC-------CEEEEEEEeCCCCEEEecCCCEeccC
Confidence            5889987533       578999999 9999999999998543

; PDB: 2Y4Y_B 2Y4X_A 2IVW_A 2LC4_A.

>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins

Probab=81.55  E-value=0.73  Score=43.91  Aligned_cols=6  Identities=0%  Similarity=-0.042  Sum_probs=2.7

Q ss_pred             ccccCC
Q 030403          130 VFKKYE  135 (178)
Q Consensus       130 ~~k~~~  135 (178)
                      .|+|..
T Consensus       124 ~WtP~~  129 (458)
T PF10446_consen  124 FWTPGA  129 (458)
T ss_pred             eecccc
Confidence            445543

>COG0662 {ManC} Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]

Probab=80.94  E-value=2.3  Score=32.40  Aligned_cols=22  Identities=32%  Similarity=0.604  Sum_probs=20.1

Q ss_pred             EEEeeCCeEEEEeCCCEEEecc
Q 030403          139 AVVQIGSHQFKVSNGDSIFTER  160 (178)
Q Consensus       139 AIVeiGGKQYKV~eGD~I~VEr  160 (178)
                      |+|.++|+++-|++||.++|+.
T Consensus        68 g~v~~~~~~~~v~~gd~~~iP~   89 (127)
T COG0662          68 GKVTIGGEEVEVKAGDSVYIPA   89 (127)
T ss_pred             EEEEECCEEEEecCCCEEEECC
Confidence            6688999999999999999974

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	178
3bbo_T	257	Homology Model For The Spinach Chloroplast 50s Subu		8e-04

>pdb|3BBO|T Chain T, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 257

Iteration: 1
 Score = 39.7 bits (91), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 19/37 (51%), Positives = 24/37 (64%)
Query: 138 FAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFER 174
           FAVV IGS Q+ V  G  I+T+RLK   VNDK+   +
Sbjct: 125 FAVVVIGSRQYIVIPGRWIYTQRLKGATVNDKIVLNK 161

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	178
3bbo_T	257	Ribosomal protein L21; large ribosomal subunit, sp	9e-18
3v2d_V	101	50S ribosomal protein L21; ribosome associated inh	6e-06
3r8s_R	103	50S ribosomal protein L21; protein biosynthesis, R	6e-06
2zjr_O	100	50S ribosomal protein L21; ribosome, large ribosom	2e-05

>3bbo_T Ribosomal protein L21; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 257

 Score = 77.0 bits (189), Expect = 9e-18
 Identities = 35/174 (20%), Positives = 55/174 (31%), Gaps = 13/174 (7%)

Query: 1   MAHRRCLHVLSRHAAALLSLKTPPTLPFSTSISLKGLTPFQHRSLISSTLGPTNWSHYRH 60
           MA        S   A L   +    L  +     K  +       +S        +  R 
Sbjct: 1   MASATLAFSCSSLCATLKLPQNLNPLLLNVPPLSKPFSGVVSPPSLSRLSLLPVAAKRRR 60

Query: 61  FSSNKNDDEGEDVDEDEDEDEETADESYEGEEIGDTVPDLGREYTLEEKEAEAAEIGYKV 120
           F     + + E  +     +++        +               +  E    E    +
Sbjct: 61  FQEIPEELKAEFEEFQRPPNQKPQLSDVLPD-------------DFQAPEPGTPEYNDII 107

Query: 121 LGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFER 174
              L K      + E  FAVV IGS Q+ V  G  I+T+RLK   VNDK+   +
Sbjct: 108 NQFLPKKGPPPPREEIIFAVVVIGSRQYIVIPGRWIYTQRLKGATVNDKIVLNK 161

>3v2d_V 50S ribosomal protein L21; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 1vsp_P 2hgj_U 2hgq_U 2hgu_U 1vsa_P 2j03_V 2jl6_V 2jl8_V 2v47_V 2v49_V 2wdi_V 2wdj_V 2wdl_V 2wdn_V 2wh2_V 2wh4_V 2wrj_V 2wrl_V 2wro_V 2wrr_V ... Length = 101

 Score = 42.1 bits (100), Expect = 6e-06
 Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 1/37 (2%)

Query: 138 FAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFER 174
           FA+V+ G  Q++V  G  +  E+L   E    +    
Sbjct: 2   FAIVKTGGKQYRVEPGLKLRVEKLD-AEPGATVELPV 37

>3r8s_R 50S ribosomal protein L21; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 1vs8_R 1vs6_R 2aw4_R 2awb_R 1vt2_R 2i2v_R 2j28_R 2i2t_R* 2qao_R* 2qba_R* 2qbc_R* 2qbe_R 2qbg_R 2qbi_R* 2qbk_R* 2qov_R 2qox_R 2qoz_R* 2qp1_R* 2rdo_R ... Length = 103

 Score = 42.1 bits (100), Expect = 6e-06
 Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 1/37 (2%)

Query: 138 FAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFER 174
           +AV Q G  Q +VS G ++  E+L      + + F  
Sbjct: 2   YAVFQSGGKQHRVSEGQTVRLEKLD-IATGETVEFAE 37

>2zjr_O 50S ribosomal protein L21; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.155.1.1 PDB: 1nwx_P* 1nwy_P* 1pnu_P 1pny_P 1sm1_P* 1vor_S 1vou_S 1vow_S 1voy_S 1vp0_S 1xbp_P* 1yl3_2 2b66_V 2b9n_V 2b9p_V 2zjp_O* 2zjq_O 1nkw_P 3cf5_O* 3dll_O* ... Length = 100

 Score = 40.6 bits (96), Expect = 2e-05
 Identities = 15/37 (40%), Positives = 22/37 (59%), Gaps = 1/37 (2%)

Query: 138 FAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFER 174
           FA++Q G  Q++VS GD I  E L+  E  DK+  + 
Sbjct: 2   FAIIQTGGKQYRVSEGDVIRVESLQ-GEAGDKVELKA 37

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	178
3r8s_R	103	50S ribosomal protein L21; protein biosynthesis, R	99.58
3v2d_V	101	50S ribosomal protein L21; ribosome associated inh	99.56
3bbo_T	257	Ribosomal protein L21; large ribosomal subunit, sp	99.48
2zjr_O	100	50S ribosomal protein L21; ribosome, large ribosom	99.48
2ivw_A	113	PILP pilot protein; lipoprotein, pilus biogenesis,	83.65
2lc4_A	111	PILP protein; type IV pilus, structural protein; N	83.42
2y4x_A	93	PILP protein; biosynthetic protein; 1.70A {Pseudom	82.72

>3r8s_R 50S ribosomal protein L21; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 1vs8_R 1vs6_R 2aw4_R 2awb_R 1vt2_R 2i2v_R 2j28_R 2i2t_R* 2qao_R* 2qba_R* 2qbc_R* 2qbe_R 2qbg_R 2qbi_R* 2qbk_R* 2qov_R 2qox_R 2qoz_R* 2qp1_R* 2rdo_R ...

Probab=99.58  E-value=1e-15  Score=115.60  Aligned_cols=41  Identities=27%  Similarity=0.466  Sum_probs=39.8

Q ss_pred             eEEEEeeCCeEEEEeCCCEEEecccCCCCCCCeEEecccccC
Q 030403          137 AFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPCWF  178 (178)
Q Consensus       137 MYAIVeiGGKQYKV~eGD~I~VErL~~aEvGdkI~LdkVLLv  178 (178)
                      |||||++|||||||++||+|+||+|+ +++|++|+|++|||+
T Consensus         1 MyAIi~~gGkQykV~~Gd~i~vekl~-~~~G~~v~~~~VLlv   41 (103)
T 3r8s_R            1 MYAVFQSGGKQHRVSEGQTVRLEKLD-IATGETVEFAEVLMI   41 (103)
T ss_dssp             CEEEEECSSSEEEEETTCEEEESCCC-SCTTCEEEECCEEEE
T ss_pred             CEEEEEECCEEEEEeCCCEEEECCcC-CCCCCEEEEeEEEEE
Confidence            99999999999999999999999997 899999999999985

>3v2d_V 50S ribosomal protein L21; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 1vsp_P 2hgj_U 2hgq_U 2hgu_U 1vsa_P 2j03_V 2jl6_V 2jl8_V 2v47_V 2v49_V 2wdi_V 2wdj_V 2wdl_V 2wdn_V 2wh2_V 2wh4_V 2wrj_V 2wrl_V 2wro_V 2wrr_V ...

Probab=99.56  E-value=2.7e-15  Score=113.25  Aligned_cols=40  Identities=25%  Similarity=0.451  Sum_probs=38.8

Q ss_pred             eEEEEeeCCeEEEEeCCCEEEecccCCCCCCCeEEecccccC
Q 030403          137 AFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPCWF  178 (178)
Q Consensus       137 MYAIVeiGGKQYKV~eGD~I~VErL~~aEvGdkI~LdkVLLv  178 (178)
                      |||||++|||||||++||+|+||+|+ +++|++|+|+ |||+
T Consensus         1 MyAIi~~gGkQykV~~Gd~i~vekl~-~~~G~~v~~~-VLlv   40 (101)
T 3v2d_V            1 MFAIVKTGGKQYRVEPGLKLRVEKLD-AEPGATVELP-VLLL   40 (101)
T ss_dssp             CEEEEEETTEEEEECTTCEEEESCCS-CCTTCEEEEC-EEEE
T ss_pred             CEEEEEeCCEEEEEeCCCEEEECCcC-CCCCCEEEEE-EEEE
Confidence            99999999999999999999999997 8999999999 9985

>3bbo_T Ribosomal protein L21; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=99.48  E-value=2.5e-15  Score=129.30  Aligned_cols=49  Identities=41%  Similarity=0.480  Sum_probs=40.6

Q ss_pred             ccccCCceEEEEeeCCeEEEEeCCCEEEecccCCCCCCCeEEecccccC
Q 030403          130 VFKKYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPCWF  178 (178)
Q Consensus       130 ~~k~~~~MYAIVeiGGKQYKV~eGD~I~VErL~~aEvGdkI~LdkVLLv  178 (178)
                      ..+.+++|||||++|||||||++||+|+|++|.++++|++|+|++|||+
T Consensus       117 ~~k~~~~MYAIIetGGKQYKV~~GD~I~VEKL~~aevGd~V~LdkVLlV  165 (257)
T 3bbo_T          117 PPPREEIIFAVVVIGSRQYIVIPGRWIYTQRLKGATVNDKIVLNKVLLV  165 (257)
T ss_dssp             -------CCCCCCSSSCCCCCCTTCCCCCCCCTTSCTTCEEECTTCCCB
T ss_pred             CCCcCCCeEEEEEECCEEEEEeCCCEEEEeCCCCCCCCCEEEEEEEEEE
Confidence            3556678999999999999999999999999976899999999999985

>2zjr_O 50S ribosomal protein L21; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.155.1.1 PDB: 1nwx_P* 1nwy_P* 1pnu_P 1pny_P 1sm1_P* 1vor_S 1vou_S 1vow_S 1voy_S 1vp0_S 1xbp_P* 1yl3_2 2b66_V 2b9n_V 2b9p_V 2zjp_O* 2zjq_O 1nkw_P 3cf5_O* 3dll_O* ...

Probab=99.48  E-value=2.9e-15  Score=112.65  Aligned_cols=40  Identities=38%  Similarity=0.661  Sum_probs=34.8

Q ss_pred             eEEEEeeCCeEEEEeCCCEEEecccCCCCCCCeEEecccccC
Q 030403          137 AFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPCWF  178 (178)
Q Consensus       137 MYAIVeiGGKQYKV~eGD~I~VErL~~aEvGdkI~LdkVLLv  178 (178)
                      |||||++|||||||++||+|+||+|+ +++|++|+|+ |||+
T Consensus         1 myAIi~~gGkQykV~~Gd~i~vekl~-~~~G~~v~~~-VLlv   40 (100)
T 2zjr_O            1 MFAIIQTGGKQYRVSEGDVIRVESLQ-GEAGDKVELK-ALFV   40 (100)
T ss_dssp             ----CCSSCCSCCSCCEEEEECCSCC-SSCCEEEECC-SCEE
T ss_pred             CEEEEEECCEEEEEeCCCEEEEcccC-CCCCCEEEEE-EEEE
Confidence            99999999999999999999999997 8999999999 9984

>2ivw_A PILP pilot protein; lipoprotein, pilus biogenesis, secretin; NMR {Neisseria meningitidis}

Probab=83.65  E-value=1.1  Score=34.19  Aligned_cols=33  Identities=12%  Similarity=0.250  Sum_probs=28.1

Q ss_pred             cEEecccccCccccccCCceEEEEeeCCeEEEEeCCCEEE
Q 030403          118 YKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIF  157 (178)
Q Consensus       118 ykvvg~~~~~~~~~k~~~~MYAIVeiGGKQYKV~eGD~I~  157 (178)
                      .|.||.|...       ...+|+|+..|+=|+|+.|++|=
T Consensus        27 LkmvGtl~~~-------~~~~ALV~~dG~vyrVk~G~yiG   59 (113)
T 2ivw_A           27 MRYVGILKSG-------QKVSGFIEAEGYVYTVGVGNYLG   59 (113)
T ss_dssp             EEEEEEEECS-------SSEEEEEEETTEEEEECSSEEET
T ss_pred             eEEEEEEccC-------CeEEEEEEeCCcEEEEccCCEec
Confidence            6888887664       45899999999999999999983

>2lc4_A PILP protein; type IV pilus, structural protein; NMR {Pseudomonas aeruginosa}

Probab=83.42  E-value=1.2  Score=33.78  Aligned_cols=34  Identities=24%  Similarity=0.412  Sum_probs=28.6

Q ss_pred             CcEEecccccCccccccCCceEEEEeeCCeEEEEeCCCEEE
Q 030403          117 GYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIF  157 (178)
Q Consensus       117 gykvvg~~~~~~~~~k~~~~MYAIVeiGGKQYKV~eGD~I~  157 (178)
                      -.+.||.|...       ..++|+|+..|+=|+|+.|++|=
T Consensus        30 ~L~mvG~l~~~-------~~~~ALV~~dG~vyrVk~G~ylG   63 (111)
T 2lc4_A           30 TFEMVGTLSNA-------QGTFALVKGAGGVHRVRVGDYLG   63 (111)
T ss_dssp             SCEEEEEEEET-------TEEEEEEEETTEEEEEETTCEET
T ss_pred             heEEEEEEccC-------CeEEEEEEeCCcEEEEccCCEec
Confidence            46888887664       45899999999999999999984

>2y4x_A PILP protein; biosynthetic protein; 1.70A {Pseudomonas aeruginosa PAO1} PDB: 2y4y_A

Probab=82.72  E-value=1.4  Score=32.31  Aligned_cols=34  Identities=24%  Similarity=0.412  Sum_probs=28.6

Q ss_pred             CcEEecccccCccccccCCceEEEEeeCCeEEEEeCCCEEE
Q 030403          117 GYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIF  157 (178)
Q Consensus       117 gykvvg~~~~~~~~~k~~~~MYAIVeiGGKQYKV~eGD~I~  157 (178)
                      -.|.||.|...       ..++|+|+..|+=|+|+.|++|=
T Consensus        23 ~L~mvG~l~~~-------~~~~ALV~~dg~v~~V~~G~yiG   56 (93)
T 2y4x_A           23 TFEMVGTLSNA-------QGTFALVKGAGGVHRVRVGDYLG   56 (93)
T ss_dssp             GCEEEEEEEET-------TEEEEEEEETTEEEEECTTCEET
T ss_pred             heEEEEEEccC-------CeEEEEEEeCCCEEEEccCCEec
Confidence            36888887664       45899999999999999999984

---

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	178
d2qamr1	103	b.155.1.1 (R:1-103) Ribosomal protein L21p {Escher	1e-07
d2j01v1	101	b.155.1.1 (V:1-101) Ribosomal protein L21p {Thermu	1e-06
d2zjro1	94	b.155.1.1 (O:5-98) Ribosomal protein L21p {Deinoco	3e-04

>d2qamr1 b.155.1.1 (R:1-103) Ribosomal protein L21p {Escherichia coli [TaxId: 562]} Length = 103

class: All beta proteins
fold: L21p-like
superfamily: L21p-like
family: Ribosomal protein L21p
domain: Ribosomal protein L21p
species: Escherichia coli [TaxId: 562]

 Score = 45.9 bits (109), Expect = 1e-07
 Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 1/41 (2%)

Query: 138 FAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPCWF 178
           +AV Q G  Q +VS G ++  E+L      + + F      
Sbjct: 2   YAVFQSGGKQHRVSEGQTVRLEKLD-IATGETVEFAEVLMI 41

>d2j01v1 b.155.1.1 (V:1-101) Ribosomal protein L21p {Thermus thermophilus [TaxId: 274]} Length = 101

class: All beta proteins
fold: L21p-like
superfamily: L21p-like
family: Ribosomal protein L21p
domain: Ribosomal protein L21p
species: Thermus thermophilus [TaxId: 274]

 Score = 42.9 bits (101), Expect = 1e-06
 Identities = 10/39 (25%), Positives = 17/39 (43%), Gaps = 1/39 (2%)

Query: 138 FAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPC 176
           FA+V+ G  Q++V  G  +  E+L   E    +      
Sbjct: 2   FAIVKTGGKQYRVEPGLKLRVEKLD-AEPGATVELPVLL 39

>d2zjro1 b.155.1.1 (O:5-98) Ribosomal protein L21p {Deinococcus radiodurans [TaxId: 1299]} Length = 94

class: All beta proteins
fold: L21p-like
superfamily: L21p-like
family: Ribosomal protein L21p
domain: Ribosomal protein L21p
species: Deinococcus radiodurans [TaxId: 1299]

 Score = 36.3 bits (84), Expect = 3e-04
 Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 1/34 (2%)

Query: 141 VQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFER 174
           +Q G  Q++VS GD I  E L+  E  DK+  + 
Sbjct: 1   IQTGGKQYRVSEGDVIRVESLQ-GEAGDKVELKA 33

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	178
d2qamr1	103	Ribosomal protein L21p {Escherichia coli [TaxId: 5	99.48
d2j01v1	101	Ribosomal protein L21p {Thermus thermophilus [TaxI	99.34
d2zjro1	94	Ribosomal protein L21p {Deinococcus radiodurans [T	98.96

>d2qamr1 b.155.1.1 (R:1-103) Ribosomal protein L21p {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: L21p-like
superfamily: L21p-like
family: Ribosomal protein L21p
domain: Ribosomal protein L21p
species: Escherichia coli [TaxId: 562]

Probab=99.48  E-value=2.2e-15  Score=111.78  Aligned_cols=41  Identities=27%  Similarity=0.466  Sum_probs=39.8

Q ss_pred             eEEEEeeCCeEEEEeCCCEEEecccCCCCCCCeEEecccccC
Q 030403          137 AFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPCWF  178 (178)
Q Consensus       137 MYAIVeiGGKQYKV~eGD~I~VErL~~aEvGdkI~LdkVLLv  178 (178)
                      |||||++|||||||++||+|.||+|. +++|++|+|++|||+
T Consensus         1 MyAIi~~gGkQykV~~Gd~i~v~~l~-~~~G~~i~~~~VLlv   41 (103)
T d2qamr1           1 MYAVFQSGGKQHRVSEGQTVRLEKLD-IATGETVEFAEVLMI   41 (103)
T ss_dssp             CCCCCCSSSSCCCCCSSCCEEESCCC-CCTTCEEEECCCSCC
T ss_pred             CEEEEEECCEEEEEcCCCEEEEeccC-CCCCCcEEehhheEc
Confidence            99999999999999999999999996 899999999999986

>d2j01v1 b.155.1.1 (V:1-101) Ribosomal protein L21p {Thermus thermophilus [TaxId: 274]}

class: All beta proteins
fold: L21p-like
superfamily: L21p-like
family: Ribosomal protein L21p
domain: Ribosomal protein L21p
species: Thermus thermophilus [TaxId: 274]

Probab=99.34  E-value=7.4e-14  Score=103.00  Aligned_cols=40  Identities=25%  Similarity=0.414  Sum_probs=37.9

Q ss_pred             eEEEEeeCCeEEEEeCCCEEEecccCCCCCCCeEEeccccc
Q 030403          137 AFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPCW  177 (178)
Q Consensus       137 MYAIVeiGGKQYKV~eGD~I~VErL~~aEvGdkI~LdkVLL  177 (178)
                      |||||++|||||||++||+|.||++. +++|+.|+|+.||+
T Consensus         1 MyAVi~~gGkQykV~~Gd~l~v~~l~-~~~g~~v~~~~ll~   40 (101)
T d2j01v1           1 MFAIVKTGGKQYRVEPGLKLRVEKLD-AEPGATVELPVLLL   40 (101)
T ss_dssp             CCCEEEETTEEEECCSSCCCCCCCCS-CCSSSCCBCCCCSC
T ss_pred             CEEEEEECCEEEEEcCCCEEEEeccc-CCCCccEEEEEEEE
Confidence            99999999999999999999999997 89999999997665

>d2zjro1 b.155.1.1 (O:5-98) Ribosomal protein L21p {Deinococcus radiodurans [TaxId: 1299]}

class: All beta proteins
fold: L21p-like
superfamily: L21p-like
family: Ribosomal protein L21p
domain: Ribosomal protein L21p
species: Deinococcus radiodurans [TaxId: 1299]

Probab=98.96  E-value=3.2e-11  Score=87.68  Aligned_cols=36  Identities=36%  Similarity=0.544  Sum_probs=34.2

Q ss_pred             EeeCCeEEEEeCCCEEEecccCCCCCCCeEEeccccc
Q 030403          141 VQIGSHQFKVSNGDSIFTERLKFCEVNDKLSFERPCW  177 (178)
Q Consensus       141 VeiGGKQYKV~eGD~I~VErL~~aEvGdkI~LdkVLL  177 (178)
                      |++|||||||++||+|.||+|. +++|++|+|+.|||
T Consensus         1 I~tGGKQykV~~Gd~i~vekl~-~~~G~~i~~~~vl~   36 (94)
T d2zjro1           1 IQTGGKQYRVSEGDVIRVESLQ-GEAGDKVELKALFV   36 (94)
T ss_dssp             CCSSCCSCCSCCEEEEECCSCC-SSCCEEEECCSCEE
T ss_pred             CccCCEEEEEcCCCEEEEeccc-CccCCceEEeeeEE
Confidence            6899999999999999999997 89999999999987