Psyllid ID: psy14782

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------
Protein Sequence
MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYGSWKTKAPLKKGYSLPQPKMANTKQRVM
Secondary Structure (PSIPRED)
ccccccccccccEEEEEccccHHHHHccccccEEEccccccccccccccccccEEEEEHHHHHHHHHHHcccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccEEEccccEEEEcccccHHHHHccccccEEEEHHHHcHHEcccccccEEEEEEcHHHHHHHHHHHcccccHHHHccccccccccccccccccc
Coil and Loop (DISEMBL)
mrnrrriqrrgplvvygkdrgltkafrniPGVELISVSklnllklapgghvgrFVIWTESAFKKLDALYGswktkaplkkgyslpqpkmantkqrvm
Flexible Loop (DISEMBL)
mrnrrriqrrgplvvygkdrgltkafRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYGSWKtkaplkkgyslpqpkmantkqrvm
Low Complexity Region (SEG)
MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYGSWKTKAPLKKGYSLPQPKMANTKQRVM
Disordered region (IsUnstruct)
***********PLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYGSWKTKA*********************
Disordered Region (DISOPRED)
*******QRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYGSWKTKAPL*KGYSLPQPKMANTKQRVM
Disordered Region (DISEMBL)
********RRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYGSWKTKAPLKKGYSLPQPK*********
Disordered Region (DISPRO)
****RRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYGSWKTKAPLKKGYSLPQPK*********
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYGSWKTKAPLKKGYSLPQPKMANTKQRVM
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	97	2.2.26 [Sep-21-2011]
P49165	386	60S ribosomal protein L4	N/A	N/A	0.948	0.238	0.652	2e-33
P09180	401	60S ribosomal protein L4	yes	N/A	0.845	0.204	0.780	3e-33
Q5RCR3	427	60S ribosomal protein L4	yes	N/A	0.845	0.192	0.670	2e-29
P35679	363	60S ribosomal protein L4-	yes	N/A	0.948	0.253	0.619	2e-29
P50878	421	60S ribosomal protein L4	yes	N/A	0.845	0.194	0.670	2e-29
Q4R5P9	427	60S ribosomal protein L4	N/A	N/A	0.845	0.192	0.670	2e-29
P36578	427	60S ribosomal protein L4	yes	N/A	0.845	0.192	0.670	2e-29
Q9D8E6	419	60S ribosomal protein L4	yes	N/A	0.845	0.195	0.670	2e-29
P08429	396	60S ribosomal protein L4-	N/A	N/A	0.845	0.207	0.682	2e-29
Q58DW0	422	60S ribosomal protein L4	yes	N/A	0.845	0.194	0.670	2e-29

>sp|P49165|RL4_URECA 60S ribosomal protein L4 OS=Urechis caupo GN=RPL4 PE=2 SV=1

 Score =  140 bits (354), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 60/92 (65%), Positives = 77/92 (83%)

Query: 1   MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
           +RNRR IQRRGPL++YG D G+++AFRNIPG+ L++V++LNLL +APGGHVGRF IWTES
Sbjct: 195 LRNRRAIQRRGPLIIYGTDNGISRAFRNIPGITLVNVNRLNLLSMAPGGHVGRFCIWTES 254

Query: 61  AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
           AFK+LD +YG+WK  +  K  Y+LP PKM NT
Sbjct: 255 AFKQLDNIYGTWKRPSAEKSHYNLPMPKMTNT 286

Urechis caupo (taxid: 6431)

>sp|P09180|RL4_DROME 60S ribosomal protein L4 OS=Drosophila melanogaster GN=RpL4 PE=2 SV=2

 Score =  140 bits (352), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 64/82 (78%), Positives = 72/82 (87%)

Query: 11  GPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYG 70
           GPLVVY KD GL KAFRNIPG+E I+V KLNLLKLAPGGHVGRFVIWTESAF +L+ L+G
Sbjct: 209 GPLVVYDKDEGLRKAFRNIPGIETINVDKLNLLKLAPGGHVGRFVIWTESAFARLNDLFG 268

Query: 71  SWKTKAPLKKGYSLPQPKMANT 92
           +WK  + LKKGY+LPQPKMANT
Sbjct: 269 TWKKPSTLKKGYNLPQPKMANT 290

Drosophila melanogaster (taxid: 7227)

>sp|Q5RCR3|RL4_PONAB 60S ribosomal protein L4 OS=Pongo abelii GN=RPL4 PE=2 SV=1

 Score =  127 bits (319), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 55/82 (67%), Positives = 67/82 (81%)

Query: 11  GPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYG 70
           GP ++Y +D G+ KAFRNIPG+ L++VSKLN+LKLAPGGHVGRF IWTESAF+KLD LYG
Sbjct: 206 GPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTESAFRKLDELYG 265

Query: 71  SWKTKAPLKKGYSLPQPKMANT 92
           +W+  A LK  Y+LP  KM NT
Sbjct: 266 TWRKAASLKSNYNLPMHKMINT 287

Pongo abelii (taxid: 9601)

>sp|P35679|RL4A_SCHPO 60S ribosomal protein L4-A OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpl4a PE=1 SV=2

 Score =  127 bits (319), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 57/92 (61%), Positives = 75/92 (81%)

Query: 1   MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
           +RNRR +QRRGPLVV+ +D G+ KAFRNIPGVE+++V +LNLL+LAPGGH+GRFVIWT+S
Sbjct: 196 LRNRRHVQRRGPLVVFNEDAGIVKAFRNIPGVEIVNVRRLNLLQLAPGGHLGRFVIWTKS 255

Query: 61  AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
           AF  LD+++GS    A LKK Y LP+  ++N 
Sbjct: 256 AFGLLDSVFGSTTEAAQLKKNYFLPENIISNA 287

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

>sp|P50878|RL4_RAT 60S ribosomal protein L4 OS=Rattus norvegicus GN=Rpl4 PE=1 SV=3

 Score =  127 bits (319), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 55/82 (67%), Positives = 67/82 (81%)

Query: 11  GPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYG 70
           GP ++Y +D G+ KAFRNIPG+ L++VSKLN+LKLAPGGHVGRF IWTESAF+KLD LYG
Sbjct: 206 GPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTESAFRKLDELYG 265

Query: 71  SWKTKAPLKKGYSLPQPKMANT 92
           +W+  A LK  Y+LP  KM NT
Sbjct: 266 TWRKAASLKSNYNLPMHKMMNT 287

Rattus norvegicus (taxid: 10116)

>sp|Q4R5P9|RL4_MACFA 60S ribosomal protein L4 OS=Macaca fascicularis GN=RPL4 PE=2 SV=1

 Score =  127 bits (319), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 55/82 (67%), Positives = 67/82 (81%)

Query: 11  GPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYG 70
           GP ++Y +D G+ KAFRNIPG+ L++VSKLN+LKLAPGGHVGRF IWTESAF+KLD LYG
Sbjct: 206 GPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTESAFRKLDELYG 265

Query: 71  SWKTKAPLKKGYSLPQPKMANT 92
           +W+  A LK  Y+LP  KM NT
Sbjct: 266 TWRKAASLKSNYNLPMHKMINT 287

Macaca fascicularis (taxid: 9541)

>sp|P36578|RL4_HUMAN 60S ribosomal protein L4 OS=Homo sapiens GN=RPL4 PE=1 SV=5

 Score =  127 bits (319), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 55/82 (67%), Positives = 67/82 (81%)

Query: 11  GPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYG 70
           GP ++Y +D G+ KAFRNIPG+ L++VSKLN+LKLAPGGHVGRF IWTESAF+KLD LYG
Sbjct: 206 GPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTESAFRKLDELYG 265

Query: 71  SWKTKAPLKKGYSLPQPKMANT 92
           +W+  A LK  Y+LP  KM NT
Sbjct: 266 TWRKAASLKSNYNLPMHKMINT 287

Homo sapiens (taxid: 9606)

>sp|Q9D8E6|RL4_MOUSE 60S ribosomal protein L4 OS=Mus musculus GN=Rpl4 PE=1 SV=3

 Score =  127 bits (318), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 55/82 (67%), Positives = 67/82 (81%)

Query: 11  GPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYG 70
           GP ++Y +D G+ KAFRNIPG+ L++VSKLN+LKLAPGGHVGRF IWTESAF+KLD LYG
Sbjct: 206 GPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTESAFRKLDELYG 265

Query: 71  SWKTKAPLKKGYSLPQPKMANT 92
           +W+  A LK  Y+LP  KM NT
Sbjct: 266 TWRKAASLKSNYNLPMHKMMNT 287

Mus musculus (taxid: 10090)

>sp|P08429|RL4A_XENLA 60S ribosomal protein L4-A OS=Xenopus laevis GN=rpl4-a PE=2 SV=2

 Score =  127 bits (318), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 56/82 (68%), Positives = 67/82 (81%)

Query: 11  GPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYG 70
           GP V+Y ++ GL KAFRNIPG+ L++VSKLNLL+LAPGGHVGRF IWTESAF+KLD LYG
Sbjct: 210 GPCVIYNENNGLVKAFRNIPGITLLNVSKLNLLRLAPGGHVGRFCIWTESAFRKLDDLYG 269

Query: 71  SWKTKAPLKKGYSLPQPKMANT 92
           +W+  A LK  Y+LP  KM NT
Sbjct: 270 TWRKSAKLKADYNLPMHKMTNT 291

Xenopus laevis (taxid: 8355)

>sp|Q58DW0|RL4_BOVIN 60S ribosomal protein L4 OS=Bos taurus GN=RPL4 PE=2 SV=3

 Score =  127 bits (318), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 55/82 (67%), Positives = 67/82 (81%)

Query: 11  GPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYG 70
           GP ++Y +D G+ KAFRNIPG+ L++VSKLN+LKLAPGGHVGRF IWTESAF+KLD LYG
Sbjct: 206 GPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTESAFRKLDELYG 265

Query: 71  SWKTKAPLKKGYSLPQPKMANT 92
           +W+  A LK  Y+LP  KM NT
Sbjct: 266 TWRKAASLKSNYNLPMHKMLNT 287

Bos taurus (taxid: 9913)

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	97
70909603	404	ribosomal protein L4e [Biphyllus lunatus	0.948	0.227	0.782	7e-38
315115489	308	ribosomal protein L4 [Euphydryas aurinia	0.948	0.298	0.760	1e-37
342356435	424	ribosomal protein L4 [Heliconius melpome	0.948	0.216	0.760	2e-37
62083421	429	ribosomal protein L4 [Lysiphlebus testac	0.948	0.214	0.760	2e-37
268306392	439	ribosomal protein L4 [Manduca sexta]	0.948	0.209	0.739	6e-37
348019681	396	ribosomal protein L4 [Biston betularia]	0.948	0.232	0.760	6e-37
264667431	207	ribosomal protein L4 [Chrysomela tremula	0.938	0.439	0.769	4e-36
326493892	459	predicted protein [Hordeum vulgare subsp	0.948	0.200	0.75	4e-36
389608169	420	ribosomal protein L4 [Papilio xuthus]	0.948	0.219	0.75	6e-36
389610681	417	ribosomal protein L4 [Papilio polytes]	0.948	0.220	0.75	6e-36

>gi|70909603|emb|CAJ17227.1| ribosomal protein L4e [Biphyllus lunatus]

 Score =  160 bits (406), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 72/92 (78%), Positives = 86/92 (93%)

Query: 1   MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
           MRNRRRIQR+GPLVVY KD GL +AFRNIPG++LISV KL+LLKLAPGGHVGRFVIWTES
Sbjct: 199 MRNRRRIQRKGPLVVYSKDDGLRRAFRNIPGIDLISVDKLSLLKLAPGGHVGRFVIWTES 258

Query: 61  AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
           AF+KLD+++G+WK+ + +KKGY+LPQPKMANT
Sbjct: 259 AFQKLDSIFGNWKSSSTVKKGYNLPQPKMANT 290

Source: Biphyllus lunatus

Species: Biphyllus lunatus

Genus: Biphyllus

Family: Biphyllidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|315115489|gb|ADT80717.1| ribosomal protein L4 [Euphydryas aurinia]

 Score =  160 bits (404), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 70/92 (76%), Positives = 87/92 (94%)

Query: 1   MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
           MRNRRR+QR+GPL++Y KD+GLTKAFRNIPGVE++SV+KLNLLKLAPGGH+GRF+IWT+S
Sbjct: 88  MRNRRRLQRKGPLIIYHKDQGLTKAFRNIPGVEMLSVNKLNLLKLAPGGHLGRFIIWTQS 147

Query: 61  AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
           AF++LDAL+GSWKT +  KK ++LPQPKMANT
Sbjct: 148 AFERLDALFGSWKTPSKEKKNFNLPQPKMANT 179

Source: Euphydryas aurinia

Species: Euphydryas aurinia

Genus: Euphydryas

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|342356435|gb|AEL28876.1| ribosomal protein L4 [Heliconius melpomene cythera]

 Score =  159 bits (403), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 70/92 (76%), Positives = 87/92 (94%)

Query: 1   MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
           MRNRRR+QR+GPL++Y KD+GL+KAFRNIPGVE++SV+KLNLLKLAPGGHVGRF+IWT+S
Sbjct: 199 MRNRRRVQRKGPLIIYHKDKGLSKAFRNIPGVEMLSVNKLNLLKLAPGGHVGRFIIWTQS 258

Query: 61  AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
           AFK+LD L+GSWK+ + LKK ++LPQPKMANT
Sbjct: 259 AFKRLDNLFGSWKSPSKLKKNFNLPQPKMANT 290

Source: Heliconius melpomene cythera

Species: Heliconius melpomene

Genus: Heliconius

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|62083421|gb|AAX62435.1| ribosomal protein L4 [Lysiphlebus testaceipes]

 Score =  159 bits (402), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 70/92 (76%), Positives = 86/92 (93%)

Query: 1   MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
           MRNRR +QRRGPL++YG+D+GL KAFRNIPGV+L++V+K+NLLKLAPGGHVGRFVIWT+S
Sbjct: 198 MRNRRHVQRRGPLIIYGQDKGLKKAFRNIPGVDLMNVNKMNLLKLAPGGHVGRFVIWTKS 257

Query: 61  AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
           AF KLDALYG+W+ ++ LKKGY+LP PKMANT
Sbjct: 258 AFDKLDALYGTWRKESTLKKGYNLPYPKMANT 289

Source: Lysiphlebus testaceipes

Species: Lysiphlebus testaceipes

Genus: Lysiphlebus

Family: Braconidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|268306392|gb|ACY95317.1| ribosomal protein L4 [Manduca sexta]

 Score =  157 bits (398), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 68/92 (73%), Positives = 87/92 (94%)

Query: 1   MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
           MRNRRR+QR+GPL++Y KD+GL++AFRNIPGVE+++V+KLNLLKLAPGGH+GRF+IWT+S
Sbjct: 199 MRNRRRVQRKGPLIIYHKDKGLSRAFRNIPGVEMLNVNKLNLLKLAPGGHLGRFIIWTQS 258

Query: 61  AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
           AF +LDAL+GSWKT + LKK ++LPQPKMANT
Sbjct: 259 AFDRLDALFGSWKTPSKLKKNFNLPQPKMANT 290

Source: Manduca sexta

Species: Manduca sexta

Genus: Manduca

Family: Sphingidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|348019681|gb|AEP43782.1| ribosomal protein L4 [Biston betularia]

 Score =  157 bits (398), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 70/92 (76%), Positives = 85/92 (92%)

Query: 1   MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
           MRNRRR+QR+GPL+VY KD+GLT+AFRNIPGVE+++V KLNLLKLAPGGHVGRF+IWT+S
Sbjct: 199 MRNRRRVQRKGPLIVYHKDQGLTRAFRNIPGVEMLNVDKLNLLKLAPGGHVGRFIIWTQS 258

Query: 61  AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
           AF +LDAL+GSWKT +  KK ++LPQPKMANT
Sbjct: 259 AFDRLDALFGSWKTPSKEKKNFNLPQPKMANT 290

Source: Biston betularia

Species: Biston betularia

Genus: Biston

Family: Geometridae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|264667431|gb|ACY71301.1| ribosomal protein L4 [Chrysomela tremula]

 Score =  155 bits (391), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 70/91 (76%), Positives = 82/91 (90%)

Query: 2  RNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESA 61
          RNRRRIQR+GPLVVY KD+GL +AFRNIPG++L+ V KLNLLKLAPGGHVGRFVIWTESA
Sbjct: 1  RNRRRIQRKGPLVVYHKDQGLRRAFRNIPGIDLVGVDKLNLLKLAPGGHVGRFVIWTESA 60

Query: 62 FKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
          F +LD L+G+WKT +  KKGY+LPQPKM+NT
Sbjct: 61 FARLDKLFGNWKTPSAEKKGYNLPQPKMSNT 91

Source: Chrysomela tremula

Species: Chrysomela tremula

Genus: Chrysomela

Family: Chrysomelidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|326493892|dbj|BAJ85408.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  155 bits (391), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 69/92 (75%), Positives = 82/92 (89%)

Query: 1   MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
           MRNRR +QRRGPL+VY KD+GL KAFRNIPGV+LI++ KLNLL LAPGGHVGRF+IWT+S
Sbjct: 198 MRNRRHVQRRGPLIVYSKDQGLRKAFRNIPGVDLINIRKLNLLHLAPGGHVGRFIIWTQS 257

Query: 61  AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
           AF+KLD+LYG+W  KA LK GY+LP PKM+NT
Sbjct: 258 AFQKLDSLYGTWDKKATLKSGYNLPFPKMSNT 289

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|389608169|dbj|BAM17696.1| ribosomal protein L4 [Papilio xuthus]

 Score =  154 bits (390), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 69/92 (75%), Positives = 84/92 (91%)

Query: 1   MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
           MRNRRRIQR+GPL+VY KD+GLT+AFRNIPGV+++ V KLNLLKLAPGGHVGRF+IWT+S
Sbjct: 199 MRNRRRIQRKGPLIVYHKDQGLTRAFRNIPGVDMLKVDKLNLLKLAPGGHVGRFIIWTKS 258

Query: 61  AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
           AF++LD L+GSWKT +  KK ++LPQPKMANT
Sbjct: 259 AFERLDPLFGSWKTPSKEKKNFNLPQPKMANT 290

Source: Papilio xuthus

Species: Papilio xuthus

Genus: Papilio

Family: Papilionidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|389610681|dbj|BAM18952.1| ribosomal protein L4 [Papilio polytes]

 Score =  154 bits (389), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 69/92 (75%), Positives = 84/92 (91%)

Query: 1   MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
           MRNRRRIQR+GPL+VY KD+GLT+AFRNIPGV+++ V KLNLLKLAPGGHVGRF+IWT+S
Sbjct: 199 MRNRRRIQRKGPLIVYHKDQGLTRAFRNIPGVDMLKVDKLNLLKLAPGGHVGRFIIWTKS 258

Query: 61  AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
           AF++LD L+GSWKT +  KK ++LPQPKMANT
Sbjct: 259 AFERLDPLFGSWKTPSKEKKNFNLPQPKMANT 290

Source: Papilio polytes

Species: Papilio polytes

Genus: Papilio

Family: Papilionidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	97
FB|FBgn0003279	401	RpL4 "Ribosomal protein L4" [D	0.948	0.229	0.782	1.5e-35
UNIPROTKB|Q58DW0	422	RPL4 "60S ribosomal protein L4	0.948	0.218	0.706	2.5e-33
UNIPROTKB|H3BM89	333	RPL4 "Ribosomal protein L4, is	0.948	0.276	0.706	2.5e-33
UNIPROTKB|P36578	427	RPL4 "60S ribosomal protein L4	0.948	0.215	0.706	2.5e-33
UNIPROTKB|F1SJJ5	426	RPL4 "60S ribosomal protein L4	0.948	0.215	0.706	2.5e-33
MGI|MGI:1915141	419	Rpl4 "ribosomal protein L4" [M	0.948	0.219	0.706	2.5e-33
RGD|619824	421	Rpl4 "ribosomal protein L4" [R	0.948	0.218	0.706	2.5e-33
UNIPROTKB|Q6P3V9	421	Rpl4 "Ribosomal protein L4" [R	0.948	0.218	0.706	2.5e-33
UNIPROTKB|E2R546	412	RPL4 "60S ribosomal protein L4	0.948	0.223	0.706	3.2e-33
UNIPROTKB|F1PVZ2	422	RPL4 "60S ribosomal protein L4	0.948	0.218	0.706	3.2e-33

FB|FBgn0003279 RpL4 "Ribosomal protein L4" [Drosophila melanogaster (taxid:7227)]

 Score = 384 (140.2 bits), Expect = 1.5e-35, P = 1.5e-35
 Identities = 72/92 (78%), Positives = 81/92 (88%)

Query:     1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
             MR+RRRI RRGPLVVY KD GL KAFRNIPG+E I+V KLNLLKLAPGGHVGRFVIWTES
Sbjct:   199 MRDRRRIARRGPLVVYDKDEGLRKAFRNIPGIETINVDKLNLLKLAPGGHVGRFVIWTES 258

Query:    61 AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
             AF +L+ L+G+WK  + LKKGY+LPQPKMANT
Sbjct:   259 AFARLNDLFGTWKKPSTLKKGYNLPQPKMANT 290

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

GO:0022625 "cytosolic large ribosomal subunit" evidence=ISS

GO:0006412 "translation" evidence=ISS

GO:0005811 "lipid particle" evidence=IDA

GO:0005840 "ribosome" evidence=IDA

GO:0051298 "centrosome duplication" evidence=IMP

UNIPROTKB|Q58DW0 RPL4 "60S ribosomal protein L4" [Bos taurus (taxid:9913)]

 Score = 363 (132.8 bits), Expect = 2.5e-33, P = 2.5e-33
 Identities = 65/92 (70%), Positives = 77/92 (83%)

Query:     1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
             MRNRRRIQRRGP ++Y +D G+ KAFRNIPG+ L++VSKLN+LKLAPGGHVGRF IWTES
Sbjct:   196 MRNRRRIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTES 255

Query:    61 AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
             AF+KLD LYG+W+  A LK  Y+LP  KM NT
Sbjct:   256 AFRKLDELYGTWRKAASLKSNYNLPMHKMLNT 287

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|H3BM89 RPL4 "Ribosomal protein L4, isoform CRA_a" [Homo sapiens (taxid:9606)]

 Score = 363 (132.8 bits), Expect = 2.5e-33, P = 2.5e-33
 Identities = 65/92 (70%), Positives = 77/92 (83%)

Query:     1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
             MRNRRRIQRRGP ++Y +D G+ KAFRNIPG+ L++VSKLN+LKLAPGGHVGRF IWTES
Sbjct:   102 MRNRRRIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTES 161

Query:    61 AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
             AF+KLD LYG+W+  A LK  Y+LP  KM NT
Sbjct:   162 AFRKLDELYGTWRKAASLKSNYNLPMHKMINT 193

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

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

UNIPROTKB|P36578 RPL4 "60S ribosomal protein L4" [Homo sapiens (taxid:9606)]

 Score = 363 (132.8 bits), Expect = 2.5e-33, P = 2.5e-33
 Identities = 65/92 (70%), Positives = 77/92 (83%)

Query:     1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
             MRNRRRIQRRGP ++Y +D G+ KAFRNIPG+ L++VSKLN+LKLAPGGHVGRF IWTES
Sbjct:   196 MRNRRRIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTES 255

Query:    61 AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
             AF+KLD LYG+W+  A LK  Y+LP  KM NT
Sbjct:   256 AFRKLDELYGTWRKAASLKSNYNLPMHKMINT 287

GO:0006412 "translation" evidence=NAS;TAS

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

GO:0022625 "cytosolic large ribosomal subunit" evidence=IDA

GO:0003723 "RNA binding" evidence=TAS

GO:0030529 "ribonucleoprotein complex" evidence=IDA

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006413 "translational initiation" evidence=TAS

GO:0006414 "translational elongation" evidence=TAS

GO:0006415 "translational termination" evidence=TAS

GO:0006614 "SRP-dependent cotranslational protein targeting to membrane" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0019058 "viral infectious cycle" evidence=TAS

GO:0019083 "viral transcription" evidence=TAS

GO:0044267 "cellular protein metabolic process" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|F1SJJ5 RPL4 "60S ribosomal protein L4" [Sus scrofa (taxid:9823)]

 Score = 363 (132.8 bits), Expect = 2.5e-33, P = 2.5e-33
 Identities = 65/92 (70%), Positives = 77/92 (83%)

Query:     1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
             MRNRRRIQRRGP ++Y +D G+ KAFRNIPG+ L++VSKLN+LKLAPGGHVGRF IWTES
Sbjct:   196 MRNRRRIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTES 255

Query:    61 AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
             AF+KLD LYG+W+  A LK  Y+LP  KM NT
Sbjct:   256 AFRKLDELYGTWRKAATLKSNYNLPMHKMLNT 287

GO:0022625 "cytosolic large ribosomal subunit" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

MGI|MGI:1915141 Rpl4 "ribosomal protein L4" [Mus musculus (taxid:10090)]

 Score = 363 (132.8 bits), Expect = 2.5e-33, P = 2.5e-33
 Identities = 65/92 (70%), Positives = 77/92 (83%)

Query:     1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
             MRNRRRIQRRGP ++Y +D G+ KAFRNIPG+ L++VSKLN+LKLAPGGHVGRF IWTES
Sbjct:   196 MRNRRRIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTES 255

Query:    61 AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
             AF+KLD LYG+W+  A LK  Y+LP  KM NT
Sbjct:   256 AFRKLDELYGTWRKAASLKSNYNLPMHKMMNT 287

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

GO:0005515 "protein binding" evidence=IPI

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0015934 "large ribosomal subunit" evidence=ISO

GO:0022625 "cytosolic large ribosomal subunit" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=ISO

RGD|619824 Rpl4 "ribosomal protein L4" [Rattus norvegicus (taxid:10116)]

 Score = 363 (132.8 bits), Expect = 2.5e-33, P = 2.5e-33
 Identities = 65/92 (70%), Positives = 77/92 (83%)

Query:     1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
             MRNRRRIQRRGP ++Y +D G+ KAFRNIPG+ L++VSKLN+LKLAPGGHVGRF IWTES
Sbjct:   196 MRNRRRIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTES 255

Query:    61 AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
             AF+KLD LYG+W+  A LK  Y+LP  KM NT
Sbjct:   256 AFRKLDELYGTWRKAASLKSNYNLPMHKMMNT 287

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO

GO:0005730 "nucleolus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0015934 "large ribosomal subunit" evidence=IDA

GO:0022625 "cytosolic large ribosomal subunit" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=ISO

UNIPROTKB|Q6P3V9 Rpl4 "Ribosomal protein L4" [Rattus norvegicus (taxid:10116)]

 Score = 363 (132.8 bits), Expect = 2.5e-33, P = 2.5e-33
 Identities = 65/92 (70%), Positives = 77/92 (83%)

Query:     1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
             MRNRRRIQRRGP ++Y +D G+ KAFRNIPG+ L++VSKLN+LKLAPGGHVGRF IWTES
Sbjct:   196 MRNRRRIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTES 255

Query:    61 AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
             AF+KLD LYG+W+  A LK  Y+LP  KM NT
Sbjct:   256 AFRKLDELYGTWRKAASLKSNYNLPMHKMMNT 287

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

GO:0006412 "translation" evidence=IEA

UNIPROTKB|E2R546 RPL4 "60S ribosomal protein L4" [Canis lupus familiaris (taxid:9615)]

 Score = 362 (132.5 bits), Expect = 3.2e-33, P = 3.2e-33
 Identities = 65/92 (70%), Positives = 77/92 (83%)

Query:     1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
             MRNRRRIQRRGP ++Y +D G+ KAFRNIPG+ L++VSKLN+LKLAPGGHVGRF IWTES
Sbjct:   196 MRNRRRIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTES 255

Query:    61 AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
             AF+KLD LYG+W+  A LK  Y+LP  KM NT
Sbjct:   256 AFRKLDDLYGTWRKAASLKSNYNLPMHKMLNT 287

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

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

UNIPROTKB|F1PVZ2 RPL4 "60S ribosomal protein L4" [Canis lupus familiaris (taxid:9615)]

 Score = 362 (132.5 bits), Expect = 3.2e-33, P = 3.2e-33
 Identities = 65/92 (70%), Positives = 77/92 (83%)

Query:     1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
             MRNRRRIQRRGP ++Y +D G+ KAFRNIPG+ L++VSKLN+LKLAPGGHVGRF IWTES
Sbjct:   196 MRNRRRIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTES 255

Query:    61 AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
             AF+KLD LYG+W+  A LK  Y+LP  KM NT
Sbjct:   256 AFRKLDDLYGTWRKAASLKSNYNLPMHKMLNT 287

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P50878	RL4_RAT	No assigned EC number	0.6707	0.8453	0.1947	yes	N/A
Q58DW0	RL4_BOVIN	No assigned EC number	0.6707	0.8453	0.1943	yes	N/A
Q5RCR3	RL4_PONAB	No assigned EC number	0.6707	0.8453	0.1920	yes	N/A
Q28346	RL4_CANFA	No assigned EC number	0.6463	0.8453	0.1947	yes	N/A
P49691	RL4B_ARATH	No assigned EC number	0.6344	0.9484	0.2260	yes	N/A
P36578	RL4_HUMAN	No assigned EC number	0.6707	0.8453	0.1920	yes	N/A
Q9P784	RL4B_SCHPO	No assigned EC number	0.6195	0.9484	0.2534	yes	N/A
P10664	RL4A_YEAST	No assigned EC number	0.6547	0.8556	0.2292	yes	N/A
Q9D8E6	RL4_MOUSE	No assigned EC number	0.6707	0.8453	0.1957	yes	N/A
O02056	RL4_CAEEL	No assigned EC number	0.5913	0.9484	0.2666	yes	N/A
P09180	RL4_DROME	No assigned EC number	0.7804	0.8453	0.2044	yes	N/A
Q54Z69	RL4_DICDI	No assigned EC number	0.5777	0.9278	0.2439	yes	N/A
P49626	RL4B_YEAST	No assigned EC number	0.6547	0.8556	0.2292	yes	N/A
P35679	RL4A_SCHPO	No assigned EC number	0.6195	0.9484	0.2534	yes	N/A
Q9SF40	RL4A_ARATH	No assigned EC number	0.6451	0.9484	0.2266	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	97
PTZ00428	381	PTZ00428, PTZ00428, 60S ribosomal protein L4; Prov	2e-48
PLN00185	405	PLN00185, PLN00185, 60S ribosomal protein L4-1; Pr	1e-45
PRK04042	254	PRK04042, rpl4lp, 50S ribosomal protein L4P; Provi	1e-23
TIGR03672	251	TIGR03672, rpl4p_arch, 50S ribosomal protein L4P	7e-23
pfam00573	190	pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 f	1e-15
COG0088	214	COG0088, RplD, Ribosomal protein L4 [Translation,	3e-06
PRK05319	205	PRK05319, rplD, 50S ribosomal protein L4; Provisio	0.002

>gnl|CDD|185611 PTZ00428, PTZ00428, 60S ribosomal protein L4; Provisional

 Score =  157 bits (398), Expect = 2e-48
 Identities = 62/92 (67%), Positives = 78/92 (84%)

Query: 1   MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
           MRNRR + RRGPLVVY  D G+TKAFRNIPGV+L +V++LNLL+LAPGGHVGRF+IWT+S
Sbjct: 195 MRNRRYVMRRGPLVVYANDNGVTKAFRNIPGVDLCNVTRLNLLQLAPGGHVGRFIIWTKS 254

Query: 61  AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
           AFKKLD ++G++   + LKKGY+LP+P M N 
Sbjct: 255 AFKKLDKIFGTYTEASALKKGYTLPRPLMTNA 286

Length = 381

>gnl|CDD|177779 PLN00185, PLN00185, 60S ribosomal protein L4-1; Provisional

 Score =  150 bits (381), Expect = 1e-45
 Identities = 60/93 (64%), Positives = 76/93 (81%), Gaps = 1/93 (1%)

Query: 1   MRNRRRIQRRGPLVVYGKDRG-LTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTE 59
           MRNRR + R+GPLVVYG +   + KAFRNIPGVEL SV +LNLL+LAPGGH+GRFVIWT+
Sbjct: 200 MRNRRYVSRKGPLVVYGTEGAKIVKAFRNIPGVELCSVDRLNLLQLAPGGHLGRFVIWTK 259

Query: 60  SAFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
           SAF+KLD++YG+++  +  KKGY LP+ KM N 
Sbjct: 260 SAFEKLDSIYGTFEKPSEKKKGYVLPRAKMVNA 292

Length = 405

>gnl|CDD|235211 PRK04042, rpl4lp, 50S ribosomal protein L4P; Provisional

 Score = 89.9 bits (224), Expect = 1e-23
 Identities = 31/70 (44%), Positives = 45/70 (64%)

Query: 1   MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
           MR RR  + +  L+V   D  + KA RN+PGV++++V  LN+  LAPGGH GR  +WTES
Sbjct: 185 MRGRRYKKPKSVLIVVSDDSPIVKAARNLPGVDVVTVDNLNVEHLAPGGHPGRLTVWTES 244

Query: 61  AFKKLDALYG 70
           A ++L   + 
Sbjct: 245 AIEELRERFE 254

Length = 254

>gnl|CDD|234305 TIGR03672, rpl4p_arch, 50S ribosomal protein L4P

 Score = 88.0 bits (219), Expect = 7e-23
 Identities = 34/66 (51%), Positives = 49/66 (74%)

Query: 1   MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
           MR RR  + +  L+V G D G++KA RN+PGV++++V+ LN+  LAPGGH GR  +WTES
Sbjct: 184 MRGRRYKEPKSVLIVVGDDSGISKAARNLPGVDVVTVNNLNVEHLAPGGHPGRLTVWTES 243

Query: 61  AFKKLD 66
           A +KL+
Sbjct: 244 AIEKLE 249

One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome. Length = 251

>gnl|CDD|215999 pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 family

 Score = 67.9 bits (167), Expect = 1e-15
 Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 5/66 (7%)

Query: 3   NRRRIQRRGPLVVYG-KDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESA 61
               ++ +  L+V   KD  L  + RN+PGV++++V  LN+  L P       V+ T+SA
Sbjct: 128 KNLGLKNKKVLIVVDEKDENLYLSARNLPGVDVVTVDGLNVYDLLPADK----VVITKSA 183

Query: 62  FKKLDA 67
            +KL+ 
Sbjct: 184 LEKLEE 189

This family includes Ribosomal L4/L1 from eukaryotes and archaebacteria and L4 from eubacteria. L4 from yeast has been shown to bind rRNA. Length = 190

>gnl|CDD|223166 COG0088, RplD, Ribosomal protein L4 [Translation, ribosomal structure and biogenesis]

 Score = 43.0 bits (102), Expect = 3e-06
 Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 11/58 (18%)

Query: 1   MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWT 58
           +  R     +  LVV G           +P V+++   KL + KLAPG    R  +W 
Sbjct: 168 LSARNLKNVKVVLVVGG-----------LPVVDVLRADKLVITKLAPGKIEERLTVWE 214

Length = 214

>gnl|CDD|235404 PRK05319, rplD, 50S ribosomal protein L4; Provisional

 Score = 35.1 bits (82), Expect = 0.002
 Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 4/58 (6%)

Query: 13  LVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYG 70
           +V    D  L  + RN+P V+++    LN+  L         V+ T++A KKL+    
Sbjct: 152 IVTDEVDENLYLSARNLPNVDVLPAQGLNVYDLL----RADKVVLTKAAVKKLEERLA 205

Length = 205

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	97
3izr_D	405	Localization Of The Large Subunit Ribosomal Protein		8e-30
4a17_C	410	T.Thermophila 60s Ribosomal Subunit In Complex With		6e-29
2zkr_c	421	Structure Of A Mammalian Ribosomal 60s Subunit With		1e-28
2ww9_H	362	Cryo-Em Structure Of The Active Yeast Ssh1 Complex		2e-27
3izs_D	362	Localization Of The Large Subunit Ribosomal Protein		2e-27
1s1i_D	361	Structure Of The Ribosomal 80s-Eef2-Sordarin Comple		2e-27
3zf7_r	374	High-resolution Cryo-electron Microscopy Structure		2e-25
3jyw_D	257	Structure Of The 60s Proteins For Eukaryotic Riboso		2e-23
3j21_D	255	Promiscuous Behavior Of Proteins In Archaeal Riboso		3e-13
3cc2_C	246	The Refined Crystal Structure Of The Haloarcula Mar		3e-05
1jj2_C	246	Fully Refined Crystal Structure Of The Haloarcula M		3e-05
1ffk_C	246	Crystal Structure Of The Large Ribosomal Subunit Fr		3e-05

>pdb|3IZR|D Chain D, Localization Of The Large Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 405

Iteration: 1
 Score =  125 bits (313), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 58/93 (62%), Positives = 76/93 (81%), Gaps = 1/93 (1%)
Query: 1   MRNRRRIQRRGPLVVYGKD-RGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTE 59
           MRNRR I R+GPL+VYG +   + KAFRN+PGV++ +V +LNLL LAPGGH+GRFVIWTE
Sbjct: 200 MRNRRYINRKGPLIVYGTEGSKIVKAFRNLPGVDVANVERLNLLDLAPGGHLGRFVIWTE 259
Query: 60  SAFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
           SAFKKL+ +YG+++  +  KKG+ LP+PKMAN 
Sbjct: 260 SAFKKLEEVYGTFEAPSLKKKGFILPRPKMANA 292

>pdb|4A17|C Chain C, T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 5s Rrna, 5.8s Rrna And Proteins Of Molecule 2. Length = 410

Iteration: 1
 Score =  122 bits (305), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 56/92 (60%), Positives = 74/92 (80%), Gaps = 1/92 (1%)
Query: 1   MRNRRRIQRRGPLVVYGKDRG-LTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTE 59
           +RNRR   RRGPLVVYG ++  LT+A RNIPGV++ +V++LNLL+LAPGGHVGRF+IWTE
Sbjct: 201 LRNRRYKLRRGPLVVYGNEKSTLTRALRNIPGVDVCNVNRLNLLQLAPGGHVGRFIIWTE 260
Query: 60  SAFKKLDALYGSWKTKAPLKKGYSLPQPKMAN 91
           SAFKKL+ ++G++ T    K GY L +P +AN
Sbjct: 261 SAFKKLNEIFGTYSTTGVQKSGYQLQRPLLAN 292

>pdb|2ZKR|CC Chain c, Structure Of A Mammalian Ribosomal 60s Subunit Within An 80s Complex Obtained By Docking Homology Models Of The Rna And Proteins Into An 8.7 A Cryo-Em Map Length = 421

Iteration: 1
 Score =  121 bits (303), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 53/82 (64%), Positives = 65/82 (79%)
Query: 11  GPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYG 70
           GP ++Y +D G+ KAFR  PG+ L++VSKLN+LKLAPGGHVGRF IWTESAF+KLD LYG
Sbjct: 206 GPCIIYNEDNGIIKAFRKHPGITLLNVSKLNILKLAPGGHVGRFCIWTESAFRKLDDLYG 265
Query: 71  SWKTKAPLKKGYSLPQPKMANT 92
           +W+  A LK  Y+LP  KM NT
Sbjct: 266 TWRKAASLKSNYNLPMHKMLNT 287

>pdb|2WW9|H Chain H, Cryo-Em Structure Of The Active Yeast Ssh1 Complex Bound To The Yeast 80s Ribosome Length = 362

Iteration: 1
 Score =  117 bits (292), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 55/84 (65%), Positives = 67/84 (79%), Gaps = 1/84 (1%)
Query: 2   RNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESA 61
           RNRR  QRRGPLVVY +D G+ KA RN+PGVE  +V+ LNLL+LAPG H+GRFVIWTE+A
Sbjct: 195 RNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPGAHLGRFVIWTEAA 254
Query: 62  FKKLDALYGSWKTKAPLKKGYSLP 85
           F KLD ++GS +T A  K GY+LP
Sbjct: 255 FTKLDQVWGS-ETVASSKVGYTLP 277

>pdb|3IZS|D Chain D, Localization Of The Large Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 362

Iteration: 1
 Score =  117 bits (292), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 55/84 (65%), Positives = 67/84 (79%), Gaps = 1/84 (1%)
Query: 2   RNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESA 61
           RNRR  QRRGPLVVY +D G+ KA RN+PGVE  +V+ LNLL+LAPG H+GRFVIWTE+A
Sbjct: 195 RNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPGAHLGRFVIWTEAA 254
Query: 62  FKKLDALYGSWKTKAPLKKGYSLP 85
           F KLD ++GS +T A  K GY+LP
Sbjct: 255 FTKLDQVWGS-ETVASSKVGYTLP 277

>pdb|1S1I|D Chain D, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From Yeast Obtained By Docking Atomic Models For Rna And Protein Components Into A 11.7 A Cryo-Em Map. This File, 1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is In File 1s1h Length = 361

Iteration: 1
 Score =  117 bits (292), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 55/84 (65%), Positives = 67/84 (79%), Gaps = 1/84 (1%)
Query: 2   RNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESA 61
           RNRR  QRRGPLVVY +D G+ KA RN+PGVE  +V+ LNLL+LAPG H+GRFVIWTE+A
Sbjct: 194 RNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPGAHLGRFVIWTEAA 253
Query: 62  FKKLDALYGSWKTKAPLKKGYSLP 85
           F KLD ++GS +T A  K GY+LP
Sbjct: 254 FTKLDQVWGS-ETVASSKVGYTLP 276

>pdb|3ZF7|RR Chain r, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 374

Iteration: 1
 Score =  110 bits (275), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 52/98 (53%), Positives = 75/98 (76%), Gaps = 2/98 (2%)
Query: 1   MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
           MRNRR + RRGP++V   ++G T+AFRNI G++L +V+ LNLL LAPGGHVGRF+IWT+S
Sbjct: 195 MRNRRYVARRGPMLVMPDNKG-TRAFRNIFGLDLANVNSLNLLHLAPGGHVGRFIIWTKS 253
Query: 61  AFKKLDALYGSWKTKAPLKKGYSLPQPKMANTK-QRVM 97
           AF+KLD ++G++   + +K G+ LP P + +T   R+M
Sbjct: 254 AFEKLDKIFGTFTEPSTVKSGFMLPAPMLTSTDVTRIM 291

>pdb|3JYW|D Chain D, Structure Of The 60s Proteins For Eukaryotic Ribosome Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome At 8.9a Resolution Length = 257

Iteration: 1
 Score =  103 bits (258), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 46/65 (70%), Positives = 54/65 (83%)
Query: 2   RNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESA 61
           RNRR  QRRGPLVVY +D G+ KA RN+PGVE  +V+ LNLL+LAPG H+GRFVIWTE+A
Sbjct: 191 RNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPGAHLGRFVIWTEAA 250
Query: 62  FKKLD 66
           F KLD
Sbjct: 251 FTKLD 255

>pdb|3J21|D Chain D, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (50s Ribosomal Proteins) Length = 255

Iteration: 1
 Score = 70.5 bits (171), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 33/70 (47%), Positives = 45/70 (64%)
Query: 1   MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
           MR RR  + +GPL+V GK+ G+    RN PGV+++ V  L +  LAPG H GR  +WT S
Sbjct: 186 MRGRRYKKAKGPLIVVGKNEGIVLGARNHPGVDVVVVDNLGVEHLAPGTHPGRLTVWTVS 245
Query: 61  AFKKLDALYG 70
           A ++L  LYG
Sbjct: 246 AIERLRELYG 255

>pdb|3CC2|C Chain C, The Refined Crystal Structure Of The Haloarcula Marismortui Large Ribosomal Subunit At 2.4 Angstrom Resolution With Rrna Sequence For The 23s Rrna And Genome-Derived Sequences For R-Proteins Length = 246

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 17/43 (39%), Positives = 28/43 (65%)
Query: 23  TKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKL 65
           + A RN+ G ++ + S++N   LAPGG  GR  ++TESA  ++
Sbjct: 201 STAARNLAGADVATASEVNTEDLAPGGAPGRLTVFTESALAEV 243

>pdb|1JJ2|C Chain C, Fully Refined Crystal Structure Of The Haloarcula Marismortui Large Ribosomal Subunit At 2.4 Angstrom Resolution Length = 246

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 17/43 (39%), Positives = 28/43 (65%)
Query: 23  TKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKL 65
           + A RN+ G ++ + S++N   LAPGG  GR  ++TESA  ++
Sbjct: 201 STAARNLAGADVATASEVNTEDLAPGGAPGRLTVFTESALAEV 243

>pdb|1FFK|C Chain C, Crystal Structure Of The Large Ribosomal Subunit From Haloarcula Marismortui At 2.4 Angstrom Resolution Length = 246

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 17/43 (39%), Positives = 28/43 (65%)
Query: 23  TKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKL 65
           + A RN+ G ++ + S++N   LAPGG  GR  ++TESA  ++
Sbjct: 201 STAARNLAGADVATASEVNTEDLAPGGAPGRLTVFTESALAEV 243

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	97
2zkr_c	421	60S ribosomal protein L4; protein-RNA complex, 60S	3e-31
4a17_C	410	RPL4, ribosomal protein L3; eukaryotic ribosome, r	2e-30
2wwb_H	362	60S ribosomal protein L4-B; ribosome, protein EXIT	9e-30
3iz5_D	405	60S ribosomal protein L4 (L4P); eukaryotic ribosom	3e-29
1vq8_C	246	50S ribosomal protein L4E; ribosome 50S, protein-p	3e-20
3r8s_E	201	50S ribosomal protein L4; protein biosynthesis, RN	8e-04

>2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 421

 Score =  112 bits (281), Expect = 3e-31
 Identities = 63/92 (68%), Positives = 75/92 (81%)

Query: 1   MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
           MRNRRRIQRRGP ++Y +D G+ KAFR  PG+ L++VSKLN+LKLAPGGHVGRF IWTES
Sbjct: 196 MRNRRRIQRRGPCIIYNEDNGIIKAFRKHPGITLLNVSKLNILKLAPGGHVGRFCIWTES 255

Query: 61  AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
           AF+KLD LYG+W+  A LK  Y+LP  KM NT
Sbjct: 256 AFRKLDDLYGTWRKAASLKSNYNLPMHKMLNT 287

>4a17_C RPL4, ribosomal protein L3; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_C 4a1c_C 4a1e_C Length = 410

 Score =  110 bits (275), Expect = 2e-30
 Identities = 56/93 (60%), Positives = 72/93 (77%), Gaps = 1/93 (1%)

Query: 1   MRNRRRIQRRGPLVVYGK-DRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTE 59
           +RNRR   RRGPLVVYG     LT+A RNIPGV++ +V++LNLL+LAPGGHVGRF+IWTE
Sbjct: 201 LRNRRYKLRRGPLVVYGNEKSTLTRALRNIPGVDVCNVNRLNLLQLAPGGHVGRFIIWTE 260

Query: 60  SAFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
           SAFKKL+ ++G++ T    K GY L +P +AN 
Sbjct: 261 SAFKKLNEIFGTYSTTGVQKSGYQLQRPLLANA 293

>2wwb_H 60S ribosomal protein L4-B; ribosome, protein EXIT tunnel, cotranslational protein translocation, protein conducting channel; 6.48A {Triticum aestivum} PDB: 2wwa_H 2ww9_H 3izc_D 3izs_D 3o58_D 3o5h_D 3u5e_C 3u5i_C 1s1i_D 3jyw_D Length = 362

 Score =  107 bits (268), Expect = 9e-30
 Identities = 54/93 (58%), Positives = 68/93 (73%), Gaps = 1/93 (1%)

Query: 1   MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
            RNRR  QRRGPLVVY +D G+ KA RN+PGVE  +V+ LNLL+LAPG H+GRFVIWTE+
Sbjct: 194 YRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPGAHLGRFVIWTEA 253

Query: 61  AFKKLDALYGSWKTKAPLKKGYSLPQPKMANTK 93
           AF KLD ++GS    A  K GY+LP   ++ + 
Sbjct: 254 AFTKLDQVWGSET-VASSKVGYTLPSHIISTSD 285

>1vq8_C 50S ribosomal protein L4E; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.22.1.1 PDB: 1k73_E* 1k8a_E* 1k9m_E* 1kc8_E* 1kd1_E* 1kqs_C* 1m1k_E* 1m90_E* 1n8r_E* 1nji_E* 1q7y_E* 1q81_E* 1q82_E* 1q86_E* 1qvf_C 1qvg_C 1s72_C* 1vq4_C* 1vq5_C* 1vq6_C* ... Length = 246

 Score = 80.5 bits (198), Expect = 3e-20
 Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 2/66 (3%)

Query: 1   MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
            R R+  +    L V       + A RN+ G ++ + S++N   LAPGG  GR  ++TES
Sbjct: 181 ARGRKYRRPASILFVT--SDEPSTAARNLAGADVATASEVNTEDLAPGGAPGRLTVFTES 238

Query: 61  AFKKLD 66
           A  ++ 
Sbjct: 239 ALAEVA 244

>3r8s_E 50S ribosomal protein L4; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_C 1p86_C 1vs8_E 1vs6_E 2aw4_E 2awb_E 1vt2_E 2i2v_E 2j28_E 2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E* 2qbk_E* 2qov_E 2qox_E 2qoz_E* ... Length = 201

 Score = 35.7 bits (83), Expect = 8e-04
 Identities = 13/59 (22%), Positives = 28/59 (47%), Gaps = 5/59 (8%)

Query: 13  LVVYGK-DRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYG 70
           L++ G+ D  L  A RN+  V++   + ++ + L         V+ T  A K+++ +  
Sbjct: 147 LIITGELDENLFLAARNLHKVDVRDATGIDPVSLI----AFDKVVMTADAVKQVEEMLA 201

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	97
4a17_C	410	RPL4, ribosomal protein L3; eukaryotic ribosome, r	99.92
3iz5_D	405	60S ribosomal protein L4 (L4P); eukaryotic ribosom	99.91
2zkr_c	421	60S ribosomal protein L4; protein-RNA complex, 60S	99.9
2wwb_H	362	60S ribosomal protein L4-B; ribosome, protein EXIT	99.9
3j21_D	255	50S ribosomal protein L4P; archaea, archaeal, KINK	99.82
1vq8_C	246	50S ribosomal protein L4E; ribosome 50S, protein-p	99.75
3r8s_E	201	50S ribosomal protein L4; protein biosynthesis, RN	99.6
3v2d_F	210	50S ribosomal protein L4; ribosome associated inhi	99.58
2ftc_D	175	Mitochondrial ribosomal protein L4 isoform A, mito	99.55
1dmg_A	225	Ribosomal protein L4; alpha-beta, ribosome, RNA, S	99.52
3bbo_G	293	Ribosomal protein L4; large ribosomal subunit, spi	99.48
2zjr_C	205	50S ribosomal protein L4; ribosome, large ribosoma	99.46

>4a17_C RPL4, ribosomal protein L3; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_C 4a1c_C 4a1e_C

Probab=99.92  E-value=1.2e-25  Score=182.43  Aligned_cols=93  Identities=60%  Similarity=1.079  Sum_probs=88.6

Q ss_pred             CCCcccccCCccEEEEeC-CchHHHhhcCCCCceEEeeCCCccccccCCCCCCceEEEcHHHHHHHHHHhcccccccCcc
Q psy14782          1 MRNRRRIQRRGPLVVYGK-DRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYGSWKTKAPLK   79 (97)
Q Consensus         1 ~~~~~~~~~~k~LIV~~e-~~nl~lSaRNLp~V~v~~a~~LNvyDLL~~d~~~~~VI~TesAl~~lee~l~~~~~~~~~~   79 (97)
                      ||||||++.+++|||+++ ++++++|+||||+|+++++++||+|||++++++++.+|||++|++.|+++|+.|......|
T Consensus       201 mRgRry~~~k~~LIV~~~~d~~l~~A~RNIpgV~v~~v~~LNv~dLl~~~~~gR~vV~TksAl~~Lee~~~~~~~~s~~k  280 (410)
T 4a17_C          201 LRNRRYKLRRGPLVVYGNEKSTLTRALRNIPGVDVCNVNRLNLLQLAPGGHVGRFIIWTESAFKKLNEIFGTYSTTGVQK  280 (410)
T ss_dssp             GGTCCEEECCCCEEEECCTTCSHHHHHTTSTTCEEEETTSCCHHHHSGGGCCCCCEEECHHHHHHHHHHHCBTTBCCTTT
T ss_pred             cccccccCCCceEEEECCCchHHHHHHhCCCCcEEEEeCCccHHHHhCCCCCCceEEEEHHHHHHHHHHHccccchhhhc
Confidence            799999999999999966 5799999999999999999999999999999888999999999999999999988888899


Q ss_pred             CCCCCCCCccccCC
Q psy14782         80 KGYSLPQPKMANTK   93 (97)
Q Consensus        80 ~~~~~~~~~~~~~~   93 (97)
                      ++|+||+++|+|+-
T Consensus       281 ~~~~lp~~~~~n~d  294 (410)
T 4a17_C          281 SGYQLQRPLLANAD  294 (410)
T ss_dssp             TSCCCCCCSCSCCC
T ss_pred             cCCcCCcccccccc
Confidence            99999999999974

>2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}

Probab=99.90  E-value=3.4e-25  Score=180.24  Aligned_cols=93  Identities=68%  Similarity=1.202  Sum_probs=66.6

Q ss_pred             CCCcccccCCccEEEEeCCchHHHhhcCCCCceEEeeCCCccccccCCCCCCceEEEcHHHHHHHHHHhcccccccCccC
Q psy14782          1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYGSWKTKAPLKK   80 (97)
Q Consensus         1 ~~~~~~~~~~k~LIV~~e~~nl~lSaRNLp~V~v~~a~~LNvyDLL~~d~~~~~VI~TesAl~~lee~l~~~~~~~~~~~   80 (97)
                      ||||||++.+++|||+++++++++|+||||+|+++++++||+|||++++++|+.+|||++|++.|+++|+.|.....+|+
T Consensus       196 mRgRry~~~kg~LiV~~~d~~l~~A~RNIpgV~v~~v~~LNv~dLl~~~h~GR~vV~T~sAle~Lee~~~t~~~~s~~k~  275 (421)
T 2zkr_c          196 MRNRRRIQRRGPCIIYNEDNGIIKAFRKHPGITLLNVSKLNILKLAPGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKS  275 (421)
T ss_dssp             TTTCCEECCCCCEEEESSSSCCCHHHHTSTTCEEEEGGGCCHHHHSGGGCCCCCEEEEHHHHHHHTTC------------
T ss_pred             ccccccccCcceEEEECCChhHHHHHhCCCCcEEEeeCCccHHHHhcCCCCCcEEEEEhHHHHHHHHHHhcccccccccc
Confidence            89999999999999998888999999999999999999999999999999999999999999999999999999889999


Q ss_pred             CCCCCCCccccCC
Q psy14782         81 GYSLPQPKMANTK   93 (97)
Q Consensus        81 ~~~~~~~~~~~~~   93 (97)
                      +|.||+++|.|+-
T Consensus       276 ~~~lp~~~~~n~d  288 (421)
T 2zkr_c          276 NYNLPMHKMLNTD  288 (421)
T ss_dssp             -------------
T ss_pred             CCcCCccccchhH
Confidence            9999999999874

>2wwb_H 60S ribosomal protein L4-B; ribosome, protein EXIT tunnel, cotranslational protein translocation, protein conducting channel; 6.48A {Triticum aestivum} PDB: 2wwa_H 2ww9_H 3izc_D 3izs_D 3o58_D 3o5h_D 3u5e_C 3u5i_C 1s1i_D 3jyw_D

Probab=99.90  E-value=1.1e-24  Score=174.64  Aligned_cols=92  Identities=60%  Similarity=1.029  Sum_probs=72.1

Q ss_pred             CCCcccccCCccEEEEeCCchHHHhhcCCCCceEEeeCCCccccccCCCCCCceEEEcHHHHHHHHHHhcccccccCccC
Q psy14782          1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYGSWKTKAPLKK   80 (97)
Q Consensus         1 ~~~~~~~~~~k~LIV~~e~~nl~lSaRNLp~V~v~~a~~LNvyDLL~~d~~~~~VI~TesAl~~lee~l~~~~~~~~~~~   80 (97)
                      ||||||++.+++|||+++++++++|+||||+|+++++++||+|||++++++++.+|||++|+++|+++|+. ......|+
T Consensus       194 mRgRry~~~k~~LiV~~~d~~l~~A~RNipgV~v~~v~~LNv~dLl~~~~~gr~vV~T~sAl~~Le~~~~~-~~~s~~k~  272 (362)
T 2wwb_H          194 YRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPGAHLGRFVIWTEAAFTKLDQVWGS-ETVASSKV  272 (362)
T ss_dssp             TTSCCSCCCCCCEEEESSSCCCCTTTSCSSSCEEEESSSCCHHHHSTTSCCCCCEECCTTHHHHHHCCSSC-CCCCC---
T ss_pred             ccccccccCCceEEEEcCChhHHHHHhcCCCCcEEeeCCccHHHHhcccCcCCEEEEEHHHHHHHHHHHcc-CCcchhcc
Confidence            89999999999999998778999999999999999999999999999998899999999999999999988 66667899


Q ss_pred             CCCCCCCccccCC
Q psy14782         81 GYSLPQPKMANTK   93 (97)
Q Consensus        81 ~~~~~~~~~~~~~   93 (97)
                      +|.||+++|.|+-
T Consensus       273 ~~~lp~~~m~n~d  285 (362)
T 2wwb_H          273 GYTLPSHIISTSD  285 (362)
T ss_dssp             -------------
T ss_pred             cCcCCccccchhH
Confidence            9999999999974

>3j21_D 50S ribosomal protein L4P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=99.82  E-value=4.9e-21  Score=147.52  Aligned_cols=70  Identities=47%  Similarity=0.884  Sum_probs=66.3

Q ss_pred             CCCcccccCCccEEEEeCCchHHHhhcCCCCceEEeeCCCccccccCCCCCCceEEEcHHHHHHHHHHhc
Q psy14782          1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYG   70 (97)
Q Consensus         1 ~~~~~~~~~~k~LIV~~e~~nl~lSaRNLp~V~v~~a~~LNvyDLL~~d~~~~~VI~TesAl~~lee~l~   70 (97)
                      ||||||++.+++|||+++++++++|+||||+|+++++++||+|||++++++++.+|||++|++.|+++|+
T Consensus       186 ~r~rr~~~~~~~LiV~~~~~~~~~a~RNip~V~v~~~~~LNv~~Ll~~~~~gr~~V~T~~A~~~lee~~g  255 (255)
T 3j21_D          186 MRGRRYKKAKGPLIVVGKNEGIVLGARNHPGVDVVVVDNLGVEHLAPGTHPGRLTVWTVSAIERLRELYG  255 (255)
T ss_dssp             GGSCCSCCCCCCEEEESSSSSSCSSSSSSTTCEEEETTTCCHHHHSTTSCCCCCEEEEHHHHHHHHSCCC
T ss_pred             cccccccCCCceEEEECCCcHHHHHHhCCCCcEEEecCCccHHHHhCCCCCCceEEEEHHHHHHHHHHhC
Confidence            7999999999999999886559999999999999999999999999999888899999999999999874

>1vq8_C 50S ribosomal protein L4E; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.22.1.1 PDB: 1k73_E* 1k8a_E* 1k9m_E* 1kc8_E* 1kd1_E* 1kqs_C* 1m1k_E* 1m90_E* 1n8r_E* 1nji_E* 1q7y_E* 1q81_E* 1q82_E* 1q86_E* 1qvf_C 1qvg_C 1s72_C* 1vq4_C* 1vq5_C* 1vq6_C* ...

Probab=99.75  E-value=2.4e-19  Score=137.49  Aligned_cols=66  Identities=32%  Similarity=0.508  Sum_probs=62.5

Q ss_pred             CCCcccccCCccEEEEeCCchHHHhhcCCCCceEEeeCCCccccccCCCCCCceEEEcHHHHHHHHHH
Q psy14782          1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDAL   68 (97)
Q Consensus         1 ~~~~~~~~~~k~LIV~~e~~nl~lSaRNLp~V~v~~a~~LNvyDLL~~d~~~~~VI~TesAl~~lee~   68 (97)
                      ||||||++.+++|||++++  +++|+||||+|+++++++||+|||++++++|+.+|||++|+++|+++
T Consensus       181 ~r~rr~~~~~~~LiV~~~~--~~~a~RNip~V~v~~~~~lnv~dll~~~~~gr~~v~T~~Al~~l~e~  246 (246)
T 1vq8_C          181 ARGRKYRRPASILFVTSDE--PSTAARNLAGADVATASEVNTEDLAPGGAPGRLTVFTESALAEVAER  246 (246)
T ss_dssp             GGTCCEECCCCCEEEESSS--CCTTTTTSTTCEEEETTTCCHHHHSGGGCCCCCEEEEHHHHHHGGGC
T ss_pred             ccccccccCCcEEEEECcH--HHHHHcCCCCcEEEeeCCeeHHHHhccCCCCCeEEEEHHHHHHHhhC
Confidence            7999999999999999855  99999999999999999999999999998889999999999999873

>3r8s_E 50S ribosomal protein L4; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_C 1p86_C 1vs8_E 1vs6_E 2aw4_E 2awb_E 1vt2_E 2i2v_E 2j28_E 2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E* 2qbk_E* 2qov_E 2qox_E 2qoz_E* ...

Probab=99.60  E-value=6e-16  Score=115.45  Aligned_cols=57  Identities=23%  Similarity=0.346  Sum_probs=53.2

Q ss_pred             CccEEEEeC-CchHHHhhcCCCCceEEeeCCCccccccCCCCCCceEEEcHHHHHHHHHHhc
Q psy14782         10 RGPLVVYGK-DRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYG   70 (97)
Q Consensus        10 ~k~LIV~~e-~~nl~lSaRNLp~V~v~~a~~LNvyDLL~~d~~~~~VI~TesAl~~lee~l~   70 (97)
                      +++|||+++ ++++++|+||||+|+++++++||+||||+++    .+|||++|+++||++|+
T Consensus       144 ~~~LiV~~~~~~~~~~a~RNip~v~v~~~~~lnv~dll~~~----~~v~t~~Al~~lee~l~  201 (201)
T 3r8s_E          144 EDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSLIAFD----KVVMTADAVKQVEEMLA  201 (201)
T ss_dssp             SSEEEEESSCCHHHHHTTSSCSSEEEEEGGGCCHHHHHHSS----EEEECHHHHHHHHHHHC
T ss_pred             CceEEEECCCchHHHHHHhCCCCceEEeeCCCcHHHHhCCC----CEEEEHHHHHHHHHHhC
Confidence            578999987 5699999999999999999999999999986    79999999999999985

>3v2d_F 50S ribosomal protein L4; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2hgq_F 2hgj_F 2hgu_F 2j03_F 2jl6_F 2jl8_F 2v47_F 2v49_F 2wdi_F 2wdj_F 2wdl_F 2wdn_F 2wh2_F 2wh4_F 2wrj_F 2wrl_F 2wro_F 2wrr_F 2x9s_F 2x9u_F ...

Probab=99.58  E-value=1.2e-15  Score=114.43  Aligned_cols=58  Identities=21%  Similarity=0.303  Sum_probs=53.9

Q ss_pred             CCccEEEEeCCchHHHhhcCCCCceEEeeCCCccccccCCCCCCceEEEcHHHHHHHHHHhcc
Q psy14782          9 RRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYGS   71 (97)
Q Consensus         9 ~~k~LIV~~e~~nl~lSaRNLp~V~v~~a~~LNvyDLL~~d~~~~~VI~TesAl~~lee~l~~   71 (97)
                      .+++|||++ ++++++|+||||+|+++++++||+||||+++    .+|||++|+++|+++|+.
T Consensus       151 ~~~~LiV~~-~~~~~~a~RNip~v~v~~~~~lnv~dll~~~----~vv~t~~Al~~l~e~~~~  208 (210)
T 3v2d_F          151 SESVLLVTG-NELVRRAARNLPWVVTLAPEGLNVYDIVRTE----RLVMDLDAWEVFQNRIGG  208 (210)
T ss_dssp             SSCEEEECS-CHHHHHHHTTCTTEEEECGGGCCHHHHHHSS----EEEEEHHHHHHHHHHHC-
T ss_pred             CCceEEEeC-ChhHHHHHhCcCCceEEeeCCccHHHHhCCC----CEEEEHHHHHHHHHHhcc
Confidence            468999998 7899999999999999999999999999986    799999999999999973

>2ftc_D Mitochondrial ribosomal protein L4 isoform A, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal R ribosome; 12.10A {Bos taurus} PDB: 3iy9_D

Probab=99.55  E-value=2.6e-15  Score=109.81  Aligned_cols=55  Identities=16%  Similarity=0.155  Sum_probs=50.5

Q ss_pred             CCccEEEEeC----CchHHHhhcCCCCceEEeeCCCccccccCCCCCCceEEEcHHHHHHHHH
Q psy14782          9 RRGPLVVYGK----DRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDA   67 (97)
Q Consensus         9 ~~k~LIV~~e----~~nl~lSaRNLp~V~v~~a~~LNvyDLL~~d~~~~~VI~TesAl~~lee   67 (97)
                      ++++|||+++    ++++++|+||||+|+++++++||+||||+++    .||||++|+++|||
T Consensus       117 ~~~~LiV~~~~~~~~~~~~~a~RNip~v~v~~~~~lnv~dll~~~----~lv~t~~Al~~lee  175 (175)
T 2ftc_D          117 GDSVLLVDLTHEEMPQSIVEATSRLKTFNLIPAVGLNVHSMLKHQ----TLVLTLPTVAFLED  175 (175)
T ss_pred             CCceEEEECCCccCCHHHHHHHhCCCCcEEEeeCCEeHHHHhCCC----CEEEEHHHHHHHhC
Confidence            3579999976    5699999999999999999999999999997    69999999999985

>1dmg_A Ribosomal protein L4; alpha-beta, ribosome, RNA, S10 operon, gene regulation; HET: CIT; 1.70A {Thermotoga maritima} SCOP: c.22.1.1

Probab=99.52  E-value=1.2e-14  Score=110.00  Aligned_cols=57  Identities=21%  Similarity=0.433  Sum_probs=53.1

Q ss_pred             CccEEEEeC-Cc---hHHHhhcCCCCceEEeeCC---------------CccccccCCCCCCceEEEcHHHHHHHHHHhc
Q psy14782         10 RGPLVVYGK-DR---GLTKAFRNIPGVELISVSK---------------LNLLKLAPGGHVGRFVIWTESAFKKLDALYG   70 (97)
Q Consensus        10 ~k~LIV~~e-~~---nl~lSaRNLp~V~v~~a~~---------------LNvyDLL~~d~~~~~VI~TesAl~~lee~l~   70 (97)
                      +++|||+++ ++   ++++|+||||+|+++++++               ||+||||+++    .||||++|+++||++|+
T Consensus       150 ~~~LiV~~~~~~~~~n~~~a~RNip~v~v~~~~~~~~~~~~~~~~~~~~lNv~dll~~~----~lv~t~~Al~~lee~l~  225 (225)
T 1dmg_A          150 KKTLIVLPWKEEGYMNVKLSGRNLPDVKVIIADNPNNSKNGEKAVRIDGLNVFDMLKYD----YLVLTRDMVSKIEEVLG  225 (225)
T ss_dssp             SCEEEEECCCSHHHHHHHHHHTTCTTEEEEECCCCSSCCSSCCCCCCTTCCHHHHHHSS----EEEEEHHHHHHHHHHHC
T ss_pred             CCEEEEECCCccchHHHHHHHhCCCCCEEEecCCcccccccccccCcCcEEHHHHhCCC----cEEEeHHHHHHHHHHhC
Confidence            679999977 47   9999999999999999999               9999999996    89999999999999984

>3bbo_G Ribosomal protein L4; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=99.48  E-value=6.3e-15  Score=115.48  Aligned_cols=58  Identities=24%  Similarity=0.364  Sum_probs=53.7

Q ss_pred             CccEEEEeC-CchHHHhhcCCCCceEEeeCCCccccccCCCCCCceEEEcHHHHHHHHHHhcc
Q psy14782         10 RGPLVVYGK-DRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYGS   71 (97)
Q Consensus        10 ~k~LIV~~e-~~nl~lSaRNLp~V~v~~a~~LNvyDLL~~d~~~~~VI~TesAl~~lee~l~~   71 (97)
                      +++|||+++ ++++++|+||||+|+++++++||+||||+++    .||||++|+++|+++|+.
T Consensus       203 ~k~LlV~~~~d~nl~~A~RNIp~V~v~~v~~LNvydLl~~~----~lViT~~Al~~Lee~l~~  261 (293)
T 3bbo_G          203 EKSLFFLMDLVENVEKSGRNIRTLKLLTPRSLNLFDVLNAE----KLVFTEGTIQYLNQRYGV  261 (293)
T ss_dssp             SSSCCEECCCSSSCCTTTSSSSSCEECCSSCCCHHHHHHSS----CEECCTTHHHHHHHHSCC
T ss_pred             CceEEEEcCCChhHHHHHhCCCCcEEEeeCceeHHHhhCCC----cEEEEHHHHHHHHHHhcc
Confidence            568888866 5799999999999999999999999999996    799999999999999984

>2zjr_C 50S ribosomal protein L4; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: c.22.1.1 PDB: 1j5a_K* 1jzy_K* 1jzz_K* 1k01_K* 1nkw_C 1sm1_C* 2zjp_C* 2zjq_C 1jzx_K 3cf5_C* 3dll_C* 3pio_C* 3pip_C* 1nwy_C* 1nwx_C* 1xbp_C* 1pnu_C 1pny_C 1vor_F 1vou_F ...

Probab=99.46  E-value=2e-15  Score=112.70  Aligned_cols=57  Identities=19%  Similarity=0.295  Sum_probs=50.4

Q ss_pred             CccEEEEeCCchHHHhhcCCCCceEEeeCCCccccccCCCCCCceEEEcHHHHHHHHHHhcc
Q psy14782         10 RGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYGS   71 (97)
Q Consensus        10 ~k~LIV~~e~~nl~lSaRNLp~V~v~~a~~LNvyDLL~~d~~~~~VI~TesAl~~lee~l~~   71 (97)
                      +++|||+ +++++++|+||||+|+++++++||+||||+++    .+|||++|+++|+++|+.
T Consensus       146 ~~~LiV~-~~~~~~~a~RNip~v~v~~~~~lnv~dll~~~----~~v~t~~Al~~lee~~~~  202 (205)
T 2zjr_C          146 EKVLLVT-DDENTRRAARNVSWVSVLPVAGVNVYDILRHD----RLVIDAAALEIVEEEAGE  202 (205)
T ss_dssp             SCEEEEC-CCHHHHTSCCCSSSEEEEGGGCCCHHHHHHSS----EEECBCTTTSSCCC----
T ss_pred             CCEEEEE-cCccHHHHHhCCCCceEEeeCceeHHHHhCCC----cEEEEHHHHHHHHHHHhh
Confidence            6799999 77899999999999999999999999999987    799999999999999864

---

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	97
d1vqoc1	246	c.22.1.1 (C:1-246) Ribosomal protein L4 {Archaeon	3e-17
d1dmga_	225	c.22.1.1 (A:) Ribosomal protein L4 {Thermotoga mar	4e-05
d2j01f1	208	c.22.1.1 (F:1-208) Ribosomal protein L4 {Thermus t	1e-04

>d1vqoc1 c.22.1.1 (C:1-246) Ribosomal protein L4 {Archaeon Haloarcula marismortui [TaxId: 2238]} Length = 246

class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L4
superfamily: Ribosomal protein L4
family: Ribosomal protein L4
domain: Ribosomal protein L4
species: Archaeon Haloarcula marismortui [TaxId: 2238]

 Score = 71.3 bits (174), Expect = 3e-17
 Identities = 21/65 (32%), Positives = 35/65 (53%)

Query: 2   RNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESA 61
             R R  RR   +++      + A RN+ G ++ + S++N   LAPGG  GR  ++TESA
Sbjct: 180 SARGRKYRRPASILFVTSDEPSTAARNLAGADVATASEVNTEDLAPGGAPGRLTVFTESA 239

Query: 62  FKKLD 66
             ++ 
Sbjct: 240 LAEVA 244

>d1dmga_ c.22.1.1 (A:) Ribosomal protein L4 {Thermotoga maritima [TaxId: 2336]} Length = 225

class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L4
superfamily: Ribosomal protein L4
family: Ribosomal protein L4
domain: Ribosomal protein L4
species: Thermotoga maritima [TaxId: 2336]

 Score = 37.9 bits (87), Expect = 4e-05
 Identities = 10/63 (15%), Positives = 20/63 (31%), Gaps = 11/63 (17%)

Query: 19  DRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRF-----------VIWTESAFKKLDA 67
              +  + RN+P V++I     N  K                     ++ T     K++ 
Sbjct: 163 YMNVKLSGRNLPDVKVIIADNPNNSKNGEKAVRIDGLNVFDMLKYDYLVLTRDMVSKIEE 222

Query: 68  LYG 70
           + G
Sbjct: 223 VLG 225

>d2j01f1 c.22.1.1 (F:1-208) Ribosomal protein L4 {Thermus thermophilus [TaxId: 274]} Length = 208

class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L4
superfamily: Ribosomal protein L4
family: Ribosomal protein L4
domain: Ribosomal protein L4
species: Thermus thermophilus [TaxId: 274]

 Score = 36.7 bits (84), Expect = 1e-04
 Identities = 9/49 (18%), Positives = 20/49 (40%), Gaps = 4/49 (8%)

Query: 22  LTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYG 70
           + +A RN+P V  ++   LN+  +         ++    A++      G
Sbjct: 163 VRRAARNLPWVVTLAPEGLNVYDIVRTER----LVMDLDAWEVFQNRIG 207

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	97
d1vqoc1	246	Ribosomal protein L4 {Archaeon Haloarcula marismor	99.56
d2j01f1	208	Ribosomal protein L4 {Thermus thermophilus [TaxId:	99.52
d1dmga_	225	Ribosomal protein L4 {Thermotoga maritima [TaxId:	99.48
d2gycc1	198	Ribosomal protein L4 {Escherichia coli [TaxId: 562	99.42
d2zjrc1	197	Ribosomal protein L4 {Deinococcus radiodurans [Tax	99.32

>d1vqoc1 c.22.1.1 (C:1-246) Ribosomal protein L4 {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L4
superfamily: Ribosomal protein L4
family: Ribosomal protein L4
domain: Ribosomal protein L4
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=99.56  E-value=5.9e-16  Score=115.64  Aligned_cols=65  Identities=32%  Similarity=0.525  Sum_probs=53.4

Q ss_pred             CCCcccccCCccEEEEe-CCchHHHhhcCCCCceEEeeCCCccccccCCCCCCceEEEcHHHHHHHHHH
Q psy14782          1 MRNRRRIQRRGPLVVYG-KDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDAL   68 (97)
Q Consensus         1 ~~~~~~~~~~k~LIV~~-e~~nl~lSaRNLp~V~v~~a~~LNvyDLL~~d~~~~~VI~TesAl~~lee~   68 (97)
                      ||||++   ++.++++. .++++.+|+||||+|+++++++||+||||++++.++.||||++|++.|||+
T Consensus       181 ~~~~~~---k~~~~vl~~~~~~~~~a~rNip~v~v~~~~~lNv~dll~~~~l~r~vV~T~~Al~~leeR  246 (246)
T d1vqoc1         181 ARGRKY---RRPASILFVTSDEPSTAARNLAGADVATASEVNTEDLAPGGAPGRLTVFTESALAEVAER  246 (246)
T ss_dssp             GGTCCE---ECCCCCEEEESSSCCTTTTTSTTCEEEETTTCCHHHHSGGGCCCCCEEEEHHHHHHHTTC
T ss_pred             cccccc---ccccccccccChHHHHHHcCCCCCEEEeCCCccHHHccccCCCCceEEEeHHHHHHHhcC
Confidence            356654   33343333 367899999999999999999999999999987678899999999999975

>d2j01f1 c.22.1.1 (F:1-208) Ribosomal protein L4 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L4
superfamily: Ribosomal protein L4
family: Ribosomal protein L4
domain: Ribosomal protein L4
species: Thermus thermophilus [TaxId: 274]

Probab=99.52  E-value=4e-15  Score=108.60  Aligned_cols=57  Identities=16%  Similarity=0.240  Sum_probs=51.1

Q ss_pred             CccEEEEeCCchHHHhhcCCCCceEEeeCCCccccccCCCCCCceEEEcHHHHHHHHHHhc
Q psy14782         10 RGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYG   70 (97)
Q Consensus        10 ~k~LIV~~e~~nl~lSaRNLp~V~v~~a~~LNvyDLL~~d~~~~~VI~TesAl~~lee~l~   70 (97)
                      ++.+++++.++++++|+||||+|+++.+++||+||||+++    .||||++|++.|+|+|+
T Consensus       151 ~~~vl~v~~~en~~~s~rNi~~v~v~~~~~lNv~dlL~~~----~lvit~~Al~~L~erl~  207 (208)
T d2j01f1         151 SESVLLVTGNELVRRAARNLPWVVTLAPEGLNVYDIVRTE----RLVMDLDAWEVFQNRIG  207 (208)
T ss_dssp             SSCEEEECSCHHHHHHHTTCTTEEEECGGGCCHHHHHHSS----EEEEEHHHHHHHHHTCC
T ss_pred             ccceeeccchhHHHHHHhCCCCCEEeecCCccHHHHhcCC----cEEEEHHHHHHHHHHhC
Confidence            3455556567899999999999999999999999999997    79999999999999986

>d1dmga_ c.22.1.1 (A:) Ribosomal protein L4 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L4
superfamily: Ribosomal protein L4
family: Ribosomal protein L4
domain: Ribosomal protein L4
species: Thermotoga maritima [TaxId: 2336]

Probab=99.48  E-value=2.4e-14  Score=105.23  Aligned_cols=58  Identities=21%  Similarity=0.399  Sum_probs=50.6

Q ss_pred             CCccEEEEeCC----chHHHhhcCCCCceEEeeCC---------------CccccccCCCCCCceEEEcHHHHHHHHHHh
Q psy14782          9 RRGPLVVYGKD----RGLTKAFRNIPGVELISVSK---------------LNLLKLAPGGHVGRFVIWTESAFKKLDALY   69 (97)
Q Consensus         9 ~~k~LIV~~e~----~nl~lSaRNLp~V~v~~a~~---------------LNvyDLL~~d~~~~~VI~TesAl~~lee~l   69 (97)
                      +++.|||+..+    +|+++|+||||+|+++.+++               +|+||||+++    .||||++|++.|||+|
T Consensus       149 ~~~~llv~~~~~e~~~n~~~s~rNlp~v~v~~~~~~~~~~~~~~~~~~~~lNvydlL~~~----~lVit~~Al~~lee~L  224 (225)
T d1dmga_         149 DKKTLIVLPWKEEGYMNVKLSGRNLPDVKVIIADNPNNSKNGEKAVRIDGLNVFDMLKYD----YLVLTRDMVSKIEEVL  224 (225)
T ss_dssp             TSCEEEEECCCSHHHHHHHHHHTTCTTEEEEECCCCSSCCSSCCCCCCTTCCHHHHHHSS----EEEEEHHHHHHHHHHH
T ss_pred             ccceeeeeccccchhHHHHHHHcCCCCceEeeccccccccccccccccCCccHHHHhcCC----eEEEeHHHHHHHHHHc
Confidence            45678887653    37999999999999998766               8999999997    7999999999999998


Q ss_pred             c
Q psy14782         70 G   70 (97)
Q Consensus        70 ~   70 (97)
                      +
T Consensus       225 g  225 (225)
T d1dmga_         225 G  225 (225)
T ss_dssp             C
T ss_pred             C
Confidence            6

>d2gycc1 c.22.1.1 (C:1-198) Ribosomal protein L4 {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L4
superfamily: Ribosomal protein L4
family: Ribosomal protein L4
domain: Ribosomal protein L4
species: Escherichia coli [TaxId: 562]

Probab=99.42  E-value=4.2e-15  Score=108.26  Aligned_cols=53  Identities=25%  Similarity=0.349  Sum_probs=49.5

Q ss_pred             ccEEEEeC-CchHHHhhcCCCCceEEeeCCCccccccCCCCCCceEEEcHHHHHHHHH
Q psy14782         11 GPLVVYGK-DRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDA   67 (97)
Q Consensus        11 k~LIV~~e-~~nl~lSaRNLp~V~v~~a~~LNvyDLL~~d~~~~~VI~TesAl~~lee   67 (97)
                      ++|||+++ ++|+++|+||||+|+++++++||+||||+++    .||||++|++.|||
T Consensus       145 ~~Liv~~~~~enl~~S~RNI~~v~v~~~~~lNvydlLk~~----~lVit~~Al~~leE  198 (198)
T d2gycc1         145 DVLIITGELDENLFLAARNLHKVDVRDATGIDPVSLIAFD----KVVMTADAVKQVEE  198 (198)
T ss_dssp             GGTTTCCCCSSSCCGGGSSSSSCCCCCSSSCCHHHHTTTS----CCCEEHHHHHHHHC
T ss_pred             eeEEecCcccHHHHHHHhCcCCceEeecCCccHHHHhcCC----eEEEEHHHHHHhhC
Confidence            68888877 5799999999999999999999999999997    79999999999986

>d2zjrc1 c.22.1.1 (C:2-198) Ribosomal protein L4 {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L4
superfamily: Ribosomal protein L4
family: Ribosomal protein L4
domain: Ribosomal protein L4
species: Deinococcus radiodurans [TaxId: 1299]

Probab=99.32  E-value=3.6e-14  Score=102.95  Aligned_cols=53  Identities=15%  Similarity=0.287  Sum_probs=46.6

Q ss_pred             ccEEEEeCCchHHHhhcCCCCceEEeeCCCccccccCCCCCCceEEEcHHHHHHHHH
Q psy14782         11 GPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDA   67 (97)
Q Consensus        11 k~LIV~~e~~nl~lSaRNLp~V~v~~a~~LNvyDLL~~d~~~~~VI~TesAl~~lee   67 (97)
                      ..++++++++|+++|+||||+|+++++++||+||||+++    .||||++|++.|||
T Consensus       145 ~~vl~~~~~en~~~s~RNi~~v~v~~~~~lNvydlLk~~----~lVit~~Al~~LEE  197 (197)
T d2zjrc1         145 EKVLLVTDDENTRRAARNVSWVSVLPVAGVNVYDILRHD----RLVIDAAALEIVEE  197 (197)
T ss_dssp             SCEEEECCCHHHHTSCCCSSSEEEEGGGCCCHHHHHHSS----EEECBCTTTSSCCC
T ss_pred             cceeeeccchHHHHHHhCcCCceEeecCCccHHHHhcCC----cEEEEHHHHHHhhC
Confidence            344555556799999999999999999999999999997    89999999998875