Citrus Sinensis ID: 048058

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------
Protein Sequence
MAAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV
Secondary Structure (PSIPRED)
ccccccccEEEEcccccccccccccccccccccccccHHHHHHHHHHHHHHcccccccccccccEEEEEEcccccccccccccccccccccccccccccccccccccccccccEEEEcccHHHHHHHHHHHHHHcccHHHHHHHccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccEEEEEEcccccccccccccccccHEcccccHHHHHHHHHHHHHccccccEEcccccccccccccccccEEEEccccccccccccccccccccccccccccccHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHcccEEccccccccc
Coil and Loop (DISEMBL)
maaaarplitvqslegdmatdasstvplpdvmkasirpdivgfvhsnisknsrqpyavsrkaghqtsaeswgtgravsriprvpgggthragqgafgnmcrggrmfaptkiWRRWHRKINVNQKRYAIVSAIAASAVPSLVmarghkietvpemplv
Flexible Loop (DISEMBL)
maaaarplitvqslegdmatdaSSTVPLPDVMKASIRPDIVGFVHsnisknsrqpyavsrkaghqtsaeswgtgravsriprvpgggthragqgafgnmcrggRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGhkietvpemplv
Low Complexity Region (SEG)
MAAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYaivsaiaasavPSLVMARGHKIETVPEMPLV
Disordered region (IsUnstruct)
***********************************IRPDIVGFVH*********************************************AGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARG************
Disordered Region (DISOPRED)
***AARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYA**************************************FGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV
Disordered Region (DISEMBL)
MAAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSR*********************RAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV
Disordered Region (DISPRO)
****ARPLITVQSLEG*******STVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRK*********WGTGRAVSRIPRVPGGGTHR**Q*AFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV
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	157	2.2.26 [Sep-21-2011]
Q9SF40	406	60S ribosomal protein L4-	yes	no	0.993	0.384	0.852	2e-77
P49691	407	60S ribosomal protein L4-	yes	no	0.993	0.383	0.846	1e-76
Q9XF97	408	60S ribosomal protein L4	N/A	no	0.968	0.372	0.934	3e-76
Q28346	421	60S ribosomal protein L4	yes	no	0.968	0.361	0.709	2e-62
P49165	386	60S ribosomal protein L4	N/A	no	0.961	0.391	0.701	6e-60
P35679	363	60S ribosomal protein L4-	yes	no	0.968	0.418	0.683	1e-59
Q9P784	363	60S ribosomal protein L4-	yes	no	0.968	0.418	0.677	2e-59
Q58DW0	422	60S ribosomal protein L4	yes	no	0.968	0.360	0.729	2e-58
Q5RCR3	427	60S ribosomal protein L4	yes	no	0.968	0.355	0.729	2e-58
P36578	427	60S ribosomal protein L4	yes	no	0.968	0.355	0.729	3e-58

>sp|Q9SF40|RL4A_ARATH 60S ribosomal protein L4-1 OS=Arabidopsis thaliana GN=RPL4A PE=2 SV=1

 Score =  287 bits (734), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 133/156 (85%), Positives = 146/156 (93%)

Query: 2   AAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRK 61
           AAAARPL+T+Q+L+GDM+TD SSTV LPDVM A +RPDIV FVH+ IS NSRQPYAVS+K
Sbjct: 3   AAAARPLVTIQTLDGDMSTDQSSTVVLPDVMTAPVRPDIVNFVHAQISNNSRQPYAVSKK 62

Query: 62  AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINV 121
           AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQ AFGNMCRGGRMFAPTKIWRRWHR++NV
Sbjct: 63  AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQAAFGNMCRGGRMFAPTKIWRRWHRRVNV 122

Query: 122 NQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           N KR+AIVSAIAA+AVP+LVMARGHKIE VPEMPLV
Sbjct: 123 NMKRHAIVSAIAATAVPALVMARGHKIENVPEMPLV 158

Arabidopsis thaliana (taxid: 3702)

>sp|P49691|RL4B_ARATH 60S ribosomal protein L4-2 OS=Arabidopsis thaliana GN=RPL4D PE=1 SV=2

 Score =  284 bits (727), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 132/156 (84%), Positives = 145/156 (92%)

Query: 2   AAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRK 61
           +AAARPL+TVQ L+GDM+TD S+TV LPDVM A +RPDIV FVH+ IS NSRQPYAVS+K
Sbjct: 4   SAAARPLVTVQGLDGDMSTDQSTTVTLPDVMTAPVRPDIVNFVHAQISNNSRQPYAVSKK 63

Query: 62  AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINV 121
           AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQ AFGNMCRGGRMFAPTKIWRRWHR++NV
Sbjct: 64  AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQAAFGNMCRGGRMFAPTKIWRRWHRRVNV 123

Query: 122 NQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           N KR+AIVSAIAA+AVP+LVMARGHKIE VPEMPLV
Sbjct: 124 NMKRHAIVSAIAATAVPALVMARGHKIENVPEMPLV 159

Arabidopsis thaliana (taxid: 3702)

>sp|Q9XF97|RL4_PRUAR 60S ribosomal protein L4 OS=Prunus armeniaca GN=RPL4 PE=2 SV=1

 Score =  283 bits (724), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 142/152 (93%), Positives = 148/152 (97%)

Query: 6   RPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQ 65
           RPL+TVQSLEGDMATD + TV LPDVMKASIRPDIV FVHSNISKNSRQPYAVS+KAGHQ
Sbjct: 9   RPLVTVQSLEGDMATDQTQTVALPDVMKASIRPDIVTFVHSNISKNSRQPYAVSKKAGHQ 68

Query: 66  TSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKR 125
           TSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKR
Sbjct: 69  TSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKR 128

Query: 126 YAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           YA+VSAIAASAVPSLV+ARGHKIETVPE+PLV
Sbjct: 129 YAVVSAIAASAVPSLVLARGHKIETVPELPLV 160

Prunus armeniaca (taxid: 36596)

>sp|Q28346|RL4_CANFA 60S ribosomal protein L4 OS=Canis familiaris GN=RPL4 PE=1 SV=2

 Score =  237 bits (604), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 110/155 (70%), Positives = 129/155 (83%), Gaps = 3/155 (1%)

Query: 3   AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKA 62
           A ARPLI+V S +G+    +   V LP V KA IRPDIV FVH+N+ KN+RQPYAVS  A
Sbjct: 2   ACARPLISVYSEKGE---SSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELA 58

Query: 63  GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVN 122
           GHQTSAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCRGGRMFAPTK WRRWHR++N  
Sbjct: 59  GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTT 118

Query: 123 QKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           QKRYAI SA+A  ++P+LVM++GH+IE VPE+PLV
Sbjct: 119 QKRYAICSALACLSLPALVMSKGHRIEEVPELPLV 153

Canis familiaris (taxid: 9615)

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

 Score =  229 bits (583), Expect = 6e-60,   Method: Compositional matrix adjust.
 Identities = 108/154 (70%), Positives = 127/154 (82%), Gaps = 3/154 (1%)

Query: 4   AARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAG 63
           AARPLITV S   D    + S V LP V +A IRPDIV FVH  + KN RQPYAVS+KAG
Sbjct: 2   AARPLITVHS---DKGAASESNVTLPAVFRAPIRPDIVNFVHFELKKNGRQPYAVSQKAG 58

Query: 64  HQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQ 123
           HQTSAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCRG RMFAPTK WRRWHR++N  Q
Sbjct: 59  HQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGRRMFAPTKTWRRWHRRVNTTQ 118

Query: 124 KRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           +R+A+VSAIAA+ +P++VM++GH IE +PE+PLV
Sbjct: 119 RRHALVSAIAATGIPAVVMSKGHCIEQIPEVPLV 152

Urechis caupo (taxid: 6431)

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

 Score =  228 bits (581), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 106/155 (68%), Positives = 129/155 (83%), Gaps = 3/155 (1%)

Query: 3   AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKA 62
           AAARP +++ S +G ++   S T+ LP V KA IRPD+V  VH+ ++KN RQPYAVS KA
Sbjct: 2   AAARPTVSIYSKDGSVS---SETIALPFVFKAPIRPDLVRSVHTAVAKNKRQPYAVSEKA 58

Query: 63  GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVN 122
           GHQTSAESWGTGRA++RIPRV GGGTHR+GQ AFGNMCR GRMFAPTK WR+WH K+N N
Sbjct: 59  GHQTSAESWGTGRALARIPRVGGGGTHRSGQAAFGNMCRSGRMFAPTKTWRKWHVKVNQN 118

Query: 123 QKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           +KRYAI SA+AAS VPSL++ARGH+IE +PE+PLV
Sbjct: 119 EKRYAISSAVAASGVPSLLLARGHRIEEIPEVPLV 153

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

>sp|Q9P784|RL4B_SCHPO 60S ribosomal protein L4-B OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpl4b PE=3 SV=1

 Score =  227 bits (578), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 105/155 (67%), Positives = 129/155 (83%), Gaps = 3/155 (1%)

Query: 3   AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKA 62
           AAARP +++ + +G ++   S T+ LP V KA IRPD+V  VH+ ++KN RQPYAVS KA
Sbjct: 2   AAARPTVSIYNKDGSVS---SETLALPFVFKAPIRPDLVRSVHTAVAKNKRQPYAVSEKA 58

Query: 63  GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVN 122
           GHQTSAESWGTGRA++RIPRV GGGTHR+GQ AFGNMCR GRMFAPTK WR+WH K+N N
Sbjct: 59  GHQTSAESWGTGRALARIPRVGGGGTHRSGQAAFGNMCRSGRMFAPTKTWRKWHVKVNQN 118

Query: 123 QKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           +KRYAI SA+AAS VPSL++ARGH+IE +PE+PLV
Sbjct: 119 EKRYAIASAVAASGVPSLLLARGHRIEEIPEVPLV 153

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

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

 Score =  224 bits (571), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 113/155 (72%), Positives = 131/155 (84%), Gaps = 3/155 (1%)

Query: 3   AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKA 62
           A ARPLI+V S +G+    +   V LP V KA IRPDIV FVH+N+ KN+RQPYAVS  A
Sbjct: 2   ACARPLISVYSEKGE---SSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELA 58

Query: 63  GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVN 122
           GHQTSAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCRGGRMFAPTK WRRWHR++N  
Sbjct: 59  GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTT 118

Query: 123 QKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           QKRYAI SA+AASA+P+LVM++GH+IE VPE+PLV
Sbjct: 119 QKRYAICSALAASALPALVMSKGHRIEEVPELPLV 153

Bos taurus (taxid: 9913)

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

 Score =  224 bits (571), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 113/155 (72%), Positives = 131/155 (84%), Gaps = 3/155 (1%)

Query: 3   AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKA 62
           A ARPLI+V S +G+    +   V LP V KA IRPDIV FVH+N+ KN+RQPYAVS  A
Sbjct: 2   ACARPLISVYSEKGE---SSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELA 58

Query: 63  GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVN 122
           GHQTSAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCRGGRMFAPTK WRRWHR++N  
Sbjct: 59  GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTT 118

Query: 123 QKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           QKRYAI SA+AASA+P+LVM++GH+IE VPE+PLV
Sbjct: 119 QKRYAICSALAASALPALVMSKGHRIEEVPELPLV 153

Pongo abelii (taxid: 9601)

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

 Score =  223 bits (569), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 113/155 (72%), Positives = 131/155 (84%), Gaps = 3/155 (1%)

Query: 3   AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKA 62
           A ARPLI+V S +G+    +   V LP V KA IRPDIV FVH+N+ KN+RQPYAVS  A
Sbjct: 2   ACARPLISVYSEKGE---SSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELA 58

Query: 63  GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVN 122
           GHQTSAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCRGGRMFAPTK WRRWHR++N  
Sbjct: 59  GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTT 118

Query: 123 QKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           QKRYAI SA+AASA+P+LVM++GH+IE VPE+PLV
Sbjct: 119 QKRYAICSALAASALPALVMSKGHRIEEVPELPLV 153

Homo sapiens (taxid: 9606)

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	157
356548210	405	PREDICTED: 60S ribosomal protein L4-1-li	1.0	0.387	0.917	4e-77
449448709	405	PREDICTED: 60S ribosomal protein L4-like	1.0	0.387	0.929	5e-77
255568434	410	60S ribosomal protein L4, putative [Rici	0.968	0.370	0.876	2e-76
356537467	405	PREDICTED: 60S ribosomal protein L4-1-li	1.0	0.387	0.904	5e-76
356537469	371	PREDICTED: 60S ribosomal protein L4-1-li	1.0	0.423	0.904	5e-76
297829496	406	60S ribosomal protein L4/L1 [Arabidopsis	0.993	0.384	0.865	1e-75
15232723	406	60S ribosomal protein L4-1 [Arabidopsis	0.993	0.384	0.852	1e-75
79313167	405	60S ribosomal protein L4-1 [Arabidopsis	0.993	0.385	0.852	1e-75
449440055	405	PREDICTED: 60S ribosomal protein L4-like	1.0	0.387	0.910	2e-75
26450328	407	putative 60S ribosomal protein [Arabidop	0.993	0.383	0.846	4e-75

>gi|356548210|ref|XP_003542496.1| PREDICTED: 60S ribosomal protein L4-1-like [Glycine max]

 Score =  291 bits (746), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 144/157 (91%), Positives = 156/157 (99%)

Query: 1   MAAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSR 60
           MAAAARPL+TVQ+L+GDMATDAS+TVP+PDVMKASIRPDIV FVHSNISKNSRQPYAVSR
Sbjct: 1   MAAAARPLVTVQALDGDMATDASATVPIPDVMKASIRPDIVNFVHSNISKNSRQPYAVSR 60

Query: 61  KAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN 120
           +AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN
Sbjct: 61  RAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN 120

Query: 121 VNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           VNQKRYA+VSAIAASA+PSLV+ARGH+IE+VPE+PLV
Sbjct: 121 VNQKRYAVVSAIAASAIPSLVLARGHRIESVPELPLV 157

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449448709|ref|XP_004142108.1| PREDICTED: 60S ribosomal protein L4-like [Cucumis sativus] gi|449520008|ref|XP_004167026.1| PREDICTED: 60S ribosomal protein L4-like [Cucumis sativus]

 Score =  291 bits (746), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 146/157 (92%), Positives = 155/157 (98%)

Query: 1   MAAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSR 60
           MAAAARPL++VQSLEGDMATDA+ TVPLPDVMKASIRPDIV FVHSNISKNSRQPYAVS+
Sbjct: 1   MAAAARPLVSVQSLEGDMATDAAPTVPLPDVMKASIRPDIVSFVHSNISKNSRQPYAVSK 60

Query: 61  KAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN 120
           +AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN
Sbjct: 61  RAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN 120

Query: 121 VNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           VNQKRYA+VSAIAASAVPSLV+ARGH+IETVPE+PLV
Sbjct: 121 VNQKRYAVVSAIAASAVPSLVLARGHRIETVPELPLV 157

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255568434|ref|XP_002525191.1| 60S ribosomal protein L4, putative [Ricinus communis] gi|223535488|gb|EEF37157.1| 60S ribosomal protein L4, putative [Ricinus communis]

 Score =  289 bits (740), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 135/154 (87%), Positives = 147/154 (95%), Gaps = 2/154 (1%)

Query: 6   RPLITVQSL--EGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAG 63
           RPL+TVQSL  + DMATDA +TVPLPD MKAS+RPDIV FVH+ +SKNSRQPYAVS++AG
Sbjct: 9   RPLVTVQSLPSQNDMATDAVTTVPLPDSMKASLRPDIVSFVHAQMSKNSRQPYAVSKRAG 68

Query: 64  HQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQ 123
           HQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQ
Sbjct: 69  HQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQ 128

Query: 124 KRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           KRYA+VSAIAASA+PSLVMARGHK+E+VPEMPLV
Sbjct: 129 KRYALVSAIAASAIPSLVMARGHKVESVPEMPLV 162

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356537467|ref|XP_003537248.1| PREDICTED: 60S ribosomal protein L4-1-like isoform 1 [Glycine max]

 Score =  288 bits (737), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 142/157 (90%), Positives = 155/157 (98%)

Query: 1   MAAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSR 60
           MAAAARPL+TVQ+L+ DMATDAS+TVP+PDVMK+SIRPDIV FVHSNISKNSRQPYAVSR
Sbjct: 1   MAAAARPLVTVQALDSDMATDASATVPIPDVMKSSIRPDIVNFVHSNISKNSRQPYAVSR 60

Query: 61  KAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN 120
           +AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN
Sbjct: 61  RAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN 120

Query: 121 VNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           VNQKRYA+VSAIAASA+PSLV+ARGH+IE+VPE+PLV
Sbjct: 121 VNQKRYAVVSAIAASAIPSLVLARGHRIESVPELPLV 157

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356537469|ref|XP_003537249.1| PREDICTED: 60S ribosomal protein L4-1-like isoform 2 [Glycine max]

 Score =  288 bits (737), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 142/157 (90%), Positives = 155/157 (98%)

Query: 1   MAAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSR 60
           MAAAARPL+TVQ+L+ DMATDAS+TVP+PDVMK+SIRPDIV FVHSNISKNSRQPYAVSR
Sbjct: 1   MAAAARPLVTVQALDSDMATDASATVPIPDVMKSSIRPDIVNFVHSNISKNSRQPYAVSR 60

Query: 61  KAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN 120
           +AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN
Sbjct: 61  RAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN 120

Query: 121 VNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           VNQKRYA+VSAIAASA+PSLV+ARGH+IE+VPE+PLV
Sbjct: 121 VNQKRYAVVSAIAASAIPSLVLARGHRIESVPELPLV 157

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297829496|ref|XP_002882630.1| 60S ribosomal protein L4/L1 [Arabidopsis lyrata subsp. lyrata] gi|297328470|gb|EFH58889.1| 60S ribosomal protein L4/L1 [Arabidopsis lyrata subsp. lyrata]

 Score =  287 bits (734), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 135/156 (86%), Positives = 145/156 (92%)

Query: 2   AAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRK 61
           AAAARPL+TVQ L+GDM+TD SSTV LPDVM A +RPDIV FVH+ IS NSRQPYAVS+K
Sbjct: 3   AAAARPLVTVQVLDGDMSTDQSSTVVLPDVMTAPVRPDIVNFVHAQISNNSRQPYAVSKK 62

Query: 62  AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINV 121
           AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQ AFGNMCRGGRMFAPTKIWRRWHR++NV
Sbjct: 63  AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQAAFGNMCRGGRMFAPTKIWRRWHRRVNV 122

Query: 122 NQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           N KR+AIVSAIAA+AVPSLVMARGHKIE VPEMPLV
Sbjct: 123 NMKRHAIVSAIAATAVPSLVMARGHKIENVPEMPLV 158

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15232723|ref|NP_187574.1| 60S ribosomal protein L4-1 [Arabidopsis thaliana] gi|17369604|sp|Q9SF40.1|RL4A_ARATH RecName: Full=60S ribosomal protein L4-1; Short=L1 gi|6682241|gb|AAF23293.1|AC016661_18 putative 60S ribosomal protein L1 [Arabidopsis thaliana] gi|15982715|gb|AAL09727.1| AT3g09630/F11F8_22 [Arabidopsis thaliana] gi|27311665|gb|AAO00798.1| putative 60S ribosomal protein L1 [Arabidopsis thaliana] gi|30725664|gb|AAP37854.1| At3g09630 [Arabidopsis thaliana] gi|332641268|gb|AEE74789.1| 60S ribosomal protein L4-1 [Arabidopsis thaliana]

 Score =  287 bits (734), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 133/156 (85%), Positives = 146/156 (93%)

Query: 2   AAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRK 61
           AAAARPL+T+Q+L+GDM+TD SSTV LPDVM A +RPDIV FVH+ IS NSRQPYAVS+K
Sbjct: 3   AAAARPLVTIQTLDGDMSTDQSSTVVLPDVMTAPVRPDIVNFVHAQISNNSRQPYAVSKK 62

Query: 62  AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINV 121
           AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQ AFGNMCRGGRMFAPTKIWRRWHR++NV
Sbjct: 63  AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQAAFGNMCRGGRMFAPTKIWRRWHRRVNV 122

Query: 122 NQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           N KR+AIVSAIAA+AVP+LVMARGHKIE VPEMPLV
Sbjct: 123 NMKRHAIVSAIAATAVPALVMARGHKIENVPEMPLV 158

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|79313167|ref|NP_001030663.1| 60S ribosomal protein L4-1 [Arabidopsis thaliana] gi|332641269|gb|AEE74790.1| 60S ribosomal protein L4-1 [Arabidopsis thaliana]

 Score =  286 bits (733), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 133/156 (85%), Positives = 146/156 (93%)

Query: 2   AAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRK 61
           AAAARPL+T+Q+L+GDM+TD SSTV LPDVM A +RPDIV FVH+ IS NSRQPYAVS+K
Sbjct: 3   AAAARPLVTIQTLDGDMSTDQSSTVVLPDVMTAPVRPDIVNFVHAQISNNSRQPYAVSKK 62

Query: 62  AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINV 121
           AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQ AFGNMCRGGRMFAPTKIWRRWHR++NV
Sbjct: 63  AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQAAFGNMCRGGRMFAPTKIWRRWHRRVNV 122

Query: 122 NQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           N KR+AIVSAIAA+AVP+LVMARGHKIE VPEMPLV
Sbjct: 123 NMKRHAIVSAIAATAVPALVMARGHKIENVPEMPLV 158

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449440055|ref|XP_004137800.1| PREDICTED: 60S ribosomal protein L4-like [Cucumis sativus] gi|449519122|ref|XP_004166584.1| PREDICTED: 60S ribosomal protein L4-like [Cucumis sativus]

 Score =  286 bits (733), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 143/157 (91%), Positives = 153/157 (97%)

Query: 1   MAAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSR 60
           MAAAARPL+ VQ LEGDMATD+S TVPLPDVMKASIRPDIV FVHSNISKNSRQPYAVS+
Sbjct: 1   MAAAARPLVAVQVLEGDMATDSSPTVPLPDVMKASIRPDIVSFVHSNISKNSRQPYAVSK 60

Query: 61  KAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN 120
           +AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN
Sbjct: 61  RAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN 120

Query: 121 VNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           VNQKRYA+VSAIAASA+PSLV+ARGH+IE+VPE+PLV
Sbjct: 121 VNQKRYAVVSAIAASAIPSLVLARGHRIESVPELPLV 157

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|26450328|dbj|BAC42280.1| putative 60S ribosomal protein [Arabidopsis thaliana]

 Score =  285 bits (729), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 132/156 (84%), Positives = 145/156 (92%)

Query: 2   AAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRK 61
           +AAARPL+TVQ L+GDM+TD S+TV LPDVM A +RPDIV FVH+ IS NSRQPYAVS+K
Sbjct: 4   SAAARPLVTVQGLDGDMSTDQSTTVTLPDVMTAPVRPDIVNFVHAQISNNSRQPYAVSKK 63

Query: 62  AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINV 121
           AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQ AFGNMCRGGRMFAPTKIWRRWHR++NV
Sbjct: 64  AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQAAFGNMCRGGRMFAPTKIWRRWHRRVNV 123

Query: 122 NQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           N KR+AIVSAIAA+AVP+LVMARGHKIE VPEMPLV
Sbjct: 124 NMKRHAIVSAIAATAVPALVMARGHKIENVPEMPLV 159

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	157
TAIR|locus:2074904	406	AT3G09630 [Arabidopsis thalian	0.993	0.384	0.788	7.4e-66
TAIR|locus:2151296	407	AT5G02870 [Arabidopsis thalian	0.993	0.383	0.782	2.5e-65
ZFIN|ZDB-GENE-030131-9034	375	rpl4 "ribosomal protein L4" [D	0.968	0.405	0.690	3.7e-55
UNIPROTKB|Q5ZII1	421	RPL4 "Uncharacterized protein"	0.968	0.361	0.670	1.3e-54
UNIPROTKB|Q58DW0	422	RPL4 "60S ribosomal protein L4	0.968	0.360	0.677	1.6e-54
UNIPROTKB|E2R546	412	RPL4 "60S ribosomal protein L4	0.968	0.368	0.677	1.6e-54
UNIPROTKB|F1PVZ2	422	RPL4 "60S ribosomal protein L4	0.968	0.360	0.677	1.6e-54
UNIPROTKB|J9JHV8	422	RPL4 "60S ribosomal protein L4	0.968	0.360	0.677	1.6e-54
UNIPROTKB|P36578	427	RPL4 "60S ribosomal protein L4	0.968	0.355	0.677	1.6e-54
UNIPROTKB|F1SJJ5	426	RPL4 "60S ribosomal protein L4	0.968	0.356	0.677	1.6e-54

TAIR|locus:2074904 AT3G09630 [Arabidopsis thaliana (taxid:3702)]

 Score = 670 (240.9 bits), Expect = 7.4e-66, P = 7.4e-66
 Identities = 123/156 (78%), Positives = 135/156 (86%)

Query:     2 AAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRK 61
             AAAARPL+T+Q+L+GDM+TD SSTV LPDVM A +RPDIV FVH+ IS NSRQPYAVS+K
Sbjct:     3 AAAARPLVTIQTLDGDMSTDQSSTVVLPDVMTAPVRPDIVNFVHAQISNNSRQPYAVSKK 62

Query:    62 AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINV 121
             AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQ AFGNMCRGGRMFAPTKIWRRWHR++NV
Sbjct:    63 AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQAAFGNMCRGGRMFAPTKIWRRWHRRVNV 122

Query:   122 NQKRYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
             N KR+           P+LVMARGHKIE VPEMPLV
Sbjct:   123 NMKRHAIVSAIAATAVPALVMARGHKIENVPEMPLV 158

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

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=IDA

GO:0005773 "vacuole" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0005618 "cell wall" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0016020 "membrane" evidence=IDA

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

GO:0005829 "cytosol" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

GO:0001510 "RNA methylation" evidence=RCA

GO:0009220 "pyrimidine ribonucleotide biosynthetic process" evidence=RCA

GO:0009664 "plant-type cell wall organization" evidence=RCA

GO:0042545 "cell wall modification" evidence=RCA

TAIR|locus:2151296 AT5G02870 [Arabidopsis thaliana (taxid:3702)]

 Score = 665 (239.2 bits), Expect = 2.5e-65, P = 2.5e-65
 Identities = 122/156 (78%), Positives = 134/156 (85%)

Query:     2 AAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRK 61
             +AAARPL+TVQ L+GDM+TD S+TV LPDVM A +RPDIV FVH+ IS NSRQPYAVS+K
Sbjct:     4 SAAARPLVTVQGLDGDMSTDQSTTVTLPDVMTAPVRPDIVNFVHAQISNNSRQPYAVSKK 63

Query:    62 AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINV 121
             AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQ AFGNMCRGGRMFAPTKIWRRWHR++NV
Sbjct:    64 AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQAAFGNMCRGGRMFAPTKIWRRWHRRVNV 123

Query:   122 NQKRYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
             N KR+           P+LVMARGHKIE VPEMPLV
Sbjct:   124 NMKRHAIVSAIAATAVPALVMARGHKIENVPEMPLV 159

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

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA;ISS

GO:0015934 "large ribosomal subunit" evidence=ISS

GO:0009507 "chloroplast" evidence=IDA

GO:0005773 "vacuole" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0005774 "vacuolar membrane" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0016020 "membrane" evidence=IDA

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

GO:0005829 "cytosol" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

GO:0001510 "RNA methylation" evidence=RCA

GO:0009220 "pyrimidine ribonucleotide biosynthetic process" evidence=RCA

GO:0009664 "plant-type cell wall organization" evidence=RCA

GO:0042545 "cell wall modification" evidence=RCA

ZFIN|ZDB-GENE-030131-9034 rpl4 "ribosomal protein L4" [Danio rerio (taxid:7955)]

 Score = 569 (205.4 bits), Expect = 3.7e-55, P = 3.7e-55
 Identities = 107/155 (69%), Positives = 123/155 (79%)

Query:     3 AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKA 62
             A ARPLI+V S +G+  T   + V +P V +A IRPDIV FVH+N+ KN RQPYAVS  A
Sbjct:     2 ACARPLISVYSEKGE--TSGKNVV-MPAVFRAPIRPDIVNFVHTNMRKNKRQPYAVSELA 58

Query:    63 GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVN 122
             GHQTSAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCRGGRMFAPTK WRRWHR++NVN
Sbjct:    59 GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNVN 118

Query:   123 QKRYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
             QKRY           PSLVMA+GH+IE +PE+PLV
Sbjct:   119 QKRYAMCSALAASALPSLVMAKGHRIEEIPEVPLV 153

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|Q5ZII1 RPL4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 564 (203.6 bits), Expect = 1.3e-54, P = 1.3e-54
 Identities = 104/155 (67%), Positives = 122/155 (78%)

Query:     3 AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKA 62
             A ARPLI+V S +G+ +      V LP V KA IRPD+V FVH+N+ KN+RQPYAVS  A
Sbjct:     2 ACARPLISVYSEKGEAS---GKNVTLPAVFKAPIRPDVVNFVHTNLRKNNRQPYAVSELA 58

Query:    63 GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVN 122
             GHQTSAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCRGGRMFAPTK WRRWHR++NV 
Sbjct:    59 GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNVT 118

Query:   123 QKRYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
             QKRY           P+LVM++GH+IE +PE+PLV
Sbjct:   119 QKRYAICSALAASALPALVMSKGHRIEEIPELPLV 153

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

GO:0006412 "translation" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

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

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

 Score = 563 (203.2 bits), Expect = 1.6e-54, P = 1.6e-54
 Identities = 105/155 (67%), Positives = 121/155 (78%)

Query:     3 AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKA 62
             A ARPLI+V S +G+    +   V LP V KA IRPDIV FVH+N+ KN+RQPYAVS  A
Sbjct:     2 ACARPLISVYSEKGE---SSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELA 58

Query:    63 GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVN 122
             GHQTSAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCRGGRMFAPTK WRRWHR++N  
Sbjct:    59 GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTT 118

Query:   123 QKRYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
             QKRY           P+LVM++GH+IE VPE+PLV
Sbjct:   119 QKRYAICSALAASALPALVMSKGHRIEEVPELPLV 153

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

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

 Score = 563 (203.2 bits), Expect = 1.6e-54, P = 1.6e-54
 Identities = 105/155 (67%), Positives = 121/155 (78%)

Query:     3 AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKA 62
             A ARPLI+V S +G+    +   V LP V KA IRPDIV FVH+N+ KN+RQPYAVS  A
Sbjct:     2 ACARPLISVYSEKGE---SSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELA 58

Query:    63 GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVN 122
             GHQTSAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCRGGRMFAPTK WRRWHR++N  
Sbjct:    59 GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTT 118

Query:   123 QKRYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
             QKRY           P+LVM++GH+IE VPE+PLV
Sbjct:   119 QKRYAICSALAASALPALVMSKGHRIEEVPELPLV 153

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 = 563 (203.2 bits), Expect = 1.6e-54, P = 1.6e-54
 Identities = 105/155 (67%), Positives = 121/155 (78%)

Query:     3 AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKA 62
             A ARPLI+V S +G+    +   V LP V KA IRPDIV FVH+N+ KN+RQPYAVS  A
Sbjct:     2 ACARPLISVYSEKGE---SSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELA 58

Query:    63 GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVN 122
             GHQTSAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCRGGRMFAPTK WRRWHR++N  
Sbjct:    59 GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTT 118

Query:   123 QKRYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
             QKRY           P+LVM++GH+IE VPE+PLV
Sbjct:   119 QKRYAICSALAASALPALVMSKGHRIEEVPELPLV 153

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

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

UNIPROTKB|J9JHV8 RPL4 "60S ribosomal protein L4" [Canis lupus familiaris (taxid:9615)]

 Score = 563 (203.2 bits), Expect = 1.6e-54, P = 1.6e-54
 Identities = 105/155 (67%), Positives = 121/155 (78%)

Query:     3 AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKA 62
             A ARPLI+V S +G+    +   V LP V KA IRPDIV FVH+N+ KN+RQPYAVS  A
Sbjct:     2 ACARPLISVYSEKGE---SSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELA 58

Query:    63 GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVN 122
             GHQTSAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCRGGRMFAPTK WRRWHR++N  
Sbjct:    59 GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTT 118

Query:   123 QKRYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
             QKRY           P+LVM++GH+IE VPE+PLV
Sbjct:   119 QKRYAICSALAASALPALVMSKGHRIEEVPELPLV 153

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

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

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

 Score = 563 (203.2 bits), Expect = 1.6e-54, P = 1.6e-54
 Identities = 105/155 (67%), Positives = 121/155 (78%)

Query:     3 AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKA 62
             A ARPLI+V S +G+    +   V LP V KA IRPDIV FVH+N+ KN+RQPYAVS  A
Sbjct:     2 ACARPLISVYSEKGE---SSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELA 58

Query:    63 GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVN 122
             GHQTSAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCRGGRMFAPTK WRRWHR++N  
Sbjct:    59 GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTT 118

Query:   123 QKRYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
             QKRY           P+LVM++GH+IE VPE+PLV
Sbjct:   119 QKRYAICSALAASALPALVMSKGHRIEEVPELPLV 153

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 = 563 (203.2 bits), Expect = 1.6e-54, P = 1.6e-54
 Identities = 105/155 (67%), Positives = 121/155 (78%)

Query:     3 AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKA 62
             A ARPLI+V S +G+    +   V LP V KA IRPDIV FVH+N+ KN+RQPYAVS  A
Sbjct:     2 ACARPLISVYSEKGE---SSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELA 58

Query:    63 GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVN 122
             GHQTSAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCRGGRMFAPTK WRRWHR++N  
Sbjct:    59 GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTT 118

Query:   123 QKRYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
             QKRY           P+LVM++GH+IE VPE+PLV
Sbjct:   119 QKRYAICSALAASALPALVMSKGHRIEEVPELPLV 153

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

---

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	0.7225	0.9681	0.3610	yes	no
Q58DW0	RL4_BOVIN	No assigned EC number	0.7290	0.9681	0.3601	yes	no
Q5RCR3	RL4_PONAB	No assigned EC number	0.7290	0.9681	0.3559	yes	no
Q28346	RL4_CANFA	No assigned EC number	0.7096	0.9681	0.3610	yes	no
P49691	RL4B_ARATH	No assigned EC number	0.8461	0.9936	0.3832	yes	no
P36578	RL4_HUMAN	No assigned EC number	0.7290	0.9681	0.3559	yes	no
Q9D8E6	RL4_MOUSE	No assigned EC number	0.7290	0.9681	0.3627	yes	no
Q9SF40	RL4A_ARATH	No assigned EC number	0.8525	0.9936	0.3842	yes	no
Q9XF97	RL4_PRUAR	No assigned EC number	0.9342	0.9681	0.3725	N/A	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	fgenesh2_kg.3__983__AT3G09630.2	annotation not avaliable (406 aa)
		(Arabidopsis lyrata)
Predicted Functional Partners:
	fgenesh2_kg.1__3711__AT1G43170.1	annotation not avaliable (389 aa)	•		•	•	•	•	•		0.913
	fgenesh2_kg.2__299__AT1G61580.1	annotation not avaliable (390 aa)	•		•	•	•	•	•		0.910
	scaffold_800913.1	annotation not avaliable (375 aa)	•		•	•	•	•	•		0.888
	scaffold_603399.1	annotation not avaliable (194 aa)	•			•	•	•	•		0.860
	fgenesh2_kg.2__971__AT1G67430.1	annotation not avaliable (175 aa)	•			•	•	•			0.854
	fgenesh2_kg.1__3446__AT1G33140.1	annotation not avaliable (194 aa)	•			•	•	•	•		0.852
	fgenesh2_kg.1__2897__AT1G27400.1	annotation not avaliable (176 aa)	•			•	•	•			0.851
	fgenesh2_kg.8__2660__AT5G67510.1	annotation not avaliable (146 aa)	•			•	•	•			0.846
	Al_scaffold_0003_3767	annotation not avaliable (258 aa)	•			•	•		•		0.832
	fgenesh2_kg.7__451__AT4G36130.1	annotation not avaliable (258 aa)	•			•	•		•		0.830

---

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	157
PLN00185	405	PLN00185, PLN00185, 60S ribosomal protein L4-1; Pr	1e-113
PTZ00428	381	PTZ00428, PTZ00428, 60S ribosomal protein L4; Prov	3e-94
PRK04042	254	PRK04042, rpl4lp, 50S ribosomal protein L4P; Provi	5e-39
TIGR03672	251	TIGR03672, rpl4p_arch, 50S ribosomal protein L4P	4e-34
COG0088	214	COG0088, RplD, Ribosomal protein L4 [Translation,	2e-26
pfam00573	190	pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 f	3e-19

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

 Score =  327 bits (840), Expect = e-113
 Identities = 139/157 (88%), Positives = 149/157 (94%)

Query: 1   MAAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSR 60
            AAAARPL++VQSL+GDMATD S+TV LPDVM A IRPDIV FVH+NISKNSRQPYAVS+
Sbjct: 1   AAAAARPLVSVQSLDGDMATDKSATVALPDVMTAPIRPDIVNFVHTNISKNSRQPYAVSK 60

Query: 61  KAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN 120
           KAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTK WRRWHRK+N
Sbjct: 61  KAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKTWRRWHRKVN 120

Query: 121 VNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           VNQKRYA+VSA+AASAVPSLVMARGHKIE VPE+PLV
Sbjct: 121 VNQKRYAVVSALAASAVPSLVMARGHKIENVPEVPLV 157

Length = 405

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

 Score =  277 bits (710), Expect = 3e-94
 Identities = 106/155 (68%), Positives = 123/155 (79%), Gaps = 3/155 (1%)

Query: 3   AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKA 62
             ARP+++V S           TVPLP V  A IRPD+V FVH+N++KN RQ YAV   A
Sbjct: 1   MTARPVVSVYSASDKSVV---GTVPLPAVFTAPIRPDLVQFVHTNMAKNRRQAYAVKPLA 57

Query: 63  GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVN 122
           G Q SAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCRGGRMFAPTK WRRWHRK+N+N
Sbjct: 58  GMQHSAESWGTGRAVARIPRVSGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRKVNLN 117

Query: 123 QKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           QKR+A+ SA+AAS VP+LVMARGH+I  VPE+PLV
Sbjct: 118 QKRHAVASALAASGVPALVMARGHRISNVPEVPLV 152

Length = 381

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

 Score =  132 bits (334), Expect = 5e-39
 Identities = 61/148 (41%), Positives = 82/148 (55%), Gaps = 9/148 (6%)

Query: 10  TVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAE 69
            V  L+G++       + LP V +  +RPD++            QP      AG +TSAE
Sbjct: 4   KVYDLDGEVV----GEIELPAVFEEPVRPDLIRRAVLAAQTARLQPKGRDPLAGKRTSAE 59

Query: 70  SWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIV 129
           SWG+GR ++R+PR+ GG      + AF     GGR   P K+ +  H KIN  ++R AI 
Sbjct: 60  SWGSGRGIARVPRLKGGS-----RAAFVPQAVGGRRAHPPKVEKDLHEKINKKERRLAIR 114

Query: 130 SAIAASAVPSLVMARGHKIETVPEMPLV 157
           SAIAA+A P LV ARGH  E VPE+PLV
Sbjct: 115 SAIAATANPELVKARGHVFEGVPELPLV 142

Length = 254

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

 Score =  119 bits (301), Expect = 4e-34
 Identities = 59/149 (39%), Positives = 81/149 (54%), Gaps = 10/149 (6%)

Query: 9   ITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSA 68
             V  L+G++       + LP V +  +RPD++         N  QPY     AG +TSA
Sbjct: 3   AKVYDLDGEVV----GEIELPAVFEEPVRPDLIKRAVLAAQTNRLQPYGADPYAGKRTSA 58

Query: 69  ESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAI 128
           ESWG+GR ++R+PR+ GG      + A      GGR   P K+ +  H KIN  ++R AI
Sbjct: 59  ESWGSGRGIARVPRIKGGS-----RAARVPQAVGGRRAHPPKVEKDLHEKINKKERRLAI 113

Query: 129 VSAIAASAVPSLVMARGHKIETVPEMPLV 157
            SAIAA+A P LV ARGH  E   E+P+V
Sbjct: 114 RSAIAATADPELVKARGHVFEGD-ELPIV 141

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

 Score = 98.4 bits (246), Expect = 2e-26
 Identities = 33/149 (22%), Positives = 57/149 (38%), Gaps = 13/149 (8%)

Query: 6   RPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQ 65
              + V  L+G+   +      LP+V       D++         N RQ    ++  G  
Sbjct: 1   MMKLKVYDLDGE---EVGEVELLPEVFGPERNEDLIHRAVLAQLANRRQGTHSTKTRGEV 57

Query: 66  TSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKR 125
           +       G+  +   R     +            RGG +    K  R + +K+N  ++R
Sbjct: 58  SGGGKKPWGQKGTGRARQGSIRS---------PQWRGGGVAHGPKPERDYSQKLNKKERR 108

Query: 126 YAIVSAIAASAVP-SLVMARGHKIETVPE 153
            A+ SA++A A    LV+ RGH  E  P+
Sbjct: 109 LALRSALSAKARAGKLVVVRGHVFEDAPK 137

Length = 214

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

 Score = 79.4 bits (197), Expect = 3e-19
 Identities = 33/123 (26%), Positives = 49/123 (39%), Gaps = 22/123 (17%)

Query: 29  PDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAE--SW----GTGRAVSRIPR 82
           P V  A IRPD++         N RQ  A + K   + S          GTGRA  R   
Sbjct: 5   PAVFGAEIRPDLLHRAVVAQLANRRQGTAST-KTRSEVSGGGKKPWRQKGTGRA--RAGS 61

Query: 83  VPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVM 142
           +      R+       + RGG +    K  R +  K+N   +R A+ SA++A A    ++
Sbjct: 62  I------RS------PLWRGGGVAFGPKP-RDYSYKLNKKVRRLALRSALSAKAREGKLV 108

Query: 143 ARG 145
              
Sbjct: 109 VVD 111

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	157
PLN00185	405	60S ribosomal protein L4-1; Provisional	100.0
PRK04042	254	rpl4lp 50S ribosomal protein L4P; Provisional	100.0
TIGR03672	251	rpl4p_arch 50S ribosomal protein L4P. One of the p	100.0
PTZ00428	381	60S ribosomal protein L4; Provisional	100.0
COG0088	214	RplD Ribosomal protein L4 [Translation, ribosomal	100.0
PRK14547	298	rplD 50S ribosomal protein L4; Provisional	100.0
CHL00147	215	rpl4 ribosomal protein L4; Validated	100.0
PRK05319	205	rplD 50S ribosomal protein L4; Provisional	100.0
KOG1475	363	consensus Ribosomal protein RPL1/RPL2/RL4L4 [RNA p	100.0
PRK14907	295	rplD 50S ribosomal protein L4; Provisional	100.0
PF00573	192	Ribosomal_L4: Ribosomal protein L4/L1 family; Inte	100.0
KOG1624	290	consensus Mitochondrial/chloroplast ribosomal prot	99.97

>PLN00185 60S ribosomal protein L4-1; Provisional

Probab=100.00  E-value=3.5e-52  Score=367.20  Aligned_cols=152  Identities=80%  Similarity=1.207  Sum_probs=146.3

Q ss_pred             CcccCCCccEEeccCC----CccccCCccccccccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccc
Q 048058            1 MAAAARPLITVQSLEG----DMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRA   76 (157)
Q Consensus         1 ~~~~~~~~v~V~n~~G----~~~~~~gg~ieLp~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k   76 (157)
                      |||++||.++|||++|    +.+    ++|+||+||+.|+|+||||+||+++++|+||||+.++.||+++++||||+|++
T Consensus         1 ~~~~~rp~v~V~~~~g~~~~~~~----~~v~Lp~VF~~piR~dlv~~v~~~~~~n~RQp~~~~~~AG~qtsAeswGtGR~   76 (405)
T PLN00185          1 AAAAARPLVSVQSLDGDMATDKS----ATVALPDVMTAPIRPDIVNFVHTNISKNSRQPYAVSKKAGHQTSAESWGTGRA   76 (405)
T ss_pred             CCcccCCeeEEEcCCCCcccccc----ceeehHHHhCCCCCHHHHHHHHHHHHHhccCCCCCCcccCCcceeeecCCCCC
Confidence            7999999999999999    555    89999999999999999999999999999999999999999999999999999


Q ss_pred             cccccccCCCCcccCCCCCCCccccccccccCCcc-CcceeeccCHHHHHHHHHHHHHhccChhhHhhcCcccCCCCCCC
Q 048058           77 VSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKI-WRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMP  155 (157)
Q Consensus        77 ~~r~prqkg~GtgRar~g~rsP~~rGGg~afgPkp-~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rgh~~~~~~~~P  155 (157)
                      ++|+|||||.||+|||||++ |+|++||++|||+| ||+|++|||+|+|++|++||||+++.++||.+|||+|++++++|
T Consensus        77 vaRiPR~kggGT~RAgqGa~-~~~~rGGr~FgP~p~~R~~~~KvNkK~rRlAl~SALAa~a~~~lV~arGH~i~~v~e~p  155 (405)
T PLN00185         77 VSRIPRVPGGGTHRAGQGAF-GNMCRGGRMFAPTKTWRRWHRKVNVNQKRYAVVSALAASAVPSLVMARGHKIENVPEVP  155 (405)
T ss_pred             ceecccccCCCCCcCCccCc-CCcCCCCeeCCCCCCccccccccCHHHHHHHHHHHHHhhccchhhhcccccccccccCC
Confidence            99999999999999999988 88888888888887 69999999999999999999999999999999999999999999


Q ss_pred             CC
Q 048058          156 LV  157 (157)
Q Consensus       156 iv  157 (157)
                      ||
T Consensus       156 LV  157 (405)
T PLN00185        156 LV  157 (405)
T ss_pred             EE
Confidence            86

>PRK04042 rpl4lp 50S ribosomal protein L4P; Provisional

Probab=100.00  E-value=2.7e-50  Score=338.54  Aligned_cols=142  Identities=43%  Similarity=0.677  Sum_probs=133.9

Q ss_pred             CccEEeccCCCccccCCccccccccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCCC
Q 048058            7 PLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGG   86 (157)
Q Consensus         7 ~~v~V~n~~G~~~~~~gg~ieLp~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg~   86 (157)
                      |+++|||++|+.+    +++|||+||+.++|+||||++|++|++|+||||+.+|+|+||+|+||||+|++.+|+||||  
T Consensus         1 ~~v~v~~~~g~~~----g~i~L~~vF~~~~~~~lv~~vv~~~~an~Rqgt~~~~ta~tKtraev~G~Gr~~~Kp~rQK--   74 (254)
T PRK04042          1 MKAKVYDLDGEVV----GEIELPAVFEEPVRPDLIRRAVLAAQTARLQPKGRDPLAGKRTSAESWGSGRGIARVPRLK--   74 (254)
T ss_pred             CeeEEEcCCCCCc----ceEehhHhhCCCCcHHHHHHHHHHHHHhccCCCCCCccccCccceeEcCCCCCcCcCCccC--
Confidence            4799999999999    8999999999999999999999999999999999999999999999999999887778855  


Q ss_pred             CcccCCCCCCCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccChhhHhhcCcccCCCCCCCCC
Q 048058           87 GTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV  157 (157)
Q Consensus        87 GtgRar~g~rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rgh~~~~~~~~Piv  157 (157)
                      |||||+   +||+|||||++|||+|+|+|++|||||+|++||+||||+++.++||++|||.|++++|||||
T Consensus        75 GTGrAr---rsP~~rGGgv~fgPkp~R~y~~klnkK~rrlAlrsALs~k~~~~lv~~~~~~~~~~~e~~lv  142 (254)
T PRK04042         75 GGSRAA---FVPQAVGGRRAHPPKVEKDLHEKINKKERRLAIRSAIAATANPELVKARGHVFEGVPELPLV  142 (254)
T ss_pred             CCCCcc---ccCccCcCCeeCCCCCCcccccccCHHHHHHHHHHHHHHhhhhhhhhhcCccccCCCccCEE
Confidence            555554   89999999999999999999999999999999999999999999999999999999999985

>TIGR03672 rpl4p_arch 50S ribosomal protein L4P

Probab=100.00  E-value=1.3e-48  Score=327.85  Aligned_cols=141  Identities=43%  Similarity=0.665  Sum_probs=132.8

Q ss_pred             CccEEeccCCCccccCCccccccccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCCC
Q 048058            7 PLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGG   86 (157)
Q Consensus         7 ~~v~V~n~~G~~~~~~gg~ieLp~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg~   86 (157)
                      |+++|||++|+.+    ++++||+||+.|++++|||++|++|++|+||||+++|.|+||+|+||||+|++++|+||||| 
T Consensus         1 m~~~v~~~~g~~~----~~i~l~~vF~~~~~~~lv~~vv~~~~an~Rqgt~~~~~a~tKtraev~G~Grg~aKp~rQKG-   75 (251)
T TIGR03672         1 MKAKVYDLDGEVV----GEIELPAVFEEPVRPDLIKRAVLAAQTNRLQPYGADPYAGKRTSAESWGSGRGIARVPRIKG-   75 (251)
T ss_pred             CceEEEccCCCCc----ceEehHHhhCCCccHHHHHHHHHHHHHhccCCCCCCcccCcccceeEccCCCCcCCCCccCC-
Confidence            4789999999998    89999999999999999999999999999999999899999999999999998888888555 


Q ss_pred             CcccCCCCCCCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccChhhHhhcCcccCCCCCCCCC
Q 048058           87 GTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV  157 (157)
Q Consensus        87 GtgRar~g~rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rgh~~~~~~~~Piv  157 (157)
                       ||||   .+||+|||||++|||+|||+|++|||||+|++|++||||+++.++||.+|||.|+++ ++|||
T Consensus        76 -TGrA---~rsP~~rGGGv~fgPkp~R~y~~klNkK~rrlAl~sALs~k~~~~lv~~~~~~~~~~-e~~lv  141 (251)
T TIGR03672        76 -GSRA---ARVPQAVGGRRAHPPKVEKDLHEKINKKERRLAIRSAIAATADPELVKARGHVFEGD-ELPIV  141 (251)
T ss_pred             -CCcc---eecCccCcCCeeCCCCCCcccceecCHHHHHHHHHHHHHHhcchhhhhhcccccccc-cccEE
Confidence             5555   689999999999999999999999999999999999999999999999999999999 88875

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.

>PTZ00428 60S ribosomal protein L4; Provisional

Probab=100.00  E-value=2.4e-47  Score=334.80  Aligned_cols=150  Identities=67%  Similarity=1.119  Sum_probs=143.6

Q ss_pred             ccCCCccEEeccCC-CccccCCccccccccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeecccccccccc
Q 048058            3 AAARPLITVQSLEG-DMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIP   81 (157)
Q Consensus         3 ~~~~~~v~V~n~~G-~~~~~~gg~ieLp~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~p   81 (157)
                      |++||+++|||++| +.+    ++|+||+||+.|+|+||||+||+++++|+||||++++++++++++|+||||++.+|+|
T Consensus         1 ~~~r~~v~V~~~~g~~~~----~~v~Lp~VF~~pir~dlV~~vv~~~~aN~RQgta~s~~ag~~tsakswGTGRA~arip   76 (381)
T PTZ00428          1 MTARPVVSVYSASDKSVV----GTVPLPAVFTAPIRPDLVQFVHTNMAKNRRQAYAVKPLAGMQHSAESWGTGRAVARIP   76 (381)
T ss_pred             CCCCCeeEEEcCCCCccc----ceEehHHhhCCCCcHHHHHHHHHHHHHhccCCCCcCCCCCCCCCceecCCCCCccccc
Confidence            67899999999999 556    8999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCcccCCCCCCCccccccccccCCcc-CcceeeccCHHHHHHHHHHHHHhccChhhHhhcCcccCCCCCCCCC
Q 048058           82 RVPGGGTHRAGQGAFGNMCRGGRMFAPTKI-WRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV  157 (157)
Q Consensus        82 rqkg~GtgRar~g~rsP~~rGGg~afgPkp-~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rgh~~~~~~~~Piv  157 (157)
                      ||+|.||+|+++|+++|+|+||+ +|||+| ||+|++|||+|+|++|++||||+++.+.||++|||+||+++|+|||
T Consensus        77 R~kg~GT~Rs~qGa~~n~~rGG~-~FgP~~~~R~~~~KvNkK~rR~Al~SALaa~a~~~lv~argh~i~~v~e~plV  152 (381)
T PTZ00428         77 RVSGGGTHRSGQGAFGNMCRGGR-MFAPTKTWRRWHRKVNLNQKRHAVASALAASGVPALVMARGHRISNVPEVPLV  152 (381)
T ss_pred             cccCCCCCcCcccccCCcCCCce-EcCCCCCccccccccCHHHHHHHHHHHHHhhccchhhhcccccccccccCCEE
Confidence            99999999999999999999888 666666 7999999999999999999999999999999999999999999986

>COG0088 RplD Ribosomal protein L4 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=2.9e-44  Score=295.69  Aligned_cols=131  Identities=31%  Similarity=0.373  Sum_probs=120.8

Q ss_pred             CCccEEeccCCCccccCCcccccc-ccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccC
Q 048058            6 RPLITVQSLEGDMATDASSTVPLP-DVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVP   84 (157)
Q Consensus         6 ~~~v~V~n~~G~~~~~~gg~ieLp-~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqk   84 (157)
                      ||+++|||++|+.+    ++++++ +||..+.+.||||++|++|++|+|||||+     +++++|++|+|+|    || +
T Consensus         1 m~k~~v~~~~G~~~----g~~~~~~~vf~~~~~~dli~~av~a~~a~~RQgt~~-----~k~rgevs~~g~K----p~-~   66 (214)
T COG0088           1 MMKLKVYDLDGEEV----GEVELLPEVFGPERNEDLIHRAVLAQLANRRQGTHS-----TKTRGEVSGGGKK----PW-G   66 (214)
T ss_pred             CCcceEeCCCCCCc----cccccChhhccCCchHHHHHHHHHHHHHhhhccCCC-----CCCcccccccCcC----CC-C
Confidence            45999999999999    997775 79998888999999999999999999876     4789999999997    54 6


Q ss_pred             CCCcccCCCCC-CCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccCh-hhHhhcCcccCC
Q 048058           85 GGGTHRAGQGA-FGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVP-SLVMARGHKIET  150 (157)
Q Consensus        85 g~GtgRar~g~-rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~-~~v~~rgh~~~~  150 (157)
                      |+||||||+|+ ++|+|||||++|||+|+|||++|||||||+|||+||||+++++ +||..+||.|++
T Consensus        67 QkgtgraR~gs~rsP~~rGGg~a~gPkp~r~~~~klnkK~rrlAl~sAls~ka~~~~lv~~~~~~~~~  134 (214)
T COG0088          67 QKGTGRARQGSIRSPQWRGGGVAHGPKPERDYSQKLNKKERRLALRSALSAKARAGKLVVVRGHVFED  134 (214)
T ss_pred             CCcCCcCCCCCCCCCeeecCccccCCCCccchhhhcCHHHHHHHHHHHHHHhccCCCEEEEecccccC
Confidence            77888888886 9999999999999999999999999999999999999999999 999999999994

>PRK14547 rplD 50S ribosomal protein L4; Provisional

Probab=100.00  E-value=4.5e-42  Score=294.28  Aligned_cols=117  Identities=23%  Similarity=0.295  Sum_probs=109.7

Q ss_pred             CccEEeccCCCccccCCcccccc-ccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCC
Q 048058            7 PLITVQSLEGDMATDASSTVPLP-DVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPG   85 (157)
Q Consensus         7 ~~v~V~n~~G~~~~~~gg~ieLp-~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg   85 (157)
                      ++++|||++|+.+    ++|+|| +||+.++|.||||++|++|++|+||||+     +||+|+||+|+|+|    || +|
T Consensus         2 ~~~~v~~~~g~~~----g~ieL~~~vF~~~~r~dllh~vv~~q~a~~Rqgt~-----~tKtRaEV~G~GkK----P~-rQ   67 (298)
T PRK14547          2 ATCDVLDWQGKKV----GSAELPLKVFDVETNIPLIHQVVVAQMAAARQGTH-----HTKTRAEVRGGGKK----PW-RQ   67 (298)
T ss_pred             ceeEEeccCCCCc----ceEECCHHHhCCCccHHHHHHHHHHHHHhhhcCCC-----CCCceeeccCCCCC----cc-CC
Confidence            4999999999999    999998 7999999999999999999999999975     67999999999997    55 68


Q ss_pred             CCcccCCCCC-CCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccCh
Q 048058           86 GGTHRAGQGA-FGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVP  138 (157)
Q Consensus        86 ~GtgRar~g~-rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~  138 (157)
                      |||||||+|+ +||+|||||++|||+| |+|++|||||+|+|||+||||+++..
T Consensus        68 KGTGrAR~Gs~rsP~wrGGGvafGPkp-R~y~~klNKK~rrlAlrsALS~k~~~  120 (298)
T PRK14547         68 KGTGRARQGSIRAPQWRGGGTVHGPRP-REYNQRTPKKMRQAALRGALSDRARD  120 (298)
T ss_pred             CCCcccCcCCccCCceeCCeeecCCCC-chhhhhcCHHHHHHHHHHHHHHHHhc
Confidence            8888899887 8999999999999999 99999999999999999999999865

>CHL00147 rpl4 ribosomal protein L4; Validated

Probab=100.00  E-value=7.2e-42  Score=281.54  Aligned_cols=117  Identities=24%  Similarity=0.307  Sum_probs=106.6

Q ss_pred             CCccEEeccCCCc-cccCCcccccc-ccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeecccccccccccc
Q 048058            6 RPLITVQSLEGDM-ATDASSTVPLP-DVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRV   83 (157)
Q Consensus         6 ~~~v~V~n~~G~~-~~~~gg~ieLp-~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prq   83 (157)
                      -++++|+|++|+. +    +++||+ +|| .++++||||++|+||++|+||||+     .||+|+||+|+|+|    || 
T Consensus         6 ~~~~~v~~~~g~~~~----~~~~l~~~vf-~~~~~~ll~~~v~~~~a~~R~gt~-----~tKtR~eV~G~grK----p~-   70 (215)
T CHL00147          6 FLNYPVIDLTGKEKS----ETIKLKLNVL-EKSGNYLLHRALVRQNNNQRQGTA-----STKTRSEVRGGGRK----PW-   70 (215)
T ss_pred             eeeEEEEccCCCeec----ceEEeCHHHh-CCchHhHHHHHHHHHHHHHhhccc-----ccCccccccCCCCC----Cc-
Confidence            3579999999999 8    899998 599 567799999999999999999975     57999999999997    55 


Q ss_pred             CCCCcccCCCCC-CCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccCh
Q 048058           84 PGGGTHRAGQGA-FGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVP  138 (157)
Q Consensus        84 kg~GtgRar~g~-rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~  138 (157)
                      +||||||||+|+ +||+|||||++|||+| |+|+++||||+|++|+++|||+++..
T Consensus        71 ~QKGTGrAR~Gs~rsP~~rgGG~afgP~p-R~y~~klnKKvrrlAl~sALS~k~~~  125 (215)
T CHL00147         71 KQKGTGRARAGSNRSPLWKGGGVIFGPKP-KTYSNKLNKKERRLALRTLLYNKSNN  125 (215)
T ss_pred             ccCCCCccCCCCCcCCcccCCEeecCCCC-cchhhhcCHHHHHHHHHHHHHHhhCC
Confidence            688888888887 9999999999999999 99999999999999999999999764

>PRK05319 rplD 50S ribosomal protein L4; Provisional

Probab=100.00  E-value=9.6e-42  Score=278.56  Aligned_cols=120  Identities=28%  Similarity=0.333  Sum_probs=110.0

Q ss_pred             CccEEeccCCCccccCCcccccc-ccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCC
Q 048058            7 PLITVQSLEGDMATDASSTVPLP-DVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPG   85 (157)
Q Consensus         7 ~~v~V~n~~G~~~~~~gg~ieLp-~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg   85 (157)
                      |+++|||++|+.+    ++|+|| +||+.|+|.||||++|++|++|+||||+     +||+|+||+|+|+|    || +|
T Consensus         1 ~~~~v~~~~g~~~----~~i~l~~~vF~~~~r~dll~~~v~~~~~~~Rqgta-----~tk~r~ev~GsgrK----~~-~Q   66 (205)
T PRK05319          1 MELKVLNLDGKEA----GEVELSDAVFGVEPNEALLHQVVVAQLANARQGTH-----ATKTRSEVSGGGKK----PW-RQ   66 (205)
T ss_pred             CeeEEEcCCCCCc----ceEEcCHHHhCCCccHHHHHHHHHHHHHhcccCcc-----cCCcccccCCCCCC----CC-CC
Confidence            4789999999998    899998 7999999999999999999999999964     67999999999987    44 57


Q ss_pred             CCcccCCCCC-CCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccChhhH
Q 048058           86 GGTHRAGQGA-FGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLV  141 (157)
Q Consensus        86 ~GtgRar~g~-rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~v  141 (157)
                      |||||||+|+ +||+|||||++|||+| |+|++|||||+|+||+++|||+++.+.-+
T Consensus        67 KGTGrAR~Gs~rsP~~rGGg~afgpkp-r~~~~klnkK~~~lAl~~aLs~k~~~~~l  122 (205)
T PRK05319         67 KGTGRARQGSIRSPQWRGGGVVFGPKP-RDYSQKLNKKVRRLALRSALSEKAREGRL  122 (205)
T ss_pred             CCCCccCcCcccCCcccCCeeeCCCCc-cchhhhcCHHHHHHHHHHHHHHHHhcCCe
Confidence            7888888887 9999999999999999 89999999999999999999999987433

>KOG1475 consensus Ribosomal protein RPL1/RPL2/RL4L4 [RNA processing and modification]

Probab=100.00  E-value=1e-41  Score=291.82  Aligned_cols=152  Identities=78%  Similarity=1.273  Sum_probs=148.8

Q ss_pred             ccCCCccEEeccCCCccccCCccccccccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccc
Q 048058            3 AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPR   82 (157)
Q Consensus         3 ~~~~~~v~V~n~~G~~~~~~gg~ieLp~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~pr   82 (157)
                      |++|+.++||+.||+.++   +++.||+||..|+|+||++.++..+..|+||+|+.++.||+++++|+||+|+.++|+||
T Consensus         1 ~~arp~vtvy~~~g~~s~---~~l~lp~vf~aPiRpdlv~~v~~~~~~n~rQpyAVs~kAG~QtSAESWGTGRAvaRiPR   77 (363)
T KOG1475|consen    1 AAARPLVTVYSLDGEASK---KTLTLPAVFSAPIRPDLVNFVHTQVRKNRRQPYAVSEKAGHQTSAESWGTGRAVARIPR   77 (363)
T ss_pred             CCccceeeEEeccccccc---ccccccceeccCCcHHHHHHHHHHHhhccccchhhhhhhccccchhhcccccceecccc
Confidence            578999999999999984   68999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCcccCCCCCCCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccChhhHhhcCcccCCCCCCCCC
Q 048058           83 VPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV  157 (157)
Q Consensus        83 qkg~GtgRar~g~rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rgh~~~~~~~~Piv  157 (157)
                      .+|.||+|+|||.+.++||||++++|.+.||.|+.++|-.++++|+.||+++++.+.||++|||+||+++|||||
T Consensus        78 V~GGGT~RsGQgAFgNmCR~GrMfaPtKt~RrW~rkVn~n~Kr~A~asaiaasavpaLv~arGHrIe~VpelPlV  152 (363)
T KOG1475|consen   78 VGGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRKVNENEKRYAIASAIAASAVPALVMARGHRIEEVPELPLV  152 (363)
T ss_pred             cCCCCcccccchhhhhhcccccccCchhhHHHHhhhhhhhhhhhHHHhhhhhhhhhHHHHhcCccccccccCceE
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999997

>PRK14907 rplD 50S ribosomal protein L4; Provisional

Probab=100.00  E-value=2.9e-39  Score=276.24  Aligned_cols=107  Identities=27%  Similarity=0.240  Sum_probs=98.1

Q ss_pred             ccccc-cccccc-CChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCCCCcccCCCCC-CCcccc
Q 048058           25 TVPLP-DVMKAS-IRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGA-FGNMCR  101 (157)
Q Consensus        25 ~ieLp-~vF~~~-~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg~GtgRar~g~-rsP~~r  101 (157)
                      .|+|+ +||+.+ ++++|||++|+||++|+||||+     .+|+|+||+|+|+|    || +|+||||||+|+ +||+||
T Consensus       103 ~ieL~~~vF~~e~~~~~llh~~V~~q~A~~RqGT~-----~TKtRsEVsGggkK----Pw-rQKGTGRAR~GS~RSP~wr  172 (295)
T PRK14907        103 TSKLPKKLFASEKIYSQAIFDTILSERASRRQGTH-----KVKTRAEVSGTGKK----PW-RQKGTGRARAGSTRSPIFV  172 (295)
T ss_pred             eEEeCHHHhCCCccchhHHHHHHHHHHHHhccccc-----cccchhhccCCCCC----Cc-ccCCCCccCCCCCcCCccc
Confidence            48997 699999 7999999999999999999976     57999999999997    55 688888888887 999999


Q ss_pred             ccccccCCccCcceeeccCHHHHHHHHHHHHHhccChhhH
Q 048058          102 GGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLV  141 (157)
Q Consensus       102 GGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~v  141 (157)
                      |||++|||+|+|+|+++||||+|+|||++|||+++..+||
T Consensus       173 GGGvaFGPkP~RdY~~KLNKKvRrLALrsALS~ka~~~Lv  212 (295)
T PRK14907        173 GGGRAFGPTPERNYKLKVNKKVRFNAFVSALTLLANSKAV  212 (295)
T ss_pred             CCeeecCCCCccchhhhcCHHHHHHHHHHHHHHhccCCEE
Confidence            9999999999999999999999999999999999987655

>PF00573 Ribosomal_L4: Ribosomal protein L4/L1 family; InterPro: IPR002136 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=100.00  E-value=1.1e-38  Score=258.04  Aligned_cols=110  Identities=33%  Similarity=0.408  Sum_probs=100.8

Q ss_pred             cccc-ccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCCCCcccCCCCC-CCcccccc
Q 048058           26 VPLP-DVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGA-FGNMCRGG  103 (157)
Q Consensus        26 ieLp-~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg~GtgRar~g~-rsP~~rGG  103 (157)
                      |||+ +||+.|+|+||||++|++|++|+||||++     +|+|+||+|+|+|    || +||||||||+|+ +||+||||
T Consensus         1 i~L~~~vF~~~~r~~llh~~v~~~~~~~Rqgt~~-----tktr~ev~g~grK----p~-~QKGTGrAR~Gs~rsP~~rgG   70 (192)
T PF00573_consen    1 IELSPDVFNVPVRPDLLHRAVVWQLANRRQGTAS-----TKTRSEVSGSGRK----PW-PQKGTGRARQGSIRSPQWRGG   70 (192)
T ss_dssp             -ES-CGGGGSSTSHHHHHHHHHHHHHHTSSBT-S-----SSTSTTSSSSSSS----SS-SSSSSSSSSSSSCTSTTSTTS
T ss_pred             CCCCHHHhCCCCcHHHHHHHHHHHHHhccCCccC-----CccceEEecccCc----cc-CCCCCcccccCccccceeecc
Confidence            6894 79999999999999999999999999764     6899999999987    65 788888888887 99999999


Q ss_pred             ccccCCccCcceeeccCHHHHHHHHHHHHHhccChhhHhhcC
Q 048058          104 RMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARG  145 (157)
Q Consensus       104 g~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rg  145 (157)
                      |++|||+|+|+|+++||||+|++||++|||+++.++.+.-.+
T Consensus        71 g~afgPkp~r~~~~klnkK~r~lAl~~aLs~k~~~~~l~vvd  112 (192)
T PF00573_consen   71 GVAFGPKPPRDYSYKLNKKVRRLALRSALSAKAAEGNLIVVD  112 (192)
T ss_dssp             SBSSSSSSTSBCSHHHHHHHHHHHHHHHHHHHHHTTHHHHCT
T ss_pred             EEecCCcccccceecCChHHHHHHHHHHHHHhhcccceEEee
Confidence            999999999999999999999999999999999999998876

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 [, ]. This family includes ribosomal L4/L1 from eukaryotes and plants and L4 from bacteria. L4 from yeast has been shown to bind rRNA []. These proteins have 246 (plant) to 427 (human) amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZR_D 1VSA_D 3D5D_F 3MS1_E 3F1F_F 3PYO_E 3MRZ_E 3F1H_F 3PYR_E 1VSP_D ....

>KOG1624 consensus Mitochondrial/chloroplast ribosomal protein L4 [Translation, ribosomal structure and biogenesis]

Probab=99.97  E-value=7.9e-32  Score=228.45  Aligned_cols=127  Identities=26%  Similarity=0.310  Sum_probs=112.0

Q ss_pred             cEEeccCCCccccCCcccccc-ccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCCCC
Q 048058            9 ITVQSLEGDMATDASSTVPLP-DVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGGG   87 (157)
Q Consensus         9 v~V~n~~G~~~~~~gg~ieLp-~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg~G   87 (157)
                      +++.+.++|++    |.++|+ ++|.+++|-||||++|+|++.|+|+|+     |++|+|+|+.|+|+|    || .|||
T Consensus        56 ~~~~~~e~E~~----gl~~l~~dvf~~~~RrDIlhrav~wq~~nrrvgt-----astktRaEv~ggGrK----p~-~QKg  121 (290)
T KOG1624|consen   56 EPLDFFELEKV----GLVDLHPDVFAEPPRRDILHRAVVWQLDNRRVGT-----ASTKTRAEVRGGGRK----PW-PQKG  121 (290)
T ss_pred             eeccccccccc----eeeecChhhhccchHHHHHHHHHHHhhccccccc-----ccCCccccccCCCCC----cC-cccC
Confidence            35567899999    999997 899999999999999999999999996     567999999999997    54 6778


Q ss_pred             cccCCCCC-CCccccccccccCCc-cCcceeeccCHHHHHHHHHHHHHhccChhhHhhcCcccCCCCCCC
Q 048058           88 THRAGQGA-FGNMCRGGRMFAPTK-IWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMP  155 (157)
Q Consensus        88 tgRar~g~-rsP~~rGGg~afgPk-p~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rgh~~~~~~~~P  155 (157)
                      |||||.|+ +||+++|||++|||+ | |+|+++||.|+|.|||+.|||++..++..    |.+|+.. ||
T Consensus       122 tGrAr~Gs~rsP~r~gGg~~~gpr~P-~d~~~~Lp~kvr~lgl~~ALS~~~a~~~l----~I~d~~~-L~  185 (290)
T KOG1624|consen  122 TGRARVGSLRSPQRRGGGVAHGPRGP-RDYSYKLPSKVRSLGLKIALSAKLAQDDL----HIVDELG-LP  185 (290)
T ss_pred             CCcccccCccCcccCCCccccCCCCC-cchhhhccHHHHHHHHHHHHHHHHhCCce----EEecccC-CC
Confidence            88899897 999999999999999 7 99999999999999999999988877653    6666653 44

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	157
3izr_D	405	Localization Of The Large Subunit Ribosomal Protein		1e-64
2zkr_c	421	Structure Of A Mammalian Ribosomal 60s Subunit With		4e-59
3zf7_r	374	High-resolution Cryo-electron Microscopy Structure		4e-50
2ww9_H	362	Cryo-Em Structure Of The Active Yeast Ssh1 Complex		4e-46
3izs_D	362	Localization Of The Large Subunit Ribosomal Protein		5e-46
1s1i_D	361	Structure Of The Ribosomal 80s-Eef2-Sordarin Comple		5e-46
3jyw_D	257	Structure Of The 60s Proteins For Eukaryotic Riboso		2e-44
4a17_C	410	T.Thermophila 60s Ribosomal Subunit In Complex With		4e-35
3j21_D	255	Promiscuous Behavior Of Proteins In Archaeal Riboso		5e-08
1jj2_C	246	Fully Refined Crystal Structure Of The Haloarcula M		1e-07
1ffk_C	246	Crystal Structure Of The Large Ribosomal Subunit Fr		2e-07
3cc2_C	246	The Refined Crystal Structure Of The Haloarcula Mar		3e-07

>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 =  241 bits (615), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 110/157 (70%), Positives = 130/157 (82%)
Query: 1   MAAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSR 60
           MA   RPL++V++LEGDMATD SS++ L +V +A +RPD+V FVH  +S N RQPYAVSR
Sbjct: 1   MATQTRPLVSVKALEGDMATDNSSSLALAEVFRAPLRPDVVRFVHRLLSCNKRQPYAVSR 60
Query: 61  KAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN 120
           +AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTK WR+WHR++N
Sbjct: 61  RAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKTWRKWHRRVN 120
Query: 121 VNQKRYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
           V+ +R            PSLV+ARGH+IETVPE+PLV
Sbjct: 121 VHLRRVAVASALAATSVPSLVLARGHRIETVPELPLV 157

>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 =  223 bits (568), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 105/155 (67%), Positives = 121/155 (78%), Gaps = 3/155 (1%)
Query: 3   AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKA 62
           A ARPLI+V S +G+    +   V LP V KA IRPDIV FVH+N+ KN+RQPYAVS  A
Sbjct: 2   ACARPLISVYSEKGE---SSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELA 58
Query: 63  GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVN 122
           GHQTSAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCRGGRMFAPTK WRRWHR++N  
Sbjct: 59  GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTT 118
Query: 123 QKRYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
           QKRY           P+LVM++GH+IE VPE+PLV
Sbjct: 119 QKRYAICSALACLSLPALVMSKGHRIEEVPELPLV 153

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

Iteration: 1
 Score =  193 bits (490), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 94/153 (61%), Positives = 113/153 (73%), Gaps = 3/153 (1%)
Query: 5   ARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGH 64
           ARP ++V S   D       T  LP V  A IR D+V FVH+N++KNSRQPYAV+R +G 
Sbjct: 3   ARPSVSVYSASEDKVV---GTCSLPAVFTAPIRHDVVQFVHTNMAKNSRQPYAVNRLSGM 59
Query: 65  QTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQK 124
           + SAESWGTGRAV+RIPR+ GGGT  +G GAFGNMCRGGRMFAPTKI+RRWHRKIN++QK
Sbjct: 60  KHSAESWGTGRAVARIPRIHGGGTSMSGAGAFGNMCRGGRMFAPTKIFRRWHRKINLHQK 119
Query: 125 RYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
           R+           P+LVM+RGHKIE V E+PLV
Sbjct: 120 RFAVVSALAASSLPALVMSRGHKIENVAEVPLV 152

>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 =  179 bits (455), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 96/153 (62%), Positives = 116/153 (75%), Gaps = 3/153 (1%)
Query: 5   ARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGH 64
           +RP +TV SL G+   +A   +PLP V  A IRPDIV  V ++++KN RQ YAVS KAGH
Sbjct: 2   SRPQVTVHSLTGEATANA---LPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGH 58
Query: 65  QTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQK 124
           QTSAESWGTGRAV+RIPRV GGGT R+GQGAFGNMCRGGRMFAPTK WR+W+ K+N N+K
Sbjct: 59  QTSAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEK 118
Query: 125 RYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
           RY            SLV+ARGH++E +PE+PLV
Sbjct: 119 RYATASAIAATAVASLVLARGHRVEKIPEIPLV 151

>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 =  179 bits (455), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 96/153 (62%), Positives = 116/153 (75%), Gaps = 3/153 (1%)
Query: 5   ARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGH 64
           +RP +TV SL G+   +A   +PLP V  A IRPDIV  V ++++KN RQ YAVS KAGH
Sbjct: 2   SRPQVTVHSLTGEATANA---LPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGH 58
Query: 65  QTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQK 124
           QTSAESWGTGRAV+RIPRV GGGT R+GQGAFGNMCRGGRMFAPTK WR+W+ K+N N+K
Sbjct: 59  QTSAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEK 118
Query: 125 RYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
           RY            SLV+ARGH++E +PE+PLV
Sbjct: 119 RYATASAIAATAVASLVLARGHRVEKIPEIPLV 151

>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 =  179 bits (455), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 96/153 (62%), Positives = 116/153 (75%), Gaps = 3/153 (1%)
Query: 5   ARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGH 64
           +RP +TV SL G+   +A   +PLP V  A IRPDIV  V ++++KN RQ YAVS KAGH
Sbjct: 1   SRPQVTVHSLTGEATANA---LPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGH 57
Query: 65  QTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQK 124
           QTSAESWGTGRAV+RIPRV GGGT R+GQGAFGNMCRGGRMFAPTK WR+W+ K+N N+K
Sbjct: 58  QTSAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEK 117
Query: 125 RYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
           RY            SLV+ARGH++E +PE+PLV
Sbjct: 118 RYATASAIAATAVASLVLARGHRVEKIPEIPLV 150

>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 =  174 bits (441), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 94/149 (63%), Positives = 113/149 (75%), Gaps = 3/149 (2%)
Query: 9   ITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSA 68
           +TV SL G+   +A   +PLP V  A IRPDIV  V ++++KN RQ YAVS KAGHQTSA
Sbjct: 2   VTVHSLTGEATANA---LPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQTSA 58
Query: 69  ESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYXX 128
           ESWGTGRAV+RIPRV GGGT R+GQGAFGNMCRGGRMFAPTK WR+W+ K+N N+KRY  
Sbjct: 59  ESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRYAT 118
Query: 129 XXXXXXXXXPSLVMARGHKIETVPEMPLV 157
                     SLV+ARGH++E +PE+PLV
Sbjct: 119 ASAIAATAVASLVLARGHRVEKIPEIPLV 147

>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 =  143 bits (360), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 77/157 (49%), Positives = 96/157 (61%), Gaps = 5/157 (3%)
Query: 5   ARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRK--- 61
           +RP I V   + +     ++ + LP V  A IR DIV  V ++++KN +Q   V      
Sbjct: 3   SRPQIHVHDAK-EANKQTATKLTLPAVFTAPIRTDIVHKVFTDLNKNRKQASGVKISTRG 61
Query: 62  -AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN 120
            AG   SAESWGTGRAV+RIPRV G GTHR+GQ AFGN CR GRMFAP K +RR HR++N
Sbjct: 62  TAGMGHSAESWGTGRAVARIPRVGGSGTHRSGQAAFGNQCRKGRMFAPLKTYRRVHRRVN 121
Query: 121 VNQKRYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
           VNQKR+             LV ARGH+I  V E+P V
Sbjct: 122 VNQKRHAVAAALAASALVPLVFARGHRISNVQELPYV 158

>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 = 53.5 bits (127), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 39/141 (27%), Positives = 59/141 (41%), Gaps = 4/141 (2%)
Query: 17  DMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRA 76
           D+       + LP V     RPD++         +  QP      AG +   E+ G G +
Sbjct: 7   DLNGQPVGEIELPKVFFTPFRPDLIRRAVIASWTHRIQPQGRDPMAGKRRVTENIGKGHS 66
Query: 77  VSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYXXXXXXXXXX 136
           ++R+ R+     +     AF    RGGR   P K+ +     IN  +KR           
Sbjct: 67  MARVERLKTPPRY----AAFVPFARGGRRTHPPKVEKIIWEDINKKEKRLALMSAIAATA 122
Query: 137 XPSLVMARGHKIETVPEMPLV 157
              LV ARGH I+ VP++PL+
Sbjct: 123 NYDLVRARGHIIDNVPQLPLI 143

>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 = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 38/141 (26%), Positives = 61/141 (43%), Gaps = 8/141 (5%)
Query: 17  DMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRA 76
           D+  +    V LPDV +  +R D++G        N +Q Y     AG +T AES+G+GR 
Sbjct: 7   DLDGNTDGEVDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESFGSGRG 66
Query: 77  VSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYXXXXXXXXXX 136
            + +P++ G    R  Q         GR   P K  +     +N  +++           
Sbjct: 67  QAHVPKLDGRA-RRVPQAV------KGRSAHPPKTEKDRSLDLNDKERQLAVRSALAATA 119
Query: 137 XPSLVMARGHKIETVPEMPLV 157
              LV  RGH+ +   E+P+V
Sbjct: 120 DADLVADRGHEFDR-DEVPVV 139

>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 = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 38/141 (26%), Positives = 61/141 (43%), Gaps = 8/141 (5%)
Query: 17  DMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRA 76
           D+  +    V LPDV +  +R D++G        N +Q Y     AG +T AES+G+GR 
Sbjct: 7   DLDGNTDGEVDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESFGSGRG 66
Query: 77  VSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYXXXXXXXXXX 136
            + +P++ G    R  Q         GR   P K  +     +N  +++           
Sbjct: 67  QAHVPKLDGRA-RRVPQAV------KGRSAHPPKTEKDRSLDLNDKERQLAVRSALAATA 119
Query: 137 XPSLVMARGHKIETVPEMPLV 157
              LV  RGH+ +   E+P+V
Sbjct: 120 DADLVADRGHEFDR-DEVPVV 139

>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 = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 38/141 (26%), Positives = 60/141 (42%), Gaps = 8/141 (5%)
Query: 17  DMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRA 76
           D+  +    V LPDV +  +R D++G        N +Q Y     AG +T AES+G+GR 
Sbjct: 7   DLDGNTDGEVDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESFGSGRG 66
Query: 77  VSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYXXXXXXXXXX 136
            + +P+   G   R  Q         GR   P K  +     +N  +++           
Sbjct: 67  QAHVPK-QDGRARRVPQAV------KGRSAHPPKTEKDRSLDLNDKERQLAVRSALAATA 119
Query: 137 XPSLVMARGHKIETVPEMPLV 157
              LV  RGH+ +   E+P+V
Sbjct: 120 DADLVADRGHEFDR-DEVPVV 139

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	157
3iz5_D	405	60S ribosomal protein L4 (L4P); eukaryotic ribosom	3e-57
2zkr_c	421	60S ribosomal protein L4; protein-RNA complex, 60S	2e-55
2wwb_H	362	60S ribosomal protein L4-B; ribosome, protein EXIT	1e-52
4a17_C	410	RPL4, ribosomal protein L3; eukaryotic ribosome, r	2e-51
1vq8_C	246	50S ribosomal protein L4E; ribosome 50S, protein-p	1e-41

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

 Score =  178 bits (452), Expect = 2e-55
 Identities = 110/155 (70%), Positives = 129/155 (83%), Gaps = 3/155 (1%)

Query: 3   AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKA 62
           A ARPLI+V S +G+    +   V LP V KA IRPDIV FVH+N+ KN+RQPYAVS  A
Sbjct: 2   ACARPLISVYSEKGE---SSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELA 58

Query: 63  GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVN 122
           GHQTSAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCRGGRMFAPTK WRRWHR++N  
Sbjct: 59  GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTT 118

Query: 123 QKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           QKRYAI SA+A  ++P+LVM++GH+IE VPE+PLV
Sbjct: 119 QKRYAICSALACLSLPALVMSKGHRIEEVPELPLV 153

>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 =  169 bits (430), Expect = 1e-52
 Identities = 103/153 (67%), Positives = 125/153 (81%), Gaps = 3/153 (1%)

Query: 5   ARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGH 64
           +RP +TV SL G+     ++ +PLP V  A IRPDIV  V ++++KN RQ YAVS KAGH
Sbjct: 2   SRPQVTVHSLTGE---ATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGH 58

Query: 65  QTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQK 124
           QTSAESWGTGRAV+RIPRV GGGT R+GQGAFGNMCRGGRMFAPTK WR+W+ K+N N+K
Sbjct: 59  QTSAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEK 118

Query: 125 RYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           RYA  SAIAA+AV SLV+ARGH++E +PE+PLV
Sbjct: 119 RYATASAIAATAVASLVLARGHRVEKIPEIPLV 151

>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 =  168 bits (425), Expect = 2e-51
 Identities = 83/158 (52%), Positives = 106/158 (67%), Gaps = 5/158 (3%)

Query: 4   AARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVS---- 59
            +RP I V   + +     ++ + LP V  A IR DIV  V ++++KN +Q   V     
Sbjct: 2   TSRPQIHVHDAK-EANKQTATKLTLPAVFTAPIRTDIVHKVFTDLNKNRKQASGVKISTR 60

Query: 60  RKAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKI 119
             AG   SAESWGTGRAV+RIPRV G GTHR+GQ AFGN CR GRMFAP K +RR HR++
Sbjct: 61  GTAGMGHSAESWGTGRAVARIPRVGGSGTHRSGQAAFGNQCRKGRMFAPLKTYRRVHRRV 120

Query: 120 NVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV 157
           NVNQKR+A+ +A+AASA+  LV ARGH+I  V E+P V
Sbjct: 121 NVNQKRHAVAAALAASALVPLVFARGHRISNVQELPYV 158

>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 =  138 bits (348), Expect = 1e-41
 Identities = 46/149 (30%), Positives = 73/149 (48%), Gaps = 12/149 (8%)

Query: 9   ITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSA 68
            T+  L+G+        V LPDV +  +R D++G        N +Q Y     AG +T A
Sbjct: 3   ATIYDLDGN----TDGEVDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPA 58

Query: 69  ESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAI 128
           ES+G+GR  + +P++ G    R  Q         GR   P K  +     +N  +++ A+
Sbjct: 59  ESFGSGRGQAHVPKLDGRA-RRVPQ------AVKGRSAHPPKTEKDRSLDLNDKERQLAV 111

Query: 129 VSAIAASAVPSLVMARGHKIETVPEMPLV 157
            SA+AA+A   LV  RGH+ +   E+P+V
Sbjct: 112 RSALAATADADLVADRGHEFDR-DEVPVV 139

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	157
3j21_D	255	50S ribosomal protein L4P; archaea, archaeal, KINK	100.0
2zkr_c	421	60S ribosomal protein L4; protein-RNA complex, 60S	100.0
3iz5_D	405	60S ribosomal protein L4 (L4P); eukaryotic ribosom	100.0
4a17_C	410	RPL4, ribosomal protein L3; eukaryotic ribosome, r	100.0
1vq8_C	246	50S ribosomal protein L4E; ribosome 50S, protein-p	100.0
2wwb_H	362	60S ribosomal protein L4-B; ribosome, protein EXIT	100.0
3bbo_G	293	Ribosomal protein L4; large ribosomal subunit, spi	100.0
3v2d_F	210	50S ribosomal protein L4; ribosome associated inhi	100.0
1dmg_A	225	Ribosomal protein L4; alpha-beta, ribosome, RNA, S	100.0
2zjr_C	205	50S ribosomal protein L4; ribosome, large ribosoma	100.0
3r8s_E	201	50S ribosomal protein L4; protein biosynthesis, RN	100.0
2ftc_D	175	Mitochondrial ribosomal protein L4 isoform A, mito	100.0
2wwb_H	362	60S ribosomal protein L4-B; ribosome, protein EXIT	92.3

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

Probab=100.00  E-value=8.4e-53  Score=352.74  Aligned_cols=143  Identities=34%  Similarity=0.494  Sum_probs=135.3

Q ss_pred             CccEEeccCCCccccCCccccccccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCCC
Q 048058            7 PLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGG   86 (157)
Q Consensus         7 ~~v~V~n~~G~~~~~~gg~ieLp~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg~   86 (157)
                      |+++|||++|+++    ++||||+||+.|+|+||||++|+++++|+||||+.++.|++|+++||||+|+|.+|+|||||+
T Consensus         1 m~v~V~~~~G~~~----g~v~Lp~vF~~~~r~dli~~~v~~~~an~Rq~~Gt~~~ag~ktraev~G~Gr~~ar~~RqKGt   76 (255)
T 3j21_D            1 MKVKVFDLNGQPV----GEIELPKVFFTPFRPDLIRRAVIASWTHRIQPQGRDPMAGKRRVTENIGKGHSMARVERLKTP   76 (255)
T ss_dssp             CEEEEECTTSCEE----EEEECCGGGGSCCCHHHHHHHHHHHHHHTCCCCCCCSSTTSSSCCBCCCSSSSSCCCCBCSSS
T ss_pred             CeeEEEcCCCCEe----eEEEhHHhhCCCCcHHHHHHHHHHHHHhccccccCCcccCcccceeecCCCCCcCcCCccCCC
Confidence            4899999999999    999999999999999999999999999999988888899999999999999999999997766


Q ss_pred             CcccCCCCCCCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccChhhHhhcCcccCCCCCCCCC
Q 048058           87 GTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV  157 (157)
Q Consensus        87 GtgRar~g~rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rgh~~~~~~~~Piv  157 (157)
                      | |||+   ++|+|||||++|||+|||+|+++||||+|++||+||||+++.++||++|||+|+++++||||
T Consensus        77 g-GrAr---rsP~~rGGg~~~gPkp~R~~~~klNkK~rrlAl~sALsa~~~~~lv~~rgh~~~~~~~~~lv  143 (255)
T 3j21_D           77 P-RYAA---FVPFARGGRRTHPPKVEKIIWEDINKKEKRLALMSAIAATANYDLVRARGHIIDNVPQLPLI  143 (255)
T ss_dssp             C-CCCS---SCSSSTTCCCSSCCCTTSCCCCCCCHHHHHHHHHHHHHHTTCHHHHHHHTCCCSCTTCSSEE
T ss_pred             C-Cccc---cCccccCCeeecCCCCCcccceecCHHHHHHHHHHHHHHHhhcccchhcccccccccceeEE
Confidence            3 5554   89999999999999999999999999999999999999999999999999999999999986

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

Probab=100.00  E-value=2.9e-52  Score=368.10  Aligned_cols=151  Identities=68%  Similarity=1.141  Sum_probs=140.1

Q ss_pred             cccCCCccEEeccCCCccccCCc-cccccccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccc
Q 048058            2 AAAARPLITVQSLEGDMATDASS-TVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRI   80 (157)
Q Consensus         2 ~~~~~~~v~V~n~~G~~~~~~gg-~ieLp~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~   80 (157)
                      ||++||+++|||++|+.+    + +|+||+||+.|+|+||||++|+++++|+||||++++.||+++|+||||+|+|++|+
T Consensus         1 ~~~~rm~v~V~~~~G~~~----g~~ieLp~VF~~piR~dlIh~vV~~~~an~RQgta~t~~AG~KTraEv~G~GRKp~Ri   76 (421)
T 2zkr_c            1 MACARPLISVYSEKGESS----GKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQTSAESWGTGRAVARI   76 (421)
T ss_dssp             ------CCEEECTTSSEE----EECSSCCGGGGSCCCHHHHHHHHHHHHHTTCCCCCCCSCTTTCSCCCCCCSSSSSCCS
T ss_pred             CCCcCceeEEEcCCCCcc----ccEEehhHhhCCCccHHHHHHHHHHHHHhccCCCCcCcccCCcceeEecCCCCCcCCc
Confidence            678899999999999997    5 89999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCcccCCCCCCCccccccccccCCc-cCcceeeccCHHHHHHHHHHHHHhccChhhHhhcCcccCCCCCCCCC
Q 048058           81 PRVPGGGTHRAGQGAFGNMCRGGRMFAPTK-IWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV  157 (157)
Q Consensus        81 prqkg~GtgRar~g~rsP~~rGGg~afgPk-p~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rgh~~~~~~~~Piv  157 (157)
                      ||.+|+||||||+|++.++|| ||++|||+ |||+|+++||+|+|++||+||||+++.++||++|||+|+++.++|||
T Consensus        77 PRv~QKGTGRARqGs~rs~~R-GGr~fgP~kp~R~~~~KlNkK~rrlAlrSALSaka~~~LV~aRGH~i~~~~e~~LV  153 (421)
T 2zkr_c           77 PRVRGGGTHRSGQGAFGNMCR-GGRMFAPTKTWRRWHRRVNTTQKRYAICSALACLSLPALVMSKGHRIEEVPELPLV  153 (421)
T ss_dssp             CCBTTTTBCCCSTTCCTTSTT-CCCCSSCCCSSSCCCCCCCHHHHHHHHHHHHHHHTCHHHHHHTTCCCCSCSCCSEE
T ss_pred             ccccCCCCCccCccccccccc-cceeeCCCCCCcchhhhcCHHHHHHHHHHHHHhcccchhhhhccccccccccCCEE
Confidence            999999999999998555999 88888888 89999999999999999999999999999999999999999999985

>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=100.00  E-value=6.4e-51  Score=358.57  Aligned_cols=151  Identities=52%  Similarity=0.794  Sum_probs=143.0

Q ss_pred             ccCCCccEEe-ccCCCccccCCcc-ccccccccccCChhhHHHHHHHHHHhcCCCCCcCcc----Ccccceeeeeccccc
Q 048058            3 AAARPLITVQ-SLEGDMATDASST-VPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRK----AGHQTSAESWGTGRA   76 (157)
Q Consensus         3 ~~~~~~v~V~-n~~G~~~~~~gg~-ieLp~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~----a~~k~raev~G~g~k   76 (157)
                      |++||+++|| |++|+.+   +++ |+||+||+.|+|+||||++|+++++|+||||+.++.    +++++|+||||+|+|
T Consensus         1 m~~~p~v~V~~~~~G~~~---~g~~veLp~VF~~~ir~dlIh~vV~~~~anrRQ~~~~~~~~rGTa~tktraEv~GtGRk   77 (410)
T 4a17_C            1 MTSRPQIHVHDAKEANKQ---TATKLTLPAVFTAPIRTDIVHKVFTDLNKNRKQASGVKISTRGTAGMGHSAESWGTGRA   77 (410)
T ss_dssp             -CCCCEEEEEESSSTTEE---EEEEEECCGGGGSCCCHHHHHHHHHHHHHTTCCCCCCCBCSSCBTTCCSCEEECCGGGS
T ss_pred             CCCCCeeEEEECCCCCcc---CCceEehhHhhCCCCcHHHHHHHHHHHHHhCcCcccCCCcccccccCCccceeCCCCCC
Confidence            6789999999 8999984   267 999999999999999999999999999999999988    999999999999999


Q ss_pred             cccccccCCCCcccCCCCCCCccccccccccCCcc-CcceeeccCHHHHHHHHHHHHHhccChhhHhhcCcccCCCCCCC
Q 048058           77 VSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKI-WRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMP  155 (157)
Q Consensus        77 ~~r~prqkg~GtgRar~g~rsP~~rGGg~afgPkp-~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rgh~~~~~~~~P  155 (157)
                      ++|+|||+|+||||||+|++.|+|| ||++|||+| ||+|+++||+|+|++||+||||+++.++||++|||+|+++.++|
T Consensus        78 ~~RiPR~~QKGTGRARqGs~rP~~r-GGr~fgP~p~~R~y~~KlNKK~rrlAlrSALSaka~~~lV~aRgh~i~~v~e~~  156 (410)
T 4a17_C           78 VARIPRVGGSGTHRSGQAAFGNQCR-KGRMFAPLKTYRRVHRRVNVNQKRHAVAAALAASALVPLVFARGHRISNVQELP  156 (410)
T ss_dssp             SCSSEEECCSSSTTTTCBCSSTTSS-SCCCSSCCCSCCCCCCCCCHHHHHHHHHHHHHHHTCHHHHHHTTCCCTTCCSSS
T ss_pred             ccccccccCCCCCcccccccCCccC-CeEEcCCCCCccchhhhhCHHHHHHHHHHHHHHhcchhhhhhccccccccCcCC
Confidence            9999999999999999999559998 889999997 79999999999999999999999999999999999999999999


Q ss_pred             CC
Q 048058          156 LV  157 (157)
Q Consensus       156 iv  157 (157)
                      ||
T Consensus       157 LV  158 (410)
T 4a17_C          157 YV  158 (410)
T ss_dssp             EE
T ss_pred             EE
Confidence            86

>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=100.00  E-value=1.7e-50  Score=337.35  Aligned_cols=139  Identities=32%  Similarity=0.502  Sum_probs=132.6

Q ss_pred             CccEEeccCCCccccCCccccccccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCCC
Q 048058            7 PLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGG   86 (157)
Q Consensus         7 ~~v~V~n~~G~~~~~~gg~ieLp~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg~   86 (157)
                      |+++|||++|+++    ++|+||+||+.|+|+||||++|++|++|+||||++++.||+|+++|+||+|++++|+||||  
T Consensus         1 m~v~v~~~~g~~~----g~v~Lp~vF~~~~r~dli~~~v~~~~an~Rqgt~~~~~aG~kt~ae~~GtGR~~ari~rqK--   74 (246)
T 1vq8_C            1 MQATIYDLDGNTD----GEVDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESFGSGRGQAHVPKLD--   74 (246)
T ss_dssp             CEEEEECTTSCEE----EEEECCGGGGSCCCHHHHHHHHHHHHHHTCCCCCCCTTTTTCCCCBCCCSSSSCCCCCEET--
T ss_pred             CeeEEEcCCCCCc----cEEEhhHhhCCCccHHHHHHHHHHHHHhcccCcccccccCcccceeeccCCCCcccccccc--
Confidence            3689999999999    9999999999999999999999999999999999999999999999999999999999988  


Q ss_pred             CcccCCCCCCCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccChhhHhhcCcccCCCCCCCCC
Q 048058           87 GTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV  157 (157)
Q Consensus        87 GtgRar~g~rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rgh~~~~~~~~Piv  157 (157)
                      |.|     .+||+|||||++|||+|||+|++|||||+|++||+||||+++.++||++|||+|+++ +.|||
T Consensus        75 G~a-----rrsP~~rGGg~~~gPkp~R~~~~klnkK~rrlAl~sALsa~~~~~lv~~rGh~~~~~-e~~lv  139 (246)
T 1vq8_C           75 GRA-----RRVPQAVKGRSAHPPKTEKDRSLDLNDKERQLAVRSALAATADADLVADRGHEFDRD-EVPVV  139 (246)
T ss_dssp             TEE-----CSSTTSTTCCCSSCCCTTCCCCCCCCHHHHHHHHHHHHHHTTCHHHHHHHTCCCCCS-SCSEE
T ss_pred             Ccc-----ccCCccCCCeeecCCCCCccchhhcCHHHHHHHHHHHHHHhhhhhhhhhcccccccc-cccEE
Confidence            443     379999999999999999999999999999999999999999999999999999998 88875

>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=100.00  E-value=7e-46  Score=323.04  Aligned_cols=148  Identities=62%  Similarity=1.016  Sum_probs=140.8

Q ss_pred             CCCccEEeccCCCccccCCcc-ccccccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeecccccccccccc
Q 048058            5 ARPLITVQSLEGDMATDASST-VPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRV   83 (157)
Q Consensus         5 ~~~~v~V~n~~G~~~~~~gg~-ieLp~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prq   83 (157)
                      +|++++|||++|+.+    ++ |+||+||+.|+|+||||++|+++++|+||||+++++++..+.+++||||+..+|+||.
T Consensus         2 ~r~~v~V~~~~G~~~----g~~i~Lp~VF~~p~r~dlih~vv~~~~an~RQgt~~tk~rgevtg~K~wGTGRAraripRv   77 (362)
T 2wwb_H            2 SRPQVTVHSLTGEAT----ANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQTSAESWGTGRAVARIPRV   77 (362)
T ss_dssp             CSSCCCCCCSSCSCC----SCCCCCCGGGCSCCCHHHHHHHHHHHHHHHCCCCCCCSSSSCSSCCSSCCCCSSSCSCSCC
T ss_pred             CCCeeEEEcCCCcCc----CceEehhHhhCCCccHHHHHHHHHHHHHhccCCCCCCCcccccccceecCCCCCeeecccc
Confidence            589999999999998    88 9999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcccCCCCCCCccccccccccCCcc-CcceeeccCHHHHHHHHHHHHHhccChhhHhhcCcccCCCCCCCCC
Q 048058           84 PGGGTHRAGQGAFGNMCRGGRMFAPTKI-WRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV  157 (157)
Q Consensus        84 kg~GtgRar~g~rsP~~rGGg~afgPkp-~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rgh~~~~~~~~Piv  157 (157)
                      +|+|+.|+++|++.| |+|||++|||+| ||+|+++||||+|++||+||||+++.++||++|||+|+++.++|||
T Consensus        78 ~g~Gs~RSp~ga~~~-~~gGG~~fgP~p~~R~~~~klNkK~rrlAl~SALsaka~~~lv~arGH~i~~~~e~~Lv  151 (362)
T 2wwb_H           78 GGGGTGRSGQGAFGN-MCRGGRMFAPTKTWRKWNVKVNHNEKRYATASAIAATAVASLVLARGHRVEKIPEIPLV  151 (362)
T ss_dssp             CSCSSSSCSSTTTSS-SCSSSCCSSSSCSSCCCCCCCCHHHHHHHHHHHHHGGGCSTHHHHHTCCCCSCSSCSBC
T ss_pred             cCCCCCCCcccccCC-ccCCeEECCCCCCCcchhhhcCHHHHHHHHHHHHHhccchhhhhhccccccccccCcEE
Confidence            999998888877766 788999999986 6999999999999999999999999999999999999999999986

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

Probab=100.00  E-value=2.2e-44  Score=306.71  Aligned_cols=119  Identities=25%  Similarity=0.308  Sum_probs=108.8

Q ss_pred             ccCCCccEEeccCCCccccCCcccccc-ccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeecccccccccc
Q 048058            3 AAARPLITVQSLEGDMATDASSTVPLP-DVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIP   81 (157)
Q Consensus         3 ~~~~~~v~V~n~~G~~~~~~gg~ieLp-~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~p   81 (157)
                      |+.|++++|||++|+.+    |+|+|| +||+.|+|+||||++|++|++|+||||     +++|+|+||||+|||    |
T Consensus        49 ~~~M~~v~V~~~~G~~~----g~veLp~~VF~~~~r~dlih~vV~~q~an~RQGT-----a~tKtRaEV~GgGRK----p  115 (293)
T 3bbo_G           49 KSELIPLPILNFSGEKV----GETFLNLKTAPPEKARAVVHRGLITHLQNKRRGT-----ASTLTRAEVRGGGRK----P  115 (293)
T ss_dssp             --CCEEEECCCSSSCCC----SEEEECSSSSSSCCCTTTTTTHHHHHHHHHCCCC-----CCCCSSTTCSSSCCC----C
T ss_pred             hhcCceeEEEcCCCCEe----eeEEcCHHHhCCCccHHHHHHHHHHHHHhccccc-----ccCceeeeeccCCCc----e
Confidence            34456899999999999    899999 799999999999999999999999996     578999999999997    4


Q ss_pred             ccCCCCcccCCCCC-CCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhcc
Q 048058           82 RVPGGGTHRAGQGA-FGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASA  136 (157)
Q Consensus        82 rqkg~GtgRar~g~-rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka  136 (157)
                      | +||||||||+|+ ++|+|||||++|||+| |+|++|||||+|++||+||||+++
T Consensus       116 ~-RQKGTGRAR~Gs~rsP~~rGGGvafGPkP-Rdy~~klNKK~rrlAlrsALSak~  169 (293)
T 3bbo_G          116 Y-PQKKTGRARRGSQGSPLRPGGGVIFGPKP-RDWTIKMNKKERRLALSTAIASAV  169 (293)
T ss_dssp             C-CCSSSCSCSCCSSSCSSSSSSCCSSCCCS-CCCCCCCCSHHHHHHHHHHHHHHH
T ss_pred             e-ccCCCCccccCcccCCceecCceecCCcC-cchhhhcCHHHHHHHHHHHHHHHc
Confidence            4 677778888886 9999999999999997 999999999999999999999999

>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=100.00  E-value=1.9e-43  Score=288.78  Aligned_cols=124  Identities=23%  Similarity=0.205  Sum_probs=110.4

Q ss_pred             CCCccEEeccCCCccccCCccccccccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccC
Q 048058            5 ARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVP   84 (157)
Q Consensus         5 ~~~~v~V~n~~G~~~~~~gg~ieLp~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqk   84 (157)
                      .||+++|||++|+++    |+||||+    |+|+||||++|++|++|+||||+     .+|+|+||||+|+|    || +
T Consensus         5 ~m~~v~V~~~~G~~~----g~i~L~~----~~r~dlih~~v~~~~a~~Rqgt~-----~tktraEv~G~grK----p~-r   66 (210)
T 3v2d_F            5 AVYQIPVLSPSGRRE----LAADLPA----EINPHLLWEVVRWQLAKRRRGTA-----STKTRGEVAYSGRK----IW-P   66 (210)
T ss_dssp             -CCCCCEECSSSCCC----CCCCCCS----CCCHHHHHHHHHHHHHHTCCCCC-----CCCCTTTSSCCCCC----SS-C
T ss_pred             ccceeEEEcCCCCEe----eeEecCC----cccHHHHHHHHHHHHHhccCCcc-----CCCccccccCCCCC----CC-C
Confidence            467999999999999    9999998    99999999999999999999986     46899999999997    43 5


Q ss_pred             CCCcccCCCCC-CCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccChhhHhhcCcccCCC
Q 048058           85 GGGTHRAGQGA-FGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETV  151 (157)
Q Consensus        85 g~GtgRar~g~-rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rgh~~~~~  151 (157)
                      ||||||||+|+ +||+|||||++|||+| |+|+++||||+|++|++||||+++.++    +-|.+|+.
T Consensus        67 QKGTGrAR~Gs~rsP~~~gGG~~fgP~p-R~~~~klnkK~rrlAl~sALs~k~~~~----~l~Vvd~~  129 (210)
T 3v2d_F           67 QKHTGRARHGDIGAPIFVGGGVVFGPKP-RDYSYTLPKKVRKKGLAMAVADRAREG----KLLLVEAF  129 (210)
T ss_dssp             SSSSSSCCCCCTTSTTSTTCCCSSCCCC-CCCCCCCCHHHHHHHHHHHHHHHHHTT----CEEEESCC
T ss_pred             CCCCCccCCCcccCCcccCCeeeCCCCC-ccceeeCCHHHHHHHHHHHHHHHHhcC----CEEEeccc
Confidence            77778888887 9999999999999999 999999999999999999999999764    33666654

>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=100.00  E-value=2.1e-44  Score=297.00  Aligned_cols=117  Identities=23%  Similarity=0.257  Sum_probs=62.6

Q ss_pred             CccEEeccCCCccccCCcccccc-ccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCC
Q 048058            7 PLITVQSLEGDMATDASSTVPLP-DVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPG   85 (157)
Q Consensus         7 ~~v~V~n~~G~~~~~~gg~ieLp-~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg   85 (157)
                      |+++|||++|+++    ++|||| +||+.|+|+||||++|++|++|+||||++     +|+|+||||+|+|+   ||  |
T Consensus         1 ~~~~v~~~~g~~~----g~v~L~~~vF~~~~r~dlih~~v~~~~a~~Rqgt~~-----tktRaEv~G~GrKp---~r--Q   66 (225)
T 1dmg_A            1 AQVDLLNVKGEKV----GTLEISDFVFNIDPNYDVMWRYVDMQLSNRRAGTAS-----TKTRGEVSGGGRKP---WP--Q   66 (225)
T ss_dssp             CEEEEECTTSCEE----EEEECCHHHHSSCCCHHHHHHHHHHHHC-----------------------------------
T ss_pred             CeeEEEcCCCCEe----eEEEcCHHHhCCCccHHHHHHHHHHHHHhccCCccc-----cceeeEeecCCCCC---CC--C
Confidence            3789999999999    999999 79999999999999999999999999864     79999999999973   44  6


Q ss_pred             CCcccCCCCC-CCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccCh
Q 048058           86 GGTHRAGQGA-FGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVP  138 (157)
Q Consensus        86 ~GtgRar~g~-rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~  138 (157)
                      |||||||+|+ +||+|||||++|||+| |+|+++||||+|++||+||||+++.+
T Consensus        67 KGTGrAR~Gs~rsP~~rGGG~~fgPkp-R~~~~klnkK~rrlAl~sALs~k~~~  119 (225)
T 1dmg_A           67 KHTGRARHGSIRSPIWRHGGVVHGPKP-RDWSKKLNKKMKKLALRSALSVKYRE  119 (225)
T ss_dssp             -----------------------------CHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCccccccccCCceecCceecCCcC-ccccccCCHHHHHHHHHHHHHHHHhC
Confidence            6677777776 9999999999999999 99999999999999999999999986

>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=100.00  E-value=1.2e-42  Score=282.86  Aligned_cols=112  Identities=22%  Similarity=0.229  Sum_probs=103.2

Q ss_pred             ccEEeccCCCccccCCccccccccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCCCC
Q 048058            8 LITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGGG   87 (157)
Q Consensus         8 ~v~V~n~~G~~~~~~gg~ieLp~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg~G   87 (157)
                      +++|||++|+++    |+||||+     +|+||||++|++|++|+||||++     +|+|+||||+|+|    || +|||
T Consensus         3 ~v~v~~~~g~~~----g~i~L~~-----~r~dlih~~v~~~~a~~Rqgt~~-----tktraEv~G~GrK----p~-rQKG   63 (205)
T 2zjr_C            3 QINVIGQNGGRT----IELPLPE-----VNSGVLHEVVTWQLASRRRGTAS-----TRTRAQVSKTGRK----MY-GQKG   63 (205)
T ss_dssp             CCCCSSCCCCCC----CCCCTTT-----CCHHHHHHHHHHHHHHHCCCCCC-----CCCCTTTSCCCSC----CS-CSSS
T ss_pred             eeEEEcCCCCEe----eeEECCC-----chHHHHHHHHHHHHHhccccccc-----cceeeeccCCCCC----CC-CcCC
Confidence            799999999999    8999998     99999999999999999999864     6899999999997    43 5777


Q ss_pred             cccCCCCC-CCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccChh
Q 048058           88 THRAGQGA-FGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPS  139 (157)
Q Consensus        88 tgRar~g~-rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~  139 (157)
                      |||||+|+ +||+|||||++|||+| |+|+++||||+|++||+||||+++.++
T Consensus        64 TGrAR~Gs~rsP~~~gGG~~fgP~p-R~~~~klnkK~rrlAl~sALs~k~~~~  115 (205)
T 2zjr_C           64 TGNARHGDRSVPTFVGGGVAFGPKP-RSYDYTLPRQVRQLGLAMAIASRQEGG  115 (205)
T ss_dssp             SSSCCCSCSCSTTSTTSCCTTCCCC-CCCCCCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCcccCcccCCcccCCeeecCCCC-cchhhhcCHHHHHHHHHHHHHHHhhcC
Confidence            77778886 9999999999999999 999999999999999999999999754

>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=100.00  E-value=8e-42  Score=277.69  Aligned_cols=113  Identities=22%  Similarity=0.258  Sum_probs=101.1

Q ss_pred             cccccc-ccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCCCCcccCCCCC-CCcccc
Q 048058           24 STVPLP-DVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGA-FGNMCR  101 (157)
Q Consensus        24 g~ieLp-~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg~GtgRar~g~-rsP~~r  101 (157)
                      ++|||| +||+.|+|+||||++|++|++|+||||+     .+|+|+||||+|+|    || +||||||||+|+ +||+||
T Consensus        10 ~~i~L~~~vF~~~~r~dlih~~v~~~~a~~Rqgt~-----~tktraEv~G~grK----p~-rQKGTGrAR~Gs~rsP~~~   79 (201)
T 3r8s_E           10 SALTVSETTFGRDFNEALVHQVVVAYAAGARQGTR-----AQKTRAEVTGSGKK----PW-RQKGTGRARSGSIKSPIWR   79 (201)
T ss_dssp             CCEECCHHHHSSCCCHHHHHHHHHHHHTTSCCCCC-----CCCBTTTSSCCCCC----SS-CSSSSSSCCCCCTTCTTST
T ss_pred             ceEECCHHHhCCCCCHHHHHHHHHHHHHhCcCCCC-----CCcceeeecCCCCC----CC-ccCCCCccccCcCcCCcee
Confidence            579998 7999999999999999999999999986     46899999999997    43 577788888887 999999


Q ss_pred             ccccccCCccCcceeeccCHHHHHHHHHHHHHhccChhhHhhcCcccCCC
Q 048058          102 GGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETV  151 (157)
Q Consensus       102 GGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rgh~~~~~  151 (157)
                      |||++|||+| |+|+++||||+|++|++||||+++.++    +-|.+|+.
T Consensus        80 gGG~~fgP~p-R~~~~klnkK~rrlAl~sALs~k~~~~----~l~Vvd~~  124 (201)
T 3r8s_E           80 SGGVTFAARP-QDHSQKVNKKMYRGALKSILSELVRQD----RLIVVEKF  124 (201)
T ss_dssp             TCCBTTCCCC-CCCCCCCCHHHHHHHHHHHHHHHHHHT----CEEECSCC
T ss_pred             CCEeecCCcc-ccceeccCHHHHHHHHHHHHHHHhhcC----CEEEeccc
Confidence            9999999999 999999999999999999999999764    34666664

>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=100.00  E-value=1.3e-34  Score=230.78  Aligned_cols=88  Identities=24%  Similarity=0.278  Sum_probs=79.0

Q ss_pred             HHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCCCCcccCCCCC-CCccccccccccCCccCcceeeccC
Q 048058           42 GFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGA-FGNMCRGGRMFAPTKIWRRWHRKIN  120 (157)
Q Consensus        42 ~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg~GtgRar~g~-rsP~~rGGg~afgPkp~r~~~~kiN  120 (157)
                      |++|+||++|+||||++     +|+|+||||+|+|    || +||||||||+|+ +||+|||||++|||+++|||+++||
T Consensus         1 h~~v~~~~a~~Rqgt~~-----tktraEv~G~grK----p~-rQKGTGrAR~Gs~rsP~~~gGG~~fgP~~pR~~~~kln   70 (175)
T 2ftc_D            1 HQVAMWQKNFKRISYAK-----TKTRAEVRGGGRK----PW-PQKGTGRARHGSIRSPLWRGGGVAHGPRGPTSYYYMLP   70 (175)
T ss_pred             CHHHHHHHHHhhcCCCC-----CcceeeecCCCCC----CC-CcCCCCccccCCCcCCcccCCEeecCCCCccchhhhcC
Confidence            78999999999999864     7999999999997    43 577777788886 9999999999999993399999999


Q ss_pred             HHHHHHHHHHHHHhccChh
Q 048058          121 VNQKRYAIVSAIAASAVPS  139 (157)
Q Consensus       121 kK~rrlAl~sALs~ka~~~  139 (157)
                      ||+|++||+||||+++.++
T Consensus        71 kK~rrlAl~sALs~k~~~~   89 (175)
T 2ftc_D           71 MKVRALGLKVALTVKLAQD   89 (175)
T ss_pred             HHHHHHHHHHHHHHhccCC
Confidence            9999999999999999864

>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=92.30  E-value=0.06  Score=46.94  Aligned_cols=51  Identities=18%  Similarity=-0.014  Sum_probs=30.6

Q ss_pred             HHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCCCCcccCCCCCCCcccccccccc
Q 048058           45 HSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFA  107 (157)
Q Consensus        45 v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg~GtgRar~g~rsP~~rGGg~af  107 (157)
                      ++.+--..-+-..+.+++.+++++|+  +|+|    ||    |||||++  +.|=..|||..-
T Consensus        34 lih~vv~~~~an~RQgt~~tk~rgev--tg~K----~w----GTGRAra--ripRv~g~Gs~R   84 (362)
T 2wwb_H           34 IVHTVFTSVNKNKRQAYAVSEKAGHQ--TSAE----SW----GTGRAVA--RIPRVGGGGTGR   84 (362)
T ss_dssp             HHHHHHHHHHHHHCCCCCCCSSSSCS--SCCS----SC----CCCSSSC--SCSCCCSCSSSS
T ss_pred             HHHHHHHHHHHhccCCCCCCCccccc--ccce----ec----CCCCCee--ecccccCCCCCC
Confidence            33333333334456789999999999  5665    77    5666665  345555554333

---

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	157
d1vqoc1	246	c.22.1.1 (C:1-246) Ribosomal protein L4 {Archaeon	2e-29
d1dmga_	225	c.22.1.1 (A:) Ribosomal protein L4 {Thermotoga mar	1e-08
d2j01f1	208	c.22.1.1 (F:1-208) Ribosomal protein L4 {Thermus t	4e-08

>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 =  105 bits (263), Expect = 2e-29
 Identities = 44/149 (29%), Positives = 70/149 (46%), Gaps = 12/149 (8%)

Query: 9   ITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSA 68
            T+  L+G+        V LPDV +  +R D++G        N +Q Y     AG +T A
Sbjct: 3   ATIYDLDGN----TDGEVDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPA 58

Query: 69  ESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAI 128
           ES+G+GR  + +P++ G                 GR   P K  +     +N  +++ A+
Sbjct: 59  ESFGSGRGQAHVPKLDGRARRV-------PQAVKGRSAHPPKTEKDRSLDLNDKERQLAV 111

Query: 129 VSAIAASAVPSLVMARGHKIETVPEMPLV 157
            SA+AA+A   LV  RGH+     E+P+V
Sbjct: 112 RSALAATADADLVADRGHEF-DRDEVPVV 139

>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 = 49.8 bits (118), Expect = 1e-08
 Identities = 30/144 (20%), Positives = 53/144 (36%), Gaps = 16/144 (11%)

Query: 9   ITVQSLEGDMATDASSTVPLPD-VMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTS 67
           + + +++G+       T+ + D V       D++         N R        A  +T 
Sbjct: 3   VDLLNVKGE----KVGTLEISDFVFNIDPNYDVMWRYVDMQLSNRRAGT-----ASTKTR 53

Query: 68  AESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYA 127
            E  G GR   +       G  R G         GG +  P    R W +K+N   K+ A
Sbjct: 54  GEVSGGGR---KPWPQKHTGRARHGSIRSPIWRHGGVVHGPKP--RDWSKKLNKKMKKLA 108

Query: 128 IVSAIAASAVPS-LVMARGHKIET 150
           + SA++     + L++    K+E 
Sbjct: 109 LRSALSVKYRENKLLVLDDLKLER 132

>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 = 48.3 bits (114), Expect = 4e-08
 Identities = 24/122 (19%), Positives = 40/122 (32%), Gaps = 10/122 (8%)

Query: 21  DASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRI 80
             S    L   + A I P ++  V        R+       A  +T  E   +GR   +I
Sbjct: 13  SPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGT-----ASTKTRGEVAYSGR---KI 64

Query: 81  PRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSL 140
                 G  R G         GG +F P    R +   +    ++  +  A+A  A    
Sbjct: 65  WPQKHTGRARHGDIGAPIFVGGGVVFGPKP--RDYSYTLPKKVRKKGLAMAVADRAREGK 122

Query: 141 VM 142
           ++
Sbjct: 123 LL 124

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	157
d1vqoc1	246	Ribosomal protein L4 {Archaeon Haloarcula marismor	100.0
d2gycc1	198	Ribosomal protein L4 {Escherichia coli [TaxId: 562	100.0
d2zjrc1	197	Ribosomal protein L4 {Deinococcus radiodurans [Tax	100.0
d1dmga_	225	Ribosomal protein L4 {Thermotoga maritima [TaxId:	100.0
d2j01f1	208	Ribosomal protein L4 {Thermus thermophilus [TaxId:	100.0

>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=100.00  E-value=1.2e-46  Score=310.47  Aligned_cols=138  Identities=31%  Similarity=0.461  Sum_probs=128.3

Q ss_pred             CccEEeccCCCccccCCccccccccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCCC
Q 048058            7 PLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGG   86 (157)
Q Consensus         7 ~~v~V~n~~G~~~~~~gg~ieLp~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg~   86 (157)
                      |+++|||++|+++    |+||||+||+.|+|.||||++|+||++|+||||++++++++++++|++|+|++        |+
T Consensus         1 Mk~~v~~~~gk~~----g~i~lpdvF~~~~r~dlvh~~v~~~~an~Rqgt~~~k~~g~~t~a~~~g~g~~--------qk   68 (246)
T d1vqoc1           1 MQATIYDLDGNTD----GEVDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESFGSGRG--------QA   68 (246)
T ss_dssp             CEEEEECTTSCEE----EEEECCGGGGSCCCHHHHHHHHHHHHHHTCCCCCCCTTTTTCCCCBCCCSSSS--------CC
T ss_pred             CceEEEcCCCCEe----eEEEChhhhCCCCCHHHHHHHHHHHHHhcccCcCCCchhheeeeeeecCcccc--------cc
Confidence            5899999999999    99999999999999999999999999999999999999999999999999863        44


Q ss_pred             CcccCCCCC-CCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccChhhHhhcCcccCCCCCCCCC
Q 048058           87 GTHRAGQGA-FGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIETVPEMPLV  157 (157)
Q Consensus        87 GtgRar~g~-rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rgh~~~~~~~~Piv  157 (157)
                      ||+|++.|+ ++|+|||||++|||+|+|+|+++||||+|++|+++|||+++.+++|.+|||+|++ .+||||
T Consensus        69 ~tgrar~g~rrsP~~rGGG~a~gPkp~r~~~~klnkK~r~lAl~~aLs~k~~~~~v~~~g~~~~~-~~~~iV  139 (246)
T d1vqoc1          69 HVPKLDGRARRVPQAVKGRSAHPPKTEKDRSLDLNDKERQLAVRSALAATADADLVADRGHEFDR-DEVPVV  139 (246)
T ss_dssp             CCCEETTEECSSTTSTTCCCSSCCCTTCCCCCCCCHHHHHHHHHHHHHHTTCHHHHHHHTCCCCC-SSCSEE
T ss_pred             CCCccccCCccCCCcCCCceecCCCCccchhHHHHHHHHHHHHHHHHHHhhcccceeeecccccC-CCCCEE
Confidence            455555554 9999999999999999999999999999999999999999999999999999988 589986

>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=100.00  E-value=1.1e-41  Score=273.49  Aligned_cols=115  Identities=20%  Similarity=0.243  Sum_probs=104.0

Q ss_pred             CccEEeccCCCccccCCcccccc-ccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCC
Q 048058            7 PLITVQSLEGDMATDASSTVPLP-DVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPG   85 (157)
Q Consensus         7 ~~v~V~n~~G~~~~~~gg~ieLp-~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg   85 (157)
                      |+++|+|.+        ++|||+ +||+.|+|.||||++|+||++|+||||+     .||+|+||+|+|+|    || +|
T Consensus         1 m~l~~~~~~--------~~i~l~~~vF~~~~~~~llh~~v~~~~a~~R~gt~-----~tKtRseV~g~gkK----p~-~Q   62 (198)
T d2gycc1           1 MELVLKDAQ--------SALTVSETTFGRDFNEALVHQVVVAYAAGARQGTR-----AQKTRAEVTGSGKK----PW-RQ   62 (198)
T ss_dssp             CCEEEECTT--------CCSCCCEECCCSCCCHHHHTTTSSSCTTCCSCCCC-----SSCSCCCCCCSCSS----CS-CC
T ss_pred             CeeEecCCC--------CeEEeCHHHhCCCcCHHHHHHHHHHHHHhccCCCc-----ccceehhccCCccC----cc-cc
Confidence            477887754        679998 6999999999999999999999999975     56899999999997    55 78


Q ss_pred             CCcccCCCCC-CCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccChhh
Q 048058           86 GGTHRAGQGA-FGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSL  140 (157)
Q Consensus        86 ~GtgRar~g~-rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~  140 (157)
                      |||||||+|+ +||+|||||++|||+| |+|+++||||+|++|+++|||+++.++-
T Consensus        63 KGTGrAR~Gs~rsP~~~gGGva~GP~p-r~~~~kl~kK~r~~al~~aLs~k~~~~~  117 (198)
T d2gycc1          63 KGTGRARSGSIKSPIWRSGGVTFAARP-QDHSQKVNKKMYRGALKSILSELVRQDR  117 (198)
T ss_dssp             CCCCCBTTBCCSCSSSSSCCCSSCSCC-SSSCCCCCTTTHHHHHHHHHHHTTSSSS
T ss_pred             cCCCCCCCcCcchhhcccCceecCccc-cCeEeeHHHHHHHHHHHHHHHHHHhcCC
Confidence            8888888887 9999999999999999 9999999999999999999999998743

>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=100.00  E-value=7.8e-41  Score=268.05  Aligned_cols=113  Identities=22%  Similarity=0.217  Sum_probs=103.1

Q ss_pred             ccEEeccCCCccccCCccccccccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCCCC
Q 048058            8 LITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGGG   87 (157)
Q Consensus         8 ~v~V~n~~G~~~~~~gg~ieLp~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg~G   87 (157)
                      +++|+|.+|+++    ++++|+     ++|+||||++|+||++|+||||+     .||+|+||+|+|+|    || +|||
T Consensus         2 ~~~v~~~~g~~~----~~~~~~-----e~~~~ll~~~v~~~~a~~R~gt~-----~tk~R~ev~gsgkK----p~-~QKG   62 (197)
T d2zjrc1           2 QINVIGQNGGRT----IELPLP-----EVNSGVLHEVVTWQLASRRRGTA-----STRTRAQVSKTGRK----MY-GQKG   62 (197)
T ss_dssp             CCCCSSCCCCCC----CCCCTT-----TCCHHHHHHHHHHHHHHHCCCCC-----CCCCCTTTSCCCSC----CS-CSSS
T ss_pred             eeeeecCCCCeE----Eeeccc-----cccHHHHHHHHHHHHHhhhccCc-----cCCchhhccCCCCC----cc-cCCC
Confidence            789999999998    888887     58999999999999999999975     57999999999997    55 6888


Q ss_pred             cccCCCCC-CCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccChhh
Q 048058           88 THRAGQGA-FGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSL  140 (157)
Q Consensus        88 tgRar~g~-rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~  140 (157)
                      |||||+|+ +||+|||||++|||+| |+|.++||||+|++||++|||+++.++-
T Consensus        63 tGrAR~Gs~rsP~~rgGg~afgp~p-r~~~~~lnkK~r~lal~~aLS~K~~~~~  115 (197)
T d2zjrc1          63 TGNARHGDRSVPTFVGGGVAFGPKP-RSYDYTLPRQVRQLGLAMAIASRQEGGK  115 (197)
T ss_dssp             SSSCCCSCSCSTTSTTSCCTTCCCC-CCCCCCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCcccccccccccceeeccccc-cchhhhccHHHHHHHHHHHHHHHHhcCc
Confidence            88888886 9999999999999998 9999999999999999999999986643

>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=100.00  E-value=3.4e-41  Score=274.01  Aligned_cols=119  Identities=24%  Similarity=0.317  Sum_probs=63.2

Q ss_pred             ccEEeccCCCccccCCcccccc-ccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccccccCCC
Q 048058            8 LITVQSLEGDMATDASSTVPLP-DVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGG   86 (157)
Q Consensus         8 ~v~V~n~~G~~~~~~gg~ieLp-~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~prqkg~   86 (157)
                      +|+|||++|+++    ++|||| +||+.|+|+||||++|++|++|+||||+     +||+|+||+|+|+|    || +|+
T Consensus         2 ~v~v~~~~g~~~----g~i~L~~~vF~~~~r~dli~~~v~~~~~~~Rqgt~-----~tk~rsev~g~gkK----~~-~QK   67 (225)
T d1dmga_           2 QVDLLNVKGEKV----GTLEISDFVFNIDPNYDVMWRYVDMQLSNRRAGTA-----STKTRGEVSGGGRK----PW-PQK   67 (225)
T ss_dssp             EEEEECTTSCEE----EEEECCHHHHSSCCCHHHHHHHHHHHHC------------------------------------
T ss_pred             eeEEEcCCCCEe----eEEEeCHHHhCCCccHHHHHHHHHHHHHhcccCcc-----ccccceeeeccccc----cc-ccC
Confidence            899999999999    999998 6999999999999999999999999975     57999999999997    44 577


Q ss_pred             CcccCCCCC-CCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccChhhH
Q 048058           87 GTHRAGQGA-FGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLV  141 (157)
Q Consensus        87 GtgRar~g~-rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~v  141 (157)
                      ||||||+|+ ++|+|||||++|||+| |+|+++||||+|++|+++|||+++.++-|
T Consensus        68 GtG~AR~Gs~~sp~~~gGg~a~gp~p-r~~~~klnkK~r~~Al~~aLs~k~~~~~l  122 (225)
T d1dmga_          68 HTGRARHGSIRSPIWRHGGVVHGPKP-RDWSKKLNKKMKKLALRSALSVKYRENKL  122 (225)
T ss_dssp             ----------------------------CHHHHHHHHHHHHHHHHHHHHHHHTTCE
T ss_pred             CcCcccccccccceeeccccccCCCC-chhhhhHHHHHHHHHHHHHHHHHhccCCe
Confidence            778888886 9999999999999999 99999999999999999999999866443

>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=100.00  E-value=6.1e-39  Score=258.42  Aligned_cols=127  Identities=24%  Similarity=0.221  Sum_probs=110.3

Q ss_pred             CcccCCCccEEeccCCCccccCCccccccccccccCChhhHHHHHHHHHHhcCCCCCcCccCcccceeeeeccccccccc
Q 048058            1 MAAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRAVSRI   80 (157)
Q Consensus         1 ~~~~~~~~v~V~n~~G~~~~~~gg~ieLp~vF~~~~r~~li~~~v~~~~an~Rqgt~~~~~a~~k~raev~G~g~k~~r~   80 (157)
                      |.--++++++|||.+|++.    ++++||    .|+|+||||++|++|++|+||||+     ++|+|+|++|+|+|    
T Consensus         1 m~~~~~~~~~v~~~~g~~~----~~~~l~----~~v~~dli~~av~~~~a~~Rqgta-----~tk~R~ev~g~gkK----   63 (208)
T d2j01f1           1 MKEVAVYQIPVLSPSGRRE----LAADLP----AEINPHLLWEVVRWQLAKRRRGTA-----STKTRGEVAYSGRK----   63 (208)
T ss_dssp             CCCCCCCCCCSSSCCCCCC----CSTTSS----SCCCHHHHHHHHHHHHHHTCCCCC-----CCCCTTTSCCCCCC----
T ss_pred             CCceeEEeeeeecCCCCEe----eccccc----cccCHHHHHHHHHHHHHhccCCCC-----CCCccccccCcccc----
Confidence            4445678999999999998    788776    478999999999999999999975     67999999999997    


Q ss_pred             cccCCCCcccCCCCC-CCccccccccccCCccCcceeeccCHHHHHHHHHHHHHhccChhhHhhcCcccCC
Q 048058           81 PRVPGGGTHRAGQGA-FGNMCRGGRMFAPTKIWRRWHRKINVNQKRYAIVSAIAASAVPSLVMARGHKIET  150 (157)
Q Consensus        81 prqkg~GtgRar~g~-rsP~~rGGg~afgPkp~r~~~~kiNkK~rrlAl~sALs~ka~~~~v~~rgh~~~~  150 (157)
                      || +|+||||||+|+ ++|+|||||++|||+| |+|+++||||+|++|+++|||+++.++-+    +.+|+
T Consensus        64 ~~-~QKGtGrAR~Gs~rsp~~~gGg~~~gp~~-r~~~~klnkK~r~~Al~~aLs~k~~~~~l----~Vvd~  128 (208)
T d2j01f1          64 IW-PQKHTGRARHGDIGAPIFVGGGVVFGPKP-RDYSYTLPKKVRKKGLAMAVADRAREGKL----LLVEA  128 (208)
T ss_dssp             SS-CSSSSSSCCCCCTTSTTSTTSCCSSCCCC-CCCCCCCCHHHHHHHHHHHHHHHHHTTCE----EEECC
T ss_pred             cC-cccccccccccccccccccccceecCcch-hhHHHHHHHHHHHHHHHHHHHHHhccCCc----eeecc
Confidence            44 577777777786 9999999999999999 99999999999999999999999887654    45555