Citrus Sinensis ID: 033538

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------
Protein Sequence
MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAEAQRVKAKKEKLDKKRKPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ
Secondary Structure (PSIPRED)
cccHHHHHHHccHHHHHHHcccccccccccccccHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHccHHHHHHHcccccccccccccccccHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHcccc
Coil and Loop (DISEMBL)
MVNADLARIINSDEVQSVVRPiktevkrapmkknplknlntllrlnpyAKTARRMSLLAEAQRVKAKKEkldkkrkpiTKEEAAAIKSAGKAWYQTmisdsdytefENFSKWLGVSQ
Flexible Loop (DISEMBL)
mvnadlariinsdevqsvvrpiktevkrapmkknplknlntllrlnPYAKTARRMSLLAEAQRVkakkekldkkrkpitkEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ
Low Complexity Region (SEG)
MVNADLARIINSDEVQSVVRPIKTEVKRApmkknplknlntllrlnpYAKTARRMSLLAEAQRVkakkekldkkrkPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ
Disordered region (IsUnstruct)
***************************************NTLLRLNPY****************************************AGKAWYQTMISDSDYTEFENFSKWL****
Disordered Region (DISOPRED)
*VNADLARIINSDEVQS******************LKNLNTLLRLNPYAKTA*******************************************TMISDSDYTEFENFSKWLGVS*
Disordered Region (DISEMBL)
MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE*****************ITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ
Disordered Region (DISPRO)
***ADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAEAQRVKAKKEKLDKKRKPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVS*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARxxxxxxxxxxxxxxxxxxxxxRKPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ
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	117	2.2.26 [Sep-21-2011]
Q9XF97	408	60S ribosomal protein L4	N/A	no	1.0	0.286	0.854	1e-46
Q9SF40	406	60S ribosomal protein L4-	yes	no	1.0	0.288	0.820	9e-45
P49691	407	60S ribosomal protein L4-	yes	no	1.0	0.287	0.829	3e-44
P02385	401	60S ribosomal protein L4-	N/A	no	0.666	0.194	0.5	9e-15
P08429	396	60S ribosomal protein L4-	N/A	no	0.666	0.196	0.5	9e-15
P36578	427	60S ribosomal protein L4	yes	no	0.598	0.163	0.471	9e-12
Q5RCR3	427	60S ribosomal protein L4	yes	no	0.598	0.163	0.471	9e-12
Q58DW0	422	60S ribosomal protein L4	yes	no	0.598	0.165	0.471	1e-11
P50878	421	60S ribosomal protein L4	yes	no	0.529	0.147	0.5	3e-11
Q9D8E6	419	60S ribosomal protein L4	yes	no	0.529	0.147	0.5	3e-11

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

 Score =  184 bits (467), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 100/117 (85%), Positives = 111/117 (94%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           MVNADLARIINSDEVQSVV PI+   KRAP+KKNPL+ LNT+L+LNPYAKTARRMSLLAE
Sbjct: 292 MVNADLARIINSDEVQSVVSPIQEGSKRAPLKKNPLRILNTMLKLNPYAKTARRMSLLAE 351

Query: 61  AQRVKAKKEKLDKKRKPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ 117
           A+RVKAKKEKLDKKRKPI+KEEA+ IK+AGKAWYQTMISDSDYTEF+NF+KWLGVSQ
Sbjct: 352 AERVKAKKEKLDKKRKPISKEEASTIKAAGKAWYQTMISDSDYTEFDNFTKWLGVSQ 408

Prunus armeniaca (taxid: 36596)

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

 Score =  178 bits (451), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 96/117 (82%), Positives = 108/117 (92%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           MVNADLARIINSDE+QSVV PIK + KRA +KKNPLKNLN +L+LNPYAKTA+RMSLLAE
Sbjct: 290 MVNADLARIINSDEIQSVVNPIKKDAKRAVLKKNPLKNLNVMLKLNPYAKTAKRMSLLAE 349

Query: 61  AQRVKAKKEKLDKKRKPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ 117
           AQRVKAKKEKL KKRK +TKEEA AIK+AGK+WY+TMISDSDYTEF+NF+KWLG SQ
Sbjct: 350 AQRVKAKKEKLAKKRKTVTKEEALAIKAAGKSWYKTMISDSDYTEFDNFTKWLGASQ 406

Arabidopsis thaliana (taxid: 3702)

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

 Score =  176 bits (447), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 97/117 (82%), Positives = 106/117 (90%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           MVNADLARIINSDEVQSVV PIK   KRA +KKNPLKNLN + +LNPYAKTA+RMSLLAE
Sbjct: 291 MVNADLARIINSDEVQSVVNPIKDGSKRAVLKKNPLKNLNVMFKLNPYAKTAKRMSLLAE 350

Query: 61  AQRVKAKKEKLDKKRKPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ 117
           A RVKAKKEKL+KKRK +TKEEA AIK+AGKAWYQTMISDSDYTEF+NF+KWLG SQ
Sbjct: 351 ASRVKAKKEKLEKKRKVVTKEEAQAIKAAGKAWYQTMISDSDYTEFDNFTKWLGASQ 407

Arabidopsis thaliana (taxid: 3702)

>sp|P02385|RL4B_XENLA 60S ribosomal protein L4-B OS=Xenopus laevis GN=rpl4-b PE=2 SV=2

 Score = 79.0 bits (193), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 41/82 (50%), Positives = 57/82 (69%), Gaps = 4/82 (4%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           M N DL RI+ S E+Q  +R    +VKR  +KKNPLKNL  ++RLNPYAKTARR ++L +
Sbjct: 288 MTNTDLTRILKSQEIQRALRAPNKKVKRRELKKNPLKNLRIMMRLNPYAKTARRHAILQQ 347

Query: 61  AQRVKAKKEKLD----KKRKPI 78
            + +KAK++K D    K +KP+
Sbjct: 348 LENIKAKEKKPDDGKPKAKKPL 369

Xenopus laevis (taxid: 8355)

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

 Score = 79.0 bits (193), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 41/82 (50%), Positives = 57/82 (69%), Gaps = 4/82 (4%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           M N DL RI+ S E+Q  +R    +VKR  +KKNPLKNL  ++RLNPYAKTARR ++L +
Sbjct: 288 MTNTDLTRILKSQEIQRALRAPNKKVKRRELKKNPLKNLRIMMRLNPYAKTARRHAILQQ 347

Query: 61  AQRVKAKKEKLD----KKRKPI 78
            + +KAK++K D    K +KP+
Sbjct: 348 LENIKAKEKKPDDGKPKAKKPL 369

Xenopus laevis (taxid: 8355)

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

 Score = 68.9 bits (167), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 33/70 (47%), Positives = 50/70 (71%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           M+N DL+RI+ S E+Q  +R  + ++ R  +KKNPLKNL  +L+LNPYAKT RR ++L +
Sbjct: 284 MINTDLSRILKSPEIQRALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQ 343

Query: 61  AQRVKAKKEK 70
           A+  K + +K
Sbjct: 344 ARNHKLRVDK 353

Homo sapiens (taxid: 9606)

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

 Score = 68.9 bits (167), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 33/70 (47%), Positives = 50/70 (71%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           M+N DL+RI+ S E+Q  +R  + ++ R  +KKNPLKNL  +L+LNPYAKT RR ++L +
Sbjct: 284 MINTDLSRILKSPEIQRALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQ 343

Query: 61  AQRVKAKKEK 70
           A+  K + +K
Sbjct: 344 ARNHKLRVDK 353

Pongo abelii (taxid: 9601)

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

 Score = 68.6 bits (166), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 33/70 (47%), Positives = 50/70 (71%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           M+N DL+RI+ S E+Q  +R  + ++ R  +KKNPLKNL  +L+LNPYAKT RR ++L +
Sbjct: 284 MLNTDLSRILKSPEIQRALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQ 343

Query: 61  AQRVKAKKEK 70
           A+  K + +K
Sbjct: 344 ARNHKIRMDK 353

Bos taurus (taxid: 9913)

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

 Score = 67.4 bits (163), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 31/62 (50%), Positives = 46/62 (74%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           M+N DL+RI+ S E+Q  +R  + ++ R  +KKNPLKNL  +L+LNPYAKT RR ++L +
Sbjct: 284 MMNTDLSRILKSPEIQRALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQ 343

Query: 61  AQ 62
           A+
Sbjct: 344 AR 345

Rattus norvegicus (taxid: 10116)

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

 Score = 67.4 bits (163), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 31/62 (50%), Positives = 46/62 (74%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           M+N DL+RI+ S E+Q  +R  + ++ R  +KKNPLKNL  +L+LNPYAKT RR ++L +
Sbjct: 284 MMNTDLSRILKSPEIQRALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQ 343

Query: 61  AQ 62
           A+
Sbjct: 344 AR 345

Mus musculus (taxid: 10090)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	117
225439761	406	PREDICTED: 60S ribosomal protein L4 [Vit	1.0	0.288	0.914	2e-55
297741490	344	unnamed protein product [Vitis vinifera]	1.0	0.340	0.914	2e-55
168415071	132	60S ribosomal protein L1 [Arachis diogoi	1.0	0.886	0.854	9e-53
297825471	394	60S ribosomal protein L4/L1 [Arabidopsis	1.0	0.296	0.811	5e-50
356572399	430	PREDICTED: 60S ribosomal protein L4-1-li	1.0	0.272	0.803	7e-50
356505182	402	PREDICTED: 60S ribosomal protein L4-1-li	1.0	0.291	0.786	5e-49
26450328	407	putative 60S ribosomal protein [Arabidop	1.0	0.287	0.820	8e-49
224068640	408	predicted protein [Populus trichocarpa]	1.0	0.286	0.854	1e-48
224144519	408	predicted protein [Populus trichocarpa]	1.0	0.286	0.854	1e-48
148905730	406	unknown [Picea sitchensis]	0.991	0.285	0.769	5e-46

>gi|225439761|ref|XP_002274975.1| PREDICTED: 60S ribosomal protein L4 [Vitis vinifera]

 Score =  219 bits (558), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 107/117 (91%), Positives = 113/117 (96%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           MVNADLARIINSDEVQSVVRPIK EVKRAPMKKNPLKNLNT+L+LNPYAKTARRM+LLAE
Sbjct: 290 MVNADLARIINSDEVQSVVRPIKKEVKRAPMKKNPLKNLNTMLKLNPYAKTARRMALLAE 349

Query: 61  AQRVKAKKEKLDKKRKPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ 117
           AQRVKAK+EKLDKKRK I KEE AAIK+AGKAWYQTMISDSDYTEF+NFSKWLGVSQ
Sbjct: 350 AQRVKAKQEKLDKKRKQIPKEEVAAIKAAGKAWYQTMISDSDYTEFDNFSKWLGVSQ 406

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297741490|emb|CBI32622.3| unnamed protein product [Vitis vinifera]

 Score =  219 bits (557), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 107/117 (91%), Positives = 113/117 (96%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           MVNADLARIINSDEVQSVVRPIK EVKRAPMKKNPLKNLNT+L+LNPYAKTARRM+LLAE
Sbjct: 228 MVNADLARIINSDEVQSVVRPIKKEVKRAPMKKNPLKNLNTMLKLNPYAKTARRMALLAE 287

Query: 61  AQRVKAKKEKLDKKRKPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ 117
           AQRVKAK+EKLDKKRK I KEE AAIK+AGKAWYQTMISDSDYTEF+NFSKWLGVSQ
Sbjct: 288 AQRVKAKQEKLDKKRKQIPKEEVAAIKAAGKAWYQTMISDSDYTEFDNFSKWLGVSQ 344

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|168415071|gb|ACA23473.1| 60S ribosomal protein L1 [Arachis diogoi]

 Score =  210 bits (534), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 100/117 (85%), Positives = 112/117 (95%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           MVNADLARIINSDEVQSVVRPIK EVKRA +KKNPLKNLN +LRLNPYAK A+RM+LLAE
Sbjct: 16  MVNADLARIINSDEVQSVVRPIKKEVKRATLKKNPLKNLNVMLRLNPYAKAAKRMALLAE 75

Query: 61  AQRVKAKKEKLDKKRKPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ 117
           AQRVKAKKEKLD+KRK ++KEEA+AI++AGKAWYQTM+SDSDYTEF+NFSKWLGVSQ
Sbjct: 76  AQRVKAKKEKLDQKRKTVSKEEASAIRAAGKAWYQTMVSDSDYTEFDNFSKWLGVSQ 132

Source: Arachis diogoi

Species: Arachis diogoi

Genus: Arachis

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297825471|ref|XP_002880618.1| 60S ribosomal protein L4/L1 [Arabidopsis lyrata subsp. lyrata] gi|297326457|gb|EFH56877.1| 60S ribosomal protein L4/L1 [Arabidopsis lyrata subsp. lyrata]

 Score =  201 bits (511), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 95/117 (81%), Positives = 109/117 (93%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           MVNADLARIINSDEVQSVVRPI+ +VKRA +KKNPLKNLN +L+LNPYAKTARRMSLLAE
Sbjct: 278 MVNADLARIINSDEVQSVVRPIEMDVKRAVLKKNPLKNLNVMLKLNPYAKTARRMSLLAE 337

Query: 61  AQRVKAKKEKLDKKRKPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ 117
           A+RVK+K EKL++KRKPI+KEEA  IK+AGK WY+TMISDSDYTEF+NF+KWLGV Q
Sbjct: 338 AERVKSKNEKLERKRKPISKEEAMKIKAAGKPWYRTMISDSDYTEFDNFTKWLGVEQ 394

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356572399|ref|XP_003554356.1| PREDICTED: 60S ribosomal protein L4-1-like [Glycine max]

 Score =  200 bits (509), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 94/117 (80%), Positives = 109/117 (93%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           MVN+DLARIINSDEVQSVVRPIK +VKRAP+KKNPL NLN +L+LNPYAKTA+RM+LLAE
Sbjct: 314 MVNSDLARIINSDEVQSVVRPIKKDVKRAPLKKNPLTNLNAMLKLNPYAKTAKRMALLAE 373

Query: 61  AQRVKAKKEKLDKKRKPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ 117
            QR+ AKKEKLDKKR  ++KEEA+AIKSAGK+WYQTM+SDSDY +F+NFSKWLGVSQ
Sbjct: 374 KQRIVAKKEKLDKKRNIVSKEEASAIKSAGKSWYQTMVSDSDYADFDNFSKWLGVSQ 430

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356505182|ref|XP_003521371.1| PREDICTED: 60S ribosomal protein L4-1-like [Glycine max]

 Score =  197 bits (502), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 92/117 (78%), Positives = 108/117 (92%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           M+N+DLARIINSDEVQSVVRPIK +VKRAP+KKNPL NLN +L+LNPYAKTA+RM+LLAE
Sbjct: 286 MINSDLARIINSDEVQSVVRPIKKDVKRAPLKKNPLTNLNAMLKLNPYAKTAKRMALLAE 345

Query: 61  AQRVKAKKEKLDKKRKPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ 117
            QR+ AKKEKL KKR  ++KEEA+AIK+AGK+WYQTM+SDSDY EF+NFSKWLGVSQ
Sbjct: 346 KQRIVAKKEKLHKKRNIVSKEEASAIKAAGKSWYQTMVSDSDYAEFDNFSKWLGVSQ 402

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  197 bits (500), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 96/117 (82%), Positives = 105/117 (89%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           MVNADLARIINSDEVQSVV PIK   KRA +KKNPLKNLN + +LNPYAKTA+RMSLLAE
Sbjct: 291 MVNADLARIINSDEVQSVVNPIKDGSKRAVLKKNPLKNLNVMFKLNPYAKTAKRMSLLAE 350

Query: 61  AQRVKAKKEKLDKKRKPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ 117
           A RVKAKKE L+KKRK +TKEEA AIK+AGKAWYQTMISDSDYTEF+NF+KWLG SQ
Sbjct: 351 ASRVKAKKEMLEKKRKVVTKEEAQAIKAAGKAWYQTMISDSDYTEFDNFTKWLGASQ 407

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224068640|ref|XP_002326163.1| predicted protein [Populus trichocarpa] gi|118486971|gb|ABK95318.1| unknown [Populus trichocarpa] gi|222833356|gb|EEE71833.1| predicted protein [Populus trichocarpa]

 Score =  196 bits (498), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 100/117 (85%), Positives = 112/117 (95%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           MVNADLARIINSDEVQSVV PIK EVKRAP+KKNPLKNLN +L+LNPYAKTARRM+LLAE
Sbjct: 292 MVNADLARIINSDEVQSVVNPIKKEVKRAPLKKNPLKNLNVMLKLNPYAKTARRMALLAE 351

Query: 61  AQRVKAKKEKLDKKRKPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ 117
           A+RVK+KKEKLD+KRKP++KEE AA K+AGKAWY+TMISDSDYTEFENF+KWLGVSQ
Sbjct: 352 AERVKSKKEKLDRKRKPVSKEELAAAKAAGKAWYKTMISDSDYTEFENFTKWLGVSQ 408

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224144519|ref|XP_002336155.1| predicted protein [Populus trichocarpa] gi|222874555|gb|EEF11686.1| predicted protein [Populus trichocarpa]

 Score =  196 bits (498), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 100/117 (85%), Positives = 112/117 (95%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           MVNADLARIINSDEVQSVV PIK EVKRAP+KKNPLKNLN +L+LNPYAKTARRM+LLAE
Sbjct: 292 MVNADLARIINSDEVQSVVNPIKKEVKRAPLKKNPLKNLNVMLKLNPYAKTARRMALLAE 351

Query: 61  AQRVKAKKEKLDKKRKPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ 117
           A+RVK+KKEKLD+KRKP++KEE AA K+AGKAWY+TMISDSDYTEFENF+KWLGVSQ
Sbjct: 352 AERVKSKKEKLDRKRKPVSKEELAAAKAAGKAWYKTMISDSDYTEFENFTKWLGVSQ 408

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|148905730|gb|ABR16029.1| unknown [Picea sitchensis]

 Score =  187 bits (476), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 90/117 (76%), Positives = 104/117 (88%), Gaps = 1/117 (0%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           MVN+DLARI+NSDE+QSVVRPI  E+KR P+KKNPLKNL  LL+LNP+AKTARRM+LLA+
Sbjct: 291 MVNSDLARIVNSDEIQSVVRPINREIKRKPLKKNPLKNLGALLKLNPHAKTARRMALLAD 350

Query: 61  AQRVKAKKEKLDKKRKPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ 117
            QR KAK+EKLDKKRK   KE   AIK+AGKAWY+TM+SDSDYTEFENFSKWLGV+Q
Sbjct: 351 EQRAKAKQEKLDKKRKE-PKENKDAIKAAGKAWYKTMVSDSDYTEFENFSKWLGVTQ 406

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

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	117
TAIR|locus:2074904	406	AT3G09630 [Arabidopsis thalian	1.0	0.288	0.615	2e-31
TAIR|locus:2151296	407	AT5G02870 [Arabidopsis thalian	1.0	0.287	0.632	6.9e-31

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

 Score = 345 (126.5 bits), Expect = 2.0e-31, P = 2.0e-31
 Identities = 72/117 (61%), Positives = 81/117 (69%)

Query:     1 MVNADLARIINSDEVQSVVRPIKTEVKRAXXXXXXXXXXXXXXXXXXYAKTARRMSLLAE 60
             MVNADLARIINSDE+QSVV PIK + KRA                  YAKTA+RMSLLAE
Sbjct:   290 MVNADLARIINSDEIQSVVNPIKKDAKRAVLKKNPLKNLNVMLKLNPYAKTAKRMSLLAE 349

Query:    61 AQRVXXXXXXXXXXXXPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ 117
             AQRV             +TKEEA AIK+AGK+WY+TMISDSDYTEF+NF+KWLG SQ
Sbjct:   350 AQRVKAKKEKLAKKRKTVTKEEALAIKAAGKSWYKTMISDSDYTEFDNFTKWLGASQ 406

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 = 340 (124.7 bits), Expect = 6.9e-31, P = 6.9e-31
 Identities = 74/117 (63%), Positives = 79/117 (67%)

Query:     1 MVNADLARIINSDEVQSVVRPIKTEVKRAXXXXXXXXXXXXXXXXXXYAKTARRMSLLAE 60
             MVNADLARIINSDEVQSVV PIK   KRA                  YAKTA+RMSLLAE
Sbjct:   291 MVNADLARIINSDEVQSVVNPIKDGSKRAVLKKNPLKNLNVMFKLNPYAKTAKRMSLLAE 350

Query:    61 AQRVXXXXXXXXXXXXPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ 117
             A RV             +TKEEA AIK+AGKAWYQTMISDSDYTEF+NF+KWLG SQ
Sbjct:   351 ASRVKAKKEKLEKKRKVVTKEEAQAIKAAGKAWYQTMISDSDYTEFDNFTKWLGASQ 407


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.314   0.124   0.338    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      117        87   0.00091  102 3  10 23  0.46    29
                                                     29  0.48    30


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  2
  No. of states in DFA:  575 (61 KB)
  Total size of DFA:  131 KB (2082 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  9.15u 0.10s 9.25t   Elapsed:  00:00:00
  Total cpu time:  9.15u 0.10s 9.25t   Elapsed:  00:00:00
  Start:  Mon May 20 23:31:40 2013   End:  Mon May 20 23:31:40 2013

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

---

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)
P49691	RL4B_ARATH	No assigned EC number	0.8290	1.0	0.2874	yes	no
Q9SF40	RL4A_ARATH	No assigned EC number	0.8205	1.0	0.2881	yes	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:
	GSVIVG00023068001	SubName- Full=Chromosome chr8 scaffold_29, whole genome shotgun sequence; (406 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00018552001	SubName- Full=Chromosome chr13 scaffold_17, whole genome shotgun sequence; (155 aa)	•			•	•	•	•		0.993
	GSVIVG00031743001	SubName- Full=Putative uncharacterized protein (Chromosome chr18 scaffold_59, whole genome shot [...] (389 aa)	•		•	•	•	•	•		0.986
	GSVIVG00010223001	SubName- Full=Chromosome undetermined scaffold_2025, whole genome shotgun sequence; Flags- Frag [...] (300 aa)	•		•	•	•	•	•		0.973
	GSVIVG00019030001	SubName- Full=Chromosome chr15 scaffold_19, whole genome shotgun sequence; (103 aa)				•	•	•	•		0.958
	GSVIVG00036802001	SubName- Full=Chromosome chr4 scaffold_83, whole genome shotgun sequence; (260 aa)	•			•	•	•	•		0.951
	GSVIVG00027466001	SubName- Full=Chromosome chr19 scaffold_4, whole genome shotgun sequence; (260 aa)	•			•	•	•	•		0.950
	GSVIVG00026101001	SubName- Full=Putative uncharacterized protein (Chromosome chr12 scaffold_36, whole genome shot [...] (260 aa)	•			•	•	•	•		0.949
	GSVIVG00025575001	SubName- Full=Chromosome chr8 scaffold_34, whole genome shotgun sequence; (307 aa)	•			•		•	•		0.947
	GSVIVG00037149001	SubName- Full=Chromosome chr16 scaffold_86, whole genome shotgun sequence; (193 aa)	•			•	•	•	•		0.943
	GSVIVG00034120001	SubName- Full=Chromosome chr9 scaffold_7, whole genome shotgun sequence; (193 aa)	•			•	•	•	•		0.943

---

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	117
PLN00185	405	PLN00185, PLN00185, 60S ribosomal protein L4-1; Pr	1e-67
pfam14374	80	pfam14374, Ribos_L4_asso_C, 60S ribosomal protein	3e-28
PTZ00428	381	PTZ00428, PTZ00428, 60S ribosomal protein L4; Prov	4e-21

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

 Score =  208 bits (530), Expect = 1e-67
 Identities = 100/117 (85%), Positives = 111/117 (94%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           MVNADLARIINSDEVQSVV PIK +VKRAP+KKNPLKNLN +L+LNPYAKTARRM+LLAE
Sbjct: 289 MVNADLARIINSDEVQSVVNPIKKDVKRAPLKKNPLKNLNAMLKLNPYAKTARRMALLAE 348

Query: 61  AQRVKAKKEKLDKKRKPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ 117
           A RVKAKKEKL KKRK ++KEEAAAIK+AGKAWY+TMISDSDYTEF+NF+KWLGVSQ
Sbjct: 349 AARVKAKKEKLAKKRKQVSKEEAAAIKAAGKAWYKTMISDSDYTEFDNFTKWLGVSQ 405

Length = 405

>gnl|CDD|222716 pfam14374, Ribos_L4_asso_C, 60S ribosomal protein L4 C-terminal domain

 Score = 97.7 bits (244), Expect = 3e-28
 Identities = 46/71 (64%), Positives = 55/71 (77%), Gaps = 1/71 (1%)

Query: 1  MVNADLARIINSDEVQSVVRPIKTEVKR-APMKKNPLKNLNTLLRLNPYAKTARRMSLLA 59
          M NADL+R+INSDE+QSV+R  K + KR    KKNPLKNL  +L+LNPYAK ARR +LLA
Sbjct: 10 MANADLSRLINSDEIQSVLRAPKKKAKRRVVQKKNPLKNLQAMLKLNPYAKVARRAALLA 69

Query: 60 EAQRVKAKKEK 70
          E +R KAK EK
Sbjct: 70 EKKRKKAKAEK 80

This family is found at the very C-terminal of 60 ribosomal L4 proteins. Length = 80

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

 Score = 85.9 bits (213), Expect = 4e-21
 Identities = 44/95 (46%), Positives = 59/95 (62%), Gaps = 2/95 (2%)

Query: 1   MVNADLARIINSDEVQSVVRPIK-TEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLA 59
           M NAD+ARIINS+EVQ+V+RP K    KR   KKNPLKN    LRLNP AK  R++++LA
Sbjct: 283 MTNADIARIINSEEVQAVLRPAKKKPAKRRVQKKNPLKNRRVRLRLNPAAKKLRKLAVLA 342

Query: 60  EAQRVKAKKEKLDKKRKPITKEEAAAIKSAGKAWY 94
           + +      +K+ K R+   K + A +    KA Y
Sbjct: 343 QEKATAKGAQKV-KNRRARKKAKKARLAKVAKALY 376

Length = 381

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	117
PLN00185	405	60S ribosomal protein L4-1; Provisional	100.0
PF14374	80	Ribos_L4_asso_C: 60S ribosomal protein L4 C-termin	99.97
PTZ00428	381	60S ribosomal protein L4; Provisional	99.93
KOG1475	363	consensus Ribosomal protein RPL1/RPL2/RL4L4 [RNA p	99.57

>PLN00185 60S ribosomal protein L4-1; Provisional

Probab=100.00  E-value=4.9e-33  Score=235.97  Aligned_cols=117  Identities=85%  Similarity=1.225  Sum_probs=111.6

Q ss_pred             CCchhhhhhhCcHHHHhhhcCCcccccCCCCCCCcchhHHHHHhcChHHHHHHHHHHHHHHHHHHHHHHhhhhcCCcCcH
Q 033538            1 MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAEAQRVKAKKEKLDKKRKPITK   80 (117)
Q Consensus         1 MtNaDl~RiInSdEIQsvlr~~k~~~kr~~~KKNPLKN~~~mlrLNPyAk~~rr~a~~~~~~r~~~k~~k~~~kr~~~~~   80 (117)
                      |||+||+|||||||||+||||++..++++++|+|||+|+++|+||||||+++|+++++.+..+..++.++.+.++....+
T Consensus       289 m~n~dl~rii~S~eiq~~lr~~~~~~~~~~~kknplkn~~~~~~lnpya~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  368 (405)
T PLN00185        289 MVNADLARIINSDEVQSVVNPIKKDVKRAPLKKNPLKNLNAMLKLNPYAKTARRMALLAEAARVKAKKEKLAKKRKQVSK  368 (405)
T ss_pred             cccccHHHHhccHHHHHHHhccCCccccchhhcCchHHHHHHHHhChHHHHHHHHHHHHHHHHHhcchhhHHHHhhhcch
Confidence            89999999999999999999999888889999999999999999999999999999999999999999988998888888


Q ss_pred             HHHHHHHHHhHHHHHHHhcCCchhHHHhhHhhhcccC
Q 033538           81 EEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ  117 (117)
Q Consensus        81 ~~~~~~~a~gk~~~~~~~~~~~~~~~~~~~~~~~~~~  117 (117)
                      ++..+++.+++.||++|.++++|++|++|++|++++|
T Consensus       369 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  405 (405)
T PLN00185        369 EEAAAIKAAGKAWYKTMISDSDYTEFDNFTKWLGVSQ  405 (405)
T ss_pred             hhHHHHHHHHHHHHHHHhhccchhhhhccccccccCC
Confidence            8888888999999999999999999999999999876

>PF14374 Ribos_L4_asso_C: 60S ribosomal protein L4 C-terminal domain; PDB: 3O5H_D 3IZS_D 3O58_D 3IZR_D 4A17_C 4A1C_C 4A1E_C 4A1A_C

Probab=99.97  E-value=1.7e-32  Score=189.03  Aligned_cols=69  Identities=64%  Similarity=0.897  Sum_probs=59.4

Q ss_pred             CCchhhhhhhCcHHHHhhhcCCcccccCC-CCCCCcchhHHHHHhcChHHHHHHHHHHHHHHHHHHHHHH
Q 033538            1 MVNADLARIINSDEVQSVVRPIKTEVKRA-PMKKNPLKNLNTLLRLNPYAKTARRMSLLAEAQRVKAKKE   69 (117)
Q Consensus         1 MtNaDl~RiInSdEIQsvlr~~k~~~kr~-~~KKNPLKN~~~mlrLNPyAk~~rr~a~~~~~~r~~~k~~   69 (117)
                      |||+||+|||||||||+||||+++.++++ ++|+|||+|+++|+||||||+++++++++.++.+..++++
T Consensus        10 MtN~Dl~RiInSdEIQsvlr~~~~~~~r~~~~kkNPLkN~~~m~rLNPya~~~kr~~~~~~~~~~~~k~~   79 (80)
T PF14374_consen   10 MTNADLSRIINSDEIQSVLRPPKKKPKRRSVQKKNPLKNLRAMLRLNPYAKVAKRAAILAQKKRKKKKAE   79 (80)
T ss_dssp             -S---HHHHHHSHHHHCCCHHHHHCSSCCHHHCCCCCC-HHHCCCHHCHHHHHHHHCHSHHSCHHHHCHS
T ss_pred             hccccHHHHhccHHHHHHHhcccccCcCCCCcCCCCcchHHHHHhcCcHHHHHHHHHHHHHHHHHHHhcc
Confidence            89999999999999999999999999887 9999999999999999999999999999998887766544

>PTZ00428 60S ribosomal protein L4; Provisional

Probab=99.93  E-value=5.2e-26  Score=192.11  Aligned_cols=97  Identities=44%  Similarity=0.635  Sum_probs=84.1

Q ss_pred             CCchhhhhhhCcHHHHhhhcCCc-ccccCCCCCCCcchhHHHHHhcChHHHHHHHHHHHHHHHHHHHHHHhhhhcCCcCc
Q 033538            1 MVNADLARIINSDEVQSVVRPIK-TEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAEAQRVKAKKEKLDKKRKPIT   79 (117)
Q Consensus         1 MtNaDl~RiInSdEIQsvlr~~k-~~~kr~~~KKNPLKN~~~mlrLNPyAk~~rr~a~~~~~~r~~~k~~k~~~kr~~~~   79 (117)
                      |||+||+|||||||||+||||++ ....++++|+|||+|+++|+||||||+++|+++++.+.++..++.++.++++... 
T Consensus       283 m~n~Dl~rii~S~eiq~~l~~~~~~~~~~~~~k~nplkn~~~~~~lnp~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  361 (381)
T PTZ00428        283 MTNADIARIINSEEVQAVLRPAKKKPAKRRVQKKNPLKNRRVRLRLNPAAKKLRKLAVLAQEKATAKGAQKVKNRRARK-  361 (381)
T ss_pred             cccccHHHHhccHHHHHHhccccccccccchhhcCCchHHHHHHhcChHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHH-
Confidence            89999999999999999999997 5667889999999999999999999999999999999999888888888766542 


Q ss_pred             HHHHHHHHHHhHHHHHHHh
Q 033538           80 KEEAAAIKSAGKAWYQTMI   98 (117)
Q Consensus        80 ~~~~~~~~a~gk~~~~~~~   98 (117)
                      +-+++.+..++++||+.+.
T Consensus       362 ~~~~~~~~~~~~~~~~~~~  380 (381)
T PTZ00428        362 KAKKARLAKVAKALYKSIK  380 (381)
T ss_pred             HHHHHHHHHHHHHHHHhhc
Confidence            2245566668889988764

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

Probab=99.57  E-value=4.3e-16  Score=130.01  Aligned_cols=60  Identities=45%  Similarity=0.499  Sum_probs=52.6

Q ss_pred             CCchhhhhhhCcHHHHhhhcCCccccc-C-CCCCCCcchhHHHHHhcChHHHHHHHHHHHHH
Q 033538            1 MVNADLARIINSDEVQSVVRPIKTEVK-R-APMKKNPLKNLNTLLRLNPYAKTARRMSLLAE   60 (117)
Q Consensus         1 MtNaDl~RiInSdEIQsvlr~~k~~~k-r-~~~KKNPLKN~~~mlrLNPyAk~~rr~a~~~~   60 (117)
                      |+|+||+|||||||||++++++..... + .+.|+|||+|.++|.+||||++....+..+..
T Consensus       283 ~~n~Dl~rii~Sdevqa~~de~~~v~~k~~~v~kKn~lk~~~v~~rlnPya~k~~aatk~~~  344 (363)
T KOG1475|consen  283 MSNADLSRIINSDELQAKSDEKGKVAGKKPVVGKKNKLKNKGVLKRLNPYAKKKAAATKKPA  344 (363)
T ss_pred             hhhhHHHHHHHHHHHHhhcccccccccccceeccccchhHHHHHHhhchHhHHHHHhhccCc
Confidence            899999999999999999999986553 3 58899999999999999999999887765443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	117
3izr_D	405	Localization Of The Large Subunit Ribosomal Protein		7e-25

>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 =  108 bits (270), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 62/117 (52%), Positives = 74/117 (63%)
Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAXXXXXXXXXXXXXXXXXXYAKTARRMSLLAE 60
           M NADL RIINSDEVQSVV+P+  EVKR                   Y  TAR+M+ LAE
Sbjct: 289 MANADLGRIINSDEVQSVVKPLNKEVKRREKRKNPLKNVAAVLKLNPYFGTARKMATLAE 348
Query: 61  AQRVXXXXXXXXXXXXPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ 117
           A R+             ++ EEAA +K+AGKAWY+TMISDSDY EF+NFSKWLGV+Q
Sbjct: 349 AARIKARKEKLDSKRTKLSPEEAAKVKAAGKAWYKTMISDSDYAEFDNFSKWLGVTQ 405

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	117
3iz5_D	405	60S ribosomal protein L4 (L4P); eukaryotic ribosom	6e-43
4a17_C	410	RPL4, ribosomal protein L3; eukaryotic ribosome, r	6e-25
2wwb_H	362	60S ribosomal protein L4-B; ribosome, protein EXIT	6e-21
2zkr_c	421	60S ribosomal protein L4; protein-RNA complex, 60S	8e-21

>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 = 96.0 bits (238), Expect = 6e-25
 Identities = 37/109 (33%), Positives = 55/109 (50%), Gaps = 3/109 (2%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           + NAD+ARIINS+EVQSVV+   T  +    KKNPL N N L +LNP AK  +  +  A 
Sbjct: 290 LANADIARIINSNEVQSVVKVAGT-TETHERKKNPLTNNNALFKLNPAAKIVKEQAKKAA 348

Query: 61  AQRVKAKKEKLDKKRKPIT--KEEAAAIKSAGKAWYQTMISDSDYTEFE 107
                 ++  L   RK     K+ + A  +A     +  I+ +   + +
Sbjct: 349 EASKAKRQATLKANRKAAKTHKKGSQAWIAAFNKANEEAIAKARQEDAD 397

>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 = 84.8 bits (209), Expect = 6e-21
 Identities = 29/78 (37%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAP--MKKNPLKNLNTLLRLNPYAKTARRMSLL 58
           +  +D+ RIINS E+QS +RP     ++    +KKNPLKN   LLRLNPYAK      L 
Sbjct: 281 ISTSDVTRIINSSEIQSAIRPAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLG 340

Query: 59  AEAQRVKAKKEKLDKKRK 76
           ++       K        
Sbjct: 341 SKKAEKTGTKPAAVFAET 358

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

 Score = 84.9 bits (209), Expect = 8e-21
 Identities = 32/105 (30%), Positives = 56/105 (53%)

Query: 1   MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAE 60
           M+N DL+RI+        +R  + ++ R  +KKNPLKNL  +L+LNPYAKT RR ++L +
Sbjct: 284 MLNTDLSRILKMPRDPRALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQ 343

Query: 61  AQRVKAKKEKLDKKRKPITKEEAAAIKSAGKAWYQTMISDSDYTE 105
           A+  K + +K     +  ++E+    K   +   +  +      +
Sbjct: 344 AKNHKLRMDKAAAALEAKSEEKGVPGKKPRRKKGKKTVGVKKPKK 388

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	117
3iz5_D	405	60S ribosomal protein L4 (L4P); eukaryotic ribosom	100.0
2zkr_c	421	60S ribosomal protein L4; protein-RNA complex, 60S	99.89
4a17_C	410	RPL4, ribosomal protein L3; eukaryotic ribosome, r	99.88
2wwb_H	362	60S ribosomal protein L4-B; ribosome, protein EXIT	99.87

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

Probab=99.89  E-value=8.9e-25  Score=185.28  Aligned_cols=88  Identities=36%  Similarity=0.574  Sum_probs=0.0

Q ss_pred             CCchhhhhhhCcHHHHhhhcCCcccccCCCCCCCcchhHHHHHhcChHHHHHHHHHHHHHHHHHHHHHHhhhhcCCcCcH
Q 033538            1 MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAEAQRVKAKKEKLDKKRKPITK   80 (117)
Q Consensus         1 MtNaDl~RiInSdEIQsvlr~~k~~~kr~~~KKNPLKN~~~mlrLNPyAk~~rr~a~~~~~~r~~~k~~k~~~kr~~~~~   80 (117)
                      |+|+||+|||||||||+||||++..++++++|+|||+|+++|+||||||+++++++++.++.+.+++.+    +++...+
T Consensus       284 ~~n~dl~rii~s~eiq~~l~~~~~~~~~~~~k~npl~n~~~~~~lnpya~~~~~~~~~~~~~~~~~~~~----~~~~~~~  359 (421)
T 2zkr_c          284 MLNTDLSRILKMPRDPRALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQAKNHKLRMD----KAAAALE  359 (421)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cchhHHHHHhcCHHHHHHhcccccccccccccCCCchhHHHHHhcCHHHHHHHHHHHHHHHHhHHHHHH----HhcccCc
Confidence            899999999999999999999988888889999999999999999999999999999999987666543    3344444


Q ss_pred             HHHHHHHHHhHH
Q 033538           81 EEAAAIKSAGKA   92 (117)
Q Consensus        81 ~~~~~~~a~gk~   92 (117)
                      ++...++.+|..
T Consensus       360 ~~~~~~~~~~~~  371 (421)
T 2zkr_c          360 AKSEEKGVPGKK  371 (421)
T ss_dssp             ------------
T ss_pred             chhhhhcccccc
Confidence            444444444433

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

Probab=99.88  E-value=1.8e-23  Score=176.88  Aligned_cols=71  Identities=42%  Similarity=0.550  Sum_probs=61.2

Q ss_pred             CCchhhhhhhCcHHHHhhhcCCcccccCCCCCCCcchhHHHHHhcChHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033538            1 MVNADLARIINSDEVQSVVRPIKTEVKRAPMKKNPLKNLNTLLRLNPYAKTARRMSLLAEAQRVKAKKEKLD   72 (117)
Q Consensus         1 MtNaDl~RiInSdEIQsvlr~~k~~~kr~~~KKNPLKN~~~mlrLNPyAk~~rr~a~~~~~~r~~~k~~k~~   72 (117)
                      |+|+||+|||||||||+||||+ ...+++++|+|||+|+++|+||||||++++++++..++......+..+.
T Consensus       290 ~~n~dl~r~i~s~eiq~~~~~~-~~~~~~~~k~npl~n~~~~~~lnp~a~~~~~~~~~~~~~~~~~~~~~~~  360 (410)
T 4a17_C          290 LANADIARIINSNEVQSVVKVA-GTTETHERKKNPLTNNNALFKLNPAAKIVKEQAKKAAEASKAKRQATLK  360 (410)
T ss_dssp             CSCCCHHHHHHSHHHHHHCCCC-CCCCCCCCCCCTTTCHHHHHHHCTHHHHHHHHHHHHHSCCHHHHHHHHH
T ss_pred             cccccHHHHhCCHHHHHHhcCc-cccccccccCCCchhHHHHHhcCHHHHHHHHHHHHhhhhhhhHHHHHHH
Confidence            8999999999999999999988 6667889999999999999999999999999999877655443333333

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

Probab=99.87  E-value=5.5e-24  Score=177.73  Aligned_cols=65  Identities=43%  Similarity=0.629  Sum_probs=0.0

Q ss_pred             CCchhhhhhhCcHHHHhhhcCCcccccC--CCCCCCcchhHHHHHhcChHHHHHHHHHHHHHHHHHH
Q 033538            1 MVNADLARIINSDEVQSVVRPIKTEVKR--APMKKNPLKNLNTLLRLNPYAKTARRMSLLAEAQRVK   65 (117)
Q Consensus         1 MtNaDl~RiInSdEIQsvlr~~k~~~kr--~~~KKNPLKN~~~mlrLNPyAk~~rr~a~~~~~~r~~   65 (117)
                      |+|+||+|||||||||+||||++..+++  +++|+|||+|+++|+||||||+++++++++.++.+..
T Consensus       281 m~n~dl~rii~S~eiq~~~r~~~~~~~~~~~~~k~npl~n~~~~~~lnpya~~~~~~~~~~~~~~~~  347 (362)
T 2wwb_H          281 ISTSDVTRIINSSEIQSAIRPAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKT  347 (362)
T ss_dssp             -------------------------------------------------------------------
T ss_pred             cchhHHHHHhccHHHHHHhcccccccccccccccCCcchhHHHHHhcCHHHHHHHHHHHHHHHhccc
Confidence            8999999999999999999999887764  6889999999999999999999999999988877543

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Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

No hit with probability above 80.00