Citrus Sinensis ID: 027581

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-
Protein Sequence
MALTVSRRLLRRFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQGWYYNARSKAQKPCYKVEQEGAAAWVEDCSICSSSRRKALGF
Secondary Structure (PSIPRED)
cHHHHHHHHHHHcccccccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccEEEEEEEccccccccccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccEEEcccccHHHHHHHHHHHHHHHccccHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHcccHHHHcccccccccHHHccccccEEEEccccccccccccHHHHHHHccccccccccccccccccccccccccccccccccccEEEEEEEEcccccEEEEEEEcHHHccccccHHHHHHHHHHHHHHHccccccccccccEcccccccccccccccccccccccccEEccccEEccccccHHHHHHHHHHHHHHHHHHHHHcHccccc
Coil and Loop (DISEMBL)
MALTVSRRLLRRfgsfsafgryespsltsrsirsppdlyvacsgdnlfplksglsflasrkfsttiltpdssegafpsdlllkktvltpditiglhqdlvipvtnffnedkgfmvlagdvfdvpirkDIIHRVVRWQLakrqqgthstktisevsgtgkkpwrqkgtgrarhgtlrgpqgwyynarskaqkpcykveqEGAAAWVEDCSICSssrrkalgf
Flexible Loop (DISEMBL)
maltvsrrllrrfgsfsafgryespsltsrsirspPDLYVACSGDNLFPLKSGLSFLASRKFSTTiltpdssegafpsDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWqlakrqqgthstktisevsgtgkkpwrqkgtgrarhgtlrgpqgwyynaRSKAQKPCYKVEQEGAAAWVEDCSICSSSRRKALGF
Low Complexity Region (SEG)
MALTVSrrllrrFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQGWYYNARSKAQKPCYKVEQEGAAAWVEDCSICSSSRRKALGF
Disordered region (IsUnstruct)
*********LRRFGSFSAF*****************DLYVACSGDNLFPLKSGLSFLASRKFSTTILTP****GAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAK************************************GPQGWYYNARSKAQKPCYKVEQEGAAAWVEDCSIC**********
Disordered Region (DISOPRED)
*****SRRLLRRFGSFSAFGRYESPSLTSRSIRSPPDLYV********************************************TVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTI**VSGTGKKPWRQKGTGRARHGTLRGPQGWYYNARSKAQKPCYKVEQEGAAAWVEDCSICSSSRRKALGF
Disordered Region (DISEMBL)
MALTVSRRLLRRFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQL**********************************GTLRGPQGWYYNARSKAQKPCYKVEQEGAAAWVEDCSIC**********
Disordered Region (DISPRO)
*********L*RFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLASRKFST*********GAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQ********************************LRGPQGWYYNARSKAQKPCYKVEQEGAAAWVEDCSICSSSR***L*F
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MALTVSRRLLRRFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQGWYYNARSKAQKPCYKVEQEGAAAWVEDCSICSSSRRKALGF
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	221	2.2.26 [Sep-21-2011]
B6IRQ7	206	50S ribosomal protein L4	yes	no	0.348	0.373	0.636	2e-22
Q2W2J2	206	50S ribosomal protein L4	yes	no	0.348	0.373	0.584	2e-19
Q2RQW1	206	50S ribosomal protein L4	yes	no	0.348	0.373	0.558	3e-19
Q5PA59	208	50S ribosomal protein L4	yes	no	0.357	0.379	0.556	7e-19
B9KJ69	208	50S ribosomal protein L4	yes	no	0.357	0.379	0.556	7e-19
Q11HQ3	206	50S ribosomal protein L4	yes	no	0.407	0.436	0.483	1e-18
A0PXU7	206	50S ribosomal protein L4	yes	no	0.411	0.441	0.484	4e-18
P61061	209	50S ribosomal protein L4	yes	no	0.343	0.363	0.552	1e-17
B1I1I9	207	50S ribosomal protein L4	yes	no	0.352	0.376	0.543	1e-17
Q8UE19	206	50S ribosomal protein L4	yes	no	0.416	0.446	0.473	2e-17

>sp|B6IRQ7|RL4_RHOCS 50S ribosomal protein L4 OS=Rhodospirillum centenum (strain ATCC 51521 / SW) GN=rplD PE=3 SV=1

 Score =  105 bits (263), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 49/77 (63%), Positives = 59/77 (76%)

Query: 103 VTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPW 162
           V N  NE  G + LA +VF +P R+DI+ R+V WQLAKR+QGTH TK ISE++GT KKPW
Sbjct: 5   VKNLNNETVGEIELADEVFGLPTRQDILTRMVLWQLAKRRQGTHKTKGISEIAGTTKKPW 64

Query: 163 RQKGTGRARHGTLRGPQ 179
           RQKGTGRAR G+ R PQ
Sbjct: 65  RQKGTGRARQGSTRSPQ 81

Forms part of the polypeptide exit tunnel.
Rhodospirillum centenum (strain ATCC 51521 / SW) (taxid: 414684)

>sp|Q2W2J2|RL4_MAGSA 50S ribosomal protein L4 OS=Magnetospirillum magneticum (strain AMB-1 / ATCC 700264) GN=rplD PE=3 SV=1

 Score = 95.5 bits (236), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 45/77 (58%), Positives = 55/77 (71%)

Query: 103 VTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPW 162
           V +  N+  G + LA ++F VP+R DI+ R V WQLAKRQ G H TKTISE+SGT KKP+
Sbjct: 5   VISLDNQTVGEIELADEIFGVPVRGDILFRAVNWQLAKRQSGNHKTKTISEISGTTKKPF 64

Query: 163 RQKGTGRARHGTLRGPQ 179
            QKG GRAR G+LR  Q
Sbjct: 65  AQKGGGRARQGSLRSAQ 81

Forms part of the polypeptide exit tunnel.

Magnetospirillum magneticum (strain AMB-1 / ATCC 700264) (taxid: 342108)

>sp|Q2RQW1|RL4_RHORT 50S ribosomal protein L4 OS=Rhodospirillum rubrum (strain ATCC 11170 / NCIB 8255) GN=rplD PE=3 SV=1

 Score = 95.1 bits (235), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 43/77 (55%), Positives = 56/77 (72%)

Query: 103 VTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPW 162
           V     +D G + L+  VF +P+R D++HR+VRWQLA+RQ GTH TK ISE+SGT  KP+
Sbjct: 5   VKTLDGKDAGSIELSDSVFGLPVRTDLLHRMVRWQLARRQAGTHKTKGISEISGTTAKPF 64

Query: 163 RQKGTGRARHGTLRGPQ 179
           +QKGTG AR G+ R PQ
Sbjct: 65  KQKGTGHARQGSKRSPQ 81

Forms part of the polypeptide exit tunnel.

Rhodospirillum rubrum (strain ATCC 11170 / NCIB 8255) (taxid: 269796)

>sp|Q5PA59|RL4_ANAMM 50S ribosomal protein L4 OS=Anaplasma marginale (strain St. Maries) GN=rplD PE=3 SV=1

 Score = 94.0 bits (232), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 44/79 (55%), Positives = 57/79 (72%)

Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
           + V N  NE  G + L+ +VF V +R+D++  VV WQLAKR+ GTH T+ IS+VSGT  K
Sbjct: 3   VNVVNIKNEVVGKVQLSAEVFGVQLRRDVLRDVVTWQLAKRRAGTHKTRCISDVSGTTAK 62

Query: 161 PWRQKGTGRARHGTLRGPQ 179
           P+RQK TGRAR G+LR PQ
Sbjct: 63  PYRQKHTGRARQGSLRSPQ 81

Forms part of the polypeptide exit tunnel.

Anaplasma marginale (strain St. Maries) (taxid: 234826)

>sp|B9KJ69|RL4_ANAMF 50S ribosomal protein L4 OS=Anaplasma marginale (strain Florida) GN=rplD PE=3 SV=1

 Score = 94.0 bits (232), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 44/79 (55%), Positives = 57/79 (72%)

Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
           + V N  NE  G + L+ +VF V +R+D++  VV WQLAKR+ GTH T+ IS+VSGT  K
Sbjct: 3   VNVVNIKNEVVGKVQLSAEVFGVQLRRDVLRDVVTWQLAKRRAGTHKTRCISDVSGTTAK 62

Query: 161 PWRQKGTGRARHGTLRGPQ 179
           P+RQK TGRAR G+LR PQ
Sbjct: 63  PYRQKHTGRARQGSLRSPQ 81

Forms part of the polypeptide exit tunnel.

Anaplasma marginale (strain Florida) (taxid: 320483)

>sp|Q11HQ3|RL4_MESSB 50S ribosomal protein L4 OS=Mesorhizobium sp. (strain BNC1) GN=rplD PE=3 SV=1

 Score = 93.2 bits (230), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 45/93 (48%), Positives = 61/93 (65%), Gaps = 3/93 (3%)

Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
           + VT    +D G + ++ ++F +  R+DI+HRVVRWQLAKRQQGTH  K  +E++ TG K
Sbjct: 3   LKVTTLAGKDAGKVEVSDEIFGLDPREDILHRVVRWQLAKRQQGTHKAKGRAEIARTGAK 62

Query: 161 PWRQKGTGRARHGTLRGPQGWYYNARSKAQKPC 193
            +RQKGTGRARH + R PQ   +    KA  P 
Sbjct: 63  MYRQKGTGRARHSSARAPQ---FRGGGKAHGPV 92

Forms part of the polypeptide exit tunnel.

Mesorhizobium sp. (strain BNC1) (taxid: 266779)

>sp|A0PXU7|RL4_CLONN 50S ribosomal protein L4 OS=Clostridium novyi (strain NT) GN=rplD PE=3 SV=1

 Score = 91.7 bits (226), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 46/95 (48%), Positives = 62/95 (65%), Gaps = 4/95 (4%)

Query: 101 IPVTNFFN---EDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGT 157
           +P  + +N   +  G + LA  VF V + +D++H+VV  QLA ++QG  S KT +EVSG 
Sbjct: 1   MPTVDLYNIEGQKVGDLQLAETVFAVEVNEDVLHQVVVAQLANKRQGNQSAKTRAEVSGG 60

Query: 158 GKKPWRQKGTGRARHGTLRGPQGWYYNARSKAQKP 192
           GKKPWRQKGTGRAR G++R PQ W +     A KP
Sbjct: 61  GKKPWRQKGTGRARQGSIRAPQ-WIHGGVVFAPKP 94

Forms part of the polypeptide exit tunnel.

Clostridium novyi (strain NT) (taxid: 386415)

>sp|P61061|RL4_BDEBA 50S ribosomal protein L4 OS=Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) GN=rplD PE=3 SV=1

 Score = 90.1 bits (222), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 42/76 (55%), Positives = 56/76 (73%)

Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
           + V N+  E  G + LA DVF+ P++K+++H VV+WQLA R+QGTH TKT   VSG GKK
Sbjct: 4   VNVLNWKKEKVGSVELAADVFETPVKKEVLHTVVQWQLAARRQGTHMTKTKGLVSGGGKK 63

Query: 161 PWRQKGTGRARHGTLR 176
           P++QKGTG AR G+ R
Sbjct: 64  PFKQKGTGGARQGSSR 79

Forms part of the polypeptide exit tunnel.

Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) (taxid: 264462)

>sp|B1I1I9|RL4_DESAP 50S ribosomal protein L4 OS=Desulforudis audaxviator (strain MP104C) GN=rplD PE=3 SV=1

 Score = 89.7 bits (221), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/81 (54%), Positives = 54/81 (66%), Gaps = 3/81 (3%)

Query: 101 IPVTNFFN---EDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGT 157
           +P    FN   +  G + L+  VF  P+   ++H VV  QLA R+QGTH TKT SEV G 
Sbjct: 1   MPTAAVFNIEGQQVGEIELSEAVFGQPVNDAVLHEVVVMQLANRRQGTHDTKTRSEVRGG 60

Query: 158 GKKPWRQKGTGRARHGTLRGP 178
           G+KPWRQKGTGRARHGT+R P
Sbjct: 61  GRKPWRQKGTGRARHGTIRSP 81

Forms part of the polypeptide exit tunnel.

Desulforudis audaxviator (strain MP104C) (taxid: 477974)

>sp|Q8UE19|RL4_AGRT5 50S ribosomal protein L4 OS=Agrobacterium tumefaciens (strain C58 / ATCC 33970) GN=rplD PE=3 SV=1

 Score = 89.4 bits (220), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 45/95 (47%), Positives = 61/95 (64%), Gaps = 3/95 (3%)

Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
           + V     +D G + L+ ++F +  R+DI+ R+VRWQLAK+QQGTH TK  SEVS TG K
Sbjct: 3   LNVKTLEGKDAGKVSLSDEIFGLDPRQDILARMVRWQLAKKQQGTHKTKNRSEVSRTGAK 62

Query: 161 PWRQKGTGRARHGTLRGPQGWYYNARSKAQKPCYK 195
            ++QKGTGRARH + R PQ   +    KA  P  +
Sbjct: 63  MYKQKGTGRARHHSARAPQ---FRGGGKAHGPVVR 94

Forms part of the polypeptide exit tunnel.

Agrobacterium tumefaciens (strain C58 / ATCC 33970) (taxid: 176299)

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	221
21553676	300	50S ribosomal protein L4 [Arabidopsis th	0.746	0.55	0.699	5e-64
18399235	300	large subunit ribosomal protein L4 [Arab	0.746	0.55	0.699	5e-64
449433990	315	PREDICTED: 50S ribosomal protein L4-like	0.809	0.568	0.695	6e-64
255554769	294	50S ribosomal protein L4, putative [Rici	0.737	0.554	0.692	4e-61
359494830	315	PREDICTED: 50S ribosomal protein L4-like	0.809	0.568	0.663	1e-58
297836242	297	50S ribosomal protein L4 [Arabidopsis ly	0.733	0.545	0.666	2e-58
363807964	312	uncharacterized protein LOC100804238 [Gl	0.809	0.573	0.642	2e-57
356532241	310	PREDICTED: 50S ribosomal protein L4-like	0.800	0.570	0.642	1e-56
224118096	285	predicted protein [Populus trichocarpa]	0.669	0.519	0.65	2e-56
255635335	224	unknown [Glycine max]	0.800	0.790	0.642	4e-56

>gi|21553676|gb|AAM62769.1| 50S ribosomal protein L4 [Arabidopsis thaliana]

 Score =  249 bits (637), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 128/183 (69%), Positives = 145/183 (79%), Gaps = 18/183 (9%)

Query: 1   MALTVSRRLLRRFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPL----KSGLSF 56
           MA ++SRR+ R FGSFSA GR  SP+L++ +           SG+ L  L    K G++ 
Sbjct: 1   MAASISRRIFRTFGSFSALGRSSSPNLSANT-----------SGNGLASLTNDLKYGMAL 49

Query: 57  LASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVL 116
           L++RK ST+ILTPD S   FPSDLL KKTVLTPD TIG +QDLVIPVTNF NE+KGFMVL
Sbjct: 50  LSNRKLSTSILTPDDS---FPSDLLTKKTVLTPDRTIGQYQDLVIPVTNFQNEEKGFMVL 106

Query: 117 AGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLR 176
           AGDVFDVPIRKDIIH VVRWQLAKRQQGTHSTKT+SEVSGTG+KPW QKGTGRARHGTLR
Sbjct: 107 AGDVFDVPIRKDIIHNVVRWQLAKRQQGTHSTKTLSEVSGTGRKPWNQKGTGRARHGTLR 166

Query: 177 GPQ 179
           GPQ
Sbjct: 167 GPQ 169

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18399235|ref|NP_565463.1| large subunit ribosomal protein L4 [Arabidopsis thaliana] gi|18252969|gb|AAL62411.1| 50S ribosomal protein L4 [Arabidopsis thaliana] gi|20197568|gb|AAD24390.2| 50S ribosomal protein L4 [Arabidopsis thaliana] gi|25084070|gb|AAN72167.1| 50S ribosomal protein L4 [Arabidopsis thaliana] gi|330251866|gb|AEC06960.1| large subunit ribosomal protein L4 [Arabidopsis thaliana]

 Score =  249 bits (636), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 128/183 (69%), Positives = 145/183 (79%), Gaps = 18/183 (9%)

Query: 1   MALTVSRRLLRRFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPL----KSGLSF 56
           MA ++SRR+ R FGSFSA GR  SP+L++ +           SG+ L  L    K G++ 
Sbjct: 1   MAASISRRIFRTFGSFSALGRSSSPNLSANT-----------SGNGLASLTNDLKYGMAL 49

Query: 57  LASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVL 116
           L++RK ST+ILTPD S   FPSDLL KKTVLTPD TIG +QDLVIPVTNF NE+KGFMVL
Sbjct: 50  LSNRKLSTSILTPDDS---FPSDLLTKKTVLTPDRTIGQYQDLVIPVTNFQNEEKGFMVL 106

Query: 117 AGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLR 176
           AGDVFDVPIRKDIIH VVRWQLAKRQQGTHSTKT+SEVSGTG+KPW QKGTGRARHGTLR
Sbjct: 107 AGDVFDVPIRKDIIHNVVRWQLAKRQQGTHSTKTLSEVSGTGRKPWNQKGTGRARHGTLR 166

Query: 177 GPQ 179
           GPQ
Sbjct: 167 GPQ 169

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449433990|ref|XP_004134779.1| PREDICTED: 50S ribosomal protein L4-like [Cucumis sativus] gi|449531047|ref|XP_004172499.1| PREDICTED: 50S ribosomal protein L4-like [Cucumis sativus]

 Score =  249 bits (636), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 128/184 (69%), Positives = 146/184 (79%), Gaps = 5/184 (2%)

Query: 1   MALTVSRRLLRRFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDN-LFPLKSGL----S 55
           MA++VSRRLLR  GS S FG+  S    SRS  +P ++Y   SG +  F  +S L    S
Sbjct: 1   MAISVSRRLLRSVGSLSTFGQCNSSCTMSRSFSNPHEIYGHVSGSSSTFASRSTLLKAGS 60

Query: 56  FLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMV 115
           FLASR F T+ILTP+SS  AFPS+LL  K V + +  IGL+QDL+IPVTNF NEDKGFMV
Sbjct: 61  FLASRGFCTSILTPESSNNAFPSELLSAKPVASEERKIGLYQDLMIPVTNFENEDKGFMV 120

Query: 116 LAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTL 175
           LAGDVFD+PIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTG+KPW+QKGTGRARHGTL
Sbjct: 121 LAGDVFDLPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGRKPWKQKGTGRARHGTL 180

Query: 176 RGPQ 179
           RGPQ
Sbjct: 181 RGPQ 184

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255554769|ref|XP_002518422.1| 50S ribosomal protein L4, putative [Ricinus communis] gi|223542267|gb|EEF43809.1| 50S ribosomal protein L4, putative [Ricinus communis]

 Score =  239 bits (611), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 124/179 (69%), Positives = 142/179 (79%), Gaps = 16/179 (8%)

Query: 1   MALTVSRRLLRRFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLASR 60
           MA+++SRR+LR F S         PSLT +S R+        S ++   +K+G + LA R
Sbjct: 1   MAVSISRRILRSFRSL--------PSLTHQSFRA--------SHESSSFIKNGAASLACR 44

Query: 61  KFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDV 120
           K ST+ILTP SS+ AFPSDLL  KT+LTP+  IGLH+DLVIPVTNF NEDKGFMVLAGDV
Sbjct: 45  KLSTSILTPGSSDDAFPSDLLSTKTLLTPEREIGLHEDLVIPVTNFLNEDKGFMVLAGDV 104

Query: 121 FDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQ 179
           FDVPI+K IIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKP+RQKGTGRARHGTLRGPQ
Sbjct: 105 FDVPIKKHIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPYRQKGTGRARHGTLRGPQ 163

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359494830|ref|XP_003634850.1| PREDICTED: 50S ribosomal protein L4-like [Vitis vinifera] gi|297741766|emb|CBI32995.3| unnamed protein product [Vitis vinifera]

 Score =  231 bits (589), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 122/184 (66%), Positives = 135/184 (73%), Gaps = 5/184 (2%)

Query: 1   MALTVSRRLLRRFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLS----- 55
           MA+++SRRLLR FG    FG   SP +     R+   L    S D LF   S        
Sbjct: 1   MAVSISRRLLRTFGPSRVFGHCNSPMIMCPLFRTSDALCGLVSQDGLFSTDSSCKTGSSF 60

Query: 56  FLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMV 115
             +    +TTILTP+SS  AFP +LL  KTVLTP+ T G +QDLVIPVTNF NEDKGFMV
Sbjct: 61  LSSRSLSTTTILTPESSGVAFPPELLSTKTVLTPERTPGHYQDLVIPVTNFHNEDKGFMV 120

Query: 116 LAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTL 175
           LAGDVFDVPIRKDI+HRVVRWQLAKRQQGTHSTKTISEVSGTG+KPWRQKGTGRARHGTL
Sbjct: 121 LAGDVFDVPIRKDIVHRVVRWQLAKRQQGTHSTKTISEVSGTGRKPWRQKGTGRARHGTL 180

Query: 176 RGPQ 179
           RGPQ
Sbjct: 181 RGPQ 184

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297836242|ref|XP_002886003.1| 50S ribosomal protein L4 [Arabidopsis lyrata subsp. lyrata] gi|297331843|gb|EFH62262.1| 50S ribosomal protein L4 [Arabidopsis lyrata subsp. lyrata]

 Score =  231 bits (589), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 122/183 (66%), Positives = 140/183 (76%), Gaps = 21/183 (11%)

Query: 1   MALTVSRRLLRRFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKS----GLSF 56
           MA ++S R+ R FGS    GR  SP+L++ +           SG+ L  L S    G++ 
Sbjct: 1   MAASISARIFRTFGSL---GRCSSPNLSANT-----------SGNGLSSLTSDLKYGMAL 46

Query: 57  LASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVL 116
           L++RK ST ILTPD +   FPSDLL KKTVLTPD TIG +QDLVIPVTNF +E+KGFMVL
Sbjct: 47  LSNRKLSTCILTPDDT---FPSDLLTKKTVLTPDRTIGQYQDLVIPVTNFQSEEKGFMVL 103

Query: 117 AGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLR 176
           AGDVFDVPIRKDIIH VVRWQLAKRQQGTHSTKT+SEVSGTG+KPW QKGTGRARHGTLR
Sbjct: 104 AGDVFDVPIRKDIIHNVVRWQLAKRQQGTHSTKTLSEVSGTGRKPWNQKGTGRARHGTLR 163

Query: 177 GPQ 179
           GPQ
Sbjct: 164 GPQ 166

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363807964|ref|NP_001242456.1| uncharacterized protein LOC100804238 [Glycine max] gi|255635327|gb|ACU18017.1| unknown [Glycine max]

 Score =  228 bits (580), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 117/182 (64%), Positives = 138/182 (75%), Gaps = 3/182 (1%)

Query: 1   MALTVSRRLLRRFG-SFSAFGR--YESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFL 57
           MA  +S+R+LR    S  + GR  ++SPS    SI  P D+  + SG+ + P    L   
Sbjct: 1   MAALISKRILRCSSWSLHSLGRCYFDSPSAGFASIYKPRDVCSSLSGERMLPADRSLVRS 60

Query: 58  ASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLA 117
             R+FST+ILTP + + AFPSDLL KKT+ T + TIGL QDL+IPVTNF NEDKG+MV  
Sbjct: 61  MVRQFSTSILTPGADDSAFPSDLLSKKTLATSERTIGLCQDLLIPVTNFHNEDKGYMVFP 120

Query: 118 GDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRG 177
           GDVFD+PIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTG+KPW QKGTGRARHG+LRG
Sbjct: 121 GDVFDLPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGRKPWNQKGTGRARHGSLRG 180

Query: 178 PQ 179
           PQ
Sbjct: 181 PQ 182

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356532241|ref|XP_003534682.1| PREDICTED: 50S ribosomal protein L4-like [Glycine max]

 Score =  224 bits (572), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 117/182 (64%), Positives = 136/182 (74%), Gaps = 5/182 (2%)

Query: 1   MALTVSRRLLR-RFGSFSAFGR--YESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFL 57
           MA  +S+R+LR   GS  + GR  ++SP   S  I  P D+    SG+ +F     L   
Sbjct: 1   MAALISKRILRCSSGSLHSLGRCYFDSPGFAS--IYKPRDVCGGLSGERMFSADRSLVGS 58

Query: 58  ASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLA 117
             R+FST+ILTP   + AFPSDLL KK + T + TIGL QDL+IPVTNF NEDKG+MVL 
Sbjct: 59  MVRQFSTSILTPGDDDSAFPSDLLSKKILATSERTIGLCQDLLIPVTNFHNEDKGYMVLP 118

Query: 118 GDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRG 177
           GDVFD+PIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTG+KPW QKGTGRARHG+LRG
Sbjct: 119 GDVFDLPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGRKPWNQKGTGRARHGSLRG 178

Query: 178 PQ 179
           PQ
Sbjct: 179 PQ 180

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224118096|ref|XP_002331557.1| predicted protein [Populus trichocarpa] gi|222873781|gb|EEF10912.1| predicted protein [Populus trichocarpa]

 Score =  224 bits (571), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 117/180 (65%), Positives = 132/180 (73%), Gaps = 32/180 (17%)

Query: 1   MALTVSRRLLRRFGSFSAFGRY-ESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLAS 59
           MAL++SRR+LR FGS S FGR  +S SLT                               
Sbjct: 1   MALSISRRVLRSFGSLSGFGRCGDSSSLT------------------------------- 29

Query: 60  RKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGD 119
           R+ ST+ +T +S++G+FPSDLL  K V+TP   IGL+QDLVIPVTNF NEDKG MVLAGD
Sbjct: 30  RQLSTSNVTSESTDGSFPSDLLSAKNVVTPQREIGLYQDLVIPVTNFHNEDKGLMVLAGD 89

Query: 120 VFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQ 179
           VFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTG+KP+RQKGTGRARHGTLRGPQ
Sbjct: 90  VFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGRKPYRQKGTGRARHGTLRGPQ 149

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255635335|gb|ACU18021.1| unknown [Glycine max]

 Score =  223 bits (569), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 117/182 (64%), Positives = 136/182 (74%), Gaps = 5/182 (2%)

Query: 1   MALTVSRRLLR-RFGSFSAFGR--YESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFL 57
           MA  +S+R+LR   GS  + GR  ++SP   S  I  P D+    SG+ +F     L   
Sbjct: 1   MAALISKRILRCSSGSLHSLGRCYFDSPGFAS--IYKPRDVCGGLSGERMFSADRSLVGS 58

Query: 58  ASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLA 117
             R+FST+ILTP   + AFPSDLL KK + T + TIGL QDL+IPVTNF NEDKG+MVL 
Sbjct: 59  MVRQFSTSILTPGDDDSAFPSDLLSKKILATSERTIGLCQDLLIPVTNFHNEDKGYMVLP 118

Query: 118 GDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRG 177
           GDVFD+PIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTG+KPW QKGTGRARHG+LRG
Sbjct: 119 GDVFDLPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGRKPWNQKGTGRARHGSLRG 178

Query: 178 PQ 179
           PQ
Sbjct: 179 PQ 180

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	221
TAIR|locus:2061659	300	AT2G20060 [Arabidopsis thalian	0.764	0.563	0.698	2.5e-58
TIGR_CMR|NSE_0267	214	NSE_0267 "ribosomal protein L4	0.316	0.327	0.578	3.2e-17
UNIPROTKB|Q3A9R7	206	rplD "50S ribosomal protein L4	0.352	0.378	0.487	5.3e-17
TIGR_CMR|CHY_2308	206	CHY_2308 "ribosomal protein L4	0.352	0.378	0.487	5.3e-17
TIGR_CMR|APH_0281	208	APH_0281 "ribosomal protein L4	0.357	0.379	0.518	6.7e-17
DICTYBASE|DDB_G0283275	258	DDB_G0283275 "ribosomal protei	0.547	0.468	0.360	9.8e-16
UNIPROTKB|P60729	223	rplD "50S ribosomal protein L4	0.307	0.304	0.573	1.3e-15
TIGR_CMR|ECH_0410	205	ECH_0410 "ribosomal protein L4	0.325	0.351	0.547	5.4e-15
UNIPROTKB|K7ELF1	163	MRPL4 "39S ribosomal protein L	0.570	0.773	0.409	8.8e-15
UNIPROTKB|K7ELQ0	220	MRPL4 "39S ribosomal protein L	0.570	0.572	0.409	8.8e-15

TAIR|locus:2061659 AT2G20060 [Arabidopsis thaliana (taxid:3702)]

 Score = 599 (215.9 bits), Expect = 2.5e-58, P = 2.5e-58
 Identities = 125/179 (69%), Positives = 142/179 (79%)

Query:     1 MALTVSXXXXXXFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLASR 60
             MA ++S      FGSFSA GR  SP+L++ +  S   L  + + D    LK G++ L++R
Sbjct:     1 MAASISRRIFRTFGSFSALGRSSSPNLSANT--SGNGL-ASLTND----LKYGMALLSNR 53

Query:    61 KFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDV 120
             K ST+ILTPD S   FPSDLL KKTVLTPD TIG +QDLVIPVTNF NE+KGFMVLAGDV
Sbjct:    54 KLSTSILTPDDS---FPSDLLTKKTVLTPDRTIGQYQDLVIPVTNFQNEEKGFMVLAGDV 110

Query:   121 FDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQ 179
             FDVPIRKDIIH VVRWQLAKRQQGTHSTKT+SEVSGTG+KPW QKGTGRARHGTLRGPQ
Sbjct:   111 FDVPIRKDIIHNVVRWQLAKRQQGTHSTKTLSEVSGTGRKPWNQKGTGRARHGTLRGPQ 169

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

GO:0005739 "mitochondrion" evidence=ISM

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA;ISS

GO:0015934 "large ribosomal subunit" evidence=ISS

GO:0006354 "DNA-dependent transcription, elongation" evidence=RCA

TIGR_CMR|NSE_0267 NSE_0267 "ribosomal protein L4" [Neorickettsia sennetsu str. Miyayama (taxid:222891)]

 Score = 211 (79.3 bits), Expect = 3.2e-17, P = 3.2e-17
 Identities = 44/76 (57%), Positives = 52/76 (68%)

Query:   110 DKGFMVLAGDV------FDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWR 163
             D G   LAG V       + P R D++  V+ WQLAKR+ GTH TK ISEVSGT +KP+R
Sbjct:    10 DFGASSLAGSVAVDRALIEAPFRPDLLSLVINWQLAKRRAGTHKTKGISEVSGTTRKPYR 69

Query:   164 QKGTGRARHGTLRGPQ 179
             QKGTGRAR G+LR PQ
Sbjct:    70 QKGTGRARQGSLRAPQ 85

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

GO:0006412 "translation" evidence=ISS

GO:0042255 "ribosome assembly" evidence=ISS

UNIPROTKB|Q3A9R7 rplD "50S ribosomal protein L4" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 209 (78.6 bits), Expect = 5.3e-17, P = 5.3e-17
 Identities = 38/78 (48%), Positives = 52/78 (66%)

Query:   101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
             +PV N      G + L  ++F  P+ K +++ V    LA +++GTH TKT  EVSG G+K
Sbjct:     4 VPVYNMEGAQVGEIELKDEIFGAPVNKAVLYEVSLMYLANQRRGTHDTKTRGEVSGGGRK 63

Query:   161 PWRQKGTGRARHGTLRGP 178
             PWRQKGTGRARHG++R P
Sbjct:    64 PWRQKGTGRARHGSIRSP 81

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|CHY_2308 CHY_2308 "ribosomal protein L4" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 209 (78.6 bits), Expect = 5.3e-17, P = 5.3e-17
 Identities = 38/78 (48%), Positives = 52/78 (66%)

Query:   101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
             +PV N      G + L  ++F  P+ K +++ V    LA +++GTH TKT  EVSG G+K
Sbjct:     4 VPVYNMEGAQVGEIELKDEIFGAPVNKAVLYEVSLMYLANQRRGTHDTKTRGEVSGGGRK 63

Query:   161 PWRQKGTGRARHGTLRGP 178
             PWRQKGTGRARHG++R P
Sbjct:    64 PWRQKGTGRARHGSIRSP 81

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|APH_0281 APH_0281 "ribosomal protein L4" [Anaplasma phagocytophilum HZ (taxid:212042)]

 Score = 208 (78.3 bits), Expect = 6.7e-17, P = 6.7e-17
 Identities = 41/79 (51%), Positives = 53/79 (67%)

Query:   101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
             + + N  NE  G + L   VF +  R+D++  VV WQLAKR+ GTH  K IS++SGT  K
Sbjct:     3 VNIVNIANEVVGSIDLNPQVFGLEPRRDVLKEVVNWQLAKRRAGTHKAKGISDISGTTAK 62

Query:   161 PWRQKGTGRARHGTLRGPQ 179
             P+RQK TGRAR G+LR PQ
Sbjct:    63 PYRQKHTGRARQGSLRSPQ 81

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

GO:0006412 "translation" evidence=ISS

GO:0042255 "ribosome assembly" evidence=ISS

DICTYBASE|DDB_G0283275 DDB_G0283275 "ribosomal protein L4P family protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 197 (74.4 bits), Expect = 9.8e-16, P = 9.8e-16
 Identities = 48/133 (36%), Positives = 68/133 (51%)

Query:    42 CSGDNLFPLKSGLSFLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVI 101
             C       ++ G  F  S K++TT  T    +    + L   KT+  P +      D + 
Sbjct:     6 CKSFQKISIQRGFEFSNSLKYTTTTTTTTVQKKT-AAQLFADKTIEVPVLNFN---DKLS 61

Query:   102 PVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKP 161
             P+ N        + L+ DVF VP+R D++HR+VR+Q AK QQGTH    +  +  T KKP
Sbjct:    62 PIEN--------IQLSKDVFSVPLRVDLLHRMVRYQRAKSQQGTHQALNMGRMERTNKKP 113

Query:   162 WRQKGTGRARHGT 174
              RQKG+G AR GT
Sbjct:   114 TRQKGSGNARKGT 126

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

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

UNIPROTKB|P60729 rplD "50S ribosomal protein L4" [Mycobacterium tuberculosis (taxid:1773)]

 Score = 196 (74.1 bits), Expect = 1.3e-15, P = 1.3e-15
 Identities = 39/68 (57%), Positives = 49/68 (72%)

Query:   112 GFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRAR 171
             G + L  ++FDVP    ++H+VV  Q A  +QGTHSTKT  EVSG G+KP+RQKGTGRAR
Sbjct:    22 GAIELPAELFDVPANIALMHQVVTAQRAAARQGTHSTKTRGEVSGGGRKPYRQKGTGRAR 81

Query:   172 HGTLRGPQ 179
              G+ R PQ
Sbjct:    82 QGSTRAPQ 89

GO:0005829 "cytosol" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0040007 "growth" evidence=IMP

TIGR_CMR|ECH_0410 ECH_0410 "ribosomal protein L4" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 40/73 (54%), Positives = 49/73 (67%)

Query:   108 NEDK-GFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKG 166
             N D+ G + L   +F V  R DI+  VV WQL+KR+ GTH  KTI ++SGT  KP RQK 
Sbjct:     9 NSDRIGTIDLNPLIFSVNYRPDILKMVVDWQLSKRRAGTHKAKTIGDISGTTAKPHRQKH 68

Query:   167 TGRARHGTLRGPQ 179
             TGRAR G+LR PQ
Sbjct:    69 TGRARQGSLRSPQ 81

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

GO:0006412 "translation" evidence=ISS

GO:0042255 "ribosome assembly" evidence=ISS

UNIPROTKB|K7ELF1 MRPL4 "39S ribosomal protein L4, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 188 (71.2 bits), Expect = 8.8e-15, P = 8.8e-15
 Identities = 54/132 (40%), Positives = 69/132 (52%)

Query:    49 PLKSGLSFLASRKFSTTILTPD--SSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNF 106
             PL+ GLS LA      T   P+  +SEG  P  +L K  +  P     + Q  V  +  F
Sbjct:    28 PLQ-GLSSLAEEAARATE-NPEQVASEG-LPEPVLRKVELPVPTHRRPV-QAWVESLRGF 83

Query:   107 FNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKG 166
               E  G   L  DVF    R DI+H+V  WQ   ++     TKT +EV G G+KPW QKG
Sbjct:    84 EQERVGLADLHPDVFATAPRLDILHQVAMWQKNFKRISYAKTKTRAEVRGGGRKPWPQKG 143

Query:   167 TGRARHGTLRGP 178
             TGRARHG++R P
Sbjct:   144 TGRARHGSIRSP 155

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

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

UNIPROTKB|K7ELQ0 MRPL4 "39S ribosomal protein L4, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 188 (71.2 bits), Expect = 8.8e-15, P = 8.8e-15
 Identities = 54/132 (40%), Positives = 69/132 (52%)

Query:    49 PLKSGLSFLASRKFSTTILTPD--SSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNF 106
             PL+ GLS LA      T   P+  +SEG  P  +L K  +  P     + Q  V  +  F
Sbjct:    16 PLQ-GLSSLAEEAARATE-NPEQVASEG-LPEPVLRKVELPVPTHRRPV-QAWVESLRGF 71

Query:   107 FNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKG 166
               E  G   L  DVF    R DI+H+V  WQ   ++     TKT +EV G G+KPW QKG
Sbjct:    72 EQERVGLADLHPDVFATAPRLDILHQVAMWQKNFKRISYAKTKTRAEVRGGGRKPWPQKG 131

Query:   167 TGRARHGTLRGP 178
             TGRARHG++R P
Sbjct:   132 TGRARHGSIRSP 143

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

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	221
PRK05319	205	PRK05319, rplD, 50S ribosomal protein L4; Provisio	3e-41
TIGR03953	188	TIGR03953, rplD_bact, 50S ribosomal protein L4, ba	9e-37
pfam00573	190	pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 f	6e-36
COG0088	214	COG0088, RplD, Ribosomal protein L4 [Translation,	3e-30
PRK14547	298	PRK14547, rplD, 50S ribosomal protein L4; Provisio	2e-22
CHL00147	215	CHL00147, rpl4, ribosomal protein L4; Validated	1e-17
PRK14907	295	PRK14907, rplD, 50S ribosomal protein L4; Provisio	1e-16
PRK04042	254	PRK04042, rpl4lp, 50S ribosomal protein L4P; Provi	0.002

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

 Score =  139 bits (352), Expect = 3e-41
 Identities = 43/79 (54%), Positives = 56/79 (70%)

Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
           + V N   ++ G + L+  VF V   + ++H+VV  QLA  +QGTH+TKT SEVSG GKK
Sbjct: 3   LKVLNLDGKEAGEVELSDAVFGVEPNEALLHQVVVAQLANARQGTHATKTRSEVSGGGKK 62

Query: 161 PWRQKGTGRARHGTLRGPQ 179
           PWRQKGTGRAR G++R PQ
Sbjct: 63  PWRQKGTGRARQGSIRSPQ 81

Length = 205

>gnl|CDD|234414 TIGR03953, rplD_bact, 50S ribosomal protein L4, bacterial/organelle

 Score =  126 bits (320), Expect = 9e-37
 Identities = 39/64 (60%), Positives = 48/64 (75%)

Query: 116 LAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTL 175
           L   VF +   + ++H+VV+ QLA R+QGTH TKT SEVSG GKKPWRQKGTGRAR G++
Sbjct: 3   LNDAVFGIEPNEHLLHQVVKAQLANRRQGTHKTKTRSEVSGGGKKPWRQKGTGRARQGSI 62

Query: 176 RGPQ 179
           R P 
Sbjct: 63  RSPL 66

Members of this protein family are ribosomal protein L4. This model recognizes bacterial and most organellar forms, but excludes homologs from the eukaryotic cytoplasm and from archaea [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 188

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

 Score =  124 bits (315), Expect = 6e-36
 Identities = 42/64 (65%), Positives = 47/64 (73%)

Query: 116 LAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTL 175
           L   VF   IR D++HR V  QLA R+QGT STKT SEVSG GKKPWRQKGTGRAR G++
Sbjct: 3   LPPAVFGAEIRPDLLHRAVVAQLANRRQGTASTKTRSEVSGGGKKPWRQKGTGRARAGSI 62

Query: 176 RGPQ 179
           R P 
Sbjct: 63  RSPL 66

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

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

 Score =  110 bits (278), Expect = 3e-30
 Identities = 44/79 (55%), Positives = 54/79 (68%)

Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
           + V +   E+ G + L  +VF     +D+IHR V  QLA R+QGTHSTKT  EVSG GKK
Sbjct: 4   LKVYDLDGEEVGEVELLPEVFGPERNEDLIHRAVLAQLANRRQGTHSTKTRGEVSGGGKK 63

Query: 161 PWRQKGTGRARHGTLRGPQ 179
           PW QKGTGRAR G++R PQ
Sbjct: 64  PWGQKGTGRARQGSIRSPQ 82

Length = 214

>gnl|CDD|184735 PRK14547, rplD, 50S ribosomal protein L4; Provisional

 Score = 92.0 bits (228), Expect = 2e-22
 Identities = 41/81 (50%), Positives = 51/81 (62%)

Query: 99  LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTG 158
               V ++  +  G   L   VFDV     +IH+VV  Q+A  +QGTH TKT +EV G G
Sbjct: 2   ATCDVLDWQGKKVGSAELPLKVFDVETNIPLIHQVVVAQMAAARQGTHHTKTRAEVRGGG 61

Query: 159 KKPWRQKGTGRARHGTLRGPQ 179
           KKPWRQKGTGRAR G++R PQ
Sbjct: 62  KKPWRQKGTGRARQGSIRAPQ 82

Length = 298

>gnl|CDD|214375 CHL00147, rpl4, ribosomal protein L4; Validated

 Score = 77.7 bits (192), Expect = 1e-17
 Identities = 29/50 (58%), Positives = 37/50 (74%)

Query: 129 IIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP 178
           ++HR +  Q   ++QGT STKT SEV G G+KPW+QKGTGRAR G+ R P
Sbjct: 37  LLHRALVRQNNNQRQGTASTKTRSEVRGGGRKPWKQKGTGRARAGSNRSP 86

Length = 215

>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional

 Score = 76.5 bits (188), Expect = 1e-16
 Identities = 30/40 (75%), Positives = 33/40 (82%)

Query: 139 AKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP 178
           A R+QGTH  KT +EVSGTGKKPWRQKGTGRAR G+ R P
Sbjct: 130 ASRRQGTHKVKTRAEVSGTGKKPWRQKGTGRARAGSTRSP 169

Length = 295

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

 Score = 38.3 bits (90), Expect = 0.002
 Identities = 19/62 (30%), Positives = 25/62 (40%), Gaps = 10/62 (16%)

Query: 119 DVFDVPIRKDIIHRVVRWQLAKRQQ--GT-------HSTKTISEVSGTGKKPWRQKGTGR 169
            VF+ P+R D+I R V      R Q  G         S ++     G  + P R KG  R
Sbjct: 20  AVFEEPVRPDLIRRAVLAAQTARLQPKGRDPLAGKRTSAESWGSGRGIARVP-RLKGGSR 78

Query: 170 AR 171
           A 
Sbjct: 79  AA 80

Length = 254

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	221
CHL00147	215	rpl4 ribosomal protein L4; Validated	100.0
PRK05319	205	rplD 50S ribosomal protein L4; Provisional	100.0
PRK14547	298	rplD 50S ribosomal protein L4; Provisional	100.0
KOG1624	290	consensus Mitochondrial/chloroplast ribosomal prot	100.0
COG0088	214	RplD Ribosomal protein L4 [Translation, ribosomal	100.0
PF00573	192	Ribosomal_L4: Ribosomal protein L4/L1 family; Inte	100.0
PRK14907	295	rplD 50S ribosomal protein L4; 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
PLN00185	405	60S ribosomal protein L4-1; Provisional	99.94
PTZ00428	381	60S ribosomal protein L4; Provisional	99.92
KOG1475	363	consensus Ribosomal protein RPL1/RPL2/RL4L4 [RNA p	98.82
PTZ00428	381	60S ribosomal protein L4; Provisional	89.86

>CHL00147 rpl4 ribosomal protein L4; Validated

Probab=100.00  E-value=2e-42  Score=300.69  Aligned_cols=111  Identities=33%  Similarity=0.432  Sum_probs=105.0

Q ss_pred             ceeeEEeccCCCe-eeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCC
Q 027581           98 DLVIPVTNFFNED-KGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLR  176 (221)
Q Consensus        98 ~m~ipV~~~~Ge~-~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~R  176 (221)
                      .++++|+|++|+. +|+++|+++|| .+++.||||++|+||++++|||||+||||+||+|||||||+||||||||||++|
T Consensus         6 ~~~~~v~~~~g~~~~~~~~l~~~vf-~~~~~~ll~~~v~~~~a~~R~gt~~tKtR~eV~G~grKp~~QKGTGrAR~Gs~r   84 (215)
T CHL00147          6 FLNYPVIDLTGKEKSETIKLKLNVL-EKSGNYLLHRALVRQNNNQRQGTASTKTRSEVRGGGRKPWKQKGTGRARAGSNR   84 (215)
T ss_pred             eeeEEEEccCCCeecceEEeCHHHh-CCchHhHHHHHHHHHHHHHhhcccccCccccccCCCCCCcccCCCCccCCCCCc
Confidence            3589999999999 89999999999 557799999999999999999999999999999999999999999999999999


Q ss_pred             CCCc--c---c-cCCCcccccCCHHHHHHHHHHHHhhcc
Q 027581          177 GPQG--W---Y-YNARSKAQKPCYKVEQEGAAAWVEDCS  209 (221)
Q Consensus       177 sP~~--G---~-PkPRdy~~kLNKKvRrlALrsALSa~~  209 (221)
                      ||+|  |   | |+||||+++||||+|++||++|||+.+
T Consensus        85 sP~~rgGG~afgP~pR~y~~klnKKvrrlAl~sALS~k~  123 (215)
T CHL00147         85 SPLWKGGGVIFGPKPKTYSNKLNKKERRLALRTLLYNKS  123 (215)
T ss_pred             CCcccCCEeecCCCCcchhhhcCHHHHHHHHHHHHHHhh
Confidence            9999  3   3 999999999999999999999999753

>PRK05319 rplD 50S ribosomal protein L4; Provisional

Probab=100.00  E-value=1.8e-41  Score=292.00  Aligned_cols=112  Identities=43%  Similarity=0.591  Sum_probs=108.2

Q ss_pred             eeeEEeccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCCCC
Q 027581           99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP  178 (221)
Q Consensus        99 m~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~RsP  178 (221)
                      |+++|+|++|+..|+|+||++||+.|+|.||||++|+||++|+||||++||+|+||+|+|+|||+||||||||+|++++|
T Consensus         1 ~~~~v~~~~g~~~~~i~l~~~vF~~~~r~dll~~~v~~~~~~~Rqgta~tk~r~ev~GsgrK~~~QKGTGrAR~Gs~rsP   80 (205)
T PRK05319          1 MELKVLNLDGKEAGEVELSDAVFGVEPNEALLHQVVVAQLANARQGTHATKTRSEVSGGGKKPWRQKGTGRARQGSIRSP   80 (205)
T ss_pred             CeeEEEcCCCCCcceEEcCHHHhCCCccHHHHHHHHHHHHHhcccCcccCCcccccCCCCCCCCCCCCCCccCcCcccCC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Cc--c---c-cCCCcccccCCHHHHHHHHHHHHhhccc
Q 027581          179 QG--W---Y-YNARSKAQKPCYKVEQEGAAAWVEDCSI  210 (221)
Q Consensus       179 ~~--G---~-PkPRdy~~kLNKKvRrlALrsALSa~~~  210 (221)
                      +|  |   | |+|++|+++||||+|++|+++||++++.
T Consensus        81 ~~rGGg~afgpkpr~~~~klnkK~~~lAl~~aLs~k~~  118 (205)
T PRK05319         81 QWRGGGVVFGPKPRDYSQKLNKKVRRLALRSALSEKAR  118 (205)
T ss_pred             cccCCeeeCCCCccchhhhcCHHHHHHHHHHHHHHHHh
Confidence            99  3   3 9999999999999999999999997765

>PRK14547 rplD 50S ribosomal protein L4; Provisional

Probab=100.00  E-value=1.4e-41  Score=307.73  Aligned_cols=112  Identities=41%  Similarity=0.526  Sum_probs=108.2

Q ss_pred             ceeeEEeccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCCC
Q 027581           98 DLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRG  177 (221)
Q Consensus        98 ~m~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~Rs  177 (221)
                      ||+++|||++|+.+|+|+||++||+.++|.||||++|+||++++||||++||+|+||+|+|||||+||||||||+|++|+
T Consensus         1 M~~~~v~~~~g~~~g~ieL~~~vF~~~~r~dllh~vv~~q~a~~Rqgt~~tKtRaEV~G~GkKP~rQKGTGrAR~Gs~rs   80 (298)
T PRK14547          1 MATCDVLDWQGKKVGSAELPLKVFDVETNIPLIHQVVVAQMAAARQGTHHTKTRAEVRGGGKKPWRQKGTGRARQGSIRA   80 (298)
T ss_pred             CceeEEeccCCCCcceEECCHHHhCCCccHHHHHHHHHHHHHhhhcCCCCCCceeeccCCCCCccCCCCCcccCcCCccC
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCc--c---c-cCCCcccccCCHHHHHHHHHHHHhhcc
Q 027581          178 PQG--W---Y-YNARSKAQKPCYKVEQEGAAAWVEDCS  209 (221)
Q Consensus       178 P~~--G---~-PkPRdy~~kLNKKvRrlALrsALSa~~  209 (221)
                      |+|  |   | |+||+|++|||||+|++||++||++..
T Consensus        81 P~wrGGGvafGPkpR~y~~klNKK~rrlAlrsALS~k~  118 (298)
T PRK14547         81 PQWRGGGTVHGPRPREYNQRTPKKMRQAALRGALSDRA  118 (298)
T ss_pred             CceeCCeeecCCCCchhhhhcCHHHHHHHHHHHHHHHH
Confidence            999  3   3 999999999999999999999999655

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

Probab=100.00  E-value=9.3e-40  Score=293.24  Aligned_cols=154  Identities=39%  Similarity=0.565  Sum_probs=134.4

Q ss_pred             hhhhhhccccccCCCCCCCCCCcccccccccCCCCcccCCc--cceeeEEeccCCCeeeeEEcCccccCCCCchhHHHHH
Q 027581           56 FLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLH--QDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRV  133 (221)
Q Consensus        56 ~~~~r~~~~~~~~~~~~e~~~P~~ll~~~~~~~~~~~~~~~--~~m~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhra  133 (221)
                      ++..|.++++..++..   .+++. |-+..+.+|+.....+  |.+.+++..+++|++|.++||+++|.+++|.||||+|
T Consensus        13 ~ss~~~l~ss~~~~~~---~~~s~-l~~~~~~~p~~p~~~~p~qa~v~~~~~~e~E~~gl~~l~~dvf~~~~RrDIlhra   88 (290)
T KOG1624|consen   13 FSSKRNLVSSTQSPPE---QITSA-LHKESTLKPELPVSIPPKQAWVEPLDFFELEKVGLVDLHPDVFAEPPRRDILHRA   88 (290)
T ss_pred             HHHHHHHHhhccCCcc---ccccc-cccccccCcCCCCCcChhhheeeeccccccccceeeecChhhhccchHHHHHHHH
Confidence            3455667888765543   66776 5666677777765555  9999999999999999999999999999999999999


Q ss_pred             HHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCCCCCc--c---c-cC-CCcccccCCHHHHHHHHHHHHh
Q 027581          134 VRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQG--W---Y-YN-ARSKAQKPCYKVEQEGAAAWVE  206 (221)
Q Consensus       134 V~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~RsP~~--G---~-Pk-PRdy~~kLNKKvRrlALrsALS  206 (221)
                      |+||.+|+|+||++||||+||.|+|+|||+||||||||||+.|+|++  |   + |+ ||||++|||+|||.|||++||+
T Consensus        89 v~wq~~nrrvgtastktRaEv~ggGrKp~~QKgtGrAr~Gs~rsP~r~gGg~~~gpr~P~d~~~~Lp~kvr~lgl~~ALS  168 (290)
T KOG1624|consen   89 VVWQLDNRRVGTASTKTRAEVRGGGRKPWPQKGTGRARVGSLRSPQRRGGGVAHGPRGPRDYSYKLPSKVRSLGLKIALS  168 (290)
T ss_pred             HHHhhcccccccccCCccccccCCCCCcCcccCCCcccccCccCcccCCCccccCCCCCcchhhhccHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999  3   2 77 9999999999999999999999


Q ss_pred             hcccccc
Q 027581          207 DCSICSS  213 (221)
Q Consensus       207 a~~~~~~  213 (221)
                      +.+.-|+
T Consensus       169 ~~~a~~~  175 (290)
T KOG1624|consen  169 AKLAQDD  175 (290)
T ss_pred             HHHhCCc
Confidence            6554443

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

Probab=100.00  E-value=1.6e-39  Score=282.55  Aligned_cols=116  Identities=41%  Similarity=0.514  Sum_probs=111.2

Q ss_pred             ceeeEEeccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCCC
Q 027581           98 DLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRG  177 (221)
Q Consensus        98 ~m~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~Rs  177 (221)
                      ||+++|+|++|+.+|++++++.||+.+++.||||+||+||++++|||||++|+|+||+|+|+|||+|||||+||+|++++
T Consensus         1 m~k~~v~~~~G~~~g~~~~~~~vf~~~~~~dli~~av~a~~a~~RQgt~~~k~rgevs~~g~Kp~~QkgtgraR~gs~rs   80 (214)
T COG0088           1 MMKLKVYDLDGEEVGEVELLPEVFGPERNEDLIHRAVLAQLANRRQGTHSTKTRGEVSGGGKKPWGQKGTGRARQGSIRS   80 (214)
T ss_pred             CCcceEeCCCCCCccccccChhhccCCchHHHHHHHHHHHHHhhhccCCCCCCcccccccCcCCCCCCcCCcCCCCCCCC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCc--c---c-cCC-CcccccCCHHHHHHHHHHHHhhcccccc
Q 027581          178 PQG--W---Y-YNA-RSKAQKPCYKVEQEGAAAWVEDCSICSS  213 (221)
Q Consensus       178 P~~--G---~-PkP-Rdy~~kLNKKvRrlALrsALSa~~~~~~  213 (221)
                      |+|  |   | |+| |||+++||||||++||++|||+++..++
T Consensus        81 P~~rGGg~a~gPkp~r~~~~klnkK~rrlAl~sAls~ka~~~~  123 (214)
T COG0088          81 PQWRGGGVAHGPKPERDYSQKLNKKERRLALRSALSAKARAGK  123 (214)
T ss_pred             CeeecCccccCCCCccchhhhcCHHHHHHHHHHHHHHhccCCC
Confidence            999  3   3 999 9999999999999999999999987643

>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=1.5e-38  Score=271.06  Aligned_cols=99  Identities=48%  Similarity=0.735  Sum_probs=91.7

Q ss_pred             EEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCCCCCc--c---c-cCC-C
Q 027581          114 MVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQG--W---Y-YNA-R  186 (221)
Q Consensus       114 IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~RsP~~--G---~-PkP-R  186 (221)
                      ||||++||++|+|.||||+||+||++++||||++||+|+||+|+|||||+|||||+||+|++++|+|  |   | |+| |
T Consensus         1 i~L~~~vF~~~~r~~llh~~v~~~~~~~Rqgt~~tktr~ev~g~grKp~~QKGTGrAR~Gs~rsP~~rgGg~afgPkp~r   80 (192)
T PF00573_consen    1 IELSPDVFNVPVRPDLLHRAVVWQLANRRQGTASTKTRSEVSGSGRKPWPQKGTGRARQGSIRSPQWRGGGVAFGPKPPR   80 (192)
T ss_dssp             -ES-CGGGGSSTSHHHHHHHHHHHHHHTSSBT-SSSTSTTSSSSSSSSSSSSSSSSSSSSSCTSTTSTTSSBSSSSSSTS
T ss_pred             CCCCHHHhCCCCcHHHHHHHHHHHHHhccCCccCCccceEEecccCcccCCCCCcccccCccccceeeccEEecCCcccc
Confidence            7999999999999999999999999999999999999999999999999999999999999999999  3   3 999 9


Q ss_pred             cccccCCHHHHHHHHHHHHhhccccc
Q 027581          187 SKAQKPCYKVEQEGAAAWVEDCSICS  212 (221)
Q Consensus       187 dy~~kLNKKvRrlALrsALSa~~~~~  212 (221)
                      ||+++||||+|++||++||++.+..+
T Consensus        81 ~~~~klnkK~r~lAl~~aLs~k~~~~  106 (192)
T PF00573_consen   81 DYSYKLNKKVRRLALRSALSAKAAEG  106 (192)
T ss_dssp             BCSHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             cceecCChHHHHHHHHHHHHHhhccc
Confidence            99999999999999999999876543

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 ....

>PRK14907 rplD 50S ribosomal protein L4; Provisional

Probab=100.00  E-value=2.6e-38  Score=286.11  Aligned_cols=98  Identities=39%  Similarity=0.473  Sum_probs=93.7

Q ss_pred             eeEEcCccccCCC-CchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCCCCCc--c---c-cC
Q 027581          112 GFMVLAGDVFDVP-IRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQG--W---Y-YN  184 (221)
Q Consensus       112 g~IeLp~~VF~~p-~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~RsP~~--G---~-Pk  184 (221)
                      ..|+|+++||+.+ ++.+|||++|+||++++|||||+||+|+||+|||+|||+||||||||||++|||+|  |   | |+
T Consensus       102 ~~ieL~~~vF~~e~~~~~llh~~V~~q~A~~RqGT~~TKtRsEVsGggkKPwrQKGTGRAR~GS~RSP~wrGGGvaFGPk  181 (295)
T PRK14907        102 NTSKLPKKLFASEKIYSQAIFDTILSERASRRQGTHKVKTRAEVSGTGKKPWRQKGTGRARAGSTRSPIFVGGGRAFGPT  181 (295)
T ss_pred             ceEEeCHHHhCCCccchhHHHHHHHHHHHHhccccccccchhhccCCCCCCcccCCCCccCCCCCcCCcccCCeeecCCC
Confidence            4599999999999 89999999999999999999999999999999999999999999999999999999  3   2 99


Q ss_pred             C-CcccccCCHHHHHHHHHHHHhhcc
Q 027581          185 A-RSKAQKPCYKVEQEGAAAWVEDCS  209 (221)
Q Consensus       185 P-Rdy~~kLNKKvRrlALrsALSa~~  209 (221)
                      | |+|+++||+|+|++||++||++.+
T Consensus       182 P~RdY~~KLNKKvRrLALrsALS~ka  207 (295)
T PRK14907        182 PERNYKLKVNKKVRFNAFVSALTLLA  207 (295)
T ss_pred             CccchhhhcCHHHHHHHHHHHHHHhc
Confidence            9 999999999999999999999765

>PRK04042 rpl4lp 50S ribosomal protein L4P; Provisional

Probab=100.00  E-value=1.8e-34  Score=256.67  Aligned_cols=108  Identities=25%  Similarity=0.237  Sum_probs=102.0

Q ss_pred             eeeEEeccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCC-----CCCceeccccCCcc---CcccccCccee
Q 027581           99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGT-----HSTKTISEVSGTGK---KPWRQKGTGRA  170 (221)
Q Consensus        99 m~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGt-----a~TKtRsEVsGsgk---KpwrQKGTGRA  170 (221)
                      |+++|||++|+..|+++||+ ||+.++|.||||++|+||++|+||||     |+||||+||+|+||   |||+|||||||
T Consensus         1 ~~v~v~~~~g~~~g~i~L~~-vF~~~~~~~lv~~vv~~~~an~Rqgt~~~~ta~tKtraev~G~Gr~~~Kp~rQKGTGrA   79 (254)
T PRK04042          1 MKAKVYDLDGEVVGEIELPA-VFEEPVRPDLIRRAVLAAQTARLQPKGRDPLAGKRTSAESWGSGRGIARVPRLKGGSRA   79 (254)
T ss_pred             CeeEEEcCCCCCcceEehhH-hhCCCCcHHHHHHHHHHHHHhccCCCCCCccccCccceeEcCCCCCcCcCCccCCCCCc
Confidence            68999999999999999995 99999999999999999999999994     89999999999999   99999999999


Q ss_pred             ccCCCCCCCc--c---c-cCC-CcccccCCHHHHHHHHHHHHhhcccc
Q 027581          171 RHGTLRGPQG--W---Y-YNA-RSKAQKPCYKVEQEGAAAWVEDCSIC  211 (221)
Q Consensus       171 R~Gs~RsP~~--G---~-PkP-Rdy~~kLNKKvRrlALrsALSa~~~~  211 (221)
                      |    |+|+|  |   + |+| |+|+++||||+|++||++||++.+..
T Consensus        80 r----rsP~~rGGgv~fgPkp~R~y~~klnkK~rrlAlrsALs~k~~~  123 (254)
T PRK04042         80 A----FVPQAVGGRRAHPPKVEKDLHEKINKKERRLAIRSAIAATANP  123 (254)
T ss_pred             c----ccCccCcCCeeCCCCCCcccccccCHHHHHHHHHHHHHHhhhh
Confidence            7    99999  3   2 999 99999999999999999999987654

>TIGR03672 rpl4p_arch 50S ribosomal protein L4P

Probab=100.00  E-value=1.7e-33  Score=250.14  Aligned_cols=108  Identities=26%  Similarity=0.250  Sum_probs=102.0

Q ss_pred             eeeEEeccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCC-----CCCceeccccCCcc---CcccccCccee
Q 027581           99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGT-----HSTKTISEVSGTGK---KPWRQKGTGRA  170 (221)
Q Consensus        99 m~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGt-----a~TKtRsEVsGsgk---KpwrQKGTGRA  170 (221)
                      |+++|+|++|+..|+++|| +||+.++|.||||++|+||++|+||||     ++||||+||+|+||   |||+|||||||
T Consensus         1 m~~~v~~~~g~~~~~i~l~-~vF~~~~~~~lv~~vv~~~~an~Rqgt~~~~~a~tKtraev~G~Grg~aKp~rQKGTGrA   79 (251)
T TIGR03672         1 MKAKVYDLDGEVVGEIELP-AVFEEPVRPDLIKRAVLAAQTNRLQPYGADPYAGKRTSAESWGSGRGIARVPRIKGGSRA   79 (251)
T ss_pred             CceEEEccCCCCcceEehH-HhhCCCccHHHHHHHHHHHHHhccCCCCCCcccCcccceeEccCCCCcCCCCccCCCCcc
Confidence            6899999999999999999 599999999999999999999999999     57999999999999   99999999999


Q ss_pred             ccCCCCCCCc--c---c-cCC-CcccccCCHHHHHHHHHHHHhhcccc
Q 027581          171 RHGTLRGPQG--W---Y-YNA-RSKAQKPCYKVEQEGAAAWVEDCSIC  211 (221)
Q Consensus       171 R~Gs~RsP~~--G---~-PkP-Rdy~~kLNKKvRrlALrsALSa~~~~  211 (221)
                          +|+|+|  |   + |+| |+|+++||||+|++||++||++.+..
T Consensus        80 ----~rsP~~rGGGv~fgPkp~R~y~~klNkK~rrlAl~sALs~k~~~  123 (251)
T TIGR03672        80 ----ARVPQAVGGRRAHPPKVEKDLHEKINKKERRLAIRSAIAATADP  123 (251)
T ss_pred             ----eecCccCcCCeeCCCCCCcccceecCHHHHHHHHHHHHHHhcch
Confidence                999999  3   2 999 99999999999999999999986653

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.

>PLN00185 60S ribosomal protein L4-1; Provisional

Probab=99.94  E-value=1.3e-27  Score=223.82  Aligned_cols=108  Identities=22%  Similarity=0.240  Sum_probs=102.6

Q ss_pred             eeEEeccCC----CeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCC-----ceeccccCCccCcc---ccc--
Q 027581          100 VIPVTNFFN----EDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHST-----KTISEVSGTGKKPW---RQK--  165 (221)
Q Consensus       100 ~ipV~~~~G----e~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~T-----KtRsEVsGsgkKpw---rQK--  165 (221)
                      .++|||++|    +.+|+|+|| +||+.|+|+||||+|++++++|+||+|+.+     +|++|++|+|+++|   +||  
T Consensus         8 ~v~V~~~~g~~~~~~~~~v~Lp-~VF~~piR~dlv~~v~~~~~~n~RQp~~~~~~AG~qtsAeswGtGR~vaRiPR~kgg   86 (405)
T PLN00185          8 LVSVQSLDGDMATDKSATVALP-DVMTAPIRPDIVNFVHTNISKNSRQPYAVSKKAGHQTSAESWGTGRAVSRIPRVPGG   86 (405)
T ss_pred             eeEEEcCCCCccccccceeehH-HHhCCCCCHHHHHHHHHHHHHhccCCCCCCcccCCcceeeecCCCCCceecccccCC
Confidence            589999999    778999999 999999999999999999999999999999     99999999999999   999  


Q ss_pred             CcceeccCCCCCCCc---cc---cCC--CcccccCCHHHHHHHHHHHHhhccc
Q 027581          166 GTGRARHGTLRGPQG---WY---YNA--RSKAQKPCYKVEQEGAAAWVEDCSI  210 (221)
Q Consensus       166 GTGRAR~Gs~RsP~~---G~---PkP--Rdy~~kLNKKvRrlALrsALSa~~~  210 (221)
                      ||||||+|..  |.|   |+   |+|  |+|+++||+|+|++|+++||++++.
T Consensus        87 GT~RAgqGa~--~~~~rGGr~FgP~p~~R~~~~KvNkK~rRlAl~SALAa~a~  137 (405)
T PLN00185         87 GTHRAGQGAF--GNMCRGGRMFAPTKTWRRWHRKVNVNQKRYAVVSALAASAV  137 (405)
T ss_pred             CCCcCCccCc--CCcCCCCeeCCCCCCccccccccCHHHHHHHHHHHHHhhcc
Confidence            9999999999  888   32   999  9999999999999999999999984

>PTZ00428 60S ribosomal protein L4; Provisional

Probab=99.92  E-value=1.1e-25  Score=209.76  Aligned_cols=106  Identities=25%  Similarity=0.290  Sum_probs=98.1

Q ss_pred             eeeEEeccCC-CeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceecc-----
Q 027581           99 LVIPVTNFFN-EDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARH-----  172 (221)
Q Consensus        99 m~ipV~~~~G-e~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~-----  172 (221)
                      ++++|||.+| +..|+|+|| +||+.|+|.||||+||+++++|+||||+.++++++  ++++|+|   ||||||+     
T Consensus         5 ~~v~V~~~~g~~~~~~v~Lp-~VF~~pir~dlV~~vv~~~~aN~RQgta~s~~ag~--~tsaksw---GTGRA~aripR~   78 (381)
T PTZ00428          5 PVVSVYSASDKSVVGTVPLP-AVFTAPIRPDLVQFVHTNMAKNRRQAYAVKPLAGM--QHSAESW---GTGRAVARIPRV   78 (381)
T ss_pred             CeeEEEcCCCCcccceEehH-HhhCCCCcHHHHHHHHHHHHHhccCCCCcCCCCCC--CCCceec---CCCCCccccccc
Confidence            6899999998 778999999 89999999999999999999999999999988888  7888999   8888888     


Q ss_pred             ---CCCCCCC-----c--c---c-cCC--CcccccCCHHHHHHHHHHHHhhccc
Q 027581          173 ---GTLRGPQ-----G--W---Y-YNA--RSKAQKPCYKVEQEGAAAWVEDCSI  210 (221)
Q Consensus       173 ---Gs~RsP~-----~--G---~-PkP--Rdy~~kLNKKvRrlALrsALSa~~~  210 (221)
                         |+.|||+     |  |   + |+|  |+|+++||+|+|++|+++||+++++
T Consensus        79 kg~GT~Rs~qGa~~n~~rGG~~FgP~~~~R~~~~KvNkK~rR~Al~SALaa~a~  132 (381)
T PTZ00428         79 SGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRKVNLNQKRHAVASALAASGV  132 (381)
T ss_pred             cCCCCCcCcccccCCcCCCceEcCCCCCccccccccCHHHHHHHHHHHHHhhcc
Confidence               8889888     7  3   2 999  9999999999999999999999974

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

Probab=98.82  E-value=4.4e-09  Score=97.13  Aligned_cols=111  Identities=22%  Similarity=0.209  Sum_probs=86.9

Q ss_pred             eeEEeccCCCee-eeEEcCccccCCCCchhHHHHHHHHHHHHcccCCC-----CCceeccccCCccCcc-----cccCcc
Q 027581          100 VIPVTNFFNEDK-GFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTH-----STKTISEVSGTGKKPW-----RQKGTG  168 (221)
Q Consensus       100 ~ipV~~~~Ge~~-g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta-----~TKtRsEVsGsgkKpw-----rQKGTG  168 (221)
                      .+.||+.+|+.. +.+.|| +||.+|+|+||++-+......|+||.|+     ...+.+|-+|+|+-.-     ++-||+
T Consensus         6 ~vtvy~~~g~~s~~~l~lp-~vf~aPiRpdlv~~v~~~~~~n~rQpyAVs~kAG~QtSAESWGTGRAvaRiPRV~GGGT~   84 (363)
T KOG1475|consen    6 LVTVYSLDGEASKKTLTLP-AVFSAPIRPDLVNFVHTQVRKNRRQPYAVSEKAGHQTSAESWGTGRAVARIPRVGGGGTH   84 (363)
T ss_pred             eeeEEeccccccccccccc-ceeccCCcHHHHHHHHHHHhhccccchhhhhhhccccchhhcccccceecccccCCCCcc
Confidence            578999999875 459999 9999999999999999999999999998     3367889888877432     445555


Q ss_pred             eeccCCCCCCCc-c---ccC-C-CcccccCCHHHHHHHHHHHHhhcccc
Q 027581          169 RARHGTLRGPQG-W---YYN-A-RSKAQKPCYKVEQEGAAAWVEDCSIC  211 (221)
Q Consensus       169 RAR~Gs~RsP~~-G---~Pk-P-Rdy~~kLNKKvRrlALrsALSa~~~~  211 (221)
                      ||=+|-...=-. |   +|. . |.|..++|..+++.|+.+|++++++.
T Consensus        85 RsGQgAFgNmCR~GrMfaPtKt~RrW~rkVn~n~Kr~A~asaiaasavp  133 (363)
T KOG1475|consen   85 RSGQGAFGNMCRGGRMFAPTKTWRRWHRKVNENEKRYAIASAIAASAVP  133 (363)
T ss_pred             cccchhhhhhcccccccCchhhHHHHhhhhhhhhhhhHHHhhhhhhhhh
Confidence            555444322222 2   264 3 89999999999999999999998864

>PTZ00428 60S ribosomal protein L4; Provisional

Probab=89.86  E-value=0.18  Score=48.32  Aligned_cols=46  Identities=22%  Similarity=0.221  Sum_probs=34.4

Q ss_pred             HHHHHHHHHHHcccCCCCCceeccccCCccCcc---ccc--CcceeccCCC
Q 027581          130 IHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPW---RQK--GTGRARHGTL  175 (221)
Q Consensus       130 IhraV~~q~anrRqGta~TKtRsEVsGsgkKpw---rQK--GTGRAR~Gs~  175 (221)
                      ....-..-+.+....++..++.+|++|+|+.++   +||  ||+||++|..
T Consensus        41 ~~~~aN~RQgta~s~~ag~~tsakswGTGRA~aripR~kg~GT~Rs~qGa~   91 (381)
T PTZ00428         41 TNMAKNRRQAYAVKPLAGMQHSAESWGTGRAVARIPRVSGGGTHRSGQGAF   91 (381)
T ss_pred             HHHHHhccCCCCcCCCCCCCCCceecCCCCCccccccccCCCCCcCccccc
Confidence            333334444555566666689999999999999   999  8889999655

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	221
1dmg_A	225	Crystal Structure Of Ribosomal Protein L4 Length =		5e-13
1p85_C	201	Real Space Refined Coordinates Of The 50s Subunit F		7e-11
3d5b_F	210	Structural Basis For Translation Termination On The		7e-11
2j01_F	210	Structure Of The Thermus Thermophilus 70s Ribosome		7e-11
3fin_F	208	T. Thermophilus 70s Ribosome In Complex With Mrna,		7e-11
2gya_C	198	Structure Of The 50s Subunit Of A Pre-Translocation		8e-11
1vsa_D	205	Crystal Structure Of A 70s Ribosome-Trna Complex Re		8e-11
3pyo_E	202	Crystal Structure Of A Complex Containing Domain 3		8e-11
3tve_F	202	Crystal Structure Analysis Of Ribosomal Decoding. T		8e-11
3uxq_F	205	The Structure Of Thermorubin In Complex With The 70		8e-11
1pnu_C	197	Crystal Structure Of A Streptomycin Dependent Ribos		1e-09
1jzx_K	205	Structural Basis For The Interaction Of Antibiotics		1e-09
1vor_F	198	Crystal Structure Of Five 70s Ribosomes From Escher		1e-09
1nwx_C	204	Complex Of The Large Ribosomal Subunit From Deinoco		1e-09
2ftc_D	175	Structural Model For The Large Subunit Of The Mamma		2e-08
3bbo_G	293	Homology Model For The Spinach Chloroplast 50s Subu		4e-07

>pdb|1DMG|A Chain A, Crystal Structure Of Ribosomal Protein L4 Length = 225

Iteration: 1
 Score = 70.9 bits (172), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 39/92 (42%), Positives = 54/92 (58%), Gaps = 1/92 (1%)
Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
           + + N   E  G + ++  VF++    D++ R V  QL+ R+ GT STKT  EVSG G+K
Sbjct: 3   VDLLNVKGEKVGTLEISDFVFNIDPNYDVMWRYVDMQLSNRRAGTASTKTRGEVSGGGRK 62
Query: 161 PWRQKGTGRARHGTLRGPQGWYYNARSKAQKP 192
           PW QK TGRARHG++R P  W +       KP
Sbjct: 63  PWPQKHTGRARHGSIRSPI-WRHGGVVHGPKP 93

>pdb|1P85|C Chain C, Real Space Refined Coordinates Of The 50s Subunit Fitted Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp State Of E. Coli 70s Ribosome Length = 201

Iteration: 1
 Score = 63.9 bits (154), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 28/50 (56%), Positives = 39/50 (78%)
Query: 129 IIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP 178
           ++H+VV    A  +QGT + KT +EV+G+GKKPWRQKGTGRAR G+++ P
Sbjct: 27  LVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSP 76

>pdb|3D5B|F Chain F, Structural Basis For Translation Termination On The 70s Ribosome. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes As Described In Remark 400. Length = 210

Iteration: 1
 Score = 63.9 bits (154), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 33/59 (55%), Positives = 42/59 (71%), Gaps = 2/59 (3%)
Query: 122 DVP--IRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP 178
           D+P  I   ++  VVRWQLAKR++GT STKT  EV+ +G+K W QK TGRARHG +  P
Sbjct: 23  DLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIWPQKHTGRARHGDIGAP 81

>pdb|2J01|F Chain F, Structure Of The Thermus Thermophilus 70s Ribosome Complexed With Mrna, Trna And Paromomycin (Part 2 Of 4). This File Contains The 50s Subunit From Molecule I. Length = 210

Iteration: 1
 Score = 63.9 bits (154), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 33/59 (55%), Positives = 42/59 (71%), Gaps = 2/59 (3%)
Query: 122 DVP--IRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP 178
           D+P  I   ++  VVRWQLAKR++GT STKT  EV+ +G+K W QK TGRARHG +  P
Sbjct: 23  DLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIWPQKHTGRARHGDIGAP 81

>pdb|3FIN|F Chain F, T. Thermophilus 70s Ribosome In Complex With Mrna, Trnas And Ef- Tu.Gdp.Kirromycin Ternary Complex, Fitted To A 6.4 A Cryo-Em Map. This File Contains The 50s Subunit. Length = 208

Iteration: 1
 Score = 63.9 bits (154), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 33/59 (55%), Positives = 42/59 (71%), Gaps = 2/59 (3%)
Query: 122 DVP--IRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP 178
           D+P  I   ++  VVRWQLAKR++GT STKT  EV+ +G+K W QK TGRARHG +  P
Sbjct: 23  DLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIWPQKHTGRARHGDIGAP 81

>pdb|2GYA|C Chain C, Structure Of The 50s Subunit Of A Pre-Translocational E. Coli Ribosome Obtained By Fitting Atomic Models For Rna And Protein Components Into Cryo-Em Map Emd-1056 Length = 198

Iteration: 1
 Score = 63.5 bits (153), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 28/50 (56%), Positives = 39/50 (78%)
Query: 129 IIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP 178
           ++H+VV    A  +QGT + KT +EV+G+GKKPWRQKGTGRAR G+++ P
Sbjct: 27  LVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSP 76

>pdb|1VSA|D Chain D, Crystal Structure Of A 70s Ribosome-Trna Complex Reveals Functional Interactions And Rearrangements. This File, 1vsa, Contains The 50s Ribosome Subunit. 30s Ribosome Subunit Is In The File 2ow8 Length = 205

Iteration: 1
 Score = 63.5 bits (153), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 33/59 (55%), Positives = 42/59 (71%), Gaps = 2/59 (3%)
Query: 122 DVP--IRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP 178
           D+P  I   ++  VVRWQLAKR++GT STKT  EV+ +G+K W QK TGRARHG +  P
Sbjct: 18  DLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIWPQKHTGRARHGDIGAP 76

>pdb|3PYO|E Chain E, Crystal Structure Of A Complex Containing Domain 3 From The Psiv Igr Ires Rna Bound To The 70s Ribosome. This File Contains The 50s Subunit Of The First 70s Ribosome. Length = 202

Iteration: 1
 Score = 63.5 bits (153), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 33/59 (55%), Positives = 42/59 (71%), Gaps = 2/59 (3%)
Query: 122 DVP--IRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP 178
           D+P  I   ++  VVRWQLAKR++GT STKT  EV+ +G+K W QK TGRARHG +  P
Sbjct: 18  DLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIWPQKHTGRARHGDIGAP 76

>pdb|3TVE|F Chain F, Crystal Structure Analysis Of Ribosomal Decoding. This Entry Contains The 50s Ribosomal Subunit Of The First 70s Molecule In The Asymmetric Unit For The Cognate Trna-Leu Complex Length = 202

Iteration: 1
 Score = 63.5 bits (153), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 33/59 (55%), Positives = 42/59 (71%), Gaps = 2/59 (3%)
Query: 122 DVP--IRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP 178
           D+P  I   ++  VVRWQLAKR++GT STKT  EV+ +G+K W QK TGRARHG +  P
Sbjct: 18  DLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIWPQKHTGRARHGDIGAP 76

>pdb|3UXQ|F Chain F, The Structure Of Thermorubin In Complex With The 70s Ribosome From Thermus Thermophilus. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes. Length = 205

Iteration: 1
 Score = 63.5 bits (153), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 33/59 (55%), Positives = 42/59 (71%), Gaps = 2/59 (3%)
Query: 122 DVP--IRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP 178
           D+P  I   ++  VVRWQLAKR++GT STKT  EV+ +G+K W QK TGRARHG +  P
Sbjct: 18  DLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIWPQKHTGRARHGDIGAP 76

>pdb|1PNU|C Chain C, Crystal Structure Of A Streptomycin Dependent Ribosome From Escherichia Coli, 50s Subunit Of 70s Ribosome. This File, 1pnu, Contains Only Molecules Of The 50s Ribosomal Subunit. The 30s Subunit, Mrna, P-Site Trna, And A-Site Trna Are In The Pdb File 1pns. Length = 197

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/59 (49%), Positives = 41/59 (69%), Gaps = 3/59 (5%)
Query: 118 GDVFDVP---IRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHG 173
           G   ++P   +   ++H VV WQLA R++GT ST+T ++VS TG+K + QKGTG ARHG
Sbjct: 11  GRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQKGTGNARHG 69

>pdb|1JZX|K Chain K, Structural Basis For The Interaction Of Antibiotics With The Peptidyl Transferase Center In Eubacteria Length = 205

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/60 (48%), Positives = 41/60 (68%), Gaps = 3/60 (5%)
Query: 117 AGDVFDVP---IRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHG 173
            G   ++P   +   ++H VV WQLA R++GT ST+T ++VS TG+K + QKGTG ARHG
Sbjct: 11  GGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQKGTGNARHG 70

>pdb|1VOR|F Chain F, Crystal Structure Of Five 70s Ribosomes From Escherichia Coli In Complex With Protein Y. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Five 70s Ribosomes And Is Described In Remark 400. Length = 198

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/60 (48%), Positives = 41/60 (68%), Gaps = 3/60 (5%)
Query: 117 AGDVFDVP---IRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHG 173
            G   ++P   +   ++H VV WQLA R++GT ST+T ++VS TG+K + QKGTG ARHG
Sbjct: 11  GGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQKGTGNARHG 70

>pdb|1NWX|C Chain C, Complex Of The Large Ribosomal Subunit From Deinococcus Radiodurans With Abt-773 Length = 204

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/60 (48%), Positives = 41/60 (68%), Gaps = 3/60 (5%)
Query: 117 AGDVFDVP---IRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHG 173
            G   ++P   +   ++H VV WQLA R++GT ST+T ++VS TG+K + QKGTG ARHG
Sbjct: 10  GGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQKGTGNARHG 69

>pdb|2FTC|D Chain D, Structural Model For The Large Subunit Of The Mammalian Mitochondrial Ribosome Length = 175

Iteration: 1
 Score = 55.8 bits (133), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 26/48 (54%), Positives = 33/48 (68%)
Query: 131 HRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP 178
           H+V  WQ   ++     TKT +EV G G+KPW QKGTGRARHG++R P
Sbjct: 1   HQVAMWQKNFKRISYAKTKTRAEVRGGGRKPWPQKGTGRARHGSIRSP 48

>pdb|3BBO|G Chain G, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 293

Iteration: 1
 Score = 51.2 bits (121), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 29/78 (37%), Positives = 42/78 (53%)
Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
           +P+ NF  E  G   L          + ++HR +   L  +++GT ST T +EV G G+K
Sbjct: 55  LPILNFSGEKVGETFLNLKTAPPEKARAVVHRGLITHLQNKRRGTASTLTRAEVRGGGRK 114
Query: 161 PWRQKGTGRARHGTLRGP 178
           P+ QK TGRAR G+   P
Sbjct: 115 PYPQKKTGRARRGSQGSP 132

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	221
1dmg_A	225	Ribosomal protein L4; alpha-beta, ribosome, RNA, S	5e-41
3bbo_G	293	Ribosomal protein L4; large ribosomal subunit, spi	3e-40
3r8s_E	201	50S ribosomal protein L4; protein biosynthesis, RN	7e-40
2zjr_C	205	50S ribosomal protein L4; ribosome, large ribosoma	1e-37
3v2d_F	210	50S ribosomal protein L4; ribosome associated inhi	7e-37
2ftc_D	175	Mitochondrial ribosomal protein L4 isoform A, mito	1e-31
1vq8_C	246	50S ribosomal protein L4E; ribosome 50S, protein-p	5e-20
2wwb_H	362	60S ribosomal protein L4-B; ribosome, protein EXIT	6e-19
4a17_C	410	RPL4, ribosomal protein L3; eukaryotic ribosome, r	4e-15
2zkr_c	421	60S ribosomal protein L4; protein-RNA complex, 60S	4e-14
3iz5_D	405	60S ribosomal protein L4 (L4P); eukaryotic ribosom	7e-13

>1dmg_A Ribosomal protein L4; alpha-beta, ribosome, RNA, S10 operon, gene regulation; HET: CIT; 1.70A {Thermotoga maritima} SCOP: c.22.1.1 Length = 225

 Score =  138 bits (350), Expect = 5e-41
 Identities = 36/79 (45%), Positives = 50/79 (63%)

Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
           + + N   E  G + ++  VF++    D++ R V  QL+ R+ GT STKT  EVSG G+K
Sbjct: 3   VDLLNVKGEKVGTLEISDFVFNIDPNYDVMWRYVDMQLSNRRAGTASTKTRGEVSGGGRK 62

Query: 161 PWRQKGTGRARHGTLRGPQ 179
           PW QK TGRARHG++R P 
Sbjct: 63  PWPQKHTGRARHGSIRSPI 81

>3bbo_G Ribosomal protein L4; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 293

 Score =  138 bits (349), Expect = 3e-40
 Identities = 35/125 (28%), Positives = 53/125 (42%), Gaps = 3/125 (2%)

Query: 58  ASRKFSTTILTPDSSEGAFPSDLLLK---KTVLTPDITIGLHQDLVIPVTNFFNEDKGFM 114
            S  F ++ L    S       +L         T        + + +P+ NF  E  G  
Sbjct: 9   LSLSFFSSSLFSSKSRNFSSKPILKLPSSSHSQTSLSLSIKSELIPLPILNFSGEKVGET 68

Query: 115 VLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGT 174
            L          + ++HR +   L  +++GT ST T +EV G G+KP+ QK TGRAR G+
Sbjct: 69  FLNLKTAPPEKARAVVHRGLITHLQNKRRGTASTLTRAEVRGGGRKPYPQKKTGRARRGS 128

Query: 175 LRGPQ 179
              P 
Sbjct: 129 QGSPL 133

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

 Score =  134 bits (340), Expect = 7e-40
 Identities = 29/72 (40%), Positives = 46/72 (63%)

Query: 108 NEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGT 167
            + +  + ++   F     + ++H+VV    A  +QGT + KT +EV+G+GKKPWRQKGT
Sbjct: 6   KDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGT 65

Query: 168 GRARHGTLRGPQ 179
           GRAR G+++ P 
Sbjct: 66  GRARSGSIKSPI 77

>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 ... Length = 205

 Score =  128 bits (325), Expect = 1e-37
 Identities = 28/63 (44%), Positives = 40/63 (63%)

Query: 117 AGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLR 176
             ++    +   ++H VV WQLA R++GT ST+T ++VS TG+K + QKGTG ARHG   
Sbjct: 14  TIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQKGTGNARHGDRS 73

Query: 177 GPQ 179
            P 
Sbjct: 74  VPT 76

>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 ... Length = 210

 Score =  127 bits (321), Expect = 7e-37
 Identities = 38/79 (48%), Positives = 47/79 (59%), Gaps = 5/79 (6%)

Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
           IPV +      G   LA D     I   ++  VVRWQLAKR++GT STKT  EV+ +G+K
Sbjct: 9   IPVLSP----SGRRELAAD-LPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRK 63

Query: 161 PWRQKGTGRARHGTLRGPQ 179
            W QK TGRARHG +  P 
Sbjct: 64  IWPQKHTGRARHGDIGAPI 82

>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 Length = 175

 Score =  112 bits (283), Expect = 1e-31
 Identities = 26/49 (53%), Positives = 33/49 (67%)

Query: 131 HRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQ 179
           H+V  WQ   ++     TKT +EV G G+KPW QKGTGRARHG++R P 
Sbjct: 1   HQVAMWQKNFKRISYAKTKTRAEVRGGGRKPWPQKGTGRARHGSIRSPL 49

>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 = 84.3 bits (208), Expect = 5e-20
 Identities = 27/85 (31%), Positives = 40/85 (47%), Gaps = 11/85 (12%)

Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHS-----TKTISEVS 155
             + +      G + L  DVF+ P+R D+I + VR   A R+Q   S      +T +E  
Sbjct: 3   ATIYDLDGNTDGEVDLP-DVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESF 61

Query: 156 GTGK-KPWRQKGTGRARHGTLRGPQ 179
           G+G+ +    K  GRAR    R PQ
Sbjct: 62  GSGRGQAHVPKLDGRAR----RVPQ 82

>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 = 82.9 bits (204), Expect = 6e-19
 Identities = 22/89 (24%), Positives = 31/89 (34%), Gaps = 8/89 (8%)

Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQG-----THSTKTISEVS 155
           + V +   E     +    VF  PIR DI+H V       ++Q          +T +E  
Sbjct: 6   VTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQTSAESW 65

Query: 156 GTGKKPW---RQKGTGRARHGTLRGPQGW 181
           GTG+      R  G G  R G        
Sbjct: 66  GTGRAVARIPRVGGGGTGRSGQGAFGNMC 94

>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 = 72.2 bits (176), Expect = 4e-15
 Identities = 19/94 (20%), Positives = 29/94 (30%), Gaps = 13/94 (13%)

Query: 100 VIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGT-- 157
           V        +    + L   VF  PIR DI+H+V       R+Q +    +    +G   
Sbjct: 9   VHDAKEANKQTATKLTLP-AVFTAPIRTDIVHKVFTDLNKNRKQASGVKISTRGTAGMGH 67

Query: 158 ----------GKKPWRQKGTGRARHGTLRGPQGW 181
                       +  R  G+G  R G        
Sbjct: 68  SAESWGTGRAVARIPRVGGSGTHRSGQAAFGNQC 101

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

 Score = 69.5 bits (169), Expect = 4e-14
 Identities = 21/91 (23%), Positives = 30/91 (32%), Gaps = 10/91 (10%)

Query: 100 VIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQG---------THSTKT 150
           +I V +   E  G  V    VF  PIR DI++ V        +Q            S ++
Sbjct: 7   LISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQTSAES 66

Query: 151 ISEVSGTGKKPWRQKGTGRARHGTLRGPQGW 181
                   + P R +G G  R G        
Sbjct: 67  WGTGRAVARIP-RVRGGGTHRSGQGAFGNMC 96

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	221
3bbo_G	293	Ribosomal protein L4; large ribosomal subunit, spi	100.0
1dmg_A	225	Ribosomal protein L4; alpha-beta, ribosome, RNA, S	100.0
3v2d_F	210	50S ribosomal protein L4; ribosome associated inhi	100.0
3r8s_E	201	50S ribosomal protein L4; protein biosynthesis, RN	100.0
2zjr_C	205	50S ribosomal protein L4; ribosome, large ribosoma	100.0
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
2ftc_D	175	Mitochondrial ribosomal protein L4 isoform A, mito	100.0
4a17_C	410	RPL4, ribosomal protein L3; eukaryotic ribosome, r	99.98
1vq8_C	246	50S ribosomal protein L4E; ribosome 50S, protein-p	99.97
3iz5_D	405	60S ribosomal protein L4 (L4P); eukaryotic ribosom	99.97
2wwb_H	362	60S ribosomal protein L4-B; ribosome, protein EXIT	99.97

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

Probab=100.00  E-value=2.9e-43  Score=316.78  Aligned_cols=114  Identities=28%  Similarity=0.355  Sum_probs=108.9

Q ss_pred             ccceeeEEeccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCC
Q 027581           96 HQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTL  175 (221)
Q Consensus        96 ~~~m~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~  175 (221)
                      ++|++++|||++|+++|+|+||++||+.|+|.||||+||+||++|+|||||+||||+||+|+|||||+||||||||+|++
T Consensus        50 ~~M~~v~V~~~~G~~~g~veLp~~VF~~~~r~dlih~vV~~q~an~RQGTa~tKtRaEV~GgGRKp~RQKGTGRAR~Gs~  129 (293)
T 3bbo_G           50 SELIPLPILNFSGEKVGETFLNLKTAPPEKARAVVHRGLITHLQNKRRGTASTLTRAEVRGGGRKPYPQKKTGRARRGSQ  129 (293)
T ss_dssp             -CCEEEECCCSSSCCCSEEEECSSSSSSCCCTTTTTTHHHHHHHHHCCCCCCCCSSTTCSSSCCCCCCCSSSCSCSCCSS
T ss_pred             hcCceeEEEcCCCCEeeeEEcCHHHhCCCccHHHHHHHHHHHHHhcccccccCceeeeeccCCCceeccCCCCccccCcc
Confidence            35668999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCc--c---c-cCCCcccccCCHHHHHHHHHHHHhhcc
Q 027581          176 RGPQG--W---Y-YNARSKAQKPCYKVEQEGAAAWVEDCS  209 (221)
Q Consensus       176 RsP~~--G---~-PkPRdy~~kLNKKvRrlALrsALSa~~  209 (221)
                      |+|+|  |   | |+||+|++|||||+|++||++||++.+
T Consensus       130 rsP~~rGGGvafGPkPRdy~~klNKK~rrlAlrsALSak~  169 (293)
T 3bbo_G          130 GSPLRPGGGVIFGPKPRDWTIKMNKKERRLALSTAIASAV  169 (293)
T ss_dssp             SCSSSSSSCCSSCCCSCCCCCCCCSHHHHHHHHHHHHHHH
T ss_pred             cCCceecCceecCCcCcchhhhcCHHHHHHHHHHHHHHHc
Confidence            99999  3   2 999999999999999999999999865

>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=1e-43  Score=309.11  Aligned_cols=112  Identities=35%  Similarity=0.444  Sum_probs=62.6

Q ss_pred             eeeEEeccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCCCC
Q 027581           99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP  178 (221)
Q Consensus        99 m~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~RsP  178 (221)
                      |+++|||++|+++|+|+||++||+.|+|.||||++|+||++|+||||++||||+||+|+|||||+||||||||+|++|+|
T Consensus         1 ~~~~v~~~~g~~~g~v~L~~~vF~~~~r~dlih~~v~~~~a~~Rqgt~~tktRaEv~G~GrKp~rQKGTGrAR~Gs~rsP   80 (225)
T 1dmg_A            1 AQVDLLNVKGEKVGTLEISDFVFNIDPNYDVMWRYVDMQLSNRRAGTASTKTRGEVSGGGRKPWPQKHTGRARHGSIRSP   80 (225)
T ss_dssp             CEEEEECTTSCEEEEEECCHHHHSSCCCHHHHHHHHHHHHC---------------------------------------
T ss_pred             CeeEEEcCCCCEeeEEEcCHHHhCCCccHHHHHHHHHHHHHhccCCccccceeeEeecCCCCCCCCCCCCccccccccCC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Cc--c---c-cCCCcccccCCHHHHHHHHHHHHhhccc
Q 027581          179 QG--W---Y-YNARSKAQKPCYKVEQEGAAAWVEDCSI  210 (221)
Q Consensus       179 ~~--G---~-PkPRdy~~kLNKKvRrlALrsALSa~~~  210 (221)
                      +|  |   | |+||||+++||||+|++||++|||+.+.
T Consensus        81 ~~rGGG~~fgPkpR~~~~klnkK~rrlAl~sALs~k~~  118 (225)
T 1dmg_A           81 IWRHGGVVHGPKPRDWSKKLNKKMKKLALRSALSVKYR  118 (225)
T ss_dssp             --------------CHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ceecCceecCCcCccccccCCHHHHHHHHHHHHHHHHh
Confidence            99  3   3 9999999999999999999999997763

>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=9.2e-42  Score=294.22  Aligned_cols=109  Identities=39%  Similarity=0.467  Sum_probs=103.8

Q ss_pred             cceeeEEeccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCC
Q 027581           97 QDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLR  176 (221)
Q Consensus        97 ~~m~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~R  176 (221)
                      -||+++|||++|+.+|+||||+     |+|.||||++|+||++|+|||||+||||+||+|+|||||+||||||||+|++|
T Consensus         5 ~m~~v~V~~~~G~~~g~i~L~~-----~~r~dlih~~v~~~~a~~Rqgt~~tktraEv~G~grKp~rQKGTGrAR~Gs~r   79 (210)
T 3v2d_F            5 AVYQIPVLSPSGRRELAADLPA-----EINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIWPQKHTGRARHGDIG   79 (210)
T ss_dssp             -CCCCCEECSSSCCCCCCCCCS-----CCCHHHHHHHHHHHHHHTCCCCCCCCCTTTSSCCCCCSSCSSSSSSCCCCCTT
T ss_pred             ccceeEEEcCCCCEeeeEecCC-----cccHHHHHHHHHHHHHhccCCccCCCccccccCCCCCCCCCCCCCccCCCccc
Confidence            4789999999999999999996     99999999999999999999999999999999999999999999999999999


Q ss_pred             CCCc--c---c-cCCCcccccCCHHHHHHHHHHHHhhccc
Q 027581          177 GPQG--W---Y-YNARSKAQKPCYKVEQEGAAAWVEDCSI  210 (221)
Q Consensus       177 sP~~--G---~-PkPRdy~~kLNKKvRrlALrsALSa~~~  210 (221)
                      +|+|  |   | |+||||+++||||+|++||++|||+.+.
T Consensus        80 sP~~~gGG~~fgP~pR~~~~klnkK~rrlAl~sALs~k~~  119 (210)
T 3v2d_F           80 APIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRAR  119 (210)
T ss_dssp             STTSTTCCCSSCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_pred             CCcccCCeeeCCCCCccceeeCCHHHHHHHHHHHHHHHHh
Confidence            9999  3   3 9999999999999999999999998653

>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=2.6e-41  Score=289.93  Aligned_cols=97  Identities=33%  Similarity=0.525  Sum_probs=94.1

Q ss_pred             eEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCCCCCc--c---c-cCCC
Q 027581          113 FMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQG--W---Y-YNAR  186 (221)
Q Consensus       113 ~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~RsP~~--G---~-PkPR  186 (221)
                      +|+||++||+.|+|.||||++|+||++|+||||++||||+||+|+|||||+||||||||+|++|+|+|  |   | |+||
T Consensus        11 ~i~L~~~vF~~~~r~dlih~~v~~~~a~~Rqgt~~tktraEv~G~grKp~rQKGTGrAR~Gs~rsP~~~gGG~~fgP~pR   90 (201)
T 3r8s_E           11 ALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQ   90 (201)
T ss_dssp             CEECCHHHHSSCCCHHHHHHHHHHHHTTSCCCCCCCCBTTTSSCCCCCSSCSSSSSSCCCCCTTCTTSTTCCBTTCCCCC
T ss_pred             eEECCHHHhCCCCCHHHHHHHHHHHHHhCcCCCCCCcceeeecCCCCCCCccCCCCccccCcCcCCceeCCEeecCCccc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999  3   3 9999


Q ss_pred             cccccCCHHHHHHHHHHHHhhcc
Q 027581          187 SKAQKPCYKVEQEGAAAWVEDCS  209 (221)
Q Consensus       187 dy~~kLNKKvRrlALrsALSa~~  209 (221)
                      ||+++||||+|++||++|||+.+
T Consensus        91 ~~~~klnkK~rrlAl~sALs~k~  113 (201)
T 3r8s_E           91 DHSQKVNKKMYRGALKSILSELV  113 (201)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHH
T ss_pred             cceeccCHHHHHHHHHHHHHHHh
Confidence            99999999999999999999765

>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-40  Score=286.11  Aligned_cols=104  Identities=36%  Similarity=0.419  Sum_probs=100.3

Q ss_pred             eeEEeccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCCCCC
Q 027581          100 VIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQ  179 (221)
Q Consensus       100 ~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~RsP~  179 (221)
                      +++|||++|+.+|+|+||+      +|.||||+||+||++|+|||||+||||+||+|+|||||+||||||||+|++|+|+
T Consensus         3 ~v~v~~~~g~~~g~i~L~~------~r~dlih~~v~~~~a~~Rqgt~~tktraEv~G~GrKp~rQKGTGrAR~Gs~rsP~   76 (205)
T 2zjr_C            3 QINVIGQNGGRTIELPLPE------VNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQKGTGNARHGDRSVPT   76 (205)
T ss_dssp             CCCCSSCCCCCCCCCCTTT------CCHHHHHHHHHHHHHHHCCCCCCCCCCTTTSCCCSCCSCSSSSSSCCCSCSCSTT
T ss_pred             eeEEEcCCCCEeeeEECCC------chHHHHHHHHHHHHHhccccccccceeeeccCCCCCCCCcCCCCCcccCcccCCc
Confidence            6899999999999999996      9999999999999999999999999999999999999999999999999999999


Q ss_pred             c--c---c-cCCCcccccCCHHHHHHHHHHHHhhcc
Q 027581          180 G--W---Y-YNARSKAQKPCYKVEQEGAAAWVEDCS  209 (221)
Q Consensus       180 ~--G---~-PkPRdy~~kLNKKvRrlALrsALSa~~  209 (221)
                      |  |   | |+||||+++||||+|++||++|||+.+
T Consensus        77 ~~gGG~~fgP~pR~~~~klnkK~rrlAl~sALs~k~  112 (205)
T 2zjr_C           77 FVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQ  112 (205)
T ss_dssp             STTSCCTTCCCCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_pred             ccCCeeecCCCCcchhhhcCHHHHHHHHHHHHHHHh
Confidence            9  3   3 999999999999999999999999766

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

Probab=100.00  E-value=7.9e-34  Score=251.32  Aligned_cols=109  Identities=20%  Similarity=0.181  Sum_probs=102.3

Q ss_pred             eeeEEeccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHccc--CCCC---CceeccccCCccC---cccccCc-ce
Q 027581           99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQ--GTHS---TKTISEVSGTGKK---PWRQKGT-GR  169 (221)
Q Consensus        99 m~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRq--Gta~---TKtRsEVsGsgkK---pwrQKGT-GR  169 (221)
                      |+++|||++|+++|+|+|| +||+.|+|.||||+||+||++|+||  ||+.   ||||+||+|+|+|   +|+|||| |+
T Consensus         1 m~v~V~~~~G~~~g~v~Lp-~vF~~~~r~dli~~~v~~~~an~Rq~~Gt~~~ag~ktraev~G~Gr~~ar~~RqKGtgGr   79 (255)
T 3j21_D            1 MKVKVFDLNGQPVGEIELP-KVFFTPFRPDLIRRAVIASWTHRIQPQGRDPMAGKRRVTENIGKGHSMARVERLKTPPRY   79 (255)
T ss_dssp             CEEEEECTTSCEEEEEECC-GGGGSCCCHHHHHHHHHHHHHHTCCCCCCCSSTTSSSCCBCCCSSSSSCCCCBCSSSCCC
T ss_pred             CeeEEEcCCCCEeeEEEhH-HhhCCCCcHHHHHHHHHHHHHhccccccCCcccCcccceeecCCCCCcCcCCccCCCCCc
Confidence            7899999999999999999 8999999999999999999999999  7776   8999999999995   9999999 99


Q ss_pred             eccCCCCCCCc--c---c-cCC-CcccccCCHHHHHHHHHHHHhhccccc
Q 027581          170 ARHGTLRGPQG--W---Y-YNA-RSKAQKPCYKVEQEGAAAWVEDCSICS  212 (221)
Q Consensus       170 AR~Gs~RsP~~--G---~-PkP-Rdy~~kLNKKvRrlALrsALSa~~~~~  212 (221)
                      ||    ++|+|  |   | |+| |+|+++||||+|++||++|||+++..+
T Consensus        80 Ar----rsP~~rGGg~~~gPkp~R~~~~klNkK~rrlAl~sALsa~~~~~  125 (255)
T 3j21_D           80 AA----FVPFARGGRRTHPPKVEKIIWEDINKKEKRLALMSAIAATANYD  125 (255)
T ss_dssp             CS----SCSSSTTCCCSSCCCTTSCCCCCCCHHHHHHHHHHHHHHTTCHH
T ss_pred             cc----cCccccCCeeecCCCCCcccceecCHHHHHHHHHHHHHHHhhcc
Confidence            98    99999  3   3 999 899999999999999999999887643

>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=3.6e-34  Score=267.59  Aligned_cols=110  Identities=24%  Similarity=0.228  Sum_probs=103.9

Q ss_pred             ceeeEEeccCCCeee-eEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCC-----ceeccccCCccCccc-----ccC
Q 027581           98 DLVIPVTNFFNEDKG-FMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHST-----KTISEVSGTGKKPWR-----QKG  166 (221)
Q Consensus        98 ~m~ipV~~~~Ge~~g-~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~T-----KtRsEVsGsgkKpwr-----QKG  166 (221)
                      .|+++|||++|+.+| +|+|| +||+.|+|.||||+||+||++|+||||+.|     |||+||+|+|+|||+     |||
T Consensus         5 rm~v~V~~~~G~~~g~~ieLp-~VF~~piR~dlIh~vV~~~~an~RQgta~t~~AG~KTraEv~G~GRKp~RiPRv~QKG   83 (421)
T 2zkr_c            5 RPLISVYSEKGESSGKNVTLP-AVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQTSAESWGTGRAVARIPRVRGGG   83 (421)
T ss_dssp             --CCEEECTTSSEEEECSSCC-GGGGSCCCHHHHHHHHHHHHHTTCCCCCCCSCTTTCSCCCCCCSSSSSCCSCCBTTTT
T ss_pred             CceeEEEcCCCCccccEEehh-HhhCCCccHHHHHHHHHHHHHhccCCCCcCcccCCcceeEecCCCCCcCCcccccCCC
Confidence            478999999999977 89999 999999999999999999999999999999     999999999999999     999


Q ss_pred             cceeccCCCCCCCc-c---c-cC-C-CcccccCCHHHHHHHHHHHHhhcc
Q 027581          167 TGRARHGTLRGPQG-W---Y-YN-A-RSKAQKPCYKVEQEGAAAWVEDCS  209 (221)
Q Consensus       167 TGRAR~Gs~RsP~~-G---~-Pk-P-Rdy~~kLNKKvRrlALrsALSa~~  209 (221)
                      |||||+|++++ +| |   + |+ | |+|+++||+|+|++||++|||+++
T Consensus        84 TGRARqGs~rs-~~RGGr~fgP~kp~R~~~~KlNkK~rrlAlrSALSaka  132 (421)
T 2zkr_c           84 THRSGQGAFGN-MCRGGRMFAPTKTWRRWHRRVNTTQKRYAICSALACLS  132 (421)
T ss_dssp             BCCCSTTCCTT-STTCCCCSSCCCSSSCCCCCCCHHHHHHHHHHHHHHHT
T ss_pred             CCccCcccccc-ccccceeeCCCCCCcchhhhcCHHHHHHHHHHHHHhcc
Confidence            99999999999 99 3   2 76 8 999999999999999999999995

>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=1.1e-33  Score=238.07  Aligned_cols=80  Identities=38%  Similarity=0.457  Sum_probs=76.5

Q ss_pred             HHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCCCCCc--c---c-cC-CCcccccCCHHHHHHHHHH
Q 027581          131 HRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQG--W---Y-YN-ARSKAQKPCYKVEQEGAAA  203 (221)
Q Consensus       131 hraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~RsP~~--G---~-Pk-PRdy~~kLNKKvRrlALrs  203 (221)
                      |++|+||++++|||||+||||+||+|+|||||+||||||||+|++|+|+|  |   | |+ ||||+++||||+|++||++
T Consensus         1 h~~v~~~~a~~Rqgt~~tktraEv~G~grKp~rQKGTGrAR~Gs~rsP~~~gGG~~fgP~~pR~~~~klnkK~rrlAl~s   80 (175)
T 2ftc_D            1 HQVAMWQKNFKRISYAKTKTRAEVRGGGRKPWPQKGTGRARHGSIRSPLWRGGGVAHGPRGPTSYYYMLPMKVRALGLKV   80 (175)
T ss_pred             CHHHHHHHHHhhcCCCCCcceeeecCCCCCCCCcCCCCccccCCCcCCcccCCEeecCCCCccchhhhcCHHHHHHHHHH
Confidence            79999999999999999999999999999999999999999999999999  3   3 99 7999999999999999999


Q ss_pred             HHhhccc
Q 027581          204 WVEDCSI  210 (221)
Q Consensus       204 ALSa~~~  210 (221)
                      |||+.+.
T Consensus        81 ALs~k~~   87 (175)
T 2ftc_D           81 ALTVKLA   87 (175)
T ss_pred             HHHHhcc
Confidence            9998664

>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=99.98  E-value=4.4e-33  Score=259.60  Aligned_cols=112  Identities=25%  Similarity=0.288  Sum_probs=104.6

Q ss_pred             cceeeEEe-ccCCCee-ee-EEcCccccCCCCchhHHHHHHHHHHHHccc---------CCCCCceeccccCCccCccc-
Q 027581           97 QDLVIPVT-NFFNEDK-GF-MVLAGDVFDVPIRKDIIHRVVRWQLAKRQQ---------GTHSTKTISEVSGTGKKPWR-  163 (221)
Q Consensus        97 ~~m~ipV~-~~~Ge~~-g~-IeLp~~VF~~p~R~DLIhraV~~q~anrRq---------Gta~TKtRsEVsGsgkKpwr-  163 (221)
                      .|++++|| |++|+.+ |+ |+|| +||+.|+|.||||+||+||++|+||         ||+++|||+||+|+|+|||+ 
T Consensus         3 ~~p~v~V~~~~~G~~~~g~~veLp-~VF~~~ir~dlIh~vV~~~~anrRQ~~~~~~~~rGTa~tktraEv~GtGRk~~Ri   81 (410)
T 4a17_C            3 SRPQIHVHDAKEANKQTATKLTLP-AVFTAPIRTDIVHKVFTDLNKNRKQASGVKISTRGTAGMGHSAESWGTGRAVARI   81 (410)
T ss_dssp             CCCEEEEEESSSTTEEEEEEEECC-GGGGSCCCHHHHHHHHHHHHHTTCCCCCCCBCSSCBTTCCSCEEECCGGGSSCSS
T ss_pred             CCCeeEEEECCCCCccCCceEehh-HhhCCCCcHHHHHHHHHHHHHhCcCcccCCCcccccccCCccceeCCCCCCcccc
Confidence            46799999 8999995 78 9996 7999999999999999999999999         77999999999999999999 


Q ss_pred             ----ccCcceeccCCCCCCCc-c---c-cCC--CcccccCCHHHHHHHHHHHHhhccc
Q 027581          164 ----QKGTGRARHGTLRGPQG-W---Y-YNA--RSKAQKPCYKVEQEGAAAWVEDCSI  210 (221)
Q Consensus       164 ----QKGTGRAR~Gs~RsP~~-G---~-PkP--Rdy~~kLNKKvRrlALrsALSa~~~  210 (221)
                          ||||||||+|+++ |+| |   + |+|  |+|+++||+|+|++||++|||+++.
T Consensus        82 PR~~QKGTGRARqGs~r-P~~rGGr~fgP~p~~R~y~~KlNKK~rrlAlrSALSaka~  138 (410)
T 4a17_C           82 PRVGGSGTHRSGQAAFG-NQCRKGRMFAPLKTYRRVHRRVNVNQKRHAVAAALAASAL  138 (410)
T ss_dssp             EEECCSSSTTTTCBCSS-TTSSSCCCSSCCCSCCCCCCCCCHHHHHHHHHHHHHHHTC
T ss_pred             ccccCCCCCcccccccC-CccCCeEEcCCCCCccchhhhhCHHHHHHHHHHHHHHhcc
Confidence                9999999999999 999 3   2 776  9999999999999999999999863

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

Probab=99.97  E-value=8.4e-32  Score=237.25  Aligned_cols=105  Identities=27%  Similarity=0.328  Sum_probs=100.0

Q ss_pred             eeeEEeccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCC-----CceeccccCCccCc---ccccCccee
Q 027581           99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHS-----TKTISEVSGTGKKP---WRQKGTGRA  170 (221)
Q Consensus        99 m~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~-----TKtRsEVsGsgkKp---wrQKGTGRA  170 (221)
                      |+++|||++|+.+|+|+|| +||+.|+|.||||+||+||++|+||||+.     +||++|++|+|+|+   |+||  |+|
T Consensus         1 m~v~v~~~~g~~~g~v~Lp-~vF~~~~r~dli~~~v~~~~an~Rqgt~~~~~aG~kt~ae~~GtGR~~ari~rqK--G~a   77 (246)
T 1vq8_C            1 MQATIYDLDGNTDGEVDLP-DVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESFGSGRGQAHVPKLD--GRA   77 (246)
T ss_dssp             CEEEEECTTSCEEEEEECC-GGGGSCCCHHHHHHHHHHHHHHTCCCCCCCTTTTTCCCCBCCCSSSSCCCCCEET--TEE
T ss_pred             CeeEEEcCCCCCccEEEhh-HhhCCCccHHHHHHHHHHHHHhcccCcccccccCcccceeeccCCCCcccccccc--Ccc
Confidence            6799999999999999999 99999999999999999999999999999     99999999999999   9999  777


Q ss_pred             ccCCCCCCCc--c---c-cCC-CcccccCCHHHHHHHHHHHHhhccc
Q 027581          171 RHGTLRGPQG--W---Y-YNA-RSKAQKPCYKVEQEGAAAWVEDCSI  210 (221)
Q Consensus       171 R~Gs~RsP~~--G---~-PkP-Rdy~~kLNKKvRrlALrsALSa~~~  210 (221)
                      |    ++|+|  |   | |+| |+|+++||||+|++||++|||+++.
T Consensus        78 r----rsP~~rGGg~~~gPkp~R~~~~klnkK~rrlAl~sALsa~~~  120 (246)
T 1vq8_C           78 R----RVPQAVKGRSAHPPKTEKDRSLDLNDKERQLAVRSALAATAD  120 (246)
T ss_dssp             C----SSTTSTTCCCSSCCCTTCCCCCCCCHHHHHHHHHHHHHHTTC
T ss_pred             c----cCCccCCCeeecCCCCCccchhhcCHHHHHHHHHHHHHHhhh
Confidence            5    89999  3   3 999 9999999999999999999999884

>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=99.97  E-value=3.8e-31  Score=243.75  Aligned_cols=107  Identities=25%  Similarity=0.317  Sum_probs=101.3

Q ss_pred             ceeeEEeccCCCeeee-EEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceecc----
Q 027581           98 DLVIPVTNFFNEDKGF-MVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARH----  172 (221)
Q Consensus        98 ~m~ipV~~~~Ge~~g~-IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~----  172 (221)
                      .++++|||++|+.+|+ |+|| +||+.|+|.||||+||+||++|+||||+.||+|+||  +|+|||   ||||||+    
T Consensus         3 r~~v~V~~~~G~~~g~~i~Lp-~VF~~p~r~dlih~vv~~~~an~RQgt~~tk~rgev--tg~K~w---GTGRAraripR   76 (362)
T 2wwb_H            3 RPQVTVHSLTGEATANALPLP-AVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQ--TSAESW---GTGRAVARIPR   76 (362)
T ss_dssp             SSCCCCCCSSCSCCSCCCCCC-GGGCSCCCHHHHHHHHHHHHHHHCCCCCCCSSSSCS--SCCSSC---CCCSSSCSCSC
T ss_pred             CCeeEEEcCCCcCcCceEehh-HhhCCCccHHHHHHHHHHHHHhccCCCCCCCccccc--ccceec---CCCCCeeeccc
Confidence            3578999999999999 9999 999999999999999999999999999999999999  889999   9999999    


Q ss_pred             ----CCCCCCC-----c--c---c-cCC--CcccccCCHHHHHHHHHHHHhhccc
Q 027581          173 ----GTLRGPQ-----G--W---Y-YNA--RSKAQKPCYKVEQEGAAAWVEDCSI  210 (221)
Q Consensus       173 ----Gs~RsP~-----~--G---~-PkP--Rdy~~kLNKKvRrlALrsALSa~~~  210 (221)
                          |++|||+     |  |   + |+|  |+|+++||+|+|++||++|||++++
T Consensus        77 v~g~Gs~RSp~ga~~~~~gGG~~fgP~p~~R~~~~klNkK~rrlAl~SALsaka~  131 (362)
T 2wwb_H           77 VGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRYATASAIAATAV  131 (362)
T ss_dssp             CCSCSSSSCSSTTTSSSCSSSCCSSSSCSSCCCCCCCCHHHHHHHHHHHHHGGGC
T ss_pred             ccCCCCCCCcccccCCccCCeEECCCCCCCcchhhhcCHHHHHHHHHHHHHhccc
Confidence                9999999     9  3   2 877  9999999999999999999999953

---

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	221
d2gycc1	198	c.22.1.1 (C:1-198) Ribosomal protein L4 {Escherich	3e-25
d2zjrc1	197	c.22.1.1 (C:2-198) Ribosomal protein L4 {Deinococc	8e-24
d1dmga_	225	c.22.1.1 (A:) Ribosomal protein L4 {Thermotoga mar	7e-23
d1vqoc1	246	c.22.1.1 (C:1-246) Ribosomal protein L4 {Archaeon	5e-21
d2j01f1	208	c.22.1.1 (F:1-208) Ribosomal protein L4 {Thermus t	1e-20

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

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]

 Score = 95.5 bits (237), Expect = 3e-25
 Identities = 35/107 (32%), Positives = 56/107 (52%), Gaps = 2/107 (1%)

Query: 108 NEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGT 167
            + +  + ++   F     + ++H+VV    A  +QGT + KT +EV+G+GKKPWRQKGT
Sbjct: 6   KDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGT 65

Query: 168 GRARHGTLRGPQGWYYNARSKAQKPC-YKVEQEGAAAWVEDCSICSS 213
           GRAR G+++ P  W     + A +P  +  +           SI S 
Sbjct: 66  GRARSGSIKSPI-WRSGGVTFAARPQDHSQKVNKKMYRGALKSILSE 111

>d2zjrc1 c.22.1.1 (C:2-198) Ribosomal protein L4 {Deinococcus radiodurans [TaxId: 1299]} Length = 197

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]

 Score = 92.1 bits (228), Expect = 8e-24
 Identities = 32/101 (31%), Positives = 51/101 (50%), Gaps = 1/101 (0%)

Query: 117 AGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLR 176
             ++    +   ++H VV WQLA R++GT ST+T ++VS TG+K + QKGTG ARHG   
Sbjct: 13  TIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQKGTGNARHGDRS 72

Query: 177 GPQGWYYNARSKAQKPCYKVEQEGAAAWVEDCSICSSSRRK 217
            P  +     +   KP                ++  +SR++
Sbjct: 73  VPT-FVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQE 112

>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 = 90.2 bits (223), Expect = 7e-23
 Identities = 39/92 (42%), Positives = 54/92 (58%), Gaps = 1/92 (1%)

Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
           + + N   E  G + ++  VF++    D++ R V  QL+ R+ GT STKT  EVSG G+K
Sbjct: 3   VDLLNVKGEKVGTLEISDFVFNIDPNYDVMWRYVDMQLSNRRAGTASTKTRGEVSGGGRK 62

Query: 161 PWRQKGTGRARHGTLRGPQGWYYNARSKAQKP 192
           PW QK TGRARHG++R P  W +       KP
Sbjct: 63  PWPQKHTGRARHGSIRSPI-WRHGGVVHGPKP 93

>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 = 85.6 bits (211), Expect = 5e-21
 Identities = 20/97 (20%), Positives = 34/97 (35%), Gaps = 4/97 (4%)

Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKT--ISEVSGTG 158
             + +      G + L  DVF+ P+R D+I + VR   A R+Q   S +   +   + + 
Sbjct: 3   ATIYDLDGNTDGEVDLP-DVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESF 61

Query: 159 KKPWRQKGTGRARHGTLRGPQGWYYNARSKAQKPCYK 195
                Q    +      R PQ       +   K    
Sbjct: 62  GSGRGQAHVPKLDGRARRVPQ-AVKGRSAHPPKTEKD 97

>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 = 83.7 bits (206), Expect = 1e-20
 Identities = 39/95 (41%), Positives = 49/95 (51%), Gaps = 6/95 (6%)

Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
           IPV +      G   LA       I   ++  VVRWQLAKR++GT STKT  EV+ +G+K
Sbjct: 9   IPVLSP----SGRRELA-ADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRK 63

Query: 161 PWRQKGTGRARHGTLRGPQGWYYNARSKAQKPCYK 195
            W QK TGRARHG +  P  +         KP   
Sbjct: 64  IWPQKHTGRARHGDIGAPI-FVGGGVVFGPKPRDY 97

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	221
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	246	Ribosomal protein L4 {Archaeon Haloarcula marismor	100.0
d1vqoc1	246	Ribosomal protein L4 {Archaeon Haloarcula marismor	83.23

>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=1.9e-42  Score=292.97  Aligned_cols=108  Identities=30%  Similarity=0.469  Sum_probs=101.6

Q ss_pred             eeeEEeccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCCCC
Q 027581           99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP  178 (221)
Q Consensus        99 m~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~RsP  178 (221)
                      |+++|.|..    |+|+|+++||+.++|.||||+||+||++|+|||||+||||+||+|||||||+||||||||||++|||
T Consensus         1 m~l~~~~~~----~~i~l~~~vF~~~~~~~llh~~v~~~~a~~R~gt~~tKtRseV~g~gkKp~~QKGTGrAR~Gs~rsP   76 (198)
T d2gycc1           1 MELVLKDAQ----SALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSP   76 (198)
T ss_dssp             CCEEEECTT----CCSCCCEECCCSCCCHHHHTTTSSSCTTCCSCCCCSSCSCCCCCCSCSSCSCCCCCCCBTTBCCSCS
T ss_pred             CeeEecCCC----CeEEeCHHHhCCCcCHHHHHHHHHHHHHhccCCCcccceehhccCCccCcccccCCCCCCCcCcchh
Confidence            688888765    4699999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Cc--c---c-cCCCcccccCCHHHHHHHHHHHHhhccc
Q 027581          179 QG--W---Y-YNARSKAQKPCYKVEQEGAAAWVEDCSI  210 (221)
Q Consensus       179 ~~--G---~-PkPRdy~~kLNKKvRrlALrsALSa~~~  210 (221)
                      +|  |   | |+||+|+++||||+|++||++|||+...
T Consensus        77 ~~~gGGva~GP~pr~~~~kl~kK~r~~al~~aLs~k~~  114 (198)
T d2gycc1          77 IWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVR  114 (198)
T ss_dssp             SSSSCCCSSCSCCSSSCCCCCTTTHHHHHHHHHHHTTS
T ss_pred             hcccCceecCccccCeEeeHHHHHHHHHHHHHHHHHHh
Confidence            99  2   2 9999999999999999999999997654

>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=3.2e-40  Score=278.50  Aligned_cols=104  Identities=36%  Similarity=0.420  Sum_probs=98.3

Q ss_pred             eeEEeccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCCCCC
Q 027581          100 VIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQ  179 (221)
Q Consensus       100 ~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~RsP~  179 (221)
                      +++|+|.+|+..++++|+      ++|.||||+||+||++|+|||||+||+|+||+|||||||+||||||||||++|+|+
T Consensus         2 ~~~v~~~~g~~~~~~~~~------e~~~~ll~~~v~~~~a~~R~gt~~tk~R~ev~gsgkKp~~QKGtGrAR~Gs~rsP~   75 (197)
T d2zjrc1           2 QINVIGQNGGRTIELPLP------EVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQKGTGNARHGDRSVPT   75 (197)
T ss_dssp             CCCCSSCCCCCCCCCCTT------TCCHHHHHHHHHHHHHHHCCCCCCCCCCTTTSCCCSCCSCSSSSSSCCCSCSCSTT
T ss_pred             eeeeecCCCCeEEeeccc------cccHHHHHHHHHHHHHhhhccCccCCchhhccCCCCCcccCCCCCCCCcccccccc
Confidence            688999999999888887      58999999999999999999999999999999999999999999999999999999


Q ss_pred             c--c---c-cCCCcccccCCHHHHHHHHHHHHhhcc
Q 027581          180 G--W---Y-YNARSKAQKPCYKVEQEGAAAWVEDCS  209 (221)
Q Consensus       180 ~--G---~-PkPRdy~~kLNKKvRrlALrsALSa~~  209 (221)
                      |  |   | |+||+|+++||||+|++||++|||+..
T Consensus        76 ~rgGg~afgp~pr~~~~~lnkK~r~lal~~aLS~K~  111 (197)
T d2zjrc1          76 FVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQ  111 (197)
T ss_dssp             STTSCCTTCCCCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_pred             cccceeeccccccchhhhccHHHHHHHHHHHHHHHH
Confidence            9  3   2 999999999999999999999998654

>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=4.9e-41  Score=287.26  Aligned_cols=111  Identities=35%  Similarity=0.455  Sum_probs=61.9

Q ss_pred             eeeEEeccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCCCC
Q 027581           99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP  178 (221)
Q Consensus        99 m~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~RsP  178 (221)
                      .+|+|||++|+++|+||||++||+.|+|.||||+||+||++|+||||++||+|+||+|+|||||+|||||+||+|+.++|
T Consensus         1 ~~v~v~~~~g~~~g~i~L~~~vF~~~~r~dli~~~v~~~~~~~Rqgt~~tk~rsev~g~gkK~~~QKGtG~AR~Gs~~sp   80 (225)
T d1dmga_           1 AQVDLLNVKGEKVGTLEISDFVFNIDPNYDVMWRYVDMQLSNRRAGTASTKTRGEVSGGGRKPWPQKHTGRARHGSIRSP   80 (225)
T ss_dssp             CEEEEECTTSCEEEEEECCHHHHSSCCCHHHHHHHHHHHHC---------------------------------------
T ss_pred             CeeEEEcCCCCEeeEEEeCHHHhCCCccHHHHHHHHHHHHHhcccCccccccceeeecccccccccCCcCcccccccccc
Confidence            37999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Cc--c---c-cCCCcccccCCHHHHHHHHHHHHhhcc
Q 027581          179 QG--W---Y-YNARSKAQKPCYKVEQEGAAAWVEDCS  209 (221)
Q Consensus       179 ~~--G---~-PkPRdy~~kLNKKvRrlALrsALSa~~  209 (221)
                      +|  |   | |+||+|+++||||+|++|+++||++..
T Consensus        81 ~~~gGg~a~gp~pr~~~~klnkK~r~~Al~~aLs~k~  117 (225)
T d1dmga_          81 IWRHGGVVHGPKPRDWSKKLNKKMKKLALRSALSVKY  117 (225)
T ss_dssp             --------------CHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             eeeccccccCCCCchhhhhHHHHHHHHHHHHHHHHHh
Confidence            99  2   3 999999999999999999999999776

>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=1.7e-38  Score=269.24  Aligned_cols=108  Identities=39%  Similarity=0.477  Sum_probs=101.4

Q ss_pred             cceeeEEeccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccccCCccCcccccCcceeccCCCC
Q 027581           97 QDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLR  176 (221)
Q Consensus        97 ~~m~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgkKpwrQKGTGRAR~Gs~R  176 (221)
                      .+++++|+|.+|+..+.++||     .|+|.||||+||+||++|+||||++||+|+||+|+|||||+||||||||+|++|
T Consensus         5 ~~~~~~v~~~~g~~~~~~~l~-----~~v~~dli~~av~~~~a~~Rqgta~tk~R~ev~g~gkK~~~QKGtGrAR~Gs~r   79 (208)
T d2j01f1           5 AVYQIPVLSPSGRRELAADLP-----AEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIWPQKHTGRARHGDIG   79 (208)
T ss_dssp             CCCCCCSSSCCCCCCCSTTSS-----SCCCHHHHHHHHHHHHHHTCCCCCCCCCTTTSCCCCCCSSCSSSSSSCCCCCTT
T ss_pred             eEEeeeeecCCCCEeeccccc-----cccCHHHHHHHHHHHHHhccCCCCCCCccccccCcccccCcccccccccccccc
Confidence            578999999999998887776     578999999999999999999999999999999999999999999999999999


Q ss_pred             CCCc--c---c-cCCCcccccCCHHHHHHHHHHHHhhcc
Q 027581          177 GPQG--W---Y-YNARSKAQKPCYKVEQEGAAAWVEDCS  209 (221)
Q Consensus       177 sP~~--G---~-PkPRdy~~kLNKKvRrlALrsALSa~~  209 (221)
                      +|+|  |   | |+||+|.++||||+|++||++|||+.+
T Consensus        80 sp~~~gGg~~~gp~~r~~~~klnkK~r~~Al~~aLs~k~  118 (208)
T d2j01f1          80 APIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRA  118 (208)
T ss_dssp             STTSTTSCCSSCCCCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_pred             cccccccceecCcchhhHHHHHHHHHHHHHHHHHHHHHh
Confidence            9999  3   2 999999999999999999999999765

>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-33  Score=244.73  Aligned_cols=111  Identities=19%  Similarity=0.157  Sum_probs=99.9

Q ss_pred             eeeEEeccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeccc--cCCccCcccccCcceeccCCCC
Q 027581           99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEV--SGTGKKPWRQKGTGRARHGTLR  176 (221)
Q Consensus        99 m~ipV~~~~Ge~~g~IeLp~~VF~~p~R~DLIhraV~~q~anrRqGta~TKtRsEV--sGsgkKpwrQKGTGRAR~Gs~R  176 (221)
                      |++.|||++|+++|+|||| +||+.|+|.||||+||+||++|+||||++||+|++.  +++..|.++||||||||+|++|
T Consensus         1 Mk~~v~~~~gk~~g~i~lp-dvF~~~~r~dlvh~~v~~~~an~Rqgt~~~k~~g~~t~a~~~g~g~~qk~tgrar~g~rr   79 (246)
T d1vqoc1           1 MQATIYDLDGNTDGEVDLP-DVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESFGSGRGQAHVPKLDGRARR   79 (246)
T ss_dssp             CEEEEECTTSCEEEEEECC-GGGGSCCCHHHHHHHHHHHHHHTCCCCCCCTTTTTCCCCBCCCSSSSCCCCCEETTEECS
T ss_pred             CceEEEcCCCCEeeEEECh-hhhCCCCCHHHHHHHHHHHHHhcccCcCCCchhheeeeeeecCccccccCCCccccCCcc
Confidence            8999999999999999998 699999999999999999999999999999866532  2444455689999999999999


Q ss_pred             CCCc--c---c-cCC-CcccccCCHHHHHHHHHHHHhhccc
Q 027581          177 GPQG--W---Y-YNA-RSKAQKPCYKVEQEGAAAWVEDCSI  210 (221)
Q Consensus       177 sP~~--G---~-PkP-Rdy~~kLNKKvRrlALrsALSa~~~  210 (221)
                      +|+|  |   | |+| |||+++||||+|++||++|||+.+.
T Consensus        80 sP~~rGGG~a~gPkp~r~~~~klnkK~r~lAl~~aLs~k~~  120 (246)
T d1vqoc1          80 VPQAVKGRSAHPPKTEKDRSLDLNDKERQLAVRSALAATAD  120 (246)
T ss_dssp             STTSTTCCCSSCCCTTCCCCCCCCHHHHHHHHHHHHHHTTC
T ss_pred             CCCcCCCceecCCCCccchhHHHHHHHHHHHHHHHHHHhhc
Confidence            9999  3   3 998 9999999999999999999998763

>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=83.23  E-value=0.14  Score=42.20  Aligned_cols=50  Identities=20%  Similarity=0.165  Sum_probs=36.8

Q ss_pred             chhHHHHHHHHHHHHcccCCCCCceeccccCCcc-CcccccCcceeccCCC
Q 027581          126 RKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGK-KPWRQKGTGRARHGTL  175 (221)
Q Consensus       126 R~DLIhraV~~q~anrRqGta~TKtRsEVsGsgk-KpwrQKGTGRAR~Gs~  175 (221)
                      ..-++++--...+......+..+++++|++|+|+ ++|.|+++|++|..-+
T Consensus        32 h~~v~~~~an~Rqgt~~~k~~g~~t~a~~~g~g~~qk~tgrar~g~rrsP~   82 (246)
T d1vqoc1          32 GKAVRAAQANRKQDYGSDEYAGLRTPAESFGSGRGQAHVPKLDGRARRVPQ   82 (246)
T ss_dssp             HHHHHHHHHHTCCCCCCCTTTTTCCCCBCCCSSSSCCCCCEETTEECSSTT
T ss_pred             HHHHHHHHHhcccCcCCCchhheeeeeeecCccccccCCCccccCCccCCC
Confidence            3444444444445556667788999999999997 8899999999985433