Citrus Sinensis ID: 031004

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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-------
Protein Sequence
MATLCTPTCVIFSSLQSSSSSSSFKTLNTGTTISSSTTPFLGFSVASAKSTSPLNTKRSFKVRCCQNLSLVPDNQRWMFEQSEVNGPDIWNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQWQ
Secondary Structure (PSIPRED)
ccccccccEEEccccccccccccccccccccccccccccccEEEEccccccccccccccEEEEEEEccccccccccccEEccccccccccccccccccccccccccEEEEEEcccccHHHHHHHHHHHHccccccccccccccccEEEEEEccccccEEEEcccccc
Secondary Structure Prediction (SSPRO)
cccEcccccEEcccccccccccccccccccccccccccccccEEEcccccccccccccEEEEEEcccEEEccHHHcHHEccccccccccccccccccccccccEEEEEEEEEcccccHHHHHHHHHHHHHcccccccccccccccEEEEEEcccHHHHEEEcccccc
Coil and Loop (DISEMBL)
matlctptcvifsslqsssssssfktlntgttisssttpflGFSVAsakstsplntkrsfkvrccqnlslvpdnqrwmfeqsevngpdiwnntwypkaadhrhsdktwyvVDATDKILGRLASTIAIHIRgknlatytpsvdmGAYVIVVCGLHAyscilflppqwq
Flexible Loop (DISEMBL)
MATLCTPTCVIFsslqsssssssfKTLNTGTTISSSTTPFLGFSVASakstsplntkrsfkVRCCQNLSLVPDNQRWMFEQSEVNGPDIWNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQWQ
Low Complexity Region (SEG)
MATLCTPTCVIFsslqsssssssFKTLNTGTTISSSTTPFLGFSVASAKSTSPLNTKRSFKVRCCQNLSLVPDNQRWMFEQSEVNGPDIWNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQWQ
Disordered region (IsUnstruct)
***LCTPTCVIF*********************************************RSFKVRCCQNLSLVPDNQRWMFEQSEVNGPDIWNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLP****
Disordered Region (DISOPRED)
*************************************TPFLGFS********************************************IWNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPP***
Disordered Region (DISEMBL)
MATLCTPTCVIFSS**************TGTTISSSTTPFLGFSVAS**********RSFKVRCCQNLSLVPDNQRWMFEQSEVNGPDIWNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQWQ
Disordered Region (DISPRO)
*************************************TPFL*F*VA*A*******TKRSFKVRCCQNLSLVPDNQRWMFEQSEVNGPDIWNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQW*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MATLCTPTCVIFSSLQSSSSSSSFKTLNTGTTISSSTTPFLGFSVASAKSTSPLNTKRSFKVRCCQNLSLVPDNQRWMFEQSEVNGPDIWNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQWQ
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	167	2.2.26 [Sep-21-2011]
Q9SYL9	241	50S ribosomal protein L13	yes	no	0.676	0.468	0.647	6e-40
P12629	250	50S ribosomal protein L13	N/A	no	0.838	0.56	0.512	2e-33
Q6KI61	144	50S ribosomal protein L13	yes	no	0.299	0.347	0.56	1e-11
Q3MF94	151	50S ribosomal protein L13	yes	no	0.275	0.304	0.673	2e-11
Q8YPK6	151	50S ribosomal protein L13	yes	no	0.275	0.304	0.673	2e-11
C5C020	147	50S ribosomal protein L13	yes	no	0.335	0.380	0.542	2e-11
B4RXK9	142	50S ribosomal protein L13	yes	no	0.269	0.316	0.644	5e-11
Q220T2	143	50S ribosomal protein L13	yes	no	0.335	0.391	0.491	8e-11
B1Y3K7	142	50S ribosomal protein L13	yes	no	0.335	0.394	0.508	1e-10
C5CC33	147	50S ribosomal protein L13	yes	no	0.335	0.380	0.491	1e-10

>sp|Q9SYL9|RK13_ARATH 50S ribosomal protein L13, chloroplastic OS=Arabidopsis thaliana GN=RPL13 PE=1 SV=1

 Score =  163 bits (412), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 79/122 (64%), Positives = 93/122 (76%), Gaps = 9/122 (7%)

Query: 38  TPFLGFSVASAKSTSP-----LNTKRSFKVRCCQN----LSLVPDNQRWMFEQSEVNGPD 88
           +PFLGFS+ +    S       N+KR  +V+C        SLVP NQRWMF++ E NGPD
Sbjct: 26  SPFLGFSLTAISKPSVRVGIYANSKRGLQVKCEAEPTTTTSLVPANQRWMFDEEEANGPD 85

Query: 89  IWNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVI 148
           IWN TWYPKA+DH ++DK W+VVDATDKILGRLASTIA HIRGKNLA+YTPSVDMGA+VI
Sbjct: 86  IWNTTWYPKASDHVNTDKPWFVVDATDKILGRLASTIANHIRGKNLASYTPSVDMGAFVI 145

Query: 149 VV 150
           VV
Sbjct: 146 VV 147

Arabidopsis thaliana (taxid: 3702)

>sp|P12629|RK13_SPIOL 50S ribosomal protein L13, chloroplastic OS=Spinacia oleracea GN=RPL13 PE=1 SV=1

 Score =  141 bits (355), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 85/166 (51%), Positives = 103/166 (62%), Gaps = 26/166 (15%)

Query: 1   MATLCTPTCVIFSSLQSSSSSSSFKTLNTGTTISSSTTPFLGF---------SVASAKST 51
           MAT+   + + F S Q+  S         GT +    TP L F         +V++ KST
Sbjct: 1   MATMACASSLTFPSAQTQKSF-------FGTNVKQ--TPVLSFPRPTVAAAVAVSARKST 51

Query: 52  SPLNTK-----RSFKVRCCQNLSL--VPDNQRWMFEQSEVNGPDIWNNTWYPKAADHRHS 104
           S  +TK     R  K    +  ++  VP +QRWMF   E  GPDIWN TWYPK+ADH  +
Sbjct: 52  S-ASTKCTEEWRQLKEAVKKEFAIPHVPLDQRWMFTLEEATGPDIWNTTWYPKSADHVPT 110

Query: 105 DKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           DK WYVVDATD ILGR+ASTIAIHIRGKNLA+YTPSVDMGA+VIVV
Sbjct: 111 DKKWYVVDATDLILGRMASTIAIHIRGKNLASYTPSVDMGAFVIVV 156

Spinacia oleracea (taxid: 3562)

>sp|Q6KI61|RL13_MYCMO 50S ribosomal protein L13 OS=Mycoplasma mobile (strain ATCC 43663 / 163K / NCTC 11711) GN=rplM PE=3 SV=1

 Score = 68.9 bits (167), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 28/50 (56%), Positives = 40/50 (80%)

Query: 101 HRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           H+ +DK W+VVDA  ++LGRLAS +A ++RGKN  T+TP+VDMG  +IV+
Sbjct: 9   HKETDKKWFVVDAEGQVLGRLASVVASYLRGKNKPTFTPNVDMGDNIIVI 58

This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.

Mycoplasma mobile (strain ATCC 43663 / 163K / NCTC 11711) (taxid: 267748)

>sp|Q3MF94|RL13_ANAVT 50S ribosomal protein L13 OS=Anabaena variabilis (strain ATCC 29413 / PCC 7937) GN=rplM PE=3 SV=1

 Score = 68.6 bits (166), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/46 (67%), Positives = 37/46 (80%)

Query: 105 DKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           ++ WYVVDATDK LGRLAS IA+ +RGKN A YTP +D G +VIVV
Sbjct: 13  ERDWYVVDATDKRLGRLASEIAMILRGKNKAHYTPHLDTGDFVIVV 58

This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.

Anabaena variabilis (strain ATCC 29413 / PCC 7937) (taxid: 240292)

>sp|Q8YPK6|RL13_NOSS1 50S ribosomal protein L13 OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=rplM PE=3 SV=1

 Score = 68.6 bits (166), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/46 (67%), Positives = 37/46 (80%)

Query: 105 DKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           ++ WYVVDATDK LGRLAS IA+ +RGKN A YTP +D G +VIVV
Sbjct: 13  ERDWYVVDATDKRLGRLASEIAMILRGKNKAHYTPHLDTGDFVIVV 58

This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.

Nostoc sp. (strain PCC 7120 / UTEX 2576) (taxid: 103690)

>sp|C5C020|RL13_BEUC1 50S ribosomal protein L13 OS=Beutenbergia cavernae (strain ATCC BAA-8 / DSM 12333 / NBRC 16432) GN=rplM PE=3 SV=1

 Score = 68.2 bits (165), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/59 (54%), Positives = 44/59 (74%), Gaps = 3/59 (5%)

Query: 92  NTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
            T+ PK +D   +++TWYV+DATD +LGRLAS +A  +RGK+ AT+ P VD G +VIVV
Sbjct: 2   RTFTPKPSD---TERTWYVIDATDVVLGRLASQVAKLLRGKHKATFAPHVDTGDFVIVV 57

This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.

Beutenbergia cavernae (strain ATCC BAA-8 / DSM 12333 / NBRC 16432) (taxid: 471853)

>sp|B4RXK9|RL13_ALTMD 50S ribosomal protein L13 OS=Alteromonas macleodii (strain DSM 17117 / Deep ecotype) GN=rplM PE=3 SV=1

 Score = 67.0 bits (162), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 29/45 (64%), Positives = 35/45 (77%)

Query: 106 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           + WYVVDATDK LGRLAS IA+ +RGK+   YTP VD G Y+IV+
Sbjct: 13  RDWYVVDATDKTLGRLASEIALRLRGKHKPEYTPHVDTGDYIIVI 57

This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.

Alteromonas macleodii (strain DSM 17117 / Deep ecotype) (taxid: 314275)

>sp|Q220T2|RL13_RHOFD 50S ribosomal protein L13 OS=Rhodoferax ferrireducens (strain DSM 15236 / ATCC BAA-621 / T118) GN=rplM PE=3 SV=1

 Score = 66.2 bits (160), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 29/59 (49%), Positives = 43/59 (72%), Gaps = 3/59 (5%)

Query: 92  NTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
            T+  KAAD  H    W+V+DATDK+LGR+AS +A+ +RGK+ A YTP VD G +++++
Sbjct: 3   KTFSAKAADVVHE---WFVIDATDKVLGRVASEVALRLRGKHKAIYTPHVDTGDFIVII 58

This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.

Rhodoferax ferrireducens (strain DSM 15236 / ATCC BAA-621 / T118) (taxid: 338969)

>sp|B1Y3K7|RL13_LEPCP 50S ribosomal protein L13 OS=Leptothrix cholodnii (strain ATCC 51168 / LMG 8142 / SP-6) GN=rplM PE=3 SV=1

 Score = 65.5 bits (158), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 30/59 (50%), Positives = 43/59 (72%), Gaps = 3/59 (5%)

Query: 92  NTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           NT+  K A+  H    W+V+DATDK+LGR+AS +A+ +RGK+ A YTP VD G +++VV
Sbjct: 2   NTFSAKPAEVVHE---WFVIDATDKVLGRVASEVALRLRGKHKAIYTPHVDTGDFIVVV 57

This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.

Leptothrix cholodnii (strain ATCC 51168 / LMG 8142 / SP-6) (taxid: 395495)

>sp|C5CC33|RL13_MICLC 50S ribosomal protein L13 OS=Micrococcus luteus (strain ATCC 4698 / DSM 20030 / JCM 1464 / NBRC 3333 / NCIMB 9278 / NCTC 2665 / VKM Ac-2230) GN=rplM PE=3 SV=1

 Score = 65.5 bits (158), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 29/59 (49%), Positives = 41/59 (69%), Gaps = 3/59 (5%)

Query: 92  NTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
            T+ PK  D   +D+ W+++DATD +LGRLAS  A  +RGK+  T+ P +DMG YVI+V
Sbjct: 2   RTYSPKPGD---ADRQWHIIDATDVVLGRLASHTATLLRGKHKPTFAPHMDMGDYVIIV 57

This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.

Micrococcus luteus (strain ATCC 4698 / DSM 20030 / JCM 1464 / NBRC 3333 / NCIMB 9278 / NCTC 2665 / VKM Ac-2230) (taxid: 465515)

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	167
302142820	374	unnamed protein product [Vitis vinifera]	0.688	0.307	0.715	5e-43
225461790	235	PREDICTED: 50S ribosomal protein L13, ch	0.688	0.489	0.715	7e-43
118489447	241	unknown [Populus trichocarpa x Populus d	0.850	0.589	0.619	4e-41
297839733	242	EMB1473 [Arabidopsis lyrata subsp. lyrat	0.826	0.570	0.55	1e-39
15218435	241	50S ribosomal protein L13 [Arabidopsis t	0.676	0.468	0.647	3e-38
449456559	248	PREDICTED: 50S ribosomal protein L13, ch	0.874	0.588	0.575	7e-36
224114752	174	predicted protein [Populus trichocarpa]	0.479	0.459	0.837	6e-35
255582683	245	50S ribosomal protein L13, putative [Ric	0.670	0.457	0.596	7e-35
115439933	233	Os01g0749200 [Oryza sativa Japonica Grou	0.532	0.381	0.711	2e-33
242054425	229	hypothetical protein SORBIDRAFT_03g03462	0.491	0.358	0.792	1e-32

>gi|302142820|emb|CBI20115.3| unnamed protein product [Vitis vinifera]

 Score =  179 bits (453), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 83/116 (71%), Positives = 99/116 (85%), Gaps = 1/116 (0%)

Query: 35  SSTTPFLGFSVASAKSTSPLNTKRSFKVRCCQNLSLVPDNQRWMFEQSEVNGPDIWNNTW 94
             TTPFLGFS+ SA +  P   ++SF+V C    ++VP +QRWMFEQSEV+GPDIWN TW
Sbjct: 166 KKTTPFLGFSI-SAANPKPSFPRQSFRVNCQDKAAVVPLDQRWMFEQSEVSGPDIWNKTW 224

Query: 95  YPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           YPKAADH +++KTWY+VDATDKILGRLASTIAI+IRGKNLATYTPSVDMG++VIVV
Sbjct: 225 YPKAADHINTEKTWYIVDATDKILGRLASTIAIYIRGKNLATYTPSVDMGSFVIVV 280

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225461790|ref|XP_002285616.1| PREDICTED: 50S ribosomal protein L13, chloroplastic [Vitis vinifera]

 Score =  178 bits (451), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 83/116 (71%), Positives = 99/116 (85%), Gaps = 1/116 (0%)

Query: 35  SSTTPFLGFSVASAKSTSPLNTKRSFKVRCCQNLSLVPDNQRWMFEQSEVNGPDIWNNTW 94
             TTPFLGFS+ SA +  P   ++SF+V C    ++VP +QRWMFEQSEV+GPDIWN TW
Sbjct: 27  KKTTPFLGFSI-SAANPKPSFPRQSFRVNCQDKAAVVPLDQRWMFEQSEVSGPDIWNKTW 85

Query: 95  YPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           YPKAADH +++KTWY+VDATDKILGRLASTIAI+IRGKNLATYTPSVDMG++VIVV
Sbjct: 86  YPKAADHINTEKTWYIVDATDKILGRLASTIAIYIRGKNLATYTPSVDMGSFVIVV 141

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118489447|gb|ABK96526.1| unknown [Populus trichocarpa x Populus deltoides]

 Score =  172 bits (437), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 96/155 (61%), Positives = 117/155 (75%), Gaps = 13/155 (8%)

Query: 1   MATLCTPTCVIFSSLQSSSSSSSFKTLNTGTTISSSTTPFL-GFSVASAKSTSPLNTKRS 59
           MA LC  +    S   S+  SSS+ T N GT+IS S  PF+ GFS  S    S  N++R 
Sbjct: 1   MAMLCASS----SFTTSTKPSSSYSTKN-GTSISPS--PFVVGFSF-SQSWFSLSNSRRG 52

Query: 60  FKVRCCQN----LSLVPDNQRWMFEQSEVNGPDIWNNTWYPKAADHRHSDKTWYVVDATD 115
           F+VRC +     ++ VP +QRW+FE+SE+NGPDIWN TWYPKAADH +++KTWY+VDATD
Sbjct: 53  FEVRCEKKDKSVVTRVPLDQRWLFEESEINGPDIWNTTWYPKAADHINTEKTWYIVDATD 112

Query: 116 KILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           KILGRLASTIAI+IRGKNLATYTPSVDMGA+VIVV
Sbjct: 113 KILGRLASTIAIYIRGKNLATYTPSVDMGAFVIVV 147

Source: Populus trichocarpa x Populus deltoides

Species: Populus trichocarpa x Populus deltoides

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297839733|ref|XP_002887748.1| EMB1473 [Arabidopsis lyrata subsp. lyrata] gi|297333589|gb|EFH64007.1| EMB1473 [Arabidopsis lyrata subsp. lyrata]

 Score =  167 bits (424), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 88/160 (55%), Positives = 104/160 (65%), Gaps = 22/160 (13%)

Query: 1   MATLCTPTCVIFSSLQSSSSSSSFKTLNTGTTISSSTTPFLGFSVASAKSTSP-----LN 55
           M  LC+ + VI  S     S S  K+            PFLGFS+ +    S       N
Sbjct: 1   MTVLCSSSTVILPSSSVKPSGSERKS------------PFLGFSLTAFSKPSVRVGIYAN 48

Query: 56  TKRSFKVRC-----CQNLSLVPDNQRWMFEQSEVNGPDIWNNTWYPKAADHRHSDKTWYV 110
           +KR  +V+C         SLVP NQRWMF++ E NGPDIWN TWYPKA+DH ++DK W+V
Sbjct: 49  SKRGLQVKCEAEETTTKTSLVPANQRWMFDEEEANGPDIWNTTWYPKASDHVNTDKPWFV 108

Query: 111 VDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           VDATDKILGRLASTIA HIRGKNLA+YTPSVDMGA+VIVV
Sbjct: 109 VDATDKILGRLASTIANHIRGKNLASYTPSVDMGAFVIVV 148

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15218435|ref|NP_177984.1| 50S ribosomal protein L13 [Arabidopsis thaliana] gi|75314103|sp|Q9SYL9.1|RK13_ARATH RecName: Full=50S ribosomal protein L13, chloroplastic; AltName: Full=CL13; AltName: Full=Protein EMBRYO DEFECTIVE 1473; Flags: Precursor gi|4836870|gb|AAD30573.1|AC007260_4 50S Ribosomal protein L13 [Arabidopsis thaliana] gi|13878111|gb|AAK44133.1|AF370318_1 putative ribosomal protein L13 [Arabidopsis thaliana] gi|7572938|emb|CAA60775.1| ribosomal protein L13 [Arabidopsis thaliana] gi|17104781|gb|AAL34279.1| putative ribosomal protein L13 [Arabidopsis thaliana] gi|332198009|gb|AEE36130.1| 50S ribosomal protein L13 [Arabidopsis thaliana]

 Score =  163 bits (412), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 79/122 (64%), Positives = 93/122 (76%), Gaps = 9/122 (7%)

Query: 38  TPFLGFSVASAKSTSP-----LNTKRSFKVRCCQN----LSLVPDNQRWMFEQSEVNGPD 88
           +PFLGFS+ +    S       N+KR  +V+C        SLVP NQRWMF++ E NGPD
Sbjct: 26  SPFLGFSLTAISKPSVRVGIYANSKRGLQVKCEAEPTTTTSLVPANQRWMFDEEEANGPD 85

Query: 89  IWNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVI 148
           IWN TWYPKA+DH ++DK W+VVDATDKILGRLASTIA HIRGKNLA+YTPSVDMGA+VI
Sbjct: 86  IWNTTWYPKASDHVNTDKPWFVVDATDKILGRLASTIANHIRGKNLASYTPSVDMGAFVI 145

Query: 149 VV 150
           VV
Sbjct: 146 VV 147

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449456559|ref|XP_004146016.1| PREDICTED: 50S ribosomal protein L13, chloroplastic-like [Cucumis sativus] gi|449518653|ref|XP_004166351.1| PREDICTED: 50S ribosomal protein L13, chloroplastic-like [Cucumis sativus]

 Score =  155 bits (391), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 91/158 (57%), Positives = 109/158 (68%), Gaps = 12/158 (7%)

Query: 1   MATLC----TPTCVIFSSL-QSSSSSSSF--KTLNTGTTISSSTTPFLGFSVASAKSTSP 53
           MA LC    TPT  + S+L   ++S+ SF   +L     +  S + FL  +  S   TS 
Sbjct: 1   MAMLCASSSTPTFSLHSTLTNGTTSNKSFPRNSLLVAFPLPHSKSSFL-LTQTSISLTS- 58

Query: 54  LNTKRS-FKVRCCQNLSLVPDNQRWMFEQSEVNGPDIWNNTWYPKAADHRHSDKTWYVVD 112
            N+KRS  +VR  Q L  VP  QRWMFE  E++GPDIWN TWYPKAADH +++K WYVVD
Sbjct: 59  -NSKRSALQVRA-QELDRVPLEQRWMFEGDELDGPDIWNKTWYPKAADHVNTEKPWYVVD 116

Query: 113 ATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           ATDKILGRLASTIA HIRGK+L TYTPSVDMGA+VIVV
Sbjct: 117 ATDKILGRLASTIANHIRGKDLPTYTPSVDMGAFVIVV 154

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224114752|ref|XP_002316846.1| predicted protein [Populus trichocarpa] gi|222859911|gb|EEE97458.1| predicted protein [Populus trichocarpa]

 Score =  152 bits (383), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 67/80 (83%), Positives = 77/80 (96%)

Query: 71  VPDNQRWMFEQSEVNGPDIWNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIR 130
           VP +QRW+FE+SE+NGPDIWN TWYPKAADH +++KTWY+VDATDKILGRLASTIAI+IR
Sbjct: 1   VPLDQRWLFEESEINGPDIWNTTWYPKAADHINTEKTWYIVDATDKILGRLASTIAIYIR 60

Query: 131 GKNLATYTPSVDMGAYVIVV 150
           GKNLATYTPSVDMGA+VIVV
Sbjct: 61  GKNLATYTPSVDMGAFVIVV 80

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255582683|ref|XP_002532120.1| 50S ribosomal protein L13, putative [Ricinus communis] gi|223528200|gb|EEF30260.1| 50S ribosomal protein L13, putative [Ricinus communis]

 Score =  151 bits (382), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 74/124 (59%), Positives = 90/124 (72%), Gaps = 12/124 (9%)

Query: 39  PFLGFSVASAKSTSPLNTKRSFKVRCCQNLSL------------VPDNQRWMFEQSEVNG 86
           P+  F   S+   S  + + SF   C ++ ++            VP +QRWMFE+ E+NG
Sbjct: 28  PYTTFIAGSSLLKSKPSVRTSFSASCSRSFTVLSEKTDKKVVPHVPVDQRWMFEEFELNG 87

Query: 87  PDIWNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAY 146
           PDIWN TWYPKAADH +++K WYVVDATDKILGRLASTIAI+IRGKNLATYTPSVDMGA+
Sbjct: 88  PDIWNKTWYPKAADHVNTEKPWYVVDATDKILGRLASTIAIYIRGKNLATYTPSVDMGAF 147

Query: 147 VIVV 150
           VIVV
Sbjct: 148 VIVV 151

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115439933|ref|NP_001044246.1| Os01g0749200 [Oryza sativa Japonica Group] gi|14209550|dbj|BAB56046.1| putative ribosomal protein L13 precursor [Oryza sativa Japonica Group] gi|113533777|dbj|BAF06160.1| Os01g0749200 [Oryza sativa Japonica Group] gi|125527707|gb|EAY75821.1| hypothetical protein OsI_03735 [Oryza sativa Indica Group] gi|125572024|gb|EAZ13539.1| hypothetical protein OsJ_03455 [Oryza sativa Japonica Group] gi|215679022|dbj|BAG96452.1| unnamed protein product [Oryza sativa Japonica Group] gi|215704294|dbj|BAG93134.1| unnamed protein product [Oryza sativa Japonica Group] gi|215704454|dbj|BAG93888.1| unnamed protein product [Oryza sativa Japonica Group] gi|215767344|dbj|BAG99572.1| unnamed protein product [Oryza sativa Japonica Group]

 Score =  146 bits (369), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 69/97 (71%), Positives = 78/97 (80%), Gaps = 8/97 (8%)

Query: 62  VRCCQNL--------SLVPDNQRWMFEQSEVNGPDIWNNTWYPKAADHRHSDKTWYVVDA 113
           VRC Q+         +LVP  QR+MFE  E+ GPDIWN TWYPKAADH  ++KTWYVVDA
Sbjct: 42  VRCEQSEKQKRQPLSALVPREQRFMFEGDELCGPDIWNTTWYPKAADHVTTEKTWYVVDA 101

Query: 114 TDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           TDKILGRLASTIA+HIRGKN ATYTPSVDMGA+V+VV
Sbjct: 102 TDKILGRLASTIAVHIRGKNEATYTPSVDMGAFVVVV 138

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242054425|ref|XP_002456358.1| hypothetical protein SORBIDRAFT_03g034620 [Sorghum bicolor] gi|241928333|gb|EES01478.1| hypothetical protein SORBIDRAFT_03g034620 [Sorghum bicolor]

 Score =  144 bits (363), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 65/82 (79%), Positives = 72/82 (87%)

Query: 69  SLVPDNQRWMFEQSEVNGPDIWNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIH 128
           +LVP  QR+MFE  E+ GPDIWN TWYPKAADH  ++KTWYVVDATDKILGRLASTIA+H
Sbjct: 54  ALVPREQRFMFEGDELCGPDIWNTTWYPKAADHVTTEKTWYVVDATDKILGRLASTIAVH 113

Query: 129 IRGKNLATYTPSVDMGAYVIVV 150
           IRGKN  TYTPSVDMGA+VIVV
Sbjct: 114 IRGKNEPTYTPSVDMGAFVIVV 135

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

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	167
TAIR|locus:2203010	241	emb1473 "embryo defective 1473	0.700	0.485	0.634	5.5e-38
UNIPROTKB|Q9KUF1	142	rplM "50S ribosomal protein L1	0.269	0.316	0.644	4.1e-10
TIGR_CMR|VC_0570	142	VC_0570 "ribosomal protein L13	0.269	0.316	0.644	4.1e-10
UNIPROTKB|P66065	147	rplM "50S ribosomal protein L1	0.329	0.374	0.5	5.2e-10
UNIPROTKB|P0AA10	142	rplM [Escherichia coli K-12 (t	0.269	0.316	0.6	8.4e-10
TIGR_CMR|CPS_4443	142	CPS_4443 "ribosomal protein L1	0.269	0.316	0.533	1.8e-09
TIGR_CMR|GSU_2876	143	GSU_2876 "ribosomal protein L1	0.323	0.377	0.5	2.2e-09
TIGR_CMR|BA_0143	145	BA_0143 "ribosomal protein L13	0.275	0.317	0.543	4.7e-09
TIGR_CMR|SO_3940	142	SO_3940 "ribosomal protein L13	0.269	0.316	0.533	5.9e-09
TIGR_CMR|SPO_1691	152	SPO_1691 "ribosomal protein L1	0.275	0.302	0.521	7.6e-09

TAIR|locus:2203010 emb1473 "embryo defective 1473" [Arabidopsis thaliana (taxid:3702)]

 Score = 407 (148.3 bits), Expect = 5.5e-38, P = 5.5e-38
 Identities = 80/126 (63%), Positives = 94/126 (74%)

Query:    34 SSSTTPFLGFSVASAKSTSP-----LNTKRSFKVRC----CQNLSLVPDNQRWMFEQSEV 84
             S   +PFLGFS+ +    S       N+KR  +V+C        SLVP NQRWMF++ E 
Sbjct:    22 SERKSPFLGFSLTAISKPSVRVGIYANSKRGLQVKCEAEPTTTTSLVPANQRWMFDEEEA 81

Query:    85 NGPDIWNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMG 144
             NGPDIWN TWYPKA+DH ++DK W+VVDATDKILGRLASTIA HIRGKNLA+YTPSVDMG
Sbjct:    82 NGPDIWNTTWYPKASDHVNTDKPWFVVDATDKILGRLASTIANHIRGKNLASYTPSVDMG 141

Query:   145 AYVIVV 150
             A+VIVV
Sbjct:   142 AFVIVV 147

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

GO:0005840 "ribosome" evidence=ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009793 "embryo development ending in seed dormancy" evidence=NAS

GO:0009579 "thylakoid" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0045036 "protein targeting to chloroplast" evidence=RCA

UNIPROTKB|Q9KUF1 rplM "50S ribosomal protein L13" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 144 (55.7 bits), Expect = 4.1e-10, P = 4.1e-10
 Identities = 29/45 (64%), Positives = 33/45 (73%)

Query:   106 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
             + WYVVDA  K LGRLAS IA  +RGK+ A YTP VD G Y+IVV
Sbjct:    13 RDWYVVDAEGKTLGRLASEIASRLRGKHKAEYTPHVDTGDYIIVV 57

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|VC_0570 VC_0570 "ribosomal protein L13" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 144 (55.7 bits), Expect = 4.1e-10, P = 4.1e-10
 Identities = 29/45 (64%), Positives = 33/45 (73%)

Query:   106 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
             + WYVVDA  K LGRLAS IA  +RGK+ A YTP VD G Y+IVV
Sbjct:    13 RDWYVVDAEGKTLGRLASEIASRLRGKHKAEYTPHVDTGDYIIVV 57

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

GO:0006412 "translation" evidence=ISS

UNIPROTKB|P66065 rplM "50S ribosomal protein L13" [Mycobacterium tuberculosis (taxid:1773)]

 Score = 143 (55.4 bits), Expect = 5.2e-10, P = 5.2e-10
 Identities = 29/58 (50%), Positives = 41/58 (70%)

Query:    93 TWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
             T+ PKA D   + ++WYV+DATD +LGRLA   A  +RGK+  T+ P+VD G +VIV+
Sbjct:     3 TYAPKAGD---TTRSWYVIDATDVVLGRLAVAAANLLRGKHKPTFAPNVDGGDFVIVI 57

GO:0005618 "cell wall" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0040007 "growth" evidence=IMP

UNIPROTKB|P0AA10 rplM [Escherichia coli K-12 (taxid:83333)]

 Score = 141 (54.7 bits), Expect = 8.4e-10, P = 8.4e-10
 Identities = 27/45 (60%), Positives = 34/45 (75%)

Query:   106 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
             + WYVVDAT K LGRLA+ +A  +RGK+ A YTP VD G Y+IV+
Sbjct:    13 RDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVL 57

GO:0008270 "zinc ion binding" evidence=IDA

GO:0006412 "translation" evidence=IEA

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

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

TIGR_CMR|CPS_4443 CPS_4443 "ribosomal protein L13" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 138 (53.6 bits), Expect = 1.8e-09, P = 1.8e-09
 Identities = 24/45 (53%), Positives = 34/45 (75%)

Query:   106 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
             + W++VDA DK LGR+A+ IA  +RGK+ A YTP VD G Y++V+
Sbjct:    13 REWFLVDAEDKTLGRIATEIATRLRGKHKAEYTPHVDTGDYIVVI 57

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

GO:0006412 "translation" evidence=ISS

GO:0015934 "large ribosomal subunit" evidence=ISS

TIGR_CMR|GSU_2876 GSU_2876 "ribosomal protein L13" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 137 (53.3 bits), Expect = 2.2e-09, P = 2.2e-09
 Identities = 27/54 (50%), Positives = 36/54 (66%)

Query:    97 KAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
             K A      + WY+VDA +K+LGR+A+ IA  +RGK    YTPSVD G +V+VV
Sbjct:     5 KVAKKEEVTRDWYLVDADNKVLGRMATEIANILRGKKKPIYTPSVDTGDFVVVV 58

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

GO:0006412 "translation" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

TIGR_CMR|BA_0143 BA_0143 "ribosomal protein L13" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 134 (52.2 bits), Expect = 4.7e-09, P = 4.7e-09
 Identities = 25/46 (54%), Positives = 34/46 (73%)

Query:   105 DKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
             ++ WYVVDA  + LGRLAS +A  +RGKN  T+TP VD G +VI++
Sbjct:    13 ERKWYVVDAEGQTLGRLASEVASILRGKNKPTFTPHVDTGDHVIII 58

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|SO_3940 SO_3940 "ribosomal protein L13" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 133 (51.9 bits), Expect = 5.9e-09, P = 5.9e-09
 Identities = 24/45 (53%), Positives = 33/45 (73%)

Query:   106 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
             + W+VVDA  K LGR+A+ IA+ +RGK+   YTP VD G Y+IV+
Sbjct:    13 RDWFVVDADGKTLGRIATEIALRLRGKHKPEYTPHVDTGDYIIVI 57

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|SPO_1691 SPO_1691 "ribosomal protein L13" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 132 (51.5 bits), Expect = 7.6e-09, P = 7.6e-09
 Identities = 24/46 (52%), Positives = 35/46 (76%)

Query:   105 DKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
             DK W ++DA   +LGRLAS +A+ +RGK+ A++TP +DMG  VIV+
Sbjct:    12 DKKWILIDAEGVVLGRLASIVAMRLRGKHKASFTPHMDMGDNVIVI 57

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

GO:0006412 "translation" evidence=ISS

GO:0042255 "ribosome assembly" evidence=ISS

---

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

Your Input:
	GSVIVG00027910001	SubName- Full=Chromosome chr19 scaffold_4, whole genome shotgun sequence; (235 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00019749001	SubName- Full=Putative uncharacterized protein (Chromosome chr5 scaffold_2, whole genome shotgu [...] (161 aa)	•		•	•	•		•		0.989
	GSVIVG00035271001	SubName- Full=Chromosome chr10 scaffold_76, whole genome shotgun sequence; (140 aa)	•		•	•	•		•		0.987
	GSVIVG00026943001	SubName- Full=Chromosome chr15 scaffold_40, whole genome shotgun sequence; (265 aa)	•			•	•		•		0.984
	GSVIVG00035173001	SubName- Full=Chromosome chr10 scaffold_76, whole genome shotgun sequence; (116 aa)	•			•	•		•		0.983
	GSVIVG00026031001	SubName- Full=Chromosome chr12 scaffold_36, whole genome shotgun sequence; (117 aa)	•			•	•		•		0.979
	GSVIVG00015322001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (167 aa)	•			•	•		•		0.977
	GSVIVG00023012001	SubName- Full=Chromosome chr6 scaffold_28, whole genome shotgun sequence; (213 aa)	•			•	•		•		0.975
	GSVIVG00014698001	SubName- Full=Putative uncharacterized protein (Chromosome chr18 scaffold_1, whole genome shotg [...] (209 aa)	•			•			•		0.972
	rps2	ribosomal protein S2 (180 aa)	•		•	•			•		0.972
	rpl20	RecName- Full=50S ribosomal protein L20, chloroplastic;; Binds directly to 23S ribosomal RNA an [...] (117 aa)	•			•	•		•		0.969

---

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	167
PRK09216	144	PRK09216, rplM, 50S ribosomal protein L13; Reviewe	5e-25
cd00392	114	cd00392, Ribosomal_L13, Ribosomal protein L13	4e-22
COG0102	148	COG0102, RplM, Ribosomal protein L13 [Translation,	8e-22
pfam00572	128	pfam00572, Ribosomal_L13, Ribosomal protein L13	3e-21
TIGR01066	140	TIGR01066, rplM_bact, ribosomal protein L13, bacte	2e-20
CHL00159	143	CHL00159, rpl13, ribosomal protein L13; Validated	2e-17
PLN00205	191	PLN00205, PLN00205, ribisomal protein L13 family p	1e-08
PRK06394	146	PRK06394, rpl13p, 50S ribosomal protein L13P; Revi	0.001

>gnl|CDD|181703 PRK09216, rplM, 50S ribosomal protein L13; Reviewed

 Score = 93.2 bits (233), Expect = 5e-25
 Identities = 28/58 (48%), Positives = 40/58 (68%), Gaps = 3/58 (5%)

Query: 93  TWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           T+  K A+    ++ WYV+DA  K+LGRLAS +A  +RGK+  T+TP VD G +VIV+
Sbjct: 3   TFSAKPAE---VERKWYVIDAEGKVLGRLASEVASILRGKHKPTFTPHVDTGDFVIVI 57

Length = 144

>gnl|CDD|238230 cd00392, Ribosomal_L13, Ribosomal protein L13

 Score = 85.2 bits (212), Expect = 4e-22
 Identities = 24/43 (55%), Positives = 32/43 (74%)

Query: 108 WYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           W+V+DA  ++LGRLAS +A  + GK+  TYTP VD G YV+VV
Sbjct: 1   WHVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVV 43

Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the polypeptide exit site. It interacts with proteins L3 and L6, and forms an extensive network of interactions with 23S rRNA. L13 has been identified as a homolog of the human breast basic conserved protein 1 (BBC1), a protein identified through its increased expression in breast cancer. L13 expression is also upregulated in a variety of human gastrointestinal cancers, suggesting it may play a role in the etiology of a variety of human malignancies. Length = 114

>gnl|CDD|223180 COG0102, RplM, Ribosomal protein L13 [Translation, ribosomal structure and biogenesis]

 Score = 85.4 bits (212), Expect = 8e-22
 Identities = 29/59 (49%), Positives = 40/59 (67%), Gaps = 3/59 (5%)

Query: 93  TWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVC 151
           T+  K ++    ++ WYV+DA  K+LGRLAS +A  +RGK+  TYTP VD G YVIV+ 
Sbjct: 3   TFTAKPSE---VERKWYVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVIN 58

Length = 148

>gnl|CDD|201314 pfam00572, Ribosomal_L13, Ribosomal protein L13

 Score = 83.3 bits (207), Expect = 3e-21
 Identities = 25/43 (58%), Positives = 33/43 (76%)

Query: 108 WYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           W+V+DA  +ILGRLAS +A  +RGK+  TYTP VD G YV+V+
Sbjct: 1   WHVIDAKGQILGRLASKVAKLLRGKHKPTYTPHVDCGDYVVVI 43

Length = 128

>gnl|CDD|162186 TIGR01066, rplM_bact, ribosomal protein L13, bacterial type

 Score = 81.6 bits (202), Expect = 2e-20
 Identities = 28/46 (60%), Positives = 33/46 (71%)

Query: 105 DKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
            + WYVVDA  K LGRLAS +A  +RGK+  TYTP VD G YVIV+
Sbjct: 10  KRKWYVVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVI 55

This model distinguishes ribosomal protein L13 of bacteria and organelles from its eukarytotic and archaeal counterparts [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 140

>gnl|CDD|177072 CHL00159, rpl13, ribosomal protein L13; Validated

 Score = 73.5 bits (181), Expect = 2e-17
 Identities = 29/60 (48%), Positives = 38/60 (63%), Gaps = 3/60 (5%)

Query: 91  NNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           N T+ P         + WY++DA D+ LGRLA+ IA  +RGKN  +Y PSVD G YVIV+
Sbjct: 2   NKTFIPSKDYKN---RKWYIIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVI 58

Length = 143

>gnl|CDD|177795 PLN00205, PLN00205, ribisomal protein L13 family protein; Provisional

 Score = 51.8 bits (124), Expect = 1e-08
 Identities = 20/43 (46%), Positives = 28/43 (65%)

Query: 108 WYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           W V DA  ++LGRLAS I+  ++GK+  TY P+ D G   IV+
Sbjct: 17  WRVFDAKGQVLGRLASQISTVLQGKDKPTYAPNRDDGDICIVL 59

Length = 191

>gnl|CDD|235793 PRK06394, rpl13p, 50S ribosomal protein L13P; Reviewed

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 11/17 (64%), Positives = 14/17 (82%)

Query: 110 VVDATDKILGRLASTIA 126
           V+DA  +ILGRLAS +A
Sbjct: 6   VIDAEGQILGRLASYVA 22

Length = 146

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	167
CHL00159	143	rpl13 ribosomal protein L13; Validated	99.97
PRK09216	144	rplM 50S ribosomal protein L13; Reviewed	99.97
TIGR01066	140	rplM_bact ribosomal protein L13, bacterial type. T	99.96
COG0102	148	RplM Ribosomal protein L13 [Translation, ribosomal	99.96
cd00392	114	Ribosomal_L13 Ribosomal protein L13. Protein L13,	99.96
PLN00205	191	ribisomal protein L13 family protein; Provisional	99.94
PF00572	128	Ribosomal_L13: Ribosomal protein L13; InterPro: IP	99.94
KOG3203	165	consensus Mitochondrial/chloroplast ribosomal prot	99.93
PRK06394	146	rpl13p 50S ribosomal protein L13P; Reviewed	99.45
PTZ00068	202	60S ribosomal protein L13a; Provisional	98.33
TIGR01077	142	L13_A_E ribosomal protein L13, archaeal/eukaryotic	97.87
KOG3204	197	consensus 60S ribosomal protein L13a [Translation,	90.84

>CHL00159 rpl13 ribosomal protein L13; Validated

Probab=99.97  E-value=1.6e-32  Score=217.43  Aligned_cols=71  Identities=41%  Similarity=0.690  Sum_probs=68.5

Q ss_pred             cceeeccCCCCcccccceEEEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCCEEEEEcCcccccccccCCCCCC
Q 031004           90 WNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQWQ  167 (167)
Q Consensus        90 ~~kT~~~k~~d~~~~~r~W~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD~VVVINA~kI~~~~a~~g~~W~  167 (167)
                      ||+||++++++   ++|+||||||+||+|||||++||++|+|||||+|||++||||+||||||++|    +|+|++|+
T Consensus         1 ~~~t~~~~~~~---~~r~W~viDA~~~~lGRlAs~iA~~L~GKhKp~ytP~~d~Gd~VVViNa~kv----~~TG~K~~   71 (143)
T CHL00159          1 MNKTFIPSKDY---KNRKWYIIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVINAEKI----KVTGNKTS   71 (143)
T ss_pred             CCccccCCchh---cCCCEEEEeCCCCchHHHHHHHHHHHhccCCCCcCCCcCCCCEEEEEeccee----EEeCchhh
Confidence            57899999888   9999999999999999999999999999999999999999999999999999    99999985

>PRK09216 rplM 50S ribosomal protein L13; Reviewed

Probab=99.97  E-value=1.2e-31  Score=212.36  Aligned_cols=70  Identities=40%  Similarity=0.687  Sum_probs=67.2

Q ss_pred             ceeeccCCCCcccccceEEEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCCEEEEEcCcccccccccCCCCCC
Q 031004           91 NNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQWQ  167 (167)
Q Consensus        91 ~kT~~~k~~d~~~~~r~W~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD~VVVINA~kI~~~~a~~g~~W~  167 (167)
                      |+||++++++   .+|+||||||+||+|||||++||++|+|||||+|+|++||||+||||||++|    .++|++|+
T Consensus         1 m~t~~~~~~~---~~~~W~viDA~~~~lGRlAs~IAk~L~GKhKp~y~p~~d~Gd~VvViNa~ki----~~tG~k~~   70 (144)
T PRK09216          1 MKTFSAKPAE---VERKWYVIDAEGKVLGRLASEVASILRGKHKPTFTPHVDTGDFVIVINAEKV----KLTGKKLT   70 (144)
T ss_pred             CCcccCChhh---cCCCEEEEeCCCCchHHHHHHHHHHHhccCCCCcCCCCCCCCEEEEEeCcee----EEcCchHh
Confidence            4689999888   8999999999999999999999999999999999999999999999999999    99999985

>TIGR01066 rplM_bact ribosomal protein L13, bacterial type

Probab=99.96  E-value=2.9e-30  Score=203.50  Aligned_cols=66  Identities=44%  Similarity=0.694  Sum_probs=61.5

Q ss_pred             ccCCCCcccccceEEEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCCEEEEEcCcccccccccCCCCCC
Q 031004           95 YPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQWQ  167 (167)
Q Consensus        95 ~~k~~d~~~~~r~W~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD~VVVINA~kI~~~~a~~g~~W~  167 (167)
                      .+++.+   +.|+||||||+||+|||||+.||++|+|||||+|+|++||||+||||||++|    .++|++|+
T Consensus         3 ~~~~~~---~~r~W~viDA~~~~lGRLAs~iAk~L~GKhKp~y~p~~d~Gd~VvViNa~ki----~~tG~k~~   68 (140)
T TIGR01066         3 AKASDD---KKRKWYVVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVINAEKV----RLTGKKLE   68 (140)
T ss_pred             cCChhh---hcccEEEEeCCCCchHHHHHHHHHHHhccCCCccCCCccCCCEEEEEeccEE----EEeCchhh
Confidence            344455   8899999999999999999999999999999999999999999999999999    99999985

This model distinguishes ribosomal protein L13 of bacteria and organelles from its eukarytotic and archaeal counterparts.

>COG0102 RplM Ribosomal protein L13 [Translation, ribosomal structure and biogenesis]

Probab=99.96  E-value=5.5e-30  Score=204.88  Aligned_cols=68  Identities=43%  Similarity=0.757  Sum_probs=65.1

Q ss_pred             ceeeccCCCCcccccceEEEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCCEEEEEcCcccccccccCCCC
Q 031004           91 NNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQ  165 (167)
Q Consensus        91 ~kT~~~k~~d~~~~~r~W~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD~VVVINA~kI~~~~a~~g~~  165 (167)
                      |+|++.++++   ..|+||||||+|++|||||+.||++|+|||||+||||+||||+|||||||||    +++|++
T Consensus         1 ~~t~~~k~~~---~~r~w~vIDA~g~vLGRLAs~VA~~Lrgkhkp~ytP~~d~Gd~ViVINAeKv----~iTG~K   68 (148)
T COG0102           1 MKTFTAKPSE---VERKWYVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKV----VITGKK   68 (148)
T ss_pred             CceeccCccc---ccceEEEEeCCCCChHHHHHHHHHHHhcCCCCCcCcCcCCCCEEEEEeceee----EEeccc
Confidence            5788899888   9999999999999999999999999999999999999999999999999999    888876

>cd00392 Ribosomal_L13 Ribosomal protein L13

Probab=99.96  E-value=2.1e-29  Score=192.23  Aligned_cols=56  Identities=45%  Similarity=0.790  Sum_probs=55.1

Q ss_pred             EEEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCCEEEEEcCcccccccccCCCCCC
Q 031004          108 WYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQWQ  167 (167)
Q Consensus       108 W~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD~VVVINA~kI~~~~a~~g~~W~  167 (167)
                      ||||||+||+|||||++||++|+|||||+|||++||||+||||||++|    .++|++|+
T Consensus         1 w~viDA~~~~lGRlAs~iA~~L~gKhKp~y~p~~d~Gd~VvViNa~~i----~~tG~k~~   56 (114)
T cd00392           1 WHVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAEKI----VITGKKWR   56 (114)
T ss_pred             CEEEeCCCCchHHHHHHHHHHHcCCCCCCcCCCccCCCEEEEEeccEE----EEeCchhh
Confidence            999999999999999999999999999999999999999999999999    99999985

Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the polypeptide exit site. It interacts with proteins L3 and L6, and forms an extensive network of interactions with 23S rRNA. L13 has been identified as a homolog of the human breast basic conserved protein 1 (BBC1), a protein identified through its increased expression in breast cancer. L13 expression is also upregulated in a variety of human gastrointestinal cancers, suggesting it may play a role in the etiology of a variety of human malignancies.

>PLN00205 ribisomal protein L13 family protein; Provisional

Probab=99.94  E-value=5.6e-28  Score=199.62  Aligned_cols=60  Identities=33%  Similarity=0.511  Sum_probs=58.1

Q ss_pred             ccceEEEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCCEEEEEcCcccccccccCCCCCC
Q 031004          104 SDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQWQ  167 (167)
Q Consensus       104 ~~r~W~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD~VVVINA~kI~~~~a~~g~~W~  167 (167)
                      ..|+||||||+||+|||||++||++|+|||||+|+|++||||+||||||++|    .++|++|+
T Consensus        13 ~~r~W~VIDA~~~iLGRLAS~IAk~L~GKhKP~ytP~~D~GD~VVVINAekI----~lTG~K~~   72 (191)
T PLN00205         13 EGLRWRVFDAKGQVLGRLASQISTVLQGKDKPTYAPNRDDGDICIVLNAKDI----SVTGRKLT   72 (191)
T ss_pred             CCCcEEEEeCCCCchHHHHHHHHHHHhccCCCCcCCCcCCCCEEEEEeccEE----EEeCChhh
Confidence            5789999999999999999999999999999999999999999999999999    99999984

>PF00572 Ribosomal_L13: Ribosomal protein L13; InterPro: IPR005822 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.94  E-value=7e-28  Score=186.71  Aligned_cols=56  Identities=46%  Similarity=0.811  Sum_probs=54.5

Q ss_pred             EEEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCCEEEEEcCcccccccccCCCCCC
Q 031004          108 WYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQWQ  167 (167)
Q Consensus       108 W~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD~VVVINA~kI~~~~a~~g~~W~  167 (167)
                      ||||||+||+|||||+.||++|+|||||+|||++|+||+||||||++|    +++|++|+
T Consensus         1 W~viDA~~~~lGRLAs~iAk~L~GKhk~~y~p~~d~Gd~VvViNae~i----~~tG~k~~   56 (128)
T PF00572_consen    1 WYVIDAKGQILGRLASKIAKLLLGKHKPTYTPNVDCGDHVVVINAEKI----VLTGKKWR   56 (128)
T ss_dssp             EEEEETTTBBHHHHHHHHHHHHCTTSSTSSBTTSSTTEEEEEECGGGB----EESSHHHH
T ss_pred             CEEEeCCCCchHHHHHHHHHHHhCCCCCccCcCccCCCEEEEEcCeee----EecCCeec
Confidence            999999999999999999999999999999999999999999999999    99998873

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L13 is one of the proteins from the large ribosomal subunit []. In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 4A17_I 4A1E_I 4A1A_I 4A1C_I 3D5B_N 3MS1_J 1VSP_H 3PYT_J 3PYO_J 3PYV_J ....

>KOG3203 consensus Mitochondrial/chloroplast ribosomal protein L13 [Translation, ribosomal structure and biogenesis]

Probab=99.93  E-value=3.5e-27  Score=191.31  Aligned_cols=65  Identities=37%  Similarity=0.577  Sum_probs=61.7

Q ss_pred             CCcccccceEEEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCCEEEEEcCcccccccccCCCCCC
Q 031004           99 ADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQWQ  167 (167)
Q Consensus        99 ~d~~~~~r~W~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD~VVVINA~kI~~~~a~~g~~W~  167 (167)
                      ..+.++.|.||+|||++|+|||||++||.+|+|||||+|||+.||||+|||+||++|    +|+|++|+
T Consensus        14 ~~~~afaRvW~vvDa~~q~lGrLAs~ia~~L~GkhKPiYhP~~DcGD~VVV~N~~~I----a~sG~K~~   78 (165)
T KOG3203|consen   14 NQWLAFARVWHVVDAKQQPLGRLASQIATTLQGKHKPIYHPSTDCGDHVVVTNCKKI----AFSGKKWE   78 (165)
T ss_pred             hHHHHHhhhheeeccccCchHHHHHHHHHHHhhccCCccCCccCCCCEEEEecchhh----eeccchhh
Confidence            445668899999999999999999999999999999999999999999999999999    99999995

>PRK06394 rpl13p 50S ribosomal protein L13P; Reviewed

Probab=99.45  E-value=6.2e-14  Score=111.63  Aligned_cols=40  Identities=38%  Similarity=0.466  Sum_probs=36.4

Q ss_pred             eEEEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCCEEEEEcCcccccc
Q 031004          107 TWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSC  158 (167)
Q Consensus       107 ~W~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD~VVVINA~kI~~~  158 (167)
                      +-|||||+||+|||||++||++|+|            ||+||||||++|.-+
T Consensus         3 ~~~viDA~~~vlGRLAs~IA~~L~~------------Gd~VVViNa~kv~~t   42 (146)
T PRK06394          3 AMVVIDAEGQILGRLASYVAKRLLE------------GEEVVIVNAEKAVIT   42 (146)
T ss_pred             ccEEEECCCCchHHHHHHHHHHHhC------------CCEEEEEechheEec
Confidence            3579999999999999999999994            999999999999644

>PTZ00068 60S ribosomal protein L13a; Provisional

Probab=98.33  E-value=3.5e-07  Score=76.80  Aligned_cols=27  Identities=33%  Similarity=0.441  Sum_probs=24.8

Q ss_pred             eEEEEeCCCCchhhHHHHHHHHHhcCC
Q 031004          107 TWYVVDATDKILGRLASTIAIHIRGKN  133 (167)
Q Consensus       107 ~W~vIDA~gq~LGRLAS~IA~~L~GKh  133 (167)
                      +|+||||+|++||||||.||+.|+.-+
T Consensus         4 ~w~vIDA~g~vLGRLAS~VAk~Ll~Gd   30 (202)
T PTZ00068          4 KVIVIDCKGHLLGRLASVVAKELLLGQ   30 (202)
T ss_pred             ceEEEECCCCcHHHHHHHHHHHHhCCC
Confidence            799999999999999999999999433

>TIGR01077 L13_A_E ribosomal protein L13, archaeal/eukaryotic

Probab=97.87  E-value=7.9e-06  Score=65.11  Aligned_cols=22  Identities=45%  Similarity=0.684  Sum_probs=21.0

Q ss_pred             EEEeCCCCchhhHHHHHHHHHh
Q 031004          109 YVVDATDKILGRLASTIAIHIR  130 (167)
Q Consensus       109 ~vIDA~gq~LGRLAS~IA~~L~  130 (167)
                      +||||+||+|||||++||++|+
T Consensus         1 ivIDA~~~vlGRLAs~IA~~L~   22 (142)
T TIGR01077         1 TVIDGSGHILGRLASVVAKQLL   22 (142)
T ss_pred             CEEeCCCCchHHHHHHHHHHHh
Confidence            4899999999999999999998

This model represents ribosomal protein of L13 from the Archaea and from the eukaryotic cytosol. Bacterial and organellar forms are represented by TIGR01066.

>KOG3204 consensus 60S ribosomal protein L13a [Translation, ribosomal structure and biogenesis]

Probab=90.84  E-value=0.16  Score=43.32  Aligned_cols=30  Identities=27%  Similarity=0.355  Sum_probs=25.8

Q ss_pred             ceEEEEeCCCCchhhHHHHHHHHHhcCCCC
Q 031004          106 KTWYVVDATDKILGRLASTIAIHIRGKNLA  135 (167)
Q Consensus       106 r~W~vIDA~gq~LGRLAS~IA~~L~GKhKP  135 (167)
                      ..-.+||+.|+++||||+.+|+.|+..-|.
T Consensus         5 ~~~~vidg~~hllGrlAa~vaK~ll~g~kv   34 (197)
T KOG3204|consen    5 VKLVVIDGRGHLLGRLAAIVAKQLLLGRKV   34 (197)
T ss_pred             EEEeeccchhhhhhhHHHHHHHHHhcCCeE
Confidence            356799999999999999999999966544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	167
3bbo_L	250	Homology Model For The Spinach Chloroplast 50s Subu		1e-33
2j28_J	140	Model Of E. Coli Srp Bound To 70s Rncs Length = 140		4e-10
1p85_H	142	Real Space Refined Coordinates Of The 50s Subunit F		4e-10
1vsa_H	163	Crystal Structure Of A 70s Ribosome-Trna Complex Re		2e-07
2j01_N	140	Structure Of The Thermus Thermophilus 70s Ribosome		3e-07
3fin_N	139	T. Thermophilus 70s Ribosome In Complex With Mrna,		3e-07
3pyo_J	137	Crystal Structure Of A Complex Containing Domain 3		3e-07
3mrz_J	139	Recognition Of The Amber Stop Codon By Release Fact		3e-07
3tve_M	138	Crystal Structure Analysis Of Ribosomal Decoding. T		3e-07
1vsp_H	140	Interactions And Dynamics Of The Shine-Dalgarno Hel		3e-07
1nkw_H	174	Crystal Structure Of The Large Ribosomal Subunit Fr		3e-06
1pnu_H	143	Crystal Structure Of A Streptomycin Dependent Ribos		5e-06

>pdb|3BBO|L Chain L, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 250

Iteration: 1
 Score =  139 bits (349), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 63/80 (78%), Positives = 69/80 (86%)
Query: 71  VPDNQRWMFEQSEVNGPDIWNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIR 130
           VP +QRWMF   E  GPDIWN TWYPK+ADH  +DK WYVVDATD ILGR+ASTIAIHIR
Sbjct: 77  VPLDQRWMFTLEEATGPDIWNTTWYPKSADHVPTDKKWYVVDATDLILGRMASTIAIHIR 136
Query: 131 GKNLATYTPSVDMGAYVIVV 150
           GKNLA+YTPSVDMGA+VIVV
Sbjct: 137 GKNLASYTPSVDMGAFVIVV 156

>pdb|2J28|J Chain J, Model Of E. Coli Srp Bound To 70s Rncs Length = 140

Iteration: 1
 Score = 60.8 bits (146), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 27/45 (60%), Positives = 34/45 (75%)
Query: 106 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           + WYVVDAT K LGRLA+ +A  +RGK+ A YTP VD G Y+IV+
Sbjct: 13  RDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVL 57

>pdb|1P85|H Chain H, 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 = 142

Iteration: 1
 Score = 60.5 bits (145), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 27/45 (60%), Positives = 34/45 (75%)
Query: 106 KTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           + WYVVDAT K LGRLA+ +A  +RGK+ A YTP VD G Y+IV+
Sbjct: 13  RDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVL 57

>pdb|1VSA|H Chain H, 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 = 163

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 37/59 (62%), Gaps = 5/59 (8%)
Query: 92  NTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
            T+ PK  + R     W ++DA  K LGRLA+ IA  +RGK+   +TP+V MG +V+VV
Sbjct: 25  KTYVPKQVEPR-----WVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVV 78

>pdb|2J01|N Chain N, 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 = 140

Iteration: 1
 Score = 51.2 bits (121), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 37/59 (62%), Gaps = 5/59 (8%)
Query: 92  NTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
            T+ PK  + R     W ++DA  K LGRLA+ IA  +RGK+   +TP+V MG +V+VV
Sbjct: 2   KTYVPKQVEPR-----WVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVV 55

>pdb|3FIN|N Chain N, 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 = 139

Iteration: 1
 Score = 51.2 bits (121), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 37/59 (62%), Gaps = 5/59 (8%)
Query: 92  NTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
            T+ PK  + R     W ++DA  K LGRLA+ IA  +RGK+   +TP+V MG +V+VV
Sbjct: 2   KTYVPKQVEPR-----WVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVV 55

>pdb|3PYO|J Chain J, 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 = 137

Iteration: 1
 Score = 51.2 bits (121), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 37/59 (62%), Gaps = 5/59 (8%)
Query: 92  NTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
            T+ PK  + R     W ++DA  K LGRLA+ IA  +RGK+   +TP+V MG +V+VV
Sbjct: 1   KTYVPKQVEPR-----WVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVV 54

>pdb|3MRZ|J Chain J, Recognition Of The Amber Stop Codon By Release Factor Rf1. This Entry 3mrz Contains 50s Ribosomal Subunit. The 30s Ribosomal Subunit Can Be Found In Pdb Entry 3ms0. Molecule A In The Same Asymmetric Unit Is Deposited As 3mr8 (50s) And 3ms1 (30s). Length = 139

Iteration: 1
 Score = 51.2 bits (121), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 37/59 (62%), Gaps = 5/59 (8%)
Query: 92  NTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
            T+ PK  + R     W ++DA  K LGRLA+ IA  +RGK+   +TP+V MG +V+VV
Sbjct: 1   KTYVPKQVEPR-----WVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVV 54

>pdb|3TVE|M Chain M, 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 = 138

Iteration: 1
 Score = 51.2 bits (121), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 37/59 (62%), Gaps = 5/59 (8%)
Query: 92  NTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
            T+ PK  + R     W ++DA  K LGRLA+ IA  +RGK+   +TP+V MG +V+VV
Sbjct: 2   KTYVPKQVEPR-----WVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVV 55

>pdb|1VSP|H Chain H, Interactions And Dynamics Of The Shine-Dalgarno Helix In The 70s Ribosome. This File, 1vsp, Contains The 50s Ribosome Subunit. 30s Ribosome Subunit Is In The File 2qnh Length = 140

Iteration: 1
 Score = 51.2 bits (121), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 37/59 (62%), Gaps = 5/59 (8%)
Query: 92  NTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
            T+ PK  + R     W ++DA  K LGRLA+ IA  +RGK+   +TP+V MG +V+VV
Sbjct: 2   KTYVPKQVEPR-----WVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVV 55

>pdb|1NKW|H Chain H, Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Length = 174

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 37/59 (62%), Gaps = 5/59 (8%)
Query: 92  NTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
            T+ PK     + ++ W VVDA+   LGRLA+ IA  IRGK+   +TP++  G +V+V+
Sbjct: 30  KTYIPK-----NDEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVI 83

>pdb|1PNU|H Chain H, 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 = 143

Iteration: 1
 Score = 47.0 bits (110), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 37/59 (62%), Gaps = 5/59 (8%)
Query: 92  NTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
            T+ PK     + ++ W VVDA+   LGRLA+ IA  IRGK+   +TP++  G +V+V+
Sbjct: 2   KTYIPK-----NDEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVI 55

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	167
3bbo_L	250	Ribosomal protein L13; large ribosomal subunit, sp	8e-39
3r8s_J	142	50S ribosomal protein L13; protein biosynthesis, R	6e-26
3f1f_N	163	50S ribosomal protein L13; RF2, ribosome, terminat	2e-24
3v2d_N	140	50S ribosomal protein L13; ribosome associated inh	2e-24
2ftc_H	148	L13MT, MRP-L13, 39S ribosomal protein L13, mitocho	3e-24
2zjr_G	174	50S ribosomal protein L13; ribosome, large ribosom	2e-23
1vq8_J	145	50S ribosomal protein L13P; ribosome 50S, protein-	2e-11
2zkr_j	203	60S ribosomal protein L13A; protein-RNA complex, 6	4e-11
4a17_I	198	RPL13A, 60S ribosomal protein L13A; eukaryotic rib	2e-10
3izc_K	199	60S ribosomal protein RPL16 (L13P); eukaryotic rib	3e-10
3iz5_K	206	60S ribosomal protein L13A (L13P); eukaryotic ribo	4e-10
1j3a_A	142	50S ribosomal protein L13P; rRNA binding, ribosoma	2e-09
3jyw_M	178	60S ribosomal protein L16(A); eukaryotic ribosome,	3e-08

>3bbo_L Ribosomal protein L13; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1 Length = 250

 Score =  131 bits (331), Expect = 8e-39
 Identities = 74/156 (47%), Positives = 95/156 (60%), Gaps = 6/156 (3%)

Query: 1   MATLCTPTCVIFSSLQSSSSSSSFKTLNTG------TTISSSTTPFLGFSVASAKSTSPL 54
           MAT+   + + F S Q+  S        T        T++++       S +++   +  
Sbjct: 1   MATMACASSLTFPSAQTQKSFFGTNVKQTPVLSFPRPTVAAAVAVSARKSTSASTKCTEE 60

Query: 55  NTKRSFKVRCCQNLSLVPDNQRWMFEQSEVNGPDIWNNTWYPKAADHRHSDKTWYVVDAT 114
             +    V+    +  VP +QRWMF   E  GPDIWN TWYPK+ADH  +DK WYVVDAT
Sbjct: 61  WRQLKEAVKKEFAIPHVPLDQRWMFTLEEATGPDIWNTTWYPKSADHVPTDKKWYVVDAT 120

Query: 115 DKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           D ILGR+ASTIAIHIRGKNLA+YTPSVDMGA+VIVV
Sbjct: 121 DLILGRMASTIAIHIRGKNLASYTPSVDMGAFVIVV 156

>3r8s_J 50S ribosomal protein L13; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_H 1p86_H 1vs8_J 1vs6_J 2aw4_J 2awb_J 2gya_H 2gyc_H 1vt2_J 2i2v_J 2i2t_J* 2qao_J* 2qba_J* 2qbc_J* 2qbe_J 2qbg_J 2qbi_J* 2qbk_J* 2qov_J 2qox_J ... Length = 142

 Score = 95.3 bits (238), Expect = 6e-26
 Identities = 29/58 (50%), Positives = 37/58 (63%), Gaps = 3/58 (5%)

Query: 93  TWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           T+  K        + WYVVDAT K LGRLA+ +A  +RGK+ A YTP VD G Y+IV+
Sbjct: 3   TFTAKPETV---KRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVL 57

>3f1f_N 50S ribosomal protein L13; RF2, ribosome, termination, tRNA; 3.00A {Thermus thermophilus} PDB: 1vsa_H 3d5d_N 3d5b_N 3f1h_N Length = 163

 Score = 92.3 bits (230), Expect = 2e-24
 Identities = 25/63 (39%), Positives = 36/63 (57%), Gaps = 5/63 (7%)

Query: 88  DIWNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYV 147
                T+ PK  +       W ++DA  K LGRLA+ IA  +RGK+   +TP+V MG +V
Sbjct: 21  RALVKTYVPKQVE-----PRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFV 75

Query: 148 IVV 150
           +VV
Sbjct: 76  VVV 78

>3v2d_N 50S ribosomal protein L13; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2hgq_M 2hgj_M 2hgu_M 2j03_N 2jl6_N 2jl8_N 2v47_N 2v49_N 2wdi_N 2wdj_N 2wdl_N 2wdn_N 2wh2_N 2wh4_N 2wrj_N 2wrl_N 2wro_N 2wrr_N 2x9s_N 2x9u_N ... Length = 140

 Score = 91.4 bits (228), Expect = 2e-24
 Identities = 25/58 (43%), Positives = 36/58 (62%), Gaps = 5/58 (8%)

Query: 93  TWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           T+ PK  +       W ++DA  K LGRLA+ IA  +RGK+   +TP+V MG +V+VV
Sbjct: 3   TYVPKQVE-----PRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVV 55

>2ftc_H L13MT, MRP-L13, 39S ribosomal protein L13, mitochondrial; mitochondrial ribosome, large ribosomal subunit, ribosomal R ribosome; 12.10A {Bos taurus} Length = 148

 Score = 91.1 bits (227), Expect = 3e-24
 Identities = 12/58 (20%), Positives = 28/58 (48%)

Query: 93  TWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           ++           + WY++D   +  G+LA+  +I ++G +   Y    D G +V+++
Sbjct: 3   SFSRAPQQWATFARIWYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIM 60

>2zjr_G 50S ribosomal protein L13; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: c.21.1.1 PDB: 1nwx_H* 1nwy_H* 1sm1_H* 1xbp_H* 2zjp_G* 2zjq_G 1nkw_H 3cf5_G* 3dll_G* 3pio_G* 3pip_G* 1pnu_H 1pny_H 1vor_K 1vou_K 1vow_K 1voy_K 1vp0_K Length = 174

 Score = 90.0 bits (224), Expect = 2e-23
 Identities = 21/46 (45%), Positives = 32/46 (69%)

Query: 105 DKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           ++ W VVDA+   LGRLA+ IA  IRGK+   +TP++  G +V+V+
Sbjct: 38  EQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVI 83

>1vq8_J 50S ribosomal protein L13P; 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.21.1.1 PDB: 1giy_M 1jj2_I 1k73_K* 1k8a_K* 1k9m_K* 1kc8_K* 1kd1_K* 1kqs_I* 1m1k_K* 1m90_K* 1ml5_m* 1n8r_K* 1nji_K* 1q7y_K* 1q81_K* 1q82_K* 1q86_K* 1qvf_I 1qvg_I 1s72_J* ... Length = 145

 Score = 57.6 bits (140), Expect = 2e-11
 Identities = 14/48 (29%), Positives = 18/48 (37%), Gaps = 12/48 (25%)

Query: 104 SDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVC 151
                 +VDA D I+GR+AS +A                 G  V VV 
Sbjct: 5   EFDADVIVDARDCIMGRVASQVAEQ------------ALDGETVAVVN 40

>2zkr_j 60S ribosomal protein L13A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 203

 Score = 57.7 bits (139), Expect = 4e-11
 Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 12/48 (25%)

Query: 104 SDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVC 151
           ++    V+D    +LGRLA+ +A  +             +G  V+VV 
Sbjct: 2   AEVQVLVLDGRGHLLGRLAAIVAKQVL------------LGRKVVVVR 37

>4a17_I RPL13A, 60S ribosomal protein L13A; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_I 4a1c_I 4a1e_I Length = 198

 Score = 55.7 bits (134), Expect = 2e-10
 Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 12/47 (25%)

Query: 105 DKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVC 151
                V+DA   +LGRLAS +A  +              G  ++VV 
Sbjct: 2   FDKLVVIDAKGHLLGRLASYVAKELL------------SGQRIVVVR 36

>1j3a_A 50S ribosomal protein L13P; rRNA binding, ribosomal assembly, ribosome; 1.60A {Pyrococcus horikoshii} SCOP: c.21.1.1 Length = 142

 Score = 52.2 bits (126), Expect = 2e-09
 Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 12/43 (27%)

Query: 109 YVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVC 151
            +++A   ILGRLAS +A  +              G  V++V 
Sbjct: 2   RIINADGLILGRLASRVAKMLLE------------GEEVVIVN 32

>3jyw_M 60S ribosomal protein L16(A); eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_M Length = 178

 Score = 49.8 bits (119), Expect = 3e-08
 Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 12/41 (29%)

Query: 110 VVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVV 150
           V+D    ++GRLAS +A  +              G  ++VV
Sbjct: 2   VIDGKGHLVGRLASVVAKQLL------------NGQKIVVV 30

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	167
3bbo_L	250	Ribosomal protein L13; large ribosomal subunit, sp	100.0
3r8s_J	142	50S ribosomal protein L13; protein biosynthesis, R	99.97
2ftc_H	148	L13MT, MRP-L13, 39S ribosomal protein L13, mitocho	99.97
3v2d_N	140	50S ribosomal protein L13; ribosome associated inh	99.97
2zjr_G	174	50S ribosomal protein L13; ribosome, large ribosom	99.97
3f1f_N	163	50S ribosomal protein L13; RF2, ribosome, terminat	99.97
1vq8_J	145	50S ribosomal protein L13P; ribosome 50S, protein-	99.72
1j3a_A	142	50S ribosomal protein L13P; rRNA binding, ribosoma	99.61
3iz5_K	206	60S ribosomal protein L13A (L13P); eukaryotic ribo	99.6
2zkr_j	203	60S ribosomal protein L13A; protein-RNA complex, 6	98.79
4a17_I	198	RPL13A, 60S ribosomal protein L13A; eukaryotic rib	98.45
4b6a_O	199	60S ribosomal protein L16-A; large ribosomal subun	98.29
3jyw_M	178	60S ribosomal protein L16(A); eukaryotic ribosome,	97.65

>3bbo_L Ribosomal protein L13; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1

Probab=100.00  E-value=1.3e-56  Score=380.02  Aligned_cols=154  Identities=51%  Similarity=0.809  Sum_probs=57.0

Q ss_pred             CccccCCceeeeccCCCCCCCCCccccccccccccccccceeecccccC--CCCccccccceEEEecccc----------
Q 031004            1 MATLCTPTCVIFSSLQSSSSSSSFKTLNTGTTISSSTTPFLGFSVASAK--STSPLNTKRSFKVRCCQNL----------   68 (167)
Q Consensus         1 m~~~~~~~~~~~~s~~~~~~~~~f~~~~~~~~~s~~~~~~~g~~~~~~~--~~~~~~~~~~~~V~C~~~~----------   68 (167)
                      ||++++++|++|||+|+  ++++|++++       +++||+||.++...  .+.+++.+++++|+|+++.          
T Consensus         1 ~~~~~~~~~~~~~~~~~--~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~   71 (250)
T 3bbo_L            1 MATMACASSLTFPSAQT--QKSFFGTNV-------KQTPVLSFPRPTVAAAVAVSARKSTSASTKCTEEWRQLKEAVKKE   71 (250)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CcceeeccceeccCCCC--CCccccccc-------ccCceeecccccccccccccccCCCcceEEeeeccchhhhhhccc
Confidence            89999999999999875  599999988       89999999886533  3345566789999999983          


Q ss_pred             ---ccccCCcchhhhhhhhcCCcccceeeccCCCCcccccceEEEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCC
Q 031004           69 ---SLVPDNQRWMFEQSEVNGPDIWNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGA  145 (167)
Q Consensus        69 ---~~Vp~d~R~m~~~~e~~gP~i~~kT~~~k~~d~~~~~r~W~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD  145 (167)
                         ++||+||||||++.|+.||||||+||++|+++..+++|+||||||+||+|||||++||++|+|||||+||||+||||
T Consensus        72 ~~~~~v~~~~~~~~~~~~~~g~d~~~kT~~~k~~~v~~~~r~W~VIDA~g~vLGRLAS~IAk~LrGKhKP~ytP~vD~GD  151 (250)
T 3bbo_L           72 FAIPHVPLDQRWMFTLEEATGPDIWNTTWYPKSADHVPTDKKWYVVDATDLILGRMASTIAIHIRGKNLASYTPSVDMGA  151 (250)
T ss_dssp             ----------------------------------------CCCCEECCSSCCSSTTHHHHTTTTTTTTTTCCCTTSCCSC
T ss_pred             cccccccccccccccchhhcCCCccceeecCChhhcccccceEEEEeCCCCchHHHHHHHHHHHccCCCCccCccccCCC
Confidence               78999999999999999999999999999999667799999999999999999999999999999999999999999


Q ss_pred             EEEEEcCcccccccccCCCCCC
Q 031004          146 YVIVVCGLHAYSCILFLPPQWQ  167 (167)
Q Consensus       146 ~VVVINA~kI~~~~a~~g~~W~  167 (167)
                      |||||||+||    .++|++|+
T Consensus       152 ~VVVINAeKI----~lTG~K~~  169 (250)
T 3bbo_L          152 FVIVVNADKV----AVSGKKRT  169 (250)
T ss_dssp             CCEESCCSSC----CCCSGGGG
T ss_pred             EEEEEecceE----EecCChhh
Confidence            9999999999    99999984

>3r8s_J 50S ribosomal protein L13; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_H 1p86_H 1vs8_J 1vs6_J 2aw4_J 2awb_J 2gya_H 2gyc_H 1vt2_J 2i2v_J 2i2t_J* 2qao_J* 2qba_J* 2qbc_J* 2qbe_J 2qbg_J 2qbi_J* 2qbk_J* 2qov_J 2qox_J ...

Probab=99.97  E-value=3.9e-33  Score=219.60  Aligned_cols=70  Identities=41%  Similarity=0.653  Sum_probs=67.8

Q ss_pred             ceeeccCCCCcccccceEEEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCCEEEEEcCcccccccccCCCCCC
Q 031004           91 NNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQWQ  167 (167)
Q Consensus        91 ~kT~~~k~~d~~~~~r~W~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD~VVVINA~kI~~~~a~~g~~W~  167 (167)
                      |+||++++++   ++|+||||||+||+|||||++||++|+|||||+|||++||||+||||||++|    .++|++|+
T Consensus         1 mkt~~~~~~~---~~r~W~viDA~g~~LGRLAs~iAk~L~GKhKp~ytP~~d~Gd~VVViNaeki----~~tG~k~~   70 (142)
T 3r8s_J            1 MKTFTAKPET---VKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKV----AVTGNKRT   70 (142)
T ss_dssp             CCCCCCCTTT---CCCCEEEEECTTCBHHHHHHHHHHHHHTTTSTTCCTTSCCCCEEEEECGGGC----BCCTTHHH
T ss_pred             CCcccCChhh---ccCcEEEEeCCCCchHHHHHHHHHHHcCCCCCccCCCccCCCEEEEEeCccc----CccCchhh
Confidence            6899999999   9999999999999999999999999999999999999999999999999999    99999874

>2ftc_H L13MT, MRP-L13, 39S ribosomal protein L13, mitochondrial; mitochondrial ribosome, large ribosomal subunit, ribosomal R ribosome; 12.10A {Bos taurus}

Probab=99.97  E-value=3.8e-33  Score=220.76  Aligned_cols=73  Identities=21%  Similarity=0.436  Sum_probs=69.8

Q ss_pred             ceeeccCCCCcccccceEEEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCCEEEEEcCcccccccccCCCCCC
Q 031004           91 NNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQWQ  167 (167)
Q Consensus        91 ~kT~~~k~~d~~~~~r~W~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD~VVVINA~kI~~~~a~~g~~W~  167 (167)
                      |.||+++++++.+++|+||||||+||+|||||++||++|+|||||+|||++||||+||||||++|    .++|++|+
T Consensus         1 m~t~~~k~~~~~~~~r~w~viDA~g~~LGRLAs~iA~~L~GKhKp~ytP~~D~Gd~VVViNaeki----~~tG~k~~   73 (148)
T 2ftc_H            1 MSSFSRAPQQWATFARIWYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIMNTRHI----AFSGNKWE   73 (148)
T ss_pred             CcccccchhhhhcccCcEEEEeCCCCchHHHHHHHHHHHhccCCCCcCccccCCCEEEEEeceee----EeccchHh
Confidence            46899999997788999999999999999999999999999999999999999999999999999    99999985

>3v2d_N 50S ribosomal protein L13; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2hgq_M 2hgj_M 2hgu_M 2j03_N 2jl6_N 2jl8_N 2v47_N 2v49_N 2wdi_N 2wdj_N 2wdl_N 2wdn_N 2wh2_N 2wh4_N 2wrj_N 2wrl_N 2wro_N 2wrr_N 2x9s_N 2x9u_N ...

Probab=99.97  E-value=1.8e-32  Score=215.39  Aligned_cols=68  Identities=37%  Similarity=0.622  Sum_probs=65.3

Q ss_pred             ceeeccCCCCcccccceEEEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCCEEEEEcCcccccccccCCCCCC
Q 031004           91 NNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQWQ  167 (167)
Q Consensus        91 ~kT~~~k~~d~~~~~r~W~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD~VVVINA~kI~~~~a~~g~~W~  167 (167)
                      |+||++|  +   ++|+||||||+||+|||||++||++|+|||||+|||++||||+|||||||+|    .++|++|+
T Consensus         1 m~t~~~~--~---~~r~w~viDA~~~~LGRLAs~iAk~L~GKhKp~ytP~~d~Gd~VVViNaeki----~~tG~k~~   68 (140)
T 3v2d_N            1 MKTYVPK--Q---VEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKI----RVTGKKLE   68 (140)
T ss_dssp             CCCCCCC--C---CCCCEEEEECSSSBTTHHHHHHHHHHHTTTSTTCCTTSCCCCEEEEECGGGC----BCCTTHHH
T ss_pred             Ccccccc--c---ccceEEEEeCCCCchHHHHHHHHHHHcCCCCCccCCCccCCCEEEEEeCcce----EccCchhh
Confidence            6899998  6   8999999999999999999999999999999999999999999999999999    99999874

>2zjr_G 50S ribosomal protein L13; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: c.21.1.1 PDB: 1nwx_H* 1nwy_H* 1sm1_H* 1xbp_H* 2zjp_G* 2zjq_G 1nkw_H 3cf5_G* 3dll_G* 3pio_G* 3pip_G* 1pnu_H 1pny_H 1vor_K 1vou_K 1vow_K 1voy_K 1vp0_K

Probab=99.97  E-value=9.8e-32  Score=217.93  Aligned_cols=74  Identities=32%  Similarity=0.515  Sum_probs=65.0

Q ss_pred             cCCcccceeeccCCCCcccccceEEEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCCEEEEEcCcccccccccCCC
Q 031004           85 NGPDIWNNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPP  164 (167)
Q Consensus        85 ~gP~i~~kT~~~k~~d~~~~~r~W~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD~VVVINA~kI~~~~a~~g~  164 (167)
                      ++-+.+|+||++|+     ++|+||||||+||+|||||++||++|+|||||+||||+||||+||||||++|    +++|+
T Consensus        23 ~~~~~~m~T~~~k~-----~~r~W~vIDA~g~~LGRLAs~IAk~L~GKhKP~ytP~~D~GD~VVVINAeki----~lTG~   93 (174)
T 2zjr_G           23 LLRSFKVKTYIPKN-----DEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQV----ALTGK   93 (174)
T ss_dssp             -------CCCCCCC-----SCCCEEEEECTTSBHHHHHHHHHHHHHCSSCSSCCSSSCCCCEEEEECCTTC----BCSSC
T ss_pred             ccccceeeeeccCc-----ccccEEEEeCCCCchHHHHHHHHHHHhccCCCccCccccCCCEEEEEeCeee----Eeccc
Confidence            44455789999987     6899999999999999999999999999999999999999999999999999    99999


Q ss_pred             CCC
Q 031004          165 QWQ  167 (167)
Q Consensus       165 ~W~  167 (167)
                      +|+
T Consensus        94 K~~   96 (174)
T 2zjr_G           94 KLD   96 (174)
T ss_dssp             SSS
T ss_pred             hhh
Confidence            995

>3f1f_N 50S ribosomal protein L13; RF2, ribosome, termination, tRNA; 3.00A {Thermus thermophilus} PDB: 1vsa_H 3d5d_N 3d5b_N 3f1h_N

Probab=99.97  E-value=9.1e-32  Score=216.38  Aligned_cols=68  Identities=37%  Similarity=0.622  Sum_probs=64.8

Q ss_pred             ceeeccCCCCcccccceEEEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCCEEEEEcCcccccccccCCCCCC
Q 031004           91 NNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQWQ  167 (167)
Q Consensus        91 ~kT~~~k~~d~~~~~r~W~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD~VVVINA~kI~~~~a~~g~~W~  167 (167)
                      |+||++|  +   ++|+||||||+|++|||||++||++|+|||||+||||+||||+|||||||+|    .++|++|+
T Consensus        24 mkt~~~k--~---~~r~W~VIDA~g~~LGRLAs~VAk~L~GKhKP~ytP~~D~GD~VVVINaekI----~iTG~K~~   91 (163)
T 3f1f_N           24 VKTYVPK--Q---VEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKI----RVTGKKLE   91 (163)
T ss_dssp             -CCCCCC--C---CCCCBCBBCCTTCBHHHHHHHHHHHHSCTTSTTCCTTTCCCCBCEECCGGGC----BCSTTHHH
T ss_pred             Ccccccc--c---ccCcEEEEeCCCCchHHHHHHHHHHHhcCCCCccCCcccCCCEEEEEeCccc----ccCCchhh
Confidence            7899998  6   8999999999999999999999999999999999999999999999999999    99999874

>1vq8_J 50S ribosomal protein L13P; 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.21.1.1 PDB: 1giy_M 1jj2_I 1k73_K* 1k8a_K* 1k9m_K* 1kc8_K* 1kd1_K* 1kqs_I* 1m1k_K* 1m90_K* 1ml5_m* 1n8r_K* 1nji_K* 1q7y_K* 1q81_K* 1q82_K* 1q86_K* 1qvf_I 1qvg_I 1s72_J* ...

Probab=99.72  E-value=9.5e-19  Score=137.94  Aligned_cols=48  Identities=33%  Similarity=0.282  Sum_probs=44.9

Q ss_pred             ccceEEEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCCEEEEEcCcccccccccCCCCCC
Q 031004          104 SDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQWQ  167 (167)
Q Consensus       104 ~~r~W~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD~VVVINA~kI~~~~a~~g~~W~  167 (167)
                      ..++||||||+||+|||||++||++|+            |||+|||||||||    .++|++|+
T Consensus         5 ~~~~w~viDA~g~~LGRLAs~vAk~L~------------~Gd~VVViNaeki----~iTG~k~~   52 (145)
T 1vq8_J            5 EFDADVIVDARDCIMGRVASQVAEQAL------------DGETVAVVNAERA----VITGREEQ   52 (145)
T ss_dssp             CCCCSEEEECTTBBHHHHHHHHHHHHH------------TTCCEEEECGGGC----EEESCHHH
T ss_pred             ccccEEEEeCCCCchHHHHHHHHHHHh------------cCCEEEEEeCEee----Eecchhhh
Confidence            456899999999999999999999999            9999999999999    99999873

>1j3a_A 50S ribosomal protein L13P; rRNA binding, ribosomal assembly, ribosome; 1.60A {Pyrococcus horikoshii} SCOP: c.21.1.1

Probab=99.61  E-value=2.6e-16  Score=123.31  Aligned_cols=39  Identities=33%  Similarity=0.401  Sum_probs=37.1

Q ss_pred             EEEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCCEEEEEcCcccccc
Q 031004          108 WYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSC  158 (167)
Q Consensus       108 W~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD~VVVINA~kI~~~  158 (167)
                      ||||||+||+|||||++||++|+            |||+|||||||||.-+
T Consensus         1 W~viDA~g~~LGRLAs~vAk~L~------------~Gd~VVViNaeki~iT   39 (142)
T 1j3a_A            1 MRIINADGLILGRLASRVAKMLL------------EGEEVVIVNAEKAVIT   39 (142)
T ss_dssp             CEEEECTTBBHHHHHHHHHHHHH------------TTCCEEEECGGGCEEE
T ss_pred             CEEEeCCCCchHHHHHHHHHHHh------------cCCEEEEEeCeeeEec
Confidence            99999999999999999999999            9999999999998643

>2zkr_j 60S ribosomal protein L13A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}

Probab=98.79  E-value=1.7e-09  Score=89.36  Aligned_cols=30  Identities=30%  Similarity=0.529  Sum_probs=24.2

Q ss_pred             ccceEEEEeCCCCchhhHHHHHHH-HHhcCC
Q 031004          104 SDKTWYVVDATDKILGRLASTIAI-HIRGKN  133 (167)
Q Consensus       104 ~~r~W~vIDA~gq~LGRLAS~IA~-~L~GKh  133 (167)
                      .+|+||||||+|++|||||+.||+ +|+|+|
T Consensus         2 ~~r~w~VIDA~g~~LGRLAS~VAk~lL~G~~   32 (203)
T 2zkr_j            2 AEVQVLVLDGRGHLLGRLAAIVAKQVLLGRK   32 (203)
T ss_dssp             -----CEEECTTBBHHHHHHHHHHHHHHTCC
T ss_pred             CCccEEEEeCCCCchHHHHHHHHHHHhCCCe
Confidence            467999999999999999999999 999975

>4a17_I RPL13A, 60S ribosomal protein L13A; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_I 4a1c_I 4a1e_I

Probab=98.45  E-value=6.6e-08  Score=79.57  Aligned_cols=25  Identities=40%  Similarity=0.566  Sum_probs=23.9

Q ss_pred             ceEEEEeCCCCchhhHHHHHHHHHh
Q 031004          106 KTWYVVDATDKILGRLASTIAIHIR  130 (167)
Q Consensus       106 r~W~vIDA~gq~LGRLAS~IA~~L~  130 (167)
                      ++||||||+|++|||||++||++|+
T Consensus         3 ~~w~VIDA~g~~LGRLAs~VAk~L~   27 (198)
T 4a17_I            3 DKLVVIDAKGHLLGRLASYVAKELL   27 (198)
T ss_dssp             SSCEEEECTTBBHHHHHHHHHHHHH
T ss_pred             ccEEEEeCCCCchHHHHHHHHHHHh
Confidence            5899999999999999999999887

>4b6a_O 60S ribosomal protein L16-A; large ribosomal subunit, ribosome biogenesis, ribosome matur factor, ribosome; 8.10A {Saccharomyces cerevisiae} PDB: 3izc_K 3izs_K 3o58_P 3o5h_P 3u5e_O 3u5i_O 1s1i_M

Probab=98.29  E-value=3.3e-07  Score=75.51  Aligned_cols=31  Identities=42%  Similarity=0.536  Sum_probs=27.1

Q ss_pred             cceEEEEeCCCCchhhHHHHHHHHHhcCCCC
Q 031004          105 DKTWYVVDATDKILGRLASTIAIHIRGKNLA  135 (167)
Q Consensus       105 ~r~W~vIDA~gq~LGRLAS~IA~~L~GKhKP  135 (167)
                      .+.|+||||+|++|||||+.||+.|++-.+.
T Consensus         3 ~~~~vVIDA~g~vLGRLAS~VAk~L~~Gd~V   33 (199)
T 4b6a_O            3 SQPVVVIDAKDHLLGRLASTIAKQLLNGQKI   33 (199)
T ss_dssp             CCSEEEEECTTBBHHHHHHHHHHHHHTTCEE
T ss_pred             CCCEEEEECCCCchHHHHHHHHHHhcCCCEE
Confidence            3589999999999999999999999975543

>3jyw_M 60S ribosomal protein L16(A); eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus}

Probab=97.65  E-value=1.4e-05  Score=64.75  Aligned_cols=22  Identities=36%  Similarity=0.623  Sum_probs=21.3

Q ss_pred             EEEeCCCCchhhHHHHHHHHHh
Q 031004          109 YVVDATDKILGRLASTIAIHIR  130 (167)
Q Consensus       109 ~vIDA~gq~LGRLAS~IA~~L~  130 (167)
                      +||||+||+|||||++||++|+
T Consensus         1 ~VIDA~g~~LGRLAs~VAk~L~   22 (178)
T 3jyw_M            1 VVIDGKGHLVGRLASVVAKQLL   22 (178)
T ss_dssp             CCCCCCSSCSHHHHHHHHHHHT
T ss_pred             CEEcCCCCchHHHHHHHHHHHh
Confidence            5899999999999999999999

---

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	167
d2zjrg1	142	c.21.1.1 (G:30-171) Ribosomal protein L13 {Deinoco	2e-17
d2gych1	140	c.21.1.1 (H:1-140) Ribosomal protein L13 {Escheric	1e-16
d2j01n1	139	c.21.1.1 (N:1-139) Ribosomal protein L13 {Thermus	3e-16
d1vqoj1	142	c.21.1.1 (J:4-145) Ribosomal protein L13 {Archaeon	1e-09
d1j3aa_	142	c.21.1.1 (A:) Ribosomal protein L13 {Archaeon Pyro	2e-07

>d2zjrg1 c.21.1.1 (G:30-171) Ribosomal protein L13 {Deinococcus radiodurans [TaxId: 1299]} Length = 142

class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L13
superfamily: Ribosomal protein L13
family: Ribosomal protein L13
domain: Ribosomal protein L13
species: Deinococcus radiodurans [TaxId: 1299]

 Score = 72.3 bits (177), Expect = 2e-17
 Identities = 26/68 (38%), Positives = 39/68 (57%), Gaps = 8/68 (11%)

Query: 93  TWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCG 152
           T+ PK       ++ W VVDA+   LGRLA+ IA  IRGK+   +TP++  G +V+V+  
Sbjct: 2   TYIPKN-----DEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVI-- 54

Query: 153 LHAYSCIL 160
            +A    L
Sbjct: 55  -NAAQVAL 61

>d2gych1 c.21.1.1 (H:1-140) Ribosomal protein L13 {Escherichia coli [TaxId: 562]} Length = 140

class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L13
superfamily: Ribosomal protein L13
family: Ribosomal protein L13
domain: Ribosomal protein L13
species: Escherichia coli [TaxId: 562]

 Score = 70.0 bits (171), Expect = 1e-16
 Identities = 29/60 (48%), Positives = 37/60 (61%), Gaps = 3/60 (5%)

Query: 93  TWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCG 152
           T+  K        + WYVVDAT K LGRLA+ +A  +RGK+ A YTP VD G Y+IV+  
Sbjct: 3   TFTAKPET---VKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNA 59

>d2j01n1 c.21.1.1 (N:1-139) Ribosomal protein L13 {Thermus thermophilus [TaxId: 274]} Length = 139

class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L13
superfamily: Ribosomal protein L13
family: Ribosomal protein L13
domain: Ribosomal protein L13
species: Thermus thermophilus [TaxId: 274]

 Score = 68.9 bits (168), Expect = 3e-16
 Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 5/60 (8%)

Query: 93  TWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCG 152
           T+ PK  +       W ++DA  K LGRLA+ IA  +RGK+   +TP+V MG +V+VV  
Sbjct: 3   TYVPKQVE-----PRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNA 57

>d1vqoj1 c.21.1.1 (J:4-145) Ribosomal protein L13 {Archaeon Haloarcula marismortui [TaxId: 2238]} Length = 142

class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L13
superfamily: Ribosomal protein L13
family: Ribosomal protein L13
domain: Ribosomal protein L13
species: Archaeon Haloarcula marismortui [TaxId: 2238]

 Score = 51.4 bits (123), Expect = 1e-09
 Identities = 15/55 (27%), Positives = 19/55 (34%), Gaps = 12/55 (21%)

Query: 104 SDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSC 158
                 +VDA D I+GR+AS +A                 G  V VV    A   
Sbjct: 2   EFDADVIVDARDCIMGRVASQVAEQ------------ALDGETVAVVNAERAVIT 44

>d1j3aa_ c.21.1.1 (A:) Ribosomal protein L13 {Archaeon Pyrococcus horikoshii [TaxId: 53953]} Length = 142

class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L13
superfamily: Ribosomal protein L13
family: Ribosomal protein L13
domain: Ribosomal protein L13
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

 Score = 45.8 bits (108), Expect = 2e-07
 Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 12/47 (25%)

Query: 110 VVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAY 156
           +++A   ILGRLAS +A  +              G  V++V    A 
Sbjct: 3   IINADGLILGRLASRVAKML------------LEGEEVVIVNAEKAV 37

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	167
d2j01n1	139	Ribosomal protein L13 {Thermus thermophilus [TaxId	99.97
d2gych1	140	Ribosomal protein L13 {Escherichia coli [TaxId: 56	99.96
d2zjrg1	142	Ribosomal protein L13 {Deinococcus radiodurans [Ta	99.96
d1vqoj1	142	Ribosomal protein L13 {Archaeon Haloarcula marismo	99.59
d1j3aa_	142	Ribosomal protein L13 {Archaeon Pyrococcus horikos	99.4

>d2j01n1 c.21.1.1 (N:1-139) Ribosomal protein L13 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L13
superfamily: Ribosomal protein L13
family: Ribosomal protein L13
domain: Ribosomal protein L13
species: Thermus thermophilus [TaxId: 274]

Probab=99.97  E-value=1.1e-31  Score=207.72  Aligned_cols=68  Identities=37%  Similarity=0.622  Sum_probs=65.0

Q ss_pred             ceeeccCCCCcccccceEEEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCCEEEEEcCcccccccccCCCCCC
Q 031004           91 NNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQWQ  167 (167)
Q Consensus        91 ~kT~~~k~~d~~~~~r~W~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD~VVVINA~kI~~~~a~~g~~W~  167 (167)
                      |+||+|+  +   .+|+||||||+||+|||||++||++|+|||||+|+|++||||+||||||++|    +++|++|+
T Consensus         1 mkt~~p~--~---~~r~W~viDA~~~~lGRLAs~iA~~L~GK~kp~y~p~~d~Gd~VvViNa~ki----~~tG~k~~   68 (139)
T d2j01n1           1 MKTYVPK--Q---VEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKI----RVTGKKLE   68 (139)
T ss_dssp             CCCCCCC--C---CCCCCCEECCTTSBTTHHHHHHHHHHTTSSSSSCCTTTCCCCCCEECSCSCC----BCSSCCSS
T ss_pred             CCccCcc--c---ccceEEEEeCCCCchHHHHHHHHHHHhccchheeeeccCCCceEEEechhHe----eeeccccc
Confidence            7899986  4   7899999999999999999999999999999999999999999999999999    99999985

>d2gych1 c.21.1.1 (H:1-140) Ribosomal protein L13 {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L13
superfamily: Ribosomal protein L13
family: Ribosomal protein L13
domain: Ribosomal protein L13
species: Escherichia coli [TaxId: 562]

Probab=99.96  E-value=1e-32  Score=214.24  Aligned_cols=70  Identities=41%  Similarity=0.653  Sum_probs=68.3

Q ss_pred             ceeeccCCCCcccccceEEEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCCEEEEEcCcccccccccCCCCCC
Q 031004           91 NNTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQWQ  167 (167)
Q Consensus        91 ~kT~~~k~~d~~~~~r~W~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD~VVVINA~kI~~~~a~~g~~W~  167 (167)
                      |+||++++++   ++|+||||||+||+|||||++||++|+|||||+|+|++||||+||||||++|    .|+|++|+
T Consensus         1 Mkt~~~k~~~---~~r~W~viDA~~~~lGRlAs~iA~~L~GK~kp~y~p~~d~Gd~VvViNaeki----~~tG~K~~   70 (140)
T d2gych1           1 MKTFTAKPET---VKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKV----AVTGNKRT   70 (140)
T ss_dssp             CCCCCSSSCC---TTCCCCCCCCSSSCSHHHHSSSSSSSTTCSSSCCCSSSCCCCCCCCSCSSSC----CCCSSCST
T ss_pred             CCcccCChhH---hCccEEEEeCCCCchHHHHHHHHHHHHhccCCccccccCCCcEEEEEechhh----cccCchhh
Confidence            7899999998   9999999999999999999999999999999999999999999999999999    99999985

>d2zjrg1 c.21.1.1 (G:30-171) Ribosomal protein L13 {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L13
superfamily: Ribosomal protein L13
family: Ribosomal protein L13
domain: Ribosomal protein L13
species: Deinococcus radiodurans [TaxId: 1299]

Probab=99.96  E-value=5.7e-30  Score=198.92  Aligned_cols=67  Identities=36%  Similarity=0.631  Sum_probs=63.4

Q ss_pred             eeeccCCCCcccccceEEEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCCEEEEEcCcccccccccCCCCCC
Q 031004           92 NTWYPKAADHRHSDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQWQ  167 (167)
Q Consensus        92 kT~~~k~~d~~~~~r~W~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD~VVVINA~kI~~~~a~~g~~W~  167 (167)
                      |||+|++     .+|+||||||+||+|||||++||++|+|||||+|+|++|+||+||||||++|    .++|++|+
T Consensus         1 kt~~~k~-----~~r~W~viDA~~~~lGRlAs~iAk~L~GK~kp~y~p~~d~Gd~ViViNa~ki----~~tG~K~~   67 (142)
T d2zjrg1           1 KTYIPKN-----DEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQV----ALTGKKLD   67 (142)
T ss_dssp             CCCCCCC-----SCCCEEEEECTTSBHHHHHHHHHHHHHCSSCSSCCSSSCCCCEEEEECCTTC----BCSSCSSS
T ss_pred             CccCCCC-----CCccEEEEECCCCchHHHHHHHHHHHhcCcccceeecccCCCEEEEcCCcee----EEcCcchh
Confidence            6888874     4699999999999999999999999999999999999999999999999999    99999995

>d1vqoj1 c.21.1.1 (J:4-145) Ribosomal protein L13 {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L13
superfamily: Ribosomal protein L13
family: Ribosomal protein L13
domain: Ribosomal protein L13
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=99.59  E-value=8.9e-17  Score=124.48  Aligned_cols=46  Identities=35%  Similarity=0.316  Sum_probs=42.7

Q ss_pred             ccceEEEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCCEEEEEcCcccccccccCCCCC
Q 031004          104 SDKTWYVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYSCILFLPPQW  166 (167)
Q Consensus       104 ~~r~W~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD~VVVINA~kI~~~~a~~g~~W  166 (167)
                      ++ +|+||||+||+|||||++||+.|+            +||+||||||++|    .++|++|
T Consensus         3 ~~-k~ivIDA~~~~lGRLAs~vAk~l~------------~Gd~ViVvNaeki----~itG~k~   48 (142)
T d1vqoj1           3 FD-ADVIVDARDCIMGRVASQVAEQAL------------DGETVAVVNAERA----VITGREE   48 (142)
T ss_dssp             CC-CSEEEECTTBBHHHHHHHHHHHHH------------TTCCEEEECGGGC----EEESCHH
T ss_pred             cc-ceEEEECCCCchHHHHHHHHHHhc------------CCCEEEEEEChhh----cccCcch
Confidence            44 789999999999999999999997            7999999999999    9999876

>d1j3aa_ c.21.1.1 (A:) Ribosomal protein L13 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L13
superfamily: Ribosomal protein L13
family: Ribosomal protein L13
domain: Ribosomal protein L13
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=99.40  E-value=5.3e-14  Score=108.26  Aligned_cols=37  Identities=35%  Similarity=0.436  Sum_probs=34.2

Q ss_pred             EEEeCCCCchhhHHHHHHHHHhcCCCCccCCCCCCCCEEEEEcCccccc
Q 031004          109 YVVDATDKILGRLASTIAIHIRGKNLATYTPSVDMGAYVIVVCGLHAYS  157 (167)
Q Consensus       109 ~vIDA~gq~LGRLAS~IA~~L~GKhKP~YtP~~D~GD~VVVINA~kI~~  157 (167)
                      -||||+|++||||||+||++|+            +||+||||||++|.=
T Consensus         2 ~vIDA~g~~lGRLAs~vAk~L~------------~Gd~ViVvNaeki~~   38 (142)
T d1j3aa_           2 RIINADGLILGRLASRVAKMLL------------EGEEVVIVNAEKAVI   38 (142)
T ss_dssp             EEEECTTBBHHHHHHHHHHHHH------------TTCCEEEECGGGCEE
T ss_pred             EEEeCCCCchHHHHHHHHHHHh------------CCCeEEEEechhhee
Confidence            3899999999999999999995            899999999999853