Citrus Sinensis ID: 028816

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200---
Protein Sequence
MANQAATAFSGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQKKAEMQQSNKDMRKNRKKEVEAEVTA
Secondary Structure (PSIPRED)
cccccccccccccccEEccccccccccccEEEEEcccccHHHHHHHHHHHHccccccccccccccccEEEEEEcccEEEEcccccccEEEEccccccccccccHHHHHHcccHHHHHHHHHcccccccHHHHHHHcccccccccccccccccccEEccccHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccccHHccccccEEEEcccccccccEEEEEEcccccHHHHHHHHHHHHHcccccccccccccccEEEEEEccEEEEEccccccEEEEEcccccccccHccHHHHHHcccHHHHHHHHHccccccccHHHHHHHcEEEcccccccccccccEEcccHHHHHHHcHHHHHHHHHHHHHHHHHHHHcHHHHccccccccEccc
Coil and Loop (DISEMBL)
MANQAATAFSGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVvqgkdkptyapnrddgdmcIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMlprnklrddrdrklrifpgsehpfgdrplepyvmpprrvreLRPRVRRAMIREQKKAEMQQSNKDMRKNRKKEVEAEVTA
Flexible Loop (DISEMBL)
manqaatafsgnmkkALAGLRRINLEGLRWRVFDAKGQVLGRLasqvatvvqgkdkptyapnrddgdmCIVLNAKDICVTGRKLKNKVYYWHTGyighlkertlkeqmerdpTEAIRKAvlrmlprnklrddrdrklrifpgsehpfgdrplepyvmpprrvrelrprVRRAMireqkkaemqqsnkdmrknrkkeveaevta
Low Complexity Region (SEG)
MANQAATAFSGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNklrddrdrklrIFPGSEHPFGDRPLEPYvmpprrvrelrprvrrAMIREQKKAEMQQSNKDMRKNRKKEVEAEVTA
Disordered region (IsUnstruct)
**************KALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKE******************************************************************************************************
Disordered Region (DISOPRED)
************MKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPP********************************************
Disordered Region (DISEMBL)
*********SGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIRE***************************
Disordered Region (DISPRO)
******T*FSGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQKKAEM*********************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MANQAATAFSGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIxxxxxxxxxxxxxxxxxxxxxEVEAEVTA
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	203	2.2.26 [Sep-21-2011]
O67722	144	50S ribosomal protein L13	yes	no	0.620	0.875	0.515	8e-31
B2GJ23	147	50S ribosomal protein L13	yes	no	0.625	0.863	0.472	3e-30
B1MG81	147	50S ribosomal protein L13	yes	no	0.620	0.857	0.460	1e-29
C1A3Z5	149	50S ribosomal protein L13	yes	no	0.581	0.791	0.512	1e-29
P66065	147	50S ribosomal protein L13	yes	no	0.620	0.857	0.476	4e-29
A5U8B9	147	50S ribosomal protein L13	yes	no	0.620	0.857	0.476	4e-29
C1AHQ2	147	50S ribosomal protein L13	yes	no	0.620	0.857	0.476	4e-29
A1KPD0	147	50S ribosomal protein L13	yes	no	0.620	0.857	0.476	4e-29
P66066	147	50S ribosomal protein L13	yes	no	0.620	0.857	0.476	4e-29
B8G6P5	143	50S ribosomal protein L13	yes	no	0.625	0.888	0.472	6e-29

>sp|O67722|RL13_AQUAE 50S ribosomal protein L13 OS=Aquifex aeolicus (strain VF5) GN=rplM PE=3 SV=1

 Score =  133 bits (334), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 65/126 (51%), Positives = 87/126 (69%)

Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
           +W V DA G+ LGRLAS++A +++GK KP Y P+ D GD  IV+NA+ I VTG+KL+ K 
Sbjct: 14  KWWVVDATGKTLGRLASEIAKILRGKHKPYYQPDVDCGDFVIVINAEKIRVTGKKLEQKK 73

Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFG 148
           YYWH+ Y G LKERTLK  +E  P E IR AV RMLP+N+L     +KL+++ G EHP  
Sbjct: 74  YYWHSRYPGGLKERTLKWMLENKPEEVIRLAVKRMLPKNRLGHRMLKKLKVYRGPEHPHQ 133

Query: 149 DRPLEP 154
            +  +P
Sbjct: 134 AQKPQP 139

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.
Aquifex aeolicus (strain VF5) (taxid: 224324)

>sp|B2GJ23|RL13_KOCRD 50S ribosomal protein L13 OS=Kocuria rhizophila (strain ATCC 9341 / DSM 348 / NBRC 103217 / DC2201) GN=rplM PE=3 SV=1

 Score =  131 bits (329), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 60/127 (47%), Positives = 87/127 (68%)

Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
           +W V DA   VLGRLASQ AT+++GK KPT+AP+ D GD  I++NA+ + +TG KL+ K 
Sbjct: 14  QWHVIDATDVVLGRLASQTATLLRGKHKPTFAPHVDTGDFVIIINAEKVALTGSKLQKKR 73

Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFG 148
            Y H+GY G LK  +  E +E++PT A+ KA+  MLP+NKL   +  KL+++ G+EHP  
Sbjct: 74  AYRHSGYPGGLKSTSYAELLEKNPTRAVEKAIKGMLPKNKLAAQQLSKLKVYAGAEHPHQ 133

Query: 149 DRPLEPY 155
            +  +PY
Sbjct: 134 AQQPKPY 140

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.

Kocuria rhizophila (strain ATCC 9341 / DSM 348 / NBRC 103217 / DC2201) (taxid: 378753)

>sp|B1MG81|RL13_MYCA9 50S ribosomal protein L13 OS=Mycobacterium abscessus (strain ATCC 19977 / DSM 44196) GN=rplM PE=3 SV=1

 Score =  129 bits (325), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 58/126 (46%), Positives = 86/126 (68%)

Query: 30  WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
           W V DA   VLGRLA Q A +++GK KPT+AP+ D GD  I++NA+ I ++G KL NK  
Sbjct: 15  WYVIDATDVVLGRLAVQAANLLRGKHKPTFAPHVDGGDFVIIINAEKIALSGNKLTNKFA 74

Query: 90  YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGD 149
           Y H+G+ G L +R++ EQ+E+ PT  + KA++ MLP+NKL    +RKL+++ G+EHP   
Sbjct: 75  YRHSGFPGGLSKRSIGEQLEKFPTRTVEKAIVGMLPKNKLGRQIERKLKVYAGAEHPHAA 134

Query: 150 RPLEPY 155
           +   P+
Sbjct: 135 QQPIPF 140

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.

Mycobacterium abscessus (strain ATCC 19977 / DSM 44196) (taxid: 561007)

>sp|C1A3Z5|RL13_GEMAT 50S ribosomal protein L13 OS=Gemmatimonas aurantiaca (strain T-27 / DSM 14586 / JCM 11422 / NBRC 100505) GN=rplM PE=3 SV=1

 Score =  129 bits (325), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 61/119 (51%), Positives = 77/119 (64%), Gaps = 1/119 (0%)

Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
           RW V DA+G VLGRLAS+VA +++GK KP Y P+ D GD  IV+NA  + VTGRK + K 
Sbjct: 14  RWYVVDAEGMVLGRLASEVAKIIRGKHKPMYTPHMDTGDFVIVINASKVQVTGRKAEQKT 73

Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKL-RDDRDRKLRIFPGSEHP 146
           Y+ HTGY+GH K       + + P   I KAV  MLP+  L R    RKLR+F G+EHP
Sbjct: 74  YFSHTGYMGHEKHTPFASVLAKHPERVIEKAVYGMLPKTALGRQVLRRKLRVFAGAEHP 132

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.

Gemmatimonas aurantiaca (strain T-27 / DSM 14586 / JCM 11422 / NBRC 100505) (taxid: 379066)

>sp|P66065|RL13_MYCTU 50S ribosomal protein L13 OS=Mycobacterium tuberculosis GN=rplM PE=3 SV=1

 Score =  127 bits (320), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 60/126 (47%), Positives = 82/126 (65%)

Query: 30  WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
           W V DA   VLGRLA   A +++GK KPT+APN D GD  IV+NA  + ++G KL++K+ 
Sbjct: 15  WYVIDATDVVLGRLAVAAANLLRGKHKPTFAPNVDGGDFVIVINADKVAISGDKLQHKMV 74

Query: 90  YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGD 149
           Y H+GY G L +RT+ E M+R P   + KA+L MLP+N+L     RKLR++ G EHP   
Sbjct: 75  YRHSGYPGGLHKRTIGELMQRHPDRVVEKAILGMLPKNRLSRQIQRKLRVYAGPEHPHSA 134

Query: 150 RPLEPY 155
           +   PY
Sbjct: 135 QQPVPY 140

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.

Mycobacterium tuberculosis (taxid: 1773)

>sp|A5U8B9|RL13_MYCTA 50S ribosomal protein L13 OS=Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) GN=rplM PE=3 SV=1

 Score =  127 bits (320), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 60/126 (47%), Positives = 82/126 (65%)

Query: 30  WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
           W V DA   VLGRLA   A +++GK KPT+APN D GD  IV+NA  + ++G KL++K+ 
Sbjct: 15  WYVIDATDVVLGRLAVAAANLLRGKHKPTFAPNVDGGDFVIVINADKVAISGDKLQHKMV 74

Query: 90  YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGD 149
           Y H+GY G L +RT+ E M+R P   + KA+L MLP+N+L     RKLR++ G EHP   
Sbjct: 75  YRHSGYPGGLHKRTIGELMQRHPDRVVEKAILGMLPKNRLSRQIQRKLRVYAGPEHPHSA 134

Query: 150 RPLEPY 155
           +   PY
Sbjct: 135 QQPVPY 140

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.

Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (taxid: 419947)

>sp|C1AHQ2|RL13_MYCBT 50S ribosomal protein L13 OS=Mycobacterium bovis (strain BCG / Tokyo 172 / ATCC 35737 / TMC 1019) GN=rplM PE=3 SV=1

 Score =  127 bits (320), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 60/126 (47%), Positives = 82/126 (65%)

Query: 30  WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
           W V DA   VLGRLA   A +++GK KPT+APN D GD  IV+NA  + ++G KL++K+ 
Sbjct: 15  WYVIDATDVVLGRLAVAAANLLRGKHKPTFAPNVDGGDFVIVINADKVAISGDKLQHKMV 74

Query: 90  YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGD 149
           Y H+GY G L +RT+ E M+R P   + KA+L MLP+N+L     RKLR++ G EHP   
Sbjct: 75  YRHSGYPGGLHKRTIGELMQRHPDRVVEKAILGMLPKNRLSRQIQRKLRVYAGPEHPHSA 134

Query: 150 RPLEPY 155
           +   PY
Sbjct: 135 QQPVPY 140

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.

Mycobacterium bovis (strain BCG / Tokyo 172 / ATCC 35737 / TMC 1019) (taxid: 561275)

>sp|A1KPD0|RL13_MYCBP 50S ribosomal protein L13 OS=Mycobacterium bovis (strain BCG / Pasteur 1173P2) GN=rplM PE=3 SV=1

 Score =  127 bits (320), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 60/126 (47%), Positives = 82/126 (65%)

Query: 30  WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
           W V DA   VLGRLA   A +++GK KPT+APN D GD  IV+NA  + ++G KL++K+ 
Sbjct: 15  WYVIDATDVVLGRLAVAAANLLRGKHKPTFAPNVDGGDFVIVINADKVAISGDKLQHKMV 74

Query: 90  YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGD 149
           Y H+GY G L +RT+ E M+R P   + KA+L MLP+N+L     RKLR++ G EHP   
Sbjct: 75  YRHSGYPGGLHKRTIGELMQRHPDRVVEKAILGMLPKNRLSRQIQRKLRVYAGPEHPHSA 134

Query: 150 RPLEPY 155
           +   PY
Sbjct: 135 QQPVPY 140

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.

Mycobacterium bovis (strain BCG / Pasteur 1173P2) (taxid: 410289)

>sp|P66066|RL13_MYCBO 50S ribosomal protein L13 OS=Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97) GN=rplM PE=3 SV=1

 Score =  127 bits (320), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 60/126 (47%), Positives = 82/126 (65%)

Query: 30  WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
           W V DA   VLGRLA   A +++GK KPT+APN D GD  IV+NA  + ++G KL++K+ 
Sbjct: 15  WYVIDATDVVLGRLAVAAANLLRGKHKPTFAPNVDGGDFVIVINADKVAISGDKLQHKMV 74

Query: 90  YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGD 149
           Y H+GY G L +RT+ E M+R P   + KA+L MLP+N+L     RKLR++ G EHP   
Sbjct: 75  YRHSGYPGGLHKRTIGELMQRHPDRVVEKAILGMLPKNRLSRQIQRKLRVYAGPEHPHSA 134

Query: 150 RPLEPY 155
           +   PY
Sbjct: 135 QQPVPY 140

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.

Mycobacterium bovis (taxid: 1765)

>sp|B8G6P5|RL13_CHLAD 50S ribosomal protein L13 OS=Chloroflexus aggregans (strain MD-66 / DSM 9485) GN=rplM PE=3 SV=1

 Score =  127 bits (319), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 60/127 (47%), Positives = 85/127 (66%)

Query: 30  WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
           W V DA G+VLGRLA+Q++T+++GK KPT+ P+ D GD  IV+NA+ I +TGRK + K+Y
Sbjct: 15  WYVIDASGKVLGRLATQISTLLRGKHKPTFTPSIDGGDFVIVVNAEKIVLTGRKPEQKIY 74

Query: 90  YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGD 149
           Y H+GY G LKE   K  + + P   +R AV RMLP+N++      KLRI+ G  HP   
Sbjct: 75  YRHSGYPGGLKEIPYKMMLAKHPERILRLAVKRMLPKNRMGRRLLSKLRIYAGPNHPHAA 134

Query: 150 RPLEPYV 156
           +  +PY+
Sbjct: 135 QQPKPYI 141

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.

Chloroflexus aggregans (strain MD-66 / DSM 9485) (taxid: 326427)

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	203
224141259	205	predicted protein [Populus trichocarpa]	0.995	0.985	0.818	4e-94
224060221	205	predicted protein [Populus trichocarpa]	0.995	0.985	0.784	5e-91
118487043	205	unknown [Populus trichocarpa]	0.995	0.985	0.779	2e-90
449487903	204	PREDICTED: 50S ribosomal protein L13-lik	1.0	0.995	0.799	2e-90
255536973	202	50S ribosomal protein L13, putative [Ric	0.985	0.990	0.788	2e-89
449448398	193	PREDICTED: 50S ribosomal protein L13-lik	0.940	0.989	0.822	1e-88
359806218	201	uncharacterized protein LOC100799712 [Gl	0.960	0.970	0.841	2e-88
351725941	200	uncharacterized protein LOC100499790 [Gl	0.960	0.975	0.841	4e-88
255542936	202	50S ribosomal protein L13, putative [Ric	0.985	0.990	0.773	6e-88
346472265	202	hypothetical protein [Amblyomma maculatu	0.965	0.970	0.785	1e-87

>gi|224141259|ref|XP_002323992.1| predicted protein [Populus trichocarpa] gi|222866994|gb|EEF04125.1| predicted protein [Populus trichocarpa]

 Score =  349 bits (895), Expect = 4e-94,   Method: Compositional matrix adjust.
 Identities = 167/204 (81%), Positives = 187/204 (91%), Gaps = 2/204 (0%)

Query: 1   MANQAA-TAFSGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTY 59
           MA+QAA +AF+GNMKKALAGL+RINLEGLRWRVFDAKGQVLGRLASQ++TV+QGKDKPTY
Sbjct: 1   MASQAAASAFNGNMKKALAGLKRINLEGLRWRVFDAKGQVLGRLASQISTVIQGKDKPTY 60

Query: 60  APNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRKA 119
           AP RDDGD+C+VLNAKD+CVTGRK+ +K Y WHTGYIGHLKER+LK+QM +DPTE IRKA
Sbjct: 61  APYRDDGDICVVLNAKDVCVTGRKMTDKFYRWHTGYIGHLKERSLKDQMAKDPTEVIRKA 120

Query: 120 VLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQKK 179
           VLRMLPRNKLRDDRDRKLRIFP SEHPFGDRPLEPYVMPPR+VRE+RPR RRAMIR QKK
Sbjct: 121 VLRMLPRNKLRDDRDRKLRIFPDSEHPFGDRPLEPYVMPPRQVREMRPRARRAMIRAQKK 180

Query: 180 AEMQ-QSNKDMRKNRKKEVEAEVT 202
           AE Q Q   D RK +K+EVEAE+T
Sbjct: 181 AEQQEQGGNDKRKGKKREVEAELT 204

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224060221|ref|XP_002300092.1| predicted protein [Populus trichocarpa] gi|222847350|gb|EEE84897.1| predicted protein [Populus trichocarpa]

 Score =  339 bits (869), Expect = 5e-91,   Method: Compositional matrix adjust.
 Identities = 160/204 (78%), Positives = 187/204 (91%), Gaps = 2/204 (0%)

Query: 1   MANQAA-TAFSGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTY 59
           MA+QAA +AF+G+MKKA AGL+RINLEGLRWRVFDAKGQVLGRLASQ++TV+QGKDKPTY
Sbjct: 1   MASQAAASAFNGSMKKAHAGLKRINLEGLRWRVFDAKGQVLGRLASQISTVIQGKDKPTY 60

Query: 60  APNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRKA 119
           AP RDDGDMC+VLNAKD+CVTGRK+ +K Y WHTGYIGHLKER+LK+QM +DPTE IRKA
Sbjct: 61  APYRDDGDMCVVLNAKDVCVTGRKMTDKFYRWHTGYIGHLKERSLKDQMAKDPTEVIRKA 120

Query: 120 VLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQKK 179
           VLRMLPRNKLRDDRDRKLRIFP SEHPFGD+P+E YVMPPR+VRE+RPR +RAMIR QKK
Sbjct: 121 VLRMLPRNKLRDDRDRKLRIFPDSEHPFGDQPVEAYVMPPRKVREMRPRAQRAMIRAQKK 180

Query: 180 AE-MQQSNKDMRKNRKKEVEAEVT 202
           AE ++Q+  D RK +K+EVEA++T
Sbjct: 181 AEQLEQAGNDKRKGKKREVEADLT 204

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118487043|gb|ABK95352.1| unknown [Populus trichocarpa]

 Score =  337 bits (864), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 159/204 (77%), Positives = 186/204 (91%), Gaps = 2/204 (0%)

Query: 1   MANQAA-TAFSGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTY 59
           MA+QAA +AF+ +MKKA AGL+RINLEGLRWRVFDAKGQVLGRLASQ++TV+QGKDKPTY
Sbjct: 1   MASQAAASAFNSSMKKAHAGLKRINLEGLRWRVFDAKGQVLGRLASQISTVIQGKDKPTY 60

Query: 60  APNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRKA 119
           AP RDDGDMC+VLNAKD+CVTGRK+ +K Y WHTGYIGHLKER+LK+QM +DPTE IRKA
Sbjct: 61  APYRDDGDMCVVLNAKDVCVTGRKMTDKFYRWHTGYIGHLKERSLKDQMAKDPTEVIRKA 120

Query: 120 VLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQKK 179
           VLRMLPRNKLRDDRDRKLRIFP SEHPFGD+P+E YVMPPR+VRE+RPR +RAMIR QKK
Sbjct: 121 VLRMLPRNKLRDDRDRKLRIFPDSEHPFGDQPVEAYVMPPRKVREMRPRAQRAMIRAQKK 180

Query: 180 AE-MQQSNKDMRKNRKKEVEAEVT 202
           AE ++Q+  D RK +K+EVEA++T
Sbjct: 181 AEQLEQAGNDKRKGKKREVEADLT 204

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449487903|ref|XP_004157858.1| PREDICTED: 50S ribosomal protein L13-like [Cucumis sativus]

 Score =  337 bits (863), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 163/204 (79%), Positives = 183/204 (89%), Gaps = 1/204 (0%)

Query: 1   MANQAATAFSGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYA 60
           MA+QAAT+ +GNMKKALAGL+RINLEGLRWRVFDAKGQVLGRLASQ++TV+QGKDKPTYA
Sbjct: 1   MASQAATSINGNMKKALAGLKRINLEGLRWRVFDAKGQVLGRLASQISTVIQGKDKPTYA 60

Query: 61  PNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRKAV 120
           PNRDDGDMCIVLNAKDI VTGRKL  K Y W   Y+G+LKERTL+EQM RDPTE IRKAV
Sbjct: 61  PNRDDGDMCIVLNAKDIAVTGRKLTKKFYAWPCRYVGNLKERTLREQMTRDPTEVIRKAV 120

Query: 121 LRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQKKA 180
           LRMLP+NKLRDDRDRKLRIF G EHPFGDRPLEPY+MPPR VRE+RP+VRRAMIR QK A
Sbjct: 121 LRMLPKNKLRDDRDRKLRIFAGDEHPFGDRPLEPYIMPPRNVREMRPQVRRAMIRAQKMA 180

Query: 181 EMQQSNKDM-RKNRKKEVEAEVTA 203
           E QQ+NK+  +++RKKE + EVTA
Sbjct: 181 EQQQNNKNEGKESRKKEEKVEVTA 204

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255536973|ref|XP_002509553.1| 50S ribosomal protein L13, putative [Ricinus communis] gi|223549452|gb|EEF50940.1| 50S ribosomal protein L13, putative [Ricinus communis]

 Score =  334 bits (856), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 160/203 (78%), Positives = 181/203 (89%), Gaps = 3/203 (1%)

Query: 1   MANQAATAFSGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYA 60
           MA+QA   F+GNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQ++TV+QGKDKPTYA
Sbjct: 1   MASQAT--FNGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQISTVIQGKDKPTYA 58

Query: 61  PNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRKAV 120
           P R+DGDMCIV+NAKD+ VTGRK+ +K Y WHTGY+G+LKER+LK+Q+ +DPTE IRKAV
Sbjct: 59  PYREDGDMCIVINAKDVSVTGRKMTDKFYRWHTGYVGNLKERSLKDQLAKDPTEVIRKAV 118

Query: 121 LRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQKKA 180
           LRMLPRNKLRDDRDRKLRIF GSEHPFGDRPLE Y+MPPR VRE+RPR RRAMIR QKKA
Sbjct: 119 LRMLPRNKLRDDRDRKLRIFAGSEHPFGDRPLESYIMPPRTVREMRPRARRAMIRAQKKA 178

Query: 181 EMQ-QSNKDMRKNRKKEVEAEVT 202
           E Q Q   +M+K RKKEVE E+T
Sbjct: 179 EQQRQGANEMQKGRKKEVEVEIT 201

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449448398|ref|XP_004141953.1| PREDICTED: 50S ribosomal protein L13-like [Cucumis sativus]

 Score =  330 bits (847), Expect = 1e-88,   Method: Compositional matrix adjust.
 Identities = 158/192 (82%), Positives = 176/192 (91%), Gaps = 1/192 (0%)

Query: 13  MKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVL 72
            +KALAGL+RINLEGLRWRVFDAKGQVLGRLASQ++TV+QGKDKPTYAPNRDDGDMCIVL
Sbjct: 2   FQKALAGLKRINLEGLRWRVFDAKGQVLGRLASQISTVIQGKDKPTYAPNRDDGDMCIVL 61

Query: 73  NAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDD 132
           NAKDI VTGRKL  KVYYWHTGY+G+LKERTL+EQM RDPTE IRKAVLRMLP+NKLRDD
Sbjct: 62  NAKDIAVTGRKLTKKVYYWHTGYVGNLKERTLREQMTRDPTEVIRKAVLRMLPKNKLRDD 121

Query: 133 RDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQKKAEMQQSNKDM-RK 191
           RDRKLRIF G EHPFGDRPLEPY+MPPR VRE+RP+VRRAMIR QK AE QQ+NK+  ++
Sbjct: 122 RDRKLRIFAGDEHPFGDRPLEPYIMPPRNVREMRPQVRRAMIRAQKMAEQQQNNKNEGKE 181

Query: 192 NRKKEVEAEVTA 203
           +RKKE + EVTA
Sbjct: 182 SRKKEEKVEVTA 193

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359806218|ref|NP_001241463.1| uncharacterized protein LOC100799712 [Glycine max] gi|255642066|gb|ACU21299.1| unknown [Glycine max]

 Score =  330 bits (845), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 165/196 (84%), Positives = 176/196 (89%), Gaps = 1/196 (0%)

Query: 6   ATAFSGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDD 65
            TAF+GNMKKA AGLRRINL+GLRWRVFDAKGQVLGRLASQ+ATVVQGKDKPTY PNRDD
Sbjct: 4   VTAFTGNMKKAAAGLRRINLDGLRWRVFDAKGQVLGRLASQIATVVQGKDKPTYTPNRDD 63

Query: 66  GDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLP 125
           GDMCIVLNAKDICVTGRKL +KVYYWHTGYIGHLK+RTLK+QM +DPTE IRKAVLRMLP
Sbjct: 64  GDMCIVLNAKDICVTGRKLTDKVYYWHTGYIGHLKQRTLKDQMAKDPTEVIRKAVLRMLP 123

Query: 126 RNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQKKAEMQQS 185
           RNKLRDDRDRKLRIFPGSEHPF DRPLEPYVMPPR VRE+RPR RRAMIR QKKAE QQ 
Sbjct: 124 RNKLRDDRDRKLRIFPGSEHPFVDRPLEPYVMPPRSVREMRPRARRAMIRAQKKAEQQQQ 183

Query: 186 NKD-MRKNRKKEVEAE 200
             D M+K +  E + E
Sbjct: 184 KADGMKKGKNGEAQEE 199

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351725941|ref|NP_001236086.1| uncharacterized protein LOC100499790 [Glycine max] gi|255626635|gb|ACU13662.1| unknown [Glycine max]

 Score =  329 bits (844), Expect = 4e-88,   Method: Compositional matrix adjust.
 Identities = 164/195 (84%), Positives = 174/195 (89%)

Query: 6   ATAFSGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDD 65
            TAF+GNMKKA AGLRRINL+GLRWRVFDAKGQVLGRLASQ+ATVVQGKDKPTY PNRDD
Sbjct: 4   VTAFNGNMKKAAAGLRRINLDGLRWRVFDAKGQVLGRLASQIATVVQGKDKPTYTPNRDD 63

Query: 66  GDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLP 125
           GDMCIVLNAKDICVTGRKL +KVYYWHTGYIGHLK+RTLK+QM +DPTE IRKAVLRMLP
Sbjct: 64  GDMCIVLNAKDICVTGRKLTDKVYYWHTGYIGHLKQRTLKDQMAKDPTEVIRKAVLRMLP 123

Query: 126 RNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQKKAEMQQS 185
           RNKLRDDRDRKLRIFPGSEHPF DRPLEPYVMPPR VRE+RPR RRAMIR QKKAE QQ 
Sbjct: 124 RNKLRDDRDRKLRIFPGSEHPFVDRPLEPYVMPPRSVREMRPRARRAMIRAQKKAEQQQQ 183

Query: 186 NKDMRKNRKKEVEAE 200
             D  K +  E + E
Sbjct: 184 KADGMKGKNGEAQEE 198

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255542936|ref|XP_002512531.1| 50S ribosomal protein L13, putative [Ricinus communis] gi|223548492|gb|EEF49983.1| 50S ribosomal protein L13, putative [Ricinus communis]

 Score =  328 bits (842), Expect = 6e-88,   Method: Compositional matrix adjust.
 Identities = 157/203 (77%), Positives = 181/203 (89%), Gaps = 3/203 (1%)

Query: 1   MANQAATAFSGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYA 60
           MA+QA+  F+GN+KKALAGLRRI+LEGLRWRVFDAKGQVLGRLASQ++TV+QGKDKP YA
Sbjct: 1   MASQAS--FNGNVKKALAGLRRISLEGLRWRVFDAKGQVLGRLASQISTVIQGKDKPIYA 58

Query: 61  PNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRKAV 120
           P R+DGDMCIV+N KD+ VTGRK+ +K Y WHTGY+G+LKER+LK+Q+ +DPTE IRKAV
Sbjct: 59  PYREDGDMCIVINTKDVSVTGRKMTDKFYRWHTGYVGNLKERSLKDQLAKDPTEVIRKAV 118

Query: 121 LRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQKKA 180
           LRMLPRNKLRDDRDRKLRIF GSEHPFGDRPLEPY+MPPR VRE+RPR RRAMIR Q+KA
Sbjct: 119 LRMLPRNKLRDDRDRKLRIFAGSEHPFGDRPLEPYIMPPRTVREIRPRARRAMIRAQRKA 178

Query: 181 EMQ-QSNKDMRKNRKKEVEAEVT 202
           E Q +   +MRK RKKEVEAEV 
Sbjct: 179 EQQVRGANEMRKGRKKEVEAEVA 201

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|346472265|gb|AEO35977.1| hypothetical protein [Amblyomma maculatum]

 Score =  328 bits (840), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 154/196 (78%), Positives = 173/196 (88%)

Query: 8   AFSGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGD 67
           AFSGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTY P R+DGD
Sbjct: 7   AFSGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYTPYREDGD 66

Query: 68  MCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRN 127
           MCI+LNAKDI VTGRKL +K Y WHTGY+GHL+ER+LK+Q+ +DPTE IRKAVLRMLPRN
Sbjct: 67  MCIILNAKDISVTGRKLTDKFYRWHTGYVGHLRERSLKDQLAKDPTEVIRKAVLRMLPRN 126

Query: 128 KLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQKKAEMQQSNK 187
           KLRDDRDRKLRIF GSEHPFGDR LEPY+MPPR+VRE+RPR RRA+IR QKKAE   S  
Sbjct: 127 KLRDDRDRKLRIFTGSEHPFGDRSLEPYIMPPRQVREMRPRARRALIRAQKKAEQSSSGT 186

Query: 188 DMRKNRKKEVEAEVTA 203
           ++ K +K++    +TA
Sbjct: 187 NITKKKKEDKVEAITA 202

Source: Amblyomma maculatum

Species: Amblyomma maculatum

Genus: Amblyomma

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	203
TAIR|locus:2082304	205	AT3G01790 [Arabidopsis thalian	1.0	0.990	0.614	1.3e-61
UNIPROTKB|P66065	147	rplM "50S ribosomal protein L1	0.620	0.857	0.436	7.6e-25
TIGR_CMR|BA_0143	145	BA_0143 "ribosomal protein L13	0.625	0.875	0.417	2.6e-24
TIGR_CMR|GSU_2876	143	GSU_2876 "ribosomal protein L1	0.576	0.818	0.418	4.8e-23
POMBASE|SPBC16G5.04	157	mrpl23 "mitochondrial ribosoma	0.581	0.751	0.445	7e-22
UNIPROTKB|P0AA10	142	rplM [Escherichia coli K-12 (t	0.571	0.816	0.439	1.1e-21
TIGR_CMR|ECH_1019	156	ECH_1019 "ribosomal protein L1	0.576	0.75	0.457	1.1e-21
TIGR_CMR|DET_0505	143	DET_0505 "ribosomal protein L1	0.576	0.818	0.384	8e-21
TIGR_CMR|SPO_1691	152	SPO_1691 "ribosomal protein L1	0.576	0.769	0.420	1e-20
TIGR_CMR|CJE_1653	141	CJE_1653 "ribosomal protein L1	0.576	0.829	0.389	2.7e-20

TAIR|locus:2082304 AT3G01790 [Arabidopsis thaliana (taxid:3702)]

 Score = 630 (226.8 bits), Expect = 1.3e-61, P = 1.3e-61
 Identities = 126/205 (61%), Positives = 146/205 (71%)

Query:     1 MANQAATA--FSGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPT 58
             MA QAA A  F GN+KKA+AG++RINL+GLRWRVFDA+GQVLGRLASQ++TV+Q KDKPT
Sbjct:     1 MATQAAAAASFKGNLKKAVAGIKRINLDGLRWRVFDARGQVLGRLASQISTVLQAKDKPT 60

Query:    59 YAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRK 118
             Y PNRDDGD+CIVLNAK+I  TGRKL +K Y WHTGYIGHLKER+LK+QM +DPTE IRK
Sbjct:    61 YCPNRDDGDICIVLNAKEIGFTGRKLTDKFYRWHTGYIGHLKERSLKDQMAKDPTEVIRK 120

Query:   119 AVLRMLPRNXXXXXXXXXXXIFPGSEHPFGDRPLEPYXXXXXXXXXXXXXXXXAMIREQK 178
             AV RMLP N           IF G EHPFGD+PLEP+                AMIR QK
Sbjct:   121 AVWRMLPSNNLRDDRDRKLRIFEGGEHPFGDKPLEPFVMPPRRVREMRPRARRAMIRAQK 180

Query:   179 KAEMQQSNKDMRKNRKKEVEAEVTA 203
             KAE  ++     K  KK   +EV A
Sbjct:   181 KAEQAENEGTEVKKGKKRTLSEVPA 205

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

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM

GO:0015934 "large ribosomal subunit" evidence=ISS

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

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

 Score = 283 (104.7 bits), Expect = 7.6e-25, P = 7.6e-25
 Identities = 55/126 (43%), Positives = 76/126 (60%)

Query:    30 WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
             W V DA   VLGRLA   A +++GK KPT+APN D GD  IV+NA  + ++G KL++K+ 
Sbjct:    15 WYVIDATDVVLGRLAVAAANLLRGKHKPTFAPNVDGGDFVIVINADKVAISGDKLQHKMV 74

Query:    90 YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEHPFGD 149
             Y H+GY G L +RT+ E M+R P   + KA+L MLP+N           ++ G EHP   
Sbjct:    75 YRHSGYPGGLHKRTIGELMQRHPDRVVEKAILGMLPKNRLSRQIQRKLRVYAGPEHPHSA 134

Query:   150 RPLEPY 155
             +   PY
Sbjct:   135 QQPVPY 140

GO:0005618 "cell wall" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0040007 "growth" evidence=IMP

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

 Score = 278 (102.9 bits), Expect = 2.6e-24, P = 2.6e-24
 Identities = 53/127 (41%), Positives = 79/127 (62%)

Query:    29 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
             +W V DA+GQ LGRLAS+VA++++GK+KPT+ P+ D GD  I++NA+ I +TG KL +K+
Sbjct:    15 KWYVVDAEGQTLGRLASEVASILRGKNKPTFTPHVDTGDHVIIINAEKIHLTGNKLNDKI 74

Query:    89 YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEHPFG 148
             YY HT + G LK+RT  E     P + +  A+  MLP+            ++ G+EHP  
Sbjct:    75 YYRHTNHPGGLKQRTALEMRTNYPVQMLELAIKGMLPKGRLGRQVSKKLNVYAGAEHPHQ 134

Query:   149 DRPLEPY 155
              +  E Y
Sbjct:   135 AQKPEVY 141

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

GO:0006412 "translation" evidence=ISS

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

 Score = 266 (98.7 bits), Expect = 4.8e-23, P = 4.8e-23
 Identities = 49/117 (41%), Positives = 74/117 (63%)

Query:    30 WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
             W + DA  +VLGR+A+++A +++GK KP Y P+ D GD  +V+NA  + +TG KL +K+Y
Sbjct:    16 WYLVDADNKVLGRMATEIANILRGKKKPIYTPSVDTGDFVVVVNAAKLQLTGNKLADKMY 75

Query:    90 YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEHP 146
             Y HTG+ G +K  T  + +E+ P + IRKAV  MLP+N           ++ G EHP
Sbjct:    76 YHHTGFPGGIKSITAGKLIEKKPEDLIRKAVKGMLPKNKLARHMLKKLKVYAGPEHP 132

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

GO:0006412 "translation" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

POMBASE|SPBC16G5.04 mrpl23 "mitochondrial ribosomal protein subunit L13 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 255 (94.8 bits), Expect = 7.0e-22, P = 7.0e-22
 Identities = 53/119 (44%), Positives = 72/119 (60%)

Query:    30 WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
             W    AK   LGRLASQ+AT + GK KP Y P  D GD+ +V +  +I ++GRKL+N  Y
Sbjct:    16 WHHVSAKNVPLGRLASQIATTLMGKHKPIYHPAADCGDVVVVTDCSEIGISGRKLENHKY 75

Query:    90 YWHTGYIGHLKERTLKEQM-ERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEHPF 147
             Y H+G  GHLKE T++E   +R   + +R+AV  MLPRN           I+ G+EHP+
Sbjct:    76 YSHSGQPGHLKEWTMEEMAAKRGHKDLLRRAVGGMLPRNKLWDRRMKRLYIYDGAEHPY 134

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

GO:0005739 "mitochondrion" evidence=IDA

GO:0005762 "mitochondrial large ribosomal subunit" evidence=ISS

GO:0006412 "translation" evidence=ISS

GO:0032543 "mitochondrial translation" evidence=NAS

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

 Score = 253 (94.1 bits), Expect = 1.1e-21, P = 1.1e-21
 Identities = 51/116 (43%), Positives = 69/116 (59%)

Query:    30 WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
             W V DA G+ LGRLA+++A  ++GK K  Y P+ D GD  IVLNA  + VTG K  +KVY
Sbjct:    15 WYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVY 74

Query:    90 YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEH 145
             Y HTG+IG +K+ T +E + R P   I  AV  MLP+            ++ G+EH
Sbjct:    75 YHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEH 130

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|ECH_1019 ECH_1019 "ribosomal protein L13" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)]

 Score = 253 (94.1 bits), Expect = 1.1e-21, P = 1.1e-21
 Identities = 54/118 (45%), Positives = 69/118 (58%)

Query:    29 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
             RW V DA G V+GRLA+ VA +++GKDKP Y P+ D GD  I++NA+ +  TG KLKNKV
Sbjct:    16 RWVVIDADGVVVGRLAAFVANILRGKDKPEYTPHMDCGDNVIIINAEKVHFTGSKLKNKV 75

Query:    89 YYWHTGYIGHLKERTLKEQ-MERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEH 145
             YY HTGY G LK  T  +  + + P   I  AV RML              ++ G EH
Sbjct:    76 YYRHTGYPGGLKSCTPADLFLNKHPERIINMAVRRMLSTGPMARRRLKNLYVYSGPEH 133

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

GO:0006412 "translation" evidence=ISS

GO:0015934 "large ribosomal subunit" evidence=ISS

TIGR_CMR|DET_0505 DET_0505 "ribosomal protein L13" [Dehalococcoides ethenogenes 195 (taxid:243164)]

 Score = 245 (91.3 bits), Expect = 8.0e-21, P = 8.0e-21
 Identities = 45/117 (38%), Positives = 66/117 (56%)

Query:    30 WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
             W V DA G+VLG +A++ A  + GK KP +  N D GD  +++NAK + VTG KL  K+Y
Sbjct:    15 WHVIDASGRVLGEVAAEAAKYLMGKHKPMFCRNLDCGDYVVIINAKKVTVTGNKLDQKIY 74

Query:    90 YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEHP 146
             Y H+G+ G  ++  L + ++  P   I  AV  M+PRN           ++ G EHP
Sbjct:    75 YRHSGFPGGFRQEKLGDLLKTKPLFVIEHAVKGMIPRNTLGAQILAKLKVYEGEEHP 131

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

GO:0006412 "translation" evidence=ISS

GO:0015934 "large ribosomal subunit" evidence=ISS

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

 Score = 244 (91.0 bits), Expect = 1.0e-20, P = 1.0e-20
 Identities = 50/119 (42%), Positives = 74/119 (62%)

Query:    29 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
             +W + DA+G VLGRLAS VA  ++GK K ++ P+ D GD  IV+NA  + +TG+K + + 
Sbjct:    14 KWILIDAEGVVLGRLASIVAMRLRGKHKASFTPHMDMGDNVIVINADKVQITGKK-REEH 72

Query:    89 YYWHTGYIGHLKERTLKEQME-RDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEHP 146
             +YWHTG+ G +K RT ++ +E   P   + +AV RMLP N           I+ G+EHP
Sbjct:    73 FYWHTGHPGGIKSRTKQQILEGAHPERVVYQAVKRMLPGNRLSRQQMTNLRIYAGTEHP 131

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

GO:0006412 "translation" evidence=ISS

GO:0042255 "ribosome assembly" evidence=ISS

TIGR_CMR|CJE_1653 CJE_1653 "ribosomal protein L13" [Campylobacter jejuni RM1221 (taxid:195099)]

 Score = 240 (89.5 bits), Expect = 2.7e-20, P = 2.7e-20
 Identities = 46/118 (38%), Positives = 71/118 (60%)

Query:    30 WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTG-RKLKNKV 88
             W V DA+G+  GRL ++VAT+++GK+KP + PN D GD  I++NA     TG  K ++K+
Sbjct:    14 WIVLDAEGKRFGRLLTEVATILRGKNKPCFTPNVDCGDYVIIINASKAVFTGANKAEDKL 73

Query:    89 YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEHP 146
             Y+ H+GY G +K     + +E++P +  + AV  MLP+            I+ GSEHP
Sbjct:    74 YHRHSGYFGSVKSEKFGDLLEKNPAKLYKLAVRGMLPKTNLGRAMLKKLKIYAGSEHP 131

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

GO:0042254 "ribosome biogenesis" 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O67722	RL13_AQUAE	No assigned EC number	0.5158	0.6206	0.875	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_fgenesh4_pg.C_LG_XVII0211	ribisomal protein L13 family protein (205 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.16155.2.1	Predicted protein (206 aa)	•			•			•		0.838
	grail3.0079001501	hypothetical protein (187 aa)	•						•		0.826
	eugene3.00141000	hypothetical protein (227 aa)	•			•	•		•		0.822
	eugene3.160500001	Predicted protein (113 aa)				•	•		•		0.810
	gw1.IV.3048.1	SubName- Full=Putative uncharacterized protein; (227 aa)	•			•			•		0.805
	fgenesh4_pm.C_LG_II000602	hypothetical protein (211 aa)	•						•		0.799
	estExt_Genewise1_v1.C_400481	SubName- Full=Putative uncharacterized protein; (211 aa)	•						•		0.798
	fgenesh4_pm.C_LG_XIV000511	hypothetical protein; Associates with the EF-Tu.GDP complex and induces the exchange of GDP to [...] (323 aa)	•			•			•		0.782
	fgenesh4_pg.C_scaffold_166000032	hypothetical protein (285 aa)	•		•	•	•		•		0.777
	fgenesh4_pm.C_LG_XIII000297	hypothetical protein (222 aa)	•			•	•		•		0.770

---

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	203
PLN00205	191	PLN00205, PLN00205, ribisomal protein L13 family p	1e-115
PRK09216	144	PRK09216, rplM, 50S ribosomal protein L13; Reviewe	7e-56
pfam00572	128	pfam00572, Ribosomal_L13, Ribosomal protein L13	3e-53
cd00392	114	cd00392, Ribosomal_L13, Ribosomal protein L13	7e-51
TIGR01066	140	TIGR01066, rplM_bact, ribosomal protein L13, bacte	6e-47
COG0102	148	COG0102, RplM, Ribosomal protein L13 [Translation,	2e-41
CHL00159	143	CHL00159, rpl13, ribosomal protein L13; Validated	1e-35
TIGR01077	142	TIGR01077, L13_A_E, ribosomal protein L13, archaea	3e-06
PRK06394	146	PRK06394, rpl13p, 50S ribosomal protein L13P; Revi	0.002

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

 Score =  324 bits (832), Expect = e-115
 Identities = 158/191 (82%), Positives = 175/191 (91%), Gaps = 1/191 (0%)

Query: 14  KKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 73
           KKALAGLRRINLEGLRWRVFDAKGQVLGRLASQ++TV+QGKDKPTYAPNRDDGD+CIVLN
Sbjct: 1   KKALAGLRRINLEGLRWRVFDAKGQVLGRLASQISTVLQGKDKPTYAPNRDDGDICIVLN 60

Query: 74  AKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDR 133
           AKDI VTGRKL +K Y WHTGYIGHLKER+LK+QM +DPTE IRKAVLRMLPRN+LRDDR
Sbjct: 61  AKDISVTGRKLTDKFYRWHTGYIGHLKERSLKDQMAKDPTEVIRKAVLRMLPRNRLRDDR 120

Query: 134 DRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQKKAEMQ-QSNKDMRKN 192
           DRKLRIF GSEHPFGD+PLEP+VMPPR+VRE+RPR RRAMIR QKKAE + Q+  + RK 
Sbjct: 121 DRKLRIFAGSEHPFGDKPLEPFVMPPRQVREMRPRARRAMIRAQKKAEQREQAANEKRKG 180

Query: 193 RKKEVEAEVTA 203
           +KKEVE EVTA
Sbjct: 181 KKKEVEVEVTA 191

Length = 191

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

 Score =  173 bits (441), Expect = 7e-56
 Identities = 59/117 (50%), Positives = 84/117 (71%)

Query: 30  WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
           W V DA+G+VLGRLAS+VA++++GK KPT+ P+ D GD  IV+NA+ + +TG+KL +K+Y
Sbjct: 15  WYVIDAEGKVLGRLASEVASILRGKHKPTFTPHVDTGDFVIVINAEKVKLTGKKLTDKIY 74

Query: 90  YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 146
           Y H+GY G LKE T  E + + P   I KAV  MLP+N L     +KL+++ G+EHP
Sbjct: 75  YRHSGYPGGLKEITFGELLAKKPERVIEKAVKGMLPKNPLGRAMFKKLKVYAGAEHP 131

Length = 144

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

 Score =  166 bits (422), Expect = 3e-53
 Identities = 61/126 (48%), Positives = 82/126 (65%)

Query: 30  WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
           W V DAKGQ+LGRLAS+VA +++GK KPTY P+ D GD  +V+NA+ I +TG+K   K Y
Sbjct: 1   WHVIDAKGQILGRLASKVAKLLRGKHKPTYTPHVDCGDYVVVINAEKIVLTGKKRDQKKY 60

Query: 90  YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGD 149
           Y HTGY G LK  T K  +ER P   + +AV  MLP+NKL     ++L+++ GS HP   
Sbjct: 61  YRHTGYPGGLKNPTAKGPLERKPERILERAVRGMLPKNKLGRAALKRLKVYAGSPHPHAA 120

Query: 150 RPLEPY 155
           +  E  
Sbjct: 121 QKPEVL 126

Length = 128

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

 Score =  159 bits (405), Expect = 7e-51
 Identities = 57/114 (50%), Positives = 77/114 (67%)

Query: 30  WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
           W V DAKGQVLGRLAS+VA ++ GK KPTY P+ D GD  +V+NA+ I +TG+K + KVY
Sbjct: 1   WHVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAEKIVITGKKWRQKVY 60

Query: 90  YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGS 143
           Y HTGY G LK  T      R P   +++AV  MLP+NKL     ++L+++ G+
Sbjct: 61  YRHTGYPGGLKNPTAGPLHPRAPERILKRAVRGMLPKNKLGRAALKRLKVYEGA 114

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|162186 TIGR01066, rplM_bact, ribosomal protein L13, bacterial type

 Score =  150 bits (382), Expect = 6e-47
 Identities = 60/118 (50%), Positives = 82/118 (69%)

Query: 30  WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
           W V DA G+ LGRLAS+VA +++GK KPTY P+ D GD  IV+NA+ + +TG+KL+ KVY
Sbjct: 13  WYVVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVINAEKVRLTGKKLEQKVY 72

Query: 90  YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPF 147
           Y H+GY G LK RT +E + R P   +  AV  MLP+N+L     +KL+++ GSEHP 
Sbjct: 73  YRHSGYPGGLKSRTFEEMIARKPERVLEHAVKGMLPKNRLGRKLFKKLKVYAGSEHPH 130

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

 Score =  137 bits (346), Expect = 2e-41
 Identities = 55/118 (46%), Positives = 77/118 (65%), Gaps = 1/118 (0%)

Query: 30  WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
           W V DA+G+VLGRLAS+VA  ++GK KPTY P+ D GD  IV+NA+ + +TG+KL +K Y
Sbjct: 15  WYVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKVVITGKKLTDKKY 74

Query: 90  YWHTGYIGHLKERTLKEQME-RDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 146
           Y H+GY G LK  T    +  R P   + +AV  MLP+N L     ++L+++ G  HP
Sbjct: 75  YRHSGYPGGLKNPTRGGPLAPRRPERILERAVRGMLPKNPLGRAALKRLKVYAGIPHP 132

Length = 148

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

 Score =  121 bits (306), Expect = 1e-35
 Identities = 53/117 (45%), Positives = 72/117 (61%)

Query: 30  WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
           W + DAK Q LGRLA+++A++++GK+KP+Y P+ D GD  IV+NA+ I VTG K   K Y
Sbjct: 16  WYIIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVINAEKIKVTGNKTSQKFY 75

Query: 90  YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 146
             H+G  G LK  T +E   R P   I KAV  MLP+  L      KL+++ G  HP
Sbjct: 76  VRHSGRPGGLKIETFEELQNRLPNRIIEKAVKGMLPKGPLGRKLFTKLKVYKGESHP 132

Length = 143

>gnl|CDD|162192 TIGR01077, L13_A_E, ribosomal protein L13, archaeal/eukaryotic

 Score = 44.7 bits (106), Expect = 3e-06
 Identities = 32/124 (25%), Positives = 50/124 (40%), Gaps = 13/124 (10%)

Query: 31  RVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYY 90
            V D  G +LGRLAS VA  +             +G+  +V+NA+ I ++G   +NK+ Y
Sbjct: 1   TVIDGSGHILGRLASVVAKQLL------------NGEKVVVVNAEKIVISGNFYRNKLKY 48

Query: 91  WHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRD-RKLRIFPGSEHPFGD 149
                   L          R P+   R+ V  MLP    R     R+L+++ G       
Sbjct: 49  KEFLRKRTLTNPRRGPFFPRAPSRIFRRTVRGMLPHKTARGRAALRRLKVYVGIPPELDK 108

Query: 150 RPLE 153
           +   
Sbjct: 109 KKRV 112

This model represents ribosomal protein of L13 from the Archaea and from the eukaryotic cytosol. Bacterial and organellar forms are represented by model TIGR01066 [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 142

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 31/131 (23%), Positives = 55/131 (41%), Gaps = 26/131 (19%)

Query: 31  RVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYY 90
            V DA+GQ+LGRLAS VA  +             +G+  +++NA+   +TG   + +V  
Sbjct: 5   VVIDAEGQILGRLASYVAKRLL------------EGEEVVIVNAEKAVITGN--RERVIE 50

Query: 91  WHTGYIGHLKERTLKEQME------RDPTEAIRKAVLRMLPRNKLRDDRD--RKLRIFPG 142
               Y    +  +            R P    ++ +  MLP  K R  R+  ++L+++ G
Sbjct: 51  K---YKQRRERGSHYNPYRNGPKYPRRPDRIFKRTIRGMLPYKKPR-GREALKRLKVYVG 106

Query: 143 SEHPFGDRPLE 153
                  +  E
Sbjct: 107 VPKELEGKEFE 117

Length = 146

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	203
PLN00205	191	ribisomal protein L13 family protein; Provisional	100.0
CHL00159	143	rpl13 ribosomal protein L13; Validated	100.0
PRK09216	144	rplM 50S ribosomal protein L13; Reviewed	100.0
TIGR01066	140	rplM_bact ribosomal protein L13, bacterial type. T	100.0
COG0102	148	RplM Ribosomal protein L13 [Translation, ribosomal	100.0
PF00572	128	Ribosomal_L13: Ribosomal protein L13; InterPro: IP	100.0
KOG3203	165	consensus Mitochondrial/chloroplast ribosomal prot	100.0
cd00392	114	Ribosomal_L13 Ribosomal protein L13. Protein L13,	100.0
TIGR01077	142	L13_A_E ribosomal protein L13, archaeal/eukaryotic	100.0
PTZ00068	202	60S ribosomal protein L13a; Provisional	100.0
PRK06394	146	rpl13p 50S ribosomal protein L13P; Reviewed	100.0
KOG3204	197	consensus 60S ribosomal protein L13a [Translation,	99.89

>PLN00205 ribisomal protein L13 family protein; Provisional

Probab=100.00  E-value=1.4e-75  Score=494.70  Aligned_cols=190  Identities=83%  Similarity=1.316  Sum_probs=184.6

Q ss_pred             HHHhhhhhhcccCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeec
Q 028816           14 KKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHT   93 (203)
Q Consensus        14 ~~~~~~~~~~~~~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~ht   93 (203)
                      ++|+|||+++|+++++||||||+||+||||||.||++|+|||||+|||++||||+||||||++|+|||+||.+|.|++||
T Consensus         1 ~~~~~~~~~~~~~~r~W~VIDA~~~iLGRLAS~IAk~L~GKhKP~ytP~~D~GD~VVVINAekI~lTG~K~~~K~Y~~ht   80 (191)
T PLN00205          1 KKALAGLRRINLEGLRWRVFDAKGQVLGRLASQISTVLQGKDKPTYAPNRDDGDICIVLNAKDISVTGRKLTDKFYRWHT   80 (191)
T ss_pred             CcccccccccccCCCcEEEEeCCCCchHHHHHHHHHHHhccCCCCcCCCcCCCCEEEEEeccEEEEeCChhhcceEEEec
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCccccChhHHhhcChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCcceecCccchhhccccchhhH
Q 028816           94 GYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAM  173 (203)
Q Consensus        94 gYpGglk~~~~~~~~~r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~pp~~~r~~r~~~~r~~  173 (203)
                      |||||+++++++++++++|++||++||+||||+|++|+.++++|+||+|++|||++|+|+++++||+++|++||+++|+|
T Consensus        81 gypGglk~~~~~~~~~r~P~~Il~kAVrGMLPkn~lr~~~~krLkVY~G~~hp~~~q~p~~~~~p~~~~~~~~~~~~~~~  160 (191)
T PLN00205         81 GYIGHLKERSLKDQMAKDPTEVIRKAVLRMLPRNRLRDDRDRKLRIFAGSEHPFGDKPLEPFVMPPRQVREMRPRARRAM  160 (191)
T ss_pred             CCCCCcccccHHHHhccCHHHHHHHHHHhcCCCCchHHHHHhCCEEECCCCCChhccCCeEecCChHHhhccCchhHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhh-HHHhhhhhhhhhhhhcC
Q 028816          174 IREQKKAEMQQSN-KDMRKNRKKEVEAEVTA  203 (203)
Q Consensus       174 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~  203 (203)
                      |+||+|+||+++. +.++++++++++.|++|
T Consensus       161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  191 (191)
T PLN00205        161 IRAQKKAEQREQAANEKRKGKKKEVEVEVTA  191 (191)
T ss_pred             HHHHHHHHHHHHHHhhhccccccccccccCC
Confidence            9999999999988 77888888888888764

>CHL00159 rpl13 ribosomal protein L13; Validated

Probab=100.00  E-value=3.3e-59  Score=380.24  Aligned_cols=133  Identities=40%  Similarity=0.640  Sum_probs=128.7

Q ss_pred             ccCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccC
Q 028816           24 NLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERT  103 (203)
Q Consensus        24 ~~~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~  103 (203)
                      +.-.|+|+||||+||+||||||.||++|+|||||+|||++||||+||||||++|+|||+||.+|.|++|||||||+++++
T Consensus        10 ~~~~r~W~viDA~~~~lGRlAs~iA~~L~GKhKp~ytP~~d~Gd~VVViNa~kv~~TG~K~~~K~y~~htg~pGg~k~~~   89 (143)
T CHL00159         10 DYKNRKWYIIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVINAEKIKVTGNKTSQKFYVRHSGRPGGLKIET   89 (143)
T ss_pred             hhcCCCEEEEeCCCCchHHHHHHHHHHHhccCCCCcCCCcCCCCEEEEEecceeEEeCchhhheEEEecCCCCCCccccc
Confidence            34468999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHhhcChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCccee
Q 028816          104 LKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYV  156 (203)
Q Consensus       104 ~~~~~~r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~  156 (203)
                      ++++++++|++||++||+||||+|.+|+.+|++|+||+|++|||++|+|++++
T Consensus        90 ~~~~~~r~P~~il~~aV~gMLPkn~lgr~~~~rLkvy~G~~hph~aq~p~~~~  142 (143)
T CHL00159         90 FEELQNRLPNRIIEKAVKGMLPKGPLGRKLFTKLKVYKGESHPHVAQKPIKIN  142 (143)
T ss_pred             HHHHhhcCHHHHHHHHHHhcCCCChhHHHHHhCCEEeCCCCCCccccCCeecC
Confidence            99999999999999999999999999999999999999999999999997665

>PRK09216 rplM 50S ribosomal protein L13; Reviewed

Probab=100.00  E-value=9.1e-59  Score=378.00  Aligned_cols=131  Identities=46%  Similarity=0.812  Sum_probs=128.5

Q ss_pred             CceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChhH
Q 028816           27 GLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKE  106 (203)
Q Consensus        27 ~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~~  106 (203)
                      .++|+||||+||+||||||.||++|+|||||+|||+.||||+|||||||+|+|||+||.+|.||+|||||||++++++++
T Consensus        12 ~~~W~viDA~~~~lGRlAs~IAk~L~GKhKp~y~p~~d~Gd~VvViNa~ki~~tG~k~~~k~y~~htg~pGglk~~~~~~   91 (144)
T PRK09216         12 ERKWYVIDAEGKVLGRLASEVASILRGKHKPTFTPHVDTGDFVIVINAEKVKLTGKKLTDKIYYRHSGYPGGLKEITFGE   91 (144)
T ss_pred             CCCEEEEeCCCCchHHHHHHHHHHHhccCCCCcCCCCCCCCEEEEEeCceeEEcCchHhheeeEEecccCCCCEEecHHH
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhcChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCcceec
Q 028816          107 QMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVM  157 (203)
Q Consensus       107 ~~~r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~  157 (203)
                      +++++|++||++||+||||+|.+|+.+|+||+||+|++|||++|+|+.+++
T Consensus        92 ~~~r~P~~il~~aVrgMLPkn~lgr~~~~rLkvy~G~~hp~~~q~p~~~~~  142 (144)
T PRK09216         92 LLAKKPERVIEKAVKGMLPKNPLGRAMFKKLKVYAGAEHPHAAQQPEVLEI  142 (144)
T ss_pred             HhhhCHHHHHHHHHHhcCCCCccHHHHHhCcEEeCCCCCCccccCCEeccc
Confidence            999999999999999999999999999999999999999999999988775

>TIGR01066 rplM_bact ribosomal protein L13, bacterial type

Probab=100.00  E-value=1.8e-58  Score=374.72  Aligned_cols=131  Identities=46%  Similarity=0.781  Sum_probs=127.6

Q ss_pred             CCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChh
Q 028816           26 EGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLK  105 (203)
Q Consensus        26 ~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~  105 (203)
                      -.|+|+||||+||+||||||.||++|+|||||+|||+.||||+|||||||+|+|||++|++|.||+|||||||+++++++
T Consensus         9 ~~r~W~viDA~~~~lGRLAs~iAk~L~GKhKp~y~p~~d~Gd~VvViNa~ki~~tG~k~~~k~y~~htg~pgg~k~~~~~   88 (140)
T TIGR01066         9 KKRKWYVVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVINAEKVRLTGKKLEQKVYYRHSGYPGGLKSRTFE   88 (140)
T ss_pred             hcccEEEEeCCCCchHHHHHHHHHHHhccCCCccCCCccCCCEEEEEeccEEEEeCchhhceeeEEEcccCCccccccHH
Confidence            35899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhcChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCccee
Q 028816          106 EQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYV  156 (203)
Q Consensus       106 ~~~~r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~  156 (203)
                      ++++++|++||++||+||||+|.+|+.+|+||+||+|++|||++|+|+.++
T Consensus        89 ~~~~r~P~~ii~~aVrGMLPkn~lgr~~l~rLkvy~G~~hp~~~q~p~~~~  139 (140)
T TIGR01066        89 EMIARKPERVLEHAVKGMLPKNRLGRKLFKKLKVYAGSEHPHEAQKPIVLD  139 (140)
T ss_pred             HhhhcCHHHHHHHHHHhcCCCCccHHHHHhCeEEeCCCCCChhhcCCeecC
Confidence            999999999999999999999999999999999999999999999987665

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=100.00  E-value=2e-56  Score=365.05  Aligned_cols=132  Identities=42%  Similarity=0.747  Sum_probs=126.3

Q ss_pred             CCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChh
Q 028816           26 EGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLK  105 (203)
Q Consensus        26 ~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~  105 (203)
                      ..++|+||||+|++||||||.||+.|+|||||+||||+||||+|||||||+|+|||+|..+|.||+|||||||+++.+++
T Consensus        11 ~~r~w~vIDA~g~vLGRLAs~VA~~Lrgkhkp~ytP~~d~Gd~ViVINAeKv~iTG~K~~~k~yy~hs~~~gglk~~t~~   90 (148)
T COG0102          11 VERKWYVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKVVITGKKLTDKKYYRHSGYPGGLKNPTRG   90 (148)
T ss_pred             ccceEEEEeCCCCChHHHHHHHHHHHhcCCCCCcCcCcCCCCEEEEEeceeeEEecccccceEEEEeeccCCcccccccc
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999999999996


Q ss_pred             HHhh-cChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCcceec
Q 028816          106 EQME-RDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVM  157 (203)
Q Consensus       106 ~~~~-r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~  157 (203)
                      .+.+ +.|++||++||+||||+|.+++++|++|+||.|++|||.+|+|+.+.+
T Consensus        91 ~~~~~r~P~ri~~~AVrGMLPk~~lGr~~~krLkVy~G~~h~~~aq~p~~l~~  143 (148)
T COG0102          91 GPLAPRRPERILERAVRGMLPKNPLGRAALKRLKVYAGIPHPHEAQKPEALEL  143 (148)
T ss_pred             cccccCCHHHHHHHHHhccCCCChhHHHHHhCceEecCCCCccccccchhhhh
Confidence            6666 999999999999999999999999999999999999999998876553

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

Probab=100.00  E-value=1.2e-55  Score=353.07  Aligned_cols=127  Identities=48%  Similarity=0.834  Sum_probs=124.4

Q ss_pred             EEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChhHHhh
Q 028816           30 WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQME  109 (203)
Q Consensus        30 W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~~~~~  109 (203)
                      |+||||+||+||||||.||++|+|||||+|||+.||||+|||||||+|+|||++|.+|.|++|||||||++..+++.+++
T Consensus         1 W~viDA~~~~lGRLAs~iAk~L~GKhk~~y~p~~d~Gd~VvViNae~i~~tG~k~~~k~y~~h~~~~g~~~~~~~~~~~~   80 (128)
T PF00572_consen    1 WYVIDAKGQILGRLASKIAKLLLGKHKPTYTPNVDCGDHVVVINAEKIVLTGKKWRQKVYYRHTGYPGGLKNPTAKGLHE   80 (128)
T ss_dssp             EEEEETTTBBHHHHHHHHHHHHCTTSSTSSBTTSSTTEEEEEECGGGBEESSHHHHHHHHHHEHSSSTSCEEEECHHHHC
T ss_pred             CEEEeCCCCchHHHHHHHHHHHhCCCCCccCcCccCCCEEEEEcCeeeEecCCeecceEEEeecccchhhcccchhhhhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCccee
Q 028816          110 RDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYV  156 (203)
Q Consensus       110 r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~  156 (203)
                      ++|++||++||+||||+|.+|+.+|+||+||+|++|||++|+++.++
T Consensus        81 ~~P~~i~~~aVrgMLP~n~~g~~~l~rL~vy~g~~hp~~~~~~~~~~  127 (128)
T PF00572_consen   81 KDPSRILKRAVRGMLPKNKLGREALKRLKVYPGEPHPHAAQKPVVLE  127 (128)
T ss_dssp             SSHHHHHHHHHHTTSTTSHHHHHHHTTEEEESSSSCSTTSSSCBEEE
T ss_pred             cCHHHHHHHHHHHHCCCChhhhHHhhceEEECCCCCChhccCCEeCC
Confidence            99999999999999999999999999999999999999999987654

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=100.00  E-value=7.9e-54  Score=351.57  Aligned_cols=137  Identities=47%  Similarity=0.749  Sum_probs=132.2

Q ss_pred             hhhhHhhhchHHHhhhhhhcccCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCccccccccc
Q 028816            4 QAATAFSGNMKKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRK   83 (203)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K   83 (203)
                      +..++|.||...|+|         |.|+||||++|+||||||+||..|+|||||+|||+.||||+|||+||++|.|||+|
T Consensus         6 a~~~~~~g~~~~afa---------RvW~vvDa~~q~lGrLAs~ia~~L~GkhKPiYhP~~DcGD~VVV~N~~~Ia~sG~K   76 (165)
T KOG3203|consen    6 AVSRSFRGNQWLAFA---------RVWHVVDAKQQPLGRLASQIATTLQGKHKPIYHPSTDCGDHVVVTNCKKIAFSGKK   76 (165)
T ss_pred             hhhccccchHHHHHh---------hhheeeccccCchHHHHHHHHHHHhhccCCccCCccCCCCEEEEecchhheeccch
Confidence            456789999999999         77999999999999999999999999999999999999999999999999999999


Q ss_pred             ccceeEeeecccCCCccccChhHHhhcChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCC
Q 028816           84 LKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGD  149 (203)
Q Consensus        84 ~~~K~Y~~htgYpGglk~~~~~~~~~r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~  149 (203)
                      |.+|+|++|||||||++..+...++.++|++|+++||+||||+|.+|++.+++|++|+|.+||+..
T Consensus        77 ~~qk~Y~~HsGyPG~lk~~~~~q~~~rdp~~Iv~~AV~gMLPkN~Lrr~~~~rL~lf~g~e~p~~~  142 (165)
T KOG3203|consen   77 WEQKIYRSHSGYPGGLKQTTADQLADRDPCRIVRLAVYGMLPKNLLRRRRMQRLHLFPGEEHPEKV  142 (165)
T ss_pred             hhhhhhhhcCCCCCchhhhHHHHHhhhCHHHHHHHHHHhhCccchHHHHHhheeeccCCccCchhh
Confidence            999999999999999998889999999999999999999999999999999999999999999654

>cd00392 Ribosomal_L13 Ribosomal protein L13

Probab=100.00  E-value=3.9e-53  Score=332.88  Aligned_cols=114  Identities=50%  Similarity=0.849  Sum_probs=112.9

Q ss_pred             EEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChhHHhh
Q 028816           30 WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQME  109 (203)
Q Consensus        30 W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~~~~~  109 (203)
                      |+||||+||+||||||.||++|+|||||+|||++||||+|||||||+|+|||++|.+|.||+|||||||+++.+++++++
T Consensus         1 w~viDA~~~~lGRlAs~iA~~L~gKhKp~y~p~~d~Gd~VvViNa~~i~~tG~k~~~k~y~~~~~~~g~~~~~~~~~~~~   80 (114)
T cd00392           1 WHVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAEKIVITGKKWRQKVYYRHTGYPGGLKNPTAGPLHP   80 (114)
T ss_pred             CEEEeCCCCchHHHHHHHHHHHcCCCCCCcCCCccCCCEEEEEeccEEEEeCchhhccceEEeccCCCCCccCCcchhhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cChhHHHHHHHhccCCCCCchhhhhcCceecCCC
Q 028816          110 RDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGS  143 (203)
Q Consensus       110 r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~  143 (203)
                      ++|++||++||+||||+|.+|+++|+||+||+|+
T Consensus        81 ~~P~~il~~aV~gMLPkn~~g~~~l~rLkvy~g~  114 (114)
T cd00392          81 RAPERILKRAVRGMLPKNKLGRAALKRLKVYEGA  114 (114)
T ss_pred             hCHHHHHHHHHHhcCCCChhHHHHHhCcEEeCCC
Confidence            9999999999999999999999999999999985

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.

>TIGR01077 L13_A_E ribosomal protein L13, archaeal/eukaryotic

Probab=100.00  E-value=3.9e-43  Score=285.58  Aligned_cols=131  Identities=27%  Similarity=0.398  Sum_probs=117.3

Q ss_pred             EEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChhHHhhc
Q 028816           31 RVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMER  110 (203)
Q Consensus        31 ~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~~~~~r  110 (203)
                      +||||+||+||||||.||++|+            |||+|||||||+|.|||+|+.+|.||+||+++|.....++++++++
T Consensus         1 ivIDA~~~vlGRLAs~IA~~L~------------~Gd~VvViNaeki~~TG~k~~~k~~y~~~~~~g~~~~~~~~~~~~r   68 (142)
T TIGR01077         1 TVIDGSGHILGRLASVVAKQLL------------NGEKVVVVNAEKIVISGNFYRNKLKYKEFLRKRTLTNPRRGPFFPR   68 (142)
T ss_pred             CEEeCCCCchHHHHHHHHHHHh------------cCCEEEEEechHheecCchhhheeEEEEECCCCCcccCCHHHhhhc
Confidence            5899999999999999999998            9999999999999999999999999999976555555589999999


Q ss_pred             ChhHHHHHHHhccCCCC-CchhhhhcCceecCCCCCCCCCCCCcceecCccchhhccccchhhHHHHH
Q 028816          111 DPTEAIRKAVLRMLPRN-KLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQ  177 (203)
Q Consensus       111 ~P~~Ii~rAVrGMLPkn-~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~pp~~~r~~r~~~~r~~~~~~  177 (203)
                      +|++||++||+||||+| .+++.+|+||+||+|+||||++|++  .++| .++ ..|+.+.|++|++-
T Consensus        69 ~P~~il~~aVrGMLPk~~~~Gr~~~krLkvy~G~~h~~~~qk~--~~~~-~a~-~~~~~~~~~~~~lg  132 (142)
T TIGR01077        69 APSRIFRRTVRGMLPHKTARGRAALRRLKVYVGIPPELDKKKR--VVVP-EAL-VSRLSPTRKYVTLG  132 (142)
T ss_pred             CHHHHHHHHHHHhCCCCChhHHHHHhCcEEecCCCCCccccCc--cccC-hhh-hhccCCCCceEEHH
Confidence            99999999999999998 5667899999999999999999987  4554 555 78899998887654

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

>PTZ00068 60S ribosomal protein L13a; Provisional

Probab=100.00  E-value=4.3e-43  Score=299.26  Aligned_cols=129  Identities=30%  Similarity=0.456  Sum_probs=118.5

Q ss_pred             eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccC-----
Q 028816           29 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERT-----  103 (203)
Q Consensus        29 ~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~-----  103 (203)
                      +|+||||+||+||||||.||+.|+            |||+|||||||+|+|||+++++|.||+|     +++.++     
T Consensus         4 ~w~vIDA~g~vLGRLAS~VAk~Ll------------~Gd~VVVVNaeki~iTG~k~~~K~~y~~-----~lk~~~~~nP~   66 (202)
T PTZ00068          4 KVIVIDCKGHLLGRLASVVAKELL------------LGQKIVVVRCEDLNISGSLFRNKVKYEE-----FLRKRMNTNPR   66 (202)
T ss_pred             ceEEEECCCCcHHHHHHHHHHHHh------------CCCEEEEEecceeEeecchhhheeeeEe-----eeEeeccCCCC
Confidence            799999999999999999999999            9999999999999999999999999998     466666     


Q ss_pred             hhHHhhcChhHHHHHHHhccCCC-CCchhhhhcCceecCCCCCCCCCCCCcceecCccchhhccccchhhHHHHH
Q 028816          104 LKEQMERDPTEAIRKAVLRMLPR-NKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQ  177 (203)
Q Consensus       104 ~~~~~~r~P~~Ii~rAVrGMLPk-n~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~pp~~~r~~r~~~~r~~~~~~  177 (203)
                      .+++|++.|++||++||+||||+ +.+|+++|+||+||+|+||||++++.  ++ .|.++|++|+.|.|.||+.-
T Consensus        67 ~g~~~~r~P~~Il~raVrGMLPkk~~~Gr~alkrLkVy~G~php~~~~k~--~v-vp~A~r~~rl~~~~ky~~lg  138 (202)
T PTZ00068         67 RGPFHHRAPSDIFWRTVRGMLPHKTKRGAAALKRLKVFEGVPAPYDKVKR--VV-IPSALRVLRLKPERPYTVLG  138 (202)
T ss_pred             cchhcccCHHHHHHHHHhhhCCCCChhHHHHHhCCEEecCCCCchhccCc--cc-ccchhhhhccCCCCceeeHH
Confidence            48999999999999999999998 55777899999999999999999975  44 47999999999999888653

>PRK06394 rpl13p 50S ribosomal protein L13P; Reviewed

Probab=100.00  E-value=1.1e-40  Score=272.26  Aligned_cols=130  Identities=21%  Similarity=0.295  Sum_probs=111.0

Q ss_pred             eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCcccc----Ch
Q 028816           29 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKER----TL  104 (203)
Q Consensus        29 ~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~----~~  104 (203)
                      +-+||||+||+||||||.||++|+            +||+||||||++|++||+|+.+  |++|++|+ +++..    ++
T Consensus         3 ~~~viDA~~~vlGRLAs~IA~~L~------------~Gd~VVViNa~kv~~tG~K~~~--~~~y~~~~-~~k~~~np~~~   67 (146)
T PRK06394          3 AMVVIDAEGQILGRLASYVAKRLL------------EGEEVVIVNAEKAVITGNRERV--IEKYKQRR-ERGSHYNPYRN   67 (146)
T ss_pred             ccEEEECCCCchHHHHHHHHHHHh------------CCCEEEEEechheEecCchhhh--eeeEeCCC-CCcccCCCCCh
Confidence            468999999999999999999999            7999999999999999999877  55566676 46666    78


Q ss_pred             hHHhhcChhHHHHHHHhccCC-CCCchhhhhcCceecCCCCCCCCCCCCcceecCccchhhccccchhhHHHHHH
Q 028816          105 KEQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQK  178 (203)
Q Consensus       105 ~~~~~r~P~~Ii~rAVrGMLP-kn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~pp~~~r~~r~~~~r~~~~~~~  178 (203)
                      +++++++|++||++||+|||| +|.+++.+|+||+||+|+||||++|+|+.+.+   +.+ .++. .|.+|+.-+
T Consensus        68 ~~~~~r~P~~il~~AV~gMLP~kn~~gr~~~~rLkvy~G~~h~~~~qkp~~~~~---a~~-~~~~-~~k~~~lge  137 (146)
T PRK06394         68 GPKYPRRPDRIFKRTIRGMLPYKKPRGREALKRLKVYVGVPKELEGKEFEVIDE---ADL-SRLS-TIKYVTLGE  137 (146)
T ss_pred             HHhhhcCHHHHHHHHHHhcCCCCChhHHHHHhCcEEecCCCCCcccCCCEEecH---HHH-hccC-CCCcEEHHH
Confidence            999999999999999999999 78888899999999999999999998854443   333 3555 577877644

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

Probab=99.89  E-value=4.2e-24  Score=181.39  Aligned_cols=127  Identities=26%  Similarity=0.393  Sum_probs=111.8

Q ss_pred             eEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChhHHh
Q 028816           29 RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQM  108 (203)
Q Consensus        29 ~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~~~~  108 (203)
                      +-.+||+.||++||||+.||+.|+            .|+.||||.||.|.|||+.+++|.|-.+      .-. ..+++|
T Consensus         6 ~~~vidg~~hllGrlAa~vaK~ll------------~g~kvvvvr~E~i~isg~f~r~k~~lrk------~~~-~ng~~h   66 (197)
T KOG3204|consen    6 KLVVIDGRGHLLGRLAAIVAKQLL------------LGRKVVVVRCEEINISGNFYRNKLFLRK------RLN-RNGPFH   66 (197)
T ss_pred             EEeeccchhhhhhhHHHHHHHHHh------------cCCeEEEEEEeEEEEecceecchHHHhh------hhc-ccCcch
Confidence            567999999999999999999999            9999999999999999999999844222      111 238999


Q ss_pred             hcChhHHHHHHHhccCCCCCchh-hhhcCceecCCCCCCCCCCCCcceecCccchhhccccchhhHHHHH
Q 028816          109 ERDPTEAIRKAVLRMLPRNKLRD-DRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQ  177 (203)
Q Consensus       109 ~r~P~~Ii~rAVrGMLPkn~lr~-~~l~rLkvy~G~~hp~~~qk~~~~~~pp~~~r~~r~~~~r~~~~~~  177 (203)
                      ++-|++|++++|+||+|+++.++ ..+++|++|+|.|+|++.+++  ++ .|.+++++|+.+.|++|..=
T Consensus        67 fr~ps~i~~~~vrgm~~~kt~rg~aal~~l~~~eGip~~~dk~~r--~v-~p~a~~v~~lk~~~K~c~lG  133 (197)
T KOG3204|consen   67 FRAPSRILQKAVRGMYPHKTKRGRAALERLRVFEGIPPPYDKQKR--LV-VPVAFQVLRLKPYKKYCLLG  133 (197)
T ss_pred             hhhHHHHHHHhhccccccCCCccHHHHHHHHHhCCCCChhhhcCC--cc-CCcceeeecccCCceeEEec
Confidence            99999999999999999998877 579999999999999999987  44 57999999999999998654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	203
2j28_J	140	Model Of E. Coli Srp Bound To 70s Rncs Length = 140		8e-23
1p85_H	142	Real Space Refined Coordinates Of The 50s Subunit F		8e-23
1pnu_H	143	Crystal Structure Of A Streptomycin Dependent Ribos		1e-21
1nkw_H	174	Crystal Structure Of The Large Ribosomal Subunit Fr		1e-21
1vsa_H	163	Crystal Structure Of A 70s Ribosome-Trna Complex Re		2e-20
3fin_N	139	T. Thermophilus 70s Ribosome In Complex With Mrna,		2e-20
2j01_N	140	Structure Of The Thermus Thermophilus 70s Ribosome		2e-20
3tve_M	138	Crystal Structure Analysis Of Ribosomal Decoding. T		2e-20
1vsp_H	140	Interactions And Dynamics Of The Shine-Dalgarno Hel		2e-20
3pyo_J	137	Crystal Structure Of A Complex Containing Domain 3		2e-20
3mrz_J	139	Recognition Of The Amber Stop Codon By Release Fact		2e-20
3bbo_L	250	Homology Model For The Spinach Chloroplast 50s Subu		1e-17
2ftc_H	148	Structural Model For The Large Subunit Of The Mamma		2e-15

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

Iteration: 1
 Score =  103 bits (256), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 51/116 (43%), Positives = 69/116 (59%)
Query: 30  WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
           W V DA G+ LGRLA+++A  ++GK K  Y P+ D GD  IVLNA  + VTG K  +KVY
Sbjct: 15  WYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVY 74
Query: 90  YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEH 145
           Y HTG+IG +K+ T +E + R P   I  AV  MLP+            ++ G+EH
Sbjct: 75  YHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEH 130

>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 =  103 bits (256), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 51/116 (43%), Positives = 69/116 (59%)
Query: 30  WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
           W V DA G+ LGRLA+++A  ++GK K  Y P+ D GD  IVLNA  + VTG K  +KVY
Sbjct: 15  WYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVY 74
Query: 90  YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEH 145
           Y HTG+IG +K+ T +E + R P   I  AV  MLP+            ++ G+EH
Sbjct: 75  YHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEH 130

>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 = 99.4 bits (246), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 46/117 (39%), Positives = 66/117 (56%)
Query: 30  WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
           W V DA G  LGRLA+ +A+ ++GK +P + PN   GD  +V+NA  + +TG+KL +KVY
Sbjct: 13  WVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKVY 72
Query: 90  YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEHP 146
             +TGY G LK  T +E + + P   I  AV  MLP+            ++ G  HP
Sbjct: 73  TRYTGYQGGLKTETAREALSKHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHP 129

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

Iteration: 1
 Score = 99.0 bits (245), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 46/117 (39%), Positives = 66/117 (56%)
Query: 30  WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
           W V DA G  LGRLA+ +A+ ++GK +P + PN   GD  +V+NA  + +TG+KL +KVY
Sbjct: 41  WVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKVY 100
Query: 90  YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEHP 146
             +TGY G LK  T +E + + P   I  AV  MLP+            ++ G  HP
Sbjct: 101 TRYTGYQGGLKTETAREALSKHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHP 157

>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 = 95.5 bits (236), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 45/118 (38%), Positives = 72/118 (61%)
Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
           RW + DA+G+ LGRLA+++AT+++GK +P + PN   GD  +V+NA  I VTG+KL+ K+
Sbjct: 35  RWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKI 94
Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEHP 146
           Y  ++GY G LK+  L++ +   P   +  AV  MLP+            ++ G +HP
Sbjct: 95  YTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHP 152

>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 = 95.1 bits (235), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 45/118 (38%), Positives = 72/118 (61%)
Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
           RW + DA+G+ LGRLA+++AT+++GK +P + PN   GD  +V+NA  I VTG+KL+ K+
Sbjct: 12  RWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKI 71
Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEHP 146
           Y  ++GY G LK+  L++ +   P   +  AV  MLP+            ++ G +HP
Sbjct: 72  YTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHP 129

>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 = 95.1 bits (235), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 45/118 (38%), Positives = 72/118 (61%)
Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
           RW + DA+G+ LGRLA+++AT+++GK +P + PN   GD  +V+NA  I VTG+KL+ K+
Sbjct: 12  RWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKI 71
Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEHP 146
           Y  ++GY G LK+  L++ +   P   +  AV  MLP+            ++ G +HP
Sbjct: 72  YTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHP 129

>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 = 95.1 bits (235), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 45/118 (38%), Positives = 72/118 (61%)
Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
           RW + DA+G+ LGRLA+++AT+++GK +P + PN   GD  +V+NA  I VTG+KL+ K+
Sbjct: 12  RWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKI 71
Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEHP 146
           Y  ++GY G LK+  L++ +   P   +  AV  MLP+            ++ G +HP
Sbjct: 72  YTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHP 129

>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 = 95.1 bits (235), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 45/118 (38%), Positives = 72/118 (61%)
Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
           RW + DA+G+ LGRLA+++AT+++GK +P + PN   GD  +V+NA  I VTG+KL+ K+
Sbjct: 12  RWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKI 71
Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEHP 146
           Y  ++GY G LK+  L++ +   P   +  AV  MLP+            ++ G +HP
Sbjct: 72  YTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHP 129

>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 = 95.1 bits (235), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 45/118 (38%), Positives = 72/118 (61%)
Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
           RW + DA+G+ LGRLA+++AT+++GK +P + PN   GD  +V+NA  I VTG+KL+ K+
Sbjct: 11  RWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKI 70
Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEHP 146
           Y  ++GY G LK+  L++ +   P   +  AV  MLP+            ++ G +HP
Sbjct: 71  YTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHP 128

>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 = 95.1 bits (235), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 45/118 (38%), Positives = 72/118 (61%)
Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
           RW + DA+G+ LGRLA+++AT+++GK +P + PN   GD  +V+NA  I VTG+KL+ K+
Sbjct: 11  RWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKI 70
Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEHP 146
           Y  ++GY G LK+  L++ +   P   +  AV  MLP+            ++ G +HP
Sbjct: 71  YTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHP 128

>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 = 85.9 bits (211), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/118 (37%), Positives = 65/118 (55%)
Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
           +W V DA   +LGR+AS +A  ++GK+  +Y P+ D G   IV+NA  + V+G+K   K+
Sbjct: 113 KWYVVDATDLILGRMASTIAIHIRGKNLASYTPSVDMGAFVIVVNADKVAVSGKKRTQKL 172
Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEHP 146
           Y  H+G  G LKE T  +  +R P   I  AV  MLP+            ++ G+EHP
Sbjct: 173 YRRHSGRPGGLKEETFDQLQKRIPERIIEHAVRGMLPKGRLGRYLFNHLKVYKGAEHP 230

>pdb|2FTC|H Chain H, Structural Model For The Large Subunit Of The Mammalian Mitochondrial Ribosome Length = 148

Iteration: 1
 Score = 79.0 bits (193), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 38/112 (33%), Positives = 57/112 (50%)
Query: 30  WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
           W + D K Q  G+LA+  +  +QG  KP Y    D GD  +++N + I  +G K + KVY
Sbjct: 18  WYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIMNTRHIAFSGNKWEQKVY 77
Query: 90  YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFP 141
             HTGY G  ++ T  +   RDP   ++ A+  MLP+N           +FP
Sbjct: 78  SSHTGYPGGFRQVTAAQLHLRDPVAIVKLAIYGMLPKNLHRRTMMERLHLFP 129

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	203
2ftc_H	148	L13MT, MRP-L13, 39S ribosomal protein L13, mitocho	3e-57
3v2d_N	140	50S ribosomal protein L13; ribosome associated inh	4e-56
3r8s_J	142	50S ribosomal protein L13; protein biosynthesis, R	1e-55
3f1f_N	163	50S ribosomal protein L13; RF2, ribosome, terminat	9e-55
2zjr_G	174	50S ribosomal protein L13; ribosome, large ribosom	1e-54
3bbo_L	250	Ribosomal protein L13; large ribosomal subunit, sp	4e-53
1j3a_A	142	50S ribosomal protein L13P; rRNA binding, ribosoma	1e-32
1vq8_J	145	50S ribosomal protein L13P; ribosome 50S, protein-	1e-31
3jyw_M	178	60S ribosomal protein L16(A); eukaryotic ribosome,	2e-27
4a17_I	198	RPL13A, 60S ribosomal protein L13A; eukaryotic rib	7e-26
3iz5_K	206	60S ribosomal protein L13A (L13P); eukaryotic ribo	2e-25
3izc_K	199	60S ribosomal protein RPL16 (L13P); eukaryotic rib	1e-24
2zkr_j	203	60S ribosomal protein L13A; protein-RNA complex, 6	5e-21
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-04

>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 =  176 bits (449), Expect = 3e-57
 Identities = 41/118 (34%), Positives = 61/118 (51%)

Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
            W + D K Q  G+LA+  +  +QG  KP Y    D GD  +++N + I  +G K + KV
Sbjct: 17  IWYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIMNTRHIAFSGNKWEQKV 76

Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 146
           Y  HTGY G  ++ T  +   RDP   ++ A+  MLP+N  R     +L +FP    P
Sbjct: 77  YSSHTGYPGGFRQVTAAQLHLRDPVAIVKLAIYGMLPKNLHRRTMMERLHLFPDEYIP 134

>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 =  173 bits (441), Expect = 4e-56
 Identities = 47/118 (39%), Positives = 77/118 (65%)

Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
           RW + DA+G+ LGRLA+++AT+++GK +P + PN   GD  +V+NA  I VTG+KL+ K+
Sbjct: 12  RWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKI 71

Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 146
           Y  ++GY G LK+  L++ +   P   +  AV  MLP+  L     ++L+++ G +HP
Sbjct: 72  YTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHP 129

>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 =  172 bits (439), Expect = 1e-55
 Identities = 55/118 (46%), Positives = 74/118 (62%)

Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
            W V DA G+ LGRLA+++A  ++GK K  Y P+ D GD  IVLNA  + VTG K  +KV
Sbjct: 14  DWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKV 73

Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 146
           YY HTG+IG +K+ T +E + R P   I  AV  MLP+  L     RKL+++ G+EH 
Sbjct: 74  YYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHN 131

>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 =  170 bits (434), Expect = 9e-55
 Identities = 47/118 (39%), Positives = 77/118 (65%)

Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
           RW + DA+G+ LGRLA+++AT+++GK +P + PN   GD  +V+NA  I VTG+KL+ K+
Sbjct: 35  RWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKI 94

Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 146
           Y  ++GY G LK+  L++ +   P   +  AV  MLP+  L     ++L+++ G +HP
Sbjct: 95  YTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHP 152

>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 =  171 bits (435), Expect = 1e-54
 Identities = 47/118 (39%), Positives = 70/118 (59%)

Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
            W V DA G  LGRLA+ +A+ ++GK +P + PN   GD  +V+NA  + +TG+KL +KV
Sbjct: 40  NWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKV 99

Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 146
           Y  +TGY G LK  T +E + + P   I  AV  MLP+ +       +L+++ G  HP
Sbjct: 100 YTRYTGYQGGLKTETAREALSKHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHP 157

>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 =  169 bits (430), Expect = 4e-53
 Identities = 46/118 (38%), Positives = 69/118 (58%)

Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
           +W V DA   +LGR+AS +A  ++GK+  +Y P+ D G   IV+NA  + V+G+K   K+
Sbjct: 113 KWYVVDATDLILGRMASTIAIHIRGKNLASYTPSVDMGAFVIVVNADKVAVSGKKRTQKL 172

Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 146
           Y  H+G  G LKE T  +  +R P   I  AV  MLP+ +L       L+++ G+EHP
Sbjct: 173 YRRHSGRPGGLKEETFDQLQKRIPERIIEHAVRGMLPKGRLGRYLFNHLKVYKGAEHP 230

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

 Score =  113 bits (286), Expect = 1e-32
 Identities = 30/139 (21%), Positives = 57/139 (41%), Gaps = 16/139 (11%)

Query: 32  VFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYW 91
           + +A G +LGRLAS+VA ++              G+  +++NA+   +TG +      Y 
Sbjct: 3   IINADGLILGRLASRVAKMLLE------------GEEVVIVNAEKAVITGNREVIFSKYK 50

Query: 92  HTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPGSEHPFGDR 150
               +  L          +   E +R+ +  MLP +        R+L+++ G    F D+
Sbjct: 51  QRTGLRTLTNPRRGPFYPKRSDEIVRRTIRGMLPWKTDRGRKAFRRLKVYVGIPKEFQDK 110

Query: 151 PLEPYVMPP-RRVRELRPR 168
             +   +      R  RP+
Sbjct: 111 --QLETIVEAHVSRLSRPK 127

>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 =  111 bits (279), Expect = 1e-31
 Identities = 27/137 (19%), Positives = 54/137 (39%), Gaps = 20/137 (14%)

Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
              + DA+  ++GR+ASQVA                DG+   V+NA+   +TGR+ +   
Sbjct: 8   ADVIVDARDCIMGRVASQVAEQA------------LDGETVAVVNAERAVITGREEQIVE 55

Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPGSEHPF 147
            Y     IG+           + P    ++ +  MLP + +   +    +R++ G+ +  
Sbjct: 56  KYEKRVDIGNDNGYFY----PKRPDGIFKRTIRGMLPHKKQRGREAFESVRVYLGNPYDE 111

Query: 148 GDRPLEPY---VMPPRR 161
               L+      +   +
Sbjct: 112 DGEVLDGTSLDRLSNIK 128

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

 Score =  101 bits (253), Expect = 2e-27
 Identities = 34/139 (24%), Positives = 60/139 (43%), Gaps = 16/139 (11%)

Query: 32  VFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYW 91
           V D KG ++GRLAS VA  +             +G   +V+ A+++ ++G   +NK+ Y 
Sbjct: 2   VIDGKGHLVGRLASVVAKQL------------LNGQKIVVVRAEELNISGEFFRNKLKYH 49

Query: 92  HTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPGSEHPFGDR 150
                     +T      R P+    KA+  M+  +         +L++F G   P+  +
Sbjct: 50  DFLRKATAFNKTRGPFHFRAPSRIFYKALRGMVSHKTARGKAALERLKVFEGIPPPYDKK 109

Query: 151 PLEPYVMP-PRRVRELRPR 168
             +  V+P   RV  L+P 
Sbjct: 110 --KRVVVPQALRVLRLKPG 126

>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 = 98.1 bits (244), Expect = 7e-26
 Identities = 43/196 (21%), Positives = 69/196 (35%), Gaps = 33/196 (16%)

Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
           +  V DAKG +LGRLAS VA  +              G   +V+  + I ++G   +N+V
Sbjct: 4   KLVVIDAKGHLLGRLASYVAKELLS------------GQRIVVVRTEAINISGSLFRNRV 51

Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPGSEHPF 147
            +                Q  R P+    +AV  MLP +         +L+IF G   P+
Sbjct: 52  KFSEFLNKWMNHNPRRGVQHFRAPSRIFWRAVRGMLPHKTPKGAAALERLKIFEGIPTPY 111

Query: 148 GDRPLE--PYVMPPRRVRELRPRVR------------RAMI------REQKKAEMQQSNK 187
                +     +  +R+R  RP  +            + +I      R  +         
Sbjct: 112 DRVKKQVVVDALKVQRLRNSRPVCKLGDLSASVGWGKQTLIEKLEEKRRARAKTYHDKKV 171

Query: 188 DMRKNRKKEVEAEVTA 203
                RKKE+ A    
Sbjct: 172 KQADARKKELAAPALK 187

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

 Score = 85.5 bits (211), Expect = 5e-21
 Identities = 32/141 (22%), Positives = 53/141 (37%), Gaps = 13/141 (9%)

Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
           +  V D +G +LGRLA+ VA  V              G   +V+  + I ++G   +NK+
Sbjct: 5   QVLVLDGRGHLLGRLAAIVAKQV------------LLGRKVVVVRCEGINISGNFYRNKL 52

Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPGSEHPF 147
            Y            +      R P+    + V  MLP + K       +L++F G   P+
Sbjct: 53  NYLAFLRKRMNTNPSRGPYDFRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPY 112

Query: 148 GDRPLEPYVMPPRRVRELRPR 168
             +         + VR    R
Sbjct: 113 DKKKRMVVPAALKVVRLKPTR 133

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 39.1 bits (90), Expect = 7e-04
 Identities = 24/109 (22%), Positives = 38/109 (34%), Gaps = 22/109 (20%)

Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVL--RMLPRNKLRDDRDRKLRIFPGSEHP 146
           +Y H G+  HLK     E  ER      R   L  R L   K+R   D       GS   
Sbjct: 473 FYSHIGH--HLKN---IEHPERM--TLFRMVFLDFRFL-EQKIR--HDSTAWNASGSILN 522

Query: 147 -FGD-RPLEPYV-----MPPRRVRELR---PRVRRAMIREQKKAEMQQS 185
                +  +PY+        R V  +    P++   +I  +    ++ +
Sbjct: 523 TLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIA 571

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

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

>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=100.00  E-value=2.8e-61  Score=390.09  Aligned_cols=132  Identities=36%  Similarity=0.678  Sum_probs=128.7

Q ss_pred             CCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChh
Q 028816           26 EGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLK  105 (203)
Q Consensus        26 ~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~  105 (203)
                      -.|+|+||||+||+||||||.||++|+|||||+|||++||||+|||||||+|+|||+||++|.||+|||||||+++++++
T Consensus         9 ~~r~w~viDA~~~~LGRLAs~iAk~L~GKhKp~ytP~~d~Gd~VVViNaeki~~tG~k~~~K~yy~htgypGglk~~~~~   88 (140)
T 3v2d_N            9 VEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLE   88 (140)
T ss_dssp             CCCCEEEEECSSSBTTHHHHHHHHHHHTTTSTTCCTTSCCCCEEEEECGGGCBCCTTHHHHCEEEEECSSTTCEEEEEHH
T ss_pred             ccceEEEEeCCCCchHHHHHHHHHHHcCCCCCccCCCccCCCEEEEEeCcceEccCchhhheeeEEecccCCcceeccHH
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhcChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCcceec
Q 028816          106 EQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVM  157 (203)
Q Consensus       106 ~~~~r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~  157 (203)
                      ++++++|++||++||+||||+|.+|+.+|+||+||+|++|||++|+|+++++
T Consensus        89 ~~~~r~P~~ii~~aVrGMLPk~~lgr~~l~rLkVy~G~~hph~aq~p~~~~~  140 (140)
T 3v2d_N           89 KMLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKLEV  140 (140)
T ss_dssp             HHHHHCTHHHHHHHHHHTSCSSHHHHHHHHTEEECSSSCCSCGGGCCEEECC
T ss_pred             HhhhhCHHHHHHHHHHhcCCCChhHHHHHhCCEEeCCCCCCcccCCCeecCC
Confidence            9999999999999999999999999999999999999999999999987764

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

Probab=100.00  E-value=1.2e-60  Score=389.40  Aligned_cols=136  Identities=31%  Similarity=0.459  Sum_probs=131.7

Q ss_pred             cccCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCcccc
Q 028816           23 INLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKER  102 (203)
Q Consensus        23 ~~~~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~  102 (203)
                      +....|+|+||||+||+||||||.||++|+|||||+|||++||||+|||||||+|+|||+||++|.||+|||||||++++
T Consensus        11 ~~~~~r~w~viDA~g~~LGRLAs~iA~~L~GKhKp~ytP~~D~Gd~VVViNaeki~~tG~k~~~K~yy~htg~pGg~k~~   90 (148)
T 2ftc_H           11 WATFARIWYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIMNTRHIAFSGNKWEQKVYSSHTGYPGGFRQV   90 (148)
T ss_pred             hhcccCcEEEEeCCCCchHHHHHHHHHHHhccCCCCcCccccCCCEEEEEeceeeEeccchHhhheeeeeeCCcCCceec
Confidence            44557999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ChhHHhhcChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCcceecC
Q 028816          103 TLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMP  158 (203)
Q Consensus       103 ~~~~~~~r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~p  158 (203)
                      +++++++++|++||++||+||||+|.+|+.+|+||+||+|++|||++|+|+.++++
T Consensus        91 ~~~~~~~r~P~~ii~~aVrGMLPkn~lgr~~l~rLkVy~G~~hP~~aq~p~~~~i~  146 (148)
T 2ftc_H           91 TAAQLHLRDPVAIVKLAIYGMLPKNLHRRTMMERLHLFPDEYIPEDILKNLVEELP  146 (148)
T ss_pred             cHHHHhhcCHHHHHHHHHHhcCCCCchHHHHHhCcEEeCCCCCChHHhCCeeeccC
Confidence            99999999999999999999999999999999999999999999999999888874

>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=100.00  E-value=7.7e-61  Score=388.30  Aligned_cols=133  Identities=41%  Similarity=0.671  Sum_probs=129.0

Q ss_pred             cCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccCh
Q 028816           25 LEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTL  104 (203)
Q Consensus        25 ~~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~  104 (203)
                      .-.|+|+||||+||+||||||.||++|+|||||+|||++||||+|||||||+|+|||+||++|.||+|||||||++++++
T Consensus        10 ~~~r~W~viDA~g~~LGRLAs~iAk~L~GKhKp~ytP~~d~Gd~VVViNaeki~~tG~k~~~K~yy~htgypGg~k~~~~   89 (142)
T 3r8s_J           10 TVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVYYHHTGHIGGIKQATF   89 (142)
T ss_dssp             TCCCCEEEEECTTCBHHHHHHHHHHHHHTTTSTTCCTTSCCCCEEEEECGGGCBCCTTHHHHCBCCEECSSTTCEECCBH
T ss_pred             hccCcEEEEeCCCCchHHHHHHHHHHHcCCCCCccCCCccCCCEEEEEeCcccCccCchhhceEEEEecCcCCCccccCH
Confidence            34699999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHhhcChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCcceec
Q 028816          105 KEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVM  157 (203)
Q Consensus       105 ~~~~~r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~  157 (203)
                      +++++++|++||++||+||||+|.+|+.+|+||+||+|++|||++|+|+++++
T Consensus        90 ~~~~~r~P~~ii~~aVrGMLPkn~lgr~~l~rLkVy~G~~hph~aq~p~~l~~  142 (142)
T 3r8s_J           90 EEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI  142 (142)
T ss_dssp             HHHHHHCSHHHHHHHHHHHSCSSHHHHHHHTTEEECSSSCCSCGGGCCEECCC
T ss_pred             HHHHhhCHHHHHHHHHHhcCCCChhHHHHHhCCEEECCCCCCcccCCCeecCC
Confidence            99999999999999999999999999999999999999999999999987753

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

Probab=100.00  E-value=4.2e-60  Score=391.16  Aligned_cols=133  Identities=36%  Similarity=0.668  Sum_probs=128.0

Q ss_pred             cCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccCh
Q 028816           25 LEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTL  104 (203)
Q Consensus        25 ~~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~  104 (203)
                      .-.|+|+||||+||+||||||.||++|+|||||+|||++||||+|||||||+|+|||+||++|.||+|||||||++++++
T Consensus        31 ~~~r~W~VIDA~g~~LGRLAs~VAk~L~GKhKP~ytP~~D~GD~VVVINaekI~iTG~K~~~K~yy~htgypGglk~~t~  110 (163)
T 3f1f_N           31 QVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPL  110 (163)
T ss_dssp             CCCCCBCBBCCTTCBHHHHHHHHHHHHSCTTSTTCCTTTCCCCBCEECCGGGCBCSTTHHHHCEECCBCSSTTCBCCEEH
T ss_pred             cccCcEEEEeCCCCchHHHHHHHHHHHhcCCCCccCCcccCCCEEEEEeCcccccCCchhhheeeEEecCcCCcceeeeh
Confidence            34699999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHhhcChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCcceec
Q 028816          105 KEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVM  157 (203)
Q Consensus       105 ~~~~~r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~  157 (203)
                      +++++++|++||++||+||||+|.+|+.+|+||+||+|++|||++|+|+++++
T Consensus       111 ~~~~~r~P~~Ii~~AVrGMLPkn~lGr~~l~rLkVY~G~~hPh~aQ~P~~l~~  163 (163)
T 3f1f_N          111 EKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKLEV  163 (163)
T ss_dssp             HHHHHSSCHHHHHHHHHTTSCSSHHHHHHHHTCEECSSSCCCCCSCCCBCC--
T ss_pred             HHhhhcCHHHHHHHHHHhcCCCChhHHHHHhCCEEECCCCCCcccCCCeecCC
Confidence            99999999999999999999999999999999999999999999999987764

>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=100.00  E-value=4.4e-59  Score=388.48  Aligned_cols=132  Identities=36%  Similarity=0.677  Sum_probs=129.5

Q ss_pred             CCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChh
Q 028816           26 EGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLK  105 (203)
Q Consensus        26 ~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~  105 (203)
                      -.|+|+||||+||+||||||.||++|+|||||+|||++||||+|||||||+|+|||+||++|.||+|||||||+++++++
T Consensus        37 ~~r~W~vIDA~g~~LGRLAs~IAk~L~GKhKP~ytP~~D~GD~VVVINAeki~lTG~K~~~K~yy~htgypGGlk~~~~~  116 (174)
T 2zjr_G           37 DEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKVYTRYTGYQGGLKTETAR  116 (174)
T ss_dssp             SCCCEEEEECTTSBHHHHHHHHHHHHHCSSCSSCCSSSCCCCEEEEECCTTCBCSSCSSSSCEEEECCSSCSSCCEEEES
T ss_pred             ccccEEEEeCCCCchHHHHHHHHHHHhccCCCccCccccCCCEEEEEeCeeeEeccchhhceEEEEecCcCCCcccccHH
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhcChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCcceec
Q 028816          106 EQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVM  157 (203)
Q Consensus       106 ~~~~r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~  157 (203)
                      ++++++|++||++||+||||+|.+|+++|+||+||+|++|||++|+|+.+++
T Consensus       117 ~~~~r~P~~Ii~~AVrGMLPkn~lGr~~l~rLkVy~G~~hph~aqkp~~l~~  168 (174)
T 2zjr_G          117 EALSKHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPHSAQKPQVLKT  168 (174)
T ss_dssp             TTTTSCHHHHHHHHHGGGSCCSHHHHHHHTTCEECSCSTGGGGSCCSCCCCC
T ss_pred             HHhhcChHHHHHHHHHhcCCCChhHHHHHhCeEEECCCCCChhccCCeEEec
Confidence            9999999999999999999999999999999999999999999999988886

>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=9.3e-57  Score=390.62  Aligned_cols=131  Identities=35%  Similarity=0.597  Sum_probs=124.2

Q ss_pred             CceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChhH
Q 028816           27 GLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKE  106 (203)
Q Consensus        27 ~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~~  106 (203)
                      .|+||||||+||+||||||.||++|+|||||+||||+||||+|||||||+|+|||+||++|.|++|||||||++++++++
T Consensus       111 ~r~W~VIDA~g~vLGRLAS~IAk~LrGKhKP~ytP~vD~GD~VVVINAeKI~lTG~K~~~K~Y~rHsgyPGGlK~~t~~~  190 (250)
T 3bbo_L          111 DKKWYVVDATDLILGRMASTIAIHIRGKNLASYTPSVDMGAFVIVVNADKVAVSGKKRTQKLYRRHSGRPGGLKEETFDQ  190 (250)
T ss_dssp             -CCCCEECCSSCCSSTTHHHHTTTTTTTTTTCCCTTSCCSCCCEESCCSSCCCCSGGGGTCCCBCCCSSSSCCCBCCHHH
T ss_pred             cceEEEEeCCCCchHHHHHHHHHHHccCCCCccCccccCCCEEEEEecceEEecCChhhceEEEEecCcCCCcccccHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhcChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCcceec
Q 028816          107 QMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVM  157 (203)
Q Consensus       107 ~~~r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~  157 (203)
                      +++++|++||++||+||||+|.+|+.+|+||+||+|.+|||++|+++.+++
T Consensus       191 l~~r~PerIi~kAVrGMLPkn~lGr~~lkrLkVY~G~~HPh~aQkp~~l~i  241 (250)
T 3bbo_L          191 LQKRIPERIIEHAVRGMLPKGRLGRYLFNHLKVYKGAEHPHQAQQPIDLPL  241 (250)
T ss_dssp             HTTSCTTHHHHHHHHTTSCSSSSHHHHHTTCCCCSSSCCSCTTSCC-----
T ss_pred             hhhcChHHHHHHHHHhcCCCCchHHHHHhCcEEeCCCCCCHHHcCCeeech
Confidence            999999999999999999999999999999999999999999999866554

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

Probab=100.00  E-value=1.1e-48  Score=316.91  Aligned_cols=133  Identities=26%  Similarity=0.401  Sum_probs=109.5

Q ss_pred             EEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccc-cChhHHh
Q 028816           30 WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKE-RTLKEQM  108 (203)
Q Consensus        30 W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~-~~~~~~~  108 (203)
                      |+||||+||+||||||.||++|+            |||+|||||||+|+|||+|+++|.||+|||||||++. ++ ++++
T Consensus         1 W~viDA~g~~LGRLAs~vAk~L~------------~Gd~VVViNaeki~iTG~k~~~K~yy~h~g~~gg~~~~~~-~~~~   67 (142)
T 1j3a_A            1 MRIINADGLILGRLASRVAKMLL------------EGEEVVIVNAEKAVITGNREVIFSKYKQRTGLRTLTNPRR-GPFY   67 (142)
T ss_dssp             CEEEECTTBBHHHHHHHHHHHHH------------TTCCEEEECGGGCEEESCHHHHHHHHHHHC--------------C
T ss_pred             CEEEeCCCCchHHHHHHHHHHHh------------cCCEEEEEeCeeeEecccHHhheeeeeecCCCCCCcCCcc-Cccc
Confidence            99999999999999999999999            9999999999999999999999999999999999766 77 9999


Q ss_pred             hcChhHHHHHHHhccCC-CCCchhhhhcCceecCCCCCCCCCCCCcceecCccchhhccccchhhHHHHHHHH
Q 028816          109 ERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQKKA  180 (203)
Q Consensus       109 ~r~P~~Ii~rAVrGMLP-kn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~pp~~~r~~r~~~~r~~~~~~~~~  180 (203)
                      +++|++||++||+|||| +|.+|+++|+||+||+|+||||++|+|+.+  | .+.+ .|+. .|+||.+-.-+
T Consensus        68 ~r~P~~ii~~aVrGMLP~k~~lgr~~l~rLkVy~G~~hp~~aqkp~~~--~-~a~~-~~~~-~~k~~~lg~ls  135 (142)
T 1j3a_A           68 PKRSDEIVRRTIRGMLPWKTDRGRKAFRRLKVYVGIPKEFQDKQLETI--V-EAHV-SRLS-RPKYVTVGEVA  135 (142)
T ss_dssp             CCSHHHHHHHHHHTTTTTTSHHHHHHHTTEEECSSCCGGGTTSCCBCC--G-GGBG-GGSS-SCCEEEHHHHH
T ss_pred             ccCHHHHHHHHHHhhccCCCHHHHHHHhCcEEeCCCCCCccccCcEec--c-HHHh-hccC-CCCeEEHHHHH
Confidence            99999999999999999 788899999999999999999999998543  3 3444 5654 78888765443

>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=100.00  E-value=3.7e-46  Score=303.12  Aligned_cols=131  Identities=22%  Similarity=0.244  Sum_probs=117.4

Q ss_pred             CCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChh
Q 028816           26 EGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLK  105 (203)
Q Consensus        26 ~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~  105 (203)
                      +.++|+||||+||+||||||.||++|+            |||+|||||||+|+|||+|+++|.||+||||||+    +++
T Consensus         5 ~~~~w~viDA~g~~LGRLAs~vAk~L~------------~Gd~VVViNaeki~iTG~k~~~K~yy~htg~~g~----~~~   68 (145)
T 1vq8_J            5 EFDADVIVDARDCIMGRVASQVAEQAL------------DGETVAVVNAERAVITGREEQIVEKYEKRVDIGN----DNG   68 (145)
T ss_dssp             CCCCSEEEECTTBBHHHHHHHHHHHHH------------TTCCEEEECGGGCEEESCHHHHHHHHHHHHHCCC----SSC
T ss_pred             ccccEEEEeCCCCchHHHHHHHHHHHh------------cCCEEEEEeCEeeEecchhhhheeeeEEeCCCCC----CHH
Confidence            457899999999999999999999999            9999999999999999999999999999999998    889


Q ss_pred             HHhhcChhHHHHHHHhccCC-CCCchhhhhcCceecCCCCCCCCCCCCcceecCccchhhccccchhhHHHHHHHH
Q 028816          106 EQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQKKA  180 (203)
Q Consensus       106 ~~~~r~P~~Ii~rAVrGMLP-kn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~pp~~~r~~r~~~~r~~~~~~~~~  180 (203)
                      ++++++|++||++||+|||| ||++|+++|+||+||+|+|||   |++  .++|.+ .+ .|+. .|+||.+-.-+
T Consensus        69 ~~~~r~P~~i~~~aVrGMLP~K~~lgr~~l~rLkVy~G~~~p---~k~--~vv~~a-~~-~~l~-~~k~~~lg~ls  136 (145)
T 1vq8_J           69 YFYPKRPDGIFKRTIRGMLPHKKQRGREAFESVRVYLGNPYD---EDG--EVLDGT-SL-DRLS-NIKFVTLGEIS  136 (145)
T ss_dssp             CCCCCSHHHHHHHHHHTTTTTTSHHHHHHHHTEEECSSCCSS---SCC--BCCTTC-BC-CTTS-CCSEEEHHHHH
T ss_pred             HHhhcChHHHHHHHHHhhcCCCCHHHHHHHhCeEEECCCCCC---CCc--eeeehh-hh-hccC-CCCeEEHHHHH
Confidence            99999999999999999999 888999999999999999999   544  565544 44 5664 78888775544

>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=100.00  E-value=4.8e-46  Score=315.45  Aligned_cols=138  Identities=26%  Similarity=0.308  Sum_probs=127.2

Q ss_pred             ceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChhHH
Q 028816           28 LRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQ  107 (203)
Q Consensus        28 r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~~~  107 (203)
                      ++|+||||+||+||||||.||++|+            |||+|||||||+|+|||++|++|.||+|+.++++....+.+++
T Consensus         3 ~~w~VIDA~g~~LGRLAs~VAk~L~------------~GD~VVVINAekI~iTG~K~~~K~yy~~~l~~~~~~~~~~g~~   70 (198)
T 4a17_I            3 DKLVVIDAKGHLLGRLASYVAKELL------------SGQRIVVVRTEAINISGSLFRNRVKFSEFLNKWMNHNPRRGVQ   70 (198)
T ss_dssp             SSCEEEECTTBBHHHHHHHHHHHHH------------TTCCEEEECGGGCEEESCHHHHHHHHHHHHTCCCSSCTTSSCC
T ss_pred             ccEEEEeCCCCchHHHHHHHHHHHh------------CCCEEEEEcCccccccCchhhheeeeeeccccccCCCCccccc
Confidence            6899999999999999999999999            9999999999999999999999999999988998887788999


Q ss_pred             hhcChhHHHHHHHhccCCC-CCchhhhhcCceecCCCCCCCCCCCCcceecCccchhhccccchhhHHHHHHHH
Q 028816          108 MERDPTEAIRKAVLRMLPR-NKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQKKA  180 (203)
Q Consensus       108 ~~r~P~~Ii~rAVrGMLPk-n~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~pp~~~r~~r~~~~r~~~~~~~~~  180 (203)
                      ++++|++||++||+||||+ |.+|+.+|+||+||+|+||||++|+.  ++ .|.+++++|+.+.|+||.+-.=+
T Consensus        71 ~~r~P~rIi~~AVrGMLPkK~~lGr~~l~rLkVy~G~~hph~aqk~--~v-vp~al~v~rl~~~rk~~~lg~ls  141 (198)
T 4a17_I           71 HFRAPSRIFWRAVRGMLPHKTPKGAAALERLKIFEGIPTPYDRVKK--QV-VVDALKVQRLRNSRPVCKLGDLS  141 (198)
T ss_dssp             CCCSHHHHHHHHHHTTTTTTSHHHHHHHHHCEECSSCCGGGTTSCC--BC-CGGGBHHHHSCTTSCEEEHHHHH
T ss_pred             cccCHHHHHHHHHhccCCCCChhHHHHHhCcEEecCCCCChhhccc--cc-cchHhhhhhcCCCCCeEEHHHHH
Confidence            9999999999999999996 77888999999999999999999975  44 47999999999999888654433

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

Probab=100.00  E-value=4.8e-44  Score=304.20  Aligned_cols=128  Identities=27%  Similarity=0.432  Sum_probs=113.0

Q ss_pred             CceEEEEeCCCCcchhhHHHHHH-HHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEe-eec-------ccCC
Q 028816           27 GLRWRVFDAKGQVLGRLASQVAT-VVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYY-WHT-------GYIG   97 (203)
Q Consensus        27 ~r~W~vIDA~gqvLGRLAS~VAk-~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~-~ht-------gYpG   97 (203)
                      .++|+||||+||+||||||.||+ +|+             ||+|||||||+|+|||++|++|.|| +|+       ||||
T Consensus         3 ~r~w~VIDA~g~~LGRLAS~VAk~lL~-------------G~~VVVINaeki~iTG~k~~~K~yy~~h~~~~~~~n~~~G   69 (203)
T 2zkr_j            3 EVQVLVLDGRGHLLGRLAAIVAKQVLL-------------GRKVVVVRCEGINISGNFYRNKLNYLAFLRKRMNTNPSRG   69 (203)
T ss_dssp             ----CEEECTTBBHHHHHHHHHHHHHH-------------TCCEEEECGGGCEEESCHHHHHHHSSSSSCHHHHCCCSSC
T ss_pred             CccEEEEeCCCCchHHHHHHHHHHHhC-------------CCeEEEEchHHeecCchHHHHHHHHHHHHhhcccCCCCCC
Confidence            47899999999999999999999 666             6899999999999999999999999 998       7877


Q ss_pred             CccccChhHHhhcChhHHHHHHHhccCCC-CCchhhhhcCceecCCCCCCCCCCCCcceecCccchhhccccchhhHHHH
Q 028816           98 HLKERTLKEQMERDPTEAIRKAVLRMLPR-NKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIRE  176 (203)
Q Consensus        98 glk~~~~~~~~~r~P~~Ii~rAVrGMLPk-n~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~pp~~~r~~r~~~~r~~~~~  176 (203)
                      +        +++++|++||++||+||||+ |.+|+.+|+||+||+|+||||++|+|  .++ |.+++++|+++.|.||.+
T Consensus        70 ~--------~~~r~P~~I~~~AVrGMLPkk~~lGr~~l~rLkVy~G~~hp~~aqkp--~vv-p~a~~v~~~~~~~ky~~l  138 (203)
T 2zkr_j           70 P--------YDFRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKR--MVV-PAALKVVRLKPTRKFAYL  138 (203)
T ss_dssp             C--------CCCCSHHHHHHHHHHHHSCTTSHHHHHHHHTEEECSCSSCSSSSCCB--CCG-GGBCCSSSSSCCSCEEEH
T ss_pred             c--------cccCChHHHHHHHHHhhCCCCChhHHHHHhCcEEeCCCCCchhhcCC--ccc-chhhhhhhcCCCCceEEH
Confidence            7        57899999999999999999 67888999999999999999999987  444 689999999999998865


Q ss_pred             HH
Q 028816          177 QK  178 (203)
Q Consensus       177 ~~  178 (203)
                      -.
T Consensus       139 g~  140 (203)
T 2zkr_j          139 GR  140 (203)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

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

Probab=100.00  E-value=1.2e-43  Score=296.57  Aligned_cols=132  Identities=27%  Similarity=0.427  Sum_probs=118.5

Q ss_pred             EEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCcc--ccChhHHh
Q 028816           31 RVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLK--ERTLKEQM  108 (203)
Q Consensus        31 ~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk--~~~~~~~~  108 (203)
                      +||||+||+||||||.||++|+            |||+|||||||+|+|||+||++|.||+|  |++...  ..+.++++
T Consensus         1 ~VIDA~g~~LGRLAs~VAk~L~------------~GD~VVVINaeki~iTG~K~~~K~yy~h--~l~~~~~~~~~~~~~~   66 (178)
T 3jyw_M            1 VVIDGKGHLVGRLASVVAKQLL------------NGQKIVVVRAEELNISGEFFRNKLKYHD--FLRKATAFNKTRGPFH   66 (178)
T ss_dssp             CCCCCCSSCSHHHHHHHHHHHT------------TTCCCCEECSTTSCCCCCSSHHHHSCSS--SSSSTTSCCCSSSCCC
T ss_pred             CEEcCCCCchHHHHHHHHHHHh------------CCCEEEEEeCeeeEEcCchHhhEhheec--cCcccccCCccccccc
Confidence            5899999999999999999999            9999999999999999999999999998  554332  33468999


Q ss_pred             hcChhHHHHHHHhccCCC-CCchhhhhcCceecCCCCCCCCCCCCcceecCccchhhccccchhhHHHHHHH
Q 028816          109 ERDPTEAIRKAVLRMLPR-NKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQKK  179 (203)
Q Consensus       109 ~r~P~~Ii~rAVrGMLPk-n~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~pp~~~r~~r~~~~r~~~~~~~~  179 (203)
                      +++|++||+++|+||||+ |.+|+.+|+||+||+|.||||++|++  ++ .|.+++++|+++.|++|.+..-
T Consensus        67 ~r~P~~Il~~AVrGMLP~K~~lGr~~l~rLkVy~G~~hp~~aqk~--~v-vp~Alrv~RLkp~rKy~tLGel  135 (178)
T 3jyw_M           67 FRAPSRIFYKALRGMVSHKTARGKAALERLKVFEGIPPPYDKKKR--VV-VPQALRVLRLKPGRKYTTLGKL  135 (178)
T ss_dssp             CSSTTTHHHHHTTSSSCSSSHHHHHHHHHCCEESSCCCCSCCSCS--SS-CCSSCCCCCSSSCSCCCCHHHH
T ss_pred             cCCHHHHHHHHHHHHhhcccHhHHHHHhCCeeeCCCCCchhhccc--cc-CchHhhhhccCCCCceEEcchh
Confidence            999999999999999995 77888999999999999999999986  34 4789999999999999987654

---

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	203
d2zjrg1	142	c.21.1.1 (G:30-171) Ribosomal protein L13 {Deinoco	1e-35
d2j01n1	139	c.21.1.1 (N:1-139) Ribosomal protein L13 {Thermus	5e-35
d2gych1	140	c.21.1.1 (H:1-140) Ribosomal protein L13 {Escheric	2e-33
d1vqoj1	142	c.21.1.1 (J:4-145) Ribosomal protein L13 {Archaeon	5e-24
d1j3aa_	142	c.21.1.1 (A:) Ribosomal protein L13 {Archaeon Pyro	2e-22

>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 =  120 bits (302), Expect = 1e-35
 Identities = 47/119 (39%), Positives = 70/119 (58%)

Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
            W V DA G  LGRLA+ +A+ ++GK +P + PN   GD  +V+NA  + +TG+KL +KV
Sbjct: 11  NWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKV 70

Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPF 147
           Y  +TGY G LK  T +E + + P   I  AV  MLP+ +       +L+++ G  HP 
Sbjct: 71  YTRYTGYQGGLKTETAREALSKHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPH 129

>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 =  118 bits (297), Expect = 5e-35
 Identities = 47/119 (39%), Positives = 77/119 (64%)

Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
           RW + DA+G+ LGRLA+++AT+++GK +P + PN   GD  +V+NA  I VTG+KL+ K+
Sbjct: 12  RWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKI 71

Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPF 147
           Y  ++GY G LK+  L++ +   P   +  AV  MLP+  L     ++L+++ G +HP 
Sbjct: 72  YTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHPH 130

>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 =  114 bits (287), Expect = 2e-33
 Identities = 55/118 (46%), Positives = 74/118 (62%)

Query: 30  WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 89
           W V DA G+ LGRLA+++A  ++GK K  Y P+ D GD  IVLNA  + VTG K  +KVY
Sbjct: 15  WYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVY 74

Query: 90  YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPF 147
           Y HTG+IG +K+ T +E + R P   I  AV  MLP+  L     RKL+++ G+EH  
Sbjct: 75  YHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNH 132

>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 = 90.3 bits (224), Expect = 5e-24
 Identities = 29/130 (22%), Positives = 52/130 (40%), Gaps = 17/130 (13%)

Query: 29  RWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKV 88
              + DA+  ++GR+ASQVA                DG+   V+NA+   +TGR+ +   
Sbjct: 5   ADVIVDARDCIMGRVASQVAEQA------------LDGETVAVVNAERAVITGREEQIVE 52

Query: 89  YYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRD-RKLRIFPGSEHPF 147
            Y     IG+           + P    ++ +  MLP  K R       +R++ G+ +  
Sbjct: 53  KYEKRVDIGNDNGYF----YPKRPDGIFKRTIRGMLPHKKQRGREAFESVRVYLGNPYDE 108

Query: 148 GDRPLEPYVM 157
               L+   +
Sbjct: 109 DGEVLDGTSL 118

>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 = 86.6 bits (214), Expect = 2e-22
 Identities = 30/139 (21%), Positives = 57/139 (41%), Gaps = 15/139 (10%)

Query: 31  RVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYY 90
           R+ +A G +LGRLAS+VA ++             +G+  +++NA+   +TG +      Y
Sbjct: 2   RIINADGLILGRLASRVAKML------------LEGEEVVIVNAEKAVITGNREVIFSKY 49

Query: 91  WHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPGSEHPFGD 149
                +  L          +   E +R+ +  MLP +        R+L+++ G    F D
Sbjct: 50  KQRTGLRTLTNPRRGPFYPKRSDEIVRRTIRGMLPWKTDRGRKAFRRLKVYVGIPKEFQD 109

Query: 150 RPLEPYVMPPRRVRELRPR 168
           +  +   +    V  L   
Sbjct: 110 K--QLETIVEAHVSRLSRP 126

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	203
d2j01n1	139	Ribosomal protein L13 {Thermus thermophilus [TaxId	100.0
d2zjrg1	142	Ribosomal protein L13 {Deinococcus radiodurans [Ta	100.0
d2gych1	140	Ribosomal protein L13 {Escherichia coli [TaxId: 56	100.0
d1j3aa_	142	Ribosomal protein L13 {Archaeon Pyrococcus horikos	100.0
d1vqoj1	142	Ribosomal protein L13 {Archaeon Haloarcula marismo	100.0

>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=100.00  E-value=3.3e-58  Score=369.47  Aligned_cols=130  Identities=37%  Similarity=0.689  Sum_probs=126.5

Q ss_pred             CceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChhH
Q 028816           27 GLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKE  106 (203)
Q Consensus        27 ~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~~  106 (203)
                      .|+||||||+||+||||||.||++|+|||||+|||+.||||+||||||++|+|||+||.++.||+|||||||+++.++++
T Consensus        10 ~r~W~viDA~~~~lGRLAs~iA~~L~GK~kp~y~p~~d~Gd~VvViNa~ki~~tG~k~~~k~y~~hsgypGg~k~~~~~~   89 (139)
T d2j01n1          10 EPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEK   89 (139)
T ss_dssp             CCCCCEECCTTSBTTHHHHHHHHHHTTSSSSSCCTTTCCCCCCEECSCSCCBCSSCCSSSSBCCCCCCSSSCCCCCBHHH
T ss_pred             cceEEEEeCCCCchHHHHHHHHHHHhccchheeeeccCCCceEEEechhHeeeeccccceeeeeeeccccCccccccHHH
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhcChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCccee
Q 028816          107 QMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYV  156 (203)
Q Consensus       107 ~~~r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~  156 (203)
                      +++++|++||++||+||||+|++|+.+|+||+||+|++|||++|+|+.++
T Consensus        90 ~~~k~P~~il~~aV~gMLPkn~lg~~~l~rLkvy~g~~hp~~aq~p~~l~  139 (139)
T d2j01n1          90 MLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKLE  139 (139)
T ss_dssp             HHHSSCSHHHHHHHHTTSCSSHHHHHHHTTCEECSSSCCTTCSCCCCCC-
T ss_pred             hcccCHHHHHHHHHHhcCCCChhHHHHHhCCEEeCCCCCCcccCCCEeCC
Confidence            99999999999999999999999999999999999999999999987653

>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=100.00  E-value=9.3e-58  Score=368.04  Aligned_cols=131  Identities=36%  Similarity=0.676  Sum_probs=128.2

Q ss_pred             CceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChhH
Q 028816           27 GLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKE  106 (203)
Q Consensus        27 ~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~~  106 (203)
                      +|+||||||+||+||||||.||++|+|||||+|||+.||||+||||||++|++||+||.+|.|++|||||||++++++++
T Consensus         9 ~r~W~viDA~~~~lGRlAs~iAk~L~GK~kp~y~p~~d~Gd~ViViNa~ki~~tG~K~~~k~y~~htg~pgg~k~~~~~~   88 (142)
T d2zjrg1           9 EQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKVYTRYTGYQGGLKTETARE   88 (142)
T ss_dssp             CCCEEEEECTTSBHHHHHHHHHHHHHCSSCSSCCSSSCCCCEEEEECCTTCBCSSCSSSSCEEEECCSSCSSCCEEEEST
T ss_pred             CccEEEEECCCCchHHHHHHHHHHHhcCcccceeecccCCCEEEEcCCceeEEcCcchhhheehhhcccccccccccHHH
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhcChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCcceec
Q 028816          107 QMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVM  157 (203)
Q Consensus       107 ~~~r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~  157 (203)
                      +++++|++||++||+||||+|.+|+.+|+||+||+|++|||++|+|+.+++
T Consensus        89 ~~~r~P~~ii~~aV~gMLPkn~lgr~~lkrLkvy~G~~hp~~~q~P~~l~~  139 (142)
T d2zjrg1          89 ALSKHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPHSAQKPQVLKT  139 (142)
T ss_dssp             TTTSCHHHHHHHHHGGGSCCSHHHHHHHTTCEECSCSTGGGGSCCSCCCCC
T ss_pred             HhccchHHHHHHHHHhcCCCChhHHHHHhCCeEeCCCCCCccccCCceecc
Confidence            999999999999999999999999999999999999999999999987775

>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=100.00  E-value=1.2e-58  Score=372.53  Aligned_cols=130  Identities=42%  Similarity=0.688  Sum_probs=126.9

Q ss_pred             cCCceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccCh
Q 028816           25 LEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTL  104 (203)
Q Consensus        25 ~~~r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~  104 (203)
                      .-.++||||||+||+||||||.||++|+|||||+|||+.||||+|||||||+|+|||+||.+|.||+|||||||+++.++
T Consensus        10 ~~~r~W~viDA~~~~lGRlAs~iA~~L~GK~kp~y~p~~d~Gd~VvViNaeki~~tG~K~~~k~y~~~sgypgg~k~~~~   89 (140)
T d2gych1          10 TVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVYYHHTGHIGGIKQATF   89 (140)
T ss_dssp             CTTCCCCCCCCSSSCSHHHHSSSSSSSTTCSSSCCCSSSCCCCCCCCSCSSSCCCCSSCSTTCCCCCCCSSCSSCCCCCC
T ss_pred             HhCccEEEEeCCCCchHHHHHHHHHHHHhccCCccccccCCCcEEEEEechhhcccCchhhhhhhhccccCCCCcccccH
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHhhcChhHHHHHHHhccCCCCCchhhhhcCceecCCCCCCCCCCCCcc
Q 028816          105 KEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEP  154 (203)
Q Consensus       105 ~~~~~r~P~~Ii~rAVrGMLPkn~lr~~~l~rLkvy~G~~hp~~~qk~~~  154 (203)
                      +++++++|++||++||+||||+|.+|+++|+||+||+|++|||++|+|++
T Consensus        90 ~~~~~k~P~~il~~aV~gMLPkn~lgr~~lkrLkvy~g~~hph~aQ~P~~  139 (140)
T d2gych1          90 EEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQV  139 (140)
T ss_dssp             HHHHTTCSSSSTTTSSSSCSCSSSTTSSTTTSSCCCCCCTTTTTSCCCCC
T ss_pred             HHHHhhHHHHHHHHHHHhcCCCChhHHHHHhCCEEeCCCCCCccccCCcc
Confidence            99999999999999999999999999999999999999999999999865

>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=100.00  E-value=1.9e-43  Score=284.19  Aligned_cols=121  Identities=26%  Similarity=0.438  Sum_probs=99.4

Q ss_pred             EEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChhHHhhc
Q 028816           31 RVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMER  110 (203)
Q Consensus        31 ~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~~~~~r  110 (203)
                      -||||+|++||||||.||++|+            +||+|||||||+|+|||+|+.++.||+|+||||+++..++++++++
T Consensus         2 ~vIDA~g~~lGRLAs~vAk~L~------------~Gd~ViVvNaeki~~tG~K~~~k~~~~~~~~~g~~~~~~~~~~~~~   69 (142)
T d1j3aa_           2 RIINADGLILGRLASRVAKMLL------------EGEEVVIVNAEKAVITGNREVIFSKYKQRTGLRTLTNPRRGPFYPK   69 (142)
T ss_dssp             EEEECTTBBHHHHHHHHHHHHH------------TTCCEEEECGGGCEEESCHHHHHHHHHHHC-------------CCC
T ss_pred             EEEeCCCCchHHHHHHHHHHHh------------CCCeEEEEechhheecCcchhhhhhhhhhcccccccCcchhhhccc
Confidence            4899999999999999999997            9999999999999999999999999999999999999999999999


Q ss_pred             ChhHHHHHHHhccCC-CCCchhhhhcCceecCCCCCCCCCCCCcceecCccchhhc
Q 028816          111 DPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVREL  165 (203)
Q Consensus       111 ~P~~Ii~rAVrGMLP-kn~lr~~~l~rLkvy~G~~hp~~~qk~~~~~~pp~~~r~~  165 (203)
                      +|++||++||+|||| +|.+++++|+||+||+|.||||++|+++.+  |.+.+...
T Consensus        70 ~P~~il~~aVrGMLP~k~~lgr~~~krLkvy~G~~h~~~~q~~~~~--~~a~~~~~  123 (142)
T d1j3aa_          70 RSDEIVRRTIRGMLPWKTDRGRKAFRRLKVYVGIPKEFQDKQLETI--VEAHVSRL  123 (142)
T ss_dssp             SHHHHHHHHHHTTTTTTSHHHHHHHTTEEECSSCCGGGTTSCCBCC--GGGBGGGS
T ss_pred             ChHHHHHHHHHcccCCCChHHHHHHhCCEEecCCCCChhhcCCccc--cHHHHhhh
Confidence            999999999999999 687888999999999999999999988654  44555433

>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=100.00  E-value=1.1e-42  Score=279.91  Aligned_cols=113  Identities=25%  Similarity=0.307  Sum_probs=104.0

Q ss_pred             ceEEEEeCCCCcchhhHHHHHHHHhCCCCCCCCCCCCCCCEEEEEeCcccccccccccceeEeeecccCCCccccChhHH
Q 028816           28 LRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQ  107 (203)
Q Consensus        28 r~W~vIDA~gqvLGRLAS~VAk~L~GKhKp~ytP~~d~Gd~VVVVNaekI~iTG~K~~~K~Y~~htgYpGglk~~~~~~~  107 (203)
                      .+|+||||+||+||||||.||+.|+            +||+|||||||+|+|||+|+.++.||+|++|||+.+    +++
T Consensus         4 ~k~ivIDA~~~~lGRLAs~vAk~l~------------~Gd~ViVvNaeki~itG~k~~~k~~y~~~~~~g~~k----g~~   67 (142)
T d1vqoj1           4 DADVIVDARDCIMGRVASQVAEQAL------------DGETVAVVNAERAVITGREEQIVEKYEKRVDIGNDN----GYF   67 (142)
T ss_dssp             CCSEEEECTTBBHHHHHHHHHHHHH------------TTCCEEEECGGGCEEESCHHHHHHHHHHHHHCCCSS----CCC
T ss_pred             cceEEEECCCCchHHHHHHHHHHhc------------CCCEEEEEEChhhcccCcchhhhheeeeeecCCCcc----cee
Confidence            4899999999999999999999998            999999999999999999999999999999999965    667


Q ss_pred             hhcChhHHHHHHHhccCCCCC-chhhhhcCceecCCCCCCCCCCCCccee
Q 028816          108 MERDPTEAIRKAVLRMLPRNK-LRDDRDRKLRIFPGSEHPFGDRPLEPYV  156 (203)
Q Consensus       108 ~~r~P~~Ii~rAVrGMLPkn~-lr~~~l~rLkvy~G~~hp~~~qk~~~~~  156 (203)
                      ++++|++||++||+||||+++ +++++|+||+||.|.||||++|.+++..
T Consensus        68 ~~r~P~~il~raVrGMLP~k~~~gr~~~krLkvy~G~~h~~~~q~~~~~~  117 (142)
T d1vqoj1          68 YPKRPDGIFKRTIRGMLPHKKQRGREAFESVRVYLGNPYDEDGEVLDGTS  117 (142)
T ss_dssp             CCCSHHHHHHHHHHTTTTTTSHHHHHHHTTEEECSSCCSSSCCBCCTTCB
T ss_pred             hhcCHHHHHHHHHhCcCCCCChhHHHHHhCcEEeCCCCCccccCcCChhh
Confidence            899999999999999999655 4567999999999999999999775433