Citrus Sinensis ID: 032581

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------
Protein Sequence
MISIYVVFFILRNLFILSLNDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQKKAEMQQSNKDMRKNRKKEVEAEVTA
Secondary Structure (PSIPRED)
ccccEEEEEEcccEEEcccccccccccccccccccccHHHHHHHcHHHHHHHHHHccccccHHHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cEEEEEEEEEccHEEEEccccccEEEEEcccccccccHHHHHHccHHHHHHHHHHccccccccHHHHHHHHEEccccccccccccccccccccHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEccc
Coil and Loop (DISEMBL)
MISIYVVFFILRNLFILSLNDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMlprnklrddrdrklrifpgsehpfgdrplepyvmpprrvreLRPRVRRAMIREQKKAEMQQSNKDMRKNRKKEVEAEVTA
Flexible Loop (DISEMBL)
MISIYVVFFILRNLFILSLNDEMSVSYRYIGHLkertlkeqmerdpteairkavlrmlprnklrddrdrklrifpgsehpfgdrplepyvmpprrvrelrprVRRAMireqkkaemqqsnkdmrknrkkeveaevta
Low Complexity Region (SEG)
MISIYVVFFILRNLFILSLNDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNklrddrdrklrIFPGSEHPFGDRPLEPYvmpprrvrelrprvrrAMIREQKKAEMQQSNKDMRKNRKKEVEAEVTA
Disordered region (IsUnstruct)
*ISIYVVFFILRNLFILSLNDEMSVSYRYIGHLK*******************************************************************************************************
Disordered Region (DISOPRED)
MISIYVVFFILRNLFILSLNDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVM**********************************************
Disordered Region (DISEMBL)
MISIYVVFFILRNLFILSLNDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIRE***************************
Disordered Region (DISPRO)
MISIYVVFFILRNLFILSLNDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQKKAEM*********************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MISIYVVFFILRNLFILSLNDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIxxxxxxxxxxxxxxxxxxxxxEVEAEVTA
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	137	2.2.26 [Sep-21-2011]
P66065	147	50S ribosomal protein L13	yes	no	0.547	0.510	0.375	3e-08
A5U8B9	147	50S ribosomal protein L13	yes	no	0.547	0.510	0.375	3e-08
C1AHQ2	147	50S ribosomal protein L13	yes	no	0.547	0.510	0.375	3e-08
A1KPD0	147	50S ribosomal protein L13	yes	no	0.547	0.510	0.375	3e-08
P66066	147	50S ribosomal protein L13	yes	no	0.547	0.510	0.375	3e-08
B1MG81	147	50S ribosomal protein L13	yes	no	0.364	0.340	0.46	3e-08
B2GJ23	147	50S ribosomal protein L13	yes	no	0.445	0.414	0.409	5e-08
O67722	144	50S ribosomal protein L13	yes	no	0.386	0.368	0.547	5e-08
Q6ANL8	142	50S ribosomal protein L13	yes	no	0.379	0.366	0.461	1e-07
B2HCZ0	147	50S ribosomal protein L13	yes	no	0.532	0.496	0.367	2e-07

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

 Score = 57.0 bits (136), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 33/88 (37%), Positives = 50/88 (56%), Gaps = 13/88 (14%)

Query: 15  FILSLN-DEMSVS---------YR---YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRN 61
           F++ +N D++++S         YR   Y G L +RT+ E M+R P   + KA+L MLP+N
Sbjct: 53  FVIVINADKVAISGDKLQHKMVYRHSGYPGGLHKRTIGELMQRHPDRVVEKAILGMLPKN 112

Query: 62  KLRDDRDRKLRIFPGSEHPFGDRPLEPY 89
           +L     RKLR++ G EHP   +   PY
Sbjct: 113 RLSRQIQRKLRVYAGPEHPHSAQQPVPY 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 = 57.0 bits (136), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 33/88 (37%), Positives = 50/88 (56%), Gaps = 13/88 (14%)

Query: 15  FILSLN-DEMSVS---------YR---YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRN 61
           F++ +N D++++S         YR   Y G L +RT+ E M+R P   + KA+L MLP+N
Sbjct: 53  FVIVINADKVAISGDKLQHKMVYRHSGYPGGLHKRTIGELMQRHPDRVVEKAILGMLPKN 112

Query: 62  KLRDDRDRKLRIFPGSEHPFGDRPLEPY 89
           +L     RKLR++ G EHP   +   PY
Sbjct: 113 RLSRQIQRKLRVYAGPEHPHSAQQPVPY 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 = 57.0 bits (136), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 33/88 (37%), Positives = 50/88 (56%), Gaps = 13/88 (14%)

Query: 15  FILSLN-DEMSVS---------YR---YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRN 61
           F++ +N D++++S         YR   Y G L +RT+ E M+R P   + KA+L MLP+N
Sbjct: 53  FVIVINADKVAISGDKLQHKMVYRHSGYPGGLHKRTIGELMQRHPDRVVEKAILGMLPKN 112

Query: 62  KLRDDRDRKLRIFPGSEHPFGDRPLEPY 89
           +L     RKLR++ G EHP   +   PY
Sbjct: 113 RLSRQIQRKLRVYAGPEHPHSAQQPVPY 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 = 57.0 bits (136), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 33/88 (37%), Positives = 50/88 (56%), Gaps = 13/88 (14%)

Query: 15  FILSLN-DEMSVS---------YR---YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRN 61
           F++ +N D++++S         YR   Y G L +RT+ E M+R P   + KA+L MLP+N
Sbjct: 53  FVIVINADKVAISGDKLQHKMVYRHSGYPGGLHKRTIGELMQRHPDRVVEKAILGMLPKN 112

Query: 62  KLRDDRDRKLRIFPGSEHPFGDRPLEPY 89
           +L     RKLR++ G EHP   +   PY
Sbjct: 113 RLSRQIQRKLRVYAGPEHPHSAQQPVPY 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 = 57.0 bits (136), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 33/88 (37%), Positives = 50/88 (56%), Gaps = 13/88 (14%)

Query: 15  FILSLN-DEMSVS---------YR---YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRN 61
           F++ +N D++++S         YR   Y G L +RT+ E M+R P   + KA+L MLP+N
Sbjct: 53  FVIVINADKVAISGDKLQHKMVYRHSGYPGGLHKRTIGELMQRHPDRVVEKAILGMLPKN 112

Query: 62  KLRDDRDRKLRIFPGSEHPFGDRPLEPY 89
           +L     RKLR++ G EHP   +   PY
Sbjct: 113 RLSRQIQRKLRVYAGPEHPHSAQQPVPY 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|B1MG81|RL13_MYCA9 50S ribosomal protein L13 OS=Mycobacterium abscessus (strain ATCC 19977 / DSM 44196) GN=rplM PE=3 SV=1

 Score = 57.0 bits (136), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 37/50 (74%)

Query: 31  GHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 80
           G L +R++ EQ+E+ PT  + KA++ MLP+NKL    +RKL+++ G+EHP
Sbjct: 82  GGLSKRSIGEQLEKFPTRTVEKAIVGMLPKNKLGRQIERKLKVYAGAEHP 131

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|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 = 56.6 bits (135), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 39/61 (63%)

Query: 29  YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEP 88
           Y G LK  +  E +E++PT A+ KA+  MLP+NKL   +  KL+++ G+EHP   +  +P
Sbjct: 80  YPGGLKSTSYAELLEKNPTRAVEKAIKGMLPKNKLAAQQLSKLKVYAGAEHPHQAQQPKP 139

Query: 89  Y 89
           Y
Sbjct: 140 Y 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|O67722|RL13_AQUAE 50S ribosomal protein L13 OS=Aquifex aeolicus (strain VF5) GN=rplM PE=3 SV=1

 Score = 56.2 bits (134), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 29/53 (54%), Positives = 36/53 (67%)

Query: 28  RYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 80
           RY G LKERTLK  +E  P E IR AV RMLP+N+L     +KL+++ G EHP
Sbjct: 79  RYPGGLKERTLKWMLENKPEEVIRLAVKRMLPKNRLGHRMLKKLKVYRGPEHP 131

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|Q6ANL8|RL13_DESPS 50S ribosomal protein L13 OS=Desulfotalea psychrophila (strain LSv54 / DSM 12343) GN=rplM PE=3 SV=1

 Score = 55.1 bits (131), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/52 (46%), Positives = 37/52 (71%)

Query: 29  YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 80
           YIG +KE + KE +E+ PT+ I KAV  MLP+NK+   + +KL+++ G+ HP
Sbjct: 80  YIGGIKETSAKELLEKHPTDLITKAVRGMLPKNKMGRAQLKKLKVYVGAAHP 131

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.

Desulfotalea psychrophila (strain LSv54 / DSM 12343) (taxid: 177439)

>sp|B2HCZ0|RL13_MYCMM 50S ribosomal protein L13 OS=Mycobacterium marinum (strain ATCC BAA-535 / M) GN=rplM PE=3 SV=1

 Score = 54.7 bits (130), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 48/79 (60%), Gaps = 6/79 (7%)

Query: 8   FFILRNLFILSLNDE-----MSVSYR-YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRN 61
           F I+ N   +++++E     M+ S+  Y G L++R++ E ME+ P   + KA++ MLP+N
Sbjct: 53  FVIVINADKVAISNEKLRNKMAYSHSGYPGGLRKRSIGELMEKHPDRVVEKAIVGMLPKN 112

Query: 62  KLRDDRDRKLRIFPGSEHP 80
           KL      KLR++ G EHP
Sbjct: 113 KLSRQIQSKLRVYAGPEHP 131

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 marinum (strain ATCC BAA-535 / M) (taxid: 216594)

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	137
224141259	205	predicted protein [Populus trichocarpa]	0.788	0.526	0.816	6e-44
449487903	204	PREDICTED: 50S ribosomal protein L13-lik	0.802	0.539	0.783	5e-42
255542936	202	50S ribosomal protein L13, putative [Ric	0.788	0.534	0.779	8e-42
118487043	205	unknown [Populus trichocarpa]	0.788	0.526	0.761	1e-41
224060221	205	predicted protein [Populus trichocarpa]	0.788	0.526	0.761	1e-41
255536973	202	50S ribosomal protein L13, putative [Ric	0.788	0.534	0.770	2e-41
449448398	193	PREDICTED: 50S ribosomal protein L13-lik	0.795	0.564	0.781	3e-41
357469935	200	50S ribosomal protein L13 [Medicago trun	0.715	0.49	0.785	2e-40
357462507	273	50S ribosomal protein L13 [Medicago trun	0.715	0.358	0.785	2e-40
346472265	202	hypothetical protein [Amblyomma maculatu	0.795	0.539	0.697	1e-38

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

 Score =  181 bits (460), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 89/109 (81%), Positives = 97/109 (88%), Gaps = 1/109 (0%)

Query: 29  YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEP 88
           YIGHLKER+LK+QM +DPTE IRKAVLRMLPRNKLRDDRDRKLRIFP SEHPFGDRPLEP
Sbjct: 96  YIGHLKERSLKDQMAKDPTEVIRKAVLRMLPRNKLRDDRDRKLRIFPDSEHPFGDRPLEP 155

Query: 89  YVMPPRRVRELRPRVRRAMIREQKKAEMQ-QSNKDMRKNRKKEVEAEVT 136
           YVMPPR+VRE+RPR RRAMIR QKKAE Q Q   D RK +K+EVEAE+T
Sbjct: 156 YVMPPRQVREMRPRARRAMIRAQKKAEQQEQGGNDKRKGKKREVEAELT 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 =  175 bits (443), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 87/111 (78%), Positives = 98/111 (88%), Gaps = 1/111 (0%)

Query: 28  RYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLE 87
           RY+G+LKERTL+EQM RDPTE IRKAVLRMLP+NKLRDDRDRKLRIF G EHPFGDRPLE
Sbjct: 94  RYVGNLKERTLREQMTRDPTEVIRKAVLRMLPKNKLRDDRDRKLRIFAGDEHPFGDRPLE 153

Query: 88  PYVMPPRRVRELRPRVRRAMIREQKKAEMQQSNKDMRK-NRKKEVEAEVTA 137
           PY+MPPR VRE+RP+VRRAMIR QK AE QQ+NK+  K +RKKE + EVTA
Sbjct: 154 PYIMPPRNVREMRPQVRRAMIRAQKMAEQQQNNKNEGKESRKKEEKVEVTA 204

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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 =  174 bits (442), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 85/109 (77%), Positives = 96/109 (88%), Gaps = 1/109 (0%)

Query: 29  YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEP 88
           Y+G+LKER+LK+Q+ +DPTE IRKAVLRMLPRNKLRDDRDRKLRIF GSEHPFGDRPLEP
Sbjct: 93  YVGNLKERSLKDQLAKDPTEVIRKAVLRMLPRNKLRDDRDRKLRIFAGSEHPFGDRPLEP 152

Query: 89  YVMPPRRVRELRPRVRRAMIREQKKAEMQ-QSNKDMRKNRKKEVEAEVT 136
           Y+MPPR VRE+RPR RRAMIR Q+KAE Q +   +MRK RKKEVEAEV 
Sbjct: 153 YIMPPRTVREIRPRARRAMIRAQRKAEQQVRGANEMRKGRKKEVEAEVA 201

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  174 bits (441), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 83/109 (76%), Positives = 98/109 (89%), Gaps = 1/109 (0%)

Query: 29  YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEP 88
           YIGHLKER+LK+QM +DPTE IRKAVLRMLPRNKLRDDRDRKLRIFP SEHPFGD+P+E 
Sbjct: 96  YIGHLKERSLKDQMAKDPTEVIRKAVLRMLPRNKLRDDRDRKLRIFPDSEHPFGDQPVEA 155

Query: 89  YVMPPRRVRELRPRVRRAMIREQKKAE-MQQSNKDMRKNRKKEVEAEVT 136
           YVMPPR+VRE+RPR +RAMIR QKKAE ++Q+  D RK +K+EVEA++T
Sbjct: 156 YVMPPRKVREMRPRAQRAMIRAQKKAEQLEQAGNDKRKGKKREVEADLT 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 =  174 bits (441), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 83/109 (76%), Positives = 98/109 (89%), Gaps = 1/109 (0%)

Query: 29  YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEP 88
           YIGHLKER+LK+QM +DPTE IRKAVLRMLPRNKLRDDRDRKLRIFP SEHPFGD+P+E 
Sbjct: 96  YIGHLKERSLKDQMAKDPTEVIRKAVLRMLPRNKLRDDRDRKLRIFPDSEHPFGDQPVEA 155

Query: 89  YVMPPRRVRELRPRVRRAMIREQKKAE-MQQSNKDMRKNRKKEVEAEVT 136
           YVMPPR+VRE+RPR +RAMIR QKKAE ++Q+  D RK +K+EVEA++T
Sbjct: 156 YVMPPRKVREMRPRAQRAMIRAQKKAEQLEQAGNDKRKGKKREVEADLT 204

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  173 bits (439), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 84/109 (77%), Positives = 95/109 (87%), Gaps = 1/109 (0%)

Query: 29  YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEP 88
           Y+G+LKER+LK+Q+ +DPTE IRKAVLRMLPRNKLRDDRDRKLRIF GSEHPFGDRPLE 
Sbjct: 93  YVGNLKERSLKDQLAKDPTEVIRKAVLRMLPRNKLRDDRDRKLRIFAGSEHPFGDRPLES 152

Query: 89  YVMPPRRVRELRPRVRRAMIREQKKAEMQ-QSNKDMRKNRKKEVEAEVT 136
           Y+MPPR VRE+RPR RRAMIR QKKAE Q Q   +M+K RKKEVE E+T
Sbjct: 153 YIMPPRTVREMRPRARRAMIRAQKKAEQQRQGANEMQKGRKKEVEVEIT 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 =  172 bits (437), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 86/110 (78%), Positives = 97/110 (88%), Gaps = 1/110 (0%)

Query: 29  YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEP 88
           Y+G+LKERTL+EQM RDPTE IRKAVLRMLP+NKLRDDRDRKLRIF G EHPFGDRPLEP
Sbjct: 84  YVGNLKERTLREQMTRDPTEVIRKAVLRMLPKNKLRDDRDRKLRIFAGDEHPFGDRPLEP 143

Query: 89  YVMPPRRVRELRPRVRRAMIREQKKAEMQQSNKDMRK-NRKKEVEAEVTA 137
           Y+MPPR VRE+RP+VRRAMIR QK AE QQ+NK+  K +RKKE + EVTA
Sbjct: 144 YIMPPRNVREMRPQVRRAMIRAQKMAEQQQNNKNEGKESRKKEEKVEVTA 193

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357469935|ref|XP_003605252.1| 50S ribosomal protein L13 [Medicago truncatula] gi|355506307|gb|AES87449.1| 50S ribosomal protein L13 [Medicago truncatula]

 Score =  170 bits (430), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 77/98 (78%), Positives = 88/98 (89%)

Query: 29  YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEP 88
           Y+GHLK+RTLK+QM +DPT+ IRKA+LRM+P+N LRDDRDRKLRIFPGSEHPFGDRPLEP
Sbjct: 91  YVGHLKQRTLKDQMAKDPTDVIRKAILRMIPKNNLRDDRDRKLRIFPGSEHPFGDRPLEP 150

Query: 89  YVMPPRRVRELRPRVRRAMIREQKKAEMQQSNKDMRKN 126
           YVMPPR VRE+RPR RRAMIR QKKAE QQ N + R+N
Sbjct: 151 YVMPPRTVREMRPRARRAMIRAQKKAEQQQENAEQRQN 188

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357462507|ref|XP_003601535.1| 50S ribosomal protein L13 [Medicago truncatula] gi|355490583|gb|AES71786.1| 50S ribosomal protein L13 [Medicago truncatula]

 Score =  169 bits (429), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 77/98 (78%), Positives = 88/98 (89%)

Query: 29  YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEP 88
           Y+GHLK+RTLK+QM +DPT+ IRKA+LRM+P+N LRDDRDRKLRIFPGSEHPFGDRPLEP
Sbjct: 164 YVGHLKQRTLKDQMAKDPTDVIRKAILRMIPKNNLRDDRDRKLRIFPGSEHPFGDRPLEP 223

Query: 89  YVMPPRRVRELRPRVRRAMIREQKKAEMQQSNKDMRKN 126
           YVMPPR VRE+RPR RRAMIR QKKAE QQ N + R+N
Sbjct: 224 YVMPPRTVREMRPRARRAMIRAQKKAEQQQENAEQRQN 261

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  164 bits (415), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 76/109 (69%), Positives = 92/109 (84%)

Query: 29  YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEP 88
           Y+GHL+ER+LK+Q+ +DPTE IRKAVLRMLPRNKLRDDRDRKLRIF GSEHPFGDR LEP
Sbjct: 94  YVGHLRERSLKDQLAKDPTEVIRKAVLRMLPRNKLRDDRDRKLRIFTGSEHPFGDRSLEP 153

Query: 89  YVMPPRRVRELRPRVRRAMIREQKKAEMQQSNKDMRKNRKKEVEAEVTA 137
           Y+MPPR+VRE+RPR RRA+IR QKKAE   S  ++ K +K++    +TA
Sbjct: 154 YIMPPRQVREMRPRARRALIRAQKKAEQSSSGTNITKKKKEDKVEAITA 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	137
TAIR|locus:2082304	205	AT3G01790 [Arabidopsis thalian	0.795	0.531	0.495	6.3e-21
UNIPROTKB|P66065	147	rplM "50S ribosomal protein L1	0.445	0.414	0.360	2.1e-06
POMBASE|SPBC16G5.04	157	mrpl23 "mitochondrial ribosoma	0.372	0.324	0.403	0.0001
TIGR_CMR|GSU_2876	143	GSU_2876 "ribosomal protein L1	0.452	0.433	0.333	0.00045
TIGR_CMR|BA_0143	145	BA_0143 "ribosomal protein L13	0.503	0.475	0.297	0.00057

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

 Score = 246 (91.7 bits), Expect = 6.3e-21, P = 6.3e-21
 Identities = 54/109 (49%), Positives = 62/109 (56%)

Query:    29 YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEHPFGDRPLEP 88
             YIGHLKER+LK+QM +DPTE IRKAV RMLP N           IF G EHPFGD+PLEP
Sbjct:    97 YIGHLKERSLKDQMAKDPTEVIRKAVWRMLPSNNLRDDRDRKLRIFEGGEHPFGDKPLEP 156

Query:    89 YXXXXXXXXXXXXXXXXAMIREQKKAEMQQSNKDMRKNRKKEVEAEVTA 137
             +                AMIR QKKAE  ++     K  KK   +EV A
Sbjct:   157 FVMPPRRVREMRPRARRAMIRAQKKAEQAENEGTEVKKGKKRTLSEVPA 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 = 109 (43.4 bits), Expect = 2.1e-06, P = 2.1e-06
 Identities = 22/61 (36%), Positives = 31/61 (50%)

Query:    29 YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEHPFGDRPLEP 88
             Y G L +RT+ E M+R P   + KA+L MLP+N           ++ G EHP   +   P
Sbjct:    80 YPGGLHKRTIGELMQRHPDRVVEKAILGMLPKNRLSRQIQRKLRVYAGPEHPHSAQQPVP 139

Query:    89 Y 89
             Y
Sbjct:   140 Y 140

GO:0005618 "cell wall" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0040007 "growth" evidence=IMP

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

 Score = 93 (37.8 bits), Expect = 0.00010, P = 0.00010
 Identities = 21/52 (40%), Positives = 30/52 (57%)

Query:    31 GHLKERTLKEQM-ERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGSEHPF 81
             GHLKE T++E   +R   + +R+AV  MLPRN           I+ G+EHP+
Sbjct:    83 GHLKEWTMEEMAAKRGHKDLLRRAVGGMLPRNKLWDRRMKRLYIYDGAEHPY 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

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

 Score = 87 (35.7 bits), Expect = 0.00045, P = 0.00045
 Identities = 21/63 (33%), Positives = 32/63 (50%)

Query:    19 LNDEMSVSYR-YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFPGS 77
             L D+M   +  + G +K  T  + +E+ P + IRKAV  MLP+N           ++ G 
Sbjct:    70 LADKMYYHHTGFPGGIKSITAGKLIEKKPEDLIRKAVKGMLPKNKLARHMLKKLKVYAGP 129

Query:    78 EHP 80
             EHP
Sbjct:   130 EHP 132

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

GO:0006412 "translation" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

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

 Score = 86 (35.3 bits), Expect = 0.00057, P = 0.00057
 Identities = 22/74 (29%), Positives = 34/74 (45%)

Query:    19 LNDEMSVSYRYIGH---LKERTLKEQMERDPTEAIRKAVLRMLPRNXXXXXXXXXXXIFP 75
             LND+  + YR+  H   LK+RT  E     P + +  A+  MLP+            ++ 
Sbjct:    70 LNDK--IYYRHTNHPGGLKQRTALEMRTNYPVQMLELAIKGMLPKGRLGRQVSKKLNVYA 127

Query:    76 GSEHPFGDRPLEPY 89
             G+EHP   +  E Y
Sbjct:   128 GAEHPHQAQKPEVY 141


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.321   0.135   0.375    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      137       110   0.00091  102 3  11 22  0.42    30
                                                     29  0.42    32


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  5
  No. of states in DFA:  484 (52 KB)
  Total size of DFA:  94 KB (2069 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  12.05u 0.19s 12.24t   Elapsed:  00:00:00
  Total cpu time:  12.05u 0.19s 12.24t   Elapsed:  00:00:00
  Start:  Thu May  9 17:03:03 2013   End:  Thu May  9 17:03:03 2013

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

GO:0006412 "translation" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	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	137
PLN00205	191	PLN00205, PLN00205, ribisomal protein L13 family p	4e-55
PRK09216	144	PRK09216, rplM, 50S ribosomal protein L13; Reviewe	8e-17
pfam00572	128	pfam00572, Ribosomal_L13, Ribosomal protein L13	2e-16
TIGR01066	140	TIGR01066, rplM_bact, ribosomal protein L13, bacte	8e-14
cd00392	114	cd00392, Ribosomal_L13, Ribosomal protein L13	2e-13
COG0102	148	COG0102, RplM, Ribosomal protein L13 [Translation,	1e-09
CHL00159	143	CHL00159, rpl13, ribosomal protein L13; Validated	8e-07

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

 Score =  170 bits (432), Expect = 4e-55
 Identities = 86/110 (78%), Positives = 98/110 (89%), Gaps = 1/110 (0%)

Query: 29  YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEP 88
           YIGHLKER+LK+QM +DPTE IRKAVLRMLPRN+LRDDRDRKLRIF GSEHPFGD+PLEP
Sbjct: 82  YIGHLKERSLKDQMAKDPTEVIRKAVLRMLPRNRLRDDRDRKLRIFAGSEHPFGDKPLEP 141

Query: 89  YVMPPRRVRELRPRVRRAMIREQKKAEMQ-QSNKDMRKNRKKEVEAEVTA 137
           +VMPPR+VRE+RPR RRAMIR QKKAE + Q+  + RK +KKEVE EVTA
Sbjct: 142 FVMPPRQVREMRPRARRAMIRAQKKAEQREQAANEKRKGKKKEVEVEVTA 191

Length = 191

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

 Score = 71.3 bits (176), Expect = 8e-17
 Identities = 25/57 (43%), Positives = 33/57 (57%), Gaps = 3/57 (5%)

Query: 27  YR---YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 80
           YR   Y 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 = 69.9 bits (172), Expect = 2e-16
 Identities = 23/63 (36%), Positives = 33/63 (52%)

Query: 27  YRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGDRPL 86
             Y G LK  T K  +ER P   + +AV  MLP+NKL     ++L+++ GS HP   +  
Sbjct: 64  TGYPGGLKNPTAKGPLERKPERILERAVRGMLPKNKLGRAALKRLKVYAGSPHPHAAQKP 123

Query: 87  EPY 89
           E  
Sbjct: 124 EVL 126

Length = 128

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

 Score = 63.5 bits (155), Expect = 8e-14
 Identities = 23/54 (42%), Positives = 32/54 (59%)

Query: 28  RYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPF 81
            Y G LK RT +E + R P   +  AV  MLP+N+L     +KL+++ GSEHP 
Sbjct: 77  GYPGGLKSRTFEEMIARKPERVLEHAVKGMLPKNRLGRKLFKKLKVYAGSEHPH 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|238230 cd00392, Ribosomal_L13, Ribosomal protein L13

 Score = 61.8 bits (151), Expect = 2e-13
 Identities = 17/51 (33%), Positives = 27/51 (52%)

Query: 27  YRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGS 77
             Y G LK  T      R P   +++AV  MLP+NKL     ++L+++ G+
Sbjct: 64  TGYPGGLKNPTAGPLHPRAPERILKRAVRGMLPKNKLGRAALKRLKVYEGA 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|223180 COG0102, RplM, Ribosomal protein L13 [Translation, ribosomal structure and biogenesis]

 Score = 52.6 bits (127), Expect = 1e-09
 Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 27  YRYIGHLKERTLKEQME-RDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 80
             Y G LK  T    +  R P   + +AV  MLP+N L     ++L+++ G  HP
Sbjct: 78  SGYPGGLKNPTRGGPLAPRRPERILERAVRGMLPKNPLGRAALKRLKVYAGIPHP 132

Length = 148

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

 Score = 45.0 bits (107), Expect = 8e-07
 Identities = 20/50 (40%), Positives = 25/50 (50%)

Query: 31  GHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 80
           G LK  T +E   R P   I KAV  MLP+  L      KL+++ G  HP
Sbjct: 83  GGLKIETFEELQNRLPNRIIEKAVKGMLPKGPLGRKLFTKLKVYKGESHP 132

Length = 143

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	137
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
TIGR01077	142	L13_A_E ribosomal protein L13, archaeal/eukaryotic	100.0
PRK06394	146	rpl13p 50S ribosomal protein L13P; Reviewed	99.97
PTZ00068	202	60S ribosomal protein L13a; Provisional	99.97
KOG3203	165	consensus Mitochondrial/chloroplast ribosomal prot	99.97
cd00392	114	Ribosomal_L13 Ribosomal protein L13. Protein L13,	99.97
KOG3204	197	consensus 60S ribosomal protein L13a [Translation,	99.71

>PLN00205 ribisomal protein L13 family protein; Provisional

Probab=100.00  E-value=7.4e-47  Score=300.24  Aligned_cols=135  Identities=62%  Similarity=0.978  Sum_probs=125.9

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCCCChhHHHHhccceeeCCCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSE   78 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLPKn~lGr~~lkrLkVy~G~~   78 (137)
                      .|||||||||++|+|||+   ++.|++|||||||+++++++++++++|++||++||+||||+|.+|+.+|+||+||+|++
T Consensus        52 ~GD~VVVINAekI~lTG~K~~~K~Y~~htgypGglk~~~~~~~~~r~P~~Il~kAVrGMLPkn~lr~~~~krLkVY~G~~  131 (191)
T PLN00205         52 DGDICIVLNAKDISVTGRKLTDKFYRWHTGYIGHLKERSLKDQMAKDPTEVIRKAVLRMLPRNRLRDDRDRKLRIFAGSE  131 (191)
T ss_pred             CCCEEEEEeccEEEEeCChhhcceEEEecCCCCCcccccHHHHhccCHHHHHHHHHHhcCCCCchHHHHHhCCEEECCCC
Confidence            589999999999999999   89999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCccceecCCccccccccccchhHHHhhhHHHHHHhh-HHHhhhhhhhhhhhhc
Q 032581           79 HPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQKKAEMQQSN-KDMRKNRKKEVEAEVT  136 (137)
Q Consensus        79 Hph~aQkp~~l~~~p~~~r~~~~~~~r~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~  136 (137)
                      |||++|+|+++++||+.+|+||++++|+||+||||+||++.. +++.++..++...+.+
T Consensus       132 hp~~~q~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  190 (191)
T PLN00205        132 HPFGDKPLEPFVMPPRQVREMRPRARRAMIRAQKKAEQREQAANEKRKGKKKEVEVEVT  190 (191)
T ss_pred             CChhccCCeEecCChHHhhccCchhHHHHHHHHHHHHHHHHHHhhhccccccccccccC
Confidence            999999999999999999999999999999999999998876 6666666666555544

>CHL00159 rpl13 ribosomal protein L13; Validated

Probab=100.00  E-value=1.1e-37  Score=238.47  Aligned_cols=89  Identities=25%  Similarity=0.270  Sum_probs=86.6

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCCCChhHHHHhccceeeCCCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSE   78 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLPKn~lGr~~lkrLkVy~G~~   78 (137)
                      -||+||||||++|++||+   ++.|++|||||||+++++++++++++|++||++||+||||||.+|+.+|+||+||+|++
T Consensus        51 ~Gd~VVViNa~kv~~TG~K~~~K~y~~htg~pGg~k~~~~~~~~~r~P~~il~~aV~gMLPkn~lgr~~~~rLkvy~G~~  130 (143)
T CHL00159         51 TGDYVIVINAEKIKVTGNKTSQKFYVRHSGRPGGLKIETFEELQNRLPNRIIEKAVKGMLPKGPLGRKLFTKLKVYKGES  130 (143)
T ss_pred             CCCEEEEEecceeEEeCchhhheEEEecCCCCCCcccccHHHHhhcCHHHHHHHHHHhcCCCChhHHHHHhCCEEeCCCC
Confidence            489999999999999999   78999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCcccee
Q 032581           79 HPFGDRPLEPYV   90 (137)
Q Consensus        79 Hph~aQkp~~l~   90 (137)
                      |||+||+|+.++
T Consensus       131 hph~aq~p~~~~  142 (143)
T CHL00159        131 HPHVAQKPIKIN  142 (143)
T ss_pred             CCccccCCeecC
Confidence            999999999875

>PRK09216 rplM 50S ribosomal protein L13; Reviewed

Probab=100.00  E-value=2.4e-37  Score=236.75  Aligned_cols=91  Identities=27%  Similarity=0.406  Sum_probs=88.0

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCCCChhHHHHhccceeeCCCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSE   78 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLPKn~lGr~~lkrLkVy~G~~   78 (137)
                      -||||||||||+|+|||+   ++.||+|||||||+++++++++++++|++||++||+||||||.+|+.+|+||+||+|++
T Consensus        50 ~Gd~VvViNa~ki~~tG~k~~~k~y~~htg~pGglk~~~~~~~~~r~P~~il~~aVrgMLPkn~lgr~~~~rLkvy~G~~  129 (144)
T PRK09216         50 TGDFVIVINAEKVKLTGKKLTDKIYYRHSGYPGGLKEITFGELLAKKPERVIEKAVKGMLPKNPLGRAMFKKLKVYAGAE  129 (144)
T ss_pred             CCCEEEEEeCceeEEcCchHhheeeEEecccCCCCEEecHHHHhhhCHHHHHHHHHHhcCCCCccHHHHHhCcEEeCCCC
Confidence            489999999999999999   78999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCccceecC
Q 032581           79 HPFGDRPLEPYVMP   92 (137)
Q Consensus        79 Hph~aQkp~~l~~~   92 (137)
                      |||++|+|+.+++.
T Consensus       130 hp~~~q~p~~~~~~  143 (144)
T PRK09216        130 HPHAAQQPEVLEIK  143 (144)
T ss_pred             CCccccCCEecccC
Confidence            99999999988753

>TIGR01066 rplM_bact ribosomal protein L13, bacterial type

Probab=100.00  E-value=7.1e-37  Score=233.18  Aligned_cols=90  Identities=28%  Similarity=0.419  Sum_probs=87.0

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCCCChhHHHHhccceeeCCCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSE   78 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLPKn~lGr~~lkrLkVy~G~~   78 (137)
                      -||+|||||||+|+|||+   ++.|++|||||||+++++++++++++|++||++||+||||||.+|+.+|+||+||+|++
T Consensus        48 ~Gd~VvViNa~ki~~tG~k~~~k~y~~htg~pgg~k~~~~~~~~~r~P~~ii~~aVrGMLPkn~lgr~~l~rLkvy~G~~  127 (140)
T TIGR01066        48 CGDYVIVINAEKVRLTGKKLEQKVYYRHSGYPGGLKSRTFEEMIARKPERVLEHAVKGMLPKNRLGRKLFKKLKVYAGSE  127 (140)
T ss_pred             CCCEEEEEeccEEEEeCchhhceeeEEEcccCCccccccHHHhhhcCHHHHHHHHHHhcCCCCccHHHHHhCeEEeCCCC
Confidence            489999999999999999   78999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCccceec
Q 032581           79 HPFGDRPLEPYVM   91 (137)
Q Consensus        79 Hph~aQkp~~l~~   91 (137)
                      |||++|+|+.+++
T Consensus       128 hp~~~q~p~~~~~  140 (140)
T TIGR01066       128 HPHEAQKPIVLDI  140 (140)
T ss_pred             CChhhcCCeecCC
Confidence            9999999988753

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=2.5e-35  Score=226.44  Aligned_cols=89  Identities=25%  Similarity=0.405  Sum_probs=85.2

Q ss_pred             CcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhh-cChhHHHHHHHHccCCCChhHHHHhccceeeCCCC
Q 032581            3 SIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQME-RDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSE   78 (137)
Q Consensus         3 ~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~-r~P~~Il~rAVrGMLPKn~lGr~~lkrLkVy~G~~   78 (137)
                      ||+|||||||+|+|||+   ++.||+|||||||+++.+++.+.. +.|++||++||+||||||++||++|+||+||.|++
T Consensus        51 Gd~ViVINAeKv~iTG~K~~~k~yy~hs~~~gglk~~t~~~~~~~r~P~ri~~~AVrGMLPk~~lGr~~~krLkVy~G~~  130 (148)
T COG0102          51 GDYVIVINAEKVVITGKKLTDKKYYRHSGYPGGLKNPTRGGPLAPRRPERILERAVRGMLPKNPLGRAALKRLKVYAGIP  130 (148)
T ss_pred             CCEEEEEeceeeEEecccccceEEEEeeccCCcccccccccccccCCHHHHHHHHHhccCCCChhHHHHHhCceEecCCC
Confidence            79999999999999999   889999999999999999977777 99999999999999999999999999999999999


Q ss_pred             CCCCCCCccceec
Q 032581           79 HPFGDRPLEPYVM   91 (137)
Q Consensus        79 Hph~aQkp~~l~~   91 (137)
                      |||.+|+|+.+++
T Consensus       131 h~~~aq~p~~l~~  143 (148)
T COG0102         131 HPHEAQKPEALEL  143 (148)
T ss_pred             Cccccccchhhhh
Confidence            9999999998764

>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=7.5e-35  Score=218.80  Aligned_cols=89  Identities=27%  Similarity=0.411  Sum_probs=86.6

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCCCChhHHHHhccceeeCCCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSE   78 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLPKn~lGr~~lkrLkVy~G~~   78 (137)
                      .||+|||||||+|+|||+   ++.|++|||||||++..+++++++++|++||++||+||||+|.+|+.+|+||+||+|++
T Consensus        36 ~Gd~VvViNae~i~~tG~k~~~k~y~~h~~~~g~~~~~~~~~~~~~~P~~i~~~aVrgMLP~n~~g~~~l~rL~vy~g~~  115 (128)
T PF00572_consen   36 CGDHVVVINAEKIVLTGKKWRQKVYYRHTGYPGGLKNPTAKGLHEKDPSRILKRAVRGMLPKNKLGREALKRLKVYPGEP  115 (128)
T ss_dssp             TTEEEEEECGGGBEESSHHHHHHHHHHEHSSSTSCEEEECHHHHCSSHHHHHHHHHHTTSTTSHHHHHHHTTEEEESSSS
T ss_pred             CCCEEEEEcCeeeEecCCeecceEEEeecccchhhcccchhhhhhcCHHHHHHHHHHHHCCCChhhhHHhhceEEECCCC
Confidence            589999999999999999   78999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCcccee
Q 032581           79 HPFGDRPLEPYV   90 (137)
Q Consensus        79 Hph~aQkp~~l~   90 (137)
                      |||++|+|+.++
T Consensus       116 hp~~~~~~~~~~  127 (128)
T PF00572_consen  116 HPHAAQKPVVLE  127 (128)
T ss_dssp             CSTTSSSCBEEE
T ss_pred             CChhccCCEeCC
Confidence            999999999886

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 ....

>TIGR01077 L13_A_E ribosomal protein L13, archaeal/eukaryotic

Probab=100.00  E-value=2.5e-33  Score=214.07  Aligned_cols=103  Identities=17%  Similarity=0.185  Sum_probs=91.8

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCCCC-hhHHHHhccceeeCCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRN-KLRDDRDRKLRIFPGS   77 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLPKn-~lGr~~lkrLkVy~G~   77 (137)
                      -||||||||||+|.+||+   ++.||+||+++|+....+++++++++|++||++||+||||+| .+|+.+|+||+||+|+
T Consensus        23 ~Gd~VvViNaeki~~TG~k~~~k~~y~~~~~~g~~~~~~~~~~~~r~P~~il~~aVrGMLPk~~~~Gr~~~krLkvy~G~  102 (142)
T TIGR01077        23 NGEKVVVVNAEKIVISGNFYRNKLKYKEFLRKRTLTNPRRGPFFPRAPSRIFRRTVRGMLPHKTARGRAALRRLKVYVGI  102 (142)
T ss_pred             cCCEEEEEechHheecCchhhheeEEEEECCCCCcccCCHHHhhhcCHHHHHHHHHHHhCCCCChhHHHHHhCcEEecCC
Confidence            489999999999999999   789999996555554448899999999999999999999986 8999999999999999


Q ss_pred             CCCCCCCCccceecCCccccccccccchhHH
Q 032581           78 EHPFGDRPLEPYVMPPRRVRELRPRVRRAMI  108 (137)
Q Consensus        78 ~Hph~aQkp~~l~~~p~~~r~~~~~~~r~~~  108 (137)
                      +|||++|+|+.+   |.++ ..++.+.|.++
T Consensus       103 ~h~~~~qk~~~~---~~a~-~~~~~~~~~~~  129 (142)
T TIGR01077       103 PPELDKKKRVVV---PEAL-VSRLSPTRKYV  129 (142)
T ss_pred             CCCccccCcccc---Chhh-hhccCCCCceE
Confidence            999999999987   5666 78888888664

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

>PRK06394 rpl13p 50S ribosomal protein L13P; Reviewed

Probab=99.97  E-value=5.9e-32  Score=207.40  Aligned_cols=102  Identities=12%  Similarity=0.116  Sum_probs=89.5

Q ss_pred             CCcEEEEEeccceEeecC-CceeEEecCccCccccc----ChhHHhhcChhHHHHHHHHccCC-CChhHHHHhccceeeC
Q 032581            2 ISIYVVFFILRNLFILSL-NDEMSVSYRYIGHLKER----TLKEQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFP   75 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~-~k~Y~~hsgypGGlk~~----t~~~~~~r~P~~Il~rAVrGMLP-Kn~lGr~~lkrLkVy~   75 (137)
                      -|||||||||++|++||+ .+.|++|++|+ |++..    +++++++++|++||++||+|||| ||.+|+.+|+||+||+
T Consensus        27 ~Gd~VVViNa~kv~~tG~K~~~~~~y~~~~-~~k~~~np~~~~~~~~r~P~~il~~AV~gMLP~kn~~gr~~~~rLkvy~  105 (146)
T PRK06394         27 EGEEVVIVNAEKAVITGNRERVIEKYKQRR-ERGSHYNPYRNGPKYPRRPDRIFKRTIRGMLPYKKPRGREALKRLKVYV  105 (146)
T ss_pred             CCCEEEEEechheEecCchhhheeeEeCCC-CCcccCCCCChHHhhhcCHHHHHHHHHHhcCCCCChhHHHHHhCcEEec
Confidence            389999999999999999 67799999998 68877    78999999999999999999999 8999999999999999


Q ss_pred             CCCCCCCCCCccceecCCccccccccccchhHHH
Q 032581           76 GSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIR  109 (137)
Q Consensus        76 G~~Hph~aQkp~~l~~~p~~~r~~~~~~~r~~~~  109 (137)
                      |++|||++|+|+.+++   +.. .++. +|.|+.
T Consensus       106 G~~h~~~~qkp~~~~~---a~~-~~~~-~~k~~~  134 (146)
T PRK06394        106 GVPKELEGKEFEVIDE---ADL-SRLS-TIKYVT  134 (146)
T ss_pred             CCCCCcccCCCEEecH---HHH-hccC-CCCcEE
Confidence            9999999999999865   333 2554 465553

>PTZ00068 60S ribosomal protein L13a; Provisional

Probab=99.97  E-value=1.9e-31  Score=213.71  Aligned_cols=100  Identities=22%  Similarity=0.299  Sum_probs=92.1

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccC-----hhHHhhcChhHHHHHHHHccCCC-ChhHHHHhccce
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERT-----LKEQMERDPTEAIRKAVLRMLPR-NKLRDDRDRKLR   72 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t-----~~~~~~r~P~~Il~rAVrGMLPK-n~lGr~~lkrLk   72 (137)
                      -||+|||||||+|+|||+   ++.||+|     |++..+     .++++++.|++||++||+||||+ |++|+.+|+||+
T Consensus        28 ~Gd~VVVVNaeki~iTG~k~~~K~~y~~-----~lk~~~~~nP~~g~~~~r~P~~Il~raVrGMLPkk~~~Gr~alkrLk  102 (202)
T PTZ00068         28 LGQKIVVVRCEDLNISGSLFRNKVKYEE-----FLRKRMNTNPRRGPFHHRAPSDIFWRTVRGMLPHKTKRGAAALKRLK  102 (202)
T ss_pred             CCCEEEEEecceeEeecchhhheeeeEe-----eeEeeccCCCCcchhcccCHHHHHHHHHhhhCCCCChhHHHHHhCCE
Confidence            489999999999999999   8899998     466666     48999999999999999999995 999999999999


Q ss_pred             eeCCCCCCCCCCCccceecCCccccccccccchhHHH
Q 032581           73 IFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIR  109 (137)
Q Consensus        73 Vy~G~~Hph~aQkp~~l~~~p~~~r~~~~~~~r~~~~  109 (137)
                      ||+|+||||++++++++   |+++|..|++|+|.||.
T Consensus       103 Vy~G~php~~~~k~~vv---p~A~r~~rl~~~~ky~~  136 (202)
T PTZ00068        103 VFEGVPAPYDKVKRVVI---PSALRVLRLKPERPYTV  136 (202)
T ss_pred             EecCCCCchhccCcccc---cchhhhhccCCCCceee
Confidence            99999999999999876   89999999999997763

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

Probab=99.97  E-value=8.3e-32  Score=208.33  Aligned_cols=82  Identities=33%  Similarity=0.452  Sum_probs=78.6

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCCCChhHHHHhccceeeCCCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSE   78 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLPKn~lGr~~lkrLkVy~G~~   78 (137)
                      -||||||+||++|.+||+   +++|++|||||||++.+++++++.++|++|+++||+||||||.||+.+|++|+||+|++
T Consensus        58 cGD~VVV~N~~~Ia~sG~K~~qk~Y~~HsGyPG~lk~~~~~q~~~rdp~~Iv~~AV~gMLPkN~Lrr~~~~rL~lf~g~e  137 (165)
T KOG3203|consen   58 CGDHVVVTNCKKIAFSGKKWEQKIYRSHSGYPGGLKQTTADQLADRDPCRIVRLAVYGMLPKNLLRRRRMQRLHLFPGEE  137 (165)
T ss_pred             CCCEEEEecchhheeccchhhhhhhhhcCCCCCchhhhHHHHHhhhCHHHHHHHHHHhhCccchHHHHHhheeeccCCcc
Confidence            389999999999999999   89999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 032581           79 HPFGD   83 (137)
Q Consensus        79 Hph~a   83 (137)
                      ||+..
T Consensus       138 ~p~~~  142 (165)
T KOG3203|consen  138 HPEKV  142 (165)
T ss_pred             Cchhh
Confidence            99443

>cd00392 Ribosomal_L13 Ribosomal protein L13

Probab=99.97  E-value=1.4e-30  Score=192.40  Aligned_cols=76  Identities=28%  Similarity=0.399  Sum_probs=74.1

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCCCChhHHHHhccceeeCCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGS   77 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLPKn~lGr~~lkrLkVy~G~   77 (137)
                      .||||||||||+|++||+   ++.|++||+||||++..+++++++++|++||++||+||||||.+|+.+|+||+||+|+
T Consensus        36 ~Gd~VvViNa~~i~~tG~k~~~k~y~~~~~~~g~~~~~~~~~~~~~~P~~il~~aV~gMLPkn~~g~~~l~rLkvy~g~  114 (114)
T cd00392          36 CGDYVVVVNAEKIVITGKKWRQKVYYRHTGYPGGLKNPTAGPLHPRAPERILKRAVRGMLPKNKLGRAALKRLKVYEGA  114 (114)
T ss_pred             CCCEEEEEeccEEEEeCchhhccceEEeccCCCCCccCCcchhhhhCHHHHHHHHHHhcCCCChhHHHHHhCcEEeCCC
Confidence            489999999999999999   8899999999999999999999999999999999999999999999999999999985

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.

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

Probab=99.71  E-value=2.5e-18  Score=137.37  Aligned_cols=102  Identities=20%  Similarity=0.235  Sum_probs=89.4

Q ss_pred             CCCcEEEEEeccceEeecCCceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCC-CChhHHHHhccceeeCCCCC
Q 032581            1 MISIYVVFFILRNLFILSLNDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPGSEH   79 (137)
Q Consensus         1 ~~~~~VVVVNaekI~isG~~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLP-Kn~lGr~~lkrLkVy~G~~H   79 (137)
                      |-|..||||.||.|+|||+   |+++.+|-+-.--+. +++|.+-|++||+++|+||+| +++.|+.++++|.+|.|.++
T Consensus        29 l~g~kvvvvr~E~i~isg~---f~r~k~~lrk~~~~n-g~~hfr~ps~i~~~~vrgm~~~kt~rg~aal~~l~~~eGip~  104 (197)
T KOG3204|consen   29 LLGRKVVVVRCEEINISGN---FYRNKLFLRKRLNRN-GPFHFRAPSRILQKAVRGMYPHKTKRGRAALERLRVFEGIPP  104 (197)
T ss_pred             hcCCeEEEEEEeEEEEecc---eecchHHHhhhhccc-CcchhhhHHHHHHHhhccccccCCCccHHHHHHHHHhCCCCC
Confidence            3578999999999999999   888776654322222 899999999999999999999 79999999999999999999


Q ss_pred             CCCCCCccceecCCccccccccccchhHHH
Q 032581           80 PFGDRPLEPYVMPPRRVRELRPRVRRAMIR  109 (137)
Q Consensus        80 ph~aQkp~~l~~~p~~~r~~~~~~~r~~~~  109 (137)
                      |++.|++.+   .|.++++++++|+|.||.
T Consensus       105 ~~dk~~r~v---~p~a~~v~~lk~~~K~c~  131 (197)
T KOG3204|consen  105 PYDKQKRLV---VPVAFQVLRLKPYKKYCL  131 (197)
T ss_pred             hhhhcCCcc---CCcceeeecccCCceeEE
Confidence            999999854   699999999999999875

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	137
2ftc_H	148	L13MT, MRP-L13, 39S ribosomal protein L13, mitocho	2e-18
3v2d_N	140	50S ribosomal protein L13; ribosome associated inh	2e-17
3r8s_J	142	50S ribosomal protein L13; protein biosynthesis, R	4e-17
2zjr_G	174	50S ribosomal protein L13; ribosome, large ribosom	1e-16
3f1f_N	163	50S ribosomal protein L13; RF2, ribosome, terminat	2e-16
3bbo_L	250	Ribosomal protein L13; large ribosomal subunit, sp	1e-15
1j3a_A	142	50S ribosomal protein L13P; rRNA binding, ribosoma	2e-09
1vq8_J	145	50S ribosomal protein L13P; ribosome 50S, protein-	1e-06
3iz5_K	206	60S ribosomal protein L13A (L13P); eukaryotic ribo	2e-06
3jyw_M	178	60S ribosomal protein L16(A); eukaryotic ribosome,	3e-06
4a17_I	198	RPL13A, 60S ribosomal protein L13A; eukaryotic rib	5e-06
3izc_K	199	60S ribosomal protein RPL16 (L13P); eukaryotic rib	7e-06

>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 = 75.3 bits (186), Expect = 2e-18
 Identities = 16/52 (30%), Positives = 25/52 (48%)

Query: 29  YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 80
           Y G  ++ T  +   RDP   ++ A+  MLP+N  R     +L +FP    P
Sbjct: 83  YPGGFRQVTAAQLHLRDPVAIVKLAIYGMLPKNLHRRTMMERLHLFPDEYIP 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 = 72.5 bits (179), Expect = 2e-17
 Identities = 16/52 (30%), Positives = 28/52 (53%)

Query: 29  YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 80
           Y G LK+  L++ +   P   +  AV  MLP+  L     ++L+++ G +HP
Sbjct: 78  YPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHP 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 = 71.4 bits (176), Expect = 4e-17
 Identities = 20/52 (38%), Positives = 30/52 (57%)

Query: 29  YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 80
           +IG +K+ T +E + R P   I  AV  MLP+  L     RKL+++ G+EH 
Sbjct: 80  HIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHN 131

>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 = 71.1 bits (175), Expect = 1e-16
 Identities = 17/52 (32%), Positives = 26/52 (50%)

Query: 29  YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 80
           Y G LK  T +E + + P   I  AV  MLP+ +       +L+++ G  HP
Sbjct: 106 YQGGLKTETAREALSKHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHP 157

>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 = 70.3 bits (173), Expect = 2e-16
 Identities = 16/52 (30%), Positives = 28/52 (53%)

Query: 29  YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 80
           Y G LK+  L++ +   P   +  AV  MLP+  L     ++L+++ G +HP
Sbjct: 101 YPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHP 152

>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 = 69.8 bits (171), Expect = 1e-15
 Identities = 19/52 (36%), Positives = 27/52 (51%)

Query: 29  YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 80
             G LKE T  +  +R P   I  AV  MLP+ +L       L+++ G+EHP
Sbjct: 179 RPGGLKEETFDQLQKRIPERIIEHAVRGMLPKGRLGRYLFNHLKVYKGAEHP 230

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

 Score = 51.5 bits (124), Expect = 2e-09
 Identities = 14/78 (17%), Positives = 28/78 (35%), Gaps = 4/78 (5%)

Query: 27  YRYIGHLKERTLKEQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPGSEHPFGDRP 85
              +  L          +   E +R+ +  MLP +        R+L+++ G    F D+ 
Sbjct: 52  RTGLRTLTNPRRGPFYPKRSDEIVRRTIRGMLPWKTDRGRKAFRRLKVYVGIPKEFQDK- 110

Query: 86  LEPYVMPP-RRVRELRPR 102
            +   +      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 = 43.8 bits (104), Expect = 1e-06
 Identities = 9/71 (12%), Positives = 25/71 (35%), Gaps = 8/71 (11%)

Query: 29  YIGHLKERTLKEQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPGSEHPFGDRPLE 87
            IG+           + P    ++ +  MLP + +   +    +R++ G+ +      L+
Sbjct: 62  DIGNDNGYFY----PKRPDGIFKRTIRGMLPHKKQRGREAFESVRVYLGNPYDEDGEVLD 117

Query: 88  PY---VMPPRR 95
                 +   +
Sbjct: 118 GTSLDRLSNIK 128

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

 Score = 43.2 bits (102), Expect = 3e-06
 Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 4/78 (5%)

Query: 27  YRYIGHLKERTLKEQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPGSEHPFGDRP 85
           +        +T      R P+    KA+  M+  +         +L++F G   P+  + 
Sbjct: 51  FLRKATAFNKTRGPFHFRAPSRIFYKALRGMVSHKTARGKAALERLKVFEGIPPPYDKK- 109

Query: 86  LEPYVMP-PRRVRELRPR 102
            +  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 = 43.0 bits (101), Expect = 5e-06
 Identities = 24/132 (18%), Positives = 40/132 (30%), Gaps = 21/132 (15%)

Query: 27  YRYIGHLKERTLKEQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPGSEHPFGDRP 85
           +             Q  R P+    +AV  MLP +         +L+IF G   P+    
Sbjct: 56  FLNKWMNHNPRRGVQHFRAPSRIFWRAVRGMLPHKTPKGAAALERLKIFEGIPTPYDRVK 115

Query: 86  LE--PYVMPPRRVRELRPRVR------------RAMI------REQKKAEMQQSNKDMRK 125
            +     +  +R+R  RP  +            + +I      R  +             
Sbjct: 116 KQVVVDALKVQRLRNSRPVCKLGDLSASVGWGKQTLIEKLEEKRRARAKTYHDKKVKQAD 175

Query: 126 NRKKEVEAEVTA 137
            RKKE+ A    
Sbjct: 176 ARKKELAAPALK 187

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	137
3v2d_N	140	50S ribosomal protein L13; ribosome associated inh	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
2ftc_H	148	L13MT, MRP-L13, 39S ribosomal protein L13, mitocho	100.0
2zjr_G	174	50S ribosomal protein L13; ribosome, large ribosom	100.0
4b6a_O	199	60S ribosomal protein L16-A; large ribosomal subun	100.0
1j3a_A	142	50S ribosomal protein L13P; rRNA binding, ribosoma	100.0
3bbo_L	250	Ribosomal protein L13; large ribosomal subunit, sp	100.0
4a17_I	198	RPL13A, 60S ribosomal protein L13A; eukaryotic rib	99.98
3jyw_M	178	60S ribosomal protein L16(A); eukaryotic ribosome,	99.97
1vq8_J	145	50S ribosomal protein L13P; ribosome 50S, protein-	99.97
2zkr_j	203	60S ribosomal protein L13A; protein-RNA complex, 6	99.97
3iz5_K	206	60S ribosomal protein L13A (L13P); eukaryotic ribo	99.97

>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=1e-39  Score=247.79  Aligned_cols=90  Identities=21%  Similarity=0.362  Sum_probs=87.6

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCCCChhHHHHhccceeeCCCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSE   78 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLPKn~lGr~~lkrLkVy~G~~   78 (137)
                      -||+|||||||+|+|||+   ++.||+|||||||+++++++++++++|++||++||+||||||++|+.+|+||+||+|++
T Consensus        48 ~Gd~VVViNaeki~~tG~k~~~K~yy~htgypGglk~~~~~~~~~r~P~~ii~~aVrGMLPk~~lgr~~l~rLkVy~G~~  127 (140)
T 3v2d_N           48 MGDFVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPD  127 (140)
T ss_dssp             CCCEEEEECGGGCBCCTTHHHHCEEEEECSSTTCEEEEEHHHHHHHCTHHHHHHHHHHTSCSSHHHHHHHHTEEECSSSC
T ss_pred             CCCEEEEEeCcceEccCchhhheeeEEecccCCcceeccHHHhhhhCHHHHHHHHHHhcCCCChhHHHHHhCCEEeCCCC
Confidence            489999999999999999   89999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCccceec
Q 032581           79 HPFGDRPLEPYVM   91 (137)
Q Consensus        79 Hph~aQkp~~l~~   91 (137)
                      |||++|+|++|++
T Consensus       128 hph~aq~p~~~~~  140 (140)
T 3v2d_N          128 HPHQAQRPEKLEV  140 (140)
T ss_dssp             CSCGGGCCEEECC
T ss_pred             CCcccCCCeecCC
Confidence            9999999998864

>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=2.4e-39  Score=246.31  Aligned_cols=90  Identities=23%  Similarity=0.356  Sum_probs=87.6

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCCCChhHHHHhccceeeCCCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSE   78 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLPKn~lGr~~lkrLkVy~G~~   78 (137)
                      -||+|||||||+|+|||+   ++.||+|||||||+++++++++++++|++||++||+||||||++|+.+|+||+||+|++
T Consensus        50 ~Gd~VVViNaeki~~tG~k~~~K~yy~htgypGg~k~~~~~~~~~r~P~~ii~~aVrGMLPkn~lgr~~l~rLkVy~G~~  129 (142)
T 3r8s_J           50 TGDYIIVLNADKVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNE  129 (142)
T ss_dssp             CCCEEEEECGGGCBCCTTHHHHCBCCEECSSTTCEECCBHHHHHHHCSHHHHHHHHHHHSCSSHHHHHHHTTEEECSSSC
T ss_pred             CCCEEEEEeCcccCccCchhhceEEEEecCcCCCccccCHHHHHhhCHHHHHHHHHHhcCCCChhHHHHHhCCEEECCCC
Confidence            489999999999999999   89999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCccceec
Q 032581           79 HPFGDRPLEPYVM   91 (137)
Q Consensus        79 Hph~aQkp~~l~~   91 (137)
                      |||++|+|++|++
T Consensus       130 hph~aq~p~~l~~  142 (142)
T 3r8s_J          130 HNHAAQQPQVLDI  142 (142)
T ss_dssp             CSCGGGCCEECCC
T ss_pred             CCcccCCCeecCC
Confidence            9999999998864

>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=7.5e-39  Score=248.21  Aligned_cols=90  Identities=21%  Similarity=0.362  Sum_probs=86.4

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCCCChhHHHHhccceeeCCCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSE   78 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLPKn~lGr~~lkrLkVy~G~~   78 (137)
                      .||+|||||||+|+|||+   ++.||+|||||||+++++++++++++|++||++||+||||||++|+.+|+||+||+|++
T Consensus        71 ~GD~VVVINaekI~iTG~K~~~K~yy~htgypGglk~~t~~~~~~r~P~~Ii~~AVrGMLPkn~lGr~~l~rLkVY~G~~  150 (163)
T 3f1f_N           71 MGDFVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPD  150 (163)
T ss_dssp             CCCBCEECCGGGCBCSTTHHHHCEECCBCSSTTCBCCEEHHHHHHSSCHHHHHHHHHTTSCSSHHHHHHHHTCEECSSSC
T ss_pred             CCCEEEEEeCcccccCCchhhheeeEEecCcCCcceeeehHHhhhcCHHHHHHHHHHhcCCCChhHHHHHhCCEEECCCC
Confidence            489999999999999999   89999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCccceec
Q 032581           79 HPFGDRPLEPYVM   91 (137)
Q Consensus        79 Hph~aQkp~~l~~   91 (137)
                      |||++|+|++|++
T Consensus       151 hPh~aQ~P~~l~~  163 (163)
T 3f1f_N          151 HPHQAQRPEKLEV  163 (163)
T ss_dssp             CCCCSCCCBCC--
T ss_pred             CCcccCCCeecCC
Confidence            9999999998864

>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=1.7e-38  Score=242.97  Aligned_cols=92  Identities=23%  Similarity=0.250  Sum_probs=89.0

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCCCChhHHHHhccceeeCCCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSE   78 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLPKn~lGr~~lkrLkVy~G~~   78 (137)
                      -||||||||||+|+|||+   ++.||+|||||||+++++++++++++|++||++||+||||||++|+.+|+||+||+|++
T Consensus        53 ~Gd~VVViNaeki~~tG~k~~~K~yy~htg~pGg~k~~~~~~~~~r~P~~ii~~aVrGMLPkn~lgr~~l~rLkVy~G~~  132 (148)
T 2ftc_H           53 CGDHVVIMNTRHIAFSGNKWEQKVYSSHTGYPGGFRQVTAAQLHLRDPVAIVKLAIYGMLPKNLHRRTMMERLHLFPDEY  132 (148)
T ss_pred             CCCEEEEEeceeeEeccchHhhheeeeeeCCcCCceeccHHHHhhcCHHHHHHHHHHhcCCCCchHHHHHhCcEEeCCCC
Confidence            489999999999999999   89999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCccceecCC
Q 032581           79 HPFGDRPLEPYVMPP   93 (137)
Q Consensus        79 Hph~aQkp~~l~~~p   93 (137)
                      |||++|+|++++++.
T Consensus       133 hP~~aq~p~~~~i~~  147 (148)
T 2ftc_H          133 IPEDILKNLVEELPQ  147 (148)
T ss_pred             CChHHhCCeeeccCC
Confidence            999999999988753

>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=7.3e-38  Score=244.79  Aligned_cols=91  Identities=21%  Similarity=0.373  Sum_probs=88.4

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCCCChhHHHHhccceeeCCCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSE   78 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLPKn~lGr~~lkrLkVy~G~~   78 (137)
                      -||||||||||+|+|||+   ++.||+|||||||+++++++++++++|++||++||+||||||++|+.+|+||+||+|++
T Consensus        76 ~GD~VVVINAeki~lTG~K~~~K~yy~htgypGGlk~~~~~~~~~r~P~~Ii~~AVrGMLPkn~lGr~~l~rLkVy~G~~  155 (174)
T 2zjr_G           76 QGDFVVVINAAQVALTGKKLDDKVYTRYTGYQGGLKTETAREALSKHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGET  155 (174)
T ss_dssp             CCCEEEEECCTTCBCSSCSSSSCEEEECCSSCSSCCEEEESTTTTSCHHHHHHHHHGGGSCCSHHHHHHHTTCEECSCST
T ss_pred             CCCEEEEEeCeeeEeccchhhceEEEEecCcCCCcccccHHHHhhcChHHHHHHHHHhcCCCChhHHHHHhCeEEECCCC
Confidence            489999999999999999   89999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCccceecC
Q 032581           79 HPFGDRPLEPYVMP   92 (137)
Q Consensus        79 Hph~aQkp~~l~~~   92 (137)
                      |||++|+|+++++.
T Consensus       156 hph~aqkp~~l~~~  169 (174)
T 2zjr_G          156 HPHSAQKPQVLKTQ  169 (174)
T ss_dssp             GGGGSCCSCCCCCC
T ss_pred             CChhccCCeEEecc
Confidence            99999999998863

>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=1.4e-37  Score=236.33  Aligned_cols=101  Identities=20%  Similarity=0.211  Sum_probs=80.4

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccc-cChhHHhhcChhHHHHHHHHccCC-CChhHHHHhccceeeCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKE-RTLKEQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPG   76 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~-~t~~~~~~r~P~~Il~rAVrGMLP-Kn~lGr~~lkrLkVy~G   76 (137)
                      -||||||||||+|+|||+   ++.||+|||||||++. ++ +++++++|++||++||+|||| ||++|+.+|+||+||+|
T Consensus        24 ~Gd~VVViNaeki~iTG~k~~~K~yy~h~g~~gg~~~~~~-~~~~~r~P~~ii~~aVrGMLP~k~~lgr~~l~rLkVy~G  102 (142)
T 1j3a_A           24 EGEEVVIVNAEKAVITGNREVIFSKYKQRTGLRTLTNPRR-GPFYPKRSDEIVRRTIRGMLPWKTDRGRKAFRRLKVYVG  102 (142)
T ss_dssp             TTCCEEEECGGGCEEESCHHHHHHHHHHHC--------------CCCSHHHHHHHHHHTTTTTTSHHHHHHHTTEEECSS
T ss_pred             cCCEEEEEeCeeeEecccHHhheeeeeecCCCCCCcCCcc-CcccccCHHHHHHHHHHhhccCCCHHHHHHHhCcEEeCC
Confidence            389999999999999999   8899999999999776 77 999999999999999999999 99999999999999999


Q ss_pred             CCCCCCCCCccceecCCccccccccccchhHH
Q 032581           77 SEHPFGDRPLEPYVMPPRRVRELRPRVRRAMI  108 (137)
Q Consensus        77 ~~Hph~aQkp~~l~~~p~~~r~~~~~~~r~~~  108 (137)
                      ++|||++|+|++++   .++. .++. +|.+|
T Consensus       103 ~~hp~~aqkp~~~~---~a~~-~~~~-~~k~~  129 (142)
T 1j3a_A          103 IPKEFQDKQLETIV---EAHV-SRLS-RPKYV  129 (142)
T ss_dssp             CCGGGTTSCCBCCG---GGBG-GGSS-SCCEE
T ss_pred             CCCCccccCcEecc---HHHh-hccC-CCCeE
Confidence            99999999999874   4554 4553 66655

>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=1e-36  Score=248.68  Aligned_cols=96  Identities=23%  Similarity=0.344  Sum_probs=83.7

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCCCChhHHHHhccceeeCCCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSE   78 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLPKn~lGr~~lkrLkVy~G~~   78 (137)
                      -||||||||||+|+|||+   ++.|++|||||||+++++++++++++|++||++||+||||||++|+.+|+||+||+|++
T Consensus       149 ~GD~VVVINAeKI~lTG~K~~~K~Y~rHsgyPGGlK~~t~~~l~~r~PerIi~kAVrGMLPkn~lGr~~lkrLkVY~G~~  228 (250)
T 3bbo_L          149 MGAFVIVVNADKVAVSGKKRTQKLYRRHSGRPGGLKEETFDQLQKRIPERIIEHAVRGMLPKGRLGRYLFNHLKVYKGAE  228 (250)
T ss_dssp             CSCCCEESCCSSCCCCSGGGGTCCCBCCCSSSSCCCBCCHHHHTTSCTTHHHHHHHHTTSCSSSSHHHHHTTCCCCSSSC
T ss_pred             CCCEEEEEecceEEecCChhhceEEEEecCcCCCcccccHHHhhhcChHHHHHHHHHhcCCCCchHHHHHhCcEEeCCCC
Confidence            489999999999999999   88999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCccceecCCcccc
Q 032581           79 HPFGDRPLEPYVMPPRRVR   97 (137)
Q Consensus        79 Hph~aQkp~~l~~~p~~~r   97 (137)
                      |||++|+|+++++....++
T Consensus       229 HPh~aQkp~~l~ia~k~v~  247 (250)
T 3bbo_L          229 HPHQAQQPIDLPLRDKRIR  247 (250)
T ss_dssp             CSCTTSCC-----------
T ss_pred             CCHHHcCCeeechhhheee
Confidence            9999999999876554443

>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=99.98  E-value=2.3e-34  Score=228.83  Aligned_cols=104  Identities=18%  Similarity=0.148  Sum_probs=97.8

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCC-CChhHHHHhccceeeCCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPGS   77 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLP-Kn~lGr~~lkrLkVy~G~   77 (137)
                      -||||||||||+|+|||+   ++.||+|+.++++....+++++++++|++||++||+|||| ||++|+.+|+||+||+|+
T Consensus        28 ~GD~VVVINAekI~iTG~K~~~K~yy~~~l~~~~~~~~~~g~~~~r~P~rIi~~AVrGMLPkK~~lGr~~l~rLkVy~G~  107 (198)
T 4a17_I           28 SGQRIVVVRTEAINISGSLFRNRVKFSEFLNKWMNHNPRRGVQHFRAPSRIFWRAVRGMLPHKTPKGAAALERLKIFEGI  107 (198)
T ss_dssp             TTCCEEEECGGGCEEESCHHHHHHHHHHHHTCCCSSCTTSSCCCCCSHHHHHHHHHHTTTTTTSHHHHHHHHHCEECSSC
T ss_pred             CCCEEEEEcCccccccCchhhheeeeeeccccccCCCCccccccccCHHHHHHHHHhccCCCCChhHHHHHhCcEEecCC
Confidence            489999999999999999   7899999989998887788999999999999999999999 599999999999999999


Q ss_pred             CCCCCCCCccceecCCccccccccccchhHH
Q 032581           78 EHPFGDRPLEPYVMPPRRVRELRPRVRRAMI  108 (137)
Q Consensus        78 ~Hph~aQkp~~l~~~p~~~r~~~~~~~r~~~  108 (137)
                      ||||++|+++++   |++++..|++|+|.||
T Consensus       108 ~hph~aqk~~vv---p~al~v~rl~~~rk~~  135 (198)
T 4a17_I          108 PTPYDRVKKQVV---VDALKVQRLRNSRPVC  135 (198)
T ss_dssp             CGGGTTSCCBCC---GGGBHHHHSCTTSCEE
T ss_pred             CCChhhcccccc---chHhhhhhcCCCCCeE
Confidence            999999998875   8999999999999876

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

Probab=99.97  E-value=5.3e-34  Score=223.57  Aligned_cols=105  Identities=18%  Similarity=0.202  Sum_probs=93.4

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccc--cChhHHhhcChhHHHHHHHHccCC-CChhHHHHhccceeeC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKE--RTLKEQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFP   75 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~--~t~~~~~~r~P~~Il~rAVrGMLP-Kn~lGr~~lkrLkVy~   75 (137)
                      -||||||||||+|+|||+   ++.||+|  |++....  .+.+++++++|++||++||+|||| ||++|+.+|+||+||+
T Consensus        23 ~GD~VVVINaeki~iTG~K~~~K~yy~h--~l~~~~~~~~~~~~~~~r~P~~Il~~AVrGMLP~K~~lGr~~l~rLkVy~  100 (178)
T 3jyw_M           23 NGQKIVVVRAEELNISGEFFRNKLKYHD--FLRKATAFNKTRGPFHFRAPSRIFYKALRGMVSHKTARGKAALERLKVFE  100 (178)
T ss_dssp             TTCCCCEECSTTSCCCCCSSHHHHSCSS--SSSSTTSCCCSSSCCCCSSTTTHHHHHTTSSSCSSSHHHHHHHHHCCEES
T ss_pred             CCCEEEEEeCeeeEEcCchHhhEhheec--cCcccccCCccccccccCCHHHHHHHHHHHHhhcccHhHHHHHhCCeeeC
Confidence            489999999999999999   7899998  5544332  346899999999999999999999 6999999999999999


Q ss_pred             CCCCCCCCCCccceecCCccccccccccchhHHHhh
Q 032581           76 GSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQ  111 (137)
Q Consensus        76 G~~Hph~aQkp~~l~~~p~~~r~~~~~~~r~~~~~~  111 (137)
                      |++|||++|+++++   |++++.+|++|+|.||.-.
T Consensus       101 G~~hp~~aqk~~vv---p~Alrv~RLkp~rKy~tLG  133 (178)
T 3jyw_M          101 GIPPPYDKKKRVVV---PQALRVLRLKPGRKYTTLG  133 (178)
T ss_dssp             SCCCCSCCSCSSSC---CSSCCCCCSSSCSCCCCHH
T ss_pred             CCCCchhhcccccC---chHhhhhccCCCCceEEcc
Confidence            99999999999876   8999999999999887544

>1vq8_J 50S ribosomal protein L13P; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.21.1.1 PDB: 1giy_M 1jj2_I 1k73_K* 1k8a_K* 1k9m_K* 1kc8_K* 1kd1_K* 1kqs_I* 1m1k_K* 1m90_K* 1ml5_m* 1n8r_K* 1nji_K* 1q7y_K* 1q81_K* 1q82_K* 1q86_K* 1qvf_I 1qvg_I 1s72_J* ...

Probab=99.97  E-value=9.5e-34  Score=216.02  Aligned_cols=96  Identities=14%  Similarity=0.070  Sum_probs=85.4

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCC-CChhHHHHhccceeeCCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPGS   77 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLP-Kn~lGr~~lkrLkVy~G~   77 (137)
                      -||||||||||+|+|||+   ++.||+|||||||    +++++++++|++||++||+|||| ||++|+.+|+||+||+|+
T Consensus        32 ~Gd~VVViNaeki~iTG~k~~~K~yy~htg~~g~----~~~~~~~r~P~~i~~~aVrGMLP~K~~lgr~~l~rLkVy~G~  107 (145)
T 1vq8_J           32 DGETVAVVNAERAVITGREEQIVEKYEKRVDIGN----DNGYFYPKRPDGIFKRTIRGMLPHKKQRGREAFESVRVYLGN  107 (145)
T ss_dssp             TTCCEEEECGGGCEEESCHHHHHHHHHHHHHCCC----SSCCCCCCSHHHHHHHHHHTTTTTTSHHHHHHHHTEEECSSC
T ss_pred             cCCEEEEEeCEeeEecchhhhheeeeEEeCCCCC----CHHHHhhcChHHHHHHHHHhhcCCCCHHHHHHHhCeEEECCC
Confidence            389999999999999999   8999999999998    78999999999999999999999 999999999999999999


Q ss_pred             CCCCCCCCccceecCCccccccccccchhHHH
Q 032581           78 EHPFGDRPLEPYVMPPRRVRELRPRVRRAMIR  109 (137)
Q Consensus        78 ~Hph~aQkp~~l~~~p~~~r~~~~~~~r~~~~  109 (137)
                      |||   |+|+++   |.+.. .++. +|.+|.
T Consensus       108 ~~p---~k~~vv---~~a~~-~~l~-~~k~~~  131 (145)
T 1vq8_J          108 PYD---EDGEVL---DGTSL-DRLS-NIKFVT  131 (145)
T ss_dssp             CSS---SCCBCC---TTCBC-CTTS-CCSEEE
T ss_pred             CCC---CCceee---ehhhh-hccC-CCCeEE
Confidence            999   788776   44544 4554 666653

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

Probab=99.97  E-value=4.3e-33  Score=222.23  Aligned_cols=95  Identities=20%  Similarity=0.224  Sum_probs=89.3

Q ss_pred             CcEEEEEeccceEeecC---CceeE-Eec-------CccCcccccChhHHhhcChhHHHHHHHHccCCC-ChhHHHHhcc
Q 032581            3 SIYVVFFILRNLFILSL---NDEMS-VSY-------RYIGHLKERTLKEQMERDPTEAIRKAVLRMLPR-NKLRDDRDRK   70 (137)
Q Consensus         3 ~~~VVVVNaekI~isG~---~k~Y~-~hs-------gypGGlk~~t~~~~~~r~P~~Il~rAVrGMLPK-n~lGr~~lkr   70 (137)
                      |+||||||||+|+|||+   ++.|| +|+       +||||        +++++|++||++||+||||+ |++|+.+|+|
T Consensus        30 G~~VVVINaeki~iTG~k~~~K~yy~~h~~~~~~~n~~~G~--------~~~r~P~~I~~~AVrGMLPkk~~lGr~~l~r  101 (203)
T 2zkr_j           30 GRKVVVVRCEGINISGNFYRNKLNYLAFLRKRMNTNPSRGP--------YDFRAPSRIFWRTVRGMLPHKTKRGQAALDR  101 (203)
T ss_dssp             TCCEEEECGGGCEEESCHHHHHHHSSSSSCHHHHCCCSSCC--------CCCCSHHHHHHHHHHHHSCTTSHHHHHHHHT
T ss_pred             CCeEEEEchHHeecCchHHHHHHHHHHHHhhcccCCCCCCc--------cccCChHHHHHHHHHhhCCCCChhHHHHHhC
Confidence            79999999999999999   78999 998       78887        57899999999999999998 8999999999


Q ss_pred             ceeeCCCCCCCCCCCccceecCCccccccccccchhHH
Q 032581           71 LRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMI  108 (137)
Q Consensus        71 LkVy~G~~Hph~aQkp~~l~~~p~~~r~~~~~~~r~~~  108 (137)
                      |+||+|+||||++|+|+++   |++++.++++++|.||
T Consensus       102 LkVy~G~~hp~~aqkp~vv---p~a~~v~~~~~~~ky~  136 (203)
T 2zkr_j          102 LKVFDGIPPPYDKKKRMVV---PAALKVVRLKPTRKFA  136 (203)
T ss_dssp             EEECSCSSCSSSSCCBCCG---GGBCCSSSSSCCSCEE
T ss_pred             cEEeCCCCCchhhcCCccc---chhhhhhhcCCCCceE
Confidence            9999999999999999886   7999999999999887

---

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	137
d2j01n1	139	c.21.1.1 (N:1-139) Ribosomal protein L13 {Thermus	7e-12
d2zjrg1	142	c.21.1.1 (G:30-171) Ribosomal protein L13 {Deinoco	5e-11
d2gych1	140	c.21.1.1 (H:1-140) Ribosomal protein L13 {Escheric	4e-10
d1j3aa_	142	c.21.1.1 (A:) Ribosomal protein L13 {Archaeon Pyro	2e-06
d1vqoj1	142	c.21.1.1 (J:4-145) Ribosomal protein L13 {Archaeon	2e-06

>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 = 56.6 bits (136), Expect = 7e-12
 Identities = 16/55 (29%), Positives = 28/55 (50%)

Query: 27  YRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPF 81
             Y G LK+  L++ +   P   +  AV  MLP+  L     ++L+++ G +HP 
Sbjct: 76  SGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHPH 130

>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 = 54.6 bits (131), Expect = 5e-11
 Identities = 17/55 (30%), Positives = 26/55 (47%)

Query: 27  YRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPF 81
             Y G LK  T +E + + P   I  AV  MLP+ +       +L+++ G  HP 
Sbjct: 75  TGYQGGLKTETAREALSKHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPH 129

>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 = 51.9 bits (124), Expect = 4e-10
 Identities = 20/55 (36%), Positives = 30/55 (54%)

Query: 27  YRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPF 81
             +IG +K+ T +E + R P   I  AV  MLP+  L     RKL+++ G+EH  
Sbjct: 78  TGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNH 132

>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 = 42.3 bits (99), Expect = 2e-06
 Identities = 17/102 (16%), Positives = 33/102 (32%), Gaps = 6/102 (5%)

Query: 5   YVVFFILRNLFILSLNDEMSVSYR---YIGHLKERTLKEQMERDPTEAIRKAVLRMLP-R 60
            VV        I    + +   Y+    +  L          +   E +R+ +  MLP +
Sbjct: 27  EVVIVNAEKAVITGNREVIFSKYKQRTGLRTLTNPRRGPFYPKRSDEIVRRTIRGMLPWK 86

Query: 61  NKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPR 102
                   R+L+++ G    F D+  +   +    V  L   
Sbjct: 87  TDRGRKAFRRLKVYVGIPKEFQDK--QLETIVEAHVSRLSRP 126

>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 = 42.2 bits (99), Expect = 2e-06
 Identities = 12/95 (12%), Positives = 28/95 (29%), Gaps = 5/95 (5%)

Query: 5   YVVFFILRNLFILSLNDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLR 64
            V         I    +++   Y     +          + P    ++ +  MLP  K R
Sbjct: 32  TVAVVNAERAVITGREEQIVEKYEKRVDIG-NDNGYFYPKRPDGIFKRTIRGMLPHKKQR 90

Query: 65  DDRD-RKLRIFPGSEHPFGDRPLEPY---VMPPRR 95
                  +R++ G+ +      L+      +   +
Sbjct: 91  GREAFESVRVYLGNPYDEDGEVLDGTSLDRLSNIK 125

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	137
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	99.98
d1vqoj1	142	Ribosomal protein L13 {Archaeon Haloarcula marismo	99.96

>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=1.4e-37  Score=233.76  Aligned_cols=89  Identities=21%  Similarity=0.360  Sum_probs=86.0

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCCCChhHHHHhccceeeCCCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSE   78 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLPKn~lGr~~lkrLkVy~G~~   78 (137)
                      .||+||||||++|+|||+   ++.|++|||||||+++.+++++++++|++||++||+||||||++|+.+|+||+||+|++
T Consensus        48 ~Gd~VvViNa~ki~~tG~k~~~k~y~~hsgypGg~k~~~~~~~~~k~P~~il~~aV~gMLPkn~lg~~~l~rLkvy~g~~  127 (139)
T d2j01n1          48 MGDFVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPD  127 (139)
T ss_dssp             CCCCCEECSCSCCBCSSCCSSSSBCCCCCCSSSCCCCCBHHHHHHSSCSHHHHHHHHTTSCSSHHHHHHHTTCEECSSSC
T ss_pred             CCceEEEechhHeeeeccccceeeeeeeccccCccccccHHHhcccCHHHHHHHHHHhcCCCChhHHHHHhCCEEeCCCC
Confidence            589999999999999999   78999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCcccee
Q 032581           79 HPFGDRPLEPYV   90 (137)
Q Consensus        79 Hph~aQkp~~l~   90 (137)
                      |||++|+|+.|+
T Consensus       128 hp~~aq~p~~l~  139 (139)
T d2j01n1         128 HPHQAQRPEKLE  139 (139)
T ss_dssp             CTTCSCCCCCC-
T ss_pred             CCcccCCCEeCC
Confidence            999999999874

>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=3.1e-37  Score=232.57  Aligned_cols=91  Identities=21%  Similarity=0.373  Sum_probs=87.9

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCCCChhHHHHhccceeeCCCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSE   78 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLPKn~lGr~~lkrLkVy~G~~   78 (137)
                      .||+||||||++|++||+   ++.|++|||||||+++++++++++++|++||++||+||||||++|+.+|+||+||+|++
T Consensus        47 ~Gd~ViViNa~ki~~tG~K~~~k~y~~htg~pgg~k~~~~~~~~~r~P~~ii~~aV~gMLPkn~lgr~~lkrLkvy~G~~  126 (142)
T d2zjrg1          47 QGDFVVVINAAQVALTGKKLDDKVYTRYTGYQGGLKTETAREALSKHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGET  126 (142)
T ss_dssp             CCCEEEEECCTTCBCSSCSSSSCEEEECCSSCSSCCEEEESTTTTSCHHHHHHHHHGGGSCCSHHHHHHHTTCEECSCST
T ss_pred             CCCEEEEcCCceeEEcCcchhhheehhhcccccccccccHHHHhccchHHHHHHHHHhcCCCChhHHHHHhCCeEeCCCC
Confidence            589999999999999999   78999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCccceecC
Q 032581           79 HPFGDRPLEPYVMP   92 (137)
Q Consensus        79 Hph~aQkp~~l~~~   92 (137)
                      |||++|+|+.|++-
T Consensus       127 hp~~~q~P~~l~~~  140 (142)
T d2zjrg1         127 HPHSAQKPQVLKTQ  140 (142)
T ss_dssp             GGGGSCCSCCCCCC
T ss_pred             CCccccCCceeccc
Confidence            99999999988753

>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=7.5e-38  Score=235.58  Aligned_cols=88  Identities=24%  Similarity=0.365  Sum_probs=85.6

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCCCChhHHHHhccceeeCCCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSE   78 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLPKn~lGr~~lkrLkVy~G~~   78 (137)
                      .||||||||||+|+|||+   ++.|++|||||||+++.+++++++++|++||++||+||||||++|+.+|+||+||+|++
T Consensus        50 ~Gd~VvViNaeki~~tG~K~~~k~y~~~sgypgg~k~~~~~~~~~k~P~~il~~aV~gMLPkn~lgr~~lkrLkvy~g~~  129 (140)
T d2gych1          50 TGDYIIVLNADKVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNE  129 (140)
T ss_dssp             CCCCCCCSCSSSCCCCSSCSTTCCCCCCCSSCSSCCCCCCHHHHTTCSSSSTTTSSSSCSCSSSTTSSTTTSSCCCCCCT
T ss_pred             CCcEEEEEechhhcccCchhhhhhhhccccCCCCcccccHHHHHhhHHHHHHHHHHHhcCCCChhHHHHHhCCEEeCCCC
Confidence            589999999999999999   78999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCccce
Q 032581           79 HPFGDRPLEPY   89 (137)
Q Consensus        79 Hph~aQkp~~l   89 (137)
                      |||++|+|++|
T Consensus       130 hph~aQ~P~~l  140 (140)
T d2gych1         130 HNHAAQQPQVL  140 (140)
T ss_dssp             TTTTSCCCCCC
T ss_pred             CCccccCCccC
Confidence            99999999864

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

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

Probab=99.98  E-value=2.3e-34  Score=216.72  Aligned_cols=89  Identities=19%  Similarity=0.202  Sum_probs=73.0

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCC-CChhHHHHhccceeeCCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPGS   77 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLP-Kn~lGr~~lkrLkVy~G~   77 (137)
                      -||||||||||+|+|||+   ++.||+|++||||++..+++++++++|++||++||+|||| ||++|+.+|+||+||+|+
T Consensus        24 ~Gd~ViVvNaeki~~tG~K~~~k~~~~~~~~~g~~~~~~~~~~~~~~P~~il~~aVrGMLP~k~~lgr~~~krLkvy~G~  103 (142)
T d1j3aa_          24 EGEEVVIVNAEKAVITGNREVIFSKYKQRTGLRTLTNPRRGPFYPKRSDEIVRRTIRGMLPWKTDRGRKAFRRLKVYVGI  103 (142)
T ss_dssp             TTCCEEEECGGGCEEESCHHHHHHHHHHHC-------------CCCSHHHHHHHHHHTTTTTTSHHHHHHHTTEEECSSC
T ss_pred             CCCeEEEEechhheecCcchhhhhhhhhhcccccccCcchhhhcccChHHHHHHHHHcccCCCChHHHHHHhCCEEecCC
Confidence            489999999999999999   7789999999999999999999999999999999999999 899999999999999999


Q ss_pred             CCCCCCCCcccee
Q 032581           78 EHPFGDRPLEPYV   90 (137)
Q Consensus        78 ~Hph~aQkp~~l~   90 (137)
                      +|||++|+|+.++
T Consensus       104 ~h~~~~q~~~~~~  116 (142)
T d1j3aa_         104 PKEFQDKQLETIV  116 (142)
T ss_dssp             CGGGTTSCCBCCG
T ss_pred             CCChhhcCCcccc
Confidence            9999999999874

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

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

Probab=99.96  E-value=8.8e-32  Score=202.76  Aligned_cols=86  Identities=14%  Similarity=0.107  Sum_probs=79.7

Q ss_pred             CCcEEEEEeccceEeecC---CceeEEecCccCcccccChhHHhhcChhHHHHHHHHccCC-CChhHHHHhccceeeCCC
Q 032581            2 ISIYVVFFILRNLFILSL---NDEMSVSYRYIGHLKERTLKEQMERDPTEAIRKAVLRMLP-RNKLRDDRDRKLRIFPGS   77 (137)
Q Consensus         2 ~~~~VVVVNaekI~isG~---~k~Y~~hsgypGGlk~~t~~~~~~r~P~~Il~rAVrGMLP-Kn~lGr~~lkrLkVy~G~   77 (137)
                      -||+|||||||+|+|||+   ++.||+|++||||.+    +++++++|++||++||+|||| |+.+|+.+|+||+||.|+
T Consensus        29 ~Gd~ViVvNaeki~itG~k~~~k~~y~~~~~~g~~k----g~~~~r~P~~il~raVrGMLP~k~~~gr~~~krLkvy~G~  104 (142)
T d1vqoj1          29 DGETVAVVNAERAVITGREEQIVEKYEKRVDIGNDN----GYFYPKRPDGIFKRTIRGMLPHKKQRGREAFESVRVYLGN  104 (142)
T ss_dssp             TTCCEEEECGGGCEEESCHHHHHHHHHHHHHCCCSS----CCCCCCSHHHHHHHHHHTTTTTTSHHHHHHHTTEEECSSC
T ss_pred             CCCEEEEEEChhhcccCcchhhhheeeeeecCCCcc----ceehhcCHHHHHHHHHhCcCCCCChhHHHHHhCcEEeCCC
Confidence            489999999999999999   678999999999976    678999999999999999999 799999999999999999


Q ss_pred             CCCCCCCCccceec
Q 032581           78 EHPFGDRPLEPYVM   91 (137)
Q Consensus        78 ~Hph~aQkp~~l~~   91 (137)
                      ||||++|.|+++.+
T Consensus       105 ~h~~~~q~~~~~~~  118 (142)
T d1vqoj1         105 PYDEDGEVLDGTSL  118 (142)
T ss_dssp             CSSSCCBCCTTCBC
T ss_pred             CCccccCcCChhhh
Confidence            99999999876543