Citrus Sinensis ID: 033270

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120---
Protein Sequence
MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYAIKV
Secondary Structure (PSIPRED)
ccccccHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHcHHHHHHccHHHHHHccHHHHHHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
cccEEHHHHccccHHHHHHHHHHHHHHHHHHHEEEEccccccEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHcHHHHHHHHHHHHHHHHHccccEEEEcc
Coil and Loop (DISEMBL)
MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVtggapnklskIKVVRLSIAQVLTVISQKQKAALREAYknkkflpldlrpkkTRAIRRRLTKHQASLKTEREKKREMYFPMRKYAIKV
Flexible Loop (DISEMBL)
marvkvhelrtksktdllNQLKDLKAELALLRVAkvtggapnklskikVVRLSIAQVLTVISQKQKAALReayknkkflpldlrpkktrairrrltkhqaslkterekkremyfpmrkyaikv
Low Complexity Region (SEG)
MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYAIKV
Disordered region (IsUnstruct)
****************LLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAALREAYKNKKFLPL******************************************
Disordered Region (DISOPRED)
***VKVH*LR******LLNQLKDLKAELA********************VRLSIAQVLTVISQ**************FLPLDLRPKKTRAIRRRL*****************YFPMRKYAIKV
Disordered Region (DISEMBL)
********LRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYAIKV
Disordered Region (DISPRO)
*ARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYAIKV
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MARVKVHELRTKSxxxxxxxxxxxxxxxxxxxxxKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYAIKV
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	123	2.2.26 [Sep-21-2011]
Q9M5L0	123	60S ribosomal protein L35	N/A	no	1.0	1.0	0.934	3e-59
Q9LZ41	123	60S ribosomal protein L35	yes	no	1.0	1.0	0.918	8e-58
Q9SF53	123	60S ribosomal protein L35	yes	no	1.0	1.0	0.910	3e-57
O80626	123	60S ribosomal protein L35	yes	no	1.0	1.0	0.902	1e-56
Q9M3D2	123	60S ribosomal protein L35	no	no	1.0	1.0	0.886	2e-55
P17078	123	60S ribosomal protein L35	yes	no	0.991	0.991	0.647	2e-37
Q6ZWV7	123	60S ribosomal protein L35	yes	no	0.991	0.991	0.647	2e-37
Q3MHM7	123	60S ribosomal protein L35	yes	no	0.991	0.991	0.639	3e-37
Q98TF7	123	60S ribosomal protein L35	yes	no	0.991	0.991	0.647	3e-37
P42766	123	60S ribosomal protein L35	yes	no	0.991	0.991	0.639	3e-37

>sp|Q9M5L0|RL35_EUPES 60S ribosomal protein L35 OS=Euphorbia esula GN=RPL35 PE=2 SV=1

 Score =  226 bits (576), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 115/123 (93%), Positives = 119/123 (96%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MAR+KVHELR K+K +LLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV
Sbjct: 1   MARIKVHELRQKTKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
           ISQKQK ALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQ SLKTEREKK+EMYFPMRKYA
Sbjct: 61  ISQKQKLALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQQSLKTEREKKKEMYFPMRKYA 120

Query: 121 IKV 123
           IKV
Sbjct: 121 IKV 123

Euphorbia esula (taxid: 3993)

>sp|Q9LZ41|RL354_ARATH 60S ribosomal protein L35-4 OS=Arabidopsis thaliana GN=RPL35D PE=2 SV=1

 Score =  221 bits (564), Expect = 8e-58,   Method: Compositional matrix adjust.
 Identities = 113/123 (91%), Positives = 118/123 (95%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MAR+KVHELR KSKTDL NQLK+ KAELALLRVAKVTGGAPNKLSKIKVVR SIAQVLTV
Sbjct: 1   MARIKVHELRDKSKTDLQNQLKEFKAELALLRVAKVTGGAPNKLSKIKVVRKSIAQVLTV 60

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
           ISQKQK+ALREAYKNKK LPLDLRPKKTRAIRRRLTKHQASLKTEREKK+EMYFP+RKYA
Sbjct: 61  ISQKQKSALREAYKNKKLLPLDLRPKKTRAIRRRLTKHQASLKTEREKKKEMYFPVRKYA 120

Query: 121 IKV 123
           IKV
Sbjct: 121 IKV 123

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SF53|RL351_ARATH 60S ribosomal protein L35-1 OS=Arabidopsis thaliana GN=RPL35A PE=1 SV=1

 Score =  219 bits (559), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 112/123 (91%), Positives = 118/123 (95%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MAR+KVHELR KSK+DL NQLK+LKAELALLRVAKVTGGAPNKLSKIKVVR SIAQVLTV
Sbjct: 1   MARIKVHELREKSKSDLQNQLKELKAELALLRVAKVTGGAPNKLSKIKVVRKSIAQVLTV 60

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
            SQKQK+ALREAYKNKK LPLDLRPKKTRAIRRRLTKHQASLKTEREKK+EMYFP+RKYA
Sbjct: 61  SSQKQKSALREAYKNKKLLPLDLRPKKTRAIRRRLTKHQASLKTEREKKKEMYFPIRKYA 120

Query: 121 IKV 123
           IKV
Sbjct: 121 IKV 123

Arabidopsis thaliana (taxid: 3702)

>sp|O80626|RL352_ARATH 60S ribosomal protein L35-2 OS=Arabidopsis thaliana GN=RPL35B PE=2 SV=1

 Score =  217 bits (553), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 111/123 (90%), Positives = 116/123 (94%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MAR+KVHELR KSK DL  QLK+ KAELALLRVAKVTGGAPNKLSKIKVVR SIAQVLTV
Sbjct: 1   MARIKVHELREKSKADLSGQLKEFKAELALLRVAKVTGGAPNKLSKIKVVRKSIAQVLTV 60

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
           ISQKQK+ALREAYKNKK LPLDLRPKKTRAIRRRLTKHQASLKTEREKK+EMYFP+RKYA
Sbjct: 61  ISQKQKSALREAYKNKKLLPLDLRPKKTRAIRRRLTKHQASLKTEREKKKEMYFPIRKYA 120

Query: 121 IKV 123
           IKV
Sbjct: 121 IKV 123

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M3D2|RL353_ARATH 60S ribosomal protein L35-3 OS=Arabidopsis thaliana GN=RPL35C PE=1 SV=1

 Score =  213 bits (542), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 109/123 (88%), Positives = 116/123 (94%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MAR+KVHELR KSK+DL  QLK+LKAELA LRVAKVTGGAPNKLSKIKVVR SIAQVLTV
Sbjct: 1   MARIKVHELRDKSKSDLSTQLKELKAELASLRVAKVTGGAPNKLSKIKVVRKSIAQVLTV 60

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
            SQKQK+ALREAYKNKK LPLDLRPKKTRAIRRRLTKHQASLKTEREKK++MYFP+RKYA
Sbjct: 61  SSQKQKSALREAYKNKKLLPLDLRPKKTRAIRRRLTKHQASLKTEREKKKDMYFPIRKYA 120

Query: 121 IKV 123
           IKV
Sbjct: 121 IKV 123

Arabidopsis thaliana (taxid: 3702)

>sp|P17078|RL35_RAT 60S ribosomal protein L35 OS=Rattus norvegicus GN=Rpl35 PE=1 SV=3

 Score =  154 bits (389), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 79/122 (64%), Positives = 101/122 (82%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MA++K  +LR K K +LL QL DLK EL+ LRVAKVTGGA +KLSKI+VVR SIA+VLTV
Sbjct: 1   MAKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTV 60

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
           I+Q QK  LR+ YK KK+ PLDLRPKKTRA+RRRLTKH+  LKT++++++E  +P+RKYA
Sbjct: 61  INQTQKENLRKFYKGKKYKPLDLRPKKTRAMRRRLTKHEEKLKTKKQQRKERLYPLRKYA 120

Query: 121 IK 122
           +K
Sbjct: 121 VK 122

Rattus norvegicus (taxid: 10116)

>sp|Q6ZWV7|RL35_MOUSE 60S ribosomal protein L35 OS=Mus musculus GN=Rpl35 PE=2 SV=1

 Score =  154 bits (389), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 79/122 (64%), Positives = 101/122 (82%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MA++K  +LR K K +LL QL DLK EL+ LRVAKVTGGA +KLSKI+VVR SIA+VLTV
Sbjct: 1   MAKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTV 60

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
           I+Q QK  LR+ YK KK+ PLDLRPKKTRA+RRRLTKH+  LKT++++++E  +P+RKYA
Sbjct: 61  INQTQKENLRKFYKGKKYKPLDLRPKKTRAMRRRLTKHEEKLKTKKQQRKERLYPLRKYA 120

Query: 121 IK 122
           +K
Sbjct: 121 VK 122

Mus musculus (taxid: 10090)

>sp|Q3MHM7|RL35_BOVIN 60S ribosomal protein L35 OS=Bos taurus GN=RPL35 PE=2 SV=3

 Score =  153 bits (387), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 78/122 (63%), Positives = 102/122 (83%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MA++K  +LR K K +LL QL+DLK EL+ LRVAKVTGGA +KLSKI+VVR SIA+VLTV
Sbjct: 1   MAKIKARDLRGKKKEELLKQLEDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTV 60

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
           I+Q QK  LR+ YK KK+ PLDLRPKKTRA+RRRL KH+ +LKT++++++E  +P+RKYA
Sbjct: 61  INQTQKENLRKFYKGKKYKPLDLRPKKTRAMRRRLNKHEENLKTKKQQRKERLYPLRKYA 120

Query: 121 IK 122
           +K
Sbjct: 121 VK 122

Bos taurus (taxid: 9913)

>sp|Q98TF7|RL35_CHICK 60S ribosomal protein L35 OS=Gallus gallus GN=RPL35 PE=2 SV=3

 Score =  153 bits (386), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 79/122 (64%), Positives = 101/122 (82%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MA++K  +LR K K +LL QL DLK EL+ LRVAKVTGGA +KLSKI+VVR SIA+VLTV
Sbjct: 1   MAKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTV 60

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
           I+Q QK  LR+ YK KK+ PLDLRPKKTRA+RRRL KH+ +LKT++++++E  +P+RKYA
Sbjct: 61  INQTQKENLRKFYKGKKYKPLDLRPKKTRAMRRRLNKHEENLKTKKQQRKERLYPVRKYA 120

Query: 121 IK 122
           IK
Sbjct: 121 IK 122

Gallus gallus (taxid: 9031)

>sp|P42766|RL35_HUMAN 60S ribosomal protein L35 OS=Homo sapiens GN=RPL35 PE=1 SV=2

 Score =  153 bits (386), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 78/122 (63%), Positives = 101/122 (82%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MA++K  +LR K K +LL QL DLK EL+ LRVAKVTGGA +KLSKI+VVR SIA+VLTV
Sbjct: 1   MAKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTV 60

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
           I+Q QK  LR+ YK KK+ PLDLRPKKTRA+RRRL KH+ +LKT++++++E  +P+RKYA
Sbjct: 61  INQTQKENLRKFYKGKKYKPLDLRPKKTRAMRRRLNKHEENLKTKKQQRKERLYPLRKYA 120

Query: 121 IK 122
           +K
Sbjct: 121 VK 122

Homo sapiens (taxid: 9606)

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	123
224109602	123	predicted protein [Populus trichocarpa]	1.0	1.0	0.951	2e-58
224088583	123	predicted protein [Populus trichocarpa]	1.0	1.0	0.943	6e-58
46397044	123	RecName: Full=60S ribosomal protein L35	1.0	1.0	0.934	1e-57
255580548	123	60S ribosomal protein L35, putative [Ric	1.0	1.0	0.943	1e-57
224100907	123	predicted protein [Populus trichocarpa]	1.0	1.0	0.934	3e-57
224088581	123	predicted protein [Populus trichocarpa]	1.0	1.0	0.926	4e-57
296086941	174	unnamed protein product [Vitis vinifera]	1.0	0.706	0.926	6e-57
225448819	123	PREDICTED: 60S ribosomal protein L35-lik	1.0	1.0	0.926	7e-57
350539055	123	60S ribosomal protein L35-like [Solanum	1.0	1.0	0.918	1e-56
297806197	123	60S ribosomal protein L35 [Arabidopsis l	1.0	1.0	0.926	1e-56

>gi|224109602|ref|XP_002315252.1| predicted protein [Populus trichocarpa] gi|118483689|gb|ABK93738.1| unknown [Populus trichocarpa] gi|118485344|gb|ABK94531.1| unknown [Populus trichocarpa] gi|222864292|gb|EEF01423.1| predicted protein [Populus trichocarpa]

 Score =  228 bits (582), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 117/123 (95%), Positives = 119/123 (96%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MAR+KVHELR KSKTDLL QLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV
Sbjct: 1   MARIKVHELRQKSKTDLLAQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
           ISQKQKA LREAYKNKKFLPLDLRPKKTRAIRRRLTKHQ SLKTEREKKRE+YFPMRKYA
Sbjct: 61  ISQKQKAVLREAYKNKKFLPLDLRPKKTRAIRRRLTKHQQSLKTEREKKREIYFPMRKYA 120

Query: 121 IKV 123
           IKV
Sbjct: 121 IKV 123

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224088583|ref|XP_002308484.1| predicted protein [Populus trichocarpa] gi|118482513|gb|ABK93179.1| unknown [Populus trichocarpa] gi|118483135|gb|ABK93474.1| unknown [Populus trichocarpa] gi|118489825|gb|ABK96712.1| unknown [Populus trichocarpa x Populus deltoides] gi|222854460|gb|EEE92007.1| predicted protein [Populus trichocarpa]

 Score =  227 bits (579), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 116/123 (94%), Positives = 121/123 (98%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MAR+KVHELR KSKT+LL QLK+LKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV
Sbjct: 1   MARIKVHELREKSKTELLAQLKELKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
           ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKT+RE+KREMYFPMRKYA
Sbjct: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTKREEKREMYFPMRKYA 120

Query: 121 IKV 123
           IKV
Sbjct: 121 IKV 123

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|46397044|sp|Q9M5L0.1|RL35_EUPES RecName: Full=60S ribosomal protein L35 gi|6984224|gb|AAF34800.1|AF227980_1 60S ribosomal protein L35 [Euphorbia esula]

 Score =  226 bits (576), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 115/123 (93%), Positives = 119/123 (96%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MAR+KVHELR K+K +LLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV
Sbjct: 1   MARIKVHELRQKTKAELLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
           ISQKQK ALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQ SLKTEREKK+EMYFPMRKYA
Sbjct: 61  ISQKQKLALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQQSLKTEREKKKEMYFPMRKYA 120

Query: 121 IKV 123
           IKV
Sbjct: 121 IKV 123

Source: Euphorbia esula

Species: Euphorbia esula

Genus: Euphorbia

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255580548|ref|XP_002531098.1| 60S ribosomal protein L35, putative [Ricinus communis] gi|223529294|gb|EEF31263.1| 60S ribosomal protein L35, putative [Ricinus communis]

 Score =  226 bits (576), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 116/123 (94%), Positives = 120/123 (97%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MAR+KVHELR KSKT+LL+QLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV
Sbjct: 1   MARIKVHELRNKSKTELLSQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
           ISQKQKAALREAYKNKK LPLDLRPKKTRAIRRRLTKH ASLKTEREKKREMYFP+RKYA
Sbjct: 61  ISQKQKAALREAYKNKKLLPLDLRPKKTRAIRRRLTKHLASLKTEREKKREMYFPVRKYA 120

Query: 121 IKV 123
           IKV
Sbjct: 121 IKV 123

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224100907|ref|XP_002312062.1| predicted protein [Populus trichocarpa] gi|118485616|gb|ABK94658.1| unknown [Populus trichocarpa] gi|222851882|gb|EEE89429.1| predicted protein [Populus trichocarpa]

 Score =  225 bits (573), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 115/123 (93%), Positives = 117/123 (95%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MAR+KVHELR KSK DLL QLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV
Sbjct: 1   MARIKVHELRNKSKADLLAQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
           ISQKQKA LR+AYKNKKFLPLDLRPKKTRAIRRRLTKHQ SLKTEREK REMYFPMRKYA
Sbjct: 61  ISQKQKAILRDAYKNKKFLPLDLRPKKTRAIRRRLTKHQLSLKTEREKNREMYFPMRKYA 120

Query: 121 IKV 123
           IKV
Sbjct: 121 IKV 123

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224088581|ref|XP_002308483.1| predicted protein [Populus trichocarpa] gi|118484398|gb|ABK94076.1| unknown [Populus trichocarpa] gi|222854459|gb|EEE92006.1| predicted protein [Populus trichocarpa]

 Score =  224 bits (572), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 114/123 (92%), Positives = 121/123 (98%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MAR++VHELR KSKT+LL QLK+LKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV
Sbjct: 1   MARIRVHELREKSKTELLAQLKELKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
           ISQKQK+ALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKRE+YFP+RKYA
Sbjct: 61  ISQKQKSALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREIYFPIRKYA 120

Query: 121 IKV 123
           IKV
Sbjct: 121 IKV 123

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296086941|emb|CBI33174.3| unnamed protein product [Vitis vinifera]

 Score =  224 bits (570), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 114/123 (92%), Positives = 119/123 (96%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MAR+KVHELR K+K DLL QLK+LKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV
Sbjct: 52  MARIKVHELRGKTKADLLVQLKELKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 111

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
           ISQKQKAALREAYKNKK+LPLDLRPKKTRAIR+RLTKHQ SLKTEREKKREMYFPMRKYA
Sbjct: 112 ISQKQKAALREAYKNKKYLPLDLRPKKTRAIRKRLTKHQVSLKTEREKKREMYFPMRKYA 171

Query: 121 IKV 123
           IKV
Sbjct: 172 IKV 174

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225448819|ref|XP_002282289.1| PREDICTED: 60S ribosomal protein L35-like [Vitis vinifera]

 Score =  224 bits (570), Expect = 7e-57,   Method: Compositional matrix adjust.
 Identities = 114/123 (92%), Positives = 119/123 (96%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MAR+KVHELR K+K DLL QLK+LKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV
Sbjct: 1   MARIKVHELRGKTKADLLVQLKELKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
           ISQKQKAALREAYKNKK+LPLDLRPKKTRAIR+RLTKHQ SLKTEREKKREMYFPMRKYA
Sbjct: 61  ISQKQKAALREAYKNKKYLPLDLRPKKTRAIRKRLTKHQVSLKTEREKKREMYFPMRKYA 120

Query: 121 IKV 123
           IKV
Sbjct: 121 IKV 123

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|350539055|ref|NP_001234116.1| 60S ribosomal protein L35-like [Solanum lycopersicum] gi|62751093|dbj|BAD95794.1| similar to 60S ribosomal protein L35 [Solanum lycopersicum]

 Score =  223 bits (568), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 113/123 (91%), Positives = 120/123 (97%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MAR+KVHELR KSKT+LL QLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV
Sbjct: 1   MARIKVHELRNKSKTELLAQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
           ISQKQK ALREAYKNKK+LPLDLRPKKTRAIR+RLTKHQASLKTEREKK+E+YFP+RKYA
Sbjct: 61  ISQKQKLALREAYKNKKYLPLDLRPKKTRAIRKRLTKHQASLKTEREKKKELYFPLRKYA 120

Query: 121 IKV 123
           IKV
Sbjct: 121 IKV 123

Source: Solanum lycopersicum

Species: Solanum lycopersicum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297806197|ref|XP_002870982.1| 60S ribosomal protein L35 [Arabidopsis lyrata subsp. lyrata] gi|297316819|gb|EFH47241.1| 60S ribosomal protein L35 [Arabidopsis lyrata subsp. lyrata]

 Score =  223 bits (567), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 114/123 (92%), Positives = 118/123 (95%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MAR+KVHELR KSKTDL NQLK+ KAELALLRVAKVTGGAPNKLSKIKVVR SIAQVLTV
Sbjct: 1   MARIKVHELRDKSKTDLQNQLKEFKAELALLRVAKVTGGAPNKLSKIKVVRKSIAQVLTV 60

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
           ISQKQK ALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKK+EMYFP+RKYA
Sbjct: 61  ISQKQKYALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKKEMYFPVRKYA 120

Query: 121 IKV 123
           IKV
Sbjct: 121 IKV 123

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	123
TAIR|locus:2074974	123	AT3G09500 [Arabidopsis thalian	1.0	1.0	0.910	6.3e-53
TAIR|locus:2039802	123	AT2G39390 [Arabidopsis thalian	1.0	1.0	0.902	2.1e-52
TAIR|locus:2100686	123	AT3G55170 [Arabidopsis thalian	1.0	1.0	0.886	2.4e-51
RGD|1303007	123	Rpl35 "ribosomal protein L35"	0.991	0.991	0.647	2.4e-37
UNIPROTKB|Q3MHM7	123	RPL35 "60S ribosomal protein L	0.991	0.991	0.639	3.9e-37
UNIPROTKB|Q98TF7	123	RPL35 "60S ribosomal protein L	0.991	0.991	0.647	6.3e-37
UNIPROTKB|P42766	123	RPL35 "60S ribosomal protein L	0.991	0.991	0.639	6.3e-37
UNIPROTKB|Q29361	123	RPL35 "60S ribosomal protein L	0.991	0.991	0.631	1e-36
UNIPROTKB|E2RPE5	123	RPL35 "Uncharacterized protein	0.983	0.983	0.636	1.3e-36
UNIPROTKB|E1BFM3	123	Bt.62501 "Uncharacterized prot	0.991	0.991	0.631	1.7e-36

TAIR|locus:2074974 AT3G09500 [Arabidopsis thaliana (taxid:3702)]

 Score = 548 (198.0 bits), Expect = 6.3e-53, P = 6.3e-53
 Identities = 112/123 (91%), Positives = 118/123 (95%)

Query:     1 MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
             MAR+KVHELR KSK+DL NQLK+LKAELALLRVAKVTGGAPNKLSKIKVVR SIAQVLTV
Sbjct:     1 MARIKVHELREKSKSDLQNQLKELKAELALLRVAKVTGGAPNKLSKIKVVRKSIAQVLTV 60

Query:    61 ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
              SQKQK+ALREAYKNKK LPLDLRPKKTRAIRRRLTKHQASLKTEREKK+EMYFP+RKYA
Sbjct:    61 SSQKQKSALREAYKNKKLLPLDLRPKKTRAIRRRLTKHQASLKTEREKKKEMYFPIRKYA 120

Query:   121 IKV 123
             IKV
Sbjct:   121 IKV 123

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

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

GO:0005730 "nucleolus" evidence=IDA

GO:0022625 "cytosolic large ribosomal subunit" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

GO:0001510 "RNA methylation" evidence=RCA

TAIR|locus:2039802 AT2G39390 [Arabidopsis thaliana (taxid:3702)]

 Score = 543 (196.2 bits), Expect = 2.1e-52, P = 2.1e-52
 Identities = 111/123 (90%), Positives = 116/123 (94%)

Query:     1 MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
             MAR+KVHELR KSK DL  QLK+ KAELALLRVAKVTGGAPNKLSKIKVVR SIAQVLTV
Sbjct:     1 MARIKVHELREKSKADLSGQLKEFKAELALLRVAKVTGGAPNKLSKIKVVRKSIAQVLTV 60

Query:    61 ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
             ISQKQK+ALREAYKNKK LPLDLRPKKTRAIRRRLTKHQASLKTEREKK+EMYFP+RKYA
Sbjct:    61 ISQKQKSALREAYKNKKLLPLDLRPKKTRAIRRRLTKHQASLKTEREKKKEMYFPIRKYA 120

Query:   121 IKV 123
             IKV
Sbjct:   121 IKV 123

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

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0022625 "cytosolic large ribosomal subunit" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

TAIR|locus:2100686 AT3G55170 [Arabidopsis thaliana (taxid:3702)]

 Score = 533 (192.7 bits), Expect = 2.4e-51, P = 2.4e-51
 Identities = 109/123 (88%), Positives = 116/123 (94%)

Query:     1 MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
             MAR+KVHELR KSK+DL  QLK+LKAELA LRVAKVTGGAPNKLSKIKVVR SIAQVLTV
Sbjct:     1 MARIKVHELRDKSKSDLSTQLKELKAELASLRVAKVTGGAPNKLSKIKVVRKSIAQVLTV 60

Query:    61 ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
              SQKQK+ALREAYKNKK LPLDLRPKKTRAIRRRLTKHQASLKTEREKK++MYFP+RKYA
Sbjct:    61 SSQKQKSALREAYKNKKLLPLDLRPKKTRAIRRRLTKHQASLKTEREKKKDMYFPIRKYA 120

Query:   121 IKV 123
             IKV
Sbjct:   121 IKV 123

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

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

GO:0022625 "cytosolic large ribosomal subunit" evidence=IDA

RGD|1303007 Rpl35 "ribosomal protein L35" [Rattus norvegicus (taxid:10116)]

 Score = 401 (146.2 bits), Expect = 2.4e-37, P = 2.4e-37
 Identities = 79/122 (64%), Positives = 101/122 (82%)

Query:     1 MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
             MA++K  +LR K K +LL QL DLK EL+ LRVAKVTGGA +KLSKI+VVR SIA+VLTV
Sbjct:     1 MAKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTV 60

Query:    61 ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
             I+Q QK  LR+ YK KK+ PLDLRPKKTRA+RRRLTKH+  LKT++++++E  +P+RKYA
Sbjct:    61 INQTQKENLRKFYKGKKYKPLDLRPKKTRAMRRRLTKHEEKLKTKKQQRKERLYPLRKYA 120

Query:   121 IK 122
             +K
Sbjct:   121 VK 122

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

GO:0005737 "cytoplasm" evidence=ISO

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0022625 "cytosolic large ribosomal subunit" evidence=ISO

UNIPROTKB|Q3MHM7 RPL35 "60S ribosomal protein L35" [Bos taurus (taxid:9913)]

 Score = 399 (145.5 bits), Expect = 3.9e-37, P = 3.9e-37
 Identities = 78/122 (63%), Positives = 102/122 (83%)

Query:     1 MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
             MA++K  +LR K K +LL QL+DLK EL+ LRVAKVTGGA +KLSKI+VVR SIA+VLTV
Sbjct:     1 MAKIKARDLRGKKKEELLKQLEDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTV 60

Query:    61 ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
             I+Q QK  LR+ YK KK+ PLDLRPKKTRA+RRRL KH+ +LKT++++++E  +P+RKYA
Sbjct:    61 INQTQKENLRKFYKGKKYKPLDLRPKKTRAMRRRLNKHEENLKTKKQQRKERLYPLRKYA 120

Query:   121 IK 122
             +K
Sbjct:   121 VK 122

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|Q98TF7 RPL35 "60S ribosomal protein L35" [Gallus gallus (taxid:9031)]

 Score = 397 (144.8 bits), Expect = 6.3e-37, P = 6.3e-37
 Identities = 79/122 (64%), Positives = 101/122 (82%)

Query:     1 MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
             MA++K  +LR K K +LL QL DLK EL+ LRVAKVTGGA +KLSKI+VVR SIA+VLTV
Sbjct:     1 MAKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTV 60

Query:    61 ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
             I+Q QK  LR+ YK KK+ PLDLRPKKTRA+RRRL KH+ +LKT++++++E  +P+RKYA
Sbjct:    61 INQTQKENLRKFYKGKKYKPLDLRPKKTRAMRRRLNKHEENLKTKKQQRKERLYPVRKYA 120

Query:   121 IK 122
             IK
Sbjct:   121 IK 122

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

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

UNIPROTKB|P42766 RPL35 "60S ribosomal protein L35" [Homo sapiens (taxid:9606)]

 Score = 397 (144.8 bits), Expect = 6.3e-37, P = 6.3e-37
 Identities = 78/122 (63%), Positives = 101/122 (82%)

Query:     1 MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
             MA++K  +LR K K +LL QL DLK EL+ LRVAKVTGGA +KLSKI+VVR SIA+VLTV
Sbjct:     1 MAKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTV 60

Query:    61 ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
             I+Q QK  LR+ YK KK+ PLDLRPKKTRA+RRRL KH+ +LKT++++++E  +P+RKYA
Sbjct:    61 INQTQKENLRKFYKGKKYKPLDLRPKKTRAMRRRLNKHEENLKTKKQQRKERLYPLRKYA 120

Query:   121 IK 122
             +K
Sbjct:   121 VK 122

GO:0006412 "translation" evidence=NAS;TAS

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

GO:0022625 "cytosolic large ribosomal subunit" evidence=IDA

GO:0003729 "mRNA binding" evidence=TAS

GO:0005730 "nucleolus" evidence=TAS

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006413 "translational initiation" evidence=TAS

GO:0006414 "translational elongation" evidence=TAS

GO:0006415 "translational termination" evidence=TAS

GO:0006614 "SRP-dependent cotranslational protein targeting to membrane" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0019058 "viral infectious cycle" evidence=TAS

GO:0019083 "viral transcription" evidence=TAS

GO:0044267 "cellular protein metabolic process" evidence=TAS

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|Q29361 RPL35 "60S ribosomal protein L35" [Sus scrofa (taxid:9823)]

 Score = 395 (144.1 bits), Expect = 1.0e-36, P = 1.0e-36
 Identities = 77/122 (63%), Positives = 102/122 (83%)

Query:     1 MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
             MA++K  +LR K K +LL QL+DLK EL+ LRVAKVTGGA +KLSKI+VVR SIA+VLTV
Sbjct:     1 MAKIKARDLRGKKKEELLKQLEDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTV 60

Query:    61 ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
             I+Q QK  LR+ YK KK+ PLDLRPKKTRA+RRRL KH+ +LKT++++++E  +P+RK+A
Sbjct:    61 INQTQKENLRKFYKGKKYKPLDLRPKKTRAMRRRLNKHEENLKTKKQQRKERLYPLRKFA 120

Query:   121 IK 122
             +K
Sbjct:   121 VK 122

GO:0022625 "cytosolic large ribosomal subunit" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|E2RPE5 RPL35 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 394 (143.8 bits), Expect = 1.3e-36, P = 1.3e-36
 Identities = 77/121 (63%), Positives = 101/121 (83%)

Query:     2 ARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVI 61
             A++K  +LR K K +LL QL+DLK EL+ LRVAKVTGGA +KLSKI+VVR SIA+VLTVI
Sbjct:     2 AKIKARDLRGKKKEELLKQLEDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTVI 61

Query:    62 SQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYAI 121
             +Q QK  LR+ YK KK+ PLDLRPKKTRA+RRRL KH+ +LKT++++++E  +P+RKYA+
Sbjct:    62 NQTQKENLRKFYKGKKYKPLDLRPKKTRAMRRRLNKHEENLKTKKQQRKERLYPLRKYAV 121

Query:   122 K 122
             K
Sbjct:   122 K 122

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

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

UNIPROTKB|E1BFM3 Bt.62501 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 393 (143.4 bits), Expect = 1.7e-36, P = 1.7e-36
 Identities = 77/122 (63%), Positives = 101/122 (82%)

Query:     1 MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
             MA++K  +LR K K +LL QL+DLK EL+ LRVAKVTGGA +KLSKI+VVR SIA+VLTV
Sbjct:     1 MAKIKARDLRGKKKEELLKQLEDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTV 60

Query:    61 ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
              +Q QK  LR+ YK KK+ PLDLRPKKTRA+RRRL KH+ +LKT++++++E  +P+RKYA
Sbjct:    61 TNQTQKENLRKFYKGKKYEPLDLRPKKTRAMRRRLNKHEENLKTKKQQRKERLYPLRKYA 120

Query:   121 IK 122
             +K
Sbjct:   121 VK 122

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9M5L0	RL35_EUPES	No assigned EC number	0.9349	1.0	1.0	N/A	no
Q98TF7	RL35_CHICK	No assigned EC number	0.6475	0.9918	0.9918	yes	no
P0CX85	RL35B_YEAST	No assigned EC number	0.5819	0.9674	0.9916	yes	no
P0CX84	RL35A_YEAST	No assigned EC number	0.5819	0.9674	0.9916	yes	no
O80626	RL352_ARATH	No assigned EC number	0.9024	1.0	1.0	yes	no
Q69CJ9	RL35_OPHHA	No assigned EC number	0.6341	1.0	1.0	N/A	no
Q2VA69	RL36_THELE	No assigned EC number	0.5041	0.9837	0.9837	N/A	no
Q4N756	RL35_THEPA	No assigned EC number	0.5040	1.0	1.0	yes	no
Q9LZ41	RL354_ARATH	No assigned EC number	0.9186	1.0	1.0	yes	no
Q5DVH6	RL35_PLAFE	No assigned EC number	0.5901	0.9918	0.9918	N/A	no
O74904	RL35_SCHPO	No assigned EC number	0.5666	0.9756	0.9836	yes	no
Q90YT4	RL35_ICTPU	No assigned EC number	0.6065	0.9918	0.9918	N/A	no
Q9SF53	RL351_ARATH	No assigned EC number	0.9105	1.0	1.0	yes	no
Q9M3D2	RL353_ARATH	No assigned EC number	0.8861	1.0	1.0	no	no
Q6ZWV7	RL35_MOUSE	No assigned EC number	0.6475	0.9918	0.9918	yes	no
P42766	RL35_HUMAN	No assigned EC number	0.6393	0.9918	0.9918	yes	no
Q8JHJ1	RL35_DANRE	No assigned EC number	0.6147	0.9918	0.9918	yes	no
Q29361	RL35_PIG	No assigned EC number	0.6311	0.9918	0.9918	yes	no
Q6UZF7	RL35_HIPCM	No assigned EC number	0.6147	0.9918	0.9918	N/A	no
P17078	RL35_RAT	No assigned EC number	0.6475	0.9918	0.9918	yes	no
Q4UIF8	RL35_THEAN	No assigned EC number	0.5042	0.9674	0.8380	yes	no
P34662	RL35_CAEEL	No assigned EC number	0.5121	1.0	1.0	yes	no
Q6PBC1	RL35_XENTR	No assigned EC number	0.6147	0.9918	0.9918	yes	no
Q3MHM7	RL35_BOVIN	No assigned EC number	0.6393	0.9918	0.9918	yes	no
Q8L805	RL35_WHEAT	No assigned EC number	0.5491	0.9837	0.9758	N/A	no
Q54J23	RL35_DICDI	No assigned EC number	0.5245	0.9756	0.9523	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_Genewise1_v1.C_LG_X2368	SubName- Full=Putative uncharacterized protein; (124 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	estExt_fgenesh4_pm.C_LG_XVII0043	SubName- Full=Putative uncharacterized protein; (206 aa)				•	•				0.494
	eugene3.00002480	SubName- Full=Putative uncharacterized protein; (206 aa)				•	•				0.493
	estExt_fgenesh4_pg.C_LG_VII0552	SubName- Full=Putative uncharacterized protein; (146 aa)				•	•				0.474
	estExt_fgenesh4_pm.C_LG_III0216	SubName- Full=Putative uncharacterized protein; (146 aa)				•	•				0.472
	eugene3.00011799	RecName- Full=60S ribosomal protein L6; (232 aa)				•	•	•			0.472
	eugene3.00190574	SubName- Full=Putative uncharacterized protein; (132 aa)				•		•			0.471
	estExt_Genewise1_v1.C_LG_XIII3119	SubName- Full=Putative uncharacterized protein; (131 aa)				•		•			0.471
	fgenesh4_pm.C_LG_III000548	RecName- Full=Ribosomal protein S27; (86 aa)				•		•			0.458
	estExt_fgenesh4_pg.C_LG_I0594	RecName- Full=Ribosomal protein S27; (86 aa)				•		•			0.458
	estExt_fgenesh4_pg.C_LG_IX0938	RecName- Full=60S ribosomal protein L6; (232 aa)				•	•	•			0.454

---

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	123
cd00427	57	cd00427, Ribosomal_L29_HIP, Ribosomal L29 protein/	6e-10
pfam00831	58	pfam00831, Ribosomal_L29, Ribosomal L29 protein	5e-09
COG0255	69	COG0255, RpmC, Ribosomal protein L29 [Translation,	3e-08
PRK14549	69	PRK14549, PRK14549, 50S ribosomal protein L29P; Pr	9e-08
PRK00306	66	PRK00306, PRK00306, 50S ribosomal protein L29; Rev	2e-07
TIGR00012	55	TIGR00012, L29, ribosomal protein L29	3e-07
PRK00461	87	PRK00461, rpmC, 50S ribosomal protein L29; Reviewe	0.002

>gnl|CDD|238243 cd00427, Ribosomal_L29_HIP, Ribosomal L29 protein/HIP

 Score = 50.9 bits (123), Expect = 6e-10
 Identities = 24/57 (42%), Positives = 34/57 (59%), Gaps = 1/57 (1%)

Query: 8  ELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQK 64
          ELR KS  +L  +L +LK EL  LR  K TG       +I+ VR  IA++ TV+++K
Sbjct: 2  ELREKSDEELQEKLDELKKELFNLRFQKATGQ-LENPHRIRKVRKDIARIKTVLNEK 57

L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it participates in forming a protein ring that surrounds the polypeptide exit channel, providing structural support for the ribosome. L29 is involved in forming the translocon binding site, along with L19, L22, L23, L24, and L31e. In addition, L29 and L23 form the interaction site for trigger factor (TF) on the ribosomal surface, adjacent to the exit tunnel. L29 forms numerous interactions with L23 and with the 23S rRNA. In some eukaryotes, L29 is referred to as L35, which is distinct from L35 found in bacteria and some eukaryotes (primarily plastids and mitochondria). The mammalian homolog, HIP, is found on the surface of many tissues and cell lines. It is believed to play a role in cell adhesion and modulation of blood coagulation. It has also been shown to inhibit apoptosis in cancer cells. Length = 57

>gnl|CDD|201463 pfam00831, Ribosomal_L29, Ribosomal L29 protein

 Score = 48.3 bits (116), Expect = 5e-09
 Identities = 25/57 (43%), Positives = 34/57 (59%), Gaps = 1/57 (1%)

Query: 8  ELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQK 64
          ELR  S  +L  +LK+LK EL  LR  K TG       +IK VR  IA++LTV+ ++
Sbjct: 3  ELRELSDEELKEKLKELKKELFNLRFQKATGQL-ENPHRIKEVRRDIARILTVLRER 58

Length = 58

>gnl|CDD|223333 COG0255, RpmC, Ribosomal protein L29 [Translation, ribosomal structure and biogenesis]

 Score = 46.5 bits (111), Expect = 3e-08
 Identities = 28/67 (41%), Positives = 39/67 (58%), Gaps = 1/67 (1%)

Query: 5  KVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQK 64
          K  ELR KS  +L  +L++LK EL  LR    TG   N   +I+ VR  IA++LTV+ +K
Sbjct: 4  KRKELREKSVEELEEELRELKKELFNLRFQLATGQLEN-PHRIREVRRDIARILTVLREK 62

Query: 65 QKAALRE 71
          +  A  E
Sbjct: 63 ELEAAEE 69

Length = 69

>gnl|CDD|237751 PRK14549, PRK14549, 50S ribosomal protein L29P; Provisional

 Score = 45.4 bits (108), Expect = 9e-08
 Identities = 22/66 (33%), Positives = 39/66 (59%)

Query: 1  MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
          MA ++  E+R  S  +   +L++LK EL   R     GGAP    +I+ +R +IA++LT+
Sbjct: 1  MAILRASEIREMSPEEREEKLEELKLELLKERAQAAMGGAPENPGRIREIRRTIARILTI 60

Query: 61 ISQKQK 66
            +K++
Sbjct: 61 QREKKR 66

Length = 69

>gnl|CDD|178971 PRK00306, PRK00306, 50S ribosomal protein L29; Reviewed

 Score = 44.5 bits (106), Expect = 2e-07
 Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 1/64 (1%)

Query: 5  KVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQK 64
          K  ELR  S  +L  +L +LK EL  LR  K TG   N   +++ VR  IA++ TV+ ++
Sbjct: 2  KAKELRELSVEELNEKLLELKKELFNLRFQKATGQLENT-HRLREVRRDIARIKTVLRER 60

Query: 65 QKAA 68
          +  A
Sbjct: 61 ELGA 64

Length = 66

>gnl|CDD|129124 TIGR00012, L29, ribosomal protein L29

 Score = 43.8 bits (104), Expect = 3e-07
 Identities = 25/56 (44%), Positives = 34/56 (60%), Gaps = 1/56 (1%)

Query: 8  ELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ 63
          ELR KSK +L  +L +LK EL  LR  K TG       +I+ VR  IA++LTV+ +
Sbjct: 1  ELREKSKEELAKKLDELKKELFELRFQKATGQLAK-PHRIRQVRRDIARLLTVLRE 55

This model describes a ribosomal large subunit protein, called L29 in prokaryotic (50S) large subunits and L35 in eukaryotic (60S) large subunits [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 55

>gnl|CDD|234773 PRK00461, rpmC, 50S ribosomal protein L29; Reviewed

 Score = 34.3 bits (79), Expect = 0.002
 Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 1/61 (1%)

Query: 8  ELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKA 67
          ELR KS  +L   + +LKAEL  LR    TG   ++  KIK +R  IA++LT++++++  
Sbjct: 4  ELRKKSVEELEKLVIELKAELFTLRFKNATGSL-DQTHKIKEIRKDIARILTILNERELE 62

Query: 68 A 68
           
Sbjct: 63 E 63

Length = 87

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	123
KOG3436	123	consensus 60S ribosomal protein L35 [Translation,	100.0
PRK14549	69	50S ribosomal protein L29P; Provisional	99.91
CHL00154	67	rpl29 ribosomal protein L29; Validated	99.9
COG0255	69	RpmC Ribosomal protein L29 [Translation, ribosomal	99.88
PRK00306	66	50S ribosomal protein L29; Reviewed	99.86
PF00831	58	Ribosomal_L29: Ribosomal L29 protein; InterPro: IP	99.85
PRK00461	87	rpmC 50S ribosomal protein L29; Reviewed	99.84
cd00427	57	Ribosomal_L29_HIP Ribosomal L29 protein/HIP. L29 i	99.82
TIGR00012	55	L29 ribosomal protein L29. called L29 in prokaryot	99.81
PF06984	87	MRP-L47: Mitochondrial 39-S ribosomal protein L47	96.82
KOG3331	213	consensus Mitochondrial/chloroplast ribosomal prot	94.95

>KOG3436 consensus 60S ribosomal protein L35 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=4.3e-51  Score=296.90  Aligned_cols=123  Identities=73%  Similarity=0.999  Sum_probs=121.9

Q ss_pred             CCCCChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCC
Q 033270            1 MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAALREAYKNKKFLP   80 (123)
Q Consensus         1 M~~mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~~lr~~y~~kk~~p   80 (123)
                      |+++++.|||+.|.+||.+||+||+.||++||+++++||..+++++|+++|++|||||||+||++.+++++||+|++|+|
T Consensus         1 M~kik~~eLr~~~ke~L~~ql~dLK~ELa~LRv~K~tgg~~~klskik~vrKsiArvLTVine~~k~~lr~~yk~~k~~p   80 (123)
T KOG3436|consen    1 MAKIKARELRGKSKEQLLKQLDDLKVELAQLRVAKVTGGAASKLSKIKVVRKSIARVLTVINEKQKEELREAYKGKKYLP   80 (123)
T ss_pred             CcchhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhhccchhhhHHHHHHHHHHHHHHHHhhhhhHHHHHHHhhcccccc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCchhhHHHHhhcChHHhhhhhHHHHHHHhhCCcchhhhcC
Q 033270           81 LDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYAIKV  123 (123)
Q Consensus        81 ~dlr~kktra~rr~Lt~~~~~~kt~k~~~k~~~~p~r~~a~ka  123 (123)
                      +|||||+||||||+||+||.|++|.+|++++++||.|+|||||
T Consensus        81 ~dLr~KktRa~rr~ltk~~~slkt~kq~~k~~~~p~rk~A~ka  123 (123)
T KOG3436|consen   81 KDLRPKKTRAIRRRLTKHQLSLKTEKQQAKERLFPLRKYAVKA  123 (123)
T ss_pred             hhhhHHHHHHHHHhccccchhHhHHHHHHHHHhchHHHhhccC
Confidence            9999999999999999999999999999999999999999997

>PRK14549 50S ribosomal protein L29P; Provisional

Probab=99.91  E-value=5.4e-24  Score=142.23  Aligned_cols=67  Identities=33%  Similarity=0.519  Sum_probs=64.3

Q ss_pred             CCCCChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHH
Q 033270            1 MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKA   67 (123)
Q Consensus         1 M~~mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~   67 (123)
                      |+.|+++||+++|.+||.++|.+++.|||+|||++++|++++|||.|+.+||+||||+||++|++++
T Consensus         1 M~~mk~~elr~ls~~eL~~~l~elk~eLf~LR~q~~~~~~l~n~~~ir~~Rk~IARi~Tvl~ek~~~   67 (69)
T PRK14549          1 MAILRASEIREMSPEEREEKLEELKLELLKERAQAAMGGAPENPGRIREIRRTIARILTIQREKKRE   67 (69)
T ss_pred             CCcCcHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhCcCccccHHHHHHHHHHHHHHHHHHHHHhc
Confidence            8899999999999999999999999999999999999955999999999999999999999998865

>CHL00154 rpl29 ribosomal protein L29; Validated

Probab=99.90  E-value=1.8e-23  Score=139.30  Aligned_cols=64  Identities=25%  Similarity=0.296  Sum_probs=62.4

Q ss_pred             CCCCChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHH
Q 033270            1 MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQ   65 (123)
Q Consensus         1 M~~mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq   65 (123)
                      |+.|+++|||++|.+||.++|.+++.|||+||||+++| +++|||.|+.+|++||||+||++|+.
T Consensus         1 M~~mk~~elr~ls~~eL~~~l~elk~elf~LRfq~atg-ql~n~~~ir~~RrdIARikTil~ek~   64 (67)
T CHL00154          1 MSLPKITDIIDLTDSEISEEIIKTKKELFDLRLKKATR-QNFKPHLFKHKKHRLAQLLTLLSSRL   64 (67)
T ss_pred             CCCCCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhC-cccChHHHHHHHHHHHHHHHHHHHHh
Confidence            78899999999999999999999999999999999999 99999999999999999999999975

>COG0255 RpmC Ribosomal protein L29 [Translation, ribosomal structure and biogenesis]

Probab=99.88  E-value=1.3e-22  Score=136.08  Aligned_cols=62  Identities=40%  Similarity=0.522  Sum_probs=59.0

Q ss_pred             HHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHHHH
Q 033270            7 HELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAAL   69 (123)
Q Consensus         7 ~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~~l   69 (123)
                      +|||++|.+||.++|.+|+.|||+||||.++| +++|||+|+.|||+||||+||++|++....
T Consensus         6 ~elR~~s~eeL~~~l~eLK~ELf~LR~q~a~g-~l~n~~~ir~vRr~IARi~Tv~~E~~~~~~   67 (69)
T COG0255           6 KELREKSVEELEEELRELKKELFNLRFQLATG-QLENPHRIREVRRDIARILTVLREKELEAA   67 (69)
T ss_pred             HHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhC-CCCCcHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            59999999999999999999999999999999 789999999999999999999999987653

>PRK00306 50S ribosomal protein L29; Reviewed

Probab=99.86  E-value=1.3e-21  Score=129.23  Aligned_cols=64  Identities=36%  Similarity=0.477  Sum_probs=61.2

Q ss_pred             CChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHHH
Q 033270            4 VKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAA   68 (123)
Q Consensus         4 mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~~   68 (123)
                      |+++||+++|.+||.++|.+++.|||+|||++++| +++|||.|+.+||+||||+||++|++.+.
T Consensus         1 Mk~~elr~ls~~eL~~~l~~lkkeL~~lR~~~~~~-~~~n~~~i~~~rk~IARi~Tvl~er~~~~   64 (66)
T PRK00306          1 MKAKELRELSVEELNEKLLELKKELFNLRFQKATG-QLENTHRLREVRRDIARIKTVLRERELGA   64 (66)
T ss_pred             CCHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHhC-CCcCcHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            68999999999999999999999999999999999 79999999999999999999999998753

>PF00831 Ribosomal_L29: Ribosomal L29 protein; InterPro: IPR001854 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.85  E-value=4.1e-21  Score=124.05  Aligned_cols=58  Identities=38%  Similarity=0.559  Sum_probs=56.1

Q ss_pred             hHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHH
Q 033270            6 VHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQK   64 (123)
Q Consensus         6 a~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ek   64 (123)
                      ++||++||.+||.++|.+++.|||+|||++++| +++|||.|+.+||+||||+||++|+
T Consensus         1 ~~elr~ls~~eL~~~l~elk~eL~~Lr~q~~~~-~l~n~~~ir~~Rr~IARi~Tvl~er   58 (58)
T PF00831_consen    1 AKELRELSDEELQEKLEELKKELFNLRFQKATG-QLENPHRIREIRRDIARILTVLRER   58 (58)
T ss_dssp             CHHHCHSHHHHHHHHHHHHHHHHHHHHHHHHHS-SSSCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhc-ccccccHHHHHHHHHHHHHHHHhcC
Confidence            579999999999999999999999999999998 7899999999999999999999986

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 L29 is one of the proteins from the large ribosomal subunit. L29 belongs to a family of ribosomal proteins of 63 to 138 amino-acid residues which, on the basis of sequence similarities [], groups: Red algal L29. Bacterial L29. Mammalian L35 Caenorhabditis elegans L35 (ZK652.4). Yeast L35. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1VSP_W 3MS1_Y 3MRZ_Y 3F1H_2 3PYT_Y 3PYO_Y 3D5D_2 3D5B_2 3PYR_Y 1VSA_W ....

>PRK00461 rpmC 50S ribosomal protein L29; Reviewed

Probab=99.84  E-value=7.5e-21  Score=132.43  Aligned_cols=66  Identities=35%  Similarity=0.482  Sum_probs=62.1

Q ss_pred             ChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHHHHHH
Q 033270            5 KVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAALRE   71 (123)
Q Consensus         5 Ka~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~~lr~   71 (123)
                      +++|||++|.+||.++|.+++.|||+|||++++| +++|||.|+.+||+||||+||++|++.++..+
T Consensus         1 ~~~elR~lS~eEL~e~L~elkkELf~LR~q~atg-ql~n~~~ir~iRR~IARilTvl~Ek~~~~~~~   66 (87)
T PRK00461          1 LFKELRKKSVEELEKLVIELKAELFTLRFKNATG-SLDQTHKIKEIRKDIARILTILNERELEEKEN   66 (87)
T ss_pred             ChHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhC-cccccHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            4689999999999999999999999999999999 89999999999999999999999999876643

>cd00427 Ribosomal_L29_HIP Ribosomal L29 protein/HIP

Probab=99.82  E-value=3.5e-20  Score=119.25  Aligned_cols=57  Identities=42%  Similarity=0.572  Sum_probs=54.8

Q ss_pred             HHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHH
Q 033270            7 HELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQK   64 (123)
Q Consensus         7 ~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ek   64 (123)
                      +||+++|.+||.++|.+++.|||+|||++++| +++|||.|+.+|++||||+||++|+
T Consensus         1 ~eir~ls~~eL~~~l~~l~~elf~Lr~q~~~~-~~~~~~~~~~~Rr~IARi~Til~er   57 (57)
T cd00427           1 KELREKSDEELQEKLDELKKELFNLRFQKATG-QLENPHRIRKVRKDIARIKTVLNEK   57 (57)
T ss_pred             ChHHHCCHHHHHHHHHHHHHHHHHHHHHHHHC-CCcCcHHHHHHHHHHHHHHHHHHcC
Confidence            48999999999999999999999999999999 7999999999999999999999974

L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it participates in forming a protein ring that surrounds the polypeptide exit channel, providing structural support for the ribosome. L29 is involved in forming the translocon binding site, along with L19, L22, L23, L24, and L31e. In addition, L29 and L23 form the interaction site for trigger factor (TF) on the ribosomal surface, adjacent to the exit tunnel. L29 forms numerous interactions with L23 and with the 23S rRNA. In some eukaryotes, L29 is referred to as L35, which is distinct from L35 found in bacteria and some eukaryotes (primarily plastids and mitochondria). The mammalian homolog, HIP, is found on the surface of many tissues and cell lines. It is believed to play a role in cell adhesion and modulat

>TIGR00012 L29 ribosomal protein L29

Probab=99.81  E-value=4.6e-20  Score=118.11  Aligned_cols=55  Identities=47%  Similarity=0.619  Sum_probs=53.1

Q ss_pred             HHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHH
Q 033270            8 ELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ   63 (123)
Q Consensus         8 ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~e   63 (123)
                      ||+++|.+||.++|.+++.|||+|||++++| +++|||.|+.+||+||||+||++|
T Consensus         1 elr~~s~~EL~~~l~~lr~eLf~Lr~~~~~~-~~~~~~~i~~~Rk~IARi~Tvl~e   55 (55)
T TIGR00012         1 ELREKSKEELAKKLDELKKELFELRFQKATG-QLAKPHRIRQVRRDIARLLTVLRE   55 (55)
T ss_pred             CHhhCCHHHHHHHHHHHHHHHHHHHHHHHhC-CcccchHHHHHHHHHHHHHHHHhC
Confidence            6899999999999999999999999999999 789999999999999999999985

called L29 in prokaryotic (50S) large subunits and L35 in eukaryotic (60S) large subunits.

>PF06984 MRP-L47: Mitochondrial 39-S ribosomal protein L47 (MRP-L47); InterPro: IPR010729 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=96.82  E-value=0.0072  Score=42.22  Aligned_cols=60  Identities=25%  Similarity=0.266  Sum_probs=40.1

Q ss_pred             ChHHHhcCCHHHHHHHHHHH---HHHHHHHH-HHHHHCCCCCccchhHHHHHHHHHHHHHHHHH
Q 033270            5 KVHELRTKSKTDLLNQLKDL---KAELALLR-VAKVTGGAPNKLSKIKVVRLSIAQVLTVISQK   64 (123)
Q Consensus         5 Ka~ELR~~s~eEL~~qL~eL---K~EL~~LR-~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ek   64 (123)
                      .+.|||.+|-+||.+-==-+   +.-|...+ .....+...+++.++..|+++-++|++|++|+
T Consensus        24 t~~ELR~KS~eDLHkLWyv~lKERN~L~T~~~e~~r~~~~~~~~~r~~kV~~sM~~Ik~Vl~ER   87 (87)
T PF06984_consen   24 TAEELRRKSFEDLHKLWYVCLKERNMLLTEEYEARRQGEGMPSPERLEKVRKSMARIKHVLTER   87 (87)
T ss_pred             cHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHHhcC
Confidence            47899999999998832222   22221111 11122223578899999999999999999984

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the N-terminal region (approximately 8 residues) of the eukaryotic mitochondrial 39-S ribosomal protein L47 (MRP-L47). Mitochondrial ribosomal proteins (MRPs) are the counterparts of the cytoplasmic ribosomal proteins, in that they fulfil similar functions in protein biosynthesis. However, they are distinct in number, features and primary structure [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005761 mitochondrial ribosome

>KOG3331 consensus Mitochondrial/chloroplast ribosomal protein L4/L29 [Translation, ribosomal structure and biogenesis]

Probab=94.95  E-value=0.16  Score=40.60  Aligned_cols=63  Identities=27%  Similarity=0.289  Sum_probs=48.0

Q ss_pred             ChHHHhcCCHHHHHHHHHHHHHH---HHHHHH--HHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHHH
Q 033270            5 KVHELRTKSKTDLLNQLKDLKAE---LALLRV--AKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAA   68 (123)
Q Consensus         5 Ka~ELR~~s~eEL~~qL~eLK~E---L~~LR~--qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~~   68 (123)
                      .+.|||-+|-.||.+.--.+-+|   |+..+-  +...| +..||-+|-.||.+.+||.+|++|++++-
T Consensus        67 ~aeELR~KS~nDLH~LWYvcLkErNmL~T~~~~~k~~~~-~~PnpERi~kV~~TM~~I~~Vl~ER~~Ay  134 (213)
T KOG3331|consen   67 SAEELRLKSFNDLHKLWYVCLKERNMLATMRHELKNIVG-SFPNPERIDKVRTTMWRIEHVLNERNLAY  134 (213)
T ss_pred             chHHHhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            57899999999998865444443   333332  23334 78899999999999999999999998753

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	123
2zkr_v	123	Structure Of A Mammalian Ribosomal 60s Subunit With		3e-38
1s1i_X	120	Structure Of The Ribosomal 80s-Eef2-Sordarin Comple		4e-29
2go5_5	124	Structure Of Signal Recognition Particle Receptor (		2e-27
4a17_U	124	T.Thermophila 60s Ribosomal Subunit In Complex With		3e-23
3zf7_k	127	High-resolution Cryo-electron Microscopy Structure		4e-13
3jyw_X	86	Structure Of The 60s Proteins For Eukaryotic Riboso		5e-09
1s72_V	71	Refined Crystal Structure Of The Haloarcula Marismo		4e-04
1ffk_S	70	Crystal Structure Of The Large Ribosomal Subunit Fr		8e-04

>pdb|2ZKR|VV Chain v, Structure Of A Mammalian Ribosomal 60s Subunit Within An 80s Complex Obtained By Docking Homology Models Of The Rna And Proteins Into An 8.7 A Cryo-Em Map Length = 123

Iteration: 1
 Score =  153 bits (386), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 78/122 (63%), Positives = 101/122 (82%)
Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MA++K  +LR K K +LL QL DLK EL+ LRVAKVTGGA +KLSKI+VVR SIA+VLTV
Sbjct: 1   MAKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTV 60
Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
           I+Q QK  LR+ YK KK+ PLDLRPKKTRA+RRRL KH+ +LKT++++++E  +P+RKYA
Sbjct: 61  INQTQKENLRKFYKGKKYKPLDLRPKKTRAMRRRLNKHEENLKTKKQQRKERLYPLRKYA 120
Query: 121 IK 122
           +K
Sbjct: 121 VK 122

>pdb|1S1I|X Chain X, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From Yeast Obtained By Docking Atomic Models For Rna And Protein Components Into A 11.7 A Cryo-Em Map. This File, 1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is In File 1s1h. Length = 120

Iteration: 1
 Score =  122 bits (307), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 71/122 (58%), Positives = 92/122 (75%), Gaps = 3/122 (2%)
Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MA VK +ELRTKSK  L +QL DLK ELA L+V K++  +   L KIK VR SIA VLTV
Sbjct: 1   MAGVKAYELRTKSKEQLASQLVDLKKELAELKVQKLSRPS---LPKIKTVRKSIACVLTV 57
Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
           I+++Q+ A+R+ YK KK+ P DLR KKTRA+RR LTK +AS  TE+++K+++ FP RKYA
Sbjct: 58  INEQQREAVRQLYKGKKYQPKDLRAKKTRALRRALTKFEASQVTEKQRKKQIAFPQRKYA 117
Query: 121 IK 122
           IK
Sbjct: 118 IK 119

>pdb|2GO5|5 Chain 5, Structure Of Signal Recognition Particle Receptor (Sr) In Complex With Signal Recognition Particle (Srp) And Ribosome Nascent Chain Complex Length = 124

Iteration: 1
 Score =  117 bits (292), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 67/122 (54%), Positives = 85/122 (69%), Gaps = 1/122 (0%)
Query: 2   ARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVI 61
            +VK  EL  KSK DL  QL +LK EL  LR+ KV     +KL++I  +R SIA+VLTVI
Sbjct: 4   GKVKAGELWNKSKDDLTKQLAELKTELGQLRIQKVASSG-SKLNRIHDIRKSIARVLTVI 62
Query: 62  SQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYAI 121
           + KQ+A LR  YKNKK+ PLDLR K+TRAIRRRL+  + S   E+ KKR ++FP RK+AI
Sbjct: 63  NAKQRAQLRLFYKNKKYAPLDLRAKQTRAIRRRLSPDEKSRVLEKTKKRTVHFPQRKFAI 122
Query: 122 KV 123
           K 
Sbjct: 123 KA 124

>pdb|4A17|U Chain U, T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 5s Rrna, 5.8s Rrna And Proteins Of Molecule 2. Length = 124

Iteration: 1
 Score =  103 bits (256), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 53/119 (44%), Positives = 85/119 (71%)
Query: 4   VKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ 63
           V+V +LRT+++  L+ +L  L+ EL+ LR+AK+ GG  NKL +I +VR +IA+ LT+I++
Sbjct: 5   VRVFKLRTQTEEQLVGELGKLQTELSQLRIAKIAGGTANKLGRIGIVRKAIAKYLTIINE 64
Query: 64  KQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYAIK 122
           K++ A+++ +K K   PLD+R KKTRAIRR+LTK Q      + +K+   F +RK+A+K
Sbjct: 65  KRRQAVKDQFKGKSLKPLDIRVKKTRAIRRKLTKKQREAVLVKTQKKLNNFGLRKFALK 123

>pdb|3ZF7|KK Chain k, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 127

Iteration: 1
 Score = 69.7 bits (169), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 45/123 (36%), Positives = 72/123 (58%), Gaps = 3/123 (2%)
Query: 4   VKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ 63
           VK+ +L+ K K DLL QL + K EL+ LRV++       +L +I+ +R  IA+++TV+++
Sbjct: 5   VKIRDLKEKGKDDLLKQLSEFKKELSQLRVSQQMNVGAARLGRIRTIRKGIARIMTVLNK 64
Query: 64  KQKAALREAYKNKKFL---PLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
            ++  LR+ Y +KK     P  LR K T   R  L  ++ + KT R+ +    FP R YA
Sbjct: 65  NERENLRKFYSDKKLRSAKPKTLRAKLTHRRRLALKANEKNRKTRRQLRMAHKFPRRIYA 124
Query: 121 IKV 123
           +KV
Sbjct: 125 VKV 127

>pdb|3JYW|X Chain X, Structure Of The 60s Proteins For Eukaryotic Ribosome Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome At 8.9a Resolution Length = 86

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 37/64 (57%), Positives = 46/64 (71%), Gaps = 3/64 (4%)
Query: 2  ARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVI 61
          A VK +ELRTKSK  L +QL DLK ELA L+V K++  +   L KIK VR SIA VLTVI
Sbjct: 1  AGVKAYELRTKSKEQLASQLVDLKKELAELKVQKLSRPS---LPKIKTVRKSIACVLTVI 57
Query: 62 SQKQ 65
          +++Q
Sbjct: 58 NEQQ 61

>pdb|1S72|V Chain V, Refined Crystal Structure Of The Haloarcula Marismortui Large Ribosomal Subunit At 2.4 Angstrom Resolution Length = 71

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 1  MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
          M  + V E+R  +  +   +L DLK EL   R  +  GGAP    +IK +R +IA++ T+
Sbjct: 1  MTVLHVQEIRDMTPAEREAELDDLKTELLNARAVQAAGGAPENPGRIKELRKAIARIKTI 60
Query: 61 ISQKQKAALRE 71
            Q ++  L+E
Sbjct: 61 --QGEEGDLQE 69

>pdb|1FFK|S Chain S, Crystal Structure Of The Large Ribosomal Subunit From Haloarcula Marismortui At 2.4 Angstrom Resolution Length = 70

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 6  VHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQ 65
          V E+R  +  +   +L DLK EL   R  +  GGAP    +IK +R +IA++ T+  Q +
Sbjct: 5  VQEIRDMTPAEREAELDDLKTELLNARAVQAAGGAPENPGRIKELRKAIARIKTI--QGE 62
Query: 66 KAALRE 71
          +  L+E
Sbjct: 63 EGDLQE 68

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	123
2zkr_v	123	60S ribosomal protein L35; protein-RNA complex, 60	9e-39
4a17_U	124	RPL35, 60S ribosomal protein L21; eukaryotic ribos	7e-38
3iz5_C	389	60S ribosomal protein L3 (L3P); eukaryotic ribosom	2e-36
3u5e_H	191	L8, RP24, YL11, 60S ribosomal protein L9-A; transl	1e-34
3jyw_X	86	60S ribosomal protein L35; eukaryotic ribosome, RA	3e-18
1vq8_V	71	50S ribosomal protein L29P; ribosome 50S, protein-	4e-17
3v2d_2	72	50S ribosomal protein L29; ribosome associated inh	9e-08
3r8s_Y	63	50S ribosomal protein L29; protein biosynthesis, R	1e-07
1r73_A	66	TM1492, 50S ribosomal protein L29; ribosome, struc	9e-07
2zjr_V	67	50S ribosomal protein L29; ribosome, large ribosom	4e-06

>2zkr_v 60S ribosomal protein L35; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 123

 Score =  125 bits (316), Expect = 9e-39
 Identities = 78/122 (63%), Positives = 101/122 (82%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           MA++K  +LR K K +LL QL DLK EL+ LRVAKVTGGA +KLSKI+VVR SIA+VLTV
Sbjct: 1   MAKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTV 60

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
           I+Q QK  LR+ YK KK+ PLDLRPKKTRA+RRRL KH+ +LKT++++++E  +P+RKYA
Sbjct: 61  INQTQKENLRKFYKGKKYKPLDLRPKKTRAMRRRLNKHEENLKTKKQQRKERLYPLRKYA 120

Query: 121 IK 122
           +K
Sbjct: 121 VK 122

>4a17_U RPL35, 60S ribosomal protein L21; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_U 4a1c_U 4a1e_U Length = 124

 Score =  123 bits (310), Expect = 7e-38
 Identities = 53/121 (43%), Positives = 85/121 (70%)

Query: 2   ARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVI 61
             V+V +LRT+++  L+ +L  L+ EL+ LR+AK+ GG  NKL +I +VR +IA+ LT+I
Sbjct: 3   KSVRVFKLRTQTEEQLVGELGKLQTELSQLRIAKIAGGTANKLGRIGIVRKAIAKYLTII 62

Query: 62  SQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYAI 121
           ++K++ A+++ +K K   PLD+R KKTRAIRR+LTK Q      + +K+   F +RK+A+
Sbjct: 63  NEKRRQAVKDQFKGKSLKPLDIRVKKTRAIRRKLTKKQREAVLVKTQKKLNNFGLRKFAL 122

Query: 122 K 122
           K
Sbjct: 123 K 123

>3u5e_H L8, RP24, YL11, 60S ribosomal protein L9-A; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3izc_F 1s1i_H 3izs_F* 3j16_F 3o5h_I 3o58_I 3u5i_H 3jyw_H Length = 191

 Score =  115 bits (289), Expect = 1e-34
 Identities = 7/122 (5%), Positives = 26/122 (21%), Gaps = 3/122 (2%)

Query: 1   MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
           M  ++  +     +   ++    +   +               +        +    + V
Sbjct: 1   MKYIQTEQQIEVPEGVTVSIKSRIVKVVGPRGTLTKNLK---HIDVTFTKVNNQLIKVAV 57

Query: 61  ISQKQKAALREAYKNKKFLPLDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYA 120
            +  +K              +     K    + R       +     +K    F   +  
Sbjct: 58  HNGGRKHVAALRTVKSLVDNMITGVTKGYKYKMRYVYAHFPINVNIVEKDGAKFIEVRNF 117

Query: 121 IK 122
           + 
Sbjct: 118 LG 119

>3jyw_X 60S ribosomal protein L35; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} Length = 86

 Score = 72.3 bits (177), Expect = 3e-18
 Identities = 40/76 (52%), Positives = 48/76 (63%), Gaps = 3/76 (3%)

Query: 2  ARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVI 61
          A VK +ELRTKSK  L +QL DLK ELA L+V K++      L KIK VR SIA VLTVI
Sbjct: 1  AGVKAYELRTKSKEQLASQLVDLKKELAELKVQKLSRP---SLPKIKTVRKSIACVLTVI 57

Query: 62 SQKQKAALREAYKNKK 77
          +++Q AA   A     
Sbjct: 58 NEQQAAAAAAAAAAAA 73

>1vq8_V 50S ribosomal protein L29P; 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: a.2.2.1 PDB: 1vq4_V* 1vq5_V* 1vq6_V* 1vq7_V* 1s72_V* 1vq9_V* 1vqk_V* 1vql_V* 1vqm_V* 1vqn_V* 1vqo_V* 1vqp_V* 1yhq_V* 1yi2_V* 1yij_V* 1yit_V* 1yj9_V* 1yjn_V* 1yjw_V* 2otj_V* ... Length = 71

 Score = 69.3 bits (170), Expect = 4e-17
 Identities = 22/71 (30%), Positives = 36/71 (50%)

Query: 1  MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
          M  + V E+R  +  +   +L DLK EL   R  +  GGAP    +IK +R +IA++ T+
Sbjct: 1  MTVLHVQEIRDMTPAEREAELDDLKTELLNARAVQAAGGAPENPGRIKELRKAIARIKTI 60

Query: 61 ISQKQKAALRE 71
            ++      E
Sbjct: 61 QGEEGDLQENE 71

>3v2d_2 50S ribosomal protein L29; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 1vsp_W 1vsa_W 2j03_2 2jl6_2 2jl8_2 2v47_2 2v49_2 2wdi_2 2wdj_2 2wdl_2 2wdn_2 2wh2_2 2wh4_2 2wrj_2 2wrl_2 2wro_2 2wrr_2 2x9s_2 2x9u_2 2xg0_2 ... Length = 72

 Score = 45.1 bits (107), Expect = 9e-08
 Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 1/68 (1%)

Query: 1  MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60
            R ++ E R  S  +L   +++ K EL  LR     G       KI+ ++  IA++LTV
Sbjct: 5  EVRKQLEEARKLSPVELEKLVREKKRELMELRFQASIGQLSQN-HKIRDLKRQIARLLTV 63

Query: 61 ISQKQKAA 68
          +++K++  
Sbjct: 64 LNEKRRQN 71

>3r8s_Y 50S ribosomal protein L29; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_W 1p86_W 1vs8_X 1vs6_X 2aw4_X 2awb_X 1vt2_Y 2i2v_Y 2j28_X 2i2t_Y* 2qao_X* 2qba_X* 2qbc_X* 2qbe_X 2qbg_X 2qbi_X* 2qbk_X* 2qov_X 2qox_X 2qoz_X* ... Length = 63

 Score = 44.2 bits (105), Expect = 1e-07
 Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 5  KVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQK 64
          K  ELR KS  +L  +L +L  E   LR+   +G        +K VR  +A+V T++++K
Sbjct: 2  KAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQS-HLLKQVRRDVARVKTLLNEK 60

Query: 65 QKA 67
            A
Sbjct: 61 AGA 63

>1r73_A TM1492, 50S ribosomal protein L29; ribosome, structural genomics, PSI, protein structure initiative, joint center for structural genomics; NMR {Thermotoga maritima} SCOP: a.2.2.1 Length = 66

 Score = 42.3 bits (100), Expect = 9e-07
 Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 5  KVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQK 64
          K  ELR  +  +L N L++ K +L  LR     G   N  S IK+ +  IA++ T++ ++
Sbjct: 2  KASELRNYTDEELKNLLEEKKRQLMELRFQLAMGQLKNT-SLIKLTKRDIARIKTILRER 60

Query: 65 QKAALR 70
          +    R
Sbjct: 61 ELGIRR 66

>2zjr_V 50S ribosomal protein L29; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: a.2.2.1 PDB: 1nwx_W* 1nwy_W* 1sm1_W* 1xbp_W* 2aar_W 2d3o_W 2zjp_V* 2zjq_V 1nkw_W 3cf5_V* 3dll_V* 3pio_V* 3pip_V* 1pnu_W 1pny_W 1vor_Y 1vou_Y 1vow_Y 1voy_Y 1vp0_Y Length = 67

 Score = 40.5 bits (95), Expect = 4e-06
 Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 1/68 (1%)

Query: 4  VKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ 63
          +K  E+R    TD   ++   K EL  LR     G       +++ +R  +AQ+ TV ++
Sbjct: 1  MKPSEMRNLQATDFAKEIDARKKELMELRFQAAAGQLAQP-HRVRQLRREVAQLNTVKAE 59

Query: 64 KQKAALRE 71
            +   ++
Sbjct: 60 LARKGEQQ 67

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	123
4a17_U	124	RPL35, 60S ribosomal protein L21; eukaryotic ribos	100.0
3u5e_h	120	60S ribosomal protein L35-A, 60S ribosomal protein	100.0
2zkr_v	123	60S ribosomal protein L35; protein-RNA complex, 60	100.0
3iz5_c	124	60S ribosomal protein L35 (L29P); eukaryotic ribos	100.0
1vq8_V	71	50S ribosomal protein L29P; ribosome 50S, protein-	99.94
3j21_W	72	50S ribosomal protein L29P; archaea, archaeal, KIN	99.92
3jyw_X	86	60S ribosomal protein L35; eukaryotic ribosome, RA	99.92
1r73_A	66	TM1492, 50S ribosomal protein L29; ribosome, struc	99.91
2zjr_V	67	50S ribosomal protein L29; ribosome, large ribosom	99.91
3v2d_2	72	50S ribosomal protein L29; ribosome associated inh	99.91
3r8s_Y	63	50S ribosomal protein L29; protein biosynthesis, R	99.9
3bbo_Z	173	Ribosomal protein L29; large ribosomal subunit, sp	99.87

>4a17_U RPL35, 60S ribosomal protein L21; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_U 4a1c_U 4a1e_U

Probab=100.00  E-value=6.2e-59  Score=340.30  Aligned_cols=123  Identities=43%  Similarity=0.693  Sum_probs=121.5

Q ss_pred             CCCCChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCC
Q 033270            1 MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAALREAYKNKKFLP   80 (123)
Q Consensus         1 M~~mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~~lr~~y~~kk~~p   80 (123)
                      |++|+++|||++|.+||.++|++|+.|||+||||++|||+++|||+|+.||++||||+||++|++.+++|+||+|++|+|
T Consensus         2 ~~~mKa~ELR~~s~eEL~~~L~eLK~ELf~LRfq~atggqlen~~rIr~vRRdIARi~Tvl~er~~~~lr~~yk~kk~~P   81 (124)
T 4a17_U            2 DKSVRVFKLRTQTEEQLVGELGKLQTELSQLRIAKIAGGTANKLGRIGIVRKAIAKYLTIINEKRRQAVKDQFKGKSLKP   81 (124)
T ss_dssp             CCCCCHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCC
T ss_pred             CcccCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhcCccCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCC
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCchhhHHHHhhcChHHhhhhhHHHHHHHhhCCcchhhhcC
Q 033270           81 LDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYAIKV  123 (123)
Q Consensus        81 ~dlr~kktra~rr~Lt~~~~~~kt~k~~~k~~~~p~r~~a~ka  123 (123)
                      +|||||+||||||+||+||+|++|.||++++.+||.|+|||||
T Consensus        82 ~dlr~kktra~rr~Lt~~e~~~kt~k~~~k~~~fp~rk~avka  124 (124)
T 4a17_U           82 LDIRVKKTRAIRRKLTKKQREAVLVKTQKKLNNFGLRKFALKA  124 (124)
T ss_dssp             TTTSCCSCHHHHHSCCHHHHHCCCHHHHHHHHHTCCCCCCCCC
T ss_pred             cccCchHHHHHHHHcCHHHHhhhhHHHHHHHHhCCchheeecC
Confidence            9999999999999999999999999999999999999999997

>3u5e_h 60S ribosomal protein L35-A, 60S ribosomal protein L33-A; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 1s1i_X 2wwa_N 2ww9_N 3izc_c 3izs_c 2wwb_N 3o5h_c 3o58_c 3u5i_h 4b6a_h

Probab=100.00  E-value=4.4e-57  Score=328.96  Aligned_cols=120  Identities=59%  Similarity=0.783  Sum_probs=117.5

Q ss_pred             CCCCChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCC
Q 033270            1 MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAALREAYKNKKFLP   80 (123)
Q Consensus         1 M~~mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~~lr~~y~~kk~~p   80 (123)
                      |+.|+++||+++|.+||.++|++|+.|||+||||++|| ++  ||+|+.||++||||+||+||++.+++|+||+|++|+|
T Consensus         1 Ma~mK~~ELR~~s~eEL~~~L~eLK~ELf~LRfq~atg-ql--~~~Ir~vRR~IARi~Tvl~er~~~~lr~~yk~kk~~p   77 (120)
T 3u5e_h            1 MAGVKAYELRTKSKEQLASQLVDLKKELAELKVQKLSR-PS--LPKIKTVRKSIACVLTVINEQQREAVRQLYKGKKYQP   77 (120)
T ss_dssp             -CCCCHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHTTS-SC--CTHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSSCCC
T ss_pred             CCcCCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHC-Cc--chhHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCC
Confidence            89999999999999999999999999999999999999 56  9999999999999999999999999999999999999


Q ss_pred             CCCCchhhHHHHhhcChHHhhhhhHHHHHHHhhCCcchhhhcC
Q 033270           81 LDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYAIKV  123 (123)
Q Consensus        81 ~dlr~kktra~rr~Lt~~~~~~kt~k~~~k~~~~p~r~~a~ka  123 (123)
                      +|||||+||||||+||+||+|++|.||++++.+||.|+|||||
T Consensus        78 ~dlr~kktra~rr~Lt~~~~~~kt~k~~~k~~~~p~r~~avka  120 (120)
T 3u5e_h           78 KDLRAKKTRALRRALTKFEASQVTEKQRKKQIAFPQRKYAIKA  120 (120)
T ss_dssp             TTTSCCSCHHHHSSCCSHHHHCCCHHHHHHHHHSCCCCEEECC
T ss_pred             cccCchHHHHHHHHcCHHHHhhhhHHHHHHHHhCCchheeecC
Confidence            9999999999999999999999999999999999999999997

>2zkr_v 60S ribosomal protein L35; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}

Probab=100.00  E-value=5.4e-58  Score=334.93  Aligned_cols=123  Identities=63%  Similarity=0.950  Sum_probs=60.3

Q ss_pred             CCCCChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCC
Q 033270            1 MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAALREAYKNKKFLP   80 (123)
Q Consensus         1 M~~mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~~lr~~y~~kk~~p   80 (123)
                      |++|+++|||++|.+||.++|.+|+.|||+||||++|||+++|||+|+.||++||||+||++|++.+++++||+|++|+|
T Consensus         1 Ma~mK~~ELR~~s~eEL~~~L~eLK~ELf~LRfq~atgq~len~~rir~vRrdIARI~Tvl~er~~~~lr~~yk~kk~~p   80 (123)
T 2zkr_v            1 MAKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTVINQTQKENLRKFYKGKKYKP   80 (123)
T ss_dssp             ---CCHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHTCSCCCHHHHHHHHHHHHHHHHHHHHC----------------
T ss_pred             CCCCCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCC
Confidence            89999999999999999999999999999999999999779999999999999999999999999999999999999999


Q ss_pred             CCCCchhhHHHHhhcChHHhhhhhHHHHHHHhhCCcchhhhcC
Q 033270           81 LDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYAIKV  123 (123)
Q Consensus        81 ~dlr~kktra~rr~Lt~~~~~~kt~k~~~k~~~~p~r~~a~ka  123 (123)
                      +|||||+||||||+||+||+|++|.||++++.+||.|+|||||
T Consensus        81 ~dlr~k~tra~rr~Lt~~~~~~kt~k~~~k~~~~p~rk~a~ka  123 (123)
T 2zkr_v           81 LDLRPKKTRAMRRRLNKHEENLKTKKQQRKERLYPLRKYAVKA  123 (123)
T ss_dssp             -------------------------------------------
T ss_pred             cccchHHHHHHHHHcCHHHHhhccHHHHHHHHhCchhhhhccC
Confidence            9999999999999999999999999999999999999999997

>1vq8_V 50S ribosomal protein L29P; 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: a.2.2.1 PDB: 1vq4_V* 1vq5_V* 1vq6_V* 1vq7_V* 1s72_V* 1vq9_V* 1vqk_V* 1vql_V* 1vqm_V* 1vqn_V* 1vqo_V* 1vqp_V* 1yhq_V* 1yi2_V* 1yij_V* 1yit_V* 1yj9_V* 1yjn_V* 1yjw_V* 2otj_V* ...

Probab=99.94  E-value=3.3e-27  Score=157.60  Aligned_cols=68  Identities=31%  Similarity=0.476  Sum_probs=63.7

Q ss_pred             CCCCChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHHH
Q 033270            1 MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAA   68 (123)
Q Consensus         1 M~~mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~~   68 (123)
                      |++|+++|||++|.+||.++|.+|+.|||+|||+++|||+++|||+|+.|||+||||+||++|++.++
T Consensus         1 Ma~mk~~elr~~s~~EL~~~l~elk~ELf~LR~q~atggql~n~~~ir~vRr~IARi~Tvl~er~~~~   68 (71)
T 1vq8_V            1 MTVLHVQEIRDMTPAEREAELDDLKTELLNARAVQAAGGAPENPGRIKELRKAIARIKTIQGEEGDLQ   68 (71)
T ss_dssp             -CCSCHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTTCCCCCHHHHHHHHHHHHHHHHHHHHHTC--
T ss_pred             CCCCCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCccChHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            89999999999999999999999999999999999997799999999999999999999999998654

>3j21_W 50S ribosomal protein L29P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=99.92  E-value=4.5e-25  Score=147.69  Aligned_cols=70  Identities=23%  Similarity=0.286  Sum_probs=66.1

Q ss_pred             CChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033270            4 VKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAALREAY   73 (123)
Q Consensus         4 mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~~lr~~y   73 (123)
                      |+++|||++|.+||.++|.+++.|||+||||++||++++|||+|+.+||+||||+||++|++.+..+...
T Consensus         1 MK~~elr~~s~~EL~~~L~elk~ELf~LR~q~atgq~l~n~~~ir~vRr~IARi~Tvl~er~~~~~~~~~   70 (72)
T 3j21_W            1 MKPSEIREMSIEEIDAKIRELRLQLAKERGLLTMGTSLENPMVIRNLRRDIARLLTIKKEKLREREKGKV   70 (72)
T ss_dssp             CCHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHCCSSCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            7899999999999999999999999999999999944999999999999999999999999998877654

>3jyw_X 60S ribosomal protein L35; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus}

Probab=99.92  E-value=8.8e-27  Score=160.95  Aligned_cols=72  Identities=56%  Similarity=0.586  Sum_probs=69.2

Q ss_pred             CCCChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 033270            2 ARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAALREAYKNK   76 (123)
Q Consensus         2 ~~mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~~lr~~y~~k   76 (123)
                      ++||++|||++|.+||.++|.+|+.|||+||||++|| ++  ||+|+.|||+||||+||++|++.+++|++|+..
T Consensus         1 ~~MKa~ELR~~S~eEL~~~L~eLK~ELf~LRfq~atg-ql--p~rIr~vRRdIARikTvl~er~~~~lr~~y~~~   72 (86)
T 3jyw_X            1 AGVKAYELRTKSKEQLASQLVDLKKELAELKVQKLSR-PS--LPKIKTVRKSIACVLTVINEQQAAAAAAAAAAA   72 (86)
T ss_dssp             CCSCHHHHHTSCHHHHHHHHHHHTTTHHHHHHHHHTC-CC--HHHHTCCSTTTHHHHTTTTHHHHHHHSSCCCSS
T ss_pred             CCCCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHC-CC--chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4799999999999999999999999999999999999 66  999999999999999999999999999999864

>1r73_A TM1492, 50S ribosomal protein L29; ribosome, structural genomics, PSI, protein structure initiative, joint center for structural genomics; NMR {Thermotoga maritima} SCOP: a.2.2.1

Probab=99.91  E-value=3.9e-25  Score=145.67  Aligned_cols=63  Identities=29%  Similarity=0.408  Sum_probs=60.7

Q ss_pred             CChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHH
Q 033270            4 VKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKA   67 (123)
Q Consensus         4 mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~   67 (123)
                      ||++|||++|.+||.++|.+++.|||+||||++|| +++|||+|+.|||+||||+||++|++.+
T Consensus         1 MK~~elr~~s~~EL~~~l~elk~ELf~LR~q~atg-ql~n~~~ir~vRr~IARi~Tvl~er~~~   63 (66)
T 1r73_A            1 MKASELRNYTDEELKNLLEEKKRQLMELRFQLAMG-QLKNTSLIKLTKRDIARIKTILRERELG   63 (66)
T ss_dssp             CCCSHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHT-CCCCHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CChHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHcc-CccCcHHHHHHHHHHHHHHHHHHHHHhh
Confidence            68899999999999999999999999999999997 9999999999999999999999999863

>2zjr_V 50S ribosomal protein L29; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: a.2.2.1 PDB: 1nwx_W* 1nwy_W* 1sm1_W* 1xbp_W* 2aar_W 2d3o_W 2zjp_V* 2zjq_V 1nkw_W 3cf5_V* 3dll_V* 3pio_V* 3pip_V* 1pnu_W 1pny_W 1vor_Y 1vou_Y 1vow_Y 1voy_Y 1vp0_Y

Probab=99.91  E-value=8.4e-25  Score=144.44  Aligned_cols=63  Identities=25%  Similarity=0.356  Sum_probs=60.7

Q ss_pred             CChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHH
Q 033270            4 VKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKA   67 (123)
Q Consensus         4 mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~   67 (123)
                      ||++|||++|.+||.++|.+++.|||+|||+++|| +++|||+|+.|||+||||+||++|++.+
T Consensus         1 Mk~~elr~~s~~EL~~~l~elk~ELf~LR~q~atg-ql~n~~~ir~vRr~IARi~Tvl~er~~~   63 (67)
T 2zjr_V            1 MKPSEMRNLQATDFAKEIDARKKELMELRFQAAAG-QLAQPHRVRQLRREVAQLNTVKAELARK   63 (67)
T ss_dssp             CCSTTTTTSCHHHHHHHHHTHHHHHHHHHHHHHHS-CCCCHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhC-CCcccHHHHHHHHHHHHHHHHHHHHHHh
Confidence            68999999999999999999999999999999997 9999999999999999999999998764

>3v2d_2 50S ribosomal protein L29; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 1vsp_W 1vsa_W 2j03_2 2jl6_2 2jl8_2 2v47_2 2v49_2 2wdi_2 2wdj_2 2wdl_2 2wdn_2 2wh2_2 2wh4_2 2wrj_2 2wrl_2 2wro_2 2wrr_2 2x9s_2 2x9u_2 2xg0_2 ...

Probab=99.91  E-value=1.3e-24  Score=145.46  Aligned_cols=65  Identities=29%  Similarity=0.409  Sum_probs=61.4

Q ss_pred             CCChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHHH
Q 033270            3 RVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAA   68 (123)
Q Consensus         3 ~mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~~   68 (123)
                      .||++|||++|.+||.++|.+++.|||+||||++|| +++||++|+.|||+||||+||++|++.+.
T Consensus         7 ~mK~~elr~~s~eEL~~~L~elk~ELf~LR~q~atg-ql~n~~~ir~vRr~IARi~Tvl~er~~~~   71 (72)
T 3v2d_2            7 RKQLEEARKLSPVELEKLVREKKRELMELRFQASIG-QLSQNHKIRDLKRQIARLLTVLNEKRRQN   71 (72)
T ss_dssp             HHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTT-CCCCTTHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             cCCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhc-CCCCcHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            489999999999999999999999999999999999 78999999999999999999999998643

>3r8s_Y 50S ribosomal protein L29; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_W 1p86_W 1vs8_X 1vs6_X 2aw4_X 2awb_X 1vt2_Y 2i2v_Y 2j28_X 2i2t_Y* 2qao_X* 2qba_X* 2qbc_X* 2qbe_X 2qbg_X 2qbi_X* 2qbk_X* 2qov_X 2qox_X 2qoz_X* ...

Probab=99.90  E-value=8.6e-25  Score=142.87  Aligned_cols=61  Identities=33%  Similarity=0.408  Sum_probs=59.2

Q ss_pred             CChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHH
Q 033270            4 VKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQ   65 (123)
Q Consensus         4 mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq   65 (123)
                      ||++|||++|.+||.++|.+++.|||+|||++++| +++||++|+.+||+||||+||++|++
T Consensus         1 MK~~elr~~s~~EL~~~l~elk~Elf~LR~q~atg-ql~n~~~ir~vRr~IARi~Tvl~er~   61 (63)
T 3r8s_Y            1 MKAKELREKSVEELNTELLNLLREQFNLRMQAASG-QLQQSHLLKQVRRDVARVKTLLNEKA   61 (63)
T ss_dssp             CCGGGTTSCHHHHHHHHHHHHTHHHHHHHHHHHTT-CCSCGGGTHHHHHHHHHHHHTTTSST
T ss_pred             CCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhC-CCcCcHHHHHHHHHHHHHHHHHHHhh
Confidence            78999999999999999999999999999999998 89999999999999999999999875

>3bbo_Z Ribosomal protein L29; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=99.87  E-value=7.8e-23  Score=156.05  Aligned_cols=76  Identities=26%  Similarity=0.389  Sum_probs=61.7

Q ss_pred             CCC--CChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Q 033270            1 MAR--VKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAALREAYKNKK   77 (123)
Q Consensus         1 M~~--mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~~lr~~y~~kk   77 (123)
                      |++  +++.|||++|.+||.++|.+|+.|||+||||++|| +++||++|+.+||+||||+||+||+++++.-..+...+
T Consensus        60 MAK~~~Ka~ELR~lS~eEL~ekL~eLKkELFnLRfQkATG-QLeNpsrIR~VRRdIARIkTVLrErel~~~~~kr~SRk  137 (173)
T 3bbo_Z           60 MSKREAELKEIRSKTTEQLQEEVVDLKGELFMLRLQKSAR-NEFKSSDFRRMKKQVARMLTVKREREIKEGIKKRLSRK  137 (173)
T ss_dssp             --CCSSCHHHHHHSCHHHHHHHHHHHTTHHHHHHHHHHHC-CCSCHHHHHHHHHHHHHHHHHHHHSCC-----------
T ss_pred             cccccCCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhc-CCCCchHHHHHHHHHHHHHHHHHHHHHHhccchhHHHH
Confidence            566  89999999999999999999999999999999999 79999999999999999999999999877655544433

---

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	123
d1vqov1	65	a.2.2.1 (V:1-65) Ribosomal protein L29 (L29p) {Arc	1e-12
d2zjrv1	66	a.2.2.1 (V:1-66) Ribosomal protein L29 (L29p) {Dei	8e-10
d2gycw1	60	a.2.2.1 (W:1-60) Ribosomal protein L29 (L29p) {Esc	5e-09
d1r73a_	66	a.2.2.1 (A:) Ribosomal protein L29 (L29p) {Thermot	9e-09
d2j0121	51	a.2.2.1 (2:12-62) Ribosomal protein L29 (L29p) {Th	8e-06

>d1vqov1 a.2.2.1 (V:1-65) Ribosomal protein L29 (L29p) {Archaeon Haloarcula marismortui [TaxId: 2238]} Length = 65

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Archaeon Haloarcula marismortui [TaxId: 2238]

 Score = 56.1 bits (136), Expect = 1e-12
 Identities = 20/61 (32%), Positives = 34/61 (55%)

Query: 4  VKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ 63
          + V E+R  +  +   +L DLK EL   R  +  GGAP    +IK +R +IA++ T+  +
Sbjct: 3  LHVQEIRDMTPAEREAELDDLKTELLNARAVQAAGGAPENPGRIKELRKAIARIKTIQGE 62

Query: 64 K 64
          +
Sbjct: 63 E 63

>d2zjrv1 a.2.2.1 (V:1-66) Ribosomal protein L29 (L29p) {Deinococcus radiodurans [TaxId: 1299]} Length = 66

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Deinococcus radiodurans [TaxId: 1299]

 Score = 49.2 bits (118), Expect = 8e-10
 Identities = 16/64 (25%), Positives = 28/64 (43%), Gaps = 1/64 (1%)

Query: 5  KVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQK 64
          K  E+R    TD   ++   K EL  LR     G       +++ +R  +AQ+ TV ++ 
Sbjct: 2  KPSEMRNLQATDFAKEIDARKKELMELRFQAAAGQLAQ-PHRVRQLRREVAQLNTVKAEL 60

Query: 65 QKAA 68
           +  
Sbjct: 61 ARKG 64

>d2gycw1 a.2.2.1 (W:1-60) Ribosomal protein L29 (L29p) {Escherichia coli [TaxId: 562]} Length = 60

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Escherichia coli [TaxId: 562]

 Score = 46.9 bits (112), Expect = 5e-09
 Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 1/60 (1%)

Query: 5  KVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQK 64
          K  ELR KS  +L  +L +L  E   LR+   +G        +K VR  +A+V T++++K
Sbjct: 2  KAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQ-SHLLKQVRRDVARVKTLLNEK 60

>d1r73a_ a.2.2.1 (A:) Ribosomal protein L29 (L29p) {Thermotoga maritima [TaxId: 2336]} Length = 66

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Thermotoga maritima [TaxId: 2336]

 Score = 46.5 bits (111), Expect = 9e-09
 Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 5  KVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQK 64
          K  ELR  +  +L N L++ K +L  LR     G   N  S IK+ +  IA++ T++ ++
Sbjct: 2  KASELRNYTDEELKNLLEEKKRQLMELRFQLAMGQLKN-TSLIKLTKRDIARIKTILRER 60

Query: 65 Q 65
          +
Sbjct: 61 E 61

>d2j0121 a.2.2.1 (2:12-62) Ribosomal protein L29 (L29p) {Thermus thermophilus [TaxId: 274]} Length = 51

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Thermus thermophilus [TaxId: 274]

 Score = 38.4 bits (90), Expect = 8e-06
 Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 8  ELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLT 59
          E R  S  +L   +++ K EL  LR      G  ++  KI+ ++  IA++LT
Sbjct: 1  EARKLSPVELEKLVREKKRELMELRFQASI-GQLSQNHKIRDLKRQIARLLT 51

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	123
d2zjrv1	66	Ribosomal protein L29 (L29p) {Deinococcus radiodur	99.88
d1r73a_	66	Ribosomal protein L29 (L29p) {Thermotoga maritima	99.88
d1vqov1	65	Ribosomal protein L29 (L29p) {Archaeon Haloarcula	99.88
d2gycw1	60	Ribosomal protein L29 (L29p) {Escherichia coli [Ta	99.87
d2j0121	51	Ribosomal protein L29 (L29p) {Thermus thermophilus	99.64

>d2zjrv1 a.2.2.1 (V:1-66) Ribosomal protein L29 (L29p) {Deinococcus radiodurans [TaxId: 1299]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Deinococcus radiodurans [TaxId: 1299]

Probab=99.88  E-value=1.2e-23  Score=136.94  Aligned_cols=63  Identities=25%  Similarity=0.356  Sum_probs=60.7

Q ss_pred             CChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHH
Q 033270            4 VKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKA   67 (123)
Q Consensus         4 mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~   67 (123)
                      ||++|||++|.+||.++|.+++.|||+|||++++| +++|||+|+.+||+||||+||++|++.+
T Consensus         1 MK~~elr~~s~~eL~~~l~~lk~elf~LRfq~~tg-ql~n~~~ik~~Rk~IARi~Tvl~er~~~   63 (66)
T d2zjrv1           1 MKPSEMRNLQATDFAKEIDARKKELMELRFQAAAG-QLAQPHRVRQLRREVAQLNTVKAELARK   63 (66)
T ss_dssp             CCSTTTTTSCHHHHHHHHHTHHHHHHHHHHHHHHS-CCCCHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHC-CCcchHHHHHHHHHHHHHHHHHHHHHHh
Confidence            78999999999999999999999999999999999 9999999999999999999999998754

>d1r73a_ a.2.2.1 (A:) Ribosomal protein L29 (L29p) {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Thermotoga maritima [TaxId: 2336]

Probab=99.88  E-value=3.4e-23  Score=134.73  Aligned_cols=62  Identities=29%  Similarity=0.411  Sum_probs=60.5

Q ss_pred             CChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHH
Q 033270            4 VKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQK   66 (123)
Q Consensus         4 mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~   66 (123)
                      |+++||+++|.+||.+.|.+++.|||+|||++++| +++|||.|+.+||+||||+||++|++.
T Consensus         1 MK~~elr~ls~~eL~~~l~~l~~el~~LRfq~~~g-ql~~~~~i~~~Rk~IARi~Tvl~er~~   62 (66)
T d1r73a_           1 MKASELRNYTDEELKNLLEEKKRQLMELRFQLAMG-QLKNTSLIKLTKRDIARIKTILREREL   62 (66)
T ss_dssp             CCCSHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHT-CCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHC-CCCChHHHHHHHHHHHHHHHHHHHHHh
Confidence            78999999999999999999999999999999998 999999999999999999999999986

>d1vqov1 a.2.2.1 (V:1-65) Ribosomal protein L29 (L29p) {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=99.88  E-value=6.9e-23  Score=132.96  Aligned_cols=62  Identities=31%  Similarity=0.453  Sum_probs=57.7

Q ss_pred             CCCChHHHhcCCHHHHHHHHHHHHHHHHHHHH-HHHHCCCCCccchhHHHHHHHHHHHHHHHHH
Q 033270            2 ARVKVHELRTKSKTDLLNQLKDLKAELALLRV-AKVTGGAPNKLSKIKVVRLSIAQVLTVISQK   64 (123)
Q Consensus         2 ~~mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~-qk~tgg~~~k~~kIr~vRK~IARvlTVl~ek   64 (123)
                      ..||++|||++|.+||.++|.+|+.|||+||+ +.++| +++|||+|+.+||+||||+||++|+
T Consensus         1 t~mK~~elr~ls~~eL~~~l~elk~El~~LR~~q~~~g-ql~~~~~ik~~Rk~IARi~Tvl~ek   63 (65)
T d1vqov1           1 TVLHVQEIRDMTPAEREAELDDLKTELLNARAVQAAGG-APENPGRIKELRKAIARIKTIQGEE   63 (65)
T ss_dssp             CCSCHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHTTC-SSCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHhC-CCCchHHHHHHHHHHHHHHHHHHHh
Confidence            36899999999999999999999999999995 55555 9999999999999999999999997

>d2gycw1 a.2.2.1 (W:1-60) Ribosomal protein L29 (L29p) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Escherichia coli [TaxId: 562]

Probab=99.87  E-value=1.3e-23  Score=134.37  Aligned_cols=60  Identities=33%  Similarity=0.416  Sum_probs=58.4

Q ss_pred             CChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHH
Q 033270            4 VKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQK   64 (123)
Q Consensus         4 mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ek   64 (123)
                      ||++|||++|.+||.+.|.+++.|||+|||++++| +++|||+|+.+||+||||+||+||+
T Consensus         1 Mk~~elr~ls~~eL~~~l~~l~~el~~lRfq~~~g-ql~~~~~i~~~Rk~IARi~Tvl~ek   60 (60)
T d2gycw1           1 MKAKELREKSVEELNTELLNLLREQFNLRMQAASG-QLQQSHLLKQVRRDVARVKTLLNEK   60 (60)
T ss_dssp             CCHHHHHHSCHHHHHHHHHHHHHHHHHCCCSTTTC-SSCCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHC-CCCchHHHHHHHHHHHHHHHHHhcC
Confidence            78999999999999999999999999999999999 8999999999999999999999984

>d2j0121 a.2.2.1 (2:12-62) Ribosomal protein L29 (L29p) {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Thermus thermophilus [TaxId: 274]

Probab=99.64  E-value=1.2e-19  Score=112.63  Aligned_cols=51  Identities=31%  Similarity=0.375  Sum_probs=48.9

Q ss_pred             HHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHH
Q 033270            8 ELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLT   59 (123)
Q Consensus         8 ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlT   59 (123)
                      |||+||.+||.++|.+++.|||+|||++++| +++|||+|+.+||+||||+|
T Consensus         1 EiR~ls~~eL~~~l~elk~el~~LRfq~atg-ql~n~~~ik~~rk~IARi~T   51 (51)
T d2j0121           1 EARKLSPVELEKLVREKKRELMELRFQASIG-QLSQNHKIRDLKRQIARLLT   51 (51)
T ss_dssp             CCTTTHHHHHHHHHHHHHHHSSSSCCTTSST-TTGGGTTSSSSSCCCCCCC-
T ss_pred             ChhhCCHHHHHHHHHHHHHHHHHHHHHHHHC-CCcchHHHHHHHHHHHHhcC
Confidence            6899999999999999999999999999998 99999999999999999987