Citrus Sinensis ID: 034832

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--
Protein Sequence
MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSIQSLSRALDQYNKVAH
Secondary Structure (PSIPRED)
cccccccccccccccccHHHHHHHHHHHHHHHHHHcccccccccccccccEEEEEEccccccEEEcHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccEEEEEEcEccccHHHHHHHHHHHHHHHHHccccHcccccccccEEEEEEEEccccccccccHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mdntsnvhvglgkvslkEELLRENVGAFVNALLLAkpaglkktskfagyvnsfhmcstmgpsfpvSIQSLSRALDQYNKVAH
Flexible Loop (DISEMBL)
mdntsnvhvglgkvslkeELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSIQSLSRALDQYNKVAH
Low Complexity Region (SEG)
MDNTSNVHVGLGKVSLKEELLRENVGAFVNalllakpaglkkTSKFAGYVNSFHMCSTMGPSFPVSIQSLSRALDQYNKVAH
Disordered region (IsUnstruct)
********VGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPV*****************
Disordered Region (DISOPRED)
MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSIQSLSRA*********
Disordered Region (DISEMBL)
MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSIQSLSRALDQYNKVAH
Disordered Region (DISPRO)
**NTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPA*LKKTSKFAGYVNSFHMCSTMGPSFPVSIQSLSRALDQYNKV**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSIQSLSRALDQYNKVAH
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	82	2.2.26 [Sep-21-2011]
B4R8K2	229	50S ribosomal protein L1	yes	no	0.719	0.257	0.484	3e-08
B6IRP3	235	50S ribosomal protein L1	yes	no	0.829	0.289	0.410	3e-08
Q5LMQ0	232	50S ribosomal protein L1	yes	no	0.731	0.258	0.476	3e-08
Q1GT68	232	50S ribosomal protein L1	yes	no	0.756	0.267	0.447	3e-08
B0T064	229	50S ribosomal protein L1	yes	no	0.731	0.262	0.476	4e-08
Q2W2H8	230	50S ribosomal protein L1	yes	no	0.731	0.260	0.446	4e-08
Q5NPL0	233	50S ribosomal protein L1	yes	no	0.829	0.291	0.410	1e-07
B8G990	237	50S ribosomal protein L1	yes	no	0.743	0.257	0.424	1e-07
B2V7M3	242	50S ribosomal protein L1	yes	no	0.853	0.289	0.373	2e-07
Q2K9M7	233	50S ribosomal protein L1	yes	no	0.756	0.266	0.402	4e-07

>sp|B4R8K2|RL1_PHEZH 50S ribosomal protein L1 OS=Phenylobacterium zucineum (strain HLK1) GN=rplA PE=3 SV=1

 Score = 57.4 bits (137), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 31/64 (48%), Positives = 37/64 (57%), Gaps = 5/64 (7%)

Query: 7   VHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVS 66
           VH G+GK S  EE L  NV A V+AL  AKP+G K T     YV    + STMGP F + 
Sbjct: 169 VHAGIGKASFTEEQLTANVKAMVDALNKAKPSGAKGT-----YVKKVSLSSTMGPGFKID 223

Query: 67  IQSL 70
           + SL
Sbjct: 224 VASL 227

Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.
Phenylobacterium zucineum (strain HLK1) (taxid: 450851)

>sp|B6IRP3|RL1_RHOCS 50S ribosomal protein L1 OS=Rhodospirillum centenum (strain ATCC 51521 / SW) GN=rplA PE=3 SV=1

 Score = 57.0 bits (136), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 30/73 (41%), Positives = 42/73 (57%), Gaps = 5/73 (6%)

Query: 2   DNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGP 61
           + T  VH G+GK S  E+ L EN+ AFV+A+  AKP+G K T     Y+    + STMGP
Sbjct: 166 EKTGIVHAGVGKASFSEQALEENIRAFVSAINRAKPSGAKGT-----YIEKVSLSSTMGP 220

Query: 62  SFPVSIQSLSRAL 74
              + I +L  +L
Sbjct: 221 GIKLDIPALVASL 233

Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.

Rhodospirillum centenum (strain ATCC 51521 / SW) (taxid: 414684)

>sp|Q5LMQ0|RL1_RUEPO 50S ribosomal protein L1 OS=Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3) GN=rplA PE=3 SV=1

 Score = 57.0 bits (136), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 31/65 (47%), Positives = 38/65 (58%), Gaps = 5/65 (7%)

Query: 7   VHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVS 66
           +H G+GKVS  E  L ENV AFV+A+  AKPAG K T     Y+    + STMGP   V 
Sbjct: 171 IHAGVGKVSFDEAKLVENVRAFVDAVAKAKPAGAKGT-----YLKKIALSSTMGPGVSVD 225

Query: 67  IQSLS 71
           + S S
Sbjct: 226 VASAS 230

Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.

Silicibacter pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3) (taxid: 246200)

>sp|Q1GT68|RL1_SPHAL 50S ribosomal protein L1 OS=Sphingopyxis alaskensis (strain DSM 13593 / LMG 18877 / RB2256) GN=rplA PE=3 SV=1

 Score = 57.0 bits (136), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 30/67 (44%), Positives = 39/67 (58%), Gaps = 5/67 (7%)

Query: 7   VHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVS 66
           +H GLGK+S  EE LR+N  AFV+A++ AKPAG K       YV    + S+MGP   V 
Sbjct: 171 IHAGLGKLSFGEEKLRQNFDAFVDAIVKAKPAGAKGK-----YVRKVALSSSMGPGVKVD 225

Query: 67  IQSLSRA 73
              L+ A
Sbjct: 226 TAELTGA 232

Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.

Sphingopyxis alaskensis (strain DSM 13593 / LMG 18877 / RB2256) (taxid: 317655)

>sp|B0T064|RL1_CAUSK 50S ribosomal protein L1 OS=Caulobacter sp. (strain K31) GN=rplA PE=3 SV=1

 Score = 57.0 bits (136), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 31/65 (47%), Positives = 39/65 (60%), Gaps = 5/65 (7%)

Query: 7   VHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVS 66
           VH G+GKVS  +E L  NV A V+AL+ AKPAG K       YV    + STMGP F + 
Sbjct: 169 VHAGIGKVSFTDEALLINVKAMVDALVKAKPAGAKGI-----YVKRIGLSSTMGPGFKID 223

Query: 67  IQSLS 71
           I S++
Sbjct: 224 IASVN 228

Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.

Caulobacter sp. (strain K31) (taxid: 366602)

>sp|Q2W2H8|RL1_MAGSA 50S ribosomal protein L1 OS=Magnetospirillum magneticum (strain AMB-1 / ATCC 700264) GN=rplA PE=3 SV=1

 Score = 56.6 bits (135), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 29/65 (44%), Positives = 38/65 (58%), Gaps = 5/65 (7%)

Query: 7   VHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVS 66
           VH G+GK S  EE L ENV AFV+A+  AKP G K T     Y+    + STMGP   + 
Sbjct: 171 VHAGIGKASFSEEKLAENVKAFVDAITKAKPQGAKGT-----YLKKVSLSSTMGPGVKLD 225

Query: 67  IQSLS 71
           + +L+
Sbjct: 226 VATLA 230

Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.

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

>sp|Q5NPL0|RL1_ZYMMO 50S ribosomal protein L1 OS=Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) GN=rplA PE=3 SV=1

 Score = 55.5 bits (132), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/73 (41%), Positives = 38/73 (52%), Gaps = 5/73 (6%)

Query: 1   MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
           +D T  +H G+GK S   E +R N  A ++ALL AKPAG K       YV    + STMG
Sbjct: 165 VDRTGIIHSGIGKASFSAEDIRANFDALIDALLKAKPAGAKGR-----YVKKVAISSTMG 219

Query: 61  PSFPVSIQSLSRA 73
           P   + I  L  A
Sbjct: 220 PGVSIDIADLPAA 232

Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.

Zymomonas mobilis (strain ATCC 31821 / ZM4 / CP4) (taxid: 264203)

>sp|B8G990|RL1_CHLAD 50S ribosomal protein L1 OS=Chloroflexus aggregans (strain MD-66 / DSM 9485) GN=rplA PE=3 SV=1

 Score = 55.1 bits (131), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/66 (42%), Positives = 38/66 (57%), Gaps = 5/66 (7%)

Query: 2   DNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGP 61
           D T  +HV +GKVS   + L EN+ A + A+  AKP+G K T     Y+ S  + STMGP
Sbjct: 169 DKTGILHVAIGKVSFTSQQLSENLAALMEAVKAAKPSGAKGT-----YIRSVTLTSTMGP 223

Query: 62  SFPVSI 67
             PV +
Sbjct: 224 GVPVDL 229

Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.

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

>sp|B2V7M3|RL1_SULSY 50S ribosomal protein L1 OS=Sulfurihydrogenibium sp. (strain YO3AOP1) GN=rplA PE=3 SV=1

 Score = 54.3 bits (129), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/75 (37%), Positives = 46/75 (61%), Gaps = 5/75 (6%)

Query: 1   MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
           +D T N+HV +GK+S ++  L+EN+ A V+A+L AKP G K       Y+ +  + +TM 
Sbjct: 169 VDKTGNLHVPVGKISFEDHKLKENILAVVDAVLKAKPPGAK-----GQYIRNVVLKTTMS 223

Query: 61  PSFPVSIQSLSRALD 75
           PS  ++   L +AL+
Sbjct: 224 PSVKLNPAELQKALE 238

Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.

Sulfurihydrogenibium sp. (strain YO3AOP1) (taxid: 436114)

>sp|Q2K9M7|RL1_RHIEC 50S ribosomal protein L1 OS=Rhizobium etli (strain CFN 42 / ATCC 51251) GN=rplA PE=3 SV=1

 Score = 53.5 bits (127), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 27/67 (40%), Positives = 38/67 (56%), Gaps = 5/67 (7%)

Query: 7   VHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVS 66
           VH G+GK S   + L EN+ AF +A++ AKPAG K       YV    + STMGP   + 
Sbjct: 169 VHAGIGKASFDAKALEENIRAFADAVIKAKPAGAK-----GNYVKRVAISSTMGPGVKIE 223

Query: 67  IQSLSRA 73
           + S++ A
Sbjct: 224 VGSVTAA 230

Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.

Rhizobium etli (strain CFN 42 / ATCC 51251) (taxid: 347834)

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	82
225446639	429	PREDICTED: 50S ribosomal protein L1-like	0.975	0.186	0.8	4e-31
302143437	274	unnamed protein product [Vitis vinifera]	0.975	0.291	0.8	7e-31
255580108	372	50S ribosomal protein L1p, putative [Ric	0.975	0.215	0.8	6e-30
449468920	424	PREDICTED: 50S ribosomal protein L1-like	0.963	0.186	0.772	1e-29
224128760	356	predicted protein [Populus trichocarpa]	0.975	0.224	0.8	4e-29
30689119	415	ribosomal protein .1/L10 family protein	0.975	0.192	0.75	1e-27
297824237	401	ribosomal protein L1 family protein [Ara	0.975	0.199	0.75	1e-27
357124299	405	PREDICTED: 50S ribosomal protein L1-like	0.975	0.197	0.712	2e-25
356517326	399	PREDICTED: 50S ribosomal protein L1-like	0.975	0.200	0.7	5e-25
357474637	407	50S ribosomal protein L1 [Medicago trunc	0.987	0.199	0.707	1e-24

>gi|225446639|ref|XP_002281125.1| PREDICTED: 50S ribosomal protein L1-like [Vitis vinifera]

 Score =  138 bits (348), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 64/80 (80%), Positives = 72/80 (90%)

Query: 1   MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
           MD T+ VHVGLGKVS  E++LREN+GAFVNALLLAKPAGLKKTSK+AGYVN+FH+CSTMG
Sbjct: 347 MDKTAIVHVGLGKVSFSEKVLRENIGAFVNALLLAKPAGLKKTSKYAGYVNAFHLCSTMG 406

Query: 61  PSFPVSIQSLSRALDQYNKV 80
           P FPVSIQSLS A D YNK+
Sbjct: 407 PGFPVSIQSLSMAADHYNKL 426

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302143437|emb|CBI21998.3| unnamed protein product [Vitis vinifera]

 Score =  137 bits (345), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 64/80 (80%), Positives = 72/80 (90%)

Query: 1   MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
           MD T+ VHVGLGKVS  E++LREN+GAFVNALLLAKPAGLKKTSK+AGYVN+FH+CSTMG
Sbjct: 192 MDKTAIVHVGLGKVSFSEKVLRENIGAFVNALLLAKPAGLKKTSKYAGYVNAFHLCSTMG 251

Query: 61  PSFPVSIQSLSRALDQYNKV 80
           P FPVSIQSLS A D YNK+
Sbjct: 252 PGFPVSIQSLSMAADHYNKL 271

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255580108|ref|XP_002530886.1| 50S ribosomal protein L1p, putative [Ricinus communis] gi|223529539|gb|EEF31492.1| 50S ribosomal protein L1p, putative [Ricinus communis]

 Score =  134 bits (337), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 64/80 (80%), Positives = 71/80 (88%)

Query: 1   MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
           MD TS VHVGLGKVS  EE LRENVGAF+NA+L AKPAGLKKTSK+AGYVN+ H+CSTMG
Sbjct: 287 MDKTSIVHVGLGKVSFSEESLRENVGAFMNAILQAKPAGLKKTSKYAGYVNTVHICSTMG 346

Query: 61  PSFPVSIQSLSRALDQYNKV 80
           P FPVSIQSLS+A+D YNKV
Sbjct: 347 PGFPVSIQSLSKAVDHYNKV 366

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449468920|ref|XP_004152169.1| PREDICTED: 50S ribosomal protein L1-like [Cucumis sativus] gi|449484790|ref|XP_004156980.1| PREDICTED: 50S ribosomal protein L1-like [Cucumis sativus]

 Score =  133 bits (335), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 61/79 (77%), Positives = 70/79 (88%)

Query: 1   MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
           MD+TS VHVGLGKVS  EE LREN+GAFVNALLLAKP GLKK SK+AGY+NSFH+CSTMG
Sbjct: 338 MDSTSIVHVGLGKVSHSEEFLRENIGAFVNALLLAKPVGLKKASKYAGYLNSFHICSTMG 397

Query: 61  PSFPVSIQSLSRALDQYNK 79
           P FP++IQSLS+  DQYN+
Sbjct: 398 PGFPITIQSLSKVADQYNR 416

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224128760|ref|XP_002320415.1| predicted protein [Populus trichocarpa] gi|222861188|gb|EEE98730.1| predicted protein [Populus trichocarpa]

 Score =  132 bits (331), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 64/80 (80%), Positives = 71/80 (88%)

Query: 1   MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
           MD T+ VHVGLGKVS  EE LRENVGAF+NALL AKPAGLKKTSK+AGYVNSFH+CSTMG
Sbjct: 274 MDKTAIVHVGLGKVSFTEESLRENVGAFMNALLQAKPAGLKKTSKYAGYVNSFHICSTMG 333

Query: 61  PSFPVSIQSLSRALDQYNKV 80
             FPVSIQSLS+A+D Y+KV
Sbjct: 334 QGFPVSIQSLSKAVDYYSKV 353

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30689119|ref|NP_850375.1| ribosomal protein .1/L10 family protein [Arabidopsis thaliana] gi|20268740|gb|AAM14073.1| unknown protein [Arabidopsis thaliana] gi|21280899|gb|AAM45043.1| unknown protein [Arabidopsis thaliana] gi|26451659|dbj|BAC42926.1| unknown protein [Arabidopsis thaliana] gi|330255065|gb|AEC10159.1| ribosomal protein .1/L10 family protein [Arabidopsis thaliana]

 Score =  127 bits (318), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 60/80 (75%), Positives = 69/80 (86%)

Query: 1   MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
           MD TS +HV LGK+S  EE LRENVGAF+NALLLAKPAGLKKTSK+AGYVN+FH+CSTMG
Sbjct: 333 MDKTSILHVPLGKMSFSEEALRENVGAFMNALLLAKPAGLKKTSKYAGYVNAFHLCSTMG 392

Query: 61  PSFPVSIQSLSRALDQYNKV 80
             +PVSIQSLSRA D + K+
Sbjct: 393 KGYPVSIQSLSRAADLHTKL 412

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297824237|ref|XP_002880001.1| ribosomal protein L1 family protein [Arabidopsis lyrata subsp. lyrata] gi|297325840|gb|EFH56260.1| ribosomal protein L1 family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  127 bits (318), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 60/80 (75%), Positives = 69/80 (86%)

Query: 1   MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
           MD TS +HV LGK+S  EE LRENVGAF+NALLLAKPAGLKKTSK+AGYVN+FH+CSTMG
Sbjct: 319 MDKTSILHVPLGKMSFPEEALRENVGAFMNALLLAKPAGLKKTSKYAGYVNAFHLCSTMG 378

Query: 61  PSFPVSIQSLSRALDQYNKV 80
             +PVSIQSLSRA D + K+
Sbjct: 379 KGYPVSIQSLSRAADLHTKL 398

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357124299|ref|XP_003563838.1| PREDICTED: 50S ribosomal protein L1-like [Brachypodium distachyon]

 Score =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 57/80 (71%), Positives = 64/80 (80%)

Query: 1   MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
           +D T+ VHVGLGKV+  EE LREN+GAFVNALLLAKP GLKKTSK+ GYV  F + STMG
Sbjct: 323 IDKTAIVHVGLGKVNFSEESLRENIGAFVNALLLAKPVGLKKTSKYVGYVKKFTLSSTMG 382

Query: 61  PSFPVSIQSLSRALDQYNKV 80
           P FPV+I SLS A D YNKV
Sbjct: 383 PGFPVTIPSLSAAADHYNKV 402

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356517326|ref|XP_003527339.1| PREDICTED: 50S ribosomal protein L1-like [Glycine max]

 Score =  118 bits (295), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 56/80 (70%), Positives = 67/80 (83%)

Query: 1   MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
           M++ S +HVGLGKVS KEE LREN+ AF+NA+LLAKPAGLKKTSK+AGYV S H+ STMG
Sbjct: 317 MESKSILHVGLGKVSYKEEALRENISAFMNAVLLAKPAGLKKTSKYAGYVLSVHISSTMG 376

Query: 61  PSFPVSIQSLSRALDQYNKV 80
           P  PVSIQS+S+A D Y K+
Sbjct: 377 PGLPVSIQSISKAADNYKKM 396

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357474637|ref|XP_003607603.1| 50S ribosomal protein L1 [Medicago truncatula] gi|355508658|gb|AES89800.1| 50S ribosomal protein L1 [Medicago truncatula]

 Score =  116 bits (291), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 58/82 (70%), Positives = 69/82 (84%), Gaps = 1/82 (1%)

Query: 1   MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
           M++ S +HVG+GKVS KEE LREN+GAF+NA+L AKPAGLKKTSK+AGYV S H+CST+G
Sbjct: 325 MESKSILHVGVGKVSYKEENLRENIGAFMNAVLQAKPAGLKKTSKYAGYVLSVHICSTIG 384

Query: 61  PSFPVSIQSLSRALDQYNKVAH 82
           P  PVSIQSLS+A D Y K AH
Sbjct: 385 PGIPVSIQSLSKAADNYKK-AH 405

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	82
TAIR|locus:2041519	415	AT2G42710 [Arabidopsis thalian	0.975	0.192	0.6	4.3e-20
TIGR_CMR|SPO_3513	232	SPO_3513 "ribosomal protein L1	0.731	0.258	0.369	0.00042

TAIR|locus:2041519 AT2G42710 [Arabidopsis thaliana (taxid:3702)]

 Score = 242 (90.2 bits), Expect = 4.3e-20, P = 4.3e-20
 Identities = 48/80 (60%), Positives = 57/80 (71%)

Query:     1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNXXXXXXXXXXXXTSKFAGYVNSFHMCSTMG 60
             MD TS +HV LGK+S  EE LRENVGAF+N            TSK+AGYVN+FH+CSTMG
Sbjct:   333 MDKTSILHVPLGKMSFSEEALRENVGAFMNALLLAKPAGLKKTSKYAGYVNAFHLCSTMG 392

Query:    61 PSFPVSIQSLSRALDQYNKV 80
               +PVSIQSLSRA D + K+
Sbjct:   393 KGYPVSIQSLSRAADLHTKL 412

GO:0003723 "RNA binding" evidence=IEA

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

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM

GO:0015934 "large ribosomal subunit" evidence=IEA;ISS

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

TIGR_CMR|SPO_3513 SPO_3513 "ribosomal protein L1" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 92 (37.4 bits), Expect = 0.00042, P = 0.00042
 Identities = 24/65 (36%), Positives = 30/65 (46%)

Query:     7 VHVGLGKVSLKEELLRENVGAFVNXXXXXXXXXXXXTSKFAGYVNSFHMCSTMGPSFPVS 66
             +H G+GKVS  E  L ENV AFV+            T     Y+    + STMGP   V 
Sbjct:   171 IHAGVGKVSFDEAKLVENVRAFVDAVAKAKPAGAKGT-----YLKKIALSSTMGPGVSVD 225

Query:    67 IQSLS 71
             + S S
Sbjct:   226 VASAS 230


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.317   0.129   0.368    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0       82        70   0.00091  102 3  11 22  0.46    28
                                                     29  0.41    29


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  2
  No. of states in DFA:  490 (52 KB)
  Total size of DFA:  83 KB (2064 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  6.81u 0.14s 6.95t   Elapsed:  00:00:00
  Total cpu time:  6.81u 0.14s 6.95t   Elapsed:  00:00:00
  Start:  Fri May 10 02:10:50 2013   End:  Fri May 10 02:10:50 2013

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

GO:0006412 "translation" evidence=ISS

GO:0042255 "ribosome assembly" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	82
PRK05424	230	PRK05424, rplA, 50S ribosomal protein L1; Validate	2e-17
TIGR01169	227	TIGR01169, rplA_bact, ribosomal protein L1, bacter	4e-16
COG0081	228	COG0081, RplA, Ribosomal protein L1 [Translation,	1e-11
CHL00129	229	CHL00129, rpl1, ribosomal protein L1; Reviewed	1e-11
cd00403	208	cd00403, Ribosomal_L1, Ribosomal protein L1	2e-11
pfam00687	200	pfam00687, Ribosomal_L1, Ribosomal protein L1p/L10	5e-08

>gnl|CDD|180071 PRK05424, rplA, 50S ribosomal protein L1; Validated

 Score = 72.5 bits (179), Expect = 2e-17
 Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 5/70 (7%)

Query: 2   DNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGP 61
           D    +H  +GKVS   E L+EN+ A ++A+  AKPA  K T     Y+ S  + STMGP
Sbjct: 165 DKAGIIHAPIGKVSFDAEKLKENLKALIDAIKKAKPATAKGT-----YIKSVSLSSTMGP 219

Query: 62  SFPVSIQSLS 71
              V   SL+
Sbjct: 220 GVKVDPSSLA 229

Length = 230

>gnl|CDD|211630 TIGR01169, rplA_bact, ribosomal protein L1, bacterial/chloroplast

 Score = 69.2 bits (170), Expect = 4e-16
 Identities = 27/69 (39%), Positives = 39/69 (56%), Gaps = 5/69 (7%)

Query: 2   DNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGP 61
           D   N+H  +GKVS   E L+EN+ A ++A+  AKP+G K       Y+ +  + STMGP
Sbjct: 164 DKAGNIHAPIGKVSFDSEKLKENLEALLDAIKKAKPSGAK-----GQYIKNIALSSTMGP 218

Query: 62  SFPVSIQSL 70
              V + SL
Sbjct: 219 GIKVDLNSL 227

This model describes bacterial (and chloroplast) ribosomal protein L1. The apparent mitochondrial L1 is sufficiently diverged to be the subject of a separate model [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 227

>gnl|CDD|223159 COG0081, RplA, Ribosomal protein L1 [Translation, ribosomal structure and biogenesis]

 Score = 57.2 bits (139), Expect = 1e-11
 Identities = 27/65 (41%), Positives = 38/65 (58%), Gaps = 5/65 (7%)

Query: 1   MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
            D    +HV +GKVS  +E L EN+ A +NA++ AKPAG K       Y+ S ++ +TMG
Sbjct: 166 ADKAGVIHVPIGKVSFDDEKLAENIEALLNAIVKAKPAGAKGQ-----YIKSVYVSTTMG 220

Query: 61  PSFPV 65
           P   V
Sbjct: 221 PGVKV 225

Length = 228

>gnl|CDD|177051 CHL00129, rpl1, ribosomal protein L1; Reviewed

 Score = 56.9 bits (138), Expect = 1e-11
 Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 5/70 (7%)

Query: 2   DNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGP 61
           D T  VHV  GK +  EE L EN+ A   ++   +P+G+K       Y  SF++CSTMGP
Sbjct: 165 DKTGIVHVLFGKSNFTEEDLLENLQAIYESIEQNRPSGVK-----GKYWKSFYICSTMGP 219

Query: 62  SFPVSIQSLS 71
           S  + I  L 
Sbjct: 220 SIQIDISLLR 229

Length = 229

>gnl|CDD|238235 cd00403, Ribosomal_L1, Ribosomal protein L1

 Score = 56.0 bits (136), Expect = 2e-11
 Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 6/65 (9%)

Query: 1   MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
           +D    +HV +GKVS+  E L EN+ A +NAL+   P+   +       + S ++ +TMG
Sbjct: 150 LDKGGCIHVPVGKVSMSPEQLVENIEAVINALVKKLPSKKGQ------NIKSIYLKTTMG 203

Query: 61  PSFPV 65
           PS P+
Sbjct: 204 PSLPI 208

The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds its own mRNA. Like several other large ribosomal subunit proteins, L1 displays RNA chaperone activity. L1 is one of the largest ribosomal proteins. It is composed of two domains that cycle between open and closed conformations via a hinge motion. The RNA-binding site of L1 is highly conserved, with both mRNA and rRNA binding the same binding site. Length = 208

>gnl|CDD|216061 pfam00687, Ribosomal_L1, Ribosomal protein L1p/L10e family

 Score = 47.2 bits (113), Expect = 5e-08
 Identities = 24/61 (39%), Positives = 34/61 (55%), Gaps = 7/61 (11%)

Query: 2   DNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGP 61
           D    +HV +GKVS+  E L EN+ A +NAL       +KK  K    + S ++ +TMGP
Sbjct: 147 DKGGCIHVKVGKVSMSPEELVENIEAVINAL-------VKKLPKGWQNIKSVYLKTTMGP 199

Query: 62  S 62
           S
Sbjct: 200 S 200

This family includes prokaryotic L1 and eukaryotic L10. Length = 200

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	82
COG0081	228	RplA Ribosomal protein L1 [Translation, ribosomal	99.89
CHL00129	229	rpl1 ribosomal protein L1; Reviewed	99.88
PRK05424	230	rplA 50S ribosomal protein L1; Validated	99.87
TIGR01169	227	rplA_bact ribosomal protein L1, bacterial/chloropl	99.86
PTZ00225	214	60S ribosomal protein L10a; Provisional	99.78
PRK04203	215	rpl1P 50S ribosomal protein L1P; Reviewed	99.77
PTZ00029	216	60S ribosomal protein L10a; Provisional	99.74
cd00403	208	Ribosomal_L1 Ribosomal protein L1. The L1 protein,	99.61
KOG1569	323	consensus 50S ribosomal protein L1 [Translation, r	99.5
PF00687	220	Ribosomal_L1: Ribosomal protein L1p/L10e family; I	99.41
KOG1570	218	consensus 60S ribosomal protein L10A [Translation,	97.67
KOG1685	343	consensus Uncharacterized conserved protein [Funct	97.48

>COG0081 RplA Ribosomal protein L1 [Translation, ribosomal structure and biogenesis]

Probab=99.89  E-value=2.8e-23  Score=152.40  Aligned_cols=62  Identities=44%  Similarity=0.716  Sum_probs=60.3

Q ss_pred             CCCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEeeh
Q 034832            1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSI   67 (82)
Q Consensus         1 ~Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~id~   67 (82)
                      +|+.|+||++||++||++|+|.||+.+++++|.+++|+++||+     ||+++||||||||||+|++
T Consensus       166 ~dk~g~ih~~iGk~sf~~e~L~eNi~a~l~~i~~~~p~~~kg~-----~ik~v~vstTMGP~v~v~~  227 (228)
T COG0081         166 ADKAGVIHVPIGKVSFDDEKLAENIEALLNAIVKAKPAGAKGQ-----YIKSVYVSTTMGPGVKVDL  227 (228)
T ss_pred             ECCCceEEEEecCCCCCHHHHHHHHHHHHHHHHHhCcCCcccc-----eEeEEEEecCCCCCEEecc
Confidence            5899999999999999999999999999999999999999999     9999999999999999985

>CHL00129 rpl1 ribosomal protein L1; Reviewed

Probab=99.88  E-value=7.9e-23  Score=149.55  Aligned_cols=65  Identities=43%  Similarity=0.655  Sum_probs=62.4

Q ss_pred             CCCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEeehhhH
Q 034832            1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSIQSL   70 (82)
Q Consensus         1 ~Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~id~~~~   70 (82)
                      +|+.|+||++||+++|++|||+||+.+++++|.+.+|++.||.     ||+++||||||||||+||+.++
T Consensus       164 ~dk~g~i~~~VG~~~m~~~~l~eNi~a~l~~i~~~~p~~~kg~-----~ik~v~issTMGp~v~i~~~~~  228 (229)
T CHL00129        164 ADKTGIVHVLFGKSNFTEEDLLENLQAIYESIEQNRPSGVKGK-----YWKSFYICSTMGPSIQIDISLL  228 (229)
T ss_pred             ecCCcEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhCcccccCc-----eEEEEEEECCCCCCEEeccccc
Confidence            4899999999999999999999999999999999999999998     9999999999999999998765

>PRK05424 rplA 50S ribosomal protein L1; Validated

Probab=99.87  E-value=5.2e-22  Score=145.04  Aligned_cols=65  Identities=43%  Similarity=0.646  Sum_probs=62.7

Q ss_pred             CCCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEeehhhH
Q 034832            1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSIQSL   70 (82)
Q Consensus         1 ~Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~id~~~~   70 (82)
                      +|+.|+||++||+++|++|||.||+.+++++|.+.+|.+.||+     ||+++|||||||||++||+.++
T Consensus       164 ~~k~g~i~~~IG~~~m~~e~i~eNi~a~l~~i~~~~p~~~kg~-----~Ik~v~lssTmGp~~~i~~~~~  228 (230)
T PRK05424        164 VDKAGIIHAPIGKVSFDAEKLKENLKALIDAIKKAKPATAKGT-----YIKSVSLSSTMGPGVKVDPSSL  228 (230)
T ss_pred             ecCCCEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhCccccCCC-----EEEEEEEECCCCCCEEechHHh
Confidence            4899999999999999999999999999999999999999998     9999999999999999999876

>TIGR01169 rplA_bact ribosomal protein L1, bacterial/chloroplast

Probab=99.86  E-value=5e-22  Score=144.92  Aligned_cols=64  Identities=41%  Similarity=0.712  Sum_probs=61.4

Q ss_pred             CCCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEeehhh
Q 034832            1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSIQS   69 (82)
Q Consensus         1 ~Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~id~~~   69 (82)
                      +|+.|+||++||+++|++|||.||+.+++++|.+.+|.+.||+     ||+++|||||||||++||+.+
T Consensus       163 ~~k~g~i~~~VG~~~m~~e~i~eNi~a~l~~i~~~~p~~~kg~-----~Ik~v~lssTmGp~~~i~~~~  226 (227)
T TIGR01169       163 ADKAGNIHASIGKVSFDSEKLKENLEALLDAIKKAKPSGAKGQ-----YIKNIALSSTMGPGIKVDLSS  226 (227)
T ss_pred             eCCCCEEEEEEecCCCCHHHHHHHHHHHHHHHHHhCccccCCC-----EEEEEEEECCCCCCEEeccCC
Confidence            4899999999999999999999999999999999999999998     999999999999999999864

This model describes bacterial (and chloroplast) ribosomal protein L1. The apparent mitochondrial L1 is sufficiently diverged to be the subject of a separate model.

>PTZ00225 60S ribosomal protein L10a; Provisional

Probab=99.78  E-value=3.2e-19  Score=129.39  Aligned_cols=58  Identities=26%  Similarity=0.265  Sum_probs=54.9

Q ss_pred             CCCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEe
Q 034832            1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPV   65 (82)
Q Consensus         1 ~Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~i   65 (82)
                      +|+.|++|++||+++|++|||+||+.|+++.|.+.+|.  +++     ||+++||||||||+++|
T Consensus       156 ~~k~~~~~~~VGk~~m~~e~i~eNi~a~l~~l~~~~p~--k~~-----nIksv~iktTMGp~~~~  213 (214)
T PTZ00225        156 LKKVLCLGTCVGHVEMTEEQLRQNVVMAINFLVSLLKK--NWQ-----NLKSAYIKSTMGKPQRI  213 (214)
T ss_pred             ecCccEEEeEEccCCCCHHHHHHHHHHHHHHHHHhCCc--CCc-----eEeEEEEECCCCCCEeC
Confidence            48999999999999999999999999999999999995  776     99999999999999985

>PRK04203 rpl1P 50S ribosomal protein L1P; Reviewed

Probab=99.77  E-value=1.1e-18  Score=126.03  Aligned_cols=59  Identities=27%  Similarity=0.407  Sum_probs=54.7

Q ss_pred             CCCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEee
Q 034832            1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVS   66 (82)
Q Consensus         1 ~Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~id   66 (82)
                      +|+.|++|++||+++|++|||+||+.+++++|.+.+|.+.+       ||+++|||||||||++|-
T Consensus       156 ~~k~~~i~v~VG~~~m~~e~l~eNi~avl~~i~~~~p~g~~-------~Iksi~lktTmgp~i~i~  214 (215)
T PRK04203        156 TKDQPTFHVRVGTEDMSPEELAENIDAVLNRIESKLEKGRQ-------NIKSVYVKTTMGPAVKVE  214 (215)
T ss_pred             eCCCCEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhCccccc-------cEEEEEEECCCCCCEEee
Confidence            37889999999999999999999999999999999997643       999999999999999984

>PTZ00029 60S ribosomal protein L10a; Provisional

Probab=99.74  E-value=4.8e-18  Score=123.04  Aligned_cols=57  Identities=28%  Similarity=0.416  Sum_probs=52.7

Q ss_pred             CCCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCC-CcccccccceEEEecCCCCceEe
Q 034832            1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKK-TSKFAGYVNSFHMCSTMGPSFPV   65 (82)
Q Consensus         1 ~Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg-~~~~~~~I~~v~lsSTMGPgi~i   65 (82)
                      +|+.|++|++||+++|++|||+||+.+++++|.+.+|   || .     ||+++||+||||||++|
T Consensus       158 ~~k~~~i~v~VG~~~~~~e~l~eNi~avl~~i~~~~~---kg~~-----~Iksv~lktTmgp~v~v  215 (216)
T PTZ00029        158 LKKVLCLGVAVGNVEMTEEQLRQNIVLSINFLVSLLK---KNWQ-----NIKTLHIKSTMGKPQRI  215 (216)
T ss_pred             ECCCCEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHhc---cccc-----cEeEEEEECCCCCCEeC
Confidence            4789999999999999999999999999999999886   44 3     99999999999999986

>cd00403 Ribosomal_L1 Ribosomal protein L1

Probab=99.61  E-value=1.7e-15  Score=107.00  Aligned_cols=58  Identities=41%  Similarity=0.631  Sum_probs=53.0

Q ss_pred             CCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEe
Q 034832            2 DNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPV   65 (82)
Q Consensus         2 Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~i   65 (82)
                      +++|+++++||+++|++|||+||+.+++++|....|. .++.     +|+++||+||||||+.|
T Consensus       151 ~~~~~~~v~VG~~~m~~~~l~eNi~~vi~~i~~~~~~-~~~~-----~i~~v~lktt~~~~lpI  208 (208)
T cd00403         151 DKGGCIHVPVGKVSMSPEQLVENIEAVINALVKKLPS-KKGQ-----NIKSIYLKTTMGPSLPI  208 (208)
T ss_pred             CCCCEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhCCc-ccCe-----EEEEEEEECCCCCCeEC
Confidence            5788999999999999999999999999999999995 3334     99999999999999975

The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds its own mRNA. Like several other large ribosomal subunit proteins, L1 displays RNA chaperone activity. L1 is one of the largest ribosomal proteins. It is composed of two domains that cycle between open and closed conformations via a hinge motion. The RNA-binding site of L1 is highly conserved, with both mRNA and rRNA binding the same binding site.

>KOG1569 consensus 50S ribosomal protein L1 [Translation, ribosomal structure and biogenesis]

Probab=99.50  E-value=4.1e-14  Score=107.83  Aligned_cols=64  Identities=19%  Similarity=0.321  Sum_probs=60.1

Q ss_pred             CCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEeehhhHH
Q 034832            2 DNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSIQSLS   71 (82)
Q Consensus         2 Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~id~~~~~   71 (82)
                      ++.+++|++||+++|++|||.+||.+++.++...+|. .+|.     ||.++.|+||||||+.||+..+.
T Consensus       246 ~~~~~~~~~vGkl~mt~e~i~~Ni~a~i~av~t~rp~-~~G~-----fv~ra~L~Ss~g~~i~l~i~p~i  309 (323)
T KOG1569|consen  246 ERENILQIKVGKLDMTSEQILANIQAVIAAVCTHRPK-ALGP-----FVVRALLRSSPGEGILLKIDPLI  309 (323)
T ss_pred             ccCceeeeeeeeecCCHHHHHHHHHHHHHHHHhcCCc-ccCc-----eeeeeEeecCCCCceeEeccccc
Confidence            5778999999999999999999999999999999998 7998     99999999999999999987663

>PF00687 Ribosomal_L1: Ribosomal protein L1p/L10e family; InterPro: IPR002143 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.41  E-value=5.1e-13  Score=94.78  Aligned_cols=54  Identities=28%  Similarity=0.415  Sum_probs=48.4

Q ss_pred             CCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhh-CCCCCCCCcccccccceEEEecCCCCc
Q 034832            2 DNTSNVHVGLGKVSLKEELLRENVGAFVNALLLA-KPAGLKKTSKFAGYVNSFHMCSTMGPS   62 (82)
Q Consensus         2 Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~-kp~~~Kg~~~~~~~I~~v~lsSTMGPg   62 (82)
                      ++.++++++||+++|+++||.||+.+++++|.+. .|.   |.    .+|+++||+||||||
T Consensus       166 ~~~~~~~v~VG~~~~~~~~i~eNi~~~i~~i~~~~~~~---g~----~~I~~i~ikst~s~~  220 (220)
T PF00687_consen  166 GKGGCISVKVGHLSMTDEQIVENIKAVIKAIVSKPLPK---GW----KNIKSIYIKSTMSPS  220 (220)
T ss_dssp             BTSSEEEEEEEETTSCHHHHHHHHHHHHHHHHHTTTSS---SS----GSEEEEEEEESSSEE
T ss_pred             ccCCeeecCccCCCCCHHHHHHHHHHHHHHHHHhhhcc---Cc----ceEEEEEEECCCCCC
Confidence            4789999999999999999999999999999999 443   33    289999999999997

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 L1 is the largest protein from the large ribosomal subunit. The L1 protein contains two domains: 2-layer alpha/beta domain and a 3-layer alpha/beta domain (interrupts the first domain). In Escherichia coli, L1 is known to bind to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L1. Algal and plant chloroplast L1. Cyanelle L1. Archaebacterial L1. Vertebrate L10A. Yeast SSM1. ; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3QOY_A 3BBO_D 1VSA_A 1VSP_A 2NOQ_G 3IZS_A 1S1I_A 3O5H_A 3O58_A 2WRL_C ....

>KOG1570 consensus 60S ribosomal protein L10A [Translation, ribosomal structure and biogenesis]

Probab=97.67  E-value=7.1e-05  Score=55.11  Aligned_cols=52  Identities=27%  Similarity=0.306  Sum_probs=43.3

Q ss_pred             eeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEe
Q 034832            7 VHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPV   65 (82)
Q Consensus         7 Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~i   65 (82)
                      ..++||-+.|++|+|.+||.--++.+.......-+       .++..++.|||||+.++
T Consensus       166 GavaVGhv~M~d~el~~nI~l~vnFlVSlLKknwQ-------Nvral~iKst~g~p~~l  217 (218)
T KOG1570|consen  166 LAVAVGHVGMTDEELVYNIHLAVNFLVSLLKKNWQ-------NVRALYIKSTMGKPQRL  217 (218)
T ss_pred             eeeeecCCCCCHHHHHHhhhhhhhhHHHHHhhccc-------chhheeeccCCCCceec
Confidence            67899999999999999998887777765433233       79999999999999875

>KOG1685 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.48  E-value=0.0001  Score=57.40  Aligned_cols=54  Identities=28%  Similarity=0.469  Sum_probs=48.8

Q ss_pred             ceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEe
Q 034832            5 SNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPV   65 (82)
Q Consensus         5 G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~i   65 (82)
                      -.+-+.+|.++++.++|.||+.++++.|....|.+.+       +|+++||.+.-+|++.|
T Consensus       205 ~~~~i~vg~l~~~~~~l~ENv~~vlk~l~e~~P~~~~-------~Irsl~lKt~~s~aLPl  258 (343)
T KOG1685|consen  205 TSSAIKVGHLGNTSEELAENVVAVLKGLSEILPGGWK-------NIRSLHLKTSRSPALPL  258 (343)
T ss_pred             ceeEEEeccccccHHHHHHHHHHHHHHHHHHccchHh-------HhHHHhhhccCCcccce
Confidence            3566789999999999999999999999988897666       89999999999999877

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	82
2ov7_A	137	50S ribosomal protein L1; 2.30A {Thermus thermophi	1e-16
2wwq_5	234	50S ribosomal protein L1; ribosomal protein, ribon	2e-16
3bbo_D	352	Ribosomal protein L1; large ribosomal subunit, spi	2e-16
3qoy_A	242	50S ribosomal protein L1; beta-alpha-beta, structu	3e-16
4f9t_A	229	50S ribosomal protein L1; rossman fold, RNA; HET:	8e-16
2ftc_A	189	Mitochondrial ribosomal protein L1; mitochondrial	6e-15
1i2a_A	219	50S ribosomal protein L1P; primary rRNA-binding pr	4e-14
3iz5_A	216	60S ribosomal protein L1 (L1P); eukaryotic ribosom	1e-13
2zkr_5	212	60S ribosomal protein L10A; protein-RNA complex, 6	2e-13
1mzp_A	217	50S ribosomal protein L1P; ribosome, RNA-protein c	4e-13
3o58_A	217	L10A, 60S ribosomal protein L1; ribosomal RNA and	1e-12

>2ov7_A 50S ribosomal protein L1; 2.30A {Thermus thermophilus} PDB: 2oum_A 2vpl_A Length = 137

 Score = 68.1 bits (167), Expect = 1e-16
 Identities = 25/68 (36%), Positives = 37/68 (54%), Gaps = 5/68 (7%)

Query: 2   DNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGP 61
           D T  +H  +GK S   E L +N+ AF+ AL   KP G K T     ++ S ++ +TMGP
Sbjct: 75  DKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGT-----FLRSVYVTTTMGP 129

Query: 62  SFPVSIQS 69
           S  ++  S
Sbjct: 130 SVRINPHS 137

>2wwq_5 50S ribosomal protein L1; ribosomal protein, ribonucleoprotein, nucleotide-binding, protein biosynthesis, translation, zinc-finger; HET: 5MU; 5.80A {Escherichia coli} PDB: 3fik_5 3izt_C* 3izu_C* 3j01_5 3j0t_C* 3j0w_C* 3j0y_C* 3j11_C* 3j12_C* 3j14_C* 3kcr_5 2rdo_9 2gya_2 2gyc_2 Length = 234

 Score = 69.6 bits (171), Expect = 2e-16
 Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 5/74 (6%)

Query: 2   DNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGP 61
           D    +H  +GKV    + L+EN+ A + AL  AKP   K       Y+    + +TMG 
Sbjct: 166 DKNGIIHTTIGKVDFDADKLKENLEALLVALKKAKPTQAKGV-----YIKKVSISTTMGA 220

Query: 62  SFPVSIQSLSRALD 75
              V    LS +++
Sbjct: 221 GVAVDQAGLSASVN 234

>3bbo_D Ribosomal protein L1; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 352

 Score = 70.7 bits (173), Expect = 2e-16
 Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 5/69 (7%)

Query: 2   DNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGP 61
           D T  VH+  GK++ +EE L  N+ A + ++   KP G K       Y  S H+ S+MGP
Sbjct: 280 DKTGIVHIPFGKLNFEEEDLLINLFATIKSVETNKPTGAKGV-----YWKSAHISSSMGP 334

Query: 62  SFPVSIQSL 70
           S  ++I+ +
Sbjct: 335 SIRLNIREM 343

>3qoy_A 50S ribosomal protein L1; beta-alpha-beta, structural constituent of ribosome, rRNA BI regulation of translation, translation, ribosomal RNA; 2.10A {Aquifex aeolicus} Length = 242

 Score = 68.9 bits (169), Expect = 3e-16
 Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 5/75 (6%)

Query: 2   DNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGP 61
           D   NVH+ +GK+S ++E L +N+ A ++A++ AKP G K       Y+ +  +  TM P
Sbjct: 170 DKAGNVHMPVGKISFEKEKLIDNLYAAIDAVVRAKPPGAKGQ-----YIKNMAVSLTMSP 224

Query: 62  SFPVSIQSLSRALDQ 76
           S  + I  + + L +
Sbjct: 225 SVKLDINEVLKKLQE 239

>4f9t_A 50S ribosomal protein L1; rossman fold, RNA; HET: MPD; 1.46A {Thermus thermophilus} PDB: 3u4m_A 1eg0_N 1vsp_A 2hgj_C 2hgq_C 2hgu_C 1vsa_A 4abs_C 3zvp_C 1zho_A 1ml5_c* 1yl3_C 1giy_C 2hw8_A 2j01_C 2j03_C 2jl6_C 2jl8_C 2om7_K* 2v47_C ... Length = 229

 Score = 67.7 bits (166), Expect = 8e-16
 Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 5/68 (7%)

Query: 2   DNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGP 61
           D T  +H  +GK S   E L +N+ AF+ AL   KP G K T     ++ S ++ + MGP
Sbjct: 167 DKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGT-----FLRSVYVTTAMGP 221

Query: 62  SFPVSIQS 69
           S  ++  S
Sbjct: 222 SVRINPHS 229

>2ftc_A Mitochondrial ribosomal protein L1; mitochondrial ribosome, large ribosomal subunit, ribosomal R ribosome; 12.10A {Bos taurus} Length = 189

 Score = 65.0 bits (159), Expect = 6e-15
 Identities = 9/70 (12%), Positives = 25/70 (35%), Gaps = 8/70 (11%)

Query: 2   DNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAG-YVNSFHMCSTMG 60
           +  + +   +  + +  + +  N+ A +N +   +P          G +V    + S+  
Sbjct: 126 ERENFLQTKIATLDMSSDQIAANLQAVINEVCRHRPLN-------LGPFVVRAFLRSSTS 178

Query: 61  PSFPVSIQSL 70
               + I  L
Sbjct: 179 EGLLLKIDPL 188

>1i2a_A 50S ribosomal protein L1P; primary rRNA-binding protein, translation repressor, ribosome; 1.85A {Methanocaldococcus jannaschii} SCOP: e.24.1.1 PDB: 1cjs_A 1u63_A 1dwu_A Length = 219

 Score = 63.2 bits (154), Expect = 4e-14
 Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 7/72 (9%)

Query: 1   MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
             +     V +G   + +E + +N+ A +N +      GL        ++   ++  TMG
Sbjct: 154 TRDKPYFQVLVGNEKMTDEQIVDNIEAVLNVVAKKYEKGLY-------HIKDAYVKLTMG 206

Query: 61  PSFPVSIQSLSR 72
           P+  V  +   +
Sbjct: 207 PAVKVKKEKAKK 218

>2zkr_5 60S ribosomal protein L10A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 212

 Score = 60.8 bits (148), Expect = 2e-13
 Identities = 11/66 (16%), Positives = 25/66 (37%), Gaps = 7/66 (10%)

Query: 1   MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
                  H  +G   +  E + +N+   +  L      G          +++ ++ +TMG
Sbjct: 154 SGERRTFHTRVGAEDMSAENIADNIDVILRRLHADLEKGPL-------NIDTVYVKTTMG 206

Query: 61  PSFPVS 66
           P+  V+
Sbjct: 207 PAMEVA 212

>1mzp_A 50S ribosomal protein L1P; ribosome, RNA-protein complex; 2.65A {Sulfolobus acidocaldarius} SCOP: e.24.1.1 PDB: 1pnu_5 1pny_5 1vor_7 1vou_7 1vow_7 1voy_7 1vp0_7 3e1b_Z 3e1d_Z Length = 217

 Score = 60.5 bits (147), Expect = 4e-13
 Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 8/65 (12%)

Query: 1   MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
             +   V V +G   +K E L EN  A +NA+                 + + ++ +TMG
Sbjct: 159 TKDQPQVQVFIGTEDMKPEDLAENAIAVLNAIENKAKVET--------NLRNIYVKTTMG 210

Query: 61  PSFPV 65
            +  V
Sbjct: 211 KAVKV 215

>3o58_A L10A, 60S ribosomal protein L1; ribosomal RNA and proteins, ribosome; 4.00A {Saccharomyces cerevisiae} PDB: 3izc_A 3izs_A 1s1i_A 3o5h_A 2noq_G 3j0l_B 3j0o_B 3j0p_B 3j0q_B 3jyw_A Length = 217

 Score = 59.0 bits (143), Expect = 1e-12
 Identities = 14/65 (21%), Positives = 28/65 (43%), Gaps = 7/65 (10%)

Query: 1   MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
           +     + V +G V ++E++L   +   VN  +       +        V S  + S+MG
Sbjct: 159 LKKVLCLAVAVGNVEMEEDVLVNQILMSVNFFVSLLKKNWQ-------NVGSLVVKSSMG 211

Query: 61  PSFPV 65
           P+F +
Sbjct: 212 PAFRL 216

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	82
2ov7_A	137	50S ribosomal protein L1; 2.30A {Thermus thermophi	99.92
3u42_A	229	50S ribosomal protein L1; rossmann fold, rRNA bind	99.9
2ftc_A	189	Mitochondrial ribosomal protein L1; mitochondrial	99.87
2wwq_5	234	50S ribosomal protein L1; ribosomal protein, ribon	99.87
3qoy_A	242	50S ribosomal protein L1; beta-alpha-beta, structu	99.86
3bbo_D	352	Ribosomal protein L1; large ribosomal subunit, spi	99.82
2zkr_5	212	60S ribosomal protein L10A; protein-RNA complex, 6	99.81
1mzp_A	217	50S ribosomal protein L1P; ribosome, RNA-protein c	99.8
3j21_A	216	50S ribosomal protein L1P; archaea, archaeal, KINK	99.8
1i2a_A	219	50S ribosomal protein L1P; primary rRNA-binding pr	99.78
3iz5_A	216	60S ribosomal protein L1 (L1P); eukaryotic ribosom	99.77
3o58_A	217	L10A, 60S ribosomal protein L1; ribosomal RNA and	99.7

>2ov7_A 50S ribosomal protein L1; 2.30A {Thermus thermophilus} PDB: 2oum_A 2vpl_A

Probab=99.92  E-value=2.4e-25  Score=151.76  Aligned_cols=63  Identities=38%  Similarity=0.593  Sum_probs=61.1

Q ss_pred             CCCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEeehh
Q 034832            1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSIQ   68 (82)
Q Consensus         1 ~Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~id~~   68 (82)
                      +||.|+||++||+++|++|||+||+.|++++|.+.+|.+.||+     ||+++|||||||||++||..
T Consensus        74 ~dk~~~ih~~VGk~sf~~e~L~eNi~a~i~~l~~~kp~~~kg~-----~ik~v~issTMGp~i~id~~  136 (137)
T 2ov7_A           74 NDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGT-----FLRSVYVTTTMGPSVRINPH  136 (137)
T ss_dssp             CCTTSEEEEEEEETTSCHHHHHHHHHHHHHHHHTTSCSSCCSC-----SEEEEEEEETTSCCEEBCTT
T ss_pred             ECCCCEEEEEEecCCCCHHHHHHHHHHHHHHHHHhCcccccCc-----eEEEEEEECCCCCCEEecCC
Confidence            5999999999999999999999999999999999999999999     99999999999999999974

>3u42_A 50S ribosomal protein L1; rossmann fold, rRNA binding, RNA binding; 1.35A {Thermus thermophilus} PDB: 3u56_A 3u4m_A 1eg0_N 1vsp_A 2hgj_C 2hgq_C 2hgu_C 1vsa_A 4f9t_A* 4abs_C 3zvp_C 1zho_A 1ml5_c* 1yl3_C 1giy_C 3umy_A 2hw8_A 2j01_C 2j03_C 2om7_K* ...

Probab=99.90  E-value=4.1e-24  Score=155.17  Aligned_cols=64  Identities=38%  Similarity=0.582  Sum_probs=61.6

Q ss_pred             CCCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEeehhh
Q 034832            1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSIQS   69 (82)
Q Consensus         1 ~Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~id~~~   69 (82)
                      +||.|+||++||+++|++|||.||+.+++++|.+.+|++.||+     ||+++||||||||||+||+.+
T Consensus       166 ~dk~g~i~~~IGk~~f~~e~L~eNi~a~i~~i~~~kp~~~kg~-----~ik~v~lssTmGp~i~id~~s  229 (229)
T 3u42_A          166 NDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGT-----FLRSVYVTTVMGPSVRINPHS  229 (229)
T ss_dssp             CCTTSEEEEEEEETTSCHHHHHHHHHHHHHHHHHTCCTTCCSC-----SEEEEEEECSSSCCEEBCTTC
T ss_pred             eCCCCeecccccCCCCCHHHHHHHHHHHHHHHHHhCccccCCC-----eEEEEEEECCCCcCeEeCCCC
Confidence            5899999999999999999999999999999999999999998     999999999999999999864

>2ftc_A Mitochondrial ribosomal protein L1; mitochondrial ribosome, large ribosomal subunit, ribosomal R ribosome; 12.10A {Bos taurus}

Probab=99.87  E-value=2.2e-22  Score=142.12  Aligned_cols=64  Identities=16%  Similarity=0.315  Sum_probs=60.9

Q ss_pred             CCCcc--eeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEeehhhH
Q 034832            1 MDNTS--NVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSIQSL   70 (82)
Q Consensus         1 ~Dk~G--~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~id~~~~   70 (82)
                      +||.|  ++|++||+++|++|||.||+.+++++|.+++|.+. |+     ||++++|||||||||+||+.++
T Consensus       123 ~~k~~~~~i~v~VG~~~~~~e~L~eNi~a~i~~l~~~~p~~~-g~-----~ik~v~lssTmgp~i~i~~~~l  188 (189)
T 2ftc_A          123 VDEERENFLQTKIATLDMSSDQIAANLQAVINEVCRHRPLNL-GP-----FVVRAFLRSSTSEGLLLKIDPL  188 (189)
T ss_pred             eccCCCcEEEEEEECCCCCHHHHHHHHHHHHHHHHHhCchhc-Cc-----cEEEEEEECCCCCCEEEehhhc
Confidence            47888  99999999999999999999999999999999988 88     9999999999999999998875

>2wwq_5 50S ribosomal protein L1; ribosomal protein, ribonucleoprotein, nucleotide-binding, protein biosynthesis, translation, zinc-finger; HET: 5MU; 5.80A {Escherichia coli} PDB: 3fik_5 3izt_C* 3izu_C* 3j01_5 3j0t_C* 3j0w_C* 3j0y_C* 3j11_C* 3j12_C* 3j14_C* 3kcr_5 2rdo_9 2gya_2 2gyc_2

Probab=99.87  E-value=1e-22  Score=148.16  Aligned_cols=67  Identities=33%  Similarity=0.509  Sum_probs=63.7

Q ss_pred             CCCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEeehhhHHH
Q 034832            1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSIQSLSR   72 (82)
Q Consensus         1 ~Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~id~~~~~~   72 (82)
                      +||.|+||++||+++|++|||.||+.+++++|.+.+|.+.||+     ||+++|||||||||++||+.++..
T Consensus       165 ~~k~~~i~v~VG~~~f~~e~L~eNi~a~i~~l~~~~p~~~kg~-----~Ik~v~lksTmgp~i~id~~~~~~  231 (234)
T 2wwq_5          165 NDKNGIIHTTIGKVDFDADKLKENLEALLVALKKAKPTQAKGV-----YIKKVSISTTMGAGVAVDQAGLSA  231 (234)
T ss_dssp             CSSSCEEEEEEEETTSCHHHHHHHHHHHHHHHHHSCCSSCCSC-----CEEEEEEEESSSCEEEESSSCCCS
T ss_pred             ecCCcEEEEEEcCCCCCHHHHHHHHHHHHHHHHHhCcccccCC-----eEEEEEEECCCCCCEEEehHHhhh
Confidence            5899999999999999999999999999999999999999998     999999999999999999887643

>3qoy_A 50S ribosomal protein L1; beta-alpha-beta, structural constituent of ribosome, rRNA BI regulation of translation, translation, ribosomal RNA; 2.10A {Aquifex aeolicus}

Probab=99.86  E-value=7.1e-22  Score=144.53  Aligned_cols=69  Identities=35%  Similarity=0.594  Sum_probs=65.1

Q ss_pred             CCCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEeehhhHHHHH
Q 034832            1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSIQSLSRAL   74 (82)
Q Consensus         1 ~Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~id~~~~~~~~   74 (82)
                      +||.|+||++||+++|++|||.||+.+++++|.+.+|.+.||+     ||+++|||||||||++||+..+...+
T Consensus       169 ~~k~~~i~v~VG~~~m~~e~L~eNi~a~i~~l~~~~p~~~kg~-----~Ik~v~lkSTmGp~i~i~~~~~~~~~  237 (242)
T 3qoy_A          169 VDKAGNVHMPVGKISFEKEKLIDNLYAAIDAVVRAKPPGAKGQ-----YIKNMAVSLTMSPSVKLDINEVLKKL  237 (242)
T ss_dssp             CCTTSEEEEEEEETTSCHHHHHHHHHHHHHHHHHTCCTTCCSC-----SEEEEEEEETTSCCEEBCHHHHHHHH
T ss_pred             ecCCcEEEEEecCCCCCHHHHHHHHHHHHHHHHHhCCcccCCc-----eEEEEEEECCCCCCEEEEhhHhChhh
Confidence            5899999999999999999999999999999999999988998     99999999999999999998885544

>3bbo_D Ribosomal protein L1; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=99.82  E-value=9.5e-21  Score=144.89  Aligned_cols=66  Identities=36%  Similarity=0.547  Sum_probs=62.0

Q ss_pred             CCCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEeehhhHH
Q 034832            1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSIQSLS   71 (82)
Q Consensus         1 ~Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~id~~~~~   71 (82)
                      +||.|+||++||+++|++|||.||+.+++++|.+.+|.+.||+     ||+++|||||||||++|+..++.
T Consensus       279 ~dK~g~ihv~VGk~sfs~EqL~ENI~Avi~~L~k~kP~~~KG~-----yIksv~LkSTMGPgi~I~~~~l~  344 (352)
T 3bbo_D          279 VDKTGIVHIPFGKLNFEEEDLLINLFATIKSVETNKPTGAKGV-----YWKSAHISSSMGPSIRLNIREML  344 (352)
T ss_dssp             CCSSCEECCCCEETTSCHHHHHHHHHHHHHHHHTTCCTTCCSC-----SEEEEECCBSSSCCCEECTTC--
T ss_pred             eCCCCEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhCcccccCc-----eEEEEEEECCCCCCEEEEhhhcc
Confidence            5899999999999999999999999999999999999999998     99999999999999999987763

>2zkr_5 60S ribosomal protein L10A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}

Probab=99.81  E-value=6.1e-20  Score=131.46  Aligned_cols=59  Identities=19%  Similarity=0.348  Sum_probs=55.3

Q ss_pred             CCCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEee
Q 034832            1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVS   66 (82)
Q Consensus         1 ~Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~id   66 (82)
                      +||.|++|++||+++|++|||.||+.+++++|.+.+|.+.  +     ||+++|||||||||++|+
T Consensus       154 ~~k~~~i~v~VG~~~~~~e~L~eNi~a~i~~l~~~~p~~~--~-----~ik~v~lksTmgp~i~i~  212 (212)
T 2zkr_5          154 SGERRTFHTRVGAEDMSAENIADNIDVILRRLHADLEKGP--L-----NIDTVYVKTTMGPAMEVA  212 (212)
T ss_dssp             CSSSSEEEEEEEETTSCHHHHHHHHHHHHHHHHTTTCCCT--T-----TEEEEEEEESSSCCEEC-
T ss_pred             ecCCCEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhCcccc--c-----cEEEEEEECCCCCCEECC
Confidence            5899999999999999999999999999999999999876  3     999999999999999985

>1mzp_A 50S ribosomal protein L1P; ribosome, RNA-protein complex; 2.65A {Sulfolobus acidocaldarius} SCOP: e.24.1.1 PDB: 1pnu_5 1pny_5 1vor_7 1vou_7 1vow_7 1voy_7 1vp0_7 3e1b_Z 3e1d_Z

Probab=99.80  E-value=1.2e-19  Score=130.42  Aligned_cols=58  Identities=28%  Similarity=0.284  Sum_probs=55.3

Q ss_pred             CCCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEee
Q 034832            1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVS   66 (82)
Q Consensus         1 ~Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~id   66 (82)
                      +|+.|++|++||+++|++|||+||+.+++++|.+.+|. .  +     ||+++|||||||||++||
T Consensus       159 ~~k~~~i~v~VG~~~~~~e~L~eNi~a~i~~l~~~~p~-~--~-----~ik~v~lksTmgp~i~i~  216 (217)
T 1mzp_A          159 TKDQPQVQVFIGTEDMKPEDLAENAIAVLNAIENKAKV-E--T-----NLRNIYVKTTMGKAVKVK  216 (217)
T ss_dssp             CSSSSEEEEEEEETTSCHHHHHHHHHHHHHHHHHHCCC-T--T-----TEEEEEEEETTSCCEECC
T ss_pred             ecCCCEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhCcc-c--h-----heEEEEEECCCCCCeeCC
Confidence            58999999999999999999999999999999999998 6  4     999999999999999987

>3j21_A 50S ribosomal protein L1P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=99.80  E-value=5.6e-20  Score=131.99  Aligned_cols=59  Identities=29%  Similarity=0.445  Sum_probs=55.6

Q ss_pred             CCCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEee
Q 034832            1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVS   66 (82)
Q Consensus         1 ~Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~id   66 (82)
                      +|+.|+||++||+++|++|||.||+.+++++|.+.+|.+.+       ||+++|||||||||++|+
T Consensus       157 ~~k~~~i~v~VG~~~~~~e~L~eNi~a~i~~l~~~~p~~~k-------~Iksi~lksTmgp~i~i~  215 (216)
T 3j21_A          157 LKNNPVVHAPVGTEKMSDEEIAENIEAVLNAIIGKLERGES-------QVKSVYVKTTMGPAVKIE  215 (216)
T ss_dssp             EETTTEEECCCEESSSCHHHHHHHHHHHHHHHHHSCCCSSC-------SEEEEEEEESSSCCEECC
T ss_pred             cCCCCEEEEEecCCCCCHHHHHHHHHHHHHHHHHhcccccc-------ceEEEEEECCCCCCEEcc
Confidence            37899999999999999999999999999999999998654       999999999999999987

>1i2a_A 50S ribosomal protein L1P; primary rRNA-binding protein, translation repressor, ribosome; 1.85A {Methanocaldococcus jannaschii} SCOP: e.24.1.1 PDB: 1cjs_A 1u63_A 1dwu_A

Probab=99.78  E-value=2.5e-19  Score=128.83  Aligned_cols=59  Identities=22%  Similarity=0.322  Sum_probs=55.2

Q ss_pred             CCCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEee
Q 034832            1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVS   66 (82)
Q Consensus         1 ~Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~id   66 (82)
                      +|+.|+||++||+++|++|||.||+.+++++|.+.+|.+.  +     ||+++|||||||||++|=
T Consensus       154 ~~k~~~i~v~VG~~~~~~e~L~eNi~a~i~~l~~~~p~~~--~-----~ik~v~lksTmgp~i~iy  212 (219)
T 1i2a_A          154 TRDKPYFQVLVGNEKMTDEQIVDNIEAVLNVVAKKYEKGL--Y-----HIKDAYVKLTMGPAVKVK  212 (219)
T ss_dssp             CTTSSEEEEEEEETTSCHHHHHHHHHHHHHHHHHHSTTGG--G-----GEEEEEEEETTSCCEECC
T ss_pred             ecCCCEEEEEEecCCCCHHHHHHHHHHHHHHHHHhCCccc--c-----ceEEEEEECCCCCCEEeE
Confidence            4889999999999999999999999999999999999765  3     999999999999999973

>3o58_A L10A, 60S ribosomal protein L1; ribosomal RNA and proteins, ribosome; 4.00A {Saccharomyces cerevisiae} PDB: 3izc_A 1s1i_A 3izs_A 3o5h_A 2noq_G 3j0l_B 3j0o_B 3j0p_B 3j0q_B 3jyw_A

Probab=99.70  E-value=7.7e-19  Score=125.91  Aligned_cols=58  Identities=24%  Similarity=0.363  Sum_probs=53.8

Q ss_pred             CCCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEe
Q 034832            1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPV   65 (82)
Q Consensus         1 ~Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~i   65 (82)
                      +|+.|++|++||+++|++|||+||+.+++++|.+.+|.  +++     ||+++|||||||||++|
T Consensus       159 ~~k~~~i~v~IG~~~~~~e~l~eNi~avi~~l~~~~pk--~~~-----~iksi~lksTmgp~i~i  216 (217)
T 3o58_A          159 LKKVLCLAVAVGNVEMEEDVLVNQILMSVNFFVSLLKK--NWQ-----NVGSLVVKSSMGPAFRL  216 (217)
T ss_dssp             CCSSSCCCCCCCSSSCCSHHHHHHHHHTCSTTTCCSSS--CSC-----CCSCCCCCSSSSCSCCC
T ss_pred             eCCCCEEEEeeccCCCCHHHHHHHHHHHHHHHHHhccc--CCc-----eEEEEEEECCCCCCEec
Confidence            48999999999999999999999999999999999985  345     99999999999999976

---

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	82
d1ad2a_	224	e.24.1.1 (A:) Ribosomal protein L1 {Thermus thermo	1e-13
d1i2aa_	212	e.24.1.1 (A:) Ribosomal protein L1 {Archaeon Metha	1e-10
d1mzpa_	217	e.24.1.1 (A:) Ribosomal protein L1 {Archaeon Sulfo	2e-10

>d1ad2a_ e.24.1.1 (A:) Ribosomal protein L1 {Thermus thermophilus [TaxId: 274]} Length = 224

class: Multi-domain proteins (alpha and beta)
fold: Ribosomal protein L1
superfamily: Ribosomal protein L1
family: Ribosomal protein L1
domain: Ribosomal protein L1
species: Thermus thermophilus [TaxId: 274]

 Score = 60.8 bits (147), Expect = 1e-13
 Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 5/69 (7%)

Query: 1   MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
            D T  +H  +GK     E L +N+ AF+ AL   KP G K T     ++ S ++ +TMG
Sbjct: 161 NDKTGAIHAPVGKACFPPEKLADNIRAFIRALEAHKPEGAKGT-----FLRSVYVTTTMG 215

Query: 61  PSFPVSIQS 69
           PS  ++  S
Sbjct: 216 PSVRINPHS 224

>d1i2aa_ e.24.1.1 (A:) Ribosomal protein L1 {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 212

class: Multi-domain proteins (alpha and beta)
fold: Ribosomal protein L1
superfamily: Ribosomal protein L1
family: Ribosomal protein L1
domain: Ribosomal protein L1
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 52.8 bits (126), Expect = 1e-10
 Identities = 13/65 (20%), Positives = 27/65 (41%), Gaps = 7/65 (10%)

Query: 1   MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
             +     V +G   + +E + +N+ A +N +      GL        ++   ++  TMG
Sbjct: 154 TRDKPYFQVLVGNEKMTDEQIVDNIEAVLNVVAKKYEKGLY-------HIKDAYVKLTMG 206

Query: 61  PSFPV 65
           P+  V
Sbjct: 207 PAVKV 211

>d1mzpa_ e.24.1.1 (A:) Ribosomal protein L1 {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]} Length = 217

class: Multi-domain proteins (alpha and beta)
fold: Ribosomal protein L1
superfamily: Ribosomal protein L1
family: Ribosomal protein L1
domain: Ribosomal protein L1
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

 Score = 52.0 bits (124), Expect = 2e-10
 Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 8/65 (12%)

Query: 1   MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
             +   V V +G   +K E L EN  A +NA        ++  +K    + + ++ +TMG
Sbjct: 159 TKDQPQVQVFIGTEDMKPEDLAENAIAVLNA--------IENKAKVETNLRNIYVKTTMG 210

Query: 61  PSFPV 65
            +  V
Sbjct: 211 KAVKV 215

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	82
d1ad2a_	224	Ribosomal protein L1 {Thermus thermophilus [TaxId:	99.88
d1mzpa_	217	Ribosomal protein L1 {Archaeon Sulfolobus acidocal	99.82
d1i2aa_	212	Ribosomal protein L1 {Archaeon Methanococcus janna	99.79

>d1ad2a_ e.24.1.1 (A:) Ribosomal protein L1 {Thermus thermophilus [TaxId: 274]}

class: Multi-domain proteins (alpha and beta)
fold: Ribosomal protein L1
superfamily: Ribosomal protein L1
family: Ribosomal protein L1
domain: Ribosomal protein L1
species: Thermus thermophilus [TaxId: 274]

Probab=99.88  E-value=2.7e-23  Score=147.68  Aligned_cols=64  Identities=38%  Similarity=0.584  Sum_probs=61.2

Q ss_pred             CCCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEeehhh
Q 034832            1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSIQS   69 (82)
Q Consensus         1 ~Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~id~~~   69 (82)
                      +||.|+||++||+++|++|||.||+.+++++|.+.+|.+.+|.     ||+++|||||||||++||..+
T Consensus       161 ~~k~g~i~~~IG~~~m~~e~i~eNi~~~i~~i~~~~p~~~k~~-----~ik~v~l~sTmGp~~~id~~s  224 (224)
T d1ad2a_         161 NDKTGAIHAPVGKACFPPEKLADNIRAFIRALEAHKPEGAKGT-----FLRSVYVTTTMGPSVRINPHS  224 (224)
T ss_dssp             CCTTSEEEEEEEETTSCHHHHHHHHHHHHHHHHTTCCTTCCSC-----SEEEEEEECTTSCCEEECTTC
T ss_pred             eCCCceeeeeeccccCCHHHHHHHHHHHHHHHHHhCccccCCC-----eEeEEEEECCCCCCEEeCCCC
Confidence            4899999999999999999999999999999999999999998     999999999999999999753

>d1mzpa_ e.24.1.1 (A:) Ribosomal protein L1 {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Multi-domain proteins (alpha and beta)
fold: Ribosomal protein L1
superfamily: Ribosomal protein L1
family: Ribosomal protein L1
domain: Ribosomal protein L1
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=99.82  E-value=1.4e-20  Score=133.23  Aligned_cols=58  Identities=28%  Similarity=0.296  Sum_probs=53.3

Q ss_pred             CCCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEee
Q 034832            1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVS   66 (82)
Q Consensus         1 ~Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~id   66 (82)
                      +|+.|+||++||+++|++|||.||+.+++++|....|   +++     ||+++||||||||||+||
T Consensus       159 ~~k~~~i~~~IG~~~m~~e~L~eNi~a~i~~i~~~~~---~~~-----~Ik~v~iksTmGp~i~i~  216 (217)
T d1mzpa_         159 TKDQPQVQVFIGTEDMKPEDLAENAIAVLNAIENKAK---VET-----NLRNIYVKTTMGKAVKVK  216 (217)
T ss_dssp             CSSSSEEEEEEEETTSCHHHHHHHHHHHHHHHHHHCC---CTT-----TEEEEEEEETTSCCEECC
T ss_pred             cccceEEEEeecccCCCHHHHHHHHHHHHHHHHhccc---cCC-----cEEEEEEECCCCCCEecC
Confidence            4889999999999999999999999999999987644   455     999999999999999997

>d1i2aa_ e.24.1.1 (A:) Ribosomal protein L1 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Multi-domain proteins (alpha and beta)
fold: Ribosomal protein L1
superfamily: Ribosomal protein L1
family: Ribosomal protein L1
domain: Ribosomal protein L1
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.79  E-value=9.6e-20  Score=128.00  Aligned_cols=57  Identities=19%  Similarity=0.248  Sum_probs=52.3

Q ss_pred             CCcceeeeeeecCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCcccccccceEEEecCCCCceEe
Q 034832            2 DNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPV   65 (82)
Q Consensus         2 Dk~G~Ih~~IGk~sF~~e~L~eNi~avl~aI~~~kp~~~Kg~~~~~~~I~~v~lsSTMGPgi~i   65 (82)
                      ++.|+||++||+++|++|||.||+.+++++|.+.+|.   |.    .+|+++||||||||||+|
T Consensus       155 ~~~~~i~~~IG~~~m~~e~i~eNi~a~~~~i~~~~pk---g~----~~Ik~v~lssTmgp~~~i  211 (212)
T d1i2aa_         155 RDKPYFQVLVGNEKMTDEQIVDNIEAVLNVVAKKYEK---GL----YHIKDAYVKLTMGPAVKV  211 (212)
T ss_dssp             TTSSEEEEEEEETTSCHHHHHHHHHHHHHHHHHHSTT---GG----GGEEEEEEEETTSCCEEC
T ss_pred             cCCceEEEeeeeccCCHHHHHHHHHHHHHHHHhhCcC---Cc----eeEEEEEEECCCCCCEec
Confidence            6789999999999999999999999999999999884   44    169999999999999987