Citrus Sinensis ID: 047111

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100------
Protein Sequence
MSREFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKVHGK
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHccEEEEEEcccccccccccccccccccccccHHHHHHHHHHHHcEEEcccccccccccccccEEEEccccccccccccccEEEEEEEEEEcc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHEEEEcccccccccccccccEEEccccHHHHHHHHHHHcccEEcccccccccccHEccEEEEccccccccccccccEEEEEEEEEEcc
Coil and Loop (DISEMBL)
MSREFEKAARRLENARLVLRrfpnieklrsreskddpielcspvtKEELVAKVASQLSisiepeylhlpsplsafgeyevpmrlsktiplpegkvqwtfNVKVHGK
Flexible Loop (DISEMBL)
MSREFEKAARrlenarlvlrrfpnieklrsreskddpielcspvtKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPMRLSKtiplpegkvqwtfnvkvhgk
Low Complexity Region (SEG)
MSREFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKVHGK
Disordered region (IsUnstruct)
*****************VL*********************C**VTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVK****
Disordered Region (DISOPRED)
*********RRLENARLVLRRFPNIE************ELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKVH**
Disordered Region (DISEMBL)
********ARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKVHGK
Disordered Region (DISPRO)
MSREFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKVHG*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSREFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKVHGK
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

No hits with e-value below 0.001 by BLAST

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	106
255634861	222	unknown [Glycine max]	1.0	0.477	0.613	3e-31
356517474	222	PREDICTED: 50S ribosomal protein L9-like	1.0	0.477	0.613	3e-31
356571485	222	PREDICTED: 50S ribosomal protein L9-like	1.0	0.477	0.613	3e-31
356558761	222	PREDICTED: 50S ribosomal protein L9-like	1.0	0.477	0.594	7e-31
255645711	150	unknown [Glycine max]	1.0	0.706	0.594	7e-31
224118314	219	predicted protein [Populus trichocarpa]	0.981	0.474	0.576	3e-29
388493818	222	unknown [Lotus japonicus]	1.0	0.477	0.594	3e-29
224146953	219	predicted protein [Populus trichocarpa]	0.981	0.474	0.567	4e-29
224115542	219	predicted protein [Populus trichocarpa]	0.981	0.474	0.567	7e-29
449456985	218	PREDICTED: 50S ribosomal protein L9-like	0.981	0.477	0.596	2e-27

>gi|255634861|gb|ACU17789.1| unknown [Glycine max]

 Score =  139 bits (349), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 65/106 (61%), Positives = 85/106 (80%)

Query: 1   MSREFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSIS 60
           M +E+EKAA RL+ A+LVLRR  N++K +SRESK+DP+EL  PVTK+ LVA+VA QL ++
Sbjct: 117 MMKEYEKAALRLDKAQLVLRRLINVQKAKSRESKEDPLELRYPVTKDTLVAEVARQLCVN 176

Query: 61  IEPEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKVHGK 106
           + P+ LHLPSPLS  GEYEVP+R+ ++IPLPEGKV W+  VKV  K
Sbjct: 177 VAPDNLHLPSPLSTLGEYEVPLRIPRSIPLPEGKVNWSLKVKVRSK 222

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356517474|ref|XP_003527412.1| PREDICTED: 50S ribosomal protein L9-like isoform 1 [Glycine max] gi|356517476|ref|XP_003527413.1| PREDICTED: 50S ribosomal protein L9-like isoform 2 [Glycine max]

 Score =  139 bits (349), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 65/106 (61%), Positives = 85/106 (80%)

Query: 1   MSREFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSIS 60
           M +E+EKAA RL+ A+LVLRR  N++K +SRESK+DP+EL  PVTK+ LVA+VA QL ++
Sbjct: 117 MMKEYEKAALRLDKAQLVLRRLINVQKAKSRESKEDPLELRYPVTKDTLVAEVARQLCVN 176

Query: 61  IEPEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKVHGK 106
           + P+ LHLPSPLS  GEYEVP+R+ ++IPLPEGKV W+  VKV  K
Sbjct: 177 VAPDNLHLPSPLSTLGEYEVPLRIPRSIPLPEGKVNWSLKVKVRSK 222

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356571485|ref|XP_003553907.1| PREDICTED: 50S ribosomal protein L9-like [Glycine max]

 Score =  138 bits (348), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 65/106 (61%), Positives = 85/106 (80%)

Query: 1   MSREFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSIS 60
           M +E+EKAA RL+ A+LVLRR  N++K +SRESK+DP+EL  PVTK+ LVA+VA QL ++
Sbjct: 117 MMKEYEKAALRLDKAKLVLRRLINVQKAKSRESKEDPLELRYPVTKDILVAEVARQLCVN 176

Query: 61  IEPEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKVHGK 106
           + P+ LHLPSPLS  GEYEVP+RL ++IPLPEGKV W+  VK+  K
Sbjct: 177 VAPDNLHLPSPLSTLGEYEVPLRLPRSIPLPEGKVNWSLKVKIRSK 222

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356558761|ref|XP_003547671.1| PREDICTED: 50S ribosomal protein L9-like [Glycine max]

 Score =  137 bits (346), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 63/106 (59%), Positives = 85/106 (80%)

Query: 1   MSREFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSIS 60
           M +E+EKAA RL+ A+LVLRR  N++K +SRESKDDP+EL  PVTK+ LVA+V+ Q+ ++
Sbjct: 117 MMKEYEKAALRLDKAKLVLRRLINVQKAKSRESKDDPLELRYPVTKDILVAEVSRQICVN 176

Query: 61  IEPEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKVHGK 106
           + P+ LHLPSPL+  GEYEVP+RL ++IPLPEGKV W+  VK+  K
Sbjct: 177 VAPDNLHLPSPLATLGEYEVPLRLPRSIPLPEGKVNWSLKVKIRSK 222

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255645711|gb|ACU23349.1| unknown [Glycine max]

 Score =  137 bits (345), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 63/106 (59%), Positives = 85/106 (80%)

Query: 1   MSREFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSIS 60
           M +E+EKAA RL+ A+LVLRR  N++K +SRESKDDP+EL  PVTK+ LVA+V+ Q+ ++
Sbjct: 45  MMKEYEKAALRLDKAKLVLRRLINVQKAKSRESKDDPLELRYPVTKDILVAEVSRQICVN 104

Query: 61  IEPEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKVHGK 106
           + P+ LHLPSPL+  GEYEVP+RL ++IPLPEGKV W+  VK+  K
Sbjct: 105 VAPDNLHLPSPLATLGEYEVPLRLPRSIPLPEGKVNWSLKVKIRSK 150

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224118314|ref|XP_002317788.1| predicted protein [Populus trichocarpa] gi|222858461|gb|EEE96008.1| predicted protein [Populus trichocarpa]

 Score =  132 bits (332), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 60/104 (57%), Positives = 79/104 (75%)

Query: 3   REFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIE 62
           +E+E AA+R   ARL  R   N  K RSRESKDDPIE+ SPVTK++++ +V  Q ++ IE
Sbjct: 116 KEYETAAKRFVKARLAFRVGINTAKFRSRESKDDPIEILSPVTKDDILKEVTRQFNVQIE 175

Query: 63  PEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKVHGK 106
           P+ +HLPSPL+A GE+EVP+R  K+IPLPEGKV+WT  VK+ GK
Sbjct: 176 PDNVHLPSPLTALGEFEVPLRFPKSIPLPEGKVKWTLQVKIRGK 219

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388493818|gb|AFK34975.1| unknown [Lotus japonicus]

 Score =  132 bits (331), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 63/106 (59%), Positives = 83/106 (78%)

Query: 1   MSREFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSIS 60
           + +E+E AA RL+ A+LVLRR  +++K ++R SKD+P+E+  PVTKE LVA+VA QL ++
Sbjct: 117 LMKEYEAAALRLDKAKLVLRRLIDVKKAKARASKDEPLEIRLPVTKEVLVAEVARQLCVN 176

Query: 61  IEPEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKVHGK 106
           I PE LHLPSPLS  GEYEVP+RL ++IPLPEGKV W+  VKV  K
Sbjct: 177 IAPENLHLPSPLSTVGEYEVPLRLPRSIPLPEGKVNWSLQVKVRSK 222

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224146953|ref|XP_002336372.1| predicted protein [Populus trichocarpa] gi|222834835|gb|EEE73284.1| predicted protein [Populus trichocarpa]

 Score =  132 bits (331), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 59/104 (56%), Positives = 80/104 (76%)

Query: 3   REFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIE 62
           +E+E AA+RL  ARL  R   N  K R+RESKDDPIE+ SPVTK++++ +V  Q ++ IE
Sbjct: 116 KEYETAAKRLVKARLAFRVGINTAKFRARESKDDPIEILSPVTKDDILKEVTRQFNVQIE 175

Query: 63  PEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKVHGK 106
           P+ +HLPSPL+A GE+EVP+R  K+IP+PEGKV+WT  VK+ GK
Sbjct: 176 PDNVHLPSPLTALGEFEVPLRFPKSIPMPEGKVKWTLKVKIRGK 219

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224115542|ref|XP_002332160.1| predicted protein [Populus trichocarpa] gi|222875210|gb|EEF12341.1| predicted protein [Populus trichocarpa]

 Score =  130 bits (328), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 59/104 (56%), Positives = 80/104 (76%)

Query: 3   REFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIE 62
           +E+E AA+RL  A+L  R   N  K R+RESKDDPIE+ SPVTK++++ +V  Q ++ IE
Sbjct: 116 KEYETAAKRLVKAQLAFRVGINTAKFRARESKDDPIEILSPVTKDDILKEVTRQFNVQIE 175

Query: 63  PEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKVHGK 106
           P+ +HLPSPL+A GE+EVP+R  K+IPLPEGKV+WT  VK+ GK
Sbjct: 176 PDNVHLPSPLTALGEFEVPLRFPKSIPLPEGKVKWTLKVKIRGK 219

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449456985|ref|XP_004146229.1| PREDICTED: 50S ribosomal protein L9-like [Cucumis sativus] gi|449517603|ref|XP_004165835.1| PREDICTED: 50S ribosomal protein L9-like [Cucumis sativus]

 Score =  126 bits (316), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 62/104 (59%), Positives = 80/104 (76%)

Query: 3   REFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIE 62
           +E+EKAARRL++ +LVLRR  + EK R+R +KD+P+ L S VT +++VA+VA Q S+ I 
Sbjct: 115 KEYEKAARRLDSKQLVLRRLIDKEKFRTRAAKDEPLALQSSVTVDDIVAEVARQFSVQIA 174

Query: 63  PEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKVHGK 106
           PE L+L SPLSA GEYEVP+R  K+IPLPEGKV WT  VKV  K
Sbjct: 175 PENLNLASPLSACGEYEVPLRFPKSIPLPEGKVYWTLKVKVRSK 218

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	106
TAIR|locus:2168377	221	AT5G53070 [Arabidopsis thalian	0.981	0.470	0.538	7.3e-27

TAIR|locus:2168377 AT5G53070 [Arabidopsis thaliana (taxid:3702)]

 Score = 302 (111.4 bits), Expect = 7.3e-27, P = 7.3e-27
 Identities = 56/104 (53%), Positives = 79/104 (75%)

Query:     2 SREFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISI 61
             ++E+EKAA+RL NA LVLR+  + EK ++R SKDD  ++ +P+TKEE+V++VA QL + I
Sbjct:   117 TKEYEKAAKRLANANLVLRKLVDKEKFKNRSSKDDKPDVQTPITKEEIVSEVARQLCVKI 176

Query:    62 EPEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKVHG 105
             +P+ + L +PL  FGEYEVP++  KTIPLP+G VQW   VKV G
Sbjct:   177 DPDNVVLAAPLETFGEYEVPLKFPKTIPLPQGTVQWILKVKVRG 220


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        0.316   0.133   0.378    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      106       106   0.00091  102 3  11 22  0.45    30
                                                     29  0.39    32


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  565 (60 KB)
  Total size of DFA:  112 KB (2074 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:  13.14u 0.10s 13.24t   Elapsed:  00:00:00
  Total cpu time:  13.14u 0.10s 13.24t   Elapsed:  00:00:00
  Start:  Fri May 10 17:22:26 2013   End:  Fri May 10 17:22:26 2013

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:0042254 "ribosome biogenesis" evidence=ISS

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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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	106
PF03948	87	Ribosomal_L9_C: Ribosomal protein L9, C-terminal d	99.92
CHL00160	153	rpl9 ribosomal protein L9; Provisional	99.84
TIGR00158	148	L9 ribosomal protein L9. Ribosomal protein L9 appe	99.83
PRK00137	147	rplI 50S ribosomal protein L9; Reviewed	99.82
COG0359	148	RplI Ribosomal protein L9 [Translation, ribosomal	99.8
PRK14538	838	putative bifunctional signaling protein/50S riboso	99.71
KOG4607	222	consensus Mitochondrial ribosomal protein L9 [Tran	88.27
PF10045	104	DUF2280: Uncharacterized conserved protein (DUF228	86.64

>PF03948 Ribosomal_L9_C: Ribosomal protein L9, C-terminal domain; InterPro: IPR020069 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.92  E-value=1.5e-24  Score=147.38  Aligned_cols=85  Identities=28%  Similarity=0.473  Sum_probs=79.4

Q ss_pred             hHHHHHHHhhhccceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEEEE
Q 047111            3 REFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPM   82 (106)
Q Consensus         3 ~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V~I   82 (106)
                      +|++..+.+|++-.|.+.+-.+..-           +||||||++||+++|++++|++|||++|.+++|||++|+|+|.|
T Consensus         2 ~~A~~l~~~l~~~~l~i~~k~g~~g-----------klfGSVt~~dIa~~l~~~~g~~Idk~~I~l~~~IK~~G~~~v~v   70 (87)
T PF03948_consen    2 AEAQALAEKLEGITLTIKRKAGENG-----------KLFGSVTSKDIAKALKEQTGIEIDKKKIELPEPIKSLGEYEVKV   70 (87)
T ss_dssp             HHHHHHHHHHCSSEEEEEECBSSCS-----------SBSSEBSHHHHHHHHHHCCSSSSSSSSBCSSSTBESSEEEEEEE
T ss_pred             HHHHHHHHHhcCCEEEEEEEecCCc-----------ceecCcCHHHHHHHHHHhhCCeEeccEEECCCchhccEEEEEEE
Confidence            5889999999999999999887443           89999999999999999999999999999999999999999999


Q ss_pred             EecCCCCCCCCcEEEEEEEEEEe
Q 047111           83 RLSKTIPLPEGKVQWTFNVKVHG  105 (106)
Q Consensus        83 kLh~~Vp~p~gkV~~~lkV~V~~  105 (106)
                      +||++       |+++|+|.|..
T Consensus        71 ~L~~~-------V~a~i~v~V~~   86 (87)
T PF03948_consen   71 KLHPE-------VSAKIKVNVVA   86 (87)
T ss_dssp             EEETT-------EEEEEEEEEEE
T ss_pred             EeCCC-------eEEEEEEEEEe
Confidence            99999       59999999974

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 L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....

>CHL00160 rpl9 ribosomal protein L9; Provisional

Probab=99.84  E-value=1.2e-20  Score=140.36  Aligned_cols=84  Identities=17%  Similarity=0.394  Sum_probs=71.7

Q ss_pred             hHHHHHHHhhhcc-ceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEEE
Q 047111            3 REFEKAARRLENA-RLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVP   81 (106)
Q Consensus         3 ~~~~~~~~~l~~~-~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V~   81 (106)
                      .|++..+..|++- .+.+++-..           +.-+||||||++||+++|++|+|++|||++|.|++ ||++|+|+|.
T Consensus        68 ~~a~~la~~l~~~~~~~i~~k~g-----------e~gklfGSVt~~dIa~~l~~~~g~~idk~~I~l~~-Ik~~G~~~v~  135 (153)
T CHL00160         68 EKCLKVKQLLEEIQKFSVKKKVG-----------ENNQIFGSVTEKEISQIIKNKTNIDLEKQNIELPE-IKTIGIYNIE  135 (153)
T ss_pred             HHHHHHHHHhhCCceEEEEEEeC-----------CCCeEEcccCHHHHHHHHHHhhCCccccceeehhh-ccccEeEEEE
Confidence            3456666777776 366665555           44599999999999999998999999999999988 9999999999


Q ss_pred             EEecCCCCCCCCcEEEEEEEEEEe
Q 047111           82 MRLSKTIPLPEGKVQWTFNVKVHG  105 (106)
Q Consensus        82 IkLh~~Vp~p~gkV~~~lkV~V~~  105 (106)
                      |+||++|       +++|+|.|+.
T Consensus       136 v~L~~~V-------~a~i~v~V~~  152 (153)
T CHL00160        136 IKLTSDV-------KANINLQILP  152 (153)
T ss_pred             EEecCCc-------EEEEEEEEEE
Confidence            9999995       9999999974

>TIGR00158 L9 ribosomal protein L9

Probab=99.83  E-value=2.9e-20  Score=137.26  Aligned_cols=84  Identities=17%  Similarity=0.256  Sum_probs=70.8

Q ss_pred             hHHHHHHHhhhccceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCCCC-CccceeEEEE
Q 047111            3 REFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSP-LSAFGEYEVP   81 (106)
Q Consensus         3 ~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~p-IKslGey~V~   81 (106)
                      .+++..+..|++-.+.+.+-...           .-+||||||++||+++|+++ |++|||++|.|++| ||++|+|+|+
T Consensus        63 ~~a~~l~~~l~~~~~~i~~k~ge-----------~gklfGSVt~~~I~~~l~~~-g~~idk~~I~l~~~~Ik~~G~y~v~  130 (148)
T TIGR00158        63 AAAARLKEVLELGTLTISKKVGD-----------EGKLFGSITTKQIADALKAA-GLDLDKKKIELPDGVIRTTGEHEVT  130 (148)
T ss_pred             HHHHHHHHHhcCcEEEEEEEeCC-----------CCeEEEeECHHHHHHHHHHc-CCcccHhhEECCCCceeceEEEEEE
Confidence            34556667777766666665543           34999999999999999866 99999999999996 9999999999


Q ss_pred             EEecCCCCCCCCcEEEEEEEEEEe
Q 047111           82 MRLSKTIPLPEGKVQWTFNVKVHG  105 (106)
Q Consensus        82 IkLh~~Vp~p~gkV~~~lkV~V~~  105 (106)
                      |+||++|       +++|+|.|..
T Consensus       131 i~L~~~V-------~a~i~v~V~~  147 (148)
T TIGR00158       131 IKLHEEV-------FAVLKVIVVP  147 (148)
T ss_pred             EEEcCCc-------EEEEEEEEEE
Confidence            9999995       9999999974

Ribosomal protein L9 appears to be universal in, but restricted to, eubacteria and chloroplast.

>PRK00137 rplI 50S ribosomal protein L9; Reviewed

Probab=99.82  E-value=5.9e-20  Score=135.00  Aligned_cols=84  Identities=29%  Similarity=0.498  Sum_probs=74.9

Q ss_pred             hHHHHHHHhhhccceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEEEE
Q 047111            3 REFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPM   82 (106)
Q Consensus         3 ~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V~I   82 (106)
                      .++++.+..|++..|.+++-.+           ++.+||||||++||+++|+++ |++|||++|.+++|||++|+|+|+|
T Consensus        63 ~~a~~l~~~l~~~~l~i~~k~g-----------~~gklfGsVt~~~I~~~l~~~-g~~idk~~I~l~~~Ik~~G~y~v~i  130 (147)
T PRK00137         63 AEAEALAEKLEGLTVTIKAKAG-----------EDGKLFGSVTTKDIAEALKKQ-GIEIDKRKIELPGPIKTLGEYEVPV  130 (147)
T ss_pred             HHHHHHHHHhhCCEEEEEEEcC-----------CCCeEEeeeCHHHHHHHHHHc-CCccCHHHeECCCcccccEEEEEEE
Confidence            5677788889988887776655           445999999999999999877 9999999999999999999999999


Q ss_pred             EecCCCCCCCCcEEEEEEEEEEe
Q 047111           83 RLSKTIPLPEGKVQWTFNVKVHG  105 (106)
Q Consensus        83 kLh~~Vp~p~gkV~~~lkV~V~~  105 (106)
                      +||++|       +++|+|.|..
T Consensus       131 ~L~~~v-------~a~l~v~V~~  146 (147)
T PRK00137        131 KLHPEV-------TATIKVNVVA  146 (147)
T ss_pred             EECCCc-------EEEEEEEEEE
Confidence            999995       9999999974

>COG0359 RplI Ribosomal protein L9 [Translation, ribosomal structure and biogenesis]

Probab=99.80  E-value=2.6e-19  Score=133.62  Aligned_cols=83  Identities=20%  Similarity=0.337  Sum_probs=69.6

Q ss_pred             HHHHHHHhhhccceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEEEEE
Q 047111            4 EFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPMR   83 (106)
Q Consensus         4 ~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V~Ik   83 (106)
                      +++.-...|+...+.+..-...+           -+||||||++||+++++++ |++|||++|.++++||++|+|+|+|+
T Consensus        64 ~a~~lk~~Le~~~~~i~~kag~~-----------GklfGSVt~~dIa~~l~~~-g~~idk~~i~l~~~ik~~G~~~V~vk  131 (148)
T COG0359          64 EAEALKEKLEGKTVEIAVKAGED-----------GKLFGSVTSKDIAEALKAA-GFKLDKRKIRLPNGIKTLGEHEVEVK  131 (148)
T ss_pred             HHHHHHHHhhCceEEEEEEcCCC-----------CceeccccHHHHHHHHHHc-CCCcchheeEcCchhhhcceeEEEEE
Confidence            44455556666546665555432           5999999999999999987 99999999999999999999999999


Q ss_pred             ecCCCCCCCCcEEEEEEEEEEe
Q 047111           84 LSKTIPLPEGKVQWTFNVKVHG  105 (106)
Q Consensus        84 Lh~~Vp~p~gkV~~~lkV~V~~  105 (106)
                      ||++|       +++++|.|..
T Consensus       132 Lh~eV-------~a~v~v~V~~  146 (148)
T COG0359         132 LHEEV-------TATVKVNVVA  146 (148)
T ss_pred             ecCce-------EEEEEEEEEe
Confidence            99995       9999999974

>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional

Probab=99.71  E-value=3e-17  Score=146.90  Aligned_cols=84  Identities=19%  Similarity=0.285  Sum_probs=74.2

Q ss_pred             hHHHHHHHhhhccceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEEEE
Q 047111            3 REFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPM   82 (106)
Q Consensus         3 ~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V~I   82 (106)
                      ++++..+..|+.-.|.+.+-..+.-           +||||||++||+++|++++|++||||+|.|++|||++|+|+|.|
T Consensus       750 ~~a~~l~~~l~~~~~~i~~k~ge~g-----------klfGSVt~~~I~~~l~~~~g~~idk~~I~l~~~Ik~~G~~~v~i  818 (838)
T PRK14538        750 LLMKKLKSEIDNKKITLDIQLGPKG-----------KIYGKITLKQIVEEFHKIHNITIDRKKISLENEIISVGIYPVDV  818 (838)
T ss_pred             HHHHHHHHHhhCcEEEEEEEeCCCC-----------eeeeccCHHHHHHHHHHhhCCccccceeeCCCcccccEEEEEEE
Confidence            3456667778877777777776444           99999999999999998999999999999999999999999999


Q ss_pred             EecCCCCCCCCcEEEEEEEEEE
Q 047111           83 RLSKTIPLPEGKVQWTFNVKVH  104 (106)
Q Consensus        83 kLh~~Vp~p~gkV~~~lkV~V~  104 (106)
                      +||++|       +++|+|.|.
T Consensus       819 ~L~~~V-------~a~i~v~V~  833 (838)
T PRK14538        819 FLTDQI-------KATFFLNVI  833 (838)
T ss_pred             EEcCCe-------EEEEEEEEE
Confidence            999995       999999987

>KOG4607 consensus Mitochondrial ribosomal protein L9 [Translation, ribosomal structure and biogenesis]

Probab=88.27  E-value=0.46  Score=38.21  Aligned_cols=56  Identities=16%  Similarity=0.271  Sum_probs=47.5

Q ss_pred             eecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEEEEEecCCCCCCCCcEEEEEEEEEE
Q 047111           41 CSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPMRLSKTIPLPEGKVQWTFNVKVH  104 (106)
Q Consensus        41 FGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V~IkLh~~Vp~p~gkV~~~lkV~V~  104 (106)
                      |++|+++.....+-+++-+.+||+-|..|. ++.-|+|...|++++++       ++-++..|+
T Consensus       138 ~~~V~~~l~~gv~~~~~t~~l~k~~vs~P~-~k~e~~~~~~V~in~~~-------~vr~~~~v~  193 (222)
T KOG4607|consen  138 PNLVKASLRKGVIVAELTIKLDKELVSGPI-TKEEGEYICEVKINPDV-------TVRVKIRVT  193 (222)
T ss_pred             HHHHHHHHhcceEeccccccCcccccCCCc-ccccceEEEEEEECCcc-------eEEeeeeee
Confidence            789999988888888889999999998765 77888999999999995       777776654

>PF10045 DUF2280: Uncharacterized conserved protein (DUF2280); InterPro: IPR018738 This entry is represented by Burkholderia phage Bups phi1, Orf2

Probab=86.64  E-value=0.26  Score=35.55  Aligned_cols=33  Identities=18%  Similarity=0.298  Sum_probs=29.2

Q ss_pred             CHHHHHHHHHhhcCCccccccccCCCCCcccee
Q 047111           45 TKEELVAKVASQLSISIEPEYLHLPSPLSAFGE   77 (106)
Q Consensus        45 TtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGe   77 (106)
                      |+.++++++++++|++|++..++.-+|=|.-|.
T Consensus        21 TPs~v~~aVk~eFgi~vsrQqve~yDPTK~aG~   53 (104)
T PF10045_consen   21 TPSEVAEAVKEEFGIDVSRQQVESYDPTKRAGR   53 (104)
T ss_pred             CHHHHHHHHHHHhCCccCHHHHHHcCchHHHHH
Confidence            789999999999999999999988888776653

36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

---

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

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	106
1div_A	149	Ribosomal protein L9; rRNA-binding; 2.60A {Geobaci	99.89
1nkw_F	146	50S ribosomal protein L9; ribosome, large subunit,	99.88
3v2d_I	148	50S ribosomal protein L9; ribosome associated inhi	99.88
3r8s_H	149	50S ribosomal protein L9; protein biosynthesis, RN	99.86
3bbo_J	197	Ribosomal protein L9; large ribosomal subunit, spi	99.8

>1div_A Ribosomal protein L9; rRNA-binding; 2.60A {Geobacillus stearothermophilus} SCOP: d.99.1.1 d.100.1.1 PDB: 1giy_K 1yl3_K 2b66_I 2b9n_I 2b9p_I 487d_K

Probab=99.89  E-value=5.6e-23  Score=150.92  Aligned_cols=85  Identities=19%  Similarity=0.314  Sum_probs=77.9

Q ss_pred             hHHHHHHHhhhccceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEEEE
Q 047111            3 REFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPM   82 (106)
Q Consensus         3 ~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V~I   82 (106)
                      .+++..+..|++-.+.+.+-...+-           +||||||++||+++|++|+|++|||++|.|++|||++|+|+|+|
T Consensus        63 ~~A~~~a~~L~~~~v~i~~k~g~~g-----------klfGSVt~~dIa~al~~~~g~~idk~~I~l~~~Ik~~G~~~v~v  131 (149)
T 1div_A           63 ANAKKLKEQLEKLTVTIPAKAGEGG-----------RLFGSITSKQIAESLQAQHGLKLDKRKIELADAIRALGYTNVPV  131 (149)
T ss_dssp             HHHHHHHHHHTTCCEEEEECBCGGG-----------EEEEEECHHHHHHHHHHHHCCCCCGGGBCCCSCEEESEEEEEEE
T ss_pred             HHHHHHHHHHcCCeEEEEEEeCCCC-----------cEEeecCHHHHHHHHHHhhCCeechheEECCCCccccEEEEEEE
Confidence            5678888999999888888776444           99999999999999999999999999999999999999999999


Q ss_pred             EecCCCCCCCCcEEEEEEEEEEe
Q 047111           83 RLSKTIPLPEGKVQWTFNVKVHG  105 (106)
Q Consensus        83 kLh~~Vp~p~gkV~~~lkV~V~~  105 (106)
                      +||++       |+++|+|+|..
T Consensus       132 kLh~~-------V~a~i~v~V~~  147 (149)
T 1div_A          132 KLHPE-------VTATLKVHVTE  147 (149)
T ss_dssp             EEETT-------EEEEEEEEEEE
T ss_pred             EECCC-------CEEEEEEEEEe
Confidence            99999       59999999974

>1nkw_F 50S ribosomal protein L9; ribosome, large subunit, X- RAY structure, peptidyl-transferase, peptide bond formation; 3.10A {Deinococcus radiodurans} SCOP: i.1.1.2 PDB: 1nwx_F* 1nwy_F* 1sm1_F* 1xbp_F* 1pnu_F 1pny_F 1vor_I 1vou_I 1vow_I 1voy_I 1vp0_I

Probab=99.88  E-value=1.3e-22  Score=148.59  Aligned_cols=84  Identities=18%  Similarity=0.357  Sum_probs=76.0

Q ss_pred             chHHHHHHHhhhccceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEEE
Q 047111            2 SREFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVP   81 (106)
Q Consensus         2 ~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V~   81 (106)
                      ..+++..+..|++-.+.+.+-.. +-           +||||||++||+++|++| |++|||++|.|++|||++|+|+|+
T Consensus        61 ~~~A~~~a~~L~~~~v~i~~k~g-~g-----------klfGSVt~~dIa~al~~~-g~~idk~~I~l~~~Ik~~G~~~v~  127 (146)
T 1nkw_F           61 KAVAEDLASRLNGVAVELSVRAG-EG-----------KIYGAVTHQDVANSLDQL-GFDVDRRKIDMPKTVKEVGEYDIA  127 (146)
T ss_pred             HHHHHHHHHHhcCCEEEEEEEcC-CC-----------ceeeccCHHHHHHHHHHc-CCeechheEECCCcccccEEEEEE
Confidence            35778888899988888877766 44           899999999999999988 999999999999999999999999


Q ss_pred             EEecCCCCCCCCcEEEEEEEEEEe
Q 047111           82 MRLSKTIPLPEGKVQWTFNVKVHG  105 (106)
Q Consensus        82 IkLh~~Vp~p~gkV~~~lkV~V~~  105 (106)
                      |+||++|       +++|+|+|..
T Consensus       128 vkLh~~V-------~a~i~v~V~~  144 (146)
T 1nkw_F          128 YRAHPEV-------TIPMKLVVHA  144 (146)
T ss_pred             EEECCCC-------EEEEEEEEEe
Confidence            9999995       9999999974

>3v2d_I 50S ribosomal protein L9; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2j03_I 2jl6_I 2jl8_I 2v47_I 2v49_I 2wdi_I 2wdj_I 2wdl_I 2wdn_I 2wh2_I 2x9s_I 2x9u_I 2xg0_I 2xg2_I 3hux_I 3huz_I 3i8f_K 3i8i_K 3i9c_K 3i9e_K ...

Probab=99.88  E-value=6.4e-23  Score=150.48  Aligned_cols=84  Identities=23%  Similarity=0.406  Sum_probs=72.5

Q ss_pred             hHHHHHHHhhhccceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEEEE
Q 047111            3 REFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVPM   82 (106)
Q Consensus         3 ~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V~I   82 (106)
                      .+++..+..|++-.+.+.+-..           +. +||||||++||+++|++|+|++|||++|.|++|||++|+|+|+|
T Consensus        63 ~~A~~~~~~L~~~~v~i~~kag-----------~~-kLfGSVt~~dIa~al~~~~g~~idk~~I~l~~pIk~~G~~~v~v  130 (148)
T 3v2d_I           63 AEAERLKEILENLTLTIPVRAG-----------ET-KIYGSVTAKDIAEALSRQHGVTIDPKRLALEKPIKELGEYVLTY  130 (148)
T ss_dssp             HHHHHHHHHSSSCCEEEECCBS-----------SS-SBSSCBCHHHHHHHHTTTTCCCCCTTSSCCSSCBCSCEEEEEEC
T ss_pred             HHHHHHHHHHcCCEEEEEEEcC-----------CC-ccccccCHHHHHHHHHHhcCCCcchheEEcCchhhceEEEEEEE
Confidence            4667777888876665544332           45 99999999999999998889999999999999999999999999


Q ss_pred             EecCCCCCCCCcEEEEEEEEEEe
Q 047111           83 RLSKTIPLPEGKVQWTFNVKVHG  105 (106)
Q Consensus        83 kLh~~Vp~p~gkV~~~lkV~V~~  105 (106)
                      +||++|       +++|+|+|..
T Consensus       131 ~Lh~~V-------~a~i~v~V~~  146 (148)
T 3v2d_I          131 KPHPEV-------PIQLKVSVVA  146 (148)
T ss_dssp             CSBTTB-------CCEEEEEEEC
T ss_pred             EECCCc-------EEEEEEEEEe
Confidence            999995       9999999973

>3r8s_H 50S ribosomal protein L9; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_F 1p86_F 1vs8_H 1vs6_H 2aw4_H 2awb_H 2gya_F 2gyc_F 1vt2_H 2i2v_H 2j28_H 2i2t_H* 2qao_H* 2qba_H* 2qbc_H* 2qbe_H 2qbg_H 2qbi_H* 2qbk_H* 2qov_H ...

Probab=99.86  E-value=4.3e-22  Score=146.21  Aligned_cols=84  Identities=15%  Similarity=0.232  Sum_probs=74.6

Q ss_pred             hHHHHHHHhhhcc-ceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCCC-CCccceeEEE
Q 047111            3 REFEKAARRLENA-RLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPS-PLSAFGEYEV   80 (106)
Q Consensus         3 ~~~~~~~~~l~~~-~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~-pIKslGey~V   80 (106)
                      .+++..+..|++. .+.+.+-...+           -+||||||++|||++|+++ |++|||++|.|++ |||++|+|+|
T Consensus        63 ~~A~~~~~~L~~~~~v~i~~k~g~~-----------gklfGSVt~~dIa~al~~~-g~~idk~~I~l~~~pIk~~G~~~v  130 (149)
T 3r8s_H           63 AAANARAEKINALETVTIASKAGDE-----------GKLFGSIGTRDIADAVTAA-GVEVAKSEVRLPNGVLRTTGEHEV  130 (149)
T ss_dssp             HHHHHHHHHHHTTCCEEEEECBCTT-----------SEEEEEECHHHHHHHHHTT-SCCCCTTSEECSSCCEEESEEEEE
T ss_pred             HHHHHHHHHhcCCcEEEEEEEcCCC-----------CceEcccCHHHHHHHHHHc-CCceehheEEcCCccccceEEEEE
Confidence            5778888999985 88887766533           3999999999999999876 9999999999987 9999999999


Q ss_pred             EEEecCCCCCCCCcEEEEEEEEEEe
Q 047111           81 PMRLSKTIPLPEGKVQWTFNVKVHG  105 (106)
Q Consensus        81 ~IkLh~~Vp~p~gkV~~~lkV~V~~  105 (106)
                      +|+||++|       +++|+|+|..
T Consensus       131 ~v~Lh~~V-------~a~i~v~V~~  148 (149)
T 3r8s_H          131 SFQVHSEV-------FAKVIVNVVA  148 (149)
T ss_dssp             EECSSSSC-------CCCEEEEEEE
T ss_pred             EEEECCCC-------EEEEEEEEEE
Confidence            99999995       9999999974

>3bbo_J Ribosomal protein L9; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1

Probab=99.80  E-value=5.7e-21  Score=146.18  Aligned_cols=85  Identities=21%  Similarity=0.334  Sum_probs=73.3

Q ss_pred             chHHHHHHHhhhcc-ceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEE
Q 047111            2 SREFEKAARRLENA-RLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEV   80 (106)
Q Consensus         2 ~~~~~~~~~~l~~~-~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V   80 (106)
                      ..|++..+..|++- .+.+.+-..           +.-+||||||++||+++|++|+|++|||++|.|++ ||++|+|+|
T Consensus       111 ~~~A~~la~~L~~~~~v~i~~kaG-----------e~GkLFGSVT~~dIa~al~~~~Gi~Idk~~I~L~~-IK~lG~y~V  178 (197)
T 3bbo_J          111 KEEAQQLAMVFQTVGAFKVKRKGG-----------KGKLIFGSVTAQDLVDIIKSQLQKDIDKRLVSLPE-IRETGEYIA  178 (197)
T ss_dssp             THHHHTHHHHSSSCCCCBCCCCBC-----------TTSSBSSCCSSHHHHGGGTSSSSCCCCSTTCCSCC-CSSSSCEEE
T ss_pred             HHHHHHHHHHhcCCceEEEEEEeC-----------CCCcEecccCHHHHHHHHHHhhCCeeeeeEEEecc-ccceEEEEE
Confidence            45677888888887 476666554           33499999999999999998999999999999985 999999999


Q ss_pred             EEEecCCCCCCCCcEEEEEEEEEEe
Q 047111           81 PMRLSKTIPLPEGKVQWTFNVKVHG  105 (106)
Q Consensus        81 ~IkLh~~Vp~p~gkV~~~lkV~V~~  105 (106)
                      +|+||++|       +++|+|+|..
T Consensus       179 ~VkLh~eV-------~a~i~V~V~~  196 (197)
T 3bbo_J          179 ELKLHPDV-------TARVKINVFA  196 (197)
T ss_dssp             CCCCBTTB-------CCCEEEBCCC
T ss_pred             EEEECCCc-------EEEEEEEEEe
Confidence            99999995       9999999864

---

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	106
d1diva1	94	d.99.1.1 (A:56-149) Ribosomal protein L9 C-domain	3e-04

>d1diva1 d.99.1.1 (A:56-149) Ribosomal protein L9 C-domain {Bacillus stearothermophilus [TaxId: 1422]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein L9 C-domain
superfamily: Ribosomal protein L9 C-domain
family: Ribosomal protein L9 C-domain
domain: Ribosomal protein L9 C-domain
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 34.8 bits (80), Expect = 3e-04
 Identities = 14/82 (17%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 7  KAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYL 66
          +AA  L NA+ +  +   +      ++ +    L   +T +++   + +Q  + ++   +
Sbjct: 2  QAAEELANAKKLKEQLEKLTVTIPAKAGEGG-RLFGSITSKQIAESLQAQHGLKLDKRKI 60

Query: 67 HLPSPLSAFGEYEVPMRLSKTI 88
           L   + A G   VP++L   +
Sbjct: 61 ELADAIRALGYTNVPVKLHPEV 82

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	106
d1diva1	94	Ribosomal protein L9 C-domain {Bacillus stearother	99.9
d2j01i1	91	Ribosomal protein L9 C-domain {Thermus thermophilu	99.89
d2gycf1	91	Ribosomal protein L9 C-domain {Escherichia coli [T	99.87

>d1diva1 d.99.1.1 (A:56-149) Ribosomal protein L9 C-domain {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein L9 C-domain
superfamily: Ribosomal protein L9 C-domain
family: Ribosomal protein L9 C-domain
domain: Ribosomal protein L9 C-domain
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.90  E-value=5e-24  Score=144.10  Aligned_cols=86  Identities=19%  Similarity=0.302  Sum_probs=79.2

Q ss_pred             chHHHHHHHhhhccceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEEE
Q 047111            2 SREFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVP   81 (106)
Q Consensus         2 ~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V~   81 (106)
                      ..+++..+..|++-.+.+..-.+.+-           +||||||++||+++|.+++|++|||++|.|++|||++|+|+|.
T Consensus         7 ~~~A~~la~~L~~~~i~i~~k~ge~G-----------kLfGSVt~~dI~~~l~~~~g~~idk~~I~l~~~IK~~G~y~v~   75 (94)
T d1diva1           7 LANAKKLKEQLEKLTVTIPAKAGEGG-----------RLFGSITSKQIAESLQAQHGLKLDKRKIELADAIRALGYTNVP   75 (94)
T ss_dssp             HHHHHHHHHHHTTCCEEEEECBCGGG-----------EEEEEECHHHHHHHHHHHHCCCCCGGGBCCCSCEEESEEEEEE
T ss_pred             HHHHHHHHHHhhCCEEEEEEEECCCC-----------eeEecccHHHHHHHHHHccCceecHHHhhccCchhhcEeEEEE
Confidence            35778889999999998888887655           9999999999999999899999999999999999999999999


Q ss_pred             EEecCCCCCCCCcEEEEEEEEEEe
Q 047111           82 MRLSKTIPLPEGKVQWTFNVKVHG  105 (106)
Q Consensus        82 IkLh~~Vp~p~gkV~~~lkV~V~~  105 (106)
                      |+||++       |+++|+|.|..
T Consensus        76 i~Lh~~-------V~a~i~v~V~~   92 (94)
T d1diva1          76 VKLHPE-------VTATLKVHVTE   92 (94)
T ss_dssp             EEEETT-------EEEEEEEEEEE
T ss_pred             EEecCC-------eEEEEEEEEEe
Confidence            999999       59999999974

>d2j01i1 d.99.1.1 (I:56-146) Ribosomal protein L9 C-domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein L9 C-domain
superfamily: Ribosomal protein L9 C-domain
family: Ribosomal protein L9 C-domain
domain: Ribosomal protein L9 C-domain
species: Thermus thermophilus [TaxId: 274]

Probab=99.89  E-value=2.2e-24  Score=145.20  Aligned_cols=84  Identities=23%  Similarity=0.401  Sum_probs=73.5

Q ss_pred             chHHHHHHHhhhccceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCCCCCccceeEEEE
Q 047111            2 SREFEKAARRLENARLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPSPLSAFGEYEVP   81 (106)
Q Consensus         2 ~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~pIKslGey~V~   81 (106)
                      ..|++..+..|++-.+.+.+-.+           | .+||||||++||+++|++|+|++|||++|.|+.|||++|+|+|.
T Consensus         7 ~~~A~~l~~~L~~~~i~i~~k~~-----------e-gkLfGSVt~~dIa~~l~~~~g~~Idk~~I~l~~~IK~~G~~~v~   74 (91)
T d2j01i1           7 KAEAERLKEILENLTLTIPVRAG-----------E-TKIYGSVTAKDIAEALSRQHGVTIDPKRLALEKPIKELGEYVLT   74 (91)
T ss_dssp             TTTTHHHHHHHTTCBCCCCCCBC-----------S-SSBSSCCCHHHHHHHHHTTTCCCCCTTTTCCSSCCCSCEEEECC
T ss_pred             HHHHHHHHHHhcCCEEEEEEEec-----------C-CceecccCHHHHHHHHHhccCceechHHhhccccccceEEEEEE
Confidence            35778888999987765544333           3 48999999999999999999999999999999999999999999


Q ss_pred             EEecCCCCCCCCcEEEEEEEEEE
Q 047111           82 MRLSKTIPLPEGKVQWTFNVKVH  104 (106)
Q Consensus        82 IkLh~~Vp~p~gkV~~~lkV~V~  104 (106)
                      |+||++|       +++|+|.|+
T Consensus        75 i~L~~~V-------~a~i~v~Vv   90 (91)
T d2j01i1          75 YKPHPEV-------PIQLKVSVV   90 (91)
T ss_dssp             CSSSSCC-------CCEEEECCC
T ss_pred             EEecCCE-------EEEEEEEEE
Confidence            9999996       999999875

>d2gycf1 d.99.1.1 (F:59-149) Ribosomal protein L9 C-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein L9 C-domain
superfamily: Ribosomal protein L9 C-domain
family: Ribosomal protein L9 C-domain
domain: Ribosomal protein L9 C-domain
species: Escherichia coli [TaxId: 562]

Probab=99.87  E-value=1.7e-22  Score=136.29  Aligned_cols=85  Identities=15%  Similarity=0.234  Sum_probs=75.7

Q ss_pred             chHHHHHHHhhhcc-ceeeEeecchhhcccccCCCCCceeeecCCHHHHHHHHHhhcCCccccccccCCC-CCccceeEE
Q 047111            2 SREFEKAARRLENA-RLVLRRFPNIEKLRSRESKDDPIELCSPVTKEELVAKVASQLSISIEPEYLHLPS-PLSAFGEYE   79 (106)
Q Consensus         2 ~~~~~~~~~~l~~~-~l~~~~~~~~~~~~~~~~~~~~~kLFGSVTtkdIaeaL~~q~gIeIDKkkI~L~~-pIKslGey~   79 (106)
                      +++++..+..|+.- .+.+.+-.+.+-           +||||||++||+++|+++ |++|||++|.|++ |||++|+|+
T Consensus         4 l~~A~~~a~kl~~~~~i~i~~kage~G-----------kLfGSVt~~dI~~~l~~~-g~~Idk~~I~l~~~~IK~lG~y~   71 (91)
T d2gycf1           4 LAAANARAEKINALETVTIASKAGDEG-----------KLFGSIGTRDIADAVTAA-GVEVAKSEVRLPNGVLRTTGEHE   71 (91)
T ss_dssp             HHHHHHHHHHHTTTCCCEEEECEEETT-----------EESSCCCHHHHHHHHTTT-TCCCCSTTSCCSSCCCCBSSEEE
T ss_pred             HHHHHHHHHHhcCCcEEEEEEEeCCCC-----------eeeeecCHHHHHHHHHHc-CCcccHHHEECCCccccccEEEE
Confidence            56788889999985 588887776554           999999999999999976 9999999999987 799999999


Q ss_pred             EEEEecCCCCCCCCcEEEEEEEEEEe
Q 047111           80 VPMRLSKTIPLPEGKVQWTFNVKVHG  105 (106)
Q Consensus        80 V~IkLh~~Vp~p~gkV~~~lkV~V~~  105 (106)
                      |.|+||++|       +++++|.|..
T Consensus        72 v~i~Lh~~V-------~~~i~v~Vv~   90 (91)
T d2gycf1          72 VSFQVHSEV-------FAKVIVNVVA   90 (91)
T ss_dssp             EEECSSSSC-------CEEEEEEEEE
T ss_pred             EEEEEcCCE-------EEEEEEEEEE
Confidence            999999995       9999999974