Citrus Sinensis ID: 044565

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------10
Protein Sequence
GGLRTFFATIVTTGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPYDIKKDDPLVMARQEQERLSKLEILKRRGKGPPKKGQGRRAAKRSK
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHcccccHHHHHcccccccccccccccHHHHHHHHHHHHHHHccccccccccccHHHHccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHccHHHHHHccccccccccccccHHHHHHHHHHHHHHHcccccccccccccHHHccc
Coil and Loop (DISEMBL)
GGLRTFFATIVTTGLTEARAKIFGHVlnltgqrsphKILRKKLiddkvagwypydikkddplVMARQEQERLSKLEILKrrgkgppkkgqgrraakrsk
Flexible Loop (DISEMBL)
GGLRTFFATIVTTGLTEARAKIFGHvlnltgqrsphkilrkkliddkvagwypydikkddplVMARQEQERLSkleilkrrgkgppkkgqgrraakrsk
Low Complexity Region (SEG)
GGLRTFFATIVTTGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPYDIKKDDPLVMARQEQERLSKLEILkrrgkgppkkgqgrrAAKRSK
Disordered region (IsUnstruct)
***RTFFATIVTTGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPYDIKKDD*L*************************************
Disordered Region (DISOPRED)
*************GLTEARAKIFGHVLNLTGQRS***ILRKKLIDDKVAGWYPYDIKKDDPLVMARQEQERLSK*************************
Disordered Region (DISEMBL)
GGLRTFFATIVTTGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPYDIKKDDPLVMARQEQERLSKLEILKRR******************
Disordered Region (DISPRO)
*GLRTFFATIVTTGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPYDIKKDDPLVMARQEQERLSKLEILKRR******************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
GGLRTFFATIVTTGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPYDIKKDDPLVMARQEQERLSKLEILKRRGKGPPKKGQGRRAAKRSK
Positional Conservation
no confident homologs detected

---

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	99	2.2.26 [Sep-21-2011]
P53305	110	Mitochondral 37S ribosoma	yes	no	0.747	0.672	0.409	0.0003

>sp|P53305|RT27_YEAST Mitochondral 37S ribosomal protein S27 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RSM27 PE=1 SV=1

 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 34/83 (40%), Positives = 43/83 (51%), Gaps = 9/83 (10%)

Query: 15 LTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPY-DIKK--------DDPLVMA 65
          + E  AKIF    N +G R+  KIL ++L    VA +Y   DI K         D   + 
Sbjct: 11 VAELSAKIFDQNFNPSGIRTGSKILNERLKGPSVASYYGNPDILKFRHLKTLYPDIEFVD 70

Query: 66 RQEQERLSKLEILKRRGKGPPKK 88
           +EQ RLS +E  KRRGKG PKK
Sbjct: 71 LEEQYRLSMVEAKKRRGKGAPKK 93

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

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	99
449454784	102	PREDICTED: mitochondral 37S ribosomal pr	1.0	0.970	0.777	1e-37
449503345	141	PREDICTED: mitochondral 37S ribosomal pr	0.979	0.687	0.793	1e-37
225423583	102	PREDICTED: mitochondral 37S ribosomal pr	0.898	0.872	0.876	2e-37
449474433	94	PREDICTED: mitochondral 37S ribosomal pr	0.949	1.0	0.808	2e-36
388497468	102	unknown [Lotus japonicus]	1.0	0.970	0.737	3e-36
255574452	105	conserved hypothetical protein [Ricinus	1.0	0.942	0.757	4e-36
388512665	102	unknown [Lotus japonicus]	1.0	0.970	0.737	4e-36
297794891	102	hypothetical protein ARALYDRAFT_494514 [	1.0	0.970	0.727	1e-35
356520428	102	PREDICTED: mitochondral 37S ribosomal pr	1.0	0.970	0.717	2e-35
356504678	102	PREDICTED: mitochondral 37S ribosomal pr	1.0	0.970	0.717	4e-35

>gi|449454784|ref|XP_004145134.1| PREDICTED: mitochondral 37S ribosomal protein S27-like isoform 1 [Cucumis sativus] gi|449454786|ref|XP_004145135.1| PREDICTED: mitochondral 37S ribosomal protein S27-like isoform 2 [Cucumis sativus] gi|449454788|ref|XP_004145136.1| PREDICTED: mitochondral 37S ribosomal protein S27-like isoform 3 [Cucumis sativus]

 Score =  160 bits (404), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 77/99 (77%), Positives = 86/99 (86%)

Query: 1   GGLRTFFATIVTTGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPYDIKKDD 60
             L++  A  V  G+TEARA+IFGH+LN TGQRS HK+LRKKLI DKV+ WYPYDIKKDD
Sbjct: 4   NSLKSMIAAAVNKGVTEARARIFGHILNPTGQRSTHKLLRKKLIGDKVSQWYPYDIKKDD 63

Query: 61  PLVMARQEQERLSKLEILKRRGKGPPKKGQGRRAAKRSK 99
           PLVMAR EQERLSKLE+LKRRGKGPPKKGQGRRAAKR+K
Sbjct: 64  PLVMARLEQERLSKLEMLKRRGKGPPKKGQGRRAAKRNK 102

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449503345|ref|XP_004161956.1| PREDICTED: mitochondral 37S ribosomal protein S27-like [Cucumis sativus]

 Score =  160 bits (404), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 77/97 (79%), Positives = 86/97 (88%)

Query: 3   LRTFFATIVTTGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPYDIKKDDPL 62
           L++  A  V  G+TEARA+IFGH+LN TGQRS HK+LRKKLI DKV+ WYPYDIKKDDPL
Sbjct: 45  LKSMIAAAVNKGVTEARARIFGHILNPTGQRSTHKLLRKKLIGDKVSQWYPYDIKKDDPL 104

Query: 63  VMARQEQERLSKLEILKRRGKGPPKKGQGRRAAKRSK 99
           VMAR EQERLSKLE+LKRRGKGPPKKGQGRRAAKR+K
Sbjct: 105 VMARLEQERLSKLEMLKRRGKGPPKKGQGRRAAKRNK 141

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225423583|ref|XP_002273533.1| PREDICTED: mitochondral 37S ribosomal protein S27 [Vitis vinifera] gi|297738035|emb|CBI27236.3| unnamed protein product [Vitis vinifera]

 Score =  159 bits (402), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 78/89 (87%), Positives = 84/89 (94%)

Query: 11  VTTGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPYDIKKDDPLVMARQEQE 70
           V  G+TEARA+IFGHVLN TGQRSPHKILRKKLI +KVA WYPYDIKKDDPLVMARQEQE
Sbjct: 14  VKGGVTEARARIFGHVLNPTGQRSPHKILRKKLIGEKVAQWYPYDIKKDDPLVMARQEQE 73

Query: 71  RLSKLEILKRRGKGPPKKGQGRRAAKRSK 99
           RLSKLE+LKRRGKGPPKKGQG+RAAKR+K
Sbjct: 74  RLSKLEMLKRRGKGPPKKGQGKRAAKRNK 102

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449474433|ref|XP_004154171.1| PREDICTED: mitochondral 37S ribosomal protein S27-like [Cucumis sativus]

 Score =  156 bits (394), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 76/94 (80%), Positives = 83/94 (88%)

Query: 6  FFATIVTTGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPYDIKKDDPLVMA 65
            A  V  G+TEARA+IFGH+LN TGQRS HK+LRKKLI DKV+ WYPYDIKKDDPLVMA
Sbjct: 1  MIAAAVNKGVTEARARIFGHILNPTGQRSTHKLLRKKLIGDKVSQWYPYDIKKDDPLVMA 60

Query: 66 RQEQERLSKLEILKRRGKGPPKKGQGRRAAKRSK 99
          R EQERLSKLE+LKRRGKGPPKKGQGRRAAKR+K
Sbjct: 61 RLEQERLSKLEMLKRRGKGPPKKGQGRRAAKRNK 94

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388497468|gb|AFK36800.1| unknown [Lotus japonicus]

 Score =  155 bits (392), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 73/99 (73%), Positives = 85/99 (85%)

Query: 1   GGLRTFFATIVTTGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPYDIKKDD 60
           GGL+      +T G+TEARA IFGH LNLTG++SPHK+LR KL  +KVA WYP+DIKKDD
Sbjct: 4   GGLKRMLTAAITGGVTEARASIFGHQLNLTGEKSPHKVLRMKLFGEKVAQWYPHDIKKDD 63

Query: 61  PLVMARQEQERLSKLEILKRRGKGPPKKGQGRRAAKRSK 99
           PLVMAR++QERLSKLE+LKRRGKGPPKKG GRRAAKR+K
Sbjct: 64  PLVMAREQQERLSKLEMLKRRGKGPPKKGHGRRAAKRNK 102

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255574452|ref|XP_002528138.1| conserved hypothetical protein [Ricinus communis] gi|223532436|gb|EEF34229.1| conserved hypothetical protein [Ricinus communis]

 Score =  155 bits (391), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 75/99 (75%), Positives = 86/99 (86%)

Query: 1   GGLRTFFATIVTTGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPYDIKKDD 60
           G L+   A  VTTG+ EARA+IFGH+LN TG +SPHKILRKKLI +KVA WYP+DIK+DD
Sbjct: 5   GCLKGILAAAVTTGVAEARARIFGHILNPTGLKSPHKILRKKLIGEKVAQWYPHDIKRDD 64

Query: 61  PLVMARQEQERLSKLEILKRRGKGPPKKGQGRRAAKRSK 99
           PLVMARQEQERLSKLE+LKRRGKGPPKKGQG+ A KR+K
Sbjct: 65  PLVMARQEQERLSKLEMLKRRGKGPPKKGQGKGAMKRNK 103

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388512665|gb|AFK44394.1| unknown [Lotus japonicus]

 Score =  155 bits (391), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 73/99 (73%), Positives = 85/99 (85%)

Query: 1   GGLRTFFATIVTTGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPYDIKKDD 60
           GGL+      +T G+TEARA IFGH LNLTG++SPHK+LR KL  +KVA WYP+DIKKDD
Sbjct: 4   GGLKRMLTAAITGGVTEARASIFGHQLNLTGKKSPHKVLRMKLFGEKVAQWYPHDIKKDD 63

Query: 61  PLVMARQEQERLSKLEILKRRGKGPPKKGQGRRAAKRSK 99
           PLVMAR++QERLSKLE+LKRRGKGPPKKG GRRAAKR+K
Sbjct: 64  PLVMAREQQERLSKLEMLKRRGKGPPKKGHGRRAAKRNK 102

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297794891|ref|XP_002865330.1| hypothetical protein ARALYDRAFT_494514 [Arabidopsis lyrata subsp. lyrata] gi|297311165|gb|EFH41589.1| hypothetical protein ARALYDRAFT_494514 [Arabidopsis lyrata subsp. lyrata]

 Score =  153 bits (387), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 72/99 (72%), Positives = 86/99 (86%)

Query: 1   GGLRTFFATIVTTGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPYDIKKDD 60
           G L++  ++ V  G+TEARA+IFGH+LN TGQRSPHKILRKKLI DKVA WYPYDIK +D
Sbjct: 4   GSLKSLISSAVGRGVTEARARIFGHMLNPTGQRSPHKILRKKLIGDKVAEWYPYDIKNED 63

Query: 61  PLVMARQEQERLSKLEILKRRGKGPPKKGQGRRAAKRSK 99
           P V+AR+EQER+SKLE+LKRR KGPPKKG G+RAAKR+K
Sbjct: 64  PNVLAREEQERISKLEMLKRRNKGPPKKGHGKRAAKRNK 102

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356520428|ref|XP_003528864.1| PREDICTED: mitochondral 37S ribosomal protein S27-like [Glycine max]

 Score =  152 bits (384), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 71/99 (71%), Positives = 84/99 (84%)

Query: 1   GGLRTFFATIVTTGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPYDIKKDD 60
           G L+   +  +  G+ E+RA+IFGH LN TGQ++PHK+LR KL  +KVA WYP+DIKKDD
Sbjct: 4   GSLKNMLSEAINKGVVESRARIFGHQLNPTGQQTPHKLLRMKLFGEKVAQWYPHDIKKDD 63

Query: 61  PLVMARQEQERLSKLEILKRRGKGPPKKGQGRRAAKRSK 99
           PLVMARQEQERLSKLE+LKRRGKGPPKKGQGRRAAKR+K
Sbjct: 64  PLVMARQEQERLSKLEMLKRRGKGPPKKGQGRRAAKRNK 102

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356504678|ref|XP_003521122.1| PREDICTED: mitochondral 37S ribosomal protein S27-like isoform 1 [Glycine max]

 Score =  151 bits (382), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 71/99 (71%), Positives = 83/99 (83%)

Query: 1   GGLRTFFATIVTTGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPYDIKKDD 60
           G L+   +  +  G+ EARA+IFGH LN TG ++PHK+LR KL  +KVA WYP+DIKKDD
Sbjct: 4   GSLKNMLSVAMNQGVVEARARIFGHQLNPTGMKTPHKLLRMKLFGEKVAQWYPHDIKKDD 63

Query: 61  PLVMARQEQERLSKLEILKRRGKGPPKKGQGRRAAKRSK 99
           PLVMARQEQERLSKLE+LKRRGKGPPKKGQGRRAAKR+K
Sbjct: 64  PLVMARQEQERLSKLEMLKRRGKGPPKKGQGRRAAKRNK 102

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	99
TAIR|locus:2156359	102	AT5G44710 "AT5G44710" [Arabido	1.0	0.970	0.595	4e-26

TAIR|locus:2156359 AT5G44710 "AT5G44710" [Arabidopsis thaliana (taxid:3702)]

 Score = 295 (108.9 bits), Expect = 4.0e-26, P = 4.0e-26
 Identities = 59/99 (59%), Positives = 73/99 (73%)

Query:     1 GGLRTFFATIVTTGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPYDIKKDD 60
             G L++  ++ V  G+TEARA+IFGH+LN TGQRSPHKILRKKLI DKVA WYPYDIK +D
Sbjct:     4 GSLKSLISSAVGRGVTEARARIFGHMLNPTGQRSPHKILRKKLIGDKVAEWYPYDIKNED 63

Query:    61 PLVMARQEQERLSKLEILXXXXXXXXXXXXXXXAAKRSK 99
             P V+AR+E+ER+SKLE+L               AAKR+K
Sbjct:    64 PNVLAREEKERISKLEMLKRRDKGPPKKGHGKRAAKRNK 102


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.321   0.137   0.394    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       99        84   0.00091  102 3  11 22  0.42    29
                                                     29  0.45    30


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:  498 (53 KB)
  Total size of DFA:  88 KB (2066 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:  9.07u 0.07s 9.14t   Elapsed:  00:00:01
  Total cpu time:  9.07u 0.07s 9.14t   Elapsed:  00:00:01
  Start:  Fri May 10 00:05:38 2013   End:  Fri May 10 00:05:39 2013

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

GO:0009086 "methionine biosynthetic process" evidence=RCA

GO:0016925 "protein sumoylation" evidence=RCA

---

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	99
pfam08293	87	pfam08293, MRP-S33, Mitochondrial ribosomal subuni	7e-21

>gnl|CDD|116877 pfam08293, MRP-S33, Mitochondrial ribosomal subunit S27

 Score = 78.5 bits (194), Expect = 7e-21
 Identities = 36/84 (42%), Positives = 47/84 (55%), Gaps = 8/84 (9%)

Query: 13 TGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYP------YDIKKDDPLVMAR 66
            +    A+IFG V N TG RS  KILR++L   ++A +YP       D+KK  P ++ R
Sbjct: 4  LRMARLSARIFGEVFNPTGSRSGKKILRQRLKGPELASYYPNHMPTFKDLKKLYPDLLFR 63

Query: 67 QEQE--RLSKLEILKRRGKGPPKK 88
           E E  RL  L + K RGKG PKK
Sbjct: 64 DEHEDFRLEMLRLRKLRGKGAPKK 87

This family of proteins corresponds to mitochondrial ribosomal subunit S27 in prokaryotes and to subunit S33 in humans. It is a small 106 residue protein.The evolutionary history of the mitoribosomal proteome that is encoded by a diverse subset of eukaryotic genomes, reveals an ancestral ribosome of alpha-proteobacterial descent that more than doubled its protein content in most eukaryotic lineages. Several new MRPs have originated via duplication of existing MRPs as well as by recruitment from outside of the mitoribosomal proteome. Length = 87

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	99
PF08293	87	MRP-S33: Mitochondrial ribosomal subunit S27; Inte	100.0
KOG4844	102	consensus Mitochondrial ribosomal protein S27 [Tra	99.97
KOG4104	113	consensus Ganglioside-induced differentiation asso	99.95

>PF08293 MRP-S33: Mitochondrial ribosomal subunit S27; InterPro: IPR013219 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=100.00  E-value=2.4e-36  Score=201.47  Aligned_cols=79  Identities=47%  Similarity=0.654  Sum_probs=73.6

Q ss_pred             HHHHHHHHHHHhhhCcCCCCCCCCchhhHhhccccchhhhccCCCCCc--------ccCCCCcChHHHHHHHHHHHHHhc
Q 044565           10 IVTTGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPYDIK--------KDDPLVMARQEQERLSKLEILKRR   81 (99)
Q Consensus        10 ~r~~~l~~ls~rIFg~~~nPt~~Rsg~kvlr~~lkg~~~~~YYP~~~~--------r~~g~~~De~e~~R~~~~~~~k~R   81 (99)
                      .|+++|++|||+|||+++|||++|||+|||+++|+|++|++|||+++.        ..+++|+||||++|+++++++++|
T Consensus         1 ~r~~~l~~ls~rIFg~~~nP~~~Rsg~Kilr~~lkg~~~~~YYP~~~~~~~~l~~l~~~~~~~De~e~~R~e~~~~rk~R   80 (87)
T PF08293_consen    1 NRLLRLARLSARIFGTVYNPTGSRSGNKILRKRLKGPKLASYYPPHIVTFKLLKRLRPDGLFRDEHEDFREEMVELRKRR   80 (87)
T ss_pred             CHHHHHHHHHHHHhCCCCCCccchHHHHHHhhcCCCchHhHhCCCcchHHHHHHHHccccCcCChhHHHHHHHHHHHHhC
Confidence            378999999999999999999999999999999999999999998763        344569999999999999999999


Q ss_pred             CCCCCCC
Q 044565           82 GKGPPKK   88 (99)
Q Consensus        82 GKg~PKK   88 (99)
                      |||+|||
T Consensus        81 GKg~PKK   87 (87)
T PF08293_consen   81 GKGPPKK   87 (87)
T ss_pred             CCCCCCC
Confidence            9999997

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a mitochondrial ribosomal subunit annotated as S27 in yeast and S33 in humans [, ]. It is a small 106 residue protein. The evolutionary history of the mitoribosomal proteome that is encoded by a diverse subset of eukaryotic genomes, reveals an ancestral ribosome of alpha-proteobacterial descent that more than doubled its protein content in most eukaryotic lineages. Several new MRPs have originated via duplication of existing MRPs as well as by recruitment from outside of the mitoribosomal proteome [].

>KOG4844 consensus Mitochondrial ribosomal protein S27 [Translation, ribosomal structure and biogenesis]

Probab=99.97  E-value=2.5e-31  Score=180.41  Aligned_cols=93  Identities=59%  Similarity=0.807  Sum_probs=85.3

Q ss_pred             ch-HHHHHHHHHHHHhhhCcCCCCCCCCchhhHhhccccchhhhccCCCCC-cccCC------CCcChHHHHHHHHHHHH
Q 044565            7 FA-TIVTTGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPYDI-KKDDP------LVMARQEQERLSKLEIL   78 (99)
Q Consensus         7 ~s-~~r~~~l~~ls~rIFg~~~nPt~~Rsg~kvlr~~lkg~~~~~YYP~~~-~r~~g------~~~De~e~~R~~~~~~~   78 (99)
                      .| +|+++.++.||++||||.||||++|||+|||+++|+|+.|++|||+.+ ++.++      .|.|-+|+.|+++++++
T Consensus         2 as~kAvl~~v~elsakIFg~~~np~g~Rtg~Kil~~~LkG~kvasyYp~~~~~r~l~tll~d~ef~d~~e~~R~s~~e~~   81 (102)
T KOG4844|consen    2 ASGKAVLRGVTELSAKIFGHMLNPTGQRTGHKILRKKLKGDKVASYYPPYDIKRELPTLLADEEFDDIAEWGRISKLEML   81 (102)
T ss_pred             cchHHHHHHHHHHHHHHHhcccCCCCCcchhHHHHHHhccchHhhhcchHHhhhhhhhhhcccccccHHHHHHHHHHHHH
Confidence            44 899999999999999999999999999999999999999999999854 46555      28889999999999999


Q ss_pred             HhcCCCCCCCCCchhHhhhcC
Q 044565           79 KRRGKGPPKKGQGRRAAKRSK   99 (99)
Q Consensus        79 k~RGKg~PKKg~gkra~kkk~   99 (99)
                      ++||||+|||+++++|.+.++
T Consensus        82 kRrgKGapKk~kk~~aa~~~~  102 (102)
T KOG4844|consen   82 KRRGKGAPKKGKKKRAAKRNK  102 (102)
T ss_pred             HHccCCCCcccchhhhhhccC
Confidence            999999999999999998764

>KOG4104 consensus Ganglioside-induced differentiation associated protein 3 [Signal transduction mechanisms]

Probab=99.95  E-value=7.6e-29  Score=170.24  Aligned_cols=92  Identities=25%  Similarity=0.413  Sum_probs=83.9

Q ss_pred             cchHHHHHHHHHHHHhhhCcCCCCCCCCchhhH--hhccc--cchhhhccCCCCCc--------ccCCCCcChHHHHHHH
Q 044565            6 FFATIVTTGLTEARAKIFGHVLNLTGQRSPHKI--LRKKL--IDDKVAGWYPYDIK--------KDDPLVMARQEQERLS   73 (99)
Q Consensus         6 ~~s~~r~~~l~~ls~rIFg~~~nPt~~Rsg~kv--lr~~l--kg~~~~~YYP~~~~--------r~~g~~~De~e~~R~~   73 (99)
                      .||. +..+|++||++|||+|.+|||.+|+++|  ||+.|  +-+++.+|||++..        |++|+|+|||++|+.+
T Consensus        10 ~~t~-ya~RM~rLSnRvfGEV~rpTn~KSmKVVr~fSeeP~~kk~~~~~wYPnh~~~h~Lmk~LRf~GLfrDeHqdF~de   88 (113)
T KOG4104|consen   10 QPTP-YAKRMDRLSNRVFGEVVRPTNTKSMKVVRVFSEEPYEKKEQLSKWYPNHPMFHYLMKMLRFHGLFRDEHQDFRDE   88 (113)
T ss_pred             CccH-HHHHHHHHHHHHHhhccccCCCcceehhhhccccchhhHHHHHHhccCchHHHHHHHHHHHhhhhhhhHHHHHHH
Confidence            3444 7889999999999999999999999976  99999  56889999999642        9999999999999999


Q ss_pred             HHHHHHhcCCCCCCCCCchhHhhhc
Q 044565           74 KLEILKRRGKGPPKKGQGRRAAKRS   98 (99)
Q Consensus        74 ~~~~~k~RGKg~PKKg~gkra~kkk   98 (99)
                      +.+++++|||.+||||+||||++++
T Consensus        89 qkrLkklRGK~~PkkGeGKRA~kr~  113 (113)
T KOG4104|consen   89 QKRLKKLRGKVVPKKGEGKRAQKRG  113 (113)
T ss_pred             HHHHHHhcCCCCCCCCcchhhhhcC
Confidence            9999999999999999999999864

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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

No hit with probability above 80.00

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Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

No hit with probability above 80.00