Citrus Sinensis ID: 036429

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70----
Protein Sequence
MAGTQALKRIPRIKFPQRHPKSSGSASQSQAGANVDPNNWSKVSTTVGGKASLQPKRIPPSNEEIEAILLGGCI
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccc
Coil and Loop (DISEMBL)
magtqalkriprikfpqrhpkssgsasqsqaganvdpnnwskvsttvggkaslqpkrippsnEEIEAILLGGCI
Flexible Loop (DISEMBL)
magtqalkriprikfpqrhpkssgsasqsqaganvdpnnwSKVSTTVGGkaslqpkrippsneeIEAILLGGCI
Low Complexity Region (SEG)
MAGTQALKRIPRIKFPQRHPKssgsasqsqagaNVDPNNWSKVSTTVGGKASLQPKRIPPSNEEIEAILLGGCI
Disordered region (IsUnstruct)
**************************************************************************
Disordered Region (DISOPRED)
***********RI*************************************************EEIEAILLGGCI
Disordered Region (DISEMBL)
MAGTQALKRIPRIKF*******************VDPNNWSKVSTTVGGKASLQPKRIPPSNEEIEAILLGGCI
Disordered Region (DISPRO)
*********IPR*KFP******************************************PPSNEEIEAILLGGCI
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAGTQALKRIPRIKFPQRHPKSSGSASQSQAGANVDPNNWSKVSTTVGGKASLQPKRIPPSNEEIEAILLGGCI
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	74
255537799	80	conserved hypothetical protein [Ricinus	0.986	0.912	0.701	7e-19
388495966	79	unknown [Lotus japonicus]	1.0	0.936	0.670	9e-19
388506798	79	unknown [Lotus japonicus]	1.0	0.936	0.645	5e-18
449452210	79	PREDICTED: uncharacterized protein LOC10	1.0	0.936	0.620	2e-17
224072198	80	predicted protein [Populus trichocarpa]	1.0	0.925	0.675	4e-17
356497315	80	PREDICTED: uncharacterized protein LOC10	1.0	0.925	0.625	5e-17
356539313	79	PREDICTED: uncharacterized protein LOC10	1.0	0.936	0.620	2e-16
255638041	80	unknown [Glycine max]	1.0	0.925	0.612	2e-16
255630706	79	unknown [Glycine max]	1.0	0.936	0.607	5e-16
388522833	79	unknown [Lotus japonicus]	1.0	0.936	0.632	6e-16

>gi|255537799|ref|XP_002509966.1| conserved hypothetical protein [Ricinus communis] gi|223549865|gb|EEF51353.1| conserved hypothetical protein [Ricinus communis]

 Score = 97.8 bits (242), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 54/77 (70%), Positives = 58/77 (75%), Gaps = 4/77 (5%)

Query: 2  AGTQALKRIPRIKFPQRHPKSSGSASQSQAGA----NVDPNNWSKVSTTVGGKASLQPKR 57
           G QALKRIP IKFPQRH KSSGSAS+S   A    N+   + SK S TVGGKASLQPKR
Sbjct: 4  GGLQALKRIPLIKFPQRHLKSSGSASKSHESAVGNGNLPFFSSSKASMTVGGKASLQPKR 63

Query: 58 IPPSNEEIEAILLGGCI 74
           P SN+EIEAILLGGCI
Sbjct: 64 TPVSNDEIEAILLGGCI 80

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388495966|gb|AFK36049.1| unknown [Lotus japonicus]

 Score = 97.4 bits (241), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 53/79 (67%), Positives = 57/79 (72%), Gaps = 5/79 (6%)

Query: 1  MAGTQALKRIPRIKFPQRHPKSSGSA-----SQSQAGANVDPNNWSKVSTTVGGKASLQP 55
          M G QALKRIPRIKFP RH KSSGSA     S S   AN+   + SK ST++GGKASLQP
Sbjct: 1  MGGAQALKRIPRIKFPNRHGKSSGSAPDKQPSSSATDANLSFFSSSKASTSLGGKASLQP 60

Query: 56 KRIPPSNEEIEAILLGGCI 74
          KR P S EEIEAILLGGC 
Sbjct: 61 KRTPVSKEEIEAILLGGCF 79

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388506798|gb|AFK41465.1| unknown [Lotus japonicus]

 Score = 95.1 bits (235), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 51/79 (64%), Positives = 58/79 (73%), Gaps = 5/79 (6%)

Query: 1  MAGTQALKRIPRIKFPQRHPKSSGSASQSQAGANVDPN-----NWSKVSTTVGGKASLQP 55
          M G  ALKRIPRIKFP RH KSSGSAS++ A ++         + SK STT+GGKASLQP
Sbjct: 1  MGGAHALKRIPRIKFPNRHSKSSGSASEAPALSSASDASSTFFSSSKASTTLGGKASLQP 60

Query: 56 KRIPPSNEEIEAILLGGCI 74
          KR P SNEEIEA+LLGGC 
Sbjct: 61 KRTPVSNEEIEAVLLGGCF 79

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449452210|ref|XP_004143853.1| PREDICTED: uncharacterized protein LOC101205349 [Cucumis sativus] gi|449501773|ref|XP_004161454.1| PREDICTED: uncharacterized LOC101205349 [Cucumis sativus]

 Score = 92.8 bits (229), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 49/79 (62%), Positives = 56/79 (70%), Gaps = 5/79 (6%)

Query: 1  MAGTQALKRIPRIKFPQRHPKSSGSASQSQAGANVDPNNW-----SKVSTTVGGKASLQP 55
          M G QA+KRIPRIKFP+RH  SSGS S++ +    D + +        S TVGGKASLQP
Sbjct: 1  MGGAQAIKRIPRIKFPKRHLSSSGSTSKTPSSHGGDDHVFFSSLEKDASKTVGGKASLQP 60

Query: 56 KRIPPSNEEIEAILLGGCI 74
          KR P SNEEIEAILLGGCI
Sbjct: 61 KRTPLSNEEIEAILLGGCI 79

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224072198|ref|XP_002303648.1| predicted protein [Populus trichocarpa] gi|222841080|gb|EEE78627.1| predicted protein [Populus trichocarpa]

 Score = 92.0 bits (227), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 54/80 (67%), Positives = 58/80 (72%), Gaps = 6/80 (7%)

Query: 1  MAGTQALKRIPRIKFPQRH-PKSSGSASQSQ----AGANVDPNNWS-KVSTTVGGKASLQ 54
          M G QALKRIPRIKFPQRH  KSSG+ SQ +    +G+       S K ST VGGKASLQ
Sbjct: 1  MGGAQALKRIPRIKFPQRHSTKSSGNGSQPEEALTSGSAYQAFFSSLKASTAVGGKASLQ 60

Query: 55 PKRIPPSNEEIEAILLGGCI 74
          PKR P SNEEIEAILLGGCI
Sbjct: 61 PKRTPVSNEEIEAILLGGCI 80

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356497315|ref|XP_003517506.1| PREDICTED: uncharacterized protein LOC100816379 [Glycine max]

 Score = 91.7 bits (226), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 50/80 (62%), Positives = 57/80 (71%), Gaps = 6/80 (7%)

Query: 1  MAGTQALKRIPRIKFPQRHPK-SSGSASQSQAGANVDPNNW-----SKVSTTVGGKASLQ 54
          M   QA+KRIPRIKFPQRHPK SSGS  ++QA ++    +      S  ST+VGGKASLQ
Sbjct: 1  MGAGQAMKRIPRIKFPQRHPKPSSGSTPETQASSSTTDVSLAFFSSSNASTSVGGKASLQ 60

Query: 55 PKRIPPSNEEIEAILLGGCI 74
          PKR P S EEIEAILLGGC 
Sbjct: 61 PKRTPVSKEEIEAILLGGCF 80

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356539313|ref|XP_003538143.1| PREDICTED: uncharacterized protein LOC100500589 [Glycine max]

 Score = 89.7 bits (221), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 49/79 (62%), Positives = 55/79 (69%), Gaps = 5/79 (6%)

Query: 1  MAGTQALKRIPRIKFPQRHPKSSGSASQSQAGANVDPNNW-----SKVSTTVGGKASLQP 55
          M   QALKRIPRIKFPQRHPK SGSA + QA ++    +      S  S++VGGKASLQP
Sbjct: 1  MGAGQALKRIPRIKFPQRHPKPSGSAPEIQASSSTTDASLAFFKSSNASSSVGGKASLQP 60

Query: 56 KRIPPSNEEIEAILLGGCI 74
          KR P S EEIEAILLGG  
Sbjct: 61 KRTPVSKEEIEAILLGGSF 79

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255638041|gb|ACU19335.1| unknown [Glycine max]

 Score = 89.7 bits (221), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 49/80 (61%), Positives = 56/80 (70%), Gaps = 6/80 (7%)

Query: 1  MAGTQALKRIPRIKFPQRHPK-SSGSASQSQAGANVDPNNW-----SKVSTTVGGKASLQ 54
          M   QA+KRIPRIKFPQRHPK  SGS  ++QA ++    +      S  ST+VGGKASLQ
Sbjct: 1  MGAGQAMKRIPRIKFPQRHPKPFSGSTPETQASSSTTDVSLAFFSSSNASTSVGGKASLQ 60

Query: 55 PKRIPPSNEEIEAILLGGCI 74
          PKR P S EEIEAILLGGC 
Sbjct: 61 PKRTPVSKEEIEAILLGGCF 80

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255630706|gb|ACU15714.1| unknown [Glycine max]

 Score = 88.2 bits (217), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 48/79 (60%), Positives = 55/79 (69%), Gaps = 5/79 (6%)

Query: 1  MAGTQALKRIPRIKFPQRHPKSSGSASQSQAGANVDPNNW-----SKVSTTVGGKASLQP 55
          M   QALKRIPRI+FPQRHPK SGSA + QA ++    +      S  S++VGGKASLQP
Sbjct: 1  MGAGQALKRIPRIEFPQRHPKPSGSAPEIQASSSTTDASLAFFKSSNASSSVGGKASLQP 60

Query: 56 KRIPPSNEEIEAILLGGCI 74
          KR P S EEIEAILLGG  
Sbjct: 61 KRTPVSKEEIEAILLGGSF 79

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388522833|gb|AFK49478.1| unknown [Lotus japonicus]

 Score = 88.2 bits (217), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 50/79 (63%), Positives = 57/79 (72%), Gaps = 5/79 (6%)

Query: 1  MAGTQALKRIPRIKFPQRHPKSSGSASQSQAGANVDPNNWSKVS-----TTVGGKASLQP 55
          M G  ALKRIPRIKFP RH KSSGSAS++ A ++    + S  S     TT+GGKASLQP
Sbjct: 1  MGGAHALKRIPRIKFPNRHSKSSGSASEAPALSSASDASSSFFSSSEASTTLGGKASLQP 60

Query: 56 KRIPPSNEEIEAILLGGCI 74
          KR P SNEEIEA+LLGGC 
Sbjct: 61 KRTPVSNEEIEAVLLGGCF 79

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

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	74
TAIR|locus:505006518	77	AT4G23885 "AT4G23885" [Arabido	0.918	0.883	0.549	6.2e-14
TAIR|locus:505006633	75	AT5G24165 "AT5G24165" [Arabido	0.918	0.906	0.493	1.2e-10

TAIR|locus:505006518 AT4G23885 "AT4G23885" [Arabidopsis thaliana (taxid:3702)]

 Score = 180 (68.4 bits), Expect = 6.2e-14, P = 6.2e-14
 Identities = 39/71 (54%), Positives = 43/71 (60%)

Query:     7 LKRIPRIKFPQRHPKXXXXXXXXXXXXNVDP---NNWSKVSTTVGGKASLQPKRIPPSNE 63
             LKRIPRIKFPQRH                D    +N + +  T GGKAS QPKR P SNE
Sbjct:     7 LKRIPRIKFPQRHINPSASEGKSQVANEADTLFFSNLNNIQKTTGGKASSQPKRTPVSNE 66

Query:    64 EIEAILLGGCI 74
             E+EAILLGGCI
Sbjct:    67 EMEAILLGGCI 77

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0005739 "mitochondrion" evidence=IDA

TAIR|locus:505006633 AT5G24165 "AT5G24165" [Arabidopsis thaliana (taxid:3702)]

 Score = 149 (57.5 bits), Expect = 1.2e-10, P = 1.2e-10
 Identities = 37/75 (49%), Positives = 44/75 (58%)

Query:     7 LKRIPRIKFPQRHPKXXXXXXXXXXXXNVDPNNW--SKV-----STTVGGKASLQPKRIP 59
             ++RIPRIKFPQRH               V  N    S V     +T  GGKASLQPKR P
Sbjct:     1 MRRIPRIKFPQRHSISSGSGPAPGSVSGVKKNVTASSDVPAAPKNTADGGKASLQPKRTP 60

Query:    60 PSNEEIEAILLGGCI 74
              S++EIE+I+LGGCI
Sbjct:    61 VSDKEIESIMLGGCI 75


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        0.315   0.134   0.406    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       74        62   0.00091  102 3  11 23  0.45    28
                                                     29  0.41    28


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:  495 (53 KB)
  Total size of DFA:  91 KB (2067 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:  7.11u 0.15s 7.26t   Elapsed:  00:00:00
  Total cpu time:  7.11u 0.15s 7.26t   Elapsed:  00:00:00
  Start:  Mon May 20 22:31:02 2013   End:  Mon May 20 22:31:02 2013

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

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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	74
PF10937	112	DUF2638: Protein of unknown function (DUF2638); In	98.03

>PF10937 DUF2638: Protein of unknown function (DUF2638); InterPro: IPR020373 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=98.03  E-value=1.2e-05  Score=54.61  Aligned_cols=24  Identities=54%  Similarity=0.631  Sum_probs=20.5

Q ss_pred             cCCCCCC---cCCCCHHHHHHHHhcCC
Q 036429           50 KASLQPK---RIPPSNEEIEAILLGGC   73 (74)
Q Consensus        50 ~as~~Pk---R~p~s~~EieaI~lGG~   73 (74)
                      +.+.+|.   |.||+++|||+|+.||+
T Consensus        86 ~~~eLP~Rfrr~p~se~EiE~InsGGA  112 (112)
T PF10937_consen   86 DRSELPARFRRKPISEEEIEAINSGGA  112 (112)
T ss_pred             eHHHcCHhHccCCCCHHHHHHHHcCCC
Confidence            5666776   67999999999999995

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 component of the mitochondrial small ribosomal subunit. Mature mitochondrial ribosomes consist of a small (37S) and a large (54S) subunit. The 37S subunit contains at least 33 different proteins and 1 molecule of RNA (15S). The 54S subunit contains at least 45 different proteins and 1 molecule of RNA (21S). This entry is represented by a mitochondrial ribosomal protein of the small subunit, which has similarity to human mitochondrial ribosomal protein MRP-S36 [, , ].

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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