Citrus Sinensis ID: 035376

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60------
Protein Sequence
MSWLIFEGLLPLGIIAAMLTIAGNAQYQIHKAAHGRPKHVGNDMWDVAMERRDKKLVEQLSGASSN
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
mswlifegLLPLGIIAAMLTIAGNAQYQIHkaahgrpkhvgndmwDVAMERRDKKLVEQLSGASSN
Flexible Loop (DISEMBL)
MSWLIFEGLLPLGIIAAMLTIAGNAQYQIHKaahgrpkhVGNDMWDVAMERRDKKLveqlsgassn
Low Complexity Region (SEG)
MSWLIFEGLLPLGIIAAMLTIAGNAQYQIHKAAHGRPKHVGNDMWDVAMERRDKKLVEQLSGASSN
Disordered region (IsUnstruct)
**WLIFEGLLPLGIIAAMLTIAGNAQYQIHKAAHGRPKHVGNDMWDV*******************
Disordered Region (DISOPRED)
**WLIFEGLLPLGIIAAMLTIAGNAQYQIHKAAHGRPKHVGNDMWDVAMER***************
Disordered Region (DISEMBL)
MSWLIFEGLLPLGIIAAMLTIAGNAQYQIHKAAHGRPKHVGNDMWDVAMERRDKKL**********
Disordered Region (DISPRO)
*SWLIFEGLLPLGIIAAMLTIAGNAQYQIHKAAHGRPKHVGNDMWDVAMERRDKKLVEQLS*****
Transmembrane Helix (TMHMM)
oooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSWLIFEGLLPLGIIAAMLTIAGNAQYQIHKAAHGRPKHVGNDMWDVAMERRDKKLVEQLSGASSN
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	66	2.2.26 [Sep-21-2011]
Q9C9Z5	65	NADH dehydrogenase [ubiqu	yes	no	0.984	1.0	0.661	4e-19

>sp|Q9C9Z5|NDUA1_ARATH NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 OS=Arabidopsis thaliana GN=At3g08610 PE=3 SV=1

 Score = 93.2 bits (230), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 43/65 (66%), Positives = 51/65 (78%)

Query: 1  MSWLIFEGLLPLGIIAAMLTIAGNAQYQIHKAAHGRPKHVGNDMWDVAMERRDKKLVEQL 60
          MS +  E +LPLGII  ML I GN+QY IHKA HGRPKH+G+D WDVAMERRDKK+VE+ 
Sbjct: 1  MSLVWLEAMLPLGIIGGMLCIMGNSQYYIHKAYHGRPKHIGHDEWDVAMERRDKKVVEKA 60

Query: 61 SGASS 65
          +  SS
Sbjct: 61 AAPSS 65


  Database: swissprot
    Posted date:  Mar 23, 2013  2:32 AM
  Number of letters in database: 191,569,459
  Number of sequences in database:  539,616
  
Lambda     K      H
   0.320    0.133    0.405 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,793,707
Number of Sequences: 539616
Number of extensions: 760748
Number of successful extensions: 1486
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1485
Number of HSP's gapped (non-prelim): 1
length of query: 66
length of database: 191,569,459
effective HSP length: 38
effective length of query: 28
effective length of database: 171,064,051
effective search space: 4789793428
effective search space used: 4789793428
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)

Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.
Arabidopsis thaliana (taxid: 3702)

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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	66
TAIR|locus:2077813	65	AT3G08610 "AT3G08610" [Arabido	0.984	1.0	0.661	6.5e-19
ASPGD|ASPL0000028074	86	AN11487 [Emericella nidulans (	0.924	0.709	0.338	0.0001
UNIPROTKB|G4MSW5	86	MGG_04614 "Uncharacterized pro	0.909	0.697	0.380	0.00045

TAIR|locus:2077813 AT3G08610 "AT3G08610" [Arabidopsis thaliana (taxid:3702)]

 Score = 227 (85.0 bits), Expect = 6.5e-19, P = 6.5e-19
 Identities = 43/65 (66%), Positives = 51/65 (78%)

Query:     1 MSWLIFEGLLPLGIIAAMLTIAGNAQYQIHKAAHGRPKHVGNDMWDVAMERRDKKLVEQL 60
             MS +  E +LPLGII  ML I GN+QY IHKA HGRPKH+G+D WDVAMERRDKK+VE+ 
Sbjct:     1 MSLVWLEAMLPLGIIGGMLCIMGNSQYYIHKAYHGRPKHIGHDEWDVAMERRDKKVVEKA 60

Query:    61 SGASS 65
             +  SS
Sbjct:    61 AAPSS 65

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0005739 "mitochondrion" evidence=IDA

GO:0005747 "mitochondrial respiratory chain complex I" evidence=IDA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=RCA

GO:0009853 "photorespiration" evidence=RCA

GO:0051788 "response to misfolded protein" evidence=RCA

GO:0080129 "proteasome core complex assembly" evidence=RCA

ASPGD|ASPL0000028074 AN11487 [Emericella nidulans (taxid:162425)]

 Score = 93 (37.8 bits), Expect = 0.00010, P = 0.00010
 Identities = 21/62 (33%), Positives = 30/62 (48%)

Query:     6 FEGLLPLGIIAAMLTIAGNAQYQIHKAAH-GRPKHVGNDMWDVAMERRDKKLVEQLSGAS 64
             FE L+P GI+  M  + G     +   A+ G+      D+WD  M  RD +L   L G S
Sbjct:     5 FEALIPYGIVVVMFGVTGVGLSVVKTYANDGKKARWNRDLWDRQMMERDLRLTGSLRGQS 64

Query:    65 SN 66
             +N
Sbjct:    65 TN 66

GO:0008150 "biological_process" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|G4MSW5 MGG_04614 "Uncharacterized protein" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 87 (35.7 bits), Expect = 0.00045, P = 0.00045
 Identities = 24/63 (38%), Positives = 31/63 (49%)

Query:     6 FEGLLPLGIIAAMLTIAGNAQYQIHKAAHG--RPKHVGNDMWDVAMERRDKKLVEQLSGA 63
             FE L+P  II AM  I+G     +    +G  RP+    D WD  M  RD++L   L G 
Sbjct:     5 FETLIPYAIITAMFGISGAGISTVRWYTNGGKRPRR-SIDQWDRQMMDRDRRLTGFLRGQ 63

Query:    64 SSN 66
             S N
Sbjct:    64 SDN 66


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        0.320   0.133   0.405    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       66        66   0.00091  102 3  11 22  0.42    28
                                                     29  0.48    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:  3
  No. of states in DFA:  539 (57 KB)
  Total size of DFA:  101 KB (2070 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:  7.45u 0.14s 7.59t   Elapsed:  00:00:01
  Total cpu time:  7.45u 0.14s 7.59t   Elapsed:  00:00:01
  Start:  Thu May  9 14:09:41 2013   End:  Thu May  9 14:09:42 2013

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

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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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9C9Z5	NDUA1_ARATH	No assigned EC number	0.6615	0.9848	1.0	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00001539001	SubName- Full=Chromosome chr11 scaffold_118, whole genome shotgun sequence; (66 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00035362001	SubName- Full=Chromosome undetermined scaffold_77, whole genome shotgun sequence; (70 aa)				•			•		0.693
	GSVIVG00028496001	SubName- Full=Chromosome chr7 scaffold_44, whole genome shotgun sequence; (399 aa)							•		0.485
	GSVIVG00008632001	SubName- Full=Chromosome undetermined scaffold_203, whole genome shotgun sequence; (65 aa)				•					0.417

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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	66
cd00922	136	Cyt_c_Oxidase_IV Cytochrome c oxidase subunit IV.	92.66
PF02936	142	COX4: Cytochrome c oxidase subunit IV; InterPro: I	84.91

>cd00922 Cyt_c_Oxidase_IV Cytochrome c oxidase subunit IV

Probab=92.66  E-value=0.58  Score=30.80  Aligned_cols=50  Identities=20%  Similarity=0.146  Sum_probs=42.4

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHhCCCCccccCcHHHHHHHHhhhhh
Q 035376            7 EGLLPLGIIAAMLTIAGNAQYQIHKAAHGRPKHVGNDMWDVAMERRDKKL   56 (66)
Q Consensus         7 E~Lpp~gIi~~~~~v~G~~~~~i~~~~~Gk~~R~~~D~wd~~mm~RD~RL   56 (66)
                      |-..-++....++++.++....++.+.+|-+++.-.+.|+....||-+..
T Consensus        73 ewk~v~~~~~~~i~~s~~~~~~~r~~~~~~~P~T~t~Ewqea~~er~~~~  122 (136)
T cd00922          73 EWKTVFGGVLAFIGITGVIFGLQRAFVYGPKPHTFTEEWQEAQLERMLDM  122 (136)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCcCHHHHHHHHHHHHHh
Confidence            55667888888889999999999999888888888889999999987764

Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit IV is the largest of the nuclear-encoded subunits. It binds ATP at the matrix side, leading to an allosteric inhibition of enzyme activity at high intramitochondrial ATP/ADP ratios. In mammals, subunit IV has a lung-specific isoform and a ubiquitously expressed isoform.

>PF02936 COX4: Cytochrome c oxidase subunit IV; InterPro: IPR004203 Cytochrome c oxidase, a 13 sub-unit complex (1

Probab=84.91  E-value=4.7  Score=26.70  Aligned_cols=49  Identities=12%  Similarity=-0.032  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHhCCCCccccCcHHHHHHHHhhhh
Q 035376            7 EGLLPLGIIAAMLTIAGNAQYQIHKAAHGRPKHVGNDMWDVAMERRDKK   55 (66)
Q Consensus         7 E~Lpp~gIi~~~~~v~G~~~~~i~~~~~Gk~~R~~~D~wd~~mm~RD~R   55 (66)
                      |--..++.+..++++++.+...++.+.++..++--.+.|+....+|=..
T Consensus        73 ewk~v~~~~~~~i~~s~~l~~~~r~~~~~~~P~T~~~Ew~ea~~~~m~~  121 (142)
T PF02936_consen   73 EWKKVFGGVFIFIGFSVLLFIWQRSYVYPPLPHTFSKEWQEAQNERMLD  121 (142)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHT-----GGGSHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHH
Confidence            3345678888888899999999998888776777788999988877444

9.3.1 from EC) is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit IV. The Dictyostelium discoideum (Slime mould) member of this family is called COX VI. The Saccharomyces cerevisiae protein YGX6_YEAST appears to be the yeast COX IV subunit.; GO: 0004129 cytochrome-c oxidase activity; PDB: 3ABK_Q 3AG1_Q 3ASN_Q 1OCZ_D 2EIN_Q 2OCC_D 2YBB_O 3AG3_D 1OCO_Q 1V55_Q ....

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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

ID	Length	Definition	Probability
Query	66
1v54_D	147	Cytochrome C oxidase subunit IV isoform 1; oxidore	88.58
2y69_D	169	Cytochrome C oxidase subunit 4 isoform 1; electron	86.89

>1v54_D Cytochrome C oxidase subunit IV isoform 1; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: f.23.1.1 PDB: 1oco_D* 1occ_D* 1ocz_D* 1ocr_D* 1v55_D* 2dyr_D* 2dys_D* 2eij_D* 2eik_D* 2eil_D* 2eim_D* 2ein_D* 2occ_D* 2ybb_O* 2zxw_D* 3abk_D* 3abl_D* 3abm_D* 3ag1_D* 3ag2_D* ...

Probab=88.58  E-value=1.8  Score=28.19  Aligned_cols=47  Identities=11%  Similarity=0.049  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHhCCCCccccCcHHHHHHHHhhhh
Q 035376            9 LLPLGIIAAMLTIAGNAQYQIHKAAHGRPKHVGNDMWDVAMERRDKK   55 (66)
Q Consensus         9 Lpp~gIi~~~~~v~G~~~~~i~~~~~Gk~~R~~~D~wd~~mm~RD~R   55 (66)
                      -+-+|.+..++++++.....++.+.++.+++--.+.|+....+|=..
T Consensus        79 K~v~g~v~~~i~~s~~~f~~~r~~v~~p~P~T~~~Ewqeaq~erm~~  125 (147)
T 1v54_D           79 KTVVGAAMFFIGFTALLLIWEKHYVYGPIPHTFEEEWVAKQTKRMLD  125 (147)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTCCCCCGGGSHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCCCHHHHHHHHHHHHH
Confidence            44577777888888888888999988888888899999888877444

>2y69_D Cytochrome C oxidase subunit 4 isoform 1; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=86.89  E-value=2.5  Score=28.15  Aligned_cols=47  Identities=11%  Similarity=0.049  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHhCCCCccccCcHHHHHHHHhhhh
Q 035376            9 LLPLGIIAAMLTIAGNAQYQIHKAAHGRPKHVGNDMWDVAMERRDKK   55 (66)
Q Consensus         9 Lpp~gIi~~~~~v~G~~~~~i~~~~~Gk~~R~~~D~wd~~mm~RD~R   55 (66)
                      -+-+|.+..++++++.....++.+.++.+++--.+.|+....+|=..
T Consensus       101 K~V~ggv~~~i~~s~~~f~~~r~~v~~p~P~T~~~Ewqeaq~erml~  147 (169)
T 2y69_D          101 KTVVGAAMFFIGFTALLLIWEKHYVYGPIPHTFEEEWVAKQTKRMLD  147 (169)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTCCCCCGGGSHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCCCHHHHHHHHHHHHH
Confidence            34577777888888888888999988888888899999888877444

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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

ID	Length	Definition	Probability
Query	66
d1v54d_	144	Mitochondrial cytochrome c oxidase subunit IV {Cow	89.32

>d1v54d_ f.23.1.1 (D:) Mitochondrial cytochrome c oxidase subunit IV {Cow (Bos taurus) [TaxId: 9913]}

class: Membrane and cell surface proteins and peptides
fold: Single transmembrane helix
superfamily: Mitochondrial cytochrome c oxidase subunit IV
family: Mitochondrial cytochrome c oxidase subunit IV
domain: Mitochondrial cytochrome c oxidase subunit IV
species: Cow (Bos taurus) [TaxId: 9913]

Probab=89.32  E-value=0.72  Score=28.51  Aligned_cols=47  Identities=11%  Similarity=0.049  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHhCCCCccccCcHHHHHHHHhhhh
Q 035376            9 LLPLGIIAAMLTIAGNAQYQIHKAAHGRPKHVGNDMWDVAMERRDKK   55 (66)
Q Consensus         9 Lpp~gIi~~~~~v~G~~~~~i~~~~~Gk~~R~~~D~wd~~mm~RD~R   55 (66)
                      -.-+|.+..++++++.....++.+.++.+++--.+.|+..+.+|=..
T Consensus        76 K~v~g~~~~~i~~s~~i~~~~r~~v~p~~P~T~~~Ewqeaq~erm~~  122 (144)
T d1v54d_          76 KTVVGAAMFFIGFTALLLIWEKHYVYGPIPHTFEEEWVAKQTKRMLD  122 (144)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTCCCCCGGGSHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHH
Confidence            34567777788888888889999999988888899999998887443