Citrus Sinensis ID: 035119

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70---
Protein Sequence
MGHTGEFFRRRDGWRKHPLLTSNLRQATPGLGIALVAFGIYLVGEQVYNRVIAPSPSHSHHTHHQHSAASSSH
Secondary Structure (PSIPRED)
cccccccHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHHHccccccccHHccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccc
Coil and Loop (DISEMBL)
mghtgeffrrrdgwrkhplltsnlrqatpGLGIALVAFGIYLVGEqvynrviapspshshhthhqhsaasssh
Flexible Loop (DISEMBL)
mghtgeffrrrdgwrkhpLLTSNLRQATPGLGIALVAFGIYLVGEQVYNRVIAPSPSHShhthhqhsaasssh
Low Complexity Region (SEG)
MGHTGEFFRRRDGWRKHPLLTSNLRQATPGLGIALVAFGIYLVGEQVYNRVIapspshshhthhqhsaasssh
Disordered region (IsUnstruct)
**********RDGWRKHPLLTSNLRQATPGLGIALVAFGIYLVGEQVYNRVIA********************
Disordered Region (DISOPRED)
****GEFFRRRDGWRKHPLLTSNLRQATPGLGIALVAFGIYLVGEQVY*************************
Disordered Region (DISEMBL)
MGHTGEFFRRRDGWRKHPLLTSNLRQATPGLGIALVAFGIYLVGEQVYNRVIAPS******************
Disordered Region (DISPRO)
***TGEFFRRRDGWRKHPLLTSNLRQATPGLGIALVAFGIYLVGEQVYNRVIA********************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MGHTGEFFRRRDGWRKHPLLTSNLRQATPGLGIALVAFGIYLVGEQVYNRVIAPSPSHSHHTHHQHSAASSSH
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	73	2.2.26 [Sep-21-2011]
Q9M9R9	73	NADH dehydrogenase [ubiqu	yes	no	0.931	0.931	0.619	6e-19
O64725	72	NADH dehydrogenase [ubiqu	no	no	0.863	0.875	0.571	2e-17

>sp|Q9M9R9|NDB3B_ARATH NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-B OS=Arabidopsis thaliana GN=At1g14450 PE=3 SV=1

 Score = 92.4 bits (228), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 44/71 (61%), Positives = 54/71 (76%), Gaps = 3/71 (4%)

Query: 1  MGHTGEFFRRRDGWRKHPLLTSNLRQATPGLGIALVAFGIYLVGEQVYNRVIAPSPSHSH 60
          +G TGEFFRRRD WRKHP+L++ +R A PGLGI + AF +YLVGEQ+YN+ +APS S SH
Sbjct: 5  LGTTGEFFRRRDEWRKHPMLSNQMRHALPGLGIGVAAFCVYLVGEQIYNKALAPSKS-SH 63

Query: 61 HTHHQHSAASS 71
            HHQ   A S
Sbjct: 64 --HHQEQTAPS 72

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)

>sp|O64725|NDB3A_ARATH NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A OS=Arabidopsis thaliana GN=At2g02510 PE=3 SV=1

 Score = 87.4 bits (215), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 36/63 (57%), Positives = 49/63 (77%)

Query: 1  MGHTGEFFRRRDGWRKHPLLTSNLRQATPGLGIALVAFGIYLVGEQVYNRVIAPSPSHSH 60
          +G TGEFFRRRD WRKHP+L++ +R A PG+GI + AF +YLVGEQ+Y++++APS   SH
Sbjct: 5  LGTTGEFFRRRDEWRKHPMLSNQMRHALPGIGIGVGAFCVYLVGEQIYSKLMAPSSQSSH 64

Query: 61 HTH 63
             
Sbjct: 65 QKQ 67

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	73
TAIR|locus:2012592	73	AT1G14450 [Arabidopsis thalian	0.712	0.712	0.634	1.3e-15
TAIR|locus:2065243	72	AT2G02510 [Arabidopsis thalian	0.712	0.722	0.596	1.4e-14

TAIR|locus:2012592 AT1G14450 [Arabidopsis thaliana (taxid:3702)]

 Score = 196 (74.1 bits), Expect = 1.3e-15, P = 1.3e-15
 Identities = 33/52 (63%), Positives = 43/52 (82%)

Query:     1 MGHTGEFFRRRDGWRKHPLLTSNLRQATPGLGIALVAFGIYLVGEQVYNRVI 52
             +G TGEFFRRRD WRKHP+L++ +R A PGLGI + AF +YLVGEQ+YN+ +
Sbjct:     5 LGTTGEFFRRRDEWRKHPMLSNQMRHALPGLGIGVAAFCVYLVGEQIYNKAL 56

GO:0005739 "mitochondrion" evidence=ISM;IEA

GO:0008137 "NADH dehydrogenase (ubiquinone) activity" evidence=IEA

GO:0009853 "photorespiration" evidence=RCA;TAS

GO:0031966 "mitochondrial membrane" evidence=IDA

GO:0045271 "respiratory chain complex I" evidence=IDA

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

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

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

TAIR|locus:2065243 AT2G02510 [Arabidopsis thaliana (taxid:3702)]

 Score = 186 (70.5 bits), Expect = 1.4e-14, P = 1.4e-14
 Identities = 31/52 (59%), Positives = 44/52 (84%)

Query:     1 MGHTGEFFRRRDGWRKHPLLTSNLRQATPGLGIALVAFGIYLVGEQVYNRVI 52
             +G TGEFFRRRD WRKHP+L++ +R A PG+GI + AF +YLVGEQ+Y++++
Sbjct:     5 LGTTGEFFRRRDEWRKHPMLSNQMRHALPGIGIGVGAFCVYLVGEQIYSKLM 56


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        0.328   0.146   0.462    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       73        52   0.00091  102 3  11 22  0.39    27
                                                     29  0.47    26


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:  474 (50 KB)
  Total size of DFA:  80 KB (2063 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  6.73u 0.14s 6.87t   Elapsed:  00:00:00
  Total cpu time:  6.73u 0.14s 6.87t   Elapsed:  00:00:00
  Start:  Fri May 10 05:45:46 2013   End:  Fri May 10 05:45:46 2013

GO:0005739 "mitochondrion" evidence=IEA;IDA

GO:0008137 "NADH dehydrogenase (ubiquinone) activity" evidence=IEA

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

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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)
Q9M9R9	NDB3B_ARATH	No assigned EC number	0.6197	0.9315	0.9315	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:
	eugene3.00860085	SubName- Full=Putative uncharacterized protein; (68 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	eugene3.00161359	SubName- Full=Putative uncharacterized protein; (63 aa)				•			•		0.633

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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	73
PF08122	57	NDUF_B12: NADH-ubiquinone oxidoreductase B12 subun	99.92
KOG4631	100	consensus NADH:ubiquinone oxidoreductase, NDUFB3/B	99.74

>PF08122 NDUF_B12: NADH-ubiquinone oxidoreductase B12 subunit family; InterPro: IPR012576 NADH:ubiquinone oxidoreductase (complex I) (1

Probab=99.92  E-value=5.3e-26  Score=136.87  Aligned_cols=41  Identities=32%  Similarity=0.755  Sum_probs=38.7

Q ss_pred             cCCCcchhhhhcCCCccc---hhhhhcCchhHHHHHHHHHHHHH
Q 035119            5 GEFFRRRDGWRKHPLLTS---NLRQATPGLGIALVAFGIYLVGE   45 (73)
Q Consensus         5 ~DPW~R~EaWRy~p~f~~---~~~~~fPGlgig~~AF~vyv~~E   45 (73)
                      ||||+|||||||+|.|++   +++.+|||||||++||++||++|
T Consensus         2 kDPW~RneaWRy~~~f~~~~~~~~~~fpG~~~G~aaf~~~v~~E   45 (57)
T PF08122_consen    2 KDPWARNEAWRYHPQFSRWNSFFKNMFPGFGIGFAAFAVYVAVE   45 (57)
T ss_pred             CChHhhhHHHhCCcccCchHHHHHHhcCCcHHHHHHHHHHHHHH
Confidence            899999999999999973   56889999999999999999999

6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family consists of the B12 subunit of NADH:ubiquinone oxidoreductase proteins. The function of this subunit is unclear [].; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion

>KOG4631 consensus NADH:ubiquinone oxidoreductase, NDUFB3/B12 subunit [Energy production and conversion]

Probab=99.74  E-value=2.1e-18  Score=114.39  Aligned_cols=58  Identities=16%  Similarity=0.194  Sum_probs=46.2

Q ss_pred             CcCCCcchhhhhcCC--Ccc--chhhh-hcCchhHHHHHHHHHHHHHHHHhhhcCC-CCCCCCC
Q 035119            4 TGEFFRRRDGWRKHP--LLT--SNLRQ-ATPGLGIALVAFGIYLVGEQVYNRVIAP-SPSHSHH   61 (73)
Q Consensus         4 ~~DPW~R~EaWRy~p--~f~--~~~~~-~fPGlgig~~AF~vyv~~E~~~~~~~~p-~~~~~hh   61 (73)
                      -||||.|||+|||.+  .++  .+|+. +||||++||+||++.|++|+++...... .+|++||
T Consensus        37 LkDPW~RNevwrY~~ph~~~~~~~f~~~~f~G~k~Gfaaf~a~v~vEyal~~~~Hgtt~dkgHH  100 (100)
T KOG4631|consen   37 LKDPWGRNEVWRYMGPHGFAKSVSFSDVFFKGFKWGFAAFVAAVGVEYALESLNHGTTKDKGHH  100 (100)
T ss_pred             ccCchhcchhhhccCcccceeeeeehhhhcccchHHHHHHHHHHHHHHHHHhcccCccCCcCCC
Confidence            389999999999999  454  45665 9999999999999999999999853211 1556665

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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	73
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	80.19

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=80.19  E-value=0.68  Score=33.13  Aligned_cols=28  Identities=18%  Similarity=0.142  Sum_probs=12.7

Q ss_pred             HHHHHHHHHHHhhhcCCCCCCCCCcccc
Q 035119           38 FGIYLVGEQVYNRVIAPSPSHSHHTHHQ   65 (73)
Q Consensus        38 F~vyv~~E~~~~~~~~p~~~~~hh~~~~   65 (73)
                      +.-++++|.+++.+..+..|.+||.||.
T Consensus       314 ~~P~~~~~~~~~~~~~~~~~~~~~~~~~  341 (341)
T 2p67_A          314 LSPRTGLRQLSEFIQTQYFDEGHHHHHH  341 (341)
T ss_dssp             SCHHHHHHHHHHHHHC------------
T ss_pred             CCHHHHHHHHHHHHhhhcccccccccCC
Confidence            5567788888888888888999988873

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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