Citrus Sinensis ID: 044560

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------
Protein Sequence
MILVNVQVIDMLLFKGTEELNNILEHAKQRHHVIGQYVLGPQGLVQDLDPKDQGLSSFLKNFYKSNYF
Secondary Structure (PSIPRED)
ccccccEEEEEEEEccHHHHHHHHHHHHHHcEEEEEEEEccccccccccccccccHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHHccHHHHHHHHHHHHHccEEEEEEEEcccccHHccccccccccHHHHHHHccccc
Coil and Loop (DISEMBL)
MILVNVQVIDMLLFKGTEELNNILEHAKQRHHVIgqyvlgpqglvqdldpkdqglSSFLKnfyksnyf
Flexible Loop (DISEMBL)
MILVNVQVIDMLLFKGTEELNNILEHAKQRHHVIGQYVLGPQGLVQDLDPKDQGLSsflknfyksnyf
Low Complexity Region (SEG)
MILVNVQVIDMLLFKGTEELNNILEHAKQRHHVIGQYVLGPQGLVQDLDPKDQGLSSFLKNFYKSNYF
Disordered region (IsUnstruct)
*ILVNVQVIDMLLFKGTEELNNILEHAKQRHHVIGQYVLGPQGLVQDL*********FLK*F******
Disordered Region (DISOPRED)
***VNVQVIDMLLFKGTEELNNILEHAKQRHHVIGQYVLG*****************FLKNFYKS***
Disordered Region (DISEMBL)
MILVNVQVIDMLLFKGTEELNNILEHAKQRHHVIGQYVLGPQGLVQDLDPKDQGLSSFLKNFYKSNYF
Disordered Region (DISPRO)
MILVNVQVIDMLLFKGTEELNNILEHAKQRHHVIGQYVLGPQGLVQDL***DQGLSSFLKNFYKSNYF
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MILVNVQVIDMLLFKGTEELNNILEHAKQRHHVIGQYVLGPQGLVQDLDPKDQGLSSFLKNFYKSNYF
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	68	2.2.26 [Sep-21-2011]
Q9LHI0	133	NADH dehydrogenase [ubiqu	yes	no	0.955	0.488	0.636	1e-18

>sp|Q9LHI0|NDUA6_ARATH NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 OS=Arabidopsis thaliana GN=At3g12260 PE=2 SV=1

 Score = 91.3 bits (225), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 42/66 (63%), Positives = 55/66 (83%), Gaps = 1/66 (1%)

Query: 3   LVNVQVIDMLLFKGTEELNNILEHAKQRHHVIGQYVLGPQGLVQDLDPKDQGLSSFLKNF 62
           + + +VID+L+FKG EEL +I++HAKQRHH+IGQYV+G +GLVQ+   KDQG + FLKNF
Sbjct: 69  ITDPKVIDLLIFKGMEELTDIVDHAKQRHHIIGQYVVG-EGLVQNTGNKDQGKTDFLKNF 127

Query: 63  YKSNYF 68
           Y SNYF
Sbjct: 128 YTSNYF 133

Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed to be not 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	68
TAIR|locus:2082209	133	AT3G12260 "AT3G12260" [Arabido	0.955	0.488	0.636	6.5e-19

TAIR|locus:2082209 AT3G12260 "AT3G12260" [Arabidopsis thaliana (taxid:3702)]

 Score = 227 (85.0 bits), Expect = 6.5e-19, P = 6.5e-19
 Identities = 42/66 (63%), Positives = 55/66 (83%)

Query:     3 LVNVQVIDMLLFKGTEELNNILEHAKQRHHVIGQYVLGPQGLVQDLDPKDQGLSSFLKNF 62
             + + +VID+L+FKG EEL +I++HAKQRHH+IGQYV+G +GLVQ+   KDQG + FLKNF
Sbjct:    69 ITDPKVIDLLIFKGMEELTDIVDHAKQRHHIIGQYVVG-EGLVQNTGNKDQGKTDFLKNF 127

Query:    63 YKSNYF 68
             Y SNYF
Sbjct:   128 YTSNYF 133


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        0.322   0.142   0.409    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       68        68   0.00091  102 3  11 22  0.44    28
                                                     29  0.38    29


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:  442 (47 KB)
  Total size of DFA:  79 KB (2064 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:  8.84u 0.10s 8.94t   Elapsed:  00:00:01
  Total cpu time:  8.84u 0.10s 8.94t   Elapsed:  00:00:01
  Start:  Mon May 20 16:41:59 2013   End:  Mon May 20 16:42:00 2013

GO:0003824 "catalytic activity" evidence=ISS

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0016020 "membrane" evidence=IDA

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

GO:0006096 "glycolysis" evidence=RCA

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

GO:0009060 "aerobic respiration" evidence=RCA

GO:0009853 "photorespiration" evidence=RCA

GO:0046686 "response to cadmium ion" 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

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	68
KOG3426	124	consensus NADH:ubiquinone oxidoreductase, NDUFA6/B	99.97
PF05347	59	Complex1_LYR: Complex 1 protein (LYR family); Inte	91.94
PF13232	61	Complex1_LYR_1: Complex1_LYR-like	81.61

>KOG3426 consensus NADH:ubiquinone oxidoreductase, NDUFA6/B14 subunit [Energy production and conversion]

Probab=99.97  E-value=5e-31  Score=174.43  Aligned_cols=57  Identities=46%  Similarity=0.824  Sum_probs=54.8

Q ss_pred             ccchhHHHHHHHhhHHHHHHHHHHhhcccchhhhhhcCCCccccCCCCCCCCcchHHHHHhhcCCC
Q 044560            3 LVNVQVIDMLLFKGTEELNNILEHAKQRHHVIGQYVLGPQGLVQDLDPKDQGLSSFLKNFYKSNYF   68 (68)
Q Consensus         3 VtD~rVID~Lv~KG~~EL~e~~~~wKQ~~Hvm~~~~~~~~~~~~~~g~~~~~~sdFL~kFy~G~~~   68 (68)
                      ||||||||+||+||+|||+|++.+|||+||||+||..|         +++|+|+|||||||.|+||
T Consensus        68 vTD~rViDlLV~kg~~elkeiv~~~kqr~Him~y~f~e---------n~d~kptDFLskF~~g~~~  124 (124)
T KOG3426|consen   68 VTDPRVIDLLVIKGMEELKEIVDHWKQRHHIMRYYFTE---------NKDPKPTDFLSKFYTGNYF  124 (124)
T ss_pred             cCCchhhhHHHHhhHHHHHHHHHHHhCchHHHHHhhcc---------cCCCCchhHHHHHhccCCC
Confidence            89999999999999999999999999999999998866         7899999999999999997

>PF05347 Complex1_LYR: Complex 1 protein (LYR family); InterPro: IPR008011 This family of short proteins includes proteins from the NADH-ubiquinone oxidoreductase complex I

Probab=91.94  E-value=0.12  Score=28.70  Aligned_cols=19  Identities=42%  Similarity=0.506  Sum_probs=17.9

Q ss_pred             ccchhHHHHHHHhhHHHHH
Q 044560            3 LVNVQVIDMLLFKGTEELN   21 (68)
Q Consensus         3 VtD~rVID~Lv~KG~~EL~   21 (68)
                      +|||..|+.|+-+|+++|+
T Consensus        40 ~~d~~~I~~~l~~g~~~l~   58 (59)
T PF05347_consen   40 ETDPEKIEELLKKGEEELE   58 (59)
T ss_pred             CCCHHHHHHHHHHHHHHhc
Confidence            7899999999999999986

The family includes the B14 subunit from bovine NADH-ubiquinone oxidoreductase B14 subunit Q02366 from SWISSPROT, and the B22 subunit from the human enzyme Q9Y6M9 from SWISSPROT. The family has been named LYR after a highly conserved tripeptide motif close to the N terminus of these proteins. Members of this family also found in yeast which do contain this complex. In these organisms they are believed to be be required for iron-sulphur custer biogenesis.

>PF13232 Complex1_LYR_1: Complex1_LYR-like

Probab=81.61  E-value=1.8  Score=24.29  Aligned_cols=20  Identities=30%  Similarity=0.393  Sum_probs=18.6

Q ss_pred             ccchhHHHHHHHhhHHHHHH
Q 044560            3 LVNVQVIDMLLFKGTEELNN   22 (68)
Q Consensus         3 VtD~rVID~Lv~KG~~EL~e   22 (68)
                      +|||.-|+-++-+|+.+|..
T Consensus        40 ~td~~~i~~~l~~~~~~L~~   59 (61)
T PF13232_consen   40 VTDPEKIAKLLKEGRKELEL   59 (61)
T ss_pred             CCCHHHHHHHHHHHHHHHHH
Confidence            78999999999999999976

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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