Citrus Sinensis ID: 035197

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70

MAGEASMLKFLKPKSRLQPVDVQAAAFWGVAAVSGALYLIQVFSFSFVHFVLPLIHDLLYLCSSFPHPLL

cccccccccccccccccccHHHHHHHHHHHHHHHEEEEEEEEcccHHHHHHHHHHHHHHHHHHccccccc

cccHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHcccccccc

mageasmlkflkpksrlqpvdvQAAAFWGVAAVSGALYLIQVFSFSFVHFVLPLIHDLLylcssfphpll

mageasmlkflkpksrlQPVDVQAAAFWGVAAVSGALYLIQVFSFSFVHFVLPLIHDLLYLCssfphpll

MAGEASMLKFLKPKSRLQPVDVQAAAFWGVAAVSGALYLIQVFSFSFVHFVLPLIHDLLYLCSSFPHPLL

*****************QPVDVQAAAFWGVAAVSGALYLIQVFSFSFVHFVLPLIHDLLYLCSSF*****

************PKSRLQPVDVQAAAFWGVAAVSGALYLIQVFSFSFVHFVLPLIHDLLYLCSSFPHPLL

MAGEASMLKFLKPKSRLQPVDVQAAAFWGVAAVSGALYLIQVFSFSFVHFVLPLIHDLLYLCSSFPHPLL

*******LK*LKPKSRLQPVDVQAAAFWGVAAVSGALYLIQVFSFSFVHFVLPLIHDLLYLCSSFPHP**

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iiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooo

iiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooHHHHHHHHHHHHHHHHiiiiiii

iiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHoooooHHHHHHHHHHHHHHHHHHHHiiiii

SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooo

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MAGEASMLKFLKPKSRLQPVDVQAAAFWGVAAVSGALYLIQVFSFSFVHFVLPLIHDLLYLCSSFPHPLL

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

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	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		70
224145008		59	predicted protein [Populus trichocarpa]	0.642	0.762	0.6	1e-07
356509088		52	PREDICTED: uncharacterized protein LOC10	0.428	0.576	0.666	0.0006

>gi\|224145008\|ref\|XP_002325493.1\| predicted protein [Populus trichocarpa] gi\|118482907\|gb\|ABK93367.1\| unknown [Populus trichocarpa] gi\|118483491\|gb\|ABK93644.1\| unknown [Populus trichocarpa] gi\|118487244\|gb\|ABK95450.1\| unknown [Populus trichocarpa] gi\|118488463\|gb\|ABK96046.1\| unknown [Populus trichocarpa] gi\|222862368\|gb\|EEE99874.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score = 60.8 bits (146), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/45 (60%), Positives = 34/45 (75%)

Query: 1  MAGEASMLKFLKPKSRLQPVDVQAAAFWGVAAVSGALYLIQVFSF 45
          MAGE +M KFL P+ RLQ  D+Q AAFWGVAA + AL+L+Q F +
Sbjct: 1  MAGENAMFKFLSPRLRLQSTDIQTAAFWGVAAGTTALWLVQPFDW 45

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|356509088\|ref\|XP_003523284.1\| PREDICTED: uncharacterized protein LOC100811454 [Glycine max]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		70
TAIR\|locus:505006312		57	AT2G40765 "AT2G40765" [Arabido	0.728	0.894	0.433	2.3e-07

TAIR\|locus:505006312 AT2G40765 "AT2G40765" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 118 (46.6 bits), Expect = 2.3e-07, P = 2.3e-07
 Identities = 23/53 (43%), Positives = 37/53 (69%)

Query:     1 MAGEASMLKFLKPKSRLQPVDVQAAAFWGVAAVSGALYLIQVFSFSFVHFVLP 53
             MAG + +L  +KPK  +Q +D+QAAA WG+AA +GA++++Q F +    F+ P
Sbjct:     1 MAGTSGLLNAVKPK--IQTIDIQAAAGWGIAAAAGAIWVVQPFGWIKKTFIDP 51


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        0.331   0.142   0.443    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       70        70   0.00091  102 3  11 21  0.36    28
                                                     29  0.41    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:  440 (47 KB)
  Total size of DFA:  81 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:  7.29u 0.19s 7.48t   Elapsed:  00:00:01
  Total cpu time:  7.29u 0.19s 7.48t   Elapsed:  00:00:01
  Start:  Fri May 10 06:26:29 2013   End:  Fri May 10 06:26:30 2013

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0005739 "mitochondrion" evidence=IDA

GO:0005750 "mitochondrial respiratory chain complex III" evidence=IDA

GO:0009627 "systemic acquired resistance" evidence=RCA

GO:0009853 "photorespiration" evidence=RCA

GO:0034976 "response to endoplasmic reticulum stress" 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

No confident hit detected by STRING

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	Alignment Graph	Length	Definition	Probability
Query		70
PF08997		56	UCR_6-4kD: Ubiquinol-cytochrome C reductase comple	86.72
PF09796		64	QCR10: Ubiquinol-cytochrome-c reductase complex su	80.67

>PF08997 UCR_6-4kD: Ubiquinol-cytochrome C reductase complex, 6	Back alignment and domain information

Probab=86.72  E-value=0.16  Score=31.31  Aligned_cols=22  Identities=27%  Similarity=0.436  Sum_probs=19.3

Q ss_pred             hhHHHHHHhhhhhhheeeeeee
Q 035197           20 VDVQAAAFWGVAAVSGALYLIQ   41 (70)
Q Consensus        20 tDi~aaA~WGvaa~~gAlwLVQ   41 (70)
                      .=+.+++.||.+++++.+|+++
T Consensus        16 ~w~ps~~~~G~~~~l~lvy~TD   37 (56)
T PF08997_consen   16 NWIPSAAAWGAAGGLALVYFTD   37 (56)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HhchhHHHHhhhhhhheeeecc
Confidence            3467899999999999999986

4kD protein; InterPro: IPR015089 The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is an essential component of the mitochondrial cellular respiratory chain. This family represents the 6.4 kDa protein, which may be closely linked to the iron-sulphur protein in the complex and function as an iron-sulphur protein-binding factor []. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0009055 electron carrier activity; PDB: 1NTM_K 1SQV_K 1SQB_K 1NU1_K 1SQQ_K 1BE3_K 1BGY_W 2YBB_k 2FYU_K 1L0N_K ....

>PF09796 QCR10: Ubiquinol-cytochrome-c reductase complex subunit (QCR10); InterPro: IPR019182 This entry represents subunit 10 of the cytochrome b-c1 complex (also known as the ubiquinol-cytochrome c reductase complex or complex III)	Back alignment and domain information

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	Alignment Graph	Length	Definition	Probability
Query		70
2fyu_K		56	Ubiquinol-cytochrome C reductase complex 6.4 kDa;	92.65

>2fyu_K Ubiquinol-cytochrome C reductase complex 6.4 kDa; transmembrane helices, 11 protein complex, oxidoreductase; HET: HEM FDN; 2.26A {Bos taurus} SCOP: f.23.15.1 PDB: 1sqq_K* 1sqv_K* 1sqx_K* 1l0l_K* 1ntk_K* 1ntm_K* 1ntz_K* 1nu1_K* 1sqp_K* 1sqb_K* 1be3_K* 1bgy_K* 2ybb_K* 1l0n_K* 1qcr_K*	Back alignment and structure

Probab=92.65  E-value=0.017  Score=34.39  Aligned_cols=20  Identities=25%  Similarity=0.672  Sum_probs=18.6

Q ss_pred             HHHHHHhhhhhhheeeeeee
Q 035197           22 VQAAAFWGVAAVSGALYLIQ   41 (70)
Q Consensus        22 i~aaA~WGvaa~~gAlwLVQ   41 (70)
                      +-+++.||.+++++++|+++
T Consensus        18 ~psa~~~Gaaa~v~~ly~td   37 (56)
T 2fyu_K           18 VPTASLWGAVGAVGLVWATD   37 (56)
T ss_dssp             HHHHHHHHHHHHHHHHHHHT
T ss_pred             hhhhhhhhhhhhhheeeecc
Confidence            56799999999999999998

PyMOL of 2fyu

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	Alignment Graph	Length	Definition	Probability
Query		70
d2fyuk1		53	Subunit XI (6.4 kDa protein) of cytochrome bc1 com	80.24

>d2fyuk1 f.23.15.1 (K:1-53) Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) {Cow (Bos taurus) [TaxId: 9913]}	Back information, alignment and structure

class: Membrane and cell surface proteins and peptides
fold: Single transmembrane helix
superfamily: Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
family: Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
domain: Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=80.24  E-value=0.14  Score=29.17  Aligned_cols=21  Identities=24%  Similarity=0.509  Sum_probs=17.9

Q ss_pred             hhHHHHHHhhhhhhheeeeee
Q 035197           20 VDVQAAAFWGVAAVSGALYLI   40 (70)
Q Consensus        20 tDi~aaA~WGvaa~~gAlwLV   40 (70)
                      +=|-+++.||.+++++.+|.+
T Consensus        16 ~wips~~~~G~a~gl~lvy~T   36 (53)
T d2fyuk1          16 NWVPTASLWGAVGAVGLVWAT   36 (53)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhhhhhhhhhhhheeeeeee
Confidence            346789999999999999876

PyMOL of d2fyuk1