Citrus Sinensis ID: 035316

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------
Protein Sequence
MAMKSALKSIRERGLGSFLRELKEEGFLRALLDGNLMQTKLHNRGATLVGVDKFGNKYYQKLDEQFGQ
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHHHHHHHccHHHccccccHHHHHHccccEEEEEcccHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHccHHHHHHHHHHcccHEEccccccHHEEEEccccEEEcEcccccHHHHHHHccccc
Coil and Loop (DISEMBL)
MAMKSALKSIRERGLGSFLRELKEEGFLRALLDGNLMQTKLHNRGATLVGVDKFGNKYYQKLDEQFGQ
Flexible Loop (DISEMBL)
mamksalksirergLGSFLRELKEEGFLRALLDGNLMQTKLHNRGATLVGVDKFGNKYYQKLDEQFGQ
Low Complexity Region (SEG)
MAMKSALKSIRERGLGSFLRELKEEGFLRALLDGNLMQTKLHNRGATLVGVDKFGNKYYQKLDEQFGQ
Disordered region (IsUnstruct)
***************GSFLRELKEEGFLRALLDGNLMQTKLHNRGATLVGVDKFGNKYYQK*******
Disordered Region (DISOPRED)
*******KSIRERGLGSFLRELKEEGFLRALLDGNLMQTKLHNRGATLVGVDKFGNKYYQK*******
Disordered Region (DISEMBL)
*********IRERGLGSFLRELKEEGFLRALLDGNLMQTKLHNRGATLVGVDKFGNKYYQKLDEQFGQ
Disordered Region (DISPRO)
MAMKSALKSIRERGLGSFLRELKEEGFLRALLDGNLMQTKLHNRGATLVGVDKFGNKYYQKLDE****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAMKSALKSIRERGLGSFLRELKEEGFLRALLDGNLMQTKLHNRGATLVGVDKFGNKYYQKLDEQFGQ
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]
Q9M9M9	159	Probable NADH dehydrogena	yes	no	0.955	0.408	0.727	8e-22

>sp|Q9M9M9|NDUAC_ARATH Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 OS=Arabidopsis thaliana GN=At3g03100 PE=1 SV=1

 Score =  102 bits (254), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 48/66 (72%), Positives = 59/66 (89%), Gaps = 1/66 (1%)

Query: 4  KSALKSIRERGLGSFLRELKEEGFLRALLDGNLMQTKLHNRGATLVGVDKFGNKYYQKL- 62
          KSAL++IRE+GLG F+R ++EEGF+R L DGNL+QTK+HN GATLVGVDKFGNKYYQKL 
Sbjct: 7  KSALEAIREKGLGGFMRMIREEGFMRCLPDGNLLQTKIHNIGATLVGVDKFGNKYYQKLG 66

Query: 63 DEQFGQ 68
          D Q+G+
Sbjct: 67 DTQYGR 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)

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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:2097765	159	AT3G03100 [Arabidopsis thalian	0.955	0.408	0.727	9e-22
ASPGD|ASPL0000048093	136	AN2260 [Emericella nidulans (t	0.647	0.323	0.382	0.00045

TAIR|locus:2097765 AT3G03100 [Arabidopsis thaliana (taxid:3702)]

 Score = 254 (94.5 bits), Expect = 9.0e-22, P = 9.0e-22
 Identities = 48/66 (72%), Positives = 59/66 (89%)

Query:     4 KSALKSIRERGLGSFLRELKEEGFLRALLDGNLMQTKLHNRGATLVGVDKFGNKYYQKL- 62
             KSAL++IRE+GLG F+R ++EEGF+R L DGNL+QTK+HN GATLVGVDKFGNKYYQKL 
Sbjct:     7 KSALEAIREKGLGGFMRMIREEGFMRCLPDGNLLQTKIHNIGATLVGVDKFGNKYYQKLG 66

Query:    63 DEQFGQ 68
             D Q+G+
Sbjct:    67 DTQYGR 72

GO:0005739 "mitochondrion" evidence=ISM;IDA

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

GO:0009055 "electron carrier activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016491 "oxidoreductase activity" evidence=ISS

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

GO:0050897 "cobalt ion binding" 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|ASPL0000048093 AN2260 [Emericella nidulans (taxid:162425)]

 Score = 87 (35.7 bits), Expect = 0.00045, P = 0.00045
 Identities = 18/47 (38%), Positives = 28/47 (59%)

Query:    19 LRELKEEGFLRALLDGNLMQTKLHNRGATLVGVDKFGNKYYQKLDEQ 65
             LR L+  GF      G+ MQ     +  TL+G D++GNKYY+ ++E+
Sbjct:     8 LRNLRRIGFKEY---GHQMQYIGDTKAGTLIGTDRYGNKYYENMEEE 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        0.320   0.138   0.382    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:  2
  No. of states in DFA:  371 (40 KB)
  Total size of DFA:  65 KB (2061 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:  7.78u 0.14s 7.92t   Elapsed:  00:00:01
  Total cpu time:  7.78u 0.14s 7.92t   Elapsed:  00:00:01
  Start:  Fri May 10 07:30:07 2013   End:  Fri May 10 07:30:08 2013

GO:0008150 "biological_process" evidence=ND

GO:0016020 "membrane" evidence=IEA

GO:0009055 "electron carrier activity" evidence=IEA

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

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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)
Q9M9M9	NDUAC_ARATH	No assigned EC number	0.7272	0.9558	0.4088	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

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

ID	Length	Definition	E-value
Query	68
PLN02732	159	PLN02732, PLN02732, Probable NADH dehydrogenase [u	1e-33
pfam05071	100	pfam05071, NDUFA12, NADH ubiquinone oxidoreductase	7e-07
PLN03095	115	PLN03095, PLN03095, NADH:ubiquinone oxidoreductase	1e-04

>gnl|CDD|215389 PLN02732, PLN02732, Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit

 Score =  111 bits (280), Expect = 1e-33
 Identities = 50/67 (74%), Positives = 60/67 (89%), Gaps = 1/67 (1%)

Query: 3  MKSALKSIRERGLGSFLRELKEEGFLRALLDGNLMQTKLHNRGATLVGVDKFGNKYYQKL 62
          +KSAL++IRE+GLG FLR L+EEG+LR L DGNL+QTK+HN GATLVGVDKFGNKYYQKL
Sbjct: 6  VKSALEAIREKGLGGFLRMLREEGYLRCLADGNLLQTKIHNIGATLVGVDKFGNKYYQKL 65

Query: 63 -DEQFGQ 68
           D Q+G+
Sbjct: 66 GDTQYGR 72

Length = 159

>gnl|CDD|218414 pfam05071, NDUFA12, NADH ubiquinone oxidoreductase subunit NDUFA12

 Score = 42.2 bits (100), Expect = 7e-07
 Identities = 14/22 (63%), Positives = 17/22 (77%)

Query: 47 TLVGVDKFGNKYYQKLDEQFGQ 68
          TLVG D+FGNKYY+  DE  G+
Sbjct: 2  TLVGEDEFGNKYYENKDELGGR 23

This family contains the 17.2 kD subunit of complex I (NDUFA12) and its homologues. The family also contains a second related eukaryotic protein of unknown function, . Length = 100

>gnl|CDD|215571 PLN03095, PLN03095, NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional

 Score = 36.8 bits (85), Expect = 1e-04
 Identities = 14/28 (50%), Positives = 18/28 (64%)

Query: 41 LHNRGATLVGVDKFGNKYYQKLDEQFGQ 68
          L +R   LVG D+FGNKYY+    Q G+
Sbjct: 5  LASRAGRLVGEDEFGNKYYENPSYQSGR 32

Length = 115

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	68
PLN02732	159	Probable NADH dehydrogenase [ubiquinone] 1 alpha s	99.9
KOG3382	151	consensus NADH:ubiquinone oxidoreductase, B17.2 su	99.69
PRK08183	133	NADH dehydrogenase; Validated	99.64
COG3761	118	NADH:ubiquinone oxidoreductase 17.2 kD subunit [En	99.0
PRK06630	99	hypothetical protein; Provisional	98.96
PLN03095	115	NADH:ubiquinone oxidoreductase 18 kDa subunit; Pro	98.78
PF05071	105	NDUFA12: NADH ubiquinone oxidoreductase subunit ND	98.58
PF15613	38	WHIM2: WSTF, HB1, Itc1p, MBD9 motif 2	92.73

>PLN02732 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit

Probab=99.90  E-value=3.3e-24  Score=149.60  Aligned_cols=67  Identities=73%  Similarity=1.188  Sum_probs=63.2

Q ss_pred             hHHHHHHHHHHhcHHHHHHHHHHcCchhhhcCCcccceeeeecCceEeeeeCCCceeeccCc-cccCC
Q 035316            2 AMKSALKSIRERGLGSFLRELKEEGFLRALLDGNLMQTKLHNRGATLVGVDKFGNKYYQKLD-EQFGQ   68 (68)
Q Consensus         2 ~~~~~~~~i~~~G~~~fl~~l~~~G~~~tww~g~t~~t~~~~~~G~lVGeD~~GNkYYE~~~-~~~gr   68 (68)
                      +|+++|++|+++|++.|+++|+++||++||.||+|++|++|++.|+|||+|+|||||||+.+ ..+||
T Consensus         5 ~~~~~~~~~~~~G~~~~~~~l~~~g~~k~~~~g~t~gt~~~~~~G~lVG~D~~GNkYYE~~~~~~~gr   72 (159)
T PLN02732          5 VVKSALEAIREKGLGGFLRMLREEGYLRCLADGNLLQTKIHNIGATLVGVDKFGNKYYQKLGDTQYGR   72 (159)
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHccchhhccCcceeeeEEEeeCcEEEEecCCCCeeeecCCCCCCCc
Confidence            68999999999999999999999999999999999999999999999999999999999874 56665

>KOG3382 consensus NADH:ubiquinone oxidoreductase, B17

Probab=99.69  E-value=1.3e-17  Score=115.72  Aligned_cols=65  Identities=52%  Similarity=0.841  Sum_probs=59.9

Q ss_pred             hHHHHHHHHHHhcHHHHHHHHHHcCchhhhcCCcccceeeeecCceEeeeeCCCceeeccCccccCC
Q 035316            2 AMKSALKSIRERGLGSFLRELKEEGFLRALLDGNLMQTKLHNRGATLVGVDKFGNKYYQKLDEQFGQ   68 (68)
Q Consensus         2 ~~~~~~~~i~~~G~~~fl~~l~~~G~~~tww~g~t~~t~~~~~~G~lVGeD~~GNkYYE~~~~~~gr   68 (68)
                      |.+++++.+...|+.+|+.+++++|.++|..+ +.+.|..|.+ |+|||+|+||||||||+++||||
T Consensus         5 ~~~s~~~~l~i~~l~k~~qmire~Gglr~~~~-k~yrtd~~ki-GTLVG~DkfGNkYyen~~~fygR   69 (151)
T KOG3382|consen    5 VAKSALEALGIKGLGKFMQMIREEGGLRCLLD-KLYRTDDHKI-GTLVGVDKFGNKYYENNDYFYGR   69 (151)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHHhhccHHHHHH-HHHhcccccc-eeeeeecccccchhcccceeccc
Confidence            56788999999999999999999999999998 7888877777 89999999999999999999998

2 subunit [Energy production and conversion]

>PRK08183 NADH dehydrogenase; Validated

Probab=99.64  E-value=9.7e-17  Score=109.28  Aligned_cols=41  Identities=32%  Similarity=0.566  Sum_probs=37.3

Q ss_pred             HHHHHHHHcCchhhhcCCcccceeeeec-CceEeeeeCCCceeeccCc
Q 035316           17 SFLRELKEEGFLRALLDGNLMQTKLHNR-GATLVGVDKFGNKYYQKLD   63 (68)
Q Consensus        17 ~fl~~l~~~G~~~tww~g~t~~t~~~~~-~G~lVGeD~~GNkYYE~~~   63 (68)
                      ++|.++      +|||+|+|++|+|+++ .|+|||+|++||||||+.+
T Consensus         2 ~~~~~i------f~ww~g~t~~t~~~~~r~g~lVG~D~~GNkYYE~~~   43 (133)
T PRK08183          2 SFLLQI------FTWWNGQTLGTRFFTWRKGERVGEDEFGNVYYRTKG   43 (133)
T ss_pred             cHHHHH------HHHhccCchhheeehhccCeEeEecCCCCeeeecCC
Confidence            466777      9999999999999999 5999999999999999766

>COG3761 NADH:ubiquinone oxidoreductase 17

Probab=99.00  E-value=3.9e-11  Score=80.81  Aligned_cols=35  Identities=31%  Similarity=0.530  Sum_probs=29.7

Q ss_pred             hhhcCCcccceeeeecCceEeeeeCCCceeecc-CccccCC
Q 035316           29 RALLDGNLMQTKLHNRGATLVGVDKFGNKYYQK-LDEQFGQ   68 (68)
Q Consensus        29 ~tww~g~t~~t~~~~~~G~lVGeD~~GNkYYE~-~~~~~gr   68 (68)
                      +|||| ++++|+||    +.||||||||.|||. +....||
T Consensus         1 ftWwn-qt~gTrfh----~kvGeDefgN~Yye~r~~ds~gr   36 (118)
T COG3761           1 FTWWN-QTFGTRFH----KKVGEDEFGNVYYEGRNIDSEGR   36 (118)
T ss_pred             CchHH-hHHHHHHH----HhccchhccceeeeccCCccCCC
Confidence            48999 99999999    679999999999997 4455555

2 kD subunit [Energy production and conversion]

>PRK06630 hypothetical protein; Provisional

Probab=98.96  E-value=2.3e-10  Score=75.45  Aligned_cols=24  Identities=33%  Similarity=0.465  Sum_probs=20.9

Q ss_pred             eeeec-CceEeeeeCCCceeeccCc
Q 035316           40 KLHNR-GATLVGVDKFGNKYYQKLD   63 (68)
Q Consensus        40 ~~~~~-~G~lVGeD~~GNkYYE~~~   63 (68)
                      +|+|+ .|+|||+|+|||+|||+.+
T Consensus         6 ~~~t~r~G~lVG~D~~GNkYYE~~~   30 (99)
T PRK06630          6 KFFITFFHKKVGEDEFLNQYYESRN   30 (99)
T ss_pred             hhhhhccCeEeEEeCCCChhcccCC
Confidence            57777 5999999999999999854

>PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional

Probab=98.78  E-value=4e-09  Score=70.75  Aligned_cols=24  Identities=50%  Similarity=0.847  Sum_probs=20.8

Q ss_pred             CceEeeeeCCCceeeccCccccCC
Q 035316           45 GATLVGVDKFGNKYYQKLDEQFGQ   68 (68)
Q Consensus        45 ~G~lVGeD~~GNkYYE~~~~~~gr   68 (68)
                      .|+|||+|+|||||||+.++..||
T Consensus         9 ~g~lVG~D~~GNkYYE~~~~~~~r   32 (115)
T PLN03095          9 AGRLVGEDEFGNKYYENPSYQSGR   32 (115)
T ss_pred             cceEeEEcCCCCeeeEcCCCCCCC
Confidence            699999999999999988766554

>PF05071 NDUFA12: NADH ubiquinone oxidoreductase subunit NDUFA12; InterPro: IPR007763 NADH:ubiquinone oxidoreductase (complex I) (1

Probab=98.58  E-value=2.8e-08  Score=64.30  Aligned_cols=17  Identities=65%  Similarity=1.161  Sum_probs=16.1

Q ss_pred             ceEeeeeCCCceeeccC
Q 035316           46 ATLVGVDKFGNKYYQKL   62 (68)
Q Consensus        46 G~lVGeD~~GNkYYE~~   62 (68)
                      |+|||+|++||+|||+.
T Consensus         1 G~lVG~D~~GN~YyE~~   17 (105)
T PF05071_consen    1 GTLVGTDEFGNKYYENP   17 (105)
T ss_pred             CCEeeEeCCCCEEEeec
Confidence            78999999999999987

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 entry represents the 17.2kDa subunit from NADH:ubiquinone oxidoreductase and its homologues []. This subunit is believed to be one of the 36 structural complex I proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0009055 electron carrier activity, 0016020 membrane

>PF15613 WHIM2: WSTF, HB1, Itc1p, MBD9 motif 2

Probab=92.73  E-value=0.051  Score=30.18  Aligned_cols=14  Identities=36%  Similarity=0.935  Sum_probs=12.1

Q ss_pred             eEeeeeCCCceeec
Q 035316           47 TLVGVDKFGNKYYQ   60 (68)
Q Consensus        47 ~lVGeD~~GNkYYE   60 (68)
                      +.+|.|.+||+||-
T Consensus         3 ~pLG~DR~~NrYww   16 (38)
T PF15613_consen    3 KPLGKDRYGNRYWW   16 (38)
T ss_pred             ccccccCCCceEEE
Confidence            46899999999985

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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