Citrus Sinensis ID: 033442

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------12
Protein Sequence
MWRRICSSQLKAQALALAQYSCRSAPVNPSIASRSLISRPLFASRHFSADSGTSVKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGG
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccccccccccccccccccEEEEcccccEEEEccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHccccccccHHHHccccccccccccHHHcccccccccccccccccccccHHHHHHHHHHHcccccccccccEcccccccccEEEEEcccEEEEEEcccccc
Coil and Loop (DISEMBL)
MWRRICSSQLKAQALALAQYScrsapvnpsiasrslisrplfasrhfsadsgtsvkkrvedvnpvatgheREELEAElegknileidyptgpfgtkdapaVVKSYydkrivgcpggegg
Flexible Loop (DISEMBL)
MWRRICSSQLKAQALALAQYSCRSAPVNPSIASRSLISRPLFASRhfsadsgtsvkkrvedvnpvatghereeleaelegknILEIDYPTGPFGTKDAPAVVKSYYDKRivgcpggegg
Low Complexity Region (SEG)
MWRRICSSqlkaqalalaqYSCRSAPVNPSIASRSLISRPLFASRHFSADSGTSVKKRVEDVNPVATGHereeleaeleGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGG
Disordered region (IsUnstruct)
***********AQALALAQYSC***********************************************************NILEIDYPTGPFGTKDAPAVVKSYYDKRIVGC******
Disordered Region (DISOPRED)
*WR**********************************************************VNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPG****
Disordered Region (DISEMBL)
MWRRICSSQLKAQALALAQYSCRSAPVNPSIASRSLISRPLFASRHFSADSGTSVKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGG
Disordered Region (DISPRO)
*W**ICSSQLKAQALAL*****************************************VEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGG***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MWRRICSSQLKAQALALAQYSCRSAPVNPSIASRSLISRPLFASRHFSADSGTSVKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGG
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	119	2.2.26 [Sep-21-2011]
Q9SSB8	171	Cytochrome c oxidase subu	yes	no	0.991	0.690	0.571	7e-31
Q9LW15	176	Cytochrome c oxidase subu	no	no	0.991	0.670	0.598	2e-25
Q9SSS5	90	Putative cytochrome c oxi	no	no	0.378	0.5	0.6	2e-10

>sp|Q9SSB8|CX5B2_ARATH Cytochrome c oxidase subunit 5b-2, mitochondrial OS=Arabidopsis thaliana GN=COX5B-2 PE=2 SV=1

 Score =  132 bits (332), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 72/126 (57%), Positives = 89/126 (70%), Gaps = 8/126 (6%)

Query: 1   MWRRICSSQLKAQAL--ALAQYSCRSAPVNPSIASRSLISRPL------FASRHFSADSG 52
           MWRRI SS LK+ +   + A  SCR A V  +  S S  +  +      F+    SA + 
Sbjct: 1   MWRRIVSSHLKSISAVGSCAAPSCRHAVVESTHLSLSTRASSIPAYSSIFSRLIGSAAAD 60

Query: 53  TSVKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVG 112
           T+VKKRVEDV P+ATGHE+EEL+AELEG+ + +ID+P GPFGTK+APAVVKSYYD RIVG
Sbjct: 61  TAVKKRVEDVMPIATGHEKEELQAELEGRKLDDIDFPEGPFGTKEAPAVVKSYYDMRIVG 120

Query: 113 CPGGEG 118
           CPGGEG
Sbjct: 121 CPGGEG 126

This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9LW15|CX5B1_ARATH Cytochrome c oxidase subunit 5b-1, mitochondrial OS=Arabidopsis thaliana GN=COX5B-1 PE=2 SV=1

 Score =  114 bits (284), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 76/127 (59%), Positives = 90/127 (70%), Gaps = 9/127 (7%)

Query: 1   MWRRICSSQLKAQALALAQYSCR------SAPVNPSIAS-RSLISRPLFA-SRHFSADS- 51
           MWRRI SSQLK  A  +   S R      + PV   +A+ RS IS   F   R FS+DS 
Sbjct: 1   MWRRIVSSQLKTLAADVVAASPRRSIAATTRPVGFYLAANRSAISASSFVIPRRFSSDSV 60

Query: 52  GTSVKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIV 111
            T   K+VEDV P+ATGHE+EELEAELEG+ + +ID+P GPFGTK+APA+VKSYYDKRIV
Sbjct: 61  ETPATKKVEDVMPIATGHEKEELEAELEGRRLDDIDFPEGPFGTKEAPAIVKSYYDKRIV 120

Query: 112 GCPGGEG 118
           GCPGGEG
Sbjct: 121 GCPGGEG 127

This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SSS5|CX5BL_ARATH Putative cytochrome c oxidase subunit 5b-like OS=Arabidopsis thaliana GN=At1g52710 PE=2 SV=2

 Score = 64.7 bits (156), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 27/45 (60%), Positives = 37/45 (82%)

Query: 74  LEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEG 118
           L+ E  G+ +L+ID+P  PFGTK++PAVV+SY+DKR +GC GGEG
Sbjct: 4   LDKEYSGRRLLDIDHPESPFGTKESPAVVQSYFDKRNIGCRGGEG 48

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	119
352091163	140	cytochrome c oxidase subunit Vb [Dimocar	0.974	0.828	0.703	1e-32
388512435	153	unknown [Lotus japonicus]	0.899	0.699	0.627	5e-31
351721897	153	uncharacterized protein LOC100527520 [Gl	0.882	0.686	0.583	6e-30
21592567	171	cytochrome c oxidase subunit, putative [	0.991	0.690	0.571	1e-29
358248215	160	uncharacterized protein LOC100780886 [Gl	0.941	0.7	0.625	2e-29
15220092	171	cytochrome c oxidase subunit Vb [Arabido	0.991	0.690	0.571	3e-29
357455121	150	Cytochrome c oxidase subunit 5B [Medicag	0.890	0.706	0.611	5e-29
388510728	156	unknown [Medicago truncatula]	0.907	0.692	0.605	6e-29
113734311	150	cytochrome c oxidase subunit Vb [Pisum s	0.915	0.726	0.576	8e-29
113734315	155	cytochrome c oxidase subunit Vb [Pisum s	0.915	0.703	0.576	2e-28

>gi|352091163|gb|AEQ61828.1| cytochrome c oxidase subunit Vb [Dimocarpus longan]

 Score =  143 bits (361), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 83/118 (70%), Positives = 96/118 (81%), Gaps = 2/118 (1%)

Query: 1   MWRRICSSQLKAQALALAQYSCRSAPVNPSIASRSLISRPLFASRHFSADSGTSVKKRVE 60
           MWRRICSS LKA  LAL+     S+    + A+RSL S PLF +R  S+DSGTSVKK+VE
Sbjct: 1   MWRRICSSHLKA--LALSHSRSASSIAVSAAANRSLASPPLFTARLLSSDSGTSVKKKVE 58

Query: 61  DVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEG 118
           DV P+ATGHEREEL AELEG+ +L+ID+P GPFGTK+APAVVKSYYDKRIVGCPGGEG
Sbjct: 59  DVMPIATGHEREELAAELEGRKLLDIDFPVGPFGTKEAPAVVKSYYDKRIVGCPGGEG 116

Source: Dimocarpus longan

Species: Dimocarpus longan

Genus: Dimocarpus

Family: Sapindaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388512435|gb|AFK44279.1| unknown [Lotus japonicus]

 Score =  138 bits (347), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 74/118 (62%), Positives = 86/118 (72%), Gaps = 11/118 (9%)

Query: 1   MWRRICSSQLKAQALALAQYSCRSAPVNPSIASRSLISRPLFASRHFSADSGTSVKKRVE 60
           MWRR+ SS LK  A    Q     A +N S  S SL+       RHFS    TS+KK+VE
Sbjct: 1   MWRRLLSSHLKTLATCSPQSVSTVAALNCS--SVSLL-------RHFS--DTTSIKKKVE 49

Query: 61  DVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEG 118
           DV P+ATGHEREEL+A LEG++ILEI++P GPFGTK+APAVVKSYYDKRIVGCPGGEG
Sbjct: 50  DVMPIATGHEREELQANLEGRDILEINHPVGPFGTKEAPAVVKSYYDKRIVGCPGGEG 107

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351721897|ref|NP_001237225.1| uncharacterized protein LOC100527520 [Glycine max] gi|255632532|gb|ACU16616.1| unknown [Glycine max]

 Score =  134 bits (338), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 70/120 (58%), Positives = 92/120 (76%), Gaps = 15/120 (12%)

Query: 1   MWRRI-CSSQLKAQALALAQYSCRSAPVNPSIASRSLISRPLFASRHFSADSG-TSVKKR 58
           MWRR+  SS LKA    L+       P  P +A+++L++R      HF+A SG +S+KKR
Sbjct: 1   MWRRLFSSSNLKALHTTLS-------PSRPRLAAQTLLAR------HFTAQSGASSLKKR 47

Query: 59  VEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEG 118
           VEDV P+ATGHEREE++A+LEG++ILEI++P GPFGTK+APAVVKSY+D+RIVGCPG EG
Sbjct: 48  VEDVVPIATGHEREEIQADLEGRDILEINHPVGPFGTKEAPAVVKSYFDRRIVGCPGDEG 107

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|21592567|gb|AAM64516.1| cytochrome c oxidase subunit, putative [Arabidopsis thaliana]

 Score =  133 bits (334), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 72/126 (57%), Positives = 90/126 (71%), Gaps = 8/126 (6%)

Query: 1   MWRRICSSQLKAQAL--ALAQYSCRSAPVNPSIASRSLISRPL------FASRHFSADSG 52
           MWRRI SS LK+ +   + A  SCR A V  +  S S  +  +      F+ +  SA + 
Sbjct: 1   MWRRIVSSHLKSISAVGSCAAPSCRHAVVESTHLSLSTRASSIPAYSSIFSRQIGSAAAD 60

Query: 53  TSVKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVG 112
           T+VKKRVEDV P+ATGHE+EEL+AELEG+ + +ID+P GPFGTK+APAVVKSYYD RIVG
Sbjct: 61  TAVKKRVEDVMPIATGHEKEELQAELEGRKLDDIDFPEGPFGTKEAPAVVKSYYDMRIVG 120

Query: 113 CPGGEG 118
           CPGGEG
Sbjct: 121 CPGGEG 126

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358248215|ref|NP_001240096.1| uncharacterized protein LOC100780886 [Glycine max] gi|255637280|gb|ACU18970.1| unknown [Glycine max]

 Score =  132 bits (333), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 75/120 (62%), Positives = 89/120 (74%), Gaps = 8/120 (6%)

Query: 1   MWRRICSSQLKAQALALAQYSCRSAPVNPSIASRSLISRPLFASRHFSADS--GTSVKKR 58
           M RR+ SS LK     LA  +  S P + S A+R        +SR+FS  S   T++KK+
Sbjct: 1   MLRRLLSSHLKT----LAATASSSTPRSASAAARFAALS--RSSRYFSTQSEDATAIKKK 54

Query: 59  VEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEG 118
           VEDV P+ATGHEREEL+AELEG+NILEID+P GPFGTK+APAVVKSYYDKRIVGCPGGEG
Sbjct: 55  VEDVMPIATGHEREELQAELEGRNILEIDHPEGPFGTKEAPAVVKSYYDKRIVGCPGGEG 114

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15220092|ref|NP_178140.1| cytochrome c oxidase subunit Vb [Arabidopsis thaliana] gi|75207492|sp|Q9SSB8.1|CX5B2_ARATH RecName: Full=Cytochrome c oxidase subunit 5b-2, mitochondrial; Short=AtCOX5b-2; Flags: Precursor gi|5902388|gb|AAD55490.1|AC009322_30 Unknown protein [Arabidopsis thaliana] gi|30102586|gb|AAP21211.1| At1g80230 [Arabidopsis thaliana] gi|110743472|dbj|BAE99622.1| hypothetical protein [Arabidopsis thaliana] gi|332198252|gb|AEE36373.1| cytochrome c oxidase subunit Vb [Arabidopsis thaliana]

 Score =  132 bits (332), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 72/126 (57%), Positives = 89/126 (70%), Gaps = 8/126 (6%)

Query: 1   MWRRICSSQLKAQAL--ALAQYSCRSAPVNPSIASRSLISRPL------FASRHFSADSG 52
           MWRRI SS LK+ +   + A  SCR A V  +  S S  +  +      F+    SA + 
Sbjct: 1   MWRRIVSSHLKSISAVGSCAAPSCRHAVVESTHLSLSTRASSIPAYSSIFSRLIGSAAAD 60

Query: 53  TSVKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVG 112
           T+VKKRVEDV P+ATGHE+EEL+AELEG+ + +ID+P GPFGTK+APAVVKSYYD RIVG
Sbjct: 61  TAVKKRVEDVMPIATGHEKEELQAELEGRKLDDIDFPEGPFGTKEAPAVVKSYYDMRIVG 120

Query: 113 CPGGEG 118
           CPGGEG
Sbjct: 121 CPGGEG 126

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357455121|ref|XP_003597841.1| Cytochrome c oxidase subunit 5B [Medicago truncatula] gi|355486889|gb|AES68092.1| Cytochrome c oxidase subunit 5B [Medicago truncatula] gi|388495938|gb|AFK36035.1| unknown [Medicago truncatula]

 Score =  131 bits (330), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 74/121 (61%), Positives = 86/121 (71%), Gaps = 15/121 (12%)

Query: 1   MWRRICSS-QLKAQALALAQYSCRSAPVNPSIASRSLISRPLFA--SRHFSADSGTSVKK 57
           MWRRI SS  LK  A      S  S P       RS ++   FA  SRH +  S  SVKK
Sbjct: 1   MWRRIVSSPHLKTLA-----SSSHSHP-------RSAVAGLRFAGLSRHVATQSAGSVKK 48

Query: 58  RVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGE 117
            VEDV P+ATGHEREE++A+LEG+NILEID+P GPFGTK+APAVVKSYY++RIVGCPGGE
Sbjct: 49  TVEDVVPIATGHEREEIQADLEGRNILEIDHPEGPFGTKEAPAVVKSYYNRRIVGCPGGE 108

Query: 118 G 118
           G
Sbjct: 109 G 109

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388510728|gb|AFK43430.1| unknown [Medicago truncatula]

 Score =  131 bits (329), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 72/119 (60%), Positives = 90/119 (75%), Gaps = 11/119 (9%)

Query: 1   MWRRIC-SSQLKAQALALAQYSCRSAPVNPSIASRSLISRPLFASRHFSADSGTSVKKRV 59
           M RR+  SSQLK         + R +P   S  + SL+SR  F+++  S DS T +KK+V
Sbjct: 1   MLRRLLISSQLKT-------LTSRRSP--SSAVAVSLLSRHHFSTQ-SSDDSTTGIKKKV 50

Query: 60  EDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEG 118
           EDV P+ATGHEREE++A+LEG++ILEID+P GPFGTK+APAVVKSYYDKRIVGCPGGEG
Sbjct: 51  EDVVPIATGHEREEIQAQLEGRDILEIDHPEGPFGTKEAPAVVKSYYDKRIVGCPGGEG 109

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|113734311|dbj|BAF30481.1| cytochrome c oxidase subunit Vb [Pisum sativum] gi|113734317|dbj|BAF30484.1| cytochrome c oxidase subunit Vb [Pisum sativum]

 Score =  130 bits (328), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 68/118 (57%), Positives = 82/118 (69%), Gaps = 9/118 (7%)

Query: 1   MWRRICSSQLKAQALALAQYSCRSAPVNPSIASRSLISRPLFASRHFSADSGTSVKKRVE 60
           MWRR+ +S       + +    RSA             R +  SRH +  S  SVKKRVE
Sbjct: 1   MWRRLFTSPHLKTLSSSSLSHPRSAVAG---------IRCVDLSRHVATQSAASVKKRVE 51

Query: 61  DVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEG 118
           DV P+ATGHEREE++AELEG+NILEID+P GPFGTKDAPAVV+S+YD+RIVGCPGGEG
Sbjct: 52  DVVPIATGHEREEIQAELEGRNILEIDHPEGPFGTKDAPAVVRSFYDRRIVGCPGGEG 109

Source: Pisum sativum

Species: Pisum sativum

Genus: Pisum

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|113734315|dbj|BAF30483.1| cytochrome c oxidase subunit Vb [Pisum sativum]

 Score =  129 bits (325), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 68/118 (57%), Positives = 86/118 (72%), Gaps = 9/118 (7%)

Query: 1   MWRRICSSQLKAQALALAQYSCRSAPVNPSIASRSLISRPLFASRHFSADSGTSVKKRVE 60
           M RR+ SSQLK    + +     S  V  S+ S       LF+++   +D  T VKK+VE
Sbjct: 1   MLRRLISSQLKTLTSSSSPLRSPSPAVAVSLLS------CLFSTQ---SDDSTVVKKKVE 51

Query: 61  DVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEG 118
           D+ P+ATGHEREEL+A++EG++ILEID+P GPFGTK+APAVVKSYYDKRIVGCPGGEG
Sbjct: 52  DIVPIATGHEREELQAQIEGRDILEIDHPEGPFGTKEAPAVVKSYYDKRIVGCPGGEG 109

Source: Pisum sativum

Species: Pisum sativum

Genus: Pisum

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	119
TAIR|locus:2093267	176	AT3G15640 [Arabidopsis thalian	0.991	0.670	0.496	1.4e-23
TAIR|locus:2016284	171	AT1G80230 [Arabidopsis thalian	0.983	0.684	0.503	2.3e-23
UNIPROTKB|P92683	169	coxVb "Cytochrome c oxidase su	0.991	0.698	0.388	7.7e-16
TAIR|locus:2035069	90	AT1G52710 [Arabidopsis thalian	0.327	0.433	0.641	5.8e-11
DICTYBASE|DDB_G0269118	120	cxeA "cytochrome c oxidase sub	0.243	0.241	0.517	0.00057

TAIR|locus:2093267 AT3G15640 [Arabidopsis thaliana (taxid:3702)]

 Score = 271 (100.5 bits), Expect = 1.4e-23, P = 1.4e-23
 Identities = 63/127 (49%), Positives = 74/127 (58%)

Query:     1 MWRRICSSXXXXXXXXXXXYSCR---SAPVNPS----IASRSLISRPLFA-SRHFSADS- 51
             MWRRI SS            S R   +A   P      A+RS IS   F   R FS+DS 
Sbjct:     1 MWRRIVSSQLKTLAADVVAASPRRSIAATTRPVGFYLAANRSAISASSFVIPRRFSSDSV 60

Query:    52 GTSVKKRVEDVNPVATGHXXXXXXXXXXGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIV 111
              T   K+VEDV P+ATGH          G+ + +ID+P GPFGTK+APA+VKSYYDKRIV
Sbjct:    61 ETPATKKVEDVMPIATGHEKEELEAELEGRRLDDIDFPEGPFGTKEAPAIVKSYYDKRIV 120

Query:   112 GCPGGEG 118
             GCPGGEG
Sbjct:   121 GCPGGEG 127

GO:0004129 "cytochrome-c oxidase activity" evidence=IEA;ISS

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0005740 "mitochondrial envelope" evidence=IEA;ISS

GO:0046872 "metal ion binding" evidence=IDA

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0008270 "zinc ion binding" evidence=IDA

GO:0050897 "cobalt ion binding" evidence=IDA

GO:0006007 "glucose catabolic process" evidence=RCA

TAIR|locus:2016284 AT1G80230 [Arabidopsis thaliana (taxid:3702)]

 Score = 269 (99.8 bits), Expect = 2.3e-23, P = 2.3e-23
 Identities = 64/127 (50%), Positives = 78/127 (61%)

Query:     1 MWRRICSSXXXXXXXXXX--XYSCRSAPVNP---SIASRSLISRPLFAS---RHF-SADS 51
             MWRRI SS              SCR A V     S+++R+  S P ++S   R   SA +
Sbjct:     1 MWRRIVSSHLKSISAVGSCAAPSCRHAVVESTHLSLSTRAS-SIPAYSSIFSRLIGSAAA 59

Query:    52 GTSVKKRVEDVNPVATGHXXXXXXXXXXGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIV 111
              T+VKKRVEDV P+ATGH          G+ + +ID+P GPFGTK+APAVVKSYYD RIV
Sbjct:    60 DTAVKKRVEDVMPIATGHEKEELQAELEGRKLDDIDFPEGPFGTKEAPAVVKSYYDMRIV 119

Query:   112 GCPGGEG 118
             GCPGGEG
Sbjct:   120 GCPGGEG 126

GO:0004129 "cytochrome-c oxidase activity" evidence=IEA;ISS

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0005740 "mitochondrial envelope" evidence=IEA;ISS

UNIPROTKB|P92683 coxVb "Cytochrome c oxidase subunit Vb" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 198 (74.8 bits), Expect = 7.7e-16, P = 7.7e-16
 Identities = 47/121 (38%), Positives = 61/121 (50%)

Query:     1 MWRRICSSXXXXXXXXXXXYSCR-SAPVNPSIASRS--LISRPLFASRHFSADSGTSVKK 57
             MWRR+ +             S   S    P+  +R+  L +    A R  S         
Sbjct:     1 MWRRLQTLAPALRRAASASASAAASGAAGPASLARAAPLSTAAAAAFRRTSPLLSGDKPA 60

Query:    58 RVEDVNPVATGHXXXXXXXXXXGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGE 117
              VEDV P+ATG           G+   ++D P GPFGTK+APAV++SYY+KRIVGCPGGE
Sbjct:    61 TVEDVMPIATGLEREELAAELKGEKRFDMDPPVGPFGTKEAPAVIESYYNKRIVGCPGGE 120

Query:   118 G 118
             G
Sbjct:   121 G 121

GO:0005739 "mitochondrion" evidence=IC;ISS

TAIR|locus:2035069 AT1G52710 [Arabidopsis thaliana (taxid:3702)]

 Score = 152 (58.6 bits), Expect = 5.8e-11, P = 5.8e-11
 Identities = 25/39 (64%), Positives = 34/39 (87%)

Query:    80 GKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEG 118
             G+ +L+ID+P  PFGTK++PAVV+SY+DKR +GC GGEG
Sbjct:    10 GRRLLDIDHPESPFGTKESPAVVQSYFDKRNIGCRGGEG 48

GO:0004129 "cytochrome-c oxidase activity" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0005740 "mitochondrial envelope" evidence=IEA

DICTYBASE|DDB_G0269118 cxeA "cytochrome c oxidase subunit V" [Dictyostelium discoideum (taxid:44689)]

 Score = 86 (35.3 bits), Expect = 0.00057, P = 0.00057
 Identities = 15/29 (51%), Positives = 20/29 (68%)

Query:    90 TGPFGTKDAPAVVKSYYDKRIVGCPGGEG 118
             TG FGT  +P +V+S +  RIV C GG+G
Sbjct:    53 TGAFGTLKSPVIVESIFHSRIVACEGGDG 81


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        0.317   0.134   0.417    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      119        98   0.00091  102 3  11 22  0.42    30
                                                     29  0.45    31


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:  5
  No. of states in DFA:  535 (57 KB)
  Total size of DFA:  110 KB (2075 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:  9.48u 0.09s 9.57t   Elapsed:  00:00:01
  Total cpu time:  9.48u 0.09s 9.57t   Elapsed:  00:00:01
  Start:  Sat May 11 03:22:21 2013   End:  Sat May 11 03:22:22 2013

GO:0045335 "phagocytic vesicle" evidence=IDA

GO:0009617 "response to bacterium" evidence=IEP

GO:0005740 "mitochondrial envelope" evidence=IEA

GO:0004129 "cytochrome-c oxidase activity" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0005743 "mitochondrial inner membrane" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0044351 "macropinocytosis" 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9SSB8	CX5B2_ARATH	No assigned EC number	0.5714	0.9915	0.6900	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!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

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	119
PLN02294	174	PLN02294, PLN02294, cytochrome c oxidase subunit V	1e-56
cd00924	97	cd00924, Cyt_c_Oxidase_Vb, Cytochrome c oxidase su	2e-20
pfam01215	136	pfam01215, COX5B, Cytochrome c oxidase subunit Vb	4e-12
PTZ00043	268	PTZ00043, PTZ00043, cytochrome c oxidase subunit;	2e-04

>gnl|CDD|177931 PLN02294, PLN02294, cytochrome c oxidase subunit Vb

 Score =  173 bits (439), Expect = 1e-56
 Identities = 79/125 (63%), Positives = 92/125 (73%), Gaps = 7/125 (5%)

Query: 1   MWRRICSSQLKAQALALAQYSCR---SAPVNPSIASRSLISRPLFAS---RHFSADS-GT 53
           MWRRI SS LK  A ++   S R    A   P   SRS  S    +S   R+FS++S  T
Sbjct: 1   MWRRIVSSHLKTLAASVVAASPRRTVVATTRPLYLSRSRSSISASSSVFSRYFSSESADT 60

Query: 54  SVKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGC 113
           +VKKRVEDV P+ATGHEREELEAELEG+ +L+ID+P GPFGTK+APAVVKSYYDKRIVGC
Sbjct: 61  AVKKRVEDVMPIATGHEREELEAELEGRKLLDIDFPEGPFGTKEAPAVVKSYYDKRIVGC 120

Query: 114 PGGEG 118
           PGGEG
Sbjct: 121 PGGEG 125

Length = 174

>gnl|CDD|238464 cd00924, Cyt_c_Oxidase_Vb, Cytochrome c oxidase subunit Vb

 Score = 78.9 bits (195), Expect = 2e-20
 Identities = 28/65 (43%), Positives = 38/65 (58%)

Query: 54  SVKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGC 113
           + +  V      ATG ER+EL A+LEG +  ++    GPFGTK+ P +V S +DKRIVGC
Sbjct: 1   AAEGEVPTDLEQATGLERKELLAKLEGIDDFDMKPLKGPFGTKEDPNLVPSAFDKRIVGC 60

Query: 114 PGGEG 118
                
Sbjct: 61  ICEPD 65

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 Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly. Length = 97

>gnl|CDD|201667 pfam01215, COX5B, Cytochrome c oxidase subunit Vb

 Score = 58.4 bits (141), Expect = 4e-12
 Identities = 24/54 (44%), Positives = 31/54 (57%)

Query: 66  ATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGG 119
           ATG EREEL A L+G++  +I       GT   P +V+S  + RIVGC G   G
Sbjct: 45  ATGLEREELLAALKGRDPFDIKPLDASKGTLKDPIIVESIDNYRIVGCTGSPDG 98

Length = 136

>gnl|CDD|240240 PTZ00043, PTZ00043, cytochrome c oxidase subunit; Provisional

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 15/28 (53%), Positives = 19/28 (67%)

Query: 91  GPFGTKDAPAVVKSYYDKRIVGCPGGEG 118
           GPFGT + P +V S   +R+VGC GG G
Sbjct: 138 GPFGTIENPVLVPSVGTERVVGCTGGTG 165

Length = 268

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	119
PLN02294	174	cytochrome c oxidase subunit Vb	100.0
cd00924	97	Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb.	99.97
PF01215	136	COX5B: Cytochrome c oxidase subunit Vb This family	99.97
KOG3352	153	consensus Cytochrome c oxidase, subunit Vb/COX4 [E	99.96
PTZ00043	268	cytochrome c oxidase subunit; Provisional	99.58

>PLN02294 cytochrome c oxidase subunit Vb

Probab=100.00  E-value=3.9e-43  Score=272.38  Aligned_cols=116  Identities=64%  Similarity=0.988  Sum_probs=97.8

Q ss_pred             ChhhHhhhhhHHHHHHhhhccCCCCCC-CCc----ccc-cccccccccccccccCCCC-CCccccCCCCCccccchhHHH
Q 033442            1 MWRRICSSQLKAQALALAQYSCRSAPV-NPS----IAS-RSLISRPLFASRHFSADSG-TSVKKRVEDVNPVATGHEREE   73 (119)
Q Consensus         1 mwrr~~~~~l~~~~~~~~~~~~~~~~~-~~~----~~~-~~~~~~~~~~s~~~~~~~~-~~~~g~vpdd~EqATGlER~E   73 (119)
                      ||||++++|||+|+++.++.++++.++ ++.    +++ +++.++.++|+|+|++.++ +.++++|+|++||||||||+|
T Consensus         1 MwRr~~ss~L~~la~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~d~~~~ATGLER~E   80 (174)
T PLN02294          1 MWRRIVSSHLKTLAASVVAASPRRTVVATTRPLYLSRSRSSISASSSVFSRYFSSESADTAVKKRVEDVMPIATGHEREE   80 (174)
T ss_pred             ChhhHHHHHHHHHHHhhcccCcccccccccccccccccccccCchhhhhhhccccccccccccccCCCchhhccchHHHH
Confidence            999999999999998866554454442 221    112 3333444899999998877 678999999999999999999


Q ss_pred             HHHHHhCCCCCCCCCCCCCCCCCCCCeeeeccCCceeEeeCCC
Q 033442           74 LEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGG  116 (119)
Q Consensus        74 Lla~~~G~DpFdm~~~~~~~GTke~P~lVpS~~~~RIVGC~g~  116 (119)
                      |+++++|+|||||+++++++||||||+||||++|+|||||+|+
T Consensus        81 Lla~leG~D~Fd~~~~~gp~GTke~P~lVpS~~d~RiVGCtg~  123 (174)
T PLN02294         81 LEAELEGRKLLDIDFPEGPFGTKEAPAVVKSYYDKRIVGCPGG  123 (174)
T ss_pred             HHHHHcCCCccccccccCCCCCccCCcEeccCCCceEEeeCCC
Confidence            9999999999999999999999999999999999999999993

>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb

Probab=99.97  E-value=8.7e-32  Score=191.98  Aligned_cols=65  Identities=43%  Similarity=0.624  Sum_probs=62.9

Q ss_pred             ccccCCCCCccccchhHHHHHHHHhCCCCCCCCCCCCCCCCCCCCeeeeccCCceeEeeCCCCCC
Q 033442           55 VKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGG  119 (119)
Q Consensus        55 ~~g~vpdd~EqATGlER~ELla~~~G~DpFdm~~~~~~~GTke~P~lVpS~~~~RIVGC~g~p~e  119 (119)
                      ++|+||||+||||||||+||+++++|+|+|+|+++++++||++||+||||++++|||||+|+|++
T Consensus         2 ~~g~vp~d~e~aTGlEr~ELl~~~~G~d~f~~~~~~~~~GT~e~P~lVpS~~~~RiVGC~g~~~~   66 (97)
T cd00924           2 AEGEVPTDLEQATGLERKELLAKLEGIDDFDMKPLKGPFGTKEDPNLVPSAFDKRIVGCICEPDS   66 (97)
T ss_pred             CCcccCCchHhhhccHHHHHHHHHcCCccccccccccCCCCccCCeEecCCCCCeEEeeeCCCCC
Confidence            67899999999999999999999999999999999999999999999999999999999999873

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 Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.

>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1

Probab=99.97  E-value=3.7e-32  Score=204.02  Aligned_cols=67  Identities=43%  Similarity=0.664  Sum_probs=45.6

Q ss_pred             CCccccCCCCCccccchhHHHHHHHHhCCCCCCCCCCCCCCCCCCCCeeeeccCCceeEeeCCCCCC
Q 033442           53 TSVKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGG  119 (119)
Q Consensus        53 ~~~~g~vpdd~EqATGlER~ELla~~~G~DpFdm~~~~~~~GTke~P~lVpS~~~~RIVGC~g~p~e  119 (119)
                      ++++|+||||+||||||||+||+++++|+|||||+++++++||+||||||||++++|||||+|+|++
T Consensus        32 ~a~~G~vptd~eqATGlER~Ella~~~G~D~Fd~~~~~~~~GT~e~P~lVpS~~~~RiVGC~g~~~~   98 (136)
T PF01215_consen   32 GAKPGTVPTDLEQATGLEREELLAKLEGIDPFDMKPLKAPFGTKEDPILVPSYFDERIVGCTGEPDD   98 (136)
T ss_dssp             -----BS--HHHH--HHHHHHHHHHHTT--TT--S--B----SSSS-CEEEESSSCEEEEESSSTT-
T ss_pred             cccCCCCCChhHhhhHHHHHHHHHHhcCcCcccccCccCCCCCccCCeEccCCCCceEEeeccCCCC
Confidence            6789999999999999999999999999999999999999999999999999999999999999975

9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....

>KOG3352 consensus Cytochrome c oxidase, subunit Vb/COX4 [Energy production and conversion]

Probab=99.96  E-value=9.6e-31  Score=199.92  Aligned_cols=67  Identities=49%  Similarity=0.745  Sum_probs=64.6

Q ss_pred             CCccccCCCCCccccchhHHHHHHHHhCCCCCCCCCCCCCCCCCCCCeeeeccCCceeEeeCCCCCC
Q 033442           53 TSVKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGG  119 (119)
Q Consensus        53 ~~~~g~vpdd~EqATGlER~ELla~~~G~DpFdm~~~~~~~GTke~P~lVpS~~~~RIVGC~g~p~e  119 (119)
                      +++.|+||||+||||||||+|||++++|.|||||+.+++++||||||||||||||+|||||.|++|+
T Consensus        54 ~~~~g~vpddle~aTGlEk~eLla~l~G~d~~d~k~~~~~~GTkedP~lV~S~~d~RiVGC~c~eD~  120 (153)
T KOG3352|consen   54 MAKGGGVPDDLEQATGLEKEELLAELEGRDPFDMKVPRGPSGTKEDPNLVPSYYDKRIVGCGCEEDS  120 (153)
T ss_pred             cccCCCCCCchhhhhhHHHHHHHHHhhCCCccccccccCCCCcccCCccccccCCceEEeecccCCC
Confidence            7789999999999999999999999999999999988999999999999999999999999999874

>PTZ00043 cytochrome c oxidase subunit; Provisional

Probab=99.58  E-value=1.1e-15  Score=124.70  Aligned_cols=63  Identities=32%  Similarity=0.467  Sum_probs=55.3

Q ss_pred             ccCCCCCc-cccchhHHHHHHHHhCCCCCCCCCCCCCCCCCCCCeeeeccCCceeEeeCCCCCC
Q 033442           57 KRVEDVNP-VATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGG  119 (119)
Q Consensus        57 g~vpdd~E-qATGlER~ELla~~~G~DpFdm~~~~~~~GTke~P~lVpS~~~~RIVGC~g~p~e  119 (119)
                      +.+.-||. |...-+.++|+|.++|.+.+.++++.+|+||+|+|+||||++++|||||+|+++|
T Consensus       103 kqla~d~gmqi~~~~~~hm~~~le~y~~Lk~~~~~GPfGTkEdPiLVpSy~deRyVGCTGg~~E  166 (268)
T PTZ00043        103 KQLARDMGMQIVNEPSEHMLGLLELYEYLKSSSFVGPFGTIENPVLVPSVGTERVVGCTGGTGE  166 (268)
T ss_pred             HHHHHHhCceecCCchHHHHHHHHHHHhcCcCCCCCCCCCccCCeEeccCCCceEEeccCCCcc
Confidence            33444555 6777889999999999999999999999999999999999999999999996554

---

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

ID	Length	Definition	E-value
Query	119
2y69_F	129	Cytochrome C oxidase subunit 5B; electron transpor	4e-21
1v54_F	98	VI, cytochrome C oxidase polypeptide VB; oxidoredu	7e-20
2odx_A	80	Cytochrome C oxidase polypeptide IV; all beta-prot	3e-09

>2y69_F Cytochrome C oxidase subunit 5B; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus} Length = 129

 Score = 80.9 bits (199), Expect = 4e-21
 Identities = 29/89 (32%), Positives = 42/89 (47%), Gaps = 3/89 (3%)

Query: 30  SIASRSLISRPLFASRHFSADSGTSVKKRVEDVNPVATGHEREELEAELEGKNILEIDYP 89
           ++AS++L +R        S     +    V      ATG ERE + A  +G++   I  P
Sbjct: 11  ALASQALRAR---GPNGVSVVRSMASGGGVPTDEEQATGLEREVMLAARKGQDPYNILAP 67

Query: 90  TGPFGTKDAPAVVKSYYDKRIVGCPGGEG 118
               GTK+ P +V S  +KRIVGC   E 
Sbjct: 68  KATSGTKEDPNLVPSITNKRIVGCICEED 96

>1v54_F VI, cytochrome C oxidase polypeptide VB; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: g.41.5.3 PDB: 1oco_F* 1occ_F* 1ocz_F* 1ocr_F* 1v55_F* 2dyr_F* 2dys_F* 2eij_F* 2eik_F* 2eil_F* 2eim_F* 2ein_F* 2occ_F* 2ybb_Q* 2zxw_F* 3abk_F* 3abl_F* 3abm_F* 3ag1_F* 3ag2_F* ... Length = 98

 Score = 76.9 bits (189), Expect = 7e-20
 Identities = 24/65 (36%), Positives = 32/65 (49%)

Query: 54  SVKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGC 113
           +    V      ATG ERE + A  +G++   I  P    GTK+ P +V S  +KRIVGC
Sbjct: 1   ASGGGVPTDEEQATGLEREVMLAARKGQDPYNILAPKATSGTKEDPNLVPSITNKRIVGC 60

Query: 114 PGGEG 118
              E 
Sbjct: 61  ICEED 65

>2odx_A Cytochrome C oxidase polypeptide IV; all beta-protein, metallo-protein, oxidoreductase; NMR {Saccharomyces cerevisiae} Length = 80

 Score = 49.0 bits (117), Expect = 3e-09
 Identities = 12/27 (44%), Positives = 15/27 (55%)

Query: 93  FGTKDAPAVVKSYYDKRIVGCPGGEGG 119
            GT   P +++SY D R VGC G   G
Sbjct: 16  KGTMKDPIIIESYDDYRYVGCTGSPAG 42

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	119
1v54_F	98	VI, cytochrome C oxidase polypeptide VB; oxidoredu	99.97
2y69_F	129	Cytochrome C oxidase subunit 5B; electron transpor	99.97
2odx_A	80	Cytochrome C oxidase polypeptide IV; all beta-prot	99.74

>1v54_F VI, cytochrome C oxidase polypeptide VB; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: g.41.5.3 PDB: 1oco_F* 1occ_F* 1ocz_F* 1ocr_F* 1v55_F* 2dyr_F* 2dys_F* 2eij_F* 2eik_F* 2eil_F* 2eim_F* 2ein_F* 2occ_F* 2ybb_Q* 2zxw_F* 3abk_F* 3abl_F* 3abm_F* 3ag1_F* 3ag2_F* ...

Probab=99.97  E-value=1.8e-32  Score=194.74  Aligned_cols=65  Identities=37%  Similarity=0.453  Sum_probs=62.1

Q ss_pred             ccccCCCCCccccchhHHHHHHHHhCCCCCCCCCCCCCCCCCCCCeeeeccCCceeEeeCCCCCC
Q 033442           55 VKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGG  119 (119)
Q Consensus        55 ~~g~vpdd~EqATGlER~ELla~~~G~DpFdm~~~~~~~GTke~P~lVpS~~~~RIVGC~g~p~e  119 (119)
                      +.|+||||+||||||||+||+++++|+|||||+++++++|||||||||||++++|||||+|++++
T Consensus         2 ~~g~iPtd~eqATGlEr~Ella~~~G~Dpfd~~~~~~~~GTke~P~lVpS~~~~RiVGC~~~~D~   66 (98)
T 1v54_F            2 SGGGVPTDEEQATGLEREVMLAARKGQDPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDN   66 (98)
T ss_dssp             CCCBCCCHHHHCCHHHHHHHHHHHTTCCTTCCSCCCCCCCCSSSCEEEECSSSEEEEEECCSTTC
T ss_pred             CCCCCCChHHhccCHHHHHHHHHHcCCCcccccCCCCCCCcccCCeEeecCCCCeEEeecCCCCC
Confidence            46899999999999999999999999999999999999999999999999999999999998763

>2y69_F Cytochrome C oxidase subunit 5B; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=99.97  E-value=1.2e-31  Score=198.84  Aligned_cols=65  Identities=37%  Similarity=0.453  Sum_probs=61.2

Q ss_pred             ccccCCCCCccccchhHHHHHHHHhCCCCCCCCCCCCCCCCCCCCeeeeccCCceeEeeCCCCCC
Q 033442           55 VKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGG  119 (119)
Q Consensus        55 ~~g~vpdd~EqATGlER~ELla~~~G~DpFdm~~~~~~~GTke~P~lVpS~~~~RIVGC~g~p~e  119 (119)
                      ++|+||||+||||||||+||+++++|+|||||+++++++|||||||||||++|+|||||+|++++
T Consensus        33 ~~g~iPtd~eqATGlER~ELla~~~G~DpFd~~~~~~~~GTkedP~lVpS~~d~RiVGC~~~~Ds   97 (129)
T 2y69_F           33 SGGGVPTDEEQATGLEREVMLAARKGQDPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDN   97 (129)
T ss_dssp             --CBCCCHHHHCCHHHHHHHHHHHTTCCTTCCSCCCCCCCCSSSCEEEEESSSEEEEEECCSTTC
T ss_pred             CCCCCCCHHHhccCHHHHHHHHHHcCCCccccCCCCCCCCcccCCeEeecCCCCeEEeecCCCCC
Confidence            67999999999999999999999999999999999999999999999999999999999998764

>2odx_A Cytochrome C oxidase polypeptide IV; all beta-protein, metallo-protein, oxidoreductase; NMR {Saccharomyces cerevisiae}

Probab=99.74  E-value=3e-19  Score=122.79  Aligned_cols=40  Identities=28%  Similarity=0.495  Sum_probs=21.9

Q ss_pred             hCCCCCCCCCCCC-CCCCCCCCeeeeccCCceeEeeCCCCC
Q 033442           79 EGKNILEIDYPTG-PFGTKDAPAVVKSYYDKRIVGCPGGEG  118 (119)
Q Consensus        79 ~G~DpFdm~~~~~-~~GTke~P~lVpS~~~~RIVGC~g~p~  118 (119)
                      +|.|||||+++++ ++|||||||||||++++|||||+|+|+
T Consensus         1 ~G~D~fd~~p~~~~~~GT~e~P~lVpS~~~~RiVGC~g~p~   41 (80)
T 2odx_A            1 MMADVFDTKPLDSSRKGTMKDPIIIESYDDYRYVGCTGSPA   41 (80)
T ss_dssp             ------------------CCSCSEECCSSSSCCEEESSSTT
T ss_pred             CCcCcccccccccCCCCCccCCeEecCCCCCeEEeeeCCCC
Confidence            6999999999985 899999999999999999999999954

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	119
d1v54f_	98	g.41.5.3 (F:) Cytochrome c oxidase Subunit F {Cow	4e-22

>d1v54f_ g.41.5.3 (F:) Cytochrome c oxidase Subunit F {Cow (Bos taurus) [TaxId: 9913]} Length = 98

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Cytochrome c oxidase Subunit F
domain: Cytochrome c oxidase Subunit F
species: Cow (Bos taurus) [TaxId: 9913]

 Score = 81.3 bits (201), Expect = 4e-22
 Identities = 23/52 (44%), Positives = 30/52 (57%)

Query: 66  ATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGE 117
           ATG ERE + A  +G++   I  P    GTK+ P +V S  +KRIVGC   E
Sbjct: 13  ATGLEREVMLAARKGQDPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEE 64

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	119
d1v54f_	98	Cytochrome c oxidase Subunit F {Cow (Bos taurus) [	100.0

>d1v54f_ g.41.5.3 (F:) Cytochrome c oxidase Subunit F {Cow (Bos taurus) [TaxId: 9913]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Cytochrome c oxidase Subunit F
domain: Cytochrome c oxidase Subunit F
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=4.2e-34  Score=201.97  Aligned_cols=66  Identities=36%  Similarity=0.452  Sum_probs=62.9

Q ss_pred             CccccCCCCCccccchhHHHHHHHHhCCCCCCCCCCCCCCCCCCCCeeeeccCCceeEeeCCCCCC
Q 033442           54 SVKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGG  119 (119)
Q Consensus        54 ~~~g~vpdd~EqATGlER~ELla~~~G~DpFdm~~~~~~~GTke~P~lVpS~~~~RIVGC~g~p~e  119 (119)
                      ++.|+||||+||||||||+||+++++|+|||||+++++++|||||||||||++++|||||+|++++
T Consensus         1 a~~g~iptd~EqATGlEr~ella~~~g~D~fd~~~~~~~~GTke~P~lVpS~~~~RiVGC~~~~D~   66 (98)
T d1v54f_           1 ASGGGVPTDEEQATGLEREVMLAARKGQDPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDN   66 (98)
T ss_dssp             CCCCBCCCHHHHCCHHHHHHHHHHHTTCCTTCCSCCCCCCCCSSSCEEEECSSSEEEEEECCSTTC
T ss_pred             CCCCcCCChHHHhhhHHHHHHHHHhcCCChhhccCCcCCCCCCcCCcEecCCCCceEEeecCCCCC
Confidence            467999999999999999999999999999999999999999999999999999999999997764