Psyllid ID: psy2945

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130----
Protein Sequence
MAVFFRSLVLSPNTRYLARSVTATGNSFSTCAQRWNKNDLDELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINWMWLYEGKPKRCMCGHWFKLVYKAPI
Secondary Structure (PSIPRED)
ccHHHHHHHccccccHHHccccccccccEEEcccccccccccccccccccccHHHHHHHHHHccccccccccccccccccccccEEEccccccEEEEEccccccccEEEEEEEccccEEEccccEEEEEEEccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHcHHHHHHHHHHHHcccccccccccEcccccccccEEEEEcccEEEEEEcccccccccEEEEEEccccEEcccccEEEEEEcccc
Coil and Loop (DISEMBL)
mavffrslvlspntRYLARSVtatgnsfstCAQRwnkndldelpdpldlaTGLEKRELLAElagdpdpfnvkirkrglgtktqptevpsaFEARIVGciceeespsinwmwlyegkpkrcmcghwfklvykapi
Flexible Loop (DISEMBL)
MAVFFRSlvlspntrYLARSvtatgnsfstcaqrwnkndldelpdPLDLATGLEKRELLaelagdpdpfnvkirkrglgtktqptevpsafEARIVGCICEEESPSINWMWLYEGKPKRCMCGHWFKLVYKAPI
Low Complexity Region (SEG)
MAVFFRSLVLSPNTRYLARSVTATGNSFSTCAQRWNKNdldelpdpldlATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINWMWLYEGKPKRCMCGHWFKLVYKAPI
Disordered region (IsUnstruct)
**VFFRSLVLSPNTRYLARSVTATGNSFSTCAQRWNKNDLD*****LDLATGL****LLA**********V*I**************PSAFEARIVGCICEEESPSINWMWLYEGKPKRCMCGHWFKLVYK***
Disordered Region (DISOPRED)
********************************************DPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINWMWLYEGKPKRCMCGHWFKLVYKAP*
Disordered Region (DISEMBL)
MAVFFRSLVLSPNTRYLARSVTATGNSFSTCAQRWNKNDLDELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINWMWLYEGKPKRCMCGHWFKLVYKAPI
Disordered Region (DISPRO)
*AVFFRSLVLSPNTRYLARSVT*******************ELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINWMWLYEGKPKRCMCGHWFKLVYKAP*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAVFFRSLVLSPNTRYLARSVTATGNSFSTCAQRWNKNDLDELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINWMWLYEGKPKRCMCGHWFKLVYKAPI
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	134	2.2.26 [Sep-21-2011]
P00428	129	Cytochrome c oxidase subu	yes	N/A	0.641	0.666	0.454	1e-14
P10606	129	Cytochrome c oxidase subu	yes	N/A	0.641	0.666	0.465	2e-14
Q710D6	128	Cytochrome c oxidase subu	N/A	N/A	0.641	0.671	0.443	3e-14
Q5REG2	129	Cytochrome c oxidase subu	yes	N/A	0.641	0.666	0.465	3e-14
Q5S3G4	129	Cytochrome c oxidase subu	yes	N/A	0.641	0.666	0.431	6e-14
P12075	129	Cytochrome c oxidase subu	yes	N/A	0.641	0.666	0.443	2e-13
P19536	128	Cytochrome c oxidase subu	yes	N/A	0.641	0.671	0.443	3e-13
P79010	164	Cytochrome c oxidase subu	yes	N/A	0.656	0.536	0.402	2e-07
Q9SSB8	171	Cytochrome c oxidase subu	yes	N/A	0.634	0.497	0.382	8e-07
P06809	186	Cytochrome c oxidase subu	N/A	N/A	0.671	0.483	0.326	0.0008

>sp|P00428|COX5B_BOVIN Cytochrome c oxidase subunit 5B, mitochondrial OS=Bos taurus GN=COX5B PE=1 SV=2

 Score = 78.2 bits (191), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 40/88 (45%), Positives = 55/88 (62%), Gaps = 2/88 (2%)

Query: 43  LPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEE 102
           +P   + ATGLE+  +LA   G  DP+N+   K   GTK  P  VPS    RIVGCICEE
Sbjct: 37  VPTDEEQATGLEREVMLAARKGQ-DPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEE 95

Query: 103 ESPSINWMWLYEGKPKRC-MCGHWFKLV 129
           ++ ++ W WL++G+ +RC  CG  +KLV
Sbjct: 96  DNSTVIWFWLHKGEAQRCPSCGTHYKLV 123

This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport.
Bos taurus (taxid: 9913)

>sp|P10606|COX5B_HUMAN Cytochrome c oxidase subunit 5B, mitochondrial OS=Homo sapiens GN=COX5B PE=1 SV=2

 Score = 77.4 bits (189), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 41/88 (46%), Positives = 55/88 (62%), Gaps = 2/88 (2%)

Query: 43  LPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEE 102
           +P   + ATGLE+  +LA   G  DP+NV   K   GT+  P  VPS    RIVGCICEE
Sbjct: 37  VPTDEEQATGLEREIMLAAKKG-LDPYNVLAPKGASGTREDPNLVPSISNKRIVGCICEE 95

Query: 103 ESPSINWMWLYEGKPKRC-MCGHWFKLV 129
           ++ S+ W WL++G+ +RC  CG  +KLV
Sbjct: 96  DNTSVVWFWLHKGEAQRCPRCGAHYKLV 123

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

Homo sapiens (taxid: 9606)

>sp|Q710D6|COX5B_VULVU Cytochrome c oxidase subunit 5B, mitochondrial OS=Vulpes vulpes GN=COX5B PE=1 SV=1

 Score = 77.0 bits (188), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 39/88 (44%), Positives = 55/88 (62%), Gaps = 2/88 (2%)

Query: 43  LPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEE 102
           +P   + ATGLE+  ++A   G  DP+N+   K   GTK  P  VPS    RIVGCICEE
Sbjct: 36  VPTDDEQATGLEREVMMAARKG-LDPYNILAPKAAAGTKEDPNLVPSITNKRIVGCICEE 94

Query: 103 ESPSINWMWLYEGKPKRC-MCGHWFKLV 129
           ++ ++ W WL++G+ +RC  CG  +KLV
Sbjct: 95  DNSTVIWFWLHKGEAQRCPSCGTHYKLV 122

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

Vulpes vulpes (taxid: 9627)

>sp|Q5REG2|COX5B_PONAB Cytochrome c oxidase subunit 5B, mitochondrial OS=Pongo abelii GN=COX5B PE=2 SV=1

 Score = 77.0 bits (188), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 41/88 (46%), Positives = 55/88 (62%), Gaps = 2/88 (2%)

Query: 43  LPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEE 102
           +P   + ATGLE+  +LA   G  DP+NV   K   GT+  P  VPS    RIVGCICEE
Sbjct: 37  VPTDEEQATGLEREIMLAAKKG-LDPYNVLAPKGASGTREDPNLVPSISNKRIVGCICEE 95

Query: 103 ESPSINWMWLYEGKPKRC-MCGHWFKLV 129
           ++ S+ W WL++G+ +RC  CG  +KLV
Sbjct: 96  DNTSVVWFWLHKGEAQRCPRCGAHYKLV 123

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

Pongo abelii (taxid: 9601)

>sp|Q5S3G4|COX5B_PIG Cytochrome c oxidase subunit 5B, mitochondrial OS=Sus scrofa GN=COX5B PE=2 SV=1

 Score = 76.3 bits (186), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 38/88 (43%), Positives = 55/88 (62%), Gaps = 2/88 (2%)

Query: 43  LPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEE 102
           +P   + ATGLE+  ++A   G  DP+N+   K   GTK  P  VPS    RIVGCICEE
Sbjct: 37  VPTDEEQATGLEREVMMAARKG-LDPYNILAPKAASGTKEDPNLVPSITNKRIVGCICEE 95

Query: 103 ESPSINWMWLYEGKPKRC-MCGHWFKLV 129
           ++ ++ W W+++G+ +RC  CG  +KLV
Sbjct: 96  DNSTVIWFWVHKGETQRCPSCGTHYKLV 123

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

Sus scrofa (taxid: 9823)

>sp|P12075|COX5B_RAT Cytochrome c oxidase subunit 5B, mitochondrial OS=Rattus norvegicus GN=Cox5b PE=1 SV=2

 Score = 73.9 bits (180), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 39/88 (44%), Positives = 55/88 (62%), Gaps = 2/88 (2%)

Query: 43  LPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEE 102
           +P   + ATGLE+  ++A   G  DP+N+   K   GTK  P  VPS    RIVGCICEE
Sbjct: 37  VPTDEEQATGLEREIMIAAQRGL-DPYNMLPPKAASGTKEDPNLVPSVSNKRIVGCICEE 95

Query: 103 ESPSINWMWLYEGKPKRC-MCGHWFKLV 129
           ++ ++ W WL++G+ +RC  CG  +KLV
Sbjct: 96  DNCTVIWFWLHQGESQRCPNCGTHYKLV 123

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

Rattus norvegicus (taxid: 10116)

>sp|P19536|COX5B_MOUSE Cytochrome c oxidase subunit 5B, mitochondrial OS=Mus musculus GN=Cox5b PE=1 SV=1

 Score = 73.6 bits (179), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 39/88 (44%), Positives = 55/88 (62%), Gaps = 2/88 (2%)

Query: 43  LPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEE 102
           +P   + ATGLE+  ++A   G  DP+N+   K   GTK  P  VPS    RIVGCICEE
Sbjct: 36  VPTDEEQATGLEREIMIAAQKG-LDPYNMLPPKAASGTKEDPNLVPSISNKRIVGCICEE 94

Query: 103 ESPSINWMWLYEGKPKRC-MCGHWFKLV 129
           ++ ++ W WL++G+ +RC  CG  +KLV
Sbjct: 95  DNCTVIWFWLHKGESQRCPNCGTHYKLV 122

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

Mus musculus (taxid: 10090)

>sp|P79010|COX4_SCHPO Cytochrome c oxidase subunit 4, mitochondrial OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=cox4 PE=2 SV=1

 Score = 54.7 bits (130), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 37/92 (40%), Positives = 53/92 (57%), Gaps = 4/92 (4%)

Query: 42  ELPDPLDLATGLEKRELLAELAGDPDPFNVK-IRKRGLGTKTQPTEVPSAFEARIVGCIC 100
           E+P  L+ ATGLE+ ELL+EL+G  D F++K +     GT T P  V S    R +GC  
Sbjct: 64  EVPTDLEQATGLERYELLSELSGR-DAFDMKPLDASRKGTLTDPIMVTSLDPYRHIGCTG 122

Query: 101 E-EESPSINWMWLYEGKPKRC-MCGHWFKLVY 130
               S ++ WM +Y+ K +RC  CG  +KL +
Sbjct: 123 SPSGSHNLIWMTVYKDKLRRCPECGSVYKLKF 154

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

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

 Score = 52.4 bits (124), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 34/89 (38%), Positives = 47/89 (52%), Gaps = 4/89 (4%)

Query: 43  LPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCIC-- 100
           + D + +ATG EK EL AEL G     ++   +   GTK  P  V S ++ RIVGC    
Sbjct: 67  VEDVMPIATGHEKEELQAELEGRKLD-DIDFPEGPFGTKEAPAVVKSYYDMRIVGCPGGE 125

Query: 101 EEESPSINWMWLYEGKPKRC-MCGHWFKL 128
            E+   + W WL +GK   C +C  +FKL
Sbjct: 126 GEDEHDVVWFWLEKGKSFECPVCTQYFKL 154

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|P06809|COX4_NEUCR Cytochrome c oxidase subunit 4, mitochondrial OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=cox-4 PE=3 SV=2

 Score = 42.4 bits (98), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 31/95 (32%), Positives = 52/95 (54%), Gaps = 5/95 (5%)

Query: 43  LPDPLDLATGLEKRELLAELAGDPDPFNVK-IRKRGLGTKTQPTEVPSAFEARIVGCIC- 100
           +P  L+ ATGLE+ E+L ++ G  D F++K +     GT   P  V SA + +  GC   
Sbjct: 63  VPTDLEQATGLERLEILGKMEG-VDVFDMKPLDASRRGTMENPISVRSAGDEQYAGCTGF 121

Query: 101 EEESPSINWMWLYEGKP-KRC-MCGHWFKLVYKAP 133
             +S ++ W+ +   +P +RC  CG+ +K+ Y  P
Sbjct: 122 PADSHNVIWLTMTRERPVERCPECGNVYKMDYVGP 156

Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (taxid: 367110)

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	134
240848562	128	cytochrome c oxidase subunit 5B, mitocho	0.798	0.835	0.616	3e-35
91086119	121	PREDICTED: similar to AGAP008724-PA [Tri	0.686	0.760	0.663	2e-33
332373650	121	unknown [Dendroctonus ponderosae]	0.686	0.760	0.630	9e-33
193620134	128	PREDICTED: cytochrome c oxidase subunit	0.798	0.835	0.570	2e-32
90820020	119	putative mitochondrial cytochrome c oxid	0.686	0.773	0.619	5e-31
149689144	118	putative mitochondrial cytochrome oxidas	0.708	0.805	0.610	6e-31
170037183	119	cytochrome c oxidase, subunit VB [Culex	0.686	0.773	0.652	1e-30
58386537	119	AGAP008724-PA [Anopheles gambiae str. PE	0.671	0.756	0.633	2e-30
307168272	470	Cytochrome c oxidase subunit 5B, mitocho	0.686	0.195	0.608	2e-30
157119566	119	cytochrome c oxidase, subunit VB, putati	0.686	0.773	0.641	3e-30

>gi|240848562|ref|NP_001155834.1| cytochrome c oxidase subunit 5B, mitochondrial [Acyrthosiphon pisum] gi|239788733|dbj|BAH71033.1| ACYPI010196 [Acyrthosiphon pisum]

 Score =  152 bits (385), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 66/107 (61%), Positives = 84/107 (78%)

Query: 28  FSTCAQRWNKNDLDELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEV 87
           F+T A R + +  +  PDPLDLATG+EK+E+L  LAG+ DP+N+K  KRG+GTK  P E+
Sbjct: 21  FTTSAARLSTSKDEGFPDPLDLATGIEKKEMLLRLAGNDDPYNLKSIKRGVGTKETPNEI 80

Query: 88  PSAFEARIVGCICEEESPSINWMWLYEGKPKRCMCGHWFKLVYKAPI 134
           PSAFEARIVGC+CEE+S  + WMWL+ G+PKRC CGHWFKLVYK  +
Sbjct: 81  PSAFEARIVGCVCEEDSSHVKWMWLHSGEPKRCFCGHWFKLVYKEAL 127

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91086119|ref|XP_968221.1| PREDICTED: similar to AGAP008724-PA [Tribolium castaneum] gi|270011057|gb|EFA07505.1| hypothetical protein TcasGA2_TC009596 [Tribolium castaneum]

 Score =  147 bits (370), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 61/92 (66%), Positives = 82/92 (89%)

Query: 43  LPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEE 102
           + DP++ ATGLEKREL+A++AG+ +PF++K+ KRG GTK +P E+PSAF+AR+VGCICEE
Sbjct: 30  MGDPVEHATGLEKRELMAKVAGNENPFDLKVIKRGPGTKDKPNEIPSAFDARLVGCICEE 89

Query: 103 ESPSINWMWLYEGKPKRCMCGHWFKLVYKAPI 134
           ES S+NWMWLY+G+P+RC CGHWF LV+KAP+
Sbjct: 90  ESTSVNWMWLYKGQPRRCECGHWFNLVHKAPV 121

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332373650|gb|AEE61966.1| unknown [Dendroctonus ponderosae]

 Score =  144 bits (364), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 58/92 (63%), Positives = 83/92 (90%)

Query: 43  LPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEE 102
           L DP++ ATGLEKRE+LA+LAG+ +PF++++ KRG+G+K QPT +PSAF++R+VGC+CEE
Sbjct: 30  LGDPVEHATGLEKREILAKLAGNDNPFDMRVIKRGVGSKAQPTPIPSAFDSRLVGCVCEE 89

Query: 103 ESPSINWMWLYEGKPKRCMCGHWFKLVYKAPI 134
           E+ +INWMWL++G+P+RC CGHWF LV+KAP+
Sbjct: 90  EATTINWMWLHKGEPRRCECGHWFNLVHKAPV 121

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193620134|ref|XP_001950954.1| PREDICTED: cytochrome c oxidase subunit 5B, mitochondrial-like isoform 1 [Acyrthosiphon pisum]

 Score =  143 bits (361), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 61/107 (57%), Positives = 82/107 (76%)

Query: 28  FSTCAQRWNKNDLDELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEV 87
           FS    ++ K + +  PDPLDLATG+EK+E+L  LAG+ DP+N+K  KRG+GT  +PT V
Sbjct: 21  FSASNAKFTKVNDEGFPDPLDLATGIEKKEMLLRLAGNDDPYNLKAIKRGVGTSDKPTLV 80

Query: 88  PSAFEARIVGCICEEESPSINWMWLYEGKPKRCMCGHWFKLVYKAPI 134
           PSAFEARI+GC+CEE++  + WMWL+ G+PKRC CGHWFKL +K  +
Sbjct: 81  PSAFEARIIGCVCEEDASHVKWMWLHSGEPKRCYCGHWFKLEFKEAL 127

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|90820020|gb|ABD98768.1| putative mitochondrial cytochrome c oxidase polypeptide Vb [Graphocephala atropunctata]

 Score =  139 bits (349), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 57/92 (61%), Positives = 80/92 (86%)

Query: 43  LPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEE 102
           L +P+++ATG+EKRELLA+ AG+ DPF++++ KRG GTK  P EVPSA +ARI+GCICEE
Sbjct: 28  LDEPINIATGIEKRELLAKAAGNEDPFDLRVLKRGKGTKDCPNEVPSATDARIIGCICEE 87

Query: 103 ESPSINWMWLYEGKPKRCMCGHWFKLVYKAPI 134
           ++ +++WMWL++G+P+RC CGHWFKLVYK P+
Sbjct: 88  DATTVSWMWLHQGQPRRCNCGHWFKLVYKPPV 119

Source: Graphocephala atropunctata

Species: Graphocephala atropunctata

Genus: Graphocephala

Family: Cicadellidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|149689144|gb|ABR27922.1| putative mitochondrial cytochrome oxidase polypeptide Vb [Triatoma infestans]

 Score =  138 bits (348), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 58/95 (61%), Positives = 79/95 (83%)

Query: 40  LDELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCI 99
           L  +PDP++ ATGLEKRELLA ++G  +PF++K+ KRG GTK  P +VPS F+AR++GC+
Sbjct: 24  LANMPDPVEHATGLEKRELLAIVSGIENPFDMKVLKRGPGTKDCPNQVPSCFDARLLGCV 83

Query: 100 CEEESPSINWMWLYEGKPKRCMCGHWFKLVYKAPI 134
           C E++ +I WMWL++GKPKRC CGHWF+LVYKAP+
Sbjct: 84  CNEDATNIQWMWLHQGKPKRCHCGHWFQLVYKAPV 118

Source: Triatoma infestans

Species: Triatoma infestans

Genus: Triatoma

Family: Reduviidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170037183|ref|XP_001846439.1| cytochrome c oxidase, subunit VB [Culex quinquefasciatus] gi|167880193|gb|EDS43576.1| cytochrome c oxidase, subunit VB [Culex quinquefasciatus]

 Score =  137 bits (346), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 60/92 (65%), Positives = 74/92 (80%)

Query: 43  LPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEE 102
           + DP++ ATGLEKRELLA  AGD DPF++++ KRG GTK  P  +PSAFE+R+VGC+CEE
Sbjct: 28  MNDPIEHATGLEKRELLAHRAGDTDPFDMRVFKRGPGTKENPNMIPSAFESRLVGCVCEE 87

Query: 103 ESPSINWMWLYEGKPKRCMCGHWFKLVYKAPI 134
           +   I WMWL++G PKRC CGHWFKLV KAPI
Sbjct: 88  DQTYIQWMWLHQGHPKRCECGHWFKLVEKAPI 119

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|58386537|ref|XP_314835.2| AGAP008724-PA [Anopheles gambiae str. PEST] gi|55239920|gb|EAA10211.2| AGAP008724-PA [Anopheles gambiae str. PEST]

 Score =  137 bits (344), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 57/90 (63%), Positives = 76/90 (84%)

Query: 45  DPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEES 104
           DP++ ATG+EKRELLA+ AG+PDPF++++ KRG GTK  P  +PSAF+AR+VGC+CEE+ 
Sbjct: 30  DPIEHATGIEKRELLAKQAGNPDPFDMRVFKRGPGTKDSPNLIPSAFDARLVGCVCEEDQ 89

Query: 105 PSINWMWLYEGKPKRCMCGHWFKLVYKAPI 134
             + WMWL++G+PKRC CGHWFKLV KAP+
Sbjct: 90  TYVQWMWLHQGQPKRCECGHWFKLVEKAPV 119

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307168272|gb|EFN61486.1| Cytochrome c oxidase subunit 5B, mitochondrial [Camponotus floridanus]

 Score =  137 bits (344), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 56/92 (60%), Positives = 74/92 (80%)

Query: 43  LPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEE 102
           + +PLD ATGLEKRE+LA LAG+ DP+N+ I++R   TK  P  V SAFE+RI+GCIC+E
Sbjct: 379 IAEPLDHATGLEKREMLARLAGNEDPYNLTIKRRPDSTKENPNIVYSAFESRIMGCICDE 438

Query: 103 ESPSINWMWLYEGKPKRCMCGHWFKLVYKAPI 134
           ++  +NWMWL++G P+RC CGHWFKLV KAP+
Sbjct: 439 DALHVNWMWLHQGPPRRCECGHWFKLVEKAPL 470

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157119566|ref|XP_001659427.1| cytochrome c oxidase, subunit VB, putative [Aedes aegypti] gi|157134235|ref|XP_001663201.1| cytochrome c oxidase, subunit VB, putative [Aedes aegypti] gi|108870556|gb|EAT34781.1| AAEL013007-PA [Aedes aegypti] gi|108875295|gb|EAT39520.1| AAEL008697-PA [Aedes aegypti]

 Score =  136 bits (343), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 59/92 (64%), Positives = 74/92 (80%)

Query: 43  LPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEE 102
           + DP++ ATGLEKRELLA  AGD DPF++++ KRG GTK  P  +PSAFE+R+VGC+CEE
Sbjct: 28  MNDPIEHATGLEKRELLARQAGDNDPFDMRVFKRGPGTKESPNMIPSAFESRLVGCVCEE 87

Query: 103 ESPSINWMWLYEGKPKRCMCGHWFKLVYKAPI 134
           +   I WMWL++G PKRC CGHWFKLV KAP+
Sbjct: 88  DQTYIQWMWLHQGHPKRCECGHWFKLVEKAPV 119

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

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	134
FB|FBgn0031830	154	CoVb "Cytochrome c oxidase sub	0.634	0.551	0.623	2.2e-27
WB|WBGene00000371	132	cco-1 [Caenorhabditis elegans	0.619	0.628	0.505	9.5e-18
UNIPROTKB|P90849	132	cco-1 "Protein CCO-1" [Caenorh	0.619	0.628	0.505	9.5e-18
FB|FBgn0031831	154	CG11043 [Drosophila melanogast	0.611	0.532	0.459	1.8e-16
UNIPROTKB|P00428	129	COX5B "Cytochrome c oxidase su	0.589	0.612	0.481	7.7e-16
UNIPROTKB|B7ZDP5	128	cox5b "Cytochrome c oxidase po	0.589	0.617	0.469	1.3e-15
UNIPROTKB|E2RHV9	129	COX5B "Uncharacterized protein	0.589	0.612	0.469	1.3e-15
UNIPROTKB|P10606	129	COX5B "Cytochrome c oxidase su	0.589	0.612	0.493	1.3e-15
UNIPROTKB|Q5S3G4	129	COX5B "Cytochrome c oxidase su	0.589	0.612	0.456	3.3e-15
RGD|620608	129	Cox5b "cytochrome c oxidase su	0.589	0.612	0.469	6.9e-15

FB|FBgn0031830 CoVb "Cytochrome c oxidase subunit Vb" [Drosophila melanogaster (taxid:7227)]

 Score = 307 (113.1 bits), Expect = 2.2e-27, P = 2.2e-27
 Identities = 53/85 (62%), Positives = 66/85 (77%)

Query:    50 ATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINW 109
             ATG+EKRELL + AG+ +PF++K+ KRG GTK  P  +PSAF+ARIVGCICEE+   + W
Sbjct:    70 ATGIEKRELLLKAAGNDNPFDMKVFKRGAGTKENPNLIPSAFDARIVGCICEEDQTYVQW 129

Query:   110 MWLYEGKPKRCMCGHWFKLVYKAPI 134
             MWL +G  KRC CGHWFKLV KA +
Sbjct:   130 MWLQKGNQKRCECGHWFKLVEKAAV 154

GO:0005739 "mitochondrion" evidence=ISS

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

GO:0005751 "mitochondrial respiratory chain complex IV" evidence=ISS

GO:0006123 "mitochondrial electron transport, cytochrome c to oxygen" evidence=ISS

GO:0005811 "lipid particle" evidence=IDA

WB|WBGene00000371 cco-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 216 (81.1 bits), Expect = 9.5e-18, P = 9.5e-18
 Identities = 43/85 (50%), Positives = 57/85 (67%)

Query:    50 ATGLEKRELLAELAGDPDPFNVKIRKRG-LGTKTQPTEVPSAFEARIVGCICEEESPSIN 108
             ATG EK+ LLA LAGD D +  K+  R    TK +P  VPS ++ RI+GC+CE++S  +N
Sbjct:    46 ATGREKKMLLARLAGD-DRYEPKVYYRAEASTKQKPNLVPSHYDFRIIGCMCEQDSGHVN 104

Query:   109 WMWLYEGKPKRCMCGHWFKLVYKAP 133
             +M + +G PKRC CGHWFK V   P
Sbjct:   105 FMTIRKGDPKRCECGHWFKGVDADP 129

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

GO:0005740 "mitochondrial envelope" evidence=IEA

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0008340 "determination of adult lifespan" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0006629 "lipid metabolic process" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0019915 "lipid storage" evidence=IMP

GO:0042776 "mitochondrial ATP synthesis coupled proton transport" evidence=IMP

UNIPROTKB|P90849 cco-1 "Protein CCO-1" [Caenorhabditis elegans (taxid:6239)]

 Score = 216 (81.1 bits), Expect = 9.5e-18, P = 9.5e-18
 Identities = 43/85 (50%), Positives = 57/85 (67%)

Query:    50 ATGLEKRELLAELAGDPDPFNVKIRKRG-LGTKTQPTEVPSAFEARIVGCICEEESPSIN 108
             ATG EK+ LLA LAGD D +  K+  R    TK +P  VPS ++ RI+GC+CE++S  +N
Sbjct:    46 ATGREKKMLLARLAGD-DRYEPKVYYRAEASTKQKPNLVPSHYDFRIIGCMCEQDSGHVN 104

Query:   109 WMWLYEGKPKRCMCGHWFKLVYKAP 133
             +M + +G PKRC CGHWFK V   P
Sbjct:   105 FMTIRKGDPKRCECGHWFKGVDADP 129

GO:0008340 "determination of adult lifespan" evidence=IMP

FB|FBgn0031831 CG11043 [Drosophila melanogaster (taxid:7227)]

 Score = 204 (76.9 bits), Expect = 1.8e-16, P = 1.8e-16
 Identities = 40/87 (45%), Positives = 57/87 (65%)

Query:    51 TGLEKRELLAELAGDPDPFNV-KIRKRGLGTKTQPTEVPSAFEARIVGCIC-EEESPSIN 108
             TG++KRE+L    G  DP+   K+ +RG G +  PT VPSAF+AR+VGC+C ++  P   
Sbjct:    70 TGIQKREMLLAKQGCEDPWGFSKVIRRGSGRENDPTVVPSAFDARLVGCLCLDDRLPK-- 127

Query:   109 WMWLYEGK-PKRCMCGHWFKLVYKAPI 134
             WMW+ + + PKRC CGH+F L    P+
Sbjct:   128 WMWIEKDEGPKRCECGHYFILKNVPPV 154

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

GO:0005739 "mitochondrion" evidence=ISS

GO:0006123 "mitochondrial electron transport, cytochrome c to oxygen" evidence=ISS

GO:0005751 "mitochondrial respiratory chain complex IV" evidence=ISS

UNIPROTKB|P00428 COX5B "Cytochrome c oxidase subunit 5B, mitochondrial" [Bos taurus (taxid:9913)]

 Score = 198 (74.8 bits), Expect = 7.7e-16, P = 7.7e-16
 Identities = 39/81 (48%), Positives = 52/81 (64%)

Query:    50 ATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINW 109
             ATGLE+  +LA   G  DP+N+   K   GTK  P  VPS    RIVGCICEE++ ++ W
Sbjct:    44 ATGLEREVMLAARKGQ-DPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIW 102

Query:   110 MWLYEGKPKRC-MCGHWFKLV 129
              WL++G+ +RC  CG  +KLV
Sbjct:   103 FWLHKGEAQRCPSCGTHYKLV 123

GO:0005743 "mitochondrial inner membrane" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

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

UNIPROTKB|B7ZDP5 cox5b "Cytochrome c oxidase polypeptide Vb" [Canis lupus familiaris (taxid:9615)]

 Score = 196 (74.1 bits), Expect = 1.3e-15, P = 1.3e-15
 Identities = 38/81 (46%), Positives = 52/81 (64%)

Query:    50 ATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINW 109
             ATGLE+  ++A   G  DP+N+   K   GTK  P  VPS    RIVGCICEE++ ++ W
Sbjct:    43 ATGLEREVMMAARKG-LDPYNILAPKAAAGTKEDPNLVPSITNKRIVGCICEEDNSTVIW 101

Query:   110 MWLYEGKPKRC-MCGHWFKLV 129
              WL++G+ +RC  CG  +KLV
Sbjct:   102 FWLHKGEAQRCPSCGTHYKLV 122

GO:0005740 "mitochondrial envelope" evidence=IEA

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

UNIPROTKB|E2RHV9 COX5B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 196 (74.1 bits), Expect = 1.3e-15, P = 1.3e-15
 Identities = 38/81 (46%), Positives = 52/81 (64%)

Query:    50 ATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINW 109
             ATGLE+  ++A   G  DP+N+   K   GTK  P  VPS    RIVGCICEE++ ++ W
Sbjct:    44 ATGLEREVMMAARKG-LDPYNILAPKAAAGTKEDPNLVPSITNKRIVGCICEEDNSTVIW 102

Query:   110 MWLYEGKPKRC-MCGHWFKLV 129
              WL++G+ +RC  CG  +KLV
Sbjct:   103 FWLHKGEAQRCPSCGTHYKLV 123

GO:0005740 "mitochondrial envelope" evidence=IEA

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

UNIPROTKB|P10606 COX5B "Cytochrome c oxidase subunit 5B, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 196 (74.1 bits), Expect = 1.3e-15, P = 1.3e-15
 Identities = 40/81 (49%), Positives = 52/81 (64%)

Query:    50 ATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINW 109
             ATGLE+  +LA   G  DP+NV   K   GT+  P  VPS    RIVGCICEE++ S+ W
Sbjct:    44 ATGLEREIMLAAKKG-LDPYNVLAPKGASGTREDPNLVPSISNKRIVGCICEEDNTSVVW 102

Query:   110 MWLYEGKPKRC-MCGHWFKLV 129
              WL++G+ +RC  CG  +KLV
Sbjct:   103 FWLHKGEAQRCPRCGAHYKLV 123

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0007585 "respiratory gaseous exchange" evidence=TAS

GO:0005743 "mitochondrial inner membrane" evidence=TAS

GO:0022904 "respiratory electron transport chain" evidence=TAS

GO:0044281 "small molecule metabolic process" evidence=TAS

GO:0005739 "mitochondrion" evidence=IDA

UNIPROTKB|Q5S3G4 COX5B "Cytochrome c oxidase subunit 5B, mitochondrial" [Sus scrofa (taxid:9823)]

 Score = 192 (72.6 bits), Expect = 3.3e-15, P = 3.3e-15
 Identities = 37/81 (45%), Positives = 52/81 (64%)

Query:    50 ATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINW 109
             ATGLE+  ++A   G  DP+N+   K   GTK  P  VPS    RIVGCICEE++ ++ W
Sbjct:    44 ATGLEREVMMAARKG-LDPYNILAPKAASGTKEDPNLVPSITNKRIVGCICEEDNSTVIW 102

Query:   110 MWLYEGKPKRC-MCGHWFKLV 129
              W+++G+ +RC  CG  +KLV
Sbjct:   103 FWVHKGETQRCPSCGTHYKLV 123

GO:0005743 "mitochondrial inner membrane" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

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

RGD|620608 Cox5b "cytochrome c oxidase subunit Vb" [Rattus norvegicus (taxid:10116)]

 Score = 189 (71.6 bits), Expect = 6.9e-15, P = 6.9e-15
 Identities = 38/81 (46%), Positives = 52/81 (64%)

Query:    50 ATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINW 109
             ATGLE+  ++A   G  DP+N+   K   GTK  P  VPS    RIVGCICEE++ ++ W
Sbjct:    44 ATGLEREIMIAAQRG-LDPYNMLPPKAASGTKEDPNLVPSVSNKRIVGCICEEDNCTVIW 102

Query:   110 MWLYEGKPKRCM-CGHWFKLV 129
              WL++G+ +RC  CG  +KLV
Sbjct:   103 FWLHQGESQRCPNCGTHYKLV 123

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

GO:0005575 "cellular_component" evidence=ND

GO:0005739 "mitochondrion" evidence=ISO

GO:0005743 "mitochondrial inner membrane" evidence=IEA;ISO

GO:0009725 "response to hormone stimulus" evidence=IEP

GO:0043434 "response to peptide hormone stimulus" evidence=IEP

GO:0046872 "metal ion binding" evidence=IEA

---

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)
P00428	COX5B_BOVIN	No assigned EC number	0.4545	0.6417	0.6666	yes	N/A
P10606	COX5B_HUMAN	No assigned EC number	0.4659	0.6417	0.6666	yes	N/A
P12075	COX5B_RAT	No assigned EC number	0.4431	0.6417	0.6666	yes	N/A
Q5REG2	COX5B_PONAB	No assigned EC number	0.4659	0.6417	0.6666	yes	N/A
P19536	COX5B_MOUSE	No assigned EC number	0.4431	0.6417	0.6718	yes	N/A
Q5S3G4	COX5B_PIG	No assigned EC number	0.4318	0.6417	0.6666	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	134
cd00924	97	cd00924, Cyt_c_Oxidase_Vb, Cytochrome c oxidase su	3e-44
pfam01215	136	pfam01215, COX5B, Cytochrome c oxidase subunit Vb	9e-23
PLN02294	174	PLN02294, PLN02294, cytochrome c oxidase subunit V	7e-11

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

 Score =  139 bits (353), Expect = 3e-44
 Identities = 54/94 (57%), Positives = 65/94 (69%), Gaps = 2/94 (2%)

Query: 42  ELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICE 101
           E+P  L+ ATGLE++ELLA+L G  D F++K  K   GTK  P  VPSAF+ RIVGCICE
Sbjct: 5   EVPTDLEQATGLERKELLAKLEGI-DDFDMKPLKGPFGTKEDPNLVPSAFDKRIVGCICE 63

Query: 102 EESPSINWMWLYEGKPKRC-MCGHWFKLVYKAPI 134
            +S  + WMWL +GKPKRC  CGH FKLV   P 
Sbjct: 64  PDSHDVIWMWLEKGKPKRCPECGHVFKLVDVGPP 97

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 = 86.5 bits (214), Expect = 9e-23
 Identities = 37/91 (40%), Positives = 49/91 (53%), Gaps = 3/91 (3%)

Query: 42  ELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICE 101
            +P  L+ ATGLE+ ELLA L G  DPF++K      GT   P  V S    RIVGC   
Sbjct: 37  GVPTDLEQATGLEREELLAALKGR-DPFDIKPLDASKGTLKDPIIVESIDNYRIVGCTGS 95

Query: 102 E-ESPSINWMWLYEGKPKRCM-CGHWFKLVY 130
              S +I W  +++G+ +RC  CG  +KL  
Sbjct: 96  PDGSHTIIWFTVHKGEAQRCPECGSVYKLKP 126

Length = 136

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

 Score = 56.4 bits (136), Expect = 7e-11
 Identities = 45/139 (32%), Positives = 67/139 (48%), Gaps = 25/139 (17%)

Query: 6   RSLVLSPNTRYLARSVTATGNSFSTCAQRWNKNDLD-----ELPDPLDLATGLEKRELLA 60
           R++V +    YL+RS ++   S S  ++ ++    D      + D + +ATG E+ EL A
Sbjct: 24  RTVVATTRPLYLSRSRSSISASSSVFSRYFSSESADTAVKKRVEDVMPIATGHEREELEA 83

Query: 61  ELAG----DPD----PFNVKIRKRGLGTKTQPTEVPSAFEARIVGCIC--EEESPSINWM 110
           EL G    D D    PF         GTK  P  V S ++ RIVGC     E+   + W 
Sbjct: 84  ELEGRKLLDIDFPEGPF---------GTKEAPAVVKSYYDKRIVGCPGGEGEDEHDVVWF 134

Query: 111 WLYEGKPKRC-MCGHWFKL 128
           WL +GK   C +C  +F+L
Sbjct: 135 WLEKGKSFECPVCTQYFEL 153

Length = 174

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	134
cd00924	97	Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb.	100.0
PF01215	136	COX5B: Cytochrome c oxidase subunit Vb This family	100.0
KOG3352|consensus	153		100.0
PLN02294	174	cytochrome c oxidase subunit Vb	100.0
PTZ00043	268	cytochrome c oxidase subunit; Provisional	99.95
KOG3456|consensus	120		96.83
PF10276	40	zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Z	96.28
COG4391	62	Uncharacterized protein conserved in bacteria [Fun	84.5

>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb

Probab=100.00  E-value=3.2e-49  Score=284.23  Aligned_cols=95  Identities=57%  Similarity=0.994  Sum_probs=91.8

Q ss_pred             CCCCCCCcccccccHHHHHHHHHHcCCCCCCCcccccCCCCCCCCCeeeeCCCCCeEEeeeCCCCCCcceEEEeecCCce
Q psy2945          39 DLDELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINWMWLYEGKPK  118 (134)
Q Consensus        39 ~~g~vptd~eqATGlEr~ELla~~~G~~D~fd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g~~dsh~v~W~~l~~g~p~  118 (134)
                      +.|+||||+||||||||+||+++++|+ |+|||+|+++++||++|||+|||++++|||||+|++|+|+|+||||++|+|+
T Consensus         2 ~~g~vp~d~e~aTGlEr~ELl~~~~G~-d~f~~~~~~~~~GT~e~P~lVpS~~~~RiVGC~g~~~~h~v~W~~l~~g~~~   80 (97)
T cd00924           2 AEGEVPTDLEQATGLERKELLAKLEGI-DDFDMKPLKGPFGTKEDPNLVPSAFDKRIVGCICEPDSHDVIWMWLEKGKPK   80 (97)
T ss_pred             CCcccCCchHhhhccHHHHHHHHHcCC-ccccccccccCCCCccCCeEecCCCCCeEEeeeCCCCCceEEEEEEeCCCce
Confidence            578999999999999999999999999 7799999999999999999999999999999999888999999999999999


Q ss_pred             ee-eCCCEEEEEEeCCC
Q psy2945         119 RC-MCGHWFKLVYKAPI  134 (134)
Q Consensus       119 RC-eCG~~FkL~~~~p~  134 (134)
                      || +|||||||++++|.
T Consensus        81 rC~eCG~~fkL~~v~~~   97 (97)
T cd00924          81 RCPECGHVFKLVDVGPP   97 (97)
T ss_pred             eCCCCCcEEEEEECCCC
Confidence            99 89999999999985

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=100.00  E-value=1.5e-49  Score=300.71  Aligned_cols=98  Identities=48%  Similarity=0.871  Sum_probs=69.7

Q ss_pred             ccCCCCCCCCCcccccccHHHHHHHHHHcCCCCCCCcccccCCCCCCCCCeeeeCCCCCeEEeeeC-CCCCCcceEEEee
Q psy2945          35 WNKNDLDELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCIC-EEESPSINWMWLY  113 (134)
Q Consensus        35 ~~~~~~g~vptd~eqATGlEr~ELla~~~G~~D~fd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g-~~dsh~v~W~~l~  113 (134)
                      .++++.|+||||+||||||||+|||++++|+ |||||+|++.++||+||||||||++++|||||+| +.|+|+|+||||+
T Consensus        30 ~~~a~~G~vptd~eqATGlER~Ella~~~G~-D~Fd~~~~~~~~GT~e~P~lVpS~~~~RiVGC~g~~~~sH~v~W~~l~  108 (136)
T PF01215_consen   30 GPGAKPGTVPTDLEQATGLEREELLAKLEGI-DPFDMKPLKAPFGTKEDPILVPSYFDERIVGCTGEPDDSHDVIWFWLH  108 (136)
T ss_dssp             -------BS--HHHH--HHHHHHHHHHHTT---TT--S--B----SSSS-CEEEESSSCEEEEESSSTT-SSS-EEEEEE
T ss_pred             cccccCCCCCChhHhhhHHHHHHHHHHhcCc-CcccccCccCCCCCccCCeEccCCCCceEEeeccCCCCcceeEEEEEe
Confidence            3456789999999999999999999999998 9999999999999999999999999999999999 6678899999999


Q ss_pred             cCCceee-eCCCEEEEEEeCC
Q psy2945         114 EGKPKRC-MCGHWFKLVYKAP  133 (134)
Q Consensus       114 ~g~p~RC-eCG~~FkL~~~~p  133 (134)
                      +|+|+|| +||+||||+++|+
T Consensus       109 ~g~~~RCpeCG~~fkL~~vg~  129 (136)
T PF01215_consen  109 KGKPQRCPECGQVFKLKYVGP  129 (136)
T ss_dssp             TTSEEEETTTEEEEEEEE---
T ss_pred             CCCccCCCCCCeEEEEEEcCC
Confidence            9999999 9999999999987

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

Probab=100.00  E-value=5.8e-48  Score=295.71  Aligned_cols=97  Identities=53%  Similarity=0.986  Sum_probs=92.8

Q ss_pred             CCCCCCCCCcccccccHHHHHHHHHHcCCCCCCCcccccCCCCCCCCCeeeeCCCCCeEEeeeCCCCCCcceEEEeecCC
Q psy2945          37 KNDLDELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINWMWLYEGK  116 (134)
Q Consensus        37 ~~~~g~vptd~eqATGlEr~ELla~~~G~~D~fd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g~~dsh~v~W~~l~~g~  116 (134)
                      ..+.|.||||+|||||+||+|||++++|+ ||||++.+++++|||+|||||||++|+|||||.|++|+|+|+||||+||+
T Consensus        54 ~~~~g~vpddle~aTGlEk~eLla~l~G~-d~~d~k~~~~~~GTkedP~lV~S~~d~RiVGC~c~eD~~~V~Wmwl~Kge  132 (153)
T KOG3352|consen   54 MAKGGGVPDDLEQATGLEKEELLAELEGR-DPFDMKVPRGPSGTKEDPNLVPSYYDKRIVGCGCEEDSHAVVWMWLEKGE  132 (153)
T ss_pred             cccCCCCCCchhhhhhHHHHHHHHHhhCC-CccccccccCCCCcccCCccccccCCceEEeecccCCCcceEEEEEEcCC
Confidence            34678999999999999999999999999 89999977789999999999999999999999999999999999999999


Q ss_pred             ceee-eCCCEEEEEEeCCC
Q psy2945         117 PKRC-MCGHWFKLVYKAPI  134 (134)
Q Consensus       117 p~RC-eCG~~FkL~~~~p~  134 (134)
                      .+|| ||||||||+.+||+
T Consensus       133 ~~rc~eCG~~fkL~~v~~~  151 (153)
T KOG3352|consen  133 TQRCPECGHYFKLVPVGPV  151 (153)
T ss_pred             cccCCcccceEEeeecCCC
Confidence            9998 99999999999985

>PLN02294 cytochrome c oxidase subunit Vb

Probab=100.00  E-value=5.5e-47  Score=295.45  Aligned_cols=94  Identities=35%  Similarity=0.686  Sum_probs=91.4

Q ss_pred             CCCCCCCcccccccHHHHHHHHHHcCCCCCCCcccccCCCCCCCCCeeeeCCCCCeEEeeeC--CCCCCcceEEEeecCC
Q psy2945          39 DLDELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCIC--EEESPSINWMWLYEGK  116 (134)
Q Consensus        39 ~~g~vptd~eqATGlEr~ELla~~~G~~D~fd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g--~~dsh~v~W~~l~~g~  116 (134)
                      .+++|+|+++|||||||+|||++++|+ |||||++++.++|||||||+|||++++|||||+|  ++|+|+|+||||++|+
T Consensus        62 ~~~~~~d~~~~ATGLER~ELla~leG~-D~Fd~~~~~gp~GTke~P~lVpS~~d~RiVGCtg~~~eDsh~v~Wf~L~kGk  140 (174)
T PLN02294         62 VKKRVEDVMPIATGHEREELEAELEGR-KLLDIDFPEGPFGTKEAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGK  140 (174)
T ss_pred             ccccCCCchhhccchHHHHHHHHHcCC-CccccccccCCCCCccCCcEeccCCCceEEeeCCCCCCCCceeEEEEecCCC
Confidence            467899999999999999999999999 9999999988999999999999999999999999  7999999999999999


Q ss_pred             ceee-eCCCEEEEEEeCC
Q psy2945         117 PKRC-MCGHWFKLVYKAP  133 (134)
Q Consensus       117 p~RC-eCG~~FkL~~~~p  133 (134)
                      |+|| +||+||||+++||
T Consensus       141 p~RCpeCG~~fkL~~vG~  158 (174)
T PLN02294        141 SFECPVCTQYFELEVVGP  158 (174)
T ss_pred             ceeCCCCCCEEEEEEeCC
Confidence            9999 9999999999998

>PTZ00043 cytochrome c oxidase subunit; Provisional

Probab=99.95  E-value=7.1e-29  Score=201.93  Aligned_cols=87  Identities=26%  Similarity=0.346  Sum_probs=80.0

Q ss_pred             CCCccc-ccccHHHHHHHHHHcCCCCCCCcccccCCCCCCCCCeeeeCCCCCeEEeeeC--CCCCCcceEEEeecCCcee
Q psy2945          43 LPDPLD-LATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCIC--EEESPSINWMWLYEGKPKR  119 (134)
Q Consensus        43 vptd~e-qATGlEr~ELla~~~G~~D~fd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g--~~dsh~v~W~~l~~g~p~R  119 (134)
                      +..|+. |...-+.+.|+|.++|. +.+..+++.+++||+|||+||||++++|||||+|  ++|+|+|+|||+++|+++|
T Consensus       105 la~d~gmqi~~~~~~hm~~~le~y-~~Lk~~~~~GPfGTkEdPiLVpSy~deRyVGCTGg~~EDeH~VvWFwLrEGkpqR  183 (268)
T PTZ00043        105 LARDMGMQIVNEPSEHMLGLLELY-EYLKSSSFVGPFGTIENPVLVPSVGTERVVGCTGGTGEHEHVPLWFRCREGFLYR  183 (268)
T ss_pred             HHHHhCceecCCchHHHHHHHHHH-HhcCcCCCCCCCCCccCCeEeccCCCceEEeccCCCccCCceeEEEEecCCCCcc
Confidence            333454 67777889999999998 9999999999999999999999999999999999  7889999999999999999


Q ss_pred             e-eCCCEEEEEE
Q psy2945         120 C-MCGHWFKLVY  130 (134)
Q Consensus       120 C-eCG~~FkL~~  130 (134)
                      | +||+||||++
T Consensus       184 CpECGqVFKLVr  195 (268)
T PTZ00043        184 CGECDQIFMLVR  195 (268)
T ss_pred             CCCCCcEEEEEE
Confidence            9 9999999998

>KOG3456|consensus

Probab=96.83  E-value=0.0034  Score=46.80  Aligned_cols=40  Identities=23%  Similarity=0.410  Sum_probs=35.2

Q ss_pred             CCCCCeEEeeeC--CCCCCcceEEEeecCCceee-eCCCEEEE
Q psy2945          89 SAFEARIVGCIC--EEESPSINWMWLYEGKPKRC-MCGHWFKL  128 (134)
Q Consensus        89 S~~~~RiVGC~g--~~dsh~v~W~~l~~g~p~RC-eCG~~FkL  128 (134)
                      +.-++|||-|-|  ++=-|-..|+.|.+..++-| -||.-|.-
T Consensus        74 ~e~d~RVV~CdGg~~aLGHPkvyInLDk~~~~~CgYCGlrf~~  116 (120)
T KOG3456|consen   74 IEVDGRVVACDGGTPALGHPKVYINLDKPGPHICGYCGLRFVQ  116 (120)
T ss_pred             hhccceEEEecCCCCCCCCCeEEEEcCCCCCcccccchhhhhh
Confidence            455999999999  68889999999999989999 99987753

>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=96.28  E-value=0.0068  Score=37.43  Aligned_cols=36  Identities=22%  Similarity=0.425  Sum_probs=29.5

Q ss_pred             CCeEEeeeC--CCCCCcceEEEeec-CCceee-eCCCEEE
Q psy2945          92 EARIVGCIC--EEESPSINWMWLYE-GKPKRC-MCGHWFK  127 (134)
Q Consensus        92 ~~RiVGC~g--~~dsh~v~W~~l~~-g~p~RC-eCG~~Fk  127 (134)
                      +.|+|-|-|  .+-.|-.+|+.|.+ +++..| -||.-|+
T Consensus         1 ~~~~v~CdG~~~~lgHPrVyl~l~~~~~~~~CpYCg~~yv   40 (40)
T PF10276_consen    1 DGRRVSCDGGGGALGHPRVYLNLDDEPGPVVCPYCGTRYV   40 (40)
T ss_dssp             -SSEEEEEESSTTSCCCCEEEE-TTTTCEEEETTTTEEEE
T ss_pred             CCcEEEeCCCCCCCCCCeEEEecCCCCCeEECCCCCCEEC
Confidence            468999998  46788899999998 478999 9999885

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.

>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=84.50  E-value=1.7  Score=29.34  Aligned_cols=44  Identities=9%  Similarity=0.142  Sum_probs=32.4

Q ss_pred             CeeeeCCCCCeEEeeeC--CCCCCcceEEEeecCCceee-eCCCEEEEE
Q psy2945          84 PTEVPSAFEARIVGCIC--EEESPSINWMWLYEGKPKRC-MCGHWFKLV  129 (134)
Q Consensus        84 P~lVpS~~~~RiVGC~g--~~dsh~v~W~~l~~g~p~RC-eCG~~FkL~  129 (134)
                      ++.|.+.+  --+-|.|  ++-+|-=+|+-+.+..-.-| -||..|+|.
T Consensus        15 ~~~I~~~~--~~l~C~g~~~p~~HPrV~L~mg~~gev~CPYC~t~y~l~   61 (62)
T COG4391          15 HETIEIGD--LPLMCPGPEPPNDHPRVFLDMGDEGEVVCPYCSTRYRLN   61 (62)
T ss_pred             ceEEEeCC--eeEEcCCCCCCCCCCEEEEEcCCCCcEecCccccEEEec
Confidence            44454432  2367988  57888889999966556899 999999985

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	134
2y69_F	129	Bovine Heart Cytochrome C Oxidase Re-Refined With M		2e-15
1occ_F	98	Structure Of Bovine Heart Cytochrome C Oxidase At T		5e-15

>pdb|2Y69|F Chain F, Bovine Heart Cytochrome C Oxidase Re-Refined With Molecular Oxygen Length = 129

Iteration: 1
 Score = 77.4 bits (189), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 39/81 (48%), Positives = 52/81 (64%), Gaps = 2/81 (2%)
Query: 50  ATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINW 109
           ATGLE+  +LA   G  DP+N+   K   GTK  P  VPS    RIVGCICEE++ ++ W
Sbjct: 44  ATGLEREVMLAARKGQ-DPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIW 102
Query: 110 MWLYEGKPKRC-MCGHWFKLV 129
            WL++G+ +RC  CG  +KLV
Sbjct: 103 FWLHKGEAQRCPSCGTHYKLV 123

>pdb|1OCC|F Chain F, Structure Of Bovine Heart Cytochrome C Oxidase At The Fully Oxidized State Length = 98

Iteration: 1
 Score = 76.3 bits (186), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 39/81 (48%), Positives = 52/81 (64%), Gaps = 2/81 (2%)
Query: 50  ATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINW 109
           ATGLE+  +LA   G  DP+N+   K   GTK  P  VPS    RIVGCICEE++ ++ W
Sbjct: 13  ATGLEREVMLAARKGQ-DPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIW 71
Query: 110 MWLYEGKPKRC-MCGHWFKLV 129
            WL++G+ +RC  CG  +KLV
Sbjct: 72  FWLHKGEAQRCPSCGTHYKLV 92

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	134
2y69_F	129	Cytochrome C oxidase subunit 5B; electron transpor	6e-37
1v54_F	98	VI, cytochrome C oxidase polypeptide VB; oxidoredu	7e-37
2odx_A	80	Cytochrome C oxidase polypeptide IV; all beta-prot	5e-26

>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 =  121 bits (305), Expect = 6e-37
 Identities = 39/91 (42%), Positives = 54/91 (59%), Gaps = 2/91 (2%)

Query: 42  ELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICE 101
            +P   + ATGLE+  +LA      DP+N+   K   GTK  P  VPS    RIVGCICE
Sbjct: 36  GVPTDEEQATGLEREVMLAAR-KGQDPYNILAPKATSGTKEDPNLVPSITNKRIVGCICE 94

Query: 102 EESPSINWMWLYEGKPKRCM-CGHWFKLVYK 131
           E++ ++ W WL++G+ +RC  CG  +KLV  
Sbjct: 95  EDNSTVIWFWLHKGEAQRCPSCGTHYKLVPH 125

>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 =  120 bits (302), Expect = 7e-37
 Identities = 39/92 (42%), Positives = 54/92 (58%), Gaps = 2/92 (2%)

Query: 42  ELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICE 101
            +P   + ATGLE+  +LA      DP+N+   K   GTK  P  VPS    RIVGCICE
Sbjct: 5   GVPTDEEQATGLEREVMLAAR-KGQDPYNILAPKATSGTKEDPNLVPSITNKRIVGCICE 63

Query: 102 EESPSINWMWLYEGKPKRCM-CGHWFKLVYKA 132
           E++ ++ W WL++G+ +RC  CG  +KLV   
Sbjct: 64  EDNSTVIWFWLHKGEAQRCPSCGTHYKLVPHQ 95

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

 Score = 92.5 bits (230), Expect = 5e-26
 Identities = 20/70 (28%), Positives = 28/70 (40%), Gaps = 3/70 (4%)

Query: 67  DPFNVK-IRKRGLGTKTQPTEVPSAFEARIVGCI-CEEESPSINWMWLYEGKPKRCM-CG 123
           D F+ K +     GT   P  + S  + R VGC      S +I W+     +  RC  CG
Sbjct: 4   DVFDTKPLDSSRKGTMKDPIIIESYDDYRYVGCTGSPAGSHTIMWLKPTVNEVARCWECG 63

Query: 124 HWFKLVYKAP 133
             +KL     
Sbjct: 64  SVYKLNPVGV 73

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	134
2y69_F	129	Cytochrome C oxidase subunit 5B; electron transpor	100.0
1v54_F	98	VI, cytochrome C oxidase polypeptide VB; oxidoredu	100.0
2odx_A	80	Cytochrome C oxidase polypeptide IV; all beta-prot	100.0
2jrr_A	67	Uncharacterized protein; solution structure, SIR90	98.16
2jvm_A	80	Uncharacterized protein; alpha+beta, structural ge	97.75
2jz8_A	87	Uncharacterized protein BH09830; zinc binding, str	93.55
1gh9_A	71	8.3 kDa protein (gene MTH1184); beta+alpha complex	80.91

>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=100.00  E-value=2.5e-50  Score=301.56  Aligned_cols=93  Identities=43%  Similarity=0.831  Sum_probs=88.4

Q ss_pred             CCCCCCCCcccccccHHHHHHHHHHcCCCCCCCcccccCCCCCCCCCeeeeCCCCCeEEeeeCCCCCCcceEEEeecCCc
Q psy2945          38 NDLDELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINWMWLYEGKP  117 (134)
Q Consensus        38 ~~~g~vptd~eqATGlEr~ELla~~~G~~D~fd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g~~dsh~v~W~~l~~g~p  117 (134)
                      ++.|+||||+||||||||+||+++++|+ |||||+++++++|||||||+|||++++|||||+|++|+|+|+||||++|+|
T Consensus        32 a~~g~iPtd~eqATGlER~ELla~~~G~-DpFd~~~~~~~~GTkedP~lVpS~~d~RiVGC~~~~Dsh~v~Wf~L~kg~p  110 (129)
T 2y69_F           32 ASGGGVPTDEEQATGLEREVMLAARKGQ-DPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEA  110 (129)
T ss_dssp             ---CBCCCHHHHCCHHHHHHHHHHHTTC-CTTCCSCCCCCCCCSSSCEEEEESSSEEEEEECCSTTCSCCEEEEEESSSC
T ss_pred             cCCCCCCCHHHhccCHHHHHHHHHHcCC-CccccCCCCCCCCcccCCeEeecCCCCeEEeecCCCCCceeEEEEEeCCCc
Confidence            3568999999999999999999999997 999999999999999999999999999999999999999999999999999


Q ss_pred             eee-eCCCEEEEEEe
Q psy2945         118 KRC-MCGHWFKLVYK  131 (134)
Q Consensus       118 ~RC-eCG~~FkL~~~  131 (134)
                      +|| +||+||||+++
T Consensus       111 ~RCpeCG~~fkL~~~  125 (129)
T 2y69_F          111 QRCPSCGTHYKLVPH  125 (129)
T ss_dssp             EECTTTCCEEEEEEC
T ss_pred             eeCCCCCeEEEEeee
Confidence            999 99999999975

>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=100.00  E-value=1.5e-49  Score=285.37  Aligned_cols=92  Identities=43%  Similarity=0.841  Sum_probs=89.2

Q ss_pred             CCCCCCCcccccccHHHHHHHHHHcCCCCCCCcccccCCCCCCCCCeeeeCCCCCeEEeeeCCCCCCcceEEEeecCCce
Q psy2945          39 DLDELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINWMWLYEGKPK  118 (134)
Q Consensus        39 ~~g~vptd~eqATGlEr~ELla~~~G~~D~fd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g~~dsh~v~W~~l~~g~p~  118 (134)
                      +.|+||||+||||||||+||+++++|+ |||||+++++++|||||||+|||++++|||||+|++|+|+|+||||++|+|+
T Consensus         2 ~~g~iPtd~eqATGlEr~Ella~~~G~-Dpfd~~~~~~~~GTke~P~lVpS~~~~RiVGC~~~~D~h~v~W~~l~~g~~~   80 (98)
T 1v54_F            2 SGGGVPTDEEQATGLEREVMLAARKGQ-DPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQ   80 (98)
T ss_dssp             CCCBCCCHHHHCCHHHHHHHHHHHTTC-CTTCCSCCCCCCCCSSSCEEEECSSSEEEEEECCSTTCSCCEEEEEESSSCE
T ss_pred             CCCCCCChHHhccCHHHHHHHHHHcCC-CcccccCCCCCCCcccCCeEeecCCCCeEEeecCCCCCceeEEEEEeCCCce
Confidence            468999999999999999999999997 9999999999999999999999999999999999999999999999999999


Q ss_pred             ee-eCCCEEEEEEe
Q psy2945         119 RC-MCGHWFKLVYK  131 (134)
Q Consensus       119 RC-eCG~~FkL~~~  131 (134)
                      || +||+||||++.
T Consensus        81 RC~eCG~~fkL~~~   94 (98)
T 1v54_F           81 RCPSCGTHYKLVPH   94 (98)
T ss_dssp             ECTTTCCEEEEECC
T ss_pred             ECCCCCeEEEEeee
Confidence            99 99999999975

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

Probab=100.00  E-value=1.8e-37  Score=215.49  Aligned_cols=70  Identities=29%  Similarity=0.387  Sum_probs=51.1

Q ss_pred             cCCCCCCCcccccC-CCCCCCCCeeeeCCCCCeEEeeeC-CCCCCcceEEEeecCCceee-eCCCEEEEEEeCC
Q psy2945          63 AGDPDPFNVKIRKR-GLGTKTQPTEVPSAFEARIVGCIC-EEESPSINWMWLYEGKPKRC-MCGHWFKLVYKAP  133 (134)
Q Consensus        63 ~G~~D~fd~~~~~~-~~GTke~P~lVpS~~~~RiVGC~g-~~dsh~v~W~~l~~g~p~RC-eCG~~FkL~~~~p  133 (134)
                      +|+ |||||+|+++ ++|||||||||||++++|||||+| ++|+|+|+||||++|+++|| +||+||||+++||
T Consensus         1 ~G~-D~fd~~p~~~~~~GT~e~P~lVpS~~~~RiVGC~g~p~d~h~v~W~~l~~g~~~RC~eCG~~fkL~~vg~   73 (80)
T 2odx_A            1 MMA-DVFDTKPLDSSRKGTMKDPIIIESYDDYRYVGCTGSPAGSHTIMWLKPTVNEVARCWECGSVYKLNPVGV   73 (80)
T ss_dssp             -------------------CCSCSEECCSSSSCCEEESSSTTCCSCCEEECCCTTCEEECSSSCCEEEECCCC-
T ss_pred             CCc-CcccccccccCCCCCccCCeEecCCCCCeEEeeeCCCCCcceEEEEEecCCCCeECCCCCeEEEEEEcCC
Confidence            487 9999999986 799999999999999999999999 49999999999999999999 9999999999997

>2jrr_A Uncharacterized protein; solution structure, SIR90, structural genomics, PSI-2, protein structure initiative; NMR {Silicibacter pomeroyi}

Probab=98.16  E-value=9.5e-07  Score=59.20  Aligned_cols=50  Identities=16%  Similarity=0.232  Sum_probs=40.8

Q ss_pred             CCCCCeeeeCCCCCeEEeeeC--CCCCCcceEEEe-ecCCceee-eCCCEEEEEEe
Q psy2945          80 TKTQPTEVPSAFEARIVGCIC--EEESPSINWMWL-YEGKPKRC-MCGHWFKLVYK  131 (134)
Q Consensus        80 Tke~P~lVpS~~~~RiVGC~g--~~dsh~v~W~~l-~~g~p~RC-eCG~~FkL~~~  131 (134)
                      |++.|-+|  ..+.|+|.|-|  .+..|-.+|++| .++.+..| -||..|+|+..
T Consensus         2 ~~~ape~i--~v~~r~v~CdGg~g~lgHPrVyl~ld~~~g~~~CpYCg~~f~l~~~   55 (67)
T 2jrr_A            2 TIQAPETK--IVDKSRVACDGGEGALGHPRVWLQIPEDTGWVECPYCDCKYVLKGS   55 (67)
T ss_dssp             CCCCCEEE--EESSSEEEEEESSTTSEEEEEEEECCTTTSEEEETTTTEEEEETTS
T ss_pred             CCCCCceE--EECCCEEEeCCCCCCCCCCEEEEEccCCCCeEECCCCCCEEEECCC
Confidence            55667666  44789999988  456899999999 56788999 99999999743

>2jvm_A Uncharacterized protein; alpha+beta, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Rhodobacter sphaeroides 2}

Probab=97.75  E-value=2.7e-05  Score=53.76  Aligned_cols=49  Identities=16%  Similarity=0.248  Sum_probs=38.5

Q ss_pred             CCCCCeeeeCCCCCeEEeeeC--CCCCCcceEEEe-ecCCceee-eCCCEEEEEE
Q psy2945          80 TKTQPTEVPSAFEARIVGCIC--EEESPSINWMWL-YEGKPKRC-MCGHWFKLVY  130 (134)
Q Consensus        80 Tke~P~lVpS~~~~RiVGC~g--~~dsh~v~W~~l-~~g~p~RC-eCG~~FkL~~  130 (134)
                      |.+-|-+|.  .+.|+|.|-|  .+..|-.+|++| .++.+..| -||..|+|+.
T Consensus        15 ~~~apevI~--V~~~~V~CdGg~g~LGHPrVyL~ld~~~g~~~CpYCg~~f~l~~   67 (80)
T 2jvm_A           15 SIEAPETVV--VSTWKVACDGGEGALGHPRVWLSIPHETGFVECGYCDRRYIHES   67 (80)
T ss_dssp             CCSCCSEEE--ESCSEEEECCCSTTCCCCCEEEECCTTTCEEECSSSSCEEEEHH
T ss_pred             ccCCCCeEE--ECCcEEEcCCCCCCCCCCEEEEEccCCCCeEECCCCCCEEEecC
Confidence            445554442  3369999988  467999999999 57888999 9999999863

>2jz8_A Uncharacterized protein BH09830; zinc binding, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Bartonella henselae str}

Probab=93.55  E-value=0.047  Score=38.04  Aligned_cols=38  Identities=11%  Similarity=0.221  Sum_probs=32.0

Q ss_pred             CeEEeeeC--CCCCCcceEEEeecCCceee-eCCCEEEEEE
Q psy2945          93 ARIVGCIC--EEESPSINWMWLYEGKPKRC-MCGHWFKLVY  130 (134)
Q Consensus        93 ~RiVGC~g--~~dsh~v~W~~l~~g~p~RC-eCG~~FkL~~  130 (134)
                      .|.|-|.|  .+-.|--+|+.|.+.....| -||.-|+++.
T Consensus        22 ~~~v~CdG~~~plgHPrVyL~i~~~g~~~CpYCg~~y~~~~   62 (87)
T 2jz8_A           22 VKEFMCVGATQPFDHPHIFIDMGSTDEKICPYCSTLYRYDP   62 (87)
T ss_dssp             CSEEECCCSSCSSSSSSCEEECTTCCEECCTTTCCEEECCT
T ss_pred             CcEEEcCCCCCCCCCCEEEEEcCCCCeEECCCCCCEeEcCC
Confidence            35589988  35578889999999888999 9999999874

>1gh9_A 8.3 kDa protein (gene MTH1184); beta+alpha complex structure, structural genomics, PSI, protein structure initiative; NMR {Methanothermobacterthermautotrophicus} SCOP: g.41.6.1

Probab=80.91  E-value=1.2  Score=29.51  Aligned_cols=32  Identities=28%  Similarity=0.601  Sum_probs=22.4

Q ss_pred             CeEEeeeCCCCCCcceEEEeecC-CceeeeCCCEEEEEE
Q psy2945          93 ARIVGCICEEESPSINWMWLYEG-KPKRCMCGHWFKLVY  130 (134)
Q Consensus        93 ~RiVGC~g~~dsh~v~W~~l~~g-~p~RCeCG~~FkL~~  130 (134)
                      |-||||.|..     .|. ++.+ +.+.|.||..++++.
T Consensus         2 Y~vv~C~C~~-----~~~-~~~~~kT~~C~CG~~~~~~k   34 (71)
T 1gh9_A            2 YIIFRCDCGR-----ALY-SREGAKTRKCVCGRTVNVKD   34 (71)
T ss_dssp             EEEEEETTSC-----CEE-EETTCSEEEETTTEEEECCS
T ss_pred             eEEEECCCCC-----EEE-EcCCCcEEECCCCCeeeece
Confidence            5799998743     143 3333 569999999988753

---

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	134
d1v54f_	98	g.41.5.3 (F:) Cytochrome c oxidase Subunit F {Cow	3e-41

>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 =  130 bits (329), Expect = 3e-41
 Identities = 40/90 (44%), Positives = 55/90 (61%), Gaps = 2/90 (2%)

Query: 41  DELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCIC 100
             +P   + ATGLE+  +LA   G  DP+N+   K   GTK  P  VPS    RIVGCIC
Sbjct: 4   GGVPTDEEQATGLEREVMLAARKGQ-DPYNILAPKATSGTKEDPNLVPSITNKRIVGCIC 62

Query: 101 EEESPSINWMWLYEGKPKRCM-CGHWFKLV 129
           EE++ ++ W WL++G+ +RC  CG  +KLV
Sbjct: 63  EEDNSTVIWFWLHKGEAQRCPSCGTHYKLV 92

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	134
d1v54f_	98	Cytochrome c oxidase Subunit F {Cow (Bos taurus) [	100.0
d1x6ea2	26	Zinc finger protein 24 {Human (Homo sapiens) [TaxI	91.26

>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=2e-51  Score=293.50  Aligned_cols=93  Identities=43%  Similarity=0.831  Sum_probs=90.1

Q ss_pred             CCCCCCCcccccccHHHHHHHHHHcCCCCCCCcccccCCCCCCCCCeeeeCCCCCeEEeeeCCCCCCcceEEEeecCCce
Q psy2945          39 DLDELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPSINWMWLYEGKPK  118 (134)
Q Consensus        39 ~~g~vptd~eqATGlEr~ELla~~~G~~D~fd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g~~dsh~v~W~~l~~g~p~  118 (134)
                      +.|+||||+||||||||+|||++++|+ |||||+++++++||+||||||||++++|||||+|++|+|+|+||||++|+|+
T Consensus         2 ~~g~iptd~EqATGlEr~ella~~~g~-D~fd~~~~~~~~GTke~P~lVpS~~~~RiVGC~~~~D~h~v~W~~l~~g~p~   80 (98)
T d1v54f_           2 SGGGVPTDEEQATGLEREVMLAARKGQ-DPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQ   80 (98)
T ss_dssp             CCCBCCCHHHHCCHHHHHHHHHHHTTC-CTTCCSCCCCCCCCSSSCEEEECSSSEEEEEECCSTTCSCCEEEEEESSSCE
T ss_pred             CCCcCCChHHHhhhHHHHHHHHHhcCC-ChhhccCCcCCCCCCcCCcEecCCCCceEEeecCCCCCceeEEEEEeCCCCc
Confidence            578999999999999999999999998 9999999999999999999999999999999999999999999999999999


Q ss_pred             ee-eCCCEEEEEEeC
Q psy2945         119 RC-MCGHWFKLVYKA  132 (134)
Q Consensus       119 RC-eCG~~FkL~~~~  132 (134)
                      || +||+||||+++.
T Consensus        81 RC~eCG~~fkL~~~~   95 (98)
T d1v54f_          81 RCPSCGTHYKLVPHQ   95 (98)
T ss_dssp             ECTTTCCEEEEECCC
T ss_pred             ccCCCCcEEEEeecc
Confidence            99 999999999764

>d1x6ea2 g.37.1.1 (A:41-66) Zinc finger protein 24 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Zinc finger protein 24
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.26  E-value=0.04  Score=28.97  Aligned_cols=12  Identities=50%  Similarity=1.196  Sum_probs=10.6

Q ss_pred             Cceee-eCCCEEE
Q psy2945         116 KPKRC-MCGHWFK  127 (134)
Q Consensus       116 ~p~RC-eCG~~Fk  127 (134)
                      +|..| +||..|.
T Consensus         1 KPy~C~eCgK~F~   13 (26)
T d1x6ea2           1 KPYKCLECGKAFS   13 (26)
T ss_dssp             CCEECSSSCCEES
T ss_pred             CCccCCCCcCeec
Confidence            68999 9999994