Psyllid ID: psy7214

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-
Protein Sequence
DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWFKLKLICRGGVHVAIGSNWSKWILSSVGYLGQSDNLTKKDSNEQSVKPIQQMTRTKSTKFSTQLKASTLCGQLDMALESLLPTPGSLLSKLVLGRDPKVHHFNRFRIRFGSGGNRTERLQGKGNVFQATRLVVVKKEISHLH
Secondary Structure (PSIPRED)
ccccccccccccccccccEEEccccccEEEEEccccccccEEEEEEEccccEEcccccEEEEEEEccccccEEEcccccHHHHHHcccccccccccccccccccccHHHHHHccccccccccccccccccHHHHHHHHccccccHHHHHHHHccccccccccEEEEEEccccccccEEcccccEEEEEEEEEEEEcccccc
Secondary Structure Prediction (SSPRO)
ccccccccEcccccccccEEEEEcccEEEEEEcccccccccEEEEEEccccEEcccccEEEEEEEcccccEEEEcccHHHHHHHcccccccccccccccccccccccHHHcccccccccccHHHHHHHHHHHHHHHHHcccccccHHHHHHccccccEccccEEEEEEccccccccHccccccEEEEEEEEEEEHHHHccc
Coil and Loop (DISEMBL)
dpyyngpfkrtsgtrddpnlvRSAFKSrlvgcvceedQYHIVWMWVEadmprrcacghwfkLKLICRGGVHVAIGSNWSKWILSSVgylgqsdnltkkdsneqsvkpiqqmtrtkstkFSTQLKASTLCGQLDMALesllptpgsllsklvlgrdpkvhhfnrfrirfgsggnrterlqgkgnvfqATRLVVVKKEISHLH
Flexible Loop (DISEMBL)
dpyyngpfkrtsgtrddpnlvRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWFKLKLICRGGVHVAIGSNWSKWILSSVGYLGQSdnltkkdsneqsvkpiqqmtrtkstkfsTQLKASTLCGQLDMALESLLPTPGSLLSKLVLGRDPKVHHFNrfrirfgsggnrterlqgkgnvfqatrlvvvkkeishlh
Low Complexity Region (SEG)
DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWFKLKLICRGGVHVAIGSNWSKWILSSVGYLGQSDNLTKKDSNEQSVKPIQQMTRTKSTKFSTQLKASTLCGQLDMALESLLPTPGSLLSKLVLGRDPKVHHFNRFRIRFGSGGNRTERLQGKGNVFQATRLVVVKKEISHLH
Disordered region (IsUnstruct)
********************VRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWFKLKLICRGGVHVAIGSNWSKWILSSVGYLG***********************************STLCGQLDMALESLLPTPGSLLSKLVLGRDPKVHHFNRFRIRFGSGGNRTERLQGKGNVFQATRLVVVK*******
Disordered Region (DISOPRED)
DPYYNG*FK****TRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWFKLKLICRGGVHVAIGSNWSKWILSSVG***************************************TLCGQLDMALESLLPTPGSLLSKLVLGRDPKVHHFNRFRIRFGSGG******QGKGNVFQATRLVVVKKEIS***
Disordered Region (DISEMBL)
DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWFKLKLICRGGVHVAIGSNWSKWILSSVGYLGQSDNLTK*************************LKASTLCGQLDMALESLLPTPGSLLSKLVLGRDPKVHHFNRFRIRFGSGGNRTERLQGKGNVFQATRLVVVKKEISHLH
Disordered Region (DISPRO)
*PYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWFKLKLICRGGVHVAIGSNWSKWILSSVGYL*Q*D**T*******S************TKFSTQLKASTLCGQLDMALESLLPTPGSLLSKLVLGRDPKVHHFNRFRIRFGSGGNRTERLQGKGNVFQATRLVVVKKEIS***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWFKLKLICRGGVHVAIGSNWSKWILSSVGYLGQSDNLTKKDSNEQSVKPIQQMTRTKSTKFSTQLKASTLCGQLDMALESLLPTPGSLLSKLVLGRDPKVHHFNRFRIRFGSGGNRTERLQGKGNVFQATRLVVVKKEISHLH
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	201	2.2.26 [Sep-21-2011]
P19536	128	Cytochrome c oxidase subu	yes	N/A	0.308	0.484	0.476	4e-11
P12075	129	Cytochrome c oxidase subu	yes	N/A	0.308	0.480	0.476	4e-11
P00428	129	Cytochrome c oxidase subu	yes	N/A	0.308	0.480	0.476	6e-11
P10606	129	Cytochrome c oxidase subu	yes	N/A	0.308	0.480	0.492	9e-11
Q5S3G4	129	Cytochrome c oxidase subu	yes	N/A	0.308	0.480	0.476	9e-11
Q5REG2	129	Cytochrome c oxidase subu	yes	N/A	0.308	0.480	0.492	1e-10
Q710D6	128	Cytochrome c oxidase subu	N/A	N/A	0.308	0.484	0.444	5e-10
Q9SSB8	171	Cytochrome c oxidase subu	yes	N/A	0.293	0.345	0.348	8e-05
Q9LW15	176	Cytochrome c oxidase subu	no	N/A	0.293	0.335	0.333	0.0001

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

 Score = 68.2 bits (165), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 30/63 (47%), Positives = 39/63 (61%), Gaps = 1/63 (1%)

Query: 1   DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCA-CGHW 59
           DPY   P K  SGT++DPNLV S    R+VGC+CEED   ++W W+     +RC  CG  
Sbjct: 59  DPYNMLPPKAASGTKEDPNLVPSISNKRIVGCICEEDNCTVIWFWLHKGESQRCPNCGTH 118

Query: 60  FKL 62
           +KL
Sbjct: 119 YKL 121

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

 Score = 68.2 bits (165), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 30/63 (47%), Positives = 39/63 (61%), Gaps = 1/63 (1%)

Query: 1   DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCA-CGHW 59
           DPY   P K  SGT++DPNLV S    R+VGC+CEED   ++W W+     +RC  CG  
Sbjct: 60  DPYNMLPPKAASGTKEDPNLVPSVSNKRIVGCICEEDNCTVIWFWLHQGESQRCPNCGTH 119

Query: 60  FKL 62
           +KL
Sbjct: 120 YKL 122

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

 Score = 67.4 bits (163), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 30/63 (47%), Positives = 40/63 (63%), Gaps = 1/63 (1%)

Query: 1   DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRC-ACGHW 59
           DPY     K TSGT++DPNLV S    R+VGC+CEED   ++W W+     +RC +CG  
Sbjct: 60  DPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQRCPSCGTH 119

Query: 60  FKL 62
           +KL
Sbjct: 120 YKL 122

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 = 67.0 bits (162), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 31/63 (49%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 1   DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCA-CGHW 59
           DPY     K  SGTR+DPNLV S    R+VGC+CEED   +VW W+     +RC  CG  
Sbjct: 60  DPYNVLAPKGASGTREDPNLVPSISNKRIVGCICEEDNTSVVWFWLHKGEAQRCPRCGAH 119

Query: 60  FKL 62
           +KL
Sbjct: 120 YKL 122

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

 Score = 67.0 bits (162), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 30/63 (47%), Positives = 39/63 (61%), Gaps = 1/63 (1%)

Query: 1   DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRC-ACGHW 59
           DPY     K  SGT++DPNLV S    R+VGC+CEED   ++W WV     +RC +CG  
Sbjct: 60  DPYNILAPKAASGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWVHKGETQRCPSCGTH 119

Query: 60  FKL 62
           +KL
Sbjct: 120 YKL 122

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

 Score = 66.6 bits (161), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 31/63 (49%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 1   DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCA-CGHW 59
           DPY     K  SGTR+DPNLV S    R+VGC+CEED   +VW W+     +RC  CG  
Sbjct: 60  DPYNVLAPKGASGTREDPNLVPSISNKRIVGCICEEDNTSVVWFWLHKGEAQRCPRCGAH 119

Query: 60  FKL 62
           +KL
Sbjct: 120 YKL 122

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

 Score = 64.3 bits (155), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 28/63 (44%), Positives = 39/63 (61%), Gaps = 1/63 (1%)

Query: 1   DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRC-ACGHW 59
           DPY     K  +GT++DPNLV S    R+VGC+CEED   ++W W+     +RC +CG  
Sbjct: 59  DPYNILAPKAAAGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQRCPSCGTH 118

Query: 60  FKL 62
           +KL
Sbjct: 119 YKL 121

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

 Score = 47.0 bits (110), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 38/66 (57%), Gaps = 7/66 (10%)

Query: 3   YYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVC--EEDQYHIVWMWVEADMPRRC-ACGHW 59
           +  GPF    GT++ P +V+S +  R+VGC     ED++ +VW W+E      C  C  +
Sbjct: 96  FPEGPF----GTKEAPAVVKSYYDMRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQY 151

Query: 60  FKLKLI 65
           FKL+++
Sbjct: 152 FKLEVV 157

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 = 46.2 bits (108), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 38/66 (57%), Gaps = 7/66 (10%)

Query: 3   YYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVC--EEDQYHIVWMWVEADMPRRC-ACGHW 59
           +  GPF    GT++ P +V+S +  R+VGC     ED++ +VW W+E      C  C  +
Sbjct: 97  FPEGPF----GTKEAPAIVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQY 152

Query: 60  FKLKLI 65
           F+L+++
Sbjct: 153 FELEVV 158

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)

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	201
289740249	120	cytochrome c oxidase subunit Vb COX4 [Gl	0.308	0.516	0.564	5e-17
58386537	119	AGAP008724-PA [Anopheles gambiae str. PE	0.308	0.521	0.612	8e-17
170037183	119	cytochrome c oxidase, subunit VB [Culex	0.308	0.521	0.612	9e-17
288856322	122	cytochrome c oxidase subunit 5B, mitocho	0.308	0.508	0.629	1e-16
157119566	119	cytochrome c oxidase, subunit VB, putati	0.308	0.521	0.612	2e-16
193620134	128	PREDICTED: cytochrome c oxidase subunit	0.318	0.5	0.562	5e-16
307168272	470	Cytochrome c oxidase subunit 5B, mitocho	0.308	0.131	0.532	9e-16
269146716	119	cytochrome c oxidase subunit Vb/COX4 [Si	0.308	0.521	0.564	2e-15
240848562	128	cytochrome c oxidase subunit 5B, mitocho	0.308	0.484	0.564	2e-15
195118826	120	GI20346 [Drosophila mojavensis] gi|19391	0.308	0.516	0.532	2e-15

>gi|289740249|gb|ADD18872.1| cytochrome c oxidase subunit Vb COX4 [Glossina morsitans morsitans]

 Score = 93.6 bits (231), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 35/62 (56%), Positives = 51/62 (82%)

Query: 1   DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWF 60
           +P+    FKR +GT+++PNL+ SAF++R+VGC+CEEDQ ++ WMW++ D P+RC CGHWF
Sbjct: 53  NPFDMKVFKRGAGTKENPNLIPSAFEARIVGCICEEDQTYVQWMWLQKDSPKRCECGHWF 112

Query: 61  KL 62
           KL
Sbjct: 113 KL 114

Source: Glossina morsitans morsitans

Species: Glossina morsitans

Genus: Glossina

Family: Glossinidae

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 = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 38/62 (61%), Positives = 46/62 (74%)

Query: 1   DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWF 60
           DP+    FKR  GT+D PNL+ SAF +RLVGCVCEEDQ ++ WMW+    P+RC CGHWF
Sbjct: 52  DPFDMRVFKRGPGTKDSPNLIPSAFDARLVGCVCEEDQTYVQWMWLHQGQPKRCECGHWF 111

Query: 61  KL 62
           KL
Sbjct: 112 KL 113

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

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 = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 38/62 (61%), Positives = 48/62 (77%)

Query: 1   DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWF 60
           DP+    FKR  GT+++PN++ SAF+SRLVGCVCEEDQ +I WMW+    P+RC CGHWF
Sbjct: 52  DPFDMRVFKRGPGTKENPNMIPSAFESRLVGCVCEEDQTYIQWMWLHQGHPKRCECGHWF 111

Query: 61  KL 62
           KL
Sbjct: 112 KL 113

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|288856322|ref|NP_001165813.1| cytochrome c oxidase subunit 5B, mitochondrial [Nasonia vitripennis]

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 39/62 (62%), Positives = 45/62 (72%)

Query: 1   DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWF 60
           DP+     KR  GT++ PNLV S FKSRLVGC+CEEDQ H+ WMW+    PRRC CGHWF
Sbjct: 53  DPFDTKVMKRGPGTKECPNLVGSFFKSRLVGCICEEDQLHVNWMWLHKGKPRRCECGHWF 112

Query: 61  KL 62
           KL
Sbjct: 113 KL 114

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 38/62 (61%), Positives = 47/62 (75%)

Query: 1   DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWF 60
           DP+    FKR  GT++ PN++ SAF+SRLVGCVCEEDQ +I WMW+    P+RC CGHWF
Sbjct: 52  DPFDMRVFKRGPGTKESPNMIPSAFESRLVGCVCEEDQTYIQWMWLHQGHPKRCECGHWF 111

Query: 61  KL 62
           KL
Sbjct: 112 KL 113

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

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 = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 36/64 (56%), Positives = 45/64 (70%)

Query: 1   DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWF 60
           DPY     KR  GT D P LV SAF++R++GCVCEED  H+ WMW+ +  P+RC CGHWF
Sbjct: 60  DPYNLKAIKRGVGTSDKPTLVPSAFEARIIGCVCEEDASHVKWMWLHSGEPKRCYCGHWF 119

Query: 61  KLKL 64
           KL+ 
Sbjct: 120 KLEF 123

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 33/62 (53%), Positives = 45/62 (72%)

Query: 1   DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWF 60
           DPY     +R   T+++PN+V SAF+SR++GC+C+ED  H+ WMW+    PRRC CGHWF
Sbjct: 403 DPYNLTIKRRPDSTKENPNIVYSAFESRIMGCICDEDALHVNWMWLHQGPPRRCECGHWF 462

Query: 61  KL 62
           KL
Sbjct: 463 KL 464

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|269146716|gb|ACZ28304.1| cytochrome c oxidase subunit Vb/COX4 [Simulium nigrimanum]

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 35/62 (56%), Positives = 46/62 (74%)

Query: 1   DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWF 60
           +P+    FKR +GT++ PNL+ SAF +RLVGC+CEEDQ  + WMW+    P+RC CGHWF
Sbjct: 52  NPFDMKVFKRGAGTKESPNLIPSAFDARLVGCICEEDQTFVQWMWLYQGTPKRCECGHWF 111

Query: 61  KL 62
           KL
Sbjct: 112 KL 113

Source: Simulium nigrimanum

Species: Simulium nigrimanum

Genus: Simulium

Family: Simuliidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 35/62 (56%), Positives = 45/62 (72%)

Query: 1   DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWF 60
           DPY     KR  GT++ PN + SAF++R+VGCVCEED  H+ WMW+ +  P+RC CGHWF
Sbjct: 60  DPYNLKSIKRGVGTKETPNEIPSAFEARIVGCVCEEDSSHVKWMWLHSGEPKRCFCGHWF 119

Query: 61  KL 62
           KL
Sbjct: 120 KL 121

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195118826|ref|XP_002003937.1| GI20346 [Drosophila mojavensis] gi|193914512|gb|EDW13379.1| GI20346 [Drosophila mojavensis]

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 33/62 (53%), Positives = 48/62 (77%)

Query: 1   DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWF 60
           +P+    FKR +GT+++PNL+ SAF +R+VGC+CEEDQ ++ WMW++    +RC CGHWF
Sbjct: 53  NPFDMKVFKRGAGTKENPNLIPSAFDARIVGCICEEDQTYVQWMWLQKGNQKRCECGHWF 112

Query: 61  KL 62
           KL
Sbjct: 113 KL 114

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

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	201
FB|FBgn0031830	154	CoVb "Cytochrome c oxidase sub	0.308	0.402	0.532	1.6e-17
FB|FBgn0031831	154	CG11043 [Drosophila melanogast	0.308	0.402	0.492	9.1e-13
RGD|620608	129	Cox5b "cytochrome c oxidase su	0.308	0.480	0.476	1.5e-12
UNIPROTKB|P00428	129	COX5B "Cytochrome c oxidase su	0.308	0.480	0.476	3.1e-12
UNIPROTKB|Q5S3G4	129	COX5B "Cytochrome c oxidase su	0.308	0.480	0.476	5e-12
UNIPROTKB|P10606	129	COX5B "Cytochrome c oxidase su	0.308	0.480	0.492	6.4e-12
UNIPROTKB|B7ZDP5	128	cox5b "Cytochrome c oxidase po	0.308	0.484	0.444	2.2e-11
UNIPROTKB|E2RHV9	129	COX5B "Uncharacterized protein	0.308	0.480	0.444	2.2e-11
WB|WBGene00000371	132	cco-1 [Caenorhabditis elegans	0.268	0.409	0.425	4.5e-11
UNIPROTKB|P90849	132	cco-1 "Protein CCO-1" [Caenorh	0.268	0.409	0.425	4.5e-11

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

 Score = 214 (80.4 bits), Expect = 1.6e-17, P = 1.6e-17
 Identities = 33/62 (53%), Positives = 48/62 (77%)

Query:     1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWF 60
             +P+    FKR +GT+++PNL+ SAF +R+VGC+CEEDQ ++ WMW++    +RC CGHWF
Sbjct:    87 NPFDMKVFKRGAGTKENPNLIPSAFDARIVGCICEEDQTYVQWMWLQKGNQKRCECGHWF 146

Query:    61 KL 62
             KL
Sbjct:   147 KL 148

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

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

 Score = 169 (64.5 bits), Expect = 9.1e-13, P = 9.1e-13
 Identities = 32/65 (49%), Positives = 45/65 (69%)

Query:     1 DPY-YNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADM-PRRCACGH 58
             DP+ ++   +R SG  +DP +V SAF +RLVGC+C +D+    WMW+E D  P+RC CGH
Sbjct:    86 DPWGFSKVIRRGSGRENDPTVVPSAFDARLVGCLCLDDRLP-KWMWIEKDEGPKRCECGH 144

Query:    59 WFKLK 63
             +F LK
Sbjct:   145 YFILK 149

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

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

 Score = 167 (63.8 bits), Expect = 1.5e-12, P = 1.5e-12
 Identities = 30/63 (47%), Positives = 39/63 (61%)

Query:     1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCA-CGHW 59
             DPY   P K  SGT++DPNLV S    R+VGC+CEED   ++W W+     +RC  CG  
Sbjct:    60 DPYNMLPPKAASGTKEDPNLVPSVSNKRIVGCICEEDNCTVIWFWLHQGESQRCPNCGTH 119

Query:    60 FKL 62
             +KL
Sbjct:   120 YKL 122

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

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

 Score = 164 (62.8 bits), Expect = 3.1e-12, P = 3.1e-12
 Identities = 30/63 (47%), Positives = 40/63 (63%)

Query:     1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRC-ACGHW 59
             DPY     K TSGT++DPNLV S    R+VGC+CEED   ++W W+     +RC +CG  
Sbjct:    60 DPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQRCPSCGTH 119

Query:    60 FKL 62
             +KL
Sbjct:   120 YKL 122

GO:0005743 "mitochondrial inner membrane" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

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

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

 Score = 162 (62.1 bits), Expect = 5.0e-12, P = 5.0e-12
 Identities = 30/63 (47%), Positives = 39/63 (61%)

Query:     1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRC-ACGHW 59
             DPY     K  SGT++DPNLV S    R+VGC+CEED   ++W WV     +RC +CG  
Sbjct:    60 DPYNILAPKAASGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWVHKGETQRCPSCGTH 119

Query:    60 FKL 62
             +KL
Sbjct:   120 YKL 122

GO:0005743 "mitochondrial inner membrane" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

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

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

 Score = 161 (61.7 bits), Expect = 6.4e-12, P = 6.4e-12
 Identities = 31/63 (49%), Positives = 38/63 (60%)

Query:     1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCA-CGHW 59
             DPY     K  SGTR+DPNLV S    R+VGC+CEED   +VW W+     +RC  CG  
Sbjct:    60 DPYNVLAPKGASGTREDPNLVPSISNKRIVGCICEEDNTSVVWFWLHKGEAQRCPRCGAH 119

Query:    60 FKL 62
             +KL
Sbjct:   120 YKL 122

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

 Score = 156 (60.0 bits), Expect = 2.2e-11, P = 2.2e-11
 Identities = 28/63 (44%), Positives = 39/63 (61%)

Query:     1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRC-ACGHW 59
             DPY     K  +GT++DPNLV S    R+VGC+CEED   ++W W+     +RC +CG  
Sbjct:    59 DPYNILAPKAAAGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQRCPSCGTH 118

Query:    60 FKL 62
             +KL
Sbjct:   119 YKL 121

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 = 156 (60.0 bits), Expect = 2.2e-11, P = 2.2e-11
 Identities = 28/63 (44%), Positives = 39/63 (61%)

Query:     1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRC-ACGHW 59
             DPY     K  +GT++DPNLV S    R+VGC+CEED   ++W W+     +RC +CG  
Sbjct:    60 DPYNILAPKAAAGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQRCPSCGTH 119

Query:    60 FKL 62
             +KL
Sbjct:   120 YKL 122

GO:0005740 "mitochondrial envelope" evidence=IEA

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

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

 Score = 153 (58.9 bits), Expect = 4.5e-11, P = 4.5e-11
 Identities = 23/54 (42%), Positives = 36/54 (66%)

Query:     8 FKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWFK 61
             ++  + T+  PNLV S +  R++GC+CE+D  H+ +M +    P+RC CGHWFK
Sbjct:    70 YRAEASTKQKPNLVPSHYDFRIIGCMCEQDSGHVNFMTIRKGDPKRCECGHWFK 123

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 = 153 (58.9 bits), Expect = 4.5e-11, P = 4.5e-11
 Identities = 23/54 (42%), Positives = 36/54 (66%)

Query:     8 FKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWFK 61
             ++  + T+  PNLV S +  R++GC+CE+D  H+ +M +    P+RC CGHWFK
Sbjct:    70 YRAEASTKQKPNLVPSHYDFRIIGCMCEQDSGHVNFMTIRKGDPKRCECGHWFK 123

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by 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	201
cd00924	97	cd00924, Cyt_c_Oxidase_Vb, Cytochrome c oxidase su	5e-28
pfam01215	136	pfam01215, COX5B, Cytochrome c oxidase subunit Vb	2e-15
PLN02294	174	PLN02294, PLN02294, cytochrome c oxidase subunit V	2e-08

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

 Score =  100 bits (252), Expect = 5e-28
 Identities = 33/64 (51%), Positives = 43/64 (67%), Gaps = 1/64 (1%)

Query: 1  DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRC-ACGHW 59
          D +   P K   GT++DPNLV SAF  R+VGC+CE D + ++WMW+E   P+RC  CGH 
Sbjct: 29 DDFDMKPLKGPFGTKEDPNLVPSAFDKRIVGCICEPDSHDVIWMWLEKGKPKRCPECGHV 88

Query: 60 FKLK 63
          FKL 
Sbjct: 89 FKLV 92

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 = 69.6 bits (170), Expect = 2e-15
 Identities = 26/67 (38%), Positives = 33/67 (49%), Gaps = 2/67 (2%)

Query: 1   DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYH-IVWMWVEADMPRRC-ACGH 58
           DP+   P   + GT  DP +V S    R+VGC    D  H I+W  V     +RC  CG 
Sbjct: 61  DPFDIKPLDASKGTLKDPIIVESIDNYRIVGCTGSPDGSHTIIWFTVHKGEAQRCPECGS 120

Query: 59  WFKLKLI 65
            +KLK I
Sbjct: 121 VYKLKPI 127

Length = 136

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

 Score = 51.4 bits (123), Expect = 2e-08
 Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 7/67 (10%)

Query: 6   GPFKRTSGTRDDPNLVRSAFKSRLVGCVC--EEDQYHIVWMWVEADMPRRC-ACGHWFKL 62
           GPF    GT++ P +V+S +  R+VGC     ED++ +VW W+E      C  C  +F+L
Sbjct: 98  GPF----GTKEAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYFEL 153

Query: 63  KLICRGG 69
           +++  GG
Sbjct: 154 EVVGPGG 160

Length = 174

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	201
PF01215	136	COX5B: Cytochrome c oxidase subunit Vb This family	100.0
PLN02294	174	cytochrome c oxidase subunit Vb	99.98
cd00924	97	Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb.	99.97
KOG3352|consensus	153		99.97
PTZ00043	268	cytochrome c oxidase subunit; Provisional	99.93
PF10276	40	zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Z	95.96
KOG3456|consensus	120		94.45
COG4391	62	Uncharacterized protein conserved in bacteria [Fun	80.89

>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=1.2e-33  Score=227.05  Aligned_cols=74  Identities=41%  Similarity=0.862  Sum_probs=50.6

Q ss_pred             CCCCCCCCCCCCCCCCCCeeeecCCCceeEeeeC-CCCCcceEEEEEecCCceee-cCCcEEEEEEecCCCCcccc
Q psy7214           1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVC-EEDQYHIVWMWVEADMPRRC-ACGHWFKLKLICRGGVHVAI   74 (201)
Q Consensus         1 DPFDMkPLks~~GTKEDPiLVPS~~deRIVGCtG-peDSH~VvWf~L~KGkP~RC-ECGqwFKLv~vG~~g~~~~~   74 (201)
                      |||||+|+++++||+||||||||++++|||||+| ++|+|+|+||||++|+|+|| +||+||||+++|+++++|.|
T Consensus        61 D~Fd~~~~~~~~GT~e~P~lVpS~~~~RiVGC~g~~~~sH~v~W~~l~~g~~~RCpeCG~~fkL~~vg~~~~~h~h  136 (136)
T PF01215_consen   61 DPFDMKPLKAPFGTKEDPILVPSYFDERIVGCTGEPDDSHDVIWFWLHKGKPQRCPECGQVFKLKYVGPEGDHHHH  136 (136)
T ss_dssp             -TT--S--B----SSSS-CEEEESSSCEEEEESSSTT-SSS-EEEEEETTSEEEETTTEEEEEEEE----------
T ss_pred             CcccccCccCCCCCccCCeEccCCCCceEEeeccCCCCcceeEEEEEeCCCccCCCCCCeEEEEEEcCCCCCCCCC
Confidence            8999999988899999999999999999999999 66888999999999999999 89999999999999988864

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 ....

>PLN02294 cytochrome c oxidase subunit Vb

Probab=99.98  E-value=6.1e-33  Score=231.35  Aligned_cols=76  Identities=29%  Similarity=0.630  Sum_probs=74.0

Q ss_pred             CCCCCCCCCCCCCCCCCCeeeecCCCceeEeeeC--CCCCcceEEEEEecCCceee-cCCcEEEEEEecCCCCccccCC
Q psy7214           1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVC--EEDQYHIVWMWVEADMPRRC-ACGHWFKLKLICRGGVHVAIGS   76 (201)
Q Consensus         1 DPFDMkPLks~~GTKEDPiLVPS~~deRIVGCtG--peDSH~VvWf~L~KGkP~RC-ECGqwFKLv~vG~~g~~~~~gs   76 (201)
                      |||||+++++++||+||||||||++++|||||+|  ++|+|+|+||||++|+|+|| |||+||||+++|++++|+.||-
T Consensus        89 D~Fd~~~~~gp~GTke~P~lVpS~~d~RiVGCtg~~~eDsh~v~Wf~L~kGkp~RCpeCG~~fkL~~vG~~~~~~~h~d  167 (174)
T PLN02294         89 KLLDIDFPEGPFGTKEAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYFELEVVGPGGPPDGHGD  167 (174)
T ss_pred             CccccccccCCCCCccCCcEeccCCCceEEeeCCCCCCCCceeEEEEecCCCceeCCCCCCEEEEEEeCCCCCCCCCCC
Confidence            8999999999999999999999999999999999  89999999999999999999 8999999999999999999875

>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb

Probab=99.97  E-value=3.8e-32  Score=207.46  Aligned_cols=68  Identities=49%  Similarity=1.023  Sum_probs=65.0

Q ss_pred             CCCCCCCCCCCCCCCCCCeeeecCCCceeEeeeCCCCCcceEEEEEecCCceee-cCCcEEEEEEecCC
Q psy7214           1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRC-ACGHWFKLKLICRG   68 (201)
Q Consensus         1 DPFDMkPLks~~GTKEDPiLVPS~~deRIVGCtGpeDSH~VvWf~L~KGkP~RC-ECGqwFKLv~vG~~   68 (201)
                      |+|||+|+.+++||++|||||||++++|||||+|++|+|+|+||||++|+|+|| +||+||||++++++
T Consensus        29 d~f~~~~~~~~~GT~e~P~lVpS~~~~RiVGC~g~~~~h~v~W~~l~~g~~~rC~eCG~~fkL~~v~~~   97 (97)
T cd00924          29 DDFDMKPLKGPFGTKEDPNLVPSAFDKRIVGCICEPDSHDVIWMWLEKGKPKRCPECGHVFKLVDVGPP   97 (97)
T ss_pred             ccccccccccCCCCccCCeEecCCCCCeEEeeeCCCCCceEEEEEEeCCCceeCCCCCcEEEEEECCCC
Confidence            789999999888999999999999999999999988899999999999999999 69999999999864

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.

>KOG3352|consensus

Probab=99.97  E-value=5.3e-31  Score=216.25  Aligned_cols=69  Identities=46%  Similarity=0.939  Sum_probs=66.7

Q ss_pred             CCCCCCCCCCCCCCCCCCeeeecCCCceeEeeeCCCCCcceEEEEEecCCceee-cCCcEEEEEEecCCC
Q psy7214           1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRC-ACGHWFKLKLICRGG   69 (201)
Q Consensus         1 DPFDMkPLks~~GTKEDPiLVPS~~deRIVGCtGpeDSH~VvWf~L~KGkP~RC-ECGqwFKLv~vG~~g   69 (201)
                      |||||+.+++++||++|||||||++|+|||||.|++|+|+|+||||+||+++|| ||||||||+.+|+++
T Consensus        83 d~~d~k~~~~~~GTkedP~lV~S~~d~RiVGC~c~eD~~~V~Wmwl~Kge~~rc~eCG~~fkL~~v~~~~  152 (153)
T KOG3352|consen   83 DPFDMKVPRGPSGTKEDPNLVPSYYDKRIVGCGCEEDSHAVVWMWLEKGETQRCPECGHYFKLVPVGPVN  152 (153)
T ss_pred             CccccccccCCCCcccCCccccccCCceEEeecccCCCcceEEEEEEcCCcccCCcccceEEeeecCCCC
Confidence            799999669999999999999999999999999999999999999999999998 999999999999876

>PTZ00043 cytochrome c oxidase subunit; Provisional

Probab=99.93  E-value=3.4e-26  Score=199.91  Aligned_cols=75  Identities=25%  Similarity=0.422  Sum_probs=69.8

Q ss_pred             CCCCCCCCCCCCCCCCeeeecCCCceeEeeeC--CCCCcceEEEEEecCCceee-cCCcEEEEEE----ecCCCCccccC
Q psy7214           3 YYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVC--EEDQYHIVWMWVEADMPRRC-ACGHWFKLKL----ICRGGVHVAIG   75 (201)
Q Consensus         3 FDMkPLks~~GTKEDPiLVPS~~deRIVGCtG--peDSH~VvWf~L~KGkP~RC-ECGqwFKLv~----vG~~g~~~~~g   75 (201)
                      +.++++.+++||+|||+||||++++|||||+|  ++|+|+|+|||+++|+++|| +||+||||++    ++++++|++.-
T Consensus       131 Lk~~~~~GPfGTkEdPiLVpSy~deRyVGCTGg~~EDeH~VvWFwLrEGkpqRCpECGqVFKLVr~~~s~~dg~dp~~~d  210 (268)
T PTZ00043        131 LKSSSFVGPFGTIENPVLVPSVGTERVVGCTGGTGEHEHVPLWFRCREGFLYRCGECDQIFMLVRVLYSLPDGEDPFPND  210 (268)
T ss_pred             cCcCCCCCCCCCccCCeEeccCCCceEEeccCCCccCCceeEEEEecCCCCccCCCCCcEEEEEEEEeecCCCCCCCCCC
Confidence            45678899999999999999999999999999  78899999999999999999 9999999999    99999999876


Q ss_pred             Cc
Q psy7214          76 SN   77 (201)
Q Consensus        76 s~   77 (201)
                      -.
T Consensus       211 pd  212 (268)
T PTZ00043        211 PD  212 (268)
T ss_pred             Cc
Confidence            43

>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=95.96  E-value=0.011  Score=39.63  Aligned_cols=36  Identities=22%  Similarity=0.386  Sum_probs=29.7

Q ss_pred             CceeEeeeC--CCCCcceEEEEEec-CCceee-cCCcEEE
Q psy7214          26 KSRLVGCVC--EEDQYHIVWMWVEA-DMPRRC-ACGHWFK   61 (201)
Q Consensus        26 deRIVGCtG--peDSH~VvWf~L~K-GkP~RC-ECGqwFK   61 (201)
                      +.|+|-|.|  .+-.|-.+|+.|.+ +++..| .||.-|+
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            468999999  46889999999999 478999 7999885

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.

>KOG3456|consensus

Probab=94.45  E-value=0.031  Score=45.48  Aligned_cols=40  Identities=23%  Similarity=0.382  Sum_probs=35.8

Q ss_pred             ecCCCceeEeeeC--CCCCcceEEEEEecCCceee-cCCcEEE
Q psy7214          22 RSAFKSRLVGCVC--EEDQYHIVWMWVEADMPRRC-ACGHWFK   61 (201)
Q Consensus        22 PS~~deRIVGCtG--peDSH~VvWf~L~KGkP~RC-ECGqwFK   61 (201)
                      |+--+.|+|.|-|  ++=-|-.+|+.|.+..++-| .||--|.
T Consensus        73 p~e~d~RVV~CdGg~~aLGHPkvyInLDk~~~~~CgYCGlrf~  115 (120)
T KOG3456|consen   73 PIEVDGRVVACDGGTPALGHPKVYINLDKPGPHICGYCGLRFV  115 (120)
T ss_pred             hhhccceEEEecCCCCCCCCCeEEEEcCCCCCcccccchhhhh
Confidence            4556999999999  78899999999999999999 8998775

>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=80.89  E-value=2.6  Score=31.18  Aligned_cols=44  Identities=11%  Similarity=0.197  Sum_probs=32.9

Q ss_pred             CeeeecCCCceeEeeeC--CCCCcceEEEEEecCCceee-cCCcEEEEE
Q psy7214          18 PNLVRSAFKSRLVGCVC--EEDQYHIVWMWVEADMPRRC-ACGHWFKLK   63 (201)
Q Consensus        18 PiLVPS~~deRIVGCtG--peDSH~VvWf~L~KGkP~RC-ECGqwFKLv   63 (201)
                      ++.|.+..  --+-|.|  ++-+|-=+|+-+.+..-.-| .||..|+|.
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  2367999  57899999999966567899 699999985

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	201
2y69_F	129	Bovine Heart Cytochrome C Oxidase Re-Refined With M		5e-12
1occ_F	98	Structure Of Bovine Heart Cytochrome C Oxidase At T		1e-11

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

Iteration: 1
 Score = 67.4 bits (163), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 30/63 (47%), Positives = 40/63 (63%), Gaps = 1/63 (1%)
Query: 1   DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRC-ACGHW 59
           DPY     K TSGT++DPNLV S    R+VGC+CEED   ++W W+     +RC +CG  
Sbjct: 60  DPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQRCPSCGTH 119
Query: 60  FKL 62
           +KL
Sbjct: 120 YKL 122

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

Iteration: 1
 Score = 66.2 bits (160), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 30/63 (47%), Positives = 40/63 (63%), Gaps = 1/63 (1%)
Query: 1  DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRC-ACGHW 59
          DPY     K TSGT++DPNLV S    R+VGC+CEED   ++W W+     +RC +CG  
Sbjct: 29 DPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQRCPSCGTH 88
Query: 60 FKL 62
          +KL
Sbjct: 89 YKL 91

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	201
2y69_F	129	Cytochrome C oxidase subunit 5B; electron transpor	1e-24
1v54_F	98	VI, cytochrome C oxidase polypeptide VB; oxidoredu	1e-24
2odx_A	80	Cytochrome C oxidase polypeptide IV; all beta-prot	1e-20
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-04

>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 = 92.8 bits (230), Expect = 1e-24
 Identities = 30/64 (46%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 1   DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCA-CGHW 59
           DPY     K TSGT++DPNLV S    R+VGC+CEED   ++W W+     +RC  CG  
Sbjct: 60  DPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQRCPSCGTH 119

Query: 60  FKLK 63
           +KL 
Sbjct: 120 YKLV 123

>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 = 91.5 bits (227), Expect = 1e-24
 Identities = 30/64 (46%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 1  DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCA-CGHW 59
          DPY     K TSGT++DPNLV S    R+VGC+CEED   ++W W+     +RC  CG  
Sbjct: 29 DPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQRCPSCGTH 88

Query: 60 FKLK 63
          +KL 
Sbjct: 89 YKLV 92

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

 Score = 81.0 bits (200), Expect = 1e-20
 Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 2/61 (3%)

Query: 7  PFKRTSGTRDDPNLVRSAFKSRLVGCV-CEEDQYHIVWMWVEADMPRRCA-CGHWFKLKL 64
                GT  DP ++ S    R VGC       + I+W+    +   RC  CG  +KL  
Sbjct: 11 LDSSRKGTMKDPIIIESYDDYRYVGCTGSPAGSHTIMWLKPTVNEVARCWECGSVYKLNP 70

Query: 65 I 65
          +
Sbjct: 71 V 71

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 39.1 bits (90), Expect = 7e-04
 Identities = 21/187 (11%), Positives = 54/187 (28%), Gaps = 47/187 (25%)

Query: 2   PYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQ-----YHIVWMWVEADMPRRCAC 56
             +   F      +D  ++ +S      +  +            + W  +          
Sbjct: 23  SVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLS--------- 73

Query: 57  GHWFKLKLICRGGVHVAIGSNWSKWILSSVGYLGQSDNLTKKDSNEQ------SVKPIQQ 110
               K + + +  V   +  N+ K+++S +    +  ++  +   EQ        +   +
Sbjct: 74  ----KQEEMVQKFVEEVLRINY-KFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAK 128

Query: 111 MTRTKSTKFSTQLKASTLCGQLDMALESLLPTPG-----------SLLSKLVLGRDPKVH 159
              ++   +  +L+          AL  L P              + ++  V     KV 
Sbjct: 129 YNVSRLQPY-LKLRQ---------ALLELRPAKNVLIDGVLGSGKTWVALDVC-LSYKVQ 177

Query: 160 HFNRFRI 166
               F+I
Sbjct: 178 CKMDFKI 184

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	201
2odx_A	80	Cytochrome C oxidase polypeptide IV; all beta-prot	100.0
1v54_F	98	VI, cytochrome C oxidase polypeptide VB; oxidoredu	99.98
2y69_F	129	Cytochrome C oxidase subunit 5B; electron transpor	99.97
2jrr_A	67	Uncharacterized protein; solution structure, SIR90	98.0
2jvm_A	80	Uncharacterized protein; alpha+beta, structural ge	97.56
2jz8_A	87	Uncharacterized protein BH09830; zinc binding, str	93.06
1gh9_A	71	8.3 kDa protein (gene MTH1184); beta+alpha complex	80.72

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

Probab=100.00  E-value=1.7e-36  Score=223.65  Aligned_cols=74  Identities=26%  Similarity=0.458  Sum_probs=51.2

Q ss_pred             CCCCCCCCC-CCCCCCCCCeeeecCCCceeEeeeC-CCCCcceEEEEEecCCceee-cCCcEEEEEEecCCCCcccc
Q psy7214           1 DPYYNGPFK-RTSGTRDDPNLVRSAFKSRLVGCVC-EEDQYHIVWMWVEADMPRRC-ACGHWFKLKLICRGGVHVAI   74 (201)
Q Consensus         1 DPFDMkPLk-s~~GTKEDPiLVPS~~deRIVGCtG-peDSH~VvWf~L~KGkP~RC-ECGqwFKLv~vG~~g~~~~~   74 (201)
                      |||||+|++ +++||+||||||||++++|||||+| |+|+|+|+||||++|+|+|| +||+||||+++|+++++|.|
T Consensus         4 D~fd~~p~~~~~~GT~e~P~lVpS~~~~RiVGC~g~p~d~h~v~W~~l~~g~~~RC~eCG~~fkL~~vg~~~~~hhh   80 (80)
T 2odx_A            4 DVFDTKPLDSSRKGTMKDPIIIESYDDYRYVGCTGSPAGSHTIMWLKPTVNEVARCWECGSVYKLNPVGVPNDDHHH   80 (80)
T ss_dssp             ---------------CCSCSEECCSSSSCCEEESSSTTCCSCCEEECCCTTCEEECSSSCCEEEECCCC--------
T ss_pred             CcccccccccCCCCCccCCeEecCCCCCeEEeeeCCCCCcceEEEEEecCCCCeECCCCCeEEEEEEcCCCCCCCCC
Confidence            899999995 6899999999999999999999999 59999999999999999999 99999999999999998764

>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=99.98  E-value=1.1e-32  Score=209.53  Aligned_cols=67  Identities=45%  Similarity=0.896  Sum_probs=64.5

Q ss_pred             CCCCCCCCCCCCCCCCCCeeeecCCCceeEeeeCCCCCcceEEEEEecCCceee-cCCcEEEEEEecC
Q psy7214           1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRC-ACGHWFKLKLICR   67 (201)
Q Consensus         1 DPFDMkPLks~~GTKEDPiLVPS~~deRIVGCtGpeDSH~VvWf~L~KGkP~RC-ECGqwFKLv~vG~   67 (201)
                      |||||+++++++||+||||||||++++|||||+|++|+|+|+||||++|+|+|| +||+||||++..-
T Consensus        29 Dpfd~~~~~~~~GTke~P~lVpS~~~~RiVGC~~~~D~h~v~W~~l~~g~~~RC~eCG~~fkL~~~~~   96 (98)
T 1v54_F           29 DPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQRCPSCGTHYKLVPHQL   96 (98)
T ss_dssp             CTTCCSCCCCCCCCSSSCEEEECSSSEEEEEECCSTTCSCCEEEEEESSSCEECTTTCCEEEEECCCS
T ss_pred             CcccccCCCCCCCcccCCeEeecCCCCeEEeecCCCCCceeEEEEEeCCCceECCCCCeEEEEeeecC
Confidence            899999999999999999999999999999999999999999999999999999 9999999997543

>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=8.5e-32  Score=214.01  Aligned_cols=67  Identities=45%  Similarity=0.896  Sum_probs=64.9

Q ss_pred             CCCCCCCCCCCCCCCCCCeeeecCCCceeEeeeCCCCCcceEEEEEecCCceee-cCCcEEEEEEecC
Q psy7214           1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRC-ACGHWFKLKLICR   67 (201)
Q Consensus         1 DPFDMkPLks~~GTKEDPiLVPS~~deRIVGCtGpeDSH~VvWf~L~KGkP~RC-ECGqwFKLv~vG~   67 (201)
                      |||||+|+++++||+||||||||++++|||||+|++|+|+|+||||++|+|+|| +||+||||++..-
T Consensus        60 DpFd~~~~~~~~GTkedP~lVpS~~d~RiVGC~~~~Dsh~v~Wf~L~kg~p~RCpeCG~~fkL~~~e~  127 (129)
T 2y69_F           60 DPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQRCPSCGTHYKLVPHQL  127 (129)
T ss_dssp             CTTCCSCCCCCCCCSSSCEEEEESSSEEEEEECCSTTCSCCEEEEEESSSCEECTTTCCEEEEEECCC
T ss_pred             CccccCCCCCCCCcccCCeEeecCCCCeEEeecCCCCCceeEEEEEeCCCceeCCCCCeEEEEeeecc
Confidence            899999999999999999999999999999999999999999999999999999 9999999998654

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

Probab=98.00  E-value=2.4e-06  Score=61.60  Aligned_cols=51  Identities=22%  Similarity=0.227  Sum_probs=41.8

Q ss_pred             CCCCCeeeecCCCceeEeeeC--CCCCcceEEEEE-ecCCceee-cCCcEEEEEEec
Q psy7214          14 TRDDPNLVRSAFKSRLVGCVC--EEDQYHIVWMWV-EADMPRRC-ACGHWFKLKLIC   66 (201)
Q Consensus        14 TKEDPiLVPS~~deRIVGCtG--peDSH~VvWf~L-~KGkP~RC-ECGqwFKLv~vG   66 (201)
                      |++.|-+|  ..+.|+|.|.|  .+..|-.+|++| .++.+..| .||..|+++...
T Consensus         2 ~~~ape~i--~v~~r~v~CdGg~g~lgHPrVyl~ld~~~g~~~CpYCg~~f~l~~~~   56 (67)
T 2jrr_A            2 TIQAPETK--IVDKSRVACDGGEGALGHPRVWLQIPEDTGWVECPYCDCKYVLKGSK   56 (67)
T ss_dssp             CCCCCEEE--EESSSEEEEEESSTTSEEEEEEEECCTTTSEEEETTTTEEEEETTSG
T ss_pred             CCCCCceE--EECCCEEEeCCCCCCCCCCEEEEEccCCCCeEECCCCCCEEEECCCc
Confidence            56677766  44789999988  456899999999 56789999 799999998643

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

Probab=97.56  E-value=5.5e-05  Score=56.32  Aligned_cols=51  Identities=16%  Similarity=0.240  Sum_probs=40.5

Q ss_pred             CCCCCCeeeecCCCceeEeeeC--CCCCcceEEEEE-ecCCceee-cCCcEEEEEEe
Q psy7214          13 GTRDDPNLVRSAFKSRLVGCVC--EEDQYHIVWMWV-EADMPRRC-ACGHWFKLKLI   65 (201)
Q Consensus        13 GTKEDPiLVPS~~deRIVGCtG--peDSH~VvWf~L-~KGkP~RC-ECGqwFKLv~v   65 (201)
                      -|.+.|-+|.  .+.|+|.|.|  .+..|-.+|++| .++.+..| .||..|+++..
T Consensus        14 m~~~apevI~--V~~~~V~CdGg~g~LGHPrVyL~ld~~~g~~~CpYCg~~f~l~~~   68 (80)
T 2jvm_A           14 MSIEAPETVV--VSTWKVACDGGEGALGHPRVWLSIPHETGFVECGYCDRRYIHESF   68 (80)
T ss_dssp             CCCSCCSEEE--ESCSEEEECCCSTTCCCCCEEEECCTTTCEEECSSSSCEEEEHHH
T ss_pred             cccCCCCeEE--ECCcEEEcCCCCCCCCCCEEEEEccCCCCeEECCCCCCEEEecCC
Confidence            3456665553  3479999988  468999999999 57889999 79999999863

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

Probab=93.06  E-value=0.049  Score=41.06  Aligned_cols=52  Identities=10%  Similarity=0.167  Sum_probs=38.9

Q ss_pred             ceeEeeeC--CCCCcceEEEEEecCCceee-cCCcEEEEEEecCCCCccccCCch
Q psy7214          27 SRLVGCVC--EEDQYHIVWMWVEADMPRRC-ACGHWFKLKLICRGGVHVAIGSNW   78 (201)
Q Consensus        27 eRIVGCtG--peDSH~VvWf~L~KGkP~RC-ECGqwFKLv~vG~~g~~~~~gs~~   78 (201)
                      .|.|.|.|  ++=.|--+|+.|.+.....| .||..|+++.--+.++.-+-+--|
T Consensus        22 ~~~v~CdG~~~plgHPrVyL~i~~~g~~~CpYCg~~y~~~~~~~~~et~p~~c~~   76 (87)
T 2jz8_A           22 VKEFMCVGATQPFDHPHIFIDMGSTDEKICPYCSTLYRYDPSLSYNQTNPTGCLY   76 (87)
T ss_dssp             CSEEECCCSSCSSSSSSCEEECTTCCEECCTTTCCEEECCTTSCTTCCCSSCCBC
T ss_pred             CcEEEcCCCCCCCCCCEEEEEcCCCCeEECCCCCCEeEcCCCCCcCCcCCCCcEe
Confidence            45689998  35579999999999889999 799999998654444444444433

>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=80.72  E-value=1.2  Score=31.87  Aligned_cols=33  Identities=21%  Similarity=0.486  Sum_probs=23.8

Q ss_pred             ceeEeeeCCCCCcceEEEEEecC-CceeecCCcEEEEEEe
Q psy7214          27 SRLVGCVCEEDQYHIVWMWVEAD-MPRRCACGHWFKLKLI   65 (201)
Q Consensus        27 eRIVGCtGpeDSH~VvWf~L~KG-kP~RCECGqwFKLv~v   65 (201)
                      |.||||+|..-     |. ++.+ +.++|.||..++++.+
T Consensus         2 Y~vv~C~C~~~-----~~-~~~~~kT~~C~CG~~~~~~k~   35 (71)
T 1gh9_A            2 YIIFRCDCGRA-----LY-SREGAKTRKCVCGRTVNVKDR   35 (71)
T ss_dssp             EEEEEETTSCC-----EE-EETTCSEEEETTTEEEECCSS
T ss_pred             eEEEECCCCCE-----EE-EcCCCcEEECCCCCeeeeceE
Confidence            67999988532     43 3334 5799999999988753

---

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	201
d1v54f_	98	g.41.5.3 (F:) Cytochrome c oxidase Subunit F {Cow	9e-27

>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 = 96.0 bits (239), Expect = 9e-27
 Identities = 30/64 (46%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 1  DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCA-CGHW 59
          DPY     K TSGT++DPNLV S    R+VGC+CEED   ++W W+     +RC  CG  
Sbjct: 29 DPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQRCPSCGTH 88

Query: 60 FKLK 63
          +KL 
Sbjct: 89 YKLV 92

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	201
d1v54f_	98	Cytochrome c oxidase Subunit F {Cow (Bos taurus) [	99.98
d1x6ea2	26	Zinc finger protein 24 {Human (Homo sapiens) [TaxI	84.5

>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=99.98  E-value=2.4e-33  Score=212.23  Aligned_cols=65  Identities=46%  Similarity=0.947  Sum_probs=63.0

Q ss_pred             CCCCCCCCCCCCCCCCCCeeeecCCCceeEeeeCCCCCcceEEEEEecCCceee-cCCcEEEEEEe
Q psy7214           1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRC-ACGHWFKLKLI   65 (201)
Q Consensus         1 DPFDMkPLks~~GTKEDPiLVPS~~deRIVGCtGpeDSH~VvWf~L~KGkP~RC-ECGqwFKLv~v   65 (201)
                      |||||+|+++++||+||||||||++++|||||+|++|+|+|+||||++|+|+|| +||+||||++.
T Consensus        29 D~fd~~~~~~~~GTke~P~lVpS~~~~RiVGC~~~~D~h~v~W~~l~~g~p~RC~eCG~~fkL~~~   94 (98)
T d1v54f_          29 DPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQRCPSCGTHYKLVPH   94 (98)
T ss_dssp             CTTCCSCCCCCCCCSSSCEEEECSSSEEEEEECCSTTCSCCEEEEEESSSCEECTTTCCEEEEECC
T ss_pred             ChhhccCCcCCCCCCcCCcEecCCCCceEEeecCCCCCceeEEEEEeCCCCcccCCCCcEEEEeec
Confidence            899999999999999999999999999999999999999999999999999999 89999999843

>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=84.50  E-value=0.19  Score=28.84  Aligned_cols=12  Identities=42%  Similarity=1.132  Sum_probs=10.4

Q ss_pred             Cceee-cCCcEEE
Q psy7214          50 MPRRC-ACGHWFK   61 (201)
Q Consensus        50 kP~RC-ECGqwFK   61 (201)
                      +|..| |||..|.
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 8999984