254780474

254780474

ubiquinol oxidase, subunit II

GeneID in NCBI database:8209463Locus tag:CLIBASIA_01795
Protein GI in NCBI database:254780474Protein Accession:YP_003064887.1
Gene range:-(396737, 397735)Protein Length:332aa
Gene description:ubiquinol oxidase, subunit II
COG prediction:[C] Heme/copper-type cytochrome/quinol oxidases, subunit 2
KEGG prediction:cyoA; ubiquinol oxidase, subunit II; K02297 cytochrome o ubiquinol oxidase subunit II [EC:1.10.3.-]
SEED prediction:Cytochrome O ubiquinol oxidase subunit II (EC 1.10.3.-)
Pathway involved in KEGG:Oxidative phosphorylation [PATH:las00190]
Subsystem involved in SEED:Terminal cytochrome O ubiquinol oxidase
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMM3 TM-Helix
TOPPRED4 TM-Helix
HMMTOP3 TM-Helix
MEMSAT1 TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUS3 TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330--
MSDCLNWMGVSVGKSLKFFFLFFSSVMLSGFEFIVMDPYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAWKYRSTNKKARYDPKWCHSTLLELFVWLVPLVIVGFLAVITWDATHRMDPYAPLERISESKSIAKNSKPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKSEKGFEDWISKVKRQGTFLNRQEYLLLKKPSERDSVRYFSPIEKGLYYSILNLCVHPGKICMDEMMRIDALGGGGMRGIDRHSLIYDEGYRQ
cccccccccccccHHHHHHHHHHHHHHHccccEEEEccccHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHcccccccccccccccccEEEEEEEHHHHHHHHHHHEEEcccEEEccccHHHHHcccccccccccccEEEEEEEEEEEEEEEEcccccccccEEEEccccEEEEEEEEcccEEEEEcccccccEEEccccEEEEEEEEcccEEEEEEccccccccccccEEEEEEEcHHHHHHHHHHHHHccccccHHHHHHHHHHccccccEEcccccHHHHHHHHHHHHcccccccccccccccccccccccccccEEEccccccc
ccHHHHHccccccHHHHHHHHHHHHHHHcccccEEccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHccccccccccccEEEEEEEEccEEEEEEccccEEEEcEEEEEcccEEEEEEEEccccEEEEEHHHcEEEEEEccEcEEEEEEccccEEEEEEcccccccccccccEEEEEccHHHHHHHHHHHHHccccccHHHHHHHccccccccEEEEcccccHHHHHHHHHHcccccccccHHHcHHHccccccccccccccHccHHccc
msdclnwmgvsvgKSLKFFFLFFSSVMLSGFefivmdpygdiaLQQASLIRIAVALMLLIVVPVFFSILFFAWKYRstnkkarydpkwchstLLELFVWLVPLVIVGFLAVITwdathrmdpyaplerisesksiaknskPLVVEVVALDWKWLFLLPEQQVAIINELvvpidrplefRITASSVmnsfyipglAGQIYAMAGMETKLHAVMNkkgaysgfsanysgrgfshmrfkfygksekgFEDWISKVKRQGTFLNRQEYLLlkkpserdsvryfspiekGLYYSILNLCVHPGKICMDEMMRIDalggggmrgidrhsliydegyrq
MSDCLNWMGVSVGKSLKFFFLFFSSVMLSGFEFIVMDPYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAWKYRSTNKKARYDPKWCHSTLLELFVWLVPLVIVGFLAVITWDATHRMDPYAPLERisesksiaknskpLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKSEKGFEDWISKVKRqgtflnrqeylllkkpserdsvRYFSPIEKGLYYSILNLCVHPGKICMDEMMRIDALGGGGMRGIDRHSLIYDEGYRQ
MSDCLNWMGVsvgkslkffflffssvmlsgfEFIVMDPYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAWKYRSTNKKARYDPKWCHSTLLELFVWLVPLVIVGFLAVITWDATHRMDPYAPLERISESKSIAKNSKPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKSEKGFEDWISKVKRQGTFLNRQEYLLLKKPSERDSVRYFSPIEKGLYYSILNLCVHPGKICMDEMMRIDALGGGGMRGIDRHSLIYDEGYRQ
*********VSVGKSLKFFFLFFSSVMLSGFEFIVMDPYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAWKYRS***********CHSTLLELFVWLVPLVIVGFLAVITWDATHRMDPYAPLE************KPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKSEKGFEDWIS*****************************SPIEKGLYYSILNLCV*************************************
MSDCLNWMGVSVGKSLKFFFLFFSSVMLSGFEFIVMDPYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAWKYRSTNKKARYDPKWCHSTLLELFVWLVPLVIVGFLAVITWDATHRMDPYAPLERISESKSIAKNSKPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKSEKGFEDWISKVKRQGTFLNRQEYLLLKKPSERDSVRYFSPIEKGLYYSILNLCVHPGKICMDEMMRIDALGGGGMRGIDRHSLIYDEGYRQ
MSDCLNWMGVSVGKSLKFFFLFFSSVMLSGFEFIVMDPYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAWKYRSTNKKARYDPKWCHSTLLELFVWLVPLVIVGFLAVITWDATHRMDPYAPLERISESKSIAKNSKPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKSEKGFEDWISKVKRQGTFLNRQEYLLLKKPSERDSVRYFSPIEKGLYYSILNLCVHPGKICMDEMMRIDALGGG*M****RHS*********
iiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxHHHHHHHHHHHHHHHHHHHHxxxxxxxxxxxxxxxxxHHHHHHHHHHHHHHHHHHHHxxxxxxxxxxxxxxxxxxxxxHHHHHHHHHHHHHHHHHHHHxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxhhhhhhhhhhhhhhhhhhhhxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
iiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHoooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSDCLNWMGVSVGKSLKFFFLFFSSVMLSGFEFIVMDPYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAWKYRSTNKKARYDPKWCHSTLLELFVWLVPLVIVGFLAVITWDATHRMDPYAPLERISESKSIAKNSKPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKSEKGFEDWISKVKRQGTFLNRQEYLLLKKPSERDSVRYFSPIEKGLYYSILNLCVHPGKICMDEMMRIDALGGGGMRGIDRHSLIYDEGYRQ
MSDCLNWMGVSVGKSLKFFFLFFSSVMLSGFEFIVMDPYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAWKYRSTNKKARYDPKWCHSTLLELFVWLVPLVIVGFLAVITWDATHRMDPYAPLERISESKSIAKNSKPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKSEKGFEDWISKVKRQGTFLNRQEYLLLKKPSERDSVRYFSPIEKGLYYSILNLCVHPGKICMDEMMRIDALGGGGMRGIDRHSLIYDEGYRQ
MSDCLNWMGVSVGKSLKFFFLFFSSVMLSGFEFIVMDPYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAWKYRSTNKKARYDPKWCHSTLLELFVWLVPLVIVGFLAVITWDATHRMDPYAPLERISESKSIAKNSKPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKSEKGFEDWISKVKRQGTFLNRQEYLLLKKPSERDSVRYFSPIEKGLYYSILNLCVHPGKICMDEMMRIDALGGGGMRGIDRHSLIYDEGYRQ

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target332 ubiquinol oxidase, subunit II [Candidatus Liberibacter
254780586101 BolA family protein [Candidatus Liberibacter asiat 0.016
>gi|254780586|ref|YP_003064999.1| BolA family protein [Candidatus Liberibacter asiaticus str. psy62] Length = 101 Back     alignment
 Score = 32.0 bits (71), Expect = 0.016,   Method: Composition-based stats.
 Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 13/78 (16%)

Query: 211 VMNKKGAYSGFSANYSGRGFSHMRFKFYGKSEKGFEDWISKVKRQGTFLNRQEYLLLKKP 270
           V+N+   + G    ++G G +H+R K    +  G    ISK     TF +R+ Y LL K 
Sbjct: 27  VINESHLHVGHQPQFNGLGETHIRIKIVSPTFTG----ISK-----TFRHRKIYDLLHKE 77

Query: 271 SERD----SVRYFSPIEK 284
            + +    S+  FSP EK
Sbjct: 78  IKEELHALSIEAFSPDEK 95

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target332 ubiquinol oxidase, subunit II [Candidatus Liberibacter
315122070329 ubiquinol oxidase, subunit II [Candidatus Liberibacter 1 1e-150
150376513392 ubiquinol oxidase subunit II [Sinorhizobium medicae WSM 1 1e-110
16265063386 putative cytochrome o ubiquinol oxidase chain II protei 1 1e-110
227820109385 cytochrome O ubiquinol oxidase subunit II [Sinorhizobiu 1 1e-108
116255242394 putative ubiquinol oxidase polypeptide II precursor [Rh 1 1e-107
190895347384 cytochrome O ubiquinol oxidase protein, subunit II [Rhi 1 1e-107
209546365390 ubiquinol oxidase subunit II [Rhizobium leguminosarum b 1 1e-106
241667021371 ubiquinol oxidase, subunit II [Rhizobium leguminosarum 1 1e-106
86360308371 cytochrome O ubiquinol oxidase, subunit II protein [Rhi 1 1e-106
222084387375 ubiquinol oxidase, subunit II [Agrobacterium radiobacte 1 1e-105
>gi|315122070|ref|YP_004062559.1| ubiquinol oxidase, subunit II [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 329 Back     alignment and organism information
 Score =  534 bits (1375), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 247/323 (76%), Positives = 289/323 (89%)

Query: 8   MGVSVGKSLKFFFLFFSSVMLSGFEFIVMDPYGDIALQQASLIRIAVALMLLIVVPVFFS 67
           M  ++ K++KF  LFFS V+LSGF+F+VM+PYGD+A QQA LI I+V+LMLLIVVPVFFS
Sbjct: 1   MMANMTKNMKFVALFFSIVILSGFDFVVMNPYGDVASQQAGLIYISVSLMLLIVVPVFFS 60

Query: 68  ILFFAWKYRSTNKKARYDPKWCHSTLLELFVWLVPLVIVGFLAVITWDATHRMDPYAPLE 127
           ILFFAW+YR+TNKKA YDP W HST LE FVWL+PL+I+G LA ITWDATHRMDPYAPLE
Sbjct: 61  ILFFAWRYRATNKKAHYDPAWYHSTRLEFFVWLIPLIIIGCLAAITWDATHRMDPYAPLE 120

Query: 128 RISESKSIAKNSKPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMN 187
           RISE+KSI KNSK L+VEVVALDWKWLFL PEQ++A++NELVVP+DRPLEFRITASSVMN
Sbjct: 121 RISENKSIPKNSKSLIVEVVALDWKWLFLFPEQKIAVVNELVVPVDRPLEFRITASSVMN 180

Query: 188 SFYIPGLAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKSEKGFED 247
           SFYIPGLAGQIYAM GMETKLHAVMN++GAYSGFSANYSG+GFSHMRF F+GKSEKGF+D
Sbjct: 181 SFYIPGLAGQIYAMPGMETKLHAVMNREGAYSGFSANYSGKGFSHMRFTFHGKSEKGFDD 240

Query: 248 WISKVKRQGTFLNRQEYLLLKKPSERDSVRYFSPIEKGLYYSILNLCVHPGKICMDEMMR 307
           W++KVKRQG  L+RQ YLLL+KPSE+D V YFS +E GLY +I+N CVHP KICMDE+MR
Sbjct: 241 WVAKVKRQGNCLDRQRYLLLEKPSEKDPVIYFSSVESGLYSAIMNFCVHPNKICMDEVMR 300

Query: 308 IDALGGGGMRGIDRHSLIYDEGY 330
           I+A+GGGG++GIDR  L+YDE Y
Sbjct: 301 INAMGGGGVKGIDRRFLVYDEDY 323


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|150376513|ref|YP_001313109.1| ubiquinol oxidase subunit II [Sinorhizobium medicae WSM419] Length = 392 Back     alignment and organism information
>gi|16265063|ref|NP_437855.1| putative cytochrome o ubiquinol oxidase chain II protein [Sinorhizobium meliloti 1021] Length = 386 Back     alignment and organism information
>gi|227820109|ref|YP_002824080.1| cytochrome O ubiquinol oxidase subunit II [Sinorhizobium fredii NGR234] Length = 385 Back     alignment and organism information
>gi|116255242|ref|YP_771075.1| putative ubiquinol oxidase polypeptide II precursor [Rhizobium leguminosarum bv. viciae 3841] Length = 394 Back     alignment and organism information
>gi|190895347|ref|YP_001985639.1| cytochrome O ubiquinol oxidase protein, subunit II [Rhizobium etli CIAT 652] Length = 384 Back     alignment and organism information
>gi|209546365|ref|YP_002278255.1| ubiquinol oxidase subunit II [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 390 Back     alignment and organism information
>gi|241667021|ref|YP_002985105.1| ubiquinol oxidase, subunit II [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 371 Back     alignment and organism information
>gi|86360308|ref|YP_472196.1| cytochrome O ubiquinol oxidase, subunit II protein [Rhizobium etli CFN 42] Length = 371 Back     alignment and organism information
>gi|222084387|ref|YP_002542916.1| ubiquinol oxidase, subunit II [Agrobacterium radiobacter K84] Length = 375 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target332 ubiquinol oxidase, subunit II [Candidatus Liberibacter
PRK10525315 PRK10525, PRK10525, cytochrome o ubiquinol oxidase subu 1e-86
TIGR01433226 TIGR01433, CyoA, cytochrome o ubiquinol oxidase subunit 3e-86
TIGR01432217 TIGR01432, QOXA, cytochrome aa3 quinol oxidase, subunit 7e-41
TIGR02866201 TIGR02866, CoxB, cytochrome c oxidase, subunit II 7e-25
COG1622247 COG1622, CyoA, Heme/copper-type cytochrome/quinol oxida 6e-62
pfam0648147 pfam06481, COX_ARM, COX Aromatic Rich Motif 1e-08
KOG4767231 KOG4767, KOG4767, KOG4767, Cytochrome c oxidase, subuni 8e-08
MTH00023240 MTH00023, COX2, cytochrome c oxidase subunit II; Valida 1e-04
MTH00051234 MTH00051, COX2, cytochrome c oxidase subunit II; Provis 4e-04
pfam00116120 pfam00116, COX2, Cytochrome C oxidase subunit II, perip 6e-04
MTH00027262 MTH00027, COX2, cytochrome c oxidase subunit II; Provis 8e-04
MTH00185230 MTH00185, COX2, cytochrome c oxidase subunit II; Provis 0.001
>gnl|CDD|182518 PRK10525, PRK10525, cytochrome o ubiquinol oxidase subunit II; Provisional Back     alignment and domain information
>gnl|CDD|130500 TIGR01433, CyoA, cytochrome o ubiquinol oxidase subunit II Back     alignment and domain information
>gnl|CDD|130499 TIGR01432, QOXA, cytochrome aa3 quinol oxidase, subunit II Back     alignment and domain information
>gnl|CDD|163049 TIGR02866, CoxB, cytochrome c oxidase, subunit II Back     alignment and domain information
>gnl|CDD|31809 COG1622, CyoA, Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion] Back     alignment and domain information
>gnl|CDD|148220 pfam06481, COX_ARM, COX Aromatic Rich Motif Back     alignment and domain information
>gnl|CDD|39964 KOG4767, KOG4767, KOG4767, Cytochrome c oxidase, subunit II, and related proteins [Energy production and conversion] Back     alignment and domain information
>gnl|CDD|177104 MTH00023, COX2, cytochrome c oxidase subunit II; Validated Back     alignment and domain information
>gnl|CDD|177126 MTH00051, COX2, cytochrome c oxidase subunit II; Provisional Back     alignment and domain information
>gnl|CDD|109183 pfam00116, COX2, Cytochrome C oxidase subunit II, periplasmic domain Back     alignment and domain information
>gnl|CDD|177106 MTH00027, COX2, cytochrome c oxidase subunit II; Provisional Back     alignment and domain information
>gnl|CDD|164736 MTH00185, COX2, cytochrome c oxidase subunit II; Provisional Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 332 ubiquinol oxidase, subunit II [Candidatus Liberibacter
PRK10525305 cytochrome o ubiquinol oxidase subunit II; Provisional 100.0
TIGR01433228 CyoA ubiquinol oxidase, subunit II; InterPro: IPR006333 100.0
TIGR02866249 CoxB cytochrome c oxidase, subunit II; InterPro: IPR014 100.0
TIGR01432229 QOXA cytochrome aa3 quinol oxidase, subunit II; InterPr 100.0
MTH00140227 COX2 cytochrome c oxidase subunit II; Provisional 100.0
MTH00129230 COX2 cytochrome c oxidase subunit II; Provisional 100.0
MTH00038229 COX2 cytochrome c oxidase subunit II; Provisional 100.0
MTH00154226 COX2 cytochrome c oxidase subunit II; Provisional 100.0
MTH00185229 COX2 cytochrome c oxidase subunit II; Provisional 100.0
MTH00051247 COX2 cytochrome c oxidase subunit II; Provisional 100.0
MTH00117227 COX2 cytochrome c oxidase subunit II; Provisional 100.0
MTH00139223 COX2 cytochrome c oxidase subunit II; Provisional 100.0
MTH00023247 COX2 cytochrome c oxidase subunit II; Validated 100.0
MTH00168225 COX2 cytochrome c oxidase subunit II; Provisional 100.0
MTH00076228 COX2 cytochrome c oxidase subunit II; Provisional 100.0
MTH00098227 COX2 cytochrome c oxidase subunit II; Validated 100.0
MTH00008228 COX2 cytochrome c oxidase subunit II; Validated 100.0
MTH00027249 COX2 cytochrome c oxidase subunit II; Provisional 100.0
MTH00080231 COX2 cytochrome c oxidase subunit II; Provisional 100.0
KOG4767231 consensus 100.0
COG1622247 CyoA Heme/copper-type cytochrome/quinol oxidases, subun 100.0
MTH00047193 COX2 cytochrome c oxidase subunit II; Provisional 100.0
pfam00116120 COX2 Cytochrome C oxidase subunit II, periplasmic domai 100.0
PTZ00047163 cytochrome C oxidase subunit II; Provisional 100.0
PRK02888637 nitrous-oxide reductase; Validated 98.41
TIGR03096135 nitroso_cyanin nitrosocyanin. Nitrosocyanin, as describ 97.28
COG4263637 NosZ Nitrous oxide reductase [Energy production and con 96.28
pfam0648147 COX_ARM COX Aromatic Rich Motif. COX2 (Cytochrome O ubi 98.97
pfam0279083 COX2_TM Cytochrome C oxidase subunit II, transmembrane 98.54
PRK10263 1355 DNA translocase FtsK; Provisional 93.15
TIGR01477395 RIFIN variant surface antigen, rifin family; InterPro: 92.87
PTZ00042304 stevor; Provisional 92.27
pfam02009289 Rifin_STEVOR Rifin/stevor family. Several multicopy gen 91.35
PTZ00046348 rifin; Provisional 90.25
>PRK10525 cytochrome o ubiquinol oxidase subunit II; Provisional Back     alignment and domain information
>TIGR01433 CyoA ubiquinol oxidase, subunit II; InterPro: IPR006333 Members of this domain catalyze the oxidation of ubiquinol with the concomitant reduction of molecular oxygen to water Back     alignment and domain information
>TIGR02866 CoxB cytochrome c oxidase, subunit II; InterPro: IPR014222 This entry contains subunit II (CoxB) of cytochrome c oxidase Back     alignment and domain information
>TIGR01432 QOXA cytochrome aa3 quinol oxidase, subunit II; InterPro: IPR006332 Members of this family catalyze the oxidation of quinol with the concomitant reduction of molecular oxygen to water Back     alignment and domain information
>MTH00140 COX2 cytochrome c oxidase subunit II; Provisional Back     alignment and domain information
>MTH00129 COX2 cytochrome c oxidase subunit II; Provisional Back     alignment and domain information
>MTH00038 COX2 cytochrome c oxidase subunit II; Provisional Back     alignment and domain information
>MTH00154 COX2 cytochrome c oxidase subunit II; Provisional Back     alignment and domain information
>MTH00185 COX2 cytochrome c oxidase subunit II; Provisional Back     alignment and domain information
>MTH00051 COX2 cytochrome c oxidase subunit II; Provisional Back     alignment and domain information
>MTH00117 COX2 cytochrome c oxidase subunit II; Provisional Back     alignment and domain information
>MTH00139 COX2 cytochrome c oxidase subunit II; Provisional Back     alignment and domain information
>MTH00023 COX2 cytochrome c oxidase subunit II; Validated Back     alignment and domain information
>MTH00168 COX2 cytochrome c oxidase subunit II; Provisional Back     alignment and domain information
>MTH00076 COX2 cytochrome c oxidase subunit II; Provisional Back     alignment and domain information
>MTH00098 COX2 cytochrome c oxidase subunit II; Validated Back     alignment and domain information
>MTH00008 COX2 cytochrome c oxidase subunit II; Validated Back     alignment and domain information
>MTH00027 COX2 cytochrome c oxidase subunit II; Provisional Back     alignment and domain information
>MTH00080 COX2 cytochrome c oxidase subunit II; Provisional Back     alignment and domain information
>KOG4767 consensus Back     alignment and domain information
>COG1622 CyoA Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion] Back     alignment and domain information
>MTH00047 COX2 cytochrome c oxidase subunit II; Provisional Back     alignment and domain information
>pfam00116 COX2 Cytochrome C oxidase subunit II, periplasmic domain Back     alignment and domain information
>PTZ00047 cytochrome C oxidase subunit II; Provisional Back     alignment and domain information
>PRK02888 nitrous-oxide reductase; Validated Back     alignment and domain information
>TIGR03096 nitroso_cyanin nitrosocyanin Back     alignment and domain information
>COG4263 NosZ Nitrous oxide reductase [Energy production and conversion] Back     alignment and domain information
>pfam06481 COX_ARM COX Aromatic Rich Motif Back     alignment and domain information
>pfam02790 COX2_TM Cytochrome C oxidase subunit II, transmembrane domain Back     alignment and domain information
>PRK10263 DNA translocase FtsK; Provisional Back     alignment and domain information
>TIGR01477 RIFIN variant surface antigen, rifin family; InterPro: IPR006373 Malaria is still a major cause of mortality in many areas of the world Back     alignment and domain information
>PTZ00042 stevor; Provisional Back     alignment and domain information
>pfam02009 Rifin_STEVOR Rifin/stevor family Back     alignment and domain information
>PTZ00046 rifin; Provisional Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target332 ubiquinol oxidase, subunit II [Candidatus Liberibacter
1fft_B315 The Structure Of Ubiquinol Oxidase From Escherichia 9e-86
1cyx_A205 Quinol Oxidase (Periplasmic Fragment Of Subunit Ii 2e-55
1cyw_A205 Quinol Oxidase (Periplasmic Fragment Of Subunit Ii) 4e-51
1m56_B264 Structure Of Cytochrome C Oxidase From Rhodobactor 4e-43
2gsm_B262 Catalytic Core (Subunits I And Ii) Of Cytochrome C 5e-42
3om3_B256 Catalytic Core Subunits (I And Ii) Of Cytochrome C 1e-41
1ar1_B298 Structure At 2.7 Angstrom Resolution Of The Paracoc 2e-41
1qle_B252 Cryo-Structure Of The Paracoccus Denitrificans Four 3e-41
gi|11514518|pdb|1FFT|B Chain B, The Structure Of Ubiquinol Oxidase From Escherichia Coli Length = 315 Back     alignment and structure
 Score =  321 bits (823), Expect = 9e-86,   Method: Composition-based stats.
 Identities = 130/310 (41%), Positives = 189/310 (60%), Gaps = 11/310 (3%)

Query: 14  KSLKFFFLFFSSVMLSGFEFIVMDPYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAW 73
           KSL +  LF  +V+LSG    ++DP G I L+Q SLI  A  LML++V+P     + FAW
Sbjct: 8   KSLGWLSLFAGTVLLSGCNSALLDPKGQIGLEQRSLILTAFGLMLIVVIPAILMAVGFAW 67

Query: 74  KYRSTNKKARYDPKWCHSTLLELFVWLVPLVIVGFLAVITWDATHRMDPYAPLERISESK 133
           KYR++NK A+Y P W HS  +E  VW VP++I+ FLAV+TW  TH ++P  PL       
Sbjct: 68  KYRASNKDAKYSPNWSHSNKVEAVVWTVPILIIIFLAVLTWKTTHALEPSKPLAH----- 122

Query: 134 SIAKNSKPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPG 193
               + KP+ +EVV++DWKW F+ PEQ +A +NE+  P + P+ F++T++SVMNSF+IP 
Sbjct: 123 ----DEKPITIEVVSMDWKWFFIYPEQGIATVNEIAFPANTPVYFKVTSNSVMNSFFIPR 178

Query: 194 LAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKSE-KGFEDWISKV 252
           L  QIYAMAGM+T+LH + N+ G Y G SA+YSG GFS M+FK     +   F+ W++K 
Sbjct: 179 LGSQIYAMAGMQTRLHLIANEPGTYDGISASYSGPGFSGMKFKAIATPDRAAFDQWVAKA 238

Query: 253 KRQGTFL-NRQEYLLLKKPSERDSVRYFSPIEKGLYYSILNLCVHPGKICMDEMMRIDAL 311
           K+    + +   +  L  PSE + V YFS ++  L+  ++N  +  GK         +  
Sbjct: 239 KQSPNTMSDMAAFEKLAAPSEYNQVEYFSNVKPDLFADVINKFMAHGKSMDMTQPEGEHS 298

Query: 312 GGGGMRGIDR 321
              GM G+D 
Sbjct: 299 AHEGMEGMDM 308


>gi|157830777|pdb|1CYX|A Chain A, Quinol Oxidase (Periplasmic Fragment Of Subunit Ii With Engineered Cu-A Binding Site)(Cyoa) Length = 205 Back     alignment and structure
>gi|157830776|pdb|1CYW|A Chain A, Quinol Oxidase (Periplasmic Fragment Of Subunit Ii) (Cyoa) Length = 205 Back     alignment and structure
>gi|23200455|pdb|1M56|B Chain B, Structure Of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type) Length = 264 Back     alignment and structure
>gi|118137842|pdb|2GSM|B Chain B, Catalytic Core (Subunits I And Ii) Of Cytochrome C Oxidase From Rhodobacter Sphaeroides Length = 262 Back     alignment and structure
>gi|321159890|pdb|3OM3|B Chain B, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase From Rhodobacter Sphaeroides With K362m Mutation In The Reduced State Length = 256 Back     alignment and structure
gi|2914142|pdb|1AR1|B Chain B, Structure At 2.7 Angstrom Resolution Of The Paracoccus Denitrificans Two-Subunit Cytochrome C Oxidase Complexed With An Antibody Fv Fragment Length = 298 Back     alignment and structure
>gi|6730477|pdb|1QLE|B Chain B, Cryo-Structure Of The Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase In The Completely Oxidized State Complexed With An Antibody Fv Fragment Length = 252 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target332 ubiquinol oxidase, subunit II [Candidatus Liberibacter
1fft_B315 Ubiquinol oxidase; electron transport, cytochrome oxida 5e-81
1cyx_A205 CYOA; electron transport; 2.30A {Escherichia coli} SCOP 1e-41
3hb3_B298 Cytochrome C oxidase subunit 2; electron transfer, prot 6e-29
2gsm_B262 Cytochrome C oxidase subunit 2; transmembrane protein c 3e-23
1v54_B227 Cytochrome C oxidase polypeptide II; oxidoreductase; HE 8e-19
1xme_B168 Cytochrome C oxidase polypeptide II; cytochrome oxidase 4e-17
2cua_A135 Protein (CUA); CUA center, electron transport; 1.60A {T 5e-13
>1fft_B Ubiquinol oxidase; electron transport, cytochrome oxidase, membrane protein, oxidoreductase; HET: HEM HEO; 3.50A {Escherichia coli} SCOP: b.6.1.2 f.17.2.1 Length = 315 Back     alignment and structure
 Score =  296 bits (759), Expect = 5e-81
 Identities = 132/309 (42%), Positives = 189/309 (61%), Gaps = 11/309 (3%)

Query: 14  KSLKFFFLFFSSVMLSGFEFIVMDPYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAW 73
           KSL +  LF  +V+LSG    ++DP G I L+Q SLI  A  LML++V+P     + FAW
Sbjct: 8   KSLGWLSLFAGTVLLSGCNSALLDPKGQIGLEQRSLILTAFGLMLIVVIPAILMAVGFAW 67

Query: 74  KYRSTNKKARYDPKWCHSTLLELFVWLVPLVIVGFLAVITWDATHRMDPYAPLERISESK 133
           KYR++NK A+Y P W HS  +E  VW VP++I+ FLAV+TW  TH ++P  PL       
Sbjct: 68  KYRASNKDAKYSPNWSHSNKVEAVVWTVPILIIIFLAVLTWKTTHALEPSKPL------- 120

Query: 134 SIAKNSKPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPG 193
             A + KP+ +EVV++DWKW F+ PEQ +A +NE+  P + P+ F++T++SVMNSF+IP 
Sbjct: 121 --AHDEKPITIEVVSMDWKWFFIYPEQGIATVNEIAFPANTPVYFKVTSNSVMNSFFIPR 178

Query: 194 LAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKS-EKGFEDWISKV 252
           L  QIYAMAGM+T+LH + N+ G Y G SA+YSG GFS M+FK         F+ W++K 
Sbjct: 179 LGSQIYAMAGMQTRLHLIANEPGTYDGISASYSGPGFSGMKFKAIATPDRAAFDQWVAKA 238

Query: 253 KRQG-TFLNRQEYLLLKKPSERDSVRYFSPIEKGLYYSILNLCVHPGKICMDEMMRIDAL 311
           K+   T  +   +  L  PSE + V YFS ++  L+  ++N  +  GK         +  
Sbjct: 239 KQSPNTMSDMAAFEKLAAPSEYNQVEYFSNVKPDLFADVINKFMAHGKSMDMTQPEGEHS 298

Query: 312 GGGGMRGID 320
              GM G+D
Sbjct: 299 AHEGMEGMD 307


>1cyx_A CYOA; electron transport; 2.30A {Escherichia coli} SCOP: b.6.1.2 PDB: 1cyw_A Length = 205 Back     alignment and structure
>3hb3_B Cytochrome C oxidase subunit 2; electron transfer, proton transfer, proton pumping, membrane protein, cell inner membrane, cell membrane, copper; HET: HEA LDA LMT; 2.25A {Paracoccus denitrificans} PDB: 1ar1_B* 3ehb_B* 1qle_B* Length = 298 Back     alignment and structure
>2gsm_B Cytochrome C oxidase subunit 2; transmembrane protein complex, oxidoreductase; HET: DMU HEA TRD; 2.00A {Rhodobacter sphaeroides} SCOP: b.6.1.2 f.17.2.1 PDB: 3dtu_B* 3fye_B* 3fyi_B* 1m56_B* 1m57_B* Length = 262 Back     alignment and structure
>1v54_B Cytochrome C oxidase polypeptide II; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: b.6.1.2 f.17.2.1 PDB: 1oco_B* 1occ_B* 1ocz_B* 1ocr_B* 1v55_B* 2dyr_B* 2dys_B* 2eij_B* 2eik_B* 2eil_B* 2eim_B* 2ein_B* 2occ_B* 2zxw_B* Length = 227 Back     alignment and structure
>1xme_B Cytochrome C oxidase polypeptide II; cytochrome oxidase, heme, heme-AS, integral membrane protein, oxidoreductase; HET: BNG HEM HAS; 2.30A {Thermus thermophilus} SCOP: b.6.1.2 f.17.2.1 PDB: 1ehk_B* 2qpd_B* 2qpe_B* 3bvd_B* 3eh5_B* 3eh3_B* 3eh4_B* Length = 168 Back     alignment and structure
>2cua_A Protein (CUA); CUA center, electron transport; 1.60A {Thermus thermophilus} SCOP: b.6.1.2 PDB: 2fwl_B* Length = 135 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target332 ubiquinol oxidase, subunit II [Candidatus Liberibacter
1fft_B315 Ubiquinol oxidase; electron transport, cytochrome oxida 100.0
3hb3_B298 Cytochrome C oxidase subunit 2; electron transfer, prot 100.0
2gsm_B262 Cytochrome C oxidase subunit 2; transmembrane protein c 100.0
1v54_B227 Cytochrome C oxidase polypeptide II; oxidoreductase; HE 100.0
1cyx_A205 CYOA; electron transport; 2.30A {Escherichia coli} SCOP 100.0
1xme_B168 Cytochrome C oxidase polypeptide II; cytochrome oxidase 100.0
2cua_A135 Protein (CUA); CUA center, electron transport; 1.60A {T 99.92
1fwx_A595 Nitrous oxide reductase; beta-propeller domain, cupredo 98.92
1qni_A581 Nitrous-oxide reductase; oxidoreductase, denitrificatio 98.65
1qhq_A140 Protein (auracyanin); electron transfer, cupredoxin, bl 97.19
2aan_A139 Auracyanin A; cupredoxin fold, electron transport; 1.85 97.13
3fsa_A125 Azurin; copper, cupredoxin fold, metal-binding, protein 96.58
2ov0_A105 Amicyanin; beta-sandwich, electron transport; 0.75A {Pa 95.57
1cuo_A129 Protein (azurin ISO-2); beta barrel, periplasmic, elect 95.42
2iaa_C128 Azurin; quinoprotein, tryptophan tryptophylquinone, cup 94.97
1nwp_A128 Azurin; electron transport, cupredoxin, electron transf 94.85
2ccw_A129 Azurin II, AZN-2; electron transport (cuproprotein), al 94.44
1oe1_A336 Dissimilatory copper-containing nitrite reductase; deni 91.5
3cvb_A105 Plastocyanin; cupredoxin, SELF assembly, copper, electr 90.49
1iby_A112 Nitrosocyanin; RED copper, cupredoxin, beta hairpin, me 99.34
3c75_A132 Amicyanin; copper proteins, electron transfer complex, 96.89
2dv6_A 447 Nitrite reductase; electron transfer, reduction, denitr 96.7
2cal_A154 Rusticyanin; iron respiratory electron transport chain, 96.12
1id2_A106 Amicyanin; beta barrel, type-1 blue copper protein, ele 95.18
1pcs_A98 Plastocyanin; electron transport; 2.15A {Synechocystis 93.31
3gdc_A288 Multicopper oxidase; beta sandwich, plasmid, oxidoreduc 92.79
2ux6_A122 Pseudoazurin; type-1 copper, metal-binding, redox poten 92.4
1bxv_A91 Plastocyanin; copper protein, electron transfer; 1.80A 92.28
1mzy_A333 Copper-containing nitrite reductase; mutant M182T, gati 91.56
1kdj_A102 Plastocyanin; electron transfer, photosystem, PAI-PAI s 91.46
3erx_A123 Pseudoazurin; copper protein, high-resolution, C electr 90.59
3ef4_A124 Pseudoazurin, blue copper protein; electron transfer, e 90.58
1byp_A99 Protein (plastocyanin); electron transfer, photosynthes 90.39
2zoo_A442 Probable nitrite reductase; electron transfer, electron 96.12
1pmy_A123 Pseudoazurin; electron transfer(cuproprotein); 1.50A {M 93.63
1paz_A123 Pseudoazurin precursor; electron transfer(cuproprotein) 93.55
>1fft_B Ubiquinol oxidase; electron transport, cytochrome oxidase, membrane protein, oxidoreductase; HET: HEM HEO; 3.50A {Escherichia coli} SCOP: b.6.1.2 f.17.2.1 Back     alignment and structure
Probab=100.00  E-value=0  Score=665.20  Aligned_cols=306  Identities=43%  Similarity=0.802  Sum_probs=291.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf             35668899999999998741364326898989999999999999999999999999999998853046777777875345
Q gi|254780474|r   11 SVGKSLKFFFLFFSSVMLSGFEFIVMDPYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAWKYRSTNKKARYDPKWCH   90 (332)
Q Consensus        11 ~~~k~l~~~~l~~~~~lLsGC~~~~l~P~G~ia~~~~~L~~~~~~l~liV~v~V~~l~~~~~~kyR~~~~~a~~~p~~~h   90 (332)
                      +..|.++++++++++++|+||+.++|+|+|++|+++++|+++++++|++|+++|+++++||+||||+++++++|.|+++|
T Consensus         5 ~~~r~l~~l~ll~~~~lLsGC~~~~l~P~G~~a~~~~~L~~~~~~l~l~V~v~v~~~~~~~~~ryR~~~~~~~~~p~~~~   84 (315)
T 1fft_B            5 KYNKSLGWLSLFAGTVLLSGCNSALLDPKGQIGLEQRSLILTAFGLMLIVVIPAILMAVGFAWKYRASNKDAKYSPNWSH   84 (315)
T ss_dssp             ----------------------CCCSSCCSCCHHHHHHHHHHHHHHTTTTTTHHHHHHHTTTTTTTTSTTTCSSCCCCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEEEECCCCCCCCCCCCC
T ss_conf             36789999999999999965765445999978999999999999997767767666430034678843677777986355


Q ss_pred             CCEEEEEEEHHHHHHHHHHHHHHHHHHHHHCCCCCCHHCCCCCCCCCCCCCEEEEEEEEEEEEEEEECCCCCCCCEEEEE
Q ss_conf             66125530227899999999999988775134442000012446788888668999998436999962678774306896
Q gi|254780474|r   91 STLLELFVWLVPLVIVGFLAVITWDATHRMDPYAPLERISESKSIAKNSKPLVVEVVALDWKWLFLLPEQQVAIINELVV  170 (332)
Q Consensus        91 s~~lEi~wt~iP~iIi~~L~~~t~~~~~~ldp~~p~~~~~~~~~~~~~~~~l~I~V~a~qW~W~F~YP~~giatvneL~l  170 (332)
                      |+++|++||++|++|+++|++++|++++.+|+++|.         +.+++|++|+|+|+||+|+|+||++|++|+|||++
T Consensus        85 ~~~lE~i~~~ip~iivi~l~~~~~~~~~~~~~~~~~---------~~~~~~l~I~V~g~qW~W~f~Yp~~~~~t~neL~i  155 (315)
T 1fft_B           85 SNKVEAVVWTVPILIIIFLAVLTWKTTHALEPSKPL---------AHDEKPITIEVVSMDWKWFFIYPEQGIATVNEIAF  155 (315)
T ss_dssp             CSHHHHHTTHHHHHHHHHHHHHHHHHSCTTCCSCCC---------CCCSCCCEEEEECCTTSCEEECTTTCCEEESBCCC
T ss_pred             CCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC---------CCCCCCEEEEEEEEEEEEEEECCCCCCCCCCCCCC
T ss_conf             745521567766899899999998888865124666---------67899849999866889999735666566765025


Q ss_pred             ECCCEEEEEEEECCCCHHCCCHHHCCEECCCCCCCEEEEEEECCCEEEEEECCCCCCCCCCCCEEEEEECC-HHHHHHHH
Q ss_conf             36982899998358101102201074031169851489999427748966613326576113658999708-89999999
Q gi|254780474|r  171 PIDRPLEFRITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKS-EKGFEDWI  249 (332)
Q Consensus       171 Pv~~pV~f~ltS~DViHSF~IP~l~~k~daiPG~~t~l~~~a~~~G~y~G~cae~cG~ghs~M~f~v~v~s-~~~f~~Wv  249 (332)
                      |+|+||+|+|||+|||||||||+||+|+|+||||+|++||+|+++|+|+|+||||||.|||.|+|+|+|++ ++||++|+
T Consensus       156 P~~~pV~~~ltS~DViHsF~VP~l~~k~daiPG~~~~~~~~a~~~G~y~g~Cae~CG~gHs~M~~~v~vv~~~~~f~~Wv  235 (315)
T 1fft_B          156 PANTPVYFKVTSNSVMNSFFIPRLGSQIYAMAGMQTRLHLIANEPGTYDGISASYSGPGFSGMKFKAIATPDRAAFDQWV  235 (315)
T ss_dssp             CSSSEEEEEECBSSSCEEEEEGGGTEEEEECBTSCEEEEEECCSCBCCEEBCCSCCSTTTTTCCEECCBCSSTHHHHHHH
T ss_pred             CCCCEEEEEEECCCCCCEEEECCCCCEEECCCCCEEEEEEECCCCEEEEEEEHHHCCCCCCCCEEEEEEECCHHHHHHHH
T ss_conf             65530189997487112011320085663289861899996189548999805550711335653899987889999999


Q ss_pred             HHHHCCCCCC-CHHHHHHHHHHHHCCCCEEECCCCCCHHHHHHCCCCCCCCCCCCHHHCCCCCCCCCHHHCCCCHHH
Q ss_conf             9986072456-989999976102126321720478354268731524448856602102466688523440110011
Q gi|254780474|r  250 SKVKRQGTFL-NRQEYLLLKKPSERDSVRYFSPIEKGLYYSILNLCVHPGKICMDEMMRIDALGGGGMRGIDRHSLI  325 (332)
Q Consensus       250 ~~~ka~~~~l-~~~~y~~l~~ps~~~~~~~f~~~~~~lf~~i~~~~~~~~~~~~~~~m~~~~~~g~~~~~~~~~~~~  325 (332)
                      +++|+++.++ +.++|++|++|++.++++|||+++|+||+.|+++|+++|+.+...++..++.+++||+++|+...+
T Consensus       236 ~~~k~~~~~~~~~~~~~~la~~~~~~~~~~~~~~~p~Lf~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~g~dm~~~~  312 (315)
T 1fft_B          236 AKAKQSPNTMSDMAAFEKLAAPSEYNQVEYFSNVKPDLFADVINKFMAHGKSMDMTQPEGEHSAHEGMEGMDMSHAE  312 (315)
T ss_dssp             HHHHHCSCCBCCHHHHHHHTSSCSSCCSEEESCBCTTHHHHHHHHTTC-----------------------------
T ss_pred             HHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             98661875566899999986775668853004779732889999873178877877644453447899987777654



>3hb3_B Cytochrome C oxidase subunit 2; electron transfer, proton transfer, proton pumping, membrane protein, cell inner membrane, cell membrane, copper; HET: HEA LDA LMT; 2.25A {Paracoccus denitrificans} PDB: 1ar1_B* 3ehb_B* 1qle_B* Back     alignment and structure
>2gsm_B Cytochrome C oxidase subunit 2; transmembrane protein complex, oxidoreductase; HET: DMU HEA TRD; 2.00A {Rhodobacter sphaeroides} SCOP: b.6.1.2 f.17.2.1 PDB: 3dtu_B* 3fye_B* 3fyi_B* 1m56_B* 1m57_B* Back     alignment and structure
>1v54_B Cytochrome C oxidase polypeptide II; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: b.6.1.2 f.17.2.1 PDB: 1oco_B* 1occ_B* 1ocz_B* 1ocr_B* 1v55_B* 2dyr_B* 2dys_B* 2eij_B* 2eik_B* 2eil_B* 2eim_B* 2ein_B* 2occ_B* 2zxw_B* 3abk_B* 3abl_B* 3abm_B* 3ag1_B* 3ag2_B* 3ag3_B* ... Back     alignment and structure
>1cyx_A CYOA; electron transport; 2.30A {Escherichia coli} SCOP: b.6.1.2 PDB: 1cyw_A Back     alignment and structure
>1xme_B Cytochrome C oxidase polypeptide II; cytochrome oxidase, heme, heme-AS, integral membrane protein, oxidoreductase; HET: BNG HEM HAS; 2.30A {Thermus thermophilus} SCOP: b.6.1.2 f.17.2.1 PDB: 1ehk_B* 2qpd_B* 2qpe_B* 3bvd_B* 3eh5_B* 3eh3_B* 3eh4_B* Back     alignment and structure
>2cua_A Protein (CUA); CUA center, electron transport; 1.60A {Thermus thermophilus} SCOP: b.6.1.2 PDB: 2fwl_B* Back     alignment and structure
>1fwx_A Nitrous oxide reductase; beta-propeller domain, cupredoxin domain, CUZ site, CUA site, oxidoreductase; 1.60A {Paracoccus denitrificans} SCOP: b.6.1.4 b.69.3.1 PDB: 2iwk_A 2iwf_A Back     alignment and structure
>1qni_A Nitrous-oxide reductase; oxidoreductase, denitrification, MAD, electron transfer; 2.40A {Pseudomonas nautica} SCOP: b.6.1.4 b.69.3.1 Back     alignment and structure
>1qhq_A Protein (auracyanin); electron transfer, cupredoxin, blue copper protein, azurin- like, thermophIle; 1.55A {Chloroflexus aurantiacus} SCOP: b.6.1.1 PDB: 1ov8_A Back     alignment and structure
>2aan_A Auracyanin A; cupredoxin fold, electron transport; 1.85A {Chloroflexus aurantiacus} Back     alignment and structure
>3fsa_A Azurin; copper, cupredoxin fold, metal-binding, protein-protein interaction, metal binding protein; 0.98A {Pseudomonas aeruginosa} PDB: 3fs9_A 2fta_A* 2hx7_A 2hx8_A 2hx9_A 2hxa_A 1cc3_A 2ft6_A 2ft7_A 2ft8_A 1azn_A 2iwe_A* 2ghz_A 2gi0_A 1jzg_A* 1azu_A* 1bex_A 1e5z_A 1e5y_A 1e67_A ... Back     alignment and structure
>2ov0_A Amicyanin; beta-sandwich, electron transport; 0.75A {Paracoccus denitrificans} SCOP: b.6.1.1 PDB: 1aaj_A 1aan_A 1aac_A 1mg2_C* 1mg3_C* 1t5k_A 2gc4_C* 2gc7_C* 2j55_A* 2j56_A* 2j57_A* 2mta_A* 1bxa_A 2rac_A 3l45_A 3ie9_A 3iea_A 2idq_A 2ids_A 1sf3_A ... Back     alignment and structure
>1cuo_A Protein (azurin ISO-2); beta barrel, periplasmic, electron transport; 1.60A {Methylomonas SP} SCOP: b.6.1.1 PDB: 1uat_A Back     alignment and structure
>2iaa_C Azurin; quinoprotein, tryptophan tryptophylquinone, cupredoxin, electron transfer, oxidoreductase/electron transport comple; HET: TRQ; 1.95A {Alcaligenes faecalis} PDB: 2h47_C* 2h3x_C* Back     alignment and structure
>1nwp_A Azurin; electron transport, cupredoxin, electron transfer; 1.60A {Pseudomonas putida} SCOP: b.6.1.1 PDB: 1nwo_A 1joi_A Back     alignment and structure
>2ccw_A Azurin II, AZN-2; electron transport (cuproprotein), alcaligenes xylosoxidans, electron transfer, cupredoxin, electron transport; 1.13A {Alcaligenes xylosoxydans} SCOP: b.6.1.1 PDB: 1dz0_A 1dyz_A 1aiz_A 1azb_A 1azc_A 1uri_A 2aza_A 1a4a_A 1a4b_A 1a4c_A Back     alignment and structure
>1oe1_A Dissimilatory copper-containing nitrite reductase; denitrification; HET: PG4; 1.04A {Alcaligenes xylosoxidans} SCOP: b.6.1.3 b.6.1.3 PDB: 1oe3_A* 2vn3_A 2zon_A* 1haw_A 1hau_A* 2vm4_A* 2vw4_A* 2vw6_A* 2vw7_A* 2vm3_A* 1oe2_A* 2jl0_A* 1gs8_A 1wa1_X* 1wa2_X* 2jl3_A* 1gs7_A* 2bp0_B 1gs6_X 2bo0_A* ... Back     alignment and structure
>3cvb_A Plastocyanin; cupredoxin, SELF assembly, copper, electron transport, metal-binding, transport; 1.40A {Phormidium laminosum} PDB: 3cvc_A 3cvd_A 2w8c_A 2w88_A 2q5b_A 1baw_A 3bqv_A Back     alignment and structure
>1iby_A Nitrosocyanin; RED copper, cupredoxin, beta hairpin, metal binding protein; 1.65A {Nitrosomonas europaea} SCOP: b.6.1.4 PDB: 1ibz_A 1ic0_A Back     alignment and structure
>3c75_A Amicyanin; copper proteins, electron transfer complex, TTQ, electron transport, oxidoreductase, periplasm, transport, metal- binding; HET: TRQ; 2.50A {Paracoccus versutus} Back     alignment and structure
>2dv6_A Nitrite reductase; electron transfer, reduction, denitrification, oxidoreductase; 2.20A {Hyphomicrobium denitrificans} Back     alignment and structure
>2cal_A Rusticyanin; iron respiratory electron transport chain, blue copper protein, copper, electron transport, metal- binding, periplasmic; 1.1A {Thiobacillus ferrooxidans} PDB: 1cur_A 1gy2_A 1a3z_A 1e30_A 1gy1_A 1rcy_A 1a8z_A 2cak_A Back     alignment and structure
>1id2_A Amicyanin; beta barrel, type-1 blue copper protein, electron transfer protein, electron transport; 2.15A {Paracoccus versutus} SCOP: b.6.1.1 Back     alignment and structure
>1pcs_A Plastocyanin; electron transport; 2.15A {Synechocystis SP} SCOP: b.6.1.1 PDB: 1m9w_A 1j5c_A 1j5d_A 1jxd_A 1jxf_A Back     alignment and structure
>3gdc_A Multicopper oxidase; beta sandwich, plasmid, oxidoreductase; 1.80A {Arthrobacter SP} Back     alignment and structure
>2ux6_A Pseudoazurin; type-1 copper, metal-binding, redox potential, copper, transport, cupredoxin, periplasmic, electron transport; 1.3A {Achromobacter cycloclastes} PDB: 2ux7_A 2uxf_A 2uxg_A 1bqk_A 1bqr_A 1zia_A 1zib_A 2jkw_A Back     alignment and structure
>1bxv_A Plastocyanin; copper protein, electron transfer; 1.80A {Synechococcus elongatus pcc 7942} SCOP: b.6.1.1 PDB: 1bxu_A Back     alignment and structure
>1mzy_A Copper-containing nitrite reductase; mutant M182T, gating mechanism, electron transfer, oxidoreductase; 1.46A {Rhodobacter sphaeroides} SCOP: b.6.1.3 b.6.1.3 PDB: 1mzz_A 1n70_A 1zv2_A 2a3t_A 2dws_A 2dwt_A 2dy2_A Back     alignment and structure
>1kdj_A Plastocyanin; electron transfer, photosystem, PAI-PAI stacking; 1.70A {Adiantum capillus-veneris} SCOP: b.6.1.1 PDB: 1kdi_A 2bz7_A 2bzc_A Back     alignment and structure
>3erx_A Pseudoazurin; copper protein, high-resolution, C electron transport, metal-binding, periplasm, transport; 1.25A {Paracoccus pantotrophus} PDB: 1adw_A Back     alignment and structure
>3ef4_A Pseudoazurin, blue copper protein; electron transfer, electron transport; HET: PO4; 1.18A {Hyphomicrobium denitrificans} Back     alignment and structure
>1byp_A Protein (plastocyanin); electron transfer, photosynthesis, acidic patch, double mutant, electron transport; 1.75A {Silene latifolia subsp} SCOP: b.6.1.1 PDB: 1pla_A 1plb_A Back     alignment and structure
>2zoo_A Probable nitrite reductase; electron transfer, electron transport, heme, iron, metal-binding, oxidoreductase, transport; HET: SUC HEM; 1.95A {Pseudoalteromonas haloplanktis TAC125} Back     alignment and structure
>1pmy_A Pseudoazurin; electron transfer(cuproprotein); 1.50A {Methylobacterium extorquens} SCOP: b.6.1.1 Back     alignment and structure
>1paz_A Pseudoazurin precursor; electron transfer(cuproprotein); 1.55A {Alcaligenes faecalis} SCOP: b.6.1.1 PDB: 1pza_A 1pzb_A 1pzc_A 2p80_D 3paz_A 8paz_A 4paz_A 5paz_A 6paz_A 7paz_A 1py0_A* Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 332 ubiquinol oxidase, subunit II [Candidatus Liberibacter
d1cyxa_158 b.6.1.2 (A:) Quinol oxidase (CyoA) {Escherichia coli [T 1e-31
d1fftb291 f.17.2.1 (B:27-117) Cytochrome O ubiquinol oxidase, sub 3e-23
d3dtub1152 b.6.1.2 (B:130-281) Cytochrome c oxidase {Rhodobacter s 1e-17
d3ehbb1145 b.6.1.2 (B:108-252) Cytochrome c oxidase {Paracoccus de 3e-17
d1v54b1137 b.6.1.2 (B:91-227) Cytochrome c oxidase {Cow (Bos tauru 2e-16
d2cuaa_122 b.6.1.2 (A:) Cytochrome c oxidase {Thermus thermophilus 5e-14
>d1cyxa_ b.6.1.2 (A:) Quinol oxidase (CyoA) {Escherichia coli [TaxId: 562]} Length = 158 Back     information, alignment and structure

class: All beta proteins
fold: Cupredoxin-like
superfamily: Cupredoxins
family: Periplasmic domain of cytochrome c oxidase subunit II
domain: Quinol oxidase (CyoA)
species: Escherichia coli [TaxId: 562]
 Score =  130 bits (328), Expect = 1e-31
 Identities = 65/155 (41%), Positives = 98/155 (63%), Gaps = 2/155 (1%)

Query: 140 KPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPGLAGQIY 199
           KP+ +EVV++DWKW F+ PEQ +A +NE+  P + P+ F++T++SVM+SF+IP L  QIY
Sbjct: 1   KPITIEVVSMDWKWFFIYPEQGIATVNEIAFPANTPVYFKVTSNSVMHSFFIPRLGSQIY 60

Query: 200 AMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYG-KSEKGFEDWISKVKRQG-T 257
           AMAGM+T+LH + N+ G Y G  A   G G S M+FK         F+ W++K K+   T
Sbjct: 61  AMAGMQTRLHLIANEPGTYDGICAEICGPGHSGMKFKAIATPDRAAFDQWVAKAKQSPNT 120

Query: 258 FLNRQEYLLLKKPSERDSVRYFSPIEKGLYYSILN 292
             +   +  L  PSE + V YFS ++  L+  ++N
Sbjct: 121 MSDMAAFEKLAAPSEYNQVEYFSNVKPDLFADVIN 155


>d1fftb2 f.17.2.1 (B:27-117) Cytochrome O ubiquinol oxidase, subunit II {Escherichia coli [TaxId: 562]} Length = 91 Back     information, alignment and structure
>d3dtub1 b.6.1.2 (B:130-281) Cytochrome c oxidase {Rhodobacter sphaeroides [TaxId: 1063]} Length = 152 Back     information, alignment and structure
>d3ehbb1 b.6.1.2 (B:108-252) Cytochrome c oxidase {Paracoccus denitrificans [TaxId: 266]} Length = 145 Back     information, alignment and structure
>d1v54b1 b.6.1.2 (B:91-227) Cytochrome c oxidase {Cow (Bos taurus) [TaxId: 9913]} Length = 137 Back     information, alignment and structure
>d2cuaa_ b.6.1.2 (A:) Cytochrome c oxidase {Thermus thermophilus, ba3 type [TaxId: 274]} Length = 122 Back     information, alignment and structure

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target332 ubiquinol oxidase, subunit II [Candidatus Liberibacter
d1cyxa_158 Quinol oxidase (CyoA) {Escherichia coli [TaxId: 562]} 100.0
d3ehbb1145 Cytochrome c oxidase {Paracoccus denitrificans [TaxId: 100.0
d1v54b1137 Cytochrome c oxidase {Cow (Bos taurus) [TaxId: 9913]} 100.0
d3dtub1152 Cytochrome c oxidase {Rhodobacter sphaeroides [TaxId: 1 100.0
d2cuaa_122 Cytochrome c oxidase {Thermus thermophilus, ba3 type [T 99.93
d1qnia1131 Nitrous oxide reductase, C-terminal domain {Pseudomonas 99.83
d1fwxa1132 Nitrous oxide reductase, C-terminal domain {Paracoccus 99.7
d1qhqa_139 Auracyanin {Chloroflexus aurantiacus [TaxId: 1108]} 97.33
d2ccwa1129 Azurin {Alcaligenes xylosoxidans, NCIMB (11015), differ 96.07
d1cuoa_129 Azurin {Methylomonas sp. j [TaxId: 32038]} 95.52
d1jzga_128 Azurin {Pseudomonas aeruginosa [TaxId: 287]} 95.14
d1nwpa_128 Azurin {Pseudomonas putida [TaxId: 303]} 94.69
d2ov0a1105 Amicyanin {Paracoccus denitrificans [TaxId: 266]} 94.33
d1fftb291 Cytochrome O ubiquinol oxidase, subunit II {Escherichia 99.81
d3dtub2100 Bacterial aa3 type cytochrome c oxidase subunit II {Rho 99.48
d3ehbb2107 Bacterial aa3 type cytochrome c oxidase subunit II {Par 99.42
d1v54b290 Mitochondrial cytochrome c oxidase, subunit II {Cow (Bo 98.77
d1ibya_112 Red copper protein nitrosocyanin {Nitrosomonas europaea 99.42
d1e30a_153 Rusticyanin {Thiobacillus ferrooxidans [TaxId: 920]} 95.88
d1id2a_106 Amicyanin {Paracoccus versutus (Thiobacillus versutus) 95.09
d2jxma197 Plastocyanin {Photosynthetic prokaryote (Prochlorothrix 94.43
d1bqka_124 Pseudoazurin {Achromobacter cycloclastes [TaxId: 223]} 94.42
d1pcsa_98 Plastocyanin {Cyanobacterium (Synechocystis sp.), pcc 6 92.6
d1bypa_99 Plastocyanin {White campion (Silene pratensis) [TaxId: 92.29
d1adwa_123 Pseudoazurin {Thiosphaera pantotropha [TaxId: 82367]} 92.2
d2q5ba1105 Plastocyanin {Cyanobacterium (Phormidium laminosum) [Ta 92.12
d1bxua_91 Plastocyanin {Cyanobacterium (Synechocystis sp.), pcc 7 91.44
d1kcwa2146 Ceruloplasmin {Human (Homo sapiens) [TaxId: 9606]} 91.3
d1kdja_102 Plastocyanin {Fern (Adiantum capillus-veneris) [TaxId: 90.23
d1pmya_123 Pseudoazurin {Methylobacterium extorquens, strain am1 [ 92.61
>d1cyxa_ b.6.1.2 (A:) Quinol oxidase (CyoA) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: All beta proteins
fold: Cupredoxin-like
superfamily: Cupredoxins
family: Periplasmic domain of cytochrome c oxidase subunit II
domain: Quinol oxidase (CyoA)
species: Escherichia coli [TaxId: 562]
Probab=100.00  E-value=0  Score=388.84  Aligned_cols=156  Identities=41%  Similarity=0.832  Sum_probs=151.6

Q ss_pred             CCEEEEEEEEEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEECCCCHHCCCHHHCCEECCCCCCCEEEEEEECCCEEEE
Q ss_conf             86689999984369999626787743068963698289999835810110220107403116985148999942774896
Q gi|254780474|r  140 KPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNKKGAYS  219 (332)
Q Consensus       140 ~~l~I~V~a~qW~W~F~YP~~giatvneL~lPv~~pV~f~ltS~DViHSF~IP~l~~k~daiPG~~t~l~~~a~~~G~y~  219 (332)
                      ||++|+|+|+||+|+|+||++|+.|+|||++|+|+||+|.|||.|||||||||+|++|+|+||||.|++||+++++|+|+
T Consensus         1 KP~~I~V~g~QW~W~f~Yp~~~i~t~n~l~lP~g~pV~~~ltS~DViHsF~vP~l~~k~daiPG~~~~~~~~~~~~G~y~   80 (158)
T d1cyxa_           1 KPITIEVVSMDWKWFFIYPEQGIATVNEIAFPANTPVYFKVTSNSVMHSFFIPRLGSQIYAMAGMQTRLHLIANEPGTYD   80 (158)
T ss_dssp             CCEEEEEEEETTEEEEEETTTTEEEESEEEEETTSCEEEEEEESSSCEEEEEGGGTEEEEECTTCCEEEEECCSSSEEEE
T ss_pred             CCEEEEEEEEECEEEEECCCCCCCCEEEEEEECCCEEEEEEECCCCCHHHHHHHCCEEECCCCCCEEEEEEEECCCCCEE
T ss_conf             98899999995408988089996512128960797689999759841045664100012027986055665505887388


Q ss_pred             EECCCCCCCCCCCCEEEEEEC-CHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHHHCCCCEEECCCCCCHHHHHHCCCC
Q ss_conf             661332657611365899970-8899999999986072456-989999976102126321720478354268731524
Q gi|254780474|r  220 GFSANYSGRGFSHMRFKFYGK-SEKGFEDWISKVKRQGTFL-NRQEYLLLKKPSERDSVRYFSPIEKGLYYSILNLCV  295 (332)
Q Consensus       220 G~cae~cG~ghs~M~f~v~v~-s~~~f~~Wv~~~ka~~~~l-~~~~y~~l~~ps~~~~~~~f~~~~~~lf~~i~~~~~  295 (332)
                      |+|+||||.||+.|+|+++++ ++++|++|++++|+++.++ +.++|++|++|++.+++++|+++.|+||+.|+++||
T Consensus        81 g~Cae~CG~gH~~M~~~v~vv~~~~~f~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~Lf~~vv~~~~  158 (158)
T d1cyxa_          81 GICAEICGPGHSGMKFKAIATPDRAAFDQWVAKAKQSPNTMSDMAAFEKLAAPSEYNQVEYFSNVKPDLFADVINKFM  158 (158)
T ss_dssp             EEECSCCSTTSTTCCEEEEEESSHHHHHHHHHHHHTCSCCBCSHHHHHHHHSCCSSCCCEEESCBCTTHHHHHHTTTC
T ss_pred             EECHHHCCCCCCCCCEEEEEECCHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHCC
T ss_conf             871432071224583699997999999999998673854454256799986786778815642689826999998519



>d3ehbb1 b.6.1.2 (B:108-252) Cytochrome c oxidase {Paracoccus denitrificans [TaxId: 266]} Back     information, alignment and structure
>d1v54b1 b.6.1.2 (B:91-227) Cytochrome c oxidase {Cow (Bos taurus) [TaxId: 9913]} Back     information, alignment and structure
>d3dtub1 b.6.1.2 (B:130-281) Cytochrome c oxidase {Rhodobacter sphaeroides [TaxId: 1063]} Back     information, alignment and structure
>d2cuaa_ b.6.1.2 (A:) Cytochrome c oxidase {Thermus thermophilus, ba3 type [TaxId: 274]} Back     information, alignment and structure
>d1qnia1 b.6.1.4 (A:451-581) Nitrous oxide reductase, C-terminal domain {Pseudomonas nautica [TaxId: 2743]} Back     information, alignment and structure
>d1fwxa1 b.6.1.4 (A:452-581) Nitrous oxide reductase, C-terminal domain {Paracoccus denitrificans [TaxId: 266]} Back     information, alignment and structure
>d1qhqa_ b.6.1.1 (A:) Auracyanin {Chloroflexus aurantiacus [TaxId: 1108]} Back     information, alignment and structure
>d2ccwa1 b.6.1.1 (A:1-129) Azurin {Alcaligenes xylosoxidans, NCIMB (11015), different isoforms [TaxId: 85698]} Back     information, alignment and structure
>d1cuoa_ b.6.1.1 (A:) Azurin {Methylomonas sp. j [TaxId: 32038]} Back     information, alignment and structure
>d1jzga_ b.6.1.1 (A:) Azurin {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1nwpa_ b.6.1.1 (A:) Azurin {Pseudomonas putida [TaxId: 303]} Back     information, alignment and structure
>d2ov0a1 b.6.1.1 (A:1-105) Amicyanin {Paracoccus denitrificans [TaxId: 266]} Back     information, alignment and structure
>d1fftb2 f.17.2.1 (B:27-117) Cytochrome O ubiquinol oxidase, subunit II {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d3dtub2 f.17.2.1 (B:30-129) Bacterial aa3 type cytochrome c oxidase subunit II {Rhodobacter sphaeroides [TaxId: 1063]} Back     information, alignment and structure
>d3ehbb2 f.17.2.1 (B:1-107) Bacterial aa3 type cytochrome c oxidase subunit II {Paracoccus denitrificans [TaxId: 266]} Back     information, alignment and structure
>d1v54b2 f.17.2.1 (B:1-90) Mitochondrial cytochrome c oxidase, subunit II {Cow (Bos taurus) [TaxId: 9913]} Back     information, alignment and structure
>d1ibya_ b.6.1.4 (A:) Red copper protein nitrosocyanin {Nitrosomonas europaea [TaxId: 915]} Back     information, alignment and structure
>d1e30a_ b.6.1.1 (A:) Rusticyanin {Thiobacillus ferrooxidans [TaxId: 920]} Back     information, alignment and structure
>d1id2a_ b.6.1.1 (A:) Amicyanin {Paracoccus versutus (Thiobacillus versutus) [TaxId: 34007]} Back     information, alignment and structure
>d2jxma1 b.6.1.1 (A:1-97) Plastocyanin {Photosynthetic prokaryote (Prochlorothrix hollandica) [TaxId: 1223]} Back     information, alignment and structure
>d1bqka_ b.6.1.1 (A:) Pseudoazurin {Achromobacter cycloclastes [TaxId: 223]} Back     information, alignment and structure
>d1pcsa_ b.6.1.1 (A:) Plastocyanin {Cyanobacterium (Synechocystis sp.), pcc 6803 [TaxId: 1143]} Back     information, alignment and structure
>d1bypa_ b.6.1.1 (A:) Plastocyanin {White campion (Silene pratensis) [TaxId: 52853]} Back     information, alignment and structure
>d1adwa_ b.6.1.1 (A:) Pseudoazurin {Thiosphaera pantotropha [TaxId: 82367]} Back     information, alignment and structure
>d2q5ba1 b.6.1.1 (A:1-105) Plastocyanin {Cyanobacterium (Phormidium laminosum) [TaxId: 32059]} Back     information, alignment and structure
>d1bxua_ b.6.1.1 (A:) Plastocyanin {Cyanobacterium (Synechocystis sp.), pcc 7942 [TaxId: 1143]} Back     information, alignment and structure
>d1kcwa2 b.6.1.3 (A:193-338) Ceruloplasmin {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1kdja_ b.6.1.1 (A:) Plastocyanin {Fern (Adiantum capillus-veneris) [TaxId: 13818]} Back     information, alignment and structure
>d1pmya_ b.6.1.1 (A:) Pseudoazurin {Methylobacterium extorquens, strain am1 [TaxId: 408]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 332 ubiquinol oxidase, subunit II [Candidatus Liberiba
1fft_B_119-315197 (B:119-315) Ubiquinol oxidase; electron transport, 2e-29
1cyx_A_205 (A:) CYOA; electron transport; 2.30A {Escherichia 4e-25
2gsm_B_103-262160 (B:103-262) Cytochrome C oxidase subunit 2; transm 4e-16
3hb3_B_137-298162 (B:137-298) Cytochrome C oxidase subunit 2; electr 6e-12
1v54_B_92-227136 (B:92-227) Cytochrome C oxidase polypeptide II; ox 2e-09
1xme_B_55-168114 (B:55-168) Cytochrome C oxidase polypeptide II; cy 3e-09
2cua_A_135 (A:) Protein (CUA); CUA center, electron transport 1e-07
1qni_A_453-581129 (A:453-581) Nitrous-oxide reductase; oxidoreductas 7e-07
1fwx_A_45-81_463-595170 (A:45-81,A:463-595) Nitrous oxide reductase; beta- 2e-05
>1fft_B (B:119-315) Ubiquinol oxidase; electron transport, cytochrome oxidase, membrane protein, oxidoreductase; HET: HEM HEO; 3.50A {Escherichia coli}Length = 197 Back     alignment and structure
 Score =  124 bits (311), Expect = 2e-29
 Identities = 75/185 (40%), Positives = 113/185 (61%), Gaps = 2/185 (1%)

Query: 138 NSKPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPGLAGQ 197
           + KP+ +EVV++DWKW F+ PEQ +A +NE+  P + P+ F++T++SVMNSF+IP L  Q
Sbjct: 5   DEKPITIEVVSMDWKWFFIYPEQGIATVNEIAFPANTPVYFKVTSNSVMNSFFIPRLGSQ 64

Query: 198 IYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKS-EKGFEDWISKVKRQG 256
           IYAMAGM+T+LH + N+ G Y G SA+YSG GFS M+FK         F+ W++K K+  
Sbjct: 65  IYAMAGMQTRLHLIANEPGTYDGISASYSGPGFSGMKFKAIATPDRAAFDQWVAKAKQSP 124

Query: 257 TFLNRQE-YLLLKKPSERDSVRYFSPIEKGLYYSILNLCVHPGKICMDEMMRIDALGGGG 315
             ++    +  L  PSE + V YFS ++  L+  ++N  +  GK         +     G
Sbjct: 125 NTMSDMAAFEKLAAPSEYNQVEYFSNVKPDLFADVINKFMAHGKSMDMTQPEGEHSAHEG 184

Query: 316 MRGID 320
           M G+D
Sbjct: 185 MEGMD 189


>1cyx_A (A:) CYOA; electron transport; 2.30A {Escherichia coli}Length = 205 Back     alignment and structure
>2gsm_B (B:103-262) Cytochrome C oxidase subunit 2; transmembrane protein complex, oxidoreductase; HET: DMU HEA TRD; 2.00A {Rhodobacter sphaeroides}Length = 160 Back     alignment and structure
>3hb3_B (B:137-298) Cytochrome C oxidase subunit 2; electron transfer, proton transfer, proton pumping, membrane protein, cell inner membrane, cell membrane, copper; HET: HEA LDA LMT; 2.25A {Paracoccus denitrificans} PDB: 1ar1_B* 3ehb_B* 1qle_B*Length = 162 Back     alignment and structure
>1v54_B (B:92-227) Cytochrome C oxidase polypeptide II; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus}Length = 136 Back     alignment and structure
>1xme_B (B:55-168) Cytochrome C oxidase polypeptide II; cytochrome oxidase, heme, heme-AS, integral membrane protein, oxidoreductase; HET: BNG HEM HAS; 2.30A {Thermus thermophilus}Length = 114 Back     alignment and structure
>2cua_A (A:) Protein (CUA); CUA center, electron transport; 1.60A {Thermus thermophilus}Length = 135 Back     alignment and structure
>1qni_A (A:453-581) Nitrous-oxide reductase; oxidoreductase, denitrification, MAD, electron transfer; 2.40A {Pseudomonas nautica}Length = 129 Back     alignment and structure
>1fwx_A (A:45-81,A:463-595) Nitrous oxide reductase; beta-propeller domain, cupredoxin domain, CUZ site, CUA site, oxidoreductase; 1.60A {Paracoccus denitrificans}Length = 170 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target332 ubiquinol oxidase, subunit II [Candidatus Liberibacter
1cyx_A_205 CYOA; electron transport; 2.30A {Escherichia coli} 100.0
1fft_B_119-315197 Ubiquinol oxidase; electron transport, cytochrome 100.0
3hb3_B_137-298162 Cytochrome C oxidase subunit 2; electron transfer, 100.0
2gsm_B_103-262160 Cytochrome C oxidase subunit 2; transmembrane prot 100.0
1v54_B_92-227136 Cytochrome C oxidase polypeptide II; oxidoreductas 100.0
1xme_B_55-168114 Cytochrome C oxidase polypeptide II; cytochrome ox 99.98
2cua_A_135 Protein (CUA); CUA center, electron transport; 1.6 99.97
1qni_A_453-581129 Nitrous-oxide reductase; oxidoreductase, denitrifi 99.95
1fwx_A_45-81_463-595170 Nitrous oxide reductase; beta-propeller domain, cu 99.85
1paz_A_123 Pseudoazurin precursor; electron transfer(cupropro 98.65
1pmy_A_123 Pseudoazurin; electron transfer(cuproprotein); 1.5 98.52
3erx_A_123 Pseudoazurin; copper protein, high-resolution,, co 98.41
1id2_A_106 Amicyanin; beta barrel, type-1 blue copper protein 97.7
2ov0_A_105 Amicyanin; beta-sandwich, electron transport; 0.75 97.12
2ux6_A_122 Pseudoazurin; type-1 copper, metal-binding, redox 96.19
1b3i_A_97 PETE protein, protein (plastocyanin); electron tra 95.89
2dv6_A_1-146146 Nitrite reductase; electron transfer, reduction, d 95.79
1sdd_B_188-336149 Coagulation factor V; copper-binding protein, cofa 93.39
1iby_A_112 Nitrosocyanin; RED copper, cupredoxin, beta hairpi 99.94
3ef4_A_124 Pseudoazurin, blue copper protein; electron transf 98.19
1bxv_A_91 Plastocyanin; copper protein, electron transfer; 1 97.18
1iuz_A_98 Plastocyanin; electron transport; 1.60A {Ulva pert 96.61
3fsa_A_125 Azurin; copper, cupredoxin fold, metal-binding, pr 96.36
2aan_A_139 Auracyanin A; cupredoxin fold, electron transport; 95.87
3c75_A_132 Amicyanin; copper proteins, electron transfer comp 95.55
1cuo_A_129 Protein (azurin ISO-2); beta barrel, periplasmic, 95.55
1qhq_A_140 Protein (auracyanin); electron transfer, cupredoxi 94.81
1kdj_A_102 Plastocyanin; electron transfer, photosystem, PAI- 94.78
1byp_A_99 Protein (plastocyanin); electron transfer, photosy 94.67
1plc_A_99 Plastocyanin; electron transport; 1.33A {Populus n 94.66
2j5w_A_213-363151 Ceruloplasmin, ferroxidase; oxidoreductase, plasma 92.05
2plt_A_98 Plastocyanin; electron transport; 1.50A {Chlamydom 91.93
2gim_A_106 Plastocyanin; beta sheet, Cu, helix, electron tran 91.69
1mzy_A_160-333174 Copper-containing nitrite reductase; mutant M182T, 91.48
1mzy_A_1-159159 Copper-containing nitrite reductase; mutant M182T, 91.26
3cvb_A_105 Plastocyanin; cupredoxin, SELF assembly, copper, e 90.36
3hb3_B_1-136136 Cytochrome C oxidase subunit 2; electron transfer, 99.39
>1cyx_A (A:) CYOA; electron transport; 2.30A {Escherichia coli} Back     alignment and structure
Probab=100.00  E-value=0  Score=414.41  Aligned_cols=201  Identities=38%  Similarity=0.717  Sum_probs=190.5

Q ss_pred             HHHHCCCCCCHHCCCCCCCCCCCCCEEEEEEEEEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEECCCCHHCCCHHHCC
Q ss_conf             77513444200001244678888866899999843699996267877430689636982899998358101102201074
Q gi|254780474|r  117 THRMDPYAPLERISESKSIAKNSKPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPGLAG  196 (332)
Q Consensus       117 ~~~ldp~~p~~~~~~~~~~~~~~~~l~I~V~a~qW~W~F~YP~~giatvneL~lPv~~pV~f~ltS~DViHSF~IP~l~~  196 (332)
                      |+.|+|++|+         ..++++++|+|+|+||+|.|+||++++.++|+|+||+|+||+|+|||.|||||||||+|++
T Consensus         1 T~a~~~~~~~---------~~~~~~l~I~v~g~qW~W~f~Yp~~~~~~~n~l~iP~~~~V~~~ltS~DViHsF~iP~l~~   71 (205)
T 1cyx_A            1 THALEPSKPL---------AHDEKPITIEVVSMDWKWFFIYPEQGIATVNEIAFPANTPVYFKVTSNSVMHSFFIPRLGS   71 (205)
T ss_dssp             -----------------------CCEEEEEEEETTEEEEEETTTTEEEESEEEEETTSCEEEEEEESSSCEEEEEGGGTE
T ss_pred             CCCCCCCCCC---------CCCCCCEEEEEEEEECEEEEEECCCCCCCCCEEEECCCCEEEEEEECCCCCHHHHHHHHHH
T ss_conf             9778989988---------8899988999999944089880899964011388506976899997687411243432210


Q ss_pred             EECCCCCCCEEEEEEECCCEEEEEECCCCCCCCCCCCEEEEEECC-HHHHHHHHHHHHCCCCCC-CHHHHHHHHHHHHCC
Q ss_conf             031169851489999427748966613326576113658999708-899999999986072456-989999976102126
Q gi|254780474|r  197 QIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKS-EKGFEDWISKVKRQGTFL-NRQEYLLLKKPSERD  274 (332)
Q Consensus       197 k~daiPG~~t~l~~~a~~~G~y~G~cae~cG~ghs~M~f~v~v~s-~~~f~~Wv~~~ka~~~~l-~~~~y~~l~~ps~~~  274 (332)
                      |+|+||||.|++||+++++|+|+|+|+||||.|||.|+|+|+|++ +++|++|++++|+.+..+ +.++|+.++.|++.+
T Consensus        72 k~daiPG~~~~~~~~~~~~G~y~g~Cae~CG~~Hs~M~~~v~vv~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (205)
T 1cyx_A           72 QIYAMAGMQTRLHLIANEPGTYDGICAEICGPGHSGMKFKAIATPDRAAFDQWVAKAKQSPNTMSDMAAFEKLAAPSEYN  151 (205)
T ss_dssp             EEEECTTCCEEEEECCSSSEEEEEEECSCCSTTSTTCCEEEEEESSHHHHHHHHHHHHTCSCCBCSHHHHHHHHSCCSSC
T ss_pred             EECCCCCCCEEEEECCCCCCCEEEEEHHHCCCCCCCCCEEEEEECCHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCC
T ss_conf             01006996047764047764306862112060223583699998999999999999763832354256899987776647


Q ss_pred             CCEEECCCCCCHHHHHHCCCCCCCCCCCCHHHCCCCCCCCCHHHCCCCHHHH
Q ss_conf             3217204783542687315244488566021024666885234401100112
Q gi|254780474|r  275 SVRYFSPIEKGLYYSILNLCVHPGKICMDEMMRIDALGGGGMRGIDRHSLIY  326 (332)
Q Consensus       275 ~~~~f~~~~~~lf~~i~~~~~~~~~~~~~~~m~~~~~~g~~~~~~~~~~~~~  326 (332)
                      +.+|++++.|+||+.+++++++.|+.+.+..+..++.++.+|+++|+...+.
T Consensus       152 ~~~~~~~~~p~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~m~~~~~  203 (205)
T 1cyx_A          152 QVEYFSNVKPDLFADVINKFMAHGKSMDMTQPEGEHSAHEGMEGMDMSHAES  203 (205)
T ss_dssp             CCEEESCBCTTHHHHHHTTTC-------------------------------
T ss_pred             CCEEEECCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             6126613581357789998753486655777412444468998736333334



>1fft_B (B:119-315) Ubiquinol oxidase; electron transport, cytochrome oxidase, membrane protein, oxidoreductase; HET: HEM HEO; 3.50A {Escherichia coli} Back     alignment and structure
>3hb3_B (B:137-298) Cytochrome C oxidase subunit 2; electron transfer, proton transfer, proton pumping, membrane protein, cell inner membrane, cell membrane, copper; HET: HEA LDA LMT; 2.25A {Paracoccus denitrificans} PDB: 1ar1_B* 3ehb_B* 1qle_B* Back     alignment and structure
>2gsm_B (B:103-262) Cytochrome C oxidase subunit 2; transmembrane protein complex, oxidoreductase; HET: DMU HEA TRD; 2.00A {Rhodobacter sphaeroides} Back     alignment and structure
>1v54_B (B:92-227) Cytochrome C oxidase polypeptide II; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} Back     alignment and structure
>1xme_B (B:55-168) Cytochrome C oxidase polypeptide II; cytochrome oxidase, heme, heme-AS, integral membrane protein, oxidoreductase; HET: BNG HEM HAS; 2.30A {Thermus thermophilus} Back     alignment and structure
>2cua_A (A:) Protein (CUA); CUA center, electron transport; 1.60A {Thermus thermophilus} Back     alignment and structure
>1qni_A (A:453-581) Nitrous-oxide reductase; oxidoreductase, denitrification, MAD, electron transfer; 2.40A {Pseudomonas nautica} Back     alignment and structure
>1fwx_A (A:45-81,A:463-595) Nitrous oxide reductase; beta-propeller domain, cupredoxin domain, CUZ site, CUA site, oxidoreductase; 1.60A {Paracoccus denitrificans} Back     alignment and structure
>1paz_A (A:) Pseudoazurin precursor; electron transfer(cuproprotein); 1.55A {Alcaligenes faecalis} Back     alignment and structure
>1pmy_A (A:) Pseudoazurin; electron transfer(cuproprotein); 1.50A {Methylobacterium extorquens} Back     alignment and structure
>3erx_A (A:) Pseudoazurin; copper protein, high-resolution,, copper, electron transport, metal-binding, periplasm, transport; 1.25A {Paracoccus pantotrophus} PDB: 1adw_A Back     alignment and structure
>1id2_A (A:) Amicyanin; beta barrel, type-1 blue copper protein, electron transfer protein, electron transport; 2.15A {Paracoccus versutus} Back     alignment and structure
>2ov0_A (A:) Amicyanin; beta-sandwich, electron transport; 0.75A {Paracoccus denitrificans} Back     alignment and structure
>2ux6_A (A:) Pseudoazurin; type-1 copper, metal-binding, redox potential, copper, transport, cupredoxin, periplasmic, electron transport; 1.3A {Achromobacter cycloclastes} PDB: 2ux7_A 2uxf_A 2uxg_A 1bqk_A 1bqr_A 1zia_A 1zib_A 2jkw_A Back     alignment and structure
>1b3i_A (A:) PETE protein, protein (plastocyanin); electron transport, type I copper protein, photosynthesis; NMR {Prochlorothrix hollandica} Back     alignment and structure
>2dv6_A (A:1-146) Nitrite reductase; electron transfer, reduction, denitrification, oxidoreductase; 2.20A {Hyphomicrobium denitrificans} Back     alignment and structure
>1sdd_B (B:188-336) Coagulation factor V; copper-binding protein, cofactor, blood clotting; HET: NAG NDG; 2.80A {Bos taurus} Back     alignment and structure
>1iby_A (A:) Nitrosocyanin; RED copper, cupredoxin, beta hairpin, metal binding protein; 1.65A {Nitrosomonas europaea} Back     alignment and structure
>3ef4_A (A:) Pseudoazurin, blue copper protein; electron transfer, electron transport; HET: PO4; 1.18A {Hyphomicrobium denitrificans} Back     alignment and structure
>1bxv_A (A:) Plastocyanin; copper protein, electron transfer; 1.80A {Synechococcus SP} Back     alignment and structure
>1iuz_A (A:) Plastocyanin; electron transport; 1.60A {Ulva pertusa} Back     alignment and structure
>3fsa_A (A:) Azurin; copper, cupredoxin fold, metal-binding, protein-protein interaction, metal binding protein; 0.98A {Pseudomonas aeruginosa} PDB: 3fs9_A 2fta_A* 2hx7_A 2hx8_A 2hx9_A 2hxa_A 1cc3_A 2ft6_A 2ft7_A 2ft8_A 1azn_A 2iwe_A* 2ghz_A 2gi0_A 1jzg_A* 1azu_A* 1bex_A 1e5z_A 1e5y_A 1e67_A ... Back     alignment and structure
>2aan_A (A:) Auracyanin A; cupredoxin fold, electron transport; 1.85A {Chloroflexus aurantiacus} Back     alignment and structure
>3c75_A (A:) Amicyanin; copper proteins, electron transfer complex, TTQ, electron transport, oxidoreductase, periplasm, transport, metal- binding; HET: TRQ; 2.50A {Paracoccus versutus} Back     alignment and structure
>1cuo_A (A:) Protein (azurin ISO-2); beta barrel, periplasmic, electron transport; 1.60A {Methylomonas SP} Back     alignment and structure
>1qhq_A (A:) Protein (auracyanin); electron transfer, cupredoxin, blue copper protein, azurin- like, thermophIle; 1.55A {Chloroflexus aurantiacus} Back     alignment and structure
>1kdj_A (A:) Plastocyanin; electron transfer, photosystem, PAI-PAI stacking; 1.70A {Adiantum capillus-veneris} Back     alignment and structure
>1byp_A (A:) Protein (plastocyanin); electron transfer, photosynthesis, acidic patch, double mutant; 1.75A {Silene pratensis} Back     alignment and structure
>1plc_A (A:) Plastocyanin; electron transport; 1.33A {Populus nigra} Back     alignment and structure
>2j5w_A (A:213-363) Ceruloplasmin, ferroxidase; oxidoreductase, plasma protein, copper transport, copper, transport, polymorphism, glycoprotein, multi-copper oxidase; HET: NAG; 2.80A {Homo sapiens} Back     alignment and structure
>2plt_A (A:) Plastocyanin; electron transport; 1.50A {Chlamydomonas reinhardtii} Back     alignment and structure
>2gim_A (A:) Plastocyanin; beta sheet, Cu, helix, electron transport; 1.60A {Anabaena variabilis} Back     alignment and structure
>1mzy_A (A:160-333) Copper-containing nitrite reductase; mutant M182T, gating mechanism, electron transfer, oxidoreductase; 1.46A {Rhodobacter sphaeroides} Back     alignment and structure