Citrus Sinensis ID: 035248

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------7
Protein Sequence
MSETEVPFRPREKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNMSHGIGKKE
Secondary Structure (PSIPRED)
cccccccccHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHEEccEEEccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccHHHHHHHHHHHHccccccEccccccHHHHHHHHHHHHHHHHHHHHccEEEccccccccc
Coil and Loop (DISEMBL)
msetevpfrpreKLLEKQKHFQSIHkhtylkgpmdkiTSVAIPIALAASSLYLIGRGiynmshgigkke
Flexible Loop (DISEMBL)
msetevpfrpreklleKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNmshgigkke
Low Complexity Region (SEG)
MSETEVPFRPREKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNMSHGIGKKE
Disordered region (IsUnstruct)
********************FQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNMS*******
Disordered Region (DISOPRED)
*****VP**PREKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNM*HG*****
Disordered Region (DISEMBL)
********RPREKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNMSHGIGKKE
Disordered Region (DISPRO)
*****VPFRPREKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNMS*******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHoooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhoooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSETEVPFRPREKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNMSHGIGKKE
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

No hits with e-value below 0.001 by BLAST

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	69
449456118	69	PREDICTED: uncharacterized protein LOC10	1.0	1.0	0.927	3e-29
449456116	74	PREDICTED: uncharacterized protein LOC10	1.0	0.932	0.927	3e-29
356542720	67	PREDICTED: uncharacterized protein LOC10	0.956	0.985	0.863	4e-27
356543560	67	PREDICTED: uncharacterized protein LOC10	0.956	0.985	0.893	4e-27
356539300	67	PREDICTED: uncharacterized protein LOC10	0.956	0.985	0.863	6e-27
224056767	68	predicted protein [Populus trichocarpa]	0.956	0.970	0.863	7e-27
224115602	68	predicted protein [Populus trichocarpa]	0.956	0.970	0.893	7e-27
255625953	67	unknown [Glycine max]	0.956	0.985	0.863	7e-27
297804048	68	hypothetical protein ARALYDRAFT_329492 [	0.956	0.970	0.878	1e-26
18415628	68	Acytochrome-c oxidase/ electron carrier	0.956	0.970	0.878	1e-26

>gi|449456118|ref|XP_004145797.1| PREDICTED: uncharacterized protein LOC101208002 isoform 2 [Cucumis sativus] gi|449456120|ref|XP_004145798.1| PREDICTED: uncharacterized protein LOC101208002 isoform 3 [Cucumis sativus] gi|449529188|ref|XP_004171583.1| PREDICTED: uncharacterized LOC101208002 [Cucumis sativus]

 Score =  132 bits (332), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 64/69 (92%), Positives = 66/69 (95%)

Query: 1  MSETEVPFRPREKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYN 60
          M+E E PFRPREKL+EKQK FQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYN
Sbjct: 1  MAEVEQPFRPREKLVEKQKIFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYN 60

Query: 61 MSHGIGKKE 69
          MSHGIGKKE
Sbjct: 61 MSHGIGKKE 69

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449456116|ref|XP_004145796.1| PREDICTED: uncharacterized protein LOC101208002 isoform 1 [Cucumis sativus]

 Score =  132 bits (331), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 64/69 (92%), Positives = 66/69 (95%)

Query: 1  MSETEVPFRPREKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYN 60
          M+E E PFRPREKL+EKQK FQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYN
Sbjct: 6  MAEVEQPFRPREKLVEKQKIFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYN 65

Query: 61 MSHGIGKKE 69
          MSHGIGKKE
Sbjct: 66 MSHGIGKKE 74

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356542720|ref|XP_003539813.1| PREDICTED: uncharacterized protein LOC100499812 [Glycine max] gi|255626819|gb|ACU13754.1| unknown [Glycine max]

 Score =  125 bits (314), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 57/66 (86%), Positives = 64/66 (96%)

Query: 4  TEVPFRPREKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNMSH 63
          +E PFRPREKL EKQK+FQSIH+HTYLKGPMDKITSVAIP+ALAA+S+Y+IGRGIYNMSH
Sbjct: 2  SEAPFRPREKLAEKQKYFQSIHRHTYLKGPMDKITSVAIPLALAATSIYMIGRGIYNMSH 61

Query: 64 GIGKKE 69
          GIGKKE
Sbjct: 62 GIGKKE 67

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356543560|ref|XP_003540228.1| PREDICTED: uncharacterized protein LOC100800807 [Glycine max]

 Score =  125 bits (313), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 59/66 (89%), Positives = 64/66 (96%)

Query: 4  TEVPFRPREKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNMSH 63
          TE PFRPREKL+EKQK+FQ+IHKHTYLKGP DKITSVAIP+ALAA+SLYLIGRGIYNMSH
Sbjct: 2  TEPPFRPREKLIEKQKYFQNIHKHTYLKGPYDKITSVAIPLALAATSLYLIGRGIYNMSH 61

Query: 64 GIGKKE 69
          GIGKKE
Sbjct: 62 GIGKKE 67

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356539300|ref|XP_003538137.1| PREDICTED: uncharacterized protein LOC100305574 [Glycine max]

 Score =  124 bits (312), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 57/66 (86%), Positives = 64/66 (96%)

Query: 4  TEVPFRPREKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNMSH 63
          +E PFRPREKL EKQK+FQSIH+HTYLKGPMDKITSVAIP+ALAA+S+Y+IGRGIYNMSH
Sbjct: 2  SESPFRPREKLAEKQKYFQSIHRHTYLKGPMDKITSVAIPLALAATSIYMIGRGIYNMSH 61

Query: 64 GIGKKE 69
          GIGKKE
Sbjct: 62 GIGKKE 67

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224056767|ref|XP_002299013.1| predicted protein [Populus trichocarpa] gi|118483355|gb|ABK93579.1| unknown [Populus trichocarpa] gi|118483432|gb|ABK93616.1| unknown [Populus trichocarpa] gi|118483661|gb|ABK93724.1| unknown [Populus trichocarpa] gi|222846271|gb|EEE83818.1| predicted protein [Populus trichocarpa]

 Score =  124 bits (311), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 57/66 (86%), Positives = 63/66 (95%)

Query: 4  TEVPFRPREKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNMSH 63
          TE PFRPREKL+E QK+FQSIHKHTYLKGP+DK+TSVAIPIA AA+SL+LIGRGIYNMSH
Sbjct: 3  TEAPFRPREKLVEHQKYFQSIHKHTYLKGPLDKVTSVAIPIAFAATSLFLIGRGIYNMSH 62

Query: 64 GIGKKE 69
          GIGKKE
Sbjct: 63 GIGKKE 68

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224115602|ref|XP_002317076.1| predicted protein [Populus trichocarpa] gi|118482848|gb|ABK93339.1| unknown [Populus trichocarpa] gi|222860141|gb|EEE97688.1| predicted protein [Populus trichocarpa]

 Score =  124 bits (311), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 59/66 (89%), Positives = 63/66 (95%)

Query: 4  TEVPFRPREKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNMSH 63
          TE PFRPREKLLEKQ +FQSIHKHTYLKGP+DKITSVAIP+ALA S+LYLIGRGIYNMSH
Sbjct: 3  TEEPFRPREKLLEKQIYFQSIHKHTYLKGPLDKITSVAIPLALAGSTLYLIGRGIYNMSH 62

Query: 64 GIGKKE 69
          GIGKKE
Sbjct: 63 GIGKKE 68

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255625953|gb|ACU13321.1| unknown [Glycine max]

 Score =  124 bits (311), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 57/66 (86%), Positives = 64/66 (96%)

Query: 4  TEVPFRPREKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNMSH 63
          +E PFRPREKL EKQK+FQSIH+HTYLKGPMDKITSVAIP+ALAA+S+Y+IGRGIYNMSH
Sbjct: 2  SESPFRPREKLAEKQKYFQSIHRHTYLKGPMDKITSVAIPLALAATSIYVIGRGIYNMSH 61

Query: 64 GIGKKE 69
          GIGKKE
Sbjct: 62 GIGKKE 67

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297804048|ref|XP_002869908.1| hypothetical protein ARALYDRAFT_329492 [Arabidopsis lyrata subsp. lyrata] gi|297315744|gb|EFH46167.1| hypothetical protein ARALYDRAFT_329492 [Arabidopsis lyrata subsp. lyrata]

 Score =  123 bits (308), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 58/66 (87%), Positives = 62/66 (93%)

Query: 4  TEVPFRPREKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNMSH 63
          TE PFRPREKLLEKQ+ FQSI +HTYLKGPMDKITSVAIPIALAASSLY+IG GIYNMS+
Sbjct: 3  TETPFRPREKLLEKQRLFQSIQRHTYLKGPMDKITSVAIPIALAASSLYMIGTGIYNMSN 62

Query: 64 GIGKKE 69
          GIGKKE
Sbjct: 63 GIGKKE 68

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18415628|ref|NP_567619.1| Acytochrome-c oxidase/ electron carrier [Arabidopsis thaliana] gi|15983356|gb|AAL11546.1|AF424552_1 unknown protein [Arabidopsis thaliana] gi|16930487|gb|AAL31929.1|AF419597_1 unknown protein [Arabidopsis thaliana] gi|17386156|gb|AAL38624.1|AF446891_1 At4g21108/At4g21108 [Arabidopsis thaliana] gi|26452279|dbj|BAC43226.1| unknown protein [Arabidopsis thaliana] gi|332659002|gb|AEE84402.1| Acytochrome-c oxidase/ electron carrier [Arabidopsis thaliana]

 Score =  123 bits (308), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 58/66 (87%), Positives = 62/66 (93%)

Query: 4  TEVPFRPREKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNMSH 63
          TE PFRPREKLLEKQ+ FQSI +HTYLKGPMDKITSVAIPIALAASSLY+IG GIYNMS+
Sbjct: 3  TETPFRPREKLLEKQRLFQSIQRHTYLKGPMDKITSVAIPIALAASSLYMIGTGIYNMSN 62

Query: 64 GIGKKE 69
          GIGKKE
Sbjct: 63 GIGKKE 68

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	69
TAIR|locus:505006502	68	AT4G21105 [Arabidopsis thalian	0.956	0.970	0.878	2.5e-26

TAIR|locus:505006502 AT4G21105 [Arabidopsis thaliana (taxid:3702)]

 Score = 297 (109.6 bits), Expect = 2.5e-26, P = 2.5e-26
 Identities = 58/66 (87%), Positives = 62/66 (93%)

Query:     4 TEVPFRPREKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNMSH 63
             TE PFRPREKLLEKQ+ FQSI +HTYLKGPMDKITSVAIPIALAASSLY+IG GIYNMS+
Sbjct:     3 TETPFRPREKLLEKQRLFQSIQRHTYLKGPMDKITSVAIPIALAASSLYMIGTGIYNMSN 62

Query:    64 GIGKKE 69
             GIGKKE
Sbjct:    63 GIGKKE 68


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.318   0.135   0.383    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0       69        69   0.00091  102 3  11 22  0.46    28
                                                     29  0.39    29


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  426 (45 KB)
  Total size of DFA:  76 KB (2064 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  8.31u 0.14s 8.45t   Elapsed:  00:00:00
  Total cpu time:  8.31u 0.14s 8.45t   Elapsed:  00:00:00
  Start:  Fri May 10 06:49:05 2013   End:  Fri May 10 06:49:05 2013

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

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0009055 "electron carrier activity" evidence=IEA

GO:0005774 "vacuolar membrane" evidence=IDA

GO:0006623 "protein targeting to vacuole" evidence=RCA

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	69
pfam02238	56	pfam02238, COX7a, Cytochrome c oxidase subunit VII	7e-24

>gnl|CDD|111162 pfam02238, COX7a, Cytochrome c oxidase subunit VIIa

 Score = 84.0 bits (208), Expect = 7e-24
 Identities = 25/56 (44%), Positives = 36/56 (64%), Gaps = 2/56 (3%)

Query: 11 REKLLEKQKHFQSIHKHTYLKGPM--DKITSVAIPIALAASSLYLIGRGIYNMSHG 64
          R K+ EKQK FQ  + HTYLKG +  DK+  V +P+ L  ++ +LIG GI +  +G
Sbjct: 1  RNKVPEKQKLFQEDNGHTYLKGGLPDDKLYRVTMPLTLGGTAYFLIGLGIASFPNG 56

Cytochrome c oxidase, a 13 sub-unit complex, is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of the heart and liver isoforms of cytochrome c oxidase subunit VIIa. Length = 56

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	69
PF02238	56	COX7a: Cytochrome c oxidase subunit VIIa; InterPro	99.84
cd00928	55	Cyt_c_Oxidase_VIIa Cytochrome c oxidase subunit VI	97.38
PF00382	71	TFIIB: Transcription factor TFIIB repeat; InterPro	86.82
PF13150	85	DUF3989: Protein of unknown function (DUF3989)	85.55

>PF02238 COX7a: Cytochrome c oxidase subunit VIIa; InterPro: IPR003177 Cytochrome c oxidase (1

Probab=99.84  E-value=5.6e-22  Score=120.60  Aligned_cols=54  Identities=43%  Similarity=0.580  Sum_probs=45.6

Q ss_pred             HHHHHHHHHHHhhhhhcccccCCC--CchhhhhhhHHHHHHHHHHhhhhhhhcccc
Q 035248           11 REKLLEKQKHFQSIHKHTYLKGPM--DKITSVAIPIALAASSLYLIGRGIYNMSHG   64 (69)
Q Consensus        11 Rekl~e~Q~yfQ~i~khtyLKG~~--DkItSvaIPlalaassl~ligRGiyNMShG   64 (69)
                      |||+.|+|++||+..+|+||||+.  |.++|+++||++++++.+|+++|+||||||
T Consensus         1 ~nkv~e~Qk~FQ~~~g~vhLKGg~~D~~Ly~~Tm~L~~~gt~~~l~~l~~a~~p~k   56 (56)
T PF02238_consen    1 RNKVPEKQKLFQEDNGHVHLKGGYMDDILYRVTMPLTVAGTSYCLYGLGIANMPKK   56 (56)
T ss_dssp             ---HHHHHHHHHSSSS-TTTTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTS---
T ss_pred             CcchHHHHHHHcCCCCcEEecCCcccchHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence            799999999999999999999998  999999999999999999999999999996

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. This family is composed of the heart and liver isoforms of cytochrome c oxidase subunit VIIa. ; GO: 0004129 cytochrome-c oxidase activity, 0009055 electron carrier activity, 0005746 mitochondrial respiratory chain; PDB: 2DYS_J 3AG3_W 3AG1_J 1OCC_J 3ABL_J 3AG4_J 3ABM_J 2EIL_W 3AG2_W 2EIM_W ....

>cd00928 Cyt_c_Oxidase_VIIa Cytochrome c oxidase subunit VIIa

Probab=97.38  E-value=0.00019  Score=43.81  Aligned_cols=50  Identities=30%  Similarity=0.278  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHhhhh-hcccccCC-CCchhhhhhhHHHHHHHHHHhhhhhhhcc
Q 035248           12 EKLLEKQKHFQSIH-KHTYLKGP-MDKITSVAIPIALAASSLYLIGRGIYNMS   62 (69)
Q Consensus        12 ekl~e~Q~yfQ~i~-khtyLKG~-~DkItSvaIPlalaassl~ligRGiyNMS   62 (69)
                      +|+-|+|+-||.-- ..+||||. .|+|.-. +=.+|++.++..+..-+|.||
T Consensus         3 nkv~~~Qk~FQ~~ng~PV~LKGG~~D~~LYr-~Tm~L~~vG~~~~~~~l~~~~   54 (55)
T cd00928           3 NKVKELQKKFQADDGLPVHLKGGVVDRILYR-LTMALTVVGTGYSLYLLYMLS   54 (55)
T ss_pred             chhHHHHHHhcCCCCceEEecCCchhHHHHH-HHHHHHHHhHHHHHHHHHHHh
Confidence            68999999999986 79999988 7998765 346778888888888888776

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 VIIa has two tissue-specific isoforms that are expressed in a developmental manner. VIIa-H is expressed in heart and skeletal muscle but not smooth muscle. VIIa-L is expressed in liver and non-muscle tissues.

>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs)

Probab=86.82  E-value=2.1  Score=24.70  Aligned_cols=38  Identities=24%  Similarity=0.418  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHhhhhhcccccCCCCchhhhhhhHHHHHHHHHHhhh
Q 035248           11 REKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGR   56 (69)
Q Consensus        11 Rekl~e~Q~yfQ~i~khtyLKG~~DkItSvaIPlalaassl~ligR   56 (69)
                      .+=.=...+.|+...+...++|+.        |.++||+++|+..|
T Consensus        12 ~~v~~~A~~i~~~~~~~~~~~Gr~--------~~~iaAA~iY~acr   49 (71)
T PF00382_consen   12 EDVRERAKEIYKKAQERGLLKGRS--------PESIAAACIYLACR   49 (71)
T ss_dssp             HHHHHHHHHHHHHHHHTTTSTTS---------HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCcccCC--------HHHHHHHHHHHHHH
Confidence            333445678888888888899986        89999999999887

Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.

>PF13150 DUF3989: Protein of unknown function (DUF3989)

Probab=85.55  E-value=0.99  Score=28.94  Aligned_cols=27  Identities=22%  Similarity=0.393  Sum_probs=21.2

Q ss_pred             hhhhhHHHHHHHHHHhhhhhhhccccC
Q 035248           39 SVAIPIALAASSLYLIGRGIYNMSHGI   65 (69)
Q Consensus        39 SvaIPlalaassl~ligRGiyNMShGi   65 (69)
                      =++.=+.+|+.|+|+++++|||+-.+-
T Consensus        31 vl~ml~~fa~l~ly~~~~ai~~~Gk~~   57 (85)
T PF13150_consen   31 VLVMLVLFAALCLYMTVSAIYDIGKED   57 (85)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhccCc
Confidence            345556788999999999999995443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	69
1v54_J	59	Cytochrome C oxidase polypeptide VIIA-heart; oxido	97.69
2y69_J	80	Cytochrome C oxidase polypeptide 7A1; electron tra	97.49

>1v54_J Cytochrome C oxidase polypeptide VIIA-heart; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: f.23.4.1 PDB: 1oco_J* 1occ_J* 1ocz_J* 1ocr_J* 1v55_J* 2dyr_J* 2dys_J* 2eij_J* 2eik_J* 2eil_J* 2eim_J* 2ein_J* 2occ_J* 2ybb_U* 2zxw_J* 3abk_J* 3abl_J* 3abm_J* 3ag1_J* 3ag2_J* ...

Probab=97.69  E-value=1.2e-05  Score=48.05  Aligned_cols=47  Identities=28%  Similarity=0.234  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHhhhhh-cccccCC-CCchhhhhhhHHHHHHHHHHhhhhhhhcc
Q 035248           12 EKLLEKQKHFQSIHK-HTYLKGP-MDKITSVAIPIALAASSLYLIGRGIYNMS   62 (69)
Q Consensus        12 ekl~e~Q~yfQ~i~k-htyLKG~-~DkItSvaIPlalaassl~ligRGiyNMS   62 (69)
                      +|+.|+|+.||+-.+ .+||||+ .|.+.-   + ++.+.++.=++.++|+|-
T Consensus         3 NkV~e~Qk~FQ~~~g~pv~lKgg~sd~~Ly---~-~t~~l~~~g~~~~~y~l~   51 (59)
T 1v54_J            3 NRVAEKQKLFQEDNGLPVHLKGGATDNILY---R-VTMTLCLGGTLYSLYCLG   51 (59)
T ss_dssp             CCHHHHHHHHHCSSCCCTTTTTCHHHHHHH---H-HHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHhcCCCCceeEeecCcCceeHH---H-HHHHHHHHHHHHHHHHHH
Confidence            489999999999765 8999997 888544   3 344444444778888873

>2y69_J Cytochrome C oxidase polypeptide 7A1; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=97.49  E-value=3.5e-05  Score=48.71  Aligned_cols=47  Identities=28%  Similarity=0.224  Sum_probs=34.9

Q ss_pred             HHHHHHHHHHhhhhh-cccccCC-CCchhhhhhhHHHHHHHHHHhhhhhhhcc
Q 035248           12 EKLLEKQKHFQSIHK-HTYLKGP-MDKITSVAIPIALAASSLYLIGRGIYNMS   62 (69)
Q Consensus        12 ekl~e~Q~yfQ~i~k-htyLKG~-~DkItSvaIPlalaassl~ligRGiyNMS   62 (69)
                      +|+.|+|+.||+-.+ .+||||+ .|.+.-    -++.+.++.=++-++|++-
T Consensus        24 NkVpe~Qk~FQ~~~g~PV~lKggrsd~~Ly----~~t~~l~~~G~~~~ly~l~   72 (80)
T 2y69_J           24 NRVAEKQKLFQEDNGLPVHLKGGATDNILY----RVTMTLCLGGTLYSLYCLG   72 (80)
T ss_dssp             CCHHHHHHHHTCSSCCCGGGTTCHHHHHHH----HHHHHHHHHHHHHHHHHHH
T ss_pred             cccHHHHHHhcCCCCceeeeecCccceeHH----HHHHHHHHHHHHHHHHHHH
Confidence            699999999999765 8999997 888544    3344444544777788773

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	69
d1v54j_	58	Mitochondrial cytochrome c oxidase subunit VIIa {C	96.13
d1vola1	95	Transcription factor IIB (TFIIB), core domain {Hum	85.92
d1aisb2	95	Transcription factor IIB (TFIIB), core domain {Arc	85.36
d1aisb1	98	Transcription factor IIB (TFIIB), core domain {Arc	81.9

>d1v54j_ f.23.4.1 (J:) Mitochondrial cytochrome c oxidase subunit VIIa {Cow (Bos taurus) [TaxId: 9913]}

class: Membrane and cell surface proteins and peptides
fold: Single transmembrane helix
superfamily: Mitochondrial cytochrome c oxidase subunit VIIa
family: Mitochondrial cytochrome c oxidase subunit VIIa
domain: Mitochondrial cytochrome c oxidase subunit VIIa
species: Cow (Bos taurus) [TaxId: 9913]

Probab=96.13  E-value=0.0011  Score=38.84  Aligned_cols=50  Identities=26%  Similarity=0.199  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHhhhhh-cccccCC-CCchhhhhhhHHHHHHHHHHhhhhhhhcc
Q 035248           12 EKLLEKQKHFQSIHK-HTYLKGP-MDKITSVAIPIALAASSLYLIGRGIYNMS   62 (69)
Q Consensus        12 ekl~e~Q~yfQ~i~k-htyLKG~-~DkItSvaIPlalaassl~ligRGiyNMS   62 (69)
                      +|+-|+|+-||.--. .+||||. .|+|.-. +-.+|++.++..+..-+|.+|
T Consensus         3 nkv~e~Qk~FQ~~~g~PVhLKGG~~D~~LYr-~Tm~L~~~G~~~s~~~l~~a~   54 (58)
T d1v54j_           3 NRVAEKQKLFQEDNGLPVHLKGGATDNILYR-VTMTLCLGGTLYSLYCLGWAS   54 (58)
T ss_dssp             CCHHHHHHHHHCSSCCCTTTTTCHHHHHHHH-HHHHHHHHHHHHHHHHHHHHT
T ss_pred             chhHHHHHHhcCCCCceEEecCCcchHHHHH-HHHHHHHHHHHHHHHHHHHHh
Confidence            578999999999884 8999998 8998754 345666666666666777766

>d1vola1 a.74.1.2 (A:113-207) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.92  E-value=0.61  Score=25.93  Aligned_cols=45  Identities=27%  Similarity=0.392  Sum_probs=34.8

Q ss_pred             cHHHHHHHHHHHhhhhhcccccCCCCchhhhhhhHHHHHHHHHHhhhhhhhccc
Q 035248           10 PREKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRGIYNMSH   63 (69)
Q Consensus        10 PRekl~e~Q~yfQ~i~khtyLKG~~DkItSvaIPlalaassl~ligRGiyNMSh   63 (69)
                      |..-.=+++.+|+.+.+.-.++|+        -|-+++|+++|+..| ..|+++
T Consensus        19 ~~~i~~~A~~i~~~~~~~~~~~Gr--------~~~~i~AA~iY~acr-~~~~p~   63 (95)
T d1vola1          19 PRNKVDRTNNLFRQAYEQKSLKGR--------ANDAIASACLYIACR-QEGVPR   63 (95)
T ss_dssp             CHHHHHHHHHHHHHHHHTCCCTTS--------CHHHHHHHHHHHHHH-HTTCCC
T ss_pred             CHHHHHHHHHHHHHHHHhhhhcCC--------ChHHHHHHHHHHHHH-HcCCCC
Confidence            444455788999999999888988        467899999999998 445443

>d1aisb2 a.74.1.2 (B:1206-1300) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

Probab=85.36  E-value=0.79  Score=25.52  Aligned_cols=38  Identities=18%  Similarity=0.195  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHhhhhhcccccCCCCchhhhhhhHHHHHHHHHHhhhh
Q 035248           12 EKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRG   57 (69)
Q Consensus        12 ekl~e~Q~yfQ~i~khtyLKG~~DkItSvaIPlalaassl~ligRG   57 (69)
                      +=.-+....|+.+.+...++|+.        |-++||+++|+..|-
T Consensus        19 ~i~~~A~~i~~~~~~~~~~~Gr~--------p~~vaAA~iY~a~r~   56 (95)
T d1aisb2          19 KVRRRAIEILDEAYKRGLTSGKS--------PAGLVAAALYIASLL   56 (95)
T ss_dssp             HHHHHHHHHHHHHHHTTCCTTSC--------HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCcCCCc--------HHhHHHHHHHHHHHH
Confidence            33445677888888888899875        889999999999874

>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

Probab=81.90  E-value=1.4  Score=24.54  Aligned_cols=39  Identities=15%  Similarity=0.207  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHhhhhhcccccCCCCchhhhhhhHHHHHHHHHHhhhh
Q 035248           11 REKLLEKQKHFQSIHKHTYLKGPMDKITSVAIPIALAASSLYLIGRG   57 (69)
Q Consensus        11 Rekl~e~Q~yfQ~i~khtyLKG~~DkItSvaIPlalaassl~ligRG   57 (69)
                      .+=.-+...+|+.+.++-.++|+-        |-+++|+++|+..|-
T Consensus        20 ~~i~~~A~~i~k~~~~~~~~~g~~--------~~~iaaA~iY~Acr~   58 (98)
T d1aisb1          20 RHVEEEAARLYREAVRKGLIRGRS--------IESVMAACVYAACRL   58 (98)
T ss_dssp             HHHHHHHHHHHHHHHTTTTTTTCC--------HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhhhcCCC--------HHHHHHHHHHHHHHH
Confidence            333446678889988888888875        788999999998873