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SAS results for UniProt accession no. P04038

Sequence annotated by structure

Key:
Sec. struc: By homology
  Helix Strand  
Residue contacts:   to ligand
Active sites:   (from PDB SITE records)

Secondary structure shown in red comes from a homologous protein structure which is at least 30% sequence identical to the target protein and has an alignment overlap of at least 80 residues or at least three-quarters of the length of the target sequence (whichever overlap is the larger).

Click on annotated residues to get source(s) of each annotation.

 

FASTA alignment for UniProt accession no. P04038 - coloured by no. of contacts to ligand

Below are the FASTA results from a search of the sequence of UniProt accession no. P04038 against all protein sequences in the PDB. Identical sequences are grouped together and represented by a single 'consensus' sequence (asterisked) onto which all relevant annotations are mapped. The number of sequences represented by each consensus sequence is shown by the '×n' on the right of the alignment. Use the box below to modify the annotations shown on the alignment. At the bottom of the page are given the FASTA stats for all the sequences. There you can exclude any sequences from the alignment.

Struct

FASTA

The search returned 11 unique sequences (including 3 consensus sequences) giving 34 sequence matches in all.

Modify alignment: Annotate by:
  Number:  
  Show secondary structure: Yes No  


                1         2         3         4         5         6     
       12345678901234567890123456789012345678901234567890123456789012345    Protein name
       ---------+---------+---------+---------+---------+---------+-----    ------------
P04038 -----------------------------------------------------------------    Cytochrome c oxidase subunit 6C OS=Bos taurus GN=COX6C PE=1  ...
1occ:I*-----------------------------------------------------------------×6  Structure of bovine heart cytochromE C oxidase at the fully  ...
1v54:I*-----------------------------------------------------------------×16 Bovine heart cytochromE C oxidase at the fully oxidized stat
2y69:I*-----------------------------------------------------------------×4  Bovine heart cytochromE C oxidase re-refined with molecular  ...
3j7a:1 ----------------------------------------------dqftirvkkymsnpllrrk    Cryo-em structure of the plasmodium falciparum 80s ribosome  ...
2pn1:A gmqkphllitsagrraklveyfvkefktgrvstadcsplasalymadqhyivpkideveyidhll    Crystal structure of carbamoylphosphate synthase large  ...
2o08:A -----------------------------------------------------------------    Crystal structure of a putative hd superfamily hydrolase  ...
2l5a:A -------------------liskipfarlvkevtdefttkdqdlrwqsmaimalqeaseaylvgl    Structural basis for recognition of centromere specific  ...
4hbl:A -----------------------------------------------------------------    Crystal structure of abfr of staphylococcus epidermidis
  " :D -----------------------------------------------------------------    Crystal structure of abfr of staphylococcus epidermidis
2x3g:A -----------------------------------------------------------------    Crystal structure of the hypothetical protein orf119 from  ...
3bbo:S -----------------------------------------------------------------    Homology model for the spinach chloroplast 50s subunit  ...

                                         1         1         1         1
           7         8         9         0         1         2         3
       67890123456789012345678901234567890123456789012345678901234567890    Protein name
       ----+---------+---------+---------+---------+---------+---------+    ------------
P04038 ---------mstalakpqmrgllarrl-rfhivgafmvsl-gfat----fykfavaekrkkayad    Cytochrome c oxidase subunit 6C OS=Bos taurus GN=COX6C PE=1  ...
1occ:I*----------stalakpqmrgllarrl-rfhivgafmvsl-gfat----fykfavaekrkkayad×6  Structure of bovine heart cytochromE C oxidase at the fully  ...
1v54:I*----------XTALAKPQMRGLLARRL-RFHIVGAFMVSL-GFAT----FYKFAVAEKRKKAYAD×16 Bovine heart cytochromE C oxidase at the fully oxidized stat
2y69:I*------------ALAKPQMRGLLARRL-RFHIVGAFMVSL-GFAT----FYKFAVAEKRKKAYAD×4  Bovine heart cytochromE C oxidase re-refined with molecular  ...
3j7a:1 qfaleilhpnkgsvakkevkerlakmy-klnnvnt-ivlf-gfkt----lf----gggrtkgfgl    Cryo-em structure of the plasmodium falciparum 80s ribosome  ...
2pn1:A tlcqdegvtalltlidpel-gllaqaterfqaigvtvivs-pyaacelcfdkytmyeyclrqgia    Crystal structure of carbamoylphosphate synthase large  ...
2o08:A ----gmnrgkalqlvkph---ltehry-q-htigvmetai-dlak----lyg---adqqkaelaa    Crystal structure of a putative hd superfamily hydrolase  ...
2l5a:A lehtnllalhakritimkkdmqlarri-r----gqflvpr-gsme----rhkla-denmrkvwsn    Structural basis for recognition of centromere specific  ...
4hbl:A -----------namkqeqmr--lanql-cf---saynvsr-lfaq----fy-----ekklkqfgi    Crystal structure of abfr of staphylococcus epidermidis
  " :D ------------amkqeqmr--lanql-cf---saynvsr-lfaq----fy-----ekklkqfgi    Crystal structure of abfr of staphylococcus epidermidis
2x3g:A --------------------gdlkkvl-nfhfsyiytyfi-titt----nykygdtekifrkfrs    Crystal structure of the hypothetical protein orf119 from  ...
3bbo:S --------------mtrvkrgyiarrr-rkkir-ffassfrgahs----rltrtiaqqkiralvs    Homology model for the spinach chloroplast 50s subunit  ...

                1         1         1         1         1         1     
                4         5         6         7         8         9     
       12345678901234567890123456789012345678901234567890123456789012345    Protein name
       ---------+---------+---------+---------+---------+---------+-----    ------------
P04038 fyrnydsmk-dfeemrkagifqsak----------------------------------------    Cytochrome c oxidase subunit 6C OS=Bos taurus GN=COX6C PE=1  ...
1occ:I*fyrnydsmk-dfeemrkagifqsak----------------------------------------×6  Structure of bovine heart cytochromE C oxidase at the fully  ...
1v54:I*FYRNYDSMK-DFEEMRKAGIFQSA-----------------------------------------×16 Bovine heart cytochromE C oxidase at the fully oxidized stat
2y69:I*FYRNYDSMK-DFEEMRKAGIFQSAK----------------------------------------×4  Bovine heart cytochromE C oxidase re-refined with molecular  ...
3j7a:1 iyknvdavk-kfekkyrlvreglidketkagrraskelknrrkkvrgt-----------------    Cryo-em structure of the plasmodium falciparum 80s ribosome  ...
2pn1:A hartyatma-sfeealaagevqlpvfvkprngdlivqellvgqelgvdayvdlisgkvtsifike    Crystal structure of carbamoylphosphate synthase large  ...
2o08:A ifhdyakfr-dknemrtlireklsqqdilfygdellhapcgayyvreevgiededvlqairfhtt    Crystal structure of a putative hd superfamily hydrolase  ...
2l5a:A iiskyesie-eqgdlvdlktgeivednghiktltannstkdkrtkytsvlrdiidisdeedgdkg    Structural basis for recognition of centromere specific  ...
4hbl:A tysqylvml-tlweenpqtlnsigrhldlssntltpmlkrleqsgwvkrliitltdngqqqqeav    Crystal structure of abfr of staphylococcus epidermidis
  " :D tysqylvml-tlweenpqtlnsigrhldlssntltpmlkrleqsgwvkrerqqsdkrqliitltd    Crystal structure of abfr of staphylococcus epidermidis
2x3g:A yiynhdkns-hvfsiketsnglhyhilvftnkkldysrvhkhmpshsdirielvpksisdiknvy    Crystal structure of the hypothetical protein orf119 from  ...
3bbo:S ahrdrdrqkrdfrrlwitrinaairergvyynyskfihdlykrqlllnrkilaqiailnpnciym    Homology model for the spinach chloroplast 50s subunit  ...

           2         2         2         2         2         2         2
           0         1         2         3         4         5         6
       67890123456789012345678901234567890123456789012345678901234567890    Protein name
       ----+---------+---------+---------+---------+---------+---------+    ------------
P04038 -----------------------------------------------------------------    Cytochrome c oxidase subunit 6C OS=Bos taurus GN=COX6C PE=1  ...
1occ:I*-----------------------------------------------------------------×6  Structure of bovine heart cytochromE C oxidase at the fully  ...
1v54:I*-----------------------------------------------------------------×16 Bovine heart cytochromE C oxidase at the fully oxidized stat
2y69:I*-----------------------------------------------------------------×4  Bovine heart cytochromE C oxidase re-refined with molecular  ...
3j7a:1 -----------------------------------------------------------------    Cryo-em structure of the plasmodium falciparum 80s ribosome  ...
2pn1:A kltmragetdksrsvlrddvfelvehvldgsglvgpldfdlfdvagtlylseinprfgggyphay    Crystal structure of carbamoylphosphate synthase large  ...
2o08:A grpnmsllekiifladyiepnrqfpgvekvrtqaktdlngaiisslvntitfllkknqpiypdtl    Crystal structure of a putative hd superfamily hydrolase  ...
2l5a:A gvkrisgliyeevravlksflesvirdsvtytehakrktvtsldvvyalkrqgrtlygfgg----    Structural basis for recognition of centromere specific  ...
4hbl:A feaissclpqefdtteydetkyvfeeleqtlkhlie-----------------------------    Crystal structure of abfr of staphylococcus epidermidis
  " :D ngqqqqeavfeaissclpqefdtteydetkyvfeeleqtlkhliek-------------------    Crystal structure of abfr of staphylococcus epidermidis
2x3g:A kymlktkkdikms----------------------------------------------------    Crystal structure of the hypothetical protein orf119 from  ...
3bbo:S iyneiikke--------------------------------------------------------    Homology model for the spinach chloroplast 50s subunit  ...

                2         2         2         3         3 
                7         8         9         0         1 
       123456789012345678901234567890123456789012345678901                  Protein name
       ---------+---------+---------+---------+---------+-                  ------------
P04038 ---------------------------------------------------                  Cytochrome c oxidase subunit 6C OS=Bos taurus GN=COX6C PE=1  ...
1occ:I*---------------------------------------------------              ×6  Structure of bovine heart cytochromE C oxidase at the fully  ...
1v54:I*---------------------------------------------------              ×16 Bovine heart cytochromE C oxidase at the fully oxidized stat
2y69:I*---------------------------------------------------              ×4  Bovine heart cytochromE C oxidase re-refined with molecular  ...
3j7a:1 ---------------------------------------------------                  Cryo-em structure of the plasmodium falciparum 80s ribosome  ...
2pn1:A ecgvnfpaqlyrnlmheinvpqigqylddiymlkhdtvtlisaaelqkikr                  Crystal structure of carbamoylphosphate synthase large  ...
2o08:A atynqllleq-----------------------------------------                  Crystal structure of a putative hd superfamily hydrolase  ...
2l5a:A ---------------------------------------------------                  Structural basis for recognition of centromere specific  ...
4hbl:A ---------------------------------------------------                  Crystal structure of abfr of staphylococcus epidermidis
  " :D ---------------------------------------------------                  Crystal structure of abfr of staphylococcus epidermidis
2x3g:A ---------------------------------------------------                  Crystal structure of the hypothetical protein orf119 from  ...
3bbo:S ---------------------------------------------------                  Homology model for the spinach chloroplast 50s subunit  ...

Residue colours: black = 0, purple = 1, blue = 2, green = 3, orange = 4, red = 5 or more contacts.

Sequence listing

The listing below shows the FASTA statistics for the PDB entries that matched UniProt accession no. P04038. Ditto marks indicate identical sequences represented by a single representative sequence in the alignment above. The representative is asterisked and the names of all its duplicate sequences are indented to the right.

Structures whose names are given in purple are those that are annotated above. The parameters defining which sequences can transfer their annotations are shown at the bottom of the page where they can be altered and the alignment regenerated.

Use the checkboxes to the left of the PDB codes to exclude any sequences from the alignment Then click the SELECT button at the bottom of the page to redisplay the alignment.

Aligned sequences

  Smith-
Waterman
score
%-tage
identity
a.a.
overlap
Seq
len
z-score E-
value
  PDB
code
Protein name
1. - - - 74 - - P04038 Cytochrome c oxidase subunit 6C OS=Bos taurus GN=COX6C PE=1 SV=2
2. 471 100.0% 73 73 719.3 4.3e-33 1occ:I * Structure of bovine heart cytochromE C oxidase at the fully oxidized state
3. " " " " " "  = 1oco:I *
Bovine heart cytochromE C oxidase in carbon monoxide-bound state
4. " " " " " "  = 1ocr:I *
Bovine heart cytochromE C oxidase in the fully reduced state
5. " " " " " "  = 1ocz:I *
Bovine heart cytochromE C oxidase in azide-bound state
6. " " " " " "  = 2occ:I *
Bovine heart cytochromE C oxidase at the fully oxidized stat
7. " " " " " "  = 2ybb:T *
Fitted model for bovine mitochondrial supercomplex i1iii2iv single particle cryo-em (emd-1876)
8. 466 100.0% 72 72 711.8 1.1e-32 1v54:I * Bovine heart cytochromE C oxidase at the fully oxidized stat
9. " " " " " "  = 1v55:I *
Bovine heart cytochromE C oxidase at the fully reduced state
10. " " " " " "  = 2dyr:I *
Bovine heart cytochromE C oxidase at the fully oxidized stat
11. " " " " " "  = 2dys:I *
Bovine heart cytochromE C oxidase modified by dccd
12. " " " " " "  = 2eij:I *
Bovine heart cytochromE C oxidase in the fully reduced state
13. " " " " " "  = 2eik:I *
Cadmium ion binding structure of bovine heart cytochromE C o the fully reduced state
14. " " " " " "  = 2eil:I *
Cadmium ion binding structure of bovine heart cytochromE C o the fully oxidized state
15. " " " " " "  = 2eim:I *
Zinc ion binding structure of bovine heart cytochromE C oxid fully reduced state
16. " " " " " "  = 2ein:I *
Zinc ion binding structure of bovine heart cytochromE C oxidase in the fully oxidized state
17. " " " " " "  = 3abk:I *
Bovine heart cytochromE C oxidase at the no-bound fully redu (50k)
18. " " " " " "  = 3ag1:I *
Bovine heart cytochromE C oxidase in the carbon monoxide-bou reduced state at 280 k
19. " " " " " "  = 3ag2:I *
Bovine heart cytochromE C oxidase in the carbon monoxide-bou reduced state at 100 k
20. " " " " " "  = 3ag3:I *
Bovine heart cytochromE C oxidase in the nitric oxide-bound reduced state at 100 k
21. " " " " " "  = 3ag4:I *
Bovine heart cytochromE C oxidase in the cyanide ion-bound f reduced state at 100 k
22. " " " " " "  = 3asn:I *
Bovine heart cytochromE C oxidase in the fully oxidized stat at 1.7470 angstrom wavelength
23. " " " " " "  = 3aso:I *
Bovine heart cytochromE C oxidase in the fully oxidized stat at 0.9 angstrom wavelength
24. 461 100.0% 71 71 704.5 2.9e-32 2y69:I * Bovine heart cytochromE C oxidase re-refined with molecular oxygen
25. " " " " " "  = 2zxw:I *
Bovine heart cytochromE C oxidase at the fully oxidized stat ray exposure dataset)
26. " " " " " "  = 3abl:I *
Bovine heart cytochromE C oxidase at the fully oxidized state (15-s x-ray exposure dataset)
27. " " " " " "  = 3abm:I *
Bovine heart cytochromE C oxidase at the fully oxidized state (200-s x-ray exposure dataset)
28. 83 28.3% 60 120 134.7 1.6 3j7a:1 Cryo-em structure of the plasmodium falciparum 80s ribosome the anti-protozoan drug emetine, small subunit
29. 84 30.6% 72 308 129.9 2.9 2pn1:A Crystal structure of carbamoylphosphate synthase large subun gene in mj) (zp_00538348.1) from exiguobacterium sp. 255-15 resolution
30. 76 27.9% 61 187 121.3 8.8 2o08:A Crystal structure of a putative hd superfamily hydrolase (bh bacillus halodurans at 1.90 a resolution
31. 70 31.9% 47 225 111.1 33 2l5a:A Structural basis for recognition of centromere specific hist variant by nonhistone scm3
32. 67 38.2% 55 138 109.8 38 4hbl:A Crystal structure of abfr of staphylococcus epidermidis
33. 67 38.2% 55 147 109.4 41 4hbl:D Crystal structure of abfr of staphylococcus epidermidis
34. 65 26.7% 45 116 108.0 49 2x3g:A Crystal structure of the hypothetical protein orf119 from sulfolobus islandicus rod-shaped virus 1
35. 65 30.4% 56 119 107.8 50 3bbo:S Homology model for the spinach chloroplast 50s subunit fitte cryo-em map of the 70s chlororibosome

Number of sequences: 35

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Annotation parameters

The parameters below were used in determining which structural annotations could be transferred on to the target sequence. You can change the parameters and regenerate the SAS alignments and annotation by pressing the Rerun button.

Min. seq. identity:   Min. seq. overlap   Max. E-value

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