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SAS results for UniProt accession no. P22139

Sequence annotated by structure

Key:
Sec. struc: By homology
  Helix Strand  
Residue contacts:   to metal
Active sites:   (from PDB SITE records)
PROSITE patterns: Low   High conservation

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. P22139 - coloured by no. of contacts to ligand

Below are the FASTA results from a search of the sequence of UniProt accession no. P22139 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 25 unique sequences (including 8 consensus sequences) giving 133 sequence matches in all. The 7 sequences excluded from the alignment are listed at the end.

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


                1         2         3         4         5         6     
       12345678901234567890123456789012345678901234567890123456789012345    Protein name
       ---------+---------+---------+---------+---------+---------+-----    ------------
P22139 -----------------------------------------------------------------    DNA-directed RNA polymerases I, II, and III subunit RPABC5  ...
4c2m:J*-----------------------------------------------------------------×4  Structure of RNA polymerase i at 2.8 a resolution
3fki:J -----------------------------------------------------------------    12-subunit RNA polymerase ii refined with zn-sad data
1i3q:J*-----------------------------------------------------------------×95 RNA polymerase ii crystal form i at 3.1 a resolution
1twa:J*-----------------------------------------------------------------×4  RNA polymerase ii complexed with atp
3h0g:J -----------------------------------------------------------------    RNA polymerase ii from schizosaccharomyces pombe
2pmz:N*-----------------------------------------------------------------×2  Archaeal RNA polymerase from sulfolobus solfataricus
2waq:N*-----------------------------------------------------------------×3  The complete structure of the archaeal 13-subunit DNA-  ...
4ayb:N*-----------------------------------------------------------------×3  Rnap at 3.2ang
1ef4:A -----------------------------------------------------------------    Solution structure of the essential RNA polymerase subunit  ...
2max:A -----------------------------------------------------------------    Nmr structure of the RNA polymerase alpha subunit  ...
1i11:A -----------------------------------------------------------------    Solution structure of the DNA binding domain, sox-5 hmg box  ...
3dai:A -----------------------------------------------------------------    Crystal structure of the bromodomain of the human atad2
2epw:A -----------------------------------------------------------------    Solution structure of the 24th c2h2 type zinc finger domain  ...
1hso:A*-----------------------------------------------------------------×2  Human alpha alcohol dehydrogenase (adh1a)
3tni:A svecpfcdevskyeklakigqevfkarhrktgqkvalkkvlmenekegfpitalreikilqllkh    Structure of cdk9/cyclin t f241l
2poi:A -----------------------------------------------------------------    Crystal structure of xiap bir1 domain (i222 form)
2pop:B -----------------------------------------------------------------    The crystal structure of tab1 and bir1 complex
2qra:D -----------------------------------------------------------------    Crystal structure of xiap bir1 domain (p21 form)
2vm5:A -----------------------------------------------------------------    Human bir2 domain of baculoviral inhibitor of apoptosis  ...
2pop:D -----------------------------------------------------------------    The crystal structure of tab1 and bir1 complex

                                         1         1         1         1
           7         8         9         0         1         2         3
       67890123456789012345678901234567890123456789012345678901234567890    Protein name
       ----+---------+---------+---------+---------+---------+---------+    ------------
P22139 -----------------------------------------------------------------    DNA-directed RNA polymerases I, II, and III subunit RPABC5  ...
4c2m:J*-----------------------------------------------------------------×4  Structure of RNA polymerase i at 2.8 a resolution
3fki:J -----------------------------------------------------------------    12-subunit RNA polymerase ii refined with zn-sad data
1i3q:J*-----------------------------------------------------------------×95 RNA polymerase ii crystal form i at 3.1 a resolution
1twa:J*-----------------------------------------------------------------×4  RNA polymerase ii complexed with atp
3h0g:J -----------------------------------------------------------------    RNA polymerase ii from schizosaccharomyces pombe
2pmz:N*-----------------------------------------------------------------×2  Archaeal RNA polymerase from sulfolobus solfataricus
2waq:N*-----------------------------------------------------------------×3  The complete structure of the archaeal 13-subunit DNA-  ...
4ayb:N*-----------------------------------------------------------------×3  Rnap at 3.2ang
1ef4:A -----------------------------------------------------------------    Solution structure of the essential RNA polymerase subunit  ...
2max:A -----------------------------------------------------------------    Nmr structure of the RNA polymerase alpha subunit  ...
1i11:A -----------------------------------------------------------------    Solution structure of the DNA binding domain, sox-5 hmg box  ...
3dai:A -----------------------------------------------------------------    Crystal structure of the bromodomain of the human atad2
2epw:A -----------------------------------------------------------------    Solution structure of the 24th c2h2 type zinc finger domain  ...
1hso:A*---------------------------------------------------------stagkvik×2  Human alpha alcohol dehydrogenase (adh1a)
3tni:A envvnlieicrtsiylvfdfcehdlagllsnvlvkftlseikrvmqmllnglyyihrnkilhrdm    Structure of cdk9/cyclin t f241l
2poi:A -----------------------------------------------------------------    Crystal structure of xiap bir1 domain (i222 form)
2pop:B -----------------------------------------------------------------    The crystal structure of tab1 and bir1 complex
2qra:D -----------------------------------------------------------------    Crystal structure of xiap bir1 domain (p21 form)
2vm5:A -----------------------------------------------------------------    Human bir2 domain of baculoviral inhibitor of apoptosis  ...
2pop:D -----------------------------------------------------------------    The crystal structure of tab1 and bir1 complex

                1         1         1         1         1         1     
                4         5         6         7         8         9     
       12345678901234567890123456789012345678901234567890123456789012345    Protein name
       ---------+---------+---------+---------+---------+---------+-----    ------------
P22139 -----------------------------------------------------------------    DNA-directed RNA polymerases I, II, and III subunit RPABC5  ...
4c2m:J*-----------------------------------------------------------------×4  Structure of RNA polymerase i at 2.8 a resolution
3fki:J -----------------------------------------------------------------    12-subunit RNA polymerase ii refined with zn-sad data
1i3q:J*-----------------------------------------------------------------×95 RNA polymerase ii crystal form i at 3.1 a resolution
1twa:J*-----------------------------------------------------------------×4  RNA polymerase ii complexed with atp
3h0g:J -----------------------------------------------------------------    RNA polymerase ii from schizosaccharomyces pombe
2pmz:N*-----------------------------------------------------------------×2  Archaeal RNA polymerase from sulfolobus solfataricus
2waq:N*-----------------------------------------------------------------×3  The complete structure of the archaeal 13-subunit DNA-  ...
4ayb:N*-----------------------------------------------------------------×3  Rnap at 3.2ang
1ef4:A -----------------------------------------------------------------    Solution structure of the essential RNA polymerase subunit  ...
2max:A ----------------------------------------------lgvfgerpianteysgdya    Nmr structure of the RNA polymerase alpha subunit  ...
1i11:A --------------------------------------------------------phikrpmna    Solution structure of the DNA binding domain, sox-5 hmg box  ...
3dai:A ---------------------------------------------------------smqeedtf    Crystal structure of the bromodomain of the human atad2
2epw:A -----------------------------------------------------------------    Solution structure of the 24th c2h2 type zinc finger domain  ...
1hso:A*ckaavlwelkkpfsieevevappkahevrikmvavgicgtddhvvsgtmvtplpvilgheaagiv×2  Human alpha alcohol dehydrogenase (adh1a)
3tni:A kaanvlitrdgvlkladfglarafspnryxnrvvtlwyrppelllgerdygppidlwgagcimae    Structure of cdk9/cyclin t f241l
2poi:A --------------------------------------------efveefnrlktfanfpsgspv    Crystal structure of xiap bir1 domain (i222 form)
2pop:B --------------------------------------------efveefnrlktfanfpsgspv    The crystal structure of tab1 and bir1 complex
2qra:D --------------------------------------------efveefnrlktfanfpsgspv    Crystal structure of xiap bir1 domain (p21 form)
2vm5:A ------------------------------smrvknlksrlrmryqeeearlasfrnwpfyvqgi    Human bir2 domain of baculoviral inhibitor of apoptosis  ...
2pop:D -----------------------------------------keeefveefnrlktfanfpsgspv    The crystal structure of tab1 and bir1 complex

           2         2         2         2         2         2         2
           0         1         2         3         4         5         6
       67890123456789012345678901234567890123456789012345678901234567890    Protein name
       ----+---------+---------+---------+---------+---------+---------+    ------------
P22139 --------------mivpvrcfscgkv-vgdkwesyln--llqedeldegtalsrlglkryccrr    DNA-directed RNA polymerases I, II, and III subunit RPABC5  ...
4c2m:J*--------------mivpvrcfscgkv-vgdkwesyln--llqedeldegtalsrlglkryccrr×4  Structure of RNA polymerase i at 2.8 a resolution
3fki:J --------------mivpvrcfscgkv-vgdkwesyln--llqedeldegtalsrlglkryccrr    12-subunit RNA polymerase ii refined with zn-sad data
1i3q:J*--------------mivpvrcfscgkv-vgdkwesyln--llqedeldegtalsrlglkryccrr×95 RNA polymerase ii crystal form i at 3.1 a resolution
1twa:J*--------------mivpvrcfscgkv-vgdkwesyln--llqedeldegtalsrlglkryccrr×4  RNA polymerase ii complexed with atp
3h0g:J --------------miipircfscgkv-igdkwdtylt--llqednt-egealdklglqryccrr    RNA polymerase ii from schizosaccharomyces pombe
2pmz:N*--------------mlipircftcgsl-iadkwqsfit--rvnage-npgkvlddlgvkryccrr×2  Archaeal RNA polymerase from sulfolobus solfataricus
2waq:N*--------------mmipircftcgsl-iadkwqpfit--rvnage-npgkvlddlgvkryccrr×3  The complete structure of the archaeal 13-subunit DNA-  ...
4ayb:N*--------------mmipircftcgsl-iadkwqpfit--rvnage-npgkvlddlgvkryccrr×3  Rnap at 3.2ang
1ef4:A ---------------mipvrclscgkp-vsayfneyqr--rvadge-dpkdvlddlglkryccrr    Solution structure of the essential RNA polymerase subunit  ...
2max:A qrddakdlsakiesmnlsarcfncldk-igikyvgelv--lmseeel-kg--vknmgkksydeia    Nmr structure of the RNA polymerase alpha subunit  ...
1i11:A fmvwakderrkilqafpdmhnsniski-lgsrwkamtn--lekqpyyeeqarlskqhlekypdy-    Solution structure of the DNA binding domain, sox-5 hmg box  ...
3dai:A relriflrnvthrlaidkrfrvftkpv-dpdevpdyvt--vikqp-mdlssviskidlhkyltvk    Crystal structure of the bromodomain of the human atad2
2epw:A ------gssgssgtgekpckctecgka-fc--wksqli--mhqrthvddkhsgpssg--------    Solution structure of the 24th c2h2 type zinc finger domain  ...
1hso:A*esvgegvttvkpgdkviplaipqcgkcricknpesnyc--lkndvsnpqgtlqd--gtsrftcrr×2  Human alpha alcohol dehydrogenase (adh1a)
3tni:A mwtrspimqgnteqhqlalisqlcgsi-tpevwpnvdnyelyeklelvkgqrkvkdrlkayvrdp    Structure of cdk9/cyclin t f241l
2poi:A sastlaragflytgegdtvrcfschaa-v-drwqygds--avgrhrkvspncrfingfyle----    Crystal structure of xiap bir1 domain (i222 form)
2pop:B sastlaragflytgegdtvrcfschaa-v-drwqygds--avgrhrkvspncrfingfylen---    The crystal structure of tab1 and bir1 complex
2qra:D sastlaragflytgegdtvrcfschaa-v-drwqygds--avgrhrkvspncrfingfyle----    Crystal structure of xiap bir1 domain (p21 form)
2vm5:A spcvlseagfvftgkqdtvqcfscggc-lgn-weegdd--pwkehakwfpkceflrskksseeit    Human bir2 domain of baculoviral inhibitor of apoptosis  ...
2pop:D sastlaragflytgegdtvrcfschaa-v-drwqygds--avgrhrkvspncrfingfyl-----    The crystal structure of tab1 and bir1 complex

                2         2         2         3         3         3     
                7         8         9         0         1         2     
       12345678901234567890123456789012345678901234567890123456789012345    Protein name
       ---------+---------+---------+---------+---------+---------+-----    ------------
P22139 milthvdli-ekflrynplekrd------------------------------------------    DNA-directed RNA polymerases I, II, and III subunit RPABC5  ...
4c2m:J*milthvdli-ekflrynplekr-------------------------------------------×4  Structure of RNA polymerase i at 2.8 a resolution
3fki:J milthvdli-ekflrynpl----------------------------------------------    12-subunit RNA polymerase ii refined with zn-sad data
1i3q:J*milthvdli-ekflrynp-----------------------------------------------×95 RNA polymerase ii crystal form i at 3.1 a resolution
1twa:J*milthvdli-ekflryn------------------------------------------------×4  RNA polymerase ii complexed with atp
3h0g:J milthvdli-ekllcynp-----------------------------------------------    RNA polymerase ii from schizosaccharomyces pombe
2pmz:N*mllshvdii-nevihytr-----------------------------------------------×2  Archaeal RNA polymerase from sulfolobus solfataricus
2waq:N*mllshidii-sevihytr-----------------------------------------------×3  The complete structure of the archaeal 13-subunit DNA-  ...
4ayb:N*mllshidii-sevihytrp----------------------------------------------×3  Rnap at 3.2ang
1ef4:A mlishvetw--------------------------------------------------------    Solution structure of the essential RNA polymerase subunit  ...
2max:A eklndlgyp-vgtelspeqreslkkrlekledkggnd----------------------------    Nmr structure of the RNA polymerase alpha subunit  ...
1i11:A -----------------------------------------------------------------    Solution structure of the DNA binding domain, sox-5 hmg box  ...
3dai:A dylrdidlicsnaleynpdrdpgdrlirhracalrdtayaiikeeldedfeqlceeiqesr----    Crystal structure of the bromodomain of the human atad2
2epw:A -----------------------------------------------------------------    Solution structure of the 24th c2h2 type zinc finger domain  ...
1hso:A*kpihhflgi-stfsqytvvdenavakidaasplekvcligcgfstgygsavnvakvtpgstcavf×2  Human alpha alcohol dehydrogenase (adh1a)
3tni:A yal---dli-dkllvldpaqridsddalnhdffwsdpmpsdl-----------------------    Structure of cdk9/cyclin t f241l
2poi:A -----------------------------------------------------------------    Crystal structure of xiap bir1 domain (i222 form)
2pop:B -----------------------------------------------------------------    The crystal structure of tab1 and bir1 complex
2qra:D -----------------------------------------------------------------    Crystal structure of xiap bir1 domain (p21 form)
2vm5:A qyiqsyk----------------------------------------------------------    Human bir2 domain of baculoviral inhibitor of apoptosis  ...
2pop:D -----------------------------------------------------------------    The crystal structure of tab1 and bir1 complex

           3         3         3         3         3         3         3
           3         4         5         6         7         8         9
       67890123456789012345678901234567890123456789012345678901234567890    Protein name
       ----+---------+---------+---------+---------+---------+---------+    ------------
P22139 -----------------------------------------------------------------    DNA-directed RNA polymerases I, II, and III subunit RPABC5  ...
4c2m:J*-----------------------------------------------------------------×4  Structure of RNA polymerase i at 2.8 a resolution
3fki:J -----------------------------------------------------------------    12-subunit RNA polymerase ii refined with zn-sad data
1i3q:J*-----------------------------------------------------------------×95 RNA polymerase ii crystal form i at 3.1 a resolution
1twa:J*-----------------------------------------------------------------×4  RNA polymerase ii complexed with atp
3h0g:J -----------------------------------------------------------------    RNA polymerase ii from schizosaccharomyces pombe
2pmz:N*-----------------------------------------------------------------×2  Archaeal RNA polymerase from sulfolobus solfataricus
2waq:N*-----------------------------------------------------------------×3  The complete structure of the archaeal 13-subunit DNA-  ...
4ayb:N*-----------------------------------------------------------------×3  Rnap at 3.2ang
1ef4:A -----------------------------------------------------------------    Solution structure of the essential RNA polymerase subunit  ...
2max:A -----------------------------------------------------------------    Nmr structure of the RNA polymerase alpha subunit  ...
1i11:A -----------------------------------------------------------------    Solution structure of the DNA binding domain, sox-5 hmg box  ...
3dai:A -----------------------------------------------------------------    Crystal structure of the bromodomain of the human atad2
2epw:A -----------------------------------------------------------------    Solution structure of the 24th c2h2 type zinc finger domain  ...
1hso:A*glggvglsaimgckaagaariiavdinkdkfakakelgatecinpqdykkpiqevlkemtdggvd×2  Human alpha alcohol dehydrogenase (adh1a)
3tni:A -----------------------------------------------------------------    Structure of cdk9/cyclin t f241l
2poi:A -----------------------------------------------------------------    Crystal structure of xiap bir1 domain (i222 form)
2pop:B -----------------------------------------------------------------    The crystal structure of tab1 and bir1 complex
2qra:D -----------------------------------------------------------------    Crystal structure of xiap bir1 domain (p21 form)
2vm5:A -----------------------------------------------------------------    Human bir2 domain of baculoviral inhibitor of apoptosis  ...
2pop:D -----------------------------------------------------------------    The crystal structure of tab1 and bir1 complex

                4         4         4         4         4         4     
                0         1         2         3         4         5     
       12345678901234567890123456789012345678901234567890123456789012345    Protein name
       ---------+---------+---------+---------+---------+---------+-----    ------------
P22139 -----------------------------------------------------------------    DNA-directed RNA polymerases I, II, and III subunit RPABC5  ...
4c2m:J*-----------------------------------------------------------------×4  Structure of RNA polymerase i at 2.8 a resolution
3fki:J -----------------------------------------------------------------    12-subunit RNA polymerase ii refined with zn-sad data
1i3q:J*-----------------------------------------------------------------×95 RNA polymerase ii crystal form i at 3.1 a resolution
1twa:J*-----------------------------------------------------------------×4  RNA polymerase ii complexed with atp
3h0g:J -----------------------------------------------------------------    RNA polymerase ii from schizosaccharomyces pombe
2pmz:N*-----------------------------------------------------------------×2  Archaeal RNA polymerase from sulfolobus solfataricus
2waq:N*-----------------------------------------------------------------×3  The complete structure of the archaeal 13-subunit DNA-  ...
4ayb:N*-----------------------------------------------------------------×3  Rnap at 3.2ang
1ef4:A -----------------------------------------------------------------    Solution structure of the essential RNA polymerase subunit  ...
2max:A -----------------------------------------------------------------    Nmr structure of the RNA polymerase alpha subunit  ...
1i11:A -----------------------------------------------------------------    Solution structure of the DNA binding domain, sox-5 hmg box  ...
3dai:A -----------------------------------------------------------------    Crystal structure of the bromodomain of the human atad2
2epw:A -----------------------------------------------------------------    Solution structure of the 24th c2h2 type zinc finger domain  ...
1hso:A*fsfevigrldtmmasllccheacgtsvivgvppdsqnlsmnpmllltgrtwkgailggfkskecv×2  Human alpha alcohol dehydrogenase (adh1a)
3tni:A -----------------------------------------------------------------    Structure of cdk9/cyclin t f241l
2poi:A -----------------------------------------------------------------    Crystal structure of xiap bir1 domain (i222 form)
2pop:B -----------------------------------------------------------------    The crystal structure of tab1 and bir1 complex
2qra:D -----------------------------------------------------------------    Crystal structure of xiap bir1 domain (p21 form)
2vm5:A -----------------------------------------------------------------    Human bir2 domain of baculoviral inhibitor of apoptosis  ...
2pop:D -----------------------------------------------------------------    The crystal structure of tab1 and bir1 complex

           4         4         4         4         5 
           6         7         8         9         0 
       6789012345678901234567890123456789012345678901                       Protein name
       ----+---------+---------+---------+---------+-                       ------------
P22139 ----------------------------------------------                       DNA-directed RNA polymerases I, II, and III subunit RPABC5  ...
4c2m:J*----------------------------------------------                   ×4  Structure of RNA polymerase i at 2.8 a resolution
3fki:J ----------------------------------------------                       12-subunit RNA polymerase ii refined with zn-sad data
1i3q:J*----------------------------------------------                   ×95 RNA polymerase ii crystal form i at 3.1 a resolution
1twa:J*----------------------------------------------                   ×4  RNA polymerase ii complexed with atp
3h0g:J ----------------------------------------------                       RNA polymerase ii from schizosaccharomyces pombe
2pmz:N*----------------------------------------------                   ×2  Archaeal RNA polymerase from sulfolobus solfataricus
2waq:N*----------------------------------------------                   ×3  The complete structure of the archaeal 13-subunit DNA-  ...
4ayb:N*----------------------------------------------                   ×3  Rnap at 3.2ang
1ef4:A ----------------------------------------------                       Solution structure of the essential RNA polymerase subunit  ...
2max:A ----------------------------------------------                       Nmr structure of the RNA polymerase alpha subunit  ...
1i11:A ----------------------------------------------                       Solution structure of the DNA binding domain, sox-5 hmg box  ...
3dai:A ----------------------------------------------                       Crystal structure of the bromodomain of the human atad2
2epw:A ----------------------------------------------                       Solution structure of the 24th c2h2 type zinc finger domain  ...
1hso:A*pklvadfmakkfsldalithvlpfekinegfdllhsgksirtilmf                   ×2  Human alpha alcohol dehydrogenase (adh1a)
3tni:A ----------------------------------------------                       Structure of cdk9/cyclin t f241l
2poi:A ----------------------------------------------                       Crystal structure of xiap bir1 domain (i222 form)
2pop:B ----------------------------------------------                       The crystal structure of tab1 and bir1 complex
2qra:D ----------------------------------------------                       Crystal structure of xiap bir1 domain (p21 form)
2vm5:A ----------------------------------------------                       Human bir2 domain of baculoviral inhibitor of apoptosis  ...
2pop:D ----------------------------------------------                       The crystal structure of tab1 and bir1 complex

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. P22139. 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 (or to add back any sequences in the Excluded list). 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. - - - 70 - - P22139 DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPB10 PE=1 SV=2
2. 476 100.0% 69 69 677.2 9.4e-31 4c2m:J * Structure of RNA polymerase i at 2.8 a resolution
3. " " " " " "  = 4c3h:J *
Structure of 14-subunit RNA polymerase i at 3.27 a resolutio crystal form c2-93
4. " " " " " "  = 4c3i:J *
Structure of 14-subunit RNA polymerase i at 3.0 a resolution crystal form c2-100
5. " " " " " "  = 4c3j:J *
Structure of 14-subunit RNA polymerase i at 3.35 a resolutio crystal form c2-90
6. 457 100.0% 66 66 650.9 2.7e-29 3fki:J 12-subunit RNA polymerase ii refined with zn-sad data
7. 452 100.0% 65 65 644.1 6.6e-29 1i3q:J * RNA polymerase ii crystal form i at 3.1 a resolution
8. " " " " " "  = 1i50:J *
RNA polymerase ii crystal form ii at 2.8 a resolution
9. " " " " " "  = 1i6h:J *
RNA polymerase ii elongation complex
10. " " " " " "  = 1k83:J *
Crystal structure of yeast RNA polymerase ii complexed with inhibitor alpha amanitin
11. " " " " " "  = 1nik:J *
Wild type RNA polymerase ii
12. " " " " " "  = 1nt9:J *
Complete 12-subunit RNA polymerase ii
13. " " " " " "  = 1pqv:J *
RNA polymerase ii-tfiis complex
14. " " " " " "  = 1r5u:J *
RNA polymerase ii tfiib complex
15. " " " " " "  = 1r9r:J *
RNA polymerase ii strand separated elongation complex
16. " " " " " "  = 1r9s:J *
RNA polymerase ii strand separated elongation complex, matched nucleotide
17. " " " " " "  = 1r9t:J *
RNA polymerase ii strand separated elongation complex, mismatched nucleotide
18. " " " " " "  = 1sfo:J *
RNA polymerase ii strand separated elongation complex
19. " " " " " "  = 1twf:J *
RNA polymerase ii complexed with utp at 2.3 a resolution
20. " " " " " "  = 1wcm:J *
Complete 12-subunit RNA polymerase ii at 3.8 ang
21. " " " " " "  = 1y1v:J *
Refined RNA polymerase ii-tfiis complex
22. " " " " " "  = 1y1w:J *
Complete RNA polymerase ii elongation complex
23. " " " " " "  = 1y1y:J *
RNA polymerase ii-tfiis-DNA/RNA complex
24. " " " " " "  = 1y77:J *
Complete RNA polymerase ii elongation complex with substrate gmpcpp
25. " " " " " "  = 2b63:J *
Complete RNA polymerase ii-RNA inhibitor complex
26. " " " " " "  = 2b8k:J *
12-subunit RNA polymerase ii
27. " " " " " "  = 2e2h:J *
RNA polymerase ii elongation complex at 5 mm mg2+ with gtp
28. " " " " " "  = 2e2i:J *
RNA polymerase ii elongation complex in 5 mm mg+2 with 2'- dgtp
29. " " " " " "  = 2e2j:J *
RNA polymerase ii elongation complex in 5 mm mg+2 with gmpcpp
30. " " " " " "  = 2ja5:J *
Cpd lesion containing RNA polymerase ii elongation complex a
31. " " " " " "  = 2ja6:J *
Cpd lesion containing RNA polymerase ii elongation complex b
32. " " " " " "  = 2ja7:J *
Cpd lesion containing RNA polymerase ii elongation complex c
33. " " " " " "  = 2ja8:J *
Cpd lesion containing RNA polymerase ii elongation complex d
34. " " " " " "  = 2nvq:J *
RNA polymerase ii elongation complex in 150 mm mg+2 with 2'dutp
35. " " " " " "  = 2nvs:J *
RNA polymerase ii elongation complex in 150 mm mg+2 with utp
36. " " " " " "  = 2nvt:J *
RNA polymerase ii elongation complex in 150 mm mg+2 with gmpcpp
37. " " " " " "  = 2nvx:J *
RNA polymerase ii elongation complex in 5 mm mg+2 with 2'- dutp
38. " " " " " "  = 2nvy:J *
RNA polymerase ii form ii in 150 mm mn+2
39. " " " " " "  = 2nvz:J *
RNA polymerase ii elongation complex with utp, updated 11/2006
40. " " " " " "  = 2r7z:J *
Cisplatin lesion containing RNA polymerase ii elongation com
41. " " " " " "  = 2r92:J *
Elongation complex of RNA polymerase ii with artificial rdrp scaffold
42. " " " " " "  = 2r93:J *
Elongation complex of RNA polymerase ii with a hepatitis delta virus-derived RNA stem loop
43. " " " " " "  = 2vum:J *
Alpha-amanitin inhibited complete RNA polymerase ii elongation complex
44. " " " " " "  = 2yu9:J *
RNA polymerase ii elongation complex in 150 mm mg+2 with utp
45. " " " " " "  = 3cqz:J *
Crystal structure of 10 subunit RNA polymerase ii in complex inhibitor alpha-amanitin
46. " " " " " "  = 3gtg:J *
Backtracked RNA polymerase ii complex with 12mer RNA
47. " " " " " "  = 3gtj:J *
Backtracked RNA polymerase ii complex with 13mer RNA
48. " " " " " "  = 3gtk:J *
Backtracked RNA polymerase ii complex with 18mer RNA
49. " " " " " "  = 3gtl:J *
Backtracked RNA polymerase ii complex with 13mer with g<>u m
50. " " " " " "  = 3gtm:J *
Co-complex of backtracked RNA polymerase ii with tfiis
51. " " " " " "  = 3gto:J *
Backtracked RNA polymerase ii complex with 15mer RNA
52. " " " " " "  = 3gtp:J *
Backtracked RNA polymerase ii complex with 24mer RNA
53. " " " " " "  = 3gtq:J *
Backtracked RNA polymerase ii complex induced by damage
54. " " " " " "  = 3h3v:K *
Yeast rnap ii containing poly(a)-signal sequence in the acti
55. " " " " " "  = 3hou:J *
Complete RNA polymerase ii elongation complex i with a t-u mismatch
56. " " " " " "  = 3hov:J *
Complete RNA polymerase ii elongation complex ii
57. " " " " " "  = 3how:J *
Complete RNA polymerase ii elongation complex iii with a t-u mismatch and a frayed RNA 3'-uridine
58. " " " " " "  = 3hox:J *
Complete RNA polymerase ii elongation complex v
59. " " " " " "  = 3hoy:J *
Complete RNA polymerase ii elongation complex vi
60. " " " " " "  = 3hoz:J *
Complete RNA polymerase ii elongation complex iv with a t-u mismatch and a frayed RNA 3'-guanine
61. " " " " " "  = 3i4m:J *
8-oxoguanine containing RNA polymerase ii elongation complex
62. " " " " " "  = 3i4n:J *
8-oxoguanine containing RNA polymerase ii elongation complex
63. " " " " " "  = 3j0k:J *
Orientation of RNA polymerase ii within the human vp16-media ii-tfiif assembly
64. " " " " " "  = 3j1n:J *
Cryo-em map of a yeast minimal preinitiation complex interac the mediator head module
65. " " " " " "  = 3k1f:J *
Crystal structure of RNA polymerase ii in complex with tfiib
66. " " " " " "  = 3k7a:J *
Crystal structure of an RNA polymerase ii-tfiib complex
67. " " " " " "  = 3m3y:J *
RNA polymerase ii elongation complex c
68. " " " " " "  = 3m4o:J *
RNA polymerase ii elongation complex b
69. " " " " " "  = 3po2:J *
Arrested RNA polymerase ii elongation complex
70. " " " " " "  = 3po3:J *
Arrested RNA polymerase ii reactivation intermediate
71. " " " " " "  = 3qt1:J *
RNA polymerase ii variant containing a chimeric rpb9-c11 sub
72. " " " " " "  = 3rzd:J *
RNA polymerase ii initiation complex with a 5-nt RNA
73. " " " " " "  = 3rzo:J *
RNA polymerase ii initiation complex with a 4-nt RNA
74. " " " " " "  = 3s14:J *
RNA polymerase ii initiation complex with a 6-nt RNA
75. " " " " " "  = 3s15:J *
RNA polymerase ii initiation complex with a 7-nt RNA
76. " " " " " "  = 3s16:J *
RNA polymerase ii initiation complex with an 8-nt RNA
77. " " " " " "  = 3s17:J *
RNA polymerase ii initiation complex with a 9-nt RNA
78. " " " " " "  = 3s1m:J *
RNA polymerase ii initiation complex with a 5-nt RNA (varian
79. " " " " " "  = 3s1n:J *
RNA polymerase ii initiation complex with a 5-nt RNA (varian
80. " " " " " "  = 3s1q:J *
RNA polymerase ii initiation complex with a 5-nt 3'-deoxy rn with atp
81. " " " " " "  = 3s1r:J *
RNA polymerase ii initiation complex with a 5-nt 3'-deoxy rn with gtp
82. " " " " " "  = 3s2d:J *
RNA polymerase ii initiation complex with a 5-nt RNA contain u
83. " " " " " "  = 3s2h:J *
RNA polymerase ii initiation complex with a 6-nt RNA contain 2[prime]-iodo atp
84. " " " " " "  = 4a3b:J *
RNA polymerase ii initial transcribing complex with a 4nt DNA-RNA hybrid
85. " " " " " "  = 4a3c:J *
RNA polymerase ii initial transcribing complex with a 5nt dn hybrid
86. " " " " " "  = 4a3d:J *
RNA polymerase ii initial transcribing complex with a 6nt dn hybrid
87. " " " " " "  = 4a3e:J *
RNA polymerase ii initial transcribing complex with a 5nt dn hybrid and soaked with ampcpp
88. " " " " " "  = 4a3f:J *
RNA polymerase ii initial transcribing complex with a 6nt dn hybrid and soaked with ampcpp
89. " " " " " "  = 4a3g:J *
RNA polymerase ii initial transcribing complex with a 2nt DNA-RNA hybrid
90. " " " " " "  = 4a3i:J *
RNA polymerase ii binary complex with DNA
91. " " " " " "  = 4a3j:J *
RNA polymerase ii initial transcribing complex with a 2nt DNA-RNA hybrid and soaked with gmpcpp
92. " " " " " "  = 4a3k:J *
RNA polymerase ii initial transcribing complex with a 7nt DNA-RNA hybrid
93. " " " " " "  = 4a3l:J *
RNA polymerase ii initial transcribing complex with a 7nt DNA-RNA hybrid and soaked with ampcpp
94. " " " " " "  = 4a3m:J *
RNA polymerase ii initial transcribing complex with a 4nt DNA-RNA hybrid and soaked with ampcpp
95. " " " " " "  = 4a93:J *
RNA polymerase ii elongation complex containing a cpd lesion
96. " " " " " "  = 4bbr:J *
Structure of RNA polymerase ii-tfiib complex
97. " " " " " "  = 4bbs:J *
Structure of an initially transcribing RNA polymerase ii- tfiib complex
98. " " " " " "  = 4bxx:J *
Arrested RNA polymerase ii-bye1 complex
99. " " " " " "  = 4bxz:J *
RNA polymerase ii-bye1 complex
100. " " " " " "  = 4by1:J *
Elongating RNA polymerase ii-bye1 tld complex soaked with am
101. " " " " " "  = 4by7:J *
Elongating RNA polymerase ii-bye1 tld complex
102. 442 100.0% 64 64 630.2 3.9e-28 1twa:J * RNA polymerase ii complexed with atp
103. " " " " " "  = 1twc:J *
RNA polymerase ii complexed with gtp
104. " " " " " "  = 1twg:J *
RNA polymerase ii complexed with ctp
105. " " " " " "  = 1twh:J *
RNA polymerase ii complexed with 2'datp
106. 366 76.9% 65 64 524.3 3.1e-22 3h0g:J RNA polymerase ii from schizosaccharomyces pombe
107. 257 47.6% 63 64 372.5 8.8e-14 2pmz:N * Archaeal RNA polymerase from sulfolobus solfataricus
108. " " " " " "  = 3hkz:N *
The x-ray crystal structure of RNA polymerase from archaea
109. 249 44.4% 63 64 361.4 3.7e-13 2waq:N * The complete structure of the archaeal 13-subunit DNA- directed RNA polymerase
110. " " " " " "  = 2wb1:N *
The complete structure of the archaeal 13-subunit DNA- directed RNA polymerase
111. " " " " " "  = 2y0s:N *
Crystal structure of sulfolobus shibatae RNA polymerase in p21 space group
112. 249 44.4% 63 65 361.3 3.7e-13 4ayb:N * Rnap at 3.2ang
113. " " " " " "  = 4b1o:N *
Archaeal rnap-DNA binary complex at 4.32ang
114. " " " " " "  = 4b1p:O *
Archaeal rnap-DNA binary complex at 4.32ang
115. 185 48.1% 54 55 273.0 3.1e-08 1ef4:A Solution structure of the essential RNA polymerase subunit rpb10 from methanobacterium thermoautotrophicum
116. 82 36.4% 44 114 125.8 4.9 2max:A Nmr structure of the RNA polymerase alpha subunit c-terminal from helicobacter pylori
117. 77 30.3% 33 70 121.3 8.6 1i11:A Solution structure of the DNA binding domain, sox-5 hmg box from mouse
118. 76 27.5% 51 130 116.8 16 3dai:A Crystal structure of the bromodomain of the human atad2
119. 70 34.5% 29 46 113.7 23 2epw:A Solution structure of the 24th c2h2 type zinc finger domain of zinc finger protein 268
120. 76 26.5% 68 374 111.3 31 1hso:A * Human alpha alcohol dehydrogenase (adh1a)
121. " " " " " "  = 1u3t:A *
Crystal structure of human alcohol dehydrogenase alpha- alpha isoform complexed with n-cyclopentyl-n- cyclobutylformamide determined to 2.5 angstrom resolution
122. 74 30.2% 63 297 109.7 38 3tni:A Structure of cdk9/cyclin t f241l
123. 69 60.0% 15 78 109.6 39 2poi:A Crystal structure of xiap bir1 domain (i222 form)
124. 69 60.0% 15 79 109.6 39 2pop:B The crystal structure of tab1 and bir1 complex
125. 69 60.0% 15 78 109.6 39 2qra:D Crystal structure of xiap bir1 domain (p21 form)
126. 70 60.0% 15 103 109.6 39 2vm5:A Human bir2 domain of baculoviral inhibitor of apoptosis repeat-containing 1 (birc1)
127. 69 60.0% 15 80 109.5 39 2pop:D The crystal structure of tab1 and bir1 complex

Number of sequences: 127

Excluded sequences

  Smith-
Waterman
score
%-tage
identity
a.a.
overlap
Seq
len
z-score E-
value
  PDB
code
Protein name
1. 70 36.4% 44 104 109.5 39 4itk:A The structure of c.Reinhardtii ferredoxin 2
2. 73 27.9% 68 267 108.9 43 1zar:A Crystal structure of a.Fulgidus rio2 kinase complexed with adp and manganese ions
3. 73 27.9% 68 269 108.8 43 1tqi:A * Crystal structure of a. Fulgidus rio2 serine protein kinase
4. " " " " " "  = 1tqm:A *
Crystal structure of a. Fulgidus rio2 serine protein kinase amppnp
5. " " " " " "  = 1tqp:A *
Crystal structure of a. Fulgidus rio2 serine protein kinase atp
6. 73 27.9% 68 271 108.8 43 1zao:A Crystal structure of a.Fulgidus rio2 kinase complexed with atp and manganese ions
7. 66 53.8% 13 46 108.2 47 2ytm:A Solution structure of the c2h2 type zinc finger (region 696- 728) of human zinc finger protein 28 homolog

Number of sequences: 7

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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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