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SAS results for UniProt accession no. P27999

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. P27999 - coloured by no. of contacts to ligand

Below are the FASTA results from a search of the sequence of UniProt accession no. P27999 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 49 unique sequences (including 8 consensus sequences) giving 146 sequence matches in all. The 30 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
       ---------+---------+---------+---------+---------+---------+-----    ------------
P27999 -----------------------------------------------------------------    DNA-directed RNA polymerase II subunit RPB9  ...
1i3q:I*-----------------------------------------------------------------×5  RNA polymerase ii crystal form i at 3.1 a resolution
1twa:I*-----------------------------------------------------------------×4  RNA polymerase ii complexed with atp
3cqz:I -----------------------------------------------------------------    Crystal structure of 10 subunit RNA polymerase ii in  ...
1i6h:I*-----------------------------------------------------------------×77 RNA polymerase ii elongation complex
3i4n:I -----------------------------------------------------------------    8-oxoguanine containing RNA polymerase ii elongation complex
2ja5:I*-----------------------------------------------------------------×7  Cpd lesion containing RNA polymerase ii elongation complex a
1r5u:I*-----------------------------------------------------------------×3  RNA polymerase ii tfiib complex
3how:I -----------------------------------------------------------------    Complete RNA polymerase ii elongation complex iii with a  ...
3h0g:I -----------------------------------------------------------------    RNA polymerase ii from schizosaccharomyces pombe
3qt1:I -----------------------------------------------------------------    RNA polymerase ii variant containing a chimeric rpb9-c11 sub
1qyp:A -----------------------------------------------------------------    Thermococcus celer rpb9, nmr, 25 structures
4c2m:I*-----------------------------------------------------------------×4  Structure of RNA polymerase i at 2.8 a resolution
1pqv:S*-----------------------------------------------------------------×3  RNA polymerase ii-tfiis complex
3gtm:S -----------------------------------------------------------------    Co-complex of backtracked RNA polymerase ii with tfiis
1tfi:A -----------------------------------------------------------------    A novel zn finger motif in the basal transcriptional  ...
3po3:S -----------------------------------------------------------------    Arrested RNA polymerase ii reactivation intermediate
1fwq:A -----------------------------------------------------------------    Solution structure of human mss4, a guanine nucleotide  ...
2k3r:A -----------------------------------------------------------------    Pfu rpp21 structure and assignments
2ki7:B -----------------------------------------------------------------    The solution structure of rpp29-rpp21 complex from  ...
4i1h:A siynsfyvyckgpcqrvqpgklrvqcstcrqatltltqgpscwddvlipnrmsgecqsphcpgts    Structure of parkin e3 ligase

                                         1         1         1         1
           7         8         9         0         1         2         3
       67890123456789012345678901234567890123456789012345678901234567890    Protein name
       ----+---------+---------+---------+---------+---------+---------+    ------------
P27999 -----------------------------------------------------------------    DNA-directed RNA polymerase II subunit RPB9  ...
1i3q:I*-----------------------------------------------------------------×5  RNA polymerase ii crystal form i at 3.1 a resolution
1twa:I*-----------------------------------------------------------------×4  RNA polymerase ii complexed with atp
3cqz:I -----------------------------------------------------------------    Crystal structure of 10 subunit RNA polymerase ii in  ...
1i6h:I*-----------------------------------------------------------------×77 RNA polymerase ii elongation complex
3i4n:I -----------------------------------------------------------------    8-oxoguanine containing RNA polymerase ii elongation complex
2ja5:I*-----------------------------------------------------------------×7  Cpd lesion containing RNA polymerase ii elongation complex a
1r5u:I*-----------------------------------------------------------------×3  RNA polymerase ii tfiib complex
3how:I -----------------------------------------------------------------    Complete RNA polymerase ii elongation complex iii with a  ...
3h0g:I -----------------------------------------------------------------    RNA polymerase ii from schizosaccharomyces pombe
3qt1:I -----------------------------------------------------------------    RNA polymerase ii variant containing a chimeric rpb9-c11 sub
1qyp:A -----------------------------------------------------------------    Thermococcus celer rpb9, nmr, 25 structures
4c2m:I*-----------------------------------------------------------------×4  Structure of RNA polymerase i at 2.8 a resolution
1pqv:S*----------------------------------------------------------ndgvdta×3  RNA polymerase ii-tfiis complex
3gtm:S -----------------------------------------------------------------    Co-complex of backtracked RNA polymerase ii with tfiis
1tfi:A -----------------------------------------------------------------    A novel zn finger motif in the basal transcriptional  ...
3po3:S -----------------------------------------------------------------    Arrested RNA polymerase ii reactivation intermediate
1fwq:A -----------------------------------------------------------------    Solution structure of human mss4, a guanine nucleotide  ...
2k3r:A -----------------------------------------------------------------    Pfu rpp21 structure and assignments
2ki7:B -----------------------------------------------------------------    The solution structure of rpp29-rpp21 complex from  ...
4i1h:A aefffkcgahptsdketsvalhliatnsrnitcitctdvrspvlvfqcnsrhvicldcfhlycvt    Structure of parkin e3 ligase

                1         1         1         1         1         1     
                4         5         6         7         8         9     
       12345678901234567890123456789012345678901234567890123456789012345    Protein name
       ---------+---------+---------+---------+---------+---------+-----    ------------
P27999 ---------------------------------------------------------mttfrfcr    DNA-directed RNA polymerase II subunit RPB9  ...
1i3q:I*---------------------------------------------------------mttfrfcr×5  RNA polymerase ii crystal form i at 3.1 a resolution
1twa:I*---------------------------------------------------------mttfrfcr×4  RNA polymerase ii complexed with atp
3cqz:I ----------------------------------------------------------ttfrfcr    Crystal structure of 10 subunit RNA polymerase ii in  ...
1i6h:I*----------------------------------------------------------ttfrfcr×77 RNA polymerase ii elongation complex
3i4n:I ---------------------------------------------------------mttfrfcr    8-oxoguanine containing RNA polymerase ii elongation complex
2ja5:I*----------------------------------------------------------ttfrfcr×7  Cpd lesion containing RNA polymerase ii elongation complex a
1r5u:I*----------------------------------------------------------ttfrfcr×3  RNA polymerase ii tfiib complex
3how:I ----------------------------------------------------------ttfrfcr    Complete RNA polymerase ii elongation complex iii with a  ...
3h0g:I -----------------------------------------------------------nfqyci    RNA polymerase ii from schizosaccharomyces pombe
3qt1:I ----------------------------------------------------------ttfrfcr    RNA polymerase ii variant containing a chimeric rpb9-c11 sub
1qyp:A -----------------------------------------------------------------    Thermococcus celer rpb9, nmr, 25 structures
4c2m:I*-------------------------------------------------------svvgslifcl×4  Structure of RNA polymerase i at 2.8 a resolution
1pqv:S*iyhhklrdqvlkalydvlakesehppqsilhtakaiesemnkvnncdtneaaykaryriiysnvi×3  RNA polymerase ii-tfiis complex
3gtm:S ----klrdqvlkalydvlakesehppqsilhtakaiesemnkvnncdtneaaykaryriiysnvi    Co-complex of backtracked RNA polymerase ii with tfiis
1tfi:A -----------------------------------------------------------------    A novel zn finger motif in the basal transcriptional  ...
3po3:S ---hklrdqvlkalydvlakesehppqsilhtakaiesemnkvnncdtneaaykaryriiysnvi    Arrested RNA polymerase ii reactivation intermediate
1fwq:A -----------------------------------------------------------------    Solution structure of human mss4, a guanine nucleotide  ...
2k3r:A -----------------------------------------------------------------    Pfu rpp21 structure and assignments
2ki7:B -----------------------------------------------------------------    The solution structure of rpp29-rpp21 complex from  ...
4i1h:A rlndrqfvhdpqlgyslpcvagcpnslikelhhfrilgeeqynryqqygaeecvlqmggvlcprp    Structure of parkin e3 ligase

           2         2         2         2         2         2         2
           0         1         2         3         4         5         6
       67890123456789012345678901234567890123456789012345678901234567890    Protein name
       ----+---------+---------+---------+---------+---------+---------+    ------------
P27999 dcnnmly-predkennrllfecrtc-syveeagsplvyrhelit--nigeta---------g--v    DNA-directed RNA polymerase II subunit RPB9  ...
1i3q:I*dcnnmly-predkennrllfecrtc-syveeagsplvyrhelit--nigeta---------g--v×5  RNA polymerase ii crystal form i at 3.1 a resolution
1twa:I*dcnnmly-predkennrllfecrtc-syveeagsplvyrhelit--nigeta---------g--v×4  RNA polymerase ii complexed with atp
3cqz:I dcnnmly-predkennrllfecrtc-syveeagsplvyrhelit--nigeta---------g--v    Crystal structure of 10 subunit RNA polymerase ii in  ...
1i6h:I*dcnnmly-predkennrllfecrtc-syveeagsplvyrhelit--nigeta---------g--v×77 RNA polymerase ii elongation complex
3i4n:I dcnnmly-predkennrllfecrtc-syveeagsplvyrhelit--nigeta---------g--v    8-oxoguanine containing RNA polymerase ii elongation complex
2ja5:I*dcnnmly-predkennrllfecrtc-syveeagsplvyrhelit--nigeta---------g--v×7  Cpd lesion containing RNA polymerase ii elongation complex a
1r5u:I*dcnnmly-predkennrllfecrtc-syveea-splvyrhelit--nigeta---------g--v×3  RNA polymerase ii tfiib complex
3how:I dcnnmly-predkennrllfecrtc-syveeagsplvyrhelit--nigeta---------g--v    Complete RNA polymerase ii elongation complex iii with a  ...
3h0g:I ecnnmly-predkvdrvlrlacrnc-dyseiaatskvyrhelqs--snvent---------t--v    RNA polymerase ii from schizosaccharomyces pombe
3qt1:I dcnnmly-predkennrllfecrtc-syveeagsplvyrhel-----------------------    RNA polymerase ii variant containing a chimeric rpb9-c11 sub
1qyp:A ----------------------------------------------------------------g    Thermococcus celer rpb9, nmr, 25 structures
4c2m:I*dcgdllenpnavlgsn---vecsqc-kaiypksq--fsnlkvvt--ttaddafpsslrakks--v×4  Structure of RNA polymerase i at 2.8 a resolution
1pqv:S*sknnpdl-khkiangditpeflatc-dakdlapaplkqkieeiakqnlynaq---------g--a×3  RNA polymerase ii-tfiis complex
3gtm:S sknnpdl-khkiangditpeflatc-dakdlapaplkqkieeiakqnlynaq---------g--a    Co-complex of backtracked RNA polymerase ii with tfiis
1tfi:A -----------------------------------------------------------------    A novel zn finger motif in the basal transcriptional  ...
3po3:S sknnpdl-khkiangditpeflatc-dakdlapaplkqkieeiakqnlynaq---------g--a    Arrested RNA polymerase ii reactivation intermediate
1fwq:A ------e-lvsaegrnrkavlcqrcgsrvlqpgtalfsrrqlfl--psmrkk---------p--a    Solution structure of human mss4, a guanine nucleotide  ...
2k3r:A --------------------kerid-ilfslaervfpyspelak--ryvela---------l--l    Pfu rpp21 structure and assignments
2ki7:B --------------ekkriakerid-ilfslaervfpyspelak--ryvela---------l--l    The solution structure of rpp29-rpp21 complex from  ...
4i1h:A gcgagll-pepdqrk----vtcegc-gfafcreckeay-hegec--svdera---------aeqa    Structure of parkin e3 ligase

                2         2         2         3         3         3     
                7         8         9         0         1         2     
       12345678901234567890123456789012345678901234567890123456789012345    Protein name
       ---------+---------+---------+---------+---------+---------+-----    ------------
P27999 vqdigsdptlprs---dr-ecpkch-srenvf-fqsqqrrkdtsmvlffv-clscshiftsdqkn    DNA-directed RNA polymerase II subunit RPB9  ...
1i3q:I*vqdigsdptlprs---dr-ecpkch-srenvf-fqsqqrrkdtsmvlffv-clscshiftsdqkn×5  RNA polymerase ii crystal form i at 3.1 a resolution
1twa:I*vqdigsdptlprs---dr-ecpkch-srenvf-fqsqqrrkdtsmvlffv-clscshiftsdqkn×4  RNA polymerase ii complexed with atp
3cqz:I vqdigsdptlprs---dr-ecpkch-srenvf-fqsqqrrkdtsmvlffv-clscshiftsdqkn    Crystal structure of 10 subunit RNA polymerase ii in  ...
1i6h:I*vqdigsdptlprs---dr-ecpkch-srenvf-fqsqqrrkdtsmvlffv-clscshiftsdqkn×77 RNA polymerase ii elongation complex
3i4n:I vqdigsdptlprs---dr-ecpkch-srenvf-fqsqqrrkdtsmvlffv-clscshiftsdqkn    8-oxoguanine containing RNA polymerase ii elongation complex
2ja5:I*vqdigsdptlprs---dr-ecpkch-srenvf-fqsqqrrkdtsmvlffv-clscshiftsdqkn×7  Cpd lesion containing RNA polymerase ii elongation complex a
1r5u:I*vqdigsdptlprs---dr-ecpkch-srenvf-fqsqqrrkdtsmvlffv-clscshiftsdqkn×3  RNA polymerase ii tfiib complex
3how:I vqdigsdptlprs---dr-ecpkch-srenvf-fqsqqrrkdtsmvlffv-clscshiftsdqk-    Complete RNA polymerase ii elongation complex iii with a  ...
3h0g:I shdastdptlprs---dk-ecprch-qheavf-yqthsrrgdtmmtliyv-cvhcgfafeeq---    RNA polymerase ii from schizosaccharomyces pombe
3qt1:I -----------------------------------------------------------------    RNA polymerase ii variant containing a chimeric rpb9-c11 sub
1qyp:A shmeqdlktlptt---ki-tcpkcg-ndtayw-wemqtragdepstifyk-ctkcghtwrsye--    Thermococcus celer rpb9, nmr, 25 structures
4c2m:I*vktslkknelkdgatike-kcpqcg-neemny-htlqlrsadegatvfyt-ctscgykfrtnn--×4  Structure of RNA polymerase i at 2.8 a resolution
1pqv:S*--------tiersvt-drftcgkck-ekkvsy-yqlqtrsadeplttfct-ceacgnrwkfs---×3  RNA polymerase ii-tfiis complex
3gtm:S --------tiersvt-drftcgkck-ekkvsy-yqlqtrsadhplttfct-ceacgnrwkfs---    Co-complex of backtracked RNA polymerase ii with tfiis
1tfi:A -----ktggtqtd---lf-tcgkck-kkncty-tqvqtrsadepmttfvv-cnecgnrwkfc---    A novel zn finger motif in the basal transcriptional  ...
3po3:S --------tiersvt-drftcgkck-ekkvsy-yqlqtrsaaaplttfct-ceacgnrwkfs---    Arrested RNA polymerase ii reactivation intermediate
1fwq:A lsd-gsnp--------dg-dllqehwlvedmfifenvgftkdvgnikflv-cadceigpigwhcl    Solution structure of human mss4, a guanine nucleotide  ...
2k3r:A vqq-kakvkiprkwk-rr-yckkch-aflvpg-inarvrlrqkrmphivvkclecghimrypyik    Pfu rpp21 structure and assignments
2ki7:B vqq-kakvkiprkwk-rr-yckkch-aflvpg-inarvrlrqkrmphivvkclecghimrypyik    The solution structure of rpp29-rpp21 complex from  ...
4i1h:A rweaasketikkt---tk-pcprch-vpvekn-ggcmhmkcpqpqcrlew-cwncgcewnrvcmg    Structure of parkin e3 ligase

           3         3 
           3         4 
       6789012345678901                                                     Protein name
       ----+---------+-                                                     ------------
P27999 krtqfs----------                                                     DNA-directed RNA polymerase II subunit RPB9  ...
1i3q:I*krtqfs----------                                                 ×5  RNA polymerase ii crystal form i at 3.1 a resolution
1twa:I*krtqf-----------                                                 ×4  RNA polymerase ii complexed with atp
3cqz:I krtqfs----------                                                     Crystal structure of 10 subunit RNA polymerase ii in  ...
1i6h:I*krtq------------                                                 ×77 RNA polymerase ii elongation complex
3i4n:I k---------------                                                     8-oxoguanine containing RNA polymerase ii elongation complex
2ja5:I*k---------------                                                 ×7  Cpd lesion containing RNA polymerase ii elongation complex a
1r5u:I*krtq------------                                                 ×3  RNA polymerase ii tfiib complex
3how:I ----------------                                                     Complete RNA polymerase ii elongation complex iii with a  ...
3h0g:I ----------------                                                     RNA polymerase ii from schizosaccharomyces pombe
3qt1:I ----------------                                                     RNA polymerase ii variant containing a chimeric rpb9-c11 sub
1qyp:A ----------------                                                     Thermococcus celer rpb9, nmr, 25 structures
4c2m:I*----------------                                                 ×4  Structure of RNA polymerase i at 2.8 a resolution
1pqv:S*----------------                                                 ×3  RNA polymerase ii-tfiis complex
3gtm:S ----------------                                                     Co-complex of backtracked RNA polymerase ii with tfiis
1tfi:A ----------------                                                     A novel zn finger motif in the basal transcriptional  ...
3po3:S ----------------                                                     Arrested RNA polymerase ii reactivation intermediate
1fwq:A ddknsfyvalervshe                                                     Solution structure of human mss4, a guanine nucleotide  ...
2k3r:A ----------------                                                     Pfu rpp21 structure and assignments
2ki7:B ----------------                                                     The solution structure of rpp29-rpp21 complex from  ...
4i1h:A dhwfdv----------                                                     Structure of parkin e3 ligase

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. P27999. 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. - - - 122 - - P27999 DNA-directed RNA polymerase II subunit RPB9 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPB9 PE=1 SV=1
2. 853 100.0% 122 122 1151.5 3.6e-57 1i3q:I * RNA polymerase ii crystal form i at 3.1 a resolution
3. " " " " " "  = 1i50:I *
RNA polymerase ii crystal form ii at 2.8 a resolution
4. " " " " " "  = 1k83:I *
Crystal structure of yeast RNA polymerase ii complexed with inhibitor alpha amanitin
5. " " " " " "  = 1twf:I *
RNA polymerase ii complexed with utp at 2.3 a resolution
6. " " " " " "  = 2nvy:I *
RNA polymerase ii form ii in 150 mm mn+2
7. 848 100.0% 121 121 1144.9 8.4e-57 1twa:I * RNA polymerase ii complexed with atp
8. " " " " " "  = 1twc:I *
RNA polymerase ii complexed with gtp
9. " " " " " "  = 1twg:I *
RNA polymerase ii complexed with ctp
10. " " " " " "  = 1twh:I *
RNA polymerase ii complexed with 2'datp
11. 846 100.0% 121 121 1142.2 1.2e-56 3cqz:I Crystal structure of 10 subunit RNA polymerase ii in complex inhibitor alpha-amanitin
12. 833 100.0% 119 119 1124.9 1.1e-55 1i6h:I * RNA polymerase ii elongation complex
13. " " " " " "  = 1nik:I *
Wild type RNA polymerase ii
14. " " " " " "  = 1nt9:I *
Complete 12-subunit RNA polymerase ii
15. " " " " " "  = 1pqv:I *
RNA polymerase ii-tfiis complex
16. " " " " " "  = 1r9r:I *
RNA polymerase ii strand separated elongation complex
17. " " " " " "  = 1r9s:I *
RNA polymerase ii strand separated elongation complex, matched nucleotide
18. " " " " " "  = 1r9t:I *
RNA polymerase ii strand separated elongation complex, mismatched nucleotide
19. " " " " " "  = 1sfo:I *
RNA polymerase ii strand separated elongation complex
20. " " " " " "  = 1wcm:I *
Complete 12-subunit RNA polymerase ii at 3.8 ang
21. " " " " " "  = 1y1v:I *
Refined RNA polymerase ii-tfiis complex
22. " " " " " "  = 1y1w:I *
Complete RNA polymerase ii elongation complex
23. " " " " " "  = 1y1y:I *
RNA polymerase ii-tfiis-DNA/RNA complex
24. " " " " " "  = 1y77:I *
Complete RNA polymerase ii elongation complex with substrate gmpcpp
25. " " " " " "  = 2b63:I *
Complete RNA polymerase ii-RNA inhibitor complex
26. " " " " " "  = 2b8k:I *
12-subunit RNA polymerase ii
27. " " " " " "  = 2e2h:I *
RNA polymerase ii elongation complex at 5 mm mg2+ with gtp
28. " " " " " "  = 2e2i:I *
RNA polymerase ii elongation complex in 5 mm mg+2 with 2'- dgtp
29. " " " " " "  = 2e2j:I *
RNA polymerase ii elongation complex in 5 mm mg+2 with gmpcpp
30. " " " " " "  = 2nvq:I *
RNA polymerase ii elongation complex in 150 mm mg+2 with 2'dutp
31. " " " " " "  = 2nvs:I *
RNA polymerase ii elongation complex in 150 mm mg+2 with utp
32. " " " " " "  = 2nvt:I *
RNA polymerase ii elongation complex in 150 mm mg+2 with gmpcpp
33. " " " " " "  = 2nvx:I *
RNA polymerase ii elongation complex in 5 mm mg+2 with 2'- dutp
34. " " " " " "  = 2nvz:I *
RNA polymerase ii elongation complex with utp, updated 11/2006
35. " " " " " "  = 2r7z:I *
Cisplatin lesion containing RNA polymerase ii elongation com
36. " " " " " "  = 2vum:I *
Alpha-amanitin inhibited complete RNA polymerase ii elongation complex
37. " " " " " "  = 2yu9:I *
RNA polymerase ii elongation complex in 150 mm mg+2 with utp
38. " " " " " "  = 3fki:I *
12-subunit RNA polymerase ii refined with zn-sad data
39. " " " " " "  = 3gtg:I *
Backtracked RNA polymerase ii complex with 12mer RNA
40. " " " " " "  = 3gtj:I *
Backtracked RNA polymerase ii complex with 13mer RNA
41. " " " " " "  = 3gtk:I *
Backtracked RNA polymerase ii complex with 18mer RNA
42. " " " " " "  = 3gtl:I *
Backtracked RNA polymerase ii complex with 13mer with g<>u m
43. " " " " " "  = 3gtm:I *
Co-complex of backtracked RNA polymerase ii with tfiis
44. " " " " " "  = 3gto:I *
Backtracked RNA polymerase ii complex with 15mer RNA
45. " " " " " "  = 3gtp:I *
Backtracked RNA polymerase ii complex with 24mer RNA
46. " " " " " "  = 3gtq:I *
Backtracked RNA polymerase ii complex induced by damage
47. " " " " " "  = 3h3v:J *
Yeast rnap ii containing poly(a)-signal sequence in the acti
48. " " " " " "  = 3hou:I *
Complete RNA polymerase ii elongation complex i with a t-u mismatch
49. " " " " " "  = 3hov:I *
Complete RNA polymerase ii elongation complex ii
50. " " " " " "  = 3hox:I *
Complete RNA polymerase ii elongation complex v
51. " " " " " "  = 3hoy:I *
Complete RNA polymerase ii elongation complex vi
52. " " " " " "  = 3hoz:I *
Complete RNA polymerase ii elongation complex iv with a t-u mismatch and a frayed RNA 3'-guanine
53. " " " " " "  = 3j0k:I *
Orientation of RNA polymerase ii within the human vp16-media ii-tfiif assembly
54. " " " " " "  = 3k1f:I *
Crystal structure of RNA polymerase ii in complex with tfiib
55. " " " " " "  = 3m3y:I *
RNA polymerase ii elongation complex c
56. " " " " " "  = 3m4o:I *
RNA polymerase ii elongation complex b
57. " " " " " "  = 3po2:I *
Arrested RNA polymerase ii elongation complex
58. " " " " " "  = 3po3:I *
Arrested RNA polymerase ii reactivation intermediate
59. " " " " " "  = 3rzd:I *
RNA polymerase ii initiation complex with a 5-nt RNA
60. " " " " " "  = 3rzo:I *
RNA polymerase ii initiation complex with a 4-nt RNA
61. " " " " " "  = 3s14:I *
RNA polymerase ii initiation complex with a 6-nt RNA
62. " " " " " "  = 3s15:I *
RNA polymerase ii initiation complex with a 7-nt RNA
63. " " " " " "  = 3s16:I *
RNA polymerase ii initiation complex with an 8-nt RNA
64. " " " " " "  = 3s17:I *
RNA polymerase ii initiation complex with a 9-nt RNA
65. " " " " " "  = 3s1m:I *
RNA polymerase ii initiation complex with a 5-nt RNA (varian
66. " " " " " "  = 3s1n:I *
RNA polymerase ii initiation complex with a 5-nt RNA (varian
67. " " " " " "  = 3s1q:I *
RNA polymerase ii initiation complex with a 5-nt 3'-deoxy rn with atp
68. " " " " " "  = 3s1r:I *
RNA polymerase ii initiation complex with a 5-nt 3'-deoxy rn with gtp
69. " " " " " "  = 3s2d:I *
RNA polymerase ii initiation complex with a 5-nt RNA contain u
70. " " " " " "  = 3s2h:I *
RNA polymerase ii initiation complex with a 6-nt RNA contain 2[prime]-iodo atp
71. " " " " " "  = 4a3b:I *
RNA polymerase ii initial transcribing complex with a 4nt DNA-RNA hybrid
72. " " " " " "  = 4a3c:I *
RNA polymerase ii initial transcribing complex with a 5nt dn hybrid
73. " " " " " "  = 4a3d:I *
RNA polymerase ii initial transcribing complex with a 6nt dn hybrid
74. " " " " " "  = 4a3e:I *
RNA polymerase ii initial transcribing complex with a 5nt dn hybrid and soaked with ampcpp
75. " " " " " "  = 4a3f:I *
RNA polymerase ii initial transcribing complex with a 6nt dn hybrid and soaked with ampcpp
76. " " " " " "  = 4a3g:I *
RNA polymerase ii initial transcribing complex with a 2nt DNA-RNA hybrid
77. " " " " " "  = 4a3i:I *
RNA polymerase ii binary complex with DNA
78. " " " " " "  = 4a3j:I *
RNA polymerase ii initial transcribing complex with a 2nt DNA-RNA hybrid and soaked with gmpcpp
79. " " " " " "  = 4a3k:I *
RNA polymerase ii initial transcribing complex with a 7nt DNA-RNA hybrid
80. " " " " " "  = 4a3l:I *
RNA polymerase ii initial transcribing complex with a 7nt DNA-RNA hybrid and soaked with ampcpp
81. " " " " " "  = 4a3m:I *
RNA polymerase ii initial transcribing complex with a 4nt DNA-RNA hybrid and soaked with ampcpp
82. " " " " " "  = 4a93:I *
RNA polymerase ii elongation complex containing a cpd lesion
83. " " " " " "  = 4bbr:I *
Structure of RNA polymerase ii-tfiib complex
84. " " " " " "  = 4bbs:I *
Structure of an initially transcribing RNA polymerase ii- tfiib complex
85. " " " " " "  = 4bxx:I *
Arrested RNA polymerase ii-bye1 complex
86. " " " " " "  = 4bxz:I *
RNA polymerase ii-bye1 complex
87. " " " " " "  = 4by1:I *
Elongating RNA polymerase ii-bye1 tld complex soaked with am
88. " " " " " "  = 4by7:I *
Elongating RNA polymerase ii-bye1 tld complex
89. 821 100.0% 117 117 1108.9 8.4e-55 3i4n:I 8-oxoguanine containing RNA polymerase ii elongation complex
90. 814 100.0% 116 116 1099.6 2.8e-54 2ja5:I * Cpd lesion containing RNA polymerase ii elongation complex a
91. " " " " " "  = 2ja6:I *
Cpd lesion containing RNA polymerase ii elongation complex b
92. " " " " " "  = 2ja7:I *
Cpd lesion containing RNA polymerase ii elongation complex c
93. " " " " " "  = 2ja8:I *
Cpd lesion containing RNA polymerase ii elongation complex d
94. " " " " " "  = 2r92:I *
Elongation complex of RNA polymerase ii with artificial rdrp scaffold
95. " " " " " "  = 2r93:I *
Elongation complex of RNA polymerase ii with a hepatitis delta virus-derived RNA stem loop
96. " " " " " "  = 3i4m:I *
8-oxoguanine containing RNA polymerase ii elongation complex
97. 813 99.2% 119 118 1098.2 3.3e-54 1r5u:I * RNA polymerase ii tfiib complex
98. " " " " " "  = 3j1n:I *
Cryo-em map of a yeast minimal preinitiation complex interac the mediator head module
99. " " " " " "  = 3k7a:I *
Crystal structure of an RNA polymerase ii-tfiib complex
100. 801 100.0% 114 114 1082.3 2.6e-53 3how:I Complete RNA polymerase ii elongation complex iii with a t-u mismatch and a frayed RNA 3'-uridine
101. 424 52.3% 107 111 578.3 3e-25 3h0g:I RNA polymerase ii from schizosaccharomyces pombe
102. 338 100.0% 47 47 468.0 4.2e-19 3qt1:I RNA polymerase ii variant containing a chimeric rpb9-c11 sub
103. 116 32.6% 46 57 170.1 0.017 1qyp:A Thermococcus celer rpb9, nmr, 25 structures
104. 111 22.3% 121 124 153.8 0.13 4c2m:I * Structure of RNA polymerase i at 2.8 a resolution
105. " " " " " "  = 4c3h:I *
Structure of 14-subunit RNA polymerase i at 3.27 a resolutio crystal form c2-93
106. " " " " " "  = 4c3i:I *
Structure of 14-subunit RNA polymerase i at 3.0 a resolution crystal form c2-100
107. " " " " " "  = 4c3j:I *
Structure of 14-subunit RNA polymerase i at 3.35 a resolutio crystal form c2-90
108. 103 28.9% 83 174 146.7 0.34 1pqv:S * RNA polymerase ii-tfiis complex
109. " " " " " "  = 1y1v:S *
Refined RNA polymerase ii-tfiis complex
110. " " " " " "  = 1y1y:S *
RNA polymerase ii-tfiis-DNA/RNA complex
111. 102 28.9% 83 163 145.7 0.38 3gtm:S Co-complex of backtracked RNA polymerase ii with tfiis
112. 95 35.3% 34 50 142.7 0.56 1tfi:A A novel zn finger motif in the basal transcriptional machinery: three-dimensional nmr studies of the nucleic- acid binding domain of transcriptional elongation factor tfiis
113. 94 27.7% 83 164 134.9 1.5 3po3:S Arrested RNA polymerase ii reactivation intermediate
114. 90 28.7% 87 115 131.5 2.3 1fwq:A Solution structure of human mss4, a guanine nucleotide exchange factor for rab proteins
115. 85 31.9% 69 91 126.1 4.7 2k3r:A Pfu rpp21 structure and assignments
116. 85 31.9% 69 97 125.7 4.9 2ki7:B The solution structure of rpp29-rpp21 complex from pyrococcus furiosus
117. 88 23.6% 72 306 123.5 6.5 4i1h:A Structure of parkin e3 ligase

Number of sequences: 117

Excluded sequences

  Smith-
Waterman
score
%-tage
identity
a.a.
overlap
Seq
len
z-score E-
value
  PDB
code
Protein name
1. 88 40.0% 45 317 123.3 6.7 1dbz:A C153s mutant of pea fructose-1,6-bisphosphatase
2. 88 40.0% 45 323 123.2 6.8 1d9q:A Oxidized pea fructose-1,6-bisphosphatase form 1
3. 88 40.0% 45 330 123.1 6.9 1dcu:A Redox signaling in the chloroplast: structure of oxidized pea fructose-1,6-bisphosphate phosphatase
4. 88 42.2% 45 333 123.1 6.9 1spi:A Crystal structure of spinach chloroplast fructose-1,6- bisphosphatase at 2.8 angstroms resolution
5. 87 24.0% 104 258 123.1 6.9 3laq:U Structure-based engineering of species selectivity in the up interaction
6. 82 30.0% 60 107 121.2 8.8 1wjp:A Solution structure of zf-c2h2 domains from human zinc finger protein 295
7. 81 29.5% 88 115 119.5 11 1hxr:B Crystal structure of mss4 at 1.65 angstroms
8. 85 24.7% 77 306 119.5 11 4i1f:A Structure of parkin-s223p e3 ligase
9. 80 40.6% 32 162 116.3 17 1klo:A Crystal structure of three consecutive laminin-type epidermal growth factor-like (le) modules of laminin gamma1 chain harboring the nidogen binding site
10. 80 40.6% 32 164 116.2 17 1npe:B Crystal structure of nidogen/laminin complex
11. 79 27.3% 44 141 115.7 18 2zet:C Crystal structure of the small gtpase rab27b complexed with the slp homology domain of slac2-a/melanophilin
12. 86 30.8% 65 844 115.4 19 3abz:A Crystal structure of se-met labeled beta-glucosidase from kluyveromyces marxianus
13. 86 30.8% 65 841 115.4 18 3ac0:A Crystal structure of beta-glucosidase from kluyveromyces mar complex with glucose
14. 85 24.7% 73 753 114.7 20 3vth:A Crystal structure of full-length hypf in the phosphate- and nucleotide-bound form
15. 85 24.7% 73 744 114.7 20 3vti:A Crystal structure of hype-hypf complex
16. 74 36.7% 30 91 111.4 31 2d8y:A Solution structure of the lim domain of epithelial protein lost in neoplasm
17. 71 40.0% 30 58 109.8 38 1tle:A Le (laminin-type egf-like) module giii4 in solution at ph 3.5 and 290 k, nmr, 14 structures
18. 75 25.7% 113 160 109.7 39 4msv:B Crystal structure of fasl and dcr3 complex
19. 73 29.8% 47 107 109.2 41 3c1s:A Crystal structure of grx1 in glutathionylated form
20. 73 29.8% 47 110 109.0 42 3c1r:A Crystal structure of oxidized grx1
21. 77 23.9% 71 301 108.9 42 4bm9:A Structure of the autoinhibited parkin catalytic domain
22. 76 26.4% 91 248 108.6 44 2i9b:G Crystal structure of atf-urokinase receptor complex
23. 73 35.7% 42 134 107.9 48 1yax:B Cystal structure analysis of s.Typhimurium phoq sensor domai calcium
24. 72 29.8% 47 108 107.8 49 3ctf:A * Crystal structure of oxidized grx2
25. " " " " " "  = 3ctg:A *
Crystal structure of reduced glutaredoxin 2
26. 71 29.4% 51 86 107.7 50 1fl7:A Human follicle stimulating hormone
27. 71 29.4% 51 85 107.7 49 1hcn:A Structure of human chorionic gonadotropin at 2.6 angstroms r from mad analysis of the selenomethionyl protein
28. 71 29.4% 51 86 107.7 50 1hrp:A Crystal structure of human chorionic gonadotropin
29. 71 29.4% 51 85 107.7 49 1xul:A Theoretical model of the ligand-binding region of lutropin receptor complexed with human chorionic gonadotropin
30. 72 29.8% 47 109 107.7 49 3d4m:A Glutaredoxin 2 oxidized structure

Number of sequences: 30

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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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