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SAS results for UniProt accession no. Q980Z8

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. Q980Z8 - coloured by no. of contacts to ligand

Below are the FASTA results from a search of the sequence of UniProt accession no. Q980Z8 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 24 unique sequences (including 8 consensus sequences) giving 131 sequence matches in all. The 4 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
       ---------+---------+---------+---------+---------+---------+-----    ------------
Q980Z8 -----------------------------------------------------------------    DNA-directed RNA polymerase subunit N OS=Sulfolobus  ...
2pmz:N*-----------------------------------------------------------------×2  Archaeal RNA polymerase from sulfolobus solfataricus
4ayb:N*-----------------------------------------------------------------×3  Rnap at 3.2ang
2waq:N*-----------------------------------------------------------------×3  The complete structure of the archaeal 13-subunit DNA-  ...
3h0g:J -----------------------------------------------------------------    RNA polymerase ii from schizosaccharomyces pombe
1twa:J*-----------------------------------------------------------------×4  RNA polymerase ii complexed with atp
1i3q:J*-----------------------------------------------------------------×95 RNA polymerase ii crystal form i at 3.1 a resolution
3fki:J -----------------------------------------------------------------    12-subunit RNA polymerase ii refined with zn-sad data
4c2m:J*-----------------------------------------------------------------×4  Structure of RNA polymerase i at 2.8 a resolution
1ef4:A -----------------------------------------------------------------    Solution structure of the essential RNA polymerase subunit  ...
3c9r:A*-----------------------------------------------------------------×2  Aathil complexed with atp
3c9t:A -----------------------------------------------------------------    Aathil complexed with amppcp and tmp
3c9u:A -----------------------------------------------------------------    Aathil complexed with adp and tpp
3mwg:A -----------------krvvtlyqgatdvavslgvkpvgaveswtqkpkfeyikndlkdtkivg    Crystal structure of staphylococcus aureus sira
3mwf:A ttsikhamgtteikgkpkrvvtlyqgatdvavslgvkpvgaveswtqkpkfeyikndlkdtkivg    Crystal structure of staphylococcus aureus sira complexed  ...
2ep3:A -----------------------------------------------------------------    Solution structure of the c2h2 type zinc finger (region  ...
2ep1:A -----------------------------------------------------------------    Solution structure of the c2h2 type zinc finger (region  ...
2emy:A -----------------------------------------------------------------    Solution structure of the c2h2 type zinc finger (region  ...
1hso:A*-----------------------------------------------------------stagkv×2  Human alpha alcohol dehydrogenase (adh1a)
2yrj:A -----------------------------------------------------------------    Solution structure of the c2h2-type zinc finger domain  ...
2poi:A -----------------------------------------------------------------    Crystal structure of xiap bir1 domain (i222 form)

                                         1         1         1         1
           7         8         9         0         1         2         3
       67890123456789012345678901234567890123456789012345678901234567890    Protein name
       ----+---------+---------+---------+---------+---------+---------+    ------------
Q980Z8 -----------------------------------------------------------------    DNA-directed RNA polymerase subunit N OS=Sulfolobus  ...
2pmz:N*-----------------------------------------------------------------×2  Archaeal RNA polymerase from sulfolobus solfataricus
4ayb:N*-----------------------------------------------------------------×3  Rnap at 3.2ang
2waq:N*-----------------------------------------------------------------×3  The complete structure of the archaeal 13-subunit DNA-  ...
3h0g:J -----------------------------------------------------------------    RNA polymerase ii from schizosaccharomyces pombe
1twa:J*-----------------------------------------------------------------×4  RNA polymerase ii complexed with atp
1i3q:J*-----------------------------------------------------------------×95 RNA polymerase ii crystal form i at 3.1 a resolution
3fki:J -----------------------------------------------------------------    12-subunit RNA polymerase ii refined with zn-sad data
4c2m:J*-----------------------------------------------------------------×4  Structure of RNA polymerase i at 2.8 a resolution
1ef4:A -----------------------------------------------------------------    Solution structure of the essential RNA polymerase subunit  ...
3c9r:A*-----------------------------------------------------------------×2  Aathil complexed with atp
3c9t:A -----------------------------------------------------------------    Aathil complexed with amppcp and tmp
3c9u:A -----------------------------------------------------------------    Aathil complexed with adp and tpp
3mwg:A qepapnleeisklkpdlivaskvrnekvydqlskiaptvstdtvfkfkdttklmgkalgkekeae    Crystal structure of staphylococcus aureus sira
3mwf:A qepapnleeisklkpdlivaskvrnekvydqlskiaptvstdtvfkfkdttklmgkalgkekeae    Crystal structure of staphylococcus aureus sira complexed  ...
2ep3:A -----------------------------------------------------------------    Solution structure of the c2h2 type zinc finger (region  ...
2ep1:A -----------------------------------------------------------------    Solution structure of the c2h2 type zinc finger (region  ...
2emy:A -----------------------------------------------------------------    Solution structure of the c2h2 type zinc finger (region  ...
1hso:A*ikckaavlwelkkpfsieevevappkahevrikmvavgicgtddhvvsgtmvtplpvilgheaag×2  Human alpha alcohol dehydrogenase (adh1a)
2yrj:A -----------------------------------------------------------------    Solution structure of the c2h2-type zinc finger domain  ...
2poi:A ----------------------------------------------efveefnrlktfanfpsgs    Crystal structure of xiap bir1 domain (i222 form)

                1         1         1         1         1         1     
                4         5         6         7         8         9     
       12345678901234567890123456789012345678901234567890123456789012345    Protein name
       ---------+---------+---------+---------+---------+---------+-----    ------------
Q980Z8 ----------------mlipircftcgsl-iadkwq-sfi-t--rvnage-npgkvl-ddlgvkr    DNA-directed RNA polymerase subunit N OS=Sulfolobus  ...
2pmz:N*----------------mlipircftcgsl-iadkwq-sfi-t--rvnage-npgkvl-ddlgvkr×2  Archaeal RNA polymerase from sulfolobus solfataricus
4ayb:N*----------------mmipircftcgsl-iadkwq-pfi-t--rvnage-npgkvl-ddlgvkr×3  Rnap at 3.2ang
2waq:N*----------------mmipircftcgsl-iadkwq-pfi-t--rvnage-npgkvl-ddlgvkr×3  The complete structure of the archaeal 13-subunit DNA-  ...
3h0g:J ----------------miipircfscgkv-igdkwd-tyl-t--llqedn-tegeal-dklglqr    RNA polymerase ii from schizosaccharomyces pombe
1twa:J*----------------mivpvrcfscgkv-vgdkwe-syl-n--llqedeldegtal-srlglkr×4  RNA polymerase ii complexed with atp
1i3q:J*----------------mivpvrcfscgkv-vgdkwe-syl-n--llqedeldegtal-srlglkr×95 RNA polymerase ii crystal form i at 3.1 a resolution
3fki:J ----------------mivpvrcfscgkv-vgdkwe-syl-n--llqedeldegtal-srlglkr    12-subunit RNA polymerase ii refined with zn-sad data
4c2m:J*----------------mivpvrcfscgkv-vgdkwe-syl-n--llqedeldegtal-srlglkr×4  Structure of RNA polymerase i at 2.8 a resolution
1ef4:A -----------------mipvrclscgkp-vsayfn-eyq-r--rvadge-dpkdvl-ddlglkr    Solution structure of the essential RNA polymerase subunit  ...
3c9r:A*-----------------------gsftmr-lkelge-fgl-i--dlikkt-leskvigddtapve×2  Aathil complexed with atp
3c9t:A --------------------------tmr-lkelge-fgl-i--dlikkt-leskvigddtapve    Aathil complexed with amppcp and tmp
3c9u:A -------------------------ftmr-lkelge-fgl-i--dlikkt-leskvigddtapve    Aathil complexed with adp and tpp
3mwg:A dllkkyddkvaafqkdakakykdawplka-svvnfr-adh-t--riyagg-yageil-ndlgfkr    Crystal structure of staphylococcus aureus sira
3mwf:A dllkkyddkvaafqkdakakykdawplka-svvnfr-adh-t--riyagg-yageil-ndlgfkr    Crystal structure of staphylococcus aureus sira complexed  ...
2ep3:A --------gssgssgtgekpyrcaecgka-ftdrsn-lfthq--kihtge-kpsgps-sg-----    Solution structure of the c2h2 type zinc finger (region  ...
2ep1:A --------gssgssgtgekpyecsdcgks-fikksq-lhvhq--rihtge-npsgps-sg-----    Solution structure of the c2h2 type zinc finger (region  ...
2emy:A --------gssgssgtgenpyechecgka-fsrkyq--li-shqrthage-kpsgps-sg-----    Solution structure of the c2h2 type zinc finger (region  ...
1hso:A*ivesvgegvttvkpgdkviplaipqcgkcricknpe-sny-c--lkndvs-npqgtl-qd-gtsr×2  Human alpha alcohol dehydrogenase (adh1a)
2yrj:A --------gssgssgtgekpyrcgecgka-faqkanltqh-q--rihtge-kpsgps-sg-----    Solution structure of the c2h2-type zinc finger domain  ...
2poi:A pvsastlaragflytgegdtvrcfschaa-v-drwq-ygd-s--avgrhr-kvspnc-rfingfy    Crystal structure of xiap bir1 domain (i222 form)

           2         2         2         2         2         2         2
           0         1         2         3         4         5         6
       67890123456789012345678901234567890123456789012345678901234567890    Protein name
       ----+---------+---------+---------+---------+---------+---------+    ------------
Q980Z8 yccrrmllshvdiinevihytrpi-----------------------------------------    DNA-directed RNA polymerase subunit N OS=Sulfolobus  ...
2pmz:N*yccrrmllshvdiinevihytr-------------------------------------------×2  Archaeal RNA polymerase from sulfolobus solfataricus
4ayb:N*yccrrmllshidiisevihytrp------------------------------------------×3  Rnap at 3.2ang
2waq:N*yccrrmllshidiisevihytr-------------------------------------------×3  The complete structure of the archaeal 13-subunit DNA-  ...
3h0g:J yccrrmilthvdliekllcynp-------------------------------------------    RNA polymerase ii from schizosaccharomyces pombe
1twa:J*yccrrmilthvdliekflryn--------------------------------------------×4  RNA polymerase ii complexed with atp
1i3q:J*yccrrmilthvdliekflrynp-------------------------------------------×95 RNA polymerase ii crystal form i at 3.1 a resolution
3fki:J yccrrmilthvdliekflrynpl------------------------------------------    12-subunit RNA polymerase ii refined with zn-sad data
4c2m:J*yccrrmilthvdliekflrynplekr---------------------------------------×4  Structure of RNA polymerase i at 2.8 a resolution
1ef4:A yccrrmlishvetw---------------------------------------------------    Solution structure of the essential RNA polymerase subunit  ...
3c9r:A*ycskklllt-tdvlnegvhflrsyipeavgwkaisvnvsdviangglpkwalislnlpedlevsy×2  Aathil complexed with atp
3c9t:A ycskklllt-tdvlnegvhflrsyipeavgwkaisvnvsdviangglpkwalislnlpedlevsy    Aathil complexed with amppcp and tmp
3c9u:A ycskklllt-tdvlnegvhflrsyipeavgwkaisvnvsdviangglpkwalislnlpedlevsy    Aathil complexed with adp and tpp
3mwg:A ---nkdlqkqvdngkdiiqltskesiplmnadhifvvksdpnakdaalvkktesewtsskewknl    Crystal structure of staphylococcus aureus sira
3mwf:A ---nkdlqkqvdngkdiiqltskesiplmnadhifvvksdpnakdaalvkktesewtsskewknl    Crystal structure of staphylococcus aureus sira complexed  ...
2ep3:A -----------------------------------------------------------------    Solution structure of the c2h2 type zinc finger (region  ...
2ep1:A -----------------------------------------------------------------    Solution structure of the c2h2 type zinc finger (region  ...
2emy:A -----------------------------------------------------------------    Solution structure of the c2h2 type zinc finger (region  ...
1hso:A*ftcrrkpihhflgistfsqytvvdenavakidaasplekvcligcgfstgygsavnvakvtpgst×2  Human alpha alcohol dehydrogenase (adh1a)
2yrj:A -----------------------------------------------------------------    Solution structure of the c2h2-type zinc finger domain  ...
2poi:A le---------------------------------------------------------------    Crystal structure of xiap bir1 domain (i222 form)

                2         2         2         3         3         3     
                7         8         9         0         1         2     
       12345678901234567890123456789012345678901234567890123456789012345    Protein name
       ---------+---------+---------+---------+---------+---------+-----    ------------
Q980Z8 -----------------------------------------------------------------    DNA-directed RNA polymerase subunit N OS=Sulfolobus  ...
2pmz:N*-----------------------------------------------------------------×2  Archaeal RNA polymerase from sulfolobus solfataricus
4ayb:N*-----------------------------------------------------------------×3  Rnap at 3.2ang
2waq:N*-----------------------------------------------------------------×3  The complete structure of the archaeal 13-subunit DNA-  ...
3h0g:J -----------------------------------------------------------------    RNA polymerase ii from schizosaccharomyces pombe
1twa:J*-----------------------------------------------------------------×4  RNA polymerase ii complexed with atp
1i3q:J*-----------------------------------------------------------------×95 RNA polymerase ii crystal form i at 3.1 a resolution
3fki:J -----------------------------------------------------------------    12-subunit RNA polymerase ii refined with zn-sad data
4c2m:J*-----------------------------------------------------------------×4  Structure of RNA polymerase i at 2.8 a resolution
1ef4:A -----------------------------------------------------------------    Solution structure of the essential RNA polymerase subunit  ...
3c9r:A*verfyigvkracefykcevvggnisksekigisvflvgeterfvgrdgarlgdsvfvsgtlgdsr×2  Aathil complexed with atp
3c9t:A verfyigvkracefykcevvggnisksekigisvflvgeterfvgrdgarlgdsvfvsgtlgdsr    Aathil complexed with amppcp and tmp
3c9u:A verfyigvkracefykcevvggnisksekigisvflvgeterfvgrdgarlgdsvfvsgtlgdsr    Aathil complexed with adp and tpp
3mwg:A davknnqvsddldeitwnlaggyksslkliddlyeklniekqs----------------------    Crystal structure of staphylococcus aureus sira
3mwf:A davknnqvsddldeitwnlaggyksslkliddlyeklniekq-----------------------    Crystal structure of staphylococcus aureus sira complexed  ...
2ep3:A -----------------------------------------------------------------    Solution structure of the c2h2 type zinc finger (region  ...
2ep1:A -----------------------------------------------------------------    Solution structure of the c2h2 type zinc finger (region  ...
2emy:A -----------------------------------------------------------------    Solution structure of the c2h2 type zinc finger (region  ...
1hso:A*cavfglggvglsaimgckaagaariiavdinkdkfakakelgatecinpqdykkpiqevlkemtd×2  Human alpha alcohol dehydrogenase (adh1a)
2yrj:A -----------------------------------------------------------------    Solution structure of the c2h2-type zinc finger domain  ...
2poi:A -----------------------------------------------------------------    Crystal structure of xiap bir1 domain (i222 form)

           3         3         3         3         3         3         3
           3         4         5         6         7         8         9
       67890123456789012345678901234567890123456789012345678901234567890    Protein name
       ----+---------+---------+---------+---------+---------+---------+    ------------
Q980Z8 -----------------------------------------------------------------    DNA-directed RNA polymerase subunit N OS=Sulfolobus  ...
2pmz:N*-----------------------------------------------------------------×2  Archaeal RNA polymerase from sulfolobus solfataricus
4ayb:N*-----------------------------------------------------------------×3  Rnap at 3.2ang
2waq:N*-----------------------------------------------------------------×3  The complete structure of the archaeal 13-subunit DNA-  ...
3h0g:J -----------------------------------------------------------------    RNA polymerase ii from schizosaccharomyces pombe
1twa:J*-----------------------------------------------------------------×4  RNA polymerase ii complexed with atp
1i3q:J*-----------------------------------------------------------------×95 RNA polymerase ii crystal form i at 3.1 a resolution
3fki:J -----------------------------------------------------------------    12-subunit RNA polymerase ii refined with zn-sad data
4c2m:J*-----------------------------------------------------------------×4  Structure of RNA polymerase i at 2.8 a resolution
1ef4:A -----------------------------------------------------------------    Solution structure of the essential RNA polymerase subunit  ...
3c9r:A*aglelllmekeeyepfelaliqrhlrptaridyvkhiqkyanasmdisdglvadanhlaqrsgvk×2  Aathil complexed with atp
3c9t:A aglelllmekeeyepfelaliqrhlrptaridyvkhiqkyanasmdisdglvadanhlaqrsgvk    Aathil complexed with amppcp and tmp
3c9u:A aglelllmekeeyepfelaliqrhlrptaridyvkhiqkyanasmdisdglvadanhlaqrsgvk    Aathil complexed with adp and tpp
3mwg:A -----------------------------------------------------------------    Crystal structure of staphylococcus aureus sira
3mwf:A -----------------------------------------------------------------    Crystal structure of staphylococcus aureus sira complexed  ...
2ep3:A -----------------------------------------------------------------    Solution structure of the c2h2 type zinc finger (region  ...
2ep1:A -----------------------------------------------------------------    Solution structure of the c2h2 type zinc finger (region  ...
2emy:A -----------------------------------------------------------------    Solution structure of the c2h2 type zinc finger (region  ...
1hso:A*ggvdfsfevigrldtmmasllccheacgtsvivgvppdsqnlsmnpmllltgrtwkgailggfks×2  Human alpha alcohol dehydrogenase (adh1a)
2yrj:A -----------------------------------------------------------------    Solution structure of the c2h2-type zinc finger domain  ...
2poi:A -----------------------------------------------------------------    Crystal structure of xiap bir1 domain (i222 form)

                4         4         4         4         4         4     
                0         1         2         3         4         5     
       12345678901234567890123456789012345678901234567890123456789012345    Protein name
       ---------+---------+---------+---------+---------+---------+-----    ------------
Q980Z8 -----------------------------------------------------------------    DNA-directed RNA polymerase subunit N OS=Sulfolobus  ...
2pmz:N*-----------------------------------------------------------------×2  Archaeal RNA polymerase from sulfolobus solfataricus
4ayb:N*-----------------------------------------------------------------×3  Rnap at 3.2ang
2waq:N*-----------------------------------------------------------------×3  The complete structure of the archaeal 13-subunit DNA-  ...
3h0g:J -----------------------------------------------------------------    RNA polymerase ii from schizosaccharomyces pombe
1twa:J*-----------------------------------------------------------------×4  RNA polymerase ii complexed with atp
1i3q:J*-----------------------------------------------------------------×95 RNA polymerase ii crystal form i at 3.1 a resolution
3fki:J -----------------------------------------------------------------    12-subunit RNA polymerase ii refined with zn-sad data
4c2m:J*-----------------------------------------------------------------×4  Structure of RNA polymerase i at 2.8 a resolution
1ef4:A -----------------------------------------------------------------    Solution structure of the essential RNA polymerase subunit  ...
3c9r:A*ieilseklplsnelkmycekygknpieyalfggedyqllfthpkerwnpfldmteigrveegegv×2  Aathil complexed with atp
3c9t:A ieilseklplsnelkmycekygknpieyalfggedyqllfthpkerwnpfldmteigrveegegv    Aathil complexed with amppcp and tmp
3c9u:A ieilseklplsnelkmycekygknpieyalfggedyqllfthpkerwnpfldmteigrveegegv    Aathil complexed with adp and tpp
3mwg:A -----------------------------------------------------------------    Crystal structure of staphylococcus aureus sira
3mwf:A -----------------------------------------------------------------    Crystal structure of staphylococcus aureus sira complexed  ...
2ep3:A -----------------------------------------------------------------    Solution structure of the c2h2 type zinc finger (region  ...
2ep1:A -----------------------------------------------------------------    Solution structure of the c2h2 type zinc finger (region  ...
2emy:A -----------------------------------------------------------------    Solution structure of the c2h2 type zinc finger (region  ...
1hso:A*kecvpklvadfmakkfsldalithvlpfekinegfdllhsgksirtilmf---------------×2  Human alpha alcohol dehydrogenase (adh1a)
2yrj:A -----------------------------------------------------------------    Solution structure of the c2h2-type zinc finger domain  ...
2poi:A -----------------------------------------------------------------    Crystal structure of xiap bir1 domain (i222 form)

           4         4
           6         7
       678901234567890                                                      Protein name
       ----+---------+                                                      ------------
Q980Z8 ---------------                                                      DNA-directed RNA polymerase subunit N OS=Sulfolobus  ...
2pmz:N*---------------                                                  ×2  Archaeal RNA polymerase from sulfolobus solfataricus
4ayb:N*---------------                                                  ×3  Rnap at 3.2ang
2waq:N*---------------                                                  ×3  The complete structure of the archaeal 13-subunit DNA-  ...
3h0g:J ---------------                                                      RNA polymerase ii from schizosaccharomyces pombe
1twa:J*---------------                                                  ×4  RNA polymerase ii complexed with atp
1i3q:J*---------------                                                  ×95 RNA polymerase ii crystal form i at 3.1 a resolution
3fki:J ---------------                                                      12-subunit RNA polymerase ii refined with zn-sad data
4c2m:J*---------------                                                  ×4  Structure of RNA polymerase i at 2.8 a resolution
1ef4:A ---------------                                                      Solution structure of the essential RNA polymerase subunit  ...
3c9r:A*fvdgkkvep------                                                  ×2  Aathil complexed with atp
3c9t:A fvdgkkvepkgwkhf                                                      Aathil complexed with amppcp and tmp
3c9u:A fvdgkkvepkgwkhf                                                      Aathil complexed with adp and tpp
3mwg:A ---------------                                                      Crystal structure of staphylococcus aureus sira
3mwf:A ---------------                                                      Crystal structure of staphylococcus aureus sira complexed  ...
2ep3:A ---------------                                                      Solution structure of the c2h2 type zinc finger (region  ...
2ep1:A ---------------                                                      Solution structure of the c2h2 type zinc finger (region  ...
2emy:A ---------------                                                      Solution structure of the c2h2 type zinc finger (region  ...
1hso:A*---------------                                                  ×2  Human alpha alcohol dehydrogenase (adh1a)
2yrj:A ---------------                                                      Solution structure of the c2h2-type zinc finger domain  ...
2poi:A ---------------                                                      Crystal structure of xiap bir1 domain (i222 form)

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. Q980Z8. 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. - - - 66 - - Q980Z8 DNA-directed RNA polymerase subunit N OS=Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) GN=rpoN PE=1 SV=1
2. 447 100.0% 64 64 638.1 1.4e-28 2pmz:N * Archaeal RNA polymerase from sulfolobus solfataricus
3. " " " " " "  = 3hkz:N *
The x-ray crystal structure of RNA polymerase from archaea
4. 442 93.8% 65 65 631.0 3.6e-28 4ayb:N * Rnap at 3.2ang
5. " " " " " "  = 4b1o:N *
Archaeal rnap-DNA binary complex at 4.32ang
6. " " " " " "  = 4b1p:O *
Archaeal rnap-DNA binary complex at 4.32ang
7. 432 93.8% 64 64 617.2 2.1e-27 2waq:N * The complete structure of the archaeal 13-subunit DNA- directed RNA polymerase
8. " " " " " "  = 2wb1:N *
The complete structure of the archaeal 13-subunit DNA- directed RNA polymerase
9. " " " " " "  = 2y0s:N *
Crystal structure of sulfolobus shibatae RNA polymerase in p21 space group
10. 270 51.6% 62 64 391.3 8e-15 3h0g:J RNA polymerase ii from schizosaccharomyces pombe
11. 257 47.6% 63 64 373.2 8.2e-14 1twa:J * RNA polymerase ii complexed with atp
12. " " " " " "  = 1twc:J *
RNA polymerase ii complexed with gtp
13. " " " " " "  = 1twg:J *
RNA polymerase ii complexed with ctp
14. " " " " " "  = 1twh:J *
RNA polymerase ii complexed with 2'datp
15. 257 47.6% 63 65 373.1 8.3e-14 1i3q:J * RNA polymerase ii crystal form i at 3.1 a resolution
16. " " " " " "  = 1i50:J *
RNA polymerase ii crystal form ii at 2.8 a resolution
17. " " " " " "  = 1i6h:J *
RNA polymerase ii elongation complex
18. " " " " " "  = 1k83:J *
Crystal structure of yeast RNA polymerase ii complexed with inhibitor alpha amanitin
19. " " " " " "  = 1nik:J *
Wild type RNA polymerase ii
20. " " " " " "  = 1nt9:J *
Complete 12-subunit RNA polymerase ii
21. " " " " " "  = 1pqv:J *
RNA polymerase ii-tfiis complex
22. " " " " " "  = 1r5u:J *
RNA polymerase ii tfiib complex
23. " " " " " "  = 1r9r:J *
RNA polymerase ii strand separated elongation complex
24. " " " " " "  = 1r9s:J *
RNA polymerase ii strand separated elongation complex, matched nucleotide
25. " " " " " "  = 1r9t:J *
RNA polymerase ii strand separated elongation complex, mismatched nucleotide
26. " " " " " "  = 1sfo:J *
RNA polymerase ii strand separated elongation complex
27. " " " " " "  = 1twf:J *
RNA polymerase ii complexed with utp at 2.3 a resolution
28. " " " " " "  = 1wcm:J *
Complete 12-subunit RNA polymerase ii at 3.8 ang
29. " " " " " "  = 1y1v:J *
Refined RNA polymerase ii-tfiis complex
30. " " " " " "  = 1y1w:J *
Complete RNA polymerase ii elongation complex
31. " " " " " "  = 1y1y:J *
RNA polymerase ii-tfiis-DNA/RNA complex
32. " " " " " "  = 1y77:J *
Complete RNA polymerase ii elongation complex with substrate gmpcpp
33. " " " " " "  = 2b63:J *
Complete RNA polymerase ii-RNA inhibitor complex
34. " " " " " "  = 2b8k:J *
12-subunit RNA polymerase ii
35. " " " " " "  = 2e2h:J *
RNA polymerase ii elongation complex at 5 mm mg2+ with gtp
36. " " " " " "  = 2e2i:J *
RNA polymerase ii elongation complex in 5 mm mg+2 with 2'- dgtp
37. " " " " " "  = 2e2j:J *
RNA polymerase ii elongation complex in 5 mm mg+2 with gmpcpp
38. " " " " " "  = 2ja5:J *
Cpd lesion containing RNA polymerase ii elongation complex a
39. " " " " " "  = 2ja6:J *
Cpd lesion containing RNA polymerase ii elongation complex b
40. " " " " " "  = 2ja7:J *
Cpd lesion containing RNA polymerase ii elongation complex c
41. " " " " " "  = 2ja8:J *
Cpd lesion containing RNA polymerase ii elongation complex d
42. " " " " " "  = 2nvq:J *
RNA polymerase ii elongation complex in 150 mm mg+2 with 2'dutp
43. " " " " " "  = 2nvs:J *
RNA polymerase ii elongation complex in 150 mm mg+2 with utp
44. " " " " " "  = 2nvt:J *
RNA polymerase ii elongation complex in 150 mm mg+2 with gmpcpp
45. " " " " " "  = 2nvx:J *
RNA polymerase ii elongation complex in 5 mm mg+2 with 2'- dutp
46. " " " " " "  = 2nvy:J *
RNA polymerase ii form ii in 150 mm mn+2
47. " " " " " "  = 2nvz:J *
RNA polymerase ii elongation complex with utp, updated 11/2006
48. " " " " " "  = 2r7z:J *
Cisplatin lesion containing RNA polymerase ii elongation com
49. " " " " " "  = 2r92:J *
Elongation complex of RNA polymerase ii with artificial rdrp scaffold
50. " " " " " "  = 2r93:J *
Elongation complex of RNA polymerase ii with a hepatitis delta virus-derived RNA stem loop
51. " " " " " "  = 2vum:J *
Alpha-amanitin inhibited complete RNA polymerase ii elongation complex
52. " " " " " "  = 2yu9:J *
RNA polymerase ii elongation complex in 150 mm mg+2 with utp
53. " " " " " "  = 3cqz:J *
Crystal structure of 10 subunit RNA polymerase ii in complex inhibitor alpha-amanitin
54. " " " " " "  = 3gtg:J *
Backtracked RNA polymerase ii complex with 12mer RNA
55. " " " " " "  = 3gtj:J *
Backtracked RNA polymerase ii complex with 13mer RNA
56. " " " " " "  = 3gtk:J *
Backtracked RNA polymerase ii complex with 18mer RNA
57. " " " " " "  = 3gtl:J *
Sequence with no PDB entry
58. " " " " " "  = 3gtm:J *
Sequence with no PDB entry
59. " " " " " "  = 3gto:J *
Backtracked RNA polymerase ii complex with 15mer RNA
60. " " " " " "  = 3gtp:J *
Backtracked RNA polymerase ii complex with 24mer RNA
61. " " " " " "  = 3gtq:J *
Backtracked RNA polymerase ii complex induced by damage
62. " " " " " "  = 3h3v:K *
Yeast rnap ii containing poly(a)-signal sequence in the acti
63. " " " " " "  = 3hou:J *
Complete RNA polymerase ii elongation complex i with a t-u mismatch
64. " " " " " "  = 3hov:J *
Complete RNA polymerase ii elongation complex ii
65. " " " " " "  = 3how:J *
Complete RNA polymerase ii elongation complex iii with a t-u mismatch and a frayed RNA 3'-uridine
66. " " " " " "  = 3hox:J *
Complete RNA polymerase ii elongation complex v
67. " " " " " "  = 3hoy:J *
Complete RNA polymerase ii elongation complex vi
68. " " " " " "  = 3hoz:J *
Complete RNA polymerase ii elongation complex iv with a t-u mismatch and a frayed RNA 3'-guanine
69. " " " " " "  = 3i4m:J *
8-oxoguanine containing RNA polymerase ii elongation complex
70. " " " " " "  = 3i4n:J *
8-oxoguanine containing RNA polymerase ii elongation complex
71. " " " " " "  = 3j0k:J *
Orientation of RNA polymerase ii within the human vp16-media ii-tfiif assembly
72. " " " " " "  = 3j1n:J *
Cryo-em map of a yeast minimal preinitiation complex interac the mediator head module
73. " " " " " "  = 3k1f:J *
Crystal structure of RNA polymerase ii in complex with tfiib
74. " " " " " "  = 3k7a:J *
Crystal structure of an RNA polymerase ii-tfiib complex
75. " " " " " "  = 3m3y:J *
RNA polymerase ii elongation complex c
76. " " " " " "  = 3m4o:J *
RNA polymerase ii elongation complex b
77. " " " " " "  = 3po2:J *
Arrested RNA polymerase ii elongation complex
78. " " " " " "  = 3po3:J *
Arrested RNA polymerase ii reactivation intermediate
79. " " " " " "  = 3qt1:J *
RNA polymerase ii variant containing a chimeric rpb9-c11 sub
80. " " " " " "  = 3rzd:J *
RNA polymerase ii initiation complex with a 5-nt RNA
81. " " " " " "  = 3rzo:J *
RNA polymerase ii initiation complex with a 4-nt RNA
82. " " " " " "  = 3s14:J *
RNA polymerase ii initiation complex with a 6-nt RNA
83. " " " " " "  = 3s15:J *
RNA polymerase ii initiation complex with a 7-nt RNA
84. " " " " " "  = 3s16:J *
RNA polymerase ii initiation complex with an 8-nt RNA
85. " " " " " "  = 3s17:J *
RNA polymerase ii initiation complex with a 9-nt RNA
86. " " " " " "  = 3s1m:J *
RNA polymerase ii initiation complex with a 5-nt RNA (varian
87. " " " " " "  = 3s1n:J *
RNA polymerase ii initiation complex with a 5-nt RNA (varian
88. " " " " " "  = 3s1q:J *
RNA polymerase ii initiation complex with a 5-nt 3'-deoxy rn with atp
89. " " " " " "  = 3s1r:J *
RNA polymerase ii initiation complex with a 5-nt 3'-deoxy rn with gtp
90. " " " " " "  = 3s2d:J *
RNA polymerase ii initiation complex with a 5-nt RNA contain u
91. " " " " " "  = 3s2h:J *
RNA polymerase ii initiation complex with a 6-nt RNA contain 2[prime]-iodo atp
92. " " " " " "  = 4a3b:J *
RNA polymerase ii initial transcribing complex with a 4nt DNA-RNA hybrid
93. " " " " " "  = 4a3c:J *
RNA polymerase ii initial transcribing complex with a 5nt dn hybrid
94. " " " " " "  = 4a3d:J *
RNA polymerase ii initial transcribing complex with a 6nt dn hybrid
95. " " " " " "  = 4a3e:J *
RNA polymerase ii initial transcribing complex with a 5nt dn hybrid and soaked with ampcpp
96. " " " " " "  = 4a3f:J *
RNA polymerase ii initial transcribing complex with a 6nt dn hybrid and soaked with ampcpp
97. " " " " " "  = 4a3g:J *
RNA polymerase ii initial transcribing complex with a 2nt DNA-RNA hybrid
98. " " " " " "  = 4a3i:J *
RNA polymerase ii binary complex with DNA
99. " " " " " "  = 4a3j:J *
RNA polymerase ii initial transcribing complex with a 2nt DNA-RNA hybrid and soaked with gmpcpp
100. " " " " " "  = 4a3k:J *
RNA polymerase ii initial transcribing complex with a 7nt DNA-RNA hybrid
101. " " " " " "  = 4a3l:J *
RNA polymerase ii initial transcribing complex with a 7nt DNA-RNA hybrid and soaked with ampcpp
102. " " " " " "  = 4a3m:J *
RNA polymerase ii initial transcribing complex with a 4nt DNA-RNA hybrid and soaked with ampcpp
103. " " " " " "  = 4a93:J *
RNA polymerase ii elongation complex containing a cpd lesion
104. " " " " " "  = 4bbr:J *
Structure of RNA polymerase ii-tfiib complex
105. " " " " " "  = 4bbs:J *
Structure of an initially transcribing RNA polymerase ii- tfiib complex
106. " " " " " "  = 4bxx:J *
Arrested RNA polymerase ii-bye1 complex
107. " " " " " "  = 4bxz:J *
RNA polymerase ii-bye1 complex
108. " " " " " "  = 4by1:J *
Elongating RNA polymerase ii-bye1 tld complex soaked with am
109. " " " " " "  = 4by7:J *
Elongating RNA polymerase ii-bye1 tld complex
110. 257 47.6% 63 66 373.0 8.4e-14 3fki:J 12-subunit RNA polymerase ii refined with zn-sad data
111. 257 47.6% 63 69 372.8 8.7e-14 4c2m:J * Structure of RNA polymerase i at 2.8 a resolution
112. " " " " " "  = 4c3h:J *
Structure of 14-subunit RNA polymerase i at 3.27 a resolutio crystal form c2-93
113. " " " " " "  = 4c3i:J *
Structure of 14-subunit RNA polymerase i at 3.0 a resolution crystal form c2-100
114. " " " " " "  = 4c3j:J *
Structure of 14-subunit RNA polymerase i at 3.35 a resolutio crystal form c2-90
115. 232 54.7% 53 55 339.2 6.5e-12 1ef4:A Solution structure of the essential RNA polymerase subunit rpb10 from methanobacterium thermoautotrophicum
116. 86 39.4% 33 304 126.3 4.6 3c9r:A * Aathil complexed with atp
117. " " " " " "  = 3c9s:A *
Aathil complexed with amppcp
118. 86 39.4% 33 307 126.3 4.7 3c9t:A Aathil complexed with amppcp and tmp
119. 86 39.4% 33 308 126.2 4.7 3c9u:A Aathil complexed with adp and tpp
120. 82 39.0% 41 276 121.3 8.9 3mwg:A Crystal structure of staphylococcus aureus sira
121. 82 39.0% 41 292 121.0 9.2 3mwf:A Crystal structure of staphylococcus aureus sira complexed wi staphyloferrin b
122. 74 34.5% 29 46 119.9 11 2ep3:A Solution structure of the c2h2 type zinc finger (region 631- 663) of human zinc finger protein 484
123. 73 37.9% 29 46 118.5 13 2ep1:A Solution structure of the c2h2 type zinc finger (region 435- 467) of human zinc finger protein 484
124. 72 40.0% 30 46 117.1 15 2emy:A Solution structure of the c2h2 type zinc finger (region 551- 583) of human zinc finger protein 268
125. 80 31.7% 63 374 116.8 16 1hso:A * Human alpha alcohol dehydrogenase (adh1a)
126. " " " " " "  = 1u3t:A *
Crystal structure of human alcohol dehydrogenase alpha- alpha isoform complexed with n-cyclopentyl-n- cyclobutylformamide determined to 2.5 angstrom resolution
127. 68 37.9% 29 46 111.5 31 2yrj:A Solution structure of the c2h2-type zinc finger domain (781- 813) from zinc finger protein 473
128. 69 46.7% 15 78 110.0 37 2poi:A Crystal structure of xiap bir1 domain (i222 form)

Number of sequences: 128

Excluded sequences

  Smith-
Waterman
score
%-tage
identity
a.a.
overlap
Seq
len
z-score E-
value
  PDB
code
Protein name
1. 69 46.7% 15 79 110.0 38 2pop:B The crystal structure of tab1 and bir1 complex
2. 69 46.7% 15 78 110.0 37 2qra:D Crystal structure of xiap bir1 domain (p21 form)
3. 69 46.7% 15 80 109.9 38 2pop:D The crystal structure of tab1 and bir1 complex
4. 70 32.0% 50 151 107.8 50 2i13:A Aart, a six finger zinc finger designed to recognize ann tri

Number of sequences: 4

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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

  spacer

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