Conserved Domains in CDD Database Detected by RPS-BLAST and HHsearch
Conserved Domains in CDD Database Detected by RPS-BLAST
Original result of RPS-BLAST against CDD database part I
Original result of RPS-BLASTagainst CDD database part II
Identity Alignment graph Length
Definition
E-value
Target 122
DNA-directed RNA polymerase subunit omega [Candidatus L
PRK00392 69
PRK00392, rpoZ, DNA-directed RNA polymerase subunit ome
1e-21
pfam01192 57
pfam01192, RNA_pol_Rpb6, RNA polymerase Rpb6
2e-09
TIGR00690 59
TIGR00690, rpoZ, DNA-directed RNA polymerase, omega sub
5e-09
COG1758 74
COG1758, RpoZ, DNA-directed RNA polymerase, subunit K/o
2e-15
>gnl|CDD|178998 PRK00392, rpoZ, DNA-directed RNA polymerase subunit omega; Reviewed
Back Show alignment and domain information
Score = 96.9 bits (242), Expect = 1e-21
Identities = 39/69 (56%), Positives = 48/69 (69%)
Query: 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSP 60
MAR T+ED ++KVDNR+ LVLLA+ R R L GAKP VD DK V+ALREIA G ++
Sbjct: 1 MARPTIEDLLEKVDNRYELVLLAAKRARQLRAGAKPPVDKSSDKPVVIALREIAEGKVTY 60
Query: 61 DDLEEDFIH 69
+ LEE I
Sbjct: 61 EILEEVEIE 69
>gnl|CDD|144692 pfam01192, RNA_pol_Rpb6, RNA polymerase Rpb6
Back Show alignment and domain information
Score = 56.5 bits (137), Expect = 2e-09
Identities = 22/56 (39%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 7 EDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVD-VGKDKNTVVALREIASGTLSPD 61
E K NR+ L + + R + LS GA P VD + K V+AL EIA G + P+
Sbjct: 1 ERLTSKYLNRYELARIIAKRAKQLSYGAPPLVDEESEIKPVVIALEEIADGKIPPE 56
Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and III. This family also contains the bacterial equivalent to Rpb6, the omega subunit. Rpb6 and omega are structurally conserved and both function in polymerase assembly. Length = 57
>gnl|CDD|161999 TIGR00690, rpoZ, DNA-directed RNA polymerase, omega subunit
Back Show alignment and domain information
Score = 55.2 bits (133), Expect = 5e-09
Identities = 26/59 (44%), Positives = 38/59 (64%), Gaps = 1/59 (1%)
Query: 2 ARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGK-DKNTVVALREIASGTLS 59
AR T+ED + K+ +R+ LVL+A+ R R L + + DK TV+ALREIA+G +S
Sbjct: 1 ARPTIEDAMKKIGSRYDLVLVAARRARQLQLKGTDPIVPEENDKPTVIALREIAAGLVS 59
The trusted cutoff excludes archaeal homologs but captures some organellar sequences. Length = 59
>gnl|CDD|31944 COG1758, RpoZ, DNA-directed RNA polymerase, subunit K/omega [Transcription]
Back Show alignment and domain information
Score = 76.1 bits (187), Expect = 2e-15
Identities = 40/74 (54%), Positives = 50/74 (67%), Gaps = 2/74 (2%)
Query: 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDV--GKDKNTVVALREIASGTL 58
MAR T+ED +DKV NR+ LV++A+ R R L+ GA P VD KDK V+ALREIA G +
Sbjct: 1 MARPTIEDLLDKVGNRYELVVVAAKRARQLAAGAPPLVDDEENKDKPVVIALREIAEGKI 60
Query: 59 SPDDLEEDFIHSLQ 72
+ L E IHSLQ
Sbjct: 61 PIEILRELLIHSLQ 74
Conserved Domains in CDD Database Detected by HHsearch
Original result of HHsearch against CDD database
Identity Alignment graph Length
Definition
Probability
Target
122
DNA-directed RNA polymerase subunit omega [Candidatus L
PRK02756 128
DNA-directed RNA polymerase subunit omega; Provisional
100.0
PRK01481 127
rpoZ DNA-directed RNA polymerase subunit omega; Provisi
100.0
PRK00392 87
rpoZ DNA-directed RNA polymerase subunit omega; Reviewe
100.0
PRK04474 99
DNA-directed RNA polymerase subunit omega; Provisional
99.97
PRK04951 91
rpoZ DNA-directed RNA polymerase subunit omega; Validat
99.97
PRK02128 67
DNA-directed RNA polymerase subunit omega; Provisional
99.97
PRK00425 69
rpoZ DNA-directed RNA polymerase subunit omega; Reviewe
99.88
PRK02544 98
DNA-directed RNA polymerase subunit omega; Provisional
99.87
COG1758 74
RpoZ DNA-directed RNA polymerase, subunit K/omega [Tran
99.8
PRK02950 89
DNA-directed RNA polymerase subunit omega; Provisional
99.7
pfam01192 57
RNA_pol_Rpb6 RNA polymerase Rpb6. Rpb6 is an essential
99.59
PRK03853 73
DNA-directed RNA polymerase subunit omega; Provisional
99.46
PRK01814 67
rpoZ DNA-directed RNA polymerase subunit omega; Validat
99.44
TIGR00690 73
rpoZ DNA-directed RNA polymerase, omega subunit; InterP
98.92
PRK01099 106
rpoK DNA-directed RNA polymerase subunit K; Provisional
96.7
PRK03721 57
rpoK DNA-directed RNA polymerase subunit K; Provisional
95.9
PRK01168 61
rpoK DNA-directed RNA polymerase subunit K; Provisional
95.9
KOG3405 136
consensus
94.55
>PRK02756 DNA-directed RNA polymerase subunit omega; Provisional
Back Show alignment and domain information
Probab=100.00 E-value=7e-45 Score=272.99 Aligned_cols=122 Identities=60% Similarity=0.864 Sum_probs=112.3
Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 96000899851287899999999999999857887767744685411567565405879999999999998411646657
Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDDLEEDFIHSLQKHVEIDEP 80 (122)
Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~~G~~~~v~~~ndK~~ViALREIa~gki~~~~l~e~~I~~lq~~~e~~E~ 80 (122)
T Consensus 1 MARvTVEDCl~kv~NRF~LVllAs~RArql~~G~~~~v~~dnDK~tViALREIA~~~i~~~~L~e~li~slQ~~~e~de~ 80 (128)
T PRK02756 1 MARVTVEDCIDKVPNRFELVLLAAHRARQISAGAPLTVDRDNDKNPVVALREIADETISPEDLKEDLIHSLQKHVEVDEP 80 (128)
T ss_pred CCEEEHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCC
T ss_conf 97233999887178778999999999999867999764866886612016876507768999999999997347888884
Q ss_pred CHHHHHHHHH-----CCCHHHCCCCCCCHHHHHHHHHHCCCCCCCCC
Q ss_conf 8566676530-----25101101011498887865531168400279
Q gi|254780937|r 81 DSPTENSDFS-----WHKPEALSFGQMSEGDLLEGINNIVTPDKRDD 122 (122)
Q Consensus 81 e~~~~~~~~~-----~~~~~~~~~~~~se~e~~~~~~~~i~p~k~~d 122 (122)
T Consensus 81 e~d~~~~~~~~~~~~~~~~~~~~~d~msEe~lLr~l~~~~~~~~~d~ 127 (128)
T PRK02756 81 EPDTVPLLSSAGAAEDAEDDDVAFDRMSEEELLRGLEGLVPPEKDDD 127 (128)
T ss_pred CHHHHHHHCCCCCCCCCCCCCCCHHHCCHHHHHHHHHCCCCCCCCCC
T ss_conf 15667651467777766644300100689999999873499765678
>PRK01481 rpoZ DNA-directed RNA polymerase subunit omega; Provisional
Back Show alignment and domain information
Probab=100.00 E-value=6.9e-38 Score=233.74 Aligned_cols=86 Identities=37% Similarity=0.538 Sum_probs=77.8
Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCC--CCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf 9600089985128789999999999999985788776--77446854115675654058799999999999984116466
Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPT--VDVGKDKNTVVALREIASGTLSPDDLEEDFIHSLQKHVEID 78 (122)
Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~~G~~~~--v~~~ndK~~ViALREIa~gki~~~~l~e~~I~~lq~~~e~~ 78 (122)
T Consensus 1 MARVTVEDCl~kI~NRFeLVl~As~RARqL~~g~~~~~~~~~~nDK~tViALREIA~g~v~~e~Lke~lI~slQk~~~ie 80 (127)
T PRK01481 1 MARITAEDCNKIIPDRFRLVVLATRYAKLLNYKVETNQIKKEKRDKPPVIALRRIAAGKVSVAQLEQDLINSLRTRTMIE 80 (127)
T ss_pred CCEEEHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEHHHHHHCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf 97153999887377678999999999999854799886670006877530258877278899999999999987501147
Q ss_pred CCCHHHHH
Q ss_conf 57856667
Q gi|254780937|r 79 EPDSPTEN 86 (122)
Q Consensus 79 E~e~~~~~ 86 (122)
T Consensus 81 ~~~~~d~~ 88 (127)
T PRK01481 81 PLVNQDES 88 (127)
T ss_pred CCCCCHHH
T ss_conf 31010023
>PRK00392 rpoZ DNA-directed RNA polymerase subunit omega; Reviewed
Back Show alignment and domain information
Probab=100.00 E-value=6.8e-34 Score=211.22 Aligned_cols=83 Identities=45% Similarity=0.637 Sum_probs=76.2
Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCC-CCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCC
Q ss_conf 9600089985128789999999999999985788-776774468541156756540587999999999999841164665
Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGA-KPTVDVGKDKNTVVALREIASGTLSPDDLEEDFIHSLQKHVEIDE 79 (122)
Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~~G~-~~~v~~~ndK~~ViALREIa~gki~~~~l~e~~I~~lq~~~e~~E 79 (122)
T Consensus 1 MARvTVEDCleki~NRF~LvllAs~RArql~~g~~~p~v~~~ndKptViALREIa~g~v~~~~L~e~~i~e~~~~~~~~e 80 (87)
T PRK00392 1 MARVTVEDCLEHVDNRFELVMLSTKRARQLATGGKEPKVAWENDKPTVVALREIAEGLVDYEVIAQEEIVEDEPLFAAFE 80 (87)
T ss_pred CCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCC
T ss_conf 98352999987079888999999999999984798875575368642045899882788999987999887775033245
Q ss_pred CCHH
Q ss_conf 7856
Q gi|254780937|r 80 PDSP 83 (122)
Q Consensus 80 ~e~~ 83 (122)
T Consensus 81 eE~~ 84 (87)
T PRK00392 81 DESN 84 (87)
T ss_pred CCCC
T ss_conf 3101
>PRK04474 DNA-directed RNA polymerase subunit omega; Provisional
Back Show alignment and domain information
Probab=99.97 E-value=1.2e-32 Score=204.13 Aligned_cols=65 Identities=49% Similarity=0.796 Sum_probs=61.8
Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCC--CCCCCHHHHHHHHHCCCCCHHHHHH
Q ss_conf 9600089985128789999999999999985788776774--4685411567565405879999999
Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDV--GKDKNTVVALREIASGTLSPDDLEE 65 (122)
Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~~G~~~~v~~--~ndK~~ViALREIa~gki~~~~l~e 65 (122)
T Consensus 1 MARvTVEDCl~~i~NRF~Lvl~A~~RArql~~G~~p~v~~~~~~DKptViALREIa~g~v~~~~l~~ 67 (99)
T PRK04474 1 MARITVEDCLEVVNNRFELVMMASKRARQLANGVQPLIENADASDKPTVMALREIAARRIDNALIDE 67 (99)
T ss_pred CCEEEHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEHHHHHHCCCCHHHHHH
T ss_conf 9714399988617888899999999999986699970377544798723104887747678999989
>PRK04951 rpoZ DNA-directed RNA polymerase subunit omega; Validated
Back Show alignment and domain information
Probab=99.97 E-value=2.4e-31 Score=196.86 Aligned_cols=73 Identities=42% Similarity=0.626 Sum_probs=66.7
Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHH-CCCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf 9600089985128789999999999999985-788776774468541156756540587999999999999841
Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLS-QGAKPTVDVGKDKNTVVALREIASGTLSPDDLEEDFIHSLQK 73 (122)
Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~-~G~~~~v~~~ndK~~ViALREIa~gki~~~~l~e~~I~~lq~ 73 (122)
T Consensus 1 MARvTVEDCl~~v~NRF~LVllAskRARql~~~g~~p~v~~~ndKptViALREIaeG~i~~~~l~~~~~~~~~e 74 (91)
T PRK04951 1 MARVTVQDAVEKIGNRFDLILVAARRARQLQVGGKDPLVPEENDKPTVIALREIEEGLINNQILDARERQEQQE 74 (91)
T ss_pred CCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf 98344999998478788999999999999982998884687589541345998884678999999889899999
>PRK02128 DNA-directed RNA polymerase subunit omega; Provisional
Back Show alignment and domain information
Probab=99.97 E-value=2.8e-31 Score=196.49 Aligned_cols=65 Identities=51% Similarity=0.793 Sum_probs=62.6
Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHH
Q ss_conf 960008998512878999999999999998578877677446854115675654058799999999
Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDDLEED 66 (122)
Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~~G~~~~v~~~ndK~~ViALREIa~gki~~~~l~e~ 66 (122)
T Consensus 1 MARvTVEDCl~~i~NRF~Lvl~A~~Rarql~~G~~~~ve-~~dK~tViALREIa~g~v~~e~L~e~ 65 (67)
T PRK02128 1 MARITVEDCLKQIPNRFELALAATYRARQLAQGHTPKIE-SRDKPTVVALREIAAGQVGLEMLKKV 65 (67)
T ss_pred CCEEEHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCC-CCCCCCCHHHHHHHHCCCCHHHHHHC
T ss_conf 982539998872798999999999999999669988656-68986221158878179799998417
>PRK00425 rpoZ DNA-directed RNA polymerase subunit omega; Reviewed
Back Show alignment and domain information
Probab=99.88 E-value=1.5e-23 Score=153.05 Aligned_cols=66 Identities=30% Similarity=0.568 Sum_probs=63.2
Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHH
Q ss_conf 960008998512878999999999999998578877677446854115675654058799999999
Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDDLEED 66 (122)
Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~~G~~~~v~~~ndK~~ViALREIa~gki~~~~l~e~ 66 (122)
T Consensus 2 M~~Psid~ll~kvdsrY~LV~~aAKRARqL~~g~~plv~~~~~Kpv~iALeEI~~gkvt~e~~~eG 67 (69)
T PRK00425 2 MINPSIVDLLEKVDDRYSLVILTAKRARQIIAGDEKLVDIESNKPLTIAINEVDQGLVTYERPEEG 67 (69)
T ss_pred CCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCEEECCCCC
T ss_conf 877879999984578424689999999998759976668878860879999998599645406555
>PRK02544 DNA-directed RNA polymerase subunit omega; Provisional
Back Show alignment and domain information
Probab=99.87 E-value=7e-23 Score=149.20 Aligned_cols=62 Identities=34% Similarity=0.553 Sum_probs=60.0
Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHH
Q ss_conf 96000899851287899999999999999857887767744685411567565405879999
Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDD 62 (122)
Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~~G~~~~v~~~ndK~~ViALREIa~gki~~~~ 62 (122)
T Consensus 1 Ml~PSId~Ll~KVdSrYsLVilAaKRARqL~~Ga~Pt~~~ds~K~t~~ALeEIaaG~V~idP 62 (98)
T PRK02544 1 MLKPSIDTLLDKVPSKYSLVILQAKRAHELEAGATPTQEFKSVKSTLQALEEIESGNVVIHP 62 (98)
T ss_pred CCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCEEECC
T ss_conf 98677999998558701568899989999865898765445765799999999839814489
>COG1758 RpoZ DNA-directed RNA polymerase, subunit K/omega [Transcription]
Back Show alignment and domain information
Probab=99.80 E-value=5.8e-20 Score=132.77 Aligned_cols=72 Identities=54% Similarity=0.770 Sum_probs=65.0
Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCC--CCCHHHHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 960008998512878999999999999998578877677446--854115675654058799999999999984
Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGK--DKNTVVALREIASGTLSPDDLEEDFIHSLQ 72 (122)
Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~~G~~~~v~~~n--dK~~ViALREIa~gki~~~~l~e~~I~~lq 72 (122)
T Consensus 1 m~~~~~~~l~~~~~~ryelv~~aa~RA~Ql~~ga~~~~~~~~~~~kpv~iAl~Ei~~g~i~~~i~~~~~~~~~~ 74 (74)
T COG1758 1 MARPTIEDLLDKVGNRYELVVVAAKRARQLAAGAPPLVDDEENKDKPVVIALREIAEGKIPIEILRELLIHSLQ 74 (74)
T ss_pred CCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCHHHHCCCCC
T ss_conf 98567999862035788999999999999983999765563336784899999998299782101122210239
>PRK02950 DNA-directed RNA polymerase subunit omega; Provisional
Back Show alignment and domain information
Probab=99.70 E-value=5.7e-18 Score=121.53 Aligned_cols=62 Identities=31% Similarity=0.586 Sum_probs=54.2
Q ss_pred EEEHHHHHCCCCCHHHHHHHHHHHHHHHHC-----------CCCCCCCCCC-CCCHHHHHHHHHCCCCCHHHHH
Q ss_conf 000899851287899999999999999857-----------8877677446-8541156756540587999999
Q gi|254780937|r 3 RTTVEDCIDKVDNRFLLVLLASHRTRHLSQ-----------GAKPTVDVGK-DKNTVVALREIASGTLSPDDLE 64 (122)
Q Consensus 3 RvTvEdcl~kv~nrf~LVllAa~RArql~~-----------G~~~~v~~~n-dK~~ViALREIa~gki~~~~l~ 64 (122)
T Consensus 14 ~P~id~Ll~kvdsky~LVi~aakRARqin~Y~~qL~eGl~e~vgPlV~~~~~~KPLsIAlrEI~eg~l~~e~~e 87 (89)
T PRK02950 14 NPPIDELLDRVDSKYALVIYAAKRARQINDYYNQLGEGLLEYVGPLVEPGLQEKPLSIALREINADLLTAEHTE 87 (89)
T ss_pred CCCHHHHHHHCCCCEEHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEHHHHHHCCCCCCCCCC
T ss_conf 88899999854871100468788898888888886011003478855677788861113999876886441356
>pfam01192 RNA_pol_Rpb6 RNA polymerase Rpb6
Back Show alignment and domain information
Probab=99.59 E-value=6.1e-16 Score=110.10 Aligned_cols=55 Identities=40% Similarity=0.601 Sum_probs=51.0
Q ss_pred HHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCC-CCHHHHHHHHHCCCCCHH
Q ss_conf 9985128789999999999999985788776774468-541156756540587999
Q gi|254780937|r 7 EDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKD-KNTVVALREIASGTLSPD 61 (122)
Q Consensus 7 Edcl~kv~nrf~LVllAa~RArql~~G~~~~v~~~nd-K~~ViALREIa~gki~~~ 61 (122)
T Consensus 1 e~l~~~~~nryel~~~~a~RA~Ql~~ga~~~v~~~~~~kp~~iAl~Ei~~g~i~~~ 56 (57)
T pfam01192 1 ERLTSKYLNRYELARIIAKRAKQLSYGAPPLVDEESEIKPVVIALEEIADGKIPPE 56 (57)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEECCCCCCCHHHHHHHHHHCCCCCCC
T ss_conf 98677763799999999999999985998725577897889999999992899999
Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and III. This family also contains the bacterial equivalent to Rpb6, the omega subunit. Rpb6 and omega are structurally conserved and both function in polymerase assembly.
>PRK03853 DNA-directed RNA polymerase subunit omega; Provisional
Back Show alignment and domain information
Probab=99.46 E-value=3.5e-14 Score=100.23 Aligned_cols=59 Identities=41% Similarity=0.625 Sum_probs=52.4
Q ss_pred HHHHCCCCC-HHHHHHHHHHHHHHHHCCCCCCCCCC--CCCCHHHHHHHHHCCCCCHHHHHH
Q ss_conf 998512878-99999999999999857887767744--685411567565405879999999
Q gi|254780937|r 7 EDCIDKVDN-RFLLVLLASHRTRHLSQGAKPTVDVG--KDKNTVVALREIASGTLSPDDLEE 65 (122)
Q Consensus 7 Edcl~kv~n-rf~LVllAa~RArql~~G~~~~v~~~--ndK~~ViALREIa~gki~~~~l~e 65 (122)
T Consensus 10 aKALe~v~~DRY~Ls~~vakRa~qLanGA~PLv~~d~~k~K~tdIAL~EIAeGKI~le~i~e 71 (73)
T PRK03853 10 AKALKNVGNDRYKLSLLVFKRAEQLANGAKPLVDMDPKKHKLADIALREIAEGKIDLERIVE 71 (73)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCEEEEEC
T ss_conf 99998728608999999999999986688642246845554899999999817520134201
>PRK01814 rpoZ DNA-directed RNA polymerase subunit omega; Validated
Back Show alignment and domain information
Probab=99.44 E-value=4e-14 Score=99.86 Aligned_cols=59 Identities=25% Similarity=0.350 Sum_probs=52.1
Q ss_pred EEHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCC-CCCHHHHHHHHHCCCCCHHH
Q ss_conf 008998512878999999999999998578877677446-85411567565405879999
Q gi|254780937|r 4 TTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGK-DKNTVVALREIASGTLSPDD 62 (122)
Q Consensus 4 vTvEdcl~kv~nrf~LVllAa~RArql~~G~~~~v~~~n-dK~~ViALREIa~gki~~~~ 62 (122)
T Consensus 4 PSiD~Ll~kvdSkYsLV~~AaKRAreL~~~~~~~l~~~~S~K~Vg~ALEEI~ag~lt~~p 63 (67)
T PRK01814 4 PSIDSLLTKIDSKYTLVTVAAKRAREMQLANNCVVEKPVSHKCVGKALEEIDAEALSYVP 63 (67)
T ss_pred CCHHHHHHHCCCCEEEHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEECC
T ss_conf 779999986278413313777788997618854233576667099999999849536257
>TIGR00690 rpoZ DNA-directed RNA polymerase, omega subunit; InterPro: IPR003716 Bacterial DNA-dependent RNA polymerase (RNAP) has the core composition of alpha(2)-beta-beta'-omega, where omega is the smallest of the subunits
Back Show alignment and domain information
Probab=98.92 E-value=6.3e-10 Score=76.24 Aligned_cols=63 Identities=46% Similarity=0.653 Sum_probs=59.2
Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHH------CCCCCCCC--CCCCCCHHHHHHHHHCCCCCHHHH
Q ss_conf 9600089985128789999999999999985------78877677--446854115675654058799999
Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLS------QGAKPTVD--VGKDKNTVVALREIASGTLSPDDL 63 (122)
Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~------~G~~~~v~--~~ndK~~ViALREIa~gki~~~~l 63 (122)
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~ 71 (73)
T TIGR00690 1 MARPPIDDLLEKVDSRYSLVLLAAKRARQLLVYYQLGEGEDLLVPPGEESDKPLGIALREIAAGKLKVELL 71 (73)
T ss_pred CCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 98752667875326401345665567777777653034410021000000013567776654111100001
The omega subunit is required to promote RNAP assembly by acting like a chaperone to maintain beta' in the correct conformation and to recruit it to the alpha(2)beta subassembly to form a functional core enzyme .; GO: 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
>PRK01099 rpoK DNA-directed RNA polymerase subunit K; Provisional
Back Show alignment and domain information
Probab=96.70 E-value=0.0023 Score=39.31 Aligned_cols=46 Identities=22% Similarity=0.460 Sum_probs=39.0
Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCCC--CCC-HHHHHHHHHCCCCCH
Q ss_conf 8999999999999998578877677446--854-115675654058799
Q gi|254780937|r 15 NRFLLVLLASHRTRHLSQGAKPTVDVGK--DKN-TVVALREIASGTLSP 60 (122)
Q Consensus 15 nrf~LVllAa~RArql~~G~~~~v~~~n--dK~-~ViALREIa~gki~~ 60 (122)
T Consensus 32 TKYEkarIiG~RA~Qi~~GA~p~I~i~~~~~~D~~~IA~~EL~qkkIPf 80 (106)
T PRK01099 32 TKYEIARIIGARALQLAMGAQPLIDIRELGSTDPVLIAEEELRRGLLDF 80 (106)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCEEECCCCCCCCHHHHHHHHHHHCCCCE
T ss_conf 3889999998999998679996686787888688999999998399977
>PRK03721 rpoK DNA-directed RNA polymerase subunit K; Provisional
Back Show alignment and domain information
Probab=95.90 E-value=0.012 Score=35.25 Aligned_cols=46 Identities=22% Similarity=0.331 Sum_probs=39.2
Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHH-HHHHHHHCCCCCH
Q ss_conf 899999999999999857887767744685411-5675654058799
Q gi|254780937|r 15 NRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTV-VALREIASGTLSP 60 (122)
Q Consensus 15 nrf~LVllAa~RArql~~G~~~~v~~~ndK~~V-iALREIa~gki~~ 60 (122)
T Consensus 5 TryEkARIiGaRALQIsmGAPvli~~~~~~dpl~IA~~El~~~~iPi 51 (57)
T PRK03721 5 TRFEKARIIGARALQIAMGAPVLIDVPEGITPLEAAILEFEKGVIPI 51 (57)
T ss_pred HHHHHHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHCCCCCE
T ss_conf 27799998859999987599857718898798999999998699745
>PRK01168 rpoK DNA-directed RNA polymerase subunit K; Provisional
Back Show alignment and domain information
Probab=95.90 E-value=0.011 Score=35.39 Aligned_cols=46 Identities=17% Similarity=0.309 Sum_probs=38.6
Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCCCC-CCH-HHHHHHHHCCCCCH
Q ss_conf 89999999999999985788776774468-541-15675654058799
Q gi|254780937|r 15 NRFLLVLLASHRTRHLSQGAKPTVDVGKD-KNT-VVALREIASGTLSP 60 (122)
Q Consensus 15 nrf~LVllAa~RArql~~G~~~~v~~~nd-K~~-ViALREIa~gki~~ 60 (122)
T Consensus 4 TryEkARIiGaRAlQIsmGAP~li~~~~~~~Dpl~IA~~El~~~~iPi 51 (61)
T PRK01168 4 TKFEKARIIGARALQIAMGAPVIIDIPKNIIDPVDIAMIEFENNVIPI 51 (61)
T ss_pred HHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHCCCCCE
T ss_conf 068999998599999876998378188887698999999998699877
>KOG3405 consensus
Back Show alignment and domain information
Probab=94.55 E-value=0.044 Score=32.08 Aligned_cols=46 Identities=13% Similarity=0.281 Sum_probs=41.2
Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHH-HHHHHHHCCCCCH
Q ss_conf 899999999999999857887767744685411-5675654058799
Q gi|254780937|r 15 NRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTV-VALREIASGTLSP 60 (122)
Q Consensus 15 nrf~LVllAa~RArql~~G~~~~v~~~ndK~~V-iALREIa~gki~~ 60 (122)
T Consensus 67 TKYErArvLGtRAlQIsm~APvmVeLegETdPL~IAmkEL~qkKIP~ 113 (136)
T KOG3405 67 TKYERARVLGTRALQISMNAPVMVELEGETDPLEIAMKELKQKKIPF 113 (136)
T ss_pred HHHHHHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHCCCCE
T ss_conf 37778776647778875389728851787788999999986365866
Homologous Domains in SCOP and MMDB Database Detected by RPS-BLAST and HHsearch
Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch
Original result of HHsearch against SCOP70(version1.75) database
Identity Alignment graph Length
Definition
Probability
Target 122
DNA-directed RNA polymerase subunit omega [Candidatus L
d1twff_ 84
RPB6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId:
97.54
d1qkla_ 127
RPB6 {Human (Homo sapiens) [TaxId: 9606]}
97.49
d1smye_ 95
RNA polymerase omega subunit {Thermus thermophilus [Tax
96.15
>d1twff_ a.143.1.2 (F:) RPB6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
Back Hide information, alignment and structure
class: All alpha proteins
fold: RPB6/omega subunit-like
superfamily: RPB6/omega subunit-like
family: RPB6
domain: RPB6
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
Probab=97.54 E-value=6.4e-05 Score=45.46 Aligned_cols=47 Identities=17% Similarity=0.294 Sum_probs=41.3
Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHH-HHHHHHHCCCCCH
Q ss_conf 7899999999999999857887767744685411-5675654058799
Q gi|254780937|r 14 DNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTV-VALREIASGTLSP 60 (122)
Q Consensus 14 ~nrf~LVllAa~RArql~~G~~~~v~~~ndK~~V-iALREIa~gki~~ 60 (122)
=++|+..-+-+.||.||+.|++|+|+.++..+++ ||..|.-.|++-+
T Consensus 14 LTkYE~ariiG~Ra~Ql~~Ga~p~I~~~~~~d~~~IA~~El~~~kiP~ 61 (84)
T d1twff_ 14 MTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPL 61 (84)
T ss_dssp CCHHHHHHHHHHHHHHHHTTCCCSSCCSSCCSHHHHHHHHHHTTCCCE
T ss_pred CCHHHHHHHHHHHHHHHHCCCCCEECCCCCCCHHHHHHHHHHCCCCCE
T ss_conf 229999999999999997699824547888799999999998399877
>d1qkla_ a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId: 9606]}
Back Show information, alignment and structure
class: All alpha proteins
fold: RPB6/omega subunit-like
superfamily: RPB6/omega subunit-like
family: RPB6
domain: RPB6
species: Human (Homo sapiens) [TaxId: 9606]
Probab=97.49 E-value=6.2e-05 Score=45.54 Aligned_cols=47 Identities=11% Similarity=0.244 Sum_probs=41.1
Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCH-HHHHHHHHCCCCCH
Q ss_conf 789999999999999985788776774468541-15675654058799
Q gi|254780937|r 14 DNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNT-VVALREIASGTLSP 60 (122)
Q Consensus 14 ~nrf~LVllAa~RArql~~G~~~~v~~~ndK~~-ViALREIa~gki~~ 60 (122)
=++|+..-+-+.||.||+.|++|+|+.++...+ .||+.|...+||-+
T Consensus 57 lTkYE~arilG~Ra~Qi~~ga~~~i~~~~~~d~~~IA~~EL~~kkiPf 104 (127)
T d1qkla_ 57 MTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPI 104 (127)
T ss_dssp CCHHHHHHHHHHHHHHHHHSCCSSSCSSSSCSSSHHHHHHHHHTCCCE
T ss_pred CCHHHHHHHHHHHHHHHHCCCCCEECCCCCCCHHHHHHHHHHCCCCCE
T ss_conf 219899999999999985699835668888799999999998399877
>d1smye_ a.143.1.1 (E:) RNA polymerase omega subunit {Thermus thermophilus [TaxId: 274]}
Back Show information, alignment and structure
class: All alpha proteins
fold: RPB6/omega subunit-like
superfamily: RPB6/omega subunit-like
family: RNA polymerase omega subunit
domain: RNA polymerase omega subunit
species: Thermus thermophilus [TaxId: 274]
Probab=96.15 E-value=0.0061 Score=34.32 Aligned_cols=54 Identities=24% Similarity=0.449 Sum_probs=40.2
Q ss_pred HHHHCCCCCHHHHHHHHHHHHHH-HHCCCC-CCCCCC------------CCCCHH-HHHHHHHCCCCCH
Q ss_conf 99851287899999999999999-857887-767744------------685411-5675654058799
Q gi|254780937|r 7 EDCIDKVDNRFLLVLLASHRTRH-LSQGAK-PTVDVG------------KDKNTV-VALREIASGTLSP 60 (122)
Q Consensus 7 Edcl~kv~nrf~LVllAa~RArq-l~~G~~-~~v~~~------------ndK~~V-iALREIa~gki~~ 60 (122)
...+.-.+|||.|.++.++||-| |.+|.+ .+++.+ .|-|+| .|.+|..-|++..
T Consensus 6 D~ll~ltDSkYRLsvVvakRA~QlLr~g~~ntvL~pde~p~~~tleg~~~dpN~vt~AMkEL~tGrl~~ 74 (95)
T d1smye_ 6 DKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAETWAMKELLTGRLVF 74 (95)
T ss_dssp HHHHHTSSSHHHHHHHHHHHHHHHHHTCTTCCSCCSSSCCCCSSSSGGGTSSCSHHHHHHHHTTTCEEE
T ss_pred HHHHHCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCEEE
T ss_conf 778631444224413548989999871798563696562556402556799758899999987373553
Homologous Domains in MMDB70 Database Detected by RPS-BLAST
Original result of RPS-BLAST against MMDB70 database
Identity Alignment graph Length
Definition
E-value
Target
122
DNA-directed RNA polymerase subunit omega [Candida
3iyd_E_ 90
(E:) DNA-directed RNA polymerase subunit omega; tr
9e-21
2a6h_E_1-77 77
(E:1-77) RNA polymerase omega chain; RNA polymeras
3e-18
>3iyd_E (E:) DNA-directed RNA polymerase subunit omega; transcription, initiation, class I, activator, RNA polymerase, holoenzyme, sigma70, open complex, CAP, CRP, CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli k-12}Length = 90
Back Hide alignment and structure
Score = 93.6 bits (233), Expect = 9e-21
Identities = 31/81 (38%), Positives = 45/81 (55%), Gaps = 4/81 (4%)
Query: 2 ARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKP-TVDVGKDKNTVVALREIASGTLSP 60
AR TV+D ++K+ NRF LVL+A+ R R + G K V DK TV+ALREI G ++
Sbjct: 1 ARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINN 60
Query: 61 DDLEEDFIHSLQKHVEIDEPD 81
L+ Q+ E + +
Sbjct: 61 QILDVR---ERQEQQEQEAAE 78
>2a6h_E (E:1-77) RNA polymerase omega chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus}Length = 77
Back Show alignment and structure
Score = 84.9 bits (210), Expect = 3e-18
Identities = 11/77 (14%), Positives = 27/77 (35%), Gaps = 15/77 (19%)
Query: 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVG---------------KDKN 45
MA ++ VD+++ L ++ + R + L + +
Sbjct: 1 MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNA 60
Query: 46 TVVALREIASGTLSPDD 62
A++E+ +G L +
Sbjct: 61 ETWAMKELLTGRLVFGE 77
Homologous Domains in MMDB70 Database Detected by HHsearch
Original result of HHsearch against MMDB70 database
Identity Alignment graph Length
Definition
Probability
Target 122
DNA-directed RNA polymerase subunit omega [Candidatus L
2a6h_E_1-77 77
RNA polymerase omega chain; RNA polymerase holoenz
99.84
3iyd_E_ 90
DNA-directed RNA polymerase subunit omega; transcr
99.83
3h0g_F_ 142
DNA-directed RNA polymerases I, II, and III subuni
97.27
1twf_F_ 155
ABC23, DNA-directed RNA polymerases I, II, and III
97.23
1qkl_A_ 127
RPB6, DNA-directed RNA polymerase II 14.4 KD polyp
97.1
2waq_K_27-95 69
DNA-directed RNA polymerase RPO6 subunit; multi-su
96.74
>2a6h_E (E:1-77) RNA polymerase omega chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus}
Back Hide alignment and structure
Probab=99.84 E-value=1.6e-21 Score=141.25 Aligned_cols=61 Identities=18% Similarity=0.322 Sum_probs=57.0
Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCC---------------CCCCCHHHHHHHHHCCCCCHH
Q ss_conf 9600089985128789999999999999985788776774---------------468541156756540587999
Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDV---------------GKDKNTVVALREIASGTLSPD 61 (122)
Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~~G~~~~v~~---------------~ndK~~ViALREIa~gki~~~ 61 (122)
|+|.++++|++||+|||.||++||+|||||++|++|+++. +++|++++||+|||+|+|+++
T Consensus 1 M~~psid~ll~kv~srY~Lvi~aAKRArql~~g~~~~~~~~~~~~~~~~~~~~~~~~~Kpv~~Al~EIa~gkv~~~ 76 (77)
T 2a6h_E 1 MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAETWAMKELLTGRLVFG 76 (77)
T ss_dssp -CCTTHHHHHHHSSSHHHHHHHHHHHHHHHHHTCTTCCSCCSSSCCCCSSSSGGGTSSCSHHHHHHHHTTTCCEEE
T ss_pred CCCCCHHHHHHCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCEEEC
T ss_conf 9863577886224442244135389899998716985636965625564025567997588999999873735533
>3iyd_E (E:) DNA-directed RNA polymerase subunit omega; transcription, initiation, class I, activator, RNA polymerase, holoenzyme, sigma70, open complex, CAP, CRP, CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli k-12}
Back Show alignment and structure
Probab=99.83 E-value=1.6e-22 Score=146.84 Aligned_cols=64 Identities=44% Similarity=0.660 Sum_probs=59.8
Q ss_pred CEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCC-CCCCCCHHHHHHHHHCCCCCHHHHHH
Q ss_conf 60008998512878999999999999998578877677-44685411567565405879999999
Q gi|254780937|r 2 ARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVD-VGKDKNTVVALREIASGTLSPDDLEE 65 (122)
Q Consensus 2 ARvTvEdcl~kv~nrf~LVllAa~RArql~~G~~~~v~-~~ndK~~ViALREIa~gki~~~~l~e 65 (122)
||+||+|||++|+|||.||++||||||||+.|++|++. .+++|++++|||||++|||+++.+.+
T Consensus 1 Arptid~ll~~v~sRy~Lv~~aaKRARqL~~g~~p~v~~~~~~K~~~iAL~EIa~Gkv~~~~~~e 65 (90)
T 3iyd_E 1 ARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDV 65 (90)
T ss_dssp CCSSSSSHHHHSSCSHHHHHHTTTTHHHHHHTCSTTCCSCTTSCCCCCBTTBCCCCCCSSCTTSC
T ss_pred CCEEHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHHCCH
T ss_conf 91419999985477879999999999998749988767887896088999999908976787331
>3h0g_F (F:) DNA-directed RNA polymerases I, II, and III subunit rpabc2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Back Show alignment and structure
Probab=97.27 E-value=0.00054 Score=42.47 Aligned_cols=47 Identities=17% Similarity=0.300 Sum_probs=42.6
Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHH-HHHHHHHCCCCCH
Q ss_conf 7899999999999999857887767744685411-5675654058799
Q gi|254780937|r 14 DNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTV-VALREIASGTLSP 60 (122)
Q Consensus 14 ~nrf~LVllAa~RArql~~G~~~~v~~~ndK~~V-iALREIa~gki~~ 60 (122)
=.||+..-+-.-||.||+.|++++|+..+...|+ ||..|...|+|.+
T Consensus 75 lTkyE~ARilG~RAlQis~gAp~~v~~~~~tdPl~IA~~El~~~~iP~ 122 (142)
T 3h0g_F 75 MTKYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKKIPL 122 (142)
T ss_dssp CCHHHHHHHHHHHHHHHHTCCCCCSCCCSCCCTTHHHHHHHHTTCCCC
T ss_pred CCHHHHHHHHHHHHHHHHCCCCCEECCCCCCCHHHHHHHHHHCCCCCE
T ss_conf 129899999999999997799825657888699999999998499877
>1twf_F (F:) ABC23, DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae}
Back Show alignment and structure
Probab=97.23 E-value=0.00062 Score=42.11 Aligned_cols=47 Identities=17% Similarity=0.294 Sum_probs=42.7
Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHH-HHHHHHHCCCCCH
Q ss_conf 7899999999999999857887767744685411-5675654058799
Q gi|254780937|r 14 DNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTV-VALREIASGTLSP 60 (122)
Q Consensus 14 ~nrf~LVllAa~RArql~~G~~~~v~~~ndK~~V-iALREIa~gki~~ 60 (122)
=.||+..-+-.-||.||+.|++++|+..+.-.|+ ||..|...|+|.+
T Consensus 85 lTkyE~aRi~g~RalQis~~ap~~v~~~~~~dpl~iA~~El~~~~ip~ 132 (155)
T 1twf_F 85 MTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPL 132 (155)
T ss_dssp CCHHHHHHHHHHHHHHHHTTCCCSSCCSSCCSHHHHHHHHHHTTCCCE
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCHHHHHHHHHHCCCCCE
T ss_conf 319999999999999997799825657888799999999998399877
>1qkl_A (A:) RPB6, DNA-directed RNA polymerase II 14.4 KD polypeptide; transcription; NMR {Homo sapiens}
Back Show alignment and structure
Probab=97.10 E-value=0.00078 Score=41.56 Aligned_cols=47 Identities=11% Similarity=0.244 Sum_probs=42.5
Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHH-HHHHHHHCCCCCH
Q ss_conf 7899999999999999857887767744685411-5675654058799
Q gi|254780937|r 14 DNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTV-VALREIASGTLSP 60 (122)
Q Consensus 14 ~nrf~LVllAa~RArql~~G~~~~v~~~ndK~~V-iALREIa~gki~~ 60 (122)
=.||+..-+-.-||.||+.|++++|+..+.-.|+ ||..|...|+|.+
T Consensus 57 lTkyE~ARilG~RAlQis~gAp~~v~~~~~~dpl~IA~~El~~~~iP~ 104 (127)
T 1qkl_A 57 MTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPI 104 (127)
T ss_dssp CCHHHHHHHHHHHHHHHHHSCCSSSCSSSSCSSSHHHHHHHHHTCCCE
T ss_pred CCHHHHHHHHHHHHHHHHCCCCCEECCCCCCCHHHHHHHHHHCCCCCE
T ss_conf 219899999999999985699844668888799999999998399877
>2waq_K (K:27-95) DNA-directed RNA polymerase RPO6 subunit; multi-subunit, transcription; 3.35A {Sulfolobus shibatae} PDB: 2wb1_I 2pmz_K 3hkz_K
Back Show alignment and structure
Probab=96.74 E-value=0.0029 Score=38.38 Aligned_cols=46 Identities=24% Similarity=0.338 Sum_probs=39.7
Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCCCC---CCHHHHHHHHHCCCCCH
Q ss_conf 89999999999999985788776774468---54115675654058799
Q gi|254780937|r 15 NRFLLVLLASHRTRHLSQGAKPTVDVGKD---KNTVVALREIASGTLSP 60 (122)
Q Consensus 15 nrf~LVllAa~RArql~~G~~~~v~~~nd---K~~ViALREIa~gki~~ 60 (122)
.||+-.-+-.-||.||+.|++++|+.++. -|..||..|...|+|.+
T Consensus 2 TkyE~ARIiG~RAlQismgAp~li~~~~~~~~dPl~IA~~El~~~~iP~ 50 (69)
T 2waq_K 2 TRYEIARVISARALQLAMGAPALIDINNLSSTDVISIAEEEFRRGVLPI 50 (69)
T ss_dssp CHHHHHHHHHHHHHHHTTTCCCTTCCCSSSCCSSSHHHHHHHHTTCSCE
T ss_pred CHHHHHHHHHHHHHHHHCCCCCEEECCCCCCCCHHHHHHHHHHCCCCCE
T ss_conf 5999999999999999779985787787788799999999998199877