Query psy6965
Match_columns 1764
No_of_seqs 314 out of 1070
Neff 1.9
Searched_HMMs 46136
Date Fri Aug 16 23:18:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6965.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6965hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0260|consensus 100.0 2.1E-71 4.6E-76 653.5 24.0 267 1384-1691 1165-1433(1605)
2 cd02584 RNAP_II_Rpb1_C Largest 100.0 4.8E-62 1E-66 543.4 21.7 268 1385-1677 141-410 (410)
3 TIGR02389 RNA_pol_rpoA2 DNA-di 100.0 3.1E-54 6.7E-59 475.9 18.5 226 1401-1677 140-367 (367)
4 cd02737 RNAP_IV_NRPD1_C Larges 100.0 7.5E-54 1.6E-58 474.5 16.3 240 1385-1676 122-381 (381)
5 PRK04309 DNA-directed RNA poly 100.0 9.5E-53 2.1E-57 465.9 17.4 226 1401-1680 155-382 (383)
6 cd06528 RNAP_A'' A'' subunit o 100.0 1.1E-52 2.3E-57 463.0 17.6 227 1399-1677 134-362 (363)
7 PRK14897 unknown domain/DNA-di 100.0 1.8E-52 3.8E-57 474.8 18.6 228 1401-1679 277-505 (509)
8 cd02736 RNAP_III_Rpc1_C Larges 100.0 4.1E-50 8.8E-55 433.9 15.7 175 1482-1672 126-300 (300)
9 cd02735 RNAP_I_Rpa1_C Largest 100.0 1.6E-49 3.4E-54 430.2 18.3 193 1453-1675 116-309 (309)
10 PRK14898 DNA-directed RNA poly 100.0 1.1E-48 2.4E-53 465.4 18.9 222 1419-1680 629-852 (858)
11 PRK14977 bifunctional DNA-dire 100.0 4E-47 8.6E-52 465.5 20.3 225 1424-1680 1088-1319(1321)
12 KOG0262|consensus 100.0 1E-39 2.2E-44 388.1 15.0 202 1448-1679 1435-1637(1640)
13 KOG0261|consensus 100.0 9.4E-40 2E-44 382.0 10.1 221 1424-1680 1139-1364(1386)
14 cd00630 RNAP_largest_subunit_C 100.0 9.5E-36 2.1E-40 299.4 9.6 110 1562-1671 49-158 (158)
15 cd02655 RNAP_beta'_C Largest s 100.0 2.3E-30 5E-35 269.4 9.9 109 1561-1671 54-204 (204)
16 PRK00566 DNA-directed RNA poly 99.9 2.8E-25 6.1E-30 270.6 10.8 123 1541-1673 977-1139(1156)
17 PRK02597 rpoC2 DNA-directed RN 99.9 1.8E-24 3.9E-29 265.5 15.0 125 1541-1673 1047-1225(1331)
18 TIGR02386 rpoC_TIGR DNA-direct 99.9 1.2E-24 2.7E-29 264.8 12.2 124 1539-1672 973-1136(1140)
19 PRK14844 bifunctional DNA-dire 99.9 4.4E-24 9.5E-29 270.4 9.4 123 1539-1671 2622-2784(2836)
20 TIGR02388 rpoC2_cyan DNA-direc 99.9 1.2E-23 2.7E-28 256.6 11.8 125 1538-1672 1043-1223(1227)
21 CHL00117 rpoC2 RNA polymerase 99.9 3.7E-23 7.9E-28 255.4 7.4 134 1541-1676 1151-1322(1364)
22 PF04998 RNA_pol_Rpb1_5: RNA p 99.9 9.6E-23 2.1E-27 207.1 6.7 99 1531-1629 177-276 (277)
23 PRK14906 DNA-directed RNA poly 99.9 2.7E-22 5.8E-27 246.4 10.5 128 1535-1672 1070-1237(1460)
24 PRK09603 bifunctional DNA-dire 99.8 5.2E-21 1.1E-25 243.6 9.6 123 1539-1671 2711-2873(2890)
25 PF04990 RNA_pol_Rpb1_7: RNA p 99.8 1.2E-19 2.6E-24 179.8 2.0 99 1385-1500 35-135 (135)
26 KOG0260|consensus 99.7 1.8E-17 4E-22 199.4 6.7 101 1-117 1196-1296(1605)
27 PF04990 RNA_pol_Rpb1_7: RNA p 99.5 8.4E-15 1.8E-19 145.6 3.9 69 1-72 67-135 (135)
28 COG0086 RpoC DNA-directed RNA 99.3 7.6E-14 1.7E-18 168.0 -5.9 148 1531-1679 599-747 (808)
29 cd02584 RNAP_II_Rpb1_C Largest 99.2 2.2E-11 4.8E-16 138.4 8.0 110 2-119 174-289 (410)
30 cd02737 RNAP_IV_NRPD1_C Larges 98.0 5.4E-06 1.2E-10 94.7 4.9 91 11-122 147-258 (381)
31 TIGR02389 RNA_pol_rpoA2 DNA-di 97.6 7.4E-05 1.6E-09 85.3 5.9 88 1-118 158-245 (367)
32 PRK04309 DNA-directed RNA poly 97.2 0.00048 1E-08 79.2 5.8 88 1-121 173-260 (383)
33 PRK14977 bifunctional DNA-dire 96.8 0.0022 4.8E-08 82.7 7.1 97 2-119 1093-1189(1321)
34 cd06528 RNAP_A'' A'' subunit o 96.8 0.0014 3.1E-08 74.9 4.9 88 1-119 154-241 (363)
35 PRK14898 DNA-directed RNA poly 96.7 0.002 4.3E-08 80.1 6.0 87 2-117 640-726 (858)
36 PRK14897 unknown domain/DNA-di 96.7 0.0028 6E-08 75.4 6.8 86 2-118 296-381 (509)
37 cd02735 RNAP_I_Rpa1_C Largest 96.7 0.0025 5.4E-08 71.6 5.7 88 4-119 103-191 (309)
38 cd02736 RNAP_III_Rpc1_C Larges 95.7 0.0086 1.9E-07 67.3 3.8 59 54-119 126-184 (300)
39 KOG1999|consensus 52.2 20 0.00043 46.7 5.2 24 1720-1743 805-835 (1024)
40 KOG1999|consensus 44.1 43 0.00094 43.9 6.4 14 1727-1740 862-877 (1024)
41 COG3688 Predicted RNA-binding 32.6 53 0.0012 36.0 4.0 48 1536-1599 5-52 (173)
42 PRK13926 ribonuclease HII; Pro 27.9 40 0.00086 37.1 2.2 51 1575-1644 151-206 (207)
43 CHL00077 rps18 ribosomal prote 27.1 42 0.00091 33.4 2.0 32 1591-1622 25-56 (86)
44 PF01084 Ribosomal_S18: Riboso 24.5 25 0.00055 31.9 0.1 33 1590-1622 3-35 (54)
45 PRK13401 30S ribosomal protein 23.2 51 0.0011 32.6 1.8 34 1588-1621 19-53 (82)
46 PRK00391 rpsR 30S ribosomal pr 21.3 66 0.0014 31.4 2.1 33 1589-1621 21-54 (79)
47 PF04998 RNA_pol_Rpb1_5: RNA p 20.1 62 0.0013 34.2 1.8 33 86-119 170-202 (277)
No 1
>KOG0260|consensus
Probab=100.00 E-value=2.1e-71 Score=653.45 Aligned_cols=267 Identities=61% Similarity=0.957 Sum_probs=257.5
Q ss_pred CCCCChhHHhhccCcchhhhHhhhccccchhhHHHH-HHhcCCCCccchHHHHhc-cCCCCcEEEEeccCCccceEEEEE
Q psy6965 1384 SKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR-IMNSDDSKMQDEEDAVDK-MEDDMFLRCIEANMLSDMTLQFIR 1461 (1764)
Q Consensus 1384 ~~m~DEE~al~k~~~~~~L~~iE~nm~~d~~l~~~R-~MiDkdLtM~~iaekI~~-f~dd~DL~VIfSDDNAEKLVIRIR 1461 (1764)
-+||||++. ++|| ||+||||+ | +|++++|+|++||++|+. |+++ ++|||+++||+|+|+|||
T Consensus 1165 ~e~pd~D~~--~isp--wlLrlelD----------r~~m~dk~ltm~~ia~~i~~~f~~d--~~~i~~ddna~klv~r~r 1228 (1605)
T KOG0260|consen 1165 YEMPDEDVG--RISP--WLLRLELD----------RASMTDKKLTMEQIAEKINRGFGSD--LACIFSDDNAEKLVLRLR 1228 (1605)
T ss_pred hcCcccchh--hcCh--HHHHhhhh----------hhhcccccccHHHHHHHHHhhccCC--CceeecccCCcceEEEEE
Confidence 379999998 9999 99999999 9 999999999999999999 9988 999999999999999999
Q ss_pred EecCCCCccchhhhhhhchhhhHHHHHHHHhhccCceeccccCcceEEecccccCCCceEEEcCCCcccccceEEEEeec
Q psy6965 1462 IMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDG 1541 (1764)
Q Consensus 1462 I~~ded~k~eeeee~vD~~EDDvFLRrIEanMLsdItLRGIPGIkKVfI~ePetdkKKRIVITEDGefkak~EWVLETDG 1541 (1764)
+.+++ ++|+||++||+++|.+++++||++|.||||+ ++++|+|+...||+|+|+|
T Consensus 1229 i~~~~--------------e~D~~l~~Ie~~ml~~~~l~G~~~i~kV~m~-----------~~~~G~f~~~~ew~LeTdg 1283 (1605)
T KOG0260|consen 1229 IAKEE--------------EDDVFLKCIEANMLGDMTLRGIPDIFKVYMS-----------PTEDGEFKPVDEWDLETDG 1283 (1605)
T ss_pred ecCcc--------------chhHHHHHHHHhhhhhcccCCccccceEEEe-----------ecCCCceeecceeEEecCc
Confidence 99852 3689999999999999999999999999997 3578889999999999999
Q ss_pred cchhhhccCCCcccccccccCHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhccCeeccccccccc
Q psy6965 1542 TSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGIN 1621 (1764)
Q Consensus 1542 TNL~EVLS~pgVDptRTySNDI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~RG~LmgITRHGIN 1621 (1764)
+||.++++.++||+.||+|||+++|+++|||||+|+++++|+..|+.|+|+||||||++||||+||++|++++|||||+|
T Consensus 1284 ~~l~~v~s~~~vD~~rt~sn~l~ei~~vlgIea~r~a~~~e~~~vi~f~gsyVnyrhlaLl~dvmT~~g~lm~itRhg~n 1363 (1605)
T KOG0260|consen 1284 VNLRRVLSEPDVDPARTTSNDLVEIAEVLGIEAVRKALLRELLNVISFDGSYVNYRHLALLCDVMTARGHLMAITRHGIN 1363 (1605)
T ss_pred hhHHhhhccCCCCcccccccchhhhhhhhcHHHHHhhhhhhhhheEeecccchhHHHHHHHHHHHhcccceeeeeccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCChhhhhhhHHHHHHHHHHhhcCCCCCCCccccCeeccCCCCCCcceeEeecChhhhhccccccccc
Q psy6965 1622 RQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKDGIEIPLAT 1691 (1764)
Q Consensus 1622 R~dTSPLmRASFEETVEILtEAAIfGEvD~LRGVSENIILGQLIPVGTGsFDLLLD~ekLkdAiE~~~~~ 1691 (1764)
|..+|+|+||||||||++|++||+++++|.++|||||||+||++|.|||+|||++|.++|+.+++.+.++
T Consensus 1364 r~~tgaLmrcSfEetv~il~~aa~~~ekd~~rgvsEnImlgqlap~gTg~~d~~ld~e~l~~~~~~~~p~ 1433 (1605)
T KOG0260|consen 1364 RQDTGALMRCSFEETVDILMDAAAHAEKDPCRGVSENIMLGQLAPMGTGCFDLMLDAEKLKKGIEIPMPW 1433 (1605)
T ss_pred hhhccccccccHHHHHHHHHHHHhhhccCCCccceeeeeecccccCCCcceeeeccHHhhhccCccCCcc
Confidence 9999999999999999999999999999999999999999999999999999999999999999877655
No 2
>cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain. RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Probab=100.00 E-value=4.8e-62 Score=543.37 Aligned_cols=268 Identities=56% Similarity=0.883 Sum_probs=243.5
Q ss_pred CCCChhHHhhccCcchhhhHhhhccccchhhHHHH-HHhcCCCCccchHHHHhc-cCCCCcEEEEeccCCccceEEEEEE
Q psy6965 1385 KMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR-IMNSDDSKMQDEEDAVDK-MEDDMFLRCIEANMLSDMTLQFIRI 1462 (1764)
Q Consensus 1385 ~m~DEE~al~k~~~~~~L~~iE~nm~~d~~l~~~R-~MiDkdLtM~~iaekI~~-f~dd~DL~VIfSDDNAEKLVIRIRI 1462 (1764)
++||+++..+..+| |++||++| | +|.++.+++.+|+.+|++ |+++ +.|+++++|++++++|||+
T Consensus 141 ~~~d~~~~~~~~~~--~~lrl~ld----------~~~~~~~~i~~~~i~~~i~~~~~~~--~~v~~~~~~~~~~~iri~~ 206 (410)
T cd02584 141 EFPDEDVEQDRLSP--WLLRIELD----------RKKMTDKKLSMEQIAKKIKEEFKDD--LNVIFSDDNAEKLVIRIRI 206 (410)
T ss_pred ccCcccccccccCC--eeEEEEEC----------HHHHHHcCCCHHHHHHHHHHhcCCC--eEEEEcCCCcceeEEEEEe
Confidence 67899888899999 99999999 8 999999999999999998 7777 9999999999999999998
Q ss_pred ecCCCCccchhhhhhhchhhhHHHHHHHHhhccCceeccccCcceEEecccccCCCceEEEcCCCcccccceEEEEeecc
Q psy6965 1463 MNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGT 1542 (1764)
Q Consensus 1463 ~~ded~k~eeeee~vD~~EDDvFLRrIEanMLsdItLRGIPGIkKVfI~ePetdkKKRIVITEDGefkak~EWVLETDGT 1542 (1764)
........ ...+++.||+++++++|.+++|+|||||+||++... ....+..+.|.++...+|+|+|+|+
T Consensus 207 ~~~~~~~~-------~~~~~~~~l~~~~~~~l~~i~l~Gi~~I~r~~i~~~----~~~~~~~~~g~~~~~~~~~l~teG~ 275 (410)
T cd02584 207 INDDEEKE-------EDSEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREE----NKKKVDIETGEFKKREEWVLETDGV 275 (410)
T ss_pred cCcccccc-------ccchhHHHHHHHHHhhCCCcEEeCCCCceEEEEEcC----CceEecCCCCcccCCcceEEEecCc
Confidence 76432111 112356799999999999999999999999999741 2222334567777778999999999
Q ss_pred chhhhccCCCcccccccccCHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhccCeecccccccccc
Q psy6965 1543 SLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINR 1622 (1764)
Q Consensus 1543 NL~EVLS~pgVDptRTySNDI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~RG~LmgITRHGINR 1622 (1764)
||+++|++++||++||+||||++|+++|||||||++|++||++||+.||++||+|||+||||+||++|+++||||||+++
T Consensus 276 nl~~v~~~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~RHl~LiaD~MT~~G~~~~i~R~Gi~~ 355 (410)
T cd02584 276 NLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAARKALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINR 355 (410)
T ss_pred CHHHHhCCCCCccccCEeCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHhhceEEeeEeeeeeec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCChhhhhhhHHHHHHHHHHhhcCCCCCCCccccCeeccCCCCCCcceeEeecC
Q psy6965 1623 QDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLD 1677 (1764)
Q Consensus 1623 ~dTSPLmRASFEETVEILtEAAIfGEvD~LRGVSENIILGQLIPVGTGsFDLLLD 1677 (1764)
.++|||++||||+|+++|++||.+|+.|+|+||||||++||++|+|||+|||++|
T Consensus 356 ~~~S~l~~aSFE~t~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~f~l~~d 410 (410)
T cd02584 356 QDTGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTGCFDLLLD 410 (410)
T ss_pred cCCChhhhccchhHHHHHHHHHhcCCCCcCCCchHheeecCccccccceEEEEeC
Confidence 8899999999999999999999999999999999999999999999999999986
No 3
>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=100.00 E-value=3.1e-54 Score=475.85 Aligned_cols=226 Identities=35% Similarity=0.499 Sum_probs=202.8
Q ss_pred hhhHhhhccccchhhHHHH-HHhcCCCCccchHHHHhc-cCCCCcEEEEeccCCccceEEEEEEecCCCCccchhhhhhh
Q psy6965 1401 FLRCIEANMLSDMTLQFIR-IMNSDDSKMQDEEDAVDK-MEDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVD 1478 (1764)
Q Consensus 1401 ~L~~iE~nm~~d~~l~~~R-~MiDkdLtM~~iaekI~~-f~dd~DL~VIfSDDNAEKLVIRIRI~~ded~k~eeeee~vD 1478 (1764)
|..+|++| + +|.++++++.+|..+|.+ ++.. +.++ ++++.++|||+...
T Consensus 140 ~~l~i~ld----------~~~l~~~~i~~~~i~~~i~~~~~~~--~~~~----~~~~~~i~i~~~~~------------- 190 (367)
T TIGR02389 140 MTVIIELD----------EEQLKERGITVDDVEKAIKKAKLGK--VIEI----DMDGNTITIKPPKP------------- 190 (367)
T ss_pred cEEEEEEC----------HHHHHhcCCCHHHHHHHHHHhcccc--ccee----ecCCCEEEEEecCc-------------
Confidence 78889999 7 888899999999999988 5444 3443 34578999987531
Q ss_pred chhhhHHHHHHHHhhccCceeccccCcceEEecccccCCCceEEEcCCCcccccceEEEEeeccchhhhccCCCcccccc
Q psy6965 1479 KMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRT 1558 (1764)
Q Consensus 1479 ~~EDDvFLRrIEanMLsdItLRGIPGIkKVfI~ePetdkKKRIVITEDGefkak~EWVLETDGTNL~EVLS~pgVDptRT 1558 (1764)
....|++++.. |.+++|+|+|||+||++++ . ..+|+|.|+|+||.++|.+++||++||
T Consensus 191 ---~~~~l~~l~~~-l~~~~v~Gi~gI~r~~i~~-------------~-----~~~~~l~teG~nl~~v~~~~~VD~~rt 248 (367)
T TIGR02389 191 ---SLKELRKLKEK-IKNLHIKGIKGIKRVVIRK-------------E-----GDEYVIYTEGSNLKEVLKLEGVDKTRT 248 (367)
T ss_pred ---hHHHHHHHHHH-hhhceEeCCCCceEEEEEC-------------C-----CCeEEEEEeccCHHHHHcCCCCccccC
Confidence 01248888765 5599999999999998752 0 147999999999999999999999999
Q ss_pred cccCHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhccCeecccccccccccCCChhhhhhhHHHHH
Q psy6965 1559 FSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVD 1638 (1764)
Q Consensus 1559 ySNDI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~RG~LmgITRHGINR~dTSPLmRASFEETVE 1638 (1764)
+||||++|+++|||||||++|++|+++||+.||++||+|||+||||+||++|+++||||||+++.+.|||++||||+|++
T Consensus 249 ~sNdI~ei~~~lGIEAaR~~Ii~Ei~~v~~~~Gi~Vd~RHl~LiaD~MT~~G~~~~i~R~Gi~~~~~S~l~~aSFE~t~~ 328 (367)
T TIGR02389 249 TTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVK 328 (367)
T ss_pred ccCCHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHhcCCceEEeccccccccCCCCHHHhcChHhHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcCCCCCCCccccCeeccCCCCCCcceeEeecC
Q psy6965 1639 VLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLD 1677 (1764)
Q Consensus 1639 ILtEAAIfGEvD~LRGVSENIILGQLIPVGTGsFDLLLD 1677 (1764)
+|++||.+|+.|+|+|||+||++|+++|+|||+|+|+++
T Consensus 329 ~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~~ 367 (367)
T TIGR02389 329 HLLDAAIRGEVDELAGVIENIIVGQPIPLGTGDVDLVMD 367 (367)
T ss_pred HHHHHhhcCCCCcCCChHHHhhcCCCcCCcCCeEEEeeC
Confidence 999999999999999999999999999999999999874
No 4
>cd02737 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain. Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.
Probab=100.00 E-value=7.5e-54 Score=474.55 Aligned_cols=240 Identities=20% Similarity=0.286 Sum_probs=207.4
Q ss_pred CCCChhHHhhccCcchhhhHhhhccccchhhHHHHHHhcCCCCccchHHHHhccCCCCcEEEEeccCCccceEEEEEEec
Q psy6965 1385 KMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRIMN 1464 (1764)
Q Consensus 1385 ~m~DEE~al~k~~~~~~L~~iE~nm~~d~~l~~~R~MiDkdLtM~~iaekI~~f~dd~DL~VIfSDDNAEKLVIRIRI~~ 1464 (1764)
++|++.....++|| |++|++++ |. ..++.+ +.|++.++|.+
T Consensus 122 ~~~~~~~~~~~~sp--w~~r~~l~----------~~---------------~~~~~~--~~ci~~~~~~~---------- 162 (381)
T cd02737 122 AIFSTSLKITKFSP--WVCHFHLD----------KE---------------CQKLSD--GPCLTFSVSKE---------- 162 (381)
T ss_pred cccccccccccCCc--ceEEEEEe----------hh---------------HhcCCC--CceEEeecCcc----------
Confidence 45666666788999 99999999 22 235444 88888888711
Q ss_pred CCCCccchhhhhhhchhhhHHHHHHHHhhccCceeccccCcceEEecccccCCCceEEEcCCCcccccceEEEEee----
Q psy6965 1465 SDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETD---- 1540 (1764)
Q Consensus 1465 ded~k~eeeee~vD~~EDDvFLRrIEanMLsdItLRGIPGIkKVfI~ePetdkKKRIVITEDGefkak~EWVLETD---- 1540 (1764)
. ..+ ...+.+++|++++.++|. ++|||+|||+||+|... +..+..+.+++++....||+|+|+
T Consensus 163 ~-~~~--------~~~~~~~~~~~i~~~lL~-~~lkG~~~I~kv~i~~~---~~~~~~~~~~~~~~~~~E~vLe~~~~~~ 229 (381)
T cd02737 163 V-SKS--------SEELLDVLRDRIIPFLLE-TVIKGDERIKSVNILWE---DSPSTSWVKSVGKSSRGELVLEVTVEES 229 (381)
T ss_pred c-ccc--------hhHHHHHHHHHHHHHHhh-eeecccCCeeEEEEEec---CCCcccccccccccccceEEEEEEeccc
Confidence 0 111 113456799999999996 99999999999999731 233344555556778899999988
Q ss_pred -----ccchhhhc-----cCCCcccccccccCHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhccC
Q psy6965 1541 -----GTSLMKVL-----SERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKG 1610 (1764)
Q Consensus 1541 -----GTNL~EVL-----S~pgVDptRTySNDI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~RG 1610 (1764)
|++|+.|+ .+++||++||+||||++|+++|||||||++|++||++||+.||++||||||.||||+||++|
T Consensus 230 ~~~t~G~~~~~vl~~c~~~~~~ID~~rt~sNdI~ev~~~lGIEAAR~~ii~El~~v~~~~G~~Vd~rHL~LlAD~MT~~G 309 (381)
T cd02737 230 CKKTRGNAWNVVMDACIPVMDLIDWERSMPYSIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYSG 309 (381)
T ss_pred cccccchhHHHHHHhhhcccccCcCCCcEECCHHHHHHHHhHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHhccCC
Confidence 99999999 59999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecccccccccccCC-----ChhhhhhhHHHHHHHHHHhhcCCCCCCCccccCeeccCCCCCCcce-eEeec
Q psy6965 1611 HLMAITRHGINRQDT-----GALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC-FDLLL 1676 (1764)
Q Consensus 1611 ~LmgITRHGINR~dT-----SPLmRASFEETVEILtEAAIfGEvD~LRGVSENIILGQLIPVGTGs-FDLLL 1676 (1764)
+++|||||||++.++ |||+|||||+|+++|++||.+|+.|+|+|||+||++||++|+|||+ |||++
T Consensus 310 ~~~~~nR~Gi~~~~~s~~~~spl~~asFE~t~~~l~~AA~~g~~D~l~gvs~~ii~G~~~~vGTG~~fdll~ 381 (381)
T cd02737 310 EFVGLNAKGYKAQRRSLKISAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTGSKFEILW 381 (381)
T ss_pred ceEEecchhhhhcccccccCCHHHHhhHHHHHHHHHHHHhccCCCCCCChHHheeeCCcCCCcCCcceeeeC
Confidence 999999999998765 8999999999999999999999999999999999999999999998 99974
No 5
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated
Probab=100.00 E-value=9.5e-53 Score=465.86 Aligned_cols=226 Identities=32% Similarity=0.514 Sum_probs=201.6
Q ss_pred hhhHhhhccccchhhHHHH-HHhcCCCCccchHHHHhc-cCCCCcEEEEeccCCccceEEEEEEecCCCCccchhhhhhh
Q psy6965 1401 FLRCIEANMLSDMTLQFIR-IMNSDDSKMQDEEDAVDK-MEDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVD 1478 (1764)
Q Consensus 1401 ~L~~iE~nm~~d~~l~~~R-~MiDkdLtM~~iaekI~~-f~dd~DL~VIfSDDNAEKLVIRIRI~~ded~k~eeeee~vD 1478 (1764)
|..+|++| + +|..++|++.+|..+|.+ ++.. +++. ..++++|+| ..
T Consensus 155 ~~l~i~ld----------~~~i~~~~l~~~~I~~~i~~~~~~~--~~~~-----~~~i~i~~~--~~------------- 202 (383)
T PRK04309 155 MTIIIELD----------EEMLEDRGLTVDDVKEAIEKKKGGE--VEIE-----GNTLIISPK--EP------------- 202 (383)
T ss_pred cEEEEEEC----------HHHHHHcCCCHHHHHHHHHHhcCcc--eecc-----CCeEEEEec--Cc-------------
Confidence 67888998 7 888999999999999988 5544 4332 456666665 10
Q ss_pred chhhhHHHHHHHHhhccCceeccccCcceEEecccccCCCceEEEcCCCcccccceEEEEeeccchhhhccCCCcccccc
Q psy6965 1479 KMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRT 1558 (1764)
Q Consensus 1479 ~~EDDvFLRrIEanMLsdItLRGIPGIkKVfI~ePetdkKKRIVITEDGefkak~EWVLETDGTNL~EVLS~pgVDptRT 1558 (1764)
...+|+++...+ .+++|+|+|||+||+++.. ..+|+|.|+|+||.++|.+++||++||
T Consensus 203 ---~~~~l~~l~~~l-~~~~vkGi~gI~r~~i~~~------------------~~~~~l~teG~nl~~v~~~~~VD~~rt 260 (383)
T PRK04309 203 ---SYRELRKLAEKI-RNIKIKGIKGIKRVIIRKE------------------GDEYVIYTEGSNLKEVLKVEGVDATRT 260 (383)
T ss_pred ---hHHHHHHHHHHh-cccEEECCCCceEEEEecC------------------CCeEEEEEcccCHHHHhcCCCEeeccc
Confidence 123677777554 5999999999999988531 147999999999999999999999999
Q ss_pred cccCHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhccCeecccccccccccCCChhhhhhhHHHHH
Q psy6965 1559 FSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVD 1638 (1764)
Q Consensus 1559 ySNDI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~RG~LmgITRHGINR~dTSPLmRASFEETVE 1638 (1764)
+||||++|+++|||||||++|++|+++||+.||++||+|||.||||+||++|++.||||||+++.+.|||++||||+|++
T Consensus 261 ~sNdI~ei~~vlGIEAAR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~i~R~Gi~~~~~S~l~~aSFE~T~~ 340 (383)
T PRK04309 261 TTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVK 340 (383)
T ss_pred cCCCHHHHHHHcCHHHHHHHHHHHHHHHHHHcCCeecHHHHHHHHHHhccCceEEeeechhhcCCCCCHHHhCchhhHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcCCCCCCCccccCeeccCCCCCCcceeEeecChhh
Q psy6965 1639 VLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEK 1680 (1764)
Q Consensus 1639 ILtEAAIfGEvD~LRGVSENIILGQLIPVGTGsFDLLLD~ek 1680 (1764)
+|++||.+|+.|+|+|||+||++||++|+|||+|+|++|..+
T Consensus 341 ~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~~~~~ 382 (383)
T PRK04309 341 HLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELTMDPPL 382 (383)
T ss_pred HHHHHHhcCCCCCCCCcHHHhhcCCCcCCCCceEEEEcCCCC
Confidence 999999999999999999999999999999999999998764
No 6
>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP). Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Probab=100.00 E-value=1.1e-52 Score=463.02 Aligned_cols=227 Identities=33% Similarity=0.505 Sum_probs=199.8
Q ss_pred chhhhHhhhccccchhhHHHH-HHhcCCCCccchHHHHhc-cCCCCcEEEEeccCCccceEEEEEEecCCCCccchhhhh
Q psy6965 1399 DMFLRCIEANMLSDMTLQFIR-IMNSDDSKMQDEEDAVDK-MEDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDA 1476 (1764)
Q Consensus 1399 ~~~L~~iE~nm~~d~~l~~~R-~MiDkdLtM~~iaekI~~-f~dd~DL~VIfSDDNAEKLVIRIRI~~ded~k~eeeee~ 1476 (1764)
+-|.++|++| | +|.++.++|.+|..+|.+ ++.. +.+ + +++. +++.... +
T Consensus 134 ~~~~l~i~ld----------~~~l~~~~l~~~~i~~~i~~~~~~~--~~~--~-~~~~-----~~~~~~~--~------- 184 (363)
T cd06528 134 FNMRITIELD----------EEMLEDRGITVDDVLKAIEKLKKGK--VGE--E-GDVT-----LIVLKAE--E------- 184 (363)
T ss_pred cCcEEEEEEC----------HHHHHHcCCCHHHHHHHHHHhcCCc--ccc--c-CCcc-----EEEEcCC--c-------
Confidence 3499999999 7 899999999999999988 6544 332 2 2222 2222211 0
Q ss_pred hhchhhhHHHHHHHHhhccCceeccccCcceEEecccccCCCceEEEcCCCcccccceEEEEeeccchhhhccCCCcccc
Q psy6965 1477 VDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPV 1556 (1764)
Q Consensus 1477 vD~~EDDvFLRrIEanMLsdItLRGIPGIkKVfI~ePetdkKKRIVITEDGefkak~EWVLETDGTNL~EVLS~pgVDpt 1556 (1764)
....+|++++.. |.+++|+|+|||+||+++.+ + .+|+|.|+|+||.++|.+++||++
T Consensus 185 ----~~~~~l~~l~~~-l~~~~v~Gi~gI~r~~i~~~------------~------~~~~l~teG~nl~~v~~~~~Vd~~ 241 (363)
T cd06528 185 ----PSIKELRKLAEK-ILNTKIKGIKGIKRVIVRKE------------E------DEYVIYTEGSNLKAVLKVEGVDPT 241 (363)
T ss_pred ----chHHHHHHHHHh-hcccEEeCCCCceEEEEecC------------C------ceEEEEecCcCHHHHhcCCCCccc
Confidence 123588888755 55799999999999988631 1 279999999999999999999999
Q ss_pred cccccCHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhccCeecccccccccccCCChhhhhhhHHH
Q psy6965 1557 RTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEET 1636 (1764)
Q Consensus 1557 RTySNDI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~RG~LmgITRHGINR~dTSPLmRASFEET 1636 (1764)
||+||||++|+++|||||||++|++||++||+.||++||+|||+||||+||++|++.||||||+++.++|||++||||+|
T Consensus 242 rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~i~R~gi~~~~~S~L~~aSFE~t 321 (363)
T cd06528 242 RTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLARAAFEVT 321 (363)
T ss_pred ccccCCHHHHHHhCCHHHHHHHHHHHHHHHHHhcCCeecHHHHHHHHHHhccCCceecccchhhcCCCCChhhhCchhhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999989999999999999
Q ss_pred HHHHHHHhhcCCCCCCCccccCeeccCCCCCCcceeEeecC
Q psy6965 1637 VDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLD 1677 (1764)
Q Consensus 1637 VEILtEAAIfGEvD~LRGVSENIILGQLIPVGTGsFDLLLD 1677 (1764)
+++|++||.+|+.|+|+|||+||++||++|+|||+|||++|
T Consensus 322 ~~~L~~AA~~g~~D~l~gvse~Ii~G~~~~~GTG~~~l~~d 362 (363)
T cd06528 322 VKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDVELTMD 362 (363)
T ss_pred HHHHHHHHhcCCCCcCCCcHHHeeeCCCCCCcCCeeEEEec
Confidence 99999999999999999999999999999999999999987
No 7
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=100.00 E-value=1.8e-52 Score=474.78 Aligned_cols=228 Identities=32% Similarity=0.492 Sum_probs=199.3
Q ss_pred hhhHhhhccccchhhHHHH-HHhcCCCCccchHHHHhccCCCCcEEEEeccCCccceEEEEEEecCCCCccchhhhhhhc
Q psy6965 1401 FLRCIEANMLSDMTLQFIR-IMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDK 1479 (1764)
Q Consensus 1401 ~L~~iE~nm~~d~~l~~~R-~MiDkdLtM~~iaekI~~f~dd~DL~VIfSDDNAEKLVIRIRI~~ded~k~eeeee~vD~ 1479 (1764)
|..+|++| + +|.+++|++.+|..+|.+.. +..+.+++| .+|+. ... +
T Consensus 277 ~~i~i~Ld----------~~~l~~~~l~~~~I~~~I~~~~----~~~~~~~~~----~I~i~--~~~-------~----- 324 (509)
T PRK14897 277 MSVVVELD----------EEKMKERLIEYDDILAAISKLT----FKTVEIDDG----IIRLK--PQQ-------P----- 324 (509)
T ss_pred ceEEEEEC----------HHHHHHcCCCHHHHHHHHHhcc----ceEEecCCC----EEEEE--eCc-------h-----
Confidence 66889999 7 89999999999999998842 233345555 34444 321 0
Q ss_pred hhhhHHHHHHHHhhccCceeccccCcceEEecccccCCCceEEEcCCCcccccceEEEEeeccchhhhccCCCccccccc
Q psy6965 1480 MEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTF 1559 (1764)
Q Consensus 1480 ~EDDvFLRrIEanMLsdItLRGIPGIkKVfI~ePetdkKKRIVITEDGefkak~EWVLETDGTNL~EVLS~pgVDptRTy 1559 (1764)
....|+++. ..+.+++|+|||||+||+++... + ..+|+|.|+|+||+++|++++||++||+
T Consensus 325 --~~~~L~~l~-~~l~~i~I~GipgI~r~~i~~~~------------~----~~~~~L~TeG~NL~~vl~~~~VD~~rt~ 385 (509)
T PRK14897 325 --SFKKLYLLA-EKVKSLTIKGIKGIKRAIARKEN------------D----ERRWVIYTQGSNLKDVLEIDEVDPTRTY 385 (509)
T ss_pred --HHHHHHHHH-HHhhccEEeCCCCccEEEEecCC------------C----CceeEEEeeccCHHHHhcCCCcccccCc
Confidence 113567764 45689999999999999986311 1 1469999999999999999999999999
Q ss_pred ccCHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhccCeecccccccccccCCChhhhhhhHHHHHH
Q psy6965 1560 SNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDV 1639 (1764)
Q Consensus 1560 SNDI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~RG~LmgITRHGINR~dTSPLmRASFEETVEI 1639 (1764)
||||++|+++|||||||++|++|++.||+.||++||+|||+||||+||++|++.||||||+++.+.|||+|||||+|+++
T Consensus 386 SNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vd~RHL~LIAD~MT~~G~v~~i~R~Gi~~~~~SpL~rASFE~T~~~ 465 (509)
T PRK14897 386 TNDIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLARAAFEITGKH 465 (509)
T ss_pred cCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHhCcCCcccccccccccccCCCHHHhcchHhHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999989999999999999999
Q ss_pred HHHHhhcCCCCCCCccccCeeccCCCCCCcceeEeecChh
Q psy6965 1640 LMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAE 1679 (1764)
Q Consensus 1640 LtEAAIfGEvD~LRGVSENIILGQLIPVGTGsFDLLLD~e 1679 (1764)
|++||.+|+.|+|+|||+||++||++|+|||+|+|+++..
T Consensus 466 L~~AA~~Ge~D~L~GvsenII~G~~ipvGTG~fdL~~~~~ 505 (509)
T PRK14897 466 LLRAGILGEVDKLAGVAENIIVGQPITLGTGAVSLVYKGR 505 (509)
T ss_pred HHHHhhcCCCCcCCChHHhhhcCCccCCcCceEEEEecCC
Confidence 9999999999999999999999999999999999998754
No 8
>cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain. Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=100.00 E-value=4.1e-50 Score=433.93 Aligned_cols=175 Identities=37% Similarity=0.540 Sum_probs=164.7
Q ss_pred hhHHHHHHHHhhccCceeccccCcceEEecccccCCCceEEEcCCCcccccceEEEEeeccchhhhccCCCccccccccc
Q psy6965 1482 DDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSN 1561 (1764)
Q Consensus 1482 DDvFLRrIEanMLsdItLRGIPGIkKVfI~ePetdkKKRIVITEDGefkak~EWVLETDGTNL~EVLS~pgVDptRTySN 1561 (1764)
...|+.+...++|.+++|+|+|||+||++++.+ ...+|+|+|+|+||.++|.+++||++||+||
T Consensus 126 ~~~~~~~~l~~~l~~~~v~Gi~gI~r~~i~~~~----------------~~~~~~l~teG~nl~~v~~~~~Vd~~rt~sN 189 (300)
T cd02736 126 NLYFLLQSLKRKLPDVVVSGIPEVKRAVINKDK----------------KKGKYKLLVEGYGLRAVMNTPGVIGTRTTSN 189 (300)
T ss_pred cHHHHHHHHHHHhccceEeCCCCceEEEEecCC----------------CCCcEEEEEecccHHHHhcCCcEeccCCccC
Confidence 345666777899999999999999999986411 0247999999999999999999999999999
Q ss_pred CHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhccCeecccccccccccCCChhhhhhhHHHHHHHH
Q psy6965 1562 DICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLM 1641 (1764)
Q Consensus 1562 DI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~RG~LmgITRHGINR~dTSPLmRASFEETVEILt 1641 (1764)
||++|+++|||||||++|++||++||+.||++||+|||+||||+||++|+++||||||+++.++|||++||||+|+++|+
T Consensus 190 dI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~Vd~rHl~LiaD~MT~~G~~~~itR~gi~~~~~S~l~~aSFE~t~~~L~ 269 (300)
T cd02736 190 HIMEVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLASFEKTTDHLF 269 (300)
T ss_pred CHHHHHHhcCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHhccCceeeeecccccccCCCHHHhcchHhHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999988899999999999999999
Q ss_pred HHhhcCCCCCCCccccCeeccCCCCCCccee
Q psy6965 1642 DAAAHAEADPMRGVSENIIMGQLPRMGTGCF 1672 (1764)
Q Consensus 1642 EAAIfGEvD~LRGVSENIILGQLIPVGTGsF 1672 (1764)
+||.+|+.|+|+|||+||++||++|+|||+|
T Consensus 270 ~AA~~g~~D~l~gvse~ii~G~~~~~GTG~f 300 (300)
T cd02736 270 NAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300 (300)
T ss_pred HHhhcCCCCcCCCcHHHeeeCCCcCCCCCCC
Confidence 9999999999999999999999999999997
No 9
>cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain. RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=100.00 E-value=1.6e-49 Score=430.20 Aligned_cols=193 Identities=28% Similarity=0.461 Sum_probs=175.1
Q ss_pred ccceEEEEEEecCCCCccchhhhhhhchhhhHHHHHHHHhhccCceeccccCcceEEecccccCCCceEEEcCCCccccc
Q psy6965 1453 SDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAI 1532 (1764)
Q Consensus 1453 AEKLVIRIRI~~ded~k~eeeee~vD~~EDDvFLRrIEanMLsdItLRGIPGIkKVfI~ePetdkKKRIVITEDGefkak 1532 (1764)
+.++.+++|+..+. ...|+..++..+|.+++|+|||||+||+++.++.. ..
T Consensus 116 ~~~~~~~i~~~~~~---------------~~~~~~~~~~~~l~~~~i~gi~gI~r~~i~~~~~~--------------~~ 166 (309)
T cd02735 116 GKWCEVTIKLPLSS---------------PKLLLLSIVEKLARKAVIREIPGITRCFVVEEDKG--------------GK 166 (309)
T ss_pred CCEEEEEEEecCCc---------------hhHHHHHHHHHHhcccEEeCCCCccEEEEecCcCC--------------Cc
Confidence 55778888875431 22577778889999999999999999998753210 12
Q ss_pred ceEEEEeeccchhhhccC-CCcccccccccCHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhccCe
Q psy6965 1533 ADWLLETDGTSLMKVLSE-RDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGH 1611 (1764)
Q Consensus 1533 ~EWVLETDGTNL~EVLS~-pgVDptRTySNDI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~RG~ 1611 (1764)
.+|+|.|+|+||.++|.+ ++||++||+||||++|+++|||||||++|++|+++||+.||++||+|||.||||+||++|+
T Consensus 167 ~~~~l~teG~nl~~v~~~~~~vd~~r~~sNdi~ei~~~lGIEAar~~ii~Ei~~v~~~~Gi~V~~rHl~LiaD~MT~~G~ 246 (309)
T cd02735 167 TKYLVITEGVNLAALWKFSDILDVNRIYTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGG 246 (309)
T ss_pred eEEEEEeccccHHHHHhccCccccccceeCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCCeeCHHHHHHHHHHHHhCCc
Confidence 479999999999999998 7899999999999999999999999999999999999999999999999999999999999
Q ss_pred ecccccccccccCCChhhhhhhHHHHHHHHHHhhcCCCCCCCccccCeeccCCCCCCcceeEee
Q psy6965 1612 LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLL 1675 (1764)
Q Consensus 1612 LmgITRHGINR~dTSPLmRASFEETVEILtEAAIfGEvD~LRGVSENIILGQLIPVGTGsFDLL 1675 (1764)
+.||||||| +...|||++||||+|+++|++||.+|+.|+|+|||+||++||++|+|||+|||+
T Consensus 247 ~~~~nr~gi-~~~~S~l~~asFE~t~~~L~~Aa~~g~~D~l~g~s~~ii~G~~~~~GTG~fdll 309 (309)
T cd02735 247 YRPFNRIGM-ESSTSPLQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGTGLFDLL 309 (309)
T ss_pred Eeecchhhe-ccCCCHHHhhhhhhHHHHHHHHhhcCCCCCCCChHHheeeCCccCccceeEEeC
Confidence 999999999 667999999999999999999999999999999999999999999999999985
No 10
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=100.00 E-value=1.1e-48 Score=465.40 Aligned_cols=222 Identities=35% Similarity=0.563 Sum_probs=197.4
Q ss_pred H-HHhcCCCCccchHHHHhc-cCCCCcEEEEeccCCccceEEEEEEecCCCCccchhhhhhhchhhhHHHHHHHHhhccC
Q psy6965 1419 R-IMNSDDSKMQDEEDAVDK-MEDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSD 1496 (1764)
Q Consensus 1419 R-~MiDkdLtM~~iaekI~~-f~dd~DL~VIfSDDNAEKLVIRIRI~~ded~k~eeeee~vD~~EDDvFLRrIEanMLsd 1496 (1764)
+ ++....+++.+|..+|++ |+.. +.+ ++.++|+|+.... ...+++.++ .|.+
T Consensus 629 ~~~~~~~~l~~~~i~~~i~~~~~~~--~~~-------~~~~~~~~~~~~~---------------~~~~~~~~~--~l~~ 682 (858)
T PRK14898 629 EETLADRGLTIESVEEAIEKKLGVK--IDR-------KGTVLYLKPKTPS---------------YKALRKRIP--KIKN 682 (858)
T ss_pred HHHHHHcCCCHHHHHHHHHHhcccc--ccC-------CCCEEEEEecCch---------------HHHHHHHHH--HhcC
Confidence 5 788889999999999988 6543 222 5688999875420 234677665 4789
Q ss_pred ceeccccCcceEEecccccCCCceEEEcCCCcccccceEEEEeeccchhhhccCCCcccccccccCHHHHHHHhcHHHHH
Q psy6965 1497 MTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVR 1576 (1764)
Q Consensus 1497 ItLRGIPGIkKVfI~ePetdkKKRIVITEDGefkak~EWVLETDGTNL~EVLS~pgVDptRTySNDI~EILeVLGIEAAR 1576 (1764)
++|+|||||+||++..++. . ...+|+|.|+|+||.++|.+++||++||+||||++|+++|||||||
T Consensus 683 ~~i~gi~gI~~~~i~~~~~----------~----~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar 748 (858)
T PRK14898 683 IVLKGIPGIERVLVKKEEH----------E----NDEEYVLYTQGSNLREVFKIEGVDTSRTTTNNIIEIQEVLGIEAAR 748 (858)
T ss_pred cEEECCCCccEEEEecCCC----------C----CCceEEEEecCcCHHHHhcCCCCcccccccCCHHHHHHhhCHHHHH
Confidence 9999999999999864221 0 1248999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhccCCcccchhhHHHHHHHHhccCeecccccccccccCCChhhhhhhHHHHHHHHHHhhcCCCCCCCccc
Q psy6965 1577 KSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVS 1656 (1764)
Q Consensus 1577 kAIInEIrnVFSfYGIYVNyRHLSLLADvMT~RG~LmgITRHGINR~dTSPLmRASFEETVEILtEAAIfGEvD~LRGVS 1656 (1764)
++|++||++||+.||++||+|||.||||+||++|.++||||||+++.++|||++||||+|+++|++||.+|+.|+|+|||
T Consensus 749 ~~ii~Ei~~v~~~~gi~V~~rHl~liad~MT~~G~~~~~~r~gi~~~~~s~l~~asFe~t~~~l~~Aa~~g~~D~l~g~s 828 (858)
T PRK14898 749 NAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIGRHGVAGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVI 828 (858)
T ss_pred HHHHHHHHHHHHhcCCccCHHHHHHHHHHHccCCcEEEeccCCccCCCCCHHHhcChHhHHHHHHHHhhcCCCCcCCCch
Confidence 99999999999999999999999999999999999999999999988899999999999999999999999999999999
Q ss_pred cCeeccCCCCCCcceeEeecChhh
Q psy6965 1657 ENIIMGQLPRMGTGCFDLLLDAEK 1680 (1764)
Q Consensus 1657 ENIILGQLIPVGTGsFDLLLD~ek 1680 (1764)
+||++|+++|+|||+|||++|.+.
T Consensus 829 ~~ii~G~~~~~GTG~~~l~~~~~~ 852 (858)
T PRK14898 829 ENVIVGKPIKLGTGCVDLRIDREY 852 (858)
T ss_pred HHeeeCCccCCcCceEEEEecCcc
Confidence 999999999999999999999653
No 11
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=100.00 E-value=4e-47 Score=465.45 Aligned_cols=225 Identities=28% Similarity=0.455 Sum_probs=192.0
Q ss_pred CCCCccchHHHHhc-cCCCCcEEEEeccCCccceEEEEEEecCCCCccchhhhhhhchhhhHHHHHHHHhhccCceeccc
Q psy6965 1424 DDSKMQDEEDAVDK-MEDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGI 1502 (1764)
Q Consensus 1424 kdLtM~~iaekI~~-f~dd~DL~VIfSDDNAEKLVIRIRI~~ded~k~eeeee~vD~~EDDvFLRrIEanMLsdItLRGI 1502 (1764)
..++|..|++.|.+ ++.. ...+..++| .+++++.... . ....-.+|++++..++ +++|+||
T Consensus 1088 ~~i~~~~i~~~i~~~~~~~--~~~~~~~~~----~i~~~~~~~~--~---------~~~~~~~l~~l~~~l~-~~~i~Gi 1149 (1321)
T PRK14977 1088 GCIPMERFAEIEAALAKGK--KFEMELEDD----LIILDLVEAA--D---------RDKPLATLIAIRNKIL-DKPVKGV 1149 (1321)
T ss_pred cCCCHHHHHHHHHHhhcCC--ceEEeecCC----EEEEecCccc--c---------cchHHHHHHHHHHhcC-CcEEecC
Confidence 34889899988887 5443 334444444 3444443210 0 0012357888887776 7999999
Q ss_pred cCcceEEecccccCCCceEEEcCCCcccccceEEEEeeccchhhhccCCCcccccccccCHHHHHHHhcHHHHHHHHHHH
Q psy6965 1503 EAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKE 1582 (1764)
Q Consensus 1503 PGIkKVfI~ePetdkKKRIVITEDGefkak~EWVLETDGTNL~EVLS~pgVDptRTySNDI~EILeVLGIEAARkAIInE 1582 (1764)
|||+||+++..+ .+| ..+|+|+|+|+||.+||.+++||++||+||||+||+++|||||||++|++|
T Consensus 1150 ~~I~r~~i~~~~----------~~~----~~e~~l~teG~nl~~vl~~~~Vd~~rt~sN~i~ei~~~lGIEAaR~~ii~E 1215 (1321)
T PRK14977 1150 PDIERAWVELVE----------KDG----RDEWIIQTSGSNLAAVLEMKCIDIANTITNDCFEIAGTLGIEAARNAIFNE 1215 (1321)
T ss_pred CCceEEEEEeec----------cCC----CeeEEEEecCcCHHHHhCCCCCcccccEECCHHHHHHhhhHHHHHHHHHHH
Confidence 999999885311 112 258999999999999999999999999999999999999999999999999
Q ss_pred HHHhhccCCcccchhhHHHHHHHHhccCeecccc------cccccccCCChhhhhhhHHHHHHHHHHhhcCCCCCCCccc
Q psy6965 1583 MNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAIT------RHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVS 1656 (1764)
Q Consensus 1583 IrnVFSfYGIYVNyRHLSLLADvMT~RG~LmgIT------RHGINR~dTSPLmRASFEETVEILtEAAIfGEvD~LRGVS 1656 (1764)
|++||++||++||+|||+||||+||++|++++|| ||||++.++|||++||||+|+++|++||++|+.|+|+|||
T Consensus 1216 i~~v~~~~G~~V~~rHi~LlaD~MT~~G~~~~i~~~~~~~R~Gi~~~~~s~l~~asFE~t~~~L~~AA~~g~~D~l~gvs 1295 (1321)
T PRK14977 1216 LASILEDQGLEVDNRYIMLVADIMCSRGTIEAIGLQAAGVRHGFAGEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGIL 1295 (1321)
T ss_pred HHHHHHHcCCccCHHHHHHHHHHHccCceEEeccccccccccccccCCCCHHHhcCHHHHHHHHHHHHHhcCcCccCChH
Confidence 9999999999999999999999999999999999 9999999999999999999999999999999999999999
Q ss_pred cCeeccCCCCCCcceeEeecChhh
Q psy6965 1657 ENIIMGQLPRMGTGCFDLLLDAEK 1680 (1764)
Q Consensus 1657 ENIILGQLIPVGTGsFDLLLD~ek 1680 (1764)
||||+|+++|+|||+|+|+++.++
T Consensus 1296 enii~G~~~~~GTG~~~Ll~~~~~ 1319 (1321)
T PRK14977 1296 DALIMGQNIPIGSGKVDLLMDFSG 1319 (1321)
T ss_pred HhhhcCCCccCccceEEEEecccc
Confidence 999999999999999999998764
No 12
>KOG0262|consensus
Probab=100.00 E-value=1e-39 Score=388.11 Aligned_cols=202 Identities=29% Similarity=0.456 Sum_probs=175.3
Q ss_pred eccCCccceEEEEEEecCCCCccchhhhhhhchhhhHHHHHHHHhhccCceeccccCcceEEecccccCCCceEEEcCCC
Q psy6965 1448 EANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESG 1527 (1764)
Q Consensus 1448 fSDDNAEKLVIRIRI~~ded~k~eeeee~vD~~EDDvFLRrIEanMLsdItLRGIPGIkKVfI~ePetdkKKRIVITEDG 1527 (1764)
|-..|..++-+.+-+.-. +.+. .+-.|-..++...+|+.+|||+||++.+|....
T Consensus 1435 fd~~~~~wcev~~~lp~~-~~k~--------------~mssiVe~~~~~~vI~q~~gIeRc~~~~~~~~~---------- 1489 (1640)
T KOG0262|consen 1435 FDKESGKWCEVELKLPLD-KEKL--------------DMSSIVESIAPKSVIHQVPGIERCVVSEPQDDV---------- 1489 (1640)
T ss_pred cccccCcEEEEEEEecCC-Ccch--------------HHHHHHHHHhcceeeeccCCceeeeccCCcccc----------
Confidence 347788887777766543 1221 233444567889999999999999987653211
Q ss_pred cccccceEEEEeeccchhhhccCCC-cccccccccCHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHH
Q psy6965 1528 EFKAIADWLLETDGTSLMKVLSERD-VDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVM 1606 (1764)
Q Consensus 1528 efkak~EWVLETDGTNL~EVLS~pg-VDptRTySNDI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvM 1606 (1764)
.... +|.|+|+||.++|.+.. +|.+++|||||+.|+++|||||||++|++||.+||+.|||.|+.|||+||||||
T Consensus 1490 ---k~~~-~l~TeGVnl~a~~~~~d~LDv~~lySNDI~ail~tyGVEAar~~Iv~Ev~~VF~vYGIsVd~RHLsLiADYM 1565 (1640)
T KOG0262|consen 1490 ---KEKS-VLLTEGVNLPALFDHADILDVNRLYSNDIHAILNTYGVEAARNAIVNEVNNVFKVYGISVDIRHLSLIADYM 1565 (1640)
T ss_pred ---cccc-eehhcCccHHHHHHHHhhhhhhhhccchHHHHHHHhhHHHHHHHHHHHHHHhhhheeeeecHHHHHHHHHHH
Confidence 1123 88999999999999776 699999999999999999999999999999999999999999999999999999
Q ss_pred hccCeecccccccccccCCChhhhhhhHHHHHHHHHHhhcCCCCCCCccccCeeccCCCCCCcceeEeecChh
Q psy6965 1607 TAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAE 1679 (1764)
Q Consensus 1607 T~RG~LmgITRHGINR~dTSPLmRASFEETVEILtEAAIfGEvD~LRGVSENIILGQLIPVGTGsFDLLLD~e 1679 (1764)
|+.|.+.|++|+||. .++|||+|+|||+|..+|.+||.+|+.|.|.+||++|++|.++..|||+|||+.+..
T Consensus 1566 Tf~G~y~pfnR~Gm~-~ssSP~qkMsFETt~~Fl~~Aa~~g~~D~L~sPSArLvvG~~~r~GTG~Fdll~~v~ 1637 (1640)
T KOG0262|consen 1566 TFEGGYQPFNRMGME-SSSSPLQKMSFETTCQFLKQAALFGEEDELSSPSARLVVGLPVRGGTGSFDLLQKVD 1637 (1640)
T ss_pred hhccccccccccccc-cCCChhHhhhHHHHHHHHHHHHhcCcccccCCCcceeEeccccCCCcceeeeeccCC
Confidence 999999999999995 578999999999999999999999999999999999999999999999999998753
No 13
>KOG0261|consensus
Probab=100.00 E-value=9.4e-40 Score=381.96 Aligned_cols=221 Identities=30% Similarity=0.445 Sum_probs=187.0
Q ss_pred CCCCccchHHHHhc---c-CCCCcEEEEeccCCccceEEEEEEecCCCCccchhhhhhhchhhhHHHHH-HHHhhccCce
Q psy6965 1424 DDSKMQDEEDAVDK---M-EDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRC-IEANMLSDMT 1498 (1764)
Q Consensus 1424 kdLtM~~iaekI~~---f-~dd~DL~VIfSDDNAEKLVIRIRI~~ded~k~eeeee~vD~~EDDvFLRr-IEanMLsdIt 1498 (1764)
=.+++..|+-+|-+ . -...++.|+-. ..++++.....+ . -+|++. ..+.-|++++
T Consensus 1139 L~i~~~~I~~sI~~s~~~k~~~~~v~v~~~------~~~~v~~~~~~~--~------------S~~~~lq~lk~~L~~Vv 1198 (1386)
T KOG0261|consen 1139 LEITIESIAYSILKSPKRKVKPNDVRVVGE------TTLRVTPVSDTK--S------------SVYYNLQRLKRSLPNVV 1198 (1386)
T ss_pred ccccHHHHHHHHhcCCccccCCcceEEecc------eeEEEeeccccc--c------------hhhhhHHHHHhhCCceE
Confidence 35677888877755 1 12234555532 556666554321 1 133333 2457789999
Q ss_pred eccccCcceEEecccccCCCceEEEcCCCcccccceEEEEeeccchhhhccCCCcccccccccCHHHHHHHhcHHHHHHH
Q psy6965 1499 LQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKS 1578 (1764)
Q Consensus 1499 LRGIPGIkKVfI~ePetdkKKRIVITEDGefkak~EWVLETDGTNL~EVLS~pgVDptRTySNDI~EILeVLGIEAARkA 1578 (1764)
++|+|.|.|+.++. ++.+ +-|-|-.+|++|+.|++.+||.++||+||++.||.+||||||||.+
T Consensus 1199 v~gip~vnr~vi~~-----------de~~-----~~y~L~vEG~gLr~Vm~t~GV~g~~TtsNnv~Ev~~vLGIEAAR~~ 1262 (1386)
T KOG0261|consen 1199 VKGIPEVNRAVINI-----------DEKR-----GLYKLLVEGTGLRAVMNTDGVKGRRTTSNNVLEVEKVLGIEAARTT 1262 (1386)
T ss_pred EecCcchhhhheee-----------cccC-----CceEEEEeccchHHHhccCCccccccccCceEEeehhhchHHHHHH
Confidence 99999999988764 1111 2378889999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhccCCcccchhhHHHHHHHHhccCeecccccccccccCCChhhhhhhHHHHHHHHHHhhcCCCCCCCccccC
Q psy6965 1579 VEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSEN 1658 (1764)
Q Consensus 1579 IInEIrnVFSfYGIYVNyRHLSLLADvMT~RG~LmgITRHGINR~dTSPLmRASFEETVEILtEAAIfGEvD~LRGVSEN 1658 (1764)
||+||..+++.+|+.||+||+.||||+||+||++.||||+|+.+++.|+|+.||||.|.++|++||.+|++|.+.||||+
T Consensus 1263 II~EI~ytM~~HGmsiD~RHiMLLaDvMTyrGEVlGITRfGl~KM~~SVL~lASFEkT~DhLF~AA~~~k~D~I~GVSEc 1342 (1386)
T KOG0261|consen 1263 IISEIGYTMSNHGMSIDPRHIMLLADVMTYRGEVLGITRFGLAKMKDSVLMLASFEKTADHLFDAAAYGKKDAIEGVSEC 1342 (1386)
T ss_pred HHHHHHHHHHhcCcccCHHHHHHHHHHhhhcceeeeeeehhhHHHHHHHHHHHhhhhhhHHHHHHHHhcCcccccchhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeccCCCCCCcceeEeecChhh
Q psy6965 1659 IIMGQLPRMGTGCFDLLLDAEK 1680 (1764)
Q Consensus 1659 IILGQLIPVGTGsFDLLLD~ek 1680 (1764)
||+|+++++|||.|+|+...+.
T Consensus 1343 IIlG~pm~iGTG~fkl~~~~~~ 1364 (1386)
T KOG0261|consen 1343 IILGIPMCIGTGIFKLLQRTDD 1364 (1386)
T ss_pred eecccceeccccHHHHHHhcCC
Confidence 9999999999999999987765
No 14
>cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain. RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channe
Probab=100.00 E-value=9.5e-36 Score=299.38 Aligned_cols=110 Identities=46% Similarity=0.724 Sum_probs=108.6
Q ss_pred CHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhccCeecccccccccccCCChhhhhhhHHHHHHHH
Q psy6965 1562 DICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLM 1641 (1764)
Q Consensus 1562 DI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~RG~LmgITRHGINR~dTSPLmRASFEETVEILt 1641 (1764)
||++|+++|||||||++|++||++||+.||++||+|||.||||+||++|.+.||||||+++..+|||++||||+|+++|+
T Consensus 49 dI~~i~~~lGIEAaR~~iv~El~~v~~~~Gi~V~~rHl~LIAD~MT~~G~~~ginr~g~~~~~~Spl~~aSFE~t~~~L~ 128 (158)
T cd00630 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEKTTKHLL 128 (158)
T ss_pred cHHHHHHHhCHHHHHHHHHHHHHHHHHhcCceecHHHHHHHHHHHhcCCcccccccccccccCCCHHHHcCHHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999888899999999999999999
Q ss_pred HHhhcCCCCCCCccccCeeccCCCCCCcce
Q psy6965 1642 DAAAHAEADPMRGVSENIIMGQLPRMGTGC 1671 (1764)
Q Consensus 1642 EAAIfGEvD~LRGVSENIILGQLIPVGTGs 1671 (1764)
+||.+|+.|+|+|||+||++|+++|+|||+
T Consensus 129 ~AA~~g~~D~l~g~s~~ii~Gk~~~~GTG~ 158 (158)
T cd00630 129 DAAAAGEKDELEGVSENIILGRPAPLGTGS 158 (158)
T ss_pred HHhhcCCCCCCCCcHHhhhccCCCCCCCCC
Confidence 999999999999999999999999999996
No 15
>cd02655 RNAP_beta'_C Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain. Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Probab=99.96 E-value=2.3e-30 Score=269.40 Aligned_cols=109 Identities=32% Similarity=0.530 Sum_probs=103.9
Q ss_pred cCHHHHHHHh--cHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhccCee--------------------------
Q psy6965 1561 NDICEIFQVL--GIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHL-------------------------- 1612 (1764)
Q Consensus 1561 NDI~EILeVL--GIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~RG~L-------------------------- 1612 (1764)
||++++++++ ||||||++|++|+++||+.||++||+|||+||||+||++|++
T Consensus 54 ~~~~~il~~~~~Giea~r~~iv~EIq~Vy~~qGV~I~dKHielIv~qMT~kv~i~~~g~s~~l~Ge~v~~~~~~~~N~~~ 133 (204)
T cd02655 54 INPHDLLRIKFLGPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRL 133 (204)
T ss_pred CCHHHHHHHHhHHHHHHHHHHHHHHHHHHHhcCeeecHHHHHHHHHHHhcCeEEecCCCcccCCCceeeHHHHHHHHHHH
Confidence 9999999999 999999999999999999999999999999999999999653
Q ss_pred --------------cccccccccccCCChhhhhhhHHHHHHHHHHhhcCCCCCCCccccCeeccCCCCCCcce
Q psy6965 1613 --------------MAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC 1671 (1764)
Q Consensus 1613 --------------mgITRHGINR~dTSPLmRASFEETVEILtEAAIfGEvD~LRGVSENIILGQLIPVGTGs 1671 (1764)
+||||++++. .|||++||||||+++|++||++|+.|+|+|+|||||+|+++|+|||+
T Consensus 134 ~~~~~~~~~y~p~llGItk~~l~~--~Sfls~ASFqeT~kvL~~AAi~gk~D~L~GlkeNVI~G~liPaGTG~ 204 (204)
T cd02655 134 LLLGKKPAKYEPVLLGITKASLNT--ESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204 (204)
T ss_pred HhCCCCcccccceeeeeeeccccC--CCccccCChHHHHHHHHHHHhcCCCCCCCCchhheEECCccCCCCCC
Confidence 4888888864 79999999999999999999999999999999999999999999995
No 16
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=99.92 E-value=2.8e-25 Score=270.58 Aligned_cols=123 Identities=33% Similarity=0.561 Sum_probs=113.5
Q ss_pred ccchhhhccCCCcccccccccCHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhcc-----------
Q psy6965 1541 GTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAK----------- 1609 (1764)
Q Consensus 1541 GTNL~EVLS~pgVDptRTySNDI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~R----------- 1609 (1764)
-+.-++.|+.+.|++ ++|++++||||+|++|++|+++||+.||++||+||+++|+++||++
T Consensus 977 ~v~~G~~l~~g~~~~--------~~il~v~G~~~~~~~lv~eiq~vY~~QGv~I~dKHievIvrqM~~kv~i~~~gdt~~ 1048 (1156)
T PRK00566 977 HVEAGDKLTDGSIDP--------HDILRVLGVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDF 1048 (1156)
T ss_pred EEccCCcccCCCCCH--------HHHHHhcCHHHHHHHHHHHHHHHHHhCCcccccceeehHHHHHhCCeEEecCCCcCC
Confidence 345677888888877 5999999999999999999999999999999999999999999986
Q ss_pred -----------------------------CeecccccccccccCCChhhhhhhHHHHHHHHHHhhcCCCCCCCccccCee
Q psy6965 1610 -----------------------------GHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENII 1660 (1764)
Q Consensus 1610 -----------------------------G~LmgITRHGINR~dTSPLmRASFEETVEILtEAAIfGEvD~LRGVSENII 1660 (1764)
+.++||||+++++ .|+|++||||||+++|++||+.|++|+|+|++||||
T Consensus 1049 ~~g~~v~~~~~~~~n~~~~~~g~~~~~~~~~llGItka~l~t--~SflsaASFQeTtkvLt~AAi~gk~D~L~GlkENVI 1126 (1156)
T PRK00566 1049 LPGELVDRSEFEEENRKLIAEGKEPATGRPVLLGITKASLAT--ESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVI 1126 (1156)
T ss_pred CCCceeeHHHHHHHHHHHHHCCCCCCcccceeeeeeeccccc--CcccccccccchHHHHHHHHhcCCCCcCCCcccceE
Confidence 2478999999975 699999999999999999999999999999999999
Q ss_pred ccCCCCCCcceeE
Q psy6965 1661 MGQLPRMGTGCFD 1673 (1764)
Q Consensus 1661 LGQLIPVGTGsFD 1673 (1764)
+|+++|+|||...
T Consensus 1127 iG~liPaGTG~~~ 1139 (1156)
T PRK00566 1127 IGRLIPAGTGLAR 1139 (1156)
T ss_pred ecCcccCCCCcch
Confidence 9999999999864
No 17
>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=99.91 E-value=1.8e-24 Score=265.46 Aligned_cols=125 Identities=29% Similarity=0.485 Sum_probs=108.0
Q ss_pred ccchhhhccCCCcccccccccCHHHHHHH----------------hcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHH
Q psy6965 1541 GTSLMKVLSERDVDPVRTFSNDICEIFQV----------------LGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCD 1604 (1764)
Q Consensus 1541 GTNL~EVLS~pgVDptRTySNDI~EILeV----------------LGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLAD 1604 (1764)
-++.++.|+.+.++| ++++.+ +|+||+|.+|++|+++||++||++||+|||++||+
T Consensus 1047 ~v~~g~~lt~g~~~p--------h~iL~~~f~~~~~~~g~~~aa~~~~~~~~~~lv~evq~Vy~~QGv~I~dkHieiIvr 1118 (1331)
T PRK02597 1047 QVDAGEPLTDGPINP--------HELLEIFFEDLRDRKGLYEAALEALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVR 1118 (1331)
T ss_pred EeecCccccCCCCCH--------HHHHhhhhhhhcccchhhHHHHHhHHHHHHHHHHHHHHHHHhcCeEechhhHHhHHH
Confidence 345667777777776 477777 89999999999999999999999999999999999
Q ss_pred HHhccCee-------------------------ccccc----------ccccccC---CChhhhhhhHHHHHHHHHHhhc
Q psy6965 1605 VMTAKGHL-------------------------MAITR----------HGINRQD---TGALMRCSFEETVDVLMDAAAH 1646 (1764)
Q Consensus 1605 vMT~RG~L-------------------------mgITR----------HGINR~d---TSPLmRASFEETVEILtEAAIf 1646 (1764)
+||+++.+ ++++| +||++.. .|+|++||||||+++|++||++
T Consensus 1119 qMt~kV~i~d~Gdt~~lpGeli~~~~~~~~N~~~~~~~~~~a~y~pvLlGItkasl~T~sfis~aSFqeT~rvL~~AAi~ 1198 (1331)
T PRK02597 1119 QMTSKVRIDDGGDTTMLPGELIELRQVEQVNEAMAITGGAPAEYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIE 1198 (1331)
T ss_pred HHhCcEEEeeCCCcccCCcceeeHHHHHHHHHHHHhcCCCcceeeeeeeeeeeeccccCChhhhccHHHHHHHHHHHHHc
Confidence 99999444 34444 5555532 4999999999999999999999
Q ss_pred CCCCCCCccccCeeccCCCCCCcceeE
Q psy6965 1647 AEADPMRGVSENIIMGQLPRMGTGCFD 1673 (1764)
Q Consensus 1647 GEvD~LRGVSENIILGQLIPVGTGsFD 1673 (1764)
|+.|+|+|++||||+|+++|+|||.+-
T Consensus 1199 g~~D~l~GlkENVI~G~liP~GTG~~~ 1225 (1331)
T PRK02597 1199 GKSDWLRGLKENVIIGRLIPAGTGFSG 1225 (1331)
T ss_pred CCCcccCCchhheeecCccccCcCchh
Confidence 999999999999999999999999973
No 18
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form. Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain.
Probab=99.91 E-value=1.2e-24 Score=264.84 Aligned_cols=124 Identities=34% Similarity=0.531 Sum_probs=113.4
Q ss_pred eeccchhhhccCCCcccccccccCHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhccCe-------
Q psy6965 1539 TDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGH------- 1611 (1764)
Q Consensus 1539 TDGTNL~EVLS~pgVDptRTySNDI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~RG~------- 1611 (1764)
.+-+..++.|+.+.+|| ++|++++||||+|++|++|+++||+.||++||+||+++|+++||++++
T Consensus 973 gd~V~~G~~l~~g~~~~--------~~il~v~G~~a~~~~lv~evq~vY~~QGv~I~dKHievIvrqM~~kv~i~~~gdt 1044 (1140)
T TIGR02386 973 GDSVSAGDKLTEGSIDP--------HDLLRIKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDS 1044 (1140)
T ss_pred CCEEccCCcccCCCCCH--------HHHHHhcCHHHHHHHHHHHHHHHHHhCCccccchhHhHHHHHHhCcEEEEeCCCc
Confidence 33445678888888887 599999999999999999999999999999999999999999999942
Q ss_pred ---------------------------------ecccccccccccCCChhhhhhhHHHHHHHHHHhhcCCCCCCCccccC
Q psy6965 1612 ---------------------------------LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSEN 1658 (1764)
Q Consensus 1612 ---------------------------------LmgITRHGINR~dTSPLmRASFEETVEILtEAAIfGEvD~LRGVSEN 1658 (1764)
++||||++++. .|+|++||||||+++|++||+.|++|+|+|++||
T Consensus 1045 ~~l~g~~v~~~~~~~~n~~~~~~g~~~~~~~~~llGitkasl~t--~SflsaASFqeTtkvLt~Aai~gk~D~L~GlkEN 1122 (1140)
T TIGR02386 1045 NLLPGELIDIHEFNEENRKLLEQGKKPASAIPQLLGITKASLNT--ESFLSAASFQETTKVLTDAAIKGKVDYLLGLKEN 1122 (1140)
T ss_pred CCCCCCeeeHHHHHHHHHHHHhCCCCCccceeeeeeeeehhccC--CCcccccchhhHHHHHHHHHhcCCCCCCCCcccc
Confidence 56799999964 6999999999999999999999999999999999
Q ss_pred eeccCCCCCCccee
Q psy6965 1659 IIMGQLPRMGTGCF 1672 (1764)
Q Consensus 1659 IILGQLIPVGTGsF 1672 (1764)
||+|+++|+|||..
T Consensus 1123 VIiG~liPaGTG~~ 1136 (1140)
T TIGR02386 1123 VIIGNLIPAGTGLK 1136 (1140)
T ss_pred eEecCcccCCCCcc
Confidence 99999999999963
No 19
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=99.90 E-value=4.4e-24 Score=270.45 Aligned_cols=123 Identities=33% Similarity=0.534 Sum_probs=112.5
Q ss_pred eeccchhhhccCCCcccccccccCHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhcc---------
Q psy6965 1539 TDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAK--------- 1609 (1764)
Q Consensus 1539 TDGTNL~EVLS~pgVDptRTySNDI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~R--------- 1609 (1764)
.+-+..++.|+.+.++| ++|++++||||+|++|++|+++||+.||++||+||+++|+++||++
T Consensus 2622 gd~V~~G~~l~~G~~~p--------~dil~v~G~ea~~~ylv~Evq~VYr~QGV~IndKHiEvIvrQMl~kV~I~d~Gdt 2693 (2836)
T PRK14844 2622 GDFVRKGDLLMDGDPDL--------HDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDT 2693 (2836)
T ss_pred CCEEcCCCCccCCCCCH--------HHHHHhhCHHHHHHHHHHHHHHHHHhcCeeecccEeeeehhhhhceeEEecCCCc
Confidence 33345677888887777 5999999999999999999999999999999999999999999987
Q ss_pred ----C-------------------e--------ecccccccccccCCChhhhhhhHHHHHHHHHHhhcCCCCCCCccccC
Q psy6965 1610 ----G-------------------H--------LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSEN 1658 (1764)
Q Consensus 1610 ----G-------------------~--------LmgITRHGINR~dTSPLmRASFEETVEILtEAAIfGEvD~LRGVSEN 1658 (1764)
| . ++||||++++. .|+|++|||+||+++|++||+.|++|+|+|++||
T Consensus 2694 ~~l~Ge~v~~~~~~~~n~~~~~~g~~pa~~~pvllGITkasL~t--~SflSaASFQeTtkVLt~AAi~Gk~D~L~GlKEN 2771 (2836)
T PRK14844 2694 MYLVGESIDKLEVDRENDAMSNSGKRPAHYLPILQGITRASLET--SSFISAASFQETTKVLTEAAFCGKSDPLSGLKEN 2771 (2836)
T ss_pred ccCCCceecHHHHHHHHHHHHhcCCCCceeeeeeeceeeccccC--CChhhcCCcccchHHHHHHHhcCCCCcCCCcccc
Confidence 2 2 78999999965 6999999999999999999999999999999999
Q ss_pred eeccCCCCCCcce
Q psy6965 1659 IIMGQLPRMGTGC 1671 (1764)
Q Consensus 1659 IILGQLIPVGTGs 1671 (1764)
||+|+++|+|||.
T Consensus 2772 VIiG~lIPaGTG~ 2784 (2836)
T PRK14844 2772 VIVGRLIPAGTGL 2784 (2836)
T ss_pred eEecCcccCCcCc
Confidence 9999999999994
No 20
>TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit. The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria.
Probab=99.89 E-value=1.2e-23 Score=256.65 Aligned_cols=125 Identities=30% Similarity=0.500 Sum_probs=112.8
Q ss_pred EeeccchhhhccCCCcccccccccCHHHHHHH----------------hcHHHHHHHHHHHHHHhhccCCcccchhhHHH
Q psy6965 1538 ETDGTSLMKVLSERDVDPVRTFSNDICEIFQV----------------LGIEAVRKSVEKEMNTVLQFYGLYVNYRHLAL 1601 (1764)
Q Consensus 1538 ETDGTNL~EVLS~pgVDptRTySNDI~EILeV----------------LGIEAARkAIInEIrnVFSfYGIYVNyRHLSL 1601 (1764)
+.+.+++++.++.+.++|+ +++.+ +|+||+|.+|++|+++||+.||++|++|||+|
T Consensus 1043 ~g~~v~~g~~l~dg~~~ph--------~iL~~~~~~~~~~~g~~~aa~~s~~~~q~~lv~eiq~vy~~QGv~I~~kHiei 1114 (1227)
T TIGR02388 1043 DGQQVTGGEPLTDGPINPH--------DILDVFFSYYKDQDGLYEAAQESLQKVQRFLVNEVQNVYQSQGVDISDKHIEV 1114 (1227)
T ss_pred cCcEEecCccccCCCCCHH--------HHHhhhhhhhcccchhHHHHHHHHHHHHHHHHHHHHHHHHhcceEeehhhHHH
Confidence 4455677888888888885 66666 49999999999999999999999999999999
Q ss_pred HHHHHhcc-------------Ce---------------------------ecccccccccccCCChhhhhhhHHHHHHHH
Q psy6965 1602 LCDVMTAK-------------GH---------------------------LMAITRHGINRQDTGALMRCSFEETVDVLM 1641 (1764)
Q Consensus 1602 LADvMT~R-------------G~---------------------------LmgITRHGINR~dTSPLmRASFEETVEILt 1641 (1764)
||++||++ |+ |.||||+++|. .|+|++||||||+++|+
T Consensus 1115 IvrqMtskV~i~~~G~t~~lpGeli~~~~~~~~n~~l~~~~~~~~~y~pvLlGITkasL~t--~Sfis~ASFqeTtrvL~ 1192 (1227)
T TIGR02388 1115 IVRQMTSKVRIDDAGDTTLLPGELVELRQVEQVNEAMAITGGAPAQYTPVLLGITKASLNT--DSFISAASFQETTRVLT 1192 (1227)
T ss_pred HHHHHhceEEEeeCCCcccCCcceeeHHHHHHHHHHHHhcCCCccccceeEeeeeeccccc--cchhhhccHHHHHHHHH
Confidence 99999999 65 68888888875 69999999999999999
Q ss_pred HHhhcCCCCCCCccccCeeccCCCCCCccee
Q psy6965 1642 DAAAHAEADPMRGVSENIIMGQLPRMGTGCF 1672 (1764)
Q Consensus 1642 EAAIfGEvD~LRGVSENIILGQLIPVGTGsF 1672 (1764)
+||+.|+.|+|+|++||||+|+++|+|||..
T Consensus 1193 ~Aai~g~~D~l~glkENvI~G~liP~GTG~~ 1223 (1227)
T TIGR02388 1193 EAAIEGKSDWLRGLKENVIIGRLIPAGTGFS 1223 (1227)
T ss_pred HHHHcCCcccccCchhheeecCccccCCCcc
Confidence 9999999999999999999999999999973
No 21
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed
Probab=99.88 E-value=3.7e-23 Score=255.43 Aligned_cols=134 Identities=28% Similarity=0.390 Sum_probs=109.8
Q ss_pred ccchhhhccCCCcccccccccCH-HHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhcc----------
Q psy6965 1541 GTSLMKVLSERDVDPVRTFSNDI-CEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAK---------- 1609 (1764)
Q Consensus 1541 GTNL~EVLS~pgVDptRTySNDI-~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~R---------- 1609 (1764)
++||.+-+..-..+++|++-+=- +-+---+.|||+|.+|++|+++||+.||+.|++|||++||++||++
T Consensus 1151 s~nle~~~~~wn~~i~~iLg~~wg~~~aA~lS~~~~~~~lv~eiq~vy~~qGv~i~~kHieiivrqmt~kv~i~~~g~~~ 1230 (1364)
T CHL00117 1151 SMNLEKRLEGWNERITRILGIPWGFLIGAELSIAQSQISLVNKIQKVYRSQGVQISDKHIEIIVRQMTSKVLVSEDGMSN 1230 (1364)
T ss_pred ecchhhcccccccChhhhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcEeehhhhhhhHHHhhCeEEEeecCccC
Confidence 34444444433334443333211 1134556799999999999999999999999999999999999996
Q ss_pred ----Ce-----------------------ecccccccccccCCChhhhhhhHHHHHHHHHHhhcCCCCCCCccccCeecc
Q psy6965 1610 ----GH-----------------------LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMG 1662 (1764)
Q Consensus 1610 ----G~-----------------------LmgITRHGINR~dTSPLmRASFEETVEILtEAAIfGEvD~LRGVSENIILG 1662 (1764)
|+ |+||||+++|+ .|+|++||||||+++|++||++|++|+|+|++||||+|
T Consensus 1231 v~~pge~i~~~~~~~~~~~~~~~~~~~~~llGitkasl~t--~Sfis~aSFqeT~rvL~~aai~g~~D~l~glkenvi~g 1308 (1364)
T CHL00117 1231 VFLPGELIGLLRAERINRALEEAICYRPILLGITKASLNT--QSFISEASFQETTRVLAKAALRGRIDWLKGLKENVILG 1308 (1364)
T ss_pred ccCCcceeeHHHHHHHhHHhhcCcceeeeeeeeeehhccc--cchhhhcchHHHHHHHHHHHHcCCcccccCchhheeec
Confidence 55 67999999986 69999999999999999999999999999999999999
Q ss_pred CCCCCCcceeEeec
Q psy6965 1663 QLPRMGTGCFDLLL 1676 (1764)
Q Consensus 1663 QLIPVGTGsFDLLL 1676 (1764)
+++|+|||...+..
T Consensus 1309 ~~ip~GTG~~~~~~ 1322 (1364)
T CHL00117 1309 GLIPAGTGFKGLVH 1322 (1364)
T ss_pred CcccCCCCchhhhh
Confidence 99999999976653
No 22
>PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to form the central cleft or channel where the DNA is bound [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....
Probab=99.87 E-value=9.6e-23 Score=207.08 Aligned_cols=99 Identities=43% Similarity=0.697 Sum_probs=91.3
Q ss_pred ccceEEEEeeccchhhhccCCC-cccccccccCHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhcc
Q psy6965 1531 AIADWLLETDGTSLMKVLSERD-VDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAK 1609 (1764)
Q Consensus 1531 ak~EWVLETDGTNL~EVLS~pg-VDptRTySNDI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~R 1609 (1764)
...+|++.|.|+|+..||..++ +|++|++||+|++++++|||||||++|++|++.|+..||++||+|||.|+||+||++
T Consensus 177 ~~~~~~l~~~g~~l~~v~~~qgvid~~k~~sn~I~qm~~~~GIeaar~~i~~e~~~v~~~~g~~vn~rhl~llad~mt~~ 256 (277)
T PF04998_consen 177 KSKEYVLQTEGSNLQEVYSSQGVIDNDKHISNDIRQMLSKLGIEAARNSIIKELKNVFESYGIEVNKRHLSLLADYMTYK 256 (277)
T ss_dssp CCCCCEEECCSHHHHHHTCSTT-EETCHHECSHHHHHHHHHEHHHHHHHHHHHHHCHHHHCTSCCCHHHHHHHHHHHCCC
T ss_pred hhHHHHHHHHhhhchhheecccccCCCEEEeceeEeeeeeEEEEECCCceeecCcEeeHHHHHHHHHHHHHhCCCcCeee
Confidence 3468999999999999999999 899999999999999999999999999999999999999999999999999999999
Q ss_pred CeecccccccccccCCChhh
Q psy6965 1610 GHLMAITRHGINRQDTGALM 1629 (1764)
Q Consensus 1610 G~LmgITRHGINR~dTSPLm 1629 (1764)
|.++|||||||++.++|.|+
T Consensus 257 g~~~gitR~gl~~~~~S~~~ 276 (277)
T PF04998_consen 257 GVLLGITRHGLNSNKSSFLS 276 (277)
T ss_dssp SS---CCTTTTSSSSSSHHH
T ss_pred eEEEEEEHHHhccCCCCccC
Confidence 99999999999987667654
No 23
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=99.86 E-value=2.7e-22 Score=246.38 Aligned_cols=128 Identities=23% Similarity=0.368 Sum_probs=117.2
Q ss_pred EEEEeeccchhhhccCCCcccccccccCHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhcc-----
Q psy6965 1535 WLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAK----- 1609 (1764)
Q Consensus 1535 WVLETDGTNL~EVLS~pgVDptRTySNDI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~R----- 1609 (1764)
||-+.+-+.-++.|+.+.|+| ++|+++.|++|+.++|++|+++||+.||++||.+|+++|+.+||++
T Consensus 1070 ~v~~gd~v~~G~~l~~G~~~p--------~~il~~~g~~~~~~ylv~eVQ~VYr~QGV~InDKHiEvIvRQMl~kV~I~d 1141 (1460)
T PRK14906 1070 GVEDGVEVRVGQQITRGSVNP--------HDLLRLTDPNTTLRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTN 1141 (1460)
T ss_pred ccCCCCEEccCCCccCCCCCH--------HHHHHhcCHHHHHHHHHHHHHHHHHhcCceeccccHHHHHHHHhceEEEec
Confidence 344445566788889988988 5999999999999999999999999999999999999999999987
Q ss_pred -----------------------------------CeecccccccccccCCChhhhhhhHHHHHHHHHHhhcCCCCCCCc
Q psy6965 1610 -----------------------------------GHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRG 1654 (1764)
Q Consensus 1610 -----------------------------------G~LmgITRHGINR~dTSPLmRASFEETVEILtEAAIfGEvD~LRG 1654 (1764)
..++|||+.+++. .|+|+.|||+||+++|++||+.|++|+|+|
T Consensus 1142 ~Gdt~fl~Ge~vd~~~~~~~n~~~~~~g~~pa~~~p~llGITKasL~t--~SflSaASFQeTtrVLt~AAi~gk~D~L~G 1219 (1460)
T PRK14906 1142 PGDSDYLPGRQVNRYEFEDTANNLILEGKQPPVGQPLLLGITKASLAT--DSWLSAASFQETTKVLTDAAIEGKVDHLAG 1219 (1460)
T ss_pred CCCcCCCCCCeeeHHHHHHHHHHHHHcCCCCceeeeEEeeeeeccccc--ccccccccccchHHHHHHHHhcCCCCcCCC
Confidence 2499999999975 699999999999999999999999999999
Q ss_pred cccCeeccCCCCCCccee
Q psy6965 1655 VSENIIMGQLPRMGTGCF 1672 (1764)
Q Consensus 1655 VSENIILGQLIPVGTGsF 1672 (1764)
++||||+|+++|+|||..
T Consensus 1220 LKENVIiG~lIPAGTG~~ 1237 (1460)
T PRK14906 1220 LKENVIIGKPIPAGTGLS 1237 (1460)
T ss_pred CccceEecceecCCCCcc
Confidence 999999999999999963
No 24
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=99.83 E-value=5.2e-21 Score=243.62 Aligned_cols=123 Identities=23% Similarity=0.398 Sum_probs=114.4
Q ss_pred eeccchhhhccCCCcccccccccCHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhcc---------
Q psy6965 1539 TDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAK--------- 1609 (1764)
Q Consensus 1539 TDGTNL~EVLS~pgVDptRTySNDI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~R--------- 1609 (1764)
.+-+.-++.|+.+.|+| ++|++++|++|+..+|++|+|+||+.||++||.+|+++|+.+|+++
T Consensus 2711 gd~v~~G~~l~~G~~~p--------~dil~~~g~~~~~~ylv~EVQ~VYr~QGV~InDKHIEvIvrQMl~kV~I~d~GDt 2782 (2890)
T PRK09603 2711 DEFVHAGEAMTDGVVSS--------HDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDS 2782 (2890)
T ss_pred CCEEccCCCcCCCCCCH--------HHHHHhcCHHHHHHHHHHHHHHHHHhcCEEeccceehhhHhhhheeEEEEcCCCc
Confidence 33445678888888988 5999999999999999999999999999999999999999999987
Q ss_pred -------------------------------CeecccccccccccCCChhhhhhhHHHHHHHHHHhhcCCCCCCCccccC
Q psy6965 1610 -------------------------------GHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSEN 1658 (1764)
Q Consensus 1610 -------------------------------G~LmgITRHGINR~dTSPLmRASFEETVEILtEAAIfGEvD~LRGVSEN 1658 (1764)
..|+|||+..++. .|+|+.|||+||+++|++||+.|++|+|.|++||
T Consensus 2783 ~fl~Ge~vd~~~~~~~n~~~~~~g~~pa~~~p~LlGITKAsL~t--~SfiSAASFQETTkVLteAAi~gk~D~L~glKEN 2860 (2890)
T PRK09603 2783 KFIEGDLVSKKLFKEENARVIALKGEPAIAEPVLLGITRAAIGS--DSIISAASFQETTKVLTEASIAMKKDFLEDLKEN 2860 (2890)
T ss_pred ccCCCceeeHHHHHHHHHHHHHcCCCCceeeeeeeeeehhhhcc--cchhhcccccchhHHHHHHHhcCCCCccCCcccc
Confidence 2499999999975 6999999999999999999999999999999999
Q ss_pred eeccCCCCCCcce
Q psy6965 1659 IIMGQLPRMGTGC 1671 (1764)
Q Consensus 1659 IILGQLIPVGTGs 1671 (1764)
||+|+++|+|||.
T Consensus 2861 Vi~G~liPaGTG~ 2873 (2890)
T PRK09603 2861 VVLGRMIPVGTGM 2873 (2890)
T ss_pred eEeeccccccCCc
Confidence 9999999999996
No 25
>PF04990 RNA_pol_Rpb1_7: RNA polymerase Rpb1, domain 7; InterPro: IPR007073 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 7, represents a mobile module of the RNA polymerase. Domain 7 interacts with the lobe domain of Rpb2 (IPR007642 from INTERPRO) [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_M 1Y77_A 3CQZ_A 3GTM_A 1TWA_A 4A3I_A 2NVY_A 2NVT_A 1I6H_A 1TWF_A ....
Probab=99.76 E-value=1.2e-19 Score=179.76 Aligned_cols=99 Identities=32% Similarity=0.553 Sum_probs=75.1
Q ss_pred CCCChhHHhhccCcchhhhHhhhccccchhhHHHH-HHhcCCCCccchHHHHhc-cCCCCcEEEEeccCCccceEEEEEE
Q psy6965 1385 KMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR-IMNSDDSKMQDEEDAVDK-MEDDMFLRCIEANMLSDMTLQFIRI 1462 (1764)
Q Consensus 1385 ~m~DEE~al~k~~~~~~L~~iE~nm~~d~~l~~~R-~MiDkdLtM~~iaekI~~-f~dd~DL~VIfSDDNAEKLVIRIRI 1462 (1764)
++||++.....+|| |++||||| | +|++|+|||++|+++|++ |+++ ++||||++||+++|+|||+
T Consensus 35 e~pd~~~~~~~~sp--WlLRieLd----------r~~m~dk~l~m~~I~~~I~~~f~~~--l~vi~sddNa~~lViRIRi 100 (135)
T PF04990_consen 35 EIPDEDDDPSRLSP--WLLRIELD----------RKKMIDKKLTMEDIAEKIKEEFGND--LHVIYSDDNAEKLVIRIRI 100 (135)
T ss_dssp CTT-SSTT-SSBES--EEEEEEE-----------CCCCCCTT--HHHHCCCHHHCCTTS--EEEEE--TTSSSEEEEEEE
T ss_pred hCCCcccCcccCCC--eEEEEEEc----------HHHHHhcCCCHHHHHHHHHHhcCCC--eEEEecCCCCcccEEEEEE
Confidence 68998888999999 99999999 9 999999999999999999 9988 9999999999999999999
Q ss_pred ecCCCCccchhhhhhhchhhhHHHHHHHHhhccCceec
Q psy6965 1463 MNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 1500 (1764)
Q Consensus 1463 ~~ded~k~eeeee~vD~~EDDvFLRrIEanMLsdItLR 1500 (1764)
.+++..+.+..++ ..+++.|||++|++||++++||
T Consensus 101 ~~~~~~~~~~~d~---~~~dd~~Lr~~e~~lL~~~~Lr 135 (135)
T PF04990_consen 101 IKDEDKKEEDEDE---QEEDDVFLRRLESNLLDDLTLR 135 (135)
T ss_dssp B--S---SSSSS-----S-CHHHHHHHHHHHCCS-ECC
T ss_pred ecCcccccccccc---hhhHHHHHHHHHHHhhhcCcCC
Confidence 9876433322221 2268899999999999999986
No 26
>KOG0260|consensus
Probab=99.69 E-value=1.8e-17 Score=199.42 Aligned_cols=101 Identities=48% Similarity=0.671 Sum_probs=89.1
Q ss_pred ChHHHHHHHhccCCCceEEeccCCccceEEEEEEeecCCCcccchhhhhccchhHHHHHHHHHhhccCcccccccccccc
Q psy6965 1 MEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRIMNSD 80 (1764)
Q Consensus 1 MEdIAEKIKEEFGDDL~VIfSDDNAEKLVIRIRIVndeDdkdDeEEDevDkmEDDvFLRRLESNMLSdLTLRGIP~Ir~d 80 (1764)
|++||.||+.+||+|++|||+||||+|||+|||+.+++ ++|+|||+||++||.+++|+|||.|.+-
T Consensus 1196 m~~ia~~i~~~f~~d~~~i~~ddna~klv~r~ri~~~~--------------e~D~~l~~Ie~~ml~~~~l~G~~~i~kV 1261 (1605)
T KOG0260|consen 1196 MEQIAEKINRGFGSDLACIFSDDNAEKLVLRLRIAKEE--------------EDDVFLKCIEANMLGDMTLRGIPDIFKV 1261 (1605)
T ss_pred HHHHHHHHHhhccCCCceeecccCCcceEEEEEecCcc--------------chhHHHHHHHHhhhhhcccCCccccceE
Confidence 68999999999999999999999999999999999842 4789999999999999999999965421
Q ss_pred cCccccchhhhcccCcceEEecccchhhhccccccEE
Q psy6965 81 DSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR 117 (1764)
Q Consensus 81 ~rk~~~Et~~f~K~~kEWVLdTdGtNL~eVLTlp~V~ 117 (1764)
-- ...++|+|.. .+||+|+|+|+||++||+.|+|-
T Consensus 1262 ~m-~~~~~G~f~~-~~ew~LeTdg~~l~~v~s~~~vD 1296 (1605)
T KOG0260|consen 1262 YM-SPTEDGEFKP-VDEWDLETDGVNLRRVLSEPDVD 1296 (1605)
T ss_pred EE-eecCCCceee-cceeEEecCchhHHhhhccCCCC
Confidence 10 0477888888 99999999999999999999973
No 27
>PF04990 RNA_pol_Rpb1_7: RNA polymerase Rpb1, domain 7; InterPro: IPR007073 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 7, represents a mobile module of the RNA polymerase. Domain 7 interacts with the lobe domain of Rpb2 (IPR007642 from INTERPRO) [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_M 1Y77_A 3CQZ_A 3GTM_A 1TWA_A 4A3I_A 2NVY_A 2NVT_A 1I6H_A 1TWF_A ....
Probab=99.50 E-value=8.4e-15 Score=145.63 Aligned_cols=69 Identities=57% Similarity=0.960 Sum_probs=51.6
Q ss_pred ChHHHHHHHhccCCCceEEeccCCccceEEEEEEeecCCCcccchhhhhccchhHHHHHHHHHhhccCcccc
Q psy6965 1 MEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQ 72 (1764)
Q Consensus 1 MEdIAEKIKEEFGDDL~VIfSDDNAEKLVIRIRIVndeDdkdDeEEDevDkmEDDvFLRRLESNMLSdLTLR 72 (1764)
|++||+||++.||++|+|||||+||++||||||++++++.+.+..++ ..+++.|||++|++||+++|||
T Consensus 67 m~~I~~~I~~~f~~~l~vi~sddNa~~lViRIRi~~~~~~~~~~~d~---~~~dd~~Lr~~e~~lL~~~~Lr 135 (135)
T PF04990_consen 67 MEDIAEKIKEEFGNDLHVIYSDDNAEKLVIRIRIIKDEDKKEEDEDE---QEEDDVFLRRLESNLLDDLTLR 135 (135)
T ss_dssp HHHHCCCHHHCCTTSEEEEE--TTSSSEEEEEEEB--S---SSSSS-----S-CHHHHHHHHHHHCCS-ECC
T ss_pred HHHHHHHHHHhcCCCeEEEecCCCCcccEEEEEEecCcccccccccc---hhhHHHHHHHHHHHhhhcCcCC
Confidence 57899999999999999999999999999999999976433322211 1268899999999999999997
No 28
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=99.29 E-value=7.6e-14 Score=168.00 Aligned_cols=148 Identities=30% Similarity=0.429 Sum_probs=142.5
Q ss_pred ccceEEEEeeccchhhhccCCCcccccccccCHHHHHHHhcHHHHHHHHHHHHHHhhccCCcc-cchhhHHHHHHHHhcc
Q psy6965 1531 AIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLY-VNYRHLALLCDVMTAK 1609 (1764)
Q Consensus 1531 ak~EWVLETDGTNL~EVLS~pgVDptRTySNDI~EILeVLGIEAARkAIInEIrnVFSfYGIY-VNyRHLSLLADvMT~R 1609 (1764)
.+.+|+..|+|.++..++....++++++.+|++.+++.++|+||+|+++.+++..+...+|.. +..+|+.+-++.||..
T Consensus 599 ~~~e~v~~ae~~v~~~i~~~~~g~lt~~~~~~i~e~~e~~~~e~l~~ai~~~~~~~~~~~g~~~~~i~~m~~~Gs~~n~s 678 (808)
T COG0086 599 EKDEIVIEAEGSVLKLILQYEEGDLTRTERNNIVEIIEVLGIEALRNAIIEEIKITLEEQGLDFVDIRHMGLSGARMNIS 678 (808)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcCCccccCCCCeEEEeehHHHHHHHHHHHHHHhhhHHhcCCcchhHHHHhhhhhccCHH
Confidence 346899999999999999999999999999999999999999999999999999999999999 9999999999999999
Q ss_pred CeecccccccccccCCChhhhhhhHHHHHHHHHHhhcCCCCCCCccccCeeccCCCCCCcceeEeecChh
Q psy6965 1610 GHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAE 1679 (1764)
Q Consensus 1610 G~LmgITRHGINR~dTSPLmRASFEETVEILtEAAIfGEvD~LRGVSENIILGQLIPVGTGsFDLLLD~e 1679 (1764)
|....+.|||+.....|++++++||.|+.+ ..|+.+++.+.+.|+++++++|+..++|||..|..+...
T Consensus 679 q~~~~iG~~gv~g~r~~~~~~~~Fe~~~~~-~~a~~~i~s~f~eGLt~~e~f~~~~ggR~GlvDTA~KTa 747 (808)
T COG0086 679 QIVQLIGQQGVMGEKISVLARAAFEVTVKH-LEAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALKTA 747 (808)
T ss_pred HHHHHhhhheeeccCCCccccccccccccc-ceeeeeeecccCCCCCcceEEeecCccccchHHHhhhhc
Confidence 999999999999888999999999999999 999999999999999999999999999999999987643
No 29
>cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain. RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Probab=99.20 E-value=2.2e-11 Score=138.39 Aligned_cols=110 Identities=43% Similarity=0.605 Sum_probs=90.4
Q ss_pred hHHHHHHHhccCCCceEEeccCCccceEEEEEEeecCCCcccchhhhhccchhHHHHHHHHHhhccCccccccc-----c
Q psy6965 2 EAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR-----I 76 (1764)
Q Consensus 2 EdIAEKIKEEFGDDL~VIfSDDNAEKLVIRIRIVndeDdkdDeEEDevDkmEDDvFLRRLESNMLSdLTLRGIP-----~ 76 (1764)
++|+.+|++.|+++++|+++++|++++++|||+........ ...+++.||++++.++|.+++|+||| .
T Consensus 174 ~~i~~~i~~~~~~~~~v~~~~~~~~~~~iri~~~~~~~~~~-------~~~~~~~~l~~~~~~~l~~i~l~Gi~~I~r~~ 246 (410)
T cd02584 174 EQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKE-------EDSEDDVFLKKIESNMLSDMTLKGIEGIRKVF 246 (410)
T ss_pred HHHHHHHHHhcCCCeEEEEcCCCcceeEEEEEecCcccccc-------ccchhHHHHHHHHHhhCCCcEEeCCCCceEEE
Confidence 56899999999999999999999999999999986432111 01246789999999999999999999 4
Q ss_pred cccccCccc-cchhhhcccCcceEEecccchhhhccccccEEEe
Q psy6965 77 MNSDDSKMQ-DEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRIM 119 (1764)
Q Consensus 77 Ir~d~rk~~-~Et~~f~K~~kEWVLdTdGtNL~eVLTlp~V~~~ 119 (1764)
|+++..+.+ ++.|.|.+ .++|+|.|+|+||.+||++|||-.-
T Consensus 247 i~~~~~~~~~~~~g~~~~-~~~~~l~teG~nl~~v~~~~~Vd~~ 289 (410)
T cd02584 247 IREENKKKVDIETGEFKK-REEWVLETDGVNLREVLSHPGVDPT 289 (410)
T ss_pred EEcCCceEecCCCCcccC-CcceEEEecCcCHHHHhCCCCCccc
Confidence 555555444 77888888 7899999999999999999998443
No 30
>cd02737 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain. Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.
Probab=98.00 E-value=5.4e-06 Score=94.67 Aligned_cols=91 Identities=12% Similarity=-0.014 Sum_probs=65.9
Q ss_pred ccCCCceEEeccCCccceEEEEEEeecCCCcccchhhhhccchhHHHHHHHHHhhccCccccccc-----ccc--cccCc
Q psy6965 11 GFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR-----IMN--SDDSK 83 (1764)
Q Consensus 11 EFGDDL~VIfSDDNAEKLVIRIRIVndeDdkdDeEEDevDkmEDDvFLRRLESNMLSdLTLRGIP-----~Ir--~d~rk 83 (1764)
.|++++.||++++|.+ .+. . ...+.++||++++.+||+ ++|||+| +|+ +..+.
T Consensus 147 ~~~~~~~ci~~~~~~~-----------~~~-~-------~~~~~~~~~~~i~~~lL~-~~lkG~~~I~kv~i~~~~~~~~ 206 (381)
T cd02737 147 QKLSDGPCLTFSVSKE-----------VSK-S-------SEELLDVLRDRIIPFLLE-TVIKGDERIKSVNILWEDSPST 206 (381)
T ss_pred hcCCCCceEEeecCcc-----------ccc-c-------hhHHHHHHHHHHHHHHhh-eeecccCCeeEEEEEecCCCcc
Confidence 4667788887777611 011 1 012467899999999996 9999999 666 44444
Q ss_pred cccchhhhcccCcceEEecc---------cchhhhcc-----ccccEEEecCC
Q psy6965 84 MQDEEDAVDKMEDDMFLRCI---------EANMLSDM-----TLQFIRIMNSD 122 (1764)
Q Consensus 84 ~~~Et~~f~K~~kEWVLdTd---------GtNL~eVL-----Tlp~V~~~~~~ 122 (1764)
...+.++|.+ ..||||||+ |+||..|| .+|+|-.-++-
T Consensus 207 ~~~~~~~~~~-~~E~vLe~~~~~~~~~t~G~~~~~vl~~c~~~~~~ID~~rt~ 258 (381)
T cd02737 207 SWVKSVGKSS-RGELVLEVTVEESCKKTRGNAWNVVMDACIPVMDLIDWERSM 258 (381)
T ss_pred cccccccccc-cceEEEEEEeccccccccchhHHHHHHhhhcccccCcCCCcE
Confidence 5555566777 899999988 99999999 68888654443
No 31
>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=97.61 E-value=7.4e-05 Score=85.30 Aligned_cols=88 Identities=10% Similarity=0.119 Sum_probs=67.1
Q ss_pred ChHHHHHHHhccCCCceEEeccCCccceEEEEEEeecCCCcccchhhhhccchhHHHHHHHHHhhccCcccccccccccc
Q psy6965 1 MEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRIMNSD 80 (1764)
Q Consensus 1 MEdIAEKIKEEFGDDL~VIfSDDNAEKLVIRIRIVndeDdkdDeEEDevDkmEDDvFLRRLESNMLSdLTLRGIP~Ir~d 80 (1764)
+++|.++|++.++..++++ +++++++|||+.+. ....|++++..++ ++.|+|||-|...
T Consensus 158 ~~~i~~~i~~~~~~~~~~~----~~~~~~i~i~~~~~----------------~~~~l~~l~~~l~-~~~v~Gi~gI~r~ 216 (367)
T TIGR02389 158 VDDVEKAIKKAKLGKVIEI----DMDGNTITIKPPKP----------------SLKELRKLKEKIK-NLHIKGIKGIKRV 216 (367)
T ss_pred HHHHHHHHHHhccccccee----ecCCCEEEEEecCc----------------hHHHHHHHHHHhh-hceEeCCCCceEE
Confidence 3578999999998877766 34678999997431 1235999998766 8999999977654
Q ss_pred cCccccchhhhcccCcceEEecccchhhhccccccEEE
Q psy6965 81 DSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRI 118 (1764)
Q Consensus 81 ~rk~~~Et~~f~K~~kEWVLdTdGtNL~eVLTlp~V~~ 118 (1764)
.-. + + .++|+|.|+|+||.+||.+|+|-.
T Consensus 217 ~i~---~-----~-~~~~~l~teG~nl~~v~~~~~VD~ 245 (367)
T TIGR02389 217 VIR---K-----E-GDEYVIYTEGSNLKEVLKLEGVDK 245 (367)
T ss_pred EEE---C-----C-CCeEEEEEeccCHHHHHcCCCCcc
Confidence 221 1 1 368999999999999999999843
No 32
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated
Probab=97.18 E-value=0.00048 Score=79.17 Aligned_cols=88 Identities=11% Similarity=0.197 Sum_probs=65.8
Q ss_pred ChHHHHHHHhccCCCceEEeccCCccceEEEEEEeecCCCcccchhhhhccchhHHHHHHHHHhhccCcccccccccccc
Q psy6965 1 MEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRIMNSD 80 (1764)
Q Consensus 1 MEdIAEKIKEEFGDDL~VIfSDDNAEKLVIRIRIVndeDdkdDeEEDevDkmEDDvFLRRLESNMLSdLTLRGIP~Ir~d 80 (1764)
++.|+++|+..|+.++++. ..++++|+| . .+..+|+++...++ ++.++|||.|...
T Consensus 173 ~~~I~~~i~~~~~~~~~~~-----~~~i~i~~~--~----------------~~~~~l~~l~~~l~-~~~vkGi~gI~r~ 228 (383)
T PRK04309 173 VDDVKEAIEKKKGGEVEIE-----GNTLIISPK--E----------------PSYRELRKLAEKIR-NIKIKGIKGIKRV 228 (383)
T ss_pred HHHHHHHHHHhcCcceecc-----CCeEEEEec--C----------------chHHHHHHHHHHhc-ccEEECCCCceEE
Confidence 3579999999999877553 466777776 1 02358999998766 8999999977663
Q ss_pred cCccccchhhhcccCcceEEecccchhhhccccccEEEecC
Q psy6965 81 DSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRIMNS 121 (1764)
Q Consensus 81 ~rk~~~Et~~f~K~~kEWVLdTdGtNL~eVLTlp~V~~~~~ 121 (1764)
.-. .+ .++|+|.|+|+||.+||.+|+|-.-..
T Consensus 229 ~i~---~~------~~~~~l~teG~nl~~v~~~~~VD~~rt 260 (383)
T PRK04309 229 IIR---KE------GDEYVIYTEGSNLKEVLKVEGVDATRT 260 (383)
T ss_pred EEe---cC------CCeEEEEEcccCHHHHhcCCCEeeccc
Confidence 322 11 258999999999999999999965433
No 33
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=96.76 E-value=0.0022 Score=82.66 Aligned_cols=97 Identities=12% Similarity=0.142 Sum_probs=65.6
Q ss_pred hHHHHHHHhccCCCceEEeccCCccceEEEEEEeecCCCcccchhhhhccchhHHHHHHHHHhhccCccccccccccccc
Q psy6965 2 EAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRIMNSDD 81 (1764)
Q Consensus 2 EdIAEKIKEEFGDDL~VIfSDDNAEKLVIRIRIVndeDdkdDeEEDevDkmEDDvFLRRLESNMLSdLTLRGIP~Ir~d~ 81 (1764)
+.|++.|.+.++.....+..++| .+++++.... . . ...-.+|++|+..+| +++|+|||.|....
T Consensus 1093 ~~i~~~i~~~~~~~~~~~~~~~~----~i~~~~~~~~---~--~------~~~~~~l~~l~~~l~-~~~i~Gi~~I~r~~ 1156 (1321)
T PRK14977 1093 ERFAEIEAALAKGKKFEMELEDD----LIILDLVEAA---D--R------DKPLATLIAIRNKIL-DKPVKGVPDIERAW 1156 (1321)
T ss_pred HHHHHHHHHhhcCCceEEeecCC----EEEEecCccc---c--c------chHHHHHHHHHHhcC-CcEEecCCCceEEE
Confidence 46788888888777667766655 3444443210 0 0 012368999999988 69999999776643
Q ss_pred CccccchhhhcccCcceEEecccchhhhccccccEEEe
Q psy6965 82 SKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRIM 119 (1764)
Q Consensus 82 rk~~~Et~~f~K~~kEWVLdTdGtNL~eVLTlp~V~~~ 119 (1764)
-.....+ . .++|+|+|+|+||.+||.+|||-.-
T Consensus 1157 i~~~~~~---~--~~e~~l~teG~nl~~vl~~~~Vd~~ 1189 (1321)
T PRK14977 1157 VELVEKD---G--RDEWIIQTSGSNLAAVLEMKCIDIA 1189 (1321)
T ss_pred EEeeccC---C--CeeEEEEecCcCHHHHhCCCCCccc
Confidence 2211111 1 3689999999999999999999543
No 34
>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP). Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Probab=96.76 E-value=0.0014 Score=74.94 Aligned_cols=88 Identities=10% Similarity=0.146 Sum_probs=61.8
Q ss_pred ChHHHHHHHhccCCCceEEeccCCccceEEEEEEeecCCCcccchhhhhccchhHHHHHHHHHhhccCcccccccccccc
Q psy6965 1 MEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRIMNSD 80 (1764)
Q Consensus 1 MEdIAEKIKEEFGDDL~VIfSDDNAEKLVIRIRIVndeDdkdDeEEDevDkmEDDvFLRRLESNMLSdLTLRGIP~Ir~d 80 (1764)
+++|+.+|++.|+.++.+ + +++. +++.... ..+..+|++++..++ ++.|+|||-|...
T Consensus 154 ~~~i~~~i~~~~~~~~~~--~-~~~~-----~~~~~~~-------------~~~~~~l~~l~~~l~-~~~v~Gi~gI~r~ 211 (363)
T cd06528 154 VDDVLKAIEKLKKGKVGE--E-GDVT-----LIVLKAE-------------EPSIKELRKLAEKIL-NTKIKGIKGIKRV 211 (363)
T ss_pred HHHHHHHHHHhcCCcccc--c-CCcc-----EEEEcCC-------------cchHHHHHHHHHhhc-ccEEeCCCCceEE
Confidence 467999999999987754 2 2222 2333211 013479999998766 6999999977764
Q ss_pred cCccccchhhhcccCcceEEecccchhhhccccccEEEe
Q psy6965 81 DSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRIM 119 (1764)
Q Consensus 81 ~rk~~~Et~~f~K~~kEWVLdTdGtNL~eVLTlp~V~~~ 119 (1764)
.-. .+ .++|+|.|+|+||.+||.+|+|-.-
T Consensus 212 ~i~--~~-------~~~~~l~teG~nl~~v~~~~~Vd~~ 241 (363)
T cd06528 212 IVR--KE-------EDEYVIYTEGSNLKAVLKVEGVDPT 241 (363)
T ss_pred EEe--cC-------CceEEEEecCcCHHHHhcCCCCccc
Confidence 321 11 2489999999999999999998543
No 35
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=96.72 E-value=0.002 Score=80.12 Aligned_cols=87 Identities=15% Similarity=0.237 Sum_probs=63.7
Q ss_pred hHHHHHHHhccCCCceEEeccCCccceEEEEEEeecCCCcccchhhhhccchhHHHHHHHHHhhccCccccccccccccc
Q psy6965 2 EAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRIMNSDD 81 (1764)
Q Consensus 2 EdIAEKIKEEFGDDL~VIfSDDNAEKLVIRIRIVndeDdkdDeEEDevDkmEDDvFLRRLESNMLSdLTLRGIP~Ir~d~ 81 (1764)
++|..+|+..|+..+.+ ++.++|+|.... ....+++.++. |.++.|+|||-|....
T Consensus 640 ~~i~~~i~~~~~~~~~~-------~~~~~~~~~~~~---------------~~~~~~~~~~~--l~~~~i~gi~gI~~~~ 695 (858)
T PRK14898 640 ESVEEAIEKKLGVKIDR-------KGTVLYLKPKTP---------------SYKALRKRIPK--IKNIVLKGIPGIERVL 695 (858)
T ss_pred HHHHHHHHHhccccccC-------CCCEEEEEecCc---------------hHHHHHHHHHH--hcCcEEECCCCccEEE
Confidence 57889999998876554 578999997541 13468888773 7799999999766543
Q ss_pred CccccchhhhcccCcceEEecccchhhhccccccEE
Q psy6965 82 SKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR 117 (1764)
Q Consensus 82 rk~~~Et~~f~K~~kEWVLdTdGtNL~eVLTlp~V~ 117 (1764)
-. .++. .. ..+|+|.|+|+||.+||.+|+|-
T Consensus 696 i~-~~~~---~~-~~~~~l~teG~nl~~~~~~~~vd 726 (858)
T PRK14898 696 VK-KEEH---EN-DEEYVLYTQGSNLREVFKIEGVD 726 (858)
T ss_pred Ee-cCCC---CC-CceEEEEecCcCHHHHhcCCCCc
Confidence 21 1111 11 35899999999999999999884
No 36
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=96.71 E-value=0.0028 Score=75.42 Aligned_cols=86 Identities=14% Similarity=0.164 Sum_probs=57.5
Q ss_pred hHHHHHHHhccCCCceEEeccCCccceEEEEEEeecCCCcccchhhhhccchhHHHHHHHHHhhccCccccccccccccc
Q psy6965 2 EAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRIMNSDD 81 (1764)
Q Consensus 2 EdIAEKIKEEFGDDL~VIfSDDNAEKLVIRIRIVndeDdkdDeEEDevDkmEDDvFLRRLESNMLSdLTLRGIP~Ir~d~ 81 (1764)
++|+++|.+.+ +..+.+++| + ||+.... .....|+++... |.+++|+|||.|....
T Consensus 296 ~~I~~~I~~~~---~~~~~~~~~----~--I~i~~~~--------------~~~~~L~~l~~~-l~~i~I~GipgI~r~~ 351 (509)
T PRK14897 296 DDILAAISKLT---FKTVEIDDG----I--IRLKPQQ--------------PSFKKLYLLAEK-VKSLTIKGIKGIKRAI 351 (509)
T ss_pred HHHHHHHHhcc---ceEEecCCC----E--EEEEeCc--------------hHHHHHHHHHHH-hhccEEeCCCCccEEE
Confidence 57888898753 245556665 2 4444421 012478888665 5699999999776532
Q ss_pred CccccchhhhcccCcceEEecccchhhhccccccEEE
Q psy6965 82 SKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRI 118 (1764)
Q Consensus 82 rk~~~Et~~f~K~~kEWVLdTdGtNL~eVLTlp~V~~ 118 (1764)
-. .+. . .++|+|.|+|+||.+||.+|||-.
T Consensus 352 i~--~~~----~-~~~~~L~TeG~NL~~vl~~~~VD~ 381 (509)
T PRK14897 352 AR--KEN----D-ERRWVIYTQGSNLKDVLEIDEVDP 381 (509)
T ss_pred Ee--cCC----C-CceeEEEeeccCHHHHhcCCCccc
Confidence 21 111 1 357999999999999999999844
No 37
>cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain. RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=96.65 E-value=0.0025 Score=71.61 Aligned_cols=88 Identities=11% Similarity=0.101 Sum_probs=62.8
Q ss_pred HHHHHHhccCCCceEEeccCCccceEEEEEEeecCCCcccchhhhhccchhHHHHHHHHHhhccCcccccccccccccCc
Q psy6965 4 ISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRIMNSDDSK 83 (1764)
Q Consensus 4 IAEKIKEEFGDDL~VIfSDDNAEKLVIRIRIVndeDdkdDeEEDevDkmEDDvFLRRLESNMLSdLTLRGIP~Ir~d~rk 83 (1764)
|..+|...|.+.+ +..+.+++|+..+. ...|+.++...+|.++.|+|||-|....-.
T Consensus 103 i~~~~~~~~~~~~--------~~~~~~~i~~~~~~---------------~~~~~~~~~~~~l~~~~i~gi~gI~r~~i~ 159 (309)
T cd02735 103 ILKTIERVFKKLL--------GKWCEVTIKLPLSS---------------PKLLLLSIVEKLARKAVIREIPGITRCFVV 159 (309)
T ss_pred HHHHHHHHhhhhh--------CCEEEEEEEecCCc---------------hhHHHHHHHHHHhcccEEeCCCCccEEEEe
Confidence 5667778887655 56788888875521 236888888999999999999977653221
Q ss_pred cccchhhhcccCcceEEecccchhhhcccc-ccEEEe
Q psy6965 84 MQDEEDAVDKMEDDMFLRCIEANMLSDMTL-QFIRIM 119 (1764)
Q Consensus 84 ~~~Et~~f~K~~kEWVLdTdGtNL~eVLTl-p~V~~~ 119 (1764)
.++ .. + ..+|+|.|+|+||.+++.+ |+|-.-
T Consensus 160 -~~~--~~-~-~~~~~l~teG~nl~~v~~~~~~vd~~ 191 (309)
T cd02735 160 -EED--KG-G-KTKYLVITEGVNLAALWKFSDILDVN 191 (309)
T ss_pred -cCc--CC-C-ceEEEEEeccccHHHHHhccCccccc
Confidence 111 11 1 3579999999999999998 666543
No 38
>cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain. Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=95.71 E-value=0.0086 Score=67.34 Aligned_cols=59 Identities=14% Similarity=0.003 Sum_probs=45.1
Q ss_pred hHHHHHHHHHhhccCcccccccccccccCccccchhhhcccCcceEEecccchhhhccccccEEEe
Q psy6965 54 DDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRIM 119 (1764)
Q Consensus 54 DDvFLRRLESNMLSdLTLRGIP~Ir~d~rk~~~Et~~f~K~~kEWVLdTdGtNL~eVLTlp~V~~~ 119 (1764)
...|+.+...++|.++.++|||.|....-. .++. .++|+|.|+|+||.+|+.+|+|-.-
T Consensus 126 ~~~~~~~~l~~~l~~~~v~Gi~gI~r~~i~-~~~~------~~~~~l~teG~nl~~v~~~~~Vd~~ 184 (300)
T cd02736 126 NLYFLLQSLKRKLPDVVVSGIPEVKRAVIN-KDKK------KGKYKLLVEGYGLRAVMNTPGVIGT 184 (300)
T ss_pred cHHHHHHHHHHHhccceEeCCCCceEEEEe-cCCC------CCcEEEEEecccHHHHhcCCcEecc
Confidence 456888888899999999999966643221 1110 2689999999999999999999543
No 39
>KOG1999|consensus
Probab=52.16 E-value=20 Score=46.75 Aligned_cols=24 Identities=17% Similarity=-0.072 Sum_probs=12.8
Q ss_pred CCC--CCCCCC-----cccccCCCCCccccc
Q psy6965 1720 HNT--SLTNAT-----HQSRDKAFAPSELFL 1743 (1764)
Q Consensus 1720 w~~--~~tp~~-----~~~~~~a~a~s~l~~ 1743 (1764)
|+. +.||++ +-+|.+.+.|||-.+
T Consensus 805 W~~~~~~tPa~~~~~~~~g~~g~~g~sp~~~ 835 (1024)
T KOG1999|consen 805 WNPYNGKTPARNFDNREPGFEGSGGRSPQGY 835 (1024)
T ss_pred cCCCCCCCCccccCCcccCCCCCCCCCCCCC
Confidence 553 356666 234555555677444
No 40
>KOG1999|consensus
Probab=44.12 E-value=43 Score=43.90 Aligned_cols=14 Identities=14% Similarity=0.131 Sum_probs=6.9
Q ss_pred CCccccc--CCCCCcc
Q psy6965 1727 ATHQSRD--KAFAPSE 1740 (1764)
Q Consensus 1727 ~~~~~~~--~a~a~s~ 1740 (1764)
.||++|+ ++.+||+
T Consensus 862 ~~gsa~~~~~~~sps~ 877 (1024)
T KOG1999|consen 862 GNGSAWGPSGQNSPSP 877 (1024)
T ss_pred CCccccccccCCCCCC
Confidence 4555664 3444443
No 41
>COG3688 Predicted RNA-binding protein containing a PIN domain [General function prediction only]
Probab=32.58 E-value=53 Score=36.01 Aligned_cols=48 Identities=19% Similarity=0.438 Sum_probs=36.3
Q ss_pred EEEeeccchhhhccCCCcccccccccCHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhH
Q psy6965 1536 LLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHL 1599 (1764)
Q Consensus 1536 VLETDGTNL~EVLS~pgVDptRTySNDI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHL 1599 (1764)
+|-++|.|.-..|. .+..+.+..|.|+||..||..+.+ |+++.+|+-+
T Consensus 5 iLLVDGYNmIgaWp------------~Lk~lkd~~~LE~AR~~LIe~l~~----Y~s~~g~~ii 52 (173)
T COG3688 5 ILLVDGYNMIGAWP------------ELKQLKDRNGLEAARDKLIEALAE----YQSFTGYKII 52 (173)
T ss_pred EEEeccchhccccH------------HHHHHHhhccHHHHHHHHHHHHHH----hhcccCceEE
Confidence 56679998766654 345788889999999999998865 6777666643
No 42
>PRK13926 ribonuclease HII; Provisional
Probab=27.88 E-value=40 Score=37.11 Aligned_cols=51 Identities=29% Similarity=0.389 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHhhccCCc-----ccchhhHHHHHHHHhccCeecccccccccccCCChhhhhhhHHHHHHHHHHh
Q psy6965 1575 VRKSVEKEMNTVLQFYGL-----YVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAA 1644 (1764)
Q Consensus 1575 ARkAIInEIrnVFSfYGI-----YVNyRHLSLLADvMT~RG~LmgITRHGINR~dTSPLmRASFEETVEILtEAA 1644 (1764)
.|-.++.++...|..||. |-...|+..|. +||+ .|+.|-||+ |++-+..||
T Consensus 151 ~RD~~m~~l~~~~~~yg~~~~kGY~t~~h~~~l~-------------~~G~-----~~~hR~s~~-~~~~~~~~~ 206 (207)
T PRK13926 151 ERDRLMRELDARYPGYGFARHKGYGTPAHREALA-------------ALGP-----SPVHRRSFA-PVRRLLTAA 206 (207)
T ss_pred HHHHHHHHHHHhCccCCCcCCCCCCCHHHHHHHH-------------HhCc-----CHHHcCCcH-HHHHhhhcc
Confidence 499999999999988763 44666766663 4664 778899997 555555554
No 43
>CHL00077 rps18 ribosomal protein S18
Probab=27.14 E-value=42 Score=33.39 Aligned_cols=32 Identities=16% Similarity=0.461 Sum_probs=27.8
Q ss_pred CcccchhhHHHHHHHHhccCeecccccccccc
Q psy6965 1591 GLYVNYRHLALLCDVMTAKGHLMAITRHGINR 1622 (1764)
Q Consensus 1591 GIYVNyRHLSLLADvMT~RG~LmgITRHGINR 1622 (1764)
|..|||+++.||..++|.+|.|.|=...|+..
T Consensus 25 ~~~iDYKnv~lL~~Fis~~GkIlpRriTGl~~ 56 (86)
T CHL00077 25 GDRIDYKNMSLLSRFISEQGKILSRRVTRLTL 56 (86)
T ss_pred CCcCCccCHHHHHHhcCCCCeEcCcccCCcCH
Confidence 55799999999999999999999977777643
No 44
>PF01084 Ribosomal_S18: Ribosomal protein S18; InterPro: IPR001648 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S18 is known to be involved in binding the aminoacyl-tRNA complex in Escherichia coli [], and appears to be situated at the tRNA A-site. Experimental evidence has revealed that S18 is well exposed on the surface of the E. coli ribosome, and is a secondary rRNA binding protein []. S18 belongs to a family of ribosomal proteins [] that includes: eubacterial S18; metazoan mitochondrial S18, algal and plant chloroplast S18; and cyanelle S18.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2UXD_R 3I8G_U 3UZ7_U 1N33_R 2XSY_R 3V24_R 3OGY_R 2XUY_R 2XFZ_R 3UXT_R ....
Probab=24.54 E-value=25 Score=31.86 Aligned_cols=33 Identities=18% Similarity=0.517 Sum_probs=29.3
Q ss_pred CCcccchhhHHHHHHHHhccCeecccccccccc
Q psy6965 1590 YGLYVNYRHLALLCDVMTAKGHLMAITRHGINR 1622 (1764)
Q Consensus 1590 YGIYVNyRHLSLLADvMT~RG~LmgITRHGINR 1622 (1764)
...+|||+...||.-++|..|.+.|=.+.|+..
T Consensus 3 ~~~~idykn~~lL~~Fi~~~GkIl~rr~Tgl~~ 35 (54)
T PF01084_consen 3 NNEYIDYKNVELLSQFISPTGKILPRRITGLCA 35 (54)
T ss_dssp SSSSSSSSSHHHHGCGBTTSSSBSTHHHHTSTH
T ss_pred CCCcCCcCCHHHHHHHcCcccceehhhhccccH
Confidence 457899999999999999999999988888754
No 45
>PRK13401 30S ribosomal protein S18; Provisional
Probab=23.16 E-value=51 Score=32.58 Aligned_cols=34 Identities=24% Similarity=0.490 Sum_probs=28.3
Q ss_pred ccCCc-ccchhhHHHHHHHHhccCeeccccccccc
Q psy6965 1588 QFYGL-YVNYRHLALLCDVMTAKGHLMAITRHGIN 1621 (1764)
Q Consensus 1588 SfYGI-YVNyRHLSLLADvMT~RG~LmgITRHGIN 1621 (1764)
...|+ +|||+.+.||..++|.+|.|.|=-..|+.
T Consensus 19 ~~~~~~~iDYKnv~lL~~Fis~~GkIlpRR~TGl~ 53 (82)
T PRK13401 19 DSLGIESVDYKDTALLRTFISDRGKIRSRRVTGLT 53 (82)
T ss_pred ccCCCCcCCccCHHHHHHhcCCCccCcCcccCCcC
Confidence 34565 58999999999999999999997777764
No 46
>PRK00391 rpsR 30S ribosomal protein S18; Reviewed
Probab=21.29 E-value=66 Score=31.44 Aligned_cols=33 Identities=18% Similarity=0.503 Sum_probs=27.8
Q ss_pred cCCc-ccchhhHHHHHHHHhccCeeccccccccc
Q psy6965 1589 FYGL-YVNYRHLALLCDVMTAKGHLMAITRHGIN 1621 (1764)
Q Consensus 1589 fYGI-YVNyRHLSLLADvMT~RG~LmgITRHGIN 1621 (1764)
..|+ +|||+.+.||..++|-+|.+.|=...|+.
T Consensus 21 ~~~~~~iDYKnv~lL~~Fis~~GkIlprriTG~~ 54 (79)
T PRK00391 21 AEKIEYIDYKDVELLKKFISERGKILPRRITGTS 54 (79)
T ss_pred CCCCCcCCccCHHHHHHhcCCCceEcCcccCCcC
Confidence 3454 79999999999999999999997766764
No 47
>PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to form the central cleft or channel where the DNA is bound [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....
Probab=20.11 E-value=62 Score=34.23 Aligned_cols=33 Identities=12% Similarity=0.011 Sum_probs=25.8
Q ss_pred cchhhhcccCcceEEecccchhhhccccccEEEe
Q psy6965 86 DEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRIM 119 (1764)
Q Consensus 86 ~Et~~f~K~~kEWVLdTdGtNL~eVLTlp~V~~~ 119 (1764)
+......+ ..+|++.|.|.||.+|+.+|+|.+.
T Consensus 170 ~~~~~~~~-~~~~~l~~~g~~l~~v~~~qgvid~ 202 (277)
T PF04998_consen 170 SKDILEKK-SKEYVLQTEGSNLQEVYSSQGVIDN 202 (277)
T ss_dssp HHHHCEEC-CCCCEEECCSHHHHHHTCSTT-EET
T ss_pred eeccccch-hHHHHHHHHhhhchhheecccccCC
Confidence 33444444 8999999999999999999996654
Done!