Query psy1131
Match_columns 353
No_of_seqs 349 out of 1629
Neff 6.0
Searched_HMMs 46136
Date Fri Aug 16 23:38:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1131.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1131hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK14977 bifunctional DNA-dire 100.0 9.1E-62 2E-66 537.5 12.0 215 52-266 309-562 (1321)
2 KOG0262|consensus 100.0 6.7E-62 1.5E-66 515.7 7.1 228 46-273 422-699 (1640)
3 KOG0261|consensus 100.0 5.7E-62 1.2E-66 506.5 2.8 221 47-267 333-589 (1386)
4 TIGR02390 RNA_pol_rpoA1 DNA-di 100.0 1.6E-60 3.5E-65 514.4 11.9 216 51-266 294-541 (868)
5 PRK08566 DNA-directed RNA poly 100.0 6E-60 1.3E-64 511.1 9.5 216 51-266 298-546 (882)
6 KOG0260|consensus 100.0 2.3E-58 5E-63 487.1 10.0 223 39-267 307-564 (1605)
7 smart00663 RPOLA_N RNA polymer 100.0 8.2E-57 1.8E-61 433.0 12.9 176 51-231 90-295 (295)
8 CHL00018 rpoC1 RNA polymerase 100.0 5E-52 1.1E-56 430.1 8.0 178 41-238 348-547 (663)
9 PRK02625 rpoC1 DNA-directed RN 100.0 1.1E-51 2.4E-56 424.2 7.6 218 31-268 317-558 (627)
10 TIGR02387 rpoC1_cyan DNA-direc 100.0 2.1E-51 4.6E-56 421.6 4.3 210 39-268 318-551 (619)
11 PRK00566 DNA-directed RNA poly 100.0 4.6E-48 1E-52 420.8 10.3 197 30-246 298-524 (1156)
12 TIGR02386 rpoC_TIGR DNA-direct 100.0 1.1E-47 2.5E-52 417.3 10.1 199 28-246 288-516 (1140)
13 PRK14906 DNA-directed RNA poly 100.0 2.4E-47 5.3E-52 416.5 10.3 189 28-236 384-594 (1460)
14 PRK09603 bifunctional DNA-dire 100.0 4.1E-47 8.8E-52 430.5 9.7 196 28-243 1695-1912(2890)
15 PF00623 RNA_pol_Rpb1_2: RNA p 100.0 2.4E-46 5.2E-51 334.0 9.6 125 82-206 41-166 (166)
16 PRK14844 bifunctional DNA-dire 100.0 1.5E-44 3.3E-49 408.6 8.3 194 28-241 1738-1954(2836)
17 COG0086 RpoC DNA-directed RNA 100.0 3.2E-40 7E-45 353.1 3.3 183 44-245 265-469 (808)
18 PRK14977 bifunctional DNA-dire 100.0 1.1E-38 2.3E-43 354.2 8.2 202 138-353 309-534 (1321)
19 TIGR02390 RNA_pol_rpoA1 DNA-di 100.0 6.1E-38 1.3E-42 339.2 11.2 202 138-353 295-514 (868)
20 KOG0261|consensus 100.0 2.4E-38 5.2E-43 330.5 5.9 194 148-353 348-558 (1386)
21 CHL00018 rpoC1 RNA polymerase 100.0 5.3E-38 1.1E-42 325.9 7.4 184 141-350 358-547 (663)
22 PRK08566 DNA-directed RNA poly 100.0 6.2E-38 1.3E-42 339.9 7.8 203 137-353 298-518 (882)
23 TIGR02387 rpoC1_cyan DNA-direc 100.0 6E-38 1.3E-42 322.6 6.6 183 142-350 331-519 (619)
24 PRK02625 rpoC1 DNA-directed RN 100.0 9.2E-38 2E-42 321.6 7.7 184 141-350 337-526 (627)
25 smart00663 RPOLA_N RNA polymer 100.0 2.5E-37 5.4E-42 298.0 9.6 188 137-343 90-295 (295)
26 TIGR02386 rpoC_TIGR DNA-direct 100.0 1.9E-36 4.1E-41 329.8 7.4 112 238-349 388-499 (1140)
27 PRK00566 DNA-directed RNA poly 100.0 3.9E-36 8.4E-41 327.8 7.2 183 141-349 319-507 (1156)
28 KOG0260|consensus 100.0 7.6E-36 1.6E-40 316.8 5.1 113 241-353 422-534 (1605)
29 PRK14906 DNA-directed RNA poly 100.0 4.8E-35 1E-39 320.4 7.1 179 142-349 408-596 (1460)
30 PRK09603 bifunctional DNA-dire 100.0 6.1E-35 1.3E-39 332.0 7.9 188 139-352 1716-1909(2890)
31 KOG0262|consensus 100.0 3.6E-34 7.8E-39 305.3 5.7 209 131-353 421-661 (1640)
32 PRK14844 bifunctional DNA-dire 100.0 4.3E-34 9.3E-39 324.3 6.2 107 246-352 1847-1953(2836)
33 COG0086 RpoC DNA-directed RNA 99.9 7.9E-28 1.7E-32 258.0 4.9 115 238-352 349-464 (808)
34 PF00623 RNA_pol_Rpb1_2: RNA p 99.9 4.8E-27 1E-31 209.8 4.6 77 242-318 90-166 (166)
35 PF04983 RNA_pol_Rpb1_3: RNA p 97.7 2.1E-06 4.5E-11 75.6 -3.0 56 209-264 1-61 (158)
36 PF05183 RdRP: RNA dependent R 83.5 1.4 3E-05 46.7 4.5 54 133-189 364-429 (579)
37 PF02362 B3: B3 DNA binding do 55.0 9.1 0.0002 30.2 2.1 48 14-61 33-86 (100)
38 PF05094 LEF-9: Late expressio 50.7 31 0.00067 35.7 5.4 65 139-204 211-279 (487)
39 KOG0988|consensus 42.0 30 0.00066 39.7 4.2 52 134-188 770-833 (1145)
40 PHA03396 lef-9 late expression 37.2 65 0.0014 33.6 5.4 66 138-204 213-282 (493)
41 PF05094 LEF-9: Late expressio 36.9 45 0.00098 34.5 4.2 61 255-316 215-279 (487)
42 PF10948 DUF2635: Protein of u 30.8 23 0.00051 25.4 0.8 15 46-60 32-46 (47)
43 PHA03396 lef-9 late expression 28.1 76 0.0016 33.1 4.2 61 255-316 218-282 (493)
44 PF10657 RC-P840_PscD: Photosy 23.6 46 0.00099 28.8 1.4 50 8-57 25-78 (144)
45 PF05183 RdRP: RNA dependent R 22.8 77 0.0017 33.7 3.3 50 249-301 368-429 (579)
46 PRK12442 translation initiatio 20.1 2.2E+02 0.0047 23.2 4.6 40 11-50 16-58 (87)
No 1
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=100.00 E-value=9.1e-62 Score=537.45 Aligned_cols=215 Identities=38% Similarity=0.612 Sum_probs=191.7
Q ss_pred cceeEeecCCCccccceeeeeeeeeccccc----------------------------ccch-HHHHHHHhCCCCCCCce
Q psy1131 52 GDLVIFNRQPTLHKMSMMGHRVRVLPWSTF----------------------------RMNL-RMFELVRRGNSQYPGAK 102 (353)
Q Consensus 52 ~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf----------------------------~~N~-~Lr~lV~nGp~~~pGA~ 102 (353)
|-.|.|++|+|+||+|||||||++++|+|+ .+|. +||++|.|||+.||||+
T Consensus 309 ~i~qrLkgKeGrfR~nlmGKRVdfSaRtVIspDP~L~i~EVGvP~~iA~~LT~Pe~Vt~~Ni~~l~~lv~nG~~~~pGA~ 388 (1321)
T PRK14977 309 SLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVINGPDEFPGAN 388 (1321)
T ss_pred HHHHHhccccccccccccccccccccceeEeCCCCcccccccCHHHHHHhCCCCEEEchhhHHHHHHHHHcCCcccCCcc
Confidence 567899999999999999999999888762 3454 89999999999999999
Q ss_pred EEEeCCCceEEeecCCCCCc-------cccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecCceeeeecccCC
Q psy1131 103 YIVRDNGERIDLRFHPKPSD-------LHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTS 175 (353)
Q Consensus 103 ~v~~~~g~~~~l~~~~~~~~-------~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~r~~~~~c~ 175 (353)
||++++|.++.+++..+... ..|++||+|+|||.|||+|||||||||||+|||||+|++++++||||||++|+
T Consensus 389 ~i~~~~g~~~~l~~~~~~~~~~~~~~a~~L~~g~iV~Rhl~dGD~VL~NRQPSLHk~Simah~vkvl~~kT~Rln~~vC~ 468 (1321)
T PRK14977 389 AIRKGDGTKIRLDFLEDKGKDALREAAEQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCP 468 (1321)
T ss_pred eEEcCCCceeeehhhhhccchhHHHHHHhcccCcEEEEEeecCcEEEeccCCccccccceEEEEEEecCceEEecccccC
Confidence 99999999998887654332 46899999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccceeeccccccc--cCccee
Q psy1131 176 PYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHI--RDGDLV 253 (353)
Q Consensus 176 ~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD~F~~kee~~l--~d~d~v 253 (353)
||||||||||||+|+|||++|||||.+||++++|++||++|+|++|++||+++|+|+||.+|.|+++++++. ......
T Consensus 469 pyNADFDGDEMNlHvPQS~eArAEa~~Lm~v~~niisP~~G~Pi~gliQD~l~g~~lLT~~d~fl~~~e~~~l~~~~~~~ 548 (1321)
T PRK14977 469 PYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAMLAGIT 548 (1321)
T ss_pred cccCCcccceeeeecCCCHHHHHHHHHHHhhhhcEecCCCCCeeEEeehhhhhhhhhhccCcccCCHHHHHHHHHhCCCc
Confidence 999999999999999999999999999999999999999999999999999999999999999999998752 111122
Q ss_pred eecCCcccc-cccc
Q psy1131 254 IFNRQPTLH-KMSM 266 (353)
Q Consensus 254 I~nrqPtIh-k~s~ 266 (353)
...++|+|. +|..
T Consensus 549 ~~lp~PaI~~kp~~ 562 (1321)
T PRK14977 549 DPLPEPAIKTKDGP 562 (1321)
T ss_pred cccCCCceecCCCC
Confidence 234778888 5533
No 2
>KOG0262|consensus
Probab=100.00 E-value=6.7e-62 Score=515.73 Aligned_cols=228 Identities=36% Similarity=0.495 Sum_probs=195.6
Q ss_pred eeeccccceeEeecCCCccccceeeeeeeeeccccc----------------------------ccch-HHHHHHHhCCC
Q psy1131 46 ERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF----------------------------RMNL-RMFELVRRGNS 96 (353)
Q Consensus 46 erhl~d~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf----------------------------~~N~-~Lr~lV~nGp~ 96 (353)
-|.-..|=.|+||||+||||+||||||||++.|+|+ .+|. +||++|+|||+
T Consensus 422 ~r~~~pGikQiLEKKeGLFRkhMMGKRVN~AaRSVIsPDPnI~tnEIGIP~vFA~KLTyPepVt~~NV~elr~aViNGP~ 501 (1640)
T KOG0262|consen 422 SRDSPPGIKQILEKKEGLFRKHMMGKRVNYAARSVISPDPNIETNEIGIPPVFAKKLTYPEPVTPWNVNELRKAVINGPD 501 (1640)
T ss_pred ccCCCchHHHHHHHhhhhHHHHhhccccchhhccccCCCCCccccccCCchHHHhhccCCCcCCcccHHHHHHHHhcCCC
Confidence 444457778999999999999999999998877762 3454 99999999999
Q ss_pred CCCCceEEEeCCCceEEeecCCCCC------------ccccc--cccEEeeeeccCCeeeEecCCCccccceeeeeEEEe
Q psy1131 97 QYPGAKYIVRDNGERIDLRFHPKPS------------DLHLQ--CGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVL 162 (353)
Q Consensus 97 ~~pGA~~v~~~~g~~~~l~~~~~~~------------~~~l~--~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~ 162 (353)
+||||+|+++++|....+.-...+. .-.+. -+.+|+||+++||+||+||||||||+|||||++||+
T Consensus 502 ~hPGA~~iqd~dg~~t~l~~~~~~qR~alA~qLLtpst~~~~~~~~K~V~RHvknGDvvlmNRQPTLHKPSimaHkaRVL 581 (1640)
T KOG0262|consen 502 VHPGATYIQDEDGTLTLLSPMTDEQREALANQLLTPSTGNPTEFGTKKVHRHVKNGDVVLMNRQPTLHKPSIMAHKARVL 581 (1640)
T ss_pred CCCCcceeecCCCceeecCCCCHHHHHHHHHHhhccccCCCcccCCceeeeeccCCcEEEEcCCCccccchhhhhhheec
Confidence 9999999999999988775322110 00111 357899999999999999999999999999999999
Q ss_pred cC-ceeeeecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccceeec
Q psy1131 163 PW-STFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 241 (353)
Q Consensus 163 ~~-~t~r~~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD~F~~ 241 (353)
+| +||||||++|++|||||||||||+|+||++.|||||+.|++++.|++.|++|.|++|+||||+++..+||.||.||+
T Consensus 582 ~gEktlRlHYANCkaYNADFDGDEMN~HfPQse~araEa~~ian~dsqYLvPt~G~PlrGLIQDHiVsgv~LT~rd~Fft 661 (1640)
T KOG0262|consen 582 PGEKTLRLHYANCKAYNADFDGDEMNVHFPQSEIARAEAYNIANTDSQYLVPTDGTPLRGLIQDHIVSGVLLTMRDSFFT 661 (1640)
T ss_pred CCcceeeeeecccccccCCCCcchhcccCCchhhHHHHHHHHhccCCceeccCCCCchhhhhhhheeeeEEEEecccccC
Confidence 99 99999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccc------cCcceeeecCCcccccccccceeeEE
Q psy1131 242 KVERHI------RDGDLVIFNRQPTLHKMSMMGHRVRV 273 (353)
Q Consensus 242 kee~~l------~d~d~vI~nrqPtIhk~s~~~~~~~i 273 (353)
+++|+. .+.-..|...+|||.||...+....|
T Consensus 662 re~y~qLv~~~l~~~~~rI~~lpPtIlkP~~LWTGKQV 699 (1640)
T KOG0262|consen 662 REDYQQLVFAGLSDTFKRIKLLPPTILKPAPLWTGKQV 699 (1640)
T ss_pred HHHHHHHHHHhhhhhccceeccCccccccccccccchH
Confidence 998862 23223455578999999885444333
No 3
>KOG0261|consensus
Probab=100.00 E-value=5.7e-62 Score=506.51 Aligned_cols=221 Identities=39% Similarity=0.629 Sum_probs=200.6
Q ss_pred eeccccceeEeecCCCccccceeeeeeeeecccc----------------------------cccch-HHHHHHHhCCCC
Q psy1131 47 RHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWST----------------------------FRMNL-RMFELVRRGNSQ 97 (353)
Q Consensus 47 rhl~d~~~~~~~~~~~l~r~~~mGkRv~v~p~~v----------------------------f~~N~-~Lr~lV~nGp~~ 97 (353)
.|=..|-+|.|.+|+|+||-|+-||||+++.|.| .+.|. +||+||+|||++
T Consensus 333 ~kp~RGf~QRLKGKqGRFRgNLSGKRVDFSGRTVISPDPNL~IdeVgVP~rvAkiLTfpE~Vt~~Ni~klr~lV~NGP~v 412 (1386)
T KOG0261|consen 333 KKPTRGFVQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDEVGVPIRVAKILTFPERVTRANIRKLRQLVRNGPNV 412 (1386)
T ss_pred CCchHHHHHHhcccCCceeccccCceeeccCceeeCCCCCcceeeccchHHHHHHhcchhhccHHHHHHHHHHHhcCCCC
Confidence 4556788999999999999999999999876654 25565 899999999999
Q ss_pred CCCceEEE-eCCCceEEeecCCCCC-ccccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecCceeeeecccCC
Q psy1131 98 YPGAKYIV-RDNGERIDLRFHPKPS-DLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTS 175 (353)
Q Consensus 98 ~pGA~~v~-~~~g~~~~l~~~~~~~-~~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~r~~~~~c~ 175 (353)
|||||||+ +..|.+..|+|..+.. ...|++||+|+|||.|||+|||||||||||+|||+|++|+.|++|||+|.|+|+
T Consensus 413 hPGANyv~~r~~~~kr~L~yg~R~kiA~eLk~GdvVERHL~DgDvVLFNRQPSLHkmSIM~H~akV~p~RTfRFNEcvCt 492 (1386)
T KOG0261|consen 413 HPGANYVVQRGEGFKRFLKYGNRDKIADELKIGDVVERHLMDGDVVLFNRQPSLHKMSIMSHRAKVMPWRTFRFNECVCT 492 (1386)
T ss_pred CCCcchhhhcccchhhHhhcCcHHHHHHhhccchHHHhhcccCCEEEEcCCchHHHHHHHHHHhhcccCceeeccccccC
Confidence 99999998 6677777788765432 246999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccceeecccccc-----ccCc
Q psy1131 176 PYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERH-----IRDG 250 (353)
Q Consensus 176 ~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD~F~~kee~~-----l~d~ 250 (353)
||||||||||||+|+||++||||||.+||.+++|+++|++|+|+++.+||+++|+|++|.+|+|++++++. +.++
T Consensus 493 PYNADFDGDEMNlHvPQTEEAraEA~~LMgvknNlvTPr~GEpiiAAtQDFiTg~YLlt~KDtF~dRa~~~ql~s~~~d~ 572 (1386)
T KOG0261|consen 493 PYNADFDGDEMNLHVPQTEEARAEALVLMGVKNNLVTPRNGEPIIAATQDFITGGYLLTHKDTFLDRAEFSQLCSYMSDA 572 (1386)
T ss_pred CcCCCCCcccccccCCchHHHHHHHHHHhccccccccCCCCCceeehhhhhhhcceeeecccccccHHHHHHHHHHHhcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999998763 4677
Q ss_pred ceeeecCCccccccccc
Q psy1131 251 DLVIFNRQPTLHKMSMM 267 (353)
Q Consensus 251 d~vI~nrqPtIhk~s~~ 267 (353)
...+..++|||.||...
T Consensus 573 ~~~i~lppPaI~KP~~L 589 (1386)
T KOG0261|consen 573 MTHIDLPPPAILKPVEL 589 (1386)
T ss_pred ccccCCCChhhcCceee
Confidence 77788899999998773
No 4
>TIGR02390 RNA_pol_rpoA1 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=1.6e-60 Score=514.44 Aligned_cols=216 Identities=38% Similarity=0.634 Sum_probs=192.5
Q ss_pred ccceeEeecCCCccccceeeeeeeeeccccc----------------------------ccch-HHHHHHHhCCCCCCCc
Q psy1131 51 DGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF----------------------------RMNL-RMFELVRRGNSQYPGA 101 (353)
Q Consensus 51 d~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf----------------------------~~N~-~Lr~lV~nGp~~~pGA 101 (353)
.|-.|.|++|+|+||+|||||||++++|+|+ .+|. +|+++|.|||+.||||
T Consensus 294 ~~i~~~l~gK~G~~R~nl~GKRvd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~Vt~~N~~~l~~lv~ng~~~~pga 373 (868)
T TIGR02390 294 KTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGPDSWPGA 373 (868)
T ss_pred hhhHhhhcccccccccccccccccccCCceeeCCCCCcCCeeeCcHHHHHhCCCCeEEehhhHHHHHHHHHcCCccCCCc
Confidence 4667899999999999999999999888872 3454 8999999999999999
Q ss_pred eEEEeCCCceEEeecCCCCC-ccccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecCceeeeecccCCCCCCC
Q psy1131 102 KYIVRDNGERIDLRFHPKPS-DLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNAD 180 (353)
Q Consensus 102 ~~v~~~~g~~~~l~~~~~~~-~~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~r~~~~~c~~~NAD 180 (353)
+||++++|.++++++..+.. ...|++||+|+||+.|||+|||||||||||+|||||+|++++++||||||++|+|||||
T Consensus 374 ~~i~~~~g~~~~l~~~~~~~~~~~l~~g~~v~rhl~dgd~vl~NRqPsLHr~si~a~~~~v~~~~t~r~n~~~c~~~NAD 453 (868)
T TIGR02390 374 NYVIRPDGRRIKIRDENKEELAERLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNAD 453 (868)
T ss_pred eEEEcCCCcEEechhhhHHHHHhhcccCCEEEEehhcCccceeccCCccccccceeEEEEEecCceEeeccccCCccccC
Confidence 99999999998887654321 23589999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccceeeccccccc--cCcceeeecCC
Q psy1131 181 FDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHI--RDGDLVIFNRQ 258 (353)
Q Consensus 181 FDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD~F~~kee~~l--~d~d~vI~nrq 258 (353)
|||||||+|+|||++||||+.+||++.+|++||++|+|+++++||+++|+++||.+|+|+++++++. ..+...+..++
T Consensus 454 FDGDeMn~h~Pqs~~a~aEa~~Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~~LT~~d~f~~~~~~~~l~~~~~~~~~~~~ 533 (868)
T TIGR02390 454 FDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGVAGYFGDPPE 533 (868)
T ss_pred cccceeeEecCCCHHHHHHHHHHhhchhceecCCCCCeeEEeehhhhhheeeeeeccccCCHHHHHHHHhcCCccccCCC
Confidence 9999999999999999999999999999999999999999999999999999999999999998753 12223344567
Q ss_pred cccccccc
Q psy1131 259 PTLHKMSM 266 (353)
Q Consensus 259 PtIhk~s~ 266 (353)
|+|.+|..
T Consensus 534 p~i~kp~~ 541 (868)
T TIGR02390 534 PAIEKPKE 541 (868)
T ss_pred ceecCCcc
Confidence 88877544
No 5
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated
Probab=100.00 E-value=6e-60 Score=511.06 Aligned_cols=216 Identities=38% Similarity=0.615 Sum_probs=190.7
Q ss_pred ccceeEeecCCCccccceeeeeeeeeccccc----------------------------ccch-HHHHHHHhCCCCCCCc
Q psy1131 51 DGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF----------------------------RMNL-RMFELVRRGNSQYPGA 101 (353)
Q Consensus 51 d~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf----------------------------~~N~-~Lr~lV~nGp~~~pGA 101 (353)
.|-.|.|++|+|+||+|||||||++++|+|+ .+|. +||++|.|||+.||||
T Consensus 298 ~~i~~~l~gK~G~fR~nl~GKRvd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~v~~~N~~~l~~~v~ng~~~~pga 377 (882)
T PRK08566 298 KTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKHPGA 377 (882)
T ss_pred cchHHhcccCCCccccccccccccCcCCceeeCCCCCcCCeeeCcHHHHHhCCCCeEEchhhHHHHHHHHHcCCCcCCCc
Confidence 3567899999999999999999999888872 3354 8999999999999999
Q ss_pred eEEEeCCCceEEeecCCCCC-ccccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecCceeeeecccCCCCCCC
Q psy1131 102 KYIVRDNGERIDLRFHPKPS-DLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNAD 180 (353)
Q Consensus 102 ~~v~~~~g~~~~l~~~~~~~-~~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~r~~~~~c~~~NAD 180 (353)
+||++++|.++.+....+.. ...|++||+|+||+.|||+|||||||||||+|||||+|++++++||||||++|+|||||
T Consensus 378 ~~i~~~~g~~~~l~~~~~~~~~~~l~~g~~v~Rhl~dgd~vl~NRqPsLHr~si~a~~~~v~~~~t~r~n~~~c~~~NAD 457 (882)
T PRK08566 378 NYVIRPDGRRIKLTDKNKEELAEKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNAD 457 (882)
T ss_pred eEEEcCCCceeeehhhhHHHHHHhccccceehhhhhcCceeeecCCCcccccccceeEEEEecCceEeeccccCCCccCC
Confidence 99999999988884432211 13588999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccceeecccccccc---CcceeeecC
Q psy1131 181 FDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHIR---DGDLVIFNR 257 (353)
Q Consensus 181 FDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD~F~~kee~~l~---d~d~vI~nr 257 (353)
|||||||+|+|||++||||+.+||++.+|++||++|+|++|++||+++|+|++|.+|.|+++++++.. .....+..+
T Consensus 458 FDGDeMn~h~Pqs~~a~aEa~~Lm~~~~~~~sp~~g~pi~~~~QD~l~g~~~lt~~d~f~~~~~~~~l~~~~~~~~~~~~ 537 (882)
T PRK08566 458 FDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGIDELPEP 537 (882)
T ss_pred ccCcEEEEecCCCHHHHHHHHHHhcchhcEecCCCCCeeEEeehHHHHHHHHHHhccccCCHHHHHHHHHhCCccccccC
Confidence 99999999999999999999999999999999999999999999999999999999999999987521 111224457
Q ss_pred Ccccccccc
Q psy1131 258 QPTLHKMSM 266 (353)
Q Consensus 258 qPtIhk~s~ 266 (353)
+|+|.+|..
T Consensus 538 ~pai~~p~~ 546 (882)
T PRK08566 538 EPAIENGKP 546 (882)
T ss_pred CcccCCCcc
Confidence 788887654
No 6
>KOG0260|consensus
Probab=100.00 E-value=2.3e-58 Score=487.13 Aligned_cols=223 Identities=58% Similarity=0.889 Sum_probs=200.7
Q ss_pred ccCCcEEeeeccccceeEeecCCCccccceeeeeeeeecccc----------------------------cccch-HHHH
Q psy1131 39 LQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWST----------------------------FRMNL-RMFE 89 (353)
Q Consensus 39 l~~g~~verhl~d~~~~~~~~~~~l~r~~~mGkRv~v~p~~v----------------------------f~~N~-~Lr~ 89 (353)
+|..-+-.+.| .+.+..|+|..|-++|||||+++.|.| ..+|. +|++
T Consensus 307 ~qksGrplkSi----~arlKgkegriRgnLmGKRvDFSaRTVItgDPnl~ldevGVP~sIAk~lTfpE~Vtp~NidrLqe 382 (1605)
T KOG0260|consen 307 DQKSGRPLKSI----SARLKGKEGRIRGNLMGKRVDFSARTVITGDPNLSLDEVGVPRSIAKRLTFPEHVTPFNIDRLQE 382 (1605)
T ss_pred ccccCCcccch----hhhhccccchhhhcccccccCcceeeeecCCCCcchhcccCcHHHHhhccCcceeccccHHHHHH
Confidence 44444444444 468999999999999999999876655 24565 8999
Q ss_pred HHHhCCCCCCCceEEEeCCCceEEeecCCCCCccccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecCceeee
Q psy1131 90 LVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRM 169 (353)
Q Consensus 90 lV~nGp~~~pGA~~v~~~~g~~~~l~~~~~~~~~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~r~ 169 (353)
||++||..|||||||++++|.++++++.++..+++|++||+|+||++|||.|||||||||||||||||+|||+|..||||
T Consensus 383 LV~~g~~~~pgakyiird~G~Ridlr~~~~~~d~~Lq~G~kVeRhl~DGD~VlfNRqPSlHKmSmmahrVrVlp~sTfrL 462 (1605)
T KOG0260|consen 383 LVRRGLLEHPGAKYIIRDNGDRIDLRYHKRAGDIHLQPGYKVERHLMDGDVVLFNRQPSLHKMSMMAHRVRVLPYSTFRL 462 (1605)
T ss_pred HhhCCCCCCCCcceeeecCCcEEEEeecCCccccccccccEEEEeeccCCEEEEcCCCcHHHhhhhhcEEEEccCceEEe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccceeeccccccc--
Q psy1131 170 NLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHI-- 247 (353)
Q Consensus 170 ~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD~F~~kee~~l-- 247 (353)
|++||+||||||||||||+|+|||+++|||+.+|+++++|+++|++|+|+.|++||+++|++++|.||.|+++.+.+.
T Consensus 463 NlsvtsPynADFDGDemnlhvPQS~etkAEl~EL~~vpkQiispQsnkpvmgivQDTLta~R~~t~Rd~Fl~r~~vmnLl 542 (1605)
T KOG0260|consen 463 NLSVTSPYNADFDGDEMNLHVPQSLETKAELEELAMVPKQIISPQSNKPVMGIVQDTLTAVRKMTKRDVFLNRAQVMNLL 542 (1605)
T ss_pred CeeecCCccCCCCCceeecccCcchhHHHHHHHHhhhhhhhcCCcCCCcceeeehhhHHHHHHHhhHhhhhcHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999987752
Q ss_pred ---cCcceeeecC-Cccccccccc
Q psy1131 248 ---RDGDLVIFNR-QPTLHKMSMM 267 (353)
Q Consensus 248 ---~d~d~vI~nr-qPtIhk~s~~ 267 (353)
.+.|... + +|+|.|+-.+
T Consensus 543 m~~p~~d~~~--Pa~pai~Kp~Pl 564 (1605)
T KOG0260|consen 543 MYVPDWDGPP--PAKPAILKPKPL 564 (1605)
T ss_pred hhccccCCCC--CCCcccCCCCcc
Confidence 2444443 4 6788887763
No 7
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus.
Probab=100.00 E-value=8.2e-57 Score=433.00 Aligned_cols=176 Identities=45% Similarity=0.763 Sum_probs=162.0
Q ss_pred ccceeEeecCCCccccceeeeeeeeeccccc----------------------------ccch-HHHHHHHhCCCCCCCc
Q psy1131 51 DGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF----------------------------RMNL-RMFELVRRGNSQYPGA 101 (353)
Q Consensus 51 d~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf----------------------------~~N~-~Lr~lV~nGp~~~pGA 101 (353)
.|-.|.+++|+|+||++||||||++++|+|+ .+|. +|+++|.||| |||
T Consensus 90 ~~i~~~l~gK~G~~R~nllGKRvd~s~RsVI~pdP~l~~~evgiP~~~A~~Lt~pe~v~~~n~~~l~~lv~ng~---pga 166 (295)
T smart00663 90 KSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLVRNGP---NGA 166 (295)
T ss_pred ccccccccCcCCccccccccccccccCceEEeCCCCcceeEeeCCHHHHHhCCcCEEEhHHHHHHHHHHHhcCC---CCc
Confidence 5678999999999999999999999988872 3344 7999999999 999
Q ss_pred eEEEeCCCceEEeecCCCC-CccccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecCceeeeecccCCCCCCC
Q psy1131 102 KYIVRDNGERIDLRFHPKP-SDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNAD 180 (353)
Q Consensus 102 ~~v~~~~g~~~~l~~~~~~-~~~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~r~~~~~c~~~NAD 180 (353)
+||++ |.+..+++.++. ....+++||+|+||+.|||+|||||||||||+|||||++++++++|||+||++|+|||||
T Consensus 167 ~~i~~--g~~~~l~~~~~~~~~~~l~~g~~v~r~l~dgd~Vl~NRqPsLHr~si~a~~v~v~~~~tir~n~~~c~~fNAD 244 (295)
T smart00663 167 KYIIR--GKKTNLKLAKRSKIAKHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNAD 244 (295)
T ss_pred eEEEe--CcEEEchhhhhHHHHhcCccccEeheehhcCCEEEEecCCccccccceeEEEEEecCceEEecCccCCcccCC
Confidence 99997 777777665433 345689999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeee
Q psy1131 181 FDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVR 231 (353)
Q Consensus 181 FDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~ 231 (353)
|||||||+|+|||++|++|+.+||.+.+|++||++|+|+++++||+++|+|
T Consensus 245 FDGDeMnih~pqs~~a~aEa~~Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~ 295 (295)
T smart00663 245 FDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295 (295)
T ss_pred cCCCEEEEecCCCHHHHHHHHHHhhhhhccccCCCCCeeEeeecceeeecC
Confidence 999999999999999999999999999999999999999999999999976
No 8
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=100.00 E-value=5e-52 Score=430.08 Aligned_cols=178 Identities=22% Similarity=0.337 Sum_probs=159.5
Q ss_pred CCcEEeeeccccceeEeecCCCccccceeeeeeeeeccccc---------------------ccchHHHHHHHhCCC-CC
Q psy1131 41 CGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF---------------------RMNLRMFELVRRGNS-QY 98 (353)
Q Consensus 41 ~g~~verhl~d~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf---------------------~~N~~Lr~lV~nGp~-~~ 98 (353)
.+.++.+.|. +.|++|+|+||+|||||||++++|+|+ +..+.+++|+.+|+. .+
T Consensus 348 ~~~r~~ksls----~~LkGK~GrFR~NLlGKRVDySgRSVIvpdP~L~l~e~GlP~~mA~eL~~P~~i~~Li~~~~~~~~ 423 (663)
T CHL00018 348 GHNKPYKSFS----DVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQPFVIRGLIRQHLASNI 423 (663)
T ss_pred CCCCCCCCcc----ccccCcCccccccccccccccCCCceecCCCcccccccCChHHHHHHcCcHHHHHHHHhcCccccH
Confidence 3445556664 499999999999999999999999983 334689999999976 55
Q ss_pred CCceEEEeCCCceEEeecCCCCCccccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecCceeeeecccCCCCC
Q psy1131 99 PGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYN 178 (353)
Q Consensus 99 pGA~~v~~~~g~~~~l~~~~~~~~~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~r~~~~~c~~~N 178 (353)
.+|++++++... .+|.|+||+.+||+|||||||||||+|||||++++++++||||||+||+|||
T Consensus 424 ~~Ak~~i~~~~~----------------~~~~Vlr~v~~gd~VLlNRqPTLHR~sIqAf~~~L~~gktIrLhplvC~~fN 487 (663)
T CHL00018 424 RAAKSKIREKEP----------------IVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFN 487 (663)
T ss_pred HHHHHHHHhcCC----------------cccEeeeehhcCceeeecCCCcccccccceeeEEecCCCeEEeCcccCCccc
Confidence 678776544322 3589999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccce
Q psy1131 179 ADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDV 238 (353)
Q Consensus 179 ADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD~ 238 (353)
|||||||||+|+|||++|++||+.||.+.+|++||++|+|+++++||+++|+|++|.++.
T Consensus 488 ADFDGDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~ 547 (663)
T CHL00018 488 ADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNR 547 (663)
T ss_pred CCccCcEEEEecCCCHHHHHHHHHHhcCccceeEcCCCceeEeechhhhhhhheecccCC
Confidence 999999999999999999999999999999999999999999999999999999999875
No 9
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=100.00 E-value=1.1e-51 Score=424.20 Aligned_cols=218 Identities=20% Similarity=0.324 Sum_probs=173.4
Q ss_pred CCCCCCccccCCcEEeeeccccceeEeecCCCccccceeeeeeeeeccccc---------------------ccchHHHH
Q psy1131 31 HPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF---------------------RMNLRMFE 89 (353)
Q Consensus 31 ~~~~~~~~l~~g~~verhl~d~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf---------------------~~N~~Lr~ 89 (353)
+.+++.+....+.+..+.|. +.+++|+|+||+|||||||++++|+|+ ...+.+++
T Consensus 317 n~~~g~~~~~~~~rp~ksls----~~LkGKeGRFR~NLlGKRVDySgRSVIspdP~L~l~e~GvP~~mA~eL~~Pf~i~~ 392 (627)
T PRK02625 317 NGRRGRTVVGANNRPLKSLS----DIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHR 392 (627)
T ss_pred CCCCCCCcccccCCchhhHH----HHhccCCccccccccccccccCCCceEeCCCCcccccccChHHHHHhcCcHHhHHH
Confidence 33333333333455666664 499999999999999999999999983 22346778
Q ss_pred HHHhCCC-CCCCceEEEeCCCceEEeecCCCCCccccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecCceee
Q psy1131 90 LVRRGNS-QYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFR 168 (353)
Q Consensus 90 lV~nGp~-~~pGA~~v~~~~g~~~~l~~~~~~~~~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~r 168 (353)
|+.+|.. +.++|++++...+. ..|.|+||+.+||+|||||||||||+|||||++++++++|||
T Consensus 393 L~~~g~~~~i~~ak~~i~~~~~----------------~~~~Vlr~v~~gd~VLlNRqPTLHR~sIqAf~~~l~~~ktir 456 (627)
T PRK02625 393 LIRQGIVNNIKAAKKLIQRADP----------------EVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQ 456 (627)
T ss_pred HHHcCchhhHHHHHHHHHhcCC----------------cccEEEEEeecCcEEEecCCCccccccceeEeeEEcCCCeEE
Confidence 8888863 45777776543322 237899999999999999999999999999999999999999
Q ss_pred eecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccceeecccc-ccc
Q psy1131 169 MNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVE-RHI 247 (353)
Q Consensus 169 ~~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD~F~~kee-~~l 247 (353)
|||+||+||||||||||||+|+|||++|++||+.||.+.+|++||++|+|+++++||+++|+|+||.++....+.. ..+
T Consensus 457 lhplvC~~fNADFDGDeMnvHvPqS~~A~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~llG~y~LT~~~~~~~~~~~~~f 536 (627)
T PRK02625 457 LHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPGAQKGAGRYF 536 (627)
T ss_pred eccccCCcccCCcCCCeEEEecCCCHHHHHHHHHHhcCccceEEcCCCceeEeechhhhhheeeeeccCccccCCCCcee
Confidence 9999999999999999999999999999999999999999999999999999999999999999999875432211 122
Q ss_pred cCc-ceeeecCCcccccccccc
Q psy1131 248 RDG-DLVIFNRQPTLHKMSMMG 268 (353)
Q Consensus 248 ~d~-d~vI~nrqPtIhk~s~~~ 268 (353)
.+. +...+..+-.++.++..+
T Consensus 537 ~~~~~~~~a~~~~~i~l~~~i~ 558 (627)
T PRK02625 537 ASLEDVIMAFEQGRIDLHAWVW 558 (627)
T ss_pred CCHHHHHHHHHCCCccccceEE
Confidence 232 333345556666666643
No 10
>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit. The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.
Probab=100.00 E-value=2.1e-51 Score=421.63 Aligned_cols=210 Identities=19% Similarity=0.313 Sum_probs=170.6
Q ss_pred ccCCcEEeeeccccceeEeecCCCccccceeeeeeeeeccccc---------------------ccchHHHHHHHhCCC-
Q psy1131 39 LQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF---------------------RMNLRMFELVRRGNS- 96 (353)
Q Consensus 39 l~~g~~verhl~d~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf---------------------~~N~~Lr~lV~nGp~- 96 (353)
...+.+.-+.|. +.+++|+|+||+|+|||||++++|+|+ ...+.+++|+.+|+.
T Consensus 318 ~~~~~rp~ksls----~~LkGKeGRFR~nLlGKRVDySgRSVI~pdP~L~l~qvGvP~~mA~eLf~Pf~i~~L~~~g~~~ 393 (619)
T TIGR02387 318 VGANNRPLKSLS----DIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVN 393 (619)
T ss_pred ccccCCchhhHH----HHhccCCccccccccccccccCCCceecCCCCcccceecChHHHHHhcCchHhHHHHHhcCccc
Confidence 333445666664 499999999999999999999999983 223467788889864
Q ss_pred CCCCceEEEeCCCceEEeecCCCCCccccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecCceeeeecccCCC
Q psy1131 97 QYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSP 176 (353)
Q Consensus 97 ~~pGA~~v~~~~g~~~~l~~~~~~~~~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~r~~~~~c~~ 176 (353)
..+||+++++..+.. .|.|+||+.+||+|||||||||||+|||||++++++++||||||++|+|
T Consensus 394 ~i~~ak~~i~~~~~~----------------v~~Vlr~v~~gd~VLlNRqPTLHR~sIqAf~~~l~~~ktirlhplvC~~ 457 (619)
T TIGR02387 394 NIKAAKKLIQRADDE----------------IWSVLQEVITGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPA 457 (619)
T ss_pred chHHHHHHHHhcCCh----------------hHHHHHHHhcCCEEEecCCCccchhcceeeeeEEecCCeEEECcccCCc
Confidence 557888776543321 2679999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccceeecc--ccccccCcceee
Q psy1131 177 YNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDK--VERHIRDGDLVI 254 (353)
Q Consensus 177 ~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD~F~~k--ee~~l~d~d~vI 254 (353)
|||||||||||+|+|||++|++||+.||.+.+|++||++|+|+++++||+++|+|++|.++.-..+ ..++.+-.+...
T Consensus 458 fNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~llg~y~LT~~~~~~~~~~~~~f~~~~~~~~ 537 (619)
T TIGR02387 458 FNADFDGDQMAVHVPLSLEAQTEARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALNPGAEKGRGRYFSSLEDAIH 537 (619)
T ss_pred ccCCCCCceeeeecCCCHHHHHHHHHHhhchhcEEecCCCceeEeechhhhhhhheeeccccccccCCCcccCCHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999998753222 122222223333
Q ss_pred ecCCcccccccccc
Q psy1131 255 FNRQPTLHKMSMMG 268 (353)
Q Consensus 255 ~nrqPtIhk~s~~~ 268 (353)
+..+-.|+.++..+
T Consensus 538 a~~~~~i~lhs~i~ 551 (619)
T TIGR02387 538 AYEDGRIDLHDWIW 551 (619)
T ss_pred HHHCCCccccceEE
Confidence 45556666666643
No 11
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=4.6e-48 Score=420.76 Aligned_cols=197 Identities=23% Similarity=0.371 Sum_probs=163.2
Q ss_pred cCCCCCCccccCCcEEeeeccccceeEeecCCCccccceeeeeeeeeccccc---------------------ccchHHH
Q psy1131 30 FHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF---------------------RMNLRMF 88 (353)
Q Consensus 30 ~~~~~~~~~l~~g~~verhl~d~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf---------------------~~N~~Lr 88 (353)
.+.+++......+.+..+.|.| .|++|+|+||+|+|||||++++|+|+ +.++.++
T Consensus 298 dn~~~g~~~~~~~~rplksls~----~LkGK~GrFR~NLlGKRVDySgRSVI~pdP~L~l~e~GvP~~mA~eL~~Pf~i~ 373 (1156)
T PRK00566 298 DNGRRGRPVTGPNNRPLKSLSD----MLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIMK 373 (1156)
T ss_pred ccCccCCCcccccCCchhHHHH----hhcCCCccccccccccccCCCCCceEeCCCCcccccccChHHHHHHhCcHHHHH
Confidence 3444443434445566666655 99999999999999999999999983 3346799
Q ss_pred HHHHhCCC-CCCCceEEEeCCCceEEeecCCCCCccccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecCcee
Q psy1131 89 ELVRRGNS-QYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF 167 (353)
Q Consensus 89 ~lV~nGp~-~~pGA~~v~~~~g~~~~l~~~~~~~~~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~ 167 (353)
+|+.+|+. ....|+..+... ... .|.|.|++.+||+|||||||||||+|||||++++++++||
T Consensus 374 ~L~~~g~~~~ik~ak~~~~~~---------------~~~-v~~vle~vi~gd~VLlNRqPTLHR~sIqAf~~~l~~gkti 437 (1156)
T PRK00566 374 KLVERGLATTIKSAKKMVERE---------------DPE-VWDVLEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAI 437 (1156)
T ss_pred HHHHcCCccchHhhhhhhhhh---------------cCc-ceEEEEEecCCCEEEecCCCcccccccceeEEEEecCceE
Confidence 99999973 233444432111 112 3556678889999999999999999999999999999999
Q ss_pred eeecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccc--------ee
Q psy1131 168 RMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRD--------VF 239 (353)
Q Consensus 168 r~~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD--------~F 239 (353)
||||++|+||||||||||||+|+|||++|++|++.||.+.+|++||++|+|+++++||+++|+|+||.++ .|
T Consensus 438 rLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~~F 517 (1156)
T PRK00566 438 QLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPANGKPIIVPSQDMVLGLYYLTREREGAKGEGMVF 517 (1156)
T ss_pred EECccccCccccccccceeEEecCCCHHHHHHHHHHhCCcccEEecCCCCeeEEeehhhhhhhheeecccccccCCCcee
Confidence 9999999999999999999999999999999999999999999999999999999999999999999987 56
Q ss_pred ecccccc
Q psy1131 240 LDKVERH 246 (353)
Q Consensus 240 ~~kee~~ 246 (353)
++++++.
T Consensus 518 ~~~~e~~ 524 (1156)
T PRK00566 518 SSPEEAL 524 (1156)
T ss_pred CCHHHHH
Confidence 6666553
No 12
>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=100.00 E-value=1.1e-47 Score=417.31 Aligned_cols=199 Identities=21% Similarity=0.339 Sum_probs=162.4
Q ss_pred eccCCCCCCccccCCcEEeeeccccceeEeecCCCccccceeeeeeeeeccccc---------------------ccchH
Q psy1131 28 LRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF---------------------RMNLR 86 (353)
Q Consensus 28 l~~~~~~~~~~l~~g~~verhl~d~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf---------------------~~N~~ 86 (353)
|-.+.+++.+....+.+..+.|.| .|++|+|+||+|||||||++++|+|+ +..+.
T Consensus 288 liDn~~~g~~~~~~~~rplksls~----~LkGK~GrFR~NLlGKRVDySgRSVI~pdP~L~l~e~GlP~~mA~~L~~Pf~ 363 (1140)
T TIGR02386 288 LFDNGRRGKPVVGKNNRPLKSLSD----MLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFI 363 (1140)
T ss_pred HhcccccCCCccCcCCCchhhHHH----hhcCCCCcccccccccccCCCCCCeEcCCCCcccccccChHHHHHHcCchHH
Confidence 344545554555556677777755 99999999999999999999999983 22356
Q ss_pred HHHHHHhCCCC-CCCceEEEeCCCceEEeecCCCCCccccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecCc
Q psy1131 87 MFELVRRGNSQ-YPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWS 165 (353)
Q Consensus 87 Lr~lV~nGp~~-~pGA~~v~~~~g~~~~l~~~~~~~~~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~ 165 (353)
+++|+.+|... ...|+..+.. .....|.|.+|+.+||+|||||||||||+|||||++++++++
T Consensus 364 i~~L~~~~~~~~i~~ak~~i~~----------------~~~~v~~vl~~vi~~d~VLlNRqPTLHRlsIqAf~~~l~~gk 427 (1140)
T TIGR02386 364 IKRLIDRELAANIKSAKKMIEQ----------------EDPEVWDVLEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGK 427 (1140)
T ss_pred HHHHHHcCcccchHHHHHHHHh----------------cCCccceEEEEccCCcEEEecCCCcccccccceeEEEEecCc
Confidence 77888876421 1112211100 011236677899999999999999999999999999999999
Q ss_pred eeeeecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccc--------
Q psy1131 166 TFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRD-------- 237 (353)
Q Consensus 166 t~r~~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD-------- 237 (353)
||||||+||+||||||||||||+|+|||++|++|++.||.+.+|++||++|+|+++++||+++|+|+||.++
T Consensus 428 tirlhplvC~~fNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~~~~~~~~ 507 (1140)
T TIGR02386 428 AIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTTEKPGAKGEGK 507 (1140)
T ss_pred eEEEcccccCcccCCCCcceeEeecCCCHHHHHHHHHHhCCcccEecCCCCCceEEeechhhheeeEeeeccccccCcCc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999985
Q ss_pred eeecccccc
Q psy1131 238 VFLDKVERH 246 (353)
Q Consensus 238 ~F~~kee~~ 246 (353)
.|+++++..
T Consensus 508 ~F~~~~e~~ 516 (1140)
T TIGR02386 508 IFSNVDEAI 516 (1140)
T ss_pred eeCCHHHHH
Confidence 566666554
No 13
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=100.00 E-value=2.4e-47 Score=416.48 Aligned_cols=189 Identities=23% Similarity=0.334 Sum_probs=161.2
Q ss_pred eccCCCCCCccccCCcEEeeeccccceeEeecCCCccccceeeeeeeeeccccc---------------------ccchH
Q psy1131 28 LRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF---------------------RMNLR 86 (353)
Q Consensus 28 l~~~~~~~~~~l~~g~~verhl~d~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf---------------------~~N~~ 86 (353)
|-.+.+++......|.+..+.|.| .|++|+|+||+|||||||++++|+|+ +..+.
T Consensus 384 liDN~~~g~p~~~~~~rplKsls~----~LkGK~GRFRqNLlGKRVDySgRSVIspdP~L~l~e~GlP~~mA~eLf~Pf~ 459 (1460)
T PRK14906 384 LFDNGRRGRPVTGPGNRPLKSLAD----MLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFV 459 (1460)
T ss_pred HHcCCCcCCCCccccCCchhHHHH----HhcccCcccccccccccccCcCCceEeCCCCCccccccCcHHHHHhcCchhH
Confidence 344555555555556666666654 99999999999999999999999983 33457
Q ss_pred HHHHHHhCC-CCCCCceEEEeCCCceEEeecCCCCCccccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecCc
Q psy1131 87 MFELVRRGN-SQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWS 165 (353)
Q Consensus 87 Lr~lV~nGp-~~~pGA~~v~~~~g~~~~l~~~~~~~~~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~ 165 (353)
+++|+..|. .+.++|+..+... ....|.|+||+.+||+|||||||||||+|||||++++.+++
T Consensus 460 i~~L~~~~~~~nik~ak~~i~~~----------------~~~v~~vle~vi~gd~VLlNRqPTLHRlsIqAf~~~L~~gk 523 (1460)
T PRK14906 460 MKRLVELEYAANIKAAKRAVDRG----------------ASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGK 523 (1460)
T ss_pred HHHHHHhcccccHHHHhhHHhhc----------------CCcceeeeeeeeccceeEeccCcccchhccceeeEEecCCc
Confidence 899999883 3455665543211 12347888999999999999999999999999999999999
Q ss_pred eeeeecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeecccc
Q psy1131 166 TFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKR 236 (353)
Q Consensus 166 t~r~~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~r 236 (353)
||||||++|+||||||||||||+|+|||++|++|++.||++.+|++||++|+|+++++||+++|+|+||..
T Consensus 524 tIrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~ 594 (1460)
T PRK14906 524 AIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTE 594 (1460)
T ss_pred eEEecccccCccccCCcCceeeeecCCCHHHHHHHHHHhcchhcEecCCCCCeeEEeeeeeeeeeEEeeec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999963
No 14
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=4.1e-47 Score=430.52 Aligned_cols=196 Identities=22% Similarity=0.302 Sum_probs=167.0
Q ss_pred eccCCCCCCccccCCcEEeeeccccceeEeecCCCccccceeeeeeeeeccccc---------------------ccchH
Q psy1131 28 LRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF---------------------RMNLR 86 (353)
Q Consensus 28 l~~~~~~~~~~l~~g~~verhl~d~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf---------------------~~N~~ 86 (353)
|-.+.+++......+.+..+.|.| .|++|+|+||+|||||||++++|+|+ ..++.
T Consensus 1695 l~DN~~~~~~~~~~~~rplKsls~----~LkGK~GRFRqNLlGKRVDySgRSVI~pdP~L~l~e~GvP~~mA~eL~~P~~ 1770 (2890)
T PRK09603 1695 LFDNGRSTNAVKGANKRPLKSLSE----IIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHL 1770 (2890)
T ss_pred HhccccccccccCCCCCcchhHHH----HhcCCCCccccccccccccCcCCceEeCCCCcccccccChHHHHHHhCChHH
Confidence 444555555556666677777755 99999999999999999999999983 34568
Q ss_pred HHHHHHhCCCCC-CCceEEEeCCCceEEeecCCCCCccccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecCc
Q psy1131 87 MFELVRRGNSQY-PGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWS 165 (353)
Q Consensus 87 Lr~lV~nGp~~~-pGA~~v~~~~g~~~~l~~~~~~~~~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~ 165 (353)
+++|+.+|+... ..|+.++. ......|.|+||+.+||+|||||||||||+|||||++++++|+
T Consensus 1771 i~~L~~~G~~~~lk~ak~~i~----------------~~~~~v~~vlr~vi~gd~VLlNRqPTLHR~sIqAf~~~l~~gk 1834 (2890)
T PRK09603 1771 LSKLEERGYATTLKQAKRMIE----------------QKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGK 1834 (2890)
T ss_pred HHHHHHcCCccCHHHHHHHHH----------------hccCccEEEEEeeecCCeEEecCCCccccccceeeeEEEecCc
Confidence 999999997422 23332211 1123457899999999999999999999999999999999999
Q ss_pred eeeeecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccceeeccc
Q psy1131 166 TFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKV 243 (353)
Q Consensus 166 t~r~~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD~F~~ke 243 (353)
||||||+||+||||||||||||+|+|||++|++||+.||++.+|++||++|+|+++++||+++|+|+||.++.++..+
T Consensus 1835 tIrLhplvC~~fNADFDGDqMnvHvPqS~eA~aEa~~LM~s~~nilsP~~G~Pi~~p~QD~vlG~y~LT~~~~~~~~~ 1912 (2890)
T PRK09603 1835 AIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGE 1912 (2890)
T ss_pred eEEeccccCCcccCCCCCceeEEeecCCHHHHHHHHHHhcccceEEEcCCCceeEEeecceeeeeEEeeccccCCCCc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999998765543
No 15
>PF00623 RNA_pol_Rpb1_2: RNA polymerase Rpb1, domain 2; InterPro: IPR000722 RNA polymerases catalyse the DNA dependent polymerisation of RNA from DNA, using the four ribonucleoside triphosphates as substrates. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Eukaryotic RNA polymerase I is essentially used to transcribe ribosomal RNA units, polymerase II is used for mRNA precursors, and III is used to transcribe 5S and tRNA genes. Each class of RNA polymerase is assembled from nine to fourteen different polypeptides. Members of the family include the largest subunit from eukaryotes; the gamma subunit from Cyanobacteria; the beta' subunit from bacteria; the A' subunit from archaea; and the B'' subunit from chloroplast RNA polymerases.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_M 2PMZ_Q 3HKZ_I 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N ....
Probab=100.00 E-value=2.4e-46 Score=333.98 Aligned_cols=125 Identities=52% Similarity=0.870 Sum_probs=107.2
Q ss_pred ccch-HHHHHHHhCCCCCCCceEEEeCCCceEEeecCCCCCccccccccEEeeeeccCCeeeEecCCCccccceeeeeEE
Q psy1131 82 RMNL-RMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVR 160 (353)
Q Consensus 82 ~~N~-~Lr~lV~nGp~~~pGA~~v~~~~g~~~~l~~~~~~~~~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~ 160 (353)
.+|. +|+++|.|||+.||||+|+.+.+|.++.++.........++.|++|+||+.+||+||+||||||||+|||||+++
T Consensus 41 ~~N~~~l~~~v~ng~~~~pga~~i~~~~~~~~~l~~~~~~~~~~l~~~~~v~r~l~~gd~vl~nRqPtLh~~s~~a~~~~ 120 (166)
T PF00623_consen 41 PFNIEKLRKLVINGPDKYPGANYIKRSNGNKISLRYKKFKISKKLRIGDIVERHLCDGDIVLLNRQPTLHRMSIMAHKVR 120 (166)
T ss_dssp TTTHHHHHHHHHHTTTSSSSEEEEESTTCHCCCTTSSSSCCCHHHHTT-EEEEEHTTT-EEEEEESS-SSGGGEEEEEEE
T ss_pred HHHHHHHHHHHhcCcccchhhhhhhcccCcceeeeeccccccceecchhhHHHhhhcCceeEEeccchhccceeeeeeee
Confidence 3454 899999999999999999999889888777654434457889999999999999999999999999999999999
Q ss_pred EecCceeeeecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcC
Q psy1131 161 VLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVT 206 (353)
Q Consensus 161 ~~~~~t~r~~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~ 206 (353)
+++++|||+||++|+||||||||||||+|+||+++|++|+.+||++
T Consensus 121 ~~~~~t~~~~~~~c~~~NADFDGDem~i~~p~~~~a~~E~~~L~~~ 166 (166)
T PF00623_consen 121 VLPGKTIRINPLVCSPFNADFDGDEMNIHLPQSYEARAEAKELMNV 166 (166)
T ss_dssp EESSSSEEEEGGGHHHHT--TSS-EEEEE--SSHHHHHHHHHHCBT
T ss_pred eecccEEEeeccchhhhhccCCcceEEEEecCCHHHHHHHHHHhcC
Confidence 9999999999999999999999999999999999999999999964
No 16
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=1.5e-44 Score=408.60 Aligned_cols=194 Identities=21% Similarity=0.318 Sum_probs=152.5
Q ss_pred eccCCCCCCccccCCcEE-eeeccccceeEeecCCCccccceeeeeeeeeccccc---------------------ccch
Q psy1131 28 LRFHPKPSDLHLQCGYKV-ERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF---------------------RMNL 85 (353)
Q Consensus 28 l~~~~~~~~~~l~~g~~v-erhl~d~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf---------------------~~N~ 85 (353)
|-.+.+++......+.+. .+.| .+.|.+|+|+||+|+|||||++++|+|+ ...+
T Consensus 1738 l~Dn~~~g~~~~~~~~r~~lksl----s~~LkGK~GRFR~NLlGKRVDySgRSVI~pdP~L~l~evGlP~~mA~eL~~Pf 1813 (2836)
T PRK14844 1738 LFDNSRRNALVNKAGAVGYKKSI----SDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPF 1813 (2836)
T ss_pred HhcCCCCCCCccCCCCCCccccH----HHHhcCCCCcccccccccccccCCCceEeCCCCcccceeeCCHHHHHhcccHH
Confidence 344444444444334332 3555 4599999999999999999999999883 2223
Q ss_pred HHHHHHHhCCC-CCCCceEEEeCCCceEEeecCCCCCccccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecC
Q psy1131 86 RMFELVRRGNS-QYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPW 164 (353)
Q Consensus 86 ~Lr~lV~nGp~-~~pGA~~v~~~~g~~~~l~~~~~~~~~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~ 164 (353)
.+.+|...|.. ..+.|+.+++.. ....++++ +|+.+||+|||||||||||+|||||+++++++
T Consensus 1814 ~i~~L~~~~~~~~i~~a~~li~~~---------------~~~v~dil-e~vi~gd~VLlNRqPTLHR~sIqAf~~~l~~g 1877 (2836)
T PRK14844 1814 VYSKLKMYGMAPTIKFASKLIRAE---------------KPEVWDML-EEVIKEHPVLLNRAPTLHRLGIQAFEPILIEG 1877 (2836)
T ss_pred HHHHHHHcCcccchHHHHHHHHhh---------------CCcceEEE-EEEecCCEEEecCCCccccccccceeeEeecC
Confidence 45555555532 112333322211 12234444 55567999999999999999999999999999
Q ss_pred ceeeeecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccceeec
Q psy1131 165 STFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 241 (353)
Q Consensus 165 ~t~r~~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD~F~~ 241 (353)
+||||||+||+||||||||||||+|+|||++|++|++.||++.+|++||++|+|+++++||+++|+|+||.++.+..
T Consensus 1878 ktirlhp~vC~~fNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pii~~~QD~ilG~y~LT~~~~~~~ 1954 (2836)
T PRK14844 1878 KAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLTLQEPKED 1954 (2836)
T ss_pred ceEEecccCCCcccCCCCCceeeeecCCcHHHHHHHHHHhCCcccEEecCCCceeEeehhhhhhhhhhhcccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999987654
No 17
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=100.00 E-value=3.2e-40 Score=353.06 Aligned_cols=183 Identities=33% Similarity=0.462 Sum_probs=160.9
Q ss_pred EEeeeccccceeEeecCCCccccceeeeeeeeeccccc------ccc---------------hHHHHHHHhCCCCCCCce
Q psy1131 44 KVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF------RMN---------------LRMFELVRRGNSQYPGAK 102 (353)
Q Consensus 44 ~verhl~d~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf------~~N---------------~~Lr~lV~nGp~~~pGA~ 102 (353)
+..+.|. |.|.+|+|+||.|+|||||+++.++|+ ++| +.+.+++..|-.. ||+
T Consensus 265 rPlksl~----~~LkgK~GrFR~nL~GKRVd~SgRsVI~~~P~l~~~e~GvP~~~A~~L~~p~~v~~~~~~~~~~--~a~ 338 (808)
T COG0086 265 RPLKSLS----QRLKGKQGRFRQNLLGKRVDYSGRSVISVGPNLKLNQCGVPKKMALELFKPFVVTELNIEGLRT--GAK 338 (808)
T ss_pred CccccHH----HHhcCCCceeeccccccccCCCCceeecCCCCccccccCCHHHHHHHhccCEEEEehhhhhhhc--CCc
Confidence 5566664 499999999999999999999999884 233 3445555555433 899
Q ss_pred EEEeCCCceEEeecCCCCCccccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEec-CceeeeecccCCCCCCCC
Q psy1131 103 YIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLP-WSTFRMNLSCTSPYNADF 181 (353)
Q Consensus 103 ~v~~~~g~~~~l~~~~~~~~~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~-~~t~r~~~~~c~~~NADF 181 (353)
|+++..+.+ +..+|.|+||+.+||+|+|||||||||+|||+|..++++ ++|||+|+++|.||||||
T Consensus 339 ~~~~~~~~~-------------~~~~w~Vl~evi~gd~Vl~NR~PtLHrlsImq~~e~vl~~gkt~rLh~lVc~~yNADF 405 (808)
T COG0086 339 YAKRMVERR-------------LPEVWDVLREVIDGDPVLLNRAPTLHRLSIMQAFEPVLPEGKAIRLHPLVCEAYNADF 405 (808)
T ss_pred eEEeccccc-------------ccccchHHHHHhcCCccccccCChHHHHHHHhhceeeccccceeecchhhcccccccc
Confidence 998766553 557899999999999999999999999999999999998 899999999999999999
Q ss_pred CCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccceeeccccc
Q psy1131 182 DGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVER 245 (353)
Q Consensus 182 DGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD~F~~kee~ 245 (353)
||||||+|+||+.+|+||+..+|++..|++||++|+|+++.+||++.+.|+||..|.++...+.
T Consensus 406 DGDeM~~Hvp~s~ea~AEa~~lm~tq~nilsP~~Ggpiv~~~qD~v~g~ylLt~~d~~~~~~~~ 469 (808)
T COG0086 406 DGDEMAVHVPASGEAAAEARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDAKLPSTPV 469 (808)
T ss_pred CchhhhccccchHHHHHHHHHhhccccccccCCCCCceEeecceEEeccEEEEEecccCCCCcc
Confidence 9999999999999999999999999999999999999999999999999999999886665544
No 18
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=100.00 E-value=1.1e-38 Score=354.17 Aligned_cols=202 Identities=35% Similarity=0.600 Sum_probs=151.5
Q ss_pred CCeeeEecCCCccccceeeeeEEEecCceeeeecccCCCCCCCCCCCce--------eeeccCCH--hhHHHHHHHhcCC
Q psy1131 138 GDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEM--------NLHVPQSM--ETRAEVENIHVTP 207 (353)
Q Consensus 138 gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~r~~~~~c~~~NADFDGDem--------nlh~Pqs~--~a~aE~~~l~~~~ 207 (353)
|....+...-.+.|.+|||.||.+... +|.+| +...+=||+ +|++|+.. ....++++++...
T Consensus 309 ~i~qrLkgKeGrfR~nlmGKRVdfSaR-------tVIsp-DP~L~i~EVGvP~~iA~~LT~Pe~Vt~~Ni~~l~~lv~nG 380 (1321)
T PRK14977 309 SLFQRLKGKEGRFRGNLIGKRVDFSAR-------TVISP-DPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVING 380 (1321)
T ss_pred HHHHHhccccccccccccccccccccc-------eeEeC-CCCcccccccCHHHHHHhCCCCEEEchhhHHHHHHHHHcC
Confidence 555667778899999999999886654 23232 233333443 56666553 3445555555332
Q ss_pred ceeeecCCCCceeeeeeee---eeeeeeccccc-----------eeeccccccccCcceeeecCCcccccccccceeeEE
Q psy1131 208 RQIITPQNNRPVMGIVQDT---LTAVRKMTKRD-----------VFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRV 273 (353)
Q Consensus 208 ~~~lsP~~g~Pi~gliQD~---i~g~~~LT~rD-----------~F~~kee~~l~d~d~vI~nrqPtIhk~s~~~~~~~i 273 (353)
. +..|....+.+. .........+. ...+..++|+.|||.|++||||||||+|+|||++++
T Consensus 381 ~------~~~pGA~~i~~~~g~~~~l~~~~~~~~~~~~~~a~~L~~g~iV~Rhl~dGD~VL~NRQPSLHk~Simah~vkv 454 (1321)
T PRK14977 381 P------DEFPGANAIRKGDGTKIRLDFLEDKGKDALREAAEQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKV 454 (1321)
T ss_pred C------cccCCcceEEcCCCceeeehhhhhccchhHHHHHHhcccCcEEEEEeecCcEEEeccCCccccccceEEEEEE
Confidence 1 112222222211 00010011100 123455788999999999999999999999999999
Q ss_pred ecCceeeccccccCCCCCCCCCCeeEEeecCChhHHHHHHHHhcCCCeeecCCCCCceEEeehheeeeeeeecccccccC
Q psy1131 274 LPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 353 (353)
Q Consensus 274 ~~~~ti~~~~~~~~~~naDFDGDem~~~~p~s~~a~~E~~~l~~~~~~~~s~~~g~p~~~~~QD~~~g~~~lt~~d~f~~ 353 (353)
++|+|||+|+++|+||||||||||||+|+|||++|+||+.+||.+++|++||++|+|+++++||+++|+|+||.+|+||+
T Consensus 455 l~~kT~Rln~~vC~pyNADFDGDEMNlHvPQS~eArAEa~~Lm~v~~niisP~~G~Pi~gliQD~l~g~~lLT~~d~fl~ 534 (1321)
T PRK14977 455 LPGATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFD 534 (1321)
T ss_pred ecCceEEecccccCcccCCcccceeeeecCCCHHHHHHHHHHHhhhhcEecCCCCCeeEEeehhhhhhhhhhccCcccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999986
No 19
>TIGR02390 RNA_pol_rpoA1 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=6.1e-38 Score=339.21 Aligned_cols=202 Identities=35% Similarity=0.567 Sum_probs=149.2
Q ss_pred CCeeeEecCCCccccceeeeeEEEecCceeeeecccCCCCCCCCCCCce--------eeeccCCH--hhHHHHHHHhcCC
Q psy1131 138 GDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEM--------NLHVPQSM--ETRAEVENIHVTP 207 (353)
Q Consensus 138 gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~r~~~~~c~~~NADFDGDem--------nlh~Pqs~--~a~aE~~~l~~~~ 207 (353)
|..-.+...-.+.|.+|||.||.+... +|.+| ++..+=||+ +|.+|+.. ....+++.+....
T Consensus 295 ~i~~~l~gK~G~~R~nl~GKRvd~s~R-------sVI~p-dp~l~~~evGvP~~~A~~Lt~pe~Vt~~N~~~l~~lv~ng 366 (868)
T TIGR02390 295 TLAQRLKGKEGRFRGNLSGKRVNFSAR-------TVISP-DPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNG 366 (868)
T ss_pred hhHhhhcccccccccccccccccccCC-------ceeeC-CCCCcCCeeeCcHHHHHhCCCCeEEehhhHHHHHHHHHcC
Confidence 455567778889999999999886654 23222 223333444 45555443 3344555555332
Q ss_pred ceeeecCCCCceeeeeeeeeeeeeeccc--cc------eeeccccccccCcceeeecCCcccccccccceeeEEecCcee
Q psy1131 208 RQIITPQNNRPVMGIVQDTLTAVRKMTK--RD------VFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF 279 (353)
Q Consensus 208 ~~~lsP~~g~Pi~gliQD~i~g~~~LT~--rD------~F~~kee~~l~d~d~vI~nrqPtIhk~s~~~~~~~i~~~~ti 279 (353)
. +..|....+.+.--..+.+.. +. ...+..++++.++|.|++||||||||+|+|||++++++|+||
T Consensus 367 ~------~~~pga~~i~~~~g~~~~l~~~~~~~~~~~l~~g~~v~rhl~dgd~vl~NRqPsLHr~si~a~~~~v~~~~t~ 440 (868)
T TIGR02390 367 P------DSWPGANYVIRPDGRRIKIRDENKEELAERLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTF 440 (868)
T ss_pred C------ccCCCceEEEcCCCcEEechhhhHHHHHhhcccCCEEEEehhcCccceeccCCccccccceeEEEEEecCceE
Confidence 1 111222222211000000110 00 112455788999999999999999999999999999999999
Q ss_pred eccccccCCCCCCCCCCeeEEeecCChhHHHHHHHHhcCCCeeecCCCCCceEEeehheeeeeeeecccccccC
Q psy1131 280 RMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 353 (353)
Q Consensus 280 ~~~~~~~~~~naDFDGDem~~~~p~s~~a~~E~~~l~~~~~~~~s~~~g~p~~~~~QD~~~g~~~lt~~d~f~~ 353 (353)
|+|+++|+||||||||||||+|+|||++|+||+++||.+.+|++||++|+|+++++||+++|+|+||.+|+||+
T Consensus 441 r~n~~~c~~~NADFDGDeMn~h~Pqs~~a~aEa~~Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~~LT~~d~f~~ 514 (868)
T TIGR02390 441 RLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFT 514 (868)
T ss_pred eeccccCCccccCcccceeeEecCCCHHHHHHHHHHhhchhceecCCCCCeeEEeehhhhhheeeeeeccccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999986
No 20
>KOG0261|consensus
Probab=100.00 E-value=2.4e-38 Score=330.53 Aligned_cols=194 Identities=41% Similarity=0.683 Sum_probs=151.7
Q ss_pred CccccceeeeeEEEecCceeeeecccCCCCCCCCCCCcee--------eeccCCHhhHHHHHHHhcCCceeeecCCCCce
Q psy1131 148 TLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMN--------LHVPQSMETRAEVENIHVTPRQIITPQNNRPV 219 (353)
Q Consensus 148 tLhr~s~ma~~~~~~~~~t~r~~~~~c~~~NADFDGDemn--------lh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi 219 (353)
.=.|.++-|.||.+... .|.+| +....-||+. +.+|+... ++..+.|- ..+...-+..|.
T Consensus 348 GRFRgNLSGKRVDFSGR-------TVISP-DPNL~IdeVgVP~rvAkiLTfpE~Vt-~~Ni~klr---~lV~NGP~vhPG 415 (1386)
T KOG0261|consen 348 GRFRGNLSGKRVDFSGR-------TVISP-DPNLRIDEVGVPIRVAKILTFPERVT-RANIRKLR---QLVRNGPNVHPG 415 (1386)
T ss_pred CceeccccCceeeccCc-------eeeCC-CCCcceeeccchHHHHHHhcchhhcc-HHHHHHHH---HHHhcCCCCCCC
Confidence 34566666776666543 23333 3333345543 34555442 33333332 334445566888
Q ss_pred eeeeeeeeeeeeeccc---cce------eeccccccccCcceeeecCCcccccccccceeeEEecCceeeccccccCCCC
Q psy1131 220 MGIVQDTLTAVRKMTK---RDV------FLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYN 290 (353)
Q Consensus 220 ~gliQD~i~g~~~LT~---rD~------F~~kee~~l~d~d~vI~nrqPtIhk~s~~~~~~~i~~~~ti~~~~~~~~~~n 290 (353)
..++++.-.+.+.+-. |+. .-+..|+|+.|+|.|+|||||+|||+|+|+|+++++||+|||+|.|+|.|||
T Consensus 416 ANyv~~r~~~~kr~L~yg~R~kiA~eLk~GdvVERHL~DgDvVLFNRQPSLHkmSIM~H~akV~p~RTfRFNEcvCtPYN 495 (1386)
T KOG0261|consen 416 ANYVVQRGEGFKRFLKYGNRDKIADELKIGDVVERHLMDGDVVLFNRQPSLHKMSIMSHRAKVMPWRTFRFNECVCTPYN 495 (1386)
T ss_pred cchhhhcccchhhHhhcCcHHHHHHhhccchHHHhhcccCCEEEEcCCchHHHHHHHHHHhhcccCceeeccccccCCcC
Confidence 8888877666655443 221 2344578999999999999999999999999999999999999999999999
Q ss_pred CCCCCCeeEEeecCChhHHHHHHHHhcCCCeeecCCCCCceEEeehheeeeeeeecccccccC
Q psy1131 291 ADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 353 (353)
Q Consensus 291 aDFDGDem~~~~p~s~~a~~E~~~l~~~~~~~~s~~~g~p~~~~~QD~~~g~~~lt~~d~f~~ 353 (353)
|||||||||+|+||++||+|||.+||.+++|+++|++|+|+++.+||+++|+|+||.||+|||
T Consensus 496 ADFDGDEMNlHvPQTEEAraEA~~LMgvknNlvTPr~GEpiiAAtQDFiTg~YLlt~KDtF~d 558 (1386)
T KOG0261|consen 496 ADFDGDEMNLHVPQTEEARAEALVLMGVKNNLVTPRNGEPIIAATQDFITGGYLLTHKDTFLD 558 (1386)
T ss_pred CCCCcccccccCCchHHHHHHHHHHhccccccccCCCCCceeehhhhhhhcceeeeccccccc
Confidence 999999999999999999999999999999999999999999999999999999999999997
No 21
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=100.00 E-value=5.3e-38 Score=325.86 Aligned_cols=184 Identities=20% Similarity=0.370 Sum_probs=145.3
Q ss_pred eeEecCCCccccceeeeeEE------EecCceeeeecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecC
Q psy1131 141 VIFNRQPTLHKMSMMGHRVR------VLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQ 214 (353)
Q Consensus 141 vl~nRqPtLhr~s~ma~~~~------~~~~~t~r~~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~ 214 (353)
-.+...-...|.++||.||. |.+++.+.+|.|- -| .+|++.+.+.+. ++.|.. +
T Consensus 358 ~~LkGK~GrFR~NLlGKRVDySgRSVIvpdP~L~l~e~G-lP-------~~mA~eL~~P~~----i~~Li~--~------ 417 (663)
T CHL00018 358 DVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCG-LP-------REIAIELFQPFV----IRGLIR--Q------ 417 (663)
T ss_pred ccccCcCccccccccccccccCCCceecCCCcccccccC-Ch-------HHHHHHcCcHHH----HHHHHh--c------
Confidence 34555668888888888876 5566777777733 44 455444333322 122211 1
Q ss_pred CCCceeeeeeeeeeeeeeccccceeeccccccccCcceeeecCCcccccccccceeeEEecCceeeccccccCCCCCCCC
Q psy1131 215 NNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFD 294 (353)
Q Consensus 215 ~g~Pi~gliQD~i~g~~~LT~rD~F~~kee~~l~d~d~vI~nrqPtIhk~s~~~~~~~i~~~~ti~~~~~~~~~~naDFD 294 (353)
++......|.+++..++...++..+++.++|.|++|||||||++|+|||++++++++||++||++|+|||||||
T Consensus 418 ------~~~~~~~~Ak~~i~~~~~~~~~Vlr~v~~gd~VLlNRqPTLHR~sIqAf~~~L~~gktIrLhplvC~~fNADFD 491 (663)
T CHL00018 418 ------HLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFD 491 (663)
T ss_pred ------CccccHHHHHHHHHhcCCcccEeeeehhcCceeeecCCCcccccccceeeEEecCCCeEEeCcccCCcccCCcc
Confidence 11222223344455555566677788999999999999999999999999999999999999999999999999
Q ss_pred CCeeEEeecCChhHHHHHHHHhcCCCeeecCCCCCceEEeehheeeeeeeeccccc
Q psy1131 295 GDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDV 350 (353)
Q Consensus 295 GDem~~~~p~s~~a~~E~~~l~~~~~~~~s~~~g~p~~~~~QD~~~g~~~lt~~d~ 350 (353)
|||||+|+|||++|+|||+.||.+.+|++||++|+|+++++||+++|+|+||.+|.
T Consensus 492 GDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~ 547 (663)
T CHL00018 492 GDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNR 547 (663)
T ss_pred CcEEEEecCCCHHHHHHHHHHhcCccceeEcCCCceeEeechhhhhhhheecccCC
Confidence 99999999999999999999999999999999999999999999999999999985
No 22
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated
Probab=100.00 E-value=6.2e-38 Score=339.86 Aligned_cols=203 Identities=35% Similarity=0.557 Sum_probs=149.9
Q ss_pred cCCeeeEecCCCccccceeeeeEEEecCceeeeecccCCCCCCCCCCCce--------eeeccCCH--hhHHHHHHHhcC
Q psy1131 137 DGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEM--------NLHVPQSM--ETRAEVENIHVT 206 (353)
Q Consensus 137 ~gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~r~~~~~c~~~NADFDGDem--------nlh~Pqs~--~a~aE~~~l~~~ 206 (353)
.|..-.+...-.+-|.+|||.||.+... +|.+| +...+=||+ +|.+|+.. ....+++.+...
T Consensus 298 ~~i~~~l~gK~G~fR~nl~GKRvd~s~R-------sVI~p-dp~l~~~evGvP~~~A~~Lt~pe~v~~~N~~~l~~~v~n 369 (882)
T PRK08566 298 KTLAQRLKGKEGRFRGNLSGKRVNFSAR-------TVISP-DPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLN 369 (882)
T ss_pred cchHHhcccCCCccccccccccccCcCC-------ceeeC-CCCCcCCeeeCcHHHHHhCCCCeEEchhhHHHHHHHHHc
Confidence 3555667778889999999999987665 23333 333344554 44555443 233344444432
Q ss_pred CceeeecCCCCceeeeeeeeeeeeeeccc--c------ceeeccccccccCcceeeecCCcccccccccceeeEEecCce
Q psy1131 207 PRQIITPQNNRPVMGIVQDTLTAVRKMTK--R------DVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWST 278 (353)
Q Consensus 207 ~~~~lsP~~g~Pi~gliQD~i~g~~~LT~--r------D~F~~kee~~l~d~d~vI~nrqPtIhk~s~~~~~~~i~~~~t 278 (353)
.. +..|....+.+.--....+.. + -...+..++++.++|.+++||||||||+|+|||++++++|+|
T Consensus 370 g~------~~~pga~~i~~~~g~~~~l~~~~~~~~~~~l~~g~~v~Rhl~dgd~vl~NRqPsLHr~si~a~~~~v~~~~t 443 (882)
T PRK08566 370 GP------EKHPGANYVIRPDGRRIKLTDKNKEELAEKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKT 443 (882)
T ss_pred CC------CcCCCceEEEcCCCceeeehhhhHHHHHHhccccceehhhhhcCceeeecCCCcccccccceeEEEEecCce
Confidence 11 111212222110000000110 0 012345578899999999999999999999999999999999
Q ss_pred eeccccccCCCCCCCCCCeeEEeecCChhHHHHHHHHhcCCCeeecCCCCCceEEeehheeeeeeeecccccccC
Q psy1131 279 FRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 353 (353)
Q Consensus 279 i~~~~~~~~~~naDFDGDem~~~~p~s~~a~~E~~~l~~~~~~~~s~~~g~p~~~~~QD~~~g~~~lt~~d~f~~ 353 (353)
|++|+++|+||||||||||||+|+|||++|+||+++||.+.+|++||++|+|+++++||+++|+|+||.+|+||+
T Consensus 444 ~r~n~~~c~~~NADFDGDeMn~h~Pqs~~a~aEa~~Lm~~~~~~~sp~~g~pi~~~~QD~l~g~~~lt~~d~f~~ 518 (882)
T PRK08566 444 FRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFT 518 (882)
T ss_pred EeeccccCCCccCCccCcEEEEecCCCHHHHHHHHHHhcchhcEecCCCCCeeEEeehHHHHHHHHHHhccccCC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999985
No 23
>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit. The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.
Probab=100.00 E-value=6e-38 Score=322.58 Aligned_cols=183 Identities=22% Similarity=0.408 Sum_probs=140.1
Q ss_pred eEecCCCccccceeeeeEE------EecCceeeeecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCC
Q psy1131 142 IFNRQPTLHKMSMMGHRVR------VLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQN 215 (353)
Q Consensus 142 l~nRqPtLhr~s~ma~~~~------~~~~~t~r~~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~ 215 (353)
.+...-...|.++||.||. |.+++++.+|.+- -| .+|++-+.+... +..|.. .
T Consensus 331 ~LkGKeGRFR~nLlGKRVDySgRSVI~pdP~L~l~qvG-vP-------~~mA~eLf~Pf~----i~~L~~---------~ 389 (619)
T TIGR02387 331 IIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCG-LP-------KEMAIELFQPFV----IHRLIR---------Q 389 (619)
T ss_pred HhccCCccccccccccccccCCCceecCCCCcccceec-Ch-------HHHHHhcCchHh----HHHHHh---------c
Confidence 3445567778888877776 4556677777633 44 444443333221 111211 1
Q ss_pred CCceeeeeeeeeeeeeeccccceeeccccccccCcceeeecCCcccccccccceeeEEecCceeeccccccCCCCCCCCC
Q psy1131 216 NRPVMGIVQDTLTAVRKMTKRDVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDG 295 (353)
Q Consensus 216 g~Pi~gliQD~i~g~~~LT~rD~F~~kee~~l~d~d~vI~nrqPtIhk~s~~~~~~~i~~~~ti~~~~~~~~~~naDFDG 295 (353)
| ++.....|.+++...+...+...+++.++|.|++|||||||++|+|||++.+++++||++||++|+||||||||
T Consensus 390 g-----~~~~i~~ak~~i~~~~~~v~~Vlr~v~~gd~VLlNRqPTLHR~sIqAf~~~l~~~ktirlhplvC~~fNADFDG 464 (619)
T TIGR02387 390 G-----IVNNIKAAKKLIQRADDEIWSVLQEVITGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDG 464 (619)
T ss_pred C-----cccchHHHHHHHHhcCChhHHHHHHHhcCCEEEecCCCccchhcceeeeeEEecCCeEEECcccCCcccCCCCC
Confidence 1 11111123333444444455667788999999999999999999999999999999999999999999999999
Q ss_pred CeeEEeecCChhHHHHHHHHhcCCCeeecCCCCCceEEeehheeeeeeeeccccc
Q psy1131 296 DEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDV 350 (353)
Q Consensus 296 Dem~~~~p~s~~a~~E~~~l~~~~~~~~s~~~g~p~~~~~QD~~~g~~~lt~~d~ 350 (353)
||||+|+|||.+|+|||+.||.+.+|++||++|+|+++++||+++|+|+||.++.
T Consensus 465 DeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~llg~y~LT~~~~ 519 (619)
T TIGR02387 465 DQMAVHVPLSLEAQTEARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALNP 519 (619)
T ss_pred ceeeeecCCCHHHHHHHHHHhhchhcEEecCCCceeEeechhhhhhhheeecccc
Confidence 9999999999999999999999999999999999999999999999999999873
No 24
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=100.00 E-value=9.2e-38 Score=321.57 Aligned_cols=184 Identities=24% Similarity=0.426 Sum_probs=140.3
Q ss_pred eeEecCCCccccceeeeeEEE------ecCceeeeecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecC
Q psy1131 141 VIFNRQPTLHKMSMMGHRVRV------LPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQ 214 (353)
Q Consensus 141 vl~nRqPtLhr~s~ma~~~~~------~~~~t~r~~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~ 214 (353)
-.+...-...|.++||.||.+ .+++.+.+|.+- -| .+|++.+.+... +..|. .
T Consensus 337 ~~LkGKeGRFR~NLlGKRVDySgRSVIspdP~L~l~e~G-vP-------~~mA~eL~~Pf~----i~~L~---------~ 395 (627)
T PRK02625 337 DIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCG-LP-------KEMAIELFQPFV----IHRLI---------R 395 (627)
T ss_pred HHhccCCccccccccccccccCCCceEeCCCCccccccc-Ch-------HHHHHhcCcHHh----HHHHH---------H
Confidence 345556678888899888764 455666666632 34 344333322221 11111 0
Q ss_pred CCCceeeeeeeeeeeeeeccccceeeccccccccCcceeeecCCcccccccccceeeEEecCceeeccccccCCCCCCCC
Q psy1131 215 NNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFD 294 (353)
Q Consensus 215 ~g~Pi~gliQD~i~g~~~LT~rD~F~~kee~~l~d~d~vI~nrqPtIhk~s~~~~~~~i~~~~ti~~~~~~~~~~naDFD 294 (353)
+ |++.....|.+++...+...+....++.++|.+++|||||||++|+|||++++++++||++||++|+|||||||
T Consensus 396 ~-----g~~~~i~~ak~~i~~~~~~~~~Vlr~v~~gd~VLlNRqPTLHR~sIqAf~~~l~~~ktirlhplvC~~fNADFD 470 (627)
T PRK02625 396 Q-----GIVNNIKAAKKLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFD 470 (627)
T ss_pred c-----CchhhHHHHHHHHHhcCCcccEEEEEeecCcEEEecCCCccccccceeEeeEEcCCCeEEeccccCCcccCCcC
Confidence 1 11111122333333344444555668889999999999999999999999999999999999999999999999
Q ss_pred CCeeEEeecCChhHHHHHHHHhcCCCeeecCCCCCceEEeehheeeeeeeeccccc
Q psy1131 295 GDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDV 350 (353)
Q Consensus 295 GDem~~~~p~s~~a~~E~~~l~~~~~~~~s~~~g~p~~~~~QD~~~g~~~lt~~d~ 350 (353)
|||||+|+|||++|+||++.||.+.+|++||++|+|+++++||+++|+|+||.+|.
T Consensus 471 GDeMnvHvPqS~~A~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~llG~y~LT~~~~ 526 (627)
T PRK02625 471 GDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENP 526 (627)
T ss_pred CCeEEEecCCCHHHHHHHHHHhcCccceEEcCCCceeEeechhhhhheeeeeccCc
Confidence 99999999999999999999999999999999999999999999999999999984
No 25
>smart00663 RPOLA_N RNA polymerase I subunit A N-terminus.
Probab=100.00 E-value=2.5e-37 Score=297.98 Aligned_cols=188 Identities=37% Similarity=0.588 Sum_probs=138.2
Q ss_pred cCCeeeEecCCCccccceeeeeEEEecCceeeeecccCCCCCCCCCCCce--------eeeccCCH--hhHHHHHHHhcC
Q psy1131 137 DGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEM--------NLHVPQSM--ETRAEVENIHVT 206 (353)
Q Consensus 137 ~gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~r~~~~~c~~~NADFDGDem--------nlh~Pqs~--~a~aE~~~l~~~ 206 (353)
.|..-.+.....+-|.+|||.|+.+... +|.+| +.+.+=||+ .+.+|... .....++.+...
T Consensus 90 ~~i~~~l~gK~G~~R~nllGKRvd~s~R-------sVI~p-dP~l~~~evgiP~~~A~~Lt~pe~v~~~n~~~l~~lv~n 161 (295)
T smart00663 90 KSLSQRLKGKEGRFRQNLLGKRVDFSAR-------SVITP-DPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLVRN 161 (295)
T ss_pred ccccccccCcCCccccccccccccccCc-------eEEeC-CCCcceeEeeCCHHHHHhCCcCEEEhHHHHHHHHHHHhc
Confidence 4555666778899999999998876664 33333 333344554 33333332 223333333322
Q ss_pred CceeeecCCCCceeeeeeeeeeeeeecc--------ccceeeccccccccCcceeeecCCcccccccccceeeEEecCce
Q psy1131 207 PRQIITPQNNRPVMGIVQDTLTAVRKMT--------KRDVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWST 278 (353)
Q Consensus 207 ~~~~lsP~~g~Pi~gliQD~i~g~~~LT--------~rD~F~~kee~~l~d~d~vI~nrqPtIhk~s~~~~~~~i~~~~t 278 (353)
|.|....+.+-. .+.+. ..-...+..++++.++|.+++||||||||+|+|||++++++++|
T Consensus 162 ---------g~pga~~i~~g~--~~~l~~~~~~~~~~~l~~g~~v~r~l~dgd~Vl~NRqPsLHr~si~a~~v~v~~~~t 230 (295)
T smart00663 162 ---------GPNGAKYIIRGK--KTNLKLAKRSKIAKHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKT 230 (295)
T ss_pred ---------CCCCceEEEeCc--EEEchhhhhHHHHhcCccccEeheehhcCCEEEEecCCccccccceeEEEEEecCce
Confidence 223333333200 01111 00112334567889999999999999999999999999999999
Q ss_pred eeccccccCCCCCCCCCCeeEEeecCChhHHHHHHHHhcCCCeeecCCCCCceEEeehheeeeee
Q psy1131 279 FRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVR 343 (353)
Q Consensus 279 i~~~~~~~~~~naDFDGDem~~~~p~s~~a~~E~~~l~~~~~~~~s~~~g~p~~~~~QD~~~g~~ 343 (353)
|++|++||+||||||||||||+|+|||++|++|+.+||.+.+|++||++|+|+++++||+++|+|
T Consensus 231 ir~n~~~c~~fNADFDGDeMnih~pqs~~a~aEa~~Lm~~~~~~~sp~~g~p~~~~~QD~l~g~~ 295 (295)
T smart00663 231 IRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295 (295)
T ss_pred EEecCccCCcccCCcCCCEEEEecCCCHHHHHHHHHHhhhhhccccCCCCCeeEeeecceeeecC
Confidence 99999999999999999999999999999999999999999999999999999999999999987
No 26
>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=100.00 E-value=1.9e-36 Score=329.84 Aligned_cols=112 Identities=27% Similarity=0.474 Sum_probs=105.2
Q ss_pred eeeccccccccCcceeeecCCcccccccccceeeEEecCceeeccccccCCCCCCCCCCeeEEeecCChhHHHHHHHHhc
Q psy1131 238 VFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHV 317 (353)
Q Consensus 238 ~F~~kee~~l~d~d~vI~nrqPtIhk~s~~~~~~~i~~~~ti~~~~~~~~~~naDFDGDem~~~~p~s~~a~~E~~~l~~ 317 (353)
..++....++.++++|++|||||||++|+|||++++++|+||++||++|+||||||||||||+|+|||++|++|++.||+
T Consensus 388 ~~v~~vl~~vi~~d~VLlNRqPTLHRlsIqAf~~~l~~gktirlhplvC~~fNADFDGDeMnvHvPqS~eA~aEa~~Lm~ 467 (1140)
T TIGR02386 388 PEVWDVLEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALML 467 (1140)
T ss_pred CccceEEEEccCCcEEEecCCCcccccccceeEEEEecCceEEEcccccCcccCCCCcceeEeecCCCHHHHHHHHHHhC
Confidence 33344445566789999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCeeecCCCCCceEEeehheeeeeeeecccc
Q psy1131 318 TPRQIITPQNNRPVMGIVQDTLTAVRKMTKRD 349 (353)
Q Consensus 318 ~~~~~~s~~~g~p~~~~~QD~~~g~~~lt~~d 349 (353)
+.+|++||++|+|+++++||+++|+|+||.++
T Consensus 468 ~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~ 499 (1140)
T TIGR02386 468 ASNNILNPKDGKPIVTPSQDMVLGLYYLTTEK 499 (1140)
T ss_pred CcccEecCCCCCceEEeechhhheeeEeeecc
Confidence 99999999999999999999999999999996
No 27
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=3.9e-36 Score=327.76 Aligned_cols=183 Identities=21% Similarity=0.394 Sum_probs=135.6
Q ss_pred eeEecCCCccccceeeeeEEE------ecCceeeeecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecC
Q psy1131 141 VIFNRQPTLHKMSMMGHRVRV------LPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQ 214 (353)
Q Consensus 141 vl~nRqPtLhr~s~ma~~~~~------~~~~t~r~~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~ 214 (353)
-.+...-...|.++||.||.+ .+++.+++|.|- -| -+|++-+.+... +++|..
T Consensus 319 ~~LkGK~GrFR~NLlGKRVDySgRSVI~pdP~L~l~e~G-vP-------~~mA~eL~~Pf~----i~~L~~--------- 377 (1156)
T PRK00566 319 DMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCG-LP-------KKMALELFKPFI----MKKLVE--------- 377 (1156)
T ss_pred HhhcCCCccccccccccccCCCCCceEeCCCCccccccc-Ch-------HHHHHHhCcHHH----HHHHHH---------
Confidence 344556678888888887764 455666666633 33 333222222111 122221
Q ss_pred CCCceeeeeeeeeeeeeeccccceeeccccccccCcceeeecCCcccccccccceeeEEecCceeeccccccCCCCCCCC
Q psy1131 215 NNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFD 294 (353)
Q Consensus 215 ~g~Pi~gliQD~i~g~~~LT~rD~F~~kee~~l~d~d~vI~nrqPtIhk~s~~~~~~~i~~~~ti~~~~~~~~~~naDFD 294 (353)
+| .......+.+++...+...+.....+.++|+|++|||||||++|+|||++++++++||++||++|+|||||||
T Consensus 378 ~g-----~~~~ik~ak~~~~~~~~~v~~vle~vi~gd~VLlNRqPTLHR~sIqAf~~~l~~gktirLhplvC~~fNADFD 452 (1156)
T PRK00566 378 RG-----LATTIKSAKKMVEREDPEVWDVLEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFD 452 (1156)
T ss_pred cC-----CccchHhhhhhhhhhcCcceEEEEEecCCCEEEecCCCcccccccceeEEEEecCceEEECccccCccccccc
Confidence 11 1122222222222223233333344568999999999999999999999999999999999999999999999
Q ss_pred CCeeEEeecCChhHHHHHHHHhcCCCeeecCCCCCceEEeehheeeeeeeecccc
Q psy1131 295 GDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRD 349 (353)
Q Consensus 295 GDem~~~~p~s~~a~~E~~~l~~~~~~~~s~~~g~p~~~~~QD~~~g~~~lt~~d 349 (353)
|||||+|+|||.+|++|++.||++.+|++||++|+|+++++||+++|+|+||.+|
T Consensus 453 GDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~ 507 (1156)
T PRK00566 453 GDQMAVHVPLSLEAQAEARVLMLSSNNILSPANGKPIIVPSQDMVLGLYYLTRER 507 (1156)
T ss_pred cceeEEecCCCHHHHHHHHHHhCCcccEEecCCCCeeEEeehhhhhhhheeeccc
Confidence 9999999999999999999999999999999999999999999999999999998
No 28
>KOG0260|consensus
Probab=100.00 E-value=7.6e-36 Score=316.83 Aligned_cols=113 Identities=80% Similarity=1.240 Sum_probs=110.4
Q ss_pred ccccccccCcceeeecCCcccccccccceeeEEecCceeeccccccCCCCCCCCCCeeEEeecCChhHHHHHHHHhcCCC
Q psy1131 241 DKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPR 320 (353)
Q Consensus 241 ~kee~~l~d~d~vI~nrqPtIhk~s~~~~~~~i~~~~ti~~~~~~~~~~naDFDGDem~~~~p~s~~a~~E~~~l~~~~~ 320 (353)
++.++++.|||.|++||||+|||||||||+++|++|+||++|+.||+||||||||||||+|+|||++||||+.+|+++++
T Consensus 422 ~kVeRhl~DGD~VlfNRqPSlHKmSmmahrVrVlp~sTfrLNlsvtsPynADFDGDemnlhvPQS~etkAEl~EL~~vpk 501 (1605)
T KOG0260|consen 422 YKVERHLMDGDVVLFNRQPSLHKMSMMAHRVRVLPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSLETKAELEELAMVPK 501 (1605)
T ss_pred cEEEEeeccCCEEEEcCCCcHHHhhhhhcEEEEccCceEEeCeeecCCccCCCCCceeecccCcchhHHHHHHHHhhhhh
Confidence 45678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeecCCCCCceEEeehheeeeeeeecccccccC
Q psy1131 321 QIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 353 (353)
Q Consensus 321 ~~~s~~~g~p~~~~~QD~~~g~~~lt~~d~f~~ 353 (353)
|||||++|+|++|++||.|+|++++|.||+||+
T Consensus 502 QiispQsnkpvmgivQDTLta~R~~t~Rd~Fl~ 534 (1605)
T KOG0260|consen 502 QIISPQSNKPVMGIVQDTLTAVRKMTKRDVFLN 534 (1605)
T ss_pred hhcCCcCCCcceeeehhhHHHHHHHhhHhhhhc
Confidence 999999999999999999999999999999985
No 29
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=100.00 E-value=4.8e-35 Score=320.45 Aligned_cols=179 Identities=23% Similarity=0.434 Sum_probs=134.2
Q ss_pred eEecCCCccccceeeeeEE------EecCceeeeecccCCCCCCCCCCCce--eeeccCCHhhHHHHHHHhcCCceeeec
Q psy1131 142 IFNRQPTLHKMSMMGHRVR------VLPWSTFRMNLSCTSPYNADFDGDEM--NLHVPQSMETRAEVENIHVTPRQIITP 213 (353)
Q Consensus 142 l~nRqPtLhr~s~ma~~~~------~~~~~t~r~~~~~c~~~NADFDGDem--nlh~Pqs~~a~aE~~~l~~~~~~~lsP 213 (353)
.+.......|.++||.||. |.+++.+.+|.|- -| .+| .++.|.... .|....
T Consensus 408 ~LkGK~GRFRqNLlGKRVDySgRSVIspdP~L~l~e~G-lP-------~~mA~eLf~Pf~i~------~L~~~~------ 467 (1460)
T PRK14906 408 MLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCG-LP-------SAMALELFKPFVMK------RLVELE------ 467 (1460)
T ss_pred HhcccCcccccccccccccCcCCceEeCCCCCcccccc-Cc-------HHHHHhcCchhHHH------HHHHhc------
Confidence 4556667888899988876 5566777777743 44 333 233443221 111100
Q ss_pred CCCCceeeeeeeeeeeeeec-cccceeeccccccccCcceeeecCCcccccccccceeeEEecCceeeccccccCCCCCC
Q psy1131 214 QNNRPVMGIVQDTLTAVRKM-TKRDVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNAD 292 (353)
Q Consensus 214 ~~g~Pi~gliQD~i~g~~~L-T~rD~F~~kee~~l~d~d~vI~nrqPtIhk~s~~~~~~~i~~~~ti~~~~~~~~~~naD 292 (353)
.... +.+++.+ .......+....++.++++|++||||||||+|||||++++++++||++||++|+|||||
T Consensus 468 --------~~~n-ik~ak~~i~~~~~~v~~vle~vi~gd~VLlNRqPTLHRlsIqAf~~~L~~gktIrLhplvC~~fNAD 538 (1460)
T PRK14906 468 --------YAAN-IKAAKRAVDRGASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNAD 538 (1460)
T ss_pred --------cccc-HHHHhhHHhhcCCcceeeeeeeeccceeEeccCcccchhccceeeEEecCCceEEecccccCccccC
Confidence 0000 1111111 11222333344456688999999999999999999999999999999999999999999
Q ss_pred CCCCeeEEeecCChhHHHHHHHHhcCCCeeecCCCCCceEEeehheeeeeeeecc-cc
Q psy1131 293 FDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTK-RD 349 (353)
Q Consensus 293 FDGDem~~~~p~s~~a~~E~~~l~~~~~~~~s~~~g~p~~~~~QD~~~g~~~lt~-~d 349 (353)
|||||||+|+|||.+|++|++.||++.+|++||++|+|+++++||+++|+|+||. +|
T Consensus 539 FDGDqMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~ilG~y~LT~~~~ 596 (1460)
T PRK14906 539 FDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTERD 596 (1460)
T ss_pred CcCceeeeecCCCHHHHHHHHHHhcchhcEecCCCCCeeEEeeeeeeeeeEEeeeccc
Confidence 9999999999999999999999999999999999999999999999999999996 44
No 30
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=6.1e-35 Score=332.05 Aligned_cols=188 Identities=22% Similarity=0.318 Sum_probs=141.1
Q ss_pred CeeeEecCCCccccceeeeeEEEe------cCceeeeecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeee
Q psy1131 139 DLVIFNRQPTLHKMSMMGHRVRVL------PWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIIT 212 (353)
Q Consensus 139 d~vl~nRqPtLhr~s~ma~~~~~~------~~~t~r~~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~ls 212 (353)
-.-.+.......|.++||.||.+. +++.+.+|.|- -| .+|++-+-+.+. ++.|..
T Consensus 1716 ls~~LkGK~GRFRqNLlGKRVDySgRSVI~pdP~L~l~e~G-vP-------~~mA~eL~~P~~----i~~L~~------- 1776 (2890)
T PRK09603 1716 LSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECG-LP-------KNMALELFKPHL----LSKLEE------- 1776 (2890)
T ss_pred HHHHhcCCCCccccccccccccCcCCceEeCCCCccccccc-Ch-------HHHHHHhCChHH----HHHHHH-------
Confidence 334555677888899998888654 55666666633 33 344322222211 122211
Q ss_pred cCCCCceeeeeeeeeeeeeeccccceeeccccccccCcceeeecCCcccccccccceeeEEecCceeeccccccCCCCCC
Q psy1131 213 PQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNAD 292 (353)
Q Consensus 213 P~~g~Pi~gliQD~i~g~~~LT~rD~F~~kee~~l~d~d~vI~nrqPtIhk~s~~~~~~~i~~~~ti~~~~~~~~~~naD 292 (353)
.| .......+.+++..+....+....++.+++.|++|||||||++|+|||++++++++||++||++|+|||||
T Consensus 1777 --~G-----~~~~lk~ak~~i~~~~~~v~~vlr~vi~gd~VLlNRqPTLHR~sIqAf~~~l~~gktIrLhplvC~~fNAD 1849 (2890)
T PRK09603 1777 --RG-----YATTLKQAKRMIEQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNAD 1849 (2890)
T ss_pred --cC-----CccCHHHHHHHHHhccCccEEEEEeeecCCeEEecCCCccccccceeeeEEEecCceEEeccccCCcccCC
Confidence 11 11111112222222333344455678899999999999999999999999999999999999999999999
Q ss_pred CCCCeeEEeecCChhHHHHHHHHhcCCCeeecCCCCCceEEeehheeeeeeeeccccccc
Q psy1131 293 FDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFL 352 (353)
Q Consensus 293 FDGDem~~~~p~s~~a~~E~~~l~~~~~~~~s~~~g~p~~~~~QD~~~g~~~lt~~d~f~ 352 (353)
|||||||+|+|||.+|++|++.||++.+|++||++|+|+++++||+++|+|+||.+|.|+
T Consensus 1850 FDGDqMnvHvPqS~eA~aEa~~LM~s~~nilsP~~G~Pi~~p~QD~vlG~y~LT~~~~~~ 1909 (2890)
T PRK09603 1850 FDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGV 1909 (2890)
T ss_pred CCCceeEEeecCCHHHHHHHHHHhcccceEEEcCCCceeEEeecceeeeeEEeeccccCC
Confidence 999999999999999999999999999999999999999999999999999999999764
No 31
>KOG0262|consensus
Probab=100.00 E-value=3.6e-34 Score=305.27 Aligned_cols=209 Identities=36% Similarity=0.557 Sum_probs=168.8
Q ss_pred EeeeeccCCeeeEecCCCccccceeeeeEEEecCceeeeecccCCCCCCCCCCCceee--------ec--cCCHhhHHHH
Q psy1131 131 VERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNL--------HV--PQSMETRAEV 200 (353)
Q Consensus 131 V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~r~~~~~c~~~NADFDGDemnl--------h~--Pqs~~a~aE~ 200 (353)
-.|....|...++.+.-.|.|..|||.||..... +|.+| ....+-||+.+ .+ |-+.....|+
T Consensus 421 ~~r~~~pGikQiLEKKeGLFRkhMMGKRVN~AaR-------SVIsP-DPnI~tnEIGIP~vFA~KLTyPepVt~~NV~el 492 (1640)
T KOG0262|consen 421 WSRDSPPGIKQILEKKEGLFRKHMMGKRVNYAAR-------SVISP-DPNIETNEIGIPPVFAKKLTYPEPVTPWNVNEL 492 (1640)
T ss_pred cccCCCchHHHHHHHhhhhHHHHhhccccchhhc-------cccCC-CCCccccccCCchHHHhhccCCCcCCcccHHHH
Confidence 3455558888999999999999999999999886 55555 55567788743 34 4556778888
Q ss_pred HHHhcCCceeeecCCCCceeeeeeeee---eee-------------eeccc-----cceeeccccccccCcceeeecCCc
Q psy1131 201 ENIHVTPRQIITPQNNRPVMGIVQDTL---TAV-------------RKMTK-----RDVFLDKVERHIRDGDLVIFNRQP 259 (353)
Q Consensus 201 ~~l~~~~~~~lsP~~g~Pi~gliQD~i---~g~-------------~~LT~-----rD~F~~kee~~l~d~d~vI~nrqP 259 (353)
+..... .-+-.|....+||-= +.. .++|- ++.--++..+|+.+||.+++||||
T Consensus 493 r~aViN------GP~~hPGA~~iqd~dg~~t~l~~~~~~qR~alA~qLLtpst~~~~~~~~K~V~RHvknGDvvlmNRQP 566 (1640)
T KOG0262|consen 493 RKAVIN------GPDVHPGATYIQDEDGTLTLLSPMTDEQREALANQLLTPSTGNPTEFGTKKVHRHVKNGDVVLMNRQP 566 (1640)
T ss_pred HHHHhc------CCCCCCCcceeecCCCceeecCCCCHHHHHHHHHHhhccccCCCcccCCceeeeeccCCcEEEEcCCC
Confidence 876533 233456666677631 111 11220 000122345788999999999999
Q ss_pred ccccccccceeeEEecC-ceeeccccccCCCCCCCCCCeeEEeecCChhHHHHHHHHhcCCCeeecCCCCCceEEeehhe
Q psy1131 260 TLHKMSMMGHRVRVLPW-STFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDT 338 (353)
Q Consensus 260 tIhk~s~~~~~~~i~~~-~ti~~~~~~~~~~naDFDGDem~~~~p~s~~a~~E~~~l~~~~~~~~s~~~g~p~~~~~QD~ 338 (353)
||||||||||+++|+++ +|+|+|++.|+.|||||||||||+|+|||+.||||+..|+++..|++.|++|+|+.|++||+
T Consensus 567 TLHKPSimaHkaRVL~gEktlRlHYANCkaYNADFDGDEMN~HfPQse~araEa~~ian~dsqYLvPt~G~PlrGLIQDH 646 (1640)
T KOG0262|consen 567 TLHKPSIMAHKARVLPGEKTLRLHYANCKAYNADFDGDEMNVHFPQSEIARAEAYNIANTDSQYLVPTDGTPLRGLIQDH 646 (1640)
T ss_pred ccccchhhhhhheecCCcceeeeeecccccccCCCCcchhcccCCchhhHHHHHHHHhccCCceeccCCCCchhhhhhhh
Confidence 99999999999999986 89999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeeeecccccccC
Q psy1131 339 LTAVRKMTKRDVFLD 353 (353)
Q Consensus 339 ~~g~~~lt~~d~f~~ 353 (353)
+++..+||.||.||+
T Consensus 647 iVsgv~LT~rd~Fft 661 (1640)
T KOG0262|consen 647 IVSGVLLTMRDSFFT 661 (1640)
T ss_pred eeeeEEEEecccccC
Confidence 999999999999996
No 32
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=4.3e-34 Score=324.27 Aligned_cols=107 Identities=25% Similarity=0.493 Sum_probs=103.3
Q ss_pred cccCcceeeecCCcccccccccceeeEEecCceeeccccccCCCCCCCCCCeeEEeecCChhHHHHHHHHhcCCCeeecC
Q psy1131 246 HIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITP 325 (353)
Q Consensus 246 ~l~d~d~vI~nrqPtIhk~s~~~~~~~i~~~~ti~~~~~~~~~~naDFDGDem~~~~p~s~~a~~E~~~l~~~~~~~~s~ 325 (353)
++.+++++++|||||||++|+|||++++++|+||++||++|+||||||||||||+|+|||.+|++|++.||++.+|++||
T Consensus 1847 ~vi~gd~VLlNRqPTLHR~sIqAf~~~l~~gktirlhp~vC~~fNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP 1926 (2836)
T PRK14844 1847 EVIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSP 1926 (2836)
T ss_pred EEecCCEEEecCCCccccccccceeeEeecCceEEecccCCCcccCCCCCceeeeecCCcHHHHHHHHHHhCCcccEEec
Confidence 34568999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCceEEeehheeeeeeeeccccccc
Q psy1131 326 QNNRPVMGIVQDTLTAVRKMTKRDVFL 352 (353)
Q Consensus 326 ~~g~p~~~~~QD~~~g~~~lt~~d~f~ 352 (353)
++|+|+++++||+++|+|+||.+|.|+
T Consensus 1927 ~~G~Pii~~~QD~ilG~y~LT~~~~~~ 1953 (2836)
T PRK14844 1927 SNGRPIIVPSKDIVLGIYYLTLQEPKE 1953 (2836)
T ss_pred CCCceeEeehhhhhhhhhhhccccccc
Confidence 999999999999999999999999754
No 33
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=99.94 E-value=7.9e-28 Score=258.00 Aligned_cols=115 Identities=40% Similarity=0.551 Sum_probs=107.7
Q ss_pred eeeccccccccCcceeeecCCcccccccccceeeEEec-CceeeccccccCCCCCCCCCCeeEEeecCChhHHHHHHHHh
Q psy1131 238 VFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLP-WSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIH 316 (353)
Q Consensus 238 ~F~~kee~~l~d~d~vI~nrqPtIhk~s~~~~~~~i~~-~~ti~~~~~~~~~~naDFDGDem~~~~p~s~~a~~E~~~l~ 316 (353)
...|..+++..+++.+++||+||+|++|+|++..++.+ +++|++|+++|.||||||||||||+|+|||.+|+||++.||
T Consensus 349 ~~~w~Vl~evi~gd~Vl~NR~PtLHrlsImq~~e~vl~~gkt~rLh~lVc~~yNADFDGDeM~~Hvp~s~ea~AEa~~lm 428 (808)
T COG0086 349 PEVWDVLREVIDGDPVLLNRAPTLHRLSIMQAFEPVLPEGKAIRLHPLVCEAYNADFDGDEMAVHVPASGEAAAEARGLM 428 (808)
T ss_pred cccchHHHHHhcCCccccccCChHHHHHHHhhceeeccccceeecchhhccccccccCchhhhccccchHHHHHHHHHhh
Confidence 34566677888999999999999999999888777766 89999999999999999999999999999999999999999
Q ss_pred cCCCeeecCCCCCceEEeehheeeeeeeeccccccc
Q psy1131 317 VTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFL 352 (353)
Q Consensus 317 ~~~~~~~s~~~g~p~~~~~QD~~~g~~~lt~~d~f~ 352 (353)
++..|++||++|+|+++.+||+++|.|+||..|+|+
T Consensus 429 ~tq~nilsP~~Ggpiv~~~qD~v~g~ylLt~~d~~~ 464 (808)
T COG0086 429 GTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDAKL 464 (808)
T ss_pred ccccccccCCCCCceEeecceEEeccEEEEEecccC
Confidence 999999999999999999999999999999999876
No 34
>PF00623 RNA_pol_Rpb1_2: RNA polymerase Rpb1, domain 2; InterPro: IPR000722 RNA polymerases catalyse the DNA dependent polymerisation of RNA from DNA, using the four ribonucleoside triphosphates as substrates. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Eukaryotic RNA polymerase I is essentially used to transcribe ribosomal RNA units, polymerase II is used for mRNA precursors, and III is used to transcribe 5S and tRNA genes. Each class of RNA polymerase is assembled from nine to fourteen different polypeptides. Members of the family include the largest subunit from eukaryotes; the gamma subunit from Cyanobacteria; the beta' subunit from bacteria; the A' subunit from archaea; and the B'' subunit from chloroplast RNA polymerases.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_M 2PMZ_Q 3HKZ_I 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N ....
Probab=99.93 E-value=4.8e-27 Score=209.84 Aligned_cols=77 Identities=61% Similarity=0.987 Sum_probs=66.2
Q ss_pred cccccccCcceeeecCCcccccccccceeeEEecCceeeccccccCCCCCCCCCCeeEEeecCChhHHHHHHHHhcC
Q psy1131 242 KVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVT 318 (353)
Q Consensus 242 kee~~l~d~d~vI~nrqPtIhk~s~~~~~~~i~~~~ti~~~~~~~~~~naDFDGDem~~~~p~s~~a~~E~~~l~~~ 318 (353)
+..+++.++|.+++|||||||++|+|||++++++++||++|+++|+||||||||||||+|+|||++|++|+++||.+
T Consensus 90 ~v~r~l~~gd~vl~nRqPtLh~~s~~a~~~~~~~~~t~~~~~~~c~~~NADFDGDem~i~~p~~~~a~~E~~~L~~~ 166 (166)
T PF00623_consen 90 IVERHLCDGDIVLLNRQPTLHRMSIMAHKVRVLPGKTIRINPLVCSPFNADFDGDEMNIHLPQSYEARAEAKELMNV 166 (166)
T ss_dssp EEEEEHTTT-EEEEEESS-SSGGGEEEEEEEEESSSSEEEEGGGHHHHT--TSS-EEEEE--SSHHHHHHHHHHCBT
T ss_pred hHHHhhhcCceeEEeccchhccceeeeeeeeeecccEEEeeccchhhhhccCCcceEEEEecCCHHHHHHHHHHhcC
Confidence 34567889999999999999999999999999999999999999999999999999999999999999999999864
No 35
>PF04983 RNA_pol_Rpb1_3: RNA polymerase Rpb1, domain 3; InterPro: IPR007066 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 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [, ].; 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=97.75 E-value=2.1e-06 Score=75.55 Aligned_cols=56 Identities=27% Similarity=0.398 Sum_probs=41.5
Q ss_pred eeeecCCCCceeeeeeeeeeeeeeccccceeeccccccccCcce-----eeecCCcccccc
Q psy1131 209 QIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHIRDGDL-----VIFNRQPTLHKM 264 (353)
Q Consensus 209 ~~lsP~~g~Pi~gliQD~i~g~~~LT~rD~F~~kee~~l~d~d~-----vI~nrqPtIhk~ 264 (353)
|++||++|+|+++++||+++|+|+||.++.|++++++...-... .....+|+|.++
T Consensus 1 NilSP~~G~Pii~~~QD~vlG~y~LT~~~~f~~~~e~~~~~~~~~~~~~~~~~~~~~I~~~ 61 (158)
T PF04983_consen 1 NILSPANGKPIIGPTQDMVLGAYYLTSEDTFLSRDEAQQALMNGLIDDKKIVLLHPAILKP 61 (158)
T ss_dssp GSEETTTTEESSS--SHHHHHHHHHSSTTTEESHHHHHHHHHCSST----CHCSSSSBSSS
T ss_pred CccCCCCCCceEEeccceEeEEEEEEecccccchHHHHHHHHcccccccceeccchhhhcc
Confidence 68999999999999999999999999999999988775311111 122356777776
No 36
>PF05183 RdRP: RNA dependent RNA polymerase; InterPro: IPR007855 This entry represents various eukaryotic RNA-dependent RNA polymerases (RDRP; 2.7.7.48 from EC), such as RCRP-1, RDRP-2 and RDRP-6. These enzymes are involved in the amplification of regulatory microRNAs during post-transcriptional gene silencing []; they are also required for transcriptional gene silencing. Double-stranded RNA has been shown to induce gene silencing in diverse eukaryotes and by a variety of pathways []. These enzymes also play a role in the RNA interference (RNAi) pathway, which is important for heterochromatin formation, accurate chromosome segregation, centromere cohesion and telomere function during mitosis and meiosis. RDRP enzymes are highly conserved in most eukaryotes, but are missing in archaea and bacteria. The core catalytic domain of RDRP enzymes is structurally similar to the beta' subunit of DNA-dependent RNA polymerases (DDRP), however the other domains of DDRP show no similarity to those of RDRP.; GO: 0003968 RNA-directed RNA polymerase activity; PDB: 2J7O_A 2J7N_A.
Probab=83.54 E-value=1.4 Score=46.74 Aligned_cols=54 Identities=28% Similarity=0.327 Sum_probs=29.2
Q ss_pred eeeccCCeeeEecCCCccccceeeeeEEEecC-----cee-------eeecccCCCCCCCCCCCceeee
Q psy1131 133 RHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPW-----STF-------RMNLSCTSPYNADFDGDEMNLH 189 (353)
Q Consensus 133 r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~-----~t~-------r~~~~~c~~~NADFDGDemnlh 189 (353)
..+..| .|++-|.|++|..-++-.+++-.|. ..| |=+++.|+ +.|+|||+-.+-
T Consensus 364 ~~~~~g-~VlV~R~P~~~pgDir~~~av~~p~L~~l~~vIVF~~~G~r~~~~~ls--GgDlDGD~~~V~ 429 (579)
T PF05183_consen 364 SQVLEG-DVLVTRNPCLHPGDIRKVKAVDKPELRHLKDVIVFSTKGDRPLPSELS--GGDLDGDEYFVC 429 (579)
T ss_dssp EEEEE--EEEEE-SS--SGGGEEEEEE---GGGTT--SEEEE-S-SSS-HHHHTT--T--SSS-EEEEE
T ss_pred cceeee-eEEEecCCccCcCceeEEEeeccHHHcccCCEEEeCCCCCCCchHHhc--CCCCCCceEEEE
Confidence 456677 8999999999999999888876653 011 22222333 489999998764
No 37
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=54.98 E-value=9.1 Score=30.25 Aligned_cols=48 Identities=15% Similarity=0.399 Sum_probs=33.0
Q ss_pred CceEEEe-ccCeEEeecc--CCCCCCccccCCcE---EeeeccccceeEeecCC
Q psy1131 14 GAKYIVR-DNGERIDLRF--HPKPSDLHLQCGYK---VERHIRDGDLVIFNRQP 61 (353)
Q Consensus 14 ga~~vi~-~~g~r~~l~~--~~~~~~~~l~~g~~---verhl~d~~~~~~~~~~ 61 (353)
+...++. .+|+.-.++. .+..+...|.-||+ .+.+|+.||+.+|+...
T Consensus 33 ~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~L~~GD~~~F~~~~ 86 (100)
T PF02362_consen 33 SREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLKEGDVCVFELIG 86 (100)
T ss_dssp -CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--TT-EEEEEE-S
T ss_pred CeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCCCCCEEEEEEec
Confidence 4455544 4788777766 66667788999998 78999999999999653
No 38
>PF05094 LEF-9: Late expression factor 9 (LEF-9); InterPro: IPR007786 The baculovirus Autographa californica nuclear polyhedrosis virus (AcMNPV) encodes a DNA-dependent RNA polymerase that is required for transcription of viral late genes. This polymerase is composed of four equimolar subunits, LEF-8, LEF-4, LEF-9, and p47. LEF-9 is homologous to the largest beta-subunit of prokaryotic DNA-directed RNA polymerase [].; GO: 0019083 viral transcription
Probab=50.69 E-value=31 Score=35.66 Aligned_cols=65 Identities=22% Similarity=0.218 Sum_probs=49.4
Q ss_pred CeeeEecCCCccccceeeeeEEEecC---ceeeeecccCCCCCCCCCCC-ceeeeccCCHhhHHHHHHHh
Q psy1131 139 DLVIFNRQPTLHKMSMMGHRVRVLPW---STFRMNLSCTSPYNADFDGD-EMNLHVPQSMETRAEVENIH 204 (353)
Q Consensus 139 d~vl~nRqPtLhr~s~ma~~~~~~~~---~t~r~~~~~c~~~NADFDGD-emnlh~Pqs~~a~aE~~~l~ 204 (353)
-.+.--|+|.+-..|-+-.+|+.-.. -.+++=...+.+-|+|-||| |+--++|+.. +--+++.++
T Consensus 211 ~raw~tRHPniSqlsTq~s~v~~~~~~~~wnvkvGlG~F~Gan~DCDGDKeviT~lP~PN-SLidlE~lL 279 (487)
T PF05094_consen 211 VRAWTTRHPNISQLSTQVSRVDQNDDYTDWNVKVGLGTFVGANRDCDGDKEVITYLPYPN-SLIDLESLL 279 (487)
T ss_pred eeeeecCCCCchhhchhheEeeccccCCCcceeeeeccccCCCCCCCCCceEEEecCCCc-chhhHHHHh
Confidence 45778899999999999888887654 45677777888999999999 6777788743 334555544
No 39
>KOG0988|consensus
Probab=41.98 E-value=30 Score=39.70 Aligned_cols=52 Identities=27% Similarity=0.367 Sum_probs=39.6
Q ss_pred eeccCCeeeEecCCCccccceeeee------------EEEecCceeeeecccCCCCCCCCCCCceee
Q psy1131 134 HIRDGDLVIFNRQPTLHKMSMMGHR------------VRVLPWSTFRMNLSCTSPYNADFDGDEMNL 188 (353)
Q Consensus 134 ~l~~gd~vl~nRqPtLhr~s~ma~~------------~~~~~~~t~r~~~~~c~~~NADFDGDemnl 188 (353)
.++.| .||+-|.|+||-.-+--++ |.|.|++--|=||.-|++ .||||||-.+
T Consensus 770 ~vitG-~VlvtKNPcLhpGDVRVl~AV~vp~L~h~~dvVvFPQkGpRphpdE~aG--sDLDGDeYfV 833 (1145)
T KOG0988|consen 770 EVITG-KVLVTKNPCLHPGDVRVLKAVYVPALEHMVDVVVFPQKGPRPHPDEMAG--SDLDGDEYFV 833 (1145)
T ss_pred eEEEe-eEEEecCCCCCCCceEEEEeeccHHHHhhcCEEEcCCCCCCCCcccccc--CCCCCceEEE
Confidence 34455 4778899999987775443 456677888999999987 8999999754
No 40
>PHA03396 lef-9 late expression factor 9; Provisional
Probab=37.20 E-value=65 Score=33.55 Aligned_cols=66 Identities=21% Similarity=0.228 Sum_probs=47.0
Q ss_pred CCeeeEecCCCccccceeeeeEEEecCc---eeeeecccCCCCCCCCCCC-ceeeeccCCHhhHHHHHHHh
Q psy1131 138 GDLVIFNRQPTLHKMSMMGHRVRVLPWS---TFRMNLSCTSPYNADFDGD-EMNLHVPQSMETRAEVENIH 204 (353)
Q Consensus 138 gd~vl~nRqPtLhr~s~ma~~~~~~~~~---t~r~~~~~c~~~NADFDGD-emnlh~Pqs~~a~aE~~~l~ 204 (353)
.-.+.--|+|.+-..|-+-.+|+.-..- .+++=.....+-|+|-||| |+--++|+.. +.-+++.++
T Consensus 213 ~~raw~tRHPnisqlstq~s~v~~~~~~~~wNvkvGlG~F~GanrDCDGDKeviT~lP~PN-sLidlE~lL 282 (493)
T PHA03396 213 NVRAWTTRHPNISQLSTQVSRVDQNDDYTDWNVKVGLGTFPGANRDCDGDKEVITFLPYPN-SLIDLECLL 282 (493)
T ss_pred ceEEeecCCCCchhhchhheEeeccccccccceeeeeccccCCCCCCCCCceEEEecCCCc-chhhHHHHh
Confidence 4457778999999999998888875532 2455556677889999999 6777788743 234444444
No 41
>PF05094 LEF-9: Late expression factor 9 (LEF-9); InterPro: IPR007786 The baculovirus Autographa californica nuclear polyhedrosis virus (AcMNPV) encodes a DNA-dependent RNA polymerase that is required for transcription of viral late genes. This polymerase is composed of four equimolar subunits, LEF-8, LEF-4, LEF-9, and p47. LEF-9 is homologous to the largest beta-subunit of prokaryotic DNA-directed RNA polymerase [].; GO: 0019083 viral transcription
Probab=36.90 E-value=45 Score=34.51 Aligned_cols=61 Identities=23% Similarity=0.315 Sum_probs=43.2
Q ss_pred ecCCcccccccccceeeEEecC-ceee--ccccccCCCCCCCCCC-eeEEeecCChhHHHHHHHHh
Q psy1131 255 FNRQPTLHKMSMMGHRVRVLPW-STFR--MNLSCTSPYNADFDGD-EMNLHVPQSMETRAEVENIH 316 (353)
Q Consensus 255 ~nrqPtIhk~s~~~~~~~i~~~-~ti~--~~~~~~~~~naDFDGD-em~~~~p~s~~a~~E~~~l~ 316 (353)
-.|-|.|.-.|-|-.++..... ..|. +-+....+-|+|+||| |.-.++|+. ++..+++.++
T Consensus 215 ~tRHPniSqlsTq~s~v~~~~~~~~wnvkvGlG~F~Gan~DCDGDKeviT~lP~P-NSLidlE~lL 279 (487)
T PF05094_consen 215 TTRHPNISQLSTQVSRVDQNDDYTDWNVKVGLGTFVGANRDCDGDKEVITYLPYP-NSLIDLESLL 279 (487)
T ss_pred ecCCCCchhhchhheEeeccccCCCcceeeeeccccCCCCCCCCCceEEEecCCC-cchhhHHHHh
Confidence 4678999888888877776542 3333 3466777899999999 577777774 4556777754
No 42
>PF10948 DUF2635: Protein of unknown function (DUF2635); InterPro: IPR024400 This family consists of uncharacterised proteins found in bacteria and bacteriophages. It includes protein Gp38 from Enterobacteria phage Mu.
Probab=30.76 E-value=23 Score=25.40 Aligned_cols=15 Identities=33% Similarity=0.543 Sum_probs=12.2
Q ss_pred eeeccccceeEeecC
Q psy1131 46 ERHIRDGDLVIFNRQ 60 (353)
Q Consensus 46 erhl~d~~~~~~~~~ 60 (353)
.|+|.|||+++.+.+
T Consensus 32 ~RRl~dGDV~~v~~~ 46 (47)
T PF10948_consen 32 LRRLADGDVVEVTPK 46 (47)
T ss_pred HHhhhcCCEEEecCC
Confidence 489999999987653
No 43
>PHA03396 lef-9 late expression factor 9; Provisional
Probab=28.11 E-value=76 Score=33.08 Aligned_cols=61 Identities=23% Similarity=0.333 Sum_probs=42.5
Q ss_pred ecCCcccccccccceeeEEecC-cee--eccccccCCCCCCCCCC-eeEEeecCChhHHHHHHHHh
Q psy1131 255 FNRQPTLHKMSMMGHRVRVLPW-STF--RMNLSCTSPYNADFDGD-EMNLHVPQSMETRAEVENIH 316 (353)
Q Consensus 255 ~nrqPtIhk~s~~~~~~~i~~~-~ti--~~~~~~~~~~naDFDGD-em~~~~p~s~~a~~E~~~l~ 316 (353)
..|-|.|.-.|-|-..+..-.. .-| ++-+....+-|+|+||| |.-.++|+. ++.-+++.++
T Consensus 218 ~tRHPnisqlstq~s~v~~~~~~~~wNvkvGlG~F~GanrDCDGDKeviT~lP~P-NsLidlE~lL 282 (493)
T PHA03396 218 TTRHPNISQLSTQVSRVDQNDDYTDWNVKVGLGTFPGANRDCDGDKEVITFLPYP-NSLIDLECLL 282 (493)
T ss_pred ecCCCCchhhchhheEeeccccccccceeeeeccccCCCCCCCCCceEEEecCCC-cchhhHHHHh
Confidence 4678999888888777776442 123 33466677899999999 577778874 4555666654
No 44
>PF10657 RC-P840_PscD: Photosystem P840 reaction centre protein PscD; InterPro: IPR019608 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. The photosynthetic reaction centres (RCs) of aerotolerant organisms contain a heterodimeric core, built up of two strongly homologous polypeptides each of which contributes five transmembrane peptide helices to hold a pseudo-symmetric double set of redox components. Two molecules of PscD are housed within a subunit. PscD may be involved in stabilising the PscB component since it is found to co-precipitate with FMO (Fenna-Mathews-Olson BChl a-protein) and PscB. It may also be involved in the interaction with ferredoxin [].
Probab=23.58 E-value=46 Score=28.79 Aligned_cols=50 Identities=22% Similarity=0.421 Sum_probs=41.6
Q ss_pred CCCCCCCceEEE----eccCeEEeeccCCCCCCccccCCcEEeeeccccceeEe
Q psy1131 8 GNSQYPGAKYIV----RDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIF 57 (353)
Q Consensus 8 gp~~~pga~~vi----~~~g~r~~l~~~~~~~~~~l~~g~~verhl~d~~~~~~ 57 (353)
|-..|-.-||.| |++--+..|...+..+.-.|.|--..-+.|.+|+++++
T Consensus 25 GNa~HK~eKYfITsAkRD~~g~Lql~i~pasGrrkLspt~emi~~l~~geIel~ 78 (144)
T PF10657_consen 25 GNAVHKAEKYFITSAKRDRYGKLQLTISPASGRRKLSPTPEMIDKLISGEIELF 78 (144)
T ss_pred CchhhhhheeEEeeeecccCCceEEEEecCCCccccCCcHHHHHHHhcCceEEE
Confidence 556777889987 55777888999998898899998888899999999875
No 45
>PF05183 RdRP: RNA dependent RNA polymerase; InterPro: IPR007855 This entry represents various eukaryotic RNA-dependent RNA polymerases (RDRP; 2.7.7.48 from EC), such as RCRP-1, RDRP-2 and RDRP-6. These enzymes are involved in the amplification of regulatory microRNAs during post-transcriptional gene silencing []; they are also required for transcriptional gene silencing. Double-stranded RNA has been shown to induce gene silencing in diverse eukaryotes and by a variety of pathways []. These enzymes also play a role in the RNA interference (RNAi) pathway, which is important for heterochromatin formation, accurate chromosome segregation, centromere cohesion and telomere function during mitosis and meiosis. RDRP enzymes are highly conserved in most eukaryotes, but are missing in archaea and bacteria. The core catalytic domain of RDRP enzymes is structurally similar to the beta' subunit of DNA-dependent RNA polymerases (DDRP), however the other domains of DDRP show no similarity to those of RDRP.; GO: 0003968 RNA-directed RNA polymerase activity; PDB: 2J7O_A 2J7N_A.
Probab=22.76 E-value=77 Score=33.67 Aligned_cols=50 Identities=28% Similarity=0.315 Sum_probs=24.0
Q ss_pred CcceeeecCCcccccccccceeeEEecCc-------eeec-----cccccCCCCCCCCCCeeEEe
Q psy1131 249 DGDLVIFNRQPTLHKMSMMGHRVRVLPWS-------TFRM-----NLSCTSPYNADFDGDEMNLH 301 (353)
Q Consensus 249 d~d~vI~nrqPtIhk~s~~~~~~~i~~~~-------ti~~-----~~~~~~~~naDFDGDem~~~ 301 (353)
.| .|+..|.|++|.--++-.++.-.++. .|.. .+.+| -+.|+|||+..|.
T Consensus 368 ~g-~VlV~R~P~~~pgDir~~~av~~p~L~~l~~vIVF~~~G~r~~~~~l--sGgDlDGD~~~V~ 429 (579)
T PF05183_consen 368 EG-DVLVTRNPCLHPGDIRKVKAVDKPELRHLKDVIVFSTKGDRPLPSEL--SGGDLDGDEYFVC 429 (579)
T ss_dssp E--EEEEE-SS--SGGGEEEEEE---GGGTT--SEEEE-S-SSS-HHHHT--TT--SSS-EEEEE
T ss_pred ee-eEEEecCCccCcCceeEEEeeccHHHcccCCEEEeCCCCCCCchHHh--cCCCCCCceEEEE
Confidence 45 66667999999988876666544432 1111 12223 3589999998866
No 46
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=20.09 E-value=2.2e+02 Score=23.16 Aligned_cols=40 Identities=15% Similarity=0.342 Sum_probs=23.3
Q ss_pred CCCCceEEEe-ccCeEEeeccCCC--CCCccccCCcEEeeecc
Q psy1131 11 QYPGAKYIVR-DNGERIDLRFHPK--PSDLHLQCGYKVERHIR 50 (353)
Q Consensus 11 ~~pga~~vi~-~~g~r~~l~~~~~--~~~~~l~~g~~verhl~ 50 (353)
..|+|+|-++ +||..+--....+ ...+.+.+||+|.=-+.
T Consensus 16 ~Lp~~~frV~LenG~~vla~isGKmR~~rIrIl~GD~V~VE~s 58 (87)
T PRK12442 16 VLPDSRFRVTLENGVEVGAYASGRMRKHRIRILAGDRVTLELS 58 (87)
T ss_pred ECCCCEEEEEeCCCCEEEEEeccceeeeeEEecCCCEEEEEEC
Confidence 5788888877 7887774332221 12355666666554443
Done!