Query 045123
Match_columns 219
No_of_seqs 189 out of 1363
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 10:04:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045123.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045123hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0260 RNA polymerase II, lar 100.0 6E-50 1.3E-54 393.9 9.6 197 1-219 1-198 (1605)
2 PRK08566 DNA-directed RNA poly 100.0 1.5E-43 3.2E-48 353.6 14.0 154 11-188 5-165 (882)
3 TIGR02390 RNA_pol_rpoA1 DNA-di 100.0 1.7E-42 3.8E-47 345.3 14.1 151 13-187 2-160 (868)
4 PRK14977 bifunctional DNA-dire 100.0 4.1E-42 8.8E-47 351.9 14.4 156 10-189 4-175 (1321)
5 PF04997 RNA_pol_Rpb1_1: RNA p 100.0 3.2E-42 6.9E-47 303.0 11.7 176 13-193 2-184 (337)
6 KOG0261 RNA polymerase III, la 100.0 8.4E-36 1.8E-40 290.0 10.7 157 13-194 11-180 (1386)
7 KOG0262 RNA polymerase I, larg 100.0 3.6E-31 7.8E-36 262.7 8.8 109 11-119 8-118 (1640)
8 COG0086 RpoC DNA-directed RNA 99.9 1.8E-28 3.8E-33 242.8 4.4 147 14-192 4-151 (808)
9 TIGR02386 rpoC_TIGR DNA-direct 99.8 3.4E-19 7.5E-24 180.6 6.3 105 17-121 1-136 (1140)
10 PRK00566 DNA-directed RNA poly 99.6 1.6E-15 3.5E-20 154.3 6.5 101 14-116 6-139 (1156)
11 PRK02625 rpoC1 DNA-directed RN 99.1 7.8E-11 1.7E-15 113.8 5.2 86 13-98 7-121 (627)
12 PRK14906 DNA-directed RNA poly 99.1 5.9E-11 1.3E-15 122.4 4.2 104 12-115 6-140 (1460)
13 TIGR02387 rpoC1_cyan DNA-direc 99.1 8.7E-11 1.9E-15 113.3 5.0 84 15-98 2-114 (619)
14 PRK14844 bifunctional DNA-dire 99.1 9.6E-11 2.1E-15 125.9 5.4 103 13-115 1446-1579(2836)
15 CHL00018 rpoC1 RNA polymerase 99.0 3.6E-10 7.9E-15 110.0 5.0 87 13-99 5-123 (663)
16 PRK09603 bifunctional DNA-dire 99.0 4.6E-10 9.9E-15 121.1 5.0 88 11-98 1392-1500(2890)
17 TIGR00357 methionine-R-sulfoxi 51.2 5.5 0.00012 32.1 0.2 27 53-86 79-105 (134)
18 COG1644 RPB10 DNA-directed RNA 44.6 12 0.00025 26.3 1.0 29 105-134 6-35 (63)
19 COG1579 Zn-ribbon protein, pos 41.4 11 0.00025 33.1 0.7 38 62-116 196-234 (239)
20 PHA03082 DNA-dependent RNA pol 41.3 16 0.00034 25.4 1.2 23 101-126 2-24 (63)
21 PF05864 Chordopox_RPO7: Chord 40.8 15 0.00033 25.4 1.1 32 101-139 2-33 (63)
22 PF01194 RNA_pol_N: RNA polyme 38.5 15 0.00033 25.5 0.9 20 104-124 5-24 (60)
23 KOG0856 Predicted pilin-like t 37.7 15 0.00033 29.8 0.9 10 76-85 109-118 (146)
24 COG5082 AIR1 Arginine methyltr 37.5 39 0.00084 28.8 3.3 17 61-77 58-77 (190)
25 PRK00222 methionine sulfoxide 36.9 12 0.00027 30.3 0.2 25 53-84 82-106 (142)
26 PLN00032 DNA-directed RNA poly 36.4 20 0.00043 25.8 1.2 29 104-133 5-34 (71)
27 PRK04016 DNA-directed RNA poly 34.4 21 0.00046 25.0 1.0 31 103-134 4-35 (62)
28 PF14260 zf-C4pol: C4-type zin 33.0 31 0.00067 24.0 1.7 37 104-143 14-50 (73)
29 PF01641 SelR: SelR domain; I 32.8 14 0.00031 29.3 -0.0 26 53-85 76-101 (124)
30 KOG0466 Translation initiation 28.5 81 0.0018 29.4 4.0 17 63-79 109-135 (466)
31 TIGR01623 put_zinc_LRP1 putati 28.5 19 0.00042 23.4 0.0 19 63-81 15-34 (43)
32 PF15288 zf-CCHC_6: Zinc knuck 28.3 26 0.00056 22.4 0.6 20 65-92 3-24 (40)
33 PF06463 Mob_synth_C: Molybden 25.8 33 0.0007 27.0 0.9 30 75-116 53-82 (128)
34 PF14754 IFR3_antag: Papain-li 21.8 15 0.00033 30.7 -1.7 27 63-89 38-68 (249)
35 PF14353 CpXC: CpXC protein 20.5 42 0.00091 25.9 0.6 40 65-112 3-47 (128)
36 PF08038 Tom7: TOM7 family; I 20.3 40 0.00086 21.7 0.3 17 83-99 8-24 (42)
No 1
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=100.00 E-value=6e-50 Score=393.86 Aligned_cols=197 Identities=50% Similarity=0.828 Sum_probs=178.2
Q ss_pred CCCCCCCCccccceeeeEEEEeCCHHHHhcCcccEEecCccccCCCCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcc
Q 045123 1 MENCFTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHF 80 (219)
Q Consensus 1 ~~~~~~~~~~~~~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~~~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHf 80 (219)
|+..+..+++++++|++||||++||+||++|||.+|..|++++.++|..|||.|||||++|+...|+||+.++.+|||||
T Consensus 1 m~~~~~~~~~pl~~v~~vqFgi~spdeir~mSV~~i~~~e~~e~~~pk~ggl~D~RlG~idr~~~CqTC~g~~~~CpGHF 80 (1605)
T KOG0260|consen 1 MGDDCEFSQAPLRTVKSVQFGILSPDEIRRMSVAEIEFPETMEGGRPKLGGLMDPRLGTIDRDSLCQTCGGNMFECPGHF 80 (1605)
T ss_pred CCCCcccccCcceeeeEEEeeccChhhhhcceeEEeecccccccCCCCcCCccccccCCCCccchhhhhccccccCCccc
Confidence 78899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeecccceeeeeehhhhhhhhhhhcccccccccCccCHHHHHHHHhcC-chhHHHHHHHHhccccccCCCCcccccccC
Q 045123 81 GHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRH-PKSRLEQILCACKTKNKCEGGDEIDVLSLL 159 (219)
Q Consensus 81 GhIeL~~Pv~h~~f~~~i~~iL~~vC~~C~rll~~~~~~~~~~~~~~~~-~k~r~~~i~~~ck~~~~Ce~~~~~d~~~~~ 159 (219)
|||+||+|||||+|+++|.+||+|||++|+++++++..+++.++++.+. ++.|+..||.+||++.+|+.+.+.+.+
T Consensus 81 GhieLAkPvfH~gFl~kv~kiL~cVC~~C~ki~~~~~~~~~~~~~~~~~~~k~rl~~v~~vck~k~~ce~g~~~e~~--- 157 (1605)
T KOG0260|consen 81 GHIELAKPVFHPGFLKKVKKILRCVCFYCSKILKDKFNPKEDQILRKRYCSKGRLLMVLDVCKGKVVCEGGIDVESD--- 157 (1605)
T ss_pred ceeeeccccccHHHHHHHHHHHHHhhhcchheeecccCcchhhhhhhhcCCcchHHHHHHhhccceeeecccccccc---
Confidence 9999999999999999999999999999999999998888878877666 999999999999999999875443322
Q ss_pred CCCCCCCCccCCCCCCCCCCeEEEeceEEEEEEccccccCCCCCCCCCCCCcccccCCCC
Q 045123 160 GHDGEEPLRKRKSGCGALQPTLTIDGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER 219 (219)
Q Consensus 160 ~~~~~~~~~~~~~gCG~~qP~irk~glkl~~~~k~~~~~~~~~~~~~~~~~~k~~ltae~ 219 (219)
.|+|||+.||.||+.|+++|++||.+. ++. +|+|+.|+|++
T Consensus 158 ----------g~sgcg~kqP~i~r~gl~l~a~~k~~~----e~~-----~e~k~~ls~e~ 198 (1605)
T KOG0260|consen 158 ----------GRSGCGLKQPSIRRLGLDLWAFWKQGD----EDS-----QESKRKLSAER 198 (1605)
T ss_pred ----------ccccccccCCceeccCchhhhhhhccC----ccC-----CcccccCcHHH
Confidence 358999999999999999999998521 111 23588898864
No 2
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated
Probab=100.00 E-value=1.5e-43 Score=353.60 Aligned_cols=154 Identities=36% Similarity=0.735 Sum_probs=137.0
Q ss_pred ccceeeeEEEEeCCHHHHhcCcccEEecCccccC-CCCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcceeeecccce
Q 045123 11 KVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTER-GMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPM 89 (219)
Q Consensus 11 ~~~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~-~~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIeL~~Pv 89 (219)
..++|++|+|++||++||+++||++|+++++||. ++|++|||+|||||++++...|+|||++..+||||||||+|++||
T Consensus 5 ~~~~I~~I~F~~~S~eEI~klSv~~It~~~~~d~~g~P~~gGL~D~RLG~~~~~~~C~TCg~~~~~CPGHFGhIeL~~PV 84 (882)
T PRK08566 5 IPKRIGSIKFGLLSPEEIRKMSVTKIITADTYDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPV 84 (882)
T ss_pred CceeeeeEEEecCCHHHHHHhCeEEEecccccCCCCCcCCCCCCCcccCCCCCCCCCCCCCCCCCcCCCcceEEeccccc
Confidence 3478999999999999999999999999999984 899999999999999999999999999999999999999999999
Q ss_pred eeeeehhhhhhhhhhhcccccccccCccCHH-HHHHHHhcC-----chhHHHHHHHHhccccccCCCCcccccccCCCCC
Q 045123 90 FHIGFMKTLLTIMRCVCFNCSKILADEEDDK-FKLALKIRH-----PKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDG 163 (219)
Q Consensus 90 ~h~~f~~~i~~iL~~vC~~C~rll~~~~~~~-~~~~~~~~~-----~k~r~~~i~~~ck~~~~Ce~~~~~d~~~~~~~~~ 163 (219)
|||+||+.|++||+|+|++|+||++++++.+ |...++..+ .+.+++++++.|+++.+|
T Consensus 85 fhpgf~~~v~~iL~~iC~~C~rll~~~~~~~~~~~~l~~~~~~~~~~~~l~k~i~k~~k~~~~C---------------- 148 (882)
T PRK08566 85 IHVGFAKLIYKLLRATCRECGRLKLTEEEIEEYLEKLERLKEWGSLADDLIKEVKKEAAKRMVC---------------- 148 (882)
T ss_pred cchhHHHHHHHHHHHhhhhhCceeccccchHHHHHHHhchhhhhhhHHHHHHHHHHHhcCCCCC----------------
Confidence 9999999999999999999999999876543 433333211 235789999999999999
Q ss_pred CCCCccCCCCCCCCCCeEEEeceEE
Q 045123 164 EEPLRKRKSGCGALQPTLTIDGMNM 188 (219)
Q Consensus 164 ~~~~~~~~~gCG~~qP~irk~glkl 188 (219)
++||+.||+|+++++..
T Consensus 149 --------~~Cg~~~~ki~~~~~~~ 165 (882)
T PRK08566 149 --------PHCGEKQYKIKFEKPTT 165 (882)
T ss_pred --------CCcCCCCceEEEeccee
Confidence 68999999999997643
No 3
>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=1.7e-42 Score=345.31 Aligned_cols=151 Identities=38% Similarity=0.829 Sum_probs=134.6
Q ss_pred ceeeeEEEEeCCHHHHhcCcccEEecCcccc-CCCCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcceeeecccceee
Q 045123 13 AKVRMVQFSILSPDEIRKMSVTEIDHGKTTE-RGMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPMFH 91 (219)
Q Consensus 13 ~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~-~~~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIeL~~Pv~h 91 (219)
++|++|+|++||++||+++||++|+++++|| .|+|++|||||||||++++...|+|||++..+||||||||+|++||||
T Consensus 2 ~~I~~I~F~~~S~eEI~k~Sv~~It~~~~~d~~g~P~~gGL~D~RLG~~~~~~~C~TCg~~~~~CpGHFGhIeL~~PVfh 81 (868)
T TIGR02390 2 KKIGSIKFGLLSPEEIRKMSVVEVVTADTYDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVVH 81 (868)
T ss_pred ceeeEEEEeCCCHHHHHHhCeeEEecccccCCCCCcCCCCccCcccCCCCCCCCCCCCCCCCCcCCCcceEEeccccccc
Confidence 5799999999999999999999999999998 489999999999999999999999999999999999999999999999
Q ss_pred eeehhhhhhhhhhhcccccccccCccC-HHHHHHHH-hcC----c-hhHHHHHHHHhccccccCCCCcccccccCCCCCC
Q 045123 92 IGFMKTLLTIMRCVCFNCSKILADEED-DKFKLALK-IRH----P-KSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGE 164 (219)
Q Consensus 92 ~~f~~~i~~iL~~vC~~C~rll~~~~~-~~~~~~~~-~~~----~-k~r~~~i~~~ck~~~~Ce~~~~~d~~~~~~~~~~ 164 (219)
|+|++.|++||+|+|++|+||++++++ +.+...++ .++ + +.+++++++.|+++++|
T Consensus 82 pgf~~~i~kiL~~vC~~C~rll~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~i~~~~~~~~~C----------------- 144 (868)
T TIGR02390 82 VGFAKEIYKILRATCRKCGRITLTEEEIEQYLEKINKLKEEGGDLASTLIEKIVKEAAKRMKC----------------- 144 (868)
T ss_pred hhHHHHHHHHHHHHhhhcCceeeCccccHHHHHHHHhcccchhhhHHHHHHHHHHHhhcCCCC-----------------
Confidence 999999999999999999999998754 33544433 222 1 45678899999988899
Q ss_pred CCCccCCCCCCCCCCeEEEeceE
Q 045123 165 EPLRKRKSGCGALQPTLTIDGMN 187 (219)
Q Consensus 165 ~~~~~~~~gCG~~qP~irk~glk 187 (219)
++||+.||+||++++.
T Consensus 145 -------~~Cg~~~p~ir~~~~~ 160 (868)
T TIGR02390 145 -------PHCGEEQKKIKFEKPT 160 (868)
T ss_pred -------CCCCCcCceEEEeeee
Confidence 6899999999998743
No 4
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=100.00 E-value=4.1e-42 Score=351.90 Aligned_cols=156 Identities=33% Similarity=0.691 Sum_probs=134.8
Q ss_pred cccceeeeEEEEeCCHHHHhcCcccEEecCccccC-CCCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcceeeecccc
Q 045123 10 FKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTER-GMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKP 88 (219)
Q Consensus 10 ~~~~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~-~~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIeL~~P 88 (219)
.++++|++|+|++||+|||+++||++|+++++||. ++|++|||||||||++++...|.||++++.+||||||||+|++|
T Consensus 4 ~~~~~I~~I~Fg~~S~eeIrk~Sv~~It~~~~~d~~g~P~~gGl~DprlG~~d~~~~C~TCg~~~~~CpGHFGHIELa~P 83 (1321)
T PRK14977 4 LAVKAIDGIIFGLISPADARKIGFAEITAPEAYDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAEP 83 (1321)
T ss_pred CccceeceEEEecCCHHHHHHhCeEEEecccccCCCCCcCCCCCCccccCCCCCCCCCCCCCCCCCcCCCeeEEEEccCC
Confidence 56789999999999999999999999999999985 79999999999999999999999999999999999999999999
Q ss_pred eeeeeehhhhhhhhhhhcccccccccCccCHHHHHHHH-hc-----CchhHHH-----H----HHHHhccccccCCCCcc
Q 045123 89 MFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALK-IR-----HPKSRLE-----Q----ILCACKTKNKCEGGDEI 153 (219)
Q Consensus 89 v~h~~f~~~i~~iL~~vC~~C~rll~~~~~~~~~~~~~-~~-----~~k~r~~-----~----i~~~ck~~~~Ce~~~~~ 153 (219)
||||+||+.|++||+|+|++|+||++++++.++..+++ .+ ++++|+. + ++.+|++.++|
T Consensus 84 VfHpgf~k~i~~iLr~iC~~C~rlll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~C------ 157 (1321)
T PRK14977 84 VIHIAFIDNIKDLLNSTCHKCAKLKLPQEDLNVFKLIEEAHAAARDIPEKRIDDEIIEEVRDQVKVYAKKAKEC------ 157 (1321)
T ss_pred ceecccHHHHHHHHHHHHHHhchhhcCcccHHHHHHHHHHhhhcccchhhhhhHHHHHHHHhhhhhhhccCCcC------
Confidence 99999999999999999999999999987766433322 11 2334432 2 23458888899
Q ss_pred cccccCCCCCCCCCccCCCCCCCCCCeEEEeceEEE
Q 045123 154 DVLSLLGHDGEEPLRKRKSGCGALQPTLTIDGMNMI 189 (219)
Q Consensus 154 d~~~~~~~~~~~~~~~~~~gCG~~qP~irk~glkl~ 189 (219)
++||+.||+|++++...+
T Consensus 158 ------------------~~C~~~~~~i~~~~~~~~ 175 (1321)
T PRK14977 158 ------------------PHCGAPQHELEFEEPTIF 175 (1321)
T ss_pred ------------------CCCCCCCCeEEEeeceee
Confidence 689999999999875543
No 5
>PF04997 RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; InterPro: IPR007080 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 1, represents the clamp domain, which is a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_W 3QQC_A 1YNJ_D 1HQM_D 1YNN_D 1I6V_D 2GHO_D 2AUJ_D 1ZYR_D 1SMY_D ....
Probab=100.00 E-value=3.2e-42 Score=303.02 Aligned_cols=176 Identities=43% Similarity=0.782 Sum_probs=138.1
Q ss_pred ceeeeEEEEeCCHHHHhcCcccEEecCccccC--CCCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcceeeeccccee
Q 045123 13 AKVRMVQFSILSPDEIRKMSVTEIDHGKTTER--GMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPMF 90 (219)
Q Consensus 13 ~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~--~~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIeL~~Pv~ 90 (219)
++|++|+|++||++||++|||++|+++.+|+. ++|+.|||||||||+.++...|+|||+++.+||||||||+|+.|||
T Consensus 2 ~~i~~i~f~~~s~~eI~~~Sv~~i~~~~~~~~~~~~p~~~Gl~d~rlG~~~~~~~C~tC~~~~~~CpGHfGhI~L~~PV~ 81 (337)
T PF04997_consen 2 KKIKSIQFGIYSPEEIRKLSVKEITNPETFDNLTGKPIKGGLYDPRLGPIDKKQICSTCGLNYTECPGHFGHIELALPVY 81 (337)
T ss_dssp EEEEEEEEEE--HHHHHHHEEEB--SSTSBCTSSSSCBSSSSSSSSSS-SSSSSTSSSSSSSSSSCCCSEEEEEEEEEEE
T ss_pred CeeeEEEEEeCCHHHHHHhCcEEEechhhccCCCCCCccccccChhhcCCCcccccccccccccccCCceeEEEeCHHHH
Confidence 68999999999999999999999999999995 5999999999999999999999999999999999999999999999
Q ss_pred eeeehhhhhhhhhhhcccccccccCccCHHHHH-HHH---hcCchhHHHHHHHHhccccccCCCCcccccccCCCCCCCC
Q 045123 91 HIGFMKTLLTIMRCVCFNCSKILADEEDDKFKL-ALK---IRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEP 166 (219)
Q Consensus 91 h~~f~~~i~~iL~~vC~~C~rll~~~~~~~~~~-~~~---~~~~k~r~~~i~~~ck~~~~Ce~~~~~d~~~~~~~~~~~~ 166 (219)
||+|++.+++||+++|++|+++++++.+..+.. .+. ......+++.|++.|++...|......+... ....
T Consensus 82 h~~f~~~i~~iL~~~C~~C~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~-----~~~~ 156 (337)
T PF04997_consen 82 HPGFFKEIPKILRCICKKCSRLLLSEKEKYFYLKILLKLKKKKKKERLKIISKECKKKSICSHCKAINGKI-----KKVE 156 (337)
T ss_dssp TCCCHHHHHHHHTTSCTTTSCTSTCCCCHTSCHHHCHCSHSSSHHHHHHHHHHHHHHTCSSTSTCC-SSS--------SS
T ss_pred hhcccccceeeecccccccccccccccccccccccccccccccchhHHHHHHHhhhhhhhhcccccccccc-----cccc
Confidence 999999999999999999999999987653211 111 2345678999999999999996432211100 0000
Q ss_pred CccCCCCCCCCCCeEEEec-eEEEEEEc
Q 045123 167 LRKRKSGCGALQPTLTIDG-MNMIAEYK 193 (219)
Q Consensus 167 ~~~~~~gCG~~qP~irk~g-lkl~~~~k 193 (219)
......+|+..++.++++| ..+...|+
T Consensus 157 ~~~~~~~~~~~~~~~~~~~~~~i~~~i~ 184 (337)
T PF04997_consen 157 KSKKCEGCGKKNPKIRKEGAEKIQEEIK 184 (337)
T ss_dssp SEETSSSSSSBSCEEEEESHCCCCCHHH
T ss_pred cchhcccccccCcccccchhhhcccccc
Confidence 0012368999999999998 55555554
No 6
>KOG0261 consensus RNA polymerase III, large subunit [Transcription]
Probab=100.00 E-value=8.4e-36 Score=290.00 Aligned_cols=157 Identities=41% Similarity=0.802 Sum_probs=141.7
Q ss_pred ceeeeEEEEeCCHHHHhcCcccEEecCccccC--C-CCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcceeeecccce
Q 045123 13 AKVRMVQFSILSPDEIRKMSVTEIDHGKTTER--G-MPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPM 89 (219)
Q Consensus 13 ~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~--~-~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIeL~~Pv 89 (219)
.+|++|+|+++|++||++.|+++|.+..+|+. + .|+++|++|||||++++...|.|||+++.+|+|||||+.|++||
T Consensus 11 kki~~i~F~~~s~~ei~~~a~v~v~~~~LY~~~~~~~P~~~G~LD~rMGvs~K~~~C~TCg~~la~C~GHfGy~~L~LPV 90 (1386)
T KOG0261|consen 11 KKIKHIQFSILSPEEIRQQAEVEVSSKDLYDISTQRAPLPNGPLDPRMGVSNKKDKCATCGEGLADCIGHFGYLKLALPV 90 (1386)
T ss_pred ceeeeEeeccCCHHHHHhcceEEeeccchhhhhcccCCCcCCCcCcccCCCCCCCccchhccchhhcccccceEeeccee
Confidence 69999999999999999999999999999984 2 49999999999999999999999999999999999999999999
Q ss_pred eeeeehhhhhhhhhhhcccccccccCccCHHHHHHHHhcCch-------hHHHHHHHHhccccccCCCCcccccccCCCC
Q 045123 90 FHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRHPK-------SRLEQILCACKTKNKCEGGDEIDVLSLLGHD 162 (219)
Q Consensus 90 ~h~~f~~~i~~iL~~vC~~C~rll~~~~~~~~~~~~~~~~~k-------~r~~~i~~~ck~~~~Ce~~~~~d~~~~~~~~ 162 (219)
||+|||+.+++||+|+|++|+.+|+++++.+. ...++++|. ..+++|++.||+..+|
T Consensus 91 FhiGyfk~ti~iLq~ICK~Cs~ilL~~~~k~~-fl~~lr~p~~~~l~k~~l~kri~~~CkK~~~C--------------- 154 (1386)
T KOG0261|consen 91 FHIGYFKATIQILQCICKNCSSILLSEEDKRQ-FLKKLRNPGLDNLRKKALLKRIVAKCKKVNTC--------------- 154 (1386)
T ss_pred eeehhHHHHHHHHHHHHHhhhhhhcCHHHHHH-HHHHhhCCCCChHHHHHHHHHHHHHhhccccc---------------
Confidence 99999999999999999999999999765443 344677763 3479999999999999
Q ss_pred CCCCCccCCCCCCCCCCeEEEe--ceEEEEE-Ecc
Q 045123 163 GEEPLRKRKSGCGALQPTLTID--GMNMIAE-YKA 194 (219)
Q Consensus 163 ~~~~~~~~~~gCG~~qP~irk~--glkl~~~-~k~ 194 (219)
.+||..|+.++|. +|+|+++ |+-
T Consensus 155 ---------~hCg~~NG~VKK~~~~lkIiHd~~~~ 180 (1386)
T KOG0261|consen 155 ---------SHCGALNGTVKKAAALLKIIHDRFKL 180 (1386)
T ss_pred ---------cccCCcCceeeccccceeEeeehhhc
Confidence 5799999999994 4899988 653
No 7
>KOG0262 consensus RNA polymerase I, large subunit [Transcription]
Probab=99.97 E-value=3.6e-31 Score=262.68 Aligned_cols=109 Identities=36% Similarity=0.667 Sum_probs=101.6
Q ss_pred cc-ceeeeEEEEeCCHHHHhcCcccEEecCccccC-CCCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcceeeecccc
Q 045123 11 KV-AKVRMVQFSILSPDEIRKMSVTEIDHGKTTER-GMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKP 88 (219)
Q Consensus 11 ~~-~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~-~~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIeL~~P 88 (219)
++ +.+..|+|++|+++||+++||++|++|.++|+ |+|++|||||++||+.+....|.||++...+||||||||+|+.|
T Consensus 8 pv~~~~~~v~Fg~yt~~ei~klSv~kIt~p~~~D~lGhPi~GGLYDl~LGp~~~~~~C~TC~~~~~~CPGH~GHIeL~~p 87 (1640)
T KOG0262|consen 8 PVMSFQPSVSFGSYTDQEIRKLSVKKITNPITFDNLGHPIPGGLYDLALGPLDNSDVCSTCNQDELNCPGHMGHIELPVP 87 (1640)
T ss_pred cccccccceeeeccCHHHHhhcceeEecCceeecccCCCCCCcccccccCCccchhhhhhhcchhhcCCCccCeeeeccc
Confidence 44 34555999999999999999999999999998 99999999999999888888999999999999999999999999
Q ss_pred eeeeeehhhhhhhhhhhcccccccccCccCH
Q 045123 89 MFHIGFMKTLLTIMRCVCFNCSKILADEEDD 119 (219)
Q Consensus 89 v~h~~f~~~i~~iL~~vC~~C~rll~~~~~~ 119 (219)
||||+||+.++.+|++.|++|++|.+...+-
T Consensus 88 vynPlfF~~ly~lLr~sCl~Chhf~~k~~~v 118 (1640)
T KOG0262|consen 88 VYNPLFFDFLYNLLRGSCLFCHHFRCKNVDV 118 (1640)
T ss_pred ccCHHHHHHHHHHHHHHHHhhhhcccCcHHH
Confidence 9999999999999999999999999987543
No 8
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=99.94 E-value=1.8e-28 Score=242.77 Aligned_cols=147 Identities=31% Similarity=0.550 Sum_probs=119.3
Q ss_pred eeeeEEEEeCCHHHHhcCcccEEecCccccC-CCCCCCCCccCCCCCCCCCcccCCCCCCCCccCCcceeeecccceeee
Q 045123 14 KVRMVQFSILSPDEIRKMSVTEIDHGKTTER-GMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPMFHI 92 (219)
Q Consensus 14 ~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~-~~p~~~Gl~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIeL~~Pv~h~ 92 (219)
.++ |+|+++||++|++ |+.||+.|++||. ++|..+||+|+|||..+++..| |||+....||||||||||+.||+|+
T Consensus 4 ~~~-i~~gl~sp~~ir~-~s~ev~~pet~~~~~~P~~~Gl~d~ri~~~~~~~~C-~Cg~~~~~~~~~~GhIeLa~Pv~hi 80 (808)
T COG0086 4 IFD-IKFGLASPEEIRS-WSGEVKKPETINYRTKPERGGLFDERIFGPDKDYEC-TCGKYKRICPGGFGHIELAAPVAHI 80 (808)
T ss_pred cce-eEEecCCHHHHHh-cceEEcCccccCCCCcccCCCccchhhcCCCCCcee-cCCCCcCcCCCCceeEEeecceEEe
Confidence 344 9999999999999 5599999999996 5999999999999999999999 9999999999999999999999999
Q ss_pred eehhhhhhhhhhhcccccccccCccCHHHHHHHHhcCchhHHHHHHHHhccccccCCCCcccccccCCCCCCCCCccCCC
Q 045123 93 GFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKS 172 (219)
Q Consensus 93 ~f~~~i~~iL~~vC~~C~rll~~~~~~~~~~~~~~~~~k~r~~~i~~~ck~~~~Ce~~~~~d~~~~~~~~~~~~~~~~~~ 172 (219)
+|++.+.++|++.|..|+++++.. .+ .+. . ..+.+.+-+.+.... .| ...+
T Consensus 81 ~f~k~~~~~L~~~~~~~~~v~~~~---~~--~~~-~---~~l~~~~~~~~~~~~------~~--------------~~~~ 131 (808)
T COG0086 81 WFFKSIPSLLDMTCRDCERVLYFE---AY--VVL-G---TDLEKIQLLNETEYV------YD--------------SFCA 131 (808)
T ss_pred chhhccHHHHhhhHHhhhhhhhHh---HH--HHh-c---cchhhhcccchheee------cc--------------ccCC
Confidence 999999999999999999998882 12 111 1 233333333332220 00 1126
Q ss_pred CCCCCCCeEEEeceEEEEEE
Q 045123 173 GCGALQPTLTIDGMNMIAEY 192 (219)
Q Consensus 173 gCG~~qP~irk~glkl~~~~ 192 (219)
+||+.|++++++++.+..+.
T Consensus 132 ~~Ga~~~~~~~~~~~~~~~~ 151 (808)
T COG0086 132 HCGAEAIKILLEKPDLETER 151 (808)
T ss_pred CCCchhHHHHHhCcchhhhh
Confidence 89999999999998776655
No 9
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form. Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain.
Probab=99.77 E-value=3.4e-19 Score=180.61 Aligned_cols=105 Identities=30% Similarity=0.473 Sum_probs=95.5
Q ss_pred eEEEEeCCHHHHhcCcccEEecCccccCC--CCCCCCCccCCC-CCC--------------CCCcccCCCCCCCCccC--
Q 045123 17 MVQFSILSPDEIRKMSVTEIDHGKTTERG--MPMAGGLSDLRL-GTI--------------DKRFKCETCSSNMGECP-- 77 (219)
Q Consensus 17 ~i~F~~~s~eeI~~~Sv~ei~~~~~~~~~--~p~~~Gl~D~rl-G~~--------------~~~~~C~TC~~~~~~Cp-- 77 (219)
+|+++++|||+|++||+.||++|++++.+ +|..+||+|+|+ |+. .+...|.+||..+..|+
T Consensus 1 ~i~i~laSPe~I~~ws~geV~~petiny~t~kPe~~GLfcerIFGp~k~~ec~Cgkyk~~~~~~~~C~~Cgve~t~~~vr 80 (1140)
T TIGR02386 1 AIKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVR 80 (1140)
T ss_pred CeEEEecCHHHHHhhhceEEeccceecCCCCccCCCCcccchhcCCccCceeccccccccCcCCcCCCCCCCCcccchhh
Confidence 48999999999999999999999999964 999999999999 987 45678999999999998
Q ss_pred -Ccceeeecccceeeeeehhh-----------hhhhhhhhcccccccccCccCHHH
Q 045123 78 -GHFGHLELAKPMFHIGFMKT-----------LLTIMRCVCFNCSKILADEEDDKF 121 (219)
Q Consensus 78 -GHfGhIeL~~Pv~h~~f~~~-----------i~~iL~~vC~~C~rll~~~~~~~~ 121 (219)
+|||||+|+.||+|++|++. ..+.|+++|++|+.+.+++.++.+
T Consensus 81 r~rmGhI~La~Pv~Hiwy~k~~ps~~~~ll~~~~k~le~v~y~~~~~v~~~~~~~~ 136 (1140)
T TIGR02386 81 RERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDPGDTKL 136 (1140)
T ss_pred hhcccceeecCCceeehhcCCCchHHHHHhCCCHHHhhheeeccceEEeCCCCCch
Confidence 99999999999999999998 589999999999999888754433
No 10
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=99.58 E-value=1.6e-15 Score=154.30 Aligned_cols=101 Identities=30% Similarity=0.473 Sum_probs=88.2
Q ss_pred eeeeEEEEeCCHHHHhcCcccEEecCccccC--CCCCCCCCccCCC-CCCCCCcccCCCCCCC------CccC-------
Q 045123 14 KVRMVQFSILSPDEIRKMSVTEIDHGKTTER--GMPMAGGLSDLRL-GTIDKRFKCETCSSNM------GECP------- 77 (219)
Q Consensus 14 ~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~--~~p~~~Gl~D~rl-G~~~~~~~C~TC~~~~------~~Cp------- 77 (219)
++..|++++.|||+|++||+.||++|++.+. .+|..+||+|.|+ |+. ++..| .||.-. ..|+
T Consensus 6 ~~~~i~i~laspe~I~~ws~GeV~~petinyrt~kPe~~GLfcerIFgp~-kd~eC-~Cgkyk~~~~~~~~C~~cgve~~ 83 (1156)
T PRK00566 6 DFDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPT-KDYEC-LCGKYKRVRYKGIICERCGVEVT 83 (1156)
T ss_pred CcceEEEEccCHHHHHHhhcceEccccccccCCCccCCCCcccchhcCcc-cCcEE-eCccccccCcCCcCCCCCCceee
Confidence 6889999999999999999999999999884 5999999999999 654 46677 777422 3677
Q ss_pred ------Ccceeeecccceeeeeehh-----------hhhhhhhhhcccccccccCc
Q 045123 78 ------GHFGHLELAKPMFHIGFMK-----------TLLTIMRCVCFNCSKILADE 116 (219)
Q Consensus 78 ------GHfGhIeL~~Pv~h~~f~~-----------~i~~iL~~vC~~C~rll~~~ 116 (219)
+|||||+|+.||.|++|++ ...+.|+++|++|+.+++++
T Consensus 84 ~~~vrr~rmGhI~La~Pv~Hiwy~k~~ps~i~~ll~~~~k~le~v~y~~~~~v~~~ 139 (1156)
T PRK00566 84 RSKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDP 139 (1156)
T ss_pred echhhhhhcceeeecCceeeeeecCCCchHHHHHhCCCHHHhhheeecceEEEeCC
Confidence 9999999999999999999 44899999999999987765
No 11
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=99.10 E-value=7.8e-11 Score=113.76 Aligned_cols=86 Identities=26% Similarity=0.496 Sum_probs=72.0
Q ss_pred ceeeeEEEEeCCHHHHhcCc---------ccEEecCccccC--CCCCCCCCccCCC-CCCC--------------CCccc
Q 045123 13 AKVRMVQFSILSPDEIRKMS---------VTEIDHGKTTER--GMPMAGGLSDLRL-GTID--------------KRFKC 66 (219)
Q Consensus 13 ~~i~~i~F~~~s~eeI~~~S---------v~ei~~~~~~~~--~~p~~~Gl~D~rl-G~~~--------------~~~~C 66 (219)
.++..|+.++.|||+|++|| +.||++|++++. .+|..+||++.|. |+.. +...|
T Consensus 7 ~~~~~i~I~laSPe~I~~Ws~r~lpng~i~GeV~kpeTinyrT~KPE~dGLFCerIFGP~k~~eC~CGkyk~~~~~~~~C 86 (627)
T PRK02625 7 NRFDYVKIGLASPERIRQWGQRTLPNGQVVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVC 86 (627)
T ss_pred cccceEEEEecCHHHHHHHHHhhcCCCceeeEECCCcccccCCCCCCCCCEeechhcCCccCcEEeCCCccccCcCCcCC
Confidence 46788999999999999999 999999999884 6999999999997 8763 22357
Q ss_pred CCCCCCCCcc---CCcceeeecccceeeeeehhhh
Q 045123 67 ETCSSNMGEC---PGHFGHLELAKPMFHIGFMKTL 98 (219)
Q Consensus 67 ~TC~~~~~~C---pGHfGhIeL~~Pv~h~~f~~~i 98 (219)
..||....+- .=.+|||+|+.||-|++|++.+
T Consensus 87 ~~CgvE~t~s~vRR~RMG~I~La~PV~HiWylk~~ 121 (627)
T PRK02625 87 ERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGI 121 (627)
T ss_pred CCCCcEecchhhhHhhcCceeecCCceEeeccCCC
Confidence 7887665433 4569999999999999999854
No 12
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=99.09 E-value=5.9e-11 Score=122.44 Aligned_cols=104 Identities=27% Similarity=0.417 Sum_probs=80.6
Q ss_pred cceeeeEEEEeCCHHHHhcCcccEEecCccccC--CCCCCCCCccCCC-CCCC--------------CCcccCCCCCCCC
Q 045123 12 VAKVRMVQFSILSPDEIRKMSVTEIDHGKTTER--GMPMAGGLSDLRL-GTID--------------KRFKCETCSSNMG 74 (219)
Q Consensus 12 ~~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~--~~p~~~Gl~D~rl-G~~~--------------~~~~C~TC~~~~~ 74 (219)
...+..|+.++.||++|++||+.||++|++.+. .+|..+||++.|. |+.. ++..|..||..+.
T Consensus 6 ~~~f~~i~I~lASPe~Ir~WS~GEV~kpeTINyrT~KPE~dGLFCerIFGP~kd~eC~CGKyk~~~~~g~~C~~CGVEvt 85 (1460)
T PRK14906 6 VTNFDALRISLASAEDIRSWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECACGKYKRIRFKGIVCERCGVEVT 85 (1460)
T ss_pred ccccceEEEEecCHHHHHhhhceeEcCccccccccCCCCCCCeeeceeccCccCcEEeCccccccCcCCeEcCCCCcEec
Confidence 347889999999999999999999999999885 5999999999998 8763 2335777776543
Q ss_pred cc---CCcceeeecccceeeeeehhhhh-----------hhhhhhcccccccccC
Q 045123 75 EC---PGHFGHLELAKPMFHIGFMKTLL-----------TIMRCVCFNCSKILAD 115 (219)
Q Consensus 75 ~C---pGHfGhIeL~~Pv~h~~f~~~i~-----------~iL~~vC~~C~rll~~ 115 (219)
.- .=.||||+|+.||-|++|++.+. +-|+.+.++=+.+.++
T Consensus 86 ~s~vRR~RMGhI~La~PV~HiWylk~~ps~i~~lL~~~~k~le~viYf~~~iv~~ 140 (1460)
T PRK14906 86 RAKVRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKPKDLEKVLYFASYIITS 140 (1460)
T ss_pred chHHHHHhcCcccccCcchhhhhccCCcHHHHHHhCCCHHHhhhhhccceeEEec
Confidence 22 45799999999999999998653 4445555544444443
No 13
>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=99.09 E-value=8.7e-11 Score=113.30 Aligned_cols=84 Identities=25% Similarity=0.469 Sum_probs=69.1
Q ss_pred eeeEEEEeCCHHHHhcCc---------ccEEecCccccC--CCCCCCCCccCCC-CCCC--------------CCcccCC
Q 045123 15 VRMVQFSILSPDEIRKMS---------VTEIDHGKTTER--GMPMAGGLSDLRL-GTID--------------KRFKCET 68 (219)
Q Consensus 15 i~~i~F~~~s~eeI~~~S---------v~ei~~~~~~~~--~~p~~~Gl~D~rl-G~~~--------------~~~~C~T 68 (219)
+..|+.++.|||+|++|| +.||++|++++. .+|..+||++.|. |+.. +...|..
T Consensus 2 ~~~i~I~laSPe~I~~Ws~r~lpng~i~GeV~kp~TinyrT~KPE~dGLFCerIFGP~k~~eC~CGkyk~~~~~~~~C~~ 81 (619)
T TIGR02387 2 FDYVKITIASPERVMEWGQRTLPNGQVVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCER 81 (619)
T ss_pred CceEEEEecCHHHHHHHHHhhCCCCceeeEECCCcccccCCCCCCCCCEeechhcCCCcCcEEeCCCccccCcCCcCCCC
Confidence 467999999999999999 999999999884 6999999999998 8764 2235667
Q ss_pred CCCCCCcc---CCcceeeecccceeeeeehhhh
Q 045123 69 CSSNMGEC---PGHFGHLELAKPMFHIGFMKTL 98 (219)
Q Consensus 69 C~~~~~~C---pGHfGhIeL~~Pv~h~~f~~~i 98 (219)
||....+- .=.+|||+|+.||-|++|++.+
T Consensus 82 CgvE~t~s~vRR~RMG~I~La~PV~HiWylk~~ 114 (619)
T TIGR02387 82 CGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGI 114 (619)
T ss_pred CCCEEchhhhHHHhcCceeccCcceeeeecCCC
Confidence 76554332 4469999999999999999854
No 14
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=99.08 E-value=9.6e-11 Score=125.89 Aligned_cols=103 Identities=31% Similarity=0.503 Sum_probs=83.0
Q ss_pred ceeeeEEEEeCCHHHHhcCcccEEecCccccC--CCCCCCCCccCCC-CCCC--------------CCcccCCCCCCCCc
Q 045123 13 AKVRMVQFSILSPDEIRKMSVTEIDHGKTTER--GMPMAGGLSDLRL-GTID--------------KRFKCETCSSNMGE 75 (219)
Q Consensus 13 ~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~--~~p~~~Gl~D~rl-G~~~--------------~~~~C~TC~~~~~~ 75 (219)
..+..|+.++.||++|++||+.||++|++.+. .+|..+||++.|. |+.. +...|..||..+..
T Consensus 1446 ~~~~~i~i~laSPe~I~~Ws~GeV~kpeTinyrt~kPE~dGLFcerIFGp~kd~eC~Cgkyk~~~~~g~~C~~Cgvevt~ 1525 (2836)
T PRK14844 1446 QSFNEVSISIASPESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKRRHRGRICEKCGVEVTS 1525 (2836)
T ss_pred cccceEEEEecCHHHHHhhhceeECCcccccccCCCCCCCCeehhhhcCCCcCcEEecccccccccCCcCcCCCCcEeee
Confidence 57889999999999999999999999999985 5999999999995 9864 33578889877654
Q ss_pred c---CCcceeeecccceeeeeehhhh-----------hhhhhhhcccccccccC
Q 045123 76 C---PGHFGHLELAKPMFHIGFMKTL-----------LTIMRCVCFNCSKILAD 115 (219)
Q Consensus 76 C---pGHfGhIeL~~Pv~h~~f~~~i-----------~~iL~~vC~~C~rll~~ 115 (219)
. .-.+|||+|+.||.|++|++.+ .+-|+.+.++=+.+.++
T Consensus 1526 s~vRR~RmGhI~La~PV~HiWy~k~~ps~i~~lL~~~~k~le~v~y~~~~~v~~ 1579 (2836)
T PRK14844 1526 SKVRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILYSDNYIVID 1579 (2836)
T ss_pred chhhHhhcCceeecCcceeeecccCCcHHHHHHhCCCHHHhhheeeeeeEEEec
Confidence 4 4789999999999999999855 34455555554444443
No 15
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=98.99 E-value=3.6e-10 Score=109.98 Aligned_cols=87 Identities=26% Similarity=0.420 Sum_probs=70.2
Q ss_pred ceeeeEEEEeCCHHHHhcCcc---------cEEecCccccC--CCCCCCCCccCCC-CCCCC-----------------C
Q 045123 13 AKVRMVQFSILSPDEIRKMSV---------TEIDHGKTTER--GMPMAGGLSDLRL-GTIDK-----------------R 63 (219)
Q Consensus 13 ~~i~~i~F~~~s~eeI~~~Sv---------~ei~~~~~~~~--~~p~~~Gl~D~rl-G~~~~-----------------~ 63 (219)
..+..|+.++.||++|++||. .||++|++++. .+|..+||++.|. |+... .
T Consensus 5 ~~~~~i~I~laSPe~I~~Ws~r~lpng~ivGeV~kp~TinyrT~KPE~dGLFCErIFGP~k~~~C~CGkyk~~~~~~~~~ 84 (663)
T CHL00018 5 YKHQQLRIGLASPQQIRAWAERILPNGEIVGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGDEKEDP 84 (663)
T ss_pred cCcCeEEEEecCHHHHHHHHHhhCCCCceeeEECCCccccccCCCCCCCCEeechhcCCCcCCEEeCCCccccCccccCC
Confidence 467889999999999999995 89999999884 6999999999998 88741 1
Q ss_pred cccCCCCCCCCcc---CCcceeeecccceeeeeehhhhh
Q 045123 64 FKCETCSSNMGEC---PGHFGHLELAKPMFHIGFMKTLL 99 (219)
Q Consensus 64 ~~C~TC~~~~~~C---pGHfGhIeL~~Pv~h~~f~~~i~ 99 (219)
..|..||....+- .=.+|||+|+.||-|++|++.+.
T Consensus 85 ~~C~~CgVE~t~s~vRR~RMG~I~La~PV~HiWylk~~p 123 (663)
T CHL00018 85 KFCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLP 123 (663)
T ss_pred CccCCcCCEechhhhhHhhcCceeecCcceeehhhcCCc
Confidence 2566666544322 34689999999999999998553
No 16
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=98.96 E-value=4.6e-10 Score=121.14 Aligned_cols=88 Identities=27% Similarity=0.498 Sum_probs=72.7
Q ss_pred ccceeeeEEEEeCCHHHHhcCcccEEecCccccC--CCCCCCCCccCCC-CCCC--------------CCc-ccCCCCCC
Q 045123 11 KVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTER--GMPMAGGLSDLRL-GTID--------------KRF-KCETCSSN 72 (219)
Q Consensus 11 ~~~~i~~i~F~~~s~eeI~~~Sv~ei~~~~~~~~--~~p~~~Gl~D~rl-G~~~--------------~~~-~C~TC~~~ 72 (219)
....+..|+.++.||++|++||+.||++|++.+. .+|..+||++.|. |+.. ++. .|..||..
T Consensus 1392 ~~~~~~~i~i~lASpe~I~~ws~GeV~kpeTinyrt~kPe~dGLFcerIFGp~kd~eC~Cgkyk~~~~~g~~~C~~Cgve 1471 (2890)
T PRK09603 1392 RPKDFSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDIGTCEKCGVA 1471 (2890)
T ss_pred cccCcceEEEEecCHHHHHHhhceeEccccccccccCccCCCCEeeceeccCccCcEEeCCCcccccCCCCEEcCCCCcE
Confidence 4467889999999999999999999999999885 5999999999997 8753 112 47777765
Q ss_pred CCcc---CCcceeeecccceeeeeehhhh
Q 045123 73 MGEC---PGHFGHLELAKPMFHIGFMKTL 98 (219)
Q Consensus 73 ~~~C---pGHfGhIeL~~Pv~h~~f~~~i 98 (219)
...- .-.+|||+|+.||.|++|++.+
T Consensus 1472 vt~s~vRR~RmGhI~La~Pv~HiWy~k~~ 1500 (2890)
T PRK09603 1472 ITHSKVRRFRMGHIELATPVAHIWYVNSL 1500 (2890)
T ss_pred echhHhHHHhcCceeecCcceeeeccCCC
Confidence 4322 4579999999999999999855
No 17
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=51.17 E-value=5.5 Score=32.09 Aligned_cols=27 Identities=30% Similarity=0.639 Sum_probs=17.0
Q ss_pred ccCCCCCCCCCcccCCCCCCCCccCCcceeeecc
Q 045123 53 SDLRLGTIDKRFKCETCSSNMGECPGHFGHLELA 86 (219)
Q Consensus 53 ~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIeL~ 86 (219)
-|..+|..--...|..|+ +|+||+=--
T Consensus 79 ~D~s~gm~RtEv~C~~Cg-------~HLGHVF~D 105 (134)
T TIGR00357 79 RDESHGMIRTEVRCRNCD-------AHLGHVFDD 105 (134)
T ss_pred ecCCCCcEEEEEEecCCC-------CccCcccCC
Confidence 566677443345676654 799997543
No 18
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=44.57 E-value=12 Score=26.33 Aligned_cols=29 Identities=24% Similarity=0.617 Sum_probs=17.0
Q ss_pred hcccccccccCccCHHHHHHHH-hcCchhHH
Q 045123 105 VCFNCSKILADEEDDKFKLALK-IRHPKSRL 134 (219)
Q Consensus 105 vC~~C~rll~~~~~~~~~~~~~-~~~~k~r~ 134 (219)
-|++|++++.+.= .+|++.+. -.+|+.-|
T Consensus 6 RCFsCGkvi~~~w-~~y~~rv~~ge~p~~vL 35 (63)
T COG1644 6 RCFSCGKVIGHKW-EEYKRRVEEGEDPGEVL 35 (63)
T ss_pred EeecCCCCHHHHH-HHHHHHHHcCCCHHHHH
Confidence 5999999987643 23443332 34565443
No 19
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=41.43 E-value=11 Score=33.10 Aligned_cols=38 Identities=21% Similarity=0.443 Sum_probs=24.9
Q ss_pred CCcccCCCCCCCCccCCcceeeecccceeeeeehhhhhhhhh-hhcccccccccCc
Q 045123 62 KRFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMR-CVCFNCSKILADE 116 (219)
Q Consensus 62 ~~~~C~TC~~~~~~CpGHfGhIeL~~Pv~h~~f~~~i~~iL~-~vC~~C~rll~~~ 116 (219)
.+..|.-| ||.|+ +.++..|.+=-. ..|++|||+|...
T Consensus 196 ~g~~C~GC------------~m~l~-----~~~~~~V~~~d~iv~CP~CgRILy~~ 234 (239)
T COG1579 196 EGRVCGGC------------HMKLP-----SQTLSKVRKKDEIVFCPYCGRILYYD 234 (239)
T ss_pred cCCcccCC------------eeeec-----HHHHHHHhcCCCCccCCccchHHHhh
Confidence 46678877 45554 355566665222 6799999998753
No 20
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=41.34 E-value=16 Score=25.37 Aligned_cols=23 Identities=26% Similarity=0.826 Sum_probs=14.5
Q ss_pred hhhhhcccccccccCccCHHHHHHHH
Q 045123 101 IMRCVCFNCSKILADEEDDKFKLALK 126 (219)
Q Consensus 101 iL~~vC~~C~rll~~~~~~~~~~~~~ 126 (219)
+++.+|..|+|=+ ++.+|+.+++
T Consensus 2 Vf~lVCsTCGrDl---SeeRy~Lli~ 24 (63)
T PHA03082 2 VFQLVCSTCGRDL---SEERYRLLIK 24 (63)
T ss_pred eeeeeecccCcch---hHHHHHHHHH
Confidence 3567899999843 3345655544
No 21
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=40.77 E-value=15 Score=25.45 Aligned_cols=32 Identities=25% Similarity=0.670 Sum_probs=18.4
Q ss_pred hhhhhcccccccccCccCHHHHHHHHhcCchhHHHHHHH
Q 045123 101 IMRCVCFNCSKILADEEDDKFKLALKIRHPKSRLEQILC 139 (219)
Q Consensus 101 iL~~vC~~C~rll~~~~~~~~~~~~~~~~~k~r~~~i~~ 139 (219)
+++.+|..|+|=+ ++.+|+.+++- ..++.|++
T Consensus 2 Vf~lvCSTCGrDl---SeeRy~Lli~~----~~Lk~Vl~ 33 (63)
T PF05864_consen 2 VFQLVCSTCGRDL---SEERYRLLIKE----MSLKKVLR 33 (63)
T ss_pred eeeeeecccCCcc---hHHHHHHHHHH----hhHHHHHH
Confidence 3567899999843 33456555442 23555544
No 22
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=38.54 E-value=15 Score=25.53 Aligned_cols=20 Identities=20% Similarity=0.685 Sum_probs=12.2
Q ss_pred hhcccccccccCccCHHHHHH
Q 045123 104 CVCFNCSKILADEEDDKFKLA 124 (219)
Q Consensus 104 ~vC~~C~rll~~~~~~~~~~~ 124 (219)
.-|++|++++.+.- .+|...
T Consensus 5 VRCFTCGkvi~~~~-e~y~~~ 24 (60)
T PF01194_consen 5 VRCFTCGKVIGNKW-EEYLER 24 (60)
T ss_dssp SS-STTTSBTCGHH-HHHHHH
T ss_pred eecCCCCCChhHhH-HHHHHH
Confidence 35999999987643 344433
No 23
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=37.74 E-value=15 Score=29.80 Aligned_cols=10 Identities=50% Similarity=1.095 Sum_probs=7.8
Q ss_pred cCCcceeeec
Q 045123 76 CPGHFGHLEL 85 (219)
Q Consensus 76 CpGHfGhIeL 85 (219)
|-||+|||-.
T Consensus 109 C~~HLGHVF~ 118 (146)
T KOG0856|consen 109 CGGHLGHVFK 118 (146)
T ss_pred cCCceeeeec
Confidence 4589999866
No 24
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=37.55 E-value=39 Score=28.81 Aligned_cols=17 Identities=29% Similarity=0.819 Sum_probs=13.1
Q ss_pred CCCcccCCCCCC---CCccC
Q 045123 61 DKRFKCETCSSN---MGECP 77 (219)
Q Consensus 61 ~~~~~C~TC~~~---~~~Cp 77 (219)
+....|.-||++ ..+||
T Consensus 58 ~~~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 58 EENPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred ccccccchhcccCcccccCC
Confidence 356789999876 56888
No 25
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=36.92 E-value=12 Score=30.34 Aligned_cols=25 Identities=28% Similarity=0.748 Sum_probs=15.5
Q ss_pred ccCCCCCCCCCcccCCCCCCCCccCCcceeee
Q 045123 53 SDLRLGTIDKRFKCETCSSNMGECPGHFGHLE 84 (219)
Q Consensus 53 ~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIe 84 (219)
-|..+|..--...|..|+ +|.||+=
T Consensus 82 ~D~s~gm~RtEv~C~~Cg-------~HLGHVF 106 (142)
T PRK00222 82 RDTSHGMVRTEVRCANCD-------SHLGHVF 106 (142)
T ss_pred eccCCCceEEEEEeCCCC-------CccCccc
Confidence 456666543345676654 7899864
No 26
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=36.38 E-value=20 Score=25.81 Aligned_cols=29 Identities=21% Similarity=0.440 Sum_probs=16.6
Q ss_pred hhcccccccccCccCHHHHHHHH-hcCchhH
Q 045123 104 CVCFNCSKILADEEDDKFKLALK-IRHPKSR 133 (219)
Q Consensus 104 ~vC~~C~rll~~~~~~~~~~~~~-~~~~k~r 133 (219)
.-|++|++++.+.- .+|...+. -.+|..-
T Consensus 5 VRCFTCGkvig~~w-e~y~~~~~~g~~~~~~ 34 (71)
T PLN00032 5 VRCFTCGKVIGNKW-DTYLDLLQADYSEGDA 34 (71)
T ss_pred eeecCCCCCcHHHH-HHHHHHHhcCCCHHHH
Confidence 35999999987643 34544332 2345443
No 27
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=34.45 E-value=21 Score=25.02 Aligned_cols=31 Identities=29% Similarity=0.661 Sum_probs=18.0
Q ss_pred hhhcccccccccCccCHHHHHHHHh-cCchhHH
Q 045123 103 RCVCFNCSKILADEEDDKFKLALKI-RHPKSRL 134 (219)
Q Consensus 103 ~~vC~~C~rll~~~~~~~~~~~~~~-~~~k~r~ 134 (219)
-..|++|++++.+.- .+|...++. .+|++-|
T Consensus 4 PvRCFTCGkvi~~~w-e~y~~~~~~g~~~~~vL 35 (62)
T PRK04016 4 PVRCFTCGKVIAEKW-EEFKERVEAGEDPGKVL 35 (62)
T ss_pred CeEecCCCCChHHHH-HHHHHHHHcCCCHHHHH
Confidence 356999999987642 345444432 4454433
No 28
>PF14260 zf-C4pol: C4-type zinc-finger of DNA polymerase delta
Probab=33.01 E-value=31 Score=24.05 Aligned_cols=37 Identities=22% Similarity=0.611 Sum_probs=23.5
Q ss_pred hhcccccccccCccCHHHHHHHHhcCchhHHHHHHHHhcc
Q 045123 104 CVCFNCSKILADEEDDKFKLALKIRHPKSRLEQILCACKT 143 (219)
Q Consensus 104 ~vC~~C~rll~~~~~~~~~~~~~~~~~k~r~~~i~~~ck~ 143 (219)
.+|..|.+ ++....+....+++.-.+|+..+|.+|..
T Consensus 14 ~lC~~C~~---~~~~~~~~l~~~~~~~E~~~~~l~~iC~~ 50 (73)
T PF14260_consen 14 PLCSNCRS---DPQQTIYNLLSRLRELERRFNELWTICQS 50 (73)
T ss_pred CcCcccCc---ChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57777776 22222233334556667899999999974
No 29
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=32.81 E-value=14 Score=29.29 Aligned_cols=26 Identities=27% Similarity=0.680 Sum_probs=15.9
Q ss_pred ccCCCCCCCCCcccCCCCCCCCccCCcceeeec
Q 045123 53 SDLRLGTIDKRFKCETCSSNMGECPGHFGHLEL 85 (219)
Q Consensus 53 ~D~rlG~~~~~~~C~TC~~~~~~CpGHfGhIeL 85 (219)
-|..+|..--...|..| -+|.||+=-
T Consensus 76 ~D~s~g~~R~Ev~C~~C-------g~HLGHVF~ 101 (124)
T PF01641_consen 76 EDFSHGMVRTEVRCARC-------GSHLGHVFD 101 (124)
T ss_dssp EEECTSSEEEEEEETTT-------CCEEEEEES
T ss_pred ccccCCceEEEEEecCC-------CCccccEeC
Confidence 45555544334567665 589999744
No 30
>KOG0466 consensus Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=28.49 E-value=81 Score=29.44 Aligned_cols=17 Identities=35% Similarity=0.888 Sum_probs=12.8
Q ss_pred CcccCCCCCC----------CCccCCc
Q 045123 63 RFKCETCSSN----------MGECPGH 79 (219)
Q Consensus 63 ~~~C~TC~~~----------~~~CpGH 79 (219)
...|..||.. ..+||||
T Consensus 109 ~~~c~~~g~~~~~klvRHVSfVDCPGH 135 (466)
T KOG0466|consen 109 RPPCDRPGCEGKMKLVRHVSFVDCPGH 135 (466)
T ss_pred CCCcccCCCCCceEEEEEEEeccCCch
Confidence 4578888865 3589998
No 31
>TIGR01623 put_zinc_LRP1 putative zinc finger domain, LRP1 type. This model represents a putative zinc finger domain found in plants. Arabidopsis thaliana has at least 10 distinct members. Proteins containing this domain, including LRP1, generally share the same size, about 300 amino acids, and architecture. This 43-residue domain, and a more C-terminal companion domain of similar size, appear as tightly conserved islands of sequence similarity. The remainder consists largely of low-complexity sequence. Several animal proteins have regions with matching patterns of Cys, Gly, and His residues. These are not included in the model but score between trusted and noise cutoffs.
Probab=28.47 E-value=19 Score=23.36 Aligned_cols=19 Identities=26% Similarity=0.490 Sum_probs=14.1
Q ss_pred CcccCCCCCC-CCccCCcce
Q 045123 63 RFKCETCSSN-MGECPGHFG 81 (219)
Q Consensus 63 ~~~C~TC~~~-~~~CpGHfG 81 (219)
...|.||-.. ..+|+||.-
T Consensus 15 ~~~CRtCCK~r~~DC~tHv~ 34 (43)
T TIGR01623 15 FERCRTCCKSRGFHCVTHVK 34 (43)
T ss_pred hhhhhHHhcccCcCCcchhc
Confidence 4689998654 459999964
No 32
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=28.32 E-value=26 Score=22.44 Aligned_cols=20 Identities=45% Similarity=1.127 Sum_probs=13.2
Q ss_pred ccCCCCCCCCccCCcceeeeccc--ceeee
Q 045123 65 KCETCSSNMGECPGHFGHLELAK--PMFHI 92 (219)
Q Consensus 65 ~C~TC~~~~~~CpGHfGhIeL~~--Pv~h~ 92 (219)
+|..||. |||+.-.+ |+|+.
T Consensus 3 kC~~CG~--------~GH~~t~k~CP~~~~ 24 (40)
T PF15288_consen 3 KCKNCGA--------FGHMRTNKRCPMYCW 24 (40)
T ss_pred ccccccc--------ccccccCccCCCCCC
Confidence 5777765 77876543 77664
No 33
>PF06463 Mob_synth_C: Molybdenum Cofactor Synthesis C; InterPro: IPR010505 The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cis-dithiolene moiety to molybdopterin (MPT). MoCF is ubiquitous in nature, and the pathway for MoCF biosynthesis is conserved in all three domains of life. MoCF-containing enzymes function as oxidoreductases in carbon, nitrogen, and sulphur metabolism [, ]. In Escherichia coli, biosynthesis of MoCF is a three stage process. It begins with the MoaA and MoaC conversion of GTP to the meta-stable pterin intermediate precursor Z. The second stage involves MPT synthase (MoaD and MoaE), which converts precursor Z to MPT; MoeB is involved in the recycling of MPT synthase. The final step in MoCF synthesis is the attachment of mononuclear Mo to MPT, a process that requires MoeA and which is enhanced by MogA in an Mg2 ATP-dependent manner []. MoCF is the active co-factor in eukaryotic and some prokaryotic molybdo-enzymes, but the majority of bacterial enzymes requiring MoCF, need a modification of MTP for it to be active; MobA is involved in the attachment of a nucleotide monophosphate to MPT resulting in the MGD co-factor, the active co-factor for most prokaryotic molybdo-enzymes. Bacterial two-hybrid studies have revealed the close interactions between MoeA, MogA, and MobA in the synthesis of MoCF []. Moreover the close functional association of MoeA and MogA in the synthesis of MoCF is supported by fact that the known eukaryotic homologues to MoeA and MogA exist as fusion proteins: CNX1 (Q39054 from SWISSPROT) of Arabidopsis thaliana (Mouse-ear cress), mammalian Gephryin (e.g. Q9NQX3 from SWISSPROT) and Drosophila melanogaster (Fruit fly) Cinnamon (P39205 from SWISSPROT) []. This entry represents MoaA, which belongs to a family of enzymes involved in the synthesis of metallo-cofactors (IPR000385 from INTERPRO). Each subunit of the MoaA dimer is comprised of an N-terminal SAM domain (IPR007197 from INTERPRO) that contains the [4Fe-4S] cluster typical for this family of enzymes, as well as an additional [4Fe-4S] cluster in the C-terminal domain that is unique to MoaA proteins []. The unique Fe site of the C-terminal [4Fe-4S] cluster is thought to be involved in the binding and activation of 5'-GTP. Mutations in the human MoCF biosynthesis proteins MOCS1, MOCS2 or GEPH cause MoCF Deficiency type A (MOCOD), causing the loss of activity of MoCF-containing enzymes, resulting in neurological abnormalities and death [].; GO: 0051539 4 iron, 4 sulfur cluster binding, 0006777 Mo-molybdopterin cofactor biosynthetic process, 0019008 molybdopterin synthase complex; PDB: 2FB2_A 2FB3_A 1TV8_B 1TV7_A.
Probab=25.79 E-value=33 Score=26.95 Aligned_cols=30 Identities=23% Similarity=0.544 Sum_probs=16.8
Q ss_pred ccCCcceeeecccceeeeeehhhhhhhhhhhcccccccccCc
Q 045123 75 ECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADE 116 (219)
Q Consensus 75 ~CpGHfGhIeL~~Pv~h~~f~~~i~~iL~~vC~~C~rll~~~ 116 (219)
.-||.-|.|.+..|+-|+ .|-+|.|+.++.
T Consensus 53 ~~~g~~g~vG~I~~~s~~------------FC~~CNRiRlTs 82 (128)
T PF06463_consen 53 RIPGGKGRVGFISPVSNP------------FCSSCNRIRLTS 82 (128)
T ss_dssp EETTT--EEEEE-TTTS--------------GGG--EEEE-T
T ss_pred EECCCCcEEEEEeCCCCC------------CCCcCCEEEEcc
Confidence 447777777777777775 499999998874
No 34
>PF14754 IFR3_antag: Papain-like auto-proteinase
Probab=21.84 E-value=15 Score=30.71 Aligned_cols=27 Identities=44% Similarity=0.955 Sum_probs=19.8
Q ss_pred CcccCCCCC---CCCccCCcc-eeeecccce
Q 045123 63 RFKCETCSS---NMGECPGHF-GHLELAKPM 89 (219)
Q Consensus 63 ~~~C~TC~~---~~~~CpGHf-GhIeL~~Pv 89 (219)
...|..|-. .+..|||-| |-+.|+.||
T Consensus 38 stlcaecfrgcegmeqcpglfmgllklaspv 68 (249)
T PF14754_consen 38 STLCAECFRGCEGMEQCPGLFMGLLKLASPV 68 (249)
T ss_pred ccHHHHHhccCcchhhCcHHHHHHHHhcCCC
Confidence 446777743 478999976 888888765
No 35
>PF14353 CpXC: CpXC protein
Probab=20.47 E-value=42 Score=25.92 Aligned_cols=40 Identities=15% Similarity=0.381 Sum_probs=22.7
Q ss_pred ccCCCCCCCCccCCcceeeecccc---eeeeeehhhhh--hhhhhhccccccc
Q 045123 65 KCETCSSNMGECPGHFGHLELAKP---MFHIGFMKTLL--TIMRCVCFNCSKI 112 (219)
Q Consensus 65 ~C~TC~~~~~~CpGHfGhIeL~~P---v~h~~f~~~i~--~iL~~vC~~C~rl 112 (219)
.|..|+.. +.+++..- ..+|.+...|+ ++...+|++|++.
T Consensus 3 tCP~C~~~--------~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~ 47 (128)
T PF14353_consen 3 TCPHCGHE--------FEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHK 47 (128)
T ss_pred CCCCCCCe--------eEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCc
Confidence 57777643 34444422 22344444443 4557999999983
No 36
>PF08038 Tom7: TOM7 family; InterPro: IPR012621 This family consists of TOM7 family of mitochondrial import receptors. TOM7 forms part of the translocase of the outer mitochondrial membrane (TOM) complex and it appears to function as a modulator of the dynamics of the mitochondrial protein transport machinery by promoting the dissociation of subunits of the outer membrane translocase [].; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0006886 intracellular protein transport, 0005741 mitochondrial outer membrane
Probab=20.25 E-value=40 Score=21.74 Aligned_cols=17 Identities=47% Similarity=0.962 Sum_probs=13.2
Q ss_pred eecccceeeeeehhhhh
Q 045123 83 LELAKPMFHIGFMKTLL 99 (219)
Q Consensus 83 IeL~~Pv~h~~f~~~i~ 99 (219)
++.++.++|.||+..|.
T Consensus 8 ~~~~k~~~HyGfIP~Il 24 (42)
T PF08038_consen 8 LDVAKTVFHYGFIPLIL 24 (42)
T ss_pred HHhheeeEEeeehHHHH
Confidence 45678899999988765
Done!