Query psy7584
Match_columns 67
No_of_seqs 115 out of 779
Neff 5.1
Searched_HMMs 46136
Date Fri Aug 16 22:09:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7584.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7584hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07225 DNA-directed RNA poly 99.9 9.4E-22 2E-26 153.1 6.5 58 10-67 316-373 (605)
2 TIGR03670 rpoB_arch DNA-direct 99.8 1.7E-21 3.7E-26 151.5 6.6 58 10-67 310-367 (599)
3 COG0085 RpoB DNA-directed RNA 99.8 5.9E-21 1.3E-25 155.4 6.6 56 12-67 785-844 (1060)
4 PRK08565 DNA-directed RNA poly 99.8 2E-20 4.4E-25 152.3 5.8 58 10-67 814-871 (1103)
5 PF00562 RNA_pol_Rpb2_6: RNA p 99.8 3.8E-20 8.2E-25 137.0 6.4 57 11-67 188-251 (386)
6 KOG0214|consensus 99.8 1E-19 2.3E-24 147.0 6.0 64 4-67 848-911 (1141)
7 TIGR02013 rpoB DNA-directed RN 99.8 2.3E-19 4.9E-24 146.2 6.0 57 11-67 789-852 (1065)
8 PRK00405 rpoB DNA-directed RNA 99.8 3.8E-19 8.2E-24 145.3 6.3 57 11-67 831-895 (1112)
9 CHL00001 rpoB RNA polymerase b 99.8 8.7E-19 1.9E-23 143.0 7.1 58 10-67 768-829 (1070)
10 cd00653 RNA_pol_B_RPB2 RNA pol 99.8 9.5E-19 2.1E-23 139.8 7.1 57 11-67 586-645 (866)
11 KOG0215|consensus 99.8 4.7E-20 1E-24 148.4 -1.1 58 10-67 869-926 (1153)
12 CHL00207 rpoB RNA polymerase b 99.7 1.9E-18 4.2E-23 141.1 7.0 58 10-67 761-825 (1077)
13 KOG0216|consensus 99.7 1E-16 2.2E-21 129.5 5.3 53 15-67 817-871 (1111)
14 PRK09603 bifunctional DNA-dire 99.5 3.2E-14 7E-19 123.5 6.0 29 39-67 1075-1103(2890)
15 PRK14844 bifunctional DNA-dire 99.2 2.3E-11 4.9E-16 106.1 6.6 28 40-67 1069-1096(2836)
16 PF04941 LEF-8: Late expressio 94.0 0.19 4.1E-06 41.3 6.2 30 38-67 704-733 (748)
17 PHA03394 lef-8 DNA-directed RN 93.8 0.21 4.6E-06 41.6 6.1 29 39-67 695-723 (865)
18 KOG0214|consensus 66.6 5.5 0.00012 34.3 2.7 38 25-66 856-893 (1141)
19 PF13497 DUF4121: Domain of un 51.8 8.8 0.00019 28.3 1.3 18 46-63 42-61 (262)
20 PF02470 MCE: mce related prot 28.3 1.2E+02 0.0026 17.1 4.7 21 12-32 16-36 (81)
21 cd06541 ASCH ASC-1 homology or 20.9 88 0.0019 19.0 2.0 22 37-58 14-37 (105)
No 1
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=99.85 E-value=9.4e-22 Score=153.08 Aligned_cols=58 Identities=53% Similarity=0.888 Sum_probs=55.5
Q ss_pred cceeeeeEEcCCCCCeEEEEEEEEeccCCcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584 10 FSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT 67 (67)
Q Consensus 10 ~~~rd~S~~~k~~e~g~Vd~V~~~~~~~g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv 67 (67)
...+|+|++++++|+|+||+|.++.+.+|.+.|+|++|+.|+|+||||||||||||||
T Consensus 316 ~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~vkv~ir~~R~p~iGDKfssRHGQKGv 373 (605)
T PRK07225 316 EKRRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGV 373 (605)
T ss_pred cCcceeeEEecCCCcEEEEEEEEEecCCCCEEEEEEEEEEEeccccchhhhcccCcee
Confidence 3479999999999999999999999999999999999999999999999999999997
No 2
>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B. This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Probab=99.85 E-value=1.7e-21 Score=151.52 Aligned_cols=58 Identities=55% Similarity=0.902 Sum_probs=55.4
Q ss_pred cceeeeeEEcCCCCCeEEEEEEEEeccCCcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584 10 FSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT 67 (67)
Q Consensus 10 ~~~rd~S~~~k~~e~g~Vd~V~~~~~~~g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv 67 (67)
...+|+|++++++|+|+||+|.++.++++.+.|+|++|+.|+|+||||||||||||||
T Consensus 310 ~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~vkv~~r~~R~p~iGDKfssRHGQKGv 367 (599)
T TIGR03670 310 ERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGV 367 (599)
T ss_pred ccCceEEEEecCCCcEEEEEEEEEecCCCcEEEEEEEeeeecCcchhhhhhhccCcce
Confidence 3479999999999999999999999999999999999999999999999999999997
No 3
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=99.83 E-value=5.9e-21 Score=155.40 Aligned_cols=56 Identities=46% Similarity=0.617 Sum_probs=54.4
Q ss_pred eeeeeEEcCCCCCeEEEEEEEEeccC----CcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584 12 KRDGSTFLRNSETGIVDQVMLTLNVD----GYKFCKIRVRSVRIPQIGDKFASRHGQKGT 67 (67)
Q Consensus 12 ~rd~S~~~k~~e~g~Vd~V~~~~~~~----g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv 67 (67)
+||+|++++++|+|+||+|.++++++ +++.|||++|+.|+|++|||||||||||||
T Consensus 785 ~rdtsl~~~~g~~G~V~~V~~~~~~~~~~g~~~~vkV~v~~~R~~~~GDK~a~RHG~KGV 844 (1060)
T COG0085 785 VRDTSLRVPHGEEGIVDDVQVFTREDGDPGVNKLVKVYVAQKRKPQIGDKMAGRHGNKGV 844 (1060)
T ss_pred eeccceeecCCCCeEEEEEEEEeccCCCcCceEEEEEEEEEeccCCccccccccCCCCce
Confidence 89999999999999999999999987 789999999999999999999999999997
No 4
>PRK08565 DNA-directed RNA polymerase subunit B; Provisional
Probab=99.81 E-value=2e-20 Score=152.31 Aligned_cols=58 Identities=55% Similarity=0.908 Sum_probs=55.5
Q ss_pred cceeeeeEEcCCCCCeEEEEEEEEeccCCcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584 10 FSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT 67 (67)
Q Consensus 10 ~~~rd~S~~~k~~e~g~Vd~V~~~~~~~g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv 67 (67)
...+|+|++++.+|+|+||+|.++.+.++.+.|+|++|+.|+|+||||||||||||||
T Consensus 814 ~~~~~~s~~~~~~e~g~V~~V~~~~~~~~~~~vkv~ir~~R~p~iGDKfssRhGqKGv 871 (1103)
T PRK08565 814 QERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGV 871 (1103)
T ss_pred CccccceEEecCCCceEEEEEEEEecCCCcEEEEEEEEEEecCchhhhhhhhccCcce
Confidence 3479999999999999999999999999999999999999999999999999999997
No 5
>PF00562 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; InterPro: IPR007120 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. RNA polymerases (2.7.7.6 from EC) 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 represents the hybrid-binding domain and the wall domain []. The hybrid-binding domain binds the nascent RNA strand/template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion []. This domain is also involved in binding to Rpb1 and Rpb3 []. Many of the bacterial members contain large insertions within this domain, which are known as dispensable region 2 (DRII).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_R 3HKZ_B 2PMZ_R 3H0G_B 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B ....
Probab=99.81 E-value=3.8e-20 Score=137.04 Aligned_cols=57 Identities=58% Similarity=0.865 Sum_probs=50.0
Q ss_pred ceeeeeEEcCCCCCeEEEEEEE-------EeccCCcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584 11 SKRDGSTFLRNSETGIVDQVML-------TLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT 67 (67)
Q Consensus 11 ~~rd~S~~~k~~e~g~Vd~V~~-------~~~~~g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv 67 (67)
..+|+|++++.+|.|+||+|.+ ..+.++...|+|++|+.|+|++|||||||||||||
T Consensus 188 ~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~~~~~~~~iki~ir~~R~p~iGDKfssRHGqKGV 251 (386)
T PF00562_consen 188 NYRDTSIKYKSGESGRVDKVIIFSNEKKDTSNNEGYKKIKIRIRSTRRPQIGDKFSSRHGQKGV 251 (386)
T ss_dssp SEEEEEEES-TT-EEEEEEEEEECCCSSBEEETTCEEEEEEEEEEEEE--TTEEEEETTSEEEE
T ss_pred cccceeecccccEEeEeccccccccccccccccCcceEEEEEecccccchhHHHHhhhhcCceE
Confidence 3799999999999999999999 66788899999999999999999999999999997
No 6
>KOG0214|consensus
Probab=99.79 E-value=1e-19 Score=147.04 Aligned_cols=64 Identities=66% Similarity=0.944 Sum_probs=60.3
Q ss_pred CCCCCccceeeeeEEcCCCCCeEEEEEEEEeccCCcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584 4 EGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT 67 (67)
Q Consensus 4 ~~~~~~~~~rd~S~~~k~~e~g~Vd~V~~~~~~~g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv 67 (67)
+..++.+.++|+|+.++++|.|+||+|.++.|.+|.+|++|++|+.|.|++|||||||||||||
T Consensus 848 ~~~~~~~t~~d~s~~Lr~~e~Givd~V~vt~n~~G~kF~kv~vr~~ripqiGDKfasrHgqKG~ 911 (1141)
T KOG0214|consen 848 GPEDRLYTKRDHSTKLRHTERGIVDQVWVTKNSEGPKFVKVRVRQVRIPQIGDKFASRHGQKGT 911 (1141)
T ss_pred cccccccccccceeecccCCcceEEEEEEecCCCCCceeEEEEeecccccccchhccccccCcc
Confidence 3455678899999999999999999999999999999999999999999999999999999997
No 7
>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit. This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit.
Probab=99.78 E-value=2.3e-19 Score=146.22 Aligned_cols=57 Identities=35% Similarity=0.452 Sum_probs=53.4
Q ss_pred ceeeeeEEcCCCCCeEEEEEEEEeccCC-------cEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584 11 SKRDGSTFLRNSETGIVDQVMLTLNVDG-------YKFCKIRVRSVRIPQIGDKFASRHGQKGT 67 (67)
Q Consensus 11 ~~rd~S~~~k~~e~g~Vd~V~~~~~~~g-------~~~vkV~vR~~R~P~iGDKFsSRHGQKGv 67 (67)
.++|+|++++++|+|+||+|.++.++++ ...|+|++|+.|+|+||||||||||||||
T Consensus 789 ~~~d~s~~~~~~~~g~V~~V~~~~~~~~~~~~~~~~~~vkv~ir~~R~p~iGDKfasRHGqKGv 852 (1065)
T TIGR02013 789 DVRDTSLRVPPGVEGTVIDVKVFSRKQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGV 852 (1065)
T ss_pred cccccceEccCCCCEEEEEEEEEeccCCCccCcCccEEEEEEEeecccccccchhhhcccCcee
Confidence 4789999999999999999999988776 57899999999999999999999999997
No 8
>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed
Probab=99.77 E-value=3.8e-19 Score=145.34 Aligned_cols=57 Identities=35% Similarity=0.488 Sum_probs=53.0
Q ss_pred ceeeeeEEcCCCCCeEEEEEEEEec-cCC-------cEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584 11 SKRDGSTFLRNSETGIVDQVMLTLN-VDG-------YKFCKIRVRSVRIPQIGDKFASRHGQKGT 67 (67)
Q Consensus 11 ~~rd~S~~~k~~e~g~Vd~V~~~~~-~~g-------~~~vkV~vR~~R~P~iGDKFsSRHGQKGv 67 (67)
.++|+|++++++|+|+||+|.++.+ .+| ...|+|++|+.|+|+||||||||||||||
T Consensus 831 ~~~d~s~~~~~~~~g~V~~v~~~~~~~~~~~~~~~~~~~vkv~ir~~R~p~iGDKfasRHGqKGv 895 (1112)
T PRK00405 831 DVKDTSLRVPHGEEGTVIDVKVFTRIEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGV 895 (1112)
T ss_pred ccccceEEcCCCCCEEEEEEEEeeccccCCccCcCcceEEEEEEeeecccCcccchhhccCCcee
Confidence 4799999999999999999999987 665 47899999999999999999999999997
No 9
>CHL00001 rpoB RNA polymerase beta subunit
Probab=99.76 E-value=8.7e-19 Score=143.01 Aligned_cols=58 Identities=26% Similarity=0.261 Sum_probs=53.4
Q ss_pred cceeeeeEEcCCCCCeEEEEEEEEec----cCCcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584 10 FSKRDGSTFLRNSETGIVDQVMLTLN----VDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT 67 (67)
Q Consensus 10 ~~~rd~S~~~k~~e~g~Vd~V~~~~~----~~g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv 67 (67)
..++|+|+++++++.|+|++|.++.+ .++...|+|++|+.|+|++|||||||||||||
T Consensus 768 ~~~~d~sl~~~~~~~g~V~~v~~~~~~~~~~~~~~~vkv~i~~~R~~~vGDK~asRHGqKGv 829 (1070)
T CHL00001 768 STSKETCLKLPIGGRGRVIDVRWIQKKGGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGI 829 (1070)
T ss_pred CcceeCeEECCCCCceEEEEEEEEecccCCCCCcEEEEEEEEEEecCCCCcccccccCCcce
Confidence 45899999999999999999999874 45678999999999999999999999999997
No 10
>cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Probab=99.76 E-value=9.5e-19 Score=139.79 Aligned_cols=57 Identities=53% Similarity=0.722 Sum_probs=53.9
Q ss_pred ceeeeeEEcCCCCCeEEEEEEEEe---ccCCcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584 11 SKRDGSTFLRNSETGIVDQVMLTL---NVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT 67 (67)
Q Consensus 11 ~~rd~S~~~k~~e~g~Vd~V~~~~---~~~g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv 67 (67)
..+|+|++++.+|+|+||+|.++. +.++...|+|++|+.|+|+||||||||||||||
T Consensus 586 ~~~~~~~~~~~~~~g~v~~v~~~~~~~~~~~~~~v~v~~r~~R~p~iGDKfssRhGqKGv 645 (866)
T cd00653 586 DVRDTSLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGV 645 (866)
T ss_pred cceEEEEEecCCCceEEEEEEEeccccCCCCcEEEEEEEeEEecCCcccccccccCCCcE
Confidence 479999999999999999999988 567789999999999999999999999999997
No 11
>KOG0215|consensus
Probab=99.76 E-value=4.7e-20 Score=148.36 Aligned_cols=58 Identities=38% Similarity=0.590 Sum_probs=55.9
Q ss_pred cceeeeeEEcCCCCCeEEEEEEEEeccCCcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584 10 FSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGT 67 (67)
Q Consensus 10 ~~~rd~S~~~k~~e~g~Vd~V~~~~~~~g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv 67 (67)
..|+|.++.|+..|+++||+|++++|+++...||+.+||+|.|++|||||||||||||
T Consensus 869 ~~Yk~~pitykgpepsyidkVmls~n~~dq~LIK~llRQTRrPElGDKFSSRHGQKGV 926 (1153)
T KOG0215|consen 869 VQYKAVPITYKGPEPSYIDRVMLTSNDEDQFLIKVLLRQTRRPELGDKFSSRHGQKGV 926 (1153)
T ss_pred cccccccceecCCCcchhheeEeecCccccHHHHHHHhhccCcccccccccccCCCce
Confidence 3599999999999999999999999999999999999999999999999999999997
No 12
>CHL00207 rpoB RNA polymerase beta subunit; Provisional
Probab=99.75 E-value=1.9e-18 Score=141.11 Aligned_cols=58 Identities=31% Similarity=0.396 Sum_probs=51.5
Q ss_pred cceeeeeEEcCCCCCeEEEEEEEEeccCC--c-----EEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584 10 FSKRDGSTFLRNSETGIVDQVMLTLNVDG--Y-----KFCKIRVRSVRIPQIGDKFASRHGQKGT 67 (67)
Q Consensus 10 ~~~rd~S~~~k~~e~g~Vd~V~~~~~~~g--~-----~~vkV~vR~~R~P~iGDKFsSRHGQKGv 67 (67)
...+|+|++++++++|+|++|.++.++++ . ..|+|++|+.|+|++|||||||||||||
T Consensus 761 ~~~kd~sl~~~~~~~g~V~~V~~~~~~~~~~~~~~~~~~vkv~i~~~R~p~vGDKfasRHGqKGV 825 (1077)
T CHL00207 761 KDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGI 825 (1077)
T ss_pred CcceEeEEEcCCCCcEEEEEEEEEecCCCCcccccccEEEEEEEEEEecCCcccccccccCCcee
Confidence 35799999999999999999999986433 2 3589999999999999999999999997
No 13
>KOG0216|consensus
Probab=99.65 E-value=1e-16 Score=129.45 Aligned_cols=53 Identities=47% Similarity=0.601 Sum_probs=49.1
Q ss_pred eeEEcCCCCCeEEEEEEEEeccCCc--EEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584 15 GSTFLRNSETGIVDQVMLTLNVDGY--KFCKIRVRSVRIPQIGDKFASRHGQKGT 67 (67)
Q Consensus 15 ~S~~~k~~e~g~Vd~V~~~~~~~g~--~~vkV~vR~~R~P~iGDKFsSRHGQKGv 67 (67)
.-.+|+..|+|+||.|.++.++.|. +.+.|++|.+|+|.||||||||||||||
T Consensus 817 ~~~~~~~~ep~~vd~vr~~~~~~~~~~k~~~i~~Ri~R~p~IGDKFsSRhGQKGi 871 (1111)
T KOG0216|consen 817 RIKKYHGTEPGIVDEVRVLGNDMGDQEKCATITLRIPRNPIIGDKFSSRHGQKGI 871 (1111)
T ss_pred EEEEecCCCCeeeEEEEEccccCCCccceEEEEEEecCCCcccchhhhhcccccc
Confidence 3468999999999999999998876 7899999999999999999999999997
No 14
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=99.49 E-value=3.2e-14 Score=123.49 Aligned_cols=29 Identities=41% Similarity=0.652 Sum_probs=27.3
Q ss_pred cEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584 39 YKFCKIRVRSVRIPQIGDKFASRHGQKGT 67 (67)
Q Consensus 39 ~~~vkV~vR~~R~P~iGDKFsSRHGQKGv 67 (67)
.+.|+|+||+.|+|++|||||||||||||
T Consensus 1075 ~~~VkV~ia~kR~~qvGDK~AgRHGnKGV 1103 (2890)
T PRK09603 1075 IKKVKLYIATKRKLKVGDKMAGRHGNKGI 1103 (2890)
T ss_pred ceEEEEEEEEeecccccchhhhccCCCee
Confidence 35799999999999999999999999997
No 15
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=99.21 E-value=2.3e-11 Score=106.13 Aligned_cols=28 Identities=39% Similarity=0.501 Sum_probs=26.9
Q ss_pred EEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584 40 KFCKIRVRSVRIPQIGDKFASRHGQKGT 67 (67)
Q Consensus 40 ~~vkV~vR~~R~P~iGDKFsSRHGQKGv 67 (67)
+.|+|+|.+.|++++|||+|+|||||||
T Consensus 1069 ~~VkVyia~KRkiqvGDKmAGRHGNKGV 1096 (2836)
T PRK14844 1069 MSVKVFIAVKHSLQPGDKMAGRHGNKGV 1096 (2836)
T ss_pred eEEEEEEEEeecCCccccccccCCCCce
Confidence 5799999999999999999999999997
No 16
>PF04941 LEF-8: Late expression factor 8 (LEF-8); InterPro: IPR007025 Late expression factor 8 (LEF-8) is one of the primary components of RNA polymerase produced by polyhedrosis viruses. LEF-8 shows homology to the second largest subunit of prokaryotic DNA-directed RNA polymerase[].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=94.04 E-value=0.19 Score=41.30 Aligned_cols=30 Identities=27% Similarity=0.347 Sum_probs=22.5
Q ss_pred CcEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584 38 GYKFCKIRVRSVRIPQIGDKFASRHGQKGT 67 (67)
Q Consensus 38 g~~~vkV~vR~~R~P~iGDKFsSRHGQKGv 67 (67)
+.-++|+.+--.=.--.|=|.||-||||||
T Consensus 704 d~v~vKl~~V~st~dLeGlKICgIHGQKGV 733 (748)
T PF04941_consen 704 DTVYVKLTLVTSTSDLEGLKICGIHGQKGV 733 (748)
T ss_pred CEEEEEEEEEEEecCccceEEeeeeccccc
Confidence 345566665555556679999999999997
No 17
>PHA03394 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional
Probab=93.80 E-value=0.21 Score=41.57 Aligned_cols=29 Identities=34% Similarity=0.410 Sum_probs=20.9
Q ss_pred cEEEEEEEeeecCCCcCeeeeeccCCcCC
Q psy7584 39 YKFCKIRVRSVRIPQIGDKFASRHGQKGT 67 (67)
Q Consensus 39 ~~~vkV~vR~~R~P~iGDKFsSRHGQKGv 67 (67)
.-++|+++--.=.--.|=|.||-||||||
T Consensus 695 ~v~lKl~~Vtst~dLeGlKICgIHGQKGV 723 (865)
T PHA03394 695 TVYLKIRLVTSTSDLEGLKICGIHGQKGV 723 (865)
T ss_pred EEEEEEEEEEEecCcceeEEeeecccccc
Confidence 33455555444455679999999999997
No 18
>KOG0214|consensus
Probab=66.61 E-value=5.5 Score=34.28 Aligned_cols=38 Identities=16% Similarity=0.078 Sum_probs=28.8
Q ss_pred eEEEEEEEEeccCCcEEEEEEEeeecCCCcCeeeeeccCCcC
Q psy7584 25 GIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKG 66 (67)
Q Consensus 25 g~Vd~V~~~~~~~g~~~vkV~vR~~R~P~iGDKFsSRHGQKG 66 (67)
+...++.+..++.| ...+|.++. +..|+||++.|.+++
T Consensus 856 ~~d~s~~Lr~~e~G-ivd~V~vt~---n~~G~kF~kv~vr~~ 893 (1141)
T KOG0214|consen 856 KRDHSTKLRHTERG-IVDQVWVTK---NSEGPKFVKVRVRQV 893 (1141)
T ss_pred cccceeecccCCcc-eEEEEEEec---CCCCCceeEEEEeec
Confidence 36667777777777 555666655 999999999998875
No 19
>PF13497 DUF4121: Domain of unknown function (DUF4121)
Probab=51.77 E-value=8.8 Score=28.29 Aligned_cols=18 Identities=56% Similarity=1.101 Sum_probs=15.7
Q ss_pred EeeecCCCcCe--eeeeccC
Q psy7584 46 VRSVRIPQIGD--KFASRHG 63 (67)
Q Consensus 46 vR~~R~P~iGD--KFsSRHG 63 (67)
.|+.+.|++|| .|-||||
T Consensus 42 tRs~~~Pq~GD~v~y~tr~G 61 (262)
T PF13497_consen 42 TRSERTPQVGDRVEYTTRHG 61 (262)
T ss_pred hccccCCCCCceEEEEcCCC
Confidence 68889999999 4889998
No 20
>PF02470 MCE: mce related protein; InterPro: IPR003399 This domain is found in all 24 mce genes associated with the four mammalian cell entry (mce) operons of Mycobacterium tuberculosis and their homologs in other Actinomycetales [, ]. The archetype (mce1A, Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage []. The domain is also found in: Chloroplast Ycf22 and related cyanobacterial homologs, the majority of which have an N-terminal transmembrane domain and are putative ABC transporters. Proteobacterial homologs, which include YrbD, YebT, VpsC and Ttg2C, the latter being annotated as a toluene tolerance proteins, belong to the periplasmic substrate-binding ABC transporter superfamily.
Probab=28.27 E-value=1.2e+02 Score=17.11 Aligned_cols=21 Identities=24% Similarity=0.267 Sum_probs=18.0
Q ss_pred eeeeeEEcCCCCCeEEEEEEE
Q psy7584 12 KRDGSTFLRNSETGIVDQVML 32 (67)
Q Consensus 12 ~rd~S~~~k~~e~g~Vd~V~~ 32 (67)
...++++|+.-+-|.|++|.+
T Consensus 16 ~~gs~V~~~Gv~VG~V~~i~l 36 (81)
T PF02470_consen 16 SVGSPVRYRGVEVGKVTSIEL 36 (81)
T ss_pred CCcCEEEECCEEEEEEEEEEE
Confidence 345789999999999999987
No 21
>cd06541 ASCH ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, the activating signal cointegrator 1 or thyroid hormone receptor interactor protein 4 (TRIP4). ASC-1 is conserved in many eukaryotes and has been suggested to participate in a protein complex that interacts with RNA. It has been shown that ASC-1 mediates the interaction between various transciption factors and the basal transcriptional machinery.
Probab=20.91 E-value=88 Score=19.02 Aligned_cols=22 Identities=32% Similarity=0.596 Sum_probs=16.2
Q ss_pred CCcEEEEEEEeee--cCCCcCeee
Q psy7584 37 DGYKFCKIRVRSV--RIPQIGDKF 58 (67)
Q Consensus 37 ~g~~~vkV~vR~~--R~P~iGDKF 58 (67)
+|.+.+.+++... ..|.+||..
T Consensus 14 ~G~Ktat~r~~~~~~~~~k~Gd~~ 37 (105)
T cd06541 14 SGRKTIEIRSLDIYEQLPKAGDYL 37 (105)
T ss_pred CCCCEEEEEcchhcccCCCCCCEE
Confidence 5677777777654 778999864
Done!