Query 047634
Match_columns 82
No_of_seqs 110 out of 382
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 13:08:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047634.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047634hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3298 DNA-directed RNA polym 99.9 1.1E-27 2.5E-32 167.6 8.8 80 1-81 40-137 (170)
2 PTZ00162 DNA-directed RNA poly 99.9 1.2E-26 2.6E-31 163.0 11.1 80 1-80 40-137 (176)
3 COG1095 RPB7 DNA-directed RNA 99.9 5.1E-23 1.1E-27 146.2 10.0 75 1-76 40-132 (183)
4 KOG3297 DNA-directed RNA polym 99.9 5E-23 1.1E-27 147.0 8.2 78 1-78 40-126 (202)
5 TIGR00448 rpoE DNA-directed RN 99.9 2.6E-21 5.6E-26 135.1 9.6 55 1-55 40-94 (179)
6 PRK08563 DNA-directed RNA poly 99.8 2.7E-20 5.9E-25 130.0 10.4 55 1-55 40-94 (187)
7 cd04329 RNAP_II_Rpb7_N RNAP_II 99.7 4.5E-18 9.7E-23 106.5 6.7 42 1-42 39-80 (80)
8 cd00655 RNAP_Rpb7_N_like RNAP_ 99.7 1.2E-17 2.7E-22 104.4 6.3 42 1-42 39-80 (80)
9 cd04330 RNAP_III_Rpc25_N RNAP_ 99.7 1.3E-17 2.8E-22 104.4 6.2 42 1-42 39-80 (80)
10 cd04331 RNAP_E_N RNAP_E_N: Rpo 99.7 9.8E-17 2.1E-21 100.6 6.1 42 1-42 39-80 (80)
11 PF03876 SHS2_Rpb7-N: SHS2 dom 99.3 1.5E-11 3.2E-16 73.8 6.2 37 2-38 34-70 (70)
12 cd04328 RNAP_I_Rpa43_N RNAP_I_ 98.9 6.7E-09 1.5E-13 65.4 5.5 39 4-42 49-89 (89)
13 PF08292 RNA_pol_Rbc25: RNA po 98.5 1.8E-07 3.9E-12 62.8 3.9 37 40-76 1-46 (122)
14 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.9 2.4E-05 5.2E-10 49.4 5.1 33 42-74 1-51 (88)
15 KOG4134 DNA-dependent RNA poly 97.2 0.0017 3.7E-08 48.3 7.1 53 3-55 67-120 (253)
16 PF00575 S1: S1 RNA binding do 79.8 1.9 4.1E-05 24.9 2.3 17 39-55 1-17 (74)
17 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 78.7 2.1 4.6E-05 25.6 2.3 18 38-55 2-19 (86)
18 cd04454 S1_Rrp4_like S1_Rrp4_l 74.1 3.3 7.1E-05 24.7 2.3 18 38-55 2-19 (82)
19 cd05686 S1_pNO40 S1_pNO40: pNO 55.6 12 0.00025 21.9 2.1 16 40-55 1-16 (73)
20 TIGR03591 polynuc_phos polyrib 50.2 3 6.5E-05 34.9 -1.4 46 10-55 584-631 (684)
21 smart00316 S1 Ribosomal protei 44.0 25 0.00053 19.0 2.2 14 42-55 2-15 (72)
22 cd04452 S1_IF2_alpha S1_IF2_al 43.0 25 0.00055 20.0 2.2 16 40-55 1-16 (76)
23 cd04455 S1_NusA S1_NusA: N-uti 42.1 30 0.00065 19.8 2.4 15 41-55 2-16 (67)
24 PHA02872 EFc gene family prote 39.5 51 0.0011 22.3 3.4 36 1-37 69-108 (124)
25 cd05697 S1_Rrp5_repeat_hs5 S1_ 37.9 34 0.00073 19.4 2.2 13 43-55 1-13 (69)
26 PRK04163 exosome complex RNA-b 35.5 34 0.00074 24.8 2.3 18 38-55 59-76 (235)
27 cd05791 S1_CSL4 S1_CSL4: CSL4, 35.0 34 0.00075 21.2 2.0 18 38-55 2-19 (92)
28 cd05706 S1_Rrp5_repeat_sc10 S1 33.9 45 0.00098 18.9 2.3 15 41-55 2-16 (73)
29 cd05790 S1_Rrp40 S1_Rrp40: Rrp 32.8 43 0.00094 21.0 2.2 18 38-55 2-19 (86)
30 cd05708 S1_Rrp5_repeat_sc12 S1 30.8 51 0.0011 18.6 2.1 14 42-55 2-15 (77)
31 PF07076 DUF1344: Protein of u 30.8 1.2E+02 0.0027 18.1 3.9 21 46-66 5-38 (61)
32 cd04461 S1_Rrp5_repeat_hs8_sc7 29.7 55 0.0012 19.3 2.2 16 40-55 12-27 (83)
33 cd04471 S1_RNase_R S1_RNase_R: 29.6 49 0.0011 19.0 2.0 14 42-55 1-14 (83)
34 cd05707 S1_Rrp5_repeat_sc11 S1 29.6 55 0.0012 18.4 2.1 13 43-55 1-13 (68)
35 cd05687 S1_RPS1_repeat_ec1_hs1 28.7 59 0.0013 18.3 2.2 13 43-55 1-13 (70)
36 cd05704 S1_Rrp5_repeat_hs13 S1 28.5 63 0.0014 18.7 2.3 14 42-55 3-16 (72)
37 PHA02945 interferon resistance 28.2 57 0.0012 21.0 2.1 15 40-55 9-23 (88)
38 TIGR00984 3a0801s03tim44 mitoc 28.0 1.5E+02 0.0032 23.6 4.9 41 15-55 308-352 (378)
39 cd04465 S1_RPS1_repeat_ec2_hs2 27.8 61 0.0013 18.2 2.1 13 43-55 1-13 (67)
40 cd05688 S1_RPS1_repeat_ec3 S1_ 27.8 58 0.0013 17.7 2.0 14 42-55 1-14 (68)
41 cd04453 S1_RNase_E S1_RNase_E: 27.4 66 0.0014 19.7 2.3 17 39-55 4-20 (88)
42 cd05698 S1_Rrp5_repeat_hs6_sc5 27.0 67 0.0014 18.0 2.2 13 43-55 1-13 (70)
43 cd05692 S1_RPS1_repeat_hs4 S1_ 26.3 62 0.0013 17.5 1.9 13 43-55 1-13 (69)
44 cd05691 S1_RPS1_repeat_ec6 S1_ 26.2 68 0.0015 17.9 2.1 13 43-55 1-13 (73)
45 cd05705 S1_Rrp5_repeat_hs14 S1 25.2 77 0.0017 18.7 2.3 14 42-55 3-16 (74)
46 PRK09521 exosome complex RNA-b 24.7 1.4E+02 0.003 20.7 3.8 22 34-55 56-77 (189)
47 cd05694 S1_Rrp5_repeat_hs2_sc2 24.4 82 0.0018 18.6 2.3 14 42-55 4-17 (74)
48 COG1278 CspC Cold shock protei 24.0 74 0.0016 19.3 2.0 23 15-37 13-35 (67)
49 cd05689 S1_RPS1_repeat_ec4 S1_ 23.7 78 0.0017 17.9 2.0 14 42-55 3-16 (72)
50 cd05695 S1_Rrp5_repeat_hs3 S1_ 22.4 91 0.002 17.8 2.2 13 43-55 1-13 (66)
51 cd05685 S1_Tex S1_Tex: The C-t 22.3 89 0.0019 16.8 2.1 13 43-55 1-13 (68)
52 cd00472 Ribosomal_L24e_L24 Rib 22.3 97 0.0021 17.9 2.2 27 12-38 5-31 (54)
53 cd05702 S1_Rrp5_repeat_hs11_sc 21.9 92 0.002 17.7 2.1 13 43-55 1-13 (70)
54 PF10447 EXOSC1: Exosome compo 21.8 93 0.002 19.3 2.2 16 40-55 2-17 (82)
55 cd05690 S1_RPS1_repeat_ec5 S1_ 21.2 86 0.0019 17.3 1.9 13 43-55 1-13 (69)
56 PF14208 DUF4320: Domain of un 21.0 1.3E+02 0.0029 19.8 3.0 26 16-42 70-97 (116)
57 PF00467 KOW: KOW motif; Inte 20.9 68 0.0015 16.0 1.2 15 39-55 10-24 (32)
58 cd05693 S1_Rrp5_repeat_hs1_sc1 20.7 1.3E+02 0.0028 18.9 2.8 14 42-55 3-16 (100)
59 COG3323 Uncharacterized protei 20.7 99 0.0022 20.6 2.3 15 39-55 55-69 (109)
No 1
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=99.95 E-value=1.1e-27 Score=167.64 Aligned_cols=80 Identities=48% Similarity=0.923 Sum_probs=75.2
Q ss_pred CCeEEEEEEEeccEecceeEEcCCCceEEEEEEeEEEeeecCCCeEEEEEEEccC-----------------CCCCceEE
Q 047634 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNK-----------------LIPDDMEL 63 (82)
Q Consensus 1 g~~GliV~v~di~~i~~G~I~~gdG~~~~~V~f~aivfrPf~gEVv~g~V~~v~~-----------------~~p~d~~~ 63 (82)
|++||+||++++++|++|+|.+++|.+.|+|+|+|++||||||||++|+|++|++ ++|+||+|
T Consensus 40 g~~Gyvi~vt~ld~Ig~g~I~~~~G~v~FpVky~av~FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f 119 (170)
T KOG3298|consen 40 GKYGYVIAVTTLDNIGEGRIRPGTGFVTFPVKYKAVTFKPFKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEF 119 (170)
T ss_pred ccccEEEEEEEhhhccCCccccCCceEEEEEEEEEEEEeecCCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCccc
Confidence 6899999999999999999999999999999999999999999999999999999 89999999
Q ss_pred cCCCC-CeEECCCCcEEEe
Q 047634 64 QTGDL-PNYTTSDGSVCIS 81 (82)
Q Consensus 64 ~~~~~-p~~~~~d~~~~i~ 81 (82)
+|+++ |+|+++|++ +|+
T Consensus 120 ~p~~n~P~f~~~d~s-~I~ 137 (170)
T KOG3298|consen 120 DPGENPPNFQTEDES-VIQ 137 (170)
T ss_pred CCCCCCCcccccccc-eee
Confidence 99988 599988885 443
No 2
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=99.94 E-value=1.2e-26 Score=163.03 Aligned_cols=80 Identities=36% Similarity=0.654 Sum_probs=72.7
Q ss_pred CCeEEEEEEEeccEecceeEEcCCCceEEEEEEeEEEeeecCCCeEEEEEEEccC-----------------CCCCceEE
Q 047634 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNK-----------------LIPDDMEL 63 (82)
Q Consensus 1 g~~GliV~v~di~~i~~G~I~~gdG~~~~~V~f~aivfrPf~gEVv~g~V~~v~~-----------------~~p~d~~~ 63 (82)
+++|||||++|++++++|+|.||||+++|+|+|||++||||+|||++|+|+++++ .||+|+.|
T Consensus 40 ~~~GliV~v~di~~i~~G~I~~gdG~~~~~V~FraivFrPf~gEVv~g~V~~v~~~G~~v~~Gp~~ifI~~~~l~~~~~f 119 (176)
T PTZ00162 40 RKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPFKDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPPDFVY 119 (176)
T ss_pred CcccEEEEEEEeeEecCCEEEcCCCCEEEEEEEEEEEEecCCCCEEEEEEEEEecceEEEEeeCeEEEEcHHHCCCccEE
Confidence 4789999999999999999999999999999999999999999999999999999 88999999
Q ss_pred cCCCCC-eEECCCCcEEE
Q 047634 64 QTGDLP-NYTTSDGSVCI 80 (82)
Q Consensus 64 ~~~~~p-~~~~~d~~~~i 80 (82)
++++.+ +|.+++++..|
T Consensus 120 d~~~~~~~~~~~~~~~~i 137 (176)
T PTZ00162 120 DSDSAYPCYISSDGQIQI 137 (176)
T ss_pred CCCCCcceEecCCCcEEE
Confidence 998664 88866654444
No 3
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=99.89 E-value=5.1e-23 Score=146.24 Aligned_cols=75 Identities=32% Similarity=0.542 Sum_probs=67.0
Q ss_pred CCeEEEEEEEeccEecceeEEcCCCceEEEEEEeEEEeeecCCCeEEEEEEEccC-----------------CCCCceEE
Q 047634 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNK-----------------LIPDDMEL 63 (82)
Q Consensus 1 g~~GliV~v~di~~i~~G~I~~gdG~~~~~V~f~aivfrPf~gEVv~g~V~~v~~-----------------~~p~d~~~ 63 (82)
+++|+||+++|+.++++|+|.||||++||+|+||||+|+||+|||++|+|+++++ ++++| .+
T Consensus 40 ~~~G~~v~V~~v~~igeG~I~~GDG~~y~~V~f~al~fkP~~gEVV~GeVv~~~~~G~fV~igp~dglvh~sqi~dd-~~ 118 (183)
T COG1095 40 GDVGLVVLVLDVKEIGEGIIVPGDGSTYHEVKFRALVFKPFRGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMDD-YI 118 (183)
T ss_pred cccCEEEEEEEeeEeeccEEecCCCcEEEEEEEEEEEEEeccccEEEEEEEEEeecceEEEeccccccccHhhccCc-cc
Confidence 4689999999999999999999999999999999999999999999999999999 88888 66
Q ss_pred cCCCCC-eEECCCC
Q 047634 64 QTGDLP-NYTTSDG 76 (82)
Q Consensus 64 ~~~~~p-~~~~~d~ 76 (82)
.++..+ .|..++.
T Consensus 119 ~~d~~~~~~~g~~t 132 (183)
T COG1095 119 DYDEKNKVLIGEET 132 (183)
T ss_pred ccCcccceeeeccc
Confidence 666554 7776543
No 4
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=99.89 E-value=5e-23 Score=146.96 Aligned_cols=78 Identities=23% Similarity=0.390 Sum_probs=72.1
Q ss_pred CCeEEEEEEEeccEecceeEEcCCCceEEEEEEeEEEeeecCCCeEEEEEEEccC-------CCCCceEEcCCCCC--eE
Q 047634 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNK-------LIPDDMELQTGDLP--NY 71 (82)
Q Consensus 1 g~~GliV~v~di~~i~~G~I~~gdG~~~~~V~f~aivfrPf~gEVv~g~V~~v~~-------~~p~d~~~~~~~~p--~~ 71 (82)
+++|||||++||.++++|.|.||||++|.+|.||+++||||.|||+.|+++++++ +||+|+.+|++.+| |.
T Consensus 40 ~nvGLCI~vyDi~~v~e~~v~pGDGas~~~V~FR~vVFrPF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~ 119 (202)
T KOG3297|consen 40 PNVGLCICVYDILEVEEGIVLPGDGASYARVWFRVVVFRPFVGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCV 119 (202)
T ss_pred ccccEEEEEeEeeeecceEEecCCCceEEEEEEEEEEEecccceEEEEEeecCCccceEEEEEeeeceeechhhCCCCcc
Confidence 4789999999999999999999999999999999999999999999999999999 99999999999887 65
Q ss_pred ECCCCcE
Q 047634 72 TTSDGSV 78 (82)
Q Consensus 72 ~~~d~~~ 78 (82)
...++++
T Consensus 120 f~~~e~v 126 (202)
T KOG3297|consen 120 FEPDEQV 126 (202)
T ss_pred cccccEE
Confidence 5655544
No 5
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=99.86 E-value=2.6e-21 Score=135.06 Aligned_cols=55 Identities=29% Similarity=0.485 Sum_probs=53.9
Q ss_pred CCeEEEEEEEeccEecceeEEcCCCceEEEEEEeEEEeeecCCCeEEEEEEEccC
Q 047634 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 1 g~~GliV~v~di~~i~~G~I~~gdG~~~~~V~f~aivfrPf~gEVv~g~V~~v~~ 55 (82)
+++|||||++||.++++|+|.||||+++|+|+|||++|||++||+++|+|+++++
T Consensus 40 ~~~G~~i~v~di~~i~~g~i~~gdG~~~~~V~f~~i~f~p~~gEvv~G~V~~v~~ 94 (179)
T TIGR00448 40 KNVGLCITIYDIEDIGEGKVIPGDGSAYHNVTFRALVFKPELGEIVEGEVIEIVE 94 (179)
T ss_pred CCcCEEEEEEEeEEecCCEEECCCCCEEEEEEEEEEEEeccCCCEEEEEEEEEEe
Confidence 4789999999999999999999999999999999999999999999999999999
No 6
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=99.84 E-value=2.7e-20 Score=130.03 Aligned_cols=55 Identities=31% Similarity=0.469 Sum_probs=53.9
Q ss_pred CCeEEEEEEEeccEecceeEEcCCCceEEEEEEeEEEeeecCCCeEEEEEEEccC
Q 047634 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 1 g~~GliV~v~di~~i~~G~I~~gdG~~~~~V~f~aivfrPf~gEVv~g~V~~v~~ 55 (82)
+++||||+++||+++++|+|.||||+++|+|+|||++|+|++|||++|+|+++++
T Consensus 40 ~~~G~~v~v~di~~i~~g~i~~gdg~~~~~v~f~~lvf~P~~GEVv~g~V~~v~~ 94 (187)
T PRK08563 40 KELGIIVAVLDVKVIGEGKIVPGDGATYHEVEFDALVFKPELQEVVEGEVVEVVE 94 (187)
T ss_pred CCcCEEEEEEEeEEecccEEecCCCCcEEEEEEEEEEEeccCCCEEEEEEEEEEc
Confidence 4789999999999999999999999999999999999999999999999999999
No 7
>cd04329 RNAP_II_Rpb7_N RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain. Rpb7 is a subunit of eukaryotic RNA polymerase (RNAP) II that is homologous to Rpc25 of RNAP III, RpoE of archaeal RNAP, and Rpa43 of eukaryotic RNAP I. Rpb7 heterodimerizes with Rpb4 and this heterodimer binds the 10-subunit core of RNAP II, forming part of the floor of the DNA-binding cleft. Rpb7 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which bind single-stranded RNA. Rpb7 is thought to interact with the nascent RNA strand as it exits the RNAP II complex during transcription elongation. The Rpb7/Rpb4 heterodimer is also thought to serve as an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter.
Probab=99.75 E-value=4.5e-18 Score=106.52 Aligned_cols=42 Identities=43% Similarity=0.944 Sum_probs=40.6
Q ss_pred CCeEEEEEEEeccEecceeEEcCCCceEEEEEEeEEEeeecC
Q 047634 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFR 42 (82)
Q Consensus 1 g~~GliV~v~di~~i~~G~I~~gdG~~~~~V~f~aivfrPf~ 42 (82)
+++|+|||++|+.++++|+|.+|||+++|+|+|||++||||+
T Consensus 39 ~~~G~iv~v~di~~i~~G~I~~gdG~~~~~V~F~aivfrPf~ 80 (80)
T cd04329 39 GDYGYIIAVTDIDDIGEGKILPGTGSVEFPVKYKAIVFKPFK 80 (80)
T ss_pred CceeEEEEEEEeeEecCcEEEcCCCCEEEEEEEEEEEEEccC
Confidence 478999999999999999999999999999999999999996
No 8
>cd00655 RNAP_Rpb7_N_like RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP. These proteins have, in addition to their N-terminal RNP domain, a C-terminal oligonucleotide-binding (OB) domain. Each of these subunits heterodimerizes with another RNAP subunit (Rpb7 to Rpb4, Rpc25 to Rpc17, RpoE to RpoF, and Rpa43 to Rpa14). The heterodimer is thought to tether the RNAP to a given promoter via its interactions with a promoter-bound transcription factor.The heterodimer is also thought to bind and position nascent RNA as it exits the polymerase complex.
Probab=99.72 E-value=1.2e-17 Score=104.41 Aligned_cols=42 Identities=33% Similarity=0.544 Sum_probs=40.5
Q ss_pred CCeEEEEEEEeccEecceeEEcCCCceEEEEEEeEEEeeecC
Q 047634 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFR 42 (82)
Q Consensus 1 g~~GliV~v~di~~i~~G~I~~gdG~~~~~V~f~aivfrPf~ 42 (82)
+++|+||+++|+.++++|+|.||||++||+|+|||++||||+
T Consensus 39 ~~~G~~v~v~di~~i~~G~I~~gdG~~~~~V~F~~ivFrPf~ 80 (80)
T cd00655 39 PVVGIILAIKDTKDIPEGAIRPGDGSAYVNVSFRAVVFKPFS 80 (80)
T ss_pred CCccEEEEEEEeEEEcCCEEECCCCCEEEEEEEEEEEEEcCC
Confidence 478999999999999999999999999999999999999996
No 9
>cd04330 RNAP_III_Rpc25_N RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain. Rpc25 is a subunit of eukaryotic RNA polymerase (RNAP) III and is homologous to Rpa43 of eukaryotic RNAP I, Rpb7 of eukaryotic RNAP II, and RpoE of archaeal RNAP. Rpc25 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which are thought to bind single-stranded RNA. Rpc25 heterodimerizes with Rpc17 and plays an important role in transcription initiation. RNAP III transcribes diverse structural and catalytic RNAs including 5S ribosomal RNAs, tRNAs, and a small number of snRNAs involved in RNA and protein synthesis.
Probab=99.72 E-value=1.3e-17 Score=104.42 Aligned_cols=42 Identities=26% Similarity=0.531 Sum_probs=40.4
Q ss_pred CCeEEEEEEEeccEecceeEEcCCCceEEEEEEeEEEeeecC
Q 047634 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFR 42 (82)
Q Consensus 1 g~~GliV~v~di~~i~~G~I~~gdG~~~~~V~f~aivfrPf~ 42 (82)
+++|+||+++|+.++++|+|.||||++||+|+|||++||||+
T Consensus 39 ~~~Gl~v~v~di~~i~eG~I~~gdG~~~~~V~Fr~lvFrPf~ 80 (80)
T cd04330 39 QNVGLCICLYDILEVEDGYILPGDGASHYKVTFRMVVFRPFV 80 (80)
T ss_pred CCccEEEEEEEeEEEcCCEEECCCCCEEEEEEEEEEEEECCC
Confidence 368999999999999999999999999999999999999996
No 10
>cd04331 RNAP_E_N RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain. RpoE (subunit E) is a subunit of the archaeal RNA polymerase (RNAP) that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNAP III, and Rpa43 of eukaryotic RNAP I. RpoE heterodimerizes with RpoF, another RNA polymerase subunit. RpoE has an elongated two-domain structure that includes an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Both domains of RpoE bind single-stranded RNA.
Probab=99.68 E-value=9.8e-17 Score=100.60 Aligned_cols=42 Identities=33% Similarity=0.551 Sum_probs=40.0
Q ss_pred CCeEEEEEEEeccEecceeEEcCCCceEEEEEEeEEEeeecC
Q 047634 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFR 42 (82)
Q Consensus 1 g~~GliV~v~di~~i~~G~I~~gdG~~~~~V~f~aivfrPf~ 42 (82)
+++|+||||+||.++++|+|.||||+++|+|+|||++|||..
T Consensus 39 ~~~G~iv~v~di~~i~eG~I~~gdG~~~~~V~F~~ivFrP~~ 80 (80)
T cd04331 39 KDLGKIVSVLDVKDVGEGKIVHGDGAVYHEVRFDALVFKPEL 80 (80)
T ss_pred CCCCEEEEEEEEEEecCCEEEcCCCCEEEEEEEEEEEEecCC
Confidence 478999999999999999999999999999999999999963
No 11
>PF03876 SHS2_Rpb7-N: SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; InterPro: IPR005576 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable []. This entry represents the N-terminal, heterodimerisation domain of RPB7.; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2C35_F 3HKZ_E 2PMZ_T 2CKZ_D 2Y0S_E 2RF4_A 2JA7_G 1Y1V_G 2JA5_G 4A3D_G ....
Probab=99.27 E-value=1.5e-11 Score=73.85 Aligned_cols=37 Identities=38% Similarity=0.656 Sum_probs=34.9
Q ss_pred CeEEEEEEEeccEecceeEEcCCCceEEEEEEeEEEe
Q 047634 2 RHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVF 38 (82)
Q Consensus 2 ~~GliV~v~di~~i~~G~I~~gdG~~~~~V~f~aivf 38 (82)
++|+||+++|+..+++|+|.+|||+++|+|+|+|++|
T Consensus 34 ~~G~~i~v~~i~~~~~g~I~~~~g~~~~~V~f~~lvF 70 (70)
T PF03876_consen 34 ELGVVIAVTDIKEISEGKIIPGDGFVYFKVTFRALVF 70 (70)
T ss_dssp TTEEEEEEEEEEEESCEEE-TTTSSEEEEEEEEEEEE
T ss_pred CceEEEEEeeeeEecCcEEECCCCCEEEEEEEEEEEC
Confidence 5699999999999999999999999999999999998
No 12
>cd04328 RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. Rpa43 is a subunit of eukaryotic RNA polymerase (RNAP) I that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNP III, and RpoE of archaeal RNAP. Rpa43 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Rpa43 heterodimerizes with Rpa14 and this heterodimer has genetic and biochemical characteristics similar to those of the Rpb7/Rpb4 heterodimer of RNAP II. In addition, the Rpa43/Rpa14 heterodimer binds single-stranded RNA, as is the case for the Rpb7/Rpb4 and the archaeal E/F complexes. The position of Rpa43/Rpa14 in the three-dimensional structure of RNAP I is similar to that of Rpb4/Rpb7, which forms an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter. Rpb43 binds Rrn3, an rDNA-specific transcription factor, functionally equivalent to TFIIB, invo
Probab=98.85 E-value=6.7e-09 Score=65.44 Aligned_cols=39 Identities=26% Similarity=0.376 Sum_probs=37.3
Q ss_pred EEEEEEEeccEecc--eeEEcCCCceEEEEEEeEEEeeecC
Q 047634 4 GFVVAIMGVESIGT--GLIRDGIGFVTFPVRCQCIVFRPFR 42 (82)
Q Consensus 4 GliV~v~di~~i~~--G~I~~gdG~~~~~V~f~aivfrPf~ 42 (82)
|+|++..|+..+++ |+|.+++|.++++|+||++||||++
T Consensus 49 Gv~l~~~di~~~~~~~~~i~~~~~~~~~~V~~~~lVFrP~~ 89 (89)
T cd04328 49 GVVLAYSNIKLLEGELAKIVDDSPFIFVWISADFLVFRPKI 89 (89)
T ss_pred eEEEEecceEeccccceeeeCCCcEEEEEEEEEEEEEecCC
Confidence 99999999999977 9999999999999999999999985
No 13
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=98.47 E-value=1.8e-07 Score=62.79 Aligned_cols=37 Identities=24% Similarity=0.364 Sum_probs=28.5
Q ss_pred ecCCCeEEEEEEEccC-------CCCCceEEcCCCCC--eEECCCC
Q 047634 40 PFRGEILGAAVTMVNK-------LIPDDMELQTGDLP--NYTTSDG 76 (82)
Q Consensus 40 Pf~gEVv~g~V~~v~~-------~~p~d~~~~~~~~p--~~~~~d~ 76 (82)
||+|||+.|+|+++++ +|++|+++|++.|| +..++++
T Consensus 1 PF~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~ 46 (122)
T PF08292_consen 1 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEE 46 (122)
T ss_dssp --TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCC
T ss_pred CCCCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccC
Confidence 8999999999999999 99999999999997 4434433
No 14
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=97.94 E-value=2.4e-05 Score=49.44 Aligned_cols=33 Identities=48% Similarity=0.813 Sum_probs=28.0
Q ss_pred CCCeEEEEEEEccC-----------------CCCCceEEcCC-CCCeEECC
Q 047634 42 RGEILGAAVTMVNK-----------------LIPDDMELQTG-DLPNYTTS 74 (82)
Q Consensus 42 ~gEVv~g~V~~v~~-----------------~~p~d~~~~~~-~~p~~~~~ 74 (82)
+|||++|+|++|++ .+|+|+.|+++ ..|+|.++
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip~~~~~~~~~~~~~~~~~ 51 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPCFTSN 51 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecCccceECCcCCCCeEeCC
Confidence 69999999999999 78999999985 44588744
No 15
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=97.22 E-value=0.0017 Score=48.33 Aligned_cols=53 Identities=30% Similarity=0.511 Sum_probs=48.5
Q ss_pred eEEEEEEEeccEec-ceeEEcCCCceEEEEEEeEEEeeecCCCeEEEEEEEccC
Q 047634 3 HGFVVAIMGVESIG-TGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 3 ~GliV~v~di~~i~-~G~I~~gdG~~~~~V~f~aivfrPf~gEVv~g~V~~v~~ 55 (82)
.|++++.-+|.-.+ .++|.+.++..+..++-...||+|-.|.+|+|.|-.++.
T Consensus 67 ~GivLgydnIKvLg~~aki~~D~pf~hlwi~adfyVf~Pk~Gd~LeG~Vn~vS~ 120 (253)
T KOG4134|consen 67 DGIVLGYDNIKVLGQTAKIRADDPFMHLWINADFYVFRPKAGDILEGVVNHVSR 120 (253)
T ss_pred CceEEeecceEeeccccceecCCCceEEEEeeeEEEECCCCCCeeeeeeeecch
Confidence 47888888887764 699999999999999999999999999999999999998
No 16
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=79.78 E-value=1.9 Score=24.91 Aligned_cols=17 Identities=29% Similarity=0.417 Sum_probs=15.3
Q ss_pred eecCCCeEEEEEEEccC
Q 047634 39 RPFRGEILGAAVTMVNK 55 (82)
Q Consensus 39 rPf~gEVv~g~V~~v~~ 55 (82)
+|..|++++|+|+++++
T Consensus 1 k~~~G~iv~g~V~~v~~ 17 (74)
T PF00575_consen 1 KLKEGDIVEGKVTSVED 17 (74)
T ss_dssp -SSTTSEEEEEEEEEET
T ss_pred CCCCCCEEEEEEEEEEC
Confidence 57899999999999998
No 17
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=78.74 E-value=2.1 Score=25.65 Aligned_cols=18 Identities=28% Similarity=0.342 Sum_probs=16.9
Q ss_pred eeecCCCeEEEEEEEccC
Q 047634 38 FRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 38 frPf~gEVv~g~V~~v~~ 55 (82)
|.|-+|+++.|.|+++++
T Consensus 2 y~p~~GdiV~g~V~~i~~ 19 (86)
T cd05789 2 YIPEVGDVVIGRVTEVGF 19 (86)
T ss_pred CcCCCCCEEEEEEEEECC
Confidence 678999999999999998
No 18
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=74.08 E-value=3.3 Score=24.69 Aligned_cols=18 Identities=39% Similarity=0.473 Sum_probs=17.0
Q ss_pred eeecCCCeEEEEEEEccC
Q 047634 38 FRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 38 frPf~gEVv~g~V~~v~~ 55 (82)
|.|.+|.++.|+|++++.
T Consensus 2 y~p~~GdiV~G~V~~v~~ 19 (82)
T cd04454 2 YLPDVGDIVIGIVTEVNS 19 (82)
T ss_pred CCCCCCCEEEEEEEEEcC
Confidence 679999999999999998
No 19
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=55.59 E-value=12 Score=21.90 Aligned_cols=16 Identities=25% Similarity=0.291 Sum_probs=14.7
Q ss_pred ecCCCeEEEEEEEccC
Q 047634 40 PFRGEILGAAVTMVNK 55 (82)
Q Consensus 40 Pf~gEVv~g~V~~v~~ 55 (82)
|..|++++|+|+++.+
T Consensus 1 ~~~g~~~~g~V~~i~~ 16 (73)
T cd05686 1 PALYQIFKGEVASVTE 16 (73)
T ss_pred CcCCCEEEEEEEEEEe
Confidence 5689999999999999
No 20
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=50.20 E-value=3 Score=34.91 Aligned_cols=46 Identities=22% Similarity=0.177 Sum_probs=36.1
Q ss_pred EeccEecceeEEcCCCceEEEE--EEeEEEeeecCCCeEEEEEEEccC
Q 047634 10 MGVESIGTGLIRDGIGFVTFPV--RCQCIVFRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 10 ~di~~i~~G~I~~gdG~~~~~V--~f~aivfrPf~gEVv~g~V~~v~~ 55 (82)
+||.+-|..+|...++.++.++ ..+.++..|.+|++.+|+|+++.+
T Consensus 584 I~i~ddG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~ 631 (684)
T TIGR03591 584 IDIEDDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMD 631 (684)
T ss_pred EEEecCeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeC
Confidence 4556666777777777777666 466678889999999999999999
No 21
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=43.99 E-value=25 Score=18.98 Aligned_cols=14 Identities=21% Similarity=0.463 Sum_probs=13.0
Q ss_pred CCCeEEEEEEEccC
Q 047634 42 RGEILGAAVTMVNK 55 (82)
Q Consensus 42 ~gEVv~g~V~~v~~ 55 (82)
.|+++.|.|+++++
T Consensus 2 ~G~~v~g~V~~v~~ 15 (72)
T smart00316 2 VGDVVEGTVTEITP 15 (72)
T ss_pred CCCEEEEEEEEEEc
Confidence 58999999999999
No 22
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=42.99 E-value=25 Score=20.01 Aligned_cols=16 Identities=25% Similarity=0.453 Sum_probs=14.5
Q ss_pred ecCCCeEEEEEEEccC
Q 047634 40 PFRGEILGAAVTMVNK 55 (82)
Q Consensus 40 Pf~gEVv~g~V~~v~~ 55 (82)
|-+|+++.|.|+++.+
T Consensus 1 ~~~G~~~~g~V~~v~~ 16 (76)
T cd04452 1 PEEGELVVVTVKSIAD 16 (76)
T ss_pred CCCCCEEEEEEEEEEc
Confidence 5679999999999998
No 23
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=42.06 E-value=30 Score=19.84 Aligned_cols=15 Identities=33% Similarity=0.488 Sum_probs=13.7
Q ss_pred cCCCeEEEEEEEccC
Q 047634 41 FRGEILGAAVTMVNK 55 (82)
Q Consensus 41 f~gEVv~g~V~~v~~ 55 (82)
..|++++|+|.++++
T Consensus 2 ~~g~iV~G~V~~~~~ 16 (67)
T cd04455 2 REGEIVTGIVKRVDR 16 (67)
T ss_pred CCCCEEEEEEEEEcC
Confidence 479999999999998
No 24
>PHA02872 EFc gene family protein; Provisional
Probab=39.54 E-value=51 Score=22.32 Aligned_cols=36 Identities=25% Similarity=0.614 Sum_probs=27.1
Q ss_pred CCeEEEEEEEeccEe----cceeEEcCCCceEEEEEEeEEE
Q 047634 1 GRHGFVVAIMGVESI----GTGLIRDGIGFVTFPVRCQCIV 37 (82)
Q Consensus 1 g~~GliV~v~di~~i----~~G~I~~gdG~~~~~V~f~aiv 37 (82)
|+-|||-+|-|+-.- ..|.+..|+ .+.|+..|.|++
T Consensus 69 GkG~LIfSv~dv~sp~~eedSgyv~eG~-~Vef~t~f~C~i 108 (124)
T PHA02872 69 GKGGLIFSVSDVGSPDNEEDSGYVNEGE-CVEFETDFACFI 108 (124)
T ss_pred cCCcEEEEEEecCCCCccccccceeccc-EEEEecCceEEE
Confidence 566889898888542 458888877 688888888864
No 25
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=37.91 E-value=34 Score=19.37 Aligned_cols=13 Identities=8% Similarity=0.416 Sum_probs=12.0
Q ss_pred CCeEEEEEEEccC
Q 047634 43 GEILGAAVTMVNK 55 (82)
Q Consensus 43 gEVv~g~V~~v~~ 55 (82)
|++++|+|+++.+
T Consensus 1 G~~v~g~V~~v~~ 13 (69)
T cd05697 1 GQVVKGTIRKLRP 13 (69)
T ss_pred CCEEEEEEEEEec
Confidence 6899999999998
No 26
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=35.48 E-value=34 Score=24.82 Aligned_cols=18 Identities=28% Similarity=0.335 Sum_probs=17.4
Q ss_pred eeecCCCeEEEEEEEccC
Q 047634 38 FRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 38 frPf~gEVv~g~V~~v~~ 55 (82)
|.|..|+++.|+|++++.
T Consensus 59 y~P~vGDiViG~V~~i~~ 76 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTF 76 (235)
T ss_pred ccCCCCCEEEEEEEEEeC
Confidence 899999999999999998
No 27
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=35.03 E-value=34 Score=21.24 Aligned_cols=18 Identities=39% Similarity=0.383 Sum_probs=16.8
Q ss_pred eeecCCCeEEEEEEEccC
Q 047634 38 FRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 38 frPf~gEVv~g~V~~v~~ 55 (82)
+.|..|.++-|+|++++.
T Consensus 2 ~~P~~GDiVig~V~~v~~ 19 (92)
T cd05791 2 VLPKVGSIVIARVTRINP 19 (92)
T ss_pred CCCCCCCEEEEEEEEEcC
Confidence 579999999999999998
No 28
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=33.93 E-value=45 Score=18.92 Aligned_cols=15 Identities=47% Similarity=0.501 Sum_probs=13.4
Q ss_pred cCCCeEEEEEEEccC
Q 047634 41 FRGEILGAAVTMVNK 55 (82)
Q Consensus 41 f~gEVv~g~V~~v~~ 55 (82)
.+|+++.|+|+++++
T Consensus 2 ~~G~iv~g~V~~v~~ 16 (73)
T cd05706 2 KVGDILPGRVTKVND 16 (73)
T ss_pred CCCCEEEEEEEEEeC
Confidence 379999999999988
No 29
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=32.80 E-value=43 Score=21.00 Aligned_cols=18 Identities=17% Similarity=0.276 Sum_probs=16.7
Q ss_pred eeecCCCeEEEEEEEccC
Q 047634 38 FRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 38 frPf~gEVv~g~V~~v~~ 55 (82)
|.|..|.++-|+|++++.
T Consensus 2 Y~P~~gD~VIG~V~~~~~ 19 (86)
T cd05790 2 YVPAKGDHVIGIVVAKAG 19 (86)
T ss_pred CcCCCCCEEEEEEEEEcC
Confidence 789999999999999976
No 30
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=30.79 E-value=51 Score=18.59 Aligned_cols=14 Identities=21% Similarity=0.347 Sum_probs=12.9
Q ss_pred CCCeEEEEEEEccC
Q 047634 42 RGEILGAAVTMVNK 55 (82)
Q Consensus 42 ~gEVv~g~V~~v~~ 55 (82)
.|+++.|.|+++++
T Consensus 2 ~g~~v~g~V~~i~~ 15 (77)
T cd05708 2 VGQKIDGTVRRVED 15 (77)
T ss_pred CCCEEEEEEEEEEc
Confidence 58999999999998
No 31
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=30.76 E-value=1.2e+02 Score=18.10 Aligned_cols=21 Identities=5% Similarity=0.382 Sum_probs=16.9
Q ss_pred EEEEEEEccC-------------CCCCceEEcCC
Q 047634 46 LGAAVTMVNK-------------LIPDDMELQTG 66 (82)
Q Consensus 46 v~g~V~~v~~-------------~~p~d~~~~~~ 66 (82)
++|+|+++++ .+|.++.++.-
T Consensus 5 veG~I~~id~~~~titLdDGksy~lp~ef~~~~L 38 (61)
T PF07076_consen 5 VEGTIKSIDPETMTITLDDGKSYKLPEEFDFDGL 38 (61)
T ss_pred ceEEEEEEcCCceEEEecCCCEEECCCccccccc
Confidence 6899999999 78888877644
No 32
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=29.70 E-value=55 Score=19.26 Aligned_cols=16 Identities=13% Similarity=0.084 Sum_probs=14.6
Q ss_pred ecCCCeEEEEEEEccC
Q 047634 40 PFRGEILGAAVTMVNK 55 (82)
Q Consensus 40 Pf~gEVv~g~V~~v~~ 55 (82)
+..|+++.|.|+++++
T Consensus 12 ~~~G~i~~g~V~~v~~ 27 (83)
T cd04461 12 LKPGMVVHGYVRNITP 27 (83)
T ss_pred CCCCCEEEEEEEEEee
Confidence 4589999999999999
No 33
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=29.65 E-value=49 Score=18.98 Aligned_cols=14 Identities=21% Similarity=0.318 Sum_probs=12.7
Q ss_pred CCCeEEEEEEEccC
Q 047634 42 RGEILGAAVTMVNK 55 (82)
Q Consensus 42 ~gEVv~g~V~~v~~ 55 (82)
.|++.+|.|+++++
T Consensus 1 ~g~~~~g~V~~v~~ 14 (83)
T cd04471 1 VGEEFDGVISGVTS 14 (83)
T ss_pred CCCEEEEEEEeEEe
Confidence 38899999999999
No 34
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=29.61 E-value=55 Score=18.40 Aligned_cols=13 Identities=15% Similarity=0.419 Sum_probs=11.9
Q ss_pred CCeEEEEEEEccC
Q 047634 43 GEILGAAVTMVNK 55 (82)
Q Consensus 43 gEVv~g~V~~v~~ 55 (82)
|+++.|+|+++.+
T Consensus 1 G~~v~g~V~~v~~ 13 (68)
T cd05707 1 GDVVRGFVKNIAN 13 (68)
T ss_pred CCEEEEEEEEEEC
Confidence 6889999999998
No 35
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=28.71 E-value=59 Score=18.25 Aligned_cols=13 Identities=31% Similarity=0.596 Sum_probs=11.7
Q ss_pred CCeEEEEEEEccC
Q 047634 43 GEILGAAVTMVNK 55 (82)
Q Consensus 43 gEVv~g~V~~v~~ 55 (82)
|+++.|+|+++.+
T Consensus 1 G~iv~g~V~~i~~ 13 (70)
T cd05687 1 GDIVKGTVVSVDD 13 (70)
T ss_pred CCEEEEEEEEEeC
Confidence 6889999999987
No 36
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=28.49 E-value=63 Score=18.75 Aligned_cols=14 Identities=29% Similarity=0.209 Sum_probs=12.3
Q ss_pred CCCeEEEEEEEccC
Q 047634 42 RGEILGAAVTMVNK 55 (82)
Q Consensus 42 ~gEVv~g~V~~v~~ 55 (82)
.|+++.|.|+++.+
T Consensus 3 ~G~iv~G~V~~i~~ 16 (72)
T cd05704 3 EGAVTLGMVTKVIP 16 (72)
T ss_pred CCCEEEEEEEEeeC
Confidence 68999999999875
No 37
>PHA02945 interferon resistance protein; Provisional
Probab=28.24 E-value=57 Score=20.95 Aligned_cols=15 Identities=33% Similarity=0.448 Sum_probs=13.7
Q ss_pred ecCCCeEEEEEEEccC
Q 047634 40 PFRGEILGAAVTMVNK 55 (82)
Q Consensus 40 Pf~gEVv~g~V~~v~~ 55 (82)
|-.||++.|+|.+ ..
T Consensus 9 P~~GelvigtV~~-~d 23 (88)
T PHA02945 9 PNVGDVLKGKVYE-NG 23 (88)
T ss_pred CCCCcEEEEEEEe-cC
Confidence 8999999999999 55
No 38
>TIGR00984 3a0801s03tim44 mitochondrial import inner membrane, translocase subunit. translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family is specific for the Tim proteins.
Probab=27.97 E-value=1.5e+02 Score=23.58 Aligned_cols=41 Identities=15% Similarity=0.243 Sum_probs=28.9
Q ss_pred ecceeEEcCCCceEEEEEEeE---EEeeecC-CCeEEEEEEEccC
Q 047634 15 IGTGLIRDGIGFVTFPVRCQC---IVFRPFR-GEILGAAVTMVNK 55 (82)
Q Consensus 15 i~~G~I~~gdG~~~~~V~f~a---ivfrPf~-gEVv~g~V~~v~~ 55 (82)
|-++++......+.+.|+|++ -++|=-+ |||++|--.++..
T Consensus 308 I~~ak~~e~~~~pviiV~F~aQqI~~vRd~~tGeVVeGd~d~I~~ 352 (378)
T TIGR00984 308 IASGKLLEPGDIPVLIVTFRAQEINVTKNAKSGEVVAGDPDNIQR 352 (378)
T ss_pred EEEEEecCCCCeEEEEEEEEEEEEEEEEcCCCCceeeCCCCceeE
Confidence 456666543446888999886 6788888 9999986444433
No 39
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=27.83 E-value=61 Score=18.20 Aligned_cols=13 Identities=46% Similarity=0.475 Sum_probs=11.8
Q ss_pred CCeEEEEEEEccC
Q 047634 43 GEILGAAVTMVNK 55 (82)
Q Consensus 43 gEVv~g~V~~v~~ 55 (82)
|++++|+|+++++
T Consensus 1 G~iv~g~V~~v~~ 13 (67)
T cd04465 1 GEIVEGKVTEKVK 13 (67)
T ss_pred CCEEEEEEEEEEC
Confidence 6889999999998
No 40
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=27.80 E-value=58 Score=17.73 Aligned_cols=14 Identities=14% Similarity=0.503 Sum_probs=12.5
Q ss_pred CCCeEEEEEEEccC
Q 047634 42 RGEILGAAVTMVNK 55 (82)
Q Consensus 42 ~gEVv~g~V~~v~~ 55 (82)
.|+++.|+|+++++
T Consensus 1 ~g~~~~g~V~~v~~ 14 (68)
T cd05688 1 EGDVVEGTVKSITD 14 (68)
T ss_pred CCCEEEEEEEEEEe
Confidence 47899999999998
No 41
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=27.40 E-value=66 Score=19.73 Aligned_cols=17 Identities=24% Similarity=0.323 Sum_probs=14.9
Q ss_pred eecCCCeEEEEEEEccC
Q 047634 39 RPFRGEILGAAVTMVNK 55 (82)
Q Consensus 39 rPf~gEVv~g~V~~v~~ 55 (82)
+|-.|++..|+|+++.+
T Consensus 4 ~~~~G~iy~g~V~~i~~ 20 (88)
T cd04453 4 EPIVGNIYLGRVKKIVP 20 (88)
T ss_pred cCCCCCEEEEEEEEecc
Confidence 35689999999999998
No 42
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=26.99 E-value=67 Score=17.98 Aligned_cols=13 Identities=15% Similarity=0.140 Sum_probs=11.9
Q ss_pred CCeEEEEEEEccC
Q 047634 43 GEILGAAVTMVNK 55 (82)
Q Consensus 43 gEVv~g~V~~v~~ 55 (82)
|+++.|+|+++.+
T Consensus 1 g~~~~g~V~~v~~ 13 (70)
T cd05698 1 GLKTHGTIVKVKP 13 (70)
T ss_pred CCEEEEEEEEEec
Confidence 6889999999998
No 43
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=26.30 E-value=62 Score=17.50 Aligned_cols=13 Identities=23% Similarity=0.468 Sum_probs=11.6
Q ss_pred CCeEEEEEEEccC
Q 047634 43 GEILGAAVTMVNK 55 (82)
Q Consensus 43 gEVv~g~V~~v~~ 55 (82)
|+++.|.|+++.+
T Consensus 1 G~~~~g~V~~i~~ 13 (69)
T cd05692 1 GSVVEGTVTRLKP 13 (69)
T ss_pred CCEEEEEEEEEEe
Confidence 6889999999988
No 44
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=26.19 E-value=68 Score=17.87 Aligned_cols=13 Identities=38% Similarity=0.532 Sum_probs=11.7
Q ss_pred CCeEEEEEEEccC
Q 047634 43 GEILGAAVTMVNK 55 (82)
Q Consensus 43 gEVv~g~V~~v~~ 55 (82)
|+++.|.|+++..
T Consensus 1 G~~v~g~V~~v~~ 13 (73)
T cd05691 1 GSIVTGKVTEVDA 13 (73)
T ss_pred CCEEEEEEEEEEC
Confidence 6889999999988
No 45
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=25.19 E-value=77 Score=18.65 Aligned_cols=14 Identities=36% Similarity=0.558 Sum_probs=13.0
Q ss_pred CCCeEEEEEEEccC
Q 047634 42 RGEILGAAVTMVNK 55 (82)
Q Consensus 42 ~gEVv~g~V~~v~~ 55 (82)
.|+++.|.|+++++
T Consensus 3 ~G~~V~g~V~~i~~ 16 (74)
T cd05705 3 EGQLLRGYVSSVTK 16 (74)
T ss_pred CCCEEEEEEEEEeC
Confidence 58999999999998
No 46
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=24.69 E-value=1.4e+02 Score=20.67 Aligned_cols=22 Identities=18% Similarity=0.066 Sum_probs=18.3
Q ss_pred eEEEeeecCCCeEEEEEEEccC
Q 047634 34 QCIVFRPFRGEILGAAVTMVNK 55 (82)
Q Consensus 34 ~aivfrPf~gEVv~g~V~~v~~ 55 (82)
+...+.|-.|+++.|+|+++..
T Consensus 56 ~~~~~~~~~GdiV~GkV~~i~~ 77 (189)
T PRK09521 56 KKTPPLLKKGDIVYGRVVDVKE 77 (189)
T ss_pred cCCCCCCCCCCEEEEEEEEEcC
Confidence 3345778899999999999998
No 47
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=24.37 E-value=82 Score=18.62 Aligned_cols=14 Identities=29% Similarity=0.520 Sum_probs=13.0
Q ss_pred CCCeEEEEEEEccC
Q 047634 42 RGEILGAAVTMVNK 55 (82)
Q Consensus 42 ~gEVv~g~V~~v~~ 55 (82)
.|.++.|.|+++.+
T Consensus 4 ~G~~v~g~V~si~d 17 (74)
T cd05694 4 EGMVLSGCVSSVED 17 (74)
T ss_pred CCCEEEEEEEEEeC
Confidence 58899999999999
No 48
>COG1278 CspC Cold shock proteins [Transcription]
Probab=24.02 E-value=74 Score=19.31 Aligned_cols=23 Identities=26% Similarity=0.169 Sum_probs=20.1
Q ss_pred ecceeEEcCCCceEEEEEEeEEE
Q 047634 15 IGTGLIRDGIGFVTFPVRCQCIV 37 (82)
Q Consensus 15 i~~G~I~~gdG~~~~~V~f~aiv 37 (82)
-+-|.|.|.+|+.-.-|+|+||-
T Consensus 13 KGfGFI~p~~G~~DvFVH~Sai~ 35 (67)
T COG1278 13 KGFGFITPEDGGKDVFVHISAIQ 35 (67)
T ss_pred CcceEcCCCCCCcCEEEEeeeec
Confidence 46799999999999999999984
No 49
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=23.73 E-value=78 Score=17.85 Aligned_cols=14 Identities=29% Similarity=0.237 Sum_probs=12.9
Q ss_pred CCCeEEEEEEEccC
Q 047634 42 RGEILGAAVTMVNK 55 (82)
Q Consensus 42 ~gEVv~g~V~~v~~ 55 (82)
.|++++|.|+++++
T Consensus 3 ~g~~~~g~V~~i~~ 16 (72)
T cd05689 3 EGTRLFGKVTNLTD 16 (72)
T ss_pred CCCEEEEEEEEEEe
Confidence 58899999999999
No 50
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=22.44 E-value=91 Score=17.76 Aligned_cols=13 Identities=31% Similarity=0.360 Sum_probs=11.7
Q ss_pred CCeEEEEEEEccC
Q 047634 43 GEILGAAVTMVNK 55 (82)
Q Consensus 43 gEVv~g~V~~v~~ 55 (82)
|.+++|+|+++.+
T Consensus 1 G~~V~g~V~~i~~ 13 (66)
T cd05695 1 GMLVNARVKKVLS 13 (66)
T ss_pred CCEEEEEEEEEeC
Confidence 6789999999988
No 51
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=22.35 E-value=89 Score=16.83 Aligned_cols=13 Identities=38% Similarity=0.504 Sum_probs=11.6
Q ss_pred CCeEEEEEEEccC
Q 047634 43 GEILGAAVTMVNK 55 (82)
Q Consensus 43 gEVv~g~V~~v~~ 55 (82)
|+++.|+|+++++
T Consensus 1 g~~~~g~V~~i~~ 13 (68)
T cd05685 1 GMVLEGVVTNVTD 13 (68)
T ss_pred CCEEEEEEEEEec
Confidence 6789999999998
No 52
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=22.26 E-value=97 Score=17.91 Aligned_cols=27 Identities=19% Similarity=0.007 Sum_probs=20.0
Q ss_pred ccEecceeEEcCCCceEEEEEEeEEEe
Q 047634 12 VESIGTGLIRDGIGFVTFPVRCQCIVF 38 (82)
Q Consensus 12 i~~i~~G~I~~gdG~~~~~V~f~aivf 38 (82)
.-.-++.+|.||.|..+....=+...|
T Consensus 5 ~C~f~g~~I~PG~G~~~Vr~Dgkv~~F 31 (54)
T cd00472 5 KCSFCGYKIYPGHGKMYVRNDGKVFRF 31 (54)
T ss_pred EecCcCCeecCCCccEEEecCCCEEEE
Confidence 334578899999999988776555555
No 53
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=21.86 E-value=92 Score=17.68 Aligned_cols=13 Identities=31% Similarity=0.526 Sum_probs=11.7
Q ss_pred CCeEEEEEEEccC
Q 047634 43 GEILGAAVTMVNK 55 (82)
Q Consensus 43 gEVv~g~V~~v~~ 55 (82)
|+++.|+|+++.+
T Consensus 1 G~iV~g~V~~i~~ 13 (70)
T cd05702 1 GDLVKAKVKSVKP 13 (70)
T ss_pred CCEEEEEEEEEEC
Confidence 6889999999988
No 54
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=21.78 E-value=93 Score=19.34 Aligned_cols=16 Identities=50% Similarity=0.532 Sum_probs=11.6
Q ss_pred ecCCCeEEEEEEEccC
Q 047634 40 PFRGEILGAAVTMVNK 55 (82)
Q Consensus 40 Pf~gEVv~g~V~~v~~ 55 (82)
|..|-++.|+|+++++
T Consensus 2 P~vGdiV~~rVtrv~~ 17 (82)
T PF10447_consen 2 PKVGDIVIARVTRVNP 17 (82)
T ss_dssp --TT-EEEEEEEEE-S
T ss_pred CCCCCEEEEEEEEEec
Confidence 8899999999999998
No 55
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=21.23 E-value=86 Score=17.34 Aligned_cols=13 Identities=8% Similarity=0.458 Sum_probs=11.8
Q ss_pred CCeEEEEEEEccC
Q 047634 43 GEILGAAVTMVNK 55 (82)
Q Consensus 43 gEVv~g~V~~v~~ 55 (82)
|+++.|.|+++++
T Consensus 1 G~~~~g~V~~i~~ 13 (69)
T cd05690 1 GTVVSGKIKSITD 13 (69)
T ss_pred CCEEEEEEEEEEe
Confidence 6889999999998
No 56
>PF14208 DUF4320: Domain of unknown function (DUF4320)
Probab=21.02 E-value=1.3e+02 Score=19.78 Aligned_cols=26 Identities=27% Similarity=0.326 Sum_probs=20.2
Q ss_pred cceeEEcCCCceEEEEE--EeEEEeeecC
Q 047634 16 GTGLIRDGIGFVTFPVR--CQCIVFRPFR 42 (82)
Q Consensus 16 ~~G~I~~gdG~~~~~V~--f~aivfrPf~ 42 (82)
..|+|..|+. +.++++ |+...|+||.
T Consensus 70 ~~~kVq~n~~-v~vtvt~~~~~~~F~~~~ 97 (116)
T PF14208_consen 70 TTGKVQLNEE-VTVTVTGEYKIGIFKGFG 97 (116)
T ss_pred cCCcccCCCE-EEEEEEEEEEEEEECCCC
Confidence 7899999884 555554 8889999876
No 57
>PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=20.87 E-value=68 Score=16.02 Aligned_cols=15 Identities=27% Similarity=0.829 Sum_probs=10.5
Q ss_pred eecCCCeEEEEEEEccC
Q 047634 39 RPFRGEILGAAVTMVNK 55 (82)
Q Consensus 39 rPf~gEVv~g~V~~v~~ 55 (82)
=||+|+. |+|.++++
T Consensus 10 G~~~G~~--G~I~~i~~ 24 (32)
T PF00467_consen 10 GPFKGKI--GKIVEIDR 24 (32)
T ss_dssp STTTTEE--EEEEEEET
T ss_pred cCCCCce--EEEEEEEC
Confidence 3677765 88887765
No 58
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.75 E-value=1.3e+02 Score=18.90 Aligned_cols=14 Identities=21% Similarity=0.330 Sum_probs=12.6
Q ss_pred CCCeEEEEEEEccC
Q 047634 42 RGEILGAAVTMVNK 55 (82)
Q Consensus 42 ~gEVv~g~V~~v~~ 55 (82)
.|.++.|+|+++++
T Consensus 3 ~G~vV~G~V~~v~~ 16 (100)
T cd05693 3 EGMLVLGQVKEITK 16 (100)
T ss_pred CCCEEEEEEEEEcC
Confidence 68899999999988
No 59
>COG3323 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.66 E-value=99 Score=20.59 Aligned_cols=15 Identities=33% Similarity=0.744 Sum_probs=13.2
Q ss_pred eecCCCeEEEEEEEccC
Q 047634 39 RPFRGEILGAAVTMVNK 55 (82)
Q Consensus 39 rPf~gEVv~g~V~~v~~ 55 (82)
.||.||| |++..+.+
T Consensus 55 nP~iGev--gk~e~v~E 69 (109)
T COG3323 55 NPFIGEV--GKLEFVAE 69 (109)
T ss_pred CCccccc--ceEEeeee
Confidence 5899999 99998888
Done!