Query 042741
Match_columns 166
No_of_seqs 105 out of 359
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 08:57:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042741.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042741hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00162 DNA-directed RNA poly 100.0 5.7E-51 1.2E-55 324.7 16.8 153 1-166 1-168 (176)
2 COG1095 RPB7 DNA-directed RNA 100.0 5.7E-47 1.2E-51 301.4 16.4 157 1-166 1-170 (183)
3 KOG3298 DNA-directed RNA polym 100.0 1.9E-45 4.1E-50 286.6 16.5 153 1-166 1-167 (170)
4 KOG3297 DNA-directed RNA polym 100.0 1.1E-45 2.5E-50 292.9 14.6 160 1-166 1-193 (202)
5 TIGR00448 rpoE DNA-directed RN 100.0 4.5E-45 9.8E-50 290.5 18.0 157 1-166 1-170 (179)
6 PRK08563 DNA-directed RNA poly 100.0 4.2E-42 9.2E-47 274.4 17.5 156 1-166 1-170 (187)
7 cd04329 RNAP_II_Rpb7_N RNAP_II 100.0 2.7E-30 5.8E-35 182.1 8.6 80 2-87 1-80 (80)
8 cd00655 RNAP_Rpb7_N_like RNAP_ 100.0 5.8E-30 1.3E-34 180.3 8.6 80 2-87 1-80 (80)
9 cd04330 RNAP_III_Rpc25_N RNAP_ 100.0 8E-30 1.7E-34 179.7 8.7 80 2-87 1-80 (80)
10 cd04331 RNAP_E_N RNAP_E_N: Rpo 100.0 2.5E-29 5.5E-34 177.2 8.5 80 2-87 1-80 (80)
11 PF03876 SHS2_Rpb7-N: SHS2 dom 99.8 4.7E-20 1E-24 125.6 7.5 70 8-83 1-70 (70)
12 cd04462 S1_RNAPII_Rpb7 S1_RNAP 99.8 8.6E-19 1.9E-23 125.4 9.4 74 87-166 1-87 (88)
13 PF08292 RNA_pol_Rbc25: RNA po 99.8 3.3E-18 7.1E-23 129.3 9.2 82 85-166 1-116 (122)
14 cd04328 RNAP_I_Rpa43_N RNAP_I_ 99.7 5.9E-17 1.3E-21 115.7 8.8 79 1-87 8-89 (89)
15 cd04460 S1_RpoE S1_RpoE: RpoE, 97.4 0.0009 2E-08 48.0 6.9 68 95-166 19-88 (99)
16 KOG4134 DNA-dependent RNA poly 97.1 0.0037 8E-08 52.1 8.7 84 5-94 30-114 (253)
17 PF00575 S1: S1 RNA binding do 96.7 0.008 1.7E-07 40.1 6.6 54 84-147 1-67 (74)
18 cd04471 S1_RNase_R S1_RNase_R: 96.2 0.027 6E-07 38.1 6.9 57 88-145 2-74 (83)
19 TIGR02063 RNase_R ribonuclease 92.0 0.45 9.8E-06 45.3 6.7 70 78-147 618-702 (709)
20 smart00316 S1 Ribosomal protei 91.9 0.72 1.6E-05 29.2 5.7 21 127-147 45-65 (72)
21 PRK11642 exoribonuclease R; Pr 89.8 1.6 3.5E-05 42.6 8.2 70 78-147 634-718 (813)
22 TIGR00358 3_prime_RNase VacB a 89.5 1.8 3.8E-05 41.1 8.1 70 78-147 563-647 (654)
23 TIGR03591 polynuc_phos polyrib 89.0 0.16 3.5E-06 48.4 0.8 80 54-144 584-678 (684)
24 PRK04163 exosome complex RNA-b 86.7 1.7 3.7E-05 36.0 5.6 55 83-143 59-126 (235)
25 cd05686 S1_pNO40 S1_pNO40: pNO 86.7 2.4 5.3E-05 28.3 5.4 20 126-145 46-65 (73)
26 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 86.3 0.98 2.1E-05 30.9 3.3 55 83-143 2-69 (86)
27 cd05708 S1_Rrp5_repeat_sc12 S1 85.0 2.9 6.2E-05 27.4 5.1 22 126-147 45-66 (77)
28 cd05691 S1_RPS1_repeat_ec6 S1_ 84.8 3.6 7.9E-05 26.7 5.4 21 127-147 43-63 (73)
29 cd05706 S1_Rrp5_repeat_sc10 S1 84.8 7.1 0.00015 25.6 6.9 21 127-147 46-66 (73)
30 cd04454 S1_Rrp4_like S1_Rrp4_l 84.7 2.7 5.9E-05 28.5 5.0 52 83-144 2-66 (82)
31 cd05698 S1_Rrp5_repeat_hs6_sc5 83.9 3 6.5E-05 27.1 4.7 19 127-145 43-61 (70)
32 cd05791 S1_CSL4 S1_CSL4: CSL4, 81.6 1.4 3E-05 31.4 2.5 17 127-143 59-75 (92)
33 cd04452 S1_IF2_alpha S1_IF2_al 81.0 7.3 0.00016 25.5 5.8 21 127-147 48-68 (76)
34 cd05697 S1_Rrp5_repeat_hs5 S1_ 80.9 3.7 8.1E-05 26.8 4.3 22 126-147 42-63 (69)
35 cd05687 S1_RPS1_repeat_ec1_hs1 80.8 6.4 0.00014 25.6 5.4 17 127-143 43-59 (70)
36 cd05688 S1_RPS1_repeat_ec3 S1_ 80.1 5.7 0.00012 25.1 4.9 19 127-145 43-61 (68)
37 PRK07252 hypothetical protein; 78.6 10 0.00022 28.3 6.5 21 127-147 46-66 (120)
38 cd04461 S1_Rrp5_repeat_hs8_sc7 78.4 7.2 0.00016 26.4 5.2 22 126-147 56-77 (83)
39 cd05685 S1_Tex S1_Tex: The C-t 77.9 4.9 0.00011 25.3 4.1 20 127-146 43-62 (68)
40 cd05692 S1_RPS1_repeat_hs4 S1_ 76.5 8.7 0.00019 24.2 5.0 18 127-144 43-60 (69)
41 PRK08582 hypothetical protein; 74.8 9.5 0.00021 29.2 5.5 18 127-144 48-65 (139)
42 cd05707 S1_Rrp5_repeat_sc11 S1 72.4 8.4 0.00018 25.0 4.1 20 126-145 42-61 (68)
43 cd05684 S1_DHX8_helicase S1_DH 71.8 15 0.00032 24.5 5.4 20 124-143 44-63 (79)
44 PRK05807 hypothetical protein; 69.2 10 0.00022 28.8 4.6 19 126-144 46-64 (136)
45 cd05696 S1_Rrp5_repeat_hs4 S1_ 69.2 23 0.0005 23.4 5.8 20 127-146 45-64 (71)
46 cd05694 S1_Rrp5_repeat_hs2_sc2 67.6 27 0.00058 23.5 6.0 18 127-144 42-59 (74)
47 cd05790 S1_Rrp40 S1_Rrp40: Rrp 67.6 13 0.00028 26.4 4.5 52 83-145 2-66 (86)
48 cd05690 S1_RPS1_repeat_ec5 S1_ 67.2 17 0.00037 23.3 4.8 21 126-146 43-63 (69)
49 COG1096 Predicted RNA-binding 65.9 53 0.0011 26.8 8.2 17 127-143 117-133 (188)
50 cd05704 S1_Rrp5_repeat_hs13 S1 65.4 11 0.00023 25.1 3.6 17 127-143 47-63 (72)
51 cd05702 S1_Rrp5_repeat_hs11_sc 64.9 18 0.0004 23.6 4.6 18 127-144 45-62 (70)
52 COG0557 VacB Exoribonuclease R 64.4 38 0.00082 32.5 8.3 50 98-147 647-697 (706)
53 cd04465 S1_RPS1_repeat_ec2_hs2 62.9 24 0.00052 22.7 4.9 15 131-145 44-58 (67)
54 cd05705 S1_Rrp5_repeat_hs14 S1 61.2 21 0.00045 24.0 4.4 21 127-147 49-69 (74)
55 PRK08059 general stress protei 59.8 27 0.00059 25.8 5.2 18 127-144 50-67 (123)
56 cd04455 S1_NusA S1_NusA: N-uti 57.4 49 0.0011 21.5 5.7 17 128-144 40-56 (67)
57 cd05695 S1_Rrp5_repeat_hs3 S1_ 55.5 35 0.00076 22.2 4.7 20 126-145 40-59 (66)
58 PF10447 EXOSC1: Exosome compo 55.4 12 0.00025 26.4 2.4 15 128-142 68-82 (82)
59 COG1097 RRP4 RNA-binding prote 53.7 25 0.00054 29.7 4.5 59 82-146 59-130 (239)
60 cd04472 S1_PNPase S1_PNPase: P 53.1 41 0.00089 21.1 4.7 18 127-144 43-60 (68)
61 cd05689 S1_RPS1_repeat_ec4 S1_ 52.2 62 0.0013 20.8 5.9 22 125-146 45-66 (72)
62 PRK09521 exosome complex RNA-b 48.7 20 0.00044 28.4 3.1 17 127-143 117-133 (189)
63 PRK09202 nusA transcription el 47.7 38 0.00081 31.2 5.1 19 127-145 170-188 (470)
64 PHA02945 interferon resistance 46.9 76 0.0016 22.8 5.5 57 85-144 9-72 (88)
65 cd00164 S1_like S1_like: Ribos 45.4 26 0.00056 21.3 2.7 20 126-145 39-58 (65)
66 cd04453 S1_RNase_E S1_RNase_E: 43.6 1.1E+02 0.0024 21.2 6.2 62 85-147 5-75 (88)
67 PRK03987 translation initiatio 43.3 47 0.001 28.1 4.7 61 84-146 5-72 (262)
68 PRK05054 exoribonuclease II; P 42.6 1.3E+02 0.0029 28.6 8.1 46 101-147 588-637 (644)
69 PRK11824 polynucleotide phosph 42.5 55 0.0012 31.5 5.5 52 83-144 617-681 (693)
70 PRK06676 rpsA 30S ribosomal pr 42.1 60 0.0013 28.4 5.4 18 128-145 62-79 (390)
71 PRK07400 30S ribosomal protein 39.7 74 0.0016 27.5 5.5 22 126-147 237-258 (318)
72 PRK07400 30S ribosomal protein 39.4 62 0.0013 28.0 5.0 17 128-144 75-91 (318)
73 COG0539 RpsA Ribosomal protein 39.2 57 0.0012 30.7 4.9 49 86-144 191-251 (541)
74 PRK12327 nusA transcription el 35.8 75 0.0016 28.3 5.0 21 127-147 170-190 (362)
75 cd04473 S1_RecJ_like S1_RecJ_l 35.3 1.2E+02 0.0026 20.1 5.0 16 127-142 51-66 (77)
76 PRK06676 rpsA 30S ribosomal pr 35.3 77 0.0017 27.7 5.0 18 127-144 234-251 (390)
77 PRK02268 hypothetical protein; 34.4 86 0.0019 24.3 4.5 36 127-164 34-69 (141)
78 COG1098 VacB Predicted RNA bin 34.1 34 0.00074 26.2 2.2 50 85-144 3-65 (129)
79 PRK07899 rpsA 30S ribosomal pr 33.3 90 0.0019 28.8 5.2 19 127-145 250-268 (486)
80 PF02470 MCE: mce related prot 31.4 1.6E+02 0.0034 19.5 5.1 35 127-165 13-53 (81)
81 PF12306 PixA: Inclusion body 31.3 62 0.0014 25.5 3.4 20 128-147 61-80 (172)
82 TIGR02062 RNase_B exoribonucle 30.5 1.3E+02 0.0028 28.7 5.9 46 101-147 584-633 (639)
83 PRK13806 rpsA 30S ribosomal pr 29.6 1.3E+02 0.0028 27.5 5.6 20 127-146 245-264 (491)
84 PRK06299 rpsA 30S ribosomal pr 29.1 1.4E+02 0.0029 27.6 5.7 19 127-145 243-261 (565)
85 PRK12269 bifunctional cytidyla 26.6 1.6E+02 0.0036 29.2 6.0 17 128-144 536-552 (863)
86 KOG3416 Predicted nucleic acid 26.2 58 0.0013 25.1 2.3 19 120-138 53-71 (134)
87 cd05703 S1_Rrp5_repeat_hs12_sc 25.0 1.6E+02 0.0035 19.4 4.1 21 127-147 45-65 (73)
88 PRK07899 rpsA 30S ribosomal pr 24.4 1.9E+02 0.0041 26.7 5.7 14 129-142 80-93 (486)
89 PRK00087 4-hydroxy-3-methylbut 24.1 2.2E+02 0.0048 27.0 6.2 20 127-146 605-624 (647)
90 TIGR01953 NusA transcription t 22.6 2.1E+02 0.0046 25.2 5.4 19 128-146 169-187 (341)
91 PRK06299 rpsA 30S ribosomal pr 21.4 2.3E+02 0.005 26.1 5.7 20 126-145 502-521 (565)
92 KOG3409 Exosomal 3'-5' exoribo 20.5 1.3E+02 0.0028 24.5 3.3 15 128-142 122-136 (193)
93 TIGR02696 pppGpp_PNP guanosine 20.0 1.8E+02 0.0039 28.5 4.7 52 84-143 644-710 (719)
No 1
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=100.00 E-value=5.7e-51 Score=324.74 Aligned_cols=153 Identities=22% Similarity=0.357 Sum_probs=145.6
Q ss_pred CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeE
Q 042741 1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMC 80 (166)
Q Consensus 1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~a 80 (166)
||++++|+|+|+|||++|+++ + ++++.++|+++|+|+ |.+++||||||+|++++++|+ |.||||++||+|+|||
T Consensus 1 MF~~~~l~d~v~i~P~~f~~~--~--~~~i~~~L~~~~egk-v~~~~GliV~v~di~~i~~G~-I~~gdG~~~~~V~Fra 74 (176)
T PTZ00162 1 MFFVVELWKNVSLKPSQLGPR--Y--QQIIEDMLRSQVEGQ-CTRKYGYVICVIRIIHNEPGR-VQDGTGMIVVNVKYQA 74 (176)
T ss_pred CcEEEEEEEEEEECHHHcCcc--H--HHHHHHHHHHHHCCC-CcCcccEEEEEEEeeEecCCE-EEcCCCCEEEEEEEEE
Confidence 999999999999999999998 5 999999999999999 999999999999999999999 9999999999999999
Q ss_pred EEEeeecCcEEEEE------------eCCcceEEecCCCCC-CceeeCCCceeEec--CCCCeecCCCEEEEEEEEEEEc
Q 042741 81 RTFLPVKGEILHGV------------CGPMKYALMSPRRMP-TYRHVSGKKSFFSN--DQQPKIGNGVVVQFLVTAVRWS 145 (166)
Q Consensus 81 lvFrPf~gEVv~G~------------~Gp~~~ifi~~~~m~-~~~~~~~~~~~~~~--~~~~~i~~g~~VR~RI~~~~~~ 145 (166)
+|||||+|||++|+ +|||+ +|+|.+.|| ++.||+++++|.|. +++.+|++|+.|||||++++|+
T Consensus 75 ivFrPf~gEVv~g~V~~v~~~G~~v~~Gp~~-ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~ 153 (176)
T PTZ00162 75 IVFKPFKDEVLDAIVTDVNKLGFFAQAGPLK-AFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYD 153 (176)
T ss_pred EEEecCCCCEEEEEEEEEecceEEEEeeCeE-EEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEec
Confidence 99999999999999 99999 999999996 57899999988774 5568999999999999999999
Q ss_pred CCCcCccccEEEEEEecCCCC
Q 042741 146 GEGRNLKREYLVFGRAKGESI 166 (166)
Q Consensus 146 ~~~~~~~~~~~~igti~~d~l 166 (166)
++ + ++|+|||++|||
T Consensus 154 ~~----~--~~~i~T~~~~~L 168 (176)
T PTZ00162 154 AS----N--LFAIATINSDYL 168 (176)
T ss_pred CC----C--cEEEEEecCCCc
Confidence 87 5 899999999998
No 2
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=100.00 E-value=5.7e-47 Score=301.37 Aligned_cols=157 Identities=21% Similarity=0.268 Sum_probs=143.5
Q ss_pred CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeE
Q 042741 1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMC 80 (166)
Q Consensus 1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~a 80 (166)
||++++++|+|+|||++||++ + ++++.++|+++|+|+ |++++|+||+|+|+++|++|+ |.||||++||+|+|+|
T Consensus 1 My~l~~~~d~VripP~~fg~~--~--~~~v~~~L~~k~eG~-~~~~~G~~v~V~~v~~igeG~-I~~GDG~~y~~V~f~a 74 (183)
T COG1095 1 MYKLVELEDTVRIPPSYFGED--L--EEAVKEELKEKYEGK-LDGDVGLVVLVLDVKEIGEGI-IVPGDGSTYHEVKFRA 74 (183)
T ss_pred CcEEEEEeeEEEeCHHHcCcc--H--HHHHHHHHHHHhcce-EccccCEEEEEEEeeEeeccE-EecCCCcEEEEEEEEE
Confidence 999999999999999999999 5 999999999999999 999999999999999999999 9999999999999999
Q ss_pred EEEeeecCcEEEEE------------eCCcceEEecCCCCCCce-eeCCCceeEecCCCCeecCCCEEEEEEEEEEEcCC
Q 042741 81 RTFLPVKGEILHGV------------CGPMKYALMSPRRMPTYR-HVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGE 147 (166)
Q Consensus 81 lvFrPf~gEVv~G~------------~Gp~~~ifi~~~~m~~~~-~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~~ 147 (166)
|+|+||+|||++|+ +||+|++.|.+|+|+|+. ||+....|..+++++.|++||.|||||++++++++
T Consensus 75 l~fkP~~gEVV~GeVv~~~~~G~fV~igp~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~ 154 (183)
T COG1095 75 LVFKPFRGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSR 154 (183)
T ss_pred EEEEeccccEEEEEEEEEeecceEEEeccccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccC
Confidence 99999999999999 999996666688888743 66666666777888999999999999999999876
Q ss_pred CcCccccEEEEEEecCCCC
Q 042741 148 GRNLKREYLVFGRAKGESI 166 (166)
Q Consensus 148 ~~~~~~~~~~igti~~d~l 166 (166)
. .++..+.+||+++||
T Consensus 155 -~--~~~~~I~lTmrq~~L 170 (183)
T COG1095 155 -R--PRESKIGLTMRQPGL 170 (183)
T ss_pred -c--cccceEEEEeccccC
Confidence 1 145899999999997
No 3
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=100.00 E-value=1.9e-45 Score=286.62 Aligned_cols=153 Identities=28% Similarity=0.490 Sum_probs=145.2
Q ss_pred CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeE
Q 042741 1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMC 80 (166)
Q Consensus 1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~a 80 (166)
||+...++.+|.+||++||++ + ++.+.+.|.++.+|+ |++++||+|||+++++||+|+ |.+|+|.+.|+|+|+|
T Consensus 1 mff~~~l~~~i~l~p~~~gp~--~--~~~l~~~L~~~veg~-ctg~~Gyvi~vt~ld~Ig~g~-I~~~~G~v~FpVky~a 74 (170)
T KOG3298|consen 1 MFFHKDLDLNICLHPSYFGPN--L--QAILKRKLLAEVEGK-CTGKYGYVIAVTTLDNIGEGR-IRPGTGFVTFPVKYKA 74 (170)
T ss_pred CcceeeeeeeeeecccccCch--H--HHHHHHHHHHHhhcc-ccccccEEEEEEEhhhccCCc-cccCCceEEEEEEEEE
Confidence 999999999999999999998 5 777788888889999 999999999999999999999 9999999999999999
Q ss_pred EEEeeecCcEEEEE------------eCCcceEEecCCCC-CCceeeCCCc-eeEecCCCCeecCCCEEEEEEEEEEEcC
Q 042741 81 RTFLPVKGEILHGV------------CGPMKYALMSPRRM-PTYRHVSGKK-SFFSNDQQPKIGNGVVVQFLVTAVRWSG 146 (166)
Q Consensus 81 lvFrPf~gEVv~G~------------~Gp~~~ifi~~~~m-~~~~~~~~~~-~~~~~~~~~~i~~g~~VR~RI~~~~~~~ 146 (166)
++|||||||||+|+ +||++ +|+++|.+ |||.|++++| ++|.++++.+|++|+.||++|+|++|++
T Consensus 75 v~FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~-~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~ 153 (170)
T KOG3298|consen 75 VTFKPFKGEVVDGVVTKVNKMGVFARSGPLE-VFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDE 153 (170)
T ss_pred EEEeecCCcEEEEEEEEEeeeeEEEeccceE-eeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEEee
Confidence 99999999999999 99999 99999988 6899999988 8888877779999999999999999998
Q ss_pred CCcCccccEEEEEEecCCCC
Q 042741 147 EGRNLKREYLVFGRAKGESI 166 (166)
Q Consensus 147 ~~~~~~~~~~~igti~~d~l 166 (166)
+ + |+|+|||+||||
T Consensus 154 ~----~--i~algtl~~D~L 167 (170)
T KOG3298|consen 154 T----E--IFALGTLKGDYL 167 (170)
T ss_pred e----e--EEEEEEecCccc
Confidence 8 5 999999999998
No 4
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=100.00 E-value=1.1e-45 Score=292.87 Aligned_cols=160 Identities=16% Similarity=0.273 Sum_probs=147.5
Q ss_pred CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeE
Q 042741 1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMC 80 (166)
Q Consensus 1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~a 80 (166)
||++++|+|+|||||++|.++ + +++|.++|++++.|| +.+|+||||||+||.++++|+ |.||||++|++|.||+
T Consensus 1 MF~Lsel~D~VrI~P~qf~~~--~--~~ai~~eL~~k~anK-vl~nvGLCI~vyDi~~v~e~~-v~pGDGas~~~V~FR~ 74 (202)
T KOG3297|consen 1 MFYLSELEDTVRIPPSQFEKP--L--EDAIKEELNRKLANK-VLPNVGLCICVYDILEVEEGI-VLPGDGASYARVWFRV 74 (202)
T ss_pred CeeehhcccceecChHHhCch--H--HHHHHHHHHHHHHhh-hcccccEEEEEeEeeeecceE-EecCCCceEEEEEEEE
Confidence 999999999999999999988 4 999999999999999 999999999999999999999 9999999999999999
Q ss_pred EEEeeecCcEEEEE------------eCCcceEEecCCCCCC-ceeeCCCceeEec-C------CCCeecCCCEEEEEEE
Q 042741 81 RTFLPVKGEILHGV------------CGPMKYALMSPRRMPT-YRHVSGKKSFFSN-D------QQPKIGNGVVVQFLVT 140 (166)
Q Consensus 81 lvFrPf~gEVv~G~------------~Gp~~~ifi~~~~m~~-~~~~~~~~~~~~~-~------~~~~i~~g~~VR~RI~ 140 (166)
+|||||.|||+.|+ +|+|||||||+..|++ +.|++++++|+|. + ++.+++.|+.|||||.
T Consensus 75 vVFrPF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~ 154 (202)
T KOG3297|consen 75 VVFRPFVGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVE 154 (202)
T ss_pred EEEecccceEEEEEeecCCccceEEEEEeeeceeechhhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEe
Confidence 99999999999999 8999999999999965 7799999999996 2 4568999999999999
Q ss_pred EEEEcCCCcC-------------ccccEEEEEEecCCCC
Q 042741 141 AVRWSGEGRN-------------LKREYLVFGRAKGESI 166 (166)
Q Consensus 141 ~~~~~~~~~~-------------~~~~~~~igti~~d~l 166 (166)
..+|.+.+.+ .+.+|..+|+|++|+|
T Consensus 155 ~e~f~d~~p~~~~~~~t~~e~~e~~~py~l~gs~~~~GL 193 (202)
T KOG3297|consen 155 DESFVDVSPEGNSTAITGAEDPEKESPYTLLGSMNEDGL 193 (202)
T ss_pred eecccccCccccccccccccccccCCCeEEEEEecCCCC
Confidence 9999654332 2348999999999987
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=100.00 E-value=4.5e-45 Score=290.51 Aligned_cols=157 Identities=14% Similarity=0.211 Sum_probs=145.9
Q ss_pred CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeE
Q 042741 1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMC 80 (166)
Q Consensus 1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~a 80 (166)
||++++|+|+|+|||++|+++ + ++++.++|+++|+|| |.+++||||||+|++++++|+ |.||||+++|+|+|||
T Consensus 1 Mf~~~~l~d~v~i~P~~~~~~--~--~~~i~~~l~~~~~gk-~~~~~G~~i~v~di~~i~~g~-i~~gdG~~~~~V~f~~ 74 (179)
T TIGR00448 1 MYILSKIADTVRIPPDQFGED--L--EEVITHQLNEKFEGR-LDKNVGLCITIYDIEDIGEGK-VIPGDGSAYHNVTFRA 74 (179)
T ss_pred CeEEEEEeeEEEECHHHhCcc--H--HHHHHHHHHHHhcCc-CcCCcCEEEEEEEeEEecCCE-EECCCCCEEEEEEEEE
Confidence 999999999999999999988 5 999999999999999 999999999999999999999 9999999999999999
Q ss_pred EEEeeecCcEEEEE------------eCCcceEEecCCCCCC-ceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEcCC
Q 042741 81 RTFLPVKGEILHGV------------CGPMKYALMSPRRMPT-YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGE 147 (166)
Q Consensus 81 lvFrPf~gEVv~G~------------~Gp~~~ifi~~~~m~~-~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~~ 147 (166)
++||||+|||++|+ +||+++++++++++++ +.||++++.|+|++++.+++.||.|||||.++++++.
T Consensus 75 i~f~p~~gEvv~G~V~~v~~~GifV~lg~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 154 (179)
T TIGR00448 75 LVFKPELGEIVEGEVIEIVEFGAFVSLGPFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDR 154 (179)
T ss_pred EEEeccCCCEEEEEEEEEEeeEEEEEeCCceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCC
Confidence 99999999999999 8999999999999976 5689999999998888999999999999999999754
Q ss_pred CcCccccEEEEEEecCCCC
Q 042741 148 GRNLKREYLVFGRAKGESI 166 (166)
Q Consensus 148 ~~~~~~~~~~igti~~d~l 166 (166)
.. . .-.+.+||+++||
T Consensus 155 ~~-~--~~~I~lt~k~~~L 170 (179)
T TIGR00448 155 RP-E--GSKIGLTMRQPLL 170 (179)
T ss_pred CC-C--cceEEEEeccCcC
Confidence 11 1 1356999999998
No 6
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=100.00 E-value=4.2e-42 Score=274.37 Aligned_cols=156 Identities=19% Similarity=0.231 Sum_probs=144.3
Q ss_pred CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeE
Q 042741 1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMC 80 (166)
Q Consensus 1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~a 80 (166)
||++++|+|+|+|||++|+++ + ++++.++|+++|+|+ |.+++||||||+|++++++|+ |.||||+++|+|+|+|
T Consensus 1 MF~~~~l~d~v~i~P~~~~~~--~--~~~i~~~l~~~~~~k-~~~~~G~~v~v~di~~i~~g~-i~~gdg~~~~~v~f~~ 74 (187)
T PRK08563 1 MYKLVKLEDVVRIPPEMFGED--L--EEAALEVLREKYEGR-IDKELGIIVAVLDVKVIGEGK-IVPGDGATYHEVEFDA 74 (187)
T ss_pred CeEEEEEeEEEEECHHHcCcc--H--HHHHHHHHHHHhhCc-CcCCcCEEEEEEEeEEecccE-EecCCCCcEEEEEEEE
Confidence 999999999999999999988 5 999999999999999 999999999999999999999 9999999999999999
Q ss_pred EEEeeecCcEEEEE------------eCCcceEEecCCCCCC-ceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEcCC
Q 042741 81 RTFLPVKGEILHGV------------CGPMKYALMSPRRMPT-YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGE 147 (166)
Q Consensus 81 lvFrPf~gEVv~G~------------~Gp~~~ifi~~~~m~~-~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~~ 147 (166)
+||+||+|||++|+ +||+++++++++++++ +.||++++.|+|++.+..++.|+.|||||.++++++.
T Consensus 75 lvf~P~~GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~ 154 (187)
T PRK08563 75 LVFKPELQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKER 154 (187)
T ss_pred EEEeccCCCEEEEEEEEEEccEEEEEEeCceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccC
Confidence 99999999999999 8999999999888876 6699999999999888899999999999999999765
Q ss_pred CcCcc-ccEEEEEEecCCCC
Q 042741 148 GRNLK-REYLVFGRAKGESI 166 (166)
Q Consensus 148 ~~~~~-~~~~~igti~~d~l 166 (166)
+ +...+.+||+++||
T Consensus 155 ----~~~~~~I~ls~~~~~L 170 (187)
T PRK08563 155 ----RPRGSKIGLTMRQPGL 170 (187)
T ss_pred ----CCCCCEEEEEecCCCC
Confidence 2 01366669999997
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=99.97 E-value=2.7e-30 Score=182.06 Aligned_cols=80 Identities=31% Similarity=0.514 Sum_probs=78.1
Q ss_pred eEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeEE
Q 042741 2 FFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMCR 81 (166)
Q Consensus 2 F~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~al 81 (166)
|++++++|+|+|||++||++ + ++++.++|+++++|+ |.+++||||||+|++++++|+ |.||||++||+|+|+|+
T Consensus 1 F~~~~l~d~v~i~P~~fg~~--l--~~~i~~~L~~~~egk-~~~~~G~iv~v~di~~i~~G~-I~~gdG~~~~~V~F~ai 74 (80)
T cd04329 1 FFKIELEHNILLHPSYFGPN--L--KEYLEQKLLEEVEGT-CTGDYGYIIAVTDIDDIGEGK-ILPGTGSVEFPVKYKAI 74 (80)
T ss_pred CEEEEEEEEEEECHHHhCcc--H--HHHHHHHHHHHhCCc-CcCceeEEEEEEEeeEecCcE-EEcCCCCEEEEEEEEEE
Confidence 89999999999999999988 5 999999999999999 999999999999999999999 99999999999999999
Q ss_pred EEeeec
Q 042741 82 TFLPVK 87 (166)
Q Consensus 82 vFrPf~ 87 (166)
|||||+
T Consensus 75 vfrPf~ 80 (80)
T cd04329 75 VFKPFK 80 (80)
T ss_pred EEEccC
Confidence 999996
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=99.96 E-value=5.8e-30 Score=180.31 Aligned_cols=80 Identities=21% Similarity=0.231 Sum_probs=78.0
Q ss_pred eEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeEE
Q 042741 2 FFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMCR 81 (166)
Q Consensus 2 F~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~al 81 (166)
|++++++|+|+|||++||++ + ++++.++|+++|+|+ |.+++||||||+|++++++|+ |.||||++||+|+|||+
T Consensus 1 f~l~~l~d~v~i~P~~f~~~--~--~~~i~~~L~~k~~gk-v~~~~G~~v~v~di~~i~~G~-I~~gdG~~~~~V~F~~i 74 (80)
T cd00655 1 FQILEIADLVSVPPKYFGDD--C--KGVKKCLLQEKGEGD-RTPVVGIILAIKDTKDIPEGA-IRPGDGSAYVNVSFRAV 74 (80)
T ss_pred CEEEEEEEEEEECHHHhCcc--H--HHHHHHHHHHHhCCe-EeCCccEEEEEEEeEEEcCCE-EECCCCCEEEEEEEEEE
Confidence 79999999999999999988 5 999999999999999 999999999999999999999 99999999999999999
Q ss_pred EEeeec
Q 042741 82 TFLPVK 87 (166)
Q Consensus 82 vFrPf~ 87 (166)
|||||+
T Consensus 75 vFrPf~ 80 (80)
T cd00655 75 VFKPFS 80 (80)
T ss_pred EEEcCC
Confidence 999996
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=99.96 E-value=8e-30 Score=179.65 Aligned_cols=80 Identities=16% Similarity=0.287 Sum_probs=78.0
Q ss_pred eEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeEE
Q 042741 2 FFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMCR 81 (166)
Q Consensus 2 F~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~al 81 (166)
|++++++|+|+|||++||++ + ++++.++|+++|+|+ |.+++||||||+|++++++|+ |.||||++||+|+|||+
T Consensus 1 F~~~~l~d~v~i~P~~fg~~--~--~~~i~~~L~~ky~gk-v~~~~Gl~v~v~di~~i~eG~-I~~gdG~~~~~V~Fr~l 74 (80)
T cd04330 1 FILSEIEDTVRIPPSQFSRP--L--NDAIEDELNKKYANK-VIQNVGLCICLYDILEVEDGY-ILPGDGASHYKVTFRMV 74 (80)
T ss_pred CEEEEEEEEEEECHHHcCcC--H--HHHHHHHHHHHhCCc-EeCCccEEEEEEEeEEEcCCE-EECCCCCEEEEEEEEEE
Confidence 88999999999999999988 5 999999999999999 999999999999999999999 99999999999999999
Q ss_pred EEeeec
Q 042741 82 TFLPVK 87 (166)
Q Consensus 82 vFrPf~ 87 (166)
|||||+
T Consensus 75 vFrPf~ 80 (80)
T cd04330 75 VFRPFV 80 (80)
T ss_pred EEECCC
Confidence 999996
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=99.96 E-value=2.5e-29 Score=177.16 Aligned_cols=80 Identities=26% Similarity=0.302 Sum_probs=77.4
Q ss_pred eEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeEE
Q 042741 2 FFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMCR 81 (166)
Q Consensus 2 F~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~al 81 (166)
|++++++|+|+|||++||++ + ++++.++|+++|+|+ |++++||||||+|++++++|+ |.||||++||+|+|||+
T Consensus 1 f~~~~l~d~vri~P~~fg~~--~--~~~i~~~L~~~~egk-~~~~~G~iv~v~di~~i~eG~-I~~gdG~~~~~V~F~~i 74 (80)
T cd04331 1 YKLVELEDVVRVPPELFGED--L--EEAVLEILKEKYEGR-LDKDLGKIVSVLDVKDVGEGK-IVHGDGAVYHEVRFDAL 74 (80)
T ss_pred CEEEEEEEeEEECHHHcCcC--H--HHHHHHHHHHHhcCc-CcCCCCEEEEEEEEEEecCCE-EEcCCCCEEEEEEEEEE
Confidence 78999999999999999988 5 999999999999999 999999999999999999999 99999999999999999
Q ss_pred EEeeec
Q 042741 82 TFLPVK 87 (166)
Q Consensus 82 vFrPf~ 87 (166)
||||..
T Consensus 75 vFrP~~ 80 (80)
T cd04331 75 VFKPEL 80 (80)
T ss_pred EEecCC
Confidence 999963
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=99.82 E-value=4.7e-20 Score=125.61 Aligned_cols=70 Identities=21% Similarity=0.339 Sum_probs=65.2
Q ss_pred ceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeEEEE
Q 042741 8 LRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMCRTF 83 (166)
Q Consensus 8 ~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~alvF 83 (166)
+|+|+|||++|+++ + ++.+.++|+++++|+ +.+++|+|||++|+..+++|+ |.+|||+++|+|+|+|+||
T Consensus 1 e~~v~l~P~~l~~~--~--~~~i~~~L~~~~~~k-~~~~~G~~i~v~~i~~~~~g~-I~~~~g~~~~~V~f~~lvF 70 (70)
T PF03876_consen 1 EDTVRLPPSYLGPD--L--KDGIKEQLLDKYEGK-YIPELGVVIAVTDIKEISEGK-IIPGDGFVYFKVTFRALVF 70 (70)
T ss_dssp EEEEEE-GGGTTST--H--HHHHHHHHHHHHTTE-EETTTEEEEEEEEEEEESCEE-E-TTTSSEEEEEEEEEEEE
T ss_pred CcEEEECHHHhCcC--H--HHHHHHHHHHHHhCc-CcCCceEEEEEeeeeEecCcE-EECCCCCEEEEEEEEEEEC
Confidence 68999999999977 4 899999999999999 999999999999999999999 9999999999999999998
No 12
>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=99.78 E-value=8.6e-19 Score=125.38 Aligned_cols=74 Identities=14% Similarity=0.226 Sum_probs=63.0
Q ss_pred cCcEEEEE------------eCCcceEEecCCCCCCceeeCCCceeEec-CCCCeecCCCEEEEEEEEEEEcCCCcCccc
Q 042741 87 KGEILHGV------------CGPMKYALMSPRRMPTYRHVSGKKSFFSN-DQQPKIGNGVVVQFLVTAVRWSGEGRNLKR 153 (166)
Q Consensus 87 ~gEVv~G~------------~Gp~~~ifi~~~~m~~~~~~~~~~~~~~~-~~~~~i~~g~~VR~RI~~~~~~~~~~~~~~ 153 (166)
+|||++|+ +||++.+|+..++++++.|++++++|.|. +++.+|++|+.|||||++++|+.+ +
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~----~- 75 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDAT----D- 75 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccC----c-
Confidence 69999999 99999555555555678899877888876 467899999999999999999766 4
Q ss_pred cEEEEEEecCCCC
Q 042741 154 EYLVFGRAKGESI 166 (166)
Q Consensus 154 ~~~~igti~~d~l 166 (166)
++|+|||++|||
T Consensus 76 -~~~igt~~~~~L 87 (88)
T cd04462 76 -IFAIGTIKDDYL 87 (88)
T ss_pred -eEEEEEccCCCC
Confidence 999999999998
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=99.76 E-value=3.3e-18 Score=129.35 Aligned_cols=82 Identities=20% Similarity=0.348 Sum_probs=60.2
Q ss_pred eecCcEEEEE------------eCCcceEEecCCCCCC-ceeeCCCceeEec---CCCCeecCCCEEEEEEEEEEEcCC-
Q 042741 85 PVKGEILHGV------------CGPMKYALMSPRRMPT-YRHVSGKKSFFSN---DQQPKIGNGVVVQFLVTAVRWSGE- 147 (166)
Q Consensus 85 Pf~gEVv~G~------------~Gp~~~ifi~~~~m~~-~~~~~~~~~~~~~---~~~~~i~~g~~VR~RI~~~~~~~~- 147 (166)
||+||||.|+ +|||+|||||++.|++ +.||++++.|+|. +++..++.|+.|||||.++.|.+.
T Consensus 1 PF~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f~d~~ 80 (122)
T PF08292_consen 1 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIFPDVP 80 (122)
T ss_dssp --TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE----
T ss_pred CCCCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEEecCC
Confidence 9999999999 8999999999999975 7799999999997 344689999999999999999432
Q ss_pred CcC-----------------ccccEEEEEEecCCCC
Q 042741 148 GRN-----------------LKREYLVFGRAKGESI 166 (166)
Q Consensus 148 ~~~-----------------~~~~~~~igti~~d~l 166 (166)
|.. ..-+|.++|||++++|
T Consensus 81 p~~~~~~~~~~~~~~~~~~~~~~Py~I~gs~~~~GL 116 (122)
T PF08292_consen 81 PTPPPSAEASGEEEEEEEDEPKPPYQIIGSINEDGL 116 (122)
T ss_dssp -----------------------SEEEEEEB-STT-
T ss_pred CCCcccccccccccccccccCCCCeEEEEEecCCCC
Confidence 111 1128999999999987
No 14
>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=99.71 E-value=5.9e-17 Score=115.73 Aligned_cols=79 Identities=13% Similarity=0.102 Sum_probs=74.2
Q ss_pred CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCe-eEEEEEEEecccCC--CcceecCCCceEEEEE
Q 042741 1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDH-GYFLSVTKSKSIDK--EGPTVNGPGVVSFPVI 77 (166)
Q Consensus 1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~-GliI~V~di~~i~~--G~~I~~gdG~~~~~V~ 77 (166)
||.+++++++|+|+|++|+++ .+++.++|++.+. + +..++ |+|+|.+|+..+++ |+ |.+++|.++++|+
T Consensus 8 ~f~~~~~~~~v~l~P~~~~~~-----~~~i~~~l~~~l~-k-y~~~l~Gv~l~~~di~~~~~~~~~-i~~~~~~~~~~V~ 79 (89)
T cd04328 8 CFETLTVSLYVSLAPKYLGNP-----LTGIKAQLLNPLL-K-YSPKLKGVVLAYSNIKLLEGELAK-IVDDSPFIFVWIS 79 (89)
T ss_pred cEEEEEEEEEEEECchhhcCH-----hHHHHHHHhhhHh-h-hcccCCeEEEEecceEecccccee-eeCCCcEEEEEEE
Confidence 899999999999999999987 4699999998888 7 99999 99999999999977 99 9999999999999
Q ss_pred EeEEEEeeec
Q 042741 78 FMCRTFLPVK 87 (166)
Q Consensus 78 F~alvFrPf~ 87 (166)
|+++|||||.
T Consensus 80 ~~~lVFrP~~ 89 (89)
T cd04328 80 ADFLVFRPKI 89 (89)
T ss_pred EEEEEEecCC
Confidence 9999999985
No 15
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=97.36 E-value=0.0009 Score=47.97 Aligned_cols=68 Identities=16% Similarity=0.191 Sum_probs=44.4
Q ss_pred eCCcceEEecCCCCCC-ceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEcCCCcCccccEEEEE-EecCCCC
Q 042741 95 CGPMKYALMSPRRMPT-YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNLKREYLVFG-RAKGESI 166 (166)
Q Consensus 95 ~Gp~~~ifi~~~~m~~-~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~~~~~~~~~~~~ig-ti~~d~l 166 (166)
+++.+++.+.+++.++ +.|++....|...+.+..++.||.|+++|.++..... ++.+..++ |+++++|
T Consensus 19 l~~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~----~~~~~~i~ls~k~~~~ 88 (99)
T cd04460 19 IGPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKER----RPRESKIGLTMRQPGL 88 (99)
T ss_pred EcCeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHC----cCCCceEEEEEecCCC
Confidence 5555644444555555 4566665555555666889999999999999886543 11134555 9998876
No 16
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=97.09 E-value=0.0037 Score=52.05 Aligned_cols=84 Identities=14% Similarity=0.105 Sum_probs=68.3
Q ss_pred EEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccC-CCcceecCCCceEEEEEEeEEEE
Q 042741 5 VELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID-KEGPTVNGPGVVSFPVIFMCRTF 83 (166)
Q Consensus 5 ~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~-~G~~I~~gdG~~~~~V~F~alvF 83 (166)
.+..-.+.+.|-++..+ ..++.++.+......+-.+=.|.+++.-+|+-.+ .++ |.+-|+..+..+.=..+||
T Consensus 30 ~t~dlhlalaP~yl~np-----l~~~i~ehld~~vl~y~~~l~GivLgydnIKvLg~~ak-i~~D~pf~hlwi~adfyVf 103 (253)
T KOG4134|consen 30 ITTDLHLALAPYYLANP-----LHALIEEHLDTKVLFYDSGLDGIVLGYDNIKVLGQTAK-IRADDPFMHLWINADFYVF 103 (253)
T ss_pred eeeheeeeecchhhcch-----hHHHHHHHhhHHHhhhccCCCceEEeecceEeeccccc-eecCCCceEEEEeeeEEEE
Confidence 45566789999999887 4656666666666663445568888887788766 688 9999999999999999999
Q ss_pred eeecCcEEEEE
Q 042741 84 LPVKGEILHGV 94 (166)
Q Consensus 84 rPf~gEVv~G~ 94 (166)
+|-.|.+|+|.
T Consensus 104 ~Pk~Gd~LeG~ 114 (253)
T KOG4134|consen 104 RPKAGDILEGV 114 (253)
T ss_pred CCCCCCeeeee
Confidence 99999999999
No 17
>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=96.72 E-value=0.008 Score=40.14 Aligned_cols=54 Identities=17% Similarity=0.184 Sum_probs=39.1
Q ss_pred eeecCcEEEEE------------eC-CcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEcCC
Q 042741 84 LPVKGEILHGV------------CG-PMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGE 147 (166)
Q Consensus 84 rPf~gEVv~G~------------~G-p~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~~ 147 (166)
+|..|++++|+ +| ..+ .|+|.+.+++. +..+....+..|+.|+++|.++.-+..
T Consensus 1 k~~~G~iv~g~V~~v~~~g~~V~l~~~~~-g~ip~~~l~~~---------~~~~~~~~~~~G~~v~v~v~~vd~~~~ 67 (74)
T PF00575_consen 1 KLKEGDIVEGKVTSVEDFGVFVDLGNGIE-GFIPISELSDD---------RIDDPSEVYKIGQTVRVKVIKVDKEKG 67 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEESTSSE-EEEEGGGSSSS---------EESSSHGTCETTCEEEEEEEEEETTTT
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCcEE-EEEEeehhcCc---------cccccccccCCCCEEEEEEEEEECCCC
Confidence 57789999999 66 666 77776666432 223334578999999999999887655
No 18
>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=96.22 E-value=0.027 Score=38.09 Aligned_cols=57 Identities=18% Similarity=0.239 Sum_probs=37.4
Q ss_pred CcEEEEE------------eCC--cceEEecCCCC-CC-ceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEc
Q 042741 88 GEILHGV------------CGP--MKYALMSPRRM-PT-YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWS 145 (166)
Q Consensus 88 gEVv~G~------------~Gp--~~~ifi~~~~m-~~-~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~ 145 (166)
|++.+|. +++ .+ -+++.+.+ ++ +.|++.+..+..+.....++.||.|+++|.++...
T Consensus 2 g~~~~g~V~~v~~~G~fv~l~~~~~~-G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~ 74 (83)
T cd04471 2 GEEFDGVISGVTSFGLFVELDNLTVE-GLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLD 74 (83)
T ss_pred CCEEEEEEEeEEeeeEEEEecCCCEE-EEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccc
Confidence 5666666 665 44 35554555 44 45665554334445567899999999999998763
No 19
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=92.01 E-value=0.45 Score=45.32 Aligned_cols=70 Identities=11% Similarity=0.008 Sum_probs=49.6
Q ss_pred EeEEEEeeecCcEEEEE------------eCC--cceEEecCCCCCC-ceeeCCCceeEecCCCCeecCCCEEEEEEEEE
Q 042741 78 FMCRTFLPVKGEILHGV------------CGP--MKYALMSPRRMPT-YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAV 142 (166)
Q Consensus 78 F~alvFrPf~gEVv~G~------------~Gp--~~~ifi~~~~m~~-~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~ 142 (166)
+.|.-.++..||+.+|+ +.+ .+++.|.+++-++ +.|++....+.....+..++.||.|+++|.++
T Consensus 618 ~~~~yl~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~v 697 (709)
T TIGR02063 618 KKAEYMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKA 697 (709)
T ss_pred HHHHhhhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEE
Confidence 44445667788888888 333 5666666655555 45777666666666667899999999999999
Q ss_pred EEcCC
Q 042741 143 RWSGE 147 (166)
Q Consensus 143 ~~~~~ 147 (166)
.....
T Consensus 698 d~~~~ 702 (709)
T TIGR02063 698 DLDTG 702 (709)
T ss_pred ecccC
Confidence 87544
No 20
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=91.86 E-value=0.72 Score=29.18 Aligned_cols=21 Identities=19% Similarity=0.039 Sum_probs=17.4
Q ss_pred CeecCCCEEEEEEEEEEEcCC
Q 042741 127 PKIGNGVVVQFLVTAVRWSGE 147 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~~~~ 147 (166)
..++.|+.|+++|..+.....
T Consensus 45 ~~~~~G~~v~~~V~~~~~~~~ 65 (72)
T smart00316 45 EVLKVGDEVKVKVLSVDEEKG 65 (72)
T ss_pred HeecCCCEEEEEEEEEeCCCC
Confidence 468999999999999986533
No 21
>PRK11642 exoribonuclease R; Provisional
Probab=89.77 E-value=1.6 Score=42.57 Aligned_cols=70 Identities=17% Similarity=0.191 Sum_probs=48.2
Q ss_pred EeEEEEeeecCcEEEEE------------eC--CcceEEecCCCCCC-ceeeCCCceeEecCCCCeecCCCEEEEEEEEE
Q 042741 78 FMCRTFLPVKGEILHGV------------CG--PMKYALMSPRRMPT-YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAV 142 (166)
Q Consensus 78 F~alvFrPf~gEVv~G~------------~G--p~~~ifi~~~~m~~-~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~ 142 (166)
+.|-......||+.+|+ +. ..+++.+.+++-++ |.|++.........++..++.||.|+++|..+
T Consensus 634 ~~~~~m~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~v 713 (813)
T PRK11642 634 LKCDFMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAV 713 (813)
T ss_pred HHHhhhhccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEe
Confidence 33444566788998888 32 25544444444455 56776666666666678899999999999998
Q ss_pred EEcCC
Q 042741 143 RWSGE 147 (166)
Q Consensus 143 ~~~~~ 147 (166)
.....
T Consensus 714 D~~~r 718 (813)
T PRK11642 714 NMDER 718 (813)
T ss_pred ecCCC
Confidence 87644
No 22
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=89.50 E-value=1.8 Score=41.11 Aligned_cols=70 Identities=16% Similarity=0.142 Sum_probs=48.7
Q ss_pred EeEEEEeeecCcEEEEE------------eC-C-cceEEecCCCCCC-ceeeCCCceeEecCCCCeecCCCEEEEEEEEE
Q 042741 78 FMCRTFLPVKGEILHGV------------CG-P-MKYALMSPRRMPT-YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAV 142 (166)
Q Consensus 78 F~alvFrPf~gEVv~G~------------~G-p-~~~ifi~~~~m~~-~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~ 142 (166)
+.|.-++...||+.+|+ +. + .+++.+.+++-++ |.||+.........++..++.||.|++||.++
T Consensus 563 ~~~~yl~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~v 642 (654)
T TIGR00358 563 LKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEV 642 (654)
T ss_pred HHHHhhhhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEE
Confidence 44555666778888888 22 2 4544444444444 66887777777666778999999999999998
Q ss_pred EEcCC
Q 042741 143 RWSGE 147 (166)
Q Consensus 143 ~~~~~ 147 (166)
.....
T Consensus 643 d~~~~ 647 (654)
T TIGR00358 643 NMETR 647 (654)
T ss_pred ecccC
Confidence 76554
No 23
>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=88.95 E-value=0.16 Score=48.39 Aligned_cols=80 Identities=11% Similarity=-0.002 Sum_probs=54.4
Q ss_pred EEecccCCCcceecCCCceEEEE--EEeEEEEeeecCcEEEEE------------e-CCcceEEecCCCCCCceeeCCCc
Q 042741 54 TKSKSIDKEGPTVNGPGVVSFPV--IFMCRTFLPVKGEILHGV------------C-GPMKYALMSPRRMPTYRHVSGKK 118 (166)
Q Consensus 54 ~di~~i~~G~~I~~gdG~~~~~V--~F~alvFrPf~gEVv~G~------------~-Gp~~~ifi~~~~m~~~~~~~~~~ 118 (166)
+||.+-|..+ |...++.++.++ ..+.++..|..|++++|+ + +..+++.|.+++-++
T Consensus 584 I~i~ddG~V~-i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~-------- 654 (684)
T TIGR03591 584 IDIEDDGTVK-IAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANE-------- 654 (684)
T ss_pred EEEecCeEEE-EEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCC--------
Confidence 4555556666 667778777777 667778889999999999 2 234544444443221
Q ss_pred eeEecCCCCeecCCCEEEEEEEEEEE
Q 042741 119 SFFSNDQQPKIGNGVVVQFLVTAVRW 144 (166)
Q Consensus 119 ~~~~~~~~~~i~~g~~VR~RI~~~~~ 144 (166)
++++-...++.||.|++||.++..
T Consensus 655 --~v~~~~~~~kvGD~V~VkVi~id~ 678 (684)
T TIGR03591 655 --RVEKVEDVLKEGDEVKVKVLEIDK 678 (684)
T ss_pred --cccChhhccCCCCEEEEEEEEECC
Confidence 122334568999999999998764
No 24
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=86.74 E-value=1.7 Score=36.02 Aligned_cols=55 Identities=20% Similarity=0.262 Sum_probs=33.7
Q ss_pred EeeecCcEEEEE------------eC-CcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEE
Q 042741 83 FLPVKGEILHGV------------CG-PMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVR 143 (166)
Q Consensus 83 FrPf~gEVv~G~------------~G-p~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~ 143 (166)
|.|-.|++|.|+ ++ +++++++.++........+ ..+-...+++||.|++||..+.
T Consensus 59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d------~~~~~~~~~~GDlV~akV~~i~ 126 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVE------GTDLRKYLDIGDYIIAKVKDVD 126 (235)
T ss_pred ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccc------hhhhHhhCCCCCEEEEEEEEEC
Confidence 899999999999 44 5564433333321111000 0112245899999999999875
No 25
>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=86.65 E-value=2.4 Score=28.26 Aligned_cols=20 Identities=15% Similarity=0.028 Sum_probs=16.1
Q ss_pred CCeecCCCEEEEEEEEEEEc
Q 042741 126 QPKIGNGVVVQFLVTAVRWS 145 (166)
Q Consensus 126 ~~~i~~g~~VR~RI~~~~~~ 145 (166)
...++.||.|+++|.++...
T Consensus 46 ~~~~~~Gd~v~vkv~~vd~~ 65 (73)
T cd05686 46 SEVVDVGEKVWVKVIGREMK 65 (73)
T ss_pred hhEECCCCEEEEEEEEECCC
Confidence 45689999999999887653
No 26
>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=86.31 E-value=0.98 Score=30.94 Aligned_cols=55 Identities=15% Similarity=0.203 Sum_probs=33.4
Q ss_pred EeeecCcEEEEE------------eC-CcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEE
Q 042741 83 FLPVKGEILHGV------------CG-PMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVR 143 (166)
Q Consensus 83 FrPf~gEVv~G~------------~G-p~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~ 143 (166)
|.|-+|++++|+ ++ +++++.+.+++..+. + +.+ ..+-...+++||.|++||..+.
T Consensus 2 y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~-~----~~~-~~~~~~~l~vGd~i~~~V~~~~ 69 (86)
T cd05789 2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPR-T----DED-ELNMRSYLDEGDLIVAEVQSVD 69 (86)
T ss_pred CcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCC-C----ccc-hHHHHhhCCCCCEEEEEEEEEC
Confidence 678899999999 33 455444444443210 0 000 1122346899999999998874
No 27
>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=85.04 E-value=2.9 Score=27.45 Aligned_cols=22 Identities=14% Similarity=-0.013 Sum_probs=17.7
Q ss_pred CCeecCCCEEEEEEEEEEEcCC
Q 042741 126 QPKIGNGVVVQFLVTAVRWSGE 147 (166)
Q Consensus 126 ~~~i~~g~~VR~RI~~~~~~~~ 147 (166)
...++.||.|++||..+.....
T Consensus 45 ~~~~~~Gd~v~v~i~~vd~~~~ 66 (77)
T cd05708 45 SKLFRVGDKVRAKVLKIDAEKK 66 (77)
T ss_pred hHeecCCCEEEEEEEEEeCCCC
Confidence 3568999999999999876543
No 28
>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=84.77 E-value=3.6 Score=26.71 Aligned_cols=21 Identities=19% Similarity=0.162 Sum_probs=17.1
Q ss_pred CeecCCCEEEEEEEEEEEcCC
Q 042741 127 PKIGNGVVVQFLVTAVRWSGE 147 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~~~~ 147 (166)
..++.||.|+++|..+.....
T Consensus 43 ~~~~~Gd~v~~~v~~~d~~~~ 63 (73)
T cd05691 43 ERFKVGDEVEAKITNVDRKNR 63 (73)
T ss_pred HccCCCCEEEEEEEEEeCCCC
Confidence 458999999999999876543
No 29
>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=84.75 E-value=7.1 Score=25.56 Aligned_cols=21 Identities=19% Similarity=0.132 Sum_probs=17.0
Q ss_pred CeecCCCEEEEEEEEEEEcCC
Q 042741 127 PKIGNGVVVQFLVTAVRWSGE 147 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~~~~ 147 (166)
..+..||.|+++|..+.....
T Consensus 46 ~~~~~Gd~v~~~V~~~d~~~~ 66 (73)
T cd05706 46 YKFKKNDIVRACVLSVDVPNK 66 (73)
T ss_pred cccCCCCEEEEEEEEEeCCCC
Confidence 568999999999998776533
No 30
>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=84.74 E-value=2.7 Score=28.50 Aligned_cols=52 Identities=15% Similarity=0.165 Sum_probs=31.9
Q ss_pred EeeecCcEEEEE------------eC-CcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEEE
Q 042741 83 FLPVKGEILHGV------------CG-PMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRW 144 (166)
Q Consensus 83 FrPf~gEVv~G~------------~G-p~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~ 144 (166)
|.|-.|.++.|+ +| .++ .++|...+... ...+....+++||.|++||..+.-
T Consensus 2 y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~-g~l~~~~~~~~---------~~~~~~~~~~~GD~i~~~V~~~~~ 66 (82)
T cd04454 2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGT-ARLEDSSATEK---------DKKEIRKSLQPGDLILAKVISLGD 66 (82)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEeCCCce-EEeechhccCc---------chHHHHhcCCCCCEEEEEEEEeCC
Confidence 679999999999 32 344 33333322110 011222458999999999998644
No 31
>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=83.92 E-value=3 Score=27.13 Aligned_cols=19 Identities=21% Similarity=0.132 Sum_probs=15.8
Q ss_pred CeecCCCEEEEEEEEEEEc
Q 042741 127 PKIGNGVVVQFLVTAVRWS 145 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~~ 145 (166)
..+++|+.|++||.++.-.
T Consensus 43 ~~~~~G~~i~v~v~~~d~~ 61 (70)
T cd05698 43 EHFRVGQVVKVKVLSCDPE 61 (70)
T ss_pred HcccCCCEEEEEEEEEcCC
Confidence 4588999999999887654
No 32
>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=81.58 E-value=1.4 Score=31.37 Aligned_cols=17 Identities=18% Similarity=0.153 Sum_probs=14.1
Q ss_pred CeecCCCEEEEEEEEEE
Q 042741 127 PKIGNGVVVQFLVTAVR 143 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~ 143 (166)
..+++||.||+||.+..
T Consensus 59 ~~f~~GDiV~AkVis~~ 75 (92)
T cd05791 59 KCFRPGDIVRAKVISLG 75 (92)
T ss_pred hhcCCCCEEEEEEEEcC
Confidence 34799999999998754
No 33
>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=81.03 E-value=7.3 Score=25.54 Aligned_cols=21 Identities=14% Similarity=-0.081 Sum_probs=16.7
Q ss_pred CeecCCCEEEEEEEEEEEcCC
Q 042741 127 PKIGNGVVVQFLVTAVRWSGE 147 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~~~~ 147 (166)
..++.||.|++||..+.....
T Consensus 48 ~~~~~Gd~v~vkv~~~d~~~~ 68 (76)
T cd04452 48 KLVKVGRKEVVKVIRVDKEKG 68 (76)
T ss_pred HeeCCCCEEEEEEEEEECCCC
Confidence 458999999999998766433
No 34
>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=80.87 E-value=3.7 Score=26.76 Aligned_cols=22 Identities=23% Similarity=0.218 Sum_probs=17.8
Q ss_pred CCeecCCCEEEEEEEEEEEcCC
Q 042741 126 QPKIGNGVVVQFLVTAVRWSGE 147 (166)
Q Consensus 126 ~~~i~~g~~VR~RI~~~~~~~~ 147 (166)
...++.|+.+.+||.++.....
T Consensus 42 ~~~~~~Gd~i~~~V~~id~~~~ 63 (69)
T cd05697 42 EKKFKPGLKVKCRVLSVEPERK 63 (69)
T ss_pred HHcCCCCCEEEEEEEEEECCCC
Confidence 3569999999999998876544
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=80.84 E-value=6.4 Score=25.57 Aligned_cols=17 Identities=24% Similarity=0.249 Sum_probs=14.9
Q ss_pred CeecCCCEEEEEEEEEE
Q 042741 127 PKIGNGVVVQFLVTAVR 143 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~ 143 (166)
..+++||.++++|.++.
T Consensus 43 ~~~~~Gd~i~~~i~~~~ 59 (70)
T cd05687 43 DEVKVGDEVEVYVLRVE 59 (70)
T ss_pred HcCCCCCEEEEEEEEEE
Confidence 45899999999999886
No 36
>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=80.07 E-value=5.7 Score=25.15 Aligned_cols=19 Identities=16% Similarity=0.094 Sum_probs=16.2
Q ss_pred CeecCCCEEEEEEEEEEEc
Q 042741 127 PKIGNGVVVQFLVTAVRWS 145 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~~ 145 (166)
..++.||.|+++|..+...
T Consensus 43 ~~~~~Gd~v~v~i~~vd~~ 61 (68)
T cd05688 43 EVVNVGDEVEVKVLKIDKE 61 (68)
T ss_pred HEECCCCEEEEEEEEEECC
Confidence 5689999999999998654
No 37
>PRK07252 hypothetical protein; Provisional
Probab=78.62 E-value=10 Score=28.30 Aligned_cols=21 Identities=14% Similarity=-0.075 Sum_probs=17.0
Q ss_pred CeecCCCEEEEEEEEEEEcCC
Q 042741 127 PKIGNGVVVQFLVTAVRWSGE 147 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~~~~ 147 (166)
..+..||.|+++|.++.....
T Consensus 46 ~~~~vGD~V~VkI~~iD~~~~ 66 (120)
T PRK07252 46 QLLKVGEEVLVQVVDFDEYTG 66 (120)
T ss_pred hccCCCCEEEEEEEEEeCCCC
Confidence 568999999999999875433
No 38
>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=78.41 E-value=7.2 Score=26.43 Aligned_cols=22 Identities=23% Similarity=0.089 Sum_probs=17.7
Q ss_pred CCeecCCCEEEEEEEEEEEcCC
Q 042741 126 QPKIGNGVVVQFLVTAVRWSGE 147 (166)
Q Consensus 126 ~~~i~~g~~VR~RI~~~~~~~~ 147 (166)
...+..|+.|+++|..+.....
T Consensus 56 ~~~~~~Gd~v~vkV~~id~~~~ 77 (83)
T cd04461 56 SFGFKKGQSVTAKVTSVDEEKQ 77 (83)
T ss_pred HHhcCCCCEEEEEEEEEcCCCC
Confidence 3568999999999999876543
No 39
>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=77.93 E-value=4.9 Score=25.35 Aligned_cols=20 Identities=15% Similarity=0.175 Sum_probs=16.6
Q ss_pred CeecCCCEEEEEEEEEEEcC
Q 042741 127 PKIGNGVVVQFLVTAVRWSG 146 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~~~ 146 (166)
..++.||.|+++|..+....
T Consensus 43 ~~~~~Gd~v~v~i~~vd~~~ 62 (68)
T cd05685 43 DVVSVGDIVEVKVISIDEER 62 (68)
T ss_pred HhcCCCCEEEEEEEEEECCC
Confidence 45899999999999887543
No 40
>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=76.46 E-value=8.7 Score=24.16 Aligned_cols=18 Identities=17% Similarity=0.141 Sum_probs=15.2
Q ss_pred CeecCCCEEEEEEEEEEE
Q 042741 127 PKIGNGVVVQFLVTAVRW 144 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~ 144 (166)
..++.||.|++||..+.-
T Consensus 43 ~~~~~Gd~v~v~v~~~~~ 60 (69)
T cd05692 43 DVLKEGDKVKVKVLSIDA 60 (69)
T ss_pred HccCCCCEEEEEEEEECC
Confidence 458999999999988764
No 41
>PRK08582 hypothetical protein; Provisional
Probab=74.79 E-value=9.5 Score=29.17 Aligned_cols=18 Identities=22% Similarity=0.089 Sum_probs=15.5
Q ss_pred CeecCCCEEEEEEEEEEE
Q 042741 127 PKIGNGVVVQFLVTAVRW 144 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~ 144 (166)
..+..||.|+++|..+.-
T Consensus 48 ~~l~vGD~VkvkV~~id~ 65 (139)
T PRK08582 48 DHLKVGDEVEVKVLNVED 65 (139)
T ss_pred cccCCCCEEEEEEEEECC
Confidence 568999999999999763
No 42
>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=72.36 E-value=8.4 Score=24.95 Aligned_cols=20 Identities=10% Similarity=0.140 Sum_probs=16.0
Q ss_pred CCeecCCCEEEEEEEEEEEc
Q 042741 126 QPKIGNGVVVQFLVTAVRWS 145 (166)
Q Consensus 126 ~~~i~~g~~VR~RI~~~~~~ 145 (166)
...+..||.|++||..+...
T Consensus 42 ~~~~~~Gd~v~~~v~~~d~~ 61 (68)
T cd05707 42 KKRFKVGQLVKGKIVSIDPD 61 (68)
T ss_pred hhccCCCCEEEEEEEEEeCC
Confidence 35589999999999877643
No 43
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=71.81 E-value=15 Score=24.52 Aligned_cols=20 Identities=15% Similarity=0.283 Sum_probs=16.6
Q ss_pred CCCCeecCCCEEEEEEEEEE
Q 042741 124 DQQPKIGNGVVVQFLVTAVR 143 (166)
Q Consensus 124 ~~~~~i~~g~~VR~RI~~~~ 143 (166)
+....++.|+.|+++|..+.
T Consensus 44 ~~~~~~~~Gd~v~v~v~~vd 63 (79)
T cd05684 44 NPSDVVKRGQKVKVKVISIQ 63 (79)
T ss_pred ChhheeCCCCEEEEEEEEEe
Confidence 33457899999999999987
No 44
>PRK05807 hypothetical protein; Provisional
Probab=69.18 E-value=10 Score=28.83 Aligned_cols=19 Identities=11% Similarity=0.055 Sum_probs=15.7
Q ss_pred CCeecCCCEEEEEEEEEEE
Q 042741 126 QPKIGNGVVVQFLVTAVRW 144 (166)
Q Consensus 126 ~~~i~~g~~VR~RI~~~~~ 144 (166)
...++.||.|+++|..+.-
T Consensus 46 ~~~~kvGd~V~VkV~~id~ 64 (136)
T PRK05807 46 REHLKEQDKVKVKVISIDD 64 (136)
T ss_pred cccCCCCCEEEEEEEEECC
Confidence 3568999999999988754
No 45
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: 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 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=69.17 E-value=23 Score=23.39 Aligned_cols=20 Identities=5% Similarity=-0.090 Sum_probs=16.0
Q ss_pred CeecCCCEEEEEEEEEEEcC
Q 042741 127 PKIGNGVVVQFLVTAVRWSG 146 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~~~ 146 (166)
..+++|+.+.+||.++.-..
T Consensus 45 ~~~~vG~~v~~kV~~id~~~ 64 (71)
T cd05696 45 GPFKAGTTHKARIIGYSPMD 64 (71)
T ss_pred cccCCCCEEEEEEEEEeCCC
Confidence 45899999999998765443
No 46
>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=67.64 E-value=27 Score=23.55 Aligned_cols=18 Identities=22% Similarity=0.279 Sum_probs=15.0
Q ss_pred CeecCCCEEEEEEEEEEE
Q 042741 127 PKIGNGVVVQFLVTAVRW 144 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~ 144 (166)
..+++|+.+.++|.++.-
T Consensus 42 ~~~~~Gq~v~~~V~~vd~ 59 (74)
T cd05694 42 SKLKVGQLLLCVVEKVKD 59 (74)
T ss_pred cccCCCCEEEEEEEEEEC
Confidence 558999999999987653
No 47
>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=67.62 E-value=13 Score=26.39 Aligned_cols=52 Identities=21% Similarity=0.364 Sum_probs=33.1
Q ss_pred EeeecCcEEEEE------------eC-CcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEc
Q 042741 83 FLPVKGEILHGV------------CG-PMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWS 145 (166)
Q Consensus 83 FrPf~gEVv~G~------------~G-p~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~ 145 (166)
|.|-.|.+|.|+ +| |.. .+.|. ..|... .++.+..+++||-|-+||..+.-.
T Consensus 2 Y~P~~gD~VIG~V~~~~~~~~~VdI~s~~~-a~L~~-----~~f~ga-----tk~~rp~L~~GDlV~ArV~~~~~~ 66 (86)
T cd05790 2 YVPAKGDHVIGIVVAKAGDFFKVDIGGSEP-ASLSY-----LAFEGA-----TKRNRPNLNVGDLVYARVVKANRD 66 (86)
T ss_pred CcCCCCCEEEEEEEEEcCCeEEEEcCCCcc-eEech-----HHcccc-----cccccccCCCCCEEEEEEEecCCC
Confidence 679999999999 32 222 22222 112111 233456799999999999887643
No 48
>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=67.18 E-value=17 Score=23.25 Aligned_cols=21 Identities=14% Similarity=0.091 Sum_probs=17.2
Q ss_pred CCeecCCCEEEEEEEEEEEcC
Q 042741 126 QPKIGNGVVVQFLVTAVRWSG 146 (166)
Q Consensus 126 ~~~i~~g~~VR~RI~~~~~~~ 146 (166)
...++.|+.|+++|..+....
T Consensus 43 ~~~~~~G~~v~v~v~~id~~~ 63 (69)
T cd05690 43 SEIYKKGQEVEAVVLNIDVER 63 (69)
T ss_pred hhEECCCCEEEEEEEEEECCc
Confidence 456899999999999887543
No 49
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=65.89 E-value=53 Score=26.79 Aligned_cols=17 Identities=18% Similarity=0.124 Sum_probs=14.9
Q ss_pred CeecCCCEEEEEEEEEE
Q 042741 127 PKIGNGVVVQFLVTAVR 143 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~ 143 (166)
..+++||.||+||++.-
T Consensus 117 d~f~~GDivrA~Vis~~ 133 (188)
T COG1096 117 DAFRIGDIVRARVISTG 133 (188)
T ss_pred cccccccEEEEEEEecC
Confidence 45899999999999975
No 50
>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=65.39 E-value=11 Score=25.12 Aligned_cols=17 Identities=12% Similarity=0.235 Sum_probs=14.3
Q ss_pred CeecCCCEEEEEEEEEE
Q 042741 127 PKIGNGVVVQFLVTAVR 143 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~ 143 (166)
..++.||.||++|.++.
T Consensus 47 ~~~~~Gd~v~~kV~~~~ 63 (72)
T cd05704 47 EGFKPGKIVRCCILSKK 63 (72)
T ss_pred HhCCCCCEEEEEEEEec
Confidence 45789999999998874
No 51
>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=64.91 E-value=18 Score=23.59 Aligned_cols=18 Identities=17% Similarity=-0.005 Sum_probs=14.9
Q ss_pred CeecCCCEEEEEEEEEEE
Q 042741 127 PKIGNGVVVQFLVTAVRW 144 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~ 144 (166)
..++.||.|++||.++.-
T Consensus 45 ~~~~~Gd~i~~kVl~~d~ 62 (70)
T cd05702 45 SKFKIGQKIKARVIGGHD 62 (70)
T ss_pred HhCCCCCEEEEEEEEEeC
Confidence 458999999999987643
No 52
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=64.41 E-value=38 Score=32.49 Aligned_cols=50 Identities=12% Similarity=0.061 Sum_probs=35.3
Q ss_pred cceEEecCCCCCC-ceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEcCC
Q 042741 98 MKYALMSPRRMPT-YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGE 147 (166)
Q Consensus 98 ~~~ifi~~~~m~~-~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~~ 147 (166)
+++..+++.+-++ +.|++.........++..+..|+.|++|+..+.....
T Consensus 647 ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~ 697 (706)
T COG0557 647 LEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDER 697 (706)
T ss_pred cccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEccccc
Confidence 5655555555545 5576666444555677789999999999999988655
No 53
>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=62.91 E-value=24 Score=22.68 Aligned_cols=15 Identities=13% Similarity=0.288 Sum_probs=12.8
Q ss_pred CCCEEEEEEEEEEEc
Q 042741 131 NGVVVQFLVTAVRWS 145 (166)
Q Consensus 131 ~g~~VR~RI~~~~~~ 145 (166)
+|+.+.++|..+.-.
T Consensus 44 vG~~i~~~i~~vd~~ 58 (67)
T cd04465 44 VGKELKFKIIEIDRE 58 (67)
T ss_pred CCCEEEEEEEEEeCC
Confidence 799999999888753
No 54
>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=61.18 E-value=21 Score=24.00 Aligned_cols=21 Identities=14% Similarity=0.115 Sum_probs=17.4
Q ss_pred CeecCCCEEEEEEEEEEEcCC
Q 042741 127 PKIGNGVVVQFLVTAVRWSGE 147 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~~~~ 147 (166)
..+++|+.|+++|.++.-+..
T Consensus 49 ~~~~~G~~v~~kVl~id~~~~ 69 (74)
T cd05705 49 KYLPEGKLLTAKVLSVNSEKN 69 (74)
T ss_pred cccCCCCEEEEEEEEEECCCC
Confidence 568999999999999876443
No 55
>PRK08059 general stress protein 13; Validated
Probab=59.77 E-value=27 Score=25.79 Aligned_cols=18 Identities=22% Similarity=0.071 Sum_probs=15.5
Q ss_pred CeecCCCEEEEEEEEEEE
Q 042741 127 PKIGNGVVVQFLVTAVRW 144 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~ 144 (166)
..++.||.|+++|..+.-
T Consensus 50 ~~~~vGD~I~vkI~~id~ 67 (123)
T PRK08059 50 DFLSVGDEVKVKVLSVDE 67 (123)
T ss_pred HcCCCCCEEEEEEEEEEC
Confidence 468999999999998864
No 56
>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=57.41 E-value=49 Score=21.45 Aligned_cols=17 Identities=24% Similarity=0.163 Sum_probs=14.5
Q ss_pred eecCCCEEEEEEEEEEE
Q 042741 128 KIGNGVVVQFLVTAVRW 144 (166)
Q Consensus 128 ~i~~g~~VR~RI~~~~~ 144 (166)
.+++|+.|++-|..+.-
T Consensus 40 ~~~~Gd~v~v~v~~v~~ 56 (67)
T cd04455 40 SYRPGDRIKAYVLEVRK 56 (67)
T ss_pred cCCCCCEEEEEEEEEec
Confidence 46899999999988864
No 57
>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=55.46 E-value=35 Score=22.20 Aligned_cols=20 Identities=20% Similarity=0.082 Sum_probs=16.1
Q ss_pred CCeecCCCEEEEEEEEEEEc
Q 042741 126 QPKIGNGVVVQFLVTAVRWS 145 (166)
Q Consensus 126 ~~~i~~g~~VR~RI~~~~~~ 145 (166)
...++.|+.|.+||..+...
T Consensus 40 ~~~~~~G~~i~~kVi~id~~ 59 (66)
T cd05695 40 KSTYKEGQKVRARILYVDPS 59 (66)
T ss_pred ccCcCCCCEEEEEEEEEeCC
Confidence 35689999999999876653
No 58
>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=55.38 E-value=12 Score=26.38 Aligned_cols=15 Identities=20% Similarity=0.206 Sum_probs=11.4
Q ss_pred eecCCCEEEEEEEEE
Q 042741 128 KIGNGVVVQFLVTAV 142 (166)
Q Consensus 128 ~i~~g~~VR~RI~~~ 142 (166)
.+++||.||+||+++
T Consensus 68 ~FrpGDIVrA~ViSl 82 (82)
T PF10447_consen 68 CFRPGDIVRARVISL 82 (82)
T ss_dssp T--SSSEEEEEEEEE
T ss_pred ccCCCCEEEEEEeeC
Confidence 378999999999874
No 59
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=53.70 E-value=25 Score=29.67 Aligned_cols=59 Identities=24% Similarity=0.392 Sum_probs=36.5
Q ss_pred EEeeecCcEEEEE------------e-CCcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEcC
Q 042741 82 TFLPVKGEILHGV------------C-GPMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSG 146 (166)
Q Consensus 82 vFrPf~gEVv~G~------------~-Gp~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~ 146 (166)
-|.|-.|.+|.|. + +|+. .+.|-+.++.-.++.++ .+-..++++||.|-+||..+--+.
T Consensus 59 ~YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~-A~L~ls~~~~r~~~~~~-----~~~r~~l~vGD~v~AkV~~vd~~~ 130 (239)
T COG1097 59 RYIPEVGDVVIGKIIEVGPSGWKVDIGSPYP-ALLSLSDFLRRKFENAE-----KDLRPFLNVGDLVYAKVVDVDRDG 130 (239)
T ss_pred cccCCCCCEEEEEEEEEcccceEEEcCCccc-eEeehhhhhcccccccc-----cccccccccCCEEEEEEEEccCCC
Confidence 4789999999999 2 2444 33333333222222111 233467999999999999875543
No 60
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=53.13 E-value=41 Score=21.07 Aligned_cols=18 Identities=22% Similarity=0.049 Sum_probs=15.3
Q ss_pred CeecCCCEEEEEEEEEEE
Q 042741 127 PKIGNGVVVQFLVTAVRW 144 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~ 144 (166)
..++.||.|+++|..+..
T Consensus 43 ~~~~~Gd~v~v~v~~~d~ 60 (68)
T cd04472 43 DVLKVGDEVKVKVIEVDD 60 (68)
T ss_pred HccCCCCEEEEEEEEECC
Confidence 468999999999988754
No 61
>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=52.18 E-value=62 Score=20.85 Aligned_cols=22 Identities=14% Similarity=0.116 Sum_probs=17.5
Q ss_pred CCCeecCCCEEEEEEEEEEEcC
Q 042741 125 QQPKIGNGVVVQFLVTAVRWSG 146 (166)
Q Consensus 125 ~~~~i~~g~~VR~RI~~~~~~~ 146 (166)
....++.||.|+++|..+....
T Consensus 45 ~~~~~~~Gd~v~v~v~~id~~~ 66 (72)
T cd05689 45 PSKVVSLGDEVEVMVLDIDEER 66 (72)
T ss_pred cccEeCCCCEEEEEEEEeeCCc
Confidence 3467999999999998877543
No 62
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=48.67 E-value=20 Score=28.44 Aligned_cols=17 Identities=18% Similarity=0.118 Sum_probs=14.9
Q ss_pred CeecCCCEEEEEEEEEE
Q 042741 127 PKIGNGVVVQFLVTAVR 143 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~ 143 (166)
..+++||.|++||..+.
T Consensus 117 ~~~~~GD~V~akV~~i~ 133 (189)
T PRK09521 117 DAFKIGDIVRAKVISYT 133 (189)
T ss_pred hccCCCCEEEEEEEecC
Confidence 45899999999999875
No 63
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=47.74 E-value=38 Score=31.20 Aligned_cols=19 Identities=26% Similarity=0.177 Sum_probs=15.8
Q ss_pred CeecCCCEEEEEEEEEEEc
Q 042741 127 PKIGNGVVVQFLVTAVRWS 145 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~~ 145 (166)
..+.+|+.||+.|..+.-.
T Consensus 170 E~~~~GdrIka~I~~Vd~~ 188 (470)
T PRK09202 170 ENFRPGDRVRAYVYEVRKE 188 (470)
T ss_pred ccCCCCCEEEEEEEEEecC
Confidence 3478999999999999654
No 64
>PHA02945 interferon resistance protein; Provisional
Probab=46.91 E-value=76 Score=22.80 Aligned_cols=57 Identities=19% Similarity=0.253 Sum_probs=33.3
Q ss_pred eecCcEEEEEeCCcc-eEEecCCCCCC---cee-e--CCCceeEecCCCCeecCCCEEEEEEEEEEE
Q 042741 85 PVKGEILHGVCGPMK-YALMSPRRMPT---YRH-V--SGKKSFFSNDQQPKIGNGVVVQFLVTAVRW 144 (166)
Q Consensus 85 Pf~gEVv~G~~Gp~~-~ifi~~~~m~~---~~~-~--~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~ 144 (166)
|-.||++.|+.--.+ ++|+.-.--++ +.. . +.++.|..+ ...+ .|..|-+||+.+.-
T Consensus 9 P~~GelvigtV~~~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~--rd~l-~GqkvV~KVirVd~ 72 (88)
T PHA02945 9 PNVGDVLKGKVYENGYALYIDLFDYPHSEAILAESVQMHMNRYFKY--RDKL-VGKTVKVKVIRVDY 72 (88)
T ss_pred CCCCcEEEEEEEecCceEEEEecccCCcEEEEEeehhhhccceEee--eeEe-cCCEEEEEEEEECC
Confidence 889999999911122 24443222211 221 2 124457655 5667 99999999987654
No 65
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=45.40 E-value=26 Score=21.27 Aligned_cols=20 Identities=20% Similarity=0.019 Sum_probs=16.5
Q ss_pred CCeecCCCEEEEEEEEEEEc
Q 042741 126 QPKIGNGVVVQFLVTAVRWS 145 (166)
Q Consensus 126 ~~~i~~g~~VR~RI~~~~~~ 145 (166)
...+++|+.|++||..+.-.
T Consensus 39 ~~~~~~G~~v~~~v~~~d~~ 58 (65)
T cd00164 39 SEVFKVGDEVEVKVLEVDPE 58 (65)
T ss_pred hhEeCCCCEEEEEEEEEcCC
Confidence 35689999999999998653
No 66
>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=43.63 E-value=1.1e+02 Score=21.24 Aligned_cols=62 Identities=18% Similarity=0.214 Sum_probs=34.1
Q ss_pred eecCcEEEEE---eCC-cceEEecCCC-CCCceeeCCCcee--Eec--CCCCeecCCCEEEEEEEEEEEcCC
Q 042741 85 PVKGEILHGV---CGP-MKYALMSPRR-MPTYRHVSGKKSF--FSN--DQQPKIGNGVVVQFLVTAVRWSGE 147 (166)
Q Consensus 85 Pf~gEVv~G~---~Gp-~~~ifi~~~~-m~~~~~~~~~~~~--~~~--~~~~~i~~g~~VR~RI~~~~~~~~ 147 (166)
|-.|++..|+ +-+ +.++|+--.- .+.+.... +-.| +.. .-...++.||.|.++|..+-+.+.
T Consensus 5 ~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~s-eis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K 75 (88)
T cd04453 5 PIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLS-DILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTK 75 (88)
T ss_pred CCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhH-HcCchhccccCCHHHcCCCCCEEEEEEEEecCCCC
Confidence 4578888888 333 3456665221 11122111 1112 011 113468999999999999777654
No 67
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=43.25 E-value=47 Score=28.12 Aligned_cols=61 Identities=18% Similarity=0.228 Sum_probs=33.4
Q ss_pred eeecCcEEEEE---eCCcceEEecCC---CCCCcee-eCCCceeEecCCCCeecCCCEEEEEEEEEEEcC
Q 042741 84 LPVKGEILHGV---CGPMKYALMSPR---RMPTYRH-VSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSG 146 (166)
Q Consensus 84 rPf~gEVv~G~---~Gp~~~ifi~~~---~m~~~~~-~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~ 146 (166)
.|-.|+++.|+ +.++. +|+.-. .+..+.. .+-+..|+.+ -...++.|+.|+++|..+....
T Consensus 5 ~P~~GdiV~G~V~~I~~~G-~fV~L~e~~gieGlI~iSEls~~~i~~-i~~~~kvGd~V~vkVi~VD~~k 72 (262)
T PRK03987 5 WPEEGELVVGTVKEVKDFG-AFVTLDEYPGKEGFIHISEVASGWVKN-IRDHVKEGQKVVCKVIRVDPRK 72 (262)
T ss_pred CCCCCCEEEEEEEEEECCE-EEEEECCCCCcEEEEEHHHcCcccccC-HHHhCCCCCEEEEEEEEEeccc
Confidence 37889999999 33333 444321 1111111 1111122221 2346899999999998876543
No 68
>PRK05054 exoribonuclease II; Provisional
Probab=42.62 E-value=1.3e+02 Score=28.58 Aligned_cols=46 Identities=11% Similarity=0.090 Sum_probs=29.6
Q ss_pred EEecCCCC-CC---ceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEcCC
Q 042741 101 ALMSPRRM-PT---YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGE 147 (166)
Q Consensus 101 ifi~~~~m-~~---~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~~ 147 (166)
.+|+-..| ++ +.|+.++...... +++.++.||.|+++|..+.....
T Consensus 588 glV~~~~l~~~~~~y~~~~~~~~~~~~-~~~~~~lGd~V~V~v~~vd~~~~ 637 (644)
T PRK05054 588 AFIPASFLHAVRDELVCNQENGTVQIK-GETVYKLGDVIDVTLAEVRMETR 637 (644)
T ss_pred EEEEccccCCCccceEEccccceEEEe-CCEEEcCCCEEEEEEEEEccccC
Confidence 34454444 42 3455554433333 34789999999999999987655
No 69
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=42.51 E-value=55 Score=31.47 Aligned_cols=52 Identities=15% Similarity=0.040 Sum_probs=31.5
Q ss_pred EeeecCcEEEEE------------eC-CcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEEE
Q 042741 83 FLPVKGEILHGV------------CG-PMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRW 144 (166)
Q Consensus 83 FrPf~gEVv~G~------------~G-p~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~ 144 (166)
..|..|+++.|+ ++ ..+++.|.+++-++. .+.-...++.||.|+++|.++.-
T Consensus 617 ~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~----------v~~~~~v~kvGD~V~VkV~~iD~ 681 (693)
T PRK11824 617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADER----------VEKVEDVLKEGDEVKVKVLEIDK 681 (693)
T ss_pred ccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCcc----------ccCccceeCCCCEEEEEEEEECC
Confidence 357789999999 22 233333333221111 12223568999999999999853
No 70
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=42.08 E-value=60 Score=28.36 Aligned_cols=18 Identities=17% Similarity=0.080 Sum_probs=12.7
Q ss_pred eecCCCEEEEEEEEEEEc
Q 042741 128 KIGNGVVVQFLVTAVRWS 145 (166)
Q Consensus 128 ~i~~g~~VR~RI~~~~~~ 145 (166)
.+.+|+.|+++|..+.-+
T Consensus 62 ~~~vGd~v~~~V~~v~~~ 79 (390)
T PRK06676 62 VVKVGDELEVYVLKVEDG 79 (390)
T ss_pred ccCCCCEEEEEEEEEECC
Confidence 467778888887777543
No 71
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=39.71 E-value=74 Score=27.52 Aligned_cols=22 Identities=0% Similarity=-0.010 Sum_probs=17.4
Q ss_pred CCeecCCCEEEEEEEEEEEcCC
Q 042741 126 QPKIGNGVVVQFLVTAVRWSGE 147 (166)
Q Consensus 126 ~~~i~~g~~VR~RI~~~~~~~~ 147 (166)
...++.||.|+++|..+.....
T Consensus 237 ~~~~~vGd~VkvkVl~iD~e~~ 258 (318)
T PRK07400 237 HSVFNVNDEMKVMIIDLDAERG 258 (318)
T ss_pred hhccCCCCEEEEEEEEEeCCCC
Confidence 3468999999999998876443
No 72
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=39.43 E-value=62 Score=28.01 Aligned_cols=17 Identities=6% Similarity=0.065 Sum_probs=12.0
Q ss_pred eecCCCEEEEEEEEEEE
Q 042741 128 KIGNGVVVQFLVTAVRW 144 (166)
Q Consensus 128 ~i~~g~~VR~RI~~~~~ 144 (166)
.+++|+.|+|+|+++.-
T Consensus 75 ~~~~G~~v~~~Vi~~~~ 91 (318)
T PRK07400 75 VLQPNETREFFILSDEN 91 (318)
T ss_pred ccCCCCEEEEEEEEEeC
Confidence 46778888888877543
No 73
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=39.16 E-value=57 Score=30.69 Aligned_cols=49 Identities=18% Similarity=0.124 Sum_probs=31.4
Q ss_pred ecCcEEEEE------------eCCcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEEE
Q 042741 86 VKGEILHGV------------CGPMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRW 144 (166)
Q Consensus 86 f~gEVv~G~------------~Gp~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~ 144 (166)
-.|++++|+ +|=++++.|.+++..... ..=...++.||.|-++|+.+.-
T Consensus 191 ~~G~vV~G~V~~It~~GafVdigGvdGLlHiseiS~~rv----------~~P~~vvkvGd~VkvkVi~~D~ 251 (541)
T COG0539 191 EVGEVVEGVVKNITDYGAFVDIGGVDGLLHISEISWKRV----------DHPSEVVKVGDEVKVKVISLDE 251 (541)
T ss_pred CCCceEEEEEEEeecCcEEEEecCeeeEEehhhcccccc----------CCHHHhcccCCEEEEEEEEEcc
Confidence 468899998 555777777766552111 0112457788888888877654
No 74
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=35.84 E-value=75 Score=28.26 Aligned_cols=21 Identities=14% Similarity=0.166 Sum_probs=17.3
Q ss_pred CeecCCCEEEEEEEEEEEcCC
Q 042741 127 PKIGNGVVVQFLVTAVRWSGE 147 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~~~~ 147 (166)
..+.+|+.|++-|..++....
T Consensus 170 e~~~~Gd~Ika~V~~V~~~~k 190 (362)
T PRK12327 170 ETYKHGDRIKVYVVKVEKTTK 190 (362)
T ss_pred CCCCCCCEEEEEEEEEecCCC
Confidence 458899999999999987544
No 75
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=35.32 E-value=1.2e+02 Score=20.09 Aligned_cols=16 Identities=25% Similarity=0.135 Sum_probs=14.5
Q ss_pred CeecCCCEEEEEEEEE
Q 042741 127 PKIGNGVVVQFLVTAV 142 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~ 142 (166)
..++.||.+++||..+
T Consensus 51 ~~~~iGd~v~v~I~~i 66 (77)
T cd04473 51 RDYEVGDEVIVQVTDI 66 (77)
T ss_pred CcCCCCCEEEEEEEEE
Confidence 4589999999999998
No 76
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=35.31 E-value=77 Score=27.69 Aligned_cols=18 Identities=22% Similarity=0.475 Sum_probs=14.1
Q ss_pred CeecCCCEEEEEEEEEEE
Q 042741 127 PKIGNGVVVQFLVTAVRW 144 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~ 144 (166)
..++.|+.|++||..+.-
T Consensus 234 ~~~~vGd~i~~~Vl~vd~ 251 (390)
T PRK06676 234 EVVSVGQEVEVKVLSIDW 251 (390)
T ss_pred HhcCCCCEEEEEEEEEeC
Confidence 357889999999988754
No 77
>PRK02268 hypothetical protein; Provisional
Probab=34.44 E-value=86 Score=24.31 Aligned_cols=36 Identities=11% Similarity=0.354 Sum_probs=29.3
Q ss_pred CeecCCCEEEEEEEEEEEcCCCcCccccEEEEEEecCC
Q 042741 127 PKIGNGVVVQFLVTAVRWSGEGRNLKREYLVFGRAKGE 164 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~~~~~~~~~~~~~~igti~~d 164 (166)
..+++||.|-+=+-.+++.+....|. +.|||++.+|
T Consensus 34 ~RmkpGD~ivyYsp~~~~~~~~~~qa--ftAig~V~~~ 69 (141)
T PRK02268 34 RRMKPGDWIIYYSPKTTFGGKDKLQA--FTAIGKVKDD 69 (141)
T ss_pred hcCCCCCEEEEEeceEecCCCcccce--EEEEEEEcCC
Confidence 36899999998888888876655555 9999999887
No 78
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=34.07 E-value=34 Score=26.23 Aligned_cols=50 Identities=16% Similarity=0.106 Sum_probs=31.1
Q ss_pred eecCcEEEEE---eCCcc----------eEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEEE
Q 042741 85 PVKGEILHGV---CGPMK----------YALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRW 144 (166)
Q Consensus 85 Pf~gEVv~G~---~Gp~~----------~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~ 144 (166)
+-.|+++.|+ +-||- ++.|.|++.++|+ ++=...+..|+.|-++|.++-=
T Consensus 3 ~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fV----------kdI~d~L~vG~eV~vKVl~ide 65 (129)
T COG1098 3 MKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFV----------KDIHDHLKVGQEVKVKVLDIDE 65 (129)
T ss_pred ccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhH----------HhHHHHhcCCCEEEEEEEeecc
Confidence 3468999999 22333 4445544444322 2223458899999999998753
No 79
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=33.30 E-value=90 Score=28.85 Aligned_cols=19 Identities=21% Similarity=0.111 Sum_probs=15.6
Q ss_pred CeecCCCEEEEEEEEEEEc
Q 042741 127 PKIGNGVVVQFLVTAVRWS 145 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~~ 145 (166)
..+++|+.|.+||..+...
T Consensus 250 ~~~kvGd~V~vkVl~iD~e 268 (486)
T PRK07899 250 EVVEVGQEVTVEVLDVDMD 268 (486)
T ss_pred HhcCCCCEEEEEEEEEECC
Confidence 4578999999999888654
No 80
>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=31.41 E-value=1.6e+02 Score=19.55 Aligned_cols=35 Identities=17% Similarity=0.174 Sum_probs=24.1
Q ss_pred CeecCCCEEEE------EEEEEEEcCCCcCccccEEEEEEecCCC
Q 042741 127 PKIGNGVVVQF------LVTAVRWSGEGRNLKREYLVFGRAKGES 165 (166)
Q Consensus 127 ~~i~~g~~VR~------RI~~~~~~~~~~~~~~~~~~igti~~d~ 165 (166)
.-|.+|+.||+ +|.+++++.. .+.+.+.-.|+++|
T Consensus 13 ~GL~~gs~V~~~Gv~VG~V~~i~l~~~----~~~v~v~~~i~~~~ 53 (81)
T PF02470_consen 13 GGLSVGSPVRYRGVEVGKVTSIELDPD----GNRVRVTLRIDPDY 53 (81)
T ss_pred CCCCCcCEEEECCEEEEEEEEEEEcCC----CCEEEEEEEEcCCc
Confidence 44888889988 6888877333 22377777777766
No 81
>PF12306 PixA: Inclusion body protein; InterPro: IPR021087 This entry represents bacterial proteins that are typically between 173 and 191 amino acids in length. PixA is thought to be specifically produced in Xenorhabdus nematophila. It is an inclusion body protein []. This signature also identifies AidA.
Probab=31.33 E-value=62 Score=25.50 Aligned_cols=20 Identities=20% Similarity=0.277 Sum_probs=17.1
Q ss_pred eecCCCEEEEEEEEEEEcCC
Q 042741 128 KIGNGVVVQFLVTAVRWSGE 147 (166)
Q Consensus 128 ~i~~g~~VR~RI~~~~~~~~ 147 (166)
...+||.||+|..+++-+..
T Consensus 61 ~a~~GD~Irwr~tSls~n~~ 80 (172)
T PF12306_consen 61 KANVGDTIRWRATSLSGNSE 80 (172)
T ss_pred eccCCCEEEEEEEeeccCCc
Confidence 46899999999999988654
No 82
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=30.54 E-value=1.3e+02 Score=28.67 Aligned_cols=46 Identities=13% Similarity=0.132 Sum_probs=30.0
Q ss_pred EEecCCCC-C--C-ceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEcCC
Q 042741 101 ALMSPRRM-P--T-YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGE 147 (166)
Q Consensus 101 ifi~~~~m-~--~-~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~~ 147 (166)
.+||...| + + +.|+.++........ ..++.||.|+++|..+.....
T Consensus 584 g~v~~~~l~~~~~~~~~~~~~~~~~l~g~-~~~~lgd~v~V~v~~vd~~~~ 633 (639)
T TIGR02062 584 AFIPAAFLHANREELVCNQENGTVQIKGE-TVYKIGDVIDVVLTEVRMETR 633 (639)
T ss_pred EEEEhhhcCCCCcceEEcccccEEEEecc-EEEecCCEEEEEEEEeccccC
Confidence 45555555 3 3 557766643322222 489999999999999887654
No 83
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=29.59 E-value=1.3e+02 Score=27.54 Aligned_cols=20 Identities=15% Similarity=0.194 Sum_probs=16.3
Q ss_pred CeecCCCEEEEEEEEEEEcC
Q 042741 127 PKIGNGVVVQFLVTAVRWSG 146 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~~~ 146 (166)
..+++|+.|+++|.++..+.
T Consensus 245 ~~~~vGd~i~vkVl~id~~~ 264 (491)
T PRK13806 245 EAVSVGDTVRVKVLGIERAK 264 (491)
T ss_pred HhcCCCCEEEEEEEEEeccc
Confidence 45889999999999877653
No 84
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=29.12 E-value=1.4e+02 Score=27.60 Aligned_cols=19 Identities=16% Similarity=0.038 Sum_probs=14.2
Q ss_pred CeecCCCEEEEEEEEEEEc
Q 042741 127 PKIGNGVVVQFLVTAVRWS 145 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~~ 145 (166)
..+++|+.|+++|.++.-+
T Consensus 243 ~~~kvG~~v~v~V~~~d~~ 261 (565)
T PRK06299 243 EVVNVGDEVKVKVLKFDKE 261 (565)
T ss_pred hcCCCCCEEEEEEEEEeCC
Confidence 3478889999888876543
No 85
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=26.58 E-value=1.6e+02 Score=29.22 Aligned_cols=17 Identities=12% Similarity=0.204 Sum_probs=12.2
Q ss_pred eecCCCEEEEEEEEEEE
Q 042741 128 KIGNGVVVQFLVTAVRW 144 (166)
Q Consensus 128 ~i~~g~~VR~RI~~~~~ 144 (166)
.+++|+.|++||+.+.-
T Consensus 536 ~~kvGq~v~vkVi~iD~ 552 (863)
T PRK12269 536 FVKKGQTIELKVIRLDQ 552 (863)
T ss_pred hccCCCEEEEEEEEEec
Confidence 35778888888876654
No 86
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=26.16 E-value=58 Score=25.06 Aligned_cols=19 Identities=11% Similarity=0.153 Sum_probs=15.8
Q ss_pred eEecCCCCeecCCCEEEEE
Q 042741 120 FFSNDQQPKIGNGVVVQFL 138 (166)
Q Consensus 120 ~~~~~~~~~i~~g~~VR~R 138 (166)
..|+|....|++||.||++
T Consensus 53 svW~e~~~~~~PGDIirLt 71 (134)
T KOG3416|consen 53 SVWDEEGCLIQPGDIIRLT 71 (134)
T ss_pred EEecCcCcccCCccEEEec
Confidence 4778777889999999985
No 87
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: 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 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=25.00 E-value=1.6e+02 Score=19.40 Aligned_cols=21 Identities=19% Similarity=0.110 Sum_probs=16.8
Q ss_pred CeecCCCEEEEEEEEEEEcCC
Q 042741 127 PKIGNGVVVQFLVTAVRWSGE 147 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~~~~ 147 (166)
..+++|+.|.++|.++.-+..
T Consensus 45 ~~~~vG~~v~~kV~~id~~~~ 65 (73)
T cd05703 45 KKFPIGQALKAKVVGVDKEHK 65 (73)
T ss_pred HhCCCCCEEEEEEEEEeCCCC
Confidence 458999999999998765543
No 88
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=24.40 E-value=1.9e+02 Score=26.72 Aligned_cols=14 Identities=29% Similarity=0.214 Sum_probs=8.5
Q ss_pred ecCCCEEEEEEEEE
Q 042741 129 IGNGVVVQFLVTAV 142 (166)
Q Consensus 129 i~~g~~VR~RI~~~ 142 (166)
+++|+.|.++|+.+
T Consensus 80 ~~vGd~Ie~~V~~~ 93 (486)
T PRK07899 80 VEVGDEVEALVLQK 93 (486)
T ss_pred CCCCCEEEEEEEEE
Confidence 55666666666654
No 89
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=24.10 E-value=2.2e+02 Score=27.02 Aligned_cols=20 Identities=15% Similarity=0.074 Sum_probs=16.3
Q ss_pred CeecCCCEEEEEEEEEEEcC
Q 042741 127 PKIGNGVVVQFLVTAVRWSG 146 (166)
Q Consensus 127 ~~i~~g~~VR~RI~~~~~~~ 146 (166)
..++.|+.|++||..+....
T Consensus 605 ~~~kvGd~V~vkV~~id~e~ 624 (647)
T PRK00087 605 DVLSEGEEVKAKILEVDPEE 624 (647)
T ss_pred hcCCCCCEEEEEEEEEeCCC
Confidence 45899999999999876543
No 90
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=22.55 E-value=2.1e+02 Score=25.18 Aligned_cols=19 Identities=26% Similarity=0.221 Sum_probs=16.2
Q ss_pred eecCCCEEEEEEEEEEEcC
Q 042741 128 KIGNGVVVQFLVTAVRWSG 146 (166)
Q Consensus 128 ~i~~g~~VR~RI~~~~~~~ 146 (166)
.+.+|+.|++-|..++-..
T Consensus 169 ~~~~Gd~ik~~V~~V~~~~ 187 (341)
T TIGR01953 169 KFRIGDRIKAYVYEVRKTA 187 (341)
T ss_pred CCCCCCEEEEEEEEEEcCC
Confidence 3889999999999998654
No 91
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=21.40 E-value=2.3e+02 Score=26.11 Aligned_cols=20 Identities=15% Similarity=0.062 Sum_probs=16.3
Q ss_pred CCeecCCCEEEEEEEEEEEc
Q 042741 126 QPKIGNGVVVQFLVTAVRWS 145 (166)
Q Consensus 126 ~~~i~~g~~VR~RI~~~~~~ 145 (166)
...++.|+.|++||..+..+
T Consensus 502 ~~~~~~Gd~v~~~V~~vd~~ 521 (565)
T PRK06299 502 TEVLKVGDEVEAKVINIDRK 521 (565)
T ss_pred cccCCCCCEEEEEEEEEccc
Confidence 35689999999999987654
No 92
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=20.48 E-value=1.3e+02 Score=24.47 Aligned_cols=15 Identities=20% Similarity=0.204 Sum_probs=13.1
Q ss_pred eecCCCEEEEEEEEE
Q 042741 128 KIGNGVVVQFLVTAV 142 (166)
Q Consensus 128 ~i~~g~~VR~RI~~~ 142 (166)
.+.+||.||+||++.
T Consensus 122 sFrPgDiVlAkVis~ 136 (193)
T KOG3409|consen 122 SFRPGDIVLAKVISL 136 (193)
T ss_pred ccCCCcEEEEEEeec
Confidence 378999999999983
No 93
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=20.03 E-value=1.8e+02 Score=28.45 Aligned_cols=52 Identities=15% Similarity=0.119 Sum_probs=32.1
Q ss_pred eeecCcEEEEE------------eCC-cceEEecCCCCCCceeeCCCceeEe--cCCCCeecCCCEEEEEEEEEE
Q 042741 84 LPVKGEILHGV------------CGP-MKYALMSPRRMPTYRHVSGKKSFFS--NDQQPKIGNGVVVQFLVTAVR 143 (166)
Q Consensus 84 rPf~gEVv~G~------------~Gp-~~~ifi~~~~m~~~~~~~~~~~~~~--~~~~~~i~~g~~VR~RI~~~~ 143 (166)
.|-.|++++|+ ++| .+++.|.+++.+ -.|.. .+-...+++||.|.++|.++.
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisd--------ls~~~rv~~~~dv~kvGd~V~VKVl~ID 710 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRK--------LAGGKRVENVEDVLSVGQKIQVEIADID 710 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccc--------cccccCcCCHHHcCCCCCEEEEEEEEEC
Confidence 58899999999 222 344444443321 01211 122346899999999999887
Done!