Query 032987
Match_columns 129
No_of_seqs 112 out of 440
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 08:24:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032987.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032987hhsearch_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 2.2E-46 4.9E-51 280.7 14.6 124 1-127 1-124 (176)
2 KOG3297 DNA-directed RNA polym 100.0 1E-43 2.2E-48 264.9 11.3 125 1-127 1-125 (202)
3 TIGR00448 rpoE DNA-directed RN 100.0 2.2E-42 4.8E-47 259.0 14.6 125 1-127 1-125 (179)
4 COG1095 RPB7 DNA-directed RNA 100.0 4.5E-42 9.7E-47 256.9 14.9 124 1-127 1-125 (183)
5 PRK08563 DNA-directed RNA poly 100.0 4.4E-40 9.6E-45 247.5 14.3 124 1-126 1-124 (187)
6 KOG3298 DNA-directed RNA polym 100.0 3.8E-36 8.3E-41 220.4 14.2 122 1-123 1-122 (170)
7 cd04330 RNAP_III_Rpc25_N RNAP_ 100.0 1.4E-31 2.9E-36 177.7 10.9 80 2-81 1-80 (80)
8 cd04329 RNAP_II_Rpb7_N RNAP_II 100.0 1.8E-31 4E-36 177.1 10.4 80 2-81 1-80 (80)
9 cd00655 RNAP_Rpb7_N_like RNAP_ 100.0 2.7E-31 5.8E-36 176.3 10.9 80 2-81 1-80 (80)
10 cd04331 RNAP_E_N RNAP_E_N: Rpo 100.0 1E-30 2.2E-35 173.6 10.3 80 2-81 1-80 (80)
11 PF03876 SHS2_Rpb7-N: SHS2 dom 99.9 2.7E-22 5.9E-27 129.0 10.3 70 8-77 1-70 (70)
12 cd04328 RNAP_I_Rpa43_N RNAP_I_ 99.8 8E-19 1.7E-23 118.2 9.8 79 1-81 8-89 (89)
13 PF08292 RNA_pol_Rbc25: RNA po 99.6 1E-15 2.2E-20 108.9 4.7 48 79-128 1-48 (122)
14 cd04462 S1_RNAPII_Rpb7 S1_RNAP 99.0 8E-10 1.7E-14 74.3 5.1 40 81-121 1-40 (88)
15 KOG4134 DNA-dependent RNA poly 98.8 5.8E-08 1.3E-12 75.3 10.9 114 6-121 31-147 (253)
16 PF00575 S1: S1 RNA binding do 97.7 8E-05 1.7E-09 47.2 4.5 39 78-117 1-40 (74)
17 cd04471 S1_RNase_R S1_RNase_R: 96.9 0.0018 3.9E-08 41.5 4.3 39 81-120 1-42 (83)
18 cd05698 S1_Rrp5_repeat_hs6_sc5 96.6 0.003 6.6E-08 39.4 3.3 39 82-120 1-39 (70)
19 cd05686 S1_pNO40 S1_pNO40: pNO 96.5 0.0057 1.2E-07 38.9 4.3 37 79-116 1-39 (73)
20 cd05697 S1_Rrp5_repeat_hs5 S1_ 96.5 0.0046 1E-07 38.7 3.7 36 82-117 1-36 (69)
21 cd05705 S1_Rrp5_repeat_hs14 S1 96.2 0.007 1.5E-07 39.0 3.7 36 81-116 3-38 (74)
22 cd04465 S1_RPS1_repeat_ec2_hs2 96.2 0.0072 1.6E-07 37.6 3.6 34 82-116 1-34 (67)
23 smart00316 S1 Ribosomal protei 96.2 0.0088 1.9E-07 36.3 3.8 37 81-117 2-38 (72)
24 cd04461 S1_Rrp5_repeat_hs8_sc7 96.2 0.0083 1.8E-07 39.0 3.8 38 79-116 12-49 (83)
25 cd04455 S1_NusA S1_NusA: N-uti 96.1 0.012 2.7E-07 36.9 4.3 40 80-120 2-41 (67)
26 cd05692 S1_RPS1_repeat_hs4 S1_ 96.1 0.011 2.4E-07 36.0 3.9 36 82-117 1-36 (69)
27 cd04460 S1_RpoE S1_RpoE: RpoE, 96.1 0.0091 2E-07 40.2 3.7 37 83-120 1-38 (99)
28 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 96.0 0.011 2.5E-07 38.4 4.0 37 77-114 2-39 (86)
29 cd05685 S1_Tex S1_Tex: The C-t 96.0 0.011 2.3E-07 36.0 3.6 36 82-117 1-36 (68)
30 cd05707 S1_Rrp5_repeat_sc11 S1 96.0 0.011 2.3E-07 36.9 3.6 35 82-116 1-35 (68)
31 cd05706 S1_Rrp5_repeat_sc10 S1 95.9 0.023 5E-07 35.7 4.8 37 80-116 2-38 (73)
32 cd05694 S1_Rrp5_repeat_hs2_sc2 95.8 0.015 3.2E-07 37.5 3.7 37 80-117 3-41 (74)
33 cd04454 S1_Rrp4_like S1_Rrp4_l 95.7 0.028 6.1E-07 36.3 4.9 40 77-116 2-41 (82)
34 cd05689 S1_RPS1_repeat_ec4 S1_ 95.5 0.026 5.7E-07 35.3 3.9 35 81-115 3-37 (72)
35 cd05695 S1_Rrp5_repeat_hs3 S1_ 95.4 0.023 4.9E-07 35.6 3.5 34 82-116 1-35 (66)
36 cd05690 S1_RPS1_repeat_ec5 S1_ 95.4 0.021 4.5E-07 35.3 3.3 34 82-115 1-34 (69)
37 cd04472 S1_PNPase S1_PNPase: P 95.4 0.03 6.5E-07 34.2 3.9 35 82-116 1-35 (68)
38 cd04452 S1_IF2_alpha S1_IF2_al 95.3 0.038 8.3E-07 34.7 4.4 37 79-116 1-40 (76)
39 cd05696 S1_Rrp5_repeat_hs4 S1_ 95.3 0.027 5.9E-07 35.7 3.6 34 82-116 1-37 (71)
40 PRK08582 hypothetical protein; 95.3 0.055 1.2E-06 39.1 5.5 38 79-116 3-40 (139)
41 cd05708 S1_Rrp5_repeat_sc12 S1 95.2 0.038 8.2E-07 34.7 4.1 35 81-116 2-38 (77)
42 cd05687 S1_RPS1_repeat_ec1_hs1 95.2 0.029 6.3E-07 34.9 3.5 35 82-116 1-35 (70)
43 cd05688 S1_RPS1_repeat_ec3 S1_ 95.1 0.034 7.3E-07 33.9 3.5 34 81-115 1-34 (68)
44 cd05691 S1_RPS1_repeat_ec6 S1_ 95.1 0.038 8.3E-07 34.3 3.8 35 82-116 1-35 (73)
45 cd04453 S1_RNase_E S1_RNase_E: 94.9 0.051 1.1E-06 36.1 4.1 37 78-114 4-42 (88)
46 cd05703 S1_Rrp5_repeat_hs12_sc 94.8 0.047 1E-06 34.9 3.6 35 82-116 1-35 (73)
47 COG0539 RpsA Ribosomal protein 94.7 0.039 8.4E-07 48.1 4.1 37 78-114 189-225 (541)
48 cd05684 S1_DHX8_helicase S1_DH 94.5 0.078 1.7E-06 33.9 4.2 34 82-116 1-38 (79)
49 PF13509 S1_2: S1 domain; PDB: 94.5 0.041 8.9E-07 34.2 2.7 39 81-119 1-39 (61)
50 TIGR03591 polynuc_phos polyrib 94.4 0.015 3.3E-07 51.9 0.8 64 50-113 585-651 (684)
51 PRK07252 hypothetical protein; 94.4 0.083 1.8E-06 37.3 4.4 35 81-116 3-38 (120)
52 TIGR02063 RNase_R ribonuclease 93.9 0.033 7.1E-07 49.7 2.0 47 73-120 619-668 (709)
53 PTZ00248 eukaryotic translatio 93.6 0.088 1.9E-06 43.2 3.7 34 79-112 15-51 (319)
54 cd04473 S1_RecJ_like S1_RecJ_l 93.5 0.2 4.3E-06 32.1 4.6 37 77-114 12-49 (77)
55 PRK11642 exoribonuclease R; Pr 93.2 0.11 2.4E-06 47.4 4.1 49 74-125 636-687 (813)
56 PRK05807 hypothetical protein; 93.1 0.23 5.1E-06 35.6 5.0 35 80-115 4-38 (136)
57 PHA02945 interferon resistance 93.1 0.14 3E-06 34.6 3.4 25 79-104 9-33 (88)
58 cd05702 S1_Rrp5_repeat_hs11_sc 92.5 0.27 5.8E-06 30.7 4.1 33 82-115 1-34 (70)
59 PRK08059 general stress protei 92.5 0.24 5.1E-06 34.8 4.2 38 79-116 5-42 (123)
60 TIGR02696 pppGpp_PNP guanosine 92.4 0.18 3.9E-06 45.5 4.3 35 78-112 644-679 (719)
61 cd05704 S1_Rrp5_repeat_hs13 S1 92.3 0.23 5E-06 31.4 3.6 29 81-109 3-33 (72)
62 PRK04163 exosome complex RNA-b 91.7 1 2.2E-05 35.1 7.3 38 77-115 59-97 (235)
63 COG1098 VacB Predicted RNA bin 91.4 0.24 5.1E-06 35.6 3.1 37 79-115 3-40 (129)
64 TIGR00358 3_prime_RNase VacB a 91.4 0.23 5.1E-06 44.1 3.8 52 73-126 564-617 (654)
65 cd00164 S1_like S1_like: Ribos 91.2 0.23 4.9E-06 29.3 2.6 32 85-116 1-32 (65)
66 PF03293 Pox_RNA_pol: Poxvirus 90.7 5.2 0.00011 29.4 10.6 92 7-104 8-104 (160)
67 PRK07899 rpsA 30S ribosomal pr 90.5 0.35 7.5E-06 41.8 3.9 35 81-116 208-242 (486)
68 PRK07400 30S ribosomal protein 89.8 0.5 1.1E-05 38.5 4.1 38 78-116 193-230 (318)
69 PRK07400 30S ribosomal protein 89.7 0.4 8.7E-06 39.0 3.6 38 79-116 29-66 (318)
70 PRK03987 translation initiatio 89.7 0.58 1.2E-05 37.3 4.4 37 78-115 5-44 (262)
71 PRK09202 nusA transcription el 89.5 0.39 8.4E-06 41.3 3.4 43 77-120 130-172 (470)
72 PRK09521 exosome complex RNA-b 89.5 0.54 1.2E-05 35.3 3.9 31 72-102 55-85 (189)
73 PRK06676 rpsA 30S ribosomal pr 89.5 0.52 1.1E-05 38.9 4.1 37 79-116 190-226 (390)
74 PRK11824 polynucleotide phosph 88.7 0.71 1.5E-05 41.4 4.6 40 77-116 617-656 (693)
75 COG1093 SUI2 Translation initi 88.4 0.56 1.2E-05 37.5 3.4 28 79-106 9-36 (269)
76 PRK12327 nusA transcription el 88.1 0.61 1.3E-05 38.9 3.6 39 77-116 130-169 (362)
77 PRK13806 rpsA 30S ribosomal pr 87.5 0.78 1.7E-05 39.4 4.0 36 80-115 291-326 (491)
78 PRK13806 rpsA 30S ribosomal pr 87.5 0.73 1.6E-05 39.6 3.8 39 78-116 199-237 (491)
79 cd05693 S1_Rrp5_repeat_hs1_sc1 87.3 0.71 1.5E-05 31.3 3.0 36 80-115 2-37 (100)
80 PRK06676 rpsA 30S ribosomal pr 87.1 0.77 1.7E-05 37.9 3.6 39 78-116 14-53 (390)
81 PRK07899 rpsA 30S ribosomal pr 86.8 0.88 1.9E-05 39.3 3.9 38 79-116 33-70 (486)
82 TIGR01953 NusA transcription t 85.9 1 2.2E-05 37.3 3.7 43 77-120 127-170 (341)
83 TIGR00717 rpsA ribosomal prote 85.5 1.1 2.4E-05 38.2 3.9 36 81-116 359-394 (516)
84 PLN00207 polyribonucleotide nu 84.5 1 2.2E-05 41.7 3.3 40 77-116 749-789 (891)
85 cd05790 S1_Rrp40 S1_Rrp40: Rrp 84.0 2.3 4.9E-05 28.4 4.1 38 77-114 2-39 (86)
86 TIGR00717 rpsA ribosomal prote 83.4 1.5 3.4E-05 37.3 3.9 36 80-115 271-306 (516)
87 cd05791 S1_CSL4 S1_CSL4: CSL4, 81.8 3.1 6.7E-05 27.7 4.1 38 77-114 2-48 (92)
88 PRK00087 4-hydroxy-3-methylbut 81.3 1.8 3.9E-05 38.5 3.6 35 81-116 389-423 (647)
89 PRK06299 rpsA 30S ribosomal pr 81.3 1.9 4.2E-05 37.3 3.8 36 80-115 285-320 (565)
90 PRK06299 rpsA 30S ribosomal pr 81.0 2 4.4E-05 37.2 3.8 38 79-116 28-65 (565)
91 PRK12269 bifunctional cytidyla 80.6 2.8 6.2E-05 38.7 4.7 34 81-115 493-526 (863)
92 PRK00087 4-hydroxy-3-methylbut 75.6 3.3 7.1E-05 36.8 3.5 40 76-115 297-336 (647)
93 COG0557 VacB Exoribonuclease R 75.2 4.7 0.0001 36.2 4.4 45 79-125 620-666 (706)
94 PRK12269 bifunctional cytidyla 75.0 3.8 8.3E-05 37.9 3.9 37 81-117 752-788 (863)
95 PRK12328 nusA transcription el 73.4 4.8 0.00011 33.8 3.8 43 77-120 134-177 (374)
96 COG2183 Tex Transcriptional ac 71.4 3.6 7.9E-05 37.6 2.8 39 78-116 655-693 (780)
97 PRK05054 exoribonuclease II; P 69.6 7.5 0.00016 34.7 4.4 41 77-117 555-598 (644)
98 COG1185 Pnp Polyribonucleotide 69.4 5.6 0.00012 35.9 3.5 41 75-115 613-653 (692)
99 COG0539 RpsA Ribosomal protein 67.8 5.6 0.00012 35.0 3.1 41 76-116 16-56 (541)
100 TIGR02062 RNase_B exoribonucle 67.8 9.1 0.0002 34.2 4.5 40 77-116 551-593 (639)
101 cd05699 S1_Rrp5_repeat_hs7 S1_ 64.1 24 0.00052 22.8 4.8 35 82-116 1-36 (72)
102 COG2996 Predicted RNA-bindinin 60.6 14 0.00031 29.9 4.0 38 80-117 72-110 (287)
103 PF07238 PilZ: PilZ domain; I 58.7 42 0.00092 20.9 5.8 35 67-101 7-41 (102)
104 TIGR00757 RNaseEG ribonuclease 58.2 16 0.00035 31.0 4.1 39 78-116 22-62 (414)
105 PHA02858 EIF2a-like PKR inhibi 55.5 19 0.00041 24.1 3.3 30 78-109 13-45 (86)
106 PRK12329 nusA transcription el 55.2 18 0.00038 31.2 3.9 43 77-120 148-196 (449)
107 PF01938 TRAM: TRAM domain; I 50.9 52 0.0011 19.6 5.7 23 78-100 37-59 (61)
108 PF10447 EXOSC1: Exosome compo 50.4 30 0.00066 22.8 3.7 23 79-101 2-24 (82)
109 PF05899 Cupin_3: Protein of u 42.8 63 0.0014 20.3 4.2 30 83-112 30-59 (74)
110 KOG0416 Ubiquitin-protein liga 39.1 34 0.00074 25.9 2.8 71 19-111 5-76 (189)
111 KOG2916 Translation initiation 34.7 43 0.00093 27.2 2.9 28 79-106 14-41 (304)
112 KOG1070 rRNA processing protei 34.0 74 0.0016 31.6 4.7 38 78-115 1159-1196(1710)
113 PF10246 MRP-S35: Mitochondria 30.6 93 0.002 21.6 3.7 27 77-103 19-45 (104)
114 PF09953 DUF2187: Uncharacteri 29.2 71 0.0015 19.8 2.6 22 85-106 16-37 (57)
115 PF02237 BPL_C: Biotin protein 29.1 95 0.0021 17.8 3.1 19 81-99 11-29 (48)
116 PF06059 DUF930: Domain of Unk 26.3 1.2E+02 0.0026 20.8 3.6 25 50-76 47-71 (101)
117 PRK15464 cold shock-like prote 25.9 1.6E+02 0.0035 18.6 4.0 43 54-97 16-62 (70)
118 PRK10943 cold shock-like prote 25.2 1.8E+02 0.0039 18.1 4.7 44 54-98 15-62 (69)
119 PRK15463 cold shock-like prote 25.1 1.4E+02 0.003 18.8 3.6 43 54-97 16-62 (70)
120 KOG1004 Exosomal 3'-5' exoribo 24.9 3.2E+02 0.0069 21.5 6.1 39 65-103 49-87 (230)
121 PRK14555 hypothetical protein; 24.8 1.8E+02 0.004 21.0 4.6 49 27-75 78-127 (145)
122 COG2106 Uncharacterized conser 23.9 1.2E+02 0.0026 24.6 3.7 37 78-115 102-138 (272)
123 COG1278 CspC Cold shock protei 22.7 78 0.0017 20.2 2.0 37 54-90 13-53 (67)
124 smart00700 JHBP Juvenile hormo 21.7 2.5E+02 0.0055 21.0 5.1 66 13-82 7-75 (225)
125 COG1097 RRP4 RNA-binding prote 21.2 4.3E+02 0.0092 21.0 7.7 38 76-114 59-97 (239)
126 PF03789 ELK: ELK domain ; In 20.6 49 0.0011 16.5 0.6 13 26-38 2-14 (22)
127 COG3269 Predicted RNA-binding 20.2 2.6E+02 0.0056 18.1 5.7 37 61-100 29-67 (73)
No 1
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=100.00 E-value=2.2e-46 Score=280.70 Aligned_cols=124 Identities=23% Similarity=0.361 Sum_probs=121.0
Q ss_pred CeEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEEeeec
Q 032987 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPF 80 (129)
Q Consensus 1 MF~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alvfrP~ 80 (129)
||++++++|+|+|||++|+++++++++++|+++|+||+.+++|+||||+||.++++|+|.||||+++|+|+|||+|||||
T Consensus 1 MF~~~~l~d~v~i~P~~f~~~~~~~i~~~L~~~~egkv~~~~GliV~v~di~~i~~G~I~~gdG~~~~~V~FraivFrPf 80 (176)
T PTZ00162 1 MFFVVELWKNVSLKPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPF 80 (176)
T ss_pred CcEEEEEEEEEEECHHHcCccHHHHHHHHHHHHHCCCCcCcccEEEEEEEeeEecCCEEEcCCCCEEEEEEEEEEEEecC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCCCCcCCCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGR 127 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~~~f~~d~~~~ 127 (129)
+|||++|+|++++++|+|+++||+| +|||+++||+++.| |++++
T Consensus 81 ~gEVv~g~V~~v~~~G~~v~~Gp~~-ifI~~~~l~~~~~f--d~~~~ 124 (176)
T PTZ00162 81 KDEVLDAIVTDVNKLGFFAQAGPLK-AFVSRSAIPPDFVY--DSDSA 124 (176)
T ss_pred CCCEEEEEEEEEecceEEEEeeCeE-EEEcHHHCCCccEE--CCCCC
Confidence 9999999999999999999999998 99999999999999 65544
No 2
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=100.00 E-value=1e-43 Score=264.85 Aligned_cols=125 Identities=53% Similarity=0.999 Sum_probs=122.1
Q ss_pred CeEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEEeeec
Q 032987 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPF 80 (129)
Q Consensus 1 MF~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alvfrP~ 80 (129)
||++.+++|+|||||++|.++++++|+++|++||.||+++|+|+||||+||.++++|.|.||||+++.+|.||++|||||
T Consensus 1 MF~Lsel~D~VrI~P~qf~~~~~~ai~~eL~~k~anKvl~nvGLCI~vyDi~~v~e~~v~pGDGas~~~V~FR~vVFrPF 80 (202)
T KOG3297|consen 1 MFYLSELEDTVRIPPSQFEKPLEDAIKEELNRKLANKVLPNVGLCICVYDILEVEEGIVLPGDGASYARVWFRVVVFRPF 80 (202)
T ss_pred CeeehhcccceecChHHhCchHHHHHHHHHHHHHHhhhcccccEEEEEeEeeeecceEEecCCCceEEEEEEEEEEEecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCCCCcCCCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGR 127 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~~~f~~d~~~~ 127 (129)
.|||+.|+|.+|++.|+.+++|||||||||+..||+++.| ++++|
T Consensus 81 ~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~f--~~~e~ 125 (202)
T KOG3297|consen 81 VGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCVF--EPDEQ 125 (202)
T ss_pred cceEEEEEeecCCccceEEEEEeeeceeechhhCCCCccc--ccccE
Confidence 9999999999999999999999999999999999999999 55454
No 3
>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=2.2e-42 Score=259.00 Aligned_cols=125 Identities=38% Similarity=0.654 Sum_probs=121.7
Q ss_pred CeEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEEeeec
Q 032987 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPF 80 (129)
Q Consensus 1 MF~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alvfrP~ 80 (129)
||++++++|+|+|||++|+++++++|.++|+++|+||+++++|+||||+||.++++|+|.||||+++|+|+|||++|||+
T Consensus 1 Mf~~~~l~d~v~i~P~~~~~~~~~~i~~~l~~~~~gk~~~~~G~~i~v~di~~i~~g~i~~gdG~~~~~V~f~~i~f~p~ 80 (179)
T TIGR00448 1 MYILSKIADTVRIPPDQFGEDLEEVITHQLNEKFEGRLDKNVGLCITIYDIEDIGEGKVIPGDGSAYHNVTFRALVFKPE 80 (179)
T ss_pred CeEEEEEeeEEEECHHHhCccHHHHHHHHHHHHhcCcCcCCcCEEEEEEEeEEecCCEEECCCCCEEEEEEEEEEEEecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCCCCcCCCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGR 127 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~~~f~~d~~~~ 127 (129)
+||+++|+|++++++|+|+++||+++++++++.+|+++.| |++++
T Consensus 81 ~gEvv~G~V~~v~~~GifV~lg~~~gi~~~~~l~~~~~~~--d~~~~ 125 (179)
T TIGR00448 81 LGEIVEGEVIEIVEFGAFVSLGPFDGLFHVSQVTDDYCYY--DPKES 125 (179)
T ss_pred CCCEEEEEEEEEEeeEEEEEeCCceEEEEcHHhCCCceEE--ccccc
Confidence 9999999999999999999999999999999999999999 66543
No 4
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=100.00 E-value=4.5e-42 Score=256.92 Aligned_cols=124 Identities=32% Similarity=0.577 Sum_probs=115.2
Q ss_pred CeEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEEeeec
Q 032987 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPF 80 (129)
Q Consensus 1 MF~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alvfrP~ 80 (129)
||++++++|+|+|||++||+++++++++.|+++|+||++++.|+||+|+++.++++|+|.||||++|++|+|+|++|+|+
T Consensus 1 My~l~~~~d~VripP~~fg~~~~~~v~~~L~~k~eG~~~~~~G~~v~V~~v~~igeG~I~~GDG~~y~~V~f~al~fkP~ 80 (183)
T COG1095 1 MYKLVELEDTVRIPPSYFGEDLEEAVKEELKEKYEGKLDGDVGLVVLVLDVKEIGEGIIVPGDGSTYHEVKFRALVFKPF 80 (183)
T ss_pred CcEEEEEeeEEEeCHHHcCccHHHHHHHHHHHHhcceEccccCEEEEEEEeeEeeccEEecCCCcEEEEEEEEEEEEEec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCC-CCcCCCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSP-SRSEPDPYGR 127 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~-~~f~~d~~~~ 127 (129)
+|||++|+|++++++|+|+++||+| .|+|.++++++ +.| |+..+
T Consensus 81 ~gEVV~GeVv~~~~~G~fV~igp~d-glvh~sqi~dd~~~~--d~~~~ 125 (183)
T COG1095 81 RGEVVEGEVVEVVEFGAFVRIGPLD-GLVHVSQIMDDYIDY--DEKNK 125 (183)
T ss_pred cccEEEEEEEEEeecceEEEecccc-ccccHhhccCccccc--Ccccc
Confidence 9999999999999999999999997 55555555554 555 76654
No 5
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=100.00 E-value=4.4e-40 Score=247.48 Aligned_cols=124 Identities=27% Similarity=0.500 Sum_probs=119.8
Q ss_pred CeEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEEeeec
Q 032987 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPF 80 (129)
Q Consensus 1 MF~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alvfrP~ 80 (129)
||++++++|+|+|||++|+++++++|.++|+++|+||+++++|+||||+||.++++|+|.||||+++++|+|+|++|+|+
T Consensus 1 MF~~~~l~d~v~i~P~~~~~~~~~~i~~~l~~~~~~k~~~~~G~~v~v~di~~i~~g~i~~gdg~~~~~v~f~~lvf~P~ 80 (187)
T PRK08563 1 MYKLVKLEDVVRIPPEMFGEDLEEAALEVLREKYEGRIDKELGIIVAVLDVKVIGEGKIVPGDGATYHEVEFDALVFKPE 80 (187)
T ss_pred CeEEEEEeEEEEECHHHcCccHHHHHHHHHHHHhhCcCcCCcCEEEEEEEeEEecccEEecCCCCcEEEEEEEEEEEecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCCCCcCCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYG 126 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~~~f~~d~~~ 126 (129)
+||+++|+|++++++|+|+++||+++++++++.+++++.| |+.+
T Consensus 81 ~GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~~l~~~~~~~--d~~~ 124 (187)
T PRK08563 81 LQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISY--DPKN 124 (187)
T ss_pred CCCEEEEEEEEEEccEEEEEEeCceEEEEcHHcCCCceEE--cccc
Confidence 9999999999999999999999999999998888888888 6543
No 6
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=100.00 E-value=3.8e-36 Score=220.37 Aligned_cols=122 Identities=26% Similarity=0.487 Sum_probs=119.2
Q ss_pred CeEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEEeeec
Q 032987 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPF 80 (129)
Q Consensus 1 MF~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alvfrP~ 80 (129)
||+...++..+.++|+++++++++.+++.|.++.+|||..++|++|||+++++|++|+|++++|.+.|+|+|+|++||||
T Consensus 1 mff~~~l~~~i~l~p~~~gp~~~~~l~~~L~~~veg~ctg~~Gyvi~vt~ld~Ig~g~I~~~~G~v~FpVky~av~Fkpf 80 (170)
T KOG3298|consen 1 MFFHKDLDLNICLHPSYFGPNLQAILKRKLLAEVEGKCTGKYGYVIAVTTLDNIGEGRIRPGTGFVTFPVKYKAVTFKPF 80 (170)
T ss_pred CcceeeeeeeeeecccccCchHHHHHHHHHHHHhhccccccccEEEEEEEhhhccCCccccCCceEEEEEEEEEEEEeec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCCCCcCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPD 123 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~~~f~~d 123 (129)
+|||++|+|++++++|+|+++||+. +|++++.+|++++|.|.
T Consensus 81 KGEVvdgvV~~Vnk~G~F~~~GPl~-~f~sshl~ppd~~f~p~ 122 (170)
T KOG3298|consen 81 KGEVVDGVVTKVNKMGVFARSGPLE-VFYSSHLKPPDYEFDPG 122 (170)
T ss_pred CCcEEEEEEEEEeeeeEEEeccceE-eeeecccCCCCcccCCC
Confidence 9999999999999999999999995 99999999999999554
No 7
>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=99.97 E-value=1.4e-31 Score=177.74 Aligned_cols=80 Identities=56% Similarity=1.027 Sum_probs=78.8
Q ss_pred eEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEEeeecC
Q 032987 2 FYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFV 81 (129)
Q Consensus 2 F~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alvfrP~~ 81 (129)
|++++++|+|+|||++||+++++++.++|++||+||++++.|+||+++|+.++++|+|.||||+++|+|+|||++||||+
T Consensus 1 F~~~~l~d~v~i~P~~fg~~~~~~i~~~L~~ky~gkv~~~~Gl~v~v~di~~i~eG~I~~gdG~~~~~V~Fr~lvFrPf~ 80 (80)
T cd04330 1 FILSEIEDTVRIPPSQFSRPLNDAIEDELNKKYANKVIQNVGLCICLYDILEVEDGYILPGDGASHYKVTFRMVVFRPFV 80 (80)
T ss_pred CEEEEEEEEEEECHHHcCcCHHHHHHHHHHHHhCCcEeCCccEEEEEEEeEEEcCCEEECCCCCEEEEEEEEEEEEECCC
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999985
No 8
>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=1.8e-31 Score=177.11 Aligned_cols=80 Identities=29% Similarity=0.568 Sum_probs=78.8
Q ss_pred eEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEEeeecC
Q 032987 2 FYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFV 81 (129)
Q Consensus 2 F~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alvfrP~~ 81 (129)
|++++++|+|+|||++||+++++++.++|+++|+||+.+++|+||||+||.++++|+|.+|||+++|+|+|+|++||||+
T Consensus 1 F~~~~l~d~v~i~P~~fg~~l~~~i~~~L~~~~egk~~~~~G~iv~v~di~~i~~G~I~~gdG~~~~~V~F~aivfrPf~ 80 (80)
T cd04329 1 FFKIELEHNILLHPSYFGPNLKEYLEQKLLEEVEGTCTGDYGYIIAVTDIDDIGEGKILPGTGSVEFPVKYKAIVFKPFK 80 (80)
T ss_pred CEEEEEEEEEEECHHHhCccHHHHHHHHHHHHhCCcCcCceeEEEEEEEeeEecCcEEEcCCCCEEEEEEEEEEEEEccC
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999996
No 9
>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=99.97 E-value=2.7e-31 Score=176.28 Aligned_cols=80 Identities=29% Similarity=0.479 Sum_probs=78.8
Q ss_pred eEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEEeeecC
Q 032987 2 FYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFV 81 (129)
Q Consensus 2 F~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alvfrP~~ 81 (129)
|++++++|+|+|||++||+++++++.++|+++|+||+++++|+||+++|+.++++|+|.||||+++|+|+|||++||||+
T Consensus 1 f~l~~l~d~v~i~P~~f~~~~~~~i~~~L~~k~~gkv~~~~G~~v~v~di~~i~~G~I~~gdG~~~~~V~F~~ivFrPf~ 80 (80)
T cd00655 1 FQILEIADLVSVPPKYFGDDCKGVKKCLLQEKGEGDRTPVVGIILAIKDTKDIPEGAIRPGDGSAYVNVSFRAVVFKPFS 80 (80)
T ss_pred CEEEEEEEEEEECHHHhCccHHHHHHHHHHHHhCCeEeCCccEEEEEEEeEEEcCCEEECCCCCEEEEEEEEEEEEEcCC
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999985
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=99.97 E-value=1e-30 Score=173.58 Aligned_cols=80 Identities=31% Similarity=0.599 Sum_probs=78.3
Q ss_pred eEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEEeeecC
Q 032987 2 FYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFV 81 (129)
Q Consensus 2 F~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alvfrP~~ 81 (129)
|++++++|+|+|||++||+++++++.++|+++|+||+++++|+||||+||.++++|+|.||||+++|+|+|||++|||..
T Consensus 1 f~~~~l~d~vri~P~~fg~~~~~~i~~~L~~~~egk~~~~~G~iv~v~di~~i~eG~I~~gdG~~~~~V~F~~ivFrP~~ 80 (80)
T cd04331 1 YKLVELEDVVRVPPELFGEDLEEAVLEILKEKYEGRLDKDLGKIVSVLDVKDVGEGKIVHGDGAVYHEVRFDALVFKPEL 80 (80)
T ss_pred CEEEEEEEeEEECHHHcCcCHHHHHHHHHHHHhcCcCcCCCCEEEEEEEEEEecCCEEEcCCCCEEEEEEEEEEEEecCC
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999963
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=99.88 E-value=2.7e-22 Score=128.97 Aligned_cols=70 Identities=43% Similarity=0.692 Sum_probs=66.8
Q ss_pred eEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEEe
Q 032987 8 EHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVF 77 (129)
Q Consensus 8 ~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alvf 77 (129)
+|+|+|||++|++++++++.++|+++|+||+.++.|+||++++|..+++|+|.+|||+++++|+|+|+||
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 EDTVRLPPSYLGPDLKDGIKEQLLDKYEGKYIPELGVVIAVTDIKEISEGKIIPGDGFVYFKVTFRALVF 70 (70)
T ss_dssp EEEEEE-GGGTTSTHHHHHHHHHHHHHTTEEETTTEEEEEEEEEEEESCEEE-TTTSSEEEEEEEEEEEE
T ss_pred CcEEEECHHHhCcCHHHHHHHHHHHHHhCcCcCCceEEEEEeeeeEecCcEEECCCCCEEEEEEEEEEEC
Confidence 6899999999999999999999999999999999999999999999999999999999999999999998
No 12
>cd04328 RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. Rpa43 is a subunit of eukaryotic RNA polymerase (RNAP) I that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNP III, and RpoE of archaeal RNAP. Rpa43 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Rpa43 heterodimerizes with Rpa14 and this heterodimer has genetic and biochemical characteristics similar to those of the Rpb7/Rpb4 heterodimer of RNAP II. In addition, the Rpa43/Rpa14 heterodimer binds single-stranded RNA, as is the case for the Rpb7/Rpb4 and the archaeal E/F complexes. The position of Rpa43/Rpa14 in the three-dimensional structure of RNAP I is similar to that of Rpb4/Rpb7, which forms an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter. Rpb43 binds Rrn3, an rDNA-specific transcription factor, functionally equivalent to TFIIB, invo
Probab=99.79 E-value=8e-19 Score=118.15 Aligned_cols=79 Identities=28% Similarity=0.382 Sum_probs=75.5
Q ss_pred CeEEEEeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCe-eEEEEEEEeeeeec--eeEEeCCCceEEEEEEEEEEe
Q 032987 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANL-GLCISIYDIKEIEG--GFVYPGEGASTHTVKFRLVVF 77 (129)
Q Consensus 1 MF~~~~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~-G~~I~v~~i~~i~~--g~I~~gdG~~~~~V~F~alvf 77 (129)
||.+++.+++|+|+|+++++..+ +++++|+++|. |+.++. |+|++.+|+..+++ |+|.+++|.++++|+|+++||
T Consensus 8 ~f~~~~~~~~v~l~P~~~~~~~~-~i~~~l~~~l~-ky~~~l~Gv~l~~~di~~~~~~~~~i~~~~~~~~~~V~~~~lVF 85 (89)
T cd04328 8 CFETLTVSLYVSLAPKYLGNPLT-GIKAQLLNPLL-KYSPKLKGVVLAYSNIKLLEGELAKIVDDSPFIFVWISADFLVF 85 (89)
T ss_pred cEEEEEEEEEEEECchhhcCHhH-HHHHHHhhhHh-hhcccCCeEEEEecceEeccccceeeeCCCcEEEEEEEEEEEEE
Confidence 89999999999999999998766 99999999999 999999 99999999998866 999999999999999999999
Q ss_pred eecC
Q 032987 78 RPFV 81 (129)
Q Consensus 78 rP~~ 81 (129)
||++
T Consensus 86 rP~~ 89 (89)
T cd04328 86 RPKI 89 (89)
T ss_pred ecCC
Confidence 9985
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=99.60 E-value=1e-15 Score=108.94 Aligned_cols=48 Identities=54% Similarity=1.032 Sum_probs=42.4
Q ss_pred ecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCCCCcCCCCCCCC
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRL 128 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~~~f~~d~~~~~ 128 (129)
||+|||+.|+|+++++.||+|++||||+||||+++||+++.| |+++|+
T Consensus 1 PF~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~f--d~~~~~ 48 (122)
T PF08292_consen 1 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRF--DEEEQA 48 (122)
T ss_dssp --TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEE--ECCCTE
T ss_pred CCCCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCcc--CccCCE
Confidence 899999999999999999999999999999999999999999 888774
No 14
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=98.99 E-value=8e-10 Score=74.34 Aligned_cols=40 Identities=25% Similarity=0.522 Sum_probs=34.3
Q ss_pred CCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCCCCcC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSE 121 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~~~f~ 121 (129)
+|||++|+|++++++|+|+++||++ .|++..++|++..|+
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gpl~-~f~~~~~ip~~~~~~ 40 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGPLS-IFISRHLIPSDMEFD 40 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcCce-EEEEeeecCccceEC
Confidence 6999999999999999999999886 666677777777773
No 15
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=98.83 E-value=5.8e-08 Score=75.27 Aligned_cols=114 Identities=19% Similarity=0.281 Sum_probs=96.4
Q ss_pred EeeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCC-eeEEEEEEEeeee-eceeEEeCCCceEEEEEEEEEEeeecCCC
Q 032987 6 KIEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIAN-LGLCISIYDIKEI-EGGFVYPGEGASTHTVKFRLVVFRPFVGE 83 (129)
Q Consensus 6 ~l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~-~G~~I~v~~i~~i-~~g~I~~gdG~~~~~V~F~alvfrP~~~E 83 (129)
+..-.+.+.|.++.++++..+++.|+.++ +++... .|++++.-+|.-. ..++|.+.+|..+..++-...||+|..|.
T Consensus 31 t~dlhlalaP~yl~npl~~~i~ehld~~v-l~y~~~l~GivLgydnIKvLg~~aki~~D~pf~hlwi~adfyVf~Pk~Gd 109 (253)
T KOG4134|consen 31 TTDLHLALAPYYLANPLHALIEEHLDTKV-LFYDSGLDGIVLGYDNIKVLGQTAKIRADDPFMHLWINADFYVFRPKAGD 109 (253)
T ss_pred eeheeeeecchhhcchhHHHHHHHhhHHH-hhhccCCCceEEeecceEeeccccceecCCCceEEEEeeeEEEECCCCCC
Confidence 55567899999999988888888888874 444444 4899999998876 57999999999999999999999999999
Q ss_pred EEEEEEEEEccCceEEEe-CccceEEecCCCCCCCCCcC
Q 032987 84 IIAAKLKESDANGLRLSL-GFFEDIYVPSHLLPSPSRSE 121 (129)
Q Consensus 84 Vl~g~V~~v~~~Gi~v~~-G~~~~i~i~~~~lp~~~~f~ 121 (129)
+|+|.|-.|+...|-+-+ |-|+ .-||+..+|.++.|-
T Consensus 110 ~LeG~Vn~vS~sHIglLIhg~FN-ASIpk~nip~dw~fI 147 (253)
T KOG4134|consen 110 ILEGVVNHVSRSHIGLLIHGVFN-ASIPKTNIPADWEFI 147 (253)
T ss_pred eeeeeeeecchhhhceeehhhhh-ccCCCCCCccceeee
Confidence 999999999999887544 8884 889999999887763
No 16
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=97.69 E-value=8e-05 Score=47.18 Aligned_cols=39 Identities=21% Similarity=0.369 Sum_probs=34.2
Q ss_pred eecCCCEEEEEEEEEccCceEEEeC-ccceEEecCCCCCCC
Q 032987 78 RPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSP 117 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~~G-~~~~i~i~~~~lp~~ 117 (129)
+|..|++++|+|+++++.|+|+.+| .. +-|+|...+++.
T Consensus 1 k~~~G~iv~g~V~~v~~~g~~V~l~~~~-~g~ip~~~l~~~ 40 (74)
T PF00575_consen 1 KLKEGDIVEGKVTSVEDFGVFVDLGNGI-EGFIPISELSDD 40 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEESTSS-EEEEEGGGSSSS
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCcE-EEEEEeehhcCc
Confidence 5789999999999999999999999 66 488998888864
No 17
>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=96.91 E-value=0.0018 Score=41.52 Aligned_cols=39 Identities=23% Similarity=0.164 Sum_probs=30.0
Q ss_pred CCCEEEEEEEEEccCceEEEeCc--cceEEecCCCCCC-CCCc
Q 032987 81 VGEIIAAKLKESDANGLRLSLGF--FEDIYVPSHLLPS-PSRS 120 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~--~~~i~i~~~~lp~-~~~f 120 (129)
.|++.+|+|++++++|+|+.+++ .++ +++.+.+++ ...|
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G-~v~~~~l~~~~~~~ 42 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEG-LVHVSTLGDDYYEF 42 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCCCEEE-EEEEEecCCCcEEE
Confidence 38999999999999999999997 443 555566654 3444
No 18
>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=96.55 E-value=0.003 Score=39.43 Aligned_cols=39 Identities=15% Similarity=0.095 Sum_probs=31.1
Q ss_pred CCEEEEEEEEEccCceEEEeCccceEEecCCCCCCCCCc
Q 032987 82 GEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRS 120 (129)
Q Consensus 82 ~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~~~f 120 (129)
|+++.|+|++++++|+|+.++.--.-++|.+.|.++..+
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~~ 39 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIK 39 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcC
Confidence 689999999999999999996423478888888764433
No 19
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=96.47 E-value=0.0057 Score=38.95 Aligned_cols=37 Identities=14% Similarity=0.092 Sum_probs=28.8
Q ss_pred ecCCCEEEEEEEEEccCceEEEeCc--cceEEecCCCCCC
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLGF--FEDIYVPSHLLPS 116 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G~--~~~i~i~~~~lp~ 116 (129)
|-.|++++|+|+++.++|+|+.+.- .+ -++|.+.+.+
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l~~~~~e-Glvh~sel~~ 39 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIPGCRKQ-GLVHKSHMSS 39 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEECCCCeE-EEEEchhhCC
Confidence 5689999999999999999999933 45 4555556644
No 20
>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=96.46 E-value=0.0046 Score=38.66 Aligned_cols=36 Identities=17% Similarity=0.303 Sum_probs=29.5
Q ss_pred CCEEEEEEEEEccCceEEEeCccceEEecCCCCCCC
Q 032987 82 GEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSP 117 (129)
Q Consensus 82 ~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~ 117 (129)
|++++|+|++++++|+++.++.--.-++|.+.+.++
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~ 36 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADV 36 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCc
Confidence 689999999999999999996433578887777653
No 21
>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=96.24 E-value=0.007 Score=38.98 Aligned_cols=36 Identities=11% Similarity=0.036 Sum_probs=29.5
Q ss_pred CCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
.|+++.|+|++++++|+|+++++--+-++|...|.+
T Consensus 3 ~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~ 38 (74)
T cd05705 3 EGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTK 38 (74)
T ss_pred CCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccC
Confidence 689999999999999999999875556777555543
No 22
>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=96.23 E-value=0.0072 Score=37.61 Aligned_cols=34 Identities=24% Similarity=0.421 Sum_probs=29.5
Q ss_pred CCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 82 GEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 82 ~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
|+++.|+|+++++.|++++++=+ ..|+|...|+.
T Consensus 1 G~iv~g~V~~v~~~G~~v~l~g~-~gfip~s~~~~ 34 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDIEGV-RAFLPASQVDL 34 (67)
T ss_pred CCEEEEEEEEEECCeEEEEECCE-EEEEEHHHCCC
Confidence 78999999999999999999555 48999888864
No 23
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=96.17 E-value=0.0088 Score=36.26 Aligned_cols=37 Identities=22% Similarity=0.305 Sum_probs=30.7
Q ss_pred CCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSP 117 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~ 117 (129)
.|+++.|+|.++++.|+++.++.--..++|.+.+++.
T Consensus 2 ~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~ 38 (72)
T smart00316 2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDK 38 (72)
T ss_pred CCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCcc
Confidence 5999999999999999999999433577777777664
No 24
>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=96.16 E-value=0.0083 Score=38.96 Aligned_cols=38 Identities=8% Similarity=0.019 Sum_probs=31.7
Q ss_pred ecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
+..|+++.|+|++++++|+|+.++.--.-++|.+.+..
T Consensus 12 ~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~ 49 (83)
T cd04461 12 LKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISD 49 (83)
T ss_pred CCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCc
Confidence 56899999999999999999999533457888877765
No 25
>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=96.10 E-value=0.012 Score=36.85 Aligned_cols=40 Identities=20% Similarity=0.258 Sum_probs=32.1
Q ss_pred cCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCCCCc
Q 032987 80 FVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRS 120 (129)
Q Consensus 80 ~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~~~f 120 (129)
..|++++|+|.++++.|+++.+|.. +-++|.+.+.+.-.|
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig~~-eg~lp~~e~~~~~~~ 41 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLGKV-EAILPKKEQIPGESY 41 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcCCe-EEEeeHHHCCCCCcC
Confidence 5799999999999999999999985 467777666543344
No 26
>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=96.08 E-value=0.011 Score=35.99 Aligned_cols=36 Identities=14% Similarity=0.097 Sum_probs=29.5
Q ss_pred CCEEEEEEEEEccCceEEEeCccceEEecCCCCCCC
Q 032987 82 GEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSP 117 (129)
Q Consensus 82 ~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~ 117 (129)
|+++.|+|+++.++|+|+.++.-..-++|.+.+++.
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~ 36 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHK 36 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCc
Confidence 689999999999999999998444577777777653
No 27
>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=96.06 E-value=0.0091 Score=40.19 Aligned_cols=37 Identities=11% Similarity=0.077 Sum_probs=28.4
Q ss_pred CEEEEEEEEEccCceEEEeCccceEEecCCCC-CCCCCc
Q 032987 83 EIIAAKLKESDANGLRLSLGFFEDIYVPSHLL-PSPSRS 120 (129)
Q Consensus 83 EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~l-p~~~~f 120 (129)
|++.|+|++++++|+|+.+++.+ -+++...+ ++...|
T Consensus 1 ~vv~g~V~~i~~~GifV~l~~v~-G~v~~~~l~~~~~~~ 38 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIGPVD-GLLHISQIMDDYISY 38 (99)
T ss_pred CEEEEEEEEEEeccEEEEEcCeE-EEEEEEEccCCceEe
Confidence 68999999999999999999865 55554444 445555
No 28
>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=96.02 E-value=0.011 Score=38.40 Aligned_cols=37 Identities=14% Similarity=0.453 Sum_probs=30.1
Q ss_pred eeecCCCEEEEEEEEEccCceEEEeC-ccceEEecCCCC
Q 032987 77 FRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLL 114 (129)
Q Consensus 77 frP~~~EVl~g~V~~v~~~Gi~v~~G-~~~~i~i~~~~l 114 (129)
|.|.+|++++|+|+++.+.|+++.++ .++++ +|.+.+
T Consensus 2 y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~-l~~se~ 39 (86)
T cd05789 2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAV-LPLSEV 39 (86)
T ss_pred CcCCCCCEEEEEEEEECCCEEEEECCCCeEEE-EEHHHc
Confidence 67899999999999999999999997 56544 444444
No 29
>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=96.01 E-value=0.011 Score=36.04 Aligned_cols=36 Identities=11% Similarity=0.195 Sum_probs=30.1
Q ss_pred CCEEEEEEEEEccCceEEEeCccceEEecCCCCCCC
Q 032987 82 GEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSP 117 (129)
Q Consensus 82 ~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~ 117 (129)
|+++.|+|++++++|+|+.++.-..-++|.+.|++.
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~ 36 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADR 36 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCc
Confidence 689999999999999999998665677777777653
No 30
>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=96.00 E-value=0.011 Score=36.87 Aligned_cols=35 Identities=26% Similarity=0.322 Sum_probs=28.5
Q ss_pred CCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 82 GEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 82 ~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
|+++.|+|+++.++|+|+.++.--.-++|...+++
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~ 35 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSD 35 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCc
Confidence 68999999999999999999653346777777764
No 31
>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=95.86 E-value=0.023 Score=35.68 Aligned_cols=37 Identities=14% Similarity=0.024 Sum_probs=29.8
Q ss_pred cCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 80 FVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 80 ~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
..|+++.|+|++++++|+++.++.--.-+++...+.+
T Consensus 2 ~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~ 38 (73)
T cd05706 2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALD 38 (73)
T ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccC
Confidence 3799999999999999999999754346666666664
No 32
>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=95.77 E-value=0.015 Score=37.48 Aligned_cols=37 Identities=14% Similarity=0.273 Sum_probs=30.8
Q ss_pred cCCCEEEEEEEEEccCceEEEeCc--cceEEecCCCCCCC
Q 032987 80 FVGEIIAAKLKESDANGLRLSLGF--FEDIYVPSHLLPSP 117 (129)
Q Consensus 80 ~~~EVl~g~V~~v~~~Gi~v~~G~--~~~i~i~~~~lp~~ 117 (129)
-.|.++.|+|+++.++|+|+.+|. + .-|+|.+.+...
T Consensus 3 ~~G~~v~g~V~si~d~G~~v~~g~~gv-~Gfl~~~~~~~~ 41 (74)
T cd05694 3 VEGMVLSGCVSSVEDHGYILDIGIPGT-TGFLPKKDAGNF 41 (74)
T ss_pred CCCCEEEEEEEEEeCCEEEEEeCCCCc-EEEEEHHHCCcc
Confidence 368999999999999999999974 5 378888877654
No 33
>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=95.73 E-value=0.028 Score=36.33 Aligned_cols=40 Identities=13% Similarity=0.154 Sum_probs=33.2
Q ss_pred eeecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 77 FRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 77 frP~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
|.|..|.++.|+|++++..|+++.+|---.-++|...+..
T Consensus 2 y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~ 41 (82)
T cd04454 2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATE 41 (82)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccC
Confidence 6799999999999999999999999744356777766654
No 34
>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=95.48 E-value=0.026 Score=35.32 Aligned_cols=35 Identities=14% Similarity=0.003 Sum_probs=27.7
Q ss_pred CCCEEEEEEEEEccCceEEEeCccceEEecCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLP 115 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp 115 (129)
.|+++.|+|++++++|+|+.+..--+-++|...++
T Consensus 3 ~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~ 37 (72)
T cd05689 3 EGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMD 37 (72)
T ss_pred CCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEecc
Confidence 68999999999999999999965233555656664
No 35
>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=95.43 E-value=0.023 Score=35.60 Aligned_cols=34 Identities=29% Similarity=0.335 Sum_probs=26.9
Q ss_pred CCEEEEEEEEEccCceEEEe-CccceEEecCCCCCC
Q 032987 82 GEIIAAKLKESDANGLRLSL-GFFEDIYVPSHLLPS 116 (129)
Q Consensus 82 ~EVl~g~V~~v~~~Gi~v~~-G~~~~i~i~~~~lp~ 116 (129)
|.+++|+|+++.++|+++.+ +-++ -++|...+.+
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~-g~v~~~~l~~ 35 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFT-GTVDFLHLDP 35 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCce-EEEEHHHcCC
Confidence 67999999999999999998 4465 5666655643
No 36
>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=95.41 E-value=0.021 Score=35.32 Aligned_cols=34 Identities=21% Similarity=0.175 Sum_probs=27.6
Q ss_pred CCEEEEEEEEEccCceEEEeCccceEEecCCCCC
Q 032987 82 GEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLP 115 (129)
Q Consensus 82 ~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp 115 (129)
|+++.|+|++++++|+|+.++.-.+-+++.+.++
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~ 34 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDIS 34 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCC
Confidence 6899999999999999999975444566666665
No 37
>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=95.40 E-value=0.03 Score=34.21 Aligned_cols=35 Identities=20% Similarity=0.086 Sum_probs=28.8
Q ss_pred CCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 82 GEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 82 ~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
|+++.|+|+++.++|+|+.++.-..-++|...++.
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~ 35 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSD 35 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCC
Confidence 68999999999999999999854456777767654
No 38
>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=95.33 E-value=0.038 Score=34.74 Aligned_cols=37 Identities=24% Similarity=0.199 Sum_probs=29.8
Q ss_pred ecCCCEEEEEEEEEccCceEEEeCc---cceEEecCCCCCC
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLGF---FEDIYVPSHLLPS 116 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G~---~~~i~i~~~~lp~ 116 (129)
|-.|+++.|+|+++.++|+|+.+.. .+ -++|.+.+.+
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~-gll~~s~l~~ 40 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEYGNIE-GMILLSELSR 40 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCCCCeE-EEEEhHHcCC
Confidence 5689999999999999999999953 54 5666666654
No 39
>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=95.29 E-value=0.027 Score=35.72 Aligned_cols=34 Identities=18% Similarity=0.208 Sum_probs=26.7
Q ss_pred CCEEE-EEEEEE-ccCceEEEeCc-cceEEecCCCCCC
Q 032987 82 GEIIA-AKLKES-DANGLRLSLGF-FEDIYVPSHLLPS 116 (129)
Q Consensus 82 ~EVl~-g~V~~v-~~~Gi~v~~G~-~~~i~i~~~~lp~ 116 (129)
||+++ |+|+++ .++|+|+++++ ++ -|+|.+.+++
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~-G~i~~s~l~~ 37 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLL-GFVHISHLSD 37 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCE-EEEEHHHCCc
Confidence 78999 999999 69999999965 54 5666556643
No 40
>PRK08582 hypothetical protein; Provisional
Probab=95.27 E-value=0.055 Score=39.11 Aligned_cols=38 Identities=16% Similarity=-0.014 Sum_probs=29.0
Q ss_pred ecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
...|++++|+|++++++|+||.++.--.-+++.+.+.+
T Consensus 3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~ 40 (139)
T PRK08582 3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVAD 40 (139)
T ss_pred CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCc
Confidence 35799999999999999999999753334555555543
No 41
>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=95.22 E-value=0.038 Score=34.65 Aligned_cols=35 Identities=11% Similarity=0.217 Sum_probs=27.7
Q ss_pred CCCEEEEEEEEEccCceEEEeC--ccceEEecCCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLG--FFEDIYVPSHLLPS 116 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G--~~~~i~i~~~~lp~ 116 (129)
.|+++.|+|++++++|+|+.++ ..+ -++|...+++
T Consensus 2 ~g~~v~g~V~~i~~~g~~v~l~~~~~~-g~i~~~~l~~ 38 (77)
T cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVS-GLCHKSEISD 38 (77)
T ss_pred CCCEEEEEEEEEEcceEEEEECCCCeE-EEEEHHHCCC
Confidence 5899999999999999999997 465 4555555554
No 42
>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=95.20 E-value=0.029 Score=34.93 Aligned_cols=35 Identities=14% Similarity=0.395 Sum_probs=27.2
Q ss_pred CCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 82 GEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 82 ~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
|+++.|+|.++++.|+++.+|.-..-++|.+.+..
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~ 35 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSD 35 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCc
Confidence 78999999999999999999743345666655543
No 43
>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=95.12 E-value=0.034 Score=33.89 Aligned_cols=34 Identities=15% Similarity=0.201 Sum_probs=28.0
Q ss_pred CCCEEEEEEEEEccCceEEEeCccceEEecCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLP 115 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp 115 (129)
.|+++.|+|++++++|+++.++..+ -++|.+.+.
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~~~~-g~l~~~e~~ 34 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLGGVD-GLLHISDMS 34 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEECCeE-EEEEhHHCC
Confidence 4899999999999999999999765 556655554
No 44
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=95.08 E-value=0.038 Score=34.32 Aligned_cols=35 Identities=29% Similarity=0.407 Sum_probs=27.5
Q ss_pred CCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 82 GEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 82 ~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
|+++.|+|+++.++|+++.++.--+-++|.+.+.+
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~ 35 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSR 35 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCC
Confidence 68999999999999999999533346666666654
No 45
>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=94.88 E-value=0.051 Score=36.14 Aligned_cols=37 Identities=16% Similarity=0.301 Sum_probs=29.6
Q ss_pred eecCCCEEEEEEEEEccC--ceEEEeCccceEEecCCCC
Q 032987 78 RPFVGEIIAAKLKESDAN--GLRLSLGFFEDIYVPSHLL 114 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~--Gi~v~~G~~~~i~i~~~~l 114 (129)
+|..|++..|+|+++.++ |+|+.++.=.+-|+|.+.+
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~sei 42 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDI 42 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHc
Confidence 466899999999999996 9999998643466665555
No 46
>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=94.77 E-value=0.047 Score=34.88 Aligned_cols=35 Identities=11% Similarity=0.053 Sum_probs=28.3
Q ss_pred CCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 82 GEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 82 ~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
|.++.|+|++++++|+|+++++=-+-++|...+.+
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~ 35 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSD 35 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCC
Confidence 67899999999999999999763346777766654
No 47
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=94.74 E-value=0.039 Score=48.14 Aligned_cols=37 Identities=19% Similarity=0.277 Sum_probs=32.0
Q ss_pred eecCCCEEEEEEEEEccCceEEEeCccceEEecCCCC
Q 032987 78 RPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLL 114 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~l 114 (129)
.-..|++++|+|++++++|+|+.+|=+|++.|.++.-
T Consensus 189 ~l~~G~vV~G~V~~It~~GafVdigGvdGLlHiseiS 225 (541)
T COG0539 189 KLEVGEVVEGVVKNITDYGAFVDIGGVDGLLHISEIS 225 (541)
T ss_pred cCCCCceEEEEEEEeecCcEEEEecCeeeEEehhhcc
Confidence 3457899999999999999999999899988876553
No 48
>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=94.54 E-value=0.078 Score=33.90 Aligned_cols=34 Identities=24% Similarity=0.084 Sum_probs=27.0
Q ss_pred CCEEEEEEEEEccCceEEEeC----ccceEEecCCCCCC
Q 032987 82 GEIIAAKLKESDANGLRLSLG----FFEDIYVPSHLLPS 116 (129)
Q Consensus 82 ~EVl~g~V~~v~~~Gi~v~~G----~~~~i~i~~~~lp~ 116 (129)
|++++|+|+++.++|+|+.++ ..+ -++|...+++
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~-gll~~s~l~~ 38 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKE-GLVHISQLSF 38 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcE-EEEEhHhccC
Confidence 689999999999999999998 344 5555556654
No 49
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=94.48 E-value=0.041 Score=34.18 Aligned_cols=39 Identities=23% Similarity=0.428 Sum_probs=22.1
Q ss_pred CCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSR 119 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~~~ 119 (129)
.|++...+|++.++.|+|+..|--.++++|.+.+|.+.+
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~~~~ 39 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPEPLK 39 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG------
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcCCCCC
Confidence 378899999999999999999997889999998886543
No 50
>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=94.40 E-value=0.015 Score=51.89 Aligned_cols=64 Identities=16% Similarity=0.136 Sum_probs=47.7
Q ss_pred EeeeeeceeEEeCCCceEEEE--EEEEEEeeecCCCEEEEEEEEEccCceEEEeCc-cceEEecCCC
Q 032987 50 DIKEIEGGFVYPGEGASTHTV--KFRLVVFRPFVGEIIAAKLKESDANGLRLSLGF-FEDIYVPSHL 113 (129)
Q Consensus 50 ~i~~i~~g~I~~gdG~~~~~V--~F~alvfrP~~~EVl~g~V~~v~~~Gi~v~~G~-~~~i~i~~~~ 113 (129)
||.+-|..+|...++..+.++ ..+.++..|..|++++|+|+++.++|+|+.+.+ .+++.|-++.
T Consensus 585 ~i~ddG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei 651 (684)
T TIGR03591 585 DIEDDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEI 651 (684)
T ss_pred EEecCeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHc
Confidence 344456677777777666655 556667789999999999999999999999965 5555554433
No 51
>PRK07252 hypothetical protein; Provisional
Probab=94.36 E-value=0.083 Score=37.26 Aligned_cols=35 Identities=9% Similarity=0.099 Sum_probs=28.2
Q ss_pred CCCEEEEEEEEEccCceEEEeC-ccceEEecCCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPS 116 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G-~~~~i~i~~~~lp~ 116 (129)
.|+++.|+|+++.++|+||.++ ..+ -++|...|.+
T Consensus 3 vG~iv~G~V~~V~~~G~fVei~~~~~-GllhiseLs~ 38 (120)
T PRK07252 3 IGDKLKGTITGIKPYGAFVALENGTT-GLIHISEIKT 38 (120)
T ss_pred CCCEEEEEEEEEeCcEEEEEECCCCE-EEEEHHHcCC
Confidence 5899999999999999999995 444 5666666654
No 52
>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=93.92 E-value=0.033 Score=49.72 Aligned_cols=47 Identities=15% Similarity=0.075 Sum_probs=35.0
Q ss_pred EEEEeeecCCCEEEEEEEEEccCceEEEeCc--cceEEecCCCCC-CCCCc
Q 032987 73 RLVVFRPFVGEIIAAKLKESDANGLRLSLGF--FEDIYVPSHLLP-SPSRS 120 (129)
Q Consensus 73 ~alvfrP~~~EVl~g~V~~v~~~Gi~v~~G~--~~~i~i~~~~lp-~~~~f 120 (129)
+|.-.++..||+.+|+|++++++|+||.+.. .+++.+ ...|+ +.+.|
T Consensus 619 ~~~yl~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvh-is~l~~d~~~~ 668 (709)
T TIGR02063 619 KAEYMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVH-ISTLKDDYYVF 668 (709)
T ss_pred HHHhhhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEE-eeecCCCcEEE
Confidence 3444677889999999999999999999975 555554 44554 34555
No 53
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=93.57 E-value=0.088 Score=43.16 Aligned_cols=34 Identities=21% Similarity=0.206 Sum_probs=27.9
Q ss_pred ecCCCEEEEEEEEEccCceEEEeC---ccceEEecCC
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLG---FFEDIYVPSH 112 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G---~~~~i~i~~~ 112 (129)
|..|+++.|+|+++.++|+||.++ =++++.+.++
T Consensus 15 P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSE 51 (319)
T PTZ00248 15 PEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSE 51 (319)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHH
Confidence 667999999999999999999993 4666655444
No 54
>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=93.46 E-value=0.2 Score=32.13 Aligned_cols=37 Identities=16% Similarity=0.142 Sum_probs=28.2
Q ss_pred eeecCCCEEEEEEEEEccCceEEEeCc-cceEEecCCCC
Q 032987 77 FRPFVGEIIAAKLKESDANGLRLSLGF-FEDIYVPSHLL 114 (129)
Q Consensus 77 frP~~~EVl~g~V~~v~~~Gi~v~~G~-~~~i~i~~~~l 114 (129)
...-.|++.+|+|++++++|+|+.+.. .++ +++.+.+
T Consensus 12 ~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~G-lv~~se~ 49 (77)
T cd04473 12 EDLEVGKLYKGKVNGVAKYGVFVDLNDHVRG-LIHRSNL 49 (77)
T ss_pred hhCCCCCEEEEEEEeEecceEEEEECCCcEE-EEEchhc
Confidence 345689999999999999999999965 444 4444444
No 55
>PRK11642 exoribonuclease R; Provisional
Probab=93.21 E-value=0.11 Score=47.36 Aligned_cols=49 Identities=16% Similarity=0.148 Sum_probs=35.7
Q ss_pred EEEeeecCCCEEEEEEEEEccCceEEEeCc--cceEEecCCCCCC-CCCcCCCCC
Q 032987 74 LVVFRPFVGEIIAAKLKESDANGLRLSLGF--FEDIYVPSHLLPS-PSRSEPDPY 125 (129)
Q Consensus 74 alvfrP~~~EVl~g~V~~v~~~Gi~v~~G~--~~~i~i~~~~lp~-~~~f~~d~~ 125 (129)
|-..+...||+.+|+|++++++|+||.+.. .+++ |+...|++ .+.| |+.
T Consensus 636 ~~~m~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGl-V~vs~L~~d~y~~--d~~ 687 (813)
T PRK11642 636 CDFMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGL-VHVSSLDNDYYRF--DQV 687 (813)
T ss_pred HhhhhccCCcEEEEEEEEeecCceEEEECCCCeeee-EEEeecCCcceEe--cch
Confidence 444666789999999999999999999964 5544 44455654 4556 643
No 56
>PRK05807 hypothetical protein; Provisional
Probab=93.12 E-value=0.23 Score=35.64 Aligned_cols=35 Identities=9% Similarity=0.016 Sum_probs=27.1
Q ss_pred cCCCEEEEEEEEEccCceEEEeCccceEEecCCCCC
Q 032987 80 FVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLP 115 (129)
Q Consensus 80 ~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp 115 (129)
..|++++|+|+.++++|+||.+.-.+++. +...+.
T Consensus 4 ~vG~vv~G~Vt~i~~~GafV~L~~~~Glv-hiseis 38 (136)
T PRK05807 4 KAGSILEGTVVNITNFGAFVEVEGKTGLV-HISEVA 38 (136)
T ss_pred cCCCEEEEEEEEEECCeEEEEECCEEEEE-Ehhhcc
Confidence 36999999999999999999996555444 444444
No 57
>PHA02945 interferon resistance protein; Provisional
Probab=93.09 E-value=0.14 Score=34.57 Aligned_cols=25 Identities=28% Similarity=0.486 Sum_probs=22.6
Q ss_pred ecCCCEEEEEEEEEccCceEEEeCcc
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLGFF 104 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G~~ 104 (129)
|-.||++.|+|.+ ..+|+|+++-=+
T Consensus 9 P~~GelvigtV~~-~d~ga~v~L~EY 33 (88)
T PHA02945 9 PNVGDVLKGKVYE-NGYALYIDLFDY 33 (88)
T ss_pred CCCCcEEEEEEEe-cCceEEEEeccc
Confidence 8999999999999 999999998433
No 58
>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=92.53 E-value=0.27 Score=30.70 Aligned_cols=33 Identities=18% Similarity=0.232 Sum_probs=25.6
Q ss_pred CCEEEEEEEEEccCceEEEeC-ccceEEecCCCCC
Q 032987 82 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLP 115 (129)
Q Consensus 82 ~EVl~g~V~~v~~~Gi~v~~G-~~~~i~i~~~~lp 115 (129)
|+++.|+|+++.+.|++++++ -++ -+++...+.
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~-g~i~~~~i~ 34 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVH-GRIHVSEVF 34 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcE-EEEEHHHhc
Confidence 689999999999999999995 344 455555554
No 59
>PRK08059 general stress protein 13; Validated
Probab=92.45 E-value=0.24 Score=34.81 Aligned_cols=38 Identities=16% Similarity=0.096 Sum_probs=29.4
Q ss_pred ecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
...|+++.|+|+++.++|+|+.++.--.-++|.+.++.
T Consensus 5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~ 42 (123)
T PRK08059 5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITH 42 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCc
Confidence 45799999999999999999999753335555556544
No 60
>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=92.42 E-value=0.18 Score=45.47 Aligned_cols=35 Identities=26% Similarity=0.181 Sum_probs=29.6
Q ss_pred eecCCCEEEEEEEEEccCceEEEeCc-cceEEecCC
Q 032987 78 RPFVGEIIAAKLKESDANGLRLSLGF-FEDIYVPSH 112 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~~G~-~~~i~i~~~ 112 (129)
.|-.|++++|+|+++.++|+||.+++ .+++.|.++
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISe 679 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQ 679 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhh
Confidence 58999999999999999999999965 566666553
No 61
>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=92.26 E-value=0.23 Score=31.42 Aligned_cols=29 Identities=17% Similarity=0.253 Sum_probs=23.1
Q ss_pred CCCEEEEEEEEEcc-CceEEEeCcc-ceEEe
Q 032987 81 VGEIIAAKLKESDA-NGLRLSLGFF-EDIYV 109 (129)
Q Consensus 81 ~~EVl~g~V~~v~~-~Gi~v~~G~~-~~i~i 109 (129)
.|+++.|+|+++.+ +|+|+.+++= +++.+
T Consensus 3 ~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvh 33 (72)
T cd05704 3 EGAVTLGMVTKVIPHSGLTVQLPFGKTGLVS 33 (72)
T ss_pred CCCEEEEEEEEeeCCcEEEEECCCCCEEEEE
Confidence 69999999999986 8999999643 34444
No 62
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=91.71 E-value=1 Score=35.10 Aligned_cols=38 Identities=18% Similarity=0.504 Sum_probs=31.8
Q ss_pred eeecCCCEEEEEEEEEccCceEEEeC-ccceEEecCCCCC
Q 032987 77 FRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLP 115 (129)
Q Consensus 77 frP~~~EVl~g~V~~v~~~Gi~v~~G-~~~~i~i~~~~lp 115 (129)
|.|..|+++.|+|++++++|+++.++ ++++ ++|.+.+.
T Consensus 59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g-~L~~s~i~ 97 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKA-YLPVSEVL 97 (235)
T ss_pred ccCCCCCEEEEEEEEEeCceEEEEeCCCcee-EEEHHHcC
Confidence 99999999999999999999999998 6764 44444443
No 63
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=91.39 E-value=0.24 Score=35.56 Aligned_cols=37 Identities=16% Similarity=0.067 Sum_probs=27.7
Q ss_pred ecCCCEEEEEEEEEccCceEEEeC-ccceEEecCCCCC
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLP 115 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G-~~~~i~i~~~~lp 115 (129)
+..|+++.|+|+.+.++|+||.+- =-.++.|.++...
T Consensus 3 ~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~ 40 (129)
T COG1098 3 MKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIAD 40 (129)
T ss_pred ccccceEEEEEEeeEecceEEEecCCCcceEEehHhhh
Confidence 567999999999999999999882 2335555555443
No 64
>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=91.36 E-value=0.23 Score=44.09 Aligned_cols=52 Identities=13% Similarity=-0.012 Sum_probs=37.8
Q ss_pred EEEEeeecCCCEEEEEEEEEccCceEEEeC-ccceEEecCCCCCC-CCCcCCCCCC
Q 032987 73 RLVVFRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPS-PSRSEPDPYG 126 (129)
Q Consensus 73 ~alvfrP~~~EVl~g~V~~v~~~Gi~v~~G-~~~~i~i~~~~lp~-~~~f~~d~~~ 126 (129)
.|..++...||+.+|+|++++++|+||.+. +..+-+|+...|++ .+.| |+..
T Consensus 564 ~~~yl~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~--d~~~ 617 (654)
T TIGR00358 564 KCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVF--DQEK 617 (654)
T ss_pred HHHhhhhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEE--eccc
Confidence 344567778999999999999999999997 53345555566665 3455 6543
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=91.24 E-value=0.23 Score=29.26 Aligned_cols=32 Identities=16% Similarity=0.021 Sum_probs=26.2
Q ss_pred EEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 85 IAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 85 l~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
++|+|++++++|+++.++.-...++|...+.+
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~ 32 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSD 32 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCC
Confidence 47999999999999999855567778777765
No 66
>PF03293 Pox_RNA_pol: Poxvirus DNA-directed RNA polymerase, 18 kD subunit; InterPro: IPR004973 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The Poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. The enzyme consists of at least eight subunits, this is the 18 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0019083 viral transcription
Probab=90.72 E-value=5.2 Score=29.36 Aligned_cols=92 Identities=21% Similarity=0.278 Sum_probs=63.3
Q ss_pred eeEEEEECCCCCCCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEee-----eeeceeEEeCCCceEEEEEEEEEEeeecC
Q 032987 7 IEHTLRLPPHLLRLPLNEAIKLELENVFLDKVIANLGLCISIYDIK-----EIEGGFVYPGEGASTHTVKFRLVVFRPFV 81 (129)
Q Consensus 7 l~d~V~I~P~~~~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~-----~i~~g~I~~gdG~~~~~V~F~alvfrP~~ 81 (129)
.--.|.++|+.|+-++++.|++...++|-.|-.. |+- -.+|. ...=|.|. ...+..+|--.+--=.--.
T Consensus 8 vYLpV~l~PhELtLd~~~Ni~~aV~~eYLhkE~~--G~M--akkIei~~d~~lPLGeiv--NN~ivv~VPC~vtykyYk~ 81 (160)
T PF03293_consen 8 VYLPVTLQPHELTLDIRKNIKDAVYREYLHKESG--GIM--AKKIEICEDKELPLGEIV--NNHIVVKVPCNVTYKYYKV 81 (160)
T ss_pred eEEEEecCcceeeehHHHhHHHHHHHHHhhhccc--Cce--eeeEEEEeccccchHhhc--ccEEEEEeeeEEEEEEEee
Confidence 3446789999999999999999999998876533 332 22222 23446665 4455555544332223457
Q ss_pred CCEEEEEEEEEccCceEEEeCcc
Q 032987 82 GEIIAAKLKESDANGLRLSLGFF 104 (129)
Q Consensus 82 ~EVl~g~V~~v~~~Gi~v~~G~~ 104 (129)
|.++.|+..--++.-+++.+|=+
T Consensus 82 GDvV~GtLnIedESni~V~CgDL 104 (160)
T PF03293_consen 82 GDVVRGTLNIEDESNITVQCGDL 104 (160)
T ss_pred CCEEEEEEEecccCceEEEcCcE
Confidence 99999999999999999998854
No 67
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=90.49 E-value=0.35 Score=41.76 Aligned_cols=35 Identities=17% Similarity=0.072 Sum_probs=29.9
Q ss_pred CCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
.|+++.|+|++++++|+||.+|-.+ -++|.+.|..
T Consensus 208 ~G~iv~G~V~~i~~~G~FVdlggv~-Glv~~Sels~ 242 (486)
T PRK07899 208 KGQVRKGVVSSIVNFGAFVDLGGVD-GLVHVSELSW 242 (486)
T ss_pred CCCEEEEEEEEEECCeEEEEECCEE-EEEEHHHCCC
Confidence 6999999999999999999999875 6777666653
No 68
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=89.78 E-value=0.5 Score=38.50 Aligned_cols=38 Identities=16% Similarity=0.283 Sum_probs=29.7
Q ss_pred eecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 78 RPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
+.-.|+++.|+|++++++|+|+.++..+++ +|.+.+..
T Consensus 193 ~~k~G~vv~G~V~~I~~~G~fV~i~gv~Gl-lhisels~ 230 (318)
T PRK07400 193 RLEVGEVVVGTVRGIKPYGAFIDIGGVSGL-LHISEISH 230 (318)
T ss_pred cCCCCCEEEEEEEEEECCeEEEEECCEEEE-EEHHHccc
Confidence 355699999999999999999999887654 44445543
No 69
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=89.73 E-value=0.4 Score=39.04 Aligned_cols=38 Identities=13% Similarity=0.257 Sum_probs=32.7
Q ss_pred ecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
.-.|+++.|+|.++.+.|++|.+|.-..-|+|.+.+..
T Consensus 29 ~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~ 66 (318)
T PRK07400 29 FKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSI 66 (318)
T ss_pred cCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcc
Confidence 47899999999999999999999985567888877754
No 70
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=89.72 E-value=0.58 Score=37.28 Aligned_cols=37 Identities=22% Similarity=0.292 Sum_probs=29.0
Q ss_pred eecCCCEEEEEEEEEccCceEEEeCc---cceEEecCCCCC
Q 032987 78 RPFVGEIIAAKLKESDANGLRLSLGF---FEDIYVPSHLLP 115 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~~G~---~~~i~i~~~~lp 115 (129)
.|-.|+++.|+|+++.++|+||.+.- .++ ++|.+.+.
T Consensus 5 ~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieG-lI~iSEls 44 (262)
T PRK03987 5 WPEEGELVVGTVKEVKDFGAFVTLDEYPGKEG-FIHISEVA 44 (262)
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCCCCcEE-EEEHHHcC
Confidence 38899999999999999999999952 444 44444554
No 71
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=89.51 E-value=0.39 Score=41.34 Aligned_cols=43 Identities=23% Similarity=0.328 Sum_probs=32.4
Q ss_pred eeecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCCCCc
Q 032987 77 FRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRS 120 (129)
Q Consensus 77 frP~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~~~f 120 (129)
|+...||++.|+|.++++.|+++.+|=.+ .|+|++.+.+.-.|
T Consensus 130 yk~~~GeIV~G~V~ri~~~giiVDLggve-a~LP~sE~ip~E~~ 172 (470)
T PRK09202 130 YKDRVGEIITGVVKRVERGNIIVDLGRAE-AILPRKEQIPRENF 172 (470)
T ss_pred HHhhcCCEEEEEEEEEecCCEEEEECCeE-EEecHHHcCCCccC
Confidence 44557999999999999999999998776 55555554433344
No 72
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=89.51 E-value=0.54 Score=35.29 Aligned_cols=31 Identities=10% Similarity=0.105 Sum_probs=26.7
Q ss_pred EEEEEeeecCCCEEEEEEEEEccCceEEEeC
Q 032987 72 FRLVVFRPFVGEIIAAKLKESDANGLRLSLG 102 (129)
Q Consensus 72 F~alvfrP~~~EVl~g~V~~v~~~Gi~v~~G 102 (129)
++.....|..|+++.|+|+++..+|+++.++
T Consensus 55 ~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~ 85 (189)
T PRK09521 55 FKKTPPLLKKGDIVYGRVVDVKEQRALVRIV 85 (189)
T ss_pred CcCCCCCCCCCCEEEEEEEEEcCCeEEEEEE
Confidence 3334578889999999999999999999996
No 73
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=89.47 E-value=0.52 Score=38.90 Aligned_cols=37 Identities=14% Similarity=0.125 Sum_probs=31.5
Q ss_pred ecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
.-.|+++.|+|+++++.|+|+.+|-.+ .++|.+.++.
T Consensus 190 ~~~G~~v~g~V~~v~~~G~fV~l~~v~-g~v~~sels~ 226 (390)
T PRK06676 190 LKEGDVVEGTVARLTDFGAFVDIGGVD-GLVHISELSH 226 (390)
T ss_pred CCCCCEEEEEEEEEecceEEEEeCCeE-EEEEHHHcCc
Confidence 457999999999999999999998775 7788777764
No 74
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=88.68 E-value=0.71 Score=41.44 Aligned_cols=40 Identities=23% Similarity=0.093 Sum_probs=30.6
Q ss_pred eeecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 77 FRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 77 frP~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
..|..|+++.|+|+++.++|+|+.+++-.+-+++.+.+++
T Consensus 617 ~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~ 656 (693)
T PRK11824 617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIAD 656 (693)
T ss_pred ccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccC
Confidence 4578999999999999999999999753334444455553
No 75
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=88.43 E-value=0.56 Score=37.55 Aligned_cols=28 Identities=25% Similarity=0.406 Sum_probs=24.9
Q ss_pred ecCCCEEEEEEEEEccCceEEEeCccce
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLGFFED 106 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G~~~~ 106 (129)
|-.||++.|+|.++.++|+|+.+-=+++
T Consensus 9 PeeGEiVv~tV~~V~~~GAyv~L~EY~g 36 (269)
T COG1093 9 PEEGEIVVGTVKQVADYGAYVELDEYPG 36 (269)
T ss_pred CCCCcEEEEEEEEeeccccEEEeeccCC
Confidence 8899999999999999999999865543
No 76
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=88.09 E-value=0.61 Score=38.87 Aligned_cols=39 Identities=23% Similarity=0.452 Sum_probs=32.6
Q ss_pred eeecCCCEEEEEEEEEccCceEEEeCccceEEec-CCCCCC
Q 032987 77 FRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVP-SHLLPS 116 (129)
Q Consensus 77 frP~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~-~~~lp~ 116 (129)
|+...||++.|+|.+.++.|+++.+|=.+ -++| ++++|.
T Consensus 130 f~~k~GeiV~G~V~~~~~~~~~Vdlg~vE-a~LP~~E~ip~ 169 (362)
T PRK12327 130 FSEREGDIVTGVVQRRDNRFVYVNLGKIE-AVLPPAEQIPG 169 (362)
T ss_pred HHHhcCCEEEEEEEEEeCCcEEEEeCCeE-EEecHHHcCCC
Confidence 66789999999999999999999999875 6777 555553
No 77
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=87.55 E-value=0.78 Score=39.41 Aligned_cols=36 Identities=11% Similarity=-0.022 Sum_probs=28.7
Q ss_pred cCCCEEEEEEEEEccCceEEEeCccceEEecCCCCC
Q 032987 80 FVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLP 115 (129)
Q Consensus 80 ~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp 115 (129)
..|+++.|+|++++++|+|+.+++--+-++|.+.|+
T Consensus 291 ~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels 326 (491)
T PRK13806 291 KAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMS 326 (491)
T ss_pred CCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcC
Confidence 358999999999999999999975334566666665
No 78
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=87.47 E-value=0.73 Score=39.58 Aligned_cols=39 Identities=13% Similarity=0.006 Sum_probs=31.8
Q ss_pred eecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 78 RPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
+...|++++|+|++++++|+|+.++.--..++|.+.+..
T Consensus 199 ~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~ 237 (491)
T PRK13806 199 TVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSW 237 (491)
T ss_pred hCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCC
Confidence 356899999999999999999999643357777777754
No 79
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=87.30 E-value=0.71 Score=31.34 Aligned_cols=36 Identities=25% Similarity=0.194 Sum_probs=27.3
Q ss_pred cCCCEEEEEEEEEccCceEEEeCccceEEecCCCCC
Q 032987 80 FVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLP 115 (129)
Q Consensus 80 ~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp 115 (129)
..|.++.|+|++++++|+++++++=-.-++|...+.
T Consensus 2 ~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis 37 (100)
T cd05693 2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNIS 37 (100)
T ss_pred CCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhh
Confidence 368999999999999999999953223555555554
No 80
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=87.06 E-value=0.77 Score=37.86 Aligned_cols=39 Identities=13% Similarity=0.317 Sum_probs=32.6
Q ss_pred eecCCCEEEEEEEEEccCceEEEe-CccceEEecCCCCCC
Q 032987 78 RPFVGEIIAAKLKESDANGLRLSL-GFFEDIYVPSHLLPS 116 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~~-G~~~~i~i~~~~lp~ 116 (129)
....|+++.|+|+++++.|+++.+ |+--..++|.+.+.+
T Consensus 14 ~~~~G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~ 53 (390)
T PRK06676 14 EVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSN 53 (390)
T ss_pred cccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhcc
Confidence 456899999999999999999999 744457888887754
No 81
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=86.76 E-value=0.88 Score=39.32 Aligned_cols=38 Identities=21% Similarity=0.340 Sum_probs=31.7
Q ss_pred ecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
.-.|++++|+|.++++.|+++.+|+--+-++|...|..
T Consensus 33 ~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~ 70 (486)
T PRK07899 33 FNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSI 70 (486)
T ss_pred CCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhcc
Confidence 45799999999999999999999964456788776653
No 82
>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=85.88 E-value=1 Score=37.25 Aligned_cols=43 Identities=28% Similarity=0.346 Sum_probs=32.1
Q ss_pred eeecCCCEEEEEEEEEccCc-eEEEeCccceEEecCCCCCCCCCc
Q 032987 77 FRPFVGEIIAAKLKESDANG-LRLSLGFFEDIYVPSHLLPSPSRS 120 (129)
Q Consensus 77 frP~~~EVl~g~V~~v~~~G-i~v~~G~~~~i~i~~~~lp~~~~f 120 (129)
|+...||++.|+|.++++.| +++.+|=.+ -++|+..+.+.-.|
T Consensus 127 y~~k~GeiV~G~V~~v~~~g~v~VdiG~~e-a~LP~~E~ip~E~~ 170 (341)
T TIGR01953 127 FSSKEGEIISGTVKRVNRRGNLYVELGKTE-GILPKKEQIPGEKF 170 (341)
T ss_pred HHhhcCCEEEEEEEEEecCCcEEEEECCeE-EEecHHHcCCCcCC
Confidence 45569999999999999988 699999765 56665544433335
No 83
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=85.48 E-value=1.1 Score=38.21 Aligned_cols=36 Identities=19% Similarity=0.093 Sum_probs=29.0
Q ss_pred CCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
.|+++.|+|++++++|+|+.+|+=-+.++|.+.++.
T Consensus 359 ~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~ls~ 394 (516)
T TIGR00717 359 VGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISW 394 (516)
T ss_pred CCCEEEEEEEEEecceEEEECCCCCEEEEEHHHCcC
Confidence 699999999999999999999843346666666653
No 84
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=84.52 E-value=1 Score=41.73 Aligned_cols=40 Identities=20% Similarity=0.193 Sum_probs=30.7
Q ss_pred eeecCCCEEE-EEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 77 FRPFVGEIIA-AKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 77 frP~~~EVl~-g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
..|..|++++ |+|+++.++|+||.+++--+-+++.+.|..
T Consensus 749 ~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~ 789 (891)
T PLN00207 749 MVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSS 789 (891)
T ss_pred cCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCC
Confidence 4689999996 699999999999999764444555555643
No 85
>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=83.97 E-value=2.3 Score=28.42 Aligned_cols=38 Identities=11% Similarity=0.175 Sum_probs=30.5
Q ss_pred eeecCCCEEEEEEEEEccCceEEEeCccceEEecCCCC
Q 032987 77 FRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLL 114 (129)
Q Consensus 77 frP~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~l 114 (129)
|.|..|.++.|+|++++..+-++.+|-......|...+
T Consensus 2 Y~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f 39 (86)
T cd05790 2 YVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAF 39 (86)
T ss_pred CcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHc
Confidence 68999999999999999999999996544455554433
No 86
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=83.38 E-value=1.5 Score=37.33 Aligned_cols=36 Identities=14% Similarity=0.101 Sum_probs=30.3
Q ss_pred cCCCEEEEEEEEEccCceEEEeCccceEEecCCCCC
Q 032987 80 FVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLP 115 (129)
Q Consensus 80 ~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp 115 (129)
..|+++.|+|++++++|+|+.+|+--..++|.+.+.
T Consensus 271 ~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels 306 (516)
T TIGR00717 271 PVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMS 306 (516)
T ss_pred cCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcC
Confidence 479999999999999999999986545788866665
No 87
>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=81.84 E-value=3.1 Score=27.74 Aligned_cols=38 Identities=16% Similarity=0.294 Sum_probs=30.1
Q ss_pred eeecCCCEEEEEEEEEccCceEEEe---------CccceEEecCCCC
Q 032987 77 FRPFVGEIIAAKLKESDANGLRLSL---------GFFEDIYVPSHLL 114 (129)
Q Consensus 77 frP~~~EVl~g~V~~v~~~Gi~v~~---------G~~~~i~i~~~~l 114 (129)
+-|..|.++.|+|++++...+.+.+ .++.++.+.++..
T Consensus 2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~ 48 (92)
T cd05791 2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIR 48 (92)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHcc
Confidence 5699999999999999999999987 3555666654433
No 88
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=81.33 E-value=1.8 Score=38.45 Aligned_cols=35 Identities=26% Similarity=0.385 Sum_probs=30.8
Q ss_pred CCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
.|+++.|+|+++++.|+++.+|-. +.|+|.+.+..
T Consensus 389 ~G~iv~g~V~~v~~~G~~V~lggi-~gfiP~sel~~ 423 (647)
T PRK00087 389 NGEPVKGKVKEVVKGGLLVDYGGV-RAFLPASHVEL 423 (647)
T ss_pred CCCEEEEEEEEEECCeEEEEECCE-EEEEEHHHhCc
Confidence 599999999999999999999875 58999877754
No 89
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=81.33 E-value=1.9 Score=37.30 Aligned_cols=36 Identities=17% Similarity=0.051 Sum_probs=29.9
Q ss_pred cCCCEEEEEEEEEccCceEEEeCccceEEecCCCCC
Q 032987 80 FVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLP 115 (129)
Q Consensus 80 ~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp 115 (129)
..|+++.|+|++++++|+|+.+++--+.++|.+.|.
T Consensus 285 ~~G~~v~g~V~~i~~~G~fV~l~~~v~Glv~~sel~ 320 (565)
T PRK06299 285 PVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMS 320 (565)
T ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCCEEEEEHHHcC
Confidence 459999999999999999999986445777766664
No 90
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=80.98 E-value=2 Score=37.18 Aligned_cols=38 Identities=13% Similarity=0.212 Sum_probs=32.0
Q ss_pred ecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
...|+++.|+|.++++.|++|.+|-=-.-|+|...+.+
T Consensus 28 ~~~G~~v~G~V~~v~~~~~~Vdig~k~~g~lp~~e~~~ 65 (565)
T PRK06299 28 TREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKN 65 (565)
T ss_pred CCCCCEEEEEEEEEECCEEEEEeCCCeEEEEEHHHhcC
Confidence 45899999999999999999999863357888877754
No 91
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=80.62 E-value=2.8 Score=38.70 Aligned_cols=34 Identities=15% Similarity=0.225 Sum_probs=28.6
Q ss_pred CCCEEEEEEEEEccCceEEEeCccceEEecCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLP 115 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp 115 (129)
.|++++|+|++++++|+||.+|-.+ -|+|.+.|.
T Consensus 493 ~G~~V~G~Vk~i~~~G~fVdl~Gv~-Gfvp~SeiS 526 (863)
T PRK12269 493 IEDSVSGVVKSFTSFGAFIDLGGFD-GLLHVNDMS 526 (863)
T ss_pred CCCEEEEEEEEEeCCcEEEEECCEE-EEEEchhcc
Confidence 4789999999999999999998765 677766664
No 92
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=75.58 E-value=3.3 Score=36.82 Aligned_cols=40 Identities=15% Similarity=0.239 Sum_probs=33.5
Q ss_pred EeeecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCC
Q 032987 76 VFRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLP 115 (129)
Q Consensus 76 vfrP~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp 115 (129)
......|+++.|+|.++++.|+++.+|.--.-++|...+.
T Consensus 297 ~~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els 336 (647)
T PRK00087 297 EKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELT 336 (647)
T ss_pred HhhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhc
Confidence 3457889999999999999999999987555788877665
No 93
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=75.17 E-value=4.7 Score=36.23 Aligned_cols=45 Identities=20% Similarity=0.135 Sum_probs=32.9
Q ss_pred ecCCCEEEEEEEEEccCceEEEeC-c-cceEEecCCCCCCCCCcCCCCC
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLG-F-FEDIYVPSHLLPSPSRSEPDPY 125 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G-~-~~~i~i~~~~lp~~~~f~~d~~ 125 (129)
=..||..+|.|+.++.+|+||.+- + +++..+++..-.+.+.| ++.
T Consensus 620 ~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~--~~~ 666 (706)
T COG0557 620 KRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHF--DER 666 (706)
T ss_pred HhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeee--ccc
Confidence 346799999999999999999994 3 56665554444457777 553
No 94
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=75.01 E-value=3.8 Score=37.88 Aligned_cols=37 Identities=14% Similarity=0.087 Sum_probs=29.6
Q ss_pred CCCEEEEEEEEEccCceEEEeCccceEEecCCCCCCC
Q 032987 81 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSP 117 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~~ 117 (129)
.|.+++|+|++++++|+||.++.--+-++|...++++
T Consensus 752 vG~iV~GkV~~v~~~GvFVeL~~gVeGlI~~s~lsdd 788 (863)
T PRK12269 752 VGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVEN 788 (863)
T ss_pred CCCEEEEEEEEEecCeEEEEcCCCeEEEEEHHHcCCc
Confidence 6999999999999999999995322467777777654
No 95
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=73.38 E-value=4.8 Score=33.80 Aligned_cols=43 Identities=12% Similarity=0.173 Sum_probs=33.5
Q ss_pred eeecCCCEEEEEEEEEccC-ceEEEeCccceEEecCCCCCCCCCc
Q 032987 77 FRPFVGEIIAAKLKESDAN-GLRLSLGFFEDIYVPSHLLPSPSRS 120 (129)
Q Consensus 77 frP~~~EVl~g~V~~v~~~-Gi~v~~G~~~~i~i~~~~lp~~~~f 120 (129)
|++..||++.|+|..++.. ++++.+|=.+ .+.|+...-+.-.|
T Consensus 134 y~~~~Geiv~g~V~r~~~~~~i~vdlg~~e-a~LP~~eqip~E~~ 177 (374)
T PRK12328 134 YKKKVGKIVFGTVVRVDNEENTFIEIDEIR-AVLPMKNRIKGEKF 177 (374)
T ss_pred HHHhcCcEEEEEEEEEecCCCEEEEcCCeE-EEeCHHHcCCCCcC
Confidence 7889999999999999874 5999999764 66666555545556
No 96
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=71.35 E-value=3.6 Score=37.55 Aligned_cols=39 Identities=18% Similarity=0.188 Sum_probs=32.7
Q ss_pred eecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 78 RPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
--..|-+++|+|+++.++|+||.+|-=++..|..+.|-+
T Consensus 655 dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~ 693 (780)
T COG2183 655 DLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSD 693 (780)
T ss_pred hccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhh
Confidence 356799999999999999999999998887666666654
No 97
>PRK05054 exoribonuclease II; Provisional
Probab=69.65 E-value=7.5 Score=34.69 Aligned_cols=41 Identities=20% Similarity=0.321 Sum_probs=31.0
Q ss_pred eeecCC--CEEEEEEEEEccCceEEEeCcc-ceEEecCCCCCCC
Q 032987 77 FRPFVG--EIIAAKLKESDANGLRLSLGFF-EDIYVPSHLLPSP 117 (129)
Q Consensus 77 frP~~~--EVl~g~V~~v~~~Gi~v~~G~~-~~i~i~~~~lp~~ 117 (129)
.+...| +..+|.|+.++++|+||.+--. -.-+||...|++.
T Consensus 555 ~~~~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~ 598 (644)
T PRK05054 555 LKDKAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAV 598 (644)
T ss_pred HhhccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCC
Confidence 556665 4999999999999999999522 2356777777663
No 98
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=69.37 E-value=5.6 Score=35.88 Aligned_cols=41 Identities=20% Similarity=0.025 Sum_probs=31.7
Q ss_pred EEeeecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCC
Q 032987 75 VVFRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLP 115 (129)
Q Consensus 75 lvfrP~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp 115 (129)
++=.|..||+..|+|+.+.++|+|+.+.|=.+-.+..+.+.
T Consensus 613 i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~ 653 (692)
T COG1185 613 ITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLA 653 (692)
T ss_pred HHhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhh
Confidence 34568899999999999999999999977655444444444
No 99
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=67.82 E-value=5.6 Score=34.98 Aligned_cols=41 Identities=10% Similarity=0.154 Sum_probs=35.4
Q ss_pred EeeecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCCC
Q 032987 76 VFRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 76 vfrP~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
...+..|.++.|+|+++++.++++.+|--..-+||.+.+..
T Consensus 16 ~~~~~~G~vV~G~Vv~i~~~~v~Vdig~Kseg~ip~~E~~~ 56 (541)
T COG0539 16 DEEFEPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSN 56 (541)
T ss_pred hhccCCCCEEEEEEEEEeCCeEEEEecCccccEeEHHHhcc
Confidence 45678899999999999999999999977778888777764
No 100
>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=67.81 E-value=9.1 Score=34.17 Aligned_cols=40 Identities=18% Similarity=0.276 Sum_probs=30.4
Q ss_pred eeecCC--CEEEEEEEEEccCceEEEe-CccceEEecCCCCCC
Q 032987 77 FRPFVG--EIIAAKLKESDANGLRLSL-GFFEDIYVPSHLLPS 116 (129)
Q Consensus 77 frP~~~--EVl~g~V~~v~~~Gi~v~~-G~~~~i~i~~~~lp~ 116 (129)
++...| +..+|.|+.++++|+||.+ ...-.-+||...|++
T Consensus 551 l~~~~g~~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~ 593 (639)
T TIGR02062 551 LADKAAKNTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHA 593 (639)
T ss_pred HhhccCCCcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCC
Confidence 455554 4899999999999999998 332247788888876
No 101
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: 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 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=64.06 E-value=24 Score=22.81 Aligned_cols=35 Identities=23% Similarity=0.448 Sum_probs=30.1
Q ss_pred CCEEEEEEEEEccCceEEEeCccc-eEEecCCCCCC
Q 032987 82 GEIIAAKLKESDANGLRLSLGFFE-DIYVPSHLLPS 116 (129)
Q Consensus 82 ~EVl~g~V~~v~~~Gi~v~~G~~~-~i~i~~~~lp~ 116 (129)
|.+++|+|.+-++.++.+.+++.+ .-++|...+.|
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD 36 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSD 36 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCC
Confidence 578999999999999999999853 25789888877
No 102
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=60.58 E-value=14 Score=29.91 Aligned_cols=38 Identities=34% Similarity=0.378 Sum_probs=33.8
Q ss_pred cCCCEEEEEEEEEc-cCceEEEeCccceEEecCCCCCCC
Q 032987 80 FVGEIIAAKLKESD-ANGLRLSLGFFEDIYVPSHLLPSP 117 (129)
Q Consensus 80 ~~~EVl~g~V~~v~-~~Gi~v~~G~~~~i~i~~~~lp~~ 117 (129)
-.||---++|++++ ..|+|+..|.=.++++|.+.+|..
T Consensus 72 tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~ 110 (287)
T COG2996 72 TVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTL 110 (287)
T ss_pred eecceeEEEEEEEcCCcceEEecCCCcceeeehhhcccc
Confidence 46777889999999 889999999778999999999974
No 103
>PF07238 PilZ: PilZ domain; InterPro: IPR009875 The ubiquitous bacterial second messenger cyclic-di-GMP (c-di-GMP) is associated with the regulation of biofilm formation, the control of exopolysaccharide synthesis, flagellar- and pili-based motility, gene expression, interactions of bacteria with eukaryotic hosts and multicellular behaviour in diverse bacteria. With the exception of bacterial cellulose synthases, the identities of c-di-GMP receptors and end targets of the proteins having one or more PilZ domains are mostly uncharacterised. However it was suggested that the PilZ domains present in the BcsA subunits of bacterial cellulose synthases function in c-di-GMP binding []. More recently YcgR (see IPR023787 from INTERPRO) was found to bind c-di-GMP tightly and specifically; also isolated PilZ domains from YcgR and BcsA bound c-di-GMP indicating that the PilZ domain was sufficient for binding of c-di-GMP and significantly that site-directed mutagenesis performed on YcgR implicated the most conserved residues in the PilZ domain directly in c-di-GMP binding []. It was suggested that c-di-GMP binding to PilZ brings about conformational changes in the protein that stabilise the bound ligand and probability initiates the downstream signal transduction cascade. In the case of YcgR, c-di-GMP binding regulates flagellum-based motility in a c-di-GMP-dependent manner (see IPR023787 from INTERPRO) []. The association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Binding and mutagenesis studies of several PilZ domain proteins have confirmed this observation and demonstrated that c-di-GMP binding depends on residues in RxxxR and D/NxSxxG sequence motifs. The crystal structure, at 1.7 A, of a PilZ domain::c-di-GMP complex from Vibrio cholerae shows c-di-GMP contacting seven of nine strongly conserved residues. Binding of c-di-GMP causes a conformational switch whereby the C- and N-terminal domains are brought into close opposition forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface []. ; GO: 0035438 cyclic-di-GMP binding; PDB: 2RDE_B 1YLN_A 3KYG_A 3DSG_B 2GJG_A 3KYF_A 1YWU_A 2L74_A 2L1T_A 3CNR_A ....
Probab=58.71 E-value=42 Score=20.93 Aligned_cols=35 Identities=11% Similarity=0.115 Sum_probs=27.8
Q ss_pred EEEEEEEEEEeeecCCCEEEEEEEEEccCceEEEe
Q 032987 67 THTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSL 101 (129)
Q Consensus 67 ~~~V~F~alvfrP~~~EVl~g~V~~v~~~Gi~v~~ 101 (129)
.+.+...+.......+..+.|.+.+++..|+.+.+
T Consensus 7 R~~~~~~~~~~~~~~~~~~~~~~~diS~~G~~~~~ 41 (102)
T PF07238_consen 7 RVPVNLPIRVILDPGGSSFQGTIVDISEGGCAFRS 41 (102)
T ss_dssp CEEEEEEEE-EEEETTEEEEEEEEEETTSEEEEEE
T ss_pred EEeccceEEEEEecCCcEEEEEEEEECccceEEEE
Confidence 34556666667788888999999999999999887
No 104
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=58.21 E-value=16 Score=30.97 Aligned_cols=39 Identities=10% Similarity=0.217 Sum_probs=32.0
Q ss_pred eecCCCEEEEEEEEEccC--ceEEEeCccceEEecCCCCCC
Q 032987 78 RPFVGEIIAAKLKESDAN--GLRLSLGFFEDIYVPSHLLPS 116 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~--Gi~v~~G~~~~i~i~~~~lp~ 116 (129)
++..|.|..|+|+++.+. |+||.+|.=.+-|+|.+.+.+
T Consensus 22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~ 62 (414)
T TIGR00757 22 RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGP 62 (414)
T ss_pred cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCc
Confidence 456899999999999999 999999986667777666543
No 105
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=55.54 E-value=19 Score=24.15 Aligned_cols=30 Identities=23% Similarity=0.319 Sum_probs=24.7
Q ss_pred eecCCCEEEEEEEEEccCceEEEe---CccceEEe
Q 032987 78 RPFVGEIIAAKLKESDANGLRLSL---GFFEDIYV 109 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~~---G~~~~i~i 109 (129)
-|..|+++. .|..+.+.|+++++ | ++++.+
T Consensus 13 ~P~v~dvv~-~Vv~i~d~~~YV~LleY~-iegmIl 45 (86)
T PHA02858 13 FPNINEVTK-GIVFVKDNIFYVKLIDYG-LEALIV 45 (86)
T ss_pred cCCCCeEEE-EEEEEeccEEEEEEecCc-cceEEe
Confidence 399999999 88899999999997 5 555544
No 106
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=55.19 E-value=18 Score=31.25 Aligned_cols=43 Identities=12% Similarity=0.243 Sum_probs=32.2
Q ss_pred eeecCCCEEEEEEEEEccCceEEEe----Cc--cceEEecCCCCCCCCCc
Q 032987 77 FRPFVGEIIAAKLKESDANGLRLSL----GF--FEDIYVPSHLLPSPSRS 120 (129)
Q Consensus 77 frP~~~EVl~g~V~~v~~~Gi~v~~----G~--~~~i~i~~~~lp~~~~f 120 (129)
|++..||++.|+|..++..++++.+ |- .+ .+.|+...-+.-.|
T Consensus 148 f~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~E-aiLP~~Eqip~E~y 196 (449)
T PRK12329 148 FQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVE-AELPKREQLPNDNY 196 (449)
T ss_pred HHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceE-EEecHHHcCCCCcC
Confidence 7889999999999999999999988 43 44 45555444334445
No 107
>PF01938 TRAM: TRAM domain; InterPro: IPR002792 The TRAM (after TRM2 and miaB) domain is a 60-70-residue-long module that is found in: Two distinct classes of tRNA-modifying enzymes, namely uridine methylases of the TRM2 family and enzymes of the miaB family that are involved in 2- methylthioadenine formation In several other proteins associated with the translation machinery In a family of small uncharacterised archaeal proteins that are predicted to have a role in the regulation of tRNA modification and/or translation The TRAM domain can be found alone or in association with other domains, such as the catalytic biotin/lipoate synthetase-like domain, the RNA methylase domain, the ribosomal S2 domain and the eIF2-beta domain. The TRAM domain is predicted to bind tRNA and deliver the RNA-modifying enzymatic domain to their targets []. Secondary structure prediction indicates that the TRAM domain adopts a simple beta-barrel fold. The conservation pattern of the TRAM domain consists primarily of small and hydrophobic residues that correspond to five beta-strands in the predicted secondary structure [].; PDB: 1YEZ_A 2BH2_A 1UWV_A 1YVC_A.
Probab=50.93 E-value=52 Score=19.61 Aligned_cols=23 Identities=22% Similarity=0.420 Sum_probs=16.5
Q ss_pred eecCCCEEEEEEEEEccCceEEE
Q 032987 78 RPFVGEIIAAKLKESDANGLRLS 100 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~ 100 (129)
.|..||.+..+|++.+++-++..
T Consensus 37 ~~~iG~~v~v~I~~~~~~~l~G~ 59 (61)
T PF01938_consen 37 LPLIGEFVKVRITKAKKNYLFGE 59 (61)
T ss_dssp -T--TEEEEEEEEEE-SSEEEEE
T ss_pred CCCCCCEEEEEEEEeeCCcEEEE
Confidence 46679999999999999877654
No 108
>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=50.41 E-value=30 Score=22.76 Aligned_cols=23 Identities=22% Similarity=0.548 Sum_probs=16.9
Q ss_pred ecCCCEEEEEEEEEccCceEEEe
Q 032987 79 PFVGEIIAAKLKESDANGLRLSL 101 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~ 101 (129)
|..|-++.|+|+++++.-+.+.+
T Consensus 2 P~vGdiV~~rVtrv~~~~a~v~I 24 (82)
T PF10447_consen 2 PKVGDIVIARVTRVNPRQAKVEI 24 (82)
T ss_dssp --TT-EEEEEEEEE-SSEEEEEE
T ss_pred CCCCCEEEEEEEEEeccEEEEEE
Confidence 88999999999999999887664
No 109
>PF05899 Cupin_3: Protein of unknown function (DUF861); InterPro: IPR008579 The function of the proteins in this entry are unknown. They contain the conserved barrel domain of the 'cupin' superfamily and members are specific to plants and bacteria.; PDB: 1RC6_A 3MYX_A 1O5U_A 2K9Z_A 1LKN_A 3ES4_A 1SFN_B 3BCW_A.
Probab=42.76 E-value=63 Score=20.28 Aligned_cols=30 Identities=10% Similarity=0.328 Sum_probs=25.4
Q ss_pred CEEEEEEEEEccCceEEEeCccceEEecCC
Q 032987 83 EIIAAKLKESDANGLRLSLGFFEDIYVPSH 112 (129)
Q Consensus 83 EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~ 112 (129)
-||+|.|+=..+.|-...+++=|-+++|+-
T Consensus 30 ~vleG~v~it~~~G~~~~~~aGD~~~~p~G 59 (74)
T PF05899_consen 30 YVLEGEVTITDEDGETVTFKAGDAFFLPKG 59 (74)
T ss_dssp EEEEEEEEEEETTTEEEEEETTEEEEE-TT
T ss_pred EEEEeEEEEEECCCCEEEEcCCcEEEECCC
Confidence 479999999999999999999887888763
No 110
>KOG0416 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.09 E-value=34 Score=25.94 Aligned_cols=71 Identities=20% Similarity=0.356 Sum_probs=44.1
Q ss_pred CCCHHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEEeeecCCCEEEEEEEEEccCceE
Q 032987 19 RLPLNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLR 98 (129)
Q Consensus 19 ~~~~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alvfrP~~~EVl~g~V~~v~~~Gi~ 98 (129)
++.++.-+.+.|.++|+=+++.+ |...|.|+|.-=.=.|..|=|..-.|.-=.+.=..
T Consensus 5 ~rRid~Dv~KL~~s~yeV~~ind----------------------~m~ef~V~f~GP~ds~YegGvWkv~V~lPd~YP~K 62 (189)
T KOG0416|consen 5 KRRIDTDVMKLLMSDYEVTIIND----------------------GMQEFYVKFHGPKDSPYEGGVWKVRVELPDNYPFK 62 (189)
T ss_pred ccchhhHHHHHHhcCCeEEEecC----------------------cccEEEEEeeCCCCCcccCceEEEEEECCCCCCCC
Confidence 34566677777777777655443 34444444444444666666666666554444333
Q ss_pred -EEeCccceEEecC
Q 032987 99 -LSLGFFEDIYVPS 111 (129)
Q Consensus 99 -v~~G~~~~i~i~~ 111 (129)
-|+||...||||.
T Consensus 63 SPSIGFvnKIfHPN 76 (189)
T KOG0416|consen 63 SPSIGFVNKIFHPN 76 (189)
T ss_pred CCcccceeeccCCC
Confidence 5789999999984
No 111
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=34.66 E-value=43 Score=27.21 Aligned_cols=28 Identities=21% Similarity=0.323 Sum_probs=24.4
Q ss_pred ecCCCEEEEEEEEEccCceEEEeCccce
Q 032987 79 PFVGEIIAAKLKESDANGLRLSLGFFED 106 (129)
Q Consensus 79 P~~~EVl~g~V~~v~~~Gi~v~~G~~~~ 106 (129)
|-.+|++-+-|.++-++|+++++==.++
T Consensus 14 Pev~e~VmvnV~sIaemGayv~LlEYnn 41 (304)
T KOG2916|consen 14 PEVEEIVMVNVRSIAEMGAYVKLLEYNN 41 (304)
T ss_pred CCcccEEEEEeeEehhccceEeeeecCC
Confidence 8899999999999999999999854443
No 112
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=34.03 E-value=74 Score=31.65 Aligned_cols=38 Identities=24% Similarity=0.374 Sum_probs=31.7
Q ss_pred eecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCC
Q 032987 78 RPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLP 115 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp 115 (129)
--..|+++.|.|.++...|+|+.+|.--..|+|-..+-
T Consensus 1159 Dlk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ 1196 (1710)
T KOG1070|consen 1159 DLKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLS 1196 (1710)
T ss_pred hcccCceeEEEEEEecCCcEEEEEccceEEEEEccccc
Confidence 34579999999999999999999998777888844443
No 113
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 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 [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=30.61 E-value=93 Score=21.59 Aligned_cols=27 Identities=19% Similarity=0.240 Sum_probs=23.8
Q ss_pred eeecCCCEEEEEEEEEccCceEEEeCc
Q 032987 77 FRPFVGEIIAAKLKESDANGLRLSLGF 103 (129)
Q Consensus 77 frP~~~EVl~g~V~~v~~~Gi~v~~G~ 103 (129)
.-+.+|-++.|+|..+.++-+++.+|.
T Consensus 19 lG~~~gk~V~G~I~hvv~ddLYIDfG~ 45 (104)
T PF10246_consen 19 LGDPEGKIVIGKIFHVVDDDLYIDFGG 45 (104)
T ss_pred cCCccCCEEEEEEEEEecCceEEEeCC
Confidence 346789999999999999999999984
No 114
>PF09953 DUF2187: Uncharacterized protein conserved in bacteria (DUF2187); InterPro: IPR018690 This family consists of various hypothetical bacterial proteins with known function. It includes the uncharacterised YkvS protein from Bacillus subtilis.
Probab=29.16 E-value=71 Score=19.78 Aligned_cols=22 Identities=9% Similarity=0.250 Sum_probs=19.6
Q ss_pred EEEEEEEEccCceEEEeCccce
Q 032987 85 IAAKLKESDANGLRLSLGFFED 106 (129)
Q Consensus 85 l~g~V~~v~~~Gi~v~~G~~~~ 106 (129)
+.|+|.++.++.+-+.+..+++
T Consensus 16 ~~G~V~kv~eNSVIVdIT~m~~ 37 (57)
T PF09953_consen 16 FTGIVEKVYENSVIVDITIMEN 37 (57)
T ss_pred cEEEEEEEecCcEEEEEEecCC
Confidence 7999999999999999987764
No 115
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=29.13 E-value=95 Score=17.80 Aligned_cols=19 Identities=21% Similarity=0.123 Sum_probs=16.6
Q ss_pred CCCEEEEEEEEEccCceEE
Q 032987 81 VGEIIAAKLKESDANGLRL 99 (129)
Q Consensus 81 ~~EVl~g~V~~v~~~Gi~v 99 (129)
.++.++|++..+++.|..+
T Consensus 11 ~~~~~~G~~~gId~~G~L~ 29 (48)
T PF02237_consen 11 GDGEIEGIAEGIDDDGALL 29 (48)
T ss_dssp TSCEEEEEEEEEETTSEEE
T ss_pred CCeEEEEEEEEECCCCEEE
Confidence 6888999999999998763
No 116
>PF06059 DUF930: Domain of Unknown Function (DUF930); InterPro: IPR009273 This is a family of bacterial proteins with undetermined function. All bacteria in this family are from the Rhizobiales order.
Probab=26.26 E-value=1.2e+02 Score=20.82 Aligned_cols=25 Identities=16% Similarity=0.207 Sum_probs=18.7
Q ss_pred EeeeeeceeEEeCCCceEEEEEEEEEE
Q 032987 50 DIKEIEGGFVYPGEGASTHTVKFRLVV 76 (129)
Q Consensus 50 ~i~~i~~g~I~~gdG~~~~~V~F~alv 76 (129)
++.+...|-.+ ++..+|.+.|+|-|
T Consensus 47 ~~l~a~gaAFR--s~g~WY~l~F~C~v 71 (101)
T PF06059_consen 47 NVLDAPGAAFR--SRGKWYDLSFRCEV 71 (101)
T ss_pred CEEecCCcEEe--cCCeEEEEEEEEEE
Confidence 34555666666 78899999999854
No 117
>PRK15464 cold shock-like protein CspH; Provisional
Probab=25.91 E-value=1.6e+02 Score=18.57 Aligned_cols=43 Identities=16% Similarity=0.162 Sum_probs=33.3
Q ss_pred eeceeEEeCCCceEEEEEEEEEE---e-eecCCCEEEEEEEEEccCce
Q 032987 54 IEGGFVYPGEGASTHTVKFRLVV---F-RPFVGEIIAAKLKESDANGL 97 (129)
Q Consensus 54 i~~g~I~~gdG~~~~~V~F~alv---f-rP~~~EVl~g~V~~v~~~Gi 97 (129)
-|-|.|.+.+|.--.=|.++++- + +|..|+.++-.|..-. .|.
T Consensus 16 KGfGFI~~~~g~~DvFvH~s~l~~~g~~~l~~G~~V~f~v~~~~-kG~ 62 (70)
T PRK15464 16 SGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGL-RGP 62 (70)
T ss_pred CCeEEEccCCCCccEEEEehhehhcCCCCCCCCCEEEEEEEECC-CCc
Confidence 46789999998877778888885 4 5899999998887643 344
No 118
>PRK10943 cold shock-like protein CspC; Provisional
Probab=25.19 E-value=1.8e+02 Score=18.10 Aligned_cols=44 Identities=18% Similarity=0.301 Sum_probs=34.7
Q ss_pred eeceeEEeCCCceEEEEEEEEEEe----eecCCCEEEEEEEEEccCceE
Q 032987 54 IEGGFVYPGEGASTHTVKFRLVVF----RPFVGEIIAAKLKESDANGLR 98 (129)
Q Consensus 54 i~~g~I~~gdG~~~~~V~F~alvf----rP~~~EVl~g~V~~v~~~Gi~ 98 (129)
-+-|.|.+.+|.--+-+.++++-- +|..|+.++-.+..-.+ |..
T Consensus 15 kGfGFI~~~~g~~dvFvH~s~l~~~g~~~l~~G~~V~f~~~~~~~-g~~ 62 (69)
T PRK10943 15 KGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQK-GPA 62 (69)
T ss_pred CCcEEEecCCCCeeEEEEhhHccccCCCCCCCCCEEEEEEEECCC-Cce
Confidence 477999999988777788888874 48899999998877554 544
No 119
>PRK15463 cold shock-like protein CspF; Provisional
Probab=25.09 E-value=1.4e+02 Score=18.78 Aligned_cols=43 Identities=14% Similarity=0.169 Sum_probs=33.4
Q ss_pred eeceeEEeCCCceEEEEEEEEEEe----eecCCCEEEEEEEEEccCce
Q 032987 54 IEGGFVYPGEGASTHTVKFRLVVF----RPFVGEIIAAKLKESDANGL 97 (129)
Q Consensus 54 i~~g~I~~gdG~~~~~V~F~alvf----rP~~~EVl~g~V~~v~~~Gi 97 (129)
-+-|.|.|.+|.--.=|.++++-- +|-.|+.+.=.+.. ++.|.
T Consensus 16 kGfGFI~~~~g~~DvFvH~sal~~~g~~~l~~G~~V~f~v~~-~~~G~ 62 (70)
T PRK15463 16 SGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRIN-GLRGP 62 (70)
T ss_pred CceEEEecCCCCccEEEEehhhhhcCCCCCCCCCEEEEEEEE-CCCCc
Confidence 477999999998888888888864 49999999987765 33443
No 120
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=24.95 E-value=3.2e+02 Score=21.54 Aligned_cols=39 Identities=10% Similarity=0.165 Sum_probs=35.2
Q ss_pred ceEEEEEEEEEEeeecCCCEEEEEEEEEccCceEEEeCc
Q 032987 65 ASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGF 103 (129)
Q Consensus 65 ~~~~~V~F~alvfrP~~~EVl~g~V~~v~~~Gi~v~~G~ 103 (129)
+-.+.|..+-.=|-|-+|..+.|.|++....+..|.+|=
T Consensus 49 ~~v~~vds~~kRYiP~~~D~VIGiV~~~~gd~ykVDigg 87 (230)
T KOG1004|consen 49 GGVYWVDSQQKRYIPVKGDHVIGIVTSKSGDIYKVDIGG 87 (230)
T ss_pred ceeEEEecccceecCCCCCEEEEEEEeccCceEEEecCC
Confidence 336788889999999999999999999999999999986
No 121
>PRK14555 hypothetical protein; Provisional
Probab=24.84 E-value=1.8e+02 Score=20.99 Aligned_cols=49 Identities=10% Similarity=0.018 Sum_probs=29.8
Q ss_pred HHHHHHHhcCeEeCCeeEEEEEEEeee-eeceeEEeCCCceEEEEEEEEE
Q 032987 27 KLELENVFLDKVIANLGLCISIYDIKE-IEGGFVYPGEGASTHTVKFRLV 75 (129)
Q Consensus 27 ~~~L~~k~~gk~~~~~G~~I~v~~i~~-i~~g~I~~gdG~~~~~V~F~al 75 (129)
.+.|++...-++..+..+.+-+-+-.- .|.=++..|||.++.++++++-
T Consensus 78 ~~~l~~~l~~r~de~~~l~lRldKQaAy~G~v~l~~gdd~I~v~ik~~~y 127 (145)
T PRK14555 78 LEKLLSELDERVDDEGKLYLRFDKQAAYLGELKLSDGDDVIRLKIKVKAY 127 (145)
T ss_pred HHHHHHHHHHhCcCCCEEEEEEehHHHhCCCEEeccCCccEEEEEEEeec
Confidence 334445555555545567776665432 2445555577889999888764
No 122
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=23.88 E-value=1.2e+02 Score=24.56 Aligned_cols=37 Identities=19% Similarity=0.159 Sum_probs=30.2
Q ss_pred eecCCCEEEEEEEEEccCceEEEeCccceEEecCCCCC
Q 032987 78 RPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLP 115 (129)
Q Consensus 78 rP~~~EVl~g~V~~v~~~Gi~v~~G~~~~i~i~~~~lp 115 (129)
+|-.||+-+|.|.+....|.++.+|--..+.++++ .+
T Consensus 102 ~~~~Ge~ReG~v~~~~~~~~~v~iG~~~~~~l~~~-~~ 138 (272)
T COG2106 102 SPKEGEYREGLVIRRGKKGNLVDIGKDKLAKLSSP-AP 138 (272)
T ss_pred CccceeecceEEEEecCCceEEEecCCcceeccCC-CC
Confidence 68899999999999999999999997655555554 44
No 123
>COG1278 CspC Cold shock proteins [Transcription]
Probab=22.72 E-value=78 Score=20.16 Aligned_cols=37 Identities=16% Similarity=0.225 Sum_probs=27.3
Q ss_pred eeceeEEeCCCceEEEEEEEEEE----eeecCCCEEEEEEE
Q 032987 54 IEGGFVYPGEGASTHTVKFRLVV----FRPFVGEIIAAKLK 90 (129)
Q Consensus 54 i~~g~I~~gdG~~~~~V~F~alv----frP~~~EVl~g~V~ 90 (129)
-+-|.|.|.||+.-+=|.|+||- =++..|+.+.=.+.
T Consensus 13 KGfGFI~p~~G~~DvFVH~Sai~~~g~~~L~eGQ~V~f~~~ 53 (67)
T COG1278 13 KGFGFITPEDGGKDVFVHISAIQRAGFRTLREGQKVEFEVE 53 (67)
T ss_pred CcceEcCCCCCCcCEEEEeeeeccCCCcccCCCCEEEEEEe
Confidence 47899999999999999999985 34555665554443
No 124
>smart00700 JHBP Juvenile hormone binding protein domains in insects. The juvenile hormone exerts pleiotropic functions during insect life cycles and its binding proteins regulate these functions.
Probab=21.74 E-value=2.5e+02 Score=21.00 Aligned_cols=66 Identities=27% Similarity=0.291 Sum_probs=38.4
Q ss_pred ECCCCCCCC---HHHHHHHHHHHHhcCeEeCCeeEEEEEEEeeeeeceeEEeCCCceEEEEEEEEEEeeecCC
Q 032987 13 LPPHLLRLP---LNEAIKLELENVFLDKVIANLGLCISIYDIKEIEGGFVYPGEGASTHTVKFRLVVFRPFVG 82 (129)
Q Consensus 13 I~P~~~~~~---~~~~i~~~L~~k~~gk~~~~~G~~I~v~~i~~i~~g~I~~gdG~~~~~V~F~alvfrP~~~ 82 (129)
+.|+..+.+ +.+++...+.....| .++.| |-..|-..+.+-.+..++|.+.++..|+=+..+=+.+
T Consensus 7 ~~~C~~~dp~~Ci~~~~~~~~~~~~~G--~Pe~g--ip~ldPl~i~~~~i~~~~~~~~~~~~~~n~~i~Gl~~ 75 (225)
T smart00700 7 LKPCKLGDPSECLRDAIEALLPQLKNG--IPEYG--IPPLDPLEIDDLKISIGSGVIGLRLTFKNVKIYGLSN 75 (225)
T ss_pred CCcCCCCChhHHHHHHHHHHHHHHhcC--CCccC--CCCcCCEEeeeEEEecCCCceEEEEEEEEeEEEcCcc
Confidence 456677653 455555555555555 45666 4445555555555655667777777776655555544
No 125
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=21.21 E-value=4.3e+02 Score=21.00 Aligned_cols=38 Identities=18% Similarity=0.431 Sum_probs=31.7
Q ss_pred EeeecCCCEEEEEEEEEccCceEEEeC-ccceEEecCCCC
Q 032987 76 VFRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLL 114 (129)
Q Consensus 76 vfrP~~~EVl~g~V~~v~~~Gi~v~~G-~~~~i~i~~~~l 114 (129)
-|.|-.|.++.|.|.++...+-.+.+| |+. ...|-+.+
T Consensus 59 ~YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~-A~L~ls~~ 97 (239)
T COG1097 59 RYIPEVGDVVIGKIIEVGPSGWKVDIGSPYP-ALLSLSDF 97 (239)
T ss_pred cccCCCCCEEEEEEEEEcccceEEEcCCccc-eEeehhhh
Confidence 688999999999999999999999996 564 55555555
No 126
>PF03789 ELK: ELK domain ; InterPro: IPR005539 This domain is required for the nuclear localisation of these proteins []. All of these proteins are members of the Tale/Knox homeodomain family, a subfamily, containing homeobox IPR001356 from INTERPRO.; GO: 0003677 DNA binding, 0005634 nucleus
Probab=20.62 E-value=49 Score=16.55 Aligned_cols=13 Identities=15% Similarity=0.250 Sum_probs=10.3
Q ss_pred HHHHHHHHhcCeE
Q 032987 26 IKLELENVFLDKV 38 (129)
Q Consensus 26 i~~~L~~k~~gk~ 38 (129)
++..|.+||.|.+
T Consensus 2 LK~~LlrkY~g~i 14 (22)
T PF03789_consen 2 LKHQLLRKYSGYI 14 (22)
T ss_pred HHHHHHHHHhHhH
Confidence 5778889998865
No 127
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=20.25 E-value=2.6e+02 Score=18.14 Aligned_cols=37 Identities=27% Similarity=0.391 Sum_probs=28.7
Q ss_pred eCCCceEEEEEEEEEEeee--cCCCEEEEEEEEEccCceEEE
Q 032987 61 PGEGASTHTVKFRLVVFRP--FVGEIIAAKLKESDANGLRLS 100 (129)
Q Consensus 61 ~gdG~~~~~V~F~alvfrP--~~~EVl~g~V~~v~~~Gi~v~ 100 (129)
.|||-+.++ -.+||-| -.||.+.=+|+++.++=+|..
T Consensus 29 ~GDGiarve---GfvVFVp~a~~Gd~V~vkI~~v~~~~afae 67 (73)
T COG3269 29 QGDGIARVE---GFVVFVPGAEVGDEVKVKITKVKPNFAFAE 67 (73)
T ss_pred CCCceEEEE---EEEEEeCCCCCCCeeeEEEEEeeccceeeE
Confidence 567777777 5566666 689999999999988866654
Done!