Query 002793
Match_columns 880
No_of_seqs 396 out of 1879
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 07:14:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002793.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002793hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK11642 exoribonuclease R; Pr 100.0 4E-124 8E-129 1128.7 65.3 628 43-791 75-710 (813)
2 TIGR00358 3_prime_RNase VacB a 100.0 3E-123 7E-128 1107.5 67.3 612 59-791 19-639 (654)
3 TIGR02063 RNase_R ribonuclease 100.0 2E-119 4E-124 1087.0 66.7 613 59-791 71-694 (709)
4 PRK05054 exoribonuclease II; P 100.0 1E-116 3E-121 1046.4 64.7 597 59-791 24-629 (644)
5 COG0557 VacB Exoribonuclease R 100.0 2E-115 4E-120 1049.9 63.1 625 42-791 59-689 (706)
6 TIGR02062 RNase_B exoribonucle 100.0 5E-115 1E-119 1031.2 65.1 596 59-791 21-625 (639)
7 KOG2102 Exosomal 3'-5' exoribo 100.0 5E-107 1E-111 986.0 44.3 574 115-805 338-915 (941)
8 PF00773 RNB: RNB domain CAUTI 100.0 3.2E-75 7E-80 644.1 29.2 320 276-628 1-324 (325)
9 COG4776 Rnb Exoribonuclease II 100.0 1.1E-67 2.3E-72 572.4 21.7 591 59-786 24-624 (645)
10 cd04471 S1_RNase_R S1_RNase_R: 98.2 5.6E-06 1.2E-10 73.3 8.9 66 723-790 2-67 (83)
11 cd04460 S1_RpoE S1_RpoE: RpoE, 97.1 0.0017 3.6E-08 60.1 7.7 62 725-790 2-63 (99)
12 PF08206 OB_RNB: Ribonuclease 97.1 0.00025 5.5E-09 59.4 1.8 52 61-123 4-58 (58)
13 TIGR00448 rpoE DNA-directed RN 96.9 0.00075 1.6E-08 69.3 4.2 75 713-791 72-146 (179)
14 cd05686 S1_pNO40 S1_pNO40: pNO 96.8 0.0032 7E-08 54.9 6.1 57 722-791 3-59 (73)
15 cd05684 S1_DHX8_helicase S1_DH 96.1 0.012 2.7E-07 51.8 5.8 57 723-791 1-59 (79)
16 COG1095 RPB7 DNA-directed RNA 95.7 0.017 3.8E-07 59.0 5.7 71 719-793 78-148 (183)
17 cd05689 S1_RPS1_repeat_ec4 S1_ 95.5 0.035 7.5E-07 47.9 6.2 57 722-791 3-59 (72)
18 PRK08582 hypothetical protein; 95.5 0.029 6.4E-07 55.4 6.4 57 721-791 4-60 (139)
19 PRK08563 DNA-directed RNA poly 95.5 0.042 9.1E-07 56.8 7.7 70 718-791 77-146 (187)
20 cd05706 S1_Rrp5_repeat_sc10 S1 95.5 0.035 7.5E-07 48.0 6.0 56 722-791 3-58 (73)
21 cd05697 S1_Rrp5_repeat_hs5 S1_ 95.4 0.028 6E-07 48.2 5.2 55 723-791 1-55 (69)
22 cd05708 S1_Rrp5_repeat_sc12 S1 95.3 0.04 8.8E-07 47.7 5.9 56 722-790 2-57 (77)
23 cd05690 S1_RPS1_repeat_ec5 S1_ 95.2 0.033 7.2E-07 47.4 5.1 56 723-791 1-56 (69)
24 cd04452 S1_IF2_alpha S1_IF2_al 95.2 0.047 1E-06 47.4 5.9 57 722-791 3-60 (76)
25 PF00575 S1: S1 RNA binding do 95.1 0.072 1.6E-06 46.0 6.8 57 721-791 3-59 (74)
26 cd05707 S1_Rrp5_repeat_sc11 S1 94.7 0.051 1.1E-06 46.4 4.8 55 723-791 1-55 (68)
27 cd05685 S1_Tex S1_Tex: The C-t 94.6 0.052 1.1E-06 45.5 4.6 54 723-790 1-54 (68)
28 PLN00207 polyribonucleotide nu 94.4 0.069 1.5E-06 66.6 6.9 62 715-790 746-808 (891)
29 cd05696 S1_Rrp5_repeat_hs4 S1_ 94.4 0.069 1.5E-06 46.4 4.9 55 723-791 1-57 (71)
30 PF08206 OB_RNB: Ribonuclease 94.4 0.13 2.9E-06 43.1 6.4 50 166-228 9-58 (58)
31 PRK07252 hypothetical protein; 94.1 0.097 2.1E-06 50.5 5.9 55 722-790 3-57 (120)
32 cd05698 S1_Rrp5_repeat_hs6_sc5 94.0 0.092 2E-06 44.9 4.8 55 723-791 1-55 (70)
33 cd04461 S1_Rrp5_repeat_hs8_sc7 93.8 0.1 2.2E-06 46.5 5.0 57 721-791 13-69 (83)
34 PRK05807 hypothetical protein; 93.8 0.13 2.8E-06 50.7 6.2 55 721-790 4-58 (136)
35 cd05705 S1_Rrp5_repeat_hs14 S1 93.3 0.13 2.8E-06 45.2 4.8 59 722-791 3-61 (74)
36 cd04472 S1_PNPase S1_PNPase: P 93.2 0.17 3.8E-06 42.5 5.2 54 723-790 1-54 (68)
37 cd05688 S1_RPS1_repeat_ec3 S1_ 92.3 0.32 7E-06 40.8 5.7 54 723-791 2-55 (68)
38 cd05692 S1_RPS1_repeat_hs4 S1_ 92.2 0.26 5.7E-06 41.3 5.0 54 723-790 1-54 (69)
39 smart00316 S1 Ribosomal protei 92.2 0.31 6.7E-06 40.7 5.4 56 722-791 2-57 (72)
40 cd05703 S1_Rrp5_repeat_hs12_sc 91.5 0.37 8E-06 42.1 5.2 57 723-791 1-57 (73)
41 cd05691 S1_RPS1_repeat_ec6 S1_ 91.4 0.39 8.5E-06 41.1 5.3 54 723-790 1-54 (73)
42 cd04473 S1_RecJ_like S1_RecJ_l 91.4 0.5 1.1E-05 41.6 6.0 49 721-791 15-63 (77)
43 PTZ00248 eukaryotic translatio 90.7 0.31 6.7E-06 54.5 4.9 38 722-759 17-55 (319)
44 PRK03987 translation initiatio 90.7 0.38 8.3E-06 52.5 5.5 56 722-790 8-64 (262)
45 PRK08059 general stress protei 89.9 0.56 1.2E-05 45.3 5.4 56 721-790 6-61 (123)
46 PRK11824 polynucleotide phosph 89.5 1.1 2.4E-05 55.5 8.9 58 720-791 619-676 (693)
47 PTZ00162 DNA-directed RNA poly 89.3 0.79 1.7E-05 47.2 6.2 71 718-791 77-147 (176)
48 PRK07899 rpsA 30S ribosomal pr 89.0 1.3 2.8E-05 52.5 8.6 71 721-805 292-368 (486)
49 cd05702 S1_Rrp5_repeat_hs11_sc 88.9 0.82 1.8E-05 39.3 5.2 57 723-791 1-57 (70)
50 TIGR02063 RNase_R ribonuclease 88.8 1.3 2.8E-05 55.1 8.8 58 166-235 79-137 (709)
51 cd05695 S1_Rrp5_repeat_hs3 S1_ 88.7 1 2.2E-05 38.5 5.5 53 723-791 1-53 (66)
52 TIGR03591 polynuc_phos polyrib 88.3 1.1 2.4E-05 55.3 7.7 58 720-791 616-673 (684)
53 PHA02945 interferon resistance 88.2 1.6 3.4E-05 39.8 6.4 42 721-763 10-54 (88)
54 cd05704 S1_Rrp5_repeat_hs13 S1 87.8 0.9 1.9E-05 39.5 4.7 56 722-791 3-59 (72)
55 PRK12269 bifunctional cytidyla 86.7 0.92 2E-05 57.3 5.7 60 721-791 751-810 (863)
56 cd00164 S1_like S1_like: Ribos 86.6 1.2 2.7E-05 36.2 4.8 51 727-791 2-52 (65)
57 cd04453 S1_RNase_E S1_RNase_E: 85.8 1.5 3.2E-05 39.9 5.2 59 722-791 7-67 (88)
58 cd05693 S1_Rrp5_repeat_hs1_sc1 85.5 0.51 1.1E-05 44.0 2.0 66 722-790 3-76 (100)
59 PRK07400 30S ribosomal protein 85.0 1.5 3.2E-05 49.4 5.8 56 721-791 195-250 (318)
60 cd04462 S1_RNAPII_Rpb7 S1_RNAP 84.7 4.6 0.0001 36.8 7.8 65 723-791 2-66 (88)
61 COG1098 VacB Predicted RNA bin 82.6 1.3 2.7E-05 42.9 3.3 40 721-761 4-43 (129)
62 PRK07899 rpsA 30S ribosomal pr 81.8 3.6 7.8E-05 48.9 7.5 56 721-791 207-262 (486)
63 TIGR02696 pppGpp_PNP guanosine 81.1 3.8 8.1E-05 50.7 7.5 60 721-791 646-706 (719)
64 COG0539 RpsA Ribosomal protein 80.1 3.4 7.3E-05 49.4 6.4 37 721-759 191-227 (541)
65 TIGR00717 rpsA ribosomal prote 78.5 3.3 7.2E-05 49.4 5.9 57 721-791 445-501 (516)
66 PRK13806 rpsA 30S ribosomal pr 77.9 4.6 0.0001 48.1 6.8 57 721-791 201-257 (491)
67 PRK06676 rpsA 30S ribosomal pr 77.0 5.9 0.00013 45.6 7.2 56 720-790 190-245 (390)
68 cd05687 S1_RPS1_repeat_ec1_hs1 76.7 5.7 0.00012 33.8 5.3 55 723-791 1-55 (70)
69 smart00357 CSP Cold shock prot 76.7 7 0.00015 32.1 5.7 55 166-229 10-64 (64)
70 cd05694 S1_Rrp5_repeat_hs2_sc2 76.3 7.3 0.00016 34.2 6.0 37 722-758 4-40 (74)
71 PRK13806 rpsA 30S ribosomal pr 72.4 5.9 0.00013 47.2 5.8 56 721-790 378-433 (491)
72 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 72.1 6.2 0.00013 35.1 4.6 61 721-791 5-65 (86)
73 cd04465 S1_RPS1_repeat_ec2_hs2 71.2 11 0.00023 32.0 5.6 34 723-758 1-34 (67)
74 PRK00087 4-hydroxy-3-methylbut 68.4 8.1 0.00018 47.7 6.0 56 721-790 561-616 (647)
75 PRK06299 rpsA 30S ribosomal pr 64.7 8.3 0.00018 46.7 5.0 57 721-790 372-428 (565)
76 PRK06676 rpsA 30S ribosomal pr 64.4 11 0.00024 43.4 5.7 56 721-790 276-331 (390)
77 PRK12269 bifunctional cytidyla 63.6 19 0.00041 45.9 7.9 36 721-758 492-527 (863)
78 PRK00087 4-hydroxy-3-methylbut 60.1 21 0.00046 44.1 7.4 56 721-791 476-531 (647)
79 COG0539 RpsA Ribosomal protein 56.0 18 0.00039 43.5 5.5 37 720-757 275-311 (541)
80 PRK06299 rpsA 30S ribosomal pr 55.9 26 0.00056 42.5 7.1 36 721-758 200-235 (565)
81 cd04454 S1_Rrp4_like S1_Rrp4_l 55.3 27 0.00058 30.8 5.4 56 722-791 6-61 (82)
82 TIGR00717 rpsA ribosomal prote 52.0 24 0.00051 42.2 5.8 57 721-790 358-414 (516)
83 COG1093 SUI2 Translation initi 50.4 13 0.00028 40.5 2.9 40 722-761 11-51 (269)
84 smart00357 CSP Cold shock prot 50.4 19 0.00042 29.4 3.4 36 89-124 22-64 (64)
85 PRK07400 30S ribosomal protein 45.2 60 0.0013 36.6 7.3 35 722-758 118-152 (318)
86 PF08292 RNA_pol_Rbc25: RNA po 42.4 1.9E+02 0.0041 28.1 9.3 80 722-803 3-83 (122)
87 cd05699 S1_Rrp5_repeat_hs7 S1_ 41.2 48 0.0011 29.3 4.5 38 723-761 1-38 (72)
88 PRK09521 exosome complex RNA-b 40.9 42 0.00091 34.8 4.9 57 721-790 63-128 (189)
89 KOG1067 Predicted RNA-binding 33.3 41 0.00089 40.3 3.7 37 723-760 669-705 (760)
90 PRK04163 exosome complex RNA-b 31.9 73 0.0016 34.3 5.1 61 721-791 62-122 (235)
91 PHA02858 EIF2a-like PKR inhibi 31.2 75 0.0016 29.0 4.1 36 722-758 16-52 (86)
92 TIGR00358 3_prime_RNase VacB a 31.1 1.3E+02 0.0029 37.3 7.9 105 689-803 536-643 (654)
93 PRK09202 nusA transcription el 30.9 2.5E+02 0.0053 33.7 9.6 38 717-756 129-166 (470)
94 COG4871 Uncharacterized protei 27.7 92 0.002 31.7 4.5 50 454-503 63-112 (193)
95 PRK11642 exoribonuclease R; Pr 24.4 2.5E+02 0.0053 36.0 8.6 103 688-800 606-711 (813)
96 PRK12442 translation initiatio 23.7 3.4E+02 0.0074 25.0 7.0 58 722-804 5-62 (87)
97 TIGR00156 conserved hypothetic 22.0 1.7E+02 0.0037 28.7 5.2 45 753-802 67-111 (126)
98 PRK10053 hypothetical protein; 20.2 1.9E+02 0.0042 28.5 5.1 45 753-802 71-115 (130)
No 1
>PRK11642 exoribonuclease R; Provisional
Probab=100.00 E-value=3.5e-124 Score=1128.67 Aligned_cols=628 Identities=24% Similarity=0.319 Sum_probs=547.7
Q ss_pred ccccCcCccccCCCCccc-ccccceeeeeeecccCCCCCCCCCccccccccCccchhhhhc--eeEEEEecC-CCCCccE
Q 002793 43 CTLLSEKGIHHDDDSSSE-AYNQEMIEREGYNYINGHHPSTSDSTEKVSSSQQNDGMNAIE--RLSAMISSY-PTKRPTG 118 (880)
Q Consensus 43 ~~~~~~k~~~~~~~~~g~-~~h~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~--~v~~~~~~~-~~~~p~G 118 (880)
.|.+|++..... |. ..|+.||||+.. ++. .+|+||..++++.||| +|++.+... .+++|+|
T Consensus 75 ~~~~~~~~~~~~----G~v~~~~~GfgFv~~---e~~--------~~difI~~~~l~~A~~GD~V~v~i~~~~~~~r~eg 139 (813)
T PRK11642 75 CYALPERLDLLK----GTVIGHRDGYGFLRV---EGR--------KDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREA 139 (813)
T ss_pred eEecCCcCceEE----EEEEECCCccEEEEE---CCC--------CCCEEEChHHHccCCCCCEEEEEEccCCCCCCcEE
Confidence 455555433222 88 779999999632 221 1478999999999999 888887653 3467899
Q ss_pred EEEEEEecCCCCcceEEEEEeccccccCCCCcccccccCCCCCCCCCceEEEEeCCCCCCceEEecCCCChhhhhhcccC
Q 002793 119 RVVSIIERSPRRDGIVGFLNVNQWFNYKGGSRKDAKKNRSSLSVPDREYIQLTPTHPKYPKMVVLVKDLPDSIKKRLEEG 198 (880)
Q Consensus 119 ~VV~IleR~~~~~~~vG~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~D~rip~i~i~~~~~p~~~~~~~~~g 198 (880)
+|++||+|+. +.+||++.. .. +..+++|+|+|++..+.+... ....+++|
T Consensus 140 ~Vv~IleR~~--~~~vG~~~~----------------~~--------~~~~v~P~d~r~~~~i~i~~~----~~~~~~~g 189 (813)
T PRK11642 140 RIVRVLVPKT--SQIVGRYFT----------------DA--------GVGFVVPDDSRLSFDILIPPE----QIMGARMG 189 (813)
T ss_pred EEEEEEecCC--CEEEEEEEE----------------eC--------CeEEEEECCCCCCCcEEeccc----cccCCCCC
Confidence 9999999985 679999982 22 367899999999985554221 12355666
Q ss_pred CccccceEEEEEEeecCCCCCCCcEEEEEEcCCCCChhHHHHHHHHhcCCCCCCCChhhhccCCCCCCCCChhhhccCcc
Q 002793 199 DATIEMELVAARIDEWNEESPFPQAHVLHVFGRGGEVEPQINAILYENAICCSGFSPESLSCLPCVPWEVPQEELLSRKD 278 (880)
Q Consensus 199 d~~~~~~lvvv~I~~wp~~~~~p~G~iv~~LG~~~d~~~e~~ail~e~~i~~~~F~~~vl~~~~~~~~~i~~~e~~~R~D 278 (880)
| +|+|+|++||..+.+|.|+|+++||..+++.+|++++|.+|+| +.+||++++++++.+++.+++++.++|+|
T Consensus 190 d------~V~v~I~~~p~~~~~~~g~iv~vLG~~~d~~~d~~~il~~~~i-p~~Fp~~v~~ea~~~~~~~~~~~~~~R~D 262 (813)
T PRK11642 190 F------VVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEI-PYIWPQAVEQQVAGLKEEVPEEAKAGRVD 262 (813)
T ss_pred C------EEEEEEecCCCcCCCCCEEEEEEecCCCCcchHHHHHHHHcCC-CCCCCHHHHHHHHhccccCChhHhccccc
Confidence 6 8999999999999999999999999999999999999999999 57999999999999999999999999999
Q ss_pred CCCceEEEEcCCCCCCCCceEEEEEcCCceEEEEEEEccccccccCCCHhhHHHHhCcceeecCCCcccCCChhhhhccc
Q 002793 279 LRNFCIFTIDPSTATDLDDALSIERLSDGISRVGVHIADVSYFVLPGTALDIEAQVRSTSVYMLQRKIPMLPVLLSEEVG 358 (880)
Q Consensus 279 lr~l~i~TIDp~~akDlDDAlsie~l~~G~~~lgVHIADVS~yV~~gS~LD~eA~~RgtSvYLp~rviPMLP~~Ls~~lc 358 (880)
||++++|||||++|+||||||||+++++|+|+||||||||||||++||+||+||++||||||||++++||||+.|||++|
T Consensus 263 Lr~l~~vTID~~~akD~DDAvsie~~~~g~~~L~VHIADVs~yV~~gS~LD~eA~~RgtSvYlpd~viPMLP~~Lsn~lc 342 (813)
T PRK11642 263 LRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLC 342 (813)
T ss_pred cccCcEEEECCCCCCcccceEEEEEeCCCcEEEEEEecchhheeCCCCHHHHHHHHhCCeEeCCCceeeCCCHHHhcCcc
Confidence 99999999999999999999999999888999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCceEEEEEEEEEcCCCCEEEEEEEEEEEecccccCHHHHHHHHccCCCccccCccCCCCCcccCCCchhhHHHHH
Q 002793 359 SLNPGVDRLAFSIFWDLNSAGDVVDRWIGRTVIRSCCKLSYEHAQDIIDGKFDVESSNTLGEGWPQLYGQFEWSDVVRSI 438 (880)
Q Consensus 359 SL~pg~dRlA~Sv~~~id~~G~i~~~~~~~SvIrS~~rLTY~~vq~iL~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~L 438 (880)
||+||++|+||||.|+||.+|+|++++|++|+|+|+++|||++|+++|+++... . ..+.++.++|
T Consensus 343 SL~p~~dRla~s~~~~id~~G~v~~~~~~~svI~s~~rltY~~v~~~l~~~~~~--~-------------~~~~~~~~~L 407 (813)
T PRK11642 343 SLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDL--R-------------EQYAPLVKHL 407 (813)
T ss_pred ccCCCCceeEEEEEEEECCCCCCcCCEEEEEEEEECceECHHHHHHHHcCCccc--c-------------hhhhHHHHHH
Confidence 999999999999999999999999999999999999999999999999874210 0 0245678999
Q ss_pred HHHHHHHHHHHHhHhcCCCccccCCCceeeeCCCCCeEEEEecCCCcHHHHHHHHHHHHHHHHHHHHHHhCCCceeEEeC
Q 002793 439 KSLYEVSKILKDKRFTDGALRLENSKPVFLFDEYGTPYDSVLSGREDLNFLFEEFMLLANKTAAEVIARAFPDSALLRRH 518 (880)
Q Consensus 439 ~~L~~la~~Lr~~R~~~Gal~l~~pe~~i~lDe~g~p~~i~~~~~~~a~~LIEEfMilAN~~vA~~l~~~~~~~~l~R~H 518 (880)
..|+++|++|+++|+++|+|+|+.||++|.+|++|.+..+...++.+||.|||||||+||++||+|+.++ +.|++||+|
T Consensus 408 ~~l~~la~~Lr~~R~~~Gai~~d~~E~~i~ld~~g~~~~i~~~~~~~a~~lIEE~MllAN~~vA~~l~~~-~~p~lyR~H 486 (813)
T PRK11642 408 EELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKA-KEPALFRIH 486 (813)
T ss_pred HHHHHHHHHHHHHHHHCCCcccCCCceEEEECCCCCEeeEEecccccHHHHHHHHHHHHHHHHHHHHHHC-CCCEEEEeC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999875 889999999
Q ss_pred CCCChHHHHHHHHHHHHcCCccCCC---ChhHHHHHHHHHHHhhcCCHHHHHHHHHHHhcccCCcEecccCCCCCCCCcc
Q 002793 519 PAPNMRKLREFEAFCSKHGLQLDTS---SSGQFHQSLEQAREKLKDDYVLFDILINYATRPMQLASYFCSGDFKDDTDWG 595 (880)
Q Consensus 519 ~~P~~~kl~~l~~~~~~~G~~l~~~---~~~~l~~~L~~i~~~~~~~~~~~~~l~~~~lR~m~~A~Y~~sg~~~s~~~~~ 595 (880)
+.|+++++++|.+++..+|+.++.. ++..++..|..+. +.|. ..+|..+++|+|++|.| ++++.+
T Consensus 487 ~~P~~ekl~~l~~~l~~lG~~l~~~~~~~~~~~~~ll~~~~----~~~~-~~~l~~~llRsm~~A~Y-------~~~~~g 554 (813)
T PRK11642 487 DKPSTEAITSFRSVLAELGLELPGGNKPEPRDYAELLESVA----DRPD-AEMLQTMLLRSMKQAIY-------DPENRG 554 (813)
T ss_pred CCCCHHHHHHHHHHHHHcCCcccCCCCCCHHHHHHHHHHHh----CCcH-HHHHHHHHHHhcccccc-------CCCCCC
Confidence 9999999999999999999998643 2455666666654 3443 25677888999999999 568999
Q ss_pred ccccCCCCeeeccCCCCChhhHHHHHHHHHHHHhchhhhhhhccCCCCCCcccccccccc-ccccccchhhhhhhhhHHH
Q 002793 596 HYALAFPVYTHFTSPLRRYPDLVVHRTLNAALEAEKLYWKHRRMLPKNNHREGVRGRFLT-GIFYDKDAAESLEGREALS 674 (880)
Q Consensus 596 HfgL~~~~YTHFTSPIRRY~DLiVHR~L~a~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~i~~~~~~~es~~~~~~~~ 674 (880)
|||||++.||||||||||||||+|||+|+++|.++... ..|+. ..+|..
T Consensus 555 HfGLa~~~YtHFTSPIRRY~DLivHR~Lk~~L~~~~~~-----------------~~~~~~~~~~~~------------- 604 (813)
T PRK11642 555 HFGLALQSYAHFTSPIRRYPDLSLHRAIKYLLAKEQGH-----------------KGNTTETGGYHY------------- 604 (813)
T ss_pred ccccccccccccCchhhhhHHHHHHHHHHHHHhCCCCc-----------------cccccccccccc-------------
Confidence 99999999999999999999999999999999754210 00111 011211
Q ss_pred HHhhhcCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccceEEeEEEEEeeccEEEEEEecCceEEEEEee
Q 002793 675 VAALKYGVPCADILVNVATHCNDRKLACRNVKDACVKLYMWILLKKKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYD 754 (880)
Q Consensus 675 ~~~~~~~~~~~~~l~~ia~~~N~r~~~A~~a~r~s~~l~~~~~l~~~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~ 754 (880)
..+.+..+|+|||++++.|.+|+|++.++++++||+++.|.+++|+|++|.++||+|.|+++++||+||++
T Consensus 605 ---------~~~~l~~~~~~~s~~er~A~~aeR~~~~~~~~~~m~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs 675 (813)
T PRK11642 605 ---------SMEEMLQLGQHCSMTERRADEATRDVADWLKCDFMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVS 675 (813)
T ss_pred ---------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEe
Confidence 01346789999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 755 EVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 755 ~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
+|.++||+|++.+++|+| +++++.|++||.|+++.
T Consensus 676 ~L~~d~y~~d~~~~~L~g--~~~~~~~~lGD~V~VkV 710 (813)
T PRK11642 676 SLDNDYYRFDQVGQRLIG--ESSGQTYRLGDRVEVRV 710 (813)
T ss_pred ecCCcceEecchheEEec--ccCCcEECCCCEEEEEE
Confidence 999999999999999999 67889999999888774
No 2
>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=100.00 E-value=3.2e-123 Score=1107.52 Aligned_cols=612 Identities=25% Similarity=0.328 Sum_probs=538.8
Q ss_pred cc-ccccceeeeeeecccCCCCCCCCCccccccccCccchhhhhc--eeEEEEecC-CCCCccEEEEEEEecCCCCcceE
Q 002793 59 SE-AYNQEMIEREGYNYINGHHPSTSDSTEKVSSSQQNDGMNAIE--RLSAMISSY-PTKRPTGRVVSIIERSPRRDGIV 134 (880)
Q Consensus 59 g~-~~h~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~--~v~~~~~~~-~~~~p~G~VV~IleR~~~~~~~v 134 (880)
|. ..|++||||+.. ++. .+.++||..++++.||+ +|.+.+... .+++|+|+|++||+|++ +.+|
T Consensus 19 G~i~~~~~gfgFv~~---~~~-------~~~difI~~~~~~~a~~GD~V~v~i~~~~~~~~~~g~v~~il~r~~--~~~v 86 (654)
T TIGR00358 19 GVVKAHNKGFGFLRP---DDD-------DKKDYFIPPPQMKKVMHGDLVEACPLSQPQRGRFEAEVERILEPAL--TRFV 86 (654)
T ss_pred EEEEECCCccEEEEe---CCC-------CCCcEEEchHHhCcCCCCCEEEEEEeecCCCCCceEEEEEEeccCC--CEEE
Confidence 88 779999999632 221 01468999999999999 887776543 35568999999999985 6799
Q ss_pred EEEEeccccccCCCCcccccccCCCCCCCCCceEEEEeCCCCCCceEEecCCCChhhhhhcccCCccccceEEEEEEeec
Q 002793 135 GFLNVNQWFNYKGGSRKDAKKNRSSLSVPDREYIQLTPTHPKYPKMVVLVKDLPDSIKKRLEEGDATIEMELVAARIDEW 214 (880)
Q Consensus 135 G~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~D~rip~i~i~~~~~p~~~~~~~~~gd~~~~~~lvvv~I~~w 214 (880)
|++.. .+ ++.+++|+|++++..++..... ....+++|| +|+|+|++|
T Consensus 87 G~~~~----------------~~--------~~~~v~p~~~~~~~~i~i~~~~---~~~~~~~g~------~V~v~i~~~ 133 (654)
T TIGR00358 87 GKFLG----------------EN--------DFGFVVPDDPRIYLDIIVPKAS---VKNELAEGD------KVVVELTEY 133 (654)
T ss_pred EEEEE----------------eC--------CeEEEEECCCCCCCcEEEcCCc---cccCCCCCC------EEEEEEccC
Confidence 99982 22 3678999999999855442220 112455666 899999999
Q ss_pred CCCCCCCcEEEEEEcCCCCChhHHHHHHHHhcCCCCCCCChhhhccCCCCCCCCChhhhccCccCCCceEEEEcCCCCCC
Q 002793 215 NEESPFPQAHVLHVFGRGGEVEPQINAILYENAICCSGFSPESLSCLPCVPWEVPQEELLSRKDLRNFCIFTIDPSTATD 294 (880)
Q Consensus 215 p~~~~~p~G~iv~~LG~~~d~~~e~~ail~e~~i~~~~F~~~vl~~~~~~~~~i~~~e~~~R~Dlr~l~i~TIDp~~akD 294 (880)
|..+.+|.|+|+++||..+++.+|++++|.+|+| +.+||++++++++.++|.+++++.+.|+|||++++|||||++|+|
T Consensus 134 p~~~~~~~g~i~~~lG~~~d~~~~~~~il~~~~i-~~~f~~~v~~~a~~~~~~~~~~~~~~R~Dlr~~~~~TID~~~a~D 212 (654)
T TIGR00358 134 PLRRNLFYGEITQILGNNDDPLIPWWVTLARHEI-PFEFPDGVEQQAAKLQFDVDEQAKKYREDLTDLAFVTIDGADAKD 212 (654)
T ss_pred CCCCCCceEEEEEEEcCCCCcccHHHHHHHHcCc-CCCCCHHHHHHHHhccccCChhHhhCccccccCcEEEECCCCCCc
Confidence 9999999999999999999999999999999999 579999999999999999999999999999999999999999999
Q ss_pred CCceEEEEEcCCceEEEEEEEccccccccCCCHhhHHHHhCcceeecCCCcccCCChhhhhcccCCCCCCceEEEEEEEE
Q 002793 295 LDDALSIERLSDGISRVGVHIADVSYFVLPGTALDIEAQVRSTSVYMLQRKIPMLPVLLSEEVGSLNPGVDRLAFSIFWD 374 (880)
Q Consensus 295 lDDAlsie~l~~G~~~lgVHIADVS~yV~~gS~LD~eA~~RgtSvYLp~rviPMLP~~Ls~~lcSL~pg~dRlA~Sv~~~ 374 (880)
|||||||+++++|+|+||||||||||||++||+||+||++||||||||++++||||+.||+++|||+||++|+||||.|+
T Consensus 213 ~DDAisie~~~~g~~~l~VHIADVs~~V~~~s~LD~eA~~R~tSvYlp~~~ipMLP~~Ls~~~cSL~p~~~R~a~s~~~~ 292 (654)
T TIGR00358 213 LDDAVYVKKLPDGGWKLYVAIADVSYYVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMT 292 (654)
T ss_pred ccceEEEEEeCCCcEEEEEEEechhheeCCCCHHHHHHHHhCcCccCCCCeecCCCHHHhcCccccCCCCcceEEEEEEE
Confidence 99999999998999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcCCCCEEEEEEEEEEEecccccCHHHHHHHHccCCCccccCccCCCCCcccCCCchhhHHHHHHHHHHHHHHHHHhHhc
Q 002793 375 LNSAGDVVDRWIGRTVIRSCCKLSYEHAQDIIDGKFDVESSNTLGEGWPQLYGQFEWSDVVRSIKSLYEVSKILKDKRFT 454 (880)
Q Consensus 375 id~~G~i~~~~~~~SvIrS~~rLTY~~vq~iL~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~L~~L~~la~~Lr~~R~~ 454 (880)
||++|+|++++|++|+|+|+++|||++|+++|++.... .. ..+++.++|..|+++|++||++|.+
T Consensus 293 id~~G~i~~~~~~~svI~s~~rltY~~v~~~l~~~~~~----------~~-----~~~~~~~~L~~l~~la~~lr~~R~~ 357 (654)
T TIGR00358 293 ISAQGRITDNEFYPATIESKARLTYDKVNDWLENDDEL----------QP-----EYETLVEQLKALHQLSQALGEWRHK 357 (654)
T ss_pred ECCCCCEeEEEEEEEEEEECcEEcHHHHHHHHcCCccc----------ch-----hhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999874210 00 1356788999999999999999999
Q ss_pred CCCccccCCCceeeeCCCCCeEEEEecCCCcHHHHHHHHHHHHHHHHHHHHHHhCCCceeEEeCCCCChHHHHHHHHHHH
Q 002793 455 DGALRLENSKPVFLFDEYGTPYDSVLSGREDLNFLFEEFMLLANKTAAEVIARAFPDSALLRRHPAPNMRKLREFEAFCS 534 (880)
Q Consensus 455 ~Gal~l~~pe~~i~lDe~g~p~~i~~~~~~~a~~LIEEfMilAN~~vA~~l~~~~~~~~l~R~H~~P~~~kl~~l~~~~~ 534 (880)
+|+++|+.||++|.+|++|.+.++...++.+||.|||||||+||++||+|+.++ +.|++||+|++|+.+++++|.+++.
T Consensus 358 ~Gai~~~~~e~~~~~d~~g~~~~i~~~~~~~a~~lIeE~MilAN~~vA~~~~~~-~~p~iyR~h~~p~~~~~~~l~~~~~ 436 (654)
T TIGR00358 358 RGLIDFEHPETKFIVDEEGRVIDIVAEVRRIAEKIIEEAMIVANICAARFLHNH-KVPGIYRVHPGPSKKKLQSLLEFLA 436 (654)
T ss_pred CCCcccCCCceeEEECCCCCeeEEEeccCcHHHHHHHHHHHHHHHHHHHHHHHc-CCCeEEecCCCCCHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999986 7899999999999999999999999
Q ss_pred HcCCccCCC-----ChhHHHHHHHHHHHhhcCCHHHHHHHHHHHhcccCCcEecccCCCCCCCCccccccCCCCeeeccC
Q 002793 535 KHGLQLDTS-----SSGQFHQSLEQAREKLKDDYVLFDILINYATRPMQLASYFCSGDFKDDTDWGHYALAFPVYTHFTS 609 (880)
Q Consensus 535 ~~G~~l~~~-----~~~~l~~~L~~i~~~~~~~~~~~~~l~~~~lR~m~~A~Y~~sg~~~s~~~~~HfgL~~~~YTHFTS 609 (880)
.+|+.++.. ++.+++..|.++. +.+. ..++..+++|+|++|+| +.+|.+|||||++.||||||
T Consensus 437 ~~g~~~~~~~~~~~~~~~~~~~l~~~~----~~~~-~~~l~~~llr~m~~A~y-------~~~~~~HfgL~~~~YthfTS 504 (654)
T TIGR00358 437 ELGLTLPGGNAENVTTLDGACWLREVK----DRPE-YEILVTRLLRSLSQAEY-------SPEPLGHFGLGLEHYAHFTS 504 (654)
T ss_pred HcCCCccCCCcCCCChHHHHHHHHHhh----CCCH-HHHHHHHHHHhhccccc-------CCCCCCccccccccccccCC
Confidence 999987432 2445666666554 3332 34677788999999999 45799999999999999999
Q ss_pred CCCChhhHHHHHHHHHHHHhchhhhhhhccCCCCCCccccccccccccccccchhhhhhhhhHHHHHhhhcCCCchhHHH
Q 002793 610 PLRRYPDLVVHRTLNAALEAEKLYWKHRRMLPKNNHREGVRGRFLTGIFYDKDAAESLEGREALSVAALKYGVPCADILV 689 (880)
Q Consensus 610 PIRRY~DLiVHR~L~a~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~es~~~~~~~~~~~~~~~~~~~~~l~ 689 (880)
|||||+||+|||||+++|.+++... . . ....+.+.
T Consensus 505 PIRRY~DLivHr~L~a~l~~~~~~~----~-~----------------------------------------~~~~~~l~ 539 (654)
T TIGR00358 505 PIRRYPDLTNHRLIKAVLAKEQTDT----E-R----------------------------------------YQPQDELL 539 (654)
T ss_pred ccccchHHHHHHHHHHHHcCCCCcc----c-c----------------------------------------hhhHHHHH
Confidence 9999999999999999998642100 0 0 00134578
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccce
Q 002793 690 NVATHCNDRKLACRNVKDACVKLYMWILLKKKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTST 769 (880)
Q Consensus 690 ~ia~~~N~r~~~A~~a~r~s~~l~~~~~l~~~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~ 769 (880)
.+|++||++++.|++|||++.++|+|+||+++.|..++|+|++|.++|++|.|+++++||+||++++++++|+|++.++.
T Consensus 540 ~~~~~~~~~er~a~~aer~~~~~~~~~yl~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~ 619 (654)
T TIGR00358 540 QIAEHCSDTERRARDAERDVADWLKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMA 619 (654)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeeecccceeecCCCceEEe
Q 002793 770 LVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 770 lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
|++ +++++.|++||.|+++.
T Consensus 620 l~g--~~~~~~~~lGD~V~Vki 639 (654)
T TIGR00358 620 LIG--KGTGKVYRIGDRVTVKL 639 (654)
T ss_pred EEe--ccCCcEECCCCEEEEEE
Confidence 999 57778899999887765
No 3
>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=100.00 E-value=1.8e-119 Score=1086.99 Aligned_cols=613 Identities=29% Similarity=0.389 Sum_probs=538.1
Q ss_pred cc-ccccceeeeeeecccCCCCCCCCCccccccccCccchhhhhc--eeEEEEecC--CCCCccEEEEEEEecCCCCcce
Q 002793 59 SE-AYNQEMIEREGYNYINGHHPSTSDSTEKVSSSQQNDGMNAIE--RLSAMISSY--PTKRPTGRVVSIIERSPRRDGI 133 (880)
Q Consensus 59 g~-~~h~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~--~v~~~~~~~--~~~~p~G~VV~IleR~~~~~~~ 133 (880)
|. ..|+.|+||+.. ++ ....++||...+++.|++ +|.+.+... ++++++|+|++||+|.. +.+
T Consensus 71 G~i~~~~~g~gFv~~---~~-------~~~~di~I~~~~~~~a~~GD~Vlv~I~~~~~~~~~~eg~Vv~Il~r~~--~~~ 138 (709)
T TIGR02063 71 GTVIAHRDGFGFLRP---ED-------DDEDDIFIPPRQMNGAMHGDRVLVRITGKPDGGDRFEARVIKILERAN--DQI 138 (709)
T ss_pred EEEEECCCccEEEEE---CC-------CCCCcEEEChHHhCcCCCCCEEEEEEecccCCCCCceEEEEEEEeeCC--CEE
Confidence 88 668999999522 11 011468999899999999 887777654 35778999999999984 789
Q ss_pred EEEEEeccccccCCCCcccccccCCCCCCCCCceEEEEeCCCCCCce-EEecCCCChhhhhhcccCCccccceEEEEEEe
Q 002793 134 VGFLNVNQWFNYKGGSRKDAKKNRSSLSVPDREYIQLTPTHPKYPKM-VVLVKDLPDSIKKRLEEGDATIEMELVAARID 212 (880)
Q Consensus 134 vG~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~D~rip~i-~i~~~~~p~~~~~~~~~gd~~~~~~lvvv~I~ 212 (880)
||++.. .+ ++.||+|+|+|+|.. .++..+ ...+++|| +|+|+|+
T Consensus 139 VG~~~~----------------~~--------~~~~v~p~d~~~~~~I~i~~~~-----~~~~~~g~------~v~v~i~ 183 (709)
T TIGR02063 139 VGTFYI----------------EN--------GIGFVIPDDKRIYLDIFIPPEQ-----ILGAEEGD------KVLVEIT 183 (709)
T ss_pred EEEEEE----------------cC--------cEEEEEECCCCCCCCEEECCcc-----ccCCCCCC------EEEEEEc
Confidence 999982 22 367899999999874 454322 12455565 8999999
Q ss_pred ecCCCCCCCcEEEEEEcCCCCChhHHHHHHHHhcCCCCCCCChhhhccCCCCCCCCChhhhccCccCCCceEEEEcCCCC
Q 002793 213 EWNEESPFPQAHVLHVFGRGGEVEPQINAILYENAICCSGFSPESLSCLPCVPWEVPQEELLSRKDLRNFCIFTIDPSTA 292 (880)
Q Consensus 213 ~wp~~~~~p~G~iv~~LG~~~d~~~e~~ail~e~~i~~~~F~~~vl~~~~~~~~~i~~~e~~~R~Dlr~l~i~TIDp~~a 292 (880)
+||..+.+|.|+|+++||..+++.+|++++|.+|+| +.+||++++++++.++|.+++++.++|+|||++++|||||++|
T Consensus 184 ~~p~~~~~~~g~i~~~lg~~~d~~~~~~~il~~~~i-~~~f~~~v~~~a~~~~~~~~~~~~~~R~Dl~~~~~~tID~~~a 262 (709)
T TIGR02063 184 KYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGI-PYEFPEEVLDEAAKIPEEVPEEEIKGRKDLRDLPFVTIDGEDA 262 (709)
T ss_pred cCCCCCCCceEEEEEEeCCCCcccchHHHHHHHcCc-CCCCCHHHHHHHHhCCCCCChhHhhcccccccCcEEEECCCCC
Confidence 999999999999999999999999999999999999 5799999999999999999989999999999999999999999
Q ss_pred CCCCceEEEEEcCCceEEEEEEEccccccccCCCHhhHHHHhCcceeecCCCcccCCChhhhhcccCCCCCCceEEEEEE
Q 002793 293 TDLDDALSIERLSDGISRVGVHIADVSYFVLPGTALDIEAQVRSTSVYMLQRKIPMLPVLLSEEVGSLNPGVDRLAFSIF 372 (880)
Q Consensus 293 kDlDDAlsie~l~~G~~~lgVHIADVS~yV~~gS~LD~eA~~RgtSvYLp~rviPMLP~~Ls~~lcSL~pg~dRlA~Sv~ 372 (880)
+|+||||||++.++|+|+||||||||||||++||+||+||++||||||||++++||||+.||+++|||+||++|+||||.
T Consensus 263 ~D~DDAisie~~~~g~~~l~VhIADVs~~V~~~s~lD~eA~~R~tSvYlp~~~ipMLP~~Ls~~~cSL~p~~~r~a~s~~ 342 (709)
T TIGR02063 263 KDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCE 342 (709)
T ss_pred cccccEEEEEEcCCCCEEEEEEEechhhEeCCCChHHHHHHHhCeeEeCCCCcccCCChHHccCccccCCCCceEEEEEE
Confidence 99999999999988999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEcCCCCEEEEEEEEEEEecccccCHHHHHHHHccCCCccccCccCCCCCcccCCCchhhHHHHHHHHHHHHHHHHHhH
Q 002793 373 WDLNSAGDVVDRWIGRTVIRSCCKLSYEHAQDIIDGKFDVESSNTLGEGWPQLYGQFEWSDVVRSIKSLYEVSKILKDKR 452 (880)
Q Consensus 373 ~~id~~G~i~~~~~~~SvIrS~~rLTY~~vq~iL~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~L~~L~~la~~Lr~~R 452 (880)
|+||++|+|++++|++|+|+|+++|||++|+++|+++.... . ...++.++|..|+++|++||++|
T Consensus 343 ~~id~~G~i~~~~~~~svI~s~~~ltY~~v~~~l~~~~~~~----------~-----~~~~~~~~L~~l~~la~~l~~~R 407 (709)
T TIGR02063 343 MEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEGKDALD----------K-----KEPPLKEMLKNLFELYKILRKKR 407 (709)
T ss_pred EEECCCCCEEEeEEEEEEEEeCeEEcHHHHHHHHcCCcccc----------c-----hhhHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999998742110 0 12457789999999999999999
Q ss_pred hcCCCccccCCCceeeeCCCCCeEEEEecCCCcHHHHHHHHHHHHHHHHHHHHHHhCCCceeEEeCCCCChHHHHHHHHH
Q 002793 453 FTDGALRLENSKPVFLFDEYGTPYDSVLSGREDLNFLFEEFMLLANKTAAEVIARAFPDSALLRRHPAPNMRKLREFEAF 532 (880)
Q Consensus 453 ~~~Gal~l~~pe~~i~lDe~g~p~~i~~~~~~~a~~LIEEfMilAN~~vA~~l~~~~~~~~l~R~H~~P~~~kl~~l~~~ 532 (880)
.++|+|+|+.|+++|.+|++|.+..+...++.+||.|||||||+||++||+|+.+ ++.|++||+|+.|+.+++++|.++
T Consensus 408 ~~~G~i~~~~~e~~~~~d~~g~~~~i~~~~~~~a~~lIeE~MllAN~~vA~~l~~-~~~p~iyR~h~~P~~~~~~~l~~~ 486 (709)
T TIGR02063 408 KKRGAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIEEFMIAANETVAEHLEK-AKLPFIYRVHERPSEEKLQNLREF 486 (709)
T ss_pred HhCCCcccCCccceeEECCCCCeEEEEeccchHHHHHHHHHHHHHHHHHHHHHHh-CCCCeEEecCCCCCHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999986 489999999999999999999999
Q ss_pred HHHcCCccCC-----CChhHHHHHHHHHHHhhcCCHHHHHHHHHHHhcccCCcEecccCCCCCCCCccccccCCCCeeec
Q 002793 533 CSKHGLQLDT-----SSSGQFHQSLEQAREKLKDDYVLFDILINYATRPMQLASYFCSGDFKDDTDWGHYALAFPVYTHF 607 (880)
Q Consensus 533 ~~~~G~~l~~-----~~~~~l~~~L~~i~~~~~~~~~~~~~l~~~~lR~m~~A~Y~~sg~~~s~~~~~HfgL~~~~YTHF 607 (880)
+..+|+.++. .++..++.+|.++. +.|. ..++..+++|+|++|.| ++.+.+|||||++.||||
T Consensus 487 ~~~~g~~~~~~~~~~~~~~~~~~~l~~~~----~~~~-~~~l~~~llr~m~~A~y-------~~~~~~HfgL~~~~Ythf 554 (709)
T TIGR02063 487 LKTLGITLKGGTSDKPQPKDFQKLLEKVK----GRPE-EELINTVLLRSMQQAKY-------SPENIGHFGLALEYYTHF 554 (709)
T ss_pred HHHcCCCccCCCCCCCCHHHHHHHHHHhh----CCcH-HHHHHHHHHHHhcCccc-------CCCCCCcccccccccccc
Confidence 9999998853 24556766666654 3443 25677888999999999 457999999999999999
Q ss_pred cCCCCChhhHHHHHHHHHHHHhchhhhhhhccCCCCCCccccccccccccccccchhhhhhhhhHHHHHhhhcCCCchhH
Q 002793 608 TSPLRRYPDLVVHRTLNAALEAEKLYWKHRRMLPKNNHREGVRGRFLTGIFYDKDAAESLEGREALSVAALKYGVPCADI 687 (880)
Q Consensus 608 TSPIRRY~DLiVHR~L~a~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~es~~~~~~~~~~~~~~~~~~~~~ 687 (880)
|||||||+||+|||||+++|.+++..... .. . + ...+.
T Consensus 555 TSPIRRY~DLivHr~L~~~l~~~~~~~~~------~~------------~-------------~-----------~~~~~ 592 (709)
T TIGR02063 555 TSPIRRYPDLIVHRLIKKALFGGENTTTE------KE------------R-------------E-----------YLEAK 592 (709)
T ss_pred CCccccchHHHHHHHHHHHHcCCCCCCcc------cc------------c-------------h-----------hhHHH
Confidence 99999999999999999999864210000 00 0 0 01345
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEeccc
Q 002793 688 LVNVATHCNDRKLACRNVKDACVKLYMWILLKKKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETT 767 (880)
Q Consensus 688 l~~ia~~~N~r~~~A~~a~r~s~~l~~~~~l~~~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~ 767 (880)
+..+|++||.+++.|++|||++.++|+|+||+.+.|..++|+|++|.++|++|.++.+|+||+||++++.++||+|++..
T Consensus 593 l~~~~~~~~~~er~a~~aer~~~~~~~~~yl~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~ 672 (709)
T TIGR02063 593 LEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKG 672 (709)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccc
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceEEEeeecccceeecCCCceEEe
Q 002793 768 STLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 768 ~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
+.|++ +++++.|++||.|+++.
T Consensus 673 ~~l~g--~~~~~~~~lGd~V~Vkv 694 (709)
T TIGR02063 673 LALVG--ERTGKVFRLGDRVKVRV 694 (709)
T ss_pred eEEEe--ccCCcEECCCCEEEEEE
Confidence 99998 57778899999887764
No 4
>PRK05054 exoribonuclease II; Provisional
Probab=100.00 E-value=1.3e-116 Score=1046.36 Aligned_cols=597 Identities=21% Similarity=0.253 Sum_probs=506.2
Q ss_pred cc-ccccceeeeeeecccCCCCCCCCCccccccccCccchhhhhc--eeEEEEecCCCCCccEEEEEEEecCCCCcceEE
Q 002793 59 SE-AYNQEMIEREGYNYINGHHPSTSDSTEKVSSSQQNDGMNAIE--RLSAMISSYPTKRPTGRVVSIIERSPRRDGIVG 135 (880)
Q Consensus 59 g~-~~h~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~--~v~~~~~~~~~~~p~G~VV~IleR~~~~~~~vG 135 (880)
|. ..|++||||+.. +| . +|+||..++++.||+ +|.+.+.+. +++++|+|++||+|+. +.+||
T Consensus 24 G~~~~~~~gfgFv~~---~~--------~-~difI~~~~l~~a~~GD~V~v~i~~~-~~r~~g~v~~il~r~~--~~~vG 88 (644)
T PRK05054 24 GVVKATEKGFGFLEV---DA--------Q-KSYFIPPPQMKKVMHGDRIIAVIHTE-KDREIAEPEELIEPFL--TRFVG 88 (644)
T ss_pred EEEEECCCccEEEEE---CC--------C-CcEEEChHHHccCCCCCEEEEEEecC-CCCcEEEEEEEEecCC--CEEEE
Confidence 88 779999999622 11 1 368999999999999 777776554 4567999999999974 68999
Q ss_pred EEEeccccccCCCCcccccccCCCCCCCCCceEEEEeCCCCCCceEEecCCCChhhhhhcccCCccccceEEEEEEeecC
Q 002793 136 FLNVNQWFNYKGGSRKDAKKNRSSLSVPDREYIQLTPTHPKYPKMVVLVKDLPDSIKKRLEEGDATIEMELVAARIDEWN 215 (880)
Q Consensus 136 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~D~rip~i~i~~~~~p~~~~~~~~~gd~~~~~~lvvv~I~~wp 215 (880)
++.. .+ +..+++|+|++++..+..... +.....+++|| +|+|+|++||
T Consensus 89 ~~~~----------------~~--------~~~~~~p~d~~~~~~i~i~~~--~~~~~~~~~gd------~V~v~i~~~p 136 (644)
T PRK05054 89 RVQK----------------KD--------DRLSIVPDHPLLKDAIPCRAA--KGLNHEFKEGD------WVVAELRRHP 136 (644)
T ss_pred EEEE----------------eC--------ceEEEEECCCCCCccEEeccc--cccccCCCCCC------EEEEEEecCC
Confidence 9982 22 367899999999986655211 11112456676 7999999999
Q ss_pred CC-CCCCcEEEEEEcCCCCChhHHHHHHHHhcCCCCCCCChhhhccCCCCCCCCChhhhccCccCCCceEEEEcCCCCCC
Q 002793 216 EE-SPFPQAHVLHVFGRGGEVEPQINAILYENAICCSGFSPESLSCLPCVPWEVPQEELLSRKDLRNFCIFTIDPSTATD 294 (880)
Q Consensus 216 ~~-~~~p~G~iv~~LG~~~d~~~e~~ail~e~~i~~~~F~~~vl~~~~~~~~~i~~~e~~~R~Dlr~l~i~TIDp~~akD 294 (880)
.. ...|.|+|+++||..+++.+|+++++.+|++ +.+|++++++ |++++++. +|+|||++++|||||++|+|
T Consensus 137 ~~~~~~~~g~i~~~lG~~~d~~~d~~~il~~~~l-~~~f~~~~~~------~~~~~~~~-~R~Dlr~~~~~TID~~~akD 208 (644)
T PRK05054 137 LKGDRGFYAEITQFITDADDHFAPWWVTLARHNL-EREAPAGGVA------WEMLDEGL-EREDLTALDFVTIDSASTED 208 (644)
T ss_pred CCCCCCceEEEEEEECCCCCCccHHHHHHHHcCC-CCCCCchhhh------ccCChhcc-CcccccCCcEEEECCCCCCc
Confidence 85 4569999999999999999999999999999 6899998754 23344443 79999999999999999999
Q ss_pred CCceEEEEEcCCceEEEEEEEccccccccCCCHhhHHHHhCcceeecCCCcccCCChhhhhcccCCCCCCceEEEEEEEE
Q 002793 295 LDDALSIERLSDGISRVGVHIADVSYFVLPGTALDIEAQVRSTSVYMLQRKIPMLPVLLSEEVGSLNPGVDRLAFSIFWD 374 (880)
Q Consensus 295 lDDAlsie~l~~G~~~lgVHIADVS~yV~~gS~LD~eA~~RgtSvYLp~rviPMLP~~Ls~~lcSL~pg~dRlA~Sv~~~ 374 (880)
|||||||+++++|+|+||||||||||||++||+||+||++||||||||++++||||+.||+++|||+||++|+||||.|+
T Consensus 209 ~DDAisve~~~~g~~~l~VHIADVs~yV~~gS~LD~eA~~RgtSvYlp~~vipMLP~~Ls~~~cSL~p~~~R~als~~~~ 288 (644)
T PRK05054 209 MDDALYVEKLPDGGLQLTVAIADPTAYIAEGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVT 288 (644)
T ss_pred ccceEEEEEeCCCCEEEEEEEcchhhEeCCCCHHHHHHHHhCceEeCCCCcccCCChHHhcCccccCCCCCceEEEEEEE
Confidence 99999999998899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcCCCCEEE-EEEEEEEEecccccCHHHHHHHHccCCCccccCccCCCCCcccCCCchhhHHHHHHHHHHHHHHHHHhHh
Q 002793 375 LNSAGDVVD-RWIGRTVIRSCCKLSYEHAQDIIDGKFDVESSNTLGEGWPQLYGQFEWSDVVRSIKSLYEVSKILKDKRF 453 (880)
Q Consensus 375 id~~G~i~~-~~~~~SvIrS~~rLTY~~vq~iL~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~L~~L~~la~~Lr~~R~ 453 (880)
||++|++++ ++|++|+|+|+++|||++|+++|+++.+. .| ..+++.++|..|.+++++|+++|.
T Consensus 289 id~~G~i~~~~~~~~svI~s~~rltY~~v~~~l~~~~~~---------~~------~~~~i~~~l~~L~~l~~~l~~~R~ 353 (644)
T PRK05054 289 IDADGTIEDDIRFFAAWIESKAKLAYDNVSDWLENGGDW---------QP------ESEAIAEQIRLLHQFCLARSEWRK 353 (644)
T ss_pred EeCCCCcccccEEEEEEEEcCCeecHHHHHHHHhCCCcc---------cc------chhHHHHHHHHHHHHHHHHHHHHH
Confidence 999999998 89999999999999999999999874210 00 235688899999999999999999
Q ss_pred cCCCccccCCCceeeeCCCCCeEEEEecCCCcHHHHHHHHHHHHHHHHHHHHHHhCCCceeEEeCCCCChHHHHHHHHHH
Q 002793 454 TDGALRLENSKPVFLFDEYGTPYDSVLSGREDLNFLFEEFMLLANKTAAEVIARAFPDSALLRRHPAPNMRKLREFEAFC 533 (880)
Q Consensus 454 ~~Gal~l~~pe~~i~lDe~g~p~~i~~~~~~~a~~LIEEfMilAN~~vA~~l~~~~~~~~l~R~H~~P~~~kl~~l~~~~ 533 (880)
++|++.|+.||+++.+|++|.+.++...++.+||+|||||||+||++||+|+.++ +.|++||+|+.|+++++++|.+++
T Consensus 354 ~~G~i~~d~~e~~i~ld~~g~~~~i~~~~~~~a~~lIeE~MllAN~~vA~~l~~~-~~p~iyRvH~~P~~~~l~~l~~~~ 432 (644)
T PRK05054 354 QHALVFKDRPDYRFELGEKGEVLDIVAEPRRIANRIVEESMIAANICAARVLRDK-LGFGIYNVHSGFDPANAEQAVALL 432 (644)
T ss_pred hCCCccccCCceEEEECCCCCEEEEEEecCcHHHHHHHHHHHHHHHHHHHHHHHc-CCCEEEECCCCCCHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999986 689999999999999999999999
Q ss_pred HHcCCccCCCChhHHHHHHHHHHHhhcCCHHHHHHHHHHHhcccCCcEecccCCCCCCCCccccccCCCCeeeccCCCCC
Q 002793 534 SKHGLQLDTSSSGQFHQSLEQAREKLKDDYVLFDILINYATRPMQLASYFCSGDFKDDTDWGHYALAFPVYTHFTSPLRR 613 (880)
Q Consensus 534 ~~~G~~l~~~~~~~l~~~L~~i~~~~~~~~~~~~~l~~~~lR~m~~A~Y~~sg~~~s~~~~~HfgL~~~~YTHFTSPIRR 613 (880)
..+|+.++..+..++. .+..+.+.+...+. +.+...++|+|++|.| ++++.+|||||++.||||||||||
T Consensus 433 ~~~g~~~~~~~~~~l~-~~~~~~~~l~~~~~--~~l~~~llr~~~~a~y-------s~~~~gHfgL~~~~YthfTSPIRR 502 (644)
T PRK05054 433 KEHGLHFDAEELLTLE-GFCKLRRELDAQPT--GYLDSRIRRFQSFAEI-------STEPGPHFGLGLEAYATWTSPIRK 502 (644)
T ss_pred HHCCCCcCCCcccChH-HHHHHHHHHhcchH--HHHHHHHHHHHhceec-------CCCCcCccccccccccccCChhhh
Confidence 9999998654333322 22223222223332 2344456899999999 568999999999999999999999
Q ss_pred hhhHHHHHHHHHHHHhchhhhhhhccCCCCCCccccccccccccccccchhhhhhhhhHHHHHhhhcCCCchhHHHHHHH
Q 002793 614 YPDLVVHRTLNAALEAEKLYWKHRRMLPKNNHREGVRGRFLTGIFYDKDAAESLEGREALSVAALKYGVPCADILVNVAT 693 (880)
Q Consensus 614 Y~DLiVHR~L~a~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~es~~~~~~~~~~~~~~~~~~~~~l~~ia~ 693 (880)
|+||+|||||+++|.+++. ...+..+|+
T Consensus 503 Y~DLivHR~L~a~l~~~~~----------------------------------------------------~~~~~~~~~ 530 (644)
T PRK05054 503 YGDMINHRLLKAVIKGETA----------------------------------------------------ERPQDEITV 530 (644)
T ss_pred hHHHHHHHHHHHHHcCCCC----------------------------------------------------CccHHHHHH
Confidence 9999999999999975421 001346899
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhccc--eEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEe--cccce
Q 002793 694 HCNDRKLACRNVKDACVKLYMWILLKKKEV--LLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWL--ETTST 769 (880)
Q Consensus 694 ~~N~r~~~A~~a~r~s~~l~~~~~l~~~~~--~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~--~~~~~ 769 (880)
+||++++.|++|+|++.++++++||+++.| +.++|+|++|+++||+|.|+++|+||.||+++|.++|++|. +.+..
T Consensus 531 ~~s~~er~a~~aer~~~~~~~~~y~~~~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~ 610 (644)
T PRK05054 531 QLAERRRLNRMAERDVGDWLYARYLKDKAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGT 610 (644)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccce
Confidence 999999999999999999999999999985 59999999999999999999999999999999999876653 33334
Q ss_pred EEEeeecccceeecCCCceEEe
Q 002793 770 LVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 770 lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
+.+ .+++.|++||+|+++.
T Consensus 611 ~~~---~~~~~~~lGd~V~V~v 629 (644)
T PRK05054 611 VQI---KGETVYKLGDVIDVTL 629 (644)
T ss_pred EEE---eCCEEEcCCCEEEEEE
Confidence 333 4557888888776654
No 5
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=100.00 E-value=1.7e-115 Score=1049.93 Aligned_cols=625 Identities=33% Similarity=0.457 Sum_probs=546.1
Q ss_pred cccccCcCccccCCCCccc-ccccceeeeeeecccCCCCCCCCCccccccccCccchhhhhc--eeEEEEecCC-CC-Cc
Q 002793 42 NCTLLSEKGIHHDDDSSSE-AYNQEMIEREGYNYINGHHPSTSDSTEKVSSSQQNDGMNAIE--RLSAMISSYP-TK-RP 116 (880)
Q Consensus 42 ~~~~~~~k~~~~~~~~~g~-~~h~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~--~v~~~~~~~~-~~-~p 116 (880)
+.|.+|+++.... |. ..|..||||+ ..++. ....|+++....++.|++ +|++.+.... .+ .+
T Consensus 59 ~~~~~~~~~~~~~----~~~~~~~~gf~f~---~~~~~------~~~~d~~v~~~~~~~a~~gD~V~v~~~~~~~~~~~~ 125 (706)
T COG0557 59 GRYLLPEELDLVE----GIVEASAKGFGFL---SPDDS------KDADDIFVPKDPLNRALHGDRVLVELLPSDKRGRFK 125 (706)
T ss_pred ccccccccccccc----ceEEeccCCceee---ccCcc------CCCCcEEeccccccccccCCEEEEEECcccccCCCc
Confidence 4666777666444 66 6789999884 22222 111467888888999998 7777765553 33 38
Q ss_pred cEEEEEEEecCCCCcceEEEEEeccccccCCCCcccccccCCCCCCCCCceEEEEeCCCCCC-ceEEecCCCChhhhhhc
Q 002793 117 TGRVVSIIERSPRRDGIVGFLNVNQWFNYKGGSRKDAKKNRSSLSVPDREYIQLTPTHPKYP-KMVVLVKDLPDSIKKRL 195 (880)
Q Consensus 117 ~G~VV~IleR~~~~~~~vG~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~D~rip-~i~i~~~~~p~~~~~~~ 195 (880)
+|+|++|++|.+ ..+||++... .++.+++|.|+|++ .+.|++++.+ .+
T Consensus 126 ~~~v~~il~r~~--~~~vG~~~~~------------------------~~~~~~~p~d~r~~~~i~i~~~~~~-----~~ 174 (706)
T COG0557 126 EAAVVRILERAN--SALVGELRPS------------------------QGIGRVLPDDKRLPFLIAIPPEQAP-----GA 174 (706)
T ss_pred eEEEEeeecccc--ceeEEEEEec------------------------CCeEEEEecCCCCccceeecccccc-----cc
Confidence 999999999986 5799999931 13789999999999 5777765553 33
Q ss_pred ccCCccccceEEEEEEeecCCCCCCCcEEEEEEcCCCCChhHHHHHHHHhcCCCCCCCChhhhccCCCCCCCCChhhhcc
Q 002793 196 EEGDATIEMELVAARIDEWNEESPFPQAHVLHVFGRGGEVEPQINAILYENAICCSGFSPESLSCLPCVPWEVPQEELLS 275 (880)
Q Consensus 196 ~~gd~~~~~~lvvv~I~~wp~~~~~p~G~iv~~LG~~~d~~~e~~ail~e~~i~~~~F~~~vl~~~~~~~~~i~~~e~~~ 275 (880)
+.| .+|+|+|++||.++.+|.|+++++||..+++..++++++++|++ +.+|+++++++++..++.+++++.++
T Consensus 175 ~~~------~~v~~~i~~~~~~~~~~~g~v~~~lG~~~~~~~~~~~il~~~~i-~~~f~~~v~~~a~~~~~~~~~~~~~~ 247 (706)
T COG0557 175 EEG------HLVVVEITRWPDTSRPPFGEVVEVLGDLGDPGADIEAILRDHGI-PSEFPEKVLDEAAALPDEVPEEDLKG 247 (706)
T ss_pred ccC------CEEEEEecccCCcCCCCceeEEEeecCCCCcchhHHHHHHHcCC-CCCCCHHHHHHHHhccCcCChhhhcC
Confidence 444 48999999999999999999999999999999999999999999 56799999999999999999999999
Q ss_pred CccCCCceEEEEcCCCCCCCCceEEEEEcCCceEEEEEEEccccccccCCCHhhHHHHhCcceeecCCCcccCCChhhhh
Q 002793 276 RKDLRNFCIFTIDPSTATDLDDALSIERLSDGISRVGVHIADVSYFVLPGTALDIEAQVRSTSVYMLQRKIPMLPVLLSE 355 (880)
Q Consensus 276 R~Dlr~l~i~TIDp~~akDlDDAlsie~l~~G~~~lgVHIADVS~yV~~gS~LD~eA~~RgtSvYLp~rviPMLP~~Ls~ 355 (880)
|.|||++++|||||++|+|+|||||++++.||+|+||||||||||||+|||+||+||++||||||||++++||||+.||+
T Consensus 248 R~Dlr~l~~~TID~~~akD~DDAv~~~~l~~g~~~LgVhIADVs~yV~p~s~LD~EA~~RgtSVYlp~~vipMLPe~Ls~ 327 (706)
T COG0557 248 RVDLRDLPIFTIDPEDAKDLDDAVSVEKLRNGGYRLGVHIADVSHYVQPGSALDKEARKRGTSVYLPDRVIPMLPEALSN 327 (706)
T ss_pred ccccccCCEEEECCCCCccccceEEEEEeCCCcEEEEEEEecceeecCCCChhhHHHHHcCCeEEcCCcccCCCchhhcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCceEEEEEEEEEcCCCCEEEEEEEEEEEecccccCHHHHHHHHccCCCccccCccCCCCCcccCCCchhhHH
Q 002793 356 EVGSLNPGVDRLAFSIFWDLNSAGDVVDRWIGRTVIRSCCKLSYEHAQDIIDGKFDVESSNTLGEGWPQLYGQFEWSDVV 435 (880)
Q Consensus 356 ~lcSL~pg~dRlA~Sv~~~id~~G~i~~~~~~~SvIrS~~rLTY~~vq~iL~~~~~~~~~~~~~~~~p~~~~~~~~~~~~ 435 (880)
++|||+||++|+|+||.|+||.+|+|.+++|++|+|+|++||||++||++|+++.+ . ....+.
T Consensus 328 ~lcSL~p~~dRla~s~~m~ld~~g~v~~~~~~~svI~s~~rltY~~v~~~l~~~~~---~--------------~~~~l~ 390 (706)
T COG0557 328 GLCSLNPGVDRLALSCEMTLDSEGRVKKYEIYPSVIKSAARLTYEEVQAILDGKED---D--------------KYAPLL 390 (706)
T ss_pred CccccCCCCceEEEEEEEEECCCCCEEEEEEEEEEEeccccCCHHHHHHHHhcCcc---h--------------hcccch
Confidence 99999999999999999999999999999999999999999999999999998421 0 134566
Q ss_pred HHHHHHHHHHHHHHHhHhcCCCccccCCCceeeeCCCCCeEEEEecCCCcHHHHHHHHHHHHHHHHHHHHHHhCCCceeE
Q 002793 436 RSIKSLYEVSKILKDKRFTDGALRLENSKPVFLFDEYGTPYDSVLSGREDLNFLFEEFMLLANKTAAEVIARAFPDSALL 515 (880)
Q Consensus 436 ~~L~~L~~la~~Lr~~R~~~Gal~l~~pe~~i~lDe~g~p~~i~~~~~~~a~~LIEEfMilAN~~vA~~l~~~~~~~~l~ 515 (880)
+.|..|.+++++++++|.++|+|+|+.+|.++.+|++|.|..+...++.++|.||||||++||++||+++.++ ..|.+|
T Consensus 391 ~~l~~~~~l~~~l~~~R~~rg~i~~~~~E~ki~~d~~~~~~~i~~~~r~~a~~lIee~Ml~AN~~vA~~l~~~-~~~~~~ 469 (706)
T COG0557 391 DSLLELLELAKILKKKRLSRGAIDFDTPEAKIVLDEEGRPVEIEIRERLDAEKLIEEFMLLANETVAEHLEKH-KIPLLY 469 (706)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCcccCCcceeEEECCCCCeeeEEEecccHHHHHHHHHHHHHHHHHHHHHHHc-CCCcce
Confidence 8899999999999999999999999999999999999999999999999999999999999999999999987 457899
Q ss_pred EeCCCCChHHHHHHHHHHHHcCCccCCCChhHHHHHHHHHHHhhcCCHHHHHHHHHHHhcccCCcEecccCCCCCCCCcc
Q 002793 516 RRHPAPNMRKLREFEAFCSKHGLQLDTSSSGQFHQSLEQAREKLKDDYVLFDILINYATRPMQLASYFCSGDFKDDTDWG 595 (880)
Q Consensus 516 R~H~~P~~~kl~~l~~~~~~~G~~l~~~~~~~l~~~L~~i~~~~~~~~~~~~~l~~~~lR~m~~A~Y~~sg~~~s~~~~~ 595 (880)
|+|+.|+.++++.|.+++..+|+.++.......+..+..+.+..++.|. ..++..+++|+|++|+| ++.+.+
T Consensus 470 R~h~~P~~ek~~~l~~~l~~lg~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~v~~~~~lRsm~~a~Y-------s~~~~~ 541 (706)
T COG0557 470 RTHERPSTEKLQSLREFLQNLGLVLPLGGSKPQPQDYQILLETVKGRPL-EAVLQTLLLRSMKQAEY-------SPDNVG 541 (706)
T ss_pred eCCCCCCHHHHHHHHHHHHHcCceecCCCCcCCHHHHHHHHhhccCChH-HHHHHHHHHHhhhcCee-------cCCCCC
Confidence 9999999999999999999999999855433223334444444444443 35677788999999999 467999
Q ss_pred ccccCCCCeeeccCCCCChhhHHHHHHHHHHHHhchhhhhhhccCCCCCCccccccccccccccccchhhhhhhhhHHHH
Q 002793 596 HYALAFPVYTHFTSPLRRYPDLVVHRTLNAALEAEKLYWKHRRMLPKNNHREGVRGRFLTGIFYDKDAAESLEGREALSV 675 (880)
Q Consensus 596 HfgL~~~~YTHFTSPIRRY~DLiVHR~L~a~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~es~~~~~~~~~ 675 (880)
|||||++.|||||||||||+||||||||+++|.++......
T Consensus 542 HfgL~~~~YtHFTSPIRRY~DLivHR~L~~~l~~~~~~~~~--------------------------------------- 582 (706)
T COG0557 542 HFGLALDYYTHFTSPIRRYPDLIVHRQLKALLSGEPIPEKK--------------------------------------- 582 (706)
T ss_pred ceeccccchhccCCchhhchHHHHHHHHHHHhcCCCCCccc---------------------------------------
Confidence 99999999999999999999999999999999865321000
Q ss_pred HhhhcCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccceEEeEEEEEeeccEEEEEEecCceEEEEEeee
Q 002793 676 AALKYGVPCADILVNVATHCNDRKLACRNVKDACVKLYMWILLKKKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDE 755 (880)
Q Consensus 676 ~~~~~~~~~~~~l~~ia~~~N~r~~~A~~a~r~s~~l~~~~~l~~~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~ 755 (880)
...+.+..+|.+||.++++|.+|+|++.++|++.||+++.|.+++|+|++|.++||+|.+|++++||+||++.
T Consensus 583 -------~~~~~l~~i~~~~s~~er~a~~aer~~~~~~~~~~m~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~ 655 (706)
T COG0557 583 -------TSEEELDELAAHISSAERRAQEAERDVIDLLKAEYMKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISS 655 (706)
T ss_pred -------hhHHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEEeccEEEEecccccccceEccc
Confidence 0135788999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 756 VEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 756 l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
|++++|.|++....+++ +++.+.|+.||.|+++.
T Consensus 656 L~~d~y~~~~~~~~l~~--~~~~~~~~lgd~v~v~v 689 (706)
T COG0557 656 LPDDYYHFDERGQALVG--EKSGKVYRLGDEVKVKV 689 (706)
T ss_pred CCCceeeeccccceeec--cccccccccCCEEEEEE
Confidence 99999999999988888 68888999998887775
No 6
>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=100.00 E-value=4.8e-115 Score=1031.23 Aligned_cols=596 Identities=19% Similarity=0.232 Sum_probs=506.1
Q ss_pred cc-ccccceeeeeeecccCCCCCCCCCccccccccCccchhhhhc--eeEEEEecCCCCCccEEEEEEEecCCCCcceEE
Q 002793 59 SE-AYNQEMIEREGYNYINGHHPSTSDSTEKVSSSQQNDGMNAIE--RLSAMISSYPTKRPTGRVVSIIERSPRRDGIVG 135 (880)
Q Consensus 59 g~-~~h~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~--~v~~~~~~~~~~~p~G~VV~IleR~~~~~~~vG 135 (880)
|. ..|+.||||+. .+| . +|+||..++++.||+ +|++.+.+. +++++|+|++|++|+. ..+||
T Consensus 21 G~i~~~~kGfgFv~---~~~--------~-~difI~~~~l~~A~~GD~V~v~i~~~-~~r~~~~v~~iver~~--~~~vG 85 (639)
T TIGR02062 21 GVVKATEKGFGFLE---VDA--------Q-KSYFIPPPQMKKVMHGDKIIAVIHSE-KERESAEPEELIEPFL--TRFVG 85 (639)
T ss_pred EEEEECCCccEEEE---ECC--------C-CcEEEChHHHccCCCCCEEEEEEecC-CCCcEEEEEEEEccCC--CEEEE
Confidence 88 77999999951 111 1 479999999999999 888887654 3567999999999984 68999
Q ss_pred EEEeccccccCCCCcccccccCCCCCCCCCceEEEEeCCCCCCceEEecCCCChhhhhhcccCCccccceEEEEEEeecC
Q 002793 136 FLNVNQWFNYKGGSRKDAKKNRSSLSVPDREYIQLTPTHPKYPKMVVLVKDLPDSIKKRLEEGDATIEMELVAARIDEWN 215 (880)
Q Consensus 136 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~D~rip~i~i~~~~~p~~~~~~~~~gd~~~~~~lvvv~I~~wp 215 (880)
++.. .+ +..+++|+|++++.++.... ++.....+++|| +|+|+|++||
T Consensus 86 ~~~~----------------~~--------~~~~v~p~d~~~~~~i~~~~--~~~~~~~~~~gd------~V~v~I~~~p 133 (639)
T TIGR02062 86 KVQG----------------KD--------DKLAIVPDHPLLKDAIPCRA--AKGLNHEFQEGD------WAVAELRRHP 133 (639)
T ss_pred EEEE----------------eC--------CeEEEEECCCCCCccEEecC--ccccccCCCCCC------EEEEEEeccC
Confidence 9982 22 35789999999988744311 111112455676 7889999999
Q ss_pred CCC-CCCcEEEEEEcCCCCChhHHHHHHHHhcCCCCCCCChhhhccCCCCCCCCChhhhccCccCCCceEEEEcCCCCCC
Q 002793 216 EES-PFPQAHVLHVFGRGGEVEPQINAILYENAICCSGFSPESLSCLPCVPWEVPQEELLSRKDLRNFCIFTIDPSTATD 294 (880)
Q Consensus 216 ~~~-~~p~G~iv~~LG~~~d~~~e~~ail~e~~i~~~~F~~~vl~~~~~~~~~i~~~e~~~R~Dlr~l~i~TIDp~~akD 294 (880)
... ..|.|+|+++||..+++.+|+++++.+|+| +.+|++++++++.. + .++|+|||++++|||||++|+|
T Consensus 134 ~~~~~~~~~~I~~vLG~~~d~~~d~~~il~~~~l-~~~f~~~v~~ea~~-------~-~~~R~DLr~~~~~TID~~~akD 204 (639)
T TIGR02062 134 LKGDRSFYAELTQYITFADDHLAPWWVTLARHNL-EREEPDGVADEMLL-------D-GLVREDLTALDFVTIDSESTKD 204 (639)
T ss_pred CCCCCCceEEEEEEeCCCCCCccHHHHHHHHcCc-CCCCCHHHHHhhhh-------c-cccCcccccCCEEEECCCCCCc
Confidence 865 559999999999999999999999999999 68999999988732 1 2579999999999999999999
Q ss_pred CCceEEEEEcCCceEEEEEEEccccccccCCCHhhHHHHhCcceeecCCCcccCCChhhhhcccCCCCCCceEEEEEEEE
Q 002793 295 LDDALSIERLSDGISRVGVHIADVSYFVLPGTALDIEAQVRSTSVYMLQRKIPMLPVLLSEEVGSLNPGVDRLAFSIFWD 374 (880)
Q Consensus 295 lDDAlsie~l~~G~~~lgVHIADVS~yV~~gS~LD~eA~~RgtSvYLp~rviPMLP~~Ls~~lcSL~pg~dRlA~Sv~~~ 374 (880)
||||||++++++|+|+||||||||||||++||+||+||++||||||||++++||||+.||+++|||+||++|+||||.|+
T Consensus 205 ~DDAisie~~~~g~~~L~VHIADVs~yV~~gS~LD~eA~~RgtSvYLp~~vipMLP~~Ls~~~cSL~p~e~R~als~~~~ 284 (639)
T TIGR02062 205 MDDALFAEALPNGKLQLIVAIADPTAYIAEGSKLDKAAKIRGFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRIT 284 (639)
T ss_pred ccceEEEEEeCCCcEEEEEEEcCccccCCCCCHHHHHHHHhCCcEeCCCceecCCCHHHhcCccccCCCCCeeEEEEEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcCCCCEEE-EEEEEEEEecccccCHHHHHHHHccCCCccccCccCCCCCcccCCCchhhHHHHHHHHHHHHHHHHHhHh
Q 002793 375 LNSAGDVVD-RWIGRTVIRSCCKLSYEHAQDIIDGKFDVESSNTLGEGWPQLYGQFEWSDVVRSIKSLYEVSKILKDKRF 453 (880)
Q Consensus 375 id~~G~i~~-~~~~~SvIrS~~rLTY~~vq~iL~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~L~~L~~la~~Lr~~R~ 453 (880)
||++|++++ ++|++|+|||+++|||++|+++|+++... .| ..+++.++|..|.++|++|+++|.
T Consensus 285 ld~~G~i~~~~~~~~svIrs~~rltY~~v~~~l~~~~~~---------~~------~~~~i~~~L~~L~~la~~l~~~R~ 349 (639)
T TIGR02062 285 ISKDGNIEDKIEFFAATIKSKAKLVYDQVSDWLENTSDW---------QP------ESEEIAQQVRLLHQFCQARIEWRH 349 (639)
T ss_pred EcCCCcEeecCEEEEEEEEeCcEEeHHHHHHHHhCCccc---------cc------chHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999 79999999999999999999999874210 00 135678899999999999999999
Q ss_pred cCCCccccCCCceeeeCCCCCeEEEEecCCCcHHHHHHHHHHHHHHHHHHHHHHhCCCceeEEeCCCCChHHHHHHHHHH
Q 002793 454 TDGALRLENSKPVFLFDEYGTPYDSVLSGREDLNFLFEEFMLLANKTAAEVIARAFPDSALLRRHPAPNMRKLREFEAFC 533 (880)
Q Consensus 454 ~~Gal~l~~pe~~i~lDe~g~p~~i~~~~~~~a~~LIEEfMilAN~~vA~~l~~~~~~~~l~R~H~~P~~~kl~~l~~~~ 533 (880)
++|++.|+.||+++.+|++|.+..+...++.+||+|||||||+||++||+|+.++ ..|++||+|+.|+++++++|.+++
T Consensus 350 ~~G~i~ld~pE~~~~ld~~g~~~~i~~~~~~~a~~lIeE~MllAN~~vA~~l~~~-~~p~iyR~H~~P~~~~l~~l~~~~ 428 (639)
T TIGR02062 350 THALVFKDRPDYRFILSEKGEVLDIVAEPRRIANRIVEEAMIIANICAARFLRDK-LGFGIYNTHAGFDPANAENVVALL 428 (639)
T ss_pred hCCcccccCCceEEEECCCCCEEEEEEecCCHHHHHHHHHHHHHHHHHHHHHHHh-CCCeEEecCCCCCHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999987 468999999999999999999999
Q ss_pred HHcCCccCCCChhHHHHHHHHHHHhhcCCHHHHHHHHHHHhcccCCcEecccCCCCCCCCccccccCCCCeeeccCCCCC
Q 002793 534 SKHGLQLDTSSSGQFHQSLEQAREKLKDDYVLFDILINYATRPMQLASYFCSGDFKDDTDWGHYALAFPVYTHFTSPLRR 613 (880)
Q Consensus 534 ~~~G~~l~~~~~~~l~~~L~~i~~~~~~~~~~~~~l~~~~lR~m~~A~Y~~sg~~~s~~~~~HfgL~~~~YTHFTSPIRR 613 (880)
..+|+.++..+...+ ..+..+...+.+.+. ..+..+++|+|++|.| ++++.+|||||++.||||||||||
T Consensus 429 ~~~g~~~~~~~~~~~-~~~~~~~~~~~~~~~--~~l~~~~~r~~~~a~y-------s~~~~~HfgL~~~~YthfTSPIRR 498 (639)
T TIGR02062 429 KTNGLHVDAEELATL-DGFCKLRRELDAQET--GYLDSRIRRYQSFAEI-------STEPGPHFGLGLEAYATWTSPIRK 498 (639)
T ss_pred HHcCCCCCcccccCH-HHHHHHHHHhhcchH--HHHHHHHHHHhhhccc-------CCCCcCcchhccccccccCChhhh
Confidence 999998864322111 122233333333332 3466677899999999 568999999999999999999999
Q ss_pred hhhHHHHHHHHHHHHhchhhhhhhccCCCCCCccccccccccccccccchhhhhhhhhHHHHHhhhcCCCchhHHHHHHH
Q 002793 614 YPDLVVHRTLNAALEAEKLYWKHRRMLPKNNHREGVRGRFLTGIFYDKDAAESLEGREALSVAALKYGVPCADILVNVAT 693 (880)
Q Consensus 614 Y~DLiVHR~L~a~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~es~~~~~~~~~~~~~~~~~~~~~l~~ia~ 693 (880)
|+||+|||||+++|.+++. . ..+..++.
T Consensus 499 Y~DLivHR~L~~~l~~~~~--------~--------------------------------------------~~~~~~~~ 526 (639)
T TIGR02062 499 YGDMINHRLLKAVIKGETA--------T--------------------------------------------RPQEDITV 526 (639)
T ss_pred hHHHHHHHHHHHHHcCCCC--------C--------------------------------------------CCHHHHHH
Confidence 9999999999999975320 0 01356799
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhccc--eEEeEEEEEeeccEEEEEEecCceEEEEEeeecCC--eEEEEecccce
Q 002793 694 HCNDRKLACRNVKDACVKLYMWILLKKKEV--LLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEG--LIVEWLETTST 769 (880)
Q Consensus 694 ~~N~r~~~A~~a~r~s~~l~~~~~l~~~~~--~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~--~~~e~~~~~~~ 769 (880)
+||++++.|++|+|++.++|+++||+++.| +.|+|+|+++.+.||+|.+++.|+||.||+..|.+ ++|+|+++..+
T Consensus 527 ~~s~~er~a~~aeR~~~~~~~~~yl~~~~g~~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~ 606 (639)
T TIGR02062 527 QLAERRRLNRIAERDVADWLYARFLADKAAKNTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGT 606 (639)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccE
Confidence 999999999999999999999999999985 48999999999999999999999999999999988 77888887754
Q ss_pred EEEeeecccceeecCCCceEEe
Q 002793 770 LVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 770 lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
+.+. .++.|++||+|+++.
T Consensus 607 ~~l~---g~~~~~lgd~v~V~v 625 (639)
T TIGR02062 607 VQIK---GETVYKIGDVIDVVL 625 (639)
T ss_pred EEEe---ccEEEecCCEEEEEE
Confidence 4331 123777777666554
No 7
>KOG2102 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp44/Dis3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.9e-107 Score=986.02 Aligned_cols=574 Identities=42% Similarity=0.672 Sum_probs=504.9
Q ss_pred CccEEEEEEEecCCCCcceEEEEEeccccccCCCCcccccccCCCCCCCCCceEEEEeCCCCCCceEEecC-CCChhhhh
Q 002793 115 RPTGRVVSIIERSPRRDGIVGFLNVNQWFNYKGGSRKDAKKNRSSLSVPDREYIQLTPTHPKYPKMVVLVK-DLPDSIKK 193 (880)
Q Consensus 115 ~p~G~VV~IleR~~~~~~~vG~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~D~rip~i~i~~~-~~p~~~~~ 193 (880)
.|+|+||+|++|+|++ ++|.+....+. .. + .....++||+|.|+|+|++.|+++ +..
T Consensus 338 ~~~~~VV~il~r~~~~--~~~~l~~~~~~--------~~-~------~~~~~~~~~~p~DkRvP~i~i~t~~~~~----- 395 (941)
T KOG2102|consen 338 QPTGKVVAILRRNWRQ--YVGGLLPLSEQ--------AL-K------GSSALIVLFIPSDKRVPLIRILTDDQAQ----- 395 (941)
T ss_pred cccceEEEEEecCcee--eeccccCcccc--------cc-c------ccccceeeeccccCCCCeeecccccccc-----
Confidence 4599999999999964 56655521110 00 0 123478999999999999999987 432
Q ss_pred hcccCCccccceEEEEEEeecCCCCCCCcEEEEEEcCCCCChhHHHHHHHHhcCCCCCCCChhhhccCCC-CCCCCChhh
Q 002793 194 RLEEGDATIEMELVAARIDEWNEESPFPQAHVLHVFGRGGEVEPQINAILYENAICCSGFSPESLSCLPC-VPWEVPQEE 272 (880)
Q Consensus 194 ~~~~gd~~~~~~lvvv~I~~wp~~~~~p~G~iv~~LG~~~d~~~e~~ail~e~~i~~~~F~~~vl~~~~~-~~~~i~~~e 272 (880)
.+.+.++++.|++||.++.||.|++++.||..++.++++++||.+|+++..+|+++++.|++. .+|.+++++
T Consensus 396 -------~~~~~~~~~~I~~W~~ts~~p~g~~v~~lG~i~~~~~e~~aLL~en~v~~~~f~~~~~~~lp~~~~~~~~~~~ 468 (941)
T KOG2102|consen 396 -------DLIDKRIVAAIDRWPRTSLYPFGHLVRELGTIGDTETETEALLLENGVPHKPFSQALLDCLPRSHPWPITEEE 468 (941)
T ss_pred -------chhceeEEEEecccccCCcccCceehhhccCcCCccchhhhhhhcCCCcccccCHHHHhcCCccCCCCcChHH
Confidence 233568999999999999999999999999999999999999999999989999999999999 999999999
Q ss_pred hcc-CccCCCceEEEEcCCCCCCCCceEEEEEcCCceEEEEEEEccccccccCCCHhhHHHHhCcceeecCCCcccCCCh
Q 002793 273 LLS-RKDLRNFCIFTIDPSTATDLDDALSIERLSDGISRVGVHIADVSYFVLPGTALDIEAQVRSTSVYMLQRKIPMLPV 351 (880)
Q Consensus 273 ~~~-R~Dlr~l~i~TIDp~~akDlDDAlsie~l~~G~~~lgVHIADVS~yV~~gS~LD~eA~~RgtSvYLp~rviPMLP~ 351 (880)
... |+|||++.+|+|||++|.|||||||++.++||+|+||||||||||||+|||+||+||++|||||||++++|||||+
T Consensus 469 ~~~~R~Dlr~~~i~~IDp~~~~dlDdAL~~~~l~nG~~evGVHIADVt~fV~pgs~lD~eA~~R~ttvyL~q~~i~MLP~ 548 (941)
T KOG2102|consen 469 LQKLRKDLRDLLIFSIDPPGATDLDDALHVRNLPNGNLEVGVHIADVTHFVKPGSALDREAARRGTTVYLVQKRIPMLPK 548 (941)
T ss_pred hhhhhhhhhhceEEeecCCCccchhhhhheeecCCCcEEEEEEeccchhhcCCCCccCHHHHhhcceEEeccccccCCch
Confidence 998 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhcccCCCCCCceEEEEEEEEEcCCCCEEEEEEEEEEEecccccCHHHHHHHHccCCCccccCccCCCCCcccCCCch
Q 002793 352 LLSEEVGSLNPGVDRLAFSIFWDLNSAGDVVDRWIGRTVIRSCCKLSYEHAQDIIDGKFDVESSNTLGEGWPQLYGQFEW 431 (880)
Q Consensus 352 ~Ls~~lcSL~pg~dRlA~Sv~~~id~~G~i~~~~~~~SvIrS~~rLTY~~vq~iL~~~~~~~~~~~~~~~~p~~~~~~~~ 431 (880)
.||+++|||+||+||+||||.|+++.+|.|++.||++|+|+|+++|+|++||++|+++.. .
T Consensus 549 ~L~~~lcSL~~g~dr~aFSvvwel~~~~~i~~~~f~ksvI~s~~~lsye~Aq~~id~~~~-------------------~ 609 (941)
T KOG2102|consen 549 LLSEELCSLRPGVDRLAFSVVWELDSDGSILKTWFGKSVIRSKAALSYEEAQDILDTPNS-------------------S 609 (941)
T ss_pred hhhhhheeccCCCceeeEEEEEEEcCCCceeeceecchhcccchhhhHHHHHHHhcCCcc-------------------c
Confidence 999999999999999999999999999999999999999999999999999999998421 1
Q ss_pred hhHHHHHHHHHHHHHHHHHhHhcCCCccccCCCceeeeCCCC-CeEEEEecCCCcHHHHHHHHHHHHHHHHHHHHHHhCC
Q 002793 432 SDVVRSIKSLYEVSKILKDKRFTDGALRLENSKPVFLFDEYG-TPYDSVLSGREDLNFLFEEFMLLANKTAAEVIARAFP 510 (880)
Q Consensus 432 ~~~~~~L~~L~~la~~Lr~~R~~~Gal~l~~pe~~i~lDe~g-~p~~i~~~~~~~a~~LIEEfMilAN~~vA~~l~~~~~ 510 (880)
.++...|+.|++||+.||++|+.+|++.+..+|+.+.+|+.+ .|.++..++..+++.||||||++||..||++|.+.||
T Consensus 610 ~~v~~~l~~l~~ia~~lr~~R~~~gal~l~~~e~~~~~d~~~~~p~~~e~~~~~~~n~lveEfmllaN~~vA~~I~~~f~ 689 (941)
T KOG2102|consen 610 DPLTSSLRLLHEIAKILRQKRLDNGALLLRSPELRFLLDEEKPNPQDVEVKELTETNFLVEEFMLLANISVAEKILASFP 689 (941)
T ss_pred chhhhhHHHHHHHHHHHHHHHhccCCcccccHhHHhhhccCCCCccccceeeeehhhhHHHHHHHHHhHHHHHHHHHhCC
Confidence 367789999999999999999999999999999999999877 7888888999999999999999999999999999999
Q ss_pred CceeEEeCCCCChHHHHHHHHHHHHcCCccCCCChhHHHHHHHHHHHhhcCCHHHHHHHHHHHhcccCCcEecccCCCCC
Q 002793 511 DSALLRRHPAPNMRKLREFEAFCSKHGLQLDTSSSGQFHQSLEQAREKLKDDYVLFDILINYATRPMQLASYFCSGDFKD 590 (880)
Q Consensus 511 ~~~l~R~H~~P~~~kl~~l~~~~~~~G~~l~~~~~~~l~~~L~~i~~~~~~~~~~~~~l~~~~lR~m~~A~Y~~sg~~~s 590 (880)
.++++|+||.|....++.+.++|..+|+.++.++++.|+.+|.++.+.. .|....+|..+++|+|++|+|||+|.. .
T Consensus 690 ~~alLR~hp~P~~~~~~~~~~~~~~~g~~ld~sS~~~L~~Sl~r~~~~~--~p~~~~~l~~l~~r~m~~A~yf~sg~~-~ 766 (941)
T KOG2102|consen 690 SLALLRRHPSPPPENFKPLVSLCLELGFNLDTSSSKSLADSLDRIRDDD--KPYLNTLLRILATRSMTRAVYFCSGSS-D 766 (941)
T ss_pred chhhhccCCCCccccccHHHHHHHHcCCCccccchHHHhhhHhhhcCCc--hHHHHHHHHHHHhhhhhceeEEeeccc-C
Confidence 9999999999999999999999999999999999999999999998753 367777889999999999999999973 5
Q ss_pred CCCccccccCCCCeeeccCCCCChhhHHHHHHHHHHHHhchhhhhhhccCCCCCCccccccccccccccccchhhhhhhh
Q 002793 591 DTDWGHYALAFPVYTHFTSPLRRYPDLVVHRTLNAALEAEKLYWKHRRMLPKNNHREGVRGRFLTGIFYDKDAAESLEGR 670 (880)
Q Consensus 591 ~~~~~HfgL~~~~YTHFTSPIRRY~DLiVHR~L~a~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~es~~~~ 670 (880)
...++|||||++.|||||||||||+||+|||||++....... .
T Consensus 767 ~~~~~HygLa~p~YTHFTsPiRRY~DIivHrqL~~~~~~~~~------~------------------------------- 809 (941)
T KOG2102|consen 767 TPQFHHYGLASPLYTHFTSPIRRYADIIVHRQLAAAFLERSP------T------------------------------- 809 (941)
T ss_pred cchhhchhhcccchhhccCcccccchHHHHHHHHHHhhccCc------c-------------------------------
Confidence 678999999999999999999999999999999963221100 0
Q ss_pred hHHHHHhhhcCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccceEEeEEEEEeeccEEEEEEecCceEEE
Q 002793 671 EALSVAALKYGVPCADILVNVATHCNDRKLACRNVKDACVKLYMWILLKKKEVLLSEARVLALGPRFMTIYIEKLAIERR 750 (880)
Q Consensus 671 ~~~~~~~~~~~~~~~~~l~~ia~~~N~r~~~A~~a~r~s~~l~~~~~l~~~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~ 750 (880)
.+....+..+|.+||+|+++|+.|+++|.++|++.|++++ ....+|+|+.|.++||.|+||+||+||+
T Consensus 810 -----------~~~~~~l~~i~~~~N~r~~~a~~a~~~S~~l~~~~~~k~~-~~~~~a~v~~V~~~~~~v~ipe~G~e~~ 877 (941)
T KOG2102|consen 810 -----------APDRPNLSSLAANCNERKKAAKKAQEASTELYLCEYLKDK-QVLEEAVVLFVRPNGIDVVIPEYGLEGR 877 (941)
T ss_pred -----------ccccccHHHHHhhhhhhHHHHHHHHHhhHHHHHHHHHHhc-ccccceEEEEEecCceEEEEcccCceEE
Confidence 0112357889999999999999999999999999999988 5678999999999999999999999999
Q ss_pred EEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEeceeEEEEEecCCCc
Q 002793 751 IYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRALEEVALVVRPNDLK 805 (880)
Q Consensus 751 V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~~d~v~v~~~~~~~~ 805 (880)
||++.+ ..+.++..+ +. + ..+++.++.|.+.+..+...
T Consensus 878 v~l~~~--------~~~~~~~~~--~~------~-~~~~~~~~~v~~~~~~~~~~ 915 (941)
T KOG2102|consen 878 VYLDLL--------KPSQTFFLD--DE------V-SLRFEESDPVVVRIKLDKLV 915 (941)
T ss_pred EEeccc--------CCccceeec--cc------c-cccccccCCceeeecccccc
Confidence 999932 333344432 11 1 11166777777777755554
No 8
>PF00773 RNB: RNB domain CAUTION: The Prosite pattern does not correspond to this Pfam.; InterPro: IPR001900 This entry represents the catalytic domain of ribonuclease II []. It includes characterised and related sequences to exoribonuclease II (RNase II) and ribonuclease R, a bacterial 3' --> 5' exoribonuclease homologous to RNase II [,,].; GO: 0003723 RNA binding, 0004540 ribonuclease activity; PDB: 2R7D_A 2R7F_A 2ID0_D 2IX1_A 2IX0_A 2VNU_D 2WP8_J.
Probab=100.00 E-value=3.2e-75 Score=644.13 Aligned_cols=320 Identities=42% Similarity=0.673 Sum_probs=255.3
Q ss_pred CccCCCceEEEEcCCCCCCCCceEEEEEcCCceEEEEEEEccccccccCCCHhhHHHHhCcceeecCCCcccCCChhhhh
Q 002793 276 RKDLRNFCIFTIDPSTATDLDDALSIERLSDGISRVGVHIADVSYFVLPGTALDIEAQVRSTSVYMLQRKIPMLPVLLSE 355 (880)
Q Consensus 276 R~Dlr~l~i~TIDp~~akDlDDAlsie~l~~G~~~lgVHIADVS~yV~~gS~LD~eA~~RgtSvYLp~rviPMLP~~Ls~ 355 (880)
|+|||++++|||||++|+|+||||||+++++|+|+|||||||||+||++||+||++|++||+|+|||++++||||+.|++
T Consensus 1 R~Dl~~~~~~tID~~~~~d~DDAisie~~~~~~~~v~VHIaDvt~~i~~~s~ld~~A~~r~~s~Ylp~~~~pMlP~~l~~ 80 (325)
T PF00773_consen 1 RKDLRDLPVFTIDPPGAKDIDDAISIEKLPDGKYEVGVHIADVTSFIPPDSPLDREARKRGTSVYLPEKVVPMLPPELSE 80 (325)
T ss_dssp SEECTTSEEEEEESTTSS---EEEEEEEETTTEEEEEEEEE-GGGTS-TTSHHHHHHHHH-B-EEETTEEE-SS-HHHHC
T ss_pred CccCCCCCEEEEcCCCCCCCCCeEEEEECCCCcEEEEEEcCCHHHhhccChHHHHHHHhcCccEECCCCccccCChhHhc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCceEEEEEEEEEcCCCCEEEEEEEEEEEecccccCHHHHHHHHccCCCccccCccCCCCCcccCCCchhhHH
Q 002793 356 EVGSLNPGVDRLAFSIFWDLNSAGDVVDRWIGRTVIRSCCKLSYEHAQDIIDGKFDVESSNTLGEGWPQLYGQFEWSDVV 435 (880)
Q Consensus 356 ~lcSL~pg~dRlA~Sv~~~id~~G~i~~~~~~~SvIrS~~rLTY~~vq~iL~~~~~~~~~~~~~~~~p~~~~~~~~~~~~ 435 (880)
++|||.||++|+|||+.|+||++|+|++++|++|+|+|+++|||++|+++|++...... ...+.
T Consensus 81 ~~~SL~~~~~r~a~S~~~~l~~~G~i~~~~i~~s~I~~~~~lty~~v~~~l~~~~~~~~----------------~~~~~ 144 (325)
T PF00773_consen 81 DLCSLNPGKDRLAFSVIFTLDEDGEILDYEIYPSIIRSVARLTYEEVDEILEGKSQEEP----------------ESPIE 144 (325)
T ss_dssp TTSSTTBTSEEEEEEEEEEE-TTS-EEEEEEEEEEEEBSEEEEHHHHHHHHHTTTS--H----------------CSHCH
T ss_pred ccccCCCCCCceEEEEEEEEeeCCeEeeeEEEEEEEecccccCHHHHHHHHhcCcccch----------------hhHHH
Confidence 99999999999999999999999999999999999999999999999999998432100 00135
Q ss_pred HHHHHHHHHHHHHHHhHhcCCCccc-cCCCceeeeCCCCCeEEEEecC---CCcHHHHHHHHHHHHHHHHHHHHHHhCCC
Q 002793 436 RSIKSLYEVSKILKDKRFTDGALRL-ENSKPVFLFDEYGTPYDSVLSG---REDLNFLFEEFMLLANKTAAEVIARAFPD 511 (880)
Q Consensus 436 ~~L~~L~~la~~Lr~~R~~~Gal~l-~~pe~~i~lDe~g~p~~i~~~~---~~~a~~LIEEfMilAN~~vA~~l~~~~~~ 511 (880)
++|..|+++|+.|+++|..+|++.+ +.|+..+.+++++.+....... ...|+.||+|||++||++||+|+.+ ++.
T Consensus 145 ~~L~~l~~la~~l~~~R~~~Ga~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~lV~E~MilAN~~vA~~~~~-~~i 223 (325)
T PF00773_consen 145 EDLKLLYELAKALRKKRLSRGAIELFNSPELKFSLDEDGPPKEINRESSDESSPAHSLVEELMILANRAVAQFLSE-NGI 223 (325)
T ss_dssp HHHHHHHHHHHHHHHHHHHTTS-----SHCEEEEEETTTTEEEEEEE------HHHHHHHHHHHHHHHHHHHHHHH-CTT
T ss_pred HHHHHHHHHHHHHHHhhhhccCccccCCCceEEEEecCCCcceEEEEeccCCchHHHHHHHHHHHHHHHHHHHHHH-cCC
Confidence 7899999999999999999999999 8889999999999888887765 8999999999999999999999996 489
Q ss_pred ceeEEeCCCCChHHHHHHHHHHHHcCCccCCCChhHHHHHHHHHHHhhcCCHHHHHHHHHHHhcccCCcEecccCCCCCC
Q 002793 512 SALLRRHPAPNMRKLREFEAFCSKHGLQLDTSSSGQFHQSLEQAREKLKDDYVLFDILINYATRPMQLASYFCSGDFKDD 591 (880)
Q Consensus 512 ~~l~R~H~~P~~~kl~~l~~~~~~~G~~l~~~~~~~l~~~L~~i~~~~~~~~~~~~~l~~~~lR~m~~A~Y~~sg~~~s~ 591 (880)
|++||+|+.|+..+++++.+.+ +++++. .+.+ .++++... .+.+ ....+..+++++|.+|+| +.
T Consensus 224 p~iyR~~~~p~~~~~~~~~~~~---~~~~~~--~~~~--~~~~~~~~-~~~~-~~~~~~~~l~~~l~~a~y-------~~ 287 (325)
T PF00773_consen 224 PAIYRVQPEPDPERLEELLKLL---KLDLDE--TKSL--TLQNLLQA-ENPP-NSLALRYLLLKTLPPAEY-------ST 287 (325)
T ss_dssp TSEEEEB-SSSCCCHHHHHHHH---T---ST--CHHH--CHHCHHCC-CCTT-SSHHHHHHHHCCC--EEE-------ES
T ss_pred CceeeeCCCCCHHHHHHHHHHh---cCCCCC--cchh--hHHHHHHh-cCCh-HHHHHHHHHHHhhccccc-------cc
Confidence 9999999999999988887776 444433 3332 23333322 2222 123455677899999999 46
Q ss_pred CCccccccCCCCeeeccCCCCChhhHHHHHHHHHHHH
Q 002793 592 TDWGHYALAFPVYTHFTSPLRRYPDLVVHRTLNAALE 628 (880)
Q Consensus 592 ~~~~HfgL~~~~YTHFTSPIRRY~DLiVHR~L~a~L~ 628 (880)
.+.+|||||++.|||||||||||+||+|||||+++|.
T Consensus 288 ~p~~H~~L~l~~Yt~~TSPlRRY~Dl~~hrql~~~L~ 324 (325)
T PF00773_consen 288 EPSGHFGLGLPAYTHFTSPLRRYADLVVHRQLKAALR 324 (325)
T ss_dssp SGC-BTTTTBSS-B--S-TTTBHHHHHHHHHHHHHHH
T ss_pred CCCcceeeeccccccccChhhhhHHHHHHHHHHHHhh
Confidence 7899999999999999999999999999999999986
No 9
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=100.00 E-value=1.1e-67 Score=572.43 Aligned_cols=591 Identities=21% Similarity=0.256 Sum_probs=435.5
Q ss_pred cc-ccccceeeeeeecccCCCCCCCCCccccccccCccchhhhhceeEEEEecCCCC---CccEEEEEEEecCCCCcceE
Q 002793 59 SE-AYNQEMIEREGYNYINGHHPSTSDSTEKVSSSQQNDGMNAIERLSAMISSYPTK---RPTGRVVSIIERSPRRDGIV 134 (880)
Q Consensus 59 g~-~~h~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~v~~~~~~~~~~---~p~G~VV~IleR~~~~~~~v 134 (880)
|- -....||||+-....-.+|+.++- +.-.||++ |+...+..+..+ .|+.-|---| +.||
T Consensus 24 GvVK~tekgfGFLEvD~qkSYFIpPp~---MKkvMHGD-------kIiA~i~te~erE~aEPe~LiEp~L------tRFv 87 (645)
T COG4776 24 GVVKATEKGFGFLEVDAQKSYFIPPPQ---MKKVMHGD-------KIIAVIHTEKERESAEPEELIEPFL------TRFV 87 (645)
T ss_pred eeeeeccccceeEEEcCccccccCCHH---HhhhcccC-------eEEEEEEecCcccccChHHHHHHHH------HHHH
Confidence 44 446789999877767778876665 44567776 777777665432 2333332222 3378
Q ss_pred EEEEeccccccCCCCcccccccCCCCCCCCCceEEEEeCCCCCCceEEecCCCChhhhhhcccCCccccceEEEEEEeec
Q 002793 135 GFLNVNQWFNYKGGSRKDAKKNRSSLSVPDREYIQLTPTHPKYPKMVVLVKDLPDSIKKRLEEGDATIEMELVAARIDEW 214 (880)
Q Consensus 135 G~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~D~rip~i~i~~~~~p~~~~~~~~~gd~~~~~~lvvv~I~~w 214 (880)
|.++. +. +...++|+.+-+... |.-.+ .+.....+++|| .+|+++.+.
T Consensus 88 gkV~~---------------kd---------~rL~i~pDhP~lk~~-i~~~~-~k~l~~~fQeGD------W~VA~lk~H 135 (645)
T COG4776 88 GKVQG---------------KD---------DRLQIVPDHPLLKDA-IPCRA-AKGLNEEFQEGD------WAVAELKRH 135 (645)
T ss_pred HHHhc---------------cC---------CceEEcCCChhhhhh-ccccc-ccchhhhhhcCc------eehhhhhcC
Confidence 88772 11 356788888776554 33222 244456678888 688999999
Q ss_pred CCCC-CCCcEEEEEEcCCCCChhHHHHHHHHhcCCCCCCCChhhhccCCCCCCCCChhhhccCccCCCceEEEEcCCCCC
Q 002793 215 NEES-PFPQAHVLHVFGRGGEVEPQINAILYENAICCSGFSPESLSCLPCVPWEVPQEELLSRKDLRNFCIFTIDPSTAT 293 (880)
Q Consensus 215 p~~~-~~p~G~iv~~LG~~~d~~~e~~ail~e~~i~~~~F~~~vl~~~~~~~~~i~~~e~~~R~Dlr~l~i~TIDp~~ak 293 (880)
|... +.-.+.|.+.+-..+|.-+--=.-|..|++.. +++. ...+|.+.++. -.|+||+.+.++|||+++++
T Consensus 136 pLkgDr~F~a~lt~~It~~dD~l~PWWVTLArh~l~r--~~p~-----g~~d~~m~d~~-l~RedLTaL~FvTID~~sT~ 207 (645)
T COG4776 136 PLKGDRSFYAELTQKITFADDHLAPWWVTLARHNLER--EAPA-----GIVDTEMLDEG-LVREDLTALDFVTIDSESTE 207 (645)
T ss_pred CCCCchhHHHHHHHHhhccCCcccceeeehhhccCCc--cCCC-----cccchhhhhhh-hhhccccccceEEecCcccc
Confidence 8643 33444555555555554333333456666632 2111 11234443333 47999999999999999999
Q ss_pred CCCceEEEEEcCCceEEEEEEEccccccccCCCHhhHHHHhCcceeecCCCcccCCChhhhhcccCCCCCCceEEEEEEE
Q 002793 294 DLDDALSIERLSDGISRVGVHIADVSYFVLPGTALDIEAQVRSTSVYMLQRKIPMLPVLLSEEVGSLNPGVDRLAFSIFW 373 (880)
Q Consensus 294 DlDDAlsie~l~~G~~~lgVHIADVS~yV~~gS~LD~eA~~RgtSvYLp~rviPMLP~~Ls~~lcSL~pg~dRlA~Sv~~ 373 (880)
|+|||+.++++++|.|.|-|.|||++.||.+||.||++|++|+.|.|||+.-|||||+.||+++|||+|++-|+++.|.+
T Consensus 208 DmDDALy~~~~~~~~~~L~vAIADPTAyI~~~s~ld~~A~~R~FTnYLPGfNIPMLPreLsd~lCSL~~ne~RPaL~C~i 287 (645)
T COG4776 208 DMDDALYAEPLPDGDWQLIVAIADPTAYIAEGSKLDKEAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPALACRI 287 (645)
T ss_pred ccchhhhccccCCCcEEEEEEecCCccccCCcchhhHHHHHHHHhhcCCCCCCCCCChhhhhhhhhccccccCceEEEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEcCCCCEE-EEEEEEEEEecccccCHHHHHHHHccCCCccccCccCCCCCcccCCCchhhHHHHHHHHHHHHHHHHHhH
Q 002793 374 DLNSAGDVV-DRWIGRTVIRSCCKLSYEHAQDIIDGKFDVESSNTLGEGWPQLYGQFEWSDVVRSIKSLYEVSKILKDKR 452 (880)
Q Consensus 374 ~id~~G~i~-~~~~~~SvIrS~~rLTY~~vq~iL~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~L~~L~~la~~Lr~~R 452 (880)
+++.+|+|. +.+|..+.|+|+++|.|++|.++|++..+ + .| +..++.+.++.|+.+++..-+.|
T Consensus 288 t~~~~G~I~~~i~F~aA~i~SkakL~YdhVSDwlE~~~~-----W----qP------e~~~iAqqi~~L~~~~~aR~~WR 352 (645)
T COG4776 288 TIDKDGNITDKIRFFAATIESKAKLVYDHVSDWLENTGD-----W----QP------ESEAIAQQIRLLHQFCQARIEWR 352 (645)
T ss_pred EEecCCccccchhhHHHhhhhhhhhhhhhHHHHHhcCCC-----C----CC------CCHHHHHHHHHHHHHHHHHHHHH
Confidence 999999998 47899999999999999999999998421 1 12 24578899999999999999999
Q ss_pred hcCCCccccCCCceeeeCCCCCeEEEEecCCCcHHHHHHHHHHHHHHHHHHHHHHhCCCceeEEeCCCCChHHHHHHHHH
Q 002793 453 FTDGALRLENSKPVFLFDEYGTPYDSVLSGREDLNFLFEEFMLLANKTAAEVIARAFPDSALLRRHPAPNMRKLREFEAF 532 (880)
Q Consensus 453 ~~~Gal~l~~pe~~i~lDe~g~p~~i~~~~~~~a~~LIEEfMilAN~~vA~~l~~~~~~~~l~R~H~~P~~~kl~~l~~~ 532 (880)
....-+.=+.|+.+|.+.|+|.++++....|..||+||||.||+||.++|++|.+++ ..++|-+|..-++.+++....+
T Consensus 353 k~hal~FkdrpdYrF~l~e~g~V~~I~ae~RRiAnriVEE~MI~ANIcAa~~L~~~~-gfGI~N~HsGFd~~~~e~a~~~ 431 (645)
T COG4776 353 KTHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEESMIAANICAARVLREKL-GFGIYNVHSGFDPANAEAAAAL 431 (645)
T ss_pred hhceeeccCCCceEEEecCCCceEeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CcceeeccccCCHHHHHHHHHH
Confidence 877666668999999999999999999999999999999999999999999999986 4799999999999999999999
Q ss_pred HHHcCCccCCCChhHHHHHHHHHHHhhcCCHHHHHHHHHHHhcccCCcEecccCCCCCCCCccccccCCCCeeeccCCCC
Q 002793 533 CSKHGLQLDTSSSGQFHQSLEQAREKLKDDYVLFDILINYATRPMQLASYFCSGDFKDDTDWGHYALAFPVYTHFTSPLR 612 (880)
Q Consensus 533 ~~~~G~~l~~~~~~~l~~~L~~i~~~~~~~~~~~~~l~~~~lR~m~~A~Y~~sg~~~s~~~~~HfgL~~~~YTHFTSPIR 612 (880)
+...|...+...-.++ ..+.+++..+...+. +.|-.-+-|...-|++ ++++.+|||||++.|+.||||||
T Consensus 432 l~~~~~~~~~e~l~Tl-~Gfc~lRr~l~~~~t--~yld~RiRrfqsfae~-------~t~p~PHFglGl~~YATWTSPIR 501 (645)
T COG4776 432 LKTNGLNVDAEELLTL-EGFCKLRRELDAQPT--GYLDSRIRRFQSFAEI-------STEPGPHFGLGLEAYATWTSPIR 501 (645)
T ss_pred HHhcCcCCCHHHHhhh-HHHHHHHHHhhcccc--chHHHHHHHHHhHHhh-------ccCcCccccccchheeeccchhh
Confidence 9999986653221122 123333322221110 1121112222233443 56899999999999999999999
Q ss_pred ChhhHHHHHHHHHHHHhchhhhhhhccCCCCCCccccccccccccccccchhhhhhhhhHHHHHhhhcCCCchhHHHHHH
Q 002793 613 RYPDLVVHRTLNAALEAEKLYWKHRRMLPKNNHREGVRGRFLTGIFYDKDAAESLEGREALSVAALKYGVPCADILVNVA 692 (880)
Q Consensus 613 RY~DLiVHR~L~a~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~es~~~~~~~~~~~~~~~~~~~~~l~~ia 692 (880)
+|.|+|+||+|+|+|.++... + | -+.+.
T Consensus 502 KY~DMiNHRLlKavi~~~~~~-k-----------------------------------------------P----qedi~ 529 (645)
T COG4776 502 KYGDMINHRLLKAVIKGETAE-K-----------------------------------------------P----QEDIT 529 (645)
T ss_pred hhhhHHHHHHHHHHHcCCCcC-C-----------------------------------------------C----chHHH
Confidence 999999999999999865310 0 1 12345
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhccce--EEeEEEEEeeccEEEEEEecCceEEEEEeeecCCe--EEEEecccc
Q 002793 693 THCNDRKLACRNVKDACVKLYMWILLKKKEVL--LSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGL--IVEWLETTS 768 (880)
Q Consensus 693 ~~~N~r~~~A~~a~r~s~~l~~~~~l~~~~~~--~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~--~~e~~~~~~ 768 (880)
..+.+++|.-|.|||+.-+...|+||+.+.+. .|.|-|..+...|+.|-+-+-|--..|--.-+.+. ..++..++.
T Consensus 530 v~lae~Rr~nrmaERdv~DWLY~r~L~~k~~~~~~F~AEI~Di~R~G~RvrLleNGA~~FIPa~lih~~reei~~n~e~g 609 (645)
T COG4776 530 VQLAERRRLNRMAERDVADWLYARFLADKAGTNTRFAAEIQDISRGGMRVRLLENGAIAFIPAPLIHANREELVCNQENG 609 (645)
T ss_pred HHHHHHHHhhhhhhhhhHHHHHHHHhccccccCchhhhhhhhhccCceEEEeccCCcceecchhhhccchhheEecCCCc
Confidence 56778889999999999999999999887653 58888888887777777666665554443333322 234444444
Q ss_pred eEEEeeecccceeecCCC
Q 002793 769 TLVLSLCAHKRSFKRGGP 786 (880)
Q Consensus 769 ~lv~~~~~~k~~~~~g~~ 786 (880)
++-. +....|++||.
T Consensus 610 tv~I---~ge~~Yk~~D~ 624 (645)
T COG4776 610 TVQI---KGETVYKVGDV 624 (645)
T ss_pred eEEE---ccEEEEeeccE
Confidence 4444 23344444543
No 10
>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=98.23 E-value=5.6e-06 Score=73.27 Aligned_cols=66 Identities=14% Similarity=0.086 Sum_probs=57.5
Q ss_pred ceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEE
Q 002793 723 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 790 (880)
Q Consensus 723 ~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r 790 (880)
|.+++|.|+++.++|++|.++.+++||.||+++++++++.|++.+..+.+ +.....|+.||.++++
T Consensus 2 g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~--~~~~~~~~~gd~v~v~ 67 (83)
T cd04471 2 GEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVG--ERTGKVFRLGDKVKVR 67 (83)
T ss_pred CCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEe--ccCCCEEcCCCEEEEE
Confidence 56899999999999999999999999999999999989999999888877 4556777778766655
No 11
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=97.11 E-value=0.0017 Score=60.12 Aligned_cols=62 Identities=15% Similarity=0.111 Sum_probs=54.6
Q ss_pred EEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEE
Q 002793 725 LSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 790 (880)
Q Consensus 725 ~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r 790 (880)
++.|.|+++.++|++|.+. +++|.||++++.++++.|++.+..+++ ...+..|++||.++++
T Consensus 2 vv~g~V~~i~~~GifV~l~--~v~G~v~~~~l~~~~~~~~~~~~~~~~--~~~~~~~~~Gd~v~vk 63 (99)
T cd04460 2 VVEGEVVEVVDFGAFVRIG--PVDGLLHISQIMDDYISYDPKNKRLIG--EETKRVLKVGDVVRAR 63 (99)
T ss_pred EEEEEEEEEEeccEEEEEc--CeEEEEEEEEccCCceEechhheeecc--cCcCCEECCCCEEEEE
Confidence 5789999999999988886 599999999999999999999888888 4677889999977765
No 12
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=97.07 E-value=0.00025 Score=59.38 Aligned_cols=52 Identities=15% Similarity=0.106 Sum_probs=36.5
Q ss_pred ccccceeeeeeecccCCCCCCCCCccccccccCccchhhhhc--eeEEEEec-CCCCCccEEEEEE
Q 002793 61 AYNQEMIEREGYNYINGHHPSTSDSTEKVSSSQQNDGMNAIE--RLSAMISS-YPTKRPTGRVVSI 123 (880)
Q Consensus 61 ~~h~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~--~v~~~~~~-~~~~~p~G~VV~I 123 (880)
..|++||||+.. ++ ...|+||..++++.|++ +|.+.+.. ..+++|+|+|+.|
T Consensus 4 ~~~~~GfGFv~~---~~--------~~~DifIp~~~l~~A~~gD~V~v~i~~~~~~~~~eg~vv~V 58 (58)
T PF08206_consen 4 KIHPKGFGFVIP---DD--------GGEDIFIPPRNLNGAMDGDKVLVRITPPSRGKRPEGEVVEV 58 (58)
T ss_dssp EE-SSS-EEEEE---CT---------TEEEEE-HHHHTTS-TT-EEEEEEEESSSEEEEEEEEEE-
T ss_pred EEEcCCCEEEEE---CC--------CCCCEEECHHHHCCCCCCCEEEEEEecCCCCCCCCEEEEeC
Confidence 458999999543 33 22689999999999999 88887776 3467899999987
No 13
>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=96.95 E-value=0.00075 Score=69.31 Aligned_cols=75 Identities=12% Similarity=0.072 Sum_probs=64.7
Q ss_pred HHHHHHhhccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 713 YMWILLKKKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 713 ~~~~~l~~~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
|.+.+++...|++++|+|+++.+.|++|-+ . .+++.++.+++.+++++|++.+..+++ +.++..++.|+.|++|.
T Consensus 72 f~~i~f~p~~gEvv~G~V~~v~~~GifV~l-g-~~~gi~~~~~l~~~~~~~d~~~~~~~~--~~~~~~~~~Gd~VrvrV 146 (179)
T TIGR00448 72 FRALVFKPELGEIVEGEVIEIVEFGAFVSL-G-PFDGLFHVSQVTDDYCYYDPKESALIG--KETKKVLDEGDKVRARI 146 (179)
T ss_pred EEEEEEeccCCCEEEEEEEEEEeeEEEEEe-C-CceEEEEcHHhCCCceEEccccceEEE--ccCCeEEcCCCEEEEEE
Confidence 344467778899999999999999999988 3 399999999999999999999998988 46778999999888875
No 14
>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=96.75 E-value=0.0032 Score=54.87 Aligned_cols=57 Identities=7% Similarity=-0.102 Sum_probs=45.1
Q ss_pred cceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 722 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 722 ~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
.|.+++|.|+++.++|++|.++.++.||+||++++.+..+ + ..+..++.||+++++.
T Consensus 3 ~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~--~-----------~~~~~~~~Gd~v~vkv 59 (73)
T cd05686 3 LYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRV--D-----------DPSEVVDVGEKVWVKV 59 (73)
T ss_pred CCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcc--c-----------CHhhEECCCCEEEEEE
Confidence 3678999999999999999997777899999999876422 1 3344578899887763
No 15
>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=96.08 E-value=0.012 Score=51.79 Aligned_cols=57 Identities=14% Similarity=0.004 Sum_probs=45.0
Q ss_pred ceEEeEEEEEeeccEEEEEEecC--ceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 723 VLLSEARVLALGPRFMTIYIEKL--AIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 723 ~~~~~a~V~~v~~~~~~V~Ip~~--giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
|.++.|.|..+.++|++|.+.+. +++|++|+++++..++ +. .....|++||.++++.
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~---------~~---~~~~~~~~Gd~v~v~v 59 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGR---------VA---NPSDVVKRGQKVKVKV 59 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCC---------cC---ChhheeCCCCEEEEEE
Confidence 45789999999999999999876 8999999999986543 11 2345688999887763
No 16
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=95.72 E-value=0.017 Score=58.96 Aligned_cols=71 Identities=15% Similarity=0.105 Sum_probs=61.4
Q ss_pred hhccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEece
Q 002793 719 KKKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRALE 793 (880)
Q Consensus 719 ~~~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~~d 793 (880)
+-..+++.+|.|+.+.+.|++|-|- -+.|+||.+++.|+++.|++....+++ +.+|+.++.||.|++|...
T Consensus 78 kP~~gEVV~GeVv~~~~~G~fV~ig--p~dglvh~sqi~dd~~~~d~~~~~~~g--~~tk~~i~~gd~VR~RIv~ 148 (183)
T COG1095 78 KPFRGEVVEGEVVEVVEFGAFVRIG--PLDGLVHVSQIMDDYIDYDEKNKVLIG--EETKRVLKVGDKVRARIVG 148 (183)
T ss_pred EeccccEEEEEEEEEeecceEEEec--cccccccHhhccCcccccCcccceeee--cccceEEecCCEEEEEEEE
Confidence 4445788999999999988777666 688999999999999999999999999 5899999999999888733
No 17
>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=95.52 E-value=0.035 Score=47.88 Aligned_cols=57 Identities=12% Similarity=-0.014 Sum_probs=43.1
Q ss_pred cceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 722 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 722 ~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
.|..+.|.|.++.++|++|.++. ++||++|+++++. .++ . ......|++||.++++.
T Consensus 3 ~g~~~~g~V~~i~~~G~fv~l~~-~~~Gl~~~~~l~~--~~~-------~---~~~~~~~~~Gd~v~v~v 59 (72)
T cd05689 3 EGTRLFGKVTNLTDYGCFVELEE-GVEGLVHVSEMDW--TNK-------N---IHPSKVVSLGDEVEVMV 59 (72)
T ss_pred CCCEEEEEEEEEEeeEEEEEcCC-CCEEEEEEEeccC--ccc-------c---cCcccEeCCCCEEEEEE
Confidence 46789999999999999999976 7999999999842 111 0 12345689999777663
No 18
>PRK08582 hypothetical protein; Provisional
Probab=95.51 E-value=0.029 Score=55.42 Aligned_cols=57 Identities=11% Similarity=-0.021 Sum_probs=45.0
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
+.|.+++|.|++|.+.|++|.|+. +++|+||++++.+.++.- ....|+.||.|+++.
T Consensus 4 kvG~iv~G~V~~I~~fG~fV~L~~-~~~GlVhiSels~~~v~~-------------~~~~l~vGD~VkvkV 60 (139)
T PRK08582 4 EVGSKLQGKVTGITNFGAFVELPE-GKTGLVHISEVADNYVKD-------------INDHLKVGDEVEVKV 60 (139)
T ss_pred cCCCEEEEEEEEEECCeEEEEECC-CCEEEEEeeccCcccccc-------------cccccCCCCEEEEEE
Confidence 467899999999999999998865 799999999998765311 124578899887763
No 19
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=95.47 E-value=0.042 Score=56.78 Aligned_cols=70 Identities=14% Similarity=0.093 Sum_probs=60.4
Q ss_pred HhhccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 718 LKKKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 718 l~~~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
++...|++++|.|+++.+.|++|-+. .+++.++.+++.+++++|++.+..++. ...+..++.|+.+++|.
T Consensus 77 f~P~~GEVv~g~V~~v~~~Gi~V~lg--~~~g~v~~~~l~~~~~~~d~~~~~~~~--~~~~~~i~~Gd~VrvrV 146 (187)
T PRK08563 77 FKPELQEVVEGEVVEVVEFGAFVRIG--PVDGLLHISQIMDDYISYDPKNGRLIG--KESKRVLKVGDVVRARI 146 (187)
T ss_pred EeccCCCEEEEEEEEEEccEEEEEEe--CceEEEEcHHcCCCceEEccccceEEE--ccCCeEEcCCCEEEEEE
Confidence 45667899999999999999998886 499999999999999999999888887 35678899999888875
No 20
>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=95.46 E-value=0.035 Score=48.00 Aligned_cols=56 Identities=13% Similarity=0.102 Sum_probs=44.1
Q ss_pred cceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 722 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 722 ~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
.|.++.|.|.++.++|++|.++. ++||.||.+++.+++.+ .....|+.||.++++.
T Consensus 3 ~G~iv~g~V~~v~~~gi~v~l~~-~~~g~v~~s~l~~~~~~-------------~~~~~~~~Gd~v~~~V 58 (73)
T cd05706 3 VGDILPGRVTKVNDRYVLVQLGN-KVTGPSFITDALDDYSE-------------ALPYKFKKNDIVRACV 58 (73)
T ss_pred CCCEEEEEEEEEeCCeEEEEeCC-CcEEEEEhhhccCcccc-------------ccccccCCCCEEEEEE
Confidence 47889999999999999998876 69999999999876421 1134588899777653
No 21
>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=95.42 E-value=0.028 Score=48.17 Aligned_cols=55 Identities=13% Similarity=0.138 Sum_probs=43.9
Q ss_pred ceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 723 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 723 ~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
|.+++|.|.+|.++|++|.++. +++|.||.+++.++++. +....|+.||.++++.
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~-~v~g~i~~~~l~~~~~~-------------~~~~~~~~Gd~i~~~V 55 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSD-HIKGLVPPMHLADVRLK-------------HPEKKFKPGLKVKCRV 55 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecC-CcEEEEEHHHCCCcccc-------------CHHHcCCCCCEEEEEE
Confidence 4678999999999999998864 69999999999876542 2234688899887764
No 22
>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=95.28 E-value=0.04 Score=47.71 Aligned_cols=56 Identities=13% Similarity=0.014 Sum_probs=44.6
Q ss_pred cceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEE
Q 002793 722 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 790 (880)
Q Consensus 722 ~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r 790 (880)
.|.++.|.|.++.+.|++|.+...+++|.+|.+++.+++. . .....|++||.++++
T Consensus 2 ~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~---~----------~~~~~~~~Gd~v~v~ 57 (77)
T cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRV---A----------DASKLFRVGDKVRAK 57 (77)
T ss_pred CCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCcc---C----------CHhHeecCCCEEEEE
Confidence 4678999999999999999888778999999999976531 1 124568899977765
No 23
>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=95.24 E-value=0.033 Score=47.38 Aligned_cols=56 Identities=5% Similarity=0.057 Sum_probs=41.8
Q ss_pred ceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 723 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 723 ~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
|..+.|.|.++.++|++|.++. ++||+||.++++. .. .. ......|++||+++++.
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~-~~~Glv~~~~l~~-----~~-----~~--~~~~~~~~~G~~v~v~v 56 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDG-GIDGLVHISDISW-----TQ-----RV--RHPSEIYKKGQEVEAVV 56 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCC-CCEEEEEHHHCCC-----cc-----cc--CChhhEECCCCEEEEEE
Confidence 4578999999999998888864 7999999999861 11 11 23345789999887763
No 24
>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=95.16 E-value=0.047 Score=47.39 Aligned_cols=57 Identities=16% Similarity=0.071 Sum_probs=44.9
Q ss_pred cceEEeEEEEEeeccEEEEEEecC-ceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 722 EVLLSEARVLALGPRFMTIYIEKL-AIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 722 ~~~~~~a~V~~v~~~~~~V~Ip~~-giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
.|..+.|.|.++.++|++|.+..+ +++|+||.+++.++++.. ....|++||.++++.
T Consensus 3 ~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~-------------~~~~~~~Gd~v~vkv 60 (76)
T cd04452 3 EGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRS-------------IRKLVKVGRKEVVKV 60 (76)
T ss_pred CCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCC-------------HHHeeCCCCEEEEEE
Confidence 467899999999999999998776 699999999998765422 134578898777663
No 25
>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=95.08 E-value=0.072 Score=46.01 Aligned_cols=57 Identities=18% Similarity=0.085 Sum_probs=47.0
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
+.|..++|.|..+.++|++|-+. .+++|.|+.+++.+.+. ......++.|++++++.
T Consensus 3 ~~G~iv~g~V~~v~~~g~~V~l~-~~~~g~ip~~~l~~~~~-------------~~~~~~~~~G~~v~v~v 59 (74)
T PF00575_consen 3 KEGDIVEGKVTSVEDFGVFVDLG-NGIEGFIPISELSDDRI-------------DDPSEVYKIGQTVRVKV 59 (74)
T ss_dssp STTSEEEEEEEEEETTEEEEEES-TSSEEEEEGGGSSSSEE-------------SSSHGTCETTCEEEEEE
T ss_pred CCCCEEEEEEEEEECCEEEEEEC-CcEEEEEEeehhcCccc-------------cccccccCCCCEEEEEE
Confidence 56889999999999999999998 99999999999987621 23456788898777664
No 26
>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=94.70 E-value=0.051 Score=46.42 Aligned_cols=55 Identities=13% Similarity=0.144 Sum_probs=42.7
Q ss_pred ceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 723 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 723 ~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
|..+.|.|+++.++|++|.++. +++|+||.+++.+++++ .....|+.||.++++.
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~-~~~G~v~~s~l~~~~~~-------------~~~~~~~~Gd~v~~~v 55 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGR-GVDARVRVSELSDSYLK-------------DWKKRFKVGQLVKGKI 55 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCC-CCEEEEEHHHCCchhhc-------------CHhhccCCCCEEEEEE
Confidence 4568999999999998888875 69999999999876542 2234578898776653
No 27
>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=94.59 E-value=0.052 Score=45.52 Aligned_cols=54 Identities=11% Similarity=-0.021 Sum_probs=42.2
Q ss_pred ceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEE
Q 002793 723 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 790 (880)
Q Consensus 723 ~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r 790 (880)
|..+.|.|.++.++|++|.+.. +++|.+|.+++.++++. .....+++||.++++
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~-~~~g~~~~~~l~~~~~~-------------~~~~~~~~Gd~v~v~ 54 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGV-KQDGLIHISKMADRFVS-------------HPSDVVSVGDIVEVK 54 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCC-CCEEEEEHHHCCCcccc-------------CHHHhcCCCCEEEEE
Confidence 3578999999999999998864 59999999999876542 123457889877765
No 28
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=94.43 E-value=0.069 Score=66.63 Aligned_cols=62 Identities=13% Similarity=0.049 Sum_probs=48.8
Q ss_pred HHHHhhccceEEe-EEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEE
Q 002793 715 WILLKKKEVLLSE-ARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 790 (880)
Q Consensus 715 ~~~l~~~~~~~~~-a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r 790 (880)
..++..+.|.+++ |.|++|.++|++|.|.. |+||+||++++..+++++.+ ..|+.||.|+++
T Consensus 746 ~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~-g~EGLVHISeLs~~rv~~~~-------------dv~kvGD~V~Vk 808 (891)
T PLN00207 746 SLTMVPTVGDIYRNCEIKSIAPYGAFVEIAP-GREGLCHISELSSNWLAKPE-------------DAFKVGDRIDVK 808 (891)
T ss_pred HHhcCcCCCcEEECcEEEEEeccEEEEEeCC-CCEEEEEhhhcCCccccCHH-------------HhcCCCCEEEEE
Confidence 3345567889995 69999999998888854 79999999999887765543 357889977776
No 29
>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=94.39 E-value=0.069 Score=46.38 Aligned_cols=55 Identities=11% Similarity=0.044 Sum_probs=41.6
Q ss_pred ceEEe-EEEEEe-eccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 723 VLLSE-ARVLAL-GPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 723 ~~~~~-a~V~~v-~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
|.+++ |.|+.+ .++|++|-+++ |++|+||.+++.+...+. ....++.|+.++++.
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~-gv~G~i~~s~l~~~~~~~-------------~~~~~~vG~~v~~kV 57 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKD-GLLGFVHISHLSDDKVPS-------------DTGPFKAGTTHKARI 57 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCC-CCEEEEEHHHCCcchhcC-------------cccccCCCCEEEEEE
Confidence 45677 999998 79999998877 899999999987543221 123578898777764
No 30
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=94.39 E-value=0.13 Score=43.07 Aligned_cols=50 Identities=20% Similarity=0.277 Sum_probs=34.9
Q ss_pred ceEEEEeCCCCCCceEEecCCCChhhhhhcccCCccccceEEEEEEeecCCCCCCCcEEEEEE
Q 002793 166 EYIQLTPTHPKYPKMVVLVKDLPDSIKKRLEEGDATIEMELVAARIDEWNEESPFPQAHVLHV 228 (880)
Q Consensus 166 ~~~~~~P~D~rip~i~i~~~~~p~~~~~~~~~gd~~~~~~lvvv~I~~wp~~~~~p~G~iv~~ 228 (880)
++.|++|+| ....+++ |+.-.+.+.+|| .|+|+|.. +.....|.|+|+++
T Consensus 9 GfGFv~~~~--~~~DifI----p~~~l~~A~~gD------~V~v~i~~-~~~~~~~eg~vv~V 58 (58)
T PF08206_consen 9 GFGFVIPDD--GGEDIFI----PPRNLNGAMDGD------KVLVRITP-PSRGKRPEGEVVEV 58 (58)
T ss_dssp S-EEEEECT---TEEEEE-----HHHHTTS-TT-------EEEEEEEE-SSSEEEEEEEEEE-
T ss_pred CCEEEEECC--CCCCEEE----CHHHHCCCCCCC------EEEEEEec-CCCCCCCCEEEEeC
Confidence 689999999 5455544 344456777888 79999998 88888999999985
No 31
>PRK07252 hypothetical protein; Provisional
Probab=94.15 E-value=0.097 Score=50.48 Aligned_cols=55 Identities=11% Similarity=0.010 Sum_probs=43.6
Q ss_pred cceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEE
Q 002793 722 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 790 (880)
Q Consensus 722 ~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r 790 (880)
.|.++.|+|++|.++|++|.|+. +++|.||++++.++++.. ....|++||.++++
T Consensus 3 vG~iv~G~V~~V~~~G~fVei~~-~~~GllhiseLs~~~~~~-------------~~~~~~vGD~V~Vk 57 (120)
T PRK07252 3 IGDKLKGTITGIKPYGAFVALEN-GTTGLIHISEIKTGFIDN-------------IHQLLKVGEEVLVQ 57 (120)
T ss_pred CCCEEEEEEEEEeCcEEEEEECC-CCEEEEEHHHcCCccccC-------------hhhccCCCCEEEEE
Confidence 47789999999999999998865 699999999998754411 12458899977776
No 32
>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=93.96 E-value=0.092 Score=44.89 Aligned_cols=55 Identities=9% Similarity=0.103 Sum_probs=41.7
Q ss_pred ceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 723 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 723 ~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
|.++.|.|.++.++|++|.++. +++|+||.+++..++. .+ ....++.||.++++.
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~-~~~gli~~s~l~~~~~-~~------------~~~~~~~G~~i~v~v 55 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYN-NVKGFLPKSELSEAFI-KD------------PEEHFRVGQVVKVKV 55 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECC-CCEEEEEHHHcChhhc-CC------------HHHcccCCCEEEEEE
Confidence 4578999999999998888865 6999999999876431 11 124578898887764
No 33
>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=93.84 E-value=0.1 Score=46.48 Aligned_cols=57 Identities=12% Similarity=0.070 Sum_probs=45.0
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
+.|.++.|.|.++.++|++|.+.. +++|.||.+++.++++. .....|+.||.++++.
T Consensus 13 ~~G~i~~g~V~~v~~~G~fv~l~~-~~~g~v~~~el~~~~~~-------------~~~~~~~~Gd~v~vkV 69 (83)
T cd04461 13 KPGMVVHGYVRNITPYGVFVEFLG-GLTGLAPKSYISDEFVT-------------DPSFGFKKGQSVTAKV 69 (83)
T ss_pred CCCCEEEEEEEEEeeceEEEEcCC-CCEEEEEHHHCCccccc-------------CHHHhcCCCCEEEEEE
Confidence 568899999999999888887754 69999999999765431 2345789999887764
No 34
>PRK05807 hypothetical protein; Provisional
Probab=93.81 E-value=0.13 Score=50.66 Aligned_cols=55 Identities=13% Similarity=0.013 Sum_probs=43.1
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEE
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 790 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r 790 (880)
+.|.+++|.|++++++|++|.+ -+.+|+||++++.+.++.- -...+++||.++++
T Consensus 4 ~vG~vv~G~Vt~i~~~GafV~L--~~~~Glvhiseis~~~v~~-------------~~~~~kvGd~V~Vk 58 (136)
T PRK05807 4 KAGSILEGTVVNITNFGAFVEV--EGKTGLVHISEVADTYVKD-------------IREHLKEQDKVKVK 58 (136)
T ss_pred cCCCEEEEEEEEEECCeEEEEE--CCEEEEEEhhhcccccccC-------------ccccCCCCCEEEEE
Confidence 4688999999999999999999 3789999999998755320 12247889977765
No 35
>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=93.35 E-value=0.13 Score=45.16 Aligned_cols=59 Identities=14% Similarity=0.114 Sum_probs=43.8
Q ss_pred cceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 722 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 722 ~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
.|....|.|..+.++|++|.|.. +++|+||++++.+.+. -+...-...|+.|+.++++.
T Consensus 3 ~G~~V~g~V~~i~~~G~fV~l~~-~v~G~v~~~~ls~~~~----------~~~~~~~~~~~~G~~v~~kV 61 (74)
T cd05705 3 EGQLLRGYVSSVTKQGVFFRLSS-SIVGRVLFQNVTKYFV----------SDPSLYNKYLPEGKLLTAKV 61 (74)
T ss_pred CCCEEEEEEEEEeCCcEEEEeCC-CCEEEEEHHHccCccc----------cChhhHhcccCCCCEEEEEE
Confidence 46789999999999998888864 9999999999876531 11011135688999877764
No 36
>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=93.22 E-value=0.17 Score=42.51 Aligned_cols=54 Identities=13% Similarity=0.023 Sum_probs=41.1
Q ss_pred ceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEE
Q 002793 723 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 790 (880)
Q Consensus 723 ~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r 790 (880)
|..+.|.|..+.++|++|.+.. +.+|.+|++++..+++ ......|++||.++++
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~-~~~g~l~~~~l~~~~~-------------~~~~~~~~~Gd~v~v~ 54 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILP-GKDGLVHISELSDERV-------------EKVEDVLKVGDEVKVK 54 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCC-CCEEEEEhHHcCCccc-------------cCHHHccCCCCEEEEE
Confidence 4578999999999888888864 6999999999876542 1223467888877665
No 37
>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=92.32 E-value=0.32 Score=40.80 Aligned_cols=54 Identities=7% Similarity=-0.049 Sum_probs=40.2
Q ss_pred ceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 723 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 723 ~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
|..+.|.|+++.++|++|-+. ++||.+|.+++...+. +..+..|++||.++++.
T Consensus 2 g~~~~g~V~~v~~~g~~v~l~--~~~g~l~~~e~~~~~~-------------~~~~~~~~~Gd~v~v~i 55 (68)
T cd05688 2 GDVVEGTVKSITDFGAFVDLG--GVDGLLHISDMSWGRV-------------KHPSEVVNVGDEVEVKV 55 (68)
T ss_pred CCEEEEEEEEEEeeeEEEEEC--CeEEEEEhHHCCCccc-------------cCHhHEECCCCEEEEEE
Confidence 567999999999988777764 7999999998863110 22345688998777664
No 38
>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=92.20 E-value=0.26 Score=41.26 Aligned_cols=54 Identities=17% Similarity=0.085 Sum_probs=40.7
Q ss_pred ceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEE
Q 002793 723 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 790 (880)
Q Consensus 723 ~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r 790 (880)
|..+.|.|.++.++|++|.+.. +.+|.+|.+++.+++. ......+++||.++++
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~-~~~g~l~~~~l~~~~~-------------~~~~~~~~~Gd~v~v~ 54 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGG-GISGLVHISQIAHKRV-------------KDVKDVLKEGDKVKVK 54 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECC-CCEEEEEhHHcCCccc-------------CCHHHccCCCCEEEEE
Confidence 4578999999999998888854 6999999999876531 1122457888877665
No 39
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=92.17 E-value=0.31 Score=40.68 Aligned_cols=56 Identities=14% Similarity=0.070 Sum_probs=43.0
Q ss_pred cceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 722 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 722 ~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
.|..+.|.|.++.++|+.|.+.. +++|.++.+++.+.+ .......|+.||.++++.
T Consensus 2 ~G~~v~g~V~~v~~~g~~v~i~~-~~~g~l~~~~~~~~~-------------~~~~~~~~~~G~~v~~~V 57 (72)
T smart00316 2 VGDVVEGTVTEITPFGAFVDLGN-GVEGLIPISELSDKR-------------VKDPEEVLKVGDEVKVKV 57 (72)
T ss_pred CCCEEEEEEEEEEccEEEEEeCC-CCEEEEEHHHCCccc-------------cCCHHHeecCCCEEEEEE
Confidence 46789999999999988887753 799999999987643 123345688898777654
No 40
>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=91.47 E-value=0.37 Score=42.13 Aligned_cols=57 Identities=14% Similarity=0.098 Sum_probs=42.3
Q ss_pred ceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 723 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 723 ~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
|.+..|.|..+.++|++|.+.+ +++|+|+++++.++. .. . ..-...|+.|+.++++.
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~-~i~G~i~~~~ls~~~-~~--------~--~~~~~~~~vG~~v~~kV 57 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISP-DVKGRIPLLDLSDDV-SV--------L--EHPEKKFPIGQALKAKV 57 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCC-CcEEEEEHHHcCCcc-cc--------c--cCHHHhCCCCCEEEEEE
Confidence 3567899999999999999866 899999999986421 00 0 12345688999887764
No 41
>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=91.45 E-value=0.39 Score=41.10 Aligned_cols=54 Identities=15% Similarity=0.116 Sum_probs=41.2
Q ss_pred ceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEE
Q 002793 723 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 790 (880)
Q Consensus 723 ~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r 790 (880)
|.++.|.|.++.++|++|-+.. +++|.+|.+++.++++ ......|+.||.++++
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~-~~~g~i~~~~~~~~~~-------------~~~~~~~~~Gd~v~~~ 54 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGD-GVEGFLRAAELSRDRV-------------EDATERFKVGDEVEAK 54 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCC-CCEEEEEHHHCCCccc-------------cCHHHccCCCCEEEEE
Confidence 3568999999999998888754 5999999999987643 1223457889877765
No 42
>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=91.39 E-value=0.5 Score=41.60 Aligned_cols=49 Identities=10% Similarity=0.070 Sum_probs=40.2
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
+.|..++|.|.++.+.|++|.+.. +.+|++|.+++. ..++.||+++++.
T Consensus 15 ~~G~~~~g~V~~i~~~G~fV~l~~-~~~Glv~~se~~---------------------~~~~iGd~v~v~I 63 (77)
T cd04473 15 EVGKLYKGKVNGVAKYGVFVDLND-HVRGLIHRSNLL---------------------RDYEVGDEVIVQV 63 (77)
T ss_pred CCCCEEEEEEEeEecceEEEEECC-CcEEEEEchhcc---------------------CcCCCCCEEEEEE
Confidence 457899999999999999999876 599999998752 2478888777764
No 43
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=90.73 E-value=0.31 Score=54.50 Aligned_cols=38 Identities=18% Similarity=0.093 Sum_probs=34.3
Q ss_pred cceEEeEEEEEeeccEEEEEEecC-ceEEEEEeeecCCe
Q 002793 722 EVLLSEARVLALGPRFMTIYIEKL-AIERRIYYDEVEGL 759 (880)
Q Consensus 722 ~~~~~~a~V~~v~~~~~~V~Ip~~-giE~~V~~~~l~~~ 759 (880)
.|.+..|.|..|.++|.+|.|.+| |+||+||++++.-.
T Consensus 17 ~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ 55 (319)
T PTZ00248 17 EDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKR 55 (319)
T ss_pred CCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhccc
Confidence 378999999999999999999999 99999999998543
No 44
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=90.70 E-value=0.38 Score=52.54 Aligned_cols=56 Identities=18% Similarity=0.055 Sum_probs=46.1
Q ss_pred cceEEeEEEEEeeccEEEEEEecC-ceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEE
Q 002793 722 EVLLSEARVLALGPRFMTIYIEKL-AIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 790 (880)
Q Consensus 722 ~~~~~~a~V~~v~~~~~~V~Ip~~-giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r 790 (880)
.|..+.|.|.++.++|++|.+.+| |+||.||++++..+|+... ...++.||.+.++
T Consensus 8 ~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i-------------~~~~kvGd~V~vk 64 (262)
T PRK03987 8 EGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNI-------------RDHVKEGQKVVCK 64 (262)
T ss_pred CCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCH-------------HHhCCCCCEEEEE
Confidence 478899999999999999999999 9999999999987765332 2357889877665
No 45
>PRK08059 general stress protein 13; Validated
Probab=89.94 E-value=0.56 Score=45.29 Aligned_cols=56 Identities=9% Similarity=0.055 Sum_probs=43.3
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEE
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 790 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r 790 (880)
+.|.++.|.|.++.++|++|.|.. +++|++|++++..++. ......++.||.++++
T Consensus 6 k~G~iv~G~V~~i~~~G~fV~i~~-~~~Gli~~sel~~~~~-------------~~~~~~~~vGD~I~vk 61 (123)
T PRK08059 6 EVGSVVTGKVTGIQPYGAFVALDE-ETQGLVHISEITHGFV-------------KDIHDFLSVGDEVKVK 61 (123)
T ss_pred CCCCEEEEEEEEEecceEEEEECC-CCEEEEEHHHCCcccc-------------cCHHHcCCCCCEEEEE
Confidence 357889999999999999988864 7999999999876532 1123467889977765
No 46
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=89.55 E-value=1.1 Score=55.48 Aligned_cols=58 Identities=14% Similarity=0.055 Sum_probs=45.6
Q ss_pred hccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 720 KKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 720 ~~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
.+.|.++.|.|+++.++|++|.|.. +.+|+||++++...++. +....++.||.++++.
T Consensus 619 ~~vG~v~~G~V~~I~~fGafVei~~-~~~GllhiSels~~~v~-------------~~~~v~kvGD~V~VkV 676 (693)
T PRK11824 619 PEVGEIYEGKVVRIVDFGAFVEILP-GKDGLVHISEIADERVE-------------KVEDVLKEGDEVKVKV 676 (693)
T ss_pred CcCCeEEEEEEEEEECCeEEEEECC-CCEEEEEeeeccCcccc-------------CccceeCCCCEEEEEE
Confidence 4678999999999999998888864 89999999999754421 2234678899777764
No 47
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=89.31 E-value=0.79 Score=47.17 Aligned_cols=71 Identities=8% Similarity=-0.092 Sum_probs=55.4
Q ss_pred HhhccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 718 LKKKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 718 l~~~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
++-..+++.+|.|+++.+.|++|-+-.+. +.||.++++++ +.|++.++........++...+.|+.|++|.
T Consensus 77 FrPf~gEVv~g~V~~v~~~G~~v~~Gp~~--ifI~~~~l~~~-~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV 147 (176)
T PTZ00162 77 FKPFKDEVLDAIVTDVNKLGFFAQAGPLK--AFVSRSAIPPD-FVYDSDSAYPCYISSDGQIQIKPNTEVRLRL 147 (176)
T ss_pred EecCCCCEEEEEEEEEecceEEEEeeCeE--EEEcHHHCCCc-cEECCCCCcceEecCCCcEEECCCCEEEEEE
Confidence 45556889999999999999999885444 99999999876 8898876655443245578889999888886
No 48
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=89.00 E-value=1.3 Score=52.55 Aligned_cols=71 Identities=15% Similarity=0.151 Sum_probs=51.5
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe--ce----e
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA--LE----E 794 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~--~d----~ 794 (880)
..|.++.|.|+.+.++|++|.+.+ |++|+||.+++.+..++. .+..|+.||.++++. +| +
T Consensus 292 ~vG~vv~G~V~~I~~fGvFVeL~~-gieGLvh~SeLs~~~v~~-------------~~~~~kvGd~V~VkIi~ID~e~rr 357 (486)
T PRK07899 292 AIGQIVPGKVTKLVPFGAFVRVEE-GIEGLVHISELAERHVEV-------------PEQVVQVGDEVFVKVIDIDLERRR 357 (486)
T ss_pred CCCCEEEEEEEEEeccEEEEEeCC-CcEEEEEHHHcCcccccC-------------ccceeCCCCEEEEEEEEEECCCCE
Confidence 357899999999999999998865 899999999998654322 234689999887763 34 3
Q ss_pred EEEEEecCCCc
Q 002793 795 VALVVRPNDLK 805 (880)
Q Consensus 795 v~v~~~~~~~~ 805 (880)
+.+-+.....+
T Consensus 358 I~LSlK~~~~~ 368 (486)
T PRK07899 358 ISLSLKQANEG 368 (486)
T ss_pred EEEEEEEcccC
Confidence 55555444433
No 49
>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=88.93 E-value=0.82 Score=39.32 Aligned_cols=57 Identities=21% Similarity=0.177 Sum_probs=40.6
Q ss_pred ceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 723 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 723 ~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
|.+..|.|+.+.++++.|-++. ++||++|.+++.++|.+ . ......|+.||.+.++.
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~-~i~g~i~~~~i~~~~~~--~---------~~~~~~~~~Gd~i~~kV 57 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLAD-NVHGRIHVSEVFDEWPD--G---------KNPLSKFKIGQKIKARV 57 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCC-CcEEEEEHHHhcccccc--c---------cChhHhCCCCCEEEEEE
Confidence 3467899999999988888764 89999999998765410 0 11123478888776664
No 50
>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=88.83 E-value=1.3 Score=55.14 Aligned_cols=58 Identities=17% Similarity=0.203 Sum_probs=43.3
Q ss_pred ceEEEEeCCCCCCc-eEEecCCCChhhhhhcccCCccccceEEEEEEeecCCCCCCCcEEEEEEcCCCCCh
Q 002793 166 EYIQLTPTHPKYPK-MVVLVKDLPDSIKKRLEEGDATIEMELVAARIDEWNEESPFPQAHVLHVFGRGGEV 235 (880)
Q Consensus 166 ~~~~~~P~D~rip~-i~i~~~~~p~~~~~~~~~gd~~~~~~lvvv~I~~wp~~~~~p~G~iv~~LG~~~d~ 235 (880)
++.|+.|.| +.+. +.|+ +....++.+|| .|+|+|..|+.....|.|+|+++||...+.
T Consensus 79 g~gFv~~~~-~~~~di~I~-----~~~~~~a~~GD------~Vlv~I~~~~~~~~~~eg~Vv~Il~r~~~~ 137 (709)
T TIGR02063 79 GFGFLRPED-DDEDDIFIP-----PRQMNGAMHGD------RVLVRITGKPDGGDRFEARVIKILERANDQ 137 (709)
T ss_pred ccEEEEECC-CCCCcEEEC-----hHHhCcCCCCC------EEEEEEecccCCCCCceEEEEEEEeeCCCE
Confidence 578899988 4444 4453 22335677788 799999999866667899999999998764
No 51
>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=88.70 E-value=1 Score=38.50 Aligned_cols=53 Identities=15% Similarity=0.137 Sum_probs=41.0
Q ss_pred ceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 723 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 723 ~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
|...+|.|..+.++|++|.+.+ +++|.|+.+++...+.. ...|+.|+++++|.
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~-~v~g~v~~~~l~~~~~~---------------~~~~~~G~~i~~kV 53 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLS-SFTGTVDFLHLDPEKSS---------------KSTYKEGQKVRARI 53 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcC-CceEEEEHHHcCCccCc---------------ccCcCCCCEEEEEE
Confidence 3467899999999999999876 79999999988543211 33588898887764
No 52
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=88.27 E-value=1.1 Score=55.33 Aligned_cols=58 Identities=14% Similarity=0.059 Sum_probs=44.8
Q ss_pred hccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 720 KKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 720 ~~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
.+.|.++.|.|+++.++|.+|.|.. +++|+||++++.+.++. +.+..++.||.++++.
T Consensus 616 ~~~G~i~~G~V~~I~~~GafVei~~-g~~GllHiSei~~~~v~-------------~~~~~~kvGD~V~VkV 673 (684)
T TIGR03591 616 PEVGKIYEGKVVRIMDFGAFVEILP-GKDGLVHISEIANERVE-------------KVEDVLKEGDEVKVKV 673 (684)
T ss_pred cccCcEEEEEEEEEeCCEEEEEECC-CcEEEEEHHHcCCCccc-------------ChhhccCCCCEEEEEE
Confidence 3568999999999999888888754 79999999999654331 2345678899777764
No 53
>PHA02945 interferon resistance protein; Provisional
Probab=88.15 E-value=1.6 Score=39.81 Aligned_cols=42 Identities=7% Similarity=-0.083 Sum_probs=36.6
Q ss_pred ccceEEeEEEEEeeccEEEEEEecC-ceEEEEEeeec--CCeEEEE
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKL-AIERRIYYDEV--EGLIVEW 763 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~-giE~~V~~~~l--~~~~~e~ 763 (880)
..|...-|+|.. .++|++|.+++| |+||.||.+.. ...|..+
T Consensus 10 ~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~ 54 (88)
T PHA02945 10 NVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY 54 (88)
T ss_pred CCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee
Confidence 457888999999 999999999999 99999999965 7777755
No 54
>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=87.80 E-value=0.9 Score=39.51 Aligned_cols=56 Identities=14% Similarity=0.054 Sum_probs=39.4
Q ss_pred cceEEeEEEEEeec-cEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 722 EVLLSEARVLALGP-RFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 722 ~~~~~~a~V~~v~~-~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
.|.++.|.|..+.+ .|++|.+ ..+.+|++|++++.++|. .. -...|+.||.++++.
T Consensus 3 ~G~iv~G~V~~i~~~~g~~v~l-~~~~~Glvhis~~s~~~~---~~----------~~~~~~~Gd~v~~kV 59 (72)
T cd05704 3 EGAVTLGMVTKVIPHSGLTVQL-PFGKTGLVSIFHLSDSYT---EN----------PLEGFKPGKIVRCCI 59 (72)
T ss_pred CCCEEEEEEEEeeCCcEEEEEC-CCCCEEEEEHHHhcCccc---CC----------HHHhCCCCCEEEEEE
Confidence 47789999999986 5655553 337999999999877542 11 123578898777664
No 55
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=86.67 E-value=0.92 Score=57.31 Aligned_cols=60 Identities=8% Similarity=-0.125 Sum_probs=47.6
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
..|..++|+|+++.++|++|.+++ |++|+||.+++.+++.+. .+ .....|+.||.+++..
T Consensus 751 ~vG~iV~GkV~~v~~~GvFVeL~~-gVeGlI~~s~lsdd~~~~-------~~---~~~~~f~vGD~V~v~V 810 (863)
T PRK12269 751 GVGSTVEGEVSSVTDFGIFVRVPG-GVEGLVRKQHLVENRDGD-------PG---EALRKYAVGDRVKAVI 810 (863)
T ss_pred CCCCEEEEEEEEEecCeEEEEcCC-CeEEEEEHHHcCCccccc-------ch---hhccccCCCCEEEEEE
Confidence 468999999999999999999987 899999999998764322 11 1245689999888764
No 56
>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=86.65 E-value=1.2 Score=36.23 Aligned_cols=51 Identities=16% Similarity=0.172 Sum_probs=38.4
Q ss_pred eEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 727 EARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 727 ~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
.|+|.++.+++++|.+. -+++|.++.+++.+.+. ...+..|+.||.++++.
T Consensus 2 ~g~V~~v~~~g~~v~l~-~~~~g~~~~~~~~~~~~-------------~~~~~~~~~G~~v~~~v 52 (65)
T cd00164 2 TGKVVSITKFGVFVELE-DGVEGLVHISELSDKFV-------------KDPSEVFKVGDEVEVKV 52 (65)
T ss_pred EEEEEEEEeeeEEEEec-CCCEEEEEHHHCCCccc-------------cCHhhEeCCCCEEEEEE
Confidence 69999999988887765 46999999999876432 12345688898777765
No 57
>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=85.81 E-value=1.5 Score=39.93 Aligned_cols=59 Identities=10% Similarity=-0.063 Sum_probs=39.9
Q ss_pred cceEEeEEEEEeecc--EEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 722 EVLLSEARVLALGPR--FMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 722 ~~~~~~a~V~~v~~~--~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
.|.++.|.|..+.++ |.+|-+.. |.+|++|++++....|... ..-...++.||.+.++.
T Consensus 7 ~G~iy~g~V~~i~~~~~GaFV~l~~-g~~Gllh~seis~~~~~~v----------~~~~~~~~~Gd~v~VqV 67 (88)
T cd04453 7 VGNIYLGRVKKIVPGLQAAFVDIGL-GKNGFLHLSDILPAYFKKH----------KKIAKLLKEGQEILVQV 67 (88)
T ss_pred CCCEEEEEEEEeccCCcEEEEEeCC-CCEEEEEhHHcCchhcccc----------CCHHHcCCCCCEEEEEE
Confidence 578899999999997 77776654 7999999998743222111 01123467787666654
No 58
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=85.47 E-value=0.51 Score=44.00 Aligned_cols=66 Identities=15% Similarity=0.104 Sum_probs=44.7
Q ss_pred cceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccc--------eEEEeeecccceeecCCCceEE
Q 002793 722 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTS--------TLVLSLCAHKRSFKRGGPGNYR 790 (880)
Q Consensus 722 ~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~--------~lv~~~~~~k~~~~~g~~~~~r 790 (880)
.|.+..|.|..+.+.+++|.+|. |++|.|+++++.+++-.|.+..+ .... ..-...|+.||.++++
T Consensus 3 ~G~vV~G~V~~v~~~gl~v~L~~-g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~f~vGd~V~~k 76 (100)
T cd05693 3 EGMLVLGQVKEITKLDLVISLPN-GLTGYVPITNISDAYTERLEELDEESEEEDDEEEL--PDLEDLFSVGQLVRCK 76 (100)
T ss_pred CCCEEEEEEEEEcCCCEEEECCC-CcEEEEEHHHhhHHHHHHHHHhhhhcccccccccc--CCHHHhccCCCEEEEE
Confidence 46788999999999998888774 99999999998765422211100 0000 1123568899977765
No 59
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=85.05 E-value=1.5 Score=49.38 Aligned_cols=56 Identities=13% Similarity=0.008 Sum_probs=43.7
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
+.|.++.|.|.++.++|++|-+ .|++|+||.+++..++. . .....|+.||.++++.
T Consensus 195 k~G~vv~G~V~~I~~~G~fV~i--~gv~Gllhisels~~~~---~----------~~~~~~~vGd~VkvkV 250 (318)
T PRK07400 195 EVGEVVVGTVRGIKPYGAFIDI--GGVSGLLHISEISHEHI---E----------TPHSVFNVNDEMKVMI 250 (318)
T ss_pred CCCCEEEEEEEEEECCeEEEEE--CCEEEEEEHHHcccccc---c----------ChhhccCCCCEEEEEE
Confidence 5588999999999998888876 48999999999876532 1 1234688999887763
No 60
>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=84.68 E-value=4.6 Score=36.80 Aligned_cols=65 Identities=9% Similarity=-0.015 Sum_probs=48.2
Q ss_pred ceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 723 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 723 ~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
+++.+|+|+.+.+.|++|-+ =.+++.++-..++++ +.|+..+..-+.. ..++..+..|+.|++|.
T Consensus 2 gEVi~g~V~~v~~~G~~v~~--Gpl~~f~~~~~ip~~-~~~~~~~~~~~~~-~~~~~~i~~g~~VR~rV 66 (88)
T cd04462 2 GEVVDAIVTSVNKTGFFAEV--GPLSIFISRHLIPSD-MEFDPNASPPCFT-SNEDIVIKKDTEVRLKI 66 (88)
T ss_pred CcEEEEEEEEEeccEEEEEE--cCceEEEEeeecCcc-ceECCcCCCCeEe-CCCcEEECCCCEEEEEE
Confidence 57889999999998877765 346678888889887 7888743333443 23577888888888876
No 61
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=82.60 E-value=1.3 Score=42.87 Aligned_cols=40 Identities=13% Similarity=0.053 Sum_probs=32.7
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEE
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIV 761 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~ 761 (880)
..|....|.|++++++|-||.++. |-.|+||++++.+.|+
T Consensus 4 kvG~~l~GkItgI~~yGAFV~l~~-g~tGLVHISEIa~~fV 43 (129)
T COG1098 4 KVGSKLKGKITGITPYGAFVELEG-GKTGLVHISEIADGFV 43 (129)
T ss_pred cccceEEEEEEeeEecceEEEecC-CCcceEEehHhhhhhH
Confidence 357789999999999887777654 5669999999987655
No 62
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=81.84 E-value=3.6 Score=48.94 Aligned_cols=56 Identities=5% Similarity=-0.055 Sum_probs=42.6
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
+.|.+..|+|+++.++|++|.|. |++|+||.+++...+. .+....++.|+.++++.
T Consensus 207 k~G~iv~G~V~~i~~~G~FVdlg--gv~Glv~~Sels~~~v-------------~~~~~~~kvGd~V~vkV 262 (486)
T PRK07899 207 QKGQVRKGVVSSIVNFGAFVDLG--GVDGLVHVSELSWKHI-------------DHPSEVVEVGQEVTVEV 262 (486)
T ss_pred cCCCEEEEEEEEEECCeEEEEEC--CEEEEEEHHHCCCccc-------------CCHHHhcCCCCEEEEEE
Confidence 46889999999999999888884 8999999999864221 12234578888887774
No 63
>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=81.05 E-value=3.8 Score=50.66 Aligned_cols=60 Identities=7% Similarity=-0.125 Sum_probs=43.4
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCe-EEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGL-IVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~-~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
..|.++.|.|..+.++|.+|.|. -|+||+||++++.+. |..+.. .-...++.||+|+++.
T Consensus 646 ~vG~i~~GkV~~I~dfGaFVel~-~G~eGLvHISeisdls~~~rv~----------~~~dv~kvGd~V~VKV 706 (719)
T TIGR02696 646 EVGERFLGTVVKTTAFGAFVSLL-PGKDGLLHISQIRKLAGGKRVE----------NVEDVLSVGQKIQVEI 706 (719)
T ss_pred CCCCEEEEEEEEEECceEEEEec-CCceEEEEhhhccccccccCcC----------CHHHcCCCCCEEEEEE
Confidence 46889999999999988888775 489999999988532 211111 2234578899887764
No 64
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=80.08 E-value=3.4 Score=49.45 Aligned_cols=37 Identities=8% Similarity=-0.006 Sum_probs=31.3
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCe
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGL 759 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~ 759 (880)
..|++.+|+|.+++++| +||.-.|+.|+||++++...
T Consensus 191 ~~G~vV~G~V~~It~~G--afVdigGvdGLlHiseiS~~ 227 (541)
T COG0539 191 EVGEVVEGVVKNITDYG--AFVDIGGVDGLLHISEISWK 227 (541)
T ss_pred CCCceEEEEEEEeecCc--EEEEecCeeeEEehhhcccc
Confidence 56889999999999955 67777789999999998643
No 65
>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=78.46 E-value=3.3 Score=49.39 Aligned_cols=57 Identities=12% Similarity=0.004 Sum_probs=45.4
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
..|..+.|.|++++++|++|.+.. +++|+||.+++.+++. ......|+.||.++++.
T Consensus 445 ~~G~~v~g~V~~v~~~G~fV~l~~-~~~Glv~~s~l~~~~~-------------~~~~~~~~~Gd~v~~~V 501 (516)
T TIGR00717 445 KVGSVVKGKVTEIKDFGAFVELPG-GVEGLIRNSELSENRD-------------EDKTDEIKVGDEVEAKV 501 (516)
T ss_pred CcceEEEEEEEEEecceEEEEcCC-CeEEEEEHHHcCcccc-------------ccccccCCCCCEEEEEE
Confidence 468899999999999998888865 7999999999986542 12345689999887764
No 66
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=77.87 E-value=4.6 Score=48.11 Aligned_cols=57 Identities=18% Similarity=0.115 Sum_probs=42.4
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
+.|.+++|+|+++.++|++|.|. .|++|+||.+++...+.. .....|+.|+.++++.
T Consensus 201 ~~G~iv~G~V~~v~~~G~fV~l~-~gv~g~v~~sels~~~~~-------------~~~~~~~vGd~i~vkV 257 (491)
T PRK13806 201 KEGDVVEGTVTRLAPFGAFVELA-PGVEGMVHISELSWSRVQ-------------KADEAVSVGDTVRVKV 257 (491)
T ss_pred CCCCEEEEEEEEEeCCeEEEEcC-CCcEEEEEHHHCCCcccc-------------ChhHhcCCCCEEEEEE
Confidence 56889999999999988777664 389999999998753221 1123478899888774
No 67
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=76.96 E-value=5.9 Score=45.60 Aligned_cols=56 Identities=18% Similarity=0.031 Sum_probs=42.1
Q ss_pred hccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEE
Q 002793 720 KKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 790 (880)
Q Consensus 720 ~~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r 790 (880)
-+.|...+|.|.++.+.|++|.+ .+++|.||.+++...+. . .....++.|+.++++
T Consensus 190 ~~~G~~v~g~V~~v~~~G~fV~l--~~v~g~v~~sels~~~~---~----------~~~~~~~vGd~i~~~ 245 (390)
T PRK06676 190 LKEGDVVEGTVARLTDFGAFVDI--GGVDGLVHISELSHERV---E----------KPSEVVSVGQEVEVK 245 (390)
T ss_pred CCCCCEEEEEEEEEecceEEEEe--CCeEEEEEHHHcCcccc---C----------CHHHhcCCCCEEEEE
Confidence 35688999999999999988887 47999999999875321 1 223346778877666
No 68
>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=76.68 E-value=5.7 Score=33.78 Aligned_cols=55 Identities=15% Similarity=0.047 Sum_probs=39.2
Q ss_pred ceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 723 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 723 ~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
|.+..|.|..+.+.+++|-+ ..+.||.++.+++...+.. .-...++.||.++++.
T Consensus 1 G~iv~g~V~~i~~~~~~v~l-~~~~~g~l~~~e~~~~~~~-------------~~~~~~~~Gd~i~~~i 55 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDI-GYKSEGIIPISEFSDDPIE-------------NGEDEVKVGDEVEVYV 55 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEe-CCCceEEEEHHHhCccccC-------------CHhHcCCCCCEEEEEE
Confidence 35678999999998888887 3479999999988653211 1123478888776663
No 69
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=76.68 E-value=7 Score=32.12 Aligned_cols=55 Identities=18% Similarity=0.167 Sum_probs=35.0
Q ss_pred ceEEEEeCCCCCCceEEecCCCChhhhhhcccCCccccceEEEEEEeecCCCCCCCcEEEEEEc
Q 002793 166 EYIQLTPTHPKYPKMVVLVKDLPDSIKKRLEEGDATIEMELVAARIDEWNEESPFPQAHVLHVF 229 (880)
Q Consensus 166 ~~~~~~P~D~rip~i~i~~~~~p~~~~~~~~~gd~~~~~~lvvv~I~~wp~~~~~p~G~iv~~L 229 (880)
++.|+.|.+.. +.+.++..++.. -...+.+|| .|.++|..|. ....|.|.++++|
T Consensus 10 g~gfv~~~~~~-~~i~v~~~~~~~-~~~~~~~Gd------~V~~~i~~~~-~~~~~~a~~v~~~ 64 (64)
T smart00357 10 GFGFIRPDDGG-KDVFVHPSQIQG-GLKSLREGD------EVEFKVVSPR-GGGKPEAENVVKL 64 (64)
T ss_pred CeeEEecCCCC-ccEEEEhHHhhc-CCCcCCCCC------EEEEEEEEcc-CCCCcEEEEEEeC
Confidence 46788887654 456665332100 023456676 7999998883 4456899999875
No 70
>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=76.32 E-value=7.3 Score=34.20 Aligned_cols=37 Identities=8% Similarity=-0.056 Sum_probs=31.2
Q ss_pred cceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCC
Q 002793 722 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEG 758 (880)
Q Consensus 722 ~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~ 758 (880)
.|....|.|.++.++|++|.+..-|++|.++.+++..
T Consensus 4 ~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~ 40 (74)
T cd05694 4 EGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGN 40 (74)
T ss_pred CCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCc
Confidence 3567899999999999999884458999999998764
No 71
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=72.41 E-value=5.9 Score=47.24 Aligned_cols=56 Identities=7% Similarity=-0.104 Sum_probs=43.3
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEE
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 790 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r 790 (880)
..|...+|.|..+.++|.+|.+.+ |++|+||.+++..... ......++.||.++++
T Consensus 378 ~vG~~v~G~V~~i~~~G~FV~l~~-gv~Gli~~se~s~~~~-------------~~~~~~~~~Gd~v~~~ 433 (491)
T PRK13806 378 APGTTVTGTVEKRAQFGLFVNLAP-GVTGLLPASVISRAGK-------------PATYEKLKPGDSVTLV 433 (491)
T ss_pred CCCCEEEEEEEEEecCceEEEcCC-CcEEEEEHHHcCcccc-------------cchhhcCCCCCEEEEE
Confidence 458899999999999998888865 9999999999864221 1123457889988776
No 72
>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=72.06 E-value=6.2 Score=35.11 Aligned_cols=61 Identities=13% Similarity=-0.015 Sum_probs=41.6
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
+.|.+..|.|+++.+.++.|.|. .++||.+|.+++....+.-.. ......++.||.+.++.
T Consensus 5 ~~GdiV~g~V~~i~~~g~~v~i~-~~~~G~l~~se~~~~~~~~~~---------~~~~~~l~vGd~i~~~V 65 (86)
T cd05789 5 EVGDVVIGRVTEVGFKRWKVDIN-SPYDAVLPLSEVNLPRTDEDE---------LNMRSYLDEGDLIVAEV 65 (86)
T ss_pred CCCCEEEEEEEEECCCEEEEECC-CCeEEEEEHHHccCCCCccch---------HHHHhhCCCCCEEEEEE
Confidence 35778899999999999888775 479999999988532110000 11233478888776664
No 73
>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=71.18 E-value=11 Score=31.96 Aligned_cols=34 Identities=12% Similarity=-0.020 Sum_probs=29.5
Q ss_pred ceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCC
Q 002793 723 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEG 758 (880)
Q Consensus 723 ~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~ 758 (880)
|...+|.|..+.+.|+.|-+ -|++|.|+.+++..
T Consensus 1 G~iv~g~V~~v~~~G~~v~l--~g~~gfip~s~~~~ 34 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI--EGVRAFLPASQVDL 34 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE--CCEEEEEEHHHCCC
Confidence 45689999999999998888 48999999998864
No 74
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=68.40 E-value=8.1 Score=47.67 Aligned_cols=56 Identities=7% Similarity=0.056 Sum_probs=44.1
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEE
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 790 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r 790 (880)
+.|.++.|.|.++.++|++|.+.. +++|++|.+++.+... ...+..|+.||.++++
T Consensus 561 ~~G~~v~g~V~~i~~~G~fV~l~~-~i~Gli~~sel~~~~~-------------~~~~~~~kvGd~V~vk 616 (647)
T PRK00087 561 PVGSIVLGKVVRIAPFGAFVELEP-GVDGLVHISQISWKRI-------------DKPEDVLSEGEEVKAK 616 (647)
T ss_pred cCCeEEEEEEEEEECCeEEEEECC-CCEEEEEhhhcCcccc-------------CCHhhcCCCCCEEEEE
Confidence 458899999999999999998854 8999999999875331 2334568999977766
No 75
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=64.65 E-value=8.3 Score=46.67 Aligned_cols=57 Identities=11% Similarity=-0.047 Sum_probs=43.6
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEE
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 790 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r 790 (880)
..|..+.|+|.++.++|++|.|+. +++|+||++++...+ ++ ......|+.|+.++++
T Consensus 372 ~~G~~v~g~V~~v~~~G~fV~l~~-~v~g~i~~s~l~~~~----------~~--~~~~~~~~~Gd~v~v~ 428 (565)
T PRK06299 372 PVGDVVEGKVKNITDFGAFVGLEG-GIDGLVHLSDISWDK----------KG--EEAVELYKKGDEVEAV 428 (565)
T ss_pred CCCCEEEEEEEEEecceEEEECCC-CCEEEEEHHHcCccc----------cc--cChHhhCCCCCEEEEE
Confidence 458899999999999998888855 799999999987421 11 2334568889977765
No 76
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=64.40 E-value=11 Score=43.36 Aligned_cols=56 Identities=11% Similarity=0.026 Sum_probs=41.7
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEE
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 790 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r 790 (880)
+.|.++.|.|.++.++|++|.+.. |++|++|.+++.... +. .....|+.||.++++
T Consensus 276 ~~G~~v~g~V~~i~~~G~fV~l~~-gi~Glv~~se~~~~~----------~~---~~~~~~~~Gd~v~v~ 331 (390)
T PRK06676 276 PEGDVIEGTVKRLTDFGAFVEVLP-GVEGLVHISQISHKH----------IA---TPSEVLEEGQEVKVK 331 (390)
T ss_pred cCCcEEEEEEEEEeCceEEEEECC-CCeEEEEhHHcCccc----------cC---ChhhccCCCCEEEEE
Confidence 457889999999999888887753 899999999886421 11 223458899977655
No 77
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=63.60 E-value=19 Score=45.93 Aligned_cols=36 Identities=6% Similarity=-0.156 Sum_probs=31.0
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCC
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEG 758 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~ 758 (880)
..|....|.|..+.++|++|.+ -|++|+||.+++..
T Consensus 492 ~~G~~V~G~Vk~i~~~G~fVdl--~Gv~Gfvp~SeiS~ 527 (863)
T PRK12269 492 HIEDSVSGVVKSFTSFGAFIDL--GGFDGLLHVNDMSW 527 (863)
T ss_pred CCCCEEEEEEEEEeCCcEEEEE--CCEEEEEEchhccc
Confidence 4578899999999999988887 49999999998754
No 78
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=60.07 E-value=21 Score=44.10 Aligned_cols=56 Identities=18% Similarity=0.001 Sum_probs=42.3
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
+.|....|+|.++.++|++|.+ -|++|+||.+++.+.+. . +....|+.|+.++++.
T Consensus 476 ~~G~iV~g~V~~v~~~G~fV~l--~gv~Gll~~sels~~~~---~----------~~~~~~~vGd~V~vkV 531 (647)
T PRK00087 476 EEGDVVEGEVKRLTDFGAFVDI--GGVDGLLHVSEISWGRV---E----------KPSDVLKVGDEIKVYI 531 (647)
T ss_pred CCCCEEEEEEEEEeCCcEEEEE--CCEEEEEEHHHcCcccc---C----------CHHHhcCCCCEEEEEE
Confidence 4688999999999999988888 58999999999863211 1 2234578888777663
No 79
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=56.01 E-value=18 Score=43.52 Aligned_cols=37 Identities=16% Similarity=0.002 Sum_probs=29.8
Q ss_pred hccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecC
Q 002793 720 KKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVE 757 (880)
Q Consensus 720 ~~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~ 757 (880)
...|....|+|+.+.++|.+|.| .-|+||+||++++.
T Consensus 275 ~~~g~~v~G~Vt~i~~~GafVei-~~GvEGlvhvSEis 311 (541)
T COG0539 275 YPVGDKVEGKVTNLTDYGAFVEI-EEGVEGLVHVSEIS 311 (541)
T ss_pred cCCCCEEEEEEEEeecCcEEEEe-cCCccceeechhhc
Confidence 35577899999999998866654 33999999999874
No 80
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=55.94 E-value=26 Score=42.49 Aligned_cols=36 Identities=8% Similarity=0.023 Sum_probs=31.2
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCC
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEG 758 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~ 758 (880)
+.|...+|.|..+.++|++|-+. |++|+||.+++..
T Consensus 200 ~~G~iv~g~V~~v~~~G~~V~i~--g~~glv~~se~s~ 235 (565)
T PRK06299 200 EEGQVVEGVVKNITDYGAFVDLG--GVDGLLHITDISW 235 (565)
T ss_pred CCCCEEEEEEEEEeCCeEEEEEC--CEEEEEEHHHhcc
Confidence 56888999999999999888775 9999999998753
No 81
>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=55.27 E-value=27 Score=30.80 Aligned_cols=56 Identities=13% Similarity=-0.028 Sum_probs=41.5
Q ss_pred cceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 722 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 722 ~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
.|.+..|.|+++..+++.|-| -.+.||.++.+++...+- ......++.||.+.++.
T Consensus 6 ~GdiV~G~V~~v~~~~~~V~i-~~~~~g~l~~~~~~~~~~-------------~~~~~~~~~GD~i~~~V 61 (82)
T cd04454 6 VGDIVIGIVTEVNSRFWKVDI-LSRGTARLEDSSATEKDK-------------KEIRKSLQPGDLILAKV 61 (82)
T ss_pred CCCEEEEEEEEEcCCEEEEEe-CCCceEEeechhccCcch-------------HHHHhcCCCCCEEEEEE
Confidence 467789999999999988887 457999999998865310 12234578898776653
No 82
>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=51.97 E-value=24 Score=42.20 Aligned_cols=57 Identities=9% Similarity=-0.077 Sum_probs=42.8
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEE
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 790 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r 790 (880)
..|....|.|..+.+.|++|-+.. |++|+||.+++...+. . ...+..|+.|+.++++
T Consensus 358 ~~G~~v~g~V~~v~~~G~fV~l~~-~v~glv~~s~ls~~~~----------~--~~~~~~~~~G~~V~~~ 414 (516)
T TIGR00717 358 PVGDRVTGKIKKITDFGAFVELEG-GIDGLIHLSDISWDKD----------G--READHLYKKGDEIEAV 414 (516)
T ss_pred CCCCEEEEEEEEEecceEEEECCC-CCEEEEEHHHCcCccc----------C--CCHhHccCCCCEEEEE
Confidence 458899999999999888887763 8999999999863211 1 1223568889987776
No 83
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=50.41 E-value=13 Score=40.50 Aligned_cols=40 Identities=18% Similarity=0.018 Sum_probs=35.6
Q ss_pred cceEEeEEEEEeeccEEEEEEecC-ceEEEEEeeecCCeEE
Q 002793 722 EVLLSEARVLALGPRFMTIYIEKL-AIERRIYYDEVEGLIV 761 (880)
Q Consensus 722 ~~~~~~a~V~~v~~~~~~V~Ip~~-giE~~V~~~~l~~~~~ 761 (880)
.|...-|+|..|.++|-+|.+.+| |+||.||++++.--|+
T Consensus 11 eGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wV 51 (269)
T COG1093 11 EGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWV 51 (269)
T ss_pred CCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHH
Confidence 367888999999999999999999 6999999999876654
No 84
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=50.39 E-value=19 Score=29.45 Aligned_cols=36 Identities=11% Similarity=-0.013 Sum_probs=24.2
Q ss_pred ccccCccc----hhhhhc--eeEEEEecC-CCCCccEEEEEEE
Q 002793 89 VSSSQQND----GMNAIE--RLSAMISSY-PTKRPTGRVVSII 124 (880)
Q Consensus 89 ~~~~~~~~----~~~a~~--~v~~~~~~~-~~~~p~G~VV~Il 124 (880)
++|++... ...+.+ +|.+.+... +.+++.|+|+.|+
T Consensus 22 ~i~v~~~~~~~~~~~~~~Gd~V~~~i~~~~~~~~~~a~~v~~~ 64 (64)
T smart00357 22 DVFVHPSQIQGGLKSLREGDEVEFKVVSPRGGGKPEAENVVKL 64 (64)
T ss_pred cEEEEhHHhhcCCCcCCCCCEEEEEEEEccCCCCcEEEEEEeC
Confidence 57777666 455544 777776542 4567889998875
No 85
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=45.18 E-value=60 Score=36.64 Aligned_cols=35 Identities=17% Similarity=0.053 Sum_probs=30.8
Q ss_pred cceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCC
Q 002793 722 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEG 758 (880)
Q Consensus 722 ~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~ 758 (880)
.+...+|.|.++.+.|++|.+. |++|+|+.+++..
T Consensus 118 ~~~~V~g~V~~~~~~G~~V~l~--Gv~gfip~s~ls~ 152 (318)
T PRK07400 118 EDATVRSEVFATNRGGALVRIE--GLRGFIPGSHIST 152 (318)
T ss_pred CCCEEEEEEEEEECCeEEEEEC--CEEEEEEHHHcCc
Confidence 3678899999999999999884 9999999999864
No 86
>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=42.36 E-value=1.9e+02 Score=28.15 Aligned_cols=80 Identities=11% Similarity=0.016 Sum_probs=42.9
Q ss_pred cceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEee-ecccceeecCCCceEEeceeEEEEEe
Q 002793 722 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSL-CAHKRSFKRGGPGNYRALEEVALVVR 800 (880)
Q Consensus 722 ~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~-~~~k~~~~~g~~~~~r~~d~v~v~~~ 800 (880)
.|++..|+|++-.+.|+.|-+ .|-=.-.|--+.|+. -..|++.++.-+.+. ..++--+..|+.|++|.-+..=..+.
T Consensus 3 ~gEvl~g~I~~~~~~Gi~vsl-gFFddI~IP~~~L~~-ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f~d~~ 80 (122)
T PF08292_consen 3 VGEVLTGKIKSSTAEGIRVSL-GFFDDIFIPPSLLPE-PSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIFPDVP 80 (122)
T ss_dssp TT-EEEEEEEEEETTEEEEEE-CCEEEEEEECCCC-T-TEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE----
T ss_pred CCCEEEEEEEecCCCcEEEEe-cccccEEECHHHCCC-CCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEEecCC
Confidence 467888999999988876654 232222222223332 234666666666654 45566678899999998766665555
Q ss_pred cCC
Q 002793 801 PND 803 (880)
Q Consensus 801 ~~~ 803 (880)
|..
T Consensus 81 p~~ 83 (122)
T PF08292_consen 81 PTP 83 (122)
T ss_dssp ---
T ss_pred CCC
Confidence 544
No 87
>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=41.22 E-value=48 Score=29.34 Aligned_cols=38 Identities=21% Similarity=0.042 Sum_probs=34.4
Q ss_pred ceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEE
Q 002793 723 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIV 761 (880)
Q Consensus 723 ~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~ 761 (880)
|...+|.|+.-.+.++.|.+.+.|+.|+++...|.| .+
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD-~~ 38 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSD-HV 38 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCC-ch
Confidence 356799999999999999999999999999999998 44
No 88
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=40.86 E-value=42 Score=34.82 Aligned_cols=57 Identities=19% Similarity=0.103 Sum_probs=41.7
Q ss_pred ccceEEeEEEEEeeccEEEEEEec---------CceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEE
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEK---------LAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 790 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~---------~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r 790 (880)
..|.+..|.|+++..++++|-|.. .+++|.+|.+++...+. . .-...++.||.+.++
T Consensus 63 ~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~---~----------~~~~~~~~GD~V~ak 128 (189)
T PRK09521 63 KKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYV---E----------SLTDAFKIGDIVRAK 128 (189)
T ss_pred CCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhh---h----------hHHhccCCCCEEEEE
Confidence 457889999999999999999864 36999999998764211 0 113457788876665
No 89
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=33.30 E-value=41 Score=40.33 Aligned_cols=37 Identities=3% Similarity=-0.100 Sum_probs=32.4
Q ss_pred ceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeE
Q 002793 723 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLI 760 (880)
Q Consensus 723 ~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~ 760 (880)
|-+|.|.|+.+.++|.+|.++. |.++++|.++|.-.|
T Consensus 669 g~vy~~tIt~~rd~G~~V~l~p-~~~~Llh~sqL~~e~ 705 (760)
T KOG1067|consen 669 GGVYTATITEIRDTGVMVELYP-MQQGLLHNSQLDQEK 705 (760)
T ss_pred eeEEEEEEeeecccceEEEecC-Cchhhccchhccccc
Confidence 4467999999999999999888 999999999987544
No 90
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=31.88 E-value=73 Score=34.34 Aligned_cols=61 Identities=15% Similarity=-0.028 Sum_probs=44.9
Q ss_pred ccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEe
Q 002793 721 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 791 (880)
Q Consensus 721 ~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~ 791 (880)
+.|.+..|+|+++..++++|-|.. +++|.+|++++...+.+.++ ...+..++.||-|..|.
T Consensus 62 ~vGDiViG~V~~i~~~~~~vdI~~-~~~g~L~~s~i~~~~~~~d~---------~~~~~~~~~GDlV~akV 122 (235)
T PRK04163 62 KVGDLVIGKVTDVTFSGWEVDINS-PYKAYLPVSEVLGRPVNVEG---------TDLRKYLDIGDYIIAKV 122 (235)
T ss_pred CCCCEEEEEEEEEeCceEEEEeCC-CceeEEEHHHcCCCccccch---------hhhHhhCCCCCEEEEEE
Confidence 456788999999999998888754 47899999998654433222 23455688999887775
No 91
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=31.16 E-value=75 Score=29.01 Aligned_cols=36 Identities=11% Similarity=0.174 Sum_probs=28.6
Q ss_pred cceEEeEEEEEeeccEEEEEEecCceEEEEE-eeecCC
Q 002793 722 EVLLSEARVLALGPRFMTIYIEKLAIERRIY-YDEVEG 758 (880)
Q Consensus 722 ~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~-~~~l~~ 758 (880)
.+.... -|..+.+.++.|.+.+|++||.|- ++++.-
T Consensus 16 v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr 52 (86)
T PHA02858 16 INEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNA 52 (86)
T ss_pred CCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhH
Confidence 455566 555789999999999999999988 777653
No 92
>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=31.08 E-value=1.3e+02 Score=37.28 Aligned_cols=105 Identities=12% Similarity=0.109 Sum_probs=55.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccc
Q 002793 689 VNVATHCNDRKLACRNVKDACVKLYMWILLKKKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTS 768 (880)
Q Consensus 689 ~~ia~~~N~r~~~A~~a~r~s~~l~~~~~l~~~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~ 768 (880)
..+...|..-..+.+.|.++..+.-.+.+++-.... -|-+. .|..+-|.++|+-..+-=..+++. +.+.+-..
T Consensus 536 ~~l~~~~~~~~~~er~a~~aer~~~~~~~~~yl~~~--iG~~~----~g~I~~v~~~GifV~L~~~~veGl-V~~s~l~~ 608 (654)
T TIGR00358 536 DELLQIAEHCSDTERRARDAERDVADWLKCRYLLDK--VGTEF----SGEISSVTRFGMFVRLDDNGIDGL-IHISTLHN 608 (654)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhC--CCcEE----EEEEEeEEcCcEEEEecCCceEEE-EEeEeCCC
Confidence 557777777777777777777777766666655433 23222 245666788886443320112222 11111110
Q ss_pred -eEEEeeecccceeecCC--CceEEeceeEEEEEecCC
Q 002793 769 -TLVLSLCAHKRSFKRGG--PGNYRALEEVALVVRPND 803 (880)
Q Consensus 769 -~lv~~~~~~k~~~~~g~--~~~~r~~d~v~v~~~~~~ 803 (880)
...+| ...... .|. ...|+.-|+|.|++.-.+
T Consensus 609 d~y~~d--~~~~~l-~g~~~~~~~~lGD~V~Vki~~vd 643 (654)
T TIGR00358 609 DYYVFD--QEKMAL-IGKGTGKVYRIGDRVTVKLTEVN 643 (654)
T ss_pred cceEEe--ccccEE-EeccCCcEECCCCEEEEEEEEEe
Confidence 11221 111111 121 246899999999987443
No 93
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=30.86 E-value=2.5e+02 Score=33.65 Aligned_cols=38 Identities=11% Similarity=-0.067 Sum_probs=30.0
Q ss_pred HHhhccceEEeEEEEEeeccEEEEEEecCceEEEEEeeec
Q 002793 717 LLKKKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEV 756 (880)
Q Consensus 717 ~l~~~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l 756 (880)
.++.+.|.+..|+|..+...|+.|-+ -|+|+.++.+++
T Consensus 129 eyk~~~GeIV~G~V~ri~~~giiVDL--ggvea~LP~sE~ 166 (470)
T PRK09202 129 EYKDRVGEIITGVVKRVERGNIIVDL--GRAEAILPRKEQ 166 (470)
T ss_pred HHHhhcCCEEEEEEEEEecCCEEEEE--CCeEEEecHHHc
Confidence 34556688999999999987766655 589999998774
No 94
>COG4871 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.65 E-value=92 Score=31.73 Aligned_cols=50 Identities=14% Similarity=0.236 Sum_probs=41.9
Q ss_pred cCCCccccCCCceeeeCCCCCeEEEEecCCCcHHHHHHHHHHHHHHHHHH
Q 002793 454 TDGALRLENSKPVFLFDEYGTPYDSVLSGREDLNFLFEEFMLLANKTAAE 503 (880)
Q Consensus 454 ~~Gal~l~~pe~~i~lDe~g~p~~i~~~~~~~a~~LIEEfMilAN~~vA~ 503 (880)
++++|.|...+.-+.+-++|.+.--......+|..+.+|+|-.+|+++|+
T Consensus 63 kk~~l~~~kgerIitiy~sGkVsm~~ikdedEAkeilgel~d~ineA~~k 112 (193)
T COG4871 63 KKNILILQKGERIITIYGSGKVSMTMIKDEDEAKEILGELMDIINEAIAK 112 (193)
T ss_pred ccceEEEeeccEEEEEccCCeEEeeeecCHHHHHHHHHHHHHHHHHHHHc
Confidence 46788888888777788888765555677789999999999999999996
No 95
>PRK11642 exoribonuclease R; Provisional
Probab=24.39 E-value=2.5e+02 Score=36.01 Aligned_cols=103 Identities=12% Similarity=0.082 Sum_probs=57.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEeccc
Q 002793 688 LVNVATHCNDRKLACRNVKDACVKLYMWILLKKKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETT 767 (880)
Q Consensus 688 l~~ia~~~N~r~~~A~~a~r~s~~l~~~~~l~~~~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~ 767 (880)
+..+...|..-....+.|.++..++-.|...+-... ..|-+. .|..+-|..||+-..+--..+++.- ...+-.
T Consensus 606 ~~~l~~~~~~~s~~er~A~~aeR~~~~~~~~~~m~~--~iGe~f----~G~Is~V~~fGifVeL~~~~vEGlV-~vs~L~ 678 (813)
T PRK11642 606 MEEMLQLGQHCSMTERRADEATRDVADWLKCDFMLD--QVGNVF----KGVISSVTGFGFFVRLDDLFIDGLV-HVSSLD 678 (813)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc--cCCcEE----EEEEEEeecCceEEEECCCCeeeeE-EEeecC
Confidence 466777788888888888888888887777765543 233332 2456677888886544211133321 111100
Q ss_pred c-eEEEeeecccceeecCC--CceEEeceeEEEEEe
Q 002793 768 S-TLVLSLCAHKRSFKRGG--PGNYRALEEVALVVR 800 (880)
Q Consensus 768 ~-~lv~~~~~~k~~~~~g~--~~~~r~~d~v~v~~~ 800 (880)
. -...+ .....-.|. .-.|+..|+|.|++.
T Consensus 679 ~d~y~~d---~~~~~L~g~~~~~~~~lGD~V~VkV~ 711 (813)
T PRK11642 679 NDYYRFD---QVGQRLIGESSGQTYRLGDRVEVRVE 711 (813)
T ss_pred CcceEec---chheEEecccCCcEECCCCEEEEEEE
Confidence 0 01111 111111232 246899999999995
No 96
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=23.73 E-value=3.4e+02 Score=25.03 Aligned_cols=58 Identities=21% Similarity=0.135 Sum_probs=35.4
Q ss_pred cceEEeEEEEEeeccEEEEEEecCceEEEEEeeecCCeEEEEecccceEEEeeecccceeecCCCceEEeceeEEEEEec
Q 002793 722 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRALEEVALVVRP 801 (880)
Q Consensus 722 ~~~~~~a~V~~v~~~~~~V~Ip~~giE~~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~~d~v~v~~~~ 801 (880)
...+.+|+|+.+-+++.+..-.+-|.+.+-|++. -++++ .+++..=|+|.|.++|
T Consensus 5 ~~ie~~G~V~e~Lp~~~frV~LenG~~vla~isG-----------------KmR~~--------rIrIl~GD~V~VE~sp 59 (87)
T PRK12442 5 ELIELDGIVDEVLPDSRFRVTLENGVEVGAYASG-----------------RMRKH--------RIRILAGDRVTLELSP 59 (87)
T ss_pred ceEEEEEEEEEECCCCEEEEEeCCCCEEEEEecc-----------------ceeee--------eEEecCCCEEEEEECc
Confidence 4567899999998877554333445555555542 11121 2344566777888888
Q ss_pred CCC
Q 002793 802 NDL 804 (880)
Q Consensus 802 ~~~ 804 (880)
.++
T Consensus 60 YDl 62 (87)
T PRK12442 60 YDL 62 (87)
T ss_pred ccC
Confidence 775
No 97
>TIGR00156 conserved hypothetical protein TIGR00156. As of the last revision, this family consists only of two proteins from Escherichia coli and one from the related species Haemophilus influenzae.
Probab=21.95 E-value=1.7e+02 Score=28.72 Aligned_cols=45 Identities=7% Similarity=0.046 Sum_probs=28.1
Q ss_pred eeecCCeEEEEecccceEEEeeecccceeecCCCceEEeceeEEEEEecC
Q 002793 753 YDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRALEEVALVVRPN 802 (880)
Q Consensus 753 ~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~~d~v~v~~~~~ 802 (880)
++.+.++.|+|++.++++..++... ...|. .+.+=++|.+.-..+
T Consensus 67 v~~l~~d~Y~F~D~TG~I~VeId~~---~w~G~--~v~p~d~V~I~GeVD 111 (126)
T TIGR00156 67 ISHIGDDRYVFRDKSGEINVVIPAA---VWNGR--EVQPKDMVNISGSLD 111 (126)
T ss_pred EEEeCCceEEEECCCCCEEEEECHH---HcCCC--cCCCCCEEEEEEEEC
Confidence 3567789999999999988865321 22343 234445555555544
No 98
>PRK10053 hypothetical protein; Provisional
Probab=20.22 E-value=1.9e+02 Score=28.53 Aligned_cols=45 Identities=7% Similarity=-0.010 Sum_probs=28.9
Q ss_pred eeecCCeEEEEecccceEEEeeecccceeecCCCceEEeceeEEEEEecC
Q 002793 753 YDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRALEEVALVVRPN 802 (880)
Q Consensus 753 ~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~~~~r~~d~v~v~~~~~ 802 (880)
++++.++.|+|++.++++..++... .+.|.. +.+-++|.+.-..+
T Consensus 71 v~~lg~d~Y~F~D~tG~I~VeID~~---~w~G~~--v~p~~kV~I~GevD 115 (130)
T PRK10053 71 IDHKGDDRYVFRDKSGEINVIIPAA---VFDGRE--VQPDQMININGSLD 115 (130)
T ss_pred EEEeCCceEEEECCCCcEEEEeCHH---HcCCCc--CCCCCEEEEEEEEC
Confidence 4667899999999999988865422 234532 34455555555433
Done!