Query 001256
Match_columns 1113
No_of_seqs 410 out of 1917
Neff 5.6
Searched_HMMs 46136
Date Thu Mar 28 20:00:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001256.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001256hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2102 Exosomal 3'-5' exoribo 100.0 2E-124 4E-129 1163.8 50.5 659 157-987 219-881 (941)
2 TIGR00358 3_prime_RNase VacB a 100.0 1E-121 3E-126 1117.7 69.1 621 175-1024 13-639 (654)
3 PRK11642 exoribonuclease R; Pr 100.0 2E-120 4E-125 1120.5 68.9 625 176-1024 82-710 (813)
4 TIGR02063 RNase_R ribonuclease 100.0 4E-117 9E-122 1089.9 69.9 621 177-1024 67-694 (709)
5 PRK05054 exoribonuclease II; P 100.0 3E-113 7E-118 1040.4 68.8 553 349-1024 71-629 (644)
6 COG0557 VacB Exoribonuclease R 100.0 1E-113 3E-118 1056.1 64.4 619 178-1025 69-690 (706)
7 TIGR02062 RNase_B exoribonucle 100.0 9E-112 2E-116 1025.8 68.9 552 349-1024 68-625 (639)
8 PF00773 RNB: RNB domain CAUTI 100.0 5.3E-74 1.1E-78 648.4 28.6 320 509-861 1-324 (325)
9 COG4776 Rnb Exoribonuclease II 100.0 4E-63 8.6E-68 549.9 23.3 527 400-1023 96-628 (645)
10 cd04471 S1_RNase_R S1_RNase_R: 98.1 1.1E-05 2.4E-10 73.4 8.7 67 956-1024 2-68 (83)
11 PF08206 OB_RNB: Ribonuclease 97.7 3.8E-05 8.3E-10 66.5 3.8 45 181-228 1-45 (58)
12 cd04460 S1_RpoE S1_RpoE: RpoE, 96.9 0.0031 6.8E-08 60.1 7.5 63 958-1024 2-64 (99)
13 TIGR00448 rpoE DNA-directed RN 96.7 0.0013 2.9E-08 69.4 4.1 74 947-1024 73-146 (179)
14 cd05686 S1_pNO40 S1_pNO40: pNO 96.4 0.0071 1.5E-07 54.4 5.9 57 955-1024 3-59 (73)
15 cd05684 S1_DHX8_helicase S1_DH 95.7 0.022 4.8E-07 51.8 5.7 57 956-1024 1-59 (79)
16 PRK08563 DNA-directed RNA poly 94.9 0.07 1.5E-06 56.8 7.6 71 950-1024 76-146 (187)
17 PRK08582 hypothetical protein; 94.9 0.051 1.1E-06 55.4 6.1 57 954-1024 4-60 (139)
18 COG1095 RPB7 DNA-directed RNA 94.9 0.043 9.3E-07 58.0 5.6 78 953-1034 79-156 (183)
19 cd05706 S1_Rrp5_repeat_sc10 S1 94.8 0.065 1.4E-06 47.8 5.9 56 955-1024 3-58 (73)
20 cd05697 S1_Rrp5_repeat_hs5 S1_ 94.7 0.058 1.2E-06 47.7 5.1 55 956-1024 1-55 (69)
21 cd05689 S1_RPS1_repeat_ec4 S1_ 94.6 0.086 1.9E-06 46.9 6.2 57 955-1024 3-59 (72)
22 cd05708 S1_Rrp5_repeat_sc12 S1 94.6 0.073 1.6E-06 47.5 5.7 57 955-1024 2-58 (77)
23 cd04452 S1_IF2_alpha S1_IF2_al 94.6 0.065 1.4E-06 48.0 5.3 57 955-1024 3-60 (76)
24 PF00575 S1: S1 RNA binding do 94.4 0.11 2.5E-06 46.2 6.6 57 954-1024 3-59 (74)
25 cd05690 S1_RPS1_repeat_ec5 S1_ 94.4 0.066 1.4E-06 47.0 4.8 56 956-1024 1-56 (69)
26 cd05707 S1_Rrp5_repeat_sc11 S1 93.7 0.1 2.2E-06 46.0 4.6 55 956-1024 1-55 (68)
27 PLN00207 polyribonucleotide nu 93.7 0.11 2.4E-06 66.7 6.6 62 949-1024 747-809 (891)
28 cd05685 S1_Tex S1_Tex: The C-t 93.6 0.1 2.2E-06 45.2 4.4 55 956-1024 1-55 (68)
29 cd05696 S1_Rrp5_repeat_hs4 S1_ 93.3 0.14 3.1E-06 45.9 5.0 55 956-1024 1-57 (71)
30 PRK07252 hypothetical protein; 93.1 0.17 3.7E-06 50.4 5.7 56 955-1024 3-58 (120)
31 cd05698 S1_Rrp5_repeat_hs6_sc5 92.8 0.17 3.8E-06 44.6 4.7 55 956-1024 1-55 (70)
32 PRK05807 hypothetical protein; 92.8 0.22 4.7E-06 50.7 6.0 56 954-1024 4-59 (136)
33 cd04461 S1_Rrp5_repeat_hs8_sc7 92.7 0.18 3.9E-06 46.4 4.9 57 954-1024 13-69 (83)
34 cd04472 S1_PNPase S1_PNPase: P 91.9 0.29 6.3E-06 42.5 5.0 55 956-1024 1-55 (68)
35 cd05705 S1_Rrp5_repeat_hs14 S1 91.4 0.29 6.3E-06 44.4 4.6 59 955-1024 3-61 (74)
36 cd05688 S1_RPS1_repeat_ec3 S1_ 90.9 0.51 1.1E-05 40.8 5.5 54 956-1024 2-55 (68)
37 PF08206 OB_RNB: Ribonuclease 90.8 0.76 1.6E-05 39.9 6.4 50 399-461 9-58 (58)
38 cd05692 S1_RPS1_repeat_hs4 S1_ 90.6 0.43 9.2E-06 41.2 4.8 55 956-1024 1-55 (69)
39 smart00316 S1 Ribosomal protei 90.5 0.52 1.1E-05 40.5 5.2 56 955-1024 2-57 (72)
40 cd05691 S1_RPS1_repeat_ec6 S1_ 89.5 0.64 1.4E-05 41.0 5.1 55 956-1024 1-55 (73)
41 cd04473 S1_RecJ_like S1_RecJ_l 89.4 0.84 1.8E-05 41.6 5.8 49 954-1024 15-63 (77)
42 PRK03987 translation initiatio 89.4 0.46 1E-05 53.5 5.0 57 955-1024 8-65 (262)
43 PTZ00248 eukaryotic translatio 89.1 0.47 1E-05 54.7 4.8 39 955-993 17-56 (319)
44 cd05703 S1_Rrp5_repeat_hs12_sc 89.0 0.74 1.6E-05 41.6 5.1 57 956-1024 1-57 (73)
45 PRK08059 general stress protei 87.9 0.86 1.9E-05 45.5 5.3 57 954-1024 6-62 (123)
46 PRK11824 polynucleotide phosph 87.3 1.7 3.7E-05 55.4 8.6 58 953-1024 619-676 (693)
47 PTZ00162 DNA-directed RNA poly 87.2 1.1 2.4E-05 47.6 5.9 71 951-1024 77-147 (176)
48 TIGR03591 polynuc_phos polyrib 85.7 1.8 3.9E-05 55.1 7.7 57 954-1024 617-673 (684)
49 cd05702 S1_Rrp5_repeat_hs11_sc 85.6 1.5 3.3E-05 39.0 5.0 57 956-1024 1-57 (70)
50 cd05695 S1_Rrp5_repeat_hs3 S1_ 85.0 1.8 4E-05 38.2 5.2 52 957-1024 2-53 (66)
51 PHA02945 interferon resistance 84.9 2.9 6.3E-05 39.5 6.6 42 954-996 10-54 (88)
52 cd05704 S1_Rrp5_repeat_hs13 S1 84.1 1.7 3.6E-05 39.1 4.6 56 955-1024 3-59 (72)
53 PRK07899 rpsA 30S ribosomal pr 83.4 2 4.4E-05 52.4 6.4 57 954-1024 292-348 (486)
54 cd00164 S1_like S1_like: Ribos 83.1 2.2 4.8E-05 35.8 4.9 51 960-1024 2-52 (65)
55 TIGR02063 RNase_R ribonuclease 82.8 3.8 8.2E-05 52.5 8.8 58 399-468 79-137 (709)
56 PRK12269 bifunctional cytidyla 82.7 2.1 4.5E-05 55.8 6.4 60 954-1024 751-810 (863)
57 smart00357 CSP Cold shock prot 82.6 1.8 3.8E-05 37.0 4.0 45 180-227 1-49 (64)
58 cd04453 S1_RNase_E S1_RNase_E: 82.3 2.5 5.4E-05 39.8 5.2 61 955-1026 7-69 (88)
59 cd04462 S1_RNAPII_Rpb7 S1_RNAP 82.3 5.5 0.00012 37.6 7.5 65 956-1024 2-66 (88)
60 PRK07400 30S ribosomal protein 81.6 2.4 5.3E-05 49.1 5.9 56 954-1024 195-250 (318)
61 PRK07899 rpsA 30S ribosomal pr 78.6 4.9 0.00011 49.2 7.4 56 954-1024 207-262 (486)
62 cd05693 S1_Rrp5_repeat_hs1_sc1 78.4 1.1 2.4E-05 43.2 1.5 67 955-1024 3-77 (100)
63 COG1098 VacB Predicted RNA bin 77.8 2.1 4.5E-05 42.9 3.2 57 954-1024 4-60 (129)
64 TIGR02696 pppGpp_PNP guanosine 76.5 5.7 0.00012 50.6 7.3 60 954-1024 646-706 (719)
65 PRK13806 rpsA 30S ribosomal pr 72.9 7 0.00015 48.0 6.7 57 954-1024 201-257 (491)
66 TIGR00717 rpsA ribosomal prote 72.8 5.4 0.00012 49.0 5.7 57 954-1024 445-501 (516)
67 PRK06676 rpsA 30S ribosomal pr 72.6 8.2 0.00018 45.7 7.1 57 953-1024 190-246 (390)
68 COG0539 RpsA Ribosomal protein 71.7 6.3 0.00014 48.6 5.8 37 954-992 191-227 (541)
69 cd05694 S1_Rrp5_repeat_hs2_sc2 71.3 10 0.00022 34.5 5.8 37 955-991 4-40 (74)
70 cd05687 S1_RPS1_repeat_ec1_hs1 71.2 8.8 0.00019 33.8 5.3 55 956-1024 1-55 (70)
71 smart00357 CSP Cold shock prot 66.6 15 0.00033 31.2 5.7 55 399-462 10-64 (64)
72 PRK13806 rpsA 30S ribosomal pr 65.7 9.2 0.0002 47.0 5.6 57 954-1024 378-434 (491)
73 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 63.1 12 0.00026 34.5 4.6 60 955-1024 6-65 (86)
74 PRK00087 4-hydroxy-3-methylbut 60.5 15 0.00032 46.7 6.3 57 954-1024 561-617 (647)
75 COG1093 SUI2 Translation initi 57.2 8.5 0.00019 43.2 2.9 40 955-994 11-51 (269)
76 PRK06676 rpsA 30S ribosomal pr 56.8 17 0.00036 43.1 5.6 56 954-1023 276-331 (390)
77 PRK12269 bifunctional cytidyla 56.2 28 0.00061 45.7 7.8 36 954-991 492-527 (863)
78 PRK00087 4-hydroxy-3-methylbut 50.5 32 0.00068 43.9 6.9 56 954-1024 476-531 (647)
79 PRK06299 rpsA 30S ribosomal pr 49.9 34 0.00074 42.6 7.0 36 954-991 200-235 (565)
80 cd04454 S1_Rrp4_like S1_Rrp4_l 49.1 37 0.0008 31.0 5.4 56 955-1024 6-61 (82)
81 cd04465 S1_RPS1_repeat_ec2_hs2 48.2 32 0.0007 30.1 4.7 34 956-991 1-34 (67)
82 COG0539 RpsA Ribosomal protein 46.0 30 0.00066 42.9 5.5 36 954-990 276-311 (541)
83 TIGR00717 rpsA ribosomal prote 45.3 33 0.00071 42.2 5.8 57 954-1023 358-414 (516)
84 PRK06299 rpsA 30S ribosomal pr 44.9 34 0.00074 42.7 5.9 57 954-1024 459-515 (565)
85 PF08292 RNA_pol_Rbc25: RNA po 42.7 1.7E+02 0.0037 29.5 9.3 80 955-1036 3-83 (122)
86 PRK07400 30S ribosomal protein 42.5 1.3E+02 0.0029 35.0 9.8 35 955-991 118-152 (318)
87 PRK09521 exosome complex RNA-b 38.1 49 0.0011 35.5 5.0 58 954-1024 63-129 (189)
88 cd05699 S1_Rrp5_repeat_hs7 S1_ 31.6 79 0.0017 29.2 4.5 37 957-994 2-38 (72)
89 PHA02858 EIF2a-like PKR inhibi 26.0 94 0.002 29.5 4.0 36 955-991 16-52 (86)
90 KOG1067 Predicted RNA-binding 25.0 69 0.0015 39.7 3.7 37 956-993 669-705 (760)
91 PRK04163 exosome complex RNA-b 24.2 1.1E+02 0.0024 34.0 5.0 61 954-1024 62-122 (235)
92 PRK09202 nusA transcription el 23.0 3.8E+02 0.0083 33.1 9.6 38 950-989 129-166 (470)
93 PF00313 CSD: 'Cold-shock' DNA 21.4 3.4E+02 0.0074 23.7 6.6 48 180-227 2-53 (66)
No 1
>KOG2102 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp44/Dis3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.8e-124 Score=1163.78 Aligned_cols=659 Identities=40% Similarity=0.647 Sum_probs=567.6
Q ss_pred ccCccCCCCHHHHHHHHHcCCeEEEEEEeccCCceeEEEEeCCcceeEEEeCcCCccccCCCCEEEEEEccchhhhhccC
Q 001256 157 CKIFAPHWSMEAVNEALEKGDAFKALYRVNAHNRLEAYCKIEGVQTDVLITGIAAQNRAVEGDFVLIKVDRLSLWAKMKG 236 (1113)
Q Consensus 157 k~~F~~hl~~~~v~~gLk~G~l~~G~lrVn~~N~~eAyV~~~g~~~Dv~I~G~~~rNRAl~GDvVaVeLlp~~~W~~~~~ 236 (1113)
|.+|++|||++.+..||++|++++|+||||++|+.||||.++++..+|+|+|.++||||++||+|||||+|..+|.....
T Consensus 219 k~~~~~~l~~~~~~~~~~~g~~~~g~l~i~~~n~~e~~v~~~~~~~~v~i~G~~~~NRa~~gdvVavell~~~~~~~~~~ 298 (941)
T KOG2102|consen 219 KLLFSPYLPMAKIKAGIKSGRLVQGTLRISRKNLSEAFVRVQGLDHPVLICGSKDRNRALDGDVVAVELLPVDEWRVELS 298 (941)
T ss_pred ceeeccccchhhHhhhhcccceeeceEEecccccccceeeccccCCceEEeCchhhhhhhcCCeEEEEeccchhccccch
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999952111
Q ss_pred CCCCCcccccCCCcccccCCCccccccCccccccccccccccccccCCCCCCCCchhhhhhhhhhhccccccCCCCCCCC
Q 001256 237 FSNNSSIVEDSNLPTEANGMHSDICKGKSKVDVSYEYSNCTLLSEKGIHHDDDSSSEAYNQEMIEREGYNYINGHHPSTS 316 (1113)
Q Consensus 237 ~~~~~~~~e~~~~~~e~~e~~~~~~~~k~~~d~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 316 (1113)
. ... + . ....+. .+.. -+++
T Consensus 299 ~---------~~~--~-~----------~~~~~~----------~~~~-~~~~--------------------------- 318 (941)
T KOG2102|consen 299 S---------IFL--D-S----------VKVSSN----------IKES-DDED--------------------------- 318 (941)
T ss_pred h---------hhc--c-c----------cccccc----------cccc-cccc---------------------------
Confidence 0 000 0 0 000000 0000 0000
Q ss_pred CccccccccccccchhhHhhhheeeccCCCCCccEEEEEEEecCCCCcceEEEEEeccccccCCCCcccccccCCCCCCC
Q 001256 317 DSTEKVSSSQQNDGMNAIERLSAMISSYPTKRPTGRVVSIIERSPRRDGIVGFLNVNQWFNYKGGSRKDAKKNRSSLSVP 396 (1113)
Q Consensus 317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~G~VV~IleR~~~~~~~vG~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 396 (1113)
.++.. . ......+.... .-.|+|+||+|++|+|++ ++|.+....+. +.+. .
T Consensus 319 -------e~~~~---~-~~~~~~~~~~~-~~~~~~~VV~il~r~~~~--~~~~l~~~~~~---------~~~~------~ 369 (941)
T KOG2102|consen 319 -------EDGTL---N-LRGKAVLSDPL-PVQPTGKVVAILRRNWRQ--YVGGLLPLSEQ---------ALKG------S 369 (941)
T ss_pred -------ccccc---c-ccccccccccc-cccccceEEEEEecCcee--eeccccCcccc---------cccc------c
Confidence 00000 0 00000000000 124699999999999964 56655521110 0001 1
Q ss_pred CCceEEEEeCCCCCCceEEecC-CCChhhhhhcccCCccccceEEEEEEeecCCCCCCCcEEEEEEcCCCCChHHHHHHH
Q 001256 397 DREYIQLTPTHPKYPKMVVLVK-DLPDSIKKRLEEGDATIEMELVAARIDEWNEESPFPQAHVLHVFGRGGEVEPQINAI 475 (1113)
Q Consensus 397 ~~~~~~~~P~D~riP~i~i~~~-~~p~~~~~~~~~gd~~~~~~lvvv~I~~Wp~~s~~P~G~Iv~~LG~~gd~~~e~~aI 475 (1113)
...++||+|.|+|+|+|.|+++ +.. .+.+.+++|.|++||.++.||.|++++.||.+|+.++++++|
T Consensus 370 ~~~~~~~~p~DkRvP~i~i~t~~~~~------------~~~~~~~~~~I~~W~~ts~~p~g~~v~~lG~i~~~~~e~~aL 437 (941)
T KOG2102|consen 370 SALIVLFIPSDKRVPLIRILTDDQAQ------------DLIDKRIVAAIDRWPRTSLYPFGHLVRELGTIGDTETETEAL 437 (941)
T ss_pred ccceeeeccccCCCCeeecccccccc------------chhceeEEEEecccccCCcccCceehhhccCcCCccchhhhh
Confidence 2468999999999999999987 432 234568999999999999999999999999999999999999
Q ss_pred HHhcCcCCCCCChhhhccCCC-CCCCCChhhhcc-CccCCCceEEEEcCCCCCCCCceEEEEEcCCCeEEEEEEeccccc
Q 001256 476 LYENAICCSGFSPESLSCLPC-VPWEVPQEELLS-RKDLRNFCIFTIDPSTATDLDDALSIERLSDGISRVGVHIADVSY 553 (1113)
Q Consensus 476 L~e~~i~~~~Fs~~vl~~l~~-~~~~i~~~e~~~-R~DLr~l~vfTIDp~~AkDlDDAlSie~l~~G~~~lgVHIADVS~ 553 (1113)
|.+|+++..+|+++++.|+|. .+|.+++++... |+|||++.||+|||++|+|||||||++.++||+|+||||||||||
T Consensus 438 L~en~v~~~~f~~~~~~~lp~~~~~~~~~~~~~~~R~Dlr~~~i~~IDp~~~~dlDdAL~~~~l~nG~~evGVHIADVt~ 517 (941)
T KOG2102|consen 438 LLENGVPHKPFSQALLDCLPRSHPWPITEEELQKLRKDLRDLLIFSIDPPGATDLDDALHVRNLPNGNLEVGVHIADVTH 517 (941)
T ss_pred hhcCCCcccccCHHHHhcCCccCCCCcChHHhhhhhhhhhhceEEeecCCCccchhhhhheeecCCCcEEEEEEeccchh
Confidence 999999889999999999999 999999999998 999999999999999999999999999999999999999999999
Q ss_pred cccCCCHhhHHHHhccceeecCCCcccCCChhhhhcccCCCCCCceeEEEEEEEEcCCCCEEEEEEEEEEEecccccCHH
Q 001256 554 FVLPGTALDIEAQVRSTSVYMLQRKIPMLPVLLSEEVGSLNPGVDRLAFSIFWDLNSAGDVVDRWIGRTVIRSCCKLSYE 633 (1113)
Q Consensus 554 fV~pgS~LD~eA~~RgtSVYLpdrviPMLP~~Ls~~lcSL~pg~dRlAfSv~~~id~~G~I~d~~f~~SvIrS~~rLTYe 633 (1113)
||+|||+||+||++|||||||++++|||||+.||+++|||+||+||+||||.|+|+.+|.|++.||++|+|+|+++|+|+
T Consensus 518 fV~pgs~lD~eA~~R~ttvyL~q~~i~MLP~~L~~~lcSL~~g~dr~aFSvvwel~~~~~i~~~~f~ksvI~s~~~lsye 597 (941)
T KOG2102|consen 518 FVKPGSALDREAARRGTTVYLVQKRIPMLPKLLSEELCSLRPGVDRLAFSVVWELDSDGSILKTWFGKSVIRSKAALSYE 597 (941)
T ss_pred hcCCCCccCHHHHhhcceEEeccccccCCchhhhhhheeccCCCceeeEEEEEEEcCCCceeeceecchhcccchhhhHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHccCCCccccCccCCCCCcccCCCchhhHHHHHHHHHHHHHHHHHHHhcCCCccccCCCceeecCCCC-CeEEeE
Q 001256 634 HAQDIIDGKFDVESSNTLGEGWPQLYGQFEWSDVVRSIKSLYEVSKILKDKRFTDGALRLENSKPVFLFDEYG-TPYDSV 712 (1113)
Q Consensus 634 ~vq~iLd~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~L~~L~~lA~~Lr~~R~~~Gal~ld~pe~~~~lDe~g-~p~~v~ 712 (1113)
+||++|+++.. ..++...|+.|++||+.||++|+.+||+.+..+|+.|.+|+.+ .|.++.
T Consensus 598 ~Aq~~id~~~~-------------------~~~v~~~l~~l~~ia~~lr~~R~~~gal~l~~~e~~~~~d~~~~~p~~~e 658 (941)
T KOG2102|consen 598 EAQDILDTPNS-------------------SDPLTSSLRLLHEIAKILRQKRLDNGALLLRSPELRFLLDEEKPNPQDVE 658 (941)
T ss_pred HHHHHhcCCcc-------------------cchhhhhHHHHHHHHHHHHHHHhccCCcccccHhHHhhhccCCCCccccc
Confidence 99999998421 2367789999999999999999999999999999999999876 789998
Q ss_pred ecCCccHHHHHHHHHHHHHHHHHHHHHHhCCCcceEEecCCCCHHHHHHHHHHHHHcCCccCCCChhHHHHHHHHHHHhh
Q 001256 713 LSGREDLNFLFEEFMLLANKTAAEVIARAFPDSALLRRHPAPNMRKLREFEAFCSKHGLQLDTSSSGQFHQSLEQAREKL 792 (1113)
Q Consensus 713 ~~~~~~a~~LIEEfMllAN~~VA~~l~~~~p~~allR~H~~P~~~kl~~l~~~~~~~G~~l~~ss~~~l~~sL~~i~~~~ 792 (1113)
.++..++|.||||||++||.+||++|.+.||.+++||+||.|....++.+.++|..+|+.++.++++.|+.+|.++.+..
T Consensus 659 ~~~~~~~n~lveEfmllaN~~vA~~I~~~f~~~alLR~hp~P~~~~~~~~~~~~~~~g~~ld~sS~~~L~~Sl~r~~~~~ 738 (941)
T KOG2102|consen 659 VKELTETNFLVEEFMLLANISVAEKILASFPSLALLRRHPSPPPENFKPLVSLCLELGFNLDTSSSKSLADSLDRIRDDD 738 (941)
T ss_pred eeeeehhhhHHHHHHHHHhHHHHHHHHHhCCchhhhccCCCCccccccHHHHHHHHcCCCccccchHHHhhhHhhhcCCc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999998753
Q ss_pred cCCHHHHHHHHHHHhcccCCcEecccCCCCCCCCcCccccCCCcccccccCCCchhhHHHHHHHHHHHHhhhhhhhhhcc
Q 001256 793 KDDYVLFDILINYATRPMQLASYFCSGDFKDDTDWGHYALAFPVYTHFTSPLRRYPDLVVHRTLNAALEAEKLYWKHRRM 872 (1113)
Q Consensus 793 ~~~p~~~~~L~~~~lR~M~~A~Y~~sg~~~s~~~~~HfgLa~~~YTHFTSPIRRYaDLIVHR~L~a~L~~~~~~~~~~~~ 872 (1113)
.|....+|..+++|+|.+|.|||+|.. +...++|||||+|+|||||||||||+||+|||||++....... .
T Consensus 739 --~p~~~~~l~~l~~r~m~~A~yf~sg~~-~~~~~~HygLa~p~YTHFTsPiRRY~DIivHrqL~~~~~~~~~------~ 809 (941)
T KOG2102|consen 739 --KPYLNTLLRILATRSMTRAVYFCSGSS-DTPQFHHYGLASPLYTHFTSPIRRYADIIVHRQLAAAFLERSP------T 809 (941)
T ss_pred --hHHHHHHHHHHHhhhhhceeEEeeccc-CcchhhchhhcccchhhccCcccccchHHHHHHHHHHhhccCc------c
Confidence 377778899999999999999999973 5678999999999999999999999999999999973221110 0
Q ss_pred CCCCCCccccccccccccccccchhhhhhhhhHHHHHhhhcCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001256 873 LPKNNHREGVRGRFLTGIFYDKDAAESLEGREALSVAALKYGVPCADILVNVATHCNDRKLACRNVKDACVKLYMWILLK 952 (1113)
Q Consensus 873 ~~~~~~~~~~~~~~~~~i~~~~~~~es~~~~e~l~~~~~k~~lp~~~~l~~ia~~~N~r~~~Ar~A~r~s~~l~~~~~lk 952 (1113)
.++...+..+|.+||.|+++|+.|+++|.++|++.|++
T Consensus 810 ------------------------------------------~~~~~~l~~i~~~~N~r~~~a~~a~~~S~~l~~~~~~k 847 (941)
T KOG2102|consen 810 ------------------------------------------APDRPNLSSLAANCNERKKAAKKAQEASTELYLCEYLK 847 (941)
T ss_pred ------------------------------------------ccccccHHHHHhhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence 01123578899999999999999999999999999999
Q ss_pred hccceEEEEEEeeecCcEEEEEEecCCeEEEEEee
Q 001256 953 KKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYD 987 (1113)
Q Consensus 953 ~~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~ 987 (1113)
.+ ....+|+|+.|.++||.||||+||+||+||++
T Consensus 848 ~~-~~~~~a~v~~V~~~~~~v~ipe~G~e~~v~l~ 881 (941)
T KOG2102|consen 848 DK-QVLEEAVVLFVRPNGIDVVIPEYGLEGRVYLD 881 (941)
T ss_pred hc-ccccceEEEEEecCceEEEEcccCceEEEEec
Confidence 98 56789999999999999999999999999999
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=1.5e-121 Score=1117.66 Aligned_cols=621 Identities=25% Similarity=0.352 Sum_probs=547.5
Q ss_pred cCCeEEEEEEeccCCceeEEEEeCCc-ceeEEEeCcCCccccCCCCEEEEEEccchhhhhccCCCCCCcccccCCCcccc
Q 001256 175 KGDAFKALYRVNAHNRLEAYCKIEGV-QTDVLITGIAAQNRAVEGDFVLIKVDRLSLWAKMKGFSNNSSIVEDSNLPTEA 253 (1113)
Q Consensus 175 ~G~l~~G~lrVn~~N~~eAyV~~~g~-~~Dv~I~G~~~rNRAl~GDvVaVeLlp~~~W~~~~~~~~~~~~~e~~~~~~e~ 253 (1113)
...+++|+|+++++.+ |||..++. ..||||.+. ++|+|+|||.|.|++.+...
T Consensus 13 ~~~~~~G~i~~~~~gf--gFv~~~~~~~~difI~~~-~~~~a~~GD~V~v~i~~~~~----------------------- 66 (654)
T TIGR00358 13 KDDLVKGVVKAHNKGF--GFLRPDDDDKKDYFIPPP-QMKKVMHGDLVEACPLSQPQ----------------------- 66 (654)
T ss_pred CCCeEEEEEEECCCcc--EEEEeCCCCCCcEEEchH-HhCcCCCCCEEEEEEeecCC-----------------------
Confidence 3457999999998876 89988763 579999985 99999999999999643100
Q ss_pred cCCCccccccCccccccccccccccccccCCCCCCCCchhhhhhhhhhhccccccCCCCCCCCCccccccccccccchhh
Q 001256 254 NGMHSDICKGKSKVDVSYEYSNCTLLSEKGIHHDDDSSSEAYNQEMIEREGYNYINGHHPSTSDSTEKVSSSQQNDGMNA 333 (1113)
Q Consensus 254 ~e~~~~~~~~k~~~d~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 (1113)
T Consensus 67 -------------------------------------------------------------------------------- 66 (654)
T TIGR00358 67 -------------------------------------------------------------------------------- 66 (654)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred HhhhheeeccCCCCCccEEEEEEEecCCCCcceEEEEEeccccccCCCCcccccccCCCCCCCCCceEEEEeCCCCCCce
Q 001256 334 IERLSAMISSYPTKRPTGRVVSIIERSPRRDGIVGFLNVNQWFNYKGGSRKDAKKNRSSLSVPDREYIQLTPTHPKYPKM 413 (1113)
Q Consensus 334 ~~~~~~~~~~~~~~~p~G~VV~IleR~~~~~~~vG~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~D~riP~i 413 (1113)
+++|+|+|++||+|++ +.+||++.. .+ +..+|+|.|++++..
T Consensus 67 ------------~~~~~g~v~~il~r~~--~~~vG~~~~----------------~~--------~~~~v~p~~~~~~~~ 108 (654)
T TIGR00358 67 ------------RGRFEAEVERILEPAL--TRFVGKFLG----------------EN--------DFGFVVPDDPRIYLD 108 (654)
T ss_pred ------------CCCceEEEEEEeccCC--CEEEEEEEE----------------eC--------CeEEEEECCCCCCCc
Confidence 1237999999999986 579999982 22 367899999999984
Q ss_pred EEecCCCChhhhhhcccCCccccceEEEEEEeecCCCCCCCcEEEEEEcCCCCChHHHHHHHHHhcCcCCCCCChhhhcc
Q 001256 414 VVLVKDLPDSIKKRLEEGDATIEMELVAARIDEWNEESPFPQAHVLHVFGRGGEVEPQINAILYENAICCSGFSPESLSC 493 (1113)
Q Consensus 414 ~i~~~~~p~~~~~~~~~gd~~~~~~lvvv~I~~Wp~~s~~P~G~Iv~~LG~~gd~~~e~~aIL~e~~i~~~~Fs~~vl~~ 493 (1113)
++.... .....+++|| +|+|+|++||..+.+|.|+|+++||..+++.+|++++|.+|+| +.+||++++++
T Consensus 109 i~i~~~---~~~~~~~~g~------~V~v~i~~~p~~~~~~~g~i~~~lG~~~d~~~~~~~il~~~~i-~~~f~~~v~~~ 178 (654)
T TIGR00358 109 IIVPKA---SVKNELAEGD------KVVVELTEYPLRRNLFYGEITQILGNNDDPLIPWWVTLARHEI-PFEFPDGVEQQ 178 (654)
T ss_pred EEEcCC---ccccCCCCCC------EEEEEEccCCCCCCCceEEEEEEEcCCCCcccHHHHHHHHcCc-CCCCCHHHHHH
Confidence 443221 0111344454 8999999999999999999999999999999999999999999 56999999999
Q ss_pred CCCCCCCCChhhhccCccCCCceEEEEcCCCCCCCCceEEEEEcCCCeEEEEEEeccccccccCCCHhhHHHHhccceee
Q 001256 494 LPCVPWEVPQEELLSRKDLRNFCIFTIDPSTATDLDDALSIERLSDGISRVGVHIADVSYFVLPGTALDIEAQVRSTSVY 573 (1113)
Q Consensus 494 l~~~~~~i~~~e~~~R~DLr~l~vfTIDp~~AkDlDDAlSie~l~~G~~~lgVHIADVS~fV~pgS~LD~eA~~RgtSVY 573 (1113)
++.++|.+++++.++|+|||++++|||||++|+||||||||+++++|+|+||||||||||||++||+||+||++||||||
T Consensus 179 a~~~~~~~~~~~~~~R~Dlr~~~~~TID~~~a~D~DDAisie~~~~g~~~l~VHIADVs~~V~~~s~LD~eA~~R~tSvY 258 (654)
T TIGR00358 179 AAKLQFDVDEQAKKYREDLTDLAFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSYYVAENSPLDKEAKHRGFSVY 258 (654)
T ss_pred HHhccccCChhHhhCccccccCcEEEECCCCCCcccceEEEEEeCCCcEEEEEEEechhheeCCCCHHHHHHHHhCcCcc
Confidence 99999999999999999999999999999999999999999999899999999999999999999999999999999999
Q ss_pred cCCCcccCCChhhhhcccCCCCCCceeEEEEEEEEcCCCCEEEEEEEEEEEecccccCHHHHHHHHccCCCccccCccCC
Q 001256 574 MLQRKIPMLPVLLSEEVGSLNPGVDRLAFSIFWDLNSAGDVVDRWIGRTVIRSCCKLSYEHAQDIIDGKFDVESSNTLGE 653 (1113)
Q Consensus 574 LpdrviPMLP~~Ls~~lcSL~pg~dRlAfSv~~~id~~G~I~d~~f~~SvIrS~~rLTYe~vq~iLd~~~~~~~~~~~~~ 653 (1113)
||++++||||+.||+++|||+||++|+||||.|+||.+|+|++++|++|+|+|+++|||++|+++|++....
T Consensus 259 lp~~~ipMLP~~Ls~~~cSL~p~~~R~a~s~~~~id~~G~i~~~~~~~svI~s~~rltY~~v~~~l~~~~~~-------- 330 (654)
T TIGR00358 259 LPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYDKVNDWLENDDEL-------- 330 (654)
T ss_pred CCCCeecCCCHHHhcCccccCCCCcceEEEEEEEECCCCCEeEEEEEEEEEEECcEEcHHHHHHHHcCCccc--------
Confidence 999999999999999999999999999999999999999999999999999999999999999999874211
Q ss_pred CCCcccCCCchhhHHHHHHHHHHHHHHHHHHHhcCCCccccCCCceeecCCCCCeEEeEecCCccHHHHHHHHHHHHHHH
Q 001256 654 GWPQLYGQFEWSDVVRSIKSLYEVSKILKDKRFTDGALRLENSKPVFLFDEYGTPYDSVLSGREDLNFLFEEFMLLANKT 733 (1113)
Q Consensus 654 ~~p~~~~~~~~~~~~~~L~~L~~lA~~Lr~~R~~~Gal~ld~pe~~~~lDe~g~p~~v~~~~~~~a~~LIEEfMllAN~~ 733 (1113)
. ...+++.++|..|++||++||++|.++|+|+|+.|+++|.+|++|.+.++...++.+||.|||||||+||++
T Consensus 331 --~-----~~~~~~~~~L~~l~~la~~lr~~R~~~Gai~~~~~e~~~~~d~~g~~~~i~~~~~~~a~~lIeE~MilAN~~ 403 (654)
T TIGR00358 331 --Q-----PEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEEGRVIDIVAEVRRIAEKIIEEAMIVANIC 403 (654)
T ss_pred --c-----hhhHHHHHHHHHHHHHHHHHHHHHHHCCCcccCCCceeEEECCCCCeeEEEeccCcHHHHHHHHHHHHHHHH
Confidence 0 023567889999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhCCCcceEEecCCCCHHHHHHHHHHHHHcCCccCCC-----ChhHHHHHHHHHHHhhcCCHHHHHHHHHHHhc
Q 001256 734 AAEVIARAFPDSALLRRHPAPNMRKLREFEAFCSKHGLQLDTS-----SSGQFHQSLEQAREKLKDDYVLFDILINYATR 808 (1113)
Q Consensus 734 VA~~l~~~~p~~allR~H~~P~~~kl~~l~~~~~~~G~~l~~s-----s~~~l~~sL~~i~~~~~~~p~~~~~L~~~~lR 808 (1113)
||+|+.++ +.|++||+|++|+.+++++|.+++..+|+.++.. ++..++..|.++. +.+. ..+|..+++|
T Consensus 404 vA~~~~~~-~~p~iyR~h~~p~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~l~~~~----~~~~-~~~l~~~llr 477 (654)
T TIGR00358 404 AARFLHNH-KVPGIYRVHPGPSKKKLQSLLEFLAELGLTLPGGNAENVTTLDGACWLREVK----DRPE-YEILVTRLLR 477 (654)
T ss_pred HHHHHHHc-CCCeEEecCCCCCHHHHHHHHHHHHHcCCCccCCCcCCCChHHHHHHHHHhh----CCCH-HHHHHHHHHH
Confidence 99999987 7899999999999999999999999999987432 2445666666554 3333 3467788899
Q ss_pred ccCCcEecccCCCCCCCCcCccccCCCcccccccCCCchhhHHHHHHHHHHHHhhhhhhhhhccCCCCCCcccccccccc
Q 001256 809 PMQLASYFCSGDFKDDTDWGHYALAFPVYTHFTSPLRRYPDLVVHRTLNAALEAEKLYWKHRRMLPKNNHREGVRGRFLT 888 (1113)
Q Consensus 809 ~M~~A~Y~~sg~~~s~~~~~HfgLa~~~YTHFTSPIRRYaDLIVHR~L~a~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 888 (1113)
+|++|.|. ..+.+|||||++.|||||||||||+||+|||||+++|.+++.....
T Consensus 478 ~m~~A~y~-------~~~~~HfgL~~~~YthfTSPIRRY~DLivHr~L~a~l~~~~~~~~~------------------- 531 (654)
T TIGR00358 478 SLSQAEYS-------PEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQTDTER------------------- 531 (654)
T ss_pred hhcccccC-------CCCCCccccccccccccCCccccchHHHHHHHHHHHHcCCCCcccc-------------------
Confidence 99999993 5799999999999999999999999999999999999864310000
Q ss_pred ccccccchhhhhhhhhHHHHHhhhcCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceEEEEEEeeecC
Q 001256 889 GIFYDKDAAESLEGREALSVAALKYGVPCADILVNVATHCNDRKLACRNVKDACVKLYMWILLKKKEVLLSEARVLALGP 968 (1113)
Q Consensus 889 ~i~~~~~~~es~~~~e~l~~~~~k~~lp~~~~l~~ia~~~N~r~~~Ar~A~r~s~~l~~~~~lk~~~g~~~~a~V~~V~~ 968 (1113)
..+.+.+..+|++||++++.|++|+|++.++|++.||+++.|.+++|+|++|.+
T Consensus 532 --------------------------~~~~~~l~~~~~~~~~~er~a~~aer~~~~~~~~~yl~~~iG~~~~g~I~~v~~ 585 (654)
T TIGR00358 532 --------------------------YQPQDELLQIAEHCSDTERRARDAERDVADWLKCRYLLDKVGTEFSGEISSVTR 585 (654)
T ss_pred --------------------------hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCcEEEEEEEeEEc
Confidence 001345789999999999999999999999999999999999999999999999
Q ss_pred cEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 969 RFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 969 ~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
+|++|.|+++|+||+||++++++++|+|++.++.|++ +++++.|++||.|+++.
T Consensus 586 ~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g--~~~~~~~~lGD~V~Vki 639 (654)
T TIGR00358 586 FGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIG--KGTGKVYRIGDRVTVKL 639 (654)
T ss_pred CcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEe--ccCCcEECCCCEEEEEE
Confidence 9999999999999999999999999999999999999 57778999999888875
No 3
>PRK11642 exoribonuclease R; Provisional
Probab=100.00 E-value=2.1e-120 Score=1120.50 Aligned_cols=625 Identities=24% Similarity=0.342 Sum_probs=546.7
Q ss_pred CCeEEEEEEeccCCceeEEEEeCCcceeEEEeCcCCccccCCCCEEEEEEccchhhhhccCCCCCCcccccCCCcccccC
Q 001256 176 GDAFKALYRVNAHNRLEAYCKIEGVQTDVLITGIAAQNRAVEGDFVLIKVDRLSLWAKMKGFSNNSSIVEDSNLPTEANG 255 (1113)
Q Consensus 176 G~l~~G~lrVn~~N~~eAyV~~~g~~~Dv~I~G~~~rNRAl~GDvVaVeLlp~~~W~~~~~~~~~~~~~e~~~~~~e~~e 255 (1113)
..++.|+++++++.+ +||..++-..||||... ++|.|+|||.|.|.+.+..
T Consensus 82 ~~~~~G~v~~~~~Gf--gFv~~e~~~~difI~~~-~l~~A~~GD~V~v~i~~~~-------------------------- 132 (813)
T PRK11642 82 LDLLKGTVIGHRDGY--GFLRVEGRKDDLYLSSE-QMKTCIHGDQVLAQPLGAD-------------------------- 132 (813)
T ss_pred CceEEEEEEECCCcc--EEEEECCCCCCEEEChH-HHccCCCCCEEEEEEccCC--------------------------
Confidence 357899999987655 68888765569999776 8999999999999853200
Q ss_pred CCccccccCccccccccccccccccccCCCCCCCCchhhhhhhhhhhccccccCCCCCCCCCccccccccccccchhhHh
Q 001256 256 MHSDICKGKSKVDVSYEYSNCTLLSEKGIHHDDDSSSEAYNQEMIEREGYNYINGHHPSTSDSTEKVSSSQQNDGMNAIE 335 (1113)
Q Consensus 256 ~~~~~~~~k~~~d~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 335 (1113)
T Consensus 133 -------------------------------------------------------------------------------- 132 (813)
T PRK11642 133 -------------------------------------------------------------------------------- 132 (813)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred hhheeeccCCCCCccEEEEEEEecCCCCcceEEEEEeccccccCCCCcccccccCCCCCCCCCceEEEEeCCCCCCceEE
Q 001256 336 RLSAMISSYPTKRPTGRVVSIIERSPRRDGIVGFLNVNQWFNYKGGSRKDAKKNRSSLSVPDREYIQLTPTHPKYPKMVV 415 (1113)
Q Consensus 336 ~~~~~~~~~~~~~p~G~VV~IleR~~~~~~~vG~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~D~riP~i~i 415 (1113)
.+++|+|+||+||+|+. ..+||++.. .+ +..+++|.|+|++..+.
T Consensus 133 ---------~~~r~eg~Vv~IleR~~--~~~vG~~~~----------------~~--------~~~~v~P~d~r~~~~i~ 177 (813)
T PRK11642 133 ---------RKGRREARIVRVLVPKT--SQIVGRYFT----------------DA--------GVGFVVPDDSRLSFDIL 177 (813)
T ss_pred ---------CCCCcEEEEEEEEecCC--CEEEEEEEE----------------eC--------CeEEEEECCCCCCCcEE
Confidence 01247999999999985 579999982 21 35789999999998554
Q ss_pred ecCCCChhhhhhcccCCccccceEEEEEEeecCCCCCCCcEEEEEEcCCCCChHHHHHHHHHhcCcCCCCCChhhhccCC
Q 001256 416 LVKDLPDSIKKRLEEGDATIEMELVAARIDEWNEESPFPQAHVLHVFGRGGEVEPQINAILYENAICCSGFSPESLSCLP 495 (1113)
Q Consensus 416 ~~~~~p~~~~~~~~~gd~~~~~~lvvv~I~~Wp~~s~~P~G~Iv~~LG~~gd~~~e~~aIL~e~~i~~~~Fs~~vl~~l~ 495 (1113)
... .-...+++|+ +|+|+|++||..+.+|.|+|+++||..+++.++++++|.+|+| +.+||++|++++.
T Consensus 178 i~~----~~~~~~~~gd------~V~v~I~~~p~~~~~~~g~iv~vLG~~~d~~~d~~~il~~~~i-p~~Fp~~v~~ea~ 246 (813)
T PRK11642 178 IPP----EQIMGARMGF------VVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEI-PYIWPQAVEQQVA 246 (813)
T ss_pred ecc----ccccCCCCCC------EEEEEEecCCCcCCCCCEEEEEEecCCCCcchHHHHHHHHcCC-CCCCCHHHHHHHH
Confidence 321 1122445555 8999999999999999999999999999999999999999999 5689999999999
Q ss_pred CCCCCCChhhhccCccCCCceEEEEcCCCCCCCCceEEEEEcCCCeEEEEEEeccccccccCCCHhhHHHHhccceeecC
Q 001256 496 CVPWEVPQEELLSRKDLRNFCIFTIDPSTATDLDDALSIERLSDGISRVGVHIADVSYFVLPGTALDIEAQVRSTSVYML 575 (1113)
Q Consensus 496 ~~~~~i~~~e~~~R~DLr~l~vfTIDp~~AkDlDDAlSie~l~~G~~~lgVHIADVS~fV~pgS~LD~eA~~RgtSVYLp 575 (1113)
.++|.+++++.++|+|||++++|||||++|+||||||||+++++|+|+||||||||||||++||+||+||++||||||||
T Consensus 247 ~~~~~~~~~~~~~R~DLr~l~~vTID~~~akD~DDAvsie~~~~g~~~L~VHIADVs~yV~~gS~LD~eA~~RgtSvYlp 326 (813)
T PRK11642 247 GLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFP 326 (813)
T ss_pred hccccCChhHhccccccccCcEEEECCCCCCcccceEEEEEeCCCcEEEEEEecchhheeCCCCHHHHHHHHhCCeEeCC
Confidence 99999999999999999999999999999999999999999988999999999999999999999999999999999999
Q ss_pred CCcccCCChhhhhcccCCCCCCceeEEEEEEEEcCCCCEEEEEEEEEEEecccccCHHHHHHHHccCCCccccCccCCCC
Q 001256 576 QRKIPMLPVLLSEEVGSLNPGVDRLAFSIFWDLNSAGDVVDRWIGRTVIRSCCKLSYEHAQDIIDGKFDVESSNTLGEGW 655 (1113)
Q Consensus 576 drviPMLP~~Ls~~lcSL~pg~dRlAfSv~~~id~~G~I~d~~f~~SvIrS~~rLTYe~vq~iLd~~~~~~~~~~~~~~~ 655 (1113)
++++||||+.||+++|||+||++|+||||.|+||.+|+|++++|++|+|+|+++|||++|+++|+++....
T Consensus 327 d~viPMLP~~Lsn~lcSL~p~~dRla~s~~~~id~~G~v~~~~~~~svI~s~~rltY~~v~~~l~~~~~~~--------- 397 (813)
T PRK11642 327 SQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLR--------- 397 (813)
T ss_pred CceeeCCCHHHhcCccccCCCCceeEEEEEEEECCCCCCcCCEEEEEEEEECceECHHHHHHHHcCCcccc---------
Confidence 99999999999999999999999999999999999999999999999999999999999999998742110
Q ss_pred CcccCCCchhhHHHHHHHHHHHHHHHHHHHhcCCCccccCCCceeecCCCCCeEEeEecCCccHHHHHHHHHHHHHHHHH
Q 001256 656 PQLYGQFEWSDVVRSIKSLYEVSKILKDKRFTDGALRLENSKPVFLFDEYGTPYDSVLSGREDLNFLFEEFMLLANKTAA 735 (1113)
Q Consensus 656 p~~~~~~~~~~~~~~L~~L~~lA~~Lr~~R~~~Gal~ld~pe~~~~lDe~g~p~~v~~~~~~~a~~LIEEfMllAN~~VA 735 (1113)
..+.++.++|..|+++|++|+++|+++|+|+|+.||++|.+|++|.+..+...++.+||.|||||||+||++||
T Consensus 398 ------~~~~~~~~~L~~l~~la~~Lr~~R~~~Gai~~d~~E~~i~ld~~g~~~~i~~~~~~~a~~lIEE~MllAN~~vA 471 (813)
T PRK11642 398 ------EQYAPLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAA 471 (813)
T ss_pred ------hhhhHHHHHHHHHHHHHHHHHHHHHHCCCcccCCCceEEEECCCCCEeeEEecccccHHHHHHHHHHHHHHHHH
Confidence 02456789999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhCCCcceEEecCCCCHHHHHHHHHHHHHcCCccCCC---ChhHHHHHHHHHHHhhcCCHHHHHHHHHHHhcccCC
Q 001256 736 EVIARAFPDSALLRRHPAPNMRKLREFEAFCSKHGLQLDTS---SSGQFHQSLEQAREKLKDDYVLFDILINYATRPMQL 812 (1113)
Q Consensus 736 ~~l~~~~p~~allR~H~~P~~~kl~~l~~~~~~~G~~l~~s---s~~~l~~sL~~i~~~~~~~p~~~~~L~~~~lR~M~~ 812 (1113)
+|+.++ +.|++||+|+.|++++++.|.+++..+|+.++.. +++.++..|..+. +.|. ..+|..+++|+|++
T Consensus 472 ~~l~~~-~~p~lyR~H~~P~~ekl~~l~~~l~~lG~~l~~~~~~~~~~~~~ll~~~~----~~~~-~~~l~~~llRsm~~ 545 (813)
T PRK11642 472 RFVEKA-KEPALFRIHDKPSTEAITSFRSVLAELGLELPGGNKPEPRDYAELLESVA----DRPD-AEMLQTMLLRSMKQ 545 (813)
T ss_pred HHHHHC-CCCEEEEeCCCCCHHHHHHHHHHHHHcCCcccCCCCCCHHHHHHHHHHHh----CCcH-HHHHHHHHHHhccc
Confidence 999875 8899999999999999999999999999998643 2455666666654 4443 25678889999999
Q ss_pred cEecccCCCCCCCCcCccccCCCcccccccCCCchhhHHHHHHHHHHHHhhhhhhhhhccCCCCCCcccccccccc-ccc
Q 001256 813 ASYFCSGDFKDDTDWGHYALAFPVYTHFTSPLRRYPDLVVHRTLNAALEAEKLYWKHRRMLPKNNHREGVRGRFLT-GIF 891 (1113)
Q Consensus 813 A~Y~~sg~~~s~~~~~HfgLa~~~YTHFTSPIRRYaDLIVHR~L~a~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~i~ 891 (1113)
|.| ++++.+|||||++.||||||||||||||||||+|+++|.++.-. ..|++ ...
T Consensus 546 A~Y-------~~~~~gHfGLa~~~YtHFTSPIRRY~DLivHR~Lk~~L~~~~~~-----------------~~~~~~~~~ 601 (813)
T PRK11642 546 AIY-------DPENRGHFGLALQSYAHFTSPIRRYPDLSLHRAIKYLLAKEQGH-----------------KGNTTETGG 601 (813)
T ss_pred ccc-------CCCCCCccccccccccccCchhhhhHHHHHHHHHHHHHhCCCCc-----------------ccccccccc
Confidence 999 46899999999999999999999999999999999999754210 00111 011
Q ss_pred cccchhhhhhhhhHHHHHhhhcCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceEEEEEEeeecCcEE
Q 001256 892 YDKDAAESLEGREALSVAALKYGVPCADILVNVATHCNDRKLACRNVKDACVKLYMWILLKKKEVLLSEARVLALGPRFM 971 (1113)
Q Consensus 892 ~~~~~~es~~~~e~l~~~~~k~~lp~~~~l~~ia~~~N~r~~~Ar~A~r~s~~l~~~~~lk~~~g~~~~a~V~~V~~~~f 971 (1113)
|.. ..+.+..+|+|||++++.|.+|+|++++++++.||+++.|.+++|+|++|.++||
T Consensus 602 ~~~----------------------~~~~l~~~~~~~s~~er~A~~aeR~~~~~~~~~~m~~~iGe~f~G~Is~V~~fGi 659 (813)
T PRK11642 602 YHY----------------------SMEEMLQLGQHCSMTERRADEATRDVADWLKCDFMLDQVGNVFKGVISSVTGFGF 659 (813)
T ss_pred ccc----------------------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCCcEEEEEEEEeecCce
Confidence 211 0134778999999999999999999999999999999999999999999999999
Q ss_pred EEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 972 TIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 972 ~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
+|.|+.+++||.||+++|.++||+|++.+++|+| +++++.|++||.|+++.
T Consensus 660 fVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g--~~~~~~~~lGD~V~VkV 710 (813)
T PRK11642 660 FVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIG--ESSGQTYRLGDRVEVRV 710 (813)
T ss_pred EEEECCCCeeeeEEEeecCCcceEecchheEEec--ccCCcEECCCCEEEEEE
Confidence 9999999999999999999999999999999999 57889999999888875
No 4
>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=4.1e-117 Score=1089.91 Aligned_cols=621 Identities=30% Similarity=0.420 Sum_probs=544.8
Q ss_pred CeEEEEEEeccCCceeEEEEeCC-cceeEEEeCcCCccccCCCCEEEEEEccchhhhhccCCCCCCcccccCCCcccccC
Q 001256 177 DAFKALYRVNAHNRLEAYCKIEG-VQTDVLITGIAAQNRAVEGDFVLIKVDRLSLWAKMKGFSNNSSIVEDSNLPTEANG 255 (1113)
Q Consensus 177 ~l~~G~lrVn~~N~~eAyV~~~g-~~~Dv~I~G~~~rNRAl~GDvVaVeLlp~~~W~~~~~~~~~~~~~e~~~~~~e~~e 255 (1113)
..+.|+++++++.+ |||..++ .+.||||.. .+.|+|++||.|.|++.+ |..
T Consensus 67 ~~~~G~i~~~~~g~--gFv~~~~~~~~di~I~~-~~~~~a~~GD~Vlv~I~~---~~~---------------------- 118 (709)
T TIGR02063 67 KLVKGTVIAHRDGF--GFLRPEDDDEDDIFIPP-RQMNGAMHGDRVLVRITG---KPD---------------------- 118 (709)
T ss_pred CeEEEEEEECCCcc--EEEEECCCCCCcEEECh-HHhCcCCCCCEEEEEEec---ccC----------------------
Confidence 46889999976654 8998876 467999987 589999999999999743 100
Q ss_pred CCccccccCccccccccccccccccccCCCCCCCCchhhhhhhhhhhccccccCCCCCCCCCccccccccccccchhhHh
Q 001256 256 MHSDICKGKSKVDVSYEYSNCTLLSEKGIHHDDDSSSEAYNQEMIEREGYNYINGHHPSTSDSTEKVSSSQQNDGMNAIE 335 (1113)
Q Consensus 256 ~~~~~~~~k~~~d~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 335 (1113)
T Consensus 119 -------------------------------------------------------------------------------- 118 (709)
T TIGR02063 119 -------------------------------------------------------------------------------- 118 (709)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred hhheeeccCCCCCccEEEEEEEecCCCCcceEEEEEeccccccCCCCcccccccCCCCCCCCCceEEEEeCCCCCCc-eE
Q 001256 336 RLSAMISSYPTKRPTGRVVSIIERSPRRDGIVGFLNVNQWFNYKGGSRKDAKKNRSSLSVPDREYIQLTPTHPKYPK-MV 414 (1113)
Q Consensus 336 ~~~~~~~~~~~~~p~G~VV~IleR~~~~~~~vG~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~D~riP~-i~ 414 (1113)
.+++++|+|+.||+|.. +.+||++.. .+ ++.||+|.|+|+|. +.
T Consensus 119 ---------~~~~~eg~Vv~Il~r~~--~~~VG~~~~----------------~~--------~~~~v~p~d~~~~~~I~ 163 (709)
T TIGR02063 119 ---------GGDRFEARVIKILERAN--DQIVGTFYI----------------EN--------GIGFVIPDDKRIYLDIF 163 (709)
T ss_pred ---------CCCCceEEEEEEEeeCC--CEEEEEEEE----------------cC--------cEEEEEECCCCCCCCEE
Confidence 01246899999999985 679999982 11 46789999999987 55
Q ss_pred EecCCCChhhhhhcccCCccccceEEEEEEeecCCCCCCCcEEEEEEcCCCCChHHHHHHHHHhcCcCCCCCChhhhccC
Q 001256 415 VLVKDLPDSIKKRLEEGDATIEMELVAARIDEWNEESPFPQAHVLHVFGRGGEVEPQINAILYENAICCSGFSPESLSCL 494 (1113)
Q Consensus 415 i~~~~~p~~~~~~~~~gd~~~~~~lvvv~I~~Wp~~s~~P~G~Iv~~LG~~gd~~~e~~aIL~e~~i~~~~Fs~~vl~~l 494 (1113)
|+..+. ..+.+|+ +|+|+|++||..+.+|.|+|+++||..+++.+|++++|.+|+| +.+||+++++++
T Consensus 164 i~~~~~-----~~~~~g~------~v~v~i~~~p~~~~~~~g~i~~~lg~~~d~~~~~~~il~~~~i-~~~f~~~v~~~a 231 (709)
T TIGR02063 164 IPPEQI-----LGAEEGD------KVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGI-PYEFPEEVLDEA 231 (709)
T ss_pred ECCccc-----cCCCCCC------EEEEEEccCCCCCCCceEEEEEEeCCCCcccchHHHHHHHcCc-CCCCCHHHHHHH
Confidence 543221 2344444 8999999999999999999999999999999999999999999 569999999999
Q ss_pred CCCCCCCChhhhccCccCCCceEEEEcCCCCCCCCceEEEEEcCCCeEEEEEEeccccccccCCCHhhHHHHhccceeec
Q 001256 495 PCVPWEVPQEELLSRKDLRNFCIFTIDPSTATDLDDALSIERLSDGISRVGVHIADVSYFVLPGTALDIEAQVRSTSVYM 574 (1113)
Q Consensus 495 ~~~~~~i~~~e~~~R~DLr~l~vfTIDp~~AkDlDDAlSie~l~~G~~~lgVHIADVS~fV~pgS~LD~eA~~RgtSVYL 574 (1113)
..++|.+++++.++|+|||++++|||||++|+||||||||+++++|+|+||||||||||||++||+||+||++|||||||
T Consensus 232 ~~~~~~~~~~~~~~R~Dl~~~~~~tID~~~a~D~DDAisie~~~~g~~~l~VhIADVs~~V~~~s~lD~eA~~R~tSvYl 311 (709)
T TIGR02063 232 AKIPEEVPEEEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYL 311 (709)
T ss_pred HhCCCCCChhHhhcccccccCcEEEECCCCCcccccEEEEEEcCCCCEEEEEEEechhhEeCCCChHHHHHHHhCeeEeC
Confidence 99999999888999999999999999999999999999999998999999999999999999999999999999999999
Q ss_pred CCCcccCCChhhhhcccCCCCCCceeEEEEEEEEcCCCCEEEEEEEEEEEecccccCHHHHHHHHccCCCccccCccCCC
Q 001256 575 LQRKIPMLPVLLSEEVGSLNPGVDRLAFSIFWDLNSAGDVVDRWIGRTVIRSCCKLSYEHAQDIIDGKFDVESSNTLGEG 654 (1113)
Q Consensus 575 pdrviPMLP~~Ls~~lcSL~pg~dRlAfSv~~~id~~G~I~d~~f~~SvIrS~~rLTYe~vq~iLd~~~~~~~~~~~~~~ 654 (1113)
|++++||||+.||+++|||+||++|+||||.|+||.+|+|++++|++|+|+|+++|||++|+++|+++.....
T Consensus 312 p~~~ipMLP~~Ls~~~cSL~p~~~r~a~s~~~~id~~G~i~~~~~~~svI~s~~~ltY~~v~~~l~~~~~~~~------- 384 (709)
T TIGR02063 312 PDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEGKDALDK------- 384 (709)
T ss_pred CCCcccCCChHHccCccccCCCCceEEEEEEEEECCCCCEEEeEEEEEEEEeCeEEcHHHHHHHHcCCccccc-------
Confidence 9999999999999999999999999999999999999999999999999999999999999999988421100
Q ss_pred CCcccCCCchhhHHHHHHHHHHHHHHHHHHHhcCCCccccCCCceeecCCCCCeEEeEecCCccHHHHHHHHHHHHHHHH
Q 001256 655 WPQLYGQFEWSDVVRSIKSLYEVSKILKDKRFTDGALRLENSKPVFLFDEYGTPYDSVLSGREDLNFLFEEFMLLANKTA 734 (1113)
Q Consensus 655 ~p~~~~~~~~~~~~~~L~~L~~lA~~Lr~~R~~~Gal~ld~pe~~~~lDe~g~p~~v~~~~~~~a~~LIEEfMllAN~~V 734 (1113)
...++.++|..|++||++||++|.++|+|+|+.|+++|.+|++|.+..+...++.+||.|||||||+||++|
T Consensus 385 --------~~~~~~~~L~~l~~la~~l~~~R~~~G~i~~~~~e~~~~~d~~g~~~~i~~~~~~~a~~lIeE~MllAN~~v 456 (709)
T TIGR02063 385 --------KEPPLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIEEFMIAANETV 456 (709)
T ss_pred --------hhhHHHHHHHHHHHHHHHHHHHHHhCCCcccCCccceeEECCCCCeEEEEeccchHHHHHHHHHHHHHHHHH
Confidence 124577899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhCCCcceEEecCCCCHHHHHHHHHHHHHcCCccCC-----CChhHHHHHHHHHHHhhcCCHHHHHHHHHHHhcc
Q 001256 735 AEVIARAFPDSALLRRHPAPNMRKLREFEAFCSKHGLQLDT-----SSSGQFHQSLEQAREKLKDDYVLFDILINYATRP 809 (1113)
Q Consensus 735 A~~l~~~~p~~allR~H~~P~~~kl~~l~~~~~~~G~~l~~-----ss~~~l~~sL~~i~~~~~~~p~~~~~L~~~~lR~ 809 (1113)
|+|+.+ ++.|++||+|+.|+.+++++|.+++..+|+.++. .++..++..|.++. +.|. ..++..+++|+
T Consensus 457 A~~l~~-~~~p~iyR~h~~P~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~l~~~~----~~~~-~~~l~~~llr~ 530 (709)
T TIGR02063 457 AEHLEK-AKLPFIYRVHERPSEEKLQNLREFLKTLGITLKGGTSDKPQPKDFQKLLEKVK----GRPE-EELINTVLLRS 530 (709)
T ss_pred HHHHHh-CCCCeEEecCCCCCHHHHHHHHHHHHHcCCCccCCCCCCCCHHHHHHHHHHhh----CCcH-HHHHHHHHHHH
Confidence 999986 4899999999999999999999999999998853 24566776666654 4443 25677888999
Q ss_pred cCCcEecccCCCCCCCCcCccccCCCcccccccCCCchhhHHHHHHHHHHHHhhhhhhhhhccCCCCCCccccccccccc
Q 001256 810 MQLASYFCSGDFKDDTDWGHYALAFPVYTHFTSPLRRYPDLVVHRTLNAALEAEKLYWKHRRMLPKNNHREGVRGRFLTG 889 (1113)
Q Consensus 810 M~~A~Y~~sg~~~s~~~~~HfgLa~~~YTHFTSPIRRYaDLIVHR~L~a~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 889 (1113)
|++|.|. +.+.+|||||++.|||||||||||+||+|||||+++|.+++......
T Consensus 531 m~~A~y~-------~~~~~HfgL~~~~YthfTSPIRRY~DLivHr~L~~~l~~~~~~~~~~------------------- 584 (709)
T TIGR02063 531 MQQAKYS-------PENIGHFGLALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENTTTEK------------------- 584 (709)
T ss_pred hcCcccC-------CCCCCccccccccccccCCccccchHHHHHHHHHHHHcCCCCCCccc-------------------
Confidence 9999994 57999999999999999999999999999999999997642100000
Q ss_pred cccccchhhhhhhhhHHHHHhhhcCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceEEEEEEeeecCc
Q 001256 890 IFYDKDAAESLEGREALSVAALKYGVPCADILVNVATHCNDRKLACRNVKDACVKLYMWILLKKKEVLLSEARVLALGPR 969 (1113)
Q Consensus 890 i~~~~~~~es~~~~e~l~~~~~k~~lp~~~~l~~ia~~~N~r~~~Ar~A~r~s~~l~~~~~lk~~~g~~~~a~V~~V~~~ 969 (1113)
+ .+ ...+.+..+|.|||.+++.|++|+|++.++|+|+||+.+.|.+++|+|++|.++
T Consensus 585 --------~----~~-----------~~~~~l~~~~~~~~~~er~a~~aer~~~~~~~~~yl~~~iG~~~~g~V~~v~~f 641 (709)
T TIGR02063 585 --------E----RE-----------YLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGEEFEGVISGVTSF 641 (709)
T ss_pred --------c----ch-----------hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCcEEEEEEEEEEeC
Confidence 0 00 013457899999999999999999999999999999999999999999999999
Q ss_pred EEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 970 FMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 970 ~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
|++|.++.+|+||+||++++.+++|+|++..+.|++ ++.++.|++||.|+++.
T Consensus 642 GifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g--~~~~~~~~lGd~V~Vkv 694 (709)
T TIGR02063 642 GLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVG--ERTGKVFRLGDRVKVRV 694 (709)
T ss_pred CEEEEecCCceEEEEEeeecCCCcEEEcccceEEEe--ccCCcEECCCCEEEEEE
Confidence 999999999999999999999999999999999998 57778899999888875
No 5
>PRK05054 exoribonuclease II; Provisional
Probab=100.00 E-value=3.1e-113 Score=1040.42 Aligned_cols=553 Identities=22% Similarity=0.269 Sum_probs=473.5
Q ss_pred ccEEEEEEEecCCCCcceEEEEEeccccccCCCCcccccccCCCCCCCCCceEEEEeCCCCCCceEEecCCCChhhhhhc
Q 001256 349 PTGRVVSIIERSPRRDGIVGFLNVNQWFNYKGGSRKDAKKNRSSLSVPDREYIQLTPTHPKYPKMVVLVKDLPDSIKKRL 428 (1113)
Q Consensus 349 p~G~VV~IleR~~~~~~~vG~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~D~riP~i~i~~~~~p~~~~~~~ 428 (1113)
++|+|++||+|+. +.+||++.. .+ +..+++|.|++++..+.... +......+
T Consensus 71 ~~g~v~~il~r~~--~~~vG~~~~----------------~~--------~~~~~~p~d~~~~~~i~i~~--~~~~~~~~ 122 (644)
T PRK05054 71 EIAEPEELIEPFL--TRFVGRVQK----------------KD--------DRLSIVPDHPLLKDAIPCRA--AKGLNHEF 122 (644)
T ss_pred cEEEEEEEEecCC--CEEEEEEEE----------------eC--------ceEEEEECCCCCCccEEecc--ccccccCC
Confidence 4899999999984 579999982 22 35789999999998555421 11111134
Q ss_pred ccCCccccceEEEEEEeecCCC-CCCCcEEEEEEcCCCCChHHHHHHHHHhcCcCCCCCChhhhccCCCCCCCCChhhhc
Q 001256 429 EEGDATIEMELVAARIDEWNEE-SPFPQAHVLHVFGRGGEVEPQINAILYENAICCSGFSPESLSCLPCVPWEVPQEELL 507 (1113)
Q Consensus 429 ~~gd~~~~~~lvvv~I~~Wp~~-s~~P~G~Iv~~LG~~gd~~~e~~aIL~e~~i~~~~Fs~~vl~~l~~~~~~i~~~e~~ 507 (1113)
++|| +|+|+|++||.. ...|.|+|+++||..+++.+|+++++.+|+| +.+|++++++ |++++++.
T Consensus 123 ~~gd------~V~v~i~~~p~~~~~~~~g~i~~~lG~~~d~~~d~~~il~~~~l-~~~f~~~~~~------~~~~~~~~- 188 (644)
T PRK05054 123 KEGD------WVVAELRRHPLKGDRGFYAEITQFITDADDHFAPWWVTLARHNL-EREAPAGGVA------WEMLDEGL- 188 (644)
T ss_pred CCCC------EEEEEEecCCCCCCCCceEEEEEEECCCCCCccHHHHHHHHcCC-CCCCCchhhh------ccCChhcc-
Confidence 5565 899999999985 4569999999999999999999999999999 6799998754 33444443
Q ss_pred cCccCCCceEEEEcCCCCCCCCceEEEEEcCCCeEEEEEEeccccccccCCCHhhHHHHhccceeecCCCcccCCChhhh
Q 001256 508 SRKDLRNFCIFTIDPSTATDLDDALSIERLSDGISRVGVHIADVSYFVLPGTALDIEAQVRSTSVYMLQRKIPMLPVLLS 587 (1113)
Q Consensus 508 ~R~DLr~l~vfTIDp~~AkDlDDAlSie~l~~G~~~lgVHIADVS~fV~pgS~LD~eA~~RgtSVYLpdrviPMLP~~Ls 587 (1113)
+|+|||++++|||||++|+||||||||+++++|+|+||||||||||||++||+||+||++||||||||++++||||+.||
T Consensus 189 ~R~Dlr~~~~~TID~~~akD~DDAisve~~~~g~~~l~VHIADVs~yV~~gS~LD~eA~~RgtSvYlp~~vipMLP~~Ls 268 (644)
T PRK05054 189 EREDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADPTAYIAEGSKLDKAARQRAFTNYLPGFNIPMLPRELS 268 (644)
T ss_pred CcccccCCcEEEECCCCCCcccceEEEEEeCCCCEEEEEEEcchhhEeCCCCHHHHHHHHhCceEeCCCCcccCCChHHh
Confidence 79999999999999999999999999999989999999999999999999999999999999999999999999999999
Q ss_pred hcccCCCCCCceeEEEEEEEEcCCCCEEE-EEEEEEEEecccccCHHHHHHHHccCCCccccCccCCCCCcccCCCchhh
Q 001256 588 EEVGSLNPGVDRLAFSIFWDLNSAGDVVD-RWIGRTVIRSCCKLSYEHAQDIIDGKFDVESSNTLGEGWPQLYGQFEWSD 666 (1113)
Q Consensus 588 ~~lcSL~pg~dRlAfSv~~~id~~G~I~d-~~f~~SvIrS~~rLTYe~vq~iLd~~~~~~~~~~~~~~~p~~~~~~~~~~ 666 (1113)
+++|||+||++|+||||.|+||++|+|++ ++|++|+|+|+++|||++|+++|+++.+. .| ..++
T Consensus 269 ~~~cSL~p~~~R~als~~~~id~~G~i~~~~~~~~svI~s~~rltY~~v~~~l~~~~~~---------~~------~~~~ 333 (644)
T PRK05054 269 DDLCSLRPNERRPALACRVTIDADGTIEDDIRFFAAWIESKAKLAYDNVSDWLENGGDW---------QP------ESEA 333 (644)
T ss_pred cCccccCCCCCceEEEEEEEEeCCCCcccccEEEEEEEEcCCeecHHHHHHHHhCCCcc---------cc------chhH
Confidence 99999999999999999999999999998 89999999999999999999999974210 01 2356
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCccccCCCceeecCCCCCeEEeEecCCccHHHHHHHHHHHHHHHHHHHHHHhCCCcc
Q 001256 667 VVRSIKSLYEVSKILKDKRFTDGALRLENSKPVFLFDEYGTPYDSVLSGREDLNFLFEEFMLLANKTAAEVIARAFPDSA 746 (1113)
Q Consensus 667 ~~~~L~~L~~lA~~Lr~~R~~~Gal~ld~pe~~~~lDe~g~p~~v~~~~~~~a~~LIEEfMllAN~~VA~~l~~~~p~~a 746 (1113)
+.+.|..|.+|+++|+++|.++|++.|+.||++|.+|++|.+.++...++.+||+|||||||+||++||+|+.++ +.|+
T Consensus 334 i~~~l~~L~~l~~~l~~~R~~~G~i~~d~~e~~i~ld~~g~~~~i~~~~~~~a~~lIeE~MllAN~~vA~~l~~~-~~p~ 412 (644)
T PRK05054 334 IAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFELGEKGEVLDIVAEPRRIANRIVEESMIAANICAARVLRDK-LGFG 412 (644)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCccccCCceEEEECCCCCEEEEEEecCcHHHHHHHHHHHHHHHHHHHHHHHc-CCCE
Confidence 888999999999999999999999999999999999999999999999999999999999999999999999986 6799
Q ss_pred eEEecCCCCHHHHHHHHHHHHHcCCccCCCChhHHHHHHHHHHHhhcCCHHHHHHHHHHHhcccCCcEecccCCCCCCCC
Q 001256 747 LLRRHPAPNMRKLREFEAFCSKHGLQLDTSSSGQFHQSLEQAREKLKDDYVLFDILINYATRPMQLASYFCSGDFKDDTD 826 (1113)
Q Consensus 747 llR~H~~P~~~kl~~l~~~~~~~G~~l~~ss~~~l~~sL~~i~~~~~~~p~~~~~L~~~~lR~M~~A~Y~~sg~~~s~~~ 826 (1113)
+||+|+.|+++++++|.+++..+|+.++..+..++. .+..+...+...+. ..+...++|+|++|.| ++.+
T Consensus 413 iyRvH~~P~~~~l~~l~~~~~~~g~~~~~~~~~~l~-~~~~~~~~l~~~~~--~~l~~~llr~~~~a~y-------s~~~ 482 (644)
T PRK05054 413 IYNVHSGFDPANAEQAVALLKEHGLHFDAEELLTLE-GFCKLRRELDAQPT--GYLDSRIRRFQSFAEI-------STEP 482 (644)
T ss_pred EEECCCCCCHHHHHHHHHHHHHCCCCcCCCcccChH-HHHHHHHHHhcchH--HHHHHHHHHHHhceec-------CCCC
Confidence 999999999999999999999999998654433322 22333333333332 2344456899999999 4689
Q ss_pred cCccccCCCcccccccCCCchhhHHHHHHHHHHHHhhhhhhhhhccCCCCCCccccccccccccccccchhhhhhhhhHH
Q 001256 827 WGHYALAFPVYTHFTSPLRRYPDLVVHRTLNAALEAEKLYWKHRRMLPKNNHREGVRGRFLTGIFYDKDAAESLEGREAL 906 (1113)
Q Consensus 827 ~~HfgLa~~~YTHFTSPIRRYaDLIVHR~L~a~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~es~~~~e~l 906 (1113)
.+|||||++.|||||||||||+||+|||||+++|.+++.
T Consensus 483 ~gHfgL~~~~YthfTSPIRRY~DLivHR~L~a~l~~~~~----------------------------------------- 521 (644)
T PRK05054 483 GPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETA----------------------------------------- 521 (644)
T ss_pred cCccccccccccccCChhhhhHHHHHHHHHHHHHcCCCC-----------------------------------------
Confidence 999999999999999999999999999999999975321
Q ss_pred HHHhhhcCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc--eEEEEEEeeecCcEEEEEEecCCeEEEE
Q 001256 907 SVAALKYGVPCADILVNVATHCNDRKLACRNVKDACVKLYMWILLKKKEV--LLSEARVLALGPRFMTIYIEKLAIERRI 984 (1113)
Q Consensus 907 ~~~~~k~~lp~~~~l~~ia~~~N~r~~~Ar~A~r~s~~l~~~~~lk~~~g--~~~~a~V~~V~~~~f~V~Ip~~giEg~V 984 (1113)
...+..+|++||++++.|++|+|++.+++++.||+++.| +.++|+|++|+++||+|.|+++|+||.|
T Consensus 522 -----------~~~~~~~~~~~s~~er~a~~aer~~~~~~~~~y~~~~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV 590 (644)
T PRK05054 522 -----------ERPQDEITVQLAERRRLNRMAERDVGDWLYARYLKDKAGTDTRFAAEIIDISRGGMRVRLLENGAVAFI 590 (644)
T ss_pred -----------CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCeEEEEEEEeeecCcEEEEEeCCceEEEE
Confidence 011456899999999999999999999999999999985 5999999999999999999999999999
Q ss_pred EeeecCCcEEEE--ecccceEEEeeecccceeecCCCceEEE
Q 001256 985 YYDEVEGLIVEW--LETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 985 ~~~~l~~~~~e~--~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
|++.|.++|++| +..+..+.+ ++++.|++||+|+++.
T Consensus 591 ~~~~l~~~~~~y~~~~~~~~~~~---~~~~~~~lGd~V~V~v 629 (644)
T PRK05054 591 PASFLHAVRDELVCNQENGTVQI---KGETVYKLGDVIDVTL 629 (644)
T ss_pred EccccCCCccceEEccccceEEE---eCCEEEcCCCEEEEEE
Confidence 999999987665 444444443 4558899999887765
No 6
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=100.00 E-value=1.4e-113 Score=1056.08 Aligned_cols=619 Identities=34% Similarity=0.482 Sum_probs=550.9
Q ss_pred eEEEEEEeccCCceeEEEEeCC--cceeEEEeCcCCccccCCCCEEEEEEccchhhhhccCCCCCCcccccCCCcccccC
Q 001256 178 AFKALYRVNAHNRLEAYCKIEG--VQTDVLITGIAAQNRAVEGDFVLIKVDRLSLWAKMKGFSNNSSIVEDSNLPTEANG 255 (1113)
Q Consensus 178 l~~G~lrVn~~N~~eAyV~~~g--~~~Dv~I~G~~~rNRAl~GDvVaVeLlp~~~W~~~~~~~~~~~~~e~~~~~~e~~e 255 (1113)
+++|++..+++++ +|+..++ ...|+||.... +|+|++||.|.|++.+.+.|
T Consensus 69 ~~~~~~~~~~~gf--~f~~~~~~~~~~d~~v~~~~-~~~a~~gD~V~v~~~~~~~~------------------------ 121 (706)
T COG0557 69 LVEGIVEASAKGF--GFLSPDDSKDADDIFVPKDP-LNRALHGDRVLVELLPSDKR------------------------ 121 (706)
T ss_pred cccceEEeccCCc--eeeccCccCCCCcEEecccc-ccccccCCEEEEEECccccc------------------------
Confidence 7899999999999 8888887 67899999985 99999999999998221000
Q ss_pred CCccccccCccccccccccccccccccCCCCCCCCchhhhhhhhhhhccccccCCCCCCCCCccccccccccccchhhHh
Q 001256 256 MHSDICKGKSKVDVSYEYSNCTLLSEKGIHHDDDSSSEAYNQEMIEREGYNYINGHHPSTSDSTEKVSSSQQNDGMNAIE 335 (1113)
Q Consensus 256 ~~~~~~~~k~~~d~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 335 (1113)
T Consensus 122 -------------------------------------------------------------------------------- 121 (706)
T COG0557 122 -------------------------------------------------------------------------------- 121 (706)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred hhheeeccCCCCCccEEEEEEEecCCCCcceEEEEEeccccccCCCCcccccccCCCCCCCCCceEEEEeCCCCCC-ceE
Q 001256 336 RLSAMISSYPTKRPTGRVVSIIERSPRRDGIVGFLNVNQWFNYKGGSRKDAKKNRSSLSVPDREYIQLTPTHPKYP-KMV 414 (1113)
Q Consensus 336 ~~~~~~~~~~~~~p~G~VV~IleR~~~~~~~vG~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~D~riP-~i~ 414 (1113)
++.++|+|++|++|.+ ..+||++... .++.+++|.|+|++ .+.
T Consensus 122 ----------~~~~~~~v~~il~r~~--~~~vG~~~~~------------------------~~~~~~~p~d~r~~~~i~ 165 (706)
T COG0557 122 ----------GRFKEAAVVRILERAN--SALVGELRPS------------------------QGIGRVLPDDKRLPFLIA 165 (706)
T ss_pred ----------CCCceEEEEeeecccc--ceeEEEEEec------------------------CCeEEEEecCCCCcccee
Confidence 0036899999999986 4699999931 13789999999999 588
Q ss_pred EecCCCChhhhhhcccCCccccceEEEEEEeecCCCCCCCcEEEEEEcCCCCChHHHHHHHHHhcCcCCCCCChhhhccC
Q 001256 415 VLVKDLPDSIKKRLEEGDATIEMELVAARIDEWNEESPFPQAHVLHVFGRGGEVEPQINAILYENAICCSGFSPESLSCL 494 (1113)
Q Consensus 415 i~~~~~p~~~~~~~~~gd~~~~~~lvvv~I~~Wp~~s~~P~G~Iv~~LG~~gd~~~e~~aIL~e~~i~~~~Fs~~vl~~l 494 (1113)
|++++.+ ..+. +.+|+|+|+.||..+.+|.|+++++||..+++..++++++++|++ +.+|++++++++
T Consensus 166 i~~~~~~-----~~~~------~~~v~~~i~~~~~~~~~~~g~v~~~lG~~~~~~~~~~~il~~~~i-~~~f~~~v~~~a 233 (706)
T COG0557 166 IPPEQAP-----GAEE------GHLVVVEITRWPDTSRPPFGEVVEVLGDLGDPGADIEAILRDHGI-PSEFPEKVLDEA 233 (706)
T ss_pred ecccccc-----cccc------CCEEEEEecccCCcCCCCceeEEEeecCCCCcchhHHHHHHHcCC-CCCCCHHHHHHH
Confidence 8766554 2233 458999999999999999999999999999999999999999999 567999999999
Q ss_pred CCCCCCCChhhhccCccCCCceEEEEcCCCCCCCCceEEEEEcCCCeEEEEEEeccccccccCCCHhhHHHHhccceeec
Q 001256 495 PCVPWEVPQEELLSRKDLRNFCIFTIDPSTATDLDDALSIERLSDGISRVGVHIADVSYFVLPGTALDIEAQVRSTSVYM 574 (1113)
Q Consensus 495 ~~~~~~i~~~e~~~R~DLr~l~vfTIDp~~AkDlDDAlSie~l~~G~~~lgVHIADVS~fV~pgS~LD~eA~~RgtSVYL 574 (1113)
...++.+++++.++|.|||++++|||||++|+|||||||++++.||+|+||||||||||||+|||+||+||++|||||||
T Consensus 234 ~~~~~~~~~~~~~~R~Dlr~l~~~TID~~~akD~DDAv~~~~l~~g~~~LgVhIADVs~yV~p~s~LD~EA~~RgtSVYl 313 (706)
T COG0557 234 AALPDEVPEEDLKGRVDLRDLPIFTIDPEDAKDLDDAVSVEKLRNGGYRLGVHIADVSHYVQPGSALDKEARKRGTSVYL 313 (706)
T ss_pred HhccCcCChhhhcCccccccCCEEEECCCCCccccceEEEEEeCCCcEEEEEEEecceeecCCCChhhHHHHHcCCeEEc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcccCCChhhhhcccCCCCCCceeEEEEEEEEcCCCCEEEEEEEEEEEecccccCHHHHHHHHccCCCccccCccCCC
Q 001256 575 LQRKIPMLPVLLSEEVGSLNPGVDRLAFSIFWDLNSAGDVVDRWIGRTVIRSCCKLSYEHAQDIIDGKFDVESSNTLGEG 654 (1113)
Q Consensus 575 pdrviPMLP~~Ls~~lcSL~pg~dRlAfSv~~~id~~G~I~d~~f~~SvIrS~~rLTYe~vq~iLd~~~~~~~~~~~~~~ 654 (1113)
|+++|||||+.||+++|||+||++|+|+||.|+||.+|+|.+++|++|+|+|+++|||++||++|+++.+.
T Consensus 314 p~~vipMLPe~Ls~~lcSL~p~~dRla~s~~m~ld~~g~v~~~~~~~svI~s~~rltY~~v~~~l~~~~~~--------- 384 (706)
T COG0557 314 PDRVIPMLPEALSNGLCSLNPGVDRLALSCEMTLDSEGRVKKYEIYPSVIKSAARLTYEEVQAILDGKEDD--------- 384 (706)
T ss_pred CCcccCCCchhhcCCccccCCCCceEEEEEEEEECCCCCEEEEEEEEEEEeccccCCHHHHHHHHhcCcch---------
Confidence 99999999999999999999999999999999999999999999999999999999999999999984210
Q ss_pred CCcccCCCchhhHHHHHHHHHHHHHHHHHHHhcCCCccccCCCceeecCCCCCeEEeEecCCccHHHHHHHHHHHHHHHH
Q 001256 655 WPQLYGQFEWSDVVRSIKSLYEVSKILKDKRFTDGALRLENSKPVFLFDEYGTPYDSVLSGREDLNFLFEEFMLLANKTA 734 (1113)
Q Consensus 655 ~p~~~~~~~~~~~~~~L~~L~~lA~~Lr~~R~~~Gal~ld~pe~~~~lDe~g~p~~v~~~~~~~a~~LIEEfMllAN~~V 734 (1113)
....+.+.|..|..|+++++++|.++|+|+|+.+|.++.+|++|.|..+...++.++|.|||||||+||++|
T Consensus 385 --------~~~~l~~~l~~~~~l~~~l~~~R~~rg~i~~~~~E~ki~~d~~~~~~~i~~~~r~~a~~lIee~Ml~AN~~v 456 (706)
T COG0557 385 --------KYAPLLDSLLELLELAKILKKKRLSRGAIDFDTPEAKIVLDEEGRPVEIEIRERLDAEKLIEEFMLLANETV 456 (706)
T ss_pred --------hcccchHHHHHHHHHHHHHHHHHHhCCCcccCCcceeEEECCCCCeeeEEEecccHHHHHHHHHHHHHHHHH
Confidence 134566889999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhCCCcceEEecCCCCHHHHHHHHHHHHHcCCccCCCChhHHHHHHHHHHHhhcCCHHHHHHHHHHHhcccCCcE
Q 001256 735 AEVIARAFPDSALLRRHPAPNMRKLREFEAFCSKHGLQLDTSSSGQFHQSLEQAREKLKDDYVLFDILINYATRPMQLAS 814 (1113)
Q Consensus 735 A~~l~~~~p~~allR~H~~P~~~kl~~l~~~~~~~G~~l~~ss~~~l~~sL~~i~~~~~~~p~~~~~L~~~~lR~M~~A~ 814 (1113)
|+++.+++ .|.+||+|+.|+.++++.|.+++..+|+.+........+..+..+.+..++.|. ..++..+++|+|++|+
T Consensus 457 A~~l~~~~-~~~~~R~h~~P~~ek~~~l~~~l~~lg~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~v~~~~~lRsm~~a~ 534 (706)
T COG0557 457 AEHLEKHK-IPLLYRTHERPSTEKLQSLREFLQNLGLVLPLGGSKPQPQDYQILLETVKGRPL-EAVLQTLLLRSMKQAE 534 (706)
T ss_pred HHHHHHcC-CCcceeCCCCCCHHHHHHHHHHHHHcCceecCCCCcCCHHHHHHHHhhccCChH-HHHHHHHHHHhhhcCe
Confidence 99999884 577999999999999999999999999999855433233344444444444453 3567788899999999
Q ss_pred ecccCCCCCCCCcCccccCCCcccccccCCCchhhHHHHHHHHHHHHhhhhhhhhhccCCCCCCcccccccccccccccc
Q 001256 815 YFCSGDFKDDTDWGHYALAFPVYTHFTSPLRRYPDLVVHRTLNAALEAEKLYWKHRRMLPKNNHREGVRGRFLTGIFYDK 894 (1113)
Q Consensus 815 Y~~sg~~~s~~~~~HfgLa~~~YTHFTSPIRRYaDLIVHR~L~a~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~ 894 (1113)
|. +.+.+|||||++.|||||||||||+||||||||+++|.++......
T Consensus 535 Ys-------~~~~~HfgL~~~~YtHFTSPIRRY~DLivHR~L~~~l~~~~~~~~~------------------------- 582 (706)
T COG0557 535 YS-------PDNVGHFGLALDYYTHFTSPIRRYPDLIVHRQLKALLSGEPIPEKK------------------------- 582 (706)
T ss_pred ec-------CCCCCceeccccchhccCCchhhchHHHHHHHHHHHhcCCCCCccc-------------------------
Confidence 94 5799999999999999999999999999999999999865321000
Q ss_pred chhhhhhhhhHHHHHhhhcCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceEEEEEEeeecCcEEEEE
Q 001256 895 DAAESLEGREALSVAALKYGVPCADILVNVATHCNDRKLACRNVKDACVKLYMWILLKKKEVLLSEARVLALGPRFMTIY 974 (1113)
Q Consensus 895 ~~~es~~~~e~l~~~~~k~~lp~~~~l~~ia~~~N~r~~~Ar~A~r~s~~l~~~~~lk~~~g~~~~a~V~~V~~~~f~V~ 974 (1113)
.....+..+|.+||.+++.|..|+|++.++|++.||+++.|.+++|+|++|..+||+|.
T Consensus 583 ---------------------~~~~~l~~i~~~~s~~er~a~~aer~~~~~~~~~~m~~~vg~~f~g~V~~v~~~g~~V~ 641 (706)
T COG0557 583 ---------------------TSEEELDELAAHISSAERRAQEAERDVIDLLKAEYMKKRVGEEFDGVVTGVTSFGFFVE 641 (706)
T ss_pred ---------------------hhHHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEEeccEEEE
Confidence 01356899999999999999999999999999999999999999999999999999999
Q ss_pred EecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEEe
Q 001256 975 IEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRAL 1025 (1113)
Q Consensus 975 Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~~ 1025 (1113)
++.+++||+||++.|++++|.|++....+++ +++.+.|++||.|+++..
T Consensus 642 l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~--~~~~~~~~lgd~v~v~v~ 690 (706)
T COG0557 642 LPELGLEGLVHISSLPDDYYHFDERGQALVG--EKSGKVYRLGDEVKVKVT 690 (706)
T ss_pred ecccccccceEcccCCCceeeeccccceeec--cccccccccCCEEEEEEE
Confidence 9999999999999999999999999988888 699999999999888863
No 7
>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=9.4e-112 Score=1025.78 Aligned_cols=552 Identities=20% Similarity=0.250 Sum_probs=473.1
Q ss_pred ccEEEEEEEecCCCCcceEEEEEeccccccCCCCcccccccCCCCCCCCCceEEEEeCCCCCCceEEecCCCChhhhhhc
Q 001256 349 PTGRVVSIIERSPRRDGIVGFLNVNQWFNYKGGSRKDAKKNRSSLSVPDREYIQLTPTHPKYPKMVVLVKDLPDSIKKRL 428 (1113)
Q Consensus 349 p~G~VV~IleR~~~~~~~vG~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~D~riP~i~i~~~~~p~~~~~~~ 428 (1113)
++|+|++|++|+. ..+||++.. .+ +..+++|.|++++.++.... ++.....+
T Consensus 68 ~~~~v~~iver~~--~~~vG~~~~----------------~~--------~~~~v~p~d~~~~~~i~~~~--~~~~~~~~ 119 (639)
T TIGR02062 68 ESAEPEELIEPFL--TRFVGKVQG----------------KD--------DKLAIVPDHPLLKDAIPCRA--AKGLNHEF 119 (639)
T ss_pred cEEEEEEEEccCC--CEEEEEEEE----------------eC--------CeEEEEECCCCCCccEEecC--ccccccCC
Confidence 4899999999985 579999982 22 35789999999988743311 11111234
Q ss_pred ccCCccccceEEEEEEeecCCCC-CCCcEEEEEEcCCCCChHHHHHHHHHhcCcCCCCCChhhhccCCCCCCCCChhhhc
Q 001256 429 EEGDATIEMELVAARIDEWNEES-PFPQAHVLHVFGRGGEVEPQINAILYENAICCSGFSPESLSCLPCVPWEVPQEELL 507 (1113)
Q Consensus 429 ~~gd~~~~~~lvvv~I~~Wp~~s-~~P~G~Iv~~LG~~gd~~~e~~aIL~e~~i~~~~Fs~~vl~~l~~~~~~i~~~e~~ 507 (1113)
++|| +|+|+|++||... ..|.|+|+++||..+++.+|++++|.+|+| +.+|++++++++.. + ..
T Consensus 120 ~~gd------~V~v~I~~~p~~~~~~~~~~I~~vLG~~~d~~~d~~~il~~~~l-~~~f~~~v~~ea~~-------~-~~ 184 (639)
T TIGR02062 120 QEGD------WAVAELRRHPLKGDRSFYAELTQYITFADDHLAPWWVTLARHNL-EREEPDGVADEMLL-------D-GL 184 (639)
T ss_pred CCCC------EEEEEEeccCCCCCCCceEEEEEEeCCCCCCccHHHHHHHHcCc-CCCCCHHHHHhhhh-------c-cc
Confidence 4565 7889999999865 569999999999999999999999999999 67999999988732 1 25
Q ss_pred cCccCCCceEEEEcCCCCCCCCceEEEEEcCCCeEEEEEEeccccccccCCCHhhHHHHhccceeecCCCcccCCChhhh
Q 001256 508 SRKDLRNFCIFTIDPSTATDLDDALSIERLSDGISRVGVHIADVSYFVLPGTALDIEAQVRSTSVYMLQRKIPMLPVLLS 587 (1113)
Q Consensus 508 ~R~DLr~l~vfTIDp~~AkDlDDAlSie~l~~G~~~lgVHIADVS~fV~pgS~LD~eA~~RgtSVYLpdrviPMLP~~Ls 587 (1113)
+|+|||++++|||||++|+||||||||+++++|+|+||||||||||||++||+||+||++||||||||++++||||+.||
T Consensus 185 ~R~DLr~~~~~TID~~~akD~DDAisie~~~~g~~~L~VHIADVs~yV~~gS~LD~eA~~RgtSvYLp~~vipMLP~~Ls 264 (639)
T TIGR02062 185 VREDLTALDFVTIDSESTKDMDDALFAEALPNGKLQLIVAIADPTAYIAEGSKLDKAAKIRGFTNYLPGFNIPMLPRELS 264 (639)
T ss_pred cCcccccCCEEEECCCCCCcccceEEEEEeCCCcEEEEEEEcCccccCCCCCHHHHHHHHhCCcEeCCCceecCCCHHHh
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcccCCCCCCceeEEEEEEEEcCCCCEEE-EEEEEEEEecccccCHHHHHHHHccCCCccccCccCCCCCcccCCCchhh
Q 001256 588 EEVGSLNPGVDRLAFSIFWDLNSAGDVVD-RWIGRTVIRSCCKLSYEHAQDIIDGKFDVESSNTLGEGWPQLYGQFEWSD 666 (1113)
Q Consensus 588 ~~lcSL~pg~dRlAfSv~~~id~~G~I~d-~~f~~SvIrS~~rLTYe~vq~iLd~~~~~~~~~~~~~~~p~~~~~~~~~~ 666 (1113)
+++|||+||++|+||||.|+||++|+|++ ++|++|+|||+++|||++|+++|+++.... | ..++
T Consensus 265 ~~~cSL~p~e~R~als~~~~ld~~G~i~~~~~~~~svIrs~~rltY~~v~~~l~~~~~~~---------~------~~~~ 329 (639)
T TIGR02062 265 DDLCSLRANEVRPVLACRITISKDGNIEDKIEFFAATIKSKAKLVYDQVSDWLENTSDWQ---------P------ESEE 329 (639)
T ss_pred cCccccCCCCCeeEEEEEEEEcCCCcEeecCEEEEEEEEeCcEEeHHHHHHHHhCCcccc---------c------chHH
Confidence 99999999999999999999999999999 799999999999999999999999742110 1 1356
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCccccCCCceeecCCCCCeEEeEecCCccHHHHHHHHHHHHHHHHHHHHHHhCCCcc
Q 001256 667 VVRSIKSLYEVSKILKDKRFTDGALRLENSKPVFLFDEYGTPYDSVLSGREDLNFLFEEFMLLANKTAAEVIARAFPDSA 746 (1113)
Q Consensus 667 ~~~~L~~L~~lA~~Lr~~R~~~Gal~ld~pe~~~~lDe~g~p~~v~~~~~~~a~~LIEEfMllAN~~VA~~l~~~~p~~a 746 (1113)
+.++|..|.++|++|+++|.++|++.|+.||++|.+|++|.+..+...++.+||+|||||||+||++||+|+.++ ..|+
T Consensus 330 i~~~L~~L~~la~~l~~~R~~~G~i~ld~pE~~~~ld~~g~~~~i~~~~~~~a~~lIeE~MllAN~~vA~~l~~~-~~p~ 408 (639)
T TIGR02062 330 IAQQVRLLHQFCQARIEWRHTHALVFKDRPDYRFILSEKGEVLDIVAEPRRIANRIVEEAMIIANICAARFLRDK-LGFG 408 (639)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCcccccCCceEEEECCCCCEEEEEEecCCHHHHHHHHHHHHHHHHHHHHHHHh-CCCe
Confidence 788999999999999999999999999999999999999999999999999999999999999999999999987 4689
Q ss_pred eEEecCCCCHHHHHHHHHHHHHcCCccCCCChhHHHHHHHHHHHhhcCCHHHHHHHHHHHhcccCCcEecccCCCCCCCC
Q 001256 747 LLRRHPAPNMRKLREFEAFCSKHGLQLDTSSSGQFHQSLEQAREKLKDDYVLFDILINYATRPMQLASYFCSGDFKDDTD 826 (1113)
Q Consensus 747 llR~H~~P~~~kl~~l~~~~~~~G~~l~~ss~~~l~~sL~~i~~~~~~~p~~~~~L~~~~lR~M~~A~Y~~sg~~~s~~~ 826 (1113)
+||+|+.|+++++++|.+++..+|+.++..+..++ ..+..+...+...+. ..+..+++|+|.+|.| ++.+
T Consensus 409 iyR~H~~P~~~~l~~l~~~~~~~g~~~~~~~~~~~-~~~~~~~~~~~~~~~--~~l~~~~~r~~~~a~y-------s~~~ 478 (639)
T TIGR02062 409 IYNTHAGFDPANAENVVALLKTNGLHVDAEELATL-DGFCKLRRELDAQET--GYLDSRIRRYQSFAEI-------STEP 478 (639)
T ss_pred EEecCCCCCHHHHHHHHHHHHHcCCCCCcccccCH-HHHHHHHHHhhcchH--HHHHHHHHHHhhhccc-------CCCC
Confidence 99999999999999999999999998864322112 122333333333332 3466677899999999 4689
Q ss_pred cCccccCCCcccccccCCCchhhHHHHHHHHHHHHhhhhhhhhhccCCCCCCccccccccccccccccchhhhhhhhhHH
Q 001256 827 WGHYALAFPVYTHFTSPLRRYPDLVVHRTLNAALEAEKLYWKHRRMLPKNNHREGVRGRFLTGIFYDKDAAESLEGREAL 906 (1113)
Q Consensus 827 ~~HfgLa~~~YTHFTSPIRRYaDLIVHR~L~a~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~es~~~~e~l 906 (1113)
.+|||||++.|||||||||||+||+|||||+++|.+++.
T Consensus 479 ~~HfgL~~~~YthfTSPIRRY~DLivHR~L~~~l~~~~~----------------------------------------- 517 (639)
T TIGR02062 479 GPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETA----------------------------------------- 517 (639)
T ss_pred cCcchhccccccccCChhhhhHHHHHHHHHHHHHcCCCC-----------------------------------------
Confidence 999999999999999999999999999999999975320
Q ss_pred HHHhhhcCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc--eEEEEEEeeecCcEEEEEEecCCeEEEE
Q 001256 907 SVAALKYGVPCADILVNVATHCNDRKLACRNVKDACVKLYMWILLKKKEV--LLSEARVLALGPRFMTIYIEKLAIERRI 984 (1113)
Q Consensus 907 ~~~~~k~~lp~~~~l~~ia~~~N~r~~~Ar~A~r~s~~l~~~~~lk~~~g--~~~~a~V~~V~~~~f~V~Ip~~giEg~V 984 (1113)
...+..++.+||++++.|++|+|++.++|++.||+++.| +.++|+|++|.+.||+|.+++.|+||.|
T Consensus 518 -----------~~~~~~~~~~~s~~er~a~~aeR~~~~~~~~~yl~~~~g~~~~f~g~I~~v~~~g~~v~l~~~~~~g~v 586 (639)
T TIGR02062 518 -----------TRPQEDITVQLAERRRLNRIAERDVADWLYARFLADKAAKNTRFAAEIVDISRGGMRVRLLENGAIAFI 586 (639)
T ss_pred -----------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcEEEEEEEeeeCCcEEEEEecCceEEEE
Confidence 001456799999999999999999999999999999985 4899999999999999999999999999
Q ss_pred EeeecCC--cEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 985 YYDEVEG--LIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 985 ~~~~l~~--~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
++..|.+ ++|+|++...++.+. .++.|++||+|+++.
T Consensus 587 ~~~~l~~~~~~~~~~~~~~~~~l~---g~~~~~lgd~v~V~v 625 (639)
T TIGR02062 587 PAAFLHANREELVCNQENGTVQIK---GETVYKIGDVIDVVL 625 (639)
T ss_pred EhhhcCCCCcceEEcccccEEEEe---ccEEEecCCEEEEEE
Confidence 9999998 778888877644431 124788888887765
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=5.3e-74 Score=648.39 Aligned_cols=320 Identities=42% Similarity=0.673 Sum_probs=255.9
Q ss_pred CccCCCceEEEEcCCCCCCCCceEEEEEcCCCeEEEEEEeccccccccCCCHhhHHHHhccceeecCCCcccCCChhhhh
Q 001256 509 RKDLRNFCIFTIDPSTATDLDDALSIERLSDGISRVGVHIADVSYFVLPGTALDIEAQVRSTSVYMLQRKIPMLPVLLSE 588 (1113)
Q Consensus 509 R~DLr~l~vfTIDp~~AkDlDDAlSie~l~~G~~~lgVHIADVS~fV~pgS~LD~eA~~RgtSVYLpdrviPMLP~~Ls~ 588 (1113)
|+|||++++|||||++|+|+||||||+++++|+|+|||||||||+||++||+||++|++||+|+|||++++||||+.|++
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 001256 589 EVGSLNPGVDRLAFSIFWDLNSAGDVVDRWIGRTVIRSCCKLSYEHAQDIIDGKFDVESSNTLGEGWPQLYGQFEWSDVV 668 (1113)
Q Consensus 589 ~lcSL~pg~dRlAfSv~~~id~~G~I~d~~f~~SvIrS~~rLTYe~vq~iLd~~~~~~~~~~~~~~~p~~~~~~~~~~~~ 668 (1113)
++|||.||++|+||||.|+||.+|+|++++|++|+|+|+++|||++|+++|++...... ...+.
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-cCCCceeecCCCCCeEEeEecC---CccHHHHHHHHHHHHHHHHHHHHHHhCCC
Q 001256 669 RSIKSLYEVSKILKDKRFTDGALRL-ENSKPVFLFDEYGTPYDSVLSG---REDLNFLFEEFMLLANKTAAEVIARAFPD 744 (1113)
Q Consensus 669 ~~L~~L~~lA~~Lr~~R~~~Gal~l-d~pe~~~~lDe~g~p~~v~~~~---~~~a~~LIEEfMllAN~~VA~~l~~~~p~ 744 (1113)
++|..|+++|+.|+++|..+|++.+ +.|+..+.+++++.+....... ...|+.||+||||+||++||+|+.+ ++.
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 8899999999999888887766 8999999999999999999999996 499
Q ss_pred cceEEecCCCCHHHHHHHHHHHHHcCCccCCCChhHHHHHHHHHHHhhcCCHHHHHHHHHHHhcccCCcEecccCCCCCC
Q 001256 745 SALLRRHPAPNMRKLREFEAFCSKHGLQLDTSSSGQFHQSLEQAREKLKDDYVLFDILINYATRPMQLASYFCSGDFKDD 824 (1113)
Q Consensus 745 ~allR~H~~P~~~kl~~l~~~~~~~G~~l~~ss~~~l~~sL~~i~~~~~~~p~~~~~L~~~~lR~M~~A~Y~~sg~~~s~ 824 (1113)
|++||+|+.|+..+++++.+.+ +++++. .+.+ .++++... .+.+ ....+..+++++|.+|+| +.
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 9999999999999988887777 444443 3332 23333322 2222 123456677899999999 45
Q ss_pred CCcCccccCCCcccccccCCCchhhHHHHHHHHHHHH
Q 001256 825 TDWGHYALAFPVYTHFTSPLRRYPDLVVHRTLNAALE 861 (1113)
Q Consensus 825 ~~~~HfgLa~~~YTHFTSPIRRYaDLIVHR~L~a~L~ 861 (1113)
.+.+|||||++.|||||||||||+||+|||||+++|.
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 7889999999999999999999999999999999986
No 9
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=100.00 E-value=4e-63 Score=549.89 Aligned_cols=527 Identities=22% Similarity=0.272 Sum_probs=401.2
Q ss_pred eEEEEeCCCCCCceEEecCCCChhhhhhcccCCccccceEEEEEEeecCCCC-CCCcEEEEEEcCCCCChHHHHHHHHHh
Q 001256 400 YIQLTPTHPKYPKMVVLVKDLPDSIKKRLEEGDATIEMELVAARIDEWNEES-PFPQAHVLHVFGRGGEVEPQINAILYE 478 (1113)
Q Consensus 400 ~~~~~P~D~riP~i~i~~~~~p~~~~~~~~~gd~~~~~~lvvv~I~~Wp~~s-~~P~G~Iv~~LG~~gd~~~e~~aIL~e 478 (1113)
...++|+-+-+... |.-. ..+.....+++|| ++|+++.+.|... ..-.+.|.+.+-..+|.-+---.-|..
T Consensus 96 rL~i~pDhP~lk~~-i~~~-~~k~l~~~fQeGD------W~VA~lk~HpLkgDr~F~a~lt~~It~~dD~l~PWWVTLAr 167 (645)
T COG4776 96 RLQIVPDHPLLKDA-IPCR-AAKGLNEEFQEGD------WAVAELKRHPLKGDRSFYAELTQKITFADDHLAPWWVTLAR 167 (645)
T ss_pred ceEEcCCChhhhhh-cccc-cccchhhhhhcCc------eehhhhhcCCCCCchhHHHHHHHHhhccCCcccceeeehhh
Confidence 45677776655443 3322 2344455677888 7889999988642 333334444444444433333334556
Q ss_pred cCcCCCCCChhhhccCCCCCCCCChhhhccCccCCCceEEEEcCCCCCCCCceEEEEEcCCCeEEEEEEeccccccccCC
Q 001256 479 NAICCSGFSPESLSCLPCVPWEVPQEELLSRKDLRNFCIFTIDPSTATDLDDALSIERLSDGISRVGVHIADVSYFVLPG 558 (1113)
Q Consensus 479 ~~i~~~~Fs~~vl~~l~~~~~~i~~~e~~~R~DLr~l~vfTIDp~~AkDlDDAlSie~l~~G~~~lgVHIADVS~fV~pg 558 (1113)
|++.. +.+. -..+|.+.++. -.|+||+.+.++|||+++++|+||||.++++++|.|.|-|.|||++.||.+|
T Consensus 168 h~l~r--~~p~-----g~~d~~m~d~~-l~RedLTaL~FvTID~~sT~DmDDALy~~~~~~~~~~L~vAIADPTAyI~~~ 239 (645)
T COG4776 168 HNLER--EAPA-----GIVDTEMLDEG-LVREDLTALDFVTIDSESTEDMDDALYAEPLPDGDWQLIVAIADPTAYIAEG 239 (645)
T ss_pred ccCCc--cCCC-----cccchhhhhhh-hhhccccccceEEecCccccccchhhhccccCCCcEEEEEEecCCccccCCc
Confidence 66532 1111 11234444333 4799999999999999999999999999999999999999999999999999
Q ss_pred CHhhHHHHhccceeecCCCcccCCChhhhhcccCCCCCCceeEEEEEEEEcCCCCEE-EEEEEEEEEecccccCHHHHHH
Q 001256 559 TALDIEAQVRSTSVYMLQRKIPMLPVLLSEEVGSLNPGVDRLAFSIFWDLNSAGDVV-DRWIGRTVIRSCCKLSYEHAQD 637 (1113)
Q Consensus 559 S~LD~eA~~RgtSVYLpdrviPMLP~~Ls~~lcSL~pg~dRlAfSv~~~id~~G~I~-d~~f~~SvIrS~~rLTYe~vq~ 637 (1113)
|.||++|++|+.|.|||+.-|||||+.||.++|||.|++-|+|+.|.++++.+|+|. +.+|..+.|+|+++|.|++|.+
T Consensus 240 s~ld~~A~~R~FTnYLPGfNIPMLPreLsd~lCSL~~ne~RPaL~C~it~~~~G~I~~~i~F~aA~i~SkakL~YdhVSD 319 (645)
T COG4776 240 SKLDKEAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPALACRITIDKDGNITDKIRFFAATIESKAKLVYDHVSD 319 (645)
T ss_pred chhhHHHHHHHHhhcCCCCCCCCCChhhhhhhhhccccccCceEEEEEEEecCCccccchhhHHHhhhhhhhhhhhhHHH
Confidence 999999999999999999999999999999999999999999999999999999998 5789999999999999999999
Q ss_pred HHccCCCccccCccCCCCCcccCCCchhhHHHHHHHHHHHHHHHHHHHhcCCCccccCCCceeecCCCCCeEEeEecCCc
Q 001256 638 IIDGKFDVESSNTLGEGWPQLYGQFEWSDVVRSIKSLYEVSKILKDKRFTDGALRLENSKPVFLFDEYGTPYDSVLSGRE 717 (1113)
Q Consensus 638 iLd~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~L~~L~~lA~~Lr~~R~~~Gal~ld~pe~~~~lDe~g~p~~v~~~~~~ 717 (1113)
+|++..+ + -| ...++.+.++.|+.+++..-+.|..+.-+.-+.|+.+|.+.|+|.++++....+.
T Consensus 320 wlE~~~~-----W----qP------e~~~iAqqi~~L~~~~~aR~~WRk~hal~FkdrpdYrF~l~e~g~V~~I~ae~RR 384 (645)
T COG4776 320 WLENTGD-----W----QP------ESEAIAQQIRLLHQFCQARIEWRKTHALVFKDRPDYRFILGEKGEVLDIVAEPRR 384 (645)
T ss_pred HHhcCCC-----C----CC------CCHHHHHHHHHHHHHHHHHHHHHhhceeeccCCCceEEEecCCCceEeeehhHHH
Confidence 9998421 1 12 2457889999999999999999988776666899999999999999999999999
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHhCCCcceEEecCCCCHHHHHHHHHHHHHcCCccCCCChhHHHHHHHHHHHhhcCCHH
Q 001256 718 DLNFLFEEFMLLANKTAAEVIARAFPDSALLRRHPAPNMRKLREFEAFCSKHGLQLDTSSSGQFHQSLEQAREKLKDDYV 797 (1113)
Q Consensus 718 ~a~~LIEEfMllAN~~VA~~l~~~~p~~allR~H~~P~~~kl~~l~~~~~~~G~~l~~ss~~~l~~sL~~i~~~~~~~p~ 797 (1113)
.||+||||.||+||.++|++|.+++ ..++|-.|..-++..++....++...|...+...-.+| ..+.+++..+.-.+.
T Consensus 385 iAnriVEE~MI~ANIcAa~~L~~~~-gfGI~N~HsGFd~~~~e~a~~~l~~~~~~~~~e~l~Tl-~Gfc~lRr~l~~~~t 462 (645)
T COG4776 385 IANRIVEESMIAANICAARVLREKL-GFGIYNVHSGFDPANAEAAAALLKTNGLNVDAEELLTL-EGFCKLRRELDAQPT 462 (645)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhc-CcceeeccccCCHHHHHHHHHHHHhcCcCCCHHHHhhh-HHHHHHHHHhhcccc
Confidence 9999999999999999999999986 48999999999999999999999999986654322222 223333332221110
Q ss_pred HHHHHHHHHhcccCCcEecccCCCCCCCCcCccccCCCcccccccCCCchhhHHHHHHHHHHHHhhhhhhhhhccCCCCC
Q 001256 798 LFDILINYATRPMQLASYFCSGDFKDDTDWGHYALAFPVYTHFTSPLRRYPDLVVHRTLNAALEAEKLYWKHRRMLPKNN 877 (1113)
Q Consensus 798 ~~~~L~~~~lR~M~~A~Y~~sg~~~s~~~~~HfgLa~~~YTHFTSPIRRYaDLIVHR~L~a~L~~~~~~~~~~~~~~~~~ 877 (1113)
..|-.-+-|...-|++ +.++.+|||||++.|+.||||||+|.|+|+||+|+|+|.+++.. +
T Consensus 463 --~yld~RiRrfqsfae~-------~t~p~PHFglGl~~YATWTSPIRKY~DMiNHRLlKavi~~~~~~-k--------- 523 (645)
T COG4776 463 --GYLDSRIRRFQSFAEI-------STEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAE-K--------- 523 (645)
T ss_pred --chHHHHHHHHHhHHhh-------ccCcCccccccchheeeccchhhhhhhHHHHHHHHHHHcCCCcC-C---------
Confidence 1111111222223333 56899999999999999999999999999999999999865310 0
Q ss_pred CccccccccccccccccchhhhhhhhhHHHHHhhhcCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccce
Q 001256 878 HREGVRGRFLTGIFYDKDAAESLEGREALSVAALKYGVPCADILVNVATHCNDRKLACRNVKDACVKLYMWILLKKKEVL 957 (1113)
Q Consensus 878 ~~~~~~~~~~~~i~~~~~~~es~~~~e~l~~~~~k~~lp~~~~l~~ia~~~N~r~~~Ar~A~r~s~~l~~~~~lk~~~g~ 957 (1113)
| -+.+...+.++.|.-|.|+|+.-+...++||+.+.+.
T Consensus 524 --------------------------------------P----qedi~v~lae~Rr~nrmaERdv~DWLY~r~L~~k~~~ 561 (645)
T COG4776 524 --------------------------------------P----QEDITVQLAERRRLNRMAERDVADWLYARFLADKAGT 561 (645)
T ss_pred --------------------------------------C----chHHHHHHHHHHHhhhhhhhhhHHHHHHHHhcccccc
Confidence 1 1234556677888899999999999999999887654
Q ss_pred --EEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCc--EEEEecccceEEEeeecccceeecCCCceEE
Q 001256 958 --LSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGL--IVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 1023 (1113)
Q Consensus 958 --~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~--~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r 1023 (1113)
.|.|-|..|...|+.|-+-+-|--..|--.-+.+. ..++..++.++-. +....|++||.+.++
T Consensus 562 ~~~F~AEI~Di~R~G~RvrLleNGA~~FIPa~lih~~reei~~n~e~gtv~I---~ge~~Yk~~D~i~V~ 628 (645)
T COG4776 562 NTRFAAEIQDISRGGMRVRLLENGAIAFIPAPLIHANREELVCNQENGTVQI---KGETVYKVGDVIDVT 628 (645)
T ss_pred CchhhhhhhhhccCceEEEeccCCcceecchhhhccchhheEecCCCceEEE---ccEEEEeeccEEEEE
Confidence 68899988888888887777776665554444332 3456666666655 455677888765554
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=98.12 E-value=1.1e-05 Score=73.40 Aligned_cols=67 Identities=13% Similarity=0.085 Sum_probs=59.6
Q ss_pred ceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 956 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 956 g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
|.+++|.|+++.++|++|.++.+|+||.||+++++++++.|++.+..+.+ +.....|+.||.++++.
T Consensus 2 g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~--~~~~~~~~~gd~v~v~v 68 (83)
T cd04471 2 GEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVG--ERTGKVFRLGDKVKVRV 68 (83)
T ss_pred CCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEe--ccCCCEEcCCCEEEEEE
Confidence 56899999999999999999999999999999999999999999888887 45667889998777763
No 11
>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=97.67 E-value=3.8e-05 Score=66.47 Aligned_cols=45 Identities=18% Similarity=0.314 Sum_probs=36.0
Q ss_pred EEEEeccCCceeEEEEeCCcceeEEEeCcCCccccCCCCEEEEEEccc
Q 001256 181 ALYRVNAHNRLEAYCKIEGVQTDVLITGIAAQNRAVEGDFVLIKVDRL 228 (1113)
Q Consensus 181 G~lrVn~~N~~eAyV~~~g~~~Dv~I~G~~~rNRAl~GDvVaVeLlp~ 228 (1113)
|+|+++++.+ |||.+++...||||... ++|.|+|||.|.|++.+.
T Consensus 1 G~~~~~~~Gf--GFv~~~~~~~DifIp~~-~l~~A~~gD~V~v~i~~~ 45 (58)
T PF08206_consen 1 GTLKIHPKGF--GFVIPDDGGEDIFIPPR-NLNGAMDGDKVLVRITPP 45 (58)
T ss_dssp EEEEE-SSS---EEEEECT-TEEEEE-HH-HHTTS-TT-EEEEEEEES
T ss_pred CEEEEEcCCC--EEEEECCCCCCEEECHH-HHCCCCCCCEEEEEEecC
Confidence 8999998877 99999999999999995 999999999999999883
No 12
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=96.87 E-value=0.0031 Score=60.09 Aligned_cols=63 Identities=14% Similarity=0.105 Sum_probs=55.3
Q ss_pred EEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 958 LSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 958 ~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
++.|.|+++.+.|++|.+. +++|.||++++.++++.|++.+..+++ ...+..|++||.++++.
T Consensus 2 vv~g~V~~i~~~GifV~l~--~v~G~v~~~~l~~~~~~~~~~~~~~~~--~~~~~~~~~Gd~v~vkI 64 (99)
T cd04460 2 VVEGEVVEVVDFGAFVRIG--PVDGLLHISQIMDDYISYDPKNKRLIG--EETKRVLKVGDVVRARI 64 (99)
T ss_pred EEEEEEEEEEeccEEEEEc--CeEEEEEEEEccCCceEechhheeecc--cCcCCEECCCCEEEEEE
Confidence 5789999999999999886 599999999999999999999888888 46678899999887763
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=96.73 E-value=0.0013 Score=69.45 Aligned_cols=74 Identities=12% Similarity=0.050 Sum_probs=64.5
Q ss_pred HHHHHHhccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 947 MWILLKKKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 947 ~~~~lk~~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
.+.+++...|.+++|+|+++.+.|++|-+ . .+++.++.+++.++++.|++.++.+++ ..+++.|+.|+.|++|.
T Consensus 73 ~~i~f~p~~gEvv~G~V~~v~~~GifV~l-g-~~~gi~~~~~l~~~~~~~d~~~~~~~~--~~~~~~~~~Gd~VrvrV 146 (179)
T TIGR00448 73 RALVFKPELGEIVEGEVIEIVEFGAFVSL-G-PFDGLFHVSQVTDDYCYYDPKESALIG--KETKKVLDEGDKVRARI 146 (179)
T ss_pred EEEEEeccCCCEEEEEEEEEEeeEEEEEe-C-CceEEEEcHHhCCCceEEccccceEEE--ccCCeEEcCCCEEEEEE
Confidence 34456777899999999999999999988 3 499999999999999999999999998 46778999999998886
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=96.39 E-value=0.0071 Score=54.44 Aligned_cols=57 Identities=7% Similarity=-0.102 Sum_probs=45.5
Q ss_pred cceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 955 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 955 ~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
.|.+++|.|+++.++|++|.++.+++||+||++++.+..+ + ..+..|+.||.++++.
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 3678999999999999999997777899999999876432 1 3344589999887764
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=95.66 E-value=0.022 Score=51.82 Aligned_cols=57 Identities=14% Similarity=0.004 Sum_probs=45.5
Q ss_pred ceEEEEEEeeecCcEEEEEEecC--CeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 956 VLLSEARVLALGPRFMTIYIEKL--AIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 956 g~~~~a~V~~V~~~~f~V~Ip~~--giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
|.++.|.|+++.++|++|.+... +++|.+|++++...++ +. .....|++||.++++.
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 2345689999888764
No 16
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=94.93 E-value=0.07 Score=56.77 Aligned_cols=71 Identities=14% Similarity=0.100 Sum_probs=61.1
Q ss_pred HHHhccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 950 LLKKKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 950 ~lk~~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
.++...|.+.+|.|+++.+.|++|-+. .+++.++..++.+++++|++.++.++. ...+..++.|+.+++|.
T Consensus 76 vf~P~~GEVv~g~V~~v~~~Gi~V~lg--~~~g~v~~~~l~~~~~~~d~~~~~~~~--~~~~~~i~~Gd~VrvrV 146 (187)
T PRK08563 76 VFKPELQEVVEGEVVEVVEFGAFVRIG--PVDGLLHISQIMDDYISYDPKNGRLIG--KESKRVLKVGDVVRARI 146 (187)
T ss_pred EEeccCCCEEEEEEEEEEccEEEEEEe--CceEEEEcHHcCCCceEEccccceEEE--ccCCeEEcCCCEEEEEE
Confidence 345567899999999999999999886 499999999999999999999888887 35678899999888885
No 17
>PRK08582 hypothetical protein; Provisional
Probab=94.90 E-value=0.051 Score=55.44 Aligned_cols=57 Identities=11% Similarity=-0.021 Sum_probs=45.3
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
+.|.+++|+|++|.+.|++|.|+. +++|+||++++.+.++.- ....|+.||.|+++.
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 457899999999999999998865 799999999998765311 124588999888764
No 18
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=94.87 E-value=0.043 Score=57.99 Aligned_cols=78 Identities=15% Similarity=0.095 Sum_probs=64.5
Q ss_pred hccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEEeeeEEEEE
Q 001256 953 KKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRALEEVALVV 1032 (1113)
Q Consensus 953 ~~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~~~~v~~~~ 1032 (1113)
-..+++.+|.|+.+.+.|++|-|- -+.|+||.+++.|+++.|++....+++ +.+|+.++.||.|++|.........
T Consensus 79 P~~gEVV~GeVv~~~~~G~fV~ig--p~dglvh~sqi~dd~~~~d~~~~~~~g--~~tk~~i~~gd~VR~RIv~~s~~~~ 154 (183)
T COG1095 79 PFRGEVVEGEVVEVVEFGAFVRIG--PLDGLVHVSQIMDDYIDYDEKNKVLIG--EETKRVLKVGDKVRARIVGVSLKSR 154 (183)
T ss_pred eccccEEEEEEEEEeecceEEEec--cccccccHhhccCcccccCcccceeee--cccceEEecCCEEEEEEEEEecccC
Confidence 344788999999999988887766 688999999999999999999999999 5799999999999988744444443
Q ss_pred ec
Q 001256 1033 RP 1034 (1113)
Q Consensus 1033 ~~ 1034 (1113)
+|
T Consensus 155 ~~ 156 (183)
T COG1095 155 RP 156 (183)
T ss_pred cc
Confidence 33
No 19
>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=94.79 E-value=0.065 Score=47.80 Aligned_cols=56 Identities=11% Similarity=0.066 Sum_probs=44.5
Q ss_pred cceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 955 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 955 ~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
.|.++.|.|+++.++|++|.++. +++|.||.+++.+++.+. ....|+.||.++++.
T Consensus 3 ~G~iv~g~V~~v~~~gi~v~l~~-~~~g~v~~s~l~~~~~~~-------------~~~~~~~Gd~v~~~V 58 (73)
T cd05706 3 VGDILPGRVTKVNDRYVLVQLGN-KVTGPSFITDALDDYSEA-------------LPYKFKKNDIVRACV 58 (73)
T ss_pred CCCEEEEEEEEEeCCeEEEEeCC-CcEEEEEhhhccCccccc-------------cccccCCCCEEEEEE
Confidence 47889999999999999999876 699999999998764221 134589999877764
No 20
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=94.65 E-value=0.058 Score=47.73 Aligned_cols=55 Identities=13% Similarity=0.138 Sum_probs=44.3
Q ss_pred ceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 956 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 956 g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
|.+++|.|++|.++|++|.++. +++|.||.+++.++++. +....|+.||.++++.
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 4678999999999999998874 69999999999877542 2234689999888775
No 21
>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=94.63 E-value=0.086 Score=46.90 Aligned_cols=57 Identities=12% Similarity=-0.014 Sum_probs=43.7
Q ss_pred cceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 955 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 955 ~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
.|..+.|.|+++.++|++|.++. +++|++|+++++. .++ . ......|++||.++++.
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 12345689999887764
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=94.60 E-value=0.073 Score=47.55 Aligned_cols=57 Identities=12% Similarity=0.014 Sum_probs=45.4
Q ss_pred cceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 955 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 955 ~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
.|.++.|.|+++.+.|++|.+...+++|.+|.+++.+++. . .....|++||.++++.
T Consensus 2 ~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~---~----------~~~~~~~~Gd~v~v~i 58 (77)
T cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRV---A----------DASKLFRVGDKVRAKV 58 (77)
T ss_pred CCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCcc---C----------CHhHeecCCCEEEEEE
Confidence 4678999999999999999888778999999999976532 1 1235689999887763
No 23
>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=94.56 E-value=0.065 Score=47.98 Aligned_cols=57 Identities=16% Similarity=0.071 Sum_probs=45.5
Q ss_pred cceEEEEEEeeecCcEEEEEEecC-CeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 955 EVLLSEARVLALGPRFMTIYIEKL-AIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 955 ~g~~~~a~V~~V~~~~f~V~Ip~~-giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
.|..+.|.|.++.++|++|.+..+ +++|.||.+++.++++.. ....|++||.++++.
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 699999999998765432 134578899887764
No 24
>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=94.43 E-value=0.11 Score=46.20 Aligned_cols=57 Identities=18% Similarity=0.085 Sum_probs=47.4
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
+.|..+.|.|..+.++|++|-+. .+++|.|+.+++.+.+. ......|+.|+.+.++.
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 56889999999999999999999 99999999999987621 23456788999887765
No 25
>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=94.37 E-value=0.066 Score=47.01 Aligned_cols=56 Identities=5% Similarity=0.057 Sum_probs=42.2
Q ss_pred ceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 956 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 956 g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
|..+.|.|.++.++|++|.++. ++||+||.+++.. .. .. ......|++||+++++.
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 23345689999888774
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=93.66 E-value=0.1 Score=46.02 Aligned_cols=55 Identities=13% Similarity=0.144 Sum_probs=43.1
Q ss_pred ceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 956 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 956 g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
|..+.|.|++|.++|++|.++. +++|.||.+++.+++++ .....|+.||.++++.
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 3568999999999998888875 69999999999877542 2234588898777664
No 27
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=93.66 E-value=0.11 Score=66.72 Aligned_cols=62 Identities=13% Similarity=0.060 Sum_probs=49.0
Q ss_pred HHHHhccceEEE-EEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 949 ILLKKKEVLLSE-ARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 949 ~~lk~~~g~~~~-a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
.++..+.|.+++ |.|++|.++|++|.|.. |+||+||++++...++.+.+ ..|+.||.|+++.
T Consensus 747 l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~-g~EGLVHISeLs~~rv~~~~-------------dv~kvGD~V~VkV 809 (891)
T PLN00207 747 LTMVPTVGDIYRNCEIKSIAPYGAFVEIAP-GREGLCHISELSSNWLAKPE-------------DAFKVGDRIDVKL 809 (891)
T ss_pred HhcCcCCCcEEECcEEEEEeccEEEEEeCC-CCEEEEEhhhcCCccccCHH-------------HhcCCCCEEEEEE
Confidence 344567789995 69999999999888854 79999999999887765543 3578899887774
No 28
>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=93.56 E-value=0.1 Score=45.16 Aligned_cols=55 Identities=11% Similarity=-0.020 Sum_probs=43.1
Q ss_pred ceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 956 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 956 g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
|..+.|.|.++.++|++|.+.. +++|.+|.+++.++++. .....|++||.++++.
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~-~~~g~~~~~~l~~~~~~-------------~~~~~~~~Gd~v~v~i 55 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGV-KQDGLIHISKMADRFVS-------------HPSDVVSVGDIVEVKV 55 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCC-CCEEEEEHHHCCCcccc-------------CHHHhcCCCCEEEEEE
Confidence 3578999999999999998864 69999999999876542 1234588999777763
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=93.29 E-value=0.14 Score=45.91 Aligned_cols=55 Identities=11% Similarity=0.018 Sum_probs=42.0
Q ss_pred ceEEE-EEEeee-cCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 956 VLLSE-ARVLAL-GPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 956 g~~~~-a~V~~V-~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
|.+++ |.|+.+ .++|++|-+++ |++|.||.+++.+...+.. ...++.|+.+.++.
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-GLLGFVHISHLSDDKVPSD-------------TGPFKAGTTHKARI 57 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCC-CCEEEEEHHHCCcchhcCc-------------ccccCCCCEEEEEE
Confidence 45677 999998 79999999877 8999999999875433221 23488899887774
No 30
>PRK07252 hypothetical protein; Provisional
Probab=93.10 E-value=0.17 Score=50.39 Aligned_cols=56 Identities=11% Similarity=0.011 Sum_probs=44.5
Q ss_pred cceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 955 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 955 ~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
.|.++.|+|++|.++|++|.|+. +++|.||++++.+.++.. ....|++||.|+++.
T Consensus 3 vG~iv~G~V~~V~~~G~fVei~~-~~~GllhiseLs~~~~~~-------------~~~~~~vGD~V~VkI 58 (120)
T PRK07252 3 IGDKLKGTITGIKPYGAFVALEN-GTTGLIHISEIKTGFIDN-------------IHQLLKVGEEVLVQV 58 (120)
T ss_pred CCCEEEEEEEEEeCcEEEEEECC-CCEEEEEHHHcCCccccC-------------hhhccCCCCEEEEEE
Confidence 47789999999999999998865 699999999998765411 124589999887763
No 31
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=92.77 E-value=0.17 Score=44.60 Aligned_cols=55 Identities=9% Similarity=0.103 Sum_probs=42.1
Q ss_pred ceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 956 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 956 g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
|.++.|.|.++.++|++|.++. +++|.||.+++..++. ++ ....++.|+.++++.
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 6999999999876531 11 124588899888774
No 32
>PRK05807 hypothetical protein; Provisional
Probab=92.76 E-value=0.22 Score=50.71 Aligned_cols=56 Identities=13% Similarity=0.013 Sum_probs=43.7
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
..|.+++|.|++++++|++|.+ -+.+|+||++++.+.++.- -...|++||.|+++.
T Consensus 4 ~vG~vv~G~Vt~i~~~GafV~L--~~~~Glvhiseis~~~v~~-------------~~~~~kvGd~V~VkV 59 (136)
T PRK05807 4 KAGSILEGTVVNITNFGAFVEV--EGKTGLVHISEVADTYVKD-------------IREHLKEQDKVKVKV 59 (136)
T ss_pred cCCCEEEEEEEEEECCeEEEEE--CCEEEEEEhhhcccccccC-------------ccccCCCCCEEEEEE
Confidence 4678999999999999999999 3789999999998755320 122478899877663
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=92.72 E-value=0.18 Score=46.36 Aligned_cols=57 Identities=12% Similarity=0.070 Sum_probs=45.4
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
+.|.++.|.|.+|.++|++|.+.. +++|.||.+++.++++. .....|+.||.++++.
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 468899999999999998887754 69999999999765431 2345689999888875
No 34
>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=91.88 E-value=0.29 Score=42.47 Aligned_cols=55 Identities=15% Similarity=0.063 Sum_probs=42.3
Q ss_pred ceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 956 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 956 g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
|..+.|.|+.+.++|++|.+.. +.+|.+|++++..+++. .....|++||.++++.
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~-~~~g~l~~~~l~~~~~~-------------~~~~~~~~Gd~v~v~v 55 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILP-GKDGLVHISELSDERVE-------------KVEDVLKVGDEVKVKV 55 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCC-CCEEEEEhHHcCCcccc-------------CHHHccCCCCEEEEEE
Confidence 3578999999999998888864 69999999998766431 2234688999877763
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=91.39 E-value=0.29 Score=44.43 Aligned_cols=59 Identities=14% Similarity=0.114 Sum_probs=44.1
Q ss_pred cceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 955 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 955 ~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
.|....|.|..+.++|++|.+.. +++|+||++++.+.+. -+...-...|+.|+.++++.
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 46788999999999998888864 9999999999876542 11111134689999887765
No 36
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=90.86 E-value=0.51 Score=40.85 Aligned_cols=54 Identities=7% Similarity=-0.049 Sum_probs=40.7
Q ss_pred ceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 956 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 956 g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
|..+.|.|+++.++|++|-+. +++|.+|.+++...+. +.....|++||.++++.
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 567899999999988877764 7999999998863111 12345689999887764
No 37
>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=90.82 E-value=0.76 Score=39.91 Aligned_cols=50 Identities=20% Similarity=0.277 Sum_probs=33.8
Q ss_pred ceEEEEeCCCCCCceEEecCCCChhhhhhcccCCccccceEEEEEEeecCCCCCCCcEEEEEE
Q 001256 399 EYIQLTPTHPKYPKMVVLVKDLPDSIKKRLEEGDATIEMELVAARIDEWNEESPFPQAHVLHV 461 (1113)
Q Consensus 399 ~~~~~~P~D~riP~i~i~~~~~p~~~~~~~~~gd~~~~~~lvvv~I~~Wp~~s~~P~G~Iv~~ 461 (1113)
++.|++|.| ....++. |+...+.+.+|| .|+|+|.. +.....|.|+|+++
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 4444433 334445666777 79999998 88888999999985
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=90.63 E-value=0.43 Score=41.24 Aligned_cols=55 Identities=16% Similarity=0.084 Sum_probs=41.7
Q ss_pred ceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 956 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 956 g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
|..+.|.|.++.++|++|.+.. +.+|.+|.+++.+++. ......|++||.++++.
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~-~~~g~l~~~~l~~~~~-------------~~~~~~~~~Gd~v~v~v 55 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGG-GISGLVHISQIAHKRV-------------KDVKDVLKEGDKVKVKV 55 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECC-CCEEEEEhHHcCCccc-------------CCHHHccCCCCEEEEEE
Confidence 4578999999999998888854 6999999999876541 11224688898777763
No 39
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=90.51 E-value=0.52 Score=40.51 Aligned_cols=56 Identities=14% Similarity=0.070 Sum_probs=43.3
Q ss_pred cceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 955 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 955 ~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
.|..+.|.|.++.++|+.|.+.. +++|.++++++.+.+ .......|+.||.++++.
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 46789999999999998887753 799999999987643 123345689999777764
No 40
>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=89.55 E-value=0.64 Score=41.04 Aligned_cols=55 Identities=15% Similarity=0.109 Sum_probs=41.9
Q ss_pred ceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 956 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 956 g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
|.++.|.|+++.++|++|-+.. +++|.+|.+++.++++ ......|+.||.++++.
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~-~~~g~i~~~~~~~~~~-------------~~~~~~~~~Gd~v~~~v 55 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGD-GVEGFLRAAELSRDRV-------------EDATERFKVGDEVEAKI 55 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCC-CCEEEEEHHHCCCccc-------------cCHHHccCCCCEEEEEE
Confidence 3568999999999998888754 5999999999887643 12234578899777763
No 41
>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=89.44 E-value=0.84 Score=41.58 Aligned_cols=49 Identities=10% Similarity=0.070 Sum_probs=40.5
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
+.|..++|.|.++.+.|++|.+.. +.+|.+|.+++. ..|++||.++++.
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 2478898887764
No 42
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=89.40 E-value=0.46 Score=53.50 Aligned_cols=57 Identities=18% Similarity=0.054 Sum_probs=46.8
Q ss_pred cceEEEEEEeeecCcEEEEEEecC-CeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 955 EVLLSEARVLALGPRFMTIYIEKL-AIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 955 ~g~~~~a~V~~V~~~~f~V~Ip~~-giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
.|..+.|.|.+|.++|++|.+.+| |++|.||++++...++... ...++.||.+.++.
T Consensus 8 ~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i-------------~~~~kvGd~V~vkV 65 (262)
T PRK03987 8 EGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNI-------------RDHVKEGQKVVCKV 65 (262)
T ss_pred CCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCH-------------HHhCCCCCEEEEEE
Confidence 477899999999999999999999 9999999999987765432 23578898777663
No 43
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=89.11 E-value=0.47 Score=54.67 Aligned_cols=39 Identities=18% Similarity=0.071 Sum_probs=34.7
Q ss_pred cceEEEEEEeeecCcEEEEEEecC-CeEEEEEeeecCCcE
Q 001256 955 EVLLSEARVLALGPRFMTIYIEKL-AIERRIYYDEVEGLI 993 (1113)
Q Consensus 955 ~g~~~~a~V~~V~~~~f~V~Ip~~-giEg~V~~~~l~~~~ 993 (1113)
.|.+..|.|+.|.++|.+|.|.+| |+||.||++++.-.+
T Consensus 17 ~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~r 56 (319)
T PTZ00248 17 EDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRR 56 (319)
T ss_pred CCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccc
Confidence 378899999999999999999999 999999999986433
No 44
>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=88.96 E-value=0.74 Score=41.61 Aligned_cols=57 Identities=14% Similarity=0.098 Sum_probs=42.4
Q ss_pred ceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 956 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 956 g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
|....|.|..+.++|++|.+.+ +++|+|+++++..+. .. . ..-...|+.|+.++++.
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 3467899999999999999866 899999999986431 00 0 12334689999887774
No 45
>PRK08059 general stress protein 13; Validated
Probab=87.92 E-value=0.86 Score=45.47 Aligned_cols=57 Identities=9% Similarity=0.032 Sum_probs=44.1
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
+.|.++.|.|+++.++|++|.|. .+++|.||++++..+++ ......|+.||.+.++.
T Consensus 6 k~G~iv~G~V~~i~~~G~fV~i~-~~~~Gli~~sel~~~~~-------------~~~~~~~~vGD~I~vkI 62 (123)
T PRK08059 6 EVGSVVTGKVTGIQPYGAFVALD-EETQGLVHISEITHGFV-------------KDIHDFLSVGDEVKVKV 62 (123)
T ss_pred CCCCEEEEEEEEEecceEEEEEC-CCCEEEEEHHHCCcccc-------------cCHHHcCCCCCEEEEEE
Confidence 35788999999999999999886 47999999999876532 11234688999877763
No 46
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=87.29 E-value=1.7 Score=55.39 Aligned_cols=58 Identities=14% Similarity=0.055 Sum_probs=46.1
Q ss_pred hccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 953 KKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 953 ~~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
.+.|.++.|.|++|.++|++|.|.. |.+|+||++++...++. +....|+.||.|+++.
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 3568999999999999999998864 89999999999755431 2234689999888774
No 47
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=87.20 E-value=1.1 Score=47.57 Aligned_cols=71 Identities=8% Similarity=-0.092 Sum_probs=55.9
Q ss_pred HHhccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 951 LKKKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 951 lk~~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
++-..+++.+|.|+++.+.|++|-+-.+- +.|+.++++++ +.|++.++..++....++..+..|+.|++|.
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 44556889999999999999999885444 89999999876 8899877655443245578899999988886
No 48
>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=85.70 E-value=1.8 Score=55.07 Aligned_cols=57 Identities=14% Similarity=0.064 Sum_probs=45.1
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
+.|.++.|.|+++.++|++|.+.. |++|+||++++.+.++. ..+..|+.||.++++.
T Consensus 617 ~~G~i~~G~V~~I~~~GafVei~~-g~~GllHiSei~~~~v~-------------~~~~~~kvGD~V~VkV 673 (684)
T TIGR03591 617 EVGKIYEGKVVRIMDFGAFVEILP-GKDGLVHISEIANERVE-------------KVEDVLKEGDEVKVKV 673 (684)
T ss_pred ccCcEEEEEEEEEeCCEEEEEECC-CcEEEEEHHHcCCCccc-------------ChhhccCCCCEEEEEE
Confidence 568999999999999998888754 79999999999654431 2345689999888775
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=85.57 E-value=1.5 Score=38.96 Aligned_cols=57 Identities=21% Similarity=0.177 Sum_probs=40.9
Q ss_pred ceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 956 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 956 g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
|....|.|+.+.++++.|-++. ++||.||.+++.+.|.+ . ......|+.||.+.++.
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 3467899999999998888764 89999999998765410 0 11123478898777664
No 50
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=84.98 E-value=1.8 Score=38.24 Aligned_cols=52 Identities=15% Similarity=0.161 Sum_probs=40.9
Q ss_pred eEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 957 LLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 957 ~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
...+|.|+.+.++|++|.+.. +++|.|+.+++...+.. ...|+.|+.+++|.
T Consensus 2 ~~V~g~V~~i~~~G~~v~l~~-~v~g~v~~~~l~~~~~~---------------~~~~~~G~~i~~kV 53 (66)
T cd05695 2 MLVNARVKKVLSNGLILDFLS-SFTGTVDFLHLDPEKSS---------------KSTYKEGQKVRARI 53 (66)
T ss_pred CEEEEEEEEEeCCcEEEEEcC-CceEEEEHHHcCCccCc---------------ccCcCCCCEEEEEE
Confidence 457899999999999999876 79999999988543211 33588999888775
No 51
>PHA02945 interferon resistance protein; Provisional
Probab=84.87 E-value=2.9 Score=39.51 Aligned_cols=42 Identities=7% Similarity=-0.083 Sum_probs=36.5
Q ss_pred ccceEEEEEEeeecCcEEEEEEecC-CeEEEEEeeec--CCcEEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKL-AIERRIYYDEV--EGLIVEW 996 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~-giEg~V~~~~l--~~~~~e~ 996 (1113)
..|...-|+|.. .++|++|.+++| |+||.||.+.+ ..-|..+
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 357788999999 999999999999 99999999965 7777755
No 52
>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=84.05 E-value=1.7 Score=39.13 Aligned_cols=56 Identities=14% Similarity=0.054 Sum_probs=40.0
Q ss_pred cceEEEEEEeeecC-cEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 955 EVLLSEARVLALGP-RFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 955 ~g~~~~a~V~~V~~-~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
.|..+.|.|..+.+ .|++|.+ ..|.+|++|++++.+.+. .. -...|+.||.++++.
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 5765554 237999999999877642 11 123578898777664
No 53
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=83.36 E-value=2 Score=52.44 Aligned_cols=57 Identities=18% Similarity=0.098 Sum_probs=45.4
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
..|.++.|.|+.+.++|++|.+.. |++|+||.+++....++. .+..|+.||.|+++.
T Consensus 292 ~vG~vv~G~V~~I~~fGvFVeL~~-gieGLvh~SeLs~~~v~~-------------~~~~~kvGd~V~VkI 348 (486)
T PRK07899 292 AIGQIVPGKVTKLVPFGAFVRVEE-GIEGLVHISELAERHVEV-------------PEQVVQVGDEVFVKV 348 (486)
T ss_pred CCCCEEEEEEEEEeccEEEEEeCC-CcEEEEEHHHcCcccccC-------------ccceeCCCCEEEEEE
Confidence 357899999999999999998865 899999999998654422 134589999888774
No 54
>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=83.14 E-value=2.2 Score=35.82 Aligned_cols=51 Identities=16% Similarity=0.172 Sum_probs=39.0
Q ss_pred EEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 960 EARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 960 ~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
.|+|.++.++|++|.+. .+++|.++.+++.+.++ ...+..|+.||.++++.
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 69999999988888775 46999999999876432 12345688999887775
No 55
>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=82.79 E-value=3.8 Score=52.52 Aligned_cols=58 Identities=17% Similarity=0.196 Sum_probs=42.6
Q ss_pred ceEEEEeCCCCCC-ceEEecCCCChhhhhhcccCCccccceEEEEEEeecCCCCCCCcEEEEEEcCCCCCh
Q 001256 399 EYIQLTPTHPKYP-KMVVLVKDLPDSIKKRLEEGDATIEMELVAARIDEWNEESPFPQAHVLHVFGRGGEV 468 (1113)
Q Consensus 399 ~~~~~~P~D~riP-~i~i~~~~~p~~~~~~~~~gd~~~~~~lvvv~I~~Wp~~s~~P~G~Iv~~LG~~gd~ 468 (1113)
++.|+.|.| +.+ .+.|+. ....++.+|| .|+|+|..|+.....|.|+|+++||...+.
T Consensus 79 g~gFv~~~~-~~~~di~I~~-----~~~~~a~~GD------~Vlv~I~~~~~~~~~~eg~Vv~Il~r~~~~ 137 (709)
T TIGR02063 79 GFGFLRPED-DDEDDIFIPP-----RQMNGAMHGD------RVLVRITGKPDGGDRFEARVIKILERANDQ 137 (709)
T ss_pred ccEEEEECC-CCCCcEEECh-----HHhCcCCCCC------EEEEEEecccCCCCCceEEEEEEEeeCCCE
Confidence 578899988 434 355542 2334566677 799999999866667899999999998764
No 56
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=82.72 E-value=2.1 Score=55.78 Aligned_cols=60 Identities=8% Similarity=-0.125 Sum_probs=47.6
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
..|..++|.|+++.++|++|.++. |++|.||++++.+++.+. .+ .....|+.||.+++..
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 1244699999888764
No 57
>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=82.59 E-value=1.8 Score=36.97 Aligned_cols=45 Identities=18% Similarity=0.111 Sum_probs=34.6
Q ss_pred EEEEEeccCCceeEEEEeCCcceeEEEeCcCC----ccccCCCCEEEEEEcc
Q 001256 180 KALYRVNAHNRLEAYCKIEGVQTDVLITGIAA----QNRAVEGDFVLIKVDR 227 (1113)
Q Consensus 180 ~G~lrVn~~N~~eAyV~~~g~~~Dv~I~G~~~----rNRAl~GDvVaVeLlp 227 (1113)
+|+++...+ ..+||..++.+.||||.-. + .+.+.+||.|.+++..
T Consensus 1 ~G~i~~~~~--g~gfv~~~~~~~~i~v~~~-~~~~~~~~~~~Gd~V~~~i~~ 49 (64)
T smart00357 1 TGVVKWFNK--GFGFIRPDDGGKDVFVHPS-QIQGGLKSLREGDEVEFKVVS 49 (64)
T ss_pred CeEEEEEcC--CeeEEecCCCCccEEEEhH-HhhcCCCcCCCCCEEEEEEEE
Confidence 477777664 4689988866579999644 4 7889999999999854
No 58
>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=82.35 E-value=2.5 Score=39.82 Aligned_cols=61 Identities=10% Similarity=-0.044 Sum_probs=42.2
Q ss_pred cceEEEEEEeeecCc--EEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEEee
Q 001256 955 EVLLSEARVLALGPR--FMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRALE 1026 (1113)
Q Consensus 955 ~g~~~~a~V~~V~~~--~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~~~ 1026 (1113)
.|.++.|.|..+.++ |.+|-+.. |.+|.+|++++....|... ..-...++.||.+.++...
T Consensus 7 ~G~iy~g~V~~i~~~~~GaFV~l~~-g~~Gllh~seis~~~~~~v----------~~~~~~~~~Gd~v~VqV~~ 69 (88)
T cd04453 7 VGNIYLGRVKKIVPGLQAAFVDIGL-GKNGFLHLSDILPAYFKKH----------KKIAKLLKEGQEILVQVVK 69 (88)
T ss_pred CCCEEEEEEEEeccCCcEEEEEeCC-CCEEEEEhHHcCchhcccc----------CCHHHcCCCCCEEEEEEEE
Confidence 578899999999997 77777755 7999999998743222111 1112357788877776543
No 59
>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=82.33 E-value=5.5 Score=37.60 Aligned_cols=65 Identities=9% Similarity=-0.015 Sum_probs=48.9
Q ss_pred ceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 956 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 956 g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
+++.+|+|+.+.+.|++|-+ =.+++.++-..++++ +.|+..+..-++. ..++..+..|+.|++|.
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 336678888889887 7888743333443 23578889999888886
No 60
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=81.56 E-value=2.4 Score=49.08 Aligned_cols=56 Identities=13% Similarity=0.008 Sum_probs=43.9
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
+.|.++.|.|.++.++|++|.+ .|++|+||.+++..++. . .....|+.||.++++.
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 4578999999999999988877 58999999999876542 1 1234589999888764
No 61
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=78.58 E-value=4.9 Score=49.21 Aligned_cols=56 Identities=5% Similarity=-0.055 Sum_probs=42.3
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
+.|.+..|+|+++.++|++|.|. |++|+||.+++...+. .+....|+.|+.|+++.
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 45889999999999999888883 8999999999864221 12223477888777764
No 62
>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=78.37 E-value=1.1 Score=43.18 Aligned_cols=67 Identities=15% Similarity=0.103 Sum_probs=45.4
Q ss_pred cceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccc--------eEEEeeecccceeecCCCceEEE
Q 001256 955 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTS--------TLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 955 ~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~--------~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
.|.+..|.|..|.+.|++|.+|. |++|.|++.++.+++..|.+..+ .... ..-...|+.||.++++.
T Consensus 3 ~G~vV~G~V~~v~~~gl~v~L~~-g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~f~vGd~V~~kV 77 (100)
T cd05693 3 EGMLVLGQVKEITKLDLVISLPN-GLTGYVPITNISDAYTERLEELDEESEEEDDEEEL--PDLEDLFSVGQLVRCKV 77 (100)
T ss_pred CCCEEEEEEEEEcCCCEEEECCC-CcEEEEEHHHhhHHHHHHHHHhhhhcccccccccc--CCHHHhccCCCEEEEEE
Confidence 46788999999999998888874 99999999998765433222100 0111 11234588999777663
No 63
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=77.75 E-value=2.1 Score=42.88 Aligned_cols=57 Identities=12% Similarity=0.074 Sum_probs=41.2
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
..|....|.|+|++++|.||.++. |-.|+||++++.+.++.-.. ...+.|+.|.+++
T Consensus 4 kvG~~l~GkItgI~~yGAFV~l~~-g~tGLVHISEIa~~fVkdI~-------------d~L~vG~eV~vKV 60 (129)
T COG1098 4 KVGSKLKGKITGITPYGAFVELEG-GKTGLVHISEIADGFVKDIH-------------DHLKVGQEVKVKV 60 (129)
T ss_pred cccceEEEEEEeeEecceEEEecC-CCcceEEehHhhhhhHHhHH-------------HHhcCCCEEEEEE
Confidence 357788999999999998887654 56799999999876652211 1235677776664
No 64
>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=76.46 E-value=5.7 Score=50.56 Aligned_cols=60 Identities=7% Similarity=-0.125 Sum_probs=44.1
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCc-EEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGL-IVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~-~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
..|.++.|.|..+.++|.+|.|. -|++|+||++++.+. |..+.. .-...++.||.|+++.
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 46889999999999988888875 489999999988532 211111 1234588999888875
No 65
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=72.91 E-value=7 Score=47.99 Aligned_cols=57 Identities=18% Similarity=0.115 Sum_probs=42.4
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
+.|..+.|.|+++.++|++|.|. .|++|.||.+++...+.. .-...|+.|+.++++.
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 1123478888887774
No 66
>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=72.76 E-value=5.4 Score=48.97 Aligned_cols=57 Identities=14% Similarity=0.042 Sum_probs=45.7
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
..|.+..|.|+++.++|++|.+.. +++|+||.+++.+++.+ .....|+.||.++++.
T Consensus 445 ~~G~~v~g~V~~v~~~G~fV~l~~-~~~Glv~~s~l~~~~~~-------------~~~~~~~~Gd~v~~~V 501 (516)
T TIGR00717 445 KVGSVVKGKVTEIKDFGAFVELPG-GVEGLIRNSELSENRDE-------------DKTDEIKVGDEVEAKV 501 (516)
T ss_pred CcceEEEEEEEEEecceEEEEcCC-CeEEEEEHHHcCccccc-------------cccccCCCCCEEEEEE
Confidence 458899999999999998888865 79999999999865421 2345689999888774
No 67
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=72.63 E-value=8.2 Score=45.70 Aligned_cols=57 Identities=18% Similarity=0.031 Sum_probs=42.2
Q ss_pred hccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 953 KKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 953 ~~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
-+.|....|.|.++.+.|++|.+ .|++|.||.+++...++ . .....|+.|+.++++.
T Consensus 190 ~~~G~~v~g~V~~v~~~G~fV~l--~~v~g~v~~sels~~~~---~----------~~~~~~~vGd~i~~~V 246 (390)
T PRK06676 190 LKEGDVVEGTVARLTDFGAFVDI--GGVDGLVHISELSHERV---E----------KPSEVVSVGQEVEVKV 246 (390)
T ss_pred CCCCCEEEEEEEEEecceEEEEe--CCeEEEEEHHHcCcccc---C----------CHHHhcCCCCEEEEEE
Confidence 35688999999999999988887 48999999999875321 1 1223467787776663
No 68
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=71.65 E-value=6.3 Score=48.63 Aligned_cols=37 Identities=8% Similarity=-0.006 Sum_probs=31.2
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCc
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGL 992 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~ 992 (1113)
..|+..+|+|.+++++| +||.-.|+.|+||++++...
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 45889999999999966 66777889999999988643
No 69
>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=71.26 E-value=10 Score=34.46 Aligned_cols=37 Identities=8% Similarity=-0.056 Sum_probs=31.3
Q ss_pred cceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCC
Q 001256 955 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEG 991 (1113)
Q Consensus 955 ~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~ 991 (1113)
.|....|.|.++.++|++|.+..-|++|.++.+++..
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 70
>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=71.15 E-value=8.8 Score=33.77 Aligned_cols=55 Identities=15% Similarity=0.047 Sum_probs=39.5
Q ss_pred ceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 956 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 956 g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
|....|.|..+.+.+++|-+ ..+.||.++.+++...+.. .-...|+.||.++++.
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 34678999999999888887 3479999999988653221 1123478888777663
No 71
>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=66.59 E-value=15 Score=31.16 Aligned_cols=55 Identities=18% Similarity=0.167 Sum_probs=34.5
Q ss_pred ceEEEEeCCCCCCceEEecCCCChhhhhhcccCCccccceEEEEEEeecCCCCCCCcEEEEEEc
Q 001256 399 EYIQLTPTHPKYPKMVVLVKDLPDSIKKRLEEGDATIEMELVAARIDEWNEESPFPQAHVLHVF 462 (1113)
Q Consensus 399 ~~~~~~P~D~riP~i~i~~~~~p~~~~~~~~~gd~~~~~~lvvv~I~~Wp~~s~~P~G~Iv~~L 462 (1113)
++.|+.|.+.. +.+.|+..++.. -...+.+|| .|.++|..|. ....|.|+++++|
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 56788887653 456665332110 023345565 7899999883 4556899999875
No 72
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=65.66 E-value=9.2 Score=46.97 Aligned_cols=57 Identities=7% Similarity=-0.101 Sum_probs=43.6
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
..|...+|.|..+.++|.+|.+.+ |++|+||.+++..... ......++.||.|+++.
T Consensus 378 ~vG~~v~G~V~~i~~~G~FV~l~~-gv~Gli~~se~s~~~~-------------~~~~~~~~~Gd~v~~~V 434 (491)
T PRK13806 378 APGTTVTGTVEKRAQFGLFVNLAP-GVTGLLPASVISRAGK-------------PATYEKLKPGDSVTLVV 434 (491)
T ss_pred CCCCEEEEEEEEEecCceEEEcCC-CcEEEEEHHHcCcccc-------------cchhhcCCCCCEEEEEE
Confidence 457899999999999999988865 9999999999864321 01223578899887763
No 73
>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=63.13 E-value=12 Score=34.45 Aligned_cols=60 Identities=13% Similarity=0.014 Sum_probs=41.5
Q ss_pred cceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 955 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 955 ~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
.|....|.|+++.+.|+.|.|. .+++|.+|.+++....+. .. + ......++.||.+.++.
T Consensus 6 ~GdiV~g~V~~i~~~g~~v~i~-~~~~G~l~~se~~~~~~~--~~----~---~~~~~~l~vGd~i~~~V 65 (86)
T cd05789 6 VGDVVIGRVTEVGFKRWKVDIN-SPYDAVLPLSEVNLPRTD--ED----E---LNMRSYLDEGDLIVAEV 65 (86)
T ss_pred CCCEEEEEEEEECCCEEEEECC-CCeEEEEEHHHccCCCCc--cc----h---HHHHhhCCCCCEEEEEE
Confidence 5778899999999999888775 479999999988632110 00 0 11233478888777664
No 74
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=60.50 E-value=15 Score=46.72 Aligned_cols=57 Identities=7% Similarity=0.051 Sum_probs=44.6
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
..|.++.|.|.++.++|++|.+.. |++|++|.+++.+... ......|+.||.++++.
T Consensus 561 ~~G~~v~g~V~~i~~~G~fV~l~~-~i~Gli~~sel~~~~~-------------~~~~~~~kvGd~V~vkV 617 (647)
T PRK00087 561 PVGSIVLGKVVRIAPFGAFVELEP-GVDGLVHISQISWKRI-------------DKPEDVLSEGEEVKAKI 617 (647)
T ss_pred cCCeEEEEEEEEEECCeEEEEECC-CCEEEEEhhhcCcccc-------------CCHhhcCCCCCEEEEEE
Confidence 458899999999999999998854 8999999999875431 23345689999887763
No 75
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=57.18 E-value=8.5 Score=43.18 Aligned_cols=40 Identities=18% Similarity=0.018 Sum_probs=35.7
Q ss_pred cceEEEEEEeeecCcEEEEEEecC-CeEEEEEeeecCCcEE
Q 001256 955 EVLLSEARVLALGPRFMTIYIEKL-AIERRIYYDEVEGLIV 994 (1113)
Q Consensus 955 ~g~~~~a~V~~V~~~~f~V~Ip~~-giEg~V~~~~l~~~~~ 994 (1113)
.|...-|.|..|.++|.+|.+.+| |+||.||++++.--|+
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 367788999999999999999999 6999999999887665
No 76
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=56.79 E-value=17 Score=43.15 Aligned_cols=56 Identities=11% Similarity=0.026 Sum_probs=42.0
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 1023 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r 1023 (1113)
..|.+..|.|.++.++|++|.+.. |++|++|.+++.... +. .....|+.||.++++
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 357889999999999998887753 899999999886421 11 223458899977765
No 77
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=56.23 E-value=28 Score=45.70 Aligned_cols=36 Identities=6% Similarity=-0.156 Sum_probs=30.9
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCC
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEG 991 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~ 991 (1113)
..|....|+|..+.++|++|.+ -|++|+||.+++..
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 3577899999999999988887 49999999998754
No 78
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=50.46 E-value=32 Score=43.87 Aligned_cols=56 Identities=18% Similarity=0.001 Sum_probs=42.2
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
+.|....|+|.++.++|++|.+ -|++|+||.+++...+. . +....|+.|+.++++.
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 1233578888777663
No 79
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=49.87 E-value=34 Score=42.64 Aligned_cols=36 Identities=8% Similarity=0.023 Sum_probs=31.2
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCC
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEG 991 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~ 991 (1113)
+.|...+|.|+.+.++|++|-+. |++|+||.+++..
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 46888999999999999888875 9999999998753
No 80
>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=49.05 E-value=37 Score=30.98 Aligned_cols=56 Identities=13% Similarity=-0.028 Sum_probs=41.6
Q ss_pred cceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 955 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 955 ~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
.|....|.|+++..+++.|-| -.++++.++.+++...+. ......++.||.+.++.
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 467789999999999999887 457999999998865411 12234478888777664
No 81
>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=48.23 E-value=32 Score=30.06 Aligned_cols=34 Identities=12% Similarity=-0.020 Sum_probs=29.5
Q ss_pred ceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCC
Q 001256 956 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEG 991 (1113)
Q Consensus 956 g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~ 991 (1113)
|....|.|..+.+.|+.|-+ -|++|.|+.+++..
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 35679999999999999988 48999999998864
No 82
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=46.03 E-value=30 Score=42.90 Aligned_cols=36 Identities=17% Similarity=0.021 Sum_probs=29.7
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecC
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVE 990 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~ 990 (1113)
..|....|+|+.+.++|.+|.| .-|+||+||++++.
T Consensus 276 ~~g~~v~G~Vt~i~~~GafVei-~~GvEGlvhvSEis 311 (541)
T COG0539 276 PVGDKVEGKVTNLTDYGAFVEI-EEGVEGLVHVSEIS 311 (541)
T ss_pred CCCCEEEEEEEEeecCcEEEEe-cCCccceeechhhc
Confidence 4578899999999998866654 23999999999874
No 83
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=45.28 E-value=33 Score=42.21 Aligned_cols=57 Identities=9% Similarity=-0.096 Sum_probs=42.7
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYR 1023 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r 1023 (1113)
..|....|.|..+.++|++|-+. .|++|+||++++...+. . ...+..|+.|+.|+++
T Consensus 358 ~~G~~v~g~V~~v~~~G~fV~l~-~~v~glv~~s~ls~~~~----------~--~~~~~~~~~G~~V~~~ 414 (516)
T TIGR00717 358 PVGDRVTGKIKKITDFGAFVELE-GGIDGLIHLSDISWDKD----------G--READHLYKKGDEIEAV 414 (516)
T ss_pred CCCCEEEEEEEEEecceEEEECC-CCCEEEEEHHHCcCccc----------C--CCHhHccCCCCEEEEE
Confidence 45889999999999999888776 38999999999863211 0 1223568889887776
No 84
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=44.92 E-value=34 Score=42.65 Aligned_cols=57 Identities=16% Similarity=0.085 Sum_probs=44.4
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
+.|.+..|+|..+.++|.+|.+.. |++|.||.+++.+.+. ..-...|+.|+.++++.
T Consensus 459 ~~G~vV~G~V~~v~~~G~fV~l~~-gi~g~i~~se~s~~~~-------------~~~~~~~~~Gd~v~~~V 515 (565)
T PRK06299 459 KKGSIVTGTVTEVKDKGAFVELED-GVEGLIRASELSRDRV-------------EDATEVLKVGDEVEAKV 515 (565)
T ss_pred CCCCEEEEEEEEEecCceEEecCC-CcEEEEEHHHhcchhc-------------cCccccCCCCCEEEEEE
Confidence 468899999999999998888764 9999999999865432 12234588999888764
No 85
>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=42.66 E-value=1.7e+02 Score=29.53 Aligned_cols=80 Identities=11% Similarity=0.016 Sum_probs=44.5
Q ss_pred cceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEee-ecccceeecCCCceEEEeeeEEEEEe
Q 001256 955 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSL-CAHKRSFKRGGPGNYRALEEVALVVR 1033 (1113)
Q Consensus 955 ~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~-~~~k~~~~~g~~v~~r~~~~v~~~~~ 1033 (1113)
.|++..|.|++-.+.|+.|-+ .|-=.-.|--+.|+. -..|++.++.-+... ..++-.+..|+.|++|+-++...-+.
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 367888999999988876654 222222222233332 235677777766665 55666778899999998777776566
Q ss_pred cCC
Q 001256 1034 PND 1036 (1113)
Q Consensus 1034 ~~~ 1036 (1113)
|-.
T Consensus 81 p~~ 83 (122)
T PF08292_consen 81 PTP 83 (122)
T ss_dssp ---
T ss_pred CCC
Confidence 544
No 86
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=42.53 E-value=1.3e+02 Score=34.97 Aligned_cols=35 Identities=17% Similarity=0.053 Sum_probs=30.8
Q ss_pred cceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCC
Q 001256 955 EVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEG 991 (1113)
Q Consensus 955 ~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~ 991 (1113)
.+...+|.|+++.+.|++|.+. |++|.|+.+++..
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 9999999998864
No 87
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=38.11 E-value=49 Score=35.48 Aligned_cols=58 Identities=19% Similarity=0.125 Sum_probs=42.2
Q ss_pred ccceEEEEEEeeecCcEEEEEEecC---------CeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKL---------AIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~---------giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
..|.+..|.|+++..++++|-|..+ +++|.+|.+++...+.. .-...|+.||.+..+.
T Consensus 63 ~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~-------------~~~~~~~~GD~V~akV 129 (189)
T PRK09521 63 KKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVE-------------SLTDAFKIGDIVRAKV 129 (189)
T ss_pred CCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhh-------------hHHhccCCCCEEEEEE
Confidence 3578899999999999999998643 69999999987643210 1133477888776663
No 88
>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=31.63 E-value=79 Score=29.15 Aligned_cols=37 Identities=22% Similarity=0.073 Sum_probs=34.1
Q ss_pred eEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEE
Q 001256 957 LLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIV 994 (1113)
Q Consensus 957 ~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~ 994 (1113)
...+|.|+.-.+.++.|.+.+.|+.|+++...|.| .+
T Consensus 2 ~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD-~~ 38 (72)
T cd05699 2 KLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSD-HV 38 (72)
T ss_pred ceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCC-ch
Confidence 56799999999999999999999999999999998 54
No 89
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=25.97 E-value=94 Score=29.52 Aligned_cols=36 Identities=11% Similarity=0.174 Sum_probs=28.5
Q ss_pred cceEEEEEEeeecCcEEEEEEecCCeEEEEE-eeecCC
Q 001256 955 EVLLSEARVLALGPRFMTIYIEKLAIERRIY-YDEVEG 991 (1113)
Q Consensus 955 ~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~-~~~l~~ 991 (1113)
.+.... -|..+.+.++.|.+.+||+||.|- ++++.-
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 345556 556789999999999999999988 776653
No 90
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=25.03 E-value=69 Score=39.73 Aligned_cols=37 Identities=3% Similarity=-0.100 Sum_probs=32.4
Q ss_pred ceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcE
Q 001256 956 VLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLI 993 (1113)
Q Consensus 956 g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~ 993 (1113)
|-++.|.|+.+.++|.+|.++. |.++++|.++|.-.|
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 91
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=24.20 E-value=1.1e+02 Score=34.01 Aligned_cols=61 Identities=15% Similarity=-0.028 Sum_probs=45.0
Q ss_pred ccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeecCCcEEEEecccceEEEeeecccceeecCCCceEEE
Q 001256 954 KEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEVEGLIVEWLETTSTLVLSLCAHKRSFKRGGPGNYRA 1024 (1113)
Q Consensus 954 ~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l~~~~~e~~~~~~~lv~~~~~~k~~~~~g~~v~~r~ 1024 (1113)
+.|.+..|+|+++..++++|-|.. +++|.+|++++...+.+.++ ...+..|+.||-|..|.
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 346788999999999999888754 47899999998654432222 23455689999887775
No 92
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=22.95 E-value=3.8e+02 Score=33.10 Aligned_cols=38 Identities=11% Similarity=-0.067 Sum_probs=30.1
Q ss_pred HHHhccceEEEEEEeeecCcEEEEEEecCCeEEEEEeeec
Q 001256 950 LLKKKEVLLSEARVLALGPRFMTIYIEKLAIERRIYYDEV 989 (1113)
Q Consensus 950 ~lk~~~g~~~~a~V~~V~~~~f~V~Ip~~giEg~V~~~~l 989 (1113)
.++.+.|....|+|..+...|+.|-+ -|+|+.++.+++
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 34555678899999999988766655 589999998764
No 93
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=21.45 E-value=3.4e+02 Score=23.65 Aligned_cols=48 Identities=15% Similarity=0.151 Sum_probs=34.6
Q ss_pred EEEEEeccCCceeEEEEeCCcceeEEEeCcCCcc---cc-CCCCEEEEEEcc
Q 001256 180 KALYRVNAHNRLEAYCKIEGVQTDVLITGIAAQN---RA-VEGDFVLIKVDR 227 (1113)
Q Consensus 180 ~G~lrVn~~N~~eAyV~~~g~~~Dv~I~G~~~rN---RA-l~GDvVaVeLlp 227 (1113)
+|++.--..+..-+||..++-..|||+.-..-.+ |. -.||.|.+++..
T Consensus 2 ~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~~~~l~~G~~V~F~~~~ 53 (66)
T PF00313_consen 2 TGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNGFRSLKEGDRVEFEVEE 53 (66)
T ss_dssp EEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSSSTS--TTSEEEEEEEE
T ss_pred eEEEEEEECCCCceEEEEcccceeEEeccccccccccccCCCCCEEEEEEEE
Confidence 6777655555678999999988899996553333 34 499999998744
Done!