Query psy4856
Match_columns 654
No_of_seqs 337 out of 1893
Neff 6.6
Searched_HMMs 46136
Date Fri Aug 16 19:24:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4856.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4856hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2102|consensus 100.0 3.5E-94 7.7E-99 843.4 36.5 583 2-641 105-881 (941)
2 PRK11642 exoribonuclease R; Pr 100.0 4.4E-81 9.5E-86 728.0 40.5 432 133-651 82-685 (813)
3 TIGR00358 3_prime_RNase VacB a 100.0 5E-81 1.1E-85 718.8 39.3 424 133-651 14-614 (654)
4 TIGR02063 RNase_R ribonuclease 100.0 2E-77 4.3E-82 696.5 40.9 425 133-651 66-669 (709)
5 PRK05054 exoribonuclease II; P 100.0 9.9E-76 2.1E-80 672.2 38.1 412 134-652 20-604 (644)
6 COG0557 VacB Exoribonuclease R 100.0 1.4E-75 3E-80 679.3 36.1 423 135-652 69-665 (706)
7 TIGR02062 RNase_B exoribonucle 100.0 9.3E-74 2E-78 654.8 38.1 413 133-652 16-602 (639)
8 COG4776 Rnb Exoribonuclease II 100.0 3.7E-37 7.9E-42 323.8 14.1 392 123-622 8-576 (645)
9 PF00773 RNB: RNB domain CAUTI 100.0 2.8E-31 6.1E-36 283.3 10.1 161 349-511 8-324 (325)
10 PF08206 OB_RNB: Ribonuclease 99.2 1.5E-11 3.2E-16 98.6 2.9 45 138-185 1-45 (58)
11 smart00357 CSP Cold shock prot 97.4 0.00035 7.6E-09 55.9 6.2 45 137-184 1-49 (64)
12 PF08206 OB_RNB: Ribonuclease 96.7 0.0021 4.5E-08 51.5 4.0 50 253-304 8-58 (58)
13 PF13638 PIN_4: PIN domain; PD 96.6 0.0027 5.9E-08 58.8 4.9 48 34-85 86-133 (133)
14 cd04471 S1_RNase_R S1_RNase_R: 96.6 0.002 4.4E-08 54.5 3.3 42 607-651 2-43 (83)
15 cd05686 S1_pNO40 S1_pNO40: pNO 96.1 0.0035 7.5E-08 52.3 2.5 40 606-648 3-42 (73)
16 smart00670 PINc Large family o 95.5 0.0088 1.9E-07 53.2 2.3 59 2-70 50-109 (111)
17 PRK08582 hypothetical protein; 95.3 0.011 2.4E-07 55.9 2.7 42 603-648 2-43 (139)
18 PLN00207 polyribonucleotide nu 95.0 0.023 4.9E-07 68.1 4.4 53 595-650 742-794 (891)
19 cd05684 S1_DHX8_helicase S1_DH 94.9 0.015 3.3E-07 49.1 2.1 40 607-648 1-41 (79)
20 TIGR00448 rpoE DNA-directed RN 94.8 0.007 1.5E-07 59.7 -0.3 50 597-651 72-121 (179)
21 cd04452 S1_IF2_alpha S1_IF2_al 94.8 0.018 3.9E-07 47.9 2.3 42 606-649 3-44 (76)
22 cd05689 S1_RPS1_repeat_ec4 S1_ 94.4 0.034 7.5E-07 45.8 2.9 36 606-645 3-38 (72)
23 cd05697 S1_Rrp5_repeat_hs5 S1_ 94.3 0.029 6.2E-07 46.0 2.2 39 607-649 1-39 (69)
24 cd05707 S1_Rrp5_repeat_sc11 S1 94.3 0.026 5.5E-07 46.2 1.9 39 607-649 1-39 (68)
25 PRK05807 hypothetical protein; 94.2 0.026 5.5E-07 53.3 1.9 42 602-648 1-42 (136)
26 TIGR02063 RNase_R ribonuclease 93.9 0.13 2.8E-06 61.3 7.5 70 240-312 68-138 (709)
27 cd05706 S1_Rrp5_repeat_sc10 S1 93.8 0.048 1E-06 45.1 2.7 40 605-648 2-41 (73)
28 cd05685 S1_Tex S1_Tex: The C-t 93.6 0.047 1E-06 43.9 2.2 38 607-648 1-38 (68)
29 PRK07252 hypothetical protein; 93.5 0.047 1E-06 50.4 2.4 41 605-649 2-42 (120)
30 cd05690 S1_RPS1_repeat_ec5 S1_ 93.5 0.045 9.8E-07 44.5 2.0 34 607-644 1-34 (69)
31 COG1098 VacB Predicted RNA bin 93.3 0.046 9.9E-07 50.2 1.8 39 605-647 4-42 (129)
32 cd05708 S1_Rrp5_repeat_sc12 S1 93.1 0.063 1.4E-06 44.5 2.2 40 606-648 2-41 (77)
33 cd04461 S1_Rrp5_repeat_hs8_sc7 93.0 0.07 1.5E-06 45.5 2.4 41 604-648 12-52 (83)
34 smart00357 CSP Cold shock prot 92.7 0.37 8.1E-06 38.1 6.2 51 253-305 9-64 (64)
35 cd04460 S1_RpoE S1_RpoE: RpoE, 92.5 0.088 1.9E-06 46.6 2.6 38 609-651 2-39 (99)
36 cd05698 S1_Rrp5_repeat_hs6_sc5 91.9 0.096 2.1E-06 42.8 1.9 37 607-647 1-37 (70)
37 PTZ00248 eukaryotic translatio 91.7 0.085 1.8E-06 56.5 1.7 50 598-649 6-58 (319)
38 cd05704 S1_Rrp5_repeat_hs13 S1 91.6 0.13 2.9E-06 42.8 2.4 39 606-648 3-42 (72)
39 cd05705 S1_Rrp5_repeat_hs14 S1 91.6 0.12 2.7E-06 43.3 2.2 39 605-647 2-40 (74)
40 cd04472 S1_PNPase S1_PNPase: P 91.0 0.15 3.4E-06 41.0 2.2 38 607-648 1-38 (68)
41 PHA02945 interferon resistance 90.1 0.27 5.9E-06 42.6 3.0 42 606-650 11-54 (88)
42 PF00575 S1: S1 RNA binding do 89.7 0.3 6.5E-06 40.3 2.9 39 604-646 2-40 (74)
43 cd05692 S1_RPS1_repeat_hs4 S1_ 89.2 0.26 5.7E-06 39.4 2.1 37 607-647 1-37 (69)
44 cd04473 S1_RecJ_like S1_RecJ_l 88.7 0.32 7E-06 40.9 2.4 37 605-645 15-51 (77)
45 cd05691 S1_RPS1_repeat_ec6 S1_ 88.1 0.34 7.4E-06 39.7 2.1 38 607-648 1-38 (73)
46 PRK08059 general stress protei 87.3 0.39 8.4E-06 44.4 2.3 40 605-648 6-45 (123)
47 COG0539 RpsA Ribosomal protein 87.0 0.59 1.3E-05 53.4 3.9 38 605-647 191-228 (541)
48 cd05696 S1_Rrp5_repeat_hs4 S1_ 86.7 0.48 1E-05 39.3 2.3 32 613-647 7-39 (71)
49 COG1095 RPB7 DNA-directed RNA 86.4 0.32 6.9E-06 47.9 1.2 50 597-651 72-121 (183)
50 PRK08563 DNA-directed RNA poly 85.7 0.55 1.2E-05 46.5 2.6 50 597-651 72-121 (187)
51 PRK11824 polynucleotide phosph 85.2 0.92 2E-05 54.0 4.5 42 603-648 618-659 (693)
52 TIGR03591 polynuc_phos polyrib 84.2 1 2.2E-05 53.4 4.3 41 604-648 616-656 (684)
53 cd05688 S1_RPS1_repeat_ec3 S1_ 83.0 0.77 1.7E-05 36.8 1.9 34 607-645 2-35 (68)
54 PRK11642 exoribonuclease R; Pr 82.5 5.1 0.00011 48.6 9.2 56 125-184 140-198 (813)
55 cd05703 S1_Rrp5_repeat_hs12_sc 82.3 0.91 2E-05 37.9 2.1 36 607-646 1-36 (73)
56 PRK07899 rpsA 30S ribosomal pr 81.9 0.89 1.9E-05 51.8 2.5 41 605-649 292-332 (486)
57 PRK07400 30S ribosomal protein 79.2 1.1 2.4E-05 48.3 1.9 38 605-647 195-232 (318)
58 TIGR02696 pppGpp_PNP guanosine 78.2 2.1 4.6E-05 50.7 4.0 37 604-644 645-681 (719)
59 smart00316 S1 Ribosomal protei 77.8 1.8 3.9E-05 34.4 2.4 38 606-647 2-39 (72)
60 COG0539 RpsA Ribosomal protein 77.7 1.7 3.7E-05 49.8 3.0 55 128-185 17-76 (541)
61 cd04453 S1_RNase_E S1_RNase_E: 76.8 2 4.3E-05 37.4 2.5 37 605-645 6-44 (88)
62 PF07497 Rho_RNA_bind: Rho ter 76.7 9.2 0.0002 32.7 6.4 50 135-186 2-57 (78)
63 cd05694 S1_Rrp5_repeat_hs2_sc2 75.1 2.3 5E-05 35.7 2.4 38 606-646 4-41 (74)
64 PRK07899 rpsA 30S ribosomal pr 75.0 3 6.5E-05 47.6 4.0 38 605-647 207-244 (486)
65 TIGR00358 3_prime_RNase VacB a 74.9 7.8 0.00017 46.0 7.6 65 240-308 16-81 (654)
66 cd05702 S1_Rrp5_repeat_hs11_sc 73.1 2.5 5.5E-05 34.6 2.1 36 608-647 2-37 (70)
67 PRK12269 bifunctional cytidyla 72.2 2.6 5.6E-05 51.3 2.7 43 601-647 746-789 (863)
68 PRK13806 rpsA 30S ribosomal pr 70.9 4.7 0.0001 46.1 4.4 41 604-648 200-240 (491)
69 PF00313 CSD: 'Cold-shock' DNA 70.0 13 0.00028 30.1 5.6 46 137-184 2-53 (66)
70 cd05695 S1_Rrp5_repeat_hs3 S1_ 69.7 3.2 7E-05 33.8 2.0 35 608-646 2-36 (66)
71 PRK13806 rpsA 30S ribosomal pr 69.6 2.9 6.2E-05 47.8 2.3 36 605-644 291-326 (491)
72 cd05693 S1_Rrp5_repeat_hs1_sc1 65.4 3.5 7.5E-05 36.8 1.5 37 606-646 3-39 (100)
73 cd00164 S1_like S1_like: Ribos 63.7 4.9 0.00011 31.1 1.9 32 613-647 3-34 (65)
74 PRK06676 rpsA 30S ribosomal pr 63.2 6.9 0.00015 43.2 3.6 41 601-646 187-227 (390)
75 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 62.1 6.5 0.00014 33.4 2.5 37 605-645 5-41 (86)
76 TIGR00717 rpsA ribosomal prote 61.6 5 0.00011 45.9 2.3 40 605-648 445-484 (516)
77 PTZ00162 DNA-directed RNA poly 61.0 5.1 0.00011 39.5 1.9 50 597-652 72-121 (176)
78 cd04458 CSP_CDS Cold-Shock Pro 60.6 21 0.00046 28.7 5.2 47 137-185 2-54 (65)
79 PRK09890 cold shock protein Cs 59.5 27 0.00059 29.0 5.7 48 136-185 5-58 (70)
80 cd04465 S1_RPS1_repeat_ec2_hs2 57.5 6.5 0.00014 31.8 1.6 36 607-647 1-36 (67)
81 PRK05054 exoribonuclease II; P 56.9 47 0.001 39.5 9.2 56 126-184 75-134 (644)
82 PRK10354 RNA chaperone/anti-te 56.9 33 0.00071 28.4 5.8 47 137-185 6-58 (70)
83 TIGR02062 RNase_B exoribonucle 56.6 46 0.001 39.5 9.1 51 130-183 76-130 (639)
84 COG1412 Uncharacterized protei 56.4 14 0.00031 34.9 3.9 38 38-85 87-124 (136)
85 PRK06676 rpsA 30S ribosomal pr 56.1 7.4 0.00016 42.9 2.4 38 605-646 276-313 (390)
86 PRK09937 stationary phase/star 54.7 27 0.00059 29.4 4.9 48 137-186 3-56 (74)
87 KOG1067|consensus 54.6 14 0.00031 42.3 4.1 36 609-648 671-706 (760)
88 cd04462 S1_RNAPII_Rpb7 S1_RNAP 53.4 14 0.00029 32.2 3.1 39 607-651 2-40 (88)
89 PRK09507 cspE cold shock prote 52.9 51 0.0011 27.3 6.3 50 135-186 3-58 (69)
90 PRK12269 bifunctional cytidyla 51.4 16 0.00035 44.6 4.3 40 604-648 491-530 (863)
91 PRK14998 cold shock-like prote 50.4 34 0.00075 28.7 4.9 47 137-185 3-55 (73)
92 cd05687 S1_RPS1_repeat_ec1_hs1 50.3 12 0.00025 30.4 2.1 37 607-647 1-37 (70)
93 PRK00087 4-hydroxy-3-methylbut 49.5 12 0.00026 44.3 2.8 39 605-647 561-599 (647)
94 PRK06299 rpsA 30S ribosomal pr 49.0 11 0.00025 43.6 2.5 38 605-646 372-409 (565)
95 cd04459 Rho_CSD Rho_CSD: Rho p 48.5 32 0.0007 28.6 4.4 47 137-185 2-54 (68)
96 COG1278 CspC Cold shock protei 47.3 27 0.00059 29.0 3.7 41 143-185 11-55 (67)
97 KOG2102|consensus 47.1 12 0.00025 46.3 2.2 37 615-651 473-509 (941)
98 TIGR00717 rpsA ribosomal prote 46.7 18 0.0004 41.3 3.7 37 605-645 358-394 (516)
99 COG2183 Tex Transcriptional ac 45.9 9.4 0.0002 45.4 1.1 40 606-649 658-697 (780)
100 PRK00215 LexA repressor; Valid 40.9 1.8E+02 0.004 28.8 9.4 41 227-272 149-189 (205)
101 TIGR02381 cspD cold shock doma 40.7 37 0.00081 27.9 3.6 48 137-186 3-56 (68)
102 PRK00087 4-hydroxy-3-methylbut 39.4 24 0.00052 41.8 3.2 37 605-646 476-512 (647)
103 PRK15463 cold shock-like prote 38.5 97 0.0021 25.8 5.8 49 136-186 5-59 (70)
104 PRK10943 cold shock-like prote 38.4 83 0.0018 26.0 5.4 49 136-186 4-58 (69)
105 PRK12423 LexA repressor; Provi 37.5 1.4E+02 0.0031 29.7 8.1 41 227-272 145-185 (202)
106 PRK06299 rpsA 30S ribosomal pr 36.7 34 0.00073 39.8 3.8 38 605-647 200-237 (565)
107 PRK15464 cold shock-like prote 34.7 1.1E+02 0.0025 25.4 5.6 47 136-185 5-58 (70)
108 COG1185 Pnp Polyribonucleotide 32.5 56 0.0012 38.6 4.6 39 604-646 617-655 (692)
109 PF05991 NYN_YacP: YacP-like N 30.8 90 0.002 30.3 5.2 67 58-128 94-160 (166)
110 COG1158 Rho Transcription term 30.7 84 0.0018 34.4 5.2 59 126-186 42-108 (422)
111 PRK07400 30S ribosomal protein 30.4 42 0.00091 36.2 3.0 35 606-645 118-152 (318)
112 cd04455 S1_NusA S1_NusA: N-uti 30.3 41 0.00089 27.2 2.3 36 605-645 2-37 (67)
113 PRK10276 DNA polymerase V subu 29.6 3.3E+02 0.0071 25.4 8.6 40 227-272 82-121 (139)
114 PRK09521 exosome complex RNA-b 27.4 33 0.00072 34.0 1.5 40 605-646 63-110 (189)
115 cd04454 S1_Rrp4_like S1_Rrp4_l 26.3 60 0.0013 27.2 2.7 38 605-646 5-42 (82)
116 TIGR00498 lexA SOS regulatory 24.6 3E+02 0.0065 27.1 7.8 41 227-272 142-182 (199)
117 COG0234 GroS Co-chaperonin Gro 24.1 1E+02 0.0022 27.4 3.7 39 175-235 7-45 (96)
118 PRK14533 groES co-chaperonin G 22.2 1.3E+02 0.0028 26.5 4.0 40 174-235 6-45 (91)
119 PRK09202 nusA transcription el 20.4 1.6E+02 0.0035 33.6 5.4 57 588-649 116-173 (470)
No 1
>KOG2102|consensus
Probab=100.00 E-value=3.5e-94 Score=843.35 Aligned_cols=583 Identities=37% Similarity=0.584 Sum_probs=482.5
Q ss_pred cccccCCC-CcEEEEecCccccccccCCCCCCccchhhHHHHHHHHHhHhhhhhhcc-CCeEEEEeCC---hhhHHHHhh
Q psy4856 2 KDLISNPS-RKFYVFVNEHHYETYVEQEPGESVNDRNDRALRRVATWYVKYEEHLES-AVRVILLSED---VRNRDLATQ 76 (654)
Q Consensus 2 r~l~~~~~-~~~~vF~Ne~~~~t~v~~~~~es~~drn~r~i~~aa~wY~~~~~Hl~~-~~~vvllt~d---~~~~~~a~~ 76 (654)
+.++.+.. ++|++|+||+++.||+++.++|+.++||+|+++.++.|| ..|++. .++++++|+| ..+..++..
T Consensus 105 ~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~---~~h~~~~~~~~~~~~~d~~~~~~~~~~~~ 181 (941)
T KOG2102|consen 105 RPLISADSTKRFILFHNEFSRSTFAERAKDESANDRNDRAIRPAANWY---DVHLPSLGPRVILVTTDVPSSVSRDNAVE 181 (941)
T ss_pred ccccccccccceeecccCCCchhhcccccCCCcchhcccccccccccc---hhcccccCcceEEEeccchhhhhhhcccc
Confidence 44555554 999999999999999999999999999999999999999 999994 5779999999 666778889
Q ss_pred cCcceeeHHHHHhhCCCCchhhhhhcccchhhccccCCCCCCCCCCHHHHHHhhhcCCeEEEEEEEecCCCceeEEeecC
Q psy4856 77 SGLLTSSIEGYISTLSNGEPLLDKLSKKEAVVETSVKDSLYPLHATPSEIHAGIKNQSLLQGSFQASRENFLEGQVNCEG 156 (654)
Q Consensus 77 ~gi~~~s~~~yv~~~~~~~~l~d~l~~~~~~~~~~~~~~~y~ehl~~~~l~~gik~g~l~~G~l~v~~~n~~egfV~~~~ 156 (654)
.|+...++++|++.+...+.+.|.+.+........+.+.+|++|||++.+.+||++|++++|+|+++++|+.||||..++
T Consensus 182 ~~i~~~~~~~y~~~~~~~~~l~~~l~~~~~~~~~~~~k~~~~~~l~~~~~~~~~~~g~~~~g~l~i~~~n~~e~~v~~~~ 261 (941)
T KOG2102|consen 182 HGIEPQTIKEYQKPLSPNHLLRDSLLQRVLESNFGSDKLLFSPYLPMAKIKAGIKSGRLVQGTLRISRKNLSEAFVRVQG 261 (941)
T ss_pred cccchhhhhhhccccCcchhhhhhhhhhcccccccccceeeccccchhhHhhhhcccceeeceEEecccccccceeeccc
Confidence 99999999999999987788999998655433222347899999999999999999999999999999999999999999
Q ss_pred CCcCeEecCCCCCCcCCCCCEEEEEEccCCCcCCccccccccC----CCCC-Ccccccc-ccccC--CCCCCCCCCCCce
Q psy4856 157 YDKPILVQGREGLNRAIDGDTVAVRLLPESQWSAPLELVLEDE----GSGE-DEEGEDG-KLIKG--NKTVPPAERRPTG 228 (654)
Q Consensus 157 ~~~dI~I~g~~~~NRAl~GD~V~Vellp~~~w~~~~~~~~~~~----~~~~-~~~~~~~-~~l~~--~~~~~~~~~~ptG 228 (654)
...+|+|.|.+++|||++||+|+|+++|.++|......+..+. ...+ .+..+|+ ..... .+........|+|
T Consensus 262 ~~~~v~i~G~~~~NRa~~gdvVavell~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~ 341 (941)
T KOG2102|consen 262 LDHPVLICGSKDRNRALDGDVVAVELLPVDEWRVELSSIFLDSVKVSSNIKESDDEDEDGTLNLRGKAVLSDPLPVQPTG 341 (941)
T ss_pred cCCceEEeCchhhhhhhcCCeEEEEeccchhccccchhhhcccccccccccccccccccccccccccccccccccccccc
Confidence 8889999999999999999999999999999953332222220 0000 0010111 10100 0011111135699
Q ss_pred eEEEEEeecCceeeeeecCCCC-----CCCceEEEEeCCCCCCcEEEccc-cccccCCCEEEEEEeecCCCCCCccEEEE
Q psy4856 229 QIVGIIKRKWRQYCGILQPNPL-----AGSSRHLFVPAERKIPKIRVETR-QIATLSGQRIVVAIDSWPRHSRYPQGHFV 302 (654)
Q Consensus 229 kVVgIi~R~~r~~vG~l~~~~~-----~~~~~~l~vP~D~riP~I~I~t~-q~~~l~~~rvvV~Id~Wp~~s~~P~Ghiv 302 (654)
+||+|++|+|++|||.+.+... +....++|+|.|+|+|+|+|+++ |+..+.+++++|.|+.||..|.||.||++
T Consensus 342 ~VV~il~r~~~~~~~~l~~~~~~~~~~~~~~~~~~~p~DkRvP~i~i~t~~~~~~~~~~~~~~~I~~W~~ts~~p~g~~v 421 (941)
T KOG2102|consen 342 KVVAILRRNWRQYVGGLLPLSEQALKGSSALIVLFIPSDKRVPLIRILTDDQAQDLIDKRIVAAIDRWPRTSLYPFGHLV 421 (941)
T ss_pred eEEEEEecCceeeeccccCcccccccccccceeeeccccCCCCeeeccccccccchhceeEEEEecccccCCcccCceeh
Confidence 9999999999999998876543 24779999999999999999999 99999999999999999999999999999
Q ss_pred EecCCCCChhhHHHHHhhcCCCCCCCCcHHHHhcCCC-CCCCCCC----C-C------ceeeeCCCCce---------ec
Q psy4856 303 RALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLPP-MPWEKST----G-R------PWCSGTSIGLS---------QI 361 (654)
Q Consensus 303 ~~LG~~gd~~~E~~~iL~e~~i~~~~Fs~~vl~~l~~-~~~~i~~----~-R------~~~tIDp~~~~---------~l 361 (654)
+.||.+|+.++|+++||.+|++++.+|+++++.|+|. .+|.+++ + | .+|+|||++|. .+
T Consensus 422 ~~lG~i~~~~~e~~aLL~en~v~~~~f~~~~~~~lp~~~~~~~~~~~~~~~R~Dlr~~~i~~IDp~~~~dlDdAL~~~~l 501 (941)
T KOG2102|consen 422 RELGTIGDTETETEALLLENGVPHKPFSQALLDCLPRSHPWPITEEELQKLRKDLRDLLIFSIDPPGATDLDDALHVRNL 501 (941)
T ss_pred hhccCcCCccchhhhhhhcCCCcccccCHHHHhcCCccCCCCcChHHhhhhhhhhhhceEEeecCCCccchhhhhheeec
Confidence 9999999999999999999999999999999999999 9999985 4 6 99999999998 46
Q ss_pred cCCeEEEEEEe-ccCCccCCCc----------eeeec-c-----CCcchhhhHHHH------Hhh---------------
Q psy4856 362 STGVISVGLEQ-GFPSLLKPRT----------TFVFY-D-----FPRTTRTNFILL------FLF--------------- 403 (654)
Q Consensus 362 ~~g~~~lgVHI-DVs~~V~~~s----------tsvYL-d-----LP~~Ls~~lcSL------la~--------------- 403 (654)
+||+|+||||| ||||||+||| ||||| + ||+.|++++||| +||
T Consensus 502 ~nG~~evGVHIADVt~fV~pgs~lD~eA~~R~ttvyL~q~~i~MLP~~L~~~lcSL~~g~dr~aFSvvwel~~~~~i~~~ 581 (941)
T KOG2102|consen 502 PNGNLEVGVHIADVTHFVKPGSALDREAARRGTTVYLVQKRIPMLPKLLSEELCSLRPGVDRLAFSVVWELDSDGSILKT 581 (941)
T ss_pred CCCcEEEEEEeccchhhcCCCCccCHHHHhhcceEEeccccccCCchhhhhhheeccCCCceeeEEEEEEEcCCCceeec
Confidence 79999999999 9999999999 99999 7 999999999999 565
Q ss_pred ------------------h----------------------------------hhcccccCCC---------ccc-----
Q psy4856 404 ------------------Q----------------------------------AVYFSSGMLQ---------QSD----- 417 (654)
Q Consensus 404 ------------------q----------------------------------al~l~~pe~~---------~~d----- 417 (654)
| |+.+.++|.. +.+
T Consensus 582 ~f~ksvI~s~~~lsye~Aq~~id~~~~~~~v~~~l~~l~~ia~~lr~~R~~~gal~l~~~e~~~~~d~~~~~p~~~e~~~ 661 (941)
T KOG2102|consen 582 WFGKSVIRSKAALSYEEAQDILDTPNSSDPLTSSLRLLHEIAKILRQKRLDNGALLLRSPELRFLLDEEKPNPQDVEVKE 661 (941)
T ss_pred eecchhcccchhhhHHHHHHHhcCCcccchhhhhHHHHHHHHHHHHHHHhccCCcccccHhHHhhhccCCCCccccceee
Confidence 0 7777777711 111
Q ss_pred -------------HHHHHHHHHHHhcCCc--eeeeCCChH------HHHHHHHhhcC---------------------CC
Q psy4856 418 -------------FHHYGLATPIYTHFTS--PIRRYADII------VHRLLAACIGA---------------------DA 455 (654)
Q Consensus 418 -------------~AN~~vA~~~~~~~p~--l~R~h~~p~------l~~~l~~~~g~---------------------~~ 455 (654)
+||.+||++|.+.||. ++|+||.|. +.+++.. .|+ .|
T Consensus 662 ~~~~n~lveEfmllaN~~vA~~I~~~f~~~alLR~hp~P~~~~~~~~~~~~~~-~g~~ld~sS~~~L~~Sl~r~~~~~~p 740 (941)
T KOG2102|consen 662 LTETNFLVEEFMLLANISVAEKILASFPSLALLRRHPSPPPENFKPLVSLCLE-LGFNLDTSSSKSLADSLDRIRDDDKP 740 (941)
T ss_pred eehhhhHHHHHHHHHhHHHHHHHHHhCCchhhhccCCCCccccccHHHHHHHH-cCCCccccchHHHhhhHhhhcCCchH
Confidence 4999999999999887 999998774 4444544 355 24
Q ss_pred chhHHHHHHhh--cc----cccc--cCCccccccCCCCCcccccCccccchhHHHHHHHHHHHhCCCCCCCccCHHHHHH
Q psy4856 456 TYPSLLDKKAS--TA----LCYN--LVSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLDKKASTA 527 (654)
Q Consensus 456 ~~~~llr~l~~--m~----~~s~--s~~~~~H~gLa~~~YTHfTSPIRRY~DLivHR~L~a~l~~~~~~~~~~~~~~l~~ 527 (654)
+++.++++|+. |+ ||+| +++.++|||||+++|||||||||||||++|||||++..... .+...+...+..
T Consensus 741 ~~~~~l~~l~~r~m~~A~yf~sg~~~~~~~~HygLa~p~YTHFTsPiRRY~DIivHrqL~~~~~~~--~~~~~~~~~l~~ 818 (941)
T KOG2102|consen 741 YLNTLLRILATRSMTRAVYFCSGSSDTPQFHHYGLASPLYTHFTSPIRRYADIIVHRQLAAAFLER--SPTAPDRPNLSS 818 (941)
T ss_pred HHHHHHHHHHhhhhhceeEEeecccCcchhhchhhcccchhhccCcccccchHHHHHHHHHHhhcc--CccccccccHHH
Confidence 67777777765 65 7888 67789999999999999999999999999999999633322 222334445666
Q ss_pred HHhcCCCCCCcCcccccCCCCCCCcccccCCccCccchhhHHHHHHHHhHHhhHHHHHHHHHHHHHHHHHHHHHhhcccC
Q psy4856 528 LCYNLPGCTDIDDALHCRPLPNGNIEVTYPSLGMSQSCKDIQACLLELGYNLNYRNRQAQYAGRASVALHTHLFFRRKSI 607 (654)
Q Consensus 528 ~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ln~r~r~A~~aer~~~~l~~~~~l~~~~g 607 (654)
+|. +||.|++.|+.|++++..+|.+.|++++ .
T Consensus 819 i~~-----------------------------------------------~~N~r~~~a~~a~~~S~~l~~~~~~k~~-~ 850 (941)
T KOG2102|consen 819 LAA-----------------------------------------------NCNERKKAAKKAQEASTELYLCEYLKDK-Q 850 (941)
T ss_pred HHh-----------------------------------------------hhhhhHHHHHHHHHhhHHHHHHHHHHhc-c
Confidence 666 9999999999999999999999999999 4
Q ss_pred cccceEEEcccccceEEEECCCCcccccceeeec
Q psy4856 608 TEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCR 641 (654)
Q Consensus 608 ~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~ 641 (654)
.... |+|++|.+-|+-++ ++-+ ++||.|+..
T Consensus 851 ~~~~-a~v~~V~~~~~~v~-ipe~-G~e~~v~l~ 881 (941)
T KOG2102|consen 851 VLEE-AVVLFVRPNGIDVV-IPEY-GLEGRVYLD 881 (941)
T ss_pred cccc-eEEEEEecCceEEE-Eccc-CceEEEEec
Confidence 5566 99999998887755 5544 489999998
No 2
>PRK11642 exoribonuclease R; Provisional
Probab=100.00 E-value=4.4e-81 Score=728.04 Aligned_cols=432 Identities=21% Similarity=0.288 Sum_probs=359.5
Q ss_pred CCeEEEEEEEecCCCceeEEeecCCCcCeEecCCCCCCcCCCCCEEEEEEccCCCcCCccccccccCCCCCCcccccccc
Q psy4856 133 QSLLQGSFQASRENFLEGQVNCEGYDKPILVQGREGLNRAIDGDTVAVRLLPESQWSAPLELVLEDEGSGEDEEGEDGKL 212 (654)
Q Consensus 133 g~l~~G~l~v~~~n~~egfV~~~~~~~dI~I~g~~~~NRAl~GD~V~Vellp~~~w~~~~~~~~~~~~~~~~~~~~~~~~ 212 (654)
..++.|+++++++|| |||..++.++||||++. +||.|||||+|.|++.+.+.
T Consensus 82 ~~~~~G~v~~~~~Gf--gFv~~e~~~~difI~~~-~l~~A~~GD~V~v~i~~~~~------------------------- 133 (813)
T PRK11642 82 LDLLKGTVIGHRDGY--GFLRVEGRKDDLYLSSE-QMKTCIHGDQVLAQPLGADR------------------------- 133 (813)
T ss_pred CceEEEEEEECCCcc--EEEEECCCCCCEEEChH-HHccCCCCCEEEEEEccCCC-------------------------
Confidence 458999999999999 99999865679999997 99999999999999875431
Q ss_pred ccCCCCCCCCCCCCceeEEEEEeecCceeeeeecCCCCCCCceEEEEeCCCCCC-cEEEcccccc-ccCCCEEEEEEeec
Q psy4856 213 IKGNKTVPPAERRPTGQIVGIIKRKWRQYCGILQPNPLAGSSRHLFVPAERKIP-KIRVETRQIA-TLSGQRIVVAIDSW 290 (654)
Q Consensus 213 l~~~~~~~~~~~~ptGkVVgIi~R~~r~~vG~l~~~~~~~~~~~l~vP~D~riP-~I~I~t~q~~-~l~~~rvvV~Id~W 290 (654)
..+|+|+||.|++|++..+||++... .+..+++|.|+|++ .|.|+..... ...|++|+|+|++|
T Consensus 134 ----------~~r~eg~Vv~IleR~~~~~vG~~~~~----~~~~~v~P~d~r~~~~i~i~~~~~~~~~~gd~V~v~I~~~ 199 (813)
T PRK11642 134 ----------KGRREARIVRVLVPKTSQIVGRYFTD----AGVGFVVPDDSRLSFDILIPPEQIMGARMGFVVVVELTQR 199 (813)
T ss_pred ----------CCCcEEEEEEEEecCCCEEEEEEEEe----CCeEEEEECCCCCCCcEEeccccccCCCCCCEEEEEEecC
Confidence 13589999999999999999999865 46788999999999 5999776554 34799999999999
Q ss_pred CCCCCCccEEEEEecCCCCChhhHHHHHhhcCCCCCCCCcHHHHhcCCCCCCCCCC----CC------ceeeeCCCCcee
Q psy4856 291 PRHSRYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLPPMPWEKST----GR------PWCSGTSIGLSQ 360 (654)
Q Consensus 291 p~~s~~P~Ghiv~~LG~~gd~~~E~~~iL~e~~i~~~~Fs~~vl~~l~~~~~~i~~----~R------~~~tIDp~~~~~ 360 (654)
|..+..|.|+|+++||..+|+.+|++++|.+|+||.. ||++|+++++.++|.+++ +| ++|||||++|++
T Consensus 200 p~~~~~~~g~iv~vLG~~~d~~~d~~~il~~~~ip~~-Fp~~v~~ea~~~~~~~~~~~~~~R~DLr~l~~vTID~~~akD 278 (813)
T PRK11642 200 PTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYI-WPQAVEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARD 278 (813)
T ss_pred CCcCCCCCEEEEEEecCCCCcchHHHHHHHHcCCCCC-CCHHHHHHHHhccccCChhHhccccccccCcEEEECCCCCCc
Confidence 9999999999999999999999999999999999997 999999999999998865 45 999999999983
Q ss_pred ---------ccCCeEEEEEEe-ccCCccCCCc----------eeeec-c-----CCcchhhhHHHH------Hhh-----
Q psy4856 361 ---------ISTGVISVGLEQ-GFPSLLKPRT----------TFVFY-D-----FPRTTRTNFILL------FLF----- 403 (654)
Q Consensus 361 ---------l~~g~~~lgVHI-DVs~~V~~~s----------tsvYL-d-----LP~~Ls~~lcSL------la~----- 403 (654)
+++|+|+||||| ||||||++|| ||+|| + ||+.||+++||| +||
T Consensus 279 ~DDAvsie~~~~g~~~L~VHIADVs~yV~~gS~LD~eA~~RgtSvYlpd~viPMLP~~Lsn~lcSL~p~~dRla~s~~~~ 358 (813)
T PRK11642 279 FDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMT 358 (813)
T ss_pred ccceEEEEEeCCCcEEEEEEecchhheeCCCCHHHHHHHHhCCeEeCCCceeeCCCHHHhcCccccCCCCceeEEEEEEE
Confidence 457899999999 9999999999 99999 7 999999999999 443
Q ss_pred ----------------------------h--------------------------------------hhcccccCCC---
Q psy4856 404 ----------------------------Q--------------------------------------AVYFSSGMLQ--- 414 (654)
Q Consensus 404 ----------------------------q--------------------------------------al~l~~pe~~--- 414 (654)
| ||+|++||.+
T Consensus 359 id~~G~v~~~~~~~svI~s~~rltY~~v~~~l~~~~~~~~~~~~~~~~L~~l~~la~~Lr~~R~~~Gai~~d~~E~~i~l 438 (813)
T PRK11642 359 ISSKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLREQYAPLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIF 438 (813)
T ss_pred ECCCCCCcCCEEEEEEEEECceECHHHHHHHHcCCcccchhhhHHHHHHHHHHHHHHHHHHHHHHCCCcccCCCceEEEE
Confidence 0 8999998832
Q ss_pred -----c---------------cc---HHHHHHHHHHHh-cCCceeeeCCChH------HHHHHHHhhcCC--------C-
Q psy4856 415 -----Q---------------SD---FHHYGLATPIYT-HFTSPIRRYADII------VHRLLAACIGAD--------A- 455 (654)
Q Consensus 415 -----~---------------~d---~AN~~vA~~~~~-~~p~l~R~h~~p~------l~~~l~~~~g~~--------~- 455 (654)
+ ++ +||++||+|+.+ ++|++||+|+.|+ |.+++... |+. +
T Consensus 439 d~~g~~~~i~~~~~~~a~~lIEE~MllAN~~vA~~l~~~~~p~lyR~H~~P~~ekl~~l~~~l~~l-G~~l~~~~~~~~~ 517 (813)
T PRK11642 439 NAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKPSTEAITSFRSVLAEL-GLELPGGNKPEPR 517 (813)
T ss_pred CCCCCEeeEEecccccHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEeCCCCCHHHHHHHHHHHHHc-CCcccCCCCCCHH
Confidence 0 01 499999999998 5999999999997 33444444 652 1
Q ss_pred chhHHHHHH--------------hhcc-cccccCCccccccCCCCCcccccCccccchhHHHHHHHHHHHhCCCCCCCcc
Q psy4856 456 TYPSLLDKK--------------ASTA-LCYNLVSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLL 520 (654)
Q Consensus 456 ~~~~llr~l--------------~~m~-~~s~s~~~~~H~gLa~~~YTHfTSPIRRY~DLivHR~L~a~l~~~~~~~~~~ 520 (654)
.++.+++.+ ++|+ ..+ ++++.+|||||++.||||||||||||||+|||+|+++|.+++.....+
T Consensus 518 ~~~~ll~~~~~~~~~~~l~~~llRsm~~A~Y-~~~~~gHfGLa~~~YtHFTSPIRRY~DLivHR~Lk~~L~~~~~~~~~~ 596 (813)
T PRK11642 518 DYAELLESVADRPDAEMLQTMLLRSMKQAIY-DPENRGHFGLALQSYAHFTSPIRRYPDLSLHRAIKYLLAKEQGHKGNT 596 (813)
T ss_pred HHHHHHHHHhCCcHHHHHHHHHHHhcccccc-CCCCCCccccccccccccCchhhhhHHHHHHHHHHHHHhCCCCccccc
Confidence 255555433 2344 222 588999999999999999999999999999999999997653210000
Q ss_pred CHHHHHHHHhcCCCCCCcCcccccCCCCCCCcccccCCccCccchhhHHHHHHHHhHHhhHHHHHHHHHHHHHHHHHHHH
Q psy4856 521 DKKASTALCYNLPGCTDIDDALHCRPLPNGNIEVTYPSLGMSQSCKDIQACLLELGYNLNYRNRQAQYAGRASVALHTHL 600 (654)
Q Consensus 521 ~~~~l~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ln~r~r~A~~aer~~~~l~~~~ 600 (654)
. ...+|.. ..+.|..++.|||.++|+|.+|+|++++++++.
T Consensus 597 ~---------------~~~~~~~------------------------~~~~l~~~~~~~s~~er~A~~aeR~~~~~~~~~ 637 (813)
T PRK11642 597 T---------------ETGGYHY------------------------SMEEMLQLGQHCSMTERRADEATRDVADWLKCD 637 (813)
T ss_pred c---------------ccccccc------------------------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 0 0011110 012345666799999999999999999999999
Q ss_pred HhhcccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccEEec
Q psy4856 601 FFRRKSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEVT 651 (654)
Q Consensus 601 ~l~~~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~~~~ 651 (654)
||++++|++|. |+|+++++||+| |+.+.. ++||+||+++|++|||+|+
T Consensus 638 ~m~~~iGe~f~-G~Is~V~~fGif-VeL~~~-~vEGlV~vs~L~~d~y~~d 685 (813)
T PRK11642 638 FMLDQVGNVFK-GVISSVTGFGFF-VRLDDL-FIDGLVHVSSLDNDYYRFD 685 (813)
T ss_pred hhhccCCcEEE-EEEEEeecCceE-EEECCC-CeeeeEEEeecCCcceEec
Confidence 99999999999 999999999999 877643 4999999999999999986
No 3
>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=5e-81 Score=718.84 Aligned_cols=424 Identities=19% Similarity=0.265 Sum_probs=356.4
Q ss_pred CCeEEEEEEEecCCCceeEEeecC-CCcCeEecCCCCCCcCCCCCEEEEEEccCCCcCCccccccccCCCCCCccccccc
Q psy4856 133 QSLLQGSFQASRENFLEGQVNCEG-YDKPILVQGREGLNRAIDGDTVAVRLLPESQWSAPLELVLEDEGSGEDEEGEDGK 211 (654)
Q Consensus 133 g~l~~G~l~v~~~n~~egfV~~~~-~~~dI~I~g~~~~NRAl~GD~V~Vellp~~~w~~~~~~~~~~~~~~~~~~~~~~~ 211 (654)
..+++|+++++++|| |||..++ .++||||++. +||+|||||+|.|+++++..
T Consensus 14 ~~~~~G~i~~~~~gf--gFv~~~~~~~~difI~~~-~~~~a~~GD~V~v~i~~~~~------------------------ 66 (654)
T TIGR00358 14 DDLVKGVVKAHNKGF--GFLRPDDDDKKDYFIPPP-QMKKVMHGDLVEACPLSQPQ------------------------ 66 (654)
T ss_pred CCeEEEEEEECCCcc--EEEEeCCCCCCcEEEchH-HhCcCCCCCEEEEEEeecCC------------------------
Confidence 457999999999999 9999976 3579999997 99999999999999987532
Q ss_pred cccCCCCCCCCCCCCceeEEEEEeecCceeeeeecCCCCCCCceEEEEeCCCCCCc-EEEccccc--cccCCCEEEEEEe
Q psy4856 212 LIKGNKTVPPAERRPTGQIVGIIKRKWRQYCGILQPNPLAGSSRHLFVPAERKIPK-IRVETRQI--ATLSGQRIVVAID 288 (654)
Q Consensus 212 ~l~~~~~~~~~~~~ptGkVVgIi~R~~r~~vG~l~~~~~~~~~~~l~vP~D~riP~-I~I~t~q~--~~l~~~rvvV~Id 288 (654)
+.+|+|+|++|++|+++.+||++... .+..+|+|.|+|++. |.|+.... ....|++|+|+|+
T Consensus 67 -----------~~~~~g~v~~il~r~~~~~vG~~~~~----~~~~~v~p~~~~~~~~i~i~~~~~~~~~~~g~~V~v~i~ 131 (654)
T TIGR00358 67 -----------RGRFEAEVERILEPALTRFVGKFLGE----NDFGFVVPDDPRIYLDIIVPKASVKNELAEGDKVVVELT 131 (654)
T ss_pred -----------CCCceEEEEEEeccCCCEEEEEEEEe----CCeEEEEECCCCCCCcEEEcCCccccCCCCCCEEEEEEc
Confidence 13489999999999999999999876 467899999999995 99976532 4568999999999
Q ss_pred ecCCCCCCccEEEEEecCCCCChhhHHHHHhhcCCCCCCCCcHHHHhcCCCCCCCCCC----CC------ceeeeCCCCc
Q psy4856 289 SWPRHSRYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLPPMPWEKST----GR------PWCSGTSIGL 358 (654)
Q Consensus 289 ~Wp~~s~~P~Ghiv~~LG~~gd~~~E~~~iL~e~~i~~~~Fs~~vl~~l~~~~~~i~~----~R------~~~tIDp~~~ 358 (654)
+||..+..|.|+|+++||..||+.+|++++|.+|+||.. ||++|+++++.++|.+++ .| ++|||||++|
T Consensus 132 ~~p~~~~~~~g~i~~~lG~~~d~~~~~~~il~~~~i~~~-f~~~v~~~a~~~~~~~~~~~~~~R~Dlr~~~~~TID~~~a 210 (654)
T TIGR00358 132 EYPLRRNLFYGEITQILGNNDDPLIPWWVTLARHEIPFE-FPDGVEQQAAKLQFDVDEQAKKYREDLTDLAFVTIDGADA 210 (654)
T ss_pred cCCCCCCCceEEEEEEEcCCCCcccHHHHHHHHcCcCCC-CCHHHHHHHHhccccCChhHhhCccccccCcEEEECCCCC
Confidence 999999999999999999999999999999999999986 999999999999998865 45 9999999999
Q ss_pred ee---------ccCCeEEEEEEe-ccCCccCCCc----------eeeec-c-----CCcchhhhHHHH------Hhh---
Q psy4856 359 SQ---------ISTGVISVGLEQ-GFPSLLKPRT----------TFVFY-D-----FPRTTRTNFILL------FLF--- 403 (654)
Q Consensus 359 ~~---------l~~g~~~lgVHI-DVs~~V~~~s----------tsvYL-d-----LP~~Ls~~lcSL------la~--- 403 (654)
++ +++|+|+||||| ||||||+||| ||+|| + ||+.||+++||| +||
T Consensus 211 ~D~DDAisie~~~~g~~~l~VHIADVs~~V~~~s~LD~eA~~R~tSvYlp~~~ipMLP~~Ls~~~cSL~p~~~R~a~s~~ 290 (654)
T TIGR00358 211 KDLDDAVYVKKLPDGGWKLYVAIADVSYYVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCE 290 (654)
T ss_pred CcccceEEEEEeCCCcEEEEEEEechhheeCCCCHHHHHHHHhCcCccCCCCeecCCCHHHhcCccccCCCCcceEEEEE
Confidence 93 467899999999 9999999999 99999 7 999999999999 444
Q ss_pred ------------------------------h--------------------------------------hhcccccCCC-
Q psy4856 404 ------------------------------Q--------------------------------------AVYFSSGMLQ- 414 (654)
Q Consensus 404 ------------------------------q--------------------------------------al~l~~pe~~- 414 (654)
| ||+|++||.+
T Consensus 291 ~~id~~G~i~~~~~~~svI~s~~rltY~~v~~~l~~~~~~~~~~~~~~~~L~~l~~la~~lr~~R~~~Gai~~~~~e~~~ 370 (654)
T TIGR00358 291 MTISAQGRITDNEFYPATIESKARLTYDKVNDWLENDDELQPEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKF 370 (654)
T ss_pred EEECCCCCEeEEEEEEEEEEECcEEcHHHHHHHHcCCcccchhhHHHHHHHHHHHHHHHHHHHHHHHCCCcccCCCceeE
Confidence 0 7889888832
Q ss_pred -------cc---------------c---HHHHHHHHHHHh-cCCceeeeCCChH---H---HHHHHHhhcCC-----C--
Q psy4856 415 -------QS---------------D---FHHYGLATPIYT-HFTSPIRRYADII---V---HRLLAACIGAD-----A-- 455 (654)
Q Consensus 415 -------~~---------------d---~AN~~vA~~~~~-~~p~l~R~h~~p~---l---~~~l~~~~g~~-----~-- 455 (654)
+. + +||++||+|+.+ .+|++||+|++|+ + .++++.. |+. .
T Consensus 371 ~~d~~g~~~~i~~~~~~~a~~lIeE~MilAN~~vA~~~~~~~~p~iyR~h~~p~~~~~~~l~~~~~~~-g~~~~~~~~~~ 449 (654)
T TIGR00358 371 IVDEEGRVIDIVAEVRRIAEKIIEEAMIVANICAARFLHNHKVPGIYRVHPGPSKKKLQSLLEFLAEL-GLTLPGGNAEN 449 (654)
T ss_pred EECCCCCeeEEEeccCcHHHHHHHHHHHHHHHHHHHHHHHcCCCeEEecCCCCCHHHHHHHHHHHHHc-CCCccCCCcCC
Confidence 10 0 499999999999 5899999999987 2 2334433 542 0
Q ss_pred ----chhHHHHH--------------Hhhcc-cccccCCccccccCCCCCcccccCccccchhHHHHHHHHHHHhCCCCC
Q psy4856 456 ----TYPSLLDK--------------KASTA-LCYNLVSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATY 516 (654)
Q Consensus 456 ----~~~~llr~--------------l~~m~-~~s~s~~~~~H~gLa~~~YTHfTSPIRRY~DLivHR~L~a~l~~~~~~ 516 (654)
.++.+++. +++|+ ..+ +++|.+|||||++.|||||||||||+||+|||||+++|.+++..
T Consensus 450 ~~~~~~~~~l~~~~~~~~~~~l~~~llr~m~~A~y-~~~~~~HfgL~~~~YthfTSPIRRY~DLivHr~L~a~l~~~~~~ 528 (654)
T TIGR00358 450 VTTLDGACWLREVKDRPEYEILVTRLLRSLSQAEY-SPEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQTD 528 (654)
T ss_pred CChHHHHHHHHHhhCCCHHHHHHHHHHHhhccccc-CCCCCCccccccccccccCCccccchHHHHHHHHHHHHcCCCCc
Confidence 12223221 23344 122 57899999999999999999999999999999999999876422
Q ss_pred C-CccCHHHHHHHHhcCCCCCCcCcccccCCCCCCCcccccCCccCccchhhHHHHHHHHhHHhhHHHHHHHHHHHHHHH
Q psy4856 517 P-SLLDKKASTALCYNLPGCTDIDDALHCRPLPNGNIEVTYPSLGMSQSCKDIQACLLELGYNLNYRNRQAQYAGRASVA 595 (654)
Q Consensus 517 ~-~~~~~~~l~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ln~r~r~A~~aer~~~~ 595 (654)
. ...+.+.+..+|. +||.++|+|.+|||++.+
T Consensus 529 ~~~~~~~~~l~~~~~-----------------------------------------------~~~~~er~a~~aer~~~~ 561 (654)
T TIGR00358 529 TERYQPQDELLQIAE-----------------------------------------------HCSDTERRARDAERDVAD 561 (654)
T ss_pred ccchhhHHHHHHHHH-----------------------------------------------HHHHHHHHHHHHHHHHHH
Confidence 1 1123344444444 999999999999999999
Q ss_pred HHHHHHhhcccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccEEec
Q psy4856 596 LHTHLFFRRKSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEVT 651 (654)
Q Consensus 596 l~~~~~l~~~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~~~~ 651 (654)
+|++.||++++|+++. |+|++++++|+| |+.+... +||+||++.|++++|+|+
T Consensus 562 ~~~~~yl~~~iG~~~~-g~I~~v~~~Gif-V~L~~~~-veGlV~~s~l~~d~y~~d 614 (654)
T TIGR00358 562 WLKCRYLLDKVGTEFS-GEISSVTRFGMF-VRLDDNG-IDGLIHISTLHNDYYVFD 614 (654)
T ss_pred HHHHHhhhhCCCcEEE-EEEEeEEcCcEE-EEecCCc-eEEEEEeEeCCCcceEEe
Confidence 9999999999999999 999999999999 7776554 999999999999999985
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=2e-77 Score=696.51 Aligned_cols=425 Identities=23% Similarity=0.360 Sum_probs=355.4
Q ss_pred CCeEEEEEEEecCCCceeEEeecC-CCcCeEecCCCCCCcCCCCCEEEEEEccCCCcCCccccccccCCCCCCccccccc
Q psy4856 133 QSLLQGSFQASRENFLEGQVNCEG-YDKPILVQGREGLNRAIDGDTVAVRLLPESQWSAPLELVLEDEGSGEDEEGEDGK 211 (654)
Q Consensus 133 g~l~~G~l~v~~~n~~egfV~~~~-~~~dI~I~g~~~~NRAl~GD~V~Vellp~~~w~~~~~~~~~~~~~~~~~~~~~~~ 211 (654)
..++.|++++++++| |||.+++ .+.+|||++. ++|+|+|||+|+|++++...
T Consensus 66 ~~~~~G~i~~~~~g~--gFv~~~~~~~~di~I~~~-~~~~a~~GD~Vlv~I~~~~~------------------------ 118 (709)
T TIGR02063 66 LKLVKGTVIAHRDGF--GFLRPEDDDEDDIFIPPR-QMNGAMHGDRVLVRITGKPD------------------------ 118 (709)
T ss_pred CCeEEEEEEECCCcc--EEEEECCCCCCcEEEChH-HhCcCCCCCEEEEEEecccC------------------------
Confidence 458999999999999 9999876 3579999986 99999999999999986421
Q ss_pred cccCCCCCCCCCCCCceeEEEEEeecCceeeeeecCCCCCCCceEEEEeCCCCCC-cEEEcccccc-ccCCCEEEEEEee
Q psy4856 212 LIKGNKTVPPAERRPTGQIVGIIKRKWRQYCGILQPNPLAGSSRHLFVPAERKIP-KIRVETRQIA-TLSGQRIVVAIDS 289 (654)
Q Consensus 212 ~l~~~~~~~~~~~~ptGkVVgIi~R~~r~~vG~l~~~~~~~~~~~l~vP~D~riP-~I~I~t~q~~-~l~~~rvvV~Id~ 289 (654)
...+++|+|+.|++|....+||++... .+..+|+|.|+|+| .|.|++.+.. ...|++|+|+|++
T Consensus 119 ----------~~~~~eg~Vv~Il~r~~~~~VG~~~~~----~~~~~v~p~d~~~~~~I~i~~~~~~~~~~g~~v~v~i~~ 184 (709)
T TIGR02063 119 ----------GGDRFEARVIKILERANDQIVGTFYIE----NGIGFVIPDDKRIYLDIFIPPEQILGAEEGDKVLVEITK 184 (709)
T ss_pred ----------CCCCceEEEEEEEeeCCCEEEEEEEEc----CcEEEEEECCCCCCCCEEECCccccCCCCCCEEEEEEcc
Confidence 124579999999999999999999876 46789999999998 5999877654 4579999999999
Q ss_pred cCCCCCCccEEEEEecCCCCChhhHHHHHhhcCCCCCCCCcHHHHhcCCCCCCCCCC----CC------ceeeeCCCCce
Q psy4856 290 WPRHSRYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLPPMPWEKST----GR------PWCSGTSIGLS 359 (654)
Q Consensus 290 Wp~~s~~P~Ghiv~~LG~~gd~~~E~~~iL~e~~i~~~~Fs~~vl~~l~~~~~~i~~----~R------~~~tIDp~~~~ 359 (654)
||..+.+|.|+|+++||..||+.+|++++|.+|+|+.. ||+++++++..++|.+++ +| ++|||||++|+
T Consensus 185 ~p~~~~~~~g~i~~~lg~~~d~~~~~~~il~~~~i~~~-f~~~v~~~a~~~~~~~~~~~~~~R~Dl~~~~~~tID~~~a~ 263 (709)
T TIGR02063 185 YPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPYE-FPEEVLDEAAKIPEEVPEEEIKGRKDLRDLPFVTIDGEDAK 263 (709)
T ss_pred CCCCCCCceEEEEEEeCCCCcccchHHHHHHHcCcCCC-CCHHHHHHHHhCCCCCChhHhhcccccccCcEEEECCCCCc
Confidence 99999999999999999999999999999999999996 999999999999998864 45 99999999998
Q ss_pred e---------ccCCeEEEEEEe-ccCCccCCCc----------eeeec-c-----CCcchhhhHHHH------Hhh----
Q psy4856 360 Q---------ISTGVISVGLEQ-GFPSLLKPRT----------TFVFY-D-----FPRTTRTNFILL------FLF---- 403 (654)
Q Consensus 360 ~---------l~~g~~~lgVHI-DVs~~V~~~s----------tsvYL-d-----LP~~Ls~~lcSL------la~---- 403 (654)
+ +++|+|+||||| ||||||+||| ||+|| + ||+.||+++||| +||
T Consensus 264 D~DDAisie~~~~g~~~l~VhIADVs~~V~~~s~lD~eA~~R~tSvYlp~~~ipMLP~~Ls~~~cSL~p~~~r~a~s~~~ 343 (709)
T TIGR02063 264 DFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEM 343 (709)
T ss_pred ccccEEEEEEcCCCCEEEEEEEechhhEeCCCChHHHHHHHhCeeEeCCCCcccCCChHHccCccccCCCCceEEEEEEE
Confidence 3 457889999999 9999999999 99999 7 999999999999 444
Q ss_pred -----------------------------h--------------------------------------hhcccccCCC--
Q psy4856 404 -----------------------------Q--------------------------------------AVYFSSGMLQ-- 414 (654)
Q Consensus 404 -----------------------------q--------------------------------------al~l~~pe~~-- 414 (654)
| ||+|+.||.+
T Consensus 344 ~id~~G~i~~~~~~~svI~s~~~ltY~~v~~~l~~~~~~~~~~~~~~~~L~~l~~la~~l~~~R~~~G~i~~~~~e~~~~ 423 (709)
T TIGR02063 344 EIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEGKDALDKKEPPLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKII 423 (709)
T ss_pred EECCCCCEEEeEEEEEEEEeCeEEcHHHHHHHHcCCccccchhhHHHHHHHHHHHHHHHHHHHHHhCCCcccCCccceeE
Confidence 0 7888888832
Q ss_pred ------c---------------cc---HHHHHHHHHHHh-cCCceeeeCCChH------HHHHHHHhhcCCC--------
Q psy4856 415 ------Q---------------SD---FHHYGLATPIYT-HFTSPIRRYADII------VHRLLAACIGADA-------- 455 (654)
Q Consensus 415 ------~---------------~d---~AN~~vA~~~~~-~~p~l~R~h~~p~------l~~~l~~~~g~~~-------- 455 (654)
+ ++ +||++||+|+.+ ++|++||+|++|+ +.++++.. |+..
T Consensus 424 ~d~~g~~~~i~~~~~~~a~~lIeE~MllAN~~vA~~l~~~~~p~iyR~h~~P~~~~~~~l~~~~~~~-g~~~~~~~~~~~ 502 (709)
T TIGR02063 424 LDENGKPIDIVPRERGDAHKLIEEFMIAANETVAEHLEKAKLPFIYRVHERPSEEKLQNLREFLKTL-GITLKGGTSDKP 502 (709)
T ss_pred ECCCCCeEEEEeccchHHHHHHHHHHHHHHHHHHHHHHhCCCCeEEecCCCCCHHHHHHHHHHHHHc-CCCccCCCCCCC
Confidence 0 01 499999999998 5899999999987 22334433 5421
Q ss_pred ---chhHHHHH--------------Hhhcc-cccccCCccccccCCCCCcccccCccccchhHHHHHHHHHHHhCCCCCC
Q psy4856 456 ---TYPSLLDK--------------KASTA-LCYNLVSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYP 517 (654)
Q Consensus 456 ---~~~~llr~--------------l~~m~-~~s~s~~~~~H~gLa~~~YTHfTSPIRRY~DLivHR~L~a~l~~~~~~~ 517 (654)
.++.+++. +++|+ ..+ ++.+.+|||||++.|||||||||||+||+|||||+++|.+++..+
T Consensus 503 ~~~~~~~~l~~~~~~~~~~~l~~~llr~m~~A~y-~~~~~~HfgL~~~~YthfTSPIRRY~DLivHr~L~~~l~~~~~~~ 581 (709)
T TIGR02063 503 QPKDFQKLLEKVKGRPEEELINTVLLRSMQQAKY-SPENIGHFGLALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENTT 581 (709)
T ss_pred CHHHHHHHHHHhhCCcHHHHHHHHHHHHhcCccc-CCCCCCccccccccccccCCccccchHHHHHHHHHHHHcCCCCCC
Confidence 13334332 23344 112 578999999999999999999999999999999999998664211
Q ss_pred C----ccCHHHHHHHHhcCCCCCCcCcccccCCCCCCCcccccCCccCccchhhHHHHHHHHhHHhhHHHHHHHHHHHHH
Q psy4856 518 S----LLDKKASTALCYNLPGCTDIDDALHCRPLPNGNIEVTYPSLGMSQSCKDIQACLLELGYNLNYRNRQAQYAGRAS 593 (654)
Q Consensus 518 ~----~~~~~~l~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ln~r~r~A~~aer~~ 593 (654)
+ ......+ .+++.|||.++|+|++|||++
T Consensus 582 ~~~~~~~~~~~l-----------------------------------------------~~~~~~~~~~er~a~~aer~~ 614 (709)
T TIGR02063 582 TEKEREYLEAKL-----------------------------------------------EEIAEHSSKTERRADEAERDV 614 (709)
T ss_pred ccccchhhHHHH-----------------------------------------------HHHHHHHHHHHHHHHHHHHHH
Confidence 0 1122334 444449999999999999999
Q ss_pred HHHHHHHHhhcccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccEEec
Q psy4856 594 VALHTHLFFRRKSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEVT 651 (654)
Q Consensus 594 ~~l~~~~~l~~~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~~~~ 651 (654)
.++|++.||++++|+++. |.|+++++||+| |+.+++ ++||+||+|.|+++||+|+
T Consensus 615 ~~~~~~~yl~~~iG~~~~-g~V~~v~~fGif-V~L~~~-~~eGlvhis~l~~d~~~~d 669 (709)
T TIGR02063 615 NDWKKAEYMSEKIGEEFE-GVISGVTSFGLF-VELENN-TIEGLVHISTLKDDYYVFD 669 (709)
T ss_pred HHHHHHHhhhccCCcEEE-EEEEEEEeCCEE-EEecCC-ceEEEEEeeecCCCcEEEc
Confidence 999999999999999999 999999999999 777654 3899999999999999885
No 5
>PRK05054 exoribonuclease II; Provisional
Probab=100.00 E-value=9.9e-76 Score=672.20 Aligned_cols=412 Identities=16% Similarity=0.178 Sum_probs=337.3
Q ss_pred CeEEEEEEEecCCCceeEEeecCCCcCeEecCCCCCCcCCCCCEEEEEEccCCCcCCccccccccCCCCCCccccccccc
Q psy4856 134 SLLQGSFQASRENFLEGQVNCEGYDKPILVQGREGLNRAIDGDTVAVRLLPESQWSAPLELVLEDEGSGEDEEGEDGKLI 213 (654)
Q Consensus 134 ~l~~G~l~v~~~n~~egfV~~~~~~~dI~I~g~~~~NRAl~GD~V~Vellp~~~w~~~~~~~~~~~~~~~~~~~~~~~~l 213 (654)
.+++|+++++++|| |||..++ .+||||++. +||.|||||+|.|++.++.
T Consensus 20 ~~~~G~~~~~~~gf--gFv~~~~-~~difI~~~-~l~~a~~GD~V~v~i~~~~--------------------------- 68 (644)
T PRK05054 20 PRVEGVVKATEKGF--GFLEVDA-QKSYFIPPP-QMKKVMHGDRIIAVIHTEK--------------------------- 68 (644)
T ss_pred CeEEEEEEECCCcc--EEEEECC-CCcEEEChH-HHccCCCCCEEEEEEecCC---------------------------
Confidence 57999999999999 9998755 469999997 9999999999999986431
Q ss_pred cCCCCCCCCCCCCceeEEEEEeecCceeeeeecCCCCCCCceEEEEeCCCCCC-cEEEccc-c-c-cccCCCEEEEEEee
Q psy4856 214 KGNKTVPPAERRPTGQIVGIIKRKWRQYCGILQPNPLAGSSRHLFVPAERKIP-KIRVETR-Q-I-ATLSGQRIVVAIDS 289 (654)
Q Consensus 214 ~~~~~~~~~~~~ptGkVVgIi~R~~r~~vG~l~~~~~~~~~~~l~vP~D~riP-~I~I~t~-q-~-~~l~~~rvvV~Id~ 289 (654)
.+++|+|++|++|+...+||++... .+..+++|.|.+++ .|.|+.. . . ....|++|+|+|++
T Consensus 69 ----------~r~~g~v~~il~r~~~~~vG~~~~~----~~~~~~~p~d~~~~~~i~i~~~~~~~~~~~~gd~V~v~i~~ 134 (644)
T PRK05054 69 ----------DREIAEPEELIEPFLTRFVGRVQKK----DDRLSIVPDHPLLKDAIPCRAAKGLNHEFKEGDWVVAELRR 134 (644)
T ss_pred ----------CCcEEEEEEEEecCCCEEEEEEEEe----CceEEEEECCCCCCccEEeccccccccCCCCCCEEEEEEec
Confidence 3469999999999999999999865 46789999999998 5898532 2 2 34579999999999
Q ss_pred cCCC-CCCccEEEEEecCCCCChhhHHHHHhhcCCCCCCCCcHHHHhc-CCCCCCCCCCCC------ceeeeCCCCce--
Q psy4856 290 WPRH-SRYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSY-LPPMPWEKSTGR------PWCSGTSIGLS-- 359 (654)
Q Consensus 290 Wp~~-s~~P~Ghiv~~LG~~gd~~~E~~~iL~e~~i~~~~Fs~~vl~~-l~~~~~~i~~~R------~~~tIDp~~~~-- 359 (654)
||.. ...|.|+|+++||..+|+.+|++++|.+|+||.+ ||+++++. ++. ... +| ++|||||++|+
T Consensus 135 ~p~~~~~~~~g~i~~~lG~~~d~~~d~~~il~~~~l~~~-f~~~~~~~~~~~--~~~--~R~Dlr~~~~~TID~~~akD~ 209 (644)
T PRK05054 135 HPLKGDRGFYAEITQFITDADDHFAPWWVTLARHNLERE-APAGGVAWEMLD--EGL--EREDLTALDFVTIDSASTEDM 209 (644)
T ss_pred CCCCCCCCceEEEEEEECCCCCCccHHHHHHHHcCCCCC-CCchhhhccCCh--hcc--CcccccCCcEEEECCCCCCcc
Confidence 9985 4569999999999999999999999999999997 99998752 221 111 33 99999999999
Q ss_pred -------eccCCeEEEEEEe-ccCCccCCCc----------eeeec-c-----CCcchhhhHHHH------Hhh------
Q psy4856 360 -------QISTGVISVGLEQ-GFPSLLKPRT----------TFVFY-D-----FPRTTRTNFILL------FLF------ 403 (654)
Q Consensus 360 -------~l~~g~~~lgVHI-DVs~~V~~~s----------tsvYL-d-----LP~~Ls~~lcSL------la~------ 403 (654)
++++|+|+||||| ||||||+||| ||+|| + ||+.||+++||| +||
T Consensus 210 DDAisve~~~~g~~~l~VHIADVs~yV~~gS~LD~eA~~RgtSvYlp~~vipMLP~~Ls~~~cSL~p~~~R~als~~~~i 289 (644)
T PRK05054 210 DDALYVEKLPDGGLQLTVAIADPTAYIAEGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTI 289 (644)
T ss_pred cceEEEEEeCCCCEEEEEEEcchhhEeCCCCHHHHHHHHhCceEeCCCCcccCCChHHhcCccccCCCCCceEEEEEEEE
Confidence 3467899999999 9999999999 99999 7 999999999999 443
Q ss_pred ----------------------------h--------------------------------------hhcccccCCC---
Q psy4856 404 ----------------------------Q--------------------------------------AVYFSSGMLQ--- 414 (654)
Q Consensus 404 ----------------------------q--------------------------------------al~l~~pe~~--- 414 (654)
| +++|++||.+
T Consensus 290 d~~G~i~~~~~~~~svI~s~~rltY~~v~~~l~~~~~~~~~~~~i~~~l~~L~~l~~~l~~~R~~~G~i~~d~~e~~i~l 369 (644)
T PRK05054 290 DADGTIEDDIRFFAAWIESKAKLAYDNVSDWLENGGDWQPESEAIAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFEL 369 (644)
T ss_pred eCCCCcccccEEEEEEEEcCCeecHHHHHHHHhCCCccccchhHHHHHHHHHHHHHHHHHHHHHhCCCccccCCceEEEE
Confidence 0 7888888722
Q ss_pred -----cc---------------c---HHHHHHHHHHHhc-CCceeeeCCChH------HHHHHHHhhcCCC---------
Q psy4856 415 -----QS---------------D---FHHYGLATPIYTH-FTSPIRRYADII------VHRLLAACIGADA--------- 455 (654)
Q Consensus 415 -----~~---------------d---~AN~~vA~~~~~~-~p~l~R~h~~p~------l~~~l~~~~g~~~--------- 455 (654)
+. + +||++||+|+.++ +|++||+|+.|+ +.++++.. |++.
T Consensus 370 d~~g~~~~i~~~~~~~a~~lIeE~MllAN~~vA~~l~~~~~p~iyRvH~~P~~~~l~~l~~~~~~~-g~~~~~~~~~~l~ 448 (644)
T PRK05054 370 GEKGEVLDIVAEPRRIANRIVEESMIAANICAARVLRDKLGFGIYNVHSGFDPANAEQAVALLKEH-GLHFDAEELLTLE 448 (644)
T ss_pred CCCCCEEEEEEecCcHHHHHHHHHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHHHC-CCCcCCCcccChH
Confidence 10 1 4999999999994 899999999887 33444444 6521
Q ss_pred chhHHHHH-------------HhhcccccccCCccccccCCCCCcccccCccccchhHHHHHHHHHHHhCCCCCCCccCH
Q psy4856 456 TYPSLLDK-------------KASTALCYNLVSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLDK 522 (654)
Q Consensus 456 ~~~~llr~-------------l~~m~~~s~s~~~~~H~gLa~~~YTHfTSPIRRY~DLivHR~L~a~l~~~~~~~~~~~~ 522 (654)
.++.+++. ++.|+....++++.+|||||++.|||||||||||+||+|||||+++|.+++.+.
T Consensus 449 ~~~~~~~~l~~~~~~~l~~~llr~~~~a~ys~~~~gHfgL~~~~YthfTSPIRRY~DLivHR~L~a~l~~~~~~~----- 523 (644)
T PRK05054 449 GFCKLRRELDAQPTGYLDSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAER----- 523 (644)
T ss_pred HHHHHHHHHhcchHHHHHHHHHHHHhceecCCCCcCccccccccccccCChhhhhHHHHHHHHHHHHHcCCCCCc-----
Confidence 12233332 223431111688999999999999999999999999999999999998765321
Q ss_pred HHHHHHHhcCCCCCCcCcccccCCCCCCCcccccCCccCccchhhHHHHHHHHhHHhhHHHHHHHHHHHHHHHHHHHHHh
Q psy4856 523 KASTALCYNLPGCTDIDDALHCRPLPNGNIEVTYPSLGMSQSCKDIQACLLELGYNLNYRNRQAQYAGRASVALHTHLFF 602 (654)
Q Consensus 523 ~~l~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ln~r~r~A~~aer~~~~l~~~~~l 602 (654)
.++++|. ++|.++|+|++|+|++.+++++.||
T Consensus 524 -~~~~~~~-----------------------------------------------~~s~~er~a~~aer~~~~~~~~~y~ 555 (644)
T PRK05054 524 -PQDEITV-----------------------------------------------QLAERRRLNRMAERDVGDWLYARYL 555 (644)
T ss_pred -cHHHHHH-----------------------------------------------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1344555 9999999999999999999999999
Q ss_pred hcccCc--ccceEEEcccccceEEEECCCCcccccceeeeccCCCccEEecC
Q psy4856 603 RRKSIT--EEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEVTY 652 (654)
Q Consensus 603 ~~~~g~--~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~~~~~ 652 (654)
++++|+ +|. |+|+++++|||| |+.... .+||+||+++|+++||+|.|
T Consensus 556 ~~~~G~~~~f~-g~I~~v~~~G~f-V~l~~~-~veglV~~~~l~~~~~~y~~ 604 (644)
T PRK05054 556 KDKAGTDTRFA-AEIIDISRGGMR-VRLLEN-GAVAFIPASFLHAVRDELVC 604 (644)
T ss_pred hhccCCCeEEE-EEEEeeecCcEE-EEEeCC-ceEEEEEccccCCCccceEE
Confidence 999975 999 999999999999 766644 59999999999999877643
No 6
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=100.00 E-value=1.4e-75 Score=679.32 Aligned_cols=423 Identities=27% Similarity=0.433 Sum_probs=365.8
Q ss_pred eEEEEEEEecCCCceeEEeecC--CCcCeEecCCCCCCcCCCCCEEEEEEccCCCcCCccccccccCCCCCCcccccccc
Q psy4856 135 LLQGSFQASRENFLEGQVNCEG--YDKPILVQGREGLNRAIDGDTVAVRLLPESQWSAPLELVLEDEGSGEDEEGEDGKL 212 (654)
Q Consensus 135 l~~G~l~v~~~n~~egfV~~~~--~~~dI~I~g~~~~NRAl~GD~V~Vellp~~~w~~~~~~~~~~~~~~~~~~~~~~~~ 212 (654)
+++|++..++.|| ||+..++ ...|++|+.. .||+|++||.|.|++.+.+.+.
T Consensus 69 ~~~~~~~~~~~gf--~f~~~~~~~~~~d~~v~~~-~~~~a~~gD~V~v~~~~~~~~~----------------------- 122 (706)
T COG0557 69 LVEGIVEASAKGF--GFLSPDDSKDADDIFVPKD-PLNRALHGDRVLVELLPSDKRG----------------------- 122 (706)
T ss_pred cccceEEeccCCc--eeeccCccCCCCcEEeccc-cccccccCCEEEEEECcccccC-----------------------
Confidence 8999999999999 9999987 5679999997 8999999999999997765421
Q ss_pred ccCCCCCCCCCCCCceeEEEEEeecCceeeeeecCCCCCCCceEEEEeCCCCCC-cEEEcccccc-ccCCCEEEEEEeec
Q psy4856 213 IKGNKTVPPAERRPTGQIVGIIKRKWRQYCGILQPNPLAGSSRHLFVPAERKIP-KIRVETRQIA-TLSGQRIVVAIDSW 290 (654)
Q Consensus 213 l~~~~~~~~~~~~ptGkVVgIi~R~~r~~vG~l~~~~~~~~~~~l~vP~D~riP-~I~I~t~q~~-~l~~~rvvV~Id~W 290 (654)
..++|+|++|++|+++.++|++.+. .+..+++|.|+|+| .|.|++.+.. ...|++++|+|+.|
T Consensus 123 -----------~~~~~~v~~il~r~~~~~vG~~~~~----~~~~~~~p~d~r~~~~i~i~~~~~~~~~~~~~v~~~i~~~ 187 (706)
T COG0557 123 -----------RFKEAAVVRILERANSALVGELRPS----QGIGRVLPDDKRLPFLIAIPPEQAPGAEEGHLVVVEITRW 187 (706)
T ss_pred -----------CCceEEEEeeeccccceeEEEEEec----CCeEEEEecCCCCccceeeccccccccccCCEEEEEeccc
Confidence 1489999999999999999999987 46899999999999 7999998877 66899999999999
Q ss_pred CCCCCCccEEEEEecCCCCChhhHHHHHhhcCCCCCCCCcHHHHhcCCCCCCCCCC----CC------ceeeeCCCCce-
Q psy4856 291 PRHSRYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLPPMPWEKST----GR------PWCSGTSIGLS- 359 (654)
Q Consensus 291 p~~s~~P~Ghiv~~LG~~gd~~~E~~~iL~e~~i~~~~Fs~~vl~~l~~~~~~i~~----~R------~~~tIDp~~~~- 359 (654)
|..+++|.|+++++||..+++.++++++|++|++++. ||++|++|+...++.+++ +| ++|||||++|+
T Consensus 188 ~~~~~~~~g~v~~~lG~~~~~~~~~~~il~~~~i~~~-f~~~v~~~a~~~~~~~~~~~~~~R~Dlr~l~~~TID~~~akD 266 (706)
T COG0557 188 PDTSRPPFGEVVEVLGDLGDPGADIEAILRDHGIPSE-FPEKVLDEAAALPDEVPEEDLKGRVDLRDLPIFTIDPEDAKD 266 (706)
T ss_pred CCcCCCCceeEEEeecCCCCcchhHHHHHHHcCCCCC-CCHHHHHHHHhccCcCChhhhcCccccccCCEEEECCCCCcc
Confidence 9999999999999999999999999999999999998 999999999998887755 55 89999999998
Q ss_pred --------eccCCeEEEEEEe-ccCCccCCCc----------eeeec-c-----CCcchhhhHHHH------Hhh-----
Q psy4856 360 --------QISTGVISVGLEQ-GFPSLLKPRT----------TFVFY-D-----FPRTTRTNFILL------FLF----- 403 (654)
Q Consensus 360 --------~l~~g~~~lgVHI-DVs~~V~~~s----------tsvYL-d-----LP~~Ls~~lcSL------la~----- 403 (654)
++.||+|+||||| ||||||+||| ||||| + ||+.||+++||| ||+
T Consensus 267 ~DDAv~~~~l~~g~~~LgVhIADVs~yV~p~s~LD~EA~~RgtSVYlp~~vipMLPe~Ls~~lcSL~p~~dRla~s~~m~ 346 (706)
T COG0557 267 LDDAVSVEKLRNGGYRLGVHIADVSHYVQPGSALDKEARKRGTSVYLPDRVIPMLPEALSNGLCSLNPGVDRLALSCEMT 346 (706)
T ss_pred ccceEEEEEeCCCcEEEEEEEecceeecCCCChhhHHHHHcCCeEEcCCcccCCCchhhcCCccccCCCCceEEEEEEEE
Confidence 4578999999999 9999999999 99999 7 999999999999 444
Q ss_pred ----------------------------h------------------------------------hhcccccCCC-----
Q psy4856 404 ----------------------------Q------------------------------------AVYFSSGMLQ----- 414 (654)
Q Consensus 404 ----------------------------q------------------------------------al~l~~pe~~----- 414 (654)
| ||+|+++|.+
T Consensus 347 ld~~g~v~~~~~~~svI~s~~rltY~~v~~~l~~~~~~~~~~l~~~l~~~~~l~~~l~~~R~~rg~i~~~~~E~ki~~d~ 426 (706)
T COG0557 347 LDSEGRVKKYEIYPSVIKSAARLTYEEVQAILDGKEDDKYAPLLDSLLELLELAKILKKKRLSRGAIDFDTPEAKIVLDE 426 (706)
T ss_pred ECCCCCEEEEEEEEEEEeccccCCHHHHHHHHhcCcchhcccchHHHHHHHHHHHHHHHHHHhCCCcccCCcceeEEECC
Confidence 0 7999999832
Q ss_pred ---ccc------------------HHHHHHHHHHHhc-CCceeeeCCChH------HHHHHHHhhcCC---------C-c
Q psy4856 415 ---QSD------------------FHHYGLATPIYTH-FTSPIRRYADII------VHRLLAACIGAD---------A-T 456 (654)
Q Consensus 415 ---~~d------------------~AN~~vA~~~~~~-~p~l~R~h~~p~------l~~~l~~~~g~~---------~-~ 456 (654)
+.+ +||++||+++.++ .|.+||+|+.|+ +.+++... |+. + .
T Consensus 427 ~~~~~~i~~~~r~~a~~lIee~Ml~AN~~vA~~l~~~~~~~~~R~h~~P~~ek~~~l~~~l~~l-g~~~~~~~~~~~~~~ 505 (706)
T COG0557 427 EGRPVEIEIRERLDAEKLIEEFMLLANETVAEHLEKHKIPLLYRTHERPSTEKLQSLREFLQNL-GLVLPLGGSKPQPQD 505 (706)
T ss_pred CCCeeeEEEecccHHHHHHHHHHHHHHHHHHHHHHHcCCCcceeCCCCCCHHHHHHHHHHHHHc-CceecCCCCcCCHHH
Confidence 111 4999999999995 588999999996 34555554 651 1 2
Q ss_pred hhHHHHH--------------Hhhcc--cccccCCccccccCCCCCcccccCccccchhHHHHHHHHHHHhCCCCCCCcc
Q psy4856 457 YPSLLDK--------------KASTA--LCYNLVSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLL 520 (654)
Q Consensus 457 ~~~llr~--------------l~~m~--~~s~s~~~~~H~gLa~~~YTHfTSPIRRY~DLivHR~L~a~l~~~~~~~~~~ 520 (654)
++.++.. +++|+ .| ++.+.+|||||++.|||||||||||+||+|||||+++|.+++.+.+..
T Consensus 506 ~~~~l~~~~~~~~~~v~~~~~lRsm~~a~Y--s~~~~~HfgL~~~~YtHFTSPIRRY~DLivHR~L~~~l~~~~~~~~~~ 583 (706)
T COG0557 506 YQILLETVKGRPLEAVLQTLLLRSMKQAEY--SPDNVGHFGLALDYYTHFTSPIRRYPDLIVHRQLKALLSGEPIPEKKT 583 (706)
T ss_pred HHHHHhhccCChHHHHHHHHHHHhhhcCee--cCCCCCceeccccchhccCCchhhchHHHHHHHHHHHhcCCCCCccch
Confidence 3333322 22244 23 578999999999999999999999999999999999999876554332
Q ss_pred CHHHHHHHHhcCCCCCCcCcccccCCCCCCCcccccCCccCccchhhHHHHHHHHhHHhhHHHHHHHHHHHHHHHHHHHH
Q psy4856 521 DKKASTALCYNLPGCTDIDDALHCRPLPNGNIEVTYPSLGMSQSCKDIQACLLELGYNLNYRNRQAQYAGRASVALHTHL 600 (654)
Q Consensus 521 ~~~~l~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ln~r~r~A~~aer~~~~l~~~~ 600 (654)
....+..+|. ++|.++|+|++|+|++..+|++.
T Consensus 584 ~~~~l~~i~~-----------------------------------------------~~s~~er~a~~aer~~~~~~~~~ 616 (706)
T COG0557 584 SEEELDELAA-----------------------------------------------HISSAERRAQEAERDVIDLLKAE 616 (706)
T ss_pred hHHHHHHHHH-----------------------------------------------HhCHHHHHHHHHHHHHHHHHHHH
Confidence 3455666665 99999999999999999999999
Q ss_pred HhhcccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccEEecC
Q psy4856 601 FFRRKSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEVTY 652 (654)
Q Consensus 601 ~l~~~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~~~~~ 652 (654)
||++++|++|. |+|++|.++|+| |+.+.+. +||+||+++|+++||.|..
T Consensus 617 ~m~~~vg~~f~-g~V~~v~~~g~~-V~l~~~~-ieglV~~s~L~~d~y~~~~ 665 (706)
T COG0557 617 YMKKRVGEEFD-GVVTGVTSFGFF-VELPELG-LEGLVHISSLPDDYYHFDE 665 (706)
T ss_pred HHHHhcCCEEE-EEEEEEEeccEE-EEecccc-cccceEcccCCCceeeecc
Confidence 99999999999 999999999999 7677654 8999999999999999976
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=9.3e-74 Score=654.78 Aligned_cols=413 Identities=16% Similarity=0.182 Sum_probs=336.8
Q ss_pred CCeEEEEEEEecCCCceeEEeecCCCcCeEecCCCCCCcCCCCCEEEEEEccCCCcCCccccccccCCCCCCcccccccc
Q psy4856 133 QSLLQGSFQASRENFLEGQVNCEGYDKPILVQGREGLNRAIDGDTVAVRLLPESQWSAPLELVLEDEGSGEDEEGEDGKL 212 (654)
Q Consensus 133 g~l~~G~l~v~~~n~~egfV~~~~~~~dI~I~g~~~~NRAl~GD~V~Vellp~~~w~~~~~~~~~~~~~~~~~~~~~~~~ 212 (654)
..+++|+++++++|| |||..++ .+||||++. +||.|||||+|.|++.++.
T Consensus 16 ~~~~~G~i~~~~kGf--gFv~~~~-~~difI~~~-~l~~A~~GD~V~v~i~~~~-------------------------- 65 (639)
T TIGR02062 16 TPRVEGVVKATEKGF--GFLEVDA-QKSYFIPPP-QMKKVMHGDKIIAVIHSEK-------------------------- 65 (639)
T ss_pred CceEEEEEEECCCcc--EEEEECC-CCcEEEChH-HHccCCCCCEEEEEEecCC--------------------------
Confidence 357999999999999 9997655 569999997 9999999999999987532
Q ss_pred ccCCCCCCCCCCCCceeEEEEEeecCceeeeeecCCCCCCCceEEEEeCCCCCCc-EEEccc-cc--cccCCCEEEEEEe
Q psy4856 213 IKGNKTVPPAERRPTGQIVGIIKRKWRQYCGILQPNPLAGSSRHLFVPAERKIPK-IRVETR-QI--ATLSGQRIVVAID 288 (654)
Q Consensus 213 l~~~~~~~~~~~~ptGkVVgIi~R~~r~~vG~l~~~~~~~~~~~l~vP~D~riP~-I~I~t~-q~--~~l~~~rvvV~Id 288 (654)
.+++|+|++|++|+...++|++... .+..+++|.|++++. |.+... .. ....|++|+|+|+
T Consensus 66 -----------~r~~~~v~~iver~~~~~vG~~~~~----~~~~~v~p~d~~~~~~i~~~~~~~~~~~~~~gd~V~v~I~ 130 (639)
T TIGR02062 66 -----------ERESAEPEELIEPFLTRFVGKVQGK----DDKLAIVPDHPLLKDAIPCRAAKGLNHEFQEGDWAVAELR 130 (639)
T ss_pred -----------CCcEEEEEEEEccCCCEEEEEEEEe----CCeEEEEECCCCCCccEEecCccccccCCCCCCEEEEEEe
Confidence 3468999999999999999999876 467899999999986 444322 21 2337999999999
Q ss_pred ecCCCC-CCccEEEEEecCCCCChhhHHHHHhhcCCCCCCCCcHHHHhcCCCCCCCCCCCC------ceeeeCCCCce--
Q psy4856 289 SWPRHS-RYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLPPMPWEKSTGR------PWCSGTSIGLS-- 359 (654)
Q Consensus 289 ~Wp~~s-~~P~Ghiv~~LG~~gd~~~E~~~iL~e~~i~~~~Fs~~vl~~l~~~~~~i~~~R------~~~tIDp~~~~-- 359 (654)
+||... ..|.|+|+++||..+|+.+|++++|.+|+||.+ ||+++++++.. .. .+| ++|||||++|+
T Consensus 131 ~~p~~~~~~~~~~I~~vLG~~~d~~~d~~~il~~~~l~~~-f~~~v~~ea~~--~~--~~R~DLr~~~~~TID~~~akD~ 205 (639)
T TIGR02062 131 RHPLKGDRSFYAELTQYITFADDHLAPWWVTLARHNLERE-EPDGVADEMLL--DG--LVREDLTALDFVTIDSESTKDM 205 (639)
T ss_pred ccCCCCCCCceEEEEEEeCCCCCCccHHHHHHHHcCcCCC-CCHHHHHhhhh--cc--ccCcccccCCEEEECCCCCCcc
Confidence 999855 569999999999999999999999999999997 99999998854 11 134 99999999998
Q ss_pred -------eccCCeEEEEEEe-ccCCccCCCc----------eeeec-c-----CCcchhhhHHHH------Hhh------
Q psy4856 360 -------QISTGVISVGLEQ-GFPSLLKPRT----------TFVFY-D-----FPRTTRTNFILL------FLF------ 403 (654)
Q Consensus 360 -------~l~~g~~~lgVHI-DVs~~V~~~s----------tsvYL-d-----LP~~Ls~~lcSL------la~------ 403 (654)
++++|+|+||||| ||||||+||| ||+|| + ||+.||+++||| +||
T Consensus 206 DDAisie~~~~g~~~L~VHIADVs~yV~~gS~LD~eA~~RgtSvYLp~~vipMLP~~Ls~~~cSL~p~e~R~als~~~~l 285 (639)
T TIGR02062 206 DDALFAEALPNGKLQLIVAIADPTAYIAEGSKLDKAAKIRGFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRITI 285 (639)
T ss_pred cceEEEEEeCCCcEEEEEEEcCccccCCCCCHHHHHHHHhCCcEeCCCceecCCCHHHhcCccccCCCCCeeEEEEEEEE
Confidence 3467899999999 9999999999 99999 7 999999999999 443
Q ss_pred ----------------------------h--------------------------------------hhcccccCCC---
Q psy4856 404 ----------------------------Q--------------------------------------AVYFSSGMLQ--- 414 (654)
Q Consensus 404 ----------------------------q--------------------------------------al~l~~pe~~--- 414 (654)
| ++.|++||.+
T Consensus 286 d~~G~i~~~~~~~~svIrs~~rltY~~v~~~l~~~~~~~~~~~~i~~~L~~L~~la~~l~~~R~~~G~i~ld~pE~~~~l 365 (639)
T TIGR02062 286 SKDGNIEDKIEFFAATIKSKAKLVYDQVSDWLENTSDWQPESEEIAQQVRLLHQFCQARIEWRHTHALVFKDRPDYRFIL 365 (639)
T ss_pred cCCCcEeecCEEEEEEEEeCcEEeHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHhCCcccccCCceEEEE
Confidence 0 6777888722
Q ss_pred -----cc---------------c---HHHHHHHHHHHh-cCCceeeeCCChH---H---HHHHHHhhcCCC---------
Q psy4856 415 -----QS---------------D---FHHYGLATPIYT-HFTSPIRRYADII---V---HRLLAACIGADA--------- 455 (654)
Q Consensus 415 -----~~---------------d---~AN~~vA~~~~~-~~p~l~R~h~~p~---l---~~~l~~~~g~~~--------- 455 (654)
+. + +||++||+|+.+ .+|++||+|+.|+ + .+++... |+..
T Consensus 366 d~~g~~~~i~~~~~~~a~~lIeE~MllAN~~vA~~l~~~~~p~iyR~H~~P~~~~l~~l~~~~~~~-g~~~~~~~~~~~~ 444 (639)
T TIGR02062 366 SEKGEVLDIVAEPRRIANRIVEEAMIIANICAARFLRDKLGFGIYNTHAGFDPANAENVVALLKTN-GLHVDAEELATLD 444 (639)
T ss_pred CCCCCEEEEEEecCCHHHHHHHHHHHHHHHHHHHHHHHhCCCeEEecCCCCCHHHHHHHHHHHHHc-CCCCCcccccCHH
Confidence 10 1 499999999998 5899999999997 2 2334333 5521
Q ss_pred chhHHHHHH-------------hhcccccccCCccccccCCCCCcccccCccccchhHHHHHHHHHHHhCCCCCCCccCH
Q psy4856 456 TYPSLLDKK-------------ASTALCYNLVSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLDK 522 (654)
Q Consensus 456 ~~~~llr~l-------------~~m~~~s~s~~~~~H~gLa~~~YTHfTSPIRRY~DLivHR~L~a~l~~~~~~~~~~~~ 522 (654)
.++.+++.+ ++|.....++++.+|||||++.|||||||||||+||+|||||+++|.+++.+.
T Consensus 445 ~~~~~~~~~~~~~~~~l~~~~~r~~~~a~ys~~~~~HfgL~~~~YthfTSPIRRY~DLivHR~L~~~l~~~~~~~----- 519 (639)
T TIGR02062 445 GFCKLRRELDAQETGYLDSRIRRYQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATR----- 519 (639)
T ss_pred HHHHHHHHhhcchHHHHHHHHHHHhhhcccCCCCcCcchhccccccccCChhhhhHHHHHHHHHHHHHcCCCCCC-----
Confidence 122233222 22331111688999999999999999999999999999999999998664321
Q ss_pred HHHHHHHhcCCCCCCcCcccccCCCCCCCcccccCCccCccchhhHHHHHHHHhHHhhHHHHHHHHHHHHHHHHHHHHHh
Q psy4856 523 KASTALCYNLPGCTDIDDALHCRPLPNGNIEVTYPSLGMSQSCKDIQACLLELGYNLNYRNRQAQYAGRASVALHTHLFF 602 (654)
Q Consensus 523 ~~l~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ln~r~r~A~~aer~~~~l~~~~~l 602 (654)
.++++|. +||.++|+|++|+|++.++|++.||
T Consensus 520 -~~~~~~~-----------------------------------------------~~s~~er~a~~aeR~~~~~~~~~yl 551 (639)
T TIGR02062 520 -PQEDITV-----------------------------------------------QLAERRRLNRIAERDVADWLYARFL 551 (639)
T ss_pred -CHHHHHH-----------------------------------------------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1344555 9999999999999999999999999
Q ss_pred hcccCc--ccceEEEcccccceEEEECCCCcccccceeeeccCCC--ccEEecC
Q psy4856 603 RRKSIT--EEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPN--GNIEVTY 652 (654)
Q Consensus 603 ~~~~g~--~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~--~~~~~~~ 652 (654)
++++|+ +|. |+|+++.++|+| |+... +.+||+||+++|++ |+|+|.+
T Consensus 552 ~~~~g~~~~f~-g~I~~v~~~g~~-v~l~~-~~~~g~v~~~~l~~~~~~~~~~~ 602 (639)
T TIGR02062 552 ADKAAKNTRFA-AEIVDISRGGMR-VRLLE-NGAIAFIPAAFLHANREELVCNQ 602 (639)
T ss_pred hhccCCCcEEE-EEEEeeeCCcEE-EEEec-CceEEEEEhhhcCCCCcceEEcc
Confidence 999965 899 999999999999 76654 46999999999999 7787775
No 8
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=100.00 E-value=3.7e-37 Score=323.80 Aligned_cols=392 Identities=18% Similarity=0.221 Sum_probs=287.8
Q ss_pred HHHHHHhhhcCC-eEEEEEEEecCCCceeEEeecCCCcCeEecCCCCCCcCCCCCEEEEEEccCCCcCCccccccccCCC
Q psy4856 123 PSEIHAGIKNQS-LLQGSFQASRENFLEGQVNCEGYDKPILVQGREGLNRAIDGDTVAVRLLPESQWSAPLELVLEDEGS 201 (654)
Q Consensus 123 ~~~l~~gik~g~-l~~G~l~v~~~n~~egfV~~~~~~~dI~I~g~~~~NRAl~GD~V~Vellp~~~w~~~~~~~~~~~~~ 201 (654)
+++|.+.|.+.+ -+.|++..+.++| ||+.++. .+..||++. +|...||||.+..-|..+.+..
T Consensus 8 LaQLKqqlh~~~prvEGvVK~tekgf--GFLEvD~-qkSYFIpPp-~MKkvMHGDkIiA~i~te~erE------------ 71 (645)
T COG4776 8 LAQLKQQLHSQTPRVEGVVKATEKGF--GFLEVDA-QKSYFIPPP-QMKKVMHGDKIIAVIHTEKERE------------ 71 (645)
T ss_pred HHHHHHHHhhcCcccceeeeeccccc--eeEEEcC-ccccccCCH-HHhhhcccCeEEEEEEecCccc------------
Confidence 466777777764 6889999999999 9999985 578999997 9999999999999887654310
Q ss_pred CCCccccccccccCCCCCCCCCCCCceeEEEEEeecCceeeeeecCCCCCCCceEEEEeCCCCCCcEEEccccccc----
Q psy4856 202 GEDEEGEDGKLIKGNKTVPPAERRPTGQIVGIIKRKWRQYCGILQPNPLAGSSRHLFVPAERKIPKIRVETRQIAT---- 277 (654)
Q Consensus 202 ~~~~~~~~~~~l~~~~~~~~~~~~ptGkVVgIi~R~~r~~vG~l~~~~~~~~~~~l~vP~D~riP~I~I~t~q~~~---- 277 (654)
...|+. .|+-....|||.++.. .+...++|+.+.+-+- |+.++...
T Consensus 72 ---------------------~aEPe~----LiEp~LtRFvgkV~~k----d~rL~i~pDhP~lk~~-i~~~~~k~l~~~ 121 (645)
T COG4776 72 ---------------------SAEPEE----LIEPFLTRFVGKVQGK----DDRLQIVPDHPLLKDA-IPCRAAKGLNEE 121 (645)
T ss_pred ---------------------ccChHH----HHHHHHHHHHHHHhcc----CCceEEcCCChhhhhh-cccccccchhhh
Confidence 011222 3344455688888765 5678889988877653 55555442
Q ss_pred -cCCCEEEEEEeecCC-CCCCccEEEEEecCCCCChhhHHHHHhhcCCCCCCCCcHHHHhcCCCCCCCCCC---CC----
Q psy4856 278 -LSGQRIVVAIDSWPR-HSRYPQGHFVRALGPIGDKDTENEVLLLEHDVPHSKFSDLVLSYLPPMPWEKST---GR---- 348 (654)
Q Consensus 278 -l~~~rvvV~Id~Wp~-~s~~P~Ghiv~~LG~~gd~~~E~~~iL~e~~i~~~~Fs~~vl~~l~~~~~~i~~---~R---- 348 (654)
..|+++|+.+...|- +.+.....+.+.+-..+|.-+-+++.|.+|+++.++ +.. ..+|.+-+ .|
T Consensus 122 fQeGDW~VA~lk~HpLkgDr~F~a~lt~~It~~dD~l~PWWVTLArh~l~r~~--p~g-----~~d~~m~d~~l~RedLT 194 (645)
T COG4776 122 FQEGDWAVAELKRHPLKGDRSFYAELTQKITFADDHLAPWWVTLARHNLEREA--PAG-----IVDTEMLDEGLVREDLT 194 (645)
T ss_pred hhcCceehhhhhcCCCCCchhHHHHHHHHhhccCCcccceeeehhhccCCccC--CCc-----ccchhhhhhhhhhcccc
Confidence 379999999999986 456666778888888999999999999999999762 111 12333322 34
Q ss_pred --ceeeeCCCCce---------eccCCeEEEEEEe-ccCCccCCCc----------eeeec-c-----CCcchhhhHHHH
Q psy4856 349 --PWCSGTSIGLS---------QISTGVISVGLEQ-GFPSLLKPRT----------TFVFY-D-----FPRTTRTNFILL 400 (654)
Q Consensus 349 --~~~tIDp~~~~---------~l~~g~~~lgVHI-DVs~~V~~~s----------tsvYL-d-----LP~~Ls~~lcSL 400 (654)
.++|||.++++ .+++|.|.|-|+| |.|.|+++|| .|.|| . ||+.||.++|||
T Consensus 195 aL~FvTID~~sT~DmDDALy~~~~~~~~~~L~vAIADPTAyI~~~s~ld~~A~~R~FTnYLPGfNIPMLPreLsd~lCSL 274 (645)
T COG4776 195 ALDFVTIDSESTEDMDDALYAEPLPDGDWQLIVAIADPTAYIAEGSKLDKEAKIRAFTNYLPGFNIPMLPRELSDDLCSL 274 (645)
T ss_pred ccceEEecCccccccchhhhccccCCCcEEEEEEecCCccccCCcchhhHHHHHHHHhhcCCCCCCCCCChhhhhhhhhc
Confidence 89999999887 4678999999999 9999999999 78999 6 999999999999
Q ss_pred ------Hhh-----------------------------------------------------h-----------------
Q psy4856 401 ------FLF-----------------------------------------------------Q----------------- 404 (654)
Q Consensus 401 ------la~-----------------------------------------------------q----------------- 404 (654)
+|+ |
T Consensus 275 ~~ne~RPaL~C~it~~~~G~I~~~i~F~aA~i~SkakL~YdhVSDwlE~~~~WqPe~~~iAqqi~~L~~~~~aR~~WRk~ 354 (645)
T COG4776 275 RANEVRPALACRITIDKDGNITDKIRFFAATIESKAKLVYDHVSDWLENTGDWQPESEAIAQQIRLLHQFCQARIEWRKT 354 (645)
T ss_pred cccccCceEEEEEEEecCCccccchhhHHHhhhhhhhhhhhhHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 222 0
Q ss_pred -hhccc-ccCCC--------ccc------------------HHHHHHHHHHHhcCCc-eeeeCCChH------HHHHHHH
Q psy4856 405 -AVYFS-SGMLQ--------QSD------------------FHHYGLATPIYTHFTS-PIRRYADII------VHRLLAA 449 (654)
Q Consensus 405 -al~l~-~pe~~--------~~d------------------~AN~~vA~~~~~~~p~-l~R~h~~p~------l~~~l~~ 449 (654)
|+-|. .|++. ..+ +||.|+|+++.+++.+ +|-+|..-+ ...+++.
T Consensus 355 hal~FkdrpdYrF~l~e~g~V~~I~ae~RRiAnriVEE~MI~ANIcAa~~L~~~~gfGI~N~HsGFd~~~~e~a~~~l~~ 434 (645)
T COG4776 355 HALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEESMIAANICAARVLREKLGFGIYNVHSGFDPANAEAAAALLKT 434 (645)
T ss_pred ceeeccCCCceEEEecCCCceEeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcceeeccccCCHHHHHHHHHHHHh
Confidence 55543 35522 111 4999999999998765 999999443 2334443
Q ss_pred hhcCCC---------chhHHHHHHhhc------------c-cccccCCccccccCCCCCcccccCccccchhHHHHHHHH
Q psy4856 450 CIGADA---------TYPSLLDKKAST------------A-LCYNLVSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLA 507 (654)
Q Consensus 450 ~~g~~~---------~~~~llr~l~~m------------~-~~s~s~~~~~H~gLa~~~YTHfTSPIRRY~DLivHR~L~ 507 (654)
. |..- .|.+|-|-+... + |..-+.++.+|||||++.|+.||||||+|.|+|+||+|+
T Consensus 435 ~-~~~~~~e~l~Tl~Gfc~lRr~l~~~~t~yld~RiRrfqsfae~~t~p~PHFglGl~~YATWTSPIRKY~DMiNHRLlK 513 (645)
T COG4776 435 N-GLNVDAEELLTLEGFCKLRRELDAQPTGYLDSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLK 513 (645)
T ss_pred c-CcCCCHHHHhhhHHHHHHHHHhhccccchHHHHHHHHHhHHhhccCcCccccccchheeeccchhhhhhhHHHHHHHH
Confidence 3 3311 122232222221 1 111167899999999999999999999999999999999
Q ss_pred HHHhCCCCCCCccCHHHHHHHHhcCCCCCCcCcccccCCCCCCCcccccCCccCccchhhHHHHHHHHhHHhhHHHHHHH
Q psy4856 508 ACIGADATYPSLLDKKASTALCYNLPGCTDIDDALHCRPLPNGNIEVTYPSLGMSQSCKDIQACLLELGYNLNYRNRQAQ 587 (654)
Q Consensus 508 a~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ln~r~r~A~ 587 (654)
++|.+++... ... .+.. .|.++.|..+
T Consensus 514 avi~~~~~~k--Pqe----di~v-----------------------------------------------~lae~Rr~nr 540 (645)
T COG4776 514 AVIKGETAEK--PQE----DITV-----------------------------------------------QLAERRRLNR 540 (645)
T ss_pred HHHcCCCcCC--Cch----HHHH-----------------------------------------------HHHHHHHhhh
Confidence 9998775322 111 1222 6788899999
Q ss_pred HHHHHHHHHHHHHHhhcccCc--ccceEEEcccccce
Q psy4856 588 YAGRASVALHTHLFFRRKSIT--EEEVARRTDLRHLD 622 (654)
Q Consensus 588 ~aer~~~~l~~~~~l~~~~g~--~~~~~~i~~~~~~g 622 (654)
.|||++-++.-++||+++.++ .|. |-|.++.--|
T Consensus 541 maERdv~DWLY~r~L~~k~~~~~~F~-AEI~Di~R~G 576 (645)
T COG4776 541 MAERDVADWLYARFLADKAGTNTRFA-AEIQDISRGG 576 (645)
T ss_pred hhhhhhHHHHHHHHhccccccCchhh-hhhhhhccCc
Confidence 999999999999999999876 466 7777665444
No 9
>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=99.97 E-value=2.8e-31 Score=283.30 Aligned_cols=161 Identities=27% Similarity=0.414 Sum_probs=110.2
Q ss_pred ceeeeCCCCce---------eccCCeEEEEEEe-ccCCccCCCc----------eeeec-c-----CCcchhhhHHHH--
Q psy4856 349 PWCSGTSIGLS---------QISTGVISVGLEQ-GFPSLLKPRT----------TFVFY-D-----FPRTTRTNFILL-- 400 (654)
Q Consensus 349 ~~~tIDp~~~~---------~l~~g~~~lgVHI-DVs~~V~~~s----------tsvYL-d-----LP~~Ls~~lcSL-- 400 (654)
++|||||++++ .+++|+|+||||| |||+||+||| +|+|| + ||+.|++++|||
T Consensus 8 ~~~tID~~~~~d~DDAisie~~~~~~~~v~VHIaDvt~~i~~~s~ld~~A~~r~~s~Ylp~~~~pMlP~~l~~~~~SL~~ 87 (325)
T PF00773_consen 8 PVFTIDPPGAKDIDDAISIEKLPDGKYEVGVHIADVTSFIPPDSPLDREARKRGTSVYLPEKVVPMLPPELSEDLCSLNP 87 (325)
T ss_dssp EEEEEESTTSS---EEEEEEEETTTEEEEEEEEE-GGGTS-TTSHHHHHHHHH-B-EEETTEEE-SS-HHHHCTTSSTTB
T ss_pred CEEEEcCCCCCCCCCeEEEEECCCCcEEEEEEcCCHHHhhccChHHHHHHHhcCccEECCCCccccCChhHhcccccCCC
Confidence 79999999998 4567889999999 9999999999 99999 6 999999999999
Q ss_pred ----Hhh---------------------------------h-------------------------------------hh
Q psy4856 401 ----FLF---------------------------------Q-------------------------------------AV 406 (654)
Q Consensus 401 ----la~---------------------------------q-------------------------------------al 406 (654)
+|| + |+
T Consensus 88 ~~~r~a~S~~~~l~~~G~i~~~~i~~s~I~~~~~lty~~v~~~l~~~~~~~~~~~~~~~L~~l~~la~~l~~~R~~~Ga~ 167 (325)
T PF00773_consen 88 GKDRLAFSVIFTLDEDGEILDYEIYPSIIRSVARLTYEEVDEILEGKSQEEPESPIEEDLKLLYELAKALRKKRLSRGAI 167 (325)
T ss_dssp TSEEEEEEEEEEE-TTS-EEEEEEEEEEEEBSEEEEHHHHHHHHHTTTS--HCSHCHHHHHHHHHHHHHHHHHHHHTTS-
T ss_pred CCCceEEEEEEEEeeCCeEeeeEEEEEEEecccccCHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHHhhhhccCc
Confidence 333 0 56
Q ss_pred cc-cccCCC--------------cc---c------------HHHHHHHHHHHh-cCCceeeeCCChH---HHHHHHHhhc
Q psy4856 407 YF-SSGMLQ--------------QS---D------------FHHYGLATPIYT-HFTSPIRRYADII---VHRLLAACIG 452 (654)
Q Consensus 407 ~l-~~pe~~--------------~~---d------------~AN~~vA~~~~~-~~p~l~R~h~~p~---l~~~l~~~~g 452 (654)
.+ +.|+.. .. . +||.+||+|+.+ ++|++||+|+.|+ ++++++.. +
T Consensus 168 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~lV~E~MilAN~~vA~~~~~~~ip~iyR~~~~p~~~~~~~~~~~~-~ 246 (325)
T PF00773_consen 168 ELFNSPELKFSLDEDGPPKEINRESSDESSPAHSLVEELMILANRAVAQFLSENGIPAIYRVQPEPDPERLEELLKLL-K 246 (325)
T ss_dssp ----SHCEEEEEETTTTEEEEEEE------HHHHHHHHHHHHHHHHHHHHHHHCTTTSEEEEB-SSSCCCHHHHHHHH-T
T ss_pred cccCCCceEEEEecCCCcceEEEEeccCCchHHHHHHHHHHHHHHHHHHHHHHcCCCceeeeCCCCCHHHHHHHHHHh-c
Confidence 66 445410 01 1 499999999998 5999999999886 55555544 2
Q ss_pred C-----------------CCchhHHHH--HHhhcc-cccccCCccccccCCCCCcccccCccccchhHHHHHHHHHHHh
Q psy4856 453 A-----------------DATYPSLLD--KKASTA-LCYNLVSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIG 511 (654)
Q Consensus 453 ~-----------------~~~~~~llr--~l~~m~-~~s~s~~~~~H~gLa~~~YTHfTSPIRRY~DLivHR~L~a~l~ 511 (654)
+ ++.....+. .++.|+ ..+ ++.|.+|||||++.|||||||||||+||+|||||+++|.
T Consensus 247 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~a~y-~~~p~~H~~L~l~~Yt~~TSPlRRY~Dl~~hrql~~~L~ 324 (325)
T PF00773_consen 247 LDLDETKSLTLQNLLQAENPPNSLALRYLLLKTLPPAEY-STEPSGHFGLGLPAYTHFTSPLRRYADLVVHRQLKAALR 324 (325)
T ss_dssp ---STCHHHCHHCHHCCCCTTSSHHHHHHHHCCC--EEE-ESSGC-BTTTTBSS-B--S-TTTBHHHHHHHHHHHHHHH
T ss_pred CCCCCcchhhHHHHHHhcCChHHHHHHHHHHHhhccccc-ccCCCcceeeeccccccccChhhhhHHHHHHHHHHHHhh
Confidence 1 111111111 122243 111 578899999999999999999999999999999999985
No 10
>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=99.16 E-value=1.5e-11 Score=98.63 Aligned_cols=45 Identities=36% Similarity=0.581 Sum_probs=37.0
Q ss_pred EEEEEecCCCceeEEeecCCCcCeEecCCCCCCcCCCCCEEEEEEccC
Q psy4856 138 GSFQASRENFLEGQVNCEGYDKPILVQGREGLNRAIDGDTVAVRLLPE 185 (654)
Q Consensus 138 G~l~v~~~n~~egfV~~~~~~~dI~I~g~~~~NRAl~GD~V~Vellp~ 185 (654)
|+|++++++| |||.+++..+||||+.. +||.|||||+|.|++.+.
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 8999999999 99999988899999997 999999999999999983
No 11
>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=97.44 E-value=0.00035 Score=55.94 Aligned_cols=45 Identities=20% Similarity=0.352 Sum_probs=38.8
Q ss_pred EEEEEEecCCCceeEEeecCCCcCeEecCCCC----CCcCCCCCEEEEEEcc
Q psy4856 137 QGSFQASRENFLEGQVNCEGYDKPILVQGREG----LNRAIDGDTVAVRLLP 184 (654)
Q Consensus 137 ~G~l~v~~~n~~egfV~~~~~~~dI~I~g~~~----~NRAl~GD~V~Vellp 184 (654)
+|++.....+| ||+..++...+|||... + ++.+++||.|.+++..
T Consensus 1 ~G~i~~~~~g~--gfv~~~~~~~~i~v~~~-~~~~~~~~~~~Gd~V~~~i~~ 49 (64)
T smart00357 1 TGVVKWFNKGF--GFIRPDDGGKDVFVHPS-QIQGGLKSLREGDEVEFKVVS 49 (64)
T ss_pred CeEEEEEcCCe--eEEecCCCCccEEEEhH-HhhcCCCcCCCCCEEEEEEEE
Confidence 58999988898 99999765569999876 5 8899999999999875
No 12
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=96.68 E-value=0.0021 Score=51.54 Aligned_cols=50 Identities=20% Similarity=0.486 Sum_probs=39.0
Q ss_pred CceEEEEeCCCCCCcEEEcccccc-ccCCCEEEEEEeecCCCCCCccEEEEEe
Q psy4856 253 SSRHLFVPAERKIPKIRVETRQIA-TLSGQRIVVAIDSWPRHSRYPQGHFVRA 304 (654)
Q Consensus 253 ~~~~l~vP~D~riP~I~I~t~q~~-~l~~~rvvV~Id~Wp~~s~~P~Ghiv~~ 304 (654)
+++.|++|.| .-..|+|+.+++. ++.|++|+|+|.. +...+.|+|.|+++
T Consensus 8 ~GfGFv~~~~-~~~DifIp~~~l~~A~~gD~V~v~i~~-~~~~~~~eg~vv~V 58 (58)
T PF08206_consen 8 KGFGFVIPDD-GGEDIFIPPRNLNGAMDGDKVLVRITP-PSRGKRPEGEVVEV 58 (58)
T ss_dssp SS-EEEEECT--TEEEEE-HHHHTTS-TT-EEEEEEEE-SSSEEEEEEEEEE-
T ss_pred CCCEEEEECC-CCCCEEECHHHHCCCCCCCEEEEEEec-CCCCCCCCEEEEeC
Confidence 5789999999 4457999998765 6799999999999 88889999999985
No 13
>PF13638 PIN_4: PIN domain; PDB: 2HWW_C 2HWX_A 2DOK_B 2HWY_B 2WP8_J.
Probab=96.60 E-value=0.0027 Score=58.78 Aligned_cols=48 Identities=27% Similarity=0.349 Sum_probs=36.6
Q ss_pred cchhhHHHHHHHHHhHhhhhhhccCCeEEEEeCChhhHHHHhhcCcceeeHH
Q psy4856 34 NDRNDRALRRVATWYVKYEEHLESAVRVILLSEDVRNRDLATQSGLLTSSIE 85 (654)
Q Consensus 34 ~drn~r~i~~aa~wY~~~~~Hl~~~~~vvllt~d~~~~~~a~~~gi~~~s~~ 85 (654)
..++|..|..+|.|| +.+.+ ..+|||||+|...+.+|...||.+.|++
T Consensus 86 ~~~~D~~Il~~a~~~---~~~~~-~~~vvLvT~D~~l~~~A~~~gi~~~~~~ 133 (133)
T PF13638_consen 86 AQRNDDRILNCALYL---QEENP-GRKVVLVTNDKNLRLKARAEGIPAVSYE 133 (133)
T ss_dssp --HHHHHHHHHHHHH---HHHCG-CEEEEEEE--HHHHHHHHHTT--EE---
T ss_pred ccccHHHHHHHHHHH---HHhcC-CCeEEEEeCCHHHHHHHhhcccccccCC
Confidence 459999999999999 88875 5899999999999999999999999864
No 14
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=96.55 E-value=0.002 Score=54.52 Aligned_cols=42 Identities=12% Similarity=0.166 Sum_probs=36.2
Q ss_pred CcccceEEEcccccceEEEECCCCcccccceeeeccCCCccEEec
Q psy4856 607 ITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEVT 651 (654)
Q Consensus 607 g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~~~~ 651 (654)
|+.+. |.|+.++.+|+| |+.+.+ .++|+||++++++++|.|+
T Consensus 2 g~~~~-g~V~~v~~~G~f-v~l~~~-~~~G~v~~~~l~~~~~~~d 43 (83)
T cd04471 2 GEEFD-GVISGVTSFGLF-VELDNL-TVEGLVHVSTLGDDYYEFD 43 (83)
T ss_pred CCEEE-EEEEeEEeeeEE-EEecCC-CEEEEEEEEecCCCcEEEc
Confidence 67788 999999999999 766644 4899999999999988775
No 15
>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=96.15 E-value=0.0035 Score=52.35 Aligned_cols=40 Identities=13% Similarity=0.225 Sum_probs=34.3
Q ss_pred cCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccE
Q psy4856 606 SITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNI 648 (654)
Q Consensus 606 ~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~ 648 (654)
.|+.+. |.|+++.+||.| |+.++. ++||+||+|.+.+.++
T Consensus 3 ~g~~~~-g~V~~i~~fG~f-v~l~~~-~~eGlvh~sel~~~~~ 42 (73)
T cd05686 3 LYQIFK-GEVASVTEYGAF-VKIPGC-RKQGLVHKSHMSSCRV 42 (73)
T ss_pred CCCEEE-EEEEEEEeeeEE-EEECCC-CeEEEEEchhhCCCcc
Confidence 688898 999999999999 877654 3799999999988754
No 16
>smart00670 PINc Large family of predicted nucleotide-binding domains. From similarities to 5'-exonucleases, these domains are predicted to be RNases. PINc domains in nematode SMG-5 and yeast NMD4p are predicted to be involved in RNAi.
Probab=95.47 E-value=0.0088 Score=53.15 Aligned_cols=59 Identities=20% Similarity=0.115 Sum_probs=48.7
Q ss_pred cccccCCCCcEEEEecCc-cccccccCCCCCCccchhhHHHHHHHHHhHhhhhhhccCCeEEEEeCChhh
Q psy4856 2 KDLISNPSRKFYVFVNEH-HYETYVEQEPGESVNDRNDRALRRVATWYVKYEEHLESAVRVILLSEDVRN 70 (654)
Q Consensus 2 r~l~~~~~~~~~vF~Ne~-~~~t~v~~~~~es~~drn~r~i~~aa~wY~~~~~Hl~~~~~vvllt~d~~~ 70 (654)
+.++....+.+.+|.|++ ++.+++++...++..+++|..|..+|.|| . .++++|+|.+.
T Consensus 50 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~D~~il~~a~~~---~-------~~~lvT~D~~l 109 (111)
T smart00670 50 EELALEGKIKLKVLKEERKLEEEILERLSLKLELLPNDALILATAKEL---G-------NVVLVTNDRDL 109 (111)
T ss_pred HHHHHhcccccceeecCCCeEEEecccCChhhcCCCChHHHHHHHHHC---C-------CCEEEeCCccc
Confidence 445555678899999997 78889988877777888999999999999 3 58899999864
No 17
>PRK08582 hypothetical protein; Provisional
Probab=95.34 E-value=0.011 Score=55.93 Aligned_cols=42 Identities=10% Similarity=0.189 Sum_probs=35.8
Q ss_pred hcccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccE
Q psy4856 603 RRKSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNI 648 (654)
Q Consensus 603 ~~~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~ 648 (654)
.-++|+.+. |.|+++.++|+| |+.++ .++|+||+|.+.++++
T Consensus 2 ~~kvG~iv~-G~V~~I~~fG~f-V~L~~--~~~GlVhiSels~~~v 43 (139)
T PRK08582 2 SIEVGSKLQ-GKVTGITNFGAF-VELPE--GKTGLVHISEVADNYV 43 (139)
T ss_pred CCcCCCEEE-EEEEEEECCeEE-EEECC--CCEEEEEeeccCcccc
Confidence 446799998 999999999999 76653 4899999999998875
No 18
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=94.97 E-value=0.023 Score=68.09 Aligned_cols=53 Identities=9% Similarity=-0.002 Sum_probs=42.0
Q ss_pred HHHHHHHhhcccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccEEe
Q psy4856 595 ALHTHLFFRRKSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEV 650 (654)
Q Consensus 595 ~l~~~~~l~~~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~~~ 650 (654)
++.+..|+..++|+.+.-|.|+++.+||.| |+..+ .+|||||+|.|+++||++
T Consensus 742 ~~I~~l~~~~~vG~iy~~g~V~~I~~FGaF-VeL~~--g~EGLVHISeLs~~rv~~ 794 (891)
T PLN00207 742 AIISSLTMVPTVGDIYRNCEIKSIAPYGAF-VEIAP--GREGLCHISELSSNWLAK 794 (891)
T ss_pred HHHHHHhcCcCCCcEEECcEEEEEeccEEE-EEeCC--CCEEEEEhhhcCCccccC
Confidence 334455567889999931799999999999 87753 489999999999988754
No 19
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=94.95 E-value=0.015 Score=49.08 Aligned_cols=40 Identities=13% Similarity=0.068 Sum_probs=33.1
Q ss_pred CcccceEEEcccccceEEEECCCCc-ccccceeeeccCCCccE
Q psy4856 607 ITEEEVARRTDLRHLDVCSVDPPGC-TDIDDALHCRPLPNGNI 648 (654)
Q Consensus 607 g~~~~~~~i~~~~~~g~~~v~~~~~-~~~eg~vh~~~~~~~~~ 648 (654)
|+.+. |.|+.+.+||+| |+..+. ..++|++|++.++++|+
T Consensus 1 G~~~~-g~V~~v~~~G~f-v~l~~~~~~~~gll~~s~l~~~~~ 41 (79)
T cd05684 1 GKIYK-GKVTSIMDFGCF-VQLEGLKGRKEGLVHISQLSFEGR 41 (79)
T ss_pred CCEEE-EEEEEEEeeeEE-EEEeCCCCCcEEEEEhHhccCCCC
Confidence 46777 999999999999 766543 25899999999998876
No 20
>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=94.83 E-value=0.007 Score=59.65 Aligned_cols=50 Identities=14% Similarity=0.179 Sum_probs=43.9
Q ss_pred HHHHHhhcccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccEEec
Q psy4856 597 HTHLFFRRKSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEVT 651 (654)
Q Consensus 597 ~~~~~l~~~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~~~~ 651 (654)
+.+.+|+.+.|+.+. |.|++++++|+| |+. + +++|++|.+.+.+++++|+
T Consensus 72 f~~i~f~p~~gEvv~-G~V~~v~~~Gif-V~l-g--~~~gi~~~~~l~~~~~~~d 121 (179)
T TIGR00448 72 FRALVFKPELGEIVE-GEVIEIVEFGAF-VSL-G--PFDGLFHVSQVTDDYCYYD 121 (179)
T ss_pred EEEEEEeccCCCEEE-EEEEEEEeeEEE-EEe-C--CceEEEEcHHhCCCceEEc
Confidence 456778999999999 999999999999 765 3 4899999999999998885
No 21
>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=94.82 E-value=0.018 Score=47.87 Aligned_cols=42 Identities=10% Similarity=0.041 Sum_probs=34.8
Q ss_pred cCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccEE
Q psy4856 606 SITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIE 649 (654)
Q Consensus 606 ~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~~ 649 (654)
.|+.+. |.|+++..+|.| |+..+...++|+||+|.++++++.
T Consensus 3 ~G~~~~-g~V~~v~~~g~~-v~l~~~~~~~gll~~s~l~~~~~~ 44 (76)
T cd04452 3 EGELVV-VTVKSIADMGAY-VSLLEYGNIEGMILLSELSRRRIR 44 (76)
T ss_pred CCCEEE-EEEEEEEccEEE-EEEcCCCCeEEEEEhHHcCCcccC
Confidence 578888 999999999999 766544358999999999988764
No 22
>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=94.35 E-value=0.034 Score=45.83 Aligned_cols=36 Identities=14% Similarity=0.134 Sum_probs=31.0
Q ss_pred cCcccceEEEcccccceEEEECCCCcccccceeeeccCCC
Q psy4856 606 SITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPN 645 (654)
Q Consensus 606 ~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~ 645 (654)
.|+.+. |.|+++.++|+| |+.++ .++|++|++.|+.
T Consensus 3 ~g~~~~-g~V~~i~~~G~f-v~l~~--~~~Gl~~~~~l~~ 38 (72)
T cd05689 3 EGTRLF-GKVTNLTDYGCF-VELEE--GVEGLVHVSEMDW 38 (72)
T ss_pred CCCEEE-EEEEEEEeeEEE-EEcCC--CCEEEEEEEeccC
Confidence 578888 999999999999 76654 4899999999963
No 23
>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=94.28 E-value=0.029 Score=46.02 Aligned_cols=39 Identities=13% Similarity=0.064 Sum_probs=32.5
Q ss_pred CcccceEEEcccccceEEEECCCCcccccceeeeccCCCccEE
Q psy4856 607 ITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIE 649 (654)
Q Consensus 607 g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~~ 649 (654)
|+.+. |.|+++.++|+| |+..+ .++|+||++.+++++++
T Consensus 1 G~~v~-g~V~~v~~~Gv~-V~l~~--~v~g~i~~~~l~~~~~~ 39 (69)
T cd05697 1 GQVVK-GTIRKLRPSGIF-VKLSD--HIKGLVPPMHLADVRLK 39 (69)
T ss_pred CCEEE-EEEEEEeccEEE-EEecC--CcEEEEEHHHCCCcccc
Confidence 46677 999999999999 76653 48999999999988653
No 24
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=94.27 E-value=0.026 Score=46.18 Aligned_cols=39 Identities=10% Similarity=0.084 Sum_probs=32.7
Q ss_pred CcccceEEEcccccceEEEECCCCcccccceeeeccCCCccEE
Q psy4856 607 ITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIE 649 (654)
Q Consensus 607 g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~~ 649 (654)
|+... |.|+++.++|+| |+..+ .++|++|+|.++++|++
T Consensus 1 G~~v~-g~V~~v~~~Gv~-V~l~~--~~~G~v~~s~l~~~~~~ 39 (68)
T cd05707 1 GDVVR-GFVKNIANNGVF-VTLGR--GVDARVRVSELSDSYLK 39 (68)
T ss_pred CCEEE-EEEEEEECccEE-EEeCC--CCEEEEEHHHCCchhhc
Confidence 45666 999999999999 76653 48999999999998865
No 25
>PRK05807 hypothetical protein; Provisional
Probab=94.19 E-value=0.026 Score=53.28 Aligned_cols=42 Identities=10% Similarity=0.128 Sum_probs=35.3
Q ss_pred hhcccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccE
Q psy4856 602 FRRKSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNI 648 (654)
Q Consensus 602 l~~~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~ 648 (654)
|+-++|+.+. |.|++++.+|+| |+.. ..+|+||+|.++++|+
T Consensus 1 m~~~vG~vv~-G~Vt~i~~~Gaf-V~L~---~~~Glvhiseis~~~v 42 (136)
T PRK05807 1 MTLKAGSILE-GTVVNITNFGAF-VEVE---GKTGLVHISEVADTYV 42 (136)
T ss_pred CCccCCCEEE-EEEEEEECCeEE-EEEC---CEEEEEEhhhcccccc
Confidence 3456899999 999999999999 7663 3699999999998775
No 26
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=93.88 E-value=0.13 Score=61.31 Aligned_cols=70 Identities=17% Similarity=0.271 Sum_probs=53.7
Q ss_pred eeeeeecCCCCCCCceEEEEeCCCCCCcEEEcccccc-ccCCCEEEEEEeecCCCCCCccEEEEEecCCCCChh
Q psy4856 240 QYCGILQPNPLAGSSRHLFVPAERKIPKIRVETRQIA-TLSGQRIVVAIDSWPRHSRYPQGHFVRALGPIGDKD 312 (654)
Q Consensus 240 ~~vG~l~~~~~~~~~~~l~vP~D~riP~I~I~t~q~~-~l~~~rvvV~Id~Wp~~s~~P~Ghiv~~LG~~gd~~ 312 (654)
.++|++.... ++++|++|.|..-..|+|+..+.. .+.|++|+|+|..|+...+.|.|+|+++||+..+.-
T Consensus 68 ~~~G~i~~~~---~g~gFv~~~~~~~~di~I~~~~~~~a~~GD~Vlv~I~~~~~~~~~~eg~Vv~Il~r~~~~~ 138 (709)
T TIGR02063 68 LVKGTVIAHR---DGFGFLRPEDDDEDDIFIPPRQMNGAMHGDRVLVRITGKPDGGDRFEARVIKILERANDQI 138 (709)
T ss_pred eEEEEEEECC---CccEEEEECCCCCCcEEEChHHhCcCCCCCEEEEEEecccCCCCCceEEEEEEEeeCCCEE
Confidence 4667776432 578899998832247999887764 679999999999998666778999999999876543
No 27
>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=93.81 E-value=0.048 Score=45.07 Aligned_cols=40 Identities=13% Similarity=-0.051 Sum_probs=33.6
Q ss_pred ccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccE
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNI 648 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~ 648 (654)
+.|+.+. |.|+++.++|+| |+.+. .++|++|++.+++++.
T Consensus 2 ~~G~iv~-g~V~~v~~~gi~-v~l~~--~~~g~v~~s~l~~~~~ 41 (73)
T cd05706 2 KVGDILP-GRVTKVNDRYVL-VQLGN--KVTGPSFITDALDDYS 41 (73)
T ss_pred CCCCEEE-EEEEEEeCCeEE-EEeCC--CcEEEEEhhhccCccc
Confidence 3688888 999999999999 76553 4899999999998764
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=0.047 Score=43.85 Aligned_cols=38 Identities=16% Similarity=0.111 Sum_probs=32.1
Q ss_pred CcccceEEEcccccceEEEECCCCcccccceeeeccCCCccE
Q psy4856 607 ITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNI 648 (654)
Q Consensus 607 g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~ 648 (654)
|+.+. |.|+++.++|+| |+... .++|++|.+.++++++
T Consensus 1 g~~~~-g~V~~i~~~G~f-v~l~~--~~~g~~~~~~l~~~~~ 38 (68)
T cd05685 1 GMVLE-GVVTNVTDFGAF-VDIGV--KQDGLIHISKMADRFV 38 (68)
T ss_pred CCEEE-EEEEEEecccEE-EEcCC--CCEEEEEHHHCCCccc
Confidence 45677 999999999999 76653 4899999999998876
No 29
>PRK07252 hypothetical protein; Provisional
Probab=93.53 E-value=0.047 Score=50.38 Aligned_cols=41 Identities=15% Similarity=0.163 Sum_probs=34.6
Q ss_pred ccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccEE
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIE 649 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~~ 649 (654)
+.|+.+. |.|+++.++|+| |+..+ .++|+||+|.|+++++.
T Consensus 2 kvG~iv~-G~V~~V~~~G~f-Vei~~--~~~GllhiseLs~~~~~ 42 (120)
T PRK07252 2 KIGDKLK-GTITGIKPYGAF-VALEN--GTTGLIHISEIKTGFID 42 (120)
T ss_pred CCCCEEE-EEEEEEeCcEEE-EEECC--CCEEEEEHHHcCCcccc
Confidence 3688888 999999999999 76653 48999999999988763
No 30
>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=93.51 E-value=0.045 Score=44.55 Aligned_cols=34 Identities=18% Similarity=0.266 Sum_probs=28.8
Q ss_pred CcccceEEEcccccceEEEECCCCcccccceeeeccCC
Q psy4856 607 ITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLP 644 (654)
Q Consensus 607 g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~ 644 (654)
|+.+. |.|+++++||+| |+..+ .++|++|++.|+
T Consensus 1 G~~~~-g~V~~i~~~G~f-v~l~~--~~~Glv~~~~l~ 34 (69)
T cd05690 1 GTVVS-GKIKSITDFGIF-VGLDG--GIDGLVHISDIS 34 (69)
T ss_pred CCEEE-EEEEEEEeeeEE-EEeCC--CCEEEEEHHHCC
Confidence 46677 999999999999 76653 489999999987
No 31
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=93.31 E-value=0.046 Score=50.17 Aligned_cols=39 Identities=15% Similarity=0.214 Sum_probs=32.7
Q ss_pred ccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCcc
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGN 647 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~ 647 (654)
.+|.... |-|||.++||-| |+.++-. .||||+|...+++
T Consensus 4 kvG~~l~-GkItgI~~yGAF-V~l~~g~--tGLVHISEIa~~f 42 (129)
T COG1098 4 KVGSKLK-GKITGITPYGAF-VELEGGK--TGLVHISEIADGF 42 (129)
T ss_pred cccceEE-EEEEeeEecceE-EEecCCC--cceEEehHhhhhh
Confidence 5788888 999999999999 8777533 7999999887765
No 32
>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=93.05 E-value=0.063 Score=44.51 Aligned_cols=40 Identities=10% Similarity=0.204 Sum_probs=33.4
Q ss_pred cCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccE
Q psy4856 606 SITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNI 648 (654)
Q Consensus 606 ~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~ 648 (654)
.|+.+. |.|++++++|+| |+..+. .++|++|.+.++++++
T Consensus 2 ~g~~v~-g~V~~i~~~g~~-v~l~~~-~~~g~i~~~~l~~~~~ 41 (77)
T cd05708 2 VGQKID-GTVRRVEDYGVF-IDIDGT-NVSGLCHKSEISDNRV 41 (77)
T ss_pred CCCEEE-EEEEEEEcceEE-EEECCC-CeEEEEEHHHCCCCcc
Confidence 578888 999999999999 766543 4899999999988653
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=92.96 E-value=0.07 Score=45.47 Aligned_cols=41 Identities=10% Similarity=0.006 Sum_probs=35.1
Q ss_pred cccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccE
Q psy4856 604 RKSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNI 648 (654)
Q Consensus 604 ~~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~ 648 (654)
-+.|+.+. |.|+.+.++|+| |+..+ .++|+||++.++++++
T Consensus 12 ~~~G~i~~-g~V~~v~~~G~f-v~l~~--~~~g~v~~~el~~~~~ 52 (83)
T cd04461 12 LKPGMVVH-GYVRNITPYGVF-VEFLG--GLTGLAPKSYISDEFV 52 (83)
T ss_pred CCCCCEEE-EEEEEEeeceEE-EEcCC--CCEEEEEHHHCCcccc
Confidence 35799998 999999999999 76643 5899999999988865
No 34
>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=92.70 E-value=0.37 Score=38.12 Aligned_cols=51 Identities=16% Similarity=0.155 Sum_probs=38.7
Q ss_pred CceEEEEeCCCCCCcEEEcccc----cc-ccCCCEEEEEEeecCCCCCCccEEEEEec
Q psy4856 253 SSRHLFVPAERKIPKIRVETRQ----IA-TLSGQRIVVAIDSWPRHSRYPQGHFVRAL 305 (654)
Q Consensus 253 ~~~~l~vP~D~riP~I~I~t~q----~~-~l~~~rvvV~Id~Wp~~s~~P~Ghiv~~L 305 (654)
.++.|+.|.+.. +.|+|+.++ .. ...|++|+++|..|. ...-|.++++++|
T Consensus 9 ~g~gfv~~~~~~-~~i~v~~~~~~~~~~~~~~Gd~V~~~i~~~~-~~~~~~a~~v~~~ 64 (64)
T smart00357 9 KGFGFIRPDDGG-KDVFVHPSQIQGGLKSLREGDEVEFKVVSPR-GGGKPEAENVVKL 64 (64)
T ss_pred CCeeEEecCCCC-ccEEEEhHHhhcCCCcCCCCCEEEEEEEEcc-CCCCcEEEEEEeC
Confidence 357788887654 689997776 44 357999999999984 4456899999875
No 35
>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=92.55 E-value=0.088 Score=46.57 Aligned_cols=38 Identities=16% Similarity=0.184 Sum_probs=32.4
Q ss_pred ccceEEEcccccceEEEECCCCcccccceeeeccCCCccEEec
Q psy4856 609 EEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEVT 651 (654)
Q Consensus 609 ~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~~~~ 651 (654)
++. |.|+++.++|+| |+.. .++|+||++.+++++|+|.
T Consensus 2 vv~-g~V~~i~~~Gif-V~l~---~v~G~v~~~~l~~~~~~~~ 39 (99)
T cd04460 2 VVE-GEVVEVVDFGAF-VRIG---PVDGLLHISQIMDDYISYD 39 (99)
T ss_pred EEE-EEEEEEEeccEE-EEEc---CeEEEEEEEEccCCceEec
Confidence 456 999999999999 7664 3899999999999998764
No 36
>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=91.91 E-value=0.096 Score=42.85 Aligned_cols=37 Identities=8% Similarity=-0.028 Sum_probs=30.8
Q ss_pred CcccceEEEcccccceEEEECCCCcccccceeeeccCCCcc
Q psy4856 607 ITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGN 647 (654)
Q Consensus 607 g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~ 647 (654)
|.... |.|+++.++|+| |+..+ .++|++|.|.+++++
T Consensus 1 g~~~~-g~V~~v~~~G~~-V~l~~--~~~gli~~s~l~~~~ 37 (70)
T cd05698 1 GLKTH-GTIVKVKPNGCI-VSFYN--NVKGFLPKSELSEAF 37 (70)
T ss_pred CCEEE-EEEEEEecCcEE-EEECC--CCEEEEEHHHcChhh
Confidence 45677 999999999999 76653 489999999998764
No 37
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=91.72 E-value=0.085 Score=56.47 Aligned_cols=50 Identities=14% Similarity=0.178 Sum_probs=39.9
Q ss_pred HHHHhhcc---cCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccEE
Q psy4856 598 THLFFRRK---SITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIE 649 (654)
Q Consensus 598 ~~~~l~~~---~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~~ 649 (654)
.|+|..+. .|+... |.|+.+.+||.| |+..++.++||+||+|.|+-+|++
T Consensus 6 ~cr~~~~~~P~~GdvV~-g~V~~I~d~Gaf-V~L~EY~gvEGlIhiSElS~~ri~ 58 (319)
T PTZ00248 6 DCRFYEQKFPEEDDLVM-VKVVRITEMGAY-VSLLEYDDIEGMILMSELSKRRIR 58 (319)
T ss_pred cccchhhhCCCCCCEEE-EEEEEEeCCeEE-EEecCCCCcEEEEEHHHhcccccC
Confidence 34555554 366776 999999999999 878766679999999999988864
No 38
>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=91.63 E-value=0.13 Score=42.76 Aligned_cols=39 Identities=10% Similarity=-0.071 Sum_probs=32.0
Q ss_pred cCcccceEEEccccc-ceEEEECCCCcccccceeeeccCCCccE
Q psy4856 606 SITEEEVARRTDLRH-LDVCSVDPPGCTDIDDALHCRPLPNGNI 648 (654)
Q Consensus 606 ~g~~~~~~~i~~~~~-~g~~~v~~~~~~~~eg~vh~~~~~~~~~ 648 (654)
.|+... |.|+.+.+ +|.| ++.+. ..+|++|+|.++++|.
T Consensus 3 ~G~iv~-G~V~~i~~~~g~~-v~l~~--~~~Glvhis~~s~~~~ 42 (72)
T cd05704 3 EGAVTL-GMVTKVIPHSGLT-VQLPF--GKTGLVSIFHLSDSYT 42 (72)
T ss_pred CCCEEE-EEEEEeeCCcEEE-EECCC--CCEEEEEHHHhcCccc
Confidence 578887 99999885 8999 76542 4799999999988764
No 39
>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=91.62 E-value=0.12 Score=43.34 Aligned_cols=39 Identities=8% Similarity=-0.079 Sum_probs=32.6
Q ss_pred ccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCcc
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGN 647 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~ 647 (654)
+.|+... |.|+.++++|.| |+..+ .++|+||++.++++|
T Consensus 2 k~G~~V~-g~V~~i~~~G~f-V~l~~--~v~G~v~~~~ls~~~ 40 (74)
T cd05705 2 KEGQLLR-GYVSSVTKQGVF-FRLSS--SIVGRVLFQNVTKYF 40 (74)
T ss_pred CCCCEEE-EEEEEEeCCcEE-EEeCC--CCEEEEEHHHccCcc
Confidence 3577888 999999999999 76542 699999999998877
No 40
>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=91.01 E-value=0.15 Score=40.97 Aligned_cols=38 Identities=13% Similarity=0.170 Sum_probs=31.7
Q ss_pred CcccceEEEcccccceEEEECCCCcccccceeeeccCCCccE
Q psy4856 607 ITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNI 648 (654)
Q Consensus 607 g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~ 648 (654)
|+.+. |.|+++.++|+| |+... ..+|++|++.++++++
T Consensus 1 g~~~~-g~V~~v~~~G~~-v~l~~--~~~g~l~~~~l~~~~~ 38 (68)
T cd04472 1 GKIYE-GKVVKIKDFGAF-VEILP--GKDGLVHISELSDERV 38 (68)
T ss_pred CCEEE-EEEEEEEEeEEE-EEeCC--CCEEEEEhHHcCCccc
Confidence 45677 999999999999 76653 3899999999998875
No 41
>PHA02945 interferon resistance protein; Provisional
Probab=90.13 E-value=0.27 Score=42.56 Aligned_cols=42 Identities=7% Similarity=-0.090 Sum_probs=34.8
Q ss_pred cCcccceEEEcccccceEEEECCCCcccccceeeeccC--CCccEEe
Q psy4856 606 SITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPL--PNGNIEV 650 (654)
Q Consensus 606 ~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~--~~~~~~~ 650 (654)
.|+-. +|.|.. .+||.| |..+.+.+.||++|.|.. .++|+.+
T Consensus 11 ~Gelv-igtV~~-~d~ga~-v~L~EY~g~eg~i~~seveva~~wvK~ 54 (88)
T PHA02945 11 VGDVL-KGKVYE-NGYALY-IDLFDYPHSEAILAESVQMHMNRYFKY 54 (88)
T ss_pred CCcEE-EEEEEe-cCceEE-EEecccCCcEEEEEeehhhhccceEee
Confidence 34444 589999 899999 778888889999999966 9999986
No 42
>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=89.68 E-value=0.3 Score=40.27 Aligned_cols=39 Identities=21% Similarity=0.199 Sum_probs=33.7
Q ss_pred cccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCc
Q psy4856 604 RKSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNG 646 (654)
Q Consensus 604 ~~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~ 646 (654)
-+.|+... |.|+.+.++|+| |+.. ..++|.||.+.++++
T Consensus 2 ~~~G~iv~-g~V~~v~~~g~~-V~l~--~~~~g~ip~~~l~~~ 40 (74)
T PF00575_consen 2 LKEGDIVE-GKVTSVEDFGVF-VDLG--NGIEGFIPISELSDD 40 (74)
T ss_dssp SSTTSEEE-EEEEEEETTEEE-EEES--TSSEEEEEGGGSSSS
T ss_pred CCCCCEEE-EEEEEEECCEEE-EEEC--CcEEEEEEeehhcCc
Confidence 46789998 999999999999 7555 368999999999986
No 43
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=89.17 E-value=0.26 Score=39.44 Aligned_cols=37 Identities=19% Similarity=0.240 Sum_probs=30.0
Q ss_pred CcccceEEEcccccceEEEECCCCcccccceeeeccCCCcc
Q psy4856 607 ITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGN 647 (654)
Q Consensus 607 g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~ 647 (654)
|+.+. |.|+++.++|+| |+... .++|++|.+.+++++
T Consensus 1 G~~~~-g~V~~i~~~g~~-v~i~~--~~~g~l~~~~l~~~~ 37 (69)
T cd05692 1 GSVVE-GTVTRLKPFGAF-VELGG--GISGLVHISQIAHKR 37 (69)
T ss_pred CCEEE-EEEEEEEeeeEE-EEECC--CCEEEEEhHHcCCcc
Confidence 45677 999999999999 65542 489999999998765
No 44
>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=88.72 E-value=0.32 Score=40.93 Aligned_cols=37 Identities=14% Similarity=0.114 Sum_probs=30.8
Q ss_pred ccCcccceEEEcccccceEEEECCCCcccccceeeeccCCC
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPN 645 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~ 645 (654)
+.|+.+. |.|++++++|+| |+..+ ..+|++|.|.++.
T Consensus 15 ~~G~~~~-g~V~~i~~~G~f-V~l~~--~~~Glv~~se~~~ 51 (77)
T cd04473 15 EVGKLYK-GKVNGVAKYGVF-VDLND--HVRGLIHRSNLLR 51 (77)
T ss_pred CCCCEEE-EEEEeEecceEE-EEECC--CcEEEEEchhccC
Confidence 5789998 999999999999 65543 4899999998753
No 45
>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=88.09 E-value=0.34 Score=39.66 Aligned_cols=38 Identities=11% Similarity=0.116 Sum_probs=30.9
Q ss_pred CcccceEEEcccccceEEEECCCCcccccceeeeccCCCccE
Q psy4856 607 ITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNI 648 (654)
Q Consensus 607 g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~ 648 (654)
|+... |.|+++.++|+| |+..+ .++|++|++.++++++
T Consensus 1 G~~v~-g~V~~v~~~g~~-v~l~~--~~~g~i~~~~~~~~~~ 38 (73)
T cd05691 1 GSIVT-GKVTEVDAKGAT-VKLGD--GVEGFLRAAELSRDRV 38 (73)
T ss_pred CCEEE-EEEEEEECCeEE-EEeCC--CCEEEEEHHHCCCccc
Confidence 45566 999999999999 76543 4899999999998765
No 46
>PRK08059 general stress protein 13; Validated
Probab=87.34 E-value=0.39 Score=44.40 Aligned_cols=40 Identities=10% Similarity=0.149 Sum_probs=33.2
Q ss_pred ccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccE
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNI 648 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~ 648 (654)
+.|+.+. |.|+++.++|+| |+... .++|++|+|.++++++
T Consensus 6 k~G~iv~-G~V~~i~~~G~f-V~i~~--~~~Gli~~sel~~~~~ 45 (123)
T PRK08059 6 EVGSVVT-GKVTGIQPYGAF-VALDE--ETQGLVHISEITHGFV 45 (123)
T ss_pred CCCCEEE-EEEEEEecceEE-EEECC--CCEEEEEHHHCCcccc
Confidence 4688888 999999999999 65543 4899999999987754
No 47
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=86.95 E-value=0.59 Score=53.44 Aligned_cols=38 Identities=16% Similarity=0.128 Sum_probs=32.3
Q ss_pred ccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCcc
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGN 647 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~ 647 (654)
..|+... |+|+.+++||.| |++- .++||||+|.++.+.
T Consensus 191 ~~G~vV~-G~V~~It~~Gaf-Vdig---GvdGLlHiseiS~~r 228 (541)
T COG0539 191 EVGEVVE-GVVKNITDYGAF-VDIG---GVDGLLHISEISWKR 228 (541)
T ss_pred CCCceEE-EEEEEeecCcEE-EEec---CeeeEEehhhccccc
Confidence 4688888 999999999999 8776 489999999887554
No 48
>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=86.75 E-value=0.48 Score=39.28 Aligned_cols=32 Identities=13% Similarity=0.199 Sum_probs=26.1
Q ss_pred EEEccc-ccceEEEECCCCcccccceeeeccCCCcc
Q psy4856 613 ARRTDL-RHLDVCSVDPPGCTDIDDALHCRPLPNGN 647 (654)
Q Consensus 613 ~~i~~~-~~~g~~~v~~~~~~~~eg~vh~~~~~~~~ 647 (654)
|.|+.+ .++|.| |+.++ .++|+||+|.++++.
T Consensus 7 g~V~~v~~~~G~~-V~l~~--gv~G~i~~s~l~~~~ 39 (71)
T cd05696 7 VKVTKVEPDLGAV-FELKD--GLLGFVHISHLSDDK 39 (71)
T ss_pred eEEEEEccCceEE-EEeCC--CCEEEEEHHHCCcch
Confidence 788887 799999 76654 489999999997654
No 49
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=86.41 E-value=0.32 Score=47.87 Aligned_cols=50 Identities=14% Similarity=0.176 Sum_probs=40.7
Q ss_pred HHHHHhhcccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccEEec
Q psy4856 597 HTHLFFRRKSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEVT 651 (654)
Q Consensus 597 ~~~~~l~~~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~~~~ 651 (654)
|.++.|+...|+... |.|+.++.+|+| |-. .+.+|+||+|-+.||+|.|+
T Consensus 72 f~al~fkP~~gEVV~-GeVv~~~~~G~f-V~i---gp~dglvh~sqi~dd~~~~d 121 (183)
T COG1095 72 FRALVFKPFRGEVVE-GEVVEVVEFGAF-VRI---GPLDGLVHVSQIMDDYIDYD 121 (183)
T ss_pred EEEEEEEeccccEEE-EEEEEEeecceE-EEe---ccccccccHhhccCcccccC
Confidence 345567777888888 999999999999 633 25799999999999977765
No 50
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=85.73 E-value=0.55 Score=46.47 Aligned_cols=50 Identities=16% Similarity=0.201 Sum_probs=43.2
Q ss_pred HHHHHhhcccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccEEec
Q psy4856 597 HTHLFFRRKSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEVT 651 (654)
Q Consensus 597 ~~~~~l~~~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~~~~ 651 (654)
+.+..++.+.|+.+. |.|+++..+|+| |+.. +++|++|.+.+++++++|+
T Consensus 72 f~~lvf~P~~GEVv~-g~V~~v~~~Gi~-V~lg---~~~g~v~~~~l~~~~~~~d 121 (187)
T PRK08563 72 FDALVFKPELQEVVE-GEVVEVVEFGAF-VRIG---PVDGLLHISQIMDDYISYD 121 (187)
T ss_pred EEEEEEeccCCCEEE-EEEEEEEccEEE-EEEe---CceEEEEcHHcCCCceEEc
Confidence 666777889999999 999999999999 7553 4899999999999988874
No 51
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=85.18 E-value=0.92 Score=53.96 Aligned_cols=42 Identities=10% Similarity=0.097 Sum_probs=36.0
Q ss_pred hcccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccE
Q psy4856 603 RRKSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNI 648 (654)
Q Consensus 603 ~~~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~ 648 (654)
..+.|+.+. |.|+++.+||.| |+..+ ..+|+||+|.++++++
T Consensus 618 ~~~vG~v~~-G~V~~I~~fGaf-Vei~~--~~~GllhiSels~~~v 659 (693)
T PRK11824 618 EPEVGEIYE-GKVVRIVDFGAF-VEILP--GKDGLVHISEIADERV 659 (693)
T ss_pred cCcCCeEEE-EEEEEEECCeEE-EEECC--CCEEEEEeeeccCccc
Confidence 357899998 999999999999 77653 4899999999987765
No 52
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=84.21 E-value=1 Score=53.45 Aligned_cols=41 Identities=12% Similarity=0.113 Sum_probs=35.4
Q ss_pred cccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccE
Q psy4856 604 RKSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNI 648 (654)
Q Consensus 604 ~~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~ 648 (654)
.+.|+.+. |.|+++.+||.| |+..+ .++|+||+|.++++++
T Consensus 616 ~~~G~i~~-G~V~~I~~~Gaf-Vei~~--g~~GllHiSei~~~~v 656 (684)
T TIGR03591 616 PEVGKIYE-GKVVRIMDFGAF-VEILP--GKDGLVHISEIANERV 656 (684)
T ss_pred cccCcEEE-EEEEEEeCCEEE-EEECC--CcEEEEEHHHcCCCcc
Confidence 46899998 999999999999 76643 4899999999988765
No 53
>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=83.03 E-value=0.77 Score=36.75 Aligned_cols=34 Identities=18% Similarity=0.171 Sum_probs=28.7
Q ss_pred CcccceEEEcccccceEEEECCCCcccccceeeeccCCC
Q psy4856 607 ITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPN 645 (654)
Q Consensus 607 g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~ 645 (654)
|+.+. |.|+++.++|+| |+.. .++|++|.+.++.
T Consensus 2 g~~~~-g~V~~v~~~g~~-v~l~---~~~g~l~~~e~~~ 35 (68)
T cd05688 2 GDVVE-GTVKSITDFGAF-VDLG---GVDGLLHISDMSW 35 (68)
T ss_pred CCEEE-EEEEEEEeeeEE-EEEC---CeEEEEEhHHCCC
Confidence 66777 999999999999 7653 4899999998873
No 54
>PRK11642 exoribonuclease R; Provisional
Probab=82.47 E-value=5.1 Score=48.63 Aligned_cols=56 Identities=21% Similarity=0.173 Sum_probs=40.3
Q ss_pred HHHHhhhcC-CeEEEEEEEecCCCceeEEeecCC--CcCeEecCCCCCCcCCCCCEEEEEEcc
Q psy4856 125 EIHAGIKNQ-SLLQGSFQASRENFLEGQVNCEGY--DKPILVQGREGLNRAIDGDTVAVRLLP 184 (654)
Q Consensus 125 ~l~~gik~g-~l~~G~l~v~~~n~~egfV~~~~~--~~dI~I~g~~~~NRAl~GD~V~Vellp 184 (654)
++..-|+.+ +.+.|++.... ++ +||.+.+. ..+|+|+.. ..+.|-+||+|+|+|..
T Consensus 140 ~Vv~IleR~~~~~vG~~~~~~-~~--~~v~P~d~r~~~~i~i~~~-~~~~~~~gd~V~v~I~~ 198 (813)
T PRK11642 140 RIVRVLVPKTSQIVGRYFTDA-GV--GFVVPDDSRLSFDILIPPE-QIMGARMGFVVVVELTQ 198 (813)
T ss_pred EEEEEEecCCCEEEEEEEEeC-Ce--EEEEECCCCCCCcEEeccc-cccCCCCCCEEEEEEec
Confidence 344444443 57888887643 44 88887763 468999875 77889999999999974
No 55
>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=82.30 E-value=0.91 Score=37.87 Aligned_cols=36 Identities=11% Similarity=0.023 Sum_probs=28.5
Q ss_pred CcccceEEEcccccceEEEECCCCcccccceeeeccCCCc
Q psy4856 607 ITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNG 646 (654)
Q Consensus 607 g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~ 646 (654)
|.... |.|+.+.++|+| |+..+ .++|+||++.++++
T Consensus 1 G~~V~-g~V~~i~~~g~~-V~l~~--~i~G~i~~~~ls~~ 36 (73)
T cd05703 1 GQEVT-GFVNNVSKEFVW-LTISP--DVKGRIPLLDLSDD 36 (73)
T ss_pred CCEEE-EEEEEEeCCEEE-EEeCC--CcEEEEEHHHcCCc
Confidence 34556 899999999999 65543 59999999999754
No 56
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=81.92 E-value=0.89 Score=51.76 Aligned_cols=41 Identities=17% Similarity=0.152 Sum_probs=34.5
Q ss_pred ccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccEE
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIE 649 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~~ 649 (654)
..|+.+. |.|+.+.+||+| |+..+ .++||+|.|.++++.++
T Consensus 292 ~vG~vv~-G~V~~I~~fGvF-VeL~~--gieGLvh~SeLs~~~v~ 332 (486)
T PRK07899 292 AIGQIVP-GKVTKLVPFGAF-VRVEE--GIEGLVHISELAERHVE 332 (486)
T ss_pred CCCCEEE-EEEEEEeccEEE-EEeCC--CcEEEEEHHHcCccccc
Confidence 4699999 999999999999 76543 48999999999887653
No 57
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=79.20 E-value=1.1 Score=48.33 Aligned_cols=38 Identities=8% Similarity=0.100 Sum_probs=27.3
Q ss_pred ccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCcc
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGN 647 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~ 647 (654)
+.|+... |.|+.+.+||.| |+.. +++|+||+|.+++++
T Consensus 195 k~G~vv~-G~V~~I~~~G~f-V~i~---gv~Gllhisels~~~ 232 (318)
T PRK07400 195 EVGEVVV-GTVRGIKPYGAF-IDIG---GVSGLLHISEISHEH 232 (318)
T ss_pred CCCCEEE-EEEEEEECCeEE-EEEC---CEEEEEEHHHccccc
Confidence 4577777 888888888888 6543 467888888777665
No 58
>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=78.25 E-value=2.1 Score=50.67 Aligned_cols=37 Identities=11% Similarity=-0.018 Sum_probs=32.0
Q ss_pred cccCcccceEEEcccccceEEEECCCCcccccceeeeccCC
Q psy4856 604 RKSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLP 644 (654)
Q Consensus 604 ~~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~ 644 (654)
-..|+.+. |.|+.+.+||.| |+.. ..++||||+|.+.
T Consensus 645 ~~vG~i~~-GkV~~I~dfGaF-Vel~--~G~eGLvHISeis 681 (719)
T TIGR02696 645 PEVGERFL-GTVVKTTAFGAF-VSLL--PGKDGLLHISQIR 681 (719)
T ss_pred CCCCCEEE-EEEEEEECceEE-EEec--CCceEEEEhhhcc
Confidence 46899999 999999999999 8764 3589999999885
No 59
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=77.84 E-value=1.8 Score=34.37 Aligned_cols=38 Identities=13% Similarity=0.141 Sum_probs=31.3
Q ss_pred cCcccceEEEcccccceEEEECCCCcccccceeeeccCCCcc
Q psy4856 606 SITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGN 647 (654)
Q Consensus 606 ~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~ 647 (654)
.|+... |.|+.+.++|+| |+... .++|++|.+.+++.+
T Consensus 2 ~G~~v~-g~V~~v~~~g~~-v~i~~--~~~g~l~~~~~~~~~ 39 (72)
T smart00316 2 VGDVVE-GTVTEITPFGAF-VDLGN--GVEGLIPISELSDKR 39 (72)
T ss_pred CCCEEE-EEEEEEEccEEE-EEeCC--CCEEEEEHHHCCccc
Confidence 577888 999999999999 65542 489999999998764
No 60
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=77.67 E-value=1.7 Score=49.77 Aligned_cols=55 Identities=18% Similarity=0.221 Sum_probs=39.2
Q ss_pred HhhhcCCeEEEEEEEecCCCceeEEeecCCCcCeEecCCCCCCcCCC-----CCEEEEEEccC
Q psy4856 128 AGIKNQSLLQGSFQASRENFLEGQVNCEGYDKPILVQGREGLNRAID-----GDTVAVRLLPE 185 (654)
Q Consensus 128 ~gik~g~l~~G~l~v~~~n~~egfV~~~~~~~dI~I~g~~~~NRAl~-----GD~V~Vellp~ 185 (654)
.-++.|..+.|++---..++ ++|.... ..+=+|+=.+-.|.... ||.|.|.++..
T Consensus 17 ~~~~~G~vV~G~Vv~i~~~~--v~Vdig~-Kseg~ip~~E~~~~~~~~~~~~gd~v~v~v~~~ 76 (541)
T COG0539 17 EEFEPGDVVKGTVVSIEKDG--VLVDIGG-KSEGVIPISEFSNEPVEDVVQVGDEVEVLVLRV 76 (541)
T ss_pred hccCCCCEEEEEEEEEeCCe--EEEEecC-ccccEeEHHHhccccccceecCCCEEEEEEEEE
Confidence 34567999999888777776 8888865 34444554445666667 99999988743
No 61
>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=76.76 E-value=2 Score=37.37 Aligned_cols=37 Identities=14% Similarity=-0.110 Sum_probs=30.5
Q ss_pred ccCcccceEEEcccccc--eEEEECCCCcccccceeeeccCCC
Q psy4856 605 KSITEEEVARRTDLRHL--DVCSVDPPGCTDIDDALHCRPLPN 645 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~--g~~~v~~~~~~~~eg~vh~~~~~~ 645 (654)
..|+.+. |.|+.+.++ |.| |+..+ ..+|+||+|.++.
T Consensus 6 ~~G~iy~-g~V~~i~~~~~GaF-V~l~~--g~~Gllh~seis~ 44 (88)
T cd04453 6 IVGNIYL-GRVKKIVPGLQAAF-VDIGL--GKNGFLHLSDILP 44 (88)
T ss_pred CCCCEEE-EEEEEeccCCcEEE-EEeCC--CCEEEEEhHHcCc
Confidence 4688888 999999986 999 76653 4899999998853
No 62
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=76.71 E-value=9.2 Score=32.70 Aligned_cols=50 Identities=14% Similarity=0.207 Sum_probs=33.1
Q ss_pred eEEEEEEEecCCCceeEEeec--C---CCcCeEecCCCCC-CcCCCCCEEEEEEccCC
Q psy4856 135 LLQGSFQASRENFLEGQVNCE--G---YDKPILVQGREGL-NRAIDGDTVAVRLLPES 186 (654)
Q Consensus 135 l~~G~l~v~~~n~~egfV~~~--~---~~~dI~I~g~~~~-NRAl~GD~V~Vellp~~ 186 (654)
+..|+|.+..+|| ||++.. + ..+||||+...-+ ..==.||.|.-.+-+..
T Consensus 2 ~~~GvLei~~dGy--GFLR~~~~~y~~~~~DvYVs~~qIrrf~LR~GD~V~G~vr~p~ 57 (78)
T PF07497_consen 2 YVEGVLEILPDGY--GFLRSPDNNYLPSPDDVYVSPSQIRRFGLRTGDLVEGQVRPPR 57 (78)
T ss_dssp EEEEEEEE-TTS---EEEE-GGGTTS-STTSEEE-CCCCCCTT--TTEEEEEEEE--S
T ss_pred EEEEEEEECCCCc--EEeECCCcCCCCCCCCEEECHHHHHHcCCCCCCEEEEEEeCCC
Confidence 5789999999999 999998 3 3689999986332 33347999998887653
No 63
>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=75.10 E-value=2.3 Score=35.68 Aligned_cols=38 Identities=11% Similarity=-0.066 Sum_probs=30.4
Q ss_pred cCcccceEEEcccccceEEEECCCCcccccceeeeccCCCc
Q psy4856 606 SITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNG 646 (654)
Q Consensus 606 ~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~ 646 (654)
.|.... |.|..+..+|.| |+. +...++|++|.+.++.+
T Consensus 4 ~G~~v~-g~V~si~d~G~~-v~~-g~~gv~Gfl~~~~~~~~ 41 (74)
T cd05694 4 EGMVLS-GCVSSVEDHGYI-LDI-GIPGTTGFLPKKDAGNF 41 (74)
T ss_pred CCCEEE-EEEEEEeCCEEE-EEe-CCCCcEEEEEHHHCCcc
Confidence 456677 999999999999 765 33358999999988864
No 64
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=74.99 E-value=3 Score=47.57 Aligned_cols=38 Identities=13% Similarity=0.157 Sum_probs=31.6
Q ss_pred ccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCcc
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGN 647 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~ 647 (654)
+.|+... |.|+.+.+||.| |+.. .++|+||+|.|+..+
T Consensus 207 k~G~iv~-G~V~~i~~~G~F-Vdlg---gv~Glv~~Sels~~~ 244 (486)
T PRK07899 207 QKGQVRK-GVVSSIVNFGAF-VDLG---GVDGLVHVSELSWKH 244 (486)
T ss_pred cCCCEEE-EEEEEEECCeEE-EEEC---CEEEEEEHHHCCCcc
Confidence 4788898 999999999999 7663 489999999988544
No 65
>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=74.94 E-value=7.8 Score=45.95 Aligned_cols=65 Identities=14% Similarity=0.192 Sum_probs=46.5
Q ss_pred eeeeeecCCCCCCCceEEEEeCCCCCCcEEEcccccc-ccCCCEEEEEEeecCCCCCCccEEEEEecCCC
Q psy4856 240 QYCGILQPNPLAGSSRHLFVPAERKIPKIRVETRQIA-TLSGQRIVVAIDSWPRHSRYPQGHFVRALGPI 308 (654)
Q Consensus 240 ~~vG~l~~~~~~~~~~~l~vP~D~riP~I~I~t~q~~-~l~~~rvvV~Id~Wp~~s~~P~Ghiv~~LG~~ 308 (654)
.+.|++.-.+ ++++|++|.+..-..|+|+..+.. ++.|++|.|+|..-... +.|+|.|+++|-..
T Consensus 16 ~~~G~i~~~~---~gfgFv~~~~~~~~difI~~~~~~~a~~GD~V~v~i~~~~~~-~~~~g~v~~il~r~ 81 (654)
T TIGR00358 16 LVKGVVKAHN---KGFGFLRPDDDDKKDYFIPPPQMKKVMHGDLVEACPLSQPQR-GRFEAEVERILEPA 81 (654)
T ss_pred eEEEEEEECC---CccEEEEeCCCCCCcEEEchHHhCcCCCCCEEEEEEeecCCC-CCceEEEEEEeccC
Confidence 3557776543 578899997643348999887764 67999999998642222 34999999998763
No 66
>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=73.09 E-value=2.5 Score=34.61 Aligned_cols=36 Identities=8% Similarity=0.137 Sum_probs=28.9
Q ss_pred cccceEEEcccccceEEEECCCCcccccceeeeccCCCcc
Q psy4856 608 TEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGN 647 (654)
Q Consensus 608 ~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~ 647 (654)
.... |.|+.+.++|+| |+.+ ..++|++|.+.+.++|
T Consensus 2 ~iV~-g~V~~i~~~gi~-v~l~--~~i~g~i~~~~i~~~~ 37 (70)
T cd05702 2 DLVK-AKVKSVKPTQLN-VQLA--DNVHGRIHVSEVFDEW 37 (70)
T ss_pred CEEE-EEEEEEECCcEE-EEeC--CCcEEEEEHHHhcccc
Confidence 3444 899999999999 7554 2489999999998876
No 67
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=72.16 E-value=2.6 Score=51.34 Aligned_cols=43 Identities=14% Similarity=0.252 Sum_probs=36.2
Q ss_pred Hhhc-ccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCcc
Q psy4856 601 FFRR-KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGN 647 (654)
Q Consensus 601 ~l~~-~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~ 647 (654)
|.++ ..|..+. |.|+++.++|+| |+.++ .++|+||+|.|+++.
T Consensus 746 ~~~~~~vG~iV~-GkV~~v~~~GvF-VeL~~--gVeGlI~~s~lsdd~ 789 (863)
T PRK12269 746 FANAYGVGSTVE-GEVSSVTDFGIF-VRVPG--GVEGLVRKQHLVENR 789 (863)
T ss_pred HHhhCCCCCEEE-EEEEEEecCeEE-EEcCC--CeEEEEEHHHcCCcc
Confidence 4444 4799999 999999999999 87764 499999999998764
No 68
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=70.95 E-value=4.7 Score=46.13 Aligned_cols=41 Identities=17% Similarity=0.159 Sum_probs=33.7
Q ss_pred cccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccE
Q psy4856 604 RKSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNI 648 (654)
Q Consensus 604 ~~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~ 648 (654)
-+.|+... |.|+++.++|.| |+..+ .++|+||+|.++.+++
T Consensus 200 l~~G~iv~-G~V~~v~~~G~f-V~l~~--gv~g~v~~sels~~~~ 240 (491)
T PRK13806 200 VKEGDVVE-GTVTRLAPFGAF-VELAP--GVEGMVHISELSWSRV 240 (491)
T ss_pred CCCCCEEE-EEEEEEeCCeEE-EEcCC--CcEEEEEHHHCCCccc
Confidence 46899998 999999999999 76642 4899999999986543
No 69
>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=70.03 E-value=13 Score=30.07 Aligned_cols=46 Identities=13% Similarity=0.230 Sum_probs=33.1
Q ss_pred EEEEEEec--CCCceeEEeecCCCcCeEecCCCCCCc---C-CCCCEEEEEEcc
Q psy4856 137 QGSFQASR--ENFLEGQVNCEGYDKPILVQGREGLNR---A-IDGDTVAVRLLP 184 (654)
Q Consensus 137 ~G~l~v~~--~n~~egfV~~~~~~~dI~I~g~~~~NR---A-l~GD~V~Vellp 184 (654)
+|++.--. ++| ||+.+++.++|||+.-..-.+. . -.||.|..++..
T Consensus 2 ~G~V~~~~~~kgy--GFI~~~~~~~diFfh~s~~~~~~~~~l~~G~~V~F~~~~ 53 (66)
T PF00313_consen 2 TGTVKWFDDEKGY--GFITSDDGGEDIFFHISDLSGNGFRSLKEGDRVEFEVEE 53 (66)
T ss_dssp EEEEEEEETTTTE--EEEEETTSSSEEEEEGGGBCSSSSTS--TTSEEEEEEEE
T ss_pred eEEEEEEECCCCc--eEEEEcccceeEEeccccccccccccCCCCCEEEEEEEE
Confidence 67776544 477 9999998888999876522222 2 489999999876
No 70
>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=69.73 E-value=3.2 Score=33.80 Aligned_cols=35 Identities=11% Similarity=0.014 Sum_probs=27.9
Q ss_pred cccceEEEcccccceEEEECCCCcccccceeeeccCCCc
Q psy4856 608 TEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNG 646 (654)
Q Consensus 608 ~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~ 646 (654)
.... |.|+.+.++|.| |+..+ .++|+||.+.++..
T Consensus 2 ~~V~-g~V~~i~~~G~~-v~l~~--~v~g~v~~~~l~~~ 36 (66)
T cd05695 2 MLVN-ARVKKVLSNGLI-LDFLS--SFTGTVDFLHLDPE 36 (66)
T ss_pred CEEE-EEEEEEeCCcEE-EEEcC--CceEEEEHHHcCCc
Confidence 3455 889999999999 76654 48999999988754
No 71
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=69.65 E-value=2.9 Score=47.84 Aligned_cols=36 Identities=14% Similarity=0.180 Sum_probs=31.2
Q ss_pred ccCcccceEEEcccccceEEEECCCCcccccceeeeccCC
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLP 644 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~ 644 (654)
..|+... |.|+.+.+||+| |+..+ .++|+||+|.|+
T Consensus 291 ~~G~~v~-G~V~~v~~~G~f-V~l~~--gv~Glvh~sels 326 (491)
T PRK13806 291 KAGDKVT-GKVVRLAPFGAF-VEILP--GIEGLVHVSEMS 326 (491)
T ss_pred CCCCEEE-EEEEEEeCceEE-EEeCC--CcEEEEEHHHcC
Confidence 5799999 999999999999 76532 489999999986
No 72
>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=65.40 E-value=3.5 Score=36.75 Aligned_cols=37 Identities=8% Similarity=0.170 Sum_probs=30.5
Q ss_pred cCcccceEEEcccccceEEEECCCCcccccceeeeccCCCc
Q psy4856 606 SITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNG 646 (654)
Q Consensus 606 ~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~ 646 (654)
.|.... |.|+.+..+|.| |+.++ .++|+||++.+.++
T Consensus 3 ~G~vV~-G~V~~v~~~gl~-v~L~~--g~~G~v~~seis~~ 39 (100)
T cd05693 3 EGMLVL-GQVKEITKLDLV-ISLPN--GLTGYVPITNISDA 39 (100)
T ss_pred CCCEEE-EEEEEEcCCCEE-EECCC--CcEEEEEHHHhhHH
Confidence 566776 999999999999 76653 58999999988764
No 73
>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=63.71 E-value=4.9 Score=31.12 Aligned_cols=32 Identities=13% Similarity=0.274 Sum_probs=26.2
Q ss_pred EEEcccccceEEEECCCCcccccceeeeccCCCcc
Q psy4856 613 ARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGN 647 (654)
Q Consensus 613 ~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~ 647 (654)
|.|+++.++|+| |+.. ..++|++|.+.+.+++
T Consensus 3 g~V~~v~~~g~~-v~l~--~~~~g~~~~~~~~~~~ 34 (65)
T cd00164 3 GKVVSITKFGVF-VELE--DGVEGLVHISELSDKF 34 (65)
T ss_pred EEEEEEEeeeEE-EEec--CCCEEEEEHHHCCCcc
Confidence 889999999999 6554 2489999999998754
No 74
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=63.16 E-value=6.9 Score=43.17 Aligned_cols=41 Identities=20% Similarity=0.174 Sum_probs=29.1
Q ss_pred HhhcccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCc
Q psy4856 601 FFRRKSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNG 646 (654)
Q Consensus 601 ~l~~~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~ 646 (654)
+.+-+.|+... |.|+++.++|+| |+.. .++|+||.|.++++
T Consensus 187 ~~~~~~G~~v~-g~V~~v~~~G~f-V~l~---~v~g~v~~sels~~ 227 (390)
T PRK06676 187 LSSLKEGDVVE-GTVARLTDFGAF-VDIG---GVDGLVHISELSHE 227 (390)
T ss_pred HhhCCCCCEEE-EEEEEEecceEE-EEeC---CeEEEEEHHHcCcc
Confidence 33345677887 888888888888 5553 37888888877754
No 75
>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=62.08 E-value=6.5 Score=33.41 Aligned_cols=37 Identities=16% Similarity=-0.023 Sum_probs=30.5
Q ss_pred ccCcccceEEEcccccceEEEECCCCcccccceeeeccCCC
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPN 645 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~ 645 (654)
+.|+... |.|+++.++|.+ |+... ..+|++|.|.+..
T Consensus 5 ~~GdiV~-g~V~~i~~~g~~-v~i~~--~~~G~l~~se~~~ 41 (86)
T cd05789 5 EVGDVVI-GRVTEVGFKRWK-VDINS--PYDAVLPLSEVNL 41 (86)
T ss_pred CCCCEEE-EEEEEECCCEEE-EECCC--CeEEEEEHHHccC
Confidence 4678887 999999999999 65542 4899999999874
No 76
>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=61.58 E-value=5 Score=45.91 Aligned_cols=40 Identities=15% Similarity=0.303 Sum_probs=33.9
Q ss_pred ccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccE
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNI 648 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~ 648 (654)
+.|+... |.|++++++|+| |+..+ .++|++|.|.+++++.
T Consensus 445 ~~G~~v~-g~V~~v~~~G~f-V~l~~--~~~Glv~~s~l~~~~~ 484 (516)
T TIGR00717 445 KVGSVVK-GKVTEIKDFGAF-VELPG--GVEGLIRNSELSENRD 484 (516)
T ss_pred CcceEEE-EEEEEEecceEE-EEcCC--CeEEEEEHHHcCcccc
Confidence 5799999 999999999999 76653 4899999999987653
No 77
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=61.02 E-value=5.1 Score=39.50 Aligned_cols=50 Identities=14% Similarity=0.162 Sum_probs=40.8
Q ss_pred HHHHHhhcccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccEEecC
Q psy4856 597 HTHLFFRRKSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEVTY 652 (654)
Q Consensus 597 ~~~~~l~~~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~~~~~ 652 (654)
|.+..|+...|+... |.|+.+..+|+| |.. | ++++.||.+.++++ ++|+.
T Consensus 72 FraivFrPf~gEVv~-g~V~~v~~~G~~-v~~-G--p~~ifI~~~~l~~~-~~fd~ 121 (176)
T PTZ00162 72 YQAIVFKPFKDEVLD-AIVTDVNKLGFF-AQA-G--PLKAFVSRSAIPPD-FVYDS 121 (176)
T ss_pred EEEEEEecCCCCEEE-EEEEEEecceEE-EEe-e--CeEEEEcHHHCCCc-cEECC
Confidence 456678889999999 999999999999 633 3 45799999999876 77753
No 78
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=60.60 E-value=21 Score=28.68 Aligned_cols=47 Identities=17% Similarity=0.251 Sum_probs=34.6
Q ss_pred EEEEEE-ec-CCCceeEEeecCCCcCeEecCCCC----CCcCCCCCEEEEEEccC
Q psy4856 137 QGSFQA-SR-ENFLEGQVNCEGYDKPILVQGREG----LNRAIDGDTVAVRLLPE 185 (654)
Q Consensus 137 ~G~l~v-~~-~n~~egfV~~~~~~~dI~I~g~~~----~NRAl~GD~V~Vellp~ 185 (654)
+|++.- +. ++| ||+..++.++|||+.-..- ..+.-.||.|..++-..
T Consensus 2 ~G~Vk~~~~~kGf--GFI~~~~~g~diffh~~~~~~~~~~~~~~G~~V~f~~~~~ 54 (65)
T cd04458 2 TGTVKWFDDEKGF--GFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEG 54 (65)
T ss_pred cEEEEEEECCCCe--EEEecCCCCcCEEEEhhHhhccCCCcCCCCCEEEEEEEEC
Confidence 466643 33 588 9999998889999887622 23468899999998764
No 79
>PRK09890 cold shock protein CspG; Provisional
Probab=59.46 E-value=27 Score=28.97 Aligned_cols=48 Identities=13% Similarity=0.176 Sum_probs=34.5
Q ss_pred EEEEEEE-e-cCCCceeEEeecCCCcCeEecCCCC----CCcCCCCCEEEEEEccC
Q psy4856 136 LQGSFQA-S-RENFLEGQVNCEGYDKPILVQGREG----LNRAIDGDTVAVRLLPE 185 (654)
Q Consensus 136 ~~G~l~v-~-~~n~~egfV~~~~~~~dI~I~g~~~----~NRAl~GD~V~Vellp~ 185 (654)
.+|++.- + .++| ||+.+++.++|||+.-..- ..+--.||.|..++...
T Consensus 5 ~~G~Vk~f~~~kGf--GFI~~~~g~~dvFvH~s~l~~~~~~~l~~G~~V~f~~~~~ 58 (70)
T PRK09890 5 MTGLVKWFNADKGF--GFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQG 58 (70)
T ss_pred ceEEEEEEECCCCc--EEEecCCCCceEEEEEeeeccCCCCCCCCCCEEEEEEEEC
Confidence 3788776 3 3688 9999998788999875411 12335899999988654
No 80
>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=57.46 E-value=6.5 Score=31.75 Aligned_cols=36 Identities=14% Similarity=-0.014 Sum_probs=28.5
Q ss_pred CcccceEEEcccccceEEEECCCCcccccceeeeccCCCcc
Q psy4856 607 ITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGN 647 (654)
Q Consensus 607 g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~ 647 (654)
|+... |.|+.+.++|+| |+.. .++|++|.|.++..+
T Consensus 1 G~iv~-g~V~~v~~~G~~-v~l~---g~~gfip~s~~~~~~ 36 (67)
T cd04465 1 GEIVE-GKVTEKVKGGLI-VDIE---GVRAFLPASQVDLRP 36 (67)
T ss_pred CCEEE-EEEEEEECCeEE-EEEC---CEEEEEEHHHCCCcc
Confidence 45566 899999999999 7662 489999999887554
No 81
>PRK05054 exoribonuclease II; Provisional
Probab=56.88 E-value=47 Score=39.46 Aligned_cols=56 Identities=20% Similarity=0.155 Sum_probs=38.2
Q ss_pred HHHhhhcC-CeEEEEEEEecCCCceeEEeecCC--CcCeEecCCCCCC-cCCCCCEEEEEEcc
Q psy4856 126 IHAGIKNQ-SLLQGSFQASRENFLEGQVNCEGY--DKPILVQGREGLN-RAIDGDTVAVRLLP 184 (654)
Q Consensus 126 l~~gik~g-~l~~G~l~v~~~n~~egfV~~~~~--~~dI~I~g~~~~N-RAl~GD~V~Vellp 184 (654)
+..-|+.+ ..+.|++.... ++ +||.+.+. ..+|+|......+ .+-+||+|.|+|..
T Consensus 75 v~~il~r~~~~~vG~~~~~~-~~--~~~~p~d~~~~~~i~i~~~~~~~~~~~~gd~V~v~i~~ 134 (644)
T PRK05054 75 PEELIEPFLTRFVGRVQKKD-DR--LSIVPDHPLLKDAIPCRAAKGLNHEFKEGDWVVAELRR 134 (644)
T ss_pred EEEEEecCCCEEEEEEEEeC-ce--EEEEECCCCCCccEEeccccccccCCCCCCEEEEEEec
Confidence 44444444 48899998653 34 78888753 5689996432333 58899999999973
No 82
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=56.85 E-value=33 Score=28.44 Aligned_cols=47 Identities=15% Similarity=0.189 Sum_probs=34.4
Q ss_pred EEEEEE-e-cCCCceeEEeecCCCcCeEecCCCCC----CcCCCCCEEEEEEccC
Q psy4856 137 QGSFQA-S-RENFLEGQVNCEGYDKPILVQGREGL----NRAIDGDTVAVRLLPE 185 (654)
Q Consensus 137 ~G~l~v-~-~~n~~egfV~~~~~~~dI~I~g~~~~----NRAl~GD~V~Vellp~ 185 (654)
+|++.- + .+|| ||+.+++.++|||+.-..-. .+--.||.|..++...
T Consensus 6 ~G~Vk~f~~~kGf--GFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~ 58 (70)
T PRK10354 6 TGIVKWFNADKGF--GFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESG 58 (70)
T ss_pred eEEEEEEeCCCCc--EEEecCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEEC
Confidence 788765 2 3688 99999987889997665221 2347899999998754
No 83
>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=56.57 E-value=46 Score=39.45 Aligned_cols=51 Identities=20% Similarity=0.206 Sum_probs=34.7
Q ss_pred hhcC-CeEEEEEEEecCCCceeEEeecCC--CcCeEecCCCCCC-cCCCCCEEEEEEc
Q psy4856 130 IKNQ-SLLQGSFQASRENFLEGQVNCEGY--DKPILVQGREGLN-RAIDGDTVAVRLL 183 (654)
Q Consensus 130 ik~g-~l~~G~l~v~~~n~~egfV~~~~~--~~dI~I~g~~~~N-RAl~GD~V~Vell 183 (654)
|+.+ ..+.|++..... + +||.+.+. ...|++...+..+ .+-+||.|+|+|.
T Consensus 76 ver~~~~~vG~~~~~~~-~--~~v~p~d~~~~~~i~~~~~~~~~~~~~~gd~V~v~I~ 130 (639)
T TIGR02062 76 IEPFLTRFVGKVQGKDD-K--LAIVPDHPLLKDAIPCRAAKGLNHEFQEGDWAVAELR 130 (639)
T ss_pred EccCCCEEEEEEEEeCC-e--EEEEECCCCCCccEEecCccccccCCCCCCEEEEEEe
Confidence 4444 689999987544 4 78888653 3457774432333 5668999999998
No 84
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=56.40 E-value=14 Score=34.87 Aligned_cols=38 Identities=18% Similarity=0.198 Sum_probs=30.9
Q ss_pred hHHHHHHHHHhHhhhhhhccCCeEEEEeCChhhHHHHhhcCcceeeHH
Q psy4856 38 DRALRRVATWYVKYEEHLESAVRVILLSEDVRNRDLATQSGLLTSSIE 85 (654)
Q Consensus 38 ~r~i~~aa~wY~~~~~Hl~~~~~vvllt~d~~~~~~a~~~gi~~~s~~ 85 (654)
|-+|..+|.=+ -..++.|||.+-++++++.||+++++.
T Consensus 87 De~i~~~a~~~----------~~~iVaTnD~eLk~rlr~~GIPvi~lr 124 (136)
T COG1412 87 DECLLEAALKH----------GRYIVATNDKELKRRLRENGIPVITLR 124 (136)
T ss_pred HHHHHHHHHHc----------CCEEEEeCCHHHHHHHHHcCCCEEEEe
Confidence 55666666544 258999999999999999999999886
No 85
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=56.10 E-value=7.4 Score=42.90 Aligned_cols=38 Identities=11% Similarity=0.113 Sum_probs=31.5
Q ss_pred ccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCc
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNG 646 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~ 646 (654)
+.|.... |.|+.+.++|+| |+..+ .++|++|.|.+++.
T Consensus 276 ~~G~~v~-g~V~~i~~~G~f-V~l~~--gi~Glv~~se~~~~ 313 (390)
T PRK06676 276 PEGDVIE-GTVKRLTDFGAF-VEVLP--GVEGLVHISQISHK 313 (390)
T ss_pred cCCcEEE-EEEEEEeCceEE-EEECC--CCeEEEEhHHcCcc
Confidence 4688999 999999999999 65542 48999999988753
No 86
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=54.67 E-value=27 Score=29.44 Aligned_cols=48 Identities=19% Similarity=0.299 Sum_probs=33.8
Q ss_pred EEEEEE-e-cCCCceeEEeecCCCcCeEecCCC----CCCcCCCCCEEEEEEccCC
Q psy4856 137 QGSFQA-S-RENFLEGQVNCEGYDKPILVQGRE----GLNRAIDGDTVAVRLLPES 186 (654)
Q Consensus 137 ~G~l~v-~-~~n~~egfV~~~~~~~dI~I~g~~----~~NRAl~GD~V~Vellp~~ 186 (654)
+|++.- | .++| ||+.+++.++|||+.=.. ..-+--.||.|..++-...
T Consensus 3 ~G~Vkwfn~~KGf--GFI~~~~gg~dVFvH~s~i~~~g~~~l~~G~~V~f~~~~~~ 56 (74)
T PRK09937 3 KGTVKWFNNAKGF--GFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGP 56 (74)
T ss_pred CeEEEEEeCCCCe--EEEeeCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEECC
Confidence 466554 2 3678 999999888999977431 1234678999999987543
No 87
>KOG1067|consensus
Probab=54.65 E-value=14 Score=42.27 Aligned_cols=36 Identities=25% Similarity=0.181 Sum_probs=30.5
Q ss_pred ccceEEEcccccceEEEECCCCcccccceeeeccCCCccE
Q psy4856 609 EEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNI 648 (654)
Q Consensus 609 ~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~ 648 (654)
... |.|+..++||.| |+..+ +-+||+|.|.|+..|+
T Consensus 671 vy~-~tIt~~rd~G~~-V~l~p--~~~~Llh~sqL~~e~i 706 (760)
T KOG1067|consen 671 VYT-ATITEIRDTGVM-VELYP--MQQGLLHNSQLDQEKI 706 (760)
T ss_pred EEE-EEEeeecccceE-EEecC--Cchhhccchhcccccc
Confidence 346 889999999999 76665 5799999999999886
No 88
>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=53.37 E-value=14 Score=32.20 Aligned_cols=39 Identities=10% Similarity=0.078 Sum_probs=31.2
Q ss_pred CcccceEEEcccccceEEEECCCCcccccceeeeccCCCccEEec
Q psy4856 607 ITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEVT 651 (654)
Q Consensus 607 g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~~~~ 651 (654)
|+... |.|+.+...|+| |.. .+++|.+|.+..+++ |.|.
T Consensus 2 gEVi~-g~V~~v~~~G~~-v~~---Gpl~~f~~~~~ip~~-~~~~ 40 (88)
T cd04462 2 GEVVD-AIVTSVNKTGFF-AEV---GPLSIFISRHLIPSD-MEFD 40 (88)
T ss_pred CcEEE-EEEEEEeccEEE-EEE---cCceEEEEeeecCcc-ceEC
Confidence 66777 999999999999 533 247899999999888 6654
No 89
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=52.92 E-value=51 Score=27.26 Aligned_cols=50 Identities=18% Similarity=0.313 Sum_probs=36.2
Q ss_pred eEEEEEEEe--cCCCceeEEeecCCCcCeEecCCC----CCCcCCCCCEEEEEEccCC
Q psy4856 135 LLQGSFQAS--RENFLEGQVNCEGYDKPILVQGRE----GLNRAIDGDTVAVRLLPES 186 (654)
Q Consensus 135 l~~G~l~v~--~~n~~egfV~~~~~~~dI~I~g~~----~~NRAl~GD~V~Vellp~~ 186 (654)
-++|++.-- .++| ||+.+++.++|||+.-.. ...+--.||.|..++....
T Consensus 3 ~~~G~Vk~f~~~kGy--GFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~~ 58 (69)
T PRK09507 3 KIKGNVKWFNESKGF--GFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGA 58 (69)
T ss_pred ccceEEEEEeCCCCc--EEEecCCCCeeEEEEeecccccCCCCCCCCCEEEEEEEECC
Confidence 356777652 4688 999999878899987542 2234578999999987543
No 90
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=51.37 E-value=16 Score=44.65 Aligned_cols=40 Identities=13% Similarity=0.180 Sum_probs=33.1
Q ss_pred cccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccE
Q psy4856 604 RKSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNI 648 (654)
Q Consensus 604 ~~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~ 648 (654)
-..|+... |.|..+.+||.| |+.. .++|+||+|.++.++.
T Consensus 491 l~~G~~V~-G~Vk~i~~~G~f-Vdl~---Gv~Gfvp~SeiS~~~v 530 (863)
T PRK12269 491 VHIEDSVS-GVVKSFTSFGAF-IDLG---GFDGLLHVNDMSWGHV 530 (863)
T ss_pred CCCCCEEE-EEEEEEeCCcEE-EEEC---CEEEEEEchhcccccc
Confidence 45788888 999999999999 7663 5899999999876653
No 91
>PRK14998 cold shock-like protein CspD; Provisional
Probab=50.37 E-value=34 Score=28.71 Aligned_cols=47 Identities=17% Similarity=0.211 Sum_probs=33.0
Q ss_pred EEEEEE-e-cCCCceeEEeecCCCcCeEecCCCC----CCcCCCCCEEEEEEccC
Q psy4856 137 QGSFQA-S-RENFLEGQVNCEGYDKPILVQGREG----LNRAIDGDTVAVRLLPE 185 (654)
Q Consensus 137 ~G~l~v-~-~~n~~egfV~~~~~~~dI~I~g~~~----~NRAl~GD~V~Vellp~ 185 (654)
+|++.- | .++| ||+.+++.++|||+.=..- .-+--.||.|..++...
T Consensus 3 ~G~Vkwfn~~kGf--GFI~~~~g~~dVFvH~s~l~~~g~~~l~~G~~V~f~~~~~ 55 (73)
T PRK14998 3 TGTVKWFNNAKGF--GFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQG 55 (73)
T ss_pred CeEEEEEeCCCce--EEEecCCCCccEEEEeeeecccCCCCCCCCCEEEEEEEEC
Confidence 355554 2 3678 9999998889999764411 12456899999998754
No 92
>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=50.29 E-value=12 Score=30.37 Aligned_cols=37 Identities=8% Similarity=0.013 Sum_probs=28.5
Q ss_pred CcccceEEEcccccceEEEECCCCcccccceeeeccCCCcc
Q psy4856 607 ITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGN 647 (654)
Q Consensus 607 g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~ 647 (654)
|+... |.|+.+.++|.| |+.. . ..+|++|.+.+.+.+
T Consensus 1 G~iv~-g~V~~i~~~~~~-v~l~-~-~~~g~l~~~e~~~~~ 37 (70)
T cd05687 1 GDIVK-GTVVSVDDDEVL-VDIG-Y-KSEGIIPISEFSDDP 37 (70)
T ss_pred CCEEE-EEEEEEeCCEEE-EEeC-C-CceEEEEHHHhCccc
Confidence 34455 899999999999 7664 2 479999999887653
No 93
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=49.53 E-value=12 Score=44.31 Aligned_cols=39 Identities=8% Similarity=0.045 Sum_probs=32.8
Q ss_pred ccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCcc
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGN 647 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~ 647 (654)
+.|++.. |.|+++.++|+| |+..+ +++|++|.+.++++.
T Consensus 561 ~~G~~v~-g~V~~i~~~G~f-V~l~~--~i~Gli~~sel~~~~ 599 (647)
T PRK00087 561 PVGSIVL-GKVVRIAPFGAF-VELEP--GVDGLVHISQISWKR 599 (647)
T ss_pred cCCeEEE-EEEEEEECCeEE-EEECC--CCEEEEEhhhcCccc
Confidence 5799999 999999999999 65543 589999999988653
No 94
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=49.02 E-value=11 Score=43.61 Aligned_cols=38 Identities=16% Similarity=0.192 Sum_probs=32.2
Q ss_pred ccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCc
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNG 646 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~ 646 (654)
..|+... |.|+++.++|+| |+... .++|++|+|.++++
T Consensus 372 ~~G~~v~-g~V~~v~~~G~f-V~l~~--~v~g~i~~s~l~~~ 409 (565)
T PRK06299 372 PVGDVVE-GKVKNITDFGAF-VGLEG--GIDGLVHLSDISWD 409 (565)
T ss_pred CCCCEEE-EEEEEEecceEE-EECCC--CCEEEEEHHHcCcc
Confidence 4699998 999999999999 76653 48999999998853
No 95
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=48.53 E-value=32 Score=28.59 Aligned_cols=47 Identities=23% Similarity=0.321 Sum_probs=36.5
Q ss_pred EEEEEEecCCCceeEEeecC-----CCcCeEecCCC-CCCcCCCCCEEEEEEccC
Q psy4856 137 QGSFQASRENFLEGQVNCEG-----YDKPILVQGRE-GLNRAIDGDTVAVRLLPE 185 (654)
Q Consensus 137 ~G~l~v~~~n~~egfV~~~~-----~~~dI~I~g~~-~~NRAl~GD~V~Vellp~ 185 (654)
.|+|.+...|| ||++..+ .++||||+... .+..==.||.|.-++-+.
T Consensus 2 ~GiLdi~~~g~--GFLR~~~~~y~~~~~DvyVs~~~Irr~~LR~GD~V~G~vr~p 54 (68)
T cd04459 2 SGVLEILPDGF--GFLRSSGYNYLPGPDDIYVSPSQIRRFNLRTGDTVVGQIRPP 54 (68)
T ss_pred cEEEEEcCCCc--eEEecCCcCCCCCCCCEEECHHHHHHhCCCCCCEEEEEEeCC
Confidence 59999999999 9999873 26799998852 224445899999998764
No 96
>COG1278 CspC Cold shock proteins [Transcription]
Probab=47.33 E-value=27 Score=29.01 Aligned_cols=41 Identities=20% Similarity=0.315 Sum_probs=30.5
Q ss_pred ecCCCceeEEeecCCCcCeEecCCC----CCCcCCCCCEEEEEEccC
Q psy4856 143 SRENFLEGQVNCEGYDKPILVQGRE----GLNRAIDGDTVAVRLLPE 185 (654)
Q Consensus 143 ~~~n~~egfV~~~~~~~dI~I~g~~----~~NRAl~GD~V~Vellp~ 185 (654)
..++| ||+.+++.++||||.=.. .+-+=..|+.|..++...
T Consensus 11 ~~KGf--GFI~p~~G~~DvFVH~Sai~~~g~~~L~eGQ~V~f~~~~g 55 (67)
T COG1278 11 ATKGF--GFITPEDGGKDVFVHISAIQRAGFRTLREGQKVEFEVEQG 55 (67)
T ss_pred CCCcc--eEcCCCCCCcCEEEEeeeeccCCCcccCCCCEEEEEEecC
Confidence 45788 999999988999987541 223446899999988654
No 97
>KOG2102|consensus
Probab=47.13 E-value=12 Score=46.30 Aligned_cols=37 Identities=68% Similarity=1.110 Sum_probs=33.5
Q ss_pred EcccccceEEEECCCCcccccceeeeccCCCccEEec
Q psy4856 615 RTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEVT 651 (654)
Q Consensus 615 i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~~~~ 651 (654)
..+.+..-+|.|+|+++.+++..|||..++||.||.|
T Consensus 473 R~Dlr~~~i~~IDp~~~~dlDdAL~~~~l~nG~~evG 509 (941)
T KOG2102|consen 473 RKDLRDLLIFSIDPPGATDLDDALHVRNLPNGNLEVG 509 (941)
T ss_pred hhhhhhceEEeecCCCccchhhhhheeecCCCcEEEE
Confidence 4566788899999999999999999999999999986
No 98
>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=46.73 E-value=18 Score=41.34 Aligned_cols=37 Identities=14% Similarity=0.197 Sum_probs=31.7
Q ss_pred ccCcccceEEEcccccceEEEECCCCcccccceeeeccCCC
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPN 645 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~ 645 (654)
..|+... |.|+.+.++|+| |+..+ .++|+||.+.|+.
T Consensus 358 ~~G~~v~-g~V~~v~~~G~f-V~l~~--~v~glv~~s~ls~ 394 (516)
T TIGR00717 358 PVGDRVT-GKIKKITDFGAF-VELEG--GIDGLIHLSDISW 394 (516)
T ss_pred CCCCEEE-EEEEEEecceEE-EECCC--CCEEEEEHHHCcC
Confidence 5799998 999999999999 76652 5899999999874
No 99
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=45.87 E-value=9.4 Score=45.44 Aligned_cols=40 Identities=18% Similarity=0.184 Sum_probs=33.2
Q ss_pred cCcccceEEEcccccceEEEECCCCcccccceeeeccCCCccEE
Q psy4856 606 SITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIE 649 (654)
Q Consensus 606 ~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~~~ 649 (654)
.|.... |+|+.|..||.| |++ |+. .+|+||+|.+.+..+.
T Consensus 658 ~Gm~le-g~Vrnv~~fgaf-VdI-gv~-qDglvHis~ls~~fv~ 697 (780)
T COG2183 658 PGMILE-GTVRNVVDFGAF-VDI-GVH-QDGLVHISQLSDKFVK 697 (780)
T ss_pred CCCEEE-EEEEEeeeccce-EEe-ccc-cceeeeHHHhhhhhcC
Confidence 588888 999999999999 644 454 7999999999887654
No 100
>PRK00215 LexA repressor; Validated
Probab=40.90 E-value=1.8e+02 Score=28.75 Aligned_cols=41 Identities=17% Similarity=0.146 Sum_probs=26.8
Q ss_pred ceeEEEEEeecCceeeeeecCCCCCCCceEEEEeCCCCCCcEEEcc
Q psy4856 227 TGQIVGIIKRKWRQYCGILQPNPLAGSSRHLFVPAERKIPKIRVET 272 (654)
Q Consensus 227 tGkVVgIi~R~~r~~vG~l~~~~~~~~~~~l~vP~D~riP~I~I~t 272 (654)
.|+||-+.- +...+|-.|... .+...+.|.++..|.|.+..
T Consensus 149 ~G~ivv~~~-~~~~~vKrl~~~----~~~~~L~s~Np~y~~~~~~~ 189 (205)
T PRK00215 149 NGQIVVALI-DDEATVKRFRRE----GGHIRLEPENPAYEPIIVDP 189 (205)
T ss_pred CCCEEEEEE-CCEEEEEEEEEe----CCEEEEEcCCCCCCCEEeCC
Confidence 476664432 224456666554 45688999999998887754
No 101
>TIGR02381 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.
Probab=40.70 E-value=37 Score=27.93 Aligned_cols=48 Identities=19% Similarity=0.222 Sum_probs=33.7
Q ss_pred EEEEEE--ecCCCceeEEeecCCCcCeEecCCCCC----CcCCCCCEEEEEEccCC
Q psy4856 137 QGSFQA--SRENFLEGQVNCEGYDKPILVQGREGL----NRAIDGDTVAVRLLPES 186 (654)
Q Consensus 137 ~G~l~v--~~~n~~egfV~~~~~~~dI~I~g~~~~----NRAl~GD~V~Vellp~~ 186 (654)
+|++.- ..++| ||+.+++.++|||+.-..-. -+--.||.|..++....
T Consensus 3 ~G~Vk~f~~~kGf--GFI~~~~g~~dvfvH~s~~~~~g~~~l~~G~~V~f~~~~~~ 56 (68)
T TIGR02381 3 IGIVKWFNNAKGF--GFICPEGVDGDIFAHYSTIQMDGYRTLKAGQKVQFEVVQGP 56 (68)
T ss_pred CeEEEEEeCCCCe--EEEecCCCCccEEEEHHHhhhcCCCCCCCCCEEEEEEEECC
Confidence 365554 24688 99999987899998765222 23467999999886543
No 102
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=39.38 E-value=24 Score=41.81 Aligned_cols=37 Identities=22% Similarity=0.247 Sum_probs=31.7
Q ss_pred ccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCc
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNG 646 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~ 646 (654)
+.|+... |.|+++.++|+| |+.. .++|+||.|.+++.
T Consensus 476 ~~G~iV~-g~V~~v~~~G~f-V~l~---gv~Gll~~sels~~ 512 (647)
T PRK00087 476 EEGDVVE-GEVKRLTDFGAF-VDIG---GVDGLLHVSEISWG 512 (647)
T ss_pred CCCCEEE-EEEEEEeCCcEE-EEEC---CEEEEEEHHHcCcc
Confidence 5799998 999999999999 6663 58999999999753
No 103
>PRK15463 cold shock-like protein CspF; Provisional
Probab=38.49 E-value=97 Score=25.76 Aligned_cols=49 Identities=12% Similarity=0.079 Sum_probs=35.2
Q ss_pred EEEEEEEe--cCCCceeEEeecCCCcCeEecCCC----CCCcCCCCCEEEEEEccCC
Q psy4856 136 LQGSFQAS--RENFLEGQVNCEGYDKPILVQGRE----GLNRAIDGDTVAVRLLPES 186 (654)
Q Consensus 136 ~~G~l~v~--~~n~~egfV~~~~~~~dI~I~g~~----~~NRAl~GD~V~Vellp~~ 186 (654)
++|++.-- .++| ||+.+++.++|||+.=.. ..-+--.||.|..++....
T Consensus 5 ~~G~Vk~fn~~kGf--GFI~~~~g~~DvFvH~sal~~~g~~~l~~G~~V~f~v~~~~ 59 (70)
T PRK15463 5 MTGIVKTFDGKSGK--GLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGL 59 (70)
T ss_pred ceEEEEEEeCCCce--EEEecCCCCccEEEEehhhhhcCCCCCCCCCEEEEEEEECC
Confidence 36777653 3577 999999888999987431 1234668999999987543
No 104
>PRK10943 cold shock-like protein CspC; Provisional
Probab=38.44 E-value=83 Score=26.01 Aligned_cols=49 Identities=14% Similarity=0.228 Sum_probs=34.9
Q ss_pred EEEEEEEe--cCCCceeEEeecCCCcCeEecCCCC----CCcCCCCCEEEEEEccCC
Q psy4856 136 LQGSFQAS--RENFLEGQVNCEGYDKPILVQGREG----LNRAIDGDTVAVRLLPES 186 (654)
Q Consensus 136 ~~G~l~v~--~~n~~egfV~~~~~~~dI~I~g~~~----~NRAl~GD~V~Vellp~~ 186 (654)
++|++.-- .++| ||+.+++.++|||+.=..- ..+--.||.|..++-...
T Consensus 4 ~~G~Vk~f~~~kGf--GFI~~~~g~~dvFvH~s~l~~~g~~~l~~G~~V~f~~~~~~ 58 (69)
T PRK10943 4 IKGQVKWFNESKGF--GFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQ 58 (69)
T ss_pred cceEEEEEeCCCCc--EEEecCCCCeeEEEEhhHccccCCCCCCCCCEEEEEEEECC
Confidence 46777652 3678 9999988788999765421 123468999999986543
No 105
>PRK12423 LexA repressor; Provisional
Probab=37.54 E-value=1.4e+02 Score=29.72 Aligned_cols=41 Identities=22% Similarity=0.155 Sum_probs=26.7
Q ss_pred ceeEEEEEeecCceeeeeecCCCCCCCceEEEEeCCCCCCcEEEcc
Q psy4856 227 TGQIVGIIKRKWRQYCGILQPNPLAGSSRHLFVPAERKIPKIRVET 272 (654)
Q Consensus 227 tGkVVgIi~R~~r~~vG~l~~~~~~~~~~~l~vP~D~riP~I~I~t 272 (654)
.|.||-+.- +...+|-.|... .+.+.+.|.++..|.|.+..
T Consensus 145 ~Gdivv~~~-~~~~~vKrl~~~----~~~~~L~s~N~~y~~i~~~~ 185 (202)
T PRK12423 145 DGQIVVARL-DGEVTIKRLERS----GDRIRLLPRNPAYAPIVVAP 185 (202)
T ss_pred CCCEEEEEE-CCEEEEEEEEEe----CCEEEEEcCCCCCCCEEcCC
Confidence 466554432 334456666554 35688999999998887764
No 106
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=36.66 E-value=34 Score=39.77 Aligned_cols=38 Identities=16% Similarity=0.140 Sum_probs=29.0
Q ss_pred ccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCcc
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGN 647 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~~ 647 (654)
+.|.... |.|+.+.++|.| |+.. .++|+||.|.++.++
T Consensus 200 ~~G~iv~-g~V~~v~~~G~~-V~i~---g~~glv~~se~s~~~ 237 (565)
T PRK06299 200 EEGQVVE-GVVKNITDYGAF-VDLG---GVDGLLHITDISWKR 237 (565)
T ss_pred CCCCEEE-EEEEEEeCCeEE-EEEC---CEEEEEEHHHhcccc
Confidence 4678887 888888888888 6553 478888888876554
No 107
>PRK15464 cold shock-like protein CspH; Provisional
Probab=34.68 E-value=1.1e+02 Score=25.43 Aligned_cols=47 Identities=15% Similarity=0.097 Sum_probs=34.8
Q ss_pred EEEEEEEe--cCCCceeEEeecCCCcCeEecCCCCC-----CcCCCCCEEEEEEccC
Q psy4856 136 LQGSFQAS--RENFLEGQVNCEGYDKPILVQGREGL-----NRAIDGDTVAVRLLPE 185 (654)
Q Consensus 136 ~~G~l~v~--~~n~~egfV~~~~~~~dI~I~g~~~~-----NRAl~GD~V~Vellp~ 185 (654)
.+|++.-- .+|| ||+.+++.++|||+.=. .+ -+--.||.|..++...
T Consensus 5 ~~G~Vk~fn~~KGf--GFI~~~~g~~DvFvH~s-~l~~~g~~~l~~G~~V~f~v~~~ 58 (70)
T PRK15464 5 MTGIVKTFDRKSGK--GFIIPSDGRKEVQVHIS-AFTPRDAEVLIPGLRVEFCRVNG 58 (70)
T ss_pred ceEEEEEEECCCCe--EEEccCCCCccEEEEeh-hehhcCCCCCCCCCEEEEEEEEC
Confidence 37877653 3577 99999988889997654 22 2467899999998754
No 108
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=32.45 E-value=56 Score=38.62 Aligned_cols=39 Identities=13% Similarity=0.048 Sum_probs=32.3
Q ss_pred cccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCc
Q psy4856 604 RKSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNG 646 (654)
Q Consensus 604 ~~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~ 646 (654)
-.+|+.+. |.|+-...||-| |+..+ .-+||||+|.+.+.
T Consensus 617 ~evg~iy~-G~V~ri~~fGaF-v~l~~--gkdgl~hiS~~~~~ 655 (692)
T COG1185 617 VEVGEVYE-GTVVRIVDFGAF-VELLP--GKDGLVHISQLAKE 655 (692)
T ss_pred cccccEEE-EEEEEEeecceE-EEecC--CcceeEEehhhhhh
Confidence 35789998 999999999999 76653 46999999988764
No 109
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=30.85 E-value=90 Score=30.32 Aligned_cols=67 Identities=18% Similarity=0.211 Sum_probs=44.2
Q ss_pred CCeEEEEeCChhhHHHHhhcCcceeeHHHHHhhCCCCchhhhhhcccchhhccccCCCCCCCCCCHHHHHH
Q psy4856 58 AVRVILLSEDVRNRDLATQSGLLTSSIEGYISTLSNGEPLLDKLSKKEAVVETSVKDSLYPLHATPSEIHA 128 (654)
Q Consensus 58 ~~~vvllt~d~~~~~~a~~~gi~~~s~~~yv~~~~~~~~l~d~l~~~~~~~~~~~~~~~y~ehl~~~~l~~ 128 (654)
...|+++|+|..-...+...|..++|..+|...+.....-... ... ......++.-...||.+++..
T Consensus 94 ~~~v~VVTSD~~iq~~~~~~GA~~iss~ef~~~l~~~~~~~~~---~~~-~~~~~~~~~~~~~ls~~~~~~ 160 (166)
T PF05991_consen 94 PRQVTVVTSDREIQRAARGRGAKRISSEEFLRELKAAKREIRK---EAR-ERSSKKKKKLDDRLSPEELEK 160 (166)
T ss_pred CCeEEEEeCCHHHHHHHhhCCCEEEcHHHHHHHHHHHHHHHHH---HHH-hhhhhccccccCCCCHHHHHH
Confidence 4789999999999999999999999999999986432111111 000 001113445556788777654
No 110
>COG1158 Rho Transcription termination factor [Transcription]
Probab=30.74 E-value=84 Score=34.36 Aligned_cols=59 Identities=19% Similarity=0.244 Sum_probs=41.0
Q ss_pred HHHhhhcCCeE--EEEEEEecCCCceeEEeecCC-----CcCeEecCCCCC-CcCCCCCEEEEEEccCC
Q psy4856 126 IHAGIKNQSLL--QGSFQASRENFLEGQVNCEGY-----DKPILVQGREGL-NRAIDGDTVAVRLLPES 186 (654)
Q Consensus 126 l~~gik~g~l~--~G~l~v~~~n~~egfV~~~~~-----~~dI~I~g~~~~-NRAl~GD~V~Vellp~~ 186 (654)
+.+..++|.++ .|+|.+-+.|| ||++..+. .+||||...+-+ ..--.||.|.=++-+..
T Consensus 42 lk~~~e~g~~~~~~GvLeil~dGf--GFLR~~~~~yl~~~~DiYvSpSQIRrf~LrtGD~v~G~vR~Pk 108 (422)
T COG1158 42 LKAQAEQGEEIFGDGVLEILPDGF--GFLRSADSSYLPGPDDIYVSPSQIRRFNLRTGDTVEGKVRPPK 108 (422)
T ss_pred HHHHhhcCceEeeeeEEEeccCCc--ceeecCccccCCCCCceEECHHHHhhccCccCCEEeeeecCCC
Confidence 34444555443 38999999999 99998762 589999986332 22236999988876543
No 111
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=30.37 E-value=42 Score=36.23 Aligned_cols=35 Identities=3% Similarity=-0.104 Sum_probs=29.7
Q ss_pred cCcccceEEEcccccceEEEECCCCcccccceeeeccCCC
Q psy4856 606 SITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPN 645 (654)
Q Consensus 606 ~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~ 645 (654)
.|.... |.|+++..+|+| |+.. .++|+||.|.++.
T Consensus 118 ~~~~V~-g~V~~~~~~G~~-V~l~---Gv~gfip~s~ls~ 152 (318)
T PRK07400 118 EDATVR-SEVFATNRGGAL-VRIE---GLRGFIPGSHIST 152 (318)
T ss_pred CCCEEE-EEEEEEECCeEE-EEEC---CEEEEEEHHHcCc
Confidence 467788 999999999999 7664 5899999998875
No 112
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=30.27 E-value=41 Score=27.23 Aligned_cols=36 Identities=11% Similarity=-0.028 Sum_probs=29.3
Q ss_pred ccCcccceEEEcccccceEEEECCCCcccccceeeeccCCC
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPN 645 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~ 645 (654)
+.|+... |.|......|+| |+..+ +||.++.+.+..
T Consensus 2 ~~g~iV~-G~V~~~~~~~~~-vdig~---~eg~lp~~e~~~ 37 (67)
T cd04455 2 REGEIVT-GIVKRVDRGNVI-VDLGK---VEAILPKKEQIP 37 (67)
T ss_pred CCCCEEE-EEEEEEcCCCEE-EEcCC---eEEEeeHHHCCC
Confidence 4577777 999999999999 77742 799999998764
No 113
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=29.64 E-value=3.3e+02 Score=25.38 Aligned_cols=40 Identities=18% Similarity=0.147 Sum_probs=24.7
Q ss_pred ceeEEEEEeecCceeeeeecCCCCCCCceEEEEeCCCCCCcEEEcc
Q psy4856 227 TGQIVGIIKRKWRQYCGILQPNPLAGSSRHLFVPAERKIPKIRVET 272 (654)
Q Consensus 227 tGkVVgIi~R~~r~~vG~l~~~~~~~~~~~l~vP~D~riP~I~I~t 272 (654)
.|.+|-+ ..+-...|-.|... ....+.|.++..|.|.+..
T Consensus 82 ~Gdivv~-~~~g~~~vKrl~~~-----~~~~L~s~N~~y~~i~i~~ 121 (139)
T PRK10276 82 HGDIVIA-AVDGEFTVKKLQLR-----PTVQLIPMNSAYSPITISS 121 (139)
T ss_pred CCCEEEE-EECCEEEEEEEEEC-----CcEEEEcCCCCCCCEEcCC
Confidence 4666543 23333455555543 2477899999998887754
No 114
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=27.41 E-value=33 Score=34.00 Aligned_cols=40 Identities=18% Similarity=0.113 Sum_probs=30.9
Q ss_pred ccCcccceEEEcccccceEEEECCCC--------cccccceeeeccCCCc
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPG--------CTDIDDALHCRPLPNG 646 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~--------~~~~eg~vh~~~~~~~ 646 (654)
+.|.... |.|+++..+|+| |++.. ...++|++|++.+.+.
T Consensus 63 ~~GdiV~-GkV~~i~~~g~~-V~I~~~~~~~~~l~~~~~G~l~~s~i~~~ 110 (189)
T PRK09521 63 KKGDIVY-GRVVDVKEQRAL-VRIVSIEGSERELATSKLAYIHISQVSDG 110 (189)
T ss_pred CCCCEEE-EEEEEEcCCeEE-EEEEEecccccccCCCceeeEEhhHcChh
Confidence 4688887 999999999999 66532 1257999999988754
No 115
>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=26.29 E-value=60 Score=27.19 Aligned_cols=38 Identities=11% Similarity=-0.200 Sum_probs=30.3
Q ss_pred ccCcccceEEEcccccceEEEECCCCcccccceeeeccCCCc
Q psy4856 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNG 646 (654)
Q Consensus 605 ~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~~~~ 646 (654)
+.|..-. |.|+++.+.+.+ |++-. ..+|.+|.+.+..+
T Consensus 5 ~~GdiV~-G~V~~v~~~~~~-V~i~~--~~~g~l~~~~~~~~ 42 (82)
T cd04454 5 DVGDIVI-GIVTEVNSRFWK-VDILS--RGTARLEDSSATEK 42 (82)
T ss_pred CCCCEEE-EEEEEEcCCEEE-EEeCC--CceEEeechhccCc
Confidence 4567776 999999999999 76642 47999999988754
No 116
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=24.64 E-value=3e+02 Score=27.09 Aligned_cols=41 Identities=12% Similarity=0.182 Sum_probs=26.0
Q ss_pred ceeEEEEEeecCceeeeeecCCCCCCCceEEEEeCCCCCCcEEEcc
Q psy4856 227 TGQIVGIIKRKWRQYCGILQPNPLAGSSRHLFVPAERKIPKIRVET 272 (654)
Q Consensus 227 tGkVVgIi~R~~r~~vG~l~~~~~~~~~~~l~vP~D~riP~I~I~t 272 (654)
.|.+|-+.- +-..+|-.|... .+.+.+.|.|+..|.|.+..
T Consensus 142 ~G~ivvv~~-~~~~~vKrl~~~----~~~i~L~s~N~~y~~i~~~~ 182 (199)
T TIGR00498 142 NGEIVAAMI-DGEVTVKRFYKD----GTKVELKPENPEFDPIVLNA 182 (199)
T ss_pred CCCEEEEEE-CCEEEEEEEEEE----CCEEEEEcCCCCCcCCcCCC
Confidence 466654433 333355555544 45688999999998877654
No 117
>COG0234 GroS Co-chaperonin GroES (HSP10) [Posttranslational modification, protein turnover, chaperones]
Probab=24.08 E-value=1e+02 Score=27.45 Aligned_cols=39 Identities=28% Similarity=0.453 Sum_probs=25.1
Q ss_pred CCEEEEEEccCCCcCCccccccccCCCCCCccccccccccCCCCCCCCCCCCceeEEEEEe
Q psy4856 175 GDTVAVRLLPESQWSAPLELVLEDEGSGEDEEGEDGKLIKGNKTVPPAERRPTGQIVGIIK 235 (654)
Q Consensus 175 GD~V~Vellp~~~w~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ptGkVVgIi~ 235 (654)
||+|+|+.....+ ++.+..++.+.. ..+...|+||.+=.
T Consensus 7 ~DRVlVk~~e~Ee-kT~gGIvlpdsa---------------------keK~~~g~VvAVG~ 45 (96)
T COG0234 7 GDRVLVKRVEEEE-KTAGGIVLPDSA---------------------KEKPQEGEVVAVGP 45 (96)
T ss_pred CCEEEEEEchhhc-cccCcEEecCcc---------------------ccCCcceEEEEEcc
Confidence 8999999987643 445555555432 12335799998764
No 118
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=22.18 E-value=1.3e+02 Score=26.49 Aligned_cols=40 Identities=20% Similarity=0.339 Sum_probs=23.7
Q ss_pred CCCEEEEEEccCCCcCCccccccccCCCCCCccccccccccCCCCCCCCCCCCceeEEEEEe
Q psy4856 174 DGDTVAVRLLPESQWSAPLELVLEDEGSGEDEEGEDGKLIKGNKTVPPAERRPTGQIVGIIK 235 (654)
Q Consensus 174 ~GD~V~Vellp~~~w~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ptGkVVgIi~ 235 (654)
-||+|+|+.....+ ++.+..++.+.. ..+..+|+||.|=.
T Consensus 6 l~DRVLVk~~~~e~-~T~gGI~Lp~~a---------------------~ek~~~G~VvavG~ 45 (91)
T PRK14533 6 LGERLLIKPIKEEK-KTEGGIVLPDSA---------------------KEKPMKAEVVAVGK 45 (91)
T ss_pred cCCEEEEEEccccc-eecccEEecccc---------------------cCCcceEEEEEECC
Confidence 48999999875432 333344443322 12335799998764
No 119
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=20.43 E-value=1.6e+02 Score=33.64 Aligned_cols=57 Identities=11% Similarity=0.017 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHHHhhcccCcccceEEEcccccceEEEECCCCcccccceeeeccC-CCccEE
Q psy4856 588 YAGRASVALHTHLFFRRKSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPL-PNGNIE 649 (654)
Q Consensus 588 ~aer~~~~l~~~~~l~~~~g~~~~~~~i~~~~~~g~~~v~~~~~~~~eg~vh~~~~-~~~~~~ 649 (654)
+.-|+..+=....-++++.|+... |.|..+..+|+| |+. ..++|++|-|.+ +++.|.
T Consensus 116 Qkire~ere~i~~eyk~~~GeIV~-G~V~ri~~~gii-VDL---ggvea~LP~sE~ip~E~~~ 173 (470)
T PRK09202 116 QKIREAERERVYEEYKDRVGEIIT-GVVKRVERGNII-VDL---GRAEAILPRKEQIPRENFR 173 (470)
T ss_pred HHHHHHHHHHHHHHHHhhcCCEEE-EEEEEEecCCEE-EEE---CCeEEEecHHHcCCCccCC
Confidence 334444444556667778899998 999999999988 765 358999999954 444443
Done!