Query 048593
Match_columns 150
No_of_seqs 112 out of 292
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 10:59:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048593.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048593hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00162 DNA-directed RNA poly 100.0 1.7E-36 3.7E-41 239.6 15.9 120 3-129 23-172 (176)
2 KOG3298 DNA-directed RNA polym 100.0 5.2E-36 1.1E-40 233.8 14.5 118 4-128 24-170 (170)
3 COG1095 RPB7 DNA-directed RNA 100.0 7.6E-35 1.6E-39 231.4 15.3 126 4-135 24-178 (183)
4 KOG3297 DNA-directed RNA polym 100.0 1.9E-34 4.2E-39 229.0 14.4 129 4-135 24-201 (202)
5 TIGR00448 rpoE DNA-directed RN 100.0 1.1E-33 2.4E-38 222.6 16.2 125 4-134 24-177 (179)
6 PRK08563 DNA-directed RNA poly 100.0 1.2E-33 2.7E-38 222.8 14.0 127 3-135 23-178 (187)
7 cd04329 RNAP_II_Rpb7_N RNAP_II 99.8 3.3E-21 7.1E-26 135.1 7.9 59 3-62 22-80 (80)
8 cd04330 RNAP_III_Rpc25_N RNAP_ 99.8 3.5E-21 7.6E-26 134.9 7.8 59 3-62 22-80 (80)
9 cd00655 RNAP_Rpb7_N_like RNAP_ 99.8 4.6E-21 9.9E-26 134.2 7.9 59 3-62 22-80 (80)
10 cd04331 RNAP_E_N RNAP_E_N: Rpo 99.8 4.5E-20 9.8E-25 129.4 7.7 58 4-62 23-80 (80)
11 PF08292 RNA_pol_Rbc25: RNA po 99.7 4.5E-18 9.7E-23 128.0 8.5 72 60-133 1-122 (122)
12 PF03876 SHS2_Rpb7-N: SHS2 dom 99.5 4.5E-14 9.7E-19 95.2 8.0 53 5-58 18-70 (70)
13 cd04462 S1_RNAPII_Rpb7 S1_RNAP 99.5 4.4E-13 9.6E-18 95.2 8.6 59 62-126 1-88 (88)
14 cd04328 RNAP_I_Rpa43_N RNAP_I_ 99.2 6.3E-11 1.4E-15 83.9 6.8 56 5-62 31-89 (89)
15 cd04460 S1_RpoE S1_RpoE: RpoE, 97.5 0.00025 5.5E-09 50.4 5.9 42 85-130 51-93 (99)
16 cd04454 S1_Rrp4_like S1_Rrp4_l 96.2 0.014 3E-07 39.8 5.3 62 58-128 2-82 (82)
17 KOG4134 DNA-dependent RNA poly 96.2 0.037 8.1E-07 46.2 8.7 97 4-102 49-161 (253)
18 cd05790 S1_Rrp40 S1_Rrp40: Rrp 95.9 0.026 5.6E-07 40.2 5.7 66 58-128 2-86 (86)
19 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 95.8 0.037 8.1E-07 37.8 5.9 61 58-127 2-85 (86)
20 PF00575 S1: S1 RNA binding do 95.7 0.041 8.9E-07 36.2 5.6 45 59-103 1-64 (74)
21 cd05791 S1_CSL4 S1_CSL4: CSL4, 95.3 0.032 6.9E-07 39.6 4.4 62 58-128 2-92 (92)
22 PRK04163 exosome complex RNA-b 95.0 0.065 1.4E-06 44.1 5.9 63 58-129 59-144 (235)
23 COG1096 Predicted RNA-binding 94.1 0.33 7.1E-06 39.4 7.9 82 36-128 30-148 (188)
24 TIGR03591 polynuc_phos polyrib 91.9 0.075 1.6E-06 50.1 1.3 73 29-102 584-677 (684)
25 smart00316 S1 Ribosomal protei 91.7 0.52 1.1E-05 29.5 4.8 42 62-103 2-62 (72)
26 cd05706 S1_Rrp5_repeat_sc10 S1 90.8 0.89 1.9E-05 29.8 5.4 18 86-103 46-63 (73)
27 cd05686 S1_pNO40 S1_pNO40: pNO 90.4 0.87 1.9E-05 30.3 5.1 17 87-103 48-64 (73)
28 cd04452 S1_IF2_alpha S1_IF2_al 89.8 0.98 2.1E-05 29.6 5.0 44 60-103 1-65 (76)
29 cd05691 S1_RPS1_repeat_ec6 S1_ 89.8 0.89 1.9E-05 29.4 4.7 18 86-103 43-60 (73)
30 cd05697 S1_Rrp5_repeat_hs5 S1_ 89.4 0.96 2.1E-05 29.4 4.6 18 86-103 43-60 (69)
31 cd05708 S1_Rrp5_repeat_sc12 S1 89.1 1.2 2.6E-05 29.0 5.0 18 86-103 46-63 (77)
32 cd04471 S1_RNase_R S1_RNase_R: 89.1 1.7 3.8E-05 28.7 5.8 18 86-103 56-73 (83)
33 cd05707 S1_Rrp5_repeat_sc11 S1 88.6 0.96 2.1E-05 29.3 4.2 18 86-103 43-60 (68)
34 cd05687 S1_RPS1_repeat_ec1_hs1 88.4 1.2 2.5E-05 28.9 4.5 16 87-102 44-59 (70)
35 COG1097 RRP4 RNA-binding prote 87.9 6.1 0.00013 33.2 9.4 47 57-103 59-128 (239)
36 cd05688 S1_RPS1_repeat_ec3 S1_ 87.8 1.9 4.1E-05 27.2 5.1 18 86-103 43-60 (68)
37 cd05704 S1_Rrp5_repeat_hs13 S1 87.2 1.2 2.6E-05 29.7 4.0 16 87-102 48-63 (72)
38 cd05692 S1_RPS1_repeat_hs4 S1_ 86.1 1.8 4E-05 27.1 4.3 17 87-103 44-60 (69)
39 PF10447 EXOSC1: Exosome compo 86.1 2.3 5.1E-05 29.9 5.2 14 60-73 2-15 (82)
40 cd05702 S1_Rrp5_repeat_hs11_sc 86.0 2.3 5E-05 27.8 4.9 16 87-102 46-61 (70)
41 cd05690 S1_RPS1_repeat_ec5 S1_ 84.8 3.9 8.4E-05 26.1 5.5 18 86-103 44-61 (69)
42 KOG3409 Exosomal 3'-5' exoribo 84.2 2.9 6.3E-05 33.9 5.5 52 49-102 57-137 (193)
43 PRK09521 exosome complex RNA-b 84.1 3.3 7.2E-05 32.7 5.8 46 57-102 59-133 (189)
44 cd05685 S1_Tex S1_Tex: The C-t 84.0 2.8 6.1E-05 26.2 4.5 17 87-103 44-60 (68)
45 cd05698 S1_Rrp5_repeat_hs6_sc5 83.8 2.3 5E-05 27.4 4.1 18 86-103 43-60 (70)
46 cd05705 S1_Rrp5_repeat_hs14 S1 83.7 3.9 8.4E-05 27.5 5.3 18 86-103 49-66 (74)
47 cd04461 S1_Rrp5_repeat_hs8_sc7 83.4 2.7 5.9E-05 28.4 4.4 44 60-103 12-74 (83)
48 PRK08582 hypothetical protein; 82.3 4 8.6E-05 31.1 5.4 41 62-102 5-64 (139)
49 cd04472 S1_PNPase S1_PNPase: P 81.5 4.1 8.9E-05 25.7 4.6 16 87-102 44-59 (68)
50 cd05689 S1_RPS1_repeat_ec4 S1_ 80.6 7.8 0.00017 25.1 5.8 18 86-103 47-64 (72)
51 cd05695 S1_Rrp5_repeat_hs3 S1_ 80.1 6.6 0.00014 25.6 5.2 18 86-103 41-58 (66)
52 cd04455 S1_NusA S1_NusA: N-uti 80.0 9.6 0.00021 24.8 6.0 42 61-102 2-55 (67)
53 cd04453 S1_RNase_E S1_RNase_E: 79.9 11 0.00024 26.2 6.6 49 59-107 4-76 (88)
54 cd05696 S1_Rrp5_repeat_hs4 S1_ 79.7 8 0.00017 25.5 5.6 17 87-103 46-62 (71)
55 PRK08059 general stress protei 79.6 4.5 9.7E-05 29.9 4.8 44 60-103 5-67 (123)
56 PRK05807 hypothetical protein; 79.6 5.1 0.00011 30.3 5.2 42 62-103 5-64 (136)
57 cd05703 S1_Rrp5_repeat_hs12_sc 75.9 8 0.00017 25.8 4.8 18 86-103 45-62 (73)
58 PRK07252 hypothetical protein; 75.2 7.9 0.00017 28.7 5.1 18 86-103 46-63 (120)
59 PRK03987 translation initiatio 73.9 6.5 0.00014 33.1 4.8 45 59-103 5-70 (262)
60 PRK09202 nusA transcription el 73.4 10 0.00022 34.6 6.1 46 58-103 130-187 (470)
61 cd05684 S1_DHX8_helicase S1_DH 73.0 14 0.00031 24.5 5.4 17 86-102 47-63 (79)
62 cd00164 S1_like S1_like: Ribos 72.5 8.3 0.00018 23.3 4.0 18 86-103 40-57 (65)
63 PF10246 MRP-S35: Mitochondria 71.5 11 0.00024 27.9 4.9 45 59-103 20-76 (104)
64 cd04473 S1_RecJ_like S1_RecJ_l 71.4 9.5 0.00021 25.5 4.3 44 58-101 12-66 (77)
65 TIGR01953 NusA transcription t 71.2 13 0.00029 32.4 6.2 46 58-103 127-185 (341)
66 KOG1004 Exosomal 3'-5' exoribo 71.1 25 0.00054 29.4 7.4 79 46-129 49-146 (230)
67 cd05694 S1_Rrp5_repeat_hs2_sc2 70.1 17 0.00036 24.4 5.3 41 62-102 4-58 (74)
68 TIGR02063 RNase_R ribonuclease 67.2 6.9 0.00015 37.0 3.9 18 86-103 682-699 (709)
69 cd05693 S1_Rrp5_repeat_hs1_sc1 66.7 20 0.00044 25.5 5.4 17 87-103 66-82 (100)
70 PRK12327 nusA transcription el 66.3 20 0.00042 31.7 6.3 47 58-104 130-188 (362)
71 TIGR00358 3_prime_RNase VacB a 66.1 14 0.0003 34.7 5.6 19 85-103 626-644 (654)
72 PRK11642 exoribonuclease R; Pr 63.3 7.8 0.00017 37.6 3.5 19 85-103 697-715 (813)
73 PRK11824 polynucleotide phosph 63.1 15 0.00032 34.9 5.3 45 58-102 617-680 (693)
74 PHA02945 interferon resistance 60.8 29 0.00063 25.0 5.2 40 60-102 9-71 (88)
75 PRK12328 nusA transcription el 58.5 32 0.00069 30.7 6.2 48 58-105 134-194 (374)
76 PTZ00248 eukaryotic translatio 54.8 21 0.00046 31.1 4.4 43 60-102 15-78 (319)
77 PRK07400 30S ribosomal protein 54.6 22 0.00048 30.5 4.5 15 88-102 76-90 (318)
78 COG1098 VacB Predicted RNA bin 51.7 39 0.00084 26.0 4.9 43 60-102 3-64 (129)
79 PRK07400 30S ribosomal protein 50.3 34 0.00074 29.3 5.0 44 60-103 194-255 (318)
80 PRK09750 hypothetical protein; 45.9 17 0.00037 24.5 1.9 23 112-134 2-24 (64)
81 TIGR02696 pppGpp_PNP guanosine 44.9 37 0.0008 32.8 4.7 44 59-102 644-710 (719)
82 cd04465 S1_RPS1_repeat_ec2_hs2 44.5 41 0.00088 21.4 3.6 14 90-103 44-57 (67)
83 PLN00207 polyribonucleotide nu 44.4 24 0.00052 34.9 3.4 47 56-102 747-813 (891)
84 COG1093 SUI2 Translation initi 43.2 50 0.0011 28.3 4.8 43 60-102 9-72 (269)
85 PRK13806 rpsA 30S ribosomal pr 41.4 61 0.0013 29.4 5.4 42 62-103 379-439 (491)
86 KOG4078 Putative mitochondrial 39.6 36 0.00078 26.9 3.1 50 55-104 75-136 (173)
87 PRK06299 rpsA 30S ribosomal pr 39.1 51 0.0011 30.0 4.6 42 62-103 460-520 (565)
88 PRK13806 rpsA 30S ribosomal pr 37.3 44 0.00095 30.3 3.8 15 88-102 113-127 (491)
89 TIGR00717 rpsA ribosomal prote 35.5 99 0.0021 27.7 5.7 43 60-102 16-72 (516)
90 PRK12329 nusA transcription el 35.2 82 0.0018 28.9 5.1 47 58-104 148-212 (449)
91 COG5256 TEF1 Translation elong 35.0 1E+02 0.0023 28.1 5.7 74 21-106 229-306 (428)
92 PRK06299 rpsA 30S ribosomal pr 34.7 79 0.0017 28.8 5.1 42 62-103 373-434 (565)
93 PRK06676 rpsA 30S ribosomal pr 34.4 70 0.0015 27.6 4.5 43 61-103 191-251 (390)
94 TIGR00717 rpsA ribosomal prote 32.3 82 0.0018 28.2 4.7 42 62-103 446-506 (516)
95 COG0539 RpsA Ribosomal protein 29.0 1.1E+02 0.0024 28.7 5.0 76 61-137 191-316 (541)
96 PRK06676 rpsA 30S ribosomal pr 28.7 1.2E+02 0.0026 26.1 5.0 42 62-103 277-337 (390)
97 PRK15052 D-tagatose-1,6-bispho 28.4 33 0.00071 31.2 1.4 22 121-146 85-106 (421)
98 PF08013 Tagatose_6_P_K: Tagat 26.8 25 0.00055 31.9 0.5 22 121-146 88-109 (424)
99 PRK07899 rpsA 30S ribosomal pr 26.7 1.1E+02 0.0025 27.9 4.7 42 62-103 208-267 (486)
100 COG2100 Predicted Fe-S oxidore 25.9 1.2E+02 0.0026 27.3 4.4 44 59-102 350-405 (414)
101 PRK00087 4-hydroxy-3-methylbut 25.8 1.3E+02 0.0027 28.4 4.9 42 62-103 562-622 (647)
102 PF07238 PilZ: PilZ domain; I 25.3 2E+02 0.0043 18.6 7.4 48 49-98 8-55 (102)
103 PRK07899 rpsA 30S ribosomal pr 24.7 1.7E+02 0.0036 26.9 5.3 42 62-103 293-353 (486)
104 PRK15458 tagatose 6-phosphate 24.6 42 0.00091 30.5 1.4 22 121-146 88-109 (426)
105 TIGR02810 agaZ_gatZ D-tagatose 23.1 47 0.001 30.1 1.5 22 121-146 84-105 (420)
106 PRK00087 4-hydroxy-3-methylbut 22.5 2.2E+02 0.0048 26.7 5.8 45 58-102 298-361 (647)
107 PF07076 DUF1344: Protein of u 21.5 2E+02 0.0044 19.3 3.9 31 66-96 5-46 (61)
108 PRK12269 bifunctional cytidyla 21.4 1.8E+02 0.0038 28.8 5.1 41 62-102 321-372 (863)
109 PF09926 DUF2158: Uncharacteri 21.1 78 0.0017 20.4 1.8 41 88-139 1-42 (53)
110 PRK05610 rpsQ 30S ribosomal pr 21.0 2E+02 0.0044 20.2 4.1 11 87-97 53-63 (84)
111 KOG0459 Polypeptide release fa 20.9 1.8E+02 0.0038 27.0 4.6 32 87-123 361-392 (501)
112 PF06688 DUF1187: Protein of u 20.6 57 0.0012 22.0 1.1 21 114-134 1-21 (61)
No 1
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=100.00 E-value=1.7e-36 Score=239.57 Aligned_cols=120 Identities=15% Similarity=0.296 Sum_probs=108.3
Q ss_pred HHHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEe---------
Q 048593 3 AIFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIA--------- 73 (150)
Q Consensus 3 ~~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v--------- 73 (150)
..+++++|+++|+|||.+++||||||+|++++++|+|.| |||++||+|+|||+|||||+|||++|+|++|
T Consensus 23 ~~~i~~~L~~~~egkv~~~~GliV~v~di~~i~~G~I~~-gdG~~~~~V~FraivFrPf~gEVv~g~V~~v~~~G~~v~~ 101 (176)
T PTZ00162 23 QQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQD-GTGMIVVNVKYQAIVFKPFKDEVLDAIVTDVNKLGFFAQA 101 (176)
T ss_pred HHHHHHHHHHHHCCCCcCcccEEEEEEEeeEecCCEEEc-CCCCEEEEEEEEEEEEecCCCCEEEEEEEEEecceEEEEe
Confidence 357899999999999999999999999999999999999 9999999999999999999999999999999
Q ss_pred -------------------cCCCceee--ccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEEEccCCcccccc
Q 048593 74 -------------------VCEQPFFS--NEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVS 129 (150)
Q Consensus 74 -------------------~~~~~~~~--~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igsi~~d~LG~i~ 129 (150)
+++++|.| ++++.+|++|+.|||||++++|+.. .++++|||++||||++.
T Consensus 102 Gp~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~------~~~~i~T~~~~~LG~~~ 172 (176)
T PTZ00162 102 GPLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDAS------NLFAIATINSDYLGPIE 172 (176)
T ss_pred eCeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCC------CcEEEEEecCCCcCccc
Confidence 33455655 3445789999999999999999543 58999999999999983
No 2
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=100.00 E-value=5.2e-36 Score=233.80 Aligned_cols=118 Identities=31% Similarity=0.566 Sum_probs=108.8
Q ss_pred HHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEe----------
Q 048593 4 IFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIA---------- 73 (150)
Q Consensus 4 ~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v---------- 73 (150)
.++.++|.+..+|||++++||+|||+++++||+|+|+| ++|.+.|+|+|+|++||||||||++|+|++|
T Consensus 24 ~~l~~~L~~~veg~ctg~~Gyvi~vt~ld~Ig~g~I~~-~~G~v~FpVky~av~FkpfKGEVvdgvV~~Vnk~G~F~~~G 102 (170)
T KOG3298|consen 24 AILKRKLLAEVEGKCTGKYGYVIAVTTLDNIGEGRIRP-GTGFVTFPVKYKAVTFKPFKGEVVDGVVTKVNKMGVFARSG 102 (170)
T ss_pred HHHHHHHHHHhhccccccccEEEEEEEhhhccCCcccc-CCceEEEEEEEEEEEEeecCCcEEEEEEEEEeeeeEEEecc
Confidence 46788888888899999999999999999999999999 9999999999999999999999999999999
Q ss_pred ------------------cCCC-ceeeccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEEEccCCccccc
Q 048593 74 ------------------VCEQ-PFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPV 128 (150)
Q Consensus 74 ------------------~~~~-~~~~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igsi~~d~LG~i 128 (150)
+++| |.|..++...|++|+.||++|+|++| +. ++|+|+|||++|||||+
T Consensus 103 Pl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~-~~-----~~i~algtl~~D~LG~i 170 (170)
T KOG3298|consen 103 PLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRV-DE-----TEIFALGTLKGDYLGPI 170 (170)
T ss_pred ceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEE-ee-----eeEEEEEEecCcccccC
Confidence 5556 77887776799999999999999999 44 37999999999999986
No 3
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=100.00 E-value=7.6e-35 Score=231.35 Aligned_cols=126 Identities=19% Similarity=0.208 Sum_probs=111.8
Q ss_pred HHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEe----------
Q 048593 4 IFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIA---------- 73 (150)
Q Consensus 4 ~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v---------- 73 (150)
-++++.|++.|+|||++++|+||+|+|+++|++|+|.| |||++||+|+||||+|+||+|||++|+|++|
T Consensus 24 ~~v~~~L~~k~eG~~~~~~G~~v~V~~v~~igeG~I~~-GDG~~y~~V~f~al~fkP~~gEVV~GeVv~~~~~G~fV~ig 102 (183)
T COG1095 24 EAVKEELKEKYEGKLDGDVGLVVLVLDVKEIGEGIIVP-GDGSTYHEVKFRALVFKPFRGEVVEGEVVEVVEFGAFVRIG 102 (183)
T ss_pred HHHHHHHHHHhcceEccccCEEEEEEEeeEeeccEEec-CCCcEEEEEEEEEEEEEeccccEEEEEEEEEeecceEEEec
Confidence 46889999999999999999999999999999999999 9999999999999999999999999999999
Q ss_pred -----------------cCCCc--eeeccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEEEccCCccccccCCCCC
Q 048593 74 -----------------VCEQP--FFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVSLSGWA 134 (150)
Q Consensus 74 -----------------~~~~~--~~~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igsi~~d~LG~i~w~~w~ 134 (150)
.++++ |..++++++|++||.|||||+++++.+.. .....|.+||+++|||...| |.
T Consensus 103 p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~---~~~~~I~lTmrq~~LGklew--~~ 177 (183)
T COG1095 103 PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRR---PRESKIGLTMRQPGLGKLEW--IE 177 (183)
T ss_pred cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCc---cccceEEEEeccccCCcchh--hh
Confidence 22233 33466777999999999999999996542 24689999999999999999 85
Q ss_pred C
Q 048593 135 G 135 (150)
Q Consensus 135 ~ 135 (150)
+
T Consensus 178 ~ 178 (183)
T COG1095 178 E 178 (183)
T ss_pred h
Confidence 3
No 4
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=100.00 E-value=1.9e-34 Score=229.02 Aligned_cols=129 Identities=19% Similarity=0.307 Sum_probs=116.3
Q ss_pred HHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEe----------
Q 048593 4 IFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIA---------- 73 (150)
Q Consensus 4 ~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v---------- 73 (150)
.+|++.|+.++.+|+..|+|||||||||.++++|.|.| |||+.|++|.||++|||||.|||+.|+|+++
T Consensus 24 ~ai~~eL~~k~anKvl~nvGLCI~vyDi~~v~e~~v~p-GDGas~~~V~FR~vVFrPF~gEVi~gki~~cs~eG~rvtl~ 102 (202)
T KOG3297|consen 24 DAIKEELNRKLANKVLPNVGLCICVYDILEVEEGIVLP-GDGASYARVWFRVVVFRPFVGEVITGKIKECSEEGLRVTLG 102 (202)
T ss_pred HHHHHHHHHHHHhhhcccccEEEEEeEeeeecceEEec-CCCceEEEEEEEEEEEecccceEEEEEeecCCccceEEEEE
Confidence 57899999999999999999999999999999999999 9999999999999999999999999999999
Q ss_pred -------------------cCCCceeeccc-------cceecCCCEEEEEEEEEEeeecCcC-------------ccCcE
Q 048593 74 -------------------VCEQPFFSNEQ-------QAKIRNGLVVQFLVTAVQWIDEGRN-------------LKKKY 114 (150)
Q Consensus 74 -------------------~~~~~~~~~~~-------~~~i~~gd~VR~RI~~v~~~d~~~~-------------~~~~~ 114 (150)
+++..|+|... +.+++.|+.|||||...+|.|.++. ..+||
T Consensus 103 FFdDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e~f~d~~p~~~~~~~t~~e~~e~~~py 182 (202)
T KOG3297|consen 103 FFDDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDESFVDVSPEGNSTAITGAEDPEKESPY 182 (202)
T ss_pred eeeceeechhhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEeeecccccCccccccccccccccccCCCe
Confidence 45567887433 3479999999999999999876532 45899
Q ss_pred EEEEEccCCccccccCCCCCC
Q 048593 115 LVFGRVEGESLGPVSLSGWAG 135 (150)
Q Consensus 115 ~~igsi~~d~LG~i~w~~w~~ 135 (150)
.++|+|++|||||++| |..
T Consensus 183 ~l~gs~~~~GLG~lsW--W~~ 201 (202)
T KOG3297|consen 183 TLLGSMNEDGLGPLSW--WDS 201 (202)
T ss_pred EEEEEecCCCCccchh--hhc
Confidence 9999999999999999 964
No 5
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=100.00 E-value=1.1e-33 Score=222.63 Aligned_cols=125 Identities=18% Similarity=0.231 Sum_probs=110.2
Q ss_pred HHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEe----------
Q 048593 4 IFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIA---------- 73 (150)
Q Consensus 4 ~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v---------- 73 (150)
-++++.|.++|+|||.+++||||||+|++++++|+|.| |||++||+|+|||++||||+|||++|+|+++
T Consensus 24 ~~i~~~l~~~~~gk~~~~~G~~i~v~di~~i~~g~i~~-gdG~~~~~V~f~~i~f~p~~gEvv~G~V~~v~~~GifV~lg 102 (179)
T TIGR00448 24 EVITHQLNEKFEGRLDKNVGLCITIYDIEDIGEGKVIP-GDGSAYHNVTFRALVFKPELGEIVEGEVIEIVEFGAFVSLG 102 (179)
T ss_pred HHHHHHHHHHhcCcCcCCcCEEEEEEEeEEecCCEEEC-CCCCEEEEEEEEEEEEeccCCCEEEEEEEEEEeeEEEEEeC
Confidence 47889999999999999999999999999999999999 9999999999999999999999999999999
Q ss_pred -------------------cCCCceeeccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEEEccCCccccccCCCCC
Q 048593 74 -------------------VCEQPFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVSLSGWA 134 (150)
Q Consensus 74 -------------------~~~~~~~~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igsi~~d~LG~i~w~~w~ 134 (150)
..++.|++++.+.++++||.|||||.++++.+..+ ..-.+.+||+++|||++.| ++
T Consensus 103 ~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~---~~~~I~lt~k~~~LG~~~w--~~ 177 (179)
T TIGR00448 103 PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRP---EGSKIGLTMRQPLLGKLEW--IE 177 (179)
T ss_pred CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCC---CcceEEEEeccCcCCcccc--cc
Confidence 22234556666678999999999999999865421 2455799999999999999 74
No 6
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=100.00 E-value=1.2e-33 Score=222.80 Aligned_cols=127 Identities=17% Similarity=0.189 Sum_probs=109.2
Q ss_pred HHHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEe---------
Q 048593 3 AIFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIA--------- 73 (150)
Q Consensus 3 ~~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v--------- 73 (150)
.-++.++|+++|+|||.+++||||||+|++++++|+|.| |||+++|+|+|||++|+||+|||++|+|+++
T Consensus 23 ~~~i~~~l~~~~~~k~~~~~G~~v~v~di~~i~~g~i~~-gdg~~~~~v~f~~lvf~P~~GEVv~g~V~~v~~~Gi~V~l 101 (187)
T PRK08563 23 EEAALEVLREKYEGRIDKELGIIVAVLDVKVIGEGKIVP-GDGATYHEVEFDALVFKPELQEVVEGEVVEVVEFGAFVRI 101 (187)
T ss_pred HHHHHHHHHHHhhCcCcCCcCEEEEEEEeEEecccEEec-CCCCcEEEEEEEEEEEeccCCCEEEEEEEEEEccEEEEEE
Confidence 346899999999999999999999999999999999999 9999999999999999999999999999999
Q ss_pred --------------------cCCCceeeccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEEEccCCccccccCCCC
Q 048593 74 --------------------VCEQPFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVSLSGW 133 (150)
Q Consensus 74 --------------------~~~~~~~~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igsi~~d~LG~i~w~~w 133 (150)
+.++.|.+++....+++|+.||+||.++++.+.. + ....+.+||+++|||+++| |
T Consensus 102 g~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~--~-~~~~I~ls~~~~~LG~~~w--~ 176 (187)
T PRK08563 102 GPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERR--P-RGSKIGLTMRQPGLGKLEW--I 176 (187)
T ss_pred eCceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCC--C-CCCEEEEEecCCCCCcHHH--H
Confidence 1112234455556899999999999999985432 0 1147888999999999999 9
Q ss_pred CC
Q 048593 134 AG 135 (150)
Q Consensus 134 ~~ 135 (150)
++
T Consensus 177 ~~ 178 (187)
T PRK08563 177 EE 178 (187)
T ss_pred HH
Confidence 64
No 7
>cd04329 RNAP_II_Rpb7_N RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain. Rpb7 is a subunit of eukaryotic RNA polymerase (RNAP) II that is homologous to Rpc25 of RNAP III, RpoE of archaeal RNAP, and Rpa43 of eukaryotic RNAP I. Rpb7 heterodimerizes with Rpb4 and this heterodimer binds the 10-subunit core of RNAP II, forming part of the floor of the DNA-binding cleft. Rpb7 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which bind single-stranded RNA. Rpb7 is thought to interact with the nascent RNA strand as it exits the RNAP II complex during transcription elongation. The Rpb7/Rpb4 heterodimer is also thought to serve as an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter.
Probab=99.85 E-value=3.3e-21 Score=135.06 Aligned_cols=59 Identities=25% Similarity=0.426 Sum_probs=56.4
Q ss_pred HHHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeec
Q 048593 3 AIFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVK 62 (150)
Q Consensus 3 ~~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~ 62 (150)
.-++.+.|+++++||+.+++||||||+|++++++|+|.| |||++||+|+|||++||||+
T Consensus 22 ~~~i~~~L~~~~egk~~~~~G~iv~v~di~~i~~G~I~~-gdG~~~~~V~F~aivfrPf~ 80 (80)
T cd04329 22 KEYLEQKLLEEVEGTCTGDYGYIIAVTDIDDIGEGKILP-GTGSVEFPVKYKAIVFKPFK 80 (80)
T ss_pred HHHHHHHHHHHhCCcCcCceeEEEEEEEeeEecCcEEEc-CCCCEEEEEEEEEEEEEccC
Confidence 347889999999999999999999999999999999999 99999999999999999996
No 8
>cd04330 RNAP_III_Rpc25_N RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain. Rpc25 is a subunit of eukaryotic RNA polymerase (RNAP) III and is homologous to Rpa43 of eukaryotic RNAP I, Rpb7 of eukaryotic RNAP II, and RpoE of archaeal RNAP. Rpc25 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which are thought to bind single-stranded RNA. Rpc25 heterodimerizes with Rpc17 and plays an important role in transcription initiation. RNAP III transcribes diverse structural and catalytic RNAs including 5S ribosomal RNAs, tRNAs, and a small number of snRNAs involved in RNA and protein synthesis.
Probab=99.85 E-value=3.5e-21 Score=134.91 Aligned_cols=59 Identities=14% Similarity=0.130 Sum_probs=56.9
Q ss_pred HHHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeec
Q 048593 3 AIFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVK 62 (150)
Q Consensus 3 ~~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~ 62 (150)
.-++++.|+++|+||+++++||||||+|+.++++|+|.| |||++||+|+|||++||||+
T Consensus 22 ~~~i~~~L~~ky~gkv~~~~Gl~v~v~di~~i~eG~I~~-gdG~~~~~V~Fr~lvFrPf~ 80 (80)
T cd04330 22 NDAIEDELNKKYANKVIQNVGLCICLYDILEVEDGYILP-GDGASHYKVTFRMVVFRPFV 80 (80)
T ss_pred HHHHHHHHHHHhCCcEeCCccEEEEEEEeEEEcCCEEEC-CCCCEEEEEEEEEEEEECCC
Confidence 457899999999999999999999999999999999999 99999999999999999996
No 9
>cd00655 RNAP_Rpb7_N_like RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP. These proteins have, in addition to their N-terminal RNP domain, a C-terminal oligonucleotide-binding (OB) domain. Each of these subunits heterodimerizes with another RNAP subunit (Rpb7 to Rpb4, Rpc25 to Rpc17, RpoE to RpoF, and Rpa43 to Rpa14). The heterodimer is thought to tether the RNAP to a given promoter via its interactions with a promoter-bound transcription factor.The heterodimer is also thought to bind and position nascent RNA as it exits the polymerase complex.
Probab=99.84 E-value=4.6e-21 Score=134.25 Aligned_cols=59 Identities=17% Similarity=0.142 Sum_probs=56.6
Q ss_pred HHHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeec
Q 048593 3 AIFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVK 62 (150)
Q Consensus 3 ~~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~ 62 (150)
.-++.++|+++|+||+.+++||||||+|++++++|+|.| |||++||+|+|||++||||+
T Consensus 22 ~~~i~~~L~~k~~gkv~~~~G~~v~v~di~~i~~G~I~~-gdG~~~~~V~F~~ivFrPf~ 80 (80)
T cd00655 22 KGVKKCLLQEKGEGDRTPVVGIILAIKDTKDIPEGAIRP-GDGSAYVNVSFRAVVFKPFS 80 (80)
T ss_pred HHHHHHHHHHHhCCeEeCCccEEEEEEEeEEEcCCEEEC-CCCCEEEEEEEEEEEEEcCC
Confidence 357899999999999999999999999999999999999 99999999999999999996
No 10
>cd04331 RNAP_E_N RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain. RpoE (subunit E) is a subunit of the archaeal RNA polymerase (RNAP) that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNAP III, and Rpa43 of eukaryotic RNAP I. RpoE heterodimerizes with RpoF, another RNA polymerase subunit. RpoE has an elongated two-domain structure that includes an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Both domains of RpoE bind single-stranded RNA.
Probab=99.82 E-value=4.5e-20 Score=129.44 Aligned_cols=58 Identities=26% Similarity=0.301 Sum_probs=55.3
Q ss_pred HHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeec
Q 048593 4 IFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVK 62 (150)
Q Consensus 4 ~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~ 62 (150)
-++.+.|+++++|||.+++||||||+|++++|+|+|.| |||++||+|+|||++|||..
T Consensus 23 ~~i~~~L~~~~egk~~~~~G~iv~v~di~~i~eG~I~~-gdG~~~~~V~F~~ivFrP~~ 80 (80)
T cd04331 23 EAVLEILKEKYEGRLDKDLGKIVSVLDVKDVGEGKIVH-GDGAVYHEVRFDALVFKPEL 80 (80)
T ss_pred HHHHHHHHHHhcCcCcCCCCEEEEEEEEEEecCCEEEc-CCCCEEEEEEEEEEEEecCC
Confidence 46889999999999999999999999999999999999 99999999999999999963
No 11
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=99.75 E-value=4.5e-18 Score=127.96 Aligned_cols=72 Identities=29% Similarity=0.439 Sum_probs=49.8
Q ss_pred eecCcEEEEEEEEe-----------------------------cCCCceeecc---ccceecCCCEEEEEEEEEEeeecC
Q 048593 60 PVKGEILHGVIHIA-----------------------------VCEQPFFSNE---QQAKIRNGLVVQFLVTAVQWIDEG 107 (150)
Q Consensus 60 Pf~gEVv~G~V~~v-----------------------------~~~~~~~~~~---~~~~i~~gd~VR~RI~~v~~~d~~ 107 (150)
||+||||.|+|+++ .+++.|+|.. +..+++.|+.|||||.++.|.|.+
T Consensus 1 PF~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f~d~~ 80 (122)
T PF08292_consen 1 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIFPDVP 80 (122)
T ss_dssp --TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE----
T ss_pred CCCCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEEecCC
Confidence 99999999999999 4556687754 334799999999999999997533
Q ss_pred ------------------cCccCcEEEEEEccCCccccccCCCC
Q 048593 108 ------------------RNLKKKYLVFGRVEGESLGPVSLSGW 133 (150)
Q Consensus 108 ------------------~~~~~~~~~igsi~~d~LG~i~w~~w 133 (150)
.++++||.++|||+++|||+++| |
T Consensus 81 p~~~~~~~~~~~~~~~~~~~~~~Py~I~gs~~~~GLG~~sW--W 122 (122)
T PF08292_consen 81 PTPPPSAEASGEEEEEEEDEPKPPYQIIGSINEDGLGLVSW--W 122 (122)
T ss_dssp -----------------------SEEEEEEB-STT-EEGGG--C
T ss_pred CCCcccccccccccccccccCCCCeEEEEEecCCCCccccc--C
Confidence 23679999999999999999999 9
No 12
>PF03876 SHS2_Rpb7-N: SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; InterPro: IPR005576 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable []. This entry represents the N-terminal, heterodimerisation domain of RPB7.; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2C35_F 3HKZ_E 2PMZ_T 2CKZ_D 2Y0S_E 2RF4_A 2JA7_G 1Y1V_G 2JA5_G 4A3D_G ....
Probab=99.53 E-value=4.5e-14 Score=95.16 Aligned_cols=53 Identities=25% Similarity=0.308 Sum_probs=49.2
Q ss_pred HHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEe
Q 048593 5 FVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTF 58 (150)
Q Consensus 5 ~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivF 58 (150)
.+.+.|.+.++||+.+++|+|||++|+..+++|+|.+ +||.++|+|+|+|++|
T Consensus 18 ~i~~~L~~~~~~k~~~~~G~~i~v~~i~~~~~g~I~~-~~g~~~~~V~f~~lvF 70 (70)
T PF03876_consen 18 GIKEQLLDKYEGKYIPELGVVIAVTDIKEISEGKIIP-GDGFVYFKVTFRALVF 70 (70)
T ss_dssp HHHHHHHHHHTTEEETTTEEEEEEEEEEEESCEEE-T-TTSSEEEEEEEEEEEE
T ss_pred HHHHHHHHHHhCcCcCCceEEEEEeeeeEecCcEEEC-CCCCEEEEEEEEEEEC
Confidence 5677888888899999999999999999999999999 9999999999999998
No 13
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=99.45 E-value=4.4e-13 Score=95.24 Aligned_cols=59 Identities=17% Similarity=0.356 Sum_probs=49.6
Q ss_pred cCcEEEEEEEEe----------------------------cCCCceeec-cccceecCCCEEEEEEEEEEeeecCcCccC
Q 048593 62 KGEILHGVIHIA----------------------------VCEQPFFSN-EQQAKIRNGLVVQFLVTAVQWIDEGRNLKK 112 (150)
Q Consensus 62 ~gEVv~G~V~~v----------------------------~~~~~~~~~-~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~ 112 (150)
+|||++|+|++| +++++|.|. +++.+|++|+.|||||++++| ++ .
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~-~~-----~ 74 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRV-DA-----T 74 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEE-cc-----C
Confidence 699999999999 224556553 456789999999999999999 55 3
Q ss_pred cEEEEEEccCCccc
Q 048593 113 KYLVFGRVEGESLG 126 (150)
Q Consensus 113 ~~~~igsi~~d~LG 126 (150)
.++++|||++||||
T Consensus 75 ~~~~igt~~~~~LG 88 (88)
T cd04462 75 DIFAIGTIKDDYLG 88 (88)
T ss_pred ceEEEEEccCCCCC
Confidence 79999999999998
No 14
>cd04328 RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. Rpa43 is a subunit of eukaryotic RNA polymerase (RNAP) I that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNP III, and RpoE of archaeal RNAP. Rpa43 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Rpa43 heterodimerizes with Rpa14 and this heterodimer has genetic and biochemical characteristics similar to those of the Rpb7/Rpb4 heterodimer of RNAP II. In addition, the Rpa43/Rpa14 heterodimer binds single-stranded RNA, as is the case for the Rpb7/Rpb4 and the archaeal E/F complexes. The position of Rpa43/Rpa14 in the three-dimensional structure of RNAP I is similar to that of Rpb4/Rpb7, which forms an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter. Rpb43 binds Rrn3, an rDNA-specific transcription factor, functionally equivalent to TFIIB, invo
Probab=99.18 E-value=6.3e-11 Score=83.86 Aligned_cols=56 Identities=16% Similarity=0.085 Sum_probs=52.7
Q ss_pred HHHHHHHhHHhceecCCc-eEEEEEeeeceeCC--eeeeeCCCcceEEEEEEEEEEeeeec
Q 048593 5 FVTRLLKGLINEKACKDQ-CYFLSVTNLKSIGR--ERGTVNESGVVFFPVTFLCRTFLPVK 62 (150)
Q Consensus 5 ~i~~ll~~~~~gk~~~~~-GliV~V~di~~i~~--G~I~~~gdG~v~~~V~FraivFrPf~ 62 (150)
+|++.|...+- |+.+++ |+|+|.+|+..+++ |+|.+ ++|..+++|+||++|||||.
T Consensus 31 ~i~~~l~~~l~-ky~~~l~Gv~l~~~di~~~~~~~~~i~~-~~~~~~~~V~~~~lVFrP~~ 89 (89)
T cd04328 31 GIKAQLLNPLL-KYSPKLKGVVLAYSNIKLLEGELAKIVD-DSPFIFVWISADFLVFRPKI 89 (89)
T ss_pred HHHHHHhhhHh-hhcccCCeEEEEecceEeccccceeeeC-CCcEEEEEEEEEEEEEecCC
Confidence 68888899988 999999 99999999999977 99999 99999999999999999985
No 15
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=97.55 E-value=0.00025 Score=50.39 Aligned_cols=42 Identities=19% Similarity=0.207 Sum_probs=31.9
Q ss_pred cceecCCCEEEEEEEEEEeeecCcCccCcEE-EEEEccCCccccccC
Q 048593 85 QAKIRNGLVVQFLVTAVQWIDEGRNLKKKYL-VFGRVEGESLGPVSL 130 (150)
Q Consensus 85 ~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~-~igsi~~d~LG~i~w 130 (150)
...++.||.|+++|.++.. +.. .|... +.-|+++++|||+.|
T Consensus 51 ~~~~~~Gd~v~vkI~~vd~-~~~---~~~~~~i~ls~k~~~~g~~~~ 93 (99)
T cd04460 51 KRVLKVGDVVRARIVAVSL-KER---RPRESKIGLTMRQPGLGKLEW 93 (99)
T ss_pred CCEECCCCEEEEEEEEEeH-HHC---cCCCceEEEEEecCCCCcHHH
Confidence 4679999999999999885 321 01234 444999999999999
No 16
>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=96.21 E-value=0.014 Score=39.79 Aligned_cols=62 Identities=19% Similarity=0.244 Sum_probs=42.8
Q ss_pred eeeecCcEEEEEEEEecCCCce---------------eec----cccceecCCCEEEEEEEEEEeeecCcCccCcEEEEE
Q 048593 58 FLPVKGEILHGVIHIAVCEQPF---------------FSN----EQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFG 118 (150)
Q Consensus 58 FrPf~gEVv~G~V~~v~~~~~~---------------~~~----~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~ig 118 (150)
|.|.+|.++.|+|+++.++... +.. +-...+++||.|++||..+.- + ..+.=
T Consensus 2 y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~-~--------~~i~L 72 (82)
T cd04454 2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGD-D--------MNVLL 72 (82)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCC-C--------CCEEE
Confidence 6799999999999999333211 111 112358999999999998652 1 23666
Q ss_pred EccCCccccc
Q 048593 119 RVEGESLGPV 128 (150)
Q Consensus 119 si~~d~LG~i 128 (150)
|++++.||.+
T Consensus 73 S~~~~~~Gvi 82 (82)
T cd04454 73 TTADNELGVI 82 (82)
T ss_pred EECCCCCccC
Confidence 7788888864
No 17
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=96.20 E-value=0.037 Score=46.17 Aligned_cols=97 Identities=13% Similarity=0.096 Sum_probs=70.5
Q ss_pred HHHHHHHHhHHhceecCCc-eEEEEEeeecee-CCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEecCC-----
Q 048593 4 IFVTRLLKGLINEKACKDQ-CYFLSVTNLKSI-GRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIAVCE----- 76 (150)
Q Consensus 4 ~~i~~ll~~~~~gk~~~~~-GliV~V~di~~i-~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v~~~----- 76 (150)
+++++.|..+.. ++...+ |++++.-+|+-. ..++|.+ .||..+-.+.=..+||+|-.|.+|+|.|-.+...
T Consensus 49 ~~i~ehld~~vl-~y~~~l~GivLgydnIKvLg~~aki~~-D~pf~hlwi~adfyVf~Pk~Gd~LeG~Vn~vS~sHIglL 126 (253)
T KOG4134|consen 49 ALIEEHLDTKVL-FYDSGLDGIVLGYDNIKVLGQTAKIRA-DDPFMHLWINADFYVFRPKAGDILEGVVNHVSRSHIGLL 126 (253)
T ss_pred HHHHHHhhHHHh-hhccCCCceEEeecceEeeccccceec-CCCceEEEEeeeEEEECCCCCCeeeeeeeecchhhhcee
Confidence 356677777764 666554 788888778765 4589999 9999999999999999999999999999887111
Q ss_pred -----Ccee----eccccceecCCCEEEEEEEEEE
Q 048593 77 -----QPFF----SNEQQAKIRNGLVVQFLVTAVQ 102 (150)
Q Consensus 77 -----~~~~----~~~~~~~i~~gd~VR~RI~~v~ 102 (150)
|+.. ...+-..|..++..-+||....
T Consensus 127 Ihg~FNASIpk~nip~dw~fI~md~eee~~v~ntD 161 (253)
T KOG4134|consen 127 IHGVFNASIPKTNIPADWEFIAMDQEEEIRVKNTD 161 (253)
T ss_pred ehhhhhccCCCCCCccceeeecCCchhhhceeecc
Confidence 1111 1222336788888888887654
No 18
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=95.91 E-value=0.026 Score=40.17 Aligned_cols=66 Identities=18% Similarity=0.409 Sum_probs=46.5
Q ss_pred eeeecCcEEEEEEEEecC---------CCc-e-----e---eccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEEE
Q 048593 58 FLPVKGEILHGVIHIAVC---------EQP-F-----F---SNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGR 119 (150)
Q Consensus 58 FrPf~gEVv~G~V~~v~~---------~~~-~-----~---~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igs 119 (150)
|.|-.|.+|-|+|+++.. ..+ . | .+..+..+++||.|-+||..+.- +. .+...++.+
T Consensus 2 Y~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~gatk~~rp~L~~GDlV~ArV~~~~~-~~----~~eLtc~~~ 76 (86)
T cd05790 2 YVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANR-DM----EPELSCVDS 76 (86)
T ss_pred CcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccccccccccCCCCCEEEEEEEecCC-CC----CeEEEEeCC
Confidence 789999999999999911 111 1 1 12334579999999999988764 32 257778764
Q ss_pred c-cCCccccc
Q 048593 120 V-EGESLGPV 128 (150)
Q Consensus 120 i-~~d~LG~i 128 (150)
- +.++||+.
T Consensus 77 ~~k~~g~G~L 86 (86)
T cd05790 77 SGKADGFGPL 86 (86)
T ss_pred CCcccccccC
Confidence 3 67889874
No 19
>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=95.76 E-value=0.037 Score=37.81 Aligned_cols=61 Identities=15% Similarity=0.146 Sum_probs=40.1
Q ss_pred eeeecCcEEEEEEEEecCCCce---------ee-----c---------cccceecCCCEEEEEEEEEEeeecCcCccCcE
Q 048593 58 FLPVKGEILHGVIHIAVCEQPF---------FS-----N---------EQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKY 114 (150)
Q Consensus 58 FrPf~gEVv~G~V~~v~~~~~~---------~~-----~---------~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~ 114 (150)
|.|-+|+++.|+|+++.+.... +. . +-...+.+||.|++||..+.- .-
T Consensus 2 y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~---------~~ 72 (86)
T cd05789 2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDS---------DG 72 (86)
T ss_pred CcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECC---------CC
Confidence 6799999999999999222110 10 0 011258999999999988641 13
Q ss_pred EEEEEccCCcccc
Q 048593 115 LVFGRVEGESLGP 127 (150)
Q Consensus 115 ~~igsi~~d~LG~ 127 (150)
.+.=|++..+||.
T Consensus 73 ~i~LS~~~~~~g~ 85 (86)
T cd05789 73 SVSLHTRSLKYGK 85 (86)
T ss_pred CEEEEeCcccccC
Confidence 4455667777775
No 20
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=95.67 E-value=0.041 Score=36.25 Aligned_cols=45 Identities=20% Similarity=0.228 Sum_probs=32.1
Q ss_pred eeecCcEEEEEEEEecCCCce---------ee----------ccccceecCCCEEEEEEEEEEe
Q 048593 59 LPVKGEILHGVIHIAVCEQPF---------FS----------NEQQAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 59 rPf~gEVv~G~V~~v~~~~~~---------~~----------~~~~~~i~~gd~VR~RI~~v~~ 103 (150)
+|..|++++|+|+++...+.+ |. .+....+.+|+.|+++|.++..
T Consensus 1 k~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~ 64 (74)
T PF00575_consen 1 KLKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDK 64 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEET
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEEC
Confidence 578999999999999322111 11 1123479999999999999875
No 21
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=95.34 E-value=0.032 Score=39.65 Aligned_cols=62 Identities=23% Similarity=0.274 Sum_probs=41.1
Q ss_pred eeeecCcEEEEEEEEecCCC---------------ce---ee-c---c---c----cceecCCCEEEEEEEEEEeeecCc
Q 048593 58 FLPVKGEILHGVIHIAVCEQ---------------PF---FS-N---E---Q----QAKIRNGLVVQFLVTAVQWIDEGR 108 (150)
Q Consensus 58 FrPf~gEVv~G~V~~v~~~~---------------~~---~~-~---~---~----~~~i~~gd~VR~RI~~v~~~d~~~ 108 (150)
+.|..|.++-|+|+++.... ++ +- + + + ...+++||.||+||.+.. +.
T Consensus 2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~--~~-- 77 (92)
T cd05791 2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLG--DA-- 77 (92)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcC--CC--
Confidence 67999999999999991110 10 00 0 0 0 135899999999999865 32
Q ss_pred CccCcEEEEEEccCCccccc
Q 048593 109 NLKKKYLVFGRVEGESLGPV 128 (150)
Q Consensus 109 ~~~~~~~~igsi~~d~LG~i 128 (150)
++|. =|++++.||.+
T Consensus 78 ---~~~~--Lst~~~~lGVv 92 (92)
T cd05791 78 ---SSYY--LSTAENELGVV 92 (92)
T ss_pred ---CCcE--EEecCCCCccC
Confidence 2333 46688888864
No 22
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=94.98 E-value=0.065 Score=44.09 Aligned_cols=63 Identities=16% Similarity=0.333 Sum_probs=42.7
Q ss_pred eeeecCcEEEEEEEEecCCC----------cee------ec-------cccceecCCCEEEEEEEEEEeeecCcCccCcE
Q 048593 58 FLPVKGEILHGVIHIAVCEQ----------PFF------SN-------EQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKY 114 (150)
Q Consensus 58 FrPf~gEVv~G~V~~v~~~~----------~~~------~~-------~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~ 114 (150)
|.|..|.+|.|+|+++.... ..+ +. +-...+++||.|++||..+.- +. +
T Consensus 59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~-~~------~- 130 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDR-TR------D- 130 (235)
T ss_pred ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECC-CC------c-
Confidence 89999999999999992111 111 11 111258999999999998762 21 2
Q ss_pred EEEEEccCCcccccc
Q 048593 115 LVFGRVEGESLGPVS 129 (150)
Q Consensus 115 ~~igsi~~d~LG~i~ 129 (150)
+.=|+++++||.+.
T Consensus 131 -~~LS~k~~~lG~L~ 144 (235)
T PRK04163 131 -VVLTLKGKGLGKIE 144 (235)
T ss_pred -EEEEEcCCCCCccC
Confidence 34456888899876
No 23
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=94.14 E-value=0.33 Score=39.37 Aligned_cols=82 Identities=21% Similarity=0.178 Sum_probs=50.6
Q ss_pred CeeeeeCCCcceEEEEEEEEEEeeeecC--------cEEEEEEEEe------------cC-C------Cce-e--e----
Q 048593 36 RERGTVNESGVVFFPVTFLCRTFLPVKG--------EILHGVIHIA------------VC-E------QPF-F--S---- 81 (150)
Q Consensus 36 ~G~I~~~gdG~v~~~V~FraivFrPf~g--------EVv~G~V~~v------------~~-~------~~~-~--~---- 81 (150)
+|.|...-.|-+.++..=+.+.-+|++. -++-|.|+++ .+ + +.- + +
T Consensus 30 ~g~i~Aa~~G~~~~d~~n~~~~V~p~~~~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~ 109 (188)
T COG1096 30 GGEIRAAATGVVRRDDKNRVISVKPGKKTPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRD 109 (188)
T ss_pred CCEEEEeecccEEEcccceEEEeccCCCCCCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEeccc
Confidence 4555532357777766656665555554 8999999999 11 1 110 1 1
Q ss_pred ---ccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEEEccCCccccc
Q 048593 82 ---NEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPV 128 (150)
Q Consensus 82 ---~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igsi~~d~LG~i 128 (150)
+.....|+.||.||+||++.- + ||++ |+++..||.+
T Consensus 110 ~~~~~~~d~f~~GDivrA~Vis~~--~-------~~~L--st~~~dlGVI 148 (188)
T COG1096 110 GYVEKLSDAFRIGDIVRARVISTG--D-------PIQL--STKGNDLGVI 148 (188)
T ss_pred ccccccccccccccEEEEEEEecC--C-------CeEE--EecCCcceEE
Confidence 122236999999999999976 2 3433 4566677766
No 24
>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=91.86 E-value=0.075 Score=50.09 Aligned_cols=73 Identities=15% Similarity=0.145 Sum_probs=51.7
Q ss_pred eeeceeCCeeeeeCCCcceEEEE--EEEEEEeeeecCcEEEEEEEEecCCCcee-------------------eccccce
Q 048593 29 TNLKSIGRERGTVNESGVVFFPV--TFLCRTFLPVKGEILHGVIHIAVCEQPFF-------------------SNEQQAK 87 (150)
Q Consensus 29 ~di~~i~~G~I~~~gdG~v~~~V--~FraivFrPf~gEVv~G~V~~v~~~~~~~-------------------~~~~~~~ 87 (150)
+||.+-|..+|.. .++..+..+ .++.+++.|.+|+++.|+|+++.+...++ .+.-...
T Consensus 584 I~i~ddG~V~i~~-~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~~ 662 (684)
T TIGR03591 584 IDIEDDGTVKIAA-SDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDV 662 (684)
T ss_pred EEEecCeEEEEEE-CcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhhc
Confidence 3455556666667 788777777 67777889999999999999992221111 1111235
Q ss_pred ecCCCEEEEEEEEEE
Q 048593 88 IRNGLVVQFLVTAVQ 102 (150)
Q Consensus 88 i~~gd~VR~RI~~v~ 102 (150)
++.||.|++||.++.
T Consensus 663 ~kvGD~V~VkVi~id 677 (684)
T TIGR03591 663 LKEGDEVKVKVLEID 677 (684)
T ss_pred cCCCCEEEEEEEEEC
Confidence 899999999999876
No 25
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=91.66 E-value=0.52 Score=29.47 Aligned_cols=42 Identities=14% Similarity=0.158 Sum_probs=28.2
Q ss_pred cCcEEEEEEEEecCCCc---------eee-----cc-----ccceecCCCEEEEEEEEEEe
Q 048593 62 KGEILHGVIHIAVCEQP---------FFS-----NE-----QQAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 62 ~gEVv~G~V~~v~~~~~---------~~~-----~~-----~~~~i~~gd~VR~RI~~v~~ 103 (150)
.|+++.|+|+++.+... .+. .+ ....++.|+.|+++|..+..
T Consensus 2 ~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~ 62 (72)
T smart00316 2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDE 62 (72)
T ss_pred CCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeC
Confidence 58899999999822211 111 00 11358999999999999874
No 26
>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=90.79 E-value=0.89 Score=29.75 Aligned_cols=18 Identities=22% Similarity=0.206 Sum_probs=15.5
Q ss_pred ceecCCCEEEEEEEEEEe
Q 048593 86 AKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 86 ~~i~~gd~VR~RI~~v~~ 103 (150)
..+.+||.|+++|..+..
T Consensus 46 ~~~~~Gd~v~~~V~~~d~ 63 (73)
T cd05706 46 YKFKKNDIVRACVLSVDV 63 (73)
T ss_pred cccCCCCEEEEEEEEEeC
Confidence 358999999999998774
No 27
>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=90.41 E-value=0.87 Score=30.25 Aligned_cols=17 Identities=18% Similarity=0.036 Sum_probs=14.7
Q ss_pred eecCCCEEEEEEEEEEe
Q 048593 87 KIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 87 ~i~~gd~VR~RI~~v~~ 103 (150)
.++.||.|++||..+..
T Consensus 48 ~~~~Gd~v~vkv~~vd~ 64 (73)
T cd05686 48 VVDVGEKVWVKVIGREM 64 (73)
T ss_pred EECCCCEEEEEEEEECC
Confidence 58999999999988764
No 28
>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=89.83 E-value=0.98 Score=29.59 Aligned_cols=44 Identities=14% Similarity=0.062 Sum_probs=28.6
Q ss_pred eecCcEEEEEEEEecCCCc-----------eee----------ccccceecCCCEEEEEEEEEEe
Q 048593 60 PVKGEILHGVIHIAVCEQP-----------FFS----------NEQQAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 60 Pf~gEVv~G~V~~v~~~~~-----------~~~----------~~~~~~i~~gd~VR~RI~~v~~ 103 (150)
|-+|+++.|+|+++.+... -+. .+....+..||.|++||..+..
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~ 65 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDK 65 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEEC
Confidence 5578899999998821111 111 0111358999999999998764
No 29
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=89.78 E-value=0.89 Score=29.40 Aligned_cols=18 Identities=22% Similarity=0.254 Sum_probs=15.6
Q ss_pred ceecCCCEEEEEEEEEEe
Q 048593 86 AKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 86 ~~i~~gd~VR~RI~~v~~ 103 (150)
..+++||.|++||..+..
T Consensus 43 ~~~~~Gd~v~~~v~~~d~ 60 (73)
T cd05691 43 ERFKVGDEVEAKITNVDR 60 (73)
T ss_pred HccCCCCEEEEEEEEEeC
Confidence 358999999999999875
No 30
>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=89.39 E-value=0.96 Score=29.39 Aligned_cols=18 Identities=33% Similarity=0.366 Sum_probs=15.7
Q ss_pred ceecCCCEEEEEEEEEEe
Q 048593 86 AKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 86 ~~i~~gd~VR~RI~~v~~ 103 (150)
..+..|+.+.+||.++..
T Consensus 43 ~~~~~Gd~i~~~V~~id~ 60 (69)
T cd05697 43 KKFKPGLKVKCRVLSVEP 60 (69)
T ss_pred HcCCCCCEEEEEEEEEEC
Confidence 469999999999999874
No 31
>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=89.08 E-value=1.2 Score=28.99 Aligned_cols=18 Identities=22% Similarity=0.086 Sum_probs=15.6
Q ss_pred ceecCCCEEEEEEEEEEe
Q 048593 86 AKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 86 ~~i~~gd~VR~RI~~v~~ 103 (150)
..+.+||.|++||..+..
T Consensus 46 ~~~~~Gd~v~v~i~~vd~ 63 (77)
T cd05708 46 KLFRVGDKVRAKVLKIDA 63 (77)
T ss_pred HeecCCCEEEEEEEEEeC
Confidence 368999999999999874
No 32
>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=89.08 E-value=1.7 Score=28.70 Aligned_cols=18 Identities=28% Similarity=0.200 Sum_probs=16.1
Q ss_pred ceecCCCEEEEEEEEEEe
Q 048593 86 AKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 86 ~~i~~gd~VR~RI~~v~~ 103 (150)
..++.||.||+||.++..
T Consensus 56 ~~~~~gd~v~v~v~~vd~ 73 (83)
T cd04471 56 KVFRLGDKVKVRVVRVDL 73 (83)
T ss_pred CEEcCCCEEEEEEEEecc
Confidence 578999999999999875
No 33
>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=88.62 E-value=0.96 Score=29.33 Aligned_cols=18 Identities=11% Similarity=0.213 Sum_probs=15.0
Q ss_pred ceecCCCEEEEEEEEEEe
Q 048593 86 AKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 86 ~~i~~gd~VR~RI~~v~~ 103 (150)
..+.+||.|++||..+..
T Consensus 43 ~~~~~Gd~v~~~v~~~d~ 60 (68)
T cd05707 43 KRFKVGQLVKGKIVSIDP 60 (68)
T ss_pred hccCCCCEEEEEEEEEeC
Confidence 358999999999988763
No 34
>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=88.43 E-value=1.2 Score=28.94 Aligned_cols=16 Identities=25% Similarity=0.362 Sum_probs=14.5
Q ss_pred eecCCCEEEEEEEEEE
Q 048593 87 KIRNGLVVQFLVTAVQ 102 (150)
Q Consensus 87 ~i~~gd~VR~RI~~v~ 102 (150)
.+++||.++++|..+.
T Consensus 44 ~~~~Gd~i~~~i~~~~ 59 (70)
T cd05687 44 EVKVGDEVEVYVLRVE 59 (70)
T ss_pred cCCCCCEEEEEEEEEE
Confidence 5899999999999876
No 35
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=87.90 E-value=6.1 Score=33.19 Aligned_cols=47 Identities=19% Similarity=0.276 Sum_probs=33.7
Q ss_pred EeeeecCcEEEEEEEEec---------CCCcee-----------e---ccccceecCCCEEEEEEEEEEe
Q 048593 57 TFLPVKGEILHGVIHIAV---------CEQPFF-----------S---NEQQAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 57 vFrPf~gEVv~G~V~~v~---------~~~~~~-----------~---~~~~~~i~~gd~VR~RI~~v~~ 103 (150)
-|.|-.|.+|-|.|.++. ...+.+ . .+-+.++++||.|-+||..+--
T Consensus 59 ~YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~ 128 (239)
T COG1097 59 RYIPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDR 128 (239)
T ss_pred cccCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccC
Confidence 588999999999999991 100101 1 1223479999999999998763
No 36
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=87.79 E-value=1.9 Score=27.19 Aligned_cols=18 Identities=17% Similarity=0.104 Sum_probs=15.5
Q ss_pred ceecCCCEEEEEEEEEEe
Q 048593 86 AKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 86 ~~i~~gd~VR~RI~~v~~ 103 (150)
..++.||.|+++|..+..
T Consensus 43 ~~~~~Gd~v~v~i~~vd~ 60 (68)
T cd05688 43 EVVNVGDEVEVKVLKIDK 60 (68)
T ss_pred HEECCCCEEEEEEEEEEC
Confidence 368999999999999864
No 37
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=87.22 E-value=1.2 Score=29.70 Aligned_cols=16 Identities=13% Similarity=0.306 Sum_probs=13.9
Q ss_pred eecCCCEEEEEEEEEE
Q 048593 87 KIRNGLVVQFLVTAVQ 102 (150)
Q Consensus 87 ~i~~gd~VR~RI~~v~ 102 (150)
.+++||.||++|.++.
T Consensus 48 ~~~~Gd~v~~kV~~~~ 63 (72)
T cd05704 48 GFKPGKIVRCCILSKK 63 (72)
T ss_pred hCCCCCEEEEEEEEec
Confidence 5889999999998864
No 38
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=86.14 E-value=1.8 Score=27.12 Aligned_cols=17 Identities=18% Similarity=0.239 Sum_probs=14.6
Q ss_pred eecCCCEEEEEEEEEEe
Q 048593 87 KIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 87 ~i~~gd~VR~RI~~v~~ 103 (150)
.++.||.|++||..+..
T Consensus 44 ~~~~Gd~v~v~v~~~~~ 60 (69)
T cd05692 44 VLKEGDKVKVKVLSIDA 60 (69)
T ss_pred ccCCCCEEEEEEEEECC
Confidence 58999999999988763
No 39
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=86.12 E-value=2.3 Score=29.90 Aligned_cols=14 Identities=21% Similarity=0.385 Sum_probs=10.5
Q ss_pred eecCcEEEEEEEEe
Q 048593 60 PVKGEILHGVIHIA 73 (150)
Q Consensus 60 Pf~gEVv~G~V~~v 73 (150)
|-.|-++.|+|+++
T Consensus 2 P~vGdiV~~rVtrv 15 (82)
T PF10447_consen 2 PKVGDIVIARVTRV 15 (82)
T ss_dssp --TT-EEEEEEEEE
T ss_pred CCCCCEEEEEEEEE
Confidence 88899999999999
No 40
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=85.95 E-value=2.3 Score=27.83 Aligned_cols=16 Identities=19% Similarity=0.183 Sum_probs=14.3
Q ss_pred eecCCCEEEEEEEEEE
Q 048593 87 KIRNGLVVQFLVTAVQ 102 (150)
Q Consensus 87 ~i~~gd~VR~RI~~v~ 102 (150)
.+..||.|++||.++.
T Consensus 46 ~~~~Gd~i~~kVl~~d 61 (70)
T cd05702 46 KFKIGQKIKARVIGGH 61 (70)
T ss_pred hCCCCCEEEEEEEEEe
Confidence 5899999999998875
No 41
>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=84.84 E-value=3.9 Score=26.14 Aligned_cols=18 Identities=17% Similarity=0.217 Sum_probs=15.6
Q ss_pred ceecCCCEEEEEEEEEEe
Q 048593 86 AKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 86 ~~i~~gd~VR~RI~~v~~ 103 (150)
..+++|+.|+++|..+..
T Consensus 44 ~~~~~G~~v~v~v~~id~ 61 (69)
T cd05690 44 EIYKKGQEVEAVVLNIDV 61 (69)
T ss_pred hEECCCCEEEEEEEEEEC
Confidence 468999999999998874
No 42
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=84.20 E-value=2.9 Score=33.85 Aligned_cols=52 Identities=21% Similarity=0.235 Sum_probs=33.5
Q ss_pred EEEEEEEEEeeeecCcEEEEEEEEe-----------cCCC---cee---e-cc-------cc----ceecCCCEEEEEEE
Q 048593 49 FPVTFLCRTFLPVKGEILHGVIHIA-----------VCEQ---PFF---S-NE-------QQ----AKIRNGLVVQFLVT 99 (150)
Q Consensus 49 ~~V~FraivFrPf~gEVv~G~V~~v-----------~~~~---~~~---~-~~-------~~----~~i~~gd~VR~RI~ 99 (150)
.+..|..+ -||.|-|+.++|+.+ -++. ..| . ++ ++ ..+++||.||+||+
T Consensus 57 ~~~~~~~~--LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVi 134 (193)
T KOG3409|consen 57 EKQLFNEL--LPFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVI 134 (193)
T ss_pred cccchhhc--CCccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEe
Confidence 44455554 599999999999998 1110 011 1 11 11 14889999999999
Q ss_pred EEE
Q 048593 100 AVQ 102 (150)
Q Consensus 100 ~v~ 102 (150)
+..
T Consensus 135 s~~ 137 (193)
T KOG3409|consen 135 SLG 137 (193)
T ss_pred ecC
Confidence 943
No 43
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=84.11 E-value=3.3 Score=32.68 Aligned_cols=46 Identities=17% Similarity=0.221 Sum_probs=31.9
Q ss_pred EeeeecCcEEEEEEEEecCCCce-------------------ee--c---cc-----cceecCCCEEEEEEEEEE
Q 048593 57 TFLPVKGEILHGVIHIAVCEQPF-------------------FS--N---EQ-----QAKIRNGLVVQFLVTAVQ 102 (150)
Q Consensus 57 vFrPf~gEVv~G~V~~v~~~~~~-------------------~~--~---~~-----~~~i~~gd~VR~RI~~v~ 102 (150)
.+.|-.|+++.|+|+++.+.... +. + +. ...+.+||.|++||..+.
T Consensus 59 ~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~ 133 (189)
T PRK09521 59 PPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT 133 (189)
T ss_pred CCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC
Confidence 47788999999999999222111 10 0 00 235899999999999875
No 44
>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=83.98 E-value=2.8 Score=26.23 Aligned_cols=17 Identities=18% Similarity=0.225 Sum_probs=15.0
Q ss_pred eecCCCEEEEEEEEEEe
Q 048593 87 KIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 87 ~i~~gd~VR~RI~~v~~ 103 (150)
.+++||.|++||..+..
T Consensus 44 ~~~~Gd~v~v~i~~vd~ 60 (68)
T cd05685 44 VVSVGDIVEVKVISIDE 60 (68)
T ss_pred hcCCCCEEEEEEEEEEC
Confidence 58999999999998874
No 45
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=83.78 E-value=2.3 Score=27.44 Aligned_cols=18 Identities=28% Similarity=0.270 Sum_probs=15.3
Q ss_pred ceecCCCEEEEEEEEEEe
Q 048593 86 AKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 86 ~~i~~gd~VR~RI~~v~~ 103 (150)
..+.+|+.+++||.++..
T Consensus 43 ~~~~~G~~i~v~v~~~d~ 60 (70)
T cd05698 43 EHFRVGQVVKVKVLSCDP 60 (70)
T ss_pred HcccCCCEEEEEEEEEcC
Confidence 358999999999998763
No 46
>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=83.72 E-value=3.9 Score=27.52 Aligned_cols=18 Identities=17% Similarity=0.150 Sum_probs=15.8
Q ss_pred ceecCCCEEEEEEEEEEe
Q 048593 86 AKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 86 ~~i~~gd~VR~RI~~v~~ 103 (150)
..+.+|+.|+++|.++.-
T Consensus 49 ~~~~~G~~v~~kVl~id~ 66 (74)
T cd05705 49 KYLPEGKLLTAKVLSVNS 66 (74)
T ss_pred cccCCCCEEEEEEEEEEC
Confidence 468999999999999874
No 47
>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=83.39 E-value=2.7 Score=28.35 Aligned_cols=44 Identities=18% Similarity=0.154 Sum_probs=28.7
Q ss_pred eecCcEEEEEEEEecCCCc---------eee----------ccccceecCCCEEEEEEEEEEe
Q 048593 60 PVKGEILHGVIHIAVCEQP---------FFS----------NEQQAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 60 Pf~gEVv~G~V~~v~~~~~---------~~~----------~~~~~~i~~gd~VR~RI~~v~~ 103 (150)
+-.|+++.|+|+++.+... -|. .+-...+.+|+.|++||..+..
T Consensus 12 ~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~ 74 (83)
T cd04461 12 LKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDE 74 (83)
T ss_pred CCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcC
Confidence 4578888888888822111 111 1112368999999999999774
No 48
>PRK08582 hypothetical protein; Provisional
Probab=82.30 E-value=4 Score=31.07 Aligned_cols=41 Identities=20% Similarity=0.261 Sum_probs=27.1
Q ss_pred cCcEEEEEEEEecCCCce-------------------eeccccceecCCCEEEEEEEEEE
Q 048593 62 KGEILHGVIHIAVCEQPF-------------------FSNEQQAKIRNGLVVQFLVTAVQ 102 (150)
Q Consensus 62 ~gEVv~G~V~~v~~~~~~-------------------~~~~~~~~i~~gd~VR~RI~~v~ 102 (150)
.|++++|+|+++.....+ +..+....+.+||.|+++|..+.
T Consensus 5 vG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id 64 (139)
T PRK08582 5 VGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVE 64 (139)
T ss_pred CCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEEC
Confidence 588888888888111111 01111246899999999999976
No 49
>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=81.54 E-value=4.1 Score=25.65 Aligned_cols=16 Identities=25% Similarity=0.258 Sum_probs=14.2
Q ss_pred eecCCCEEEEEEEEEE
Q 048593 87 KIRNGLVVQFLVTAVQ 102 (150)
Q Consensus 87 ~i~~gd~VR~RI~~v~ 102 (150)
.++.||.|+++|..+.
T Consensus 44 ~~~~Gd~v~v~v~~~d 59 (68)
T cd04472 44 VLKVGDEVKVKVIEVD 59 (68)
T ss_pred ccCCCCEEEEEEEEEC
Confidence 5799999999998875
No 50
>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=80.64 E-value=7.8 Score=25.09 Aligned_cols=18 Identities=17% Similarity=0.150 Sum_probs=15.5
Q ss_pred ceecCCCEEEEEEEEEEe
Q 048593 86 AKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 86 ~~i~~gd~VR~RI~~v~~ 103 (150)
..+++|+.|+++|..+..
T Consensus 47 ~~~~~Gd~v~v~v~~id~ 64 (72)
T cd05689 47 KVVSLGDEVEVMVLDIDE 64 (72)
T ss_pred cEeCCCCEEEEEEEEeeC
Confidence 468999999999988774
No 51
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=80.06 E-value=6.6 Score=25.62 Aligned_cols=18 Identities=17% Similarity=0.126 Sum_probs=15.3
Q ss_pred ceecCCCEEEEEEEEEEe
Q 048593 86 AKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 86 ~~i~~gd~VR~RI~~v~~ 103 (150)
..++.|+.|.+||..+..
T Consensus 41 ~~~~~G~~i~~kVi~id~ 58 (66)
T cd05695 41 STYKEGQKVRARILYVDP 58 (66)
T ss_pred cCcCCCCEEEEEEEEEeC
Confidence 469999999999998763
No 52
>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=80.03 E-value=9.6 Score=24.80 Aligned_cols=42 Identities=21% Similarity=0.274 Sum_probs=29.4
Q ss_pred ecCcEEEEEEEEecCCCcee--------e--cc--ccceecCCCEEEEEEEEEE
Q 048593 61 VKGEILHGVIHIAVCEQPFF--------S--NE--QQAKIRNGLVVQFLVTAVQ 102 (150)
Q Consensus 61 f~gEVv~G~V~~v~~~~~~~--------~--~~--~~~~i~~gd~VR~RI~~v~ 102 (150)
..|+++.|+|.++.+...++ . ++ ....+++|+.|++-|..+.
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig~~eg~lp~~e~~~~~~~~~Gd~v~v~v~~v~ 55 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIPGESYRPGDRIKAYVLEVR 55 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcCCeEEEeeHHHCCCCCcCCCCCEEEEEEEEEe
Confidence 57999999999994433222 1 00 0125799999999999987
No 53
>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=79.94 E-value=11 Score=26.25 Aligned_cols=49 Identities=20% Similarity=0.255 Sum_probs=32.8
Q ss_pred eeecCcEEEEEEEEecCC-Ccee----------e--cc-----------ccceecCCCEEEEEEEEEEeeecC
Q 048593 59 LPVKGEILHGVIHIAVCE-QPFF----------S--NE-----------QQAKIRNGLVVQFLVTAVQWIDEG 107 (150)
Q Consensus 59 rPf~gEVv~G~V~~v~~~-~~~~----------~--~~-----------~~~~i~~gd~VR~RI~~v~~~d~~ 107 (150)
+|-.|++..|+|+++.+. +..| . ++ -...+.+||.|.++|...-+.+..
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~ 76 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKG 76 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCC
Confidence 356899999999999442 1111 1 00 013589999999999997775543
No 54
>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=79.70 E-value=8 Score=25.52 Aligned_cols=17 Identities=6% Similarity=0.006 Sum_probs=14.8
Q ss_pred eecCCCEEEEEEEEEEe
Q 048593 87 KIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 87 ~i~~gd~VR~RI~~v~~ 103 (150)
.+++|+.+++||.++.-
T Consensus 46 ~~~vG~~v~~kV~~id~ 62 (71)
T cd05696 46 PFKAGTTHKARIIGYSP 62 (71)
T ss_pred ccCCCCEEEEEEEEEeC
Confidence 59999999999988763
No 55
>PRK08059 general stress protein 13; Validated
Probab=79.64 E-value=4.5 Score=29.86 Aligned_cols=44 Identities=16% Similarity=0.090 Sum_probs=28.5
Q ss_pred eecCcEEEEEEEEecCCCcee-------------------eccccceecCCCEEEEEEEEEEe
Q 048593 60 PVKGEILHGVIHIAVCEQPFF-------------------SNEQQAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 60 Pf~gEVv~G~V~~v~~~~~~~-------------------~~~~~~~i~~gd~VR~RI~~v~~ 103 (150)
.-.|+++.|+|+++.....++ ..+....+.+||.|+++|..+..
T Consensus 5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~ 67 (123)
T PRK08059 5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDE 67 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEEC
Confidence 346889999999882211110 11112368999999999999863
No 56
>PRK05807 hypothetical protein; Provisional
Probab=79.62 E-value=5.1 Score=30.31 Aligned_cols=42 Identities=17% Similarity=0.221 Sum_probs=27.2
Q ss_pred cCcEEEEEEEEecCCCcee------------------eccccceecCCCEEEEEEEEEEe
Q 048593 62 KGEILHGVIHIAVCEQPFF------------------SNEQQAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 62 ~gEVv~G~V~~v~~~~~~~------------------~~~~~~~i~~gd~VR~RI~~v~~ 103 (150)
.|+++.|+|+.+.....++ ..+....+.+|+.|+++|..+.-
T Consensus 5 vG~vv~G~Vt~i~~~GafV~L~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~ 64 (136)
T PRK05807 5 AGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD 64 (136)
T ss_pred CCCEEEEEEEEEECCeEEEEECCEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC
Confidence 4788888888882221111 11112468999999999988763
No 57
>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=75.90 E-value=8 Score=25.76 Aligned_cols=18 Identities=22% Similarity=0.165 Sum_probs=15.4
Q ss_pred ceecCCCEEEEEEEEEEe
Q 048593 86 AKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 86 ~~i~~gd~VR~RI~~v~~ 103 (150)
..+.+|+.|.+||.++..
T Consensus 45 ~~~~vG~~v~~kV~~id~ 62 (73)
T cd05703 45 KKFPIGQALKAKVVGVDK 62 (73)
T ss_pred HhCCCCCEEEEEEEEEeC
Confidence 359999999999998764
No 58
>PRK07252 hypothetical protein; Provisional
Probab=75.24 E-value=7.9 Score=28.74 Aligned_cols=18 Identities=17% Similarity=0.058 Sum_probs=15.7
Q ss_pred ceecCCCEEEEEEEEEEe
Q 048593 86 AKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 86 ~~i~~gd~VR~RI~~v~~ 103 (150)
..+.+||.|++||.++..
T Consensus 46 ~~~~vGD~V~VkI~~iD~ 63 (120)
T PRK07252 46 QLLKVGEEVLVQVVDFDE 63 (120)
T ss_pred hccCCCCEEEEEEEEEeC
Confidence 468999999999999874
No 59
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=73.93 E-value=6.5 Score=33.08 Aligned_cols=45 Identities=22% Similarity=0.309 Sum_probs=31.0
Q ss_pred eeecCcEEEEEEEEecCCCce-----------ee----------ccccceecCCCEEEEEEEEEEe
Q 048593 59 LPVKGEILHGVIHIAVCEQPF-----------FS----------NEQQAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 59 rPf~gEVv~G~V~~v~~~~~~-----------~~----------~~~~~~i~~gd~VR~RI~~v~~ 103 (150)
.|-+|+++.|+|+++.+...+ +. .+-...++.|+.|++||..+..
T Consensus 5 ~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~ 70 (262)
T PRK03987 5 WPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDP 70 (262)
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEec
Confidence 488999999999999222111 10 0111258999999999998764
No 60
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=73.38 E-value=10 Score=34.64 Aligned_cols=46 Identities=22% Similarity=0.235 Sum_probs=32.2
Q ss_pred eeeecCcEEEEEEEEecCCCcee--------ec-c---ccceecCCCEEEEEEEEEEe
Q 048593 58 FLPVKGEILHGVIHIAVCEQPFF--------SN-E---QQAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 58 FrPf~gEVv~G~V~~v~~~~~~~--------~~-~---~~~~i~~gd~VR~RI~~v~~ 103 (150)
|++..||++.|+|+++...+..+ .. . .+..+.+|+.||+.|..+.-
T Consensus 130 yk~~~GeIV~G~V~ri~~~giiVDLggvea~LP~sE~ip~E~~~~GdrIka~I~~Vd~ 187 (470)
T PRK09202 130 YKDRVGEIITGVVKRVERGNIIVDLGRAEAILPRKEQIPRENFRPGDRVRAYVYEVRK 187 (470)
T ss_pred HHhhcCCEEEEEEEEEecCCEEEEECCeEEEecHHHcCCCccCCCCCEEEEEEEEEec
Confidence 44457999999999994333222 11 1 12368999999999999975
No 61
>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=72.97 E-value=14 Score=24.45 Aligned_cols=17 Identities=24% Similarity=0.393 Sum_probs=14.9
Q ss_pred ceecCCCEEEEEEEEEE
Q 048593 86 AKIRNGLVVQFLVTAVQ 102 (150)
Q Consensus 86 ~~i~~gd~VR~RI~~v~ 102 (150)
..++.|+.|+++|..+.
T Consensus 47 ~~~~~Gd~v~v~v~~vd 63 (79)
T cd05684 47 DVVKRGQKVKVKVISIQ 63 (79)
T ss_pred heeCCCCEEEEEEEEEe
Confidence 46899999999999876
No 62
>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=72.51 E-value=8.3 Score=23.32 Aligned_cols=18 Identities=22% Similarity=0.095 Sum_probs=15.8
Q ss_pred ceecCCCEEEEEEEEEEe
Q 048593 86 AKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 86 ~~i~~gd~VR~RI~~v~~ 103 (150)
..+++|+.|++||..+..
T Consensus 40 ~~~~~G~~v~~~v~~~d~ 57 (65)
T cd00164 40 EVFKVGDEVEVKVLEVDP 57 (65)
T ss_pred hEeCCCCEEEEEEEEEcC
Confidence 479999999999999864
No 63
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=71.53 E-value=11 Score=27.89 Aligned_cols=45 Identities=18% Similarity=0.224 Sum_probs=31.5
Q ss_pred eeecCcEEEEEEEEecCCCcee---------e---ccccceecCCCEEEEEEEEEEe
Q 048593 59 LPVKGEILHGVIHIAVCEQPFF---------S---NEQQAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 59 rPf~gEVv~G~V~~v~~~~~~~---------~---~~~~~~i~~gd~VR~RI~~v~~ 103 (150)
-|++|-++.|+|..+.++..+. - ..+...+..|+.||+|+.....
T Consensus 20 G~~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~~~~y~~G~rV~lrLkdlEL 76 (104)
T PF10246_consen 20 GDPEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVNGEKYVRGSRVRLRLKDLEL 76 (104)
T ss_pred CCccCCEEEEEEEEEecCceEEEeCCceeEEEecccccccccccCCEEEEEECCHhh
Confidence 4678899999999984443322 1 1223468899999999987665
No 64
>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=71.38 E-value=9.5 Score=25.51 Aligned_cols=44 Identities=16% Similarity=0.050 Sum_probs=29.9
Q ss_pred eeeecCcEEEEEEEEecCCCcee-----------eccccceecCCCEEEEEEEEE
Q 048593 58 FLPVKGEILHGVIHIAVCEQPFF-----------SNEQQAKIRNGLVVQFLVTAV 101 (150)
Q Consensus 58 FrPf~gEVv~G~V~~v~~~~~~~-----------~~~~~~~i~~gd~VR~RI~~v 101 (150)
..+-.|++++|+|+++.+...+. .++-...++.|+.+++||..+
T Consensus 12 ~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~~~~~iGd~v~v~I~~i 66 (77)
T cd04473 12 EDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDYEVGDEVIVQVTDI 66 (77)
T ss_pred hhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhccCcCCCCCEEEEEEEEE
Confidence 34557899999999983222111 122224689999999999998
No 65
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=71.16 E-value=13 Score=32.42 Aligned_cols=46 Identities=24% Similarity=0.328 Sum_probs=33.3
Q ss_pred eeeecCcEEEEEEEEecCCCceeec-----------c--ccceecCCCEEEEEEEEEEe
Q 048593 58 FLPVKGEILHGVIHIAVCEQPFFSN-----------E--QQAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 58 FrPf~gEVv~G~V~~v~~~~~~~~~-----------~--~~~~i~~gd~VR~RI~~v~~ 103 (150)
|+...||++.|+|.++...+.++.+ + .+..+.+|+.+++-|..++-
T Consensus 127 y~~k~GeiV~G~V~~v~~~g~v~VdiG~~ea~LP~~E~ip~E~~~~Gd~ik~~V~~V~~ 185 (341)
T TIGR01953 127 FSSKEGEIISGTVKRVNRRGNLYVELGKTEGILPKKEQIPGEKFRIGDRIKAYVYEVRK 185 (341)
T ss_pred HHhhcCCEEEEEEEEEecCCcEEEEECCeEEEecHHHcCCCcCCCCCCEEEEEEEEEEc
Confidence 5667999999999999554322211 1 11258999999999999985
No 66
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=71.06 E-value=25 Score=29.38 Aligned_cols=79 Identities=14% Similarity=0.221 Sum_probs=57.6
Q ss_pred ceEEEEEEEEEEeeeecCcEEEEEEEEecCCCc---------------eee---ccccceecCCCEEEEEEEEEEeeecC
Q 048593 46 VVFFPVTFLCRTFLPVKGEILHGVIHIAVCEQP---------------FFS---NEQQAKIRNGLVVQFLVTAVQWIDEG 107 (150)
Q Consensus 46 ~v~~~V~FraivFrPf~gEVv~G~V~~v~~~~~---------------~~~---~~~~~~i~~gd~VR~RI~~v~~~d~~ 107 (150)
.-.+.|.++-.=|-|-++..|-|+|++..++.- .|. +..+..+++||.|-+||.-..- |.+
T Consensus 49 ~~v~~vds~~kRYiP~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe~AtkrNrPnl~vGdliyakv~~a~~-~~E 127 (230)
T KOG1004|consen 49 GGVYWVDSQQKRYIPVKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFEGATKRNRPNLQVGDLIYAKVVDANK-DME 127 (230)
T ss_pred ceeEEEecccceecCCCCCEEEEEEEeccCceEEEecCCCCeeeeeeccccCccccCCCccccccEEEEEEEecCC-CcC
Confidence 346788999999999999999999999822211 122 3334579999999999987552 333
Q ss_pred cCccCcEEEEEEc-cCCcccccc
Q 048593 108 RNLKKKYLVFGRV-EGESLGPVS 129 (150)
Q Consensus 108 ~~~~~~~~~igsi-~~d~LG~i~ 129 (150)
|.+.++.+- +..++|++-
T Consensus 128 ----pel~Cids~graaGfG~Lk 146 (230)
T KOG1004|consen 128 ----PELTCIDSTGRAAGFGVLK 146 (230)
T ss_pred ----cceEEEcccCcccCccccc
Confidence 789999884 446777664
No 67
>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=70.12 E-value=17 Score=24.44 Aligned_cols=41 Identities=20% Similarity=0.337 Sum_probs=28.2
Q ss_pred cCcEEEEEEEEecCCCce----------ee-ccc---cceecCCCEEEEEEEEEE
Q 048593 62 KGEILHGVIHIAVCEQPF----------FS-NEQ---QAKIRNGLVVQFLVTAVQ 102 (150)
Q Consensus 62 ~gEVv~G~V~~v~~~~~~----------~~-~~~---~~~i~~gd~VR~RI~~v~ 102 (150)
.|.++.|.|+++.+...+ |. ..+ ...+.+|+.+.++|.++.
T Consensus 4 ~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~~~~~~Gq~v~~~V~~vd 58 (74)
T cd05694 4 EGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNFSKLKVGQLLLCVVEKVK 58 (74)
T ss_pred CCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcccccCCCCEEEEEEEEEE
Confidence 588999999999333221 21 111 146999999999998775
No 68
>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=67.18 E-value=6.9 Score=36.96 Aligned_cols=18 Identities=22% Similarity=0.137 Sum_probs=16.1
Q ss_pred ceecCCCEEEEEEEEEEe
Q 048593 86 AKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 86 ~~i~~gd~VR~RI~~v~~ 103 (150)
..++.||.|++||.++..
T Consensus 682 ~~~~lGd~V~Vkv~~vd~ 699 (709)
T TIGR02063 682 KVFRLGDRVKVRVVKADL 699 (709)
T ss_pred cEECCCCEEEEEEEEEec
Confidence 468999999999999875
No 69
>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=66.67 E-value=20 Score=25.54 Aligned_cols=17 Identities=18% Similarity=0.179 Sum_probs=15.1
Q ss_pred eecCCCEEEEEEEEEEe
Q 048593 87 KIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 87 ~i~~gd~VR~RI~~v~~ 103 (150)
.+.+|+.||++|+++.-
T Consensus 66 ~f~vGd~V~~kVi~~d~ 82 (100)
T cd05693 66 LFSVGQLVRCKVVSLDK 82 (100)
T ss_pred hccCCCEEEEEEEEccC
Confidence 58999999999999774
No 70
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=66.32 E-value=20 Score=31.73 Aligned_cols=47 Identities=17% Similarity=0.247 Sum_probs=33.9
Q ss_pred eeeecCcEEEEEEEEecCCCcee--------ec-c---ccceecCCCEEEEEEEEEEee
Q 048593 58 FLPVKGEILHGVIHIAVCEQPFF--------SN-E---QQAKIRNGLVVQFLVTAVQWI 104 (150)
Q Consensus 58 FrPf~gEVv~G~V~~v~~~~~~~--------~~-~---~~~~i~~gd~VR~RI~~v~~~ 104 (150)
|++-.|+++.|+|.+....+.++ .. . .+..+.+|+.||+-|..++..
T Consensus 130 f~~k~GeiV~G~V~~~~~~~~~Vdlg~vEa~LP~~E~ip~e~~~~Gd~Ika~V~~V~~~ 188 (362)
T PRK12327 130 FSEREGDIVTGVVQRRDNRFVYVNLGKIEAVLPPAEQIPGETYKHGDRIKVYVVKVEKT 188 (362)
T ss_pred HHHhcCCEEEEEEEEEeCCcEEEEeCCeEEEecHHHcCCCCCCCCCCEEEEEEEEEecC
Confidence 67789999999999984332221 11 1 123689999999999999863
No 71
>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=66.05 E-value=14 Score=34.74 Aligned_cols=19 Identities=26% Similarity=0.134 Sum_probs=16.6
Q ss_pred cceecCCCEEEEEEEEEEe
Q 048593 85 QAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 85 ~~~i~~gd~VR~RI~~v~~ 103 (150)
+..++.||.|++||.++..
T Consensus 626 ~~~~~lGD~V~Vki~~vd~ 644 (654)
T TIGR00358 626 GKVYRIGDRVTVKLTEVNM 644 (654)
T ss_pred CcEECCCCEEEEEEEEEec
Confidence 3579999999999999875
No 72
>PRK11642 exoribonuclease R; Provisional
Probab=63.26 E-value=7.8 Score=37.58 Aligned_cols=19 Identities=32% Similarity=0.218 Sum_probs=16.7
Q ss_pred cceecCCCEEEEEEEEEEe
Q 048593 85 QAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 85 ~~~i~~gd~VR~RI~~v~~ 103 (150)
+..++.||.|++||..+..
T Consensus 697 ~~~~~lGD~V~VkV~~vD~ 715 (813)
T PRK11642 697 GQTYRLGDRVEVRVEAVNM 715 (813)
T ss_pred CcEECCCCEEEEEEEEeec
Confidence 3579999999999999876
No 73
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=63.06 E-value=15 Score=34.92 Aligned_cols=45 Identities=22% Similarity=0.256 Sum_probs=31.4
Q ss_pred eeeecCcEEEEEEEEecCCCcee-------------------eccccceecCCCEEEEEEEEEE
Q 048593 58 FLPVKGEILHGVIHIAVCEQPFF-------------------SNEQQAKIRNGLVVQFLVTAVQ 102 (150)
Q Consensus 58 FrPf~gEVv~G~V~~v~~~~~~~-------------------~~~~~~~i~~gd~VR~RI~~v~ 102 (150)
..|..|+++.|+|+++.+...++ .+.-...++.||.|++||.++.
T Consensus 617 ~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD 680 (693)
T PRK11824 617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID 680 (693)
T ss_pred ccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEEC
Confidence 45889999999999992221111 0111236899999999999875
No 74
>PHA02945 interferon resistance protein; Provisional
Probab=60.85 E-value=29 Score=24.96 Aligned_cols=40 Identities=25% Similarity=0.411 Sum_probs=29.1
Q ss_pred eecCcEEEEEEEEe-------------------cC----CCceeeccccceecCCCEEEEEEEEEE
Q 048593 60 PVKGEILHGVIHIA-------------------VC----EQPFFSNEQQAKIRNGLVVQFLVTAVQ 102 (150)
Q Consensus 60 Pf~gEVv~G~V~~v-------------------~~----~~~~~~~~~~~~i~~gd~VR~RI~~v~ 102 (150)
|-.||++.|+|++- .. .+.|+.+ +..+ .|..|-+||+-+.
T Consensus 9 P~~GelvigtV~~~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~--rd~l-~GqkvV~KVirVd 71 (88)
T PHA02945 9 PNVGDVLKGKVYENGYALYIDLFDYPHSEAILAESVQMHMNRYFKY--RDKL-VGKTVKVKVIRVD 71 (88)
T ss_pred CCCCcEEEEEEEecCceEEEEecccCCcEEEEEeehhhhccceEee--eeEe-cCCEEEEEEEEEC
Confidence 88999999999985 11 1123333 4567 9999999998875
No 75
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=58.54 E-value=32 Score=30.71 Aligned_cols=48 Identities=21% Similarity=0.254 Sum_probs=35.3
Q ss_pred eeeecCcEEEEEEEEecCCCceee----------cc---ccceecCCCEEEEEEEEEEeee
Q 048593 58 FLPVKGEILHGVIHIAVCEQPFFS----------NE---QQAKIRNGLVVQFLVTAVQWID 105 (150)
Q Consensus 58 FrPf~gEVv~G~V~~v~~~~~~~~----------~~---~~~~i~~gd~VR~RI~~v~~~d 105 (150)
|++..||++.|+|.++...+..+. .. .+..+.+|+.+|+=|..|+-..
T Consensus 134 y~~~~Geiv~g~V~r~~~~~~i~vdlg~~ea~LP~~eqip~E~~~~Gdrik~~i~~V~~~~ 194 (374)
T PRK12328 134 YKKKVGKIVFGTVVRVDNEENTFIEIDEIRAVLPMKNRIKGEKFKVGDVVKAVLKRVKIDK 194 (374)
T ss_pred HHHhcCcEEEEEEEEEecCCCEEEEcCCeEEEeCHHHcCCCCcCCCCCEEEEEEEEEecCC
Confidence 789999999999999854322221 11 1236999999999999998643
No 76
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=54.78 E-value=21 Score=31.10 Aligned_cols=43 Identities=16% Similarity=0.138 Sum_probs=30.3
Q ss_pred eecCcEEEEEEEEecCCCceee---------------------ccccceecCCCEEEEEEEEEE
Q 048593 60 PVKGEILHGVIHIAVCEQPFFS---------------------NEQQAKIRNGLVVQFLVTAVQ 102 (150)
Q Consensus 60 Pf~gEVv~G~V~~v~~~~~~~~---------------------~~~~~~i~~gd~VR~RI~~v~ 102 (150)
|..|+++.|+|+++.+-..++. .+-...+++|+.|.++|..+.
T Consensus 15 P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD 78 (319)
T PTZ00248 15 PEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVD 78 (319)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEe
Confidence 6679999999999933332221 011135899999999999874
No 77
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=54.60 E-value=22 Score=30.51 Aligned_cols=15 Identities=7% Similarity=0.255 Sum_probs=8.2
Q ss_pred ecCCCEEEEEEEEEE
Q 048593 88 IRNGLVVQFLVTAVQ 102 (150)
Q Consensus 88 i~~gd~VR~RI~~v~ 102 (150)
+.+|+.|+++|+++.
T Consensus 76 ~~~G~~v~~~Vi~~~ 90 (318)
T PRK07400 76 LQPNETREFFILSDE 90 (318)
T ss_pred cCCCCEEEEEEEEEe
Confidence 455555555555543
No 78
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=51.69 E-value=39 Score=25.96 Aligned_cols=43 Identities=19% Similarity=0.202 Sum_probs=30.3
Q ss_pred eecCcEEEEEEEEecCCCceee-------------------ccccceecCCCEEEEEEEEEE
Q 048593 60 PVKGEILHGVIHIAVCEQPFFS-------------------NEQQAKIRNGLVVQFLVTAVQ 102 (150)
Q Consensus 60 Pf~gEVv~G~V~~v~~~~~~~~-------------------~~~~~~i~~gd~VR~RI~~v~ 102 (150)
+-.|+++.|+|+.+.+-.+++. ++=...+.+|+.|.++|.++-
T Consensus 3 ~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~id 64 (129)
T COG1098 3 MKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDID 64 (129)
T ss_pred ccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeec
Confidence 4579999999999933333321 111235899999999999875
No 79
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=50.35 E-value=34 Score=29.35 Aligned_cols=44 Identities=9% Similarity=0.113 Sum_probs=29.1
Q ss_pred eecCcEEEEEEEEecCCCceee------------------ccccceecCCCEEEEEEEEEEe
Q 048593 60 PVKGEILHGVIHIAVCEQPFFS------------------NEQQAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 60 Pf~gEVv~G~V~~v~~~~~~~~------------------~~~~~~i~~gd~VR~RI~~v~~ 103 (150)
.-.|+++.|+|+++.+...++. .+-...+++||.|+++|..+..
T Consensus 194 ~k~G~vv~G~V~~I~~~G~fV~i~gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~ 255 (318)
T PRK07400 194 LEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDA 255 (318)
T ss_pred CCCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeC
Confidence 3458899999999832222110 1112358999999999998764
No 80
>PRK09750 hypothetical protein; Provisional
Probab=45.87 E-value=17 Score=24.52 Aligned_cols=23 Identities=17% Similarity=0.306 Sum_probs=19.8
Q ss_pred CcEEEEEEccCCccccccCCCCC
Q 048593 112 KKYLVFGRVEGESLGPVSLSGWA 134 (150)
Q Consensus 112 ~~~~~igsi~~d~LG~i~w~~w~ 134 (150)
..|.|.|+|+-++=+|++|.-..
T Consensus 2 ykY~I~Ati~KpGg~P~~W~r~s 24 (64)
T PRK09750 2 YMYKITATIEKEGGTPTNWTRYS 24 (64)
T ss_pred ceeEEEEEEECCCCCccceeEec
Confidence 46999999999999999996553
No 81
>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=44.90 E-value=37 Score=32.81 Aligned_cols=44 Identities=16% Similarity=0.308 Sum_probs=30.7
Q ss_pred eeecCcEEEEEEEEecCCCce----------e----------e---ccccceecCCCEEEEEEEEEE
Q 048593 59 LPVKGEILHGVIHIAVCEQPF----------F----------S---NEQQAKIRNGLVVQFLVTAVQ 102 (150)
Q Consensus 59 rPf~gEVv~G~V~~v~~~~~~----------~----------~---~~~~~~i~~gd~VR~RI~~v~ 102 (150)
.|-.|+++.|+|+++.+-..+ . + .+-...+++||.|.+||.++.
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID 710 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADID 710 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEEC
Confidence 589999999999999111111 0 0 111126899999999999876
No 82
>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=44.46 E-value=41 Score=21.42 Aligned_cols=14 Identities=14% Similarity=0.323 Sum_probs=12.2
Q ss_pred CCCEEEEEEEEEEe
Q 048593 90 NGLVVQFLVTAVQW 103 (150)
Q Consensus 90 ~gd~VR~RI~~v~~ 103 (150)
+|+.+.++|..+.-
T Consensus 44 vG~~i~~~i~~vd~ 57 (67)
T cd04465 44 VGKELKFKIIEIDR 57 (67)
T ss_pred CCCEEEEEEEEEeC
Confidence 79999999988773
No 83
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=44.41 E-value=24 Score=34.87 Aligned_cols=47 Identities=17% Similarity=0.224 Sum_probs=30.9
Q ss_pred EEeeeecCcEEE-EEEEEecCCCcee-------------------eccccceecCCCEEEEEEEEEE
Q 048593 56 RTFLPVKGEILH-GVIHIAVCEQPFF-------------------SNEQQAKIRNGLVVQFLVTAVQ 102 (150)
Q Consensus 56 ivFrPf~gEVv~-G~V~~v~~~~~~~-------------------~~~~~~~i~~gd~VR~RI~~v~ 102 (150)
++..|..|++.+ |+|+++.+-..++ .......+++||.|+++|.++.
T Consensus 747 l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID 813 (891)
T PLN00207 747 LTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVN 813 (891)
T ss_pred HhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEEC
Confidence 344688999995 5999981111111 0111236999999999999875
No 84
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=43.22 E-value=50 Score=28.27 Aligned_cols=43 Identities=21% Similarity=0.288 Sum_probs=31.9
Q ss_pred eecCcEEEEEEEEecCCCceee--cc-------------------ccceecCCCEEEEEEEEEE
Q 048593 60 PVKGEILHGVIHIAVCEQPFFS--NE-------------------QQAKIRNGLVVQFLVTAVQ 102 (150)
Q Consensus 60 Pf~gEVv~G~V~~v~~~~~~~~--~~-------------------~~~~i~~gd~VR~RI~~v~ 102 (150)
|-.||++-|+|+++.+-+++.. .. =+.+++.|..|-++|+.|.
T Consensus 9 PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd 72 (269)
T COG1093 9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVD 72 (269)
T ss_pred CCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEc
Confidence 8899999999999933333221 11 1237999999999999886
No 85
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=41.44 E-value=61 Score=29.41 Aligned_cols=42 Identities=17% Similarity=0.244 Sum_probs=29.1
Q ss_pred cCcEEEEEEEEecCCCceee-------------------ccccceecCCCEEEEEEEEEEe
Q 048593 62 KGEILHGVIHIAVCEQPFFS-------------------NEQQAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 62 ~gEVv~G~V~~v~~~~~~~~-------------------~~~~~~i~~gd~VR~RI~~v~~ 103 (150)
.|.+++|+|+++.+...+.. .+....++.|+.|++||..+..
T Consensus 379 vG~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~~~~~~~~~~~~~Gd~v~~~V~~id~ 439 (491)
T PRK13806 379 PGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDT 439 (491)
T ss_pred CCCEEEEEEEEEecCceEEEcCCCcEEEEEHHHcCcccccchhhcCCCCCEEEEEEEEEeC
Confidence 58999999999933222211 0112368999999999998764
No 86
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=39.55 E-value=36 Score=26.90 Aligned_cols=50 Identities=18% Similarity=0.239 Sum_probs=33.6
Q ss_pred EEEeeeecCcEEEEEEEEecCCCce--e-------e---ccccceecCCCEEEEEEEEEEee
Q 048593 55 CRTFLPVKGEILHGVIHIAVCEQPF--F-------S---NEQQAKIRNGLVVQFLVTAVQWI 104 (150)
Q Consensus 55 aivFrPf~gEVv~G~V~~v~~~~~~--~-------~---~~~~~~i~~gd~VR~RI~~v~~~ 104 (150)
++=.-|++|.++.|+|-.+.++... | - .-+...+++|..||+|++...+.
T Consensus 75 l~qlg~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~n~e~Y~~GaRVrlRl~DlELs 136 (173)
T KOG4078|consen 75 LMQLGDAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPALNGEAYQKGARVRLRLIDLELS 136 (173)
T ss_pred cccccCcCCcEEEeeeeeeeccceEEecCCeEEEEEcCcCcCHHHhhcCceEEEEEcChhHh
Confidence 4445688999999998887333221 1 0 11224689999999999987653
No 87
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=39.14 E-value=51 Score=30.03 Aligned_cols=42 Identities=19% Similarity=0.275 Sum_probs=29.1
Q ss_pred cCcEEEEEEEEecCCCcee---------e----------ccccceecCCCEEEEEEEEEEe
Q 048593 62 KGEILHGVIHIAVCEQPFF---------S----------NEQQAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 62 ~gEVv~G~V~~v~~~~~~~---------~----------~~~~~~i~~gd~VR~RI~~v~~ 103 (150)
.|+++.|+|+++.+...+. . ++-...+..|+.|++||..+..
T Consensus 460 ~G~vV~G~V~~v~~~G~fV~l~~gi~g~i~~se~s~~~~~~~~~~~~~Gd~v~~~V~~vd~ 520 (565)
T PRK06299 460 KGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDR 520 (565)
T ss_pred CCCEEEEEEEEEecCceEEecCCCcEEEEEHHHhcchhccCccccCCCCCEEEEEEEEEcc
Confidence 6999999999993332211 1 1112358999999999998764
No 88
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=37.35 E-value=44 Score=30.32 Aligned_cols=15 Identities=33% Similarity=0.266 Sum_probs=9.3
Q ss_pred ecCCCEEEEEEEEEE
Q 048593 88 IRNGLVVQFLVTAVQ 102 (150)
Q Consensus 88 i~~gd~VR~RI~~v~ 102 (150)
++.|+.|..+|.++.
T Consensus 113 ~~~g~~v~g~V~~~~ 127 (491)
T PRK13806 113 YENGVPVEGKVTGTC 127 (491)
T ss_pred HhCCCEEEEEEEEEE
Confidence 456666666666655
No 89
>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=35.52 E-value=99 Score=27.69 Aligned_cols=43 Identities=19% Similarity=0.302 Sum_probs=30.3
Q ss_pred eecCcEEEEEEEEecCCCcee----------ec----cccceecCCCEEEEEEEEEE
Q 048593 60 PVKGEILHGVIHIAVCEQPFF----------SN----EQQAKIRNGLVVQFLVTAVQ 102 (150)
Q Consensus 60 Pf~gEVv~G~V~~v~~~~~~~----------~~----~~~~~i~~gd~VR~RI~~v~ 102 (150)
...|+++.|+|+++.+...+. .. +....+.+|+.|.++|..+.
T Consensus 16 ~~~G~~v~g~V~~i~~~~~~v~~g~k~~g~i~~~E~~~~~~~~~vGd~i~~~V~~~~ 72 (516)
T TIGR00717 16 TRPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLDAPLEIQVGDEVEVYLDRVE 72 (516)
T ss_pred CCCCCEEEEEEEEEECCEEEEEcCCCcEEEEEHHHhcCCccCCCCCCEEEEEEEEEe
Confidence 467999999999995443222 11 11134799999999999876
No 90
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=35.17 E-value=82 Score=28.89 Aligned_cols=47 Identities=9% Similarity=0.106 Sum_probs=35.0
Q ss_pred eeeecCcEEEEEEEEecCCCceee---------------cc---ccceecCCCEEEEEEEEEEee
Q 048593 58 FLPVKGEILHGVIHIAVCEQPFFS---------------NE---QQAKIRNGLVVQFLVTAVQWI 104 (150)
Q Consensus 58 FrPf~gEVv~G~V~~v~~~~~~~~---------------~~---~~~~i~~gd~VR~RI~~v~~~ 104 (150)
|++-.||++.|+|.+++..+..+. .. .+..+++|+.||+=|..|+-.
T Consensus 148 f~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqip~E~y~~Gdrika~i~~V~~~ 212 (449)
T PRK12329 148 FQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQLPNDNYRANATFKVFLKEVSEG 212 (449)
T ss_pred HHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcCCCCcCCCCCEEEEEEEEeecC
Confidence 889999999999999944433221 01 123699999999999999863
No 91
>COG5256 TEF1 Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and biogenesis]
Probab=35.03 E-value=1e+02 Score=28.07 Aligned_cols=74 Identities=27% Similarity=0.245 Sum_probs=43.4
Q ss_pred CceEEEEEeeecee-CCeeeeeCC---CcceEEEEEEEEEEeeeecCcEEEEEEEEecCCCceeeccccceecCCCEEEE
Q 048593 21 DQCYFLSVTNLKSI-GRERGTVNE---SGVVFFPVTFLCRTFLPVKGEILHGVIHIAVCEQPFFSNEQQAKIRNGLVVQF 96 (150)
Q Consensus 21 ~~GliV~V~di~~i-~~G~I~~~g---dG~v~~~V~FraivFrPf~gEVv~G~V~~v~~~~~~~~~~~~~~i~~gd~VR~ 96 (150)
|.=|.+.|.|+.+| +.|.|.. | +|...- =+-++|.|-. +.|+|+++... .+....-..||.|.|
T Consensus 229 d~Plr~pI~~v~~i~~~gtv~v-GrVEsG~i~~---g~~v~~~p~~---~~~evksie~~-----~~~~~~a~~GD~i~~ 296 (428)
T COG5256 229 DKPLRLPIQDVYSISGIGTVPV-GRVESGVIKP---GQKVTFMPAG---VVGEVKSIEMH-----HEEISQAEPGDNVGF 296 (428)
T ss_pred CCCeEeEeeeEEEecCCceEEE-EEEeeeeecc---CCEEEEecCc---ceEEEeeeeec-----ccccccCCCCCeEEE
Confidence 34477777777662 3333322 1 111110 0235667766 88999998444 333345678999999
Q ss_pred EEEEEEeeec
Q 048593 97 LVTAVQWIDE 106 (150)
Q Consensus 97 RI~~v~~~d~ 106 (150)
+|.++.-.|.
T Consensus 297 ~vrgv~~~dI 306 (428)
T COG5256 297 NVRGVEKNDI 306 (428)
T ss_pred EecCCchhcc
Confidence 9999876553
No 92
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=34.71 E-value=79 Score=28.79 Aligned_cols=42 Identities=19% Similarity=0.209 Sum_probs=28.8
Q ss_pred cCcEEEEEEEEecCCCcee----------------e----ccccceecCCCEEEEEEEEEEe
Q 048593 62 KGEILHGVIHIAVCEQPFF----------------S----NEQQAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 62 ~gEVv~G~V~~v~~~~~~~----------------~----~~~~~~i~~gd~VR~RI~~v~~ 103 (150)
.|+++.|+|+++.+...++ + ++....++.|+.|++||..+..
T Consensus 373 ~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~ 434 (565)
T PRK06299 373 VGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDV 434 (565)
T ss_pred CCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeC
Confidence 5999999999992221111 0 1112368999999999998863
No 93
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=34.35 E-value=70 Score=27.62 Aligned_cols=43 Identities=16% Similarity=0.361 Sum_probs=28.9
Q ss_pred ecCcEEEEEEEEecCCCcee--------e----------ccccceecCCCEEEEEEEEEEe
Q 048593 61 VKGEILHGVIHIAVCEQPFF--------S----------NEQQAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 61 f~gEVv~G~V~~v~~~~~~~--------~----------~~~~~~i~~gd~VR~RI~~v~~ 103 (150)
-.|+++.|+|+++.+.+.++ . .+-...+.+|+.|++||..+.-
T Consensus 191 ~~G~~v~g~V~~v~~~G~fV~l~~v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~ 251 (390)
T PRK06676 191 KEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDW 251 (390)
T ss_pred CCCCEEEEEEEEEecceEEEEeCCeEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeC
Confidence 36999999999993322211 1 0111257899999999988753
No 94
>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=32.27 E-value=82 Score=28.21 Aligned_cols=42 Identities=17% Similarity=0.209 Sum_probs=28.7
Q ss_pred cCcEEEEEEEEecCCCcee---------e----------ccccceecCCCEEEEEEEEEEe
Q 048593 62 KGEILHGVIHIAVCEQPFF---------S----------NEQQAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 62 ~gEVv~G~V~~v~~~~~~~---------~----------~~~~~~i~~gd~VR~RI~~v~~ 103 (150)
.|.++.|.|+++.+...++ . ++....+..|+.|++||..+..
T Consensus 446 ~G~~v~g~V~~v~~~G~fV~l~~~~~Glv~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~id~ 506 (516)
T TIGR00717 446 VGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDK 506 (516)
T ss_pred cceEEEEEEEEEecceEEEEcCCCeEEEEEHHHcCccccccccccCCCCCEEEEEEEEEeC
Confidence 5999999999992221111 0 1122468999999999998764
No 95
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=29.03 E-value=1.1e+02 Score=28.67 Aligned_cols=76 Identities=22% Similarity=0.317 Sum_probs=48.5
Q ss_pred ecCcEEEEEEEEecCCCceee------------------ccccceecCCCEEEEEEEEEEeeecC-------------c-
Q 048593 61 VKGEILHGVIHIAVCEQPFFS------------------NEQQAKIRNGLVVQFLVTAVQWIDEG-------------R- 108 (150)
Q Consensus 61 f~gEVv~G~V~~v~~~~~~~~------------------~~~~~~i~~gd~VR~RI~~v~~~d~~-------------~- 108 (150)
-.|++++|+|+++.+-+.+.. +.-...+++||.|.++|+.+-- +.. +
T Consensus 191 ~~G~vV~G~V~~It~~GafVdigGvdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~-e~~RVsLSlK~l~~dPw~ 269 (541)
T COG0539 191 EVGEVVEGVVKNITDYGAFVDIGGVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDE-ERGRVSLSLKQLEEDPWE 269 (541)
T ss_pred CCCceEEEEEEEeecCcEEEEecCeeeEEehhhccccccCCHHHhcccCCEEEEEEEEEcc-CCCeEEEEehhcccCcHH
Confidence 468999999999944433321 1112379999999999998762 211 0
Q ss_pred ----------------CccCcEEEEEEccC--CccccccCCCCCCCc
Q 048593 109 ----------------NLKKKYLVFGRVEG--ESLGPVSLSGWAGTD 137 (150)
Q Consensus 109 ----------------~~~~~~~~igsi~~--d~LG~i~w~~w~~~~ 137 (150)
+...||-|+..+.. .+|-++|=-+|.-..
T Consensus 270 ~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~ 316 (541)
T COG0539 270 GIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKN 316 (541)
T ss_pred HHhhhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhhcccccC
Confidence 03367777777765 667777644575443
No 96
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=28.69 E-value=1.2e+02 Score=26.13 Aligned_cols=42 Identities=17% Similarity=0.268 Sum_probs=28.1
Q ss_pred cCcEEEEEEEEecCCCce---------ee----------ccccceecCCCEEEEEEEEEEe
Q 048593 62 KGEILHGVIHIAVCEQPF---------FS----------NEQQAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 62 ~gEVv~G~V~~v~~~~~~---------~~----------~~~~~~i~~gd~VR~RI~~v~~ 103 (150)
.|+++.|.|+++.+...+ +. ......++.|+.|++||..+..
T Consensus 277 ~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~v~V~~id~ 337 (390)
T PRK06676 277 EGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNE 337 (390)
T ss_pred CCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCccccCChhhccCCCCEEEEEEEEEEC
Confidence 599999999999222111 10 0111358999999999998863
No 97
>PRK15052 D-tagatose-1,6-bisphosphate aldolase subunit GatZ; Provisional
Probab=28.36 E-value=33 Score=31.16 Aligned_cols=22 Identities=23% Similarity=0.367 Sum_probs=17.6
Q ss_pred cCCccccccCCCCCCCchhhhhhhhh
Q 048593 121 EGESLGPVSLSGWAGTDDINLKMLVH 146 (150)
Q Consensus 121 ~~d~LG~i~w~~w~~~~~~~~~~~~~ 146 (150)
.+|+|||-.| ..+..+|.|..+
T Consensus 85 ggDHlGPn~W----q~~pa~eAM~~A 106 (421)
T PRK15052 85 GGDHLGPNCW----QQEPADAAMEKS 106 (421)
T ss_pred ecCCCCCccc----cCCCHHHHHHHH
Confidence 6899999999 677777777654
No 98
>PF08013 Tagatose_6_P_K: Tagatose 6 phosphate kinase; InterPro: IPR012062 Escherichia coli and other enteric bacteria contain two closely related D-tagatose 1,6-bisphosphate (TagBP)-specific aldolases involved in catabolism of galactitol (genes gatY gatZ) and of N-acetyl-galactosamine and D-galactosamine (genes kbaY, kbaZ, also called agaY, agaZ). The catalytic subunits GatY/KbaY alone are sufficient to show aldolase activity and contain most or all of the residues that have been identified as essential in substrate/product recognition and catalysis for class II aldolases [, ]. However, these aldolases differ from other Class II aldolases (which are homodimeric enzymes) in that they require subunits GatZ/KbaZ for full activity and for good in vivo and in vitro stability. The Z subunits alone do not show any aldolase activity []. It should be noted that the previous suggestion of a tagatose 6P-kinase function for AgaZ [] and other members of this family turned out to be erroneous [, ].; GO: 0019402 galactitol metabolic process; PDB: 2FIQ_A 3TXV_A.
Probab=26.79 E-value=25 Score=31.90 Aligned_cols=22 Identities=23% Similarity=0.237 Sum_probs=17.4
Q ss_pred cCCccccccCCCCCCCchhhhhhhhh
Q 048593 121 EGESLGPVSLSGWAGTDDINLKMLVH 146 (150)
Q Consensus 121 ~~d~LG~i~w~~w~~~~~~~~~~~~~ 146 (150)
.+|+|||-.| .....++.|..+
T Consensus 88 GGDHLGP~~w----~~lpaeeAM~~A 109 (424)
T PF08013_consen 88 GGDHLGPNPW----QHLPAEEAMAKA 109 (424)
T ss_dssp EEEEESSCCC----TTSBHHHHHHHH
T ss_pred cCCCCCcccc----cCCCHHHHHHHH
Confidence 5799999999 677777777654
No 99
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=26.67 E-value=1.1e+02 Score=27.95 Aligned_cols=42 Identities=24% Similarity=0.299 Sum_probs=28.7
Q ss_pred cCcEEEEEEEEecCCCcee--------e----------ccccceecCCCEEEEEEEEEEe
Q 048593 62 KGEILHGVIHIAVCEQPFF--------S----------NEQQAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 62 ~gEVv~G~V~~v~~~~~~~--------~----------~~~~~~i~~gd~VR~RI~~v~~ 103 (150)
.|+++.|+|+++.+-+.++ . ++-...+++|+.|.+||..+..
T Consensus 208 ~G~iv~G~V~~i~~~G~FVdlggv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~ 267 (486)
T PRK07899 208 KGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDM 267 (486)
T ss_pred CCCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEEC
Confidence 5999999999992222211 0 1111358999999999998764
No 100
>COG2100 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=25.86 E-value=1.2e+02 Score=27.32 Aligned_cols=44 Identities=16% Similarity=0.325 Sum_probs=25.9
Q ss_pred eee-cCcEEEEEEEEe---------cCCCcee--eccccceecCCCEEEEEEEEEE
Q 048593 59 LPV-KGEILHGVIHIA---------VCEQPFF--SNEQQAKIRNGLVVQFLVTAVQ 102 (150)
Q Consensus 59 rPf-~gEVv~G~V~~v---------~~~~~~~--~~~~~~~i~~gd~VR~RI~~v~ 102 (150)
+|| +||++.++|+-= ...+... .+.+.....+|+.||+||+..+
T Consensus 350 ~PF~rGevv~aevV~~Gr~kGEmlavArdRvIav~~~~~~~~~vG~~vkvrIvr~k 405 (414)
T COG2100 350 KPFKRGEVVKAEVVLPGRLKGEMLAVARDRVIAVINSNEGALLVGDRVKVRIVRTK 405 (414)
T ss_pred CccccCcEEEEEEEecceecceEEEEecccEEEEecCchhhhccCceEEEEEEEcc
Confidence 455 478887777643 1112111 1222125789999999998754
No 101
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=25.78 E-value=1.3e+02 Score=28.36 Aligned_cols=42 Identities=17% Similarity=0.162 Sum_probs=28.4
Q ss_pred cCcEEEEEEEEecCCCcee---------e----------ccccceecCCCEEEEEEEEEEe
Q 048593 62 KGEILHGVIHIAVCEQPFF---------S----------NEQQAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 62 ~gEVv~G~V~~v~~~~~~~---------~----------~~~~~~i~~gd~VR~RI~~v~~ 103 (150)
.|+++.|+|+++.+.+.++ . ......+++|+.|++||..+..
T Consensus 562 ~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id~ 622 (647)
T PRK00087 562 VGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDP 622 (647)
T ss_pred CCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEeC
Confidence 5899999999992222111 0 1111358999999999998763
No 102
>PF07238 PilZ: PilZ domain; InterPro: IPR009875 The ubiquitous bacterial second messenger cyclic-di-GMP (c-di-GMP) is associated with the regulation of biofilm formation, the control of exopolysaccharide synthesis, flagellar- and pili-based motility, gene expression, interactions of bacteria with eukaryotic hosts and multicellular behaviour in diverse bacteria. With the exception of bacterial cellulose synthases, the identities of c-di-GMP receptors and end targets of the proteins having one or more PilZ domains are mostly uncharacterised. However it was suggested that the PilZ domains present in the BcsA subunits of bacterial cellulose synthases function in c-di-GMP binding []. More recently YcgR (see IPR023787 from INTERPRO) was found to bind c-di-GMP tightly and specifically; also isolated PilZ domains from YcgR and BcsA bound c-di-GMP indicating that the PilZ domain was sufficient for binding of c-di-GMP and significantly that site-directed mutagenesis performed on YcgR implicated the most conserved residues in the PilZ domain directly in c-di-GMP binding []. It was suggested that c-di-GMP binding to PilZ brings about conformational changes in the protein that stabilise the bound ligand and probability initiates the downstream signal transduction cascade. In the case of YcgR, c-di-GMP binding regulates flagellum-based motility in a c-di-GMP-dependent manner (see IPR023787 from INTERPRO) []. The association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Binding and mutagenesis studies of several PilZ domain proteins have confirmed this observation and demonstrated that c-di-GMP binding depends on residues in RxxxR and D/NxSxxG sequence motifs. The crystal structure, at 1.7 A, of a PilZ domain::c-di-GMP complex from Vibrio cholerae shows c-di-GMP contacting seven of nine strongly conserved residues. Binding of c-di-GMP causes a conformational switch whereby the C- and N-terminal domains are brought into close opposition forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface []. ; GO: 0035438 cyclic-di-GMP binding; PDB: 2RDE_B 1YLN_A 3KYG_A 3DSG_B 2GJG_A 3KYF_A 1YWU_A 2L74_A 2L1T_A 3CNR_A ....
Probab=25.33 E-value=2e+02 Score=18.61 Aligned_cols=48 Identities=21% Similarity=0.232 Sum_probs=32.7
Q ss_pred EEEEEEEEEeeeecCcEEEEEEEEecCCCceeeccccceecCCCEEEEEE
Q 048593 49 FPVTFLCRTFLPVKGEILHGVIHIAVCEQPFFSNEQQAKIRNGLVVQFLV 98 (150)
Q Consensus 49 ~~V~FraivFrPf~gEVv~G~V~~v~~~~~~~~~~~~~~i~~gd~VR~RI 98 (150)
+++...+....+..+....|.++++...+..+.-+. .+.+|+.|++++
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~diS~~G~~~~~~~--~~~~~~~v~l~~ 55 (102)
T PF07238_consen 8 VPVNLPIRVILDPGGSSFQGTIVDISEGGCAFRSPK--PLEPGDRVRLSF 55 (102)
T ss_dssp EEEEEEEE-EEEETTEEEEEEEEEETTSEEEEEECT--G--TTSEEEEEE
T ss_pred EeccceEEEEEecCCcEEEEEEEEECccceEEEECC--CCCCCCEEEEEE
Confidence 445555566888889999999999977776654433 678888886665
No 103
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=24.72 E-value=1.7e+02 Score=26.92 Aligned_cols=42 Identities=19% Similarity=0.188 Sum_probs=28.3
Q ss_pred cCcEEEEEEEEecCCCcee---------e----------ccccceecCCCEEEEEEEEEEe
Q 048593 62 KGEILHGVIHIAVCEQPFF---------S----------NEQQAKIRNGLVVQFLVTAVQW 103 (150)
Q Consensus 62 ~gEVv~G~V~~v~~~~~~~---------~----------~~~~~~i~~gd~VR~RI~~v~~ 103 (150)
.|+++.|+|+++.+...++ . ......+++|+.|++||..+..
T Consensus 293 vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID~ 353 (486)
T PRK07899 293 IGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDL 353 (486)
T ss_pred CCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEEC
Confidence 4899999999992211111 0 1112368999999999988764
No 104
>PRK15458 tagatose 6-phosphate aldolase subunit KbaZ; Provisional
Probab=24.63 E-value=42 Score=30.53 Aligned_cols=22 Identities=23% Similarity=0.232 Sum_probs=17.3
Q ss_pred cCCccccccCCCCCCCchhhhhhhhh
Q 048593 121 EGESLGPVSLSGWAGTDDINLKMLVH 146 (150)
Q Consensus 121 ~~d~LG~i~w~~w~~~~~~~~~~~~~ 146 (150)
.+|+|||-.| .....+|.|..+
T Consensus 88 GGDHLGPn~W----q~lpa~eAM~~A 109 (426)
T PRK15458 88 GGDHLGPNRW----QNLPAAQAMANA 109 (426)
T ss_pred ecCCCCCccc----cCCCHHHHHHHH
Confidence 6899999999 577777777643
No 105
>TIGR02810 agaZ_gatZ D-tagatose-bisphosphate aldolase, class II, non-catalytic subunit. Aldolases specific for D-tagatose-bisphosphate occur in distinct pathways in Escherichia coli and other bacteria, one for the degradation of galactitol (formerly dulcitol) and one for degradation of N-acetyl-galactosamine and D-galactosamine. This family represents a protein of both systems that behaves as a non-catalytic subunit of D-tagatose-bisphosphate aldolase, required both for full activity and for good stability of the aldolase. Note that members of this protein family appear in public databases annotated as putative tagatose 6-phosphate kinases, possibly in error.
Probab=23.10 E-value=47 Score=30.14 Aligned_cols=22 Identities=23% Similarity=0.256 Sum_probs=17.2
Q ss_pred cCCccccccCCCCCCCchhhhhhhhh
Q 048593 121 EGESLGPVSLSGWAGTDDINLKMLVH 146 (150)
Q Consensus 121 ~~d~LG~i~w~~w~~~~~~~~~~~~~ 146 (150)
.+|+|||-.| .....+|.|..+
T Consensus 84 ggDHlGPn~W----q~lpa~eAM~~A 105 (420)
T TIGR02810 84 GGDHLGPNPW----QHLPADEAMAKA 105 (420)
T ss_pred ecCCCCCccc----cCCCHHHHHHHH
Confidence 6899999999 566777777643
No 106
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=22.55 E-value=2.2e+02 Score=26.74 Aligned_cols=45 Identities=13% Similarity=0.235 Sum_probs=29.1
Q ss_pred eeeecCcEEEEEEEEecCCCceee-------------------ccccceecCCCEEEEEEEEEE
Q 048593 58 FLPVKGEILHGVIHIAVCEQPFFS-------------------NEQQAKIRNGLVVQFLVTAVQ 102 (150)
Q Consensus 58 FrPf~gEVv~G~V~~v~~~~~~~~-------------------~~~~~~i~~gd~VR~RI~~v~ 102 (150)
...-.|+++.|+|+++.+...++. .+....+.+|+.|+++|..+.
T Consensus 298 ~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els~~~~~~~~~~~~vGd~V~v~V~~vd 361 (647)
T PRK00087 298 KQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLE 361 (647)
T ss_pred hhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcccccCChhhccCCCCEEEEEEEEEE
Confidence 345678888888888833322210 011135889999999999976
No 107
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=21.54 E-value=2e+02 Score=19.27 Aligned_cols=31 Identities=16% Similarity=0.204 Sum_probs=19.4
Q ss_pred EEEEEEEecCCCceeecccc-----------ceecCCCEEEE
Q 048593 66 LHGVIHIAVCEQPFFSNEQQ-----------AKIRNGLVVQF 96 (150)
Q Consensus 66 v~G~V~~v~~~~~~~~~~~~-----------~~i~~gd~VR~ 96 (150)
++|+|++++.+...+.-+++ ..|++|..|++
T Consensus 5 veG~I~~id~~~~titLdDGksy~lp~ef~~~~L~~G~kV~V 46 (61)
T PF07076_consen 5 VEGTIKSIDPETMTITLDDGKSYKLPEEFDFDGLKPGMKVVV 46 (61)
T ss_pred ceEEEEEEcCCceEEEecCCCEEECCCcccccccCCCCEEEE
Confidence 68999999555443321111 24888888875
No 108
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=21.45 E-value=1.8e+02 Score=28.79 Aligned_cols=41 Identities=20% Similarity=0.257 Sum_probs=24.6
Q ss_pred cCcEEEEEEEEecCCCceee---ccc--------cceecCCCEEEEEEEEEE
Q 048593 62 KGEILHGVIHIAVCEQPFFS---NEQ--------QAKIRNGLVVQFLVTAVQ 102 (150)
Q Consensus 62 ~gEVv~G~V~~v~~~~~~~~---~~~--------~~~i~~gd~VR~RI~~v~ 102 (150)
+|++++|+|+++.++..++. +.+ ....++||.|.+.|..+.
T Consensus 321 ~G~iV~G~Vv~i~~~~v~VdiG~K~eGiI~~~E~~~~~kvGd~i~~~V~~~~ 372 (863)
T PRK12269 321 PGSVRMGTVVQVNAGTVFVDIGGKSEGRVPVEEFEAPPKAGDGVRVYVERVT 372 (863)
T ss_pred CCCEEEEEEEEEECCEEEEEeCCCceEEeEHHHhccCCCCCCEEEEEEEEEc
Confidence 48888888888854433321 000 112467888888877654
No 109
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=21.06 E-value=78 Score=20.43 Aligned_cols=41 Identities=20% Similarity=0.155 Sum_probs=23.7
Q ss_pred ecCCCEEEEEEEEEEeeecCcCccCcEEEEEEccC-CccccccCCCCCCCchh
Q 048593 88 IRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEG-ESLGPVSLSGWAGTDDI 139 (150)
Q Consensus 88 i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igsi~~-d~LG~i~w~~w~~~~~~ 139 (150)
+.+||.|++|= . + |+|.+..-... .+.+.-.+|-|......
T Consensus 1 f~~GDvV~LKS------G-G----p~MTV~~v~~~~~~~~~~v~C~WFd~~~~ 42 (53)
T PF09926_consen 1 FKIGDVVQLKS------G-G----PRMTVTEVGPNAGASGGWVECQWFDGHGE 42 (53)
T ss_pred CCCCCEEEEcc------C-C----CCeEEEEccccccCCCCeEEEEeCCCCCc
Confidence 45788888762 2 2 46666644333 45555566667665544
No 110
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=21.03 E-value=2e+02 Score=20.16 Aligned_cols=11 Identities=27% Similarity=0.456 Sum_probs=8.7
Q ss_pred eecCCCEEEEE
Q 048593 87 KIRNGLVVQFL 97 (150)
Q Consensus 87 ~i~~gd~VR~R 97 (150)
....||.|+++
T Consensus 53 ~~k~GD~V~I~ 63 (84)
T PRK05610 53 EAKIGDVVRIM 63 (84)
T ss_pred CCCCCCEEEEE
Confidence 58899998764
No 111
>KOG0459 consensus Polypeptide release factor 3 [Translation, ribosomal structure and biogenesis]
Probab=20.87 E-value=1.8e+02 Score=26.98 Aligned_cols=32 Identities=9% Similarity=0.132 Sum_probs=24.6
Q ss_pred eecCCCEEEEEEEEEEeeecCcCccCcEEEEEEccCC
Q 048593 87 KIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGE 123 (150)
Q Consensus 87 ~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igsi~~d 123 (150)
....|+.||+|+.++.-.|.. |-+++++.+.+
T Consensus 361 ~~~pGenvk~rlkgieeedi~-----~GfiL~~~~n~ 392 (501)
T KOG0459|consen 361 RVAPGENVKLRLKGIEEEDIS-----PGFILCSPNNP 392 (501)
T ss_pred eccCCcceEEEecccchhhcc-----CceEEecCCCc
Confidence 578999999999998866653 55777776554
No 112
>PF06688 DUF1187: Protein of unknown function (DUF1187); InterPro: IPR009572 This family consists of several short, hypothetical bacterial proteins of around 62 residues in length. Members of this family are found in Escherichia coli and Salmonella typhi. The function of this family is unknown.
Probab=20.60 E-value=57 Score=21.96 Aligned_cols=21 Identities=14% Similarity=0.302 Sum_probs=17.7
Q ss_pred EEEEEEccCCccccccCCCCC
Q 048593 114 YLVFGRVEGESLGPVSLSGWA 134 (150)
Q Consensus 114 ~~~igsi~~d~LG~i~w~~w~ 134 (150)
|.|+|+|.-.|=.|+.|.-..
T Consensus 1 YkItAtI~KpG~~Pv~W~rys 21 (61)
T PF06688_consen 1 YKITATIIKPGNTPVNWTRYS 21 (61)
T ss_pred CceEEEEEcCCCCCeeeEEec
Confidence 678999999999999995543
Done!