Query 022898
Match_columns 290
No_of_seqs 266 out of 935
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 06:57:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022898.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022898hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2191 RNA-binding protein NO 99.7 2.1E-18 4.6E-23 154.1 5.8 164 53-238 39-208 (402)
2 KOG1677 CCCH-type Zn-finger pr 99.6 1.1E-15 2.5E-20 142.1 6.6 76 35-127 87-163 (332)
3 KOG1677 CCCH-type Zn-finger pr 99.4 7.3E-14 1.6E-18 130.0 4.4 81 28-127 126-207 (332)
4 cd02396 PCBP_like_KH K homolog 99.3 6.3E-12 1.4E-16 89.3 6.3 63 166-228 1-64 (65)
5 COG5063 CTH1 CCCH-type Zn-fing 99.2 1.6E-11 3.5E-16 109.2 4.9 74 29-127 223-304 (351)
6 COG5063 CTH1 CCCH-type Zn-fing 99.1 9.2E-11 2E-15 104.4 6.6 93 29-121 148-260 (351)
7 KOG1676 K-homology type RNA bi 99.1 2.2E-10 4.8E-15 110.3 8.6 78 162-239 227-305 (600)
8 KOG2192 PolyC-binding hnRNP-K 99.1 5.9E-10 1.3E-14 97.8 9.5 75 161-235 311-385 (390)
9 cd02394 vigilin_like_KH K homo 99.0 7.1E-10 1.5E-14 77.8 6.1 61 166-228 1-61 (62)
10 cd00105 KH-I K homology RNA-bi 99.0 1.7E-09 3.7E-14 75.9 6.9 62 167-228 2-63 (64)
11 PF00013 KH_1: KH domain syndr 99.0 2.8E-10 6.2E-15 79.3 2.5 60 166-228 1-60 (60)
12 cd02393 PNPase_KH Polynucleoti 98.9 2.3E-09 4.9E-14 75.2 6.1 57 166-228 3-60 (61)
13 KOG1676 K-homology type RNA bi 98.9 2.8E-10 6.1E-15 109.6 1.4 153 59-236 236-391 (600)
14 PF00642 zf-CCCH: Zinc finger 98.8 6E-10 1.3E-14 65.1 -0.5 26 32-57 1-26 (27)
15 KOG2190 PolyC-binding proteins 98.7 3.5E-08 7.7E-13 95.6 8.5 73 164-236 137-210 (485)
16 KOG1040 Polyadenylation factor 98.7 1.7E-08 3.6E-13 92.8 4.1 56 31-121 74-129 (325)
17 PF00642 zf-CCCH: Zinc finger 98.6 3.1E-09 6.8E-14 62.0 -1.0 26 257-282 1-27 (27)
18 KOG2191 RNA-binding protein NO 98.6 8E-08 1.7E-12 86.8 7.1 74 164-237 38-114 (402)
19 KOG2193 IGF-II mRNA-binding pr 98.6 9.2E-08 2E-12 88.9 6.8 75 164-238 410-485 (584)
20 KOG1595 CCCH-type Zn-finger pr 98.6 3.3E-08 7.1E-13 94.6 3.2 77 20-128 222-298 (528)
21 PF13014 KH_3: KH domain 98.5 1.1E-07 2.3E-12 61.8 4.3 42 175-216 1-43 (43)
22 smart00322 KH K homology RNA-b 98.5 5.1E-07 1.1E-11 63.2 7.5 66 165-232 3-68 (69)
23 KOG1595 CCCH-type Zn-finger pr 98.4 2.3E-07 5.1E-12 88.9 3.6 31 255-288 267-297 (528)
24 KOG2193 IGF-II mRNA-binding pr 98.4 4.9E-07 1.1E-11 84.2 5.1 71 164-234 198-269 (584)
25 smart00356 ZnF_C3H1 zinc finge 98.3 4.4E-07 9.5E-12 52.6 1.8 26 31-57 1-26 (27)
26 smart00356 ZnF_C3H1 zinc finge 98.2 7.7E-07 1.7E-11 51.6 2.2 26 257-282 2-27 (27)
27 KOG2333 Uncharacterized conser 98.1 5.9E-07 1.3E-11 85.2 0.1 61 33-120 75-137 (614)
28 TIGR03665 arCOG04150 arCOG0415 98.0 4.5E-06 9.8E-11 70.7 4.1 61 169-234 2-65 (172)
29 cd02395 SF1_like-KH Splicing f 98.0 1.6E-05 3.4E-10 63.3 6.6 63 174-236 15-97 (120)
30 PRK13763 putative RNA-processi 98.0 1.3E-05 2.7E-10 68.5 5.5 64 165-233 3-70 (180)
31 KOG1492 C3H1-type Zn-finger pr 97.9 3E-06 6.6E-11 73.1 0.8 72 13-121 185-256 (377)
32 TIGR03665 arCOG04150 arCOG0415 97.8 3.7E-05 8.1E-10 65.1 5.0 55 174-235 98-152 (172)
33 KOG2190 PolyC-binding proteins 97.7 0.00012 2.7E-09 71.3 8.9 74 164-237 42-124 (485)
34 PRK13763 putative RNA-processi 97.6 9.6E-05 2.1E-09 63.0 4.8 55 174-235 104-158 (180)
35 KOG1040 Polyadenylation factor 97.4 7.9E-05 1.7E-09 68.8 2.9 53 32-119 103-155 (325)
36 KOG2192 PolyC-binding hnRNP-K 97.4 0.00011 2.3E-09 65.2 3.4 72 165-236 123-195 (390)
37 COG5084 YTH1 Cleavage and poly 97.4 0.0002 4.3E-09 64.8 5.0 58 31-121 101-158 (285)
38 TIGR02696 pppGpp_PNP guanosine 97.2 0.00063 1.4E-08 68.9 6.3 65 164-234 577-642 (719)
39 KOG1763 Uncharacterized conser 97.2 0.00012 2.6E-09 65.6 0.8 32 26-58 84-115 (343)
40 COG5252 Uncharacterized conser 97.1 0.00013 2.8E-09 63.4 -0.2 82 29-121 80-175 (299)
41 KOG0336 ATP-dependent RNA heli 97.0 0.0014 2.9E-08 61.9 5.6 72 160-234 42-113 (629)
42 KOG2494 C3H1-type Zn-finger pr 96.9 0.0004 8.6E-09 63.3 1.5 64 30-125 33-97 (331)
43 PF14608 zf-CCCH_2: Zinc finge 96.7 0.0012 2.6E-08 35.0 1.9 19 261-281 1-19 (19)
44 TIGR03591 polynuc_phos polyrib 96.6 0.0024 5.2E-08 65.2 5.1 66 164-235 550-616 (684)
45 KOG0119 Splicing factor 1/bran 96.6 0.0053 1.1E-07 58.9 6.3 74 164-237 137-233 (554)
46 KOG4791 Uncharacterized conser 96.5 0.0014 3.1E-08 62.3 2.3 22 261-282 120-141 (667)
47 cd02134 NusA_KH NusA_K homolog 96.2 0.0072 1.6E-07 42.1 4.0 37 164-200 24-60 (61)
48 KOG2185 Predicted RNA-processi 96.1 0.0019 4.2E-08 60.3 0.9 26 258-283 139-164 (486)
49 KOG2185 Predicted RNA-processi 96.1 0.002 4.3E-08 60.3 0.9 25 33-58 139-163 (486)
50 PF14608 zf-CCCH_2: Zinc finge 96.1 0.0032 6.9E-08 33.4 1.2 19 36-57 1-19 (19)
51 KOG2494 C3H1-type Zn-finger pr 96.0 0.0034 7.3E-08 57.4 1.9 26 261-287 73-98 (331)
52 PLN00207 polyribonucleotide nu 95.9 0.0084 1.8E-07 62.3 4.5 69 164-238 684-754 (891)
53 COG1185 Pnp Polyribonucleotide 95.7 0.014 3.1E-07 58.3 5.1 69 164-238 551-620 (692)
54 KOG2113 Predicted RNA binding 95.4 0.032 7E-07 50.8 5.5 67 161-230 22-88 (394)
55 COG5152 Uncharacterized conser 95.3 0.0077 1.7E-07 51.3 1.3 28 31-58 138-165 (259)
56 KOG2333 Uncharacterized conser 95.2 0.011 2.3E-07 57.0 2.0 25 96-120 75-101 (614)
57 COG1094 Predicted RNA-binding 94.7 0.073 1.6E-06 45.5 5.7 55 176-237 113-167 (194)
58 KOG2279 Kinase anchor protein 94.5 0.017 3.6E-07 56.2 1.4 74 164-237 139-212 (608)
59 KOG1492 C3H1-type Zn-finger pr 94.4 0.029 6.3E-07 48.8 2.6 52 33-121 232-283 (377)
60 COG5152 Uncharacterized conser 94.1 0.022 4.7E-07 48.6 1.0 31 255-285 137-168 (259)
61 KOG2279 Kinase anchor protein 93.6 0.073 1.6E-06 51.9 3.8 74 164-238 67-140 (608)
62 PRK11824 polynucleotide phosph 93.2 0.087 1.9E-06 54.0 3.9 66 165-236 554-620 (693)
63 KOG1763 Uncharacterized conser 93.1 0.027 5.7E-07 50.8 -0.0 36 253-288 86-121 (343)
64 PRK04163 exosome complex RNA-b 92.9 0.22 4.9E-06 44.2 5.7 67 164-236 144-211 (235)
65 KOG2202 U2 snRNP splicing fact 92.4 0.088 1.9E-06 46.8 2.3 29 254-282 147-175 (260)
66 KOG1039 Predicted E3 ubiquitin 92.3 0.16 3.5E-06 47.5 4.1 28 255-282 89-116 (344)
67 COG5176 MSL5 Splicing factor ( 92.2 0.2 4.4E-06 43.2 4.2 40 164-203 147-192 (269)
68 KOG4369 RTK signaling protein 92.1 0.056 1.2E-06 56.9 0.8 75 164-238 1339-1414(2131)
69 COG5084 YTH1 Cleavage and poly 91.1 0.16 3.4E-06 46.2 2.5 55 34-122 134-190 (285)
70 COG5252 Uncharacterized conser 91.1 0.051 1.1E-06 47.6 -0.6 34 255-288 81-114 (299)
71 KOG1813 Predicted E3 ubiquitin 89.6 0.1 2.2E-06 47.3 -0.0 35 30-65 182-216 (313)
72 PRK08406 transcription elongat 89.3 0.39 8.4E-06 39.2 3.2 37 165-201 32-68 (140)
73 KOG2814 Transcription coactiva 89.1 0.63 1.4E-05 42.9 4.7 71 165-236 57-127 (345)
74 KOG1588 RNA-binding protein Sa 88.3 0.52 1.1E-05 42.1 3.6 39 164-202 91-135 (259)
75 PRK00468 hypothetical protein; 87.7 0.57 1.2E-05 34.0 2.8 30 164-193 29-58 (75)
76 COG1837 Predicted RNA-binding 87.5 0.59 1.3E-05 34.0 2.8 30 164-193 29-58 (76)
77 PRK01064 hypothetical protein; 87.4 0.71 1.5E-05 33.8 3.2 30 164-193 29-58 (78)
78 KOG1813 Predicted E3 ubiquitin 87.4 0.18 3.8E-06 45.8 0.0 33 253-285 180-213 (313)
79 PRK02821 hypothetical protein; 87.4 0.59 1.3E-05 34.1 2.8 33 164-196 30-62 (77)
80 TIGR03319 YmdA_YtgF conserved 87.0 1.7 3.8E-05 43.0 6.7 54 164-223 203-257 (514)
81 PRK12704 phosphodiesterase; Pr 86.7 1.9 4.2E-05 42.8 6.9 64 164-233 209-275 (520)
82 PRK00106 hypothetical protein; 86.2 2.2 4.8E-05 42.5 6.9 54 164-223 224-278 (535)
83 PRK08406 transcription elongat 85.8 0.59 1.3E-05 38.1 2.3 38 164-201 98-135 (140)
84 PF10650 zf-C3H1: Putative zin 84.8 0.52 1.1E-05 26.1 1.0 22 35-57 1-22 (23)
85 PF13184 KH_5: NusA-like KH do 84.0 1 2.2E-05 32.1 2.6 35 167-201 5-45 (69)
86 TIGR01952 nusA_arch NusA famil 82.7 1.1 2.5E-05 36.5 2.7 36 166-201 34-69 (141)
87 KOG0153 Predicted RNA-binding 82.0 0.89 1.9E-05 42.2 2.0 25 259-283 161-185 (377)
88 cd02409 KH-II KH-II (K homolo 81.7 2.3 4.9E-05 29.1 3.7 33 166-198 26-58 (68)
89 KOG3273 Predicted RNA-binding 81.5 1 2.2E-05 38.7 2.1 59 173-238 177-235 (252)
90 KOG1039 Predicted E3 ubiquitin 81.4 0.67 1.5E-05 43.4 1.0 24 35-59 9-32 (344)
91 COG1094 Predicted RNA-binding 81.1 3.3 7.2E-05 35.5 5.1 63 164-231 7-74 (194)
92 PRK12705 hypothetical protein; 78.3 3.2 6.9E-05 41.1 4.6 41 164-204 197-238 (508)
93 TIGR01952 nusA_arch NusA famil 78.0 1.5 3.2E-05 35.9 1.9 38 164-201 99-136 (141)
94 KOG2208 Vigilin [Lipid transpo 76.8 3.9 8.4E-05 42.5 5.0 72 164-237 346-417 (753)
95 TIGR01953 NusA transcription t 76.8 2.3 4.9E-05 40.0 3.0 39 164-202 300-338 (341)
96 PF07650 KH_2: KH domain syndr 76.4 0.82 1.8E-05 33.0 -0.0 35 165-199 25-59 (78)
97 KOG2202 U2 snRNP splicing fact 76.4 1.1 2.3E-05 40.0 0.7 27 30-57 148-174 (260)
98 cd02413 40S_S3_KH K homology R 76.0 3 6.5E-05 30.7 2.9 35 165-199 30-64 (81)
99 PRK12328 nusA transcription el 75.6 2.8 6.1E-05 39.7 3.3 39 164-202 307-345 (374)
100 cd02414 jag_KH jag_K homology 75.5 3.9 8.6E-05 29.5 3.4 36 164-199 23-58 (77)
101 COG0195 NusA Transcription elo 74.9 2.2 4.7E-05 36.7 2.2 37 166-202 143-179 (190)
102 PRK06418 transcription elongat 74.6 3.3 7.1E-05 34.8 3.1 38 164-202 60-97 (166)
103 PF13083 KH_4: KH domain; PDB: 74.2 1 2.2E-05 32.1 0.0 33 164-196 28-60 (73)
104 KOG4791 Uncharacterized conser 72.6 1.7 3.7E-05 42.1 1.0 25 96-121 60-84 (667)
105 PRK13764 ATPase; Provisional 71.1 3.7 8E-05 41.5 3.1 42 163-204 479-520 (602)
106 KOG1067 Predicted RNA-binding 69.9 6.4 0.00014 39.2 4.3 67 164-237 596-663 (760)
107 COG1855 ATPase (PilT family) [ 67.9 4 8.6E-05 39.8 2.4 40 164-203 485-524 (604)
108 PRK12327 nusA transcription el 67.7 4.9 0.00011 38.1 3.0 39 164-202 302-340 (362)
109 PRK09202 nusA transcription el 67.5 4.4 9.6E-05 39.7 2.8 39 164-202 301-339 (470)
110 COG0092 RpsC Ribosomal protein 67.2 5.3 0.00011 35.3 2.9 29 165-193 51-79 (233)
111 PRK12329 nusA transcription el 66.0 4.9 0.00011 38.9 2.7 39 164-202 334-372 (449)
112 cd02411 archeal_30S_S3_KH K ho 63.2 7.4 0.00016 28.7 2.7 29 166-194 39-67 (85)
113 cd02412 30S_S3_KH K homology R 62.1 6 0.00013 30.7 2.1 31 165-195 61-91 (109)
114 COG0195 NusA Transcription elo 60.5 8.2 0.00018 33.2 2.8 35 167-201 78-112 (190)
115 cd02410 archeal_CPSF_KH The ar 54.5 14 0.00031 30.2 3.1 38 165-202 76-113 (145)
116 COG5175 MOT2 Transcriptional r 49.5 7.4 0.00016 36.2 0.8 24 34-58 202-225 (480)
117 PF14611 SLS: Mitochondrial in 47.0 84 0.0018 26.9 7.0 66 165-235 26-91 (210)
118 TIGR00436 era GTP-binding prot 44.1 21 0.00045 32.0 2.9 29 166-194 222-251 (270)
119 KOG2208 Vigilin [Lipid transpo 43.2 29 0.00064 36.2 4.1 102 165-273 420-522 (753)
120 KOG2874 rRNA processing protei 42.0 45 0.00098 30.4 4.5 47 179-232 163-209 (356)
121 PRK12329 nusA transcription el 39.7 38 0.00083 32.9 4.0 27 174-200 277-304 (449)
122 PRK15494 era GTPase Era; Provi 36.8 31 0.00067 32.2 2.9 28 167-194 275-303 (339)
123 KOG3702 Nuclear polyadenylated 36.5 40 0.00088 34.2 3.7 24 94-121 622-645 (681)
124 KOG2113 Predicted RNA binding 35.4 34 0.00073 31.7 2.7 59 164-225 114-173 (394)
125 COG1159 Era GTPase [General fu 35.0 32 0.0007 31.6 2.6 31 167-197 231-262 (298)
126 PRK00089 era GTPase Era; Revie 34.5 35 0.00075 30.8 2.8 29 167-195 228-257 (292)
127 PF10283 zf-CCHH: Zinc-finger 34.2 11 0.00024 21.5 -0.3 9 45-53 2-10 (26)
128 KOG4369 RTK signaling protein 33.6 26 0.00057 38.1 1.9 66 164-229 780-845 (2131)
129 PRK12327 nusA transcription el 33.6 33 0.00072 32.5 2.5 27 174-200 245-272 (362)
130 TIGR01953 NusA transcription t 33.4 37 0.00079 32.0 2.8 28 174-201 243-271 (341)
131 COG1097 RRP4 RNA-binding prote 31.6 56 0.0012 29.1 3.4 40 164-203 145-184 (239)
132 PRK04191 rps3p 30S ribosomal p 30.7 46 0.001 28.9 2.8 30 167-196 42-71 (207)
133 TIGR01008 rpsC_E_A ribosomal p 30.4 46 0.001 28.7 2.7 30 166-195 39-68 (195)
134 CHL00048 rps3 ribosomal protei 30.0 52 0.0011 28.8 3.0 30 165-194 66-95 (214)
135 PRK12328 nusA transcription el 29.2 32 0.0007 32.7 1.6 28 174-201 251-279 (374)
136 KOG0153 Predicted RNA-binding 28.4 31 0.00067 32.3 1.3 27 34-61 161-187 (377)
137 PTZ00084 40S ribosomal protein 28.0 49 0.0011 29.1 2.5 30 166-195 45-74 (220)
138 COG1908 FrhD Coenzyme F420-red 26.7 30 0.00065 27.5 0.8 13 44-57 60-72 (132)
139 PRK09202 nusA transcription el 24.8 47 0.001 32.6 2.0 27 174-200 245-272 (470)
140 COG1782 Predicted metal-depend 22.2 94 0.002 31.0 3.4 39 164-202 98-136 (637)
141 TIGR03675 arCOG00543 arCOG0054 21.4 1.1E+02 0.0023 31.4 3.8 39 164-202 92-130 (630)
142 KOG1423 Ras-like GTPase ERA [C 20.0 1.1E+02 0.0023 28.7 3.1 31 164-194 327-358 (379)
No 1
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.74 E-value=2.1e-18 Score=154.11 Aligned_cols=164 Identities=21% Similarity=0.194 Sum_probs=127.9
Q ss_pred eEecccCCCchhhhhhccCCCCCCCCCCCCCC---CCCCCCCCCcccccccccccccccCCCCCcccccccccccCCCcc
Q 022898 53 HFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAV---PPPASNGPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIA 129 (290)
Q Consensus 53 ~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~---~s~~~~~~~~~ktr~C~~~~~~g~C~~G~~C~f~H~~~el~~~~~ 129 (290)
.|+..|+|+|+++++|+++|++|.++|+++++ +|.+.+++|++.+|+|.+.++..... ..+-...+
T Consensus 39 y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~---av~efI~d-------- 107 (402)
T KOG2191|consen 39 YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALN---AVHEFIAD-------- 107 (402)
T ss_pred eEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHH---HHHHHHHH--------
Confidence 88999999999999999999999999999998 78999999999999999988876444 11211212
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCceEEEEecccccceeeCCCCCchhhHHHhhCCceeecc-CCC--C
Q 022898 130 ISHDDPRAFGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD-HEA--D 206 (290)
Q Consensus 130 ~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~s~~~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~-~~~--~ 206 (290)
+++..+..........++.. -....++++.||++.+|+||||+|.+||.|+++++++|+|++ .+. .
T Consensus 108 ----Kire~p~~~~k~v~~~~pqt-------~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~s 176 (402)
T KOG2191|consen 108 ----KIREKPQAVAKPVDILQPQT-------PDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGIS 176 (402)
T ss_pred ----HHHHhHHhhcCCccccCCCC-------ccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCcc
Confidence 12222222222222222211 123577999999999999999999999999999999999984 333 3
Q ss_pred CCcceeEEcCCHHHHHHHHHHHHHHHHhcCCC
Q 022898 207 PNLRNIELEGSFEQIKQASAMVRELIVRIGPA 238 (290)
Q Consensus 207 ~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~~ 238 (290)
..+|+++++|++++..+|..+|.++|.|++..
T Consensus 177 Lqervvt~sge~e~~~~A~~~IL~Ki~eDpqs 208 (402)
T KOG2191|consen 177 LQERVVTVSGEPEQNMKAVSLILQKIQEDPQS 208 (402)
T ss_pred ceeEEEEecCCHHHHHHHHHHHHHHhhcCCcc
Confidence 34899999999999999999999999988765
No 2
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=99.60 E-value=1.1e-15 Score=142.11 Aligned_cols=76 Identities=29% Similarity=0.625 Sum_probs=59.6
Q ss_pred ccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCcccccccccccccccCCC-CC
Q 022898 35 KPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCKF-GD 113 (290)
Q Consensus 35 ~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~C~~-G~ 113 (290)
..|.+|...+.|.++..|+|.|..- .....+.. .......+..+||.+|..|...|.|+| |+
T Consensus 87 ~~~~~~~~~~~~~~~s~~~~~~p~~----------~~~~~~~~-------~~~~~~~p~~~kt~lc~~~~~~g~c~y~ge 149 (332)
T KOG1677|consen 87 GDCSAYLRTGVCGYGSSCRYNHPDL----------RLRPRPVR-------RSRGERKPERYKTPLCRSFRKSGTCKYRGE 149 (332)
T ss_pred cccccccccCCCCCCCCCCccCccc----------ccccCCcc-------ccccccCcccccCCcceeeecCccccccCc
Confidence 7999999999999999999999740 11110000 012335678999999999999999999 99
Q ss_pred cccccccccccCCC
Q 022898 114 KCHFAHGEWELGKP 127 (290)
Q Consensus 114 ~C~f~H~~~el~~~ 127 (290)
+|+|+|+.++++.+
T Consensus 150 ~crfah~~~e~r~~ 163 (332)
T KOG1677|consen 150 QCRFAHGLEELRLP 163 (332)
T ss_pred hhhhcCCccccccc
Confidence 99999999888765
No 3
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=99.43 E-value=7.3e-14 Score=129.99 Aligned_cols=81 Identities=27% Similarity=0.587 Sum_probs=66.1
Q ss_pred CCCccccccccccccCCCCCC-CCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCccccccccccccc
Q 022898 28 SGVGSKSKPCTKFFSTAGCPF-GESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSA 106 (290)
Q Consensus 28 ~~~~~Kt~lC~~~~~~g~C~~-G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~ 106 (290)
....|||.+|.+|..+|+|+| |++|+|+|++ .+++... .......++.|||++|.+|..+
T Consensus 126 ~p~~~kt~lc~~~~~~g~c~y~ge~crfah~~----------~e~r~~~---------~~~~~~~~~~~kt~lC~~f~~t 186 (332)
T KOG1677|consen 126 KPERYKTPLCRSFRKSGTCKYRGEQCRFAHGL----------EELRLPS---------SENQVGNPPKYKTKLCPKFQKT 186 (332)
T ss_pred CcccccCCcceeeecCccccccCchhhhcCCc----------ccccccc---------cchhhcCCCCCCCcCCCccccC
Confidence 367899999999999999999 9999999986 2332110 0012346899999999999999
Q ss_pred ccCCCCCcccccccccccCCC
Q 022898 107 EGCKFGDKCHFAHGEWELGKP 127 (290)
Q Consensus 107 g~C~~G~~C~f~H~~~el~~~ 127 (290)
|.|+||.+|+|+|+..++...
T Consensus 187 G~C~yG~rC~F~H~~~~~~~~ 207 (332)
T KOG1677|consen 187 GLCKYGSRCRFIHGEPEDRAS 207 (332)
T ss_pred CCCCCCCcCeecCCCcccccc
Confidence 999999999999999877764
No 4
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.29 E-value=6.3e-12 Score=89.31 Aligned_cols=63 Identities=32% Similarity=0.502 Sum_probs=58.2
Q ss_pred eEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCC-CCCcceeEEcCCHHHHHHHHHHH
Q 022898 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEA-DPNLRNIELEGSFEQIKQASAMV 228 (290)
Q Consensus 166 t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~-~~~~r~v~i~G~~~~i~~A~~~I 228 (290)
+.+|.||.+.+|.|||++|.+|+.|++.||+.|.|.+... +..+|.|+|.|+++++..|..||
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence 4689999999999999999999999999999999976654 67789999999999999999987
No 5
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=99.19 E-value=1.6e-11 Score=109.17 Aligned_cols=74 Identities=23% Similarity=0.487 Sum_probs=61.5
Q ss_pred CCcccc--ccccccccCCCCCC---CCCceEe---cccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCccccccc
Q 022898 29 GVGSKS--KPCTKFFSTAGCPF---GESCHFL---HYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMC 100 (290)
Q Consensus 29 ~~~~Kt--~lC~~~~~~g~C~~---G~~C~F~---H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C 100 (290)
...||| .||.-|...|+|+| |++|+|+ |++-+ + .....-.+|+|+.|
T Consensus 223 ~~L~kt~~~lc~~ft~kg~~p~~~sG~~~q~a~~~HGlN~----------l---------------~~k~k~~~frTePc 277 (351)
T COG5063 223 KPLYKTNPELCESFTRKGTCPYWISGVKCQFACRGHGLNE----------L---------------KSKKKKQNFRTEPC 277 (351)
T ss_pred chhhcCCHHHhhccCcCCCCcccccccccccccccccccc----------c---------------cccccccccccCCc
Confidence 778999 99999999999999 9999999 98711 1 01124578999999
Q ss_pred ccccccccCCCCCcccccccccccCCC
Q 022898 101 NRLNSAEGCKFGDKCHFAHGEWELGKP 127 (290)
Q Consensus 101 ~~~~~~g~C~~G~~C~f~H~~~el~~~ 127 (290)
..|...|+|+||.+|-|+|+.+++..+
T Consensus 278 inwe~sGyc~yg~Rc~F~hgd~~~ie~ 304 (351)
T COG5063 278 INWEKSGYCPYGLRCCFKHGDDSDIEM 304 (351)
T ss_pred cchhhcccCccccccccccCChhhccc
Confidence 999999999999999999988655543
No 6
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=99.13 E-value=9.2e-11 Score=104.38 Aligned_cols=93 Identities=17% Similarity=0.357 Sum_probs=55.5
Q ss_pred CCccccccccccccCCCCCCCCCceEecccCCCchhhhhhc---cCCCCCC--CCCCCCCCC-------CCCCCCCCccc
Q 022898 29 GVGSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMM---NLPQAVP--APSRNMAVP-------PPASNGPTVVK 96 (290)
Q Consensus 29 ~~~~Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~---~~g~~~~--~~~~~~~~~-------s~~~~~~~~~k 96 (290)
..+|||+-|.-|.+-+.|+++.+|-|.|.---..+...++. +++.... ...++..+. ......-+.++
T Consensus 148 ~~K~kt~slev~in~~~vp~s~~~~~~slP~t~~~~q~l~~rkpks~~~~~s~t~~kes~a~P~~~~~~~~~e~n~~L~k 227 (351)
T COG5063 148 HPKYKTESLEVFINPGYVPYSKRCCFISLPLTDINLQPLSQRKPKSGKNCTSYTLGKESDAHPHDELIYQKQEQNKPLYK 227 (351)
T ss_pred CccccccceeEEecCCccccccccccccccccccCcchhhccCcccCcCccccccccccccCchhhhhhhhhhccchhhc
Confidence 67788888888888788888888888874211111111111 1110000 111111110 01223456677
Q ss_pred c--cccccccccccCCC---CCccccc---ccc
Q 022898 97 S--RMCNRLNSAEGCKF---GDKCHFA---HGE 121 (290)
Q Consensus 97 t--r~C~~~~~~g~C~~---G~~C~f~---H~~ 121 (290)
+ .+|.-|-..|.|+| |.+|.|+ |+.
T Consensus 228 t~~~lc~~ft~kg~~p~~~sG~~~q~a~~~HGl 260 (351)
T COG5063 228 TNPELCESFTRKGTCPYWISGVKCQFACRGHGL 260 (351)
T ss_pred CCHHHhhccCcCCCCcccccccccccccccccc
Confidence 7 89999999999999 9999999 864
No 7
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.10 E-value=2.2e-10 Score=110.29 Aligned_cols=78 Identities=33% Similarity=0.536 Sum_probs=71.8
Q ss_pred CCCceEEEEecccccceeeCCCCCchhhHHHhhCCceee-ccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCCCC
Q 022898 162 GASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAH 239 (290)
Q Consensus 162 ~~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v-~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~~p 239 (290)
+.+.+.+|.||...||+||||+|++||.|+..||++|++ .+.++.+.+|.+.|.|+.++|.+|..+|.++|.+.+...
T Consensus 227 g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~~ 305 (600)
T KOG1676|consen 227 GGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAGA 305 (600)
T ss_pred cccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhccC
Confidence 346689999999999999999999999999999999999 566677889999999999999999999999999988863
No 8
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.08 E-value=5.9e-10 Score=97.82 Aligned_cols=75 Identities=31% Similarity=0.493 Sum_probs=70.3
Q ss_pred CCCCceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhc
Q 022898 161 FGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI 235 (290)
Q Consensus 161 ~~~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~ 235 (290)
.++..+.+|.||.++.|.||||||..|++|++++||+|.|.....+..+|+++|+|+.+||+.|+.++.+.+.+.
T Consensus 311 GGPitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 311 GGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY 385 (390)
T ss_pred CCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence 356899999999999999999999999999999999999998888889999999999999999999999988753
No 9
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.02 E-value=7.1e-10 Score=77.79 Aligned_cols=61 Identities=28% Similarity=0.460 Sum_probs=55.4
Q ss_pred eEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHH
Q 022898 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMV 228 (290)
Q Consensus 166 t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I 228 (290)
+..+.||.++++.|||++|++|+.|++.+|+.|.+.+.. ..++.|+|+|+.+++..|..+|
T Consensus 1 ~~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--SKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred CeEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--CCCCEEEEEcCHHHHHHHHHHh
Confidence 357899999999999999999999999999999997655 5678899999999999999876
No 10
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.98 E-value=1.7e-09 Score=75.95 Aligned_cols=62 Identities=35% Similarity=0.597 Sum_probs=57.4
Q ss_pred EEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHH
Q 022898 167 AKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMV 228 (290)
Q Consensus 167 ~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I 228 (290)
.++.||...++.|||++|++|+.|++.||+.|.|.....+..++.|.|.|+.+++..|..+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHh
Confidence 67999999999999999999999999999999998766667889999999999999998876
No 11
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=98.97 E-value=2.8e-10 Score=79.31 Aligned_cols=60 Identities=43% Similarity=0.635 Sum_probs=54.9
Q ss_pred eEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHH
Q 022898 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMV 228 (290)
Q Consensus 166 t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I 228 (290)
|.+|.||.+.++.|||++|++|+.|++.||+.|.+.+. + ....+.|.|+.++++.|..+|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~--~-~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD--D-ERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--T-EEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--C-CcEEEEEEeCHHHHHHHHhhC
Confidence 57899999999999999999999999999999999765 3 556999999999999999876
No 12
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.94 E-value=2.3e-09 Score=75.19 Aligned_cols=57 Identities=26% Similarity=0.421 Sum_probs=52.1
Q ss_pred eEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCC-HHHHHHHHHHH
Q 022898 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGS-FEQIKQASAMV 228 (290)
Q Consensus 166 t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~-~~~i~~A~~~I 228 (290)
...+.||.+.++.|||++|++|++|++.||+.|.|.+ ++.|.|.|+ .+.++.|..+|
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~------~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED------DGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC------CCEEEEEeCCHHHHHHHHHHh
Confidence 5679999999999999999999999999999999976 257999998 99999999887
No 13
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=98.92 E-value=2.8e-10 Score=109.56 Aligned_cols=153 Identities=20% Similarity=0.235 Sum_probs=104.7
Q ss_pred CCCchhhhhhccCCCCCCCCCCCCCCCC-CCCCCCCcccccccccccccccCCCCCcccccccccccCCCcccCCCCCCC
Q 022898 59 PGGYNAVAQMMNLPQAVPAPSRNMAVPP-PASNGPTVVKSRMCNRLNSAEGCKFGDKCHFAHGEWELGKPIAISHDDPRA 137 (290)
Q Consensus 59 ~~~~~~~~~~~~~g~~~~~~~~~~~~~s-~~~~~~~~~ktr~C~~~~~~g~C~~G~~C~f~H~~~el~~~~~~~~~~~~~ 137 (290)
++....+.+|++.|++|.-++.++++-- ---+-.+.+.+|.-.+.+....|- .| ++...||...+..
T Consensus 236 VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie---~A--a~lI~eii~~~~~------- 303 (600)
T KOG1676|consen 236 VPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIE---HA--AELINEIIAEAEA------- 303 (600)
T ss_pred ccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHH---HH--HHHHHHHHHHHhc-------
Confidence 4667778899999999988888777521 000111255667777777776665 33 3333333332111
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCcCCCCceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccC--CCCCCcceeEEc
Q 022898 138 FGAVPGRMGGRYEPPPAPGPAASFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH--EADPNLRNIELE 215 (290)
Q Consensus 138 ~~p~~~~~~~~~~~~~~p~~~~s~~~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~--~~~~~~r~v~i~ 215 (290)
...++ .++.. | +.-....|.||++++|+||||||++||+|+.+|||++++... ..+..+|.|.|.
T Consensus 304 -~~~~~--~~~G~----P------~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~Ir 370 (600)
T KOG1676|consen 304 -GAGGG--MGGGA----P------GLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIR 370 (600)
T ss_pred -cCCCC--cCCCC----c------cceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEe
Confidence 00011 11110 0 011278899999999999999999999999999999999543 456679999999
Q ss_pred CCHHHHHHHHHHHHHHHHhcC
Q 022898 216 GSFEQIKQASAMVRELIVRIG 236 (290)
Q Consensus 216 G~~~~i~~A~~~I~~~i~~~~ 236 (290)
|+..+|+.|..||..++-...
T Consensus 371 G~~~QIdhAk~LIr~kvg~~~ 391 (600)
T KOG1676|consen 371 GDKRQIDHAKQLIRDKVGDIA 391 (600)
T ss_pred cCcccchHHHHHHHHHhcccC
Confidence 999999999999999997643
No 14
>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....
Probab=98.80 E-value=6e-10 Score=65.07 Aligned_cols=26 Identities=46% Similarity=0.991 Sum_probs=21.9
Q ss_pred cccccccccccCCCCCCCCCceEecc
Q 022898 32 SKSKPCTKFFSTAGCPFGESCHFLHY 57 (290)
Q Consensus 32 ~Kt~lC~~~~~~g~C~~G~~C~F~H~ 57 (290)
|||++|++|+.+|.|+||++|+|+|+
T Consensus 1 ~k~~~C~~f~~~g~C~~G~~C~f~H~ 26 (27)
T PF00642_consen 1 YKTKLCRFFMRTGTCPFGDKCRFAHG 26 (27)
T ss_dssp TTSSB-HHHHHTS--TTGGGSSSBSS
T ss_pred CccccChhhccCCccCCCCCcCccCC
Confidence 79999999999999999999999996
No 15
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=98.72 E-value=3.5e-08 Score=95.61 Aligned_cols=73 Identities=27% Similarity=0.447 Sum_probs=68.0
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeec-cCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcC
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR-DHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG 236 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~-~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~ 236 (290)
..+.+|.||.+.+|.||||+|..|++|++.|||+|+|. +..+...+|.|+|+|.+++|..|+..|...|.+..
T Consensus 137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~L~~~~ 210 (485)
T KOG2190|consen 137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSRLLENP 210 (485)
T ss_pred ceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHHHHhcC
Confidence 46899999999999999999999999999999999995 44788889999999999999999999999999964
No 16
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=98.66 E-value=1.7e-08 Score=92.80 Aligned_cols=56 Identities=27% Similarity=0.689 Sum_probs=50.0
Q ss_pred ccccccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCcccccccccccccccCC
Q 022898 31 GSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCK 110 (290)
Q Consensus 31 ~~Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~C~ 110 (290)
..++.+|++|++ |.|..||.|.|+|.. ...+-+.|.+|...|.|.
T Consensus 74 ~~~~~vcK~~l~-glC~kgD~C~Flhe~----------------------------------~~~k~rec~ff~~~g~c~ 118 (325)
T KOG1040|consen 74 SRGKVVCKHWLR-GLCKKGDQCEFLHEY----------------------------------DLTKMRECKFFSLFGECT 118 (325)
T ss_pred cCCceeehhhhh-hhhhccCcCcchhhh----------------------------------hhcccccccccccccccc
Confidence 678999999995 699999999999964 556677899999999999
Q ss_pred CCCcccccccc
Q 022898 111 FGDKCHFAHGE 121 (290)
Q Consensus 111 ~G~~C~f~H~~ 121 (290)
.+.+|.|.|+.
T Consensus 119 ~~~~c~y~h~d 129 (325)
T KOG1040|consen 119 NGKDCPYLHGD 129 (325)
T ss_pred cccCCcccCCC
Confidence 99999999966
No 17
>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....
Probab=98.64 E-value=3.1e-09 Score=62.01 Aligned_cols=26 Identities=62% Similarity=1.364 Sum_probs=21.1
Q ss_pred cccccCCCCC-CCCCCCCCCCcCCCCh
Q 022898 257 FKTKLCGNFA-KGSCTFGDRCHFAHGA 282 (290)
Q Consensus 257 ~k~~~C~~~~-~g~C~~g~~C~f~Hg~ 282 (290)
||+++|.+|. .|.|++|++|.|+|++
T Consensus 1 ~k~~~C~~f~~~g~C~~G~~C~f~H~~ 27 (27)
T PF00642_consen 1 YKTKLCRFFMRTGTCPFGDKCRFAHGE 27 (27)
T ss_dssp TTSSB-HHHHHTS--TTGGGSSSBSSG
T ss_pred CccccChhhccCCccCCCCCcCccCCC
Confidence 6889999999 6999999999999985
No 18
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=98.62 E-value=8e-08 Score=86.81 Aligned_cols=74 Identities=23% Similarity=0.362 Sum_probs=67.8
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccC---CCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH---EADPNLRNIELEGSFEQIKQASAMVRELIVRIGP 237 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~---~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~ 237 (290)
...++|+||+-.+|.||||||.+|.+++.++|++|+++.+ -++..+|++.|+|+.+.+....+.|.++|.|...
T Consensus 38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~ 114 (402)
T KOG2191|consen 38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQ 114 (402)
T ss_pred ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHH
Confidence 4779999999999999999999999999999999999755 3888899999999999999999999999987544
No 19
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=98.60 E-value=9.2e-08 Score=88.90 Aligned_cols=75 Identities=27% Similarity=0.276 Sum_probs=69.1
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccC-CCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCCC
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH-EADPNLRNIELEGSFEQIKQASAMVRELIVRIGPA 238 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~-~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~~ 238 (290)
..++++.||...||+|||+.|.+||+|...+||.|+|... -+|..+|.|.|+|.+++..+|+..|..+|.|....
T Consensus 410 ~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikEenf~ 485 (584)
T KOG2193|consen 410 QEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEENFF 485 (584)
T ss_pred hhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhccC
Confidence 6788999999999999999999999999999999999655 47778999999999999999999999999887665
No 20
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=98.57 E-value=3.3e-08 Score=94.62 Aligned_cols=77 Identities=25% Similarity=0.473 Sum_probs=64.9
Q ss_pred ccccCCCCCCCccccccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCcccccc
Q 022898 20 KKSKHESESGVGSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRM 99 (290)
Q Consensus 20 ~~~~~~~~~~~~~Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~ 99 (290)
.|.|..+..+..|.-..|+.|.+ |.|..||.|.|+|++.+-| ..|..|+|+.
T Consensus 222 EkARRRDPRkyhYs~tpCPefrk-G~C~rGD~CEyaHgvfEcw---------------------------LHPa~YRT~~ 273 (528)
T KOG1595|consen 222 EKARRRDPRKYHYSSTPCPEFRK-GSCERGDSCEYAHGVFECW---------------------------LHPARYRTRK 273 (528)
T ss_pred cccccCCcccccccCccCccccc-CCCCCCCccccccceehhh---------------------------cCHHHhcccc
Confidence 34555788899999999999986 7999999999999985533 4678999999
Q ss_pred cccccccccCCCCCcccccccccccCCCc
Q 022898 100 CNRLNSAEGCKFGDKCHFAHGEWELGKPI 128 (290)
Q Consensus 100 C~~~~~~g~C~~G~~C~f~H~~~el~~~~ 128 (290)
|+- .++|+- .-|.|||..++||...
T Consensus 274 CkD---g~~C~R-rvCfFAH~~eqLR~l~ 298 (528)
T KOG1595|consen 274 CKD---GGYCPR-RVCFFAHSPEQLRPLP 298 (528)
T ss_pred ccC---CCCCcc-ceEeeecChHHhcccC
Confidence 974 489996 9999999999997653
No 21
>PF13014 KH_3: KH domain
Probab=98.55 E-value=1.1e-07 Score=61.76 Aligned_cols=42 Identities=43% Similarity=0.692 Sum_probs=37.5
Q ss_pred ccceeeCCCCCchhhHHHhhCCceeecc-CCCCCCcceeEEcC
Q 022898 175 LAGAIIGKGGVNSKQICRQTGAKLSIRD-HEADPNLRNIELEG 216 (290)
Q Consensus 175 ~vg~iIGkgG~~Ik~i~~~sga~i~v~~-~~~~~~~r~v~i~G 216 (290)
++|+|||++|++|++|+++|+++|+|.+ ..++..++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 4789999999999999999999999977 56677789999987
No 22
>smart00322 KH K homology RNA-binding domain.
Probab=98.51 E-value=5.1e-07 Score=63.22 Aligned_cols=66 Identities=32% Similarity=0.562 Sum_probs=58.1
Q ss_pred ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHH
Q 022898 165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELI 232 (290)
Q Consensus 165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i 232 (290)
.+.++.||...++.+||++|.+|+.|++.+++.|.+..... ....+.|.|..+++..|..+|...+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--EERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC--CccEEEEEcCHHHHHHHHHHHHHHh
Confidence 46789999999999999999999999999999999964332 5678999999999999999887764
No 23
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=98.37 E-value=2.3e-07 Score=88.85 Aligned_cols=31 Identities=32% Similarity=0.715 Sum_probs=28.0
Q ss_pred cccccccCCCCCCCCCCCCCCCcCCCChhhhccc
Q 022898 255 SNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKT 288 (290)
Q Consensus 255 ~~~k~~~C~~~~~g~C~~g~~C~f~Hg~~el~~~ 288 (290)
..|||++|+.= |+|+. --|.|||..+|||..
T Consensus 267 a~YRT~~CkDg--~~C~R-rvCfFAH~~eqLR~l 297 (528)
T KOG1595|consen 267 ARYRTRKCKDG--GYCPR-RVCFFAHSPEQLRPL 297 (528)
T ss_pred HHhccccccCC--CCCcc-ceEeeecChHHhccc
Confidence 57999999985 89998 889999999999975
No 24
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=98.35 E-value=4.9e-07 Score=84.18 Aligned_cols=71 Identities=27% Similarity=0.424 Sum_probs=66.1
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceee-ccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHh
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI-RDHEADPNLRNIELEGSFEQIKQASAMVRELIVR 234 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v-~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~ 234 (290)
.-..++.||..++|+|||+.|++|++|..+|.++|.| +....+..++.++|.+++|....|..+|.++|..
T Consensus 198 D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~s~Ac~~ILeimqk 269 (584)
T KOG2193|consen 198 DWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGTSKACKMILEIMQK 269 (584)
T ss_pred CcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccchHHHHHHHHHHHHH
Confidence 5678999999999999999999999999999999999 5667888899999999999999999999999864
No 25
>smart00356 ZnF_C3H1 zinc finger.
Probab=98.27 E-value=4.4e-07 Score=52.64 Aligned_cols=26 Identities=35% Similarity=0.851 Sum_probs=23.4
Q ss_pred ccccccccccccCCCCCCCCCceEecc
Q 022898 31 GSKSKPCTKFFSTAGCPFGESCHFLHY 57 (290)
Q Consensus 31 ~~Kt~lC~~~~~~g~C~~G~~C~F~H~ 57 (290)
.+|+.+|++| .+|.|++|++|.|+|+
T Consensus 1 ~~k~~~C~~~-~~g~C~~g~~C~~~H~ 26 (27)
T smart00356 1 KYKTELCKFF-KRGYCPYGDRCKFAHP 26 (27)
T ss_pred CCCCCcCcCc-cCCCCCCCCCcCCCCc
Confidence 3689999999 6789999999999996
No 26
>smart00356 ZnF_C3H1 zinc finger.
Probab=98.22 E-value=7.7e-07 Score=51.59 Aligned_cols=26 Identities=54% Similarity=1.212 Sum_probs=23.7
Q ss_pred cccccCCCCCCCCCCCCCCCcCCCCh
Q 022898 257 FKTKLCGNFAKGSCTFGDRCHFAHGA 282 (290)
Q Consensus 257 ~k~~~C~~~~~g~C~~g~~C~f~Hg~ 282 (290)
+|+.+|.+|.+|.|.+|++|.|+|..
T Consensus 2 ~k~~~C~~~~~g~C~~g~~C~~~H~~ 27 (27)
T smart00356 2 YKTELCKFFKRGYCPYGDRCKFAHPL 27 (27)
T ss_pred CCCCcCcCccCCCCCCCCCcCCCCcC
Confidence 57889999999999999999999973
No 27
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=98.11 E-value=5.9e-07 Score=85.22 Aligned_cols=61 Identities=25% Similarity=0.644 Sum_probs=45.5
Q ss_pred ccccccccccC--CCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCcccccccccccccccCC
Q 022898 33 KSKPCTKFFST--AGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCK 110 (290)
Q Consensus 33 Kt~lC~~~~~~--g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~C~ 110 (290)
+-.||+....+ ..|+|||+|+|.|++ +-|- ..+++... --|.+|.+.|.|+
T Consensus 75 ~n~LCPsli~g~~~~C~f~d~Crf~HDi-~ayL-------------------------atK~~Dig-~~Cp~f~s~G~Cp 127 (614)
T KOG2333|consen 75 QNRLCPSLIQGDISKCSFGDNCRFVHDI-EAYL-------------------------ATKAPDIG-PSCPVFESLGFCP 127 (614)
T ss_pred hhccChHhhcCCCccCcccccccccccH-HHHH-------------------------hccCcccC-CccceeeccccCC
Confidence 46899999988 689999999999986 1111 01122222 2499999999999
Q ss_pred CCCccccccc
Q 022898 111 FGDKCHFAHG 120 (290)
Q Consensus 111 ~G~~C~f~H~ 120 (290)
||.+|||+-.
T Consensus 128 ~G~~CRFl~a 137 (614)
T KOG2333|consen 128 YGFKCRFLGA 137 (614)
T ss_pred ccceeehhhc
Confidence 9999999743
No 28
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=98.04 E-value=4.5e-06 Score=70.66 Aligned_cols=61 Identities=25% Similarity=0.421 Sum_probs=53.5
Q ss_pred EEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEE---cCCHHHHHHHHHHHHHHHHh
Q 022898 169 ISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIEL---EGSFEQIKQASAMVRELIVR 234 (290)
Q Consensus 169 i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i---~G~~~~i~~A~~~I~~~i~~ 234 (290)
+.||.+.+++|||++|++|+.|++.+|++|+|.+. ...|.| +++++++..|..+|..+...
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~i~kA~~~I~~i~~g 65 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLAVMKAREVVKAIGRG 65 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence 57899999999999999999999999999999753 245666 88999999999999987653
No 29
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.02 E-value=1.6e-05 Score=63.31 Aligned_cols=63 Identities=27% Similarity=0.380 Sum_probs=49.1
Q ss_pred cccceeeCCCCCchhhHHHhhCCceeeccCCCCC-----------------CcceeEEcC-C--HHHHHHHHHHHHHHHH
Q 022898 174 SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADP-----------------NLRNIELEG-S--FEQIKQASAMVRELIV 233 (290)
Q Consensus 174 ~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~-----------------~~r~v~i~G-~--~~~i~~A~~~I~~~i~ 233 (290)
.++|.|||.+|.+|++|++.||++|.|....... ..--|.|++ + .+.++.|..+|..++.
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~ 94 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK 94 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence 5778999999999999999999999997542110 113466666 5 6999999999999988
Q ss_pred hcC
Q 022898 234 RIG 236 (290)
Q Consensus 234 ~~~ 236 (290)
...
T Consensus 95 ~~~ 97 (120)
T cd02395 95 PAI 97 (120)
T ss_pred cCC
Confidence 443
No 30
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.96 E-value=1.3e-05 Score=68.46 Aligned_cols=64 Identities=22% Similarity=0.309 Sum_probs=56.4
Q ss_pred ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEE----cCCHHHHHHHHHHHHHHHH
Q 022898 165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIEL----EGSFEQIKQASAMVRELIV 233 (290)
Q Consensus 165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i----~G~~~~i~~A~~~I~~~i~ 233 (290)
....+.||.+.++.|||++|.+|+.|++.+|++|+|.+. ...|.| +++++++.+|..+|..++.
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~i~kA~~~I~ai~~ 70 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLAVLKARDIVKAIGR 70 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence 357899999999999999999999999999999999753 245666 5899999999999998876
No 31
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=97.91 E-value=3e-06 Score=73.06 Aligned_cols=72 Identities=22% Similarity=0.495 Sum_probs=52.9
Q ss_pred CCCCCccccccCCCCCCCccccccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCC
Q 022898 13 INANGVFKKSKHESESGVGSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGP 92 (290)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~ 92 (290)
++..-.-||+|+-.|-+-.....-|+||..+|.|-.|..|+|.|.
T Consensus 185 nnksyllkkkrflkevgnspsavycryynangicgkgaacrfvhe----------------------------------- 229 (377)
T KOG1492|consen 185 NNKSYLLKKKRFLKEVGNSPSAVYCRYYNANGICGKGAACRFVHE----------------------------------- 229 (377)
T ss_pred cChhHHHHHHHHHHHhCCCCceeEEEEecCCCcccCCceeeeecc-----------------------------------
Confidence 333334456665555555556778999999999999999999995
Q ss_pred CcccccccccccccccCCCCCcccccccc
Q 022898 93 TVVKSRMCNRLNSAEGCKFGDKCHFAHGE 121 (290)
Q Consensus 93 ~~~ktr~C~~~~~~g~C~~G~~C~f~H~~ 121 (290)
+..|| +|.+|.. |.|...++|...|..
T Consensus 230 ptrkt-icpkfln-grcnkaedcnlshel 256 (377)
T KOG1492|consen 230 PTRKT-ICPKFLN-GRCNKAEDCNLSHEL 256 (377)
T ss_pred ccccc-cChHHhc-CccCchhcCCccccc
Confidence 33343 7998865 689999999999944
No 32
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=97.76 E-value=3.7e-05 Score=65.07 Aligned_cols=55 Identities=29% Similarity=0.469 Sum_probs=49.7
Q ss_pred cccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhc
Q 022898 174 SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI 235 (290)
Q Consensus 174 ~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~ 235 (290)
..+|.|||++|.+++.|+..||+.|+|.+ +.|.|.|++++++.|..+|..++...
T Consensus 98 ~~~griIG~~G~t~~~ie~~t~~~i~i~~-------~~v~i~G~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 98 RIKGRIIGEGGKTRRIIEELTGVSISVYG-------KTVGIIGDPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred HHHhhhcCCCcHHHHHHHHHHCCeEEEcC-------CEEEEECCHHHHHHHHHHHHHHHcCC
Confidence 36889999999999999999999999974 57999999999999999999988544
No 33
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.74 E-value=0.00012 Score=71.25 Aligned_cols=74 Identities=22% Similarity=0.253 Sum_probs=67.0
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcC---------CHHHHHHHHHHHHHHHHh
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG---------SFEQIKQASAMVRELIVR 234 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G---------~~~~i~~A~~~I~~~i~~ 234 (290)
..+.|+..+...+|.||||.|..|++|+..+.++|.|.+...+..+|+|+|+| ..+++.+|..+|...+.+
T Consensus 42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~ 121 (485)
T KOG2190|consen 42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEE 121 (485)
T ss_pred cceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhcccc
Confidence 44579999999999999999999999999999999999999999999999999 999999999999887664
Q ss_pred cCC
Q 022898 235 IGP 237 (290)
Q Consensus 235 ~~~ 237 (290)
.+.
T Consensus 122 d~~ 124 (485)
T KOG2190|consen 122 DDE 124 (485)
T ss_pred ccc
Confidence 333
No 34
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.57 E-value=9.6e-05 Score=63.02 Aligned_cols=55 Identities=29% Similarity=0.475 Sum_probs=48.7
Q ss_pred cccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhc
Q 022898 174 SLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI 235 (290)
Q Consensus 174 ~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~ 235 (290)
...|.|||++|.+++.|++.||++|+|.+ +.+.|.|+++++..|...|..++...
T Consensus 104 r~~griIG~~G~~~k~ie~~t~~~i~i~~-------~~v~i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 104 RIKGRIIGEGGKTRRIIEELTGVDISVYG-------KTVAIIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred HHhhheeCCCcHHHHHHHHHHCcEEEEcC-------CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence 36789999999999999999999999974 24889999999999999999988443
No 35
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=97.45 E-value=7.9e-05 Score=68.77 Aligned_cols=53 Identities=25% Similarity=0.494 Sum_probs=44.8
Q ss_pred cccccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCcccccccccccccccCCC
Q 022898 32 SKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCKF 111 (290)
Q Consensus 32 ~Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~C~~ 111 (290)
.|+..|.+|...|.|..+.+|.|.|+. +.++-+.|. |+..|.|.-
T Consensus 103 ~k~rec~ff~~~g~c~~~~~c~y~h~d----------------------------------pqt~~k~c~-~~~~g~c~~ 147 (325)
T KOG1040|consen 103 TKMRECKFFSLFGECTNGKDCPYLHGD----------------------------------PQTAIKKCK-WYKEGFCRG 147 (325)
T ss_pred cccccccccccccccccccCCcccCCC----------------------------------hhhhhhccc-hhhhccCCC
Confidence 356689999999999999999999974 344556785 778899999
Q ss_pred CCcccccc
Q 022898 112 GDKCHFAH 119 (290)
Q Consensus 112 G~~C~f~H 119 (290)
|..|++.|
T Consensus 148 g~~c~~~h 155 (325)
T KOG1040|consen 148 GPSCKKRH 155 (325)
T ss_pred cchhhhhh
Confidence 99999999
No 36
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=97.44 E-value=0.00011 Score=65.16 Aligned_cols=72 Identities=22% Similarity=0.363 Sum_probs=63.9
Q ss_pred ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccC-CCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcC
Q 022898 165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH-EADPNLRNIELEGSFEQIKQASAMVRELIVRIG 236 (290)
Q Consensus 165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~-~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~ 236 (290)
-.++++|.++++|.|||+.|+.||++++.+.|+++|... -+...+|++.|.|.+..|-.....|...+.+.+
T Consensus 123 ce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~p 195 (390)
T KOG2192|consen 123 CELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISESP 195 (390)
T ss_pred hhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCC
Confidence 357899999999999999999999999999999999654 577889999999999999888888888887653
No 37
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=97.42 E-value=0.0002 Score=64.82 Aligned_cols=58 Identities=28% Similarity=0.541 Sum_probs=46.1
Q ss_pred ccccccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCcccccccccccccccCC
Q 022898 31 GSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCK 110 (290)
Q Consensus 31 ~~Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~C~ 110 (290)
.+....|++|.. |.|+-++.|.|+|+... -.. ..-.|..|...|.|.
T Consensus 101 ~~s~V~c~~~~~-g~c~s~~~c~~lh~~d~-------------------------------~~s-~~~~c~~Fs~~G~cs 147 (285)
T COG5084 101 LSSSVVCKFFLR-GLCKSGFSCEFLHEYDL-------------------------------RSS-QGPPCRSFSLKGSCS 147 (285)
T ss_pred ccCCcccchhcc-ccCcCCCccccccCCCc-------------------------------ccc-cCCCcccccccceec
Confidence 578899998885 69999999999997511 010 234699999999999
Q ss_pred CCCcccccccc
Q 022898 111 FGDKCHFAHGE 121 (290)
Q Consensus 111 ~G~~C~f~H~~ 121 (290)
.|..|.|.|..
T Consensus 148 ~g~~c~~~h~d 158 (285)
T COG5084 148 SGPSCGYSHID 158 (285)
T ss_pred cCCCCCccccC
Confidence 99999999954
No 38
>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=97.20 E-value=0.00063 Score=68.88 Aligned_cols=65 Identities=23% Similarity=0.306 Sum_probs=56.8
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcC-CHHHHHHHHHHHHHHHHh
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVR 234 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G-~~~~i~~A~~~I~~~i~~ 234 (290)
-....+.||.+.++.|||.||.+|+.|++.||+.|.|.+ +..|.|.+ +.++++.|..+|..++..
T Consensus 577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 456789999999999999999999999999999999976 24566666 789999999999998884
No 39
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=97.18 E-value=0.00012 Score=65.56 Aligned_cols=32 Identities=34% Similarity=0.654 Sum_probs=26.9
Q ss_pred CCCCCccccccccccccCCCCCCCCCceEeccc
Q 022898 26 SESGVGSKSKPCTKFFSTAGCPFGESCHFLHYF 58 (290)
Q Consensus 26 ~~~~~~~Kt~lC~~~~~~g~C~~G~~C~F~H~~ 58 (290)
.+..+-.|+.+|.+|. .|.|..|++|+|+|++
T Consensus 84 v~~gvDPKSvvCafFk-~g~C~KG~kCKFsHdl 115 (343)
T KOG1763|consen 84 VPKGVDPKSVVCAFFK-QGTCTKGDKCKFSHDL 115 (343)
T ss_pred cccCCCchHHHHHHHh-ccCCCCCCcccccchH
Confidence 3347788999997665 5799999999999997
No 40
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=97.06 E-value=0.00013 Score=63.44 Aligned_cols=82 Identities=23% Similarity=0.478 Sum_probs=48.8
Q ss_pred CCccccccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCC----CCCCCCCCCCCCCCCCccccccccccc
Q 022898 29 GVGSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPA----PSRNMAVPPPASNGPTVVKSRMCNRLN 104 (290)
Q Consensus 29 ~~~~Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~----~~~~~~~~s~~~~~~~~~ktr~C~~~~ 104 (290)
.+-.|+..|.-|. .+.|..|+.|+|+|+.- +.+.+... .-++....-+-...|--...++|.+|.
T Consensus 80 gvdpK~~vcalF~-~~~c~kg~~ckF~h~~e----------e~r~~eK~DLYsDvRd~~ed~pl~krP~intd~VCkffi 148 (299)
T COG5252 80 GVDPKTVVCALFL-NKTCAKGDACKFAHGKE----------EARKTEKPDLYSDVRDKEEDVPLGKRPWINTDRVCKFFI 148 (299)
T ss_pred ccCchhHHHHHhc-cCccccCchhhhhcchH----------HHhhhcccchhhhhhhhhccCCcccCCCCChhHHHHHHH
Confidence 6778999998777 57999999999999851 11111000 000000000111223344567898763
Q ss_pred ------ccc---cCCCC-Ccccccccc
Q 022898 105 ------SAE---GCKFG-DKCHFAHGE 121 (290)
Q Consensus 105 ------~~g---~C~~G-~~C~f~H~~ 121 (290)
..| .|++| .+|-|.|.-
T Consensus 149 eA~e~GkYgw~W~CPng~~~C~y~H~L 175 (299)
T COG5252 149 EAMESGKYGWGWTCPNGNMRCSYIHKL 175 (299)
T ss_pred HHHhcCCccceeeCCCCCceeeeeecc
Confidence 222 79996 799999954
No 41
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.96 E-value=0.0014 Score=61.93 Aligned_cols=72 Identities=21% Similarity=0.316 Sum_probs=55.5
Q ss_pred cCCCCceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHh
Q 022898 160 SFGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVR 234 (290)
Q Consensus 160 s~~~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~ 234 (290)
..+.....-+.|-+.+||.|||+||++|+.||..++++|+|..-+... .|.|-|.-..-.+|...|...+..
T Consensus 42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~~e~---kv~ifg~~~m~~kaka~id~~~~k 113 (629)
T KOG0336|consen 42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDLEV---KVTIFGINHMRKKAKASIDRGQDK 113 (629)
T ss_pred cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccCcee---EEEEechHHHHHHHHhhHhhhhhh
Confidence 444577788899999999999999999999999999999997655443 455667666666666666555543
No 42
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=96.90 E-value=0.0004 Score=63.28 Aligned_cols=64 Identities=19% Similarity=0.390 Sum_probs=42.0
Q ss_pred CccccccccccccCCCCCCCCC-ceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCccccccccccccccc
Q 022898 30 VGSKSKPCTKFFSTAGCPFGES-CHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEG 108 (290)
Q Consensus 30 ~~~Kt~lC~~~~~~g~C~~G~~-C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~ 108 (290)
.+..-..|+.|+++ .|..||. |+|+|.. ..-. + .+-+---| +-.+.|.
T Consensus 33 ~wl~~eVCReF~rn-~C~R~d~~CkfaHP~--~~~~---V------------------------~~g~v~aC-~Ds~kgr 81 (331)
T KOG2494|consen 33 KWLTLEVCREFLRN-TCSRGDRECKFAHPP--KNCQ---V------------------------SNGRVIAC-FDSQKGR 81 (331)
T ss_pred chhHHHHHHHHHhc-cccCCCccccccCCC--CCCC---c------------------------cCCeEEEE-eccccCc
Confidence 44456899999975 9999999 9999953 1000 0 00011136 4456778
Q ss_pred CCCCCcccccccccccC
Q 022898 109 CKFGDKCHFAHGEWELG 125 (290)
Q Consensus 109 C~~G~~C~f~H~~~el~ 125 (290)
|. .++|+|+|.-.+++
T Consensus 82 Cs-R~nCkylHpp~hlk 97 (331)
T KOG2494|consen 82 CS-RENCKYLHPPQHLK 97 (331)
T ss_pred cC-cccceecCCChhhh
Confidence 98 57799999765543
No 43
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=96.72 E-value=0.0012 Score=35.04 Aligned_cols=19 Identities=42% Similarity=0.812 Sum_probs=16.4
Q ss_pred cCCCCCCCCCCCCCCCcCCCC
Q 022898 261 LCGNFAKGSCTFGDRCHFAHG 281 (290)
Q Consensus 261 ~C~~~~~g~C~~g~~C~f~Hg 281 (290)
+|+||.. |+++++|.|.|+
T Consensus 1 ~Ck~~~~--C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGPN--CTNGDNCPFSHP 19 (19)
T ss_pred CCcCcCC--CCCCCcCccCCc
Confidence 4888774 999999999995
No 44
>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=96.64 E-value=0.0024 Score=65.18 Aligned_cols=66 Identities=23% Similarity=0.388 Sum_probs=54.1
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEc-CCHHHHHHHHHHHHHHHHhc
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELE-GSFEQIKQASAMVRELIVRI 235 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~-G~~~~i~~A~~~I~~~i~~~ 235 (290)
-....+.||.+.++.|||+||.+|+.|.++||+.|.|.+. ..|.|. .+.+.++.|..+|..+....
T Consensus 550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd------G~V~i~~~~~~~~~~a~~~I~~~~~~~ 616 (684)
T TIGR03591 550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD------GTVKIAASDGEAAEAAIKMIEGITAEP 616 (684)
T ss_pred CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC------eEEEEEECcHHHHHHHHHHHHhhhccc
Confidence 3456799999999999999999999999999999999752 233443 46788999999998886643
No 45
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.55 E-value=0.0053 Score=58.88 Aligned_cols=74 Identities=31% Similarity=0.443 Sum_probs=56.5
Q ss_pred CceEEEEecc------cccceeeCCCCCchhhHHHhhCCceeeccCC---------CC--------CCcceeEEcCCHHH
Q 022898 164 SATAKISVDA------SLAGAIIGKGGVNSKQICRQTGAKLSIRDHE---------AD--------PNLRNIELEGSFEQ 220 (290)
Q Consensus 164 ~~t~~i~VP~------~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~---------~~--------~~~r~v~i~G~~~~ 220 (290)
..+.+|.||. .+||+|||..|.+.|.+..+|||+|.|.... .+ ..........+.|.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek 216 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK 216 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence 3456666654 6899999999999999999999999996521 10 11244556668999
Q ss_pred HHHHHHHHHHHHHhcCC
Q 022898 221 IKQASAMVRELIVRIGP 237 (290)
Q Consensus 221 i~~A~~~I~~~i~~~~~ 237 (290)
|++|+.+|.++|.+.-.
T Consensus 217 i~~Ai~vienli~~av~ 233 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSAVS 233 (554)
T ss_pred HHHHHHHHHHHHHhhcc
Confidence 99999999999987433
No 46
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.52 E-value=0.0014 Score=62.34 Aligned_cols=22 Identities=14% Similarity=-0.245 Sum_probs=20.1
Q ss_pred cCCCCCCCCCCCCCCCcCCCCh
Q 022898 261 LCGNFAKGSCTFGDRCHFAHGA 282 (290)
Q Consensus 261 ~C~~~~~g~C~~g~~C~f~Hg~ 282 (290)
.|.+|..+.|.-+|.|.|.|.-
T Consensus 120 P~l~~~K~~e~~~D~~s~Lh~P 141 (667)
T KOG4791|consen 120 PQLRSVKKVESSEDVPSPLHPP 141 (667)
T ss_pred hHHHHhhhhhhhccccccCCCC
Confidence 5999999999999999999974
No 47
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=96.22 E-value=0.0072 Score=42.08 Aligned_cols=37 Identities=32% Similarity=0.515 Sum_probs=33.9
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceee
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSI 200 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v 200 (290)
.....+.|+.+.++.+|||+|.+|+.++..++..|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3678999999999999999999999999999988776
No 48
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=96.14 E-value=0.0019 Score=60.35 Aligned_cols=26 Identities=42% Similarity=1.028 Sum_probs=22.9
Q ss_pred ccccCCCCCCCCCCCCCCCcCCCChh
Q 022898 258 KTKLCGNFAKGSCTFGDRCHFAHGAA 283 (290)
Q Consensus 258 k~~~C~~~~~g~C~~g~~C~f~Hg~~ 283 (290)
...+|+||..|.|+|+.+|+|.||..
T Consensus 139 sMkpC~ffLeg~CRF~enCRfSHG~~ 164 (486)
T KOG2185|consen 139 SMKPCKFFLEGRCRFGENCRFSHGLD 164 (486)
T ss_pred hhccchHhhccccccCcccccccCcc
Confidence 34569999999999999999999963
No 49
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=96.11 E-value=0.002 Score=60.27 Aligned_cols=25 Identities=44% Similarity=1.015 Sum_probs=22.1
Q ss_pred ccccccccccCCCCCCCCCceEeccc
Q 022898 33 KSKPCTKFFSTAGCPFGESCHFLHYF 58 (290)
Q Consensus 33 Kt~lC~~~~~~g~C~~G~~C~F~H~~ 58 (290)
-+++|+||+. |.|+|+++|+|.|++
T Consensus 139 sMkpC~ffLe-g~CRF~enCRfSHG~ 163 (486)
T KOG2185|consen 139 SMKPCKFFLE-GRCRFGENCRFSHGL 163 (486)
T ss_pred hhccchHhhc-cccccCcccccccCc
Confidence 3689999884 699999999999996
No 50
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=96.07 E-value=0.0032 Score=33.39 Aligned_cols=19 Identities=37% Similarity=0.775 Sum_probs=15.5
Q ss_pred cccccccCCCCCCCCCceEecc
Q 022898 36 PCTKFFSTAGCPFGESCHFLHY 57 (290)
Q Consensus 36 lC~~~~~~g~C~~G~~C~F~H~ 57 (290)
+|++|. .|+++++|.|.|.
T Consensus 1 ~Ck~~~---~C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGP---NCTNGDNCPFSHP 19 (19)
T ss_pred CCcCcC---CCCCCCcCccCCc
Confidence 587554 4999999999994
No 51
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=96.01 E-value=0.0034 Score=57.35 Aligned_cols=26 Identities=27% Similarity=0.703 Sum_probs=22.4
Q ss_pred cCCCCCCCCCCCCCCCcCCCChhhhcc
Q 022898 261 LCGNFAKGSCTFGDRCHFAHGAAELRK 287 (290)
Q Consensus 261 ~C~~~~~g~C~~g~~C~f~Hg~~el~~ 287 (290)
-|-.+.+|.|.. ++|+|+|+-.+|+.
T Consensus 73 aC~Ds~kgrCsR-~nCkylHpp~hlkd 98 (331)
T KOG2494|consen 73 ACFDSQKGRCSR-ENCKYLHPPQHLKD 98 (331)
T ss_pred EEeccccCccCc-ccceecCCChhhhh
Confidence 499999999995 57999999988864
No 52
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=95.93 E-value=0.0084 Score=62.26 Aligned_cols=69 Identities=19% Similarity=0.374 Sum_probs=57.5
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCc-eeeccCCCCCCcceeEEcC-CHHHHHHHHHHHHHHHHhcCCC
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAK-LSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGPA 238 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~-i~v~~~~~~~~~r~v~i~G-~~~~i~~A~~~I~~~i~~~~~~ 238 (290)
-....+.||.+.++.|||.||.+|+.|.+++|+. |.|.+. -.|.|.+ +.+.++.|..+|.+++.....+
T Consensus 684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd------g~V~I~a~d~~~i~~A~~~I~~l~~~~~vG 754 (891)
T PLN00207 684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD------GTVKITAKDLSSLEKSKAIISSLTMVPTVG 754 (891)
T ss_pred CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC------eeEEEEeCCHHHHHHHHHHHHHHhcCcCCC
Confidence 4567899999999999999999999999999999 888762 3445555 8899999999999998765443
No 53
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=95.74 E-value=0.014 Score=58.32 Aligned_cols=69 Identities=23% Similarity=0.392 Sum_probs=58.2
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcC-CHHHHHHHHHHHHHHHHhcCCC
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIGPA 238 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G-~~~~i~~A~~~I~~~i~~~~~~ 238 (290)
-.-..+.|+.+.+.-+||+||.+|+.|.+.+|++|+|.+. ..|.|.+ +.+.+..|...|.++..+.+.+
T Consensus 551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idiedd------Gtv~i~~s~~~~~~~ak~~I~~i~~e~evg 620 (692)
T COG1185 551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD------GTVKIAASDGESAKKAKERIEAITREVEVG 620 (692)
T ss_pred CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCC------CcEEEEecchHHHHHHHHHHHHHHhhcccc
Confidence 4557789999999999999999999999999999999732 2455555 4588999999999999888775
No 54
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=95.37 E-value=0.032 Score=50.76 Aligned_cols=67 Identities=16% Similarity=0.305 Sum_probs=57.4
Q ss_pred CCCCceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHH
Q 022898 161 FGASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRE 230 (290)
Q Consensus 161 ~~~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~ 230 (290)
++...+..+.||...|+.|+|++|..||.++..|...|.....+ .+-+|.++|-.+.+++|...|..
T Consensus 22 ~p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~---eePiF~vTg~~edv~~aRrei~s 88 (394)
T KOG2113|consen 22 IGQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG---EEPIFPVTGRHEDVRRARREIPS 88 (394)
T ss_pred CCCccceeeecCcccceeecccCccccchhhhhhcceeccCCCC---CCCcceeccCchhHHHHhhcCcc
Confidence 34577889999999999999999999999999999999875443 34789999999999999877755
No 55
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=95.29 E-value=0.0077 Score=51.30 Aligned_cols=28 Identities=32% Similarity=0.772 Sum_probs=24.8
Q ss_pred ccccccccccccCCCCCCCCCceEeccc
Q 022898 31 GSKSKPCTKFFSTAGCPFGESCHFLHYF 58 (290)
Q Consensus 31 ~~Kt~lC~~~~~~g~C~~G~~C~F~H~~ 58 (290)
-|.-..|+-|..+|.|-|||.|+|+|..
T Consensus 138 D~qpdVCKdyk~TGYCGYGDsCKflH~R 165 (259)
T COG5152 138 DTQPDVCKDYKETGYCGYGDSCKFLHDR 165 (259)
T ss_pred ecCcccccchhhcccccCCchhhhhhhh
Confidence 3556799999999999999999999974
No 56
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=95.18 E-value=0.011 Score=56.97 Aligned_cols=25 Identities=40% Similarity=1.030 Sum_probs=20.9
Q ss_pred ccccccccccc--ccCCCCCccccccc
Q 022898 96 KSRMCNRLNSA--EGCKFGDKCHFAHG 120 (290)
Q Consensus 96 ktr~C~~~~~~--g~C~~G~~C~f~H~ 120 (290)
+-++|.-.-+. ..|.||++|+|.|.
T Consensus 75 ~n~LCPsli~g~~~~C~f~d~Crf~HD 101 (614)
T KOG2333|consen 75 QNRLCPSLIQGDISKCSFGDNCRFVHD 101 (614)
T ss_pred hhccChHhhcCCCccCccccccccccc
Confidence 56789877666 69999999999994
No 57
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=94.73 E-value=0.073 Score=45.52 Aligned_cols=55 Identities=31% Similarity=0.466 Sum_probs=48.2
Q ss_pred cceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898 176 AGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP 237 (290)
Q Consensus 176 vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~ 237 (290)
.|-|||++|.+-+.|.+.|++.|.|.+ ..|.|-|.+++++.|...|..++.-...
T Consensus 113 kgRIIG~~GkTr~~IE~lt~~~I~V~g-------~tVaiiG~~~~v~iAr~AVemli~G~~h 167 (194)
T COG1094 113 KGRIIGREGKTRRAIEELTGVYISVYG-------KTVAIIGGFEQVEIAREAVEMLINGAPH 167 (194)
T ss_pred hceeeCCCchHHHHHHHHhCCeEEEeC-------cEEEEecChhhhHHHHHHHHHHHcCCCc
Confidence 356999999999999999999999976 3699999999999999999888765543
No 58
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=94.48 E-value=0.017 Score=56.22 Aligned_cols=74 Identities=24% Similarity=0.422 Sum_probs=65.7
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP 237 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~ 237 (290)
.......+|...++.|+|++|..|.+|+..++|+|.+..+..+...+.+.|.+.......|..++.+.+.+.+.
T Consensus 139 pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edee 212 (608)
T KOG2279|consen 139 PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEE 212 (608)
T ss_pred cccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccchhH
Confidence 56677889999999999999999999999999999999887777789999999998888999999888875543
No 59
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=94.44 E-value=0.029 Score=48.76 Aligned_cols=52 Identities=21% Similarity=0.557 Sum_probs=38.5
Q ss_pred ccccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCcccccccccccccccCCCC
Q 022898 33 KSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLNSAEGCKFG 112 (290)
Q Consensus 33 Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~~~g~C~~G 112 (290)
+..+|++|+ +|.|...+.|...|.+.+ . .-..|++|. .|.|. .
T Consensus 232 rkticpkfl-ngrcnkaedcnlsheldp---------------------------------r-ripacryfl-lgkcn-n 274 (377)
T KOG1492|consen 232 RKTICPKFL-NGRCNKAEDCNLSHELDP---------------------------------R-RIPACRYFL-LGKCN-N 274 (377)
T ss_pred ccccChHHh-cCccCchhcCCcccccCc---------------------------------c-ccchhhhhh-hccCC-C
Confidence 456899999 579999999999998721 1 112487664 57887 5
Q ss_pred Ccccccccc
Q 022898 113 DKCHFAHGE 121 (290)
Q Consensus 113 ~~C~f~H~~ 121 (290)
..|+|.|..
T Consensus 275 pncryvhih 283 (377)
T KOG1492|consen 275 PNCRYVHIH 283 (377)
T ss_pred CCceEEEEe
Confidence 799999954
No 60
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=94.06 E-value=0.022 Score=48.62 Aligned_cols=31 Identities=26% Similarity=0.860 Sum_probs=25.9
Q ss_pred cccccccCCCCC-CCCCCCCCCCcCCCChhhh
Q 022898 255 SNFKTKLCGNFA-KGSCTFGDRCHFAHGAAEL 285 (290)
Q Consensus 255 ~~~k~~~C~~~~-~g~C~~g~~C~f~Hg~~el 285 (290)
-.|....|..|. +|+|-||+.|.|.|.-++.
T Consensus 137 iD~qpdVCKdyk~TGYCGYGDsCKflH~R~D~ 168 (259)
T COG5152 137 IDTQPDVCKDYKETGYCGYGDSCKFLHDRSDF 168 (259)
T ss_pred eecCcccccchhhcccccCCchhhhhhhhhhh
Confidence 345566799998 9999999999999987654
No 61
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=93.62 E-value=0.073 Score=51.93 Aligned_cols=74 Identities=26% Similarity=0.395 Sum_probs=61.9
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCCC
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPA 238 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~~ 238 (290)
.....+.|+...|..|||++|++|+.+...++++|.+.+.+.+ .++.-.++|-+.++..|...+.+++.+.+..
T Consensus 67 ~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g-~e~~~~~~~~p~~v~~a~a~~~~~~~~~~pv 140 (608)
T KOG2279|consen 67 DIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG-DERVLLISGFPVQVCKAKAAIHQILTENTPV 140 (608)
T ss_pred heeeeEeecccceeeeeccccCCcchhhcccccceecCcccCC-cccchhhccCCCCCChHHHHHHHHHhcCCcc
Confidence 5678899999999999999999999999999999999754333 3456666778888889999999998877665
No 62
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=93.22 E-value=0.087 Score=54.05 Aligned_cols=66 Identities=21% Similarity=0.363 Sum_probs=53.4
Q ss_pred ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcC-CHHHHHHHHHHHHHHHHhcC
Q 022898 165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIG 236 (290)
Q Consensus 165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G-~~~~i~~A~~~I~~~i~~~~ 236 (290)
....+.|+.+.++.+||.||.+|+.|.+++|+.|.+.+. -.+.|.+ +.+.++.|..+|..+.....
T Consensus 554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~------G~v~i~~~~~~~~~~a~~~I~~~~~~~~ 620 (693)
T PRK11824 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD------GTVKIAATDGEAAEAAKERIEGITAEPE 620 (693)
T ss_pred hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC------ceEEEEcccHHHHHHHHHHHHHhcccCc
Confidence 445778899999999999999999999999999888542 2345555 78899999999998886533
No 63
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=93.08 E-value=0.027 Score=50.83 Aligned_cols=36 Identities=39% Similarity=0.751 Sum_probs=31.2
Q ss_pred CCcccccccCCCCCCCCCCCCCCCcCCCChhhhccc
Q 022898 253 LSSNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKT 288 (290)
Q Consensus 253 ~~~~~k~~~C~~~~~g~C~~g~~C~f~Hg~~el~~~ 288 (290)
.....|+.+|-+|..|.|.-|+.|.|+|+...-|+.
T Consensus 86 ~gvDPKSvvCafFk~g~C~KG~kCKFsHdl~~~~k~ 121 (343)
T KOG1763|consen 86 KGVDPKSVVCAFFKQGTCTKGDKCKFSHDLAVERKK 121 (343)
T ss_pred cCCCchHHHHHHHhccCCCCCCcccccchHHHhhhc
Confidence 335679999999999999999999999999877653
No 64
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=92.95 E-value=0.22 Score=44.19 Aligned_cols=67 Identities=15% Similarity=0.227 Sum_probs=53.7
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcC-CHHHHHHHHHHHHHHHHhcC
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEG-SFEQIKQASAMVRELIVRIG 236 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G-~~~~i~~A~~~I~~~i~~~~ 236 (290)
..-..+.||.++++.+||++|..|+.|.+.+++.|.|..+ -.|.|.+ +.+.+..|..+|...-.++.
T Consensus 144 ~~G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N------G~VwI~~~~~~~~~~a~~~I~~~e~~~~ 211 (235)
T PRK04163 144 EGGTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN------GRIWIKGPDEEDEEIAIEAIKKIEREAH 211 (235)
T ss_pred CCCEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC------cEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence 3457799999999999999999999999999999999653 3455555 66688888888877655543
No 65
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=92.45 E-value=0.088 Score=46.75 Aligned_cols=29 Identities=31% Similarity=0.913 Sum_probs=26.2
Q ss_pred CcccccccCCCCCCCCCCCCCCCcCCCCh
Q 022898 254 SSNFKTKLCGNFAKGSCTFGDRCHFAHGA 282 (290)
Q Consensus 254 ~~~~k~~~C~~~~~g~C~~g~~C~f~Hg~ 282 (290)
...++...|..|..+.|.+|..|.|.|-.
T Consensus 147 vT~~rea~C~~~e~~~C~rG~~CnFmH~k 175 (260)
T KOG2202|consen 147 VTDFREAICGQFERTECSRGGACNFMHVK 175 (260)
T ss_pred cCchhhhhhcccccccCCCCCcCcchhhh
Confidence 37789999999998899999999999954
No 66
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.32 E-value=0.16 Score=47.51 Aligned_cols=28 Identities=21% Similarity=0.267 Sum_probs=23.4
Q ss_pred cccccccCCCCCCCCCCCCCCCcCCCCh
Q 022898 255 SNFKTKLCGNFAKGSCTFGDRCHFAHGA 282 (290)
Q Consensus 255 ~~~k~~~C~~~~~g~C~~g~~C~f~Hg~ 282 (290)
..-++++|.+-..|.|.+|..|.++|+.
T Consensus 89 ~~s~~~~~~~~~~~~~~~g~~~~~~~~~ 116 (344)
T KOG1039|consen 89 EPSSTQENPYSNHGQCRFGNGDVTLNGN 116 (344)
T ss_pred cccccccCccccccccccCCcccccccc
Confidence 4446788999889999999999999963
No 67
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=92.25 E-value=0.2 Score=43.16 Aligned_cols=40 Identities=33% Similarity=0.473 Sum_probs=33.2
Q ss_pred CceEEEEecc------cccceeeCCCCCchhhHHHhhCCceeeccC
Q 022898 164 SATAKISVDA------SLAGAIIGKGGVNSKQICRQTGAKLSIRDH 203 (290)
Q Consensus 164 ~~t~~i~VP~------~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~ 203 (290)
..+-++.||- .+||+|||..|++.+++...|+|+|-|...
T Consensus 147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 4455566653 689999999999999999999999999654
No 68
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=92.05 E-value=0.056 Score=56.92 Aligned_cols=75 Identities=17% Similarity=0.177 Sum_probs=62.2
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeecc-CCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCCC
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD-HEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPA 238 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~-~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~~ 238 (290)
.....+.+|.-.+.-|||+||+||..++..+|+.|.|.. .+.+..+|.+.+.|.++.++.|-.+|.-.+...+..
T Consensus 1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i~Dpdv~ 1414 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPIIDPDVS 1414 (2131)
T ss_pred ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccceeecCCcC
Confidence 455567778777888999999999999999999999977 455567999999999999999988887766655544
No 69
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=91.12 E-value=0.16 Score=46.23 Aligned_cols=55 Identities=27% Similarity=0.619 Sum_probs=41.8
Q ss_pred cccccccccCCCCCCCCCceEecccCCCchhhhhhccCCCCCCCCCCCCCCCCCCCCCCCccccccccccc--ccccCCC
Q 022898 34 SKPCTKFFSTAGCPFGESCHFLHYFPGGYNAVAQMMNLPQAVPAPSRNMAVPPPASNGPTVVKSRMCNRLN--SAEGCKF 111 (290)
Q Consensus 34 t~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~~~~~~~g~~~~~~~~~~~~~s~~~~~~~~~ktr~C~~~~--~~g~C~~ 111 (290)
+-.|++|..-|.|..|..|.+.|.+|. ...-.|..|- +.+.|++
T Consensus 134 ~~~c~~Fs~~G~cs~g~~c~~~h~dp~----------------------------------~~~~~~~~~~~~~~~f~p~ 179 (285)
T COG5084 134 GPPCRSFSLKGSCSSGPSCGYSHIDPD----------------------------------SFAGNCDQYSGATYGFCPL 179 (285)
T ss_pred CCCcccccccceeccCCCCCccccCcc----------------------------------cccccccccCcccccccCC
Confidence 678999977899999999999997622 1222343322 3789999
Q ss_pred CCccccccccc
Q 022898 112 GDKCHFAHGEW 122 (290)
Q Consensus 112 G~~C~f~H~~~ 122 (290)
|..|+|-|...
T Consensus 180 g~~c~~~H~~~ 190 (285)
T COG5084 180 GASCKFSHTLK 190 (285)
T ss_pred CCccccccccc
Confidence 99999999764
No 70
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=91.05 E-value=0.051 Score=47.59 Aligned_cols=34 Identities=47% Similarity=0.835 Sum_probs=30.5
Q ss_pred cccccccCCCCCCCCCCCCCCCcCCCChhhhccc
Q 022898 255 SNFKTKLCGNFAKGSCTFGDRCHFAHGAAELRKT 288 (290)
Q Consensus 255 ~~~k~~~C~~~~~g~C~~g~~C~f~Hg~~el~~~ 288 (290)
...|+..|-.|..+.|-.|+.|.|+|+.+|.|+.
T Consensus 81 vdpK~~vcalF~~~~c~kg~~ckF~h~~ee~r~~ 114 (299)
T COG5252 81 VDPKTVVCALFLNKTCAKGDACKFAHGKEEARKT 114 (299)
T ss_pred cCchhHHHHHhccCccccCchhhhhcchHHHhhh
Confidence 4558999999999999999999999999998864
No 71
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.62 E-value=0.1 Score=47.31 Aligned_cols=35 Identities=31% Similarity=0.686 Sum_probs=27.9
Q ss_pred CccccccccccccCCCCCCCCCceEecccCCCchhh
Q 022898 30 VGSKSKPCTKFFSTAGCPFGESCHFLHYFPGGYNAV 65 (290)
Q Consensus 30 ~~~Kt~lC~~~~~~g~C~~G~~C~F~H~~~~~~~~~ 65 (290)
.-|---+|+-|-.+|.|-||+.|.|+|.. .+|.++
T Consensus 182 ~d~qpDicKdykeTgycg~gdSckFlh~r-~DyK~G 216 (313)
T KOG1813|consen 182 IDYQPDICKDYKETGYCGYGDSCKFLHDR-SDYKAG 216 (313)
T ss_pred eecCchhhhhhHhhCcccccchhhhhhhh-hhcccc
Confidence 33556799999999999999999999985 444433
No 72
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=89.32 E-value=0.39 Score=39.23 Aligned_cols=37 Identities=27% Similarity=0.400 Sum_probs=33.5
Q ss_pred ceEEEEecccccceeeCCCCCchhhHHHhhCCceeec
Q 022898 165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR 201 (290)
Q Consensus 165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~ 201 (290)
..+.+.|+...+|+.||++|++|+.|++..|-+|.|-
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVv 68 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELV 68 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEE
Confidence 5677888999999999999999999999999998883
No 73
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=89.08 E-value=0.63 Score=42.95 Aligned_cols=71 Identities=21% Similarity=0.180 Sum_probs=56.9
Q ss_pred ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcC
Q 022898 165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIG 236 (290)
Q Consensus 165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~ 236 (290)
.+..+.|++...+.|||+.|.+-+.|.+++++.|.+..+..+. ..++.+.+..++|.+|...|.-+|.+..
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~-~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNK-EEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCc-ceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 4556889999999999999999999999999999996543332 2344445588999999999988887665
No 74
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=88.34 E-value=0.52 Score=42.12 Aligned_cols=39 Identities=33% Similarity=0.524 Sum_probs=34.0
Q ss_pred CceEEEEeccc------ccceeeCCCCCchhhHHHhhCCceeecc
Q 022898 164 SATAKISVDAS------LAGAIIGKGGVNSKQICRQTGAKLSIRD 202 (290)
Q Consensus 164 ~~t~~i~VP~~------~vg~iIGkgG~~Ik~i~~~sga~i~v~~ 202 (290)
..+.+|.||-. +||-|||..|.++++++++|+++|-|..
T Consensus 91 k~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrG 135 (259)
T KOG1588|consen 91 KLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRG 135 (259)
T ss_pred eEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEec
Confidence 56677888764 8999999999999999999999999953
No 75
>PRK00468 hypothetical protein; Provisional
Probab=87.70 E-value=0.57 Score=34.03 Aligned_cols=30 Identities=30% Similarity=0.353 Sum_probs=26.3
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHh
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQ 193 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~ 193 (290)
....++.+..+-+|-||||+|.+|+.|+.-
T Consensus 29 ~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 29 SVILELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred eEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence 456778899999999999999999999874
No 76
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=87.50 E-value=0.59 Score=34.02 Aligned_cols=30 Identities=27% Similarity=0.365 Sum_probs=26.6
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHh
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQ 193 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~ 193 (290)
....++.|..+-+|-||||+|.+|+.|+..
T Consensus 29 ~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 29 TVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred eEEEEEEECcccccceecCCChhHHHHHHH
Confidence 456888999999999999999999999863
No 77
>PRK01064 hypothetical protein; Provisional
Probab=87.39 E-value=0.71 Score=33.80 Aligned_cols=30 Identities=30% Similarity=0.348 Sum_probs=26.4
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHh
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQ 193 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~ 193 (290)
....++.|..+-.|.+|||+|.+|+.|+.-
T Consensus 29 ~~~~~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 29 TIIYELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred EEEEEEEECcccceEEECCCCccHHHHHHH
Confidence 456778889999999999999999999874
No 78
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.38 E-value=0.18 Score=45.76 Aligned_cols=33 Identities=24% Similarity=0.841 Sum_probs=27.7
Q ss_pred CCcccccccCCCCC-CCCCCCCCCCcCCCChhhh
Q 022898 253 LSSNFKTKLCGNFA-KGSCTFGDRCHFAHGAAEL 285 (290)
Q Consensus 253 ~~~~~k~~~C~~~~-~g~C~~g~~C~f~Hg~~el 285 (290)
....|...+|..|. +|+|-||+.|.|.|--...
T Consensus 180 ~~~d~qpDicKdykeTgycg~gdSckFlh~r~Dy 213 (313)
T KOG1813|consen 180 ERIDYQPDICKDYKETGYCGYGDSCKFLHDRSDY 213 (313)
T ss_pred ceeecCchhhhhhHhhCcccccchhhhhhhhhhc
Confidence 44677788999998 9999999999999976543
No 79
>PRK02821 hypothetical protein; Provisional
Probab=87.37 E-value=0.59 Score=34.12 Aligned_cols=33 Identities=24% Similarity=0.422 Sum_probs=28.0
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCC
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGA 196 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga 196 (290)
.....+.|.++-+|-||||+|.+|+.|+.--.+
T Consensus 30 ~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 30 GRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred cEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 456788899999999999999999999975443
No 80
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=86.96 E-value=1.7 Score=43.04 Aligned_cols=54 Identities=26% Similarity=0.487 Sum_probs=40.3
Q ss_pred CceEEEEeccccc-ceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHH
Q 022898 164 SATAKISVDASLA-GAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQ 223 (290)
Q Consensus 164 ~~t~~i~VP~~~v-g~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~ 223 (290)
.....|.+|++-+ |-|||+.|.||+.+...||+-|-|.+. ...|.|++ ++.|++
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt-----p~~v~ls~-fdp~rr 257 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT-----PEAVILSG-FDPVRR 257 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC-----CCeEEecC-CchHHH
Confidence 4455688899555 889999999999999999999999763 22455555 555533
No 81
>PRK12704 phosphodiesterase; Provisional
Probab=86.73 E-value=1.9 Score=42.80 Aligned_cols=64 Identities=27% Similarity=0.446 Sum_probs=45.0
Q ss_pred CceEEEEeccccc-ceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHH--HHHHHHHHHHH
Q 022898 164 SATAKISVDASLA-GAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIK--QASAMVRELIV 233 (290)
Q Consensus 164 ~~t~~i~VP~~~v-g~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~--~A~~~I~~~i~ 233 (290)
.....|.+|++-+ |-|||+.|.||+-+...||+-|-|.+. .-.|.|++ ++.++ .|...+...+.
T Consensus 209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt-----p~~v~ls~-~~~~rre~a~~~l~~l~~ 275 (520)
T PRK12704 209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT-----PEAVILSG-FDPIRREIARLALEKLVQ 275 (520)
T ss_pred hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC-----CCeEEEec-CChhhHHHHHHHHHHHHh
Confidence 3445678898555 889999999999999999999999763 23455666 33443 55555544443
No 82
>PRK00106 hypothetical protein; Provisional
Probab=86.21 E-value=2.2 Score=42.46 Aligned_cols=54 Identities=26% Similarity=0.456 Sum_probs=40.4
Q ss_pred CceEEEEeccccc-ceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHH
Q 022898 164 SATAKISVDASLA-GAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQ 223 (290)
Q Consensus 164 ~~t~~i~VP~~~v-g~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~ 223 (290)
.....|.+|++-+ |-|||+-|.||+-+...||+-|-|.+. ...|.|++ |+.|++
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt-----p~~v~lS~-fdpvRR 278 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDT-----PEVVVLSG-FDPIRR 278 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCC-----CCeEEEeC-CChHHH
Confidence 4455688899555 889999999999999999999999753 23455665 444443
No 83
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=85.80 E-value=0.59 Score=38.13 Aligned_cols=38 Identities=24% Similarity=0.281 Sum_probs=33.4
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeec
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR 201 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~ 201 (290)
.....+.|+.+..+.+|||+|.||+.++..++-.+.|.
T Consensus 98 ~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 98 DKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred cEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 34567889999999999999999999999999888764
No 84
>PF10650 zf-C3H1: Putative zinc-finger domain; InterPro: IPR019607 This domain is conserved in fungi and might be a zinc-finger domain as it contains three conserved Cs and an H in the C-x8-C-x5-C-x3-H conformation typical of a zinc-finger.
Probab=84.76 E-value=0.52 Score=26.11 Aligned_cols=22 Identities=23% Similarity=0.628 Sum_probs=17.9
Q ss_pred ccccccccCCCCCCCCCceEecc
Q 022898 35 KPCTKFFSTAGCPFGESCHFLHY 57 (290)
Q Consensus 35 ~lC~~~~~~g~C~~G~~C~F~H~ 57 (290)
.||.|-+.+|.|. -+.|.|.|.
T Consensus 1 ~lC~yEl~Gg~Cn-d~~C~~QHf 22 (23)
T PF10650_consen 1 PLCPYELTGGVCN-DPDCEFQHF 22 (23)
T ss_pred CCCccccCCCeeC-CCCCCcccc
Confidence 3899888888995 469999994
No 85
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=83.99 E-value=1 Score=32.14 Aligned_cols=35 Identities=34% Similarity=0.537 Sum_probs=27.1
Q ss_pred EEEEecccc-----cceeeCCCCCchhhHHHhh-CCceeec
Q 022898 167 AKISVDASL-----AGAIIGKGGVNSKQICRQT-GAKLSIR 201 (290)
Q Consensus 167 ~~i~VP~~~-----vg~iIGkgG~~Ik~i~~~s-ga~i~v~ 201 (290)
..+.|-... +|+.||++|..|+.|.+.. |.+|.|-
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence 455555555 8999999999999999999 8888873
No 86
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=82.74 E-value=1.1 Score=36.52 Aligned_cols=36 Identities=31% Similarity=0.441 Sum_probs=32.2
Q ss_pred eEEEEecccccceeeCCCCCchhhHHHhhCCceeec
Q 022898 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR 201 (290)
Q Consensus 166 t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~ 201 (290)
..-+.|....+|+.||++|++|+.+++..|-+|.|-
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVV 69 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELI 69 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEE
Confidence 566778889999999999999999999999888883
No 87
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=82.04 E-value=0.89 Score=42.19 Aligned_cols=25 Identities=32% Similarity=0.860 Sum_probs=21.9
Q ss_pred cccCCCCCCCCCCCCCCCcCCCChh
Q 022898 259 TKLCGNFAKGSCTFGDRCHFAHGAA 283 (290)
Q Consensus 259 ~~~C~~~~~g~C~~g~~C~f~Hg~~ 283 (290)
..+|.+|..|+|+.|+.|.|.|-.-
T Consensus 161 p~Icsf~v~geckRG~ec~yrhEkp 185 (377)
T KOG0153|consen 161 PHICSFFVKGECKRGAECPYRHEKP 185 (377)
T ss_pred CccccceeeccccccccccccccCC
Confidence 3479999999999999999999653
No 88
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=81.70 E-value=2.3 Score=29.06 Aligned_cols=33 Identities=27% Similarity=0.336 Sum_probs=25.6
Q ss_pred eEEEEecccccceeeCCCCCchhhHHHhhCCce
Q 022898 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKL 198 (290)
Q Consensus 166 t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i 198 (290)
...+.+.....+.+||+.|.+++.++..++..+
T Consensus 26 ~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 26 EIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 444555555689999999999999999887554
No 89
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=81.51 E-value=1 Score=38.72 Aligned_cols=59 Identities=31% Similarity=0.469 Sum_probs=50.7
Q ss_pred ccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCCC
Q 022898 173 ASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPA 238 (290)
Q Consensus 173 ~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~~ 238 (290)
...+|-|+||+|.+-..|...|.++|.+.+ ..|.|-|.++.++.|...|..+|.-++++
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad-------~kIHiLG~~~niriAR~avcsLIlGsppg 235 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD-------SKIHILGAFQNIRIARDAVCSLILGSPPG 235 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecC-------ceEEEeecchhhHHHHHhhHhhhccCCch
Confidence 455678999999999999999999999865 36899999999999999999988766553
No 90
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.40 E-value=0.67 Score=43.41 Aligned_cols=24 Identities=29% Similarity=0.851 Sum_probs=21.5
Q ss_pred ccccccccCCCCCCCCCceEecccC
Q 022898 35 KPCTKFFSTAGCPFGESCHFLHYFP 59 (290)
Q Consensus 35 ~lC~~~~~~g~C~~G~~C~F~H~~~ 59 (290)
.+|+||. .|.|+||+.|+|.|.++
T Consensus 9 tic~~~~-~g~c~~g~~cr~~h~~~ 32 (344)
T KOG1039|consen 9 TICKYYQ-KGNCKFGDLCRLSHSLP 32 (344)
T ss_pred hhhhhcc-cccccccceeeeeccCc
Confidence 7998777 57999999999999987
No 91
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=81.13 E-value=3.3 Score=35.53 Aligned_cols=63 Identities=22% Similarity=0.351 Sum_probs=49.1
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEc-----CCHHHHHHHHHHHHHH
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELE-----GSFEQIKQASAMVREL 231 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~-----G~~~~i~~A~~~I~~~ 231 (290)
..+..+.||.+.++++||+.|..-+.|.+.++.++.|... ...|.|. .+|-.+..|...|..+
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~-----~~~V~i~~~~~t~Dp~~~~ka~d~VkAI 74 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTEDPLALLKARDVVKAI 74 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCChHHHHHHHHHHHHH
Confidence 4566799999999999999999999999999999999643 2233332 3677777887777655
No 92
>PRK12705 hypothetical protein; Provisional
Probab=78.27 E-value=3.2 Score=41.06 Aligned_cols=41 Identities=27% Similarity=0.412 Sum_probs=34.2
Q ss_pred CceEEEEeccccc-ceeeCCCCCchhhHHHhhCCceeeccCC
Q 022898 164 SATAKISVDASLA-GAIIGKGGVNSKQICRQTGAKLSIRDHE 204 (290)
Q Consensus 164 ~~t~~i~VP~~~v-g~iIGkgG~~Ik~i~~~sga~i~v~~~~ 204 (290)
.....+.+|++.+ |-|||+.|.||+.+...||..|-|.+..
T Consensus 197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp 238 (508)
T PRK12705 197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP 238 (508)
T ss_pred heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc
Confidence 3445678888666 8899999999999999999999997653
No 93
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=78.03 E-value=1.5 Score=35.87 Aligned_cols=38 Identities=26% Similarity=0.307 Sum_probs=33.6
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeec
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR 201 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~ 201 (290)
.....+.|+.+..+..|||+|.||+-..+.++-.+.|.
T Consensus 99 ~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 99 KKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred CEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 45677889999999999999999999999999888764
No 94
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=76.78 E-value=3.9 Score=42.52 Aligned_cols=72 Identities=19% Similarity=0.253 Sum_probs=60.1
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCC
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGP 237 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~ 237 (290)
...+.+.+-......|+||+|.+|..|.+.+.+.|.+.. .+.....+.+.+....+..|...+...+.+...
T Consensus 346 n~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~--~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n 417 (753)
T KOG2208|consen 346 NENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK--QGSNNKKVVITGVSANDEKAVEDVEKIIAEILN 417 (753)
T ss_pred ceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc--ccCCCCCeEEeccccchhHHHHHHHHHHHhhhc
Confidence 567788889999999999999999999999999999976 334566788888888888888888777766544
No 95
>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=76.77 E-value=2.3 Score=39.96 Aligned_cols=39 Identities=26% Similarity=0.430 Sum_probs=36.1
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeecc
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 202 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~ 202 (290)
.....+.||.+..+..|||+|.|++-.+..+|.+|.|..
T Consensus 300 ~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 300 KHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred CcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 467889999999999999999999999999999999954
No 96
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=76.43 E-value=0.82 Score=33.01 Aligned_cols=35 Identities=34% Similarity=0.451 Sum_probs=29.6
Q ss_pred ceEEEEecccccceeeCCCCCchhhHHHhhCCcee
Q 022898 165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLS 199 (290)
Q Consensus 165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~ 199 (290)
....+.+-.+..+.|||++|++|+.|.......++
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 45778888999999999999999999987766654
No 97
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=76.39 E-value=1.1 Score=40.04 Aligned_cols=27 Identities=30% Similarity=0.700 Sum_probs=23.6
Q ss_pred CccccccccccccCCCCCCCCCceEecc
Q 022898 30 VGSKSKPCTKFFSTAGCPFGESCHFLHY 57 (290)
Q Consensus 30 ~~~Kt~lC~~~~~~g~C~~G~~C~F~H~ 57 (290)
..++...|..|..+ .|++|..|+|.|-
T Consensus 148 T~~rea~C~~~e~~-~C~rG~~CnFmH~ 174 (260)
T KOG2202|consen 148 TDFREAICGQFERT-ECSRGGACNFMHV 174 (260)
T ss_pred Cchhhhhhcccccc-cCCCCCcCcchhh
Confidence 45678899999876 9999999999995
No 98
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=75.96 E-value=3 Score=30.67 Aligned_cols=35 Identities=11% Similarity=0.316 Sum_probs=28.7
Q ss_pred ceEEEEecccccceeeCCCCCchhhHHHhhCCcee
Q 022898 165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLS 199 (290)
Q Consensus 165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~ 199 (290)
...++.|-....|+|||++|.+|+.+++.-.....
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~ 64 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFN 64 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhC
Confidence 34788899999999999999999999886544443
No 99
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=75.59 E-value=2.8 Score=39.70 Aligned_cols=39 Identities=21% Similarity=0.354 Sum_probs=36.1
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeecc
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 202 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~ 202 (290)
.....+.||.+..++.|||+|.|++-....+|.+|.|..
T Consensus 307 ~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s 345 (374)
T PRK12328 307 EKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNE 345 (374)
T ss_pred CcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEE
Confidence 467889999999999999999999999999999999954
No 100
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=75.46 E-value=3.9 Score=29.48 Aligned_cols=36 Identities=19% Similarity=0.301 Sum_probs=28.7
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCcee
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLS 199 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~ 199 (290)
.....+.|..+..|.+|||.|.++..||--....+.
T Consensus 23 ~~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 23 GDTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred CCEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 345678888899999999999999999876554433
No 101
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=74.89 E-value=2.2 Score=36.69 Aligned_cols=37 Identities=30% Similarity=0.402 Sum_probs=34.5
Q ss_pred eEEEEecccccceeeCCCCCchhhHHHhhCCceeecc
Q 022898 166 TAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 202 (290)
Q Consensus 166 t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~ 202 (290)
...+.||.+..+.+|||+|.|++-+++.||..+.|..
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 6788899999999999999999999999999999854
No 102
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=74.61 E-value=3.3 Score=34.79 Aligned_cols=38 Identities=26% Similarity=0.396 Sum_probs=32.0
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeecc
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 202 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~ 202 (290)
...+-+.|-... |+.|||+|.+|+.+++..|-.|.|-.
T Consensus 60 ddrvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 60 DDLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred CCEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 445667777777 99999999999999999999998843
No 103
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=74.23 E-value=1 Score=32.14 Aligned_cols=33 Identities=27% Similarity=0.364 Sum_probs=28.1
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCC
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGA 196 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga 196 (290)
.....+.+..+..|.||||.|.+++.||.-...
T Consensus 28 ~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 28 GDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred ceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 567888999999999999999999999875443
No 104
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=72.56 E-value=1.7 Score=42.08 Aligned_cols=25 Identities=28% Similarity=0.587 Sum_probs=18.4
Q ss_pred cccccccccccccCCCCCcccccccc
Q 022898 96 KSRMCNRLNSAEGCKFGDKCHFAHGE 121 (290)
Q Consensus 96 ktr~C~~~~~~g~C~~G~~C~f~H~~ 121 (290)
..++|.+|.+...|. -.+|-|-|..
T Consensus 60 ~e~~CYwe~~p~gC~-k~~CgfRH~~ 84 (667)
T KOG4791|consen 60 SEIPCYWENQPTGCQ-KLNCGFRHNR 84 (667)
T ss_pred CcccceeecCCCccC-CCccccccCC
Confidence 567887666665687 5799999944
No 105
>PRK13764 ATPase; Provisional
Probab=71.07 E-value=3.7 Score=41.51 Aligned_cols=42 Identities=26% Similarity=0.416 Sum_probs=37.7
Q ss_pred CCceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCC
Q 022898 163 ASATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHE 204 (290)
Q Consensus 163 ~~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~ 204 (290)
....+.+.||...++.+|||+|.+|+.|.+..|..|.|...+
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~ 520 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLD 520 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcc
Confidence 367788999999999999999999999999999999996543
No 106
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=69.89 E-value=6.4 Score=39.18 Aligned_cols=67 Identities=21% Similarity=0.311 Sum_probs=53.1
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEE-cCCHHHHHHHHHHHHHHHHhcCC
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIEL-EGSFEQIKQASAMVRELIVRIGP 237 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i-~G~~~~i~~A~~~I~~~i~~~~~ 237 (290)
-....+.|+++..-.+||.+|...|.|..+||+.-+|.+ ..|.| .-++.+.+.|++.|..++.....
T Consensus 596 P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vDe-------~t~~i~A~~~~am~~Ak~~I~~i~~~~~~ 663 (760)
T KOG1067|consen 596 PVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVDE-------GTFSIFAPTQAAMEEAKEFIDGIIKDDQV 663 (760)
T ss_pred ceeeEEeecchhhheeecCccceeeeEeeeccceeeecC-------ceEEEEecCHHHHHHHHHHHHHHhcCccc
Confidence 345678889999999999999999999999997766643 23333 34788999999999999876444
No 107
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=67.90 E-value=4 Score=39.81 Aligned_cols=40 Identities=28% Similarity=0.467 Sum_probs=36.3
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccC
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH 203 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~ 203 (290)
.....+.||...++.||||+|.+|+.|....|-.|.|...
T Consensus 485 d~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~ 524 (604)
T COG1855 485 DGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL 524 (604)
T ss_pred CCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence 4567899999999999999999999999999999999544
No 108
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=67.75 E-value=4.9 Score=38.07 Aligned_cols=39 Identities=31% Similarity=0.427 Sum_probs=36.1
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeecc
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 202 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~ 202 (290)
.....+.||.+..+..|||+|.|++-.+..+|..|.|..
T Consensus 302 ~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 302 EKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred CcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 467889999999999999999999999999999999954
No 109
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=67.47 E-value=4.4 Score=39.72 Aligned_cols=39 Identities=28% Similarity=0.363 Sum_probs=35.9
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeecc
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 202 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~ 202 (290)
...+.+.||.+..+..|||+|.||+-.+..+|..|.|..
T Consensus 301 ~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 301 EHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred CCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 457889999999999999999999999999999999954
No 110
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=67.22 E-value=5.3 Score=35.32 Aligned_cols=29 Identities=24% Similarity=0.552 Sum_probs=25.6
Q ss_pred ceEEEEecccccceeeCCCCCchhhHHHh
Q 022898 165 ATAKISVDASLAGAIIGKGGVNSKQICRQ 193 (290)
Q Consensus 165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~ 193 (290)
..++|.|-...-|+|||++|++|..|+..
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 45788999999999999999999998873
No 111
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=66.01 E-value=4.9 Score=38.90 Aligned_cols=39 Identities=33% Similarity=0.435 Sum_probs=35.9
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeecc
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 202 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~ 202 (290)
.....+.||.+..++.|||+|.|++-....+|..|.|..
T Consensus 334 ~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 334 GRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred CcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 456889999999999999999999999999999999964
No 112
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=63.21 E-value=7.4 Score=28.68 Aligned_cols=29 Identities=28% Similarity=0.543 Sum_probs=24.3
Q ss_pred eEEEEecccccceeeCCCCCchhhHHHhh
Q 022898 166 TAKISVDASLAGAIIGKGGVNSKQICRQT 194 (290)
Q Consensus 166 t~~i~VP~~~vg~iIGkgG~~Ik~i~~~s 194 (290)
...+.|-....|++||++|.+|..++..-
T Consensus 39 ~i~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 39 GTQITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred cEEEEEEECCCCceECCCchhHHHHHHHH
Confidence 36777777889999999999999998753
No 113
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=62.14 E-value=6 Score=30.69 Aligned_cols=31 Identities=19% Similarity=0.452 Sum_probs=26.5
Q ss_pred ceEEEEecccccceeeCCCCCchhhHHHhhC
Q 022898 165 ATAKISVDASLAGAIIGKGGVNSKQICRQTG 195 (290)
Q Consensus 165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sg 195 (290)
....|.|-....|+|||+.|..|+.+++...
T Consensus 61 ~~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~ 91 (109)
T cd02412 61 DRVEVTIHTARPGIIIGKKGAGIEKLRKELQ 91 (109)
T ss_pred CCEEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence 3478888899999999999999999987543
No 114
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=60.49 E-value=8.2 Score=33.17 Aligned_cols=35 Identities=29% Similarity=0.426 Sum_probs=29.3
Q ss_pred EEEEecccccceeeCCCCCchhhHHHhhCCceeec
Q 022898 167 AKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIR 201 (290)
Q Consensus 167 ~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~ 201 (290)
..+.+-.+.+|+.||++|++|+.|++..|-+|.|-
T Consensus 78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVV 112 (190)
T COG0195 78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVV 112 (190)
T ss_pred EEeecCcCchhhhccCCChHHHHHHHHhCCceEEE
Confidence 34445567889999999999999999999888873
No 115
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=54.47 E-value=14 Score=30.24 Aligned_cols=38 Identities=32% Similarity=0.551 Sum_probs=33.4
Q ss_pred ceEEEEecccccceeeCCCCCchhhHHHhhCCceeecc
Q 022898 165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 202 (290)
Q Consensus 165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~ 202 (290)
.+-.+.|-+...|++||++|.++..|...+|=.-.|-.
T Consensus 76 ~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvR 113 (145)
T cd02410 76 DTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVR 113 (145)
T ss_pred CCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence 45678888999999999999999999999999888843
No 116
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=49.52 E-value=7.4 Score=36.23 Aligned_cols=24 Identities=38% Similarity=0.776 Sum_probs=21.6
Q ss_pred cccccccccCCCCCCCCCceEeccc
Q 022898 34 SKPCTKFFSTAGCPFGESCHFLHYF 58 (290)
Q Consensus 34 t~lC~~~~~~g~C~~G~~C~F~H~~ 58 (290)
||-|..|+++-.|+.+ +|-|+|.-
T Consensus 202 TKYCtsYLRn~~CpNp-~CMyLHEp 225 (480)
T COG5175 202 TKYCTSYLRNAVCPNP-DCMYLHEP 225 (480)
T ss_pred hHHHHHHHcCCCCCCC-CeeeecCC
Confidence 6899999999999977 89999964
No 117
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=46.96 E-value=84 Score=26.92 Aligned_cols=66 Identities=14% Similarity=0.225 Sum_probs=53.9
Q ss_pred ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhc
Q 022898 165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRI 235 (290)
Q Consensus 165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~ 235 (290)
....+.++....-+++..+|..+.++....|++|.+... ...+.|+|+...+..+...|.+.+...
T Consensus 26 g~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~-----~~~i~I~g~k~~~~~i~~~i~~~l~~i 91 (210)
T PF14611_consen 26 GDLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS-----ENRIRITGTKSTAEYIEASINEILSNI 91 (210)
T ss_pred ceeEEEecchheeeeecCCchHHHHHHHhcCceEEEecC-----CcEEEEEccHHHHHHHHHHHHHHHhhc
Confidence 345566678888889999999999998888999999642 357899999999988888888888654
No 118
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=44.12 E-value=21 Score=32.00 Aligned_cols=29 Identities=38% Similarity=0.355 Sum_probs=20.9
Q ss_pred eEEEEeccc-ccceeeCCCCCchhhHHHhh
Q 022898 166 TAKISVDAS-LAGAIIGKGGVNSKQICRQT 194 (290)
Q Consensus 166 t~~i~VP~~-~vg~iIGkgG~~Ik~i~~~s 194 (290)
.+.+.|..+ .-+.|||++|+.|++|....
T Consensus 222 ~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 222 HALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 344555544 44779999999999998744
No 119
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=43.20 E-value=29 Score=36.17 Aligned_cols=102 Identities=10% Similarity=0.144 Sum_probs=58.7
Q ss_pred ceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHHHhcCCCCCCCCC
Q 022898 165 ATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELIVRIGPAHAKNPA 244 (290)
Q Consensus 165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i~~~~~~p~~~~~ 244 (290)
....+.+|......|||.+|..|..|-..++. ++|.-.+........++.|....+..+..++...........-.-.
T Consensus 420 ~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~-v~i~f~~~~~~~~~~~~~~~~~dv~~~~~~~~~~~~~a~~~~~~~~- 497 (753)
T KOG2208|consen 420 VKEEVQIPTKSHKRIIGTKGALINYIMGKHGG-VHIKFQNNNNSSDMVTIRGISKDVEKSVSLLKALKADAKNLKFRDV- 497 (753)
T ss_pred ccceeecCccchhhhhccccccHHHHHhhcCc-EEEecCCCCcccccceEeccccccchhHHHHHhhhhhhhcchhhhh-
Confidence 35668999999999999999999999999996 5553333333344455555444444444333333322221100000
Q ss_pred CCCCCCCCCCcccccccCCCCC-CCCCCCC
Q 022898 245 TAGSAAHPLSSNFKTKLCGNFA-KGSCTFG 273 (290)
Q Consensus 245 ~~~p~~~p~~~~~k~~~C~~~~-~g~C~~g 273 (290)
..-.....+..+|..+. .+.|...
T Consensus 498 -----~~~d~~~~~~~~~~~~g~~~~i~d~ 522 (753)
T KOG2208|consen 498 -----VTKDKLLPVKYIGKEIGKNGTIRDS 522 (753)
T ss_pred -----hhccccchHHhhcccccCceeeecc
Confidence 00011344666788887 5666643
No 120
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=42.05 E-value=45 Score=30.38 Aligned_cols=47 Identities=19% Similarity=0.394 Sum_probs=36.9
Q ss_pred eeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHHHHH
Q 022898 179 IIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVRELI 232 (290)
Q Consensus 179 iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~~~i 232 (290)
+||..|++++.|...|.+.|-|..+ .|++.|.+.-+..+...+.+.|
T Consensus 163 LiGpng~TLKAlelLT~CYilVqG~-------TVsaiGpfkGlkevr~IV~DcM 209 (356)
T KOG2874|consen 163 LIGPNGSTLKALELLTNCYILVQGN-------TVSAIGPFKGLKEVRKIVEDCM 209 (356)
T ss_pred hcCCCchhHHHHHHHhhcEEEeeCc-------EEEeecCcchHHHHHHHHHHHH
Confidence 7999999999999999999999653 5677777776666665555544
No 121
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=39.75 E-value=38 Score=32.93 Aligned_cols=27 Identities=26% Similarity=0.505 Sum_probs=24.4
Q ss_pred cccceeeCCCCCchhhHHHhh-CCceee
Q 022898 174 SLAGAIIGKGGVNSKQICRQT-GAKLSI 200 (290)
Q Consensus 174 ~~vg~iIGkgG~~Ik~i~~~s-ga~i~v 200 (290)
+.+|+.||++|++|+.|.+.. |-+|.|
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDV 304 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDV 304 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEE
Confidence 678999999999999998887 888887
No 122
>PRK15494 era GTPase Era; Provisional
Probab=36.82 E-value=31 Score=32.22 Aligned_cols=28 Identities=29% Similarity=0.397 Sum_probs=20.7
Q ss_pred EEEEeccc-ccceeeCCCCCchhhHHHhh
Q 022898 167 AKISVDAS-LAGAIIGKGGVNSKQICRQT 194 (290)
Q Consensus 167 ~~i~VP~~-~vg~iIGkgG~~Ik~i~~~s 194 (290)
..|.|..+ .-+.|||++|..|++|....
T Consensus 275 ~~i~v~~~sqk~iiiG~~g~~ik~i~~~a 303 (339)
T PRK15494 275 QVIVVSRESYKTIILGKNGSKIKEIGAKS 303 (339)
T ss_pred EEEEECCCCceeEEEcCCcHHHHHHHHHH
Confidence 45566554 44778999999999997644
No 123
>KOG3702 consensus Nuclear polyadenylated RNA binding protein [RNA processing and modification]
Probab=36.54 E-value=40 Score=34.18 Aligned_cols=24 Identities=21% Similarity=0.549 Sum_probs=15.0
Q ss_pred cccccccccccccccCCCCCcccccccc
Q 022898 94 VVKSRMCNRLNSAEGCKFGDKCHFAHGE 121 (290)
Q Consensus 94 ~~ktr~C~~~~~~g~C~~G~~C~f~H~~ 121 (290)
..-..+|.|+ +.|+ -..|+|.|..
T Consensus 622 ~ti~~~CrY~---pnCr-nm~C~F~HPk 645 (681)
T KOG3702|consen 622 GTIRGLCRYR---PNCR-NMQCKFYHPK 645 (681)
T ss_pred CCccccceec---cCcC-CccccccCCc
Confidence 3445567654 4566 4578899854
No 124
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=35.39 E-value=34 Score=31.68 Aligned_cols=59 Identities=20% Similarity=0.263 Sum_probs=44.5
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHH-HHHHH
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQ-IKQAS 225 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~-i~~A~ 225 (290)
..+..+.||...+|+|.|..|..|+.|++.+...|...-. ..+-++.++|.+.. +++|.
T Consensus 114 qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~---~~~~Vf~Vtg~~~nC~kra~ 173 (394)
T KOG2113|consen 114 QTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR---CGEPVFCVTGAPKNCVKRAR 173 (394)
T ss_pred CCceeeeccceeeeeccccccCccchheecccceEeeecc---CCCceEEEecCCcchhhhcc
Confidence 5677889999999999999999999999999998876432 23445666775554 44443
No 125
>COG1159 Era GTPase [General function prediction only]
Probab=35.01 E-value=32 Score=31.60 Aligned_cols=31 Identities=35% Similarity=0.439 Sum_probs=22.4
Q ss_pred EEEEeccccc-ceeeCCCCCchhhHHHhhCCc
Q 022898 167 AKISVDASLA-GAIIGKGGVNSKQICRQTGAK 197 (290)
Q Consensus 167 ~~i~VP~~~v-g~iIGkgG~~Ik~i~~~sga~ 197 (290)
..+.|+.+.- +.||||+|+.||.|-..+...
T Consensus 231 a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ 262 (298)
T COG1159 231 ATIYVERESQKGIIIGKNGAMIKKIGTAARKD 262 (298)
T ss_pred EEEEEecCCccceEECCCcHHHHHHHHHHHHH
Confidence 4466666444 779999999999997754433
No 126
>PRK00089 era GTPase Era; Reviewed
Probab=34.48 E-value=35 Score=30.77 Aligned_cols=29 Identities=45% Similarity=0.583 Sum_probs=20.5
Q ss_pred EEEEecc-cccceeeCCCCCchhhHHHhhC
Q 022898 167 AKISVDA-SLAGAIIGKGGVNSKQICRQTG 195 (290)
Q Consensus 167 ~~i~VP~-~~vg~iIGkgG~~Ik~i~~~sg 195 (290)
+.|.|.. +.-+.|||++|+.|+.|...+.
T Consensus 228 ~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar 257 (292)
T PRK00089 228 ATIYVERDSQKGIIIGKGGAMLKKIGTEAR 257 (292)
T ss_pred EEEEEccCCceeEEEeCCcHHHHHHHHHHH
Confidence 3445544 3347789999999999987443
No 127
>PF10283 zf-CCHH: Zinc-finger (CX5CX6HX5H) motif; InterPro: IPR019406 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type Znf motif that in humans is part of the APLF (aprataxin- and PNK-like) forkead association domain-containing protein []. The Znf is highly conserved both in primary sequence and in the spacing between the putative zinc coordinating residues, and is configured CX5CX6HX5H. Many of the proteins containing this Znf are involved in DNA strand break repair and/or contain domains implicated in DNA metabolism. This Znf motif appears to be specialised for the non-covalent binding of poly ADP-ribose; Aprataxin also appears to covalently bind poly ADP-ribose, but not through its Znf motif [].; PDB: 2KQC_A 2KUO_A 2KQE_A 2KQD_A 2KQB_A.
Probab=34.21 E-value=11 Score=21.51 Aligned_cols=9 Identities=33% Similarity=1.124 Sum_probs=5.2
Q ss_pred CCCCCCCce
Q 022898 45 GCPFGESCH 53 (290)
Q Consensus 45 ~C~~G~~C~ 53 (290)
.|+||.+|-
T Consensus 2 ~C~YG~~CY 10 (26)
T PF10283_consen 2 PCKYGAKCY 10 (26)
T ss_dssp E-TTGGG-S
T ss_pred CCCcchhhh
Confidence 488888884
No 128
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=33.55 E-value=26 Score=38.09 Aligned_cols=66 Identities=8% Similarity=0.020 Sum_probs=53.1
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccCCCCCCcceeEEcCCHHHHHHHHHHHH
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDHEADPNLRNIELEGSFEQIKQASAMVR 229 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~~~~~~~r~v~i~G~~~~i~~A~~~I~ 229 (290)
...+...++..++.+||+..+.+|+-|+..+++.+.|.....-..++.++|.+.-...+.+..+|.
T Consensus 780 ganiehrdkkgf~plImaatagh~tvV~~llk~ha~veaQsdrtkdt~lSlacsggr~~vvelLl~ 845 (2131)
T KOG4369|consen 780 GANIEHRDKKGFVPLIMAATAGHITVVQDLLKAHADVEAQSDRTKDTMLSLACSGGRTRVVELLLN 845 (2131)
T ss_pred cccccccccccchhhhhhcccCchHHHHHHHhhhhhhhhhcccccCceEEEecCCCcchHHHHHHH
Confidence 456778889999999999999999999999999999976555566788888887666655554443
No 129
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=33.55 E-value=33 Score=32.50 Aligned_cols=27 Identities=30% Similarity=0.528 Sum_probs=24.4
Q ss_pred cccceeeCCCCCchhhHHHhh-CCceee
Q 022898 174 SLAGAIIGKGGVNSKQICRQT-GAKLSI 200 (290)
Q Consensus 174 ~~vg~iIGkgG~~Ik~i~~~s-ga~i~v 200 (290)
+.+|+.||++|+.|+.|.+.. |-.|.|
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdi 272 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDI 272 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEE
Confidence 678999999999999998877 888887
No 130
>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=33.44 E-value=37 Score=31.95 Aligned_cols=28 Identities=29% Similarity=0.495 Sum_probs=24.8
Q ss_pred cccceeeCCCCCchhhHHHhh-CCceeec
Q 022898 174 SLAGAIIGKGGVNSKQICRQT-GAKLSIR 201 (290)
Q Consensus 174 ~~vg~iIGkgG~~Ik~i~~~s-ga~i~v~ 201 (290)
+.+|+.||++|+.|+.|.+.. |-+|.|-
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv 271 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDII 271 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEE
Confidence 678999999999999999887 8888873
No 131
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=31.65 E-value=56 Score=29.08 Aligned_cols=40 Identities=18% Similarity=0.294 Sum_probs=35.5
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeeccC
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRDH 203 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~~ 203 (290)
..-.-+.|++..|.-+||+.|+.++-+.+.+++.|-|..+
T Consensus 145 ~~G~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N 184 (239)
T COG1097 145 KNGQIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN 184 (239)
T ss_pred cCCEEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC
Confidence 4457789999999999999999999999999999988655
No 132
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=30.70 E-value=46 Score=28.94 Aligned_cols=30 Identities=27% Similarity=0.537 Sum_probs=24.8
Q ss_pred EEEEecccccceeeCCCCCchhhHHHhhCC
Q 022898 167 AKISVDASLAGAIIGKGGVNSKQICRQTGA 196 (290)
Q Consensus 167 ~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga 196 (290)
..+.|-....|++||++|.+|+.+++.-..
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk 71 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEK 71 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHH
Confidence 666777788899999999999999886543
No 133
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=30.43 E-value=46 Score=28.69 Aligned_cols=30 Identities=23% Similarity=0.458 Sum_probs=25.6
Q ss_pred eEEEEecccccceeeCCCCCchhhHHHhhC
Q 022898 166 TAKISVDASLAGAIIGKGGVNSKQICRQTG 195 (290)
Q Consensus 166 t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sg 195 (290)
..++.|-....|+|||+.|.+|+++++.-.
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~ 68 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKLQ 68 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHHH
Confidence 478888888899999999999999887543
No 134
>CHL00048 rps3 ribosomal protein S3
Probab=29.96 E-value=52 Score=28.80 Aligned_cols=30 Identities=7% Similarity=0.144 Sum_probs=25.4
Q ss_pred ceEEEEecccccceeeCCCCCchhhHHHhh
Q 022898 165 ATAKISVDASLAGAIIGKGGVNSKQICRQT 194 (290)
Q Consensus 165 ~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~s 194 (290)
...++.|-....++|||++|.+|+++++.-
T Consensus 66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 66 DLIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred CeEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 347788888888999999999999998754
No 135
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=29.16 E-value=32 Score=32.72 Aligned_cols=28 Identities=21% Similarity=0.421 Sum_probs=24.7
Q ss_pred cccceeeCCCCCchhhHHHhh-CCceeec
Q 022898 174 SLAGAIIGKGGVNSKQICRQT-GAKLSIR 201 (290)
Q Consensus 174 ~~vg~iIGkgG~~Ik~i~~~s-ga~i~v~ 201 (290)
+.+|+.||++|++|+.|.+.. |-+|.|-
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI 279 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCI 279 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEE
Confidence 678999999999999998887 8888873
No 136
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=28.39 E-value=31 Score=32.34 Aligned_cols=27 Identities=26% Similarity=0.584 Sum_probs=22.4
Q ss_pred cccccccccCCCCCCCCCceEecccCCC
Q 022898 34 SKPCTKFFSTAGCPFGESCHFLHYFPGG 61 (290)
Q Consensus 34 t~lC~~~~~~g~C~~G~~C~F~H~~~~~ 61 (290)
-.+|.+|..+ .|+.|+.|.|.|..+++
T Consensus 161 p~Icsf~v~g-eckRG~ec~yrhEkp~d 187 (377)
T KOG0153|consen 161 PHICSFFVKG-ECKRGAECPYRHEKPPD 187 (377)
T ss_pred Cccccceeec-cccccccccccccCCCC
Confidence 4589888865 99999999999987643
No 137
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=27.96 E-value=49 Score=29.09 Aligned_cols=30 Identities=13% Similarity=0.285 Sum_probs=25.5
Q ss_pred eEEEEecccccceeeCCCCCchhhHHHhhC
Q 022898 166 TAKISVDASLAGAIIGKGGVNSKQICRQTG 195 (290)
Q Consensus 166 t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sg 195 (290)
..+|.|-....|+|||++|..|+++++.-.
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L~ 74 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLLQ 74 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHHH
Confidence 477888888899999999999999987543
No 138
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=26.74 E-value=30 Score=27.50 Aligned_cols=13 Identities=54% Similarity=1.339 Sum_probs=11.4
Q ss_pred CCCCCCCCceEecc
Q 022898 44 AGCPFGESCHFLHY 57 (290)
Q Consensus 44 g~C~~G~~C~F~H~ 57 (290)
..|++|+ |+|.|+
T Consensus 60 ~GC~~ge-CHy~~G 72 (132)
T COG1908 60 AGCKIGE-CHYISG 72 (132)
T ss_pred ecccccc-eeeecc
Confidence 3699997 999997
No 139
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=24.85 E-value=47 Score=32.64 Aligned_cols=27 Identities=30% Similarity=0.505 Sum_probs=24.4
Q ss_pred cccceeeCCCCCchhhHHHhh-CCceee
Q 022898 174 SLAGAIIGKGGVNSKQICRQT-GAKLSI 200 (290)
Q Consensus 174 ~~vg~iIGkgG~~Ik~i~~~s-ga~i~v 200 (290)
+.+|+.||++|++|+.|.... |-+|.|
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idi 272 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDI 272 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEE
Confidence 678999999999999999887 888887
No 140
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=22.20 E-value=94 Score=30.95 Aligned_cols=39 Identities=31% Similarity=0.503 Sum_probs=33.9
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeecc
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 202 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~ 202 (290)
..+-.+.|-+..-|+||||+|++.+.|...+|-.-.|-.
T Consensus 98 ~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR 136 (637)
T COG1782 98 DDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVR 136 (637)
T ss_pred CCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeee
Confidence 445678888999999999999999999999998888743
No 141
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=21.40 E-value=1.1e+02 Score=31.41 Aligned_cols=39 Identities=28% Similarity=0.503 Sum_probs=34.3
Q ss_pred CceEEEEecccccceeeCCCCCchhhHHHhhCCceeecc
Q 022898 164 SATAKISVDASLAGAIIGKGGVNSKQICRQTGAKLSIRD 202 (290)
Q Consensus 164 ~~t~~i~VP~~~vg~iIGkgG~~Ik~i~~~sga~i~v~~ 202 (290)
..+-.+.|-+..-|+||||+|.+.+.|...+|=...|-.
T Consensus 92 ~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~ 130 (630)
T TIGR03675 92 DVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVR 130 (630)
T ss_pred CCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEe
Confidence 445678889999999999999999999999999988843
No 142
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=20.04 E-value=1.1e+02 Score=28.71 Aligned_cols=31 Identities=23% Similarity=0.311 Sum_probs=22.7
Q ss_pred CceEEEEeccccc-ceeeCCCCCchhhHHHhh
Q 022898 164 SATAKISVDASLA-GAIIGKGGVNSKQICRQT 194 (290)
Q Consensus 164 ~~t~~i~VP~~~v-g~iIGkgG~~Ik~i~~~s 194 (290)
-.+..+.+|.... .+|||+||..|++|-..-
T Consensus 327 ~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a 358 (379)
T KOG1423|consen 327 FIQVEVVCPKNSQKKLLIGKGGKKISQIGTRA 358 (379)
T ss_pred EEEEEEEcCCCcceeEEEcCCCccHHHHHHHH
Confidence 3455667776555 568899999999997643
Done!