Query 010611
Match_columns 506
No_of_seqs 350 out of 1575
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 02:32:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010611.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010611hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2190 PolyC-binding proteins 100.0 4.6E-31 1E-35 282.3 25.6 167 183-353 40-210 (485)
2 KOG1676 K-homology type RNA bi 100.0 1.3E-31 2.9E-36 283.7 19.5 215 111-352 80-301 (600)
3 KOG2192 PolyC-binding hnRNP-K 100.0 2.1E-29 4.6E-34 243.9 19.8 288 182-505 44-351 (390)
4 KOG2192 PolyC-binding hnRNP-K 100.0 4E-29 8.6E-34 242.0 14.5 217 91-352 63-385 (390)
5 KOG2190 PolyC-binding proteins 99.9 6.2E-27 1.3E-31 250.7 20.0 213 113-351 73-409 (485)
6 KOG2191 RNA-binding protein NO 99.9 3.7E-25 8E-30 220.0 19.5 166 184-356 37-209 (402)
7 KOG2193 IGF-II mRNA-binding pr 99.9 1E-25 2.2E-30 229.4 12.7 161 181-356 194-357 (584)
8 KOG2193 IGF-II mRNA-binding pr 99.9 1.1E-25 2.3E-30 229.3 10.9 246 121-504 238-528 (584)
9 KOG1676 K-homology type RNA bi 99.9 7.4E-25 1.6E-29 232.6 15.9 215 183-505 51-266 (600)
10 KOG2191 RNA-binding protein NO 99.7 9.8E-17 2.1E-21 160.2 12.3 74 277-353 38-113 (402)
11 TIGR03665 arCOG04150 arCOG0415 99.5 3.8E-14 8.2E-19 133.9 9.9 139 190-353 2-153 (172)
12 PRK13763 putative RNA-processi 99.5 3.9E-13 8.6E-18 127.9 11.2 142 186-352 3-158 (180)
13 cd02396 PCBP_like_KH K homolog 99.3 1.9E-12 4.1E-17 102.9 6.7 65 279-346 1-65 (65)
14 KOG2279 Kinase anchor protein 99.2 3.5E-11 7.6E-16 127.6 10.8 147 183-353 65-211 (608)
15 cd02396 PCBP_like_KH K homolog 99.2 1.5E-11 3.2E-16 97.8 5.2 63 187-255 1-64 (65)
16 TIGR03665 arCOG04150 arCOG0415 99.1 7.1E-11 1.5E-15 111.7 6.9 61 282-351 2-65 (172)
17 PF00013 KH_1: KH domain syndr 99.1 1.4E-10 3E-15 90.4 5.5 60 279-345 1-60 (60)
18 PRK13763 putative RNA-processi 99.1 3.8E-10 8.3E-15 107.4 9.7 65 278-351 3-71 (180)
19 cd02394 vigilin_like_KH K homo 99.1 1.6E-10 3.5E-15 90.6 5.7 60 280-345 2-61 (62)
20 cd02393 PNPase_KH Polynucleoti 99.0 6.6E-10 1.4E-14 87.4 7.1 58 278-345 2-60 (61)
21 cd00105 KH-I K homology RNA-bi 99.0 1.9E-09 4.1E-14 84.4 7.0 62 280-345 2-63 (64)
22 PF00013 KH_1: KH domain syndr 98.9 1.4E-09 3.1E-14 84.6 3.8 51 187-240 1-51 (60)
23 PF13014 KH_3: KH domain 98.9 3.4E-09 7.3E-14 77.4 4.7 42 196-237 1-43 (43)
24 cd02394 vigilin_like_KH K homo 98.8 2.5E-09 5.3E-14 83.9 3.9 51 188-240 2-52 (62)
25 cd00105 KH-I K homology RNA-bi 98.8 5.9E-09 1.3E-13 81.5 5.6 53 188-240 2-54 (64)
26 PF13014 KH_3: KH domain 98.8 6.8E-09 1.5E-13 75.7 4.5 43 288-333 1-43 (43)
27 cd02393 PNPase_KH Polynucleoti 98.7 1.6E-08 3.4E-13 79.6 5.4 47 186-238 2-48 (61)
28 smart00322 KH K homology RNA-b 98.7 5.9E-08 1.3E-12 75.5 8.1 66 278-349 3-68 (69)
29 COG1094 Predicted RNA-binding 98.6 4.8E-07 1E-11 86.2 10.9 146 185-353 7-166 (194)
30 smart00322 KH K homology RNA-b 98.4 1.2E-06 2.7E-11 68.0 6.9 54 185-240 2-55 (69)
31 KOG2279 Kinase anchor protein 98.3 4.4E-07 9.6E-12 97.0 2.7 72 275-351 65-136 (608)
32 KOG2208 Vigilin [Lipid transpo 98.2 7.2E-06 1.6E-10 93.6 12.5 199 118-352 161-415 (753)
33 cd02395 SF1_like-KH Splicing f 98.0 1.2E-05 2.7E-10 71.8 7.2 67 286-352 14-96 (120)
34 PRK08406 transcription elongat 97.7 0.00011 2.4E-09 67.4 8.0 102 187-313 33-134 (140)
35 cd02395 SF1_like-KH Splicing f 97.6 8.6E-05 1.9E-09 66.3 5.0 36 189-224 3-44 (120)
36 TIGR02696 pppGpp_PNP guanosine 97.5 0.00039 8.5E-09 78.5 9.7 66 276-351 576-642 (719)
37 KOG2113 Predicted RNA binding 97.5 5.1E-05 1.1E-09 76.5 2.4 140 184-342 24-173 (394)
38 KOG2208 Vigilin [Lipid transpo 97.5 0.0003 6.5E-09 80.6 8.7 141 185-350 346-487 (753)
39 PRK08406 transcription elongat 97.5 0.0003 6.5E-09 64.5 6.9 37 278-314 32-68 (140)
40 TIGR01952 nusA_arch NusA famil 97.4 0.00053 1.2E-08 62.9 7.2 102 187-313 34-135 (141)
41 KOG2113 Predicted RNA binding 97.4 0.00026 5.6E-09 71.6 5.4 64 275-346 23-87 (394)
42 KOG0119 Splicing factor 1/bran 97.1 0.0023 5E-08 68.4 10.1 76 277-352 137-231 (554)
43 TIGR03591 polynuc_phos polyrib 97.1 0.0014 3.1E-08 74.5 8.4 66 276-351 549-615 (684)
44 COG1094 Predicted RNA-binding 96.9 0.0025 5.4E-08 61.1 6.7 65 278-351 8-77 (194)
45 COG0195 NusA Transcription elo 96.7 0.0047 1E-07 59.5 7.6 99 190-314 80-178 (190)
46 KOG0336 ATP-dependent RNA heli 96.7 0.0017 3.7E-08 68.4 4.7 68 275-349 44-111 (629)
47 TIGR01952 nusA_arch NusA famil 96.4 0.0068 1.5E-07 55.7 5.8 36 279-314 34-69 (141)
48 PLN00207 polyribonucleotide nu 96.4 0.0068 1.5E-07 70.2 7.0 67 276-352 683-751 (891)
49 TIGR02696 pppGpp_PNP guanosine 96.3 0.0056 1.2E-07 69.4 6.2 51 184-240 576-626 (719)
50 cd02134 NusA_KH NusA_K homolog 96.3 0.0045 9.8E-08 48.6 3.9 36 186-221 25-60 (61)
51 cd02134 NusA_KH NusA_K homolog 96.1 0.0064 1.4E-07 47.7 3.8 36 469-504 25-60 (61)
52 KOG1588 RNA-binding protein Sa 96.0 0.0072 1.6E-07 60.3 4.4 41 183-223 89-135 (259)
53 KOG0336 ATP-dependent RNA heli 95.8 0.0044 9.6E-08 65.3 2.1 56 181-239 42-97 (629)
54 PRK12328 nusA transcription el 95.7 0.025 5.5E-07 59.6 7.2 93 195-314 251-344 (374)
55 TIGR03591 polynuc_phos polyrib 95.7 0.015 3.3E-07 66.3 5.9 50 184-239 549-598 (684)
56 TIGR01953 NusA transcription t 95.6 0.03 6.5E-07 58.7 7.2 94 195-314 243-337 (341)
57 COG1185 Pnp Polyribonucleotide 95.6 0.03 6.4E-07 62.7 7.4 70 277-356 551-621 (692)
58 PRK04163 exosome complex RNA-b 95.6 0.028 6E-07 56.0 6.5 67 279-355 146-213 (235)
59 KOG2814 Transcription coactiva 95.5 0.017 3.6E-07 59.4 4.6 69 278-352 57-126 (345)
60 PRK12327 nusA transcription el 95.4 0.038 8.2E-07 58.4 7.2 94 195-314 245-339 (362)
61 PRK12329 nusA transcription el 95.3 0.035 7.6E-07 59.6 6.5 94 195-314 277-371 (449)
62 PRK00468 hypothetical protein; 95.3 0.018 3.8E-07 47.4 3.3 34 182-215 26-59 (75)
63 COG0195 NusA Transcription elo 95.1 0.061 1.3E-06 51.9 7.1 36 470-505 143-178 (190)
64 PRK11824 polynucleotide phosph 95.1 0.033 7.2E-07 63.7 6.0 65 277-351 553-618 (693)
65 PRK09202 nusA transcription el 95.0 0.052 1.1E-06 59.3 7.0 93 195-314 245-338 (470)
66 PRK02821 hypothetical protein; 94.8 0.024 5.3E-07 46.7 3.0 35 183-217 28-62 (77)
67 COG1837 Predicted RNA-binding 94.7 0.032 6.9E-07 45.9 3.3 33 183-215 27-59 (76)
68 KOG1588 RNA-binding protein Sa 94.6 0.035 7.5E-07 55.6 3.9 76 275-350 89-190 (259)
69 KOG2814 Transcription coactiva 94.5 0.043 9.4E-07 56.5 4.6 52 186-239 57-108 (345)
70 TIGR03319 YmdA_YtgF conserved 94.5 0.076 1.6E-06 58.7 6.7 66 277-351 203-270 (514)
71 KOG0119 Splicing factor 1/bran 94.5 0.04 8.7E-07 59.3 4.2 39 185-223 137-181 (554)
72 KOG4369 RTK signaling protein 94.5 0.032 7E-07 65.0 3.7 70 279-351 1341-1410(2131)
73 PRK12704 phosphodiesterase; Pr 94.3 0.09 1.9E-06 58.2 6.7 65 278-351 210-276 (520)
74 PRK00106 hypothetical protein; 94.2 0.1 2.2E-06 57.9 6.9 66 277-351 224-291 (535)
75 PRK00468 hypothetical protein; 94.1 0.051 1.1E-06 44.7 3.2 33 275-307 27-59 (75)
76 PRK01064 hypothetical protein; 94.0 0.053 1.2E-06 44.9 3.1 33 183-215 27-59 (78)
77 COG5176 MSL5 Splicing factor ( 93.7 0.11 2.4E-06 50.2 5.3 78 275-352 145-241 (269)
78 PRK02821 hypothetical protein; 93.4 0.07 1.5E-06 44.1 2.9 30 469-498 31-60 (77)
79 COG1837 Predicted RNA-binding 93.0 0.1 2.2E-06 43.0 3.2 32 275-306 27-58 (76)
80 PRK12328 nusA transcription el 92.9 0.23 5E-06 52.6 6.7 37 469-505 308-344 (374)
81 PLN00207 polyribonucleotide nu 92.5 0.12 2.7E-06 60.1 4.3 51 184-240 683-734 (891)
82 PRK01064 hypothetical protein; 92.1 0.17 3.6E-06 42.0 3.4 33 275-307 27-59 (78)
83 COG1185 Pnp Polyribonucleotide 91.8 0.21 4.5E-06 56.2 4.9 50 185-240 551-600 (692)
84 PRK09202 nusA transcription el 91.7 0.32 7E-06 53.2 6.1 36 470-505 303-338 (470)
85 PF14611 SLS: Mitochondrial in 91.5 6.6 0.00014 38.0 14.6 124 192-350 32-164 (210)
86 PRK12327 nusA transcription el 91.5 0.41 8.9E-06 50.7 6.6 37 469-505 303-339 (362)
87 PRK04163 exosome complex RNA-b 91.3 0.34 7.4E-06 48.2 5.4 47 188-240 147-193 (235)
88 PF13083 KH_4: KH domain; PDB: 90.8 0.17 3.6E-06 40.9 2.1 35 183-217 26-60 (73)
89 PRK12704 phosphodiesterase; Pr 90.8 0.29 6.2E-06 54.3 4.7 47 187-238 211-258 (520)
90 TIGR03319 YmdA_YtgF conserved 90.7 0.29 6.3E-06 54.2 4.6 48 186-238 204-252 (514)
91 PRK00106 hypothetical protein; 90.2 0.34 7.4E-06 53.8 4.7 48 186-238 225-273 (535)
92 PRK12329 nusA transcription el 90.2 0.49 1.1E-05 51.1 5.6 36 470-505 336-371 (449)
93 COG5176 MSL5 Splicing factor ( 89.6 0.31 6.8E-06 47.2 3.3 38 468-505 147-190 (269)
94 cd02409 KH-II KH-II (K homolo 89.1 0.46 1E-05 36.7 3.4 34 186-219 25-58 (68)
95 KOG1067 Predicted RNA-binding 89.1 1.7 3.6E-05 48.1 8.6 67 275-352 594-661 (760)
96 PF13184 KH_5: NusA-like KH do 88.6 0.36 7.7E-06 39.0 2.5 34 189-222 6-45 (69)
97 PRK12705 hypothetical protein; 87.9 0.98 2.1E-05 49.9 6.1 63 278-349 198-262 (508)
98 PF07650 KH_2: KH domain syndr 87.2 0.42 9.1E-06 38.9 2.2 34 186-219 25-58 (78)
99 PRK11824 polynucleotide phosph 85.7 0.65 1.4E-05 53.3 3.4 49 185-239 553-601 (693)
100 KOG3273 Predicted RNA-binding 85.5 0.68 1.5E-05 44.7 2.9 55 286-351 177-231 (252)
101 PF13184 KH_5: NusA-like KH do 85.2 0.71 1.5E-05 37.3 2.5 35 280-314 5-45 (69)
102 cd02409 KH-II KH-II (K homolo 83.9 1.3 2.9E-05 34.0 3.5 33 278-310 25-57 (68)
103 PF07650 KH_2: KH domain syndr 83.7 0.66 1.4E-05 37.8 1.7 32 469-500 25-56 (78)
104 PRK12705 hypothetical protein; 83.5 0.89 1.9E-05 50.2 3.1 38 468-505 197-235 (508)
105 PF13083 KH_4: KH domain; PDB: 82.7 0.64 1.4E-05 37.4 1.3 30 469-498 29-58 (73)
106 KOG4369 RTK signaling protein 81.2 0.68 1.5E-05 54.7 1.2 170 67-241 1199-1396(2131)
107 cd02414 jag_KH jag_K homology 81.0 1.4 2.9E-05 36.1 2.6 33 188-220 26-58 (77)
108 cd02413 40S_S3_KH K homology R 79.2 1.9 4E-05 35.9 2.9 35 187-221 31-65 (81)
109 PRK06418 transcription elongat 79.2 2 4.3E-05 40.7 3.4 34 189-223 64-97 (166)
110 TIGR01953 NusA transcription t 78.4 2.1 4.6E-05 45.0 3.7 37 469-505 301-337 (341)
111 COG1855 ATPase (PilT family) [ 78.0 1.5 3.3E-05 47.5 2.5 37 187-223 487-523 (604)
112 PF14611 SLS: Mitochondrial in 75.5 20 0.00043 34.6 9.4 65 279-352 27-91 (210)
113 PRK13764 ATPase; Provisional 74.9 2.2 4.8E-05 48.2 2.9 37 187-223 482-518 (602)
114 cd02414 jag_KH jag_K homology 74.3 3 6.4E-05 34.1 2.8 30 470-499 25-54 (77)
115 cd02413 40S_S3_KH K homology R 74.2 3.2 7E-05 34.5 3.0 29 469-497 30-58 (81)
116 COG1097 RRP4 RNA-binding prote 74.0 6 0.00013 39.5 5.3 58 280-347 148-206 (239)
117 PRK13764 ATPase; Provisional 73.7 2.7 5.9E-05 47.5 3.2 39 467-505 479-517 (602)
118 cd02412 30S_S3_KH K homology R 73.3 3.2 7E-05 36.3 2.9 30 188-217 63-92 (109)
119 COG1855 ATPase (PilT family) [ 71.8 2.9 6.3E-05 45.5 2.7 37 469-505 486-522 (604)
120 cd02411 archeal_30S_S3_KH K ho 69.8 4.4 9.5E-05 33.8 2.9 28 188-215 40-67 (85)
121 PRK06418 transcription elongat 66.9 5.9 0.00013 37.5 3.4 35 279-314 62-96 (166)
122 COG0092 RpsC Ribosomal protein 64.5 5.2 0.00011 39.8 2.6 31 185-215 50-80 (233)
123 cd02410 archeal_CPSF_KH The ar 64.3 28 0.00062 32.2 7.2 93 200-314 20-112 (145)
124 cd02410 archeal_CPSF_KH The ar 63.8 8.3 0.00018 35.7 3.6 35 189-223 79-113 (145)
125 COG1097 RRP4 RNA-binding prote 61.6 6.6 0.00014 39.2 2.7 45 190-240 150-194 (239)
126 COG0092 RpsC Ribosomal protein 59.8 7.4 0.00016 38.7 2.7 28 469-496 51-78 (233)
127 KOG2874 rRNA processing protei 59.6 15 0.00031 37.6 4.8 51 290-351 161-211 (356)
128 cd02411 archeal_30S_S3_KH K ho 58.5 9.3 0.0002 31.8 2.8 27 471-497 40-66 (85)
129 cd02412 30S_S3_KH K homology R 56.7 9.4 0.0002 33.4 2.6 28 470-497 62-89 (109)
130 PRK13916 plasmid segregation p 55.1 8.1 0.00018 32.4 1.8 35 59-97 16-50 (97)
131 KOG1067 Predicted RNA-binding 51.6 25 0.00055 39.3 5.3 49 184-239 595-643 (760)
132 PRK15494 era GTPase Era; Provi 47.9 22 0.00047 37.3 4.1 36 186-221 273-317 (339)
133 TIGR00436 era GTP-binding prot 47.3 17 0.00038 36.4 3.2 29 186-214 221-250 (270)
134 COG1782 Predicted metal-depend 46.5 46 0.00099 37.0 6.3 93 199-314 42-135 (637)
135 KOG1423 Ras-like GTPase ERA [C 45.4 15 0.00033 38.3 2.3 34 183-216 325-359 (379)
136 TIGR00436 era GTP-binding prot 42.5 22 0.00047 35.7 3.1 30 469-498 221-251 (270)
137 COG5166 Uncharacterized conser 41.7 31 0.00067 38.2 4.1 127 185-314 448-607 (657)
138 TIGR01008 rpsC_E_A ribosomal p 39.6 26 0.00056 34.1 2.9 31 187-217 39-69 (195)
139 PTZ00084 40S ribosomal protein 38.2 28 0.0006 34.5 2.9 32 187-218 45-76 (220)
140 PRK04191 rps3p 30S ribosomal p 37.9 28 0.00061 34.1 2.9 30 188-217 42-71 (207)
141 CHL00048 rps3 ribosomal protei 37.5 29 0.00062 34.2 2.9 30 187-216 67-96 (214)
142 PRK00089 era GTPase Era; Revie 37.2 30 0.00066 34.9 3.2 36 186-221 226-270 (292)
143 PRK15494 era GTPase Era; Provi 35.9 31 0.00068 36.1 3.1 30 469-498 273-303 (339)
144 PRK00089 era GTPase Era; Revie 35.5 31 0.00067 34.8 2.9 30 277-306 225-255 (292)
145 COG1159 Era GTPase [General fu 34.4 39 0.00085 34.9 3.4 30 185-214 228-258 (298)
146 TIGR03675 arCOG00543 arCOG0054 33.2 1.1E+02 0.0024 35.0 7.1 94 199-314 36-129 (630)
147 COG1159 Era GTPase [General fu 32.1 40 0.00086 34.9 3.0 31 277-307 228-259 (298)
148 TIGR01008 rpsC_E_A ribosomal p 30.5 43 0.00093 32.6 2.8 29 469-497 38-66 (195)
149 COG1847 Jag Predicted RNA-bind 30.0 37 0.0008 33.3 2.2 35 187-221 92-126 (208)
150 TIGR03675 arCOG00543 arCOG0054 29.2 51 0.0011 37.7 3.6 35 189-223 96-130 (630)
151 COG1782 Predicted metal-depend 29.1 51 0.0011 36.6 3.3 34 189-222 102-135 (637)
152 PRK04191 rps3p 30S ribosomal p 28.5 47 0.001 32.5 2.7 28 471-498 42-69 (207)
153 CHL00048 rps3 ribosomal protei 28.3 49 0.0011 32.6 2.9 29 469-497 66-94 (214)
154 KOG3273 Predicted RNA-binding 26.8 46 0.001 32.5 2.2 41 194-241 177-217 (252)
155 TIGR01009 rpsC_bact ribosomal 26.0 59 0.0013 31.9 2.9 29 188-216 64-92 (211)
156 PTZ00084 40S ribosomal protein 26.0 55 0.0012 32.5 2.7 28 470-497 45-72 (220)
157 KOG1423 Ras-like GTPase ERA [C 25.0 59 0.0013 34.1 2.8 32 468-499 327-359 (379)
158 COG1847 Jag Predicted RNA-bind 23.8 61 0.0013 31.8 2.5 30 469-498 91-120 (208)
159 COG5166 Uncharacterized conser 22.6 81 0.0017 35.1 3.3 72 279-353 450-526 (657)
No 1
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.98 E-value=4.6e-31 Score=282.31 Aligned_cols=167 Identities=38% Similarity=0.636 Sum_probs=143.2
Q ss_pred CCeeEEEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhhc
Q 010611 183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEG 262 (506)
Q Consensus 183 ~~~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e~ 262 (506)
....++||||+.+.+|.||||+|..||+||.+|.++|+|.+..++|.||+++|+|..... ..+++++|+.+++++++..
T Consensus 40 ~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~-~~~~~~~al~ka~~~iv~~ 118 (485)
T KOG2190|consen 40 DETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVEL-NLSPATDALFKAFDMIVFK 118 (485)
T ss_pred CCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccc-cCCchHHHHHHHHHHHhhc
Confidence 445569999999999999999999999999999999999998999999999999953222 6788999999999988763
Q ss_pred cc---ccCCCcC-CCCCceeEEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeCHHHH
Q 010611 263 TS---EKGLDFS-SNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKV 338 (506)
Q Consensus 263 ~~---~~g~~~~-~~~~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~~~V 338 (506)
.. ....+.+ ......++++|+||.+++|+||||+|+.||+|+++|||+|++..+.+|. +++|.|+|.|.+++|
T Consensus 119 ~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~---ster~V~IsG~~~av 195 (485)
T KOG2190|consen 119 LEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPN---STERAVTISGEPDAV 195 (485)
T ss_pred ccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCc---ccceeEEEcCchHHH
Confidence 21 1111111 1123368999999999999999999999999999999999999888998 689999999999999
Q ss_pred HHHHHHHHHHhhccc
Q 010611 339 KDAVYNVTGRLRDNH 353 (506)
Q Consensus 339 ~~A~~~I~~~L~e~~ 353 (506)
.+|+..|..+|.++.
T Consensus 196 ~~al~~Is~~L~~~~ 210 (485)
T KOG2190|consen 196 KKALVQISSRLLENP 210 (485)
T ss_pred HHHHHHHHHHHHhcC
Confidence 999999999999964
No 2
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.98 E-value=1.3e-31 Score=283.69 Aligned_cols=215 Identities=21% Similarity=0.289 Sum_probs=169.6
Q ss_pred CCCCcceeec--cCCCCceeeEeeccCchhHHHHhhhccccCCCCCCCCCCcCCCCCCCCccccccccccccccCCeeEE
Q 010611 111 SHRSSEALSI--ETQHRLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQEVSF 188 (506)
Q Consensus 111 ~~~~~~~ini--s~~~~PeRivti~g~~~~i~~af~~i~~~l~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~vtl 188 (506)
+..|+|+|-| +++..++|-|.++|.++.+..|..||.......- ....|... .....+|.
T Consensus 80 qq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~aK~li~evv~r~~--------~~~~~~~~----------q~~~~ttq 141 (600)
T KOG1676|consen 80 QQKSGCRVQIAADPSGIGYRSVDLTGSPENVEVAKQLIGEVVSRGR--------PPGGFPDN----------QGSVETTQ 141 (600)
T ss_pred hhhcCCccccCCCCCCcccccccccCCcccHHHHHHhhhhhhhccC--------CCCCcccc----------CCccceee
Confidence 4568888775 4456699999999999999999999875543321 00112111 11456899
Q ss_pred EEEeecccccccccccchHHHHHHhhcCceEEEcCC--CCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhhcccc-
Q 010611 189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT--MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE- 265 (506)
Q Consensus 189 rllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~--~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e~~~~- 265 (506)
.|+||+++||+||||+|++||+|++.+||++.+-.+ ......+.+.|+|.++. ++.|..++.+.+.+..-+
T Consensus 142 eI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~------ve~a~~lV~dil~e~~~~~ 215 (600)
T KOG1676|consen 142 EILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDK------VEQAKQLVADILREEDDEV 215 (600)
T ss_pred eeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHH------HHHHHHHHHHHHHhcccCC
Confidence 999999999999999999999999999999988764 22337889999999875 456777777766643221
Q ss_pred --cCCCcCCCCCceeEEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeCHHHHHHHHH
Q 010611 266 --KGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVY 343 (506)
Q Consensus 266 --~g~~~~~~~~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~~~V~~A~~ 343 (506)
.+...+.......+.+|.||.+.||.||||+|++||+|+.+||++|+|..|+.|. +.||.+.|.|+.++|..|.+
T Consensus 216 ~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~---speR~~~IiG~~d~ie~Aa~ 292 (600)
T KOG1676|consen 216 PGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPS---SPERPAQIIGTVDQIEHAAE 292 (600)
T ss_pred CccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCC---CccceeeeecCHHHHHHHHH
Confidence 1122333445566999999999999999999999999999999999999777764 89999999999999999999
Q ss_pred HHHHHhhcc
Q 010611 344 NVTGRLRDN 352 (506)
Q Consensus 344 ~I~~~L~e~ 352 (506)
+|+++|++.
T Consensus 293 lI~eii~~~ 301 (600)
T KOG1676|consen 293 LINEIIAEA 301 (600)
T ss_pred HHHHHHHHH
Confidence 999999774
No 3
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.97 E-value=2.1e-29 Score=243.87 Aligned_cols=288 Identities=24% Similarity=0.368 Sum_probs=186.9
Q ss_pred cCCeeEEEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhh
Q 010611 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE 261 (506)
Q Consensus 182 ~~~~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e 261 (506)
.+..+.+|||+.++.+|+||||||++||.|+.+++|+|+|.+ .+..||+++|+...+ .+..|+..++.
T Consensus 44 k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpd--s~~peri~tisad~~----------ti~~ilk~iip 111 (390)
T KOG2192|consen 44 KRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPD--SSGPERILTISADIE----------TIGEILKKIIP 111 (390)
T ss_pred hhcceeEEEEEecccccceeccccccHHHHhhhccceeeccC--CCCCceeEEEeccHH----------HHHHHHHHHhh
Confidence 356799999999999999999999999999999999999986 667899999998644 45555554432
Q ss_pred cccccCCCcCCCCCceeEEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeCHHHHHHH
Q 010611 262 GTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDA 341 (506)
Q Consensus 262 ~~~~~g~~~~~~~~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~~~V~~A 341 (506)
. .+.++. ....+.++|+|..+++|.|||++|++||++|+++.|+.+|..+.. ..++||+|.|.|.+..|..+
T Consensus 112 ~-lee~f~----~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~---p~stdrv~l~~g~~k~v~~~ 183 (390)
T KOG2192|consen 112 T-LEEGFQ----LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECC---PHSTDRVVLIGGKPKRVVEC 183 (390)
T ss_pred h-hhhCCC----CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccC---CCCcceEEEecCCcchHHHH
Confidence 1 122222 345689999999999999999999999999999999999986644 45999999999999999999
Q ss_pred HHHHHHHhhccccCCCccccccCCCCCccccCCCCCCCC----------CCCC-cCcCCcccccCC----CCCCC----C
Q 010611 342 VYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLK----------DPAS-FGVHSSVAVSHD----FSQPP----L 402 (506)
Q Consensus 342 ~~~I~~~L~e~~~~~~~~~~~~r~~~s~~~~~~py~~~~----------~p~~-~g~~~~~g~~~~----~~r~~----~ 402 (506)
++.|.+.|.|.+.++...+- ++.|.+.+..|.-.. .|++ -+++++++.... .+|.+ -
T Consensus 184 i~~il~~i~e~pikgsa~py----~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~r 259 (390)
T KOG2192|consen 184 IKIILDLISESPIKGSAQPY----DPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDR 259 (390)
T ss_pred HHHHHHHhhcCCcCCcCCcC----CccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCcc
Confidence 99999999998877642211 223444455443221 1111 122222221110 11111 0
Q ss_pred CCCCCccCCCCCCCCCCCCccccccc-cccccCCCCCCCCCCCcCCCCCCCCCcccCCCCccccccceEEEEEecccccc
Q 010611 403 TQGMDHLGLSHSLDCPSSPKLWTAQT-VTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIG 481 (506)
Q Consensus 403 ~~g~~~~~~s~~~~~p~~p~~~~~~~-~~g~~~~~~~d~~~g~~~g~~~~~~g~~~~sg~~~a~vt~~T~eI~VP~~~vG 481 (506)
+-+|. .|+..-.-|+.-..|.+.. .++|.|.+ ++.+..+..++...+ |... ..-+|.++.||.++-|
T Consensus 260 ydg~v--dFs~detw~saidtw~~SewqmaYePQg-------Gs~ydysyAG~~GsY-GdlG--GPitTaQvtip~dlgg 327 (390)
T KOG2192|consen 260 YDGMV--DFSADETWPSAIDTWSPSEWQMAYEPQG-------GSGYDYSYAGGYGSY-GDLG--GPITTAQVTIPKDLGG 327 (390)
T ss_pred ccccc--cccccccCCCcCCCcCccccccccCCCC-------CCCCCcccccccccc-CCCC--CceeeeeEecccccCc
Confidence 00111 1111101111112222211 12222221 111112222211111 1111 1346899999999999
Q ss_pred ccccCCCchHHHHHhhcCCeEEEe
Q 010611 482 SVYGENGSNLLRLRQVSCILNVFA 505 (506)
Q Consensus 482 ~IIGkgG~~Ik~Irq~SGA~I~I~ 505 (506)
.||||||..|++|+++|||.|+|.
T Consensus 328 siigkggqri~~ir~esGA~Ikid 351 (390)
T KOG2192|consen 328 SIIGKGGQRIKQIRHESGASIKID 351 (390)
T ss_pred ceecccchhhhhhhhccCceEEec
Confidence 999999999999999999999984
No 4
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.96 E-value=4e-29 Score=241.96 Aligned_cols=217 Identities=19% Similarity=0.363 Sum_probs=178.1
Q ss_pred hhcCccccccccccccCCCCCCCCcceeeccCCCCceeeEeeccCchhHHHHhhhccccCCCCCCCCCCcCCCCCCCCcc
Q 010611 91 LESGPQEILRRPLEVFAPESSHRSSEALSIETQHRLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLE 170 (506)
Q Consensus 91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~inis~~~~PeRivti~g~~~~i~~af~~i~~~l~~~~~~~n~~~~~~~~~~~~ 170 (506)
+-+|+.||+++|-||+| .|+|+|+|.||||++|+++.++|.+++..|...|+.-.
T Consensus 63 igkgg~nik~lr~d~na---------~v~vpds~~peri~tisad~~ti~~ilk~iip~lee~f---------------- 117 (390)
T KOG2192|consen 63 IGKGGKNIKALRTDYNA---------SVSVPDSSGPERILTISADIETIGEILKKIIPTLEEGF---------------- 117 (390)
T ss_pred eccccccHHHHhhhccc---------eeeccCCCCCceeEEEeccHHHHHHHHHHHhhhhhhCC----------------
Confidence 57899999999999999 99999999999999999999999999999864443311
Q ss_pred ccccccccccccCCeeEEEEEeecccccccccccchHHHHHHhhcCceEEEcC-CCCCCCcceEEEeccCCCCcCCChHH
Q 010611 171 SDRVATLDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA-TMPECDERLITVTASEGPESRYSPAQ 249 (506)
Q Consensus 171 ~~~~~~~~~~~~~~~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~-~~p~s~eRvVtIsG~~~~i~~~s~a~ 249 (506)
....++.+||||+++.+|.|||++|++||+|||++.|++++.. +.|.+++|+|.|.|.++. +.
T Consensus 118 ----------~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~------v~ 181 (390)
T KOG2192|consen 118 ----------QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKR------VV 181 (390)
T ss_pred ----------CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcch------HH
Confidence 1124689999999999999999999999999999999999975 579999999999998876 34
Q ss_pred HHHHHHHHHHhhccc-------------------------c------------------------------cC-------
Q 010611 250 KAVVLVFSRLIEGTS-------------------------E------------------------------KG------- 267 (506)
Q Consensus 250 ~Av~~i~~~i~e~~~-------------------------~------------------------------~g------- 267 (506)
..+..+++.+.+..+ . .+
T Consensus 182 ~~i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~ryd 261 (390)
T KOG2192|consen 182 ECIKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYD 261 (390)
T ss_pred HHHHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCcccc
Confidence 556566655433100 0 00
Q ss_pred --CC-----------------------------------------cCCCCCceeEEEEEeeccccceecccCcchHHhhh
Q 010611 268 --LD-----------------------------------------FSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMR 304 (506)
Q Consensus 268 --~~-----------------------------------------~~~~~~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr 304 (506)
.+ .+.-.+...+.++.||.++-|.||||+|+.|++|+
T Consensus 262 g~vdFs~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir 341 (390)
T KOG2192|consen 262 GMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIR 341 (390)
T ss_pred ccccccccccCCCcCCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhh
Confidence 00 00113456788999999999999999999999999
Q ss_pred hhcCceEEEccCcccccCCCCCeEEEEEeCHHHHHHHHHHHHHHhhcc
Q 010611 305 KVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN 352 (506)
Q Consensus 305 ~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~~~V~~A~~~I~~~L~e~ 352 (506)
+++||+|+|. +.+ .++.||+++|+|+.++++.|++++++.++..
T Consensus 342 ~esGA~Ikid-epl---eGsedrIitItGTqdQIqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 342 HESGASIKID-EPL---EGSEDRIITITGTQDQIQNAQYLLQNSVKQY 385 (390)
T ss_pred hccCceEEec-CcC---CCCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence 9999999996 212 4588999999999999999999999999754
No 5
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.95 E-value=6.2e-27 Score=250.68 Aligned_cols=213 Identities=28% Similarity=0.433 Sum_probs=166.8
Q ss_pred CCcceeeccCCCCceeeEeecc---------CchhHHHHhhhccccCCCCCCCCCCcCCCCCCCCccccccccccccccC
Q 010611 113 RSSEALSIETQHRLFGAVSQEI---------LPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQ 183 (506)
Q Consensus 113 ~~~~~inis~~~~PeRivti~g---------~~~~i~~af~~i~~~l~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~ 183 (506)
.++++|+.+.++|||||++++| .+++++|+|.+|+.+++...... .+. ......
T Consensus 73 ~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~d~~~~----------~d~-------~~~~~~ 135 (485)
T KOG2190|consen 73 ESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEEDDEAA----------EDN-------GEDASG 135 (485)
T ss_pred cccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhccccccccc----------ccC-------CccccC
Confidence 4567899999999999999999 99999999999998876322111 000 001112
Q ss_pred CeeEEEEEeecccccccccccchHHHHHHhhcCceEEEcCC-CCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhhc
Q 010611 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT-MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEG 262 (506)
Q Consensus 184 ~~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~-~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e~ 262 (506)
.++++|||||+++||+||||+|++||+|+++|||+|+|.++ +|.|+||.|+|.|.++. +.+|+..+...+.+.
T Consensus 136 ~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~a------v~~al~~Is~~L~~~ 209 (485)
T KOG2190|consen 136 PEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDA------VKKALVQISSRLLEN 209 (485)
T ss_pred CceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHH------HHHHHHHHHHHHHhc
Confidence 37999999999999999999999999999999999999987 89999999999999875 445666665554441
Q ss_pred c----c---------c-----------cC---------------------------------------------------
Q 010611 263 T----S---------E-----------KG--------------------------------------------------- 267 (506)
Q Consensus 263 ~----~---------~-----------~g--------------------------------------------------- 267 (506)
. . . .+
T Consensus 210 ~~~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i 289 (485)
T KOG2190|consen 210 PPRSPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASI 289 (485)
T ss_pred CCcCCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCce
Confidence 0 0 0 00
Q ss_pred ------CC----------cC---------------------CCC-CceeEEEEEeeccccceecccCcchHHhhhhhcCc
Q 010611 268 ------LD----------FS---------------------SNK-GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGT 309 (506)
Q Consensus 268 ------~~----------~~---------------------~~~-~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA 309 (506)
.+ +. ... ...++.+|+||++++||||||+|++|.+||+.|||
T Consensus 290 ~v~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA 369 (485)
T KOG2190|consen 290 SVGDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGA 369 (485)
T ss_pred EeccccCcceeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccchHHHHHhcCC
Confidence 00 00 000 34478999999999999999999999999999999
Q ss_pred eEEEc-cCcccccCCCCCeEEEEEeCHHHHHHHHHHHHHHhhc
Q 010611 310 SIRII-SDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD 351 (506)
Q Consensus 310 ~I~I~-~d~~P~~~~s~eR~VtItGt~~~V~~A~~~I~~~L~e 351 (506)
.|+|. +++. ....|+.++|+|...+...|++++..++..
T Consensus 370 ~I~I~~~~~~---~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~ 409 (485)
T KOG2190|consen 370 SISILNKEEV---SGVREALVQITGMLREDLLAQYLIRARLSA 409 (485)
T ss_pred ceEEcccccc---CCcceeEEEecchhHHHHhhhhhccccccc
Confidence 99999 4432 136899999999999999999999777754
No 6
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.93 E-value=3.7e-25 Score=219.98 Aligned_cols=166 Identities=26% Similarity=0.421 Sum_probs=129.9
Q ss_pred CeeEEEEEeecccccccccccchHHHHHHhhcCceEEEcCC---CCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHh
Q 010611 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT---MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLI 260 (506)
Q Consensus 184 ~~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~---~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~ 260 (506)
..+.+|+|||+..+|+||||||++|.+||.+|||+|++++. .|+.+||+|.|+|+-+. ....+..|++++.
T Consensus 37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~ea------i~av~efI~dKir 110 (402)
T KOG2191|consen 37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEA------LNAVHEFIADKIR 110 (402)
T ss_pred CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHH------HHHHHHHHHHHHH
Confidence 44999999999999999999999999999999999999874 69999999999998553 1222334555554
Q ss_pred hcccc-cC-CCc-CCC-CCceeEEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeCHH
Q 010611 261 EGTSE-KG-LDF-SSN-KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFS 336 (506)
Q Consensus 261 e~~~~-~g-~~~-~~~-~~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~~ 336 (506)
+.... .+ .+- ... ....-.++++||+..+|.||||+|++||.|++++||.|+|+. +.|..-+-.||+|++.|+++
T Consensus 111 e~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisP-qkpt~~sLqervvt~sge~e 189 (402)
T KOG2191|consen 111 EKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISP-QKPTGISLQERVVTVSGEPE 189 (402)
T ss_pred HhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecc-cCCCCccceeEEEEecCCHH
Confidence 43211 11 000 000 111235899999999999999999999999999999999982 33444456899999999999
Q ss_pred HHHHHHHHHHHHhhccccCC
Q 010611 337 KVKDAVYNVTGRLRDNHFSG 356 (506)
Q Consensus 337 ~V~~A~~~I~~~L~e~~~~~ 356 (506)
+..+|..+|.++|.|++...
T Consensus 190 ~~~~A~~~IL~Ki~eDpqs~ 209 (402)
T KOG2191|consen 190 QNMKAVSLILQKIQEDPQSG 209 (402)
T ss_pred HHHHHHHHHHHHhhcCCccc
Confidence 99999999999999987543
No 7
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.93 E-value=1e-25 Score=229.40 Aligned_cols=161 Identities=23% Similarity=0.381 Sum_probs=131.4
Q ss_pred ccCCeeEEEEEeecccccccccccchHHHHHHhhcCceEEEcCC-CCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHH
Q 010611 181 TQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT-MPECDERLITVTASEGPESRYSPAQKAVVLVFSRL 259 (506)
Q Consensus 181 ~~~~~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~-~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i 259 (506)
....++.+|+|||...+|.||||.|++||.|...|.|+|.|... ..+..||+|||.|+++. +-+|+.+|++-+
T Consensus 194 ~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg------~s~Ac~~ILeim 267 (584)
T KOG2193|consen 194 QQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG------TSKACKMILEIM 267 (584)
T ss_pred ccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc------hHHHHHHHHHHH
Confidence 34567899999999999999999999999999999999999864 56889999999999886 345666666544
Q ss_pred hhcccccCCCcCCCCCceeEEEEEeeccccceecccCcchHHhhhhhcCceEEEc--cCcccccCCCCCeEEEEEeCHHH
Q 010611 260 IEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII--SDQLLKCISENDRVVQISGEFSK 337 (506)
Q Consensus 260 ~e~~~~~g~~~~~~~~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~--~d~~P~~~~s~eR~VtItGt~~~ 337 (506)
..+..+.. -...+.++++-.+++||+||||.|.+||+|.++||++|.|. .| +. .-..||.|++.|+.++
T Consensus 268 qkEA~~~k------~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqe-ls--~ynpERTItVkGsiEa 338 (584)
T KOG2193|consen 268 QKEAVDDK------VAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQE-LS--LYNPERTITVKGSIEA 338 (584)
T ss_pred HHhhhccc------hhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhh-hc--ccCccceEEecccHHH
Confidence 33221111 12456789999999999999999999999999999999998 33 21 2257999999999999
Q ss_pred HHHHHHHHHHHhhccccCC
Q 010611 338 VKDAVYNVTGRLRDNHFSG 356 (506)
Q Consensus 338 V~~A~~~I~~~L~e~~~~~ 356 (506)
|..|-.+|..+|+++...+
T Consensus 339 c~~AE~eImkKlre~yEnD 357 (584)
T KOG2193|consen 339 CVQAEAEIMKKLRECYEND 357 (584)
T ss_pred HHHHHHHHHHHHHHHHhhh
Confidence 9999999999999975433
No 8
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.92 E-value=1.1e-25 Score=229.27 Aligned_cols=246 Identities=23% Similarity=0.356 Sum_probs=186.9
Q ss_pred cCCCCceeeEeeccCchhHHHHhhhccccCCCCCCCCCCcCCCCCCCCccccccccccccccCCeeEEEEEeeccccccc
Q 010611 121 ETQHRLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQEVSFRILCSNDKVGAV 200 (506)
Q Consensus 121 s~~~~PeRivti~g~~~~i~~af~~i~~~l~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~vtlrllIP~~~vG~I 200 (506)
+..+.-|+++|+-+.++-..+|..||.+.+-. ++. +.+. ..++.||++..+..||+|
T Consensus 238 en~Gaaek~itvh~tpEg~s~Ac~~ILeimqk-----------------EA~-----~~k~-~~e~pLk~lAHN~lvGRL 294 (584)
T KOG2193|consen 238 ENAGAAEKIITVHSTPEGTSKACKMILEIMQK-----------------EAV-----DDKV-AEEIPLKILAHNNLVGRL 294 (584)
T ss_pred ccCCcccCceEEecCccchHHHHHHHHHHHHH-----------------hhh-----ccch-hhhcchhhhhhcchhhhh
Confidence 44477999999999999999999998543311 000 0111 267999999999999999
Q ss_pred ccccchHHHHHHhhcCceEEEcCC---CCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhh---cccc---------
Q 010611 201 IGKGGTIIRALQSEAGAFISVGAT---MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE---GTSE--------- 265 (506)
Q Consensus 201 IGKgGs~IK~IreeTGa~I~V~~~---~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e---~~~~--------- 265 (506)
|||.|.+||+|+.+||++|.|+.- .--..||.|++.|.-++ +..|-.+|..++.+ .++.
T Consensus 295 IGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEa------c~~AE~eImkKlre~yEnDl~a~s~q~~l~ 368 (584)
T KOG2193|consen 295 IGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEA------CVQAEAEIMKKLRECYENDLAAMSLQCHLP 368 (584)
T ss_pred hhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHH------HHHHHHHHHHHHHHHHhhhHHHhhccCCCC
Confidence 999999999999999999999863 23456999999995443 23344444444332 2210
Q ss_pred cC-----C---CcC---------C-------------CCCceeEEEEEeeccccceecccCcchHHhhhhhcCceEEEcc
Q 010611 266 KG-----L---DFS---------S-------------NKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIIS 315 (506)
Q Consensus 266 ~g-----~---~~~---------~-------------~~~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~ 315 (506)
.+ + ++. + .......++|.||...||+||||+|.+||.|.+.+||.|+|..
T Consensus 369 P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIap 448 (584)
T KOG2193|consen 369 PGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAP 448 (584)
T ss_pred cccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecC
Confidence 00 0 000 0 0112346899999999999999999999999999999999985
Q ss_pred CcccccCCCCCeEEEEEeCHHHHHHHHHHHHHHhhccccCCCccccccCCCCCccccCCCCCCCCCCCCcCcCCcccccC
Q 010611 316 DQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSH 395 (506)
Q Consensus 316 d~~P~~~~s~eR~VtItGt~~~V~~A~~~I~~~L~e~~~~~~~~~~~~r~~~s~~~~~~py~~~~~p~~~g~~~~~g~~~ 395 (506)
...|. ..+|.|+|+|.+++..+|+-.|..+|.|..|..
T Consensus 449 pE~pd---vseRMViItGppeaqfKAQgrifgKikEenf~~--------------------------------------- 486 (584)
T KOG2193|consen 449 PEIPD---VSERMVIITGPPEAQFKAQGRIFGKIKEENFFL--------------------------------------- 486 (584)
T ss_pred CCCCC---cceeEEEecCChHHHHhhhhhhhhhhhhhccCC---------------------------------------
Confidence 44554 789999999999999999999999998853211
Q ss_pred CCCCCCCCCCCCccCCCCCCCCCCCCccccccccccccCCCCCCCCCCCcCCCCCCCCCcccCCCCccccccceEEEEEe
Q 010611 396 DFSQPPLTQGMDHLGLSHSLDCPSSPKLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIV 475 (506)
Q Consensus 396 ~~~r~~~~~g~~~~~~s~~~~~p~~p~~~~~~~~~g~~~~~~~d~~~g~~~g~~~~~~g~~~~sg~~~a~vt~~T~eI~V 475 (506)
|.- . -+..++|.|
T Consensus 487 -------------------------Pke------------------------------e------------vklethirV 499 (584)
T KOG2193|consen 487 -------------------------PKE------------------------------E------------VKLETHIRV 499 (584)
T ss_pred -------------------------chh------------------------------h------------heeeeeeec
Confidence 100 0 125679999
Q ss_pred ccccccccccCCCchHHHHHhhcCCeEEE
Q 010611 476 PENVIGSVYGENGSNLLRLRQVSCILNVF 504 (506)
Q Consensus 476 P~~~vG~IIGkgG~~Ik~Irq~SGA~I~I 504 (506)
|...+|+||||||.++++++..|+|.|.|
T Consensus 500 Ps~~aGRvIGKGGktVnELQnlt~AeV~v 528 (584)
T KOG2193|consen 500 PSSAAGRVIGKGGKTVNELQNLTSAEVVV 528 (584)
T ss_pred cchhhhhhhccccccHHHHhccccceEEc
Confidence 99999999999999999999999999987
No 9
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.92 E-value=7.4e-25 Score=232.59 Aligned_cols=215 Identities=23% Similarity=0.387 Sum_probs=162.7
Q ss_pred CCeeEEEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhhc
Q 010611 183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEG 262 (506)
Q Consensus 183 ~~~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e~ 262 (506)
...++.+..||.+.+|.||||+|+.|..|+.++||+|++........+|.+.++|.++++ ..|..+ ...++..
T Consensus 51 ~~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v------~~aK~l-i~evv~r 123 (600)
T KOG1676|consen 51 DTVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENV------EVAKQL-IGEVVSR 123 (600)
T ss_pred ccccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccH------HHHHHh-hhhhhhc
Confidence 356788899999999999999999999999999999998776667789999999998874 233322 2223322
Q ss_pred ccccCCCcCC-CCCceeEEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeCHHHHHHH
Q 010611 263 TSEKGLDFSS-NKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDA 341 (506)
Q Consensus 263 ~~~~g~~~~~-~~~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~~~V~~A 341 (506)
.... ..+.. .....++.+++||++.+|.||||+|++||.|++.+||++.+..|.. .+...++.+.|+|++++|+.|
T Consensus 124 ~~~~-~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~--~~~~~~KplritGdp~~ve~a 200 (600)
T KOG1676|consen 124 GRPP-GGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGS--IATGADKPLRITGDPDKVEQA 200 (600)
T ss_pred cCCC-CCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCC--cCCCCCCceeecCCHHHHHHH
Confidence 2100 01111 1235679999999999999999999999999999999999985431 122478899999999999999
Q ss_pred HHHHHHHhhccccCCCccccccCCCCCccccCCCCCCCCCCCCcCcCCcccccCCCCCCCCCCCCCccCCCCCCCCCCCC
Q 010611 342 VYNVTGRLRDNHFSGTLNTARTRSTSSVLTETSPYSRLKDPASFGVHSSVAVSHDFSQPPLTQGMDHLGLSHSLDCPSSP 421 (506)
Q Consensus 342 ~~~I~~~L~e~~~~~~~~~~~~r~~~s~~~~~~py~~~~~p~~~g~~~~~g~~~~~~r~~~~~g~~~~~~s~~~~~p~~p 421 (506)
..|+.++|+|... +.+ +.
T Consensus 201 ~~lV~dil~e~~~-~~~----------------------------------------------g~--------------- 218 (600)
T KOG1676|consen 201 KQLVADILREEDD-EVP----------------------------------------------GS--------------- 218 (600)
T ss_pred HHHHHHHHHhccc-CCC----------------------------------------------cc---------------
Confidence 9999999987321 000 00
Q ss_pred ccccccccccccCCCCCCCCCCCcCCCCCCCCCcccCCCCccccccceEEEEEeccccccccccCCCchHHHHHhhcCCe
Q 010611 422 KLWTAQTVTGVHLRGSSDVGRGWSQGLSHHKGGLELGSGSKSAIVTNTTVEIIVPENVIGSVYGENGSNLLRLRQVSCIL 501 (506)
Q Consensus 422 ~~~~~~~~~g~~~~~~~d~~~g~~~g~~~~~~g~~~~sg~~~a~vt~~T~eI~VP~~~vG~IIGkgG~~Ik~Irq~SGA~ 501 (506)
....|.. + + ..++.+|.||...||.||||+|++||+|+..|||+
T Consensus 219 -----~~~~g~~------------~------g-------------~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~K 262 (600)
T KOG1676|consen 219 -----GGHAGVR------------G------G-------------GSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAK 262 (600)
T ss_pred -----ccccCcC------------c------c-------------ccceeEEeccccceeeEEecCchHHHHHhhccCce
Confidence 0000000 0 0 12488999999999999999999999999999999
Q ss_pred EEEe
Q 010611 502 NVFA 505 (506)
Q Consensus 502 I~I~ 505 (506)
|+|-
T Consensus 263 IQfk 266 (600)
T KOG1676|consen 263 IQFK 266 (600)
T ss_pred eEee
Confidence 9984
No 10
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.70 E-value=9.8e-17 Score=160.21 Aligned_cols=74 Identities=23% Similarity=0.432 Sum_probs=70.4
Q ss_pred eeEEEEEeeccccceecccCcchHHhhhhhcCceEEEc--cCcccccCCCCCeEEEEEeCHHHHHHHHHHHHHHhhccc
Q 010611 277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII--SDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNH 353 (506)
Q Consensus 277 ~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~--~d~~P~~~~s~eR~VtItGt~~~V~~A~~~I~~~L~e~~ 353 (506)
.+.++++||+..+|.||||||++|.++|++|||+|+++ +|.+|+ .+||+|.|+|+.+++......|.++|+|.+
T Consensus 38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPG---TTeRvcli~Gt~eai~av~efI~dKire~p 113 (402)
T KOG2191|consen 38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPG---TTERVCLIQGTVEALNAVHEFIADKIREKP 113 (402)
T ss_pred ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCC---ccceEEEEeccHHHHHHHHHHHHHHHHHhH
Confidence 38899999999999999999999999999999999999 677887 899999999999999999999999999975
No 11
>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=99.52 E-value=3.8e-14 Score=133.90 Aligned_cols=139 Identities=19% Similarity=0.264 Sum_probs=97.9
Q ss_pred EEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEe---ccCCCCcCCChHHHHHHHHHHHHhhccccc
Q 010611 190 ILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVT---ASEGPESRYSPAQKAVVLVFSRLIEGTSEK 266 (506)
Q Consensus 190 llIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIs---G~~~~i~~~s~a~~Av~~i~~~i~e~~~~~ 266 (506)
+.||.+.+|.|||+||++||.|+++|||+|++.+ .+..|.|. +.++ .+++|...+.........+.
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~-----~~g~V~I~~~t~d~~------~i~kA~~~I~~i~~gf~~e~ 70 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS-----ETGEVKIEEEDEDPL------AVMKAREVVKAIGRGFSPEK 70 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc-----CCceEEEecCCCCHH------HHHHHHHHHHHHHcCCCHHH
Confidence 5689999999999999999999999999999984 33568883 3222 24555555543221100110
Q ss_pred CCCcCCCCCceeEEE-EEeec---------cccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeCHH
Q 010611 267 GLDFSSNKGLLVNAR-LVVAS---------NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFS 336 (506)
Q Consensus 267 g~~~~~~~~~~vt~~-l~VP~---------~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~~ 336 (506)
.+ .. ....+..+ +-|+. ..+|.|||++|++++.|++.|||+|.|. ++.|.|.|+++
T Consensus 71 A~--~l-~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~-----------~~~v~i~G~~~ 136 (172)
T TIGR03665 71 AL--KL-LDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY-----------GKTVGIIGDPE 136 (172)
T ss_pred HH--Hh-cCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc-----------CCEEEEECCHH
Confidence 00 00 01111222 22332 3789999999999999999999999994 25799999999
Q ss_pred HHHHHHHHHHHHhhccc
Q 010611 337 KVKDAVYNVTGRLRDNH 353 (506)
Q Consensus 337 ~V~~A~~~I~~~L~e~~ 353 (506)
+++.|..+|.+++....
T Consensus 137 ~~~~A~~~i~~li~~~~ 153 (172)
T TIGR03665 137 QVQIAREAIEMLIEGAP 153 (172)
T ss_pred HHHHHHHHHHHHHcCCC
Confidence 99999999999996543
No 12
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.45 E-value=3.9e-13 Score=127.85 Aligned_cols=142 Identities=18% Similarity=0.208 Sum_probs=99.4
Q ss_pred eEEEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEe----ccCCCCcCCChHHHHHHHHHHHHhh
Q 010611 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVT----ASEGPESRYSPAQKAVVLVFSRLIE 261 (506)
Q Consensus 186 vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIs----G~~~~i~~~s~a~~Av~~i~~~i~e 261 (506)
+...+.||.+.+|.|||++|++||.|+++|||+|++.+ .+..|.|. +.++ .+++|...+.+....
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~-----~~g~V~I~~~~~~d~~------~i~kA~~~I~ai~~g 71 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS-----ETGEVIIEPTDGEDPL------AVLKARDIVKAIGRG 71 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC-----CCCeEEEEeCCCCCHH------HHHHHHHHHHHHhcC
Confidence 46678999999999999999999999999999999985 24677786 2222 244555554432221
Q ss_pred cccccCCCcCCCCCceeEEEE-E----ee-----ccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEE
Q 010611 262 GTSEKGLDFSSNKGLLVNARL-V----VA-----SNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQI 331 (506)
Q Consensus 262 ~~~~~g~~~~~~~~~~vt~~l-~----VP-----~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtI 331 (506)
...+..+. . .+..+..++ - .+ ...+|.|||++|++++.|++.|||+|.|. ++.|.|
T Consensus 72 f~~e~A~~--l-~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~-----------~~~v~i 137 (180)
T PRK13763 72 FSPEKALR--L-LDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVY-----------GKTVAI 137 (180)
T ss_pred CCHHHHHH--H-hCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEc-----------CCEEEE
Confidence 00110000 0 001111111 1 11 13689999999999999999999999995 234999
Q ss_pred EeCHHHHHHHHHHHHHHhhcc
Q 010611 332 SGEFSKVKDAVYNVTGRLRDN 352 (506)
Q Consensus 332 tGt~~~V~~A~~~I~~~L~e~ 352 (506)
.|++++++.|...|..+++..
T Consensus 138 ~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 138 IGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred EeCHHHHHHHHHHHHHHHcCC
Confidence 999999999999999999654
No 13
>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=99.34 E-value=1.9e-12 Score=102.90 Aligned_cols=65 Identities=42% Similarity=0.647 Sum_probs=57.9
Q ss_pred EEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeCHHHHHHHHHHHH
Q 010611 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVT 346 (506)
Q Consensus 279 t~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~~~V~~A~~~I~ 346 (506)
+++|+||.+.+|+||||+|++|++|+++|||+|++.++..+ +..+|+|+|+|+++++.+|+.+|.
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLP---GSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCC---CCCceEEEEEeCHHHHHHHHHhhC
Confidence 36899999999999999999999999999999999844322 378999999999999999999873
No 14
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.23 E-value=3.5e-11 Score=127.63 Aligned_cols=147 Identities=24% Similarity=0.407 Sum_probs=115.8
Q ss_pred CCeeEEEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhhc
Q 010611 183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEG 262 (506)
Q Consensus 183 ~~~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e~ 262 (506)
..++.++++|++..+-.+|||+|++||.|++.++++|.+.... -..+++.++.|.+.+ ++++..+ ++..+.+
T Consensus 65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p~~---v~~a~a~---~~~~~~~- 136 (608)
T KOG2279|consen 65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFPVQ---VCKAKAA---IHQILTE- 136 (608)
T ss_pred hhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCCCC---CChHHHH---HHHHHhc-
Confidence 4678999999999999999999999999999999999997532 235677777776654 3333322 3333332
Q ss_pred ccccCCCcCCCCCceeEEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeCHHHHHHHH
Q 010611 263 TSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAV 342 (506)
Q Consensus 263 ~~~~g~~~~~~~~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~~~V~~A~ 342 (506)
...+...+-+|...++.|+|++|.++.+|+..++|+|.+..+. . ....+...|.|....+..|+
T Consensus 137 ------------~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ng--r--~g~~~~~~i~~qqk~~~~a~ 200 (608)
T KOG2279|consen 137 ------------NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNG--R--LGLSRLIKISGQQKEVAAAK 200 (608)
T ss_pred ------------CCcccccccchhhhcccccccchhhhcchhccccccccccccc--c--cccccceecccccchHHHHH
Confidence 3456778889999999999999999999999999999997321 1 14578888889988888999
Q ss_pred HHHHHHhhccc
Q 010611 343 YNVTGRLRDNH 353 (506)
Q Consensus 343 ~~I~~~L~e~~ 353 (506)
.++.+++.+..
T Consensus 201 ~~~~~~~~ede 211 (608)
T KOG2279|consen 201 HLILEKVSEDE 211 (608)
T ss_pred hhhhccccchh
Confidence 99999987653
No 15
>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=99.21 E-value=1.5e-11 Score=97.76 Aligned_cols=63 Identities=35% Similarity=0.718 Sum_probs=54.5
Q ss_pred EEEEEeecccccccccccchHHHHHHhhcCceEEEcCCC-CCCCcceEEEeccCCCCcCCChHHHHHHHH
Q 010611 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATM-PECDERLITVTASEGPESRYSPAQKAVVLV 255 (506)
Q Consensus 187 tlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~-p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i 255 (506)
++||+||.+.+|+||||+|++|++|+++|||+|++.+.. ++..+|+|+|.|..++ +++|+.++
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 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSA------VQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHH------HHHHHHhh
Confidence 479999999999999999999999999999999998754 4788999999998664 45666544
No 16
>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=99.14 E-value=7.1e-11 Score=111.65 Aligned_cols=61 Identities=28% Similarity=0.367 Sum_probs=54.1
Q ss_pred EEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEE---EeCHHHHHHHHHHHHHHhhc
Q 010611 282 LVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQI---SGEFSKVKDAVYNVTGRLRD 351 (506)
Q Consensus 282 l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtI---tGt~~~V~~A~~~I~~~L~e 351 (506)
+.||.+.+|.|||++|++|++|+++|||+|+|.. .+..|.| +++++++.+|+.+|..+.+.
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 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS---------ETGEVKIEEEDEDPLAVMKAREVVKAIGRG 65 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc---------CCceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence 5789999999999999999999999999999952 2356888 78999999999999998753
No 17
>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=99.09 E-value=1.4e-10 Score=90.37 Aligned_cols=60 Identities=35% Similarity=0.528 Sum_probs=53.9
Q ss_pred EEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeCHHHHHHHHHHH
Q 010611 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNV 345 (506)
Q Consensus 279 t~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~~~V~~A~~~I 345 (506)
|.+|.||.+++|+|||++|++|++|+++|||+|.|+.+ ..+..|+|+|++++|++|+.+|
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-------DERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST-------TEEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC-------CCcEEEEEEeCHHHHHHHHhhC
Confidence 57899999999999999999999999999999999733 1345899999999999999886
No 18
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.09 E-value=3.8e-10 Score=107.43 Aligned_cols=65 Identities=25% Similarity=0.270 Sum_probs=57.4
Q ss_pred eEEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEE----eCHHHHHHHHHHHHHHhhc
Q 010611 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQIS----GEFSKVKDAVYNVTGRLRD 351 (506)
Q Consensus 278 vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtIt----Gt~~~V~~A~~~I~~~L~e 351 (506)
....+.||.+.+|.|||++|++|+.|+++|||+|.+.. .+..|.|. ++++++.+|+.+|..+++.
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~---------~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~g 71 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS---------ETGEVIIEPTDGEDPLAVLKARDIVKAIGRG 71 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC---------CCCeEEEEeCCCCCHHHHHHHHHHHHHHhcC
Confidence 45789999999999999999999999999999999952 23678885 8999999999999998863
No 19
>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=99.09 E-value=1.6e-10 Score=90.58 Aligned_cols=60 Identities=20% Similarity=0.333 Sum_probs=54.3
Q ss_pred EEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeCHHHHHHHHHHH
Q 010611 280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNV 345 (506)
Q Consensus 280 ~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~~~V~~A~~~I 345 (506)
.++.||.+++|+|||++|++|++|+++|||+|.|++.. +.++.|+|+|+.++|..|+.+|
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~------~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG------SKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC------CCCCEEEEEcCHHHHHHHHHHh
Confidence 57899999999999999999999999999999997321 4688999999999999999886
No 20
>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=99.03 E-value=6.6e-10 Score=87.41 Aligned_cols=58 Identities=21% Similarity=0.313 Sum_probs=52.5
Q ss_pred eEEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeC-HHHHHHHHHHH
Q 010611 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNV 345 (506)
Q Consensus 278 vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt-~~~V~~A~~~I 345 (506)
....+.||.+++|+||||+|++|++|+++|||+|.|.+ ++.|.|+|+ .++++.|+.+|
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~----------~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED----------DGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC----------CCEEEEEeCCHHHHHHHHHHh
Confidence 45678999999999999999999999999999999952 467999998 99999999887
No 21
>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=98.96 E-value=1.9e-09 Score=84.36 Aligned_cols=62 Identities=35% Similarity=0.578 Sum_probs=55.1
Q ss_pred EEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeCHHHHHHHHHHH
Q 010611 280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNV 345 (506)
Q Consensus 280 ~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~~~V~~A~~~I 345 (506)
.++.||.+++|.|||++|++|++|+++|||+|.|..... ...++.|+|.|+.+++..|+.+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~----~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS----GSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC----CCCceEEEEEcCHHHHHHHHHHh
Confidence 579999999999999999999999999999999973211 25789999999999999999886
No 22
>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=98.88 E-value=1.4e-09 Score=84.63 Aligned_cols=51 Identities=27% Similarity=0.511 Sum_probs=45.5
Q ss_pred EEEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCC
Q 010611 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240 (506)
Q Consensus 187 tlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~ 240 (506)
|.+|.||.+.+|+||||+|++||+|+++|||+|++++. + .+..|+|+|.++
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~--~-~~~~v~I~G~~~ 51 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD--D-ERDIVTISGSPE 51 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--T-EEEEEEEEESHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--C-CcEEEEEEeCHH
Confidence 67899999999999999999999999999999999864 3 455999999654
No 23
>PF13014 KH_3: KH domain
Probab=98.85 E-value=3.4e-09 Score=77.36 Aligned_cols=42 Identities=40% Similarity=0.743 Sum_probs=39.1
Q ss_pred cccccccccchHHHHHHhhcCceEEEcC-CCCCCCcceEEEec
Q 010611 196 KVGAVIGKGGTIIRALQSEAGAFISVGA-TMPECDERLITVTA 237 (506)
Q Consensus 196 ~vG~IIGKgGs~IK~IreeTGa~I~V~~-~~p~s~eRvVtIsG 237 (506)
++|+||||+|++|++|+++|||+|+|++ ..++..+|.|+|+|
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 4799999999999999999999999998 46888999999987
No 24
>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=98.84 E-value=2.5e-09 Score=83.85 Aligned_cols=51 Identities=24% Similarity=0.264 Sum_probs=46.2
Q ss_pred EEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCC
Q 010611 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240 (506)
Q Consensus 188 lrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~ 240 (506)
.+|.||.+++|.|||++|++|++|+++|||+|.+++.. ..++.|+|+|.++
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--~~~~~v~I~G~~~ 52 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--SKSDTITITGPKE 52 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--CCCCEEEEEcCHH
Confidence 57899999999999999999999999999999998633 6789999999855
No 25
>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=98.83 E-value=5.9e-09 Score=81.52 Aligned_cols=53 Identities=34% Similarity=0.616 Sum_probs=48.1
Q ss_pred EEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCC
Q 010611 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240 (506)
Q Consensus 188 lrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~ 240 (506)
.++.||.+++|.|||++|++|++|+++|||+|.|.+...+..++.|.|.|..+
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~ 54 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPE 54 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHH
Confidence 57999999999999999999999999999999998755567899999999854
No 26
>PF13014 KH_3: KH domain
Probab=98.79 E-value=6.8e-09 Score=75.75 Aligned_cols=43 Identities=44% Similarity=0.737 Sum_probs=37.7
Q ss_pred ccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEe
Q 010611 288 QVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG 333 (506)
Q Consensus 288 ~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItG 333 (506)
++|+|||++|++|++|+++|||+|+|+++..+ .+.++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~---~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEP---GSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCC---CCCceEEEEEC
Confidence 58999999999999999999999999863333 37899999998
No 27
>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=98.74 E-value=1.6e-08 Score=79.56 Aligned_cols=47 Identities=28% Similarity=0.413 Sum_probs=42.7
Q ss_pred eEEEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEecc
Q 010611 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS 238 (506)
Q Consensus 186 vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~ 238 (506)
.+..+.||.+++|.||||+|++||+|+++|||+|.+.+ ++.|+|+|.
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~------~g~v~I~G~ 48 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED------DGTVYIAAS 48 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC------CCEEEEEeC
Confidence 45678999999999999999999999999999999974 467999996
No 28
>smart00322 KH K homology RNA-binding domain.
Probab=98.72 E-value=5.9e-08 Score=75.50 Aligned_cols=66 Identities=32% Similarity=0.553 Sum_probs=58.9
Q ss_pred eEEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeCHHHHHHHHHHHHHHh
Q 010611 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRL 349 (506)
Q Consensus 278 vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~~~V~~A~~~I~~~L 349 (506)
.+.++.||.+++|.+||++|++|++|++.+|++|.+..+. .....|+|.|+.+++..|..+|.+.+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~------~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG------SEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 5789999999999999999999999999999999997321 25788999999999999999998876
No 29
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.56 E-value=4.8e-07 Score=86.15 Aligned_cols=146 Identities=20% Similarity=0.276 Sum_probs=101.1
Q ss_pred eeEEEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhhccc
Q 010611 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTS 264 (506)
Q Consensus 185 ~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e~~~ 264 (506)
...+.+.||.+.+|.+||+.|+..|.|.+.+++++.+. +.+..|+|.......++ ...++|...+.+-
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD-----~~~~~V~i~~~~~t~Dp-~~~~ka~d~VkAI------ 74 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID-----SKTGSVTIRTTRKTEDP-LALLKARDVVKAI------ 74 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEE-----CCCCeEEEEecCCCCCh-HHHHHHHHHHHHH------
Confidence 34567999999999999999999999999999999997 56788998876321111 1233343333221
Q ss_pred ccCCCcCCC---CCceeEEEE------Ee-ec----cccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEE
Q 010611 265 EKGLDFSSN---KGLLVNARL------VV-AS----NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQ 330 (506)
Q Consensus 265 ~~g~~~~~~---~~~~vt~~l------~V-P~----~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~Vt 330 (506)
..|+++..+ ....+.+.+ .- ++ ...|.|||++|.+-+-|.+.|||.|-|. +..|.
T Consensus 75 grGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~-----------g~tVa 143 (194)
T COG1094 75 GRGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY-----------GKTVA 143 (194)
T ss_pred hcCCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe-----------CcEEE
Confidence 111111100 000111111 11 11 2469999999999999999999999995 34699
Q ss_pred EEeCHHHHHHHHHHHHHHhhccc
Q 010611 331 ISGEFSKVKDAVYNVTGRLRDNH 353 (506)
Q Consensus 331 ItGt~~~V~~A~~~I~~~L~e~~ 353 (506)
|.|.+++|+.|...|..++...+
T Consensus 144 iiG~~~~v~iAr~AVemli~G~~ 166 (194)
T COG1094 144 IIGGFEQVEIAREAVEMLINGAP 166 (194)
T ss_pred EecChhhhHHHHHHHHHHHcCCC
Confidence 99999999999999999997654
No 30
>smart00322 KH K homology RNA-binding domain.
Probab=98.36 E-value=1.2e-06 Score=67.95 Aligned_cols=54 Identities=33% Similarity=0.645 Sum_probs=46.8
Q ss_pred eeEEEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCC
Q 010611 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240 (506)
Q Consensus 185 ~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~ 240 (506)
.++.++.||...+|.+||++|++|++|++.||++|.+... ......+.|.|..+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~--~~~~~~v~i~g~~~ 55 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPED--GSEERVVEITGPPE 55 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCC--CCCccEEEEEcCHH
Confidence 3578899999999999999999999999999999999752 22678899999854
No 31
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=98.25 E-value=4.4e-07 Score=97.00 Aligned_cols=72 Identities=26% Similarity=0.378 Sum_probs=62.8
Q ss_pred CceeEEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeCHHHHHHHHHHHHHHhhc
Q 010611 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD 351 (506)
Q Consensus 275 ~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~~~V~~A~~~I~~~L~e 351 (506)
...+..++.|+...|-+++||+|.+|+.|+..++++|.+..++.+ .++.-.+.|-+.++..|.+++..++.+
T Consensus 65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g-----~e~~~~~~~~p~~v~~a~a~~~~~~~~ 136 (608)
T KOG2279|consen 65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG-----DERVLLISGFPVQVCKAKAAIHQILTE 136 (608)
T ss_pred hhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCC-----cccchhhccCCCCCChHHHHHHHHHhc
Confidence 356789999999999999999999999999999999999855443 467777888999999999999998854
No 32
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.24 E-value=7.2e-06 Score=93.57 Aligned_cols=199 Identities=15% Similarity=0.152 Sum_probs=129.7
Q ss_pred eeccCCCCceeeEeeccCchhHHHHhhhccccCCCCCCCCCCcCCCCCCCCccccccccccccccCCeeEEEEEeecccc
Q 010611 118 LSIETQHRLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDARTQQQEVSFRILCSNDKV 197 (506)
Q Consensus 118 inis~~~~PeRivti~g~~~~i~~af~~i~~~l~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~vtlrllIP~~~v 197 (506)
+.+.+...-+.-+.+.|.++.+..|...+...++... ..-+..++.+-....
T Consensus 161 ~~~~~~~~~~~~i~~~G~~e~V~~a~~~~~~~~~~~~----------------------------~r~~~~k~~v~~~~~ 212 (753)
T KOG2208|consen 161 LKIGEKAKKDPQIKLQGVVESVERAREPILNLIDRKN----------------------------ERSVFEKMNVGITLH 212 (753)
T ss_pred hhhhhhcccCCeeeeecchhhhhhhhhhhhhhhhccc----------------------------ceeEEEEeeccccch
Confidence 3344445557778999999999988888653332211 233677888888999
Q ss_pred cccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCCCCcC-CChHHHHHHHHHHH---------H--------
Q 010611 198 GAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESR-YSPAQKAVVLVFSR---------L-------- 259 (506)
Q Consensus 198 G~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~~i~~-~s~a~~Av~~i~~~---------i-------- 259 (506)
.++||++|.+++.+++++.+.+.++... -......|.|..+.... ..-.+.++.++-.. .
T Consensus 213 ~~~~g~g~~~~~~~~d~~~~~i~ip~sn--~~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~~~~~~~~~~~~~~ 290 (753)
T KOG2208|consen 213 SHIIGRGGSNISIIMDETKVHIHIPDSN--KSSPSNKIDGRLNSSSSINVEIQEALTRLESEFDYDEIIYRRLPRFIRGI 290 (753)
T ss_pred hhhccccccccccccccceeEEEccccc--ccchhhhhccccccceehhhhhHHHHHHhcChhhhhhhhhcccccccccc
Confidence 9999999999999999999999998631 11112222232111100 00011111111100 0
Q ss_pred --------hhcc------ccc-----------CCCcC-------------CCCCceeEEEEEeeccccceecccCcchHH
Q 010611 260 --------IEGT------SEK-----------GLDFS-------------SNKGLLVNARLVVASNQVGCLLGKGGTIIS 301 (506)
Q Consensus 260 --------~e~~------~~~-----------g~~~~-------------~~~~~~vt~~l~VP~~~vG~IIGkgG~~Ik 301 (506)
.... +.. +.+.+ .-....+.+.+.+-...+..++||+|.+|.
T Consensus 291 ~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~~~~v~GK~~~ni~ 370 (753)
T KOG2208|consen 291 PGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPEELKFVIGKKGANIE 370 (753)
T ss_pred ccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHHhhhhhcCCCCccHH
Confidence 0000 000 00000 002344778889999999999999999999
Q ss_pred hhhhhcCceEEEccCcccccCCCCCeEEEEEeCHHHHHHHHHHHHHHhhcc
Q 010611 302 EMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN 352 (506)
Q Consensus 302 eIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~~~V~~A~~~I~~~L~e~ 352 (506)
+|++.+.+.|.+.. .++.+..+.++|....+.+|...+.....+.
T Consensus 371 ki~e~~~~~i~~~~------~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei 415 (753)
T KOG2208|consen 371 KIREESQVKIDLPK------QGSNNKKVVITGVSANDEKAVEDVEKIIAEI 415 (753)
T ss_pred HHHHhhhhceeccc------ccCCCCCeEEeccccchhHHHHHHHHHHHhh
Confidence 99999999999973 1267888999999999999999999888653
No 33
>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=98.05 E-value=1.2e-05 Score=71.75 Aligned_cols=67 Identities=27% Similarity=0.302 Sum_probs=51.3
Q ss_pred ccccceecccCcchHHhhhhhcCceEEEccCcc------------cccC-CCCCeEEEEEeC---HHHHHHHHHHHHHHh
Q 010611 286 SNQVGCLLGKGGTIISEMRKVTGTSIRIISDQL------------LKCI-SENDRVVQISGE---FSKVKDAVYNVTGRL 349 (506)
Q Consensus 286 ~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~------------P~~~-~s~eR~VtItGt---~~~V~~A~~~I~~~L 349 (506)
-+++|.|||.+|++||+|+++|||+|.|..+.. |..+ ...+-.|.|++. .+++.+|..+|..++
T Consensus 14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll 93 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL 93 (120)
T ss_pred CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence 368899999999999999999999999983210 0000 112256999995 599999999999999
Q ss_pred hcc
Q 010611 350 RDN 352 (506)
Q Consensus 350 ~e~ 352 (506)
.+.
T Consensus 94 ~~~ 96 (120)
T cd02395 94 KPA 96 (120)
T ss_pred ccC
Confidence 753
No 34
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.74 E-value=0.00011 Score=67.37 Aligned_cols=102 Identities=20% Similarity=0.284 Sum_probs=69.6
Q ss_pred EEEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhhccccc
Q 010611 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEK 266 (506)
Q Consensus 187 tlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e~~~~~ 266 (506)
.+.++|+...+|..||++|++|+.|++..|-+|.|-.- +++ +...+.+.+.......
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~-------------s~d----------~~~fI~n~l~Pa~V~~ 89 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY-------------SDD----------PEEFIKNIFAPAAVRS 89 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc-------------CCC----------HHHHHHHHcCCCEEEE
Confidence 56688999999999999999999999999988887531 111 1122222111110000
Q ss_pred CCCcCCCCCceeEEEEEeeccccceecccCcchHHhhhhhcCceEEE
Q 010611 267 GLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRI 313 (506)
Q Consensus 267 g~~~~~~~~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I 313 (506)
... ..........+.|+.+..|..|||+|++|+.++.-+|-++.|
T Consensus 90 -v~I-~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 90 -VTI-KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred -EEE-EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 000 001223466788999999999999999999999999988766
No 35
>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=97.59 E-value=8.6e-05 Score=66.34 Aligned_cols=36 Identities=28% Similarity=0.537 Sum_probs=30.9
Q ss_pred EEEeec------ccccccccccchHHHHHHhhcCceEEEcCC
Q 010611 189 RILCSN------DKVGAVIGKGGTIIRALQSEAGAFISVGAT 224 (506)
Q Consensus 189 rllIP~------~~vG~IIGKgGs~IK~IreeTGa~I~V~~~ 224 (506)
++.||. .++|.|||++|++||+|+++|||+|.|.+.
T Consensus 3 ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~ 44 (120)
T cd02395 3 KVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGK 44 (120)
T ss_pred EEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecC
Confidence 455554 468999999999999999999999999864
No 36
>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=97.50 E-value=0.00039 Score=78.53 Aligned_cols=66 Identities=18% Similarity=0.275 Sum_probs=58.7
Q ss_pred ceeEEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEe-CHHHHHHHHHHHHHHhhc
Q 010611 276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD 351 (506)
Q Consensus 276 ~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItG-t~~~V~~A~~~I~~~L~e 351 (506)
.+....+.||.+.+|.|||.||++||+|+++|||+|.|. .+..|.|.+ +.+++++|+.+|..++..
T Consensus 576 aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~----------d~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 576 APRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE----------DDGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred CCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe----------cCcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 456778999999999999999999999999999999994 256799988 678999999999999974
No 37
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.49 E-value=5.1e-05 Score=76.55 Aligned_cols=140 Identities=21% Similarity=0.284 Sum_probs=97.9
Q ss_pred CeeEEEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhhcc
Q 010611 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGT 263 (506)
Q Consensus 184 ~~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e~~ 263 (506)
+.++..+-+|...++.|.|++|.+||.|+.+|...|+-+. -..|-+..++|..+.++ .|-..+-. ..+.
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPs---r~eePiF~vTg~~edv~------~aRrei~s--aaeH 92 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPS---RGEEPIFPVTGRHEDVR------RARREIPS--AAEH 92 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCC---CCCCCcceeccCchhHH------HHhhcCcc--ccce
Confidence 6788889999999999999999999999999999988652 23446777899877532 22221111 0001
Q ss_pred c---------ccCCCcCCCCCceeEEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeC
Q 010611 264 S---------EKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE 334 (506)
Q Consensus 264 ~---------~~g~~~~~~~~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt 334 (506)
+ ..+.. +.......+...-+|-..+|.+.|..|++|+.|++.+...|.-.-. ..+-++.++|-
T Consensus 93 ~~l~~~s~s~Sgg~~-~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~-------~~~~Vf~Vtg~ 164 (394)
T KOG2113|consen 93 FGLIRASRSFSGGTN-GASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR-------CGEPVFCVTGA 164 (394)
T ss_pred eeeeeecccccCCCc-cccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc-------CCCceEEEecC
Confidence 1 01111 1112334567788999999999999999999999999998887611 24667888887
Q ss_pred HHH-HHHHH
Q 010611 335 FSK-VKDAV 342 (506)
Q Consensus 335 ~~~-V~~A~ 342 (506)
+.+ +++|.
T Consensus 165 ~~nC~kra~ 173 (394)
T KOG2113|consen 165 PKNCVKRAR 173 (394)
T ss_pred Ccchhhhcc
Confidence 777 45554
No 38
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=97.48 E-value=0.0003 Score=80.59 Aligned_cols=141 Identities=18% Similarity=0.244 Sum_probs=103.2
Q ss_pred eeEEEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhhccc
Q 010611 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTS 264 (506)
Q Consensus 185 ~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e~~~ 264 (506)
.+...+-+-......++||+|.+|.+|+++++|.+.+.. .++++..+.++|...++ .+|...+.....+.
T Consensus 346 n~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~--~~~~~~~v~~~~~~~~~------~ka~~~v~~~~~ei-- 415 (753)
T KOG2208|consen 346 NENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK--QGSNNKKVVITGVSAND------EKAVEDVEKIIAEI-- 415 (753)
T ss_pred ceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc--ccCCCCCeEEeccccch------hHHHHHHHHHHHhh--
Confidence 355666677788999999999999999999999999985 56778889999986653 34444443322221
Q ss_pred ccCCCcCCCCCceeEEEEEeeccccceecccCcchHHhhhhhcC-ceEEEccCcccccCCCCCeEEEEEeCHHHHHHHHH
Q 010611 265 EKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTG-TSIRIISDQLLKCISENDRVVQISGEFSKVKDAVY 343 (506)
Q Consensus 265 ~~g~~~~~~~~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TG-A~I~I~~d~~P~~~~s~eR~VtItGt~~~V~~A~~ 343 (506)
..+.....+.+|...+..|||.+|..|+.|..++| .+|+...+. +....+++.|....+..++.
T Consensus 416 ---------~n~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~------~~~~~~~~~~~~~dv~~~~~ 480 (753)
T KOG2208|consen 416 ---------LNSIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN------NSSDMVTIRGISKDVEKSVS 480 (753)
T ss_pred ---------hcccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC------cccccceEeccccccchhHH
Confidence 11145677999999999999999999999999999 666665321 33445777777777666666
Q ss_pred HHHHHhh
Q 010611 344 NVTGRLR 350 (506)
Q Consensus 344 ~I~~~L~ 350 (506)
+...+..
T Consensus 481 ~~~~~~~ 487 (753)
T KOG2208|consen 481 LLKALKA 487 (753)
T ss_pred HHHhhhh
Confidence 5555443
No 39
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.47 E-value=0.0003 Score=64.52 Aligned_cols=37 Identities=24% Similarity=0.496 Sum_probs=33.9
Q ss_pred eEEEEEeeccccceecccCcchHHhhhhhcCceEEEc
Q 010611 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (506)
Q Consensus 278 vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~ 314 (506)
-.+.++|+...+|..||++|++|+.|++..|-+|.+.
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 3678889999999999999999999999999999886
No 40
>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=97.36 E-value=0.00053 Score=62.94 Aligned_cols=102 Identities=24% Similarity=0.303 Sum_probs=68.5
Q ss_pred EEEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhhccccc
Q 010611 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEK 266 (506)
Q Consensus 187 tlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e~~~~~ 266 (506)
-+-++|....+|..||++|++|+.|++..|-+|.|-. - +++. ...+.+.+.......
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe-----------y--s~D~----------~~fI~N~l~PA~V~~ 90 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE-----------Y--SENL----------EEFVANKLAPAEVKN 90 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE-----------c--CCCH----------HHHHHHcCCCceEEE
Confidence 4557888899999999999999999999998888753 1 1111 111111111100000
Q ss_pred CCCcCCCCCceeEEEEEeeccccceecccCcchHHhhhhhcCceEEE
Q 010611 267 GLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRI 313 (506)
Q Consensus 267 g~~~~~~~~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I 313 (506)
... ..........+.||.+..+..|||+|.+|+...+-+|-++.|
T Consensus 91 -V~i-~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI 135 (141)
T TIGR01952 91 -VTV-SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI 135 (141)
T ss_pred -EEE-EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence 000 001123567888999999999999999999999999987766
No 41
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.35 E-value=0.00026 Score=71.60 Aligned_cols=64 Identities=23% Similarity=0.380 Sum_probs=55.7
Q ss_pred CceeEEEEEeeccccceecccCcchHHhhhhhcCceEEEc-cCcccccCCCCCeEEEEEeCHHHHHHHHHHHH
Q 010611 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII-SDQLLKCISENDRVVQISGEFSKVKDAVYNVT 346 (506)
Q Consensus 275 ~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~-~d~~P~~~~s~eR~VtItGt~~~V~~A~~~I~ 346 (506)
...++..+.||..+|+.+.|++|++||.++.+|...|+-+ +. .|-++.++|..+.|..|+..|.
T Consensus 23 p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~--------eePiF~vTg~~edv~~aRrei~ 87 (394)
T KOG2113|consen 23 GQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG--------EEPIFPVTGRHEDVRRARREIP 87 (394)
T ss_pred CCccceeeecCcccceeecccCccccchhhhhhcceeccCCCC--------CCCcceeccCchhHHHHhhcCc
Confidence 3678999999999999999999999999999999999887 32 3456889999999999987753
No 42
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.15 E-value=0.0023 Score=68.42 Aligned_cols=76 Identities=21% Similarity=0.285 Sum_probs=58.0
Q ss_pred eeEEEEEeec------cccceecccCcchHHhhhhhcCceEEEcc-----Ccc------cccCCCC-CeEEEEEe-CHHH
Q 010611 277 LVNARLVVAS------NQVGCLLGKGGTIISEMRKVTGTSIRIIS-----DQL------LKCISEN-DRVVQISG-EFSK 337 (506)
Q Consensus 277 ~vt~~l~VP~------~~vG~IIGkgG~~IkeIr~~TGA~I~I~~-----d~~------P~~~~s~-eR~VtItG-t~~~ 337 (506)
..+-++.||- ++||.|||..|.+.|+|.++|||+|.|-. +.. ....... +-.|.|++ +.+.
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 5677888884 58999999999999999999999999972 111 0001122 23488888 6788
Q ss_pred HHHHHHHHHHHhhcc
Q 010611 338 VKDAVYNVTGRLRDN 352 (506)
Q Consensus 338 V~~A~~~I~~~L~e~ 352 (506)
|++|+.+|..+|.+.
T Consensus 217 i~~Ai~vienli~~a 231 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSA 231 (554)
T ss_pred HHHHHHHHHHHHHhh
Confidence 999999999999863
No 43
>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=97.07 E-value=0.0014 Score=74.51 Aligned_cols=66 Identities=21% Similarity=0.371 Sum_probs=56.4
Q ss_pred ceeEEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEe-CHHHHHHHHHHHHHHhhc
Q 010611 276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD 351 (506)
Q Consensus 276 ~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItG-t~~~V~~A~~~I~~~L~e 351 (506)
.+....+.||.+.+|.|||+||++||+|+++|||+|.|. .+-.|.|.+ ..+.+.+|..+|..+..+
T Consensus 549 ~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~----------ddG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 549 APRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE----------DDGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred CCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEe----------cCeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 346778999999999999999999999999999999995 245677777 677899999999888754
No 44
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=96.87 E-value=0.0025 Score=61.11 Aligned_cols=65 Identities=22% Similarity=0.283 Sum_probs=53.6
Q ss_pred eEEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEe-----CHHHHHHHHHHHHHHhhc
Q 010611 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-----EFSKVKDAVYNVTGRLRD 351 (506)
Q Consensus 278 vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItG-----t~~~V~~A~~~I~~~L~e 351 (506)
....+.||.+.+|.+||+.|+.-+.|.+.+|+++.+. +.+..|+|.. +|..+.+|...|..+=+-
T Consensus 8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD---------~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrG 77 (194)
T COG1094 8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID---------SKTGSVTIRTTRKTEDPLALLKARDVVKAIGRG 77 (194)
T ss_pred ceeeeecCchhheeeecccccchHHHHhhcCeEEEEE---------CCCCeEEEEecCCCCChHHHHHHHHHHHHHhcC
Confidence 3556899999999999999999999999999999995 3455677755 477889999888776643
No 45
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.74 E-value=0.0047 Score=59.45 Aligned_cols=99 Identities=29% Similarity=0.368 Sum_probs=66.4
Q ss_pred EEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhhcccccCCC
Q 010611 190 ILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLD 269 (506)
Q Consensus 190 llIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e~~~~~g~~ 269 (506)
+.+-.+.+|..||++|++|+.|+++.|=+|.|-. -++++ ...+.+.+....... ..
T Consensus 80 ~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe-------------~s~d~----------~~fI~nal~Pa~v~~-V~ 135 (190)
T COG0195 80 NVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVE-------------WSEDP----------AEFIKNALAPAEVLS-VN 135 (190)
T ss_pred eecCcCchhhhccCCChHHHHHHHHhCCceEEEE-------------eCCCH----------HHHHHHhcCcceEeE-EE
Confidence 4444678999999999999999999997777642 22222 111111111000000 00
Q ss_pred cCCCCCceeEEEEEeeccccceecccCcchHHhhhhhcCceEEEc
Q 010611 270 FSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (506)
Q Consensus 270 ~~~~~~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~ 314 (506)
... .... ...+.||.++.+..|||+|.+++-+.+-||-++.|.
T Consensus 136 ~~~-~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~ 178 (190)
T COG0195 136 IKE-DDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIE 178 (190)
T ss_pred EEe-CCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEE
Confidence 000 0111 778889999999999999999999999999999996
No 46
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.72 E-value=0.0017 Score=68.37 Aligned_cols=68 Identities=26% Similarity=0.295 Sum_probs=55.2
Q ss_pred CceeEEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeCHHHHHHHHHHHHHHh
Q 010611 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRL 349 (506)
Q Consensus 275 ~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~~~V~~A~~~I~~~L 349 (506)
.......+.|-+++||.+||++|++|+.||..|+++|+|.+. ..+-.|+|-|...--.+|...|....
T Consensus 44 ~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~-------~~e~kv~ifg~~~m~~kaka~id~~~ 111 (629)
T KOG0336|consen 44 GGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC-------DLEVKVTIFGINHMRKKAKASIDRGQ 111 (629)
T ss_pred CCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc-------CceeEEEEechHHHHHHHHhhHhhhh
Confidence 445677888999999999999999999999999999999743 35778999998776666665555444
No 47
>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=96.37 E-value=0.0068 Score=55.70 Aligned_cols=36 Identities=31% Similarity=0.637 Sum_probs=33.1
Q ss_pred EEEEEeeccccceecccCcchHHhhhhhcCceEEEc
Q 010611 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (506)
Q Consensus 279 t~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~ 314 (506)
.+-++|....+|..||++|++|+.|++..|-+|.+.
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 667889999999999999999999999999988886
No 48
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.36 E-value=0.0068 Score=70.21 Aligned_cols=67 Identities=18% Similarity=0.283 Sum_probs=58.0
Q ss_pred ceeEEEEEeeccccceecccCcchHHhhhhhcCce-EEEccCcccccCCCCCeEEEEEe-CHHHHHHHHHHHHHHhhcc
Q 010611 276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTS-IRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRDN 352 (506)
Q Consensus 276 ~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~-I~I~~d~~P~~~~s~eR~VtItG-t~~~V~~A~~~I~~~L~e~ 352 (506)
.+....+.||.+.+|.|||.||.+||.|.++||+. |.+. .+-.|.|.+ +.+++++|+.+|.++..+.
T Consensus 683 aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~----------ddg~V~I~a~d~~~i~~A~~~I~~l~~~~ 751 (891)
T PLN00207 683 APLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ----------DDGTVKITAKDLSSLEKSKAIISSLTMVP 751 (891)
T ss_pred CCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC----------CCeeEEEEeCCHHHHHHHHHHHHHHhcCc
Confidence 45678899999999999999999999999999999 8884 245688888 7889999999999988653
No 49
>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=96.35 E-value=0.0056 Score=69.42 Aligned_cols=51 Identities=31% Similarity=0.507 Sum_probs=44.7
Q ss_pred CeeEEEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCC
Q 010611 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240 (506)
Q Consensus 184 ~~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~ 240 (506)
-+-...+.||.+++|.|||+||++||+|+++|||+|.+.+ +..|.|.+...
T Consensus 576 aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------~G~V~I~a~d~ 626 (719)
T TIGR02696 576 APRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADG 626 (719)
T ss_pred CCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCH
Confidence 3567778999999999999999999999999999999974 67799998643
No 50
>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=96.34 E-value=0.0045 Score=48.61 Aligned_cols=36 Identities=31% Similarity=0.541 Sum_probs=33.6
Q ss_pred eEEEEEeecccccccccccchHHHHHHhhcCceEEE
Q 010611 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV 221 (506)
Q Consensus 186 vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V 221 (506)
....+.|+.+.+|..|||+|.+|+.+++.+|-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 578899999999999999999999999999988876
No 51
>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=96.15 E-value=0.0064 Score=47.73 Aligned_cols=36 Identities=17% Similarity=0.300 Sum_probs=34.0
Q ss_pred eEEEEEeccccccccccCCCchHHHHHhhcCCeEEE
Q 010611 469 TTVEIIVPENVIGSVYGENGSNLLRLRQVSCILNVF 504 (506)
Q Consensus 469 ~T~eI~VP~~~vG~IIGkgG~~Ik~Irq~SGA~I~I 504 (506)
....+.||.+.+|.+|||+|.||+.+++.+|-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 478999999999999999999999999999999987
No 52
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.02 E-value=0.0072 Score=60.34 Aligned_cols=41 Identities=22% Similarity=0.438 Sum_probs=36.7
Q ss_pred CCeeEEEEEeecc------cccccccccchHHHHHHhhcCceEEEcC
Q 010611 183 QQEVSFRILCSND------KVGAVIGKGGTIIRALQSEAGAFISVGA 223 (506)
Q Consensus 183 ~~~vtlrllIP~~------~vG~IIGKgGs~IK~IreeTGa~I~V~~ 223 (506)
.-.++.|++||.+ .||.|+|.+|.++|+|+++|||+|.|-.
T Consensus 89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrG 135 (259)
T KOG1588|consen 89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRG 135 (259)
T ss_pred ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEec
Confidence 4567889999986 6999999999999999999999999864
No 53
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=95.84 E-value=0.0044 Score=65.34 Aligned_cols=56 Identities=23% Similarity=0.325 Sum_probs=47.6
Q ss_pred ccCCeeEEEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccC
Q 010611 181 TQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239 (506)
Q Consensus 181 ~~~~~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~ 239 (506)
....+..+.|.|-+++||.|||++|++||.||..|+++|++-.+ ..+-.|+|-|..
T Consensus 42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~ 97 (629)
T KOG0336|consen 42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGIN 97 (629)
T ss_pred cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechH
Confidence 45677888899999999999999999999999999999999753 345668888863
No 54
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.73 E-value=0.025 Score=59.65 Aligned_cols=93 Identities=25% Similarity=0.283 Sum_probs=63.0
Q ss_pred ccccccccccchHHHHHHhhc-CceEEEcCCCCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhhcccccCCCcCCC
Q 010611 195 DKVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN 273 (506)
Q Consensus 195 ~~vG~IIGKgGs~IK~IreeT-Ga~I~V~~~~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e~~~~~g~~~~~~ 273 (506)
+-+|..||++|++|+.|.++. |=+|.|-. =++++ ...+...+....... .. .
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~-------------~s~D~----------~~fI~Nal~Pa~V~~-V~--i- 303 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIE-------------YSNVP----------EIFIARALAPAIISS-VK--I- 303 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEE-------------cCCCH----------HHHHHHhCCCceeeE-EE--E-
Confidence 458999999999999999988 66666642 11221 111222111100000 00 0
Q ss_pred CCceeEEEEEeeccccceecccCcchHHhhhhhcCceEEEc
Q 010611 274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (506)
Q Consensus 274 ~~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~ 314 (506)
........+.||.++.+..|||+|.+++-..+-||.+|.|.
T Consensus 304 ~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~ 344 (374)
T PRK12328 304 EEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELN 344 (374)
T ss_pred cCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEE
Confidence 01124678899999999999999999999999999999998
No 55
>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=95.70 E-value=0.015 Score=66.30 Aligned_cols=50 Identities=32% Similarity=0.497 Sum_probs=43.4
Q ss_pred CeeEEEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccC
Q 010611 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239 (506)
Q Consensus 184 ~~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~ 239 (506)
.+-...+.||.+++|.|||+||++||+|+++|||+|.+.+ +-.|.|.+..
T Consensus 549 ~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------dG~V~i~~~~ 598 (684)
T TIGR03591 549 APRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------DGTVKIAASD 598 (684)
T ss_pred CCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec------CeEEEEEECc
Confidence 3567778999999999999999999999999999999974 5668887754
No 56
>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=95.61 E-value=0.03 Score=58.72 Aligned_cols=94 Identities=28% Similarity=0.384 Sum_probs=62.9
Q ss_pred ccccccccccchHHHHHHhhc-CceEEEcCCCCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhhcccccCCCcCCC
Q 010611 195 DKVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN 273 (506)
Q Consensus 195 ~~vG~IIGKgGs~IK~IreeT-Ga~I~V~~~~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e~~~~~g~~~~~~ 273 (506)
+-+|+.||++|++|+.|.++. |=+|.|-. =+.++ ...+...+.......- . -.+
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~-------------~s~d~----------~~fi~nal~Pa~v~~v-~-i~~ 297 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIE-------------YSDDP----------AEFIANALSPAKVISV-E-VLD 297 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEE-------------cCCCH----------HHHHHHhcCCceEEEE-E-EEc
Confidence 458999999999999999988 66776642 11121 1111111111000000 0 000
Q ss_pred CCceeEEEEEeeccccceecccCcchHHhhhhhcCceEEEc
Q 010611 274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (506)
Q Consensus 274 ~~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~ 314 (506)
. ......+.||.++.+..|||+|.+++-..+-||.+|.|.
T Consensus 298 ~-~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~ 337 (341)
T TIGR01953 298 E-DKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVK 337 (341)
T ss_pred C-CCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEE
Confidence 1 124788999999999999999999999999999999996
No 57
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=95.60 E-value=0.03 Score=62.71 Aligned_cols=70 Identities=20% Similarity=0.299 Sum_probs=59.4
Q ss_pred eeEEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeCH-HHHHHHHHHHHHHhhccccC
Q 010611 277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEF-SKVKDAVYNVTGRLRDNHFS 355 (506)
Q Consensus 277 ~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~-~~V~~A~~~I~~~L~e~~~~ 355 (506)
+....+.|+.+.++-+||++|++|++|.++|||+|.|. .+-.|.|.++. +.+.+|+..|.++.++....
T Consensus 551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie----------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg 620 (692)
T COG1185 551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE----------DDGTVKIAASDGESAKKAKERIEAITREVEVG 620 (692)
T ss_pred CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec----------CCCcEEEEecchHHHHHHHHHHHHHHhhcccc
Confidence 44677889999999999999999999999999999995 24468999965 78899999999999776543
Q ss_pred C
Q 010611 356 G 356 (506)
Q Consensus 356 ~ 356 (506)
.
T Consensus 621 ~ 621 (692)
T COG1185 621 E 621 (692)
T ss_pred c
Confidence 3
No 58
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.57 E-value=0.028 Score=55.96 Aligned_cols=67 Identities=21% Similarity=0.284 Sum_probs=55.9
Q ss_pred EEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeC-HHHHHHHHHHHHHHhhccccC
Q 010611 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRLRDNHFS 355 (506)
Q Consensus 279 t~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt-~~~V~~A~~~I~~~L~e~~~~ 355 (506)
-+.+.||.++++.+||++|..|+.|.+.++++|.+- .+-.|.|.|+ .+++.+|..+|..+-++....
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig----------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~~ 213 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG----------QNGRIWIKGPDEEDEEIAIEAIKKIEREAHTS 213 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc----------CCcEEEEeeCCHHHHHHHHHHHHHHHhhhhcc
Confidence 357889999999999999999999999999999884 2346889885 558899999998888776543
No 59
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=95.48 E-value=0.017 Score=59.42 Aligned_cols=69 Identities=22% Similarity=0.331 Sum_probs=56.8
Q ss_pred eEEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEe-CHHHHHHHHHHHHHHhhcc
Q 010611 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRDN 352 (506)
Q Consensus 278 vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItG-t~~~V~~A~~~I~~~L~e~ 352 (506)
....+.|++.+.|.|||++|.+-++|+++|+++|.++.. . .+...++|+| ..++|..|...|...|.+.
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p---~---~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP---N---TNKEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC---C---CCcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 456788999999999999999999999999999999832 1 2344455555 7889999999999998765
No 60
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.43 E-value=0.038 Score=58.41 Aligned_cols=94 Identities=28% Similarity=0.305 Sum_probs=63.0
Q ss_pred ccccccccccchHHHHHHhhc-CceEEEcCCCCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhhcccccCCCcCCC
Q 010611 195 DKVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN 273 (506)
Q Consensus 195 ~~vG~IIGKgGs~IK~IreeT-Ga~I~V~~~~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e~~~~~g~~~~~~ 273 (506)
+-+|+.||++|++|+.|.++. |=+|.|-. =++++ ...+...+.......- . -.
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~-------------~s~d~----------~~fi~nal~Pa~v~~v-~-i~- 298 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIID-------------WSEDP----------AEFVANALSPAKVVSV-E-VD- 298 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEE-------------cCCCH----------HHHHHHhCCCceEEEE-E-EE-
Confidence 459999999999999999988 77777642 11121 1111111111000000 0 00
Q ss_pred CCceeEEEEEeeccccceecccCcchHHhhhhhcCceEEEc
Q 010611 274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (506)
Q Consensus 274 ~~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~ 314 (506)
........+.||.++.+.-|||+|.+++-..+-||.+|.|.
T Consensus 299 ~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~ 339 (362)
T PRK12327 299 DEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIK 339 (362)
T ss_pred cCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEE
Confidence 01124688999999999999999999999999999999997
No 61
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.30 E-value=0.035 Score=59.60 Aligned_cols=94 Identities=28% Similarity=0.343 Sum_probs=62.4
Q ss_pred ccccccccccchHHHHHHhhc-CceEEEcCCCCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhhcccccCCCcCCC
Q 010611 195 DKVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN 273 (506)
Q Consensus 195 ~~vG~IIGKgGs~IK~IreeT-Ga~I~V~~~~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e~~~~~g~~~~~~ 273 (506)
+-+|+.||++|++|+.|.++. |=+|.|-. =++++ ...+...+.......- .. .+
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~-------------ys~Dp----------~~fI~NaLsPA~V~~V-~i-~~ 331 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIR-------------WSPDP----------ATYIANALSPARVDEV-RL-VD 331 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEE-------------cCCCH----------HHHHHHhcCCceeeEE-EE-Ec
Confidence 559999999999999999988 66666632 12221 1112111111000000 00 00
Q ss_pred CCceeEEEEEeeccccceecccCcchHHhhhhhcCceEEEc
Q 010611 274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (506)
Q Consensus 274 ~~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~ 314 (506)
.......+.||.++.+.-|||+|.+++-..+-||.+|.|.
T Consensus 332 -~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~ 371 (449)
T PRK12329 332 -PEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIK 371 (449)
T ss_pred -CCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccc
Confidence 1123578999999999999999999999999999999986
No 62
>PRK00468 hypothetical protein; Provisional
Probab=95.27 E-value=0.018 Score=47.36 Aligned_cols=34 Identities=29% Similarity=0.534 Sum_probs=30.1
Q ss_pred cCCeeEEEEEeecccccccccccchHHHHHHhhc
Q 010611 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEA 215 (506)
Q Consensus 182 ~~~~vtlrllIP~~~vG~IIGKgGs~IK~IreeT 215 (506)
.+..+.++|.|..+.+|.||||+|.+|+.||.--
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 3456899999999999999999999999999754
No 63
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=95.13 E-value=0.061 Score=51.85 Aligned_cols=36 Identities=17% Similarity=0.231 Sum_probs=34.1
Q ss_pred EEEEEeccccccccccCCCchHHHHHhhcCCeEEEe
Q 010611 470 TVEIIVPENVIGSVYGENGSNLLRLRQVSCILNVFA 505 (506)
Q Consensus 470 T~eI~VP~~~vG~IIGkgG~~Ik~Irq~SGA~I~I~ 505 (506)
...+.||.+..+.+|||+|.|++-+.+.||-++.|.
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~ 178 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIE 178 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEE
Confidence 678899999999999999999999999999999885
No 64
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.08 E-value=0.033 Score=63.71 Aligned_cols=65 Identities=22% Similarity=0.352 Sum_probs=54.6
Q ss_pred eeEEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEe-CHHHHHHHHHHHHHHhhc
Q 010611 277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD 351 (506)
Q Consensus 277 ~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItG-t~~~V~~A~~~I~~~L~e 351 (506)
+....+.||.+.++.+||.||.+||+|.++||+.|.+. .+-.|.|.+ ..+.+.+|..+|..+..+
T Consensus 553 p~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~----------d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 553 PRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE----------DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred chheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC----------CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 34566778999999999999999999999999987773 245688888 678899999999988864
No 65
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.03 E-value=0.052 Score=59.28 Aligned_cols=93 Identities=28% Similarity=0.386 Sum_probs=62.9
Q ss_pred ccccccccccchHHHHHHhhc-CceEEEcCCCCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhhcccccCCCcCCC
Q 010611 195 DKVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN 273 (506)
Q Consensus 195 ~~vG~IIGKgGs~IK~IreeT-Ga~I~V~~~~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e~~~~~g~~~~~~ 273 (506)
+-+|+.||++|++|+.|.++. |=+|.|-. =++++ ...+...+.......- -.+
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~-------------~s~d~----------~~fi~nal~pa~v~~v---~~~ 298 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIIL-------------WSDDP----------AQFIINALSPAEVSSV---VVD 298 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEE-------------cCCCH----------HHHHHHhCCCCEEEEE---EEe
Confidence 348999999999999999988 66776642 11221 1112221111100000 000
Q ss_pred CCceeEEEEEeeccccceecccCcchHHhhhhhcCceEEEc
Q 010611 274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (506)
Q Consensus 274 ~~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~ 314 (506)
. ..-.+.+.||.++.+.-|||+|.+++-..+-||.+|.|.
T Consensus 299 ~-~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~ 338 (470)
T PRK09202 299 E-DEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIM 338 (470)
T ss_pred C-CCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEE
Confidence 0 123788999999999999999999999999999999997
No 66
>PRK02821 hypothetical protein; Provisional
Probab=94.84 E-value=0.024 Score=46.75 Aligned_cols=35 Identities=29% Similarity=0.531 Sum_probs=30.4
Q ss_pred CCeeEEEEEeecccccccccccchHHHHHHhhcCc
Q 010611 183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGA 217 (506)
Q Consensus 183 ~~~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa 217 (506)
...+.+.|.|..+.+|.||||+|.+|+.||.--.+
T Consensus 28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 44578999999999999999999999999986543
No 67
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.68 E-value=0.032 Score=45.89 Aligned_cols=33 Identities=27% Similarity=0.535 Sum_probs=29.9
Q ss_pred CCeeEEEEEeecccccccccccchHHHHHHhhc
Q 010611 183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEA 215 (506)
Q Consensus 183 ~~~vtlrllIP~~~vG~IIGKgGs~IK~IreeT 215 (506)
+..+.++|-+..+.+|.||||+|.+|+.||.--
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 567899999999999999999999999999753
No 68
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=94.57 E-value=0.035 Score=55.55 Aligned_cols=76 Identities=20% Similarity=0.253 Sum_probs=52.3
Q ss_pred CceeEEEEEeec------cccceecccCcchHHhhhhhcCceEEEcc-----Cc--------ccccCCCCC---eEEEEE
Q 010611 275 GLLVNARLVVAS------NQVGCLLGKGGTIISEMRKVTGTSIRIIS-----DQ--------LLKCISEND---RVVQIS 332 (506)
Q Consensus 275 ~~~vt~~l~VP~------~~vG~IIGkgG~~IkeIr~~TGA~I~I~~-----d~--------~P~~~~s~e---R~VtIt 332 (506)
.-..+.+|+||- ++||.|+|..|.++|+|+++|||+|-|-. |. .|+++--++ -.|...
T Consensus 89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~ 168 (259)
T KOG1588|consen 89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETE 168 (259)
T ss_pred ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEe
Confidence 445688899985 48999999999999999999999999971 10 122221122 235556
Q ss_pred eCHHHH----HHHHHHHHHHhh
Q 010611 333 GEFSKV----KDAVYNVTGRLR 350 (506)
Q Consensus 333 Gt~~~V----~~A~~~I~~~L~ 350 (506)
+++.-+ ..|+..|..+|.
T Consensus 169 ~p~~ea~~rl~~AleeI~klL~ 190 (259)
T KOG1588|consen 169 APPAEAYARLAYALEEIKKLLV 190 (259)
T ss_pred CCHHHHHHHHHHHHHHHHHhcC
Confidence 666544 457777777774
No 69
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=94.55 E-value=0.043 Score=56.46 Aligned_cols=52 Identities=25% Similarity=0.346 Sum_probs=43.2
Q ss_pred eEEEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccC
Q 010611 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239 (506)
Q Consensus 186 vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~ 239 (506)
...-++++....|.|||++|.+-|+|+++|+++|.++. |+...-.|+|+|..
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~--p~~n~~~i~i~~~~ 108 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPR--PNTNKEEIKIIGIS 108 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccC--CCCCcceEEEeehh
Confidence 44568899999999999999999999999999999986 55455557777653
No 70
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=94.49 E-value=0.076 Score=58.72 Aligned_cols=66 Identities=20% Similarity=0.306 Sum_probs=51.1
Q ss_pred eeEEEEEeec-cccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEe-CHHHHHHHHHHHHHHhhc
Q 010611 277 LVNARLVVAS-NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD 351 (506)
Q Consensus 277 ~vt~~l~VP~-~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItG-t~~~V~~A~~~I~~~L~e 351 (506)
.....+.+|+ ++-|.||||.|.+|+-+...||+.|-| |+.| ..|+|+| .|-.-+.|...+..++.+
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~ii--ddtp-------~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLII--DDTP-------EAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEE--cCCC-------CeEEecCCchHHHHHHHHHHHHHHHc
Confidence 3455677887 677999999999999999999999999 4334 3577888 666666677777776654
No 71
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=94.45 E-value=0.04 Score=59.27 Aligned_cols=39 Identities=26% Similarity=0.421 Sum_probs=34.0
Q ss_pred eeEEEEEeecc------cccccccccchHHHHHHhhcCceEEEcC
Q 010611 185 EVSFRILCSND------KVGAVIGKGGTIIRALQSEAGAFISVGA 223 (506)
Q Consensus 185 ~vtlrllIP~~------~vG~IIGKgGs~IK~IreeTGa~I~V~~ 223 (506)
.++-|+.||.+ +||+|||..|.+.|+|+++|||||.|-.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRG 181 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRG 181 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEec
Confidence 45567888864 6999999999999999999999999965
No 72
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=94.45 E-value=0.032 Score=64.97 Aligned_cols=70 Identities=17% Similarity=0.150 Sum_probs=58.7
Q ss_pred EEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeCHHHHHHHHHHHHHHhhc
Q 010611 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD 351 (506)
Q Consensus 279 t~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~~~V~~A~~~I~~~L~e 351 (506)
.-++.+|-....++||++|.+|+.++..|||.|.+.+-+ |. ...||.+.+.|.++.+..|...|.-.+.|
T Consensus 1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq-~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ-PD--NQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred ccccccchhhhhhhhccCcchhhhHhhccceEEehhhcC-Cc--cchhhhcccCCCChhhhhhhccccceeec
Confidence 346778888899999999999999999999999997321 11 25799999999999999999888777755
No 73
>PRK12704 phosphodiesterase; Provisional
Probab=94.26 E-value=0.09 Score=58.25 Aligned_cols=65 Identities=20% Similarity=0.309 Sum_probs=50.0
Q ss_pred eEEEEEeec-cccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEe-CHHHHHHHHHHHHHHhhc
Q 010611 278 VNARLVVAS-NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD 351 (506)
Q Consensus 278 vt~~l~VP~-~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItG-t~~~V~~A~~~I~~~L~e 351 (506)
....+.+|+ ++-|.||||.|.+|+-+...||+.|-| |+.| ..|.|+| ++-.-+.|...+..++.+
T Consensus 210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~ii--ddtp-------~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLII--DDTP-------EAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEE--cCCC-------CeEEEecCChhhHHHHHHHHHHHHhc
Confidence 345567787 678999999999999999999999999 4333 4688998 565555677776666654
No 74
>PRK00106 hypothetical protein; Provisional
Probab=94.23 E-value=0.1 Score=57.87 Aligned_cols=66 Identities=23% Similarity=0.352 Sum_probs=51.4
Q ss_pred eeEEEEEeec-cccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEe-CHHHHHHHHHHHHHHhhc
Q 010611 277 LVNARLVVAS-NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD 351 (506)
Q Consensus 277 ~vt~~l~VP~-~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItG-t~~~V~~A~~~I~~~L~e 351 (506)
.....+.+|+ ++-|.||||.|.+|+-+...||+.+-| |+.| ..|+|+| +|-.-+-|...+..++.+
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdlii--ddtp-------~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVII--DDTP-------EVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEE--cCCC-------CeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 3455677888 677999999999999999999999999 4333 3577998 666666677777666654
No 75
>PRK00468 hypothetical protein; Provisional
Probab=94.06 E-value=0.051 Score=44.66 Aligned_cols=33 Identities=33% Similarity=0.454 Sum_probs=29.2
Q ss_pred CceeEEEEEeeccccceecccCcchHHhhhhhc
Q 010611 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVT 307 (506)
Q Consensus 275 ~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~T 307 (506)
...+.+++.+..+.+|.||||+|.+|+.||.--
T Consensus 27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 455788999999999999999999999998754
No 76
>PRK01064 hypothetical protein; Provisional
Probab=93.95 E-value=0.053 Score=44.87 Aligned_cols=33 Identities=21% Similarity=0.538 Sum_probs=30.1
Q ss_pred CCeeEEEEEeecccccccccccchHHHHHHhhc
Q 010611 183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEA 215 (506)
Q Consensus 183 ~~~vtlrllIP~~~vG~IIGKgGs~IK~IreeT 215 (506)
...+.+++.|..+..|.+|||+|.+|+.||.-.
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 567899999999999999999999999999854
No 77
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=93.73 E-value=0.11 Score=50.22 Aligned_cols=78 Identities=17% Similarity=0.309 Sum_probs=51.9
Q ss_pred CceeEEEEEee------ccccceecccCcchHHhhhhhcCceEEEccC----------cccccCCCCCeE--EEE-EeCH
Q 010611 275 GLLVNARLVVA------SNQVGCLLGKGGTIISEMRKVTGTSIRIISD----------QLLKCISENDRV--VQI-SGEF 335 (506)
Q Consensus 275 ~~~vt~~l~VP------~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d----------~~P~~~~s~eR~--VtI-tGt~ 335 (506)
....+-+++|| .++||.|||..|.+.|++++.|+|+|.|-.. ++|......+.+ +.| --+.
T Consensus 145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adse 224 (269)
T COG5176 145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSE 224 (269)
T ss_pred cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchh
Confidence 34556678887 5699999999999999999999999999621 111111111111 223 3355
Q ss_pred HHHHHHHHHHHHHhhcc
Q 010611 336 SKVKDAVYNVTGRLRDN 352 (506)
Q Consensus 336 ~~V~~A~~~I~~~L~e~ 352 (506)
+.++.++..+.+.++++
T Consensus 225 dki~~~ik~~~n~I~~a 241 (269)
T COG5176 225 DKICRLIKSQLNAIREA 241 (269)
T ss_pred hhHHHHHHHHHHHHHHH
Confidence 66777777777777665
No 78
>PRK02821 hypothetical protein; Provisional
Probab=93.38 E-value=0.07 Score=44.05 Aligned_cols=30 Identities=33% Similarity=0.490 Sum_probs=27.6
Q ss_pred eEEEEEeccccccccccCCCchHHHHHhhc
Q 010611 469 TTVEIIVPENVIGSVYGENGSNLLRLRQVS 498 (506)
Q Consensus 469 ~T~eI~VP~~~vG~IIGkgG~~Ik~Irq~S 498 (506)
...++.|..+-+|+||||+|.+|+.||..-
T Consensus 31 ~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv 60 (77)
T PRK02821 31 RTLEVRVHPDDLGKVIGRGGRTATALRTVV 60 (77)
T ss_pred EEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence 578999999999999999999999999864
No 79
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=92.95 E-value=0.1 Score=42.96 Aligned_cols=32 Identities=31% Similarity=0.493 Sum_probs=29.0
Q ss_pred CceeEEEEEeeccccceecccCcchHHhhhhh
Q 010611 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKV 306 (506)
Q Consensus 275 ~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~ 306 (506)
.....+++.+....+|.+|||+|.+|+.||.-
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 45678999999999999999999999999864
No 80
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=92.95 E-value=0.23 Score=52.57 Aligned_cols=37 Identities=11% Similarity=0.086 Sum_probs=34.5
Q ss_pred eEEEEEeccccccccccCCCchHHHHHhhcCCeEEEe
Q 010611 469 TTVEIIVPENVIGSVYGENGSNLLRLRQVSCILNVFA 505 (506)
Q Consensus 469 ~T~eI~VP~~~vG~IIGkgG~~Ik~Irq~SGA~I~I~ 505 (506)
....+.||.+..+..|||+|.|++-..+.+|.+|.|.
T Consensus 308 ~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~ 344 (374)
T PRK12328 308 KKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELN 344 (374)
T ss_pred cEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEE
Confidence 3678899999999999999999999999999999985
No 81
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=92.50 E-value=0.12 Score=60.10 Aligned_cols=51 Identities=22% Similarity=0.384 Sum_probs=44.0
Q ss_pred CeeEEEEEeecccccccccccchHHHHHHhhcCce-EEEcCCCCCCCcceEEEeccCC
Q 010611 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAF-ISVGATMPECDERLITVTASEG 240 (506)
Q Consensus 184 ~~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~-I~V~~~~p~s~eRvVtIsG~~~ 240 (506)
-+....+.||.+++|.|||.||.+||.|.++||++ |.+.+ +-.|.|.+...
T Consensus 683 aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d------dg~V~I~a~d~ 734 (891)
T PLN00207 683 APLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD------DGTVKITAKDL 734 (891)
T ss_pred CCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC------CeeEEEEeCCH
Confidence 46677899999999999999999999999999999 88864 56688888643
No 82
>PRK01064 hypothetical protein; Provisional
Probab=92.09 E-value=0.17 Score=41.98 Aligned_cols=33 Identities=27% Similarity=0.438 Sum_probs=29.4
Q ss_pred CceeEEEEEeeccccceecccCcchHHhhhhhc
Q 010611 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVT 307 (506)
Q Consensus 275 ~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~T 307 (506)
...+.+++.|..+..|.+|||+|.+|+.||.-.
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 456789999999999999999999999998754
No 83
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=91.81 E-value=0.21 Score=56.18 Aligned_cols=50 Identities=34% Similarity=0.535 Sum_probs=42.7
Q ss_pred eeEEEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCC
Q 010611 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240 (506)
Q Consensus 185 ~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~ 240 (506)
+-...+.++.+.++-+||+||.+||+|.++|||+|++. ++-.|.|.+...
T Consensus 551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie------ddGtv~i~~s~~ 600 (692)
T COG1185 551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE------DDGTVKIAASDG 600 (692)
T ss_pred CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec------CCCcEEEEecch
Confidence 34556788999999999999999999999999999996 355688888754
No 84
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=91.68 E-value=0.32 Score=53.22 Aligned_cols=36 Identities=17% Similarity=0.345 Sum_probs=34.2
Q ss_pred EEEEEeccccccccccCCCchHHHHHhhcCCeEEEe
Q 010611 470 TVEIIVPENVIGSVYGENGSNLLRLRQVSCILNVFA 505 (506)
Q Consensus 470 T~eI~VP~~~vG~IIGkgG~~Ik~Irq~SGA~I~I~ 505 (506)
...+.||.+..+..|||+|.|++..++.+|.+|.|.
T Consensus 303 ~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~ 338 (470)
T PRK09202 303 SADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIM 338 (470)
T ss_pred EEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEE
Confidence 778999999999999999999999999999999884
No 85
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=91.55 E-value=6.6 Score=38.01 Aligned_cols=124 Identities=16% Similarity=0.168 Sum_probs=80.2
Q ss_pred eecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhhcccccCCCcC
Q 010611 192 CSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFS 271 (506)
Q Consensus 192 IP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e~~~~~g~~~~ 271 (506)
++....-.|...+|..++.|-...||+|.+.. .+..|.|+|++.. .+.+....+.+..
T Consensus 32 l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-----~~~~i~I~g~k~~-------~~~i~~~i~~~l~---------- 89 (210)
T PF14611_consen 32 LQPDEFFLLLTGNGRILENLAARNGAKIEVSR-----SENRIRITGTKST-------AEYIEASINEILS---------- 89 (210)
T ss_pred ecchheeeeecCCchHHHHHHHhcCceEEEec-----CCcEEEEEccHHH-------HHHHHHHHHHHHh----------
Confidence 34677788889999999999888899999973 5678999997653 2333333333322
Q ss_pred CCCCceeEEEEEeeccccceec----ccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEE-----eCHHHHHHHH
Q 010611 272 SNKGLLVNARLVVASNQVGCLL----GKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQIS-----GEFSKVKDAV 342 (506)
Q Consensus 272 ~~~~~~vt~~l~VP~~~vG~II----GkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtIt-----Gt~~~V~~A~ 342 (506)
...+.++-++.-.--.-- -.....++.|++.|++.|....+ +..+.|+ -....+..|.
T Consensus 90 ----~i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~---------~~~~~i~~~~~~~~~~~~~~a~ 156 (210)
T PF14611_consen 90 ----NIRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD---------GNKLKISWLASPENEKRADRAK 156 (210)
T ss_pred ----hcEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC---------CCeEEEEEEeeccccchHHHHH
Confidence 123334444421110000 12356799999999999988632 2334444 4667888999
Q ss_pred HHHHHHhh
Q 010611 343 YNVTGRLR 350 (506)
Q Consensus 343 ~~I~~~L~ 350 (506)
.++...+.
T Consensus 157 RlL~~a~~ 164 (210)
T PF14611_consen 157 RLLLWALD 164 (210)
T ss_pred HHHHHhcc
Confidence 99888774
No 86
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=91.53 E-value=0.41 Score=50.68 Aligned_cols=37 Identities=14% Similarity=0.222 Sum_probs=34.4
Q ss_pred eEEEEEeccccccccccCCCchHHHHHhhcCCeEEEe
Q 010611 469 TTVEIIVPENVIGSVYGENGSNLLRLRQVSCILNVFA 505 (506)
Q Consensus 469 ~T~eI~VP~~~vG~IIGkgG~~Ik~Irq~SGA~I~I~ 505 (506)
....+.||.+..+..|||+|.|++-..+.+|.+|.|.
T Consensus 303 ~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~ 339 (362)
T PRK12327 303 KAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIK 339 (362)
T ss_pred cEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEE
Confidence 3678999999999999999999999999999999884
No 87
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=91.30 E-value=0.34 Score=48.23 Aligned_cols=47 Identities=32% Similarity=0.386 Sum_probs=40.0
Q ss_pred EEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCC
Q 010611 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240 (506)
Q Consensus 188 lrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~ 240 (506)
+.+.||.++++.+||++|..|+.|.++++++|.+.. +-.|.|.+...
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~------NG~VwI~~~~~ 193 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ------NGRIWIKGPDE 193 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC------CcEEEEeeCCH
Confidence 347789999999999999999999999999999973 35588888643
No 88
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=90.77 E-value=0.17 Score=40.91 Aligned_cols=35 Identities=26% Similarity=0.376 Sum_probs=29.1
Q ss_pred CCeeEEEEEeecccccccccccchHHHHHHhhcCc
Q 010611 183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGA 217 (506)
Q Consensus 183 ~~~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa 217 (506)
.....+.+-|..+..|.||||+|.+++.||.-.+.
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 34567778889999999999999999999976543
No 89
>PRK12704 phosphodiesterase; Provisional
Probab=90.75 E-value=0.29 Score=54.31 Aligned_cols=47 Identities=21% Similarity=0.329 Sum_probs=39.4
Q ss_pred EEEEEeec-ccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEecc
Q 010611 187 SFRILCSN-DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS 238 (506)
Q Consensus 187 tlrllIP~-~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~ 238 (506)
+--+-+|+ ++-|.||||.|.+||.++..||+.|-|.+ +.-+|+|+|.
T Consensus 211 ~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd-----tp~~v~ls~~ 258 (520)
T PRK12704 211 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-----TPEAVILSGF 258 (520)
T ss_pred eeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC-----CCCeEEEecC
Confidence 34466787 78999999999999999999999999975 3456778885
No 90
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=90.66 E-value=0.29 Score=54.18 Aligned_cols=48 Identities=21% Similarity=0.322 Sum_probs=39.7
Q ss_pred eEEEEEeec-ccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEecc
Q 010611 186 VSFRILCSN-DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS 238 (506)
Q Consensus 186 vtlrllIP~-~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~ 238 (506)
++--+-+|+ ++-|.||||.|.+||.++..||+.|-|.+ +--.|+|+|.
T Consensus 204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd-----tp~~v~ls~f 252 (514)
T TIGR03319 204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-----TPEAVILSGF 252 (514)
T ss_pred eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC-----CCCeEEecCC
Confidence 344477787 78999999999999999999999999975 3445778885
No 91
>PRK00106 hypothetical protein; Provisional
Probab=90.25 E-value=0.34 Score=53.76 Aligned_cols=48 Identities=19% Similarity=0.340 Sum_probs=39.9
Q ss_pred eEEEEEeec-ccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEecc
Q 010611 186 VSFRILCSN-DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS 238 (506)
Q Consensus 186 vtlrllIP~-~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~ 238 (506)
++--+-+|+ ++-|.||||-|.+||.++..||+.+-|.+ +.-.|+|+|.
T Consensus 225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd-----tp~~v~lS~f 273 (535)
T PRK00106 225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD-----TPEVVVLSGF 273 (535)
T ss_pred eeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC-----CCCeEEEeCC
Confidence 344577887 78999999999999999999999999975 3445778885
No 92
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=90.16 E-value=0.49 Score=51.06 Aligned_cols=36 Identities=14% Similarity=0.247 Sum_probs=33.7
Q ss_pred EEEEEeccccccccccCCCchHHHHHhhcCCeEEEe
Q 010611 470 TVEIIVPENVIGSVYGENGSNLLRLRQVSCILNVFA 505 (506)
Q Consensus 470 T~eI~VP~~~vG~IIGkgG~~Ik~Irq~SGA~I~I~ 505 (506)
...+.||.+..+..|||+|.|++-..+.+|-+|.|.
T Consensus 336 ~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~ 371 (449)
T PRK12329 336 HAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIK 371 (449)
T ss_pred EEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccc
Confidence 568999999999999999999999999999999874
No 93
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=89.58 E-value=0.31 Score=47.23 Aligned_cols=38 Identities=26% Similarity=0.400 Sum_probs=33.3
Q ss_pred ceEEEEEecc------ccccccccCCCchHHHHHhhcCCeEEEe
Q 010611 468 NTTVEIIVPE------NVIGSVYGENGSNLLRLRQVSCILNVFA 505 (506)
Q Consensus 468 ~~T~eI~VP~------~~vG~IIGkgG~~Ik~Irq~SGA~I~I~ 505 (506)
..+-.+.||. +.||.+||-.|.++|+++.+|+|+|.|-
T Consensus 147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIR 190 (269)
T COG5176 147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIR 190 (269)
T ss_pred cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEe
Confidence 4567888885 4899999999999999999999999873
No 94
>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=89.15 E-value=0.46 Score=36.65 Aligned_cols=34 Identities=35% Similarity=0.506 Sum_probs=27.4
Q ss_pred eEEEEEeecccccccccccchHHHHHHhhcCceE
Q 010611 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFI 219 (506)
Q Consensus 186 vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I 219 (506)
....+.+.....|.+|||+|.+++.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 4555666666789999999999999999988443
No 95
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=89.08 E-value=1.7 Score=48.10 Aligned_cols=67 Identities=19% Similarity=0.307 Sum_probs=56.2
Q ss_pred CceeEEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEe-CHHHHHHHHHHHHHHhhcc
Q 010611 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRDN 352 (506)
Q Consensus 275 ~~~vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItG-t~~~V~~A~~~I~~~L~e~ 352 (506)
..++...+.|+.+..-.+||.+|...|+|..+||+.-.+ +|..++|.. ++.+.++|+..|..++.+.
T Consensus 594 y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v-----------De~t~~i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 594 YSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV-----------DEGTFSIFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred cCceeeEEeecchhhheeecCccceeeeEeeeccceeee-----------cCceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence 356778899999999999999999999999999964444 245688877 6788899999999998764
No 96
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=88.59 E-value=0.36 Score=39.00 Aligned_cols=34 Identities=38% Similarity=0.585 Sum_probs=26.9
Q ss_pred EEEeeccc-----ccccccccchHHHHHHhhc-CceEEEc
Q 010611 189 RILCSNDK-----VGAVIGKGGTIIRALQSEA-GAFISVG 222 (506)
Q Consensus 189 rllIP~~~-----vG~IIGKgGs~IK~IreeT-Ga~I~V~ 222 (506)
++.|-... +|..||++|++||.|.++. |-+|.|-
T Consensus 6 kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 6 KVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp EEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred EEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence 45555555 9999999999999999999 8888874
No 97
>PRK12705 hypothetical protein; Provisional
Probab=87.88 E-value=0.98 Score=49.91 Aligned_cols=63 Identities=21% Similarity=0.219 Sum_probs=42.9
Q ss_pred eEEEEEeec-cccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEe-CHHHHHHHHHHHHHHh
Q 010611 278 VNARLVVAS-NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRL 349 (506)
Q Consensus 278 vt~~l~VP~-~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItG-t~~~V~~A~~~I~~~L 349 (506)
....+.+|+ ++-|.||||.|.+|+.+...||+.+-|. +.|. .|+|.+ .+..-+.|...+..++
T Consensus 198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid--dtp~-------~V~ls~fdp~rreia~~~l~~Li 262 (508)
T PRK12705 198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID--DTPE-------AVVISSFNPIRREIARLTLEKLL 262 (508)
T ss_pred eeeeeecCChHhhccccCccchhHHHHHHhhCCceEec--CCcc-------chhhcccCccchHHHHHHHHHHH
Confidence 344566776 5679999999999999999999999994 4443 355555 3333344444444444
No 98
>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=87.21 E-value=0.42 Score=38.91 Aligned_cols=34 Identities=26% Similarity=0.379 Sum_probs=28.6
Q ss_pred eEEEEEeecccccccccccchHHHHHHhhcCceE
Q 010611 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFI 219 (506)
Q Consensus 186 vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I 219 (506)
-...+.+..++.|.|||++|++|++|++..+-.+
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 3456788899999999999999999998876554
No 99
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=85.67 E-value=0.65 Score=53.31 Aligned_cols=49 Identities=31% Similarity=0.475 Sum_probs=40.1
Q ss_pred eeEEEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccC
Q 010611 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239 (506)
Q Consensus 185 ~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~ 239 (506)
+....+.||.++++.+||.||.+||+|.++||++|.+.+ +-.|.|.+..
T Consensus 553 p~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d------~G~v~i~~~~ 601 (693)
T PRK11824 553 PRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED------DGTVKIAATD 601 (693)
T ss_pred chheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC------CceEEEEccc
Confidence 344556779999999999999999999999999988853 4567777753
No 100
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=85.48 E-value=0.68 Score=44.74 Aligned_cols=55 Identities=29% Similarity=0.417 Sum_probs=48.5
Q ss_pred ccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeCHHHHHHHHHHHHHHhhc
Q 010611 286 SNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD 351 (506)
Q Consensus 286 ~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~~~V~~A~~~I~~~L~e 351 (506)
+..+|.|+||+|.+---|.+.|-.+|.+. +..|.|-|..+++..|...|+.+|--
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVla-----------d~kIHiLG~~~niriAR~avcsLIlG 231 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA-----------DSKIHILGAFQNIRIARDAVCSLILG 231 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEec-----------CceEEEeecchhhHHHHHhhHhhhcc
Confidence 45789999999999889999999999884 45699999999999999999999943
No 101
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=85.20 E-value=0.71 Score=37.28 Aligned_cols=35 Identities=29% Similarity=0.561 Sum_probs=28.8
Q ss_pred EEEEeeccc-----cceecccCcchHHhhhhhc-CceEEEc
Q 010611 280 ARLVVASNQ-----VGCLLGKGGTIISEMRKVT-GTSIRII 314 (506)
Q Consensus 280 ~~l~VP~~~-----vG~IIGkgG~~IkeIr~~T-GA~I~I~ 314 (506)
..+.|-... +|..||++|.+|+.|.++. |-+|++.
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 456666666 9999999999999999999 9999997
No 102
>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=83.86 E-value=1.3 Score=33.96 Aligned_cols=33 Identities=30% Similarity=0.455 Sum_probs=27.0
Q ss_pred eEEEEEeeccccceecccCcchHHhhhhhcCce
Q 010611 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTS 310 (506)
Q Consensus 278 vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~ 310 (506)
....+.+.....|.+|||+|++++.++..++-.
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~ 57 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKL 57 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHH
Confidence 455666666678999999999999999988744
No 103
>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=83.66 E-value=0.66 Score=37.75 Aligned_cols=32 Identities=25% Similarity=0.416 Sum_probs=27.9
Q ss_pred eEEEEEeccccccccccCCCchHHHHHhhcCC
Q 010611 469 TTVEIIVPENVIGSVYGENGSNLLRLRQVSCI 500 (506)
Q Consensus 469 ~T~eI~VP~~~vG~IIGkgG~~Ik~Irq~SGA 500 (506)
..+.+.+-...-|.|||++|++|++|++..+-
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k 56 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRK 56 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHH
Confidence 46788899999999999999999999887643
No 104
>PRK12705 hypothetical protein; Provisional
Probab=83.50 E-value=0.89 Score=50.24 Aligned_cols=38 Identities=13% Similarity=0.364 Sum_probs=32.5
Q ss_pred ceEEEEEeccccc-cccccCCCchHHHHHhhcCCeEEEe
Q 010611 468 NTTVEIIVPENVI-GSVYGENGSNLLRLRQVSCILNVFA 505 (506)
Q Consensus 468 ~~T~eI~VP~~~v-G~IIGkgG~~Ik~Irq~SGA~I~I~ 505 (506)
.++.-+.+|++-+ |+||||.|.||+.+...||..|.|-
T Consensus 197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid 235 (508)
T PRK12705 197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID 235 (508)
T ss_pred heeeeeecCChHhhccccCccchhHHHHHHhhCCceEec
Confidence 3556677898655 9999999999999999999999873
No 105
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=82.68 E-value=0.64 Score=37.45 Aligned_cols=30 Identities=20% Similarity=0.351 Sum_probs=27.0
Q ss_pred eEEEEEeccccccccccCCCchHHHHHhhc
Q 010611 469 TTVEIIVPENVIGSVYGENGSNLLRLRQVS 498 (506)
Q Consensus 469 ~T~eI~VP~~~vG~IIGkgG~~Ik~Irq~S 498 (506)
....+.|..+..|.||||.|.+++.||...
T Consensus 29 ~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~ 58 (73)
T PF13083_consen 29 DTIVVNIDGEDAGRLIGKHGKTLNALQYLV 58 (73)
T ss_dssp TEEEEEEESCCCHHHCTTHHHHHHHHHHHH
T ss_pred eEEEEEECCCccceEECCCCeeHHHHHHHH
Confidence 578888999999999999999999998764
No 106
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=81.20 E-value=0.68 Score=54.66 Aligned_cols=170 Identities=19% Similarity=0.100 Sum_probs=96.5
Q ss_pred hcccCccccccccccchH-HHHHHHhhcCcccc---ccccccccCCCCCCCCcce--------eec--cCC-----CCce
Q 010611 67 LEAVPHDTIARPVEAVPQ-EILWRSLESGPQEI---LRRPLEVFAPESSHRSSEA--------LSI--ETQ-----HRLF 127 (506)
Q Consensus 67 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~--------ini--s~~-----~~Pe 127 (506)
|+++++-+. --||.-|- +-+.|.+..+.||- ..-+..|.+|--++++.-+ .+| ++. -.|-
T Consensus 1199 l~p~~~P~~-~vve~pP~T~p~kr~~~~~kqdps~~pk~pk~V~~P~~s~~~qps~~~ys~v~~~ip~~~~~sa~~~nP~ 1277 (2131)
T KOG4369|consen 1199 LSPMSMPFA-SVVEPPPLTLPSKRMVAADKQDPSNLPKGPKAVPAPRVSHRMQPSGSFYSMVPNAIPHHDPQSAFVTNPV 1277 (2131)
T ss_pred cCcCCCCcc-cccCCCCcCCCchhhhhccccCcccCCCCcccccCcccccccCcccCccccccccCCCCCCccceecCCc
Confidence 677776543 23444444 56677777777664 3345788887777765443 122 221 1244
Q ss_pred eeEeeccCchhHHHHhhhccccCC--CCCCCCCCcC------CCCCCCCccccccccccccccCCeeEEEEEeecccccc
Q 010611 128 GAVSQEILPDLHVDILSQRNSVLT--TAPSSSISYV------SAVRPLSLESDRVATLDARTQQQEVSFRILCSNDKVGA 199 (506)
Q Consensus 128 Rivti~g~~~~i~~af~~i~~~l~--~~~~~~n~~~------~~~~~~~~~~~~~~~~~~~~~~~~vtlrllIP~~~vG~ 199 (506)
...-..|.+.++-+.-+.-+.+-. ..++.-++.. .....|.. -.+..+. ........++-+|.....+
T Consensus 1278 t~Te~~gw~~avq~ssav~~~~~s~~gapssA~ssq~a~~Ss~~sS~~~~---~Ts~~~s-s~~~~~~~k~~~P~~a~SR 1353 (2131)
T KOG4369|consen 1278 TLTEPQGWPAAVQLSSAVNIMNGSQMGAPSSANSSQPAKPSSGPSSLFNH---FTSLFDS-SQVPANQGKGDGPLYASSR 1353 (2131)
T ss_pred cccCCcccHHHhhhhhhheeccccccCCCCCccccCcCCCCCCccchhcc---ccccccc-ccCcccccccccchhhhhh
Confidence 444555667766644433221111 1111111100 00000100 0011111 1123445678889999999
Q ss_pred cccccchHHHHHHhhcCceEEEcCC-CCCCCcceEEEeccCCC
Q 010611 200 VIGKGGTIIRALQSEAGAFISVGAT-MPECDERLITVTASEGP 241 (506)
Q Consensus 200 IIGKgGs~IK~IreeTGa~I~V~~~-~p~s~eRvVtIsG~~~~ 241 (506)
|||+||++|..++..|||.|.+.+- ..+..||.+++.|.++.
T Consensus 1354 Vig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~ 1396 (2131)
T KOG4369|consen 1354 VIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPS 1396 (2131)
T ss_pred hhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChh
Confidence 9999999999999999999999873 44568999999998764
No 107
>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=80.98 E-value=1.4 Score=36.09 Aligned_cols=33 Identities=33% Similarity=0.494 Sum_probs=26.0
Q ss_pred EEEEeecccccccccccchHHHHHHhhcCceEE
Q 010611 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFIS 220 (506)
Q Consensus 188 lrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~ 220 (506)
+.+-+..+..|.||||+|.+++.||--+..-++
T Consensus 26 i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 26 VEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred EEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 445556788999999999999999987665443
No 108
>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=79.21 E-value=1.9 Score=35.93 Aligned_cols=35 Identities=23% Similarity=0.298 Sum_probs=28.8
Q ss_pred EEEEEeecccccccccccchHHHHHHhhcCceEEE
Q 010611 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV 221 (506)
Q Consensus 187 tlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V 221 (506)
..++.|....-|.|||++|+.|++|+++-.-...+
T Consensus 31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~ 65 (81)
T cd02413 31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF 65 (81)
T ss_pred eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence 46788888999999999999999999886544433
No 109
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=79.19 E-value=2 Score=40.67 Aligned_cols=34 Identities=32% Similarity=0.472 Sum_probs=29.2
Q ss_pred EEEeecccccccccccchHHHHHHhhcCceEEEcC
Q 010611 189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA 223 (506)
Q Consensus 189 rllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~ 223 (506)
-++|-... |.-|||+|.+||++++..|-+|.+-.
T Consensus 64 IfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 64 ILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 35666666 99999999999999999999998853
No 110
>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=78.44 E-value=2.1 Score=45.04 Aligned_cols=37 Identities=16% Similarity=0.297 Sum_probs=34.8
Q ss_pred eEEEEEeccccccccccCCCchHHHHHhhcCCeEEEe
Q 010611 469 TTVEIIVPENVIGSVYGENGSNLLRLRQVSCILNVFA 505 (506)
Q Consensus 469 ~T~eI~VP~~~vG~IIGkgG~~Ik~Irq~SGA~I~I~ 505 (506)
....+.||.+..+..|||+|.|++-..+.+|.+|.|.
T Consensus 301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~ 337 (341)
T TIGR01953 301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVK 337 (341)
T ss_pred cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEE
Confidence 3679999999999999999999999999999999984
No 111
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=78.02 E-value=1.5 Score=47.55 Aligned_cols=37 Identities=27% Similarity=0.418 Sum_probs=33.7
Q ss_pred EEEEEeecccccccccccchHHHHHHhhcCceEEEcC
Q 010611 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA 223 (506)
Q Consensus 187 tlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~ 223 (506)
...+.+|.+.++.+|||+|.+|++|+++.|-+|.|-.
T Consensus 487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~ 523 (604)
T COG1855 487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKP 523 (604)
T ss_pred eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEE
Confidence 3457899999999999999999999999999999964
No 112
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=75.49 E-value=20 Score=34.63 Aligned_cols=65 Identities=15% Similarity=0.250 Sum_probs=54.6
Q ss_pred EEEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeCHHHHHHHHHHHHHHhhcc
Q 010611 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN 352 (506)
Q Consensus 279 t~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~~~V~~A~~~I~~~L~e~ 352 (506)
.+.+.++....-.|...+|..++.|....||+|.+.. .+..+.|+|+...+..+...|.+.+...
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~---------~~~~i~I~g~k~~~~~i~~~i~~~l~~i 91 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR---------SENRIRITGTKSTAEYIEASINEILSNI 91 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEec---------CCcEEEEEccHHHHHHHHHHHHHHHhhc
Confidence 4455566888889999999999999888999999962 3567999999999999999999888654
No 113
>PRK13764 ATPase; Provisional
Probab=74.95 E-value=2.2 Score=48.17 Aligned_cols=37 Identities=27% Similarity=0.450 Sum_probs=33.9
Q ss_pred EEEEEeecccccccccccchHHHHHHhhcCceEEEcC
Q 010611 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA 223 (506)
Q Consensus 187 tlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~ 223 (506)
..-+.||.+.++.+|||+|.+|++|+++.|.+|.|-.
T Consensus 482 ~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~ 518 (602)
T PRK13764 482 KAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP 518 (602)
T ss_pred eEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence 4457899999999999999999999999999999964
No 114
>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=74.32 E-value=3 Score=34.06 Aligned_cols=30 Identities=30% Similarity=0.457 Sum_probs=25.1
Q ss_pred EEEEEeccccccccccCCCchHHHHHhhcC
Q 010611 470 TVEIIVPENVIGSVYGENGSNLLRLRQVSC 499 (506)
Q Consensus 470 T~eI~VP~~~vG~IIGkgG~~Ik~Irq~SG 499 (506)
...+.|..+..|.+|||.|.+++.||-...
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~ 54 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLAN 54 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHH
Confidence 567777788899999999999999986543
No 115
>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=74.23 E-value=3.2 Score=34.50 Aligned_cols=29 Identities=31% Similarity=0.481 Sum_probs=25.3
Q ss_pred eEEEEEeccccccccccCCCchHHHHHhh
Q 010611 469 TTVEIIVPENVIGSVYGENGSNLLRLRQV 497 (506)
Q Consensus 469 ~T~eI~VP~~~vG~IIGkgG~~Ik~Irq~ 497 (506)
..+++.|-...-|.|||++|.+|++|++.
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~ 58 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSL 58 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHH
Confidence 45788888888899999999999999875
No 116
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=74.02 E-value=6 Score=39.47 Aligned_cols=58 Identities=17% Similarity=0.308 Sum_probs=42.9
Q ss_pred EEEEeeccccceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeCHHH-HHHHHHHHHH
Q 010611 280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK-VKDAVYNVTG 347 (506)
Q Consensus 280 ~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~~~-V~~A~~~I~~ 347 (506)
+-+.|+...|-.+||++|+.++-+.+.++|+|.+-.+ -.|-|.|..+. ...|...|..
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N----------G~IWV~~~~~~~e~~~~~aI~~ 206 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN----------GRIWVDGENESLEELAIEAIRK 206 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC----------CEEEecCCCcchHHHHHHHHHH
Confidence 5677899999999999999999999999999999522 23566665553 3344444433
No 117
>PRK13764 ATPase; Provisional
Probab=73.73 E-value=2.7 Score=47.48 Aligned_cols=39 Identities=21% Similarity=0.291 Sum_probs=36.0
Q ss_pred cceEEEEEeccccccccccCCCchHHHHHhhcCCeEEEe
Q 010611 467 TNTTVEIIVPENVIGSVYGENGSNLLRLRQVSCILNVFA 505 (506)
Q Consensus 467 t~~T~eI~VP~~~vG~IIGkgG~~Ik~Irq~SGA~I~I~ 505 (506)
......+.||.+.++.+|||+|.+|++|.+..|-.|.|.
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~ 517 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVR 517 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEE
Confidence 456788999999999999999999999999999999874
No 118
>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=73.31 E-value=3.2 Score=36.32 Aligned_cols=30 Identities=27% Similarity=0.412 Sum_probs=25.6
Q ss_pred EEEEeecccccccccccchHHHHHHhhcCc
Q 010611 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGA 217 (506)
Q Consensus 188 lrllIP~~~vG~IIGKgGs~IK~IreeTGa 217 (506)
+++.+-...-|.|||++|+.|++|++....
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence 567778888999999999999999987543
No 119
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=71.75 E-value=2.9 Score=45.48 Aligned_cols=37 Identities=22% Similarity=0.258 Sum_probs=33.9
Q ss_pred eEEEEEeccccccccccCCCchHHHHHhhcCCeEEEe
Q 010611 469 TTVEIIVPENVIGSVYGENGSNLLRLRQVSCILNVFA 505 (506)
Q Consensus 469 ~T~eI~VP~~~vG~IIGkgG~~Ik~Irq~SGA~I~I~ 505 (506)
...-+.||.+.++.+|||+|.+|++|.+..|-+|.|.
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~ 522 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVK 522 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEE
Confidence 4567889999999999999999999999999999874
No 120
>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=69.82 E-value=4.4 Score=33.77 Aligned_cols=28 Identities=36% Similarity=0.529 Sum_probs=23.3
Q ss_pred EEEEeecccccccccccchHHHHHHhhc
Q 010611 188 FRILCSNDKVGAVIGKGGTIIRALQSEA 215 (506)
Q Consensus 188 lrllIP~~~vG~IIGKgGs~IK~IreeT 215 (506)
+++.+....-|.+||++|..|++|++..
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHHH
Confidence 4556666888999999999999998864
No 121
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=66.85 E-value=5.9 Score=37.50 Aligned_cols=35 Identities=29% Similarity=0.523 Sum_probs=30.8
Q ss_pred EEEEEeeccccceecccCcchHHhhhhhcCceEEEc
Q 010611 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (506)
Q Consensus 279 t~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~ 314 (506)
.+-++|.... |.-|||+|.+|+.+++..|-+|++.
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevV 96 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVV 96 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEE
Confidence 4566776667 9999999999999999999999997
No 122
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=64.47 E-value=5.2 Score=39.80 Aligned_cols=31 Identities=32% Similarity=0.434 Sum_probs=26.9
Q ss_pred eeEEEEEeecccccccccccchHHHHHHhhc
Q 010611 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEA 215 (506)
Q Consensus 185 ~vtlrllIP~~~vG~IIGKgGs~IK~IreeT 215 (506)
+...++.|....-|.||||+|+.|++|++..
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l 80 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKEL 80 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHH
Confidence 4467788899999999999999999998764
No 123
>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=64.29 E-value=28 Score=32.22 Aligned_cols=93 Identities=16% Similarity=0.388 Sum_probs=58.0
Q ss_pred cccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhhcccccCCCcCCCCCceeE
Q 010611 200 VIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVN 279 (506)
Q Consensus 200 IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e~~~~~g~~~~~~~~~~vt 279 (506)
.+-..|..|++|-.+..-+|.|-.+ +.. ..+-.+|...|.+.+-++.--.+..| ...+
T Consensus 20 ~~~~~~dli~~lAk~lrKRIvvR~d--------------ps~---l~~~e~A~~~I~~ivP~ea~i~di~F-----d~~t 77 (145)
T cd02410 20 LFAEDGDLVKDLAKDLRKRIVIRPD--------------PSV---LKPPEEAIKIILEIVPEEAGITDIYF-----DDDT 77 (145)
T ss_pred HHhcccHHHHHHHHHHhceEEEcCC--------------hhh---cCCHHHHHHHHHHhCCCccCceeeEe-----cCCC
Confidence 3445678888888888777777421 110 01112455555442221100011111 1235
Q ss_pred EEEEeeccccceecccCcchHHhhhhhcCceEEEc
Q 010611 280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (506)
Q Consensus 280 ~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~ 314 (506)
-++.|-...-|.+|||+|.++++|..+||-.-++.
T Consensus 78 GEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vv 112 (145)
T cd02410 78 GEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVV 112 (145)
T ss_pred cEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEE
Confidence 57888888999999999999999999999988886
No 124
>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=63.78 E-value=8.3 Score=35.67 Aligned_cols=35 Identities=34% Similarity=0.552 Sum_probs=29.7
Q ss_pred EEEeecccccccccccchHHHHHHhhcCceEEEcC
Q 010611 189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA 223 (506)
Q Consensus 189 rllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~ 223 (506)
.+.|-.+.-|.+|||+|.++++|..+||-+-.|-.
T Consensus 79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvR 113 (145)
T cd02410 79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVR 113 (145)
T ss_pred EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence 35566788899999999999999999998877753
No 125
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=61.56 E-value=6.6 Score=39.19 Aligned_cols=45 Identities=33% Similarity=0.496 Sum_probs=36.9
Q ss_pred EEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCC
Q 010611 190 ILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240 (506)
Q Consensus 190 llIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~ 240 (506)
+.|+...+-.+|||+|+.++.|.++|+|.|-|.. +-| |-|.+..+
T Consensus 150 v~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-----NG~-IWV~~~~~ 194 (239)
T COG1097 150 VKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-----NGR-IWVDGENE 194 (239)
T ss_pred EEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-----CCE-EEecCCCc
Confidence 5688899999999999999999999999999973 233 55666554
No 126
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=59.81 E-value=7.4 Score=38.71 Aligned_cols=28 Identities=29% Similarity=0.481 Sum_probs=24.7
Q ss_pred eEEEEEeccccccccccCCCchHHHHHh
Q 010611 469 TTVEIIVPENVIGSVYGENGSNLLRLRQ 496 (506)
Q Consensus 469 ~T~eI~VP~~~vG~IIGkgG~~Ik~Irq 496 (506)
..++|.|-...-|.||||+|++|++|++
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~ 78 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRK 78 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHH
Confidence 4678888889999999999999988875
No 127
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=59.62 E-value=15 Score=37.59 Aligned_cols=51 Identities=20% Similarity=0.331 Sum_probs=45.3
Q ss_pred ceecccCcchHHhhhhhcCceEEEccCcccccCCCCCeEEEEEeCHHHHHHHHHHHHHHhhc
Q 010611 290 GCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD 351 (506)
Q Consensus 290 G~IIGkgG~~IkeIr~~TGA~I~I~~d~~P~~~~s~eR~VtItGt~~~V~~A~~~I~~~L~e 351 (506)
-.|||.+|.+++.|+--|.|.|-|.. ..|.+.|....+..+...+.+++..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG-----------~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG-----------NTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC-----------cEEEeecCcchHHHHHHHHHHHHhc
Confidence 57999999999999999999998852 3588999999999999999999865
No 128
>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=58.51 E-value=9.3 Score=31.81 Aligned_cols=27 Identities=26% Similarity=0.455 Sum_probs=21.2
Q ss_pred EEEEeccccccccccCCCchHHHHHhh
Q 010611 471 VEIIVPENVIGSVYGENGSNLLRLRQV 497 (506)
Q Consensus 471 ~eI~VP~~~vG~IIGkgG~~Ik~Irq~ 497 (506)
+++.|-...-|.+||++|.+|+++++.
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~ 66 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEI 66 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHH
Confidence 455555577799999999999988764
No 129
>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=56.66 E-value=9.4 Score=33.39 Aligned_cols=28 Identities=25% Similarity=0.491 Sum_probs=23.1
Q ss_pred EEEEEeccccccccccCCCchHHHHHhh
Q 010611 470 TVEIIVPENVIGSVYGENGSNLLRLRQV 497 (506)
Q Consensus 470 T~eI~VP~~~vG~IIGkgG~~Ik~Irq~ 497 (506)
.++|.|-...-|.|||+.|++|++|++.
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~ 89 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKE 89 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHH
Confidence 3566666777899999999999998875
No 130
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=55.11 E-value=8.1 Score=32.37 Aligned_cols=35 Identities=29% Similarity=0.283 Sum_probs=29.6
Q ss_pred chHHHhhhhcccCccccccccccchHHHHHHHhhcCccc
Q 010611 59 SHETIRRSLEAVPHDTIARPVEAVPQEILWRSLESGPQE 97 (506)
Q Consensus 59 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 97 (506)
.|-.|-.-|++||.||.-.|| .|+|+|.|++++-+
T Consensus 16 ~~~~iF~FL~~~P~GT~~~~i----R~~L~rYI~~~G~~ 50 (97)
T PRK13916 16 DYPQIFDFLENVPRGTKTAHI----REALRRYIEEIGEN 50 (97)
T ss_pred ccHHHHHHHHHCCCCCccHHH----HHHHHHHHHhcCCC
Confidence 466788889999999988776 58999999999854
No 131
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=51.59 E-value=25 Score=39.27 Aligned_cols=49 Identities=27% Similarity=0.387 Sum_probs=40.8
Q ss_pred CeeEEEEEeecccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccC
Q 010611 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239 (506)
Q Consensus 184 ~~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~ 239 (506)
.++...|.++.++...+||.+|.+.|+|+.|||+.-++. |-.++|-...
T Consensus 595 ~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD-------e~t~~i~A~~ 643 (760)
T KOG1067|consen 595 SPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD-------EGTFSIFAPT 643 (760)
T ss_pred CceeeEEeecchhhheeecCccceeeeEeeeccceeeec-------CceEEEEecC
Confidence 467888999999999999999999999999999655553 5567777653
No 132
>PRK15494 era GTPase Era; Provisional
Probab=47.86 E-value=22 Score=37.27 Aligned_cols=36 Identities=19% Similarity=0.356 Sum_probs=27.9
Q ss_pred eEEEEEeec-ccccccccccchHHHHHHhh--------cCceEEE
Q 010611 186 VSFRILCSN-DKVGAVIGKGGTIIRALQSE--------AGAFISV 221 (506)
Q Consensus 186 vtlrllIP~-~~vG~IIGKgGs~IK~Iree--------TGa~I~V 221 (506)
+...|+|.. ++-+-||||+|+.||+|..+ .|++|.+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l 317 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHL 317 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEE
Confidence 556677774 78899999999999988765 5666655
No 133
>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=47.30 E-value=17 Score=36.40 Aligned_cols=29 Identities=24% Similarity=0.417 Sum_probs=24.0
Q ss_pred eEEEEEeec-ccccccccccchHHHHHHhh
Q 010611 186 VSFRILCSN-DKVGAVIGKGGTIIRALQSE 214 (506)
Q Consensus 186 vtlrllIP~-~~vG~IIGKgGs~IK~Iree 214 (506)
+...++|.. ++-+-||||+|+.||+|..+
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ 250 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIA 250 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence 566677774 77899999999999998765
No 134
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=46.50 E-value=46 Score=36.95 Aligned_cols=93 Identities=20% Similarity=0.417 Sum_probs=61.7
Q ss_pred ccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhhcc-cccCCCcCCCCCce
Q 010611 199 AVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGT-SEKGLDFSSNKGLL 277 (506)
Q Consensus 199 ~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e~~-~~~g~~~~~~~~~~ 277 (506)
.++-+.|..||+|-.+..-+|.+-.+ |. + ..+..+|...|.+-+-++. +.+ ..| ..
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~d-Ps-----v-----------l~~~e~A~~~I~eivP~ea~i~~-i~F-----d~ 98 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPD-PS-----V-----------LKPPEEARKIILEIVPEEAGITD-IYF-----DD 98 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccC-ch-----h-----------cCCHHHHHHHHHHhCccccCcee-EEe-----cC
Confidence 46678899999999998888888531 11 0 1112345555554332111 100 111 12
Q ss_pred eEEEEEeeccccceecccCcchHHhhhhhcCceEEEc
Q 010611 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (506)
Q Consensus 278 vt~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~ 314 (506)
.+-+++|-...=|.+|||+|++.++|..+||-.-+|.
T Consensus 99 ~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~iv 135 (637)
T COG1782 99 DTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIV 135 (637)
T ss_pred CCceEEEEecCCceEEecCchHHHHHHHHhCCcceee
Confidence 3568888899999999999999999999999877776
No 135
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=45.36 E-value=15 Score=38.35 Aligned_cols=34 Identities=24% Similarity=0.484 Sum_probs=27.2
Q ss_pred CCeeEEEEEeec-ccccccccccchHHHHHHhhcC
Q 010611 183 QQEVSFRILCSN-DKVGAVIGKGGTIIRALQSEAG 216 (506)
Q Consensus 183 ~~~vtlrllIP~-~~vG~IIGKgGs~IK~IreeTG 216 (506)
.-.+..+++||. ++.-.||||||.+|++|-++.+
T Consensus 325 ~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 325 VLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 345778899996 6677899999999999976643
No 136
>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=42.54 E-value=22 Score=35.69 Aligned_cols=30 Identities=20% Similarity=0.211 Sum_probs=24.3
Q ss_pred eEEEEEeccccc-cccccCCCchHHHHHhhc
Q 010611 469 TTVEIIVPENVI-GSVYGENGSNLLRLRQVS 498 (506)
Q Consensus 469 ~T~eI~VP~~~v-G~IIGkgG~~Ik~Irq~S 498 (506)
....|.|..+.. +-|||++|+.||+|...+
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 567788887755 999999999999887654
No 137
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=41.68 E-value=31 Score=38.16 Aligned_cols=127 Identities=15% Similarity=0.118 Sum_probs=82.0
Q ss_pred eeEEEEEeecccccccccccchHHHHHHhhcCceEEEcCC--CCCCCcce-EEEeccCCCCcCCChHHHHHHHHHHHHhh
Q 010611 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT--MPECDERL-ITVTASEGPESRYSPAQKAVVLVFSRLIE 261 (506)
Q Consensus 185 ~vtlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~--~p~s~eRv-VtIsG~~~~i~~~s~a~~Av~~i~~~i~e 261 (506)
+-.+.+.||.+.+-.|||.||..|.+...+.++.|++... .+.+..+- |.|..+..+.+.++-+-+.++.+.. +
T Consensus 448 pae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~---~ 524 (657)
T COG5166 448 PAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVK---Q 524 (657)
T ss_pred chheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHh---h
Confidence 4456789999999999999999999999999999988753 45555444 7888877666554444333333222 1
Q ss_pred cc-cc-cC---CCcC----------C--------C----CCceeEEEEEeeccccceecc---cCcchHHhhhhhcCceE
Q 010611 262 GT-SE-KG---LDFS----------S--------N----KGLLVNARLVVASNQVGCLLG---KGGTIISEMRKVTGTSI 311 (506)
Q Consensus 262 ~~-~~-~g---~~~~----------~--------~----~~~~vt~~l~VP~~~vG~IIG---kgG~~IkeIr~~TGA~I 311 (506)
.+ +. ++ +.++ . + ..-+....+.+|++.++..+| -.|++|..+.....-.|
T Consensus 525 ~c~f~~Kgdirf~~~~~sI~~v~~~~~~I~rv~kne~v~~~~p~~~~~y~~se~h~~g~gena~R~~ni~~~t~~y~~~i 604 (657)
T COG5166 525 QCRFNLKGDIRFCPQSTSIFTVDIYSDEIERVIKNETVLLEFPAEMHFYVPSEIHKKGIGENAFRGENIQRVTKLYNSYI 604 (657)
T ss_pred hcccccccceEEcCCceEEEEEcccccHHHHHhhccceEEecccccccccchhhhhccCCcccccccchhhhhhhhhccc
Confidence 11 10 00 0000 0 0 112334567788888888888 67888888777766666
Q ss_pred EEc
Q 010611 312 RII 314 (506)
Q Consensus 312 ~I~ 314 (506)
...
T Consensus 605 e~~ 607 (657)
T COG5166 605 EFS 607 (657)
T ss_pred eee
Confidence 654
No 138
>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=39.61 E-value=26 Score=34.07 Aligned_cols=31 Identities=29% Similarity=0.543 Sum_probs=26.2
Q ss_pred EEEEEeecccccccccccchHHHHHHhhcCc
Q 010611 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGA 217 (506)
Q Consensus 187 tlrllIP~~~vG~IIGKgGs~IK~IreeTGa 217 (506)
..++.|....-|.|||++|..|++|+++-.-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k 69 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKLQK 69 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHHHH
Confidence 4677888888999999999999999987543
No 139
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=38.21 E-value=28 Score=34.52 Aligned_cols=32 Identities=25% Similarity=0.287 Sum_probs=26.4
Q ss_pred EEEEEeecccccccccccchHHHHHHhhcCce
Q 010611 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAF 218 (506)
Q Consensus 187 tlrllIP~~~vG~IIGKgGs~IK~IreeTGa~ 218 (506)
-.++.|-...-|.|||++|..|++|+++..-.
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~ 76 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLLQKR 76 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHHHHH
Confidence 36677778888999999999999999876543
No 140
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=37.86 E-value=28 Score=34.08 Aligned_cols=30 Identities=37% Similarity=0.516 Sum_probs=24.8
Q ss_pred EEEEeecccccccccccchHHHHHHhhcCc
Q 010611 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGA 217 (506)
Q Consensus 188 lrllIP~~~vG~IIGKgGs~IK~IreeTGa 217 (506)
.++.|-...-|.+||++|++|++|++...-
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 455666688999999999999999987654
No 141
>CHL00048 rps3 ribosomal protein S3
Probab=37.52 E-value=29 Score=34.22 Aligned_cols=30 Identities=17% Similarity=0.147 Sum_probs=25.6
Q ss_pred EEEEEeecccccccccccchHHHHHHhhcC
Q 010611 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAG 216 (506)
Q Consensus 187 tlrllIP~~~vG~IIGKgGs~IK~IreeTG 216 (506)
..++.|-...-|.|||++|..|++|++...
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 466777788889999999999999998763
No 142
>PRK00089 era GTPase Era; Reviewed
Probab=37.17 E-value=30 Score=34.85 Aligned_cols=36 Identities=25% Similarity=0.577 Sum_probs=26.8
Q ss_pred eEEEEEee-cccccccccccchHHHHHHhh--------cCceEEE
Q 010611 186 VSFRILCS-NDKVGAVIGKGGTIIRALQSE--------AGAFISV 221 (506)
Q Consensus 186 vtlrllIP-~~~vG~IIGKgGs~IK~Iree--------TGa~I~V 221 (506)
+...++|. .++-+-||||+|+.||+|..+ .|++|.+
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l 270 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL 270 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 44556666 467899999999999988765 4666555
No 143
>PRK15494 era GTPase Era; Provisional
Probab=35.89 E-value=31 Score=36.07 Aligned_cols=30 Identities=23% Similarity=0.353 Sum_probs=24.0
Q ss_pred eEEEEEeccccc-cccccCCCchHHHHHhhc
Q 010611 469 TTVEIIVPENVI-GSVYGENGSNLLRLRQVS 498 (506)
Q Consensus 469 ~T~eI~VP~~~v-G~IIGkgG~~Ik~Irq~S 498 (506)
....|.|..+.. +-|||++|+.||+|...+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~a 303 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKS 303 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHH
Confidence 456788887755 899999999999886543
No 144
>PRK00089 era GTPase Era; Reviewed
Probab=35.47 E-value=31 Score=34.79 Aligned_cols=30 Identities=27% Similarity=0.576 Sum_probs=23.5
Q ss_pred eeEEEEEeec-cccceecccCcchHHhhhhh
Q 010611 277 LVNARLVVAS-NQVGCLLGKGGTIISEMRKV 306 (506)
Q Consensus 277 ~vt~~l~VP~-~~vG~IIGkgG~~IkeIr~~ 306 (506)
.+...++|.. ++-+.||||+|+.||+|...
T Consensus 225 ~i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ 255 (292)
T PRK00089 225 RIEATIYVERDSQKGIIIGKGGAMLKKIGTE 255 (292)
T ss_pred EEEEEEEEccCCceeEEEeCCcHHHHHHHHH
Confidence 3566777774 56799999999999988554
No 145
>COG1159 Era GTPase [General function prediction only]
Probab=34.35 E-value=39 Score=34.94 Aligned_cols=30 Identities=23% Similarity=0.543 Sum_probs=23.4
Q ss_pred eeEEEEEeec-ccccccccccchHHHHHHhh
Q 010611 185 EVSFRILCSN-DKVGAVIGKGGTIIRALQSE 214 (506)
Q Consensus 185 ~vtlrllIP~-~~vG~IIGKgGs~IK~Iree 214 (506)
.+...++|+. ++=|-||||+|+.||+|-..
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~ 258 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKIGTA 258 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHHHHH
Confidence 4455577774 78899999999999988654
No 146
>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=33.21 E-value=1.1e+02 Score=34.96 Aligned_cols=94 Identities=18% Similarity=0.351 Sum_probs=60.0
Q ss_pred ccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCCCCcCCChHHHHHHHHHHHHhhcccccCCCcCCCCCcee
Q 010611 199 AVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLV 278 (506)
Q Consensus 199 ~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~~i~~~s~a~~Av~~i~~~i~e~~~~~g~~~~~~~~~~v 278 (506)
..+-+.|..||+|-.+..-+|.|-.+ |. +.-. -.+|...|.+.+-++.--.+..| ...
T Consensus 36 ~~~~~~~~~~~~~~~~~~~r~~~~~~-~~-------~~~~---------~~~~~~~i~~~~~~~~~~~~~~f-----~~~ 93 (630)
T TIGR03675 36 ELFAKDDDLVKELAKKLRKRIVIRPD-PS-------VLLP---------PEEAIEKIKEIVPEEAGITDIYF-----DDV 93 (630)
T ss_pred HHhccchHHHHHHHHHhhceEEEecC-hh-------hcCC---------HHHHHHHHHHhCCCcCCceeEEe-----cCC
Confidence 34556789999999888888877531 11 0011 12455444432211100001111 123
Q ss_pred EEEEEeeccccceecccCcchHHhhhhhcCceEEEc
Q 010611 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (506)
Q Consensus 279 t~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~ 314 (506)
+-+++|-...-|.+|||+|.++++|.++||-.-++.
T Consensus 94 ~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~ 129 (630)
T TIGR03675 94 TGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVV 129 (630)
T ss_pred CceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEE
Confidence 568888899999999999999999999999988887
No 147
>COG1159 Era GTPase [General function prediction only]
Probab=32.12 E-value=40 Score=34.91 Aligned_cols=31 Identities=26% Similarity=0.536 Sum_probs=23.9
Q ss_pred eeEEEEEeec-cccceecccCcchHHhhhhhc
Q 010611 277 LVNARLVVAS-NQVGCLLGKGGTIISEMRKVT 307 (506)
Q Consensus 277 ~vt~~l~VP~-~~vG~IIGkgG~~IkeIr~~T 307 (506)
.+...++|+. ++=|.||||+|++||+|-..+
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~A 259 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKIGTAA 259 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHHHHHH
Confidence 4556677875 577999999999999885443
No 148
>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=30.54 E-value=43 Score=32.58 Aligned_cols=29 Identities=21% Similarity=0.319 Sum_probs=24.1
Q ss_pred eEEEEEeccccccccccCCCchHHHHHhh
Q 010611 469 TTVEIIVPENVIGSVYGENGSNLLRLRQV 497 (506)
Q Consensus 469 ~T~eI~VP~~~vG~IIGkgG~~Ik~Irq~ 497 (506)
..++|.|-...-|.|||++|.+|++|++.
T Consensus 38 ~~~~I~I~~~rPg~vIG~~g~~i~~l~~~ 66 (195)
T TIGR01008 38 LGTKVIIFAERPGLVIGRGGRRIRELTEK 66 (195)
T ss_pred CcEEEEEEECCCceEECCCchHHHHHHHH
Confidence 34677777778899999999999998765
No 149
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=30.05 E-value=37 Score=33.31 Aligned_cols=35 Identities=26% Similarity=0.416 Sum_probs=27.4
Q ss_pred EEEEEeecccccccccccchHHHHHHhhcCceEEE
Q 010611 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV 221 (506)
Q Consensus 187 tlrllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V 221 (506)
.+.+-+-.+..|.||||.|.++..||--+.+-++-
T Consensus 92 ~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 92 RVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred EEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 44455566669999999999999999887765543
No 150
>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=29.21 E-value=51 Score=37.69 Aligned_cols=35 Identities=34% Similarity=0.565 Sum_probs=30.6
Q ss_pred EEEeecccccccccccchHHHHHHhhcCceEEEcC
Q 010611 189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA 223 (506)
Q Consensus 189 rllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~~ 223 (506)
.++|-+++-|.+|||+|+++++|..+||-+-.|-.
T Consensus 96 ~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~ 130 (630)
T TIGR03675 96 EVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVR 130 (630)
T ss_pred eEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEe
Confidence 46677788899999999999999999998887754
No 151
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=29.11 E-value=51 Score=36.63 Aligned_cols=34 Identities=32% Similarity=0.562 Sum_probs=29.7
Q ss_pred EEEeecccccccccccchHHHHHHhhcCceEEEc
Q 010611 189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVG 222 (506)
Q Consensus 189 rllIP~~~vG~IIGKgGs~IK~IreeTGa~I~V~ 222 (506)
.++|-+++-|.+|||+|++.++|..+||-.-.|-
T Consensus 102 EViIea~KPGlvigk~g~~~reI~~~tgW~p~iv 135 (637)
T COG1782 102 EVIIEAKKPGLVIGKGGSTLREITAETGWAPKIV 135 (637)
T ss_pred eEEEEecCCceEEecCchHHHHHHHHhCCcceee
Confidence 4677788999999999999999999999776664
No 152
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=28.45 E-value=47 Score=32.49 Aligned_cols=28 Identities=25% Similarity=0.399 Sum_probs=22.0
Q ss_pred EEEEeccccccccccCCCchHHHHHhhc
Q 010611 471 VEIIVPENVIGSVYGENGSNLLRLRQVS 498 (506)
Q Consensus 471 ~eI~VP~~~vG~IIGkgG~~Ik~Irq~S 498 (506)
.++.|-...-|.+||++|.+|+++++.-
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~L 69 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEIL 69 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHH
Confidence 4455555778999999999999988753
No 153
>CHL00048 rps3 ribosomal protein S3
Probab=28.32 E-value=49 Score=32.57 Aligned_cols=29 Identities=10% Similarity=0.178 Sum_probs=23.6
Q ss_pred eEEEEEeccccccccccCCCchHHHHHhh
Q 010611 469 TTVEIIVPENVIGSVYGENGSNLLRLRQV 497 (506)
Q Consensus 469 ~T~eI~VP~~~vG~IIGkgG~~Ik~Irq~ 497 (506)
..++|.|=...-|.|||++|.+|++|++.
T Consensus 66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~ 94 (214)
T CHL00048 66 DLIQVIIYTGFPKLLIERKGRGIEELQIN 94 (214)
T ss_pred CeEEEEEEECCCceEECCCcHhHHHHHHH
Confidence 34667776777899999999999998865
No 154
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=26.77 E-value=46 Score=32.54 Aligned_cols=41 Identities=20% Similarity=0.292 Sum_probs=34.2
Q ss_pred cccccccccccchHHHHHHhhcCceEEEcCCCCCCCcceEEEeccCCC
Q 010611 194 NDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGP 241 (506)
Q Consensus 194 ~~~vG~IIGKgGs~IK~IreeTGa~I~V~~~~p~s~eRvVtIsG~~~~ 241 (506)
+..+|.|+||+|.+--.|++.|.++|.+.+ ..|.|-|.-++
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad-------~kIHiLG~~~n 217 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD-------SKIHILGAFQN 217 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecC-------ceEEEeecchh
Confidence 346899999999999999999999999973 44777786554
No 155
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=25.99 E-value=59 Score=31.94 Aligned_cols=29 Identities=31% Similarity=0.515 Sum_probs=24.6
Q ss_pred EEEEeecccccccccccchHHHHHHhhcC
Q 010611 188 FRILCSNDKVGAVIGKGGTIIRALQSEAG 216 (506)
Q Consensus 188 lrllIP~~~vG~IIGKgGs~IK~IreeTG 216 (506)
+++.+....-|.|||++|..|++|++...
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l~ 92 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDLQ 92 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHHH
Confidence 56777788889999999999999997653
No 156
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=25.95 E-value=55 Score=32.48 Aligned_cols=28 Identities=25% Similarity=0.450 Sum_probs=23.1
Q ss_pred EEEEEeccccccccccCCCchHHHHHhh
Q 010611 470 TVEIIVPENVIGSVYGENGSNLLRLRQV 497 (506)
Q Consensus 470 T~eI~VP~~~vG~IIGkgG~~Ik~Irq~ 497 (506)
.++|.|-...-|.|||++|..|++|++.
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~ 72 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSL 72 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHH
Confidence 4567777777899999999999988764
No 157
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=24.99 E-value=59 Score=34.13 Aligned_cols=32 Identities=19% Similarity=0.357 Sum_probs=26.0
Q ss_pred ceEEEEEeccccc-cccccCCCchHHHHHhhcC
Q 010611 468 NTTVEIIVPENVI-GSVYGENGSNLLRLRQVSC 499 (506)
Q Consensus 468 ~~T~eI~VP~~~v-G~IIGkgG~~Ik~Irq~SG 499 (506)
.+.+++.||.... -.||||||..|++|-+.-+
T Consensus 327 ~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 327 FIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 3688999998866 5679999999999876543
No 158
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=23.78 E-value=61 Score=31.83 Aligned_cols=30 Identities=20% Similarity=0.348 Sum_probs=25.0
Q ss_pred eEEEEEeccccccccccCCCchHHHHHhhc
Q 010611 469 TTVEIIVPENVIGSVYGENGSNLLRLRQVS 498 (506)
Q Consensus 469 ~T~eI~VP~~~vG~IIGkgG~~Ik~Irq~S 498 (506)
.++.+.+-.+..|.+||+.|.+++.||-..
T Consensus 91 ~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~ 120 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGKHGKTLDALQYLA 120 (208)
T ss_pred cEEEEEecCCchhhhhccCCcchHHHHHHH
Confidence 367777788889999999999999987543
No 159
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=22.64 E-value=81 Score=35.07 Aligned_cols=72 Identities=11% Similarity=0.145 Sum_probs=51.2
Q ss_pred EEEEEeeccccceecccCcchHHhhhhhcCceEEEccC-cccccCCCCCe-EEEEEeCH---HHHHHHHHHHHHHhhccc
Q 010611 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISD-QLLKCISENDR-VVQISGEF---SKVKDAVYNVTGRLRDNH 353 (506)
Q Consensus 279 t~~l~VP~~~vG~IIGkgG~~IkeIr~~TGA~I~I~~d-~~P~~~~s~eR-~VtItGt~---~~V~~A~~~I~~~L~e~~ 353 (506)
...+.||...+-.|||-||..|+++....++.|++... ..+. +.-+ -|.|.-+. +++.-++.-+.+++.+..
T Consensus 450 e~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~q---s~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~~c 526 (657)
T COG5166 450 EIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQ---SQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQQC 526 (657)
T ss_pred heEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcch---hhhhcceEEECCccCccchhcccccHHHHHhhhc
Confidence 56789999999999999999999999999999998732 1232 2222 26666543 445556666667776543
Done!