Query 046946
Match_columns 650
No_of_seqs 397 out of 2064
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 06:06:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046946.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046946hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1676 K-homology type RNA bi 100.0 7.7E-46 1.7E-50 398.0 33.9 332 126-556 52-389 (600)
2 KOG2190 PolyC-binding proteins 100.0 1.9E-42 4.1E-47 378.6 37.1 363 127-557 42-410 (485)
3 KOG2193 IGF-II mRNA-binding pr 100.0 2.4E-40 5.3E-45 339.3 21.3 361 124-556 195-564 (584)
4 KOG1676 K-homology type RNA bi 100.0 2.4E-37 5.2E-42 332.7 20.8 301 56-462 76-384 (600)
5 KOG2192 PolyC-binding hnRNP-K 100.0 1.5E-31 3.3E-36 260.6 24.6 294 126-473 46-384 (390)
6 KOG2191 RNA-binding protein NO 100.0 1.2E-29 2.6E-34 254.4 16.2 188 397-602 38-238 (402)
7 KOG2191 RNA-binding protein NO 100.0 3.1E-27 6.7E-32 237.2 21.8 240 127-437 38-283 (402)
8 KOG2192 PolyC-binding hnRNP-K 99.9 7.6E-25 1.6E-29 213.9 18.3 225 238-555 46-383 (390)
9 KOG2193 IGF-II mRNA-binding pr 99.9 6.7E-26 1.5E-30 233.3 10.1 241 239-562 198-487 (584)
10 KOG2190 PolyC-binding proteins 99.8 6.2E-19 1.3E-23 193.8 17.3 157 397-560 42-212 (485)
11 TIGR03665 arCOG04150 arCOG0415 99.5 4.5E-14 9.7E-19 136.6 13.1 138 132-315 2-152 (172)
12 PRK13763 putative RNA-processi 99.5 4E-14 8.7E-19 137.8 11.4 142 128-315 3-158 (180)
13 TIGR03665 arCOG04150 arCOG0415 99.5 2E-14 4.3E-19 139.0 6.9 135 402-556 2-151 (172)
14 PRK13763 putative RNA-processi 99.5 1.2E-13 2.7E-18 134.4 8.9 139 398-556 3-157 (180)
15 cd02396 PCBP_like_KH K homolog 99.3 5.5E-12 1.2E-16 102.2 7.1 64 482-551 2-65 (65)
16 KOG2279 Kinase anchor protein 99.3 1.1E-11 2.4E-16 133.3 10.6 272 123-451 63-352 (608)
17 cd02396 PCBP_like_KH K homolog 99.3 5.5E-12 1.2E-16 102.2 5.3 59 129-187 1-60 (65)
18 KOG2279 Kinase anchor protein 99.2 6.5E-11 1.4E-15 127.5 10.2 228 237-554 65-366 (608)
19 cd02394 vigilin_like_KH K homo 99.2 4.7E-11 1E-15 95.7 5.6 61 482-551 2-62 (62)
20 cd02393 PNPase_KH Polynucleoti 99.1 1.6E-10 3.5E-15 92.3 7.6 59 480-551 2-61 (61)
21 PF00013 KH_1: KH domain syndr 99.1 5.6E-11 1.2E-15 94.6 3.2 60 481-550 1-60 (60)
22 cd00105 KH-I K homology RNA-bi 99.1 3.6E-10 7.8E-15 90.8 7.5 63 482-551 2-64 (64)
23 KOG2208 Vigilin [Lipid transpo 99.0 1.6E-09 3.4E-14 126.3 14.4 318 128-517 347-746 (753)
24 cd02394 vigilin_like_KH K homo 99.0 5.8E-10 1.3E-14 89.3 6.1 61 242-309 2-62 (62)
25 KOG2208 Vigilin [Lipid transpo 99.0 1.3E-09 2.8E-14 127.1 11.3 328 128-557 201-563 (753)
26 PF00013 KH_1: KH domain syndr 99.0 3.9E-10 8.4E-15 89.8 4.6 60 241-308 1-60 (60)
27 cd02393 PNPase_KH Polynucleoti 99.0 2.1E-09 4.5E-14 85.9 7.7 59 240-309 2-61 (61)
28 cd00105 KH-I K homology RNA-bi 98.9 3.6E-09 7.9E-14 84.9 7.8 62 242-308 2-63 (64)
29 PF13014 KH_3: KH domain 98.9 3.3E-09 7E-14 78.6 5.2 42 138-179 1-43 (43)
30 COG1094 Predicted RNA-binding 98.8 6.4E-08 1.4E-12 93.3 12.2 145 127-317 7-167 (194)
31 smart00322 KH K homology RNA-b 98.8 4.2E-08 9E-13 78.9 9.0 66 480-554 3-68 (69)
32 PF13014 KH_3: KH domain 98.8 1.5E-08 3.3E-13 75.0 5.5 43 490-538 1-43 (43)
33 smart00322 KH K homology RNA-b 98.7 1.4E-07 3.1E-12 75.8 9.2 68 239-313 2-69 (69)
34 COG1094 Predicted RNA-binding 98.6 3.7E-07 8.1E-12 88.1 11.4 142 397-557 7-165 (194)
35 KOG2113 Predicted RNA binding 98.4 3.2E-07 6.9E-12 93.0 5.7 145 396-553 24-180 (394)
36 cd02395 SF1_like-KH Splicing f 98.2 4.9E-06 1.1E-10 75.6 7.8 69 488-556 14-95 (120)
37 cd02395 SF1_like-KH Splicing f 98.2 7.6E-06 1.6E-10 74.4 8.2 68 248-315 14-96 (120)
38 PRK08406 transcription elongat 98.0 2.3E-05 5E-10 73.2 7.6 104 128-276 32-135 (140)
39 KOG2113 Predicted RNA binding 97.9 2E-05 4.3E-10 80.3 7.1 144 238-453 24-167 (394)
40 PRK08406 transcription elongat 97.7 3.8E-05 8.3E-10 71.8 4.6 102 398-516 32-135 (140)
41 TIGR02696 pppGpp_PNP guanosine 97.6 0.00016 3.4E-09 83.5 8.9 68 476-556 574-642 (719)
42 TIGR02696 pppGpp_PNP guanosine 97.5 0.00053 1.2E-08 79.2 10.7 92 208-314 550-642 (719)
43 TIGR01952 nusA_arch NusA famil 97.5 0.00044 9.6E-09 64.5 8.2 103 129-276 34-136 (141)
44 KOG0119 Splicing factor 1/bran 97.4 0.00091 2E-08 72.5 11.2 77 238-314 136-230 (554)
45 KOG0336 ATP-dependent RNA heli 97.3 0.00024 5.3E-09 75.4 4.8 59 125-186 44-102 (629)
46 TIGR03591 polynuc_phos polyrib 97.3 0.00038 8.3E-09 81.4 6.8 66 477-555 548-614 (684)
47 KOG0119 Splicing factor 1/bran 97.1 0.0021 4.6E-08 69.7 9.9 77 479-556 137-230 (554)
48 TIGR03591 polynuc_phos polyrib 97.1 0.0018 3.8E-08 75.9 9.1 92 209-314 523-615 (684)
49 TIGR01952 nusA_arch NusA famil 97.0 0.00054 1.2E-08 64.0 3.3 101 399-516 34-136 (141)
50 COG0195 NusA Transcription elo 97.0 0.0021 4.5E-08 63.0 7.4 102 130-277 78-179 (190)
51 PLN00207 polyribonucleotide nu 96.9 0.00094 2E-08 78.9 4.8 66 477-555 682-749 (891)
52 COG1185 Pnp Polyribonucleotide 96.6 0.0029 6.4E-08 71.8 6.0 67 477-556 549-616 (692)
53 KOG1588 RNA-binding protein Sa 96.6 0.0024 5.3E-08 64.6 4.5 41 124-164 88-134 (259)
54 COG0195 NusA Transcription elo 96.5 0.0028 6E-08 62.2 4.3 99 401-517 79-179 (190)
55 PLN00207 polyribonucleotide nu 96.4 0.0062 1.4E-07 72.1 7.5 92 209-314 657-750 (891)
56 PRK12328 nusA transcription el 96.4 0.0078 1.7E-07 64.7 7.5 96 137-279 251-347 (374)
57 KOG0336 ATP-dependent RNA heli 96.4 0.0034 7.4E-08 67.0 4.7 66 480-555 47-112 (629)
58 TIGR01953 NusA transcription t 96.4 0.0073 1.6E-07 64.8 6.9 95 137-277 243-338 (341)
59 cd02134 NusA_KH NusA_K homolog 96.3 0.0057 1.2E-07 48.8 4.3 36 128-163 25-60 (61)
60 COG1185 Pnp Polyribonucleotide 96.3 0.012 2.6E-07 67.0 8.1 93 208-314 523-616 (692)
61 KOG2814 Transcription coactiva 96.1 0.0063 1.4E-07 63.4 4.5 69 481-558 58-127 (345)
62 PRK12327 nusA transcription el 96.1 0.012 2.6E-07 63.5 6.7 95 137-277 245-340 (362)
63 KOG2814 Transcription coactiva 96.0 0.0085 1.8E-07 62.4 5.1 70 240-316 57-127 (345)
64 KOG4369 RTK signaling protein 96.0 0.0089 1.9E-07 70.4 5.5 70 480-555 1340-1409(2131)
65 PRK12329 nusA transcription el 95.9 0.013 2.8E-07 64.1 5.8 95 137-277 277-372 (449)
66 cd02134 NusA_KH NusA_K homolog 95.8 0.014 3.1E-07 46.5 4.5 36 480-515 25-60 (61)
67 PRK11824 polynucleotide phosph 95.7 0.0081 1.8E-07 70.6 3.7 66 478-556 552-618 (693)
68 PRK04163 exosome complex RNA-b 95.6 0.019 4.2E-07 58.6 5.5 62 482-556 147-209 (235)
69 TIGR01953 NusA transcription t 95.5 0.012 2.7E-07 63.0 4.1 93 408-517 244-338 (341)
70 PRK11824 polynucleotide phosph 95.4 0.024 5.2E-07 66.7 6.4 93 208-314 525-618 (693)
71 PRK09202 nusA transcription el 95.4 0.041 9E-07 61.5 7.7 93 138-277 246-339 (470)
72 KOG1588 RNA-binding protein Sa 95.2 0.021 4.6E-07 58.0 4.4 79 237-315 89-192 (259)
73 PRK12328 nusA transcription el 95.2 0.018 3.9E-07 62.0 3.9 91 408-517 252-345 (374)
74 PRK00468 hypothetical protein; 95.1 0.023 5.1E-07 47.2 3.5 32 126-157 28-59 (75)
75 COG5176 MSL5 Splicing factor ( 95.1 0.095 2.1E-06 51.1 8.1 80 235-314 143-240 (269)
76 PRK12327 nusA transcription el 95.0 0.021 4.5E-07 61.8 4.0 92 408-517 246-340 (362)
77 PRK12329 nusA transcription el 95.0 0.02 4.4E-07 62.6 3.9 93 408-517 278-372 (449)
78 PRK04163 exosome complex RNA-b 95.0 0.052 1.1E-06 55.4 6.4 66 242-318 147-213 (235)
79 TIGR03319 YmdA_YtgF conserved 94.9 0.088 1.9E-06 59.8 8.7 66 480-557 204-271 (514)
80 PF14611 SLS: Mitochondrial in 94.9 0.28 6E-06 49.1 11.3 128 400-555 28-164 (210)
81 PRK02821 hypothetical protein; 94.9 0.053 1.1E-06 45.3 5.0 35 477-511 28-62 (77)
82 PRK00106 hypothetical protein; 94.8 0.1 2.2E-06 59.1 9.0 66 480-557 225-292 (535)
83 TIGR03319 YmdA_YtgF conserved 94.7 0.11 2.4E-06 59.0 8.9 63 242-314 206-270 (514)
84 PRK02821 hypothetical protein; 94.6 0.033 7.2E-07 46.5 3.3 33 127-159 30-62 (77)
85 PRK00106 hypothetical protein; 94.6 0.13 2.8E-06 58.3 9.1 63 242-314 227-291 (535)
86 PRK12704 phosphodiesterase; Pr 94.4 0.13 2.9E-06 58.4 8.7 65 480-556 210-276 (520)
87 PF14611 SLS: Mitochondrial in 94.4 0.88 1.9E-05 45.4 13.6 131 131-317 29-168 (210)
88 PRK09202 nusA transcription el 94.3 0.037 7.9E-07 62.0 3.8 92 408-517 246-339 (470)
89 PRK12704 phosphodiesterase; Pr 94.3 0.14 3.1E-06 58.2 8.4 62 243-314 213-276 (520)
90 COG1837 Predicted RNA-binding 94.1 0.076 1.7E-06 44.1 4.2 32 237-268 27-58 (76)
91 COG1837 Predicted RNA-binding 94.0 0.056 1.2E-06 44.9 3.4 31 126-156 28-58 (76)
92 PRK00468 hypothetical protein; 94.0 0.065 1.4E-06 44.6 3.7 34 236-269 26-59 (75)
93 PRK01064 hypothetical protein; 93.9 0.061 1.3E-06 45.1 3.4 32 126-157 28-59 (78)
94 COG5176 MSL5 Splicing factor ( 93.2 0.12 2.7E-06 50.3 4.8 41 479-519 147-193 (269)
95 PRK01064 hypothetical protein; 93.1 0.12 2.5E-06 43.4 3.9 34 477-510 27-60 (78)
96 KOG1067 Predicted RNA-binding 92.3 0.43 9.3E-06 53.2 7.9 92 209-315 569-661 (760)
97 PF13083 KH_4: KH domain; PDB: 91.2 0.13 2.9E-06 42.3 2.0 33 127-159 28-60 (73)
98 KOG1067 Predicted RNA-binding 90.9 0.51 1.1E-05 52.6 6.6 68 477-558 594-662 (760)
99 PRK12705 hypothetical protein; 89.3 0.67 1.5E-05 52.4 6.2 65 480-556 198-264 (508)
100 cd02409 KH-II KH-II (K homolo 89.1 0.58 1.3E-05 37.1 4.1 34 128-161 25-58 (68)
101 COG5166 Uncharacterized conser 88.7 1.4 3.1E-05 48.7 7.9 102 400-516 499-607 (657)
102 KOG3273 Predicted RNA-binding 88.5 0.31 6.7E-06 47.4 2.3 55 488-556 177-231 (252)
103 PRK12705 hypothetical protein; 88.4 0.9 2E-05 51.4 6.4 62 243-314 201-264 (508)
104 KOG4369 RTK signaling protein 88.0 0.21 4.5E-06 59.6 1.1 65 127-191 1339-1404(2131)
105 PF13184 KH_5: NusA-like KH do 87.9 0.44 9.5E-06 39.0 2.6 37 130-166 5-47 (69)
106 KOG2874 rRNA processing protei 87.9 0.84 1.8E-05 46.7 5.1 54 492-559 161-214 (356)
107 KOG3273 Predicted RNA-binding 86.2 0.47 1E-05 46.2 2.2 57 248-316 177-233 (252)
108 cd02409 KH-II KH-II (K homolo 86.1 1.3 2.7E-05 35.1 4.4 35 479-513 24-58 (68)
109 PF13184 KH_5: NusA-like KH do 85.1 0.55 1.2E-05 38.4 1.8 37 481-517 4-46 (69)
110 cd02410 archeal_CPSF_KH The ar 84.4 4 8.7E-05 38.2 7.3 93 143-277 21-113 (145)
111 PF13083 KH_4: KH domain; PDB: 84.1 0.66 1.4E-05 38.2 1.9 34 238-271 27-60 (73)
112 PF07650 KH_2: KH domain syndr 84.0 0.65 1.4E-05 38.6 1.8 34 129-162 26-59 (78)
113 cd02414 jag_KH jag_K homology 82.4 1.2 2.7E-05 37.1 2.9 33 130-162 26-58 (77)
114 PRK06418 transcription elongat 82.4 1.6 3.5E-05 42.0 4.0 36 130-166 63-98 (166)
115 cd02410 archeal_CPSF_KH The ar 81.8 3 6.5E-05 39.0 5.5 89 415-517 23-113 (145)
116 COG1782 Predicted metal-depend 80.9 4.9 0.00011 44.8 7.5 95 141-277 42-136 (637)
117 COG1855 ATPase (PilT family) [ 80.4 3.5 7.6E-05 45.5 6.1 39 241-279 487-525 (604)
118 cd02414 jag_KH jag_K homology 80.3 1.9 4.2E-05 35.9 3.4 33 481-513 25-57 (77)
119 COG1097 RRP4 RNA-binding prote 80.1 3.4 7.3E-05 41.9 5.5 59 242-311 148-207 (239)
120 COG1855 ATPase (PilT family) [ 79.9 1.2 2.7E-05 48.9 2.6 37 129-165 487-523 (604)
121 cd02413 40S_S3_KH K homology R 79.3 2 4.3E-05 36.3 3.1 36 129-164 31-66 (81)
122 COG1097 RRP4 RNA-binding prote 78.7 4.7 0.0001 40.9 6.0 57 482-551 148-205 (239)
123 PRK13764 ATPase; Provisional 78.5 3.2 7E-05 48.1 5.5 42 240-281 481-522 (602)
124 PF07650 KH_2: KH domain syndr 78.3 1.3 2.9E-05 36.7 1.8 33 241-273 26-58 (78)
125 KOG2874 rRNA processing protei 77.3 4.1 8.9E-05 41.8 5.2 51 252-314 161-211 (356)
126 cd02413 40S_S3_KH K homology R 74.5 3.5 7.5E-05 34.8 3.3 34 479-512 29-62 (81)
127 PRK13764 ATPase; Provisional 74.3 2.3 5.1E-05 49.2 2.9 38 128-165 481-518 (602)
128 COG1782 Predicted metal-depend 74.0 3.9 8.4E-05 45.6 4.3 102 397-517 33-136 (637)
129 cd02412 30S_S3_KH K homology R 71.4 3.6 7.9E-05 36.7 2.9 30 130-159 63-92 (109)
130 cd02411 archeal_30S_S3_KH K ho 68.6 5 0.00011 34.1 3.0 28 130-157 40-67 (85)
131 PRK06418 transcription elongat 67.3 7.3 0.00016 37.5 4.1 35 242-277 63-97 (166)
132 TIGR03675 arCOG00543 arCOG0054 65.4 15 0.00032 43.1 7.0 95 142-278 37-131 (630)
133 COG0092 RpsC Ribosomal protein 64.0 5.6 0.00012 40.2 2.8 30 128-157 51-80 (233)
134 TIGR03675 arCOG00543 arCOG0054 62.6 10 0.00022 44.5 5.0 91 413-517 38-130 (630)
135 cd02412 30S_S3_KH K homology R 61.4 6.1 0.00013 35.3 2.3 30 481-510 62-91 (109)
136 cd02411 archeal_30S_S3_KH K ho 60.6 8 0.00017 32.8 2.8 28 482-509 40-67 (85)
137 COG0092 RpsC Ribosomal protein 58.7 8.3 0.00018 39.0 2.9 38 479-516 50-92 (233)
138 COG5166 Uncharacterized conser 54.8 15 0.00033 41.0 4.3 95 409-517 391-486 (657)
139 TIGR00436 era GTP-binding prot 51.7 16 0.00035 37.8 3.9 30 480-509 221-251 (270)
140 PRK15494 era GTPase Era; Provi 47.0 21 0.00045 38.5 3.9 29 480-508 273-302 (339)
141 TIGR00436 era GTP-binding prot 46.8 22 0.00049 36.7 4.1 31 239-269 220-251 (270)
142 PRK00089 era GTPase Era; Revie 44.8 23 0.0005 37.0 3.8 30 480-509 226-256 (292)
143 COG1159 Era GTPase [General fu 44.7 23 0.00049 37.3 3.6 31 479-509 228-259 (298)
144 KOG1423 Ras-like GTPase ERA [C 44.1 19 0.00042 38.1 2.9 32 127-158 327-359 (379)
145 PRK15494 era GTPase Era; Provi 41.7 29 0.00063 37.4 4.0 29 240-268 273-302 (339)
146 COG1159 Era GTPase [General fu 41.6 32 0.00068 36.3 4.1 30 239-268 228-258 (298)
147 PRK00089 era GTPase Era; Revie 41.0 30 0.00065 36.1 4.0 30 240-269 226-256 (292)
148 TIGR01008 rpsC_E_A ribosomal p 38.3 29 0.00064 34.4 3.1 31 129-159 39-69 (195)
149 KOG1960 Predicted RNA-binding 38.1 2.5E+02 0.0054 30.8 10.0 139 404-556 220-375 (531)
150 PRK04191 rps3p 30S ribosomal p 37.5 30 0.00065 34.7 3.1 31 130-160 42-72 (207)
151 CHL00048 rps3 ribosomal protei 37.2 31 0.00066 34.8 3.1 30 129-158 67-96 (214)
152 KOG1423 Ras-like GTPase ERA [C 35.9 37 0.00081 36.0 3.5 32 479-510 327-359 (379)
153 PTZ00084 40S ribosomal protein 35.8 33 0.00072 34.6 3.1 31 130-160 46-76 (220)
154 TIGR01008 rpsC_E_A ribosomal p 30.6 45 0.00097 33.1 3.0 31 479-509 37-67 (195)
155 COG1847 Jag Predicted RNA-bind 30.5 36 0.00078 33.9 2.3 35 129-163 92-126 (208)
156 PRK03818 putative transporter; 29.6 5.3E+02 0.011 29.9 11.9 62 240-307 290-358 (552)
157 PRK04191 rps3p 30S ribosomal p 29.3 48 0.001 33.2 3.0 29 482-510 42-70 (207)
158 COG0490 Putative regulatory, l 29.1 68 0.0015 30.7 3.8 66 481-551 89-158 (162)
159 CHL00048 rps3 ribosomal protei 29.0 51 0.0011 33.2 3.2 31 479-509 65-95 (214)
160 PF09869 DUF2096: Uncharacteri 28.9 1.5E+02 0.0033 28.5 6.0 59 236-312 109-167 (169)
161 PTZ00084 40S ribosomal protein 28.2 48 0.001 33.5 2.8 30 480-509 44-73 (220)
162 TIGR03802 Asp_Ala_antiprt aspa 26.9 4.7E+02 0.01 30.3 10.9 63 241-309 304-377 (562)
163 COG1702 PhoH Phosphate starvat 26.2 1.3E+02 0.0028 32.5 5.7 56 486-555 21-78 (348)
164 COG1847 Jag Predicted RNA-bind 24.2 71 0.0015 31.9 3.1 35 240-274 91-125 (208)
165 TIGR01009 rpsC_bact ribosomal 24.1 68 0.0015 32.2 3.0 29 130-158 64-92 (211)
166 COG1702 PhoH Phosphate starvat 23.7 1.4E+02 0.0031 32.2 5.4 58 245-314 20-79 (348)
167 PF02080 TrkA_C: TrkA-C domain 22.1 1.2E+02 0.0026 23.9 3.6 52 499-550 14-70 (71)
168 PF08052 PyrBI_leader: PyrBI o 21.8 35 0.00076 24.5 0.3 11 6-16 15-25 (44)
169 PRK10224 pyrBI operon leader p 21.3 36 0.00079 24.3 0.3 13 6-18 15-27 (44)
170 KOG1960 Predicted RNA-binding 20.2 1.5E+02 0.0032 32.4 4.6 64 492-555 227-294 (531)
No 1
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=7.7e-46 Score=397.97 Aligned_cols=332 Identities=22% Similarity=0.369 Sum_probs=265.9
Q ss_pred CceEEEEEecCccccceeccCchHHHHHHHHhCceEEEecCCCCCCceEEEEecChhhhhhccCCccchhhhhhcccCCc
Q 046946 126 ADTVYRILCPSRKIGGVIGKAGNIVKSLREETQAKITVADTIPGSEERVIIIYSSPTKIAKTQNKDDDSAAETKKESMEP 205 (650)
Q Consensus 126 ~~~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~~~~~g~~eRvI~I~G~~e~v~~a~~~~~~~~~e~~~~~~~~ 205 (650)
..++.+..||.++||+||||+|+.|..|..++||+|+|.....+..+|-|.++|.+++|++++.++.+
T Consensus 52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~aK~li~e------------ 119 (600)
T KOG1676|consen 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEVAKQLIGE------------ 119 (600)
T ss_pred cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHHHHHHhhhh------------
Confidence 35778899999999999999999999999999999998876668899999999999998876554432
Q ss_pred ccHHHHHHHHHHHHHhhhhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCC
Q 046946 206 HCAAQDALLKVHDRIIEEDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCA 285 (650)
Q Consensus 206 ~~~a~~Al~~v~~~i~e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~ 285 (650)
|.++.. ... ..........++.+|+||.+.+|+||||+|++||.|++++||++.+..+.....
T Consensus 120 ----------vv~r~~---~~~--~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~-- 182 (600)
T KOG1676|consen 120 ----------VVSRGR---PPG--GFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIAT-- 182 (600)
T ss_pred ----------hhhccC---CCC--CccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCC--
Confidence 333332 011 111222245688999999999999999999999999999999999997655433
Q ss_pred CCCCceEEEecCHHHHHHHHHHHHHHHccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 046946 286 MNTDEMVQISGKPNVAKRALYEVSTLLHQNPRKDKPPSSFPQAYGGQNFHSPPAPMADMHPLGNSSWPARNSSLHGMPST 365 (650)
Q Consensus 286 ~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~ 365 (650)
..++.+.|+|+++.|+.|+.+|.++|++..... . +.
T Consensus 183 -~~~KplritGdp~~ve~a~~lV~dil~e~~~~~-~---------g~--------------------------------- 218 (600)
T KOG1676|consen 183 -GADKPLRITGDPDKVEQAKQLVADILREEDDEV-P---------GS--------------------------------- 218 (600)
T ss_pred -CCCCceeecCCHHHHHHHHHHHHHHHHhcccCC-C---------cc---------------------------------
Confidence 478899999999999999999999998632211 0 00
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEecCCccceecccCccchhchhhhcCceEEecCCC-CCCCccE
Q 046946 366 PWMGGYGDQPSRMGSGSINSCPPGQMGEVSAEFSMKILCSAGKIGGVIGKGGFNVKQLQQETGASIHVEDAP-TDSDERV 444 (650)
Q Consensus 366 p~~~~yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~~~~-~~~~eri 444 (650)
.+.+|..+ ....+++|.||...||.||||+|++||+|+.+||++|+|..++ +.+.||.
T Consensus 219 --~~~~g~~~-------------------g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~ 277 (600)
T KOG1676|consen 219 --GGHAGVRG-------------------GGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERP 277 (600)
T ss_pred --ccccCcCc-------------------cccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccce
Confidence 00111110 0134789999999999999999999999999999999998554 4889999
Q ss_pred EEEeccCCCcCccchHHHHHHHHhhhccccc---cCCce--EEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCc
Q 046946 445 IRASAFEGLWNPRSQTIDAILQLQNKTSEFS---EKGTI--TTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGAR 519 (650)
Q Consensus 445 i~I~G~~~~~~~~~~~~~ai~~~~~~i~~~~---~~~~~--~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~ 519 (650)
+.|.|+.+.+..+..++.+|+.-.+...... ..... ...+.||+++||+||||||++||.|..+|||+|++++.
T Consensus 278 ~~IiG~~d~ie~Aa~lI~eii~~~~~~~~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~- 356 (600)
T KOG1676|consen 278 AQIIGTVDQIEHAAELINEIIAEAEAGAGGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ- 356 (600)
T ss_pred eeeecCHHHHHHHHHHHHHHHHHHhccCCCCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC-
Confidence 9999999888877777777766554432111 11122 78999999999999999999999999999999999963
Q ss_pred cccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 046946 520 VKLQDPHPGSSECIVDIRGSSEHLISAHGTYQSFMTS 556 (650)
Q Consensus 520 ~~l~~p~~~~~er~V~I~G~~e~V~~A~~lI~~~i~~ 556 (650)
.|..+..+++|+|+|++.+|+.|++||+++|..
T Consensus 357 ----~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~ 389 (600)
T KOG1676|consen 357 ----PPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGD 389 (600)
T ss_pred ----CCCCCccceEEEEecCcccchHHHHHHHHHhcc
Confidence 256788999999999999999999999999964
No 2
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=1.9e-42 Score=378.58 Aligned_cols=363 Identities=37% Similarity=0.590 Sum_probs=286.2
Q ss_pred ceEEEEEecCccccceeccCchHHHHHHHHhCceEEEecCCCCCCceEEEEecChhhhhhccCCccchhhhhhcccCCcc
Q 046946 127 DTVYRILCPSRKIGGVIGKAGNIVKSLREETQAKITVADTIPGSEERVIIIYSSPTKIAKTQNKDDDSAAETKKESMEPH 206 (650)
Q Consensus 127 ~~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~~~~~g~~eRvI~I~G~~e~v~~a~~~~~~~~~e~~~~~~~~~ 206 (650)
..++||||+.+++|.||||+|.+||+||++|.++|+|.+..++|.||+++|+|...+ .+.
T Consensus 42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~--------------------~~~ 101 (485)
T KOG2190|consen 42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVE--------------------LNL 101 (485)
T ss_pred cceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEeccccc--------------------ccC
Confidence 455999999999999999999999999999999999999999999999999997111 156
Q ss_pred cHHHHHHHHHHHHHhhh---hccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCC
Q 046946 207 CAAQDALLKVHDRIIEE---DLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPP 283 (650)
Q Consensus 207 ~~a~~Al~~v~~~i~e~---~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~ 283 (650)
+++++|+++++++|... +.....+...+.....++++|+||.+++|+||||+|++||+|+++|||+|+|.++ .+|.
T Consensus 102 ~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~ 180 (485)
T KOG2190|consen 102 SPATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN 180 (485)
T ss_pred CchHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCc
Confidence 78999999999999963 1111111121122226899999999999999999999999999999999999965 8887
Q ss_pred CCCCCCceEEEecCHHHHHHHHHHHHHHHccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 046946 284 CAMNTDEMVQISGKPNVAKRALYEVSTLLHQNPRKDKPPSSFPQAYGGQNFHSPPAPMADMHPLGNSSWPARNSSLHGMP 363 (650)
Q Consensus 284 ~~~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~ 363 (650)
.++|.|+|.|.+++|.+|+..|..+|.+++....+......+|.. ..+.+.+..+
T Consensus 181 ---ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~y~P------------~~~~~~~~~~---------- 235 (485)
T KOG2190|consen 181 ---STERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIPYRP------------SASQGGPVLP---------- 235 (485)
T ss_pred ---ccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCcccCCC------------cccccCcccc----------
Confidence 568889999999999999999999999975443111000011110 0000000000
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEecCCccceecccCccchhchhhhcCceEEecCCCCCCCcc
Q 046946 364 STPWMGGYGDQPSRMGSGSINSCPPGQMGEVSAEFSMKILCSAGKIGGVIGKGGFNVKQLQQETGASIHVEDAPTDSDER 443 (650)
Q Consensus 364 ~~p~~~~yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~er 443 (650)
..+. .....++........++.+++.||...++.|||++|..|+.|+.++++.|.+.+...+ |
T Consensus 236 ------s~~~--------~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~---~ 298 (485)
T KOG2190|consen 236 ------STAQ--------TSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTD---R 298 (485)
T ss_pred ------cccc--------CCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccCc---c
Confidence 0000 0001122233334557888999999999999999999999999999999999987653 9
Q ss_pred EEEEeccCCCcCccchHHHHHHHHhhhcccccc---CCceEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCcc
Q 046946 444 VIRASAFEGLWNPRSQTIDAILQLQNKTSEFSE---KGTITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARV 520 (650)
Q Consensus 444 ii~I~G~~~~~~~~~~~~~ai~~~~~~i~~~~~---~~~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~ 520 (650)
+++++..+...+..+++++++++++.++.+... ...++.+|+||++++||||||+|++|.+||+.|||.|+|..+.
T Consensus 299 ~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~- 377 (485)
T KOG2190|consen 299 IVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKE- 377 (485)
T ss_pred eeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccchHHHHHhcCCceEEcccc-
Confidence 999999988888888999999999999887653 3458899999999999999999999999999999999999754
Q ss_pred ccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 046946 521 KLQDPHPGSSECIVDIRGSSEHLISAHGTYQSFMTSG 557 (650)
Q Consensus 521 ~l~~p~~~~~er~V~I~G~~e~V~~A~~lI~~~i~~~ 557 (650)
......++.++|+|...+...|+.+|...+...
T Consensus 378 ----~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~ 410 (485)
T KOG2190|consen 378 ----EVSGVREALVQITGMLREDLLAQYLIRARLSAP 410 (485)
T ss_pred ----ccCCcceeEEEecchhHHHHhhhhhcccccccC
Confidence 113678999999999999999999998887654
No 3
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=2.4e-40 Score=339.26 Aligned_cols=361 Identities=24% Similarity=0.384 Sum_probs=271.3
Q ss_pred CCCceEEEEEecCccccceeccCchHHHHHHHHhCceEEEec-CCCCCCceEEEEecChhhhhhccCCccchhhhhhccc
Q 046946 124 QPADTVYRILCPSRKIGGVIGKAGNIVKSLREETQAKITVAD-TIPGSEERVIIIYSSPTKIAKTQNKDDDSAAETKKES 202 (650)
Q Consensus 124 ~~~~~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~~-~~~g~~eRvI~I~G~~e~v~~a~~~~~~~~~e~~~~~ 202 (650)
...+..+|+|||...+|.||||.|.|||.|-+.|.|+|+|.. ...|..||+|+|.+++|..
T Consensus 195 q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~------------------ 256 (584)
T KOG2193|consen 195 QLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGT------------------ 256 (584)
T ss_pred cccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccch------------------
Confidence 356799999999999999999999999999999999999994 4458999999999998874
Q ss_pred CCcccHHHHHHHHHHHHHhhhhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCC
Q 046946 203 MEPHCAAQDALLKVHDRIIEEDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLP 282 (650)
Q Consensus 203 ~~~~~~a~~Al~~v~~~i~e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p 282 (650)
.+|+.++++.+..+... +.....+.++++..+.+||+||||.|.+||+|+++||++|.|++-.++.
T Consensus 257 -------s~Ac~~ILeimqkEA~~-------~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels 322 (584)
T KOG2193|consen 257 -------SKACKMILEIMQKEAVD-------DKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELS 322 (584)
T ss_pred -------HHHHHHHHHHHHHhhhc-------cchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhc
Confidence 45777888877765332 2223567789999999999999999999999999999999999844443
Q ss_pred CCCCCCCceEEEecCHHHHHHHHHHHHHHHccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CC
Q 046946 283 PCAMNTDEMVQISGKPNVAKRALYEVSTLLHQNPRKDKPPSSFPQAYGGQNFHSPPAPMADMHPLGNSSWPARNSSL-HG 361 (650)
Q Consensus 283 ~~~~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~-~~ 361 (650)
. ...||.|++.|+.|+|.+|..+|+.+|+++...|... ...+..++|.+.+..+.+ ++.....+ +.
T Consensus 323 ~--ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl~a------~s~q~~l~P~l~~~~l~~-----f~ssS~~~~Ph 389 (584)
T KOG2193|consen 323 L--YNPERTITVKGSIEACVQAEAEIMKKLRECYENDLAA------MSLQCHLPPGLNLPALGL-----FPSSSAVSPPH 389 (584)
T ss_pred c--cCccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHH------hhccCCCCcccCccccCC-----CCcccccCCCC
Confidence 3 3569999999999999999999999999977666211 111222333322221111 11111000 00
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEecCCccceecccCccchhchhhhcCceEEecCC-CCCC
Q 046946 362 MPSTPWMGGYGDQPSRMGSGSINSCPPGQMGEVSAEFSMKILCSAGKIGGVIGKGGFNVKQLQQETGASIHVEDA-PTDS 440 (650)
Q Consensus 362 ~~~~p~~~~yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~~~-~~~~ 440 (650)
.++.|. .+.+.++. .+ .. .+.-.++|.||...+|+|||++|.+||+|..++||+|+|... .++.
T Consensus 390 ~~Ps~v----------~~a~p~~~---~h-q~-pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdv 454 (584)
T KOG2193|consen 390 FPPSPV----------TFASPYPL---FH-QN-PEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDV 454 (584)
T ss_pred CCCCcc----------ccCCCchh---hh-cC-cchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCc
Confidence 000000 00000000 00 11 124478999999999999999999999999999999999864 4567
Q ss_pred CccEEEEeccCCCcCccchHHHHHHHHhhhccccc-----cCCceEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEE
Q 046946 441 DERVIRASAFEGLWNPRSQTIDAILQLQNKTSEFS-----EKGTITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRV 515 (650)
Q Consensus 441 ~erii~I~G~~~~~~~~~~~~~ai~~~~~~i~~~~-----~~~~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i 515 (650)
.+|.++|+|.+ .+..+|--+++.++.+.+ ++-.+.+.+.||++.+|+||||||.+++|+++-|+|.|.|
T Consensus 455 seRMViItGpp------eaqfKAQgrifgKikEenf~~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~v 528 (584)
T KOG2193|consen 455 SERMVIITGPP------EAQFKAQGRIFGKIKEENFFLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVV 528 (584)
T ss_pred ceeEEEecCCh------HHHHhhhhhhhhhhhhhccCCchhhheeeeeeeccchhhhhhhccccccHHHHhccccceEEc
Confidence 89999999987 444566667777776633 3345678899999999999999999999999999999999
Q ss_pred eCCccccCCCCCC-CCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 046946 516 VGARVKLQDPHPG-SSECIVDIRGSSEHLISAHGTYQSFMTS 556 (650)
Q Consensus 516 ~~~~~~l~~p~~~-~~er~V~I~G~~e~V~~A~~lI~~~i~~ 556 (650)
+++. .++ .+.-+|.|.|..-+.+.|+..|.+++..
T Consensus 529 Prdq------tpdEnd~vivriiGhfyatq~aQrki~~iv~q 564 (584)
T KOG2193|consen 529 PRDQ------TPDENDQVIVRIIGHFYATQNAQRKIAHIVNQ 564 (584)
T ss_pred cccC------CCCccceeeeeeechhhcchHHHHHHHHHHHH
Confidence 9753 233 4566899999999999999999998854
No 4
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=2.4e-37 Score=332.66 Aligned_cols=301 Identities=24% Similarity=0.344 Sum_probs=226.5
Q ss_pred EEEeeecccceEEEeecCCCc-eeeEEecCccccccc-CCCCCccccCCCcCCCCCCCCCCCccCCCCCCCCCceEEEEE
Q 046946 56 IYLFSISFSCAFHLLSHSRCI-RFCCIMDASKRNFFK-KRPNNQFKRKGVVGIKKGNWSNSSREQSFGNSQPADTVYRIL 133 (650)
Q Consensus 56 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~r~~~~-~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ril 133 (650)
|-.++-.|+|+||+.++.+++ +|.|+++|...+... |+..++...+++ .....++ +.....++.+|+
T Consensus 76 I~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~aK~li~evv~r~~-------~~~~~~~----~q~~~~ttqeI~ 144 (600)
T KOG1676|consen 76 IQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEVAKQLIGEVVSRGR-------PPGGFPD----NQGSVETTQEIL 144 (600)
T ss_pred hhhhhhhcCCccccCCCCCCcccccccccCCcccHHHHHHhhhhhhhccC-------CCCCccc----cCCccceeeeec
Confidence 334556899999999999998 999999999999955 444444333222 1111111 111457999999
Q ss_pred ecCccccceeccCchHHHHHHHHhCceEEEecCC--CCCCceEEEEecChhhhhhccCCccchhhhhhcccCCcccHHHH
Q 046946 134 CPSRKIGGVIGKAGNIVKSLREETQAKITVADTI--PGSEERVIIIYSSPTKIAKTQNKDDDSAAETKKESMEPHCAAQD 211 (650)
Q Consensus 134 vP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~~~~--~g~~eRvI~I~G~~e~v~~a~~~~~~~~~e~~~~~~~~~~~a~~ 211 (650)
||.+++|+||||+|++||+|++++||++.+.... .....+.+.|+|++++|+.
T Consensus 145 IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~------------------------- 199 (600)
T KOG1676|consen 145 IPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQ------------------------- 199 (600)
T ss_pred cCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHH-------------------------
Confidence 9999999999999999999999999999988432 2336789999999998765
Q ss_pred HHHHHHHHHhhhhccCCC--CCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCC
Q 046946 212 ALLKVHDRIIEEDLFGGM--ASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTD 289 (650)
Q Consensus 212 Al~~v~~~i~e~~~~~~~--~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~d 289 (650)
|..+|++.+.|++..... ...........+.+|.||++.||.||||+|++||+|+.+||++|+|.+++. | .+.|
T Consensus 200 a~~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~-p---~spe 275 (600)
T KOG1676|consen 200 AKQLVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD-P---SSPE 275 (600)
T ss_pred HHHHHHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCC-C---CCcc
Confidence 455566666643322111 111122234458999999999999999999999999999999999998654 3 3789
Q ss_pred ceEEEecCHHHHHHHHHHHHHHHccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 046946 290 EMVQISGKPNVAKRALYEVSTLLHQNPRKDKPPSSFPQAYGGQNFHSPPAPMADMHPLGNSSWPARNSSLHGMPSTPWMG 369 (650)
Q Consensus 290 r~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~p~~~ 369 (650)
|.+.|.|+.++|++|.++|.++|++.....
T Consensus 276 R~~~IiG~~d~ie~Aa~lI~eii~~~~~~~-------------------------------------------------- 305 (600)
T KOG1676|consen 276 RPAQIIGTVDQIEHAAELINEIIAEAEAGA-------------------------------------------------- 305 (600)
T ss_pred ceeeeecCHHHHHHHHHHHHHHHHHHhccC--------------------------------------------------
Confidence 999999999999999999999998743221
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEecCCccceecccCccchhchhhhcCceEEecCC--CCCCCccEEEE
Q 046946 370 GYGDQPSRMGSGSINSCPPGQMGEVSAEFSMKILCSAGKIGGVIGKGGFNVKQLQQETGASIHVEDA--PTDSDERVIRA 447 (650)
Q Consensus 370 ~yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~~~--~~~~~erii~I 447 (650)
+ ++|+..++. .-..+.|.||..++|.||||+|+|||+|.+++||++.+.+. ..+..|++++|
T Consensus 306 ~----------~~~~~G~P~------~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~I 369 (600)
T KOG1676|consen 306 G----------GGMGGGAPG------LVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVI 369 (600)
T ss_pred C----------CCcCCCCcc------ceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEE
Confidence 0 001100010 11267899999999999999999999999999999999976 23567899999
Q ss_pred eccCCCcCccchHHH
Q 046946 448 SAFEGLWNPRSQTID 462 (650)
Q Consensus 448 ~G~~~~~~~~~~~~~ 462 (650)
.|.+.+++.+..+++
T Consensus 370 rG~~~QIdhAk~LIr 384 (600)
T KOG1676|consen 370 RGDKRQIDHAKQLIR 384 (600)
T ss_pred ecCcccchHHHHHHH
Confidence 999977776655544
No 5
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=1.5e-31 Score=260.61 Aligned_cols=294 Identities=27% Similarity=0.420 Sum_probs=208.5
Q ss_pred CceEEEEEecCccccceeccCchHHHHHHHHhCceEEEecCCCCCCceEEEEecChhhhhhccCCccchhhhhhcccCCc
Q 046946 126 ADTVYRILCPSRKIGGVIGKAGNIVKSLREETQAKITVADTIPGSEERVIIIYSSPTKIAKTQNKDDDSAAETKKESMEP 205 (650)
Q Consensus 126 ~~~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~~~~~g~~eRvI~I~G~~e~v~~a~~~~~~~~~e~~~~~~~~ 205 (650)
..+.+|||+.++.+|.||||||++||.|+.+.+|.|.|.|. ..+||+++|+...+.|
T Consensus 46 ~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri~tisad~~ti--------------------- 102 (390)
T KOG2192|consen 46 SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILTISADIETI--------------------- 102 (390)
T ss_pred cceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCceeEEEeccHHHH---------------------
Confidence 35999999999999999999999999999999999999986 4789999999874432
Q ss_pred ccHHHHHHHHHHHHHhhhhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCC
Q 046946 206 HCAAQDALLKVHDRIIEEDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCA 285 (650)
Q Consensus 206 ~~~a~~Al~~v~~~i~e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~ 285 (650)
-+.|.+|+-++.+. ......++++|||..+++|.|||++|++||+|++++.|+++|.. ..|.
T Consensus 103 ----~~ilk~iip~lee~----------f~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift----~c~p 164 (390)
T KOG2192|consen 103 ----GEILKKIIPTLEEG----------FQLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFT----ECCP 164 (390)
T ss_pred ----HHHHHHHhhhhhhC----------CCCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhh----ccCC
Confidence 33555555555532 23456789999999999999999999999999999999999985 5778
Q ss_pred CCCCceEEEecCHHHHHHHHHHHHHHHccCCCCCCCCCCCCC------cCCCCCCCCCCCC--CCCCCCCC--CCCCC--
Q 046946 286 MNTDEMVQISGKPNVAKRALYEVSTLLHQNPRKDKPPSSFPQ------AYGGQNFHSPPAP--MADMHPLG--NSSWP-- 353 (650)
Q Consensus 286 ~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~------~~~~~~~~~~~~~--~~~~~p~~--~~~~~-- 353 (650)
.++||+|.|.|.+..|..+++.|+++|.+.|.+.......|. +|++..++..+.+ ....++.+ ++..+
T Consensus 165 ~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~ 244 (390)
T KOG2192|consen 165 HSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRG 244 (390)
T ss_pred CCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCc
Confidence 899999999999999999999999999999988864433332 3555443211111 11111111 00000
Q ss_pred -------CCCCC---CC-----------------------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEE
Q 046946 354 -------ARNSS---LH-----------------------GMPSTPWMGGYGDQPSRMGSGSINSCPPGQMGEVSAEFSM 400 (650)
Q Consensus 354 -------~~~~~---~~-----------------------~~~~~p~~~~yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 400 (650)
++... .. .|+-.|..+..+++.. .+.+.+..+++ ..-.+.
T Consensus 245 sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQgGs~ydysy---AG~~GsYGdlG----GPitTa 317 (390)
T KOG2192|consen 245 SDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSY---AGGYGSYGDLG----GPITTA 317 (390)
T ss_pred cccceeccCCCCCccccccccccccccCCCcCCCcCccccccccCCCCCCCCCccc---cccccccCCCC----Cceeee
Confidence 00000 00 0000010000000000 00011111111 125678
Q ss_pred EEEecCCccceecccCccchhchhhhcCceEEecCCCCCCCccEEEEeccCCCcCccchHHHHHHHHhhhccc
Q 046946 401 KILCSAGKIGGVIGKGGFNVKQLQQETGASIHVEDAPTDSDERVIRASAFEGLWNPRSQTIDAILQLQNKTSE 473 (650)
Q Consensus 401 ~v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~erii~I~G~~~~~~~~~~~~~ai~~~~~~i~~ 473 (650)
.|.||.+.-|.||||+|+.|++|++++||.|++.....++++|+++|+|+. .++..|..+++..+..
T Consensus 318 Qvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTq------dQIqnAQYLlQn~Vkq 384 (390)
T KOG2192|consen 318 QVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ------DQIQNAQYLLQNSVKQ 384 (390)
T ss_pred eEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccH------HHHhhHHHHHHHHHHh
Confidence 899999999999999999999999999999999998889999999999998 4555666666665543
No 6
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.96 E-value=1.2e-29 Score=254.44 Aligned_cols=188 Identities=26% Similarity=0.382 Sum_probs=152.4
Q ss_pred eeEEEEEecCCccceecccCccchhchhhhcCceEEecC---CCCCCCccEEEEeccCCCcCc-cchHHHHHHHH---hh
Q 046946 397 EFSMKILCSAGKIGGVIGKGGFNVKQLQQETGASIHVED---APTDSDERVIRASAFEGLWNP-RSQTIDAILQL---QN 469 (650)
Q Consensus 397 ~~~~~v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~~---~~~~~~erii~I~G~~~~~~~-~~~~~~ai~~~---~~ 469 (650)
.+.++++||+..+|.||||+|++|.+|++++||+|++++ .++++.||+|.|+|+-+.+.+ .+.+.|.|.+. +.
T Consensus 38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~~~ 117 (402)
T KOG2191|consen 38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQAVA 117 (402)
T ss_pred ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHhhc
Confidence 389999999999999999999999999999999999995 578999999999998632221 11222222211 11
Q ss_pred hcccc----ccCCceEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcCHHHHHH
Q 046946 470 KTSEF----SEKGTITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGSSEHLIS 545 (650)
Q Consensus 470 ~i~~~----~~~~~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~~e~V~~ 545 (650)
++.+. ..++..+++|+||++.+|+||||+|++||.|++++||+|+|++.. ...-+..+|+|+++|++|+..+
T Consensus 118 k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqk----pt~~sLqervvt~sge~e~~~~ 193 (402)
T KOG2191|consen 118 KPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQK----PTGISLQERVVTVSGEPEQNMK 193 (402)
T ss_pred CCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccC----CCCccceeEEEEecCCHHHHHH
Confidence 11111 123446689999999999999999999999999999999999521 1225678999999999999999
Q ss_pred HHHHHHHHHhcCCCCCCCCCCccCCCCCCCCCCCCCCC--CCcCCCCCCCCCCcccCCC
Q 046946 546 AHGTYQSFMTSGQSMKVQPSSYQNINPQQSSCQTMSSH--QSSYQNMNTQQSPYHRVNA 602 (650)
Q Consensus 546 A~~lI~~~i~~~~~~~~~~~~~~~~~p~~~~~~~~~~~--~g~~~~~~~~~sp~~~~~~ 602 (650)
|..+|+++| ++|||+++|.|.+|. .|+.++++|+++||+...+
T Consensus 194 A~~~IL~Ki--------------~eDpqs~scln~sya~vsGpvaNsnPtGspya~~~~ 238 (402)
T KOG2191|consen 194 AVSLILQKI--------------QEDPQSGSCLNISYANVSGPVANSNPTGSPYAYQAH 238 (402)
T ss_pred HHHHHHHHh--------------hcCCcccceeccchhcccCcccccCCCCCCCCCCCc
Confidence 999999999 799999999998866 7899999999999976554
No 7
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.95 E-value=3.1e-27 Score=237.16 Aligned_cols=240 Identities=27% Similarity=0.447 Sum_probs=172.7
Q ss_pred ceEEEEEecCccccceeccCchHHHHHHHHhCceEEEe---cCCCCCCceEEEEecChhhhhhccCCccchhhhhhcccC
Q 046946 127 DTVYRILCPSRKIGGVIGKAGNIVKSLREETQAKITVA---DTIPGSEERVIIIYSSPTKIAKTQNKDDDSAAETKKESM 203 (650)
Q Consensus 127 ~~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~---~~~~g~~eRvI~I~G~~e~v~~a~~~~~~~~~e~~~~~~ 203 (650)
.+++|+|||+..+|.||||||++|.+|+++|||+|+++ |.+||++||||.|+|+.+++..+..
T Consensus 38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~e-------------- 103 (402)
T KOG2191|consen 38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHE-------------- 103 (402)
T ss_pred ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHH--------------
Confidence 49999999999999999999999999999999999998 6889999999999999665443222
Q ss_pred CcccHHHHHHHHHHHHHhhhhccCCC--C-CCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCC
Q 046946 204 EPHCAAQDALLKVHDRIIEEDLFGGM--A-SDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADR 280 (650)
Q Consensus 204 ~~~~~a~~Al~~v~~~i~e~~~~~~~--~-~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~ 280 (650)
-+.+.|.|.....+. + .+....+....++++||+..+|+||||+|.+||.|++++||+|+|++.
T Consensus 104 -----------fI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPq-- 170 (402)
T KOG2191|consen 104 -----------FIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQ-- 170 (402)
T ss_pred -----------HHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEeccc--
Confidence 222222222111111 1 112223445668999999999999999999999999999999999962
Q ss_pred CCCCCCCCCceEEEecCHHHHHHHHHHHHHHHccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 046946 281 LPPCAMNTDEMVQISGKPNVAKRALYEVSTLLHQNPRKDKPPSSFPQAYGGQNFHSPPAPMADMHPLGNSSWPARNSSLH 360 (650)
Q Consensus 281 ~p~~~~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~ 360 (650)
.|......||+|++.|++|+..+|+.+|.++|.++|+...+.+. +|.-.. .+..+..|.|
T Consensus 171 kpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~---sya~vs-----GpvaNsnPtG------------ 230 (402)
T KOG2191|consen 171 KPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNI---SYANVS-----GPVANSNPTG------------ 230 (402)
T ss_pred CCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceecc---chhccc-----CcccccCCCC------------
Confidence 23334578999999999999999999999999999887765431 111100 0111111111
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEecCCccceecccCccchhchhhhcCceEEecCCC
Q 046946 361 GMPSTPWMGGYGDQPSRMGSGSINSCPPGQMGEVSAEFSMKILCSAGKIGGVIGKGGFNVKQLQQETGASIHVEDAP 437 (650)
Q Consensus 361 ~~~~~p~~~~yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~~~~ 437 (650)
.+|+... .. ..........++....|..-|.+|.++-.|-.-+|+.+.+++..
T Consensus 231 --------spya~~~-----~~-----------~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l 283 (402)
T KOG2191|consen 231 --------SPYAYQA-----HV-----------LPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQAL 283 (402)
T ss_pred --------CCCCCCC-----cc-----------ccccchhhccccccccccccccccccceeeecccccceeecccc
Confidence 1222110 00 01123445677888899999999999999999999999888653
No 8
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.93 E-value=7.6e-25 Score=213.95 Aligned_cols=225 Identities=23% Similarity=0.423 Sum_probs=185.0
Q ss_pred CceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCceEEEecCHHHHHHHHHHHHHHHccCCC
Q 046946 238 STITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDEMVQISGKPNVAKRALYEVSTLLHQNPR 317 (650)
Q Consensus 238 ~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~~~ 317 (650)
..++++||+.++.+|.||||+|++||.|+.+++|.|.|... +..+|+++|+.+.+.|-.-++.|.-.|++.+.
T Consensus 46 ~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds-------~~peri~tisad~~ti~~ilk~iip~lee~f~ 118 (390)
T KOG2192|consen 46 SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS-------SGPERILTISADIETIGEILKKIIPTLEEGFQ 118 (390)
T ss_pred cceeEEEEEecccccceeccccccHHHHhhhccceeeccCC-------CCCceeEEEeccHHHHHHHHHHHhhhhhhCCC
Confidence 34789999999999999999999999999999999999732 25689999999999999888888888887432
Q ss_pred CCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCce
Q 046946 318 KDKPPSSFPQAYGGQNFHSPPAPMADMHPLGNSSWPARNSSLHGMPSTPWMGGYGDQPSRMGSGSINSCPPGQMGEVSAE 397 (650)
Q Consensus 318 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~p~~~~yg~~~~~~~~~~~~~~~~~~~~~~~~~ 397 (650)
.. ..
T Consensus 119 ~~----------------------------------------------------------------------------~p 122 (390)
T KOG2192|consen 119 LP----------------------------------------------------------------------------SP 122 (390)
T ss_pred CC----------------------------------------------------------------------------Cc
Confidence 21 13
Q ss_pred eEEEEEecCCccceecccCccchhchhhhcCceEEec-CCCCCCCccEEEEeccCCCcCccchHHHHHHHHhhhcc----
Q 046946 398 FSMKILCSAGKIGGVIGKGGFNVKQLQQETGASIHVE-DAPTDSDERVIRASAFEGLWNPRSQTIDAILQLQNKTS---- 472 (650)
Q Consensus 398 ~~~~v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~-~~~~~~~erii~I~G~~~~~~~~~~~~~ai~~~~~~i~---- 472 (650)
..++|+|....+|.|||++|++||+|++++.|+++|- ...+.+.+|++.|.|... .+-.+++.|+.+.+.+.
T Consensus 123 ce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k---~v~~~i~~il~~i~e~pikgs 199 (390)
T KOG2192|consen 123 CELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPK---RVVECIKIILDLISESPIKGS 199 (390)
T ss_pred hhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcc---hHHHHHHHHHHHhhcCCcCCc
Confidence 5689999999999999999999999999999999986 445678999999999872 22334444444322110
Q ss_pred -------------c------------------------------------------------------------------
Q 046946 473 -------------E------------------------------------------------------------------ 473 (650)
Q Consensus 473 -------------~------------------------------------------------------------------ 473 (650)
+
T Consensus 200 a~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw 279 (390)
T KOG2192|consen 200 AQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTW 279 (390)
T ss_pred CCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCc
Confidence 0
Q ss_pred ----cc-------------------------cCCceEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCC
Q 046946 474 ----FS-------------------------EKGTITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQD 524 (650)
Q Consensus 474 ----~~-------------------------~~~~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~ 524 (650)
|. .....|.++.||.++-|.||||||++|++|++++||.|.|. +
T Consensus 280 ~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikid-------e 352 (390)
T KOG2192|consen 280 SPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKID-------E 352 (390)
T ss_pred CccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEec-------C
Confidence 00 01245678999999999999999999999999999999887 4
Q ss_pred CCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 046946 525 PHPGSSECIVDIRGSSEHLISAHGTYQSFMT 555 (650)
Q Consensus 525 p~~~~~er~V~I~G~~e~V~~A~~lI~~~i~ 555 (650)
|..++.+|+++|+|+.+|++.|++|++..+.
T Consensus 353 pleGsedrIitItGTqdQIqnAQYLlQn~Vk 383 (390)
T KOG2192|consen 353 PLEGSEDRIITITGTQDQIQNAQYLLQNSVK 383 (390)
T ss_pred cCCCCCceEEEEeccHHHHhhHHHHHHHHHH
Confidence 6688899999999999999999999999986
No 9
>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=6.7e-26 Score=233.32 Aligned_cols=241 Identities=24% Similarity=0.399 Sum_probs=192.8
Q ss_pred ceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCceEEEecCHHHHHHHHHHHHHHHccCCCC
Q 046946 239 TITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDEMVQISGKPNVAKRALYEVSTLLHQNPRK 318 (650)
Q Consensus 239 ~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~~~~ 318 (650)
...+|++||-.+||.||||.|++||.|...|-|+|.|...++. +..|+.|+|-|++|...+|+++|++++.....+
T Consensus 198 D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~----Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~~ 273 (584)
T KOG2193|consen 198 DWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENA----GAAEKIITVHSTPEGTSKACKMILEIMQKEAVD 273 (584)
T ss_pred CcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccC----CcccCceEEecCccchHHHHHHHHHHHHHhhhc
Confidence 3458999999999999999999999999999999999976553 467999999999999999999999999875443
Q ss_pred CCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcee
Q 046946 319 DKPPSSFPQAYGGQNFHSPPAPMADMHPLGNSSWPARNSSLHGMPSTPWMGGYGDQPSRMGSGSINSCPPGQMGEVSAEF 398 (650)
Q Consensus 319 ~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~p~~~~yg~~~~~~~~~~~~~~~~~~~~~~~~~~ 398 (650)
++. .+++
T Consensus 274 ~k~-------------------------------------------------------------------------~~e~ 280 (584)
T KOG2193|consen 274 DKV-------------------------------------------------------------------------AEEI 280 (584)
T ss_pred cch-------------------------------------------------------------------------hhhc
Confidence 311 1267
Q ss_pred EEEEEecCCccceecccCccchhchhhhcCceEEecCC---CCCCCccEEEEeccCCCcCccchHHHHHHH-Hhh-hccc
Q 046946 399 SMKILCSAGKIGGVIGKGGFNVKQLQQETGASIHVEDA---PTDSDERVIRASAFEGLWNPRSQTIDAILQ-LQN-KTSE 473 (650)
Q Consensus 399 ~~~v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~~~---~~~~~erii~I~G~~~~~~~~~~~~~ai~~-~~~-~i~~ 473 (650)
.++++-.+.++|++|||.|.+||+|.++||++|.|.+- ..-..||.|++.|+-+.+-.++..+-+.++ -++ .+..
T Consensus 281 pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl~a 360 (584)
T KOG2193|consen 281 PLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDLAA 360 (584)
T ss_pred chhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHH
Confidence 78899999999999999999999999999999999852 223479999999976544433332222211 111 0000
Q ss_pred ------------------------cc--------------------cCCceEEEEEeCCCCceeEecCCCchHHHHHHhc
Q 046946 474 ------------------------FS--------------------EKGTITTRLLVPSSKVGCILGQGGHVINEMRRRT 509 (650)
Q Consensus 474 ------------------------~~--------------------~~~~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~T 509 (650)
.. .....+++|.||...+|.||||+|.+||.|.+.+
T Consensus 361 ~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~Rfa 440 (584)
T KOG2193|consen 361 MSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFA 440 (584)
T ss_pred hhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhc
Confidence 00 1134468999999999999999999999999999
Q ss_pred CCeEEEeCCccccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCCCCCC
Q 046946 510 QADIRVVGARVKLQDPHPGSSECIVDIRGSSEHLISAHGTYQSFMTSGQSMKV 562 (650)
Q Consensus 510 GA~I~i~~~~~~l~~p~~~~~er~V~I~G~~e~V~~A~~lI~~~i~~~~~~~~ 562 (650)
||.|.|.+.+. ++..+|+|+|+|.+++.-+|+..|..+|+++....|
T Consensus 441 gASiKIappE~------pdvseRMViItGppeaqfKAQgrifgKikEenf~~P 487 (584)
T KOG2193|consen 441 GASIKIAPPEI------PDVSERMVIITGPPEAQFKAQGRIFGKIKEENFFLP 487 (584)
T ss_pred cceeeecCCCC------CCcceeEEEecCChHHHHhhhhhhhhhhhhhccCCc
Confidence 99999997542 667999999999999999999999999988655433
No 10
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.80 E-value=6.2e-19 Score=193.82 Aligned_cols=157 Identities=31% Similarity=0.450 Sum_probs=131.1
Q ss_pred eeEEEEEecCCccceecccCccchhchhhhcCceEEecCCCCCCCccEEEEeccCCCcCccchHHHHHHHHhhhcccc--
Q 046946 397 EFSMKILCSAGKIGGVIGKGGFNVKQLQQETGASIHVEDAPTDSDERVIRASAFEGLWNPRSQTIDAILQLQNKTSEF-- 474 (650)
Q Consensus 397 ~~~~~v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~erii~I~G~~~~~~~~~~~~~ai~~~~~~i~~~-- 474 (650)
..++|++|+...+|.||||+|..|++|++++.++|+|.+..+++.||+++|+|+.... ..+.+.+++.+.++.+...
T Consensus 42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~-~~~~~~~al~ka~~~iv~~~~ 120 (485)
T KOG2190|consen 42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVEL-NLSPATDALFKAFDMIVFKLE 120 (485)
T ss_pred cceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccc-cCCchHHHHHHHHHHHhhccc
Confidence 4458999999999999999999999999999999999999999999999999942211 3344566666655544321
Q ss_pred ---------c---cCCceEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcCHHH
Q 046946 475 ---------S---EKGTITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGSSEH 542 (650)
Q Consensus 475 ---------~---~~~~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~~e~ 542 (650)
. +...++++|+||.+++|+||||+|+.||+|++.|||+|+|.++. .+..++|.|+|.|++++
T Consensus 121 ~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~------lP~ster~V~IsG~~~a 194 (485)
T KOG2190|consen 121 EDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDM------LPNSTERAVTISGEPDA 194 (485)
T ss_pred ccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCC------CCcccceeEEEcCchHH
Confidence 0 12247899999999999999999999999999999999999753 27789999999999999
Q ss_pred HHHHHHHHHHHHhcCCCC
Q 046946 543 LISAHGTYQSFMTSGQSM 560 (650)
Q Consensus 543 V~~A~~lI~~~i~~~~~~ 560 (650)
|.+|...|..+|.+....
T Consensus 195 v~~al~~Is~~L~~~~~~ 212 (485)
T KOG2190|consen 195 VKKALVQISSRLLENPPR 212 (485)
T ss_pred HHHHHHHHHHHHHhcCCc
Confidence 999999999999875433
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=99.55 E-value=4.5e-14 Score=136.56 Aligned_cols=138 Identities=21% Similarity=0.350 Sum_probs=99.1
Q ss_pred EEecCccccceeccCchHHHHHHHHhCceEEEecCCCCCCceEEEE---ecChhhhhhccCCccchhhhhhcccCCcccH
Q 046946 132 ILCPSRKIGGVIGKAGNIVKSLREETQAKITVADTIPGSEERVIII---YSSPTKIAKTQNKDDDSAAETKKESMEPHCA 208 (650)
Q Consensus 132 ilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~~~~~g~~eRvI~I---~G~~e~v~~a~~~~~~~~~e~~~~~~~~~~~ 208 (650)
+.||.+++|.|||+||++|++|+++|||+|+|.+. +..|.| +++++++.+|.+++..+...- .
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf---------~ 67 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLAVMKAREVVKAIGRGF---------S 67 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHHHHHHHHHHHHHHcCC---------C
Confidence 46899999999999999999999999999999953 356777 566666655544433211100 0
Q ss_pred HHHHHHHHHHHHhhhhccCCCCCCCCCCCCceEEE-EEEcC---------CccceeecCCchHHHHHHHHhCCeEEEccC
Q 046946 209 AQDALLKVHDRIIEEDLFGGMASDDDNENSTITAR-LLVPN---------NMVGCLLGKRGDVIQRLRSETGANIRVLPA 278 (650)
Q Consensus 209 a~~Al~~v~~~i~e~~~~~~~~~~~~~~~~~vt~~-llVP~---------~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~ 278 (650)
..+|+. +. .+.+..+ +-|.. ..+|+|||++|++++.|++.|||+|.|.
T Consensus 68 ~e~A~~-----l~---------------gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~-- 125 (172)
T TIGR03665 68 PEKALK-----LL---------------DDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY-- 125 (172)
T ss_pred HHHHHH-----hc---------------CCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc--
Confidence 011110 00 0111111 22222 3789999999999999999999999996
Q ss_pred CCCCCCCCCCCceEEEecCHHHHHHHHHHHHHHHccC
Q 046946 279 DRLPPCAMNTDEMVQISGKPNVAKRALYEVSTLLHQN 315 (650)
Q Consensus 279 ~~~p~~~~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~ 315 (650)
++.|.|.|++++++.|+.+|.+++...
T Consensus 126 ----------~~~v~i~G~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 126 ----------GKTVGIIGDPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred ----------CCEEEEECCHHHHHHHHHHHHHHHcCC
Confidence 357999999999999999999999664
No 12
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.53 E-value=4e-14 Score=137.82 Aligned_cols=142 Identities=21% Similarity=0.341 Sum_probs=103.0
Q ss_pred eEEEEEecCccccceeccCchHHHHHHHHhCceEEEecCCCCCCceEEEEe----cChhhhhhccCCccchhhhhhcccC
Q 046946 128 TVYRILCPSRKIGGVIGKAGNIVKSLREETQAKITVADTIPGSEERVIIIY----SSPTKIAKTQNKDDDSAAETKKESM 203 (650)
Q Consensus 128 ~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~~~~~g~~eRvI~I~----G~~e~v~~a~~~~~~~~~e~~~~~~ 203 (650)
+...+.||.+++|.|||++|++|+.|+++|||+|++.+. +..|.|. ++++++.+|.++++.+...-
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf----- 72 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLAVLKARDIVKAIGRGF----- 72 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCC-----
Confidence 567889999999999999999999999999999999953 3567775 67777666555444322210
Q ss_pred CcccHHHHHHHHHHHHHhhhhccCCCCCCCCCCCCceEEEE-E----Ec-----CCccceeecCCchHHHHHHHHhCCeE
Q 046946 204 EPHCAAQDALLKVHDRIIEEDLFGGMASDDDNENSTITARL-L----VP-----NNMVGCLLGKRGDVIQRLRSETGANI 273 (650)
Q Consensus 204 ~~~~~a~~Al~~v~~~i~e~~~~~~~~~~~~~~~~~vt~~l-l----VP-----~~~vg~IIGk~G~~Ik~I~~~tGa~I 273 (650)
...+|+. +..+ .+..++ - .+ ...+|+|||++|++++.|++.|||+|
T Consensus 73 ----~~e~A~~-----l~gd---------------~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i 128 (180)
T PRK13763 73 ----SPEKALR-----LLDD---------------DYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDI 128 (180)
T ss_pred ----CHHHHHH-----HhCC---------------CceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEE
Confidence 0111111 0000 011111 0 11 13789999999999999999999999
Q ss_pred EEccCCCCCCCCCCCCceEEEecCHHHHHHHHHHHHHHHccC
Q 046946 274 RVLPADRLPPCAMNTDEMVQISGKPNVAKRALYEVSTLLHQN 315 (650)
Q Consensus 274 ~i~~~~~~p~~~~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~ 315 (650)
.|. ++.|.|.|++++++.|+.+|.++++..
T Consensus 129 ~i~------------~~~v~i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 129 SVY------------GKTVAIIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred EEc------------CCEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence 996 235999999999999999999999663
No 13
>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=99.51 E-value=2e-14 Score=139.01 Aligned_cols=135 Identities=19% Similarity=0.284 Sum_probs=97.2
Q ss_pred EEecCCccceecccCccchhchhhhcCceEEecCCCCCCCccEEEE---eccCCCcCccchHHHHHHHHhhhccc---cc
Q 046946 402 ILCSAGKIGGVIGKGGFNVKQLQQETGASIHVEDAPTDSDERVIRA---SAFEGLWNPRSQTIDAILQLQNKTSE---FS 475 (650)
Q Consensus 402 v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~erii~I---~G~~~~~~~~~~~~~ai~~~~~~i~~---~~ 475 (650)
+.||.+.+|.|||++|++|+.|+++||++|++.+. +..|.| ++.++.+..+...++++..-++ .++ .-
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~-~e~A~~l~ 75 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLAVMKAREVVKAIGRGFS-PEKALKLL 75 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHHHHHHHHHHHHHHcCCC-HHHHHHhc
Confidence 56899999999999999999999999999999753 346777 3444333333333443332111 110 00
Q ss_pred cCCceEEEEEeCC---------CCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcCHHHHHHH
Q 046946 476 EKGTITTRLLVPS---------SKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGSSEHLISA 546 (650)
Q Consensus 476 ~~~~~~~~l~VP~---------~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~~e~V~~A 546 (650)
.+.....-+.|+. ..+|+|||++|++++.|++.|||+|.|.. +.|.|.|++++++.|
T Consensus 76 gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~--------------~~v~i~G~~~~~~~A 141 (172)
T TIGR03665 76 DDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG--------------KTVGIIGDPEQVQIA 141 (172)
T ss_pred CCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC--------------CEEEEECCHHHHHHH
Confidence 1111112233443 37999999999999999999999999862 579999999999999
Q ss_pred HHHHHHHHhc
Q 046946 547 HGTYQSFMTS 556 (650)
Q Consensus 547 ~~lI~~~i~~ 556 (650)
+++|.+++..
T Consensus 142 ~~~i~~li~~ 151 (172)
T TIGR03665 142 REAIEMLIEG 151 (172)
T ss_pred HHHHHHHHcC
Confidence 9999999944
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.47 E-value=1.2e-13 Score=134.42 Aligned_cols=139 Identities=19% Similarity=0.232 Sum_probs=100.1
Q ss_pred eEEEEEecCCccceecccCccchhchhhhcCceEEecCCCCCCCccEEEEe----ccCCCcCccchHHHHHHHHhhhccc
Q 046946 398 FSMKILCSAGKIGGVIGKGGFNVKQLQQETGASIHVEDAPTDSDERVIRAS----AFEGLWNPRSQTIDAILQLQNKTSE 473 (650)
Q Consensus 398 ~~~~v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~erii~I~----G~~~~~~~~~~~~~ai~~~~~~i~~ 473 (650)
+...+.||.+.++.|||++|++|+.|+++||++|++.+. +..|.|. ++++.+..+...++++..-++ .++
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~-~e~ 76 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLAVLKARDIVKAIGRGFS-PEK 76 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCC-HHH
Confidence 467899999999999999999999999999999999853 3566675 444444444444454443111 110
Q ss_pred -cc-cCCceEEE-EEeC---------CCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcCHH
Q 046946 474 -FS-EKGTITTR-LLVP---------SSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGSSE 541 (650)
Q Consensus 474 -~~-~~~~~~~~-l~VP---------~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~~e 541 (650)
+. ....+..+ +.|. ...+|+|||++|+++|.|++.|||+|.|.. +.|.|.|+++
T Consensus 77 A~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~--------------~~v~i~G~~~ 142 (180)
T PRK13763 77 ALRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG--------------KTVAIIGDPE 142 (180)
T ss_pred HHHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC--------------CEEEEEeCHH
Confidence 00 00111111 1111 147999999999999999999999999973 3499999999
Q ss_pred HHHHHHHHHHHHHhc
Q 046946 542 HLISAHGTYQSFMTS 556 (650)
Q Consensus 542 ~V~~A~~lI~~~i~~ 556 (650)
+++.|+..|.+++..
T Consensus 143 ~~~~A~~~I~~li~g 157 (180)
T PRK13763 143 QVEIAREAIEMLIEG 157 (180)
T ss_pred HHHHHHHHHHHHHcC
Confidence 999999999999844
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=99.30 E-value=5.5e-12 Score=102.22 Aligned_cols=64 Identities=44% Similarity=0.623 Sum_probs=58.0
Q ss_pred EEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 046946 482 TRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGSSEHLISAHGTYQ 551 (650)
Q Consensus 482 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~~e~V~~A~~lI~ 551 (650)
.+|+||.+.+|+||||+|++|++|+++|||+|++.+.. .....+|+|+|.|++++++.|+.+|.
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~------~~~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSV------LPGSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCC------CCCCCceEEEEEeCHHHHHHHHHhhC
Confidence 68999999999999999999999999999999998642 14678999999999999999999873
No 16
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.29 E-value=1.1e-11 Score=133.31 Aligned_cols=272 Identities=21% Similarity=0.306 Sum_probs=167.3
Q ss_pred CCCCceEEEEEecCccccceeccCchHHHHHHHHhCceEEEecCCCCCCceEEEEecChhhhhhccCCccchhhhhhccc
Q 046946 123 SQPADTVYRILCPSRKIGGVIGKAGNIVKSLREETQAKITVADTIPGSEERVIIIYSSPTKIAKTQNKDDDSAAETKKES 202 (650)
Q Consensus 123 ~~~~~~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~~~~~g~~eRvI~I~G~~e~v~~a~~~~~~~~~e~~~~~ 202 (650)
...+++.+++.++...|-++|||+|++|+.|++.|++||.+.+.. -.++++.++.|.+..
T Consensus 63 e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p~~------------------- 122 (608)
T KOG2279|consen 63 KPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFPVQ------------------- 122 (608)
T ss_pred CchhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCCCC-------------------
Confidence 345689999999999999999999999999999999999998543 235566666654332
Q ss_pred CCcccHHHHHHHHHHHHHhhhhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCC
Q 046946 203 MEPHCAAQDALLKVHDRIIEEDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLP 282 (650)
Q Consensus 203 ~~~~~~a~~Al~~v~~~i~e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p 282 (650)
.|.+..++ +..+.+ +..+...+.+|...++.|+|++|++++.|+.-++|+|.+.... .
T Consensus 123 ---v~~a~a~~---~~~~~~--------------~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ng--r 180 (608)
T KOG2279|consen 123 ---VCKAKAAI---HQILTE--------------NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNG--R 180 (608)
T ss_pred ---CChHHHHH---HHHHhc--------------CCcccccccchhhhcccccccchhhhcchhccccccccccccc--c
Confidence 33344333 333332 2456678899999999999999999999999999999997431 1
Q ss_pred CCCCCCCceEEEecCHHHHHHHHHHHHHHHccCCCCC--CC-----CCCCCCcCCCCCCCCCCCCCCCCCCCCCCC----
Q 046946 283 PCAMNTDEMVQISGKPNVAKRALYEVSTLLHQNPRKD--KP-----PSSFPQAYGGQNFHSPPAPMADMHPLGNSS---- 351 (650)
Q Consensus 283 ~~~~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~~~~~--~~-----~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~---- 351 (650)
...++...|.|...-++.|+.++.+.++++...- .+ ......+... .-.+++..+...
T Consensus 181 ---~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~--------~~~~m~~~~~s~~~h~ 249 (608)
T KOG2279|consen 181 ---LGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINV--------RREDMTEPGGAGEPHL 249 (608)
T ss_pred ---cccccceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCccc--------cchhhcccccCCcccc
Confidence 2457888888888888899999999887642211 00 0000000000 001111111110
Q ss_pred CCCCCCC-CCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCCceeEEEEEecCCccceecccCccchhchhhhc
Q 046946 352 WPARNSS-LHGMPSTPWMGGYGDQPSRMG---SGSINSCPPGQMGEVSAEFSMKILCSAGKIGGVIGKGGFNVKQLQQET 427 (650)
Q Consensus 352 ~~~~~~~-~~~~~~~p~~~~yg~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~v~iP~~~~g~IIGkgG~~Ik~I~~~s 427 (650)
|++.... +++ .|... .++..+..+ .+.|.....+-...........|.+|...+|.+||+.|++++.+...+
T Consensus 250 ~~~t~~s~spg---~~~~~-~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssas 325 (608)
T KOG2279|consen 250 WKNTSSSMSPG---APLVT-KEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSAS 325 (608)
T ss_pred CccchhccCCC---CCCcc-cCCCcceeEEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhcc
Confidence 1111000 000 00000 000000000 011211111111122234456799999999999999999999999999
Q ss_pred CceEEecCCCCCCCc---cEEEEeccC
Q 046946 428 GASIHVEDAPTDSDE---RVIRASAFE 451 (650)
Q Consensus 428 ga~I~i~~~~~~~~e---rii~I~G~~ 451 (650)
++.+.|.-......- .+|.+.|+-
T Consensus 326 n~~~hi~t~pyt~~v~~~qic~~egkq 352 (608)
T KOG2279|consen 326 NHPNHIWTQPYTSRVLQLQICVNEGKQ 352 (608)
T ss_pred CccceEEeccccchhhhhhhheecchh
Confidence 999999855332211 367777764
No 17
>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=99.26 E-value=5.5e-12 Score=102.17 Aligned_cols=59 Identities=44% Similarity=0.754 Sum_probs=53.3
Q ss_pred EEEEEecCccccceeccCchHHHHHHHHhCceEEEecCCC-CCCceEEEEecChhhhhhc
Q 046946 129 VYRILCPSRKIGGVIGKAGNIVKSLREETQAKITVADTIP-GSEERVIIIYSSPTKIAKT 187 (650)
Q Consensus 129 ~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~~~~~-g~~eRvI~I~G~~e~v~~a 187 (650)
++||+||.+++|.||||+|++|++|+++|||+|.+.+... +..+|+|+|.|+++++.+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A 60 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKA 60 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHH
Confidence 4799999999999999999999999999999999997544 7889999999998886654
No 18
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.19 E-value=6.5e-11 Score=127.55 Aligned_cols=228 Identities=18% Similarity=0.299 Sum_probs=168.6
Q ss_pred CCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCceEEEecCHHHHHHHHHHHHHHHccCC
Q 046946 237 NSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDEMVQISGKPNVAKRALYEVSTLLHQNP 316 (650)
Q Consensus 237 ~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~~ 316 (650)
...+.++++|+...+-+++||.|.+|+.|+..++++|.+..++ . ..++...+.|-+.+|.+|+.++.+++..+.
T Consensus 65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~-----g~e~~~~~~~~p~~v~~a~a~~~~~~~~~~ 138 (608)
T KOG2279|consen 65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-V-----GDERVLLISGFPVQVCKAKAAIHQILTENT 138 (608)
T ss_pred hhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-C-----CcccchhhccCCCCCChHHHHHHHHHhcCC
Confidence 4567899999999999999999999999999999999998543 2 346666777789999999999999987631
Q ss_pred CCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc
Q 046946 317 RKDKPPSSFPQAYGGQNFHSPPAPMADMHPLGNSSWPARNSSLHGMPSTPWMGGYGDQPSRMGSGSINSCPPGQMGEVSA 396 (650)
Q Consensus 317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~p~~~~yg~~~~~~~~~~~~~~~~~~~~~~~~ 396 (650)
T Consensus 139 -------------------------------------------------------------------------------- 138 (608)
T KOG2279|consen 139 -------------------------------------------------------------------------------- 138 (608)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred eeEEEEEecCCccceecccCccchhchhhhcCceEEecCCCCCCCccEEEEeccCCCcCccchH-HHHHHH---Hhhhcc
Q 046946 397 EFSMKILCSAGKIGGVIGKGGFNVKQLQQETGASIHVEDAPTDSDERVIRASAFEGLWNPRSQT-IDAILQ---LQNKTS 472 (650)
Q Consensus 397 ~~~~~v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~erii~I~G~~~~~~~~~~~-~~ai~~---~~~~i~ 472 (650)
.+.....+|...+++|+|++|++++.++..++|+|.+.+.....-.+.+.|.+....++.+... .+.+.. +.+++.
T Consensus 139 pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~ 218 (608)
T KOG2279|consen 139 PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKRIA 218 (608)
T ss_pred cccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccchhHHhhhch
Confidence 3345677788899999999999999999999999999987655567788888765322111110 011100 001100
Q ss_pred c------------------------------c-------------------------------c---------cCCceEE
Q 046946 473 E------------------------------F-------------------------------S---------EKGTITT 482 (650)
Q Consensus 473 ~------------------------------~-------------------------------~---------~~~~~~~ 482 (650)
+ + . .......
T Consensus 219 e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~ 298 (608)
T KOG2279|consen 219 ESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIP 298 (608)
T ss_pred hhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccccccccc
Confidence 0 0 0 0012235
Q ss_pred EEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 046946 483 RLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGSSEHLISAHGTYQSFM 554 (650)
Q Consensus 483 ~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~~e~V~~A~~lI~~~i 554 (650)
+|.||...+|.|||+.|++|+.+...+++.+.|..... -..-..-.++.+.|...-+..|..|+....
T Consensus 299 e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~py----t~~v~~~qic~~egkqh~~n~vl~ml~~~~ 366 (608)
T KOG2279|consen 299 EMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPY----TSRVLQLQICVNEGKQHYENSVLEMLTVHV 366 (608)
T ss_pred eeecCcccccchhhhhhhhhhhhhhccCccceEEeccc----cchhhhhhhheecchhHHHHHHHhhhhccC
Confidence 78999999999999999999999999999999985321 011112256889999999999999998655
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=99.15 E-value=4.7e-11 Score=95.68 Aligned_cols=61 Identities=23% Similarity=0.340 Sum_probs=55.5
Q ss_pred EEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 046946 482 TRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGSSEHLISAHGTYQ 551 (650)
Q Consensus 482 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~~e~V~~A~~lI~ 551 (650)
.+|.||.+++|+|||++|++|++|+++|||+|.+++. ...++.|+|+|+.++|..|+.+|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~---------~~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDP---------GSKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCC---------CCCCCEEEEEcCHHHHHHHHHHhC
Confidence 5799999999999999999999999999999999853 246789999999999999999874
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=99.13 E-value=1.6e-10 Score=92.31 Aligned_cols=59 Identities=22% Similarity=0.337 Sum_probs=53.4
Q ss_pred eEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcC-HHHHHHHHHHHH
Q 046946 480 ITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGS-SEHLISAHGTYQ 551 (650)
Q Consensus 480 ~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~-~e~V~~A~~lI~ 551 (650)
....+.||.+++|+||||+|++||+|+++|||+|.|+. ++.|.|+|+ +++++.|+.+|.
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-------------~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-------------DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-------------CCEEEEEeCCHHHHHHHHHHhC
Confidence 35689999999999999999999999999999999873 368999998 999999999873
No 21
>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=5.6e-11 Score=94.61 Aligned_cols=60 Identities=37% Similarity=0.498 Sum_probs=54.6
Q ss_pred EEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 046946 481 TTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGSSEHLISAHGTY 550 (650)
Q Consensus 481 ~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~~e~V~~A~~lI 550 (650)
|.+|.||.+++|+|||++|++|++|+++|||+|+|+.+ + .+..|+|+|++++|+.|+++|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~---------~-~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD---------D-ERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST---------T-EEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC---------C-CcEEEEEEeCHHHHHHHHhhC
Confidence 57899999999999999999999999999999999842 2 455999999999999999987
No 22
>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=99.08 E-value=3.6e-10 Score=90.82 Aligned_cols=63 Identities=43% Similarity=0.633 Sum_probs=56.7
Q ss_pred EEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 046946 482 TRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGSSEHLISAHGTYQ 551 (650)
Q Consensus 482 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~~e~V~~A~~lI~ 551 (650)
.++.||.+++|+|||++|++|++|+++|||+|.|+... .+..++.|+|.|+.+++..|+.+|+
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~-------~~~~~~~v~i~G~~~~v~~a~~~i~ 64 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSG-------SGSEERIVTITGTPEAVEKAKELIL 64 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCC-------CCCCceEEEEEcCHHHHHHHHHHhC
Confidence 57999999999999999999999999999999998532 2457899999999999999998873
No 23
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.05 E-value=1.6e-09 Score=126.32 Aligned_cols=318 Identities=18% Similarity=0.262 Sum_probs=179.4
Q ss_pred eEEEEEecCccccceeccCchHHHHHHHHhCceEEEecCCCCCCceEEEEecChhhhhhccCCccchhhhhhcccCCccc
Q 046946 128 TVYRILCPSRKIGGVIGKAGNIVKSLREETQAKITVADTIPGSEERVIIIYSSPTKIAKTQNKDDDSAAETKKESMEPHC 207 (650)
Q Consensus 128 ~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~~~~~g~~eRvI~I~G~~e~v~~a~~~~~~~~~e~~~~~~~~~~ 207 (650)
+...+-+-...+..|+||+|.+|.+|++++.|+|.+.+. +.+...+.++|...++.+|
T Consensus 347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~~~~ka-------------------- 404 (753)
T KOG2208|consen 347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSANDEKA-------------------- 404 (753)
T ss_pred eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccccchhHH--------------------
Confidence 556666778999999999999999999999999999973 5677889999987665542
Q ss_pred HHHHHHHHHHHHHhhhhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhC-CeEEEccCCCCCCCCC
Q 046946 208 AAQDALLKVHDRIIEEDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETG-ANIRVLPADRLPPCAM 286 (650)
Q Consensus 208 ~a~~Al~~v~~~i~e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tG-a~I~i~~~~~~p~~~~ 286 (650)
.+.+.++...+.. ..+...+.+|...+.+|||.+|..|..|..+++ ..|.+....
T Consensus 405 --~~~v~~~~~ei~n---------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~------- 460 (753)
T KOG2208|consen 405 --VEDVEKIIAEILN---------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN------- 460 (753)
T ss_pred --HHHHHHHHHhhhc---------------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC-------
Confidence 2233333333221 134457899999999999999999999999999 666554321
Q ss_pred CCCceEEEecCHHHHHHHHHHHHHHHcc----------------------------------CCCCCCCCCCCCCc----
Q 046946 287 NTDEMVQISGKPNVAKRALYEVSTLLHQ----------------------------------NPRKDKPPSSFPQA---- 328 (650)
Q Consensus 287 ~~dr~V~I~G~~~~V~~A~~~I~~~l~~----------------------------------~~~~~~~~~~~~~~---- 328 (650)
.....+++.|....|.+++.++..+... ...+...+...+..
T Consensus 461 ~~~~~~~~~~~~~dv~~~~~~~~~~~~~a~~~~~~~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~~~i~~~~~~~~~~~i 540 (753)
T KOG2208|consen 461 NSSDMVTIRGISKDVEKSVSLLKALKADAKNLKFRDVVTKDKLLPVKYIGKEIGKNGTIRDSLGDKSIFPPNEDEDHEKI 540 (753)
T ss_pred cccccceEeccccccchhHHHHHhhhhhhhcchhhhhhhccccchHHhhcccccCceeeeccCCceeeccccccccccee
Confidence 2233344444433333333222222210 00000001100000
Q ss_pred --------CCCC----CCCCCCC-CC---CCCCCC---------------------CC--CCCCCCCCCCCCCCCCCCCC
Q 046946 329 --------YGGQ----NFHSPPA-PM---ADMHPL---------------------GN--SSWPARNSSLHGMPSTPWMG 369 (650)
Q Consensus 329 --------~~~~----~~~~~~~-~~---~~~~p~---------------------~~--~~~~~~~~~~~~~~~~p~~~ 369 (650)
.... ....+.. .. .-..+. ++ ..+|.....+..+
T Consensus 541 ~i~gk~~~v~~a~~~L~~~~~~~~~~~~~~v~~~~~~~~~~l~~~~~~~~~~~e~~~gv~~~fp~~~~~~~e~------- 613 (753)
T KOG2208|consen 541 TIEGKLELVLEAPAELKALIEALIKATLLEVNNPPGQHRPFLIGKGIENRTYVEVFGGVVVPFPRSPTSSDEV------- 613 (753)
T ss_pred eecccccchhhhHHHHHhcchhhhhhhhhhccCcchheeeeeeccccccccceeecCcccccCCCCCCchhhh-------
Confidence 0000 0000000 00 000000 00 0011110000000
Q ss_pred CCCCCCCCCCCCCCCCCCCCCC----CCCCceeEEEEEecCCccceecccCccchhchhhhcCceEEecCCCCCCCccEE
Q 046946 370 GYGDQPSRMGSGSINSCPPGQM----GEVSAEFSMKILCSAGKIGGVIGKGGFNVKQLQQETGASIHVEDAPTDSDERVI 445 (650)
Q Consensus 370 ~yg~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~erii 445 (650)
...+....+.. +.... .......+..+.+|..++..+.|.+|..+++++..+++.+.+.+.........+
T Consensus 614 -----~i~g~~~~v~a-a~~~~~~i~~~~~~~~~~~~~i~~~~~~~~~~~~g~~~~~~t~~~~~~~~~~~~~~~~s~~~~ 687 (753)
T KOG2208|consen 614 -----SIKGAKDEVKA-AKGRLEEIVEYLSAYATTNTKIPDKFHRSIVGYRGHIIEEITSKFGVGGYFGDAPTEGSVNTI 687 (753)
T ss_pred -----ccchhHHHHHH-hhccchhhhhhcccccceeeecccccceeeecCCCcccccceeecCccceeCCCCCccccCcc
Confidence 00000000000 00000 011234455699999999999999999999999999999999876532111112
Q ss_pred EEeccCCCcCccchHHHHHHHHhhhccccccCCceEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeC
Q 046946 446 RASAFEGLWNPRSQTIDAILQLQNKTSEFSEKGTITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVG 517 (650)
Q Consensus 446 ~I~G~~~~~~~~~~~~~ai~~~~~~i~~~~~~~~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~ 517 (650)
.+.|.....+ ..+... .....++..+.+|.++++.|||.+|++++.+..++++.+.++.
T Consensus 688 ~~~~~~~~~e-----------~~~~~~--~~~~~~~~~~~~p~~~~~~~ig~~g~~~r~~~~~~~~~~~~~~ 746 (753)
T KOG2208|consen 688 HVSGEKMQSE-----------IAKIAL--EAKNLVTKEIEIPRSLHRYLIGPKGSNLRQLEKEFNVNIVVPN 746 (753)
T ss_pred hhhhhhhhhh-----------hccccc--ccccceeeEEeccHHHhhhccCCCCccHHHHHHHhccceecCC
Confidence 2222211111 111111 1346788899999999999999999999999999999998874
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=99.01 E-value=5.8e-10 Score=89.34 Aligned_cols=61 Identities=23% Similarity=0.468 Sum_probs=55.0
Q ss_pred EEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCceEEEecCHHHHHHHHHHHH
Q 046946 242 ARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDEMVQISGKPNVAKRALYEVS 309 (650)
Q Consensus 242 ~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr~V~I~G~~~~V~~A~~~I~ 309 (650)
.++.||.+++++|||++|++|++|+++|||+|.|...+ ..++.|+|+|+.++|.+|+.+|.
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-------~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-------SKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-------CCCCEEEEEcCHHHHHHHHHHhC
Confidence 57899999999999999999999999999999998532 45789999999999999998873
No 25
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.01 E-value=1.3e-09 Score=127.08 Aligned_cols=328 Identities=14% Similarity=0.212 Sum_probs=197.0
Q ss_pred eEEEEEecCccccceeccCchHHHHHHHHhCceEEEecCCCCCC-----ceEEEEecChhhhhhccCCcc-----chhhh
Q 046946 128 TVYRILCPSRKIGGVIGKAGNIVKSLREETQAKITVADTIPGSE-----ERVIIIYSSPTKIAKTQNKDD-----DSAAE 197 (650)
Q Consensus 128 ~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~~~~~g~~-----eRvI~I~G~~e~v~~a~~~~~-----~~~~e 197 (650)
+..++.+....+.++||+||.+++.++.++.+.|+|++.....+ .+...+....-++..+...++ ++...
T Consensus 201 ~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~~~~ 280 (753)
T KOG2208|consen 201 VFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSSPSNKIDGRLNSSSSINVEIQEALTRLESEFDYDEIIY 280 (753)
T ss_pred EEEEeeccccchhhhccccccccccccccceeEEEcccccccchhhhhccccccceehhhhhHHHHHHhcChhhhhhhhh
Confidence 77889999999999999999999999999999999995321111 122222222222222211111 11000
Q ss_pred hhc------ccCCcccHHHHHHHHHHHHHhh---h-hcc--CCCCC------------CCCCCCCceEEEEEEcCCccce
Q 046946 198 TKK------ESMEPHCAAQDALLKVHDRIIE---E-DLF--GGMAS------------DDDNENSTITARLLVPNNMVGC 253 (650)
Q Consensus 198 ~~~------~~~~~~~~a~~Al~~v~~~i~e---~-~~~--~~~~~------------~~~~~~~~vt~~llVP~~~vg~ 253 (650)
... ..........+...++.-.... . +.. .+... -.......+.+.+.+....+..
T Consensus 281 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~~~~ 360 (753)
T KOG2208|consen 281 RRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPEELKF 360 (753)
T ss_pred ccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHHhhhh
Confidence 000 0000000000000000000000 0 000 00000 0000123367788889999999
Q ss_pred eecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCceEEEecCHHHHHHHHHHHHHHHccCCCCCCCCCCCCCcCCCCC
Q 046946 254 LLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDEMVQISGKPNVAKRALYEVSTLLHQNPRKDKPPSSFPQAYGGQN 333 (650)
Q Consensus 254 IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~ 333 (650)
++||+|..|.+|++++.+.|.+... .+.+..+.++|....+.+|...+...+.+-+..
T Consensus 361 v~GK~~~ni~ki~e~~~~~i~~~~~-------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~--------------- 418 (753)
T KOG2208|consen 361 VIGKKGANIEKIREESQVKIDLPKQ-------GSNNKKVVITGVSANDEKAVEDVEKIIAEILNS--------------- 418 (753)
T ss_pred hcCCCCccHHHHHHhhhhceecccc-------cCCCCCeEEeccccchhHHHHHHHHHHHhhhcc---------------
Confidence 9999999999999999999999741 256788999999999999999999999762210
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEecCCccceec
Q 046946 334 FHSPPAPMADMHPLGNSSWPARNSSLHGMPSTPWMGGYGDQPSRMGSGSINSCPPGQMGEVSAEFSMKILCSAGKIGGVI 413 (650)
Q Consensus 334 ~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~p~~~~yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~iP~~~~g~II 413 (650)
.+...+.+|...+..+|
T Consensus 419 ---------------------------------------------------------------~~~~~~~iP~k~~~~ii 435 (753)
T KOG2208|consen 419 ---------------------------------------------------------------IVKEEVQIPTKSHKRII 435 (753)
T ss_pred ---------------------------------------------------------------cccceeecCccchhhhh
Confidence 12345889999999999
Q ss_pred ccCccchhchhhhcC-ceEEecCCCCCCCccEEEEeccCCCcCccchHHHHHHHHhhhccccccCCceEEEEEeCCCCce
Q 046946 414 GKGGFNVKQLQQETG-ASIHVEDAPTDSDERVIRASAFEGLWNPRSQTIDAILQLQNKTSEFSEKGTITTRLLVPSSKVG 492 (650)
Q Consensus 414 GkgG~~Ik~I~~~sg-a~I~i~~~~~~~~erii~I~G~~~~~~~~~~~~~ai~~~~~~i~~~~~~~~~~~~l~VP~~~vG 492 (650)
|.+|..|..|..+++ ..|++..... ...-.++.|....+..+ ...+..+.....+.......+...+.|..+.+
T Consensus 436 g~~g~~i~~I~~k~~~v~i~f~~~~~--~~~~~~~~~~~~dv~~~---~~~~~~~~~~a~~~~~~~~~~~d~~~~~~~~~ 510 (753)
T KOG2208|consen 436 GTKGALINYIMGKHGGVHIKFQNNNN--SSDMVTIRGISKDVEKS---VSLLKALKADAKNLKFRDVVTKDKLLPVKYIG 510 (753)
T ss_pred ccccccHHHHHhhcCcEEEecCCCCc--ccccceEeccccccchh---HHHHHhhhhhhhcchhhhhhhccccchHHhhc
Confidence 999999999999999 6666654432 33345566654333221 11111111101111111234456677777777
Q ss_pred eEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 046946 493 CILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGSSEHLISAHGTYQSFMTSG 557 (650)
Q Consensus 493 ~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~~e~V~~A~~lI~~~i~~~ 557 (650)
..+|+.|..+....+ ..-++.. ...++..++|.|..+.|..|.+.+..++...
T Consensus 511 ~~~g~~~~i~d~~~~----~~i~~~~--------~~~~~~~i~i~gk~~~v~~a~~~L~~~~~~~ 563 (753)
T KOG2208|consen 511 KEIGKNGTIRDSLGD----KSIFPPN--------EDEDHEKITIEGKLELVLEAPAELKALIEAL 563 (753)
T ss_pred ccccCceeeeccCCc----eeecccc--------cccccceeeecccccchhhhHHHHHhcchhh
Confidence 777777766554444 4444322 2346779999999999999999998877643
No 26
>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=99.00 E-value=3.9e-10 Score=89.75 Aligned_cols=60 Identities=33% Similarity=0.642 Sum_probs=53.9
Q ss_pred EEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCceEEEecCHHHHHHHHHHH
Q 046946 241 TARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDEMVQISGKPNVAKRALYEV 308 (650)
Q Consensus 241 t~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr~V~I~G~~~~V~~A~~~I 308 (650)
|.+|.||.+++++|||++|++|++|+++|||+|.|..+ ..+..|+|+|+.++|++|+++|
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 57899999999999999999999999999999999742 1245899999999999999886
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=98.97 E-value=2.1e-09 Score=85.91 Aligned_cols=59 Identities=22% Similarity=0.376 Sum_probs=53.2
Q ss_pred eEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCceEEEecC-HHHHHHHHHHHH
Q 046946 240 ITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDEMVQISGK-PNVAKRALYEVS 309 (650)
Q Consensus 240 vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr~V~I~G~-~~~V~~A~~~I~ 309 (650)
+...+.||.+.+|+|||++|++|++|+++|||+|.|.. ++.|.|+|+ +++|++|+.+|.
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----------~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-----------DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-----------CCEEEEEeCCHHHHHHHHHHhC
Confidence 45678999999999999999999999999999999963 457999999 999999999873
No 28
>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=98.93 E-value=3.6e-09 Score=84.93 Aligned_cols=62 Identities=34% Similarity=0.655 Sum_probs=55.6
Q ss_pred EEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCceEEEecCHHHHHHHHHHH
Q 046946 242 ARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDEMVQISGKPNVAKRALYEV 308 (650)
Q Consensus 242 ~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr~V~I~G~~~~V~~A~~~I 308 (650)
.++.||.+++++|||++|++|++|+++|||+|.|..... ...++.|.|.|+.+++.+|+.+|
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 589999999999999999999999999999999985322 25688999999999999999887
No 29
>PF13014 KH_3: KH domain
Probab=98.87 E-value=3.3e-09 Score=78.58 Aligned_cols=42 Identities=48% Similarity=0.766 Sum_probs=39.1
Q ss_pred cccceeccCchHHHHHHHHhCceEEEec-CCCCCCceEEEEec
Q 046946 138 KIGGVIGKAGNIVKSLREETQAKITVAD-TIPGSEERVIIIYS 179 (650)
Q Consensus 138 ~vG~IIGKgG~~Ik~Ir~~TgakI~I~~-~~~g~~eRvI~I~G 179 (650)
++|+||||+|++|++|+++|+|+|+|++ ..++..+|+|+|+|
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 5899999999999999999999999997 66788999999987
No 30
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.78 E-value=6.4e-08 Score=93.29 Aligned_cols=145 Identities=23% Similarity=0.353 Sum_probs=100.6
Q ss_pred ceEEEEEecCccccceeccCchHHHHHHHHhCceEEEecCCCCCCceEEEEecC-----hhhhhhccCCccchhhhhhcc
Q 046946 127 DTVYRILCPSRKIGGVIGKAGNIVKSLREETQAKITVADTIPGSEERVIIIYSS-----PTKIAKTQNKDDDSAAETKKE 201 (650)
Q Consensus 127 ~~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~~~~~g~~eRvI~I~G~-----~e~v~~a~~~~~~~~~e~~~~ 201 (650)
...+.+.||...++.+||+.|++.+.|++.++++|.++ +.+..|.|... |-.+.+|.+.+..+.
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD-----~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIg------ 75 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID-----SKTGSVTIRTTRKTEDPLALLKARDVVKAIG------ 75 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEE-----CCCCeEEEEecCCCCChHHHHHHHHHHHHHh------
Confidence 35677999999999999999999999999999999998 45667888765 112222222111000
Q ss_pred cCCcccHHHHHHHHHHHHHhhhhccCCCCCCCCCCCCceEEEE-----EEc------CCccceeecCCchHHHHHHHHhC
Q 046946 202 SMEPHCAAQDALLKVHDRIIEEDLFGGMASDDDNENSTITARL-----LVP------NNMVGCLLGKRGDVIQRLRSETG 270 (650)
Q Consensus 202 ~~~~~~~a~~Al~~v~~~i~e~~~~~~~~~~~~~~~~~vt~~l-----lVP------~~~vg~IIGk~G~~Ik~I~~~tG 270 (650)
.-.+-.+|+..+-+ ...+.+ ++- ....|+|||++|.+-+.|++-||
T Consensus 76 ---rGF~pe~A~~LL~d--------------------~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~ 132 (194)
T COG1094 76 ---RGFPPEKALKLLED--------------------DYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTG 132 (194)
T ss_pred ---cCCCHHHHHHHhcC--------------------CcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhC
Confidence 00011112211100 111111 111 23569999999999999999999
Q ss_pred CeEEEccCCCCCCCCCCCCceEEEecCHHHHHHHHHHHHHHHccCCC
Q 046946 271 ANIRVLPADRLPPCAMNTDEMVQISGKPNVAKRALYEVSTLLHQNPR 317 (650)
Q Consensus 271 a~I~i~~~~~~p~~~~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~~~ 317 (650)
|.|.|. +..|.|-|..++|+.|+.+|..++...++
T Consensus 133 ~~I~V~------------g~tVaiiG~~~~v~iAr~AVemli~G~~h 167 (194)
T COG1094 133 VYISVY------------GKTVAIIGGFEQVEIAREAVEMLINGAPH 167 (194)
T ss_pred CeEEEe------------CcEEEEecChhhhHHHHHHHHHHHcCCCc
Confidence 999997 45799999999999999999999987543
No 31
>smart00322 KH K homology RNA-binding domain.
Probab=98.76 E-value=4.2e-08 Score=78.94 Aligned_cols=66 Identities=30% Similarity=0.542 Sum_probs=59.3
Q ss_pred eEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 046946 480 ITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGSSEHLISAHGTYQSFM 554 (650)
Q Consensus 480 ~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~~e~V~~A~~lI~~~i 554 (650)
.+.++.||...+|++||++|++|++|++.||++|.+.... .....|+|.|+.++++.|+.+|.+.+
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 4678999999999999999999999999999999997521 15689999999999999999999876
No 32
>PF13014 KH_3: KH domain
Probab=98.75 E-value=1.5e-08 Score=74.99 Aligned_cols=43 Identities=44% Similarity=0.746 Sum_probs=38.4
Q ss_pred CceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEc
Q 046946 490 KVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRG 538 (650)
Q Consensus 490 ~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G 538 (650)
+||+|||++|++|++|+++|||+|+|++ +..++..++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~------~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP------ENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC------ccCCCCCceEEEEEC
Confidence 5899999999999999999999999996 233677899999998
No 33
>smart00322 KH K homology RNA-binding domain.
Probab=98.66 E-value=1.4e-07 Score=75.76 Aligned_cols=68 Identities=28% Similarity=0.577 Sum_probs=59.8
Q ss_pred ceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCceEEEecCHHHHHHHHHHHHHHHc
Q 046946 239 TITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDEMVQISGKPNVAKRALYEVSTLLH 313 (650)
Q Consensus 239 ~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr~V~I~G~~~~V~~A~~~I~~~l~ 313 (650)
.++.++.||...++++||++|++|++|++.||++|.+.... .....+.|.|+.+++..|+.+|.+.++
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------~~~~~v~i~g~~~~v~~a~~~i~~~~~ 69 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------SEERVVEITGPPENVEKAAELILEILE 69 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-------CCccEEEEEcCHHHHHHHHHHHHHHhC
Confidence 35789999999999999999999999999999999997421 146789999999999999999998763
No 34
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.60 E-value=3.7e-07 Score=88.06 Aligned_cols=142 Identities=19% Similarity=0.231 Sum_probs=100.3
Q ss_pred eeEEEEEecCCccceecccCccchhchhhhcCceEEecCCCCCCCccEEEEeccCCCcCc-----cchHHHHHHHHhhhc
Q 046946 397 EFSMKILCSAGKIGGVIGKGGFNVKQLQQETGASIHVEDAPTDSDERVIRASAFEGLWNP-----RSQTIDAILQLQNKT 471 (650)
Q Consensus 397 ~~~~~v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~erii~I~G~~~~~~~-----~~~~~~ai~~~~~~i 471 (650)
.....+.||.+..+.+||+.|+.-+.|.+.+++.|.++. .+..+.|..++...++ +...++||-+-++--
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~-----~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe 81 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS-----KTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPE 81 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC-----CCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHH
Confidence 345679999999999999999999999999999999953 4567777766422222 122334443211110
Q ss_pred cccc--cCCceEEEEEe------C----CCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcC
Q 046946 472 SEFS--EKGTITTRLLV------P----SSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGS 539 (650)
Q Consensus 472 ~~~~--~~~~~~~~l~V------P----~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~ 539 (650)
..+. +++..-..+.+ + ....|+|||++|.+-+-|.+.|||+|.|.. ..|.|.|.
T Consensus 82 ~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g--------------~tVaiiG~ 147 (194)
T COG1094 82 KALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG--------------KTVAIIGG 147 (194)
T ss_pred HHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC--------------cEEEEecC
Confidence 0000 11111111111 1 135699999999999999999999999985 47999999
Q ss_pred HHHHHHHHHHHHHHHhcC
Q 046946 540 SEHLISAHGTYQSFMTSG 557 (650)
Q Consensus 540 ~e~V~~A~~lI~~~i~~~ 557 (650)
+++|+.|++.|..+|...
T Consensus 148 ~~~v~iAr~AVemli~G~ 165 (194)
T COG1094 148 FEQVEIAREAVEMLINGA 165 (194)
T ss_pred hhhhHHHHHHHHHHHcCC
Confidence 999999999999999653
No 35
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.41 E-value=3.2e-07 Score=93.03 Aligned_cols=145 Identities=17% Similarity=0.249 Sum_probs=111.9
Q ss_pred ceeEEEEEecCCccceecccCccchhchhhhcCceEEecCCCCCCCccEEEEeccCCCcCccchHHHHHHHHhhhccc--
Q 046946 396 AEFSMKILCSAGKIGGVIGKGGFNVKQLQQETGASIHVEDAPTDSDERVIRASAFEGLWNPRSQTIDAILQLQNKTSE-- 473 (650)
Q Consensus 396 ~~~~~~v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~erii~I~G~~~~~~~~~~~~~ai~~~~~~i~~-- 473 (650)
+.++..+.+|...++.|.|++|.+||.|+.+|..+|+-+... .|.++.++|..+.++.+...+++..+.+..+..
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~---eePiF~vTg~~edv~~aRrei~saaeH~~l~~~s~ 100 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG---EEPIFPVTGRHEDVRRARREIPSAAEHFGLIRASR 100 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC---CCCcceeccCchhHHHHhhcCccccceeeeeeecc
Confidence 367889999999999999999999999999999999988654 458999999987776555444443222222211
Q ss_pred -c-------ccCCceEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcCHHH-HH
Q 046946 474 -F-------SEKGTITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGSSEH-LI 544 (650)
Q Consensus 474 -~-------~~~~~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~~e~-V~ 544 (650)
+ ......+....||...+|.|.|.+|++|+.|++.+...|..+-. ..+.++.++|.+++ ++
T Consensus 101 s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~----------~~~~Vf~Vtg~~~nC~k 170 (394)
T KOG2113|consen 101 SFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR----------CGEPVFCVTGAPKNCVK 170 (394)
T ss_pred cccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc----------CCCceEEEecCCcchhh
Confidence 1 12346677899999999999999999999999999999877632 26789999998888 66
Q ss_pred HHH-HHHHHH
Q 046946 545 SAH-GTYQSF 553 (650)
Q Consensus 545 ~A~-~lI~~~ 553 (650)
+|. ..|+..
T Consensus 171 ra~s~eie~t 180 (394)
T KOG2113|consen 171 RARSCEIEQT 180 (394)
T ss_pred hccccchhhh
Confidence 666 555544
No 36
>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=98.19 E-value=4.9e-06 Score=75.58 Aligned_cols=69 Identities=23% Similarity=0.313 Sum_probs=52.5
Q ss_pred CCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCC--------CC--CCCCceEEEEEcC---HHHHHHHHHHHHHHH
Q 046946 488 SSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQD--------PH--PGSSECIVDIRGS---SEHLISAHGTYQSFM 554 (650)
Q Consensus 488 ~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~--------p~--~~~~er~V~I~G~---~e~V~~A~~lI~~~i 554 (650)
.+++|.|||++|.+||+|+++|||+|.|..+.-.-.. +. .....-.|.|++. .+.+++|+++|.+++
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 3789999999999999999999999999975210000 00 1123357999995 599999999999998
Q ss_pred hc
Q 046946 555 TS 556 (650)
Q Consensus 555 ~~ 556 (650)
..
T Consensus 94 ~~ 95 (120)
T cd02395 94 KP 95 (120)
T ss_pred cc
Confidence 64
No 37
>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=98.15 E-value=7.6e-06 Score=74.35 Aligned_cols=68 Identities=29% Similarity=0.475 Sum_probs=52.2
Q ss_pred CCccceeecCCchHHHHHHHHhCCeEEEccCCCCC-----------CCC-CCCCceEEEecCH---HHHHHHHHHHHHHH
Q 046946 248 NNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLP-----------PCA-MNTDEMVQISGKP---NVAKRALYEVSTLL 312 (650)
Q Consensus 248 ~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p-----------~~~-~~~dr~V~I~G~~---~~V~~A~~~I~~~l 312 (650)
.+.+|.|||++|.+||+|+++|||+|.|..+.... ..+ ....-.|.|++.. +++.+|+.+|..++
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 35789999999999999999999999998542111 000 0122578999965 88999999999999
Q ss_pred ccC
Q 046946 313 HQN 315 (650)
Q Consensus 313 ~~~ 315 (650)
...
T Consensus 94 ~~~ 96 (120)
T cd02395 94 KPA 96 (120)
T ss_pred ccC
Confidence 853
No 38
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.96 E-value=2.3e-05 Score=73.24 Aligned_cols=104 Identities=20% Similarity=0.274 Sum_probs=71.5
Q ss_pred eEEEEEecCccccceeccCchHHHHHHHHhCceEEEecCCCCCCceEEEEecChhhhhhccCCccchhhhhhcccCCccc
Q 046946 128 TVYRILCPSRKIGGVIGKAGNIVKSLREETQAKITVADTIPGSEERVIIIYSSPTKIAKTQNKDDDSAAETKKESMEPHC 207 (650)
Q Consensus 128 ~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~~~~~g~~eRvI~I~G~~e~v~~a~~~~~~~~~e~~~~~~~~~~ 207 (650)
-.+.++|+...+|..||++|++|+.|++..|-+|.|-+... .+
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~-----------d~-------------------------- 74 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSD-----------DP-------------------------- 74 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCC-----------CH--------------------------
Confidence 35678889999999999999999999999999999886421 10
Q ss_pred HHHHHHHHHHHHHhhhhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEc
Q 046946 208 AAQDALLKVHDRIIEEDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVL 276 (650)
Q Consensus 208 ~a~~Al~~v~~~i~e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~ 276 (650)
.+ ....+.......... -...+....+.+.|+.+..|.+|||+|++|+.++.-++-++.|.
T Consensus 75 --~~----fI~n~l~Pa~V~~v~--I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 75 --EE----FIKNIFAPAAVRSVT--IKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred --HH----HHHHHcCCCEEEEEE--EEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 11 111111000000000 00112235567889999999999999999999999999888764
No 39
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.93 E-value=2e-05 Score=80.32 Aligned_cols=144 Identities=22% Similarity=0.274 Sum_probs=105.3
Q ss_pred CceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCceEEEecCHHHHHHHHHHHHHHHccCCC
Q 046946 238 STITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDEMVQISGKPNVAKRALYEVSTLLHQNPR 317 (650)
Q Consensus 238 ~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~~~ 317 (650)
..++..+.||...++.|.|++|.+||.|+.+|...|.-+..+ .+.+..++|..+.|+.|++.|...-+-.-.
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~--------eePiF~vTg~~edv~~aRrei~saaeH~~l 95 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG--------EEPIFPVTGRHEDVRRARREIPSAAEHFGL 95 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC--------CCCcceeccCchhHHHHhhcCccccceeee
Confidence 678889999999999999999999999999999999876543 346789999999999999987653221000
Q ss_pred CCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCce
Q 046946 318 KDKPPSSFPQAYGGQNFHSPPAPMADMHPLGNSSWPARNSSLHGMPSTPWMGGYGDQPSRMGSGSINSCPPGQMGEVSAE 397 (650)
Q Consensus 318 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~p~~~~yg~~~~~~~~~~~~~~~~~~~~~~~~~ 397 (650)
. ++ ... ++++.+.+. .+..
T Consensus 96 ~------------------------------------~~-s~s------------------~Sgg~~~~s------~s~q 114 (394)
T KOG2113|consen 96 I------------------------------------RA-SRS------------------FSGGTNGAS------ASGQ 114 (394)
T ss_pred e------------------------------------ee-ccc------------------ccCCCcccc------ccCC
Confidence 0 00 000 011111111 1113
Q ss_pred eEEEEEecCCccceecccCccchhchhhhcCceEEecCCCCCCCccEEEEeccCCC
Q 046946 398 FSMKILCSAGKIGGVIGKGGFNVKQLQQETGASIHVEDAPTDSDERVIRASAFEGL 453 (650)
Q Consensus 398 ~~~~v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~erii~I~G~~~~ 453 (650)
.+..+.+|...+|.|.|..|.+|+.+++.+...|...... .+.++.++|....
T Consensus 115 t~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~---~~~Vf~Vtg~~~n 167 (394)
T KOG2113|consen 115 TTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRC---GEPVFCVTGAPKN 167 (394)
T ss_pred CceeeeccceeeeeccccccCccchheecccceEeeeccC---CCceEEEecCCcc
Confidence 4567788888899999999999999999999999887543 5679999996654
No 40
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.70 E-value=3.8e-05 Score=71.78 Aligned_cols=102 Identities=23% Similarity=0.389 Sum_probs=70.6
Q ss_pred eEEEEEecCCccceecccCccchhchhhhcCceEEecCCCCCCCccEEEEeccCCCcCccchHHHHHHHHhhhcc-cc-c
Q 046946 398 FSMKILCSAGKIGGVIGKGGFNVKQLQQETGASIHVEDAPTDSDERVIRASAFEGLWNPRSQTIDAILQLQNKTS-EF-S 475 (650)
Q Consensus 398 ~~~~v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~erii~I~G~~~~~~~~~~~~~ai~~~~~~i~-~~-~ 475 (650)
-.+.+.|+...+|..||++|++|+.|++..|-+|.+-.-.. +. ...+..++.-..-.. .. .
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~----------------d~-~~fI~n~l~Pa~V~~v~I~~ 94 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSD----------------DP-EEFIKNIFAPAAVRSVTIKK 94 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCC----------------CH-HHHHHHHcCCCEEEEEEEEe
Confidence 35678899999999999999999999999988877753211 11 111121211111000 00 1
Q ss_pred cCCceEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEe
Q 046946 476 EKGTITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVV 516 (650)
Q Consensus 476 ~~~~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~ 516 (650)
..+.....+.|+....|..|||+|++|+.++.-+|-++.|.
T Consensus 95 ~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 95 KNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred cCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 22345567889999999999999999999999999887664
No 41
>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=97.62 E-value=0.00016 Score=83.54 Aligned_cols=68 Identities=19% Similarity=0.327 Sum_probs=60.6
Q ss_pred cCCceEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHH
Q 046946 476 EKGTITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRG-SSEHLISAHGTYQSFM 554 (650)
Q Consensus 476 ~~~~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G-~~e~V~~A~~lI~~~i 554 (650)
...+....+.||.+++|.|||+||.+||+|.++|||+|.|. ++..|.|.+ +.+.+++|+.+|..++
T Consensus 574 ~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~-------------d~G~V~I~a~d~~~~~~A~~~I~~i~ 640 (719)
T TIGR02696 574 PYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE-------------DDGTVYIGAADGPSAEAARAMINAIA 640 (719)
T ss_pred cCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe-------------cCcEEEEEeCCHHHHHHHHHHHHHhh
Confidence 33466788999999999999999999999999999999998 457899999 6899999999999998
Q ss_pred hc
Q 046946 555 TS 556 (650)
Q Consensus 555 ~~ 556 (650)
..
T Consensus 641 ~~ 642 (719)
T TIGR02696 641 NP 642 (719)
T ss_pred Cc
Confidence 63
No 42
>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=97.48 E-value=0.00053 Score=79.23 Aligned_cols=92 Identities=24% Similarity=0.330 Sum_probs=71.9
Q ss_pred HHHHHHHHHHHHHhhhhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCC
Q 046946 208 AAQDALLKVHDRIIEEDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMN 287 (650)
Q Consensus 208 ~a~~Al~~v~~~i~e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~ 287 (650)
.+.+++..+++.+.+.-.. . .......+....+.||.+.++.|||++|.+||+|.++|||+|.|..
T Consensus 550 ~A~~g~~~Il~~m~~al~~-p---~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---------- 615 (719)
T TIGR02696 550 QARDARLAILDVMAEAIDT-P---DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---------- 615 (719)
T ss_pred HHHHHHHHHHHHHHHHHhC-c---cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec----------
Confidence 3666777777666543211 1 1223345667889999999999999999999999999999999962
Q ss_pred CCceEEEecC-HHHHHHHHHHHHHHHcc
Q 046946 288 TDEMVQISGK-PNVAKRALYEVSTLLHQ 314 (650)
Q Consensus 288 ~dr~V~I~G~-~~~V~~A~~~I~~~l~~ 314 (650)
+..|.|.+. .+.+++|+.+|..++..
T Consensus 616 -~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 616 -DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred -CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 567899886 88899999999999974
No 43
>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=97.47 E-value=0.00044 Score=64.55 Aligned_cols=103 Identities=19% Similarity=0.229 Sum_probs=70.1
Q ss_pred EEEEEecCccccceeccCchHHHHHHHHhCceEEEecCCCCCCceEEEEecChhhhhhccCCccchhhhhhcccCCcccH
Q 046946 129 VYRILCPSRKIGGVIGKAGNIVKSLREETQAKITVADTIPGSEERVIIIYSSPTKIAKTQNKDDDSAAETKKESMEPHCA 208 (650)
Q Consensus 129 ~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~~~~~g~~eRvI~I~G~~e~v~~a~~~~~~~~~e~~~~~~~~~~~ 208 (650)
-+-++|....+|..||++|++|+.|++..|=+|.|-+... +++.
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~-----------D~~~------------------------- 77 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSE-----------NLEE------------------------- 77 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCC-----------CHHH-------------------------
Confidence 4556788899999999999999999999999999886321 1111
Q ss_pred HHHHHHHHHHHHhhhhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEc
Q 046946 209 AQDALLKVHDRIIEEDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVL 276 (650)
Q Consensus 209 a~~Al~~v~~~i~e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~ 276 (650)
-+...+.-... ... .....++.....+.|+.+..+..|||+|++++..++-++-++.|.
T Consensus 78 ------fI~N~l~PA~V-~~V--~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 78 ------FVANKLAPAEV-KNV--TVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred ------HHHHcCCCceE-EEE--EEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 00000000000 000 000112345678899999999999999999999999999888764
No 44
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.45 E-value=0.00091 Score=72.49 Aligned_cols=77 Identities=25% Similarity=0.427 Sum_probs=58.6
Q ss_pred CceEEEEEEcC------CccceeecCCchHHHHHHHHhCCeEEEccCCCCCCC----------CCC-CCceEEEecC-HH
Q 046946 238 STITARLLVPN------NMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPC----------AMN-TDEMVQISGK-PN 299 (650)
Q Consensus 238 ~~vt~~llVP~------~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~----------~~~-~dr~V~I~G~-~~ 299 (650)
..++-+|.||. ++||+|||.+|.|.|+|+++|||+|.|.-+...... .+. .+-.+.|+++ .|
T Consensus 136 ~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~e 215 (554)
T KOG0119|consen 136 AKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQE 215 (554)
T ss_pred cccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHH
Confidence 36677888884 589999999999999999999999999862211111 111 2235778887 67
Q ss_pred HHHHHHHHHHHHHcc
Q 046946 300 VAKRALYEVSTLLHQ 314 (650)
Q Consensus 300 ~V~~A~~~I~~~l~~ 314 (650)
.|++|+..|..+|.+
T Consensus 216 ki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 216 KIKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHHh
Confidence 899999999999986
No 45
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.30 E-value=0.00024 Score=75.39 Aligned_cols=59 Identities=20% Similarity=0.326 Sum_probs=49.2
Q ss_pred CCceEEEEEecCccccceeccCchHHHHHHHHhCceEEEecCCCCCCceEEEEecChhhhhh
Q 046946 125 PADTVYRILCPSRKIGGVIGKAGNIVKSLREETQAKITVADTIPGSEERVIIIYSSPTKIAK 186 (650)
Q Consensus 125 ~~~~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~~~~~g~~eRvI~I~G~~e~v~~ 186 (650)
.+++.+.+-+-+.+||.|||+||++|+.|+..|+++|+|... ..|-.|+|.|...--.+
T Consensus 44 ~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~~m~~k 102 (629)
T KOG0336|consen 44 GGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGINHMRKK 102 (629)
T ss_pred CCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechHHHHHH
Confidence 457888888999999999999999999999999999999963 35667889997543333
No 46
>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=97.29 E-value=0.00038 Score=81.40 Aligned_cols=66 Identities=21% Similarity=0.310 Sum_probs=57.9
Q ss_pred CCceEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHh
Q 046946 477 KGTITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRG-SSEHLISAHGTYQSFMT 555 (650)
Q Consensus 477 ~~~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G-~~e~V~~A~~lI~~~i~ 555 (650)
.......+.||.+++|.|||+||.+||+|.++|||+|.|. ++..|.|.+ +.+.+++|+++|..+..
T Consensus 548 ~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~-------------ddG~V~i~~~~~~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 548 YAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE-------------DDGTVKIAASDGEAAEAAIKMIEGITA 614 (684)
T ss_pred cCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEe-------------cCeEEEEEECcHHHHHHHHHHHHhhhc
Confidence 3466788999999999999999999999999999999997 346788877 67899999999998865
No 47
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.14 E-value=0.0021 Score=69.69 Aligned_cols=77 Identities=23% Similarity=0.408 Sum_probs=57.2
Q ss_pred ceEEEEEeCC------CCceeEecCCCchHHHHHHhcCCeEEEeCCccccC------C-CC--CCCCc-eEEEEEc-CHH
Q 046946 479 TITTRLLVPS------SKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQ------D-PH--PGSSE-CIVDIRG-SSE 541 (650)
Q Consensus 479 ~~~~~l~VP~------~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~------~-p~--~~~~e-r~V~I~G-~~e 541 (650)
.++.+|.||- ++||+|||..|.|.|.|+++|||+|.|-.+. .+- + +. ..+.| =-+.|++ +.|
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkg-SvkEgk~~~~d~~~~~~~~epLH~~Isadt~e 215 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKG-SVKEGKGRSDDLSYIPKENEPLHCLISADTQE 215 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccc-cccccccCCcccccccccccceeEEEecchHH
Confidence 4556677764 7999999999999999999999999999732 110 1 11 12222 2366777 679
Q ss_pred HHHHHHHHHHHHHhc
Q 046946 542 HLISAHGTYQSFMTS 556 (650)
Q Consensus 542 ~V~~A~~lI~~~i~~ 556 (650)
.|++|.++|+.+|.+
T Consensus 216 ki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 216 KIKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHHh
Confidence 999999999999985
No 48
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.05 E-value=0.0018 Score=75.91 Aligned_cols=92 Identities=17% Similarity=0.237 Sum_probs=67.3
Q ss_pred HHHHHHHHHHHHhhhhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCC
Q 046946 209 AQDALLKVHDRIIEEDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNT 288 (650)
Q Consensus 209 a~~Al~~v~~~i~e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~ 288 (650)
|.++..++++.+.+.-.... .......+....+.||.+.++.|||++|++||+|.++|||+|.|..
T Consensus 523 a~~~~~~I~~~m~~~l~~~~---~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d----------- 588 (684)
T TIGR03591 523 AKEGRLHILGEMNKVISEPR---AELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED----------- 588 (684)
T ss_pred HHHHHHHHHHHHHHHHhhhh---ccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-----------
Confidence 45566666655543211111 1122344667889999999999999999999999999999999962
Q ss_pred CceEEEecC-HHHHHHHHHHHHHHHcc
Q 046946 289 DEMVQISGK-PNVAKRALYEVSTLLHQ 314 (650)
Q Consensus 289 dr~V~I~G~-~~~V~~A~~~I~~~l~~ 314 (650)
+..|.|.+. .+.+.+|+..|..+...
T Consensus 589 dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 589 DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 456777775 78899999999988653
No 49
>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=97.00 E-value=0.00054 Score=63.98 Aligned_cols=101 Identities=23% Similarity=0.352 Sum_probs=69.3
Q ss_pred EEEEEecCCccceecccCccchhchhhhcCceEEecCCCCCCCccEEEEeccCCCcCccchHHHHHHHHh--hhcccccc
Q 046946 399 SMKILCSAGKIGGVIGKGGFNVKQLQQETGASIHVEDAPTDSDERVIRASAFEGLWNPRSQTIDAILQLQ--NKTSEFSE 476 (650)
Q Consensus 399 ~~~v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~erii~I~G~~~~~~~~~~~~~ai~~~~--~~i~~~~~ 476 (650)
.+-+.|....+|..||++|++|+.|++..|-+|.+-.-.. +. ...+..++.-. ..+.-...
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~----------------D~-~~fI~N~l~PA~V~~V~i~~~ 96 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSE----------------NL-EEFVANKLAPAEVKNVTVSEF 96 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCC----------------CH-HHHHHHcCCCceEEEEEEEcC
Confidence 5668889999999999999999999888888877753211 00 11111111100 01100011
Q ss_pred CCceEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEe
Q 046946 477 KGTITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVV 516 (650)
Q Consensus 477 ~~~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~ 516 (650)
++.....+.||.+..+..|||+|.+|+-..+-+|-++.|.
T Consensus 97 ~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 97 NGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred CCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 2345677899999999999999999999999999887664
No 50
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.98 E-value=0.0021 Score=63.05 Aligned_cols=102 Identities=24% Similarity=0.369 Sum_probs=68.9
Q ss_pred EEEEecCccccceeccCchHHHHHHHHhCceEEEecCCCCCCceEEEEecChhhhhhccCCccchhhhhhcccCCcccHH
Q 046946 130 YRILCPSRKIGGVIGKAGNIVKSLREETQAKITVADTIPGSEERVIIIYSSPTKIAKTQNKDDDSAAETKKESMEPHCAA 209 (650)
Q Consensus 130 ~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~~~~~g~~eRvI~I~G~~e~v~~a~~~~~~~~~e~~~~~~~~~~~a 209 (650)
+-+.+-.+.+|..||++|++|+.|.++.|=+|.|-+..++ ++. -+
T Consensus 78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d-----------~~~------------------------fI 122 (190)
T COG0195 78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSED-----------PAE------------------------FI 122 (190)
T ss_pred EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCC-----------HHH------------------------HH
Confidence 3344556789999999999999999999988888764311 000 01
Q ss_pred HHHHHHHHHHHhhhhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEcc
Q 046946 210 QDALLKVHDRIIEEDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLP 277 (650)
Q Consensus 210 ~~Al~~v~~~i~e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~ 277 (650)
.+|+. -..+.. ..... . +.. ...+.||.++.+..|||+|.+++.+.+-||-++.|..
T Consensus 123 ~nal~--Pa~v~~------V~~~~-~-d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 123 KNALA--PAEVLS------VNIKE-D-DGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred HHhcC--cceEeE------EEEEe-C-CCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 11111 000000 00000 0 112 6788999999999999999999999999999999974
No 51
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.88 E-value=0.00094 Score=78.88 Aligned_cols=66 Identities=20% Similarity=0.295 Sum_probs=58.4
Q ss_pred CCceEEEEEeCCCCceeEecCCCchHHHHHHhcCCe-EEEeCCccccCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHH
Q 046946 477 KGTITTRLLVPSSKVGCILGQGGHVINEMRRRTQAD-IRVVGARVKLQDPHPGSSECIVDIRG-SSEHLISAHGTYQSFM 554 (650)
Q Consensus 477 ~~~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~-I~i~~~~~~l~~p~~~~~er~V~I~G-~~e~V~~A~~lI~~~i 554 (650)
.......+.||.+++|.|||.||.+||+|.++||+. |.+. ++..|.|.+ +.+.++.|+.+|.+++
T Consensus 682 ~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~-------------ddg~V~I~a~d~~~i~~A~~~I~~l~ 748 (891)
T PLN00207 682 YAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ-------------DDGTVKITAKDLSSLEKSKAIISSLT 748 (891)
T ss_pred cCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-------------CCeeEEEEeCCHHHHHHHHHHHHHHh
Confidence 446778899999999999999999999999999998 7665 457889998 7899999999999987
Q ss_pred h
Q 046946 555 T 555 (650)
Q Consensus 555 ~ 555 (650)
.
T Consensus 749 ~ 749 (891)
T PLN00207 749 M 749 (891)
T ss_pred c
Confidence 5
No 52
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.62 E-value=0.0029 Score=71.80 Aligned_cols=67 Identities=18% Similarity=0.291 Sum_probs=58.9
Q ss_pred CCceEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcCH-HHHHHHHHHHHHHHh
Q 046946 477 KGTITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGSS-EHLISAHGTYQSFMT 555 (650)
Q Consensus 477 ~~~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~~-e~V~~A~~lI~~~i~ 555 (650)
......++.|+.+.++.+||+||.+||+|.++|||+|+|. ++..|.|.++. +.++.|+..|.++..
T Consensus 549 ~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-------------ddGtv~i~~s~~~~~~~ak~~I~~i~~ 615 (692)
T COG1185 549 YAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-------------DDGTVKIAASDGESAKKAKERIEAITR 615 (692)
T ss_pred cCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-------------CCCcEEEEecchHHHHHHHHHHHHHHh
Confidence 3456678999999999999999999999999999999997 44689999965 888999999999985
Q ss_pred c
Q 046946 556 S 556 (650)
Q Consensus 556 ~ 556 (650)
+
T Consensus 616 e 616 (692)
T COG1185 616 E 616 (692)
T ss_pred h
Confidence 4
No 53
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.57 E-value=0.0024 Score=64.60 Aligned_cols=41 Identities=34% Similarity=0.631 Sum_probs=37.2
Q ss_pred CCCceEEEEEecCc------cccceeccCchHHHHHHHHhCceEEEe
Q 046946 124 QPADTVYRILCPSR------KIGGVIGKAGNIVKSLREETQAKITVA 164 (650)
Q Consensus 124 ~~~~~~~rilvP~~------~vG~IIGKgG~~Ik~Ir~~TgakI~I~ 164 (650)
++..++.|++||.+ +||.|+|..|.++|+|+++|+|||.|.
T Consensus 88 ~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 88 KPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred CceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 34468999999987 699999999999999999999999988
No 54
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.50 E-value=0.0028 Score=62.20 Aligned_cols=99 Identities=22% Similarity=0.359 Sum_probs=67.5
Q ss_pred EEEecCCccceecccCccchhchhhhcCceEEecCCCCCCCccEEEEeccCCCcCccchHHHHHHHHhhh--ccccccCC
Q 046946 401 KILCSAGKIGGVIGKGGFNVKQLQQETGASIHVEDAPTDSDERVIRASAFEGLWNPRSQTIDAILQLQNK--TSEFSEKG 478 (650)
Q Consensus 401 ~v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~erii~I~G~~~~~~~~~~~~~ai~~~~~~--i~~~~~~~ 478 (650)
.+.+-.+.+|..||++|.+|+.|.++.|-+|.+-.-. + +.+..+.+++. -.+. +.-...+.
T Consensus 79 ~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s-------------~---d~~~fI~nal~-Pa~v~~V~~~~~d~ 141 (190)
T COG0195 79 SNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS-------------E---DPAEFIKNALA-PAEVLSVNIKEDDG 141 (190)
T ss_pred EeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeC-------------C---CHHHHHHHhcC-cceEeEEEEEeCCC
Confidence 3445566789999999999999999999666664321 1 11122222222 0000 00001112
Q ss_pred ceEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeC
Q 046946 479 TITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVG 517 (650)
Q Consensus 479 ~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~ 517 (650)
. ...+.||.+..+..|||+|.+++-+.+-||-++.|..
T Consensus 142 ~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 142 H-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred c-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 2 6788899999999999999999999999999998874
No 55
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.44 E-value=0.0062 Score=72.14 Aligned_cols=92 Identities=18% Similarity=0.214 Sum_probs=69.4
Q ss_pred HHHHHHHHHHHHhhhhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCe-EEEccCCCCCCCCCC
Q 046946 209 AQDALLKVHDRIIEEDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGAN-IRVLPADRLPPCAMN 287 (650)
Q Consensus 209 a~~Al~~v~~~i~e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~-I~i~~~~~~p~~~~~ 287 (650)
|.+++..+++.+.+..... ........+....+.||.+.++.|||.||.+||+|.++||++ |.+.
T Consensus 657 A~~g~~~Il~~M~~~i~~p---r~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~----------- 722 (891)
T PLN00207 657 AKDGRKHILAEMSKCSPPP---SKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ----------- 722 (891)
T ss_pred HHHHHHHHHHHHHHHHhhh---hhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-----------
Confidence 5666666666655432111 111233456678899999999999999999999999999999 8775
Q ss_pred CCceEEEecC-HHHHHHHHHHHHHHHcc
Q 046946 288 TDEMVQISGK-PNVAKRALYEVSTLLHQ 314 (650)
Q Consensus 288 ~dr~V~I~G~-~~~V~~A~~~I~~~l~~ 314 (650)
.+-.|.|.+. .+.+++|+.+|..++.+
T Consensus 723 ddg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 723 DDGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 2457888885 88899999999999863
No 56
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.43 E-value=0.0078 Score=64.68 Aligned_cols=96 Identities=18% Similarity=0.177 Sum_probs=65.6
Q ss_pred ccccceeccCchHHHHHHHHh-CceEEEecCCCCCCceEEEEecChhhhhhccCCccchhhhhhcccCCcccHHHHHHHH
Q 046946 137 RKIGGVIGKAGNIVKSLREET-QAKITVADTIPGSEERVIIIYSSPTKIAKTQNKDDDSAAETKKESMEPHCAAQDALLK 215 (650)
Q Consensus 137 ~~vG~IIGKgG~~Ik~Ir~~T-gakI~I~~~~~g~~eRvI~I~G~~e~v~~a~~~~~~~~~e~~~~~~~~~~~a~~Al~~ 215 (650)
+-+|..||++|++|+.|.++. |=+|.|-+...+ ++. =..+|+
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D-----------~~~------------------------fI~Nal-- 293 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNV-----------PEI------------------------FIARAL-- 293 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCC-----------HHH------------------------HHHHhC--
Confidence 458999999999999999998 788888754211 000 000010
Q ss_pred HHHHHhhhhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCC
Q 046946 216 VHDRIIEEDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPAD 279 (650)
Q Consensus 216 v~~~i~e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~ 279 (650)
.-... ... ... +....+.+.||.++.+..|||+|.+++-..+-||.+|.|.+-+
T Consensus 294 -----~Pa~V-~~V---~i~-~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~ 347 (374)
T PRK12328 294 -----APAII-SSV---KIE-EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG 347 (374)
T ss_pred -----CCcee-eEE---EEc-CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence 00000 000 000 1224678999999999999999999999999999999999843
No 57
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.42 E-value=0.0034 Score=66.96 Aligned_cols=66 Identities=21% Similarity=0.304 Sum_probs=56.2
Q ss_pred eEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 046946 480 ITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGSSEHLISAHGTYQSFMT 555 (650)
Q Consensus 480 ~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~~e~V~~A~~lI~~~i~ 555 (650)
....+.|-+.+||.|||++|+.||.|+..|.++|+|.+.+ .+-.|+|-|..+--.+|+..|...+.
T Consensus 47 ~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~----------~e~kv~ifg~~~m~~kaka~id~~~~ 112 (629)
T KOG0336|consen 47 FPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD----------LEVKVTIFGINHMRKKAKASIDRGQD 112 (629)
T ss_pred CchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC----------ceeEEEEechHHHHHHHHhhHhhhhh
Confidence 3456778899999999999999999999999999999654 67789999998888888888776654
No 58
>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=96.36 E-value=0.0073 Score=64.78 Aligned_cols=95 Identities=22% Similarity=0.397 Sum_probs=64.7
Q ss_pred ccccceeccCchHHHHHHHHh-CceEEEecCCCCCCceEEEEecChhhhhhccCCccchhhhhhcccCCcccHHHHHHHH
Q 046946 137 RKIGGVIGKAGNIVKSLREET-QAKITVADTIPGSEERVIIIYSSPTKIAKTQNKDDDSAAETKKESMEPHCAAQDALLK 215 (650)
Q Consensus 137 ~~vG~IIGKgG~~Ik~Ir~~T-gakI~I~~~~~g~~eRvI~I~G~~e~v~~a~~~~~~~~~e~~~~~~~~~~~a~~Al~~ 215 (650)
+-+|..||++|++|+.|.++. |=+|.|-+...+ ++. =..+|+.-
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d-----------~~~------------------------fi~nal~P 287 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDD-----------PAE------------------------FIANALSP 287 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCC-----------HHH------------------------HHHHhcCC
Confidence 458999999999999999998 788888754211 000 00001000
Q ss_pred HHHHHhhhhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEcc
Q 046946 216 VHDRIIEEDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLP 277 (650)
Q Consensus 216 v~~~i~e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~ 277 (650)
..+. ... -.......+.+.||.++.+..|||+|.+++-...-||.+|.|.+
T Consensus 288 --a~v~------~v~---i~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 288 --AKVI------SVE---VLDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred --ceEE------EEE---EEcCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 0000 000 00012246899999999999999999999999999999999975
No 59
>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=96.30 E-value=0.0057 Score=48.79 Aligned_cols=36 Identities=28% Similarity=0.443 Sum_probs=33.8
Q ss_pred eEEEEEecCccccceeccCchHHHHHHHHhCceEEE
Q 046946 128 TVYRILCPSRKIGGVIGKAGNIVKSLREETQAKITV 163 (650)
Q Consensus 128 ~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I 163 (650)
....+.|+.+..|.+|||+|.+|+.+++.++-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 678899999999999999999999999999998876
No 60
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.26 E-value=0.012 Score=67.05 Aligned_cols=93 Identities=18% Similarity=0.227 Sum_probs=69.4
Q ss_pred HHHHHHHHHHHHHhhhhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCC
Q 046946 208 AAQDALLKVHDRIIEEDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMN 287 (650)
Q Consensus 208 ~a~~Al~~v~~~i~e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~ 287 (650)
.|..|.+.++..+.+..... .............+.|+.+.+.-+||++|.+|++|.++|||+|.|.
T Consensus 523 QAk~aRlhIL~~M~~ai~~p---r~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie----------- 588 (692)
T COG1185 523 QAKGARLHILIVMNEAISEP---RKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE----------- 588 (692)
T ss_pred HHHHHHHHHHHHHHHHHhhh---hhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-----------
Confidence 36667777766665431110 0011223445578889999999999999999999999999999996
Q ss_pred CCceEEEecCH-HHHHHHHHHHHHHHcc
Q 046946 288 TDEMVQISGKP-NVAKRALYEVSTLLHQ 314 (650)
Q Consensus 288 ~dr~V~I~G~~-~~V~~A~~~I~~~l~~ 314 (650)
.+..|.|.+.. +.+.+|+..|.++.++
T Consensus 589 ddGtv~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 589 DDGTVKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred CCCcEEEEecchHHHHHHHHHHHHHHhh
Confidence 24569999985 7799999999999965
No 61
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.10 E-value=0.0063 Score=63.37 Aligned_cols=69 Identities=25% Similarity=0.414 Sum_probs=58.4
Q ss_pred EEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcCC
Q 046946 481 TTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRG-SSEHLISAHGTYQSFMTSGQ 558 (650)
Q Consensus 481 ~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G-~~e~V~~A~~lI~~~i~~~~ 558 (650)
...+.|++...|.|||+.|.|-|.|+++|+++|.+++ +..+...|+|+| ..++|..|...|.-+|.+..
T Consensus 58 ~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~---------p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 58 SSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPR---------PNTNKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred hhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccC---------CCCCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 4568999999999999999999999999999999885 444555666666 78999999999999887643
No 62
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.05 E-value=0.012 Score=63.53 Aligned_cols=95 Identities=21% Similarity=0.334 Sum_probs=65.1
Q ss_pred ccccceeccCchHHHHHHHHh-CceEEEecCCCCCCceEEEEecChhhhhhccCCccchhhhhhcccCCcccHHHHHHHH
Q 046946 137 RKIGGVIGKAGNIVKSLREET-QAKITVADTIPGSEERVIIIYSSPTKIAKTQNKDDDSAAETKKESMEPHCAAQDALLK 215 (650)
Q Consensus 137 ~~vG~IIGKgG~~Ik~Ir~~T-gakI~I~~~~~g~~eRvI~I~G~~e~v~~a~~~~~~~~~e~~~~~~~~~~~a~~Al~~ 215 (650)
+-+|..||++|++|+.|.++. |=+|.|-+...+ ++. .
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d-----------~~~-------------------------------f 282 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSED-----------PAE-------------------------------F 282 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCCC-----------HHH-------------------------------H
Confidence 458999999999999999998 889988854211 000 0
Q ss_pred HHHHHhhhhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEcc
Q 046946 216 VHDRIIEEDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLP 277 (650)
Q Consensus 216 v~~~i~e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~ 277 (650)
+...+.-... ... ....+....+.+.||.++.+..|||+|.+++--..-||.+|.|.+
T Consensus 283 i~nal~Pa~v-~~v---~i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 283 VANALSPAKV-VSV---EVDDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred HHHhCCCceE-EEE---EEEcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 0000000000 000 000012346889999999999999999999999999999999986
No 63
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.03 E-value=0.0085 Score=62.42 Aligned_cols=70 Identities=27% Similarity=0.496 Sum_probs=57.8
Q ss_pred eEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCceEEEec-CHHHHHHHHHHHHHHHccCC
Q 046946 240 ITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDEMVQISG-KPNVAKRALYEVSTLLHQNP 316 (650)
Q Consensus 240 vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr~V~I~G-~~~~V~~A~~~I~~~l~~~~ 316 (650)
....+.|++...++|||++|.|.++|+++|+++|.++... .....|.|+| ..++|.+|...|..+|.+..
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~-------~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN-------TNKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC-------CCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 4567899999999999999999999999999999998522 2344555555 58889999999999998754
No 64
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=95.98 E-value=0.0089 Score=70.40 Aligned_cols=70 Identities=19% Similarity=0.100 Sum_probs=60.3
Q ss_pred eEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 046946 480 ITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGSSEHLISAHGTYQSFMT 555 (650)
Q Consensus 480 ~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~~e~V~~A~~lI~~~i~ 555 (650)
..-++.+|.....+|||+||.+|+.++..|||.|+|.+- +. .+..||.+.+.|.++.++.|..+|.-.|.
T Consensus 1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekm----q~--~Nqaers~~~kg~p~~~r~a~~~I~~~i~ 1409 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKM----QP--DNQAERSKAPKGRPPSQRVATSPIGLPII 1409 (2131)
T ss_pred cccccccchhhhhhhhccCcchhhhHhhccceEEehhhc----CC--ccchhhhcccCCCChhhhhhhccccceee
Confidence 345788999999999999999999999999999999852 21 33689999999999999999999988774
No 65
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.86 E-value=0.013 Score=64.08 Aligned_cols=95 Identities=23% Similarity=0.329 Sum_probs=64.2
Q ss_pred ccccceeccCchHHHHHHHHh-CceEEEecCCCCCCceEEEEecChhhhhhccCCccchhhhhhcccCCcccHHHHHHHH
Q 046946 137 RKIGGVIGKAGNIVKSLREET-QAKITVADTIPGSEERVIIIYSSPTKIAKTQNKDDDSAAETKKESMEPHCAAQDALLK 215 (650)
Q Consensus 137 ~~vG~IIGKgG~~Ik~Ir~~T-gakI~I~~~~~g~~eRvI~I~G~~e~v~~a~~~~~~~~~e~~~~~~~~~~~a~~Al~~ 215 (650)
+-+|..||++|.+|+.|.++. |=+|.|.....+ ++. =..+|+
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~D-----------p~~------------------------fI~NaL-- 319 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPD-----------PAT------------------------YIANAL-- 319 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCC-----------HHH------------------------HHHHhc--
Confidence 458999999999999999998 788888754211 000 000010
Q ss_pred HHHHHhhhhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEcc
Q 046946 216 VHDRIIEEDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLP 277 (650)
Q Consensus 216 v~~~i~e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~ 277 (650)
.-... .... ... +....+.+.||.++.++.|||+|.+++--..-||.+|.|..
T Consensus 320 -----sPA~V-~~V~--i~~-~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 320 -----SPARV-DEVR--LVD-PEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred -----CCcee-eEEE--EEc-CCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 00000 0000 000 12245789999999999999999999999999999999974
No 66
>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=95.83 E-value=0.014 Score=46.49 Aligned_cols=36 Identities=22% Similarity=0.505 Sum_probs=33.2
Q ss_pred eEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEE
Q 046946 480 ITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRV 515 (650)
Q Consensus 480 ~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i 515 (650)
....+.|+.+..|..|||+|.+|+.+++.+|-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 567899999999999999999999999999988765
No 67
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.67 E-value=0.0081 Score=70.62 Aligned_cols=66 Identities=21% Similarity=0.365 Sum_probs=56.4
Q ss_pred CceEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 046946 478 GTITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRG-SSEHLISAHGTYQSFMTS 556 (650)
Q Consensus 478 ~~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G-~~e~V~~A~~lI~~~i~~ 556 (650)
......+.||.+.++.+||+||.+||+|.++||+.|.+. ++..|.|.+ +.+.+++|+++|..+...
T Consensus 552 ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-------------d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 552 APRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-------------DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred CchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-------------CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 345567888999999999999999999999999987664 456788888 689999999999998753
No 68
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.57 E-value=0.019 Score=58.56 Aligned_cols=62 Identities=24% Similarity=0.272 Sum_probs=53.5
Q ss_pred EEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhc
Q 046946 482 TRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGS-SEHLISAHGTYQSFMTS 556 (650)
Q Consensus 482 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~-~e~V~~A~~lI~~~i~~ 556 (650)
+.+.||.++++.+||++|.+|+.|.+.+++.|.+- .+..|.|.+. .+.++.|+.+|.++-+.
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig-------------~NG~VwI~~~~~~~~~~a~~~I~~~e~~ 209 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG-------------QNGRIWIKGPDEEDEEIAIEAIKKIERE 209 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc-------------CCcEEEEeeCCHHHHHHHHHHHHHHHhh
Confidence 57899999999999999999999999999999886 3468999995 66889999999876543
No 69
>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=95.53 E-value=0.012 Score=63.05 Aligned_cols=93 Identities=17% Similarity=0.362 Sum_probs=63.0
Q ss_pred ccceecccCccchhchhhhc-CceEEecCCCCCCCccEEEEeccCCCcCccchHHHHHHHHh-hhccccccCCceEEEEE
Q 046946 408 KIGGVIGKGGFNVKQLQQET-GASIHVEDAPTDSDERVIRASAFEGLWNPRSQTIDAILQLQ-NKTSEFSEKGTITTRLL 485 (650)
Q Consensus 408 ~~g~IIGkgG~~Ik~I~~~s-ga~I~i~~~~~~~~erii~I~G~~~~~~~~~~~~~ai~~~~-~~i~~~~~~~~~~~~l~ 485 (650)
-+|..||++|.+|+.|.++. |-+|.+-.-.. +....+.+++.-.. ..+. ..+.......+.
T Consensus 244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~----------------d~~~fi~nal~Pa~v~~v~-i~~~~~~~~~v~ 306 (341)
T TIGR01953 244 PVGACVGPKGSRIQAISKELNGEKIDIIEYSD----------------DPAEFIANALSPAKVISVE-VLDEDKHSAEVV 306 (341)
T ss_pred cceeeECCCCchHHHHHHHhCCCeEEEEEcCC----------------CHHHHHHHhcCCceEEEEE-EEcCCCcEEEEE
Confidence 48999999999999999998 66666643211 11111112111000 0010 011123567899
Q ss_pred eCCCCceeEecCCCchHHHHHHhcCCeEEEeC
Q 046946 486 VPSSKVGCILGQGGHVINEMRRRTQADIRVVG 517 (650)
Q Consensus 486 VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~ 517 (650)
||.+..+..|||+|.+++-..+-||.+|.|..
T Consensus 307 V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 307 VPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred EChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 99999999999999999999999999999874
No 70
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.42 E-value=0.024 Score=66.71 Aligned_cols=93 Identities=18% Similarity=0.270 Sum_probs=67.4
Q ss_pred HHHHHHHHHHHHHhhhhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCC
Q 046946 208 AAQDALLKVHDRIIEEDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMN 287 (650)
Q Consensus 208 ~a~~Al~~v~~~i~e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~ 287 (650)
.|.++..++++.+.+.-.. . ..+..........+.|+.+.++.+||.+|.+||+|.++||++|.+.
T Consensus 525 ~a~~g~~~I~~~M~~aI~~-~--r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~----------- 590 (693)
T PRK11824 525 QAKEGRLHILGKMNEAISE-P--RAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE----------- 590 (693)
T ss_pred HHHHHHHHHHHHHHHHhcC-C--hhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------
Confidence 3566777777776643111 1 0111223344566777999999999999999999999999988774
Q ss_pred CCceEEEecC-HHHHHHHHHHHHHHHcc
Q 046946 288 TDEMVQISGK-PNVAKRALYEVSTLLHQ 314 (650)
Q Consensus 288 ~dr~V~I~G~-~~~V~~A~~~I~~~l~~ 314 (650)
.+-.|.|.+. .+.+++|+..|..+..+
T Consensus 591 d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 591 DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 2456888885 78899999999988853
No 71
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.37 E-value=0.041 Score=61.54 Aligned_cols=93 Identities=17% Similarity=0.345 Sum_probs=63.9
Q ss_pred cccceeccCchHHHHHHHHh-CceEEEecCCCCCCceEEEEecChhhhhhccCCccchhhhhhcccCCcccHHHHHHHHH
Q 046946 138 KIGGVIGKAGNIVKSLREET-QAKITVADTIPGSEERVIIIYSSPTKIAKTQNKDDDSAAETKKESMEPHCAAQDALLKV 216 (650)
Q Consensus 138 ~vG~IIGKgG~~Ik~Ir~~T-gakI~I~~~~~g~~eRvI~I~G~~e~v~~a~~~~~~~~~e~~~~~~~~~~~a~~Al~~v 216 (650)
-+|..||++|++|+.|.++. |=+|.|....++ ++. -+
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d-----------~~~-------------------------------fi 283 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIILWSDD-----------PAQ-------------------------------FI 283 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEEcCCC-----------HHH-------------------------------HH
Confidence 48999999999999999998 788988754211 000 00
Q ss_pred HHHHhhhhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEcc
Q 046946 217 HDRIIEEDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLP 277 (650)
Q Consensus 217 ~~~i~e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~ 277 (650)
...+.-.... .. . .......+.+.||..+.+..|||+|.+++..++-||.+|.|..
T Consensus 284 ~nal~pa~v~-~v---~-~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 284 INALSPAEVS-SV---V-VDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred HHhCCCCEEE-EE---E-EeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 0111100000 00 0 0011236789999999999999999999999999999999985
No 72
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=95.22 E-value=0.021 Score=57.96 Aligned_cols=79 Identities=29% Similarity=0.504 Sum_probs=55.1
Q ss_pred CCceEEEEEEcCC------ccceeecCCchHHHHHHHHhCCeEEEccCCCC------------CCCCCCCCc---eEEEe
Q 046946 237 NSTITARLLVPNN------MVGCLLGKRGDVIQRLRSETGANIRVLPADRL------------PPCAMNTDE---MVQIS 295 (650)
Q Consensus 237 ~~~vt~~llVP~~------~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~------------p~~~~~~dr---~V~I~ 295 (650)
.-.++.+|+||-. .||+|+|.+|.++|+|+++|||+|.|.-+... |..+.-.+. .|...
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 3456788999954 89999999999999999999999999763222 111111121 35556
Q ss_pred cCHHH----HHHHHHHHHHHHccC
Q 046946 296 GKPNV----AKRALYEVSTLLHQN 315 (650)
Q Consensus 296 G~~~~----V~~A~~~I~~~l~~~ 315 (650)
++++- +.+|+..|..+|...
T Consensus 169 ~p~~ea~~rl~~AleeI~klL~P~ 192 (259)
T KOG1588|consen 169 APPAEAYARLAYALEEIKKLLVPD 192 (259)
T ss_pred CCHHHHHHHHHHHHHHHHHhcCCC
Confidence 66543 456888888888653
No 73
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.17 E-value=0.018 Score=61.99 Aligned_cols=91 Identities=18% Similarity=0.222 Sum_probs=62.7
Q ss_pred ccceecccCccchhchhhhc-CceEEecCCCCCCCccEEEEeccCCCcCccchHHHHHHHHhh--hccccccCCceEEEE
Q 046946 408 KIGGVIGKGGFNVKQLQQET-GASIHVEDAPTDSDERVIRASAFEGLWNPRSQTIDAILQLQN--KTSEFSEKGTITTRL 484 (650)
Q Consensus 408 ~~g~IIGkgG~~Ik~I~~~s-ga~I~i~~~~~~~~erii~I~G~~~~~~~~~~~~~ai~~~~~--~i~~~~~~~~~~~~l 484 (650)
-+|..||++|.+|+.|.++. |-+|.|-.-.. +....+.+++. -.+ .+ .. ........+
T Consensus 252 PvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~----------------D~~~fI~Nal~-Pa~V~~V-~i-~~~~~~~~V 312 (374)
T PRK12328 252 PIGATVGVKGVRINAVSKELNGENIDCIEYSN----------------VPEIFIARALA-PAIISSV-KI-EEEEKKAIV 312 (374)
T ss_pred hHHhhcCCCcchHHHHHHHhCCCeEEEEEcCC----------------CHHHHHHHhCC-CceeeEE-EE-cCCCcEEEE
Confidence 48999999999999999998 66666643211 11111111111 000 00 00 122346789
Q ss_pred EeCCCCceeEecCCCchHHHHHHhcCCeEEEeC
Q 046946 485 LVPSSKVGCILGQGGHVINEMRRRTQADIRVVG 517 (650)
Q Consensus 485 ~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~ 517 (650)
.||....+..|||+|.+++-..+.||.+|.|-.
T Consensus 313 ~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s 345 (374)
T PRK12328 313 TLLSDQKSKAIGKNGINIRLASMLTGYEIELNE 345 (374)
T ss_pred EEChHHhhhhhcCCChhHHHHHHHhCCEEEEEE
Confidence 999999999999999999999999999999985
No 74
>PRK00468 hypothetical protein; Provisional
Probab=95.07 E-value=0.023 Score=47.20 Aligned_cols=32 Identities=28% Similarity=0.541 Sum_probs=28.7
Q ss_pred CceEEEEEecCccccceeccCchHHHHHHHHh
Q 046946 126 ADTVYRILCPSRKIGGVIGKAGNIVKSLREET 157 (650)
Q Consensus 126 ~~~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~T 157 (650)
..+.+++.|..+-+|.||||+|.+|+.||.--
T Consensus 28 ~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 28 QSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 35889999999999999999999999999643
No 75
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.07 E-value=0.095 Score=51.14 Aligned_cols=80 Identities=19% Similarity=0.335 Sum_probs=53.4
Q ss_pred CCCCceEEEEEEc------CCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCc-----------eEEEecC
Q 046946 235 NENSTITARLLVP------NNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDE-----------MVQISGK 297 (650)
Q Consensus 235 ~~~~~vt~~llVP------~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr-----------~V~I~G~ 297 (650)
......+-++.|| ...||+|||..|.|+|++++.|+|+|-|-.......|..+.|- .+.|+.+
T Consensus 143 ~rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~ad 222 (269)
T COG5176 143 IRPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEAD 222 (269)
T ss_pred cCcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcc
Confidence 3444556677777 5689999999999999999999999999865444444433331 1223333
Q ss_pred -HHHHHHHHHHHHHHHcc
Q 046946 298 -PNVAKRALYEVSTLLHQ 314 (650)
Q Consensus 298 -~~~V~~A~~~I~~~l~~ 314 (650)
.+.+.+++..+...+.+
T Consensus 223 sedki~~~ik~~~n~I~~ 240 (269)
T COG5176 223 SEDKICRLIKSQLNAIRE 240 (269)
T ss_pred hhhhHHHHHHHHHHHHHH
Confidence 44466666666666655
No 76
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.04 E-value=0.021 Score=61.76 Aligned_cols=92 Identities=20% Similarity=0.323 Sum_probs=62.8
Q ss_pred ccceecccCccchhchhhhc-CceEEecCCCCCCCccEEEEeccCCCcCccchHHHHHHHHhh--hccccccCCceEEEE
Q 046946 408 KIGGVIGKGGFNVKQLQQET-GASIHVEDAPTDSDERVIRASAFEGLWNPRSQTIDAILQLQN--KTSEFSEKGTITTRL 484 (650)
Q Consensus 408 ~~g~IIGkgG~~Ik~I~~~s-ga~I~i~~~~~~~~erii~I~G~~~~~~~~~~~~~ai~~~~~--~i~~~~~~~~~~~~l 484 (650)
-+|..||++|.+|+.|.++. |-+|.+-.-.. +....+.+++. -.. .+. ..+.......+
T Consensus 246 pvGa~iG~~G~rI~~i~~el~gekIdiv~~s~----------------d~~~fi~nal~-Pa~v~~v~-i~~~~~~~~~v 307 (362)
T PRK12327 246 AKGACVGPKGQRVQNIVSELKGEKIDIIDWSE----------------DPAEFVANALS-PAKVVSVE-VDDEEEKAARV 307 (362)
T ss_pred chheeECCCChhHHHHHHHhCCCeEEEEEcCC----------------CHHHHHHHhCC-CceEEEEE-EEcCCCcEEEE
Confidence 48999999999999999998 66666643211 00111111111 000 000 00122356789
Q ss_pred EeCCCCceeEecCCCchHHHHHHhcCCeEEEeC
Q 046946 485 LVPSSKVGCILGQGGHVINEMRRRTQADIRVVG 517 (650)
Q Consensus 485 ~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~ 517 (650)
.||.+..+..|||+|.+++--.+-||.+|.|-.
T Consensus 308 ~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 308 VVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred EEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 999999999999999999999999999999885
No 77
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.04 E-value=0.02 Score=62.60 Aligned_cols=93 Identities=19% Similarity=0.332 Sum_probs=62.1
Q ss_pred ccceecccCccchhchhhhc-CceEEecCCCCCCCccEEEEeccCCCcCccchHHHHHHHH-hhhccccccCCceEEEEE
Q 046946 408 KIGGVIGKGGFNVKQLQQET-GASIHVEDAPTDSDERVIRASAFEGLWNPRSQTIDAILQL-QNKTSEFSEKGTITTRLL 485 (650)
Q Consensus 408 ~~g~IIGkgG~~Ik~I~~~s-ga~I~i~~~~~~~~erii~I~G~~~~~~~~~~~~~ai~~~-~~~i~~~~~~~~~~~~l~ 485 (650)
-+|..||++|.+|+.|.++. |=+|.|-.-.. +....+.+++.-. ...+. ..+.......+.
T Consensus 278 PvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~----------------Dp~~fI~NaLsPA~V~~V~-i~~~~~k~a~V~ 340 (449)
T PRK12329 278 PVGACIGARGSRIQAVVNELRGEKIDVIRWSP----------------DPATYIANALSPARVDEVR-LVDPEGRHAHVL 340 (449)
T ss_pred hhhccCCCCcchHHHHHHHhCCCeEEEEEcCC----------------CHHHHHHHhcCCceeeEEE-EEcCCCcEEEEE
Confidence 48999999999999999998 66666543211 0111111111100 00000 001223457899
Q ss_pred eCCCCceeEecCCCchHHHHHHhcCCeEEEeC
Q 046946 486 VPSSKVGCILGQGGHVINEMRRRTQADIRVVG 517 (650)
Q Consensus 486 VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~ 517 (650)
||.+..+..|||+|.+++--.+.||-+|.|..
T Consensus 341 V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 341 VPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred EChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 99999999999999999999999999998874
No 78
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=94.95 E-value=0.052 Score=55.40 Aligned_cols=66 Identities=21% Similarity=0.302 Sum_probs=55.7
Q ss_pred EEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCceEEEecC-HHHHHHHHHHHHHHHccCCCC
Q 046946 242 ARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDEMVQISGK-PNVAKRALYEVSTLLHQNPRK 318 (650)
Q Consensus 242 ~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr~V~I~G~-~~~V~~A~~~I~~~l~~~~~~ 318 (650)
+.+.||.++++.+||++|.+|+.|.++++++|.+-. +-.|.|.+. .+.+.+|+.+|..+-++....
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-----------NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~~ 213 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-----------NGRIWIKGPDEEDEEIAIEAIKKIEREAHTS 213 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-----------CcEEEEeeCCHHHHHHHHHHHHHHHhhhhcc
Confidence 568899999999999999999999999999998852 356889988 568899999998877765443
No 79
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=94.91 E-value=0.088 Score=59.80 Aligned_cols=66 Identities=18% Similarity=0.270 Sum_probs=55.7
Q ss_pred eEEEEEeCC-CCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcC
Q 046946 480 ITTRLLVPS-SKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRG-SSEHLISAHGTYQSFMTSG 557 (650)
Q Consensus 480 ~~~~l~VP~-~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G-~~e~V~~A~~lI~~~i~~~ 557 (650)
....+.+|+ ++-|+|||+.|.+||-+...||++|-|+. +...|+|+| +|---+.|+..+..+|..+
T Consensus 204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd------------tp~~v~ls~fdp~rreia~~~l~~li~dg 271 (514)
T TIGR03319 204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD------------TPEAVILSGFDPVRREIARMALEKLIQDG 271 (514)
T ss_pred eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC------------CCCeEEecCCchHHHHHHHHHHHHHHHcC
Confidence 345678898 67799999999999999999999998873 446888999 8888899999888888654
No 80
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=94.86 E-value=0.28 Score=49.08 Aligned_cols=128 Identities=13% Similarity=0.065 Sum_probs=86.3
Q ss_pred EEEEecCCccceecccCccchhchhhhcCceEEecCCCCCCCccEEEEeccCCCcCccchHHHHHHHHhhhccccccCCc
Q 046946 400 MKILCSAGKIGGVIGKGGFNVKQLQQETGASIHVEDAPTDSDERVIRASAFEGLWNPRSQTIDAILQLQNKTSEFSEKGT 479 (650)
Q Consensus 400 ~~v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~erii~I~G~~~~~~~~~~~~~ai~~~~~~i~~~~~~~~ 479 (650)
+.+.++....-.+...+|..+++|....||+|.+.. ++..+.|+|++..++. +...|..+...+
T Consensus 28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-----~~~~i~I~g~k~~~~~---i~~~i~~~l~~i-------- 91 (210)
T PF14611_consen 28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR-----SENRIRITGTKSTAEY---IEASINEILSNI-------- 91 (210)
T ss_pred eEEEecchheeeeecCCchHHHHHHHhcCceEEEec-----CCcEEEEEccHHHHHH---HHHHHHHHHhhc--------
Confidence 344455777888889999999999888899999965 4558999999844432 223333333322
Q ss_pred eEEEEEeCCCCceeEe----cCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEE-----cCHHHHHHHHHHH
Q 046946 480 ITTRLLVPSSKVGCIL----GQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIR-----GSSEHLISAHGTY 550 (650)
Q Consensus 480 ~~~~l~VP~~~vG~II----GkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~-----G~~e~V~~A~~lI 550 (650)
.+..+.++.-.--.-. -.....+++|++.|++.|+...++ ..+.|+ -....++.|++++
T Consensus 92 ~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~~------------~~~~i~~~~~~~~~~~~~~a~RlL 159 (210)
T PF14611_consen 92 RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPDG------------NKLKISWLASPENEKRADRAKRLL 159 (210)
T ss_pred EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCCC------------CeEEEEEEeeccccchHHHHHHHH
Confidence 3345555533221111 124788999999999999887532 344444 4678889999999
Q ss_pred HHHHh
Q 046946 551 QSFMT 555 (650)
Q Consensus 551 ~~~i~ 555 (650)
...+.
T Consensus 160 ~~a~~ 164 (210)
T PF14611_consen 160 LWALD 164 (210)
T ss_pred HHhcc
Confidence 98874
No 81
>PRK02821 hypothetical protein; Provisional
Probab=94.86 E-value=0.053 Score=45.30 Aligned_cols=35 Identities=23% Similarity=0.417 Sum_probs=30.1
Q ss_pred CCceEEEEEeCCCCceeEecCCCchHHHHHHhcCC
Q 046946 477 KGTITTRLLVPSSKVGCILGQGGHVINEMRRRTQA 511 (650)
Q Consensus 477 ~~~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA 511 (650)
+......|.|..+-+|+||||+|.+|+.||.--.|
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 34577899999999999999999999999986544
No 82
>PRK00106 hypothetical protein; Provisional
Probab=94.84 E-value=0.1 Score=59.13 Aligned_cols=66 Identities=23% Similarity=0.325 Sum_probs=56.2
Q ss_pred eEEEEEeCC-CCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcC
Q 046946 480 ITTRLLVPS-SKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRG-SSEHLISAHGTYQSFMTSG 557 (650)
Q Consensus 480 ~~~~l~VP~-~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G-~~e~V~~A~~lI~~~i~~~ 557 (650)
....+.+|+ ++-|+|||+-|.+||-+...||+++-|+. +...|+|+| +|---+.|+..+..+|..+
T Consensus 225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd------------tp~~v~lS~fdpvRReiAr~~le~Li~dg 292 (535)
T PRK00106 225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD------------TPEVVVLSGFDPIRREIARMTLESLIKDG 292 (535)
T ss_pred eeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC------------CCCeEEEeCCChHHHHHHHHHHHHHHHcC
Confidence 345678898 67799999999999999999999998873 446888999 8988899999998888654
No 83
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=94.69 E-value=0.11 Score=58.97 Aligned_cols=63 Identities=29% Similarity=0.464 Sum_probs=49.1
Q ss_pred EEEEEcC-CccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCceEEEec-CHHHHHHHHHHHHHHHcc
Q 046946 242 ARLLVPN-NMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDEMVQISG-KPNVAKRALYEVSTLLHQ 314 (650)
Q Consensus 242 ~~llVP~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr~V~I~G-~~~~V~~A~~~I~~~l~~ 314 (650)
-.+.+|+ ++-|+|||+.|.+||.++..||++|.|.. +...|+|+| +|---+.|+..+..++.+
T Consensus 206 ~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd----------tp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 206 SVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD----------TPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred eeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC----------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 3466776 67799999999999999999999999972 234678888 566566677777777654
No 84
>PRK02821 hypothetical protein; Provisional
Probab=94.65 E-value=0.033 Score=46.49 Aligned_cols=33 Identities=24% Similarity=0.432 Sum_probs=29.1
Q ss_pred ceEEEEEecCccccceeccCchHHHHHHHHhCc
Q 046946 127 DTVYRILCPSRKIGGVIGKAGNIVKSLREETQA 159 (650)
Q Consensus 127 ~~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~Tga 159 (650)
.+.+++.|..+-+|.||||+|.+|+.||.--.+
T Consensus 30 ~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 30 GRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred cEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 478999999999999999999999999976543
No 85
>PRK00106 hypothetical protein; Provisional
Probab=94.64 E-value=0.13 Score=58.34 Aligned_cols=63 Identities=30% Similarity=0.501 Sum_probs=49.6
Q ss_pred EEEEEcC-CccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCceEEEec-CHHHHHHHHHHHHHHHcc
Q 046946 242 ARLLVPN-NMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDEMVQISG-KPNVAKRALYEVSTLLHQ 314 (650)
Q Consensus 242 ~~llVP~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr~V~I~G-~~~~V~~A~~~I~~~l~~ 314 (650)
-.+.+|+ ++-|+||||.|.+|+.++.-||++|.|.. +...|+|+| +|---+.|+..+..++.+
T Consensus 227 s~v~lp~demkGriIGreGrNir~~E~~tGvdliidd----------tp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 227 TTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD----------TPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred eeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC----------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 3466777 67799999999999999999999999972 234688888 566666677777777654
No 86
>PRK12704 phosphodiesterase; Provisional
Probab=94.44 E-value=0.13 Score=58.44 Aligned_cols=65 Identities=17% Similarity=0.227 Sum_probs=53.5
Q ss_pred eEEEEEeCC-CCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 046946 480 ITTRLLVPS-SKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRG-SSEHLISAHGTYQSFMTS 556 (650)
Q Consensus 480 ~~~~l~VP~-~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G-~~e~V~~A~~lI~~~i~~ 556 (650)
....+.+|+ ++-|+||||.|.+||-+...||++|-|+. +...|.|+| +|---+.|+..+..++..
T Consensus 210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd------------tp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD------------TPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC------------CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 344677888 67799999999999999999999998873 456888999 777777888888777754
No 87
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=94.35 E-value=0.88 Score=45.44 Aligned_cols=131 Identities=18% Similarity=0.170 Sum_probs=86.4
Q ss_pred EEEecCccccceeccCchHHHHHHHHhCceEEEecCCCCCCceEEEEecChhhhhhccCCccchhhhhhcccCCcccHHH
Q 046946 131 RILCPSRKIGGVIGKAGNIVKSLREETQAKITVADTIPGSEERVIIIYSSPTKIAKTQNKDDDSAAETKKESMEPHCAAQ 210 (650)
Q Consensus 131 rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~~~~~g~~eRvI~I~G~~e~v~~a~~~~~~~~~e~~~~~~~~~~~a~ 210 (650)
.+.++....-++...+|..++.|-...||+|.+.. ++..|.|+|+...++. +.
T Consensus 29 ~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-----~~~~i~I~g~k~~~~~----------------------i~ 81 (210)
T PF14611_consen 29 DVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR-----SENRIRITGTKSTAEY----------------------IE 81 (210)
T ss_pred EEEecchheeeeecCCchHHHHHHHhcCceEEEec-----CCcEEEEEccHHHHHH----------------------HH
Confidence 34445788889999999999999888899999983 4568999999655433 22
Q ss_pred HHHHHHHHHHhhhhccCCCCCCCCCCCCceEEEEEEcCCccceee----cCCchHHHHHHHHhCCeEEEccCCCCCCCCC
Q 046946 211 DALLKVHDRIIEEDLFGGMASDDDNENSTITARLLVPNNMVGCLL----GKRGDVIQRLRSETGANIRVLPADRLPPCAM 286 (650)
Q Consensus 211 ~Al~~v~~~i~e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~II----Gk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~ 286 (650)
..+..++..|. +..+-++.-.-.... -.....++.|++.|++.|....+
T Consensus 82 ~~i~~~l~~i~-------------------~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~-------- 134 (210)
T PF14611_consen 82 ASINEILSNIR-------------------TEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD-------- 134 (210)
T ss_pred HHHHHHHhhcE-------------------EEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC--------
Confidence 23333333333 223333321111111 12467799999999999998742
Q ss_pred CCCceEEEec-----CHHHHHHHHHHHHHHHccCCC
Q 046946 287 NTDEMVQISG-----KPNVAKRALYEVSTLLHQNPR 317 (650)
Q Consensus 287 ~~dr~V~I~G-----~~~~V~~A~~~I~~~l~~~~~ 317 (650)
+..+.|.. ....+..|+.++...+..++.
T Consensus 135 --~~~~~i~~~~~~~~~~~~~~a~RlL~~a~~~~~~ 168 (210)
T PF14611_consen 135 --GNKLKISWLASPENEKRADRAKRLLLWALDYNPH 168 (210)
T ss_pred --CCeEEEEEEeeccccchHHHHHHHHHHhccCCcc
Confidence 33455554 577789999999998864444
No 88
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=94.33 E-value=0.037 Score=61.95 Aligned_cols=92 Identities=17% Similarity=0.351 Sum_probs=62.6
Q ss_pred ccceecccCccchhchhhhc-CceEEecCCCCCCCccEEEEeccCCCcCccchHHHHHHHHhhhccc-cccCCceEEEEE
Q 046946 408 KIGGVIGKGGFNVKQLQQET-GASIHVEDAPTDSDERVIRASAFEGLWNPRSQTIDAILQLQNKTSE-FSEKGTITTRLL 485 (650)
Q Consensus 408 ~~g~IIGkgG~~Ik~I~~~s-ga~I~i~~~~~~~~erii~I~G~~~~~~~~~~~~~ai~~~~~~i~~-~~~~~~~~~~l~ 485 (650)
-+|..||++|.+|+.|.++. |=+|.|-.-.. +....+.+++.- .+ +.. .-+.......+.
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~----------------d~~~fi~nal~p-a~-v~~v~~~~~~~~~~v~ 307 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIILWSD----------------DPAQFIINALSP-AE-VSSVVVDEDEHSADVV 307 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEEcCC----------------CHHHHHHHhCCC-CE-EEEEEEeCCCCEEEEE
Confidence 38999999999999999998 66666643211 111111111110 00 000 001123467899
Q ss_pred eCCCCceeEecCCCchHHHHHHhcCCeEEEeC
Q 046946 486 VPSSKVGCILGQGGHVINEMRRRTQADIRVVG 517 (650)
Q Consensus 486 VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~ 517 (650)
||....+..|||+|.+|+-..+.||.+|.|-.
T Consensus 308 V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 308 VPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred ECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 99999999999999999999999999999975
No 89
>PRK12704 phosphodiesterase; Provisional
Probab=94.26 E-value=0.14 Score=58.24 Aligned_cols=62 Identities=29% Similarity=0.458 Sum_probs=48.4
Q ss_pred EEEEcC-CccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCceEEEec-CHHHHHHHHHHHHHHHcc
Q 046946 243 RLLVPN-NMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDEMVQISG-KPNVAKRALYEVSTLLHQ 314 (650)
Q Consensus 243 ~llVP~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr~V~I~G-~~~~V~~A~~~I~~~l~~ 314 (650)
.+-+|+ ++-|+||||.|.+||.++.-||++|.|.. +...|.|+| ++-.-+.|+..+..++.+
T Consensus 213 ~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd----------tp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 213 VVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD----------TPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred eeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC----------CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 456676 67799999999999999999999999972 345788998 455555677777776654
No 90
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.05 E-value=0.076 Score=44.10 Aligned_cols=32 Identities=34% Similarity=0.533 Sum_probs=29.6
Q ss_pred CCceEEEEEEcCCccceeecCCchHHHHHHHH
Q 046946 237 NSTITARLLVPNNMVGCLLGKRGDVIQRLRSE 268 (650)
Q Consensus 237 ~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~ 268 (650)
+....++|.|...-+|.||||+|.+|+.||.-
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 66788999999999999999999999999975
No 91
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.04 E-value=0.056 Score=44.89 Aligned_cols=31 Identities=23% Similarity=0.464 Sum_probs=28.1
Q ss_pred CceEEEEEecCccccceeccCchHHHHHHHH
Q 046946 126 ADTVYRILCPSRKIGGVIGKAGNIVKSLREE 156 (650)
Q Consensus 126 ~~~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~ 156 (650)
..+.+++-+..+.+|.||||+|.+|+.||.-
T Consensus 28 ~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 28 KTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 3588999999999999999999999999954
No 92
>PRK00468 hypothetical protein; Provisional
Probab=93.96 E-value=0.065 Score=44.57 Aligned_cols=34 Identities=21% Similarity=0.432 Sum_probs=29.7
Q ss_pred CCCceEEEEEEcCCccceeecCCchHHHHHHHHh
Q 046946 236 ENSTITARLLVPNNMVGCLLGKRGDVIQRLRSET 269 (650)
Q Consensus 236 ~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~t 269 (650)
.+..+.+++.|..+-+|+||||+|.+|+.||.--
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 3455788999999999999999999999998753
No 93
>PRK01064 hypothetical protein; Provisional
Probab=93.87 E-value=0.061 Score=45.05 Aligned_cols=32 Identities=28% Similarity=0.571 Sum_probs=28.8
Q ss_pred CceEEEEEecCccccceeccCchHHHHHHHHh
Q 046946 126 ADTVYRILCPSRKIGGVIGKAGNIVKSLREET 157 (650)
Q Consensus 126 ~~~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~T 157 (650)
..+.+++.|..+..|.+|||+|.+|+.||.-.
T Consensus 28 ~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 28 HTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 35899999999999999999999999999743
No 94
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=93.23 E-value=0.12 Score=50.32 Aligned_cols=41 Identities=24% Similarity=0.567 Sum_probs=34.1
Q ss_pred ceEEEEEeC------CCCceeEecCCCchHHHHHHhcCCeEEEeCCc
Q 046946 479 TITTRLLVP------SSKVGCILGQGGHVINEMRRRTQADIRVVGAR 519 (650)
Q Consensus 479 ~~~~~l~VP------~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~ 519 (650)
..+-++.|| .++||+|||..|.|+|++++.|+|+|-|-+..
T Consensus 147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g 193 (269)
T COG5176 147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSG 193 (269)
T ss_pred cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence 344556655 47999999999999999999999999998743
No 95
>PRK01064 hypothetical protein; Provisional
Probab=93.13 E-value=0.12 Score=43.39 Aligned_cols=34 Identities=29% Similarity=0.447 Sum_probs=29.5
Q ss_pred CCceEEEEEeCCCCceeEecCCCchHHHHHHhcC
Q 046946 477 KGTITTRLLVPSSKVGCILGQGGHVINEMRRRTQ 510 (650)
Q Consensus 477 ~~~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TG 510 (650)
...+..++.|..+-.|.+|||+|.+|+.||.-..
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHHHH
Confidence 4567788999999999999999999999998543
No 96
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=92.30 E-value=0.43 Score=53.21 Aligned_cols=92 Identities=21% Similarity=0.240 Sum_probs=68.0
Q ss_pred HHHHHHHHHHHHhhhhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCC
Q 046946 209 AQDALLKVHDRIIEEDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNT 288 (650)
Q Consensus 209 a~~Al~~v~~~i~e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~ 288 (650)
|.+|..++++.+.+... .. .........+...+.|+.+....+||.+|...|+|..+||+.-.+.
T Consensus 569 a~~ar~~Il~~m~k~i~-~P--r~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD------------ 633 (760)
T KOG1067|consen 569 AREARLQILDIMEKNIN-SP--RGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD------------ 633 (760)
T ss_pred hhHHHHHHHHHHHhhcC-Cc--ccCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec------------
Confidence 56666777776664321 11 1122344567788999999999999999999999999999654443
Q ss_pred CceEEEecC-HHHHHHHHHHHHHHHccC
Q 046946 289 DEMVQISGK-PNVAKRALYEVSTLLHQN 315 (650)
Q Consensus 289 dr~V~I~G~-~~~V~~A~~~I~~~l~~~ 315 (650)
+..+.|... ..+.++|+..|..++...
T Consensus 634 e~t~~i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 634 EGTFSIFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred CceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence 556788776 778999999999988663
No 97
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=91.21 E-value=0.13 Score=42.33 Aligned_cols=33 Identities=21% Similarity=0.307 Sum_probs=27.8
Q ss_pred ceEEEEEecCccccceeccCchHHHHHHHHhCc
Q 046946 127 DTVYRILCPSRKIGGVIGKAGNIVKSLREETQA 159 (650)
Q Consensus 127 ~~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~Tga 159 (650)
...+.+-|..+..|.||||.|.+++.||.-.+.
T Consensus 28 ~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 28 GDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred ceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 456777889999999999999999999965543
No 98
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=90.87 E-value=0.51 Score=52.63 Aligned_cols=68 Identities=21% Similarity=0.251 Sum_probs=57.1
Q ss_pred CCceEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHh
Q 046946 477 KGTITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRG-SSEHLISAHGTYQSFMT 555 (650)
Q Consensus 477 ~~~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G-~~e~V~~A~~lI~~~i~ 555 (650)
...+...+.|+.+....+||.+|-..|.|..+||+.-++ ++..++|-- ++...++|+++|..++.
T Consensus 594 y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v--------------De~t~~i~A~~~~am~~Ak~~I~~i~~ 659 (760)
T KOG1067|consen 594 YSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV--------------DEGTFSIFAPTQAAMEEAKEFIDGIIK 659 (760)
T ss_pred cCceeeEEeecchhhheeecCccceeeeEeeeccceeee--------------cCceEEEEecCHHHHHHHHHHHHHHhc
Confidence 346778899999999999999999999999999965444 456777777 78899999999999986
Q ss_pred cCC
Q 046946 556 SGQ 558 (650)
Q Consensus 556 ~~~ 558 (650)
..+
T Consensus 660 ~~~ 662 (760)
T KOG1067|consen 660 DDQ 662 (760)
T ss_pred Ccc
Confidence 543
No 99
>PRK12705 hypothetical protein; Provisional
Probab=89.34 E-value=0.67 Score=52.37 Aligned_cols=65 Identities=20% Similarity=0.232 Sum_probs=49.6
Q ss_pred eEEEEEeCC-CCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 046946 480 ITTRLLVPS-SKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRG-SSEHLISAHGTYQSFMTS 556 (650)
Q Consensus 480 ~~~~l~VP~-~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G-~~e~V~~A~~lI~~~i~~ 556 (650)
....+.+|+ ++-|+|||+-|.+||.+...||+.|-|+. +.+.|++++ +|.--+.|...+..+|..
T Consensus 198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd------------tp~~V~ls~fdp~rreia~~~l~~Li~d 264 (508)
T PRK12705 198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD------------TPEAVVISSFNPIRREIARLTLEKLLAD 264 (508)
T ss_pred eeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC------------CccchhhcccCccchHHHHHHHHHHHhc
Confidence 344577887 57799999999999999999999998873 334567777 566667777777766643
No 100
>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=89.13 E-value=0.58 Score=37.10 Aligned_cols=34 Identities=26% Similarity=0.337 Sum_probs=27.6
Q ss_pred eEEEEEecCccccceeccCchHHHHHHHHhCceE
Q 046946 128 TVYRILCPSRKIGGVIGKAGNIVKSLREETQAKI 161 (650)
Q Consensus 128 ~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI 161 (650)
....+.+.....|.+|||+|++|+.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 4555666666789999999999999999988554
No 101
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=88.70 E-value=1.4 Score=48.68 Aligned_cols=102 Identities=13% Similarity=0.171 Sum_probs=66.8
Q ss_pred EEEEecCCccceecccCccchhchhhhc----CceEEecCCCCCCCccEEEEeccCCCcCccchHHHHHHHHhhhccccc
Q 046946 400 MKILCSAGKIGGVIGKGGFNVKQLQQET----GASIHVEDAPTDSDERVIRASAFEGLWNPRSQTIDAILQLQNKTSEFS 475 (650)
Q Consensus 400 ~~v~iP~~~~g~IIGkgG~~Ik~I~~~s----ga~I~i~~~~~~~~erii~I~G~~~~~~~~~~~~~ai~~~~~~i~~~~ 475 (650)
+-+.+|.+..+.|+|++......+++.. ...|.+... ..++.++.+-. ..+..+......+.
T Consensus 499 V~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~~Kgdirf~~~----~~sI~~v~~~~-------~~I~rv~kne~v~~--- 564 (657)
T COG5166 499 VLIEAPRKNQDNISGKKNDKLDKVKQQCRFNLKGDIRFCPQ----STSIFTVDIYS-------DEIERVIKNETVLL--- 564 (657)
T ss_pred eEEECCccCccchhcccccHHHHHhhhcccccccceEEcCC----ceEEEEEcccc-------cHHHHHhhccceEE---
Confidence 4578899999999999988887777655 344555432 44588877754 22333332111111
Q ss_pred cCCceEEEEEeCCCCceeEec---CCCchHHHHHHhcCCeEEEe
Q 046946 476 EKGTITTRLLVPSSKVGCILG---QGGHVINEMRRRTQADIRVV 516 (650)
Q Consensus 476 ~~~~~~~~l~VP~~~vG~IIG---kgG~~IkeI~~~TGA~I~i~ 516 (650)
.-.....+.+|+..++..+| -.|++|-.+..-..-.|...
T Consensus 565 -~~p~~~~~y~~se~h~~g~gena~R~~ni~~~t~~y~~~ie~~ 607 (657)
T COG5166 565 -EFPAEMHFYVPSEIHKKGIGENAFRGENIQRVTKLYNSYIEFS 607 (657)
T ss_pred -ecccccccccchhhhhccCCcccccccchhhhhhhhhccceee
Confidence 12345568899999999999 77888877777666666555
No 102
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=88.45 E-value=0.31 Score=47.44 Aligned_cols=55 Identities=22% Similarity=0.343 Sum_probs=49.1
Q ss_pred CCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 046946 488 SSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGSSEHLISAHGTYQSFMTS 556 (650)
Q Consensus 488 ~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~~e~V~~A~~lI~~~i~~ 556 (650)
+..+|+|+||+|.+--.|.+.|..+|.+. +..|.|-|..+++..|+..|+.+|..
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 56789999999999999999999999876 34799999999999999999999843
No 103
>PRK12705 hypothetical protein; Provisional
Probab=88.37 E-value=0.9 Score=51.37 Aligned_cols=62 Identities=27% Similarity=0.386 Sum_probs=41.9
Q ss_pred EEEEcC-CccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCceEEEecC-HHHHHHHHHHHHHHHcc
Q 046946 243 RLLVPN-NMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDEMVQISGK-PNVAKRALYEVSTLLHQ 314 (650)
Q Consensus 243 ~llVP~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr~V~I~G~-~~~V~~A~~~I~~~l~~ 314 (650)
.+-+|+ ++-|+|||+.|.+||.++..||+.|.|.. +.+.|+|.+- +..-+.|...+..++.+
T Consensus 201 ~v~lp~demkGriIGreGrNir~~E~~tGvdliidd----------tp~~V~ls~fdp~rreia~~~l~~Li~d 264 (508)
T PRK12705 201 VVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD----------TPEAVVISSFNPIRREIARLTLEKLLAD 264 (508)
T ss_pred eeecCChHhhccccCccchhHHHHHHhhCCceEecC----------CccchhhcccCccchHHHHHHHHHHHhc
Confidence 355665 57799999999999999999999999973 1223445543 33334455555555443
No 104
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=88.03 E-value=0.21 Score=59.58 Aligned_cols=65 Identities=20% Similarity=0.095 Sum_probs=55.2
Q ss_pred ceEEEEEecCccccceeccCchHHHHHHHHhCceEEEecC-CCCCCceEEEEecChhhhhhccCCc
Q 046946 127 DTVYRILCPSRKIGGVIGKAGNIVKSLREETQAKITVADT-IPGSEERVIIIYSSPTKIAKTQNKD 191 (650)
Q Consensus 127 ~~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~~~-~~g~~eRvI~I~G~~e~v~~a~~~~ 191 (650)
...-++-+|...+.+|||+||.+|+.+|.-||+.|.|..- ..+-.||.+.+.|.++.++.+...+
T Consensus 1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I 1404 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPI 1404 (2131)
T ss_pred ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccc
Confidence 4556778999999999999999999999999999999863 2346799999999999988776544
No 105
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=87.91 E-value=0.44 Score=39.00 Aligned_cols=37 Identities=32% Similarity=0.531 Sum_probs=29.2
Q ss_pred EEEEecCcc-----ccceeccCchHHHHHHHHh-CceEEEecC
Q 046946 130 YRILCPSRK-----IGGVIGKAGNIVKSLREET-QAKITVADT 166 (650)
Q Consensus 130 ~rilvP~~~-----vG~IIGKgG~~Ik~Ir~~T-gakI~I~~~ 166 (650)
.++.|-+.. +|..||++|++|+.|.++. |-+|+|-+.
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~ 47 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY 47 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence 455666666 9999999999999999999 899998864
No 106
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=87.87 E-value=0.84 Score=46.68 Aligned_cols=54 Identities=19% Similarity=0.220 Sum_probs=47.9
Q ss_pred eeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCCC
Q 046946 492 GCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGSSEHLISAHGTYQSFMTSGQS 559 (650)
Q Consensus 492 G~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~~e~V~~A~~lI~~~i~~~~~ 559 (650)
-++||.+|+|+|.|+-.|.|+|-|.+ .+|.+.|....++.++..+.+.|..-+.
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG--------------~TVsaiGpfkGlkevr~IV~DcM~NiHP 214 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG--------------NTVSAIGPFKGLKEVRKIVEDCMKNIHP 214 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC--------------cEEEeecCcchHHHHHHHHHHHHhccch
Confidence 36999999999999999999998875 4799999999999999999999876443
No 107
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=86.21 E-value=0.47 Score=46.18 Aligned_cols=57 Identities=23% Similarity=0.307 Sum_probs=51.0
Q ss_pred CCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCceEEEecCHHHHHHHHHHHHHHHccCC
Q 046946 248 NNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDEMVQISGKPNVAKRALYEVSTLLHQNP 316 (650)
Q Consensus 248 ~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~~ 316 (650)
+..+|+|+||+|.+--.|++.|..+|.+. +..|.|-|.-++++.|+..|+.++-.++
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVla------------d~kIHiLG~~~niriAR~avcsLIlGsp 233 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA------------DSKIHILGAFQNIRIARDAVCSLILGSP 233 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEec------------CceEEEeecchhhHHHHHhhHhhhccCC
Confidence 56789999999999999999999999886 4579999999999999999999997643
No 108
>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=86.11 E-value=1.3 Score=35.11 Aligned_cols=35 Identities=20% Similarity=0.395 Sum_probs=28.4
Q ss_pred ceEEEEEeCCCCceeEecCCCchHHHHHHhcCCeE
Q 046946 479 TITTRLLVPSSKVGCILGQGGHVINEMRRRTQADI 513 (650)
Q Consensus 479 ~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I 513 (650)
.....+.+.....|.+|||+|++|+.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 35556777776789999999999999999988544
No 109
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=85.13 E-value=0.55 Score=38.42 Aligned_cols=37 Identities=30% Similarity=0.460 Sum_probs=29.2
Q ss_pred EEEEEeCCCC-----ceeEecCCCchHHHHHHhc-CCeEEEeC
Q 046946 481 TTRLLVPSSK-----VGCILGQGGHVINEMRRRT-QADIRVVG 517 (650)
Q Consensus 481 ~~~l~VP~~~-----vG~IIGkgG~~IkeI~~~T-GA~I~i~~ 517 (650)
.+.+.|-+.. +|..||++|.+||.|.++. |-+|+|-.
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 3466676766 9999999999999999999 88887763
No 110
>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=84.41 E-value=4 Score=38.21 Aligned_cols=93 Identities=18% Similarity=0.316 Sum_probs=58.8
Q ss_pred eccCchHHHHHHHHhCceEEEecCCCCCCceEEEEecChhhhhhccCCccchhhhhhcccCCcccHHHHHHHHHHHHHhh
Q 046946 143 IGKAGNIVKSLREETQAKITVADTIPGSEERVIIIYSSPTKIAKTQNKDDDSAAETKKESMEPHCAAQDALLKVHDRIIE 222 (650)
Q Consensus 143 IGKgG~~Ik~Ir~~TgakI~I~~~~~g~~eRvI~I~G~~e~v~~a~~~~~~~~~e~~~~~~~~~~~a~~Al~~v~~~i~e 222 (650)
+=..|..|++|-++..-+|.|..+. .. +.+..+|...+.+.+-+
T Consensus 21 ~~~~~dli~~lAk~lrKRIvvR~dp--------------s~----------------------l~~~e~A~~~I~~ivP~ 64 (145)
T cd02410 21 FAEDGDLVKDLAKDLRKRIVIRPDP--------------SV----------------------LKPPEEAIKIILEIVPE 64 (145)
T ss_pred HhcccHHHHHHHHHHhceEEEcCCh--------------hh----------------------cCCHHHHHHHHHHhCCC
Confidence 4456788888888888888876321 00 01123455555554443
Q ss_pred hhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEcc
Q 046946 223 EDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLP 277 (650)
Q Consensus 223 ~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~ 277 (650)
+....+.-+ +..+-++.|-...-|++||++|.++++|..+||=.-.|..
T Consensus 65 ea~i~di~F------d~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvR 113 (145)
T cd02410 65 EAGITDIYF------DDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVR 113 (145)
T ss_pred ccCceeeEe------cCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence 311111111 1123456666778899999999999999999998888875
No 111
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=84.14 E-value=0.66 Score=38.16 Aligned_cols=34 Identities=24% Similarity=0.297 Sum_probs=28.4
Q ss_pred CceEEEEEEcCCccceeecCCchHHHHHHHHhCC
Q 046946 238 STITARLLVPNNMVGCLLGKRGDVIQRLRSETGA 271 (650)
Q Consensus 238 ~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa 271 (650)
+...+.+-+..+..|.||||.|.+++.||.-.+.
T Consensus 27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred CceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 3456788889999999999999999999876543
No 112
>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=83.97 E-value=0.65 Score=38.64 Aligned_cols=34 Identities=32% Similarity=0.469 Sum_probs=28.6
Q ss_pred EEEEEecCccccceeccCchHHHHHHHHhCceEE
Q 046946 129 VYRILCPSRKIGGVIGKAGNIVKSLREETQAKIT 162 (650)
Q Consensus 129 ~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~ 162 (650)
...+.+...+.|.|||++|++|++|+++.+-.+.
T Consensus 26 ~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 26 QIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp EEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred eEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 4567788999999999999999999988765553
No 113
>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=82.37 E-value=1.2 Score=37.05 Aligned_cols=33 Identities=21% Similarity=0.329 Sum_probs=25.7
Q ss_pred EEEEecCccccceeccCchHHHHHHHHhCceEE
Q 046946 130 YRILCPSRKIGGVIGKAGNIVKSLREETQAKIT 162 (650)
Q Consensus 130 ~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~ 162 (650)
+.+-+..+..|.+|||.|+++..||--++.-+.
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 445566788999999999999999976654433
No 114
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=82.36 E-value=1.6 Score=41.96 Aligned_cols=36 Identities=31% Similarity=0.389 Sum_probs=31.0
Q ss_pred EEEEecCccccceeccCchHHHHHHHHhCceEEEecC
Q 046946 130 YRILCPSRKIGGVIGKAGNIVKSLREETQAKITVADT 166 (650)
Q Consensus 130 ~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~~~ 166 (650)
+-++|-... |.-|||+|++|++|++..|-+|.+.+.
T Consensus 63 vIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 63 VILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred EEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence 345666666 999999999999999999999999864
No 115
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=81.83 E-value=3 Score=39.03 Aligned_cols=89 Identities=24% Similarity=0.402 Sum_probs=57.8
Q ss_pred cCccchhchhhhcCceEEecCCCCCCCccEEEEeccCCCcCccchHHHHHHHHhhhccccc--cCCceEEEEEeCCCCce
Q 046946 415 KGGFNVKQLQQETGASIHVEDAPTDSDERVIRASAFEGLWNPRSQTIDAILQLQNKTSEFS--EKGTITTRLLVPSSKVG 492 (650)
Q Consensus 415 kgG~~Ik~I~~~sga~I~i~~~~~~~~erii~I~G~~~~~~~~~~~~~ai~~~~~~i~~~~--~~~~~~~~l~VP~~~vG 492 (650)
.+|..|++|.++..-+|.|-.+.. ....-..+.+.|..+...-.... .-+..+-++.|-...-|
T Consensus 23 ~~~dli~~lAk~lrKRIvvR~dps--------------~l~~~e~A~~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG 88 (145)
T cd02410 23 EDGDLVKDLAKDLRKRIVIRPDPS--------------VLKPPEEAIKIILEIVPEEAGITDIYFDDDTGEVIIEAEKPG 88 (145)
T ss_pred cccHHHHHHHHHHhceEEEcCChh--------------hcCCHHHHHHHHHHhCCCccCceeeEecCCCcEEEEEEcCCe
Confidence 457889999998888887753321 11111334444444432111111 11233457888889999
Q ss_pred eEecCCCchHHHHHHhcCCeEEEeC
Q 046946 493 CILGQGGHVINEMRRRTQADIRVVG 517 (650)
Q Consensus 493 ~IIGkgG~~IkeI~~~TGA~I~i~~ 517 (650)
++|||+|.++++|..+||=.-.|-+
T Consensus 89 ~ViGk~g~~~reI~~~tgW~p~vvR 113 (145)
T cd02410 89 LVIGKGGSTLREITRETGWAPKVVR 113 (145)
T ss_pred EEEecCchhHHHHHHHhCCeeEEEe
Confidence 9999999999999999998777764
No 116
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=80.87 E-value=4.9 Score=44.84 Aligned_cols=95 Identities=17% Similarity=0.303 Sum_probs=64.0
Q ss_pred ceeccCchHHHHHHHHhCceEEEecCCCCCCceEEEEecChhhhhhccCCccchhhhhhcccCCcccHHHHHHHHHHHHH
Q 046946 141 GVIGKAGNIVKSLREETQAKITVADTIPGSEERVIIIYSSPTKIAKTQNKDDDSAAETKKESMEPHCAAQDALLKVHDRI 220 (650)
Q Consensus 141 ~IIGKgG~~Ik~Ir~~TgakI~I~~~~~g~~eRvI~I~G~~e~v~~a~~~~~~~~~e~~~~~~~~~~~a~~Al~~v~~~i 220 (650)
.+|=+.|..||+|-++..-+|.|.... .. +.+..+|...+++.+
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~dP--------------sv----------------------l~~~e~A~~~I~eiv 85 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPDP--------------SV----------------------LKPPEEARKIILEIV 85 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccCc--------------hh----------------------cCCHHHHHHHHHHhC
Confidence 446688899999999888888887321 00 112345666666655
Q ss_pred hhhhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEcc
Q 046946 221 IEEDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLP 277 (650)
Q Consensus 221 ~e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~ 277 (650)
-++.......+ +..+.+++|-...-|.+|||+|++.++|..+||-.-+|..
T Consensus 86 P~ea~i~~i~F------d~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR 136 (637)
T COG1782 86 PEEAGITDIYF------DDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVR 136 (637)
T ss_pred ccccCceeEEe------cCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeee
Confidence 44322211111 1234567788888999999999999999999998777765
No 117
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=80.36 E-value=3.5 Score=45.54 Aligned_cols=39 Identities=28% Similarity=0.509 Sum_probs=35.6
Q ss_pred EEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCC
Q 046946 241 TARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPAD 279 (650)
Q Consensus 241 t~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~ 279 (650)
...+.||...++.+|||+|.+|++|+++.|-+|.|.+.+
T Consensus 487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e 525 (604)
T COG1855 487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE 525 (604)
T ss_pred eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence 467889999999999999999999999999999998643
No 118
>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=80.33 E-value=1.9 Score=35.85 Aligned_cols=33 Identities=12% Similarity=0.405 Sum_probs=27.2
Q ss_pred EEEEEeCCCCceeEecCCCchHHHHHHhcCCeE
Q 046946 481 TTRLLVPSSKVGCILGQGGHVINEMRRRTQADI 513 (650)
Q Consensus 481 ~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I 513 (650)
...+.|..+..|.+|||.|++++.|+--+..-+
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~ 57 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVL 57 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHH
Confidence 456777788899999999999999998766443
No 119
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=80.09 E-value=3.4 Score=41.90 Aligned_cols=59 Identities=20% Similarity=0.399 Sum_probs=44.2
Q ss_pred EEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCceEEEecCHHH-HHHHHHHHHHH
Q 046946 242 ARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDEMVQISGKPNV-AKRALYEVSTL 311 (650)
Q Consensus 242 ~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr~V~I~G~~~~-V~~A~~~I~~~ 311 (650)
.-+.|+...|.++||++|+.++.+.++|+|+|.+-. .-.|=|.|+.+. ...|..+|..+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-----------NG~IWV~~~~~~~e~~~~~aI~~i 207 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-----------NGRIWVDGENESLEELAIEAIRKI 207 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-----------CCEEEecCCCcchHHHHHHHHHHH
Confidence 357889999999999999999999999999998863 234667776653 34444444443
No 120
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=79.87 E-value=1.2 Score=48.90 Aligned_cols=37 Identities=30% Similarity=0.413 Sum_probs=34.0
Q ss_pred EEEEEecCccccceeccCchHHHHHHHHhCceEEEec
Q 046946 129 VYRILCPSRKIGGVIGKAGNIVKSLREETQAKITVAD 165 (650)
Q Consensus 129 ~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~~ 165 (650)
...+.+|.+.++.||||+|.+|++|+++.|-+|.|..
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 3557899999999999999999999999999999985
No 121
>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=79.30 E-value=2 Score=36.34 Aligned_cols=36 Identities=17% Similarity=0.334 Sum_probs=29.9
Q ss_pred EEEEEecCccccceeccCchHHHHHHHHhCceEEEe
Q 046946 129 VYRILCPSRKIGGVIGKAGNIVKSLREETQAKITVA 164 (650)
Q Consensus 129 ~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~ 164 (650)
..++.+....-|.|||++|+.|++|+++-.-...+.
T Consensus 31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~ 66 (81)
T cd02413 31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP 66 (81)
T ss_pred eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence 367788889999999999999999998876655543
No 122
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=78.67 E-value=4.7 Score=40.88 Aligned_cols=57 Identities=23% Similarity=0.313 Sum_probs=43.3
Q ss_pred EEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcCHHH-HHHHHHHHH
Q 046946 482 TRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGSSEH-LISAHGTYQ 551 (650)
Q Consensus 482 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~~e~-V~~A~~lI~ 551 (650)
.-+.|+...|-++||++|+.++-+.+.|+|.|-+-.+ ..|=|.|..+. ...|...|.
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N-------------G~IWV~~~~~~~e~~~~~aI~ 205 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN-------------GRIWVDGENESLEELAIEAIR 205 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC-------------CEEEecCCCcchHHHHHHHHH
Confidence 4578999999999999999999999999999998853 35666665552 333444443
No 123
>PRK13764 ATPase; Provisional
Probab=78.49 E-value=3.2 Score=48.08 Aligned_cols=42 Identities=29% Similarity=0.472 Sum_probs=37.5
Q ss_pred eEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCC
Q 046946 240 ITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRL 281 (650)
Q Consensus 240 vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~ 281 (650)
-.+.+.||.+.++.+|||+|.+|++|+++.|.+|.|.+.+..
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~ 522 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEE 522 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcccc
Confidence 356789999999999999999999999999999999975543
No 124
>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=78.28 E-value=1.3 Score=36.74 Aligned_cols=33 Identities=21% Similarity=0.503 Sum_probs=28.3
Q ss_pred EEEEEEcCCccceeecCCchHHHHHHHHhCCeE
Q 046946 241 TARLLVPNNMVGCLLGKRGDVIQRLRSETGANI 273 (650)
Q Consensus 241 t~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I 273 (650)
.+.+.+...+-+.|||++|++|++|++...-.+
T Consensus 26 ~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 26 QIIIVIKASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp EEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred eEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 467888999999999999999999988876554
No 125
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=77.29 E-value=4.1 Score=41.84 Aligned_cols=51 Identities=22% Similarity=0.189 Sum_probs=45.4
Q ss_pred ceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCceEEEecCHHHHHHHHHHHHHHHcc
Q 046946 252 GCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDEMVQISGKPNVAKRALYEVSTLLHQ 314 (650)
Q Consensus 252 g~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr~V~I~G~~~~V~~A~~~I~~~l~~ 314 (650)
-+|||.+|.|+|.|+--|.|-|-|. -..|.+.|.-..++.+...+.+.+..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVq------------G~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQ------------GNTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEee------------CcEEEeecCcchHHHHHHHHHHHHhc
Confidence 4799999999999999999999886 24699999999999999999998865
No 126
>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=74.47 E-value=3.5 Score=34.85 Aligned_cols=34 Identities=21% Similarity=0.414 Sum_probs=28.4
Q ss_pred ceEEEEEeCCCCceeEecCCCchHHHHHHhcCCe
Q 046946 479 TITTRLLVPSSKVGCILGQGGHVINEMRRRTQAD 512 (650)
Q Consensus 479 ~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~ 512 (650)
...+++.|-...-|.|||++|+.|++|++.-...
T Consensus 29 ~~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~ 62 (81)
T cd02413 29 PTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKR 62 (81)
T ss_pred CCeEEEEEEeCCCceEECCCchhHHHHHHHHHHH
Confidence 3457888899999999999999999998876443
No 127
>PRK13764 ATPase; Provisional
Probab=74.28 E-value=2.3 Score=49.19 Aligned_cols=38 Identities=26% Similarity=0.424 Sum_probs=34.6
Q ss_pred eEEEEEecCccccceeccCchHHHHHHHHhCceEEEec
Q 046946 128 TVYRILCPSRKIGGVIGKAGNIVKSLREETQAKITVAD 165 (650)
Q Consensus 128 ~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I~~ 165 (650)
-...+.||.+.++.+|||+|.+|++|+++.|.+|.|..
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~ 518 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP 518 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence 44567899999999999999999999999999999984
No 128
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=74.03 E-value=3.9 Score=45.58 Aligned_cols=102 Identities=19% Similarity=0.328 Sum_probs=65.9
Q ss_pred eeEEEEEecCCccceecccCccchhchhhhcCceEEecCCCCCCCccEEEEeccCCCcCccchHHHHHHHHhhhccccc-
Q 046946 397 EFSMKILCSAGKIGGVIGKGGFNVKQLQQETGASIHVEDAPTDSDERVIRASAFEGLWNPRSQTIDAILQLQNKTSEFS- 475 (650)
Q Consensus 397 ~~~~~v~iP~~~~g~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~erii~I~G~~~~~~~~~~~~~ai~~~~~~i~~~~- 475 (650)
++.+.+.=|. .+-+.|..|++|.++..-+|.|..+.. .....+.+.+.|.++...-....
T Consensus 33 elvvY~k~P~-----~~~~~~dlik~lAk~lrKRI~iR~dPs--------------vl~~~e~A~~~I~eivP~ea~i~~ 93 (637)
T COG1782 33 ELVVYTKNPE-----LFAKDGDLIKDLAKDLRKRIIIRPDPS--------------VLKPPEEARKIILEIVPEEAGITD 93 (637)
T ss_pred eEEEEecCHH-----HhccchhHHHHHHHHHhhceEeccCch--------------hcCCHHHHHHHHHHhCccccCcee
Confidence 4444444443 345778999999999999988864421 11112334444544443222211
Q ss_pred -cCCceEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeC
Q 046946 476 -EKGTITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVG 517 (650)
Q Consensus 476 -~~~~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~ 517 (650)
.-...+-++.|-...-|.+|||+|++.++|.++||-.-+|.+
T Consensus 94 i~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR 136 (637)
T COG1782 94 IYFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVR 136 (637)
T ss_pred EEecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeee
Confidence 112334578888999999999999999999999997666664
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=71.39 E-value=3.6 Score=36.74 Aligned_cols=30 Identities=30% Similarity=0.437 Sum_probs=25.4
Q ss_pred EEEEecCccccceeccCchHHHHHHHHhCc
Q 046946 130 YRILCPSRKIGGVIGKAGNIVKSLREETQA 159 (650)
Q Consensus 130 ~rilvP~~~vG~IIGKgG~~Ik~Ir~~Tga 159 (650)
+++.+....-|.|||++|++|++|++....
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 567777888999999999999999977554
No 130
>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=68.57 E-value=5 Score=34.07 Aligned_cols=28 Identities=29% Similarity=0.406 Sum_probs=22.7
Q ss_pred EEEEecCccccceeccCchHHHHHHHHh
Q 046946 130 YRILCPSRKIGGVIGKAGNIVKSLREET 157 (650)
Q Consensus 130 ~rilvP~~~vG~IIGKgG~~Ik~Ir~~T 157 (650)
.++.+....-|.+||++|++|++|++.-
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 4455555888999999999999998764
No 131
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=67.26 E-value=7.3 Score=37.53 Aligned_cols=35 Identities=29% Similarity=0.464 Sum_probs=30.4
Q ss_pred EEEEEcCCccceeecCCchHHHHHHHHhCCeEEEcc
Q 046946 242 ARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLP 277 (650)
Q Consensus 242 ~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~ 277 (650)
+-++|-... |.-|||+|++|+++++..|-+|.+..
T Consensus 63 vIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 63 VILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 456676666 99999999999999999999999873
No 132
>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=65.39 E-value=15 Score=43.12 Aligned_cols=95 Identities=19% Similarity=0.357 Sum_probs=60.4
Q ss_pred eeccCchHHHHHHHHhCceEEEecCCCCCCceEEEEecChhhhhhccCCccchhhhhhcccCCcccHHHHHHHHHHHHHh
Q 046946 142 VIGKAGNIVKSLREETQAKITVADTIPGSEERVIIIYSSPTKIAKTQNKDDDSAAETKKESMEPHCAAQDALLKVHDRII 221 (650)
Q Consensus 142 IIGKgG~~Ik~Ir~~TgakI~I~~~~~g~~eRvI~I~G~~e~v~~a~~~~~~~~~e~~~~~~~~~~~a~~Al~~v~~~i~ 221 (650)
.+=+.|..|++|-++..-+|.|..+. .. +.+..+|..++.+.+-
T Consensus 37 ~~~~~~~~~~~~~~~~~~r~~~~~~~--------------~~----------------------~~~~~~~~~~i~~~~~ 80 (630)
T TIGR03675 37 LFAKDDDLVKELAKKLRKRIVIRPDP--------------SV----------------------LLPPEEAIEKIKEIVP 80 (630)
T ss_pred HhccchHHHHHHHHHhhceEEEecCh--------------hh----------------------cCCHHHHHHHHHHhCC
Confidence 35567788888888888777776321 00 0112345555555544
Q ss_pred hhhccCCCCCCCCCCCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccC
Q 046946 222 EEDLFGGMASDDDNENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPA 278 (650)
Q Consensus 222 e~~~~~~~~~~~~~~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~ 278 (650)
++......-+ +..+-+++|-...-|.+|||+|.++++|..+||=.-+|...
T Consensus 81 ~~~~~~~~~f------~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 81 EEAGITDIYF------DDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred CcCCceeEEe------cCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 3321111111 12334677777888999999999999999999998888753
No 133
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=64.03 E-value=5.6 Score=40.17 Aligned_cols=30 Identities=33% Similarity=0.447 Sum_probs=25.6
Q ss_pred eEEEEEecCccccceeccCchHHHHHHHHh
Q 046946 128 TVYRILCPSRKIGGVIGKAGNIVKSLREET 157 (650)
Q Consensus 128 ~~~rilvP~~~vG~IIGKgG~~Ik~Ir~~T 157 (650)
...++.|....-|.||||+|+.|++|+++.
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~l 80 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKEL 80 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHHH
Confidence 356778889999999999999999988654
No 134
>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=62.58 E-value=10 Score=44.48 Aligned_cols=91 Identities=21% Similarity=0.360 Sum_probs=60.4
Q ss_pred cccCccchhchhhhcCceEEecCCCCCCCccEEEEeccCCCcCccchHHHHHHHHhhhccccc--cCCceEEEEEeCCCC
Q 046946 413 IGKGGFNVKQLQQETGASIHVEDAPTDSDERVIRASAFEGLWNPRSQTIDAILQLQNKTSEFS--EKGTITTRLLVPSSK 490 (650)
Q Consensus 413 IGkgG~~Ik~I~~~sga~I~i~~~~~~~~erii~I~G~~~~~~~~~~~~~ai~~~~~~i~~~~--~~~~~~~~l~VP~~~ 490 (650)
+-..|..|++|.++..-+|.|..+.. ....-+.+.+.|..+...-.... .-+..+-++.|-...
T Consensus 38 ~~~~~~~~~~~~~~~~~r~~~~~~~~--------------~~~~~~~~~~~i~~~~~~~~~~~~~~f~~~~~~v~i~~~~ 103 (630)
T TIGR03675 38 FAKDDDLVKELAKKLRKRIVIRPDPS--------------VLLPPEEAIEKIKEIVPEEAGITDIYFDDVTGEVIIEAEK 103 (630)
T ss_pred hccchHHHHHHHHHhhceEEEecChh--------------hcCCHHHHHHHHHHhCCCcCCceeEEecCCCceEEEEEcC
Confidence 34567889999999888888753321 11111334455554443221111 112345578888999
Q ss_pred ceeEecCCCchHHHHHHhcCCeEEEeC
Q 046946 491 VGCILGQGGHVINEMRRRTQADIRVVG 517 (650)
Q Consensus 491 vG~IIGkgG~~IkeI~~~TGA~I~i~~ 517 (650)
-|.+|||+|.++++|.++||=.-.|-+
T Consensus 104 p~~~~~~~~~~~~~i~~~~~w~~~~~~ 130 (630)
T TIGR03675 104 PGLVIGKGGSTLREITAETGWTPKVVR 130 (630)
T ss_pred CeEEEecCcchHHHHHHHhCCeeeEEe
Confidence 999999999999999999998877765
No 135
>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=61.44 E-value=6.1 Score=35.28 Aligned_cols=30 Identities=23% Similarity=0.513 Sum_probs=25.5
Q ss_pred EEEEEeCCCCceeEecCCCchHHHHHHhcC
Q 046946 481 TTRLLVPSSKVGCILGQGGHVINEMRRRTQ 510 (650)
Q Consensus 481 ~~~l~VP~~~vG~IIGkgG~~IkeI~~~TG 510 (650)
.+++.|-...-|.|||++|+.|++|++...
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~ 91 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQ 91 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence 367788888899999999999999987654
No 136
>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=60.61 E-value=8 Score=32.85 Aligned_cols=28 Identities=25% Similarity=0.551 Sum_probs=23.3
Q ss_pred EEEEeCCCCceeEecCCCchHHHHHHhc
Q 046946 482 TRLLVPSSKVGCILGQGGHVINEMRRRT 509 (650)
Q Consensus 482 ~~l~VP~~~vG~IIGkgG~~IkeI~~~T 509 (650)
+++.|-...-|.+||++|++|+++++.-
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 5566666888999999999999998754
No 137
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=58.70 E-value=8.3 Score=38.98 Aligned_cols=38 Identities=18% Similarity=0.440 Sum_probs=30.6
Q ss_pred ceEEEEEeCCCCceeEecCCCchHHHHHH----hcCC-eEEEe
Q 046946 479 TITTRLLVPSSKVGCILGQGGHVINEMRR----RTQA-DIRVV 516 (650)
Q Consensus 479 ~~~~~l~VP~~~vG~IIGkgG~~IkeI~~----~TGA-~I~i~ 516 (650)
...+++.|-...-|.|||++|+.|++|++ .+|. .++|.
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~~v~I~ 92 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKENVQIN 92 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCCCceEE
Confidence 56788999999999999999999998865 5665 45554
No 138
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=54.85 E-value=15 Score=41.04 Aligned_cols=95 Identities=16% Similarity=0.065 Sum_probs=62.2
Q ss_pred cceecccCccchhchhhhcCceEEecCCCCCCCccEEEE-eccCCCcCccchHHHHHHHHhhhccccccCCceEEEEEeC
Q 046946 409 IGGVIGKGGFNVKQLQQETGASIHVEDAPTDSDERVIRA-SAFEGLWNPRSQTIDAILQLQNKTSEFSEKGTITTRLLVP 487 (650)
Q Consensus 409 ~g~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~erii~I-~G~~~~~~~~~~~~~ai~~~~~~i~~~~~~~~~~~~l~VP 487 (650)
-..+-||+...+.+|.+...|.+.+.-... .+.++.++ .|..... .+ .+.-...+-.-+..+.+|
T Consensus 391 EdFl~gkkngK~TrIm~~v~c~~~~~i~~~-~gs~~~~~~~g~~~~F------~k-------~~~~~~~EFpae~~f~i~ 456 (657)
T COG5166 391 EDFLRGKKNGKATRIMKGVSCSELSSIVSS-TGSIVETNGIGEKMSF------SK-------KLSIPPTEFPAEIAFIIM 456 (657)
T ss_pred HHHhccccCcchhhhhhhcccceeeEEEec-CCcEEEEeccCcchhh------HH-------HhcCCcccCchheEEEee
Confidence 447778888889999999999955542111 12233222 2322111 01 111111122345679999
Q ss_pred CCCceeEecCCCchHHHHHHhcCCeEEEeC
Q 046946 488 SSKVGCILGQGGHVINEMRRRTQADIRVVG 517 (650)
Q Consensus 488 ~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~ 517 (650)
...|..|||-||..|.++++..++.|++..
T Consensus 457 e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n 486 (657)
T COG5166 457 ESGHEMIIGTGGIEIQENMVKHAVDIAFKN 486 (657)
T ss_pred cccceeeeccCchhhHHhhhhhhhhhhhhh
Confidence 999999999999999999999999998875
No 139
>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=51.70 E-value=16 Score=37.84 Aligned_cols=30 Identities=23% Similarity=0.362 Sum_probs=24.2
Q ss_pred eEEEEEeCC-CCceeEecCCCchHHHHHHhc
Q 046946 480 ITTRLLVPS-SKVGCILGQGGHVINEMRRRT 509 (650)
Q Consensus 480 ~~~~l~VP~-~~vG~IIGkgG~~IkeI~~~T 509 (650)
+...|.|.. ++-+.||||+|++||+|....
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 556778875 566999999999999987654
No 140
>PRK15494 era GTPase Era; Provisional
Probab=47.03 E-value=21 Score=38.51 Aligned_cols=29 Identities=31% Similarity=0.462 Sum_probs=23.2
Q ss_pred eEEEEEeCC-CCceeEecCCCchHHHHHHh
Q 046946 480 ITTRLLVPS-SKVGCILGQGGHVINEMRRR 508 (650)
Q Consensus 480 ~~~~l~VP~-~~vG~IIGkgG~~IkeI~~~ 508 (650)
+...|.|.. ++-+.||||+|++||+|...
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 456788885 56689999999999988654
No 141
>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=46.80 E-value=22 Score=36.74 Aligned_cols=31 Identities=23% Similarity=0.365 Sum_probs=24.2
Q ss_pred ceEEEEEEcC-CccceeecCCchHHHHHHHHh
Q 046946 239 TITARLLVPN-NMVGCLLGKRGDVIQRLRSET 269 (650)
Q Consensus 239 ~vt~~llVP~-~~vg~IIGk~G~~Ik~I~~~t 269 (650)
.+.+.++|.. ++-+.||||+|++||+|..+.
T Consensus 220 ~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 220 KIHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 3667778874 466899999999999986654
No 142
>PRK00089 era GTPase Era; Reviewed
Probab=44.80 E-value=23 Score=36.97 Aligned_cols=30 Identities=27% Similarity=0.593 Sum_probs=23.3
Q ss_pred eEEEEEeCC-CCceeEecCCCchHHHHHHhc
Q 046946 480 ITTRLLVPS-SKVGCILGQGGHVINEMRRRT 509 (650)
Q Consensus 480 ~~~~l~VP~-~~vG~IIGkgG~~IkeI~~~T 509 (650)
+...|.|.. ++-+.||||+|++||+|...+
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~a 256 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEA 256 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHH
Confidence 455677775 566899999999999886543
No 143
>COG1159 Era GTPase [General function prediction only]
Probab=44.70 E-value=23 Score=37.32 Aligned_cols=31 Identities=26% Similarity=0.508 Sum_probs=23.7
Q ss_pred ceEEEEEeCC-CCceeEecCCCchHHHHHHhc
Q 046946 479 TITTRLLVPS-SKVGCILGQGGHVINEMRRRT 509 (650)
Q Consensus 479 ~~~~~l~VP~-~~vG~IIGkgG~~IkeI~~~T 509 (650)
.+...|.|+. ++=|.||||+|++||+|-..+
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 3445677875 677999999999999886543
No 144
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=44.12 E-value=19 Score=38.07 Aligned_cols=32 Identities=19% Similarity=0.413 Sum_probs=25.7
Q ss_pred ceEEEEEec-CccccceeccCchHHHHHHHHhC
Q 046946 127 DTVYRILCP-SRKIGGVIGKAGNIVKSLREETQ 158 (650)
Q Consensus 127 ~~~~rilvP-~~~vG~IIGKgG~~Ik~Ir~~Tg 158 (650)
.+..+++|| .+..-.||||||..|++|-++.+
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 467788999 45677899999999999987644
No 145
>PRK15494 era GTPase Era; Provisional
Probab=41.70 E-value=29 Score=37.40 Aligned_cols=29 Identities=24% Similarity=0.462 Sum_probs=23.2
Q ss_pred eEEEEEEcCC-ccceeecCCchHHHHHHHH
Q 046946 240 ITARLLVPNN-MVGCLLGKRGDVIQRLRSE 268 (650)
Q Consensus 240 vt~~llVP~~-~vg~IIGk~G~~Ik~I~~~ 268 (650)
+.+.|+|..+ +-+.||||+|++||+|..+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 5577888854 6689999999999988654
No 146
>COG1159 Era GTPase [General function prediction only]
Probab=41.63 E-value=32 Score=36.28 Aligned_cols=30 Identities=27% Similarity=0.565 Sum_probs=22.9
Q ss_pred ceEEEEEEcC-CccceeecCCchHHHHHHHH
Q 046946 239 TITARLLVPN-NMVGCLLGKRGDVIQRLRSE 268 (650)
Q Consensus 239 ~vt~~llVP~-~~vg~IIGk~G~~Ik~I~~~ 268 (650)
.+...++|+. ++-+.||||+|++||+|-..
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 3445677774 57799999999999988544
No 147
>PRK00089 era GTPase Era; Reviewed
Probab=40.97 E-value=30 Score=36.07 Aligned_cols=30 Identities=27% Similarity=0.585 Sum_probs=23.2
Q ss_pred eEEEEEEcC-CccceeecCCchHHHHHHHHh
Q 046946 240 ITARLLVPN-NMVGCLLGKRGDVIQRLRSET 269 (650)
Q Consensus 240 vt~~llVP~-~~vg~IIGk~G~~Ik~I~~~t 269 (650)
+.+.+.|.. ++-+.||||+|++||+|..+.
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~a 256 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEA 256 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHH
Confidence 566777774 466899999999999886553
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=38.25 E-value=29 Score=34.36 Aligned_cols=31 Identities=26% Similarity=0.427 Sum_probs=25.8
Q ss_pred EEEEEecCccccceeccCchHHHHHHHHhCc
Q 046946 129 VYRILCPSRKIGGVIGKAGNIVKSLREETQA 159 (650)
Q Consensus 129 ~~rilvP~~~vG~IIGKgG~~Ik~Ir~~Tga 159 (650)
..++.+....-|.|||++|..|++|+++-.-
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 3667777888999999999999999877544
No 149
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=38.09 E-value=2.5e+02 Score=30.82 Aligned_cols=139 Identities=10% Similarity=0.083 Sum_probs=73.2
Q ss_pred ecCCcc-ceecccCccchhchhhhcCceEEecCCCC---------CCCcc-EEEEe-ccCCCcCccchHHHHHHHH-hhh
Q 046946 404 CSAGKI-GGVIGKGGFNVKQLQQETGASIHVEDAPT---------DSDER-VIRAS-AFEGLWNPRSQTIDAILQL-QNK 470 (650)
Q Consensus 404 iP~~~~-g~IIGkgG~~Ik~I~~~sga~I~i~~~~~---------~~~er-ii~I~-G~~~~~~~~~~~~~ai~~~-~~~ 470 (650)
+|..++ +..=+++-.++..++.++++.+-+.-... ++.|. -|.|+ +..+-+..+...+..+++. .-.
T Consensus 220 ~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMYI~i~h~~~~g~~~A~r~~~nl~~~v~~~ 299 (531)
T KOG1960|consen 220 DPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNEGNESNEPMYIFSTHGNGNGENGAPRRKWNLEEKVYIN 299 (531)
T ss_pred CcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccCcccccccCCceeEEeecCCchhhccchhHHHhHHHHHHHH
Confidence 444443 33336677788888888888866642211 22222 44455 4554444444333322211 111
Q ss_pred ccccccCCceEEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccc-c-CCCC--CCCCceEEEEEcCHHHHHHH
Q 046946 471 TSEFSEKGTITTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVK-L-QDPH--PGSSECIVDIRGSSEHLISA 546 (650)
Q Consensus 471 i~~~~~~~~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~-l-~~p~--~~~~er~V~I~G~~e~V~~A 546 (650)
+.. .... -.+.|.-|...+.|+..+-.++++..-.-. + ..+. .++.-.+..|.-.+..++.|
T Consensus 300 ~sr----~~~~----------~~~~~p~~~y~~~~~~~~~~~~~~~g~~s~~i~p~~~~~~~~p~~~~~~~~~~~~~~~~ 365 (531)
T KOG1960|consen 300 LSR----GFHR----------QAIVGPQGAYVKHIQQETRTRVQIKGQGSAFIEPSTNRESDEPIHLCIMSHDPNAIQRA 365 (531)
T ss_pred hhh----hhhh----------cccccCCcccccccCCCCCcceeccCccceeecCCCCCCCCCCcccccccCChhhhhhh
Confidence 111 0001 134566677778888877777776542100 0 1111 22334567788888888888
Q ss_pred HHHHHHHHhc
Q 046946 547 HGTYQSFMTS 556 (650)
Q Consensus 547 ~~lI~~~i~~ 556 (650)
+-++...|..
T Consensus 366 ~~~~~~~i~~ 375 (531)
T KOG1960|consen 366 KVLCEDLIAS 375 (531)
T ss_pred hhcccccCCc
Confidence 8888887765
No 150
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=37.50 E-value=30 Score=34.66 Aligned_cols=31 Identities=32% Similarity=0.449 Sum_probs=24.7
Q ss_pred EEEEecCccccceeccCchHHHHHHHHhCce
Q 046946 130 YRILCPSRKIGGVIGKAGNIVKSLREETQAK 160 (650)
Q Consensus 130 ~rilvP~~~vG~IIGKgG~~Ik~Ir~~Tgak 160 (650)
.++.+....-|.+||++|++|++|++.-.-.
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk~ 72 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEKK 72 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHHH
Confidence 4455555889999999999999999876543
No 151
>CHL00048 rps3 ribosomal protein S3
Probab=37.15 E-value=31 Score=34.78 Aligned_cols=30 Identities=13% Similarity=0.143 Sum_probs=25.0
Q ss_pred EEEEEecCccccceeccCchHHHHHHHHhC
Q 046946 129 VYRILCPSRKIGGVIGKAGNIVKSLREETQ 158 (650)
Q Consensus 129 ~~rilvP~~~vG~IIGKgG~~Ik~Ir~~Tg 158 (650)
..++.+-...-|.|||++|+.|++|++.-.
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 356667778889999999999999998764
No 152
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=35.94 E-value=37 Score=36.02 Aligned_cols=32 Identities=25% Similarity=0.549 Sum_probs=26.0
Q ss_pred ceEEEEEeCC-CCceeEecCCCchHHHHHHhcC
Q 046946 479 TITTRLLVPS-SKVGCILGQGGHVINEMRRRTQ 510 (650)
Q Consensus 479 ~~~~~l~VP~-~~vG~IIGkgG~~IkeI~~~TG 510 (650)
.+..++.+|. ++...||||||..|++|-++.+
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 4677889996 5667899999999999976544
No 153
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=35.76 E-value=33 Score=34.65 Aligned_cols=31 Identities=19% Similarity=0.354 Sum_probs=25.5
Q ss_pred EEEEecCccccceeccCchHHHHHHHHhCce
Q 046946 130 YRILCPSRKIGGVIGKAGNIVKSLREETQAK 160 (650)
Q Consensus 130 ~rilvP~~~vG~IIGKgG~~Ik~Ir~~Tgak 160 (650)
.++.+....-|.|||++|..|++|+++-.-.
T Consensus 46 i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~ 76 (220)
T PTZ00084 46 TEIIIRATRTREVLGDKGRRIRELTSLLQKR 76 (220)
T ss_pred EEEEEEECCCccEEcCCchHHHHHHHHHHHH
Confidence 5666777888999999999999999776543
No 154
>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=30.63 E-value=45 Score=33.10 Aligned_cols=31 Identities=23% Similarity=0.606 Sum_probs=25.8
Q ss_pred ceEEEEEeCCCCceeEecCCCchHHHHHHhc
Q 046946 479 TITTRLLVPSSKVGCILGQGGHVINEMRRRT 509 (650)
Q Consensus 479 ~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~T 509 (650)
...+++.|-...-|.|||++|+.|++|++.-
T Consensus 37 ~~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 37 PLGTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred CCcEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 3457788888889999999999999987654
No 155
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=30.47 E-value=36 Score=33.92 Aligned_cols=35 Identities=17% Similarity=0.240 Sum_probs=27.1
Q ss_pred EEEEEecCccccceeccCchHHHHHHHHhCceEEE
Q 046946 129 VYRILCPSRKIGGVIGKAGNIVKSLREETQAKITV 163 (650)
Q Consensus 129 ~~rilvP~~~vG~IIGKgG~~Ik~Ir~~TgakI~I 163 (650)
.+.+-+-.+..+.||||.|+++..||--+.+-+.-
T Consensus 92 ~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 92 RVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred EEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 34445566679999999999999999887765544
No 156
>PRK03818 putative transporter; Validated
Probab=29.61 E-value=5.3e+02 Score=29.89 Aligned_cols=62 Identities=19% Similarity=0.367 Sum_probs=34.9
Q ss_pred eEEEEEEcCCccceeecCCchHHHHH--HHHhCCeEEEccCCCCC--C---CCCCCCceEEEecCHHHHHHHHHH
Q 046946 240 ITARLLVPNNMVGCLLGKRGDVIQRL--RSETGANIRVLPADRLP--P---CAMNTDEMVQISGKPNVAKRALYE 307 (650)
Q Consensus 240 vt~~llVP~~~vg~IIGk~G~~Ik~I--~~~tGa~I~i~~~~~~p--~---~~~~~dr~V~I~G~~~~V~~A~~~ 307 (650)
....+++|+ ..++|| +++++ +++.|+.|.=..+.+.. . ..-..-.++.+.|+++++++..+.
T Consensus 290 ~~E~Vvv~~---S~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq~GD~LlVvG~~~~i~~l~~~ 358 (552)
T PRK03818 290 RSERVVVTN---EKVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLSLQFGDILNLVGRPEAIDAVANV 358 (552)
T ss_pred EEEEEEEcC---hhccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCEEecCCEEEEEECHHHHHHHHHH
Confidence 334445555 356665 67877 56677665333221111 1 001122468899999999987764
No 157
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=29.30 E-value=48 Score=33.22 Aligned_cols=29 Identities=28% Similarity=0.588 Sum_probs=23.6
Q ss_pred EEEEeCCCCceeEecCCCchHHHHHHhcC
Q 046946 482 TRLLVPSSKVGCILGQGGHVINEMRRRTQ 510 (650)
Q Consensus 482 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TG 510 (650)
+++.|-...-|.+||++|++|+++++.-.
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lk 70 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILE 70 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHH
Confidence 55666668889999999999999987653
No 158
>COG0490 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]
Probab=29.08 E-value=68 Score=30.74 Aligned_cols=66 Identities=18% Similarity=0.202 Sum_probs=41.7
Q ss_pred EEEEEeCCCCceeEecCCCchHHHHHHhcCCeEEEe-CCccccCCCCCC---CCceEEEEEcCHHHHHHHHHHHH
Q 046946 481 TTRLLVPSSKVGCILGQGGHVINEMRRRTQADIRVV-GARVKLQDPHPG---SSECIVDIRGSSEHLISAHGTYQ 551 (650)
Q Consensus 481 ~~~l~VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~-~~~~~l~~p~~~---~~er~V~I~G~~e~V~~A~~lI~ 551 (650)
..++..-+..+|.=||- -+|+++|||.|.-. ++...+-.|.+. ..-.++.+.|+..++..++.+..
T Consensus 89 ~~~i~~~s~~~GksiGd-----l~irq~TGaTIIAI~r~~e~I~SPgPy~vle~gDtlvviG~~~~~~r~~~f~~ 158 (162)
T COG0490 89 WFKIEAGSPFIGKTIGD-----LNIRQNTGATVIAIVRNEEKILSPGPYTVLEAGDTLVVIGEETGLKRAKRFLL 158 (162)
T ss_pred eeeeecCCcccCcchhh-----cccccccCcEEEEEEecCcEecCCCchhhhcCCCEEEEEecchHhHHHHHHhh
Confidence 34455555556655554 46789999887544 433333344433 23457889999999988877653
No 159
>CHL00048 rps3 ribosomal protein S3
Probab=29.02 E-value=51 Score=33.16 Aligned_cols=31 Identities=10% Similarity=0.136 Sum_probs=25.7
Q ss_pred ceEEEEEeCCCCceeEecCCCchHHHHHHhc
Q 046946 479 TITTRLLVPSSKVGCILGQGGHVINEMRRRT 509 (650)
Q Consensus 479 ~~~~~l~VP~~~vG~IIGkgG~~IkeI~~~T 509 (650)
...+++.|-...-|.|||++|+.|++|++.-
T Consensus 65 ~~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 65 IDLIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred CCeEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 3446778888888999999999999998754
No 160
>PF09869 DUF2096: Uncharacterized protein conserved in archaea (DUF2096); InterPro: IPR017098 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=28.95 E-value=1.5e+02 Score=28.53 Aligned_cols=59 Identities=22% Similarity=0.253 Sum_probs=45.4
Q ss_pred CCCceEEEEEEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCceEEEecCHHHHHHHHHHHHHHH
Q 046946 236 ENSTITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDEMVQISGKPNVAKRALYEVSTLL 312 (650)
Q Consensus 236 ~~~~vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr~V~I~G~~~~V~~A~~~I~~~l 312 (650)
..+.-++|+-++...+ =+.+++|.+-.|+-+.+. .+..|.|.|+.+.|.+|++.+..+-
T Consensus 109 p~~~~~iRv~l~~~i~-------~erl~ei~E~~gvI~Efe-----------e~~~V~I~Gdke~Ik~aLKe~s~~w 167 (169)
T PF09869_consen 109 PPGFETIRVKLKKPIQ-------EERLQEISEWHGVIFEFE-----------EDDKVVIEGDKERIKKALKEFSSFW 167 (169)
T ss_pred CCCceeEEEecCccch-------HHHHHHHHHHhceeEEec-----------CCcEEEEeccHHHHHHHHHHHHHHh
Confidence 3445567777776654 466889999999988883 2457999999999999999887653
No 161
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=28.16 E-value=48 Score=33.49 Aligned_cols=30 Identities=23% Similarity=0.460 Sum_probs=24.9
Q ss_pred eEEEEEeCCCCceeEecCCCchHHHHHHhc
Q 046946 480 ITTRLLVPSSKVGCILGQGGHVINEMRRRT 509 (650)
Q Consensus 480 ~~~~l~VP~~~vG~IIGkgG~~IkeI~~~T 509 (650)
..+++.|-...-|.|||++|..|++|++.-
T Consensus 44 ~~i~V~I~tarPg~vIG~~G~~i~~l~~~L 73 (220)
T PTZ00084 44 IRTEIIIRATRTREVLGDKGRRIRELTSLL 73 (220)
T ss_pred CcEEEEEEECCCccEEcCCchHHHHHHHHH
Confidence 346788888888999999999999987654
No 162
>TIGR03802 Asp_Ala_antiprt aspartate-alanine antiporter. All members of the seed alignment for this model are asparate-alanine anti-transporters (AspT) encoded next to the gene for aspartate 4-decarboxylase (AspD), which converts asparate to alanine, releasing CO2. The exchange of Asp for Ala is electrogenic, so the AspD/AspT system confers a proton-motive force. This transporter contains two copies of the AspT/YidE/YbjL antiporter duplication domain (TIGR01625).
Probab=26.86 E-value=4.7e+02 Score=30.33 Aligned_cols=63 Identities=19% Similarity=0.361 Sum_probs=36.4
Q ss_pred EEEEEEcCCccceeecCCchHHHHHH------HHhCCeEEEccCCCCC-----CCCCCCCceEEEecCHHHHHHHHHHHH
Q 046946 241 TARLLVPNNMVGCLLGKRGDVIQRLR------SETGANIRVLPADRLP-----PCAMNTDEMVQISGKPNVAKRALYEVS 309 (650)
Q Consensus 241 t~~llVP~~~vg~IIGk~G~~Ik~I~------~~tGa~I~i~~~~~~p-----~~~~~~dr~V~I~G~~~~V~~A~~~I~ 309 (650)
..++++|+ ..++|| ++++++ ++.|+.|.=..+++.. ...-..-.++.+.|++++++++.+.+-
T Consensus 304 ~e~VV~~~---S~liGk---TL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~GD~LlV~G~~~~l~~~~~~lG 377 (562)
T TIGR03802 304 TKDVVLTN---KEYNGK---TVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQRGDVVTLVGTPQDVDRAAKQLG 377 (562)
T ss_pred EEEEEECC---cccCCc---cHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecCCCEEEEEeCHHHHHHHHHHcC
Confidence 34455565 345555 788886 2677776444322211 111122346889999999998777644
No 163
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=26.17 E-value=1.3e+02 Score=32.46 Aligned_cols=56 Identities=13% Similarity=0.132 Sum_probs=46.0
Q ss_pred eCCCCceeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCCCCCceEEEEEcCHHHHHHHHHHHH--HHHh
Q 046946 486 VPSSKVGCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHPGSSECIVDIRGSSEHLISAHGTYQ--SFMT 555 (650)
Q Consensus 486 VP~~~vG~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~~~~er~V~I~G~~e~V~~A~~lI~--~~i~ 555 (650)
-+....-.+.|..|.+++.|.+..|++|.... +.++|+|+...|+.|...+. +++.
T Consensus 21 ~~~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG--------------~~~~i~g~~~~v~~A~~~l~~l~~~~ 78 (348)
T COG1702 21 SDDNELVALFGPTDTNLSLLEIALGVSIVARG--------------EAVRIIGARPLVDVATRVLLTLELLA 78 (348)
T ss_pred CCchhhhhhcCCCCccHHHHHHHhCcEEEeCC--------------ceEEEEechHHHHHHHHHHhHHHHHH
Confidence 34567778999999999999999999886653 47999999879999988888 5443
No 164
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=24.19 E-value=71 Score=31.89 Aligned_cols=35 Identities=17% Similarity=0.290 Sum_probs=27.9
Q ss_pred eEEEEEEcCCccceeecCCchHHHHHHHHhCCeEE
Q 046946 240 ITARLLVPNNMVGCLLGKRGDVIQRLRSETGANIR 274 (650)
Q Consensus 240 vt~~llVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~ 274 (650)
..+.+-+..+..++|||+.|.++..||--+.+-+.
T Consensus 91 ~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~ 125 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLN 125 (208)
T ss_pred cEEEEEecCCchhhhhccCCcchHHHHHHHHHHhh
Confidence 34566777777999999999999999987765443
No 165
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=24.10 E-value=68 Score=32.22 Aligned_cols=29 Identities=34% Similarity=0.538 Sum_probs=24.2
Q ss_pred EEEEecCccccceeccCchHHHHHHHHhC
Q 046946 130 YRILCPSRKIGGVIGKAGNIVKSLREETQ 158 (650)
Q Consensus 130 ~rilvP~~~vG~IIGKgG~~Ik~Ir~~Tg 158 (650)
++|.+....-|.|||++|..|++|++.-.
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 56777778889999999999999986653
No 166
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=23.70 E-value=1.4e+02 Score=32.18 Aligned_cols=58 Identities=24% Similarity=0.263 Sum_probs=46.7
Q ss_pred EEcCCccceeecCCchHHHHHHHHhCCeEEEccCCCCCCCCCCCCceEEEecCHHHHHHHHHHHH--HHHcc
Q 046946 245 LVPNNMVGCLLGKRGDVIQRLRSETGANIRVLPADRLPPCAMNTDEMVQISGKPNVAKRALYEVS--TLLHQ 314 (650)
Q Consensus 245 lVP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~dr~V~I~G~~~~V~~A~~~I~--~~l~~ 314 (650)
+-+....-.|.|..+..++.|.+..|++|... .+.++|+|+...|..|...+. +++..
T Consensus 20 ~~~~~~~~~l~G~~~~~l~l~e~~~gv~i~~r------------G~~~~i~g~~~~v~~A~~~l~~l~~~~~ 79 (348)
T COG1702 20 LSDDNELVALFGPTDTNLSLLEIALGVSIVAR------------GEAVRIIGARPLVDVATRVLLTLELLAE 79 (348)
T ss_pred cCCchhhhhhcCCCCccHHHHHHHhCcEEEeC------------CceEEEEechHHHHHHHHHHhHHHHHHH
Confidence 33466777899999999999999999988664 356999999878888888888 54443
No 167
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=22.13 E-value=1.2e+02 Score=23.93 Aligned_cols=52 Identities=15% Similarity=0.229 Sum_probs=33.0
Q ss_pred CchHHH--HHHhcCCeEEEeCCccccCCCCCC---CCceEEEEEcCHHHHHHHHHHH
Q 046946 499 GHVINE--MRRRTQADIRVVGARVKLQDPHPG---SSECIVDIRGSSEHLISAHGTY 550 (650)
Q Consensus 499 G~~Ike--I~~~TGA~I~i~~~~~~l~~p~~~---~~er~V~I~G~~e~V~~A~~lI 550 (650)
|.+|++ +++.+++.|---.+.-....|..+ .....+.|.|+.+.++++.+++
T Consensus 14 gk~l~el~l~~~~~~~i~~i~R~~~~~~p~~~~~l~~gD~l~v~g~~~~i~~~~~~~ 70 (71)
T PF02080_consen 14 GKTLKELDLPERYGVRIVAIKRGGEIIIPDGDTVLQAGDILIVVGDPEDIERFRELF 70 (71)
T ss_dssp TEBHHHCTHHCHHTEEEEEEEETEEEES--TT-BE-TTEEEEEEEEHHHHHHHHHHT
T ss_pred CCCHHHCCCCccCCEEEEEEEECCEEECCCCCCEECCCCEEEEEECHHHHHHHHHhh
Confidence 667888 777778877665433112122221 2346899999999999887654
No 168
>PF08052 PyrBI_leader: PyrBI operon leader peptide; InterPro: IPR012602 This family consists of the pyrBI operon leader peptides. The expression of the pyrBI operon, which encodes the subunits of the pyrimidine biosynthetic enzyme aspartate transcarbamylase. is regulated primarily through a UTP-sensitive transcriptional attenuation control mechanism. In this mechanism, the concentration of UTP determines the extent of coupling between transcription and translation within the pyrBI leader region, hence determining the level of rho-independent transcriptional termination at an attenuator preceding the pyrB gene [].; GO: 0019856 pyrimidine base biosynthetic process
Probab=21.85 E-value=35 Score=24.49 Aligned_cols=11 Identities=64% Similarity=1.204 Sum_probs=8.9
Q ss_pred ccCCcccccCC
Q 046946 6 KVEGLPFLFPP 16 (650)
Q Consensus 6 ~~~~~~~~~~~ 16 (650)
|-.||||.||-
T Consensus 15 ~daglpfffpl 25 (44)
T PF08052_consen 15 KDAGLPFFFPL 25 (44)
T ss_pred ccCCCceEEec
Confidence 45799999985
No 169
>PRK10224 pyrBI operon leader peptide; Provisional
Probab=21.27 E-value=36 Score=24.32 Aligned_cols=13 Identities=54% Similarity=1.047 Sum_probs=9.6
Q ss_pred ccCCcccccCCCC
Q 046946 6 KVEGLPFLFPPFP 18 (650)
Q Consensus 6 ~~~~~~~~~~~~~ 18 (650)
+-.||||.||-.+
T Consensus 15 ~daglpfffpl~~ 27 (44)
T PRK10224 15 KDAGLPFFFPLIT 27 (44)
T ss_pred ccCCCceEEeeec
Confidence 3469999998643
No 170
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=20.16 E-value=1.5e+02 Score=32.45 Aligned_cols=64 Identities=9% Similarity=0.022 Sum_probs=43.6
Q ss_pred eeEecCCCchHHHHHHhcCCeEEEeCCccccCCCCC----CCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 046946 492 GCILGQGGHVINEMRRRTQADIRVVGARVKLQDPHP----GSSECIVDIRGSSEHLISAHGTYQSFMT 555 (650)
Q Consensus 492 G~IIGkgG~~IkeI~~~TGA~I~i~~~~~~l~~p~~----~~~er~V~I~G~~e~V~~A~~lI~~~i~ 555 (650)
+..=|++-.++..++.++++++-+..+.-.-.+|+. .+..-+..+-|.++.+..|++++.++..
T Consensus 227 ~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMYI~i~h~~~~g~~~A~r~~~nl~~ 294 (531)
T KOG1960|consen 227 IVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNEGNESNEPMYIFSTHGNGNGENGAPRRKWNLEE 294 (531)
T ss_pred hhccCccchhhhhhhhhhhhhhhhccccccccCcccccccCCceeEEeecCCchhhccchhHHHhHHH
Confidence 455567777888889999988777544312224442 2233456666689999999999988765
Done!