Query 009520
Match_columns 533
No_of_seqs 330 out of 2111
Neff 8.3
Searched_HMMs 46136
Date Thu Mar 28 14:07:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009520.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009520hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2190 PolyC-binding proteins 100.0 1.1E-46 2.3E-51 392.9 35.2 398 5-447 6-412 (485)
2 KOG1676 K-homology type RNA bi 100.0 4.1E-43 8.9E-48 359.1 32.4 334 41-445 52-390 (600)
3 KOG2193 IGF-II mRNA-binding pr 100.0 1.1E-42 2.4E-47 339.2 21.6 355 39-446 195-566 (584)
4 KOG2192 PolyC-binding hnRNP-K 100.0 1.2E-34 2.7E-39 267.8 22.2 346 10-445 19-385 (390)
5 KOG1676 K-homology type RNA bi 100.0 9E-29 1.9E-33 254.0 23.1 231 39-338 135-374 (600)
6 KOG2193 IGF-II mRNA-binding pr 99.9 4.9E-28 1.1E-32 236.9 9.7 243 138-447 197-484 (584)
7 KOG2191 RNA-binding protein NO 99.9 2.9E-26 6.3E-31 218.6 21.4 238 39-322 35-282 (402)
8 KOG2192 PolyC-binding hnRNP-K 99.9 2E-22 4.3E-27 187.0 15.1 151 282-447 46-196 (390)
9 KOG2191 RNA-binding protein NO 99.9 1.5E-21 3.3E-26 186.5 20.1 172 137-447 36-207 (402)
10 KOG2190 PolyC-binding proteins 99.9 8.2E-22 1.8E-26 206.4 20.0 173 284-464 43-225 (485)
11 TIGR03665 arCOG04150 arCOG0415 99.6 1.4E-14 2.9E-19 133.4 9.5 137 47-215 2-152 (172)
12 PRK13763 putative RNA-processi 99.5 1.7E-13 3.6E-18 127.1 13.6 142 43-215 3-158 (180)
13 TIGR03665 arCOG04150 arCOG0415 99.5 8.4E-14 1.8E-18 128.2 9.8 138 288-444 2-151 (172)
14 PRK13763 putative RNA-processi 99.5 3.8E-13 8.2E-18 124.7 11.4 142 284-444 3-157 (180)
15 cd02396 PCBP_like_KH K homolog 99.4 1E-12 2.2E-17 101.0 7.8 64 371-438 1-64 (65)
16 KOG2279 Kinase anchor protein 99.3 1E-11 2.3E-16 127.2 13.0 273 38-340 63-355 (608)
17 cd02396 PCBP_like_KH K homolog 99.3 3.7E-12 8E-17 97.9 7.0 64 141-208 1-64 (65)
18 cd02393 PNPase_KH Polynucleoti 99.2 4.5E-11 9.7E-16 90.3 8.1 58 370-438 2-60 (61)
19 cd02394 vigilin_like_KH K homo 99.2 1.8E-11 3.9E-16 93.2 5.9 61 371-438 1-61 (62)
20 PF00013 KH_1: KH domain syndr 99.2 1.5E-11 3.4E-16 92.9 3.8 60 371-438 1-60 (60)
21 KOG2208 Vigilin [Lipid transpo 99.2 6.4E-11 1.4E-15 131.7 9.0 310 43-445 201-563 (753)
22 cd00105 KH-I K homology RNA-bi 99.1 2.2E-10 4.7E-15 87.7 8.2 62 372-438 2-63 (64)
23 KOG2279 Kinase anchor protein 99.1 1.8E-10 4E-15 118.1 9.9 232 136-442 64-366 (608)
24 cd02394 vigilin_like_KH K homo 99.1 8.1E-11 1.8E-15 89.6 5.4 60 142-208 2-61 (62)
25 PF00013 KH_1: KH domain syndr 99.1 6.4E-11 1.4E-15 89.5 4.1 60 141-208 1-60 (60)
26 cd02393 PNPase_KH Polynucleoti 99.1 2.9E-10 6.3E-15 85.9 7.6 58 140-208 2-60 (61)
27 cd00105 KH-I K homology RNA-bi 99.0 9E-10 1.9E-14 84.2 7.5 62 142-208 2-63 (64)
28 PF13014 KH_3: KH domain 99.0 1.5E-09 3.2E-14 76.0 5.7 42 53-94 1-43 (43)
29 PF13014 KH_3: KH domain 98.9 1.9E-09 4.1E-14 75.4 5.4 43 380-426 1-43 (43)
30 KOG2208 Vigilin [Lipid transpo 98.9 4.6E-09 9.9E-14 117.0 9.6 289 42-445 346-636 (753)
31 smart00322 KH K homology RNA-b 98.8 1.9E-08 4.1E-13 77.5 8.8 67 369-442 2-68 (69)
32 COG1094 Predicted RNA-binding 98.8 1.6E-07 3.4E-12 85.8 13.6 146 41-215 6-165 (194)
33 smart00322 KH K homology RNA-b 98.8 5.2E-08 1.1E-12 75.0 8.7 67 139-212 2-68 (69)
34 KOG2113 Predicted RNA binding 98.6 3.2E-08 7E-13 95.0 4.7 149 282-441 24-180 (394)
35 COG1094 Predicted RNA-binding 98.6 2.2E-07 4.8E-12 84.9 9.9 139 283-445 7-165 (194)
36 cd02395 SF1_like-KH Splicing f 98.4 1.9E-06 4.2E-11 74.1 8.5 67 378-444 14-95 (120)
37 cd02395 SF1_like-KH Splicing f 98.2 5.7E-06 1.2E-10 71.2 8.2 68 148-215 14-96 (120)
38 KOG2113 Predicted RNA binding 98.1 3.5E-06 7.5E-11 81.3 5.9 142 137-336 23-164 (394)
39 TIGR02696 pppGpp_PNP guanosine 98.1 1.1E-05 2.5E-10 88.4 9.4 97 106-214 545-642 (719)
40 PRK08406 transcription elongat 98.1 8.2E-06 1.8E-10 72.3 6.7 102 45-176 34-135 (140)
41 PRK08406 transcription elongat 97.9 5.1E-05 1.1E-09 67.3 8.3 103 284-405 32-134 (140)
42 TIGR02696 pppGpp_PNP guanosine 97.8 6.2E-05 1.3E-09 82.8 8.4 95 339-444 544-642 (719)
43 TIGR03591 polynuc_phos polyrib 97.7 8.8E-05 1.9E-09 82.8 8.4 97 107-214 518-615 (684)
44 KOG0119 Splicing factor 1/bran 97.7 0.00038 8.2E-09 71.7 11.7 77 369-445 137-231 (554)
45 TIGR01952 nusA_arch NusA famil 97.7 7.3E-05 1.6E-09 66.0 5.3 103 44-176 34-136 (141)
46 KOG0336 ATP-dependent RNA heli 97.6 7.9E-05 1.7E-09 75.1 5.2 65 29-96 33-97 (629)
47 PLN00207 polyribonucleotide nu 97.6 0.00015 3.2E-09 81.6 7.6 98 106-214 651-750 (891)
48 COG1185 Pnp Polyribonucleotide 97.5 0.00012 2.6E-09 78.8 6.2 97 107-214 519-616 (692)
49 KOG0119 Splicing factor 1/bran 97.4 0.0013 2.7E-08 68.0 10.9 76 139-214 137-230 (554)
50 TIGR03591 polynuc_phos polyrib 97.3 0.00033 7.1E-09 78.3 6.8 65 369-444 550-615 (684)
51 TIGR01952 nusA_arch NusA famil 97.3 0.00077 1.7E-08 59.6 7.1 102 285-405 34-135 (141)
52 COG1185 Pnp Polyribonucleotide 97.0 0.0011 2.4E-08 71.6 6.7 97 340-447 518-619 (692)
53 COG0195 NusA Transcription elo 97.0 0.0015 3.1E-08 60.8 6.6 102 45-178 78-180 (190)
54 PRK11824 polynucleotide phosph 96.9 0.001 2.2E-08 74.6 5.4 97 107-214 521-618 (693)
55 PLN00207 polyribonucleotide nu 96.9 0.0011 2.3E-08 74.9 5.0 66 368-444 683-750 (891)
56 KOG1588 RNA-binding protein Sa 96.7 0.0018 3.9E-08 62.1 4.7 42 38-79 87-134 (259)
57 cd02134 NusA_KH NusA_K homolog 96.7 0.0034 7.3E-08 47.3 4.7 37 42-78 24-60 (61)
58 KOG0336 ATP-dependent RNA heli 96.6 0.0022 4.9E-08 64.9 4.8 66 369-442 46-111 (629)
59 COG0195 NusA Transcription elo 96.6 0.0065 1.4E-07 56.5 7.5 101 286-406 78-178 (190)
60 KOG1588 RNA-binding protein Sa 96.6 0.0088 1.9E-07 57.5 8.3 76 368-443 90-190 (259)
61 KOG2814 Transcription coactiva 96.4 0.0036 7.8E-08 61.8 4.6 70 139-215 56-126 (345)
62 KOG2814 Transcription coactiva 96.4 0.0033 7.1E-08 62.1 4.3 68 42-123 56-123 (345)
63 TIGR01953 NusA transcription t 96.4 0.0063 1.4E-07 62.1 6.3 96 52-178 243-339 (341)
64 cd02134 NusA_KH NusA_K homolog 96.4 0.0056 1.2E-07 46.1 4.4 36 140-175 25-60 (61)
65 PRK12328 nusA transcription el 96.2 0.0086 1.9E-07 61.2 6.2 96 52-179 251-347 (374)
66 PRK12327 nusA transcription el 96.2 0.0078 1.7E-07 61.9 5.7 96 52-178 245-341 (362)
67 PRK04163 exosome complex RNA-b 96.1 0.013 2.7E-07 57.0 6.2 63 372-445 147-210 (235)
68 TIGR03319 YmdA_YtgF conserved 95.9 0.021 4.6E-07 61.8 7.8 65 369-443 203-269 (514)
69 PRK12704 phosphodiesterase; Pr 95.9 0.023 4.9E-07 61.7 7.8 65 369-443 209-275 (520)
70 PRK00106 hypothetical protein; 95.9 0.026 5.6E-07 60.9 8.1 65 369-443 224-290 (535)
71 PRK00468 hypothetical protein; 95.9 0.0097 2.1E-07 46.6 3.6 34 39-72 26-59 (75)
72 PRK11824 polynucleotide phosph 95.8 0.0071 1.5E-07 67.9 3.9 65 369-444 553-618 (693)
73 PRK12329 nusA transcription el 95.8 0.02 4.4E-07 59.5 6.8 95 52-177 277-372 (449)
74 TIGR01953 NusA transcription t 95.8 0.027 5.9E-07 57.5 7.6 94 293-407 243-338 (341)
75 COG5176 MSL5 Splicing factor ( 95.8 0.023 5E-07 52.3 6.1 42 38-79 143-190 (269)
76 KOG1067 Predicted RNA-binding 95.6 0.022 4.9E-07 59.9 6.2 112 91-214 544-660 (760)
77 COG5176 MSL5 Splicing factor ( 95.6 0.045 9.8E-07 50.4 7.3 41 368-408 146-192 (269)
78 PRK02821 hypothetical protein; 95.5 0.015 3.2E-07 45.8 3.4 35 39-73 27-61 (77)
79 PF14611 SLS: Mitochondrial in 95.5 0.32 7E-06 46.3 13.3 65 140-214 26-90 (210)
80 PRK12328 nusA transcription el 95.4 0.053 1.1E-06 55.6 7.8 97 293-410 251-348 (374)
81 PRK09202 nusA transcription el 95.3 0.021 4.5E-07 60.9 5.0 94 53-178 246-340 (470)
82 PRK12327 nusA transcription el 95.3 0.047 1E-06 56.2 7.4 96 293-408 245-341 (362)
83 PRK02821 hypothetical protein; 95.3 0.033 7.1E-07 43.8 4.7 35 136-170 27-61 (77)
84 PRK00468 hypothetical protein; 95.3 0.019 4.2E-07 44.9 3.4 34 367-400 27-60 (75)
85 COG1837 Predicted RNA-binding 95.1 0.046 9.9E-07 42.7 4.9 33 136-168 26-58 (76)
86 PRK12329 nusA transcription el 95.0 0.053 1.2E-06 56.5 6.5 95 293-407 277-372 (449)
87 PRK04163 exosome complex RNA-b 94.9 0.042 9.1E-07 53.4 5.2 63 142-215 147-210 (235)
88 PRK01064 hypothetical protein; 94.8 0.037 8.1E-07 43.7 3.8 33 40-72 27-59 (78)
89 COG1837 Predicted RNA-binding 94.8 0.034 7.4E-07 43.4 3.5 32 40-71 27-58 (76)
90 TIGR03319 YmdA_YtgF conserved 94.6 0.14 3.1E-06 55.4 8.9 66 139-214 203-270 (514)
91 PRK01064 hypothetical protein; 94.5 0.081 1.8E-06 41.8 5.1 34 136-169 26-59 (78)
92 PRK09202 nusA transcription el 94.4 0.071 1.5E-06 56.9 6.0 93 294-408 246-340 (470)
93 PRK00106 hypothetical protein; 94.3 0.19 4E-06 54.4 9.1 66 139-214 224-291 (535)
94 PRK12704 phosphodiesterase; Pr 94.3 0.16 3.5E-06 55.1 8.7 66 139-214 209-276 (520)
95 PF14611 SLS: Mitochondrial in 93.1 2.3 4.9E-05 40.5 13.3 130 45-215 28-166 (210)
96 PRK12705 hypothetical protein; 92.9 0.15 3.2E-06 54.8 5.3 48 369-426 197-245 (508)
97 KOG4369 RTK signaling protein 92.9 0.12 2.6E-06 58.8 4.5 70 372-445 1342-1411(2131)
98 PF13083 KH_4: KH domain; PDB: 92.5 0.07 1.5E-06 41.6 1.7 35 40-74 26-60 (73)
99 KOG3273 Predicted RNA-binding 91.1 0.1 2.3E-06 47.8 1.4 55 378-444 177-231 (252)
100 KOG1067 Predicted RNA-binding 90.4 0.39 8.4E-06 51.0 4.9 68 366-445 593-661 (760)
101 COG1855 ATPase (PilT family) [ 90.0 0.65 1.4E-05 48.5 6.1 40 140-179 486-525 (604)
102 cd02409 KH-II KH-II (K homolo 89.9 0.52 1.1E-05 35.5 4.2 35 42-76 24-58 (68)
103 KOG2874 rRNA processing protei 89.0 0.7 1.5E-05 44.8 5.1 52 382-445 161-212 (356)
104 PF13083 KH_4: KH domain; PDB: 89.0 0.21 4.6E-06 38.9 1.4 35 137-171 26-60 (73)
105 PRK12705 hypothetical protein; 88.5 1 2.2E-05 48.6 6.5 38 140-177 198-236 (508)
106 cd02409 KH-II KH-II (K homolo 88.3 0.7 1.5E-05 34.8 3.9 35 139-173 24-58 (68)
107 KOG2874 rRNA processing protei 87.5 0.94 2E-05 43.9 4.9 51 152-214 161-211 (356)
108 cd02410 archeal_CPSF_KH The ar 87.3 2.2 4.9E-05 37.7 6.8 94 59-180 22-116 (145)
109 KOG4369 RTK signaling protein 86.8 0.19 4.2E-06 57.2 -0.1 71 140-214 1340-1410(2131)
110 COG1782 Predicted metal-depend 86.2 1.8 3.9E-05 45.8 6.5 97 56-179 42-138 (637)
111 PF13184 KH_5: NusA-like KH do 86.0 0.47 1E-05 36.6 1.7 36 372-407 5-46 (69)
112 COG1097 RRP4 RNA-binding prote 85.9 1.7 3.8E-05 41.6 5.8 58 142-210 148-206 (239)
113 PRK13764 ATPase; Provisional 85.0 2.1 4.6E-05 47.2 6.8 45 138-182 479-523 (602)
114 PF13184 KH_5: NusA-like KH do 84.5 0.54 1.2E-05 36.2 1.4 37 142-178 5-47 (69)
115 COG5166 Uncharacterized conser 84.5 2.2 4.8E-05 45.0 6.2 151 140-405 449-606 (657)
116 cd02414 jag_KH jag_K homology 84.2 1.1 2.4E-05 35.3 3.2 34 371-404 25-58 (77)
117 cd02414 jag_KH jag_K homology 84.2 1 2.3E-05 35.4 3.0 34 141-174 25-58 (77)
118 KOG3273 Predicted RNA-binding 84.0 0.66 1.4E-05 42.7 2.0 56 148-215 177-232 (252)
119 PF07650 KH_2: KH domain syndr 83.5 0.5 1.1E-05 37.2 0.9 34 140-173 25-58 (78)
120 PF07650 KH_2: KH domain syndr 82.9 0.66 1.4E-05 36.6 1.4 33 44-76 26-58 (78)
121 COG1855 ATPase (PilT family) [ 82.2 0.85 1.8E-05 47.7 2.2 36 45-80 488-523 (604)
122 cd02413 40S_S3_KH K homology R 81.8 1.4 3E-05 35.1 2.8 38 44-81 31-68 (81)
123 COG1097 RRP4 RNA-binding prote 81.7 3.6 7.7E-05 39.5 6.0 47 372-429 148-194 (239)
124 PRK13764 ATPase; Provisional 81.4 1.4 3.1E-05 48.5 3.8 44 369-412 480-523 (602)
125 cd02413 40S_S3_KH K homology R 78.8 2.3 5.1E-05 33.8 3.2 36 370-405 30-65 (81)
126 PRK06418 transcription elongat 78.2 3.3 7.1E-05 37.8 4.3 36 142-178 63-98 (166)
127 PRK06418 transcription elongat 78.0 3 6.4E-05 38.0 4.0 33 46-79 64-96 (166)
128 cd02410 archeal_CPSF_KH The ar 77.2 11 0.00024 33.4 7.2 94 299-408 21-114 (145)
129 COG5166 Uncharacterized conser 77.0 6.4 0.00014 41.7 6.5 102 285-433 450-555 (657)
130 TIGR03675 arCOG00543 arCOG0054 72.3 8.9 0.00019 42.9 6.8 96 57-180 37-133 (630)
131 cd02412 30S_S3_KH K homology R 71.2 3.9 8.5E-05 34.5 2.9 30 45-74 63-92 (109)
132 cd02411 archeal_30S_S3_KH K ho 68.8 5.6 0.00012 31.9 3.2 28 45-72 40-67 (85)
133 cd02412 30S_S3_KH K homology R 66.2 4.9 0.00011 34.0 2.5 30 372-401 63-92 (109)
134 cd02411 archeal_30S_S3_KH K ho 65.9 6.3 0.00014 31.6 3.0 28 372-399 40-67 (85)
135 COG0092 RpsC Ribosomal protein 65.6 5.4 0.00012 38.2 2.9 32 42-73 50-81 (233)
136 COG0092 RpsC Ribosomal protein 63.2 6.5 0.00014 37.7 2.9 30 369-398 50-79 (233)
137 TIGR00436 era GTP-binding prot 61.6 9.5 0.00021 37.7 4.0 31 139-169 220-251 (270)
138 COG1782 Predicted metal-depend 59.6 23 0.00049 37.9 6.3 96 297-408 42-137 (637)
139 PRK15494 era GTPase Era; Provi 56.6 13 0.00028 38.3 4.0 29 140-168 273-302 (339)
140 PRK00089 era GTPase Era; Revie 55.7 14 0.00029 37.0 4.0 29 140-168 226-255 (292)
141 COG1159 Era GTPase [General fu 55.5 14 0.0003 36.9 3.8 31 138-168 227-258 (298)
142 TIGR00436 era GTP-binding prot 52.7 16 0.00035 36.1 3.9 31 369-399 220-251 (270)
143 TIGR03675 arCOG00543 arCOG0054 48.6 34 0.00074 38.3 6.0 95 298-408 37-131 (630)
144 PRK15494 era GTPase Era; Provi 46.9 22 0.00048 36.5 4.0 30 369-398 272-302 (339)
145 KOG1423 Ras-like GTPase ERA [C 46.5 19 0.00041 36.2 3.1 34 137-170 325-359 (379)
146 PRK00089 era GTPase Era; Revie 43.8 26 0.00057 34.9 3.9 31 369-399 225-256 (292)
147 COG1159 Era GTPase [General fu 43.7 28 0.0006 34.8 3.8 34 366-399 225-259 (298)
148 KOG1423 Ras-like GTPase ERA [C 40.5 29 0.00063 34.9 3.4 36 364-399 322-358 (379)
149 PRK03818 putative transporter; 40.3 3.4E+02 0.0075 29.9 12.1 133 45-207 207-358 (552)
150 CHL00048 rps3 ribosomal protei 38.6 33 0.00072 32.8 3.4 31 43-73 66-96 (214)
151 TIGR01008 rpsC_E_A ribosomal p 38.2 35 0.00075 32.1 3.4 30 44-73 39-68 (195)
152 PRK04191 rps3p 30S ribosomal p 37.9 34 0.00074 32.5 3.4 31 45-75 42-72 (207)
153 KOG0921 Dosage compensation co 36.3 68 0.0015 37.0 5.7 15 372-386 1086-1100(1282)
154 TIGR01008 rpsC_E_A ribosomal p 36.1 36 0.00078 32.0 3.2 29 371-399 39-67 (195)
155 COG0490 Putative regulatory, l 36.0 52 0.0011 29.8 4.0 61 374-439 92-158 (162)
156 COG1847 Jag Predicted RNA-bind 34.8 37 0.00081 32.0 3.0 37 369-405 90-126 (208)
157 PTZ00084 40S ribosomal protein 34.8 40 0.00086 32.3 3.3 31 45-75 46-76 (220)
158 COG1847 Jag Predicted RNA-bind 34.6 36 0.00079 32.1 2.9 37 139-175 90-126 (208)
159 PRK04191 rps3p 30S ribosomal p 34.1 39 0.00085 32.1 3.1 30 372-401 42-71 (207)
160 PF09869 DUF2096: Uncharacteri 33.3 1.3E+02 0.0027 27.4 5.9 58 137-212 110-167 (169)
161 PTZ00084 40S ribosomal protein 33.0 40 0.00086 32.3 3.0 30 371-400 45-74 (220)
162 TIGR03802 Asp_Ala_antiprt aspa 33.0 4.9E+02 0.011 28.8 11.9 62 141-208 304-376 (562)
163 CHL00048 rps3 ribosomal protei 32.9 42 0.00092 32.0 3.2 30 370-399 66-95 (214)
164 COG1702 PhoH Phosphate starvat 30.7 1.1E+02 0.0025 31.2 5.9 51 377-439 22-72 (348)
165 PF10369 ALS_ss_C: Small subun 25.6 1.4E+02 0.003 23.2 4.4 42 390-440 17-58 (75)
166 cd07055 BMC_like_2 Bacterial M 25.1 2.1E+02 0.0046 21.4 4.9 39 397-440 21-59 (61)
167 TIGR01009 rpsC_bact ribosomal 23.5 79 0.0017 30.1 3.2 28 45-72 64-91 (211)
168 PRK15468 carboxysome structura 23.0 2.1E+02 0.0046 24.0 5.1 38 169-215 63-100 (111)
169 TIGR01009 rpsC_bact ribosomal 22.2 78 0.0017 30.2 2.9 28 372-399 64-91 (211)
170 COG4010 Uncharacterized protei 20.1 3.3E+02 0.0071 24.2 5.9 43 160-213 126-168 (170)
No 1
>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=1.1e-46 Score=392.90 Aligned_cols=398 Identities=40% Similarity=0.617 Sum_probs=313.0
Q ss_pred CCcCCCCCCCCCCCCCCCCCccccCCCCCCCcccCCCceEEEEEecCCccceeecCCcHHHHHHHHHhCCeEEEcCCCCC
Q 009520 5 RNSYGKRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPG 84 (533)
Q Consensus 5 ~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~ 84 (533)
|....++........+++..+++...+..... ..+...+|||||+.+.+|.||||+|.+||+||.+|.++|+|.+..++
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~ 84 (485)
T KOG2190|consen 6 RGLPRPKNSTTSNVGDNGSIKRPSLGDPVIST-GPDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPG 84 (485)
T ss_pred ccCccccCCCcccccCCCcccccCCCCCcccC-CCCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCC
Confidence 44455666666777666666665555543333 44444459999999999999999999999999999999999999999
Q ss_pred CCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHHHhh---ccCCCC---CCCCCceEEEEEecCCceeeeeccC
Q 009520 85 SEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEE---LRGDED---SDGGHQVTAKLLVPSDQIGCVIGKG 158 (533)
Q Consensus 85 ~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~---~~~~~~---~~~~~~~~~~llVp~~~~g~IIGk~ 158 (533)
|.||+|+|+|...+ ..++++++|++++++.+.... .....+ +.....++++||||.+++|+||||+
T Consensus 85 c~eRIiti~g~~~~--------~~~~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~ 156 (485)
T KOG2190|consen 85 CPERIITITGNRVE--------LNLSPATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKG 156 (485)
T ss_pred CCcceEEEeccccc--------ccCCchHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccC
Confidence 99999999997322 168889999999999988631 111111 1222368999999999999999999
Q ss_pred chHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCccccccccccCCCC---CCC
Q 009520 159 GQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHS---SSG 235 (533)
Q Consensus 159 G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~s~~~~~~~---~gg 235 (533)
|+.||+|+++|||+|+|.++ .+|. +++|.|+|.|.+++|.+|+..|..+|+++..+....+.+..+ .+| .++
T Consensus 157 G~~Ik~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~-y~P~~~~~~ 231 (485)
T KOG2190|consen 157 GSLIKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIP-YRPSASQGG 231 (485)
T ss_pred cHHHHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCccc-CCCcccccC
Confidence 99999999999999999987 8887 578999999999999999999999999976553332222211 000 000
Q ss_pred CCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEeeecCccccccccCchhhHhhhhhcCC
Q 009520 236 SLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGA 315 (533)
Q Consensus 236 ~~~~p~~~~~~~~~~p~~~~~g~~~~d~~~~~~~~~~~~p~~~~~~~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~tga 315 (533)
.+... ++ ...+ .+.++.....+.++..++.+|...++.|+|++|..|+.|+.++++
T Consensus 232 ~~~~s---------------~~-------~~~~--~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~ 287 (485)
T KOG2190|consen 232 PVLPS---------------TA-------QTSP--DAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGA 287 (485)
T ss_pred ccccc---------------cc-------cCCc--ccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCC
Confidence 00000 00 0000 111222234456778899999999999999999999999999999
Q ss_pred eEEecCCCCCCCceeEEecCcchhhhhhhHHHHHHHHhCcccccccccccCCcceeEEEeecCCceeEEecCCChhHHHH
Q 009520 316 AIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEM 395 (533)
Q Consensus 316 ~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~~G~IIGkgG~~Ik~I 395 (533)
.|.+.....+ |+++++..+..++.++++++++++.++++.+....+. ...++.+|+||.+++||||||+|.+|.+|
T Consensus 288 ~i~v~~~~~~---~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~-~~~v~~~l~vps~~igciiGk~G~~isei 363 (485)
T KOG2190|consen 288 SISVGDSRTD---RIVTISARENPEDRYSMAQEALLLVQPRISENAGDDL-TQTVTQRLLVPSDLIGCIIGKGGAKISEI 363 (485)
T ss_pred ceEeccccCc---ceeeeccccCcccccccchhhhhhccccccccccccc-cceeeeeeccCccccceeecccccchHHH
Confidence 9999987654 9999999999999999999999999999887766555 67899999999999999999999999999
Q ss_pred HHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhccc
Q 009520 396 RRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLF 447 (533)
Q Consensus 396 ~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~~~ 447 (533)
|+.|||.|+|..+++. ...++++++|+|+..+...|..++..++.....
T Consensus 364 r~~tgA~I~I~~~~~~---~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~~ 412 (485)
T KOG2190|consen 364 RQRTGASISILNKEEV---SGVREALVQITGMLREDLLAQYLIRARLSAPKS 412 (485)
T ss_pred HHhcCCceEEcccccc---CCcceeEEEecchhHHHHhhhhhcccccccCcc
Confidence 9999999999887653 247899999999999999999999877765543
No 2
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=4.1e-43 Score=359.09 Aligned_cols=334 Identities=20% Similarity=0.376 Sum_probs=252.7
Q ss_pred CceEEEEEecCCccceeecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHH
Q 009520 41 EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVH 120 (533)
Q Consensus 41 ~~~~~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~ 120 (533)
..++-+..||.+++|+||||+|+.|..|..+++|+|.+.....+..+|-+.++|.+++++ .|. .++
T Consensus 52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~-------------~aK-~li 117 (600)
T KOG1676|consen 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVE-------------VAK-QLI 117 (600)
T ss_pred cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHH-------------HHH-Hhh
Confidence 556788999999999999999999999999999999988777778899999999999852 232 222
Q ss_pred HHHHHhhcc--CCCCCCCCCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcCH
Q 009520 121 DRVIAEELR--GDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198 (533)
Q Consensus 121 ~~i~~~~~~--~~~~~~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~ 198 (533)
..+...... ...+......++..|+||.+.+|.||||+|+|||.|+++|||++.+..+..... ..++.+.|+|++
T Consensus 118 ~evv~r~~~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~---~~~KplritGdp 194 (600)
T KOG1676|consen 118 GEVVSRGRPPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIAT---GADKPLRITGDP 194 (600)
T ss_pred hhhhhccCCCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCC---CCCCceeecCCH
Confidence 222222211 111222356789999999999999999999999999999999999998755433 478899999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009520 199 SVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDD 278 (533)
Q Consensus 199 ~~V~~A~~~I~~~l~~~~~~~~~~~~s~~~~~~~~gg~~~~p~~~~~~~~~~p~~~~~g~~~~d~~~~~~~~~~~~p~~~ 278 (533)
+.|+.|..+|.++|++... ..+..+++ +|..
T Consensus 195 ~~ve~a~~lV~dil~e~~~-----------~~~g~~~~-------------------~g~~------------------- 225 (600)
T KOG1676|consen 195 DKVEQAKQLVADILREEDD-----------EVPGSGGH-------------------AGVR------------------- 225 (600)
T ss_pred HHHHHHHHHHHHHHHhccc-----------CCCccccc-------------------cCcC-------------------
Confidence 9999999999999996311 01111100 0000
Q ss_pred CCCceEEEEEeeecCccccccccCchhhHhhhhhcCCeEEecCCCC-CCCceeEEecCcchhhhhhhHHHHHHHHhCccc
Q 009520 279 LSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSST-EGDDCLITVSSKEFFEDTLSATIEAVVRLQPRC 357 (533)
Q Consensus 279 ~~~~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~-~~~ervi~I~G~~~~~~~~~~~~~a~~~~~~~~ 357 (533)
.....+++|.||...||.||||+|++||+|+.+||++|+|..++. ...||++.|.|....-....+.+.+++......
T Consensus 226 -~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~ 304 (600)
T KOG1676|consen 226 -GGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAG 304 (600)
T ss_pred -ccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhcc
Confidence 011238899999999999999999999999999999999987654 678999999997542222122333332221111
Q ss_pred ccccccccCCcce--eEEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHH
Q 009520 358 SEKIERDSGLISF--TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDAL 435 (533)
Q Consensus 358 ~~~~~~~~~~~~~--~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~ 435 (533)
. ......+.... .+.|.||.+.||+||||||++||.|.++|||++.+.+. |+..+..+++|+|.|++.+|+.|+
T Consensus 305 ~-~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~---~p~~~~~ektf~IrG~~~QIdhAk 380 (600)
T KOG1676|consen 305 A-GGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ---PPNGNPKEKTFVIRGDKRQIDHAK 380 (600)
T ss_pred C-CCCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC---CCCCCccceEEEEecCcccchHHH
Confidence 0 00000111223 78899999999999999999999999999999998543 556778899999999999999999
Q ss_pred HHHHHHHHhc
Q 009520 436 IQVMTRLRAN 445 (533)
Q Consensus 436 ~~I~~~l~~~ 445 (533)
.||..++.+.
T Consensus 381 ~LIr~kvg~~ 390 (600)
T KOG1676|consen 381 QLIRDKVGDI 390 (600)
T ss_pred HHHHHHhccc
Confidence 9999999764
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=1.1e-42 Score=339.19 Aligned_cols=355 Identities=23% Similarity=0.387 Sum_probs=269.8
Q ss_pred CCCceEEEEEecCCccceeecCCcHHHHHHHHHhCCeEEEcC-CCCCCCceEEEEEcCCccccccccCcccCCHHHHHHH
Q 009520 39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE-TVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALF 117 (533)
Q Consensus 39 ~~~~~~~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~-~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~ 117 (533)
...++.+|+|||..++|.||||.|.|||.|...|.|+|+|.. ...|..|++|+|.|.+|. +.+|+.
T Consensus 195 q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg-------------~s~Ac~ 261 (584)
T KOG2193|consen 195 QLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG-------------TSKACK 261 (584)
T ss_pred cccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc-------------hHHHHH
Confidence 466778999999999999999999999999999999999974 456889999999999998 457888
Q ss_pred HHHHHHHHhhccCCCCCCCCCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcC
Q 009520 118 KVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGE 197 (533)
Q Consensus 118 ~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~ 197 (533)
+|++.|-.+.... .....+.++++.++..||+||||.|.+||+|+.+||++|.|++-.++.. ...+|++++.|+
T Consensus 262 ~ILeimqkEA~~~----k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~--ynpERTItVkGs 335 (584)
T KOG2193|consen 262 MILEIMQKEAVDD----KVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSL--YNPERTITVKGS 335 (584)
T ss_pred HHHHHHHHhhhcc----chhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcc--cCccceEEeccc
Confidence 8888766554332 3346788999999999999999999999999999999999998776654 367999999999
Q ss_pred HHHHHHHHHHHHHHHhcCCCCcccc------ccccc----cCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCC
Q 009520 198 ASVVKKALCQIASRLHDNPSRSQHL------LASAI----SNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDW 267 (533)
Q Consensus 198 ~~~V~~A~~~I~~~l~~~~~~~~~~------~~s~~----~~~~~~gg~~~~p~~~~~~~~~~p~~~~~g~~~~d~~~~~ 267 (533)
.|+|..|..+|..+|+++...+... +.+.. .+.|++......| .+.+..+ ..+..+
T Consensus 336 iEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~P------h~~Ps~v--------~~a~p~ 401 (584)
T KOG2193|consen 336 IEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPP------HFPPSPV--------TFASPY 401 (584)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCC------CCCCCcc--------ccCCCc
Confidence 9999999999999999976554211 11000 0111111101001 0000000 000111
Q ss_pred CCCCCCCCCCCCCCceEEEEEeeecCccccccccCchhhHhhhhhcCCeEEecCCC-CCCCceeEEecCcchhhhhhhHH
Q 009520 268 SRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSS-TEGDDCLITVSSKEFFEDTLSAT 346 (533)
Q Consensus 268 ~~~~~~~p~~~~~~~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~-~~~~ervi~I~G~~~~~~~~~~~ 346 (533)
+ + .....+...++|.||...+|.|||++|.+||+|...+||.|+|..+. ++..+|+++|+|.+
T Consensus 402 ~--~-----~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGpp--------- 465 (584)
T KOG2193|consen 402 P--L-----FHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPP--------- 465 (584)
T ss_pred h--h-----hhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCCh---------
Confidence 1 1 11123456889999999999999999999999999999999998754 55788999999965
Q ss_pred HHHHHHhCcccccccccc-----cCCcceeEEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcE
Q 009520 347 IEAVVRLQPRCSEKIERD-----SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEM 421 (533)
Q Consensus 347 ~~a~~~~~~~~~~~~~~~-----~~~~~~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~ 421 (533)
++.++.+.++..++.++ .....+...+.||...+|+||||||.+++||+..|+|.+.|+.. +.|. ..+.-+
T Consensus 466 -eaqfKAQgrifgKikEenf~~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrd-qtpd--End~vi 541 (584)
T KOG2193|consen 466 -EAQFKAQGRIFGKIKEENFFLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRD-QTPD--ENDQVI 541 (584)
T ss_pred -HHHHhhhhhhhhhhhhhccCCchhhheeeeeeeccchhhhhhhccccccHHHHhccccceEEcccc-CCCC--ccceee
Confidence 34455555554444332 22356788999999999999999999999999999999999654 4453 234457
Q ss_pred EEEEeCHHHHHHHHHHHHHHHHhcc
Q 009520 422 VQISGDLDLAKDALIQVMTRLRANL 446 (533)
Q Consensus 422 V~I~G~~~~v~~A~~~I~~~l~~~~ 446 (533)
|.|+|...+.+.|...|.+++.+..
T Consensus 542 vriiGhfyatq~aQrki~~iv~qvk 566 (584)
T KOG2193|consen 542 VRIIGHFYATQNAQRKIAHIVNQVK 566 (584)
T ss_pred eeeechhhcchHHHHHHHHHHHHHH
Confidence 8999999999999999999988754
No 4
>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=1.2e-34 Score=267.77 Aligned_cols=346 Identities=19% Similarity=0.303 Sum_probs=224.6
Q ss_pred CCCCCCCCCCCCCCCccccCCCCCCCcccCCCceEEEEEecCCccceeecCCcHHHHHHHHHhCCeEEEcCCCCCCCceE
Q 009520 10 KRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERV 89 (533)
Q Consensus 10 ~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~erv 89 (533)
||.|+..+.++. .+|...+ .+..++....+.+|||+.++.+|+||||+|++||+|+.+++|+|.|++. ..++|+
T Consensus 19 ~~~~~~e~g~~~---gkrp~~d-~~~qa~k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri 92 (390)
T KOG2192|consen 19 ETFPNTETGGEF---GKRPAED-MEEQAFKRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERI 92 (390)
T ss_pred hcCCCCcccccc---cCCcchh-hHHHHhhhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCcee
Confidence 455554444333 3555444 4556688889999999999999999999999999999999999999987 788999
Q ss_pred EEEEcCCccccccccCcccCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEecCCceeeeeccCchHHHHHHhhc
Q 009520 90 VTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSET 169 (533)
Q Consensus 90 v~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~t 169 (533)
++|+...+. .-+-|.+|+..+.+. ....+.+.++|||+.+++|.|||++|++||+|++++
T Consensus 93 ~tisad~~t-------------i~~ilk~iip~lee~-------f~~~~pce~rllihqs~ag~iigrngskikelrekc 152 (390)
T KOG2192|consen 93 LTISADIET-------------IGEILKKIIPTLEEG-------FQLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKC 152 (390)
T ss_pred EEEeccHHH-------------HHHHHHHHhhhhhhC-------CCCCCchhhhhhhhhhhccceecccchhHHHHHHhh
Confidence 999987432 223333343333221 135567999999999999999999999999999999
Q ss_pred CceEEEeecCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCcccc-ccccc-cCCCCCCCCCCC--------
Q 009520 170 GAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHL-LASAI-SNSHSSSGSLVG-------- 239 (533)
Q Consensus 170 ga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~-~~s~~-~~~~~~gg~~~~-------- 239 (533)
.|+++|... .|.+++||+|.|.|.+..|..+++.|.++|.+.+-+.... ..+.. ...|..||..|.
T Consensus 153 sarlkift~----c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~p 228 (390)
T KOG2192|consen 153 SARLKIFTE----CCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRP 228 (390)
T ss_pred hhhhhhhhc----cCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCC
Confidence 999999874 5778999999999999999999999999999987765432 11111 111223332111
Q ss_pred -CCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEeeecCccccccccCchhhHhhhhhcCCeEE
Q 009520 240 -PTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIK 318 (533)
Q Consensus 240 -p~~~~~~~~~~p~~~~~g~~~~d~~~~~~~~~~~~p~~~~~~~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~ 318 (533)
|.+..+.++.+|..+++++. +-++|..= +.+--.+.
T Consensus 229 gpapqrggqgpp~~~~sdlma---------------------------------------y~r~GrpG----~rydg~vd 265 (390)
T KOG2192|consen 229 GPAPQRGGQGPPPPRGSDLMA---------------------------------------YDRRGRPG----DRYDGMVD 265 (390)
T ss_pred CCCCCCCCCCCCCCCccccce---------------------------------------eccCCCCC----cccccccc
Confidence 11111111111111111100 00000000 00000001
Q ss_pred ecCCCCCCCceeEEecCcchhhhhhhHHHHHHHHhCcccc----------cccccccCCcceeEEEeecCCceeEEecCC
Q 009520 319 VDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCS----------EKIERDSGLISFTTRLLVPTSRIGCLIGKG 388 (533)
Q Consensus 319 i~~~~~~~~ervi~I~G~~~~~~~~~~~~~a~~~~~~~~~----------~~~~~~~~~~~~~~~l~Vp~~~~G~IIGkg 388 (533)
++..... +..+-+-..+ +......+.-. ...-.+.+....|.++.||.++-|.||||+
T Consensus 266 Fs~detw-~saidtw~~S-----------ewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkg 333 (390)
T KOG2192|consen 266 FSADETW-PSAIDTWSPS-----------EWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKG 333 (390)
T ss_pred ccccccC-CCcCCCcCcc-----------ccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceeccc
Confidence 1110000 0000000000 00000101000 001123344578899999999999999999
Q ss_pred ChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhc
Q 009520 389 GSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN 445 (533)
Q Consensus 389 G~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~ 445 (533)
|++|++|+.++||.|+|.. | ..++.+|+++|+|+.++++.|..++...++..
T Consensus 334 gqri~~ir~esGA~Ikide----p-leGsedrIitItGTqdQIqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 334 GQRIKQIRHESGASIKIDE----P-LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY 385 (390)
T ss_pred chhhhhhhhccCceEEecC----c-CCCCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence 9999999999999999964 2 24678999999999999999999999998854
No 5
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.96 E-value=9e-29 Score=253.98 Aligned_cols=231 Identities=27% Similarity=0.439 Sum_probs=180.3
Q ss_pred CCCceEEEEEecCCccceeecCCcHHHHHHHHHhCCeEEEcCC--CCCCCceEEEEEcCCccccccccCcccCCHHHHHH
Q 009520 39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGET--VPGSEERVVTVYSASDETNAFEDGDKFVSPAQDAL 116 (533)
Q Consensus 39 ~~~~~~~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~--~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~ 116 (533)
+...++..|+||.+++|+||||+|++||+|++++||++.+..+ ......+.+.|+|.++.+ +.|.
T Consensus 135 ~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~v-------------e~a~ 201 (600)
T KOG1676|consen 135 GSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKV-------------EQAK 201 (600)
T ss_pred CccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHH-------------HHHH
Confidence 3678899999999999999999999999999999999987644 222367899999998874 4566
Q ss_pred HHHHHHHHHhhccCCCC-----CCCCCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCce
Q 009520 117 FKVHDRVIAEELRGDED-----SDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDEL 191 (533)
Q Consensus 117 ~~i~~~i~~~~~~~~~~-----~~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~ 191 (533)
.++++.|.++.-..... .......+++|.||.+.||.||||+|++||+|+.+|||||+|.++++ | .+.+|.
T Consensus 202 ~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~-p---~speR~ 277 (600)
T KOG1676|consen 202 QLVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD-P---SSPERP 277 (600)
T ss_pred HHHHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCC-C---CCccce
Confidence 66777665433221111 12233458999999999999999999999999999999999988754 3 367999
Q ss_pred EEEEcCHHHHHHHHHHHHHHHhcCCCCccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCC
Q 009520 192 VQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSL 271 (533)
Q Consensus 192 v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~s~~~~~~~~gg~~~~p~~~~~~~~~~p~~~~~g~~~~d~~~~~~~~~ 271 (533)
+.|.|+.+.|+.|.++|.++|.+..... .+++.+ |
T Consensus 278 ~~IiG~~d~ie~Aa~lI~eii~~~~~~~-------------~~~~~~-------------------G------------- 312 (600)
T KOG1676|consen 278 AQIIGTVDQIEHAAELINEIIAEAEAGA-------------GGGMGG-------------------G------------- 312 (600)
T ss_pred eeeecCHHHHHHHHHHHHHHHHHHhccC-------------CCCcCC-------------------C-------------
Confidence 9999999999999999999998741100 000000 0
Q ss_pred CCCCCCCCCCceEEEEEeeecCccccccccCchhhHhhhhhcCCeEEecCCCC--CCCceeEEecCcch
Q 009520 272 YSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSST--EGDDCLITVSSKEF 338 (533)
Q Consensus 272 ~~~p~~~~~~~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~--~~~ervi~I~G~~~ 338 (533)
.|. .-..+.|.||.+.+|+|||++|++||.|..+|||++.+.+..+ +..+++|+|.|.+.
T Consensus 313 --~P~-----~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG~~~ 374 (600)
T KOG1676|consen 313 --APG-----LVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGDKR 374 (600)
T ss_pred --Ccc-----ceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEecCcc
Confidence 000 0116789999999999999999999999999999999998732 35789999999764
No 6
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.95 E-value=4.9e-28 Score=236.90 Aligned_cols=243 Identities=23% Similarity=0.383 Sum_probs=190.6
Q ss_pred CceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCC
Q 009520 138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPS 217 (533)
Q Consensus 138 ~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~ 217 (533)
....+|+|||..++|.||||.|+|||.|...|.++|+|...++. +..|+.++|-|++|...+|+++|++++.....
T Consensus 197 ~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~----Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~ 272 (584)
T KOG2193|consen 197 KDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENA----GAAEKIITVHSTPEGTSKACKMILEIMQKEAV 272 (584)
T ss_pred cCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccC----CcccCceEEecCccchHHHHHHHHHHHHHhhh
Confidence 34779999999999999999999999999999999999987653 56899999999999999999999999987532
Q ss_pred CccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEeeecCcccc
Q 009520 218 RSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGG 297 (533)
Q Consensus 218 ~~~~~~~s~~~~~~~~gg~~~~p~~~~~~~~~~p~~~~~g~~~~d~~~~~~~~~~~~p~~~~~~~~~~~~v~vp~~~~g~ 297 (533)
+. ....++.++++-.+.++|+
T Consensus 273 ~~-----------------------------------------------------------k~~~e~pLk~lAHN~lvGR 293 (584)
T KOG2193|consen 273 DD-----------------------------------------------------------KVAEEIPLKILAHNNLVGR 293 (584)
T ss_pred cc-----------------------------------------------------------chhhhcchhhhhhcchhhh
Confidence 21 1235678899999999999
Q ss_pred ccccCchhhHhhhhhcCCeEEecCCC---CCCCceeEEecCcc-hhh-------hhhhHHHHHHH---HhCcccccc---
Q 009520 298 VIGKGGAIINQIRQESGAAIKVDSSS---TEGDDCLITVSSKE-FFE-------DTLSATIEAVV---RLQPRCSEK--- 360 (533)
Q Consensus 298 IIGk~G~~Ik~i~~~tga~I~i~~~~---~~~~ervi~I~G~~-~~~-------~~~~~~~~a~~---~~~~~~~~~--- 360 (533)
+|||.|.+||+|+++||++|.|++-. .-.+||+|++.|+- .+. +.+.++.|.-+ .++..+...
T Consensus 294 LIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~ 373 (584)
T KOG2193|consen 294 LIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNL 373 (584)
T ss_pred hhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCc
Confidence 99999999999999999999999742 22479999999942 111 11111222111 111111000
Q ss_pred -----------cccc-----------------cCCcceeEEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCC
Q 009520 361 -----------IERD-----------------SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLP 412 (533)
Q Consensus 361 -----------~~~~-----------------~~~~~~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P 412 (533)
.... .......++|.||...+|.||||+|..||.|-+.+||.|+|...
T Consensus 374 ~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIapp---- 449 (584)
T KOG2193|consen 374 PALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPP---- 449 (584)
T ss_pred cccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCC----
Confidence 0000 01135678999999999999999999999999999999999754
Q ss_pred CCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhccc
Q 009520 413 KIASEDDEMVQISGDLDLAKDALIQVMTRLRANLF 447 (533)
Q Consensus 413 ~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~~~ 447 (533)
..++..+|+|+|+|++++.-+|.-.|..+|+++.+
T Consensus 450 E~pdvseRMViItGppeaqfKAQgrifgKikEenf 484 (584)
T KOG2193|consen 450 EIPDVSERMVIITGPPEAQFKAQGRIFGKIKEENF 484 (584)
T ss_pred CCCCcceeEEEecCChHHHHhhhhhhhhhhhhhcc
Confidence 34468899999999999999999999999988754
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=2.9e-26 Score=218.58 Aligned_cols=238 Identities=25% Similarity=0.396 Sum_probs=174.4
Q ss_pred CCCceEEEEEecCCccceeecCCcHHHHHHHHHhCCeEEEcCC---CCCCCceEEEEEcCCccccccccCcccCCHHHHH
Q 009520 39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGET---VPGSEERVVTVYSASDETNAFEDGDKFVSPAQDA 115 (533)
Q Consensus 39 ~~~~~~~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~---~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a 115 (533)
.++.+.+++|||+..+|+||||+|++|.+|+++|||+|++++. +|+++||+|.|.|..+++ ..-
T Consensus 35 e~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai-------------~av 101 (402)
T KOG2191|consen 35 EDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEAL-------------NAV 101 (402)
T ss_pred CCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHH-------------HHH
Confidence 3444899999999999999999999999999999999999854 899999999999996653 233
Q ss_pred HHHHHHHHHHhhccCCC-CC-----CCCCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEee-cCCCCcccCCC
Q 009520 116 LFKVHDRVIAEELRGDE-DS-----DGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILK-DEHLPSCALRS 188 (533)
Q Consensus 116 ~~~i~~~i~~~~~~~~~-~~-----~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~-~~~~p~~~~~~ 188 (533)
+..|.++|.+....... .+ ..+..-.++++||++.+|.||||+|++||.|++++||-|+|++ ++. -..-.
T Consensus 102 ~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt---~~sLq 178 (402)
T KOG2191|consen 102 HEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPT---GISLQ 178 (402)
T ss_pred HHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCC---Cccce
Confidence 44556666654332222 11 1122245999999999999999999999999999999999984 322 22357
Q ss_pred CceEEEEcCHHHHHHHHHHHHHHHhcCCCCccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCC
Q 009520 189 DELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWS 268 (533)
Q Consensus 189 dr~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~s~~~~~~~~gg~~~~p~~~~~~~~~~p~~~~~g~~~~d~~~~~~ 268 (533)
+|+|++.|++++..+|+.+|.++|.+++...+++..+.. +..| |.. -..|-..+|.. .++
T Consensus 179 ervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya---~vsG-----pva-----NsnPtGspya~-~~~------ 238 (402)
T KOG2191|consen 179 ERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYA---NVSG-----PVA-----NSNPTGSPYAY-QAH------ 238 (402)
T ss_pred eEEEEecCCHHHHHHHHHHHHHHhhcCCcccceeccchh---cccC-----ccc-----ccCCCCCCCCC-CCc------
Confidence 999999999999999999999999999887766553221 1111 110 01111111111 111
Q ss_pred CCCCCCCCCCCCCceEEEEEeeecCccccccccCchhhHhhhhhcCCeEEecCC
Q 009520 269 RSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSS 322 (533)
Q Consensus 269 ~~~~~~p~~~~~~~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~ 322 (533)
..+...+....++....|..-|.+|.++-.|-.-+|+.+.++..
T Consensus 239 ----------~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~ 282 (402)
T KOG2191|consen 239 ----------VLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQA 282 (402)
T ss_pred ----------cccccchhhccccccccccccccccccceeeecccccceeeccc
Confidence 01222355667888899999999999999999999998888764
No 8
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.89 E-value=2e-22 Score=186.98 Aligned_cols=151 Identities=27% Similarity=0.422 Sum_probs=124.5
Q ss_pred ceEEEEEeeecCccccccccCchhhHhhhhhcCCeEEecCCCCCCCceeEEecCcchhhhhhhHHHHHHHHhCccccccc
Q 009520 282 KEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKI 361 (533)
Q Consensus 282 ~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~ 361 (533)
..+.+++++.++.+|.||||+|++||+|+.+++|+|.|++.. .++++++|++.+. -..+-+..+.+.+.+..
T Consensus 46 ~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~--~peri~tisad~~------ti~~ilk~iip~lee~f 117 (390)
T KOG2192|consen 46 SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSS--GPERILTISADIE------TIGEILKKIIPTLEEGF 117 (390)
T ss_pred cceeEEEEEecccccceeccccccHHHHhhhccceeeccCCC--CCceeEEEeccHH------HHHHHHHHHhhhhhhCC
Confidence 347999999999999999999999999999999999999854 5899999998542 12223333444444332
Q ss_pred ccccCCcceeEEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHH
Q 009520 362 ERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTR 441 (533)
Q Consensus 362 ~~~~~~~~~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~~ 441 (533)
. ....+.++|+|+++++|.|||++|++||++|+...|+++|--. +.| ++++|+|.|.|.+..|..+++.|++.
T Consensus 118 ~---~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~-c~p---~stdrv~l~~g~~k~v~~~i~~il~~ 190 (390)
T KOG2192|consen 118 Q---LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE-CCP---HSTDRVVLIGGKPKRVVECIKIILDL 190 (390)
T ss_pred C---CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc-cCC---CCcceEEEecCCcchHHHHHHHHHHH
Confidence 2 2346889999999999999999999999999999999998653 434 69999999999999999999999999
Q ss_pred HHhccc
Q 009520 442 LRANLF 447 (533)
Q Consensus 442 l~~~~~ 447 (533)
|.+..+
T Consensus 191 i~e~pi 196 (390)
T KOG2192|consen 191 ISESPI 196 (390)
T ss_pred hhcCCc
Confidence 988654
No 9
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.88 E-value=1.5e-21 Score=186.47 Aligned_cols=172 Identities=26% Similarity=0.443 Sum_probs=138.7
Q ss_pred CCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCC
Q 009520 137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNP 216 (533)
Q Consensus 137 ~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~ 216 (533)
...+.++||||+..+|.||||+|++|.+++.+|||+|++++..++.+ +.+||+|.|+|+.+++...+..|.++|++.+
T Consensus 36 ~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyP--GTTeRvcli~Gt~eai~av~efI~dKire~p 113 (402)
T KOG2191|consen 36 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYP--GTTERVCLIQGTVEALNAVHEFIADKIREKP 113 (402)
T ss_pred CCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCC--CccceEEEEeccHHHHHHHHHHHHHHHHHhH
Confidence 34589999999999999999999999999999999999998766444 5899999999999999999999999999842
Q ss_pred CCccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEeeecCccc
Q 009520 217 SRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIG 296 (533)
Q Consensus 217 ~~~~~~~~s~~~~~~~~gg~~~~p~~~~~~~~~~p~~~~~g~~~~d~~~~~~~~~~~~p~~~~~~~~~~~~v~vp~~~~g 296 (533)
...
T Consensus 114 ~~~----------------------------------------------------------------------------- 116 (402)
T KOG2191|consen 114 QAV----------------------------------------------------------------------------- 116 (402)
T ss_pred Hhh-----------------------------------------------------------------------------
Confidence 110
Q ss_pred cccccCchhhHhhhhhcCCeEEecCCCCCCCceeEEecCcchhhhhhhHHHHHHHHhCcccccccccccCCcceeEEEee
Q 009520 297 GVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLV 376 (533)
Q Consensus 297 ~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l~V 376 (533)
.+ -+.+..+ ..++| .-.+++.|
T Consensus 117 ----------------~k-~v~~~~p--qt~~r---------------------------------------~kqikivv 138 (402)
T KOG2191|consen 117 ----------------AK-PVDILQP--QTPDR---------------------------------------IKQIKIVV 138 (402)
T ss_pred ----------------cC-CccccCC--CCccc---------------------------------------cceeEEec
Confidence 00 0000000 00111 12267999
Q ss_pred cCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhccc
Q 009520 377 PTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLF 447 (533)
Q Consensus 377 p~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~~~ 447 (533)
|.+-+|.||||+|.+||.|++++||.|+|.. ..|..-...+|+|++.|++++..+|+.+|+++|.++..
T Consensus 139 PNstag~iigkggAtiK~~~Eqsga~iqisP--qkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpq 207 (402)
T KOG2191|consen 139 PNSTAGMIIGKGGATIKAIQEQSGAWIQISP--QKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQ 207 (402)
T ss_pred cCCcccceecCCcchHHHHHHhhCcceEecc--cCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCc
Confidence 9999999999999999999999999999973 22444456789999999999999999999999998864
No 10
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.88 E-value=8.2e-22 Score=206.44 Aligned_cols=173 Identities=38% Similarity=0.597 Sum_probs=140.8
Q ss_pred EEEEEeeecCccccccccCchhhHhhhhhcCCeEEecCCCCCCCceeEEecCcchhhhhhhHHHHHHHHhCccccccccc
Q 009520 284 FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIER 363 (533)
Q Consensus 284 ~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~ 363 (533)
.++|++|+.+.+|.||||+|..||+||.++.++|+|....+++.+|+++|+|. ..+...+.+.+|+.+.+.++....+.
T Consensus 43 ~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~-~~~~~~~~~~~al~ka~~~iv~~~~~ 121 (485)
T KOG2190|consen 43 LTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGN-RVELNLSPATDALFKAFDMIVFKLEE 121 (485)
T ss_pred ceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecc-cccccCCchHHHHHHHHHHHhhcccc
Confidence 34899999999999999999999999999999999999888999999999994 22224455666776666655443221
Q ss_pred ----------ccCCcceeEEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHH
Q 009520 364 ----------DSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKD 433 (533)
Q Consensus 364 ----------~~~~~~~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~ 433 (533)
+.....++++|+||.+++|+||||+|++||+|++.|||+|+|.++ .+|. .++|.|+|.|.+++|.+
T Consensus 122 d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av~~ 197 (485)
T KOG2190|consen 122 DDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAVKK 197 (485)
T ss_pred cccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHHHH
Confidence 111225899999999999999999999999999999999999765 7886 78899999999999999
Q ss_pred HHHHHHHHHHhccccccCcccCCCCCCCCCC
Q 009520 434 ALIQVMTRLRANLFDREGAVSTFVPVLPYIP 464 (533)
Q Consensus 434 A~~~I~~~l~~~~~~~~~~~~~~~~~~~y~p 464 (533)
|+.+|..+|.++..+ ..+.+....+|.|
T Consensus 198 al~~Is~~L~~~~~~---~~~~~~st~~y~P 225 (485)
T KOG2190|consen 198 ALVQISSRLLENPPR---SPPPLVSTIPYRP 225 (485)
T ss_pred HHHHHHHHHHhcCCc---CCCCCCCcccCCC
Confidence 999999999987532 2233445667877
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=1.4e-14 Score=133.40 Aligned_cols=137 Identities=22% Similarity=0.256 Sum_probs=95.9
Q ss_pred EEecCCccceeecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEE---cCCccccccccCcccCCHHHHHHHHHHHHH
Q 009520 47 YLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVY---SASDETNAFEDGDKFVSPAQDALFKVHDRV 123 (533)
Q Consensus 47 ilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~---G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i 123 (533)
+.||.+.+|.|||++|++|+.|+++|||+|++.+. +..|.|+ +.++. +++|...|.. +
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~-------------i~kA~~~I~~-i 62 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLA-------------VMKAREVVKA-I 62 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHH-------------HHHHHHHHHH-H
Confidence 56899999999999999999999999999999754 3568883 33222 2333333322 1
Q ss_pred HHhhccCCCCC-CCCCceEEE-EEecC---------CceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceE
Q 009520 124 IAEELRGDEDS-DGGHQVTAK-LLVPS---------DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELV 192 (533)
Q Consensus 124 ~~~~~~~~~~~-~~~~~~~~~-llVp~---------~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v 192 (533)
... +..+... -....+..+ +-|+. ..+|+|||++|++++.|++.|||+|.|. ++.|
T Consensus 63 ~~g-f~~e~A~~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~------------~~~v 129 (172)
T TIGR03665 63 GRG-FSPEKALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY------------GKTV 129 (172)
T ss_pred HcC-CCHHHHHHhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc------------CCEE
Confidence 110 0000000 011122222 23333 3689999999999999999999999984 3679
Q ss_pred EEEcCHHHHHHHHHHHHHHHhcC
Q 009520 193 QISGEASVVKKALCQIASRLHDN 215 (533)
Q Consensus 193 ~I~G~~~~V~~A~~~I~~~l~~~ 215 (533)
.|.|.+++++.|...|.+++...
T Consensus 130 ~i~G~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 130 GIIGDPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred EEECCHHHHHHHHHHHHHHHcCC
Confidence 99999999999999999999653
No 12
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.52 E-value=1.7e-13 Score=127.06 Aligned_cols=142 Identities=20% Similarity=0.181 Sum_probs=98.6
Q ss_pred eEEEEEecCCccceeecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEE----cCCccccccccCcccCCHHHHHHHH
Q 009520 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVY----SASDETNAFEDGDKFVSPAQDALFK 118 (533)
Q Consensus 43 ~~~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~----G~~~~~~~~~~~~~~v~~a~~a~~~ 118 (533)
+...+.||.+.+|.|||++|++|+.|+++|||+|++.+. +..|.|+ +.++. +++|...
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~-------------i~kA~~~ 64 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLA-------------VLKARDI 64 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHH-------------HHHHHHH
Confidence 467899999999999999999999999999999999764 3578886 33222 2333333
Q ss_pred HHHHHHHhhccCCCCCCCCCceEEEE-Eec---------CCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCC
Q 009520 119 VHDRVIAEELRGDEDSDGGHQVTAKL-LVP---------SDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRS 188 (533)
Q Consensus 119 i~~~i~~~~~~~~~~~~~~~~~~~~l-lVp---------~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~ 188 (533)
|......-... +.-......+...+ -+. ...+|+|||++|++++.|++.|||+|.|..
T Consensus 65 I~ai~~gf~~e-~A~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~----------- 132 (180)
T PRK13763 65 VKAIGRGFSPE-KALRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG----------- 132 (180)
T ss_pred HHHHhcCCCHH-HHHHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC-----------
Confidence 33211100000 00000111222222 111 136899999999999999999999999853
Q ss_pred CceEEEEcCHHHHHHHHHHHHHHHhcC
Q 009520 189 DELVQISGEASVVKKALCQIASRLHDN 215 (533)
Q Consensus 189 dr~v~I~G~~~~V~~A~~~I~~~l~~~ 215 (533)
+.|.|.|++++++.|...|..++...
T Consensus 133 -~~v~i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 133 -KTVAIIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred -CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence 35999999999999999999999664
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=99.50 E-value=8.4e-14 Score=128.15 Aligned_cols=138 Identities=20% Similarity=0.253 Sum_probs=92.7
Q ss_pred EeeecCccccccccCchhhHhhhhhcCCeEEecCCCCCCCceeEEe---cCcchhhhhhhHHHHHHHHhCcccccccccc
Q 009520 288 LVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITV---SSKEFFEDTLSATIEAVVRLQPRCSEKIERD 364 (533)
Q Consensus 288 v~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervi~I---~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~ 364 (533)
+.||.+.++.|||++|++|+.|+++||++|.++.. +..+.| ++...........+.++.+-++ ...++.-
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- 74 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLAVMKAREVVKAIGRGFS-PEKALKL- 74 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHHHHHHHHHHHHHHcCCC-HHHHHHh-
Confidence 57899999999999999999999999999999963 234666 3322111111111222221110 0000000
Q ss_pred cCCcceeEEEeecC---------CceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHH
Q 009520 365 SGLISFTTRLLVPT---------SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDAL 435 (533)
Q Consensus 365 ~~~~~~~~~l~Vp~---------~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~ 435 (533)
.++...-.-+.|+. ..+|+|||++|++++.|+..|||+|.|.. ..|.|.|++++++.|.
T Consensus 75 ~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------------~~v~i~G~~~~~~~A~ 142 (172)
T TIGR03665 75 LDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------------KTVGIIGDPEQVQIAR 142 (172)
T ss_pred cCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------------CEEEEECCHHHHHHHH
Confidence 01111112233433 47899999999999999999999999941 4899999999999999
Q ss_pred HHHHHHHHh
Q 009520 436 IQVMTRLRA 444 (533)
Q Consensus 436 ~~I~~~l~~ 444 (533)
.+|..+|+.
T Consensus 143 ~~i~~li~~ 151 (172)
T TIGR03665 143 EAIEMLIEG 151 (172)
T ss_pred HHHHHHHcC
Confidence 999988854
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.46 E-value=3.8e-13 Score=124.65 Aligned_cols=142 Identities=18% Similarity=0.214 Sum_probs=94.3
Q ss_pred EEEEEeeecCccccccccCchhhHhhhhhcCCeEEecCCCCCCCceeEEec----CcchhhhhhhHHHHHHHHhCccccc
Q 009520 284 FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVS----SKEFFEDTLSATIEAVVRLQPRCSE 359 (533)
Q Consensus 284 ~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervi~I~----G~~~~~~~~~~~~~a~~~~~~~~~~ 359 (533)
+...+.||.+.++.|||++|++|+.|+++||++|.+... +..+.|. +...........+.++.+-++ ...
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 467899999999999999999999999999999999963 2345554 222111111112222222110 000
Q ss_pred ccccccCCcceeEEEeec---------CCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHH
Q 009520 360 KIERDSGLISFTTRLLVP---------TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL 430 (533)
Q Consensus 360 ~~~~~~~~~~~~~~l~Vp---------~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~ 430 (533)
.+.. .++...-.-+.|. ...+|+|||++|++++.|++.|||+|.|.. +.|.|.|++++
T Consensus 77 A~~l-~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~------------~~v~i~G~~~~ 143 (180)
T PRK13763 77 ALRL-LDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG------------KTVAIIGDPEQ 143 (180)
T ss_pred HHHH-hCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC------------CEEEEEeCHHH
Confidence 0000 0111111111111 147899999999999999999999999942 36999999999
Q ss_pred HHHHHHHHHHHHHh
Q 009520 431 AKDALIQVMTRLRA 444 (533)
Q Consensus 431 v~~A~~~I~~~l~~ 444 (533)
++.|...|..+++.
T Consensus 144 ~~~A~~~I~~li~g 157 (180)
T PRK13763 144 VEIAREAIEMLIEG 157 (180)
T ss_pred HHHHHHHHHHHHcC
Confidence 99999999888854
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=99.39 E-value=1e-12 Score=101.03 Aligned_cols=64 Identities=42% Similarity=0.630 Sum_probs=57.2
Q ss_pred eEEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHH
Q 009520 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQV 438 (533)
Q Consensus 371 ~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I 438 (533)
+++|+||.+.+|+|||++|++|++|+++|||+|.+.+... ...++|+|+|+|+++++..|+.+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~----~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL----PGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC----CCCCceEEEEEeCHHHHHHHHHhh
Confidence 3689999999999999999999999999999999965432 246789999999999999999887
No 16
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.33 E-value=1e-11 Score=127.16 Aligned_cols=273 Identities=22% Similarity=0.286 Sum_probs=169.4
Q ss_pred cCCCceEEEEEecCCccceeecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHH
Q 009520 38 IGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALF 117 (533)
Q Consensus 38 ~~~~~~~~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~ 117 (533)
-.++++...+.||...+..+||+.|++|+.|+..+++||.+.+.. -.++++.++.|.+.. ++++..+
T Consensus 63 e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p~~----------v~~a~a~-- 129 (608)
T KOG2279|consen 63 KPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFPVQ----------VCKAKAA-- 129 (608)
T ss_pred CchhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCCCC----------CChHHHH--
Confidence 357889999999999999999999999999999999999997552 223566666665443 4444443
Q ss_pred HHHHHHHHhhccCCCCCCCCCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcC
Q 009520 118 KVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGE 197 (533)
Q Consensus 118 ~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~ 197 (533)
+++++. ....+...+-+|...++.|+|++|++++.|+..++|+|.+..... ...++...|.+.
T Consensus 130 -~~~~~~-----------~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr-----~g~~~~~~i~~q 192 (608)
T KOG2279|consen 130 -IHQILT-----------ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGR-----LGLSRLIKISGQ 192 (608)
T ss_pred -HHHHHh-----------cCCcccccccchhhhcccccccchhhhcchhcccccccccccccc-----cccccceecccc
Confidence 333332 345677889999999999999999999999999999999876522 245788889898
Q ss_pred HHHHHHHHHHHHHHHhcCCC-------Cccccccc-ccc-----CCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCC
Q 009520 198 ASVVKKALCQIASRLHDNPS-------RSQHLLAS-AIS-----NSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTA 264 (533)
Q Consensus 198 ~~~V~~A~~~I~~~l~~~~~-------~~~~~~~s-~~~-----~~~~~gg~~~~p~~~~~~~~~~p~~~~~g~~~~d~~ 264 (533)
...++.|..++.+.+.++.. ..+..... ... ..+..++...+.-.+.....+.|-.+....-.+|+.
T Consensus 193 qk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~ 272 (608)
T KOG2279|consen 193 QKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMA 272 (608)
T ss_pred cchHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcce
Confidence 88888999998888876411 11111100 000 111111111000000000000000000000000100
Q ss_pred CCC-CCCCCCCCCCC---CCCceEEEEEeeecCccccccccCchhhHhhhhhcCCeEEecCCCCCCCc---eeEEecCcc
Q 009520 265 GDW-SRSLYSAPRDD---LSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDD---CLITVSSKE 337 (533)
Q Consensus 265 ~~~-~~~~~~~p~~~---~~~~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~e---rvi~I~G~~ 337 (533)
-.. -...++.|.++ .........|.+|...+|.+||+.|+.++.+...+++.+.|.-......- .++.+.|+.
T Consensus 273 v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~v~~~qic~~egkq 352 (608)
T KOG2279|consen 273 VVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSRVLQLQICVNEGKQ 352 (608)
T ss_pred eEEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEeccccchhhhhhhheecchh
Confidence 000 00011122221 22334567899999999999999999999999999999888765432211 356667765
Q ss_pred hhh
Q 009520 338 FFE 340 (533)
Q Consensus 338 ~~~ 340 (533)
..+
T Consensus 353 h~~ 355 (608)
T KOG2279|consen 353 HYE 355 (608)
T ss_pred HHH
Confidence 433
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=99.32 E-value=3.7e-12 Score=97.88 Aligned_cols=64 Identities=52% Similarity=0.778 Sum_probs=57.7
Q ss_pred EEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcCHHHHHHHHHHH
Q 009520 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI 208 (533)
Q Consensus 141 ~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I 208 (533)
+++|+||.+.+++|||++|++|++|+++|||+|++.+... + ...+|+|+|+|++++|.+|+.+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~-~---~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-P---GSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-C---CCCceEEEEEeCHHHHHHHHHhh
Confidence 3789999999999999999999999999999999987543 1 36799999999999999999886
No 18
>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=99.22 E-value=4.5e-11 Score=90.34 Aligned_cols=58 Identities=26% Similarity=0.342 Sum_probs=52.5
Q ss_pred eeEEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeC-HHHHHHHHHHH
Q 009520 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD-LDLAKDALIQV 438 (533)
Q Consensus 370 ~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~-~~~v~~A~~~I 438 (533)
.+..+.||.+++|+||||+|++|++|+++|||+|.|.+ ++.|.|+|+ +++++.|+.+|
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----------~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-----------DGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-----------CCEEEEEeCCHHHHHHHHHHh
Confidence 45679999999999999999999999999999999842 358999998 99999999887
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=99.22 E-value=1.8e-11 Score=93.16 Aligned_cols=61 Identities=23% Similarity=0.322 Sum_probs=54.5
Q ss_pred eEEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHH
Q 009520 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQV 438 (533)
Q Consensus 371 ~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I 438 (533)
+.+|.||.+++|+|||++|++|++|+++|||+|.++... +.++.|+|+|++++|..|+.+|
T Consensus 1 ~~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-------~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-------SKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred CeEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-------CCCCEEEEEcCHHHHHHHHHHh
Confidence 357999999999999999999999999999999996432 4567999999999999999877
No 20
>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=99.18 E-value=1.5e-11 Score=92.88 Aligned_cols=60 Identities=35% Similarity=0.511 Sum_probs=53.7
Q ss_pred eEEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHH
Q 009520 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQV 438 (533)
Q Consensus 371 ~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I 438 (533)
|.+|.||.+++|+|||++|++|++|+++|||+|.++.. + ....|+|+|++++|..|+.+|
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 67899999999999999999999999999999999542 1 344899999999999999876
No 21
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.16 E-value=6.4e-11 Score=131.70 Aligned_cols=310 Identities=21% Similarity=0.278 Sum_probs=194.5
Q ss_pred eEEEEEecCCccceeecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccc--------ccccCcccCCHH--
Q 009520 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETN--------AFEDGDKFVSPA-- 112 (533)
Q Consensus 43 ~~~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~--------~~~~~~~~v~~a-- 112 (533)
+..++.+-...++++||++|.+++.++.++.+.|+|++..... ....|.+...++. ++...+.+..-+
T Consensus 201 ~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~--~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~~ 278 (753)
T KOG2208|consen 201 VFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSS--PSNKIDGRLNSSSSINVEIQEALTRLESEFDYDEI 278 (753)
T ss_pred EEEEeeccccchhhhccccccccccccccceeEEEcccccccc--hhhhhccccccceehhhhhHHHHHHhcChhhhhhh
Confidence 6678999999999999999999999999999999998652222 2333444332211 000000000000
Q ss_pred -------------HHHHHHHHHHHHHhh-ccCC-C-----------C---------------CCCCCceEEEEEecCCce
Q 009520 113 -------------QDALFKVHDRVIAEE-LRGD-E-----------D---------------SDGGHQVTAKLLVPSDQI 151 (533)
Q Consensus 113 -------------~~a~~~i~~~i~~~~-~~~~-~-----------~---------------~~~~~~~~~~llVp~~~~ 151 (533)
-+.+..+........ +..+ + + ......+.+.+.+....+
T Consensus 279 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~~ 358 (753)
T KOG2208|consen 279 IYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPEEL 358 (753)
T ss_pred hhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHHhh
Confidence 000001100000000 0000 0 0 011223678888889999
Q ss_pred eeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCccccccccccCCC
Q 009520 152 GCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSH 231 (533)
Q Consensus 152 g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~s~~~~~~ 231 (533)
..++||+|.+|.+|++++.+.|.+... ++.+..+.++|....+.+|...+...+.+...
T Consensus 359 ~~v~GK~~~ni~ki~e~~~~~i~~~~~-------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n-------------- 417 (753)
T KOG2208|consen 359 KFVIGKKGANIEKIREESQVKIDLPKQ-------GSNNKKVVITGVSANDEKAVEDVEKIIAEILN-------------- 417 (753)
T ss_pred hhhcCCCCccHHHHHHhhhhceecccc-------cCCCCCeEEeccccchhHHHHHHHHHHHhhhc--------------
Confidence 999999999999999999999999763 35678899999999999999999998877311
Q ss_pred CCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEeeecCccccccccCchhhHhhhh
Q 009520 232 SSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQ 311 (533)
Q Consensus 232 ~~gg~~~~p~~~~~~~~~~p~~~~~g~~~~d~~~~~~~~~~~~p~~~~~~~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~ 311 (533)
......+.+|...+..|||.+|..|+.|..
T Consensus 418 --------------------------------------------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~ 447 (753)
T KOG2208|consen 418 --------------------------------------------------SIVKEEVQIPTKSHKRIIGTKGALINYIMG 447 (753)
T ss_pred --------------------------------------------------ccccceeecCccchhhhhccccccHHHHHh
Confidence 023456899999999999999999999999
Q ss_pred hcC-CeEEecCCCCCCCceeEEecCcc-hhhhhhhHHHHHHHHhCcccccccccccCCcceeEEEeecCCceeEEecCCC
Q 009520 312 ESG-AAIKVDSSSTEGDDCLITVSSKE-FFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGG 389 (533)
Q Consensus 312 ~tg-a~I~i~~~~~~~~ervi~I~G~~-~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~~G~IIGkgG 389 (533)
+++ ..|++.......+ ..++.+.. .++.... .+..+. ... .....-...+...+.|..+.+..+|+.|
T Consensus 448 k~~~v~i~f~~~~~~~~--~~~~~~~~~dv~~~~~----~~~~~~---~~a-~~~~~~~~~~~d~~~~~~~~~~~~g~~~ 517 (753)
T KOG2208|consen 448 KHGGVHIKFQNNNNSSD--MVTIRGISKDVEKSVS----LLKALK---ADA-KNLKFRDVVTKDKLLPVKYIGKEIGKNG 517 (753)
T ss_pred hcCcEEEecCCCCcccc--cceEeccccccchhHH----HHHhhh---hhh-hcchhhhhhhccccchHHhhcccccCce
Confidence 999 6777776543322 23333321 1111111 000000 000 0000112455667778888777777776
Q ss_pred hhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhc
Q 009520 390 SIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN 445 (533)
Q Consensus 390 ~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~ 445 (533)
..+...++ ...++. ....++..++|.|..+.|.+|...+..++...
T Consensus 518 ~i~d~~~~----~~i~~~------~~~~~~~~i~i~gk~~~v~~a~~~L~~~~~~~ 563 (753)
T KOG2208|consen 518 TIRDSLGD----KSIFPP------NEDEDHEKITIEGKLELVLEAPAELKALIEAL 563 (753)
T ss_pred eeeccCCc----eeeccc------ccccccceeeecccccchhhhHHHHHhcchhh
Confidence 66555544 444422 22345668999999999999999988777654
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=99.13 E-value=2.2e-10 Score=87.68 Aligned_cols=62 Identities=37% Similarity=0.599 Sum_probs=55.0
Q ss_pred EEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHH
Q 009520 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQV 438 (533)
Q Consensus 372 ~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I 438 (533)
.+|.||.+++|+|||++|++|++|+++|||+|.|..... +..++.|+|.|+.+++..|+.+|
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 579999999999999999999999999999999964321 35678999999999999998876
No 23
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.13 E-value=1.8e-10 Score=118.15 Aligned_cols=232 Identities=24% Similarity=0.359 Sum_probs=167.4
Q ss_pred CCCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 009520 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN 215 (533)
Q Consensus 136 ~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~ 215 (533)
....+.+++.||...+.+++|++|++|+.|+..|+++|.+..+ +.+ .++...+.|.+.++.+|...+..++.++
T Consensus 64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~e-d~g-----~e~~~~~~~~p~~v~~a~a~~~~~~~~~ 137 (608)
T KOG2279|consen 64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTE-DVG-----DERVLLISGFPVQVCKAKAAIHQILTEN 137 (608)
T ss_pred chhheeeeEeecccceeeeeccccCCcchhhcccccceecCcc-cCC-----cccchhhccCCCCCChHHHHHHHHHhcC
Confidence 3467889999999999999999999999999999999988654 333 3666777779999999999998888763
Q ss_pred CCCccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEeeecCcc
Q 009520 216 PSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANI 295 (533)
Q Consensus 216 ~~~~~~~~~s~~~~~~~~gg~~~~p~~~~~~~~~~p~~~~~g~~~~d~~~~~~~~~~~~p~~~~~~~~~~~~v~vp~~~~ 295 (533)
. .+.+.+.+|...+
T Consensus 138 ~------------------------------------------------------------------pvk~~lsvpqr~~ 151 (608)
T KOG2279|consen 138 T------------------------------------------------------------------PVSEQLSVPQRSV 151 (608)
T ss_pred C------------------------------------------------------------------cccccccchhhhc
Confidence 1 3455678899999
Q ss_pred ccccccCchhhHhhhhhcCCeEEecCCCCCCCceeEEecCcchhh---hh-----hhHHHHHHHHh-------Ccc---c
Q 009520 296 GGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFE---DT-----LSATIEAVVRL-------QPR---C 357 (533)
Q Consensus 296 g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervi~I~G~~~~~---~~-----~~~~~~a~~~~-------~~~---~ 357 (533)
+.|+|++|+++..++..++|+|.+..+......+...|.+..... +. ++.-.+.+.+. .++ .
T Consensus 152 ~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~ 231 (608)
T KOG2279|consen 152 GRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPI 231 (608)
T ss_pred ccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCc
Confidence 999999999999999999999999988666667777777643211 00 00000000000 000 0
Q ss_pred c---ccc------------------cc--------c-----------------------cCCcceeEEEeecCCceeEEe
Q 009520 358 S---EKI------------------ER--------D-----------------------SGLISFTTRLLVPTSRIGCLI 385 (533)
Q Consensus 358 ~---~~~------------------~~--------~-----------------------~~~~~~~~~l~Vp~~~~G~II 385 (533)
. +.+ .. + .........|.||...+|.+|
T Consensus 232 n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~li 311 (608)
T KOG2279|consen 232 NVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLI 311 (608)
T ss_pred cccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCcccccchh
Confidence 0 000 00 0 001234557899999999999
Q ss_pred cCCChhHHHHHHhcCceEEEecCCCCCCCCCC-CCcEEEEEeCHHHHHHHHHHHHHHH
Q 009520 386 GKGGSIITEMRRLTKANIRILPKENLPKIASE-DDEMVQISGDLDLAKDALIQVMTRL 442 (533)
Q Consensus 386 GkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~-~~r~V~I~G~~~~v~~A~~~I~~~l 442 (533)
|+.|+.++.+...|++.+.|.. .|..... +-.++.+.|+..-+..|..|+..+.
T Consensus 312 g~~gey~s~yssasn~~~hi~t---~pyt~~v~~~qic~~egkqh~~n~vl~ml~~~~ 366 (608)
T KOG2279|consen 312 GHAGEYLSVYSSASNHPNHIWT---QPYTSRVLQLQICVNEGKQHYENSVLEMLTVHV 366 (608)
T ss_pred hhhhhhhhhhhhccCccceEEe---ccccchhhhhhhheecchhHHHHHHHhhhhccC
Confidence 9999999999999999998854 3531111 1145779999999999998887443
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=99.12 E-value=8.1e-11 Score=89.56 Aligned_cols=60 Identities=28% Similarity=0.441 Sum_probs=54.7
Q ss_pred EEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcCHHHHHHHHHHH
Q 009520 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI 208 (533)
Q Consensus 142 ~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I 208 (533)
..|.||.+++++|||++|++|++|+++|||+|.|++.. ..++.|+|+|+.++|..|+.+|
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-------~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-------SKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-------CCCCEEEEEcCHHHHHHHHHHh
Confidence 57899999999999999999999999999999997642 4578999999999999998876
No 25
>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=99.11 E-value=6.4e-11 Score=89.48 Aligned_cols=60 Identities=40% Similarity=0.613 Sum_probs=54.0
Q ss_pred EEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcCHHHHHHHHHHH
Q 009520 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI 208 (533)
Q Consensus 141 ~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I 208 (533)
|.+|+||.+++++|||++|++|++|+++|||+|.|.++ .....|+|+|++++|.+|+.+|
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 57899999999999999999999999999999999764 1245899999999999999876
No 26
>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=99.10 E-value=2.9e-10 Score=85.90 Aligned_cols=58 Identities=34% Similarity=0.488 Sum_probs=52.5
Q ss_pred eEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcC-HHHHHHHHHHH
Q 009520 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGE-ASVVKKALCQI 208 (533)
Q Consensus 140 ~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~-~~~V~~A~~~I 208 (533)
....|.||.+++++||||+|++|++|+++|||+|.+.+ ++.|.|+|+ .+++++|+.+|
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----------~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-----------DGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-----------CCEEEEEeCCHHHHHHHHHHh
Confidence 45779999999999999999999999999999999854 467999998 99999998876
No 27
>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=99.03 E-value=9e-10 Score=84.24 Aligned_cols=62 Identities=40% Similarity=0.657 Sum_probs=55.5
Q ss_pred EEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcCHHHHHHHHHHH
Q 009520 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI 208 (533)
Q Consensus 142 ~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I 208 (533)
.+|.||.+++++|||++|++|++|+++|||+|.|..... ...++.|.|.|+.+++..|..+|
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 689999999999999999999999999999999976532 24689999999999999998776
No 28
>PF13014 KH_3: KH domain
Probab=98.95 E-value=1.5e-09 Score=75.96 Aligned_cols=42 Identities=48% Similarity=0.794 Sum_probs=38.9
Q ss_pred ccceeecCCcHHHHHHHHHhCCeEEEcC-CCCCCCceEEEEEc
Q 009520 53 KIGSIIGRGGEIVKQLRIDTKSKIRIGE-TVPGSEERVVTVYS 94 (533)
Q Consensus 53 ~~g~IIGk~G~~Ik~i~~~tga~I~i~~-~~~~~~ervv~I~G 94 (533)
++|+||||+|++|++|+++|+|+|+|++ ..++..+|+|+|+|
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 5899999999999999999999999998 56688899999987
No 29
>PF13014 KH_3: KH domain
Probab=98.93 E-value=1.9e-09 Score=75.44 Aligned_cols=43 Identities=47% Similarity=0.740 Sum_probs=37.3
Q ss_pred ceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEe
Q 009520 380 RIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG 426 (533)
Q Consensus 380 ~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G 426 (533)
+||+|||++|++|++|+++|||+|.|++ +.. .++++++|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~-~~~---~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP-ENE---PGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC-ccC---CCCCceEEEEEC
Confidence 5899999999999999999999999976 222 357889999998
No 30
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.89 E-value=4.6e-09 Score=117.05 Aligned_cols=289 Identities=19% Similarity=0.254 Sum_probs=187.0
Q ss_pred ceEEEEEecCCccceeecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHH
Q 009520 42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHD 121 (533)
Q Consensus 42 ~~~~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~ 121 (533)
-+...+-+-..++..|+||+|.+|.+|++++.|.|.+.+. +..+..+++.+...++ .+|.+.+..+..
T Consensus 346 n~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~~~----------~ka~~~v~~~~~ 413 (753)
T KOG2208|consen 346 NENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSAND----------EKAVEDVEKIIA 413 (753)
T ss_pred ceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccccch----------hHHHHHHHHHHH
Confidence 3556777888899999999999999999999999999874 5667889999987763 234444444433
Q ss_pred HHHHhhccCCCCCCCCCceEEEEEecCCceeeeeccCchHHHHHHhhcC-ceEEEeecCCCCcccCCCCceEEEEcCHHH
Q 009520 122 RVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETG-AQIRILKDEHLPSCALRSDELVQISGEASV 200 (533)
Q Consensus 122 ~i~~~~~~~~~~~~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tg-a~I~i~~~~~~p~~~~~~dr~v~I~G~~~~ 200 (533)
.+.. ......+++|...+.++||.+|..|..|.++++ ..|++.... +....+++.|....
T Consensus 414 ei~n------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~-------~~~~~~~~~~~~~d 474 (753)
T KOG2208|consen 414 EILN------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN-------NSSDMVTIRGISKD 474 (753)
T ss_pred hhhc------------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC-------cccccceEeccccc
Confidence 3221 145577999999999999999999999999999 666654432 33456888888888
Q ss_pred HHHHHHHHHHHHhcCCCCccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009520 201 VKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLS 280 (533)
Q Consensus 201 V~~A~~~I~~~l~~~~~~~~~~~~s~~~~~~~~gg~~~~p~~~~~~~~~~p~~~~~g~~~~d~~~~~~~~~~~~p~~~~~ 280 (533)
+..+..+...+........ |
T Consensus 475 v~~~~~~~~~~~~~a~~~~-----------------------------------------------~------------- 494 (753)
T KOG2208|consen 475 VEKSVSLLKALKADAKNLK-----------------------------------------------F------------- 494 (753)
T ss_pred cchhHHHHHhhhhhhhcch-----------------------------------------------h-------------
Confidence 8776655544443210000 0
Q ss_pred CceEEEEEeeecCccccccccCchhhHhhhhhcCCeEEecCCCCCCCceeEEecCcchhhhhhhHHHHHHHHhCcccccc
Q 009520 281 SKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEK 360 (533)
Q Consensus 281 ~~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~ 360 (533)
..........|..+.+..+|+.|..+..+.++. .++.... .++..+++.|.... +..+..++..+.+.+.+
T Consensus 495 ~~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~~~----i~~~~~~-~~~~~i~i~gk~~~---v~~a~~~L~~~~~~~~~- 565 (753)
T KOG2208|consen 495 RDVVTKDKLLPVKYIGKEIGKNGTIRDSLGDKS----IFPPNED-EDHEKITIEGKLEL---VLEAPAELKALIEALIK- 565 (753)
T ss_pred hhhhhccccchHHhhcccccCceeeeccCCcee----ecccccc-cccceeeecccccc---hhhhHHHHHhcchhhhh-
Confidence 001123345566666666666665555554444 4444322 25667888886522 22223333322222221
Q ss_pred cccccCCcceeEEEeecCCce-eEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHH
Q 009520 361 IERDSGLISFTTRLLVPTSRI-GCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVM 439 (533)
Q Consensus 361 ~~~~~~~~~~~~~l~Vp~~~~-G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~ 439 (533)
.....+.+|..++ -++++++....+..+...|+.+..++.. .+.+.++|.|..+.++.|...+.
T Consensus 566 --------~~~~~v~~~~~~~~~~l~~~~~~~~~~~e~~~gv~~~fp~~~-------~~~~e~~i~g~~~~v~aa~~~~~ 630 (753)
T KOG2208|consen 566 --------ATLLEVNNPPGQHRPFLIGKGIENRTYVEVFGGVVVPFPRSP-------TSSDEVSIKGAKDEVKAAKGRLE 630 (753)
T ss_pred --------hhhhhccCcchheeeeeeccccccccceeecCcccccCCCCC-------CchhhhccchhHHHHHHhhccch
Confidence 1223445555444 6777777777777777777887765432 33447999999999999988887
Q ss_pred HHHHhc
Q 009520 440 TRLRAN 445 (533)
Q Consensus 440 ~~l~~~ 445 (533)
+.++..
T Consensus 631 ~i~~~~ 636 (753)
T KOG2208|consen 631 EIVEYL 636 (753)
T ss_pred hhhhhc
Confidence 776543
No 31
>smart00322 KH K homology RNA-binding domain.
Probab=98.84 E-value=1.9e-08 Score=77.46 Aligned_cols=67 Identities=28% Similarity=0.519 Sum_probs=58.7
Q ss_pred ceeEEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHH
Q 009520 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRL 442 (533)
Q Consensus 369 ~~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l 442 (533)
..+.++.||..++|++||++|++|++|++.||++|.+... ......|+|.|+++++..|..+|.+.+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~-------~~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPED-------GSEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCC-------CCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 3678899999999999999999999999999999998532 124678999999999999999998765
No 32
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.77 E-value=1.6e-07 Score=85.82 Aligned_cols=146 Identities=25% Similarity=0.274 Sum_probs=100.2
Q ss_pred CceEEEEEecCCccceeecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHH
Q 009520 41 EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVH 120 (533)
Q Consensus 41 ~~~~~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~ 120 (533)
......+.||....+.+||+.|++.+.|++.+++++.++.. +..|.|.......++ -++.+..
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~-----~~~V~i~~~~~t~Dp------------~~~~ka~ 68 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTEDP------------LALLKAR 68 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCCh------------HHHHHHH
Confidence 34557799999999999999999999999999999999643 678999877321111 1222222
Q ss_pred HHHHHhhccCCCCC---CCCCceEEEE-----Eec-C-----CceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccC
Q 009520 121 DRVIAEELRGDEDS---DGGHQVTAKL-----LVP-S-----DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCAL 186 (533)
Q Consensus 121 ~~i~~~~~~~~~~~---~~~~~~~~~l-----lVp-~-----~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 186 (533)
+.+.+-....+++. -..+.+.+.+ ++- + ...|+|||++|.|-+.|++-|+|.|.|.
T Consensus 69 d~VkAIgrGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~---------- 138 (194)
T COG1094 69 DVVKAIGRGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY---------- 138 (194)
T ss_pred HHHHHHhcCCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe----------
Confidence 22211111111000 0011222222 111 1 2459999999999999999999999885
Q ss_pred CCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 009520 187 RSDELVQISGEASVVKKALCQIASRLHDN 215 (533)
Q Consensus 187 ~~dr~v~I~G~~~~V~~A~~~I~~~l~~~ 215 (533)
+.+|.|-|..++|..|..+|..++..-
T Consensus 139 --g~tVaiiG~~~~v~iAr~AVemli~G~ 165 (194)
T COG1094 139 --GKTVAIIGGFEQVEIAREAVEMLINGA 165 (194)
T ss_pred --CcEEEEecChhhhHHHHHHHHHHHcCC
Confidence 457999999999999999999999763
No 33
>smart00322 KH K homology RNA-binding domain.
Probab=98.75 E-value=5.2e-08 Score=74.96 Aligned_cols=67 Identities=39% Similarity=0.655 Sum_probs=59.4
Q ss_pred ceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 009520 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRL 212 (533)
Q Consensus 139 ~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l 212 (533)
.++.++.||...++++||++|++|++|++.||++|.+.... .....+.|.|..+++..|...|.+.+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------SEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 35789999999999999999999999999999999986531 14688999999999999999998876
No 34
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.62 E-value=3.2e-08 Score=95.00 Aligned_cols=149 Identities=16% Similarity=0.253 Sum_probs=105.8
Q ss_pred ceEEEEEeeecCccccccccCchhhHhhhhhcCCeEEecCCCCCCCceeEEecCcch-hhhhhhHHHHHHHHhCcccc--
Q 009520 282 KEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEF-FEDTLSATIEAVVRLQPRCS-- 358 (533)
Q Consensus 282 ~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervi~I~G~~~-~~~~~~~~~~a~~~~~~~~~-- 358 (533)
..++..+.||..+++.|.|++|++||.|+.+|.++|+-+. .+.+.++.++|... +..+.++...+..++--...
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPs---r~eePiF~vTg~~edv~~aRrei~saaeH~~l~~~s~ 100 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPS---RGEEPIFPVTGRHEDVRRARREIPSAAEHFGLIRASR 100 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCC---CCCCCcceeccCchhHHHHhhcCccccceeeeeeecc
Confidence 4567888999999999999999999999999999998874 34668999999643 22222222222222210000
Q ss_pred ---cccccccCCcceeEEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHH-HHHH
Q 009520 359 ---EKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL-AKDA 434 (533)
Q Consensus 359 ---~~~~~~~~~~~~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~-v~~A 434 (533)
.....-....+.+..+.+|...+|.|.|..|.+|+.|++.+...|.-+.++. +-++.++|.+.+ +++|
T Consensus 101 s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~~--------~~Vf~Vtg~~~nC~kra 172 (394)
T KOG2113|consen 101 SFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRCG--------EPVFCVTGAPKNCVKRA 172 (394)
T ss_pred cccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeeccCC--------CceEEEecCCcchhhhc
Confidence 0000111235678889999999999999999999999999999999765533 348999999888 5666
Q ss_pred H-HHHHHH
Q 009520 435 L-IQVMTR 441 (533)
Q Consensus 435 ~-~~I~~~ 441 (533)
. ..|...
T Consensus 173 ~s~eie~t 180 (394)
T KOG2113|consen 173 RSCEIEQT 180 (394)
T ss_pred cccchhhh
Confidence 5 444443
No 35
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.62 E-value=2.2e-07 Score=84.86 Aligned_cols=139 Identities=22% Similarity=0.329 Sum_probs=95.5
Q ss_pred eEEEEEeeecCccccccccCchhhHhhhhhcCCeEEecCCCCCCCceeEEecCcchhhhhhh-----HHHHH--------
Q 009520 283 EFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLS-----ATIEA-------- 349 (533)
Q Consensus 283 ~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervi~I~G~~~~~~~~~-----~~~~a-------- 349 (533)
..+..+.||..-.+.+||+.|+..+.|.+.+++++.++.. +..++|...+...|.+. ..+.|
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 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPE 81 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHH
Confidence 3467799999999999999999999999999999999853 34566665532222221 11111
Q ss_pred -HHHhCcccccccccccCCcceeEE--Eeec----CCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEE
Q 009520 350 -VVRLQPRCSEKIERDSGLISFTTR--LLVP----TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMV 422 (533)
Q Consensus 350 -~~~~~~~~~~~~~~~~~~~~~~~~--l~Vp----~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V 422 (533)
++++... ...++ .+.+. +.-+ ...-|+|||++|.+-+-|++.|+|+|.|.. .+|
T Consensus 82 ~A~~LL~d-~~~le------vIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g------------~tV 142 (194)
T COG1094 82 KALKLLED-DYYLE------VIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG------------KTV 142 (194)
T ss_pred HHHHHhcC-CcEEE------EEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC------------cEE
Confidence 1222111 00000 00000 0011 234699999999999999999999999963 389
Q ss_pred EEEeCHHHHHHHHHHHHHHHHhc
Q 009520 423 QISGDLDLAKDALIQVMTRLRAN 445 (533)
Q Consensus 423 ~I~G~~~~v~~A~~~I~~~l~~~ 445 (533)
-|.|.+++++.|...|..+++..
T Consensus 143 aiiG~~~~v~iAr~AVemli~G~ 165 (194)
T COG1094 143 AIIGGFEQVEIAREAVEMLINGA 165 (194)
T ss_pred EEecChhhhHHHHHHHHHHHcCC
Confidence 99999999999999998888643
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=98.35 E-value=1.9e-06 Score=74.06 Aligned_cols=67 Identities=22% Similarity=0.341 Sum_probs=51.7
Q ss_pred CCceeEEecCCChhHHHHHHhcCceEEEecCCCC-----------CCCC-CCCCcEEEEEeC---HHHHHHHHHHHHHHH
Q 009520 378 TSRIGCLIGKGGSIITEMRRLTKANIRILPKENL-----------PKIA-SEDDEMVQISGD---LDLAKDALIQVMTRL 442 (533)
Q Consensus 378 ~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~-----------P~~~-~~~~r~V~I~G~---~~~v~~A~~~I~~~l 442 (533)
.+++|.|||++|++||+|+++|||+|.|..+... |... .+..-.|.|++. .+++..|+.+|..++
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 4788999999999999999999999999765211 1111 122346999995 499999999999888
Q ss_pred Hh
Q 009520 443 RA 444 (533)
Q Consensus 443 ~~ 444 (533)
..
T Consensus 94 ~~ 95 (120)
T cd02395 94 KP 95 (120)
T ss_pred cc
Confidence 73
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=98.21 E-value=5.7e-06 Score=71.20 Aligned_cols=68 Identities=25% Similarity=0.369 Sum_probs=52.1
Q ss_pred CCceeeeeccCchHHHHHHhhcCceEEEeecCCCC-----------cc-cCCCCceEEEEcCH---HHHHHHHHHHHHHH
Q 009520 148 SDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLP-----------SC-ALRSDELVQISGEA---SVVKKALCQIASRL 212 (533)
Q Consensus 148 ~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p-----------~~-~~~~dr~v~I~G~~---~~V~~A~~~I~~~l 212 (533)
.+.+|.|||++|.+||+|+++|||+|.|..+.... .. ....+-.|.|++.. +++.+|+.+|..++
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 36789999999999999999999999997642110 00 01223578899965 99999999999999
Q ss_pred hcC
Q 009520 213 HDN 215 (533)
Q Consensus 213 ~~~ 215 (533)
...
T Consensus 94 ~~~ 96 (120)
T cd02395 94 KPA 96 (120)
T ss_pred ccC
Confidence 764
No 38
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.14 E-value=3.5e-06 Score=81.30 Aligned_cols=142 Identities=24% Similarity=0.363 Sum_probs=103.9
Q ss_pred CCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCC
Q 009520 137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNP 216 (533)
Q Consensus 137 ~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~ 216 (533)
...++..+.||..+++.+.|++|.+||.|+.+|...|.-+...+ +-+..++|..+.|+.|.++|...-+..-
T Consensus 23 p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~e--------ePiF~vTg~~edv~~aRrei~saaeH~~ 94 (394)
T KOG2113|consen 23 GQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGE--------EPIFPVTGRHEDVRRARREIPSAAEHFG 94 (394)
T ss_pred CCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCC--------CCcceeccCchhHHHHhhcCccccceee
Confidence 37788999999999999999999999999999999997765433 4568899999999999888755322210
Q ss_pred CCccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEeeecCccc
Q 009520 217 SRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIG 296 (533)
Q Consensus 217 ~~~~~~~~s~~~~~~~~gg~~~~p~~~~~~~~~~p~~~~~g~~~~d~~~~~~~~~~~~p~~~~~~~~~~~~v~vp~~~~g 296 (533)
+.-.. +.+.+ +.+ + + ..+.+.+..+.+|...++
T Consensus 95 ------l~~~s-------~s~Sg---g~~------------~-------------~------s~s~qt~sy~svP~rvvg 127 (394)
T KOG2113|consen 95 ------LIRAS-------RSFSG---GTN------------G-------------A------SASGQTTSYVSVPLRVVG 127 (394)
T ss_pred ------eeeec-------ccccC---CCc------------c-------------c------cccCCCceeeeccceeee
Confidence 00000 00000 000 0 0 012345678889999999
Q ss_pred cccccCchhhHhhhhhcCCeEEecCCCCCCCceeEEecCc
Q 009520 297 GVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSK 336 (533)
Q Consensus 297 ~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervi~I~G~ 336 (533)
.+.|.+|.+|+.+++.+...|..+-. ..+.++.++|.
T Consensus 128 lvv~~~~~ti~~iqq~tnt~I~T~v~---~~~~Vf~Vtg~ 164 (394)
T KOG2113|consen 128 LVVGPKGATIKRIQQFTNTYIATPVR---CGEPVFCVTGA 164 (394)
T ss_pred eccccccCccchheecccceEeeecc---CCCceEEEecC
Confidence 99999999999999999999987743 35678888884
No 39
>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=98.08 E-value=1.1e-05 Score=88.43 Aligned_cols=97 Identities=25% Similarity=0.322 Sum_probs=79.6
Q ss_pred cccCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCccc
Q 009520 106 DKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCA 185 (533)
Q Consensus 106 ~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~ 185 (533)
.+.+..|.+++.+|++.+.+..... .+.....+....+.||.+.++.|||++|.+||.|.++|||+|.|..
T Consensus 545 ~~aL~~A~~g~~~Il~~m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-------- 615 (719)
T TIGR02696 545 ASALKQARDARLAILDVMAEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED-------- 615 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec--------
Confidence 3567778889999988766554444 4445556778899999999999999999999999999999999854
Q ss_pred CCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009520 186 LRSDELVQISG-EASVVKKALCQIASRLHD 214 (533)
Q Consensus 186 ~~~dr~v~I~G-~~~~V~~A~~~I~~~l~~ 214 (533)
+..|.|.+ ..+++++|+.+|..++..
T Consensus 616 ---~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 616 ---DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred ---CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 56789888 578899999999988874
No 40
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.08 E-value=8.2e-06 Score=72.31 Aligned_cols=102 Identities=20% Similarity=0.278 Sum_probs=68.6
Q ss_pred EEEEecCCccceeecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHH
Q 009520 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVI 124 (533)
Q Consensus 45 ~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~ 124 (533)
+.++|+...+|..||++|++|+.|++..|-+|.|-+ -+-. +++ .+...+.
T Consensus 34 vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve-----------~s~d----------------~~~---fI~n~l~ 83 (140)
T PRK08406 34 IIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE-----------YSDD----------------PEE---FIKNIFA 83 (140)
T ss_pred EEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE-----------cCCC----------------HHH---HHHHHcC
Confidence 567889999999999999999999999998887532 1111 111 1111111
Q ss_pred HhhccCCCCCCCCCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEe
Q 009520 125 AEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRIL 176 (533)
Q Consensus 125 ~~~~~~~~~~~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~ 176 (533)
...+..-.-........+.+.|+.+..+.+|||+|++|+.++.-++-.+.|.
T Consensus 84 Pa~V~~v~I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 84 PAAVRSVTIKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred CCEEEEEEEEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 0000000000112235677889999999999999999999999999888763
No 41
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.89 E-value=5.1e-05 Score=67.26 Aligned_cols=103 Identities=21% Similarity=0.300 Sum_probs=70.9
Q ss_pred EEEEEeeecCccccccccCchhhHhhhhhcCCeEEecCCCCCCCceeEEecCcchhhhhhhHHHHHHHHhCccccccccc
Q 009520 284 FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIER 363 (533)
Q Consensus 284 ~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~ 363 (533)
..+.+.|+...+|..||++|++|+.|++..|-+|.+-.-+.+ . ..-+..++. |--.....-
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~d-------------~----~~fI~n~l~--Pa~V~~v~I 92 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDD-------------P----EEFIKNIFA--PAAVRSVTI 92 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCCC-------------H----HHHHHHHcC--CCEEEEEEE
Confidence 377889999999999999999999999999988877653221 0 001111111 100000000
Q ss_pred ccCCcceeEEEeecCCceeEEecCCChhHHHHHHhcCceEEE
Q 009520 364 DSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405 (533)
Q Consensus 364 ~~~~~~~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i 405 (533)
..........+.|+....|..|||+|++|+.++..++-++.|
T Consensus 93 ~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 93 KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 001123556788999999999999999999999999998877
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=97.78 E-value=6.2e-05 Score=82.78 Aligned_cols=95 Identities=24% Similarity=0.293 Sum_probs=69.2
Q ss_pred hhhhhhHHHHHHHHhCcccccccccc---cCCcceeEEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCC
Q 009520 339 FEDTLSATIEAVVRLQPRCSEKIERD---SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIA 415 (533)
Q Consensus 339 ~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~ 415 (533)
+++++..+.++..++...+.+.+... .........+.||.+.+|.|||+||.+||+|+++|||+|.|.
T Consensus 544 l~~aL~~A~~g~~~Il~~m~~al~~p~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~--------- 614 (719)
T TIGR02696 544 LASALKQARDARLAILDVMAEAIDTPDEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE--------- 614 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCccccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe---------
Confidence 33444445555544443332222221 122356788999999999999999999999999999999994
Q ss_pred CCCCcEEEEEe-CHHHHHHHHHHHHHHHHh
Q 009520 416 SEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (533)
Q Consensus 416 ~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~ 444 (533)
++..|.|.+ +.+.+++|+.+|...+..
T Consensus 615 --d~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 615 --DDGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred --cCcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 245899998 489999999999888874
No 43
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.71 E-value=8.8e-05 Score=82.82 Aligned_cols=97 Identities=21% Similarity=0.297 Sum_probs=73.9
Q ss_pred ccCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccC
Q 009520 107 KFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCAL 186 (533)
Q Consensus 107 ~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 186 (533)
+.+..|.++..+|++.+.+.............+....+.||.+.++.|||++|.+||+|+++|||+|.|..
T Consensus 518 ~al~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d--------- 588 (684)
T TIGR03591 518 QALEQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED--------- 588 (684)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec---------
Confidence 45566777778887765544333323334456778889999999999999999999999999999999954
Q ss_pred CCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009520 187 RSDELVQISG-EASVVKKALCQIASRLHD 214 (533)
Q Consensus 187 ~~dr~v~I~G-~~~~V~~A~~~I~~~l~~ 214 (533)
+..|.|.+ ..+.+.+|...|..+..+
T Consensus 589 --dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 589 --DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred --CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 45677776 567889998888877653
No 44
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.68 E-value=0.00038 Score=71.66 Aligned_cols=77 Identities=25% Similarity=0.393 Sum_probs=58.6
Q ss_pred ceeEEEeecC------CceeEEecCCChhHHHHHHhcCceEEEecCC----------CCCCCCCCCCc-EEEEEeC-HHH
Q 009520 369 SFTTRLLVPT------SRIGCLIGKGGSIITEMRRLTKANIRILPKE----------NLPKIASEDDE-MVQISGD-LDL 430 (533)
Q Consensus 369 ~~~~~l~Vp~------~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~----------~~P~~~~~~~r-~V~I~G~-~~~ 430 (533)
.++.+|.||. +++|+|||..|.|.|+|+++|||+|.|-.+. ++.......+. -+.|+.+ .|.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek 216 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK 216 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence 5667788874 7899999999999999999999999997621 11111122233 4788885 799
Q ss_pred HHHHHHHHHHHHHhc
Q 009520 431 AKDALIQVMTRLRAN 445 (533)
Q Consensus 431 v~~A~~~I~~~l~~~ 445 (533)
|++|+.+|..+|.+.
T Consensus 217 i~~Ai~vienli~~a 231 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSA 231 (554)
T ss_pred HHHHHHHHHHHHHhh
Confidence 999999999999864
No 45
>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=97.65 E-value=7.3e-05 Score=66.05 Aligned_cols=103 Identities=23% Similarity=0.285 Sum_probs=68.8
Q ss_pred EEEEEecCCccceeecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHH
Q 009520 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRV 123 (533)
Q Consensus 44 ~~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i 123 (533)
..-++|....+|..||++|++|+.|++..|=+|.|-+ -+..+++ .+.+.+
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe-----------ys~D~~~-------------------fI~N~l 83 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE-----------YSENLEE-------------------FVANKL 83 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE-----------cCCCHHH-------------------HHHHcC
Confidence 5667889999999999999999999988888887532 1111111 011100
Q ss_pred HHhhccCCCCCCCCCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEe
Q 009520 124 IAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRIL 176 (533)
Q Consensus 124 ~~~~~~~~~~~~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~ 176 (533)
.-..+..-............+.||.++.+..|||+|.+++....-++-++.|.
T Consensus 84 ~PA~V~~V~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 84 APAEVKNVTVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred CCceEEEEEEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 00000000000112345678899999999999999999999999999888763
No 46
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.59 E-value=7.9e-05 Score=75.15 Aligned_cols=65 Identities=28% Similarity=0.451 Sum_probs=54.8
Q ss_pred CCCCCCCcccCCCceEEEEEecCCccceeecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCC
Q 009520 29 TGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSAS 96 (533)
Q Consensus 29 ~~~~~~~~~~~~~~~~~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~ 96 (533)
..+.++..+...+++.+.+.+-++++|.|||++|++|+.|+..|+++|++.+. ..+-.|+|.|..
T Consensus 33 ~~~~~~~~aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~ 97 (629)
T KOG0336|consen 33 HRDSRDSAAAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGIN 97 (629)
T ss_pred CCCCCcccccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechH
Confidence 34455666678889999999999999999999999999999999999999764 335678999874
No 47
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.57 E-value=0.00015 Score=81.57 Aligned_cols=98 Identities=20% Similarity=0.249 Sum_probs=77.7
Q ss_pred cccCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEecCCceeeeeccCchHHHHHHhhcCce-EEEeecCCCCcc
Q 009520 106 DKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQ-IRILKDEHLPSC 184 (533)
Q Consensus 106 ~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~-I~i~~~~~~p~~ 184 (533)
.+.+..|.+++.+|++.+.+.............+....+.||.+.++.|||.+|.+||.|.++||++ |.+.+
T Consensus 651 ~eAL~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d------- 723 (891)
T PLN00207 651 ERALLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD------- 723 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC-------
Confidence 3567778888888888766544333333455567788999999999999999999999999999999 87743
Q ss_pred cCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009520 185 ALRSDELVQISG-EASVVKKALCQIASRLHD 214 (533)
Q Consensus 185 ~~~~dr~v~I~G-~~~~V~~A~~~I~~~l~~ 214 (533)
+-.|.|.+ ..+.+++|+..|..++.+
T Consensus 724 ----dg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 724 ----DGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred ----CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 56788888 578899999999888764
No 48
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.55 E-value=0.00012 Score=78.81 Aligned_cols=97 Identities=24% Similarity=0.269 Sum_probs=78.4
Q ss_pred ccCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccC
Q 009520 107 KFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCAL 186 (533)
Q Consensus 107 ~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 186 (533)
..+..|..|..+++..+.+..-..........+....+.|+.+.+.-+||++|.+|++|.++|||+|++..
T Consensus 519 ~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied--------- 589 (692)
T COG1185 519 KALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED--------- 589 (692)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC---------
Confidence 45677888888888877654433333334555667889999999999999999999999999999999952
Q ss_pred CCCceEEEEcCH-HHHHHHHHHHHHHHhc
Q 009520 187 RSDELVQISGEA-SVVKKALCQIASRLHD 214 (533)
Q Consensus 187 ~~dr~v~I~G~~-~~V~~A~~~I~~~l~~ 214 (533)
+..|.|.++. +.+.+|+..|.++.++
T Consensus 590 --dGtv~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 590 --DGTVKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred --CCcEEEEecchHHHHHHHHHHHHHHhh
Confidence 5679999986 7789999999998866
No 49
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.39 E-value=0.0013 Score=67.96 Aligned_cols=76 Identities=25% Similarity=0.389 Sum_probs=56.9
Q ss_pred ceEEEEEecC------CceeeeeccCchHHHHHHhhcCceEEEeecCC----------CCccc-CCCCceEEEEcC-HHH
Q 009520 139 QVTAKLLVPS------DQIGCVIGKGGQIVQNIRSETGAQIRILKDEH----------LPSCA-LRSDELVQISGE-ASV 200 (533)
Q Consensus 139 ~~~~~llVp~------~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~----------~p~~~-~~~dr~v~I~G~-~~~ 200 (533)
.++-+|.||- +.+|+|||..|.|.|+|+.+|||||.|..+.. +.... ...+=-|.|+++ .|.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek 216 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK 216 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence 6777888875 57899999999999999999999999976211 11111 112224678776 578
Q ss_pred HHHHHHHHHHHHhc
Q 009520 201 VKKALCQIASRLHD 214 (533)
Q Consensus 201 V~~A~~~I~~~l~~ 214 (533)
|++|+..|..+|.+
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999998886
No 50
>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=97.35 E-value=0.00033 Score=78.30 Aligned_cols=65 Identities=28% Similarity=0.354 Sum_probs=55.8
Q ss_pred ceeEEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHHh
Q 009520 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (533)
Q Consensus 369 ~~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~ 444 (533)
.....+.||.+.+|.|||+||.+||+|+++|||+|.|. ++..|.|.+ ..+.+++|+.+|......
T Consensus 550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~-----------ddG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE-----------DDGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEe-----------cCeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 56778999999999999999999999999999999994 234788877 578899999998877653
No 51
>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=97.29 E-value=0.00077 Score=59.61 Aligned_cols=102 Identities=25% Similarity=0.336 Sum_probs=70.4
Q ss_pred EEEEeeecCccccccccCchhhHhhhhhcCCeEEecCCCCCCCceeEEecCcchhhhhhhHHHHHHHHhCcccccccccc
Q 009520 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERD 364 (533)
Q Consensus 285 ~~~v~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~ 364 (533)
.+-|.|....+|..||++|.+|+.|++..|-+|.+-.-+.+. .+++..+ +.|--.....-.
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~D~---------~~fI~N~----------l~PA~V~~V~i~ 94 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSENL---------EEFVANK----------LAPAEVKNVTVS 94 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCCH---------HHHHHHc----------CCCceEEEEEEE
Confidence 677889999999999999999999988888887776432210 0111111 111110111000
Q ss_pred cCCcceeEEEeecCCceeEEecCCChhHHHHHHhcCceEEE
Q 009520 365 SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405 (533)
Q Consensus 365 ~~~~~~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i 405 (533)
..+......+.||.+..+..|||+|.+|+-..+.++-++.|
T Consensus 95 ~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI 135 (141)
T TIGR01952 95 EFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI 135 (141)
T ss_pred cCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence 01124567789999999999999999999999999998877
No 52
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.05 E-value=0.0011 Score=71.56 Aligned_cols=97 Identities=22% Similarity=0.224 Sum_probs=71.2
Q ss_pred hhhhhHHHHHHHHhCccccccccccc----CCcceeEEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCC
Q 009520 340 EDTLSATIEAVVRLQPRCSEKIERDS----GLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIA 415 (533)
Q Consensus 340 ~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~ 415 (533)
..+..++..+.+++...+.+.+.... .-......+.|+.+.++.|||++|.+|++|.++|||+|.|.
T Consensus 518 ~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie--------- 588 (692)
T COG1185 518 KKALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE--------- 588 (692)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec---------
Confidence 34444555565655544444332211 11245678999999999999999999999999999999994
Q ss_pred CCCCcEEEEEeCH-HHHHHHHHHHHHHHHhccc
Q 009520 416 SEDDEMVQISGDL-DLAKDALIQVMTRLRANLF 447 (533)
Q Consensus 416 ~~~~r~V~I~G~~-~~v~~A~~~I~~~l~~~~~ 447 (533)
++.+|.|.++. +.+..|+..|...+++...
T Consensus 589 --ddGtv~i~~s~~~~~~~ak~~I~~i~~e~ev 619 (692)
T COG1185 589 --DDGTVKIAASDGESAKKAKERIEAITREVEV 619 (692)
T ss_pred --CCCcEEEEecchHHHHHHHHHHHHHHhhccc
Confidence 23479999975 8899999999998877643
No 53
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=97.04 E-value=0.0015 Score=60.83 Aligned_cols=102 Identities=28% Similarity=0.337 Sum_probs=67.4
Q ss_pred EEEEecCCccceeecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHH
Q 009520 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVI 124 (533)
Q Consensus 45 ~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~ 124 (533)
+-..+-.+.+|..||++|++|+.|.++-|=+|.|-+- +-.+. .-+.+.+.
T Consensus 78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~-----------s~d~~-------------------~fI~nal~ 127 (190)
T COG0195 78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW-----------SEDPA-------------------EFIKNALA 127 (190)
T ss_pred EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEe-----------CCCHH-------------------HHHHHhcC
Confidence 4455566778999999999999999999977764321 11110 11111111
Q ss_pred -HhhccCCCCCCCCCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeec
Q 009520 125 -AEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (533)
Q Consensus 125 -~~~~~~~~~~~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (533)
++...-.- ...+.. ...+.||.++.+.+|||+|.+++-+.+-||-++.|...
T Consensus 128 Pa~v~~V~~-~~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~ 180 (190)
T COG0195 128 PAEVLSVNI-KEDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI 180 (190)
T ss_pred cceEeEEEE-EeCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence 00000000 011122 78889999999999999999999999999999999763
No 54
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.92 E-value=0.001 Score=74.59 Aligned_cols=97 Identities=22% Similarity=0.319 Sum_probs=73.1
Q ss_pred ccCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccC
Q 009520 107 KFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCAL 186 (533)
Q Consensus 107 ~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 186 (533)
+.+..|.++..+|++.+.+..-....+.....+....+.||.+.++.+||++|.+||.|.++||++|.+..
T Consensus 521 ~al~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d--------- 591 (693)
T PRK11824 521 EALEQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED--------- 591 (693)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC---------
Confidence 45667788888888876654333222223344556677789999999999999999999999999988732
Q ss_pred CCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009520 187 RSDELVQISG-EASVVKKALCQIASRLHD 214 (533)
Q Consensus 187 ~~dr~v~I~G-~~~~V~~A~~~I~~~l~~ 214 (533)
+..|.|.+ ..+.+.+|...|..+..+
T Consensus 592 --~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 592 --DGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred --CceEEEEcccHHHHHHHHHHHHHhccc
Confidence 56788888 568889999988877753
No 55
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.88 E-value=0.0011 Score=74.93 Aligned_cols=66 Identities=20% Similarity=0.294 Sum_probs=57.1
Q ss_pred cceeEEEeecCCceeEEecCCChhHHHHHHhcCce-EEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHHh
Q 009520 368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKAN-IRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (533)
Q Consensus 368 ~~~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~-I~i~~~~~~P~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~ 444 (533)
......+.||.+.+|.|||.||.+||+|.++||+. |.+. ++-.|.|.+ +.+.++.|+.+|.+.+.+
T Consensus 683 aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~-----------ddg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 683 APLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ-----------DDGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred CCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-----------CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 35778899999999999999999999999999999 8873 245788888 589999999999888764
No 56
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.74 E-value=0.0018 Score=62.13 Aligned_cols=42 Identities=31% Similarity=0.476 Sum_probs=36.6
Q ss_pred cCCCceEEEEEecCC------ccceeecCCcHHHHHHHHHhCCeEEEc
Q 009520 38 IGPEDTVYRYLCPIR------KIGSIIGRGGEIVKQLRIDTKSKIRIG 79 (533)
Q Consensus 38 ~~~~~~~~rilvp~~------~~g~IIGk~G~~Ik~i~~~tga~I~i~ 79 (533)
...-.++.+|+||.+ +||.|+|++|.++|+|+++|+|+|.|-
T Consensus 87 ~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 87 GKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred CCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 445566789999998 799999999999999999999998653
No 57
>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=96.65 E-value=0.0034 Score=47.28 Aligned_cols=37 Identities=30% Similarity=0.421 Sum_probs=34.1
Q ss_pred ceEEEEEecCCccceeecCCcHHHHHHHHHhCCeEEE
Q 009520 42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRI 78 (533)
Q Consensus 42 ~~~~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i 78 (533)
...+.+.|+.+..|.+|||+|.+|+.+++.++-+|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3578999999999999999999999999999988876
No 58
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.64 E-value=0.0022 Score=64.95 Aligned_cols=66 Identities=24% Similarity=0.331 Sum_probs=53.2
Q ss_pred ceeEEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHH
Q 009520 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRL 442 (533)
Q Consensus 369 ~~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l 442 (533)
.+...+.|-.++||.|||++|++|+.||..|.++|+|... +.+-.|+|-|...--.+|+..|...+
T Consensus 46 e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~--------~~e~kv~ifg~~~m~~kaka~id~~~ 111 (629)
T KOG0336|consen 46 EFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC--------DLEVKVTIFGINHMRKKAKASIDRGQ 111 (629)
T ss_pred CCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc--------CceeEEEEechHHHHHHHHhhHhhhh
Confidence 4666788889999999999999999999999999999653 23458999998877666666554433
No 59
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.64 E-value=0.0065 Score=56.55 Aligned_cols=101 Identities=24% Similarity=0.308 Sum_probs=67.1
Q ss_pred EEEeeecCccccccccCchhhHhhhhhcCCeEEecCCCCCCCceeEEecCcchhhhhhhHHHHHHHHhCccccccccccc
Q 009520 286 LRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDS 365 (533)
Q Consensus 286 ~~v~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~ 365 (533)
+-+.+-...+|..||++|.+|+.|.++.|-+|.+-.-+.+ .+ .-...++. |--.....-..
T Consensus 78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d-------------~~---~fI~nal~---Pa~v~~V~~~~ 138 (190)
T COG0195 78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSED-------------PA---EFIKNALA---PAEVLSVNIKE 138 (190)
T ss_pred EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCC-------------HH---HHHHHhcC---cceEeEEEEEe
Confidence 3445556778999999999999999999966665532211 00 00111111 11000111111
Q ss_pred CCcceeEEEeecCCceeEEecCCChhHHHHHHhcCceEEEe
Q 009520 366 GLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRIL 406 (533)
Q Consensus 366 ~~~~~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~ 406 (533)
.+.. ...+.||.+..+..|||+|.+++-+.+.||-++.|.
T Consensus 139 ~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~ 178 (190)
T COG0195 139 DDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIE 178 (190)
T ss_pred CCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEE
Confidence 0112 778899999999999999999999999999999985
No 60
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.61 E-value=0.0088 Score=57.54 Aligned_cols=76 Identities=20% Similarity=0.343 Sum_probs=53.4
Q ss_pred cceeEEEeecC------CceeEEecCCChhHHHHHHhcCceEEEecCCCC------------CCCCCCCC---cEEEEEe
Q 009520 368 ISFTTRLLVPT------SRIGCLIGKGGSIITEMRRLTKANIRILPKENL------------PKIASEDD---EMVQISG 426 (533)
Q Consensus 368 ~~~~~~l~Vp~------~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~------------P~~~~~~~---r~V~I~G 426 (533)
...+.+|+||- ++||.|+|.+|.++|+|+++|||+|-|-.+... |..+.-++ -+|+...
T Consensus 90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~ 169 (259)
T KOG1588|consen 90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEA 169 (259)
T ss_pred eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeC
Confidence 46788899984 689999999999999999999999999766321 22222222 2466777
Q ss_pred CHHHHHH----HHHHHHHHHH
Q 009520 427 DLDLAKD----ALIQVMTRLR 443 (533)
Q Consensus 427 ~~~~v~~----A~~~I~~~l~ 443 (533)
++..+.. |++.|...|.
T Consensus 170 p~~ea~~rl~~AleeI~klL~ 190 (259)
T KOG1588|consen 170 PPAEAYARLAYALEEIKKLLV 190 (259)
T ss_pred CHHHHHHHHHHHHHHHHHhcC
Confidence 7765544 5555555543
No 61
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.44 E-value=0.0036 Score=61.81 Aligned_cols=70 Identities=27% Similarity=0.401 Sum_probs=57.3
Q ss_pred ceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEE-EcCHHHHHHHHHHHHHHHhcC
Q 009520 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQI-SGEASVVKKALCQIASRLHDN 215 (533)
Q Consensus 139 ~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I-~G~~~~V~~A~~~I~~~l~~~ 215 (533)
.....++|++...++|||++|.|-++|+++|+++|.++... .....++| .+..++|-+|...|..+|...
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~-------~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN-------TNKEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC-------CCcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 45677899999999999999999999999999999887642 23344554 456788999999998888764
No 62
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.43 E-value=0.0033 Score=62.07 Aligned_cols=68 Identities=21% Similarity=0.296 Sum_probs=53.2
Q ss_pred ceEEEEEecCCccceeecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHH
Q 009520 42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHD 121 (533)
Q Consensus 42 ~~~~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~ 121 (533)
+...-+++++.+.|.|||++|.|.++|+++|+|+|.++.+ +.....|+|.|...++ +..|+.+|..
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p--~~n~~~i~i~~~~~~~------------V~~a~~Ri~~ 121 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP--NTNKEEIKIIGISRNC------------VIQALERIAK 121 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC--CCCcceEEEeehhHHH------------HHHHHHHHHH
Confidence 3556799999999999999999999999999999999877 4444577888776543 5556666655
Q ss_pred HH
Q 009520 122 RV 123 (533)
Q Consensus 122 ~i 123 (533)
.|
T Consensus 122 ~i 123 (345)
T KOG2814|consen 122 LI 123 (345)
T ss_pred HH
Confidence 44
No 63
>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=96.39 E-value=0.0063 Score=62.12 Aligned_cols=96 Identities=24% Similarity=0.350 Sum_probs=62.9
Q ss_pred CccceeecCCcHHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHHHhhccC
Q 009520 52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG 130 (533)
Q Consensus 52 ~~~g~IIGk~G~~Ik~i~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~ 130 (533)
+-+|+.||++|++|+.|.++- |=+|.|-.- +-.++. -+...+.-..+..
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~-----------s~d~~~-------------------fi~nal~Pa~v~~ 292 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEY-----------SDDPAE-------------------FIANALSPAKVIS 292 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEc-----------CCCHHH-------------------HHHHhcCCceEEE
Confidence 358999999999999999997 777765321 111100 0111000000000
Q ss_pred CCCCCCCCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeec
Q 009520 131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (533)
Q Consensus 131 ~~~~~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (533)
- .........+.+.||.++.+..|||+|.+++-...-||.+|.|.+.
T Consensus 293 v-~i~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~ 339 (341)
T TIGR01953 293 V-EVLDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE 339 (341)
T ss_pred E-EEEcCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence 0 0000122468999999999999999999999999999999999764
No 64
>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=96.38 E-value=0.0056 Score=46.08 Aligned_cols=36 Identities=44% Similarity=0.679 Sum_probs=33.8
Q ss_pred eEEEEEecCCceeeeeccCchHHHHHHhhcCceEEE
Q 009520 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRI 175 (533)
Q Consensus 140 ~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i 175 (533)
....+.|+.+.++.+|||+|.+|+.++..++-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 578999999999999999999999999999988876
No 65
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.23 E-value=0.0086 Score=61.23 Aligned_cols=96 Identities=18% Similarity=0.163 Sum_probs=63.2
Q ss_pred CccceeecCCcHHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHHHhhccC
Q 009520 52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG 130 (533)
Q Consensus 52 ~~~g~IIGk~G~~Ik~i~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~ 130 (533)
+-+|..||++|++|+.|.++- |=+|.|-.- +-.+. ..+...+.-..+..
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~-----------s~D~~-------------------~fI~Nal~Pa~V~~ 300 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEY-----------SNVPE-------------------IFIARALAPAIISS 300 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEc-----------CCCHH-------------------HHHHHhCCCceeeE
Confidence 358999999999999999997 777765321 11100 00111000000000
Q ss_pred CCCCCCCCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecC
Q 009520 131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179 (533)
Q Consensus 131 ~~~~~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~ 179 (533)
- . -....-.+.+.||.++.+..|||+|.+++-...-||.+|.|..-+
T Consensus 301 V-~-i~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~ 347 (374)
T PRK12328 301 V-K-IEEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG 347 (374)
T ss_pred E-E-EcCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence 0 0 001224688999999999999999999999999999999998743
No 66
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.18 E-value=0.0078 Score=61.87 Aligned_cols=96 Identities=23% Similarity=0.278 Sum_probs=63.3
Q ss_pred CccceeecCCcHHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHHHhhccC
Q 009520 52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG 130 (533)
Q Consensus 52 ~~~g~IIGk~G~~Ik~i~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~ 130 (533)
+-+|+.||++|++|+.|.++. |=+|.|-.- +-.++ ..+...+.-..+..
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~-----------s~d~~-------------------~fi~nal~Pa~v~~ 294 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDW-----------SEDPA-------------------EFVANALSPAKVVS 294 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEc-----------CCCHH-------------------HHHHHhCCCceEEE
Confidence 358999999999999999998 777775321 11100 00111000000000
Q ss_pred CCCCCCCCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeec
Q 009520 131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (533)
Q Consensus 131 ~~~~~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (533)
- .........+.+.||.++.+..|||+|.+++-...-||.+|.|...
T Consensus 295 v-~i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 295 V-EVDDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred E-EEEcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 0 0000123468899999999999999999999999999999999775
No 67
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.05 E-value=0.013 Score=57.02 Aligned_cols=63 Identities=21% Similarity=0.246 Sum_probs=53.1
Q ss_pred EEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeC-HHHHHHHHHHHHHHHHhc
Q 009520 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD-LDLAKDALIQVMTRLRAN 445 (533)
Q Consensus 372 ~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~-~~~v~~A~~~I~~~l~~~ 445 (533)
+.+.||.++++.+||++|.+|+.|.+.|++.|.|- .+..|.|.++ .+++..|+.+|...-++.
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig-----------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG-----------QNGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc-----------CCcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 56899999999999999999999999999999983 2357999997 568888888887665554
No 68
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.91 E-value=0.021 Score=61.78 Aligned_cols=65 Identities=25% Similarity=0.336 Sum_probs=49.4
Q ss_pred ceeEEEeecC-CceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHH
Q 009520 369 SFTTRLLVPT-SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLR 443 (533)
Q Consensus 369 ~~~~~l~Vp~-~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~ 443 (533)
..+..|.+|+ ++-|.||||-|.+|+-+...||+.|.|. +.| ..|+|++ +|---+.|..-+..+|.
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid---dtp-------~~v~ls~fdp~rreia~~~l~~li~ 269 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---DTP-------EAVILSGFDPVRREIARMALEKLIQ 269 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc---CCC-------CeEEecCCchHHHHHHHHHHHHHHH
Confidence 4666788898 5559999999999999999999999993 334 4899999 56555555555544443
No 69
>PRK12704 phosphodiesterase; Provisional
Probab=95.87 E-value=0.023 Score=61.65 Aligned_cols=65 Identities=25% Similarity=0.328 Sum_probs=49.2
Q ss_pred ceeEEEeecC-CceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHH
Q 009520 369 SFTTRLLVPT-SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLR 443 (533)
Q Consensus 369 ~~~~~l~Vp~-~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~ 443 (533)
..+..+.+|+ ++-|.||||-|.+|+-+...||+.|.|. +.| .+|.|+| +|---+.|...+...+.
T Consensus 209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid---dtp-------~~v~ls~~~~~rre~a~~~l~~l~~ 275 (520)
T PRK12704 209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---DTP-------EAVILSGFDPIRREIARLALEKLVQ 275 (520)
T ss_pred hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc---CCC-------CeEEEecCChhhHHHHHHHHHHHHh
Confidence 4566788888 5569999999999999999999999993 334 4899999 56554555555544443
No 70
>PRK00106 hypothetical protein; Provisional
Probab=95.87 E-value=0.026 Score=60.94 Aligned_cols=65 Identities=26% Similarity=0.367 Sum_probs=49.8
Q ss_pred ceeEEEeecC-CceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHH
Q 009520 369 SFTTRLLVPT-SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLR 443 (533)
Q Consensus 369 ~~~~~l~Vp~-~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~ 443 (533)
..+..+.+|+ ++-|.||||-|.+|+-+...||+.+.|. +.| ..|+|+| +|---+.|..-+..+|.
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid---dtp-------~~v~lS~fdpvRReiAr~~le~Li~ 290 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID---DTP-------EVVVLSGFDPIRREIARMTLESLIK 290 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc---CCC-------CeEEEeCCChHHHHHHHHHHHHHHH
Confidence 4666788898 5669999999999999999999999993 334 4899999 66555555555544444
No 71
>PRK00468 hypothetical protein; Provisional
Probab=95.86 E-value=0.0097 Score=46.62 Aligned_cols=34 Identities=24% Similarity=0.501 Sum_probs=29.9
Q ss_pred CCCceEEEEEecCCccceeecCCcHHHHHHHHHh
Q 009520 39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDT 72 (533)
Q Consensus 39 ~~~~~~~rilvp~~~~g~IIGk~G~~Ik~i~~~t 72 (533)
.++.+.+++.|..+-+|.||||+|.+|+.||.--
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 3455789999999999999999999999999753
No 72
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.83 E-value=0.0071 Score=67.93 Aligned_cols=65 Identities=29% Similarity=0.363 Sum_probs=54.7
Q ss_pred ceeEEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHHh
Q 009520 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (533)
Q Consensus 369 ~~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~ 444 (533)
.....+.||.+.++.+||+||.+||+|.++||+.|.+. ++-.|.|.+ ..+.+++|+.+|.....+
T Consensus 553 p~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-----------d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 553 PRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-----------DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred chheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 45567888999999999999999999999999988862 245788888 578999999999887754
No 73
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.81 E-value=0.02 Score=59.51 Aligned_cols=95 Identities=23% Similarity=0.257 Sum_probs=61.9
Q ss_pred CccceeecCCcHHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHHHhhccC
Q 009520 52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG 130 (533)
Q Consensus 52 ~~~g~IIGk~G~~Ik~i~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~ 130 (533)
+-+|..||++|++|+.|.++. |=+|.|-.- +-.++ ..|...+.-..+..
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~y-----------s~Dp~-------------------~fI~NaLsPA~V~~ 326 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRW-----------SPDPA-------------------TYIANALSPARVDE 326 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEc-----------CCCHH-------------------HHHHHhcCCceeeE
Confidence 458999999999999999998 777765321 11110 00111000000000
Q ss_pred CCCCCCCCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEee
Q 009520 131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILK 177 (533)
Q Consensus 131 ~~~~~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~ 177 (533)
- .........+.+.||.++.+..|||+|.+++-...-||-+|.|..
T Consensus 327 V-~i~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 327 V-RLVDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred E-EEEcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 0 000011235789999999999999999999999999999999865
No 74
>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=95.80 E-value=0.027 Score=57.55 Aligned_cols=94 Identities=24% Similarity=0.392 Sum_probs=63.8
Q ss_pred CccccccccCchhhHhhhhhc-CCeEEecCCCCCCCceeEEecCcchhhhhhhHHHHHHHHhCcccccc-cccccCCcce
Q 009520 293 ANIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEK-IERDSGLISF 370 (533)
Q Consensus 293 ~~~g~IIGk~G~~Ik~i~~~t-ga~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~ 370 (533)
+-+|..||++|.+|+.|.++. |-+|.+-.-+.+ . .+++. .|+.... +..- +..+ ...
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d---~------~~fi~-------nal~Pa~--v~~v~i~~~---~~~ 301 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDD---P------AEFIA-------NALSPAK--VISVEVLDE---DKH 301 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCC---H------HHHHH-------HhcCCce--EEEEEEEcC---CCc
Confidence 457999999999999999998 667766543221 0 01111 1111100 0000 1111 125
Q ss_pred eEEEeecCCceeEEecCCChhHHHHHHhcCceEEEec
Q 009520 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP 407 (533)
Q Consensus 371 ~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~ 407 (533)
...+.||.++.+..|||+|.+++-..+.||.+|.|.+
T Consensus 302 ~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 302 SAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred EEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 6889999999999999999999999999999999965
No 75
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.75 E-value=0.023 Score=52.26 Aligned_cols=42 Identities=31% Similarity=0.496 Sum_probs=36.2
Q ss_pred cCCCceEEEEEecCC------ccceeecCCcHHHHHHHHHhCCeEEEc
Q 009520 38 IGPEDTVYRYLCPIR------KIGSIIGRGGEIVKQLRIDTKSKIRIG 79 (533)
Q Consensus 38 ~~~~~~~~rilvp~~------~~g~IIGk~G~~Ik~i~~~tga~I~i~ 79 (533)
+.+..+.-++.||.+ ++|++||+.|.|+|+|++.|+|+|-|-
T Consensus 143 ~rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIR 190 (269)
T COG5176 143 IRPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIR 190 (269)
T ss_pred cCcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEe
Confidence 455667778888864 899999999999999999999999885
No 76
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=95.63 E-value=0.022 Score=59.93 Aligned_cols=112 Identities=19% Similarity=0.206 Sum_probs=79.1
Q ss_pred EEEcCCcccccccc----CcccCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEecCCceeeeeccCchHHHHHH
Q 009520 91 TVYSASDETNAFED----GDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIR 166 (533)
Q Consensus 91 ~I~G~~~~~~~~~~----~~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~ 166 (533)
.|-|..+.+.|+.. ..+.+.+|.+|...|++.+....-.+........++...+.|+.++...+||.+|...|+|.
T Consensus 544 KiAGt~dGvTA~gi~l~Iv~eal~~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~ 623 (760)
T KOG1067|consen 544 KIAGTNDGVTALGIPLKIVMEALQKAREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIE 623 (760)
T ss_pred eeccccCcceecCCcHHHHHHHHHhhhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEe
Confidence 45555555544421 12445567777777777655444333334456678889999999999999999999999999
Q ss_pred hhcCceEEEeecCCCCcccCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009520 167 SETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHD 214 (533)
Q Consensus 167 ~~tga~I~i~~~~~~p~~~~~~dr~v~I~G-~~~~V~~A~~~I~~~l~~ 214 (533)
.+||+.-++ ++.+++|.. +..+.++|...|..++..
T Consensus 624 ~EtGai~~v------------De~t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 624 VETGAISQV------------DEGTFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred eeccceeee------------cCceEEEEecCHHHHHHHHHHHHHHhcC
Confidence 999955544 245677766 467788999988888766
No 77
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.58 E-value=0.045 Score=50.41 Aligned_cols=41 Identities=27% Similarity=0.611 Sum_probs=35.3
Q ss_pred cceeEEEeec------CCceeEEecCCChhHHHHHHhcCceEEEecC
Q 009520 368 ISFTTRLLVP------TSRIGCLIGKGGSIITEMRRLTKANIRILPK 408 (533)
Q Consensus 368 ~~~~~~l~Vp------~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~ 408 (533)
..++..+.|| .+++|+|||+.|.+.|+|++.|+|+|-|-.+
T Consensus 146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 3566677777 4789999999999999999999999999654
No 78
>PRK02821 hypothetical protein; Provisional
Probab=95.52 E-value=0.015 Score=45.78 Aligned_cols=35 Identities=23% Similarity=0.374 Sum_probs=30.4
Q ss_pred CCCceEEEEEecCCccceeecCCcHHHHHHHHHhC
Q 009520 39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (533)
Q Consensus 39 ~~~~~~~rilvp~~~~g~IIGk~G~~Ik~i~~~tg 73 (533)
.++.+.+.|.|..+-+|.||||+|.+|+.||.--.
T Consensus 27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 34557899999999999999999999999997744
No 79
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=95.46 E-value=0.32 Score=46.32 Aligned_cols=65 Identities=18% Similarity=0.355 Sum_probs=56.3
Q ss_pred eEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 009520 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD 214 (533)
Q Consensus 140 ~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~ 214 (533)
-.+.+.++.....++...+|..+++|....||+|.+..+ +..|.|+|+...++.+...|.+++..
T Consensus 26 g~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~----------~~~i~I~g~k~~~~~i~~~i~~~l~~ 90 (210)
T PF14611_consen 26 GDLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS----------ENRIRITGTKSTAEYIEASINEILSN 90 (210)
T ss_pred ceeEEEecchheeeeecCCchHHHHHHHhcCceEEEecC----------CcEEEEEccHHHHHHHHHHHHHHHhh
Confidence 345566668899999999999999998899999999764 56899999999999999999888865
No 80
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.38 E-value=0.053 Score=55.56 Aligned_cols=97 Identities=22% Similarity=0.216 Sum_probs=65.2
Q ss_pred CccccccccCchhhHhhhhhc-CCeEEecCCCCCCCceeEEecCcchhhhhhhHHHHHHHHhCcccccccccccCCccee
Q 009520 293 ANIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFT 371 (533)
Q Consensus 293 ~~~g~IIGk~G~~Ik~i~~~t-ga~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ 371 (533)
+-+|..||++|.+|+.|.++. |-+|.+-.-+.+ . .+++..+++++ . +. ...-. +....
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D---~------~~fI~Nal~Pa-------~--V~-~V~i~--~~~~~ 309 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNV---P------EIFIARALAPA-------I--IS-SVKIE--EEEKK 309 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCC---H------HHHHHHhCCCc-------e--ee-EEEEc--CCCcE
Confidence 457999999999999999998 667766543221 0 01111111110 0 00 00001 11356
Q ss_pred EEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCC
Q 009520 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKEN 410 (533)
Q Consensus 372 ~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~ 410 (533)
..+.||.++.+..|||+|.+++-..+.||.+|.|.+-+.
T Consensus 310 ~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 310 AIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS 348 (374)
T ss_pred EEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence 789999999999999999999999999999999976543
No 81
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.33 E-value=0.021 Score=60.89 Aligned_cols=94 Identities=23% Similarity=0.309 Sum_probs=62.4
Q ss_pred ccceeecCCcHHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHHHhhccCC
Q 009520 53 KIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGD 131 (533)
Q Consensus 53 ~~g~IIGk~G~~Ik~i~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~~ 131 (533)
-+|+.||++|++|+.|.++- |=+|.|-.- +-.+. ..+...+.-..+..-
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~-----------s~d~~-------------------~fi~nal~pa~v~~v 295 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIILW-----------SDDPA-------------------QFIINALSPAEVSSV 295 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEEc-----------CCCHH-------------------HHHHHhCCCCEEEEE
Confidence 48999999999999999997 777775211 11100 011111100000000
Q ss_pred CCCCCCCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeec
Q 009520 132 EDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (533)
Q Consensus 132 ~~~~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (533)
.-....-.+.+.||..+.+..|||+|.+++-....||.+|.|...
T Consensus 296 --~~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 296 --VVDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred --EEeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 000012368899999999999999999999999999999999774
No 82
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.32 E-value=0.047 Score=56.17 Aligned_cols=96 Identities=27% Similarity=0.358 Sum_probs=64.2
Q ss_pred CccccccccCchhhHhhhhhc-CCeEEecCCCCCCCceeEEecCcchhhhhhhHHHHHHHHhCcccccccccccCCccee
Q 009520 293 ANIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFT 371 (533)
Q Consensus 293 ~~~g~IIGk~G~~Ik~i~~~t-ga~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ 371 (533)
+-+|..||++|.+|+.|..+. |-+|.+-.-+.+ . .+++..+.+++ . +. ...-.. .....
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d---~------~~fi~nal~Pa-------~--v~-~v~i~~-~~~~~ 304 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSED---P------AEFVANALSPA-------K--VV-SVEVDD-EEEKA 304 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCCC---H------HHHHHHhCCCc-------e--EE-EEEEEc-CCCcE
Confidence 457999999999999999998 767766543221 0 01111111110 0 00 000000 11356
Q ss_pred EEEeecCCceeEEecCCChhHHHHHHhcCceEEEecC
Q 009520 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPK 408 (533)
Q Consensus 372 ~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~ 408 (533)
..+.||.++.+..|||+|.+++--.+.||.+|.|.+.
T Consensus 305 ~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 305 ARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred EEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 8899999999999999999999999999999999653
No 83
>PRK02821 hypothetical protein; Provisional
Probab=95.28 E-value=0.033 Score=43.85 Aligned_cols=35 Identities=29% Similarity=0.498 Sum_probs=29.8
Q ss_pred CCCceEEEEEecCCceeeeeccCchHHHHHHhhcC
Q 009520 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETG 170 (533)
Q Consensus 136 ~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tg 170 (533)
....+.+.|.|..+-+|.||||+|.+|+.||.--.
T Consensus 27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 34557899999999999999999999999986543
No 84
>PRK00468 hypothetical protein; Provisional
Probab=95.28 E-value=0.019 Score=44.94 Aligned_cols=34 Identities=32% Similarity=0.435 Sum_probs=29.9
Q ss_pred CcceeEEEeecCCceeEEecCCChhHHHHHHhcC
Q 009520 367 LISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTK 400 (533)
Q Consensus 367 ~~~~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tg 400 (533)
+..+..++.+..+-+|.||||+|.+|+.||..-.
T Consensus 27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~ 60 (75)
T PRK00468 27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVK 60 (75)
T ss_pred CCeEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence 3468889999999999999999999999998644
No 85
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.09 E-value=0.046 Score=42.73 Aligned_cols=33 Identities=42% Similarity=0.658 Sum_probs=29.7
Q ss_pred CCCceEEEEEecCCceeeeeccCchHHHHHHhh
Q 009520 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSE 168 (533)
Q Consensus 136 ~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~ 168 (533)
.+....++|.|...-+|.||||+|.+|+.|+.-
T Consensus 26 ~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred cCCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 466788999999999999999999999999854
No 86
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=94.97 E-value=0.053 Score=56.50 Aligned_cols=95 Identities=25% Similarity=0.346 Sum_probs=63.0
Q ss_pred CccccccccCchhhHhhhhhc-CCeEEecCCCCCCCceeEEecCcchhhhhhhHHHHHHHHhCcccccccccccCCccee
Q 009520 293 ANIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFT 371 (533)
Q Consensus 293 ~~~g~IIGk~G~~Ik~i~~~t-ga~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ 371 (533)
+-+|..||++|.+|+.|.++. |-+|.|-.-+.+ . .+++..+++++ . +. ...-.. .....
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~D---p------~~fI~NaLsPA-------~--V~-~V~i~~-~~~k~ 336 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPD---P------ATYIANALSPA-------R--VD-EVRLVD-PEGRH 336 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCC---H------HHHHHHhcCCc-------e--ee-EEEEEc-CCCcE
Confidence 458999999999999999998 667766543221 0 01111111110 0 00 000000 11245
Q ss_pred EEEeecCCceeEEecCCChhHHHHHHhcCceEEEec
Q 009520 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP 407 (533)
Q Consensus 372 ~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~ 407 (533)
..+.||.++.+..|||+|.+++--.+.||.+|.|.+
T Consensus 337 a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 337 AHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred EEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 689999999999999999999999999999999853
No 87
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=94.86 E-value=0.042 Score=53.40 Aligned_cols=63 Identities=21% Similarity=0.289 Sum_probs=52.4
Q ss_pred EEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcCH-HHHHHHHHHHHHHHhcC
Q 009520 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA-SVVKKALCQIASRLHDN 215 (533)
Q Consensus 142 ~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~-~~V~~A~~~I~~~l~~~ 215 (533)
+.+.||.++++.+||++|.+|+.|.++|+++|.+-. +..|.|.+.. +++.+|...|..+-++.
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-----------NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-----------NGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-----------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 568899999999999999999999999999998843 4568888875 57888888887766553
No 88
>PRK01064 hypothetical protein; Provisional
Probab=94.80 E-value=0.037 Score=43.66 Aligned_cols=33 Identities=27% Similarity=0.496 Sum_probs=29.6
Q ss_pred CCceEEEEEecCCccceeecCCcHHHHHHHHHh
Q 009520 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDT 72 (533)
Q Consensus 40 ~~~~~~rilvp~~~~g~IIGk~G~~Ik~i~~~t 72 (533)
...+.+++.|..+..|.+|||+|.+|+.||.-.
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 456789999999999999999999999999753
No 89
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.80 E-value=0.034 Score=43.41 Aligned_cols=32 Identities=16% Similarity=0.367 Sum_probs=29.1
Q ss_pred CCceEEEEEecCCccceeecCCcHHHHHHHHH
Q 009520 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRID 71 (533)
Q Consensus 40 ~~~~~~rilvp~~~~g~IIGk~G~~Ik~i~~~ 71 (533)
..-+.++|-+....+|.||||+|.+|+.||.-
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 55677999999999999999999999999965
No 90
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=94.56 E-value=0.14 Score=55.45 Aligned_cols=66 Identities=21% Similarity=0.360 Sum_probs=48.6
Q ss_pred ceEEEEEecC-CceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009520 139 QVTAKLLVPS-DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHD 214 (533)
Q Consensus 139 ~~~~~llVp~-~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G-~~~~V~~A~~~I~~~l~~ 214 (533)
...-.+.+|+ ++-|+|||+.|.+|+.++.-||+.|-|.+. ...|+|+| .|---+.|...+..++.+
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt----------p~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT----------PEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC----------CCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 3445577887 677999999999999999999999988432 35688888 454445565555555544
No 91
>PRK01064 hypothetical protein; Provisional
Probab=94.53 E-value=0.081 Score=41.75 Aligned_cols=34 Identities=35% Similarity=0.603 Sum_probs=29.8
Q ss_pred CCCceEEEEEecCCceeeeeccCchHHHHHHhhc
Q 009520 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSET 169 (533)
Q Consensus 136 ~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~t 169 (533)
....+.+++.|...-.|.+|||+|.+|+.|+.-.
T Consensus 26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CCCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 4566889999999999999999999999998753
No 92
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=94.38 E-value=0.071 Score=56.91 Aligned_cols=93 Identities=26% Similarity=0.429 Sum_probs=63.5
Q ss_pred ccccccccCchhhHhhhhhc-CCeEEecCCCCCCCceeEEecCcchhhhhhhHHHHHHHHhCccccc-ccccccCCccee
Q 009520 294 NIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSE-KIERDSGLISFT 371 (533)
Q Consensus 294 ~~g~IIGk~G~~Ik~i~~~t-ga~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~~ 371 (533)
-+|..||++|.+|+.|..+. |-+|.|-.-+.+ . .++ ...++.... +.. .+... ...
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d---~------~~f-------i~nal~pa~--v~~v~~~~~----~~~ 303 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIILWSDD---P------AQF-------IINALSPAE--VSSVVVDED----EHS 303 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEEcCCC---H------HHH-------HHHhCCCCE--EEEEEEeCC----CCE
Confidence 47999999999999999998 667766543221 0 001 111111100 000 01111 247
Q ss_pred EEEeecCCceeEEecCCChhHHHHHHhcCceEEEecC
Q 009520 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPK 408 (533)
Q Consensus 372 ~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~ 408 (533)
..+.||..+.+..|||+|.+++-..+.||.+|.|...
T Consensus 304 ~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 304 ADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred EEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 7899999999999999999999999999999999764
No 93
>PRK00106 hypothetical protein; Provisional
Probab=94.34 E-value=0.19 Score=54.43 Aligned_cols=66 Identities=26% Similarity=0.412 Sum_probs=49.3
Q ss_pred ceEEEEEecC-CceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009520 139 QVTAKLLVPS-DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHD 214 (533)
Q Consensus 139 ~~~~~llVp~-~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G-~~~~V~~A~~~I~~~l~~ 214 (533)
...-.+.+|+ ++-|+|||+.|.+|+.++.-||+.+-|.+ +...|+|+| .|---+.|...+..++.+
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd----------tp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD----------TPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC----------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 4455677887 67899999999999999999999998843 235688888 455555566666555544
No 94
>PRK12704 phosphodiesterase; Provisional
Probab=94.33 E-value=0.16 Score=55.10 Aligned_cols=66 Identities=21% Similarity=0.355 Sum_probs=48.1
Q ss_pred ceEEEEEecC-CceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009520 139 QVTAKLLVPS-DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHD 214 (533)
Q Consensus 139 ~~~~~llVp~-~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G-~~~~V~~A~~~I~~~l~~ 214 (533)
...-.+.+|+ ++-|+|||+.|.+||.++.-||+.|-|.+ +..+|.|+| .+-.-+.|...+..++.+
T Consensus 209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd----------tp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD----------TPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC----------CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 3445567786 67899999999999999999999998843 245788998 444434555555555544
No 95
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=93.05 E-value=2.3 Score=40.51 Aligned_cols=130 Identities=12% Similarity=0.112 Sum_probs=84.5
Q ss_pred EEEEecCCccceeecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHH
Q 009520 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVI 124 (533)
Q Consensus 45 ~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~ 124 (533)
+.+.++....-++...+|..++.|-...||+|.+... +..|.|+|....+ +.+...++.+.
T Consensus 28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~-----~~~i~I~g~k~~~--------------~~i~~~i~~~l 88 (210)
T PF14611_consen 28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS-----ENRIRITGTKSTA--------------EYIEASINEIL 88 (210)
T ss_pred eEEEecchheeeeecCCchHHHHHHHhcCceEEEecC-----CcEEEEEccHHHH--------------HHHHHHHHHHH
Confidence 3445568888899999999999998888999999654 5689999986542 22222222222
Q ss_pred HhhccCCCCCCCCCceEEEEEecCCceeeee----ccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEE-----
Q 009520 125 AEELRGDEDSDGGHQVTAKLLVPSDQIGCVI----GKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQIS----- 195 (533)
Q Consensus 125 ~~~~~~~~~~~~~~~~~~~llVp~~~~g~II----Gk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~----- 195 (533)
.. ..+..|-++.-.--..- -.....++.|++.|++.|....+ +..+.|.
T Consensus 89 ~~------------i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~----------~~~~~i~~~~~~ 146 (210)
T PF14611_consen 89 SN------------IRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD----------GNKLKISWLASP 146 (210)
T ss_pred hh------------cEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC----------CCeEEEEEEeec
Confidence 21 22344444422111111 12467899999999999988654 3344444
Q ss_pred cCHHHHHHHHHHHHHHHhcC
Q 009520 196 GEASVVKKALCQIASRLHDN 215 (533)
Q Consensus 196 G~~~~V~~A~~~I~~~l~~~ 215 (533)
-....+..|...+...+..+
T Consensus 147 ~~~~~~~~a~RlL~~a~~~~ 166 (210)
T PF14611_consen 147 ENEKRADRAKRLLLWALDYN 166 (210)
T ss_pred cccchHHHHHHHHHHhccCC
Confidence 45677888888888777533
No 96
>PRK12705 hypothetical protein; Provisional
Probab=92.89 E-value=0.15 Score=54.81 Aligned_cols=48 Identities=27% Similarity=0.395 Sum_probs=38.0
Q ss_pred ceeEEEeecCC-ceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEe
Q 009520 369 SFTTRLLVPTS-RIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG 426 (533)
Q Consensus 369 ~~~~~l~Vp~~-~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G 426 (533)
.....+.+|.+ +-|.||||-|.+|+-++..||+.|.|. +.|. .|+|.+
T Consensus 197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid---dtp~-------~V~ls~ 245 (508)
T PRK12705 197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID---DTPE-------AVVISS 245 (508)
T ss_pred heeeeeecCChHhhccccCccchhHHHHHHhhCCceEec---CCcc-------chhhcc
Confidence 45566788874 559999999999999999999999993 3443 566666
No 97
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=92.87 E-value=0.12 Score=58.81 Aligned_cols=70 Identities=19% Similarity=0.105 Sum_probs=57.9
Q ss_pred EEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhc
Q 009520 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN 445 (533)
Q Consensus 372 ~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~ 445 (533)
..+.+|.....+|||++|.+|+.++..|||.|.|.. .-|. ...+|.+.+.|.++.++.|...|...|.+-
T Consensus 1342 ~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielek--mq~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~Dp 1411 (2131)
T KOG4369|consen 1342 GKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEK--MQPD--NQAERSKAPKGRPPSQRVATSPIGLPIIDP 1411 (2131)
T ss_pred cccccchhhhhhhhccCcchhhhHhhccceEEehhh--cCCc--cchhhhcccCCCChhhhhhhccccceeecC
Confidence 356788888999999999999999999999999853 1232 256899999999999999998887766543
No 98
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=92.50 E-value=0.07 Score=41.64 Aligned_cols=35 Identities=14% Similarity=0.218 Sum_probs=29.7
Q ss_pred CCceEEEEEecCCccceeecCCcHHHHHHHHHhCC
Q 009520 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKS 74 (533)
Q Consensus 40 ~~~~~~rilvp~~~~g~IIGk~G~~Ik~i~~~tga 74 (533)
.+...+.+-|..+..|.||||+|.+++.||.-.+.
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 45667888899999999999999999999976543
No 99
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=91.11 E-value=0.1 Score=47.83 Aligned_cols=55 Identities=22% Similarity=0.315 Sum_probs=49.1
Q ss_pred CCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHh
Q 009520 378 TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRA 444 (533)
Q Consensus 378 ~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~ 444 (533)
...+|+|+||+|.+---|+..|.++|.+.. ..|-|-|..++++.|...|+.+|-.
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad------------~kIHiLG~~~niriAR~avcsLIlG 231 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD------------SKIHILGAFQNIRIARDAVCSLILG 231 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecC------------ceEEEeecchhhHHHHHhhHhhhcc
Confidence 467899999999999999999999999852 3799999999999999999988753
No 100
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=90.42 E-value=0.39 Score=51.01 Aligned_cols=68 Identities=19% Similarity=0.207 Sum_probs=56.9
Q ss_pred CCcceeEEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEe-CHHHHHHHHHHHHHHHHh
Q 009520 366 GLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (533)
Q Consensus 366 ~~~~~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~ 444 (533)
....+...|.|+.+....+||.+|...|.|..+||+.-.+ ++.+|.|.- ++.+.++|+++|...+..
T Consensus 593 ~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 593 EYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEGTFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred ccCceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCceEEEEecCHHHHHHHHHHHHHHhcC
Confidence 3457888999999999999999999999999999965554 244788887 588999999999888765
Q ss_pred c
Q 009520 445 N 445 (533)
Q Consensus 445 ~ 445 (533)
+
T Consensus 661 ~ 661 (760)
T KOG1067|consen 661 D 661 (760)
T ss_pred c
Confidence 3
No 101
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=89.99 E-value=0.65 Score=48.52 Aligned_cols=40 Identities=35% Similarity=0.475 Sum_probs=36.3
Q ss_pred eEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecC
Q 009520 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179 (533)
Q Consensus 140 ~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~ 179 (533)
-...+.||..+++.+|||+|.+|++|+.+.|-+|.|...+
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e 525 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE 525 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence 3477899999999999999999999999999999997753
No 102
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=89.90 E-value=0.52 Score=35.52 Aligned_cols=35 Identities=14% Similarity=0.214 Sum_probs=28.1
Q ss_pred ceEEEEEecCCccceeecCCcHHHHHHHHHhCCeE
Q 009520 42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKI 76 (533)
Q Consensus 42 ~~~~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I 76 (533)
.....+.+.....|.+||++|++++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 35556666666799999999999999999988544
No 103
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=89.04 E-value=0.7 Score=44.76 Aligned_cols=52 Identities=23% Similarity=0.238 Sum_probs=46.0
Q ss_pred eEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHHHHHhc
Q 009520 382 GCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN 445 (533)
Q Consensus 382 G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~ 445 (533)
-++||.+|.+++.|+=.|.|.|-|+. .+|.+.|....++.+...+.+++..-
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG------------~TVsaiGpfkGlkevr~IV~DcM~Ni 212 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG------------NTVSAIGPFKGLKEVRKIVEDCMKNI 212 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC------------cEEEeecCcchHHHHHHHHHHHHhcc
Confidence 46899999999999999999999963 28999999999999999998887653
No 104
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=88.95 E-value=0.21 Score=38.90 Aligned_cols=35 Identities=20% Similarity=0.295 Sum_probs=29.2
Q ss_pred CCceEEEEEecCCceeeeeccCchHHHHHHhhcCc
Q 009520 137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGA 171 (533)
Q Consensus 137 ~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga 171 (533)
.....+.+-+..+..|.||||.|.|++.||--.++
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 34557888889999999999999999999876553
No 105
>PRK12705 hypothetical protein; Provisional
Probab=88.50 E-value=1 Score=48.60 Aligned_cols=38 Identities=24% Similarity=0.413 Sum_probs=31.8
Q ss_pred eEEEEEecC-CceeeeeccCchHHHHHHhhcCceEEEee
Q 009520 140 VTAKLLVPS-DQIGCVIGKGGQIVQNIRSETGAQIRILK 177 (533)
Q Consensus 140 ~~~~llVp~-~~~g~IIGk~G~~Ik~I~~~tga~I~i~~ 177 (533)
..-.+.+|+ ++-|+|||+.|.+|+.++..||+.+-|.+
T Consensus 198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd 236 (508)
T PRK12705 198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD 236 (508)
T ss_pred eeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC
Confidence 344566776 57799999999999999999999998854
No 106
>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=88.31 E-value=0.7 Score=34.77 Aligned_cols=35 Identities=26% Similarity=0.401 Sum_probs=28.7
Q ss_pred ceEEEEEecCCceeeeeccCchHHHHHHhhcCceE
Q 009520 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQI 173 (533)
Q Consensus 139 ~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I 173 (533)
...+.+.+.....+.+||++|.+++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 45666777766789999999999999999988544
No 107
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=87.46 E-value=0.94 Score=43.92 Aligned_cols=51 Identities=16% Similarity=0.185 Sum_probs=45.6
Q ss_pred eeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 009520 152 GCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD 214 (533)
Q Consensus 152 g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~ 214 (533)
-++||.+|+|+|.|+-.|.|-|-|.. .+|.+.|....+..+...|.+.+..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG------------~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG------------NTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC------------cEEEeecCcchHHHHHHHHHHHHhc
Confidence 58999999999999999999998843 4799999999999999888888876
No 108
>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=87.30 E-value=2.2 Score=37.66 Aligned_cols=94 Identities=24% Similarity=0.407 Sum_probs=58.8
Q ss_pred cCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHHHh-hccCCCCCCCC
Q 009520 59 GRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAE-ELRGDEDSDGG 137 (533)
Q Consensus 59 Gk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~-~~~~~~~~~~~ 137 (533)
=.+|..|++|-++-.-+|.|- ..+.. +.+-.+|...|.+.+-++ .+. +-.-
T Consensus 22 ~~~~dli~~lAk~lrKRIvvR--------------~dps~----------l~~~e~A~~~I~~ivP~ea~i~----di~F 73 (145)
T cd02410 22 AEDGDLVKDLAKDLRKRIVIR--------------PDPSV----------LKPPEEAIKIILEIVPEEAGIT----DIYF 73 (145)
T ss_pred hcccHHHHHHHHHHhceEEEc--------------CChhh----------cCCHHHHHHHHHHhCCCccCce----eeEe
Confidence 356788999988888777663 22111 111235555555433222 111 0011
Q ss_pred CceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCC
Q 009520 138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEH 180 (533)
Q Consensus 138 ~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~ 180 (533)
+..+-.+.|-...-|.+||++|.++++|..+||=.-.|.....
T Consensus 74 d~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 74 DDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred cCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 1223456666788899999999999999999999888877533
No 109
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=86.78 E-value=0.19 Score=57.23 Aligned_cols=71 Identities=27% Similarity=0.251 Sum_probs=59.3
Q ss_pred eEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 009520 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD 214 (533)
Q Consensus 140 ~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~ 214 (533)
...++.+|-....+|||++|.+|..++.-|||-|.+.+-. +. ...+|.+.+.|.++.++.|...|.-.+.+
T Consensus 1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq--~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ--PD--NQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcC--Cc--cchhhhcccCCCChhhhhhhccccceeec
Confidence 4567788988999999999999999999999999996511 11 24689999999999999999888777655
No 110
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=86.24 E-value=1.8 Score=45.78 Aligned_cols=97 Identities=24% Similarity=0.365 Sum_probs=63.6
Q ss_pred eeecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHHHhhccCCCCCC
Q 009520 56 SIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDSD 135 (533)
Q Consensus 56 ~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~ 135 (533)
..|=+.|..|++|-++-.-+|.|-.. +.. +.+..+|...|++.+-++.--. +-
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~d--------------Psv----------l~~~e~A~~~I~eivP~ea~i~---~i 94 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPD--------------PSV----------LKPPEEARKIILEIVPEEAGIT---DI 94 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccC--------------chh----------cCCHHHHHHHHHHhCccccCce---eE
Confidence 34567889999999998877766422 111 2223566666655432221100 01
Q ss_pred CCCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecC
Q 009520 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179 (533)
Q Consensus 136 ~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~ 179 (533)
.-...+-.++|-.+.-|.||||+|++.++|..+||-.-.|....
T Consensus 95 ~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~P 138 (637)
T COG1782 95 YFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTP 138 (637)
T ss_pred EecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecC
Confidence 11233466788889999999999999999999999887777653
No 111
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=86.01 E-value=0.47 Score=36.59 Aligned_cols=36 Identities=28% Similarity=0.450 Sum_probs=28.0
Q ss_pred EEEeecCCc-----eeEEecCCChhHHHHHHhc-CceEEEec
Q 009520 372 TRLLVPTSR-----IGCLIGKGGSIITEMRRLT-KANIRILP 407 (533)
Q Consensus 372 ~~l~Vp~~~-----~G~IIGkgG~~Ik~I~~~t-ga~I~i~~ 407 (533)
..+.|-... +|..||++|.+|+.|.++. |-+|.|-.
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 345565655 8999999999999999999 99998853
No 112
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=85.94 E-value=1.7 Score=41.62 Aligned_cols=58 Identities=22% Similarity=0.406 Sum_probs=45.0
Q ss_pred EEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcCHHH-HHHHHHHHHH
Q 009520 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASV-VKKALCQIAS 210 (533)
Q Consensus 142 ~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~-V~~A~~~I~~ 210 (533)
.-+.|++..+.++||++|+.++-|.++|+|+|-|-. ...|=|.|..+. ...|..+|..
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-----------NG~IWV~~~~~~~e~~~~~aI~~ 206 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-----------NGRIWVDGENESLEELAIEAIRK 206 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-----------CCEEEecCCCcchHHHHHHHHHH
Confidence 457899999999999999999999999999998854 345778887764 4444444443
No 113
>PRK13764 ATPase; Provisional
Probab=85.03 E-value=2.1 Score=47.24 Aligned_cols=45 Identities=31% Similarity=0.499 Sum_probs=39.0
Q ss_pred CceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCC
Q 009520 138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLP 182 (533)
Q Consensus 138 ~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p 182 (533)
..-...+.||.+.++.+|||+|.+|++|+++.|.+|.|...++.+
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 344578899999999999999999999999999999998765433
No 114
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=84.53 E-value=0.54 Score=36.25 Aligned_cols=37 Identities=32% Similarity=0.572 Sum_probs=29.7
Q ss_pred EEEEecCCc-----eeeeeccCchHHHHHHhhc-CceEEEeec
Q 009520 142 AKLLVPSDQ-----IGCVIGKGGQIVQNIRSET-GAQIRILKD 178 (533)
Q Consensus 142 ~~llVp~~~-----~g~IIGk~G~~Ik~I~~~t-ga~I~i~~~ 178 (533)
..+.|-+.. +|..||++|.+|+.|+++. |-+|+|...
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 556666666 8999999999999999999 999999764
No 115
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=84.51 E-value=2.2 Score=45.01 Aligned_cols=151 Identities=19% Similarity=0.233 Sum_probs=99.7
Q ss_pred eEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCc
Q 009520 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRS 219 (533)
Q Consensus 140 ~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~~~ 219 (533)
-.+.+.+|...+..|||-||..|++++...++.|++.-.-+++. + .-++
T Consensus 449 ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~q----------------s----------~~~d----- 497 (657)
T COG5166 449 AEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQ----------------S----------QWHD----- 497 (657)
T ss_pred hheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcch----------------h----------hhhc-----
Confidence 35789999999999999999999999999998887743222211 0 0000
Q ss_pred cccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEeeecCcccccc
Q 009520 220 QHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVI 299 (533)
Q Consensus 220 ~~~~~s~~~~~~~~gg~~~~p~~~~~~~~~~p~~~~~g~~~~d~~~~~~~~~~~~p~~~~~~~~~~~~v~vp~~~~g~II 299 (533)
.+-+.+|.+..+.|+
T Consensus 498 -----------------------------------------------------------------NV~I~~PrKn~~ni~ 512 (657)
T COG5166 498 -----------------------------------------------------------------NVLIEAPRKNQDNIS 512 (657)
T ss_pred -----------------------------------------------------------------ceEEECCccCccchh
Confidence 234678888889999
Q ss_pred ccCchhhHhhhhhcC----CeEEecCCCCCCCceeEEecCcchhhhhhhHHHHHHHHhCcccccccccccCCcceeEEEe
Q 009520 300 GKGGAIINQIRQESG----AAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLL 375 (533)
Q Consensus 300 Gk~G~~Ik~i~~~tg----a~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l~ 375 (533)
|++......+++... ..|.+.. ...+++++.+... .++.++.- +.--......+.+.
T Consensus 513 ~~KNd~~~~V~~~c~f~~Kgdirf~~----~~~sI~~v~~~~~-------~I~rv~kn--------e~v~~~~p~~~~~y 573 (657)
T COG5166 513 GKKNDKLDKVKQQCRFNLKGDIRFCP----QSTSIFTVDIYSD-------EIERVIKN--------ETVLLEFPAEMHFY 573 (657)
T ss_pred cccccHHHHHhhhcccccccceEEcC----CceEEEEEccccc-------HHHHHhhc--------cceEEecccccccc
Confidence 999888888876553 3344443 2445788777432 22222210 00001113556688
Q ss_pred ecCCceeEEec---CCChhHHHHHHhcCceEEE
Q 009520 376 VPTSRIGCLIG---KGGSIITEMRRLTKANIRI 405 (533)
Q Consensus 376 Vp~~~~G~IIG---kgG~~Ik~I~~~tga~I~i 405 (533)
+|...++.-+| -+|++|..+.....-.|..
T Consensus 574 ~~se~h~~g~gena~R~~ni~~~t~~y~~~ie~ 606 (657)
T COG5166 574 VPSEIHKKGIGENAFRGENIQRVTKLYNSYIEF 606 (657)
T ss_pred cchhhhhccCCcccccccchhhhhhhhhcccee
Confidence 99999999999 7788888877776666654
No 116
>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=84.23 E-value=1.1 Score=35.28 Aligned_cols=34 Identities=26% Similarity=0.459 Sum_probs=28.3
Q ss_pred eEEEeecCCceeEEecCCChhHHHHHHhcCceEE
Q 009520 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIR 404 (533)
Q Consensus 371 ~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~ 404 (533)
.+.+.|.....|.+|||.|++++.||-.+..-+.
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 4567777888999999999999999988776554
No 117
>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=84.16 E-value=1 Score=35.42 Aligned_cols=34 Identities=24% Similarity=0.459 Sum_probs=27.7
Q ss_pred EEEEEecCCceeeeeccCchHHHHHHhhcCceEE
Q 009520 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIR 174 (533)
Q Consensus 141 ~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~ 174 (533)
.+.+-+..+..|.+|||.|++++.|+--++.-++
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 4667777899999999999999999877665443
No 118
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=84.04 E-value=0.66 Score=42.75 Aligned_cols=56 Identities=27% Similarity=0.356 Sum_probs=49.6
Q ss_pred CCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 009520 148 SDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN 215 (533)
Q Consensus 148 ~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~ 215 (533)
+..+|+|+||+|.|--.|+.-|..+|-+. +..|.|-|..++++-|...|+.+|...
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVla------------d~kIHiLG~~~niriAR~avcsLIlGs 232 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA------------DSKIHILGAFQNIRIARDAVCSLILGS 232 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEec------------CceEEEeecchhhHHHHHhhHhhhccC
Confidence 45679999999999999999999999764 456999999999999999999999764
No 119
>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=83.49 E-value=0.5 Score=37.25 Aligned_cols=34 Identities=29% Similarity=0.474 Sum_probs=28.8
Q ss_pred eEEEEEecCCceeeeeccCchHHHHHHhhcCceE
Q 009520 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQI 173 (533)
Q Consensus 140 ~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I 173 (533)
....+.+..++.+.|||++|++|++|++...-.+
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 3467888899999999999999999988766555
No 120
>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=82.94 E-value=0.66 Score=36.55 Aligned_cols=33 Identities=18% Similarity=0.381 Sum_probs=28.2
Q ss_pred EEEEEecCCccceeecCCcHHHHHHHHHhCCeE
Q 009520 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKI 76 (533)
Q Consensus 44 ~~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I 76 (533)
...+.+.....|.|||++|++|++|+++.+-.+
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 367888999999999999999999988776554
No 121
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=82.21 E-value=0.85 Score=47.70 Aligned_cols=36 Identities=25% Similarity=0.397 Sum_probs=33.4
Q ss_pred EEEEecCCccceeecCCcHHHHHHHHHhCCeEEEcC
Q 009520 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE 80 (533)
Q Consensus 45 ~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~ 80 (533)
..+.||.++++.||||+|.+|++|++..|-+|.|..
T Consensus 488 avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~ 523 (604)
T COG1855 488 AVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKP 523 (604)
T ss_pred EEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEE
Confidence 568899999999999999999999999999999864
No 122
>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=81.79 E-value=1.4 Score=35.14 Aligned_cols=38 Identities=11% Similarity=0.239 Sum_probs=31.2
Q ss_pred EEEEEecCCccceeecCCcHHHHHHHHHhCCeEEEcCC
Q 009520 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGET 81 (533)
Q Consensus 44 ~~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~ 81 (533)
..++.+-...-|.|||++|+.|++|+++-.-...+.++
T Consensus 31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~~ 68 (81)
T cd02413 31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPEG 68 (81)
T ss_pred eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCCC
Confidence 37888889999999999999999999887666655433
No 123
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=81.71 E-value=3.6 Score=39.55 Aligned_cols=47 Identities=21% Similarity=0.418 Sum_probs=39.8
Q ss_pred EEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHH
Q 009520 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLD 429 (533)
Q Consensus 372 ~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~ 429 (533)
.-+.||+..+-.+||++|+.++-+.+.|+|+|.|-. +-.|=|.+..+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-----------NG~IWV~~~~~ 194 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-----------NGRIWVDGENE 194 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-----------CCEEEecCCCc
Confidence 458899999999999999999999999999999953 23677777655
No 124
>PRK13764 ATPase; Provisional
Probab=81.43 E-value=1.4 Score=48.52 Aligned_cols=44 Identities=27% Similarity=0.463 Sum_probs=39.0
Q ss_pred ceeEEEeecCCceeEEecCCChhHHHHHHhcCceEEEecCCCCC
Q 009520 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLP 412 (533)
Q Consensus 369 ~~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P 412 (533)
.-...+.||...++.+|||+|.+|++|.+..|.+|.|...+..|
T Consensus 480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 35677999999999999999999999999999999997766554
No 125
>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=78.82 E-value=2.3 Score=33.85 Aligned_cols=36 Identities=19% Similarity=0.413 Sum_probs=29.6
Q ss_pred eeEEEeecCCceeEEecCCChhHHHHHHhcCceEEE
Q 009520 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405 (533)
Q Consensus 370 ~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i 405 (533)
..+++.|-...-|.|||++|+.|++|++.-.....+
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~ 65 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF 65 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence 346788888888999999999999999886655554
No 126
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=78.19 E-value=3.3 Score=37.76 Aligned_cols=36 Identities=33% Similarity=0.611 Sum_probs=31.5
Q ss_pred EEEEecCCceeeeeccCchHHHHHHhhcCceEEEeec
Q 009520 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (533)
Q Consensus 142 ~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (533)
+-++|-... |..|||+|.+|+++++..|-+|.+...
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 556776666 999999999999999999999999764
No 127
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=78.00 E-value=3 Score=38.03 Aligned_cols=33 Identities=30% Similarity=0.386 Sum_probs=28.0
Q ss_pred EEEecCCccceeecCCcHHHHHHHHHhCCeEEEc
Q 009520 46 RYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIG 79 (533)
Q Consensus 46 rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~ 79 (533)
-++|-... |.-|||+|++|++|++..|-+|.+-
T Consensus 64 IfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevV 96 (166)
T PRK06418 64 ILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVV 96 (166)
T ss_pred EEEEeCCC-cccccccchHHHHHHHHhCCcEEEE
Confidence 35555566 9999999999999999999999864
No 128
>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=77.17 E-value=11 Score=33.36 Aligned_cols=94 Identities=16% Similarity=0.303 Sum_probs=58.8
Q ss_pred cccCchhhHhhhhhcCCeEEecCCCCCCCceeEEecCcchhhhhhhHHHHHHHHhCcccccccccccCCcceeEEEeecC
Q 009520 299 IGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPT 378 (533)
Q Consensus 299 IGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~ 378 (533)
+=.++..|+.|-++..-+|.|-.+..- . ..-..+.+.+..+.|.-.+-.+-.. ...+-++.|-.
T Consensus 21 ~~~~~dli~~lAk~lrKRIvvR~dps~-----l---------~~~e~A~~~I~~ivP~ea~i~di~F--d~~tGEV~Iea 84 (145)
T cd02410 21 FAEDGDLVKDLAKDLRKRIVIRPDPSV-----L---------KPPEEAIKIILEIVPEEAGITDIYF--DDDTGEVIIEA 84 (145)
T ss_pred HhcccHHHHHHHHHHhceEEEcCChhh-----c---------CCHHHHHHHHHHhCCCccCceeeEe--cCCCcEEEEEE
Confidence 334578899999988888887543110 0 0001234444444432211000000 12345677888
Q ss_pred CceeEEecCCChhHHHHHHhcCceEEEecC
Q 009520 379 SRIGCLIGKGGSIITEMRRLTKANIRILPK 408 (533)
Q Consensus 379 ~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~ 408 (533)
..-|.|||++|.++++|..+||-.-.|.+.
T Consensus 85 eKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 85 EKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred cCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 899999999999999999999998888654
No 129
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=77.00 E-value=6.4 Score=41.71 Aligned_cols=102 Identities=14% Similarity=0.181 Sum_probs=73.5
Q ss_pred EEEEeeecCccccccccCchhhHhhhhhcCCeEEecCCCCCCCceeEEecCcchhhhhhhHHHHHHHHhCcccccccccc
Q 009520 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERD 364 (533)
Q Consensus 285 ~~~v~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~ 364 (533)
.+.+.||...|..|||.+|..|++...+.++.|++...-.- +. .+.
T Consensus 450 e~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~---------~q------------s~~------------- 495 (657)
T COG5166 450 EIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKF---------GQ------------SQW------------- 495 (657)
T ss_pred heEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhc---------ch------------hhh-------------
Confidence 56789999999999999999999999999999988753110 00 000
Q ss_pred cCCcceeEEEeecCCceeEEecCCChhHHHHHHhc----CceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHH
Q 009520 365 SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLT----KANIRILPKENLPKIASEDDEMVQISGDLDLAKD 433 (533)
Q Consensus 365 ~~~~~~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~t----ga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~ 433 (533)
.-.+-+.-|.+-.+.|+|++-....-++++. ...|++. | ..-+++++-|-.+-+.+
T Consensus 496 ----~dNV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~~Kgdirf~-----~----~~~sI~~v~~~~~~I~r 555 (657)
T COG5166 496 ----HDNVLIEAPRKNQDNISGKKNDKLDKVKQQCRFNLKGDIRFC-----P----QSTSIFTVDIYSDEIER 555 (657)
T ss_pred ----hcceEEECCccCccchhcccccHHHHHhhhcccccccceEEc-----C----CceEEEEEcccccHHHH
Confidence 1124477899999999999999988888654 5677773 2 12347888776654443
No 130
>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=72.33 E-value=8.9 Score=42.89 Aligned_cols=96 Identities=24% Similarity=0.430 Sum_probs=60.8
Q ss_pred eecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHHHhh-ccCCCCCC
Q 009520 57 IIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEE-LRGDEDSD 135 (533)
Q Consensus 57 IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~-~~~~~~~~ 135 (533)
.+=.+|..|++|-++-.-+|.|-. .+.. +.+-.+|.+.|.+.+-++. +. +-
T Consensus 37 ~~~~~~~~~~~~~~~~~~r~~~~~--------------~~~~----------~~~~~~~~~~i~~~~~~~~~~~----~~ 88 (630)
T TIGR03675 37 LFAKDDDLVKELAKKLRKRIVIRP--------------DPSV----------LLPPEEAIEKIKEIVPEEAGIT----DI 88 (630)
T ss_pred HhccchHHHHHHHHHhhceEEEec--------------Chhh----------cCCHHHHHHHHHHhCCCcCCce----eE
Confidence 345678889999888877776532 2111 1112355555554332221 10 00
Q ss_pred CCCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCC
Q 009520 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEH 180 (533)
Q Consensus 136 ~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~ 180 (533)
.-+..+-.++|-...-|.||||+|.++++|..+||-+-.|.+...
T Consensus 89 ~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~~ 133 (630)
T TIGR03675 89 YFDDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTPP 133 (630)
T ss_pred EecCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecCC
Confidence 112334567777888899999999999999999999988887643
No 131
>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=71.15 E-value=3.9 Score=34.55 Aligned_cols=30 Identities=23% Similarity=0.358 Sum_probs=25.7
Q ss_pred EEEEecCCccceeecCCcHHHHHHHHHhCC
Q 009520 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKS 74 (533)
Q Consensus 45 ~rilvp~~~~g~IIGk~G~~Ik~i~~~tga 74 (533)
.++.+-...-|.|||++|++|++|++.-..
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 577888888999999999999999977543
No 132
>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=68.82 E-value=5.6 Score=31.92 Aligned_cols=28 Identities=25% Similarity=0.380 Sum_probs=23.2
Q ss_pred EEEEecCCccceeecCCcHHHHHHHHHh
Q 009520 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDT 72 (533)
Q Consensus 45 ~rilvp~~~~g~IIGk~G~~Ik~i~~~t 72 (533)
.++.+-...-|.+||++|.+|++|++.-
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 4555666889999999999999998764
No 133
>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=66.20 E-value=4.9 Score=33.99 Aligned_cols=30 Identities=30% Similarity=0.502 Sum_probs=24.8
Q ss_pred EEEeecCCceeEEecCCChhHHHHHHhcCc
Q 009520 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKA 401 (533)
Q Consensus 372 ~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga 401 (533)
+++.|-...-|.|||++|+.|++|++....
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 567777777899999999999999876543
No 134
>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=65.91 E-value=6.3 Score=31.62 Aligned_cols=28 Identities=32% Similarity=0.615 Sum_probs=22.7
Q ss_pred EEEeecCCceeEEecCCChhHHHHHHhc
Q 009520 372 TRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (533)
Q Consensus 372 ~~l~Vp~~~~G~IIGkgG~~Ik~I~~~t 399 (533)
+.+.|....-|.+||++|++|++|++.-
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 4555666788999999999999998764
No 135
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=65.59 E-value=5.4 Score=38.17 Aligned_cols=32 Identities=22% Similarity=0.333 Sum_probs=27.0
Q ss_pred ceEEEEEecCCccceeecCCcHHHHHHHHHhC
Q 009520 42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (533)
Q Consensus 42 ~~~~rilvp~~~~g~IIGk~G~~Ik~i~~~tg 73 (533)
....++.|....-|.|||++|+.|++|+++-.
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~ 81 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKELE 81 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHHH
Confidence 34468889999999999999999999987643
No 136
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=63.21 E-value=6.5 Score=37.66 Aligned_cols=30 Identities=37% Similarity=0.530 Sum_probs=25.6
Q ss_pred ceeEEEeecCCceeEEecCCChhHHHHHHh
Q 009520 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRL 398 (533)
Q Consensus 369 ~~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~ 398 (533)
...+++.|....-|.|||++|+.|++|++.
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 356778888889999999999999998764
No 137
>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=61.59 E-value=9.5 Score=37.72 Aligned_cols=31 Identities=26% Similarity=0.431 Sum_probs=25.3
Q ss_pred ceEEEEEec-CCceeeeeccCchHHHHHHhhc
Q 009520 139 QVTAKLLVP-SDQIGCVIGKGGQIVQNIRSET 169 (533)
Q Consensus 139 ~~~~~llVp-~~~~g~IIGk~G~~Ik~I~~~t 169 (533)
.+...++|. .++-+.||||+|++||+|..+.
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 367788888 5788999999999999886543
No 138
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=59.62 E-value=23 Score=37.90 Aligned_cols=96 Identities=17% Similarity=0.276 Sum_probs=61.5
Q ss_pred cccccCchhhHhhhhhcCCeEEecCCCCCCCceeEEecCcchhhhhhhHHHHHHHHhCcccccccccccCCcceeEEEee
Q 009520 297 GVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLV 376 (533)
Q Consensus 297 ~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l~V 376 (533)
.++-+.|..|++|.++..-+|.+-.+..- + ... ..+...+..+.|.-.+-.+-.. ...+-++.|
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~dPsv-----l--~~~-------e~A~~~I~eivP~ea~i~~i~F--d~~tGEViI 105 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPDPSV-----L--KPP-------EEARKIILEIVPEEAGITDIYF--DDDTGEVII 105 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccCchh-----c--CCH-------HHHHHHHHHhCccccCceeEEe--cCCCceEEE
Confidence 45667889999999999988888753211 0 111 1233344444433211100000 123456778
Q ss_pred cCCceeEEecCCChhHHHHHHhcCceEEEecC
Q 009520 377 PTSRIGCLIGKGGSIITEMRRLTKANIRILPK 408 (533)
Q Consensus 377 p~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~ 408 (533)
-.+.-|.||||+|++.++|.++||-.-+|.+.
T Consensus 106 ea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 106 EAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred EecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 88899999999999999999999988777654
No 139
>PRK15494 era GTPase Era; Provisional
Probab=56.57 E-value=13 Score=38.27 Aligned_cols=29 Identities=17% Similarity=0.419 Sum_probs=24.0
Q ss_pred eEEEEEec-CCceeeeeccCchHHHHHHhh
Q 009520 140 VTAKLLVP-SDQIGCVIGKGGQIVQNIRSE 168 (533)
Q Consensus 140 ~~~~llVp-~~~~g~IIGk~G~~Ik~I~~~ 168 (533)
+...|+|. .++-+.||||+|++||+|..+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 66778888 578899999999999987543
No 140
>PRK00089 era GTPase Era; Reviewed
Probab=55.74 E-value=14 Score=36.97 Aligned_cols=29 Identities=38% Similarity=0.723 Sum_probs=23.7
Q ss_pred eEEEEEec-CCceeeeeccCchHHHHHHhh
Q 009520 140 VTAKLLVP-SDQIGCVIGKGGQIVQNIRSE 168 (533)
Q Consensus 140 ~~~~llVp-~~~~g~IIGk~G~~Ik~I~~~ 168 (533)
+...|.|. .++-+.||||+|++||+|..+
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ 255 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTE 255 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHH
Confidence 66777787 578899999999999987544
No 141
>COG1159 Era GTPase [General function prediction only]
Probab=55.55 E-value=14 Score=36.94 Aligned_cols=31 Identities=29% Similarity=0.576 Sum_probs=24.5
Q ss_pred CceEEEEEec-CCceeeeeccCchHHHHHHhh
Q 009520 138 HQVTAKLLVP-SDQIGCVIGKGGQIVQNIRSE 168 (533)
Q Consensus 138 ~~~~~~llVp-~~~~g~IIGk~G~~Ik~I~~~ 168 (533)
-.+...++|+ .+|-+.||||+|++||+|-..
T Consensus 227 ~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~ 258 (298)
T COG1159 227 LKIHATIYVERESQKGIIIGKNGAMIKKIGTA 258 (298)
T ss_pred EEEEEEEEEecCCccceEECCCcHHHHHHHHH
Confidence 3456677888 578899999999999987433
No 142
>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=52.70 E-value=16 Score=36.07 Aligned_cols=31 Identities=26% Similarity=0.355 Sum_probs=24.5
Q ss_pred ceeEEEeecC-CceeEEecCCChhHHHHHHhc
Q 009520 369 SFTTRLLVPT-SRIGCLIGKGGSIITEMRRLT 399 (533)
Q Consensus 369 ~~~~~l~Vp~-~~~G~IIGkgG~~Ik~I~~~t 399 (533)
.+...+.|.. ++-+.|||++|+.||+|....
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 4667777875 455999999999999887654
No 143
>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=48.64 E-value=34 Score=38.34 Aligned_cols=95 Identities=16% Similarity=0.287 Sum_probs=61.0
Q ss_pred ccccCchhhHhhhhhcCCeEEecCCCCCCCceeEEecCcchhhhhhhHHHHHHHHhCcccccccccccCCcceeEEEeec
Q 009520 298 VIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVP 377 (533)
Q Consensus 298 IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l~Vp 377 (533)
.+=.++..|++|-++..-+|.|-.+..- . ..-..+.+.+..+.|.-.+-.+-. =...+-++.|-
T Consensus 37 ~~~~~~~~~~~~~~~~~~r~~~~~~~~~-----~---------~~~~~~~~~i~~~~~~~~~~~~~~--f~~~~~~v~i~ 100 (630)
T TIGR03675 37 LFAKDDDLVKELAKKLRKRIVIRPDPSV-----L---------LPPEEAIEKIKEIVPEEAGITDIY--FDDVTGEVIIE 100 (630)
T ss_pred HhccchHHHHHHHHHhhceEEEecChhh-----c---------CCHHHHHHHHHHhCCCcCCceeEE--ecCCCceEEEE
Confidence 3445678999999988888887643210 0 000224445555544321110000 01345567888
Q ss_pred CCceeEEecCCChhHHHHHHhcCceEEEecC
Q 009520 378 TSRIGCLIGKGGSIITEMRRLTKANIRILPK 408 (533)
Q Consensus 378 ~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~ 408 (533)
.+.-|.||||+|.++++|.++||-.-+|.+.
T Consensus 101 ~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 101 AEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred EcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 8899999999999999999999999888654
No 144
>PRK15494 era GTPase Era; Provisional
Probab=46.88 E-value=22 Score=36.51 Aligned_cols=30 Identities=23% Similarity=0.345 Sum_probs=23.6
Q ss_pred ceeEEEeecCC-ceeEEecCCChhHHHHHHh
Q 009520 369 SFTTRLLVPTS-RIGCLIGKGGSIITEMRRL 398 (533)
Q Consensus 369 ~~~~~l~Vp~~-~~G~IIGkgG~~Ik~I~~~ 398 (533)
.+...+.|..+ +-+.|||++|+.||+|...
T Consensus 272 ~i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 272 KINQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 46677778764 5599999999999988654
No 145
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=46.46 E-value=19 Score=36.18 Aligned_cols=34 Identities=24% Similarity=0.445 Sum_probs=28.2
Q ss_pred CCceEEEEEec-CCceeeeeccCchHHHHHHhhcC
Q 009520 137 GHQVTAKLLVP-SDQIGCVIGKGGQIVQNIRSETG 170 (533)
Q Consensus 137 ~~~~~~~llVp-~~~~g~IIGk~G~~Ik~I~~~tg 170 (533)
...+..++++| .++...||||+|..|++|-.+.+
T Consensus 325 ~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 325 VLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 34578889999 57888999999999999976654
No 146
>PRK00089 era GTPase Era; Reviewed
Probab=43.84 E-value=26 Score=34.91 Aligned_cols=31 Identities=26% Similarity=0.542 Sum_probs=23.6
Q ss_pred ceeEEEeecC-CceeEEecCCChhHHHHHHhc
Q 009520 369 SFTTRLLVPT-SRIGCLIGKGGSIITEMRRLT 399 (533)
Q Consensus 369 ~~~~~l~Vp~-~~~G~IIGkgG~~Ik~I~~~t 399 (533)
.+...+.|.. ++-+.|||++|++||+|...+
T Consensus 225 ~i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~a 256 (292)
T PRK00089 225 RIEATIYVERDSQKGIIIGKGGAMLKKIGTEA 256 (292)
T ss_pred EEEEEEEEccCCceeEEEeCCcHHHHHHHHHH
Confidence 4666677765 556999999999999886543
No 147
>COG1159 Era GTPase [General function prediction only]
Probab=43.70 E-value=28 Score=34.83 Aligned_cols=34 Identities=29% Similarity=0.593 Sum_probs=25.3
Q ss_pred CCcceeEEEeecC-CceeEEecCCChhHHHHHHhc
Q 009520 366 GLISFTTRLLVPT-SRIGCLIGKGGSIITEMRRLT 399 (533)
Q Consensus 366 ~~~~~~~~l~Vp~-~~~G~IIGkgG~~Ik~I~~~t 399 (533)
+...+...+.|+. ++=|-||||+|+.||+|-..+
T Consensus 225 ~~~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~A 259 (298)
T COG1159 225 GLLKIHATIYVERESQKGIIIGKNGAMIKKIGTAA 259 (298)
T ss_pred CeEEEEEEEEEecCCccceEECCCcHHHHHHHHHH
Confidence 3345666777876 455999999999999886544
No 148
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=40.53 E-value=29 Score=34.93 Aligned_cols=36 Identities=25% Similarity=0.511 Sum_probs=27.7
Q ss_pred ccCCcceeEEEeecCC-ceeEEecCCChhHHHHHHhc
Q 009520 364 DSGLISFTTRLLVPTS-RIGCLIGKGGSIITEMRRLT 399 (533)
Q Consensus 364 ~~~~~~~~~~l~Vp~~-~~G~IIGkgG~~Ik~I~~~t 399 (533)
..+...+..++.+|.. +.-.||||||..|++|-++-
T Consensus 322 ~~g~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a 358 (379)
T KOG1423|consen 322 PAGVLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRA 358 (379)
T ss_pred CCcEEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHH
Confidence 3345567888899974 55788999999999996654
No 149
>PRK03818 putative transporter; Validated
Probab=40.31 E-value=3.4e+02 Score=29.93 Aligned_cols=133 Identities=14% Similarity=0.232 Sum_probs=69.3
Q ss_pred EEEEecCCccceeecCCcHHHHHHHHHhCCeEEEcCC---------CCC---CCceEEEEEcCCccccccccCcccCCHH
Q 009520 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGET---------VPG---SEERVVTVYSASDETNAFEDGDKFVSPA 112 (533)
Q Consensus 45 ~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~---------~~~---~~ervv~I~G~~~~~~~~~~~~~~v~~a 112 (533)
.++.|+++. ++ |++++++.......+.|..- .++ ....++.|.|..++
T Consensus 207 r~~~V~~s~---li---GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~-------------- 266 (552)
T PRK03818 207 INIRVENPN---LH---GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPED-------------- 266 (552)
T ss_pred EEEEEeCCC---CC---CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHH--------------
Confidence 566666443 34 67999999887766655311 011 12356777777543
Q ss_pred HHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEecCCceeeeeccCchHHHHH--HhhcCceEEEeecC--CCC---ccc
Q 009520 113 QDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNI--RSETGAQIRILKDE--HLP---SCA 185 (533)
Q Consensus 113 ~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~~g~IIGk~G~~Ik~I--~~~tga~I~i~~~~--~~p---~~~ 185 (533)
+.++.+.+-.+.. .+.+..........+++|++ .++|| +++++ +++.|+.|.=.... +++ ...
T Consensus 267 ---l~~l~~~~Gl~~~-~~~~~~~~~~~~E~Vvv~~S---~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~ 336 (552)
T PRK03818 267 ---LHKAQLVIGEEVD-TSLSTRGTDLRSERVVVTNE---KVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLS 336 (552)
T ss_pred ---HHHHHHhcCCccC-ccccccCcceEEEEEEEcCh---hccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCE
Confidence 3333332221110 00111122334444555543 55555 78887 56777765433321 121 111
Q ss_pred CCCCceEEEEcCHHHHHHHHHH
Q 009520 186 LRSDELVQISGEASVVKKALCQ 207 (533)
Q Consensus 186 ~~~dr~v~I~G~~~~V~~A~~~ 207 (533)
...-.++.+.|+++++++..+.
T Consensus 337 Lq~GD~LlVvG~~~~i~~l~~~ 358 (552)
T PRK03818 337 LQFGDILNLVGRPEAIDAVANV 358 (552)
T ss_pred EecCCEEEEEECHHHHHHHHHH
Confidence 1233468899999999987664
No 150
>CHL00048 rps3 ribosomal protein S3
Probab=38.65 E-value=33 Score=32.76 Aligned_cols=31 Identities=16% Similarity=0.210 Sum_probs=25.9
Q ss_pred eEEEEEecCCccceeecCCcHHHHHHHHHhC
Q 009520 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (533)
Q Consensus 43 ~~~rilvp~~~~g~IIGk~G~~Ik~i~~~tg 73 (533)
...++.+-...-|.|||++|++|++|++.-.
T Consensus 66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 66 DLIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred CeEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 3467777788889999999999999998753
No 151
>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=38.22 E-value=35 Score=32.08 Aligned_cols=30 Identities=23% Similarity=0.417 Sum_probs=25.7
Q ss_pred EEEEEecCCccceeecCCcHHHHHHHHHhC
Q 009520 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (533)
Q Consensus 44 ~~rilvp~~~~g~IIGk~G~~Ik~i~~~tg 73 (533)
..++.+....-|.|||++|..|++|+++-.
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~ 68 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKLQ 68 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHHH
Confidence 367888888899999999999999987754
No 152
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=37.91 E-value=34 Score=32.50 Aligned_cols=31 Identities=29% Similarity=0.426 Sum_probs=24.7
Q ss_pred EEEEecCCccceeecCCcHHHHHHHHHhCCe
Q 009520 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSK 75 (533)
Q Consensus 45 ~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~ 75 (533)
.++.+-...-|.+||++|++|++|++.-.-.
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 4555555889999999999999999876443
No 153
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=36.30 E-value=68 Score=36.96 Aligned_cols=15 Identities=20% Similarity=0.607 Sum_probs=7.8
Q ss_pred EEEeecCCceeEEec
Q 009520 372 TRLLVPTSRIGCLIG 386 (533)
Q Consensus 372 ~~l~Vp~~~~G~IIG 386 (533)
++|.|.++.+.||+|
T Consensus 1086 IklqIshEaAAcItg 1100 (1282)
T KOG0921|consen 1086 IKLQISHEAAACITG 1100 (1282)
T ss_pred eeEeccHHHHHHHhh
Confidence 445555555555555
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=36.12 E-value=36 Score=31.98 Aligned_cols=29 Identities=31% Similarity=0.560 Sum_probs=24.4
Q ss_pred eEEEeecCCceeEEecCCChhHHHHHHhc
Q 009520 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (533)
Q Consensus 371 ~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~t 399 (533)
.+++.|....-|.|||++|..|++|++.-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 46777777888999999999999998764
No 155
>COG0490 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]
Probab=36.01 E-value=52 Score=29.80 Aligned_cols=61 Identities=23% Similarity=0.235 Sum_probs=37.4
Q ss_pred EeecCCceeEEecCCChhHHHHHHhcCceEE-EecCCCC-----CCCCCCCCcEEEEEeCHHHHHHHHHHHH
Q 009520 374 LLVPTSRIGCLIGKGGSIITEMRRLTKANIR-ILPKENL-----PKIASEDDEMVQISGDLDLAKDALIQVM 439 (533)
Q Consensus 374 l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~-i~~~~~~-----P~~~~~~~r~V~I~G~~~~v~~A~~~I~ 439 (533)
+..-..++|.=|| --+|+++|||.|. |.+.+++ |...-....++.+.|+...+.+++.+..
T Consensus 92 i~~~s~~~GksiG-----dl~irq~TGaTIIAI~r~~e~I~SPgPy~vle~gDtlvviG~~~~~~r~~~f~~ 158 (162)
T COG0490 92 IEAGSPFIGKTIG-----DLNIRQNTGATVIAIVRNEEKILSPGPYTVLEAGDTLVVIGEETGLKRAKRFLL 158 (162)
T ss_pred eecCCcccCcchh-----hcccccccCcEEEEEEecCcEecCCCchhhhcCCCEEEEEecchHhHHHHHHhh
Confidence 3334455566666 3567999999854 3333221 2211223458999999999998876553
No 156
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=34.80 E-value=37 Score=31.98 Aligned_cols=37 Identities=19% Similarity=0.284 Sum_probs=30.4
Q ss_pred ceeEEEeecCCceeEEecCCChhHHHHHHhcCceEEE
Q 009520 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405 (533)
Q Consensus 369 ~~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga~I~i 405 (533)
.-++.+.+-.+..|.+||+.|.+++.||-.+.+.+.-
T Consensus 90 ~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 90 GRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred CcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 3456677777889999999999999999988776653
No 157
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=34.79 E-value=40 Score=32.33 Aligned_cols=31 Identities=10% Similarity=0.250 Sum_probs=25.9
Q ss_pred EEEEecCCccceeecCCcHHHHHHHHHhCCe
Q 009520 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSK 75 (533)
Q Consensus 45 ~rilvp~~~~g~IIGk~G~~Ik~i~~~tga~ 75 (533)
.++.+-...-|.|||++|..|++|+++-.-.
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 6777778888999999999999998776443
No 158
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=34.59 E-value=36 Score=32.06 Aligned_cols=37 Identities=14% Similarity=0.253 Sum_probs=30.6
Q ss_pred ceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEE
Q 009520 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRI 175 (533)
Q Consensus 139 ~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i 175 (533)
.-.+.+-+..+..+.|||+.|.++..||--+++-++-
T Consensus 90 ~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 90 GRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred CcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 3456777888889999999999999999888876643
No 159
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=34.11 E-value=39 Score=32.09 Aligned_cols=30 Identities=33% Similarity=0.618 Sum_probs=23.8
Q ss_pred EEEeecCCceeEEecCCChhHHHHHHhcCc
Q 009520 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKA 401 (533)
Q Consensus 372 ~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tga 401 (533)
+.+.|....-|.+||++|++|+++++.-.-
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk 71 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEK 71 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHH
Confidence 455555577899999999999999887543
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=33.28 E-value=1.3e+02 Score=27.42 Aligned_cols=58 Identities=22% Similarity=0.226 Sum_probs=44.2
Q ss_pred CCceEEEEEecCCceeeeeccCchHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 009520 137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRL 212 (533)
Q Consensus 137 ~~~~~~~llVp~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l 212 (533)
.+.-++|+-++...+- +.+.+|.+-.|+-+.+ . .+..|.|.|..+.|.+|++.++.+-
T Consensus 110 ~~~~~iRv~l~~~i~~-------erl~ei~E~~gvI~Ef-e----------e~~~V~I~Gdke~Ik~aLKe~s~~w 167 (169)
T PF09869_consen 110 PGFETIRVKLKKPIQE-------ERLQEISEWHGVIFEF-E----------EDDKVVIEGDKERIKKALKEFSSFW 167 (169)
T ss_pred CCceeEEEecCccchH-------HHHHHHHHHhceeEEe-c----------CCcEEEEeccHHHHHHHHHHHHHHh
Confidence 3445666666655442 6788999999999888 2 2567999999999999999987653
No 161
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=33.05 E-value=40 Score=32.32 Aligned_cols=30 Identities=23% Similarity=0.460 Sum_probs=24.4
Q ss_pred eEEEeecCCceeEEecCCChhHHHHHHhcC
Q 009520 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTK 400 (533)
Q Consensus 371 ~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~tg 400 (533)
.+++.|....-|.|||++|..|++|++.-.
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L~ 74 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLLQ 74 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHHH
Confidence 366777777789999999999999987643
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=32.99 E-value=4.9e+02 Score=28.79 Aligned_cols=62 Identities=24% Similarity=0.384 Sum_probs=36.1
Q ss_pred EEEEEecCCceeeeeccCchHHHHHH------hhcCceEEEeecC--CCC---cccCCCCceEEEEcCHHHHHHHHHHH
Q 009520 141 TAKLLVPSDQIGCVIGKGGQIVQNIR------SETGAQIRILKDE--HLP---SCALRSDELVQISGEASVVKKALCQI 208 (533)
Q Consensus 141 ~~~llVp~~~~g~IIGk~G~~Ik~I~------~~tga~I~i~~~~--~~p---~~~~~~dr~v~I~G~~~~V~~A~~~I 208 (533)
..++.+|++ .++|| +++++. ++.|+.|.-.... +++ ......-..+.+.|++++++++.+.+
T Consensus 304 ~e~VV~~~S---~liGk---TL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~GD~LlV~G~~~~l~~~~~~l 376 (562)
T TIGR03802 304 TKDVVLTNK---EYNGK---TVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQRGDVVTLVGTPQDVDRAAKQL 376 (562)
T ss_pred EEEEEECCc---ccCCc---cHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecCCCEEEEEeCHHHHHHHHHHc
Confidence 444555543 45554 788886 3677776544321 111 11122344688999999999876653
No 163
>CHL00048 rps3 ribosomal protein S3
Probab=32.88 E-value=42 Score=32.03 Aligned_cols=30 Identities=20% Similarity=0.113 Sum_probs=24.5
Q ss_pred eeEEEeecCCceeEEecCCChhHHHHHHhc
Q 009520 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (533)
Q Consensus 370 ~~~~l~Vp~~~~G~IIGkgG~~Ik~I~~~t 399 (533)
..+++.|-...-|.|||++|..|++|++.-
T Consensus 66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 66 DLIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred CeEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 345677777778999999999999998765
No 164
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=30.68 E-value=1.1e+02 Score=31.24 Aligned_cols=51 Identities=18% Similarity=0.165 Sum_probs=42.9
Q ss_pred cCCceeEEecCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHH
Q 009520 377 PTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVM 439 (533)
Q Consensus 377 p~~~~G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~ 439 (533)
+.+..-.+.|..+.+++-|.+..|+.|... .+.++|+|+...+..|...+.
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~r------------G~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVAR------------GEAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeC------------CceEEEEechHHHHHHHHHHh
Confidence 356677899999999999999999999852 247999999778888887776
No 165
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=25.59 E-value=1.4e+02 Score=23.23 Aligned_cols=42 Identities=14% Similarity=0.224 Sum_probs=29.4
Q ss_pred hhHHHHHHhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHH
Q 009520 390 SIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMT 440 (533)
Q Consensus 390 ~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~ 440 (533)
..|.+|-+.++|+|.=..+ +.-+|+++|+++.+...+.++..
T Consensus 17 ~ei~~l~~~f~a~ivd~~~---------~~~iie~tG~~~kid~fi~~l~~ 58 (75)
T PF10369_consen 17 SEILQLAEIFRARIVDVSP---------DSIIIELTGTPEKIDAFIKLLKP 58 (75)
T ss_dssp HHHHHHHHHTT-EEEEEET---------TEEEEEEEE-HHHHHHHHHHSTG
T ss_pred HHHHHHHHHhCCEEEEECC---------CEEEEEEcCCHHHHHHHHHHhhh
Confidence 5678888999999764432 23489999999999888666543
No 166
>cd07055 BMC_like_2 Bacterial Micro-Compartment (BMC)-like domain 2. BMC like 2 domains exist in cyanobacteria, proteobacteria, and actinobacteria and are homologs of carboxysome shell proteins. They might be encoded from putative organelles involved in unknown metabolic process. Although it has been suggested that these carboxysome shell protein homologs form hexamers and further assemble into the flat facets of the polyhedral bacterial organelles shell at present no experimental evidence exists to directly support this view.
Probab=25.05 E-value=2.1e+02 Score=21.44 Aligned_cols=39 Identities=10% Similarity=0.045 Sum_probs=24.9
Q ss_pred HhcCceEEEecCCCCCCCCCCCCcEEEEEeCHHHHHHHHHHHHH
Q 009520 397 RLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMT 440 (533)
Q Consensus 397 ~~tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~ 440 (533)
+.+++.| +......|. .--.+.|+|+..+|+.|+..|.+
T Consensus 21 Kaa~V~i-~d~f~gCPq----~~~~l~i~Gdvs~Ve~Al~~i~~ 59 (61)
T cd07055 21 KASGVFV-SDIFGSCPQ----HMITLAIFGETSAVELAMREIEE 59 (61)
T ss_pred hccCeEE-EEecCCCCC----ceEEEEEEecHHHHHHHHHHHhh
Confidence 4455555 333333342 23367799999999999888764
No 167
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=23.51 E-value=79 Score=30.14 Aligned_cols=28 Identities=29% Similarity=0.457 Sum_probs=24.2
Q ss_pred EEEEecCCccceeecCCcHHHHHHHHHh
Q 009520 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDT 72 (533)
Q Consensus 45 ~rilvp~~~~g~IIGk~G~~Ik~i~~~t 72 (533)
++|.+-...-+.|||++|..|++|++.-
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l 91 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDL 91 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHH
Confidence 5677788888999999999999998664
No 168
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=23.05 E-value=2.1e+02 Score=24.02 Aligned_cols=38 Identities=26% Similarity=0.271 Sum_probs=30.6
Q ss_pred cCceEEEeecCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 009520 169 TGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN 215 (533)
Q Consensus 169 tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~ 215 (533)
.++.|-|.+. ....+.|+|.-.+|+.|+..|.+.+++.
T Consensus 63 a~V~igF~DR---------FsGslvitGdvs~Ve~Al~~V~~~l~~~ 100 (111)
T PRK15468 63 ADVHIGFLDR---------FSGALVIYGSVGAVEEALSQTVSGLGRL 100 (111)
T ss_pred cCcEEeeeec---------cceeEEEEccHHHHHHHHHHHHHHHHhh
Confidence 4577777653 3456999999999999999999999873
No 169
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=22.19 E-value=78 Score=30.15 Aligned_cols=28 Identities=39% Similarity=0.577 Sum_probs=23.1
Q ss_pred EEEeecCCceeEEecCCChhHHHHHHhc
Q 009520 372 TRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (533)
Q Consensus 372 ~~l~Vp~~~~G~IIGkgG~~Ik~I~~~t 399 (533)
+++.|-...-|.|||++|..|++|++.-
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l 91 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDL 91 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHH
Confidence 5577777777999999999999998653
No 170
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.12 E-value=3.3e+02 Score=24.19 Aligned_cols=43 Identities=35% Similarity=0.423 Sum_probs=34.8
Q ss_pred hHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHh
Q 009520 160 QIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLH 213 (533)
Q Consensus 160 ~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~ 213 (533)
+.++.|.+-.|+-|.+.. ...|.|.|..+.|.+|++.|...-+
T Consensus 126 eRlqDi~E~hgvIiE~~E-----------~D~V~i~Gd~drVk~aLke~~~~wk 168 (170)
T COG4010 126 ERLQDIAETHGVIIEFEE-----------YDLVAIYGDSDRVKKALKEIGSFWK 168 (170)
T ss_pred HHHHHHHHhhheeEEeee-----------ccEEEEeccHHHHHHHHHHHHHHHh
Confidence 566778888888888753 3579999999999999999987643
Done!