Query 009973
Match_columns 521
No_of_seqs 302 out of 1877
Neff 7.3
Searched_HMMs 46136
Date Thu Mar 28 19:32:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009973.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009973hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1676 K-homology type RNA bi 100.0 4.2E-37 9.2E-42 321.4 27.0 321 54-475 65-393 (600)
2 KOG2192 PolyC-binding hnRNP-K 100.0 6E-35 1.3E-39 277.0 26.2 311 130-472 48-385 (390)
3 KOG2190 PolyC-binding proteins 100.0 2.4E-32 5.2E-37 290.1 28.2 327 130-474 43-412 (485)
4 KOG2193 IGF-II mRNA-binding pr 100.0 5E-33 1.1E-37 278.1 16.7 284 129-473 198-483 (584)
5 KOG1676 K-homology type RNA bi 100.0 1.7E-31 3.6E-36 279.5 22.1 250 129-475 53-304 (600)
6 KOG2193 IGF-II mRNA-binding pr 100.0 5E-31 1.1E-35 263.8 13.8 317 52-478 208-571 (584)
7 KOG2191 RNA-binding protein NO 99.9 1E-26 2.2E-31 227.1 19.5 268 128-474 37-318 (402)
8 KOG2190 PolyC-binding proteins 99.9 1E-22 2.2E-27 216.7 17.6 228 53-295 53-408 (485)
9 KOG2191 RNA-binding protein NO 99.9 8.4E-22 1.8E-26 192.9 20.3 168 220-475 37-208 (402)
10 KOG2192 PolyC-binding hnRNP-K 99.8 2.7E-20 6E-25 177.4 11.9 240 33-297 43-385 (390)
11 TIGR03665 arCOG04150 arCOG0415 99.6 9.8E-16 2.1E-20 143.5 12.2 139 226-472 2-152 (172)
12 TIGR03665 arCOG04150 arCOG0415 99.6 1.9E-15 4E-20 141.6 8.9 138 134-296 2-151 (172)
13 PRK13763 putative RNA-processi 99.6 1.6E-14 3.4E-19 136.3 14.4 152 222-472 3-158 (180)
14 PRK13763 putative RNA-processi 99.6 1E-14 2.2E-19 137.5 10.3 142 130-297 3-158 (180)
15 cd02396 PCBP_like_KH K homolog 99.4 8.1E-13 1.7E-17 103.8 7.3 63 404-466 2-65 (65)
16 KOG2279 Kinase anchor protein 99.3 3.6E-11 7.9E-16 125.8 12.6 293 127-470 65-367 (608)
17 cd02396 PCBP_like_KH K homolog 99.3 1.5E-11 3.2E-16 96.6 7.2 65 223-291 1-65 (65)
18 cd02394 vigilin_like_KH K homo 99.2 1.1E-11 2.4E-16 96.2 5.9 61 404-466 2-62 (62)
19 PF00013 KH_1: KH domain syndr 99.2 8.2E-12 1.8E-16 96.3 4.9 60 403-465 1-60 (60)
20 cd00105 KH-I K homology RNA-bi 99.2 4.9E-11 1.1E-15 92.8 7.6 63 404-466 2-64 (64)
21 cd02393 PNPase_KH Polynucleoti 99.2 9.1E-11 2E-15 90.9 7.5 58 403-466 3-61 (61)
22 cd02394 vigilin_like_KH K homo 99.1 1.7E-10 3.6E-15 89.6 6.0 61 224-291 2-62 (62)
23 PF00013 KH_1: KH domain syndr 99.1 2.3E-10 5.1E-15 88.2 5.3 60 223-290 1-60 (60)
24 cd02393 PNPase_KH Polynucleoti 99.0 9.6E-10 2.1E-14 85.1 7.2 58 222-290 2-60 (61)
25 cd00105 KH-I K homology RNA-bi 99.0 2.3E-09 5E-14 83.3 7.6 62 224-290 2-63 (64)
26 PF13014 KH_3: KH domain 98.9 2.2E-09 4.8E-14 77.1 4.8 42 140-181 1-43 (43)
27 smart00322 KH K homology RNA-b 98.9 9.9E-09 2.1E-13 79.9 8.8 66 402-469 3-68 (69)
28 PF13014 KH_3: KH domain 98.9 4.3E-09 9.3E-14 75.5 5.5 42 412-453 1-43 (43)
29 KOG2208 Vigilin [Lipid transpo 98.8 2.9E-08 6.4E-13 112.2 12.5 233 130-472 201-489 (753)
30 COG1094 Predicted RNA-binding 98.8 4.5E-08 9.8E-13 91.5 11.5 146 129-296 7-164 (194)
31 KOG2279 Kinase anchor protein 98.8 3.6E-09 7.7E-14 111.1 3.6 145 220-472 66-210 (608)
32 COG1094 Predicted RNA-binding 98.7 1E-07 2.3E-12 89.1 11.6 154 222-473 8-166 (194)
33 smart00322 KH K homology RNA-b 98.7 1.3E-07 2.7E-12 73.6 8.6 66 222-294 3-68 (69)
34 KOG2208 Vigilin [Lipid transpo 98.5 1.4E-07 3E-12 106.8 7.9 217 130-473 347-564 (753)
35 KOG2113 Predicted RNA binding 98.3 5.2E-07 1.1E-11 89.0 4.3 157 126-294 22-181 (394)
36 cd02395 SF1_like-KH Splicing f 98.3 2E-06 4.4E-11 75.6 7.1 62 411-472 15-96 (120)
37 KOG2113 Predicted RNA binding 98.2 2.3E-06 4.9E-11 84.6 5.8 149 220-462 24-173 (394)
38 cd02395 SF1_like-KH Splicing f 98.1 8.5E-06 1.8E-10 71.7 7.2 67 230-296 14-95 (120)
39 PRK08406 transcription elongat 97.9 5.2E-05 1.1E-09 68.7 9.3 103 130-258 32-135 (140)
40 PRK08406 transcription elongat 97.7 0.00011 2.3E-09 66.6 7.4 38 222-259 32-69 (140)
41 TIGR01952 nusA_arch NusA famil 97.6 0.00035 7.6E-09 63.2 9.2 101 131-258 34-136 (141)
42 TIGR02696 pppGpp_PNP guanosine 97.5 0.00041 8.9E-09 77.7 10.5 63 403-471 579-642 (719)
43 TIGR02696 pppGpp_PNP guanosine 97.4 0.00052 1.1E-08 76.9 9.8 65 221-296 577-642 (719)
44 KOG0336 ATP-dependent RNA heli 97.1 0.00099 2.1E-08 69.0 6.8 71 400-473 45-115 (629)
45 TIGR03591 polynuc_phos polyrib 97.1 0.0016 3.5E-08 73.7 8.7 65 221-296 550-615 (684)
46 COG0195 NusA Transcription elo 96.9 0.0036 7.9E-08 59.4 8.4 101 131-259 77-179 (190)
47 TIGR01952 nusA_arch NusA famil 96.9 0.0023 5E-08 57.9 6.5 37 223-259 34-70 (141)
48 KOG0119 Splicing factor 1/bran 96.9 0.006 1.3E-07 64.4 10.2 76 221-296 137-230 (554)
49 TIGR03591 polynuc_phos polyrib 96.9 0.0016 3.4E-08 73.9 6.3 64 402-471 551-615 (684)
50 KOG1588 RNA-binding protein Sa 96.8 0.001 2.2E-08 65.3 4.0 40 127-166 89-134 (259)
51 KOG0119 Splicing factor 1/bran 96.7 0.0037 8E-08 66.0 7.3 63 410-472 152-231 (554)
52 KOG0336 ATP-dependent RNA heli 96.7 0.00066 1.4E-08 70.2 1.5 55 127-184 44-98 (629)
53 cd02134 NusA_KH NusA_K homolog 96.6 0.0027 5.8E-08 49.0 3.7 36 130-165 25-60 (61)
54 PLN00207 polyribonucleotide nu 96.5 0.0051 1.1E-07 70.6 7.4 63 403-471 686-750 (891)
55 PLN00207 polyribonucleotide nu 96.5 0.0062 1.4E-07 69.9 7.5 65 221-296 684-750 (891)
56 PRK12328 nusA transcription el 96.4 0.012 2.7E-07 61.2 8.6 93 139-260 251-346 (374)
57 COG1185 Pnp Polyribonucleotide 96.4 0.0075 1.6E-07 66.6 7.2 68 221-299 551-619 (692)
58 KOG4369 RTK signaling protein 96.3 0.0032 6.9E-08 72.0 4.1 71 403-473 1341-1412(2131)
59 cd02134 NusA_KH NusA_K homolog 96.2 0.0074 1.6E-07 46.6 4.4 36 402-437 25-60 (61)
60 PRK12329 nusA transcription el 96.2 0.018 3.9E-07 61.0 8.7 86 139-259 277-372 (449)
61 TIGR03319 YmdA_YtgF conserved 96.2 0.011 2.5E-07 64.7 7.4 68 400-472 202-271 (514)
62 TIGR01953 NusA transcription t 96.2 0.016 3.5E-07 60.2 8.0 86 139-259 243-338 (341)
63 PRK12704 phosphodiesterase; Pr 96.1 0.013 2.9E-07 64.3 7.6 68 400-472 208-277 (520)
64 PRK00106 hypothetical protein; 96.1 0.014 3.1E-07 63.9 7.7 68 400-472 223-292 (535)
65 KOG2814 Transcription coactiva 96.1 0.0078 1.7E-07 60.8 5.1 72 401-473 56-127 (345)
66 PF14611 SLS: Mitochondrial in 96.1 0.13 2.8E-06 49.7 13.5 65 223-297 27-91 (210)
67 PRK12327 nusA transcription el 96.0 0.02 4.3E-07 59.9 8.0 86 139-259 245-340 (362)
68 COG0195 NusA Transcription elo 95.9 0.027 5.9E-07 53.5 7.5 37 403-439 143-179 (190)
69 PRK09202 nusA transcription el 95.8 0.023 5E-07 61.5 7.6 91 140-259 246-339 (470)
70 KOG2814 Transcription coactiva 95.8 0.016 3.4E-07 58.7 5.7 70 222-297 57-126 (345)
71 COG1185 Pnp Polyribonucleotide 95.8 0.014 3.1E-07 64.4 5.7 65 403-473 553-618 (692)
72 PRK04163 exosome complex RNA-b 95.7 0.022 4.7E-07 56.3 6.3 64 404-473 147-211 (235)
73 PRK00468 hypothetical protein; 95.5 0.013 2.8E-07 47.2 3.1 29 129-157 29-57 (75)
74 KOG1588 RNA-binding protein Sa 95.5 0.017 3.7E-07 56.8 4.4 40 400-439 90-135 (259)
75 PRK11824 polynucleotide phosph 95.4 0.025 5.4E-07 64.4 6.3 64 222-296 554-618 (693)
76 PRK00106 hypothetical protein; 95.2 0.079 1.7E-06 58.2 9.1 65 221-295 224-290 (535)
77 PRK02821 hypothetical protein; 95.2 0.017 3.7E-07 46.7 2.9 32 129-160 30-61 (77)
78 TIGR03319 YmdA_YtgF conserved 95.2 0.076 1.6E-06 58.4 8.9 65 221-295 203-269 (514)
79 COG5176 MSL5 Splicing factor ( 95.1 0.028 6.1E-07 53.1 4.4 41 127-167 145-191 (269)
80 COG5176 MSL5 Splicing factor ( 95.0 0.11 2.3E-06 49.3 8.1 41 220-260 146-192 (269)
81 PRK12704 phosphodiesterase; Pr 95.0 0.084 1.8E-06 58.1 8.6 66 221-296 209-276 (520)
82 PRK04163 exosome complex RNA-b 94.9 0.05 1.1E-06 53.7 6.1 63 224-297 147-210 (235)
83 COG1837 Predicted RNA-binding 94.9 0.025 5.5E-07 45.5 3.2 29 129-157 29-57 (76)
84 PF14611 SLS: Mitochondrial in 94.8 0.49 1.1E-05 45.7 12.5 127 133-295 29-164 (210)
85 PRK12328 nusA transcription el 94.7 0.076 1.7E-06 55.5 6.8 38 403-440 309-346 (374)
86 TIGR01953 NusA transcription t 94.5 0.097 2.1E-06 54.4 7.2 37 403-439 302-338 (341)
87 PRK01064 hypothetical protein; 94.2 0.043 9.4E-07 44.5 2.9 31 128-158 28-58 (78)
88 PRK09202 nusA transcription el 94.1 0.087 1.9E-06 57.1 6.1 37 403-439 303-339 (470)
89 PRK11824 polynucleotide phosph 94.1 0.04 8.8E-07 62.7 3.6 63 403-471 555-618 (693)
90 PRK12327 nusA transcription el 94.1 0.14 3E-06 53.7 7.2 38 403-440 304-341 (362)
91 PRK00468 hypothetical protein; 93.9 0.059 1.3E-06 43.4 3.3 33 400-432 28-60 (75)
92 PRK12705 hypothetical protein; 93.7 0.081 1.8E-06 57.7 4.9 66 400-470 196-263 (508)
93 PRK12329 nusA transcription el 93.6 0.15 3.4E-06 54.1 6.7 37 403-439 336-372 (449)
94 PRK02821 hypothetical protein; 93.1 0.077 1.7E-06 42.9 2.7 32 402-433 31-62 (77)
95 COG1837 Predicted RNA-binding 92.8 0.13 2.7E-06 41.5 3.4 35 219-253 27-61 (76)
96 PRK01064 hypothetical protein; 92.4 0.13 2.8E-06 41.8 3.0 33 400-432 28-60 (78)
97 PF13083 KH_4: KH domain; PDB: 92.2 0.11 2.3E-06 41.4 2.4 32 129-160 28-59 (73)
98 cd02409 KH-II KH-II (K homolo 90.2 0.39 8.4E-06 36.8 3.8 34 130-163 25-58 (68)
99 KOG3273 Predicted RNA-binding 89.9 0.21 4.5E-06 47.2 2.3 55 230-296 177-231 (252)
100 KOG1067 Predicted RNA-binding 89.5 0.68 1.5E-05 50.3 6.0 65 220-296 595-660 (760)
101 PRK12705 hypothetical protein; 89.4 0.79 1.7E-05 50.2 6.6 39 221-259 197-236 (508)
102 PF13184 KH_5: NusA-like KH do 89.4 0.33 7.1E-06 38.4 2.7 37 131-167 4-46 (69)
103 KOG2874 rRNA processing protei 89.3 0.69 1.5E-05 45.9 5.4 51 414-471 161-211 (356)
104 KOG3273 Predicted RNA-binding 88.3 0.3 6.4E-06 46.2 2.1 54 411-471 178-231 (252)
105 KOG1067 Predicted RNA-binding 87.4 1.7 3.6E-05 47.4 7.2 65 402-473 597-662 (760)
106 PF07650 KH_2: KH domain syndr 87.2 0.4 8.6E-06 38.6 2.0 35 130-164 25-59 (78)
107 KOG4369 RTK signaling protein 87.0 0.28 6.1E-06 56.9 1.3 58 129-186 1339-1397(2131)
108 cd02409 KH-II KH-II (K homolo 86.8 1.1 2.5E-05 34.1 4.4 34 402-435 25-58 (68)
109 PF13083 KH_4: KH domain; PDB: 86.0 0.44 9.5E-06 37.9 1.6 35 221-255 28-62 (73)
110 PF13184 KH_5: NusA-like KH do 85.8 0.74 1.6E-05 36.4 2.8 37 403-439 4-46 (69)
111 cd02414 jag_KH jag_K homology 84.9 0.83 1.8E-05 36.8 2.8 34 131-164 25-58 (77)
112 COG1855 ATPase (PilT family) [ 84.8 0.62 1.4E-05 49.7 2.5 38 130-167 486-523 (604)
113 KOG2874 rRNA processing protei 84.7 1.7 3.7E-05 43.2 5.3 51 234-296 161-211 (356)
114 cd02413 40S_S3_KH K homology R 81.3 1.6 3.4E-05 35.7 3.0 36 130-165 30-65 (81)
115 PF07650 KH_2: KH domain syndr 81.2 0.98 2.1E-05 36.3 1.8 35 222-256 25-59 (78)
116 COG1855 ATPase (PilT family) [ 79.7 1.2 2.7E-05 47.5 2.4 38 403-440 487-524 (604)
117 PRK13764 ATPase; Provisional 79.5 1.4 3E-05 49.4 2.9 38 130-167 481-518 (602)
118 PRK06418 transcription elongat 79.0 2.5 5.4E-05 39.4 3.9 36 131-167 62-97 (166)
119 cd02414 jag_KH jag_K homology 78.4 2.4 5.2E-05 34.1 3.3 35 403-437 25-59 (77)
120 COG1097 RRP4 RNA-binding prote 77.8 5.1 0.00011 39.3 5.9 46 405-456 149-194 (239)
121 PRK13764 ATPase; Provisional 76.5 2.8 6.2E-05 46.9 4.2 43 222-264 481-523 (602)
122 cd02412 30S_S3_KH K homology R 75.8 2.8 6E-05 36.2 3.1 31 131-161 62-92 (109)
123 COG1097 RRP4 RNA-binding prote 74.0 8.1 0.00018 38.0 6.1 62 224-296 148-210 (239)
124 cd02411 archeal_30S_S3_KH K ho 72.8 3.7 8.1E-05 33.7 3.1 28 132-159 40-67 (85)
125 cd02413 40S_S3_KH K homology R 72.7 4.5 9.8E-05 33.0 3.5 35 403-437 31-65 (81)
126 COG5166 Uncharacterized conser 71.6 3.6 7.8E-05 44.4 3.3 72 130-201 449-523 (657)
127 cd02410 archeal_CPSF_KH The ar 71.4 4.7 0.0001 36.6 3.6 40 131-170 77-116 (145)
128 PRK06418 transcription elongat 69.9 6.2 0.00013 36.8 4.1 36 223-259 62-97 (166)
129 COG0092 RpsC Ribosomal protein 68.5 4.1 9E-05 39.8 2.8 29 130-158 51-79 (233)
130 cd02410 archeal_CPSF_KH The ar 66.8 4 8.6E-05 37.0 2.1 41 402-442 76-116 (145)
131 cd02411 archeal_30S_S3_KH K ho 62.5 8.3 0.00018 31.6 3.1 28 404-431 40-67 (85)
132 cd02412 30S_S3_KH K homology R 62.4 7.1 0.00015 33.7 2.8 30 404-433 63-92 (109)
133 COG5166 Uncharacterized conser 54.7 18 0.00039 39.3 4.7 126 142-296 392-524 (657)
134 COG0092 RpsC Ribosomal protein 53.9 12 0.00026 36.7 3.0 31 403-433 52-86 (233)
135 COG1782 Predicted metal-depend 53.1 32 0.0007 37.5 6.3 95 143-259 42-136 (637)
136 PF03991 Prion_octapep: Copper 52.2 8.8 0.00019 17.4 0.9 7 507-513 2-8 (8)
137 COG1702 PhoH Phosphate starvat 52.1 34 0.00073 35.6 6.1 56 409-471 22-79 (348)
138 TIGR00436 era GTP-binding prot 45.6 23 0.0005 35.4 3.8 31 401-431 220-251 (270)
139 TIGR03675 arCOG00543 arCOG0054 44.2 29 0.00063 39.4 4.7 38 222-259 93-130 (630)
140 PRK04191 rps3p 30S ribosomal p 43.1 22 0.00048 34.4 3.1 30 132-161 42-71 (207)
141 COG4371 Predicted membrane pro 42.2 30 0.00066 34.2 3.8 6 506-511 73-78 (334)
142 TIGR00436 era GTP-binding prot 42.1 25 0.00054 35.1 3.4 30 222-251 221-251 (270)
143 TIGR01008 rpsC_E_A ribosomal p 41.6 25 0.00054 33.7 3.1 31 130-160 38-68 (195)
144 COG1159 Era GTPase [General fu 41.3 24 0.00052 36.0 3.1 29 129-157 228-257 (298)
145 CHL00048 rps3 ribosomal protei 40.8 25 0.00055 34.2 3.1 30 130-159 66-95 (214)
146 PRK15494 era GTPase Era; Provi 40.0 31 0.00067 35.9 3.8 30 401-430 272-302 (339)
147 PTZ00084 40S ribosomal protein 39.5 27 0.00059 34.1 3.1 32 131-162 45-76 (220)
148 COG1782 Predicted metal-depend 39.3 28 0.0006 38.0 3.3 38 131-168 100-137 (637)
149 PRK00089 era GTPase Era; Revie 39.3 32 0.0007 34.6 3.7 37 401-437 225-270 (292)
150 KOG1423 Ras-like GTPase ERA [C 38.7 22 0.00048 36.5 2.3 31 129-159 327-358 (379)
151 TIGR03675 arCOG00543 arCOG0054 38.7 22 0.00049 40.3 2.7 41 402-442 93-133 (630)
152 PF02749 QRPTase_N: Quinolinat 38.0 1E+02 0.0022 25.3 5.9 66 402-471 18-86 (88)
153 COG1159 Era GTPase [General fu 37.7 37 0.00079 34.7 3.7 32 400-431 227-259 (298)
154 PRK15494 era GTPase Era; Provi 36.9 32 0.0007 35.8 3.4 29 222-250 273-302 (339)
155 COG1847 Jag Predicted RNA-bind 36.4 26 0.00057 33.7 2.4 36 130-165 91-126 (208)
156 PRK00089 era GTPase Era; Revie 35.8 34 0.00074 34.4 3.3 29 222-250 226-255 (292)
157 KOG1960 Predicted RNA-binding 33.0 2.1E+02 0.0047 30.3 8.4 66 408-473 220-297 (531)
158 PRK04191 rps3p 30S ribosomal p 30.6 48 0.001 32.1 3.2 29 404-432 42-70 (207)
159 COG1702 PhoH Phosphate starvat 30.5 1.2E+02 0.0026 31.6 6.2 51 229-291 22-72 (348)
160 TIGR01008 rpsC_E_A ribosomal p 30.2 50 0.0011 31.7 3.2 29 403-431 39-67 (195)
161 KOG1423 Ras-like GTPase ERA [C 29.9 45 0.00097 34.4 2.9 33 221-253 327-360 (379)
162 TIGR01009 rpsC_bact ribosomal 28.2 55 0.0012 31.8 3.1 28 132-159 64-91 (211)
163 PTZ00084 40S ribosomal protein 27.8 56 0.0012 31.9 3.1 28 404-431 46-73 (220)
164 CHL00048 rps3 ribosomal protei 27.4 58 0.0013 31.7 3.1 29 403-431 67-95 (214)
165 COG1847 Jag Predicted RNA-bind 25.8 51 0.0011 31.8 2.4 36 222-257 91-126 (208)
166 PF10515 APP_amyloid: beta-amy 25.5 13 0.00028 27.6 -1.3 32 4-39 17-49 (52)
167 PF09869 DUF2096: Uncharacteri 24.1 1.9E+02 0.0042 26.9 5.6 58 219-294 110-167 (169)
168 PF02749 QRPTase_N: Quinolinat 21.6 2.6E+02 0.0056 22.8 5.6 54 240-295 32-85 (88)
169 PF09849 DUF2076: Uncharacteri 21.4 3.5E+02 0.0075 27.0 7.3 15 457-471 56-70 (247)
170 PRK00310 rpsC 30S ribosomal pr 21.0 90 0.002 30.8 3.1 29 131-159 63-91 (232)
No 1
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=4.2e-37 Score=321.38 Aligned_cols=321 Identities=23% Similarity=0.360 Sum_probs=229.9
Q ss_pred CccccccccccccccccCCCCCCCCCCCC--CCcCccccCCCCCCCCCccchhhhhhhhhcccccCCCCCCCCC--CCCc
Q 009973 54 PESQVTKEQVTEDQLTEDQVPEDHVPEDQ--VPEDHVPEDQVPEDIVPEDSQLQEKQENEVNLAVGSTEKKWPG--WPGE 129 (521)
Q Consensus 54 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~p~--~~~~ 129 (521)
.+-+|+|-+.-+..+.-+|.-+..++.+. .+.|-+..+ +..+.+.++ .+...+.-...- .....+. .+.+
T Consensus 65 VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~-G~pe~v~~a----K~li~evv~r~~-~~~~~~~~q~~~~ 138 (600)
T KOG1676|consen 65 VGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLT-GSPENVEVA----KQLIGEVVSRGR-PPGGFPDNQGSVE 138 (600)
T ss_pred ceeEeeccHHHhhhhhhhcCCccccCCCCCCccccccccc-CCcccHHHH----HHhhhhhhhccC-CCCCccccCCccc
Confidence 34457888888888888999887764443 357666666 444444433 333333322110 0011111 1457
Q ss_pred eEEEEEeeccccccccccCchHHHHHHhhcCcEEEEeC-CCC-CCCccEEEEeccCCCCCCchhHHHHHHHHhhhhhcCC
Q 009973 130 SVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILD-GPP-GTTERAVMISAKEEPESSLPPAMDGLLRVHKRIVDGL 207 (521)
Q Consensus 130 ~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~-~~~-~~~er~v~I~G~~e~~~~a~~a~~~l~~~~~~i~~~l 207 (521)
++..|+||.+++|+||||+|++||+|++++||++.+.. +.. ....+.+.|+|.++.++.++..+-.|++ .-.+..
T Consensus 139 ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~---e~~~~~ 215 (600)
T KOG1676|consen 139 TTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILR---EEDDEV 215 (600)
T ss_pred eeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHH---hcccCC
Confidence 89999999999999999999999999999999988774 322 2367899999999865544333322221 100101
Q ss_pred CCCCCCCCCCCCCceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHH
Q 009973 208 DSDSSHAPSGTGGKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAM 287 (521)
Q Consensus 208 ~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~ 287 (521)
...............+.++.||+..||.||||+|++||+|+.+||++|+|.+ |+.|. +.+|++.|.|+.+.|++|.
T Consensus 216 ~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkp-Dd~p~---speR~~~IiG~~d~ie~Aa 291 (600)
T KOG1676|consen 216 PGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKP-DDDPS---SPERPAQIIGTVDQIEHAA 291 (600)
T ss_pred CccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeec-CCCCC---CccceeeeecCHHHHHHHH
Confidence 1111111222344569999999999999999999999999999999999998 55553 6899999999999999999
Q ss_pred HHHHHHHhhhcccCCccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009973 288 ELIGSHLRKFLVDRSIIPLFEMHMQMPNPQMDHIPPPQSWGPPQGLPPSGGPGYGHNPQYMPPPRQAESYYPPADLPPPM 367 (521)
Q Consensus 288 ~~I~~~l~~~~~~~~~~p~~e~~~~~~~p~~~~~~p~~~~~p~~~~~~~gg~g~~~~~~~~~~p~~~~~~~~~~~~~~~~ 367 (521)
++|.++|++...-. +++
T Consensus 292 ~lI~eii~~~~~~~--------------------------------------~~~------------------------- 308 (600)
T KOG1676|consen 292 ELINEIIAEAEAGA--------------------------------------GGG------------------------- 308 (600)
T ss_pred HHHHHHHHHHhccC--------------------------------------CCC-------------------------
Confidence 99999998742100 000
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccceEEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccC--CCCCC
Q 009973 368 EKQPHQGISAYGREAPVNVHGSSNAQSTPSMITQVTQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQET--RGVPG 445 (521)
Q Consensus 368 ~~~~~~g~~~~g~~~~~~~~g~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~--~~~~~ 445 (521)
++ + +. +. ....++|.||.+++|+||||+|+|||.|.++|||+|.+.+. .....
T Consensus 309 ----------~~----~---G~------P~--~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ 363 (600)
T KOG1676|consen 309 ----------MG----G---GA------PG--LVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPK 363 (600)
T ss_pred ----------cC----C---CC------cc--ceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCcc
Confidence 00 0 00 00 11167899999999999999999999999999999999876 34567
Q ss_pred ceEEEEEcCHHHHHHHHHHHHHHHHhccCC
Q 009973 446 EMTVEISGTASQVQTAQQLIQNFMAEAAAP 475 (521)
Q Consensus 446 er~VtI~Gt~e~V~~A~~lI~~~i~~~~~~ 475 (521)
+++|+|+|++.+|+.|++||+.+|......
T Consensus 364 ektf~IrG~~~QIdhAk~LIr~kvg~~~~n 393 (600)
T KOG1676|consen 364 EKTFVIRGDKRQIDHAKQLIRDKVGDIAPN 393 (600)
T ss_pred ceEEEEecCcccchHHHHHHHHHhcccCCC
Confidence 999999999999999999999999986543
No 2
>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=6e-35 Score=277.01 Aligned_cols=311 Identities=27% Similarity=0.415 Sum_probs=214.2
Q ss_pred eEEEEEeeccccccccccCchHHHHHHhhcCcEEEEeCCCCCCCccEEEEeccCCCCCCchhHHHHHHHHhhhhhcCCCC
Q 009973 130 SVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILDGPPGTTERAVMISAKEEPESSLPPAMDGLLRVHKRIVDGLDS 209 (521)
Q Consensus 130 ~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~~~~~~~er~v~I~G~~e~~~~a~~a~~~l~~~~~~i~~~l~~ 209 (521)
+.+|||+.++.+|.||||+|++||+|+.+++|.|+|++.. .++|+++|+...+ .+..+++.|+..|+.
T Consensus 48 ~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~--~peri~tisad~~----------ti~~ilk~iip~lee 115 (390)
T KOG2192|consen 48 VELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSS--GPERILTISADIE----------TIGEILKKIIPTLEE 115 (390)
T ss_pred eeEEEEEecccccceeccccccHHHHhhhccceeeccCCC--CCceeEEEeccHH----------HHHHHHHHHhhhhhh
Confidence 8999999999999999999999999999999999999865 7899999998644 566777777766665
Q ss_pred CCCCCCCCCCCceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHHHH
Q 009973 210 DSSHAPSGTGGKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAMEL 289 (521)
Q Consensus 210 ~~~~~~~~~~~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~ 289 (521)
.... ...+.++|+|...++|.|||++|++||+|++++.|+++|.. +..| .+++|+|.|.|.+..|..+++.
T Consensus 116 ~f~~-----~~pce~rllihqs~ag~iigrngskikelrekcsarlkift-~c~p---~stdrv~l~~g~~k~v~~~i~~ 186 (390)
T KOG2192|consen 116 GFQL-----PSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFT-ECCP---HSTDRVVLIGGKPKRVVECIKI 186 (390)
T ss_pred CCCC-----CCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhh-ccCC---CCcceEEEecCCcchHHHHHHH
Confidence 4332 34689999999999999999999999999999999999987 6655 4799999999999999999999
Q ss_pred HHHHHhhhcccCCcccc---ccccccCCCCCCCCCC---CCCCCCC-----CCCCCCCCC-------------CCCCCCC
Q 009973 290 IGSHLRKFLVDRSIIPL---FEMHMQMPNPQMDHIP---PPQSWGP-----PQGLPPSGG-------------PGYGHNP 345 (521)
Q Consensus 290 I~~~l~~~~~~~~~~p~---~e~~~~~~~p~~~~~~---p~~~~~p-----~~~~~~~gg-------------~g~~~~~ 345 (521)
|+++|.+...+.+..|+ |-.....+. .-.|+ +....+| .++.++..+ .-|-...
T Consensus 187 il~~i~e~pikgsa~py~p~fyd~t~dyg--gf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~v 264 (390)
T KOG2192|consen 187 ILDLISESPIKGSAQPYDPNFYDETYDYG--GFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMV 264 (390)
T ss_pred HHHHhhcCCcCCcCCcCCccccCcccccC--CceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccc
Confidence 99999987766654443 211110000 00000 0000000 011111000 0000001
Q ss_pred CCCCC---CCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccceEEEEEecCCCccceecCCCc
Q 009973 346 QYMPP---PRQAESYYPPADLPPPMEKQPHQGISAYGREAPVNVHGSSNAQSTPSMITQVTQQMQIPLSYADAVIGTAGA 422 (521)
Q Consensus 346 ~~~~~---p~~~~~~~~~~~~~~~~~~~~~~g~~~~g~~~~~~~~g~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~ 422 (521)
.|.+. |...+.+ .+++.. |.-.+++| +.|... .++..+++.... ...+|.++.||+++-|.||||+|+
T Consensus 265 dFs~detw~saidtw-~~Sewq--maYePQgG-s~ydys-yAG~~GsYGdlG----GPitTaQvtip~dlggsiigkggq 335 (390)
T KOG2192|consen 265 DFSADETWPSAIDTW-SPSEWQ--MAYEPQGG-SGYDYS-YAGGYGSYGDLG----GPITTAQVTIPKDLGGSIIGKGGQ 335 (390)
T ss_pred cccccccCCCcCCCc-Cccccc--cccCCCCC-CCCCcc-ccccccccCCCC----CceeeeeEecccccCcceecccch
Confidence 11000 0000000 011000 11111111 111110 012222222211 245788999999999999999999
Q ss_pred hHHHHHHHhCCeEEEccCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 009973 423 SISYIRRSSGATVTIQETRGVPGEMTVEISGTASQVQTAQQLIQNFMAEA 472 (521)
Q Consensus 423 ~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~Gt~e~V~~A~~lI~~~i~~~ 472 (521)
+|++|++++||.|+|.++...+.+|+++|+||.+|++.|++|+++.+..-
T Consensus 336 ri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 336 RIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY 385 (390)
T ss_pred hhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence 99999999999999999988899999999999999999999999999854
No 3
>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=2.4e-32 Score=290.07 Aligned_cols=327 Identities=28% Similarity=0.358 Sum_probs=218.8
Q ss_pred eEEEEEeeccccccccccCchHHHHHHhhcCcEEEEeCCCCCCCccEEEEeccCCCCCCchhHHHHHHHHhhhhhcCCCC
Q 009973 130 SVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILDGPPGTTERAVMISAKEEPESSLPPAMDGLLRVHKRIVDGLDS 209 (521)
Q Consensus 130 ~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~~~~~~~er~v~I~G~~e~~~~a~~a~~~l~~~~~~i~~~l~~ 209 (521)
.++||||+.+.+|.||||+|.+||+||.+|.++|+|.+..+++.+|+|+|+|..... ..+.+.+++++++++|+..++.
T Consensus 43 ~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~-~~~~~~~al~ka~~~iv~~~~~ 121 (485)
T KOG2190|consen 43 LTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVEL-NLSPATDALFKAFDMIVFKLEE 121 (485)
T ss_pred ceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccc-cCCchHHHHHHHHHHHhhcccc
Confidence 448999999999999999999999999999999999999999999999999953333 6677889999999999987664
Q ss_pred CCCCCCC----CCCCceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHH
Q 009973 210 DSSHAPS----GTGGKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHK 285 (521)
Q Consensus 210 ~~~~~~~----~~~~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~ 285 (521)
+...... .....++++|+||..++|+||||+|+.||+|+++|||+|+|.+ +++|. +++|.|+|.|.+++|.+
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 DDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSS-DMLPN---STERAVTISGEPDAVKK 197 (485)
T ss_pred cccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecC-CCCCc---ccceeEEEcCchHHHHH
Confidence 3322111 1123589999999999999999999999999999999999998 68887 48899999999999999
Q ss_pred HHHHHHHHHhhhcc-----cCCccccccccccCCCCCCCCCCCCCCCCCCC-------------------CCCCCCCCCC
Q 009973 286 AMELIGSHLRKFLV-----DRSIIPLFEMHMQMPNPQMDHIPPPQSWGPPQ-------------------GLPPSGGPGY 341 (521)
Q Consensus 286 A~~~I~~~l~~~~~-----~~~~~p~~e~~~~~~~p~~~~~~p~~~~~p~~-------------------~~~~~gg~g~ 341 (521)
|+..|..+|.++.. ..+.++++.. .....+...+|...- ..+.... +
T Consensus 198 al~~Is~~L~~~~~~~~~~~~st~~y~P~-------~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~--~ 268 (485)
T KOG2190|consen 198 ALVQISSRLLENPPRSPPPLVSTIPYRPS-------ASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKV--G 268 (485)
T ss_pred HHHHHHHHHHhcCCcCCCCCCCcccCCCc-------ccccCccccccccCCcccccccccccchhhhhhhcCchhhc--e
Confidence 99999999988531 2223332210 000001011111000 0000000 0
Q ss_pred CCCCCCCCCCCCCCCCCC-----CCCCCC-CCcCCCCCCCCCCCCCCCCCCCCC------CC-CCCCCCcccceEEEEEe
Q 009973 342 GHNPQYMPPPRQAESYYP-----PADLPP-PMEKQPHQGISAYGREAPVNVHGS------SN-AQSTPSMITQVTQQMQI 408 (521)
Q Consensus 342 ~~~~~~~~~p~~~~~~~~-----~~~~~~-~~~~~~~~g~~~~g~~~~~~~~g~------~~-~~~~~~~~~~~t~~i~V 408 (521)
+.....+..-+.+..... ....+. .... +....++....+..... .. ...... ...++.+|.|
T Consensus 269 ~v~g~~~~~i~~l~~~~~~~i~v~~~~~~~~i~~---s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~-~~~v~~~l~v 344 (485)
T KOG2190|consen 269 SVIGKGGLVIRALRNETGASISVGDSRTDRIVTI---SARENPEDRYSMAQEALLLVQPRISENAGDDL-TQTVTQRLLV 344 (485)
T ss_pred eeecCCCccchhhhhhcCCceEeccccCcceeee---ccccCcccccccchhhhhhccccccccccccc-cceeeeeecc
Confidence 000000000000000000 000000 0000 00000000000000000 00 000011 3568899999
Q ss_pred cCCCccceecCCCchHHHHHHHhCCeEEEccCCC--CCCceEEEEEcCHHHHHHHHHHHHHHHHhccC
Q 009973 409 PLSYADAVIGTAGASISYIRRSSGATVTIQETRG--VPGEMTVEISGTASQVQTAQQLIQNFMAEAAA 474 (521)
Q Consensus 409 P~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~--~~~er~VtI~Gt~e~V~~A~~lI~~~i~~~~~ 474 (521)
|.+++||||||+|++|.+||+.|||.|+|.+... ...++.++|+|+..+...|++++..++.....
T Consensus 345 ps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~~ 412 (485)
T KOG2190|consen 345 PSDLIGCIIGKGGAKISEIRQRTGASISILNKEEVSGVREALVQITGMLREDLLAQYLIRARLSAPKS 412 (485)
T ss_pred CccccceeecccccchHHHHHhcCCceEEccccccCCcceeEEEecchhHHHHhhhhhcccccccCcc
Confidence 9999999999999999999999999999998766 67899999999999999999999888887654
No 4
>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=5e-33 Score=278.06 Aligned_cols=284 Identities=25% Similarity=0.374 Sum_probs=205.0
Q ss_pred ceEEEEEeeccccccccccCchHHHHHHhhcCcEEEEeC-CCCCCCccEEEEeccCCCCCCchhHHHHHHHHhhhhhcCC
Q 009973 129 ESVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILD-GPPGTTERAVMISAKEEPESSLPPAMDGLLRVHKRIVDGL 207 (521)
Q Consensus 129 ~~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~-~~~~~~er~v~I~G~~e~~~~a~~a~~~l~~~~~~i~~~l 207 (521)
++.+|+|||..+||.||||.|+|||.|.+.|.|+|+|.+ .+.+..||+|+|.+++|.+..||+ .|+++...-..+.
T Consensus 198 D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~s~Ac~---~ILeimqkEA~~~ 274 (584)
T KOG2193|consen 198 DWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGTSKACK---MILEIMQKEAVDD 274 (584)
T ss_pred CcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccchHHHHH---HHHHHHHHhhhcc
Confidence 455999999999999999999999999999999999995 567889999999999997654444 3333322211100
Q ss_pred CCCCCCCCCCCCCceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHH
Q 009973 208 DSDSSHAPSGTGGKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAM 287 (521)
Q Consensus 208 ~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~ 287 (521)
+ ....+.++++-.+.+||++|||.|.+||+|+.+||++|.|.+-.++.-+ ..+|+|++.|+.++|.+|.
T Consensus 275 --k-------~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~y--npERTItVkGsiEac~~AE 343 (584)
T KOG2193|consen 275 --K-------VAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLY--NPERTITVKGSIEACVQAE 343 (584)
T ss_pred --c-------hhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhccc--CccceEEecccHHHHHHHH
Confidence 0 0236778999999999999999999999999999999999986665443 4699999999999999999
Q ss_pred HHHHHHHhhhcccCCccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009973 288 ELIGSHLRKFLVDRSIIPLFEMHMQMPNPQMDHIPPPQSWGPPQGLPPSGGPGYGHNPQYMPPPRQAESYYPPADLPPPM 367 (521)
Q Consensus 288 ~~I~~~l~~~~~~~~~~p~~e~~~~~~~p~~~~~~p~~~~~p~~~~~~~gg~g~~~~~~~~~~p~~~~~~~~~~~~~~~~ 367 (521)
.+|+.+|+++ ||.+....+-+ .+++|..+.. .++ .++..+.+++| .++|..
T Consensus 344 ~eImkKlre~---------yEnDl~a~s~q-~~l~P~l~~~---~l~------~f~ssS~~~~P----------h~~Ps~ 394 (584)
T KOG2193|consen 344 AEIMKKLREC---------YENDLAAMSLQ-CHLPPGLNLP---ALG------LFPSSSAVSPP----------HFPPSP 394 (584)
T ss_pred HHHHHHHHHH---------HhhhHHHhhcc-CCCCcccCcc---ccC------CCCcccccCCC----------CCCCCc
Confidence 9999999997 55443322211 1222222110 000 00111111111 111100
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccceEEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCC-CCCCc
Q 009973 368 EKQPHQGISAYGREAPVNVHGSSNAQSTPSMITQVTQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETR-GVPGE 446 (521)
Q Consensus 368 ~~~~~~g~~~~g~~~~~~~~g~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~-~~~~e 446 (521)
+.+.+++....+ ..+....+|.||...+|+|||++|.+||.|.+.+||.|+|..+. ++..+
T Consensus 395 ----------------v~~a~p~~~~hq--~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvse 456 (584)
T KOG2193|consen 395 ----------------VTFASPYPLFHQ--NPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSE 456 (584)
T ss_pred ----------------cccCCCchhhhc--CcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcce
Confidence 000000000000 01445678999999999999999999999999999999998764 35679
Q ss_pred eEEEEEcCHHHHHHHHHHHHHHHHhcc
Q 009973 447 MTVEISGTASQVQTAQQLIQNFMAEAA 473 (521)
Q Consensus 447 r~VtI~Gt~e~V~~A~~lI~~~i~~~~ 473 (521)
|+|+|+|.+++.-+|+..|..+|.+..
T Consensus 457 RMViItGppeaqfKAQgrifgKikEen 483 (584)
T KOG2193|consen 457 RMVIITGPPEAQFKAQGRIFGKIKEEN 483 (584)
T ss_pred eEEEecCChHHHHhhhhhhhhhhhhhc
Confidence 999999999999999999999998864
No 5
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.98 E-value=1.7e-31 Score=279.52 Aligned_cols=250 Identities=26% Similarity=0.391 Sum_probs=196.4
Q ss_pred ceEEEEEeeccccccccccCchHHHHHHhhcCcEEEEeCCCCCCCccEEEEeccCCCCCCchhHHHHHHHHhhhhhcCCC
Q 009973 129 ESVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILDGPPGTTERAVMISAKEEPESSLPPAMDGLLRVHKRIVDGLD 208 (521)
Q Consensus 129 ~~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~~~~~~~er~v~I~G~~e~~~~a~~a~~~l~~~~~~i~~~l~ 208 (521)
.++.+..||..+||.||||+|+.|..|+.++||+|++.....+..+|-|.+.|.+++++.++..++.+ ..+..
T Consensus 53 ~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~aK~li~ev---v~r~~---- 125 (600)
T KOG1676|consen 53 VQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEVAKQLIGEV---VSRGR---- 125 (600)
T ss_pred ccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHHHHHHhhhhh---hhccC----
Confidence 36788999999999999999999999999999999988766667899999999999765444333222 22221
Q ss_pred CCCCCCCC-CCCCceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHH
Q 009973 209 SDSSHAPS-GTGGKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAM 287 (521)
Q Consensus 209 ~~~~~~~~-~~~~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~ 287 (521)
+...+.. -....++.+|+||...+|+||||+|++||.|++.+||++.+....... ...++.+.|+|++++|+.|.
T Consensus 126 -~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~---~~~~KplritGdp~~ve~a~ 201 (600)
T KOG1676|consen 126 -PPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIA---TGADKPLRITGDPDKVEQAK 201 (600)
T ss_pred -CCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcC---CCCCCceeecCCHHHHHHHH
Confidence 1111111 113568999999999999999999999999999999999988733322 23678999999999999999
Q ss_pred HHHHHHHhhhcccCCccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009973 288 ELIGSHLRKFLVDRSIIPLFEMHMQMPNPQMDHIPPPQSWGPPQGLPPSGGPGYGHNPQYMPPPRQAESYYPPADLPPPM 367 (521)
Q Consensus 288 ~~I~~~l~~~~~~~~~~p~~e~~~~~~~p~~~~~~p~~~~~p~~~~~~~gg~g~~~~~~~~~~p~~~~~~~~~~~~~~~~ 367 (521)
.||.++|+++.... + +.+..+
T Consensus 202 ~lV~dil~e~~~~~-------------------------------~--g~~~~~-------------------------- 222 (600)
T KOG1676|consen 202 QLVADILREEDDEV-------------------------------P--GSGGHA-------------------------- 222 (600)
T ss_pred HHHHHHHHhcccCC-------------------------------C--cccccc--------------------------
Confidence 99999998741110 0 000000
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccceEEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCC-CCCc
Q 009973 368 EKQPHQGISAYGREAPVNVHGSSNAQSTPSMITQVTQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRG-VPGE 446 (521)
Q Consensus 368 ~~~~~~g~~~~g~~~~~~~~g~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~-~~~e 446 (521)
|.+. ....+.+|.||...||.||||+|++||+|+.+|||+|+|..+.+ .+.+
T Consensus 223 -----------g~~~----------------g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~spe 275 (600)
T KOG1676|consen 223 -----------GVRG----------------GGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPE 275 (600)
T ss_pred -----------CcCc----------------cccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCcc
Confidence 0000 02237889999999999999999999999999999999987765 6679
Q ss_pred eEEEEEcCHHHHHHHHHHHHHHHHhccCC
Q 009973 447 MTVEISGTASQVQTAQQLIQNFMAEAAAP 475 (521)
Q Consensus 447 r~VtI~Gt~e~V~~A~~lI~~~i~~~~~~ 475 (521)
|.+.|.|++++|+.|.+||.++|.++...
T Consensus 276 R~~~IiG~~d~ie~Aa~lI~eii~~~~~~ 304 (600)
T KOG1676|consen 276 RPAQIIGTVDQIEHAAELINEIIAEAEAG 304 (600)
T ss_pred ceeeeecCHHHHHHHHHHHHHHHHHHhcc
Confidence 99999999999999999999999987654
No 6
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.97 E-value=5e-31 Score=263.78 Aligned_cols=317 Identities=21% Similarity=0.302 Sum_probs=232.1
Q ss_pred CCCccccccccccccccccCCCCCCCC---CCCCCCcCccccCCCCCCCCCccchhhhhhhhhcccccCCCCCCCCCCCC
Q 009973 52 QVPESQVTKEQVTEDQLTEDQVPEDHV---PEDQVPEDHVPEDQVPEDIVPEDSQLQEKQENEVNLAVGSTEKKWPGWPG 128 (521)
Q Consensus 52 ~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~p~~~~ 128 (521)
|----+|+||+.|.+-+|--+--+..+ ...-..+++++.- .+++-+...+|..+|+........+ ..+
T Consensus 208 qyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh-----~tpEg~s~Ac~~ILeimqkEA~~~k----~~~ 278 (584)
T KOG2193|consen 208 QYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVH-----STPEGTSKACKMILEIMQKEAVDDK----VAE 278 (584)
T ss_pred ceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEe-----cCccchHHHHHHHHHHHHHhhhccc----hhh
Confidence 334568999999999998766544333 3335566666665 3445555556666666554322222 126
Q ss_pred ceEEEEEeeccccccccccCchHHHHHHhhcCcEEEEeCC---CCCCCccEEEEeccCCCCCCchhHHHHHHHHh-hhhh
Q 009973 129 ESVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILDG---PPGTTERAVMISAKEEPESSLPPAMDGLLRVH-KRIV 204 (521)
Q Consensus 129 ~~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~~---~~~~~er~v~I~G~~e~~~~a~~a~~~l~~~~-~~i~ 204 (521)
++.+|++.++.+||+||||.|.+||+|+.+||++|.|++. ..-..||.|+|.|+-|.|..|.. .|.+-+ ++.-
T Consensus 279 e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~---eImkKlre~yE 355 (584)
T KOG2193|consen 279 EIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEA---EIMKKLRECYE 355 (584)
T ss_pred hcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHH---HHHHHHHHHHh
Confidence 7899999999999999999999999999999999999951 12257999999997665543322 222111 1111
Q ss_pred cC-------------CCCC------------CCCCCC-------------CCCCceEEEEEeccccccccccCCchhHHH
Q 009973 205 DG-------------LDSD------------SSHAPS-------------GTGGKVSTKLLVPASQAGSLIGKQGGTVKS 246 (521)
Q Consensus 205 ~~-------------l~~~------------~~~~~~-------------~~~~~~t~~l~VP~~~vG~IIGk~G~~Ik~ 246 (521)
.+ |... .+++++ .......++|.||...+|.||||+|.+||.
T Consensus 356 nDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKq 435 (584)
T KOG2193|consen 356 NDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQ 435 (584)
T ss_pred hhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHH
Confidence 10 0000 001111 012446789999999999999999999999
Q ss_pred HHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHHHHHHHHHhhhcccCCccccccccccCCCCCCCCCCCCCC
Q 009973 247 IQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAMELIGSHLRKFLVDRSIIPLFEMHMQMPNPQMDHIPPPQS 326 (521)
Q Consensus 247 I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~p~~e~~~~~~~p~~~~~~p~~~ 326 (521)
|.+.+||.|+|...+ .| +..+|+|+|+|.+++..+|...|+.+|.+..+
T Consensus 436 l~RfagASiKIappE-~p---dvseRMViItGppeaqfKAQgrifgKikEenf--------------------------- 484 (584)
T KOG2193|consen 436 LSRFAGASIKIAPPE-IP---DVSERMVIITGPPEAQFKAQGRIFGKIKEENF--------------------------- 484 (584)
T ss_pred HHHhccceeeecCCC-CC---CcceeEEEecCChHHHHhhhhhhhhhhhhhcc---------------------------
Confidence 999999999999843 34 36899999999999999999999999987411
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccceEEEE
Q 009973 327 WGPPQGLPPSGGPGYGHNPQYMPPPRQAESYYPPADLPPPMEKQPHQGISAYGREAPVNVHGSSNAQSTPSMITQVTQQM 406 (521)
Q Consensus 327 ~~p~~~~~~~gg~g~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~g~~~~~~~~g~~~~~~~~~~~~~~t~~i 406 (521)
+.| . ....+...|
T Consensus 485 ~~P-------------------------------k------------------------------------eevklethi 497 (584)
T KOG2193|consen 485 FLP-------------------------------K------------------------------------EEVKLETHI 497 (584)
T ss_pred CCc-------------------------------h------------------------------------hhheeeeee
Confidence 000 0 013467789
Q ss_pred EecCCCccceecCCCchHHHHHHHhCCeEEEccCC--CCCCceEEEEEcCHHHHHHHHHHHHHHHHhccCCCcc
Q 009973 407 QIPLSYADAVIGTAGASISYIRRSSGATVTIQETR--GVPGEMTVEISGTASQVQTAQQLIQNFMAEAAAPSQA 478 (521)
Q Consensus 407 ~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~--~~~~er~VtI~Gt~e~V~~A~~lI~~~i~~~~~~~~~ 478 (521)
.||...+|+||||||.++++|+..|+|.|.|+++. +..+.-+|.|.|..-+++.|++.|.+++.+..+..+-
T Consensus 498 rVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhfyatq~aQrki~~iv~qvkq~~q~ 571 (584)
T KOG2193|consen 498 RVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHFYATQNAQRKIAHIVNQVKQSGQH 571 (584)
T ss_pred eccchhhhhhhccccccHHHHhccccceEEccccCCCCccceeeeeeechhhcchHHHHHHHHHHHHHHHhhhh
Confidence 99999999999999999999999999999999864 3334568999999999999999999999988765443
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=1e-26 Score=227.10 Aligned_cols=268 Identities=28% Similarity=0.386 Sum_probs=194.2
Q ss_pred CceEEEEEeeccccccccccCchHHHHHHhhcCcEEEEeC---CCCCCCccEEEEeccCCCCCCchhHHHHHHHHhhhhh
Q 009973 128 GESVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILD---GPPGTTERAVMISAKEEPESSLPPAMDGLLRVHKRIV 204 (521)
Q Consensus 128 ~~~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~---~~~~~~er~v~I~G~~e~~~~a~~a~~~l~~~~~~i~ 204 (521)
+.+++|+|||+..+|.||||+|++|.+|+++|||+|++++ ..|+++||+|.|+|+.+ +|..++..|+
T Consensus 37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~e----------ai~av~efI~ 106 (402)
T KOG2191|consen 37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVE----------ALNAVHEFIA 106 (402)
T ss_pred CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHH----------HHHHHHHHHH
Confidence 3489999999999999999999999999999999999994 78999999999999754 5666677777
Q ss_pred cCCCCCCCCC--------CCCCCCceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEE
Q 009973 205 DGLDSDSSHA--------PSGTGGKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEV 276 (521)
Q Consensus 205 ~~l~~~~~~~--------~~~~~~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I 276 (521)
|+++...... +...+....++++||+..+|.||||+|.+||.|++++||.|+|.+.. |..-.-.+|+|++
T Consensus 107 dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqk--pt~~sLqervvt~ 184 (402)
T KOG2191|consen 107 DKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQK--PTGISLQERVVTV 184 (402)
T ss_pred HHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccC--CCCccceeEEEEe
Confidence 6655432110 01112234589999999999999999999999999999999999522 3333457899999
Q ss_pred EcCHHHHHHHHHHHHHHHhhhcccCCccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009973 277 VGDASGVHKAMELIGSHLRKFLVDRSIIPLFEMHMQMPNPQMDHIPPPQSWGPPQGLPPSGGPGYGHNPQYMPPPRQAES 356 (521)
Q Consensus 277 ~G~~~~V~~A~~~I~~~l~~~~~~~~~~p~~e~~~~~~~p~~~~~~p~~~~~p~~~~~~~gg~g~~~~~~~~~~p~~~~~ 356 (521)
.|++++..+|..+|+.+|.+.....+++.. +|.-..+ +..++-|..
T Consensus 185 sge~e~~~~A~~~IL~Ki~eDpqs~scln~-------------------sya~vsG----------pvaNsnPtG----- 230 (402)
T KOG2191|consen 185 SGEPEQNMKAVSLILQKIQEDPQSGSCLNI-------------------SYANVSG----------PVANSNPTG----- 230 (402)
T ss_pred cCCHHHHHHHHHHHHHHhhcCCcccceecc-------------------chhcccC----------cccccCCCC-----
Confidence 999999999999999999764222222210 0100000 000000000
Q ss_pred CCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccceEEEEEecCCCccceecCCCchHHHHHHHhCCeEE
Q 009973 357 YYPPADLPPPMEKQPHQGISAYGREAPVNVHGSSNAQSTPSMITQVTQQMQIPLSYADAVIGTAGASISYIRRSSGATVT 436 (521)
Q Consensus 357 ~~~~~~~~~~~~~~~~~g~~~~g~~~~~~~~g~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~ 436 (521)
++|... ...+....+..+.++...+|..-|.+|.++-.|...+|+.|.
T Consensus 231 -------------------spya~~-------------~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~ 278 (402)
T KOG2191|consen 231 -------------------SPYAYQ-------------AHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIA 278 (402)
T ss_pred -------------------CCCCCC-------------Cccccccchhhccccccccccccccccccceeeeccccccee
Confidence 011000 000112234457789999999999999999999999999999
Q ss_pred EccCCC---CCCceEEEEEcCHHHHHHHHHHHHHHHHhccC
Q 009973 437 IQETRG---VPGEMTVEISGTASQVQTAQQLIQNFMAEAAA 474 (521)
Q Consensus 437 I~~~~~---~~~er~VtI~Gt~e~V~~A~~lI~~~i~~~~~ 474 (521)
|..--+ ....+ +.+.|.+-.+..|-.+|..++..+..
T Consensus 279 itq~l~~m~g~gy~-~n~~g~~ls~~aa~g~L~~~~~~a~t 318 (402)
T KOG2191|consen 279 ITQALNTMAGYGYN-TNILGLGLSILAAEGVLAAKVASANT 318 (402)
T ss_pred eccccccccccccc-ccccchhhhhhhhhhHHHHhhcccCc
Confidence 876532 34455 88999999999999999988876543
No 8
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.89 E-value=1e-22 Score=216.73 Aligned_cols=228 Identities=26% Similarity=0.363 Sum_probs=178.2
Q ss_pred CCccccccccccccccc--cCCCCCCCCCCCCCCcCccccCCC---------CCCCCCccchhhhhhhhhcccc-cCCC-
Q 009973 53 VPESQVTKEQVTEDQLT--EDQVPEDHVPEDQVPEDHVPEDQV---------PEDIVPEDSQLQEKQENEVNLA-VGST- 119 (521)
Q Consensus 53 ~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~k~~~~~~~~-~~~~- 119 (521)
.--++++|++..+++++ |++..+.+.+.+.||+|++++. . +.+++++.|..+-+.+++++.. ..+.
T Consensus 53 evG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~-g~~~~~~~~~~~~al~ka~~~iv~~~~~d~~~~~d~~~ 131 (485)
T KOG2190|consen 53 EVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITIT-GNRVELNLSPATDALFKAFDMIVFKLEEDDEAAEDNGE 131 (485)
T ss_pred cceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEe-cccccccCCchHHHHHHHHHHHhhcccccccccccCCc
Confidence 34589999999999999 8888999999999999999999 8 8999999998888776633332 2222
Q ss_pred -CCCCCCCCCceEEEEEeeccccccccccCchHHHHHHhhcCcEEEEeC-CCCCCCccEEEEeccCCCCCCchhHHHHHH
Q 009973 120 -EKKWPGWPGESVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILD-GPPGTTERAVMISAKEEPESSLPPAMDGLL 197 (521)
Q Consensus 120 -~~~~p~~~~~~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~-~~~~~~er~v~I~G~~e~~~~a~~a~~~l~ 197 (521)
..+| ++++|||||.+++|.||||+|++||+|+++|||+|+|.. ..|.+++|.|+|.|.++.+. .| |.
T Consensus 132 ~~~~~-----~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~---~a---l~ 200 (485)
T KOG2190|consen 132 DASGP-----EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVK---KA---LV 200 (485)
T ss_pred cccCC-----ceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHH---HH---HH
Confidence 2322 599999999999999999999999999999999999995 58999999999999988542 22 22
Q ss_pred HHhhhhhcCC-------------CC------------C--CC-----------------------C--------------
Q 009973 198 RVHKRIVDGL-------------DS------------D--SS-----------------------H-------------- 213 (521)
Q Consensus 198 ~~~~~i~~~l-------------~~------------~--~~-----------------------~-------------- 213 (521)
.+..+|.+.. .+ . .. .
T Consensus 201 ~Is~~L~~~~~~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~ 280 (485)
T KOG2190|consen 201 QISSRLLENPPRSPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRA 280 (485)
T ss_pred HHHHHHHhcCCcCCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchh
Confidence 2222222210 00 0 00 0
Q ss_pred ---------------C-----------CC---------------------C-C-CCceEEEEEeccccccccccCCchhH
Q 009973 214 ---------------A-----------PS---------------------G-T-GGKVSTKLLVPASQAGSLIGKQGGTV 244 (521)
Q Consensus 214 ---------------~-----------~~---------------------~-~-~~~~t~~l~VP~~~vG~IIGk~G~~I 244 (521)
. +. + . ...++.+|+||.+++||||||+|.+|
T Consensus 281 l~~~~~~~i~v~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~i 360 (485)
T KOG2190|consen 281 LRNETGASISVGDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKI 360 (485)
T ss_pred hhhhcCCceEeccccCcceeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccch
Confidence 0 00 0 0 22378999999999999999999999
Q ss_pred HHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 009973 245 KSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAMELIGSHLR 295 (521)
Q Consensus 245 k~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~ 295 (521)
.+|++.|||.|+|...++. ....++.++|+|.......+..++...+.
T Consensus 361 seir~~tgA~I~I~~~~~~---~~~~e~~~~I~~~~~~~~~~~~~~~~~~~ 408 (485)
T KOG2190|consen 361 SEIRQRTGASISILNKEEV---SGVREALVQITGMLREDLLAQYLIRARLS 408 (485)
T ss_pred HHHHHhcCCceEEcccccc---CCcceeEEEecchhHHHHhhhhhcccccc
Confidence 9999999999999986553 13589999999999999999999966654
No 9
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.89 E-value=8.4e-22 Score=192.86 Aligned_cols=168 Identities=26% Similarity=0.385 Sum_probs=136.0
Q ss_pred CceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHHHHHHHHHhhhcc
Q 009973 220 GKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAMELIGSHLRKFLV 299 (521)
Q Consensus 220 ~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~~ 299 (521)
....++++||...+|.||||+|++|.+|+++|||+|++.+..++ +.+.+||+|.|+|+.+++......|.++|++...
T Consensus 37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~df--yPGTTeRvcli~Gt~eai~av~efI~dKire~p~ 114 (402)
T KOG2191|consen 37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDF--YPGTTERVCLIQGTVEALNAVHEFIADKIREKPQ 114 (402)
T ss_pred CceEEEEEeecccccceeccchHHHHHHHhccCcEEEecccccc--CCCccceEEEEeccHHHHHHHHHHHHHHHHHhHH
Confidence 44899999999999999999999999999999999999985442 3468999999999999999999999999998532
Q ss_pred cCCccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCC
Q 009973 300 DRSIIPLFEMHMQMPNPQMDHIPPPQSWGPPQGLPPSGGPGYGHNPQYMPPPRQAESYYPPADLPPPMEKQPHQGISAYG 379 (521)
Q Consensus 300 ~~~~~p~~e~~~~~~~p~~~~~~p~~~~~p~~~~~~~gg~g~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~g 379 (521)
+..- +... +.|..
T Consensus 115 ~~~k-------------------------~v~~-------------------------~~pqt----------------- 127 (402)
T KOG2191|consen 115 AVAK-------------------------PVDI-------------------------LQPQT----------------- 127 (402)
T ss_pred hhcC-------------------------Cccc-------------------------cCCCC-----------------
Confidence 1100 0000 00000
Q ss_pred CCCCCCCCCCCCCCCCCCcccc-eEEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccC-CC--CCCceEEEEEcCH
Q 009973 380 REAPVNVHGSSNAQSTPSMITQ-VTQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQET-RG--VPGEMTVEISGTA 455 (521)
Q Consensus 380 ~~~~~~~~g~~~~~~~~~~~~~-~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~-~~--~~~er~VtI~Gt~ 455 (521)
..+ -..+|.||..-+|.||||+|++||.|++++||+|+|... +. .-.+|.|+++|++
T Consensus 128 -------------------~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~ 188 (402)
T KOG2191|consen 128 -------------------PDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEP 188 (402)
T ss_pred -------------------ccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCH
Confidence 011 136799999999999999999999999999999999843 22 2358999999999
Q ss_pred HHHHHHHHHHHHHHHhccCC
Q 009973 456 SQVQTAQQLIQNFMAEAAAP 475 (521)
Q Consensus 456 e~V~~A~~lI~~~i~~~~~~ 475 (521)
++..+|..||.++|.+.+..
T Consensus 189 e~~~~A~~~IL~Ki~eDpqs 208 (402)
T KOG2191|consen 189 EQNMKAVSLILQKIQEDPQS 208 (402)
T ss_pred HHHHHHHHHHHHHhhcCCcc
Confidence 99999999999999998764
No 10
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.83 E-value=2.7e-20 Score=177.37 Aligned_cols=240 Identities=23% Similarity=0.369 Sum_probs=174.2
Q ss_pred CCCCcccCCCCCccCCCCCCCCccccccccccccccccCCCCCCCCCCCCCCcCccccCCCCCCCCCccchhhhhhhhhc
Q 009973 33 YEVPEYEVPEVPQEQVPQEQVPESQVTKEQVTEDQLTEDQVPEDHVPEDQVPEDHVPEDQVPEDIVPEDSQLQEKQENEV 112 (521)
Q Consensus 33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~ 112 (521)
+--+.||++-.+|+. +---+++|-+...|.+++|.-+..++|+...|+++.+... ..+.+-+ ...|.....
T Consensus 43 ~k~~r~e~ril~~sk-----~agavigkgg~nik~lr~d~na~v~vpds~~peri~tisa-d~~ti~~---ilk~iip~l 113 (390)
T KOG2192|consen 43 FKRSRVELRILLQSK-----NAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISA-DIETIGE---ILKKIIPTL 113 (390)
T ss_pred hhhcceeEEEEEecc-----cccceeccccccHHHHhhhccceeeccCCCCCceeEEEec-cHHHHHH---HHHHHhhhh
Confidence 344556666666653 3456889999999999999999999999999999888772 3333222 222221111
Q ss_pred ccccCCCCCCCCCCCCceEEEEEeeccccccccccCchHHHHHHhhcCcEEEEe-CCCCCCCccEEEEeccCCCCCCchh
Q 009973 113 NLAVGSTEKKWPGWPGESVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKIL-DGPPGTTERAVMISAKEEPESSLPP 191 (521)
Q Consensus 113 ~~~~~~~~~~~p~~~~~~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~-~~~~~~~er~v~I~G~~e~~~~a~~ 191 (521)
... - ..++.+.+||||+.+.+|.|||++|++||+||+++.++++|- ...|.+++|+|.|.|.+..+ ..
T Consensus 114 ee~---f-----~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v---~~ 182 (390)
T KOG2192|consen 114 EEG---F-----QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRV---VE 182 (390)
T ss_pred hhC---C-----CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchH---HH
Confidence 110 1 112339999999999999999999999999999999999988 46788999999999988753 23
Q ss_pred HHHHHHHHhhhhh-cC--------C-CC--C--CCC--------------------------------------------
Q 009973 192 AMDGLLRVHKRIV-DG--------L-DS--D--SSH-------------------------------------------- 213 (521)
Q Consensus 192 a~~~l~~~~~~i~-~~--------l-~~--~--~~~-------------------------------------------- 213 (521)
+++.++++++.+- .. + +. + .+.
T Consensus 183 ~i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg 262 (390)
T KOG2192|consen 183 CIKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDG 262 (390)
T ss_pred HHHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccc
Confidence 3333333332210 00 0 00 0 000
Q ss_pred ---C-----------------------C------------------CCCCCceEEEEEeccccccccccCCchhHHHHHH
Q 009973 214 ---A-----------------------P------------------SGTGGKVSTKLLVPASQAGSLIGKQGGTVKSIQE 249 (521)
Q Consensus 214 ---~-----------------------~------------------~~~~~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~ 249 (521)
+ + ......+|..+.||.++-|.||||+|+.|+.|+.
T Consensus 263 ~vdFs~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~ 342 (390)
T KOG2192|consen 263 MVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRH 342 (390)
T ss_pred cccccccccCCCcCCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhh
Confidence 0 0 0012346889999999999999999999999999
Q ss_pred HhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHHHHHHHHHhhh
Q 009973 250 ASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAMELIGSHLRKF 297 (521)
Q Consensus 250 ~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~ 297 (521)
++||.|+|... ..++.+|+++|+|+.++|+.|++++...+++.
T Consensus 343 esGA~Ikidep-----leGsedrIitItGTqdQIqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 343 ESGASIKIDEP-----LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY 385 (390)
T ss_pred ccCceEEecCc-----CCCCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence 99999999752 34678999999999999999999999988753
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=99.65 E-value=9.8e-16 Score=143.47 Aligned_cols=139 Identities=26% Similarity=0.421 Sum_probs=107.3
Q ss_pred EEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEE---EcCHHHHHHHHHHHHHHHhhhcccCC
Q 009973 226 LLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEV---VGDASGVHKAMELIGSHLRKFLVDRS 302 (521)
Q Consensus 226 l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I---~G~~~~V~~A~~~I~~~l~~~~~~~~ 302 (521)
+.||.+.+|.|||++|++|+.|+++|||+|+|.. ++..|.| +++++++.+|+.+|..+.+.+..+..
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 71 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS----------ETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKA 71 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc----------CCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 5689999999999999999999999999999975 2367888 89999999999999998764211000
Q ss_pred ccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCC
Q 009973 303 IIPLFEMHMQMPNPQMDHIPPPQSWGPPQGLPPSGGPGYGHNPQYMPPPRQAESYYPPADLPPPMEKQPHQGISAYGREA 382 (521)
Q Consensus 303 ~~p~~e~~~~~~~p~~~~~~p~~~~~p~~~~~~~gg~g~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~g~~~ 382 (521)
+.++. +.|+
T Consensus 72 -~~l~g----------------------------------------------d~y~------------------------ 80 (172)
T TIGR03665 72 -LKLLD----------------------------------------------DDYM------------------------ 80 (172)
T ss_pred -HHhcC----------------------------------------------Ccce------------------------
Confidence 00000 0000
Q ss_pred CCCCCCCCCCCCCCCcccceEEEEEec---------CCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEc
Q 009973 383 PVNVHGSSNAQSTPSMITQVTQQMQIP---------LSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISG 453 (521)
Q Consensus 383 ~~~~~g~~~~~~~~~~~~~~t~~i~VP---------~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~G 453 (521)
-.-+.|+ ....|+|||++|.+++.|+..|||+|.|.. ..|.|.|
T Consensus 81 --------------------~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~-------~~v~i~G 133 (172)
T TIGR03665 81 --------------------LEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG-------KTVGIIG 133 (172)
T ss_pred --------------------EEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC-------CEEEEEC
Confidence 0001111 136899999999999999999999999964 5799999
Q ss_pred CHHHHHHHHHHHHHHHHhc
Q 009973 454 TASQVQTAQQLIQNFMAEA 472 (521)
Q Consensus 454 t~e~V~~A~~lI~~~i~~~ 472 (521)
++++++.|+.+|.+++...
T Consensus 134 ~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 134 DPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred CHHHHHHHHHHHHHHHcCC
Confidence 9999999999999999644
No 12
>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=99.60 E-value=1.9e-15 Score=141.60 Aligned_cols=138 Identities=22% Similarity=0.336 Sum_probs=95.3
Q ss_pred EEeeccccccccccCchHHHHHHhhcCcEEEEeCCCCCCCccEEEE---eccCCCCCCchhHHHHHHHHhhhhhcCCCCC
Q 009973 134 MLVPAQKVGSIIGRKGEFIKKIVEETRARIKILDGPPGTTERAVMI---SAKEEPESSLPPAMDGLLRVHKRIVDGLDSD 210 (521)
Q Consensus 134 llVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~~~~~~~er~v~I---~G~~e~~~~a~~a~~~l~~~~~~i~~~l~~~ 210 (521)
|.||.+.+|.|||++|++||.|+++|||+|++.+ .+..|.| +++++.+..|...+.+| ......+
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~-----~~g~V~I~~~t~d~~~i~kA~~~I~~i-------~~gf~~e 69 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS-----ETGEVKIEEEDEDPLAVMKAREVVKAI-------GRGFSPE 69 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc-----CCceEEEecCCCCHHHHHHHHHHHHHH-------HcCCCHH
Confidence 5689999999999999999999999999999984 3356888 44444322222222222 1111100
Q ss_pred CCCCCCCCCCceEEEEEecc---------ccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHH
Q 009973 211 SSHAPSGTGGKVSTKLLVPA---------SQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDAS 281 (521)
Q Consensus 211 ~~~~~~~~~~~~t~~l~VP~---------~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~ 281 (521)
......+ +......+.|+. ..+|+|||++|++++.|++.|||+|.|.. +.|.|.|+++
T Consensus 70 ~A~~l~g-d~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------------~~v~i~G~~~ 136 (172)
T TIGR03665 70 KALKLLD-DDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------------KTVGIIGDPE 136 (172)
T ss_pred HHHHhcC-CcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------------CEEEEECCHH
Confidence 0000000 011111223332 37899999999999999999999999863 6799999999
Q ss_pred HHHHHHHHHHHHHhh
Q 009973 282 GVHKAMELIGSHLRK 296 (521)
Q Consensus 282 ~V~~A~~~I~~~l~~ 296 (521)
+++.|+.+|.+++..
T Consensus 137 ~~~~A~~~i~~li~~ 151 (172)
T TIGR03665 137 QVQIAREAIEMLIEG 151 (172)
T ss_pred HHHHHHHHHHHHHcC
Confidence 999999999999854
No 13
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.60 E-value=1.6e-14 Score=136.28 Aligned_cols=152 Identities=25% Similarity=0.392 Sum_probs=109.7
Q ss_pred eEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEE----cCHHHHHHHHHHHHHHHhhh
Q 009973 222 VSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVV----GDASGVHKAMELIGSHLRKF 297 (521)
Q Consensus 222 ~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~----G~~~~V~~A~~~I~~~l~~~ 297 (521)
....+.||.+.+|.|||++|++|+.|+++|||+|+|.. ++..|.|. ++++++.+|+.+|..+++.+
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~----------~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf 72 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS----------ETGEVIIEPTDGEDPLAVLKARDIVKAIGRGF 72 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC----------CCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCC
Confidence 45689999999999999999999999999999999975 23678885 89999999999999988642
Q ss_pred cccCCccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCC
Q 009973 298 LVDRSIIPLFEMHMQMPNPQMDHIPPPQSWGPPQGLPPSGGPGYGHNPQYMPPPRQAESYYPPADLPPPMEKQPHQGISA 377 (521)
Q Consensus 298 ~~~~~~~p~~e~~~~~~~p~~~~~~p~~~~~p~~~~~~~gg~g~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~ 377 (521)
..+.. +-++. +.|+. . .- .+..
T Consensus 73 ~~e~A-~~l~g----------------------------------------------d~y~~-~-Vi---------~i~~ 94 (180)
T PRK13763 73 SPEKA-LRLLD----------------------------------------------DDYVL-E-VI---------DLSD 94 (180)
T ss_pred CHHHH-HHHhC----------------------------------------------CCceE-E-EE---------Ehhh
Confidence 11100 00000 00000 0 00 0000
Q ss_pred CCCCCCCCCCCCCCCCCCCCcccceEEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEcCHHH
Q 009973 378 YGREAPVNVHGSSNAQSTPSMITQVTQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISGTASQ 457 (521)
Q Consensus 378 ~g~~~~~~~~g~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~Gt~e~ 457 (521)
++. + .. .-...+|+|||++|.+++.|+..|||+|.|.. ..|.|.|++++
T Consensus 95 ~~~--------~---------~~-------~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~-------~~v~i~G~~~~ 143 (180)
T PRK13763 95 YGD--------S---------PN-------ALRRIKGRIIGEGGKTRRIIEELTGVDISVYG-------KTVAIIGDPEQ 143 (180)
T ss_pred ccC--------C---------hh-------HHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC-------CEEEEEeCHHH
Confidence 000 0 00 01237899999999999999999999999964 34999999999
Q ss_pred HHHHHHHHHHHHHhc
Q 009973 458 VQTAQQLIQNFMAEA 472 (521)
Q Consensus 458 V~~A~~lI~~~i~~~ 472 (521)
++.|+..|..++...
T Consensus 144 ~~~A~~~I~~li~g~ 158 (180)
T PRK13763 144 VEIAREAIEMLIEGA 158 (180)
T ss_pred HHHHHHHHHHHHcCC
Confidence 999999999998644
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.57 E-value=1e-14 Score=137.53 Aligned_cols=142 Identities=23% Similarity=0.337 Sum_probs=99.3
Q ss_pred eEEEEEeeccccccccccCchHHHHHHhhcCcEEEEeCCCCCCCccEEEEe----ccCCCCCCchhHHHHHHHHhhhhhc
Q 009973 130 SVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILDGPPGTTERAVMIS----AKEEPESSLPPAMDGLLRVHKRIVD 205 (521)
Q Consensus 130 ~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~~~~~~~er~v~I~----G~~e~~~~a~~a~~~l~~~~~~i~~ 205 (521)
+...|.||.+.+|.|||++|++||.|+++|||+|++.+ .+..|.|. ++++.+..|+..+++|..
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~-----~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~------- 70 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS-----ETGEVIIEPTDGEDPLAVLKARDIVKAIGR------- 70 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC-----CCCeEEEEeCCCCCHHHHHHHHHHHHHHhc-------
Confidence 57889999999999999999999999999999999984 33677885 444433333333333222
Q ss_pred CCCCCCCCCCCCCCCceEEE-EEec---------cccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEE
Q 009973 206 GLDSDSSHAPSGTGGKVSTK-LLVP---------ASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVE 275 (521)
Q Consensus 206 ~l~~~~~~~~~~~~~~~t~~-l~VP---------~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~ 275 (521)
..+.+..... ....+..+ +.|. ...+|+|||++|++++.|++.|||+|.|.. +.|.
T Consensus 71 gf~~e~A~~l--~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~------------~~v~ 136 (180)
T PRK13763 71 GFSPEKALRL--LDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG------------KTVA 136 (180)
T ss_pred CCCHHHHHHH--hCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC------------CEEE
Confidence 1100000000 00011111 1111 147899999999999999999999999963 4489
Q ss_pred EEcCHHHHHHHHHHHHHHHhhh
Q 009973 276 VVGDASGVHKAMELIGSHLRKF 297 (521)
Q Consensus 276 I~G~~~~V~~A~~~I~~~l~~~ 297 (521)
|.|+++++..|...|.++++..
T Consensus 137 i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 137 IIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred EEeCHHHHHHHHHHHHHHHcCC
Confidence 9999999999999999999653
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=8.1e-13 Score=103.78 Aligned_cols=63 Identities=35% Similarity=0.473 Sum_probs=58.5
Q ss_pred EEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCC-CCCceEEEEEcCHHHHHHHHHHHH
Q 009973 404 QQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRG-VPGEMTVEISGTASQVQTAQQLIQ 466 (521)
Q Consensus 404 ~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~-~~~er~VtI~Gt~e~V~~A~~lI~ 466 (521)
.+|.||..++|+|||++|++|++|++.|||+|+|.+... ...+|.|+|+|++++++.|+.||.
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhhC
Confidence 579999999999999999999999999999999998765 577899999999999999999983
No 16
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.26 E-value=3.6e-11 Score=125.81 Aligned_cols=293 Identities=21% Similarity=0.249 Sum_probs=178.2
Q ss_pred CCceEEEEEeeccccccccccCchHHHHHHhhcCcEEEEeCCCCCCCccEEEEeccCCCCCCchhHHHHHHHHhhhhhcC
Q 009973 127 PGESVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILDGPPGTTERAVMISAKEEPESSLPPAMDGLLRVHKRIVDG 206 (521)
Q Consensus 127 ~~~~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~~~~~~~er~v~I~G~~e~~~~a~~a~~~l~~~~~~i~~~ 206 (521)
+.++.+++.|+...+-.||||.|++||.|++.|+++|.+..... ..++..++.|.+.+ ++.+...+. +.+..
T Consensus 65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~-g~e~~~~~~~~p~~---v~~a~a~~~---~~~~~- 136 (608)
T KOG2279|consen 65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDV-GDERVLLISGFPVQ---VCKAKAAIH---QILTE- 136 (608)
T ss_pred hhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccC-CcccchhhccCCCC---CChHHHHHH---HHHhc-
Confidence 46799999999999999999999999999999999999985431 34566666665553 444443332 22221
Q ss_pred CCCCCCCCCCCCCCceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHH
Q 009973 207 LDSDSSHAPSGTGGKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKA 286 (521)
Q Consensus 207 l~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A 286 (521)
...+...+-+|...+++|+|++|.++++|+..++|+|.+..... ..-.+...|.+...-+..|
T Consensus 137 ------------~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr-----~g~~~~~~i~~qqk~~~~a 199 (608)
T KOG2279|consen 137 ------------NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGR-----LGLSRLIKISGQQKEVAAA 199 (608)
T ss_pred ------------CCcccccccchhhhcccccccchhhhcchhcccccccccccccc-----cccccceecccccchHHHH
Confidence 23566778899999999999999999999999999999876321 1356888899999999999
Q ss_pred HHHHHHHHhhhcccCCccccccccccCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCC
Q 009973 287 MELIGSHLRKFLVDRSIIPLFEMHMQMPNPQMDHIPPPQSWGPP-QGLPPSGGPGYG-HNPQYMPPPRQAESYYPPADLP 364 (521)
Q Consensus 287 ~~~I~~~l~~~~~~~~~~p~~e~~~~~~~p~~~~~~p~~~~~p~-~~~~~~gg~g~~-~~~~~~~~p~~~~~~~~~~~~~ 364 (521)
..++.+.+.+.-......|- -...+.|......+. ..+--.++.+-+ .+..++. ...++.
T Consensus 200 ~~~~~~~~~edeelv~~~~e---------~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~------s~spg~--- 261 (608)
T KOG2279|consen 200 KHLILEKVSEDEELVKRIAE---------SAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSS------SMSPGA--- 261 (608)
T ss_pred HhhhhccccchhHHhhhchh---------hcccCCCCCCCccccchhhcccccCCccccCccchh------ccCCCC---
Confidence 99998888652111111110 001111100000000 000000000000 0000100 000000
Q ss_pred CCCcCCCCCCCCCCCCCCCCC-----CCCCCCCCCCCCcccceEEEEEecCCCccceecCCCchHHHHHHHhCCeEEEcc
Q 009973 365 PPMEKQPHQGISAYGREAPVN-----VHGSSNAQSTPSMITQVTQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQE 439 (521)
Q Consensus 365 ~~~~~~~~~g~~~~g~~~~~~-----~~g~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~ 439 (521)
+.+ ..-|.+..++ .|.......-+......-.+|.+|...+|.|||+.|..|+.+...|++.+.|.-
T Consensus 262 ------~~~--~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t 333 (608)
T KOG2279|consen 262 ------PLV--TKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWT 333 (608)
T ss_pred ------CCc--ccCCCcceeEEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEe
Confidence 000 0000000000 011000000011123345679999999999999999999999999999999875
Q ss_pred CCCCCC---ceEEEEEcCHHHHHHHHHHHHHHHH
Q 009973 440 TRGVPG---EMTVEISGTASQVQTAQQLIQNFMA 470 (521)
Q Consensus 440 ~~~~~~---er~VtI~Gt~e~V~~A~~lI~~~i~ 470 (521)
..-... -.++.+.|+..-+..|..||...+-
T Consensus 334 ~pyt~~v~~~qic~~egkqh~~n~vl~ml~~~~p 367 (608)
T KOG2279|consen 334 QPYTSRVLQLQICVNEGKQHYENSVLEMLTVHVP 367 (608)
T ss_pred ccccchhhhhhhheecchhHHHHHHHhhhhccCC
Confidence 432222 2568899999999999999985443
No 17
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.26 E-value=1.5e-11 Score=96.58 Aligned_cols=65 Identities=46% Similarity=0.651 Sum_probs=57.8
Q ss_pred EEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHHHHHH
Q 009973 223 STKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAMELIG 291 (521)
Q Consensus 223 t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~ 291 (521)
+++|+||...+|+|||++|.+|++|+++|||+|.+.+... + ...+|+|+|+|+++++.+|+.+|.
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~-~---~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-P---GSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-C---CCCceEEEEEeCHHHHHHHHHhhC
Confidence 3689999999999999999999999999999999987332 2 357899999999999999999873
No 18
>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=99.24 E-value=1.1e-11 Score=96.21 Aligned_cols=61 Identities=23% Similarity=0.430 Sum_probs=55.8
Q ss_pred EEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 009973 404 QQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISGTASQVQTAQQLIQ 466 (521)
Q Consensus 404 ~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~Gt~e~V~~A~~lI~ 466 (521)
.+|.||..++++|||++|++|++|++.|||+|.|++.. ..++.|+|+|++++|..|+.+|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--SKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--CCCCEEEEEcCHHHHHHHHHHhC
Confidence 46899999999999999999999999999999998754 46788999999999999999873
No 19
>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=99.24 E-value=8.2e-12 Score=96.31 Aligned_cols=60 Identities=30% Similarity=0.545 Sum_probs=55.3
Q ss_pred EEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEcCHHHHHHHHHHH
Q 009973 403 TQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISGTASQVQTAQQLI 465 (521)
Q Consensus 403 t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~Gt~e~V~~A~~lI 465 (521)
|.+|.||.+++|+|||++|++|++|++.|||+|.|++. + ....|+|+|++++|+.|+.+|
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 57899999999999999999999999999999999876 2 455999999999999999987
No 20
>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=99.20 E-value=4.9e-11 Score=92.81 Aligned_cols=63 Identities=32% Similarity=0.540 Sum_probs=58.1
Q ss_pred EEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 009973 404 QQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISGTASQVQTAQQLIQ 466 (521)
Q Consensus 404 ~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~Gt~e~V~~A~~lI~ 466 (521)
.+|.||.+++++|||++|++|++|++.|||+|.|........++.|+|.|+.++++.|+.+|+
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i~ 64 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELIL 64 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHhC
Confidence 468999999999999999999999999999999998765567899999999999999999873
No 21
>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=99.17 E-value=9.1e-11 Score=90.86 Aligned_cols=58 Identities=28% Similarity=0.486 Sum_probs=53.2
Q ss_pred EEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEcC-HHHHHHHHHHHH
Q 009973 403 TQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISGT-ASQVQTAQQLIQ 466 (521)
Q Consensus 403 t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~Gt-~e~V~~A~~lI~ 466 (521)
+..+.||.+++|+|||++|++|++|++.|||+|.|++ ++.|+|+|+ +++++.|+.+|.
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~------~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED------DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC------CCEEEEEeCCHHHHHHHHHHhC
Confidence 5679999999999999999999999999999999976 357999999 999999999873
No 22
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.09 E-value=1.7e-10 Score=89.59 Aligned_cols=61 Identities=23% Similarity=0.378 Sum_probs=55.3
Q ss_pred EEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHHHHHH
Q 009973 224 TKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAMELIG 291 (521)
Q Consensus 224 ~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~ 291 (521)
.+|.||..++++|||++|++|++|+++|||+|.|++.+ ..++.|+|+|+.++|.+|+.+|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-------~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-------SKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-------CCCCEEEEEcCHHHHHHHHHHhC
Confidence 57899999999999999999999999999999998732 36799999999999999998873
No 23
>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=99.05 E-value=2.3e-10 Score=88.16 Aligned_cols=60 Identities=28% Similarity=0.550 Sum_probs=54.4
Q ss_pred EEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHHHHH
Q 009973 223 STKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAMELI 290 (521)
Q Consensus 223 t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I 290 (521)
|.+|.||..++|+|||++|.+|++|+++|||+|.|+.. + ....|+|+|++++|.+|+.+|
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 67899999999999999999999999999999999862 1 345999999999999999986
No 24
>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=99.01 E-value=9.6e-10 Score=85.14 Aligned_cols=58 Identities=22% Similarity=0.370 Sum_probs=52.8
Q ss_pred eEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcC-HHHHHHHHHHH
Q 009973 222 VSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGD-ASGVHKAMELI 290 (521)
Q Consensus 222 ~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~-~~~V~~A~~~I 290 (521)
....+.||..++|+|||++|++|++|+++|||+|.|.. ++.|+|+|+ ++++++|+.+|
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 35678999999999999999999999999999999864 367999999 89999999987
No 25
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.96 E-value=2.3e-09 Score=83.32 Aligned_cols=62 Identities=35% Similarity=0.639 Sum_probs=55.7
Q ss_pred EEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHHHHH
Q 009973 224 TKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAMELI 290 (521)
Q Consensus 224 ~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I 290 (521)
.++.||..+++.|||++|++|++|++.|||+|.|..... ...++.|+|.|+.+++..|+.+|
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 579999999999999999999999999999999987322 24689999999999999999887
No 26
>PF13014 KH_3: KH domain
Probab=98.89 E-value=2.2e-09 Score=77.05 Aligned_cols=42 Identities=50% Similarity=0.725 Sum_probs=38.8
Q ss_pred ccccccccCchHHHHHHhhcCcEEEEeC-CCCCCCccEEEEec
Q 009973 140 KVGSIIGRKGEFIKKIVEETRARIKILD-GPPGTTERAVMISA 181 (521)
Q Consensus 140 ~vG~IIGKgG~~Ik~I~e~Tga~I~i~~-~~~~~~er~v~I~G 181 (521)
+||+||||+|++|++|+++|||+|+|++ ..++..+|.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 5899999999999999999999999997 56678999999987
No 27
>smart00322 KH K homology RNA-binding domain.
Probab=98.89 E-value=9.9e-09 Score=79.92 Aligned_cols=66 Identities=32% Similarity=0.526 Sum_probs=59.5
Q ss_pred eEEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 009973 402 VTQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISGTASQVQTAQQLIQNFM 469 (521)
Q Consensus 402 ~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~Gt~e~V~~A~~lI~~~i 469 (521)
.+.++.||..+++++||++|++|++|++.||++|.+..... ....|+|.|+.++++.|+.+|.+.+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--EERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC--CccEEEEEcCHHHHHHHHHHHHHHh
Confidence 47789999999999999999999999999999999976432 5688999999999999999998876
No 28
>PF13014 KH_3: KH domain
Probab=98.86 E-value=4.3e-09 Score=75.55 Aligned_cols=42 Identities=31% Similarity=0.556 Sum_probs=38.0
Q ss_pred CccceecCCCchHHHHHHHhCCeEEEcc-CCCCCCceEEEEEc
Q 009973 412 YADAVIGTAGASISYIRRSSGATVTIQE-TRGVPGEMTVEISG 453 (521)
Q Consensus 412 ~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~-~~~~~~er~VtI~G 453 (521)
++|+|||++|++|++|++.|||+|+|++ ......++.|+|+|
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 34566789999998
No 29
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.80 E-value=2.9e-08 Score=112.18 Aligned_cols=233 Identities=24% Similarity=0.303 Sum_probs=159.2
Q ss_pred eEEEEEeeccccccccccCchHHHHHHhhcCcEEEEeCCCCCCCccEEEEeccCCCCC----CchhHHHHHHH--Hhhhh
Q 009973 130 SVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILDGPPGTTERAVMISAKEEPES----SLPPAMDGLLR--VHKRI 203 (521)
Q Consensus 130 ~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~~~~~~~er~v~I~G~~e~~~----~a~~a~~~l~~--~~~~i 203 (521)
+..++.+....+.+|||++|.+++.++.++.+.|.|++... ......|.|....+. ....++..+.- ....+
T Consensus 201 ~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~--~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~~ 278 (753)
T KOG2208|consen 201 VFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNK--SSPSNKIDGRLNSSSSINVEIQEALTRLESEFDYDEI 278 (753)
T ss_pred EEEEeeccccchhhhccccccccccccccceeEEEcccccc--cchhhhhccccccceehhhhhHHHHHHhcChhhhhhh
Confidence 67889999999999999999999999999999999996431 112233333222111 01111110000 00000
Q ss_pred h--------c------------CC------CCCCCC--------CCC----------------CCCCceEEEEEeccccc
Q 009973 204 V--------D------------GL------DSDSSH--------APS----------------GTGGKVSTKLLVPASQA 233 (521)
Q Consensus 204 ~--------~------------~l------~~~~~~--------~~~----------------~~~~~~t~~l~VP~~~v 233 (521)
+ . .+ ..+... ... -......+.+.|-...+
T Consensus 279 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~~ 358 (753)
T KOG2208|consen 279 IYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPEEL 358 (753)
T ss_pred hhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHHhh
Confidence 0 0 00 000000 000 00233677788889999
Q ss_pred cccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHHHHHHHHHhhhcccCCccccccccccC
Q 009973 234 GSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAMELIGSHLRKFLVDRSIIPLFEMHMQM 313 (521)
Q Consensus 234 G~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~p~~e~~~~~ 313 (521)
..++||+|.+|.+|++++.+.|.+... ++++..+.++|...++.+|...+...+.+.+.
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 999999999999999999999998762 24678999999999999999999998876311
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009973 314 PNPQMDHIPPPQSWGPPQGLPPSGGPGYGHNPQYMPPPRQAESYYPPADLPPPMEKQPHQGISAYGREAPVNVHGSSNAQ 393 (521)
Q Consensus 314 ~~p~~~~~~p~~~~~p~~~~~~~gg~g~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~g~~~~~~~~g~~~~~ 393 (521)
T Consensus 418 -------------------------------------------------------------------------------- 417 (753)
T KOG2208|consen 418 -------------------------------------------------------------------------------- 417 (753)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCCCcccceEEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 009973 394 STPSMITQVTQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISGTASQVQTAQQLIQNFMAEA 472 (521)
Q Consensus 394 ~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~Gt~e~V~~A~~lI~~~i~~~ 472 (521)
......+.+|..++.+|||.+|..|++|...+++ +.|...+.......+++.|....+..++.++..+...+
T Consensus 418 ------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~-v~i~f~~~~~~~~~~~~~~~~~dv~~~~~~~~~~~~~a 489 (753)
T KOG2208|consen 418 ------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGG-VHIKFQNNNNSSDMVTIRGISKDVEKSVSLLKALKADA 489 (753)
T ss_pred ------ccccceeecCccchhhhhccccccHHHHHhhcCc-EEEecCCCCcccccceEeccccccchhHHHHHhhhhhh
Confidence 0124458899999999999999999999999995 55554444455566888888887777777666655543
No 30
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.80 E-value=4.5e-08 Score=91.55 Aligned_cols=146 Identities=24% Similarity=0.367 Sum_probs=100.3
Q ss_pred ceEEEEEeeccccccccccCchHHHHHHhhcCcEEEEeCCCCCCCccEEEEeccCCCCC--CchhHHHHHHHHhhhhhcC
Q 009973 129 ESVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILDGPPGTTERAVMISAKEEPES--SLPPAMDGLLRVHKRIVDG 206 (521)
Q Consensus 129 ~~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~~~~~~~er~v~I~G~~e~~~--~a~~a~~~l~~~~~~i~~~ 206 (521)
.....+.||...++.+||+.|++.+.|.+.++++|.+. +.+..|.|..+....+ ...+|. .+.+.|..+
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD-----~~~~~V~i~~~~~t~Dp~~~~ka~----d~VkAIgrG 77 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID-----SKTGSVTIRTTRKTEDPLALLKAR----DVVKAIGRG 77 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEE-----CCCCeEEEEecCCCCChHHHHHHH----HHHHHHhcC
Confidence 35678999999999999999999999999999999998 5667888877632111 111111 122222221
Q ss_pred CCCCCCCCCCCCCCceEEEE-----Ee-c----cccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEE
Q 009973 207 LDSDSSHAPSGTGGKVSTKL-----LV-P----ASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEV 276 (521)
Q Consensus 207 l~~~~~~~~~~~~~~~t~~l-----~V-P----~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I 276 (521)
+..+..-..- .+......+ .- + ....|+|||++|.+.+-|++.|+|.|.|.. .+|.|
T Consensus 78 F~pe~A~~LL-~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g------------~tVai 144 (194)
T COG1094 78 FPPEKALKLL-EDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG------------KTVAI 144 (194)
T ss_pred CCHHHHHHHh-cCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC------------cEEEE
Confidence 1111000000 000111111 11 1 235699999999999999999999999975 67999
Q ss_pred EcCHHHHHHHHHHHHHHHhh
Q 009973 277 VGDASGVHKAMELIGSHLRK 296 (521)
Q Consensus 277 ~G~~~~V~~A~~~I~~~l~~ 296 (521)
-|.+++|..|+..|..+++.
T Consensus 145 iG~~~~v~iAr~AVemli~G 164 (194)
T COG1094 145 IGGFEQVEIAREAVEMLING 164 (194)
T ss_pred ecChhhhHHHHHHHHHHHcC
Confidence 99999999999999999975
No 31
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=98.77 E-value=3.6e-09 Score=111.13 Aligned_cols=145 Identities=28% Similarity=0.428 Sum_probs=122.9
Q ss_pred CceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHHHHHHHHHhhhcc
Q 009973 220 GKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAMELIGSHLRKFLV 299 (521)
Q Consensus 220 ~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~~ 299 (521)
..+..+++|+...+-+++||.|.+|+.|+..++++|.+.. ++.+ .++..++.|-+.++.+|..++..++...
T Consensus 66 k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~-ed~g-----~e~~~~~~~~p~~v~~a~a~~~~~~~~~-- 137 (608)
T KOG2279|consen 66 KDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDT-EDVG-----DERVLLISGFPVQVCKAKAAIHQILTEN-- 137 (608)
T ss_pred hheeeeEeecccceeeeeccccCCcchhhcccccceecCc-ccCC-----cccchhhccCCCCCChHHHHHHHHHhcC--
Confidence 3578899999999999999999999999999999999987 4433 5688888889999999999999887532
Q ss_pred cCCccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCC
Q 009973 300 DRSIIPLFEMHMQMPNPQMDHIPPPQSWGPPQGLPPSGGPGYGHNPQYMPPPRQAESYYPPADLPPPMEKQPHQGISAYG 379 (521)
Q Consensus 300 ~~~~~p~~e~~~~~~~p~~~~~~p~~~~~p~~~~~~~gg~g~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~g 379 (521)
T Consensus 138 -------------------------------------------------------------------------------- 137 (608)
T KOG2279|consen 138 -------------------------------------------------------------------------------- 137 (608)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCCCCCCCCCCCCCCCCCcccceEEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEcCHHHHH
Q 009973 380 REAPVNVHGSSNAQSTPSMITQVTQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISGTASQVQ 459 (521)
Q Consensus 380 ~~~~~~~~g~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~Gt~e~V~ 459 (521)
..+...+.+|...+++|+||+|.++..|++.++|+|.+.........+...|.|...-++
T Consensus 138 --------------------~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~ 197 (608)
T KOG2279|consen 138 --------------------TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVA 197 (608)
T ss_pred --------------------CcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHH
Confidence 123445778999999999999999999999999999998874344578888999999999
Q ss_pred HHHHHHHHHHHhc
Q 009973 460 TAQQLIQNFMAEA 472 (521)
Q Consensus 460 ~A~~lI~~~i~~~ 472 (521)
.|+.++.+++.+.
T Consensus 198 ~a~~~~~~~~~ed 210 (608)
T KOG2279|consen 198 AAKHLILEKVSED 210 (608)
T ss_pred HHHhhhhccccch
Confidence 9999998887764
No 32
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.73 E-value=1e-07 Score=89.13 Aligned_cols=154 Identities=22% Similarity=0.307 Sum_probs=109.4
Q ss_pred eEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEc-----CHHHHHHHHHHHHHHHhh
Q 009973 222 VSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVG-----DASGVHKAMELIGSHLRK 296 (521)
Q Consensus 222 ~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G-----~~~~V~~A~~~I~~~l~~ 296 (521)
....+.||.+.++.+||+.|+.-+.|.+.++++|.++. .+..|+|.- +|-.+.+|...|..+-+.
T Consensus 8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~----------~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrG 77 (194)
T COG1094 8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS----------KTGSVTIRTTRKTEDPLALLKARDVVKAIGRG 77 (194)
T ss_pred ceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC----------CCCeEEEEecCCCCChHHHHHHHHHHHHHhcC
Confidence 35568999999999999999999999999999999975 346666654 577899999999988766
Q ss_pred hcccCCccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCC
Q 009973 297 FLVDRSIIPLFEMHMQMPNPQMDHIPPPQSWGPPQGLPPSGGPGYGHNPQYMPPPRQAESYYPPADLPPPMEKQPHQGIS 376 (521)
Q Consensus 297 ~~~~~~~~p~~e~~~~~~~p~~~~~~p~~~~~p~~~~~~~gg~g~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~ 376 (521)
+..+... -+++.. ++- ..+.- .
T Consensus 78 F~pe~A~-~LL~d~------------------------------------~~l------evIdi---------------~ 99 (194)
T COG1094 78 FPPEKAL-KLLEDD------------------------------------YYL------EVIDL---------------K 99 (194)
T ss_pred CCHHHHH-HHhcCC------------------------------------cEE------EEEEH---------------H
Confidence 4222110 000000 000 00000 0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCcccceEEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEcCHH
Q 009973 377 AYGREAPVNVHGSSNAQSTPSMITQVTQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISGTAS 456 (521)
Q Consensus 377 ~~g~~~~~~~~g~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~Gt~e 456 (521)
.+ .+. ... .+ ....|+|||++|.+.+.|++.|||.|.|.. .+|.|.|.++
T Consensus 100 ~~--------~~~---------~~~-----~l-~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g-------~tVaiiG~~~ 149 (194)
T COG1094 100 DV--------VTL---------SGD-----HL-RRIKGRIIGREGKTRRAIEELTGVYISVYG-------KTVAIIGGFE 149 (194)
T ss_pred Hh--------ccC---------chh-----hh-hHhhceeeCCCchHHHHHHHHhCCeEEEeC-------cEEEEecChh
Confidence 00 000 000 00 235699999999999999999999999976 5799999999
Q ss_pred HHHHHHHHHHHHHHhcc
Q 009973 457 QVQTAQQLIQNFMAEAA 473 (521)
Q Consensus 457 ~V~~A~~lI~~~i~~~~ 473 (521)
+|+.|+..|..+|..++
T Consensus 150 ~v~iAr~AVemli~G~~ 166 (194)
T COG1094 150 QVEIAREAVEMLINGAP 166 (194)
T ss_pred hhHHHHHHHHHHHcCCC
Confidence 99999999999998654
No 33
>smart00322 KH K homology RNA-binding domain.
Probab=98.66 E-value=1.3e-07 Score=73.59 Aligned_cols=66 Identities=38% Similarity=0.616 Sum_probs=59.1
Q ss_pred eEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHHHHHHHHH
Q 009973 222 VSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAMELIGSHL 294 (521)
Q Consensus 222 ~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~l 294 (521)
.+.++.||...++.+||++|.+|++|++.||++|.+.... .....|+|.|+.+++..|+.+|.+.+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------SEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 5788999999999999999999999999999999997521 14689999999999999999998875
No 34
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.54 E-value=1.4e-07 Score=106.85 Aligned_cols=217 Identities=18% Similarity=0.293 Sum_probs=157.5
Q ss_pred eEEEEEeeccccccccccCchHHHHHHhhcCcEEEEeCCCCCCCccEEEEeccCCCCCCchhHHHHHHHHhhhhhcCCCC
Q 009973 130 SVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILDGPPGTTERAVMISAKEEPESSLPPAMDGLLRVHKRIVDGLDS 209 (521)
Q Consensus 130 ~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~~~~~~~er~v~I~G~~e~~~~a~~a~~~l~~~~~~i~~~l~~ 209 (521)
..+.+-+-...+..|+||+|.+|.+|++++.|.|.+.+. +.....+.++|...++ ..+++.+......+..
T Consensus 347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~~~---~ka~~~v~~~~~ei~n---- 417 (753)
T KOG2208|consen 347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSAND---EKAVEDVEKIIAEILN---- 417 (753)
T ss_pred eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccccch---hHHHHHHHHHHHhhhc----
Confidence 567888888999999999999999999999999999973 3677889999977654 3455555555555433
Q ss_pred CCCCCCCCCCCceEEEEEeccccccccccCCchhHHHHHHHhc-ccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHHH
Q 009973 210 DSSHAPSGTGGKVSTKLLVPASQAGSLIGKQGGTVKSIQEASN-CIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAME 288 (521)
Q Consensus 210 ~~~~~~~~~~~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tG-a~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~ 288 (521)
......+.+|...+.+|||.+|..|..|..+++ .+|+..... .....+++.|....+.++..
T Consensus 418 ----------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~-------~~~~~~~~~~~~~dv~~~~~ 480 (753)
T KOG2208|consen 418 ----------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN-------NSSDMVTIRGISKDVEKSVS 480 (753)
T ss_pred ----------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC-------cccccceEeccccccchhHH
Confidence 134567899999999999999999999999999 555554421 24466888898888888777
Q ss_pred HHHHHHhhhcccCCccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc
Q 009973 289 LIGSHLRKFLVDRSIIPLFEMHMQMPNPQMDHIPPPQSWGPPQGLPPSGGPGYGHNPQYMPPPRQAESYYPPADLPPPME 368 (521)
Q Consensus 289 ~I~~~l~~~~~~~~~~p~~e~~~~~~~p~~~~~~p~~~~~p~~~~~~~gg~g~~~~~~~~~~p~~~~~~~~~~~~~~~~~ 368 (521)
++..+........ |
T Consensus 481 ~~~~~~~~a~~~~-------------------------~----------------------------------------- 494 (753)
T KOG2208|consen 481 LLKALKADAKNLK-------------------------F----------------------------------------- 494 (753)
T ss_pred HHHhhhhhhhcch-------------------------h-----------------------------------------
Confidence 7766654211000 0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccceEEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceE
Q 009973 369 KQPHQGISAYGREAPVNVHGSSNAQSTPSMITQVTQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMT 448 (521)
Q Consensus 369 ~~~~~g~~~~g~~~~~~~~g~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~ 448 (521)
....+.+...|..+.+..+|+.|..+..+++.....+... .....
T Consensus 495 ------------------------------~~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~~~i~~~~~~-----~~~~~ 539 (753)
T KOG2208|consen 495 ------------------------------RDVVTKDKLLPVKYIGKEIGKNGTIRDSLGDKSIFPPNED-----EDHEK 539 (753)
T ss_pred ------------------------------hhhhhccccchHHhhcccccCceeeeccCCceeecccccc-----cccce
Confidence 0112444566778888888888776666555554433332 24567
Q ss_pred EEEEcCHHHHHHHHHHHHHHHHhcc
Q 009973 449 VEISGTASQVQTAQQLIQNFMAEAA 473 (521)
Q Consensus 449 VtI~Gt~e~V~~A~~lI~~~i~~~~ 473 (521)
++|.|..+.|..|+..++..+....
T Consensus 540 i~i~gk~~~v~~a~~~L~~~~~~~~ 564 (753)
T KOG2208|consen 540 ITIEGKLELVLEAPAELKALIEALI 564 (753)
T ss_pred eeecccccchhhhHHHHHhcchhhh
Confidence 9999999999999999988777543
No 35
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.30 E-value=5.2e-07 Score=89.00 Aligned_cols=157 Identities=22% Similarity=0.243 Sum_probs=110.6
Q ss_pred CCCceEEEEEeeccccccccccCchHHHHHHhhcCcEEEEeCCCCCCCccEEEEeccCCCCCCchhHHHHHHHHhhhhhc
Q 009973 126 WPGESVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILDGPPGTTERAVMISAKEEPESSLPPAMDGLLRVHKRIVD 205 (521)
Q Consensus 126 ~~~~~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~~~~~~~er~v~I~G~~e~~~~a~~a~~~l~~~~~~i~~ 205 (521)
.++.++..+-||...++.|.|++|.+||.|+.+|..+|+-+.. ..+.++.++|..+.++.|++-+++...-+.++..
T Consensus 22 ~p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr---~eePiF~vTg~~edv~~aRrei~saaeH~~l~~~ 98 (394)
T KOG2113|consen 22 IGQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---GEEPIFPVTGRHEDVRRARREIPSAAEHFGLIRA 98 (394)
T ss_pred CCCccceeeecCcccceeecccCccccchhhhhhcceeccCCC---CCCCcceeccCchhHHHHhhcCccccceeeeeee
Confidence 3577999999999999999999999999999999999998743 2457788999988655444433322211111111
Q ss_pred CCCCCCCCCC-CCCCCceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHH-H
Q 009973 206 GLDSDSSHAP-SGTGGKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASG-V 283 (521)
Q Consensus 206 ~l~~~~~~~~-~~~~~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~-V 283 (521)
........+ .......+...-+|-..+|.+.|.+|++|+.|++.++..|.-.-. ..+.++-++|.+.+ +
T Consensus 99 -s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~--------~~~~Vf~Vtg~~~nC~ 169 (394)
T KOG2113|consen 99 -SRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR--------CGEPVFCVTGAPKNCV 169 (394)
T ss_pred -cccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc--------CCCceEEEecCCcchh
Confidence 000000000 112345677788999999999999999999999999998876542 25688999999988 5
Q ss_pred HHHH-HHHHHHH
Q 009973 284 HKAM-ELIGSHL 294 (521)
Q Consensus 284 ~~A~-~~I~~~l 294 (521)
++|. ..|...+
T Consensus 170 kra~s~eie~ta 181 (394)
T KOG2113|consen 170 KRARSCEIEQTA 181 (394)
T ss_pred hhccccchhhhh
Confidence 6666 4554433
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=98.28 E-value=2e-06 Score=75.63 Aligned_cols=62 Identities=16% Similarity=0.410 Sum_probs=51.4
Q ss_pred CCccceecCCCchHHHHHHHhCCeEEEccCCC-----------------CCCceEEEEEcC---HHHHHHHHHHHHHHHH
Q 009973 411 SYADAVIGTAGASISYIRRSSGATVTIQETRG-----------------VPGEMTVEISGT---ASQVQTAQQLIQNFMA 470 (521)
Q Consensus 411 ~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~-----------------~~~er~VtI~Gt---~e~V~~A~~lI~~~i~ 470 (521)
+++|+|||.+|.+||+|++.|||+|.|..... ....-.|.|++. .++++.|..+|+.++.
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~ 94 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK 94 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence 57899999999999999999999999986410 112357999995 5999999999999988
Q ss_pred hc
Q 009973 471 EA 472 (521)
Q Consensus 471 ~~ 472 (521)
..
T Consensus 95 ~~ 96 (120)
T cd02395 95 PA 96 (120)
T ss_pred cC
Confidence 44
No 37
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.18 E-value=2.3e-06 Score=84.56 Aligned_cols=149 Identities=21% Similarity=0.331 Sum_probs=108.3
Q ss_pred CceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHHHHHHHHHhhhcc
Q 009973 220 GKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAMELIGSHLRKFLV 299 (521)
Q Consensus 220 ~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~~ 299 (521)
..++..+.||..+++.|+|++|.+||.|+.+|...|+-+... .+.++.++|..+.|..|+..|...-+.+-.
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~--------eePiF~vTg~~edv~~aRrei~saaeH~~l 95 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG--------EEPIFPVTGRHEDVRRARREIPSAAEHFGL 95 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC--------CCCcceeccCchhHHHHhhcCccccceeee
Confidence 567888999999999999999999999999999999877532 457899999999999999988764432200
Q ss_pred cCCccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCC
Q 009973 300 DRSIIPLFEMHMQMPNPQMDHIPPPQSWGPPQGLPPSGGPGYGHNPQYMPPPRQAESYYPPADLPPPMEKQPHQGISAYG 379 (521)
Q Consensus 300 ~~~~~p~~e~~~~~~~p~~~~~~p~~~~~p~~~~~~~gg~g~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~g 379 (521)
+.+ .+.. .++...|.
T Consensus 96 -----~~~--------------------------s~s~----------------------------------Sgg~~~~s 110 (394)
T KOG2113|consen 96 -----IRA--------------------------SRSF----------------------------------SGGTNGAS 110 (394)
T ss_pred -----eee--------------------------cccc----------------------------------cCCCcccc
Confidence 000 0000 00000000
Q ss_pred CCCCCCCCCCCCCCCCCCcccceEEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEcCHHH-H
Q 009973 380 REAPVNVHGSSNAQSTPSMITQVTQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISGTASQ-V 458 (521)
Q Consensus 380 ~~~~~~~~g~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~Gt~e~-V 458 (521)
...+.+.++.+|...+|.|.|..|.+|+.|++.+...|.-.-. ..+.++.++|.+.. +
T Consensus 111 ------------------~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~---~~~~Vf~Vtg~~~nC~ 169 (394)
T KOG2113|consen 111 ------------------ASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR---CGEPVFCVTGAPKNCV 169 (394)
T ss_pred ------------------ccCCCceeeeccceeeeeccccccCccchheecccceEeeecc---CCCceEEEecCCcchh
Confidence 0134577889999999999999999999999999999887543 24567888887776 4
Q ss_pred HHHH
Q 009973 459 QTAQ 462 (521)
Q Consensus 459 ~~A~ 462 (521)
++|.
T Consensus 170 kra~ 173 (394)
T KOG2113|consen 170 KRAR 173 (394)
T ss_pred hhcc
Confidence 4444
No 38
>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=98.10 E-value=8.5e-06 Score=71.75 Aligned_cols=67 Identities=19% Similarity=0.389 Sum_probs=51.9
Q ss_pred cccccccccCCchhHHHHHHHhcccEEEcCCCCCC-----------cc-cCCCCeEEEEEcCH---HHHHHHHHHHHHHH
Q 009973 230 ASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLP-----------VF-ALQDDRVVEVVGDA---SGVHKAMELIGSHL 294 (521)
Q Consensus 230 ~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P-----------~~-~~~~er~V~I~G~~---~~V~~A~~~I~~~l 294 (521)
.+++|.|||.+|.+||.|+++|||+|.|......- .. .....-.|.|++.. +++.+|+.+|..++
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 35789999999999999999999999998742110 00 01233678898865 89999999999998
Q ss_pred hh
Q 009973 295 RK 296 (521)
Q Consensus 295 ~~ 296 (521)
..
T Consensus 94 ~~ 95 (120)
T cd02395 94 KP 95 (120)
T ss_pred cc
Confidence 74
No 39
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.94 E-value=5.2e-05 Score=68.67 Aligned_cols=103 Identities=17% Similarity=0.275 Sum_probs=70.7
Q ss_pred eEEEEEeeccccccccccCchHHHHHHhhcCcEEEEeCCCCCCCccEEEEeccCCCCCCchhHHHHHHHHhhhh-hcCCC
Q 009973 130 SVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILDGPPGTTERAVMISAKEEPESSLPPAMDGLLRVHKRI-VDGLD 208 (521)
Q Consensus 130 ~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~~~~~~~er~v~I~G~~e~~~~a~~a~~~l~~~~~~i-~~~l~ 208 (521)
-.+.++|+...+|..||++|++|+.|++..|-+|.|-.... + ..+-+..++.-. +....
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~-------------d-------~~~fI~n~l~Pa~V~~v~ 91 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSD-------------D-------PEEFIKNIFAPAAVRSVT 91 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCC-------------C-------HHHHHHHHcCCCEEEEEE
Confidence 46889999999999999999999999999999999874221 0 001111111000 00000
Q ss_pred CCCCCCCCCCCCceEEEEEeccccccccccCCchhHHHHHHHhcccEEEc
Q 009973 209 SDSSHAPSGTGGKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVL 258 (521)
Q Consensus 209 ~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~ 258 (521)
-. .........+.|+....|.+|||+|++|+.++..++-++.|.
T Consensus 92 I~------~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 92 IK------KKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred EE------ecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 00 001234566779999999999999999999999999887663
No 40
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.71 E-value=0.00011 Score=66.60 Aligned_cols=38 Identities=24% Similarity=0.316 Sum_probs=34.4
Q ss_pred eEEEEEeccccccccccCCchhHHHHHHHhcccEEEcC
Q 009973 222 VSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLG 259 (521)
Q Consensus 222 ~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~ 259 (521)
-...++|+...+|..||++|++|+.|++..|-+|.|..
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE
Confidence 36778899999999999999999999999999998874
No 41
>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=97.61 E-value=0.00035 Score=63.20 Aligned_cols=101 Identities=19% Similarity=0.260 Sum_probs=69.5
Q ss_pred EEEEEeeccccccccccCchHHHHHHhhcCcEEEEeCCCCCCCccEEEEeccCCCCCCchhHHHHHHHHhh--hhhcCCC
Q 009973 131 VFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILDGPPGTTERAVMISAKEEPESSLPPAMDGLLRVHK--RIVDGLD 208 (521)
Q Consensus 131 ~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~~~~~~~er~v~I~G~~e~~~~a~~a~~~l~~~~~--~i~~~l~ 208 (521)
.+-++|....+|..||++|++|+.|++..|-+|.|-.... .++ +-+..++. .+.. +.
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~-----------D~~---------~fI~N~l~PA~V~~-V~ 92 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSE-----------NLE---------EFVANKLAPAEVKN-VT 92 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCC-----------CHH---------HHHHHcCCCceEEE-EE
Confidence 6788899999999999999999999999999999874211 100 00000000 0000 00
Q ss_pred CCCCCCCCCCCCceEEEEEeccccccccccCCchhHHHHHHHhcccEEEc
Q 009973 209 SDSSHAPSGTGGKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVL 258 (521)
Q Consensus 209 ~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~ 258 (521)
-. .........+.|+.+..+..|||+|.+|+...+.++-++.|.
T Consensus 93 i~------~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 93 VS------EFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred EE------cCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 00 001234567889999999999999999999999999887664
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=97.54 E-value=0.00041 Score=77.69 Aligned_cols=63 Identities=25% Similarity=0.442 Sum_probs=57.1
Q ss_pred EEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHh
Q 009973 403 TQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISG-TASQVQTAQQLIQNFMAE 471 (521)
Q Consensus 403 t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~G-t~e~V~~A~~lI~~~i~~ 471 (521)
...+.||.+++|.|||.||.+||.|.+.||++|.|.+ +..|.|.+ +.+++++|+.+|+.++..
T Consensus 579 ~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 579 IITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred eEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 4568999999999999999999999999999999976 35799988 679999999999999884
No 43
>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=97.45 E-value=0.00052 Score=76.89 Aligned_cols=65 Identities=18% Similarity=0.332 Sum_probs=57.4
Q ss_pred ceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEc-CHHHHHHHHHHHHHHHhh
Q 009973 221 KVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVG-DASGVHKAMELIGSHLRK 296 (521)
Q Consensus 221 ~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G-~~~~V~~A~~~I~~~l~~ 296 (521)
.....+.||.+.+|.|||.+|.+||.|.++|||+|.|.. +..|.|.+ +.+++++|+.+|..++..
T Consensus 577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-----------~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED-----------DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec-----------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 457789999999999999999999999999999999963 47788887 577899999999998863
No 44
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.12 E-value=0.00099 Score=68.96 Aligned_cols=71 Identities=20% Similarity=0.230 Sum_probs=59.4
Q ss_pred cceEEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhcc
Q 009973 400 TQVTQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISGTASQVQTAQQLIQNFMAEAA 473 (521)
Q Consensus 400 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~Gt~e~V~~A~~lI~~~i~~~~ 473 (521)
....+.+.|...+||.|||++|++|+.||..|.++|+|.+. ..+..|+|-|..+--.+|+..|...+....
T Consensus 45 ~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~~m~~kaka~id~~~~k~e 115 (629)
T KOG0336|consen 45 GEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGINHMRKKAKASIDRGQDKDE 115 (629)
T ss_pred CCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechHHHHHHHHhhHhhhhhhhh
Confidence 34566688999999999999999999999999999999873 346789999999888888888877766543
No 45
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.07 E-value=0.0016 Score=73.74 Aligned_cols=65 Identities=15% Similarity=0.312 Sum_probs=55.5
Q ss_pred ceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEc-CHHHHHHHHHHHHHHHhh
Q 009973 221 KVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVG-DASGVHKAMELIGSHLRK 296 (521)
Q Consensus 221 ~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G-~~~~V~~A~~~I~~~l~~ 296 (521)
.....+.||.+.++.|||++|++||.|.++|||+|.|.. +..|.|.+ ..+.+.+|..+|..+...
T Consensus 550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-----------dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-----------DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-----------CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 457789999999999999999999999999999999963 36677765 577899999999888653
No 46
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.93 E-value=0.0036 Score=59.44 Aligned_cols=101 Identities=22% Similarity=0.390 Sum_probs=68.0
Q ss_pred EEEEEeeccccccccccCchHHHHHHhhcCcEEEEeCCCCCCCccEEEEeccCCCCCCchhHHHHHHHHhh--hhhcCCC
Q 009973 131 VFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILDGPPGTTERAVMISAKEEPESSLPPAMDGLLRVHK--RIVDGLD 208 (521)
Q Consensus 131 ~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~~~~~~~er~v~I~G~~e~~~~a~~a~~~l~~~~~--~i~~~l~ 208 (521)
.+-+.+-.+.+|..||++|++|+.|+++.|=+|.|-... ++. .+-+..++. .+.. +.
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s-------------~d~-------~~fI~nal~Pa~v~~-V~ 135 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS-------------EDP-------AEFIKNALAPAEVLS-VN 135 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeC-------------CCH-------HHHHHHhcCcceEeE-EE
Confidence 344555567899999999999999999999888776422 110 000111110 0000 00
Q ss_pred CCCCCCCCCCCCceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcC
Q 009973 209 SDSSHAPSGTGGKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLG 259 (521)
Q Consensus 209 ~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~ 259 (521)
-. ..+.. ...+.||.+..+..|||+|.+++-+.+-||-++.|..
T Consensus 136 ~~------~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 136 IK------EDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EE------eCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 00 00112 6778899999999999999999999999999999875
No 47
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=96.90 E-value=0.0023 Score=57.90 Aligned_cols=37 Identities=24% Similarity=0.418 Sum_probs=33.4
Q ss_pred EEEEEeccccccccccCCchhHHHHHHHhcccEEEcC
Q 009973 223 STKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLG 259 (521)
Q Consensus 223 t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~ 259 (521)
..-++|....+|..||++|.+|+.|++..|-+|.|..
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 6778889999999999999999999999998888764
No 48
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.88 E-value=0.006 Score=64.42 Aligned_cols=76 Identities=21% Similarity=0.402 Sum_probs=56.4
Q ss_pred ceEEEEEecc------ccccccccCCchhHHHHHHHhcccEEEcCCC----------CCCccc-CCCCeEEEEEcC-HHH
Q 009973 221 KVSTKLLVPA------SQAGSLIGKQGGTVKSIQEASNCIVRVLGAE----------DLPVFA-LQDDRVVEVVGD-ASG 282 (521)
Q Consensus 221 ~~t~~l~VP~------~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~----------~~P~~~-~~~er~V~I~G~-~~~ 282 (521)
..+-++.||. ++||+|||..|.|.|+|+++|||+|.|-.+. ++.... ..++=-+.|+++ .+.
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 5566788874 4889999999999999999999999998621 111111 122334667765 668
Q ss_pred HHHHHHHHHHHHhh
Q 009973 283 VHKAMELIGSHLRK 296 (521)
Q Consensus 283 V~~A~~~I~~~l~~ 296 (521)
|++|+.+|..+|.+
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999999986
No 49
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=96.87 E-value=0.0016 Score=73.89 Aligned_cols=64 Identities=27% Similarity=0.420 Sum_probs=55.6
Q ss_pred eEEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHh
Q 009973 402 VTQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISG-TASQVQTAQQLIQNFMAE 471 (521)
Q Consensus 402 ~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~G-t~e~V~~A~~lI~~~i~~ 471 (521)
....+.||.++++.|||++|.+||.|.++|||+|.|.+ +..|.|.+ ..+.++.|..+|..+...
T Consensus 551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec------CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 35678999999999999999999999999999999976 24577776 578999999999988664
No 50
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.85 E-value=0.001 Score=65.30 Aligned_cols=40 Identities=38% Similarity=0.606 Sum_probs=36.5
Q ss_pred CCceEEEEEeecc------ccccccccCchHHHHHHhhcCcEEEEe
Q 009973 127 PGESVFRMLVPAQ------KVGSIIGRKGEFIKKIVEETRARIKIL 166 (521)
Q Consensus 127 ~~~~~~rllVP~~------~vG~IIGKgG~~Ik~I~e~Tga~I~i~ 166 (521)
+-.++.||+||.+ +||+|+|.+|.++|+|+++|||+|.|.
T Consensus 89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 3458999999985 799999999999999999999999997
No 51
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.73 E-value=0.0037 Score=65.97 Aligned_cols=63 Identities=22% Similarity=0.430 Sum_probs=50.7
Q ss_pred CCCccceecCCCchHHHHHHHhCCeEEEccCC---------C-------CCCceEEEEEc-CHHHHHHHHHHHHHHHHhc
Q 009973 410 LSYADAVIGTAGASISYIRRSSGATVTIQETR---------G-------VPGEMTVEISG-TASQVQTAQQLIQNFMAEA 472 (521)
Q Consensus 410 ~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~---------~-------~~~er~VtI~G-t~e~V~~A~~lI~~~i~~~ 472 (521)
-+++|+|||..|.+.|+|+++|||+|.|.... + ...+--+.|++ |.|.|++|..+|+.+|.++
T Consensus 152 ~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~a 231 (554)
T KOG0119|consen 152 INFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQSA 231 (554)
T ss_pred cceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHhh
Confidence 35899999999999999999999999997521 0 01133567777 6799999999999999974
No 52
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.70 E-value=0.00066 Score=70.24 Aligned_cols=55 Identities=33% Similarity=0.465 Sum_probs=47.9
Q ss_pred CCceEEEEEeeccccccccccCchHHHHHHhhcCcEEEEeCCCCCCCccEEEEeccCC
Q 009973 127 PGESVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILDGPPGTTERAVMISAKEE 184 (521)
Q Consensus 127 ~~~~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~~~~~~~er~v~I~G~~e 184 (521)
.+++.+.|.|-+++||.|||++|++||+||..|+++|+|.+. ..+-.|+|.|...
T Consensus 44 ~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~~ 98 (629)
T KOG0336|consen 44 GGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGINH 98 (629)
T ss_pred CCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechHH
Confidence 567889999999999999999999999999999999999864 3456788888654
No 53
>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=96.56 E-value=0.0027 Score=49.05 Aligned_cols=36 Identities=25% Similarity=0.456 Sum_probs=34.0
Q ss_pred eEEEEEeeccccccccccCchHHHHHHhhcCcEEEE
Q 009973 130 SVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKI 165 (521)
Q Consensus 130 ~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i 165 (521)
..+.+.|+.+.+|..|||+|.+|+.+++.++-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 579999999999999999999999999999988876
No 54
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.54 E-value=0.0051 Score=70.61 Aligned_cols=63 Identities=19% Similarity=0.383 Sum_probs=56.2
Q ss_pred EEEEEecCCCccceecCCCchHHHHHHHhCCe-EEEccCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHh
Q 009973 403 TQQMQIPLSYADAVIGTAGASISYIRRSSGAT-VTIQETRGVPGEMTVEISG-TASQVQTAQQLIQNFMAE 471 (521)
Q Consensus 403 t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~-I~I~~~~~~~~er~VtI~G-t~e~V~~A~~lI~~~i~~ 471 (521)
...+.||.++++.|||.||.+||.|.++||+. |.|.+ +-.|.|.+ +.+.++.|+.+|++++..
T Consensus 686 i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d------dg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 686 IHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD------DGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred eEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC------CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 56789999999999999999999999999999 99866 35688888 689999999999999864
No 55
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.47 E-value=0.0062 Score=69.92 Aligned_cols=65 Identities=25% Similarity=0.312 Sum_probs=55.8
Q ss_pred ceEEEEEeccccccccccCCchhHHHHHHHhccc-EEEcCCCCCCcccCCCCeEEEEEc-CHHHHHHHHHHHHHHHhh
Q 009973 221 KVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCI-VRVLGAEDLPVFALQDDRVVEVVG-DASGVHKAMELIGSHLRK 296 (521)
Q Consensus 221 ~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~-I~i~~~~~~P~~~~~~er~V~I~G-~~~~V~~A~~~I~~~l~~ 296 (521)
.....+.||.+.++.|||.||.+||.|.++||++ |.+.. +..|.|.+ +.+.+++|+.+|..++.+
T Consensus 684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d-----------dg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD-----------DGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC-----------CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 4577899999999999999999999999999999 87753 46778877 577899999999988753
No 56
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.39 E-value=0.012 Score=61.21 Aligned_cols=93 Identities=15% Similarity=0.223 Sum_probs=63.8
Q ss_pred cccccccccCchHHHHHHhhc-CcEEEEeCCCCCCCccEEEEeccCCCCCCchhHHHHHHHHhh--hhhcCCCCCCCCCC
Q 009973 139 QKVGSIIGRKGEFIKKIVEET-RARIKILDGPPGTTERAVMISAKEEPESSLPPAMDGLLRVHK--RIVDGLDSDSSHAP 215 (521)
Q Consensus 139 ~~vG~IIGKgG~~Ik~I~e~T-ga~I~i~~~~~~~~er~v~I~G~~e~~~~a~~a~~~l~~~~~--~i~~~l~~~~~~~~ 215 (521)
+-+|..||++|.+|+.|.++. |=+|.|-....+ .... +..++. .+.. +.-+
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D---~~~f-----------------I~Nal~Pa~V~~-V~i~----- 304 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNV---PEIF-----------------IARALAPAIISS-VKIE----- 304 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCC---HHHH-----------------HHHhCCCceeeE-EEEc-----
Confidence 459999999999999999988 888888742211 0000 000000 0000 0000
Q ss_pred CCCCCceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCC
Q 009973 216 SGTGGKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGA 260 (521)
Q Consensus 216 ~~~~~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~ 260 (521)
.......+.||.++.+..|||+|.+++-..+.||.+|.|..-
T Consensus 305 ---~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~ 346 (374)
T PRK12328 305 ---EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI 346 (374)
T ss_pred ---CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence 112366889999999999999999999999999999999763
No 57
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.38 E-value=0.0075 Score=66.55 Aligned_cols=68 Identities=22% Similarity=0.310 Sum_probs=58.7
Q ss_pred ceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCH-HHHHHHHHHHHHHHhhhcc
Q 009973 221 KVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDA-SGVHKAMELIGSHLRKFLV 299 (521)
Q Consensus 221 ~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~-~~V~~A~~~I~~~l~~~~~ 299 (521)
.....+.|+.+.+.-+||++|.+|++|.++|||+|.|.. +..|.|.++. +.+.+|+..|..+.++..+
T Consensus 551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied-----------dGtv~i~~s~~~~~~~ak~~I~~i~~e~ev 619 (692)
T COG1185 551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED-----------DGTVKIAASDGESAKKAKERIEAITREVEV 619 (692)
T ss_pred CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC-----------CCcEEEEecchHHHHHHHHHHHHHHhhccc
Confidence 346778899999999999999999999999999999962 4678888876 6799999999999987543
No 58
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=96.34 E-value=0.0032 Score=71.98 Aligned_cols=71 Identities=18% Similarity=0.241 Sum_probs=61.5
Q ss_pred EEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccC-CCCCCceEEEEEcCHHHHHHHHHHHHHHHHhcc
Q 009973 403 TQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQET-RGVPGEMTVEISGTASQVQTAQQLIQNFMAEAA 473 (521)
Q Consensus 403 t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~-~~~~~er~VtI~Gt~e~V~~A~~lI~~~i~~~~ 473 (521)
.-.+.+|.....+|||++|.||+.+|..|||.|.|.+- .+...+|.+++.|+++.+..|..+|.-.|.+..
T Consensus 1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i~Dpd 1412 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPIIDPD 1412 (2131)
T ss_pred ccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccceeecCC
Confidence 34678899999999999999999999999999999873 345679999999999999999999977666543
No 59
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=96.22 E-value=0.0074 Score=46.59 Aligned_cols=36 Identities=17% Similarity=0.330 Sum_probs=33.3
Q ss_pred eEEEEEecCCCccceecCCCchHHHHHHHhCCeEEE
Q 009973 402 VTQQMQIPLSYADAVIGTAGASISYIRRSSGATVTI 437 (521)
Q Consensus 402 ~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I 437 (521)
....+.|+.+..|.+|||+|.||+.+++.+|-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 467899999999999999999999999999988876
No 60
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.21 E-value=0.018 Score=61.01 Aligned_cols=86 Identities=26% Similarity=0.431 Sum_probs=63.1
Q ss_pred cccccccccCchHHHHHHhhc-CcEEEEeCCCCC---------CCccEEEEeccCCCCCCchhHHHHHHHHhhhhhcCCC
Q 009973 139 QKVGSIIGRKGEFIKKIVEET-RARIKILDGPPG---------TTERAVMISAKEEPESSLPPAMDGLLRVHKRIVDGLD 208 (521)
Q Consensus 139 ~~vG~IIGKgG~~Ik~I~e~T-ga~I~i~~~~~~---------~~er~v~I~G~~e~~~~a~~a~~~l~~~~~~i~~~l~ 208 (521)
+-+|..||++|.+|+.|.++. |=+|.|-....+ ++-+++.|. +. +
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp~~fI~NaLsPA~V~~V~----------------------i~---~ 331 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDPATYIANALSPARVDEVR----------------------LV---D 331 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCHHHHHHHhcCCceeeEEE----------------------EE---c
Confidence 459999999999999999988 888888743211 011111110 00 0
Q ss_pred CCCCCCCCCCCCceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcC
Q 009973 209 SDSSHAPSGTGGKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLG 259 (521)
Q Consensus 209 ~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~ 259 (521)
.......+.||.++.+..|||+|.+++-..+.||.+|.|..
T Consensus 332 ----------~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 332 ----------PEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred ----------CCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 11235689999999999999999999999999999998864
No 61
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.19 E-value=0.011 Score=64.72 Aligned_cols=68 Identities=18% Similarity=0.367 Sum_probs=56.0
Q ss_pred cceEEEEEecCC-CccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHhc
Q 009973 400 TQVTQQMQIPLS-YADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISG-TASQVQTAQQLIQNFMAEA 472 (521)
Q Consensus 400 ~~~t~~i~VP~~-~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~G-t~e~V~~A~~lI~~~i~~~ 472 (521)
..++..|.+|.+ +-|+||||.|.||+.+...||++|.|++.+ ..|+|+| .|---+.|+.-|..+|.+.
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp-----~~v~ls~fdp~rreia~~~l~~li~dg 271 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-----EAVILSGFDPVRREIARMALEKLIQDG 271 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCC-----CeEEecCCchHHHHHHHHHHHHHHHcC
Confidence 445667899985 559999999999999999999999998743 4588888 7777788888888887754
No 62
>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=96.17 E-value=0.016 Score=60.20 Aligned_cols=86 Identities=26% Similarity=0.425 Sum_probs=63.5
Q ss_pred cccccccccCchHHHHHHhhc-CcEEEEeCCCCC---------CCccEEEEeccCCCCCCchhHHHHHHHHhhhhhcCCC
Q 009973 139 QKVGSIIGRKGEFIKKIVEET-RARIKILDGPPG---------TTERAVMISAKEEPESSLPPAMDGLLRVHKRIVDGLD 208 (521)
Q Consensus 139 ~~vG~IIGKgG~~Ik~I~e~T-ga~I~i~~~~~~---------~~er~v~I~G~~e~~~~a~~a~~~l~~~~~~i~~~l~ 208 (521)
+-+|..||++|++|+.|.++. |=+|.|-....+ ++-+++.|. +.+
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~fi~nal~Pa~v~~v~----------------------i~~--- 297 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEFIANALSPAKVISVE----------------------VLD--- 297 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHHHHHHHhcCCceEEEEE----------------------EEc---
Confidence 459999999999999999988 888888743211 001111110 000
Q ss_pred CCCCCCCCCCCCceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcC
Q 009973 209 SDSSHAPSGTGGKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLG 259 (521)
Q Consensus 209 ~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~ 259 (521)
.......+.||.++.+..|||+|.+++-..+.||.+|.|..
T Consensus 298 ----------~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 298 ----------EDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred ----------CCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 11246789999999999999999999999999999999975
No 63
>PRK12704 phosphodiesterase; Provisional
Probab=96.13 E-value=0.013 Score=64.31 Aligned_cols=68 Identities=18% Similarity=0.355 Sum_probs=54.2
Q ss_pred cceEEEEEecCC-CccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHhc
Q 009973 400 TQVTQQMQIPLS-YADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISG-TASQVQTAQQLIQNFMAEA 472 (521)
Q Consensus 400 ~~~t~~i~VP~~-~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~G-t~e~V~~A~~lI~~~i~~~ 472 (521)
..++..|.+|.+ +-|+||||.|.||+.+...||++|.|++.+ ..|.|+| .|---+.|+..|..++.+.
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp-----~~v~ls~~~~~rre~a~~~l~~l~~dg 277 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-----EAVILSGFDPIRREIARLALEKLVQDG 277 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCC-----CeEEEecCChhhHHHHHHHHHHHHhcC
Confidence 445667889985 559999999999999999999999998743 4688999 6666667777777776643
No 64
>PRK00106 hypothetical protein; Provisional
Probab=96.13 E-value=0.014 Score=63.88 Aligned_cols=68 Identities=21% Similarity=0.382 Sum_probs=56.7
Q ss_pred cceEEEEEecCC-CccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHhc
Q 009973 400 TQVTQQMQIPLS-YADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISG-TASQVQTAQQLIQNFMAEA 472 (521)
Q Consensus 400 ~~~t~~i~VP~~-~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~G-t~e~V~~A~~lI~~~i~~~ 472 (521)
..++..|.+|.+ +-|+||||.|.||+.+...||++|.|++.+ ..|+|+| .|---+.|+.-|..+|.+.
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-----~~v~lS~fdpvRReiAr~~le~Li~dg 292 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP-----EVVVLSGFDPIRREIARMTLESLIKDG 292 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC-----CeEEEeCCChHHHHHHHHHHHHHHHcC
Confidence 445667899985 559999999999999999999999997743 4588999 7888888888888888764
No 65
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.11 E-value=0.0078 Score=60.81 Aligned_cols=72 Identities=13% Similarity=0.158 Sum_probs=60.0
Q ss_pred ceEEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhcc
Q 009973 401 QVTQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISGTASQVQTAQQLIQNFMAEAA 473 (521)
Q Consensus 401 ~~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~Gt~e~V~~A~~lI~~~i~~~~ 473 (521)
.....+.|++...|.|||+.|.+.+.|+++|+++|.++++.+. .+.++.+-+..++|..|...|.-+|++..
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n-~~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTN-KEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCC-cceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 3455688999999999999999999999999999999987542 33444445578999999999999998765
No 66
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=96.09 E-value=0.13 Score=49.75 Aligned_cols=65 Identities=11% Similarity=0.166 Sum_probs=55.3
Q ss_pred EEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHHHHHHHHHhhh
Q 009973 223 STKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAMELIGSHLRKF 297 (521)
Q Consensus 223 t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~ 297 (521)
.+.+.++....-.++..+|..++.|....||+|.+.. .+..|.|+|+...+..+...|.+++...
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~----------~~~~i~I~g~k~~~~~i~~~i~~~l~~i 91 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR----------SENRIRITGTKSTAEYIEASINEILSNI 91 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEec----------CCcEEEEEccHHHHHHHHHHHHHHHhhc
Confidence 3445556888889999999999999888999999976 4578999999999999999999988653
No 67
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.05 E-value=0.02 Score=59.94 Aligned_cols=86 Identities=22% Similarity=0.400 Sum_probs=63.6
Q ss_pred cccccccccCchHHHHHHhhc-CcEEEEeCCCCC---------CCccEEEEeccCCCCCCchhHHHHHHHHhhhhhcCCC
Q 009973 139 QKVGSIIGRKGEFIKKIVEET-RARIKILDGPPG---------TTERAVMISAKEEPESSLPPAMDGLLRVHKRIVDGLD 208 (521)
Q Consensus 139 ~~vG~IIGKgG~~Ik~I~e~T-ga~I~i~~~~~~---------~~er~v~I~G~~e~~~~a~~a~~~l~~~~~~i~~~l~ 208 (521)
+-+|..||++|.+|+.|.++. |-+|.|-....+ ++-+++.|. +. +
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~~fi~nal~Pa~v~~v~----------------------i~---~ 299 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPAEFVANALSPAKVVSVE----------------------VD---D 299 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCCCHHHHHHHhCCCceEEEEE----------------------EE---c
Confidence 459999999999999999888 888888743211 011111110 00 0
Q ss_pred CCCCCCCCCCCCceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcC
Q 009973 209 SDSSHAPSGTGGKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLG 259 (521)
Q Consensus 209 ~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~ 259 (521)
.......+.||.++.+..|||+|.+++-..+.||.+|.|..
T Consensus 300 ----------~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 300 ----------EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred ----------CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 11246789999999999999999999999999999999975
No 68
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=95.89 E-value=0.027 Score=53.54 Aligned_cols=37 Identities=16% Similarity=0.328 Sum_probs=34.3
Q ss_pred EEEEEecCCCccceecCCCchHHHHHHHhCCeEEEcc
Q 009973 403 TQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQE 439 (521)
Q Consensus 403 t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~ 439 (521)
...+.||.+..+.+|||+|.|++-+++.||-+|.|..
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 5678899999999999999999999999999999965
No 69
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.83 E-value=0.023 Score=61.50 Aligned_cols=91 Identities=26% Similarity=0.383 Sum_probs=63.2
Q ss_pred ccccccccCchHHHHHHhhc-CcEEEEeCCCCCCCccEEEEeccCCCCCCchhHHHHHH--HHhhhhhcCCCCCCCCCCC
Q 009973 140 KVGSIIGRKGEFIKKIVEET-RARIKILDGPPGTTERAVMISAKEEPESSLPPAMDGLL--RVHKRIVDGLDSDSSHAPS 216 (521)
Q Consensus 140 ~vG~IIGKgG~~Ik~I~e~T-ga~I~i~~~~~~~~er~v~I~G~~e~~~~a~~a~~~l~--~~~~~i~~~l~~~~~~~~~ 216 (521)
-+|..||++|++|+.|.++. |=+|.|-....+ ....|.- +|. ++...+++
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d---~~~fi~n-------------al~pa~v~~v~~~----------- 298 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIILWSDD---PAQFIIN-------------ALSPAEVSSVVVD----------- 298 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEEcCCC---HHHHHHH-------------hCCCCEEEEEEEe-----------
Confidence 49999999999999999988 888888743211 0000000 000 00000110
Q ss_pred CCCCceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcC
Q 009973 217 GTGGKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLG 259 (521)
Q Consensus 217 ~~~~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~ 259 (521)
.......+.||....+..|||+|.+++-..+.||.+|.|..
T Consensus 299 --~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 299 --EDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred --CCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 01237789999999999999999999999999999999975
No 70
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=95.79 E-value=0.016 Score=58.65 Aligned_cols=70 Identities=26% Similarity=0.287 Sum_probs=56.9
Q ss_pred eEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHHHHHHHHHhhh
Q 009973 222 VSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAMELIGSHLRKF 297 (521)
Q Consensus 222 ~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~ 297 (521)
....+.++....|+|||++|.|.++|+++|+++|.++.... ..+-++.+.+..++|.+|...|..+|.+.
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~------n~~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT------NKEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC------CcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 34567899999999999999999999999999999987321 23344445567888999999999999764
No 71
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=95.76 E-value=0.014 Score=64.40 Aligned_cols=65 Identities=23% Similarity=0.406 Sum_probs=57.2
Q ss_pred EEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEcCH-HHHHHHHHHHHHHHHhcc
Q 009973 403 TQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISGTA-SQVQTAQQLIQNFMAEAA 473 (521)
Q Consensus 403 t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~Gt~-e~V~~A~~lI~~~i~~~~ 473 (521)
..++.|+.+.++-|||++|.+|+.|.++|||+|.|.+ +-+|.|.++. +.+..|+.+|.++..+..
T Consensus 553 i~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied------dGtv~i~~s~~~~~~~ak~~I~~i~~e~e 618 (692)
T COG1185 553 IETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED------DGTVKIAASDGESAKKAKERIEAITREVE 618 (692)
T ss_pred eEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC------CCcEEEEecchHHHHHHHHHHHHHHhhcc
Confidence 3578999999999999999999999999999999974 2459999976 899999999999997654
No 72
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.70 E-value=0.022 Score=56.28 Aligned_cols=64 Identities=20% Similarity=0.324 Sum_probs=54.7
Q ss_pred EEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHHhcc
Q 009973 404 QQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISGT-ASQVQTAQQLIQNFMAEAA 473 (521)
Q Consensus 404 ~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~Gt-~e~V~~A~~lI~~~i~~~~ 473 (521)
..+.||..+++++||++|.+|+.|.+.+++.|.|.. +-.|.|.++ .+.++.|..+|+++-.++.
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~------NG~VwI~~~~~~~~~~a~~~I~~~e~~~~ 211 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ------NGRIWIKGPDEEDEEIAIEAIKKIEREAH 211 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC------CcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence 348899999999999999999999999999999965 246999986 5699999999998766654
No 73
>PRK00468 hypothetical protein; Provisional
Probab=95.46 E-value=0.013 Score=47.17 Aligned_cols=29 Identities=24% Similarity=0.572 Sum_probs=27.1
Q ss_pred ceEEEEEeeccccccccccCchHHHHHHh
Q 009973 129 ESVFRMLVPAQKVGSIIGRKGEFIKKIVE 157 (521)
Q Consensus 129 ~~~~rllVP~~~vG~IIGKgG~~Ik~I~e 157 (521)
.+.++|.|..+.+|+||||+|.+|+.||.
T Consensus 29 ~~~~~l~v~~~D~GrVIGk~Gr~i~AIRt 57 (75)
T PRK00468 29 SVILELKVAPEDMGKVIGKQGRIAKAIRT 57 (75)
T ss_pred eEEEEEEEChhhCcceecCCChhHHHHHH
Confidence 37899999999999999999999999995
No 74
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=95.45 E-value=0.017 Score=56.81 Aligned_cols=40 Identities=18% Similarity=0.564 Sum_probs=35.5
Q ss_pred cceEEEEEecCC------CccceecCCCchHHHHHHHhCCeEEEcc
Q 009973 400 TQVTQQMQIPLS------YADAVIGTAGASISYIRRSSGATVTIQE 439 (521)
Q Consensus 400 ~~~t~~i~VP~~------~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~ 439 (521)
...+.+|.||.+ +||+|+|..|.++|+|+++|||+|-|.-
T Consensus 90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrG 135 (259)
T KOG1588|consen 90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRG 135 (259)
T ss_pred eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEec
Confidence 457788888865 8999999999999999999999999953
No 75
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.41 E-value=0.025 Score=64.40 Aligned_cols=64 Identities=22% Similarity=0.367 Sum_probs=53.6
Q ss_pred eEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEc-CHHHHHHHHHHHHHHHhh
Q 009973 222 VSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVG-DASGVHKAMELIGSHLRK 296 (521)
Q Consensus 222 ~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G-~~~~V~~A~~~I~~~l~~ 296 (521)
....+.|+.+.++.+||.+|.+||+|.++||++|.+. ++..|.|.+ ..+.+.+|+.+|..+..+
T Consensus 554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-----------d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-----------DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 4556778999999999999999999999999988764 246678877 577899999999888754
No 76
>PRK00106 hypothetical protein; Provisional
Probab=95.21 E-value=0.079 Score=58.17 Aligned_cols=65 Identities=20% Similarity=0.334 Sum_probs=49.9
Q ss_pred ceEEEEEecc-ccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEc-CHHHHHHHHHHHHHHHh
Q 009973 221 KVSTKLLVPA-SQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVG-DASGVHKAMELIGSHLR 295 (521)
Q Consensus 221 ~~t~~l~VP~-~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G-~~~~V~~A~~~I~~~l~ 295 (521)
.+...+.+|+ ++-|+||||.|.+|+-+...||+.+-|+. +...|+|+| +|-.-+-|+..+..++.
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd----------tp~~v~lS~fdpvRReiAr~~le~Li~ 290 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD----------TPEVVVLSGFDPIRREIARMTLESLIK 290 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC----------CCCeEEEeCCChHHHHHHHHHHHHHHH
Confidence 4556677887 78899999999999999999999999964 236678888 55555556666665554
No 77
>PRK02821 hypothetical protein; Provisional
Probab=95.19 E-value=0.017 Score=46.73 Aligned_cols=32 Identities=19% Similarity=0.340 Sum_probs=28.3
Q ss_pred ceEEEEEeeccccccccccCchHHHHHHhhcC
Q 009973 129 ESVFRMLVPAQKVGSIIGRKGEFIKKIVEETR 160 (521)
Q Consensus 129 ~~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tg 160 (521)
.+.+.|.|..+.+|+||||+|.+|+.||.--.
T Consensus 30 ~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 30 GRTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred cEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 37899999999999999999999999996443
No 78
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.17 E-value=0.076 Score=58.35 Aligned_cols=65 Identities=14% Similarity=0.268 Sum_probs=49.3
Q ss_pred ceEEEEEecc-ccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEc-CHHHHHHHHHHHHHHHh
Q 009973 221 KVSTKLLVPA-SQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVG-DASGVHKAMELIGSHLR 295 (521)
Q Consensus 221 ~~t~~l~VP~-~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G-~~~~V~~A~~~I~~~l~ 295 (521)
.+...+.+|+ ++-|+||||.|.+||.+...||+.|-|+. +...|+|++ +|-.-+-|+..|..++.
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd----------tp~~v~ls~fdp~rreia~~~l~~li~ 269 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD----------TPEAVILSGFDPVRREIARMALEKLIQ 269 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC----------CCCeEEecCCchHHHHHHHHHHHHHHH
Confidence 4555677886 77899999999999999999999999964 235677888 45555556666665554
No 79
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.07 E-value=0.028 Score=53.13 Aligned_cols=41 Identities=29% Similarity=0.543 Sum_probs=35.9
Q ss_pred CCceEEEEEeec------cccccccccCchHHHHHHhhcCcEEEEeC
Q 009973 127 PGESVFRMLVPA------QKVGSIIGRKGEFIKKIVEETRARIKILD 167 (521)
Q Consensus 127 ~~~~~~rllVP~------~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~ 167 (521)
+..++-++.||. ++||+|||..|.|+|+|++.|+|+|-|.-
T Consensus 145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG 191 (269)
T COG5176 145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRG 191 (269)
T ss_pred cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEec
Confidence 445778888885 57999999999999999999999999973
No 80
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.02 E-value=0.11 Score=49.31 Aligned_cols=41 Identities=29% Similarity=0.563 Sum_probs=35.2
Q ss_pred CceEEEEEecc------ccccccccCCchhHHHHHHHhcccEEEcCC
Q 009973 220 GKVSTKLLVPA------SQAGSLIGKQGGTVKSIQEASNCIVRVLGA 260 (521)
Q Consensus 220 ~~~t~~l~VP~------~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~ 260 (521)
...+-++.||- ++||.|||..|.++|++++.|+|+|-|-.+
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 45666778874 589999999999999999999999999764
No 81
>PRK12704 phosphodiesterase; Provisional
Probab=95.00 E-value=0.084 Score=58.12 Aligned_cols=66 Identities=14% Similarity=0.253 Sum_probs=49.3
Q ss_pred ceEEEEEecc-ccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEc-CHHHHHHHHHHHHHHHhh
Q 009973 221 KVSTKLLVPA-SQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVG-DASGVHKAMELIGSHLRK 296 (521)
Q Consensus 221 ~~t~~l~VP~-~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G-~~~~V~~A~~~I~~~l~~ 296 (521)
.++..+.+|+ ++-|+||||.|.+||.+...||+.|-|+. +...|.|+| ++-.-+.|+..+..++.+
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 3455677886 78899999999999999999999999964 236678888 444444566666555544
No 82
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=94.94 E-value=0.05 Score=53.73 Aligned_cols=63 Identities=21% Similarity=0.286 Sum_probs=53.9
Q ss_pred EEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHH-HHHHHHHHHHHHHhhh
Q 009973 224 TKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDAS-GVHKAMELIGSHLRKF 297 (521)
Q Consensus 224 ~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~-~V~~A~~~I~~~l~~~ 297 (521)
+.+.||..+++++||++|.+|+.|.+.++++|.|-. +..|.|.+... .+.+|..+|..+-+++
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 468899999999999999999999999999998853 36788887755 7899999998887765
No 83
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.94 E-value=0.025 Score=45.45 Aligned_cols=29 Identities=24% Similarity=0.519 Sum_probs=27.1
Q ss_pred ceEEEEEeeccccccccccCchHHHHHHh
Q 009973 129 ESVFRMLVPAQKVGSIIGRKGEFIKKIVE 157 (521)
Q Consensus 129 ~~~~rllVP~~~vG~IIGKgG~~Ik~I~e 157 (521)
.+.++|.+....+|.||||+|.+|+.||.
T Consensus 29 ~~~~~l~v~~~D~GkvIGk~GRti~AIRT 57 (76)
T COG1837 29 TVTIELRVAPEDMGKVIGKQGRTIQAIRT 57 (76)
T ss_pred eEEEEEEECcccccceecCCChhHHHHHH
Confidence 47899999999999999999999999995
No 84
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=94.79 E-value=0.49 Score=45.69 Aligned_cols=127 Identities=9% Similarity=0.137 Sum_probs=83.8
Q ss_pred EEEeeccccccccccCchHHHHHHhhcCcEEEEeCCCCCCCccEEEEeccCCCCCCchhHHHHHHHHhhhhhcCCCCCCC
Q 009973 133 RMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILDGPPGTTERAVMISAKEEPESSLPPAMDGLLRVHKRIVDGLDSDSS 212 (521)
Q Consensus 133 rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~~~~~~~er~v~I~G~~e~~~~a~~a~~~l~~~~~~i~~~l~~~~~ 212 (521)
.+.++....-.|...+|..++.|-...||+|.+. ..+..|.|+|++..+ +.+......++..
T Consensus 29 ~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~-----~~~~~i~I~g~k~~~-------~~i~~~i~~~l~~------ 90 (210)
T PF14611_consen 29 DVWLQPDEFFLLLTGNGRILENLAARNGAKIEVS-----RSENRIRITGTKSTA-------EYIEASINEILSN------ 90 (210)
T ss_pred EEEecchheeeeecCCchHHHHHHHhcCceEEEe-----cCCcEEEEEccHHHH-------HHHHHHHHHHHhh------
Confidence 3334477778899999999999988899999998 455689999987632 3333333333321
Q ss_pred CCCCCCCCceEEEEEeccccccccc----cCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEE-----cCHHHH
Q 009973 213 HAPSGTGGKVSTKLLVPASQAGSLI----GKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVV-----GDASGV 283 (521)
Q Consensus 213 ~~~~~~~~~~t~~l~VP~~~vG~II----Gk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~-----G~~~~V 283 (521)
..+.++-++.-.--.-. -.....++.|++.|++.|+..+. ...+.|. -....+
T Consensus 91 --------i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~----------~~~~~i~~~~~~~~~~~~ 152 (210)
T PF14611_consen 91 --------IRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD----------GNKLKISWLASPENEKRA 152 (210)
T ss_pred --------cEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC----------CCeEEEEEEeeccccchH
Confidence 23444544432111111 12467889999999999988752 2334444 456788
Q ss_pred HHHHHHHHHHHh
Q 009973 284 HKAMELIGSHLR 295 (521)
Q Consensus 284 ~~A~~~I~~~l~ 295 (521)
..|+.+|.-.+.
T Consensus 153 ~~a~RlL~~a~~ 164 (210)
T PF14611_consen 153 DRAKRLLLWALD 164 (210)
T ss_pred HHHHHHHHHhcc
Confidence 899999888774
No 85
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=94.68 E-value=0.076 Score=55.45 Aligned_cols=38 Identities=16% Similarity=0.247 Sum_probs=34.9
Q ss_pred EEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccC
Q 009973 403 TQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQET 440 (521)
Q Consensus 403 t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~ 440 (521)
...+.||.+..+..|||+|.|++-.++.||.+|.|..-
T Consensus 309 ~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~ 346 (374)
T PRK12328 309 KAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI 346 (374)
T ss_pred EEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence 56789999999999999999999999999999999643
No 86
>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=94.52 E-value=0.097 Score=54.44 Aligned_cols=37 Identities=14% Similarity=0.365 Sum_probs=34.7
Q ss_pred EEEEEecCCCccceecCCCchHHHHHHHhCCeEEEcc
Q 009973 403 TQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQE 439 (521)
Q Consensus 403 t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~ 439 (521)
...+.||.+..+..|||+|.|++-.++.||.+|.|..
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 5679999999999999999999999999999999964
No 87
>PRK01064 hypothetical protein; Provisional
Probab=94.17 E-value=0.043 Score=44.51 Aligned_cols=31 Identities=29% Similarity=0.532 Sum_probs=28.0
Q ss_pred CceEEEEEeeccccccccccCchHHHHHHhh
Q 009973 128 GESVFRMLVPAQKVGSIIGRKGEFIKKIVEE 158 (521)
Q Consensus 128 ~~~~~rllVP~~~vG~IIGKgG~~Ik~I~e~ 158 (521)
..+.+++.|.....|.+|||+|.+|+.||.-
T Consensus 28 ~~~~~~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 28 HTIIYELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred CEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence 3488999999999999999999999999963
No 88
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=94.12 E-value=0.087 Score=57.09 Aligned_cols=37 Identities=16% Similarity=0.333 Sum_probs=34.7
Q ss_pred EEEEEecCCCccceecCCCchHHHHHHHhCCeEEEcc
Q 009973 403 TQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQE 439 (521)
Q Consensus 403 t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~ 439 (521)
...+.||....+..|||+|.||+..++.||.+|.|..
T Consensus 303 ~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 303 SADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred EEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 5679999999999999999999999999999999965
No 89
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=94.07 E-value=0.04 Score=62.72 Aligned_cols=63 Identities=29% Similarity=0.488 Sum_probs=54.3
Q ss_pred EEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHh
Q 009973 403 TQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISG-TASQVQTAQQLIQNFMAE 471 (521)
Q Consensus 403 t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~G-t~e~V~~A~~lI~~~i~~ 471 (521)
...+.||.+.++.+||.||.+||.|.++||+.|.|.+ +-.|.|.+ ..+.++.|+.+|+.+...
T Consensus 555 ~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d------~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 555 IETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED------DGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred heeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC------CceEEEEcccHHHHHHHHHHHHHhccc
Confidence 3467789999999999999999999999999988854 34688888 678999999999998864
No 90
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=94.06 E-value=0.14 Score=53.69 Aligned_cols=38 Identities=18% Similarity=0.307 Sum_probs=35.1
Q ss_pred EEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccC
Q 009973 403 TQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQET 440 (521)
Q Consensus 403 t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~ 440 (521)
...+.||.+..+..|||+|.|++-.++.||.+|.|...
T Consensus 304 ~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 304 AARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred EEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 56799999999999999999999999999999999653
No 91
>PRK00468 hypothetical protein; Provisional
Probab=93.92 E-value=0.059 Score=43.39 Aligned_cols=33 Identities=21% Similarity=0.259 Sum_probs=28.7
Q ss_pred cceEEEEEecCCCccceecCCCchHHHHHHHhC
Q 009973 400 TQVTQQMQIPLSYADAVIGTAGASISYIRRSSG 432 (521)
Q Consensus 400 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SG 432 (521)
..+..++.+..+-+|+||||+|.+|+.||..-.
T Consensus 28 ~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~ 60 (75)
T PRK00468 28 QSVILELKVAPEDMGKVIGKQGRIAKAIRTVVK 60 (75)
T ss_pred CeEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence 346788999999999999999999999987653
No 92
>PRK12705 hypothetical protein; Provisional
Probab=93.69 E-value=0.081 Score=57.71 Aligned_cols=66 Identities=21% Similarity=0.325 Sum_probs=46.7
Q ss_pred cceEEEEEecCCCc-cceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHH
Q 009973 400 TQVTQQMQIPLSYA-DAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISG-TASQVQTAQQLIQNFMA 470 (521)
Q Consensus 400 ~~~t~~i~VP~~~v-G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~G-t~e~V~~A~~lI~~~i~ 470 (521)
..+...+.+|.+-+ |+||||.|.||+.+...||+.|.|++... .|+|++ .|.--+.|...+..+|.
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp~-----~V~ls~fdp~rreia~~~l~~Li~ 263 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTPE-----AVVISSFNPIRREIARLTLEKLLA 263 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCcc-----chhhcccCccchHHHHHHHHHHHh
Confidence 34556788898654 99999999999999999999999987532 355555 34444445554444444
No 93
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=93.65 E-value=0.15 Score=54.14 Aligned_cols=37 Identities=19% Similarity=0.398 Sum_probs=34.4
Q ss_pred EEEEEecCCCccceecCCCchHHHHHHHhCCeEEEcc
Q 009973 403 TQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQE 439 (521)
Q Consensus 403 t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~ 439 (521)
...+.||.+..+..|||+|.|++-..+.||.+|.|..
T Consensus 336 ~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 336 HAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred EEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 4579999999999999999999999999999999965
No 94
>PRK02821 hypothetical protein; Provisional
Probab=93.13 E-value=0.077 Score=42.94 Aligned_cols=32 Identities=22% Similarity=0.294 Sum_probs=28.6
Q ss_pred eEEEEEecCCCccceecCCCchHHHHHHHhCC
Q 009973 402 VTQQMQIPLSYADAVIGTAGASISYIRRSSGA 433 (521)
Q Consensus 402 ~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA 433 (521)
....|.|..+-+|+||||+|.+|+.||..-.|
T Consensus 31 ~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 31 RTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred EEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 57889999999999999999999999987654
No 95
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=92.77 E-value=0.13 Score=41.50 Aligned_cols=35 Identities=31% Similarity=0.498 Sum_probs=30.2
Q ss_pred CCceEEEEEeccccccccccCCchhHHHHHHHhcc
Q 009973 219 GGKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNC 253 (521)
Q Consensus 219 ~~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa 253 (521)
......++.+...-+|.||||+|.+|+.|+..-.+
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll~a 61 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLLSA 61 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHHHHH
Confidence 34678899999999999999999999999986443
No 96
>PRK01064 hypothetical protein; Provisional
Probab=92.38 E-value=0.13 Score=41.80 Aligned_cols=33 Identities=18% Similarity=0.274 Sum_probs=28.8
Q ss_pred cceEEEEEecCCCccceecCCCchHHHHHHHhC
Q 009973 400 TQVTQQMQIPLSYADAVIGTAGASISYIRRSSG 432 (521)
Q Consensus 400 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SG 432 (521)
..+..++.|...-.|++|||+|.+|+.||....
T Consensus 28 ~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 28 HTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred CEEEEEEEECcccceEEECCCCccHHHHHHHHH
Confidence 346788999999999999999999999998643
No 97
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=92.15 E-value=0.11 Score=41.45 Aligned_cols=32 Identities=13% Similarity=0.319 Sum_probs=27.7
Q ss_pred ceEEEEEeeccccccccccCchHHHHHHhhcC
Q 009973 129 ESVFRMLVPAQKVGSIIGRKGEFIKKIVEETR 160 (521)
Q Consensus 129 ~~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tg 160 (521)
...+.+-|..+..|.||||+|.+++.||--.+
T Consensus 28 ~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 28 GDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp TTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred ceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence 35788889999999999999999999996443
No 98
>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=90.20 E-value=0.39 Score=36.82 Aligned_cols=34 Identities=21% Similarity=0.361 Sum_probs=27.9
Q ss_pred eEEEEEeeccccccccccCchHHHHHHhhcCcEE
Q 009973 130 SVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARI 163 (521)
Q Consensus 130 ~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I 163 (521)
..+.+.+.....|.+|||+|.+|+.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 5566666666789999999999999999888554
No 99
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=89.93 E-value=0.21 Score=47.21 Aligned_cols=55 Identities=16% Similarity=0.271 Sum_probs=49.2
Q ss_pred cccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 009973 230 ASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAMELIGSHLRK 296 (521)
Q Consensus 230 ~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~ 296 (521)
...+|+|+||+|.+--.|.+.|-++|.+.. ..|-|-|..+++..|+..|+.++..
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 467899999999999999999999998863 6788999999999999999999854
No 100
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=89.52 E-value=0.68 Score=50.26 Aligned_cols=65 Identities=25% Similarity=0.375 Sum_probs=53.1
Q ss_pred CceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEc-CHHHHHHHHHHHHHHHhh
Q 009973 220 GKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVG-DASGVHKAMELIGSHLRK 296 (521)
Q Consensus 220 ~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G-~~~~V~~A~~~I~~~l~~ 296 (521)
..+...+.|+.+....+||.+|...|+|..+||+.-.+ ++.+++|.. +....++|+..|..++..
T Consensus 595 ~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 595 SPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEGTFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred CceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCceEEEEecCHHHHHHHHHHHHHHhcC
Confidence 45677899999999999999999999999999964444 346677765 466789999999988754
No 101
>PRK12705 hypothetical protein; Provisional
Probab=89.42 E-value=0.79 Score=50.19 Aligned_cols=39 Identities=13% Similarity=0.354 Sum_probs=33.1
Q ss_pred ceEEEEEecc-ccccccccCCchhHHHHHHHhcccEEEcC
Q 009973 221 KVSTKLLVPA-SQAGSLIGKQGGTVKSIQEASNCIVRVLG 259 (521)
Q Consensus 221 ~~t~~l~VP~-~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~ 259 (521)
.+...+.+|+ ++-|+||||.|.+||.+...||+.|-|..
T Consensus 197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd 236 (508)
T PRK12705 197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD 236 (508)
T ss_pred heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC
Confidence 3455667775 67799999999999999999999999864
No 102
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=89.38 E-value=0.33 Score=38.45 Aligned_cols=37 Identities=35% Similarity=0.558 Sum_probs=30.1
Q ss_pred EEEEEeeccc-----cccccccCchHHHHHHhhc-CcEEEEeC
Q 009973 131 VFRMLVPAQK-----VGSIIGRKGEFIKKIVEET-RARIKILD 167 (521)
Q Consensus 131 ~~rllVP~~~-----vG~IIGKgG~~Ik~I~e~T-ga~I~i~~ 167 (521)
..++.|-+.. +|..||++|.+|+.|+++. |-+|+|-.
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 3566677777 9999999999999999999 99999874
No 103
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=89.28 E-value=0.69 Score=45.92 Aligned_cols=51 Identities=16% Similarity=0.351 Sum_probs=46.7
Q ss_pred cceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 009973 414 DAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISGTASQVQTAQQLIQNFMAE 471 (521)
Q Consensus 414 G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~Gt~e~V~~A~~lI~~~i~~ 471 (521)
-++||.+|++++.|+-.|.|.|-|+. .+|.+.|....+..+.+.+.++|..
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 57999999999999999999999976 4699999999999999999988876
No 104
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=88.28 E-value=0.3 Score=46.17 Aligned_cols=54 Identities=11% Similarity=0.255 Sum_probs=49.2
Q ss_pred CCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 009973 411 SYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISGTASQVQTAQQLIQNFMAE 471 (521)
Q Consensus 411 ~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~Gt~e~V~~A~~lI~~~i~~ 471 (521)
..+|+|+||+|.+--.|...|.++|.+.+ ..|.|-|+.+++..|+..|..+|..
T Consensus 178 RAIGRiaGk~GkTkfaIEn~trtrIVlad-------~kIHiLG~~~niriAR~avcsLIlG 231 (252)
T KOG3273|consen 178 RAIGRIAGKGGKTKFAIENVTRTRIVLAD-------SKIHILGAFQNIRIARDAVCSLILG 231 (252)
T ss_pred HHHHHhhcCCCcceeeeeccceeEEEecC-------ceEEEeecchhhHHHHHhhHhhhcc
Confidence 56899999999999999999999999965 4699999999999999999998873
No 105
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=87.39 E-value=1.7 Score=47.36 Aligned_cols=65 Identities=22% Similarity=0.347 Sum_probs=54.2
Q ss_pred eEEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHhcc
Q 009973 402 VTQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISG-TASQVQTAQQLIQNFMAEAA 473 (521)
Q Consensus 402 ~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~G-t~e~V~~A~~lI~~~i~~~~ 473 (521)
+...+.|+.+..-.+||.+|.+.|.|..+||+.-.+++ .+++|-. ++.+.+.|+.+|..++....
T Consensus 597 ~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vDe-------~t~~i~A~~~~am~~Ak~~I~~i~~~~~ 662 (760)
T KOG1067|consen 597 VLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVDE-------GTFSIFAPTQAAMEEAKEFIDGIIKDDQ 662 (760)
T ss_pred eeeEEeecchhhheeecCccceeeeEeeeccceeeecC-------ceEEEEecCHHHHHHHHHHHHHHhcCcc
Confidence 45678899999999999999999999999996555533 4677776 78899999999999988643
No 106
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=87.16 E-value=0.4 Score=38.59 Aligned_cols=35 Identities=37% Similarity=0.589 Sum_probs=29.6
Q ss_pred eEEEEEeeccccccccccCchHHHHHHhhcCcEEE
Q 009973 130 SVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIK 164 (521)
Q Consensus 130 ~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~ 164 (521)
..+.+.+...+.|.|||++|++|++|++...-.+.
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 35788899999999999999999999987665553
No 107
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=86.96 E-value=0.28 Score=56.94 Aligned_cols=58 Identities=17% Similarity=0.136 Sum_probs=50.5
Q ss_pred ceEEEEEeeccccccccccCchHHHHHHhhcCcEEEEeCC-CCCCCccEEEEeccCCCC
Q 009973 129 ESVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILDG-PPGTTERAVMISAKEEPE 186 (521)
Q Consensus 129 ~~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~~-~~~~~er~v~I~G~~e~~ 186 (521)
...-++-+|.....+|||++|.+|..++.-||+.|.|.++ ..+..||.+.+.|.++..
T Consensus 1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~ 1397 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQ 1397 (2131)
T ss_pred ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhh
Confidence 4567888999999999999999999999999999999974 334689999999998843
No 108
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=86.81 E-value=1.1 Score=34.12 Aligned_cols=34 Identities=15% Similarity=0.235 Sum_probs=27.1
Q ss_pred eEEEEEecCCCccceecCCCchHHHHHHHhCCeE
Q 009973 402 VTQQMQIPLSYADAVIGTAGASISYIRRSSGATV 435 (521)
Q Consensus 402 ~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I 435 (521)
....+.+.....|.+||++|.+|+.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 3455666655689999999999999999998554
No 109
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=86.01 E-value=0.44 Score=37.91 Aligned_cols=35 Identities=29% Similarity=0.398 Sum_probs=29.9
Q ss_pred ceEEEEEeccccccccccCCchhHHHHHHHhcccE
Q 009973 221 KVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIV 255 (521)
Q Consensus 221 ~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I 255 (521)
.....+.+..+..|.||||.|.+++.||.-.+.-+
T Consensus 28 ~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~ 62 (73)
T PF13083_consen 28 GDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAA 62 (73)
T ss_dssp TTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHH
T ss_pred ceEEEEEECCCccceEECCCCeeHHHHHHHHHHHH
Confidence 45778888999999999999999999998776533
No 110
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=85.84 E-value=0.74 Score=36.43 Aligned_cols=37 Identities=22% Similarity=0.364 Sum_probs=29.1
Q ss_pred EEEEEecCCC-----ccceecCCCchHHHHHHHh-CCeEEEcc
Q 009973 403 TQQMQIPLSY-----ADAVIGTAGASISYIRRSS-GATVTIQE 439 (521)
Q Consensus 403 t~~i~VP~~~-----vG~IIGkgG~~Ik~Ir~~S-GA~I~I~~ 439 (521)
...+.|-... +|+.||++|.+|+.|+++. |-+|.|-.
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 3456666666 8999999999999999999 99999854
No 111
>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=84.86 E-value=0.83 Score=36.80 Aligned_cols=34 Identities=12% Similarity=0.359 Sum_probs=26.8
Q ss_pred EEEEEeeccccccccccCchHHHHHHhhcCcEEE
Q 009973 131 VFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIK 164 (521)
Q Consensus 131 ~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~ 164 (521)
.+.+-+.....|.||||+|++++.||--++.-+.
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 4667777888999999999999999965554333
No 112
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=84.83 E-value=0.62 Score=49.66 Aligned_cols=38 Identities=24% Similarity=0.377 Sum_probs=35.3
Q ss_pred eEEEEEeeccccccccccCchHHHHHHhhcCcEEEEeC
Q 009973 130 SVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILD 167 (521)
Q Consensus 130 ~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~ 167 (521)
-...+.||.+.++.+|||+|.+|++|+++.|-+|.|..
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~ 523 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKP 523 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEE
Confidence 45788999999999999999999999999999999984
No 113
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=84.73 E-value=1.7 Score=43.23 Aligned_cols=51 Identities=25% Similarity=0.564 Sum_probs=45.7
Q ss_pred cccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 009973 234 GSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAMELIGSHLRK 296 (521)
Q Consensus 234 G~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~ 296 (521)
-++||.+|.+++.|+-.|.|.|-|.+ .+|.+.|....+..+...+.+.+.+
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 47999999999999999999998875 6799999999999999998888865
No 114
>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=81.30 E-value=1.6 Score=35.74 Aligned_cols=36 Identities=17% Similarity=0.434 Sum_probs=29.8
Q ss_pred eEEEEEeeccccccccccCchHHHHHHhhcCcEEEE
Q 009973 130 SVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKI 165 (521)
Q Consensus 130 ~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i 165 (521)
..+++.|....-|.|||++|++|++|++.-.-...+
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 358889999999999999999999999876554444
No 115
>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=81.20 E-value=0.98 Score=36.28 Aligned_cols=35 Identities=31% Similarity=0.469 Sum_probs=29.9
Q ss_pred eEEEEEeccccccccccCCchhHHHHHHHhcccEE
Q 009973 222 VSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVR 256 (521)
Q Consensus 222 ~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~ 256 (521)
....+.+...+-|.|||++|++|++|+....-.+.
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 35678888999999999999999999988776664
No 116
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=79.74 E-value=1.2 Score=47.48 Aligned_cols=38 Identities=24% Similarity=0.475 Sum_probs=34.8
Q ss_pred EEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccC
Q 009973 403 TQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQET 440 (521)
Q Consensus 403 t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~ 440 (521)
...+.||..+++.+|||+|.+|++|.+..|-+|.|...
T Consensus 487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~ 524 (604)
T COG1855 487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL 524 (604)
T ss_pred eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence 46688999999999999999999999999999999654
No 117
>PRK13764 ATPase; Provisional
Probab=79.53 E-value=1.4 Score=49.41 Aligned_cols=38 Identities=26% Similarity=0.415 Sum_probs=35.6
Q ss_pred eEEEEEeeccccccccccCchHHHHHHhhcCcEEEEeC
Q 009973 130 SVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILD 167 (521)
Q Consensus 130 ~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~ 167 (521)
-...+.||.+.++.+|||+|.+|++|+++.|..|.|..
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~ 518 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP 518 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence 46889999999999999999999999999999999984
No 118
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=78.99 E-value=2.5 Score=39.41 Aligned_cols=36 Identities=17% Similarity=0.406 Sum_probs=31.5
Q ss_pred EEEEEeeccccccccccCchHHHHHHhhcCcEEEEeC
Q 009973 131 VFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILD 167 (521)
Q Consensus 131 ~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~ 167 (521)
.+-++|-... |.-|||+|.+|+++++..|-+|.+-+
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 4667776667 99999999999999999999999875
No 119
>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=78.40 E-value=2.4 Score=34.11 Aligned_cols=35 Identities=14% Similarity=0.212 Sum_probs=28.0
Q ss_pred EEEEEecCCCccceecCCCchHHHHHHHhCCeEEE
Q 009973 403 TQQMQIPLSYADAVIGTAGASISYIRRSSGATVTI 437 (521)
Q Consensus 403 t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I 437 (521)
...+.|..+..|.+|||.|++++.||-.+...+.-
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~ 59 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR 59 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence 44577777888999999999999999887654443
No 120
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=77.82 E-value=5.1 Score=39.33 Aligned_cols=46 Identities=20% Similarity=0.431 Sum_probs=38.0
Q ss_pred EEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEcCHH
Q 009973 405 QMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISGTAS 456 (521)
Q Consensus 405 ~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~Gt~e 456 (521)
-+.|+...+.++||++|+.++-|.+.|+|+|.+-.+ -.|-|.|..+
T Consensus 149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N------G~IWV~~~~~ 194 (239)
T COG1097 149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN------GRIWVDGENE 194 (239)
T ss_pred EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC------CEEEecCCCc
Confidence 378999999999999999999999999999999653 2355555554
No 121
>PRK13764 ATPase; Provisional
Probab=76.52 E-value=2.8 Score=46.95 Aligned_cols=43 Identities=23% Similarity=0.357 Sum_probs=38.0
Q ss_pred eEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCC
Q 009973 222 VSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLP 264 (521)
Q Consensus 222 ~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P 264 (521)
....+.||...++.+|||+|.+|++|.++.|.+|.|-..+..+
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 4667899999999999999999999999999999998755543
No 122
>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=75.79 E-value=2.8 Score=36.24 Aligned_cols=31 Identities=29% Similarity=0.459 Sum_probs=26.2
Q ss_pred EEEEEeeccccccccccCchHHHHHHhhcCc
Q 009973 131 VFRMLVPAQKVGSIIGRKGEFIKKIVEETRA 161 (521)
Q Consensus 131 ~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga 161 (521)
.+++.|....-|.|||++|++|++|++....
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence 4778888888999999999999999975433
No 123
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=73.97 E-value=8.1 Score=37.98 Aligned_cols=62 Identities=24% Similarity=0.367 Sum_probs=47.4
Q ss_pred EEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHH-HHHHHHHHHHHHhh
Q 009973 224 TKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASG-VHKAMELIGSHLRK 296 (521)
Q Consensus 224 ~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~-V~~A~~~I~~~l~~ 296 (521)
.-+.|+...+-++||++|..++.|.+.|+|+|-+-. +..|=|.+..+. ...|...|..+-++
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-----------NG~IWV~~~~~~~e~~~~~aI~~ie~e 210 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-----------NGRIWVDGENESLEELAIEAIRKIERE 210 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-----------CCEEEecCCCcchHHHHHHHHHHHhhh
Confidence 357789999999999999999999999999998864 355777777763 45555555554433
No 124
>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=72.80 E-value=3.7 Score=33.70 Aligned_cols=28 Identities=29% Similarity=0.513 Sum_probs=23.6
Q ss_pred EEEEeeccccccccccCchHHHHHHhhc
Q 009973 132 FRMLVPAQKVGSIIGRKGEFIKKIVEET 159 (521)
Q Consensus 132 ~rllVP~~~vG~IIGKgG~~Ik~I~e~T 159 (521)
+++.|....-|.+||++|.+|++|++.-
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 6666667889999999999999998653
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=72.75 E-value=4.5 Score=33.03 Aligned_cols=35 Identities=14% Similarity=0.225 Sum_probs=28.2
Q ss_pred EEEEEecCCCccceecCCCchHHHHHHHhCCeEEE
Q 009973 403 TQQMQIPLSYADAVIGTAGASISYIRRSSGATVTI 437 (521)
Q Consensus 403 t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I 437 (521)
..++.|-...-|.|||++|++|++|++.-.....+
T Consensus 31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~ 65 (81)
T cd02413 31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF 65 (81)
T ss_pred eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence 45677777888999999999999998876555544
No 126
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=71.63 E-value=3.6 Score=44.38 Aligned_cols=72 Identities=15% Similarity=0.143 Sum_probs=54.5
Q ss_pred eEEEEEeeccccccccccCchHHHHHHhhcCcEEEEeC--CCCCCCccE-EEEeccCCCCCCchhHHHHHHHHhh
Q 009973 130 SVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILD--GPPGTTERA-VMISAKEEPESSLPPAMDGLLRVHK 201 (521)
Q Consensus 130 ~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~--~~~~~~er~-v~I~G~~e~~~~a~~a~~~l~~~~~ 201 (521)
-.+.+.||.+.+..|||.||..|++++.+.++.|++.. ..+.+..+- |.|.....+..+++-+.+.+++..+
T Consensus 449 ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~ 523 (657)
T COG5166 449 AEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVK 523 (657)
T ss_pred hheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHh
Confidence 35778899999999999999999999999999999984 223333333 8888877777776666655554443
No 127
>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=71.45 E-value=4.7 Score=36.56 Aligned_cols=40 Identities=30% Similarity=0.529 Sum_probs=33.0
Q ss_pred EEEEEeeccccccccccCchHHHHHHhhcCcEEEEeCCCC
Q 009973 131 VFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILDGPP 170 (521)
Q Consensus 131 ~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~~~~ 170 (521)
+=.+.|-...-|.+|||+|.++++|..+||-+-.|-+..|
T Consensus 77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 3455566677899999999999999999999999876543
No 128
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=69.88 E-value=6.2 Score=36.78 Aligned_cols=36 Identities=31% Similarity=0.321 Sum_probs=31.0
Q ss_pred EEEEEeccccccccccCCchhHHHHHHHhcccEEEcC
Q 009973 223 STKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLG 259 (521)
Q Consensus 223 t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~ 259 (521)
.+-++|-... |..|||+|.+|+.+++..|-+|.+..
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 4556676666 99999999999999999999998874
No 129
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=68.49 E-value=4.1 Score=39.83 Aligned_cols=29 Identities=34% Similarity=0.535 Sum_probs=26.3
Q ss_pred eEEEEEeeccccccccccCchHHHHHHhh
Q 009973 130 SVFRMLVPAQKVGSIIGRKGEFIKKIVEE 158 (521)
Q Consensus 130 ~~~rllVP~~~vG~IIGKgG~~Ik~I~e~ 158 (521)
..+++.|....-|.||||+|++|++|++.
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 56899999999999999999999999864
No 130
>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=66.84 E-value=4 Score=37.05 Aligned_cols=41 Identities=24% Similarity=0.306 Sum_probs=35.5
Q ss_pred eEEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCC
Q 009973 402 VTQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRG 442 (521)
Q Consensus 402 ~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~ 442 (521)
.|-++.|-...-|.|||++|.++++|...||-.-.|-+..+
T Consensus 76 ~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 76 DTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred CCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 35678888899999999999999999999999988876543
No 131
>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=62.46 E-value=8.3 Score=31.62 Aligned_cols=28 Identities=25% Similarity=0.294 Sum_probs=21.8
Q ss_pred EEEEecCCCccceecCCCchHHHHHHHh
Q 009973 404 QQMQIPLSYADAVIGTAGASISYIRRSS 431 (521)
Q Consensus 404 ~~i~VP~~~vG~IIGkgG~~Ik~Ir~~S 431 (521)
.++.|-...-|.+||++|++|++|+..-
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 3455555777999999999999887764
No 132
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=62.37 E-value=7.1 Score=33.67 Aligned_cols=30 Identities=23% Similarity=0.380 Sum_probs=24.1
Q ss_pred EEEEecCCCccceecCCCchHHHHHHHhCC
Q 009973 404 QQMQIPLSYADAVIGTAGASISYIRRSSGA 433 (521)
Q Consensus 404 ~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA 433 (521)
.+|.|-...-|.|||+.|++|+.|++....
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 456666777899999999999999876543
No 133
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=54.69 E-value=18 Score=39.30 Aligned_cols=126 Identities=6% Similarity=-0.047 Sum_probs=79.6
Q ss_pred ccccccCchHHHHHHhhcCcEEEEe--CCCCCCCccEEEE-eccCCCCCCchhHHHHHHHHhhhhhcCCCCCCCCCCCCC
Q 009973 142 GSIIGRKGEFIKKIVEETRARIKIL--DGPPGTTERAVMI-SAKEEPESSLPPAMDGLLRVHKRIVDGLDSDSSHAPSGT 218 (521)
Q Consensus 142 G~IIGKgG~~Ik~I~e~Tga~I~i~--~~~~~~~er~v~I-~G~~e~~~~a~~a~~~l~~~~~~i~~~l~~~~~~~~~~~ 218 (521)
-.|=||+--++.+|++...|.+.+. +.. ..++.++ .|..- +..+.++.+.+
T Consensus 392 dFl~gkkngK~TrIm~~v~c~~~~~i~~~~---gs~~~~~~~g~~~----------~F~k~~~~~~~------------- 445 (657)
T COG5166 392 DFLRGKKNGKATRIMKGVSCSELSSIVSST---GSIVETNGIGEKM----------SFSKKLSIPPT------------- 445 (657)
T ss_pred HHhccccCcchhhhhhhcccceeeEEEecC---CcEEEEeccCcch----------hhHHHhcCCcc-------------
Confidence 3566887777999999999986554 221 2233332 33221 12222222221
Q ss_pred CCceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCe-EEEEEcCHH---HHHHHHHHHHHHH
Q 009973 219 GGKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDR-VVEVVGDAS---GVHKAMELIGSHL 294 (521)
Q Consensus 219 ~~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er-~V~I~G~~~---~V~~A~~~I~~~l 294 (521)
.-.....+.||...+..|||-||..|.+++...++.|++...-+++.. ..+ -|.|..+.. ++.-++.-+.+++
T Consensus 446 EFpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs---~~~dNV~I~~PrKn~~ni~~~KNd~~~~V 522 (657)
T COG5166 446 EFPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQS---QWHDNVLIEAPRKNQDNISGKKNDKLDKV 522 (657)
T ss_pred cCchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchh---hhhcceEEECCccCccchhcccccHHHHH
Confidence 112356789999999999999999999999999999998764455432 223 266666544 4555666666666
Q ss_pred hh
Q 009973 295 RK 296 (521)
Q Consensus 295 ~~ 296 (521)
.+
T Consensus 523 ~~ 524 (657)
T COG5166 523 KQ 524 (657)
T ss_pred hh
Confidence 54
No 134
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=53.86 E-value=12 Score=36.71 Aligned_cols=31 Identities=26% Similarity=0.411 Sum_probs=25.0
Q ss_pred EEEEEecCCCccceecCCCchHHHHHH----HhCC
Q 009973 403 TQQMQIPLSYADAVIGTAGASISYIRR----SSGA 433 (521)
Q Consensus 403 t~~i~VP~~~vG~IIGkgG~~Ik~Ir~----~SGA 433 (521)
...|.|-...-|.|||++|++|+.|++ .+|.
T Consensus 52 ~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~ 86 (233)
T COG0092 52 GTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGK 86 (233)
T ss_pred ceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCC
Confidence 456778788889999999999998765 4555
No 135
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=53.08 E-value=32 Score=37.52 Aligned_cols=95 Identities=19% Similarity=0.334 Sum_probs=59.7
Q ss_pred cccccCchHHHHHHhhcCcEEEEeCCCCCCCccEEEEeccCCCCCCchhHHHHHHHHhhhhhcCCCCCCCCCCCCCCCce
Q 009973 143 SIIGRKGEFIKKIVEETRARIKILDGPPGTTERAVMISAKEEPESSLPPAMDGLLRVHKRIVDGLDSDSSHAPSGTGGKV 222 (521)
Q Consensus 143 ~IIGKgG~~Ik~I~e~Tga~I~i~~~~~~~~er~v~I~G~~e~~~~a~~a~~~l~~~~~~i~~~l~~~~~~~~~~~~~~~ 222 (521)
.+|=+.|..||+|-++-.-+|.|.... ........|.+-|.++.-.-.+ +....+ ...
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~dP--------------svl~~~e~A~~~I~eivP~ea~-i~~i~F-------d~~ 99 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPDP--------------SVLKPPEEARKIILEIVPEEAG-ITDIYF-------DDD 99 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccCc--------------hhcCCHHHHHHHHHHhCccccC-ceeEEe-------cCC
Confidence 345688999999999988888886321 1001111233222222200000 000000 123
Q ss_pred EEEEEeccccccccccCCchhHHHHHHHhcccEEEcC
Q 009973 223 STKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLG 259 (521)
Q Consensus 223 t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~ 259 (521)
+-+++|-...=|.+|||+|++.++|..+||-.-+|.+
T Consensus 100 tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR 136 (637)
T COG1782 100 TGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVR 136 (637)
T ss_pred CceEEEEecCCceEEecCchHHHHHHHHhCCcceeee
Confidence 5678889999999999999999999999999888875
No 136
>PF03991 Prion_octapep: Copper binding octapeptide repeat; InterPro: IPR020949 Prion protein (PrP-c) [, , ] is a small glycoprotein found in high quantity in the brain of animals infected with certain degenerative neurological diseases, such as sheep scrapie and bovine spongiform encephalopathy (BSE), and the human dementias Creutzfeldt-Jacob disease (CJD) and Gerstmann-Straussler syndrome (GSS). PrP-c is encoded in the host genome and is expressed both in normal and infected cells. During infection, however, the PrP-c molecule become altered (conformationally rather than at the amino acid level) to an abnormal isoform, PrP-sc. In detergent-treated brain extracts from infected individuals, fibrils composed of polymers of PrP-sc, namely scrapie-associated fibrils or prion rods, can be evidenced by electron microscopy. The precise function of the normal PrP isoform in healthy individuals remains unknown. Several results, mainly obtained in transgenic animals, indicate that PrP-c might play a role in long-term potentiation, in sleep physiology, in oxidative burst compensation (PrP can fix four Cu2+ through its octarepeat domain), in interactions with the extracellular matrix (PrP-c can bind to the precursor of the laminin receptor, LRP), in apoptosis and in signal transduction (costimulation of PrP-c induces a modulation of Fyn kinase phosphorylation) []. The normal isoform, PrP-c, is anchored at the cell membrane, in rafts, through a glycosyl phosphatidyl inositol (GPI); its half-life at the cell surface is 5 h, after which the protein is internalised through a caveolae-dependent mechanism and degraded in the endolysosome compartment. Conversion between PrP-c and PrP-sc occurs likely during the internalisation process. This repeat is found at the amino terminus of mammalian prion proteins. It has been shown to bind to copper [].
Probab=52.20 E-value=8.8 Score=17.42 Aligned_cols=7 Identities=57% Similarity=1.455 Sum_probs=5.0
Q ss_pred CCCCCCC
Q 009973 507 HAGGYGS 513 (521)
Q Consensus 507 ~~gg~g~ 513 (521)
++||||.
T Consensus 2 hgG~Wgq 8 (8)
T PF03991_consen 2 HGGGWGQ 8 (8)
T ss_pred CCCcCCC
Confidence 6788874
No 137
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=52.08 E-value=34 Score=35.62 Aligned_cols=56 Identities=20% Similarity=0.313 Sum_probs=47.5
Q ss_pred cCCCccceecCCCchHHHHHHHhCCeEEEccCCCCCCceEEEEEcCHHHHHHHHHHHH--HHHHh
Q 009973 409 PLSYADAVIGTAGASISYIRRSSGATVTIQETRGVPGEMTVEISGTASQVQTAQQLIQ--NFMAE 471 (521)
Q Consensus 409 P~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~VtI~Gt~e~V~~A~~lI~--~~i~~ 471 (521)
+...+-.|.|..+.+++.|.+..|++|.... +.++|+|+...|+.|...++ ..+..
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG-------~~~~i~g~~~~v~~A~~~l~~l~~~~~ 79 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVARG-------EAVRIIGARPLVDVATRVLLTLELLAE 79 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeCC-------ceEEEEechHHHHHHHHHHhHHHHHHH
Confidence 3567789999999999999999999988854 56999999889999999888 55554
No 138
>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=45.62 E-value=23 Score=35.36 Aligned_cols=31 Identities=16% Similarity=0.302 Sum_probs=24.4
Q ss_pred ceEEEEEecCCCc-cceecCCCchHHHHHHHh
Q 009973 401 QVTQQMQIPLSYA-DAVIGTAGASISYIRRSS 431 (521)
Q Consensus 401 ~~t~~i~VP~~~v-G~IIGkgG~~Ik~Ir~~S 431 (521)
.+...|.|..+-. +-|||++|+.||+|...+
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 4677788886655 999999999999875543
No 139
>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=44.24 E-value=29 Score=39.37 Aligned_cols=38 Identities=26% Similarity=0.521 Sum_probs=34.6
Q ss_pred eEEEEEeccccccccccCCchhHHHHHHHhcccEEEcC
Q 009973 222 VSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLG 259 (521)
Q Consensus 222 ~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~ 259 (521)
.+-+++|-...-|.+|||+|.++++|..+||-.-+|.+
T Consensus 93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~ 130 (630)
T TIGR03675 93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVR 130 (630)
T ss_pred CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEe
Confidence 45688899999999999999999999999999988876
No 140
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=43.08 E-value=22 Score=34.39 Aligned_cols=30 Identities=30% Similarity=0.514 Sum_probs=24.8
Q ss_pred EEEEeeccccccccccCchHHHHHHhhcCc
Q 009973 132 FRMLVPAQKVGSIIGRKGEFIKKIVEETRA 161 (521)
Q Consensus 132 ~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga 161 (521)
+++.|....-|.+||++|++|++|++.-.-
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 666666688999999999999999976544
No 141
>COG4371 Predicted membrane protein [Function unknown]
Probab=42.23 E-value=30 Score=34.18 Aligned_cols=6 Identities=50% Similarity=1.093 Sum_probs=2.8
Q ss_pred CCCCCC
Q 009973 506 GHAGGY 511 (521)
Q Consensus 506 ~~~gg~ 511 (521)
+.+|||
T Consensus 73 psGGgY 78 (334)
T COG4371 73 PSGGGY 78 (334)
T ss_pred CCCCCC
Confidence 334455
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=42.07 E-value=25 Score=35.15 Aligned_cols=30 Identities=33% Similarity=0.455 Sum_probs=23.4
Q ss_pred eEEEEEecc-ccccccccCCchhHHHHHHHh
Q 009973 222 VSTKLLVPA-SQAGSLIGKQGGTVKSIQEAS 251 (521)
Q Consensus 222 ~t~~l~VP~-~~vG~IIGk~G~~Ik~I~~~t 251 (521)
+...+.|.. .+-+.|||++|+.||+|....
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 566777774 577999999999999876543
No 143
>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=41.56 E-value=25 Score=33.72 Aligned_cols=31 Identities=26% Similarity=0.486 Sum_probs=26.3
Q ss_pred eEEEEEeeccccccccccCchHHHHHHhhcC
Q 009973 130 SVFRMLVPAQKVGSIIGRKGEFIKKIVEETR 160 (521)
Q Consensus 130 ~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tg 160 (521)
..+++.|....-|.|||++|..|++|++.-.
T Consensus 38 ~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~ 68 (195)
T TIGR01008 38 LGTKVIIFAERPGLVIGRGGRRIRELTEKLQ 68 (195)
T ss_pred CcEEEEEEECCCceEECCCchHHHHHHHHHH
Confidence 3488888888999999999999999986543
No 144
>COG1159 Era GTPase [General function prediction only]
Probab=41.32 E-value=24 Score=35.95 Aligned_cols=29 Identities=34% Similarity=0.481 Sum_probs=23.0
Q ss_pred ceEEEEEeec-cccccccccCchHHHHHHh
Q 009973 129 ESVFRMLVPA-QKVGSIIGRKGEFIKKIVE 157 (521)
Q Consensus 129 ~~~~rllVP~-~~vG~IIGKgG~~Ik~I~e 157 (521)
.+...++|.. ++-|-||||+|++||+|-.
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~ 257 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKIGT 257 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHHHH
Confidence 3566677774 6789999999999998754
No 145
>CHL00048 rps3 ribosomal protein S3
Probab=40.80 E-value=25 Score=34.20 Aligned_cols=30 Identities=17% Similarity=0.233 Sum_probs=25.8
Q ss_pred eEEEEEeeccccccccccCchHHHHHHhhc
Q 009973 130 SVFRMLVPAQKVGSIIGRKGEFIKKIVEET 159 (521)
Q Consensus 130 ~~~rllVP~~~vG~IIGKgG~~Ik~I~e~T 159 (521)
..+++.|.....|.|||++|.+|++|++.-
T Consensus 66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 66 DLIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred CeEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 357778888889999999999999999765
No 146
>PRK15494 era GTPase Era; Provisional
Probab=40.04 E-value=31 Score=35.90 Aligned_cols=30 Identities=17% Similarity=0.312 Sum_probs=23.5
Q ss_pred ceEEEEEecCCCc-cceecCCCchHHHHHHH
Q 009973 401 QVTQQMQIPLSYA-DAVIGTAGASISYIRRS 430 (521)
Q Consensus 401 ~~t~~i~VP~~~v-G~IIGkgG~~Ik~Ir~~ 430 (521)
.+...|.|..+-. +-|||++|+.||+|...
T Consensus 272 ~i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 272 KINQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 3667788886655 99999999999976443
No 147
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=39.52 E-value=27 Score=34.08 Aligned_cols=32 Identities=19% Similarity=0.416 Sum_probs=26.6
Q ss_pred EEEEEeeccccccccccCchHHHHHHhhcCcE
Q 009973 131 VFRMLVPAQKVGSIIGRKGEFIKKIVEETRAR 162 (521)
Q Consensus 131 ~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~ 162 (521)
.+++.|....-|.|||++|..|++|++.-.-.
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~ 76 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLLQKR 76 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHHHHH
Confidence 47788888889999999999999999765433
No 148
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=39.34 E-value=28 Score=37.99 Aligned_cols=38 Identities=29% Similarity=0.427 Sum_probs=32.2
Q ss_pred EEEEEeeccccccccccCchHHHHHHhhcCcEEEEeCC
Q 009973 131 VFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKILDG 168 (521)
Q Consensus 131 ~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i~~~ 168 (521)
+-.++|=+++-|.+|||+|++.+.|..+||-.-+|-+.
T Consensus 100 tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 100 TGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred CceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 44566777888999999999999999999998887653
No 149
>PRK00089 era GTPase Era; Reviewed
Probab=39.27 E-value=32 Score=34.59 Aligned_cols=37 Identities=19% Similarity=0.315 Sum_probs=27.0
Q ss_pred ceEEEEEecCCCc-cceecCCCchHHHHHH--------HhCCeEEE
Q 009973 401 QVTQQMQIPLSYA-DAVIGTAGASISYIRR--------SSGATVTI 437 (521)
Q Consensus 401 ~~t~~i~VP~~~v-G~IIGkgG~~Ik~Ir~--------~SGA~I~I 437 (521)
.+...|.|..+-. +-|||++|++||+|.. ..|++|.+
T Consensus 225 ~i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l 270 (292)
T PRK00089 225 RIEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL 270 (292)
T ss_pred EEEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 4667788875544 9999999999987654 45565555
No 150
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=38.73 E-value=22 Score=36.53 Aligned_cols=31 Identities=19% Similarity=0.296 Sum_probs=25.4
Q ss_pred ceEEEEEeec-cccccccccCchHHHHHHhhc
Q 009973 129 ESVFRMLVPA-QKVGSIIGRKGEFIKKIVEET 159 (521)
Q Consensus 129 ~~~~rllVP~-~~vG~IIGKgG~~Ik~I~e~T 159 (521)
.+...++||. ++...||||||..|++|-++-
T Consensus 327 ~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a 358 (379)
T KOG1423|consen 327 FIQVEVVCPKNSQKKLLIGKGGKKISQIGTRA 358 (379)
T ss_pred EEEEEEEcCCCcceeEEEcCCCccHHHHHHHH
Confidence 4678899996 567788999999999997643
No 151
>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=38.71 E-value=22 Score=40.28 Aligned_cols=41 Identities=27% Similarity=0.329 Sum_probs=36.3
Q ss_pred eEEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCC
Q 009973 402 VTQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRG 442 (521)
Q Consensus 402 ~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~ 442 (521)
.|-++.|-+.+-|.||||+|.++++|-+.||-.-+|-+..+
T Consensus 93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~~ 133 (630)
T TIGR03675 93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTPP 133 (630)
T ss_pred CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecCC
Confidence 45678898999999999999999999999999988877654
No 152
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=38.04 E-value=1e+02 Score=25.25 Aligned_cols=66 Identities=23% Similarity=0.261 Sum_probs=47.3
Q ss_pred eEEEEEecCCCccceecCCCchHHHHHHHhCCeEEEccCCC---CCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 009973 402 VTQQMQIPLSYADAVIGTAGASISYIRRSSGATVTIQETRG---VPGEMTVEISGTASQVQTAQQLIQNFMAE 471 (521)
Q Consensus 402 ~t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~---~~~er~VtI~Gt~e~V~~A~~lI~~~i~~ 471 (521)
.+..+..-.+ |.+- |=.-+.+|=+..|++++.....+ ..++.+++|+|+...+..|.+.++++|..
T Consensus 18 ~~a~i~are~--gV~a--G~~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~~ 86 (88)
T PF02749_consen 18 GTATIIARED--GVLA--GLEEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQR 86 (88)
T ss_dssp EEEEEEESSS--EEE---SHHHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred EEEEEEeCCC--EEEE--CHHHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHHH
Confidence 3444444443 3332 45567788888899988875543 34789999999999999999999999864
No 153
>COG1159 Era GTPase [General function prediction only]
Probab=37.72 E-value=37 Score=34.66 Aligned_cols=32 Identities=19% Similarity=0.309 Sum_probs=23.6
Q ss_pred cceEEEEEecCC-CccceecCCCchHHHHHHHh
Q 009973 400 TQVTQQMQIPLS-YADAVIGTAGASISYIRRSS 431 (521)
Q Consensus 400 ~~~t~~i~VP~~-~vG~IIGkgG~~Ik~Ir~~S 431 (521)
-.+...|.|+.+ +-|-||||+|++||+|-..+
T Consensus 227 ~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~A 259 (298)
T COG1159 227 LKIHATIYVERESQKGIIIGKNGAMIKKIGTAA 259 (298)
T ss_pred EEEEEEEEEecCCccceEECCCcHHHHHHHHHH
Confidence 345666888765 44999999999998764433
No 154
>PRK15494 era GTPase Era; Provisional
Probab=36.94 E-value=32 Score=35.76 Aligned_cols=29 Identities=24% Similarity=0.456 Sum_probs=22.8
Q ss_pred eEEEEEecc-ccccccccCCchhHHHHHHH
Q 009973 222 VSTKLLVPA-SQAGSLIGKQGGTVKSIQEA 250 (521)
Q Consensus 222 ~t~~l~VP~-~~vG~IIGk~G~~Ik~I~~~ 250 (521)
+...++|.. .+-+.|||++|+.||+|...
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 456777874 57789999999999987554
No 155
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=36.45 E-value=26 Score=33.72 Aligned_cols=36 Identities=11% Similarity=0.257 Sum_probs=30.1
Q ss_pred eEEEEEeeccccccccccCchHHHHHHhhcCcEEEE
Q 009973 130 SVFRMLVPAQKVGSIIGRKGEFIKKIVEETRARIKI 165 (521)
Q Consensus 130 ~~~rllVP~~~vG~IIGKgG~~Ik~I~e~Tga~I~i 165 (521)
..+.+-+..+..+.||||.|+++..||--+++.+.-
T Consensus 91 ~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 567777888889999999999999999877765554
No 156
>PRK00089 era GTPase Era; Reviewed
Probab=35.85 E-value=34 Score=34.40 Aligned_cols=29 Identities=34% Similarity=0.562 Sum_probs=22.0
Q ss_pred eEEEEEec-cccccccccCCchhHHHHHHH
Q 009973 222 VSTKLLVP-ASQAGSLIGKQGGTVKSIQEA 250 (521)
Q Consensus 222 ~t~~l~VP-~~~vG~IIGk~G~~Ik~I~~~ 250 (521)
+...+.|. ..+-+.|||++|++||+|...
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 45566676 456789999999999887554
No 157
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=33.05 E-value=2.1e+02 Score=30.35 Aligned_cols=66 Identities=15% Similarity=0.085 Sum_probs=44.0
Q ss_pred ecCCCc-cceecCCCchHHHHHHHhCCeEEEccCC--------C-CC-CceEE-EEEcCHHHHHHHHHHHHHHHHhcc
Q 009973 408 IPLSYA-DAVIGTAGASISYIRRSSGATVTIQETR--------G-VP-GEMTV-EISGTASQVQTAQQLIQNFMAEAA 473 (521)
Q Consensus 408 VP~~~v-G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~--------~-~~-~er~V-tI~Gt~e~V~~A~~lI~~~i~~~~ 473 (521)
+|..++ +.+=|++-..+..++.++++.+-+.... + .+ .-+.| .+-++++.+..|.+++.+++....
T Consensus 220 ~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMYI~i~h~~~~g~~~A~r~~~nl~~~v~ 297 (531)
T KOG1960|consen 220 DPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNEGNESNEPMYIFSTHGNGNGENGAPRRKWNLEEKVY 297 (531)
T ss_pred CcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccCcccccccCCceeEEeecCCchhhccchhHHHhHHHHHH
Confidence 555554 6666778888888888898886663211 0 11 12344 445688999999999988877643
No 158
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=30.64 E-value=48 Score=32.09 Aligned_cols=29 Identities=21% Similarity=0.261 Sum_probs=22.6
Q ss_pred EEEEecCCCccceecCCCchHHHHHHHhC
Q 009973 404 QQMQIPLSYADAVIGTAGASISYIRRSSG 432 (521)
Q Consensus 404 ~~i~VP~~~vG~IIGkgG~~Ik~Ir~~SG 432 (521)
..+.|-...-|.+||++|++|++|++.-.
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lk 70 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILE 70 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHH
Confidence 34555557789999999999999887654
No 159
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=30.49 E-value=1.2e+02 Score=31.63 Aligned_cols=51 Identities=16% Similarity=0.208 Sum_probs=43.5
Q ss_pred ccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHHHHHH
Q 009973 229 PASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAMELIG 291 (521)
Q Consensus 229 P~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~ 291 (521)
+...+-.+.|..+.+++-|.+.+|+.|.... +.++|+|+...|..|...+.
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG------------~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVARG------------EAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeCC------------ceEEEEechHHHHHHHHHHh
Confidence 3667788999999999999999998886543 67999999878888888887
No 160
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=30.16 E-value=50 Score=31.65 Aligned_cols=29 Identities=21% Similarity=0.219 Sum_probs=23.5
Q ss_pred EEEEEecCCCccceecCCCchHHHHHHHh
Q 009973 403 TQQMQIPLSYADAVIGTAGASISYIRRSS 431 (521)
Q Consensus 403 t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~S 431 (521)
..++.|-...-|.|||++|.+|++|++.-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 35677777778999999999999887654
No 161
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=29.93 E-value=45 Score=34.39 Aligned_cols=33 Identities=30% Similarity=0.438 Sum_probs=26.4
Q ss_pred ceEEEEEecc-ccccccccCCchhHHHHHHHhcc
Q 009973 221 KVSTKLLVPA-SQAGSLIGKQGGTVKSIQEASNC 253 (521)
Q Consensus 221 ~~t~~l~VP~-~~vG~IIGk~G~~Ik~I~~~tGa 253 (521)
.+..++.+|. .+...||||+|..|++|-++-+-
T Consensus 327 ~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~~ 360 (379)
T KOG1423|consen 327 FIQVEVVCPKNSQKKLLIGKGGKKISQIGTRANE 360 (379)
T ss_pred EEEEEEEcCCCcceeEEEcCCCccHHHHHHHHHH
Confidence 4677889995 56677899999999999776554
No 162
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=28.19 E-value=55 Score=31.79 Aligned_cols=28 Identities=29% Similarity=0.577 Sum_probs=24.5
Q ss_pred EEEEeeccccccccccCchHHHHHHhhc
Q 009973 132 FRMLVPAQKVGSIIGRKGEFIKKIVEET 159 (521)
Q Consensus 132 ~rllVP~~~vG~IIGKgG~~Ik~I~e~T 159 (521)
+++.|....-|.|||++|..|++|++.-
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 7788888888999999999999998654
No 163
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=27.82 E-value=56 Score=31.93 Aligned_cols=28 Identities=18% Similarity=0.260 Sum_probs=22.6
Q ss_pred EEEEecCCCccceecCCCchHHHHHHHh
Q 009973 404 QQMQIPLSYADAVIGTAGASISYIRRSS 431 (521)
Q Consensus 404 ~~i~VP~~~vG~IIGkgG~~Ik~Ir~~S 431 (521)
.+|.|-...-|.|||++|..|++|++.-
T Consensus 46 i~V~I~tarPg~vIG~~G~~i~~l~~~L 73 (220)
T PTZ00084 46 TEIIIRATRTREVLGDKGRRIRELTSLL 73 (220)
T ss_pred EEEEEEECCCccEEcCCchHHHHHHHHH
Confidence 4566666778999999999999887654
No 164
>CHL00048 rps3 ribosomal protein S3
Probab=27.41 E-value=58 Score=31.70 Aligned_cols=29 Identities=17% Similarity=0.196 Sum_probs=23.2
Q ss_pred EEEEEecCCCccceecCCCchHHHHHHHh
Q 009973 403 TQQMQIPLSYADAVIGTAGASISYIRRSS 431 (521)
Q Consensus 403 t~~i~VP~~~vG~IIGkgG~~Ik~Ir~~S 431 (521)
..+|.|-...-|.|||++|.+|++|++.-
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 34566666777999999999999987765
No 165
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=25.85 E-value=51 Score=31.81 Aligned_cols=36 Identities=28% Similarity=0.408 Sum_probs=29.7
Q ss_pred eEEEEEeccccccccccCCchhHHHHHHHhcccEEE
Q 009973 222 VSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRV 257 (521)
Q Consensus 222 ~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i 257 (521)
-++.+.|-....+++||+.|.++..||--+.+-+.-
T Consensus 91 ~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 356677777779999999999999999998875543
No 166
>PF10515 APP_amyloid: beta-amyloid precursor protein C-terminus; InterPro: IPR019543 This is the amyloid, C-terminal, protein of the beta-Amyloid precursor protein (APP) which is a conserved and ubiquitous transmembrane glycoprotein strongly implicated in the pathogenesis of Alzheimer's disease but whose normal biological function is unknown. The C-terminal 100 residues are released and aggregate into amyloid deposits which are strongly implicated in the pathology of Alzheimer's disease plaque-formation. The domain is associated with IPR008154 from INTERPRO, further towards the N terminus. ; PDB: 2ROZ_A 3DXD_D 1X11_D 2LP1_A 2LOH_A 3MXC_L 3MXY_L 3DXC_B 3DXE_D 3L81_B ....
Probab=25.53 E-value=13 Score=27.61 Aligned_cols=32 Identities=38% Similarity=0.578 Sum_probs=13.1
Q ss_pred cccccccccCCCCccCCCcchhh-hccCCCCCCCccc
Q 009973 4 ADQGFVEHDGNHDLEQIPENQEV-ENQVPGYEVPEYE 39 (521)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 39 (521)
..+||||-|-+++. |...+ .-|.-|||-|.|+
T Consensus 17 ~~~g~veVD~~~tp----Ee~h~~~mQ~nGYENPTYk 49 (52)
T PF10515_consen 17 ISHGFVEVDPCLTP----EERHLSNMQNNGYENPTYK 49 (52)
T ss_dssp -------------H----HHHHHHHHHCTEEESCTCH
T ss_pred cccceEEecCCCCh----HHHHHHHHHhcCCcCCcee
Confidence 35899999999665 44444 3488899999885
No 167
>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=24.08 E-value=1.9e+02 Score=26.93 Aligned_cols=58 Identities=19% Similarity=0.241 Sum_probs=44.5
Q ss_pred CCceEEEEEeccccccccccCCchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHHHHHHHHH
Q 009973 219 GGKVSTKLLVPASQAGSLIGKQGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAMELIGSHL 294 (521)
Q Consensus 219 ~~~~t~~l~VP~~~vG~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~l 294 (521)
.+..+.|+.++....- ..+.+|.+-.|+-+.+. ++.+|.|-|..+.|.+|+..+..+.
T Consensus 110 ~~~~~iRv~l~~~i~~-------erl~ei~E~~gvI~Efe-----------e~~~V~I~Gdke~Ik~aLKe~s~~w 167 (169)
T PF09869_consen 110 PGFETIRVKLKKPIQE-------ERLQEISEWHGVIFEFE-----------EDDKVVIEGDKERIKKALKEFSSFW 167 (169)
T ss_pred CCceeEEEecCccchH-------HHHHHHHHHhceeEEec-----------CCcEEEEeccHHHHHHHHHHHHHHh
Confidence 3456777777766543 46788999999988772 3577999999999999999887654
No 168
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=21.59 E-value=2.6e+02 Score=22.78 Aligned_cols=54 Identities=20% Similarity=0.097 Sum_probs=41.2
Q ss_pred CchhHHHHHHHhcccEEEcCCCCCCcccCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 009973 240 QGGTVKSIQEASNCIVRVLGAEDLPVFALQDDRVVEVVGDASGVHKAMELIGSHLR 295 (521)
Q Consensus 240 ~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~ 295 (521)
+=.-+.+|-+..+++++....|.... ...+.+++|.|+..++..|.+.++.+|.
T Consensus 32 G~~~~~~i~~~l~~~v~~~~~dG~~v--~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 32 GLEEAEEIFEKLGLEVEWLVKDGDRV--EPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp SHHHHHHHHHHCTEEEEESS-TT-EE--ETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhhccEEEEEEeCCCCCc--cCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 33566788888899998876444221 3467999999999999999999998875
No 169
>PF09849 DUF2076: Uncharacterized protein conserved in bacteria (DUF2076); InterPro: IPR018648 This family of hypothetical prokaryotic proteins has no known function but includes putative perimplasmic ligand-binding sensor proteins.
Probab=21.36 E-value=3.5e+02 Score=26.99 Aligned_cols=15 Identities=33% Similarity=0.390 Sum_probs=8.8
Q ss_pred HHHHHHHHHHHHHHh
Q 009973 457 QVQTAQQLIQNFMAE 471 (521)
Q Consensus 457 ~V~~A~~lI~~~i~~ 471 (521)
+++.|...|+++-.+
T Consensus 56 AL~~a~~ri~eLe~q 70 (247)
T PF09849_consen 56 ALKQAQARIQELEAQ 70 (247)
T ss_pred HHHHHHHHHHHHHHH
Confidence 556666666665544
No 170
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=21.01 E-value=90 Score=30.76 Aligned_cols=29 Identities=31% Similarity=0.532 Sum_probs=24.0
Q ss_pred EEEEEeeccccccccccCchHHHHHHhhc
Q 009973 131 VFRMLVPAQKVGSIIGRKGEFIKKIVEET 159 (521)
Q Consensus 131 ~~rllVP~~~vG~IIGKgG~~Ik~I~e~T 159 (521)
.+++.|....-+.|||++|..|++|++.-
T Consensus 63 ~i~I~I~~~rP~~iiG~~g~~i~~l~~~L 91 (232)
T PRK00310 63 RVRVTIHTARPGIVIGKKGAEIEKLRKEL 91 (232)
T ss_pred eEEEEEEECCCccccCCCcHHHHHHHHHH
Confidence 36666777778999999999999998754
Done!