Query 012477
Match_columns 462
No_of_seqs 198 out of 2077
Neff 8.8
Searched_HMMs 46136
Date Fri Mar 29 03:03:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012477.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012477hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2190 PolyC-binding proteins 100.0 1.6E-43 3.6E-48 356.7 33.9 405 5-451 6-416 (485)
2 KOG1676 K-homology type RNA bi 100.0 4.8E-43 1E-47 346.8 25.6 350 25-445 35-390 (600)
3 KOG2193 IGF-II mRNA-binding pr 100.0 2E-42 4.3E-47 326.5 23.2 369 33-447 189-567 (584)
4 KOG2192 PolyC-binding hnRNP-K 100.0 2.5E-38 5.4E-43 282.6 22.3 366 10-446 19-386 (390)
5 KOG1676 K-homology type RNA bi 100.0 1.9E-29 4E-34 250.5 21.9 243 37-348 133-384 (600)
6 KOG2193 IGF-II mRNA-binding pr 100.0 4.8E-29 1E-33 236.1 10.1 241 138-447 197-484 (584)
7 KOG2191 RNA-binding protein NO 99.9 2.2E-26 4.8E-31 212.1 20.9 237 41-322 37-282 (402)
8 KOG2191 RNA-binding protein NO 99.9 6.6E-22 1.4E-26 182.7 17.3 246 138-444 37-315 (402)
9 KOG2190 PolyC-binding proteins 99.8 4.9E-19 1.1E-23 179.4 19.1 171 283-458 42-225 (485)
10 KOG2192 PolyC-binding hnRNP-K 99.8 2.7E-18 5.8E-23 154.4 12.7 158 39-214 119-384 (390)
11 TIGR03665 arCOG04150 arCOG0415 99.6 9.9E-15 2.1E-19 129.7 9.1 138 47-215 2-152 (172)
12 TIGR03665 arCOG04150 arCOG0415 99.6 1.4E-14 2.9E-19 128.9 9.7 138 288-444 2-151 (172)
13 PRK13763 putative RNA-processi 99.5 6.9E-14 1.5E-18 125.2 11.7 141 284-444 3-157 (180)
14 PRK13763 putative RNA-processi 99.5 5.3E-14 1.1E-18 125.9 10.9 143 42-215 2-158 (180)
15 cd02396 PCBP_like_KH K homolog 99.4 5.3E-13 1.2E-17 99.0 7.5 63 372-438 2-64 (65)
16 KOG2208 Vigilin [Lipid transpo 99.4 1.6E-12 3.6E-17 139.5 9.8 305 43-445 201-563 (753)
17 cd02396 PCBP_like_KH K homolog 99.3 2.3E-12 5.1E-17 95.6 7.0 64 141-208 1-64 (65)
18 cd02394 vigilin_like_KH K homo 99.3 1.7E-12 3.6E-17 95.5 5.9 61 372-439 2-62 (62)
19 KOG2279 Kinase anchor protein 99.3 5.4E-12 1.2E-16 125.0 10.7 271 40-340 65-355 (608)
20 cd02393 PNPase_KH Polynucleoti 99.3 1E-11 2.2E-16 90.5 7.8 58 370-438 2-60 (61)
21 PF00013 KH_1: KH domain syndr 99.3 2.2E-12 4.7E-17 94.3 4.0 60 371-438 1-60 (60)
22 KOG2208 Vigilin [Lipid transpo 99.3 3.3E-11 7.3E-16 129.5 12.6 316 42-407 346-746 (753)
23 cd00105 KH-I K homology RNA-bi 99.2 4.4E-11 9.6E-16 88.5 8.0 62 372-438 2-63 (64)
24 KOG2279 Kinase anchor protein 99.2 2.6E-11 5.6E-16 120.3 7.5 229 137-440 65-364 (608)
25 PF00013 KH_1: KH domain syndr 99.2 3.8E-11 8.2E-16 87.7 4.6 60 141-208 1-60 (60)
26 cd02394 vigilin_like_KH K homo 99.1 6.8E-11 1.5E-15 86.9 5.5 60 142-208 2-61 (62)
27 cd02393 PNPase_KH Polynucleoti 99.1 3.1E-10 6.7E-15 82.7 7.7 58 140-208 2-60 (61)
28 cd00105 KH-I K homology RNA-bi 99.1 7E-10 1.5E-14 82.0 7.6 62 142-208 2-63 (64)
29 PF13014 KH_3: KH domain 99.0 9.1E-10 2E-14 74.3 5.7 42 53-94 1-43 (43)
30 smart00322 KH K homology RNA-b 99.0 3.3E-09 7.2E-14 79.1 8.8 67 369-442 2-68 (69)
31 PF13014 KH_3: KH domain 99.0 1.1E-09 2.3E-14 74.0 5.4 43 380-426 1-43 (43)
32 smart00322 KH K homology RNA-b 98.8 5.2E-08 1.1E-12 72.5 8.8 67 139-212 2-68 (69)
33 COG1094 Predicted RNA-binding 98.6 1.1E-07 2.4E-12 83.8 8.6 141 284-444 8-164 (194)
34 COG1094 Predicted RNA-binding 98.6 8.9E-07 1.9E-11 78.2 13.8 149 41-216 6-166 (194)
35 cd02395 SF1_like-KH Splicing f 98.5 3.3E-07 7.2E-12 76.0 7.8 67 378-444 14-95 (120)
36 cd02395 SF1_like-KH Splicing f 98.2 6.9E-06 1.5E-10 68.2 7.4 67 149-215 15-96 (120)
37 TIGR02696 pppGpp_PNP guanosine 98.0 1.9E-05 4.2E-10 83.9 9.3 96 107-214 546-642 (719)
38 PRK08406 transcription elongat 98.0 2.8E-05 6E-10 66.6 8.5 103 284-405 32-134 (140)
39 PRK08406 transcription elongat 98.0 1.1E-05 2.4E-10 69.0 5.1 102 44-175 33-134 (140)
40 KOG2113 Predicted RNA binding 97.9 2.6E-05 5.7E-10 72.9 6.1 140 138-335 24-163 (394)
41 KOG2113 Predicted RNA binding 97.8 1.5E-05 3.3E-10 74.4 4.3 136 282-435 24-173 (394)
42 TIGR03591 polynuc_phos polyrib 97.7 8.7E-05 1.9E-09 80.2 7.4 96 108-214 519-615 (684)
43 TIGR01952 nusA_arch NusA famil 97.6 0.00018 3.8E-09 61.4 7.4 103 285-406 34-136 (141)
44 KOG0119 Splicing factor 1/bran 97.6 0.0005 1.1E-08 68.5 11.0 77 369-445 137-231 (554)
45 TIGR02696 pppGpp_PNP guanosine 97.6 0.00014 3E-09 77.5 7.3 65 369-444 577-642 (719)
46 TIGR01952 nusA_arch NusA famil 97.6 0.00011 2.5E-09 62.6 5.1 102 44-175 34-135 (141)
47 KOG0336 ATP-dependent RNA heli 97.5 0.00012 2.6E-09 71.5 5.3 64 31-97 35-98 (629)
48 COG1185 Pnp Polyribonucleotide 97.5 0.00015 3.2E-09 75.6 6.0 99 105-214 517-616 (692)
49 KOG0119 Splicing factor 1/bran 97.5 0.00095 2.1E-08 66.6 10.6 77 138-214 136-230 (554)
50 PLN00207 polyribonucleotide nu 97.4 0.00021 4.6E-09 77.8 5.9 98 106-214 651-750 (891)
51 TIGR03591 polynuc_phos polyrib 97.1 0.00061 1.3E-08 73.7 5.8 65 369-444 550-615 (684)
52 KOG0336 ATP-dependent RNA heli 97.0 0.00083 1.8E-08 65.8 4.8 64 369-440 46-109 (629)
53 COG0195 NusA Transcription elo 97.0 0.0022 4.9E-08 57.5 7.0 100 288-407 80-179 (190)
54 COG0195 NusA Transcription elo 96.8 0.0032 6.9E-08 56.6 6.6 104 44-178 77-180 (190)
55 cd02134 NusA_KH NusA_K homolog 96.8 0.0025 5.5E-08 46.3 4.7 37 42-78 24-60 (61)
56 PRK11824 polynucleotide phosph 96.7 0.0015 3.1E-08 71.0 4.7 96 108-214 522-618 (693)
57 KOG1588 RNA-binding protein Sa 96.7 0.0021 4.6E-08 59.6 4.7 39 40-78 89-133 (259)
58 cd02134 NusA_KH NusA_K homolog 96.7 0.0029 6.3E-08 45.9 4.5 36 370-405 25-60 (61)
59 COG5176 MSL5 Splicing factor ( 96.6 0.008 1.7E-07 53.4 7.2 42 368-409 146-193 (269)
60 TIGR03319 YmdA_YtgF conserved 96.6 0.0055 1.2E-07 64.1 7.4 68 368-445 202-271 (514)
61 PRK12704 phosphodiesterase; Pr 96.6 0.0057 1.2E-07 64.0 7.5 68 368-445 208-277 (520)
62 COG1185 Pnp Polyribonucleotide 96.6 0.0031 6.8E-08 66.0 5.5 65 370-445 552-617 (692)
63 PRK00106 hypothetical protein; 96.6 0.0065 1.4E-07 63.3 7.7 68 368-445 223-292 (535)
64 KOG2814 Transcription coactiva 96.5 0.0031 6.8E-08 60.1 4.7 71 139-215 56-126 (345)
65 KOG1588 RNA-binding protein Sa 96.4 0.0034 7.3E-08 58.3 4.3 42 368-409 90-137 (259)
66 PLN00207 polyribonucleotide nu 96.4 0.0031 6.7E-08 69.0 4.5 64 369-443 684-749 (891)
67 PRK04163 exosome complex RNA-b 96.4 0.0068 1.5E-07 56.9 5.9 63 372-445 147-210 (235)
68 PRK12328 nusA transcription el 96.3 0.013 2.8E-07 57.9 7.9 96 293-409 251-347 (374)
69 TIGR01953 NusA transcription t 96.3 0.011 2.4E-07 58.4 7.4 93 294-407 244-338 (341)
70 TIGR01953 NusA transcription t 96.3 0.013 2.7E-07 58.0 7.5 96 52-178 243-339 (341)
71 PRK12327 nusA transcription el 96.1 0.013 2.8E-07 58.2 6.9 94 294-407 246-340 (362)
72 PRK00468 hypothetical protein; 96.1 0.0066 1.4E-07 45.9 3.6 33 40-72 27-59 (75)
73 PRK12328 nusA transcription el 96.1 0.016 3.5E-07 57.3 7.2 96 52-179 251-347 (374)
74 PRK12327 nusA transcription el 96.1 0.022 4.8E-07 56.6 8.2 96 52-178 245-341 (362)
75 KOG2814 Transcription coactiva 96.0 0.01 2.2E-07 56.8 5.1 71 369-446 56-127 (345)
76 PRK02821 hypothetical protein; 95.9 0.0088 1.9E-07 45.3 3.5 34 40-73 28-61 (77)
77 PRK12329 nusA transcription el 95.9 0.017 3.7E-07 58.1 6.3 94 293-407 277-372 (449)
78 PRK09202 nusA transcription el 95.8 0.022 4.7E-07 58.8 6.9 94 294-408 246-340 (470)
79 PRK12329 nusA transcription el 95.7 0.021 4.6E-07 57.4 6.2 96 52-178 277-373 (449)
80 PRK00468 hypothetical protein; 95.5 0.017 3.6E-07 43.7 3.6 34 368-401 28-61 (75)
81 COG1837 Predicted RNA-binding 95.4 0.019 4.2E-07 43.2 3.7 33 40-72 27-59 (76)
82 PRK04163 exosome complex RNA-b 95.4 0.03 6.5E-07 52.6 5.8 65 141-216 146-211 (235)
83 KOG1067 Predicted RNA-binding 95.3 0.03 6.6E-07 57.1 5.9 114 90-215 543-661 (760)
84 PF14611 SLS: Mitochondrial in 95.3 0.27 5.9E-06 45.3 11.9 131 285-445 27-166 (210)
85 PRK09202 nusA transcription el 95.3 0.044 9.5E-07 56.5 7.0 94 53-178 246-340 (470)
86 PRK02821 hypothetical protein; 95.3 0.021 4.6E-07 43.2 3.4 34 368-401 29-62 (77)
87 COG5176 MSL5 Splicing factor ( 95.2 0.052 1.1E-06 48.3 6.1 44 135-178 143-192 (269)
88 PRK01064 hypothetical protein; 95.1 0.03 6.5E-07 42.6 3.8 33 40-72 27-59 (78)
89 PRK11824 polynucleotide phosph 95.1 0.016 3.6E-07 62.9 3.4 64 370-444 554-618 (693)
90 COG1837 Predicted RNA-binding 95.0 0.03 6.6E-07 42.1 3.6 34 367-400 27-60 (76)
91 TIGR03319 YmdA_YtgF conserved 94.8 0.13 2.9E-06 53.9 9.1 66 139-214 203-270 (514)
92 PRK12704 phosphodiesterase; Pr 94.8 0.14 2.9E-06 53.9 9.0 66 139-214 209-276 (520)
93 PRK00106 hypothetical protein; 94.7 0.16 3.4E-06 53.2 9.3 68 138-215 223-292 (535)
94 PF14611 SLS: Mitochondrial in 94.3 0.98 2.1E-05 41.6 12.8 86 115-214 5-90 (210)
95 PRK01064 hypothetical protein; 94.3 0.055 1.2E-06 41.2 3.6 34 367-400 27-60 (78)
96 PRK12705 hypothetical protein; 94.0 0.067 1.4E-06 55.5 4.8 65 368-442 196-262 (508)
97 PF13083 KH_4: KH domain; PDB: 92.9 0.058 1.2E-06 40.6 1.6 34 40-73 26-59 (73)
98 KOG4369 RTK signaling protein 92.8 0.041 8.9E-07 60.5 0.8 70 371-444 1341-1410(2131)
99 PRK12705 hypothetical protein; 91.7 0.14 2.9E-06 53.3 3.1 43 39-81 194-237 (508)
100 KOG3273 Predicted RNA-binding 91.5 0.12 2.7E-06 45.7 2.2 53 378-442 177-229 (252)
101 cd02409 KH-II KH-II (K homolo 91.0 0.38 8.3E-06 35.0 4.2 35 42-76 24-58 (68)
102 PF13184 KH_5: NusA-like KH do 90.8 0.22 4.7E-06 37.1 2.6 37 371-407 4-46 (69)
103 KOG2874 rRNA processing protei 90.4 0.47 1E-05 44.4 5.0 51 152-214 161-211 (356)
104 KOG2874 rRNA processing protei 90.2 0.56 1.2E-05 43.9 5.2 51 382-444 161-211 (356)
105 cd02409 KH-II KH-II (K homolo 90.0 0.6 1.3E-05 33.9 4.5 34 370-403 25-58 (68)
106 COG1097 RRP4 RNA-binding prote 90.0 0.7 1.5E-05 42.7 5.7 47 372-429 148-194 (239)
107 PF13083 KH_4: KH domain; PDB: 89.4 0.22 4.7E-06 37.5 1.6 33 138-170 27-59 (73)
108 COG1097 RRP4 RNA-binding prote 88.8 0.92 2E-05 42.0 5.6 60 142-212 148-208 (239)
109 COG1855 ATPase (PilT family) [ 88.1 1.1 2.3E-05 45.4 5.9 41 139-179 485-525 (604)
110 cd02414 jag_KH jag_K homology 87.8 0.6 1.3E-05 35.5 3.2 33 44-76 25-57 (77)
111 KOG3273 Predicted RNA-binding 87.6 0.38 8.3E-06 42.8 2.2 57 148-216 177-233 (252)
112 PF13184 KH_5: NusA-like KH do 87.5 0.37 7.9E-06 35.8 1.8 34 45-78 5-44 (69)
113 PRK13764 ATPase; Provisional 87.2 0.67 1.5E-05 49.4 4.2 44 369-412 480-523 (602)
114 PF07650 KH_2: KH domain syndr 86.8 0.34 7.5E-06 36.8 1.3 34 43-76 25-58 (78)
115 cd02413 40S_S3_KH K homology R 85.8 0.57 1.2E-05 36.0 2.1 38 43-80 30-67 (81)
116 KOG4369 RTK signaling protein 85.1 0.32 6.9E-06 53.9 0.5 72 139-214 1339-1410(2131)
117 COG1855 ATPase (PilT family) [ 85.1 0.7 1.5E-05 46.7 2.8 41 370-410 486-526 (604)
118 cd02414 jag_KH jag_K homology 84.0 1.3 2.9E-05 33.6 3.4 34 371-404 25-58 (77)
119 PF07650 KH_2: KH domain syndr 83.7 0.59 1.3E-05 35.5 1.3 34 140-173 25-58 (78)
120 COG5166 Uncharacterized conser 83.3 2.2 4.8E-05 43.6 5.5 136 287-446 384-526 (657)
121 cd02410 archeal_CPSF_KH The ar 82.8 3.6 7.9E-05 35.1 5.8 38 141-178 77-114 (145)
122 PRK13764 ATPase; Provisional 82.7 3.2 6.8E-05 44.4 6.7 45 138-182 479-523 (602)
123 PRK06418 transcription elongat 82.7 1.5 3.3E-05 38.5 3.6 33 46-79 64-96 (166)
124 KOG1067 Predicted RNA-binding 81.7 2.3 4.9E-05 44.0 4.9 66 367-444 594-660 (760)
125 cd02410 archeal_CPSF_KH The ar 80.8 2.2 4.7E-05 36.4 3.8 94 299-408 21-114 (145)
126 cd02413 40S_S3_KH K homology R 79.6 2.4 5.1E-05 32.6 3.4 35 371-405 31-65 (81)
127 cd02412 30S_S3_KH K homology R 78.0 2.2 4.8E-05 34.8 3.0 29 45-73 63-91 (109)
128 cd02411 archeal_30S_S3_KH K ho 77.1 3 6.4E-05 32.3 3.3 28 45-72 40-67 (85)
129 COG5166 Uncharacterized conser 76.3 2.6 5.7E-05 43.1 3.5 130 53-214 390-524 (657)
130 PRK06418 transcription elongat 75.6 3.7 8.1E-05 36.1 3.9 37 141-178 62-98 (166)
131 COG0092 RpsC Ribosomal protein 75.3 6.3 0.00014 36.4 5.4 29 370-398 51-79 (233)
132 COG0092 RpsC Ribosomal protein 71.9 3.7 8E-05 37.9 3.0 31 42-72 50-80 (233)
133 COG1782 Predicted metal-depend 71.4 13 0.00029 38.3 7.0 97 55-178 41-137 (637)
134 cd02411 archeal_30S_S3_KH K ho 68.3 5.9 0.00013 30.7 3.1 28 372-399 40-67 (85)
135 cd02412 30S_S3_KH K homology R 68.2 4.7 0.0001 32.9 2.7 29 372-400 63-91 (109)
136 COG1782 Predicted metal-depend 63.7 19 0.00041 37.2 6.4 96 297-408 42-137 (637)
137 TIGR00436 era GTP-binding prot 61.9 9.4 0.0002 36.5 3.9 31 369-399 220-251 (270)
138 COG1847 Jag Predicted RNA-bind 59.3 32 0.00069 31.3 6.4 36 370-405 91-126 (208)
139 PRK15494 era GTPase Era; Provi 58.2 12 0.00025 37.3 3.9 37 369-405 272-317 (339)
140 TIGR03675 arCOG00543 arCOG0054 58.1 29 0.00062 37.7 7.1 96 297-408 36-131 (630)
141 TIGR03675 arCOG00543 arCOG0054 58.0 20 0.00042 38.9 5.8 96 56-178 36-131 (630)
142 PRK00089 era GTPase Era; Revie 55.7 13 0.00029 35.8 3.8 38 368-405 224-270 (292)
143 COG1159 Era GTPase [General fu 55.4 15 0.00033 35.4 3.9 34 365-398 224-258 (298)
144 TIGR01008 rpsC_E_A ribosomal p 47.2 22 0.00048 32.2 3.5 30 44-73 39-68 (195)
145 CHL00048 rps3 ribosomal protei 46.7 22 0.00048 32.8 3.5 32 42-73 65-96 (214)
146 PRK04191 rps3p 30S ribosomal p 46.6 22 0.00048 32.6 3.5 30 45-74 42-71 (207)
147 COG1702 PhoH Phosphate starvat 44.5 59 0.0013 32.1 6.1 51 377-439 22-72 (348)
148 PTZ00084 40S ribosomal protein 44.1 25 0.00054 32.5 3.4 32 44-75 45-76 (220)
149 COG1847 Jag Predicted RNA-bind 42.5 18 0.00039 32.9 2.1 36 42-77 90-125 (208)
150 KOG1423 Ras-like GTPase ERA [C 41.1 28 0.0006 33.9 3.2 37 364-400 322-359 (379)
151 TIGR00436 era GTP-binding prot 39.9 22 0.00049 33.9 2.6 29 43-71 221-250 (270)
152 TIGR01008 rpsC_E_A ribosomal p 37.2 36 0.00078 30.9 3.3 29 371-399 39-67 (195)
153 PRK04191 rps3p 30S ribosomal p 36.4 37 0.0008 31.1 3.3 29 372-400 42-70 (207)
154 PRK15494 era GTPase Era; Provi 34.9 45 0.00096 33.1 3.9 36 140-175 273-317 (339)
155 CHL00048 rps3 ribosomal protei 34.9 40 0.00087 31.1 3.2 29 371-399 67-95 (214)
156 PRK00089 era GTPase Era; Revie 34.0 31 0.00066 33.3 2.5 36 43-78 226-270 (292)
157 PTZ00084 40S ribosomal protein 33.8 41 0.00089 31.1 3.1 29 371-399 45-73 (220)
158 TIGR01009 rpsC_bact ribosomal 31.5 50 0.0011 30.4 3.3 29 45-73 64-92 (211)
159 COG1159 Era GTPase [General fu 31.3 39 0.00084 32.7 2.6 37 42-78 228-273 (298)
160 PRK03818 putative transporter; 29.5 7.2E+02 0.016 26.5 12.7 135 44-208 206-359 (552)
161 PF09869 DUF2096: Uncharacteri 29.1 1.8E+02 0.0038 25.6 5.9 57 138-212 111-167 (169)
162 COG0490 Putative regulatory, l 28.8 45 0.00098 29.1 2.3 62 373-439 91-158 (162)
163 PF02749 QRPTase_N: Quinolinat 28.4 1.5E+02 0.0034 22.8 5.2 54 158-213 32-85 (88)
164 KOG1423 Ras-like GTPase ERA [C 26.4 51 0.0011 32.1 2.4 33 282-314 326-359 (379)
165 COG1702 PhoH Phosphate starvat 25.1 1.4E+02 0.0029 29.7 5.1 53 145-209 20-72 (348)
166 TIGR01009 rpsC_bact ribosomal 23.0 80 0.0017 29.1 3.0 28 372-399 64-91 (211)
167 PRK00310 rpsC 30S ribosomal pr 21.3 90 0.002 29.2 3.0 30 44-73 63-92 (232)
168 PRK15468 carboxysome structura 21.1 1.6E+02 0.0035 23.8 3.9 26 420-445 75-100 (111)
169 cd07055 BMC_like_2 Bacterial M 20.3 1.1E+02 0.0024 22.0 2.6 21 420-440 39-59 (61)
No 1
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=1.6e-43 Score=356.69 Aligned_cols=405 Identities=40% Similarity=0.609 Sum_probs=313.0
Q ss_pred CCccCCCCCCCCCCCCCCCCccccCCCCCCCcccCCCceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCC
Q 012477 5 RNSYGKRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPG 84 (462)
Q Consensus 5 ~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~ 84 (462)
|..-.++....+....++..+++....+..+. ..+...++|||||.+.+|.||||+|..|++|++++.++|+|.+..++
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~ 84 (485)
T KOG2190|consen 6 RGLPRPKNSTTSNVGDNGSIKRPSLGDPVIST-GPDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPG 84 (485)
T ss_pred ccCccccCCCcccccCCCcccccCCCCCcccC-CCCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCC
Confidence 44455666666676677777777777765444 33444459999999999999999999999999999999999998999
Q ss_pred CCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHHHHhh---cc---CCCCCCCCCceEEEEEEeCCceeeeecCC
Q 012477 85 SEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEE---LR---GDEDSDGGHQVTAKLLVPSDQIGCVIGKG 158 (462)
Q Consensus 85 ~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~---~~---~~~~~~~~~~~~~~l~ip~~~~g~IIGk~ 158 (462)
+++|+++|+|...+. ..+.+.+|+.++++.+.... .. ....+.....+++||+||..++|.||||+
T Consensus 85 c~eRIiti~g~~~~~--------~~~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~ 156 (485)
T KOG2190|consen 85 CPERIITITGNRVEL--------NLSPATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKG 156 (485)
T ss_pred CCcceEEEecccccc--------cCCchHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccC
Confidence 999999999962221 35557888888888776631 11 11111222368999999999999999999
Q ss_pred chHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCcccccccccCCCCCCCCCCC
Q 012477 159 GQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLV 238 (462)
Q Consensus 159 G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~g~~~ 238 (462)
|++||+|+++|||+|++.++ ++|. +++|.|+|.|.+++|.+|+..|..+|.+++........+..+ |.
T Consensus 157 G~~Ik~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~--y~------ 224 (485)
T KOG2190|consen 157 GSLIKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIP--YR------ 224 (485)
T ss_pred cHHHHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCccc--CC------
Confidence 99999999999999999987 8887 899999999999999999999999999965332111111111 00
Q ss_pred CCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEeeeCCccccccccCChhHHhHHhhhCCeEE
Q 012477 239 GPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIK 318 (462)
Q Consensus 239 ~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~ 318 (462)
| ......+...+.+... ..+.++.....+.++..++.+|...++.|+|++|..|+.|+.++++.|.
T Consensus 225 -P----~~~~~~~~~~s~~~~~---------~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~ 290 (485)
T KOG2190|consen 225 -P----SASQGGPVLPSTAQTS---------PDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASIS 290 (485)
T ss_pred -C----cccccCccccccccCC---------cccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceE
Confidence 0 0000000000000000 0111122223455667889999999999999999999999999999999
Q ss_pred ecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccccccccCCCcceEEEEEecCCccceeecCCCchHHHHHHh
Q 012477 319 VDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRL 398 (462)
Q Consensus 319 i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~ 398 (462)
+.....+ |+++++..+...+..+.++++++..+++..+....+. ...++.++.||.+++||||||+|.+|.+||+.
T Consensus 291 v~~~~~~---~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~-~~~v~~~l~vps~~igciiGk~G~~iseir~~ 366 (485)
T KOG2190|consen 291 VGDSRTD---RIVTISARENPEDRYSMAQEALLLVQPRISENAGDDL-TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQR 366 (485)
T ss_pred eccccCc---ceeeeccccCcccccccchhhhhhccccccccccccc-cceeeeeeccCccccceeecccccchHHHHHh
Confidence 9987654 9999999999988889999999999998887766555 67899999999999999999999999999999
Q ss_pred hCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhhhccCCC
Q 012477 399 TKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLFDREG 451 (462)
Q Consensus 399 sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~ 451 (462)
|||.|+|.+.++. ....++.++|+|...+...|++++..++.......++
T Consensus 367 tgA~I~I~~~~~~---~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~~ 416 (485)
T KOG2190|consen 367 TGASISILNKEEV---SGVREALVQITGMLREDLLAQYLIRARLSAPKSSMGG 416 (485)
T ss_pred cCCceEEcccccc---CCcceeEEEecchhHHHHhhhhhcccccccCccCCCC
Confidence 9999999987543 2567899999999999999999999888887654433
No 2
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=4.8e-43 Score=346.80 Aligned_cols=350 Identities=20% Similarity=0.357 Sum_probs=264.2
Q ss_pred ccccCCCCCCCcccCC-CceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccc
Q 012477 25 KRRYTGDDRDQFIIGP-EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFE 103 (462)
Q Consensus 25 ~~~~~~~~~~~~~~~~-~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~ 103 (462)
|+...+.+...+..+. ..++.+..||.+++++||||+|+.|..|.+++||+|.+.....+..+|.+.++|.++++
T Consensus 35 ~~~~~~~~l~p~~~~s~~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v---- 110 (600)
T KOG1676|consen 35 KGPSEDTDLDPDMDPSDTVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENV---- 110 (600)
T ss_pred cCCCCccccCcccCCcccccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccH----
Confidence 4444444443333333 55678899999999999999999999999999999998766667789999999999994
Q ss_pred CCCCcCCHHHHHHHHHHHHHHHhhc--cCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCC
Q 012477 104 DGDKFVSPAQDALFKVHDRVIAEEL--RGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHL 181 (462)
Q Consensus 104 ~~~~~v~~a~~a~~~i~~~i~~~~~--~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~ 181 (462)
..|- ++++.+..... ...........++..|+||.+.+|.||||+|++||.|++.+||++.+..+...
T Consensus 111 ---------~~aK-~li~evv~r~~~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~ 180 (600)
T KOG1676|consen 111 ---------EVAK-QLIGEVVSRGRPPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSI 180 (600)
T ss_pred ---------HHHH-HhhhhhhhccCCCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCc
Confidence 2222 22222322221 11122233567899999999999999999999999999999999999888654
Q ss_pred CCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCcccccccccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCC
Q 012477 182 PSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKG 261 (462)
Q Consensus 182 p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~~~~~ 261 (462)
.. ..++.+.|+|+++.|+.|..+|.++|++.... .+..+++ +++..
T Consensus 181 ~~---~~~KplritGdp~~ve~a~~lV~dil~e~~~~-----------~~g~~~~-------------------~g~~~- 226 (600)
T KOG1676|consen 181 AT---GADKPLRITGDPDKVEQAKQLVADILREEDDE-----------VPGSGGH-------------------AGVRG- 226 (600)
T ss_pred CC---CCCCceeecCCHHHHHHHHHHHHHHHHhcccC-----------CCccccc-------------------cCcCc-
Confidence 43 47889999999999999999999999974211 1111000 11100
Q ss_pred CCCCCCCCCCCCCCCCCCCCcceEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCC-CCCceEEEEecCCccc
Q 012477 262 DTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSST-EGDDCLITVSSKEFFE 340 (462)
Q Consensus 262 ~~~~~~~~~~~~~p~~~~~~~~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~-~~~~~~i~i~G~~~~~ 340 (462)
....+++|.||...+|.||||+|++||+|+.+||++|+|-+++. .+.+|++.|.|+...-
T Consensus 227 -------------------g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~i 287 (600)
T KOG1676|consen 227 -------------------GGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQI 287 (600)
T ss_pred -------------------cccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHH
Confidence 11237899999999999999999999999999999999999765 7889999999986443
Q ss_pred ccccHHHHHHHhhcCcccccccccCCCcce--EEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCC
Q 012477 341 DTLSATIEAVVRLQPRCSEKIERDSGLISF--TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASED 418 (462)
Q Consensus 341 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~--t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~ 418 (462)
......+.+++........ ..-..+.... ..+|.||...||.||||||++||.|.++|||++.+++. |+..+..
T Consensus 288 e~Aa~lI~eii~~~~~~~~-~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~---~p~~~~~ 363 (600)
T KOG1676|consen 288 EHAAELINEIIAEAEAGAG-GGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ---PPNGNPK 363 (600)
T ss_pred HHHHHHHHHHHHHHhccCC-CCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC---CCCCCcc
Confidence 3334444444443211110 0001112223 78899999999999999999999999999999999875 4566788
Q ss_pred CceEEEEcCHHHHHHHHHHHHHHHHhh
Q 012477 419 DEMVQISGDLDLAKDALIQVMTRLRAN 445 (462)
Q Consensus 419 ~~~v~I~G~~~~v~~A~~~I~~~l~~~ 445 (462)
+++|+|+|++.+|+.|+.||..++...
T Consensus 364 ektf~IrG~~~QIdhAk~LIr~kvg~~ 390 (600)
T KOG1676|consen 364 EKTFVIRGDKRQIDHAKQLIRDKVGDI 390 (600)
T ss_pred ceEEEEecCcccchHHHHHHHHHhccc
Confidence 999999999999999999999999875
No 3
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=2e-42 Score=326.51 Aligned_cols=369 Identities=22% Similarity=0.380 Sum_probs=274.6
Q ss_pred CCCcccCCCceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcC-CCCCCCceEEEEEcCCcccccccCCCCcCCH
Q 012477 33 RDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE-TVPGSEERVVTVYSASDETNAFEDGDKFVSP 111 (462)
Q Consensus 33 ~~~~~~~~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~-~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~ 111 (462)
..+...-..+..+|+|||-.++|.|||+.|.+||.|.+.|.|+|+|.. ...+..|++|+|-|++|.
T Consensus 189 G~~~~~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg------------- 255 (584)
T KOG2193|consen 189 GPHHKQQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG------------- 255 (584)
T ss_pred CCcccccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc-------------
Confidence 344445567889999999999999999999999999999999999975 455888999999999999
Q ss_pred HHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCce
Q 012477 112 AQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDEL 191 (462)
Q Consensus 112 a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~ 191 (462)
+.+|+.+|++.+..+... +.....+.++++-++.++|++|||.|.++|+|+.+||++|.|++--++.. ...+|+
T Consensus 256 ~s~Ac~~ILeimqkEA~~----~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~--ynpERT 329 (584)
T KOG2193|consen 256 TSKACKMILEIMQKEAVD----DKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSL--YNPERT 329 (584)
T ss_pred hHHHHHHHHHHHHHhhhc----cchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcc--cCccce
Confidence 467788888876655432 23346788999999999999999999999999999999999998766655 367999
Q ss_pred EEEEcCHHHHHHHHHHHHHHHhcCCCCcccccccccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCC--CCCC-CCCCCCC
Q 012477 192 VQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYG--GYKG-DTAGDWS 268 (462)
Q Consensus 192 v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~--~~~~-~~~~~~~ 268 (462)
++++|+.++|..|..+|..+|++.++.+...+ ++. ..+.|....+..++-|..+++. .+.+ .+....+
T Consensus 330 ItVkGsiEac~~AE~eImkKlre~yEnDl~a~--s~q-------~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p 400 (584)
T KOG2193|consen 330 ITVKGSIEACVQAEAEIMKKLRECYENDLAAM--SLQ-------CHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASP 400 (584)
T ss_pred EEecccHHHHHHHHHHHHHHHHHHHhhhHHHh--hcc-------CCCCcccCccccCCCCcccccCCCCCCCCccccCCC
Confidence 99999999999999999999999877653211 100 0011111000000000000000 0000 0010111
Q ss_pred CCCCCCCCCCCCCcceEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCC-CCCCceEEEEecCCcccccccHHH
Q 012477 269 RSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSS-TEGDDCLITVSSKEFFEDTLSATI 347 (462)
Q Consensus 269 ~~~~~~p~~~~~~~~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~-~~~~~~~i~i~G~~~~~~~~~~~~ 347 (462)
+.++. .....-.+++.||...+|+|||++|.+||.|...+||+|+|.++. ++..+|.|+|+|.+
T Consensus 401 ~~~~h-----q~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGpp---------- 465 (584)
T KOG2193|consen 401 YPLFH-----QNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPP---------- 465 (584)
T ss_pred chhhh-----cCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCCh----------
Confidence 11111 111234789999999999999999999999999999999998864 56789999999975
Q ss_pred HHHHhhcCcccccccc-----cCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceE
Q 012477 348 EAVVRLQPRCSEKIER-----DSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMV 422 (462)
Q Consensus 348 ~a~~~~~~~~~~~~~~-----~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v 422 (462)
++.+..+.+++.++.. +.....+.+.+.||...+|+||||||.+++++++.|+|-+.|+++. .|. ..+.-+|
T Consensus 466 eaqfKAQgrifgKikEenf~~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdq-tpd--End~viv 542 (584)
T KOG2193|consen 466 EAQFKAQGRIFGKIKEENFFLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQ-TPD--ENDQVIV 542 (584)
T ss_pred HHHHhhhhhhhhhhhhhccCCchhhheeeeeeeccchhhhhhhccccccHHHHhccccceEEccccC-CCC--ccceeee
Confidence 3455555555544432 2234567889999999999999999999999999999999997654 443 2334568
Q ss_pred EEEcCHHHHHHHHHHHHHHHHhhhc
Q 012477 423 QISGDLDLAKDALIQVMTRLRANLF 447 (462)
Q Consensus 423 ~I~G~~~~v~~A~~~I~~~l~~~~~ 447 (462)
.|.|.+-+.+.|+..|.+.+.+...
T Consensus 543 riiGhfyatq~aQrki~~iv~qvkq 567 (584)
T KOG2193|consen 543 RIIGHFYATQNAQRKIAHIVNQVKQ 567 (584)
T ss_pred eeechhhcchHHHHHHHHHHHHHHH
Confidence 8999999999999999998887754
No 4
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=2.5e-38 Score=282.63 Aligned_cols=366 Identities=19% Similarity=0.273 Sum_probs=235.1
Q ss_pred CCCCCCCCCCCCCCCccccCCCCCCCcccCCCceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceE
Q 012477 10 KRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERV 89 (462)
Q Consensus 10 ~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~erv 89 (462)
+|.|+..+++. ..+|..++. +..++....+.++||+.++.+|+||||+|++||+|+.+++++|.|++. ..++|+
T Consensus 19 ~~~~~~e~g~~---~gkrp~~d~-~~qa~k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri 92 (390)
T KOG2192|consen 19 ETFPNTETGGE---FGKRPAEDM-EEQAFKRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERI 92 (390)
T ss_pred hcCCCCccccc---ccCCcchhh-HHHHhhhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCcee
Confidence 45555444322 333333333 445566788999999999999999999999999999999999999987 788999
Q ss_pred EEEEcCCcccccccCCCCcCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhc
Q 012477 90 VTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSET 169 (462)
Q Consensus 90 i~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~t 169 (462)
++|+...+- +-+-|++++..|.+. + ...+.|.+||||+.+++|.|||++|++||+|++++
T Consensus 93 ~tisad~~t-------------i~~ilk~iip~lee~-f------~~~~pce~rllihqs~ag~iigrngskikelrekc 152 (390)
T KOG2192|consen 93 LTISADIET-------------IGEILKKIIPTLEEG-F------QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKC 152 (390)
T ss_pred EEEeccHHH-------------HHHHHHHHhhhhhhC-C------CCCCchhhhhhhhhhhccceecccchhHHHHHHhh
Confidence 999988544 344555555555322 1 34567999999999999999999999999999999
Q ss_pred CceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCcccccccc--cCCCCCCCCCCCCCCCCCCCc
Q 012477 170 GAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASA--ISNSHSSSGSLVGPTAATPIV 247 (462)
Q Consensus 170 ga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~--~~~~~~~~g~~~~p~~~~~~~ 247 (462)
.|++.|... .|+++++|+|.|.|.+.+|..+++.|.+.|.+.|.+.....+.. ....|.+||..|.-...+.-.
T Consensus 153 sarlkift~----c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~p 228 (390)
T KOG2192|consen 153 SARLKIFTE----CCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRP 228 (390)
T ss_pred hhhhhhhhc----cCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCC
Confidence 999999876 67889999999999999999999999999999988876655433 223455666432211000000
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCC
Q 012477 248 GIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGD 327 (462)
Q Consensus 248 ~~~p~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~ 327 (462)
+.+|..++++-.+ |+.. .-+.+.. -|+-|.. +--.+.|.......
T Consensus 229 gpapqrggqgpp~--------------~~~s-------dlmay~r------~GrpG~r-------ydg~vdFs~detw~- 273 (390)
T KOG2192|consen 229 GPAPQRGGQGPPP--------------PRGS-------DLMAYDR------RGRPGDR-------YDGMVDFSADETWP- 273 (390)
T ss_pred CCCCCCCCCCCCC--------------CCcc-------ccceecc------CCCCCcc-------ccccccccccccCC-
Confidence 0011111111000 0000 0000000 0110111 00011111111100
Q ss_pred ceEEEEecCCcccccccHHHHHHHhhcCcccccccccCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEec
Q 012477 328 DCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP 407 (462)
Q Consensus 328 ~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~ 407 (462)
..+-+..-++ |...+.+..-.-..........+..+.+.+..|..|.||.++-|.||||||++|++|++++||.|+|.+
T Consensus 274 saidtw~~Se-wqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikide 352 (390)
T KOG2192|consen 274 SAIDTWSPSE-WQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDE 352 (390)
T ss_pred CcCCCcCccc-cccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecC
Confidence 0000000000 000000000000000000001112334567889999999999999999999999999999999999976
Q ss_pred CCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhhh
Q 012477 408 KENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANL 446 (462)
Q Consensus 408 ~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~ 446 (462)
+ .+++.+|.++|+|+.++++.|++|+.+.++++.
T Consensus 353 p-----leGsedrIitItGTqdQIqnAQYLlQn~Vkq~r 386 (390)
T KOG2192|consen 353 P-----LEGSEDRIITITGTQDQIQNAQYLLQNSVKQYR 386 (390)
T ss_pred c-----CCCCCceEEEEeccHHHHhhHHHHHHHHHHhhh
Confidence 4 357889999999999999999999999988653
No 5
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.97 E-value=1.9e-29 Score=250.49 Aligned_cols=243 Identities=26% Similarity=0.419 Sum_probs=186.7
Q ss_pred ccCCCceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcC--CCCCCCceEEEEEcCCcccccccCCCCcCCHHHH
Q 012477 37 IIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE--TVPGSEERVVTVYSASDETNAFEDGDKFVSPAQD 114 (462)
Q Consensus 37 ~~~~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~--~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~ 114 (462)
..+...++.+|+||.+.+|+||||+|++||+|++.+||++.+-+ .......+.+.|+|.++.+ +.
T Consensus 133 ~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~v-------------e~ 199 (600)
T KOG1676|consen 133 NQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKV-------------EQ 199 (600)
T ss_pred cCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHH-------------HH
Confidence 34467899999999999999999999999999999999998753 2333467899999999883 55
Q ss_pred HHHHHHHHHHHhhccCCC-----CCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCC
Q 012477 115 ALFKVHDRVIAEELRGDE-----DSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSD 189 (462)
Q Consensus 115 a~~~i~~~i~~~~~~~~~-----~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~ 189 (462)
|..++++.|.++.-.... ........++++.||.+.||.||||+|++||+|+.+||+||+|.++++ | .+.+
T Consensus 200 a~~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~-p---~spe 275 (600)
T KOG1676|consen 200 AKQLVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD-P---SSPE 275 (600)
T ss_pred HHHHHHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCC-C---CCcc
Confidence 666666666543311111 112233458999999999999999999999999999999999988743 4 3889
Q ss_pred ceEEEEcCHHHHHHHHHHHHHHHhcCCCCcccccccccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCC
Q 012477 190 ELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSR 269 (462)
Q Consensus 190 r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~ 269 (462)
|.+.|.|+.+.|..|.++|.++|.+..... . +++. +|.
T Consensus 276 R~~~IiG~~d~ie~Aa~lI~eii~~~~~~~----------~---~~~~-------------------~G~---------- 313 (600)
T KOG1676|consen 276 RPAQIIGTVDQIEHAAELINEIIAEAEAGA----------G---GGMG-------------------GGA---------- 313 (600)
T ss_pred ceeeeecCHHHHHHHHHHHHHHHHHHhccC----------C---CCcC-------------------CCC----------
Confidence 999999999999999999999998842110 0 0000 000
Q ss_pred CCCCCCCCCCCCcceEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCC--CCCCceEEEEecCCcccccccHHH
Q 012477 270 SLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSS--TEGDDCLITVSSKEFFEDTLSATI 347 (462)
Q Consensus 270 ~~~~~p~~~~~~~~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~--~~~~~~~i~i~G~~~~~~~~~~~~ 347 (462)
|. ....+.+.||...+|+||||+|++||.|..+|||++.+.+.. .+..+++++|.|.+...+.....+
T Consensus 314 -----P~-----~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG~~~QIdhAk~LI 383 (600)
T KOG1676|consen 314 -----PG-----LVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGDKRQIDHAKQLI 383 (600)
T ss_pred -----cc-----ceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEecCcccchHHHHHH
Confidence 00 001678999999999999999999999999999999999873 345789999999876554444443
Q ss_pred H
Q 012477 348 E 348 (462)
Q Consensus 348 ~ 348 (462)
+
T Consensus 384 r 384 (600)
T KOG1676|consen 384 R 384 (600)
T ss_pred H
Confidence 3
No 6
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.96 E-value=4.8e-29 Score=236.06 Aligned_cols=241 Identities=23% Similarity=0.397 Sum_probs=190.4
Q ss_pred CceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCC
Q 012477 138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPS 217 (462)
Q Consensus 138 ~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~ 217 (462)
....+|++||..++|.||||.|+|||.|...|-|+|+|...+.- +..|+.++|-|+++...+|+++|.+++..+..
T Consensus 197 ~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~----Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~ 272 (584)
T KOG2193|consen 197 KDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENA----GAAEKIITVHSTPEGTSKACKMILEIMQKEAV 272 (584)
T ss_pred cCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccC----CcccCceEEecCccchHHHHHHHHHHHHHhhh
Confidence 34679999999999999999999999999999999999987653 57899999999999999999999999987532
Q ss_pred CcccccccccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEeeeCCcccc
Q 012477 218 RSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGG 297 (462)
Q Consensus 218 ~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~v~ip~~~~g~ 297 (462)
.. ....++.++++-.+.++|+
T Consensus 273 ~~-----------------------------------------------------------k~~~e~pLk~lAHN~lvGR 293 (584)
T KOG2193|consen 273 DD-----------------------------------------------------------KVAEEIPLKILAHNNLVGR 293 (584)
T ss_pred cc-----------------------------------------------------------chhhhcchhhhhhcchhhh
Confidence 11 1234567889999999999
Q ss_pred ccccCChhHHhHHhhhCCeEEecCCC---CCCCceEEEEecCCcccccc----------cHHHHHH---HhhcCcccccc
Q 012477 298 VIGKGGAIINQIRQESGAAIKVDSSS---TEGDDCLITVSSKEFFEDTL----------SATIEAV---VRLQPRCSEKI 361 (462)
Q Consensus 298 IIGk~G~~Ik~I~~~sga~I~i~~~~---~~~~~~~i~i~G~~~~~~~~----------~~~~~a~---~~~~~~~~~~~ 361 (462)
+|||.|.++|+|+++||++|.|.+-- ....+|+|++.|+ ++..+ ..+.+.. +.++..+...+
T Consensus 294 LIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGs--iEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l 371 (584)
T KOG2193|consen 294 LIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGS--IEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGL 371 (584)
T ss_pred hhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEeccc--HHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCccc
Confidence 99999999999999999999999842 2346899999994 22211 1112211 12221111000
Q ss_pred --------------cc----c-------------CCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCC
Q 012477 362 --------------ER----D-------------SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKEN 410 (462)
Q Consensus 362 --------------~~----~-------------~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~ 410 (462)
.+ + .........|.||...+|+|||++|.+||.|.+.+||+|+|..+
T Consensus 372 ~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIapp-- 449 (584)
T KOG2193|consen 372 NLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPP-- 449 (584)
T ss_pred CccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCC--
Confidence 00 0 01134567899999999999999999999999999999999764
Q ss_pred CCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhhhc
Q 012477 411 LPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLF 447 (462)
Q Consensus 411 ~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~~ 447 (462)
..++..+|+|+|+|++++..+|+-.|+.+|++..+
T Consensus 450 --E~pdvseRMViItGppeaqfKAQgrifgKikEenf 484 (584)
T KOG2193|consen 450 --EIPDVSERMVIITGPPEAQFKAQGRIFGKIKEENF 484 (584)
T ss_pred --CCCCcceeEEEecCChHHHHhhhhhhhhhhhhhcc
Confidence 34467899999999999999999999999998854
No 7
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.95 E-value=2.2e-26 Score=212.11 Aligned_cols=237 Identities=25% Similarity=0.416 Sum_probs=176.8
Q ss_pred CceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcC---CCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHH
Q 012477 41 EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE---TVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALF 117 (462)
Q Consensus 41 ~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~---~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~ 117 (462)
..+.+++|||+..+|.||||+|++|.+|+++|||+|++++ ..|+++||+|.|.|+.+++ ...++
T Consensus 37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai-------------~av~e 103 (402)
T KOG2191|consen 37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEAL-------------NAVHE 103 (402)
T ss_pred CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHH-------------HHHHH
Confidence 4599999999999999999999999999999999999974 6999999999999997773 44566
Q ss_pred HHHHHHHHhhccCCC-CC-----CCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCce
Q 012477 118 KVHDRVIAEELRGDE-DS-----DGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDEL 191 (462)
Q Consensus 118 ~i~~~i~~~~~~~~~-~~-----~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~ 191 (462)
.|+++|.+....... .+ ..+..-.++++||++.+|.||||+|.+||.|++++||-|+|++.. |....-.+|+
T Consensus 104 fI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqk--pt~~sLqerv 181 (402)
T KOG2191|consen 104 FIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQK--PTGISLQERV 181 (402)
T ss_pred HHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccC--CCCccceeEE
Confidence 677787765432222 11 222334599999999999999999999999999999999999421 2233468999
Q ss_pred EEEEcCHHHHHHHHHHHHHHHhcCCCCcccccccccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCC
Q 012477 192 VQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSL 271 (462)
Q Consensus 192 v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~ 271 (462)
|++.|.+++..+|+.+|.+++.++|.....+.. .|.... +| ..-..|-+++|... .+
T Consensus 182 vt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~-----sya~vs---Gp-----vaNsnPtGspya~~-~~--------- 238 (402)
T KOG2191|consen 182 VTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNI-----SYANVS---GP-----VANSNPTGSPYAYQ-AH--------- 238 (402)
T ss_pred EEecCCHHHHHHHHHHHHHHhhcCCcccceecc-----chhccc---Cc-----ccccCCCCCCCCCC-Cc---------
Confidence 999999999999999999999999877665442 122111 00 00111111111110 01
Q ss_pred CCCCCCCCCCcceEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCC
Q 012477 272 YSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSS 322 (462)
Q Consensus 272 ~~~p~~~~~~~~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~ 322 (462)
..+...+....++....|..-|.+|.++-.|-.-+|+.+.++..
T Consensus 239 -------~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~ 282 (402)
T KOG2191|consen 239 -------VLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQA 282 (402)
T ss_pred -------cccccchhhccccccccccccccccccceeeecccccceeeccc
Confidence 01222345677888899999999999999999999998888774
No 8
>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=6.6e-22 Score=182.71 Aligned_cols=246 Identities=24% Similarity=0.339 Sum_probs=181.5
Q ss_pred CceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCC-CCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcCC
Q 012477 138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEH-LPSCALRSDELVQISGEASVVKKALCQIASRLHDNP 216 (462)
Q Consensus 138 ~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~-~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~ 216 (462)
..+.+++|||...+|.||||+|++|.+|+.+|||+|++++..+ +| +.+||+|.|+|+.+++......|.++|++.+
T Consensus 37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyP---GTTeRvcli~Gt~eai~av~efI~dKire~p 113 (402)
T KOG2191|consen 37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYP---GTTERVCLIQGTVEALNAVHEFIADKIREKP 113 (402)
T ss_pred CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCC---CccceEEEEeccHHHHHHHHHHHHHHHHHhH
Confidence 4489999999999999999999999999999999999998654 44 6999999999999999999999999999965
Q ss_pred CCcccccccccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEeeeCCccc
Q 012477 217 SRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIG 296 (462)
Q Consensus 217 ~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~v~ip~~~~g 296 (462)
..... +...+++.. .+..-.+++++|+..+|
T Consensus 114 ~~~~k----------------------------------------------~v~~~~pqt---~~r~kqikivvPNstag 144 (402)
T KOG2191|consen 114 QAVAK----------------------------------------------PVDILQPQT---PDRIKQIKIVVPNSTAG 144 (402)
T ss_pred HhhcC----------------------------------------------CccccCCCC---ccccceeEEeccCCccc
Confidence 32110 000000000 01112579999999999
Q ss_pred cccccCChhHHhHHhhhCCeEEecCCCC---CCCceEEEEecCCcccccccHHHHHHHhhc------Cc----cccc---
Q 012477 297 GVIGKGGAIINQIRQESGAAIKVDSSST---EGDDCLITVSSKEFFEDTLSATIEAVVRLQ------PR----CSEK--- 360 (462)
Q Consensus 297 ~IIGk~G~~Ik~I~~~sga~I~i~~~~~---~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~------~~----~~~~--- 360 (462)
.||||+|.+||.|++++||.|+|.+..+ .-.+|++|+.|... ....|+-.+. |+ +...
T Consensus 145 ~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e------~~~~A~~~IL~Ki~eDpqs~scln~sya~ 218 (402)
T KOG2191|consen 145 MIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPE------QNMKAVSLILQKIQEDPQSGSCLNISYAN 218 (402)
T ss_pred ceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHH------HHHHHHHHHHHHhhcCCcccceeccchhc
Confidence 9999999999999999999999996433 35789999999632 1222221111 11 1000
Q ss_pred ----c------------cccCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEE
Q 012477 361 ----I------------ERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQI 424 (462)
Q Consensus 361 ----~------------~~~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I 424 (462)
. .........+....|+....|..-|.+|.++-.|...+|+.+.+++..++-. +...+ .-+
T Consensus 219 vsGpvaNsnPtGspya~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l~~m~--g~gy~-~n~ 295 (402)
T KOG2191|consen 219 VSGPVANSNPTGSPYAYQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQALNTMA--GYGYN-TNI 295 (402)
T ss_pred ccCcccccCCCCCCCCCCCccccccchhhccccccccccccccccccceeeecccccceeecccccccc--ccccc-ccc
Confidence 0 0111123455667899999999999999999999999999999987765322 33444 778
Q ss_pred EcCHHHHHHHHHHHHHHHHh
Q 012477 425 SGDLDLAKDALIQVMTRLRA 444 (462)
Q Consensus 425 ~G~~~~v~~A~~~I~~~l~~ 444 (462)
.|.+-++..|-.+|..+...
T Consensus 296 ~g~~ls~~aa~g~L~~~~~~ 315 (402)
T KOG2191|consen 296 LGLGLSILAAEGVLAAKVAS 315 (402)
T ss_pred cchhhhhhhhhhHHHHhhcc
Confidence 88888888888777665543
No 9
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.82 E-value=4.9e-19 Score=179.43 Aligned_cols=171 Identities=36% Similarity=0.560 Sum_probs=136.8
Q ss_pred ceEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCccccccc
Q 012477 283 EFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIE 362 (462)
Q Consensus 283 ~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~ 362 (462)
+.+++++++...+|.|||++|..|++|+.++.++|+|.....++.+|+++|+|.. .+...+++.+++++.+..+.....
T Consensus 42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~-~~~~~~~~~~al~ka~~~iv~~~~ 120 (485)
T KOG2190|consen 42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNR-VELNLSPATDALFKAFDMIVFKLE 120 (485)
T ss_pred cceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEeccc-ccccCCchHHHHHHHHHHHhhccc
Confidence 3458999999999999999999999999999999999998888899999999941 122345566666666655443221
Q ss_pred ----------ccCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHH
Q 012477 363 ----------RDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAK 432 (462)
Q Consensus 363 ----------~~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~ 432 (462)
.+.....++.+|+||..++|+||||+|+.|++|++.|||+|+|..+ .+| ..++|.|+|.|.+++|.
T Consensus 121 ~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP---~ster~V~IsG~~~av~ 196 (485)
T KOG2190|consen 121 EDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLP---NSTERAVTISGEPDAVK 196 (485)
T ss_pred ccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCC---cccceeEEEcCchHHHH
Confidence 0111225789999999999999999999999999999999999876 556 47889999999999999
Q ss_pred HHHHHHHHHHHhhh---ccCCCCCCCCCC
Q 012477 433 DALIQVMTRLRANL---FDREGAVSTFVP 458 (462)
Q Consensus 433 ~A~~~I~~~l~~~~---~~~~~~~~~~~p 458 (462)
+|+..|...|.+.. ...-+....|.|
T Consensus 197 ~al~~Is~~L~~~~~~~~~~~~st~~y~P 225 (485)
T KOG2190|consen 197 KALVQISSRLLENPPRSPPPLVSTIPYRP 225 (485)
T ss_pred HHHHHHHHHHHhcCCcCCCCCCCcccCCC
Confidence 99999999999974 223444444444
No 10
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.77 E-value=2.7e-18 Score=154.44 Aligned_cols=158 Identities=28% Similarity=0.460 Sum_probs=133.4
Q ss_pred CCCceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEc-CCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHH
Q 012477 39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIG-ETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALF 117 (462)
Q Consensus 39 ~~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~-~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~ 117 (462)
.++.+.+||||+.+++|.|||++|++||+|++++.++++|- ...|++++|+|.+.|.+.+ ++..++
T Consensus 119 ~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~-------------v~~~i~ 185 (390)
T KOG2192|consen 119 LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKR-------------VVECIK 185 (390)
T ss_pred CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcch-------------HHHHHH
Confidence 46679999999999999999999999999999999999875 5788999999999999988 577888
Q ss_pred HHHHHHHHhhccC--------------------------------------------------------CC---------
Q 012477 118 KVHDRVIAEELRG--------------------------------------------------------DE--------- 132 (462)
Q Consensus 118 ~i~~~i~~~~~~~--------------------------------------------------------~~--------- 132 (462)
.+++.+.+..+.+ ++
T Consensus 186 ~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vd 265 (390)
T KOG2192|consen 186 IILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVD 265 (390)
T ss_pred HHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCcccccccc
Confidence 8877776632211 00
Q ss_pred ------------------------------------------CCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcC
Q 012477 133 ------------------------------------------DSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETG 170 (462)
Q Consensus 133 ------------------------------------------~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tg 170 (462)
.+-....++..+.||.++-|.||||+|+.|++|+.++|
T Consensus 266 Fs~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esG 345 (390)
T KOG2192|consen 266 FSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESG 345 (390)
T ss_pred ccccccCCCcCCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccC
Confidence 00123457899999999999999999999999999999
Q ss_pred ceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477 171 AQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD 214 (462)
Q Consensus 171 a~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~ 214 (462)
|.|.+... ..++.+|+++|+|+.++++.|..++...+++
T Consensus 346 A~Ikidep-----leGsedrIitItGTqdQIqnAQYLlQn~Vkq 384 (390)
T KOG2192|consen 346 ASIKIDEP-----LEGSEDRIITITGTQDQIQNAQYLLQNSVKQ 384 (390)
T ss_pred ceEEecCc-----CCCCCceEEEEeccHHHHhhHHHHHHHHHHh
Confidence 99999653 3368999999999999999999999888875
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=99.56 E-value=9.9e-15 Score=129.75 Aligned_cols=138 Identities=22% Similarity=0.214 Sum_probs=96.4
Q ss_pred EEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEE---EcCCcccccccCCCCcCCHHHHHHHHHHHHH
Q 012477 47 YLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTV---YSASDETNAFEDGDKFVSPAQDALFKVHDRV 123 (462)
Q Consensus 47 ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I---~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i 123 (462)
+.||.+.+|.|||++|++|+.|+++|||+|++.+. +..|.| +++++. +..|...+....
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~-------------i~kA~~~I~~i~ 63 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLA-------------VMKAREVVKAIG 63 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHH-------------HHHHHHHHHHHH
Confidence 56899999999999999999999999999999753 245777 444443 233333332211
Q ss_pred HHhhccCCCC-CCCCCceEEEEEEeC---------CceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEE
Q 012477 124 IAEELRGDED-SDGGHQVTAKLLVPS---------DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQ 193 (462)
Q Consensus 124 ~~~~~~~~~~-~~~~~~~~~~l~ip~---------~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~ 193 (462)
....+. +.. ...+......+-|+. ...|+|||++|++++.|++.|||+|.|.. ..|.
T Consensus 64 ~gf~~e-~A~~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------------~~v~ 130 (172)
T TIGR03665 64 RGFSPE-KALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------------KTVG 130 (172)
T ss_pred cCCCHH-HHHHhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------------CEEE
Confidence 100000 000 001111222234443 36899999999999999999999999842 5799
Q ss_pred EEcCHHHHHHHHHHHHHHHhcC
Q 012477 194 ISGEASVVKKALCQIASRLHDN 215 (462)
Q Consensus 194 I~G~~~~v~~A~~~I~~~l~~~ 215 (462)
|.|+++++..|...|.+++...
T Consensus 131 i~G~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 131 IIGDPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred EECCHHHHHHHHHHHHHHHcCC
Confidence 9999999999999999999664
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=99.56 E-value=1.4e-14 Score=128.87 Aligned_cols=138 Identities=21% Similarity=0.269 Sum_probs=91.9
Q ss_pred EeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEe--cCC-cccccccHHHHHHHhhcCccccccccc
Q 012477 288 LVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVS--SKE-FFEDTLSATIEAVVRLQPRCSEKIERD 364 (462)
Q Consensus 288 v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~--G~~-~~~~~~~~~~~a~~~~~~~~~~~~~~~ 364 (462)
+.||.+.+|.|||++|++|+.|+++||++|.+... +..|.|. +.+ .........+.++.+-++ .+....-
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~--~e~A~~l 74 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLAVMKAREVVKAIGRGFS--PEKALKL 74 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHHHHHHHHHHHHHHcCCC--HHHHHHh
Confidence 56899999999999999999999999999999973 2356662 221 111111111222211100 0000000
Q ss_pred CCCcceEEEEEecC---------CccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHH
Q 012477 365 SGLISFTTRLLVPT---------SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDAL 435 (462)
Q Consensus 365 ~~~~~~t~~i~Vp~---------~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~ 435 (462)
.+....-.-+.|+. ...|+|||++|++++.|+..|||+|.|.. +.|.|.|++++++.|.
T Consensus 75 ~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------------~~v~i~G~~~~~~~A~ 142 (172)
T TIGR03665 75 LDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------------KTVGIIGDPEQVQIAR 142 (172)
T ss_pred cCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------------CEEEEECCHHHHHHHH
Confidence 01111112233443 36899999999999999999999999941 5899999999999999
Q ss_pred HHHHHHHHh
Q 012477 436 IQVMTRLRA 444 (462)
Q Consensus 436 ~~I~~~l~~ 444 (462)
.+|...|+.
T Consensus 143 ~~i~~li~~ 151 (172)
T TIGR03665 143 EAIEMLIEG 151 (172)
T ss_pred HHHHHHHcC
Confidence 999887743
No 13
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.53 E-value=6.9e-14 Score=125.20 Aligned_cols=141 Identities=21% Similarity=0.270 Sum_probs=93.9
Q ss_pred eEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEe---cCC-cccccccHHHHHHHhhcCcccc
Q 012477 284 FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVS---SKE-FFEDTLSATIEAVVRLQPRCSE 359 (462)
Q Consensus 284 ~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~---G~~-~~~~~~~~~~~a~~~~~~~~~~ 359 (462)
+...+.||.+.++.|||++|++|+.|+++||++|.+... +..|.|. +.+ .........++++..-.+ .+
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~--~e 75 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLAVLKARDIVKAIGRGFS--PE 75 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCC--HH
Confidence 367899999999999999999999999999999999974 2455665 222 111111111222222100 00
Q ss_pred cccccCCCcceEEE-EEec---------CCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHH
Q 012477 360 KIERDSGLISFTTR-LLVP---------TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLD 429 (462)
Q Consensus 360 ~~~~~~~~~~~t~~-i~Vp---------~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~ 429 (462)
....-.+ ..+..+ +.|. ...+|.|||++|++++.|++.|||+|.|.. +.|.|.|+++
T Consensus 76 ~A~~l~g-d~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~------------~~v~i~G~~~ 142 (180)
T PRK13763 76 KALRLLD-DDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG------------KTVAIIGDPE 142 (180)
T ss_pred HHHHHhC-CCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC------------CEEEEEeCHH
Confidence 0000000 111111 1121 137899999999999999999999999942 3599999999
Q ss_pred HHHHHHHHHHHHHHh
Q 012477 430 LAKDALIQVMTRLRA 444 (462)
Q Consensus 430 ~v~~A~~~I~~~l~~ 444 (462)
+++.|...|...++.
T Consensus 143 ~~~~A~~~I~~li~g 157 (180)
T PRK13763 143 QVEIAREAIEMLIEG 157 (180)
T ss_pred HHHHHHHHHHHHHcC
Confidence 999999999887743
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.53 E-value=5.3e-14 Score=125.93 Aligned_cols=143 Identities=20% Similarity=0.174 Sum_probs=99.0
Q ss_pred ceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEE----cCCcccccccCCCCcCCHHHHHHH
Q 012477 42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVY----SASDETNAFEDGDKFVSPAQDALF 117 (462)
Q Consensus 42 ~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~----G~~e~~~~~~~~~~~v~~a~~a~~ 117 (462)
.+...+.||.+.++.|||++|++|+.|+++|||+|++.+. +..|.|. ++++. +.+|..
T Consensus 2 ~~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~-------------i~kA~~ 63 (180)
T PRK13763 2 MMMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLA-------------VLKARD 63 (180)
T ss_pred CceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHH-------------HHHHHH
Confidence 3567899999999999999999999999999999999754 2467775 44433 233333
Q ss_pred HHHHHHHHhhccCCCCCCCCCceEEEE-EEeC---------CceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCC
Q 012477 118 KVHDRVIAEELRGDEDSDGGHQVTAKL-LVPS---------DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALR 187 (462)
Q Consensus 118 ~i~~~i~~~~~~~~~~~~~~~~~~~~l-~ip~---------~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~ 187 (462)
.+...+..-.+. +........+...+ -+.. ..+|+|||++|++++.|++.|||+|.|..
T Consensus 64 ~I~ai~~gf~~e-~A~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~---------- 132 (180)
T PRK13763 64 IVKAIGRGFSPE-KALRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG---------- 132 (180)
T ss_pred HHHHHhcCCCHH-HHHHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC----------
Confidence 332211100000 00000011122221 1111 36899999999999999999999999853
Q ss_pred CCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 012477 188 SDELVQISGEASVVKKALCQIASRLHDN 215 (462)
Q Consensus 188 ~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 215 (462)
..|.|.|+++++..|...|.++++..
T Consensus 133 --~~v~i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 133 --KTVAIIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred --CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence 24999999999999999999999664
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=99.42 E-value=5.3e-13 Score=99.02 Aligned_cols=63 Identities=41% Similarity=0.627 Sum_probs=57.2
Q ss_pred EEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHH
Q 012477 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQV 438 (462)
Q Consensus 372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I 438 (462)
.+|.||...+|+|||++|++|++|+++|||+|++.+... .+.++|.|+|+|++++++.|+.||
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~----~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL----PGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC----CCCCceEEEEEeCHHHHHHHHHhh
Confidence 579999999999999999999999999999999976532 257789999999999999999987
No 16
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.36 E-value=1.6e-12 Score=139.48 Aligned_cols=305 Identities=21% Similarity=0.257 Sum_probs=199.7
Q ss_pred eEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHH-
Q 012477 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHD- 121 (462)
Q Consensus 43 ~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~- 121 (462)
+..++.+....+.++||++|.++..++.++.+.++|+..... .....+.|...++.- ...-.+.++.++-.
T Consensus 201 ~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~--~~~~~i~~~~~~~~~------~~~~i~~~~~~le~~ 272 (753)
T KOG2208|consen 201 VFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKS--SPSNKIDGRLNSSSS------INVEIQEALTRLESE 272 (753)
T ss_pred EEEEeeccccchhhhccccccccccccccceeEEEccccccc--chhhhhcccccccee------hhhhhHHHHHHhcCh
Confidence 667899999999999999999999999999999999864222 223344554333210 00001111111100
Q ss_pred ----------------------------HHHHhh-ccCC-C--------------------------CCCCCCceEEEEE
Q 012477 122 ----------------------------RVIAEE-LRGD-E--------------------------DSDGGHQVTAKLL 145 (462)
Q Consensus 122 ----------------------------~i~~~~-~~~~-~--------------------------~~~~~~~~~~~l~ 145 (462)
...... ...+ + ...........+-
T Consensus 273 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~ 352 (753)
T KOG2208|consen 273 FDYDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKRE 352 (753)
T ss_pred hhhhhhhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEe
Confidence 000000 0000 0 0012234778888
Q ss_pred EeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCccccccc
Q 012477 146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLAS 225 (462)
Q Consensus 146 ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~ 225 (462)
+...++..++||+|.++.+|++++.|.+.+... ++.+..+.++|...++.+|...+...+.+...
T Consensus 353 i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~-------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n-------- 417 (753)
T KOG2208|consen 353 IFPEELKFVIGKKGANIEKIREESQVKIDLPKQ-------GSNNKKVVITGVSANDEKAVEDVEKIIAEILN-------- 417 (753)
T ss_pred ecHHhhhhhcCCCCccHHHHHHhhhhceecccc-------cCCCCCeEEeccccchhHHHHHHHHHHHhhhc--------
Confidence 999999999999999999999999999999763 26688999999999999999999999887421
Q ss_pred ccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEeeeCCccccccccCChh
Q 012477 226 AISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAI 305 (462)
Q Consensus 226 ~~~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~v~ip~~~~g~IIGk~G~~ 305 (462)
+.....+.+|..++.+|||.+|..
T Consensus 418 --------------------------------------------------------~~~~~~~~iP~k~~~~iig~~g~~ 441 (753)
T KOG2208|consen 418 --------------------------------------------------------SIVKEEVQIPTKSHKRIIGTKGAL 441 (753)
T ss_pred --------------------------------------------------------ccccceeecCccchhhhhcccccc
Confidence 013446889999999999999999
Q ss_pred HHhHHhhhC-CeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccccccccCCCcceEEEEEecCCcccee
Q 012477 306 INQIRQESG-AAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCL 384 (462)
Q Consensus 306 Ik~I~~~sg-a~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~i~Vp~~~~g~I 384 (462)
|+.|+.+++ ..|++.+...... ..++.+.-... ..+..-...+. . ...........+.+...|..+.+..
T Consensus 442 i~~I~~k~~~v~i~f~~~~~~~~--~~~~~~~~~dv---~~~~~~~~~~~-~---~a~~~~~~~~~~~d~~~~~~~~~~~ 512 (753)
T KOG2208|consen 442 INYIMGKHGGVHIKFQNNNNSSD--MVTIRGISKDV---EKSVSLLKALK-A---DAKNLKFRDVVTKDKLLPVKYIGKE 512 (753)
T ss_pred HHHHHhhcCcEEEecCCCCcccc--cceEecccccc---chhHHHHHhhh-h---hhhcchhhhhhhccccchHHhhccc
Confidence 999999998 7777777654333 33444421110 01111011110 0 0001111234556677777777777
Q ss_pred ecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhh
Q 012477 385 IGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN 445 (462)
Q Consensus 385 IGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~ 445 (462)
+|+.|..++...+.....+ ....++..++|.|..+.|..|.+.+...++..
T Consensus 513 ~g~~~~i~d~~~~~~i~~~----------~~~~~~~~i~i~gk~~~v~~a~~~L~~~~~~~ 563 (753)
T KOG2208|consen 513 IGKNGTIRDSLGDKSIFPP----------NEDEDHEKITIEGKLELVLEAPAELKALIEAL 563 (753)
T ss_pred ccCceeeeccCCceeeccc----------ccccccceeeecccccchhhhHHHHHhcchhh
Confidence 7777776665555553322 23456678999999999999999998877666
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=99.35 E-value=2.3e-12 Score=95.56 Aligned_cols=64 Identities=50% Similarity=0.740 Sum_probs=58.1
Q ss_pred EEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHH
Q 012477 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI 208 (462)
Q Consensus 141 ~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I 208 (462)
+++|+||...+|+|||++|.+|++|+++|||+|.+.+... .+..+|+|+|+|+++++.+|+.+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~----~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL----PGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC----CCCCceEEEEEeCHHHHHHHHHhh
Confidence 3789999999999999999999999999999999987643 247899999999999999999987
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=99.34 E-value=1.7e-12 Score=95.54 Aligned_cols=61 Identities=21% Similarity=0.330 Sum_probs=54.7
Q ss_pred EEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHH
Q 012477 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVM 439 (462)
Q Consensus 372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~ 439 (462)
.++.||..++++|||++|++|++|+++|||+|.+++. .+.++.|+|+|++++|..|+.+|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~-------~~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDP-------GSKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCC-------CCCCCEEEEEcCHHHHHHHHHHhC
Confidence 5789999999999999999999999999999999643 245689999999999999998873
No 19
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.33 E-value=5.4e-12 Score=125.02 Aligned_cols=271 Identities=22% Similarity=0.285 Sum_probs=173.6
Q ss_pred CCceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHH
Q 012477 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKV 119 (462)
Q Consensus 40 ~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i 119 (462)
++++..++.||..++..+|||.|++|+.|++.++++|.+.+.. ..+++...+.|.+.. +.++..++-
T Consensus 65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p~~----------v~~a~a~~~-- 131 (608)
T KOG2279|consen 65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFPVQ----------VCKAKAAIH-- 131 (608)
T ss_pred hhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCCCC----------CChHHHHHH--
Confidence 5789999999999999999999999999999999999997542 334566666666554 344444433
Q ss_pred HHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHH
Q 012477 120 HDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEAS 199 (462)
Q Consensus 120 ~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~ 199 (462)
.++. ....+...+.+|...++.|+|++|++++.|+.-++|+|.+..+. . ....+...|.|...
T Consensus 132 -~~~~-----------~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ng--r---~g~~~~~~i~~qqk 194 (608)
T KOG2279|consen 132 -QILT-----------ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNG--R---LGLSRLIKISGQQK 194 (608)
T ss_pred -HHHh-----------cCCcccccccchhhhcccccccchhhhcchhccccccccccccc--c---cccccceecccccc
Confidence 3332 33567888999999999999999999999999999999986542 1 25688889999999
Q ss_pred HHHHHHHHHHHHHhcCCCCccccccc------------cc-CCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCC-C
Q 012477 200 VVKKALCQIASRLHDNPSRSQHLLAS------------AI-SNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTA-G 265 (462)
Q Consensus 200 ~v~~A~~~I~~~l~~~~~~~~~~~~~------------~~-~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~~~~~~~~-~ 265 (462)
-++.|..++.+.+.++...-...... .. ...+..++...+.-++.-...++|-.......+.++. .
T Consensus 195 ~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~ 274 (608)
T KOG2279|consen 195 EVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVV 274 (608)
T ss_pred hHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeE
Confidence 99999999999887753221110000 00 0011111111111111101111111111111111110 0
Q ss_pred CCCCCCCCCCCCCC---CCcceEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCc---eEEEEecCCcc
Q 012477 266 DWSRSLYSAPRDDL---SSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDD---CLITVSSKEFF 339 (462)
Q Consensus 266 ~~~~~~~~~p~~~~---~~~~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~---~~i~i~G~~~~ 339 (462)
-.....++.|.+++ .....-..|.+|+..+|.+||..|+++..+...+++.+.|......+.- .+..+.|+...
T Consensus 275 vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~v~~~qic~~egkqh~ 354 (608)
T KOG2279|consen 275 VSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSRVLQLQICVNEGKQHY 354 (608)
T ss_pred EecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEeccccchhhhhhhheecchhHH
Confidence 01112233333322 1223356789999999999999999999999999999999876544322 34556776543
Q ss_pred c
Q 012477 340 E 340 (462)
Q Consensus 340 ~ 340 (462)
.
T Consensus 355 ~ 355 (608)
T KOG2279|consen 355 E 355 (608)
T ss_pred H
Confidence 3
No 20
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.30 E-value=1e-11 Score=90.51 Aligned_cols=58 Identities=26% Similarity=0.342 Sum_probs=52.6
Q ss_pred eEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC-HHHHHHHHHHH
Q 012477 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD-LDLAKDALIQV 438 (462)
Q Consensus 370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~-~~~v~~A~~~I 438 (462)
.+..+.||.+++|+|||++|++|++|+++|||+|.|++ ++.|+|+|+ +++++.|+.+|
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 35679999999999999999999999999999999942 358999999 99999999887
No 21
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.29 E-value=2.2e-12 Score=94.26 Aligned_cols=60 Identities=35% Similarity=0.511 Sum_probs=54.1
Q ss_pred EEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHH
Q 012477 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQV 438 (462)
Q Consensus 371 t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I 438 (462)
|.+|.||.+++|+|||++|++|++|+++|||+|.++++ + +...|+|+|++++|+.|+.+|
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 67899999999999999999999999999999999642 2 345999999999999999886
No 22
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.26 E-value=3.3e-11 Score=129.50 Aligned_cols=316 Identities=16% Similarity=0.214 Sum_probs=184.6
Q ss_pred ceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHH
Q 012477 42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHD 121 (462)
Q Consensus 42 ~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~ 121 (462)
.+...+.+-..++..|+||+|.+|.+|++++.|.|.+... +..+..+.++|...++ .++.+.+..+..
T Consensus 346 n~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~~~----------~ka~~~v~~~~~ 413 (753)
T KOG2208|consen 346 NENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSAND----------EKAVEDVEKIIA 413 (753)
T ss_pred ceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccccch----------hHHHHHHHHHHH
Confidence 3667788889999999999999999999999999999874 5667789999998773 334555554443
Q ss_pred HHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcC-ceEEEecCCCCCC-----------------
Q 012477 122 RVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETG-AQIRILKDEHLPS----------------- 183 (462)
Q Consensus 122 ~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tg-a~I~i~~~~~~p~----------------- 183 (462)
.+.. +.....+.+|...+.++||.+|..|..|.++++ ..|++........
T Consensus 414 ei~n------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~~~~~~~~~~~~~~dv~~~~~~ 481 (753)
T KOG2208|consen 414 EILN------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNNNSSDMVTIRGISKDVEKSVSL 481 (753)
T ss_pred hhhc------------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCCcccccceEeccccccchhHHH
Confidence 3321 145677999999999999999999999999999 5665543211100
Q ss_pred --------------------------------------------------cCCCCCceEEEEcCHHHHHHHHHHHHHHHh
Q 012477 184 --------------------------------------------------CALRSDELVQISGEASVVKKALCQIASRLH 213 (462)
Q Consensus 184 --------------------------------------------------~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~ 213 (462)
-.......++|.|..+.|..|...+...+.
T Consensus 482 ~~~~~~~a~~~~~~~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~~~i~~~~~~~~~~~i~i~gk~~~v~~a~~~L~~~~~ 561 (753)
T KOG2208|consen 482 LKALKADAKNLKFRDVVTKDKLLPVKYIGKEIGKNGTIRDSLGDKSIFPPNEDEDHEKITIEGKLELVLEAPAELKALIE 561 (753)
T ss_pred HHhhhhhhhcchhhhhhhccccchHHhhcccccCceeeeccCCceeecccccccccceeeecccccchhhhHHHHHhcch
Confidence 000111133444444444444444433333
Q ss_pred cCCCCcccccccccCCCCCCC--CCCCCCCCC-----CC-CcCCCCCCCCCCCCCCCCC-CCCC--CCCCCC---C---C
Q 012477 214 DNPSRSQHLLASAISNSHSSS--GSLVGPTAA-----TP-IVGIAPLMGPYGGYKGDTA-GDWS--RSLYSA---P---R 276 (462)
Q Consensus 214 ~~~~~~~~~~~~~~~~~~~~~--g~~~~p~~~-----~~-~~~~~p~~~~~~~~~~~~~-~~~~--~~~~~~---p---~ 276 (462)
........ . ..++.+ -.+....+. .. ..+. ..++.....+.. ..|. ...+.. . .
T Consensus 562 ~~~~~~~~-~-----v~~~~~~~~~~l~~~~~~~~~~~e~~~gv---~~~fp~~~~~~~e~~i~g~~~~v~aa~~~~~~i 632 (753)
T KOG2208|consen 562 ALIKATLL-E-----VNNPPGQHRPFLIGKGIENRTYVEVFGGV---VVPFPRSPTSSDEVSIKGAKDEVKAAKGRLEEI 632 (753)
T ss_pred hhhhhhhh-h-----ccCcchheeeeeeccccccccceeecCcc---cccCCCCCCchhhhccchhHHHHHHhhccchhh
Confidence 32110000 0 000000 000000000 00 0000 000000000000 0000 000000 0 0
Q ss_pred CCCCCcceEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCc
Q 012477 277 DDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPR 356 (462)
Q Consensus 277 ~~~~~~~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~ 356 (462)
........+..+.+|..++..+.|.+|..+++++..++..+.++..........+.+.|.. .... .
T Consensus 633 ~~~~~~~~~~~~~i~~~~~~~~~~~~g~~~~~~t~~~~~~~~~~~~~~~~s~~~~~~~~~~--------~~~e---~--- 698 (753)
T KOG2208|consen 633 VEYLSAYATTNTKIPDKFHRSIVGYRGHIIEEITSKFGVGGYFGDAPTEGSVNTIHVSGEK--------MQSE---I--- 698 (753)
T ss_pred hhhcccccceeeecccccceeeecCCCcccccceeecCccceeCCCCCccccCcchhhhhh--------hhhh---h---
Confidence 0122444566799999999999999999999999999999999986543222112222210 0000 0
Q ss_pred ccccccccCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEec
Q 012477 357 CSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP 407 (462)
Q Consensus 357 ~~~~~~~~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~ 407 (462)
..........++.++.+|..+|+.+||++|++++.+..++++.+.+.+
T Consensus 699 ---~~~~~~~~~~~~~~~~~p~~~~~~~ig~~g~~~r~~~~~~~~~~~~~~ 746 (753)
T KOG2208|consen 699 ---AKIALEAKNLVTKEIEIPRSLHRYLIGPKGSNLRQLEKEFNVNIVVPN 746 (753)
T ss_pred ---cccccccccceeeEEeccHHHhhhccCCCCccHHHHHHHhccceecCC
Confidence 001112234688999999999999999999999999999999999854
No 23
>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=99.22 E-value=4.4e-11 Score=88.49 Aligned_cols=62 Identities=37% Similarity=0.600 Sum_probs=55.4
Q ss_pred EEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHH
Q 012477 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQV 438 (462)
Q Consensus 372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I 438 (462)
.++.||.+++++|||++|++|++|++.|||+|.|.+.. .+.+++.|+|.|+.++++.|+.+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~-----~~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSG-----SGSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCC-----CCCCceEEEEEcCHHHHHHHHHHh
Confidence 57899999999999999999999999999999997542 135678999999999999999886
No 24
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.20 E-value=2.6e-11 Score=120.26 Aligned_cols=229 Identities=22% Similarity=0.327 Sum_probs=167.6
Q ss_pred CCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcCC
Q 012477 137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNP 216 (462)
Q Consensus 137 ~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~ 216 (462)
...+.+.++|+...+..++|++|++|+.|+..+++||.+-.+ +. ..++...+.|.+.++-.|...+..++.++.
T Consensus 65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~e-d~-----g~e~~~~~~~~p~~v~~a~a~~~~~~~~~~ 138 (608)
T KOG2279|consen 65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTE-DV-----GDERVLLISGFPVQVCKAKAAIHQILTENT 138 (608)
T ss_pred hhheeeeEeecccceeeeeccccCCcchhhcccccceecCcc-cC-----CcccchhhccCCCCCChHHHHHHHHHhcCC
Confidence 356789999999999999999999999999999999998655 32 346667777799999999999999988742
Q ss_pred CCcccccccccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEeeeCCccc
Q 012477 217 SRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIG 296 (462)
Q Consensus 217 ~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~v~ip~~~~g 296 (462)
.+.....+|...++
T Consensus 139 ------------------------------------------------------------------pvk~~lsvpqr~~~ 152 (608)
T KOG2279|consen 139 ------------------------------------------------------------------PVSEQLSVPQRSVG 152 (608)
T ss_pred ------------------------------------------------------------------cccccccchhhhcc
Confidence 24667789999999
Q ss_pred cccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHH-------HHHHHhhcCccc-----------
Q 012477 297 GVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSAT-------IEAVVRLQPRCS----------- 358 (462)
Q Consensus 297 ~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~-------~~a~~~~~~~~~----------- 358 (462)
+|+|++|++++.|+.-++++|.+..+......+.+.|.+........... -+...+-.++..
T Consensus 153 ~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n 232 (608)
T KOG2279|consen 153 RIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPIN 232 (608)
T ss_pred cccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCcc
Confidence 99999999999999999999999998666666777777643211100000 000000000000
Q ss_pred ---c------------------cccc-------------------------------cCCCcceEEEEEecCCccceeec
Q 012477 359 ---E------------------KIER-------------------------------DSGLISFTTRLLVPTSRIGCLIG 386 (462)
Q Consensus 359 ---~------------------~~~~-------------------------------~~~~~~~t~~i~Vp~~~~g~IIG 386 (462)
+ .+.. ........-+|.+|.-.+|.+||
T Consensus 233 ~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig 312 (608)
T KOG2279|consen 233 VRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIG 312 (608)
T ss_pred ccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCcccccchhh
Confidence 0 0000 01123455678999999999999
Q ss_pred CCCchHHHHHHhhCceEEEecCCCCCCCCC-CCCceEEEEcCHHHHHHHHHHHHH
Q 012477 387 KGGSIITEMRRLTKANIRILPKENLPKIAS-EDDEMVQISGDLDLAKDALIQVMT 440 (462)
Q Consensus 387 k~G~~I~~I~~~sga~I~i~~~~~~P~~~~-~~~~~v~I~G~~~~v~~A~~~I~~ 440 (462)
+.|+.+..+...|++.+.|..- |-... -...++.+.|+..-+.+|..|+..
T Consensus 313 ~~gey~s~yssasn~~~hi~t~---pyt~~v~~~qic~~egkqh~~n~vl~ml~~ 364 (608)
T KOG2279|consen 313 HAGEYLSVYSSASNHPNHIWTQ---PYTSRVLQLQICVNEGKQHYENSVLEMLTV 364 (608)
T ss_pred hhhhhhhhhhhccCccceEEec---cccchhhhhhhheecchhHHHHHHHhhhhc
Confidence 9999999999999999888653 32110 112568899999999999999983
No 25
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.16 E-value=3.8e-11 Score=87.65 Aligned_cols=60 Identities=40% Similarity=0.613 Sum_probs=54.2
Q ss_pred EEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHH
Q 012477 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI 208 (462)
Q Consensus 141 ~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I 208 (462)
|.+|.||.+++++|||++|++|++|+++|||+|.|+.+ .....|+|+|++++|.+|+.+|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~--------~~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD--------DERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--------TEEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--------CCcEEEEEEeCHHHHHHHHhhC
Confidence 57899999999999999999999999999999999764 1245999999999999999876
No 26
>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=99.14 E-value=6.8e-11 Score=86.90 Aligned_cols=60 Identities=28% Similarity=0.441 Sum_probs=55.0
Q ss_pred EEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHH
Q 012477 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI 208 (462)
Q Consensus 142 ~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I 208 (462)
..|.||..++++|||++|++|++|+++|||+|.|+..+ +.++.|+|+|+.++|..|..+|
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-------~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-------SKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-------CCCCEEEEEcCHHHHHHHHHHh
Confidence 57899999999999999999999999999999997753 4688999999999999999876
No 27
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.11 E-value=3.1e-10 Score=82.74 Aligned_cols=58 Identities=34% Similarity=0.488 Sum_probs=52.5
Q ss_pred eEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcC-HHHHHHHHHHH
Q 012477 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGE-ASVVKKALCQI 208 (462)
Q Consensus 140 ~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I 208 (462)
....+.||.+++++|||++|++|+.|+++|||+|.+.. ++.|.|+|+ ++++..|..+|
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 35678999999999999999999999999999999854 457999998 99999999886
No 28
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.05 E-value=7e-10 Score=82.01 Aligned_cols=62 Identities=40% Similarity=0.657 Sum_probs=55.9
Q ss_pred EEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHH
Q 012477 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI 208 (462)
Q Consensus 142 ~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I 208 (462)
.++.||..++++|||++|++|++|+++|||+|.|..... ...++.|.|.|+.+++..|..+|
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 579999999999999999999999999999999987532 25789999999999999998876
No 29
>PF13014 KH_3: KH domain
Probab=98.99 E-value=9.1e-10 Score=74.34 Aligned_cols=42 Identities=48% Similarity=0.794 Sum_probs=39.0
Q ss_pred ccceeecCCchHHHHHHHHhCCeEEEcC-CCCCCCceEEEEEc
Q 012477 53 KIGSIIGRGGEIVKQLRIDTKSKIRIGE-TVPGSEERVVTVYS 94 (462)
Q Consensus 53 ~~g~IIGk~G~~Ik~i~~~tg~~I~v~~-~~~~~~ervi~I~G 94 (462)
+||+|||++|++|++|+++|+|+|+|++ ..++..++.|+|+|
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 66788899999997
No 30
>smart00322 KH K homology RNA-binding domain.
Probab=98.98 E-value=3.3e-09 Score=79.10 Aligned_cols=67 Identities=28% Similarity=0.519 Sum_probs=59.2
Q ss_pred ceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 012477 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRL 442 (462)
Q Consensus 369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l 442 (462)
..+.++.||..+++++||++|++|++|++.||++|.+... ..+...|+|.|+.++++.|..+|.+.+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~-------~~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPED-------GSEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCC-------CCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 3578899999999999999999999999999999999532 125678999999999999999998876
No 31
>PF13014 KH_3: KH domain
Probab=98.97 E-value=1.1e-09 Score=73.99 Aligned_cols=43 Identities=47% Similarity=0.741 Sum_probs=37.4
Q ss_pred ccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc
Q 012477 380 RIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG 426 (462)
Q Consensus 380 ~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G 426 (462)
+||+|||++|++|++|+++|||+|+|++ +. ..+.+++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~-~~---~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP-EN---EPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC-cc---CCCCCceEEEEEC
Confidence 5899999999999999999999999987 22 2357889999998
No 32
>smart00322 KH K homology RNA-binding domain.
Probab=98.76 E-value=5.2e-08 Score=72.55 Aligned_cols=67 Identities=39% Similarity=0.655 Sum_probs=59.6
Q ss_pred ceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 012477 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRL 212 (462)
Q Consensus 139 ~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l 212 (462)
..+.++.||...++.+||++|.+|++|++.||++|.+.... .....+.|.|+.+++..|..+|.+.+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------SEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 35788999999999999999999999999999999986541 25789999999999999999998876
No 33
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.65 E-value=1.1e-07 Score=83.82 Aligned_cols=141 Identities=23% Similarity=0.308 Sum_probs=93.5
Q ss_pred eEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCccccccc-----HHHHHHHhhcC-cc
Q 012477 284 FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLS-----ATIEAVVRLQP-RC 357 (462)
Q Consensus 284 ~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~-----~~~~a~~~~~~-~~ 357 (462)
.+..+.||..-.+.+||+.|+.-+.|.+.+++++.++.. +..|+|...+...+.+. ..+.|+-+-++ ..
T Consensus 8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~-----~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~ 82 (194)
T COG1094 8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEK 82 (194)
T ss_pred ceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHH
Confidence 366799999999999999999999999999999999874 34566665432222211 11111111110 00
Q ss_pred cccccccCCCcceEEEEEe------c----CCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC
Q 012477 358 SEKIERDSGLISFTTRLLV------P----TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD 427 (462)
Q Consensus 358 ~~~~~~~~~~~~~t~~i~V------p----~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~ 427 (462)
.-.+-.+ ...-..+.+ + ....|+|||++|.+-+-|++.|||+|.|.. .+|.|.|.
T Consensus 83 A~~LL~d---~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g------------~tVaiiG~ 147 (194)
T COG1094 83 ALKLLED---DYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG------------KTVAIIGG 147 (194)
T ss_pred HHHHhcC---CcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC------------cEEEEecC
Confidence 0000000 000001111 1 224599999999999999999999999953 38999999
Q ss_pred HHHHHHHHHHHHHHHHh
Q 012477 428 LDLAKDALIQVMTRLRA 444 (462)
Q Consensus 428 ~~~v~~A~~~I~~~l~~ 444 (462)
+++|+.|...|...|+.
T Consensus 148 ~~~v~iAr~AVemli~G 164 (194)
T COG1094 148 FEQVEIAREAVEMLING 164 (194)
T ss_pred hhhhHHHHHHHHHHHcC
Confidence 99999999998776643
No 34
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.63 E-value=8.9e-07 Score=78.18 Aligned_cols=149 Identities=21% Similarity=0.282 Sum_probs=99.2
Q ss_pred CceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHH
Q 012477 41 EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVH 120 (462)
Q Consensus 41 ~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~ 120 (462)
......+.||.+..+.+||+.|+..+.|.+.+++++.++.. +..|.|......-+. -.+-+|.+-+..+
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~-----~~~V~i~~~~~t~Dp-----~~~~ka~d~VkAI- 74 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTEDP-----LALLKARDVVKAI- 74 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCCh-----HHHHHHHHHHHHH-
Confidence 45567799999999999999999999999999999999643 456788776221110 0011122211111
Q ss_pred HHHHHhhccCCCCC-CCCCceEEE-E----EEe--C----CceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCC
Q 012477 121 DRVIAEELRGDEDS-DGGHQVTAK-L----LVP--S----DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRS 188 (462)
Q Consensus 121 ~~i~~~~~~~~~~~-~~~~~~~~~-l----~ip--~----~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~ 188 (462)
..++..+.+. -....+.+. + ++. . ...|+|||++|.+-+.|++-|+|.|.|..+
T Consensus 75 ----grGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~---------- 140 (194)
T COG1094 75 ----GRGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGK---------- 140 (194)
T ss_pred ----hcCCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCc----------
Confidence 1111100000 000111111 1 111 1 235999999999999999999999999654
Q ss_pred CceEEEEcCHHHHHHHHHHHHHHHhcCC
Q 012477 189 DELVQISGEASVVKKALCQIASRLHDNP 216 (462)
Q Consensus 189 ~r~v~I~G~~~~v~~A~~~I~~~l~~~~ 216 (462)
.|.|-|.+++|..|...|..++...+
T Consensus 141 --tVaiiG~~~~v~iAr~AVemli~G~~ 166 (194)
T COG1094 141 --TVAIIGGFEQVEIAREAVEMLINGAP 166 (194)
T ss_pred --EEEEecChhhhHHHHHHHHHHHcCCC
Confidence 79999999999999999999998753
No 35
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.53 E-value=3.3e-07 Score=76.04 Aligned_cols=67 Identities=21% Similarity=0.308 Sum_probs=51.8
Q ss_pred CCccceeecCCCchHHHHHHhhCceEEEecCCCCC-----------CCC-CCCCceEEEEcCH---HHHHHHHHHHHHHH
Q 012477 378 TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLP-----------KIA-SEDDEMVQISGDL---DLAKDALIQVMTRL 442 (462)
Q Consensus 378 ~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P-----------~~~-~~~~~~v~I~G~~---~~v~~A~~~I~~~l 442 (462)
.+++|.|||++|++||+|+++|||+|.|..+...- ... .++.-.|.|+++. ++++.|+.+|...|
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 56889999999999999999999999997653210 000 1223579999964 99999999999877
Q ss_pred Hh
Q 012477 443 RA 444 (462)
Q Consensus 443 ~~ 444 (462)
..
T Consensus 94 ~~ 95 (120)
T cd02395 94 KP 95 (120)
T ss_pred cc
Confidence 63
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=98.16 E-value=6.9e-06 Score=68.22 Aligned_cols=67 Identities=25% Similarity=0.391 Sum_probs=52.3
Q ss_pred CceeeeecCCchHHHHHHhhcCceEEEecCCCCCC------------cCCCCCceEEEEcCH---HHHHHHHHHHHHHHh
Q 012477 149 DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPS------------CALRSDELVQISGEA---SVVKKALCQIASRLH 213 (462)
Q Consensus 149 ~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~------------~~~~~~r~v~I~G~~---~~v~~A~~~I~~~l~ 213 (462)
+++|.|||++|.++|.|+++|||+|.|..+..... ......-.|.|++.. +++.+|..+|..++.
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 57899999999999999999999999976521100 001233578999964 999999999999998
Q ss_pred cC
Q 012477 214 DN 215 (462)
Q Consensus 214 ~~ 215 (462)
..
T Consensus 95 ~~ 96 (120)
T cd02395 95 PA 96 (120)
T ss_pred cC
Confidence 64
No 37
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.02 E-value=1.9e-05 Score=83.85 Aligned_cols=96 Identities=25% Similarity=0.327 Sum_probs=78.1
Q ss_pred CcCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCC
Q 012477 107 KFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCAL 186 (462)
Q Consensus 107 ~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 186 (462)
+++..|.+++.++++.+.+....+ .+.....+....+.||.+.++.|||++|.+||.|.++|||+|.+..
T Consensus 546 ~aL~~A~~g~~~Il~~m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d--------- 615 (719)
T TIGR02696 546 SALKQARDARLAILDVMAEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED--------- 615 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---------
Confidence 456678888888888765544333 3344556778899999999999999999999999999999999843
Q ss_pred CCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 012477 187 RSDELVQISG-EASVVKKALCQIASRLHD 214 (462)
Q Consensus 187 ~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 214 (462)
+..|.|.+ ..+++.+|+.+|..++..
T Consensus 616 --~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 616 --DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred --CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 56899988 489999999999998885
No 38
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.01 E-value=2.8e-05 Score=66.56 Aligned_cols=103 Identities=21% Similarity=0.309 Sum_probs=71.4
Q ss_pred eEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccccccc
Q 012477 284 FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIER 363 (462)
Q Consensus 284 ~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~ 363 (462)
-.+.+.|+...+|..||++|++|+.|++..|-+|.+-.-+.+. ..-+..++ .|.-.....-
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~d~-----------------~~fI~n~l--~Pa~V~~v~I 92 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDDP-----------------EEFIKNIF--APAAVRSVTI 92 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCCCH-----------------HHHHHHHc--CCCEEEEEEE
Confidence 3778899999999999999999999999999888776632221 00111111 1111000000
Q ss_pred cCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEE
Q 012477 364 DSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405 (462)
Q Consensus 364 ~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i 405 (462)
..........+.|+....|..|||+|++|+.++..+|-.+.|
T Consensus 93 ~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 93 KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 001123456788999999999999999999999999998877
No 39
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.96 E-value=1.1e-05 Score=69.00 Aligned_cols=102 Identities=19% Similarity=0.277 Sum_probs=68.2
Q ss_pred EEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHH
Q 012477 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRV 123 (462)
Q Consensus 44 ~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i 123 (462)
.+.++|+...+|..||++|++|+.|++..|-+|.|-+ .+-.+ ..-+..++.-.
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve-----------~s~d~----------------~~fI~n~l~Pa 85 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE-----------YSDDP----------------EEFIKNIFAPA 85 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE-----------cCCCH----------------HHHHHHHcCCC
Confidence 4567889999999999999999999999988887532 11111 11111111100
Q ss_pred HHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEE
Q 012477 124 IAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRI 175 (462)
Q Consensus 124 ~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i 175 (462)
.-.++. -........+.+.|+....|.+|||+|.+++.++.-++-.+.+
T Consensus 86 ~V~~v~---I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 86 AVRSVT---IKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred EEEEEE---EEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 000000 0011223466778999999999999999999999999988766
No 40
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.87 E-value=2.6e-05 Score=72.89 Aligned_cols=140 Identities=21% Similarity=0.347 Sum_probs=99.7
Q ss_pred CceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCC
Q 012477 138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPS 217 (462)
Q Consensus 138 ~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~ 217 (462)
..++..+.||..+++.+.|++|.+||.|+.+|...|.-+.... +-++.++|..+.|..|++.|...-+..-
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~e--------ePiF~vTg~~edv~~aRrei~saaeH~~- 94 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGE--------EPIFPVTGRHEDVRRARREIPSAAEHFG- 94 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCCC--------CCcceeccCchhHHHHhhcCccccceee-
Confidence 6788889999999999999999999999999999998766543 3478899999999999988754322210
Q ss_pred CcccccccccCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEeeeCCcccc
Q 012477 218 RSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGG 297 (462)
Q Consensus 218 ~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~v~ip~~~~g~ 297 (462)
+.. + ..++.+.. .. |+ .+.+.+..+.+|...+|.
T Consensus 95 ----l~~------~---------------------s~s~Sgg~----~~-----~s------~s~qt~sy~svP~rvvgl 128 (394)
T KOG2113|consen 95 ----LIR------A---------------------SRSFSGGT----NG-----AS------ASGQTTSYVSVPLRVVGL 128 (394)
T ss_pred ----eee------e---------------------cccccCCC----cc-----cc------ccCCCceeeeccceeeee
Confidence 000 0 00000000 00 00 123346678899999999
Q ss_pred ccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEec
Q 012477 298 VIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSS 335 (462)
Q Consensus 298 IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G 335 (462)
+.|..|.+|+.|++.+...|.-+-.. .+.++.++|
T Consensus 129 vv~~~~~ti~~iqq~tnt~I~T~v~~---~~~Vf~Vtg 163 (394)
T KOG2113|consen 129 VVGPKGATIKRIQQFTNTYIATPVRC---GEPVFCVTG 163 (394)
T ss_pred ccccccCccchheecccceEeeeccC---CCceEEEec
Confidence 99999999999999999988776644 334555555
No 41
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.85 E-value=1.5e-05 Score=74.40 Aligned_cols=136 Identities=18% Similarity=0.311 Sum_probs=98.0
Q ss_pred cceEEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccc--
Q 012477 282 KEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSE-- 359 (462)
Q Consensus 282 ~~~~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~-- 359 (462)
..++..+.+|..+++.|.|++|.+||.|+.+|.+.|+-+... .+.++.++|... ..+.+.+..+...+
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~---eePiF~vTg~~e-------dv~~aRrei~saaeH~ 93 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG---EEPIFPVTGRHE-------DVRRARREIPSAAEHF 93 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC---CCCcceeccCch-------hHHHHhhcCcccccee
Confidence 456788899999999999999999999999999999877643 446777888532 11122211111000
Q ss_pred ----ccc------ccC-CCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCH
Q 012477 360 ----KIE------RDS-GLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDL 428 (462)
Q Consensus 360 ----~~~------~~~-~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~ 428 (462)
++. ... ...+.+..+.+|-..+|.|.|..|.+|+.|++.+...|.-.-+ ..+.++-++|.+
T Consensus 94 ~l~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~--------~~~~Vf~Vtg~~ 165 (394)
T KOG2113|consen 94 GLIRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR--------CGEPVFCVTGAP 165 (394)
T ss_pred eeeeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc--------CCCceEEEecCC
Confidence 000 000 1246778899999999999999999999999999999876432 345689999998
Q ss_pred HH-HHHHH
Q 012477 429 DL-AKDAL 435 (462)
Q Consensus 429 ~~-v~~A~ 435 (462)
.+ +++|.
T Consensus 166 ~nC~kra~ 173 (394)
T KOG2113|consen 166 KNCVKRAR 173 (394)
T ss_pred cchhhhcc
Confidence 88 55554
No 42
>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=97.68 E-value=8.7e-05 Score=80.15 Aligned_cols=96 Identities=21% Similarity=0.295 Sum_probs=73.1
Q ss_pred cCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCC
Q 012477 108 FVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALR 187 (462)
Q Consensus 108 ~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~ 187 (462)
.+..|.++..+|++.+.+.............+....+.||.+.++.|||++|.+||.|+++|||+|.|..
T Consensus 519 al~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d---------- 588 (684)
T TIGR03591 519 ALEQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED---------- 588 (684)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec----------
Confidence 4455677777777765543333333334455678889999999999999999999999999999999954
Q ss_pred CCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 012477 188 SDELVQISG-EASVVKKALCQIASRLHD 214 (462)
Q Consensus 188 ~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 214 (462)
+..|.|.+ ..+.+.+|..+|..+...
T Consensus 589 -dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 589 -DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred -CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 45677776 588889999999888653
No 43
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=97.64 E-value=0.00018 Score=61.41 Aligned_cols=103 Identities=23% Similarity=0.283 Sum_probs=70.9
Q ss_pred EEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCccccccccc
Q 012477 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERD 364 (462)
Q Consensus 285 ~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~ 364 (462)
.+-|.|....+|..||++|++|+.|++..|-+|.+-.-+++. . .-+..+ +.|.-.....-.
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~D~-------------~----~fI~N~--l~PA~V~~V~i~ 94 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSENL-------------E----EFVANK--LAPAEVKNVTVS 94 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCCH-------------H----HHHHHc--CCCceEEEEEEE
Confidence 677889999999999999999999988888888776632221 0 000111 111111111000
Q ss_pred CCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEe
Q 012477 365 SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRIL 406 (462)
Q Consensus 365 ~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~ 406 (462)
.........+.||.+..+..|||+|++|+..++.+|-++.|.
T Consensus 95 ~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 95 EFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred cCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 011235677889999999999999999999999999988773
No 44
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.62 E-value=0.0005 Score=68.52 Aligned_cols=77 Identities=22% Similarity=0.342 Sum_probs=58.3
Q ss_pred ceEEEEEec------CCccceeecCCCchHHHHHHhhCceEEEecCCCC----------CCCC-CCCCceEEEEcC-HHH
Q 012477 369 SFTTRLLVP------TSRIGCLIGKGGSIITEMRRLTKANIRILPKENL----------PKIA-SEDDEMVQISGD-LDL 430 (462)
Q Consensus 369 ~~t~~i~Vp------~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~----------P~~~-~~~~~~v~I~G~-~~~ 430 (462)
.++.+|.|| .+++|.|||..|.|.|+|+++|||+|.|-.+... .... ..++=-+.|+++ .|.
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 567788888 6789999999999999999999999999752211 0001 112234778876 588
Q ss_pred HHHHHHHHHHHHHhh
Q 012477 431 AKDALIQVMTRLRAN 445 (462)
Q Consensus 431 v~~A~~~I~~~l~~~ 445 (462)
|++|+.+|...|++-
T Consensus 217 i~~Ai~vienli~~a 231 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSA 231 (554)
T ss_pred HHHHHHHHHHHHHhh
Confidence 999999999998863
No 45
>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=97.59 E-value=0.00014 Score=77.46 Aligned_cols=65 Identities=25% Similarity=0.287 Sum_probs=57.3
Q ss_pred ceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC-HHHHHHHHHHHHHHHHh
Q 012477 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD-LDLAKDALIQVMTRLRA 444 (462)
Q Consensus 369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~l~~ 444 (462)
.....+.||.+.+|.|||+||.+||.|.++|||+|.|.+ +..|.|.+. .+.+++|+.+|...+..
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 456789999999999999999999999999999999942 468999984 79999999999887774
No 46
>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=97.57 E-value=0.00011 Score=62.58 Aligned_cols=102 Identities=22% Similarity=0.273 Sum_probs=68.0
Q ss_pred EEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHH
Q 012477 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRV 123 (462)
Q Consensus 44 ~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i 123 (462)
.+-++|....+|..||++|++|+.|++..|-+|.|- ..+..+++. +.++ +
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVV-----------eys~D~~~f------------I~N~-------l 83 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELI-----------EYSENLEEF------------VANK-------L 83 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEE-----------EcCCCHHHH------------HHHc-------C
Confidence 566789999999999999999999988888888752 222222110 0000 0
Q ss_pred HHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEE
Q 012477 124 IAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRI 175 (462)
Q Consensus 124 ~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i 175 (462)
.--......-..........+.||....+..|||+|.+++....-++-.+.+
T Consensus 84 ~PA~V~~V~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI 135 (141)
T TIGR01952 84 APAEVKNVTVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI 135 (141)
T ss_pred CCceEEEEEEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence 0000000000011233567788999999999999999999999999888766
No 47
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.53 E-value=0.00012 Score=71.55 Aligned_cols=64 Identities=28% Similarity=0.467 Sum_probs=52.1
Q ss_pred CCCCCcccCCCceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCc
Q 012477 31 DDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASD 97 (462)
Q Consensus 31 ~~~~~~~~~~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e 97 (462)
+.+...+...+++.+++.+-++++|.|||++|++|++|+..|+++|++.+. ..+-.|+|.|...
T Consensus 35 ~~~~~~aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~~ 98 (629)
T KOG0336|consen 35 DSRDSAAAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGINH 98 (629)
T ss_pred CCCcccccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechHH
Confidence 333444556778999999999999999999999999999999999999754 2355688888743
No 48
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.51 E-value=0.00015 Score=75.61 Aligned_cols=99 Identities=23% Similarity=0.256 Sum_probs=78.6
Q ss_pred CCCcCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCc
Q 012477 105 GDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSC 184 (462)
Q Consensus 105 ~~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~ 184 (462)
+..++.+|..+..+++..+.+..-..+.......+-...+.|+...+..+||++|.+|++|.++|||+|++..
T Consensus 517 m~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied------- 589 (692)
T COG1185 517 MKKALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED------- 589 (692)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC-------
Confidence 3345667888888888876554333333444556667889999999999999999999999999999999952
Q ss_pred CCCCCceEEEEcC-HHHHHHHHHHHHHHHhc
Q 012477 185 ALRSDELVQISGE-ASVVKKALCQIASRLHD 214 (462)
Q Consensus 185 ~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~ 214 (462)
+..|.|.++ .+.+.+|+..|..+.++
T Consensus 590 ----dGtv~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 590 ----DGTVKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred ----CCcEEEEecchHHHHHHHHHHHHHHhh
Confidence 557999987 48889999999999966
No 49
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.46 E-value=0.00095 Score=66.56 Aligned_cols=77 Identities=25% Similarity=0.381 Sum_probs=58.5
Q ss_pred CceEEEEEEeC------CceeeeecCCchHHHHHHhhcCceEEEecCCC----------CCCcC-CCCCceEEEEcC-HH
Q 012477 138 HQVTAKLLVPS------DQIGCVIGKGGQIVQNIRSETGAQIRILKDEH----------LPSCA-LRSDELVQISGE-AS 199 (462)
Q Consensus 138 ~~~~~~l~ip~------~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~----------~p~~~-~~~~r~v~I~G~-~~ 199 (462)
..++.++.||. +++|+|||.+|.|.|+|+++|||||.|-.+.. +.... ...+=-|.|++. -+
T Consensus 136 ~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~e 215 (554)
T KOG0119|consen 136 AKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQE 215 (554)
T ss_pred cccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHH
Confidence 36778888886 58899999999999999999999999976211 11111 122335778875 78
Q ss_pred HHHHHHHHHHHHHhc
Q 012477 200 VVKKALCQIASRLHD 214 (462)
Q Consensus 200 ~v~~A~~~I~~~l~~ 214 (462)
.|.+|+..|..+|.+
T Consensus 216 ki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 216 KIKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHHh
Confidence 899999999999986
No 50
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.40 E-value=0.00021 Score=77.81 Aligned_cols=98 Identities=20% Similarity=0.249 Sum_probs=78.7
Q ss_pred CCcCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCce-EEEecCCCCCCc
Q 012477 106 DKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQ-IRILKDEHLPSC 184 (462)
Q Consensus 106 ~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~-I~i~~~~~~p~~ 184 (462)
.+++..|.+++.++++.+.+....+........+....+.||.+.++.|||.+|.+||.|.++||++ |.+.
T Consensus 651 ~eAL~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~-------- 722 (891)
T PLN00207 651 ERALLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ-------- 722 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC--------
Confidence 3456678888888888766544444444455667889999999999999999999999999999999 8763
Q ss_pred CCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 012477 185 ALRSDELVQISG-EASVVKKALCQIASRLHD 214 (462)
Q Consensus 185 ~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 214 (462)
.+..|.|.+ ..+.+.+|+.+|..++.+
T Consensus 723 ---ddg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 723 ---DDGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred ---CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 256788888 589999999999998874
No 51
>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=97.14 E-value=0.00061 Score=73.69 Aligned_cols=65 Identities=26% Similarity=0.326 Sum_probs=55.0
Q ss_pred ceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHh
Q 012477 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (462)
Q Consensus 369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l~~ 444 (462)
.....+.||.+.++.|||+||++||.|.++|||+|.|.. +..|.|.+ ..+.+++|+.+|......
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 456789999999999999999999999999999999942 34677777 468899999999876553
No 52
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.01 E-value=0.00083 Score=65.81 Aligned_cols=64 Identities=25% Similarity=0.354 Sum_probs=53.2
Q ss_pred ceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHH
Q 012477 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMT 440 (462)
Q Consensus 369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~ 440 (462)
.+...+.|.++++|.|||++|++|+.|+..|.++|+|.+. +.+-.|+|-|...--.+|+..|..
T Consensus 46 e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~--------~~e~kv~ifg~~~m~~kaka~id~ 109 (629)
T KOG0336|consen 46 EFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC--------DLEVKVTIFGINHMRKKAKASIDR 109 (629)
T ss_pred CCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc--------CceeEEEEechHHHHHHHHhhHhh
Confidence 3556677889999999999999999999999999999764 445789999998777777666643
No 53
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.98 E-value=0.0022 Score=57.53 Aligned_cols=100 Identities=24% Similarity=0.337 Sum_probs=66.5
Q ss_pred EeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccccccccCCC
Q 012477 288 LVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGL 367 (462)
Q Consensus 288 v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~ 367 (462)
+.+-...+|..||++|.+|+.|.++.|=+|.|-.-+++. .. -..+++ . |.-.....-...
T Consensus 80 ~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d~-------------~~---fI~nal-~--Pa~v~~V~~~~~- 139 (190)
T COG0195 80 NVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSEDP-------------AE---FIKNAL-A--PAEVLSVNIKED- 139 (190)
T ss_pred eecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCCH-------------HH---HHHHhc-C--cceEeEEEEEeC-
Confidence 334456789999999999999999999666665533221 00 011111 1 111111110000
Q ss_pred cceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEec
Q 012477 368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP 407 (462)
Q Consensus 368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~ 407 (462)
+.-...+.||.+..+..|||+|.+++-+.+.||-++.|..
T Consensus 140 d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 140 DGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred CCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 1126788899999999999999999999999999999953
No 54
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.82 E-value=0.0032 Score=56.57 Aligned_cols=104 Identities=30% Similarity=0.352 Sum_probs=68.0
Q ss_pred EEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHH
Q 012477 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRV 123 (462)
Q Consensus 44 ~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i 123 (462)
.+-..+-.+.+|..||++|++|+.|.++.|=+|.|-+- +-.+.+. +.+++.
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~-----------s~d~~~f------------I~nal~------ 127 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW-----------SEDPAEF------------IKNALA------ 127 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEe-----------CCCHHHH------------HHHhcC------
Confidence 44555667788999999999999999999977765221 1111110 111111
Q ss_pred HHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecC
Q 012477 124 IAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (462)
Q Consensus 124 ~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (462)
--...+-.-...+.. ...+.||.+..+.+|||+|.+++-+..-||-++.|...
T Consensus 128 -Pa~v~~V~~~~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~ 180 (190)
T COG0195 128 -PAEVLSVNIKEDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI 180 (190)
T ss_pred -cceEeEEEEEeCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence 000000000011112 78888999999999999999999999999999998654
No 55
>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=96.78 E-value=0.0025 Score=46.25 Aligned_cols=37 Identities=30% Similarity=0.421 Sum_probs=33.9
Q ss_pred ceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEE
Q 012477 42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRI 78 (462)
Q Consensus 42 ~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v 78 (462)
.-...+.|+.+..|..|||+|.+|+.+++.++-+|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3578899999999999999999999999999988875
No 56
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.75 E-value=0.0015 Score=70.99 Aligned_cols=96 Identities=22% Similarity=0.318 Sum_probs=72.7
Q ss_pred cCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCC
Q 012477 108 FVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALR 187 (462)
Q Consensus 108 ~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~ 187 (462)
.+..|.++..+|++.+.+....+........+....+.||.+.++.+||.+|.+||.|.++||++|.+.
T Consensus 522 al~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~----------- 590 (693)
T PRK11824 522 ALEQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE----------- 590 (693)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------
Confidence 455677888888877655433333333334455667778999999999999999999999999998872
Q ss_pred CCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 012477 188 SDELVQISG-EASVVKKALCQIASRLHD 214 (462)
Q Consensus 188 ~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 214 (462)
.+..|.|.+ ..+.+.+|..+|..+..+
T Consensus 591 d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 591 DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 256788888 588899999999887754
No 57
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.71 E-value=0.0021 Score=59.62 Aligned_cols=39 Identities=33% Similarity=0.569 Sum_probs=35.2
Q ss_pred CCceEEEEEeeCC------ccceeecCCchHHHHHHHHhCCeEEE
Q 012477 40 PEDTVYRYLCPIR------KIGSIIGRGGEIVKQLRIDTKSKIRI 78 (462)
Q Consensus 40 ~~~~~~~ilvp~~------~~g~IIGk~G~~Ik~i~~~tg~~I~v 78 (462)
.-.++.+|+||.+ ++|.|+|.+|.++|+|+++|+|+|.|
T Consensus 89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~I 133 (259)
T KOG1588|consen 89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMI 133 (259)
T ss_pred ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEE
Confidence 4467889999988 79999999999999999999999875
No 58
>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=96.69 E-value=0.0029 Score=45.94 Aligned_cols=36 Identities=33% Similarity=0.570 Sum_probs=33.6
Q ss_pred eEEEEEecCCccceeecCCCchHHHHHHhhCceEEE
Q 012477 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405 (462)
Q Consensus 370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i 405 (462)
....+.||....|..|||+|++|+.+++.+|-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 577899999999999999999999999999988876
No 59
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.58 E-value=0.008 Score=53.35 Aligned_cols=42 Identities=26% Similarity=0.590 Sum_probs=36.5
Q ss_pred cceEEEEEec------CCccceeecCCCchHHHHHHhhCceEEEecCC
Q 012477 368 ISFTTRLLVP------TSRIGCLIGKGGSIITEMRRLTKANIRILPKE 409 (462)
Q Consensus 368 ~~~t~~i~Vp------~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~ 409 (462)
..++.+++|| .+++|.|||+.|++.+++++.|+|+|.|-.+.
T Consensus 146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g 193 (269)
T COG5176 146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSG 193 (269)
T ss_pred ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence 3567778888 78999999999999999999999999996543
No 60
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.58 E-value=0.0055 Score=64.06 Aligned_cols=68 Identities=22% Similarity=0.277 Sum_probs=53.7
Q ss_pred cceEEEEEecC-CccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHhh
Q 012477 368 ISFTTRLLVPT-SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRAN 445 (462)
Q Consensus 368 ~~~t~~i~Vp~-~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l~~~ 445 (462)
...+..|.+|+ ++-|.|||+.|.+|+-+...||+.|.|+ ++...|+|+| +|---+.|...+...|.+.
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid----------dtp~~v~ls~fdp~rreia~~~l~~li~dg 271 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID----------DTPEAVILSGFDPVRREIARMALEKLIQDG 271 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc----------CCCCeEEecCCchHHHHHHHHHHHHHHHcC
Confidence 35667788998 5669999999999999999999999994 3345899999 6766677776666655543
No 61
>PRK12704 phosphodiesterase; Provisional
Probab=96.58 E-value=0.0057 Score=64.04 Aligned_cols=68 Identities=22% Similarity=0.269 Sum_probs=52.8
Q ss_pred cceEEEEEecC-CccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHhh
Q 012477 368 ISFTTRLLVPT-SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRAN 445 (462)
Q Consensus 368 ~~~t~~i~Vp~-~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l~~~ 445 (462)
...+..|.+|+ ++-|.|||+.|.+|+-+...||+.|.|+ ++...|+|+| +|---+.|...+...+.+.
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid----------dtp~~v~ls~~~~~rre~a~~~l~~l~~dg 277 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID----------DTPEAVILSGFDPIRREIARLALEKLVQDG 277 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc----------CCCCeEEEecCChhhHHHHHHHHHHHHhcC
Confidence 35667788998 5669999999999999999999999994 3345899999 6666567766665555443
No 62
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.58 E-value=0.0031 Score=66.00 Aligned_cols=65 Identities=26% Similarity=0.305 Sum_probs=57.0
Q ss_pred eEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCH-HHHHHHHHHHHHHHHhh
Q 012477 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDL-DLAKDALIQVMTRLRAN 445 (462)
Q Consensus 370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~-~~v~~A~~~I~~~l~~~ 445 (462)
-..++.|+.+.++-+||+||.+|++|.++|||.|+|. ++.+|.|.++. +.++.|+.+|.+..++.
T Consensus 552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-----------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~ 617 (692)
T COG1185 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-----------DDGTVKIAASDGESAKKAKERIEAITREV 617 (692)
T ss_pred ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-----------CCCcEEEEecchHHHHHHHHHHHHHHhhc
Confidence 4567889999999999999999999999999999994 33579999986 88999999999887665
No 63
>PRK00106 hypothetical protein; Provisional
Probab=96.56 E-value=0.0065 Score=63.29 Aligned_cols=68 Identities=24% Similarity=0.306 Sum_probs=53.7
Q ss_pred cceEEEEEecC-CccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHhh
Q 012477 368 ISFTTRLLVPT-SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRAN 445 (462)
Q Consensus 368 ~~~t~~i~Vp~-~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l~~~ 445 (462)
...+..|.+|+ ++-|.|||+.|.+|+-+...||+.+.|+ ++...|+|+| +|---+.|...+...|.+.
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid----------dtp~~v~lS~fdpvRReiAr~~le~Li~dg 292 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID----------DTPEVVVLSGFDPIRREIARMTLESLIKDG 292 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc----------CCCCeEEEeCCChHHHHHHHHHHHHHHHcC
Confidence 45677788998 5669999999999999999999999994 3445899999 7777777766666555443
No 64
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.52 E-value=0.0031 Score=60.12 Aligned_cols=71 Identities=27% Similarity=0.391 Sum_probs=58.9
Q ss_pred ceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 012477 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN 215 (462)
Q Consensus 139 ~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 215 (462)
.....++++..+.++|||++|.|-++|+++|+++|.++...+ ..+.+..+.+..++|.+|...|.-++...
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~------n~~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT------NKEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC------CcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 456778999999999999999999999999999999977531 33444455557999999999999998775
No 65
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.45 E-value=0.0034 Score=58.26 Aligned_cols=42 Identities=24% Similarity=0.458 Sum_probs=37.0
Q ss_pred cceEEEEEec------CCccceeecCCCchHHHHHHhhCceEEEecCC
Q 012477 368 ISFTTRLLVP------TSRIGCLIGKGGSIITEMRRLTKANIRILPKE 409 (462)
Q Consensus 368 ~~~t~~i~Vp------~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~ 409 (462)
...+.+|+|| .++||.|+|+.|.++|+|+++|||+|-|-.+.
T Consensus 90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrg 137 (259)
T KOG1588|consen 90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRG 137 (259)
T ss_pred eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCC
Confidence 4577888888 56899999999999999999999999997654
No 66
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.42 E-value=0.0031 Score=68.99 Aligned_cols=64 Identities=20% Similarity=0.307 Sum_probs=55.2
Q ss_pred ceEEEEEecCCccceeecCCCchHHHHHHhhCce-EEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHH
Q 012477 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKAN-IRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLR 443 (462)
Q Consensus 369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~-I~i~~~~~~P~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l~ 443 (462)
.....+.||.+.++.|||.||.+||.|.++||+. |.+. ++-.|.|.+ +.+.+++|+.+|.+...
T Consensus 684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~-----------ddg~V~I~a~d~~~i~~A~~~I~~l~~ 749 (891)
T PLN00207 684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ-----------DDGTVKITAKDLSSLEKSKAIISSLTM 749 (891)
T ss_pred CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-----------CCeeEEEEeCCHHHHHHHHHHHHHHhc
Confidence 4667899999999999999999999999999999 8873 235788888 57899999999887764
No 67
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.36 E-value=0.0068 Score=56.91 Aligned_cols=63 Identities=21% Similarity=0.239 Sum_probs=52.5
Q ss_pred EEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCH-HHHHHHHHHHHHHHHhh
Q 012477 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDL-DLAKDALIQVMTRLRAN 445 (462)
Q Consensus 372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~-~~v~~A~~~I~~~l~~~ 445 (462)
..+.||..+++.+||++|.+|+.|.+.+++.|.|. .+-.|.|.++. +++..|+.+|.+.-++.
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig-----------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG-----------QNGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc-----------CCcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 45889999999999999999999999999999983 23589999975 58889988887644433
No 68
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.34 E-value=0.013 Score=57.92 Aligned_cols=96 Identities=21% Similarity=0.192 Sum_probs=64.7
Q ss_pred CccccccccCChhHHhHHhhh-CCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccccccccCCCcceE
Q 012477 293 ANIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFT 371 (462)
Q Consensus 293 ~~~g~IIGk~G~~Ik~I~~~s-ga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t 371 (462)
+-+|..||++|.+|+.|.++. |=+|.|-.-+++.. .. ..+++ .|.-....... .....
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~-------------~f---I~Nal---~Pa~V~~V~i~--~~~~~ 309 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPE-------------IF---IARAL---APAIISSVKIE--EEEKK 309 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHH-------------HH---HHHhC---CCceeeEEEEc--CCCcE
Confidence 357999999999999999998 76776655332210 00 00111 11111011001 11246
Q ss_pred EEEEecCCccceeecCCCchHHHHHHhhCceEEEecCC
Q 012477 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKE 409 (462)
Q Consensus 372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~ 409 (462)
..+.||.+..+..|||+|++++-..+.||.+|.|-.-+
T Consensus 310 ~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~ 347 (374)
T PRK12328 310 AIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG 347 (374)
T ss_pred EEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence 78899999999999999999999999999999997644
No 69
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=96.32 E-value=0.011 Score=58.37 Aligned_cols=93 Identities=26% Similarity=0.403 Sum_probs=63.2
Q ss_pred ccccccccCChhHHhHHhhh-CCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCccccccc-ccCCCcceE
Q 012477 294 NIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIE-RDSGLISFT 371 (462)
Q Consensus 294 ~~g~IIGk~G~~Ik~I~~~s-ga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~t 371 (462)
-+|..||++|++|+.|.++. |=+|.|-.-+++.. .. ..+++ .|.-..... .+. ....
T Consensus 244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~-------------~f---i~nal---~Pa~v~~v~i~~~--~~~~ 302 (341)
T TIGR01953 244 PVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPA-------------EF---IANAL---SPAKVISVEVLDE--DKHS 302 (341)
T ss_pred cceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHH-------------HH---HHHhc---CCceEEEEEEEcC--CCcE
Confidence 57999999999999999998 76776655332210 00 00111 111111110 011 1246
Q ss_pred EEEEecCCccceeecCCCchHHHHHHhhCceEEEec
Q 012477 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP 407 (462)
Q Consensus 372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~ 407 (462)
..+.||.+..+..|||+|++++-..+.||.+|.|..
T Consensus 303 ~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 303 AEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred EEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 789999999999999999999999999999999953
No 70
>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=96.28 E-value=0.013 Score=57.97 Aligned_cols=96 Identities=29% Similarity=0.406 Sum_probs=62.7
Q ss_pred CccceeecCCchHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHHHHhhccC
Q 012477 52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG 130 (462)
Q Consensus 52 ~~~g~IIGk~G~~Ik~i~~~t-g~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~ 130 (462)
+-+|+.||++|++|+.|.++. |=+|+|-.- +-.++.. +.+|+.=. .+..-.+
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~-----------s~d~~~f------------i~nal~Pa--~v~~v~i-- 295 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEY-----------SDDPAEF------------IANALSPA--KVISVEV-- 295 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEc-----------CCCHHHH------------HHHhcCCc--eEEEEEE--
Confidence 348999999999999999998 777776221 1111100 00000000 0000000
Q ss_pred CCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecC
Q 012477 131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (462)
Q Consensus 131 ~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (462)
.....-...+.||....+..|||+|.+++-...-||.+|.|...
T Consensus 296 ----~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~ 339 (341)
T TIGR01953 296 ----LDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE 339 (341)
T ss_pred ----EcCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence 00112478899999999999999999999999999999999764
No 71
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.15 E-value=0.013 Score=58.21 Aligned_cols=94 Identities=26% Similarity=0.324 Sum_probs=63.4
Q ss_pred ccccccccCChhHHhHHhhh-CCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccccccccCCCcceEE
Q 012477 294 NIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTT 372 (462)
Q Consensus 294 ~~g~IIGk~G~~Ik~I~~~s-ga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~ 372 (462)
-+|..||++|.+|+.|..+. |-+|.+-.-+++.. . -+..+ +.|.-.....-.. ......
T Consensus 246 pvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~-------------~----fi~na--l~Pa~v~~v~i~~-~~~~~~ 305 (362)
T PRK12327 246 AKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPA-------------E----FVANA--LSPAKVVSVEVDD-EEEKAA 305 (362)
T ss_pred chheeECCCChhHHHHHHHhCCCeEEEEEcCCCHH-------------H----HHHHh--CCCceEEEEEEEc-CCCcEE
Confidence 57999999999999999998 76776665332210 0 00000 1111111110000 112467
Q ss_pred EEEecCCccceeecCCCchHHHHHHhhCceEEEec
Q 012477 373 RLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP 407 (462)
Q Consensus 373 ~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~ 407 (462)
.+.||.+..+..|||+|.+++--.+.||.+|.|..
T Consensus 306 ~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 306 RVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred EEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 89999999999999999999999999999999964
No 72
>PRK00468 hypothetical protein; Provisional
Probab=96.13 E-value=0.0066 Score=45.85 Aligned_cols=33 Identities=21% Similarity=0.450 Sum_probs=29.6
Q ss_pred CCceEEEEEeeCCccceeecCCchHHHHHHHHh
Q 012477 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDT 72 (462)
Q Consensus 40 ~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~t 72 (462)
.+.+.+++.|..+..|.||||+|.+|+.||.--
T Consensus 27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 356889999999999999999999999999764
No 73
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.12 E-value=0.016 Score=57.29 Aligned_cols=96 Identities=20% Similarity=0.154 Sum_probs=63.0
Q ss_pred CccceeecCCchHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHHHHhhccC
Q 012477 52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG 130 (462)
Q Consensus 52 ~~~g~IIGk~G~~Ik~i~~~t-g~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~ 130 (462)
+-+|+.||++|++|+.|.++. |=+|+|-.- +-.+... +.+|+. --.+..
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~-----------s~D~~~f------------I~Nal~-------Pa~V~~ 300 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEY-----------SNVPEIF------------IARALA-------PAIISS 300 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEc-----------CCCHHHH------------HHHhCC-------CceeeE
Confidence 358999999999999999998 777776321 1111000 000000 000000
Q ss_pred CCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCC
Q 012477 131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179 (462)
Q Consensus 131 ~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~ 179 (462)
. ......-...+.||....+..|||+|.+++-...-||.+|.|..-+
T Consensus 301 V--~i~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~ 347 (374)
T PRK12328 301 V--KIEEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG 347 (374)
T ss_pred E--EEcCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence 0 0001223678899999999999999999999999999999997653
No 74
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.10 E-value=0.022 Score=56.62 Aligned_cols=96 Identities=25% Similarity=0.313 Sum_probs=62.9
Q ss_pred CccceeecCCchHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHHHHhhccC
Q 012477 52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG 130 (462)
Q Consensus 52 ~~~g~IIGk~G~~Ik~i~~~t-g~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~ 130 (462)
+-+|+.||++|.+|+.|.++. |=+|+|-.- +-.++.. +.+|+. --....
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~-----------s~d~~~f------------i~nal~-------Pa~v~~ 294 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDW-----------SEDPAEF------------VANALS-------PAKVVS 294 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEc-----------CCCHHHH------------HHHhCC-------CceEEE
Confidence 358999999999999999998 778876221 1111100 000000 000000
Q ss_pred CCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecC
Q 012477 131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (462)
Q Consensus 131 ~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (462)
. .......-.+.+.||....+..|||+|.+++-...-||.+|.|...
T Consensus 295 v-~i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 295 V-EVDDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred E-EEEcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 0 0000122468899999999999999999999999999999999765
No 75
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.02 E-value=0.01 Score=56.76 Aligned_cols=71 Identities=27% Similarity=0.405 Sum_probs=57.8
Q ss_pred ceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHhhh
Q 012477 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRANL 446 (462)
Q Consensus 369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l~~~~ 446 (462)
.+...+.|++.+.|.|||++|.+-++|+++|+++|.++.+ .++...|+|+| +.++|.+|...|...|....
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 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP-------NTNKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC-------CCCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 4566789999999999999999999999999999999653 34445566666 57899999988877776654
No 76
>PRK02821 hypothetical protein; Provisional
Probab=95.92 E-value=0.0088 Score=45.33 Aligned_cols=34 Identities=24% Similarity=0.381 Sum_probs=30.2
Q ss_pred CCceEEEEEeeCCccceeecCCchHHHHHHHHhC
Q 012477 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (462)
Q Consensus 40 ~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg 73 (462)
.+.+.+++.|..+..|.||||+|.+|+.||.--.
T Consensus 28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CCcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 3457899999999999999999999999998754
No 77
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.88 E-value=0.017 Score=58.06 Aligned_cols=94 Identities=28% Similarity=0.363 Sum_probs=62.9
Q ss_pred CccccccccCChhHHhHHhhh-CCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCccccccc-ccCCCcce
Q 012477 293 ANIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIE-RDSGLISF 370 (462)
Q Consensus 293 ~~~g~IIGk~G~~Ik~I~~~s-ga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~ 370 (462)
+-+|..||.+|.+|+.|..+. |=+|.|-.-+++. .. -+..+ +.|.-..... .+ ....
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp-------------~~----fI~Na--LsPA~V~~V~i~~--~~~k 335 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDP-------------AT----YIANA--LSPARVDEVRLVD--PEGR 335 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCH-------------HH----HHHHh--cCCceeeEEEEEc--CCCc
Confidence 357999999999999999998 7677665533221 00 00000 1111111110 01 1124
Q ss_pred EEEEEecCCccceeecCCCchHHHHHHhhCceEEEec
Q 012477 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP 407 (462)
Q Consensus 371 t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~ 407 (462)
...+.||.+..+.-|||+|++++--.+.||.+|.|..
T Consensus 336 ~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 336 HAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred EEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 5679999999999999999999999999999999953
No 78
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.79 E-value=0.022 Score=58.75 Aligned_cols=94 Identities=24% Similarity=0.373 Sum_probs=63.6
Q ss_pred ccccccccCChhHHhHHhhh-CCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccccccccCCCcceEE
Q 012477 294 NIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTT 372 (462)
Q Consensus 294 ~~g~IIGk~G~~Ik~I~~~s-ga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~ 372 (462)
-+|..||.+|++|+.|..+. |=+|.|-.-+++. ... ..+++ .|.-.....-+. ..-..
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~-------------~~f---i~nal---~pa~v~~v~~~~--~~~~~ 304 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIILWSDDP-------------AQF---IINAL---SPAEVSSVVVDE--DEHSA 304 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEEcCCCH-------------HHH---HHHhC---CCCEEEEEEEeC--CCCEE
Confidence 47999999999999999998 7677666533221 000 01111 111100110001 12377
Q ss_pred EEEecCCccceeecCCCchHHHHHHhhCceEEEecC
Q 012477 373 RLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPK 408 (462)
Q Consensus 373 ~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~ 408 (462)
.+.||....+.-|||+|++|+..++.||.+|.|...
T Consensus 305 ~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 305 DVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred EEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 899999999999999999999999999999999653
No 79
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.72 E-value=0.021 Score=57.44 Aligned_cols=96 Identities=28% Similarity=0.302 Sum_probs=62.0
Q ss_pred CccceeecCCchHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHHHHhhccC
Q 012477 52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG 130 (462)
Q Consensus 52 ~~~g~IIGk~G~~Ik~i~~~t-g~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~ 130 (462)
+-+|+.||++|++|+.|.++. |=+|+|-.- +-.++.. +.+|+.=. ++..-.+
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~y-----------s~Dp~~f------------I~NaLsPA--~V~~V~i-- 329 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRW-----------SPDPATY------------IANALSPA--RVDEVRL-- 329 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEc-----------CCCHHHH------------HHHhcCCc--eeeEEEE--
Confidence 458999999999999999998 777776221 1111100 00000000 0000000
Q ss_pred CCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecC
Q 012477 131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (462)
Q Consensus 131 ~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (462)
.....-.+.+.||....+..|||+|.+++-...-||.+|.|...
T Consensus 330 ----~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s~ 373 (449)
T PRK12329 330 ----VDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKDS 373 (449)
T ss_pred ----EcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccccH
Confidence 00112357899999999999999999999999999999998543
No 80
>PRK00468 hypothetical protein; Provisional
Probab=95.52 E-value=0.017 Score=43.68 Aligned_cols=34 Identities=35% Similarity=0.486 Sum_probs=29.8
Q ss_pred cceEEEEEecCCccceeecCCCchHHHHHHhhCc
Q 012477 368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKA 401 (462)
Q Consensus 368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga 401 (462)
..+..++.+..+-+|.||||+|.+|+.||..-.+
T Consensus 28 ~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~a 61 (75)
T PRK00468 28 QSVILELKVAPEDMGKVIGKQGRIAKAIRTVVKA 61 (75)
T ss_pred CeEEEEEEEChhhCcceecCCChhHHHHHHHHHH
Confidence 4578889999999999999999999999987543
No 81
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.45 E-value=0.019 Score=43.17 Aligned_cols=33 Identities=15% Similarity=0.343 Sum_probs=29.7
Q ss_pred CCceEEEEEeeCCccceeecCCchHHHHHHHHh
Q 012477 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDT 72 (462)
Q Consensus 40 ~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~t 72 (462)
...+.+++-+..+..|.||||+|.+|+.||.--
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 456789999999999999999999999999763
No 82
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.41 E-value=0.03 Score=52.58 Aligned_cols=65 Identities=20% Similarity=0.271 Sum_probs=54.8
Q ss_pred EEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcC-HHHHHHHHHHHHHHHhcCC
Q 012477 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGE-ASVVKKALCQIASRLHDNP 216 (462)
Q Consensus 141 ~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~~ 216 (462)
-+.+.||..+++.+||++|.+|+.|.++|+++|.+-. +..|.|.+. .+++.+|..+|..+-++..
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-----------NG~VwI~~~~~~~~~~a~~~I~~~e~~~~ 211 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-----------NGRIWIKGPDEEDEEIAIEAIKKIEREAH 211 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-----------CcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence 4668899999999999999999999999999998833 457899887 6688888888887776643
No 83
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=95.35 E-value=0.03 Score=57.09 Aligned_cols=114 Identities=18% Similarity=0.209 Sum_probs=82.2
Q ss_pred EEEEcCCccccccc----CCCCcCCHHHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHH
Q 012477 90 VTVYSASDETNAFE----DGDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNI 165 (462)
Q Consensus 90 i~I~G~~e~~~~~~----~~~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I 165 (462)
+.|.|+.+.+-|+. -..+++.+|.+|..+|++.+....-.+.........+...+.++.+....+||.+|...|+|
T Consensus 543 FKiAGt~dGvTA~gi~l~Iv~eal~~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki 622 (760)
T KOG1067|consen 543 FKIAGTNDGVTALGIPLKIVMEALQKAREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKI 622 (760)
T ss_pred eeeccccCcceecCCcHHHHHHHHHhhhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeE
Confidence 34566666655542 12234556777777777766554444455556667889999999999999999999999999
Q ss_pred HhhcCceEEEecCCCCCCcCCCCCceEEEEc-CHHHHHHHHHHHHHHHhcC
Q 012477 166 RSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHDN 215 (462)
Q Consensus 166 ~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~~ 215 (462)
..+||+.-.+ ++..++|-. +..+.++|...|..++...
T Consensus 623 ~~EtGai~~v------------De~t~~i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 623 EVETGAISQV------------DEGTFSIFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred eeeccceeee------------cCceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence 9999955544 245677766 5778899999998888663
No 84
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=95.33 E-value=0.27 Score=45.26 Aligned_cols=131 Identities=17% Similarity=0.166 Sum_probs=87.7
Q ss_pred EEEEeeeCCccccccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCccccccccc
Q 012477 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERD 364 (462)
Q Consensus 285 ~~~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~ 364 (462)
.+.+.++....-.+...+|..++.|....|++|.+.. ....+.|+|++.....+...++.++.
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-----~~~~i~I~g~k~~~~~i~~~i~~~l~------------ 89 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR-----SENRIRITGTKSTAEYIEASINEILS------------ 89 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEec-----CCcEEEEEccHHHHHHHHHHHHHHHh------------
Confidence 3445556777888899999999999888899999988 34688999986433322222222222
Q ss_pred CCCcceEEEEEecCCccceeec----CCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-----CHHHHHHHH
Q 012477 365 SGLISFTTRLLVPTSRIGCLIG----KGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-----DLDLAKDAL 435 (462)
Q Consensus 365 ~~~~~~t~~i~Vp~~~~g~IIG----k~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G-----~~~~v~~A~ 435 (462)
...+.++.++.-..-.-.+ .....+++|++.|++.|..... ...+.|+. ....++.|+
T Consensus 90 ---~i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~----------~~~~~i~~~~~~~~~~~~~~a~ 156 (210)
T PF14611_consen 90 ---NIRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD----------GNKLKISWLASPENEKRADRAK 156 (210)
T ss_pred ---hcEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC----------CCeEEEEEEeeccccchHHHHH
Confidence 1245566666432211221 2467899999999999998432 23455554 568899999
Q ss_pred HHHHHHHHhh
Q 012477 436 IQVMTRLRAN 445 (462)
Q Consensus 436 ~~I~~~l~~~ 445 (462)
++++-.+...
T Consensus 157 RlL~~a~~~~ 166 (210)
T PF14611_consen 157 RLLLWALDYN 166 (210)
T ss_pred HHHHHhccCC
Confidence 9999888533
No 85
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.28 E-value=0.044 Score=56.52 Aligned_cols=94 Identities=23% Similarity=0.324 Sum_probs=62.3
Q ss_pred ccceeecCCchHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHHHHhhccCC
Q 012477 53 KIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGD 131 (462)
Q Consensus 53 ~~g~IIGk~G~~Ik~i~~~t-g~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~~ 131 (462)
-+|+.||++|++|+.|.++. |=+|.|-.- +-.+.. .+.+.+..-.+...
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~-----------s~d~~~-------------------fi~nal~pa~v~~v 295 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIILW-----------SDDPAQ-------------------FIINALSPAEVSSV 295 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEEc-----------CCCHHH-------------------HHHHhCCCCEEEEE
Confidence 48999999999999999998 777776221 111110 00000000000000
Q ss_pred CCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecC
Q 012477 132 EDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (462)
Q Consensus 132 ~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (462)
......-.+.+.||....+..|||+|.+++.....||.+|.|...
T Consensus 296 --~~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 296 --VVDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred --EEeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 000012378899999999999999999999999999999999764
No 86
>PRK02821 hypothetical protein; Provisional
Probab=95.25 E-value=0.021 Score=43.24 Aligned_cols=34 Identities=29% Similarity=0.447 Sum_probs=29.7
Q ss_pred cceEEEEEecCCccceeecCCCchHHHHHHhhCc
Q 012477 368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKA 401 (462)
Q Consensus 368 ~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga 401 (462)
......+.|..+-+|.||||+|.+|+.||..-.+
T Consensus 29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 3577889999999999999999999999987544
No 87
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.18 E-value=0.052 Score=48.32 Aligned_cols=44 Identities=20% Similarity=0.360 Sum_probs=36.5
Q ss_pred CCCCceEEEEEEeC------CceeeeecCCchHHHHHHhhcCceEEEecC
Q 012477 135 DGGHQVTAKLLVPS------DQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (462)
Q Consensus 135 ~~~~~~~~~l~ip~------~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (462)
.....++-++.||- +++|.|||..|.|.|.|++.|+|+|.|-..
T Consensus 143 ~rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 143 IRPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred cCcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 34455667777774 589999999999999999999999999654
No 88
>PRK01064 hypothetical protein; Provisional
Probab=95.09 E-value=0.03 Score=42.61 Aligned_cols=33 Identities=27% Similarity=0.496 Sum_probs=29.5
Q ss_pred CCceEEEEEeeCCccceeecCCchHHHHHHHHh
Q 012477 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDT 72 (462)
Q Consensus 40 ~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~t 72 (462)
...+.+++.|..+..|.+|||+|.+|+.|+.-.
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 356889999999999999999999999999764
No 89
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.08 E-value=0.016 Score=62.94 Aligned_cols=64 Identities=30% Similarity=0.366 Sum_probs=53.6
Q ss_pred eEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHh
Q 012477 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (462)
Q Consensus 370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l~~ 444 (462)
....+.||.+.++.+||.||.+||+|.++||+.|.+. ++-.|.|.+ ..+.+++|+.+|......
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 4556778999999999999999999999999988772 235788888 478899999999887654
No 90
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.03 E-value=0.03 Score=42.11 Aligned_cols=34 Identities=32% Similarity=0.442 Sum_probs=30.3
Q ss_pred CcceEEEEEecCCccceeecCCCchHHHHHHhhC
Q 012477 367 LISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTK 400 (462)
Q Consensus 367 ~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sg 400 (462)
......++.|...-.|.||||+|.+|+.||..-.
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll~ 60 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLLS 60 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHHHH
Confidence 4578899999999999999999999999997743
No 91
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=94.84 E-value=0.13 Score=53.90 Aligned_cols=66 Identities=21% Similarity=0.367 Sum_probs=51.4
Q ss_pred ceEEEEEEeC-CceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 012477 139 QVTAKLLVPS-DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHD 214 (462)
Q Consensus 139 ~~~~~l~ip~-~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 214 (462)
.+.-.+.+|+ .+-|+|||+.|.+|+.++..||+.+-|.. +...|.|+| .|-.-+-|...+..++.+
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd----------tp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD----------TPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC----------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 4455567777 67799999999999999999999999843 234688888 566667777777777765
No 92
>PRK12704 phosphodiesterase; Provisional
Probab=94.75 E-value=0.14 Score=53.88 Aligned_cols=66 Identities=21% Similarity=0.355 Sum_probs=49.3
Q ss_pred ceEEEEEEeC-CceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 012477 139 QVTAKLLVPS-DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHD 214 (462)
Q Consensus 139 ~~~~~l~ip~-~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 214 (462)
.+.-.+.+|+ .+-|+|||+.|.+|+.++.-||+.|-|.. +...|.|+| .+-.-+.|...+..++.+
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 3445566676 67799999999999999999999999843 244788998 455555666666666654
No 93
>PRK00106 hypothetical protein; Provisional
Probab=94.74 E-value=0.16 Score=53.16 Aligned_cols=68 Identities=25% Similarity=0.404 Sum_probs=52.8
Q ss_pred CceEEEEEEeC-CceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEc-CHHHHHHHHHHHHHHHhcC
Q 012477 138 HQVTAKLLVPS-DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHDN 215 (462)
Q Consensus 138 ~~~~~~l~ip~-~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~~ 215 (462)
..+.-.+.+|+ .+-|+|||+.|.+|+.++.-||+.+-|.. +...|.|+| .|-.-+-|...+..++.+.
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd----------tp~~v~lS~fdpvRReiAr~~le~Li~dg 292 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD----------TPEVVVLSGFDPIRREIARMTLESLIKDG 292 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC----------CCCeEEEeCCChHHHHHHHHHHHHHHHcC
Confidence 34455667777 67799999999999999999999999843 234688998 5777777777777777653
No 94
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=94.32 E-value=0.98 Score=41.55 Aligned_cols=86 Identities=15% Similarity=0.249 Sum_probs=64.8
Q ss_pred HHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEE
Q 012477 115 ALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQI 194 (462)
Q Consensus 115 a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I 194 (462)
.+..|+..++.-.+.+. -+..-.+.+.++......+...+|..++.|....||+|.+..+ +..+.|
T Consensus 5 l~~~Il~d~W~l~v~e~----v~~~g~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~----------~~~i~I 70 (210)
T PF14611_consen 5 LAERILRDCWNLEVSEE----VDELGDLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS----------ENRIRI 70 (210)
T ss_pred HHHHHHHHhcCCcccce----eeccceeEEEecchheeeeecCCchHHHHHHHhcCceEEEecC----------CcEEEE
Confidence 45566666655333211 1122345555668888999999999999998889999999764 568999
Q ss_pred EcCHHHHHHHHHHHHHHHhc
Q 012477 195 SGEASVVKKALCQIASRLHD 214 (462)
Q Consensus 195 ~G~~~~v~~A~~~I~~~l~~ 214 (462)
+|+...+..+...|.+.+..
T Consensus 71 ~g~k~~~~~i~~~i~~~l~~ 90 (210)
T PF14611_consen 71 TGTKSTAEYIEASINEILSN 90 (210)
T ss_pred EccHHHHHHHHHHHHHHHhh
Confidence 99999999999999999876
No 95
>PRK01064 hypothetical protein; Provisional
Probab=94.31 E-value=0.055 Score=41.17 Aligned_cols=34 Identities=32% Similarity=0.442 Sum_probs=29.8
Q ss_pred CcceEEEEEecCCccceeecCCCchHHHHHHhhC
Q 012477 367 LISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTK 400 (462)
Q Consensus 367 ~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sg 400 (462)
...+..++.|...-.|.+|||+|.+|+.||....
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHHHH
Confidence 3567888999999999999999999999998643
No 96
>PRK12705 hypothetical protein; Provisional
Probab=94.05 E-value=0.067 Score=55.54 Aligned_cols=65 Identities=25% Similarity=0.247 Sum_probs=45.8
Q ss_pred cceEEEEEecCC-ccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHH
Q 012477 368 ISFTTRLLVPTS-RIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRL 442 (462)
Q Consensus 368 ~~~t~~i~Vp~~-~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l 442 (462)
......+.+|++ +-|.|||+.|.+|+.+...||+.|.|++ .| +.|+|++ +|.--+.|...+...|
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd---tp-------~~V~ls~fdp~rreia~~~l~~Li 262 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD---TP-------EAVVISSFNPIRREIARLTLEKLL 262 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC---Cc-------cchhhcccCccchHHHHHHHHHHH
Confidence 345667788874 5599999999999999999999999942 23 3566766 3444444544444443
No 97
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=92.91 E-value=0.058 Score=40.62 Aligned_cols=34 Identities=15% Similarity=0.214 Sum_probs=29.3
Q ss_pred CCceEEEEEeeCCccceeecCCchHHHHHHHHhC
Q 012477 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (462)
Q Consensus 40 ~~~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg 73 (462)
.+...+.+-+..+..|.||||+|.+++.||.-.+
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence 3566778888999999999999999999997654
No 98
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=92.75 E-value=0.041 Score=60.47 Aligned_cols=70 Identities=19% Similarity=0.129 Sum_probs=57.1
Q ss_pred EEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHh
Q 012477 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRA 444 (462)
Q Consensus 371 t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~ 444 (462)
...+.+|.....+|||+||++|+.+|..|||.|.|.+-- |. ...+|.+++.|.++.+..|...|.-.|.+
T Consensus 1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq--~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ--PD--NQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred ccccccchhhhhhhhccCcchhhhHhhccceEEehhhcC--Cc--cchhhhcccCCCChhhhhhhccccceeec
Confidence 345778888899999999999999999999999996521 21 25689999999999999998887655433
No 99
>PRK12705 hypothetical protein; Provisional
Probab=91.70 E-value=0.14 Score=53.32 Aligned_cols=43 Identities=26% Similarity=0.288 Sum_probs=36.8
Q ss_pred CCCceEEEEEeeC-CccceeecCCchHHHHHHHHhCCeEEEcCC
Q 012477 39 GPEDTVYRYLCPI-RKIGSIIGRGGEIVKQLRIDTKSKIRIGET 81 (462)
Q Consensus 39 ~~~~~~~~ilvp~-~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~ 81 (462)
..+.++-.+-+|+ ++-|+||||.|.||+.++..||+.|-|++.
T Consensus 194 ~~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt 237 (508)
T PRK12705 194 ASDLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT 237 (508)
T ss_pred hhhheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC
Confidence 3556666777887 689999999999999999999999999764
No 100
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=91.54 E-value=0.12 Score=45.72 Aligned_cols=53 Identities=23% Similarity=0.337 Sum_probs=47.3
Q ss_pred CCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 012477 378 TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRL 442 (462)
Q Consensus 378 ~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l 442 (462)
+..+|.|+||+|.+---|.+.|.++|.+.. ..|-|-|..++++.|...|+..|
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad------------~kIHiLG~~~niriAR~avcsLI 229 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD------------SKIHILGAFQNIRIARDAVCSLI 229 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecC------------ceEEEeecchhhHHHHHhhHhhh
Confidence 456799999999999999999999999842 37999999999999999998765
No 101
>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=91.01 E-value=0.38 Score=34.98 Aligned_cols=35 Identities=14% Similarity=0.214 Sum_probs=27.7
Q ss_pred ceEEEEEeeCCccceeecCCchHHHHHHHHhCCeE
Q 012477 42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKI 76 (462)
Q Consensus 42 ~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I 76 (462)
.....+.+.....|.+||++|.+++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 35555666666789999999999999999987443
No 102
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=90.76 E-value=0.22 Score=37.05 Aligned_cols=37 Identities=27% Similarity=0.436 Sum_probs=30.0
Q ss_pred EEEEEecCCc-----cceeecCCCchHHHHHHhh-CceEEEec
Q 012477 371 TTRLLVPTSR-----IGCLIGKGGSIITEMRRLT-KANIRILP 407 (462)
Q Consensus 371 t~~i~Vp~~~-----~g~IIGk~G~~I~~I~~~s-ga~I~i~~ 407 (462)
...+.|-+.. +|..||++|++|+.|+++. |-+|.|-.
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 4556777777 8999999999999999999 99999864
No 103
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=90.45 E-value=0.47 Score=44.36 Aligned_cols=51 Identities=16% Similarity=0.193 Sum_probs=46.7
Q ss_pred eeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477 152 GCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD 214 (462)
Q Consensus 152 g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~ 214 (462)
-++||.+|+|++.|+-.|.|-|-|... +|.+.|....+..+...+.+++.+
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~------------TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN------------TVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc------------EEEeecCcchHHHHHHHHHHHHhc
Confidence 579999999999999999999998654 799999999999999999999977
No 104
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=90.15 E-value=0.56 Score=43.91 Aligned_cols=51 Identities=24% Similarity=0.261 Sum_probs=44.2
Q ss_pred ceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHh
Q 012477 382 GCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRA 444 (462)
Q Consensus 382 g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~ 444 (462)
-++||.+|++++.|+-.|.|.|-|+. .+|.+.|....++.+...+.+.++.
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 57899999999999999999999953 3899999999999998887765543
No 105
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=89.97 E-value=0.6 Score=33.93 Aligned_cols=34 Identities=24% Similarity=0.426 Sum_probs=27.8
Q ss_pred eEEEEEecCCccceeecCCCchHHHHHHhhCceE
Q 012477 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANI 403 (462)
Q Consensus 370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I 403 (462)
....+.+.....|.+||++|++++.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 5556666666789999999999999999988544
No 106
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=89.97 E-value=0.7 Score=42.73 Aligned_cols=47 Identities=21% Similarity=0.408 Sum_probs=40.3
Q ss_pred EEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHH
Q 012477 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLD 429 (462)
Q Consensus 372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~ 429 (462)
.-+.||...+..+||++|+.++.+.+.|+|+|-|-.+ -.|=|.|..+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N-----------G~IWV~~~~~ 194 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN-----------GRIWVDGENE 194 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC-----------CEEEecCCCc
Confidence 4578999999999999999999999999999999533 4777888765
No 107
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=89.35 E-value=0.22 Score=37.46 Aligned_cols=33 Identities=18% Similarity=0.297 Sum_probs=28.2
Q ss_pred CceEEEEEEeCCceeeeecCCchHHHHHHhhcC
Q 012477 138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETG 170 (462)
Q Consensus 138 ~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tg 170 (462)
....+.+-+.....|.||||+|.+++.|+.-.+
T Consensus 27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred CceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence 455788888999999999999999999986544
No 108
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=88.80 E-value=0.92 Score=41.97 Aligned_cols=60 Identities=22% Similarity=0.364 Sum_probs=46.8
Q ss_pred EEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHH-HHHHHHHHHHHH
Q 012477 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASV-VKKALCQIASRL 212 (462)
Q Consensus 142 ~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~-v~~A~~~I~~~l 212 (462)
.-+.|+...+.++||++|+.++.|.+.|+|+|-+-.+ ..|-|.|..+. ...|...|..+=
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N-----------G~IWV~~~~~~~e~~~~~aI~~ie 208 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN-----------GRIWVDGENESLEELAIEAIRKIE 208 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC-----------CEEEecCCCcchHHHHHHHHHHHh
Confidence 5578999999999999999999999999999998553 46888887764 444555554433
No 109
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=88.12 E-value=1.1 Score=45.44 Aligned_cols=41 Identities=34% Similarity=0.471 Sum_probs=36.8
Q ss_pred ceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCC
Q 012477 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179 (462)
Q Consensus 139 ~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~ 179 (462)
.-...+.||..+++.+|||+|.+|++|++..|-+|.|...+
T Consensus 485 d~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e 525 (604)
T COG1855 485 DGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE 525 (604)
T ss_pred CCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence 34577899999999999999999999999999999997653
No 110
>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=87.76 E-value=0.6 Score=35.47 Aligned_cols=33 Identities=18% Similarity=0.247 Sum_probs=26.6
Q ss_pred EEEEEeeCCccceeecCCchHHHHHHHHhCCeE
Q 012477 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKI 76 (462)
Q Consensus 44 ~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I 76 (462)
.+.+-+..+..|.+|||+|+++..||--.+.-+
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~ 57 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVL 57 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHH
Confidence 345666778899999999999999998766443
No 111
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=87.55 E-value=0.38 Score=42.75 Aligned_cols=57 Identities=28% Similarity=0.394 Sum_probs=50.2
Q ss_pred CCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhcCC
Q 012477 148 SDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNP 216 (462)
Q Consensus 148 ~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~ 216 (462)
...+|+|+||+|.+--.|+.-|-.+|.+. +..+.|-|..+++.-|...|+.++...+
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVla------------d~kIHiLG~~~niriAR~avcsLIlGsp 233 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA------------DSKIHILGAFQNIRIARDAVCSLILGSP 233 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEec------------CceEEEeecchhhHHHHHhhHhhhccCC
Confidence 35679999999999999999999999874 3479999999999999999999998754
No 112
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=87.48 E-value=0.37 Score=35.82 Aligned_cols=34 Identities=21% Similarity=0.378 Sum_probs=27.1
Q ss_pred EEEEeeCCc-----cceeecCCchHHHHHHHHh-CCeEEE
Q 012477 45 YRYLCPIRK-----IGSIIGRGGEIVKQLRIDT-KSKIRI 78 (462)
Q Consensus 45 ~~ilvp~~~-----~g~IIGk~G~~Ik~i~~~t-g~~I~v 78 (462)
..+.|-+.. +|..||++|+.|+.|.++. |-+|+|
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdv 44 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDV 44 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEE
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEE
Confidence 356666666 9999999999999999999 888875
No 113
>PRK13764 ATPase; Provisional
Probab=87.18 E-value=0.67 Score=49.41 Aligned_cols=44 Identities=27% Similarity=0.463 Sum_probs=39.2
Q ss_pred ceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCC
Q 012477 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLP 412 (462)
Q Consensus 369 ~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P 412 (462)
.-+..+.||..+++.+|||+|.+|++|.+..|.+|.|-..++.|
T Consensus 480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 35678999999999999999999999999999999998776544
No 114
>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=86.80 E-value=0.34 Score=36.83 Aligned_cols=34 Identities=18% Similarity=0.370 Sum_probs=28.4
Q ss_pred eEEEEEeeCCccceeecCCchHHHHHHHHhCCeE
Q 012477 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKI 76 (462)
Q Consensus 43 ~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I 76 (462)
-...+.+.....+.|||++|++|++|.+...-.+
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 3457889999999999999999999998765444
No 115
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=85.81 E-value=0.57 Score=36.03 Aligned_cols=38 Identities=13% Similarity=0.270 Sum_probs=31.3
Q ss_pred eEEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcC
Q 012477 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE 80 (462)
Q Consensus 43 ~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~ 80 (462)
...++.|....-|.|||++|+.|++|+++-.-...+++
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~ 67 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPE 67 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCC
Confidence 34788899999999999999999999998765555543
No 116
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=85.10 E-value=0.32 Score=53.90 Aligned_cols=72 Identities=26% Similarity=0.247 Sum_probs=59.7
Q ss_pred ceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 012477 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD 214 (462)
Q Consensus 139 ~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~ 214 (462)
....++.+|.....+|||++|.+|+.++..|||-|.+.+-. +. .-.||.+.+.|.++.+..|...|.-.+.+
T Consensus 1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq--~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ--PD--NQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcC--Cc--cchhhhcccCCCChhhhhhhccccceeec
Confidence 34577889999999999999999999999999999996521 11 25689999999999999998888666544
No 117
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=85.07 E-value=0.7 Score=46.75 Aligned_cols=41 Identities=32% Similarity=0.421 Sum_probs=36.7
Q ss_pred eEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCC
Q 012477 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKEN 410 (462)
Q Consensus 370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~ 410 (462)
-...+.||..+++.+|||+|.+|++|.+..|-+|.|-..+.
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 35678899999999999999999999999999999976554
No 118
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=84.00 E-value=1.3 Score=33.57 Aligned_cols=34 Identities=26% Similarity=0.459 Sum_probs=28.0
Q ss_pred EEEEEecCCccceeecCCCchHHHHHHhhCceEE
Q 012477 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIR 404 (462)
Q Consensus 371 t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~ 404 (462)
...+.|..+..|.+|||.|++++.|+-.+..-+.
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 4557777888999999999999999988766544
No 119
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=83.69 E-value=0.59 Score=35.52 Aligned_cols=34 Identities=29% Similarity=0.474 Sum_probs=28.6
Q ss_pred eEEEEEEeCCceeeeecCCchHHHHHHhhcCceE
Q 012477 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQI 173 (462)
Q Consensus 140 ~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I 173 (462)
....+.+.....+.+||++|++|++|.....-.+
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 4577889999999999999999999987655444
No 120
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=83.28 E-value=2.2 Score=43.55 Aligned_cols=136 Identities=14% Similarity=0.102 Sum_probs=86.8
Q ss_pred EEeeeCCccccccccCChhHHhHHhhhCCe--EEecCCCCCCCceEEE-EecCCcccccccHHHHHHHhhcCcccccccc
Q 012477 287 RLVCPVANIGGVIGKGGAIINQIRQESGAA--IKVDSSSTEGDDCLIT-VSSKEFFEDTLSATIEAVVRLQPRCSEKIER 363 (462)
Q Consensus 287 ~v~ip~~~~g~IIGk~G~~Ik~I~~~sga~--I~i~~~~~~~~~~~i~-i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~ 363 (462)
++.+| +.-.++-|++.-++.+|++.+.|. +.+.... + . ++.+ +.|. .......+...+.-
T Consensus 384 q~~~e-d~EdFl~gkkngK~TrIm~~v~c~~~~~i~~~~-g-s-~~~~~~~g~-------~~~F~k~~~~~~~E------ 446 (657)
T COG5166 384 QFGVE-DNEDFLRGKKNGKATRIMKGVSCSELSSIVSST-G-S-IVETNGIGE-------KMSFSKKLSIPPTE------ 446 (657)
T ss_pred eecCC-chHHHhccccCcchhhhhhhcccceeeEEEecC-C-c-EEEEeccCc-------chhhHHHhcCCccc------
Confidence 33344 334477888888899999998887 4444432 1 1 3222 2232 11222233322111
Q ss_pred cCCCcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCc-eEEEEcCH---HHHHHHHHHHH
Q 012477 364 DSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDE-MVQISGDL---DLAKDALIQVM 439 (462)
Q Consensus 364 ~~~~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~-~v~I~G~~---~~v~~A~~~I~ 439 (462)
-.-...+.+|...|..|||.||..|.+++..-++.|+....-.+|. +..+ -|.|.-+. +++-.++.-++
T Consensus 447 ----Fpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~q---s~~~dNV~I~~PrKn~~ni~~~KNd~~ 519 (657)
T COG5166 447 ----FPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQ---SQWHDNVLIEAPRKNQDNISGKKNDKL 519 (657)
T ss_pred ----CchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcch---hhhhcceEEECCccCccchhcccccHH
Confidence 1134568899999999999999999999999999999876655553 2222 27777765 55667777777
Q ss_pred HHHHhhh
Q 012477 440 TRLRANL 446 (462)
Q Consensus 440 ~~l~~~~ 446 (462)
+++.++-
T Consensus 520 ~~V~~~c 526 (657)
T COG5166 520 DKVKQQC 526 (657)
T ss_pred HHHhhhc
Confidence 8877653
No 121
>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=82.79 E-value=3.6 Score=35.09 Aligned_cols=38 Identities=32% Similarity=0.646 Sum_probs=32.7
Q ss_pred EEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecC
Q 012477 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (462)
Q Consensus 141 ~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (462)
+-.+.|-...-|.+||++|.++++|..+||-+-.+.+.
T Consensus 77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 44567778888999999999999999999988887665
No 122
>PRK13764 ATPase; Provisional
Probab=82.72 E-value=3.2 Score=44.42 Aligned_cols=45 Identities=31% Similarity=0.499 Sum_probs=39.4
Q ss_pred CceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCC
Q 012477 138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLP 182 (462)
Q Consensus 138 ~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p 182 (462)
..-...+.||...++.+|||+|.+|++|+++.|.+|.|-..++.+
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 445788899999999999999999999999999999998765433
No 123
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=82.67 E-value=1.5 Score=38.51 Aligned_cols=33 Identities=30% Similarity=0.386 Sum_probs=28.2
Q ss_pred EEEeeCCccceeecCCchHHHHHHHHhCCeEEEc
Q 012477 46 RYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIG 79 (462)
Q Consensus 46 ~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~ 79 (462)
-++|-... |.-||++|++|++|++..|-+|.+-
T Consensus 64 IfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevV 96 (166)
T PRK06418 64 ILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVV 96 (166)
T ss_pred EEEEeCCC-cccccccchHHHHHHHHhCCcEEEE
Confidence 35666666 9999999999999999999988763
No 124
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=81.65 E-value=2.3 Score=44.02 Aligned_cols=66 Identities=20% Similarity=0.202 Sum_probs=54.9
Q ss_pred CcceEEEEEecCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC-HHHHHHHHHHHHHHHHh
Q 012477 367 LISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD-LDLAKDALIQVMTRLRA 444 (462)
Q Consensus 367 ~~~~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~l~~ 444 (462)
...+...+.|+.+....+||.+|-..|+|..+||+.-.+ ++.+|+|.-. +...++|+.+|...+..
T Consensus 594 y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 594 YSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEGTFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred cCceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCceEEEEecCHHHHHHHHHHHHHHhcC
Confidence 346778899999999999999999999999999965554 2347877774 78899999999887766
No 125
>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=80.80 E-value=2.2 Score=36.43 Aligned_cols=94 Identities=18% Similarity=0.322 Sum_probs=60.6
Q ss_pred cccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccccccccCCCcceEEEEEecC
Q 012477 299 IGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPT 378 (462)
Q Consensus 299 IGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~i~Vp~ 378 (462)
+-..|..|+.|..+..-+|.|-.+...- ..-..+.+.+..+.|.-.+ + .+-.-+..|.++.|-.
T Consensus 21 ~~~~~dli~~lAk~lrKRIvvR~dps~l--------------~~~e~A~~~I~~ivP~ea~-i-~di~Fd~~tGEV~Iea 84 (145)
T cd02410 21 FAEDGDLVKDLAKDLRKRIVIRPDPSVL--------------KPPEEAIKIILEIVPEEAG-I-TDIYFDDDTGEVIIEA 84 (145)
T ss_pred HhcccHHHHHHHHHHhceEEEcCChhhc--------------CCHHHHHHHHHHhCCCccC-c-eeeEecCCCcEEEEEE
Confidence 4456788999999888888876532110 0001233344444432111 0 0011123567888999
Q ss_pred CccceeecCCCchHHHHHHhhCceEEEecC
Q 012477 379 SRIGCLIGKGGSIITEMRRLTKANIRILPK 408 (462)
Q Consensus 379 ~~~g~IIGk~G~~I~~I~~~sga~I~i~~~ 408 (462)
..-|.+||++|.++++|..+||-.-.|-+.
T Consensus 85 eKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 85 EKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred cCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 999999999999999999999999888664
No 126
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=79.60 E-value=2.4 Score=32.61 Aligned_cols=35 Identities=20% Similarity=0.446 Sum_probs=28.5
Q ss_pred EEEEEecCCccceeecCCCchHHHHHHhhCceEEE
Q 012477 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405 (462)
Q Consensus 371 t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i 405 (462)
..++.|-...-|.|||++|+.|++|++.-.-...+
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 46777888888999999999999999886554444
No 127
>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=77.97 E-value=2.2 Score=34.78 Aligned_cols=29 Identities=24% Similarity=0.369 Sum_probs=25.6
Q ss_pred EEEEeeCCccceeecCCchHHHHHHHHhC
Q 012477 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (462)
Q Consensus 45 ~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg 73 (462)
+++.+....-|.|||++|++|++|++...
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~ 91 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQ 91 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence 57888888999999999999999998754
No 128
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=77.10 E-value=3 Score=32.34 Aligned_cols=28 Identities=25% Similarity=0.380 Sum_probs=24.0
Q ss_pred EEEEeeCCccceeecCCchHHHHHHHHh
Q 012477 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDT 72 (462)
Q Consensus 45 ~~ilvp~~~~g~IIGk~G~~Ik~i~~~t 72 (462)
.++.+....-|.+||++|.+|++|++.-
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 5666777899999999999999998774
No 129
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=76.35 E-value=2.6 Score=43.05 Aligned_cols=130 Identities=9% Similarity=0.001 Sum_probs=80.5
Q ss_pred ccceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEE-EcCCcccccccCCCCcCCHHHHHHHHHHHHHHHhhccCC
Q 012477 53 KIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTV-YSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGD 131 (462)
Q Consensus 53 ~~g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I-~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~~ 131 (462)
.--+|=||+--++.+|.+...|.+.+.=...+. .++.++ .|..- +..+-+..
T Consensus 390 ~EdFl~gkkngK~TrIm~~v~c~~~~~i~~~~g-s~~~~~~~g~~~-----------------~F~k~~~~--------- 442 (657)
T COG5166 390 NEDFLRGKKNGKATRIMKGVSCSELSSIVSSTG-SIVETNGIGEKM-----------------SFSKKLSI--------- 442 (657)
T ss_pred hHHHhccccCcchhhhhhhcccceeeEEEecCC-cEEEEeccCcch-----------------hhHHHhcC---------
Confidence 334777887667999999998885443111011 133222 22211 11111111
Q ss_pred CCCCCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCce-EEEEcCHHHH---HHHHHH
Q 012477 132 EDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDEL-VQISGEASVV---KKALCQ 207 (462)
Q Consensus 132 ~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~-v~I~G~~~~v---~~A~~~ 207 (462)
...+....+.+.||...|..|||.+|..|++++...++.|.+.-.-.++. +..+- |.|..+..++ --+.--
T Consensus 443 --~~~EFpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~q---s~~~dNV~I~~PrKn~~ni~~~KNd 517 (657)
T COG5166 443 --PPTEFPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQ---SQWHDNVLIEAPRKNQDNISGKKND 517 (657)
T ss_pred --CcccCchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcch---hhhhcceEEECCccCccchhccccc
Confidence 12334557889999999999999999999999999999999865444443 33333 7777765544 444455
Q ss_pred HHHHHhc
Q 012477 208 IASRLHD 214 (462)
Q Consensus 208 I~~~l~~ 214 (462)
+.+++.+
T Consensus 518 ~~~~V~~ 524 (657)
T COG5166 518 KLDKVKQ 524 (657)
T ss_pred HHHHHhh
Confidence 5555554
No 130
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=75.63 E-value=3.7 Score=36.08 Aligned_cols=37 Identities=32% Similarity=0.583 Sum_probs=31.6
Q ss_pred EEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecC
Q 012477 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (462)
Q Consensus 141 ~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (462)
.+-++|.... |..|||+|.+|+++++..|-+|.+-..
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence 4566776667 999999999999999999999988654
No 131
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=75.26 E-value=6.3 Score=36.45 Aligned_cols=29 Identities=38% Similarity=0.543 Sum_probs=25.3
Q ss_pred eEEEEEecCCccceeecCCCchHHHHHHh
Q 012477 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRL 398 (462)
Q Consensus 370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~ 398 (462)
..+.|.|-...-|.|||++|+.|++|++.
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 45678888889999999999999999865
No 132
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=71.87 E-value=3.7 Score=37.93 Aligned_cols=31 Identities=23% Similarity=0.331 Sum_probs=26.8
Q ss_pred ceEEEEEeeCCccceeecCCchHHHHHHHHh
Q 012477 42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDT 72 (462)
Q Consensus 42 ~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~t 72 (462)
....++.|....-|.|||++|++|++|++..
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l 80 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKEL 80 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHH
Confidence 4456788999999999999999999988764
No 133
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=71.43 E-value=13 Score=38.26 Aligned_cols=97 Identities=24% Similarity=0.344 Sum_probs=62.6
Q ss_pred ceeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHHHHhhccCCCCC
Q 012477 55 GSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDS 134 (462)
Q Consensus 55 g~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~~~~~ 134 (462)
..++=+.|.-|++|-++..-+|.|-... .+.-+ ..+|...|++.+-++.-.. +
T Consensus 41 P~~~~~~~dlik~lAk~lrKRI~iR~dP--------svl~~----------------~e~A~~~I~eivP~ea~i~---~ 93 (637)
T COG1782 41 PELFAKDGDLIKDLAKDLRKRIIIRPDP--------SVLKP----------------PEEARKIILEIVPEEAGIT---D 93 (637)
T ss_pred HHHhccchhHHHHHHHHHhhceEeccCc--------hhcCC----------------HHHHHHHHHHhCccccCce---e
Confidence 4456678899999999988777763210 11122 3456665555443322100 0
Q ss_pred CCCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecC
Q 012477 135 DGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (462)
Q Consensus 135 ~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (462)
-.-...+-.++|-...-|.+|||+|++.++|..+||-.-.+.+.
T Consensus 94 i~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 94 IYFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred EEecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 01122345678888899999999999999999999977777664
No 134
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=68.30 E-value=5.9 Score=30.65 Aligned_cols=28 Identities=32% Similarity=0.615 Sum_probs=22.4
Q ss_pred EEEEecCCccceeecCCCchHHHHHHhh
Q 012477 372 TRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (462)
Q Consensus 372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~s 399 (462)
..+.|-...-|.+||++|++|+++++.-
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 4455555778999999999999998764
No 135
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=68.22 E-value=4.7 Score=32.86 Aligned_cols=29 Identities=31% Similarity=0.524 Sum_probs=24.1
Q ss_pred EEEEecCCccceeecCCCchHHHHHHhhC
Q 012477 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTK 400 (462)
Q Consensus 372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~sg 400 (462)
.++.|-...-|.|||++|+.|++|++...
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~ 91 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQ 91 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence 55667777789999999999999997753
No 136
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=63.73 E-value=19 Score=37.21 Aligned_cols=96 Identities=18% Similarity=0.273 Sum_probs=63.7
Q ss_pred cccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccccccccCCCcceEEEEEe
Q 012477 297 GVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLV 376 (462)
Q Consensus 297 ~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~i~V 376 (462)
..+-+.|..|++|..+.--+|.|-.+...- ... ..+...+..+.|.-..-. +..-...+-++.|
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~dPsvl-------~~~-------e~A~~~I~eivP~ea~i~--~i~Fd~~tGEViI 105 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPDPSVL-------KPP-------EEARKIILEIVPEEAGIT--DIYFDDDTGEVII 105 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccCchhc-------CCH-------HHHHHHHHHhCccccCce--eEEecCCCceEEE
Confidence 456678899999999999888887643210 000 123333444433211100 0111235678889
Q ss_pred cCCccceeecCCCchHHHHHHhhCceEEEecC
Q 012477 377 PTSRIGCLIGKGGSIITEMRRLTKANIRILPK 408 (462)
Q Consensus 377 p~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~ 408 (462)
-.+.-|.||||+|++.++|.++||-.-.|.+.
T Consensus 106 ea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 106 EAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred EecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 99999999999999999999999998877664
No 137
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=61.94 E-value=9.4 Score=36.50 Aligned_cols=31 Identities=23% Similarity=0.318 Sum_probs=25.4
Q ss_pred ceEEEEEecCCcc-ceeecCCCchHHHHHHhh
Q 012477 369 SFTTRLLVPTSRI-GCLIGKGGSIITEMRRLT 399 (462)
Q Consensus 369 ~~t~~i~Vp~~~~-g~IIGk~G~~I~~I~~~s 399 (462)
.+...+.|..+.+ +-|||++|+.||+|...+
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 4778888887666 889999999999987553
No 138
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=59.30 E-value=32 Score=31.34 Aligned_cols=36 Identities=19% Similarity=0.288 Sum_probs=29.8
Q ss_pred eEEEEEecCCccceeecCCCchHHHHHHhhCceEEE
Q 012477 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405 (462)
Q Consensus 370 ~t~~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I~i 405 (462)
-+..+.+-.+..+.+||+.|.+++.|+-.+.+.+.-
T Consensus 91 ~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 355677777789999999999999999988776654
No 139
>PRK15494 era GTPase Era; Provisional
Probab=58.18 E-value=12 Score=37.29 Aligned_cols=37 Identities=19% Similarity=0.307 Sum_probs=28.7
Q ss_pred ceEEEEEecCCcc-ceeecCCCchHHHHHHh--------hCceEEE
Q 012477 369 SFTTRLLVPTSRI-GCLIGKGGSIITEMRRL--------TKANIRI 405 (462)
Q Consensus 369 ~~t~~i~Vp~~~~-g~IIGk~G~~I~~I~~~--------sga~I~i 405 (462)
.+...+.|..+-+ +-|||++|+.||+|... .|++|.+
T Consensus 272 ~i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l 317 (339)
T PRK15494 272 KINQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHL 317 (339)
T ss_pred EEEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEE
Confidence 4778889987766 88999999999988644 5665554
No 140
>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=58.11 E-value=29 Score=37.67 Aligned_cols=96 Identities=17% Similarity=0.262 Sum_probs=63.5
Q ss_pred cccccCChhHHhHHhhhCCeEEecCCCCCCCceEEEEecCCcccccccHHHHHHHhhcCcccccccccCCCcceEEEEEe
Q 012477 297 GVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLV 376 (462)
Q Consensus 297 ~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~i~i~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~i~V 376 (462)
..+-..|..|++|..+..-+|.|-.+...- ..-..+.+.+..+.|.-.+- .+-.-+..+-++.|
T Consensus 36 ~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~--------------~~~~~~~~~i~~~~~~~~~~--~~~~f~~~~~~v~i 99 (630)
T TIGR03675 36 ELFAKDDDLVKELAKKLRKRIVIRPDPSVL--------------LPPEEAIEKIKEIVPEEAGI--TDIYFDDVTGEVII 99 (630)
T ss_pred HHhccchHHHHHHHHHhhceEEEecChhhc--------------CCHHHHHHHHHHhCCCcCCc--eeEEecCCCceEEE
Confidence 345567789999999998888886532110 00022344444444332110 00111345678999
Q ss_pred cCCccceeecCCCchHHHHHHhhCceEEEecC
Q 012477 377 PTSRIGCLIGKGGSIITEMRRLTKANIRILPK 408 (462)
Q Consensus 377 p~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~ 408 (462)
-.+.-|.||||+|+++++|.++||-.-.|.+.
T Consensus 100 ~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 100 EAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred EEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 99999999999999999999999999888765
No 141
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=57.95 E-value=20 Score=38.93 Aligned_cols=96 Identities=24% Similarity=0.387 Sum_probs=59.3
Q ss_pred eeecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcccccccCCCCcCCHHHHHHHHHHHHHHHhhccCCCCCC
Q 012477 56 SIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDSD 135 (462)
Q Consensus 56 ~IIGk~G~~Ik~i~~~tg~~I~v~~~~~~~~ervi~I~G~~e~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~ 135 (462)
..+=.+|..|++|-++..-+|.|-... .+.-++ .+|.+.|.+.+-++.-. .+-
T Consensus 36 ~~~~~~~~~~~~~~~~~~~r~~~~~~~--------~~~~~~----------------~~~~~~i~~~~~~~~~~---~~~ 88 (630)
T TIGR03675 36 ELFAKDDDLVKELAKKLRKRIVIRPDP--------SVLLPP----------------EEAIEKIKEIVPEEAGI---TDI 88 (630)
T ss_pred HHhccchHHHHHHHHHhhceEEEecCh--------hhcCCH----------------HHHHHHHHHhCCCcCCc---eeE
Confidence 344567888999998887777653110 012222 33444444433222100 000
Q ss_pred CCCceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecC
Q 012477 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (462)
Q Consensus 136 ~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (462)
.-...+-.++|-...-|.||||+|.++++|..+||-+-.+.+.
T Consensus 89 ~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 89 YFDDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred EecCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 1122345677888889999999999999999999988888765
No 142
>PRK00089 era GTPase Era; Reviewed
Probab=55.72 E-value=13 Score=35.80 Aligned_cols=38 Identities=21% Similarity=0.502 Sum_probs=28.9
Q ss_pred cceEEEEEecCCcc-ceeecCCCchHHHHHH--------hhCceEEE
Q 012477 368 ISFTTRLLVPTSRI-GCLIGKGGSIITEMRR--------LTKANIRI 405 (462)
Q Consensus 368 ~~~t~~i~Vp~~~~-g~IIGk~G~~I~~I~~--------~sga~I~i 405 (462)
-.+...+.|..+-+ +-|||++|++|++|.. .+|++|.+
T Consensus 224 ~~i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l 270 (292)
T PRK00089 224 VRIEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL 270 (292)
T ss_pred EEEEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 34778888886655 8899999999998874 45666555
No 143
>COG1159 Era GTPase [General function prediction only]
Probab=55.36 E-value=15 Score=35.38 Aligned_cols=34 Identities=26% Similarity=0.554 Sum_probs=26.5
Q ss_pred CCCcceEEEEEecCCcc-ceeecCCCchHHHHHHh
Q 012477 365 SGLISFTTRLLVPTSRI-GCLIGKGGSIITEMRRL 398 (462)
Q Consensus 365 ~~~~~~t~~i~Vp~~~~-g~IIGk~G~~I~~I~~~ 398 (462)
...-.+...+.|+.+-. |-||||+|++||+|-..
T Consensus 224 ~~~~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~ 258 (298)
T COG1159 224 KGLLKIHATIYVERESQKGIIIGKNGAMIKKIGTA 258 (298)
T ss_pred CCeEEEEEEEEEecCCccceEECCCcHHHHHHHHH
Confidence 34456778888986655 99999999999987644
No 144
>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=47.22 E-value=22 Score=32.20 Aligned_cols=30 Identities=23% Similarity=0.417 Sum_probs=26.1
Q ss_pred EEEEEeeCCccceeecCCchHHHHHHHHhC
Q 012477 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (462)
Q Consensus 44 ~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg 73 (462)
..++.|....-|.|||++|..|++|++.-.
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~ 68 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKLQ 68 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHHH
Confidence 467888888999999999999999987754
No 145
>CHL00048 rps3 ribosomal protein S3
Probab=46.73 E-value=22 Score=32.75 Aligned_cols=32 Identities=16% Similarity=0.164 Sum_probs=26.8
Q ss_pred ceEEEEEeeCCccceeecCCchHHHHHHHHhC
Q 012477 42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (462)
Q Consensus 42 ~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg 73 (462)
....++.|....-|.|||++|.+|++|++.-.
T Consensus 65 ~~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 65 IDLIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred CCeEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 34467788888899999999999999998764
No 146
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=46.64 E-value=22 Score=32.59 Aligned_cols=30 Identities=27% Similarity=0.405 Sum_probs=25.2
Q ss_pred EEEEeeCCccceeecCCchHHHHHHHHhCC
Q 012477 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKS 74 (462)
Q Consensus 45 ~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~ 74 (462)
.++.|....-|.+||++|.+|++|++...-
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 566677788999999999999999988643
No 147
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=44.46 E-value=59 Score=32.14 Aligned_cols=51 Identities=18% Similarity=0.165 Sum_probs=43.0
Q ss_pred cCCccceeecCCCchHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHH
Q 012477 377 PTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVM 439 (462)
Q Consensus 377 p~~~~g~IIGk~G~~I~~I~~~sga~I~i~~~~~~P~~~~~~~~~v~I~G~~~~v~~A~~~I~ 439 (462)
+.+..-.+.|..+.+++.|.+..|+.|..- .+.++|+|+.+.+..|...+.
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~r------------G~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVAR------------GEAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeC------------CceEEEEechHHHHHHHHHHh
Confidence 356778899999999999999999988752 247999999888888887776
No 148
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=44.11 E-value=25 Score=32.54 Aligned_cols=32 Identities=9% Similarity=0.222 Sum_probs=26.7
Q ss_pred EEEEEeeCCccceeecCCchHHHHHHHHhCCe
Q 012477 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSK 75 (462)
Q Consensus 44 ~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~ 75 (462)
..++.|....-|.|||++|..|++|++...-.
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 36778888889999999999999999876543
No 149
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=42.54 E-value=18 Score=32.91 Aligned_cols=36 Identities=14% Similarity=0.160 Sum_probs=28.8
Q ss_pred ceEEEEEeeCCccceeecCCchHHHHHHHHhCCeEE
Q 012477 42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIR 77 (462)
Q Consensus 42 ~~~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~ 77 (462)
.-.+.+-+..+..+.+||+.|+++..||--++.-++
T Consensus 90 ~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~ 125 (208)
T COG1847 90 GRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLN 125 (208)
T ss_pred CcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhh
Confidence 345566777788999999999999999988765544
No 150
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=41.13 E-value=28 Score=33.89 Aligned_cols=37 Identities=24% Similarity=0.491 Sum_probs=28.5
Q ss_pred cCCCcceEEEEEecCCcc-ceeecCCCchHHHHHHhhC
Q 012477 364 DSGLISFTTRLLVPTSRI-GCLIGKGGSIITEMRRLTK 400 (462)
Q Consensus 364 ~~~~~~~t~~i~Vp~~~~-g~IIGk~G~~I~~I~~~sg 400 (462)
+.+...+..++.+|.... ..||||||..|++|-++.+
T Consensus 322 ~~g~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 322 PAGVLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred CCcEEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 344567888999997755 6679999999999976543
No 151
>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=39.86 E-value=22 Score=33.88 Aligned_cols=29 Identities=21% Similarity=0.264 Sum_probs=22.8
Q ss_pred eEEEEEeeCC-ccceeecCCchHHHHHHHH
Q 012477 43 TVYRYLCPIR-KIGSIIGRGGEIVKQLRID 71 (462)
Q Consensus 43 ~~~~ilvp~~-~~g~IIGk~G~~Ik~i~~~ 71 (462)
+...++|..+ +.+.|||++|+.||+|...
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ 250 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIA 250 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence 5666777755 5688999999999988754
No 152
>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=37.25 E-value=36 Score=30.86 Aligned_cols=29 Identities=31% Similarity=0.560 Sum_probs=24.3
Q ss_pred EEEEEecCCccceeecCCCchHHHHHHhh
Q 012477 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (462)
Q Consensus 371 t~~i~Vp~~~~g~IIGk~G~~I~~I~~~s 399 (462)
..++.|-...-|.|||++|..|++|++.-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 46677777788999999999999998764
No 153
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=36.40 E-value=37 Score=31.14 Aligned_cols=29 Identities=34% Similarity=0.644 Sum_probs=22.9
Q ss_pred EEEEecCCccceeecCCCchHHHHHHhhC
Q 012477 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTK 400 (462)
Q Consensus 372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~sg 400 (462)
..+.|-...-|.+||++|++|+++++.-.
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 44555557789999999999999987753
No 154
>PRK15494 era GTPase Era; Provisional
Probab=34.94 E-value=45 Score=33.14 Aligned_cols=36 Identities=17% Similarity=0.373 Sum_probs=26.8
Q ss_pred eEEEEEEeCC-ceeeeecCCchHHHHHH--------hhcCceEEE
Q 012477 140 VTAKLLVPSD-QIGCVIGKGGQIVQNIR--------SETGAQIRI 175 (462)
Q Consensus 140 ~~~~l~ip~~-~~g~IIGk~G~~Ik~I~--------~~tga~I~i 175 (462)
+...|+|... +-+.|||++|++||+|. +-.|++|.+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l 317 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHL 317 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEE
Confidence 5566777764 66889999999999875 446666654
No 155
>CHL00048 rps3 ribosomal protein S3
Probab=34.91 E-value=40 Score=31.09 Aligned_cols=29 Identities=21% Similarity=0.169 Sum_probs=24.1
Q ss_pred EEEEEecCCccceeecCCCchHHHHHHhh
Q 012477 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (462)
Q Consensus 371 t~~i~Vp~~~~g~IIGk~G~~I~~I~~~s 399 (462)
..++.|-...-|.|||++|..|++|++.-
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 45666777778999999999999998765
No 156
>PRK00089 era GTPase Era; Reviewed
Probab=34.03 E-value=31 Score=33.27 Aligned_cols=36 Identities=22% Similarity=0.332 Sum_probs=25.5
Q ss_pred eEEEEEeeCC-ccceeecCCchHHHHHHH--------HhCCeEEE
Q 012477 43 TVYRYLCPIR-KIGSIIGRGGEIVKQLRI--------DTKSKIRI 78 (462)
Q Consensus 43 ~~~~ilvp~~-~~g~IIGk~G~~Ik~i~~--------~tg~~I~v 78 (462)
+...|+|..+ +.+.|||++|+.|++|.. -++++|.+
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l 270 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL 270 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 4455666644 568899999999998764 35666655
No 157
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=33.78 E-value=41 Score=31.12 Aligned_cols=29 Identities=24% Similarity=0.458 Sum_probs=23.8
Q ss_pred EEEEEecCCccceeecCCCchHHHHHHhh
Q 012477 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (462)
Q Consensus 371 t~~i~Vp~~~~g~IIGk~G~~I~~I~~~s 399 (462)
..++.|-...-|.|||++|..|++|++.-
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L 73 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLL 73 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHH
Confidence 35667777778999999999999998764
No 158
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=31.49 E-value=50 Score=30.41 Aligned_cols=29 Identities=28% Similarity=0.458 Sum_probs=25.0
Q ss_pred EEEEeeCCccceeecCCchHHHHHHHHhC
Q 012477 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (462)
Q Consensus 45 ~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg 73 (462)
+++.+....-+.|||++|..|++|++...
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l~ 92 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDLQ 92 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHHH
Confidence 56888888889999999999999997653
No 159
>COG1159 Era GTPase [General function prediction only]
Probab=31.27 E-value=39 Score=32.65 Aligned_cols=37 Identities=19% Similarity=0.288 Sum_probs=26.7
Q ss_pred ceEEEEEeeCC-ccceeecCCchHHHHHH--------HHhCCeEEE
Q 012477 42 DTVYRYLCPIR-KIGSIIGRGGEIVKQLR--------IDTKSKIRI 78 (462)
Q Consensus 42 ~~~~~ilvp~~-~~g~IIGk~G~~Ik~i~--------~~tg~~I~v 78 (462)
.+...++|+.+ +-+.||||+|++||+|- +-.+++|.+
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L 273 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYL 273 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEE
Confidence 34556777754 67889999999999875 445666655
No 160
>PRK03818 putative transporter; Validated
Probab=29.52 E-value=7.2e+02 Score=26.54 Aligned_cols=135 Identities=13% Similarity=0.193 Sum_probs=70.8
Q ss_pred EEEEEeeCCccceeecCCchHHHHHHHHhCCeEEEcC---------C---CCCCCceEEEEEcCCcccccccCCCCcCCH
Q 012477 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE---------T---VPGSEERVVTVYSASDETNAFEDGDKFVSP 111 (462)
Q Consensus 44 ~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg~~I~v~~---------~---~~~~~ervi~I~G~~e~~~~~~~~~~~v~~ 111 (462)
..++.|+.+. ++ |++++++.......+.|.. + ..=...+++.+.|..++
T Consensus 206 ~r~~~V~~s~---li---GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~------------- 266 (552)
T PRK03818 206 TINIRVENPN---LH---GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPED------------- 266 (552)
T ss_pred eEEEEEeCCC---CC---CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHH-------------
Confidence 3566666433 34 6789999998876665531 0 01112467888888655
Q ss_pred HHHHHHHHHHHHHHhhccCCCCCCCCCceEEEEEEeCCceeeeecCCchHHHHH--HhhcCceEEEecCCC--CCC---c
Q 012477 112 AQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNI--RSETGAQIRILKDEH--LPS---C 184 (462)
Q Consensus 112 a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~IIGk~G~~Ik~I--~~~tga~I~i~~~~~--~p~---~ 184 (462)
+.++.+....+.. .+.+.........++++|+ +.++|| +++++ ++++|+.+.--...+ ++. .
T Consensus 267 ----l~~l~~~~Gl~~~-~~~~~~~~~~~~E~Vvv~~---S~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~ 335 (552)
T PRK03818 267 ----LHKAQLVIGEEVD-TSLSTRGTDLRSERVVVTN---EKVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDL 335 (552)
T ss_pred ----HHHHHHhcCCccC-ccccccCcceEEEEEEEcC---hhccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCC
Confidence 2333222211100 0001111223444445554 366765 67776 577887754332211 111 0
Q ss_pred CCCCCceEEEEcCHHHHHHHHHHH
Q 012477 185 ALRSDELVQISGEASVVKKALCQI 208 (462)
Q Consensus 185 ~~~~~r~v~I~G~~~~v~~A~~~I 208 (462)
.-..-..+.+.|+++++++..+.+
T Consensus 336 ~Lq~GD~LlVvG~~~~i~~l~~~L 359 (552)
T PRK03818 336 SLQFGDILNLVGRPEAIDAVANVL 359 (552)
T ss_pred EEecCCEEEEEECHHHHHHHHHHh
Confidence 012234688999999999977753
No 161
>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=29.08 E-value=1.8e+02 Score=25.57 Aligned_cols=57 Identities=23% Similarity=0.239 Sum_probs=42.7
Q ss_pred CceEEEEEEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 012477 138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRL 212 (462)
Q Consensus 138 ~~~~~~l~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l 212 (462)
+..++|+-++...+ =..+.+|.+-+|+-+.+ . .+..|.|.|..+.|..|++.+...-
T Consensus 111 ~~~~iRv~l~~~i~-------~erl~ei~E~~gvI~Ef-e----------e~~~V~I~Gdke~Ik~aLKe~s~~w 167 (169)
T PF09869_consen 111 GFETIRVKLKKPIQ-------EERLQEISEWHGVIFEF-E----------EDDKVVIEGDKERIKKALKEFSSFW 167 (169)
T ss_pred CceeEEEecCccch-------HHHHHHHHHHhceeEEe-c----------CCcEEEEeccHHHHHHHHHHHHHHh
Confidence 34455665555543 25778899999999988 2 2457999999999999999987653
No 162
>COG0490 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]
Probab=28.84 E-value=45 Score=29.11 Aligned_cols=62 Identities=21% Similarity=0.231 Sum_probs=39.6
Q ss_pred EEEecCCccceeecCCCchHHHHHHhhCceE-EEecCCCCCCCCC-----CCCceEEEEcCHHHHHHHHHHHH
Q 012477 373 RLLVPTSRIGCLIGKGGSIITEMRRLTKANI-RILPKENLPKIAS-----EDDEMVQISGDLDLAKDALIQVM 439 (462)
Q Consensus 373 ~i~Vp~~~~g~IIGk~G~~I~~I~~~sga~I-~i~~~~~~P~~~~-----~~~~~v~I~G~~~~v~~A~~~I~ 439 (462)
++..-+.++|.=||- -+|++.|||.| -|-++.+.=.+++ ....++.+.|+..++..++.+..
T Consensus 91 ~i~~~s~~~GksiGd-----l~irq~TGaTIIAI~r~~e~I~SPgPy~vle~gDtlvviG~~~~~~r~~~f~~ 158 (162)
T COG0490 91 KIEAGSPFIGKTIGD-----LNIRQNTGATVIAIVRNEEKILSPGPYTVLEAGDTLVVIGEETGLKRAKRFLL 158 (162)
T ss_pred eeecCCcccCcchhh-----cccccccCcEEEEEEecCcEecCCCchhhhcCCCEEEEEecchHhHHHHHHhh
Confidence 333445566666664 46889999994 4544443111122 33468999999999999987654
No 163
>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=28.38 E-value=1.5e+02 Score=22.75 Aligned_cols=54 Identities=19% Similarity=0.183 Sum_probs=40.9
Q ss_pred CchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHHHHHh
Q 012477 158 GGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLH 213 (462)
Q Consensus 158 ~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~ 213 (462)
+=.-+.++-+..|+++.....+.-. ....+.+++++|+..++..|.+.+...|.
T Consensus 32 G~~~~~~i~~~l~~~v~~~~~dG~~--v~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 32 GLEEAEEIFEKLGLEVEWLVKDGDR--VEPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp SHHHHHHHHHHCTEEEEESS-TT-E--EETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhhccEEEEEEeCCCCC--ccCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 4457777888889999887554322 13567899999999999999998888775
No 164
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=26.39 E-value=51 Score=32.13 Aligned_cols=33 Identities=33% Similarity=0.536 Sum_probs=26.0
Q ss_pred cceEEEEeeeC-CccccccccCChhHHhHHhhhC
Q 012477 282 KEFSLRLVCPV-ANIGGVIGKGGAIINQIRQESG 314 (462)
Q Consensus 282 ~~~~~~v~ip~-~~~g~IIGk~G~~Ik~I~~~sg 314 (462)
-.+..++.+|. ++...|||++|..|++|-++-+
T Consensus 326 l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 326 LFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 44678889996 5667889999999999876543
No 165
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=25.13 E-value=1.4e+02 Score=29.69 Aligned_cols=53 Identities=19% Similarity=0.226 Sum_probs=44.3
Q ss_pred EEeCCceeeeecCCchHHHHHHhhcCceEEEecCCCCCCcCCCCCceEEEEcCHHHHHHHHHHHH
Q 012477 145 LVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIA 209 (462)
Q Consensus 145 ~ip~~~~g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~ 209 (462)
+-+....-.+.|..+.+++.|+..+|+.|... .+.++|.|....|..|...+.
T Consensus 20 ~~~~~~~~~l~G~~~~~l~l~e~~~gv~i~~r------------G~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 20 LSDDNELVALFGPTDTNLSLLEIALGVSIVAR------------GEAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred cCCchhhhhhcCCCCccHHHHHHHhCcEEEeC------------CceEEEEechHHHHHHHHHHh
Confidence 33466778899999999999999999999752 457999999878888888777
No 166
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=22.97 E-value=80 Score=29.06 Aligned_cols=28 Identities=39% Similarity=0.577 Sum_probs=23.0
Q ss_pred EEEEecCCccceeecCCCchHHHHHHhh
Q 012477 372 TRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (462)
Q Consensus 372 ~~i~Vp~~~~g~IIGk~G~~I~~I~~~s 399 (462)
.++.|-...-|.|||++|..|++|++.-
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l 91 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDL 91 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHH
Confidence 5577777777999999999999998653
No 167
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=21.30 E-value=90 Score=29.18 Aligned_cols=30 Identities=23% Similarity=0.389 Sum_probs=24.5
Q ss_pred EEEEEeeCCccceeecCCchHHHHHHHHhC
Q 012477 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (462)
Q Consensus 44 ~~~ilvp~~~~g~IIGk~G~~Ik~i~~~tg 73 (462)
.+++.|....-+.|||++|..|++|++...
T Consensus 63 ~i~I~I~~~rP~~iiG~~g~~i~~l~~~L~ 92 (232)
T PRK00310 63 RVRVTIHTARPGIVIGKKGAEIEKLRKELE 92 (232)
T ss_pred eEEEEEEECCCccccCCCcHHHHHHHHHHH
Confidence 356667777789999999999999987753
No 168
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=21.10 E-value=1.6e+02 Score=23.78 Aligned_cols=26 Identities=23% Similarity=0.277 Sum_probs=23.4
Q ss_pred ceEEEEcCHHHHHHHHHHHHHHHHhh
Q 012477 420 EMVQISGDLDLAKDALIQVMTRLRAN 445 (462)
Q Consensus 420 ~~v~I~G~~~~v~~A~~~I~~~l~~~ 445 (462)
..+.|+|+-.+|+.|+..+.+-+++.
T Consensus 75 GslvitGdvs~Ve~Al~~V~~~l~~~ 100 (111)
T PRK15468 75 GALVIYGSVGAVEEALSQTVSGLGRL 100 (111)
T ss_pred eeEEEEccHHHHHHHHHHHHHHHHhh
Confidence 46999999999999999999988874
No 169
>cd07055 BMC_like_2 Bacterial Micro-Compartment (BMC)-like domain 2. BMC like 2 domains exist in cyanobacteria, proteobacteria, and actinobacteria and are homologs of carboxysome shell proteins. They might be encoded from putative organelles involved in unknown metabolic process. Although it has been suggested that these carboxysome shell protein homologs form hexamers and further assemble into the flat facets of the polyhedral bacterial organelles shell at present no experimental evidence exists to directly support this view.
Probab=20.30 E-value=1.1e+02 Score=22.02 Aligned_cols=21 Identities=14% Similarity=0.154 Sum_probs=17.8
Q ss_pred ceEEEEcCHHHHHHHHHHHHH
Q 012477 420 EMVQISGDLDLAKDALIQVMT 440 (462)
Q Consensus 420 ~~v~I~G~~~~v~~A~~~I~~ 440 (462)
-.+.|.|+..+|+.|+..|.+
T Consensus 39 ~~l~i~Gdvs~Ve~Al~~i~~ 59 (61)
T cd07055 39 ITLAIFGETSAVELAMREIEE 59 (61)
T ss_pred EEEEEEecHHHHHHHHHHHhh
Confidence 367799999999999988765
Done!