Query 009566
Match_columns 532
No_of_seqs 326 out of 2129
Neff 8.4
Searched_HMMs 46136
Date Thu Mar 28 14:40:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009566.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009566hhsearch_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 7.1E-45 1.5E-49 378.4 34.7 404 5-450 6-415 (485)
2 KOG1676 K-homology type RNA bi 100.0 1.2E-42 2.5E-47 354.8 30.7 329 41-446 52-391 (600)
3 KOG2193 IGF-II mRNA-binding pr 100.0 7.7E-43 1.7E-47 339.3 21.4 357 38-447 194-567 (584)
4 KOG2192 PolyC-binding hnRNP-K 100.0 2.2E-33 4.9E-38 258.7 22.3 342 26-445 32-385 (390)
5 KOG1676 K-homology type RNA bi 100.0 4.2E-28 9E-33 248.5 22.6 232 38-338 134-374 (600)
6 KOG2193 IGF-II mRNA-binding pr 100.0 2.3E-28 5.1E-33 238.5 9.7 243 138-447 197-484 (584)
7 KOG2191 RNA-binding protein NO 99.9 7E-26 1.5E-30 215.4 21.2 237 41-322 37-282 (402)
8 KOG2192 PolyC-binding hnRNP-K 99.9 7.3E-23 1.6E-27 189.3 16.4 173 282-479 46-218 (390)
9 KOG2191 RNA-binding protein NO 99.9 2.1E-21 4.5E-26 185.1 23.1 173 136-447 35-207 (402)
10 KOG2190 PolyC-binding proteins 99.9 8.7E-21 1.9E-25 198.3 20.5 173 284-464 43-225 (485)
11 TIGR03665 arCOG04150 arCOG0415 99.5 2.4E-14 5.1E-19 131.5 10.2 135 288-444 2-151 (172)
12 TIGR03665 arCOG04150 arCOG0415 99.5 1.8E-14 3.9E-19 132.2 9.5 137 47-215 2-152 (172)
13 PRK13763 putative RNA-processi 99.5 9.2E-14 2E-18 128.4 12.1 143 284-445 3-158 (180)
14 PRK13763 putative RNA-processi 99.5 8.7E-14 1.9E-18 128.6 11.0 139 43-215 3-158 (180)
15 cd02396 PCBP_like_KH K homolog 99.4 9.7E-13 2.1E-17 100.8 7.6 64 372-439 2-65 (65)
16 cd02396 PCBP_like_KH K homolog 99.3 4.5E-12 9.7E-17 97.1 6.3 55 44-98 1-56 (65)
17 KOG2208 Vigilin [Lipid transpo 99.3 1.2E-11 2.6E-16 137.1 9.2 305 42-445 200-563 (753)
18 cd02394 vigilin_like_KH K homo 99.2 1.2E-11 2.5E-16 94.0 5.8 61 372-439 2-62 (62)
19 KOG2279 Kinase anchor protein 99.2 6.1E-11 1.3E-15 121.3 12.5 271 39-339 64-354 (608)
20 cd02393 PNPase_KH Polynucleoti 99.2 3.8E-11 8.2E-16 90.5 8.0 58 370-438 2-60 (61)
21 PF00013 KH_1: KH domain syndr 99.2 1.1E-11 2.4E-16 93.4 4.2 60 371-438 1-60 (60)
22 KOG2279 Kinase anchor protein 99.2 6.6E-11 1.4E-15 121.0 8.3 233 137-445 65-369 (608)
23 cd00105 KH-I K homology RNA-bi 99.1 1.8E-10 4E-15 87.9 8.1 62 372-438 2-63 (64)
24 KOG2208 Vigilin [Lipid transpo 99.1 2.3E-10 5E-15 127.0 10.9 318 42-407 346-746 (753)
25 cd02394 vigilin_like_KH K homo 99.1 1.8E-10 3.9E-15 87.4 5.1 60 142-208 2-61 (62)
26 PF00013 KH_1: KH domain syndr 99.1 1.7E-10 3.6E-15 87.0 4.5 60 141-208 1-60 (60)
27 cd02393 PNPase_KH Polynucleoti 99.0 1.4E-09 3E-14 81.9 7.9 58 140-208 2-60 (61)
28 cd00105 KH-I K homology RNA-bi 99.0 2.4E-09 5.2E-14 81.6 7.7 62 142-208 2-63 (64)
29 PF13014 KH_3: KH domain 98.9 1.7E-09 3.6E-14 75.5 5.7 42 53-94 1-43 (43)
30 PF13014 KH_3: KH domain 98.9 2.9E-09 6.2E-14 74.3 5.5 43 380-426 1-43 (43)
31 smart00322 KH K homology RNA-b 98.9 1.3E-08 2.8E-13 78.2 8.9 67 369-442 2-68 (69)
32 COG1094 Predicted RNA-binding 98.8 5E-08 1.1E-12 88.8 10.2 139 283-445 7-165 (194)
33 COG1094 Predicted RNA-binding 98.8 1.6E-07 3.4E-12 85.6 13.4 148 41-215 6-165 (194)
34 smart00322 KH K homology RNA-b 98.7 1.4E-07 3E-12 72.4 8.9 67 139-212 2-68 (69)
35 cd02395 SF1_like-KH Splicing f 98.5 3.5E-07 7.6E-12 78.4 8.1 68 378-445 14-96 (120)
36 KOG2113 Predicted RNA binding 98.3 8.2E-07 1.8E-11 85.3 4.5 149 282-441 24-180 (394)
37 cd02395 SF1_like-KH Splicing f 98.2 8.1E-06 1.8E-10 70.0 7.9 67 149-215 15-96 (120)
38 KOG0119 Splicing factor 1/bran 98.0 3.4E-05 7.4E-10 78.9 11.2 100 344-445 113-231 (554)
39 KOG2113 Predicted RNA binding 98.0 1E-05 2.2E-10 78.0 5.8 143 136-336 22-164 (394)
40 PRK08406 transcription elongat 97.9 1.3E-05 2.7E-10 70.9 5.2 102 44-175 33-134 (140)
41 TIGR02696 pppGpp_PNP guanosine 97.9 3.3E-05 7.2E-10 84.7 9.4 98 105-214 544-642 (719)
42 TIGR02696 pppGpp_PNP guanosine 97.9 2.3E-05 5.1E-10 85.8 8.0 66 368-444 576-642 (719)
43 PRK08406 transcription elongat 97.9 5.1E-05 1.1E-09 67.1 8.7 103 284-405 32-134 (140)
44 KOG0336 ATP-dependent RNA heli 97.5 0.00013 2.9E-09 73.4 5.2 64 30-96 34-97 (629)
45 TIGR03591 polynuc_phos polyrib 97.5 0.00025 5.5E-09 79.0 7.9 97 107-214 518-615 (684)
46 TIGR01952 nusA_arch NusA famil 97.5 0.00041 8.9E-09 61.2 7.4 103 285-406 34-136 (141)
47 TIGR03591 polynuc_phos polyrib 97.5 0.00018 3.9E-09 80.2 6.2 65 369-444 550-615 (684)
48 TIGR01952 nusA_arch NusA famil 97.4 0.00021 4.5E-09 63.0 5.3 103 44-176 34-136 (141)
49 KOG0119 Splicing factor 1/bran 97.4 0.0015 3.2E-08 67.3 11.3 76 139-214 137-230 (554)
50 PLN00207 polyribonucleotide nu 97.4 0.00038 8.1E-09 78.3 7.7 99 105-214 650-750 (891)
51 COG1185 Pnp Polyribonucleotide 97.3 0.00034 7.4E-09 75.2 6.3 114 90-214 491-616 (692)
52 KOG1588 RNA-binding protein Sa 97.2 0.001 2.2E-08 63.6 7.9 76 368-443 90-190 (259)
53 PLN00207 polyribonucleotide nu 97.1 0.00051 1.1E-08 77.2 4.7 66 368-444 683-750 (891)
54 COG1185 Pnp Polyribonucleotide 97.1 0.00091 2E-08 72.1 6.2 67 369-446 551-618 (692)
55 KOG0336 ATP-dependent RNA heli 96.9 0.0017 3.7E-08 65.6 6.3 67 369-443 46-112 (629)
56 COG0195 NusA Transcription elo 96.8 0.004 8.6E-08 57.8 7.6 103 285-407 77-179 (190)
57 COG0195 NusA Transcription elo 96.8 0.0029 6.2E-08 58.7 6.2 103 45-178 78-180 (190)
58 KOG1588 RNA-binding protein Sa 96.8 0.0018 3.8E-08 62.1 4.8 41 38-78 87-133 (259)
59 PRK11824 polynucleotide phosph 96.6 0.0023 5E-08 71.7 4.9 97 107-214 521-618 (693)
60 cd02134 NusA_KH NusA_K homolog 96.5 0.0046 1E-07 46.4 4.7 37 42-78 24-60 (61)
61 KOG2814 Transcription coactiva 96.4 0.0038 8.2E-08 61.5 4.8 71 369-446 56-127 (345)
62 cd02134 NusA_KH NusA_K homolog 96.4 0.0059 1.3E-07 45.8 4.6 36 370-405 25-60 (61)
63 COG5176 MSL5 Splicing factor ( 96.4 0.026 5.7E-07 51.8 9.5 42 368-409 146-193 (269)
64 KOG2814 Transcription coactiva 96.2 0.0055 1.2E-07 60.4 4.7 71 139-215 56-126 (345)
65 PRK04163 exosome complex RNA-b 96.2 0.0092 2E-07 57.8 6.2 63 372-445 147-210 (235)
66 PRK12328 nusA transcription el 96.2 0.018 3.8E-07 58.8 8.4 97 293-410 251-348 (374)
67 PRK00106 hypothetical protein; 96.2 0.015 3.2E-07 62.7 8.0 67 369-445 224-292 (535)
68 TIGR03319 YmdA_YtgF conserved 96.2 0.013 2.8E-07 63.3 7.7 67 369-445 203-271 (514)
69 TIGR01953 NusA transcription t 96.2 0.017 3.7E-07 58.9 8.1 93 293-407 243-338 (341)
70 PRK11824 polynucleotide phosph 96.1 0.0042 9E-08 69.6 3.4 65 369-444 553-618 (693)
71 PRK12704 phosphodiesterase; Pr 96.1 0.016 3.5E-07 62.6 7.7 66 369-444 209-276 (520)
72 PRK00468 hypothetical protein; 95.9 0.0095 2.1E-07 46.5 3.7 34 39-72 26-59 (75)
73 TIGR01953 NusA transcription t 95.9 0.015 3.3E-07 59.2 6.3 96 52-178 243-339 (341)
74 PRK12327 nusA transcription el 95.8 0.027 5.8E-07 57.8 7.8 96 293-408 245-341 (362)
75 PRK12328 nusA transcription el 95.7 0.021 4.5E-07 58.3 6.1 95 52-178 251-346 (374)
76 PRK12327 nusA transcription el 95.6 0.021 4.7E-07 58.5 6.0 96 52-178 245-341 (362)
77 PRK02821 hypothetical protein; 95.6 0.014 3E-07 45.8 3.5 36 39-74 27-62 (77)
78 PRK12329 nusA transcription el 95.5 0.032 7E-07 57.9 7.0 94 293-407 277-372 (449)
79 PRK09202 nusA transcription el 95.3 0.04 8.7E-07 58.6 7.0 95 293-408 245-340 (470)
80 PF14611 SLS: Mitochondrial in 95.3 0.54 1.2E-05 44.7 14.1 131 285-445 27-166 (210)
81 PRK12329 nusA transcription el 95.1 0.024 5.3E-07 58.8 4.6 95 52-177 277-372 (449)
82 PRK00468 hypothetical protein; 95.1 0.023 5.1E-07 44.3 3.4 34 367-400 27-60 (75)
83 COG5176 MSL5 Splicing factor ( 95.1 0.066 1.4E-06 49.2 6.8 44 136-179 144-193 (269)
84 PRK02821 hypothetical protein; 94.9 0.028 6E-07 44.1 3.2 34 368-401 29-62 (77)
85 PRK01064 hypothetical protein; 94.8 0.039 8.4E-07 43.4 3.9 34 40-73 27-60 (78)
86 COG1837 Predicted RNA-binding 94.8 0.037 7.9E-07 43.1 3.6 33 40-72 27-59 (76)
87 PF14611 SLS: Mitochondrial in 94.7 0.77 1.7E-05 43.6 13.5 63 142-214 28-90 (210)
88 COG1837 Predicted RNA-binding 94.5 0.046 1E-06 42.6 3.6 34 367-400 27-60 (76)
89 KOG1067 Predicted RNA-binding 94.5 0.071 1.5E-06 56.2 5.9 114 90-215 543-661 (760)
90 PRK04163 exosome complex RNA-b 94.4 0.061 1.3E-06 52.2 5.2 63 142-215 147-210 (235)
91 PRK09202 nusA transcription el 94.4 0.048 1E-06 58.0 4.8 95 52-178 245-340 (470)
92 KOG0921 Dosage compensation co 94.3 0.12 2.5E-06 57.7 7.5 28 283-310 935-962 (1282)
93 TIGR03319 YmdA_YtgF conserved 94.3 0.18 3.9E-06 54.5 9.0 67 138-214 202-270 (514)
94 PRK00106 hypothetical protein; 94.2 0.23 5.1E-06 53.6 9.3 67 138-214 223-291 (535)
95 PRK12704 phosphodiesterase; Pr 94.1 0.21 4.6E-06 54.1 9.0 66 139-214 209-276 (520)
96 PRK12705 hypothetical protein; 94.1 0.07 1.5E-06 57.2 5.1 64 369-442 197-262 (508)
97 PRK01064 hypothetical protein; 93.6 0.083 1.8E-06 41.6 3.5 34 367-400 27-60 (78)
98 PF13083 KH_4: KH domain; PDB: 92.7 0.057 1.2E-06 42.0 1.4 34 40-73 26-59 (73)
99 KOG1067 Predicted RNA-binding 92.1 0.2 4.3E-06 53.0 4.8 69 365-445 592-661 (760)
100 KOG3273 Predicted RNA-binding 90.8 0.12 2.6E-06 47.3 1.4 55 378-444 177-231 (252)
101 COG5166 Uncharacterized conser 90.3 0.79 1.7E-05 48.1 7.0 204 56-405 393-606 (657)
102 KOG4369 RTK signaling protein 90.2 0.078 1.7E-06 60.0 -0.3 70 372-445 1342-1411(2131)
103 cd02409 KH-II KH-II (K homolo 90.1 0.51 1.1E-05 35.5 4.3 35 42-76 24-58 (68)
104 cd02409 KH-II KH-II (K homolo 88.5 0.81 1.8E-05 34.3 4.4 34 370-403 25-58 (68)
105 PRK12705 hypothetical protein; 88.3 0.37 8E-06 51.7 3.1 44 38-81 193-237 (508)
106 KOG2874 rRNA processing protei 87.8 0.98 2.1E-05 43.7 5.2 52 382-445 161-212 (356)
107 PF13184 KH_5: NusA-like KH do 87.7 0.44 9.6E-06 36.6 2.4 36 372-407 5-46 (69)
108 KOG3875 Peroxisomal biogenesis 87.2 2.1 4.6E-05 42.1 7.2 23 503-525 78-100 (362)
109 PRK13764 ATPase; Provisional 87.0 1.2 2.6E-05 49.0 6.2 43 370-412 481-523 (602)
110 cd02414 jag_KH jag_K homology 86.8 0.69 1.5E-05 36.3 3.1 33 45-77 26-58 (77)
111 COG1097 RRP4 RNA-binding prote 86.2 1.7 3.6E-05 41.6 5.8 47 372-429 148-194 (239)
112 PF13083 KH_4: KH domain; PDB: 85.9 0.46 1E-05 36.9 1.6 35 138-172 27-61 (73)
113 KOG2874 rRNA processing protei 85.7 1.4 3E-05 42.7 5.0 51 152-214 161-211 (356)
114 COG1855 ATPase (PilT family) [ 85.3 1.8 3.8E-05 45.3 5.9 39 141-179 487-525 (604)
115 KOG4369 RTK signaling protein 84.8 0.38 8.3E-06 54.8 0.9 58 42-99 1339-1397(2131)
116 PF13184 KH_5: NusA-like KH do 84.7 0.58 1.2E-05 36.0 1.7 34 45-78 5-44 (69)
117 cd02413 40S_S3_KH K homology R 83.9 1 2.3E-05 35.7 2.9 37 45-81 32-68 (81)
118 COG1855 ATPase (PilT family) [ 83.4 0.77 1.7E-05 47.9 2.4 40 371-410 487-526 (604)
119 cd02410 archeal_CPSF_KH The ar 83.1 3.8 8.3E-05 36.1 6.2 91 60-178 23-114 (145)
120 PF07650 KH_2: KH domain syndr 82.6 0.64 1.4E-05 36.5 1.2 33 44-76 26-58 (78)
121 COG1097 RRP4 RNA-binding prote 81.9 4.3 9.3E-05 38.9 6.6 47 46-98 149-195 (239)
122 PF07650 KH_2: KH domain syndr 81.3 0.68 1.5E-05 36.4 0.9 35 370-404 25-59 (78)
123 cd02414 jag_KH jag_K homology 80.2 2.1 4.6E-05 33.6 3.4 34 371-404 25-58 (77)
124 COG1782 Predicted metal-depend 80.0 3.7 8.1E-05 43.4 5.9 96 56-178 42-137 (637)
125 PRK13764 ATPase; Provisional 78.1 5.2 0.00011 44.2 6.7 43 139-181 480-522 (602)
126 cd02413 40S_S3_KH K homology R 77.6 3.1 6.6E-05 33.1 3.6 35 371-405 31-65 (81)
127 PRK06418 transcription elongat 77.3 3.2 6.9E-05 37.7 4.0 33 46-79 64-96 (166)
128 KOG3273 Predicted RNA-binding 76.8 1.5 3.3E-05 40.3 1.8 56 148-215 177-232 (252)
129 cd02410 archeal_CPSF_KH The ar 75.0 4.4 9.6E-05 35.7 4.1 37 45-81 78-114 (145)
130 COG1782 Predicted metal-depend 73.9 15 0.00032 39.1 8.2 97 152-322 41-137 (637)
131 cd02412 30S_S3_KH K homology R 72.9 3.3 7.3E-05 34.9 2.9 30 45-74 63-92 (109)
132 PRK06418 transcription elongat 71.5 5.8 0.00012 36.1 4.2 35 372-407 63-97 (166)
133 cd02411 archeal_30S_S3_KH K ho 69.4 5.4 0.00012 31.9 3.2 28 45-72 40-67 (85)
134 COG0092 RpsC Ribosomal protein 65.8 5.5 0.00012 38.0 2.9 30 44-73 52-81 (233)
135 TIGR03675 arCOG00543 arCOG0054 64.8 9 0.0002 42.8 4.9 94 57-178 37-131 (630)
136 cd02411 archeal_30S_S3_KH K ho 64.1 8.3 0.00018 30.8 3.3 28 372-399 40-67 (85)
137 COG5166 Uncharacterized conser 63.9 12 0.00027 39.6 5.2 130 296-445 392-525 (657)
138 cd02412 30S_S3_KH K homology R 63.4 6.9 0.00015 33.0 2.8 29 372-400 63-91 (109)
139 COG0092 RpsC Ribosomal protein 61.1 8.3 0.00018 36.8 3.2 29 370-398 51-79 (233)
140 TIGR00436 era GTP-binding prot 54.6 15 0.00033 36.1 4.1 31 369-399 220-251 (270)
141 KOG3973 Uncharacterized conser 50.5 46 0.00099 33.6 6.4 18 395-412 286-303 (465)
142 COG1159 Era GTPase [General fu 49.4 23 0.0005 35.3 4.2 35 365-399 224-259 (298)
143 PRK15494 era GTPase Era; Provi 48.9 21 0.00045 36.6 4.1 31 369-399 272-303 (339)
144 PRK00089 era GTPase Era; Revie 45.9 25 0.00054 35.0 4.1 38 368-405 224-270 (292)
145 COG0490 Putative regulatory, l 45.9 16 0.00034 33.0 2.2 61 374-439 92-158 (162)
146 TIGR03675 arCOG00543 arCOG0054 45.8 50 0.0011 36.9 6.8 38 370-407 93-130 (630)
147 KOG3973 Uncharacterized conser 43.8 1.3E+02 0.0028 30.5 8.3 11 202-212 102-112 (465)
148 TIGR00436 era GTP-binding prot 41.9 32 0.0007 33.8 4.1 30 43-72 221-251 (270)
149 COG4907 Predicted membrane pro 40.8 23 0.0005 37.1 2.8 14 425-438 522-535 (595)
150 cd07055 BMC_like_2 Bacterial M 40.7 60 0.0013 24.2 4.2 22 419-440 38-59 (61)
151 TIGR01008 rpsC_E_A ribosomal p 39.5 32 0.0007 32.2 3.4 30 45-74 40-69 (195)
152 CHL00048 rps3 ribosomal protei 39.2 32 0.00069 32.8 3.4 30 44-73 67-96 (214)
153 PRK04191 rps3p 30S ribosomal p 38.3 33 0.00073 32.5 3.4 31 45-75 42-72 (207)
154 COG1847 Jag Predicted RNA-bind 38.0 23 0.00049 33.3 2.1 36 42-77 90-125 (208)
155 PF09869 DUF2096: Uncharacteri 36.3 1.1E+02 0.0024 27.7 6.0 57 137-211 110-166 (169)
156 PTZ00084 40S ribosomal protein 36.0 37 0.0008 32.5 3.3 31 45-75 46-76 (220)
157 COG1847 Jag Predicted RNA-bind 35.6 33 0.00072 32.2 2.8 35 141-175 92-126 (208)
158 COG1702 PhoH Phosphate starvat 35.5 87 0.0019 32.0 5.9 56 377-444 22-79 (348)
159 TIGR01008 rpsC_E_A ribosomal p 34.7 44 0.00096 31.3 3.5 29 371-399 39-67 (195)
160 KOG1423 Ras-like GTPase ERA [C 33.9 45 0.00098 33.5 3.5 35 366-400 324-359 (379)
161 KOG1423 Ras-like GTPase ERA [C 33.6 42 0.00092 33.7 3.3 34 40-73 325-359 (379)
162 CHL00048 rps3 ribosomal protei 32.1 50 0.0011 31.5 3.5 29 371-399 67-95 (214)
163 PRK04191 rps3p 30S ribosomal p 32.1 50 0.0011 31.3 3.5 29 372-400 42-70 (207)
164 PTZ00084 40S ribosomal protein 31.7 49 0.0011 31.6 3.3 29 371-399 45-73 (220)
165 PRK03818 putative transporter; 31.7 6.1E+02 0.013 27.9 12.3 133 45-207 207-358 (552)
166 PRK00089 era GTPase Era; Revie 31.5 60 0.0013 32.2 4.2 36 140-175 226-270 (292)
167 PRK15494 era GTPase Era; Provi 30.6 62 0.0013 33.1 4.2 36 140-175 273-317 (339)
168 COG1159 Era GTPase [General fu 30.3 66 0.0014 32.1 4.1 29 139-167 228-257 (298)
169 COG4010 Uncharacterized protei 25.8 2E+02 0.0043 25.4 5.7 43 160-213 126-168 (170)
170 PRK15468 carboxysome structura 24.9 1.2E+02 0.0025 25.4 3.9 27 420-446 75-101 (111)
171 TIGR01009 rpsC_bact ribosomal 24.1 75 0.0016 30.2 3.2 29 45-73 64-92 (211)
172 COG1702 PhoH Phosphate starvat 23.2 1.6E+02 0.0035 30.1 5.4 50 148-209 23-72 (348)
173 PF02749 QRPTase_N: Quinolinat 21.8 2.5E+02 0.0054 22.4 5.4 54 388-443 32-85 (88)
174 TIGR01009 rpsC_bact ribosomal 21.3 95 0.0021 29.5 3.2 28 372-399 64-91 (211)
175 PF00352 TBP: Transcription fa 20.5 2.9E+02 0.0062 21.9 5.5 35 399-444 48-84 (86)
176 PF10369 ALS_ss_C: Small subun 20.4 2.1E+02 0.0045 22.1 4.5 42 390-440 17-58 (75)
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=7.1e-45 Score=378.38 Aligned_cols=404 Identities=39% Similarity=0.599 Sum_probs=313.6
Q ss_pred cCcCCCCCCCCCCCCCCCCCccccCCCCCCCcccCCCceEEEEEecCCccceEecCCchHHHHHHHHhCCeEEEcCCCCC
Q 009566 5 RNSYGKRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPG 84 (532)
Q Consensus 5 ~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~ 84 (532)
|....++...+....+++..+++...+. ......+...++||||+.+.+|.||||+|.+||+|+++|.++|+|.+..++
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~ 84 (485)
T KOG2190|consen 6 RGLPRPKNSTTSNVGDNGSIKRPSLGDP-VISTGPDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPG 84 (485)
T ss_pred ccCccccCCCcccccCCCcccccCCCCC-cccCCCCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCC
Confidence 4455566666666666666666555554 333344555559999999999999999999999999999999999999999
Q ss_pred CCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHHHh---hhcCC--CC-CCCCCceEEEEEEeCCceeeeeccC
Q 009566 85 SEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAE---ELRGD--ED-SDGGHQVTAKLLVPSDQIGCVIGKG 158 (532)
Q Consensus 85 ~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~---~~~~~--~~-~~~~~~~~~~l~vp~~~~g~iIGk~ 158 (532)
|+||+|+|+|...+ ..++.+++|+.++++.+... +.... .. +.....++++|+||..++|.||||+
T Consensus 85 c~eRIiti~g~~~~--------~~~~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~ 156 (485)
T KOG2190|consen 85 CPERIITITGNRVE--------LNLSPATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKG 156 (485)
T ss_pred CCcceEEEeccccc--------ccCCchHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccC
Confidence 99999999997222 16788999999999988753 11111 11 1222368999999999999999999
Q ss_pred chHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCccccccccccCCCCCCCCCC
Q 009566 159 GQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLV 238 (532)
Q Consensus 159 G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~s~~~~~~~~~g~~~ 238 (532)
|..||+|+++|+|+|.+.++ .+|. ..+|.|+|.|.+++|.+|+..|...|++++.+....+.+..+ |.+ .
T Consensus 157 G~~Ik~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~--y~P----~ 226 (485)
T KOG2190|consen 157 GSLIKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIP--YRP----S 226 (485)
T ss_pred cHHHHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCccc--CCC----c
Confidence 99999999999999999987 8887 478889999999999999999999999975443222221111 100 0
Q ss_pred CCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEEeecCcccccccCCchhHHHHHhhhCCeEE
Q 009566 239 GPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIK 318 (532)
Q Consensus 239 ~p~~g~~~~~~~p~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~ 318 (532)
-+..++ ....++. ..+ .+.++.....+.++..++.+|...++.|||+++..|+.|+.++++.|.
T Consensus 227 ~~~~~~-------~~~s~~~-------~~~--~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~ 290 (485)
T KOG2190|consen 227 ASQGGP-------VLPSTAQ-------TSP--DAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASIS 290 (485)
T ss_pred ccccCc-------ccccccc-------CCc--ccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceE
Confidence 000000 0000000 000 111222233456778899999999999999999999999999999999
Q ss_pred ecCCCCCCCCeEEEEecCcchhhhhhHHHHHHHHhcccccccccccCCCcceEEEEEEecCcceeEecCCChhHHHHHHh
Q 009566 319 VDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRL 398 (532)
Q Consensus 319 i~~~~~~~~e~vi~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~ 398 (532)
+.....+ |+++++..+..++..+.++++++.+++++.+....+. ...++.+|+||.+++||||||+|++|.+||+.
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 9999999999999999999999999999988777665 77899999999999999999999999999999
Q ss_pred hCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhcccccC
Q 009566 399 TKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLFDRE 450 (532)
Q Consensus 399 Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~~~~~~ 450 (532)
|||.|+|..+++. ...++++|+|+|...+...|+.++..++........
T Consensus 367 tgA~I~I~~~~~~---~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~ 415 (485)
T KOG2190|consen 367 TGASISILNKEEV---SGVREALVQITGMLREDLLAQYLIRARLSAPKSSMG 415 (485)
T ss_pred cCCceEEcccccc---CCcceeEEEecchhHHHHhhhhhcccccccCccCCC
Confidence 9999999887653 146789999999999999999999888877654333
No 2
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=1.2e-42 Score=354.84 Aligned_cols=329 Identities=21% Similarity=0.383 Sum_probs=252.5
Q ss_pred CceEEEEEecCCccceEecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHH
Q 009566 41 EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVH 120 (532)
Q Consensus 41 ~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~ 120 (532)
..++.+..||.+++++||||+|+.|..|..+++|+|+|.....+..+|.|.++|.+++++ .|-. ++
T Consensus 52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~-------------~aK~-li 117 (600)
T KOG1676|consen 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVE-------------VAKQ-LI 117 (600)
T ss_pred cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHH-------------HHHH-hh
Confidence 456678999999999999999999999999999999988777778899999999999842 3322 22
Q ss_pred HHHHHhhhcC--CCCCCCCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCH
Q 009566 121 DRVIAEELRG--DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198 (532)
Q Consensus 121 ~~i~~~~~~~--~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~ 198 (532)
..+....... -........++.+|+||.+.++.||||+|++||.|++.+||+|.+..+..... ..++.+.|+|++
T Consensus 118 ~evv~r~~~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~---~~~KplritGdp 194 (600)
T KOG1676|consen 118 GEVVSRGRPPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIAT---GADKPLRITGDP 194 (600)
T ss_pred hhhhhccCCCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCC---CCCCceeecCCH
Confidence 2222222100 01112246689999999999999999999999999999999999988765433 478899999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009566 199 SVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDD 278 (532)
Q Consensus 199 ~~v~~A~~~I~~~l~~~~~~~~~~~~s~~~~~~~~~g~~~~p~~g~~~~~~~p~~~~~g~~~~~~~~~~~~~~~~~~~~~ 278 (532)
+.|+.|..+|.++|++.... .|..++ .+|. +
T Consensus 195 ~~ve~a~~lV~dil~e~~~~-----------~~g~~~-------------------~~g~---~---------------- 225 (600)
T KOG1676|consen 195 DKVEQAKQLVADILREEDDE-----------VPGSGG-------------------HAGV---R---------------- 225 (600)
T ss_pred HHHHHHHHHHHHHHHhcccC-----------CCcccc-------------------ccCc---C----------------
Confidence 99999999999999963211 111100 0010 0
Q ss_pred CCCceEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCC-CCCCeEEEEecCcchhhhhhHHHHHHHHhcccc
Q 009566 279 LSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSST-EGDDCLITVSSKEFFEDTLSATIEAVVRLQPRC 357 (532)
Q Consensus 279 ~~~~~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~-~~~e~vi~i~g~~~~~~~~~~~~~a~~~~~~~~ 357 (532)
.....+++|.||...||.||||+|++||+|+.+||++|+|.+++. .+.||++.|.|.... ++.+.+++..|
T Consensus 226 -~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~-------ie~Aa~lI~ei 297 (600)
T KOG1676|consen 226 -GGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQ-------IEHAAELINEI 297 (600)
T ss_pred -ccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHH-------HHHHHHHHHHH
Confidence 011238899999999999999999999999999999999987654 678999999997542 22222222222
Q ss_pred cccccccC------CCcce--EEEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHH
Q 009566 358 SEKIERDS------GLISF--TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLD 429 (532)
Q Consensus 358 ~~~~~~~~------~~~~~--~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~ 429 (532)
........ +.... ...|.||.+.||+||||+|++||.|.++|||++.+.+. |...+..+++|+|.|++.
T Consensus 298 i~~~~~~~~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~---~p~~~~~ektf~IrG~~~ 374 (600)
T KOG1676|consen 298 IAEAEAGAGGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ---PPNGNPKEKTFVIRGDKR 374 (600)
T ss_pred HHHHhccCCCCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC---CCCCCccceEEEEecCcc
Confidence 22221111 12223 78899999999999999999999999999999999764 445677899999999999
Q ss_pred HHHHHHHHHHHHHHhcc
Q 009566 430 LAKDALIQVMTRLRANL 446 (532)
Q Consensus 430 ~v~~A~~~I~~~l~~~~ 446 (532)
+|+.|+.||.+++....
T Consensus 375 QIdhAk~LIr~kvg~~~ 391 (600)
T KOG1676|consen 375 QIDHAKQLIRDKVGDIA 391 (600)
T ss_pred cchHHHHHHHHHhcccC
Confidence 99999999999998753
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=7.7e-43 Score=339.31 Aligned_cols=357 Identities=23% Similarity=0.378 Sum_probs=273.5
Q ss_pred cCCCceEEEEEecCCccceEecCCchHHHHHHHHhCCeEEEcC-CCCCCCceEEEEEcCCccccccccCcccCCHHHHHH
Q 009566 38 IGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE-TVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDAL 116 (532)
Q Consensus 38 ~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~-~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~ 116 (532)
....+..+|+|||..+||.||||.|.|||.|.+.|.|+|.|.. ...+..|++|+|-+.+|. +.+||
T Consensus 194 ~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg-------------~s~Ac 260 (584)
T KOG2193|consen 194 QQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG-------------TSKAC 260 (584)
T ss_pred ccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc-------------hHHHH
Confidence 3467888999999999999999999999999999999999974 456889999999999998 46788
Q ss_pred HHHHHHHHHhhhcCCCCCCCCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEc
Q 009566 117 FKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG 196 (532)
Q Consensus 117 ~~i~~~i~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G 196 (532)
.+|++.+..+.... .....+.++++..+.+||+||||.|.+||+|+.+||++|.|++--++.. .+.+|+|++.|
T Consensus 261 ~~ILeimqkEA~~~----k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~--ynpERTItVkG 334 (584)
T KOG2193|consen 261 KMILEIMQKEAVDD----KVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSL--YNPERTITVKG 334 (584)
T ss_pred HHHHHHHHHhhhcc----chhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcc--cCccceEEecc
Confidence 88888665443322 3346778999999999999999999999999999999999998666554 36799999999
Q ss_pred CHHHHHHHHHHHHHHHhcCCCCccccc--ccccc--------CCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCC
Q 009566 197 EASVVKKALCQIASRLHDNPSRSQHLL--ASAIS--------NSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGD 266 (532)
Q Consensus 197 ~~~~v~~A~~~I~~~l~~~~~~~~~~~--~s~~~--------~~~~~~g~~~~p~~g~~~~~~~p~~~~~g~~~~~~~~~ 266 (532)
+.|+|..|..+|+.+|++..+.+.... ....+ +.|++...+..|. +.+. -+...
T Consensus 335 siEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph------~~Ps----------~v~~a 398 (584)
T KOG2193|consen 335 SIEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPH------FPPS----------PVTFA 398 (584)
T ss_pred cHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCCC------CCCC----------ccccC
Confidence 999999999999999999766652211 01001 0111111111110 0000 00000
Q ss_pred CCCCCCCCCCCCCCCceEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCC-CCCCCeEEEEecCcchhhhhhH
Q 009566 267 WSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSS-TEGDDCLITVSSKEFFEDTLSA 345 (532)
Q Consensus 267 ~~~~~~~~~~~~~~~~~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~-~~~~e~vi~i~g~~~~~~~~~~ 345 (532)
.+.+++- .......++|.||...+|+|||++|.+||+|...+||.|+|..+. ++..+|+|+|+|.+
T Consensus 399 ~p~~~~h-----q~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGpp-------- 465 (584)
T KOG2193|consen 399 SPYPLFH-----QNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPP-------- 465 (584)
T ss_pred CCchhhh-----cCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCCh--------
Confidence 1111111 122455789999999999999999999999999999999998753 56789999999964
Q ss_pred HHHHHHHhccccccccccc-----CCCcceEEEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCc
Q 009566 346 TIEAVVRLQPRCSEKIERD-----SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDE 420 (532)
Q Consensus 346 ~~~a~~~~~~~~~~~~~~~-----~~~~~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r 420 (532)
++.++.+.++..++..+ .....+...+.||...+|+||||||.+++||+..|+|-|.|+.+ ..|. ..+..
T Consensus 466 --eaqfKAQgrifgKikEenf~~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrd-qtpd--End~v 540 (584)
T KOG2193|consen 466 --EAQFKAQGRIFGKIKEENFFLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRD-QTPD--ENDQV 540 (584)
T ss_pred --HHHHhhhhhhhhhhhhhccCCchhhheeeeeeeccchhhhhhhccccccHHHHhccccceEEcccc-CCCC--cccee
Confidence 45556666655554332 23456788999999999999999999999999999999999654 4554 34456
Q ss_pred eEEEEcCHHHHHHHHHHHHHHHHhccc
Q 009566 421 MVQISGDLDLAKDALIQVMTRLRANLF 447 (532)
Q Consensus 421 ~V~I~G~~~~v~~A~~~I~~~l~~~~~ 447 (532)
+|.|+|..-+.+.|...|.++|.+...
T Consensus 541 ivriiGhfyatq~aQrki~~iv~qvkq 567 (584)
T KOG2193|consen 541 IVRIIGHFYATQNAQRKIAHIVNQVKQ 567 (584)
T ss_pred eeeeechhhcchHHHHHHHHHHHHHHH
Confidence 799999999999999999999988653
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=2.2e-33 Score=258.69 Aligned_cols=342 Identities=19% Similarity=0.271 Sum_probs=218.1
Q ss_pred cccCCCCCCCcccCCCceEEEEEecCCccceEecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccC
Q 009566 26 RRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDG 105 (532)
Q Consensus 26 ~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~ 105 (532)
+|...+ -+..++....+.++||+.++.+|.||||+|++||+|+.+++|+|.|+++ ..+||+++|+...+.
T Consensus 32 krp~~d-~~~qa~k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri~tisad~~t------- 101 (390)
T KOG2192|consen 32 KRPAED-MEEQAFKRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILTISADIET------- 101 (390)
T ss_pred CCcchh-hHHHHhhhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCceeEEEeccHHH-------
Confidence 444444 3566788889999999999999999999999999999999999999988 788999999976332
Q ss_pred cccCCHHHHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCccc
Q 009566 106 DKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCA 185 (532)
Q Consensus 106 ~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~ 185 (532)
+-+-|++++..+.+. ......+.++|||+.++++.|||++|++||+|++++.|+++|... .|.
T Consensus 102 ------i~~ilk~iip~lee~-------f~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~----c~p 164 (390)
T KOG2192|consen 102 ------IGEILKKIIPTLEEG-------FQLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE----CCP 164 (390)
T ss_pred ------HHHHHHHHhhhhhhC-------CCCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc----cCC
Confidence 234444444444321 134567999999999999999999999999999999999999764 566
Q ss_pred CCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCcccccc-------ccccCCCCC--CCCCCCCCCCC--CcccCCCCCC
Q 009566 186 LRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLA-------SAISNSHSS--SGSLVGPTAAT--PIVGIAPLMG 254 (532)
Q Consensus 186 ~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~-------s~~~~~~~~--~g~~~~p~~g~--~~~~~~p~~~ 254 (532)
+++||+|.|.|.+..|..+++.|+++|.+.|.+.....+ ++....|++ .+....|.+.+ +.++.+|...
T Consensus 165 ~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~ 244 (390)
T KOG2192|consen 165 HSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRG 244 (390)
T ss_pred CCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCc
Confidence 799999999999999999999999999998887654211 111122221 00001111101 1111112111
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCCeEEEEe
Q 009566 255 PYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVS 334 (532)
Q Consensus 255 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~e~vi~i~ 334 (532)
++.+. +-++|..= +.+--.+.|+..... ...+-+..
T Consensus 245 sdlma---------------------------------------y~r~GrpG----~rydg~vdFs~detw-~saidtw~ 280 (390)
T KOG2192|consen 245 SDLMA---------------------------------------YDRRGRPG----DRYDGMVDFSADETW-PSAIDTWS 280 (390)
T ss_pred cccce---------------------------------------eccCCCCC----ccccccccccccccC-CCcCCCcC
Confidence 11110 00000000 000000001110000 00000000
Q ss_pred cCcchhhhhhHHHHHHHHhcccc-cccccccCCCcceEEEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCC
Q 009566 335 SKEFFEDTLSATIEAVVRLQPRC-SEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPK 413 (532)
Q Consensus 335 g~~~~~~~~~~~~~a~~~~~~~~-~~~~~~~~~~~~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~ 413 (532)
.++ +..++.++.-. .-..... ....-.+.+....|..+.||.++-|.||||+|+.|++|++++||.|+|...
T Consensus 281 ~Se-wqmaYePQgGs-~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikidep----- 353 (390)
T KOG2192|consen 281 PSE-WQMAYEPQGGS-GYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEP----- 353 (390)
T ss_pred ccc-cccccCCCCCC-CCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCc-----
Confidence 000 00000000000 0000000 000011223456788999999999999999999999999999999999642
Q ss_pred CCCCCCceEEEEcCHHHHHHHHHHHHHHHHhc
Q 009566 414 IASEDDEMVQISGDLDLAKDALIQVMTRLRAN 445 (532)
Q Consensus 414 ~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~ 445 (532)
-.++.+|.++|+|+.++++.|+.|++..++..
T Consensus 354 leGsedrIitItGTqdQIqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 354 LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY 385 (390)
T ss_pred CCCCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence 23677899999999999999999999988853
No 5
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.96 E-value=4.2e-28 Score=248.46 Aligned_cols=232 Identities=26% Similarity=0.419 Sum_probs=180.7
Q ss_pred cCCCceEEEEEecCCccceEecCCchHHHHHHHHhCCeEEEcCC--CCCCCceEEEEEcCCccccccccCcccCCHHHHH
Q 009566 38 IGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGET--VPGSEERVVTVYSASDETNAFEDGDKFVSPAQDA 115 (532)
Q Consensus 38 ~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~--~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a 115 (532)
.+...++..|+||..++|+||||+|++||+|++.+||++.+-.. ......+-+.|+|.++.+ +.|
T Consensus 134 q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~v-------------e~a 200 (600)
T KOG1676|consen 134 QGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKV-------------EQA 200 (600)
T ss_pred CCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHH-------------HHH
Confidence 34678999999999999999999999999999999999987533 222367889999998873 556
Q ss_pred HHHHHHHHHHhhhcCCC-----CCCCCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCc
Q 009566 116 LFKVHDRVIAEELRGDE-----DSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDE 190 (532)
Q Consensus 116 ~~~i~~~i~~~~~~~~~-----~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r 190 (532)
..++++.|.++.-.... ........+++|.||...||.||||+|++||+|+.+||++|+|.++++ | .+.+|
T Consensus 201 ~~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~-p---~speR 276 (600)
T KOG1676|consen 201 KQLVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD-P---SSPER 276 (600)
T ss_pred HHHHHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCC-C---CCccc
Confidence 66677766543211111 112233458999999999999999999999999999999999998755 3 36799
Q ss_pred eEEEEcCHHHHHHHHHHHHHHHhcCCCCccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCC
Q 009566 191 LVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRS 270 (532)
Q Consensus 191 ~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~s~~~~~~~~~g~~~~p~~g~~~~~~~p~~~~~g~~~~~~~~~~~~~ 270 (532)
.+.|.|+.+.|+.|.++|.++|.+..... .++. +|.
T Consensus 277 ~~~IiG~~d~ie~Aa~lI~eii~~~~~~~----------~~~~--------------------------------~~G-- 312 (600)
T KOG1676|consen 277 PAQIIGTVDQIEHAAELINEIIAEAEAGA----------GGGM--------------------------------GGG-- 312 (600)
T ss_pred eeeeecCHHHHHHHHHHHHHHHHHHhccC----------CCCc--------------------------------CCC--
Confidence 99999999999999999999998841110 0000 000
Q ss_pred CCCCCCCCCCCceEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCC--CCCCeEEEEecCcc
Q 009566 271 LYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSST--EGDDCLITVSSKEF 338 (532)
Q Consensus 271 ~~~~~~~~~~~~~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~--~~~e~vi~i~g~~~ 338 (532)
.|. ....+.|.||..++|+|||++|++||.|..+|||++.+.+..+ +..+++|+|.|.+.
T Consensus 313 ---~P~-----~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG~~~ 374 (600)
T KOG1676|consen 313 ---APG-----LVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGDKR 374 (600)
T ss_pred ---Ccc-----ceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEecCcc
Confidence 000 1116789999999999999999999999999999999998732 34789999999864
No 6
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.95 E-value=2.3e-28 Score=238.48 Aligned_cols=243 Identities=23% Similarity=0.391 Sum_probs=190.1
Q ss_pred CceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCC
Q 009566 138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPS 217 (532)
Q Consensus 138 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~ 217 (532)
..+.++++||..+++.||||.|++||+|...|.++|+|...++. +..|+.|+|-+++|.+.+|+++|++++.....
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 44779999999999999999999999999999999999887653 47899999999999999999999999988532
Q ss_pred CccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEEeecCcccc
Q 009566 218 RSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGG 297 (532)
Q Consensus 218 ~~~~~~~s~~~~~~~~~g~~~~p~~g~~~~~~~p~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~vp~~~~g~ 297 (532)
++. ...++.++++..+.++|+
T Consensus 273 ~~k-----------------------------------------------------------~~~e~pLk~lAHN~lvGR 293 (584)
T KOG2193|consen 273 DDK-----------------------------------------------------------VAEEIPLKILAHNNLVGR 293 (584)
T ss_pred ccc-----------------------------------------------------------hhhhcchhhhhhcchhhh
Confidence 221 234678899999999999
Q ss_pred cccCCchhHHHHHhhhCCeEEecCCC---CCCCCeEEEEecCc-chh-------hhhhHHHHHHH---Hhcccccccc--
Q 009566 298 VIGKGGAIINQIRQESGAAIKVDSSS---TEGDDCLITVSSKE-FFE-------DTLSATIEAVV---RLQPRCSEKI-- 361 (532)
Q Consensus 298 iIGk~G~~Ik~i~~~sga~I~i~~~~---~~~~e~vi~i~g~~-~~~-------~~~~~~~~a~~---~~~~~~~~~~-- 361 (532)
+|||.|.+||+|+++||++|+|++-. .-.+||+|++.|.- .+. +.+.++.|.-+ .++..+...+
T Consensus 294 LIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~ 373 (584)
T KOG2193|consen 294 LIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNL 373 (584)
T ss_pred hhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCc
Confidence 99999999999999999999998732 23478999999941 111 11112222111 1111110000
Q ss_pred ------------ccc-----------------CCCcceEEEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCC
Q 009566 362 ------------ERD-----------------SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLP 412 (532)
Q Consensus 362 ------------~~~-----------------~~~~~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P 412 (532)
... .....-..+|.||...+|.|||++|..||.|.+.+||.|+|.+.+
T Consensus 374 ~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE--- 450 (584)
T KOG2193|consen 374 PALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPE--- 450 (584)
T ss_pred cccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCC---
Confidence 000 001234678999999999999999999999999999999997643
Q ss_pred CCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhccc
Q 009566 413 KIASEDDEMVQISGDLDLAKDALIQVMTRLRANLF 447 (532)
Q Consensus 413 ~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~~~ 447 (532)
.++..+|+|+|+|+|++.-+|.-.|..+|.++.|
T Consensus 451 -~pdvseRMViItGppeaqfKAQgrifgKikEenf 484 (584)
T KOG2193|consen 451 -IPDVSERMVIITGPPEAQFKAQGRIFGKIKEENF 484 (584)
T ss_pred -CCCcceeEEEecCChHHHHhhhhhhhhhhhhhcc
Confidence 3467899999999999999999999999998754
No 7
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.94 E-value=7e-26 Score=215.38 Aligned_cols=237 Identities=24% Similarity=0.383 Sum_probs=172.3
Q ss_pred CceEEEEEecCCccceEecCCchHHHHHHHHhCCeEEEcC---CCCCCCceEEEEEcCCccccccccCcccCCHHHHHHH
Q 009566 41 EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE---TVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALF 117 (532)
Q Consensus 41 ~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~---~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~ 117 (532)
..+.++||||+..+|+||||+|++|.+|+++|||+|++++ .+|+++||||.|.|+.+++ ...+.
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 3499999999999999999999999999999999999975 4899999999999996652 33444
Q ss_pred HHHHHHHHhhhcCCC-CC-----CCCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCce
Q 009566 118 KVHDRVIAEELRGDE-DS-----DGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDEL 191 (532)
Q Consensus 118 ~i~~~i~~~~~~~~~-~~-----~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~ 191 (532)
.|.++|.+.....+. .+ ..+..-.++++||++.++.||||+|++||.|+++++|-|+|++.. |....-.+|+
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 555666544322211 11 111223489999999999999999999999999999999999522 2222457999
Q ss_pred EEEEcCHHHHHHHHHHHHHHHhcCCCCccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCC
Q 009566 192 VQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSL 271 (532)
Q Consensus 192 v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~s~~~~~~~~~g~~~~p~~g~~~~~~~p~~~~~g~~~~~~~~~~~~~~ 271 (532)
|++.|++++..+|+.+|+++|.++|....++..++. +.+|...+ ..|...+|... .+
T Consensus 182 vt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya---~vsGpvaN----------snPtGspya~~-~~--------- 238 (402)
T KOG2191|consen 182 VTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYA---NVSGPVAN----------SNPTGSPYAYQ-AH--------- 238 (402)
T ss_pred EEecCCHHHHHHHHHHHHHHhhcCCcccceeccchh---cccCcccc----------cCCCCCCCCCC-Cc---------
Confidence 999999999999999999999999877665443221 11111111 11111112110 00
Q ss_pred CCCCCCCCCCceEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCC
Q 009566 272 YSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSS 322 (532)
Q Consensus 272 ~~~~~~~~~~~~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~ 322 (532)
..+........++..+.|..-|.++.++-.|-.-+|+.+.++..
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 01222345567888999999999999999999999998888764
No 8
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.90 E-value=7.3e-23 Score=189.31 Aligned_cols=173 Identities=26% Similarity=0.398 Sum_probs=143.7
Q ss_pred ceEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCCeEEEEecCcchhhhhhHHHHHHHHhcccccccc
Q 009566 282 KEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKI 361 (532)
Q Consensus 282 ~~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~e~vi~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~ 361 (532)
..+.+++++..+.+|+||||+|++||.|+.+++|+|.|++++ .++++++|++... ...+-+..+++.+.+.+
T Consensus 46 ~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~--~peri~tisad~~------ti~~ilk~iip~lee~f 117 (390)
T KOG2192|consen 46 SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSS--GPERILTISADIE------TIGEILKKIIPTLEEGF 117 (390)
T ss_pred cceeEEEEEecccccceeccccccHHHHhhhccceeeccCCC--CCceeEEEeccHH------HHHHHHHHHhhhhhhCC
Confidence 457999999999999999999999999999999999999865 4789999998642 12333445555555443
Q ss_pred cccCCCcceEEEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHH
Q 009566 362 ERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTR 441 (532)
Q Consensus 362 ~~~~~~~~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~~ 441 (532)
.. ...+.++|+|.++++|.|||++|++|||||++..|+++|... +.| ++++|+|.|.|.+..|..+++.|+++
T Consensus 118 ~~---~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~-c~p---~stdrv~l~~g~~k~v~~~i~~il~~ 190 (390)
T KOG2192|consen 118 QL---PSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE-CCP---HSTDRVVLIGGKPKRVVECIKIILDL 190 (390)
T ss_pred CC---CCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc-cCC---CCcceEEEecCCcchHHHHHHHHHHH
Confidence 32 236899999999999999999999999999999999999864 334 68999999999999999999999999
Q ss_pred HHhcccccCCCcCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009566 442 LRANLFDREGAVSTFVPVLPYIPVSENGSDGLNYESRD 479 (532)
Q Consensus 442 l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~y~~~~ 479 (532)
|.+..+ ++...||+|..+|+. ..|+++.
T Consensus 191 i~e~pi--------kgsa~py~p~fyd~t--~dyggf~ 218 (390)
T KOG2192|consen 191 ISESPI--------KGSAQPYDPNFYDET--YDYGGFT 218 (390)
T ss_pred hhcCCc--------CCcCCcCCccccCcc--cccCCce
Confidence 998544 678889999999864 5677654
No 9
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.89 E-value=2.1e-21 Score=185.06 Aligned_cols=173 Identities=26% Similarity=0.442 Sum_probs=138.8
Q ss_pred CCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 009566 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN 215 (532)
Q Consensus 136 ~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 215 (532)
.+..+.++||||+..+|.||||+|++|.+|+.+|||+|++++..++.+ +++||+|.|+|+.+++...++.|+++|++.
T Consensus 35 e~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyP--GTTeRvcli~Gt~eai~av~efI~dKire~ 112 (402)
T KOG2191|consen 35 EDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYP--GTTERVCLIQGTVEALNAVHEFIADKIREK 112 (402)
T ss_pred CCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCC--CccceEEEEeccHHHHHHHHHHHHHHHHHh
Confidence 344589999999999999999999999999999999999998655433 589999999999999999999999999984
Q ss_pred CCCccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEEeecCcc
Q 009566 216 PSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANI 295 (532)
Q Consensus 216 ~~~~~~~~~s~~~~~~~~~g~~~~p~~g~~~~~~~p~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~vp~~~~ 295 (532)
+....
T Consensus 113 p~~~~--------------------------------------------------------------------------- 117 (402)
T KOG2191|consen 113 PQAVA--------------------------------------------------------------------------- 117 (402)
T ss_pred HHhhc---------------------------------------------------------------------------
Confidence 31100
Q ss_pred cccccCCchhHHHHHhhhCCeEEecCCCCCCCCeEEEEecCcchhhhhhHHHHHHHHhcccccccccccCCCcceEEEEE
Q 009566 296 GGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLL 375 (532)
Q Consensus 296 g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~e~vi~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~ 375 (532)
+ -+.+..... ++| ....++.
T Consensus 118 ------------------k-~v~~~~pqt--~~r---------------------------------------~kqikiv 137 (402)
T KOG2191|consen 118 ------------------K-PVDILQPQT--PDR---------------------------------------IKQIKIV 137 (402)
T ss_pred ------------------C-CccccCCCC--ccc---------------------------------------cceeEEe
Confidence 0 000000000 111 1235699
Q ss_pred EecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhccc
Q 009566 376 VPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLF 447 (532)
Q Consensus 376 VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~~~ 447 (532)
||..-+|.||||+|.+||.|++++||.|+|.+. .|..-...+|+|++.|++++..+|..+|+++|.++..
T Consensus 138 vPNstag~iigkggAtiK~~~Eqsga~iqisPq--kpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpq 207 (402)
T KOG2191|consen 138 VPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQ--KPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQ 207 (402)
T ss_pred ccCCcccceecCCcchHHHHHHhhCcceEeccc--CCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCc
Confidence 999999999999999999999999999999853 2333356789999999999999999999999999864
No 10
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.86 E-value=8.7e-21 Score=198.27 Aligned_cols=173 Identities=38% Similarity=0.597 Sum_probs=141.5
Q ss_pred EEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCCeEEEEecCcchhhhhhHHHHHHHHhcccccccccc
Q 009566 284 FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIER 363 (532)
Q Consensus 284 ~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~e~vi~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~ 363 (532)
.++|++|+...+|.||||+|..||+|+.++.++|+|....+++++|+++|+|. ..+...+.+.+|+++++..+...++.
T Consensus 43 ~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~-~~~~~~~~~~~al~ka~~~iv~~~~~ 121 (485)
T KOG2190|consen 43 LTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGN-RVELNLSPATDALFKAFDMIVFKLEE 121 (485)
T ss_pred ceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecc-cccccCCchHHHHHHHHHHHhhcccc
Confidence 34899999999999999999999999999999999999888899999999994 22224455667777766665544321
Q ss_pred ----------cCCCcceEEEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHH
Q 009566 364 ----------DSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKD 433 (532)
Q Consensus 364 ----------~~~~~~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~ 433 (532)
+.....++.+|+||.+++|+||||+|++||+|+++|||+|+|.++ .+|. .++|.|+|.|.+++|.+
T Consensus 122 d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av~~ 197 (485)
T KOG2190|consen 122 DDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAVKK 197 (485)
T ss_pred cccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHHHH
Confidence 112235899999999999999999999999999999999999875 7785 67889999999999999
Q ss_pred HHHHHHHHHHhcccccCCCcCCCCCCCCCCC
Q 009566 434 ALIQVMTRLRANLFDREGAVSTFVPVLPYIP 464 (532)
Q Consensus 434 A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~p 464 (532)
|+..|..+|.+.... ..+.+....+|.|
T Consensus 198 al~~Is~~L~~~~~~---~~~~~~st~~y~P 225 (485)
T KOG2190|consen 198 ALVQISSRLLENPPR---SPPPLVSTIPYRP 225 (485)
T ss_pred HHHHHHHHHHhcCCc---CCCCCCCcccCCC
Confidence 999999999997532 2334445567777
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=99.54 E-value=2.4e-14 Score=131.48 Aligned_cols=135 Identities=21% Similarity=0.257 Sum_probs=93.5
Q ss_pred EEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCCeEEEE---ecCcchhhhhhHHHHHHHHhcccccccccc-
Q 009566 288 LVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITV---SSKEFFEDTLSATIEAVVRLQPRCSEKIER- 363 (532)
Q Consensus 288 v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~e~vi~i---~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~- 363 (532)
|.||.+.++.|||++|++|+.|+++|||+|.++.. +..|.| ++.. ..+..+.+.+..+..- ...+.
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~---~~i~kA~~~I~~i~~g--f~~e~A 71 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDP---LAVMKAREVVKAIGRG--FSPEKA 71 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCH---HHHHHHHHHHHHHHcC--CCHHHH
Confidence 67899999999999999999999999999999963 245666 2221 1112222222111100 00000
Q ss_pred --cCCCcceEEEEEEec---------CcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHH
Q 009566 364 --DSGLISFTTRLLVPT---------SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAK 432 (532)
Q Consensus 364 --~~~~~~~~~~i~VP~---------~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~ 432 (532)
-.++...-.-+.|+. ..+|+|||++|++++.|+..|||+|.|. +.+|.|.|++++++
T Consensus 72 ~~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~------------~~~v~i~G~~~~~~ 139 (172)
T TIGR03665 72 LKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY------------GKTVGIIGDPEQVQ 139 (172)
T ss_pred HHhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc------------CCEEEEECCHHHHH
Confidence 011111222234443 4789999999999999999999999994 25899999999999
Q ss_pred HHHHHHHHHHHh
Q 009566 433 DALIQVMTRLRA 444 (532)
Q Consensus 433 ~A~~~I~~~l~~ 444 (532)
.|..+|.++|..
T Consensus 140 ~A~~~i~~li~~ 151 (172)
T TIGR03665 140 IAREAIEMLIEG 151 (172)
T ss_pred HHHHHHHHHHcC
Confidence 999999998854
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=99.54 E-value=1.8e-14 Score=132.23 Aligned_cols=137 Identities=22% Similarity=0.262 Sum_probs=95.6
Q ss_pred EEecCCccceEecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEE---cCCccccccccCcccCCHHHHHHHHHHHHH
Q 009566 47 YLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVY---SASDETNAFEDGDKFVSPAQDALFKVHDRV 123 (532)
Q Consensus 47 i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~---G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i 123 (532)
|.||.+.+|.|||++|++|+.|+++|+|+|.|.+. +..|.|+ +.++. +.+|...+.. +
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~-------------i~kA~~~I~~-i 62 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLA-------------VMKAREVVKA-I 62 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHH-------------HHHHHHHHHH-H
Confidence 57899999999999999999999999999999753 3578883 33222 2333333322 1
Q ss_pred HHhhhcCCCC-CCCCCceEEE-EEEeC---------CceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceE
Q 009566 124 IAEELRGDED-SDGGHQVTAK-LLVPS---------DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELV 192 (532)
Q Consensus 124 ~~~~~~~~~~-~~~~~~~~~~-l~vp~---------~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v 192 (532)
... +..+.. .-....++.+ +.|+. ..+++|||++|++++.|++.|+|+|.|. +..|
T Consensus 63 ~~g-f~~e~A~~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~------------~~~v 129 (172)
T TIGR03665 63 GRG-FSPEKALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY------------GKTV 129 (172)
T ss_pred HcC-CCHHHHHHhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc------------CCEE
Confidence 110 000000 0001122222 23332 3689999999999999999999999984 3579
Q ss_pred EEEcCHHHHHHHHHHHHHHHhcC
Q 009566 193 QISGEASVVKKALCQIASRLHDN 215 (532)
Q Consensus 193 ~I~G~~~~v~~A~~~I~~~l~~~ 215 (532)
.|.|++++++.|.++|.+++...
T Consensus 130 ~i~G~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 130 GIIGDPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred EEECCHHHHHHHHHHHHHHHcCC
Confidence 99999999999999999999653
No 13
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.52 E-value=9.2e-14 Score=128.43 Aligned_cols=143 Identities=19% Similarity=0.227 Sum_probs=95.5
Q ss_pred EEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCCeEEEEe---cCc-chhhhhhHHHHHHHHhcccccc
Q 009566 284 FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVS---SKE-FFEDTLSATIEAVVRLQPRCSE 359 (532)
Q Consensus 284 ~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~e~vi~i~---g~~-~~~~~~~~~~~a~~~~~~~~~~ 359 (532)
+...+.||.+.++.|||++|++|+.|+++|||+|.++.. +..|.|. +.+ .........++++.+-.. ...
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~-~e~ 76 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLAVLKARDIVKAIGRGFS-PEK 76 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCC-HHH
Confidence 467899999999999999999999999999999999963 2455564 221 111111122222222100 000
Q ss_pred cccccCCCcceEEEEEEe---------cCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHH
Q 009566 360 KIERDSGLISFTTRLLVP---------TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL 430 (532)
Q Consensus 360 ~~~~~~~~~~~~~~i~VP---------~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~ 430 (532)
.+ ...++...-..+.|. ...+|.|||++|++++.|++.|||+|.|.. ..|.|.|++++
T Consensus 77 A~-~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~------------~~v~i~G~~~~ 143 (180)
T PRK13763 77 AL-RLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG------------KTVAIIGDPEQ 143 (180)
T ss_pred HH-HHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC------------CEEEEEeCHHH
Confidence 00 000111111111121 147899999999999999999999999942 35999999999
Q ss_pred HHHHHHHHHHHHHhc
Q 009566 431 AKDALIQVMTRLRAN 445 (532)
Q Consensus 431 v~~A~~~I~~~l~~~ 445 (532)
++.|...|..+++..
T Consensus 144 ~~~A~~~I~~li~g~ 158 (180)
T PRK13763 144 VEIAREAIEMLIEGA 158 (180)
T ss_pred HHHHHHHHHHHHcCC
Confidence 999999999988643
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.51 E-value=8.7e-14 Score=128.60 Aligned_cols=139 Identities=22% Similarity=0.206 Sum_probs=98.3
Q ss_pred eEEEEEecCCccceEecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEE----cCCccccccccCcccCCHHHHHHHH
Q 009566 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVY----SASDETNAFEDGDKFVSPAQDALFK 118 (532)
Q Consensus 43 ~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~----G~~~~~~~~~~~~~~v~~a~~a~~~ 118 (532)
+...+.||.+.++.|||++|++|+.|+++|+|+|.|.+. +..|.|+ +.++. +.+|...
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~-------------i~kA~~~ 64 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLA-------------VLKARDI 64 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHH-------------HHHHHHH
Confidence 467899999999999999999999999999999999764 3577886 33322 2333333
Q ss_pred HHHHHHH---hhhcCCCCCCCCCceEEEE-EE----e-----CCceeeeeccCchHHHHHHhhhCceEEEecCCCCCccc
Q 009566 119 VHDRVIA---EELRGDEDSDGGHQVTAKL-LV----P-----SDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCA 185 (532)
Q Consensus 119 i~~~i~~---~~~~~~~~~~~~~~~~~~l-~v----p-----~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~ 185 (532)
+...+.. ++... .....+..++ .+ + ...+|+|||++|++++.|++.|||+|.|..
T Consensus 65 I~ai~~gf~~e~A~~----l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~-------- 132 (180)
T PRK13763 65 VKAIGRGFSPEKALR----LLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG-------- 132 (180)
T ss_pred HHHHhcCCCHHHHHH----HhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC--------
Confidence 3221110 00000 0011112221 11 1 136899999999999999999999999853
Q ss_pred CCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 009566 186 LRSDELVQISGEASVVKKALCQIASRLHDN 215 (532)
Q Consensus 186 ~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 215 (532)
+.|.|.|++++++.|...|.+++...
T Consensus 133 ----~~v~i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 133 ----KTVAIIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred ----CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence 34999999999999999999999664
No 15
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.39 E-value=9.7e-13 Score=100.83 Aligned_cols=64 Identities=41% Similarity=0.632 Sum_probs=57.4
Q ss_pred EEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHH
Q 009566 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVM 439 (532)
Q Consensus 372 ~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~ 439 (532)
.+|+||.+.+|+|||++|++|++|+++|||+|+|.+... ...++|.|+|+|++++|.+|+.+|.
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~----~~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL----PGSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC----CCCCceEEEEEeCHHHHHHHHHhhC
Confidence 679999999999999999999999999999999976432 2467899999999999999999873
No 16
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.30 E-value=4.5e-12 Score=97.13 Aligned_cols=55 Identities=44% Similarity=0.724 Sum_probs=50.6
Q ss_pred EEEEEecCCccceEecCCchHHHHHHHHhCCeEEEcCCCC-CCCceEEEEEcCCcc
Q 009566 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVP-GSEERVVTVYSASDE 98 (532)
Q Consensus 44 ~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~-~~~ervv~I~G~~~~ 98 (532)
+++|+||...+|+||||+|++|++|+++|||+|.|.+... +..+|+|+|.|++++
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~ 56 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSA 56 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHH
Confidence 4799999999999999999999999999999999987644 788999999999777
No 17
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.25 E-value=1.2e-11 Score=137.12 Aligned_cols=305 Identities=21% Similarity=0.272 Sum_probs=196.3
Q ss_pred ceEEEEEecCCccceEecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHH
Q 009566 42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHD 121 (532)
Q Consensus 42 ~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~ 121 (532)
-+..++.+-...+.++||++|.+++.++.++.+.|+|+++.... ....+.+...++.. .....+.++.++-.
T Consensus 200 ~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~--~~~~i~~~~~~~~~------~~~~i~~~~~~le~ 271 (753)
T KOG2208|consen 200 SVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSS--PSNKIDGRLNSSSS------INVEIQEALTRLES 271 (753)
T ss_pred eEEEEeeccccchhhhccccccccccccccceeEEEcccccccc--hhhhhcccccccee------hhhhhHHHHHHhcC
Confidence 36788999999999999999999999999999999998663222 23333443222110 00001111111100
Q ss_pred -----------------------------HHHHhh-hcCC-CC--------------------------CCCCCceEEEE
Q 009566 122 -----------------------------RVIAEE-LRGD-ED--------------------------SDGGHQVTAKL 144 (532)
Q Consensus 122 -----------------------------~i~~~~-~~~~-~~--------------------------~~~~~~~~~~l 144 (532)
..-... +..+ .. ......+.+.+
T Consensus 272 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~ 351 (753)
T KOG2208|consen 272 EFDYDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKR 351 (753)
T ss_pred hhhhhhhhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEE
Confidence 000000 0000 00 01223366788
Q ss_pred EEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCcccccc
Q 009566 145 LVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLA 224 (532)
Q Consensus 145 ~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~ 224 (532)
.+....+..++||+|.+|.+|++++.+.|.+... .+.+..+.++|....+.+|...+...+.+.+.
T Consensus 352 ~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~-------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n------- 417 (753)
T KOG2208|consen 352 EIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ-------GSNNKKVVITGVSANDEKAVEDVEKIIAEILN------- 417 (753)
T ss_pred eecHHhhhhhcCCCCccHHHHHHhhhhceecccc-------cCCCCCeEEeccccchhHHHHHHHHHHHhhhc-------
Confidence 8888999999999999999999999999999763 24577899999999999999999998877421
Q ss_pred ccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEEeecCcccccccCCch
Q 009566 225 SAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGA 304 (532)
Q Consensus 225 s~~~~~~~~~g~~~~p~~g~~~~~~~p~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~vp~~~~g~iIGk~G~ 304 (532)
......+.+|...+..+||.+|.
T Consensus 418 ---------------------------------------------------------~~~~~~~~iP~k~~~~iig~~g~ 440 (753)
T KOG2208|consen 418 ---------------------------------------------------------SIVKEEVQIPTKSHKRIIGTKGA 440 (753)
T ss_pred ---------------------------------------------------------ccccceeecCccchhhhhccccc
Confidence 02345689999999999999999
Q ss_pred hHHHHHhhhC-CeEEecCCCCCCCCeEEEEecCc-chhhhhhHHHHHHHHhcccccccccccCCCcceEEEEEEecCcce
Q 009566 305 IINQIRQESG-AAIKVDSSSTEGDDCLITVSSKE-FFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIG 382 (532)
Q Consensus 305 ~Ik~i~~~sg-a~I~i~~~~~~~~e~vi~i~g~~-~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~~G 382 (532)
.|+.|..+++ ..|++........ ..++.+.. .++.. ....+.+.. ...........+...+.|..+.+
T Consensus 441 ~i~~I~~k~~~v~i~f~~~~~~~~--~~~~~~~~~dv~~~----~~~~~~~~~----~a~~~~~~~~~~~d~~~~~~~~~ 510 (753)
T KOG2208|consen 441 LINYIMGKHGGVHIKFQNNNNSSD--MVTIRGISKDVEKS----VSLLKALKA----DAKNLKFRDVVTKDKLLPVKYIG 510 (753)
T ss_pred cHHHHHhhcCcEEEecCCCCcccc--cceEeccccccchh----HHHHHhhhh----hhhcchhhhhhhccccchHHhhc
Confidence 9999999998 7777776543322 22333321 11111 111111100 00000111245667778888888
Q ss_pred eEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhc
Q 009566 383 CLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN 445 (532)
Q Consensus 383 ~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~ 445 (532)
..+|+.|..+...++.....+.. ..++..++|.|..+.|.+|.+.+..++...
T Consensus 511 ~~~g~~~~i~d~~~~~~i~~~~~----------~~~~~~i~i~gk~~~v~~a~~~L~~~~~~~ 563 (753)
T KOG2208|consen 511 KEIGKNGTIRDSLGDKSIFPPNE----------DEDHEKITIEGKLELVLEAPAELKALIEAL 563 (753)
T ss_pred ccccCceeeeccCCceeeccccc----------ccccceeeecccccchhhhHHHHHhcchhh
Confidence 88888766665555444333322 345678999999999999999988777655
No 18
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.24 E-value=1.2e-11 Score=93.99 Aligned_cols=61 Identities=21% Similarity=0.323 Sum_probs=54.7
Q ss_pred EEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHH
Q 009566 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVM 439 (532)
Q Consensus 372 ~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~ 439 (532)
.+|.||.+++++|||++|++|++|+++|||+|.|+... +.++.|+|+|++++|..|+.+|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-------~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-------SKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-------CCCCEEEEEcCHHHHHHHHHHhC
Confidence 57999999999999999999999999999999996532 45789999999999999998873
No 19
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.24 E-value=6.1e-11 Score=121.30 Aligned_cols=271 Identities=21% Similarity=0.275 Sum_probs=167.2
Q ss_pred CCCceEEEEEecCCccceEecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHH
Q 009566 39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFK 118 (532)
Q Consensus 39 ~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~ 118 (532)
.++++.+.+.||...+..+|||.|++|+.|+..|++||.+.+.. -.++++.++.|-+.. ++++..+
T Consensus 64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p~~----------v~~a~a~--- 129 (608)
T KOG2279|consen 64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFPVQ----------VCKAKAA--- 129 (608)
T ss_pred chhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCCCC----------CChHHHH---
Confidence 46789999999999999999999999999999999999997552 123566666655444 4444444
Q ss_pred HHHHHHHhhhcCCCCCCCCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCH
Q 009566 119 VHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198 (532)
Q Consensus 119 i~~~i~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~ 198 (532)
+++++. ....+...+-+|...++.|+|++|++++.|...++|+|.+..... | ..++...|.+..
T Consensus 130 ~~~~~~-----------~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr---~--g~~~~~~i~~qq 193 (608)
T KOG2279|consen 130 IHQILT-----------ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGR---L--GLSRLIKISGQQ 193 (608)
T ss_pred HHHHHh-----------cCCcccccccchhhhcccccccchhhhcchhcccccccccccccc---c--ccccceeccccc
Confidence 344442 345667889999999999999999999999999999999865422 1 357778888888
Q ss_pred HHHHHHHHHHHHHHhcCCC-------Ccccccc-cccc-----CCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCC
Q 009566 199 SVVKKALCQIASRLHDNPS-------RSQHLLA-SAIS-----NSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAG 265 (532)
Q Consensus 199 ~~v~~A~~~I~~~l~~~~~-------~~~~~~~-s~~~-----~~~~~~g~~~~p~~g~~~~~~~p~~~~~g~~~~~~~~ 265 (532)
.-+..|..++.+.+.++-. ..+...+ .... ..+..+++..+.-.+.....++|-.+....-..++..
T Consensus 194 k~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v 273 (608)
T KOG2279|consen 194 KEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAV 273 (608)
T ss_pred chHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCccee
Confidence 8888999999888877411 1111110 0000 1111111110000000000000000000000000000
Q ss_pred CC-CCCCCCCCCC---CCCCceEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCC---eEEEEecCcc
Q 009566 266 DW-SRSLYSAPRD---DLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDD---CLITVSSKEF 338 (532)
Q Consensus 266 ~~-~~~~~~~~~~---~~~~~~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~e---~vi~i~g~~~ 338 (532)
.. -...++.+.. .........+|.+|...+|.|||+.|+.++.+...+++.+.|........- .++.+.|+..
T Consensus 274 ~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~v~~~qic~~egkqh 353 (608)
T KOG2279|consen 274 VVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSRVLQLQICVNEGKQH 353 (608)
T ss_pred EEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEeccccchhhhhhhheecchhH
Confidence 00 0001112221 123445577899999999999999999999999999999888764432211 3455666654
Q ss_pred h
Q 009566 339 F 339 (532)
Q Consensus 339 ~ 339 (532)
.
T Consensus 354 ~ 354 (608)
T KOG2279|consen 354 Y 354 (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=99.23 E-value=3.8e-11 Score=90.47 Aligned_cols=58 Identities=26% Similarity=0.342 Sum_probs=52.7
Q ss_pred eEEEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC-HHHHHHHHHHH
Q 009566 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD-LDLAKDALIQV 438 (532)
Q Consensus 370 ~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~-~~~v~~A~~~I 438 (532)
.+..|.||.+++|+|||++|++|++|+++|||+|.|.. ++.|.|.|+ +++++.|+.+|
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 45779999999999999999999999999999999942 368999998 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=99.21 E-value=1.1e-11 Score=93.44 Aligned_cols=60 Identities=35% Similarity=0.511 Sum_probs=54.0
Q ss_pred EEEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHH
Q 009566 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQV 438 (532)
Q Consensus 371 ~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I 438 (532)
|.+|.||.+++|+|||++|++|++|+++|||+|+++.+ + ....|+|.|++++|+.|+.+|
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 1 345899999999999999886
No 22
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.16 E-value=6.6e-11 Score=121.04 Aligned_cols=233 Identities=22% Similarity=0.327 Sum_probs=167.5
Q ss_pred CCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCC
Q 009566 137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNP 216 (532)
Q Consensus 137 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~ 216 (532)
..++.+++.|+...+.+++|+.|.+|+.|+..++++|.+..++ . ..++..++.|-+.++.+|...+..++.++
T Consensus 65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~-----g~e~~~~~~~~p~~v~~a~a~~~~~~~~~- 137 (608)
T KOG2279|consen 65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-V-----GDERVLLISGFPVQVCKAKAAIHQILTEN- 137 (608)
T ss_pred hhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-C-----CcccchhhccCCCCCChHHHHHHHHHhcC-
Confidence 4567899999999999999999999999999999999886653 2 23566667778999999999999888763
Q ss_pred CCccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEEeecCccc
Q 009566 217 SRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIG 296 (532)
Q Consensus 217 ~~~~~~~~s~~~~~~~~~g~~~~p~~g~~~~~~~p~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~vp~~~~g 296 (532)
..+.+.+.+|...++
T Consensus 138 -----------------------------------------------------------------~pvk~~lsvpqr~~~ 152 (608)
T KOG2279|consen 138 -----------------------------------------------------------------TPVSEQLSVPQRSVG 152 (608)
T ss_pred -----------------------------------------------------------------Ccccccccchhhhcc
Confidence 234566788999999
Q ss_pred ccccCCchhHHHHHhhhCCeEEecCCCCCCCCeEEEEecCcchhhh--------hhHHHHHHHHhcccccc---------
Q 009566 297 GVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDT--------LSATIEAVVRLQPRCSE--------- 359 (532)
Q Consensus 297 ~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~e~vi~i~g~~~~~~~--------~~~~~~a~~~~~~~~~~--------- 359 (532)
.|+|++|++++.++..++|+|.+..+......+.+.|.+....+.. +..-.+.+ +..++..+
T Consensus 153 ~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv-~~~~e~~q~rvprk~p~ 231 (608)
T KOG2279|consen 153 RIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELV-KRIAESAQTRVPRKQPI 231 (608)
T ss_pred cccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccchhHHh-hhchhhcccCCCCCCCc
Confidence 9999999999999999999999998766566677777764322100 00000111 00000000
Q ss_pred -----c------------------ccc--------c-----------------------CCCcceEEEEEEecCcceeEe
Q 009566 360 -----K------------------IER--------D-----------------------SGLISFTTRLLVPTSRIGCLI 385 (532)
Q Consensus 360 -----~------------------~~~--------~-----------------------~~~~~~~~~i~VP~~~~G~II 385 (532)
. ... + ......-.+|.||..++|.+|
T Consensus 232 n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~li 311 (608)
T KOG2279|consen 232 NVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLI 311 (608)
T ss_pred cccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCcccccchh
Confidence 0 000 0 011233467999999999999
Q ss_pred cCCChhHHHHHHhhCceEEEecCCCCCCCCCC-CCceEEEEcCHHHHHHHHHHHHHHHHhc
Q 009566 386 GKGGSIITEMRRLTKANIRILPKENLPKIASE-DDEMVQISGDLDLAKDALIQVMTRLRAN 445 (532)
Q Consensus 386 GkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~-~~r~V~I~G~~~~v~~A~~~I~~~l~~~ 445 (532)
|+.|++|+.+...|++.+.|.. .|....- .-.++++.|+..-+..|..|+..+.-..
T Consensus 312 g~~gey~s~yssasn~~~hi~t---~pyt~~v~~~qic~~egkqh~~n~vl~ml~~~~p~~ 369 (608)
T KOG2279|consen 312 GHAGEYLSVYSSASNHPNHIWT---QPYTSRVLQLQICVNEGKQHYENSVLEMLTVHVPDI 369 (608)
T ss_pred hhhhhhhhhhhhccCccceEEe---ccccchhhhhhhheecchhHHHHHHHhhhhccCCcc
Confidence 9999999999999999988864 2331111 1146889999999999999997544433
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=99.14 E-value=1.8e-10 Score=87.89 Aligned_cols=62 Identities=37% Similarity=0.599 Sum_probs=55.3
Q ss_pred EEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHH
Q 009566 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQV 438 (532)
Q Consensus 372 ~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I 438 (532)
.+|.||.+++++|||++|++|++|+++|||+|.|..... ++.++.|+|.|+.+++..|+.+|
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 579999999999999999999999999999999975321 35678999999999999999887
No 24
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.12 E-value=2.3e-10 Score=127.00 Aligned_cols=318 Identities=18% Similarity=0.258 Sum_probs=183.5
Q ss_pred ceEEEEEecCCccceEecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHH
Q 009566 42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHD 121 (532)
Q Consensus 42 ~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~ 121 (532)
.+...+.+-...+..|+||+|.+|.+|++++.|.|.+.+. +.....+.+++...++ ..+.+.+..+..
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 3566778889999999999999999999999999999885 5667789999987663 224444444333
Q ss_pred HHHHhhhcCCCCCCCCCceEEEEEEeCCceeeeeccCchHHHHHHhhhC-ceEEEecCCCCCcccCCCCceEEEEcCHHH
Q 009566 122 RVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETG-AQIRILKDEHLPSCALRSDELVQISGEASV 200 (532)
Q Consensus 122 ~i~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tg-a~I~i~~~~~~p~~~~~~~r~v~I~G~~~~ 200 (532)
.+.. ..+...+++|...+.++||.+|..|..|.++++ +.|.+..... ....+++.|....
T Consensus 414 ei~n------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~~-------~~~~~~~~~~~~d 474 (753)
T KOG2208|consen 414 EILN------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNNN-------SSDMVTIRGISKD 474 (753)
T ss_pred hhhc------------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCCc-------ccccceEeccccc
Confidence 3221 145577999999999999999999999999999 6666654322 2233555555444
Q ss_pred HHHHHHHHHHHHhcCCCC--------------------------------cccccccc--c-------cCCCCC------
Q 009566 201 VKKALCQIASRLHDNPSR--------------------------------SQHLLASA--I-------SNSHSS------ 233 (532)
Q Consensus 201 v~~A~~~I~~~l~~~~~~--------------------------------~~~~~~s~--~-------~~~~~~------ 233 (532)
+.++..++..+....... ....+... . ...+..
T Consensus 475 v~~~~~~~~~~~~~a~~~~~~~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~~~i~~~~~~~~~~~i~i~gk~~~v~~a~~ 554 (753)
T KOG2208|consen 475 VEKSVSLLKALKADAKNLKFRDVVTKDKLLPVKYIGKEIGKNGTIRDSLGDKSIFPPNEDEDHEKITIEGKLELVLEAPA 554 (753)
T ss_pred cchhHHHHHhhhhhhhcchhhhhhhccccchHHhhcccccCceeeeccCCceeecccccccccceeeecccccchhhhHH
Confidence 444333333222210000 00000000 0 000000
Q ss_pred -------C------CCCCCCCC-CCCc-----ccCCCCCCCCCC----CCCCCCC----CCCCC--CCCCC------CCC
Q 009566 234 -------S------GSLVGPTA-ATPI-----VGIAPLMGPYGG----YKGDTAG----DWSRS--LYSAP------RDD 278 (532)
Q Consensus 234 -------~------g~~~~p~~-g~~~-----~~~~p~~~~~g~----~~~~~~~----~~~~~--~~~~~------~~~ 278 (532)
. -.+..|.. ..+. .......-.+++ |+..... .|... .+.+. ..+
T Consensus 555 ~L~~~~~~~~~~~~~~v~~~~~~~~~~l~~~~~~~~~~~e~~~gv~~~fp~~~~~~~e~~i~g~~~~v~aa~~~~~~i~~ 634 (753)
T KOG2208|consen 555 ELKALIEALIKATLLEVNNPPGQHRPFLIGKGIENRTYVEVFGGVVVPFPRSPTSSDEVSIKGAKDEVKAAKGRLEEIVE 634 (753)
T ss_pred HHHhcchhhhhhhhhhccCcchheeeeeeccccccccceeecCcccccCCCCCCchhhhccchhHHHHHHhhccchhhhh
Confidence 0 00000000 0000 000000000000 0000000 00000 00000 001
Q ss_pred CCCceEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCCeEEEEecCcchhhhhhHHHHHHHHhccccc
Q 009566 279 LSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCS 358 (532)
Q Consensus 279 ~~~~~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~e~vi~i~g~~~~~~~~~~~~~a~~~~~~~~~ 358 (532)
......+..+.+|...+..+.|.+|..+++++..++..+.+++.........+.+.+.. .....
T Consensus 635 ~~~~~~~~~~~i~~~~~~~~~~~~g~~~~~~t~~~~~~~~~~~~~~~~s~~~~~~~~~~--------~~~e~-------- 698 (753)
T KOG2208|consen 635 YLSAYATTNTKIPDKFHRSIVGYRGHIIEEITSKFGVGGYFGDAPTEGSVNTIHVSGEK--------MQSEI-------- 698 (753)
T ss_pred hcccccceeeecccccceeeecCCCcccccceeecCccceeCCCCCccccCcchhhhhh--------hhhhh--------
Confidence 23445566799999999999999999999999999999999886533211112222211 00000
Q ss_pred ccccccCCCcceEEEEEEecCcceeEecCCChhHHHHHHhhCceEEEec
Q 009566 359 EKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP 407 (532)
Q Consensus 359 ~~~~~~~~~~~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~ 407 (532)
..........++..+.+|.+++..|||++|++++.+..++++.+.++.
T Consensus 699 -~~~~~~~~~~~~~~~~~p~~~~~~~ig~~g~~~r~~~~~~~~~~~~~~ 746 (753)
T KOG2208|consen 699 -AKIALEAKNLVTKEIEIPRSLHRYLIGPKGSNLRQLEKEFNVNIVVPN 746 (753)
T ss_pred -cccccccccceeeEEeccHHHhhhccCCCCccHHHHHHHhccceecCC
Confidence 111112234688999999999999999999999999999999998854
No 25
>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=99.07 E-value=1.8e-10 Score=87.44 Aligned_cols=60 Identities=28% Similarity=0.441 Sum_probs=54.7
Q ss_pred EEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHH
Q 009566 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI 208 (532)
Q Consensus 142 ~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I 208 (532)
..|.||..++++|||++|++|++|+++|||+|.|++.. ..++.|+|+|+.++|.+|+.+|
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-------~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-------SKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-------CCCCEEEEEcCHHHHHHHHHHh
Confidence 57899999999999999999999999999999997642 3578899999999999999876
No 26
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.06 E-value=1.7e-10 Score=86.98 Aligned_cols=60 Identities=40% Similarity=0.613 Sum_probs=54.0
Q ss_pred EEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHH
Q 009566 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI 208 (532)
Q Consensus 141 ~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I 208 (532)
|.+|.||.+++++|||++|.+|++|+++|||+|.|+.+ .....|+|+|+.++|.+|+++|
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 57899999999999999999999999999999999754 1245899999999999999876
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=99.01 E-value=1.4e-09 Score=81.94 Aligned_cols=58 Identities=34% Similarity=0.488 Sum_probs=52.4
Q ss_pred eEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcC-HHHHHHHHHHH
Q 009566 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGE-ASVVKKALCQI 208 (532)
Q Consensus 140 ~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I 208 (532)
....|.||.+++++|||++|++|++|+++|||+|.+.. ++.|.|+|+ .+++++|+.+|
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----------~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-----------DGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-----------CCEEEEEeCCHHHHHHHHHHh
Confidence 45779999999999999999999999999999999854 457999998 99999999876
No 28
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.96 E-value=2.4e-09 Score=81.65 Aligned_cols=62 Identities=40% Similarity=0.657 Sum_probs=55.5
Q ss_pred EEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHH
Q 009566 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI 208 (532)
Q Consensus 142 ~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I 208 (532)
.+|.||..++++|||++|++|++|+++|+|+|.|..... ...++.|.|.|+.+++..|+.+|
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 689999999999999999999999999999999986532 24688999999999999998876
No 29
>PF13014 KH_3: KH domain
Probab=98.95 E-value=1.7e-09 Score=75.48 Aligned_cols=42 Identities=48% Similarity=0.794 Sum_probs=38.7
Q ss_pred ccceEecCCchHHHHHHHHhCCeEEEcC-CCCCCCceEEEEEc
Q 009566 53 KIGSIIGRGGEIVKQLRIDTKSKIRIGE-TVPGSEERVVTVYS 94 (532)
Q Consensus 53 ~~g~IIGk~G~~Ik~i~~~tga~I~i~~-~~~~~~ervv~I~G 94 (532)
+||+||||+|++|++|+++|+|+|+|++ ..++..+|+|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 5899999999999999999999999998 56688899999987
No 30
>PF13014 KH_3: KH domain
Probab=98.90 E-value=2.9e-09 Score=74.30 Aligned_cols=43 Identities=49% Similarity=0.797 Sum_probs=37.3
Q ss_pred cceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc
Q 009566 380 RIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG 426 (532)
Q Consensus 380 ~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G 426 (532)
+||+|||++|++|++|+++|+|+|+|++ +..| .++++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~-~~~~---~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP-ENEP---GSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC-ccCC---CCCceEEEEEC
Confidence 5899999999999999999999999976 2222 57789999998
No 31
>smart00322 KH K homology RNA-binding domain.
Probab=98.87 E-value=1.3e-08 Score=78.23 Aligned_cols=67 Identities=28% Similarity=0.513 Sum_probs=59.1
Q ss_pred ceEEEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 009566 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRL 442 (532)
Q Consensus 369 ~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l 442 (532)
..+.++.||.+++++|||++|++|++|++.|+|+|.+.... .....|+|.|+++++..|..+|.+.+
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 36788999999999999999999999999999999995321 24678999999999999999998876
No 32
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.76 E-value=5e-08 Score=88.79 Aligned_cols=139 Identities=23% Similarity=0.328 Sum_probs=97.9
Q ss_pred eEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCCeEEEEecCcchhhhhh--H---HHHH--------
Q 009566 283 EFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLS--A---TIEA-------- 349 (532)
Q Consensus 283 ~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~e~vi~i~g~~~~~~~~~--~---~~~a-------- 349 (532)
..+..+.||.+-++.+||+.|+..+.|.+.++++|.++. .+..|+|...+...+++. . .+.|
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~-----~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe 81 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS-----KTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPE 81 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC-----CCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHH
Confidence 446779999999999999999999999999999999986 345677776543223221 1 1111
Q ss_pred -HHHhcccccccccccCCCcceEEE-EEE-e----cCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceE
Q 009566 350 -VVRLQPRCSEKIERDSGLISFTTR-LLV-P----TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMV 422 (532)
Q Consensus 350 -~~~~~~~~~~~~~~~~~~~~~~~~-i~V-P----~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V 422 (532)
++++... +.-...+... +.- + ....|+|||++|.+-+-|++.|+|+|.|.. .+|
T Consensus 82 ~A~~LL~d-------~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g------------~tV 142 (194)
T COG1094 82 KALKLLED-------DYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG------------KTV 142 (194)
T ss_pred HHHHHhcC-------CcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC------------cEE
Confidence 1222111 1000011110 111 1 234599999999999999999999999963 489
Q ss_pred EEEcCHHHHHHHHHHHHHHHHhc
Q 009566 423 QISGDLDLAKDALIQVMTRLRAN 445 (532)
Q Consensus 423 ~I~G~~~~v~~A~~~I~~~l~~~ 445 (532)
.|.|++++|+.|...|+.+|+..
T Consensus 143 aiiG~~~~v~iAr~AVemli~G~ 165 (194)
T COG1094 143 AIIGGFEQVEIAREAVEMLINGA 165 (194)
T ss_pred EEecChhhhHHHHHHHHHHHcCC
Confidence 99999999999999999988864
No 33
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.76 E-value=1.6e-07 Score=85.57 Aligned_cols=148 Identities=21% Similarity=0.270 Sum_probs=99.0
Q ss_pred CceEEEEEecCCccceEecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHH
Q 009566 41 EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVH 120 (532)
Q Consensus 41 ~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~ 120 (532)
......+.||....+.+||+.|++.+.|.+.++++|.++. .+..|.|......... -.+.+|.+-+..+
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~-----~~~~V~i~~~~~t~Dp-----~~~~ka~d~VkAI- 74 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS-----KTGSVTIRTTRKTEDP-----LALLKARDVVKAI- 74 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC-----CCCeEEEEecCCCCCh-----HHHHHHHHHHHHH-
Confidence 3455679999999999999999999999999999999953 4678999876221110 0011111111111
Q ss_pred HHHHHhhhcCCCCC-CCCCceEEEE-----EEe------CCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCC
Q 009566 121 DRVIAEELRGDEDS-DGGHQVTAKL-----LVP------SDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRS 188 (532)
Q Consensus 121 ~~i~~~~~~~~~~~-~~~~~~~~~l-----~vp------~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~ 188 (532)
...+..+... -....+.+.+ ++- ....|+|||++|.+.+.|++.|+|.|.|.
T Consensus 75 ----grGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~------------ 138 (194)
T COG1094 75 ----GRGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY------------ 138 (194)
T ss_pred ----hcCCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe------------
Confidence 1111100000 0001112221 111 13459999999999999999999999985
Q ss_pred CceEEEEcCHHHHHHHHHHHHHHHhcC
Q 009566 189 DELVQISGEASVVKKALCQIASRLHDN 215 (532)
Q Consensus 189 ~r~v~I~G~~~~v~~A~~~I~~~l~~~ 215 (532)
+.+|.|-|..++|..|.++|..++..-
T Consensus 139 g~tVaiiG~~~~v~iAr~AVemli~G~ 165 (194)
T COG1094 139 GKTVAIIGGFEQVEIAREAVEMLINGA 165 (194)
T ss_pred CcEEEEecChhhhHHHHHHHHHHHcCC
Confidence 347999999999999999999999764
No 34
>smart00322 KH K homology RNA-binding domain.
Probab=98.67 E-value=1.4e-07 Score=72.37 Aligned_cols=67 Identities=39% Similarity=0.655 Sum_probs=59.2
Q ss_pred ceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 009566 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRL 212 (532)
Q Consensus 139 ~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l 212 (532)
.++.++.||...+++|||++|.+|++|++.|+++|.+.... .....+.|.|..+++..|..+|.+.+
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 35788999999999999999999999999999999996532 14678999999999999999998876
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=98.52 E-value=3.5e-07 Score=78.42 Aligned_cols=68 Identities=22% Similarity=0.335 Sum_probs=53.2
Q ss_pred cCcceeEecCCChhHHHHHHhhCceEEEecCCCC-----------CCCC-CCCCceEEEEcC---HHHHHHHHHHHHHHH
Q 009566 378 TSRIGCLIGKGGSIITEMRRLTKANIRILPKENL-----------PKIA-SEDDEMVQISGD---LDLAKDALIQVMTRL 442 (532)
Q Consensus 378 ~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~-----------P~~~-~~~~r~V~I~G~---~~~v~~A~~~I~~~l 442 (532)
.+++|.|||++|++||+|+++|||+|.|..+... |... .++.-.|.|.++ .+++++|+.+|..+|
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 5788999999999999999999999999876321 1111 122356999994 599999999999988
Q ss_pred Hhc
Q 009566 443 RAN 445 (532)
Q Consensus 443 ~~~ 445 (532)
...
T Consensus 94 ~~~ 96 (120)
T cd02395 94 KPA 96 (120)
T ss_pred ccC
Confidence 843
No 36
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.26 E-value=8.2e-07 Score=85.28 Aligned_cols=149 Identities=16% Similarity=0.240 Sum_probs=102.8
Q ss_pred ceEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCCeEEEEecCcchhhhhhHHHHHHHHhccccc---
Q 009566 282 KEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCS--- 358 (532)
Q Consensus 282 ~~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~e~vi~i~g~~~~~~~~~~~~~a~~~~~~~~~--- 358 (532)
..++..+.||..+++.|.|++|.+||.|+.+|..+|+-+.. ..+.++.++|.....+.+...+++....+..+.
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr---~eePiF~vTg~~edv~~aRrei~saaeH~~l~~~s~ 100 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---GEEPIFPVTGRHEDVRRARREIPSAAEHFGLIRASR 100 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCC---CCCCcceeccCchhHHHHhhcCccccceeeeeeecc
Confidence 56788899999999999999999999999999999987753 255899999964322111111111111110000
Q ss_pred ---ccccccCCCcceEEEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHH-HHHH
Q 009566 359 ---EKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL-AKDA 434 (532)
Q Consensus 359 ---~~~~~~~~~~~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~-v~~A 434 (532)
..........+.+..+.+|...+|.|.|..|++|+.|++.+...|.-.-++ .+-++.++|.+.. +++|
T Consensus 101 s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~--------~~~Vf~Vtg~~~nC~kra 172 (394)
T KOG2113|consen 101 SFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRC--------GEPVFCVTGAPKNCVKRA 172 (394)
T ss_pred cccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeeccC--------CCceEEEecCCcchhhhc
Confidence 000111123467888999999999999999999999999999998876543 3458999998877 5555
Q ss_pred H-HHHHHH
Q 009566 435 L-IQVMTR 441 (532)
Q Consensus 435 ~-~~I~~~ 441 (532)
. ..|+..
T Consensus 173 ~s~eie~t 180 (394)
T KOG2113|consen 173 RSCEIEQT 180 (394)
T ss_pred cccchhhh
Confidence 4 344433
No 37
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.15 E-value=8.1e-06 Score=70.04 Aligned_cols=67 Identities=27% Similarity=0.402 Sum_probs=51.4
Q ss_pred CceeeeeccCchHHHHHHhhhCceEEEecCCCCCc-----------cc-CCCCceEEEEcCH---HHHHHHHHHHHHHHh
Q 009566 149 DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPS-----------CA-LRSDELVQISGEA---SVVKKALCQIASRLH 213 (532)
Q Consensus 149 ~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~-----------~~-~~~~r~v~I~G~~---~~v~~A~~~I~~~l~ 213 (532)
+++|.|||++|.+||+|+++|||+|.|..+..... .. ....-.|.|++.. +++.+|+.+|..++.
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 57899999999999999999999999976521110 00 0122468899865 899999999999997
Q ss_pred cC
Q 009566 214 DN 215 (532)
Q Consensus 214 ~~ 215 (532)
..
T Consensus 95 ~~ 96 (120)
T cd02395 95 PA 96 (120)
T ss_pred cC
Confidence 53
No 38
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=98.05 E-value=3.4e-05 Score=78.93 Aligned_cols=100 Identities=23% Similarity=0.334 Sum_probs=68.7
Q ss_pred hHHHHHHHHhcccccccccccCCCc-ceEEEEEEe------cCcceeEecCCChhHHHHHHhhCceEEEecCCC------
Q 009566 344 SATIEAVVRLQPRCSEKIERDSGLI-SFTTRLLVP------TSRIGCLIGKGGSIITEMRRLTKANIRILPKEN------ 410 (532)
Q Consensus 344 ~~~~~a~~~~~~~~~~~~~~~~~~~-~~~~~i~VP------~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~------ 410 (532)
...+++++++.+.-. ...+-... .++.+|.|| .++||+|||..|.+.|.|+++|||+|.|-.+..
T Consensus 113 ~e~I~~~lk~nP~fk--pP~DYk~p~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~ 190 (554)
T KOG0119|consen 113 HEIIEEILKLNPGFK--PPADYKPPAKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKG 190 (554)
T ss_pred HHHHHHHHHhCcCCC--CCcccCcccccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEecccccccccc
Confidence 345555665544321 11222212 566778888 578999999999999999999999999987431
Q ss_pred ----CCCCCCCCC-ceEEEEc-CHHHHHHHHHHHHHHHHhc
Q 009566 411 ----LPKIASEDD-EMVQISG-DLDLAKDALIQVMTRLRAN 445 (532)
Q Consensus 411 ----~P~~~~~~~-r~V~I~G-~~~~v~~A~~~I~~~l~~~ 445 (532)
+.....+.+ =-+.|+. +.|.|++|+++|..+|.+.
T Consensus 191 ~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~a 231 (554)
T KOG0119|consen 191 RSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQSA 231 (554)
T ss_pred CCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHhh
Confidence 111112223 3488888 5899999999999999874
No 39
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.99 E-value=1e-05 Score=77.97 Aligned_cols=143 Identities=23% Similarity=0.314 Sum_probs=103.7
Q ss_pred CCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 009566 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN 215 (532)
Q Consensus 136 ~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 215 (532)
....++..+.||..+++.+.|++|.+||.|+.+|...|+-+...+ +-+..++|..+.|+.|++.|...-+..
T Consensus 22 ~p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~e--------ePiF~vTg~~edv~~aRrei~saaeH~ 93 (394)
T KOG2113|consen 22 IGQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGE--------EPIFPVTGRHEDVRRARREIPSAAEHF 93 (394)
T ss_pred CCCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCC--------CCcceeccCchhHHHHhhcCcccccee
Confidence 347889999999999999999999999999999999997765433 456889999999999998876533221
Q ss_pred CCCccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEEeecCcc
Q 009566 216 PSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANI 295 (532)
Q Consensus 216 ~~~~~~~~~s~~~~~~~~~g~~~~p~~g~~~~~~~p~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~vp~~~~ 295 (532)
.+.-+. ..|.. +. + -+ ..+.+....+.+|...+
T Consensus 94 ------~l~~~s-~s~Sg---------g~------~-------------------~~------s~s~qt~sy~svP~rvv 126 (394)
T KOG2113|consen 94 ------GLIRAS-RSFSG---------GT------N-------------------GA------SASGQTTSYVSVPLRVV 126 (394)
T ss_pred ------eeeeec-ccccC---------CC------c-------------------cc------cccCCCceeeeccceee
Confidence 010000 00000 00 0 00 01334577788999999
Q ss_pred cccccCCchhHHHHHhhhCCeEEecCCCCCCCCeEEEEecC
Q 009566 296 GGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSK 336 (532)
Q Consensus 296 g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~e~vi~i~g~ 336 (532)
+.|.|.+|.+|+.+++.+...|.-+-.. .+.++.++|.
T Consensus 127 glvv~~~~~ti~~iqq~tnt~I~T~v~~---~~~Vf~Vtg~ 164 (394)
T KOG2113|consen 127 GLVVGPKGATIKRIQQFTNTYIATPVRC---GEPVFCVTGA 164 (394)
T ss_pred eeccccccCccchheecccceEeeeccC---CCceEEEecC
Confidence 9999999999999999999888766433 4568888874
No 40
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.94 E-value=1.3e-05 Score=70.94 Aligned_cols=102 Identities=18% Similarity=0.262 Sum_probs=68.7
Q ss_pred EEEEEecCCccceEecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHH
Q 009566 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRV 123 (532)
Q Consensus 44 ~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i 123 (532)
.+.++|+...+|..||++|++|+.|++..|-+|.|- .-+-. .++=+..++.-.
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVv-----------e~s~d----------------~~~fI~n~l~Pa 85 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELV-----------EYSDD----------------PEEFIKNIFAPA 85 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEE-----------EcCCC----------------HHHHHHHHcCCC
Confidence 356788999999999999999999999998888752 21111 111111111110
Q ss_pred HHhhhcCCCCCCCCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEE
Q 009566 124 IAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRI 175 (532)
Q Consensus 124 ~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i 175 (532)
.-....- ........+.+.|+....+.+|||+|.+|+.++.-++-.+.|
T Consensus 86 ~V~~v~I---~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 86 AVRSVTI---KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred EEEEEEE---EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 0000000 011223457788999999999999999999999999988876
No 41
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.93 E-value=3.3e-05 Score=84.68 Aligned_cols=98 Identities=24% Similarity=0.304 Sum_probs=78.8
Q ss_pred CcccCCHHHHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcc
Q 009566 105 GDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSC 184 (532)
Q Consensus 105 ~~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~ 184 (532)
..+.+..|.+++..|++.+.+..... .+..........+.||.+.++.|||++|.+||.|.++|||+|.|..
T Consensus 544 l~~aL~~A~~g~~~Il~~m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------- 615 (719)
T TIGR02696 544 LASALKQARDARLAILDVMAEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------- 615 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec-------
Confidence 34567788899999888765544333 3334455667889999999999999999999999999999999953
Q ss_pred cCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009566 185 ALRSDELVQISG-EASVVKKALCQIASRLHD 214 (532)
Q Consensus 185 ~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 214 (532)
+..|.|.+ +.+++++|+.+|..++..
T Consensus 616 ----~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 616 ----DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred ----CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 45788888 478899999999998874
No 42
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.92 E-value=2.3e-05 Score=85.83 Aligned_cols=66 Identities=27% Similarity=0.331 Sum_probs=59.3
Q ss_pred cceEEEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHh
Q 009566 368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (532)
Q Consensus 368 ~~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~ 444 (532)
.+....|.||.+.+|.|||.||.+||+|+++|||+|.|. ++..|.|.+ +.+++++|+.+|...+..
T Consensus 576 aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~-----------d~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 576 APRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE-----------DDGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred CCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe-----------cCcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 356788999999999999999999999999999999994 246899999 789999999999998884
No 43
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.92 E-value=5.1e-05 Score=67.07 Aligned_cols=103 Identities=22% Similarity=0.285 Sum_probs=70.2
Q ss_pred EEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCCeEEEEecCcchhhhhhHHHHHHHHhcccccccccc
Q 009566 284 FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIER 363 (532)
Q Consensus 284 ~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~e~vi~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~ 363 (532)
..+.++|+...+|..||++|++|+.|++..|-+|.+-.-+.+ + ..-+..++.-..-..-.+..
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~d-------------~----~~fI~n~l~Pa~V~~v~I~~ 94 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDD-------------P----EEFIKNIFAPAAVRSVTIKK 94 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCCC-------------H----HHHHHHHcCCCEEEEEEEEe
Confidence 367788999999999999999999999988877776542211 0 11112221111000000101
Q ss_pred cCCCcceEEEEEEecCcceeEecCCChhHHHHHHhhCceEEE
Q 009566 364 DSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405 (532)
Q Consensus 364 ~~~~~~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i 405 (532)
+ .......+.|+.+..|.+|||+|++|+.++..++-++.|
T Consensus 95 ~--~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 95 K--NGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred c--CCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 1 113456688999999999999999999999999998877
No 44
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.49 E-value=0.00013 Score=73.39 Aligned_cols=64 Identities=28% Similarity=0.459 Sum_probs=54.5
Q ss_pred CCCCCCcccCCCceEEEEEecCCccceEecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCC
Q 009566 30 GDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSAS 96 (532)
Q Consensus 30 ~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~ 96 (532)
.++++..+.+.++..+++.|-+.+||.|||++|++|++|+..|+++|+|.+. ..+-.|+|.|..
T Consensus 34 ~~~~~~~aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~ 97 (629)
T KOG0336|consen 34 RDSRDSAAAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGIN 97 (629)
T ss_pred CCCCcccccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechH
Confidence 4455666778899999999999999999999999999999999999999765 235678888863
No 45
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.48 E-value=0.00025 Score=79.03 Aligned_cols=97 Identities=21% Similarity=0.297 Sum_probs=73.3
Q ss_pred ccCCHHHHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccC
Q 009566 107 KFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCAL 186 (532)
Q Consensus 107 ~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 186 (532)
+.+..|.++...|++.+.+..................+.||.+.++.|||++|.+||.|+++|||+|.|..
T Consensus 518 ~al~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d--------- 588 (684)
T TIGR03591 518 QALEQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED--------- 588 (684)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec---------
Confidence 45667777888887765543333222233445567889999999999999999999999999999999954
Q ss_pred CCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009566 187 RSDELVQISG-EASVVKKALCQIASRLHD 214 (532)
Q Consensus 187 ~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 214 (532)
+..|.|.+ ..+.+.+|..+|..+..+
T Consensus 589 --dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 589 --DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred --CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 35677766 577889999998887653
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=97.46 E-value=0.00041 Score=61.16 Aligned_cols=103 Identities=22% Similarity=0.292 Sum_probs=69.9
Q ss_pred EEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCCeEEEEecCcchhhhhhHHHHHHHHhccccccccccc
Q 009566 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERD 364 (532)
Q Consensus 285 ~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~e~vi~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~ 364 (532)
.+-|.|....+|..||++|++|+.|++..|-+|.+-.-+.+ + ...+..+ +.|.-...+.-.
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 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSEN-------------L----EEFVANK--LAPAEVKNVTVS 94 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCC-------------H----HHHHHHc--CCCceEEEEEEE
Confidence 66788999999999999999999998888877766542211 0 0011111 111111111110
Q ss_pred CCCcceEEEEEEecCcceeEecCCChhHHHHHHhhCceEEEe
Q 009566 365 SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRIL 406 (532)
Q Consensus 365 ~~~~~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~ 406 (532)
..+......+.||.+..+..|||+|.+|+-..+.++-++.|.
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 011235567889999999999999999999999999988773
No 47
>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=97.45 E-value=0.00018 Score=80.24 Aligned_cols=65 Identities=28% Similarity=0.354 Sum_probs=56.8
Q ss_pred ceEEEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHh
Q 009566 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (532)
Q Consensus 369 ~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~ 444 (532)
....++.||.+.++.|||+||.+||+|+++|||+|.|. ++..|.|.+ +.+.+++|+.+|..+...
T Consensus 550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~-----------ddG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE-----------DDGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEe-----------cCeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 56788999999999999999999999999999999994 245788887 688999999999887664
No 48
>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=97.44 E-value=0.00021 Score=63.02 Aligned_cols=103 Identities=21% Similarity=0.282 Sum_probs=68.4
Q ss_pred EEEEEecCCccceEecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHH
Q 009566 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRV 123 (532)
Q Consensus 44 ~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i 123 (532)
.+-++|....+|..||++|++|+.|++..|-+|.| |.-+..+++. +.+++.=. ++
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdV-----------Veys~D~~~f------------I~N~l~PA--~V 88 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIEL-----------IEYSENLEEF------------VANKLAPA--EV 88 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEE-----------EEcCCCHHHH------------HHHcCCCc--eE
Confidence 56678999999999999999999999888888875 2222221110 01110000 00
Q ss_pred HHhhhcCCCCCCCCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEe
Q 009566 124 IAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRIL 176 (532)
Q Consensus 124 ~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~ 176 (532)
..+.-. .........+.||.+..+..|||+|.+++...+-++-++.|.
T Consensus 89 --~~V~i~---~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 89 --KNVTVS---EFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred --EEEEEE---cCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 000000 112234577889999999999999999999999999888763
No 49
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.39 E-value=0.0015 Score=67.27 Aligned_cols=76 Identities=24% Similarity=0.380 Sum_probs=56.9
Q ss_pred ceEEEEEEeC------CceeeeeccCchHHHHHHhhhCceEEEecCCCC----------Cccc-CCCCceEEEEcC-HHH
Q 009566 139 QVTAKLLVPS------DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHL----------PSCA-LRSDELVQISGE-ASV 200 (532)
Q Consensus 139 ~~~~~l~vp~------~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~----------p~~~-~~~~r~v~I~G~-~~~ 200 (532)
.++.++.||- +++|+|||..|.|.|+|+++|||+|.|-.+..+ .... ...+=-+.|+.+ .|.
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 6778888884 578999999999999999999999999752211 1100 112224677776 577
Q ss_pred HHHHHHHHHHHHhc
Q 009566 201 VKKALCQIASRLHD 214 (532)
Q Consensus 201 v~~A~~~I~~~l~~ 214 (532)
|++|++.|..+|.+
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999999986
No 50
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.38 E-value=0.00038 Score=78.27 Aligned_cols=99 Identities=20% Similarity=0.235 Sum_probs=77.2
Q ss_pred CcccCCHHHHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCce-EEEecCCCCCc
Q 009566 105 GDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQ-IRILKDEHLPS 183 (532)
Q Consensus 105 ~~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~-I~i~~~~~~p~ 183 (532)
..+.+..|.+++..|++.+.+..................|.||.+.++.|||.+|.+||.|.++||++ |.+..
T Consensus 650 l~eAL~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d------ 723 (891)
T PLN00207 650 MERALLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD------ 723 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC------
Confidence 34567778888888888765544333333344556778899999999999999999999999999999 87743
Q ss_pred ccCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009566 184 CALRSDELVQISG-EASVVKKALCQIASRLHD 214 (532)
Q Consensus 184 ~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 214 (532)
+-.|.|.+ +.+.+++|+.+|..++.+
T Consensus 724 -----dg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 724 -----DGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred -----CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 45688888 578899999999988864
No 51
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.33 E-value=0.00034 Score=75.22 Aligned_cols=114 Identities=23% Similarity=0.247 Sum_probs=84.2
Q ss_pred EEEEcCCccccccc-----------cCcccCCHHHHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEEeCCceeeeeccC
Q 009566 90 VTVYSASDETNAFE-----------DGDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKG 158 (532)
Q Consensus 90 v~I~G~~~~~~~~~-----------~~~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~ 158 (532)
+.|.|+.+.+.++. .....+..|..|..+++..+.+..............-...+.|+...+.-+||++
T Consensus 491 FKVAGT~~GiTAlQMDiKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~g 570 (692)
T COG1185 491 FKVAGTDDGITALQMDIKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPG 570 (692)
T ss_pred eEEecCCCcceeeeeeeeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCc
Confidence 55666655554332 1235677788888888887655443322233334445677889999999999999
Q ss_pred chHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCH-HHHHHHHHHHHHHHhc
Q 009566 159 GQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA-SVVKKALCQIASRLHD 214 (532)
Q Consensus 159 G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~-~~v~~A~~~I~~~l~~ 214 (532)
|.+|++|.++|||+|++.. +..|.|.++. +.+.+|+..|..+.++
T Consensus 571 Gk~I~~I~eetg~~Idied-----------dGtv~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 571 GKTIKAITEETGVKIDIED-----------DGTVKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred ccchhhhhhhhCcEEEecC-----------CCcEEEEecchHHHHHHHHHHHHHHhh
Confidence 9999999999999999962 5579999876 7789999999999866
No 52
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.25 E-value=0.001 Score=63.63 Aligned_cols=76 Identities=20% Similarity=0.322 Sum_probs=54.5
Q ss_pred cceEEEEEEe------cCcceeEecCCChhHHHHHHhhCceEEEecCCCC------------CCCCCCCC---ceEEEEc
Q 009566 368 ISFTTRLLVP------TSRIGCLIGKGGSIITEMRRLTKANIRILPKENL------------PKIASEDD---EMVQISG 426 (532)
Q Consensus 368 ~~~~~~i~VP------~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~------------P~~~~~~~---r~V~I~G 426 (532)
..++.+|+|| .++||+|+|.+|.++|+|+++|||+|-|-.+... |..++-++ -.|+...
T Consensus 90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~ 169 (259)
T KOG1588|consen 90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEA 169 (259)
T ss_pred eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeC
Confidence 4678899999 5699999999999999999999999999887532 22222222 3467777
Q ss_pred CHHHHH----HHHHHHHHHHH
Q 009566 427 DLDLAK----DALIQVMTRLR 443 (532)
Q Consensus 427 ~~~~v~----~A~~~I~~~l~ 443 (532)
++..+. .|++.|..+|.
T Consensus 170 p~~ea~~rl~~AleeI~klL~ 190 (259)
T KOG1588|consen 170 PPAEAYARLAYALEEIKKLLV 190 (259)
T ss_pred CHHHHHHHHHHHHHHHHHhcC
Confidence 765544 45555555544
No 53
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.08 E-value=0.00051 Score=77.25 Aligned_cols=66 Identities=20% Similarity=0.294 Sum_probs=57.8
Q ss_pred cceEEEEEEecCcceeEecCCChhHHHHHHhhCce-EEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHh
Q 009566 368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKAN-IRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (532)
Q Consensus 368 ~~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~-I~i~~~~~~P~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~ 444 (532)
......|.||.+.++.|||.||.+||+|.++||+. |.|. ++..|.|.+ +.+.+++|+.+|.+++.+
T Consensus 683 aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~-----------ddg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 683 APLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ-----------DDGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred CCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-----------CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 35678899999999999999999999999999999 8873 346789998 789999999999888764
No 54
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.07 E-value=0.00091 Score=72.06 Aligned_cols=67 Identities=25% Similarity=0.282 Sum_probs=58.7
Q ss_pred ceEEEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC-HHHHHHHHHHHHHHHHhcc
Q 009566 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD-LDLAKDALIQVMTRLRANL 446 (532)
Q Consensus 369 ~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~-~~~v~~A~~~I~~~l~~~~ 446 (532)
...+++.|+.+.+..|||++|.+|++|.++|||+|+|. ++.+|.|.++ -+.+..|+..|.+.+++..
T Consensus 551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-----------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~e 618 (692)
T COG1185 551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-----------DDGTVKIAASDGESAKKAKERIEAITREVE 618 (692)
T ss_pred CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-----------CCCcEEEEecchHHHHHHHHHHHHHHhhcc
Confidence 45678999999999999999999999999999999994 3457999995 5889999999999987764
No 55
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.93 E-value=0.0017 Score=65.64 Aligned_cols=67 Identities=24% Similarity=0.324 Sum_probs=55.2
Q ss_pred ceEEEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHH
Q 009566 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLR 443 (532)
Q Consensus 369 ~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~ 443 (532)
.+.+.|.|-+++||.|||++|++|+.||..|.++|+|... +.+-.|+|-|....-.+|+..|...+.
T Consensus 46 e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~--------~~e~kv~ifg~~~m~~kaka~id~~~~ 112 (629)
T KOG0336|consen 46 EFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC--------DLEVKVTIFGINHMRKKAKASIDRGQD 112 (629)
T ss_pred CCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc--------CceeEEEEechHHHHHHHHhhHhhhhh
Confidence 3556688899999999999999999999999999999653 335689999998887888777755544
No 56
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.84 E-value=0.004 Score=57.79 Aligned_cols=103 Identities=23% Similarity=0.312 Sum_probs=67.9
Q ss_pred EEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCCeEEEEecCcchhhhhhHHHHHHHHhccccccccccc
Q 009566 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERD 364 (532)
Q Consensus 285 ~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~e~vi~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~ 364 (532)
...+.+-.+.+|..||++|.+|+.|.++.|=+|.|-.-+.+ .+ . .+..++. |--...+.-.
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d-------------~~---~-fI~nal~--Pa~v~~V~~~ 137 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSED-------------PA---E-FIKNALA--PAEVLSVNIK 137 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCC-------------HH---H-HHHHhcC--cceEeEEEEE
Confidence 34455556778999999999999999999966655432211 10 0 1111111 1111111111
Q ss_pred CCCcceEEEEEEecCcceeEecCCChhHHHHHHhhCceEEEec
Q 009566 365 SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP 407 (532)
Q Consensus 365 ~~~~~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~ 407 (532)
..+.. ...+.||.+..+.+|||+|.+++-+.+.||-+|.|..
T Consensus 138 ~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 138 EDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred eCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 10112 6778899999999999999999999999999999953
No 57
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.79 E-value=0.0029 Score=58.73 Aligned_cols=103 Identities=29% Similarity=0.363 Sum_probs=67.1
Q ss_pred EEEEecCCccceEecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHH
Q 009566 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVI 124 (532)
Q Consensus 45 ~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~ 124 (532)
+-+.+-...+|..||++|++|+.|.++.|=+|.|-+ -+-.+.+ -+.+|+.-+ ++.
T Consensus 78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe-----------~s~d~~~------------fI~nal~Pa--~v~ 132 (190)
T COG0195 78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVE-----------WSEDPAE------------FIKNALAPA--EVL 132 (190)
T ss_pred EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEE-----------eCCCHHH------------HHHHhcCcc--eEe
Confidence 444555677899999999999999999996665421 1111111 012221100 000
Q ss_pred HhhhcCCCCCCCCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecC
Q 009566 125 AEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (532)
Q Consensus 125 ~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~ 178 (532)
.+.-. ..+.. ...+.||.++.+.+|||+|.+++.+.+-||.++.|...
T Consensus 133 --~V~~~---~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~ 180 (190)
T COG0195 133 --SVNIK---EDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI 180 (190)
T ss_pred --EEEEE---eCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence 00000 00112 67889999999999999999999999999999999653
No 58
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.77 E-value=0.0018 Score=62.06 Aligned_cols=41 Identities=32% Similarity=0.496 Sum_probs=36.2
Q ss_pred cCCCceEEEEEecCC------ccceEecCCchHHHHHHHHhCCeEEE
Q 009566 38 IGPEDTVYRYLCPIR------KIGSIIGRGGEIVKQLRIDTKSKIRI 78 (532)
Q Consensus 38 ~~~~~~~~~i~vp~~------~~g~IIGk~G~~Ik~i~~~tga~I~i 78 (532)
...-.++.+|+||.+ +||.|+|.+|.++|+|+++|+|+|.|
T Consensus 87 ~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~I 133 (259)
T KOG1588|consen 87 GKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMI 133 (259)
T ss_pred CCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEE
Confidence 345667789999997 79999999999999999999999865
No 59
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.58 E-value=0.0023 Score=71.69 Aligned_cols=97 Identities=22% Similarity=0.319 Sum_probs=72.0
Q ss_pred ccCCHHHHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccC
Q 009566 107 KFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCAL 186 (532)
Q Consensus 107 ~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 186 (532)
+.+..|.+++.+|++.+.+..-....+..........+.||.+.++.+||++|.+||+|.++||++|.+..
T Consensus 521 ~al~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d--------- 591 (693)
T PRK11824 521 EALEQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED--------- 591 (693)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC---------
Confidence 56677888888888876554322222222233445667779999999999999999999999999988732
Q ss_pred CCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009566 187 RSDELVQISG-EASVVKKALCQIASRLHD 214 (532)
Q Consensus 187 ~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 214 (532)
+-.|.|.+ ..+.+.+|+.+|..+..+
T Consensus 592 --~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 592 --DGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred --CceEEEEcccHHHHHHHHHHHHHhccc
Confidence 45688888 578889999999887754
No 60
>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=96.53 E-value=0.0046 Score=46.41 Aligned_cols=37 Identities=30% Similarity=0.421 Sum_probs=34.0
Q ss_pred ceEEEEEecCCccceEecCCchHHHHHHHHhCCeEEE
Q 009566 42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRI 78 (532)
Q Consensus 42 ~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i 78 (532)
.....+.|+.+.+|.+|||+|.+|+.+++.++-+|.|
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 61
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.44 E-value=0.0038 Score=61.49 Aligned_cols=71 Identities=27% Similarity=0.405 Sum_probs=59.8
Q ss_pred ceEEEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHhcc
Q 009566 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRANL 446 (532)
Q Consensus 369 ~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~~~ 446 (532)
.....+.|+..+.|.|||++|.+-+.|+++|+++|.++.+ .++...|+|+| ..++|..|...|...|.+..
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 4567799999999999999999999999999999998653 23445666666 78999999999988888764
No 62
>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=96.40 E-value=0.0059 Score=45.82 Aligned_cols=36 Identities=33% Similarity=0.570 Sum_probs=33.5
Q ss_pred eEEEEEEecCcceeEecCCChhHHHHHHhhCceEEE
Q 009566 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405 (532)
Q Consensus 370 ~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i 405 (532)
....+.|+.+..|.+|||+|.+|+.+++.++-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 567899999999999999999999999999988876
No 63
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.38 E-value=0.026 Score=51.75 Aligned_cols=42 Identities=26% Similarity=0.590 Sum_probs=36.8
Q ss_pred cceEEEEEEe------cCcceeEecCCChhHHHHHHhhCceEEEecCC
Q 009566 368 ISFTTRLLVP------TSRIGCLIGKGGSIITEMRRLTKANIRILPKE 409 (532)
Q Consensus 368 ~~~~~~i~VP------~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~ 409 (532)
..++..+.|| .++||.|||..|.+.|+|++.|+|+|-|-.+.
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 3567788888 67999999999999999999999999997654
No 64
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.25 E-value=0.0055 Score=60.37 Aligned_cols=71 Identities=27% Similarity=0.391 Sum_probs=57.2
Q ss_pred ceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 009566 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN 215 (532)
Q Consensus 139 ~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 215 (532)
.....++|++...++|||++|.|.++|+++|+++|.++.... ..+.++.+.+..++|.+|...|..+|...
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 345678999999999999999999999999999998876421 23344444456888999999999988775
No 65
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.24 E-value=0.0092 Score=57.84 Aligned_cols=63 Identities=22% Similarity=0.274 Sum_probs=53.1
Q ss_pred EEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHhc
Q 009566 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRAN 445 (532)
Q Consensus 372 ~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~~ 445 (532)
..+.||.++++.+||++|.+|+.|.+.|++.|.|- .+..|.|.+ +.+++..|+.+|...-++.
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig-----------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG-----------QNGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc-----------CCcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 56899999999999999999999999999999983 246899999 5678888888887655543
No 66
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.23 E-value=0.018 Score=58.85 Aligned_cols=97 Identities=22% Similarity=0.206 Sum_probs=64.8
Q ss_pred CcccccccCCchhHHHHHhhh-CCeEEecCCCCCCCCeEEEEecCcchhhhhhHHHHHHHHhcccccccccccCCCcceE
Q 009566 293 ANIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFT 371 (532)
Q Consensus 293 ~~~g~iIGk~G~~Ik~i~~~s-ga~I~i~~~~~~~~e~vi~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ 371 (532)
+-+|..||++|.+|+.|.++. |=+|.|-.-+.+ .. .-+..++ .|.-...+.-. .....
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D-------------~~----~fI~Nal--~Pa~V~~V~i~--~~~~~ 309 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNV-------------PE----IFIARAL--APAIISSVKIE--EEEKK 309 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCC-------------HH----HHHHHhC--CCceeeEEEEc--CCCcE
Confidence 458999999999999999998 666665432211 00 0111111 11111111111 11246
Q ss_pred EEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCC
Q 009566 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKEN 410 (532)
Q Consensus 372 ~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~ 410 (532)
..+.||.+..+..|||+|.+++-..+.||.+|.|.+-+.
T Consensus 310 ~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 310 AIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS 348 (374)
T ss_pred EEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence 778999999999999999999999999999999987554
No 67
>PRK00106 hypothetical protein; Provisional
Probab=96.19 E-value=0.015 Score=62.66 Aligned_cols=67 Identities=24% Similarity=0.322 Sum_probs=52.9
Q ss_pred ceEEEEEEec-CcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHhc
Q 009566 369 SFTTRLLVPT-SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRAN 445 (532)
Q Consensus 369 ~~~~~i~VP~-~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~~ 445 (532)
.....+.+|+ ++-|+||||-|.+|+-+...||+.|-|. + +...|+|++ +|---+.|...+..+|.+-
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid---d-------tp~~v~lS~fdpvRReiAr~~le~Li~dg 292 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID---D-------TPEVVVLSGFDPIRREIARMTLESLIKDG 292 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc---C-------CCCeEEEeCCChHHHHHHHHHHHHHHHcC
Confidence 4566788898 5669999999999999999999999993 2 335899999 8877777766666665543
No 68
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.19 E-value=0.013 Score=63.29 Aligned_cols=67 Identities=22% Similarity=0.292 Sum_probs=52.4
Q ss_pred ceEEEEEEec-CcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHhc
Q 009566 369 SFTTRLLVPT-SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRAN 445 (532)
Q Consensus 369 ~~~~~i~VP~-~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~~ 445 (532)
..+..+.+|+ ++-|.||||-|.+|+-+...||+.|-|. + +...|+|++ +|---+.|..-+..+|.+-
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid---d-------tp~~v~ls~fdp~rreia~~~l~~li~dg 271 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---D-------TPEAVILSGFDPVRREIARMALEKLIQDG 271 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc---C-------CCCeEEecCCchHHHHHHHHHHHHHHHcC
Confidence 4566788898 4559999999999999999999999993 2 335899999 7876677766666665543
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=96.18 E-value=0.017 Score=58.87 Aligned_cols=93 Identities=26% Similarity=0.414 Sum_probs=63.2
Q ss_pred CcccccccCCchhHHHHHhhh-CCeEEecCCCCCCCCeEEEEecCcchhhhhhHHHHHHHHhcccccccc--cccCCCcc
Q 009566 293 ANIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKI--ERDSGLIS 369 (532)
Q Consensus 293 ~~~g~iIGk~G~~Ik~i~~~s-ga~I~i~~~~~~~~e~vi~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~ 369 (532)
+-+|+.||++|++|+.|.++. |=+|.|-.-+.+. .++ ...|+ .|.-...+ ..+ ..
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~---------~~f-------i~nal---~Pa~v~~v~i~~~---~~ 300 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDP---------AEF-------IANAL---SPAKVISVEVLDE---DK 300 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCH---------HHH-------HHHhc---CCceEEEEEEEcC---CC
Confidence 458999999999999999998 6666654322110 000 11111 11111111 111 12
Q ss_pred eEEEEEEecCcceeEecCCChhHHHHHHhhCceEEEec
Q 009566 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP 407 (532)
Q Consensus 370 ~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~ 407 (532)
....+.||.+..+..|||+|.+++-..+.||.+|.|.+
T Consensus 301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 46789999999999999999999999999999999965
No 70
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.08 E-value=0.0042 Score=69.64 Aligned_cols=65 Identities=29% Similarity=0.363 Sum_probs=55.8
Q ss_pred ceEEEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHh
Q 009566 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (532)
Q Consensus 369 ~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~ 444 (532)
.....+.||.+.++.|||.||.+||+|.++||+.|.+. ++..|.|.+ +.+.+++|+.+|..+..+
T Consensus 553 p~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-----------d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 553 PRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-----------DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred chheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 45567888999999999999999999999999988772 345788888 689999999999887764
No 71
>PRK12704 phosphodiesterase; Provisional
Probab=96.07 E-value=0.016 Score=62.63 Aligned_cols=66 Identities=23% Similarity=0.286 Sum_probs=50.7
Q ss_pred ceEEEEEEec-CcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHh
Q 009566 369 SFTTRLLVPT-SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (532)
Q Consensus 369 ~~~~~i~VP~-~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~ 444 (532)
..+..+.+|+ ++-|+||||-|.+|+-+...||+.|-|. + +...|+|+| +|-.-+.|...+..++.+
T Consensus 209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid---d-------tp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---D-------TPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc---C-------CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 4556788888 5669999999999999999999999993 2 335899999 676655666665555543
No 72
>PRK00468 hypothetical protein; Provisional
Probab=95.90 E-value=0.0095 Score=46.53 Aligned_cols=34 Identities=24% Similarity=0.501 Sum_probs=30.2
Q ss_pred CCCceEEEEEecCCccceEecCCchHHHHHHHHh
Q 009566 39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDT 72 (532)
Q Consensus 39 ~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~t 72 (532)
..+.+.++|.|..+.+|.||||+|.+|+.||.--
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 3456889999999999999999999999999764
No 73
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=95.90 E-value=0.015 Score=59.19 Aligned_cols=96 Identities=30% Similarity=0.431 Sum_probs=62.5
Q ss_pred CccceEecCCchHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHHHhhhcC
Q 009566 52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG 130 (532)
Q Consensus 52 ~~~g~IIGk~G~~Ik~i~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~ 130 (532)
+-+|..||++|.+|+.|.++. |=+|.|-. -+-.++.. +.+||.-. ++..-.+.
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~-----------~s~d~~~f------------i~nal~Pa--~v~~v~i~- 296 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIE-----------YSDDPAEF------------IANALSPA--KVISVEVL- 296 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEE-----------cCCCHHHH------------HHHhcCCc--eEEEEEEE-
Confidence 458999999999999999998 67776421 11111100 01111000 00000000
Q ss_pred CCCCCCCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecC
Q 009566 131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (532)
Q Consensus 131 ~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~ 178 (532)
+ .....+.+.||..+.+..|||+|.+++-....||.+|.|...
T Consensus 297 ----~-~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~ 339 (341)
T TIGR01953 297 ----D-EDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE 339 (341)
T ss_pred ----c-CCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence 0 112368899999999999999999999999999999999764
No 74
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.84 E-value=0.027 Score=57.83 Aligned_cols=96 Identities=24% Similarity=0.307 Sum_probs=63.7
Q ss_pred CcccccccCCchhHHHHHhhh-CCeEEecCCCCCCCCeEEEEecCcchhhhhhHHHHHHHHhcccccccccccCCCcceE
Q 009566 293 ANIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFT 371 (532)
Q Consensus 293 ~~~g~iIGk~G~~Ik~i~~~s-ga~I~i~~~~~~~~e~vi~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ 371 (532)
+-+|+.||++|.+|+.|..+. |=+|.|-.-+.+ .+. -+..++ .|.-...+.-.. .....
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d-------------~~~----fi~nal--~Pa~v~~v~i~~-~~~~~ 304 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSED-------------PAE----FVANAL--SPAKVVSVEVDD-EEEKA 304 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCCC-------------HHH----HHHHhC--CCceEEEEEEEc-CCCcE
Confidence 458999999999999999998 666665432211 000 111111 111111110000 11246
Q ss_pred EEEEEecCcceeEecCCChhHHHHHHhhCceEEEecC
Q 009566 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPK 408 (532)
Q Consensus 372 ~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~ 408 (532)
..+.||.++.+..|||+|.+++-..+.||.+|.|.+.
T Consensus 305 ~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 305 ARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred EEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 7899999999999999999999999999999999753
No 75
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.67 E-value=0.021 Score=58.30 Aligned_cols=95 Identities=20% Similarity=0.187 Sum_probs=62.3
Q ss_pred CccceEecCCchHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHHHhhhcC
Q 009566 52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG 130 (532)
Q Consensus 52 ~~~g~IIGk~G~~Ik~i~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~ 130 (532)
+-+|..||++|.+|+.|.++. |=+|.|-.= .-.+... +.+||.=. ++. .+.-
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~-----------s~D~~~f------------I~Nal~Pa--~V~--~V~i 303 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEY-----------SNVPEIF------------IARALAPA--IIS--SVKI 303 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEc-----------CCCHHHH------------HHHhCCCc--eee--EEEE
Confidence 458999999999999999998 667664211 1110000 01110000 000 0000
Q ss_pred CCCCCCCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecC
Q 009566 131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (532)
Q Consensus 131 ~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~ 178 (532)
. ...-.+.+.||..+.+..|||+|.+++-....||.+|.|..-
T Consensus 304 ----~-~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~ 346 (374)
T PRK12328 304 ----E-EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI 346 (374)
T ss_pred ----c-CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence 0 112367889999999999999999999999999999999764
No 76
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.61 E-value=0.021 Score=58.53 Aligned_cols=96 Identities=27% Similarity=0.356 Sum_probs=62.8
Q ss_pred CccceEecCCchHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHHHhhhcC
Q 009566 52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG 130 (532)
Q Consensus 52 ~~~g~IIGk~G~~Ik~i~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~ 130 (532)
+-+|..||++|.+|+.|.++. |-+|.|-.- +-.++.. +.+||.=. ++..-.+.
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~-----------s~d~~~f------------i~nal~Pa--~v~~v~i~- 298 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDW-----------SEDPAEF------------VANALSPA--KVVSVEVD- 298 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEc-----------CCCHHHH------------HHHhCCCc--eEEEEEEE-
Confidence 458999999999999999998 777765211 1111000 00110000 00000000
Q ss_pred CCCCCCCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecC
Q 009566 131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (532)
Q Consensus 131 ~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~ 178 (532)
+ .....+.+.||..+.+..|||+|.|++-....||.+|.|...
T Consensus 299 ----~-~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 299 ----D-EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred ----c-CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 0 122358899999999999999999999999999999999765
No 77
>PRK02821 hypothetical protein; Provisional
Probab=95.60 E-value=0.014 Score=45.81 Aligned_cols=36 Identities=22% Similarity=0.374 Sum_probs=31.1
Q ss_pred CCCceEEEEEecCCccceEecCCchHHHHHHHHhCC
Q 009566 39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKS 74 (532)
Q Consensus 39 ~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga 74 (532)
..+.+.+.|.|..+.+|.||||+|.+|+.||.--.+
T Consensus 27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 345678999999999999999999999999977543
No 78
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.54 E-value=0.032 Score=57.90 Aligned_cols=94 Identities=27% Similarity=0.347 Sum_probs=62.5
Q ss_pred CcccccccCCchhHHHHHhhh-CCeEEecCCCCCCCCeEEEEecCcchhhhhhHHHHHHHHhccccccccc-ccCCCcce
Q 009566 293 ANIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIE-RDSGLISF 370 (532)
Q Consensus 293 ~~~g~iIGk~G~~Ik~i~~~s-ga~I~i~~~~~~~~e~vi~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~ 370 (532)
+-+|..||++|.+|+.|.++. |=+|.|-.-+.+ .+. -+..++ .|.-...+. .+ ....
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~D-------------p~~----fI~NaL--sPA~V~~V~i~~--~~~k 335 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPD-------------PAT----YIANAL--SPARVDEVRLVD--PEGR 335 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCC-------------HHH----HHHHhc--CCceeeEEEEEc--CCCc
Confidence 458999999999999999998 666665432211 000 111111 111111110 01 1124
Q ss_pred EEEEEEecCcceeEecCCChhHHHHHHhhCceEEEec
Q 009566 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP 407 (532)
Q Consensus 371 ~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~ 407 (532)
...+.||.++.+..|||+|.+|+-..+.||.+|.|..
T Consensus 336 ~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 336 HAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred EEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 5679999999999999999999999999999999954
No 79
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.30 E-value=0.04 Score=58.63 Aligned_cols=95 Identities=24% Similarity=0.374 Sum_probs=63.4
Q ss_pred CcccccccCCchhHHHHHhhh-CCeEEecCCCCCCCCeEEEEecCcchhhhhhHHHHHHHHhcccccccccccCCCcceE
Q 009566 293 ANIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFT 371 (532)
Q Consensus 293 ~~~g~iIGk~G~~Ik~i~~~s-ga~I~i~~~~~~~~e~vi~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ 371 (532)
+-+|+.||++|++|+.|..+. |=+|.|-.-+.+ .+. -...++ .|.-...+.-+.. ...
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d-------------~~~---fi~nal---~pa~v~~v~~~~~--~~~ 303 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIILWSDD-------------PAQ---FIINAL---SPAEVSSVVVDED--EHS 303 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEEcCCC-------------HHH---HHHHhC---CCCEEEEEEEeCC--CCE
Confidence 348999999999999999998 666665432211 000 011111 1111111100111 236
Q ss_pred EEEEEecCcceeEecCCChhHHHHHHhhCceEEEecC
Q 009566 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPK 408 (532)
Q Consensus 372 ~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~ 408 (532)
..+.||....+..|||+|.+|+-..+.||.+|.|...
T Consensus 304 ~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 304 ADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred EEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 7899999999999999999999999999999999764
No 80
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=95.26 E-value=0.54 Score=44.68 Aligned_cols=131 Identities=17% Similarity=0.166 Sum_probs=86.4
Q ss_pred EEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCCeEEEEecCcchhhhhhHHHHHHHHhccccccccccc
Q 009566 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERD 364 (532)
Q Consensus 285 ~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~e~vi~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~ 364 (532)
.+.+.++....-.+...+|..++.|....||+|.+.. ....+.|+|++...+.+...+..++.-
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-----~~~~i~I~g~k~~~~~i~~~i~~~l~~----------- 90 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR-----SENRIRITGTKSTAEYIEASINEILSN----------- 90 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEec-----CCcEEEEEccHHHHHHHHHHHHHHHhh-----------
Confidence 3445556788889999999999999888899999986 456889999864333222222222211
Q ss_pred CCCcceEEEEEEecCcceeEe-c---CCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-----CHHHHHHHH
Q 009566 365 SGLISFTTRLLVPTSRIGCLI-G---KGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-----DLDLAKDAL 435 (532)
Q Consensus 365 ~~~~~~~~~i~VP~~~~G~II-G---kgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G-----~~~~v~~A~ 435 (532)
..+.+|.++.-..-... + .....+++|++.|++.|..... ...+.|.. ....++.|+
T Consensus 91 ----i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~----------~~~~~i~~~~~~~~~~~~~~a~ 156 (210)
T PF14611_consen 91 ----IRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD----------GNKLKISWLASPENEKRADRAK 156 (210)
T ss_pred ----cEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC----------CCeEEEEEEeeccccchHHHHH
Confidence 24455555533211111 1 2467899999999999987432 23455554 578899999
Q ss_pred HHHHHHHHhc
Q 009566 436 IQVMTRLRAN 445 (532)
Q Consensus 436 ~~I~~~l~~~ 445 (532)
.++...+...
T Consensus 157 RlL~~a~~~~ 166 (210)
T PF14611_consen 157 RLLLWALDYN 166 (210)
T ss_pred HHHHHhccCC
Confidence 9998888533
No 81
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.13 E-value=0.024 Score=58.81 Aligned_cols=95 Identities=29% Similarity=0.326 Sum_probs=61.4
Q ss_pred CccceEecCCchHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHHHhhhcC
Q 009566 52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG 130 (532)
Q Consensus 52 ~~~g~IIGk~G~~Ik~i~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~ 130 (532)
+-+|..||++|..|+.|.++. |=+|.|-. -+-.++.. +.+||.=. ++..-.+.
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~-----------ys~Dp~~f------------I~NaLsPA--~V~~V~i~- 330 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIR-----------WSPDPATY------------IANALSPA--RVDEVRLV- 330 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEE-----------cCCCHHHH------------HHHhcCCc--eeeEEEEE-
Confidence 468999999999999999998 67776421 11111000 01110000 00000000
Q ss_pred CCCCCCCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEec
Q 009566 131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILK 177 (532)
Q Consensus 131 ~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~ 177 (532)
+ ...-.+.+.||..+.+..|||+|.|++-....||.+|.|..
T Consensus 331 ----~-~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 331 ----D-PEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred ----c-CCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 0 11234789999999999999999999999999999999864
No 82
>PRK00468 hypothetical protein; Provisional
Probab=95.13 E-value=0.023 Score=44.34 Aligned_cols=34 Identities=32% Similarity=0.435 Sum_probs=29.8
Q ss_pred CcceEEEEEEecCcceeEecCCChhHHHHHHhhC
Q 009566 367 LISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTK 400 (532)
Q Consensus 367 ~~~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tg 400 (532)
+..+..++.+..+-+|+||||+|.+|+-||.--.
T Consensus 27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~ 60 (75)
T PRK00468 27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVK 60 (75)
T ss_pred CCeEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence 3457889999999999999999999999998654
No 83
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.13 E-value=0.066 Score=49.22 Aligned_cols=44 Identities=23% Similarity=0.406 Sum_probs=36.1
Q ss_pred CCCceEEEEEEe------CCceeeeeccCchHHHHHHhhhCceEEEecCC
Q 009566 136 GGHQVTAKLLVP------SDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179 (532)
Q Consensus 136 ~~~~~~~~l~vp------~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~ 179 (532)
....++-++.|| .+.+|.|||+.|.|+++|++.|+|+|.|-...
T Consensus 144 rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g 193 (269)
T COG5176 144 RPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSG 193 (269)
T ss_pred CcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence 445556677777 45799999999999999999999999996543
No 84
>PRK02821 hypothetical protein; Provisional
Probab=94.87 E-value=0.028 Score=44.11 Aligned_cols=34 Identities=29% Similarity=0.447 Sum_probs=29.6
Q ss_pred cceEEEEEEecCcceeEecCCChhHHHHHHhhCc
Q 009566 368 ISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKA 401 (532)
Q Consensus 368 ~~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga 401 (532)
......+.|.++-+|+||||+|.+|+.||..-.+
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 3577889999999999999999999999987543
No 85
>PRK01064 hypothetical protein; Provisional
Probab=94.82 E-value=0.039 Score=43.43 Aligned_cols=34 Identities=26% Similarity=0.465 Sum_probs=30.2
Q ss_pred CCceEEEEEecCCccceEecCCchHHHHHHHHhC
Q 009566 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (532)
Q Consensus 40 ~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tg 73 (532)
...+.+++.|..+..|.+|||+|.+|+.||.-..
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 4668899999999999999999999999997543
No 86
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.76 E-value=0.037 Score=43.11 Aligned_cols=33 Identities=15% Similarity=0.343 Sum_probs=29.7
Q ss_pred CCceEEEEEecCCccceEecCCchHHHHHHHHh
Q 009566 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDT 72 (532)
Q Consensus 40 ~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~t 72 (532)
...+.++|.+..+.+|.||||+|.+|+.||.--
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 566789999999999999999999999999764
No 87
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=94.72 E-value=0.77 Score=43.64 Aligned_cols=63 Identities=19% Similarity=0.383 Sum_probs=54.3
Q ss_pred EEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 009566 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD 214 (532)
Q Consensus 142 ~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~ 214 (532)
+.+.++.....+|...+|..+++|....||+|.+..+ +..|.|+|+...|..+...|.+++..
T Consensus 28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~----------~~~i~I~g~k~~~~~i~~~i~~~l~~ 90 (210)
T PF14611_consen 28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS----------ENRIRITGTKSTAEYIEASINEILSN 90 (210)
T ss_pred eEEEecchheeeeecCCchHHHHHHHhcCceEEEecC----------CcEEEEEccHHHHHHHHHHHHHHHhh
Confidence 4455567888999999999999998899999999764 56799999999999999999888865
No 88
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.51 E-value=0.046 Score=42.55 Aligned_cols=34 Identities=32% Similarity=0.442 Sum_probs=30.2
Q ss_pred CcceEEEEEEecCcceeEecCCChhHHHHHHhhC
Q 009566 367 LISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTK 400 (532)
Q Consensus 367 ~~~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tg 400 (532)
+..+..++.|...-+|.||||+|.+|+-||..-.
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll~ 60 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLLS 60 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHHHH
Confidence 4578899999999999999999999999998643
No 89
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=94.47 E-value=0.071 Score=56.18 Aligned_cols=114 Identities=18% Similarity=0.213 Sum_probs=77.9
Q ss_pred EEEEcCCccccccccC----cccCCHHHHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEEeCCceeeeeccCchHHHHH
Q 009566 90 VTVYSASDETNAFEDG----DKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNI 165 (532)
Q Consensus 90 v~I~G~~~~~~~~~~~----~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I 165 (532)
..|.|+.+.+.++... .+.+.+|.+|-..|++.+....-...........+...+.|+.+....+||.+|...|+|
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 3455555555544211 244555666766777655433322233334556788899999999999999999999999
Q ss_pred HhhhCceEEEecCCCCCcccCCCCceEEEEcC-HHHHHHHHHHHHHHHhcC
Q 009566 166 RSETGAQIRILKDEHLPSCALRSDELVQISGE-ASVVKKALCQIASRLHDN 215 (532)
Q Consensus 166 ~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~ 215 (532)
..+||+.-.+ ++..++|... ..+.++|++.|..++..+
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 9999954443 2456777665 667789999998888663
No 90
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=94.43 E-value=0.061 Score=52.16 Aligned_cols=63 Identities=21% Similarity=0.291 Sum_probs=52.7
Q ss_pred EEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcC-HHHHHHHHHHHHHHHhcC
Q 009566 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGE-ASVVKKALCQIASRLHDN 215 (532)
Q Consensus 142 ~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~ 215 (532)
+.+.||..+++.+||++|.+|+.|.++|+++|.+-. +-.|.|.+. .+++.+|+.+|..+-++.
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-----------NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-----------NGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-----------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 558899999999999999999999999999998843 346888887 457888888888766653
No 91
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=94.42 E-value=0.048 Score=58.03 Aligned_cols=95 Identities=26% Similarity=0.357 Sum_probs=62.2
Q ss_pred CccceEecCCchHHHHHHHHh-CCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHHHhhhcC
Q 009566 52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG 130 (532)
Q Consensus 52 ~~~g~IIGk~G~~Ik~i~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~ 130 (532)
+-+|..||++|++|+.|.++. |=+|.|-. -.-.+... +.+|+.-. .+ .....
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~-----------~s~d~~~f------------i~nal~pa--~v-~~v~~- 297 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIIL-----------WSDDPAQF------------IINALSPA--EV-SSVVV- 297 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEE-----------cCCCHHHH------------HHHhCCCC--EE-EEEEE-
Confidence 358999999999999999998 67776421 11111000 01110000 00 00000
Q ss_pred CCCCCCCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecC
Q 009566 131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (532)
Q Consensus 131 ~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~ 178 (532)
+. ..-.+.+.||..+.+..|||+|.+++-....||.+|.|...
T Consensus 298 ----~~-~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 298 ----DE-DEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred ----eC-CCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 00 11268899999999999999999999999999999999764
No 92
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=94.34 E-value=0.12 Score=57.71 Aligned_cols=28 Identities=21% Similarity=0.237 Sum_probs=12.3
Q ss_pred eEEEEEEeecCcccccccCCchhHHHHH
Q 009566 283 EFSLRLVCPVANIGGVIGKGGAIINQIR 310 (532)
Q Consensus 283 ~~~~~v~vp~~~~g~iIGk~G~~Ik~i~ 310 (532)
++..++-......-.+.+..-+.+-.|+
T Consensus 935 efc~r~~l~~~~~~~t~~a~~ql~d~L~ 962 (1282)
T KOG0921|consen 935 EFCERYSLSNPVLKMTDGARRQLIDVLR 962 (1282)
T ss_pred hHhHhhhhcchhhhhhhhhHHHHHHHHH
Confidence 3333444444444444444444444444
No 93
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=94.30 E-value=0.18 Score=54.55 Aligned_cols=67 Identities=22% Similarity=0.391 Sum_probs=50.1
Q ss_pred CceEEEEEEeC-CceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009566 138 HQVTAKLLVPS-DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHD 214 (532)
Q Consensus 138 ~~~~~~l~vp~-~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 214 (532)
...+..+.+|+ .+-|+|||+.|.||+.++..||+.|-|.. .| ..|+|++ ++---+-|...|..++.+
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd---tp-------~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD---TP-------EAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC---CC-------CeEEecCCchHHHHHHHHHHHHHHHc
Confidence 33445577887 46799999999999999999999998843 23 3578888 555556676666666655
No 94
>PRK00106 hypothetical protein; Provisional
Probab=94.16 E-value=0.23 Score=53.58 Aligned_cols=67 Identities=27% Similarity=0.435 Sum_probs=50.7
Q ss_pred CceEEEEEEeC-CceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009566 138 HQVTAKLLVPS-DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHD 214 (532)
Q Consensus 138 ~~~~~~l~vp~-~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 214 (532)
...+..+.+|+ .+-|+|||+.|.||+.++..||+.+-|.. .| ..|+|++ ++---+-|...+..++.+
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd---tp-------~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD---TP-------EVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC---CC-------CeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 33455677887 46799999999999999999999998843 22 3688888 566666677776666655
No 95
>PRK12704 phosphodiesterase; Provisional
Probab=94.10 E-value=0.21 Score=54.12 Aligned_cols=66 Identities=23% Similarity=0.383 Sum_probs=48.7
Q ss_pred ceEEEEEEeC-CceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009566 139 QVTAKLLVPS-DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHD 214 (532)
Q Consensus 139 ~~~~~l~vp~-~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 214 (532)
..+-.+.+|+ .+-|+|||+.|.||+.++..||+.|-|.. .| ..|.|+| ++-.-+.|...|..++.+
T Consensus 209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd---tp-------~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD---TP-------EAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC---CC-------CeEEEecCChhhHHHHHHHHHHHHhc
Confidence 3445567887 56799999999999999999999998843 23 4688888 455545666666666554
No 96
>PRK12705 hypothetical protein; Provisional
Probab=94.07 E-value=0.07 Score=57.15 Aligned_cols=64 Identities=25% Similarity=0.285 Sum_probs=45.2
Q ss_pred ceEEEEEEecC-cceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHH
Q 009566 369 SFTTRLLVPTS-RIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRL 442 (532)
Q Consensus 369 ~~~~~i~VP~~-~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l 442 (532)
.....+.+|++ +-|.||||-|.+|+-+...||+.|-|. +.| +.|+|.+ +|..-+.|...+..+|
T Consensus 197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid---dtp-------~~V~ls~fdp~rreia~~~l~~Li 262 (508)
T PRK12705 197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID---DTP-------EAVVISSFNPIRREIARLTLEKLL 262 (508)
T ss_pred heeeeeecCChHhhccccCccchhHHHHHHhhCCceEec---CCc-------cchhhcccCccchHHHHHHHHHHH
Confidence 45566778875 459999999999999999999999883 334 3566776 4544444444443333
No 97
>PRK01064 hypothetical protein; Provisional
Probab=93.63 E-value=0.083 Score=41.57 Aligned_cols=34 Identities=32% Similarity=0.442 Sum_probs=29.9
Q ss_pred CcceEEEEEEecCcceeEecCCChhHHHHHHhhC
Q 009566 367 LISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTK 400 (532)
Q Consensus 367 ~~~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tg 400 (532)
...+..++.|..+-.|.||||+|.+|+.||....
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 3468889999999999999999999999998643
No 98
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=92.73 E-value=0.057 Score=42.04 Aligned_cols=34 Identities=15% Similarity=0.214 Sum_probs=29.6
Q ss_pred CCceEEEEEecCCccceEecCCchHHHHHHHHhC
Q 009566 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (532)
Q Consensus 40 ~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tg 73 (532)
.+...+.+.|..+..|.||||+|.+++.||.-.+
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 4566788889999999999999999999997654
No 99
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=92.13 E-value=0.2 Score=52.97 Aligned_cols=69 Identities=19% Similarity=0.204 Sum_probs=58.4
Q ss_pred CCCcceEEEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHH
Q 009566 365 SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLR 443 (532)
Q Consensus 365 ~~~~~~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~ 443 (532)
.....+..++.|+.+....+||.+|-..|.|..+||+.-++ ++.+|.|.- ++.+.++|+++|...+.
T Consensus 592 ~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~t~~i~A~~~~am~~Ak~~I~~i~~ 659 (760)
T KOG1067|consen 592 KEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEGTFSIFAPTQAAMEEAKEFIDGIIK 659 (760)
T ss_pred cccCceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCceEEEEecCHHHHHHHHHHHHHHhc
Confidence 34457888999999999999999999999999999965555 345788887 79999999999988877
Q ss_pred hc
Q 009566 444 AN 445 (532)
Q Consensus 444 ~~ 445 (532)
..
T Consensus 660 ~~ 661 (760)
T KOG1067|consen 660 DD 661 (760)
T ss_pred Cc
Confidence 64
No 100
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=90.78 E-value=0.12 Score=47.32 Aligned_cols=55 Identities=24% Similarity=0.347 Sum_probs=49.3
Q ss_pred cCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHh
Q 009566 378 TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRA 444 (532)
Q Consensus 378 ~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~ 444 (532)
...+|.|+||+|.+---|.+.|.++|.+. +..|.|-|..++++.|...|+.+|-.
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVla------------d~kIHiLG~~~niriAR~avcsLIlG 231 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA------------DSKIHILGAFQNIRIARDAVCSLILG 231 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEec------------CceEEEeecchhhHHHHHhhHhhhcc
Confidence 45789999999999999999999999884 34799999999999999999988764
No 101
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=90.31 E-value=0.79 Score=48.06 Aligned_cols=204 Identities=15% Similarity=0.125 Sum_probs=126.2
Q ss_pred eEecCCchHHHHHHHHhCCeEEE--cCCCCCCCceEEEE-EcCCccccccccCcccCCHHHHHHHHHHHHHHHhhhcCCC
Q 009566 56 SIIGRGGEIVKQLRIDTKSKIRI--GETVPGSEERVVTV-YSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGDE 132 (532)
Q Consensus 56 ~IIGk~G~~Ik~i~~~tga~I~i--~~~~~~~~ervv~I-~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~~~ 132 (532)
+|=||+--.+.+|++...|.+.+ .+. ...++.++ .|..- ++.+-++.+
T Consensus 393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~---~gs~~~~~~~g~~~-----------------~F~k~~~~~--------- 443 (657)
T COG5166 393 FLRGKKNGKATRIMKGVSCSELSSIVSS---TGSIVETNGIGEKM-----------------SFSKKLSIP--------- 443 (657)
T ss_pred HhccccCcchhhhhhhcccceeeEEEec---CCcEEEEeccCcch-----------------hhHHHhcCC---------
Confidence 67788766699999999998554 222 11233333 23211 122222211
Q ss_pred CCCCCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 009566 133 DSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRL 212 (532)
Q Consensus 133 ~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l 212 (532)
..+..-.+.+.+|...|..|||.+|..|+++....++.|.+...-+++. + .
T Consensus 444 --~~EFpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~q---s------------------------~ 494 (657)
T COG5166 444 --PTEFPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQ---S------------------------Q 494 (657)
T ss_pred --cccCchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcch---h------------------------h
Confidence 1123334789999999999999999999999999998887754322221 0 0
Q ss_pred hcCCCCccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEEeec
Q 009566 213 HDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPV 292 (532)
Q Consensus 213 ~~~~~~~~~~~~s~~~~~~~~~g~~~~p~~g~~~~~~~p~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~vp~ 292 (532)
+. ..+-+.+|.
T Consensus 495 ~~---------------------------------------------------------------------dNV~I~~Pr 505 (657)
T COG5166 495 WH---------------------------------------------------------------------DNVLIEAPR 505 (657)
T ss_pred hh---------------------------------------------------------------------cceEEECCc
Confidence 00 023467888
Q ss_pred CcccccccCCchhHHHHHhhhC----CeEEecCCCCCCCCeEEEEecCcchhhhhhHHHHHHHHhcccccccccccCCCc
Q 009566 293 ANIGGVIGKGGAIINQIRQESG----AAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLI 368 (532)
Q Consensus 293 ~~~g~iIGk~G~~Ik~i~~~sg----a~I~i~~~~~~~~e~vi~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~ 368 (532)
+..+.|+|++......+++... ..|.+... ..+++++.+-.. .++.++.- +.-....
T Consensus 506 Kn~~ni~~~KNd~~~~V~~~c~f~~Kgdirf~~~----~~sI~~v~~~~~-------~I~rv~kn--------e~v~~~~ 566 (657)
T COG5166 506 KNQDNISGKKNDKLDKVKQQCRFNLKGDIRFCPQ----STSIFTVDIYSD-------EIERVIKN--------ETVLLEF 566 (657)
T ss_pred cCccchhcccccHHHHHhhhcccccccceEEcCC----ceEEEEEccccc-------HHHHHhhc--------cceEEec
Confidence 8899999999888888876552 34445432 345777776432 22222211 0000112
Q ss_pred ceEEEEEEecCcceeEec---CCChhHHHHHHhhCceEEE
Q 009566 369 SFTTRLLVPTSRIGCLIG---KGGSIITEMRRLTKANIRI 405 (532)
Q Consensus 369 ~~~~~i~VP~~~~G~IIG---kgG~~Ik~I~~~Tga~I~i 405 (532)
...+.+.+|...++.-+| -.|++|..+.....-.|.-
T Consensus 567 p~~~~~y~~se~h~~g~gena~R~~ni~~~t~~y~~~ie~ 606 (657)
T COG5166 567 PAEMHFYVPSEIHKKGIGENAFRGENIQRVTKLYNSYIEF 606 (657)
T ss_pred ccccccccchhhhhccCCcccccccchhhhhhhhhcccee
Confidence 455678899999999999 7788888877776666654
No 102
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=90.17 E-value=0.078 Score=60.04 Aligned_cols=70 Identities=19% Similarity=0.109 Sum_probs=57.6
Q ss_pred EEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhc
Q 009566 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN 445 (532)
Q Consensus 372 ~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~ 445 (532)
-.+.+|.....+|||++|.+|+.++.-|||.|.|..- -|. ...+|.+.+.|.++.++.|...|...|.+-
T Consensus 1342 ~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekm--q~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~Dp 1411 (2131)
T KOG4369|consen 1342 GKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKM--QPD--NQAERSKAPKGRPPSQRVATSPIGLPIIDP 1411 (2131)
T ss_pred cccccchhhhhhhhccCcchhhhHhhccceEEehhhc--CCc--cchhhhcccCCCChhhhhhhccccceeecC
Confidence 3567888889999999999999999999999999541 122 346899999999999999988887666544
No 103
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=90.13 E-value=0.51 Score=35.48 Aligned_cols=35 Identities=14% Similarity=0.214 Sum_probs=28.2
Q ss_pred ceEEEEEecCCccceEecCCchHHHHHHHHhCCeE
Q 009566 42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKI 76 (532)
Q Consensus 42 ~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I 76 (532)
.....+.+.....+.+||++|.+|+.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 45556666666789999999999999999987544
No 104
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=88.49 E-value=0.81 Score=34.32 Aligned_cols=34 Identities=24% Similarity=0.426 Sum_probs=27.8
Q ss_pred eEEEEEEecCcceeEecCCChhHHHHHHhhCceE
Q 009566 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANI 403 (532)
Q Consensus 370 ~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I 403 (532)
....+.+.....|.+||++|++|+.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 4555666666789999999999999999998554
No 105
>PRK12705 hypothetical protein; Provisional
Probab=88.35 E-value=0.37 Score=51.74 Aligned_cols=44 Identities=25% Similarity=0.277 Sum_probs=37.9
Q ss_pred cCCCceEEEEEecC-CccceEecCCchHHHHHHHHhCCeEEEcCC
Q 009566 38 IGPEDTVYRYLCPI-RKIGSIIGRGGEIVKQLRIDTKSKIRIGET 81 (532)
Q Consensus 38 ~~~~~~~~~i~vp~-~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~ 81 (532)
...+.++-.+-+|+ ++-|.|||+.|.+||.|+..||+.|.|++.
T Consensus 193 ~~~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt 237 (508)
T PRK12705 193 TASDLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT 237 (508)
T ss_pred hhhhheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC
Confidence 34566777778888 678999999999999999999999999765
No 106
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=87.80 E-value=0.98 Score=43.67 Aligned_cols=52 Identities=23% Similarity=0.238 Sum_probs=45.3
Q ss_pred eeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhc
Q 009566 382 GCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN 445 (532)
Q Consensus 382 G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~ 445 (532)
-++||.+|++++.|+-.|.|.|-|+. .+|.+.|....++.+...+.+.+.+.
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG------------~TVsaiGpfkGlkevr~IV~DcM~Ni 212 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG------------NTVSAIGPFKGLKEVRKIVEDCMKNI 212 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC------------cEEEeecCcchHHHHHHHHHHHHhcc
Confidence 57899999999999999999999964 38999999999888888887777653
No 107
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=87.66 E-value=0.44 Score=36.59 Aligned_cols=36 Identities=28% Similarity=0.450 Sum_probs=28.9
Q ss_pred EEEEEecCc-----ceeEecCCChhHHHHHHhh-CceEEEec
Q 009566 372 TRLLVPTSR-----IGCLIGKGGSIITEMRRLT-KANIRILP 407 (532)
Q Consensus 372 ~~i~VP~~~-----~G~IIGkgG~~Ik~I~~~T-ga~I~i~~ 407 (532)
..+.|-... +|..||++|.+|+.|.++. |-+|+|-.
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 456677666 8999999999999999999 89998854
No 108
>KOG3875 consensus Peroxisomal biogenesis protein peroxin [Intracellular trafficking, secretion, and vesicular transport]
Probab=87.18 E-value=2.1 Score=42.15 Aligned_cols=23 Identities=43% Similarity=1.024 Sum_probs=10.1
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCC
Q 009566 503 YGSYGSSQLGGTGSAYGSYGSYS 525 (532)
Q Consensus 503 ~g~~g~~~~g~~g~~yg~~g~~~ 525 (532)
||.||++..|+.|++|+.++.|+
T Consensus 78 yg~YGgGygg~fGgGyN~~~~~g 100 (362)
T KOG3875|consen 78 YGPYGGGYGGGFGGGYNRFGPYG 100 (362)
T ss_pred CCCcCCCcCcccCcccccccccc
Confidence 34444333334445555544443
No 109
>PRK13764 ATPase; Provisional
Probab=87.01 E-value=1.2 Score=49.00 Aligned_cols=43 Identities=28% Similarity=0.470 Sum_probs=38.9
Q ss_pred eEEEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCC
Q 009566 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLP 412 (532)
Q Consensus 370 ~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P 412 (532)
-...+.||.+.++.+|||+|.+|++|.++.|..|.|...+..|
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 4567999999999999999999999999999999998877654
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=86.83 E-value=0.69 Score=36.34 Aligned_cols=33 Identities=18% Similarity=0.250 Sum_probs=26.9
Q ss_pred EEEEecCCccceEecCCchHHHHHHHHhCCeEE
Q 009566 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIR 77 (532)
Q Consensus 45 ~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~ 77 (532)
+.+.+..+..|.+|||+|++++.||--++.-++
T Consensus 26 i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 26 VEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred EEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 456667788999999999999999988765443
No 111
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=86.22 E-value=1.7 Score=41.65 Aligned_cols=47 Identities=21% Similarity=0.418 Sum_probs=39.6
Q ss_pred EEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHH
Q 009566 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLD 429 (532)
Q Consensus 372 ~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~ 429 (532)
.-+.|++..|-.+||++|+.++-|.+.|+|+|-|-. +..|-|.+..+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-----------NG~IWV~~~~~ 194 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-----------NGRIWVDGENE 194 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-----------CCEEEecCCCc
Confidence 458899999999999999999999999999999853 34677777544
No 112
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=85.87 E-value=0.46 Score=36.87 Aligned_cols=35 Identities=20% Similarity=0.301 Sum_probs=29.1
Q ss_pred CceEEEEEEeCCceeeeeccCchHHHHHHhhhCce
Q 009566 138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQ 172 (532)
Q Consensus 138 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~ 172 (532)
....+.+.+..+..|.||||.|.+++.|+.-.++-
T Consensus 27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~ 61 (73)
T PF13083_consen 27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAA 61 (73)
T ss_dssp TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHH
T ss_pred CceEEEEEECCCccceEECCCCeeHHHHHHHHHHH
Confidence 44567788899999999999999999998765543
No 113
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=85.72 E-value=1.4 Score=42.67 Aligned_cols=51 Identities=16% Similarity=0.185 Sum_probs=45.6
Q ss_pred eeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 009566 152 GCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD 214 (532)
Q Consensus 152 g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~ 214 (532)
.+|||.+|+|++.|+-.|.|-|-|.. .+|.+.|....+..+...+.+.+..
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 57999999999999999999998853 4699999999999999999988876
No 114
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=85.27 E-value=1.8 Score=45.32 Aligned_cols=39 Identities=36% Similarity=0.515 Sum_probs=35.7
Q ss_pred EEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCC
Q 009566 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179 (532)
Q Consensus 141 ~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~ 179 (532)
...+.||..+++.+|||+|.+|++|+...|-+|.|.+.+
T Consensus 487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e 525 (604)
T COG1855 487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE 525 (604)
T ss_pred eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence 467889999999999999999999999999999997753
No 115
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=84.75 E-value=0.38 Score=54.84 Aligned_cols=58 Identities=19% Similarity=0.208 Sum_probs=49.5
Q ss_pred ceEEEEEecCCccceEecCCchHHHHHHHHhCCeEEEcCC-CCCCCceEEEEEcCCccc
Q 009566 42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGET-VPGSEERVVTVYSASDET 99 (532)
Q Consensus 42 ~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~-~~~~~ervv~I~G~~~~~ 99 (532)
....++-+|......|||++|.+|+.++.-||+.|.|.+- ..+..||.+++.|.++.+
T Consensus 1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~ 1397 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQ 1397 (2131)
T ss_pred ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhh
Confidence 3445678999999999999999999999999999999873 334679999999998864
No 116
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=84.74 E-value=0.58 Score=35.97 Aligned_cols=34 Identities=21% Similarity=0.378 Sum_probs=26.9
Q ss_pred EEEEecCCc-----cceEecCCchHHHHHHHHh-CCeEEE
Q 009566 45 YRYLCPIRK-----IGSIIGRGGEIVKQLRIDT-KSKIRI 78 (532)
Q Consensus 45 ~~i~vp~~~-----~g~IIGk~G~~Ik~i~~~t-ga~I~i 78 (532)
..+.|-+.. +|..||++|..|+.|.++. |-+|.|
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 355666666 9999999999999999999 888775
No 117
>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=83.88 E-value=1 Score=35.74 Aligned_cols=37 Identities=11% Similarity=0.263 Sum_probs=30.9
Q ss_pred EEEEecCCccceEecCCchHHHHHHHHhCCeEEEcCC
Q 009566 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGET 81 (532)
Q Consensus 45 ~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~ 81 (532)
.++.|-...-|.|||++|+.|++|+++-.-...+.++
T Consensus 32 i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~~ 68 (81)
T cd02413 32 TEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPEG 68 (81)
T ss_pred EEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCCC
Confidence 6788889999999999999999999987666655433
No 118
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=83.43 E-value=0.77 Score=47.87 Aligned_cols=40 Identities=33% Similarity=0.475 Sum_probs=36.3
Q ss_pred EEEEEEecCcceeEecCCChhHHHHHHhhCceEEEecCCC
Q 009566 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKEN 410 (532)
Q Consensus 371 ~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~ 410 (532)
...+.||..+++.||||+|.+|++|.+..|-+|.|...+.
T Consensus 487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 4668999999999999999999999999999999977653
No 119
>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=83.06 E-value=3.8 Score=36.14 Aligned_cols=91 Identities=25% Similarity=0.410 Sum_probs=55.9
Q ss_pred CCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHHHh-hhcCCCCCCCCC
Q 009566 60 RGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAE-ELRGDEDSDGGH 138 (532)
Q Consensus 60 k~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~-~~~~~~~~~~~~ 138 (532)
.++..|++|-++-.-+|.|-... .+.-+ -.+|...|.+.+-++ .+.+-.. .
T Consensus 23 ~~~dli~~lAk~lrKRIvvR~dp--------s~l~~----------------~e~A~~~I~~ivP~ea~i~di~F----d 74 (145)
T cd02410 23 EDGDLVKDLAKDLRKRIVIRPDP--------SVLKP----------------PEEAIKIILEIVPEEAGITDIYF----D 74 (145)
T ss_pred cccHHHHHHHHHHhceEEEcCCh--------hhcCC----------------HHHHHHHHHHhCCCccCceeeEe----c
Confidence 56789999999988887763220 01111 234444444433211 1110000 1
Q ss_pred ceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecC
Q 009566 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (532)
Q Consensus 139 ~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~ 178 (532)
..+-++.|-...-|.+||++|.++++|..+||-.-.+...
T Consensus 75 ~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 75 DDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred CCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 1134566666788999999999999999999998888765
No 120
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=82.64 E-value=0.64 Score=36.52 Aligned_cols=33 Identities=18% Similarity=0.381 Sum_probs=28.3
Q ss_pred EEEEEecCCccceEecCCchHHHHHHHHhCCeE
Q 009566 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKI 76 (532)
Q Consensus 44 ~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I 76 (532)
...+.+.....+.|||++|++|++|+++..-.+
T Consensus 26 ~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 26 QIIIVIKASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp EEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred eEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 356788999999999999999999998876555
No 121
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=81.89 E-value=4.3 Score=38.91 Aligned_cols=47 Identities=21% Similarity=0.362 Sum_probs=39.8
Q ss_pred EEEecCCccceEecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCcc
Q 009566 46 RYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDE 98 (532)
Q Consensus 46 ~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~ 98 (532)
-+.||...+..+||++|+.++.|.++|+|+|.|... -.|-|.+..+.
T Consensus 149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N------G~IWV~~~~~~ 195 (239)
T COG1097 149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN------GRIWVDGENES 195 (239)
T ss_pred EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC------CEEEecCCCcc
Confidence 367999999999999999999999999999999543 25788887663
No 122
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=81.35 E-value=0.68 Score=36.38 Aligned_cols=35 Identities=26% Similarity=0.406 Sum_probs=29.3
Q ss_pred eEEEEEEecCcceeEecCCChhHHHHHHhhCceEE
Q 009566 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIR 404 (532)
Q Consensus 370 ~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~ 404 (532)
....+.+...+-|.|||++|++|++|++..+-.+.
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 34678899999999999999999999987765553
No 123
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=80.24 E-value=2.1 Score=33.56 Aligned_cols=34 Identities=26% Similarity=0.459 Sum_probs=27.7
Q ss_pred EEEEEEecCcceeEecCCChhHHHHHHhhCceEE
Q 009566 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIR 404 (532)
Q Consensus 371 ~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~ 404 (532)
...+.|..+..|.+|||.|++++.||--+..-+.
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 3457777888999999999999999988765444
No 124
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=80.00 E-value=3.7 Score=43.38 Aligned_cols=96 Identities=25% Similarity=0.368 Sum_probs=61.6
Q ss_pred eEecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHHHhhhcCCCCCC
Q 009566 56 SIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDSD 135 (532)
Q Consensus 56 ~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~ 135 (532)
.+|=+.|..|++|-++-.-+|.|-... .+.-+ ..+|...|++.+-++.--.+ -
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~dP--------svl~~----------------~e~A~~~I~eivP~ea~i~~---i 94 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPDP--------SVLKP----------------PEEARKIILEIVPEEAGITD---I 94 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccCc--------hhcCC----------------HHHHHHHHHHhCccccCcee---E
Confidence 345578999999999998888774321 11112 34555555554322110000 0
Q ss_pred CCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecC
Q 009566 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (532)
Q Consensus 136 ~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~ 178 (532)
.=...+-+++|-.+.-|.+|||+|++.+.|..+||-.-.|...
T Consensus 95 ~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 95 YFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred EecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 0012235677888889999999999999999999988777664
No 125
>PRK13764 ATPase; Provisional
Probab=78.14 E-value=5.2 Score=44.15 Aligned_cols=43 Identities=30% Similarity=0.465 Sum_probs=37.9
Q ss_pred ceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCC
Q 009566 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHL 181 (532)
Q Consensus 139 ~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~ 181 (532)
.-...+.||...++.+|||+|.+|++|++..|..|.|.+.++.
T Consensus 480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~ 522 (602)
T PRK13764 480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEE 522 (602)
T ss_pred CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcccc
Confidence 3457789999999999999999999999999999999876543
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=77.63 E-value=3.1 Score=33.09 Aligned_cols=35 Identities=20% Similarity=0.446 Sum_probs=28.8
Q ss_pred EEEEEEecCcceeEecCCChhHHHHHHhhCceEEE
Q 009566 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405 (532)
Q Consensus 371 ~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i 405 (532)
..++.|-...-|.|||++|+.|++|++.-.....+
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 46788888899999999999999999876554443
No 127
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=77.30 E-value=3.2 Score=37.74 Aligned_cols=33 Identities=30% Similarity=0.386 Sum_probs=27.8
Q ss_pred EEEecCCccceEecCCchHHHHHHHHhCCeEEEc
Q 009566 46 RYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIG 79 (532)
Q Consensus 46 ~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~ 79 (532)
-++|-... |.-|||+|++|++|++..|-+|.|-
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 35565566 9999999999999999999998863
No 128
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=76.84 E-value=1.5 Score=40.31 Aligned_cols=56 Identities=27% Similarity=0.356 Sum_probs=49.3
Q ss_pred CCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 009566 148 SDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN 215 (532)
Q Consensus 148 ~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 215 (532)
+..+|+|+||+|.+--.|+..|.++|.+. +..|.|-|..+++.-|...|..+|...
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVla------------d~kIHiLG~~~niriAR~avcsLIlGs 232 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA------------DSKIHILGAFQNIRIARDAVCSLILGS 232 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEec------------CceEEEeecchhhHHHHHhhHhhhccC
Confidence 35679999999999999999999999774 446999999999999999999999664
No 129
>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=75.05 E-value=4.4 Score=35.74 Aligned_cols=37 Identities=22% Similarity=0.362 Sum_probs=31.1
Q ss_pred EEEEecCCccceEecCCchHHHHHHHHhCCeEEEcCC
Q 009566 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGET 81 (532)
Q Consensus 45 ~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~ 81 (532)
=.+.|-.+.-|.|||++|.++++|..+||-+-.|-..
T Consensus 78 GEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 78 GEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred cEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 3567778899999999999999999999987666433
No 130
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=73.91 E-value=15 Score=39.11 Aligned_cols=97 Identities=20% Similarity=0.282 Sum_probs=68.5
Q ss_pred eeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCccccccccccCCC
Q 009566 152 GCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSH 231 (532)
Q Consensus 152 g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~s~~~~~~ 231 (532)
..++-+.|.-|++|..+..-+|.|-++... ...-+.|++.|.+++-++..-....+
T Consensus 41 P~~~~~~~dlik~lAk~lrKRI~iR~dPsv----------------l~~~e~A~~~I~eivP~ea~i~~i~F-------- 96 (637)
T COG1782 41 PELFAKDGDLIKDLAKDLRKRIIIRPDPSV----------------LKPPEEARKIILEIVPEEAGITDIYF-------- 96 (637)
T ss_pred HHHhccchhHHHHHHHHHhhceEeccCchh----------------cCCHHHHHHHHHHhCccccCceeEEe--------
Confidence 456778999999999999999988765221 11225688888888855321110000
Q ss_pred CCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEEEEeecCcccccccCCchhHHHHHh
Q 009566 232 SSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQ 311 (532)
Q Consensus 232 ~~~g~~~~p~~g~~~~~~~p~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~ 311 (532)
...+=+|.|-.+.-|.+|||+|++.++|.+
T Consensus 97 --------------------------------------------------d~~tGEViIea~KPGlvigk~g~~~reI~~ 126 (637)
T COG1782 97 --------------------------------------------------DDDTGEVIIEAKKPGLVIGKGGSTLREITA 126 (637)
T ss_pred --------------------------------------------------cCCCceEEEEecCCceEEecCchHHHHHHH
Confidence 112346888899999999999999999999
Q ss_pred hhCCeEEecCC
Q 009566 312 ESGAAIKVDSS 322 (532)
Q Consensus 312 ~sga~I~i~~~ 322 (532)
++|-.-+|-+.
T Consensus 127 ~tgW~p~ivR~ 137 (637)
T COG1782 127 ETGWAPKIVRT 137 (637)
T ss_pred HhCCcceeeec
Confidence 99977666553
No 131
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=72.92 E-value=3.3 Score=34.89 Aligned_cols=30 Identities=23% Similarity=0.358 Sum_probs=26.0
Q ss_pred EEEEecCCccceEecCCchHHHHHHHHhCC
Q 009566 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKS 74 (532)
Q Consensus 45 ~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga 74 (532)
+++.|-...-|.|||++|++|++|++....
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence 567888888999999999999999987644
No 132
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=71.45 E-value=5.8 Score=36.07 Aligned_cols=35 Identities=31% Similarity=0.491 Sum_probs=30.3
Q ss_pred EEEEEecCcceeEecCCChhHHHHHHhhCceEEEec
Q 009566 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP 407 (532)
Q Consensus 372 ~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~ 407 (532)
.-+.|.... |.-|||+|.+|+.+++..|-+|.|-.
T Consensus 63 vIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 63 VILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 456676666 99999999999999999999998864
No 133
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=69.39 E-value=5.4 Score=31.92 Aligned_cols=28 Identities=25% Similarity=0.380 Sum_probs=23.5
Q ss_pred EEEEecCCccceEecCCchHHHHHHHHh
Q 009566 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDT 72 (532)
Q Consensus 45 ~~i~vp~~~~g~IIGk~G~~Ik~i~~~t 72 (532)
.++.+-...-|.+||++|.+|++|++.-
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 4556666889999999999999999775
No 134
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=65.80 E-value=5.5 Score=38.01 Aligned_cols=30 Identities=23% Similarity=0.361 Sum_probs=26.1
Q ss_pred EEEEEecCCccceEecCCchHHHHHHHHhC
Q 009566 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (532)
Q Consensus 44 ~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tg 73 (532)
..++.|....-|.|||++|+.|++|+++..
T Consensus 52 ~~~V~I~aarPg~VIGk~G~~I~~L~~~l~ 81 (233)
T COG0092 52 GTRVTIHAARPGLVIGKKGSNIEKLRKELE 81 (233)
T ss_pred ceEEEEEeCCCcceEcCCCccHHHHHHHHH
Confidence 467888899999999999999999987654
No 135
>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=64.80 E-value=9 Score=42.76 Aligned_cols=94 Identities=24% Similarity=0.435 Sum_probs=58.4
Q ss_pred EecCCchHHHHHHHHhCCeEEEcCCCCCCCceEEEEEcCCccccccccCcccCCHHHHHHHHHHHHHHHh-hhcCCCCCC
Q 009566 57 IIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAE-ELRGDEDSD 135 (532)
Q Consensus 57 IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~-~~~~~~~~~ 135 (532)
.+=.++..|++|-++-.-+|.|-... .+.-+ -.+|.+.|.+.+-++ .+.+ ..
T Consensus 37 ~~~~~~~~~~~~~~~~~~r~~~~~~~--------~~~~~----------------~~~~~~~i~~~~~~~~~~~~---~~ 89 (630)
T TIGR03675 37 LFAKDDDLVKELAKKLRKRIVIRPDP--------SVLLP----------------PEEAIEKIKEIVPEEAGITD---IY 89 (630)
T ss_pred HhccchHHHHHHHHHhhceEEEecCh--------hhcCC----------------HHHHHHHHHHhCCCcCCcee---EE
Confidence 34467899999999988877763220 11111 234444444332111 1100 00
Q ss_pred CCCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecC
Q 009566 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (532)
Q Consensus 136 ~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~ 178 (532)
=...+-+++|-...-|.||||.|.++++|..+||-.-.|...
T Consensus 90 -f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 90 -FDDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred -ecCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 011235567777888999999999999999999999888765
No 136
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=64.15 E-value=8.3 Score=30.84 Aligned_cols=28 Identities=32% Similarity=0.615 Sum_probs=22.9
Q ss_pred EEEEEecCcceeEecCCChhHHHHHHhh
Q 009566 372 TRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (532)
Q Consensus 372 ~~i~VP~~~~G~IIGkgG~~Ik~I~~~T 399 (532)
..+.|....-|.+||++|+.|++|++.-
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 4566666788999999999999998764
No 137
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=63.87 E-value=12 Score=39.60 Aligned_cols=130 Identities=13% Similarity=0.101 Sum_probs=78.4
Q ss_pred cccccCCchhHHHHHhhhCCeEEecCCCCCCCCeEEEE-ecCcchhhhhhHHHHHHHHhcccccccccccCCCcceEEEE
Q 009566 296 GGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITV-SSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRL 374 (532)
Q Consensus 296 g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~e~vi~i-~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i 374 (532)
-++-||+.-.+.+|++..-|.+.+.=.... ..++.+. .|.. ......+...+. +-.-...+
T Consensus 392 dFl~gkkngK~TrIm~~v~c~~~~~i~~~~-gs~~~~~~~g~~-------~~F~k~~~~~~~----------EFpae~~f 453 (657)
T COG5166 392 DFLRGKKNGKATRIMKGVSCSELSSIVSST-GSIVETNGIGEK-------MSFSKKLSIPPT----------EFPAEIAF 453 (657)
T ss_pred HHhccccCcchhhhhhhcccceeeEEEecC-CcEEEEeccCcc-------hhhHHHhcCCcc----------cCchheEE
Confidence 478888888899999988887443321111 1133222 2221 111222222111 11345679
Q ss_pred EEecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC---HHHHHHHHHHHHHHHHhc
Q 009566 375 LVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD---LDLAKDALIQVMTRLRAN 445 (532)
Q Consensus 375 ~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~---~~~v~~A~~~I~~~l~~~ 445 (532)
.||...|..|||-||..|+++...-++.|+....-.+|+...- .-|.|.-+ .+.+.-++.-+.+++.+.
T Consensus 454 ~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~--dNV~I~~PrKn~~ni~~~KNd~~~~V~~~ 525 (657)
T COG5166 454 IIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWH--DNVLIEAPRKNQDNISGKKNDKLDKVKQQ 525 (657)
T ss_pred EeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhh--cceEEECCccCccchhcccccHHHHHhhh
Confidence 9999999999999999999999999999988765566652211 12666553 344555555555665543
No 138
>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=63.41 E-value=6.9 Score=32.98 Aligned_cols=29 Identities=31% Similarity=0.524 Sum_probs=24.6
Q ss_pred EEEEEecCcceeEecCCChhHHHHHHhhC
Q 009566 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTK 400 (532)
Q Consensus 372 ~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tg 400 (532)
.++.|-...-|.|||++|+.|++|++...
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 56777788889999999999999987654
No 139
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=61.07 E-value=8.3 Score=36.84 Aligned_cols=29 Identities=38% Similarity=0.543 Sum_probs=25.1
Q ss_pred eEEEEEEecCcceeEecCCChhHHHHHHh
Q 009566 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRL 398 (532)
Q Consensus 370 ~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~ 398 (532)
..+.+.|....-|.|||++|+.|++|++.
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 45678888999999999999999998754
No 140
>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=54.57 E-value=15 Score=36.15 Aligned_cols=31 Identities=23% Similarity=0.318 Sum_probs=25.6
Q ss_pred ceEEEEEEecCcc-eeEecCCChhHHHHHHhh
Q 009566 369 SFTTRLLVPTSRI-GCLIGKGGSIITEMRRLT 399 (532)
Q Consensus 369 ~~~~~i~VP~~~~-G~IIGkgG~~Ik~I~~~T 399 (532)
.+...+.|..+.+ +-|||++|+.||+|...+
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 4778888886655 999999999999987654
No 141
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=50.50 E-value=46 Score=33.61 Aligned_cols=18 Identities=28% Similarity=0.351 Sum_probs=8.3
Q ss_pred HHHhhCceEEEecCCCCC
Q 009566 395 MRRLTKANIRILPKENLP 412 (532)
Q Consensus 395 I~~~Tga~I~i~~~~~~P 412 (532)
+|+.|-|+|+-..-...|
T Consensus 286 ~Re~Taski~k~~igrvP 303 (465)
T KOG3973|consen 286 RRERTASKIHKLSIGRVP 303 (465)
T ss_pred hhhhhhhhhcccccccCC
Confidence 455555555443333334
No 142
>COG1159 Era GTPase [General function prediction only]
Probab=49.35 E-value=23 Score=35.28 Aligned_cols=35 Identities=26% Similarity=0.544 Sum_probs=27.1
Q ss_pred CCCcceEEEEEEecCcc-eeEecCCChhHHHHHHhh
Q 009566 365 SGLISFTTRLLVPTSRI-GCLIGKGGSIITEMRRLT 399 (532)
Q Consensus 365 ~~~~~~~~~i~VP~~~~-G~IIGkgG~~Ik~I~~~T 399 (532)
.....+...+.|+.+-. +-||||+|++||+|-..+
T Consensus 224 ~~~~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~A 259 (298)
T COG1159 224 KGLLKIHATIYVERESQKGIIIGKNGAMIKKIGTAA 259 (298)
T ss_pred CCeEEEEEEEEEecCCccceEECCCcHHHHHHHHHH
Confidence 34446777888887655 999999999999986554
No 143
>PRK15494 era GTPase Era; Provisional
Probab=48.87 E-value=21 Score=36.62 Aligned_cols=31 Identities=23% Similarity=0.382 Sum_probs=25.2
Q ss_pred ceEEEEEEecCcc-eeEecCCChhHHHHHHhh
Q 009566 369 SFTTRLLVPTSRI-GCLIGKGGSIITEMRRLT 399 (532)
Q Consensus 369 ~~~~~i~VP~~~~-G~IIGkgG~~Ik~I~~~T 399 (532)
.+...+.|..+-+ +-|||++|+.||+|..+.
T Consensus 272 ~i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~a 303 (339)
T PRK15494 272 KINQVIVVSRESYKTIILGKNGSKIKEIGAKS 303 (339)
T ss_pred EEEEEEEECCCCceeEEEcCCcHHHHHHHHHH
Confidence 4678888887655 999999999999886543
No 144
>PRK00089 era GTPase Era; Reviewed
Probab=45.89 E-value=25 Score=35.01 Aligned_cols=38 Identities=18% Similarity=0.442 Sum_probs=28.6
Q ss_pred cceEEEEEEecCcc-eeEecCCChhHHHHHHh--------hCceEEE
Q 009566 368 ISFTTRLLVPTSRI-GCLIGKGGSIITEMRRL--------TKANIRI 405 (532)
Q Consensus 368 ~~~~~~i~VP~~~~-G~IIGkgG~~Ik~I~~~--------Tga~I~i 405 (532)
-.+...+.|..+-+ +-|||++|++||+|... .+++|.+
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 34677888886555 99999999999988754 4666554
No 145
>COG0490 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]
Probab=45.85 E-value=16 Score=32.98 Aligned_cols=61 Identities=23% Similarity=0.268 Sum_probs=38.8
Q ss_pred EEEecCcceeEecCCChhHHHHHHhhCceE-EEecCCCC-----CCCCCCCCceEEEEcCHHHHHHHHHHHH
Q 009566 374 LLVPTSRIGCLIGKGGSIITEMRRLTKANI-RILPKENL-----PKIASEDDEMVQISGDLDLAKDALIQVM 439 (532)
Q Consensus 374 i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I-~i~~~~~~-----P~~~~~~~r~V~I~G~~~~v~~A~~~I~ 439 (532)
+..-..++|+=||- -+|+++|||.| -|.+.+++ |...-..-.++.++|+...+.+++.+..
T Consensus 92 i~~~s~~~GksiGd-----l~irq~TGaTIIAI~r~~e~I~SPgPy~vle~gDtlvviG~~~~~~r~~~f~~ 158 (162)
T COG0490 92 IEAGSPFIGKTIGD-----LNIRQNTGATVIAIVRNEEKILSPGPYTVLEAGDTLVVIGEETGLKRAKRFLL 158 (162)
T ss_pred eecCCcccCcchhh-----cccccccCcEEEEEEecCcEecCCCchhhhcCCCEEEEEecchHhHHHHHHhh
Confidence 33445556666664 56799999984 44444432 2211233468999999999998877653
No 146
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=45.82 E-value=50 Score=36.95 Aligned_cols=38 Identities=26% Similarity=0.466 Sum_probs=33.7
Q ss_pred eEEEEEEecCcceeEecCCChhHHHHHHhhCceEEEec
Q 009566 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP 407 (532)
Q Consensus 370 ~~~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~ 407 (532)
.+-++.|-.+.-|.||||+|.++++|.++||-+-+|.+
T Consensus 93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~ 130 (630)
T TIGR03675 93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVR 130 (630)
T ss_pred CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEe
Confidence 45678888999999999999999999999998887765
No 147
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=43.81 E-value=1.3e+02 Score=30.55 Aligned_cols=11 Identities=27% Similarity=0.066 Sum_probs=5.2
Q ss_pred HHHHHHHHHHH
Q 009566 202 KKALCQIASRL 212 (532)
Q Consensus 202 ~~A~~~I~~~l 212 (532)
.+|+.++++.|
T Consensus 102 ~~a~~lLlsyL 112 (465)
T KOG3973|consen 102 SSAKKLLLSYL 112 (465)
T ss_pred HHHHHHHHHHH
Confidence 44555444444
No 148
>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=41.87 E-value=32 Score=33.84 Aligned_cols=30 Identities=20% Similarity=0.262 Sum_probs=23.4
Q ss_pred eEEEEEecCC-ccceEecCCchHHHHHHHHh
Q 009566 43 TVYRYLCPIR-KIGSIIGRGGEIVKQLRIDT 72 (532)
Q Consensus 43 ~~~~i~vp~~-~~g~IIGk~G~~Ik~i~~~t 72 (532)
+...|+|..+ +-+.||||+|+.||+|..+.
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 5667788764 56889999999999887543
No 149
>COG4907 Predicted membrane protein [Function unknown]
Probab=40.77 E-value=23 Score=37.11 Aligned_cols=14 Identities=21% Similarity=0.131 Sum_probs=8.6
Q ss_pred EcCHHHHHHHHHHH
Q 009566 425 SGDLDLAKDALIQV 438 (532)
Q Consensus 425 ~G~~~~v~~A~~~I 438 (532)
-|-.+.|.+|.+.+
T Consensus 522 LGV~dkVvkam~~~ 535 (595)
T COG4907 522 LGVSDKVVKAMRKA 535 (595)
T ss_pred hccHHHHHHHHHHh
Confidence 35567777776544
No 150
>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=40.72 E-value=60 Score=24.20 Aligned_cols=22 Identities=14% Similarity=0.102 Sum_probs=18.5
Q ss_pred CceEEEEcCHHHHHHHHHHHHH
Q 009566 419 DEMVQISGDLDLAKDALIQVMT 440 (532)
Q Consensus 419 ~r~V~I~G~~~~v~~A~~~I~~ 440 (532)
--.+.|+|+.++|+.|+..|.+
T Consensus 38 ~~~l~i~Gdvs~Ve~Al~~i~~ 59 (61)
T cd07055 38 MITLAIFGETSAVELAMREIEE 59 (61)
T ss_pred eEEEEEEecHHHHHHHHHHHhh
Confidence 3467799999999999988865
No 151
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=39.49 E-value=32 Score=32.20 Aligned_cols=30 Identities=23% Similarity=0.454 Sum_probs=25.8
Q ss_pred EEEEecCCccceEecCCchHHHHHHHHhCC
Q 009566 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKS 74 (532)
Q Consensus 45 ~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga 74 (532)
.++.|....-|.|||++|..|++|+++-.-
T Consensus 40 ~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k 69 (195)
T TIGR01008 40 TKVIIFAERPGLVIGRGGRRIRELTEKLQK 69 (195)
T ss_pred EEEEEEECCCceEECCCchHHHHHHHHHHH
Confidence 677888888999999999999999987643
No 152
>CHL00048 rps3 ribosomal protein S3
Probab=39.21 E-value=32 Score=32.77 Aligned_cols=30 Identities=17% Similarity=0.217 Sum_probs=25.4
Q ss_pred EEEEEecCCccceEecCCchHHHHHHHHhC
Q 009566 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (532)
Q Consensus 44 ~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tg 73 (532)
..++.|-...-+.|||++|++|++|++.-.
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 356777788889999999999999998764
No 153
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=38.25 E-value=33 Score=32.46 Aligned_cols=31 Identities=29% Similarity=0.426 Sum_probs=25.0
Q ss_pred EEEEecCCccceEecCCchHHHHHHHHhCCe
Q 009566 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSK 75 (532)
Q Consensus 45 ~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~ 75 (532)
.++.|-...-|.+||++|++|++|++.-.-.
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk~ 72 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEKK 72 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHHH
Confidence 4555666889999999999999999886543
No 154
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=38.04 E-value=23 Score=33.33 Aligned_cols=36 Identities=14% Similarity=0.160 Sum_probs=29.2
Q ss_pred ceEEEEEecCCccceEecCCchHHHHHHHHhCCeEE
Q 009566 42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIR 77 (532)
Q Consensus 42 ~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~ 77 (532)
.-.+.+-+-.+..+.+||+.|+++..||--+++-++
T Consensus 90 ~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~ 125 (208)
T COG1847 90 GRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLN 125 (208)
T ss_pred CcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhh
Confidence 344566677777999999999999999988876554
No 155
>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=36.26 E-value=1.1e+02 Score=27.74 Aligned_cols=57 Identities=23% Similarity=0.234 Sum_probs=43.0
Q ss_pred CCceEEEEEEeCCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHH
Q 009566 137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASR 211 (532)
Q Consensus 137 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~ 211 (532)
...-++|+-++...+- +.+++|.+-.|+-+.+ . .+..|.|.|..+.|.+|++.+..+
T Consensus 110 ~~~~~iRv~l~~~i~~-------erl~ei~E~~gvI~Ef-e----------e~~~V~I~Gdke~Ik~aLKe~s~~ 166 (169)
T PF09869_consen 110 PGFETIRVKLKKPIQE-------ERLQEISEWHGVIFEF-E----------EDDKVVIEGDKERIKKALKEFSSF 166 (169)
T ss_pred CCceeEEEecCccchH-------HHHHHHHHHhceeEEe-c----------CCcEEEEeccHHHHHHHHHHHHHH
Confidence 3444566666655442 5678999999999988 2 145699999999999999988765
No 156
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=35.98 E-value=37 Score=32.46 Aligned_cols=31 Identities=10% Similarity=0.250 Sum_probs=26.0
Q ss_pred EEEEecCCccceEecCCchHHHHHHHHhCCe
Q 009566 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSK 75 (532)
Q Consensus 45 ~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~ 75 (532)
.++.|-...-|.|||++|..|++|+++-.-.
T Consensus 46 i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~ 76 (220)
T PTZ00084 46 TEIIIRATRTREVLGDKGRRIRELTSLLQKR 76 (220)
T ss_pred EEEEEEECCCccEEcCCchHHHHHHHHHHHH
Confidence 5677778888999999999999999876544
No 157
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=35.58 E-value=33 Score=32.23 Aligned_cols=35 Identities=14% Similarity=0.296 Sum_probs=29.0
Q ss_pred EEEEEEeCCceeeeeccCchHHHHHHhhhCceEEE
Q 009566 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRI 175 (532)
Q Consensus 141 ~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i 175 (532)
.+.+.+..+..+.|||+.|.++..||--+++-++-
T Consensus 92 ~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 92 RVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred EEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 45667777789999999999999999988866643
No 158
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=35.46 E-value=87 Score=31.95 Aligned_cols=56 Identities=18% Similarity=0.157 Sum_probs=45.0
Q ss_pred ecCcceeEecCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHH--HHHHh
Q 009566 377 PTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVM--TRLRA 444 (532)
Q Consensus 377 P~~~~G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~--~~l~~ 444 (532)
+.+..-.|.|..+.+++.|.+..|+.|... -+.++|+|+...|..|...+. +++..
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~r------------G~~~~i~g~~~~v~~A~~~l~~l~~~~~ 79 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVAR------------GEAVRIIGARPLVDVATRVLLTLELLAE 79 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeC------------CceEEEEechHHHHHHHHHHhHHHHHHH
Confidence 356678899999999999999999998752 247999999778888877776 44443
No 159
>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=34.71 E-value=44 Score=31.31 Aligned_cols=29 Identities=31% Similarity=0.560 Sum_probs=24.7
Q ss_pred EEEEEEecCcceeEecCCChhHHHHHHhh
Q 009566 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (532)
Q Consensus 371 ~~~i~VP~~~~G~IIGkgG~~Ik~I~~~T 399 (532)
..++.|....-|.|||++|..|++|++.-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 46788888888999999999999998664
No 160
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=33.93 E-value=45 Score=33.52 Aligned_cols=35 Identities=26% Similarity=0.529 Sum_probs=27.4
Q ss_pred CCcceEEEEEEecC-cceeEecCCChhHHHHHHhhC
Q 009566 366 GLISFTTRLLVPTS-RIGCLIGKGGSIITEMRRLTK 400 (532)
Q Consensus 366 ~~~~~~~~i~VP~~-~~G~IIGkgG~~Ik~I~~~Tg 400 (532)
+.-.+..++.+|.. +.-.||||+|..|++|-++.+
T Consensus 324 g~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 324 GVLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred cEEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 34567888999965 457789999999999976543
No 161
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=33.64 E-value=42 Score=33.71 Aligned_cols=34 Identities=21% Similarity=0.383 Sum_probs=27.4
Q ss_pred CCceEEEEEecCC-ccceEecCCchHHHHHHHHhC
Q 009566 40 PEDTVYRYLCPIR-KIGSIIGRGGEIVKQLRIDTK 73 (532)
Q Consensus 40 ~~~~~~~i~vp~~-~~g~IIGk~G~~Ik~i~~~tg 73 (532)
...+...+.||.. ....||||+|..|++|-++-+
T Consensus 325 ~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 325 VLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 3467788999985 567899999999999987654
No 162
>CHL00048 rps3 ribosomal protein S3
Probab=32.14 E-value=50 Score=31.47 Aligned_cols=29 Identities=21% Similarity=0.169 Sum_probs=24.6
Q ss_pred EEEEEEecCcceeEecCCChhHHHHHHhh
Q 009566 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (532)
Q Consensus 371 ~~~i~VP~~~~G~IIGkgG~~Ik~I~~~T 399 (532)
..++.|-...-|.|||++|..|++|++.-
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 46677778888999999999999998765
No 163
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=32.06 E-value=50 Score=31.29 Aligned_cols=29 Identities=34% Similarity=0.644 Sum_probs=23.6
Q ss_pred EEEEEecCcceeEecCCChhHHHHHHhhC
Q 009566 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTK 400 (532)
Q Consensus 372 ~~i~VP~~~~G~IIGkgG~~Ik~I~~~Tg 400 (532)
..+.|....-|.+||++|++|+++++.-.
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 45566668889999999999999987654
No 164
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=31.74 E-value=49 Score=31.64 Aligned_cols=29 Identities=24% Similarity=0.458 Sum_probs=24.3
Q ss_pred EEEEEEecCcceeEecCCChhHHHHHHhh
Q 009566 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (532)
Q Consensus 371 ~~~i~VP~~~~G~IIGkgG~~Ik~I~~~T 399 (532)
..++.|-...-|.|||++|..|++|++.-
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 36677778888999999999999998664
No 165
>PRK03818 putative transporter; Validated
Probab=31.66 E-value=6.1e+02 Score=27.95 Aligned_cols=133 Identities=14% Similarity=0.234 Sum_probs=68.9
Q ss_pred EEEEecCCccceEecCCchHHHHHHHHhCCeEEEcCC---------CCC---CCceEEEEEcCCccccccccCcccCCHH
Q 009566 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGET---------VPG---SEERVVTVYSASDETNAFEDGDKFVSPA 112 (532)
Q Consensus 45 ~~i~vp~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~---------~~~---~~ervv~I~G~~~~~~~~~~~~~~v~~a 112 (532)
.++.|+++. ++ |++++++.......+.|..- .++ ....++.|.|..++
T Consensus 207 r~~~V~~s~---li---GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~-------------- 266 (552)
T PRK03818 207 INIRVENPN---LH---GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPED-------------- 266 (552)
T ss_pred EEEEEeCCC---CC---CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHH--------------
Confidence 556666443 34 57999999988766665311 111 12457788887554
Q ss_pred HHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEEeCCceeeeeccCchHHHHH--HhhhCceEEEecCC--CCCc---cc
Q 009566 113 QDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNI--RSETGAQIRILKDE--HLPS---CA 185 (532)
Q Consensus 113 ~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I--~~~tga~I~i~~~~--~~p~---~~ 185 (532)
+.++.+.+-.+. ..+.+..........+++|+ ..++|| +++++ ++.+|+.|.=.... +++. ..
T Consensus 267 ---l~~l~~~~Gl~~-~~~~~~~~~~~~~E~Vvv~~---S~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~ 336 (552)
T PRK03818 267 ---LHKAQLVIGEEV-DTSLSTRGTDLRSERVVVTN---EKVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLS 336 (552)
T ss_pred ---HHHHHHhcCCcc-CccccccCcceEEEEEEEcC---hhccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCE
Confidence 333322221111 00011112233444455554 356665 67776 56777765433221 1211 01
Q ss_pred CCCCceEEEEcCHHHHHHHHHH
Q 009566 186 LRSDELVQISGEASVVKKALCQ 207 (532)
Q Consensus 186 ~~~~r~v~I~G~~~~v~~A~~~ 207 (532)
...-..+.+.|+++++++..+.
T Consensus 337 Lq~GD~LlVvG~~~~i~~l~~~ 358 (552)
T PRK03818 337 LQFGDILNLVGRPEAIDAVANV 358 (552)
T ss_pred EecCCEEEEEECHHHHHHHHHH
Confidence 1123368999999999987664
No 166
>PRK00089 era GTPase Era; Reviewed
Probab=31.46 E-value=60 Score=32.23 Aligned_cols=36 Identities=31% Similarity=0.601 Sum_probs=25.9
Q ss_pred eEEEEEEeC-CceeeeeccCchHHHHHHh--------hhCceEEE
Q 009566 140 VTAKLLVPS-DQIGCVIGKGGQIVQNIRS--------ETGAQIRI 175 (532)
Q Consensus 140 ~~~~l~vp~-~~~g~iIGk~G~~Ik~I~~--------~tga~I~i 175 (532)
+...+.|.. ++.+.|||++|++|++|.. -++++|.+
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 455666764 4679999999999998754 45666544
No 167
>PRK15494 era GTPase Era; Provisional
Probab=30.56 E-value=62 Score=33.14 Aligned_cols=36 Identities=17% Similarity=0.385 Sum_probs=26.5
Q ss_pred eEEEEEEeCC-ceeeeeccCchHHHHHHh--------hhCceEEE
Q 009566 140 VTAKLLVPSD-QIGCVIGKGGQIVQNIRS--------ETGAQIRI 175 (532)
Q Consensus 140 ~~~~l~vp~~-~~g~iIGk~G~~Ik~I~~--------~tga~I~i 175 (532)
+...++|... +-+.|||++|+.||+|.. -++++|.+
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 5566777754 678999999999998754 45655544
No 168
>COG1159 Era GTPase [General function prediction only]
Probab=30.35 E-value=66 Score=32.11 Aligned_cols=29 Identities=31% Similarity=0.633 Sum_probs=22.2
Q ss_pred ceEEEEEEeC-CceeeeeccCchHHHHHHh
Q 009566 139 QVTAKLLVPS-DQIGCVIGKGGQIVQNIRS 167 (532)
Q Consensus 139 ~~~~~l~vp~-~~~g~iIGk~G~~Ik~I~~ 167 (532)
.+...++|+. ++-+.||||+|+.||+|-.
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~ 257 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKIGT 257 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHHHH
Confidence 3455677775 4679999999999988744
No 169
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.83 E-value=2e+02 Score=25.40 Aligned_cols=43 Identities=35% Similarity=0.423 Sum_probs=34.6
Q ss_pred hHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHh
Q 009566 160 QIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLH 213 (532)
Q Consensus 160 ~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~ 213 (532)
+.++.|-+-.|+-|.+.. ...|.|.|+.+.|.+|++.|...-.
T Consensus 126 eRlqDi~E~hgvIiE~~E-----------~D~V~i~Gd~drVk~aLke~~~~wk 168 (170)
T COG4010 126 ERLQDIAETHGVIIEFEE-----------YDLVAIYGDSDRVKKALKEIGSFWK 168 (170)
T ss_pred HHHHHHHHhhheeEEeee-----------ccEEEEeccHHHHHHHHHHHHHHHh
Confidence 456778888888888753 3469999999999999999987643
No 170
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=24.93 E-value=1.2e+02 Score=25.45 Aligned_cols=27 Identities=26% Similarity=0.316 Sum_probs=24.4
Q ss_pred ceEEEEcCHHHHHHHHHHHHHHHHhcc
Q 009566 420 EMVQISGDLDLAKDALIQVMTRLRANL 446 (532)
Q Consensus 420 r~V~I~G~~~~v~~A~~~I~~~l~~~~ 446 (532)
..|.|+|+..+|+.|+..+.+.+++..
T Consensus 75 GslvitGdvs~Ve~Al~~V~~~l~~~L 101 (111)
T PRK15468 75 GALVIYGSVGAVEEALSQTVSGLGRLL 101 (111)
T ss_pred eeEEEEccHHHHHHHHHHHHHHHHhhc
Confidence 469999999999999999999999854
No 171
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=24.13 E-value=75 Score=30.20 Aligned_cols=29 Identities=28% Similarity=0.458 Sum_probs=24.6
Q ss_pred EEEEecCCccceEecCCchHHHHHHHHhC
Q 009566 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (532)
Q Consensus 45 ~~i~vp~~~~g~IIGk~G~~Ik~i~~~tg 73 (532)
++|.|-...-+.|||++|..|++|++.-.
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l~ 92 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDLQ 92 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHHH
Confidence 56777788889999999999999997653
No 172
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=23.20 E-value=1.6e+02 Score=30.07 Aligned_cols=50 Identities=18% Similarity=0.224 Sum_probs=42.3
Q ss_pred CCceeeeeccCchHHHHHHhhhCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHH
Q 009566 148 SDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIA 209 (532)
Q Consensus 148 ~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~ 209 (532)
...+-.|.|..+.+++.|.+.+|+.|... .+.++|+|+...|..|...+.
T Consensus 23 ~~~~~~l~G~~~~~l~l~e~~~gv~i~~r------------G~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 23 DNELVALFGPTDTNLSLLEIALGVSIVAR------------GEAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred chhhhhhcCCCCccHHHHHHHhCcEEEeC------------CceEEEEechHHHHHHHHHHh
Confidence 55677899999999999999999988542 456999999888888887777
No 173
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=21.79 E-value=2.5e+02 Score=22.35 Aligned_cols=54 Identities=17% Similarity=0.104 Sum_probs=40.7
Q ss_pred CChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHH
Q 009566 388 GGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLR 443 (532)
Q Consensus 388 gG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~ 443 (532)
|=..+.+|-+..++.++..-+|...- ...+.+++|.|+..++..|-+.++..|.
T Consensus 32 G~~~~~~i~~~l~~~v~~~~~dG~~v--~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 32 GLEEAEEIFEKLGLEVEWLVKDGDRV--EPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp SHHHHHHHHHHCTEEEEESS-TT-EE--ETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhhccEEEEEEeCCCCCc--cCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 55788889888899998875543221 2456899999999999999888877765
No 174
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=21.27 E-value=95 Score=29.51 Aligned_cols=28 Identities=39% Similarity=0.577 Sum_probs=23.5
Q ss_pred EEEEEecCcceeEecCCChhHHHHHHhh
Q 009566 372 TRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (532)
Q Consensus 372 ~~i~VP~~~~G~IIGkgG~~Ik~I~~~T 399 (532)
.++.|-...-|.|||++|+.|++|++.-
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 5577777788999999999999998654
No 175
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=20.48 E-value=2.9e+02 Score=21.87 Aligned_cols=35 Identities=26% Similarity=0.396 Sum_probs=28.5
Q ss_pred hCceEEEecCCCCCCCCCCCCceEEEEc--CHHHHHHHHHHHHHHHHh
Q 009566 399 TKANIRILPKENLPKIASEDDEMVQISG--DLDLAKDALIQVMTRLRA 444 (532)
Q Consensus 399 Tga~I~i~~~~~~P~~~~~~~r~V~I~G--~~~~v~~A~~~I~~~l~~ 444 (532)
..|.+.|.+. ..|+|+| +.+.++.|...|...|.+
T Consensus 48 p~~t~~IF~s-----------Gki~itGaks~~~~~~a~~~i~~~L~~ 84 (86)
T PF00352_consen 48 PKATVLIFSS-----------GKIVITGAKSEEEAKKAIEKILPILQK 84 (86)
T ss_dssp TTEEEEEETT-----------SEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred CcEEEEEEcC-----------CEEEEEecCCHHHHHHHHHHHHHHHHH
Confidence 3577888642 4799999 699999999999999876
No 176
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=20.40 E-value=2.1e+02 Score=22.14 Aligned_cols=42 Identities=14% Similarity=0.225 Sum_probs=29.1
Q ss_pred hhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHH
Q 009566 390 SIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMT 440 (532)
Q Consensus 390 ~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~V~I~G~~~~v~~A~~~I~~ 440 (532)
..|.+|-+..+|+|.-.. .+.-+|+++|+++.+...+.++..
T Consensus 17 ~ei~~l~~~f~a~ivd~~---------~~~~iie~tG~~~kid~fi~~l~~ 58 (75)
T PF10369_consen 17 SEILQLAEIFRARIVDVS---------PDSIIIELTGTPEKIDAFIKLLKP 58 (75)
T ss_dssp HHHHHHHHHTT-EEEEEE---------TTEEEEEEEE-HHHHHHHHHHSTG
T ss_pred HHHHHHHHHhCCEEEEEC---------CCEEEEEEcCCHHHHHHHHHHhhh
Confidence 457788889999964322 234689999999999887766543
Done!