Query 006320
Match_columns 650
No_of_seqs 342 out of 2115
Neff 7.8
Searched_HMMs 46136
Date Thu Mar 28 21:34:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006320.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006320hhsearch_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 4.9E-44 1.1E-48 388.4 37.5 371 74-506 38-410 (485)
2 KOG2193 IGF-II mRNA-binding pr 100.0 2E-41 4.4E-46 343.7 23.2 357 76-508 196-567 (584)
3 KOG1676 K-homology type RNA bi 100.0 1.5E-37 3.3E-42 331.3 31.4 335 78-511 53-395 (600)
4 KOG1676 K-homology type RNA bi 100.0 1.5E-36 3.3E-41 323.6 22.6 294 190-642 52-356 (600)
5 KOG2193 IGF-II mRNA-binding pr 100.0 2.4E-31 5.1E-36 270.6 14.8 284 190-642 197-531 (584)
6 KOG2192 PolyC-binding hnRNP-K 100.0 2.9E-29 6.4E-34 241.9 23.2 292 75-416 44-380 (390)
7 KOG2192 PolyC-binding hnRNP-K 100.0 1.3E-29 2.8E-34 244.4 20.2 279 346-641 46-352 (390)
8 KOG2190 PolyC-binding proteins 100.0 2.8E-27 6E-32 257.7 22.1 158 347-509 42-212 (485)
9 KOG2191 RNA-binding protein NO 99.9 1.6E-25 3.5E-30 222.5 20.4 244 75-385 35-281 (402)
10 KOG2191 RNA-binding protein NO 99.9 6.2E-21 1.3E-25 190.0 17.9 229 346-642 37-282 (402)
11 TIGR03665 arCOG04150 arCOG0415 99.5 1.6E-14 3.4E-19 138.7 8.9 140 352-508 2-154 (172)
12 TIGR03665 arCOG04150 arCOG0415 99.5 9.1E-14 2E-18 133.4 11.9 143 83-269 2-153 (172)
13 PRK13763 putative RNA-processi 99.5 6.6E-14 1.4E-18 135.3 9.6 144 348-508 3-160 (180)
14 PRK13763 putative RNA-processi 99.5 3.2E-13 6.9E-18 130.5 13.2 146 79-268 3-158 (180)
15 KOG2208 Vigilin [Lipid transpo 99.3 1.7E-11 3.7E-16 141.8 16.2 330 75-506 197-563 (753)
16 KOG2208 Vigilin [Lipid transpo 99.3 1.7E-11 3.6E-16 141.8 13.0 391 79-641 347-746 (753)
17 cd02396 PCBP_like_KH K homolog 99.2 1.5E-11 3.2E-16 98.7 6.8 63 433-499 1-64 (65)
18 cd02396 PCBP_like_KH K homolog 99.2 5.9E-11 1.3E-15 95.2 7.1 64 193-261 1-64 (65)
19 KOG2279 Kinase anchor protein 99.1 2.5E-10 5.4E-15 122.0 8.4 231 189-510 65-373 (608)
20 KOG2279 Kinase anchor protein 99.1 1.5E-09 3.2E-14 116.2 13.1 144 346-506 66-210 (608)
21 cd02394 vigilin_like_KH K homo 99.0 2.8E-10 6.1E-15 90.4 5.3 60 434-500 2-62 (62)
22 PF00013 KH_1: KH domain syndr 99.0 2.4E-10 5.2E-15 90.1 3.3 59 433-499 1-60 (60)
23 cd02394 vigilin_like_KH K homo 99.0 6.6E-10 1.4E-14 88.2 5.2 61 194-262 2-62 (62)
24 cd02393 PNPase_KH Polynucleoti 99.0 1.5E-09 3.2E-14 85.8 7.1 57 432-499 2-60 (61)
25 cd02393 PNPase_KH Polynucleoti 98.9 2.9E-09 6.2E-14 84.2 7.8 58 192-261 2-60 (61)
26 PF00013 KH_1: KH domain syndr 98.9 9.7E-10 2.1E-14 86.7 4.8 60 193-261 1-60 (60)
27 cd00105 KH-I K homology RNA-bi 98.9 4.1E-09 8.9E-14 84.0 7.3 61 434-499 2-63 (64)
28 cd00105 KH-I K homology RNA-bi 98.9 8.4E-09 1.8E-13 82.2 7.6 62 194-261 2-63 (64)
29 PF13014 KH_3: KH domain 98.8 9.9E-09 2.1E-13 75.1 5.3 42 89-130 1-43 (43)
30 COG1094 Predicted RNA-binding 98.6 1E-07 2.2E-12 90.9 8.4 139 346-507 6-166 (194)
31 smart00322 KH K homology RNA-b 98.6 1.9E-07 4.2E-12 74.7 8.1 66 431-503 2-68 (69)
32 PF13014 KH_3: KH domain 98.6 8.5E-08 1.8E-12 70.2 5.1 42 358-399 1-43 (43)
33 smart00322 KH K homology RNA-b 98.5 4.9E-07 1.1E-11 72.3 8.7 66 192-265 3-68 (69)
34 COG1094 Predicted RNA-binding 98.4 1E-06 2.2E-11 84.1 9.9 148 78-269 7-166 (194)
35 cd02395 SF1_like-KH Splicing f 98.0 2.5E-05 5.3E-10 70.3 8.3 65 88-160 15-96 (120)
36 cd02395 SF1_like-KH Splicing f 98.0 2.1E-05 4.7E-10 70.7 7.2 66 441-506 15-96 (120)
37 KOG2113 Predicted RNA binding 98.0 3.4E-05 7.3E-10 77.8 9.1 155 77-265 24-181 (394)
38 PRK08406 transcription elongat 97.7 0.00011 2.4E-09 68.0 7.8 103 80-228 33-135 (140)
39 KOG2113 Predicted RNA binding 97.6 0.00011 2.3E-09 74.3 6.4 141 190-400 24-164 (394)
40 KOG0336 ATP-dependent RNA heli 97.6 9.3E-05 2E-09 77.7 6.1 53 77-132 45-97 (629)
41 PRK08406 transcription elongat 97.5 0.00027 5.8E-09 65.5 7.1 99 348-466 32-134 (140)
42 TIGR02696 pppGpp_PNP guanosine 97.4 0.00056 1.2E-08 78.5 9.3 94 143-267 548-642 (719)
43 TIGR02696 pppGpp_PNP guanosine 97.4 0.00048 1E-08 79.1 8.3 88 407-505 548-642 (719)
44 KOG0119 Splicing factor 1/bran 97.3 0.0017 3.6E-08 69.8 11.5 78 191-268 137-231 (554)
45 TIGR01952 nusA_arch NusA famil 97.2 0.001 2.3E-08 61.4 7.0 103 80-228 34-136 (141)
46 TIGR03591 polynuc_phos polyrib 97.1 0.001 2.2E-08 77.5 7.5 65 191-267 550-615 (684)
47 KOG0119 Splicing factor 1/bran 97.0 0.0036 7.9E-08 67.3 10.1 75 431-505 137-230 (554)
48 TIGR03591 polynuc_phos polyrib 97.0 0.0011 2.3E-08 77.4 6.4 66 430-506 549-616 (684)
49 TIGR01952 nusA_arch NusA famil 96.8 0.003 6.6E-08 58.4 6.5 101 349-467 34-136 (141)
50 PLN00207 polyribonucleotide nu 96.5 0.0029 6.3E-08 74.4 5.2 95 407-512 654-757 (891)
51 PLN00207 polyribonucleotide nu 96.5 0.0039 8.4E-08 73.3 6.0 65 191-267 684-750 (891)
52 KOG2814 Transcription coactiva 96.4 0.0031 6.7E-08 64.9 4.4 71 78-160 56-126 (345)
53 COG0195 NusA Transcription elo 96.4 0.0023 4.9E-08 62.2 3.1 103 80-229 77-179 (190)
54 KOG0336 ATP-dependent RNA heli 96.3 0.0048 1E-07 65.2 4.9 73 187-268 42-114 (629)
55 COG1185 Pnp Polyribonucleotide 96.2 0.0081 1.7E-07 67.8 6.6 95 408-513 522-624 (692)
56 KOG1588 RNA-binding protein Sa 96.2 0.0059 1.3E-07 61.3 4.9 42 74-115 87-134 (259)
57 COG0195 NusA Transcription elo 96.2 0.0062 1.3E-07 59.2 4.7 100 350-468 78-179 (190)
58 COG1185 Pnp Polyribonucleotide 96.2 0.011 2.3E-07 66.9 7.0 96 143-268 521-617 (692)
59 KOG1588 RNA-binding protein Sa 95.9 0.032 6.9E-07 56.1 8.1 80 428-507 88-189 (259)
60 cd02134 NusA_KH NusA_K homolog 95.8 0.016 3.5E-07 45.6 4.7 37 78-114 24-60 (61)
61 cd02134 NusA_KH NusA_K homolog 95.7 0.012 2.7E-07 46.3 3.6 36 604-639 25-60 (61)
62 KOG2814 Transcription coactiva 95.6 0.014 3.1E-07 60.2 4.7 71 191-269 56-127 (345)
63 PRK12328 nusA transcription el 95.5 0.038 8.2E-07 59.0 7.7 98 357-473 251-350 (374)
64 TIGR01953 NusA transcription t 95.5 0.046 1E-06 58.3 8.3 38 192-229 301-338 (341)
65 TIGR01953 NusA transcription t 95.4 0.043 9.2E-07 58.5 7.6 94 357-469 243-339 (341)
66 PRK12327 nusA transcription el 95.2 0.055 1.2E-06 58.1 7.8 95 88-229 245-340 (362)
67 PRK12328 nusA transcription el 95.2 0.045 9.8E-07 58.4 7.0 96 88-231 251-347 (374)
68 PRK11824 polynucleotide phosph 95.2 0.017 3.6E-07 67.7 4.1 88 408-506 524-619 (693)
69 PRK11824 polynucleotide phosph 95.1 0.022 4.8E-07 66.6 4.9 95 143-267 523-618 (693)
70 PRK12329 nusA transcription el 95.0 0.069 1.5E-06 58.0 7.7 94 88-228 277-371 (449)
71 PF14611 SLS: Mitochondrial in 95.0 1 2.2E-05 44.8 15.6 65 193-268 27-91 (210)
72 PRK00468 hypothetical protein; 94.7 0.038 8.3E-07 45.4 3.7 33 75-107 26-58 (75)
73 PRK00468 hypothetical protein; 94.6 0.064 1.4E-06 44.1 4.8 34 428-461 26-60 (75)
74 PRK12327 nusA transcription el 94.5 0.078 1.7E-06 56.9 6.8 96 357-470 245-342 (362)
75 PRK02821 hypothetical protein; 94.3 0.074 1.6E-06 43.9 4.7 34 429-462 28-62 (77)
76 PRK04163 exosome complex RNA-b 94.1 0.077 1.7E-06 53.8 5.4 67 433-510 146-214 (235)
77 PRK04163 exosome complex RNA-b 94.1 0.1 2.2E-06 52.9 6.1 63 194-268 147-210 (235)
78 PRK09202 nusA transcription el 94.0 0.098 2.1E-06 58.2 6.4 94 88-229 245-339 (470)
79 PRK12329 nusA transcription el 94.0 0.099 2.1E-06 56.8 6.1 94 357-468 277-372 (449)
80 PRK02821 hypothetical protein; 94.0 0.06 1.3E-06 44.4 3.4 35 76-110 28-62 (77)
81 COG5176 MSL5 Splicing factor ( 93.7 0.091 2E-06 50.6 4.6 39 78-116 147-191 (269)
82 TIGR03319 YmdA_YtgF conserved 93.6 0.13 2.8E-06 58.2 6.3 50 346-400 202-252 (514)
83 PRK00106 hypothetical protein; 93.5 0.13 2.8E-06 57.9 6.3 50 346-400 223-273 (535)
84 COG1837 Predicted RNA-binding 93.5 0.087 1.9E-06 43.2 3.6 32 76-107 27-58 (76)
85 COG1837 Predicted RNA-binding 93.5 0.15 3.3E-06 41.8 5.0 33 428-460 26-59 (76)
86 PRK09202 nusA transcription el 93.4 0.15 3.3E-06 56.7 6.6 93 358-469 246-340 (470)
87 PRK01064 hypothetical protein; 93.3 0.19 4.2E-06 41.6 5.4 34 428-461 26-60 (78)
88 PRK00106 hypothetical protein; 93.2 0.34 7.4E-06 54.7 8.9 66 191-267 224-291 (535)
89 PRK01064 hypothetical protein; 93.2 0.11 2.4E-06 43.0 3.7 32 76-107 27-58 (78)
90 PRK12704 phosphodiesterase; Pr 93.1 0.17 3.8E-06 57.2 6.5 50 346-400 208-258 (520)
91 TIGR03319 YmdA_YtgF conserved 93.1 0.36 7.7E-06 54.6 8.9 66 191-267 203-270 (514)
92 PRK12704 phosphodiesterase; Pr 93.0 0.31 6.8E-06 55.1 8.4 66 192-268 210-277 (520)
93 KOG1067 Predicted RNA-binding 93.0 0.28 6E-06 54.2 7.4 94 144-268 567-661 (760)
94 KOG1067 Predicted RNA-binding 92.4 0.29 6.3E-06 54.0 6.6 71 428-510 593-665 (760)
95 COG5176 MSL5 Splicing factor ( 91.9 0.23 5.1E-06 47.9 4.7 41 190-230 146-192 (269)
96 PF14611 SLS: Mitochondrial in 91.3 4.6 9.9E-05 40.0 13.6 130 82-269 29-167 (210)
97 KOG3273 Predicted RNA-binding 90.9 0.18 3.9E-06 48.4 2.8 62 433-506 170-232 (252)
98 PRK12705 hypothetical protein; 90.0 0.45 9.7E-06 53.4 5.4 50 346-400 196-246 (508)
99 PF13083 KH_4: KH domain; PDB: 87.8 0.25 5.5E-06 40.2 1.2 32 78-109 28-59 (73)
100 COG1855 ATPase (PilT family) [ 85.1 1.7 3.7E-05 47.5 5.9 39 193-231 487-525 (604)
101 PF13083 KH_4: KH domain; PDB: 84.7 0.55 1.2E-05 38.2 1.7 34 346-379 27-60 (73)
102 PRK13764 ATPase; Provisional 84.5 1.8 3.8E-05 49.8 6.2 66 409-474 456-524 (602)
103 cd02409 KH-II KH-II (K homolo 84.4 1.6 3.6E-05 34.2 4.3 34 79-112 25-58 (68)
104 PRK12705 hypothetical protein; 83.8 2.1 4.5E-05 48.2 6.2 64 193-267 199-264 (508)
105 PF13184 KH_5: NusA-like KH do 83.2 0.85 1.8E-05 36.9 2.1 36 81-116 5-46 (69)
106 KOG4369 RTK signaling protein 82.1 0.39 8.5E-06 56.9 -0.3 70 433-506 1341-1411(2131)
107 PF13184 KH_5: NusA-like KH do 81.8 0.94 2E-05 36.6 1.9 36 433-468 4-46 (69)
108 cd02409 KH-II KH-II (K homolo 80.6 2.3 5E-05 33.3 3.8 35 191-225 24-58 (68)
109 COG1855 ATPase (PilT family) [ 80.5 2.4 5.2E-05 46.3 4.9 64 408-471 460-526 (604)
110 KOG2874 rRNA processing protei 79.7 3 6.5E-05 42.3 5.0 51 204-267 161-211 (356)
111 KOG3273 Predicted RNA-binding 79.0 1.3 2.8E-05 42.7 2.1 159 79-269 74-233 (252)
112 KOG4369 RTK signaling protein 79.0 0.58 1.3E-05 55.6 -0.2 70 193-267 1341-1410(2131)
113 PF07650 KH_2: KH domain syndr 78.1 1.1 2.5E-05 36.8 1.3 34 604-637 25-58 (78)
114 cd02414 jag_KH jag_K homology 77.3 2.5 5.3E-05 34.8 3.1 35 80-114 25-59 (77)
115 COG1097 RRP4 RNA-binding prote 76.5 5.7 0.00012 39.9 5.8 62 194-267 148-210 (239)
116 COG1782 Predicted metal-depend 76.4 11 0.00023 41.9 8.3 37 349-385 100-136 (637)
117 cd02410 archeal_CPSF_KH The ar 75.0 8.5 0.00018 35.7 6.2 37 349-385 77-113 (145)
118 PF07650 KH_2: KH domain syndr 74.3 1.7 3.6E-05 35.8 1.3 33 80-112 26-58 (78)
119 cd02410 archeal_CPSF_KH The ar 72.9 17 0.00037 33.7 7.6 89 363-468 21-113 (145)
120 cd02414 jag_KH jag_K homology 72.9 2.4 5.1E-05 35.0 1.9 44 604-647 24-67 (77)
121 cd02413 40S_S3_KH K homology R 72.3 4.1 9E-05 34.0 3.2 37 80-116 31-67 (81)
122 PRK13764 ATPase; Provisional 72.0 2.8 6E-05 48.3 2.8 43 599-641 476-518 (602)
123 PRK06418 transcription elongat 70.2 4.8 0.0001 38.3 3.5 35 81-116 63-97 (166)
124 COG1159 Era GTPase [General fu 69.5 3.5 7.6E-05 42.8 2.6 45 604-648 229-280 (298)
125 COG1782 Predicted metal-depend 69.1 18 0.00038 40.3 7.9 91 361-468 42-136 (637)
126 PRK06418 transcription elongat 68.1 5.8 0.00012 37.8 3.6 36 193-229 62-97 (166)
127 COG1097 RRP4 RNA-binding prote 67.9 11 0.00023 38.0 5.5 56 434-500 148-205 (239)
128 cd02413 40S_S3_KH K homology R 65.9 5.9 0.00013 33.1 2.9 30 604-633 30-59 (81)
129 cd02412 30S_S3_KH K homology R 62.3 6.7 0.00015 34.7 2.7 29 81-109 63-91 (109)
130 TIGR03675 arCOG00543 arCOG0054 60.9 15 0.00033 42.8 6.0 90 362-468 37-130 (630)
131 PRK00089 era GTPase Era; Revie 59.6 6.9 0.00015 40.8 2.7 44 604-647 226-276 (292)
132 KOG2874 rRNA processing protei 57.6 16 0.00035 37.3 4.6 50 444-505 161-211 (356)
133 PRK15494 era GTPase Era; Provi 56.4 8.5 0.00018 41.3 2.8 44 604-647 273-323 (339)
134 cd02411 archeal_30S_S3_KH K ho 56.0 12 0.00025 31.5 3.0 28 81-108 40-67 (85)
135 COG5166 Uncharacterized conser 54.6 14 0.00029 41.0 3.9 36 193-228 450-485 (657)
136 COG0092 RpsC Ribosomal protein 54.0 11 0.00023 37.9 2.7 40 603-642 50-94 (233)
137 COG5166 Uncharacterized conser 53.1 11 0.00025 41.6 3.0 128 361-507 393-526 (657)
138 COG0092 RpsC Ribosomal protein 52.1 12 0.00026 37.5 2.8 30 79-108 51-80 (233)
139 TIGR03675 arCOG00543 arCOG0054 50.9 38 0.00083 39.5 7.1 38 348-385 93-130 (630)
140 cd02411 archeal_30S_S3_KH K ho 50.0 14 0.00031 31.0 2.6 27 606-632 40-66 (85)
141 TIGR00436 era GTP-binding prot 48.1 12 0.00025 38.7 2.1 43 604-646 221-270 (270)
142 cd02412 30S_S3_KH K homology R 46.5 16 0.00034 32.3 2.4 30 193-222 62-91 (109)
143 TIGR00436 era GTP-binding prot 36.0 39 0.00085 34.7 3.8 29 192-220 221-250 (270)
144 KOG1423 Ras-like GTPase ERA [C 32.5 32 0.0007 36.1 2.4 32 603-634 327-359 (379)
145 PRK15494 era GTPase Era; Provi 32.3 48 0.001 35.5 3.9 29 192-220 273-302 (339)
146 PRK00089 era GTPase Era; Revie 31.8 50 0.0011 34.3 3.8 29 192-220 226-255 (292)
147 TIGR01008 rpsC_E_A ribosomal p 28.8 54 0.0012 32.2 3.2 31 80-110 39-69 (195)
148 KOG1423 Ras-like GTPase ERA [C 27.4 54 0.0012 34.5 3.0 33 190-222 326-359 (379)
149 COG1159 Era GTPase [General fu 27.4 64 0.0014 33.7 3.6 29 191-219 228-257 (298)
150 PRK04191 rps3p 30S ribosomal p 26.9 59 0.0013 32.3 3.1 31 81-111 42-72 (207)
151 CHL00048 rps3 ribosomal protei 26.9 59 0.0013 32.5 3.2 30 80-109 67-96 (214)
152 PTZ00084 40S ribosomal protein 25.9 61 0.0013 32.5 3.0 32 81-112 46-77 (220)
153 PRK15468 carboxysome structura 22.8 1.2E+02 0.0025 26.7 3.7 26 482-507 76-101 (111)
154 PRK03818 putative transporter; 22.4 1.1E+03 0.025 27.0 12.9 136 98-273 218-371 (552)
155 PF09869 DUF2096: Uncharacteri 21.9 2.4E+02 0.0051 26.9 5.8 58 189-265 110-167 (169)
156 COG1847 Jag Predicted RNA-bind 20.7 72 0.0016 31.5 2.3 26 80-105 92-117 (208)
157 TIGR01008 rpsC_E_A ribosomal p 20.2 81 0.0018 31.0 2.6 29 604-632 38-66 (195)
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=4.9e-44 Score=388.40 Aligned_cols=371 Identities=39% Similarity=0.598 Sum_probs=285.0
Q ss_pred CCCccEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHH
Q 006320 74 SLMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLI 153 (650)
Q Consensus 74 ~~~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i 153 (650)
.++...+||+||+.+.+|.||||+|.+|++||++|.++|+|.+..++|.|||++|+|...+ ...+.+++|+.++
T Consensus 38 ~p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~------~~~~~~~~al~ka 111 (485)
T KOG2190|consen 38 GPDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVE------LNLSPATDALFKA 111 (485)
T ss_pred CCCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEeccccc------ccCCchHHHHHHH
Confidence 3444556999999999999999999999999999999999999999999999999996211 1577889999999
Q ss_pred HHHhhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCC
Q 006320 154 HDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHS 233 (650)
Q Consensus 154 ~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~ 233 (650)
++.|......+. ....+.+. -....+++++|+||..++|+||||+|+.||+|+++|||+|+|.+ ++
T Consensus 112 ~~~iv~~~~~d~---~~~~d~~~---------~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~--~~ 177 (485)
T KOG2190|consen 112 FDMIVFKLEEDD---EAAEDNGE---------DASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSS--DM 177 (485)
T ss_pred HHHHhhcccccc---cccccCCc---------cccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecC--CC
Confidence 999887533111 01111110 01123689999999999999999999999999999999999986 47
Q ss_pred CCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcccCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006320 234 LPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGS 313 (650)
Q Consensus 234 lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~ 313 (650)
+|. .++|.|+|.|.+++|.+|+..|..+|+++... +|..+...-.|.|.........+..+..++
T Consensus 178 lP~---ster~V~IsG~~~av~~al~~Is~~L~~~~~~----------~~~~~~st~~y~P~~~~~~~~~~s~~~~~~-- 242 (485)
T KOG2190|consen 178 LPN---STERAVTISGEPDAVKKALVQISSRLLENPPR----------SPPPLVSTIPYRPSASQGGPVLPSTAQTSP-- 242 (485)
T ss_pred CCc---ccceeEEEcCchHHHHHHHHHHHHHHHhcCCc----------CCCCCCCcccCCCcccccCccccccccCCc--
Confidence 898 67888999999999999999999999997533 111111122233311100000000000000
Q ss_pred CCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCcc
Q 006320 314 NYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQ 393 (650)
Q Consensus 314 ~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er 393 (650)
.+ .+... ...+.+..+++.||.++++.|||++|..|+.|+.++++.|.+.++..+ +
T Consensus 243 ------------~~------~~~~~---~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~---~ 298 (485)
T KOG2190|consen 243 ------------DA------HPFGG---IVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTD---R 298 (485)
T ss_pred ------------cc------ccccc---cccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccCc---c
Confidence 00 00000 112367788999999999999999999999999999999999875443 9
Q ss_pred EEEecCCCCCCCcchHHHHHHHHHHHhhhccCCCC-CCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCC
Q 006320 394 IITISSEEGPDDELFPAQEALLHIQTRIVDLGADK-DNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREE 471 (650)
Q Consensus 394 ~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~~~-~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~ 471 (650)
+|+++..+-+.+..+.|++|+++++.++.+...+. ...++.+|+||++++||||||+|+ |.+||+.|||.|+|..+++
T Consensus 299 ~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~ 378 (485)
T KOG2190|consen 299 IVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEE 378 (485)
T ss_pred eeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccchHHHHHhcCCceEEccccc
Confidence 99999999899999999999999999988865544 667999999999999999999999 9999999999999998776
Q ss_pred CCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320 472 VPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY 506 (650)
Q Consensus 472 ~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 506 (650)
.. ..++++++|+|.......|..+|..++...
T Consensus 379 ~~---~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~ 410 (485)
T KOG2190|consen 379 VS---GVREALVQITGMLREDLLAQYLIRARLSAP 410 (485)
T ss_pred cC---CcceeEEEecchhHHHHhhhhhcccccccC
Confidence 42 357999999999988888887775544433
No 2
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=2e-41 Score=343.72 Aligned_cols=357 Identities=26% Similarity=0.392 Sum_probs=271.1
Q ss_pred CccEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecC-CCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHH
Q 006320 76 MVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHEL-IPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIH 154 (650)
Q Consensus 76 ~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~-~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~ 154 (650)
-...++|+|+|..++|.||||.|+|||.|...|.|+|+|... ..|..|++|+|.++. |+ +-+|+++|+
T Consensus 196 ~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tp----Eg-------~s~Ac~~IL 264 (584)
T KOG2193|consen 196 LKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTP----EG-------TSKACKMIL 264 (584)
T ss_pred ccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCc----cc-------hHHHHHHHH
Confidence 456899999999999999999999999999999999999753 558899999999984 33 468888888
Q ss_pred HHhhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCC
Q 006320 155 DRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSL 234 (650)
Q Consensus 155 ~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~l 234 (650)
+.|........+ ...+.++++..+.+||+||||.|.+||+|+.+||++|.|++- ..|
T Consensus 265 eimqkEA~~~k~----------------------~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~l-qel 321 (584)
T KOG2193|consen 265 EIMQKEAVDDKV----------------------AEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKL-QEL 321 (584)
T ss_pred HHHHHhhhccch----------------------hhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeeh-hhh
Confidence 888654322211 256689999999999999999999999999999999999864 334
Q ss_pred CCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcccCCCCCC------CCCCCCCCc--cCCCCCCCCCCCCCCCCCCCC
Q 006320 235 PRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHF------HGRLHSPDR--FFPDDDYVPHMNNTARRPSMD 306 (650)
Q Consensus 235 p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~------~~~~~~p~~--~~~~~~~~p~~~~~~~~~~~~ 306 (650)
... ..||+|+|.|+.|+|.+|..+|+.+|+++...|...+ .+.+..|.- |++...+.|.
T Consensus 322 s~y--npERTItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~P----------- 388 (584)
T KOG2193|consen 322 SLY--NPERTITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPP----------- 388 (584)
T ss_pred ccc--CccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCC-----------
Confidence 332 5699999999999999999999999999887664322 111111100 1100000000
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCC
Q 006320 307 GARFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADP 386 (650)
Q Consensus 307 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~ 386 (650)
.|+... ...+.++..-. ..++....+|.||...+|+|||++|..||+|...+||+|+|..+
T Consensus 389 --h~~Ps~---------------v~~a~p~~~~h--q~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIapp 449 (584)
T KOG2193|consen 389 --HFPPSP---------------VTFASPYPLFH--QNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPP 449 (584)
T ss_pred --CCCCCc---------------cccCCCchhhh--cCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCC
Confidence 000000 00001111100 11256678999999999999999999999999999999999876
Q ss_pred C-CCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccC---CCCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcC
Q 006320 387 V-DGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLG---ADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTG 461 (650)
Q Consensus 387 ~-~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~---~~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tg 461 (650)
. ++..+|+|+|+| ++++.++|+.- |+.+|.+.. +..+..+...+.||++.+|+||||||. ++|+++.|+
T Consensus 450 E~pdvseRMViItG---ppeaqfKAQgr---ifgKikEenf~~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~ 523 (584)
T KOG2193|consen 450 EIPDVSERMVIITG---PPEAQFKAQGR---IFGKIKEENFFLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTS 523 (584)
T ss_pred CCCCcceeEEEecC---ChHHHHhhhhh---hhhhhhhhccCCchhhheeeeeeeccchhhhhhhccccccHHHHhcccc
Confidence 3 677899999995 56777777765 456666543 234556788899999999999999999 999999999
Q ss_pred ceEEEecCCCCCCCCCCCCeE-EEEEecHHHHHHHHHHHHHHHHhhhh
Q 006320 462 ANIQILSREEVPACVSGTDEL-VQIVGEIQAARDALVEVTTRLRSYLY 508 (650)
Q Consensus 462 a~I~i~~~~~~p~~~~~~~r~-v~I~G~~~~v~~A~~~I~~~l~~~~~ 508 (650)
|.+.|+ +|+.|. ++|.+ |.|+|...+.+.|...|.++|.++..
T Consensus 524 AeV~vP-rdqtpd---End~vivriiGhfyatq~aQrki~~iv~qvkq 567 (584)
T KOG2193|consen 524 AEVVVP-RDQTPD---ENDQVIVRIIGHFYATQNAQRKIAHIVNQVKQ 567 (584)
T ss_pred ceEEcc-ccCCCC---ccceeeeeeechhhcchHHHHHHHHHHHHHHH
Confidence 999774 777775 45554 99999999999999999999988743
No 3
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=1.5e-37 Score=331.35 Aligned_cols=335 Identities=20% Similarity=0.315 Sum_probs=262.0
Q ss_pred cEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHh
Q 006320 78 TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRI 157 (650)
Q Consensus 78 ~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i 157 (650)
.++-+.-||...+|.||||+|+.|+.|..+++|+|+|.....+..+|-+.++|.. +.+++|..++-+.+
T Consensus 53 ~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~p-----------e~v~~aK~li~evv 121 (600)
T KOG1676|consen 53 VQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSP-----------ENVEVAKQLIGEVV 121 (600)
T ss_pred ccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCc-----------ccHHHHHHhhhhhh
Confidence 3566778899999999999999999999999999998766556799999999974 35778887777666
Q ss_pred hhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCc
Q 006320 158 LESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRC 237 (650)
Q Consensus 158 ~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~ 237 (650)
........+ .. ......++.+|+||.+.+|+||||+|++|+.|++++||++.+... ....
T Consensus 122 ~r~~~~~~~----~~-------------~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd-~~~~-- 181 (600)
T KOG1676|consen 122 SRGRPPGGF----PD-------------NQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQD-GSIA-- 181 (600)
T ss_pred hccCCCCCc----cc-------------cCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEec-CCcC--
Confidence 543211110 00 011467899999999999999999999999999999999999853 2222
Q ss_pred cCCCcceEEEEcCHHHHHHHHHHHHHHHhhcccCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006320 238 VSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSNYRS 317 (650)
Q Consensus 238 ~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~ 317 (650)
...++.+.|+|++++|+.|+.+|.++|++.... .+ ...
T Consensus 182 -~~~~KplritGdp~~ve~a~~lV~dil~e~~~~---~~-----------------g~~--------------------- 219 (600)
T KOG1676|consen 182 -TGADKPLRITGDPDKVEQAKQLVADILREEDDE---VP-----------------GSG--------------------- 219 (600)
T ss_pred -CCCCCceeecCCHHHHHHHHHHHHHHHHhcccC---CC-----------------ccc---------------------
Confidence 236889999999999999999999999974210 00 000
Q ss_pred CCCCCCCCCCCccCCCCCCCCCCCCCCCCceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCC-CCCCccEEE
Q 006320 318 NNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPV-DGSDEQIIT 396 (650)
Q Consensus 318 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~-~~~~er~i~ 396 (650)
..++... ....+++|.||..+||.||||+|++||+|+.+||++|.|.... +.+.||++.
T Consensus 220 -------~~~g~~~-------------g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~ 279 (600)
T KOG1676|consen 220 -------GHAGVRG-------------GGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQ 279 (600)
T ss_pred -------cccCcCc-------------cccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceee
Confidence 0000000 1344899999999999999999999999999999999997654 488999999
Q ss_pred ecCCCCCCCcchHHHHHHHHHHHhhhccCC---CCCC-ce--EEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecC
Q 006320 397 ISSEEGPDDELFPAQEALLHIQTRIVDLGA---DKDN-II--TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSR 469 (650)
Q Consensus 397 I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~---~~~~-~~--~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~ 469 (650)
|.| +.+.+..|.+.|-+|+........ .... .. .+.+.||.+.||.||||||+ ||.|..++||++++.+.
T Consensus 280 IiG---~~d~ie~Aa~lI~eii~~~~~~~~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~ 356 (600)
T KOG1676|consen 280 IIG---TVDQIEHAAELINEIIAEAEAGAGGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ 356 (600)
T ss_pred eec---CHHHHHHHHHHHHHHHHHHhccCCCCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC
Confidence 996 478888888888888776654310 0011 12 78899999999999999999 99999999999998753
Q ss_pred CCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhhhhhcc
Q 006320 470 EEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDF 511 (650)
Q Consensus 470 ~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~ 511 (650)
+...+..++++.|+|+..+|+.|+.+|..++-+......
T Consensus 357 ---~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~~~~n~~ 395 (600)
T KOG1676|consen 357 ---PPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGDIAPNTP 395 (600)
T ss_pred ---CCCCCccceEEEEecCcccchHHHHHHHHHhcccCCCCC
Confidence 333456799999999999999999999999988755443
No 4
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=1.5e-36 Score=323.63 Aligned_cols=294 Identities=19% Similarity=0.280 Sum_probs=231.7
Q ss_pred CcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcc
Q 006320 190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQ 269 (650)
Q Consensus 190 ~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~ 269 (650)
...+.+..||..+|+++|||+|+.|..|+.++||+|+|..... ....|.|.++|.+++|+.|+.+|.+++....
T Consensus 52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s------~~~~r~~~~~G~pe~v~~aK~li~evv~r~~ 125 (600)
T KOG1676|consen 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPS------GIGYRSVDLTGSPENVEVAKQLIGEVVSRGR 125 (600)
T ss_pred cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCC------CcccccccccCCcccHHHHHHhhhhhhhccC
Confidence 5678899999999999999999999999999999999864321 1468999999999999999999999987652
Q ss_pred cCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCceE
Q 006320 270 HRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLV 349 (650)
Q Consensus 270 ~~~~~~~~~~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 349 (650)
. +..|. ...+ ..+++
T Consensus 126 ~------------~~~~~-----------------------------------------~~q~------------~~~tt 140 (600)
T KOG1676|consen 126 P------------PGGFP-----------------------------------------DNQG------------SVETT 140 (600)
T ss_pred C------------CCCcc-----------------------------------------ccCC------------cccee
Confidence 0 00000 0000 15789
Q ss_pred EEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCC--CCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccCC-
Q 006320 350 FRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPV--DGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGA- 426 (650)
Q Consensus 350 ~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~--~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~- 426 (650)
.+|+||++++|.||||+|++||+|++.+||++.+.... ....++.+.|+|. ++.++.|.+++.+|+....+..+
T Consensus 141 qeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGd---p~~ve~a~~lV~dil~e~~~~~~g 217 (600)
T KOG1676|consen 141 QEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGD---PDKVEQAKQLVADILREEDDEVPG 217 (600)
T ss_pred eeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCC---HHHHHHHHHHHHHHHHhcccCCCc
Confidence 99999999999999999999999999999998876532 2336789999965 67788888888877664222111
Q ss_pred -------CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHH
Q 006320 427 -------DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVE 498 (650)
Q Consensus 427 -------~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~ 498 (650)
......+.+|.||++.||.||||+|+ ||+|+.+|||+|+|.+++ .| .+.+|.++|.|++++|+.|.++
T Consensus 218 ~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd-~p---~speR~~~IiG~~d~ie~Aa~l 293 (600)
T KOG1676|consen 218 SGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDD-DP---SSPERPAQIIGTVDQIEHAAEL 293 (600)
T ss_pred cccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCC-CC---CCccceeeeecCHHHHHHHHHH
Confidence 11123488999999999999999999 999999999999998654 44 3679999999999999999999
Q ss_pred HHHHHHhhhhhcccccCCCCCCCCCCCCcccccCCCCCCCCCCCccCCcCCCCCCCCCCCCCCCCCCCCcccCCCccccc
Q 006320 499 VTTRLRSYLYRDFFQKETPPSSTGPTGSALVVEAASPIDITPAREVQTVTDPPAATHQSVQIPATSQPSKEAAGSVSETV 578 (650)
Q Consensus 499 I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~~~~ 578 (650)
|.++|.+..... ++ .|.
T Consensus 294 I~eii~~~~~~~-------------~~--------------------------------------~~~------------ 310 (600)
T KOG1676|consen 294 INEIIAEAEAGA-------------GG--------------------------------------GMG------------ 310 (600)
T ss_pred HHHHHHHHhccC-------------CC--------------------------------------CcC------------
Confidence 999999883211 00 010
Q ss_pred cCCcccccCCCccccCCCCccccccceEEEEecCCcccccccCCCcchhhHHHhcCCeEEEEEe
Q 006320 579 KQNESERREDVPTVINRVPLPLVTRSTLEVVLPDYAVPKLITKSKTLLTRFSEVSLLLHLINLF 642 (650)
Q Consensus 579 ~~g~~~~~~~~~~~~~~~~~~l~t~~t~~v~IP~~~~g~vIGk~G~~I~~Ir~~SGA~i~i~~~ 642 (650)
+|.+ +. ...++|.||++.||.||||||++|++|.++|||+|.+--+
T Consensus 311 -~G~P--------------~~---~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~ 356 (600)
T KOG1676|consen 311 -GGAP--------------GL---VAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ 356 (600)
T ss_pred -CCCc--------------cc---eeeEEEeccccccccccCCCccchhhhcccCCccccccCC
Confidence 1111 00 1278999999999999999999999999999999987544
No 5
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.97 E-value=2.4e-31 Score=270.62 Aligned_cols=284 Identities=18% Similarity=0.336 Sum_probs=231.5
Q ss_pred CcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcc
Q 006320 190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQ 269 (650)
Q Consensus 190 ~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~ 269 (650)
....+|++||..+||.||||.|++|+.|...|-|+|+|..++. ++..|+.++|-|++|...+|+++|++++....
T Consensus 197 ~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken-----~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA 271 (584)
T KOG2193|consen 197 KDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKEN-----AGAAEKIITVHSTPEGTSKACKMILEIMQKEA 271 (584)
T ss_pred cCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeeccc-----CCcccCceEEecCccchHHHHHHHHHHHHHhh
Confidence 4467899999999999999999999999999999999987643 24779999999999999999999999998764
Q ss_pred cCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCceE
Q 006320 270 HRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLV 349 (650)
Q Consensus 270 ~~~~~~~~~~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 349 (650)
..+.. .+++.
T Consensus 272 ~~~k~----------------------------------------------------------------------~~e~p 281 (584)
T KOG2193|consen 272 VDDKV----------------------------------------------------------------------AEEIP 281 (584)
T ss_pred hccch----------------------------------------------------------------------hhhcc
Confidence 22110 15778
Q ss_pred EEEEeecccccceecCCchhHHHHHHHhCCeEEEeCC---CCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccC-
Q 006320 350 FRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADP---VDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLG- 425 (650)
Q Consensus 350 ~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~---~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~- 425 (650)
++++--+.++|++|||.|.+||+|.++||++|.|.+- .--+.||+|++.|+ .+++..|...|.+-+..+.+..
T Consensus 282 Lk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGs---iEac~~AE~eImkKlre~yEnDl 358 (584)
T KOG2193|consen 282 LKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGS---IEACVQAEAEIMKKLRECYENDL 358 (584)
T ss_pred hhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEeccc---HHHHHHHHHHHHHHHHHHHhhhH
Confidence 8999999999999999999999999999999999754 23467999999974 5667777666654333222110
Q ss_pred ---------------------C-------------------------CCCCceEEEEeecCCcceeeecCCCc-hhhhhh
Q 006320 426 ---------------------A-------------------------DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRR 458 (650)
Q Consensus 426 ---------------------~-------------------------~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~ 458 (650)
+ ...+.-..+|+||...+|.||||.|. ||.|.+
T Consensus 359 ~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~R 438 (584)
T KOG2193|consen 359 AAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSR 438 (584)
T ss_pred HHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHH
Confidence 0 01134567999999999999999999 999999
Q ss_pred hcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhhhhhcccccCCCCCCCCCCCCcccccCCCCCCC
Q 006320 459 STGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDFFQKETPPSSTGPTGSALVVEAASPIDI 538 (650)
Q Consensus 459 ~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 538 (650)
.+||.|+|.+.| .| +..+|+|+|+|.+++..+|.-.|..+|+|.-+ + .
T Consensus 439 fagASiKIappE-~p---dvseRMViItGppeaqfKAQgrifgKikEenf------------------~------~---- 486 (584)
T KOG2193|consen 439 FAGASIKIAPPE-IP---DVSERMVIITGPPEAQFKAQGRIFGKIKEENF------------------F------L---- 486 (584)
T ss_pred hccceeeecCCC-CC---CcceeEEEecCChHHHHhhhhhhhhhhhhhcc------------------C------C----
Confidence 999999998765 44 36799999999999999999999999998711 0 0
Q ss_pred CCCCccCCcCCCCCCCCCCCCCCCCCCCCcccCCCccccccCCcccccCCCccccCCCCccccccceEEEEecCCccccc
Q 006320 539 TPAREVQTVTDPPAATHQSVQIPATSQPSKEAAGSVSETVKQNESERREDVPTVINRVPLPLVTRSTLEVVLPDYAVPKL 618 (650)
Q Consensus 539 ~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~~~~~~g~~~~~~~~~~~~~~~~~~l~t~~t~~v~IP~~~~g~v 618 (650)
|+ + .-+...+|-||...+|.|
T Consensus 487 ---------------------------Pk-----------------------e---------evklethirVPs~~aGRv 507 (584)
T KOG2193|consen 487 ---------------------------PK-----------------------E---------EVKLETHIRVPSSAAGRV 507 (584)
T ss_pred ---------------------------ch-----------------------h---------hheeeeeeeccchhhhhh
Confidence 00 0 013577899999999999
Q ss_pred ccCCCcchhhHHHhcCCeEEEEEe
Q 006320 619 ITKSKTLLTRFSEVSLLLHLINLF 642 (650)
Q Consensus 619 IGk~G~~I~~Ir~~SGA~i~i~~~ 642 (650)
|||||.+++.++.+++|.|.|.-+
T Consensus 508 IGKGGktVnELQnlt~AeV~vPrd 531 (584)
T KOG2193|consen 508 IGKGGKTVNELQNLTSAEVVVPRD 531 (584)
T ss_pred hccccccHHHHhccccceEEcccc
Confidence 999999999999999999998755
No 6
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.97 E-value=2.9e-29 Score=241.93 Aligned_cols=292 Identities=23% Similarity=0.368 Sum_probs=200.4
Q ss_pred CCccEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHH
Q 006320 75 LMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIH 154 (650)
Q Consensus 75 ~~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~ 154 (650)
....+.+|||+.++.+|+||||+|++||+|+.+++|.|.|++. ..+|||++|+... ..+-+-++.|+
T Consensus 44 k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri~tisad~-----------~ti~~ilk~ii 110 (390)
T KOG2192|consen 44 KRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILTISADI-----------ETIGEILKKII 110 (390)
T ss_pred hhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCceeEEEeccH-----------HHHHHHHHHHh
Confidence 3446999999999999999999999999999999999999987 6799999999852 23444444455
Q ss_pred HHhhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCC
Q 006320 155 DRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSL 234 (650)
Q Consensus 155 ~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~l 234 (650)
-.+++.. .....+.++|||+.+++|.|||++|+.||+|++++.|+.+|..
T Consensus 111 p~lee~f-------------------------~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift----- 160 (390)
T KOG2192|consen 111 PTLEEGF-------------------------QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFT----- 160 (390)
T ss_pred hhhhhCC-------------------------CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhh-----
Confidence 4443321 1135688999999999999999999999999999999999873
Q ss_pred CCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcccCCCC-CCCCCCCCCCc----cC---CCC----CCCCCCC-----
Q 006320 235 PRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRS-HFHGRLHSPDR----FF---PDD----DYVPHMN----- 297 (650)
Q Consensus 235 p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~-~~~~~~~~p~~----~~---~~~----~~~p~~~----- 297 (650)
.+|..+++|+|.|.|.+..|..+++.|++.|.+.+-+... +|.+...-+.. |. ... ...|...
T Consensus 161 ~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp 240 (390)
T KOG2192|consen 161 ECCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPP 240 (390)
T ss_pred ccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCC
Confidence 5788899999999999999999999999999998876653 33322211110 10 000 0000000
Q ss_pred --CCCCCCCCCCCC------CCCCCCCC--------CCCCCC--CCCC----------CccCCCCCCCCCCCCCCCCceE
Q 006320 298 --NTARRPSMDGAR------FSGSNYRS--------NNYGPR--PSGY----------SIEAGAAPMSDSVQPFYGEDLV 349 (650)
Q Consensus 298 --~~~~~~~~~~~~------~~~~~~~~--------~~~~~~--~~g~----------~~~~~~~~~~~~~~~~~~~~~~ 349 (650)
.+...|...+.. +...++.. ..+.+. ..+| +...+..+..+ +-...++
T Consensus 241 ~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGd----lGGPitT 316 (390)
T KOG2192|consen 241 PPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGD----LGGPITT 316 (390)
T ss_pred CCCccccceeccCCCCCccccccccccccccCCCcCCCcCccccccccCCCCCCCCCccccccccccCC----CCCceee
Confidence 000011110000 00000000 000000 0111 11111111111 1134578
Q ss_pred EEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHH
Q 006320 350 FRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLH 416 (650)
Q Consensus 350 ~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~ 416 (650)
..+.||.++-|.||||+|+.|++|+.++||.|++.++..++++|+++|+|+ .+++..||-.+..
T Consensus 317 aQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGT---qdQIqnAQYLlQn 380 (390)
T KOG2192|consen 317 AQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT---QDQIQNAQYLLQN 380 (390)
T ss_pred eeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEecc---HHHHhhHHHHHHH
Confidence 899999999999999999999999999999999999999999999999976 4666666655543
No 7
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.97 E-value=1.3e-29 Score=244.42 Aligned_cols=279 Identities=22% Similarity=0.228 Sum_probs=186.8
Q ss_pred CceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccC
Q 006320 346 EDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLG 425 (650)
Q Consensus 346 ~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~ 425 (650)
..+.+++++..+.+|+||||+|++||.|+.+++|+|.|++ ...++|+++|+..+ ....+.|.+|..++++.
T Consensus 46 ~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpd--s~~peri~tisad~------~ti~~ilk~iip~lee~- 116 (390)
T KOG2192|consen 46 SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPD--SSGPERILTISADI------ETIGEILKKIIPTLEEG- 116 (390)
T ss_pred cceeEEEEEecccccceeccccccHHHHhhhccceeeccC--CCCCceeEEEeccH------HHHHHHHHHHhhhhhhC-
Confidence 5689999999999999999999999999999999999977 77889999999653 23444455566666553
Q ss_pred CCCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHH
Q 006320 426 ADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLR 504 (650)
Q Consensus 426 ~~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~ 504 (650)
+.....+++||||+++++|.|||++|+ |||++++..|+++|+. -+|+.++||+|.|.|.+..|..+++.|+.+|.
T Consensus 117 f~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift----~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~ 192 (390)
T KOG2192|consen 117 FQLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFT----ECCPHSTDRVVLIGGKPKRVVECIKIILDLIS 192 (390)
T ss_pred CCCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhh----ccCCCCcceEEEecCCcchHHHHHHHHHHHhh
Confidence 445668999999999999999999999 9999999999999983 36778999999999999999999999999999
Q ss_pred hhhhhcccccCCCCC--CCCCCCCcccccCCCCCCCCC--CCccCCcCCCC-----CCCCCCCC----------C-CCCC
Q 006320 505 SYLYRDFFQKETPPS--STGPTGSALVVEAASPIDITP--AREVQTVTDPP-----AATHQSVQ----------I-PATS 564 (650)
Q Consensus 505 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~p-----~~~~~~~~----------~-~~~~ 564 (650)
+..++.....-.|.. .++.+++|.-.-.-.|.++.| ++.+ .+..+| |..++... . ....
T Consensus 193 e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrgg-qgpp~~~~sdlmay~r~GrpG~rydg~vdFs~det 271 (390)
T KOG2192|consen 193 ESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGG-QGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADET 271 (390)
T ss_pred cCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCC-CCCCCCCccccceeccCCCCCcccccccccccccc
Confidence 998887422111111 223333332222222332222 1110 000111 11111110 0 0112
Q ss_pred CCCcccCCCcc----ccccCCccc---ccCCCccccCCCCccccccceEEEEecCCcccccccCCCcchhhHHHhcCCeE
Q 006320 565 QPSKEAAGSVS----ETVKQNESE---RREDVPTVINRVPLPLVTRSTLEVVLPDYAVPKLITKSKTLLTRFSEVSLLLH 637 (650)
Q Consensus 565 ~~~~~~g~~~~----~~~~~g~~~---~~~~~~~~~~~~~~~l~t~~t~~v~IP~~~~g~vIGk~G~~I~~Ir~~SGA~i 637 (650)
|++.-.+++.+ ..-+|+... ++.+.-..-..+.+|+ +|.+|+||.+.-|.||||||++|++||+.|||.|
T Consensus 272 w~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPi---tTaQvtip~dlggsiigkggqri~~ir~esGA~I 348 (390)
T KOG2192|consen 272 WPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPI---TTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASI 348 (390)
T ss_pred CCCcCCCcCccccccccCCCCCCCCCccccccccccCCCCCce---eeeeEecccccCcceecccchhhhhhhhccCceE
Confidence 33311111000 001111110 0000001111223455 8999999999999999999999999999999999
Q ss_pred EEEE
Q 006320 638 LINL 641 (650)
Q Consensus 638 ~i~~ 641 (650)
+|.-
T Consensus 349 kide 352 (390)
T KOG2192|consen 349 KIDE 352 (390)
T ss_pred EecC
Confidence 9974
No 8
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.95 E-value=2.8e-27 Score=257.69 Aligned_cols=158 Identities=37% Similarity=0.585 Sum_probs=136.2
Q ss_pred ceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccC-
Q 006320 347 DLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLG- 425 (650)
Q Consensus 347 ~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~- 425 (650)
..++||+|+.+.+|.||||+|.+|++|+.++.++|+|.+...++.+|+|+|+|..... ..+.+++||+++++.+....
T Consensus 42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~-~~~~~~~al~ka~~~iv~~~~ 120 (485)
T KOG2190|consen 42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVEL-NLSPATDALFKAFDMIVFKLE 120 (485)
T ss_pred cceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccc-cCCchHHHHHHHHHHHhhccc
Confidence 3458999999999999999999999999999999999998999999999999953222 66778888888887766421
Q ss_pred ----------CC-CCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHH
Q 006320 426 ----------AD-KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAAR 493 (650)
Q Consensus 426 ----------~~-~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~ 493 (650)
.+ +...+++||+||.+++|+||||+|+ ||+|+++|||+|+|.++ .+|.| ++|.|+|.|++++|.
T Consensus 121 ~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~s---ter~V~IsG~~~av~ 196 (485)
T KOG2190|consen 121 EDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPNS---TERAVTISGEPDAVK 196 (485)
T ss_pred ccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCcc---cceeEEEcCchHHHH
Confidence 01 1224899999999999999999999 99999999999999865 78985 788899999999999
Q ss_pred HHHHHHHHHHHhhhhh
Q 006320 494 DALVEVTTRLRSYLYR 509 (650)
Q Consensus 494 ~A~~~I~~~l~~~~~~ 509 (650)
+|+.+|..+|.++.-+
T Consensus 197 ~al~~Is~~L~~~~~~ 212 (485)
T KOG2190|consen 197 KALVQISSRLLENPPR 212 (485)
T ss_pred HHHHHHHHHHHhcCCc
Confidence 9999999999997533
No 9
>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=1.6e-25 Score=222.50 Aligned_cols=244 Identities=22% Similarity=0.309 Sum_probs=173.7
Q ss_pred CCccEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEe---cCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHH
Q 006320 75 LMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVH---ELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALF 151 (650)
Q Consensus 75 ~~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~---~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~ 151 (650)
.+..+.++||||+..+|.||||+|++|.+|+++|||+|+++ |.+|++.||||.|.|+. +++...+.
T Consensus 35 e~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~-----------eai~av~e 103 (402)
T KOG2191|consen 35 EDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTV-----------EALNAVHE 103 (402)
T ss_pred CCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccH-----------HHHHHHHH
Confidence 44459999999999999999999999999999999999996 46999999999999973 34555566
Q ss_pred HHHHHhhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCC
Q 006320 152 LIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRD 231 (650)
Q Consensus 152 ~i~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~ 231 (650)
.|.++|.|.........+. +.| +..++...++|+||+..+|.||||+|++||.|++++||+|+|+|.+
T Consensus 104 fI~dKire~p~~~~k~v~~---~~p---------qt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqk 171 (402)
T KOG2191|consen 104 FIADKIREKPQAVAKPVDI---LQP---------QTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQK 171 (402)
T ss_pred HHHHHHHHhHHhhcCCccc---cCC---------CCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccC
Confidence 6777776654333211111 111 2234556799999999999999999999999999999999999743
Q ss_pred CCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcccCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006320 232 HSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFS 311 (650)
Q Consensus 232 ~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~ 311 (650)
|.-....||+|++.|++++..+|+.+|+++|.++++...-. + .+|. ++.+
T Consensus 172 ---pt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scl-----n--~sya----~vsG---------------- 221 (402)
T KOG2191|consen 172 ---PTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCL-----N--ISYA----NVSG---------------- 221 (402)
T ss_pred ---CCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCccccee-----c--cchh----cccC----------------
Confidence 44445789999999999999999999999999987422110 0 0000 0000
Q ss_pred CCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeC
Q 006320 312 GSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVAD 385 (650)
Q Consensus 312 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~ 385 (650)
...|+.+.-.+|....+. .+......+-++....|..-|.+|.++-.|-..+|+.+.+++
T Consensus 222 ----pvaNsnPtGspya~~~~~----------~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq 281 (402)
T KOG2191|consen 222 ----PVANSNPTGSPYAYQAHV----------LPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQ 281 (402)
T ss_pred ----cccccCCCCCCCCCCCcc----------ccccchhhccccccccccccccccccceeeecccccceeecc
Confidence 011111111111111111 012233446678888888889999999999889998777765
No 10
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.86 E-value=6.2e-21 Score=190.00 Aligned_cols=229 Identities=19% Similarity=0.257 Sum_probs=163.1
Q ss_pred CceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCC---CCCCCccEEEecCCCCCCCcchHHHHHHH-HHHHhh
Q 006320 346 EDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADP---VDGSDEQIITISSEEGPDDELFPAQEALL-HIQTRI 421 (650)
Q Consensus 346 ~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~---~~~~~er~i~I~G~~g~~~~~~~a~~ai~-~i~~~i 421 (650)
..+.++|+||...+|.||||+|++|.+||+++||+|++++. -+++.||++.|+|+- + +..+++ .|.++|
T Consensus 37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~---e----ai~av~efI~dKi 109 (402)
T KOG2191|consen 37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTV---E----ALNAVHEFIADKI 109 (402)
T ss_pred CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccH---H----HHHHHHHHHHHHH
Confidence 44899999999999999999999999999999999999876 378999999999862 2 223332 244555
Q ss_pred hccCC--C----------CCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEec
Q 006320 422 VDLGA--D----------KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGE 488 (650)
Q Consensus 422 ~~~~~--~----------~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~ 488 (650)
.+... . .+..-.++|+||.+.+|.||||||. ||.|++++||.|+|.|.+ |..-.-.+|+|++.|+
T Consensus 110 re~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqk--pt~~sLqervvt~sge 187 (402)
T KOG2191|consen 110 REKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQK--PTGISLQERVVTVSGE 187 (402)
T ss_pred HHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccC--CCCccceeEEEEecCC
Confidence 54311 0 1112348999999999999999999 999999999999999633 3333456899999999
Q ss_pred HHHHHHHHHHHHHHHHhhhhhcccccCCCCCCCCCCCCcccccCCCCCCCCCCCccCCcCCCCCCCCCCCCCCCCCCCCc
Q 006320 489 IQAARDALVEVTTRLRSYLYRDFFQKETPPSSTGPTGSALVVEAASPIDITPAREVQTVTDPPAATHQSVQIPATSQPSK 568 (650)
Q Consensus 489 ~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~ 568 (650)
+++..+|+.+|+++|.+...-.. .++ .++.. . .+ |+ ..+.+.
T Consensus 188 ~e~~~~A~~~IL~Ki~eDpqs~s---cln--~sya~----v-------sG-pv---------------------aNsnPt 229 (402)
T KOG2191|consen 188 PEQNMKAVSLILQKIQEDPQSGS---CLN--ISYAN----V-------SG-PV---------------------ANSNPT 229 (402)
T ss_pred HHHHHHHHHHHHHHhhcCCcccc---eec--cchhc----c-------cC-cc---------------------cccCCC
Confidence 99999999999999988732210 111 11110 0 00 00 011111
Q ss_pred ccCCCccccccCCcccccCCCccccCCCCccccccceEEEEecCCcccccccCCCcchhhHHHhcCCeEEEEEe
Q 006320 569 EAAGSVSETVKQNESERREDVPTVINRVPLPLVTRSTLEVVLPDYAVPKLITKSKTLLTRFSEVSLLLHLINLF 642 (650)
Q Consensus 569 ~~g~~~~~~~~~g~~~~~~~~~~~~~~~~~~l~t~~t~~v~IP~~~~g~vIGk~G~~I~~Ir~~SGA~i~i~~~ 642 (650)
++++. + ++ ..+..+++...-+|.-..|..-|.+|.++..|..++|+.+.|.-+
T Consensus 230 Gspya----~-~~----------------~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~ 282 (402)
T KOG2191|consen 230 GSPYA----Y-QA----------------HVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQA 282 (402)
T ss_pred CCCCC----C-CC----------------ccccccchhhccccccccccccccccccceeeecccccceeeccc
Confidence 11100 0 00 012234567788899999999999999999999999998888654
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=1.6e-14 Score=138.70 Aligned_cols=140 Identities=17% Similarity=0.219 Sum_probs=102.7
Q ss_pred EEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHh--hhccCCCCC
Q 006320 352 MLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTR--IVDLGADKD 429 (650)
Q Consensus 352 i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~--i~~~~~~~~ 429 (650)
+.||.++++.|||++|++|+.|+++|||+|.+.+ ++..|.|....+.++.+.+|++.|..+..- ..+...-..
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~-----~~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~A~~l~g 76 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS-----ETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKALKLLD 76 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc-----CCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHHHHhcC
Confidence 5789999999999999999999999999999975 335678831113456777777777654331 111000011
Q ss_pred CceEEE-EeecC---------CcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHH
Q 006320 430 NIITTR-LLVPS---------SEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVE 498 (650)
Q Consensus 430 ~~~~~~-l~Vp~---------~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~ 498 (650)
..++.+ +.|+. ..+|+|||++|+ ++.|++.|||+|.|. +..|.|.|++++++.|..+
T Consensus 77 d~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~------------~~~v~i~G~~~~~~~A~~~ 144 (172)
T TIGR03665 77 DDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY------------GKTVGIIGDPEQVQIAREA 144 (172)
T ss_pred CcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc------------CCEEEEECCHHHHHHHHHH
Confidence 122222 23333 368999999999 999999999999884 2569999999999999999
Q ss_pred HHHHHHhhhh
Q 006320 499 VTTRLRSYLY 508 (650)
Q Consensus 499 I~~~l~~~~~ 508 (650)
|.+++.....
T Consensus 145 i~~li~~~~~ 154 (172)
T TIGR03665 145 IEMLIEGAPH 154 (172)
T ss_pred HHHHHcCCCC
Confidence 9999866543
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=99.51 E-value=9.1e-14 Score=133.40 Aligned_cols=143 Identities=17% Similarity=0.215 Sum_probs=102.4
Q ss_pred EEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhhcCC
Q 006320 83 ILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDG 162 (650)
Q Consensus 83 ilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e~~~ 162 (650)
|.||.+.+|.|||++|++|+.|+++|||+|++.+ ++..|.|. .... ...++++|..+|.........
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~-----~~g~V~I~-~~t~-------d~~~i~kA~~~I~~i~~gf~~ 68 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS-----ETGEVKIE-EEDE-------DPLAVMKAREVVKAIGRGFSP 68 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc-----CCceEEEe-cCCC-------CHHHHHHHHHHHHHHHcCCCH
Confidence 4579999999999999999999999999999996 23568883 1101 134677887777765442111
Q ss_pred CCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEcc---------ceeeeeecCCchHHHHHHhhcCceEEEecCCCC
Q 006320 163 GGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSR---------MHVGCLLGKGGKIIEQMRMETKTQIRILPRDHS 233 (650)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~---------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~ 233 (650)
+..+. ...+ .....-+.|+. ..+|+|||++|++++.|++.|||+|.|.
T Consensus 69 e~A~~-l~gd-----------------~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~----- 125 (172)
T TIGR03665 69 EKALK-LLDD-----------------DYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY----- 125 (172)
T ss_pred HHHHH-hcCC-----------------cceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc-----
Confidence 10000 0000 11111223333 3689999999999999999999999995
Q ss_pred CCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcc
Q 006320 234 LPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQ 269 (650)
Q Consensus 234 lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~ 269 (650)
+..|.|.|++++++.|+.+|.+++...+
T Consensus 126 --------~~~v~i~G~~~~~~~A~~~i~~li~~~~ 153 (172)
T TIGR03665 126 --------GKTVGIIGDPEQVQIAREAIEMLIEGAP 153 (172)
T ss_pred --------CCEEEEECCHHHHHHHHHHHHHHHcCCC
Confidence 2579999999999999999999996653
No 13
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.50 E-value=6.6e-14 Score=135.25 Aligned_cols=144 Identities=15% Similarity=0.201 Sum_probs=104.3
Q ss_pred eEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEec-CCCCCCCcchHHHHHHHHHHH--hhhcc
Q 006320 348 LVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITIS-SEEGPDDELFPAQEALLHIQT--RIVDL 424 (650)
Q Consensus 348 ~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~-G~~g~~~~~~~a~~ai~~i~~--~i~~~ 424 (650)
....+.||.++++.|||++|++|+.|+++|||+|.+.+ ++..|.|. +....++.+.+|++.|..+.. ...+.
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~-----~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~~e~A 77 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS-----ETGEVIIEPTDGEDPLAVLKARDIVKAIGRGFSPEKA 77 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC-----CCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCHHHH
Confidence 45779999999999999999999999999999999976 23667775 111345667777777765543 11110
Q ss_pred CCCCCCceEEEE-ee----c-----CCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHH
Q 006320 425 GADKDNIITTRL-LV----P-----SSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAAR 493 (650)
Q Consensus 425 ~~~~~~~~~~~l-~V----p-----~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~ 493 (650)
.......+..++ .+ + ...+|+|||++|+ ++.|++.|||+|.|. ++.|.|.|++++++
T Consensus 78 ~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~------------~~~v~i~G~~~~~~ 145 (180)
T PRK13763 78 LRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVY------------GKTVAIIGDPEQVE 145 (180)
T ss_pred HHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEc------------CCEEEEEeCHHHHH
Confidence 000011122222 11 1 1368999999999 999999999999884 23499999999999
Q ss_pred HHHHHHHHHHHhhhh
Q 006320 494 DALVEVTTRLRSYLY 508 (650)
Q Consensus 494 ~A~~~I~~~l~~~~~ 508 (650)
.|...|..+++....
T Consensus 146 ~A~~~I~~li~g~~~ 160 (180)
T PRK13763 146 IAREAIEMLIEGAPH 160 (180)
T ss_pred HHHHHHHHHHcCCCc
Confidence 999999999876643
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.48 E-value=3.2e-13 Score=130.55 Aligned_cols=146 Identities=18% Similarity=0.183 Sum_probs=104.9
Q ss_pred EEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhh
Q 006320 79 TTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRIL 158 (650)
Q Consensus 79 ~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~ 158 (650)
+...+.||.+.++.|||++|++|+.|+++|||+|++.+. +..|.|+-.... ....+++|..+|.....
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~-------d~~~i~kA~~~I~ai~~ 70 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGE-------DPLAVLKARDIVKAIGR 70 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCC-------CHHHHHHHHHHHHHHhc
Confidence 567889999999999999999999999999999999972 356777611100 13467788877776654
Q ss_pred hcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEE-EEc---------cceeeeeecCCchHHHHHHhhcCceEEEe
Q 006320 159 ESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRM-VVS---------RMHVGCLLGKGGKIIEQMRMETKTQIRIL 228 (650)
Q Consensus 159 e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i-~Vp---------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~ 228 (650)
..+.+..+. ... ..+..++ .+. ...+|+|||++|++++.|++.|||+|.|.
T Consensus 71 gf~~e~A~~-l~g------------------d~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~ 131 (180)
T PRK13763 71 GFSPEKALR-LLD------------------DDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVY 131 (180)
T ss_pred CCCHHHHHH-HhC------------------CCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEc
Confidence 211110000 000 1111111 111 13689999999999999999999999995
Q ss_pred cCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320 229 PRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES 268 (650)
Q Consensus 229 ~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~ 268 (650)
. ..|.|.|++++++.|...|..+++..
T Consensus 132 ~-------------~~v~i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 132 G-------------KTVAIIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred C-------------CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence 2 34899999999999999999999665
No 15
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.33 E-value=1.7e-11 Score=141.77 Aligned_cols=330 Identities=15% Similarity=0.165 Sum_probs=201.5
Q ss_pred CCccEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCC----------------C---
Q 006320 75 LMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRR----------------D--- 135 (650)
Q Consensus 75 ~~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~----------------~--- 135 (650)
....+..++.+....+..+||++|.+++.++.++.+.|.|++.....+ ...+.+...+ .
T Consensus 197 ~~r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~~--~~~i~~~~~~~~~~~~~i~~~~~~le~~~~ 274 (753)
T KOG2208|consen 197 NERSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSSP--SNKIDGRLNSSSSINVEIQEALTRLESEFD 274 (753)
T ss_pred cceeEEEEeeccccchhhhccccccccccccccceeEEEcccccccch--hhhhccccccceehhhhhHHHHHHhcChhh
Confidence 444578889999999999999999999999999999999986422111 1111111100 0
Q ss_pred ------------CCCC-CCCccHHHHHHHHHHHHhhhcCCCC---CCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEc
Q 006320 136 ------------PEGR-MPSFSPAQEALFLIHDRILESDGGG---GFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVS 199 (650)
Q Consensus 136 ------------~~~~-~~~~~~a~~A~~~i~~~i~e~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp 199 (650)
..+. ...+..+....-.+.-......... .....+.......+.....-..-....+.+.+.+.
T Consensus 275 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~ 354 (753)
T KOG2208|consen 275 YDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIF 354 (753)
T ss_pred hhhhhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeec
Confidence 0000 0012222222222111111100000 00000000000000000000000134467888899
Q ss_pred cceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcccCCCCCCCCC
Q 006320 200 RMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGR 279 (650)
Q Consensus 200 ~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~ 279 (650)
...+..++||+|.+|++|++++.|.|.+... .+.+..+.++|...++.+|...+...+.+...
T Consensus 355 ~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n--------- 417 (753)
T KOG2208|consen 355 PEELKFVIGKKGANIEKIREESQVKIDLPKQ--------GSNNKKVVITGVSANDEKAVEDVEKIIAEILN--------- 417 (753)
T ss_pred HHhhhhhcCCCCccHHHHHHhhhhceecccc--------cCCCCCeEEeccccchhHHHHHHHHHHHhhhc---------
Confidence 9999999999999999999999999999642 15678899999999999999999999988631
Q ss_pred CCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCceEEEEEeecccc
Q 006320 280 LHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKV 359 (650)
Q Consensus 280 ~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~v 359 (650)
......+.+|...+
T Consensus 418 ------------------------------------------------------------------~~~~~~~~iP~k~~ 431 (753)
T KOG2208|consen 418 ------------------------------------------------------------------SIVKEEVQIPTKSH 431 (753)
T ss_pred ------------------------------------------------------------------ccccceeecCccch
Confidence 02234588999999
Q ss_pred cceecCCchhHHHHHHHhC-CeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccCCCCCCceEEEEee
Q 006320 360 GRVIGESEGIVELLQNEIG-VDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTRLLV 438 (650)
Q Consensus 360 g~IIGk~G~~Ik~l~~~tg-a~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~~~~~~~~~~l~V 438 (650)
..|||.+|..|..|..+++ +.|.+.. ..+.....++.+. ...+..++..+..+.....+ ......++...+.
T Consensus 432 ~~iig~~g~~i~~I~~k~~~v~i~f~~--~~~~~~~~~~~~~---~~dv~~~~~~~~~~~~~a~~--~~~~~~~~~d~~~ 504 (753)
T KOG2208|consen 432 KRIIGTKGALINYIMGKHGGVHIKFQN--NNNSSDMVTIRGI---SKDVEKSVSLLKALKADAKN--LKFRDVVTKDKLL 504 (753)
T ss_pred hhhhccccccHHHHHhhcCcEEEecCC--CCcccccceEecc---ccccchhHHHHHhhhhhhhc--chhhhhhhccccc
Confidence 9999999999999999999 6666654 3444455556643 22233322222222111111 0122346667788
Q ss_pred cCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320 439 PSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY 506 (650)
Q Consensus 439 p~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 506 (650)
|..+.+..+|+.|. +....+.....+ .+ ..+...++|.|..+.|.+|...+..++...
T Consensus 505 ~~~~~~~~~g~~~~i~d~~~~~~i~~~----~~------~~~~~~i~i~gk~~~v~~a~~~L~~~~~~~ 563 (753)
T KOG2208|consen 505 PVKYIGKEIGKNGTIRDSLGDKSIFPP----NE------DEDHEKITIEGKLELVLEAPAELKALIEAL 563 (753)
T ss_pred hHHhhcccccCceeeeccCCceeeccc----cc------ccccceeeecccccchhhhHHHHHhcchhh
Confidence 88888888888777 455555444333 32 134667999999999999988887766554
No 16
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.29 E-value=1.7e-11 Score=141.81 Aligned_cols=391 Identities=16% Similarity=0.165 Sum_probs=238.7
Q ss_pred EEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhh
Q 006320 79 TTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRIL 158 (650)
Q Consensus 79 ~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~ 158 (650)
....+-+...+...|+||+|.+|.+|++++.|.|.+++. +..+..+.+++.. ...++|...+...+.
T Consensus 347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~-----------~~~~ka~~~v~~~~~ 413 (753)
T KOG2208|consen 347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVS-----------ANDEKAVEDVEKIIA 413 (753)
T ss_pred eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccc-----------cchhHHHHHHHHHHH
Confidence 556666788899999999999999999999999999984 5677778888853 345666666666665
Q ss_pred hcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcC-ceEEEecCCCCCCCc
Q 006320 159 ESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETK-TQIRILPRDHSLPRC 237 (650)
Q Consensus 159 e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tg-a~I~i~~~~~~lp~~ 237 (650)
+.. .......+.+|...+.+|||.+|+.|+.|..+++ ..|..... .
T Consensus 414 ei~---------------------------n~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~-~----- 460 (753)
T KOG2208|consen 414 EIL---------------------------NSIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN-N----- 460 (753)
T ss_pred hhh---------------------------cccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC-C-----
Confidence 431 1134667899999999999999999999999999 55555321 1
Q ss_pred cCCCcceEEEEcCHHHHHHHHHHHHHHHhhcccCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006320 238 VSMSEEIVQVVGDINNVKNAVAIISSRLRESQHRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSNYRS 317 (650)
Q Consensus 238 ~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~ 317 (650)
.....+++.|....|..++.++..+.........
T Consensus 461 --~~~~~~~~~~~~~dv~~~~~~~~~~~~~a~~~~~-------------------------------------------- 494 (753)
T KOG2208|consen 461 --NSSDMVTIRGISKDVEKSVSLLKALKADAKNLKF-------------------------------------------- 494 (753)
T ss_pred --cccccceEeccccccchhHHHHHhhhhhhhcchh--------------------------------------------
Confidence 3345678888888888877777766654321000
Q ss_pred CCCCCCCCCCCccCCCCCCCCCCCCCCCCceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEe
Q 006320 318 NNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITI 397 (650)
Q Consensus 318 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I 397 (650)
-...+...+.|..+.+..+|+.|..+..+.++..+.+.. ..++..++|
T Consensus 495 ---------------------------~~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~~~i~~~~~-----~~~~~~i~i 542 (753)
T KOG2208|consen 495 ---------------------------RDVVTKDKLLPVKYIGKEIGKNGTIRDSLGDKSIFPPNE-----DEDHEKITI 542 (753)
T ss_pred ---------------------------hhhhhccccchHHhhcccccCceeeeccCCceeeccccc-----ccccceeee
Confidence 022344566788888888888887777666666554433 235678888
Q ss_pred cCCCCCCCcchHHHHHHHHHHHhhhccCCCCCCceEEEEeecCCccee-eecCCCch-hhhhhhcCceEEEecCCCCCCC
Q 006320 398 SSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTRLLVPSSEIGC-LEGRDGSL-SEMRRSTGANIQILSREEVPAC 475 (650)
Q Consensus 398 ~G~~g~~~~~~~a~~ai~~i~~~i~~~~~~~~~~~~~~l~Vp~~~~g~-IIGkgG~I-k~I~~~Tga~I~i~~~~~~p~~ 475 (650)
.|. .+.+..+..+|..+...+.+ ...+.+.+|..++-. +++++... +..+...|+.+.++...
T Consensus 543 ~gk---~~~v~~a~~~L~~~~~~~~~-------~~~~~v~~~~~~~~~~l~~~~~~~~~~~e~~~gv~~~fp~~~----- 607 (753)
T KOG2208|consen 543 EGK---LELVLEAPAELKALIEALIK-------ATLLEVNNPPGQHRPFLIGKGIENRTYVEVFGGVVVPFPRSP----- 607 (753)
T ss_pred ccc---ccchhhhHHHHHhcchhhhh-------hhhhhccCcchheeeeeeccccccccceeecCcccccCCCCC-----
Confidence 865 34455555555433222221 234456666666554 55555555 55666666788554321
Q ss_pred CCCCCeEEEEEecHHHHHHHHHHHHHHHHhhhhhcc----cccCCCCCCCCCCCCcccccCCCCCCCCCCCccCCcCCCC
Q 006320 476 VSGTDELVQIVGEIQAARDALVEVTTRLRSYLYRDF----FQKETPPSSTGPTGSALVVEAASPIDITPAREVQTVTDPP 551 (650)
Q Consensus 476 ~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p 551 (650)
.+.+.++|.|....++.|...+.+.+....--.. .....+..+...++ +.+. ...
T Consensus 608 --~~~~e~~i~g~~~~v~aa~~~~~~i~~~~~~~~~~~~~i~~~~~~~~~~~~g------~~~~-~~t------------ 666 (753)
T KOG2208|consen 608 --TSSDEVSIKGAKDEVKAAKGRLEEIVEYLSAYATTNTKIPDKFHRSIVGYRG------HIIE-EIT------------ 666 (753)
T ss_pred --CchhhhccchhHHHHHHhhccchhhhhhcccccceeeecccccceeeecCCC------cccc-cce------------
Confidence 2233589999999999998888877765422111 11112222211111 1110 000
Q ss_pred CCCCCCCCCCCCCCCCcccCCCc--cccccCCcccccCCCccccCCCCccccccceEEEEecCCcccccccCCCcchhhH
Q 006320 552 AATHQSVQIPATSQPSKEAAGSV--SETVKQNESERREDVPTVINRVPLPLVTRSTLEVVLPDYAVPKLITKSKTLLTRF 629 (650)
Q Consensus 552 ~~~~~~~~~~~~~~~~~~~g~~~--~~~~~~g~~~~~~~~~~~~~~~~~~l~t~~t~~v~IP~~~~g~vIGk~G~~I~~I 629 (650)
..|...+-.+.. .+...+ .....+.......+++.......|.++.||.++++.+||.+|+++.++
T Consensus 667 -----------~~~~~~~~~~~~~~~~s~~~-~~~~~~~~~~e~~~~~~~~~~~~~~~~~~p~~~~~~~ig~~g~~~r~~ 734 (753)
T KOG2208|consen 667 -----------SKFGVGGYFGDAPTEGSVNT-IHVSGEKMQSEIAKIALEAKNLVTKEIEIPRSLHRYLIGPKGSNLRQL 734 (753)
T ss_pred -----------eecCccceeCCCCCccccCc-chhhhhhhhhhhcccccccccceeeEEeccHHHhhhccCCCCccHHHH
Confidence 001000000000 000000 000111111222222222223479999999999999999999999999
Q ss_pred HHhcCCeEEEEE
Q 006320 630 SEVSLLLHLINL 641 (650)
Q Consensus 630 r~~SGA~i~i~~ 641 (650)
=...+..+.+.-
T Consensus 735 ~~~~~~~~~~~~ 746 (753)
T KOG2208|consen 735 EKEFNVNIVVPN 746 (753)
T ss_pred HHHhccceecCC
Confidence 999888776653
No 17
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.24 E-value=1.5e-11 Score=98.73 Aligned_cols=63 Identities=41% Similarity=0.657 Sum_probs=56.5
Q ss_pred EEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHH
Q 006320 433 TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEV 499 (650)
Q Consensus 433 ~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I 499 (650)
+++|+||.+.+|+|||++|+ |++|+++|||+|++.+.+. + ..++|+|+|+|+++++++|+.+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~-~---~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-P---GSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-C---CCCceEEEEEeCHHHHHHHHHhh
Confidence 47899999999999999999 9999999999999976443 1 35789999999999999999987
No 18
>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=99.18 E-value=5.9e-11 Score=95.22 Aligned_cols=64 Identities=30% Similarity=0.533 Sum_probs=57.2
Q ss_pred EEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHH
Q 006320 193 ATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAII 261 (650)
Q Consensus 193 ~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I 261 (650)
+.+|+||..++++|||++|++|++|+++|||+|.+.+... ....+|+|+|+|++++|.+|+.+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~-----~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-----PGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-----CCCCceEEEEEeCHHHHHHHHHhh
Confidence 3689999999999999999999999999999999985322 236789999999999999999987
No 19
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.07 E-value=2.5e-10 Score=121.99 Aligned_cols=231 Identities=20% Similarity=0.292 Sum_probs=168.2
Q ss_pred CCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320 189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES 268 (650)
Q Consensus 189 ~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~ 268 (650)
...+.++++|+...|.+++|+.|++|+.|+..++++|.+.+.+ . ..++.-.+.|-+.+|..|+..+..++.+.
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 4778899999999999999999999999999999999997632 1 33555566668999999999999998776
Q ss_pred ccCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCce
Q 006320 269 QHRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDL 348 (650)
Q Consensus 269 ~~~~~~~~~~~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~ 348 (650)
. .+
T Consensus 138 ~-----------------------------------------------------------------------------pv 140 (608)
T KOG2279|consen 138 T-----------------------------------------------------------------------------PV 140 (608)
T ss_pred C-----------------------------------------------------------------------------cc
Confidence 3 12
Q ss_pred EEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHH-------HHHhh
Q 006320 349 VFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLH-------IQTRI 421 (650)
Q Consensus 349 ~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~-------i~~~i 421 (650)
...+.+|...+++|+|++|++++.++.-++++|.+.......-.+.+.|.+.... ...|+..+.. +.+.+
T Consensus 141 k~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~---~~~a~~~~~~~~~edeelv~~~ 217 (608)
T KOG2279|consen 141 SEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKE---VAAAKHLILEKVSEDEELVKRI 217 (608)
T ss_pred cccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccch---HHHHHhhhhccccchhHHhhhc
Confidence 3345578999999999999999999999999999987644445678888864321 1222222221 11111
Q ss_pred hccC------------------------------------C--------------------------------CCCCceE
Q 006320 422 VDLG------------------------------------A--------------------------------DKDNIIT 433 (650)
Q Consensus 422 ~~~~------------------------------------~--------------------------------~~~~~~~ 433 (650)
.+.. . .++....
T Consensus 218 ~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i 297 (608)
T KOG2279|consen 218 AESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAI 297 (608)
T ss_pred hhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCcccccccccccccc
Confidence 1000 0 0112344
Q ss_pred EEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCC--CCeEEEEEecHHHHHHHHHHHHHHHHhhhhhc
Q 006320 434 TRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSG--TDELVQIVGEIQAARDALVEVTTRLRSYLYRD 510 (650)
Q Consensus 434 ~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~--~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~~ 510 (650)
-.|.+|..++|.|||+.|+ |+.+...+++.+.|.. .|-. +. .-.++++.|+..-+..|+.++..+.-...+.+
T Consensus 298 ~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t---~pyt-~~v~~~qic~~egkqh~~n~vl~ml~~~~p~~~f~e 373 (608)
T KOG2279|consen 298 PEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWT---QPYT-SRVLQLQICVNEGKQHYENSVLEMLTVHVPDIVFAE 373 (608)
T ss_pred ceeecCcccccchhhhhhhhhhhhhhccCccceEEe---cccc-chhhhhhhheecchhHHHHHHHhhhhccCCcccccc
Confidence 5788999999999999999 9999999999998873 2220 11 12458899999999999998886555555554
No 20
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.05 E-value=1.5e-09 Score=116.24 Aligned_cols=144 Identities=23% Similarity=0.398 Sum_probs=114.9
Q ss_pred CceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccC
Q 006320 346 EDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLG 425 (650)
Q Consensus 346 ~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~ 425 (650)
+++..++.|+.+.+..+||+.|++|+.|++.++++|.+.+. .-.+++..++.| .+..+.+|+.++.+...
T Consensus 66 k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~e-d~g~e~~~~~~~---~p~~v~~a~a~~~~~~~------ 135 (608)
T KOG2279|consen 66 KDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTE-DVGDERVLLISG---FPVQVCKAKAAIHQILT------ 135 (608)
T ss_pred hheeeeEeecccceeeeeccccCCcchhhcccccceecCcc-cCCcccchhhcc---CCCCCChHHHHHHHHHh------
Confidence 67899999999999999999999999999999999999653 233456667765 35567777776654332
Q ss_pred CCCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHH
Q 006320 426 ADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLR 504 (650)
Q Consensus 426 ~~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~ 504 (650)
.+..+...+.||+..+++|+|++|. +++|+..++|+|.+.... .| .-++..+|.|....++.|..++.+++.
T Consensus 136 --~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ng---r~--g~~~~~~i~~qqk~~~~a~~~~~~~~~ 208 (608)
T KOG2279|consen 136 --ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNG---RL--GLSRLIKISGQQKEVAAAKHLILEKVS 208 (608)
T ss_pred --cCCcccccccchhhhcccccccchhhhcchhccccccccccccc---cc--ccccceecccccchHHHHHhhhhcccc
Confidence 2346788899999999999999999 999999999999875321 22 346778888888888899999988875
Q ss_pred hh
Q 006320 505 SY 506 (650)
Q Consensus 505 ~~ 506 (650)
+.
T Consensus 209 ed 210 (608)
T KOG2279|consen 209 ED 210 (608)
T ss_pred ch
Confidence 43
No 21
>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=99.04 E-value=2.8e-10 Score=90.39 Aligned_cols=60 Identities=18% Similarity=0.335 Sum_probs=53.4
Q ss_pred EEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHH
Q 006320 434 TRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVT 500 (650)
Q Consensus 434 ~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~ 500 (650)
.+|.||.+++++|||++|+ |++|+++|||+|+|++.+ +.++.|+|+|+.++|..|+.+|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-------~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-------SKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-------CCCCEEEEEcCHHHHHHHHHHhC
Confidence 5789999999999999999 999999999999987433 35778999999999999998873
No 22
>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=98.99 E-value=2.4e-10 Score=90.13 Aligned_cols=59 Identities=34% Similarity=0.523 Sum_probs=52.6
Q ss_pred EEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHH
Q 006320 433 TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEV 499 (650)
Q Consensus 433 ~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I 499 (650)
|++|.||.+++++|||++|+ |++|+++|||+|+|... +....|+|+|++++|++|+.+|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~--------~~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD--------DERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--------TEEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--------CCcEEEEEEeCHHHHHHHHhhC
Confidence 67899999999999999999 99999999999999632 1245799999999999999886
No 23
>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=98.98 E-value=6.6e-10 Score=88.24 Aligned_cols=61 Identities=21% Similarity=0.304 Sum_probs=54.9
Q ss_pred EEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHH
Q 006320 194 TRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIIS 262 (650)
Q Consensus 194 ~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~ 262 (650)
.+|.||..++++|||++|++|++|+++|||+|.|.+.. ..++.|+|+|+.++|.+|+.+|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--------~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--------SKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--------CCCCEEEEEcCHHHHHHHHHHhC
Confidence 57899999999999999999999999999999997531 45789999999999999998873
No 24
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.98 E-value=1.5e-09 Score=85.77 Aligned_cols=57 Identities=25% Similarity=0.335 Sum_probs=51.3
Q ss_pred eEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEec-HHHHHHHHHHH
Q 006320 432 ITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGE-IQAARDALVEV 499 (650)
Q Consensus 432 ~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I 499 (650)
....+.||.+.+|+|||++|+ |++|+++|||+|.|.. ++.|.|+|+ .++++.|+.+|
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 467889999999999999999 9999999999998842 457999998 99999999887
No 25
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.95 E-value=2.9e-09 Score=84.16 Aligned_cols=58 Identities=22% Similarity=0.318 Sum_probs=52.7
Q ss_pred EEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcC-HHHHHHHHHHH
Q 006320 192 VATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGD-INNVKNAVAII 261 (650)
Q Consensus 192 ~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~-~~~V~~A~~~I 261 (650)
+...+.||..++++|||++|++|++|+++|||+|.|.. ++.|.|+|+ .+++++|+.+|
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 46789999999999999999999999999999999952 357999998 99999999887
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=98.94 E-value=9.7e-10 Score=86.67 Aligned_cols=60 Identities=30% Similarity=0.449 Sum_probs=54.0
Q ss_pred EEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHH
Q 006320 193 ATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAII 261 (650)
Q Consensus 193 ~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I 261 (650)
|.+|.||..++++|||++|++|++|+++|||+|.|... ..+..|+|+|+.++|++|+.+|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~---------~~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD---------DERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST---------TEEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC---------CCcEEEEEEeCHHHHHHHHhhC
Confidence 57899999999999999999999999999999999642 1345999999999999999886
No 27
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.90 E-value=4.1e-09 Score=84.00 Aligned_cols=61 Identities=36% Similarity=0.569 Sum_probs=54.1
Q ss_pred EEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHH
Q 006320 434 TRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEV 499 (650)
Q Consensus 434 ~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I 499 (650)
.+|.||.+++++|||++|+ |++|+++|||+|.|..... .+.++.|+|.|..++++.|+.+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~-----~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-----GSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC-----CCCceEEEEEcCHHHHHHHHHHh
Confidence 6799999999999999999 9999999999999975332 34688899999999999999876
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=98.86 E-value=8.4e-09 Score=82.21 Aligned_cols=62 Identities=34% Similarity=0.549 Sum_probs=55.4
Q ss_pred EEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHH
Q 006320 194 TRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAII 261 (650)
Q Consensus 194 ~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I 261 (650)
.+|.||..++++|||++|++|++|+++|||+|.|.+... ...++.|.|.|..+++..|+.+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~------~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS------GSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC------CCCceEEEEEcCHHHHHHHHHHh
Confidence 679999999999999999999999999999999975321 25688999999999999999876
No 29
>PF13014 KH_3: KH domain
Probab=98.79 E-value=9.9e-09 Score=75.11 Aligned_cols=42 Identities=45% Similarity=0.716 Sum_probs=38.6
Q ss_pred ccceeecCCChHHHHHHHHhCCeEEEec-CCCCCCccEEEEec
Q 006320 89 KAGGVIGKSGSIIKSIRQHTGAWINVHE-LIPGDEERIIEISD 130 (650)
Q Consensus 89 ~vg~IIGk~G~~Ik~I~~~tga~I~v~~-~~~~~~ervi~I~G 130 (650)
++|+|||++|++|++|+++|+|+|+|++ ..++..+++|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 5799999999999999999999999998 56678999999987
No 30
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.63 E-value=1e-07 Score=90.90 Aligned_cols=139 Identities=21% Similarity=0.343 Sum_probs=100.5
Q ss_pred CceEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCC--cchHHHHHHHHHHH----
Q 006320 346 EDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDD--ELFPAQEALLHIQT---- 419 (650)
Q Consensus 346 ~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~--~~~~a~~ai~~i~~---- 419 (650)
....+.+.||.+..+.+||+.|++.+.|.+.+++++.+.. .+..|+|..++.+.| ...+|.+.+..|-.
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~-----~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~p 80 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS-----KTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPP 80 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC-----CCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCH
Confidence 3456779999999999999999999999999999999954 557788876643333 33444444432211
Q ss_pred ----hhhccCCCCCCceEEEE-----eec------CCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEE
Q 006320 420 ----RIVDLGADKDNIITTRL-----LVP------SSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELV 483 (650)
Q Consensus 420 ----~i~~~~~~~~~~~~~~l-----~Vp------~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v 483 (650)
++.+ + .+.+.+ ++- ....|+|||++|. -+-|++.|||.|-|. +..|
T Consensus 81 e~A~~LL~-----d-~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~------------g~tV 142 (194)
T COG1094 81 EKALKLLE-----D-DYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY------------GKTV 142 (194)
T ss_pred HHHHHHhc-----C-CcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe------------CcEE
Confidence 0111 1 111111 111 2245999999999 888999999999885 4569
Q ss_pred EEEecHHHHHHHHHHHHHHHHhhh
Q 006320 484 QIVGEIQAARDALVEVTTRLRSYL 507 (650)
Q Consensus 484 ~I~G~~~~v~~A~~~I~~~l~~~~ 507 (650)
.|.|.+++|+.|.+.|..++....
T Consensus 143 aiiG~~~~v~iAr~AVemli~G~~ 166 (194)
T COG1094 143 AIIGGFEQVEIAREAVEMLINGAP 166 (194)
T ss_pred EEecChhhhHHHHHHHHHHHcCCC
Confidence 999999999999999999887653
No 31
>smart00322 KH K homology RNA-binding domain.
Probab=98.60 E-value=1.9e-07 Score=74.67 Aligned_cols=66 Identities=24% Similarity=0.465 Sum_probs=57.8
Q ss_pred ceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHH
Q 006320 431 IITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRL 503 (650)
Q Consensus 431 ~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l 503 (650)
..+.++.||...+++|||++|+ |++|++.||++|.+.... .....|.|.|+.++++.|..+|.+.+
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 3678899999999999999999 999999999999885321 14678999999999999999998876
No 32
>PF13014 KH_3: KH domain
Probab=98.59 E-value=8.5e-08 Score=70.16 Aligned_cols=42 Identities=29% Similarity=0.610 Sum_probs=38.1
Q ss_pred cccceecCCchhHHHHHHHhCCeEEEeC-CCCCCCccEEEecC
Q 006320 358 KVGRVIGESEGIVELLQNEIGVDLKVAD-PVDGSDEQIITISS 399 (650)
Q Consensus 358 ~vg~IIGk~G~~Ik~l~~~tga~I~i~~-~~~~~~er~i~I~G 399 (650)
+|++|||++|++|++|+++|||+|.|++ ..++..++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 5799999999999999999999999988 45777889999986
No 33
>smart00322 KH K homology RNA-binding domain.
Probab=98.53 E-value=4.9e-07 Score=72.27 Aligned_cols=66 Identities=30% Similarity=0.504 Sum_probs=58.9
Q ss_pred EEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHH
Q 006320 192 VATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRL 265 (650)
Q Consensus 192 ~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l 265 (650)
.+.++.||..+++.|||++|++|++|++.||++|.+.... .....|.|.|..+++..|..+|.+.+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~--------~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG--------SEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC--------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 5788999999999999999999999999999999996421 24688999999999999999998876
No 34
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.45 E-value=1e-06 Score=84.14 Aligned_cols=148 Identities=19% Similarity=0.241 Sum_probs=102.5
Q ss_pred cEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCC-CCCCCCCCCccHHHHHHHHHHHH
Q 006320 78 TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRR-RDPEGRMPSFSPAQEALFLIHDR 156 (650)
Q Consensus 78 ~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~-~~~~~~~~~~~~a~~A~~~i~~~ 156 (650)
...+.+.||...++.+||+.|++.+.|.+.++++|.++. .+..|.|..+.. .+| ....+|...|...
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~-----~~~~V~i~~~~~t~Dp-------~~~~ka~d~VkAI 74 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS-----KTGSVTIRTTRKTEDP-------LALLKARDVVKAI 74 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC-----CCCeEEEEecCCCCCh-------HHHHHHHHHHHHH
Confidence 356778999999999999999999999999999999985 567788887632 122 2234444333221
Q ss_pred hhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEE-E----EEc------cceeeeeecCCchHHHHHHhhcCceE
Q 006320 157 ILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATR-M----VVS------RMHVGCLLGKGGKIIEQMRMETKTQI 225 (650)
Q Consensus 157 i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-i----~Vp------~~~vg~IIGk~G~~Ik~I~~~tga~I 225 (650)
=.-.+++..+.- . ...+.+. | ++- ....|+|||++|.+-+.|++.|+|.|
T Consensus 75 grGF~pe~A~~L-L------------------~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I 135 (194)
T COG1094 75 GRGFPPEKALKL-L------------------EDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYI 135 (194)
T ss_pred hcCCCHHHHHHH-h------------------cCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeE
Confidence 111111000000 0 0011111 1 111 12369999999999999999999999
Q ss_pred EEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcc
Q 006320 226 RILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQ 269 (650)
Q Consensus 226 ~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~ 269 (650)
.|. ...|.|-|.+++|+.|+.+|..++....
T Consensus 136 ~V~-------------g~tVaiiG~~~~v~iAr~AVemli~G~~ 166 (194)
T COG1094 136 SVY-------------GKTVAIIGGFEQVEIAREAVEMLINGAP 166 (194)
T ss_pred EEe-------------CcEEEEecChhhhHHHHHHHHHHHcCCC
Confidence 997 3479999999999999999999998764
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=98.00 E-value=2.5e-05 Score=70.32 Aligned_cols=65 Identities=18% Similarity=0.203 Sum_probs=46.8
Q ss_pred cccceeecCCChHHHHHHHHhCCeEEEecCCC-----------------CCCccEEEEecCCCCCCCCCCCCccHHHHHH
Q 006320 88 MKAGGVIGKSGSIIKSIRQHTGAWINVHELIP-----------------GDEERIIEISDTRRRDPEGRMPSFSPAQEAL 150 (650)
Q Consensus 88 ~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~-----------------~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~ 150 (650)
.++|.|||++|++||+|+++|||+|.|..... ..+.-.|.|++..- +..++++|+
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~--------~~e~~~~A~ 86 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETP--------PEEALAKAV 86 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCc--------HHHHHHHHH
Confidence 67999999999999999999999999975310 01235688888530 124567777
Q ss_pred HHHHHHhhhc
Q 006320 151 FLIHDRILES 160 (650)
Q Consensus 151 ~~i~~~i~e~ 160 (650)
.+|...+.+.
T Consensus 87 ~~I~~ll~~~ 96 (120)
T cd02395 87 EAIEELLKPA 96 (120)
T ss_pred HHHHHHhccC
Confidence 7777666543
No 36
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=97.96 E-value=2.1e-05 Score=70.69 Aligned_cols=66 Identities=24% Similarity=0.360 Sum_probs=50.6
Q ss_pred CcceeeecCCCc-hhhhhhhcCceEEEecCCCC-----------CCCCCCCC-eEEEEEec---HHHHHHHHHHHHHHHH
Q 006320 441 SEIGCLEGRDGS-LSEMRRSTGANIQILSREEV-----------PACVSGTD-ELVQIVGE---IQAARDALVEVTTRLR 504 (650)
Q Consensus 441 ~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~-----------p~~~~~~~-r~v~I~G~---~~~v~~A~~~I~~~l~ 504 (650)
+++|.|||.+|+ ||+|+++|||+|.|..+... |.....++ -.|.|++. .+++++|+.+|..+|.
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 567999999999 99999999999999754211 11111222 34999996 4999999999999988
Q ss_pred hh
Q 006320 505 SY 506 (650)
Q Consensus 505 ~~ 506 (650)
..
T Consensus 95 ~~ 96 (120)
T cd02395 95 PA 96 (120)
T ss_pred cC
Confidence 54
No 37
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.95 E-value=3.4e-05 Score=77.81 Aligned_cols=155 Identities=22% Similarity=0.285 Sum_probs=106.5
Q ss_pred ccEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHH
Q 006320 77 VTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDR 156 (650)
Q Consensus 77 ~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~ 156 (650)
..++...-+|..+++.|.|++|.+||.|+.+|...|+-+. ..+|-+..++|.. +.|..|. +.
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPs---r~eePiF~vTg~~-----------edv~~aR----re 85 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPS---RGEEPIFPVTGRH-----------EDVRRAR----RE 85 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCC---CCCCCcceeccCc-----------hhHHHHh----hc
Confidence 5688888889999999999999999999999999999875 3466788888853 2344443 33
Q ss_pred hhhcCCCCCCCCCcccccCCCCCCCCCCCCC-CCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCC
Q 006320 157 ILESDGGGGFYGEEEEEYGGGGGVGGGGFRG-GGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLP 235 (650)
Q Consensus 157 i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp 235 (650)
|......++..... +..++|-... .....+...-+|...+++|.|.+|++|++|++.++..|.-.-+
T Consensus 86 i~saaeH~~l~~~s-------~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~----- 153 (394)
T KOG2113|consen 86 IPSAAEHFGLIRAS-------RSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR----- 153 (394)
T ss_pred Cccccceeeeeeec-------ccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc-----
Confidence 32222122110000 0111111111 1345677788899999999999999999999999988866422
Q ss_pred CccCCCcceEEEEcCHHH-HHHHH-HHHHHHH
Q 006320 236 RCVSMSEEIVQVVGDINN-VKNAV-AIISSRL 265 (650)
Q Consensus 236 ~~~~~~er~V~I~G~~~~-V~~A~-~~I~~~l 265 (650)
..+.+..++|...+ +++|. ..|...+
T Consensus 154 ----~~~~Vf~Vtg~~~nC~kra~s~eie~ta 181 (394)
T KOG2113|consen 154 ----CGEPVFCVTGAPKNCVKRARSCEIEQTA 181 (394)
T ss_pred ----CCCceEEEecCCcchhhhccccchhhhh
Confidence 34678899998777 66666 4555544
No 38
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.71 E-value=0.00011 Score=67.98 Aligned_cols=103 Identities=19% Similarity=0.212 Sum_probs=71.2
Q ss_pred EEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhh
Q 006320 80 TYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILE 159 (650)
Q Consensus 80 ~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e 159 (650)
.+-|+++...+|..||++|++|+.|++..|-+|+|-+-.. ++...|...+..
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~----------------------------d~~~fI~n~l~P 84 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSD----------------------------DPEEFIKNIFAP 84 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCC----------------------------CHHHHHHHHcCC
Confidence 5677889999999999999999999999998888765210 122222222221
Q ss_pred cCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEe
Q 006320 160 SDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRIL 228 (650)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~ 228 (650)
...... .. ..........+.|+....+.+|||+|.+|+.++.-++-.+.|.
T Consensus 85 a~V~~v-------~I-----------~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 85 AAVRSV-------TI-----------KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred CEEEEE-------EE-----------EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 110000 00 0001234677889999999999999999999999999888764
No 39
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.61 E-value=0.00011 Score=74.28 Aligned_cols=141 Identities=22% Similarity=0.277 Sum_probs=102.4
Q ss_pred CcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhcc
Q 006320 190 NRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRESQ 269 (650)
Q Consensus 190 ~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~ 269 (650)
..++..+.||..+|+.+.|++|.+||.|+.+|.+.|.-..+ ..+.+..++|..+.|+.|++.|...-+...
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr---------~eePiF~vTg~~edv~~aRrei~saaeH~~ 94 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---------GEEPIFPVTGRHEDVRRARREIPSAAEHFG 94 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCC---------CCCCcceeccCchhHHHHhhcCccccceee
Confidence 67889999999999999999999999999999999977543 235688899999999999988766332221
Q ss_pred cCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCceE
Q 006320 270 HRDRSHFHGRLHSPDRFFPDDDYVPHMNNTARRPSMDGARFSGSNYRSNNYGPRPSGYSIEAGAAPMSDSVQPFYGEDLV 349 (650)
Q Consensus 270 ~~~~~~~~~~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 349 (650)
... + ..+|. + ...++. ...+.+
T Consensus 95 l~~---~------s~s~S------------------------g----------g~~~~s---------------~s~qt~ 116 (394)
T KOG2113|consen 95 LIR---A------SRSFS------------------------G----------GTNGAS---------------ASGQTT 116 (394)
T ss_pred eee---e------ccccc------------------------C----------CCcccc---------------ccCCCc
Confidence 000 0 00000 0 000110 014566
Q ss_pred EEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCC
Q 006320 350 FRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSE 400 (650)
Q Consensus 350 ~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~ 400 (650)
..+.+|...++.|.|..|.+|+.+++.+...|.-+- .+.+-++.++|.
T Consensus 117 sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v---~~~~~Vf~Vtg~ 164 (394)
T KOG2113|consen 117 SYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPV---RCGEPVFCVTGA 164 (394)
T ss_pred eeeeccceeeeeccccccCccchheecccceEeeec---cCCCceEEEecC
Confidence 778899999999999999999999999998887643 345677888874
No 40
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.60 E-value=9.3e-05 Score=77.68 Aligned_cols=53 Identities=26% Similarity=0.272 Sum_probs=47.5
Q ss_pred ccEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCC
Q 006320 77 VTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTR 132 (650)
Q Consensus 77 ~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~ 132 (650)
.+++++|-+-+.+||.|||++|++|+.|+..|+++|+|.. ...+-.|+|.|..
T Consensus 45 ~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~---~~~e~kv~ifg~~ 97 (629)
T KOG0336|consen 45 GEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIK---CDLEVKVTIFGIN 97 (629)
T ss_pred CCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEec---cCceeEEEEechH
Confidence 4678899999999999999999999999999999999987 4567779999964
No 41
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.50 E-value=0.00027 Score=65.48 Aligned_cols=99 Identities=18% Similarity=0.303 Sum_probs=69.8
Q ss_pred eEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHh--hhccC
Q 006320 348 LVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTR--IVDLG 425 (650)
Q Consensus 348 ~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~--i~~~~ 425 (650)
-...+.|+...+|+.||++|++|+.|++..|-+|.+-. -+ .+ +.+.|..++.. +.+..
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve-----------~s-----~d----~~~fI~n~l~Pa~V~~v~ 91 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE-----------YS-----DD----PEEFIKNIFAPAAVRSVT 91 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE-----------cC-----CC----HHHHHHHHcCCCEEEEEE
Confidence 46678889999999999999999999999988887743 11 01 11222222111 11100
Q ss_pred -CCCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEE
Q 006320 426 -ADKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQI 466 (650)
Q Consensus 426 -~~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i 466 (650)
.+.+....+.+.|+....|..|||+|+ |+.++..++-.+.|
T Consensus 92 I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 92 IKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred EEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 012334567788999999999999999 99999999999866
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=97.38 E-value=0.00056 Score=78.52 Aligned_cols=94 Identities=22% Similarity=0.270 Sum_probs=72.3
Q ss_pred ccHHHHHHHHHHHHhhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcC
Q 006320 143 FSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETK 222 (650)
Q Consensus 143 ~~~a~~A~~~i~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tg 222 (650)
+..+.++...|++.+.+.-... .+-..+ -.....+.||...++.|||+||++|+.|+++||
T Consensus 548 L~~A~~g~~~Il~~m~~al~~p----~~~s~~---------------aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg 608 (719)
T TIGR02696 548 LKQARDARLAILDVMAEAIDTP----DEMSPY---------------APRIITVKIPVDKIGEVIGPKGKMINQIQDETG 608 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHhCc----cccccC---------------CCeeEEEEeChHHhhheeCCCcHhHHHHHHHHC
Confidence 4456667777777776543211 011112 345778899999999999999999999999999
Q ss_pred ceEEEecCCCCCCCccCCCcceEEEEcC-HHHHHHHHHHHHHHHhh
Q 006320 223 TQIRILPRDHSLPRCVSMSEEIVQVVGD-INNVKNAVAIISSRLRE 267 (650)
Q Consensus 223 a~I~i~~~~~~lp~~~~~~er~V~I~G~-~~~V~~A~~~I~~~l~~ 267 (650)
++|.|.. +..|.|.+. .+++++|+.+|..++..
T Consensus 609 ~~Idi~d------------~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 609 AEISIED------------DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred CEEEEec------------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 9999952 467899885 89999999999999985
No 43
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.36 E-value=0.00048 Score=79.08 Aligned_cols=88 Identities=23% Similarity=0.251 Sum_probs=67.3
Q ss_pred chHHHHHHHHHHHhhhccC--C---CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCC
Q 006320 407 LFPAQEALLHIQTRIVDLG--A---DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTD 480 (650)
Q Consensus 407 ~~~a~~ai~~i~~~i~~~~--~---~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~ 480 (650)
+..|.++..+|++.+.+.. + ....+....+.||.+.++.|||.||. ||+|.++|||+|.|. ++
T Consensus 548 L~~A~~g~~~Il~~m~~al~~p~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~-----------d~ 616 (719)
T TIGR02696 548 LKQARDARLAILDVMAEAIDTPDEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE-----------DD 616 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHhCccccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe-----------cC
Confidence 3445555555554433321 1 12335778899999999999999999 999999999999884 25
Q ss_pred eEEEEEe-cHHHHHHHHHHHHHHHHh
Q 006320 481 ELVQIVG-EIQAARDALVEVTTRLRS 505 (650)
Q Consensus 481 r~v~I~G-~~~~v~~A~~~I~~~l~~ 505 (650)
..|.|.+ +.+++++|+.+|..++..
T Consensus 617 G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 617 GTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 6799998 589999999999999885
No 44
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.34 E-value=0.0017 Score=69.85 Aligned_cols=78 Identities=18% Similarity=0.305 Sum_probs=58.9
Q ss_pred cEEEEEEEcc------ceeeeeecCCchHHHHHHhhcCceEEEecCCCC---------CCCcc-CCCcceEEEEcC-HHH
Q 006320 191 RVATRMVVSR------MHVGCLLGKGGKIIEQMRMETKTQIRILPRDHS---------LPRCV-SMSEEIVQVVGD-INN 253 (650)
Q Consensus 191 ~~~~~i~Vp~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~---------lp~~~-~~~er~V~I~G~-~~~ 253 (650)
.++.+|.||- ++||+|||..|.+.|+|+++|||+|.|.-+... +.... ...+=.|.|+++ .|+
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 5677788875 479999999999999999999999999752111 11111 112336788886 799
Q ss_pred HHHHHHHHHHHHhhc
Q 006320 254 VKNAVAIISSRLRES 268 (650)
Q Consensus 254 V~~A~~~I~~~l~~~ 268 (650)
|++|++.|..+|.+.
T Consensus 217 i~~Ai~vienli~~a 231 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSA 231 (554)
T ss_pred HHHHHHHHHHHHHhh
Confidence 999999999999874
No 45
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=97.17 E-value=0.001 Score=61.44 Aligned_cols=103 Identities=19% Similarity=0.248 Sum_probs=69.6
Q ss_pred EEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhh
Q 006320 80 TYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILE 159 (650)
Q Consensus 80 ~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e 159 (650)
.+=|++....+|..||++|++|+.|++..|-+|+|-+-..+ -...|.+.+..
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~D----------------------------~~~fI~N~l~P 85 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSEN----------------------------LEEFVANKLAP 85 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCC----------------------------HHHHHHHcCCC
Confidence 55678899999999999999999999988988888652110 00111111111
Q ss_pred cCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEe
Q 006320 160 SDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRIL 228 (650)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~ 228 (650)
..... . .-. ..+......+.|+..+.+..|||+|.+++...+-++-++.|.
T Consensus 86 A~V~~-V---~i~--------------~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 86 AEVKN-V---TVS--------------EFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred ceEEE-E---EEE--------------cCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 00000 0 000 001335678899999999999999999999999999888764
No 46
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.09 E-value=0.001 Score=77.53 Aligned_cols=65 Identities=22% Similarity=0.347 Sum_probs=56.3
Q ss_pred cEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEc-CHHHHHHHHHHHHHHHhh
Q 006320 191 RVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVG-DINNVKNAVAIISSRLRE 267 (650)
Q Consensus 191 ~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G-~~~~V~~A~~~I~~~l~~ 267 (650)
.....+.||...++.|||++|++|+.|+++|||+|.|.. +..|.|.+ ..+.+++|+..|..+..+
T Consensus 550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------------dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------------DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec------------CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 457789999999999999999999999999999999962 45677776 489999999999988654
No 47
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.01 E-value=0.0036 Score=67.34 Aligned_cols=75 Identities=19% Similarity=0.361 Sum_probs=57.5
Q ss_pred ceEEEEeecC------CcceeeecCCCc-hhhhhhhcCceEEEecCCC----------CCCCCCCCCeE-EEEEec-HHH
Q 006320 431 IITTRLLVPS------SEIGCLEGRDGS-LSEMRRSTGANIQILSREE----------VPACVSGTDEL-VQIVGE-IQA 491 (650)
Q Consensus 431 ~~~~~l~Vp~------~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~----------~p~~~~~~~r~-v~I~G~-~~~ 491 (650)
..+.+|.||. ++||.|||-.|. .|+|+++|||+|.|..+.. +.-...+.+.+ |.|+.+ .++
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 5667788875 478999999999 9999999999999986221 11111234455 999996 689
Q ss_pred HHHHHHHHHHHHHh
Q 006320 492 ARDALVEVTTRLRS 505 (650)
Q Consensus 492 v~~A~~~I~~~l~~ 505 (650)
|++|+.+|..+|.+
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999888886
No 48
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=96.98 E-value=0.0011 Score=77.36 Aligned_cols=66 Identities=23% Similarity=0.258 Sum_probs=56.0
Q ss_pred CceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEe-cHHHHHHHHHHHHHHHHhh
Q 006320 430 NIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVG-EIQAARDALVEVTTRLRSY 506 (650)
Q Consensus 430 ~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~~ 506 (650)
.+...++.||.+.++.|||+||+ ||+|+++|||+|.|. ++..|.|.+ ..+.+++|+.+|..+..+.
T Consensus 549 ~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~-----------ddG~V~i~~~~~~~~~~a~~~I~~~~~~~ 616 (684)
T TIGR03591 549 APRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE-----------DDGTVKIAASDGEAAEAAIKMIEGITAEP 616 (684)
T ss_pred CCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEe-----------cCeEEEEEECcHHHHHHHHHHHHhhhccc
Confidence 46778899999999999999999 999999999999884 245577777 5789999999998887653
No 49
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=96.80 E-value=0.003 Score=58.38 Aligned_cols=101 Identities=14% Similarity=0.174 Sum_probs=68.1
Q ss_pred EEEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhcc-CCC
Q 006320 349 VFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDL-GAD 427 (650)
Q Consensus 349 ~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~-~~~ 427 (650)
..-+.|....+|..||++|++|+.|++..|=+|.+-.- + .|...-+..++.= .++.+. ..+
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVey-----------s-----~D~~~fI~N~l~P--A~V~~V~i~~ 95 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEY-----------S-----ENLEEFVANKLAP--AEVKNVTVSE 95 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEc-----------C-----CCHHHHHHHcCCC--ceEEEEEEEc
Confidence 56677888899999999999999999888888877431 1 0000000111100 001110 001
Q ss_pred CCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEe
Q 006320 428 KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQIL 467 (650)
Q Consensus 428 ~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~ 467 (650)
.++.....+.||.++.+..|||+|+ |+-..+.++-.+.|.
T Consensus 96 ~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 96 FNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred CCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 2334567889999999999999999 999999999888663
No 50
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.50 E-value=0.0029 Score=74.39 Aligned_cols=95 Identities=16% Similarity=0.256 Sum_probs=70.1
Q ss_pred chHHHHHHHHHHHhhhccCC------CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCce-EEEecCCCCCCCCCC
Q 006320 407 LFPAQEALLHIQTRIVDLGA------DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGAN-IQILSREEVPACVSG 478 (650)
Q Consensus 407 ~~~a~~ai~~i~~~i~~~~~------~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~-I~i~~~~~~p~~~~~ 478 (650)
+..|.++...|++.+.+..+ ....+....+.||.+.++.|||.||. ||+|.++||+. |.+.
T Consensus 654 L~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~----------- 722 (891)
T PLN00207 654 LLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ----------- 722 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-----------
Confidence 34455555555554443211 23346788899999999999999999 99999999999 8652
Q ss_pred CCeEEEEEe-cHHHHHHHHHHHHHHHHhhhhhccc
Q 006320 479 TDELVQIVG-EIQAARDALVEVTTRLRSYLYRDFF 512 (650)
Q Consensus 479 ~~r~v~I~G-~~~~v~~A~~~I~~~l~~~~~~~~~ 512 (650)
++-.|.|.+ +.+++++|+.+|.+++.+....+.|
T Consensus 723 ddg~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~iy 757 (891)
T PLN00207 723 DDGTVKITAKDLSSLEKSKAIISSLTMVPTVGDIY 757 (891)
T ss_pred CCeeEEEEeCCHHHHHHHHHHHHHHhcCcCCCcEE
Confidence 345688888 5899999999999988754443444
No 51
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.46 E-value=0.0039 Score=73.34 Aligned_cols=65 Identities=25% Similarity=0.349 Sum_probs=57.0
Q ss_pred cEEEEEEEccceeeeeecCCchHHHHHHhhcCce-EEEecCCCCCCCccCCCcceEEEEcC-HHHHHHHHHHHHHHHhh
Q 006320 191 RVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQ-IRILPRDHSLPRCVSMSEEIVQVVGD-INNVKNAVAIISSRLRE 267 (650)
Q Consensus 191 ~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~-I~i~~~~~~lp~~~~~~er~V~I~G~-~~~V~~A~~~I~~~l~~ 267 (650)
.....+.||...++.|||.||.+|+.|.++||++ |.+. .+-.|.|.+. .+++++|+.+|..++.+
T Consensus 684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~------------ddg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ------------DDGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC------------CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 4578899999999999999999999999999999 8874 2457888884 89999999999998864
No 52
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.43 E-value=0.0031 Score=64.92 Aligned_cols=71 Identities=24% Similarity=0.171 Sum_probs=59.1
Q ss_pred cEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHh
Q 006320 78 TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRI 157 (650)
Q Consensus 78 ~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i 157 (650)
..+..+++++.+++.|||+.|.|-++|++||+++|.++.+ ++....|+|.|. ..++|..|+.+|...|
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p--~~n~~~i~i~~~----------~~~~V~~a~~Ri~~~i 123 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP--NTNKEEIKIIGI----------SRNCVIQALERIAKLI 123 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC--CCCcceEEEeeh----------hHHHHHHHHHHHHHHH
Confidence 4677889999999999999999999999999999999986 444455666664 3678899999988888
Q ss_pred hhc
Q 006320 158 LES 160 (650)
Q Consensus 158 ~e~ 160 (650)
.+.
T Consensus 124 ds~ 126 (345)
T KOG2814|consen 124 DSD 126 (345)
T ss_pred Hhh
Confidence 653
No 53
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.42 E-value=0.0023 Score=62.19 Aligned_cols=103 Identities=22% Similarity=0.213 Sum_probs=70.0
Q ss_pred EEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhh
Q 006320 80 TYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILE 159 (650)
Q Consensus 80 ~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e 159 (650)
.+-++.-...+|..||++|++|+.|.++.|=+|+|-+-.++. ..-+.+|+ ..
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d~---------------------~~fI~nal-------~P 128 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSEDP---------------------AEFIKNAL-------AP 128 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCCH---------------------HHHHHHhc-------Cc
Confidence 455666778899999999999999999999888875421100 11122222 11
Q ss_pred cCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEec
Q 006320 160 SDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILP 229 (650)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~ 229 (650)
... ......+ .+.....+.||..+.+..|||+|.+++...+-||.++.|..
T Consensus 129 a~v-~~V~~~~------------------~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 129 AEV-LSVNIKE------------------DDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred ceE-eEEEEEe------------------CCCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 000 0000000 01127888999999999999999999999999999999963
No 54
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.30 E-value=0.0048 Score=65.20 Aligned_cols=73 Identities=26% Similarity=0.360 Sum_probs=60.5
Q ss_pred CCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHh
Q 006320 187 GGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLR 266 (650)
Q Consensus 187 ~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~ 266 (650)
+......+.+.+-+++||.+||++|++|++|+..|+++|+|..- ..+..|+|-|..+--.+|+..|...+.
T Consensus 42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---------~~e~kv~ifg~~~m~~kaka~id~~~~ 112 (629)
T KOG0336|consen 42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---------DLEVKVTIFGINHMRKKAKASIDRGQD 112 (629)
T ss_pred cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---------CceeEEEEechHHHHHHHHhhHhhhhh
Confidence 34466678889999999999999999999999999999999742 457789999998777777777776665
Q ss_pred hc
Q 006320 267 ES 268 (650)
Q Consensus 267 ~~ 268 (650)
..
T Consensus 113 k~ 114 (629)
T KOG0336|consen 113 KD 114 (629)
T ss_pred hh
Confidence 54
No 55
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.24 E-value=0.0081 Score=67.81 Aligned_cols=95 Identities=19% Similarity=0.216 Sum_probs=71.5
Q ss_pred hHHHHHHHHHHHhhhccCC------CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCC
Q 006320 408 FPAQEALLHIQTRIVDLGA------DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTD 480 (650)
Q Consensus 408 ~~a~~ai~~i~~~i~~~~~------~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~ 480 (650)
.+|.++-++++..+.+... ....+-..++-|+...++-+||+||+ |++|.++|||+|+|. ++
T Consensus 522 ~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-----------dd 590 (692)
T COG1185 522 EQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-----------DD 590 (692)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-----------CC
Confidence 3455555555544443211 12335667888999999999999999 999999999999884 24
Q ss_pred eEEEEEecH-HHHHHHHHHHHHHHHhhhhhcccc
Q 006320 481 ELVQIVGEI-QAARDALVEVTTRLRSYLYRDFFQ 513 (650)
Q Consensus 481 r~v~I~G~~-~~v~~A~~~I~~~l~~~~~~~~~~ 513 (650)
-+|.|.++. +.+.+|+..|.+++++......|.
T Consensus 591 Gtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~ 624 (692)
T COG1185 591 GTVKIAASDGESAKKAKERIEAITREVEVGEVYE 624 (692)
T ss_pred CcEEEEecchHHHHHHHHHHHHHHhhcccccEEE
Confidence 468999975 899999999999999887777543
No 56
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.23 E-value=0.0059 Score=61.30 Aligned_cols=42 Identities=24% Similarity=0.357 Sum_probs=37.5
Q ss_pred CCCccEEEEEEecCc------ccceeecCCChHHHHHHHHhCCeEEEe
Q 006320 74 SLMVTTTYRILCHDM------KAGGVIGKSGSIIKSIRQHTGAWINVH 115 (650)
Q Consensus 74 ~~~~~~~~rilip~~------~vg~IIGk~G~~Ik~I~~~tga~I~v~ 115 (650)
.....++.+++||.+ |||.|+|++|.++|+|+++|+|+|-|-
T Consensus 87 ~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 87 GKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred CCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 345578899999985 899999999999999999999999885
No 57
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.18 E-value=0.0062 Score=59.18 Aligned_cols=100 Identities=23% Similarity=0.363 Sum_probs=66.7
Q ss_pred EEEEeecccccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccC-CCC
Q 006320 350 FRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLG-ADK 428 (650)
Q Consensus 350 ~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~-~~~ 428 (650)
....+-.+.+|..||++|++|+.|.++.|=+|.|-.- + +|...-+..|+.- .++.... .+.
T Consensus 78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~-----------s-----~d~~~fI~nal~P--a~v~~V~~~~~ 139 (190)
T COG0195 78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW-----------S-----EDPAEFIKNALAP--AEVLSVNIKED 139 (190)
T ss_pred EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEe-----------C-----CCHHHHHHHhcCc--ceEeEEEEEeC
Confidence 3444556778999999999999999999976766431 1 1111111122210 0000000 011
Q ss_pred CCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEec
Q 006320 429 DNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILS 468 (650)
Q Consensus 429 ~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~ 468 (650)
++. ...+.||.++.+..|||+|. ++-+.+.||-+|.|..
T Consensus 140 d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 140 DGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred CCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 223 78889999999999999999 9999999999999863
No 58
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.16 E-value=0.011 Score=66.85 Aligned_cols=96 Identities=22% Similarity=0.234 Sum_probs=72.6
Q ss_pred ccHHHHHHHHHHHHhhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcC
Q 006320 143 FSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETK 222 (650)
Q Consensus 143 ~~~a~~A~~~i~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tg 222 (650)
+.+|.+|...|...+.+.-.... .+-..| ......+.|+.....-+||++|++|++|.++||
T Consensus 521 L~QAk~aRlhIL~~M~~ai~~pr---~els~~---------------aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg 582 (692)
T COG1185 521 LEQAKGARLHILIVMNEAISEPR---KELSPY---------------APRIETIKIDPDKIRDVIGPGGKTIKAITEETG 582 (692)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhh---hhhhcc---------------CCceEEEccCHHHHhhccCCcccchhhhhhhhC
Confidence 44567777777777766432211 111122 234677888999999999999999999999999
Q ss_pred ceEEEecCCCCCCCccCCCcceEEEEcC-HHHHHHHHHHHHHHHhhc
Q 006320 223 TQIRILPRDHSLPRCVSMSEEIVQVVGD-INNVKNAVAIISSRLRES 268 (650)
Q Consensus 223 a~I~i~~~~~~lp~~~~~~er~V~I~G~-~~~V~~A~~~I~~~l~~~ 268 (650)
++|+|. .+..|.|.++ .+.+.+|+..|..+.++.
T Consensus 583 ~~Idie------------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~ 617 (692)
T COG1185 583 VKIDIE------------DDGTVKIAASDGESAKKAKERIEAITREV 617 (692)
T ss_pred cEEEec------------CCCcEEEEecchHHHHHHHHHHHHHHhhc
Confidence 999996 2457899887 599999999999999774
No 59
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=95.85 E-value=0.032 Score=56.12 Aligned_cols=80 Identities=24% Similarity=0.338 Sum_probs=54.0
Q ss_pred CCCceEEEEeecCC------cceeeecCCCc-hhhhhhhcCceEEEecCCC------------CCCCCCCCCe---EEEE
Q 006320 428 KDNIITTRLLVPSS------EIGCLEGRDGS-LSEMRRSTGANIQILSREE------------VPACVSGTDE---LVQI 485 (650)
Q Consensus 428 ~~~~~~~~l~Vp~~------~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~------------~p~~~~~~~r---~v~I 485 (650)
+...++.+|+||-+ +||+|||..|. +|.|+++|||+|-|..+.. -|.++.-++. +|+.
T Consensus 88 ~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~ 167 (259)
T KOG1588|consen 88 KPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIET 167 (259)
T ss_pred CceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEE
Confidence 44567888999865 78999999999 9999999999999976443 2344333333 3667
Q ss_pred EecHHHHHHHHHHHHHHHHhhh
Q 006320 486 VGEIQAARDALVEVTTRLRSYL 507 (650)
Q Consensus 486 ~G~~~~v~~A~~~I~~~l~~~~ 507 (650)
..++.-+..=+.+-++.|+..+
T Consensus 168 ~~p~~ea~~rl~~AleeI~klL 189 (259)
T KOG1588|consen 168 EAPPAEAYARLAYALEEIKKLL 189 (259)
T ss_pred eCCHHHHHHHHHHHHHHHHHhc
Confidence 7776555443333344444443
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=95.80 E-value=0.016 Score=45.61 Aligned_cols=37 Identities=24% Similarity=0.380 Sum_probs=34.4
Q ss_pred cEEEEEEecCcccceeecCCChHHHHHHHHhCCeEEE
Q 006320 78 TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINV 114 (650)
Q Consensus 78 ~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v 114 (650)
...+.+.++.+..|.+|||+|.+|+.+++.++-+|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3688899999999999999999999999999998876
No 61
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=95.68 E-value=0.012 Score=46.30 Aligned_cols=36 Identities=22% Similarity=0.049 Sum_probs=33.6
Q ss_pred ceEEEEecCCcccccccCCCcchhhHHHhcCCeEEE
Q 006320 604 STLEVVLPDYAVPKLITKSKTLLTRFSEVSLLLHLI 639 (650)
Q Consensus 604 ~t~~v~IP~~~~g~vIGk~G~~I~~Ir~~SGA~i~i 639 (650)
....|.||.+..+.+|||+|.||+.+++..|-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 578899999999999999999999999999988865
No 62
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=95.63 E-value=0.014 Score=60.20 Aligned_cols=71 Identities=25% Similarity=0.440 Sum_probs=58.7
Q ss_pred cEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEc-CHHHHHHHHHHHHHHHhhcc
Q 006320 191 RVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVG-DINNVKNAVAIISSRLRESQ 269 (650)
Q Consensus 191 ~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G-~~~~V~~A~~~I~~~l~~~~ 269 (650)
.....+.|++...++|||++|.+-++|+++|+|+|.++. |. .....|+|+| ..++|.+|..+|...+.+..
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 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPR-----PN---TNKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccC-----CC---CCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 456778999999999999999999999999999999964 22 2344555555 68999999999999998763
No 63
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.53 E-value=0.038 Score=59.04 Aligned_cols=98 Identities=17% Similarity=0.254 Sum_probs=64.3
Q ss_pred ccccceecCCchhHHHHHHHh-CCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccCCCCCCceEEE
Q 006320 357 DKVGRVIGESEGIVELLQNEI-GVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTR 435 (650)
Q Consensus 357 ~~vg~IIGk~G~~Ik~l~~~t-ga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~~~~~~~~~~ 435 (650)
+-+|+.||++|.+|+.|.++. |=+|.|-.-..+. ..+ |. +++++|. +....-+ +..-...
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~--~~f-I~------Nal~Pa~---------V~~V~i~-~~~~~~~ 311 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVP--EIF-IA------RALAPAI---------ISSVKIE-EEEKKAI 311 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCH--HHH-HH------HhCCCce---------eeEEEEc-CCCcEEE
Confidence 447999999999999999988 6677664311000 000 00 0011110 0000001 2234778
Q ss_pred EeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCC
Q 006320 436 LLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVP 473 (650)
Q Consensus 436 l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p 473 (650)
+.||..+.+..|||+|. ++-..+.||.+|.|.+-++..
T Consensus 312 V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~~~ 350 (374)
T PRK12328 312 VTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGSKE 350 (374)
T ss_pred EEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCCCc
Confidence 99999999999999999 999999999999999865543
No 64
>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=95.50 E-value=0.046 Score=58.27 Aligned_cols=38 Identities=21% Similarity=0.274 Sum_probs=35.7
Q ss_pred EEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEec
Q 006320 192 VATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILP 229 (650)
Q Consensus 192 ~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~ 229 (650)
..+.+.||..+.+..|||+|.+++.....||.+|.|..
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 47899999999999999999999999999999999974
No 65
>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=95.40 E-value=0.043 Score=58.54 Aligned_cols=94 Identities=20% Similarity=0.417 Sum_probs=62.0
Q ss_pred ccccceecCCchhHHHHHHHh-CCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhcc-CCCCCCceEE
Q 006320 357 DKVGRVIGESEGIVELLQNEI-GVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDL-GADKDNIITT 434 (650)
Q Consensus 357 ~~vg~IIGk~G~~Ik~l~~~t-ga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~-~~~~~~~~~~ 434 (650)
+-+|+.||++|.+|+.|.++. |=+|.|-.-..+. ..+.. +++++|. +... ..+. ..-..
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~--~~fi~-------nal~Pa~---------v~~v~i~~~-~~~~~ 303 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDP--AEFIA-------NALSPAK---------VISVEVLDE-DKHSA 303 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCH--HHHHH-------HhcCCce---------EEEEEEEcC-CCcEE
Confidence 447999999999999999998 6677664311000 00000 0011110 0000 0011 23578
Q ss_pred EEeecCCcceeeecCCCc-hhhhhhhcCceEEEecC
Q 006320 435 RLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSR 469 (650)
Q Consensus 435 ~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~ 469 (650)
.+.||.++.+..|||+|. ++-..+.||.+|.|.+.
T Consensus 304 ~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~ 339 (341)
T TIGR01953 304 EVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE 339 (341)
T ss_pred EEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence 899999999999999999 99999999999999753
No 66
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.23 E-value=0.055 Score=58.11 Aligned_cols=95 Identities=18% Similarity=0.211 Sum_probs=64.3
Q ss_pred cccceeecCCChHHHHHHHHh-CCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhhcCCCCCC
Q 006320 88 MKAGGVIGKSGSIIKSIRQHT-GAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGF 166 (650)
Q Consensus 88 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e~~~~~~~ 166 (650)
+-+|..||++|+.|+.|.++. |-+|+|-.-..+ ....|...+........
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d----------------------------~~~fi~nal~Pa~v~~v- 295 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSED----------------------------PAEFVANALSPAKVVSV- 295 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCCC----------------------------HHHHHHHhCCCceEEEE-
Confidence 458999999999999999998 788887542110 00111111111000000
Q ss_pred CCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEec
Q 006320 167 YGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILP 229 (650)
Q Consensus 167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~ 229 (650)
. . .. +....+.+.||..+.++.|||+|.+++.-...||.+|.|..
T Consensus 296 ---~---i-----------~~-~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 296 ---E---V-----------DD-EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred ---E---E-----------Ec-CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 0 0 00 12246889999999999999999999999999999999975
No 67
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.21 E-value=0.045 Score=58.45 Aligned_cols=96 Identities=16% Similarity=0.099 Sum_probs=65.0
Q ss_pred cccceeecCCChHHHHHHHHh-CCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhhcCCCCCC
Q 006320 88 MKAGGVIGKSGSIIKSIRQHT-GAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGF 166 (650)
Q Consensus 88 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e~~~~~~~ 166 (650)
+-+|..||++|++|+.|.++- |=+|+|-.-.++ -...|...+........
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D----------------------------~~~fI~Nal~Pa~V~~V- 301 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNV----------------------------PEIFIARALAPAIISSV- 301 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCC----------------------------HHHHHHHhCCCceeeEE-
Confidence 458999999999999999998 788887542110 00111111111000000
Q ss_pred CCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCC
Q 006320 167 YGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRD 231 (650)
Q Consensus 167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~ 231 (650)
. . ......+.+.||..+.++.|||+|.+++.....||.+|.|..-+
T Consensus 302 ~--i-----------------~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~ 347 (374)
T PRK12328 302 K--I-----------------EEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG 347 (374)
T ss_pred E--E-----------------cCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence 0 0 01223788999999999999999999999999999999998643
No 68
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.20 E-value=0.017 Score=67.70 Aligned_cols=88 Identities=24% Similarity=0.259 Sum_probs=64.3
Q ss_pred hHHHHHHHHHHHhhhccCC------CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCC
Q 006320 408 FPAQEALLHIQTRIVDLGA------DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTD 480 (650)
Q Consensus 408 ~~a~~ai~~i~~~i~~~~~------~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~ 480 (650)
..|.++..+|++.+.+... ....+....+.||.+.++.+||.||. ||+|.++||+.|.+. ++
T Consensus 524 ~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-----------d~ 592 (693)
T PRK11824 524 EQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-----------DD 592 (693)
T ss_pred HHHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------CC
Confidence 3455555566655554211 12234556777899999999999999 999999999988652 24
Q ss_pred eEEEEEe-cHHHHHHHHHHHHHHHHhh
Q 006320 481 ELVQIVG-EIQAARDALVEVTTRLRSY 506 (650)
Q Consensus 481 r~v~I~G-~~~~v~~A~~~I~~~l~~~ 506 (650)
-.|.|.+ ..+.+++|+.+|..+..+.
T Consensus 593 G~v~i~~~~~~~~~~a~~~I~~~~~~~ 619 (693)
T PRK11824 593 GTVKIAATDGEAAEAAKERIEGITAEP 619 (693)
T ss_pred ceEEEEcccHHHHHHHHHHHHHhcccC
Confidence 5688888 5789999999998888653
No 69
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.12 E-value=0.022 Score=66.64 Aligned_cols=95 Identities=20% Similarity=0.242 Sum_probs=68.6
Q ss_pred ccHHHHHHHHHHHHhhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcC
Q 006320 143 FSPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETK 222 (650)
Q Consensus 143 ~~~a~~A~~~i~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tg 222 (650)
+..+.++...|++.|.+.-.... .+-..+ ......+.|+...++.+||.||.+|+.|.++||
T Consensus 523 l~~a~~g~~~I~~~M~~aI~~~r---~~~~~~---------------ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~ 584 (693)
T PRK11824 523 LEQAKEGRLHILGKMNEAISEPR---AELSPY---------------APRIETIKIPPDKIRDVIGPGGKTIREITEETG 584 (693)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCh---hhhccc---------------CchheeecCCHHHHHHHhcCCchhHHHHHHHHC
Confidence 34566777778877766532221 011111 233456677999999999999999999999999
Q ss_pred ceEEEecCCCCCCCccCCCcceEEEEcC-HHHHHHHHHHHHHHHhh
Q 006320 223 TQIRILPRDHSLPRCVSMSEEIVQVVGD-INNVKNAVAIISSRLRE 267 (650)
Q Consensus 223 a~I~i~~~~~~lp~~~~~~er~V~I~G~-~~~V~~A~~~I~~~l~~ 267 (650)
++|.+. .+-.|.|.+. .+.+++|+..|..+..+
T Consensus 585 ~~idi~------------d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 585 AKIDIE------------DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred CccccC------------CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 988774 2456888884 89999999999988854
No 70
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=94.98 E-value=0.069 Score=58.03 Aligned_cols=94 Identities=19% Similarity=0.186 Sum_probs=63.0
Q ss_pred cccceeecCCChHHHHHHHHh-CCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhhcCCCCCC
Q 006320 88 MKAGGVIGKSGSIIKSIRQHT-GAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGF 166 (650)
Q Consensus 88 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e~~~~~~~ 166 (650)
+-+|..||++|+.|+.|.++. |=+|+|-.-.++-.+ -+.+| +.-......
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp~~---------------------fI~Na-------LsPA~V~~V- 327 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDPAT---------------------YIANA-------LSPARVDEV- 327 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCHHH---------------------HHHHh-------cCCceeeEE-
Confidence 558999999999999999998 788887542111000 01111 111000000
Q ss_pred CCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEe
Q 006320 167 YGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRIL 228 (650)
Q Consensus 167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~ 228 (650)
. . .......+.+.||..+.++.|||+|.+++.-...||.+|.|.
T Consensus 328 ---~---i------------~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~ 371 (449)
T PRK12329 328 ---R---L------------VDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIK 371 (449)
T ss_pred ---E---E------------EcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccc
Confidence 0 0 001123578999999999999999999999999999999996
No 71
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=94.96 E-value=1 Score=44.79 Aligned_cols=65 Identities=18% Similarity=0.231 Sum_probs=56.0
Q ss_pred EEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhhc
Q 006320 193 ATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRES 268 (650)
Q Consensus 193 ~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~ 268 (650)
.+.+.++....-+|...+|..++.|....||+|.+.. .+..+.|+|+...++.+...|.+++...
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-----------~~~~i~I~g~k~~~~~i~~~i~~~l~~i 91 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR-----------SENRIRITGTKSTAEYIEASINEILSNI 91 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEec-----------CCcEEEEEccHHHHHHHHHHHHHHHhhc
Confidence 4555666888899999999999999888899999973 3568999999999999999999999774
No 72
>PRK00468 hypothetical protein; Provisional
Probab=94.69 E-value=0.038 Score=45.37 Aligned_cols=33 Identities=30% Similarity=0.344 Sum_probs=29.5
Q ss_pred CCccEEEEEEecCcccceeecCCChHHHHHHHH
Q 006320 75 LMVTTTYRILCHDMKAGGVIGKSGSIIKSIRQH 107 (650)
Q Consensus 75 ~~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~ 107 (650)
.+..+.+++.|....+|.||||+|.+|+.||.-
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence 345689999999999999999999999999975
No 73
>PRK00468 hypothetical protein; Provisional
Probab=94.58 E-value=0.064 Score=44.07 Aligned_cols=34 Identities=18% Similarity=0.362 Sum_probs=28.5
Q ss_pred CCCceEEEEeecCCcceeeecCCCc-hhhhhhhcC
Q 006320 428 KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTG 461 (650)
Q Consensus 428 ~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tg 461 (650)
.+..+.++|.|..+.+|+||||+|. |+.||.--.
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~ 60 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVK 60 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence 3456888999999999999999999 888886543
No 74
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=94.54 E-value=0.078 Score=56.94 Aligned_cols=96 Identities=23% Similarity=0.391 Sum_probs=62.5
Q ss_pred ccccceecCCchhHHHHHHHh-CCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccCCCCCCceEEE
Q 006320 357 DKVGRVIGESEGIVELLQNEI-GVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTR 435 (650)
Q Consensus 357 ~~vg~IIGk~G~~Ik~l~~~t-ga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~~~~~~~~~~ 435 (650)
+-+|+.||++|.+|+.|.++. |=+|.|-.-..+. ..+ |. +++++|. +. .+. . .+ +..-.+.
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~--~~f-i~------nal~Pa~-----v~-~v~-i-~~-~~~~~~~ 306 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDP--AEF-VA------NALSPAK-----VV-SVE-V-DD-EEEKAAR 306 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCCCH--HHH-HH------HhCCCce-----EE-EEE-E-Ec-CCCcEEE
Confidence 447999999999999999888 7677764311100 000 00 0001110 00 000 0 01 2235688
Q ss_pred EeecCCcceeeecCCCc-hhhhhhhcCceEEEecCC
Q 006320 436 LLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSRE 470 (650)
Q Consensus 436 l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~ 470 (650)
+.||..+.+.-|||+|. |+-..+.||.+|.|.+.+
T Consensus 307 v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~~ 342 (362)
T PRK12327 307 VVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSES 342 (362)
T ss_pred EEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEHH
Confidence 99999999999999999 999999999999998643
No 75
>PRK02821 hypothetical protein; Provisional
Probab=94.33 E-value=0.074 Score=43.88 Aligned_cols=34 Identities=24% Similarity=0.327 Sum_probs=28.4
Q ss_pred CCceEEEEeecCCcceeeecCCCc-hhhhhhhcCc
Q 006320 429 DNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGA 462 (650)
Q Consensus 429 ~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga 462 (650)
+....+.|.|....+|+||||+|. |+.||.--.+
T Consensus 28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 445788999999999999999999 8888865443
No 76
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=94.13 E-value=0.077 Score=53.79 Aligned_cols=67 Identities=16% Similarity=0.211 Sum_probs=54.9
Q ss_pred EEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEec-HHHHHHHHHHHHHHHHhhhhhc
Q 006320 433 TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGE-IQAARDALVEVTTRLRSYLYRD 510 (650)
Q Consensus 433 ~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~~~~~ 510 (650)
-+.+.||...++++||++|. |+.|.+.|++.|.+- .+-.|.|.+. .+++++|+..|..+-++....+
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig-----------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~~~ 214 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG-----------QNGRIWIKGPDEEDEEIAIEAIKKIEREAHTSG 214 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc-----------CCcEEEEeeCCHHHHHHHHHHHHHHHhhhhccC
Confidence 35678999999999999999 999999999999772 2446889996 5688999999888877765444
No 77
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=94.07 E-value=0.1 Score=52.95 Aligned_cols=63 Identities=22% Similarity=0.291 Sum_probs=54.4
Q ss_pred EEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcC-HHHHHHHHHHHHHHHhhc
Q 006320 194 TRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGD-INNVKNAVAIISSRLRES 268 (650)
Q Consensus 194 ~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~-~~~V~~A~~~I~~~l~~~ 268 (650)
..+.||..+++.|||++|..|+.|.++++++|.+-. +-.|.|.+. .+++.+|+.+|..+-++.
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 668899999999999999999999999999999842 346889886 678999999988877665
No 78
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=94.04 E-value=0.098 Score=58.19 Aligned_cols=94 Identities=18% Similarity=0.237 Sum_probs=63.8
Q ss_pred cccceeecCCChHHHHHHHHh-CCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhhcCCCCCC
Q 006320 88 MKAGGVIGKSGSIIKSIRQHT-GAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGGF 166 (650)
Q Consensus 88 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e~~~~~~~ 166 (650)
+-+|+.||++|+.|+.|.++- |=+|+|-.-.+ +. ...|...+........
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~---d~-------------------------~~fi~nal~pa~v~~v- 295 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIILWSD---DP-------------------------AQFIINALSPAEVSSV- 295 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEEcCC---CH-------------------------HHHHHHhCCCCEEEEE-
Confidence 448999999999999999998 78888754211 00 0111111111100000
Q ss_pred CCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEec
Q 006320 167 YGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILP 229 (650)
Q Consensus 167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~ 229 (650)
. .+ .....+.+.||..+.+..|||+|.+++.....||.+|.|..
T Consensus 296 ~--~~-----------------~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 296 V--VD-----------------EDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred E--Ee-----------------CCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 0 00 11237889999999999999999999999999999999974
No 79
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=93.97 E-value=0.099 Score=56.85 Aligned_cols=94 Identities=26% Similarity=0.367 Sum_probs=60.5
Q ss_pred ccccceecCCchhHHHHHHHh-CCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccCCCCCCceEEE
Q 006320 357 DKVGRVIGESEGIVELLQNEI-GVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTR 435 (650)
Q Consensus 357 ~~vg~IIGk~G~~Ik~l~~~t-ga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~~~~~~~~~~ 435 (650)
+-+|+.||++|.+|+.|.++. |=+|.|-.-..+ -...|. +++++| ++....-..+..-...
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~D---p~~fI~------NaLsPA---------~V~~V~i~~~~~k~a~ 338 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPD---PATYIA------NALSPA---------RVDEVRLVDPEGRHAH 338 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCC---HHHHHH------HhcCCc---------eeeEEEEEcCCCcEEE
Confidence 457999999999999999988 667766431100 000000 000110 0000000011234578
Q ss_pred EeecCCcceeeecCCCc-hhhhhhhcCceEEEec
Q 006320 436 LLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILS 468 (650)
Q Consensus 436 l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~ 468 (650)
+.||..+.+.-|||+|. |+-..+.||.+|.|.+
T Consensus 339 V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 339 VLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred EEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 99999999999999999 9999999999998853
No 80
>PRK02821 hypothetical protein; Provisional
Probab=93.96 E-value=0.06 Score=44.39 Aligned_cols=35 Identities=26% Similarity=0.359 Sum_probs=30.2
Q ss_pred CccEEEEEEecCcccceeecCCChHHHHHHHHhCC
Q 006320 76 MVTTTYRILCHDMKAGGVIGKSGSIIKSIRQHTGA 110 (650)
Q Consensus 76 ~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga 110 (650)
+..+.+.+.|...-+|.||||+|.+|+.||.--.+
T Consensus 28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 34578999999999999999999999999987543
No 81
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=93.68 E-value=0.091 Score=50.62 Aligned_cols=39 Identities=23% Similarity=0.256 Sum_probs=33.1
Q ss_pred cEEEEEEecC------cccceeecCCChHHHHHHHHhCCeEEEec
Q 006320 78 TTTYRILCHD------MKAGGVIGKSGSIIKSIRQHTGAWINVHE 116 (650)
Q Consensus 78 ~~~~rilip~------~~vg~IIGk~G~~Ik~I~~~tga~I~v~~ 116 (650)
.+.-++.||. .|||.|||+.|+|.|+|++.|+|+|-|--
T Consensus 147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG 191 (269)
T COG5176 147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRG 191 (269)
T ss_pred cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEec
Confidence 3455666664 78999999999999999999999999964
No 82
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=93.56 E-value=0.13 Score=58.17 Aligned_cols=50 Identities=30% Similarity=0.412 Sum_probs=42.2
Q ss_pred CceEEEEEeeccc-ccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCC
Q 006320 346 EDLVFRMLCPIDK-VGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSE 400 (650)
Q Consensus 346 ~~~~~~i~vp~~~-vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~ 400 (650)
+.++..|.+|++. -|+|||+.|.+|+.|+..|||.|.|++ +-..|+|||.
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd-----tp~~v~ls~f 252 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-----TPEAVILSGF 252 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC-----CCCeEEecCC
Confidence 5677788999854 599999999999999999999999976 2356779976
No 83
>PRK00106 hypothetical protein; Provisional
Probab=93.54 E-value=0.13 Score=57.93 Aligned_cols=50 Identities=24% Similarity=0.430 Sum_probs=42.3
Q ss_pred CceEEEEEeecc-cccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCC
Q 006320 346 EDLVFRMLCPID-KVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSE 400 (650)
Q Consensus 346 ~~~~~~i~vp~~-~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~ 400 (650)
+.++..|.+|++ +-|+|||+.|.+|+.|+.-|||.+.|++ +-..|+|+|.
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd-----tp~~v~lS~f 273 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD-----TPEVVVLSGF 273 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC-----CCCeEEEeCC
Confidence 567778999985 5599999999999999999999999966 3356779986
No 84
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=93.52 E-value=0.087 Score=43.17 Aligned_cols=32 Identities=34% Similarity=0.418 Sum_probs=29.3
Q ss_pred CccEEEEEEecCcccceeecCCChHHHHHHHH
Q 006320 76 MVTTTYRILCHDMKAGGVIGKSGSIIKSIRQH 107 (650)
Q Consensus 76 ~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~ 107 (650)
+..+.+++-+....+|.||||+|.+|+.||.-
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 55788999999999999999999999999975
No 85
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=93.51 E-value=0.15 Score=41.79 Aligned_cols=33 Identities=21% Similarity=0.452 Sum_probs=28.5
Q ss_pred CCCceEEEEeecCCcceeeecCCCc-hhhhhhhc
Q 006320 428 KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRST 460 (650)
Q Consensus 428 ~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~T 460 (650)
.+....++|.|....+|.||||+|. |+-||.--
T Consensus 26 ~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred cCCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 3567889999999999999999999 88888643
No 86
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=93.44 E-value=0.15 Score=56.67 Aligned_cols=93 Identities=20% Similarity=0.336 Sum_probs=61.1
Q ss_pred cccceecCCchhHHHHHHHh-CCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccCCCCCCceEEEE
Q 006320 358 KVGRVIGESEGIVELLQNEI-GVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTRL 436 (650)
Q Consensus 358 ~vg~IIGk~G~~Ik~l~~~t-ga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~~~~~~~~~~l 436 (650)
-+|+.||++|++|+.|.++. |=+|.|-.-. ++ ...-...||.- ..+....-+.+ .-.+.+
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s---~d-------------~~~fi~nal~p--a~v~~v~~~~~-~~~~~v 306 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIILWS---DD-------------PAQFIINALSP--AEVSSVVVDED-EHSADV 306 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEEcC---CC-------------HHHHHHHhCCC--CEEEEEEEeCC-CCEEEE
Confidence 37999999999999999988 6677664310 00 00000011100 00000000111 247889
Q ss_pred eecCCcceeeecCCCc-hhhhhhhcCceEEEecC
Q 006320 437 LVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSR 469 (650)
Q Consensus 437 ~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~ 469 (650)
.||..+.+.-|||+|. |+-..+.||.+|.|...
T Consensus 307 ~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 307 VVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred EECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 9999999999999999 99999999999999863
No 87
>PRK01064 hypothetical protein; Provisional
Probab=93.34 E-value=0.19 Score=41.55 Aligned_cols=34 Identities=24% Similarity=0.398 Sum_probs=29.0
Q ss_pred CCCceEEEEeecCCcceeeecCCCc-hhhhhhhcC
Q 006320 428 KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTG 461 (650)
Q Consensus 428 ~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tg 461 (650)
.+..+.+++.|.....|.+|||+|. |+.||.-..
T Consensus 26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred CCCEEEEEEEECcccceEEECCCCccHHHHHHHHH
Confidence 3556889999999999999999999 998887544
No 88
>PRK00106 hypothetical protein; Provisional
Probab=93.22 E-value=0.34 Score=54.66 Aligned_cols=66 Identities=20% Similarity=0.256 Sum_probs=50.4
Q ss_pred cEEEEEEEcc-ceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEc-CHHHHHHHHHHHHHHHhh
Q 006320 191 RVATRMVVSR-MHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVG-DINNVKNAVAIISSRLRE 267 (650)
Q Consensus 191 ~~~~~i~Vp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G-~~~~V~~A~~~I~~~l~~ 267 (650)
.+...+.+|+ .+-|.|||+.|.+|+.+...||+++-|. .+...|+|+| ++---+-|...+..++.+
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid-----------dtp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID-----------DTPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc-----------CCCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 3445566676 7889999999999999999999999996 2334678888 566666677766666655
No 89
>PRK01064 hypothetical protein; Provisional
Probab=93.18 E-value=0.11 Score=43.01 Aligned_cols=32 Identities=34% Similarity=0.510 Sum_probs=29.4
Q ss_pred CccEEEEEEecCcccceeecCCChHHHHHHHH
Q 006320 76 MVTTTYRILCHDMKAGGVIGKSGSIIKSIRQH 107 (650)
Q Consensus 76 ~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~ 107 (650)
+..+.+++.|.....|.+|||+|.+|+.||.-
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence 45689999999999999999999999999985
No 90
>PRK12704 phosphodiesterase; Provisional
Probab=93.12 E-value=0.17 Score=57.19 Aligned_cols=50 Identities=30% Similarity=0.395 Sum_probs=42.1
Q ss_pred CceEEEEEeecc-cccceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCC
Q 006320 346 EDLVFRMLCPID-KVGRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSE 400 (650)
Q Consensus 346 ~~~~~~i~vp~~-~vg~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~ 400 (650)
+.++..|.+|++ +-|+|||+.|.+|+.|+.-|||.|.|++ +-..|+|||.
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd-----tp~~v~ls~~ 258 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-----TPEAVILSGF 258 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC-----CCCeEEEecC
Confidence 566777889985 5599999999999999999999999976 2356779976
No 91
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=93.07 E-value=0.36 Score=54.63 Aligned_cols=66 Identities=17% Similarity=0.221 Sum_probs=50.0
Q ss_pred cEEEEEEEcc-ceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEc-CHHHHHHHHHHHHHHHhh
Q 006320 191 RVATRMVVSR-MHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVG-DINNVKNAVAIISSRLRE 267 (650)
Q Consensus 191 ~~~~~i~Vp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G-~~~~V~~A~~~I~~~l~~ 267 (650)
.+...+-+|+ .+-|.|||+.|.+|+.+...||++|-|.. +...|+|++ ++---+-|...+..++.+
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd-----------tp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-----------TPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC-----------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 3445566676 78899999999999999999999999962 234677888 465556677777666655
No 92
>PRK12704 phosphodiesterase; Provisional
Probab=93.04 E-value=0.31 Score=55.12 Aligned_cols=66 Identities=17% Similarity=0.202 Sum_probs=49.6
Q ss_pred EEEEEEEcc-ceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEc-CHHHHHHHHHHHHHHHhhc
Q 006320 192 VATRMVVSR-MHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVG-DINNVKNAVAIISSRLRES 268 (650)
Q Consensus 192 ~~~~i~Vp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G-~~~~V~~A~~~I~~~l~~~ 268 (650)
+...+.+|+ .+-|.|||+.|.+|+.+...||++|-|. .+...|.|+| .+---+.|...+...+.+.
T Consensus 210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid-----------dtp~~v~ls~~~~~rre~a~~~l~~l~~dg 277 (520)
T PRK12704 210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID-----------DTPEAVILSGFDPIRREIARLALEKLVQDG 277 (520)
T ss_pred ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc-----------CCCCeEEEecCChhhHHHHHHHHHHHHhcC
Confidence 344455665 7889999999999999999999999996 2335788998 4555556777776666553
No 93
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=92.96 E-value=0.28 Score=54.17 Aligned_cols=94 Identities=20% Similarity=0.296 Sum_probs=68.5
Q ss_pred cHHHHHHHHHHHHhhhcCCCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCc
Q 006320 144 SPAQEALFLIHDRILESDGGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKT 223 (650)
Q Consensus 144 ~~a~~A~~~i~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga 223 (650)
-+|.+|...|.+.+.+.-.... ..+.+| ..+...+.|+.+....+||.+|...|+|..|||+
T Consensus 567 ~~a~~ar~~Il~~m~k~i~~Pr---~~~~~y---------------~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGa 628 (760)
T KOG1067|consen 567 QKAREARLQILDIMEKNINSPR---GSDKEY---------------SPVLETLKVSPSKRATLIGPGGVLKKKIEVETGA 628 (760)
T ss_pred HhhhHHHHHHHHHHHhhcCCcc---cCcccc---------------CceeeEEeecchhhheeecCccceeeeEeeeccc
Confidence 3455566667777765432221 123333 3468889999999999999999999999999995
Q ss_pred eEEEecCCCCCCCccCCCcceEEEEc-CHHHHHHHHHHHHHHHhhc
Q 006320 224 QIRILPRDHSLPRCVSMSEEIVQVVG-DINNVKNAVAIISSRLRES 268 (650)
Q Consensus 224 ~I~i~~~~~~lp~~~~~~er~V~I~G-~~~~V~~A~~~I~~~l~~~ 268 (650)
.-.+. +..+.|.. +..+.++|+..|..++.+.
T Consensus 629 i~~vD-------------e~t~~i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 629 ISQVD-------------EGTFSIFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred eeeec-------------CceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence 44442 45677776 4889999999999998775
No 94
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=92.36 E-value=0.29 Score=53.98 Aligned_cols=71 Identities=20% Similarity=0.189 Sum_probs=58.3
Q ss_pred CCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEe-cHHHHHHHHHHHHHHHHh
Q 006320 428 KDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVG-EIQAARDALVEVTTRLRS 505 (650)
Q Consensus 428 ~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 505 (650)
+..++...|-|+.++...+||.+|. .|+|..+||+.-++ ++..++|.- ++.+.++|++.|..++..
T Consensus 593 ~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 593 EYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEGTFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred ccCceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCceEEEEecCHHHHHHHHHHHHHHhcC
Confidence 3457888999999999999999999 99999999955543 355677776 578999999999998887
Q ss_pred hhhhc
Q 006320 506 YLYRD 510 (650)
Q Consensus 506 ~~~~~ 510 (650)
....+
T Consensus 661 ~~~~~ 665 (760)
T KOG1067|consen 661 DQVQD 665 (760)
T ss_pred ccccc
Confidence 55555
No 95
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=91.90 E-value=0.23 Score=47.90 Aligned_cols=41 Identities=20% Similarity=0.389 Sum_probs=34.4
Q ss_pred CcEEEEEEEcc------ceeeeeecCCchHHHHHHhhcCceEEEecC
Q 006320 190 NRVATRMVVSR------MHVGCLLGKGGKIIEQMRMETKTQIRILPR 230 (650)
Q Consensus 190 ~~~~~~i~Vp~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 230 (650)
..++-++.||- ++||+|||..|++.++|++.|+|+|-|..+
T Consensus 146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 45566677763 579999999999999999999999999753
No 96
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=91.34 E-value=4.6 Score=40.05 Aligned_cols=130 Identities=15% Similarity=0.142 Sum_probs=82.9
Q ss_pred EEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhhcC
Q 006320 82 RILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESD 161 (650)
Q Consensus 82 rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e~~ 161 (650)
.+.++....-.+...+|..++.|....||+|.+.. ++..|.|+|++. .+..+...|.+.+ .
T Consensus 29 ~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-----~~~~i~I~g~k~-----------~~~~i~~~i~~~l-~-- 89 (210)
T PF14611_consen 29 DVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR-----SENRIRITGTKS-----------TAEYIEASINEIL-S-- 89 (210)
T ss_pred EEEecchheeeeecCCchHHHHHHHhcCceEEEec-----CCcEEEEEccHH-----------HHHHHHHHHHHHH-h--
Confidence 34445677778889999999999888899999986 456799999742 1222222222222 1
Q ss_pred CCCCCCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeee----cCCchHHHHHHhhcCceEEEecCCCCCCCc
Q 006320 162 GGGGFYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLL----GKGGKIIEQMRMETKTQIRILPRDHSLPRC 237 (650)
Q Consensus 162 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~II----Gk~G~~Ik~I~~~tga~I~i~~~~~~lp~~ 237 (650)
...+..+-++.-.-..-. -.....++.|++.|++.|...+.
T Consensus 90 ----------------------------~i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~------- 134 (210)
T PF14611_consen 90 ----------------------------NIRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD------- 134 (210)
T ss_pred ----------------------------hcEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC-------
Confidence 223444444432111111 12366889999999999998642
Q ss_pred cCCCcceEEEE-----cCHHHHHHHHHHHHHHHhhcc
Q 006320 238 VSMSEEIVQVV-----GDINNVKNAVAIISSRLRESQ 269 (650)
Q Consensus 238 ~~~~er~V~I~-----G~~~~V~~A~~~I~~~l~~~~ 269 (650)
+..+.|. -....+..|+..+...+...+
T Consensus 135 ----~~~~~i~~~~~~~~~~~~~~a~RlL~~a~~~~~ 167 (210)
T PF14611_consen 135 ----GNKLKISWLASPENEKRADRAKRLLLWALDYNP 167 (210)
T ss_pred ----CCeEEEEEEeeccccchHHHHHHHHHHhccCCc
Confidence 2234444 357888999999998885443
No 97
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=90.86 E-value=0.18 Score=48.37 Aligned_cols=62 Identities=24% Similarity=0.249 Sum_probs=49.8
Q ss_pred EEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320 433 TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY 506 (650)
Q Consensus 433 ~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 506 (650)
+++=.=-+..+|+|+||+|. =--|++.|.++|-+. +..|.|-|..++++-|...|+.+|-..
T Consensus 170 tL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVla------------d~kIHiLG~~~niriAR~avcsLIlGs 232 (252)
T KOG3273|consen 170 TLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLA------------DSKIHILGAFQNIRIARDAVCSLILGS 232 (252)
T ss_pred cccchhHHHHHHHhhcCCCcceeeeeccceeEEEec------------CceEEEeecchhhHHHHHhhHhhhccC
Confidence 44434446788999999999 456999999999553 456999999999999999999887544
No 98
>PRK12705 hypothetical protein; Provisional
Probab=89.95 E-value=0.45 Score=53.38 Aligned_cols=50 Identities=30% Similarity=0.409 Sum_probs=40.8
Q ss_pred CceEEEEEeecccc-cceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCC
Q 006320 346 EDLVFRMLCPIDKV-GRVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSE 400 (650)
Q Consensus 346 ~~~~~~i~vp~~~v-g~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~ 400 (650)
+.++..+.+|++.. |+|||+.|.+|+.|+..||+.+.|.+ ....|+|++.
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd-----tp~~V~ls~f 246 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD-----TPEAVVISSF 246 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC-----Cccchhhccc
Confidence 56677788997655 99999999999999999999999976 2244667765
No 99
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=87.85 E-value=0.25 Score=40.24 Aligned_cols=32 Identities=22% Similarity=0.335 Sum_probs=27.6
Q ss_pred cEEEEEEecCcccceeecCCChHHHHHHHHhC
Q 006320 78 TTTYRILCHDMKAGGVIGKSGSIIKSIRQHTG 109 (650)
Q Consensus 78 ~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tg 109 (650)
...+.+.|..+..|.||||.|.++++||.-.+
T Consensus 28 ~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 28 GDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp TTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred ceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence 45777888999999999999999999997654
No 100
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=85.06 E-value=1.7 Score=47.45 Aligned_cols=39 Identities=23% Similarity=0.399 Sum_probs=36.3
Q ss_pred EEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCC
Q 006320 193 ATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRD 231 (650)
Q Consensus 193 ~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~ 231 (650)
...+.||..+++.+|||+|.+|++|+++.|-+|.|.+.+
T Consensus 487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e 525 (604)
T COG1855 487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE 525 (604)
T ss_pred eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence 578899999999999999999999999999999998754
No 101
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=84.74 E-value=0.55 Score=38.23 Aligned_cols=34 Identities=18% Similarity=0.229 Sum_probs=29.2
Q ss_pred CceEEEEEeecccccceecCCchhHHHHHHHhCC
Q 006320 346 EDLVFRMLCPIDKVGRVIGESEGIVELLQNEIGV 379 (650)
Q Consensus 346 ~~~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga 379 (650)
+...+.+.|..+..|.||||.|.+++.||.-.+.
T Consensus 27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred CceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 4567888999999999999999999999876543
No 102
>PRK13764 ATPase; Provisional
Probab=84.49 E-value=1.8 Score=49.84 Aligned_cols=66 Identities=17% Similarity=0.269 Sum_probs=48.8
Q ss_pred HHHHHHHHHHHhhhccCC--CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCC
Q 006320 409 PAQEALLHIQTRIVDLGA--DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPA 474 (650)
Q Consensus 409 ~a~~ai~~i~~~i~~~~~--~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~ 474 (650)
.|.+.|.+...++..... +........+.||...++.+|||+|. |++|++..|..|+|.+.++.+.
T Consensus 456 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~~ 524 (602)
T PRK13764 456 LAEKEIEREIKRYLPGPVEVEVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEPG 524 (602)
T ss_pred HHHHHHHHHHHHhcCCceEEEEecCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcccccc
Confidence 355556655555542111 11245567889999999999999999 9999999999999998776553
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=84.42 E-value=1.6 Score=34.17 Aligned_cols=34 Identities=24% Similarity=0.333 Sum_probs=27.1
Q ss_pred EEEEEEecCcccceeecCCChHHHHHHHHhCCeE
Q 006320 79 TTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWI 112 (650)
Q Consensus 79 ~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I 112 (650)
....+.+.....|.+||++|++|+.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 4555566665689999999999999999988444
No 104
>PRK12705 hypothetical protein; Provisional
Probab=83.82 E-value=2.1 Score=48.16 Aligned_cols=64 Identities=17% Similarity=0.168 Sum_probs=43.2
Q ss_pred EEEEEEcc-ceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcC-HHHHHHHHHHHHHHHhh
Q 006320 193 ATRMVVSR-MHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGD-INNVKNAVAIISSRLRE 267 (650)
Q Consensus 193 ~~~i~Vp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~-~~~V~~A~~~I~~~l~~ 267 (650)
...+-+|+ .+-|.|||+.|.+|+.+...||+.+-|.. .| +.|.|.+- +.--+.|...+..++.+
T Consensus 199 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd----tp-------~~V~ls~fdp~rreia~~~l~~Li~d 264 (508)
T PRK12705 199 VSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD----TP-------EAVVISSFNPIRREIARLTLEKLLAD 264 (508)
T ss_pred eeeeecCChHhhccccCccchhHHHHHHhhCCceEecC----Cc-------cchhhcccCccchHHHHHHHHHHHhc
Confidence 34455554 67899999999999999999999999962 23 23445552 44444455555555444
No 105
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=83.16 E-value=0.85 Score=36.86 Aligned_cols=36 Identities=36% Similarity=0.515 Sum_probs=28.4
Q ss_pred EEEEecCcc-----cceeecCCChHHHHHHHHh-CCeEEEec
Q 006320 81 YRILCHDMK-----AGGVIGKSGSIIKSIRQHT-GAWINVHE 116 (650)
Q Consensus 81 ~rilip~~~-----vg~IIGk~G~~Ik~I~~~t-ga~I~v~~ 116 (650)
..+.+-+.. +|..||++|+.|+.|.++. |-+|+|-+
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 345566666 9999999999999999999 89998854
No 106
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=82.11 E-value=0.39 Score=56.94 Aligned_cols=70 Identities=19% Similarity=0.129 Sum_probs=57.3
Q ss_pred EEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHhh
Q 006320 433 TTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRSY 506 (650)
Q Consensus 433 ~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 506 (650)
.-++.+|-....+|||+||+ |+.++..|||-|.+.. .-|+ ...+|.+.+.|.++.++.|...|.-.+.+-
T Consensus 1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielek--mq~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~Dp 1411 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEK--MQPD--NQAERSKAPKGRPPSQRVATSPIGLPIIDP 1411 (2131)
T ss_pred ccccccchhhhhhhhccCcchhhhHhhccceEEehhh--cCCc--cchhhhcccCCCChhhhhhhccccceeecC
Confidence 34677888899999999999 9999999999999853 1232 256889999999999999988887666554
No 107
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=81.80 E-value=0.94 Score=36.62 Aligned_cols=36 Identities=25% Similarity=0.558 Sum_probs=28.5
Q ss_pred EEEEeecCCc-----ceeeecCCCc-hhhhhhhc-CceEEEec
Q 006320 433 TTRLLVPSSE-----IGCLEGRDGS-LSEMRRST-GANIQILS 468 (650)
Q Consensus 433 ~~~l~Vp~~~-----~g~IIGkgG~-Ik~I~~~T-ga~I~i~~ 468 (650)
.+.+.|-+.. +|.+||++|+ |+.|.++. |-+|+|.-
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 3456676666 8999999999 99999999 99998863
No 108
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=80.63 E-value=2.3 Score=33.32 Aligned_cols=35 Identities=26% Similarity=0.432 Sum_probs=28.1
Q ss_pred cEEEEEEEccceeeeeecCCchHHHHHHhhcCceE
Q 006320 191 RVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQI 225 (650)
Q Consensus 191 ~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I 225 (650)
.....+.+.....+.+||++|.+++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 35566677766789999999999999999887543
No 109
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=80.53 E-value=2.4 Score=46.35 Aligned_cols=64 Identities=20% Similarity=0.208 Sum_probs=45.4
Q ss_pred hHHHHHHHHHHHhhhccCC--CCCCceEEEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCC
Q 006320 408 FPAQEALLHIQTRIVDLGA--DKDNIITTRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREE 471 (650)
Q Consensus 408 ~~a~~ai~~i~~~i~~~~~--~~~~~~~~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~ 471 (650)
..|.+.+.....++..... +......+.+.||...++.+|||+|. |++|++..|-+|.|.+.+.
T Consensus 460 ~~a~~~i~~~i~r~~p~~~eVe~~gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 460 KLAEEEIEREIKRYLPGDVEVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred HHHHHHHHHHHHHhCCCCceEEEecCCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 3455555555555443111 11123457788999999999999999 9999999999999987553
No 110
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=79.72 E-value=3 Score=42.31 Aligned_cols=51 Identities=18% Similarity=0.377 Sum_probs=45.8
Q ss_pred eeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhh
Q 006320 204 GCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRE 267 (650)
Q Consensus 204 g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~ 267 (650)
-+|||.+|++++.|+-.|.|-|-|. -.+|.+.|....++++...|.+++..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVq-------------G~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQ-------------GNTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEee-------------CcEEEeecCcchHHHHHHHHHHHHhc
Confidence 4699999999999999999999985 24789999999999999999999876
No 111
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=79.05 E-value=1.3 Score=42.69 Aligned_cols=159 Identities=17% Similarity=0.159 Sum_probs=89.5
Q ss_pred EEEEEEecCcccceeecCCChHHHHHHHHhCCeEEEecCCCCCCccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhh
Q 006320 79 TTYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHELIPGDEERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRIL 158 (650)
Q Consensus 79 ~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~ 158 (650)
-+-++-||.....-+=-.==..-.-|-+..+.+|.+.- ..|-|.+.-.+.. + ..++.|++..-|...+.
T Consensus 74 e~Rkvpvpp~r~tplk~~W~kIytPive~lklqiRmNl-----K~r~VelRt~~~t-~-----D~s~Lqk~adfv~Af~l 142 (252)
T KOG3273|consen 74 ETRKVPVPPHRYTPLKDNWMKIYTPIVEHLKLQIRMNL-----KARSVELRTCKDT-E-----DPSALQKGADFVRAFIL 142 (252)
T ss_pred ceeeccCCcccCChHHHhhHhhhhHHHHhhhheeEeec-----ccceeEeecCCCC-C-----ChHHHHHHHHHHHHHHh
Confidence 34456666654422111111233446667777777763 3455666433211 1 24567777766666665
Q ss_pred hcCCCCCCCC-CcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCc
Q 006320 159 ESDGGGGFYG-EEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRC 237 (650)
Q Consensus 159 e~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~ 237 (650)
-.+.++...- ..|+-|-. .+ .-.+..+++=.=-+..+|.|+||+|.+--.|++-|.++|-+.
T Consensus 143 GF~i~DAiALlrlddlfle-------sF-Ei~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVla--------- 205 (252)
T KOG3273|consen 143 GFDIDDAIALLRLDDLFLE-------SF-EIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLA--------- 205 (252)
T ss_pred CCcchhHHHHHhhhhhhhe-------ee-eecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEec---------
Confidence 4433221100 00000000 00 000011111111234579999999999999999999999885
Q ss_pred cCCCcceEEEEcCHHHHHHHHHHHHHHHhhcc
Q 006320 238 VSMSEEIVQVVGDINNVKNAVAIISSRLRESQ 269 (650)
Q Consensus 238 ~~~~er~V~I~G~~~~V~~A~~~I~~~l~~~~ 269 (650)
+..|-|-|..++++-|...|+..+..++
T Consensus 206 ----d~kIHiLG~~~niriAR~avcsLIlGsp 233 (252)
T KOG3273|consen 206 ----DSKIHILGAFQNIRIARDAVCSLILGSP 233 (252)
T ss_pred ----CceEEEeecchhhHHHHHhhHhhhccCC
Confidence 3468999999999999999999998764
No 112
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=79.04 E-value=0.58 Score=55.59 Aligned_cols=70 Identities=16% Similarity=0.157 Sum_probs=59.2
Q ss_pred EEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHHhh
Q 006320 193 ATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRLRE 267 (650)
Q Consensus 193 ~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~~ 267 (650)
..++.+|-....++||++|++|+.++.-||+.|.|.. +-|. ...||.+.+.|.++.++.|...|...+.+
T Consensus 1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielek---mq~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEK---MQPD--NQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred ccccccchhhhhhhhccCcchhhhHhhccceEEehhh---cCCc--cchhhhcccCCCChhhhhhhccccceeec
Confidence 4567888888999999999999999999999999964 1122 15689999999999999999998887765
No 113
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=78.11 E-value=1.1 Score=36.82 Aligned_cols=34 Identities=12% Similarity=0.040 Sum_probs=29.2
Q ss_pred ceEEEEecCCcccccccCCCcchhhHHHhcCCeE
Q 006320 604 STLEVVLPDYAVPKLITKSKTLLTRFSEVSLLLH 637 (650)
Q Consensus 604 ~t~~v~IP~~~~g~vIGk~G~~I~~Ir~~SGA~i 637 (650)
....+++-.+.-+.|||++|++|+.|++.++-.+
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 5678999999999999999999999988665444
No 114
>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=77.35 E-value=2.5 Score=34.85 Aligned_cols=35 Identities=20% Similarity=0.268 Sum_probs=27.2
Q ss_pred EEEEEecCcccceeecCCChHHHHHHHHhCCeEEE
Q 006320 80 TYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINV 114 (650)
Q Consensus 80 ~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v 114 (650)
.+.+.+.....|.+|||.|+++.+||--.+.-++-
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~ 59 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR 59 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence 34455567788999999999999999887655543
No 115
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=76.47 E-value=5.7 Score=39.91 Aligned_cols=62 Identities=19% Similarity=0.248 Sum_probs=45.8
Q ss_pred EEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHH-HHHHHHHHHHHHhh
Q 006320 194 TRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINN-VKNAVAIISSRLRE 267 (650)
Q Consensus 194 ~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~-V~~A~~~I~~~l~~ 267 (650)
.-+.|+...|.++||++|+.++-|.++++|+|-|-.. -.|=|.+..+. ...|...|..+=++
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N------------G~IWV~~~~~~~e~~~~~aI~~ie~e 210 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN------------GRIWVDGENESLEELAIEAIRKIERE 210 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC------------CEEEecCCCcchHHHHHHHHHHHhhh
Confidence 4578999999999999999999999999999999532 24667776553 44455555544433
No 116
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=76.42 E-value=11 Score=41.93 Aligned_cols=37 Identities=22% Similarity=0.276 Sum_probs=31.9
Q ss_pred EEEEEeecccccceecCCchhHHHHHHHhCCeEEEeC
Q 006320 349 VFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVAD 385 (650)
Q Consensus 349 ~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~ 385 (650)
+-++.|-.++-|.+|||+|++.++|..++|-.-+|..
T Consensus 100 tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR 136 (637)
T COG1782 100 TGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVR 136 (637)
T ss_pred CceEEEEecCCceEEecCchHHHHHHHHhCCcceeee
Confidence 4568888999999999999999999999997766643
No 117
>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=75.02 E-value=8.5 Score=35.68 Aligned_cols=37 Identities=24% Similarity=0.304 Sum_probs=32.2
Q ss_pred EEEEEeecccccceecCCchhHHHHHHHhCCeEEEeC
Q 006320 349 VFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVAD 385 (650)
Q Consensus 349 ~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~ 385 (650)
+-++.|-.++-|.+||++|.++++|..++|-.-.+-.
T Consensus 77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvR 113 (145)
T cd02410 77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVR 113 (145)
T ss_pred CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence 4468888999999999999999999999998777654
No 118
>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=74.34 E-value=1.7 Score=35.80 Aligned_cols=33 Identities=36% Similarity=0.421 Sum_probs=27.8
Q ss_pred EEEEEecCcccceeecCCChHHHHHHHHhCCeE
Q 006320 80 TYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWI 112 (650)
Q Consensus 80 ~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I 112 (650)
...+.+.....+.|||++|++|+.|+++.+-.+
T Consensus 26 ~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 26 QIIIVIKASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp EEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred eEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 456778889999999999999999998865544
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=72.88 E-value=17 Score=33.73 Aligned_cols=89 Identities=21% Similarity=0.308 Sum_probs=56.8
Q ss_pred ecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHH---hhhccCCCCCCceEEEEeec
Q 006320 363 IGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQT---RIVDLGADKDNIITTRLLVP 439 (650)
Q Consensus 363 IGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~---~i~~~~~~~~~~~~~~l~Vp 439 (650)
+-.++..|++|.++..-+|.|-... . + . ..-..|.+.|.++.. .+.+..++ ..+-++.|-
T Consensus 21 ~~~~~dli~~lAk~lrKRIvvR~dp-----s-~-l-------~~~e~A~~~I~~ivP~ea~i~di~Fd---~~tGEV~Ie 83 (145)
T cd02410 21 FAEDGDLVKDLAKDLRKRIVIRPDP-----S-V-L-------KPPEEAIKIILEIVPEEAGITDIYFD---DDTGEVIIE 83 (145)
T ss_pred HhcccHHHHHHHHHHhceEEEcCCh-----h-h-c-------CCHHHHHHHHHHhCCCccCceeeEec---CCCcEEEEE
Confidence 3456789999999988777773210 0 0 0 011345555655542 23332222 234456666
Q ss_pred CCcceeeecCCCc-hhhhhhhcCceEEEec
Q 006320 440 SSEIGCLEGRDGS-LSEMRRSTGANIQILS 468 (650)
Q Consensus 440 ~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~ 468 (650)
...-|.+||++|. +++|..+||-.-.|..
T Consensus 84 aeKPG~ViGk~g~~~reI~~~tgW~p~vvR 113 (145)
T cd02410 84 AEKPGLVIGKGGSTLREITRETGWAPKVVR 113 (145)
T ss_pred EcCCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence 6778999999999 9999999999988863
No 120
>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=72.86 E-value=2.4 Score=34.96 Aligned_cols=44 Identities=23% Similarity=0.234 Sum_probs=32.0
Q ss_pred ceEEEEecCCcccccccCCCcchhhHHHhcCCeEEEEEeeeEEE
Q 006320 604 STLEVVLPDYAVPKLITKSKTLLTRFSEVSLLLHLINLFNFVKV 647 (650)
Q Consensus 604 ~t~~v~IP~~~~g~vIGk~G~~I~~Ir~~SGA~i~i~~~~~~~~ 647 (650)
....+.|..+..|.+|||.|+.|+.|+-...+.+.-+...+.+|
T Consensus 24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~~~~~~~~v 67 (77)
T cd02414 24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNRNTGEYVRI 67 (77)
T ss_pred CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhhccCCceEE
Confidence 35667777788999999999999999887665554444444443
No 121
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=72.28 E-value=4.1 Score=34.00 Aligned_cols=37 Identities=19% Similarity=0.332 Sum_probs=30.7
Q ss_pred EEEEEecCcccceeecCCChHHHHHHHHhCCeEEEec
Q 006320 80 TYRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHE 116 (650)
Q Consensus 80 ~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~ 116 (650)
..++.+....-|.|||++|+.|++|+++-.-...+++
T Consensus 31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~ 67 (81)
T cd02413 31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPE 67 (81)
T ss_pred eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCC
Confidence 4678888999999999999999999998766655543
No 122
>PRK13764 ATPase; Provisional
Probab=72.01 E-value=2.8 Score=48.26 Aligned_cols=43 Identities=16% Similarity=0.221 Sum_probs=38.4
Q ss_pred cccccceEEEEecCCcccccccCCCcchhhHHHhcCCeEEEEE
Q 006320 599 PLVTRSTLEVVLPDYAVPKLITKSKTLLTRFSEVSLLLHLINL 641 (650)
Q Consensus 599 ~l~t~~t~~v~IP~~~~g~vIGk~G~~I~~Ir~~SGA~i~i~~ 641 (650)
.+....+..|.||..+++.+|||+|.+|+.|.+.-|-+|-|-.
T Consensus 476 ~~~~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~ 518 (602)
T PRK13764 476 EVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP 518 (602)
T ss_pred EEecCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence 4446778889999999999999999999999999999998754
No 123
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=70.19 E-value=4.8 Score=38.35 Aligned_cols=35 Identities=29% Similarity=0.335 Sum_probs=30.1
Q ss_pred EEEEecCcccceeecCCChHHHHHHHHhCCeEEEec
Q 006320 81 YRILCHDMKAGGVIGKSGSIIKSIRQHTGAWINVHE 116 (650)
Q Consensus 81 ~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~ 116 (650)
+=|++.... |.-|||+|++|++|++..|-+|.|-+
T Consensus 63 vIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 63 VILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 345666677 99999999999999999999999865
No 124
>COG1159 Era GTPase [General function prediction only]
Probab=69.46 E-value=3.5 Score=42.80 Aligned_cols=45 Identities=13% Similarity=0.080 Sum_probs=35.9
Q ss_pred ceEEEEecC-CcccccccCCCcchhhHHHhcCC------eEEEEEeeeEEEe
Q 006320 604 STLEVVLPD-YAVPKLITKSKTLLTRFSEVSLL------LHLINLFNFVKVY 648 (650)
Q Consensus 604 ~t~~v~IP~-~~~g~vIGk~G~~I~~Ir~~SGA------~i~i~~~~~~~~~ 648 (650)
+...+.|+. +.=+-|||++|+.|+.|...+=. -+.++++-||||.
T Consensus 229 I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L~L~VKVk 280 (298)
T COG1159 229 IHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYLELWVKVK 280 (298)
T ss_pred EEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEEEEEEEEc
Confidence 567788888 88899999999999988665433 2457888899986
No 125
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=69.07 E-value=18 Score=40.25 Aligned_cols=91 Identities=18% Similarity=0.284 Sum_probs=60.2
Q ss_pred ceecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHH---hhhccCCCCCCceEEEEe
Q 006320 361 RVIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQT---RIVDLGADKDNIITTRLL 437 (650)
Q Consensus 361 ~IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~---~i~~~~~~~~~~~~~~l~ 437 (650)
.++-+.|..|++|.++..-+|.|-... . + .+ ....|.+.|+++.. .|.+... ...+-++.
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~dP-s-----v-l~-------~~e~A~~~I~eivP~ea~i~~i~F---d~~tGEVi 104 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPDP-S-----V-LK-------PPEEARKIILEIVPEEAGITDIYF---DDDTGEVI 104 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccCc-h-----h-cC-------CHHHHHHHHHHhCccccCceeEEe---cCCCceEE
Confidence 345578899999999998887774311 0 0 11 12345556665552 2232211 12345677
Q ss_pred ecCCcceeeecCCCc-hhhhhhhcCceEEEec
Q 006320 438 VPSSEIGCLEGRDGS-LSEMRRSTGANIQILS 468 (650)
Q Consensus 438 Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~ 468 (650)
|-...-|.+|||+|+ .++|.++||-.-+|..
T Consensus 105 Iea~KPGlvigk~g~~~reI~~~tgW~p~ivR 136 (637)
T COG1782 105 IEAKKPGLVIGKGGSTLREITAETGWAPKIVR 136 (637)
T ss_pred EEecCCceEEecCchHHHHHHHHhCCcceeee
Confidence 777888999999999 9999999998887763
No 126
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=68.13 E-value=5.8 Score=37.84 Aligned_cols=36 Identities=22% Similarity=0.403 Sum_probs=31.5
Q ss_pred EEEEEEccceeeeeecCCchHHHHHHhhcCceEEEec
Q 006320 193 ATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILP 229 (650)
Q Consensus 193 ~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~ 229 (650)
-+-++|.... |.-|||+|++|+++++..|-+|.+..
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 3557777777 99999999999999999999999973
No 127
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=67.93 E-value=11 Score=38.00 Aligned_cols=56 Identities=21% Similarity=0.369 Sum_probs=40.7
Q ss_pred EEEeecCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHH-HHHHHHHHH
Q 006320 434 TRLLVPSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQA-ARDALVEVT 500 (650)
Q Consensus 434 ~~l~Vp~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~-v~~A~~~I~ 500 (650)
.-+.|+...+-++||++|+ ++-+.+.|+|+|-|-. .-.|-|.++.+. ...|...|.
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-----------NG~IWV~~~~~~~e~~~~~aI~ 205 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-----------NGRIWVDGENESLEELAIEAIR 205 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-----------CCEEEecCCCcchHHHHHHHHH
Confidence 3467899999999999999 9999999999996632 234677776552 333433333
No 128
>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=65.91 E-value=5.9 Score=33.05 Aligned_cols=30 Identities=3% Similarity=0.205 Sum_probs=26.3
Q ss_pred ceEEEEecCCcccccccCCCcchhhHHHhc
Q 006320 604 STLEVVLPDYAVPKLITKSKTLLTRFSEVS 633 (650)
Q Consensus 604 ~t~~v~IP~~~~g~vIGk~G~~I~~Ir~~S 633 (650)
...+|.|-...-|.|||++|++|+.|++.-
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L 59 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSLV 59 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHHH
Confidence 457888888999999999999999999864
No 129
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=62.28 E-value=6.7 Score=34.68 Aligned_cols=29 Identities=28% Similarity=0.495 Sum_probs=25.3
Q ss_pred EEEEecCcccceeecCCChHHHHHHHHhC
Q 006320 81 YRILCHDMKAGGVIGKSGSIIKSIRQHTG 109 (650)
Q Consensus 81 ~rilip~~~vg~IIGk~G~~Ik~I~~~tg 109 (650)
+++.+...+-|.|||++|+.|++|++...
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 57777888899999999999999998754
No 130
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=60.91 E-value=15 Score=42.76 Aligned_cols=90 Identities=18% Similarity=0.270 Sum_probs=58.8
Q ss_pred eecCCchhHHHHHHHhCCeEEEeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHH---hhhccCCCCCCceEEEEee
Q 006320 362 VIGESEGIVELLQNEIGVDLKVADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQT---RIVDLGADKDNIITTRLLV 438 (650)
Q Consensus 362 IIGk~G~~Ik~l~~~tga~I~i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~---~i~~~~~~~~~~~~~~l~V 438 (650)
.+-.++..|++|.++..-+|.|-... . +. ..-..|.+.|.++.. .|.+... +..+-++.|
T Consensus 37 ~~~~~~~~~~~~~~~~~~r~~~~~~~-----~-~~--------~~~~~~~~~i~~~~~~~~~~~~~~f---~~~~~~v~i 99 (630)
T TIGR03675 37 LFAKDDDLVKELAKKLRKRIVIRPDP-----S-VL--------LPPEEAIEKIKEIVPEEAGITDIYF---DDVTGEVII 99 (630)
T ss_pred HhccchHHHHHHHHHhhceEEEecCh-----h-hc--------CCHHHHHHHHHHhCCCcCCceeEEe---cCCCceEEE
Confidence 44567899999999988777773210 0 00 011345555555542 2222211 233456777
Q ss_pred cCCcceeeecCCCc-hhhhhhhcCceEEEec
Q 006320 439 PSSEIGCLEGRDGS-LSEMRRSTGANIQILS 468 (650)
Q Consensus 439 p~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~ 468 (650)
-...-|.+|||+|+ +++|.++||-.-+|..
T Consensus 100 ~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~ 130 (630)
T TIGR03675 100 EAEKPGLVIGKGGSTLREITAETGWTPKVVR 130 (630)
T ss_pred EEcCCeEEEecCcchHHHHHHHhCCeeeEEe
Confidence 77788999999999 8999999999988863
No 131
>PRK00089 era GTPase Era; Reviewed
Probab=59.60 E-value=6.9 Score=40.75 Aligned_cols=44 Identities=16% Similarity=0.091 Sum_probs=35.2
Q ss_pred ceEEEEecC-CcccccccCCCcchhhHHHhcCC------eEEEEEeeeEEE
Q 006320 604 STLEVVLPD-YAVPKLITKSKTLLTRFSEVSLL------LHLINLFNFVKV 647 (650)
Q Consensus 604 ~t~~v~IP~-~~~g~vIGk~G~~I~~Ir~~SGA------~i~i~~~~~~~~ 647 (650)
+..++.|.. +.-+-|||++|+.|++|...+-. .+.|+++.||||
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~l~vkv 276 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLELWVKV 276 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEEEEEEE
Confidence 667788887 77888999999999998765543 246788888887
No 132
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=57.61 E-value=16 Score=37.29 Aligned_cols=50 Identities=20% Similarity=0.292 Sum_probs=42.4
Q ss_pred eeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEecHHHHHHHHHHHHHHHHh
Q 006320 444 GCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGEIQAARDALVEVTTRLRS 505 (650)
Q Consensus 444 g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~ 505 (650)
-+|||.+|+ +|.|+-.|.|.|-|. ..+|.+.|....++++...+.+.+..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVq------------G~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQ------------GNTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEee------------CcEEEeecCcchHHHHHHHHHHHHhc
Confidence 689999999 999999999999774 33699999999999888777776653
No 133
>PRK15494 era GTPase Era; Provisional
Probab=56.36 E-value=8.5 Score=41.27 Aligned_cols=44 Identities=20% Similarity=0.236 Sum_probs=34.7
Q ss_pred ceEEEEecC-CcccccccCCCcchhhHHHhcCC------eEEEEEeeeEEE
Q 006320 604 STLEVVLPD-YAVPKLITKSKTLLTRFSEVSLL------LHLINLFNFVKV 647 (650)
Q Consensus 604 ~t~~v~IP~-~~~g~vIGk~G~~I~~Ir~~SGA------~i~i~~~~~~~~ 647 (650)
+...+.|.. +.-+-|||++|+.|++|...+=. .+.|+++-||||
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~l~Vkv 323 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLFLFVKV 323 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEEEEEEE
Confidence 567788888 78889999999999998765432 236778888887
No 134
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=55.95 E-value=12 Score=31.51 Aligned_cols=28 Identities=25% Similarity=0.376 Sum_probs=23.3
Q ss_pred EEEEecCcccceeecCCChHHHHHHHHh
Q 006320 81 YRILCHDMKAGGVIGKSGSIIKSIRQHT 108 (650)
Q Consensus 81 ~rilip~~~vg~IIGk~G~~Ik~I~~~t 108 (650)
.++.+....-|.+||++|..|++|++.-
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHHH
Confidence 5556666888999999999999998874
No 135
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=54.63 E-value=14 Score=41.00 Aligned_cols=36 Identities=14% Similarity=0.266 Sum_probs=33.1
Q ss_pred EEEEEEccceeeeeecCCchHHHHHHhhcCceEEEe
Q 006320 193 ATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRIL 228 (650)
Q Consensus 193 ~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~ 228 (650)
++.+.+|...|..|||-||..|++++...++.|++.
T Consensus 450 e~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~ 485 (657)
T COG5166 450 EIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFK 485 (657)
T ss_pred heEEEeecccceeeeccCchhhHHhhhhhhhhhhhh
Confidence 577899999999999999999999999999988875
No 136
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=54.05 E-value=11 Score=37.89 Aligned_cols=40 Identities=13% Similarity=0.003 Sum_probs=32.6
Q ss_pred cceEEEEecCCcccccccCCCcchhhHHH----hcCC-eEEEEEe
Q 006320 603 RSTLEVVLPDYAVPKLITKSKTLLTRFSE----VSLL-LHLINLF 642 (650)
Q Consensus 603 ~~t~~v~IP~~~~g~vIGk~G~~I~~Ir~----~SGA-~i~i~~~ 642 (650)
...+.|+|-...=|.|||++|++|.+|++ ..|. .+.||..
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~~v~I~i~ 94 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKENVQINIE 94 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCCCceEEEE
Confidence 35778899999999999999999999886 5666 5776654
No 137
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=53.06 E-value=11 Score=41.55 Aligned_cols=128 Identities=13% Similarity=0.104 Sum_probs=76.7
Q ss_pred ceecCCchhHHHHHHHhCCeEE--EeCCCCCCCccEEEecCCCCCCCcchHHHHHHHHHHHhhhccCCCCCCceEEEEee
Q 006320 361 RVIGESEGIVELLQNEIGVDLK--VADPVDGSDEQIITISSEEGPDDELFPAQEALLHIQTRIVDLGADKDNIITTRLLV 438 (650)
Q Consensus 361 ~IIGk~G~~Ik~l~~~tga~I~--i~~~~~~~~er~i~I~G~~g~~~~~~~a~~ai~~i~~~i~~~~~~~~~~~~~~l~V 438 (650)
.|-||+.-.+.+|.+..-|.+. +... .++ ++.+.. . |..-..+ +++- + ...+-+-.+.+.+
T Consensus 393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~-~gs--~~~~~~-~-g~~~~F~---k~~~-~--------~~~EFpae~~f~i 455 (657)
T COG5166 393 FLRGKKNGKATRIMKGVSCSELSSIVSS-TGS--IVETNG-I-GEKMSFS---KKLS-I--------PPTEFPAEIAFII 455 (657)
T ss_pred HhccccCcchhhhhhhcccceeeEEEec-CCc--EEEEec-c-CcchhhH---HHhc-C--------CcccCchheEEEe
Confidence 6778777678888888877743 4331 122 333322 1 1111111 1111 0 1234456788999
Q ss_pred cCCcceeeecCCCc-hhhhhhhcCceEEEecCCCCCCCCCCCCeEEEEEec---HHHHHHHHHHHHHHHHhhh
Q 006320 439 PSSEIGCLEGRDGS-LSEMRRSTGANIQILSREEVPACVSGTDELVQIVGE---IQAARDALVEVTTRLRSYL 507 (650)
Q Consensus 439 p~~~~g~IIGkgG~-Ik~I~~~Tga~I~i~~~~~~p~~~~~~~r~v~I~G~---~~~v~~A~~~I~~~l~~~~ 507 (650)
|...|..|||-||. |.+++...++.|++...-..|.. ...|. |.|.-+ .+++--|+.-+++++.++.
T Consensus 456 ~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs-~~~dN-V~I~~PrKn~~ni~~~KNd~~~~V~~~c 526 (657)
T COG5166 456 MESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQS-QWHDN-VLIEAPRKNQDNISGKKNDKLDKVKQQC 526 (657)
T ss_pred ecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchh-hhhcc-eEEECCccCccchhcccccHHHHHhhhc
Confidence 99999999999999 99999999999988654444432 11121 445443 3455556666777777553
No 138
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=52.07 E-value=12 Score=37.47 Aligned_cols=30 Identities=37% Similarity=0.550 Sum_probs=26.3
Q ss_pred EEEEEEecCcccceeecCCChHHHHHHHHh
Q 006320 79 TTYRILCHDMKAGGVIGKSGSIIKSIRQHT 108 (650)
Q Consensus 79 ~~~rilip~~~vg~IIGk~G~~Ik~I~~~t 108 (650)
...++.|....-|.|||++|+.|++|+++-
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~l 80 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKEL 80 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHHH
Confidence 356788899999999999999999998874
No 139
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=50.90 E-value=38 Score=39.53 Aligned_cols=38 Identities=24% Similarity=0.309 Sum_probs=33.2
Q ss_pred eEEEEEeecccccceecCCchhHHHHHHHhCCeEEEeC
Q 006320 348 LVFRMLCPIDKVGRVIGESEGIVELLQNEIGVDLKVAD 385 (650)
Q Consensus 348 ~~~~i~vp~~~vg~IIGk~G~~Ik~l~~~tga~I~i~~ 385 (650)
.+-++.|-.++-|.||||+|.++++|.+++|-.-+|..
T Consensus 93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~ 130 (630)
T TIGR03675 93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVR 130 (630)
T ss_pred CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEe
Confidence 34568889999999999999999999999998877754
No 140
>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=50.01 E-value=14 Score=30.96 Aligned_cols=27 Identities=7% Similarity=0.148 Sum_probs=22.2
Q ss_pred EEEEecCCcccccccCCCcchhhHHHh
Q 006320 606 LEVVLPDYAVPKLITKSKTLLTRFSEV 632 (650)
Q Consensus 606 ~~v~IP~~~~g~vIGk~G~~I~~Ir~~ 632 (650)
.+|.|-...-|.+||++|.+|+.+++.
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~ 66 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEI 66 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHH
Confidence 555555578899999999999999874
No 141
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=48.06 E-value=12 Score=38.69 Aligned_cols=43 Identities=14% Similarity=0.024 Sum_probs=32.8
Q ss_pred ceEEEEecC-CcccccccCCCcchhhHHHhcCCe------EEEEEeeeEE
Q 006320 604 STLEVVLPD-YAVPKLITKSKTLLTRFSEVSLLL------HLINLFNFVK 646 (650)
Q Consensus 604 ~t~~v~IP~-~~~g~vIGk~G~~I~~Ir~~SGA~------i~i~~~~~~~ 646 (650)
+...+.|.. +.-+-|||++|+.|++|...+-.. +.+|++-|||
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ar~~l~~~~~~~v~l~l~vk 270 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIAARKDILELFDCDVFLELFVK 270 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCEEEEEEEC
Confidence 677889988 788899999999999987655432 3566666664
No 142
>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=46.50 E-value=16 Score=32.29 Aligned_cols=30 Identities=27% Similarity=0.475 Sum_probs=24.8
Q ss_pred EEEEEEccceeeeeecCCchHHHHHHhhcC
Q 006320 193 ATRMVVSRMHVGCLLGKGGKIIEQMRMETK 222 (650)
Q Consensus 193 ~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tg 222 (650)
.+++.|....-|.|||++|+.|++|++...
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~ 91 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQ 91 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence 366777777889999999999999987643
No 143
>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=35.96 E-value=39 Score=34.74 Aligned_cols=29 Identities=17% Similarity=0.416 Sum_probs=23.3
Q ss_pred EEEEEEEc-cceeeeeecCCchHHHHHHhh
Q 006320 192 VATRMVVS-RMHVGCLLGKGGKIIEQMRME 220 (650)
Q Consensus 192 ~~~~i~Vp-~~~vg~IIGk~G~~Ik~I~~~ 220 (650)
+.+.|+|. .+|-+.|||++|+.||+|..+
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ 250 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIA 250 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence 56677887 557799999999999987644
No 144
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=32.55 E-value=32 Score=36.11 Aligned_cols=32 Identities=22% Similarity=0.188 Sum_probs=26.9
Q ss_pred cceEEEEecC-CcccccccCCCcchhhHHHhcC
Q 006320 603 RSTLEVVLPD-YAVPKLITKSKTLLTRFSEVSL 634 (650)
Q Consensus 603 ~~t~~v~IP~-~~~g~vIGk~G~~I~~Ir~~SG 634 (650)
.+.++|++|. ++...|||+||.+|.+|-+.-+
T Consensus 327 ~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 327 FIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 4789999999 7777889999999999866543
No 145
>PRK15494 era GTPase Era; Provisional
Probab=32.30 E-value=48 Score=35.48 Aligned_cols=29 Identities=28% Similarity=0.412 Sum_probs=22.8
Q ss_pred EEEEEEEc-cceeeeeecCCchHHHHHHhh
Q 006320 192 VATRMVVS-RMHVGCLLGKGGKIIEQMRME 220 (650)
Q Consensus 192 ~~~~i~Vp-~~~vg~IIGk~G~~Ik~I~~~ 220 (650)
+...|+|. .+|-+.|||++|+.||+|..+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 55677787 457789999999999987643
No 146
>PRK00089 era GTPase Era; Reviewed
Probab=31.80 E-value=50 Score=34.28 Aligned_cols=29 Identities=24% Similarity=0.604 Sum_probs=22.6
Q ss_pred EEEEEEEc-cceeeeeecCCchHHHHHHhh
Q 006320 192 VATRMVVS-RMHVGCLLGKGGKIIEQMRME 220 (650)
Q Consensus 192 ~~~~i~Vp-~~~vg~IIGk~G~~Ik~I~~~ 220 (650)
+...|.|. .++-+.|||++|+.|++|..+
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ 255 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTE 255 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHH
Confidence 55667777 557789999999999987643
No 147
>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=28.79 E-value=54 Score=32.24 Aligned_cols=31 Identities=19% Similarity=0.404 Sum_probs=26.3
Q ss_pred EEEEEecCcccceeecCCChHHHHHHHHhCC
Q 006320 80 TYRILCHDMKAGGVIGKSGSIIKSIRQHTGA 110 (650)
Q Consensus 80 ~~rilip~~~vg~IIGk~G~~Ik~I~~~tga 110 (650)
.+++.+....-|.|||++|..|++|+++-.-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k 69 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKLQK 69 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHHHH
Confidence 4677888888999999999999999987543
No 148
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=27.42 E-value=54 Score=34.49 Aligned_cols=33 Identities=27% Similarity=0.417 Sum_probs=25.7
Q ss_pred CcEEEEEEEcc-ceeeeeecCCchHHHHHHhhcC
Q 006320 190 NRVATRMVVSR-MHVGCLLGKGGKIIEQMRMETK 222 (650)
Q Consensus 190 ~~~~~~i~Vp~-~~vg~IIGk~G~~Ik~I~~~tg 222 (650)
-.+..++++|. .+...||||+|..|.+|-.+.+
T Consensus 326 l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 326 LFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 34567788884 5778899999999999876544
No 149
>COG1159 Era GTPase [General function prediction only]
Probab=27.36 E-value=64 Score=33.71 Aligned_cols=29 Identities=21% Similarity=0.535 Sum_probs=22.6
Q ss_pred cEEEEEEEc-cceeeeeecCCchHHHHHHh
Q 006320 191 RVATRMVVS-RMHVGCLLGKGGKIIEQMRM 219 (650)
Q Consensus 191 ~~~~~i~Vp-~~~vg~IIGk~G~~Ik~I~~ 219 (650)
.+...|+|+ .+|-+-||||+|+.||+|-.
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 345567787 45789999999999998753
No 150
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=26.92 E-value=59 Score=32.29 Aligned_cols=31 Identities=26% Similarity=0.324 Sum_probs=25.3
Q ss_pred EEEEecCcccceeecCCChHHHHHHHHhCCe
Q 006320 81 YRILCHDMKAGGVIGKSGSIIKSIRQHTGAW 111 (650)
Q Consensus 81 ~rilip~~~vg~IIGk~G~~Ik~I~~~tga~ 111 (650)
.++.+....-|.+||++|++|++|++.-.-.
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk~ 72 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEKK 72 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHHH
Confidence 5566666888999999999999999886543
No 151
>CHL00048 rps3 ribosomal protein S3
Probab=26.91 E-value=59 Score=32.45 Aligned_cols=30 Identities=10% Similarity=0.074 Sum_probs=25.6
Q ss_pred EEEEEecCcccceeecCCChHHHHHHHHhC
Q 006320 80 TYRILCHDMKAGGVIGKSGSIIKSIRQHTG 109 (650)
Q Consensus 80 ~~rilip~~~vg~IIGk~G~~Ik~I~~~tg 109 (650)
.+++.+.....|.|||++|..|++|++.-.
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 467777788889999999999999998864
No 152
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=25.85 E-value=61 Score=32.47 Aligned_cols=32 Identities=16% Similarity=0.286 Sum_probs=26.7
Q ss_pred EEEEecCcccceeecCCChHHHHHHHHhCCeE
Q 006320 81 YRILCHDMKAGGVIGKSGSIIKSIRQHTGAWI 112 (650)
Q Consensus 81 ~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I 112 (650)
+++.+....-|.|||++|..|++|+++-.-.+
T Consensus 46 i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~ 77 (220)
T PTZ00084 46 TEIIIRATRTREVLGDKGRRIRELTSLLQKRF 77 (220)
T ss_pred EEEEEEECCCccEEcCCchHHHHHHHHHHHHh
Confidence 67777888889999999999999998865443
No 153
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=22.77 E-value=1.2e+02 Score=26.75 Aligned_cols=26 Identities=27% Similarity=0.397 Sum_probs=23.7
Q ss_pred EEEEEecHHHHHHHHHHHHHHHHhhh
Q 006320 482 LVQIVGEIQAARDALVEVTTRLRSYL 507 (650)
Q Consensus 482 ~v~I~G~~~~v~~A~~~I~~~l~~~~ 507 (650)
.+.|+|+..+|+.|++.+.+.|++.+
T Consensus 76 slvitGdvs~Ve~Al~~V~~~l~~~L 101 (111)
T PRK15468 76 ALVIYGSVGAVEEALSQTVSGLGRLL 101 (111)
T ss_pred eEEEEccHHHHHHHHHHHHHHHHhhc
Confidence 48899999999999999999999864
No 154
>PRK03818 putative transporter; Validated
Probab=22.40 E-value=1.1e+03 Score=26.97 Aligned_cols=136 Identities=16% Similarity=0.173 Sum_probs=0.0
Q ss_pred ChHHHHHHHHhCCeEEEec---------CCCCC---CccEEEEecCCCCCCCCCCCCccHHHHHHHHHHHHhhhcCCCCC
Q 006320 98 GSIIKSIRQHTGAWINVHE---------LIPGD---EERIIEISDTRRRDPEGRMPSFSPAQEALFLIHDRILESDGGGG 165 (650)
Q Consensus 98 G~~Ik~I~~~tga~I~v~~---------~~~~~---~ervi~I~G~~~~~~~~~~~~~~~a~~A~~~i~~~i~e~~~~~~ 165 (650)
|.+++++.......+.|.. +.++. ...++.|.|. .+++..+.+.+-.......
T Consensus 218 GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~---------------~e~l~~l~~~~Gl~~~~~~ 282 (552)
T PRK03818 218 GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQ---------------PEDLHKAQLVIGEEVDTSL 282 (552)
T ss_pred CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEEC---------------HHHHHHHHHhcCCccCccc
Q ss_pred CCCCcccccCCCCCCCCCCCCCCCCcEEEEEEEccceeeeeecCCchHHHHH--HhhcCceE-EEecCCCCCCCccC---
Q 006320 166 FYGEEEEEYGGGGGVGGGGFRGGGNRVATRMVVSRMHVGCLLGKGGKIIEQM--RMETKTQI-RILPRDHSLPRCVS--- 239 (650)
Q Consensus 166 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I--~~~tga~I-~i~~~~~~lp~~~~--- 239 (650)
...+.....+.+++.+ ..++|| +++++ ++..|+.| .|.+.+..++...+
T Consensus 283 --------------------~~~~~~~~~E~Vvv~~--S~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~L 337 (552)
T PRK03818 283 --------------------STRGTDLRSERVVVTN--EKVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLSL 337 (552)
T ss_pred --------------------cccCcceEEEEEEEcC--hhccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCEE
Q ss_pred CCcceEEEEcCHHHHHHHHHHHHHHHhhcccCCC
Q 006320 240 MSEEIVQVVGDINNVKNAVAIISSRLRESQHRDR 273 (650)
Q Consensus 240 ~~er~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~ 273 (650)
..-..+.+.|++++++++.+.+.+..++....+.
T Consensus 338 q~GD~LlVvG~~~~i~~l~~~Lg~~~~~~~~~~~ 371 (552)
T PRK03818 338 QFGDILNLVGRPEAIDAVANVLGNAQQKLQQVQM 371 (552)
T ss_pred ecCCEEEEEECHHHHHHHHHHhCCcccccccCCh
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=21.90 E-value=2.4e+02 Score=26.93 Aligned_cols=58 Identities=14% Similarity=0.117 Sum_probs=43.5
Q ss_pred CCcEEEEEEEccceeeeeecCCchHHHHHHhhcCceEEEecCCCCCCCccCCCcceEEEEcCHHHHHHHHHHHHHHH
Q 006320 189 GNRVATRMVVSRMHVGCLLGKGGKIIEQMRMETKTQIRILPRDHSLPRCVSMSEEIVQVVGDINNVKNAVAIISSRL 265 (650)
Q Consensus 189 ~~~~~~~i~Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~lp~~~~~~er~V~I~G~~~~V~~A~~~I~~~l 265 (650)
.+..++|+-++...+ =..++.|.+-.|+-+.+. .+..|.|.|..+.|.+|++.+..+-
T Consensus 110 ~~~~~iRv~l~~~i~-------~erl~ei~E~~gvI~Efe------------e~~~V~I~Gdke~Ik~aLKe~s~~w 167 (169)
T PF09869_consen 110 PGFETIRVKLKKPIQ-------EERLQEISEWHGVIFEFE------------EDDKVVIEGDKERIKKALKEFSSFW 167 (169)
T ss_pred CCceeEEEecCccch-------HHHHHHHHHHhceeEEec------------CCcEEEEeccHHHHHHHHHHHHHHh
Confidence 345567777776543 256678888889888872 2457999999999999999987653
No 156
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=20.69 E-value=72 Score=31.51 Aligned_cols=26 Identities=23% Similarity=0.435 Sum_probs=0.0
Q ss_pred EEEEEecCcccceeecCCChHHHHHH
Q 006320 80 TYRILCHDMKAGGVIGKSGSIIKSIR 105 (650)
Q Consensus 80 ~~rilip~~~vg~IIGk~G~~Ik~I~ 105 (650)
.+.+-+..+..+.|||+.|+++..||
T Consensus 92 ~v~~~i~~~~~~~LIG~~Gk~LdALQ 117 (208)
T COG1847 92 RVVVSIEGEDAGRLIGKHGKTLDALQ 117 (208)
T ss_pred EEEEEecCCchhhhhccCCcchHHHH
No 157
>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=20.23 E-value=81 Score=31.00 Aligned_cols=29 Identities=10% Similarity=0.069 Sum_probs=24.7
Q ss_pred ceEEEEecCCcccccccCCCcchhhHHHh
Q 006320 604 STLEVVLPDYAVPKLITKSKTLLTRFSEV 632 (650)
Q Consensus 604 ~t~~v~IP~~~~g~vIGk~G~~I~~Ir~~ 632 (650)
.-++|.|-...-|.|||+.|.+|+++++.
T Consensus 38 ~~~~I~I~~~rPg~vIG~~g~~i~~l~~~ 66 (195)
T TIGR01008 38 LGTKVIIFAERPGLVIGRGGRRIRELTEK 66 (195)
T ss_pred CcEEEEEEECCCceEECCCchHHHHHHHH
Confidence 35778888888899999999999999874
Done!