Query 009007
Match_columns 546
No_of_seqs 342 out of 2117
Neff 8.2
Searched_HMMs 46136
Date Thu Mar 28 19:16:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009007.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009007hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2190 PolyC-binding proteins 100.0 7.7E-46 1.7E-50 389.3 34.6 403 5-449 6-414 (485)
2 KOG1676 K-homology type RNA bi 100.0 3.3E-43 7.1E-48 362.6 31.8 334 41-445 52-390 (600)
3 KOG2193 IGF-II mRNA-binding pr 100.0 1.9E-41 4.2E-46 333.1 22.5 363 39-446 195-566 (584)
4 KOG2192 PolyC-binding hnRNP-K 100.0 9.5E-33 2.1E-37 257.4 22.4 350 10-444 19-384 (390)
5 KOG1676 K-homology type RNA bi 100.0 1.3E-28 2.9E-33 254.6 22.6 241 39-348 135-384 (600)
6 KOG2193 IGF-II mRNA-binding pr 100.0 5.9E-29 1.3E-33 245.2 10.1 243 138-447 197-484 (584)
7 KOG2191 RNA-binding protein NO 99.9 1.2E-25 2.6E-30 216.1 20.9 236 41-322 37-282 (402)
8 KOG2192 PolyC-binding hnRNP-K 99.9 1.5E-23 3.3E-28 196.0 17.2 174 281-479 45-218 (390)
9 KOG2190 PolyC-binding proteins 99.9 4.6E-21 9.9E-26 202.3 20.6 173 284-464 43-225 (485)
10 KOG2191 RNA-binding protein NO 99.9 6.8E-21 1.5E-25 183.5 17.6 250 138-444 37-315 (402)
11 TIGR03665 arCOG04150 arCOG0415 99.5 4.7E-14 1E-18 130.9 12.1 135 47-215 2-152 (172)
12 TIGR03665 arCOG04150 arCOG0415 99.5 3.8E-14 8.2E-19 131.5 10.3 138 288-444 2-151 (172)
13 PRK13763 putative RNA-processi 99.5 1.5E-13 3.2E-18 128.3 12.3 142 284-444 3-157 (180)
14 PRK13763 putative RNA-processi 99.5 2E-13 4.4E-18 127.4 13.0 138 43-215 3-158 (180)
15 cd02396 PCBP_like_KH K homolog 99.4 1.4E-12 3E-17 101.1 7.7 64 371-438 1-64 (65)
16 cd02396 PCBP_like_KH K homolog 99.3 6.9E-12 1.5E-16 97.2 6.3 55 44-98 1-56 (65)
17 KOG2279 Kinase anchor protein 99.3 3.4E-11 7.4E-16 124.4 12.8 271 39-339 64-354 (608)
18 cd02394 vigilin_like_KH K homo 99.2 1.3E-11 2.8E-16 94.7 5.9 61 372-439 2-62 (62)
19 KOG2279 Kinase anchor protein 99.2 3.7E-11 8E-16 124.1 9.3 232 136-442 64-366 (608)
20 KOG2208 Vigilin [Lipid transpo 99.2 3.4E-11 7.4E-16 134.8 9.1 304 43-445 201-563 (753)
21 cd02393 PNPase_KH Polynucleoti 99.2 7.2E-11 1.6E-15 90.0 8.1 58 370-438 2-60 (61)
22 PF00013 KH_1: KH domain syndr 99.2 1.5E-11 3.3E-16 93.7 3.8 60 371-438 1-60 (60)
23 cd00105 KH-I K homology RNA-bi 99.1 1.8E-10 3.9E-15 88.8 8.3 62 372-438 2-63 (64)
24 cd02394 vigilin_like_KH K homo 99.0 2.5E-10 5.4E-15 87.6 5.0 60 142-208 2-61 (62)
25 cd02393 PNPase_KH Polynucleoti 99.0 8.7E-10 1.9E-14 84.0 7.8 58 140-208 2-60 (61)
26 PF00013 KH_1: KH domain syndr 99.0 1.7E-10 3.7E-15 87.9 3.3 60 141-208 1-60 (60)
27 PF13014 KH_3: KH domain 99.0 1.3E-09 2.9E-14 76.9 5.7 42 53-94 1-43 (43)
28 cd00105 KH-I K homology RNA-bi 99.0 2.4E-09 5.3E-14 82.4 7.6 62 142-208 2-63 (64)
29 KOG2208 Vigilin [Lipid transpo 98.9 2.1E-09 4.6E-14 120.5 8.7 288 43-445 347-636 (753)
30 COG1094 Predicted RNA-binding 98.9 2.8E-08 6E-13 91.5 13.4 147 41-216 6-166 (194)
31 PF13014 KH_3: KH domain 98.9 3.3E-09 7.1E-14 74.9 5.5 43 380-426 1-43 (43)
32 smart00322 KH K homology RNA-b 98.9 1.5E-08 3.3E-13 78.5 8.9 66 370-442 3-68 (69)
33 smart00322 KH K homology RNA-b 98.7 1.1E-07 2.5E-12 73.5 8.8 67 139-212 2-68 (69)
34 COG1094 Predicted RNA-binding 98.7 1.1E-07 2.4E-12 87.5 9.4 142 283-444 7-164 (194)
35 cd02395 SF1_like-KH Splicing f 98.4 7.9E-07 1.7E-11 77.1 8.2 67 378-444 14-95 (120)
36 KOG2113 Predicted RNA binding 98.3 8.6E-07 1.9E-11 86.1 4.4 143 282-435 24-173 (394)
37 cd02395 SF1_like-KH Splicing f 98.2 4.5E-06 9.7E-11 72.4 7.8 67 149-215 15-96 (120)
38 TIGR02696 pppGpp_PNP guanosine 98.1 1.2E-05 2.7E-10 88.8 9.2 97 106-214 545-642 (719)
39 KOG0119 Splicing factor 1/bran 98.0 3.5E-05 7.7E-10 79.6 11.3 101 344-445 113-231 (554)
40 PRK08406 transcription elongat 98.0 5.7E-06 1.2E-10 73.9 4.8 102 45-176 34-135 (140)
41 KOG2113 Predicted RNA binding 98.0 1.1E-05 2.3E-10 78.7 5.9 142 137-336 23-164 (394)
42 PRK08406 transcription elongat 98.0 3.6E-05 7.9E-10 68.7 8.9 103 284-405 32-134 (140)
43 TIGR02696 pppGpp_PNP guanosine 97.8 5.5E-05 1.2E-09 83.8 8.1 65 369-444 577-642 (719)
44 TIGR03591 polynuc_phos polyrib 97.6 0.00014 3.1E-09 81.7 7.7 97 107-214 518-615 (684)
45 KOG0119 Splicing factor 1/bran 97.6 0.00053 1.1E-08 71.2 11.1 76 139-214 137-230 (554)
46 TIGR01952 nusA_arch NusA famil 97.6 0.00024 5.1E-09 63.4 7.4 102 285-405 34-135 (141)
47 TIGR01952 nusA_arch NusA famil 97.5 0.00042 9.1E-09 61.8 8.4 103 44-176 34-136 (141)
48 PLN00207 polyribonucleotide nu 97.5 0.00019 4.1E-09 81.4 7.4 98 106-214 651-750 (891)
49 KOG0336 ATP-dependent RNA heli 97.5 0.00012 2.6E-09 74.4 5.1 64 30-96 34-97 (629)
50 COG1185 Pnp Polyribonucleotide 97.5 0.00018 3.9E-09 78.1 6.3 98 106-214 518-616 (692)
51 TIGR03591 polynuc_phos polyrib 97.2 0.00054 1.2E-08 77.2 6.3 65 369-444 550-615 (684)
52 COG0195 NusA Transcription elo 97.0 0.0033 7.1E-08 59.0 8.3 103 285-407 77-179 (190)
53 COG0195 NusA Transcription elo 96.9 0.0014 2.9E-08 61.5 5.6 104 44-178 77-180 (190)
54 KOG0336 ATP-dependent RNA heli 96.9 0.0015 3.2E-08 66.7 6.0 67 369-443 46-112 (629)
55 KOG1588 RNA-binding protein Sa 96.8 0.0049 1.1E-07 59.7 8.5 76 368-443 90-190 (259)
56 COG1185 Pnp Polyribonucleotide 96.8 0.0018 3.8E-08 70.6 6.0 66 370-446 552-618 (692)
57 PLN00207 polyribonucleotide nu 96.8 0.0012 2.5E-08 75.1 4.7 65 369-444 684-750 (891)
58 PRK11824 polynucleotide phosph 96.8 0.0014 3.1E-08 73.9 5.1 97 107-214 521-618 (693)
59 KOG1588 RNA-binding protein Sa 96.7 0.0018 4E-08 62.6 4.2 39 40-78 89-133 (259)
60 cd02134 NusA_KH NusA_K homolog 96.6 0.0043 9.3E-08 47.1 4.8 36 43-78 25-60 (61)
61 COG5176 MSL5 Splicing factor ( 96.4 0.023 5E-07 52.7 9.5 42 368-409 146-193 (269)
62 KOG2814 Transcription coactiva 96.4 0.0037 8E-08 62.2 4.3 68 42-123 56-123 (345)
63 cd02134 NusA_KH NusA_K homolog 96.4 0.0063 1.4E-07 46.2 4.6 36 370-405 25-60 (61)
64 KOG2814 Transcription coactiva 96.2 0.0054 1.2E-07 61.1 4.5 70 139-215 56-126 (345)
65 PRK12328 nusA transcription el 96.2 0.02 4.4E-07 59.0 8.5 95 294-409 252-347 (374)
66 TIGR01953 NusA transcription t 96.2 0.017 3.7E-07 59.4 8.1 92 294-407 244-338 (341)
67 TIGR01953 NusA transcription t 96.1 0.021 4.5E-07 58.9 8.4 95 53-178 244-339 (341)
68 PRK12328 nusA transcription el 96.0 0.024 5.3E-07 58.4 8.2 96 52-179 251-347 (374)
69 PRK12327 nusA transcription el 96.0 0.022 4.7E-07 59.1 7.8 95 294-408 246-341 (362)
70 PRK00106 hypothetical protein; 96.0 0.022 4.7E-07 61.9 8.1 65 369-443 224-290 (535)
71 PRK04163 exosome complex RNA-b 95.9 0.015 3.3E-07 56.9 6.3 63 372-445 147-210 (235)
72 TIGR03319 YmdA_YtgF conserved 95.9 0.022 4.7E-07 62.2 7.8 65 369-443 203-269 (514)
73 PRK12327 nusA transcription el 95.9 0.011 2.5E-07 61.1 5.2 96 52-178 245-341 (362)
74 PRK12704 phosphodiesterase; Pr 95.8 0.024 5.2E-07 61.9 7.8 65 369-443 209-275 (520)
75 PRK00468 hypothetical protein; 95.7 0.012 2.5E-07 46.6 3.7 33 40-72 27-59 (75)
76 PRK11824 polynucleotide phosph 95.7 0.0078 1.7E-07 68.1 3.5 64 370-444 554-618 (693)
77 PRK12329 nusA transcription el 95.6 0.029 6.3E-07 58.8 7.1 95 293-407 277-372 (449)
78 PF14611 SLS: Mitochondrial in 95.6 0.34 7.4E-06 46.5 14.2 131 285-445 27-166 (210)
79 PRK12329 nusA transcription el 95.5 0.029 6.3E-07 58.9 6.6 95 52-177 277-372 (449)
80 PRK09202 nusA transcription el 95.4 0.034 7.5E-07 59.7 7.0 94 294-408 246-340 (470)
81 PRK02821 hypothetical protein; 95.3 0.018 4E-07 45.6 3.5 35 40-74 28-62 (77)
82 COG5176 MSL5 Splicing factor ( 95.2 0.06 1.3E-06 50.1 6.9 44 135-178 143-192 (269)
83 TIGR03319 YmdA_YtgF conserved 95.2 0.085 1.8E-06 57.6 9.2 67 138-214 202-270 (514)
84 PF14611 SLS: Mitochondrial in 95.1 0.57 1.2E-05 45.0 13.8 63 142-214 28-90 (210)
85 PRK02821 hypothetical protein; 95.1 0.041 9E-07 43.7 4.8 35 136-170 27-61 (77)
86 PRK00468 hypothetical protein; 95.0 0.042 9.1E-07 43.4 4.7 35 135-169 25-59 (75)
87 COG1837 Predicted RNA-binding 95.0 0.048 1E-06 43.0 4.9 34 135-168 25-58 (76)
88 PRK12704 phosphodiesterase; Pr 95.0 0.1 2.2E-06 57.1 9.1 66 139-214 209-276 (520)
89 KOG1067 Predicted RNA-binding 95.0 0.05 1.1E-06 57.8 6.3 113 91-215 544-661 (760)
90 PRK09202 nusA transcription el 94.9 0.041 8.9E-07 59.1 5.8 94 53-178 246-340 (470)
91 PRK01064 hypothetical protein; 94.8 0.036 7.8E-07 44.1 3.7 33 40-72 27-59 (78)
92 PRK04163 exosome complex RNA-b 94.8 0.043 9.4E-07 53.7 5.1 63 142-215 147-210 (235)
93 PRK00106 hypothetical protein; 94.8 0.14 3E-06 55.8 9.3 67 138-214 223-291 (535)
94 COG1837 Predicted RNA-binding 94.4 0.047 1E-06 43.0 3.6 33 40-72 27-59 (76)
95 PRK01064 hypothetical protein; 94.1 0.12 2.6E-06 41.2 5.2 35 135-169 25-59 (78)
96 PRK12705 hypothetical protein; 93.2 0.12 2.6E-06 55.9 5.2 38 369-406 197-235 (508)
97 PF13083 KH_4: KH domain; PDB: 93.2 0.048 1E-06 42.9 1.6 34 40-73 26-59 (73)
98 KOG0921 Dosage compensation co 93.1 0.46 1E-05 53.7 9.5 30 281-310 933-962 (1282)
99 KOG4369 RTK signaling protein 90.9 0.064 1.4E-06 61.3 -0.2 70 372-445 1342-1411(2131)
100 PRK12705 hypothetical protein; 90.7 0.56 1.2E-05 50.8 6.7 66 139-214 197-264 (508)
101 cd02409 KH-II KH-II (K homolo 90.4 0.44 9.6E-06 36.2 4.2 35 42-76 24-58 (68)
102 KOG3273 Predicted RNA-binding 89.5 0.17 3.8E-06 46.8 1.4 55 378-444 177-231 (252)
103 cd02409 KH-II KH-II (K homolo 88.8 0.76 1.6E-05 34.8 4.4 34 370-403 25-58 (68)
104 KOG0921 Dosage compensation co 88.7 1.9 4.1E-05 49.0 8.8 6 490-495 1206-1211(1282)
105 KOG1067 Predicted RNA-binding 88.1 0.9 2E-05 48.7 5.7 68 366-445 593-661 (760)
106 PF13184 KH_5: NusA-like KH do 87.4 0.41 8.8E-06 37.3 2.0 37 371-407 4-46 (69)
107 PRK13764 ATPase; Provisional 87.3 1.1 2.4E-05 49.7 6.1 43 370-412 481-523 (602)
108 cd02414 jag_KH jag_K homology 86.8 0.66 1.4E-05 36.9 3.1 33 45-77 26-58 (77)
109 COG1855 ATPase (PilT family) [ 86.7 1.3 2.8E-05 46.7 5.8 39 141-179 487-525 (604)
110 KOG2874 rRNA processing protei 86.1 1.2 2.5E-05 43.6 4.8 51 152-214 161-211 (356)
111 COG5166 Uncharacterized conser 86.0 2.8 6E-05 44.7 7.7 151 140-405 449-606 (657)
112 KOG3273 Predicted RNA-binding 85.0 3.2 6.9E-05 38.7 6.8 57 148-216 177-233 (252)
113 cd02410 archeal_CPSF_KH The ar 84.5 4 8.6E-05 36.4 7.0 93 58-178 21-114 (145)
114 PF13083 KH_4: KH domain; PDB: 84.2 0.63 1.4E-05 36.5 1.8 33 283-315 28-60 (73)
115 cd02413 40S_S3_KH K homology R 83.3 1.1 2.5E-05 36.0 2.9 35 45-79 32-66 (81)
116 COG1855 ATPase (PilT family) [ 83.3 0.83 1.8E-05 48.1 2.6 41 370-410 486-526 (604)
117 PF07650 KH_2: KH domain syndr 83.2 0.61 1.3E-05 37.1 1.3 33 44-76 26-58 (78)
118 KOG3875 Peroxisomal biogenesis 83.2 4.2 9.1E-05 40.6 7.2 22 504-525 79-100 (362)
119 COG1097 RRP4 RNA-binding prote 82.9 2.8 6.1E-05 40.5 5.9 47 372-429 148-194 (239)
120 KOG4369 RTK signaling protein 82.7 0.52 1.1E-05 54.3 1.0 59 41-99 1338-1397(2131)
121 COG1097 RRP4 RNA-binding prote 81.7 3.3 7.2E-05 40.1 5.8 58 142-210 148-206 (239)
122 cd02414 jag_KH jag_K homology 81.6 1.7 3.7E-05 34.5 3.3 34 371-404 25-58 (77)
123 PF13184 KH_5: NusA-like KH do 81.2 1.4 3.1E-05 34.2 2.7 37 285-321 4-46 (69)
124 COG1782 Predicted metal-depend 81.1 3.9 8.4E-05 43.7 6.5 129 56-216 42-174 (637)
125 KOG2874 rRNA processing protei 81.0 2.9 6.3E-05 41.0 5.2 51 382-444 161-211 (356)
126 PF07650 KH_2: KH domain syndr 80.7 0.7 1.5E-05 36.7 0.8 35 370-404 25-59 (78)
127 PRK06418 transcription elongat 80.3 2.3 4.9E-05 39.1 4.0 34 46-80 64-97 (166)
128 cd02410 archeal_CPSF_KH The ar 80.0 6.7 0.00015 35.0 6.7 91 299-407 21-113 (145)
129 PRK13764 ATPase; Provisional 79.9 4 8.6E-05 45.5 6.6 44 138-181 479-522 (602)
130 cd02413 40S_S3_KH K homology R 79.1 2.5 5.4E-05 34.0 3.5 35 371-405 31-65 (81)
131 cd02412 30S_S3_KH K homology R 72.4 3.5 7.6E-05 35.2 2.9 30 45-74 63-92 (109)
132 PRK06418 transcription elongat 71.8 4.8 0.0001 37.0 3.8 36 142-178 63-98 (166)
133 COG1782 Predicted metal-depend 71.0 7.7 0.00017 41.6 5.5 96 297-408 42-137 (637)
134 cd02411 archeal_30S_S3_KH K ho 68.9 5.5 0.00012 32.2 3.2 28 45-72 40-67 (85)
135 TIGR03675 arCOG00543 arCOG0054 66.8 10 0.00023 42.6 5.9 95 57-179 37-132 (630)
136 cd02411 archeal_30S_S3_KH K ho 66.3 6.8 0.00015 31.7 3.2 28 372-399 40-67 (85)
137 COG0092 RpsC Ribosomal protein 65.9 5.4 0.00012 38.5 2.9 31 43-73 51-81 (233)
138 cd02412 30S_S3_KH K homology R 65.7 5.5 0.00012 33.9 2.7 29 372-400 63-91 (109)
139 COG5166 Uncharacterized conser 64.0 12 0.00026 40.1 5.2 128 296-445 392-525 (657)
140 TIGR03675 arCOG00543 arCOG0054 64.0 22 0.00048 40.1 7.8 96 297-408 36-131 (630)
141 COG0092 RpsC Ribosomal protein 63.5 6.8 0.00015 37.8 3.1 29 370-398 51-79 (233)
142 TIGR00436 era GTP-binding prot 59.0 12 0.00025 37.3 4.1 31 369-399 220-251 (270)
143 COG1159 Era GTPase [General fu 54.0 9.3 0.0002 38.4 2.4 35 365-399 224-259 (298)
144 PRK15494 era GTPase Era; Provi 53.8 16 0.00034 37.9 4.2 30 369-398 272-302 (339)
145 PRK00089 era GTPase Era; Revie 50.7 19 0.00041 36.2 4.1 31 369-399 225-256 (292)
146 cd07055 BMC_like_2 Bacterial M 43.7 49 0.0011 25.0 4.2 40 397-441 21-60 (61)
147 TIGR03802 Asp_Ala_antiprt aspa 42.5 5.2E+02 0.011 28.8 14.9 62 141-208 304-376 (562)
148 TIGR00436 era GTP-binding prot 39.7 35 0.00075 33.9 4.0 29 140-168 221-250 (270)
149 CHL00048 rps3 ribosomal protei 39.6 31 0.00068 33.2 3.5 30 44-73 67-96 (214)
150 COG1847 Jag Predicted RNA-bind 39.5 20 0.00044 34.0 2.1 35 43-77 91-125 (208)
151 TIGR01008 rpsC_E_A ribosomal p 39.3 32 0.0007 32.5 3.4 30 45-74 40-69 (195)
152 PRK03818 putative transporter; 39.1 3.6E+02 0.0078 30.0 12.1 133 45-207 207-358 (552)
153 KOG1423 Ras-like GTPase ERA [C 38.9 32 0.00068 34.9 3.4 36 365-400 323-359 (379)
154 PRK04191 rps3p 30S ribosomal p 38.7 32 0.0007 32.9 3.4 31 45-75 42-72 (207)
155 TIGR01008 rpsC_E_A ribosomal p 37.4 36 0.00079 32.2 3.4 29 371-399 39-67 (195)
156 PTZ00084 40S ribosomal protein 35.6 38 0.00082 32.7 3.3 32 45-76 46-77 (220)
157 PRK04191 rps3p 30S ribosomal p 34.9 41 0.00088 32.2 3.4 29 372-400 42-70 (207)
158 CHL00048 rps3 ribosomal protei 34.5 42 0.0009 32.3 3.4 29 371-399 67-95 (214)
159 COG1159 Era GTPase [General fu 34.4 42 0.00091 33.8 3.5 37 139-175 228-273 (298)
160 PTZ00084 40S ribosomal protein 34.3 40 0.00087 32.5 3.2 29 371-399 45-73 (220)
161 PRK15494 era GTPase Era; Provi 34.1 47 0.001 34.3 4.1 36 140-175 273-317 (339)
162 PRK00089 era GTPase Era; Revie 33.9 49 0.0011 33.1 4.1 36 140-175 226-270 (292)
163 COG1702 PhoH Phosphate starvat 33.5 97 0.0021 32.0 5.9 56 377-444 22-79 (348)
164 PF09869 DUF2096: Uncharacteri 32.0 1.3E+02 0.0029 27.5 5.9 57 137-211 110-166 (169)
165 KOG3973 Uncharacterized conser 30.8 1.2E+02 0.0027 31.0 6.1 12 474-485 365-376 (465)
166 COG1847 Jag Predicted RNA-bind 29.8 48 0.001 31.5 2.9 36 140-175 91-126 (208)
167 KOG3973 Uncharacterized conser 27.4 1.8E+02 0.0039 29.8 6.5 12 395-406 286-297 (465)
168 COG0490 Putative regulatory, l 26.7 44 0.00095 30.5 1.9 62 373-439 91-158 (162)
169 PTZ00473 Plasmodium Vir superf 24.6 3E+02 0.0064 29.0 7.6 11 63-73 9-19 (420)
170 TIGR01009 rpsC_bact ribosomal 24.0 75 0.0016 30.5 3.2 29 45-73 64-92 (211)
171 KOG1423 Ras-like GTPase ERA [C 22.7 85 0.0018 32.0 3.3 34 137-170 325-359 (379)
172 TIGR01009 rpsC_bact ribosomal 22.3 84 0.0018 30.2 3.1 28 372-399 64-91 (211)
173 PF02749 QRPTase_N: Quinolinat 21.3 2.5E+02 0.0055 22.5 5.4 66 374-443 20-85 (88)
174 PRK15468 carboxysome structura 20.9 2.3E+02 0.005 24.0 5.0 39 168-215 62-100 (111)
175 COG1702 PhoH Phosphate starvat 20.8 1.9E+02 0.004 30.0 5.3 51 147-209 22-72 (348)
176 PRK15468 carboxysome structura 20.4 1.5E+02 0.0032 25.1 3.7 26 421-446 76-101 (111)
No 1
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=7.7e-46 Score=389.33 Aligned_cols=403 Identities=40% Similarity=0.605 Sum_probs=314.2
Q ss_pred cCcCCCCCCCCCCCCCCCCCccccCCCCCCCcccCCCceEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCC
Q 009007 5 RNSYGKRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPG 84 (546)
Q Consensus 5 ~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~ 84 (546)
|....++....+...+++..+++...++... ...+...++||||+.+.+|.||||+|.+||+||.+|.++|+|.+..++
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~ 84 (485)
T KOG2190|consen 6 RGLPRPKNSTTSNVGDNGSIKRPSLGDPVIS-TGPDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPG 84 (485)
T ss_pred ccCccccCCCcccccCCCcccccCCCCCccc-CCCCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCC
Confidence 4455556666666655666666555554333 333444449999999999999999999999999999999999999999
Q ss_pred CCceEEEEecCCccccccccCcccCCHHHHHHHHHHHHHHHhhh---cCCCC---CCCCCceEEEEEecCCceeEEeecC
Q 009007 85 SEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEEL---RGDED---SDGGHQVTAKLLVPSDQIGCVIGKG 158 (546)
Q Consensus 85 ~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~---~~~~~---~~~~~~~~~~l~Vp~~~vg~iIGk~ 158 (546)
|+||+|+|+|...+ ..++++++|++++++.|..... ....+ +.....++++|+||..++|+||||+
T Consensus 85 c~eRIiti~g~~~~--------~~~~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~ 156 (485)
T KOG2190|consen 85 CPERIITITGNRVE--------LNLSPATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKG 156 (485)
T ss_pred CCcceEEEeccccc--------ccCCchHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccC
Confidence 99999999997222 1688899999999999886321 11111 1122268999999999999999999
Q ss_pred chHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCccccccccccCCCCCCCCCC
Q 009007 159 GQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLV 238 (546)
Q Consensus 159 G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~s~~~~~~~~~g~~~ 238 (546)
|+.||+|+++|||+|.|.++ .+|. +++|.|+|.|.+++|.+|+..|...|++++.+....+.+..+ |.. .
T Consensus 157 G~~Ik~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~--y~P----~ 226 (485)
T KOG2190|consen 157 GSLIKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIP--YRP----S 226 (485)
T ss_pred cHHHHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCccc--CCC----c
Confidence 99999999999999999987 8887 588999999999999999999999999976553222221111 100 0
Q ss_pred CCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEEEeecCcccccccCCchhHHHHHhhhCCeEE
Q 009007 239 GPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIK 318 (546)
Q Consensus 239 ~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~~~~~p~~~~~~~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~ 318 (546)
-+..++ +...++. ..+ .+.++.....+.++.+++.+|...++.|||+++..|+.|+.++++.|.
T Consensus 227 ~~~~~~-------~~~s~~~-------~~~--~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~ 290 (485)
T KOG2190|consen 227 ASQGGP-------VLPSTAQ-------TSP--DAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASIS 290 (485)
T ss_pred ccccCc-------ccccccc-------CCc--ccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceE
Confidence 000000 0000000 000 111222334567788899999999999999999999999999999999
Q ss_pred ecCCCCCCCceEEEEecCcchhhhhhHHHHHHHHhcCccccccccccCCcceeEEEEEccCcceeEEcCCChhHHHHHHh
Q 009007 319 VDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRL 398 (546)
Q Consensus 319 i~~~~~~~~erii~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~ 398 (546)
+.+..+. |+++++..+..++..+++++++++.++++.+....+. ...++.+|+||.+++||||||+|.+|.+||+.
T Consensus 291 v~~~~~~---~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~-~~~v~~~l~vps~~igciiGk~G~~iseir~~ 366 (485)
T KOG2190|consen 291 VGDSRTD---RIVTISARENPEDRYSMAQEALLLVQPRISENAGDDL-TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQR 366 (485)
T ss_pred eccccCc---ceeeeccccCcccccccchhhhhhccccccccccccc-cceeeeeeccCccccceeecccccchHHHHHh
Confidence 9987654 9999999999999999999999999999988777655 77899999999999999999999999999999
Q ss_pred hCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhccccc
Q 009007 399 TKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLFDR 449 (546)
Q Consensus 399 Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~ 449 (546)
|||.|+|..+++. ...++++++|+|+..+...|..+|..++.......
T Consensus 367 tgA~I~I~~~~~~---~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~~~~ 414 (485)
T KOG2190|consen 367 TGASISILNKEEV---SGVREALVQITGMLREDLLAQYLIRARLSAPKSSM 414 (485)
T ss_pred cCCceEEcccccc---CCcceeEEEecchhHHHHhhhhhcccccccCccCC
Confidence 9999999887653 24678999999999999999999988887765433
No 2
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=3.3e-43 Score=362.57 Aligned_cols=334 Identities=20% Similarity=0.368 Sum_probs=253.5
Q ss_pred CceEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEecCCccccccccCcccCCHHHHHHHHHH
Q 009007 41 EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVH 120 (546)
Q Consensus 41 ~~~~~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~ 120 (546)
..++.++.||.+++|+||||+|+.|..|..+++|+|+|.....+..+|-|.++|.+++++ .| ++++
T Consensus 52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~-------------~a-K~li 117 (600)
T KOG1676|consen 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVE-------------VA-KQLI 117 (600)
T ss_pred cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHH-------------HH-HHhh
Confidence 455788999999999999999999999999999999987776677899999999999842 22 2222
Q ss_pred HHHHHhhhcC--CCCCCCCCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCH
Q 009007 121 DRVIAEELRG--DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198 (546)
Q Consensus 121 ~~i~~~~~~~--~~~~~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~ 198 (546)
..+++..... ..+.-....++..|+||.+.+|.||||+|+|||.|++.+||++.+..+..... ..++.+.|+|++
T Consensus 118 ~evv~r~~~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~---~~~KplritGdp 194 (600)
T KOG1676|consen 118 GEVVSRGRPPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIAT---GADKPLRITGDP 194 (600)
T ss_pred hhhhhccCCCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCC---CCCCceeecCCH
Confidence 3333322111 01112246689999999999999999999999999999999999988755432 478899999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009007 199 SVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDD 278 (546)
Q Consensus 199 ~~v~~A~~~I~~~l~~~~~~~~~~~~s~~~~~~~~~g~~~~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~~~~~p~~~ 278 (546)
+.|+.|+.+|.++|++.... .+..++. ++. +
T Consensus 195 ~~ve~a~~lV~dil~e~~~~-----------~~g~~~~-------------------~g~---~---------------- 225 (600)
T KOG1676|consen 195 DKVEQAKQLVADILREEDDE-----------VPGSGGH-------------------AGV---R---------------- 225 (600)
T ss_pred HHHHHHHHHHHHHHHhcccC-----------CCccccc-------------------cCc---C----------------
Confidence 99999999999999863211 1111000 000 0
Q ss_pred CCCccEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCC-CCCceEEEEecCcchhhhhhHHHHHHHHhcCcc
Q 009007 279 LSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSST-EGDDCLITVSSKEFFEDTLSATIEAVVRLQPRC 357 (546)
Q Consensus 279 ~~~~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~i~~~~~-~~~erii~i~g~~~~~~~~~~~~~a~~~~~~~~ 357 (546)
.....+++|.||...||.||||+|++||+|+.+||++|+|.+.+. .+.||++.|.|.........+.+.+++......
T Consensus 226 -~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~ 304 (600)
T KOG1676|consen 226 -GGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAG 304 (600)
T ss_pred -ccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhcc
Confidence 011238899999999999999999999999999999999987654 678999999997543333233344433321111
Q ss_pred ccccccccCCcce--eEEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHH
Q 009007 358 SEKIERDSGLISF--TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDAL 435 (546)
Q Consensus 358 ~~~~~~~~~~~~~--~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~ 435 (546)
.. ..-..+.... ...|.||.+.||+||||+|++||.|.++|||++.+.+. |+..+..+++|+|+|++.+|+.|+
T Consensus 305 ~~-~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~---~p~~~~~ektf~IrG~~~QIdhAk 380 (600)
T KOG1676|consen 305 AG-GGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ---PPNGNPKEKTFVIRGDKRQIDHAK 380 (600)
T ss_pred CC-CCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC---CCCCCccceEEEEecCcccchHHH
Confidence 00 0000112223 78899999999999999999999999999999999764 445667899999999999999999
Q ss_pred HHHHHHHHhc
Q 009007 436 IQVMTRLRAN 445 (546)
Q Consensus 436 ~~I~~~i~~~ 445 (546)
.||.+++...
T Consensus 381 ~LIr~kvg~~ 390 (600)
T KOG1676|consen 381 QLIRDKVGDI 390 (600)
T ss_pred HHHHHHhccc
Confidence 9999999874
No 3
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=1.9e-41 Score=333.06 Aligned_cols=363 Identities=23% Similarity=0.371 Sum_probs=272.5
Q ss_pred CCCceEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcC-CCCCCCceEEEEecCCccccccccCcccCCHHHHHHH
Q 009007 39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE-TVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALF 117 (546)
Q Consensus 39 ~~~~~~~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~-~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~ 117 (546)
...+..+|+|||..++|.||||.|.|||.|-..|.|+|+|.. ...+..|++|+|-+.+|. +.+||.
T Consensus 195 q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg-------------~s~Ac~ 261 (584)
T KOG2193|consen 195 QLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG-------------TSKACK 261 (584)
T ss_pred cccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc-------------hHHHHH
Confidence 467788999999999999999999999999999999999964 356889999999999998 578999
Q ss_pred HHHHHHHHhhhcCCCCCCCCCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcC
Q 009007 118 KVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGE 197 (546)
Q Consensus 118 ~i~~~i~~~~~~~~~~~~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~ 197 (546)
+|++.+..+.... .....+.++++..+.+||+||||.|.+||+|+.+||++|.|.+-.++.. .+.+|+++|.|+
T Consensus 262 ~ILeimqkEA~~~----k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~--ynpERTItVkGs 335 (584)
T KOG2193|consen 262 MILEIMQKEAVDD----KVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSL--YNPERTITVKGS 335 (584)
T ss_pred HHHHHHHHhhhcc----chhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcc--cCccceEEeccc
Confidence 9998776655432 3346778999999999999999999999999999999999998766554 367999999999
Q ss_pred HHHHHHHHHHHHHHHhcCCCCccccccccccCCCCCCCCCCCCCCC--CCcccCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009007 198 ASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAA--TPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAP 275 (546)
Q Consensus 198 ~~~v~~A~~~I~~~l~~~~~~~~~~~~s~~~~~~~~~g~~~~p~~g--~~~~~~~p~~~~~gg~~~d~~~~~~~~~~~~p 275 (546)
.|+|..|..+|+.+|++++..+. .+-+..-..+. .|+.|..| +...++.|+- ....-+....+..++
T Consensus 336 iEac~~AE~eImkKlre~yEnDl--~a~s~q~~l~P--~l~~~~l~~f~ssS~~~~Ph----~~Ps~v~~a~p~~~~--- 404 (584)
T KOG2193|consen 336 IEACVQAEAEIMKKLRECYENDL--AAMSLQCHLPP--GLNLPALGLFPSSSAVSPPH----FPPSPVTFASPYPLF--- 404 (584)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhH--HHhhccCCCCc--ccCccccCCCCcccccCCCC----CCCCccccCCCchhh---
Confidence 99999999999999999876652 11111111111 11111111 1111111100 000000000010111
Q ss_pred CCCCCCccEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCC-CCCCceEEEEecCcchhhhhhHHHHHHHHhc
Q 009007 276 RDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSS-TEGDDCLITVSSKEFFEDTLSATIEAVVRLQ 354 (546)
Q Consensus 276 ~~~~~~~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~i~~~~-~~~~erii~i~g~~~~~~~~~~~~~a~~~~~ 354 (546)
......-.+++.||...+|+|||++|.+||+|...+||.|+|..+. ++..+|+++|+|.+ ++.++.+
T Consensus 405 --hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGpp----------eaqfKAQ 472 (584)
T KOG2193|consen 405 --HQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPP----------EAQFKAQ 472 (584)
T ss_pred --hcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCCh----------HHHHhhh
Confidence 1122455889999999999999999999999999999999998754 56788999999964 3344444
Q ss_pred Ccccccccc-----ccCCcceeEEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHH
Q 009007 355 PRCSEKIER-----DSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLD 429 (546)
Q Consensus 355 ~~~~~~~~~-----~~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~ 429 (546)
.++..++.. ......+.+.+.||...+|.||||||.+++||+..|+|-+.|+.+. .|. +.++-+|.|.|...
T Consensus 473 grifgKikEenf~~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdq-tpd--End~vivriiGhfy 549 (584)
T KOG2193|consen 473 GRIFGKIKEENFFLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQ-TPD--ENDQVIVRIIGHFY 549 (584)
T ss_pred hhhhhhhhhhccCCchhhheeeeeeeccchhhhhhhccccccHHHHhccccceEEccccC-CCC--ccceeeeeeechhh
Confidence 444433322 2233467889999999999999999999999999999999997654 453 45566799999999
Q ss_pred HHHHHHHHHHHHHHhcc
Q 009007 430 LAKDALIQVMTRLRANL 446 (546)
Q Consensus 430 ~v~~A~~~I~~~i~~~~ 446 (546)
+...|...|.+.|.+..
T Consensus 550 atq~aQrki~~iv~qvk 566 (584)
T KOG2193|consen 550 ATQNAQRKIAHIVNQVK 566 (584)
T ss_pred cchHHHHHHHHHHHHHH
Confidence 99999999999998765
No 4
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=9.5e-33 Score=257.41 Aligned_cols=350 Identities=20% Similarity=0.312 Sum_probs=222.4
Q ss_pred CCCCCCCCCCCCCCCccccCCCCCCCcccCCCceEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCCceE
Q 009007 10 KRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERV 89 (546)
Q Consensus 10 ~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~erv 89 (546)
||.|+..+.++.+ +|...| -+..++....+.+|||+.++.+|.||||+|++||+|+.+++|.|.|++. ..+||+
T Consensus 19 ~~~~~~e~g~~~g---krp~~d-~~~qa~k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri 92 (390)
T KOG2192|consen 19 ETFPNTETGGEFG---KRPAED-MEEQAFKRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERI 92 (390)
T ss_pred hcCCCCccccccc---CCcchh-hHHHHhhhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCcee
Confidence 4556555543332 433334 4666778888999999999999999999999999999999999999887 788999
Q ss_pred EEEecCCccccccccCcccCCHHHHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEecCCceeEEeecCchHHHHHHhhc
Q 009007 90 VTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSET 169 (546)
Q Consensus 90 v~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~t 169 (546)
++|+...+. +-+-|.+|+..+.+. ....+.+.++|||+.+++|.|||++|+.||+|++++
T Consensus 93 ~tisad~~t-------------i~~ilk~iip~lee~-------f~~~~pce~rllihqs~ag~iigrngskikelrekc 152 (390)
T KOG2192|consen 93 LTISADIET-------------IGEILKKIIPTLEEG-------FQLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKC 152 (390)
T ss_pred EEEeccHHH-------------HHHHHHHHhhhhhhC-------CCCCCchhhhhhhhhhhccceecccchhHHHHHHhh
Confidence 999976332 234444444443321 134577999999999999999999999999999999
Q ss_pred CceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCccccccccccCC----CCCCCC-CC-CCCCC
Q 009007 170 GAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNS----HSSSGS-LV-GPTAA 243 (546)
Q Consensus 170 ga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~s~~~~~----~~~~g~-~~-~p~~g 243 (546)
.|+++|... .|..++||+|.|.|.+..|..+++.|+++|.+.|.+..... +.++. |..||. |+ .-.++
T Consensus 153 sarlkift~----c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~p--y~p~fyd~t~dyggf~M~f~d~pg 226 (390)
T KOG2192|consen 153 SARLKIFTE----CCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQP--YDPNFYDETYDYGGFTMMFDDRPG 226 (390)
T ss_pred hhhhhhhhc----cCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCc--CCccccCcccccCCceeecCCCCC
Confidence 999999764 45568999999999999999999999999999877643221 11111 222221 11 10000
Q ss_pred CCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCC
Q 009007 244 TPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSS 323 (546)
Q Consensus 244 ~~~~~~~p~~~~~gg~~~d~~~~~~~~~~~~p~~~~~~~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~i~~~~ 323 (546)
..+.+|..+..|. ++|+.. ....+-++|..= +.+--.+.|....
T Consensus 227 --~pgpapqrggqgp--------------p~~~~s----------------dlmay~r~GrpG----~rydg~vdFs~de 270 (390)
T KOG2192|consen 227 --RPGPAPQRGGQGP--------------PPPRGS----------------DLMAYDRRGRPG----DRYDGMVDFSADE 270 (390)
T ss_pred --CCCCCCCCCCCCC--------------CCCCcc----------------ccceeccCCCCC----ccccccccccccc
Confidence 0000111100000 000000 000011111000 0000001111110
Q ss_pred CCCCceEEEEecCcchhhhhhHHHHHHHHhcCccc----------cccccccCCcceeEEEEEccCcceeEEcCCChhHH
Q 009007 324 TEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCS----------EKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIIT 393 (546)
Q Consensus 324 ~~~~erii~i~g~~~~~~~~~~~~~a~~~~~~~~~----------~~~~~~~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik 393 (546)
.. +..+-+-..++ ..+...+.-. ...-.+.+.+..|..+.||.++-|.||||+|++|+
T Consensus 271 tw-~saidtw~~Se-----------wqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~ 338 (390)
T KOG2192|consen 271 TW-PSAIDTWSPSE-----------WQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIK 338 (390)
T ss_pred cC-CCcCCCcCccc-----------cccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhh
Confidence 00 00000000000 0000000000 00011233456889999999999999999999999
Q ss_pred HHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHh
Q 009007 394 EMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRA 444 (546)
Q Consensus 394 ~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~ 444 (546)
+|++++||.|+|... ..++.+|.++|+|+.++++.|+.|++..++.
T Consensus 339 ~ir~esGA~Ikidep-----leGsedrIitItGTqdQIqnAQYLlQn~Vkq 384 (390)
T KOG2192|consen 339 QIRHESGASIKIDEP-----LEGSEDRIITITGTQDQIQNAQYLLQNSVKQ 384 (390)
T ss_pred hhhhccCceEEecCc-----CCCCCceEEEEeccHHHHhhHHHHHHHHHHh
Confidence 999999999999642 2367889999999999999999999999885
No 5
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.96 E-value=1.3e-28 Score=254.65 Aligned_cols=241 Identities=26% Similarity=0.422 Sum_probs=184.4
Q ss_pred CCCceEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCC--CCCCCceEEEEecCCccccccccCcccCCHHHHHH
Q 009007 39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGET--VPGSEERVVTVYSASDETNAFEDGDKFVSPAQDAL 116 (546)
Q Consensus 39 ~~~~~~~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~--~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~ 116 (546)
++..++..|+||..++|+||||+|+|||+|++.+||++.+... ......+.+.|+|.++.+ +.|.
T Consensus 135 ~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~v-------------e~a~ 201 (600)
T KOG1676|consen 135 GSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKV-------------EQAK 201 (600)
T ss_pred CccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHH-------------HHHH
Confidence 4677999999999999999999999999999999999987543 222367889999998873 5666
Q ss_pred HHHHHHHHHhhhcCCCC-----CCCCCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCce
Q 009007 117 FKVHDRVIAEELRGDED-----SDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDEL 191 (546)
Q Consensus 117 ~~i~~~i~~~~~~~~~~-----~~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~ 191 (546)
.++++.|.+++-....+ .......+++|.||...||.||||+|++||+|+.+||++|+|.++++ | .+.+|.
T Consensus 202 ~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~-p---~speR~ 277 (600)
T KOG1676|consen 202 QLVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD-P---SSPERP 277 (600)
T ss_pred HHHHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCC-C---CCccce
Confidence 66777665433221111 12233448999999999999999999999999999999999988754 3 378999
Q ss_pred EEEEcCHHHHHHHHHHHHHHHhcCCCCccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCC
Q 009007 192 VQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSL 271 (546)
Q Consensus 192 v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~s~~~~~~~~~g~~~~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~~ 271 (546)
+.|.|+.+.|+.|.++|.++|++..... .+ + + +|.
T Consensus 278 ~~IiG~~d~ie~Aa~lI~eii~~~~~~~----------~~---~-~----------------------------~~G--- 312 (600)
T KOG1676|consen 278 AQIIGTVDQIEHAAELINEIIAEAEAGA----------GG---G-M----------------------------GGG--- 312 (600)
T ss_pred eeeecCHHHHHHHHHHHHHHHHHHhccC----------CC---C-c----------------------------CCC---
Confidence 9999999999999999999998741110 00 0 0 000
Q ss_pred CCCCCCCCCCccEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCC--CCCCceEEEEecCcchhhhhhHHHH
Q 009007 272 YSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSS--TEGDDCLITVSSKEFFEDTLSATIE 348 (546)
Q Consensus 272 ~~~p~~~~~~~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~i~~~~--~~~~erii~i~g~~~~~~~~~~~~~ 348 (546)
.| ..-..+.+.||.+++|+|||++|++||.|..++||++.+.+.. ....+++++|.|.+.-.+.....++
T Consensus 313 --~P-----~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG~~~QIdhAk~LIr 384 (600)
T KOG1676|consen 313 --AP-----GLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGDKRQIDHAKQLIR 384 (600)
T ss_pred --Cc-----cceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEecCcccchHHHHHHH
Confidence 00 0011788999999999999999999999999999999998863 2347899999998754444333333
No 6
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.95 E-value=5.9e-29 Score=245.19 Aligned_cols=243 Identities=23% Similarity=0.396 Sum_probs=190.4
Q ss_pred CceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCC
Q 009007 138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPS 217 (546)
Q Consensus 138 ~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~v~~A~~~I~~~l~~~~~ 217 (546)
....++++||..+++.||||.|+|||+|...|.|+|+|..+++. +..|+.|+|.+++|...+|+++|++++.+...
T Consensus 197 ~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~----Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~ 272 (584)
T KOG2193|consen 197 KDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENA----GAAEKIITVHSTPEGTSKACKMILEIMQKEAV 272 (584)
T ss_pred cCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccC----CcccCceEEecCccchHHHHHHHHHHHHHhhh
Confidence 45679999999999999999999999999999999999987653 46899999999999999999999999987532
Q ss_pred CccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEEEeecCcccc
Q 009007 218 RSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGG 297 (546)
Q Consensus 218 ~~~~~~~s~~~~~~~~~g~~~~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~~~~~p~~~~~~~~~~~~v~vp~~~~g~ 297 (546)
++. ...++.++++-.+.++|+
T Consensus 273 ~~k-----------------------------------------------------------~~~e~pLk~lAHN~lvGR 293 (584)
T KOG2193|consen 273 DDK-----------------------------------------------------------VAEEIPLKILAHNNLVGR 293 (584)
T ss_pred ccc-----------------------------------------------------------hhhhcchhhhhhcchhhh
Confidence 221 234678899999999999
Q ss_pred cccCCchhHHHHHhhhCCeEEecCCC---CCCCceEEEEecC-cchhh-------hhhHHHHHHHH---hcC----cccc
Q 009007 298 VIGKGGAIINQIRQESGAAIKVDSSS---TEGDDCLITVSSK-EFFED-------TLSATIEAVVR---LQP----RCSE 359 (546)
Q Consensus 298 IIGk~G~~Ik~i~~~sga~I~i~~~~---~~~~erii~i~g~-~~~~~-------~~~~~~~a~~~---~~~----~~~~ 359 (546)
+|||.|.+||+|+++||++|+|.+-. .-.+||+|++.|. |.+.. .+.++.|.-++ ++. .++-
T Consensus 294 LIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~ 373 (584)
T KOG2193|consen 294 LIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNL 373 (584)
T ss_pred hhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCc
Confidence 99999999999999999999998742 2347999999994 11111 11112221111 111 1100
Q ss_pred c----------cccc-----------------cCCcceeEEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCC
Q 009007 360 K----------IERD-----------------SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLP 412 (546)
Q Consensus 360 ~----------~~~~-----------------~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P 412 (546)
. +... .....-..+|.||...+|.||||+|.+||.|.+.+||.|+|...+
T Consensus 374 ~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE--- 450 (584)
T KOG2193|consen 374 PALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPE--- 450 (584)
T ss_pred cccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCC---
Confidence 0 0000 011345678999999999999999999999999999999997643
Q ss_pred CCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhccc
Q 009007 413 KIASEDDEMVQISGDLDLAKDALIQVMTRLRANLF 447 (546)
Q Consensus 413 ~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~ 447 (546)
.++..+|||+|+|++++.-+|.-.|..+|.|+.|
T Consensus 451 -~pdvseRMViItGppeaqfKAQgrifgKikEenf 484 (584)
T KOG2193|consen 451 -IPDVSERMVIITGPPEAQFKAQGRIFGKIKEENF 484 (584)
T ss_pred -CCCcceeEEEecCChHHHHhhhhhhhhhhhhhcc
Confidence 3467899999999999999999999999999865
No 7
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.94 E-value=1.2e-25 Score=216.10 Aligned_cols=236 Identities=25% Similarity=0.399 Sum_probs=170.4
Q ss_pred CceEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcC---CCCCCCceEEEEecCCccccccccCcccCCHHHHHHH
Q 009007 41 EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE---TVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALF 117 (546)
Q Consensus 41 ~~~~~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~---~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~ 117 (546)
..+.++||||+..+|+||||+|++|.+|+++|||+|++++ .+|+++||||.|.|+.+++ ..-+.
T Consensus 37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai-------------~av~e 103 (402)
T KOG2191|consen 37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEAL-------------NAVHE 103 (402)
T ss_pred CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHH-------------HHHHH
Confidence 4499999999999999999999999999999999999975 4899999999999986542 22233
Q ss_pred HHHHHHHHhhhcCCC-CC-----CCCCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCce
Q 009007 118 KVHDRVIAEELRGDE-DS-----DGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDEL 191 (546)
Q Consensus 118 ~i~~~i~~~~~~~~~-~~-----~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~ 191 (546)
.|.++|.+....... .+ ..+..-.++++||+..+|.||||+|.+||.|+++++|.|+|.+. .|....-.+|+
T Consensus 104 fI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPq--kpt~~sLqerv 181 (402)
T KOG2191|consen 104 FIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQ--KPTGISLQERV 181 (402)
T ss_pred HHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEeccc--CCCCccceeEE
Confidence 345555443322211 11 11122348999999999999999999999999999999999842 12223457999
Q ss_pred EEEEcCHHHHHHHHHHHHHHHhcCCCCccccccccccCCCCCCCCCC-CCCCCCCcccCCCCCCCCCCCCCCCCCCCCCC
Q 009007 192 VQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLV-GPTAATPIVGIAPLMGPYGGYKGDTAGDWSRS 270 (546)
Q Consensus 192 v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~s~~~~~~~~~g~~~-~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~ 270 (546)
|+++|++++..+|+.+|+++|.++|....++..++. +-.|+.-+ .|++ .+|.. ..+
T Consensus 182 vt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya---~vsGpvaNsnPtG-----------spya~-~~~-------- 238 (402)
T KOG2191|consen 182 VTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYA---NVSGPVANSNPTG-----------SPYAY-QAH-------- 238 (402)
T ss_pred EEecCCHHHHHHHHHHHHHHhhcCCcccceeccchh---cccCcccccCCCC-----------CCCCC-CCc--------
Confidence 999999999999999999999999877665542221 11111111 1111 11111 100
Q ss_pred CCCCCCCCCCCccEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCC
Q 009007 271 LYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSS 322 (546)
Q Consensus 271 ~~~~p~~~~~~~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~i~~~ 322 (546)
..+.......-++..+.|..-|.++.++-.|-.-+|+.+.++..
T Consensus 239 --------~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~ 282 (402)
T KOG2191|consen 239 --------VLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQA 282 (402)
T ss_pred --------cccccchhhccccccccccccccccccceeeecccccceeeccc
Confidence 01122355677888999999999999999999999998888763
No 8
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.91 E-value=1.5e-23 Score=196.00 Aligned_cols=174 Identities=26% Similarity=0.392 Sum_probs=144.1
Q ss_pred CccEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhhhhHHHHHHHHhcCccccc
Q 009007 281 SKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEK 360 (546)
Q Consensus 281 ~~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~i~~~~~~~~erii~i~g~~~~~~~~~~~~~a~~~~~~~~~~~ 360 (546)
...+.+++++..+.+|+||||+|+|||+|+.+++|+|.|++++ .++++++|++.+. ...+-+..+.+.+.+.
T Consensus 45 ~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~--~peri~tisad~~------ti~~ilk~iip~lee~ 116 (390)
T KOG2192|consen 45 RSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSS--GPERILTISADIE------TIGEILKKIIPTLEEG 116 (390)
T ss_pred hcceeEEEEEecccccceeccccccHHHHhhhccceeeccCCC--CCceeEEEeccHH------HHHHHHHHHhhhhhhC
Confidence 3458999999999999999999999999999999999999865 4789999998642 1223334455555544
Q ss_pred cccccCCcceeEEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHH
Q 009007 361 IERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMT 440 (546)
Q Consensus 361 ~~~~~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~ 440 (546)
+.. ...++++|+|+++++|.|||++|++|||||++..|+++|.-. ++| ++++|+|.|.|.+..|..+++.|++
T Consensus 117 f~~---~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~-c~p---~stdrv~l~~g~~k~v~~~i~~il~ 189 (390)
T KOG2192|consen 117 FQL---PSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE-CCP---HSTDRVVLIGGKPKRVVECIKIILD 189 (390)
T ss_pred CCC---CCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc-cCC---CCcceEEEecCCcchHHHHHHHHHH
Confidence 332 235899999999999999999999999999999999999764 444 6899999999999999999999999
Q ss_pred HHHhcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009007 441 RLRANLFDREGAVSTFVPVLPYIPVSENGSDGLNYESRD 479 (546)
Q Consensus 441 ~i~~~~~~~~~~~~~~~~~~~y~p~~~~~~~~~~yg~~~ 479 (546)
+|.+.+ .++...||+|..|++. ..||++.
T Consensus 190 ~i~e~p--------ikgsa~py~p~fyd~t--~dyggf~ 218 (390)
T KOG2192|consen 190 LISESP--------IKGSAQPYDPNFYDET--YDYGGFT 218 (390)
T ss_pred HhhcCC--------cCCcCCcCCccccCcc--cccCCce
Confidence 999854 4678889999998875 4677755
No 9
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.87 E-value=4.6e-21 Score=202.33 Aligned_cols=173 Identities=38% Similarity=0.597 Sum_probs=141.4
Q ss_pred EEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhhhhHHHHHHHHhcCcccccccc
Q 009007 284 FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIER 363 (546)
Q Consensus 284 ~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~i~~~~~~~~erii~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~ 363 (546)
.++|++|+...+|.||||+|..||+||.++.++|+|.+..++..+|+++|+|. ..+...+.+.+++.+.+.++...++.
T Consensus 43 ~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~-~~~~~~~~~~~al~ka~~~iv~~~~~ 121 (485)
T KOG2190|consen 43 LTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGN-RVELNLSPATDALFKAFDMIVFKLEE 121 (485)
T ss_pred ceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecc-cccccCCchHHHHHHHHHHHhhcccc
Confidence 34899999999999999999999999999999999999888899999999994 22224455666766666555543221
Q ss_pred ----------ccCCcceeEEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHH
Q 009007 364 ----------DSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKD 433 (546)
Q Consensus 364 ----------~~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~ 433 (546)
+.....++++|+||..++|+||||+|++||+|+++|||+|+|..+ .+|. .++|.|+|.|++++|.+
T Consensus 122 d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av~~ 197 (485)
T KOG2190|consen 122 DDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAVKK 197 (485)
T ss_pred cccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHHHH
Confidence 111225789999999999999999999999999999999999875 6775 68899999999999999
Q ss_pred HHHHHHHHHHhcccccCCCCCCCCCCCCCCC
Q 009007 434 ALIQVMTRLRANLFDREGAVSTFVPVLPYIP 464 (546)
Q Consensus 434 A~~~I~~~i~~~~~~~~~~~~~~~~~~~y~p 464 (546)
|+.+|..+|.+..-. ..+.+....+|.|
T Consensus 198 al~~Is~~L~~~~~~---~~~~~~st~~y~P 225 (485)
T KOG2190|consen 198 ALVQISSRLLENPPR---SPPPLVSTIPYRP 225 (485)
T ss_pred HHHHHHHHHHhcCCc---CCCCCCCcccCCC
Confidence 999999999986532 2334556678888
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=6.8e-21 Score=183.54 Aligned_cols=250 Identities=23% Similarity=0.319 Sum_probs=180.1
Q ss_pred CceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCC
Q 009007 138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPS 217 (546)
Q Consensus 138 ~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~v~~A~~~I~~~l~~~~~ 217 (546)
..+.+++|||+..+|.||||+|++|.+|+.+|||+|++++..++.+ ..+||+|.|+|+.+++...+..|+++|++.+.
T Consensus 37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyP--GTTeRvcli~Gt~eai~av~efI~dKire~p~ 114 (402)
T KOG2191|consen 37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYP--GTTERVCLIQGTVEALNAVHEFIADKIREKPQ 114 (402)
T ss_pred CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCC--CccceEEEEeccHHHHHHHHHHHHHHHHHhHH
Confidence 4488999999999999999999999999999999999998766443 48999999999999999999999999999643
Q ss_pred CccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEEEeecCcccc
Q 009007 218 RSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGG 297 (546)
Q Consensus 218 ~~~~~~~s~~~~~~~~~g~~~~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~~~~~p~~~~~~~~~~~~v~vp~~~~g~ 297 (546)
.... +.+.+++.. ....-+++++||+..+|.
T Consensus 115 ~~~k----------------------------------------------~v~~~~pqt---~~r~kqikivvPNstag~ 145 (402)
T KOG2191|consen 115 AVAK----------------------------------------------PVDILQPQT---PDRIKQIKIVVPNSTAGM 145 (402)
T ss_pred hhcC----------------------------------------------CccccCCCC---ccccceeEEeccCCcccc
Confidence 3211 000111110 112236899999999999
Q ss_pred cccCCchhHHHHHhhhCCeEEecCCCCC---CCceEEEEecCcchhhhhhHHHHHHHH-hc--Cc----cccccc-----
Q 009007 298 VIGKGGAIINQIRQESGAAIKVDSSSTE---GDDCLITVSSKEFFEDTLSATIEAVVR-LQ--PR----CSEKIE----- 362 (546)
Q Consensus 298 IIGk~G~~Ik~i~~~sga~I~i~~~~~~---~~erii~i~g~~~~~~~~~~~~~a~~~-~~--~~----~~~~~~----- 362 (546)
||||+|.+||.|+++++|.|+|.+..+. -.+|++++.|+..-. ..+++.++. ++ |. +...+.
T Consensus 146 iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~---~~A~~~IL~Ki~eDpqs~scln~sya~vsGp 222 (402)
T KOG2191|consen 146 IIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQN---MKAVSLILQKIQEDPQSGSCLNISYANVSGP 222 (402)
T ss_pred eecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHH---HHHHHHHHHHhhcCCcccceeccchhcccCc
Confidence 9999999999999999999999965433 378999999964211 112222221 11 00 000000
Q ss_pred --------------cccCCcceeEEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCH
Q 009007 363 --------------RDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDL 428 (546)
Q Consensus 363 --------------~~~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~ 428 (546)
........+....|+...+|..-|.+|.++-.|-..||+.|.+.+..+.-. ....+ +-+.|-+
T Consensus 223 vaNsnPtGspya~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l~~m~--g~gy~-~n~~g~~ 299 (402)
T KOG2191|consen 223 VANSNPTGSPYAYQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQALNTMA--GYGYN-TNILGLG 299 (402)
T ss_pred ccccCCCCCCCCCCCccccccchhhccccccccccccccccccceeeecccccceeecccccccc--ccccc-ccccchh
Confidence 001123345567899999999999999999999999999999987654211 22333 6677888
Q ss_pred HHHHHHHHHHHHHHHh
Q 009007 429 DLAKDALIQVMTRLRA 444 (546)
Q Consensus 429 ~~v~~A~~~I~~~i~~ 444 (546)
-++..|-.+|..++..
T Consensus 300 ls~~aa~g~L~~~~~~ 315 (402)
T KOG2191|consen 300 LSILAAEGVLAAKVAS 315 (402)
T ss_pred hhhhhhhhHHHHhhcc
Confidence 8888777776665543
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=4.7e-14 Score=130.85 Aligned_cols=135 Identities=22% Similarity=0.268 Sum_probs=95.2
Q ss_pred EEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEe---cCCccccccccCcccCCHHHHHHHHHHHHH
Q 009007 47 YLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVY---SASDETNAFEDGDKFVSPAQDALFKVHDRV 123 (546)
Q Consensus 47 ilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~---G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i 123 (546)
|.||.+.+|.|||++|++|+.|+++|+|+|+|.+. +..|.|+ +.++. +++|...+.. +
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~-------------i~kA~~~I~~-i 62 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLA-------------VMKAREVVKA-I 62 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHH-------------HHHHHHHHHH-H
Confidence 57899999999999999999999999999999643 3578884 22222 2333333322 1
Q ss_pred HHhhhcCCCCC---CCCCceEEE-EEecC---------CceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCc
Q 009007 124 IAEELRGDEDS---DGGHQVTAK-LLVPS---------DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDE 190 (546)
Q Consensus 124 ~~~~~~~~~~~---~~~~~~~~~-l~Vp~---------~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr 190 (546)
... + .+.. -....++.. +-|+. ..+|+|||++|++++.|+..|+|+|.|. +.
T Consensus 63 ~~g-f--~~e~A~~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~------------~~ 127 (172)
T TIGR03665 63 GRG-F--SPEKALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY------------GK 127 (172)
T ss_pred HcC-C--CHHHHHHhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc------------CC
Confidence 110 0 0000 011122222 23332 3689999999999999999999999984 35
Q ss_pred eEEEEcCHHHHHHHHHHHHHHHhcC
Q 009007 191 LVQISGEASVVKKALCQIASRLHDN 215 (546)
Q Consensus 191 ~v~I~G~~~~v~~A~~~I~~~l~~~ 215 (546)
.|.|.|++++++.|..+|.+++...
T Consensus 128 ~v~i~G~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 128 TVGIIGDPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred EEEEECCHHHHHHHHHHHHHHHcCC
Confidence 7999999999999999999999554
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=99.53 E-value=3.8e-14 Score=131.47 Aligned_cols=138 Identities=20% Similarity=0.252 Sum_probs=93.8
Q ss_pred EEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEE---ecCcchhhhhhHHHHHHHHhcCccccccccc
Q 009007 288 LVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITV---SSKEFFEDTLSATIEAVVRLQPRCSEKIERD 364 (546)
Q Consensus 288 v~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~i~~~~~~~~erii~i---~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~ 364 (546)
|.||.+.++.|||++|++|++|+++||++|.++.. +..+.| ++.......+...+.++.+-++ ....+ .-
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~-~e~A~-~l 74 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLAVMKAREVVKAIGRGFS-PEKAL-KL 74 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHHHHHHHHHHHHHHcCCC-HHHHH-Hh
Confidence 57899999999999999999999999999999963 245666 2222111111222222222110 00000 00
Q ss_pred cCCcceeEEEEEcc---------CcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHH
Q 009007 365 SGLISFTTRLLVPT---------SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDAL 435 (546)
Q Consensus 365 ~~~~~~~~~l~VP~---------~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~ 435 (546)
.++...-.-+.|+. ..+|.|||++|++++.|++.|||+|.|.. .+|.|.|++++++.|.
T Consensus 75 ~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------------~~v~i~G~~~~~~~A~ 142 (172)
T TIGR03665 75 LDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------------KTVGIIGDPEQVQIAR 142 (172)
T ss_pred cCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------------CEEEEECCHHHHHHHH
Confidence 01111122234443 47899999999999999999999999942 5899999999999999
Q ss_pred HHHHHHHHh
Q 009007 436 IQVMTRLRA 444 (546)
Q Consensus 436 ~~I~~~i~~ 444 (546)
.+|.++|..
T Consensus 143 ~~i~~li~~ 151 (172)
T TIGR03665 143 EAIEMLIEG 151 (172)
T ss_pred HHHHHHHcC
Confidence 999998854
No 13
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.50 E-value=1.5e-13 Score=128.35 Aligned_cols=142 Identities=19% Similarity=0.219 Sum_probs=95.6
Q ss_pred EEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEe----cCcchhhhhhHHHHHHHHhcCcccc
Q 009007 284 FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVS----SKEFFEDTLSATIEAVVRLQPRCSE 359 (546)
Q Consensus 284 ~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~i~~~~~~~~erii~i~----g~~~~~~~~~~~~~a~~~~~~~~~~ 359 (546)
+...+.||.+.++.|||++|++|+.|+++|||+|+++.. +..|.|. +.......+...++++..-++ ...
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~-~e~ 76 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLAVLKARDIVKAIGRGFS-PEK 76 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCC-HHH
Confidence 467899999999999999999999999999999999963 2455564 222111111222333322110 000
Q ss_pred ccccccCCcceeEEEEEc---------cCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHH
Q 009007 360 KIERDSGLISFTTRLLVP---------TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL 430 (546)
Q Consensus 360 ~~~~~~~~~~~~~~l~VP---------~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~ 430 (546)
.+ ...++...-.-+.|. ...+|.|||++|++++.|++.|||+|.|.. ..|.|.|++++
T Consensus 77 A~-~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~------------~~v~i~G~~~~ 143 (180)
T PRK13763 77 AL-RLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG------------KTVAIIGDPEQ 143 (180)
T ss_pred HH-HHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC------------CEEEEEeCHHH
Confidence 00 000111111111221 247899999999999999999999999942 35999999999
Q ss_pred HHHHHHHHHHHHHh
Q 009007 431 AKDALIQVMTRLRA 444 (546)
Q Consensus 431 v~~A~~~I~~~i~~ 444 (546)
++.|...|..+++.
T Consensus 144 ~~~A~~~I~~li~g 157 (180)
T PRK13763 144 VEIAREAIEMLIEG 157 (180)
T ss_pred HHHHHHHHHHHHcC
Confidence 99999999988854
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.50 E-value=2e-13 Score=127.42 Aligned_cols=138 Identities=23% Similarity=0.221 Sum_probs=97.9
Q ss_pred eEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEe----cCCccccccccCcccCCHHHHHHHH
Q 009007 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVY----SASDETNAFEDGDKFVSPAQDALFK 118 (546)
Q Consensus 43 ~~~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~----G~~~~~~~~~~~~~~v~~a~~a~~~ 118 (546)
+...+.||.+.++.|||++|++|+.|+++|+|+|++.+. +..|.|+ +.++. +.+|...
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~-------------i~kA~~~ 64 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLA-------------VLKARDI 64 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHH-------------HHHHHHH
Confidence 467899999999999999999999999999999999653 4678886 32222 2333333
Q ss_pred HHHHHH----HhhhcCCCCCCCCCceEEEE-E----ecC-----CceeEEeecCchHHHHHHhhcCceEEEecCCCCCcc
Q 009007 119 VHDRVI----AEELRGDEDSDGGHQVTAKL-L----VPS-----DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSC 184 (546)
Q Consensus 119 i~~~i~----~~~~~~~~~~~~~~~~~~~l-~----Vp~-----~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~ 184 (546)
+...+. +..+.. ....+..++ - .+. ..+|+|||++|++++.|++.|||+|.|..
T Consensus 65 I~ai~~gf~~e~A~~l-----~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~------- 132 (180)
T PRK13763 65 VKAIGRGFSPEKALRL-----LDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG------- 132 (180)
T ss_pred HHHHhcCCCHHHHHHH-----hCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC-------
Confidence 322111 000000 011112221 1 111 36899999999999999999999999953
Q ss_pred cCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 009007 185 ALRSDELVQISGEASVVKKALCQIASRLHDN 215 (546)
Q Consensus 185 ~~~~dr~v~I~G~~~~v~~A~~~I~~~l~~~ 215 (546)
+.|.|.|++++++.|...|.++++..
T Consensus 133 -----~~v~i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 133 -----KTVAIIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred -----CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence 34999999999999999999999664
No 15
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.38 E-value=1.4e-12 Score=101.11 Aligned_cols=64 Identities=42% Similarity=0.630 Sum_probs=57.3
Q ss_pred eEEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHH
Q 009007 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQV 438 (546)
Q Consensus 371 ~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I 438 (546)
+.+|+||.+.+|+|||++|++|++|+++|||+|+|.+... ....+|+|+|+|+++++..|+.+|
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 3689999999999999999999999999999999976432 246789999999999999999987
No 16
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.28 E-value=6.9e-12 Score=97.15 Aligned_cols=55 Identities=44% Similarity=0.724 Sum_probs=50.4
Q ss_pred EEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCC-CCCceEEEEecCCcc
Q 009007 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVP-GSEERVVTVYSASDE 98 (546)
Q Consensus 44 ~~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~-~~~ervv~I~G~~~~ 98 (546)
++||+||...+|.||||+|++|++|+++|||+|.+.+... +..+|+|+|.|++++
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~ 56 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSA 56 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHH
Confidence 3799999999999999999999999999999999987643 788999999999776
No 17
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.27 E-value=3.4e-11 Score=124.38 Aligned_cols=271 Identities=23% Similarity=0.288 Sum_probs=168.0
Q ss_pred CCCceEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEecCCccccccccCcccCCHHHHHHHH
Q 009007 39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFK 118 (546)
Q Consensus 39 ~~~~~~~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~ 118 (546)
.++++..++.+|.+.+..||||.|++|+.|+..|++||.+.+.. -.++++.++.|-+.. ++++..++
T Consensus 64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p~~----------v~~a~a~~-- 130 (608)
T KOG2279|consen 64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFPVQ----------VCKAKAAI-- 130 (608)
T ss_pred chhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCCCC----------CChHHHHH--
Confidence 46889999999999999999999999999999999999996542 123455566654333 55555543
Q ss_pred HHHHHHHhhhcCCCCCCCCCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCH
Q 009007 119 VHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198 (546)
Q Consensus 119 i~~~i~~~~~~~~~~~~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~ 198 (546)
++++. ....+...+-+|...++.|+|++|++++.|+..++|+|.+..... ...++...|.+..
T Consensus 131 -~~~~~-----------~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr-----~g~~~~~~i~~qq 193 (608)
T KOG2279|consen 131 -HQILT-----------ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGR-----LGLSRLIKISGQQ 193 (608)
T ss_pred -HHHHh-----------cCCcccccccchhhhcccccccchhhhcchhcccccccccccccc-----cccccceeccccc
Confidence 33332 235667888999999999999999999999999999999976422 2457788888888
Q ss_pred HHHHHHHHHHHHHHhcCCC-------Ccccccc-ccccC-----CCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCC
Q 009007 199 SVVKKALCQIASRLHDNPS-------RSQHLLA-SAISN-----SHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAG 265 (546)
Q Consensus 199 ~~v~~A~~~I~~~l~~~~~-------~~~~~~~-s~~~~-----~~~~~g~~~~p~~g~~~~~~~p~~~~~gg~~~d~~~ 265 (546)
.-++.|..++.+.+.++-. ..+.... ....+ ++..++...+...+-.-..++|-.+....-.+|+.-
T Consensus 194 k~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v 273 (608)
T KOG2279|consen 194 KEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAV 273 (608)
T ss_pred chHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCccee
Confidence 8888999999888876421 1111100 00001 111111111100000000011100000000011000
Q ss_pred CC-CCCCCCCCCCC---CCCccEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCc---eEEEEecCcc
Q 009007 266 DW-SRSLYSAPRDD---LSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDD---CLITVSSKEF 338 (546)
Q Consensus 266 ~~-~~~~~~~p~~~---~~~~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~i~~~~~~~~e---rii~i~g~~~ 338 (546)
.. -...++.|.+. ........+|.+|...+|.+||+.|+.++.+...+++.+.|.-......- .++.+.|+..
T Consensus 274 ~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~v~~~qic~~egkqh 353 (608)
T KOG2279|consen 274 VVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSRVLQLQICVNEGKQH 353 (608)
T ss_pred EEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEeccccchhhhhhhheecchhH
Confidence 00 00111222222 23444577899999999999999999999999999999888764332211 3455667654
Q ss_pred h
Q 009007 339 F 339 (546)
Q Consensus 339 ~ 339 (546)
.
T Consensus 354 ~ 354 (608)
T KOG2279|consen 354 Y 354 (608)
T ss_pred H
Confidence 3
No 18
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.24 E-value=1.3e-11 Score=94.71 Aligned_cols=61 Identities=21% Similarity=0.323 Sum_probs=54.7
Q ss_pred EEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHH
Q 009007 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVM 439 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~ 439 (546)
.+|.||..++++|||++|++|++|+++|||+|.++... +.++.|+|+|++++|..|+.+|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-------~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-------SKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-------CCCCEEEEEcCHHHHHHHHHHhC
Confidence 57999999999999999999999999999999996532 45689999999999999998873
No 19
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.21 E-value=3.7e-11 Score=124.12 Aligned_cols=232 Identities=24% Similarity=0.362 Sum_probs=167.4
Q ss_pred CCCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 009007 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN 215 (546)
Q Consensus 136 ~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~v~~A~~~I~~~l~~~ 215 (546)
....+.+++.||...+-++||+.|.+|+.|+..++++|.+..++ .+ .++...+.|-+.++.+|...+..++..+
T Consensus 64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g-----~e~~~~~~~~p~~v~~a~a~~~~~~~~~ 137 (608)
T KOG2279|consen 64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VG-----DERVLLISGFPVQVCKAKAAIHQILTEN 137 (608)
T ss_pred chhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CC-----cccchhhccCCCCCChHHHHHHHHHhcC
Confidence 34677899999999999999999999999999999999986653 22 3566666778999999999999988664
Q ss_pred CCCccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEEEeecCcc
Q 009007 216 PSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANI 295 (546)
Q Consensus 216 ~~~~~~~~~s~~~~~~~~~g~~~~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~~~~~p~~~~~~~~~~~~v~vp~~~~ 295 (546)
. .+.+.+.+|...+
T Consensus 138 ~------------------------------------------------------------------pvk~~lsvpqr~~ 151 (608)
T KOG2279|consen 138 T------------------------------------------------------------------PVSEQLSVPQRSV 151 (608)
T ss_pred C------------------------------------------------------------------cccccccchhhhc
Confidence 1 3456678899999
Q ss_pred cccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhh--------hhHHHHHHHHh----c---Cc---c
Q 009007 296 GGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDT--------LSATIEAVVRL----Q---PR---C 357 (546)
Q Consensus 296 g~IIGk~G~~Ik~i~~~sga~I~i~~~~~~~~erii~i~g~~~~~~~--------~~~~~~a~~~~----~---~~---~ 357 (546)
+.|+|++|++++.|+..++++|.++.+......+++.|.+....... +..-.+.+.+. + ++ .
T Consensus 152 ~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~ 231 (608)
T KOG2279|consen 152 GRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPI 231 (608)
T ss_pred ccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCc
Confidence 99999999999999999999999998865566677777765322110 00000000000 0 00 0
Q ss_pred c---cc------------------ccc--------c-----------------------cCCcceeEEEEEccCcceeEE
Q 009007 358 S---EK------------------IER--------D-----------------------SGLISFTTRLLVPTSRIGCLI 385 (546)
Q Consensus 358 ~---~~------------------~~~--------~-----------------------~~~~~~~~~l~VP~~~vG~II 385 (546)
+ +. ... + ........+|.||...+|.||
T Consensus 232 n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~li 311 (608)
T KOG2279|consen 232 NVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLI 311 (608)
T ss_pred cccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCcccccchh
Confidence 0 00 000 0 011234468999999999999
Q ss_pred cCCChhHHHHHHhhCceEEEecCCCCCCCCCC-CCceEEEEcCHHHHHHHHHHHHHHH
Q 009007 386 GKGGSIITEMRRLTKANIRILPKENLPKIASE-DDEMVQISGDLDLAKDALIQVMTRL 442 (546)
Q Consensus 386 GkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~-~~r~v~I~G~~~~v~~A~~~I~~~i 442 (546)
|+.|+.++.+...|++.+.|.. .|..... .-.++.+.|+..-+..|..|+..+.
T Consensus 312 g~~gey~s~yssasn~~~hi~t---~pyt~~v~~~qic~~egkqh~~n~vl~ml~~~~ 366 (608)
T KOG2279|consen 312 GHAGEYLSVYSSASNHPNHIWT---QPYTSRVLQLQICVNEGKQHYENSVLEMLTVHV 366 (608)
T ss_pred hhhhhhhhhhhhccCccceEEe---ccccchhhhhhhheecchhHHHHHHHhhhhccC
Confidence 9999999999999999988864 3431111 1145789999999999999998433
No 20
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.20 E-value=3.4e-11 Score=134.79 Aligned_cols=304 Identities=21% Similarity=0.266 Sum_probs=195.1
Q ss_pred eEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEecCCccccccccCcccCCHHHHHHHHHHH-
Q 009007 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHD- 121 (546)
Q Consensus 43 ~~~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~- 121 (546)
+..++.+-...+.+|||++|.+++.++.++.+.|+|+..... .....|.+...++.. ...-.+.++.++..
T Consensus 201 ~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~--~~~~~i~~~~~~~~~------~~~~i~~~~~~le~~ 272 (753)
T KOG2208|consen 201 VFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKS--SPSNKIDGRLNSSSS------INVEIQEALTRLESE 272 (753)
T ss_pred EEEEeeccccchhhhccccccccccccccceeEEEccccccc--chhhhhcccccccee------hhhhhHHHHHHhcCh
Confidence 667899999999999999999999999999999999755211 112333332222100 00001111111100
Q ss_pred ----------------------------HHHHhh-hcCC-C----------C----------------CCCCCceEEEEE
Q 009007 122 ----------------------------RVIAEE-LRGD-E----------D----------------SDGGHQVTAKLL 145 (546)
Q Consensus 122 ----------------------------~i~~~~-~~~~-~----------~----------------~~~~~~~~~~l~ 145 (546)
...... +..+ + . ......+.+.+.
T Consensus 273 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~ 352 (753)
T KOG2208|consen 273 FDYDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKRE 352 (753)
T ss_pred hhhhhhhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEe
Confidence 000000 0000 0 0 011233667788
Q ss_pred ecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCccccccc
Q 009007 146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLAS 225 (546)
Q Consensus 146 Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~s 225 (546)
+-...+..++||+|.+|..|++++.|.|.+... .+.+..+.++|....+.+|...|...+.+...
T Consensus 353 i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~-------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n-------- 417 (753)
T KOG2208|consen 353 IFPEELKFVIGKKGANIEKIREESQVKIDLPKQ-------GSNNKKVVITGVSANDEKAVEDVEKIIAEILN-------- 417 (753)
T ss_pred ecHHhhhhhcCCCCccHHHHHHhhhhceecccc-------cCCCCCeEEeccccchhHHHHHHHHHHHhhhc--------
Confidence 888999999999999999999999999999763 25678899999999999999999988877311
Q ss_pred cccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEEEeecCcccccccCCchh
Q 009007 226 AISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAI 305 (546)
Q Consensus 226 ~~~~~~~~~g~~~~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~~~~~p~~~~~~~~~~~~v~vp~~~~g~IIGk~G~~ 305 (546)
......+.+|...+..+||.+|..
T Consensus 418 --------------------------------------------------------~~~~~~~~iP~k~~~~iig~~g~~ 441 (753)
T KOG2208|consen 418 --------------------------------------------------------SIVKEEVQIPTKSHKRIIGTKGAL 441 (753)
T ss_pred --------------------------------------------------------ccccceeecCccchhhhhcccccc
Confidence 023556899999999999999999
Q ss_pred HHHHHhhhC-CeEEecCCCCCCCceEEEEecCcc-hhhhhhHHHHHHHHhcCccccccccccCCcceeEEEEEccCccee
Q 009007 306 INQIRQESG-AAIKVDSSSTEGDDCLITVSSKEF-FEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGC 383 (546)
Q Consensus 306 Ik~i~~~sg-a~I~i~~~~~~~~erii~i~g~~~-~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l~VP~~~vG~ 383 (546)
|+.|..+++ ..|.+.......+ ..++.+... ++. +...+..+.... .........+...+.|..+.+.
T Consensus 442 i~~I~~k~~~v~i~f~~~~~~~~--~~~~~~~~~dv~~----~~~~~~~~~~~a----~~~~~~~~~~~d~~~~~~~~~~ 511 (753)
T KOG2208|consen 442 INYIMGKHGGVHIKFQNNNNSSD--MVTIRGISKDVEK----SVSLLKALKADA----KNLKFRDVVTKDKLLPVKYIGK 511 (753)
T ss_pred HHHHHhhcCcEEEecCCCCcccc--cceEeccccccch----hHHHHHhhhhhh----hcchhhhhhhccccchHHhhcc
Confidence 999999999 7777776543322 233333211 111 111111110000 0000112356677888888888
Q ss_pred EEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhc
Q 009007 384 LIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN 445 (546)
Q Consensus 384 IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~ 445 (546)
.+|+.|..+...++.....+.. ..++..++|.|..+.|.+|.+++..++...
T Consensus 512 ~~g~~~~i~d~~~~~~i~~~~~----------~~~~~~i~i~gk~~~v~~a~~~L~~~~~~~ 563 (753)
T KOG2208|consen 512 EIGKNGTIRDSLGDKSIFPPNE----------DEDHEKITIEGKLELVLEAPAELKALIEAL 563 (753)
T ss_pred cccCceeeeccCCceeeccccc----------ccccceeeecccccchhhhHHHHHhcchhh
Confidence 8888776666555554433322 245678999999999999999887777655
No 21
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.20 E-value=7.2e-11 Score=89.98 Aligned_cols=58 Identities=26% Similarity=0.342 Sum_probs=52.5
Q ss_pred eeEEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC-HHHHHHHHHHH
Q 009007 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD-LDLAKDALIQV 438 (546)
Q Consensus 370 ~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~-~~~v~~A~~~I 438 (546)
....|.||.+++|+||||+|++|++|+++|||+|.|.. ++.|.|.|+ +++++.|+.+|
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----------~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-----------DGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-----------CCEEEEEeCCHHHHHHHHHHh
Confidence 35679999999999999999999999999999999942 358999998 99999999887
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=99.18 E-value=1.5e-11 Score=93.69 Aligned_cols=60 Identities=35% Similarity=0.511 Sum_probs=53.9
Q ss_pred eEEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHH
Q 009007 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQV 438 (546)
Q Consensus 371 ~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I 438 (546)
|.+|.||.+++|+|||++|++|++|+++|||+|+++.+ + ....|+|.|++++|+.|+.+|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~-------~-~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD-------D-ERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST-------T-EEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC-------C-CcEEEEEEeCHHHHHHHHhhC
Confidence 67899999999999999999999999999999999642 1 345899999999999999886
No 23
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.14 E-value=1.8e-10 Score=88.80 Aligned_cols=62 Identities=37% Similarity=0.599 Sum_probs=55.2
Q ss_pred EEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHH
Q 009007 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQV 438 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I 438 (546)
.+|.||.+++++|||++|++|++|+++|||+|.|..... .+.++.|+|.|+.+++..|+.+|
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 579999999999999999999999999999999965321 35678999999999999999876
No 24
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.04 E-value=2.5e-10 Score=87.56 Aligned_cols=60 Identities=28% Similarity=0.441 Sum_probs=54.7
Q ss_pred EEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHH
Q 009007 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI 208 (546)
Q Consensus 142 ~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~v~~A~~~I 208 (546)
..|.||.+++++|||++|++|++|+++|||+|.|+... ..++.|+|+|+.++|.+|+.+|
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-------~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-------SKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-------CCCCEEEEEcCHHHHHHHHHHh
Confidence 57899999999999999999999999999999997642 4578999999999999998876
No 25
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.04 E-value=8.7e-10 Score=84.01 Aligned_cols=58 Identities=34% Similarity=0.488 Sum_probs=52.5
Q ss_pred eEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcC-HHHHHHHHHHH
Q 009007 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGE-ASVVKKALCQI 208 (546)
Q Consensus 140 ~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~-~~~v~~A~~~I 208 (546)
.+..+.||.+++++||||+|++|++|+++|||+|.|.+ ++.|.|+|+ .+++++|+.+|
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 45789999999999999999999999999999999854 457999998 99999998876
No 26
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.02 E-value=1.7e-10 Score=87.88 Aligned_cols=60 Identities=40% Similarity=0.613 Sum_probs=54.0
Q ss_pred EEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHH
Q 009007 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI 208 (546)
Q Consensus 141 ~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~v~~A~~~I 208 (546)
|.+|.||.+++++|||++|++|++|+++|||+|.|+.+ .....|+|+|+.++|.+|+.+|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~--------~~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD--------DERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--------TEEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--------CCcEEEEEEeCHHHHHHHHhhC
Confidence 57899999999999999999999999999999999764 1245899999999999999876
No 27
>PF13014 KH_3: KH domain
Probab=98.96 E-value=1.3e-09 Score=76.87 Aligned_cols=42 Identities=48% Similarity=0.794 Sum_probs=38.9
Q ss_pred ccceEecCCcHHHHHHHHHhCCeEEEcC-CCCCCCceEEEEec
Q 009007 53 KIGSIIGRGGEIVKQLRIDTKSKIRIGE-TVPGSEERVVTVYS 94 (546)
Q Consensus 53 ~~g~IIGk~G~~Ik~i~~~tga~I~i~~-~~~~~~ervv~I~G 94 (546)
++|+||||+|++|++|+++|+|+|+|++ ..++..+|+|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 5899999999999999999999999998 56788899999987
No 28
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.96 E-value=2.4e-09 Score=82.44 Aligned_cols=62 Identities=40% Similarity=0.657 Sum_probs=55.5
Q ss_pred EEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHH
Q 009007 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI 208 (546)
Q Consensus 142 ~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~v~~A~~~I 208 (546)
.+|.||..++++|||++|++|++|+++|+|+|.|..... ...++.|.|.|+.+++..|+.+|
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 689999999999999999999999999999999986432 24688999999999999998776
No 29
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.92 E-value=2.1e-09 Score=120.52 Aligned_cols=288 Identities=19% Similarity=0.242 Sum_probs=190.4
Q ss_pred eEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEecCCccccccccCcccCCHHHHHHHHHHHH
Q 009007 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDR 122 (546)
Q Consensus 43 ~~~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~ 122 (546)
....+.+-...+..|+||+|.+|.+|++++.|.|.+.+. +..+..+++++...++ ..|.+.+..+...
T Consensus 347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~~~----------~ka~~~v~~~~~e 414 (753)
T KOG2208|consen 347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSAND----------EKAVEDVEKIIAE 414 (753)
T ss_pred eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccccch----------hHHHHHHHHHHHh
Confidence 566778889999999999999999999999999999875 6677899999987773 2233443333332
Q ss_pred HHHhhhcCCCCCCCCCceEEEEEecCCceeEEeecCchHHHHHHhhcC-ceEEEecCCCCCcccCCCCceEEEEcCHHHH
Q 009007 123 VIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETG-AQIRILKDEHLPSCALRSDELVQISGEASVV 201 (546)
Q Consensus 123 i~~~~~~~~~~~~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tg-a~I~i~~~~~~p~~~~~~dr~v~I~G~~~~v 201 (546)
+.. ......+.+|...+.++||.+|..|+.|.++++ +.|.+.... +....+++.|....+
T Consensus 415 i~n------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~-------~~~~~~~~~~~~~dv 475 (753)
T KOG2208|consen 415 ILN------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN-------NSSDMVTIRGISKDV 475 (753)
T ss_pred hhc------------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC-------cccccceEecccccc
Confidence 221 144577999999999999999999999999999 666654432 334568888888888
Q ss_pred HHHHHHHHHHHhcCCCCccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009007 202 KKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSS 281 (546)
Q Consensus 202 ~~A~~~I~~~l~~~~~~~~~~~~s~~~~~~~~~g~~~~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~~~~~p~~~~~~ 281 (546)
.++..++..+........ | .
T Consensus 476 ~~~~~~~~~~~~~a~~~~-----------------------------------------------~-------------~ 495 (753)
T KOG2208|consen 476 EKSVSLLKALKADAKNLK-----------------------------------------------F-------------R 495 (753)
T ss_pred chhHHHHHhhhhhhhcch-----------------------------------------------h-------------h
Confidence 877666555443211000 0 0
Q ss_pred ccEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhhhhHHHHHHHHhcCcccccc
Q 009007 282 KEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKI 361 (546)
Q Consensus 282 ~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~i~~~~~~~~erii~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~ 361 (546)
.....+...|..+.+..+|+.+..+..+.+ ...++.... .+...++|.|+.... ..+.+++..+.+.+..
T Consensus 496 ~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~----~~i~~~~~~-~~~~~i~i~gk~~~v---~~a~~~L~~~~~~~~~-- 565 (753)
T KOG2208|consen 496 DVVTKDKLLPVKYIGKEIGKNGTIRDSLGD----KSIFPPNED-EDHEKITIEGKLELV---LEAPAELKALIEALIK-- 565 (753)
T ss_pred hhhhccccchHHhhcccccCceeeeccCCc----eeecccccc-cccceeeecccccch---hhhHHHHHhcchhhhh--
Confidence 011334456666666666666665554444 444444322 256678888865322 2233333332222221
Q ss_pred ccccCCcceeEEEEEccCcc-eeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHH
Q 009007 362 ERDSGLISFTTRLLVPTSRI-GCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMT 440 (546)
Q Consensus 362 ~~~~~~~~~~~~l~VP~~~v-G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~ 440 (546)
.....+.+|..++ -+|++++....+..+...|+.+..++.. .+.+.++|.|....++.|...+.+
T Consensus 566 -------~~~~~v~~~~~~~~~~l~~~~~~~~~~~e~~~gv~~~fp~~~-------~~~~e~~i~g~~~~v~aa~~~~~~ 631 (753)
T KOG2208|consen 566 -------ATLLEVNNPPGQHRPFLIGKGIENRTYVEVFGGVVVPFPRSP-------TSSDEVSIKGAKDEVKAAKGRLEE 631 (753)
T ss_pred -------hhhhhccCcchheeeeeeccccccccceeecCcccccCCCCC-------CchhhhccchhHHHHHHhhccchh
Confidence 1334455666655 7788888888888888888888775532 334579999999999999887777
Q ss_pred HHHhc
Q 009007 441 RLRAN 445 (546)
Q Consensus 441 ~i~~~ 445 (546)
.+...
T Consensus 632 i~~~~ 636 (753)
T KOG2208|consen 632 IVEYL 636 (753)
T ss_pred hhhhc
Confidence 76643
No 30
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.90 E-value=2.8e-08 Score=91.48 Aligned_cols=147 Identities=26% Similarity=0.293 Sum_probs=102.6
Q ss_pred CceEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEecCCccccccccCcccCCHHHHHHHHHH
Q 009007 41 EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVH 120 (546)
Q Consensus 41 ~~~~~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~ 120 (546)
......+.||...++.+||+.|++.+.|++.++++|.+ +..+..|+|........ .-++.+..
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~i-----D~~~~~V~i~~~~~t~D------------p~~~~ka~ 68 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRI-----DSKTGSVTIRTTRKTED------------PLALLKAR 68 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEE-----ECCCCeEEEEecCCCCC------------hHHHHHHH
Confidence 34456799999999999999999999999999999999 56678999987732111 11222333
Q ss_pred HHHHHhhhcCCCCC---CCCCceEEEE-----Eec-C-----CceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccC
Q 009007 121 DRVIAEELRGDEDS---DGGHQVTAKL-----LVP-S-----DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCAL 186 (546)
Q Consensus 121 ~~i~~~~~~~~~~~---~~~~~~~~~l-----~Vp-~-----~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 186 (546)
+.+.+-....+++. -..+.+.+.+ ++- + ...|+|||++|.|-+.|++.|+|.|.|..
T Consensus 69 d~VkAIgrGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g--------- 139 (194)
T COG1094 69 DVVKAIGRGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG--------- 139 (194)
T ss_pred HHHHHHhcCCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC---------
Confidence 32222111111110 0011222221 111 1 24599999999999999999999999954
Q ss_pred CCCceEEEEcCHHHHHHHHHHHHHHHhcCC
Q 009007 187 RSDELVQISGEASVVKKALCQIASRLHDNP 216 (546)
Q Consensus 187 ~~dr~v~I~G~~~~v~~A~~~I~~~l~~~~ 216 (546)
..|.|.|..++|..|..+|..++...+
T Consensus 140 ---~tVaiiG~~~~v~iAr~AVemli~G~~ 166 (194)
T COG1094 140 ---KTVAIIGGFEQVEIAREAVEMLINGAP 166 (194)
T ss_pred ---cEEEEecChhhhHHHHHHHHHHHcCCC
Confidence 479999999999999999999997754
No 31
>PF13014 KH_3: KH domain
Probab=98.89 E-value=3.3e-09 Score=74.89 Aligned_cols=43 Identities=49% Similarity=0.797 Sum_probs=37.2
Q ss_pred cceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc
Q 009007 380 RIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG 426 (546)
Q Consensus 380 ~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G 426 (546)
+||+|||++|++|++|+++|+|+|+|++ +..| .++++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~-~~~~---~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP-ENEP---GSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC-ccCC---CCCceEEEEEC
Confidence 5899999999999999999999999987 2222 57789999997
No 32
>smart00322 KH K homology RNA-binding domain.
Probab=98.86 E-value=1.5e-08 Score=78.54 Aligned_cols=66 Identities=29% Similarity=0.525 Sum_probs=58.6
Q ss_pred eeEEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 009007 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRL 442 (546)
Q Consensus 370 ~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i 442 (546)
.+.+|.||..++++|||++|++|++|++.|+++|.+... ......|+|.|+.+++..|+.+|.+.+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~-------~~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPED-------GSEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCC-------CCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 678899999999999999999999999999999999532 124578999999999999999998876
No 33
>smart00322 KH K homology RNA-binding domain.
Probab=98.68 E-value=1.1e-07 Score=73.54 Aligned_cols=67 Identities=39% Similarity=0.655 Sum_probs=59.3
Q ss_pred ceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 009007 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRL 212 (546)
Q Consensus 139 ~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~v~~A~~~I~~~l 212 (546)
.++.++.||...++.|||++|.+|++|++.|+|+|.+.... .....+.|.|+.+++..|..+|.+.+
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 35788999999999999999999999999999999996531 14678999999999999999998876
No 34
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.66 E-value=1.1e-07 Score=87.49 Aligned_cols=142 Identities=23% Similarity=0.313 Sum_probs=96.7
Q ss_pred cEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhhh-----hHHHHHHHHhcCc-
Q 009007 283 EFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTL-----SATIEAVVRLQPR- 356 (546)
Q Consensus 283 ~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~i~~~~~~~~erii~i~g~~~~~~~~-----~~~~~a~~~~~~~- 356 (546)
.....+.||..-++.+||+.|+..+.|.+.++++|.++.. +..++|...+...|.+ ...+.|+-+-++-
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~-----~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe 81 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPE 81 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHH
Confidence 4467799999999999999999999999999999999863 3456666653222221 1122222111100
Q ss_pred cccccccccCCcceeEEEEE------c----cCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc
Q 009007 357 CSEKIERDSGLISFTTRLLV------P----TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG 426 (546)
Q Consensus 357 ~~~~~~~~~~~~~~~~~l~V------P----~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G 426 (546)
-.-.+-.+. .+-..+.+ + ....|.|||++|.+-+-|++.|+|+|.|.. .+|.|.|
T Consensus 82 ~A~~LL~d~---~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g------------~tVaiiG 146 (194)
T COG1094 82 KALKLLEDD---YYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG------------KTVAIIG 146 (194)
T ss_pred HHHHHhcCC---cEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC------------cEEEEec
Confidence 000000000 00001111 1 235699999999999999999999999953 3899999
Q ss_pred CHHHHHHHHHHHHHHHHh
Q 009007 427 DLDLAKDALIQVMTRLRA 444 (546)
Q Consensus 427 ~~~~v~~A~~~I~~~i~~ 444 (546)
.+++|+.|...|..+|..
T Consensus 147 ~~~~v~iAr~AVemli~G 164 (194)
T COG1094 147 GFEQVEIAREAVEMLING 164 (194)
T ss_pred ChhhhHHHHHHHHHHHcC
Confidence 999999999999888865
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=98.44 E-value=7.9e-07 Score=77.12 Aligned_cols=67 Identities=22% Similarity=0.351 Sum_probs=51.9
Q ss_pred cCcceeEEcCCChhHHHHHHhhCceEEEecCCCC-----------CCCCC-CCCceEEEEcC---HHHHHHHHHHHHHHH
Q 009007 378 TSRIGCLIGKGGSIITEMRRLTKANIRILPKENL-----------PKIAS-EDDEMVQISGD---LDLAKDALIQVMTRL 442 (546)
Q Consensus 378 ~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~-----------P~~~~-~~~r~v~I~G~---~~~v~~A~~~I~~~i 442 (546)
.+++|.|||++|++||+|+++|||+|.|..+... |...+ ++.-.|.|.++ .+++.+|+.+|..+|
T Consensus 14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll 93 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL 93 (120)
T ss_pred CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence 4688999999999999999999999999865311 11111 12246899995 599999999999888
Q ss_pred Hh
Q 009007 443 RA 444 (546)
Q Consensus 443 ~~ 444 (546)
..
T Consensus 94 ~~ 95 (120)
T cd02395 94 KP 95 (120)
T ss_pred cc
Confidence 74
No 36
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.25 E-value=8.6e-07 Score=86.09 Aligned_cols=143 Identities=17% Similarity=0.237 Sum_probs=100.9
Q ss_pred ccEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhhhhHHHHHHHHhcCcc----
Q 009007 282 KEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRC---- 357 (546)
Q Consensus 282 ~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~i~~~~~~~~erii~i~g~~~~~~~~~~~~~a~~~~~~~~---- 357 (546)
..++..+.||..+++.|.|++|.+||.|+.+|..+|+-+... .+.++.++|.....+.+...++++..-+..+
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~---eePiF~vTg~~edv~~aRrei~saaeH~~l~~~s~ 100 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG---EEPIFPVTGRHEDVRRARREIPSAAEHFGLIRASR 100 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC---CCCcceeccCchhHHHHhhcCccccceeeeeeecc
Confidence 456888999999999999999999999999999999887542 5589999996432222211222111111000
Q ss_pred --ccccccccCCcceeEEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHH-HHHH
Q 009007 358 --SEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL-AKDA 434 (546)
Q Consensus 358 --~~~~~~~~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~-v~~A 434 (546)
...........+.+..+.+|-..+|.|.|..|.+|+.|++.+...|.-+-++ .+-++.++|-+.. +++|
T Consensus 101 s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~--------~~~Vf~Vtg~~~nC~kra 172 (394)
T KOG2113|consen 101 SFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRC--------GEPVFCVTGAPKNCVKRA 172 (394)
T ss_pred cccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeeccC--------CCceEEEecCCcchhhhc
Confidence 0000111123467888999999999999999999999999999999876543 3458999998877 4444
Q ss_pred H
Q 009007 435 L 435 (546)
Q Consensus 435 ~ 435 (546)
.
T Consensus 173 ~ 173 (394)
T KOG2113|consen 173 R 173 (394)
T ss_pred c
Confidence 4
No 37
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.22 E-value=4.5e-06 Score=72.42 Aligned_cols=67 Identities=25% Similarity=0.389 Sum_probs=51.5
Q ss_pred CceeEEeecCchHHHHHHhhcCceEEEecCCCCC-----------c-ccCCCCceEEEEcCH---HHHHHHHHHHHHHHh
Q 009007 149 DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLP-----------S-CALRSDELVQISGEA---SVVKKALCQIASRLH 213 (546)
Q Consensus 149 ~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p-----------~-~~~~~dr~v~I~G~~---~~v~~A~~~I~~~l~ 213 (546)
+++|.|||++|.+||+|+++|||+|.|..+.... . ......-.|.|++.. +++.+|+.+|..++.
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 5789999999999999999999999997642110 0 001223568899864 899999999999997
Q ss_pred cC
Q 009007 214 DN 215 (546)
Q Consensus 214 ~~ 215 (546)
..
T Consensus 95 ~~ 96 (120)
T cd02395 95 PA 96 (120)
T ss_pred cC
Confidence 54
No 38
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.07 E-value=1.2e-05 Score=88.80 Aligned_cols=97 Identities=25% Similarity=0.322 Sum_probs=79.2
Q ss_pred cccCCHHHHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCccc
Q 009007 106 DKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCA 185 (546)
Q Consensus 106 ~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~ 185 (546)
.+.+..|.+++.+|++.+.+..... .+.....+....+.||.+.++.|||++|.+||.|.++|||+|.|..
T Consensus 545 ~~aL~~A~~g~~~Il~~m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-------- 615 (719)
T TIGR02696 545 ASALKQARDARLAILDVMAEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED-------- 615 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec--------
Confidence 4567788899999988765544433 3334456778899999999999999999999999999999999953
Q ss_pred CCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009007 186 LRSDELVQISG-EASVVKKALCQIASRLHD 214 (546)
Q Consensus 186 ~~~dr~v~I~G-~~~~v~~A~~~I~~~l~~ 214 (546)
+..|.|.+ +.+++++|+.+|..++..
T Consensus 616 ---~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 616 ---DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred ---CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 56789888 578899999999998864
No 39
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=98.04 E-value=3.5e-05 Score=79.61 Aligned_cols=101 Identities=23% Similarity=0.348 Sum_probs=68.7
Q ss_pred hHHHHHHHHhcCccccccccccCCcceeEEEEEc------cCcceeEEcCCChhHHHHHHhhCceEEEecCCC-------
Q 009007 344 SATIEAVVRLQPRCSEKIERDSGLISFTTRLLVP------TSRIGCLIGKGGSIITEMRRLTKANIRILPKEN------- 410 (546)
Q Consensus 344 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l~VP------~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~------- 410 (546)
.+.+++++++.+.-.-. .+-.....++.+|.|| .++||+|||..|.+.|+|+++|||+|.|-.+..
T Consensus 113 ~e~I~~~lk~nP~fkpP-~DYk~p~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~ 191 (554)
T KOG0119|consen 113 HEIIEEILKLNPGFKPP-ADYKPPAKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGR 191 (554)
T ss_pred HHHHHHHHHhCcCCCCC-cccCcccccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccC
Confidence 44566666655442211 1111112577788888 468999999999999999999999999977321
Q ss_pred ---CCCCCCCCCc-eEEEEcC-HHHHHHHHHHHHHHHHhc
Q 009007 411 ---LPKIASEDDE-MVQISGD-LDLAKDALIQVMTRLRAN 445 (546)
Q Consensus 411 ---~P~~~~~~~r-~v~I~G~-~~~v~~A~~~I~~~i~~~ 445 (546)
+.....+.+. -+.|+.+ .|.|++|+++|..+|.+.
T Consensus 192 ~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~a 231 (554)
T KOG0119|consen 192 SDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQSA 231 (554)
T ss_pred CcccccccccccceeEEEecchHHHHHHHHHHHHHHHHhh
Confidence 1111123333 3888884 789999999999999874
No 40
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.03 E-value=5.7e-06 Score=73.88 Aligned_cols=102 Identities=19% Similarity=0.265 Sum_probs=69.3
Q ss_pred EEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEecCCccccccccCcccCCHHHHHHHHHHHHHH
Q 009007 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVI 124 (546)
Q Consensus 45 ~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~ 124 (546)
+.++|+...+|..||++|++|+.|++..|-+|.|-+- +-. +++-+..++.-..
T Consensus 34 vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~-----------s~d----------------~~~fI~n~l~Pa~ 86 (140)
T PRK08406 34 IIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY-----------SDD----------------PEEFIKNIFAPAA 86 (140)
T ss_pred EEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc-----------CCC----------------HHHHHHHHcCCCE
Confidence 5678899999999999999999999999988876321 111 1122211111100
Q ss_pred HhhhcCCCCCCCCCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEe
Q 009007 125 AEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRIL 176 (546)
Q Consensus 125 ~~~~~~~~~~~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~ 176 (546)
-.++.- ........+.+.|+....+.+|||+|++|+.++.-++-.+.|.
T Consensus 87 V~~v~I---~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 87 VRSVTI---KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred EEEEEE---EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 000000 0112234577889999999999999999999999999988773
No 41
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.98 E-value=1.1e-05 Score=78.68 Aligned_cols=142 Identities=25% Similarity=0.359 Sum_probs=103.5
Q ss_pred CCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCC
Q 009007 137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNP 216 (546)
Q Consensus 137 ~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~v~~A~~~I~~~l~~~~ 216 (546)
...++..+.||..+++.+.|++|.+||.|+.+|...|.-+...+. -+..++|..+.|+.|++.|...-+..-
T Consensus 23 p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~ee--------PiF~vTg~~edv~~aRrei~saaeH~~ 94 (394)
T KOG2113|consen 23 GQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEE--------PIFPVTGRHEDVRRARREIPSAAEHFG 94 (394)
T ss_pred CCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCCC--------CcceeccCchhHHHHhhcCccccceee
Confidence 378899999999999999999999999999999999987765443 367899999999999988765332210
Q ss_pred CCccccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEEEeecCccc
Q 009007 217 SRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIG 296 (546)
Q Consensus 217 ~~~~~~~~s~~~~~~~~~g~~~~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~~~~~p~~~~~~~~~~~~v~vp~~~~g 296 (546)
+.-+.+ .|. + +. + + + ..+.+....+.+|...++
T Consensus 95 ------l~~~s~-s~S------g---g~------~------~-------------~------s~s~qt~sy~svP~rvvg 127 (394)
T KOG2113|consen 95 ------LIRASR-SFS------G---GT------N------G-------------A------SASGQTTSYVSVPLRVVG 127 (394)
T ss_pred ------eeeecc-ccc------C---CC------c------c-------------c------cccCCCceeeeccceeee
Confidence 000000 000 0 00 0 0 0 012345778889999999
Q ss_pred ccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecC
Q 009007 297 GVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSK 336 (546)
Q Consensus 297 ~IIGk~G~~Ik~i~~~sga~I~i~~~~~~~~erii~i~g~ 336 (546)
.|.|..|.+|+.|++.+...|.-+-.. .+.++.++|.
T Consensus 128 lvv~~~~~ti~~iqq~tnt~I~T~v~~---~~~Vf~Vtg~ 164 (394)
T KOG2113|consen 128 LVVGPKGATIKRIQQFTNTYIATPVRC---GEPVFCVTGA 164 (394)
T ss_pred eccccccCccchheecccceEeeeccC---CCceEEEecC
Confidence 999999999999999999988776543 4567888874
No 42
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.97 E-value=3.6e-05 Score=68.75 Aligned_cols=103 Identities=20% Similarity=0.268 Sum_probs=71.1
Q ss_pred EEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhhhhHHHHHHHHhcCcccccccc
Q 009007 284 FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIER 363 (546)
Q Consensus 284 ~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~i~~~~~~~~erii~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~ 363 (546)
..+-++|+...+|..||++|++|+.|++..|-+|.+-.-+.+ . ..-+..++.- .-.....-
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~d-------------~----~~fI~n~l~P--a~V~~v~I 92 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDD-------------P----EEFIKNIFAP--AAVRSVTI 92 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCCC-------------H----HHHHHHHcCC--CEEEEEEE
Confidence 377889999999999999999999999998988777543211 0 1122222211 11111100
Q ss_pred ccCCcceeEEEEEccCcceeEEcCCChhHHHHHHhhCceEEE
Q 009007 364 DSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405 (546)
Q Consensus 364 ~~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i 405 (546)
..........+.|+.+..|..|||+|++|+.+++.++-.+.|
T Consensus 93 ~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 93 KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 001112456788999999999999999999999999988877
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=97.78 E-value=5.5e-05 Score=83.76 Aligned_cols=65 Identities=26% Similarity=0.312 Sum_probs=57.6
Q ss_pred ceeEEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHh
Q 009007 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (546)
Q Consensus 369 ~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~ 444 (546)
.....|.||.+.+|.|||+||.+||+|.++|||+|.|.. +..|.|.+ +.+++++|+.+|...+..
T Consensus 577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-----------~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED-----------DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec-----------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 456789999999999999999999999999999999942 45788888 689999999999988874
No 44
>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=97.58 E-value=0.00014 Score=81.72 Aligned_cols=97 Identities=21% Similarity=0.297 Sum_probs=74.0
Q ss_pred ccCCHHHHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccC
Q 009007 107 KFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCAL 186 (546)
Q Consensus 107 ~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 186 (546)
+.+..|.+++.+|++.+.+.......+.....+....+.||.+.++.|||++|.+||.|+++|||+|.|..
T Consensus 518 ~al~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d--------- 588 (684)
T TIGR03591 518 QALEQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED--------- 588 (684)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec---------
Confidence 45566778888887765544333222334445667889999999999999999999999999999999954
Q ss_pred CCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009007 187 RSDELVQISG-EASVVKKALCQIASRLHD 214 (546)
Q Consensus 187 ~~dr~v~I~G-~~~~v~~A~~~I~~~l~~ 214 (546)
+..|.|.+ ..+.+.+|+..|..+...
T Consensus 589 --dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 589 --DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred --CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 45677776 578899999998887643
No 45
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.58 E-value=0.00053 Score=71.19 Aligned_cols=76 Identities=24% Similarity=0.380 Sum_probs=57.1
Q ss_pred ceEEEEEecC------CceeEEeecCchHHHHHHhhcCceEEEecCCCC----------Cccc-CCCCceEEEEcC-HHH
Q 009007 139 QVTAKLLVPS------DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHL----------PSCA-LRSDELVQISGE-ASV 200 (546)
Q Consensus 139 ~~~~~l~Vp~------~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~----------p~~~-~~~dr~v~I~G~-~~~ 200 (546)
.++.++.||. ++||+|||.+|.|.|+|+++|||+|.|-.+..+ .... ...+=.+.|+.+ .|.
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 6778888885 478999999999999999999999999752211 1000 112224677775 588
Q ss_pred HHHHHHHHHHHHhc
Q 009007 201 VKKALCQIASRLHD 214 (546)
Q Consensus 201 v~~A~~~I~~~l~~ 214 (546)
|++|+..|..+|.+
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999999976
No 46
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=97.57 E-value=0.00024 Score=63.37 Aligned_cols=102 Identities=23% Similarity=0.308 Sum_probs=70.6
Q ss_pred EEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhhhhHHHHHHHHhcCccccccccc
Q 009007 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERD 364 (546)
Q Consensus 285 ~~~v~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~i~~~~~~~~erii~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~ 364 (546)
.+-|+|....+|..||++|++|+.|++..|-+|.+-.-+.+ . ..-+..+ +.|.-...+.-.
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~D-------------~----~~fI~N~--l~PA~V~~V~i~ 94 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSEN-------------L----EEFVANK--LAPAEVKNVTVS 94 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCC-------------H----HHHHHHc--CCCceEEEEEEE
Confidence 67789999999999999999999998888877776542211 0 1111111 112111111110
Q ss_pred cCCcceeEEEEEccCcceeEEcCCChhHHHHHHhhCceEEE
Q 009007 365 SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405 (546)
Q Consensus 365 ~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i 405 (546)
..+......+.||++..+..|||+|++|+-..+.++-++.|
T Consensus 95 ~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI 135 (141)
T TIGR01952 95 EFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI 135 (141)
T ss_pred cCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence 11123557789999999999999999999999999988877
No 47
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=97.52 E-value=0.00042 Score=61.79 Aligned_cols=103 Identities=22% Similarity=0.249 Sum_probs=68.7
Q ss_pred EEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEecCCccccccccCcccCCHHHHHHHHHHHHH
Q 009007 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRV 123 (546)
Q Consensus 44 ~~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i 123 (546)
-+-++|....+|..||++|++|+.|++..|-+|.|-+ -+..+++ -+..++.
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe-----------ys~D~~~----------------fI~N~l~-- 84 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE-----------YSENLEE----------------FVANKLA-- 84 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE-----------cCCCHHH----------------HHHHcCC--
Confidence 5667889999999999999999999988888887632 1111111 0000000
Q ss_pred HHhhhcCCCCCCCCCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEe
Q 009007 124 IAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRIL 176 (546)
Q Consensus 124 ~~~~~~~~~~~~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~ 176 (546)
-..+..-.-.+........+.||.++.+.+|||+|++|+...+-++-++.|.
T Consensus 85 -PA~V~~V~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 85 -PAEVKNVTVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred -CceEEEEEEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 0000000000112335577889999999999999999999999999888763
No 48
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.51 E-value=0.00019 Score=81.38 Aligned_cols=98 Identities=20% Similarity=0.249 Sum_probs=77.6
Q ss_pred cccCCHHHHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEecCCceeEEeecCchHHHHHHhhcCce-EEEecCCCCCcc
Q 009007 106 DKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQ-IRILKDEHLPSC 184 (546)
Q Consensus 106 ~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~-I~i~~~~~~p~~ 184 (546)
.+.+..|.+++..+++.+.+.......+.....+....+.||.+.++.|||++|.+||.|.++||++ |.+..
T Consensus 651 ~eAL~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d------- 723 (891)
T PLN00207 651 ERALLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD------- 723 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC-------
Confidence 4567778888888888766544333333344566788999999999999999999999999999999 87743
Q ss_pred cCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009007 185 ALRSDELVQISG-EASVVKKALCQIASRLHD 214 (546)
Q Consensus 185 ~~~~dr~v~I~G-~~~~v~~A~~~I~~~l~~ 214 (546)
+-.|.|.+ +.+.+++|+.+|..++.+
T Consensus 724 ----dg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 724 ----DGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred ----CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 55788888 578899999999988854
No 49
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.50 E-value=0.00012 Score=74.43 Aligned_cols=64 Identities=28% Similarity=0.459 Sum_probs=54.4
Q ss_pred CCCCCCcccCCCceEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEecCC
Q 009007 30 GDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSAS 96 (546)
Q Consensus 30 ~~~~~~~~~~~~~~~~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~ 96 (546)
.+.++..+...+++.+.+.|-++++|.|||++|++|++|+..|+++|+|.+. ..+-.|+|.|..
T Consensus 34 ~~~~~~~aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~ 97 (629)
T KOG0336|consen 34 RDSRDSAAAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGIN 97 (629)
T ss_pred CCCCcccccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechH
Confidence 3555666667889999999999999999999999999999999999999654 345678999964
No 50
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.47 E-value=0.00018 Score=78.06 Aligned_cols=98 Identities=23% Similarity=0.268 Sum_probs=77.3
Q ss_pred cccCCHHHHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCccc
Q 009007 106 DKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCA 185 (546)
Q Consensus 106 ~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~ 185 (546)
...+..|..|..+++..+.+..-....+......-...+.|+.+.+.-+||++|.+|++|.++|||+|.|..
T Consensus 518 ~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied-------- 589 (692)
T COG1185 518 KKALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED-------- 589 (692)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC--------
Confidence 346677888888888876554333222333445567889999999999999999999999999999999952
Q ss_pred CCCCceEEEEcCH-HHHHHHHHHHHHHHhc
Q 009007 186 LRSDELVQISGEA-SVVKKALCQIASRLHD 214 (546)
Q Consensus 186 ~~~dr~v~I~G~~-~~v~~A~~~I~~~l~~ 214 (546)
+..|.|.++. +.+.+|+..|.++.++
T Consensus 590 ---dGtv~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 590 ---DGTVKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred ---CCcEEEEecchHHHHHHHHHHHHHHhh
Confidence 5679999876 7789999999998866
No 51
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.19 E-value=0.00054 Score=77.17 Aligned_cols=65 Identities=26% Similarity=0.326 Sum_probs=55.1
Q ss_pred ceeEEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHh
Q 009007 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (546)
Q Consensus 369 ~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~ 444 (546)
....++.||.+.++.|||++|.+||+|.++|||+|.|.. +-.|.|.+ +.+.+++|+.+|......
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 356789999999999999999999999999999999942 34677766 678899999998877654
No 52
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.97 E-value=0.0033 Score=58.97 Aligned_cols=103 Identities=23% Similarity=0.312 Sum_probs=68.5
Q ss_pred EEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhhhhHHHHHHHHhcCccccccccc
Q 009007 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERD 364 (546)
Q Consensus 285 ~~~v~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~i~~~~~~~~erii~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~ 364 (546)
.+.+.+-.+.+|..||++|.+|+.|.++.|-+|.|-.-+++ .+ .-+..++. |.-...+.-.
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d-------------~~----~fI~nal~--Pa~v~~V~~~ 137 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSED-------------PA----EFIKNALA--PAEVLSVNIK 137 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCC-------------HH----HHHHHhcC--cceEeEEEEE
Confidence 34455556778999999999999999999966655432211 00 01111111 1111111111
Q ss_pred cCCcceeEEEEEccCcceeEEcCCChhHHHHHHhhCceEEEec
Q 009007 365 SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP 407 (546)
Q Consensus 365 ~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~ 407 (546)
..+. ....+.||++..+.+|||+|.+++-+.+-||-+|.|..
T Consensus 138 ~~d~-~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 138 EDDG-HVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred eCCC-cEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 1011 26788999999999999999999999999999999953
No 53
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.95 E-value=0.0014 Score=61.52 Aligned_cols=104 Identities=30% Similarity=0.367 Sum_probs=68.2
Q ss_pred EEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEecCCccccccccCcccCCHHHHHHHHHHHHH
Q 009007 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRV 123 (546)
Q Consensus 44 ~~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i 123 (546)
.+-+.+-...+|..||++|++|+.|.++.|=+|.|-+- +-.+.+ -+.+|+.-+ ++
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~-----------s~d~~~------------fI~nal~Pa--~v 131 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW-----------SEDPAE------------FIKNALAPA--EV 131 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEe-----------CCCHHH------------HHHHhcCcc--eE
Confidence 34555666778999999999999999999977765222 111100 011211100 00
Q ss_pred HHhhhcCCCCCCCCCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecC
Q 009007 124 IAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (546)
Q Consensus 124 ~~~~~~~~~~~~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~ 178 (546)
. .+.-. +.+.. ...+.||.++.+.+|||+|.+++.+.+-||-++.|...
T Consensus 132 ~--~V~~~---~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~ 180 (190)
T COG0195 132 L--SVNIK---EDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI 180 (190)
T ss_pred e--EEEEE---eCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence 0 00000 11122 68888999999999999999999999999999999653
No 54
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.93 E-value=0.0015 Score=66.70 Aligned_cols=67 Identities=24% Similarity=0.324 Sum_probs=54.1
Q ss_pred ceeEEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHH
Q 009007 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLR 443 (546)
Q Consensus 369 ~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~ 443 (546)
.+...|.|-+.+||.|||++|++|+.||..|.++|+|... +.+-.|+|-|...--.+|...|...+.
T Consensus 46 e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~--------~~e~kv~ifg~~~m~~kaka~id~~~~ 112 (629)
T KOG0336|consen 46 EFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC--------DLEVKVTIFGINHMRKKAKASIDRGQD 112 (629)
T ss_pred CCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc--------CceeEEEEechHHHHHHHHhhHhhhhh
Confidence 3556688889999999999999999999999999999753 235689999998777777666644443
No 55
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.85 E-value=0.0049 Score=59.74 Aligned_cols=76 Identities=20% Similarity=0.343 Sum_probs=53.7
Q ss_pred cceeEEEEEcc------CcceeEEcCCChhHHHHHHhhCceEEEecCCCC------------CCCCCCCC---ceEEEEc
Q 009007 368 ISFTTRLLVPT------SRIGCLIGKGGSIITEMRRLTKANIRILPKENL------------PKIASEDD---EMVQISG 426 (546)
Q Consensus 368 ~~~~~~l~VP~------~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~------------P~~~~~~~---r~v~I~G 426 (546)
...+.+|+||- ++||.|+|..|.++|+|+++|||+|-|-.+... |.-++-++ -+|+...
T Consensus 90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~ 169 (259)
T KOG1588|consen 90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEA 169 (259)
T ss_pred eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeC
Confidence 45788999994 599999999999999999999999999877532 22112122 3477778
Q ss_pred CHHHHHH----HHHHHHHHHH
Q 009007 427 DLDLAKD----ALIQVMTRLR 443 (546)
Q Consensus 427 ~~~~v~~----A~~~I~~~i~ 443 (546)
++..+.. |++.|...|.
T Consensus 170 p~~ea~~rl~~AleeI~klL~ 190 (259)
T KOG1588|consen 170 PPAEAYARLAYALEEIKKLLV 190 (259)
T ss_pred CHHHHHHHHHHHHHHHHHhcC
Confidence 7766544 4555544443
No 56
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.84 E-value=0.0018 Score=70.61 Aligned_cols=66 Identities=26% Similarity=0.286 Sum_probs=56.8
Q ss_pred eeEEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCH-HHHHHHHHHHHHHHHhcc
Q 009007 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDL-DLAKDALIQVMTRLRANL 446 (546)
Q Consensus 370 ~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~-~~v~~A~~~I~~~i~~~~ 446 (546)
-..++.|+.+.+..|||++|.+|++|.++|||+|.|. ++-+|.|.++. +.+..|+..|...+++..
T Consensus 552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-----------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~e 618 (692)
T COG1185 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-----------DDGTVKIAASDGESAKKAKERIEAITREVE 618 (692)
T ss_pred ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-----------CCCcEEEEecchHHHHHHHHHHHHHHhhcc
Confidence 4577999999999999999999999999999999994 23478888865 888999999988887653
No 57
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.81 E-value=0.0012 Score=75.14 Aligned_cols=65 Identities=20% Similarity=0.303 Sum_probs=55.9
Q ss_pred ceeEEEEEccCcceeEEcCCChhHHHHHHhhCce-EEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHh
Q 009007 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKAN-IRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (546)
Q Consensus 369 ~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~-I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~ 444 (546)
.....|.||.+.++.|||.||.+||+|.++||+. |.|. ++-.|.|.+ +.+.+++|+.+|.+.+.+
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 4667899999999999999999999999999999 8873 235688888 689999999999888764
No 58
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.78 E-value=0.0014 Score=73.94 Aligned_cols=97 Identities=22% Similarity=0.319 Sum_probs=72.8
Q ss_pred ccCCHHHHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccC
Q 009007 107 KFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCAL 186 (546)
Q Consensus 107 ~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 186 (546)
+.+..|.+++.+|++.+.+..-....+..........+.||.+.++.+||++|.+||.|.++||++|.+.
T Consensus 521 ~al~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~---------- 590 (693)
T PRK11824 521 EALEQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE---------- 590 (693)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC----------
Confidence 4566788888888887655432222222233445567778999999999999999999999999998873
Q ss_pred CCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009007 187 RSDELVQISG-EASVVKKALCQIASRLHD 214 (546)
Q Consensus 187 ~~dr~v~I~G-~~~~v~~A~~~I~~~l~~ 214 (546)
.+-.|.|.+ ..+.+.+|+..|..+..+
T Consensus 591 -d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 591 -DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred -CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 255688888 578899999998887743
No 59
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.66 E-value=0.0018 Score=62.60 Aligned_cols=39 Identities=33% Similarity=0.569 Sum_probs=34.8
Q ss_pred CCceEEEEEecCC------ccceEecCCcHHHHHHHHHhCCeEEE
Q 009007 40 PEDTVYRYLCPIR------KIGSIIGRGGEIVKQLRIDTKSKIRI 78 (546)
Q Consensus 40 ~~~~~~rilip~~------~~g~IIGk~G~~Ik~i~~~tga~I~i 78 (546)
+-.++.+|+||.+ +||.|+|.+|.++|+|+++|+|+|-|
T Consensus 89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~I 133 (259)
T KOG1588|consen 89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMI 133 (259)
T ss_pred ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEE
Confidence 4456789999998 79999999999999999999999865
No 60
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=96.56 E-value=0.0043 Score=47.13 Aligned_cols=36 Identities=31% Similarity=0.408 Sum_probs=33.7
Q ss_pred eEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEE
Q 009007 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRI 78 (546)
Q Consensus 43 ~~~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i 78 (546)
....+.||.+..|.+|||+|.+|+.+++.++-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 578899999999999999999999999999988876
No 61
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.42 E-value=0.023 Score=52.71 Aligned_cols=42 Identities=26% Similarity=0.590 Sum_probs=37.0
Q ss_pred cceeEEEEEc------cCcceeEEcCCChhHHHHHHhhCceEEEecCC
Q 009007 368 ISFTTRLLVP------TSRIGCLIGKGGSIITEMRRLTKANIRILPKE 409 (546)
Q Consensus 368 ~~~~~~l~VP------~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~ 409 (546)
..++.++.|| .++||.|||..|.+.|+|++.|+|+|-|-.+.
T Consensus 146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g 193 (269)
T COG5176 146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSG 193 (269)
T ss_pred ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence 3577788888 57999999999999999999999999997654
No 62
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.37 E-value=0.0037 Score=62.22 Aligned_cols=68 Identities=21% Similarity=0.296 Sum_probs=52.4
Q ss_pred ceEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEecCCccccccccCcccCCHHHHHHHHHHH
Q 009007 42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHD 121 (546)
Q Consensus 42 ~~~~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~ 121 (546)
+....+++++...+.|||++|.|.++|+++|+|+|.++.+ +.....|+|.|...++ +..|+.+|..
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p--~~n~~~i~i~~~~~~~------------V~~a~~Ri~~ 121 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP--NTNKEEIKIIGISRNC------------VIQALERIAK 121 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC--CCCcceEEEeehhHHH------------HHHHHHHHHH
Confidence 3456789999999999999999999999999999999776 4444567777765442 5566666655
Q ss_pred HH
Q 009007 122 RV 123 (546)
Q Consensus 122 ~i 123 (546)
.|
T Consensus 122 ~i 123 (345)
T KOG2814|consen 122 LI 123 (345)
T ss_pred HH
Confidence 43
No 63
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=96.36 E-value=0.0063 Score=46.22 Aligned_cols=36 Identities=33% Similarity=0.570 Sum_probs=33.6
Q ss_pred eeEEEEEccCcceeEEcCCChhHHHHHHhhCceEEE
Q 009007 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405 (546)
Q Consensus 370 ~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i 405 (546)
....+.||....|.+|||+|.+|+.+++.++-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 577899999999999999999999999999988876
No 64
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.22 E-value=0.0054 Score=61.10 Aligned_cols=70 Identities=27% Similarity=0.391 Sum_probs=57.2
Q ss_pred ceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEE-cCHHHHHHHHHHHHHHHhcC
Q 009007 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQIS-GEASVVKKALCQIASRLHDN 215 (546)
Q Consensus 139 ~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~-G~~~~v~~A~~~I~~~l~~~ 215 (546)
.....++|++...++|||++|.|-+.|+++|+++|.++... .....++|+ +..++|-+|...|..+|...
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~-------~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN-------TNKEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC-------CCcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 44567899999999999999999999999999999997642 233445554 57889999999999888664
No 65
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.16 E-value=0.02 Score=59.00 Aligned_cols=95 Identities=21% Similarity=0.199 Sum_probs=64.3
Q ss_pred cccccccCCchhHHHHHhhh-CCeEEecCCCCCCCceEEEEecCcchhhhhhHHHHHHHHhcCccccccccccCCcceeE
Q 009007 294 NIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTT 372 (546)
Q Consensus 294 ~~g~IIGk~G~~Ik~i~~~s-ga~I~i~~~~~~~~erii~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~ 372 (546)
-+|..||++|.+|+.|.++. |-+|.|-.-+.+ . ..-+..++ .|.-...+.-. ......
T Consensus 252 PvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D---~--------------~~fI~Nal--~Pa~V~~V~i~--~~~~~~ 310 (374)
T PRK12328 252 PIGATVGVKGVRINAVSKELNGENIDCIEYSNV---P--------------EIFIARAL--APAIISSVKIE--EEEKKA 310 (374)
T ss_pred hHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCC---H--------------HHHHHHhC--CCceeeEEEEc--CCCcEE
Confidence 47999999999999999998 766666432211 0 00111111 11111111111 112467
Q ss_pred EEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCC
Q 009007 373 RLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKE 409 (546)
Q Consensus 373 ~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~ 409 (546)
.+.||.++.+..|||+|.+++-..+.||.+|.|.+-+
T Consensus 311 ~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~ 347 (374)
T PRK12328 311 IVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG 347 (374)
T ss_pred EEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence 8999999999999999999999999999999997654
No 66
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=96.16 E-value=0.017 Score=59.41 Aligned_cols=92 Identities=24% Similarity=0.377 Sum_probs=63.2
Q ss_pred cccccccCCchhHHHHHhhh-CCeEEecCCCCCCCceEEEEecCcchhhhhhHHHHHHHHhcCcccccc--ccccCCcce
Q 009007 294 NIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKI--ERDSGLISF 370 (546)
Q Consensus 294 ~~g~IIGk~G~~Ik~i~~~s-ga~I~i~~~~~~~~erii~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~ 370 (546)
-+|..||++|.+|+.|.++. |-+|.|-.-+.+ . ..-+..++ .|.-...+ ..+ ...
T Consensus 244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d-------------~----~~fi~nal--~Pa~v~~v~i~~~---~~~ 301 (341)
T TIGR01953 244 PVGACVGPKGSRIQAISKELNGEKIDIIEYSDD-------------P----AEFIANAL--SPAKVISVEVLDE---DKH 301 (341)
T ss_pred cceeeECCCCchHHHHHHHhCCCeEEEEEcCCC-------------H----HHHHHHhc--CCceEEEEEEEcC---CCc
Confidence 47999999999999999998 766666443211 0 00111111 11111111 111 124
Q ss_pred eEEEEEccCcceeEEcCCChhHHHHHHhhCceEEEec
Q 009007 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP 407 (546)
Q Consensus 371 ~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~ 407 (546)
...+.||.++.+..|||+|.+++-..+.||.+|.|.+
T Consensus 302 ~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 302 SAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred EEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 6789999999999999999999999999999999965
No 67
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=96.11 E-value=0.021 Score=58.86 Aligned_cols=95 Identities=31% Similarity=0.434 Sum_probs=62.5
Q ss_pred ccceEecCCcHHHHHHHHHh-CCeEEEcCCCCCCCceEEEEecCCccccccccCcccCCHHHHHHHHHHHHHHHhhhcCC
Q 009007 53 KIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGD 131 (546)
Q Consensus 53 ~~g~IIGk~G~~Ik~i~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~~ 131 (546)
-+|..||++|++|+.|.++. |=+|.|-+- .-.++.. +.+||.-. ++..-.+.
T Consensus 244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~-----------s~d~~~f------------i~nal~Pa--~v~~v~i~-- 296 (341)
T TIGR01953 244 PVGACVGPKGSRIQAISKELNGEKIDIIEY-----------SDDPAEF------------IANALSPA--KVISVEVL-- 296 (341)
T ss_pred cceeeECCCCchHHHHHHHhCCCeEEEEEc-----------CCCHHHH------------HHHhcCCc--eEEEEEEE--
Confidence 48999999999999999998 777776321 1100000 00110000 00000000
Q ss_pred CCCCCCCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecC
Q 009007 132 EDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (546)
Q Consensus 132 ~~~~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~ 178 (546)
+ .....+.+.||.++.+..|||+|.+++....-||.+|.|...
T Consensus 297 ---~-~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~ 339 (341)
T TIGR01953 297 ---D-EDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE 339 (341)
T ss_pred ---c-CCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence 0 122368899999999999999999999999999999999764
No 68
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.00 E-value=0.024 Score=58.41 Aligned_cols=96 Identities=20% Similarity=0.167 Sum_probs=63.0
Q ss_pred CccceEecCCcHHHHHHHHHh-CCeEEEcCCCCCCCceEEEEecCCccccccccCcccCCHHHHHHHHHHHHHHHhhhcC
Q 009007 52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG 130 (546)
Q Consensus 52 ~~~g~IIGk~G~~Ik~i~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~ 130 (546)
+-+|..||++|++|+.|.++. |=+|.|-+-..+ +... +.+||.-. ++. .+.-
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D-----------~~~f------------I~Nal~Pa--~V~--~V~i 303 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNV-----------PEIF------------IARALAPA--IIS--SVKI 303 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCC-----------HHHH------------HHHhCCCc--eee--EEEE
Confidence 358999999999999999998 777776321100 0000 00110000 000 0000
Q ss_pred CCCCCCCCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCC
Q 009007 131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179 (546)
Q Consensus 131 ~~~~~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~ 179 (546)
. ...-.+.+.||.++.+..|||+|.+++....-||.+|.|..-+
T Consensus 304 ----~-~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~ 347 (374)
T PRK12328 304 ----E-EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG 347 (374)
T ss_pred ----c-CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence 0 1223678899999999999999999999999999999997643
No 69
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.96 E-value=0.022 Score=59.08 Aligned_cols=95 Identities=24% Similarity=0.305 Sum_probs=63.8
Q ss_pred cccccccCCchhHHHHHhhh-CCeEEecCCCCCCCceEEEEecCcchhhhhhHHHHHHHHhcCccccccccccCCcceeE
Q 009007 294 NIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTT 372 (546)
Q Consensus 294 ~~g~IIGk~G~~Ik~i~~~s-ga~I~i~~~~~~~~erii~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~ 372 (546)
-+|..||++|.+|+.|.++. |-+|.|-.-+.+ . ..-+..++ .|.-...+.-.. ......
T Consensus 246 pvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d-------------~----~~fi~nal--~Pa~v~~v~i~~-~~~~~~ 305 (362)
T PRK12327 246 AKGACVGPKGQRVQNIVSELKGEKIDIIDWSED-------------P----AEFVANAL--SPAKVVSVEVDD-EEEKAA 305 (362)
T ss_pred chheeECCCChhHHHHHHHhCCCeEEEEEcCCC-------------H----HHHHHHhC--CCceEEEEEEEc-CCCcEE
Confidence 47999999999999999998 767766442211 0 00111111 111111110000 112467
Q ss_pred EEEEccCcceeEEcCCChhHHHHHHhhCceEEEecC
Q 009007 373 RLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPK 408 (546)
Q Consensus 373 ~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~ 408 (546)
.+.||.++.+..|||+|.+++-..+.||.+|.|...
T Consensus 306 ~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 306 RVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred EEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 899999999999999999999999999999999653
No 70
>PRK00106 hypothetical protein; Provisional
Probab=95.96 E-value=0.022 Score=61.90 Aligned_cols=65 Identities=25% Similarity=0.331 Sum_probs=49.3
Q ss_pred ceeEEEEEcc-CcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHH
Q 009007 369 SFTTRLLVPT-SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLR 443 (546)
Q Consensus 369 ~~~~~l~VP~-~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~ 443 (546)
.....|.+|+ ++-|.||||-|.+|+-+...||++|-|. + +...|+|++ +|---+.|...+..+|.
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid---d-------tp~~v~lS~fdpvRReiAr~~le~Li~ 290 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID---D-------TPEVVVLSGFDPIRREIARMTLESLIK 290 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc---C-------CCCeEEEeCCChHHHHHHHHHHHHHHH
Confidence 4667788998 5669999999999999999999999993 2 335899999 66555555544444443
No 71
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.94 E-value=0.015 Score=56.85 Aligned_cols=63 Identities=21% Similarity=0.246 Sum_probs=51.6
Q ss_pred EEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC-HHHHHHHHHHHHHHHHhc
Q 009007 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD-LDLAKDALIQVMTRLRAN 445 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~i~~~ 445 (546)
+.+.||..+++.+||++|.+|+.|.+.|++.|.|- .+-.|-|.+. .+++..|+.+|...-++.
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig-----------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG-----------QNGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc-----------CCcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 56899999999999999999999999999999983 2347888885 567788877776655443
No 72
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.89 E-value=0.022 Score=62.16 Aligned_cols=65 Identities=23% Similarity=0.302 Sum_probs=48.8
Q ss_pred ceeEEEEEccC-cceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHH
Q 009007 369 SFTTRLLVPTS-RIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLR 443 (546)
Q Consensus 369 ~~~~~l~VP~~-~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~ 443 (546)
..+..|.+|++ +-|.||||.|.+|+-+...||++|-|. + +...|+|++ +|---+.|...+..+|.
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid---d-------tp~~v~ls~fdp~rreia~~~l~~li~ 269 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---D-------TPEAVILSGFDPVRREIARMALEKLIQ 269 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc---C-------CCCeEEecCCchHHHHHHHHHHHHHHH
Confidence 46677889984 559999999999999999999999993 2 335899999 66554555444444443
No 73
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.86 E-value=0.011 Score=61.14 Aligned_cols=96 Identities=27% Similarity=0.359 Sum_probs=63.1
Q ss_pred CccceEecCCcHHHHHHHHHh-CCeEEEcCCCCCCCceEEEEecCCccccccccCcccCCHHHHHHHHHHHHHHHhhhcC
Q 009007 52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG 130 (546)
Q Consensus 52 ~~~g~IIGk~G~~Ik~i~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~ 130 (546)
+-+|..||++|+.|+.|.++. |=+|.|-+-. -.++.. +.+||.-. .+..-.+.
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s-----------~d~~~f------------i~nal~Pa--~v~~v~i~- 298 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWS-----------EDPAEF------------VANALSPA--KVVSVEVD- 298 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcC-----------CCHHHH------------HHHhCCCc--eEEEEEEE-
Confidence 358999999999999999998 7788763211 000000 00100000 00000000
Q ss_pred CCCCCCCCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecC
Q 009007 131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (546)
Q Consensus 131 ~~~~~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~ 178 (546)
+ .....+.+.||.++.+..|||+|.+++....-||.+|.|...
T Consensus 299 ----~-~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 299 ----D-EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred ----c-CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 0 122458899999999999999999999999999999999764
No 74
>PRK12704 phosphodiesterase; Provisional
Probab=95.82 E-value=0.024 Score=61.87 Aligned_cols=65 Identities=23% Similarity=0.292 Sum_probs=48.7
Q ss_pred ceeEEEEEcc-CcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHH
Q 009007 369 SFTTRLLVPT-SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLR 443 (546)
Q Consensus 369 ~~~~~l~VP~-~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~ 443 (546)
..+..|.+|+ ++-|.||||.|.+|+-+...||++|-|. + +..+|.|+| +|-.-+.|...+...+.
T Consensus 209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid---d-------tp~~v~ls~~~~~rre~a~~~l~~l~~ 275 (520)
T PRK12704 209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---D-------TPEAVILSGFDPIRREIARLALEKLVQ 275 (520)
T ss_pred hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc---C-------CCCeEEEecCChhhHHHHHHHHHHHHh
Confidence 4566788998 4569999999999999999999999993 2 335899999 66554455544444443
No 75
>PRK00468 hypothetical protein; Provisional
Probab=95.74 E-value=0.012 Score=46.58 Aligned_cols=33 Identities=21% Similarity=0.450 Sum_probs=29.6
Q ss_pred CCceEEEEEecCCccceEecCCcHHHHHHHHHh
Q 009007 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDT 72 (546)
Q Consensus 40 ~~~~~~rilip~~~~g~IIGk~G~~Ik~i~~~t 72 (546)
.+.+.+++.|..+.+|.||||+|.+|+.||.--
T Consensus 27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 456889999999999999999999999999654
No 76
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.69 E-value=0.0078 Score=68.11 Aligned_cols=64 Identities=30% Similarity=0.366 Sum_probs=54.0
Q ss_pred eeEEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHh
Q 009007 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (546)
Q Consensus 370 ~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~ 444 (546)
....+.||.+.++.|||.||.+||+|.++||+.|.+. ++-.|.|.+ +.+.+++|+.+|.....+
T Consensus 554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-----------d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-----------DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 4567888999999999999999999999999988772 234688888 688899999999887754
No 77
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.63 E-value=0.029 Score=58.82 Aligned_cols=95 Identities=25% Similarity=0.324 Sum_probs=63.0
Q ss_pred CcccccccCCchhHHHHHhhh-CCeEEecCCCCCCCceEEEEecCcchhhhhhHHHHHHHHhcCccccccccccCCccee
Q 009007 293 ANIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFT 371 (546)
Q Consensus 293 ~~~g~IIGk~G~~Ik~i~~~s-ga~I~i~~~~~~~~erii~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ 371 (546)
+-+|..||++|.+|+.|.++. |-+|.|-.-+.+ . ..-+..++ .|.-...+.-.. .....
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~D-------------p----~~fI~NaL--sPA~V~~V~i~~-~~~k~ 336 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPD-------------P----ATYIANAL--SPARVDEVRLVD-PEGRH 336 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCC-------------H----HHHHHHhc--CCceeeEEEEEc-CCCcE
Confidence 347999999999999999998 666666443211 0 00111111 111111110000 11245
Q ss_pred EEEEEccCcceeEEcCCChhHHHHHHhhCceEEEec
Q 009007 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP 407 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~ 407 (546)
..+.||.++.+..|||+|.+|+-..+.||.+|.|..
T Consensus 337 a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 337 AHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred EEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 679999999999999999999999999999999954
No 78
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=95.63 E-value=0.34 Score=46.48 Aligned_cols=131 Identities=18% Similarity=0.170 Sum_probs=87.9
Q ss_pred EEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhhhhHHHHHHHHhcCccccccccc
Q 009007 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERD 364 (546)
Q Consensus 285 ~~~v~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~i~~~~~~~~erii~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~ 364 (546)
.+.+.++....-.++..+|..++.|....||+|.+... ...+.|+|++...+.+...+..++.-
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~-----~~~i~I~g~k~~~~~i~~~i~~~l~~----------- 90 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS-----ENRIRITGTKSTAEYIEASINEILSN----------- 90 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEecC-----CcEEEEEccHHHHHHHHHHHHHHHhh-----------
Confidence 44556668888899999999999998888999999863 46899999865433333233332221
Q ss_pred cCCcceeEEEEEccCcceeEEc----CCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-----CHHHHHHHH
Q 009007 365 SGLISFTTRLLVPTSRIGCLIG----KGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-----DLDLAKDAL 435 (546)
Q Consensus 365 ~~~~~~~~~l~VP~~~vG~IIG----kgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G-----~~~~v~~A~ 435 (546)
..+..|.++.-.--.... .....+++|++.|++.|+...+ ...+.|.. ....++.|+
T Consensus 91 ----i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~----------~~~~~i~~~~~~~~~~~~~~a~ 156 (210)
T PF14611_consen 91 ----IRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD----------GNKLKISWLASPENEKRADRAK 156 (210)
T ss_pred ----cEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC----------CCeEEEEEEeeccccchHHHHH
Confidence 244555555432211111 1467899999999999998532 22455554 678899999
Q ss_pred HHHHHHHHhc
Q 009007 436 IQVMTRLRAN 445 (546)
Q Consensus 436 ~~I~~~i~~~ 445 (546)
+++...+...
T Consensus 157 RlL~~a~~~~ 166 (210)
T PF14611_consen 157 RLLLWALDYN 166 (210)
T ss_pred HHHHHhccCC
Confidence 9998888533
No 79
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.53 E-value=0.029 Score=58.86 Aligned_cols=95 Identities=29% Similarity=0.323 Sum_probs=61.8
Q ss_pred CccceEecCCcHHHHHHHHHh-CCeEEEcCCCCCCCceEEEEecCCccccccccCcccCCHHHHHHHHHHHHHHHhhhcC
Q 009007 52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG 130 (546)
Q Consensus 52 ~~~g~IIGk~G~~Ik~i~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~ 130 (546)
+-+|..||++|..|+.|.++. |=+|.|-.- +-.+... +.+||.-. ++..-.+.
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~y-----------s~Dp~~f------------I~NaLsPA--~V~~V~i~- 330 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRW-----------SPDPATY------------IANALSPA--RVDEVRLV- 330 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEc-----------CCCHHHH------------HHHhcCCc--eeeEEEEE-
Confidence 458999999999999999998 777776321 1100000 00110000 00000000
Q ss_pred CCCCCCCCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEec
Q 009007 131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILK 177 (546)
Q Consensus 131 ~~~~~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~ 177 (546)
. .....+.+.||.++.+..|||+|.+++-...-||.+|.|..
T Consensus 331 ----~-~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 331 ----D-PEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred ----c-CCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 0 11234789999999999999999999999999999999864
No 80
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.41 E-value=0.034 Score=59.69 Aligned_cols=94 Identities=23% Similarity=0.362 Sum_probs=63.5
Q ss_pred cccccccCCchhHHHHHhhh-CCeEEecCCCCCCCceEEEEecCcchhhhhhHHHHHHHHhcCccccccccccCCcceeE
Q 009007 294 NIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTT 372 (546)
Q Consensus 294 ~~g~IIGk~G~~Ik~i~~~s-ga~I~i~~~~~~~~erii~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~ 372 (546)
-+|..||++|++|+.|..+. |-+|.|-.-+.+ . ..-+..++ .|.-...+.-+.. .-..
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d---~--------------~~fi~nal--~pa~v~~v~~~~~--~~~~ 304 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIILWSDD---P--------------AQFIINAL--SPAEVSSVVVDED--EHSA 304 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEEcCCC---H--------------HHHHHHhC--CCCEEEEEEEeCC--CCEE
Confidence 37999999999999999998 667766442211 0 00111111 1111111100011 2367
Q ss_pred EEEEccCcceeEEcCCChhHHHHHHhhCceEEEecC
Q 009007 373 RLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPK 408 (546)
Q Consensus 373 ~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~ 408 (546)
.+.||....+..|||+|.+|+-..+.||.+|.|...
T Consensus 305 ~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 305 DVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred EEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 899999999999999999999999999999999764
No 81
>PRK02821 hypothetical protein; Provisional
Probab=95.33 E-value=0.018 Score=45.64 Aligned_cols=35 Identities=23% Similarity=0.380 Sum_probs=30.5
Q ss_pred CCceEEEEEecCCccceEecCCcHHHHHHHHHhCC
Q 009007 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKS 74 (546)
Q Consensus 40 ~~~~~~rilip~~~~g~IIGk~G~~Ik~i~~~tga 74 (546)
.+.+.+.|.|..+.+|.||||+|.+|+.||.--.+
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 45578999999999999999999999999976543
No 82
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.23 E-value=0.06 Score=50.05 Aligned_cols=44 Identities=20% Similarity=0.360 Sum_probs=36.7
Q ss_pred CCCCceEEEEEecC------CceeEEeecCchHHHHHHhhcCceEEEecC
Q 009007 135 DGGHQVTAKLLVPS------DQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (546)
Q Consensus 135 ~~~~~~~~~l~Vp~------~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~ 178 (546)
-....++-++.||- .+||.|||+.|.|.|+|+..|+|+|.|-..
T Consensus 143 ~rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 143 IRPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred cCcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 34556667777774 579999999999999999999999999754
No 83
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.19 E-value=0.085 Score=57.60 Aligned_cols=67 Identities=21% Similarity=0.357 Sum_probs=51.2
Q ss_pred CceEEEEEecC-CceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009007 138 HQVTAKLLVPS-DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHD 214 (546)
Q Consensus 138 ~~~~~~l~Vp~-~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G-~~~~v~~A~~~I~~~l~~ 214 (546)
...+..+.+|+ ++-|+|||+.|.+|+.++..||+.|-|... ...|+|++ ++---+-|...|..++.+
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt----------p~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT----------PEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC----------CCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 34455678888 467999999999999999999999988432 33688888 566666677777776655
No 84
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=95.10 E-value=0.57 Score=44.96 Aligned_cols=63 Identities=19% Similarity=0.383 Sum_probs=54.5
Q ss_pred EEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 009007 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD 214 (546)
Q Consensus 142 ~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~v~~A~~~I~~~l~~ 214 (546)
+.+.++....-+|...+|..+++|....||+|.+..+ +..|.|+|+...|+.+...|.+++..
T Consensus 28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~----------~~~i~I~g~k~~~~~i~~~i~~~l~~ 90 (210)
T PF14611_consen 28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS----------ENRIRITGTKSTAEYIEASINEILSN 90 (210)
T ss_pred eEEEecchheeeeecCCchHHHHHHHhcCceEEEecC----------CcEEEEEccHHHHHHHHHHHHHHHhh
Confidence 4555668888999999999999999999999999764 56899999999999999999888855
No 85
>PRK02821 hypothetical protein; Provisional
Probab=95.10 E-value=0.041 Score=43.66 Aligned_cols=35 Identities=29% Similarity=0.498 Sum_probs=29.8
Q ss_pred CCCceEEEEEecCCceeEEeecCchHHHHHHhhcC
Q 009007 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETG 170 (546)
Q Consensus 136 ~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tg 170 (546)
....+.+.+.|..+.+|.||||+|.+|+.||.--.
T Consensus 27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 34557899999999999999999999999987543
No 86
>PRK00468 hypothetical protein; Provisional
Probab=95.04 E-value=0.042 Score=43.44 Aligned_cols=35 Identities=37% Similarity=0.634 Sum_probs=30.0
Q ss_pred CCCCceEEEEEecCCceeEEeecCchHHHHHHhhc
Q 009007 135 DGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSET 169 (546)
Q Consensus 135 ~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~t 169 (546)
+....+.+++.+..+.+|.||||+|.+|+.||.--
T Consensus 25 ~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 25 EGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred eCCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 34566889999999999999999999999998743
No 87
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.03 E-value=0.048 Score=42.98 Aligned_cols=34 Identities=41% Similarity=0.665 Sum_probs=30.2
Q ss_pred CCCCceEEEEEecCCceeEEeecCchHHHHHHhh
Q 009007 135 DGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSE 168 (546)
Q Consensus 135 ~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~ 168 (546)
.....+.+++.|....+|.||||+|.+|+.||.-
T Consensus 25 ~~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 25 EGEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred ecCCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 3467788999999999999999999999999864
No 88
>PRK12704 phosphodiesterase; Provisional
Probab=94.99 E-value=0.1 Score=57.13 Aligned_cols=66 Identities=21% Similarity=0.341 Sum_probs=49.0
Q ss_pred ceEEEEEecC-CceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009007 139 QVTAKLLVPS-DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHD 214 (546)
Q Consensus 139 ~~~~~l~Vp~-~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G-~~~~v~~A~~~I~~~l~~ 214 (546)
..+-.+.+|+ ++-|+|||+.|.+|+.++..||+.|-|.. . ...|.|+| ++-.-+.|...+..++.+
T Consensus 209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd---t-------p~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD---T-------PEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC---C-------CCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 3445577887 56899999999999999999999998843 2 34688988 455545666666665544
No 89
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=94.97 E-value=0.05 Score=57.84 Aligned_cols=113 Identities=19% Similarity=0.216 Sum_probs=78.8
Q ss_pred EEecCCccccccccC----cccCCHHHHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEecCCceeEEeecCchHHHHHH
Q 009007 91 TVYSASDETNAFEDG----DKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIR 166 (546)
Q Consensus 91 ~I~G~~~~~~~~~~~----~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~ 166 (546)
.|-|+.+.+.++... .+.+-.|.+|-.+|++.+....-.....+.....+...+.|+.+....+||++|...|+|.
T Consensus 544 KiAGt~dGvTA~gi~l~Iv~eal~~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~ 623 (760)
T KOG1067|consen 544 KIAGTNDGVTALGIPLKIVMEALQKAREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIE 623 (760)
T ss_pred eeccccCcceecCCcHHHHHHHHHhhhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEe
Confidence 455665555554322 2344556667777777554443333334455677889999999999999999999999999
Q ss_pred hhcCceEEEecCCCCCcccCCCCceEEEEc-CHHHHHHHHHHHHHHHhcC
Q 009007 167 SETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHDN 215 (546)
Q Consensus 167 ~~tga~I~i~~~~~~p~~~~~~dr~v~I~G-~~~~v~~A~~~I~~~l~~~ 215 (546)
.+||+.-.+ ++..++|.. +..+.++|+..|..++..+
T Consensus 624 ~EtGai~~v------------De~t~~i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 624 VETGAISQV------------DEGTFSIFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred eeccceeee------------cCceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence 999955444 245677766 5677889999998887653
No 90
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=94.94 E-value=0.041 Score=59.11 Aligned_cols=94 Identities=27% Similarity=0.343 Sum_probs=62.1
Q ss_pred ccceEecCCcHHHHHHHHHh-CCeEEEcCCCCCCCceEEEEecCCccccccccCcccCCHHHHHHHHHHHHHHHhhhcCC
Q 009007 53 KIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGD 131 (546)
Q Consensus 53 ~~g~IIGk~G~~Ik~i~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~~ 131 (546)
-+|..||++|++|+.|.++. |=+|.|-.- .-.+... +.+|+.-. .+. .+.-
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~-----------s~d~~~f------------i~nal~pa--~v~--~v~~- 297 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIILW-----------SDDPAQF------------IINALSPA--EVS--SVVV- 297 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEEc-----------CCCHHHH------------HHHhCCCC--EEE--EEEE-
Confidence 48999999999999999998 777776321 1000000 00110000 000 0000
Q ss_pred CCCCCCCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecC
Q 009007 132 EDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (546)
Q Consensus 132 ~~~~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~ 178 (546)
+ ...-.+.+.||..+.+..|||+|.+|+.....||.+|.|...
T Consensus 298 ---~-~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 298 ---D-EDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred ---e-CCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 0 012368899999999999999999999999999999999764
No 91
>PRK01064 hypothetical protein; Provisional
Probab=94.78 E-value=0.036 Score=44.13 Aligned_cols=33 Identities=27% Similarity=0.496 Sum_probs=29.7
Q ss_pred CCceEEEEEecCCccceEecCCcHHHHHHHHHh
Q 009007 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDT 72 (546)
Q Consensus 40 ~~~~~~rilip~~~~g~IIGk~G~~Ik~i~~~t 72 (546)
.+.+.+++.|.....|.+|||+|.+|+.||.-.
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 456889999999999999999999999999754
No 92
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=94.78 E-value=0.043 Score=53.70 Aligned_cols=63 Identities=21% Similarity=0.291 Sum_probs=53.1
Q ss_pred EEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcC-HHHHHHHHHHHHHHHhcC
Q 009007 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGE-ASVVKKALCQIASRLHDN 215 (546)
Q Consensus 142 ~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~-~~~v~~A~~~I~~~l~~~ 215 (546)
+.+.||..+++.+||++|.+|+.|.++|+++|.+-. +-.|.|.+. .+++.+|+.+|..+-++.
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-----------NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-----------NGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-----------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 568899999999999999999999999999998843 456899886 457888888888766554
No 93
>PRK00106 hypothetical protein; Provisional
Probab=94.77 E-value=0.14 Score=55.85 Aligned_cols=67 Identities=25% Similarity=0.400 Sum_probs=52.0
Q ss_pred CceEEEEEecC-CceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009007 138 HQVTAKLLVPS-DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHD 214 (546)
Q Consensus 138 ~~~~~~l~Vp~-~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G-~~~~v~~A~~~I~~~l~~ 214 (546)
...+..+.+|+ ++-|+|||+.|.+|+.++..||+.|-|... ...|+|+| +|---+-|...+..++.+
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt----------p~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDT----------PEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCC----------CCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 34455678888 468999999999999999999999988432 34688888 666667777777777755
No 94
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.43 E-value=0.047 Score=43.03 Aligned_cols=33 Identities=15% Similarity=0.343 Sum_probs=29.5
Q ss_pred CCceEEEEEecCCccceEecCCcHHHHHHHHHh
Q 009007 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDT 72 (546)
Q Consensus 40 ~~~~~~rilip~~~~g~IIGk~G~~Ik~i~~~t 72 (546)
...+.++|-+....+|.||||+|.+|+.||.--
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 456789999999999999999999999999653
No 95
>PRK01064 hypothetical protein; Provisional
Probab=94.10 E-value=0.12 Score=41.21 Aligned_cols=35 Identities=34% Similarity=0.595 Sum_probs=30.2
Q ss_pred CCCCceEEEEEecCCceeEEeecCchHHHHHHhhc
Q 009007 135 DGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSET 169 (546)
Q Consensus 135 ~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~t 169 (546)
.....+.+++.|.....|.+|||+|.+|+.|+.-.
T Consensus 25 ~~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 25 QGTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred eCCCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 34567889999999999999999999999998743
No 96
>PRK12705 hypothetical protein; Provisional
Probab=93.21 E-value=0.12 Score=55.92 Aligned_cols=38 Identities=24% Similarity=0.345 Sum_probs=33.0
Q ss_pred ceeEEEEEccC-cceeEEcCCChhHHHHHHhhCceEEEe
Q 009007 369 SFTTRLLVPTS-RIGCLIGKGGSIITEMRRLTKANIRIL 406 (546)
Q Consensus 369 ~~~~~l~VP~~-~vG~IIGkgG~~Ik~I~~~Tga~I~i~ 406 (546)
.....+.+|++ +-|.||||-|.+|+-+...||+.|.|.
T Consensus 197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid 235 (508)
T PRK12705 197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID 235 (508)
T ss_pred heeeeeecCChHhhccccCccchhHHHHHHhhCCceEec
Confidence 45667888885 459999999999999999999999993
No 97
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=93.15 E-value=0.048 Score=42.92 Aligned_cols=34 Identities=15% Similarity=0.214 Sum_probs=29.6
Q ss_pred CCceEEEEEecCCccceEecCCcHHHHHHHHHhC
Q 009007 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (546)
Q Consensus 40 ~~~~~~rilip~~~~g~IIGk~G~~Ik~i~~~tg 73 (546)
.+...+.+.|..+..|.||||+|.+++.||.-.+
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence 4566788899999999999999999999997654
No 98
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=93.14 E-value=0.46 Score=53.69 Aligned_cols=30 Identities=20% Similarity=0.254 Sum_probs=14.0
Q ss_pred CccEEEEEEeecCcccccccCCchhHHHHH
Q 009007 281 SKEFSLRLVCPVANIGGVIGKGGAIINQIR 310 (546)
Q Consensus 281 ~~~~~~~v~vp~~~~g~IIGk~G~~Ik~i~ 310 (546)
..++.+++-......-.+.+..-+.|-.|+
T Consensus 933 e~efc~r~~l~~~~~~~t~~a~~ql~d~L~ 962 (1282)
T KOG0921|consen 933 EREFCERYSLSNPVLKMTDGARRQLIDVLR 962 (1282)
T ss_pred hhhHhHhhhhcchhhhhhhhhHHHHHHHHH
Confidence 334444444444444444455545555555
No 99
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=90.87 E-value=0.064 Score=61.25 Aligned_cols=70 Identities=19% Similarity=0.109 Sum_probs=58.3
Q ss_pred EEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhc
Q 009007 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN 445 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~ 445 (546)
-.+.+|-....+|||++|.+|+.++.-|||.|.|..= -|. ...||.+.+.|.++.++.|...|...|.+-
T Consensus 1342 ~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekm--q~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~Dp 1411 (2131)
T KOG4369|consen 1342 GKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKM--QPD--NQAERSKAPKGRPPSQRVATSPIGLPIIDP 1411 (2131)
T ss_pred cccccchhhhhhhhccCcchhhhHhhccceEEehhhc--CCc--cchhhhcccCCCChhhhhhhccccceeecC
Confidence 4677888899999999999999999999999999531 122 356899999999999999988887776654
No 100
>PRK12705 hypothetical protein; Provisional
Probab=90.72 E-value=0.56 Score=50.85 Aligned_cols=66 Identities=27% Similarity=0.358 Sum_probs=45.1
Q ss_pred ceEEEEEecCC-ceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009007 139 QVTAKLLVPSD-QIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHD 214 (546)
Q Consensus 139 ~~~~~l~Vp~~-~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G-~~~~v~~A~~~I~~~l~~ 214 (546)
...-.+.+|++ +-|+|||+.|.+|+.++..||+.|.|... | +.|.|++ ++..-+.|...+..+|..
T Consensus 197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt---p-------~~V~ls~fdp~rreia~~~l~~Li~d 264 (508)
T PRK12705 197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT---P-------EAVVISSFNPIRREIARLTLEKLLAD 264 (508)
T ss_pred heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC---c-------cchhhcccCccchHHHHHHHHHHHhc
Confidence 34455677775 67999999999999999999999988532 2 2355555 344444555555555544
No 101
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=90.42 E-value=0.44 Score=36.18 Aligned_cols=35 Identities=14% Similarity=0.214 Sum_probs=28.1
Q ss_pred ceEEEEEecCCccceEecCCcHHHHHHHHHhCCeE
Q 009007 42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKI 76 (546)
Q Consensus 42 ~~~~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I 76 (546)
.....+.+.....|.+|||+|++|+.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 35556666666799999999999999999988544
No 102
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=89.47 E-value=0.17 Score=46.81 Aligned_cols=55 Identities=24% Similarity=0.347 Sum_probs=49.3
Q ss_pred cCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHh
Q 009007 378 TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRA 444 (546)
Q Consensus 378 ~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~ 444 (546)
+..+|.|+||+|.+---|...|.++|.+. +..|.|-|..++++.|...|+.+|-.
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVla------------d~kIHiLG~~~niriAR~avcsLIlG 231 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA------------DSKIHILGAFQNIRIARDAVCSLILG 231 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEec------------CceEEEeecchhhHHHHHhhHhhhcc
Confidence 56789999999999999999999999884 24799999999999999999998854
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=88.77 E-value=0.76 Score=34.84 Aligned_cols=34 Identities=24% Similarity=0.426 Sum_probs=28.0
Q ss_pred eeEEEEEccCcceeEEcCCChhHHHHHHhhCceE
Q 009007 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANI 403 (546)
Q Consensus 370 ~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I 403 (546)
....+.+.....|.+||++|++|+.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 5556667666789999999999999999988544
No 104
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=88.65 E-value=1.9 Score=49.00 Aligned_cols=6 Identities=83% Similarity=1.675 Sum_probs=2.5
Q ss_pred CCCCCC
Q 009007 490 GGYGSS 495 (546)
Q Consensus 490 ~Gyg~~ 495 (546)
||||++
T Consensus 1206 GGYGgs 1211 (1282)
T KOG0921|consen 1206 GGYGGS 1211 (1282)
T ss_pred CCCCCC
Confidence 444433
No 105
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=88.13 E-value=0.9 Score=48.72 Aligned_cols=68 Identities=19% Similarity=0.207 Sum_probs=56.1
Q ss_pred CCcceeEEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHh
Q 009007 366 GLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (546)
Q Consensus 366 ~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~ 444 (546)
....+...+.|+.+..-.+||.+|...|.|..+||+.-.+ ++.+|.|.- ++.+.++|+++|...+..
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 3445778899999999999999999999999999965554 345777777 678889999999888776
Q ss_pred c
Q 009007 445 N 445 (546)
Q Consensus 445 ~ 445 (546)
.
T Consensus 661 ~ 661 (760)
T KOG1067|consen 661 D 661 (760)
T ss_pred c
Confidence 4
No 106
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=87.37 E-value=0.41 Score=37.26 Aligned_cols=37 Identities=27% Similarity=0.436 Sum_probs=29.7
Q ss_pred eEEEEEccCc-----ceeEEcCCChhHHHHHHhh-CceEEEec
Q 009007 371 TTRLLVPTSR-----IGCLIGKGGSIITEMRRLT-KANIRILP 407 (546)
Q Consensus 371 ~~~l~VP~~~-----vG~IIGkgG~~Ik~I~~~T-ga~I~i~~ 407 (546)
...+.|-... +|..||++|++|+.|.++. |-+|+|-.
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 4556777777 9999999999999999999 89998854
No 107
>PRK13764 ATPase; Provisional
Probab=87.27 E-value=1.1 Score=49.71 Aligned_cols=43 Identities=28% Similarity=0.470 Sum_probs=38.8
Q ss_pred eeEEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCC
Q 009007 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLP 412 (546)
Q Consensus 370 ~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P 412 (546)
-+..+.||.+.++.+|||+|.+|++|.++.|.+|.|...++.|
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 4677999999999999999999999999999999998776644
No 108
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=86.81 E-value=0.66 Score=36.86 Aligned_cols=33 Identities=18% Similarity=0.250 Sum_probs=26.4
Q ss_pred EEEEecCCccceEecCCcHHHHHHHHHhCCeEE
Q 009007 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIR 77 (546)
Q Consensus 45 ~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~ 77 (546)
+.+.+..+..|.+|||+|+++..||--++.-++
T Consensus 26 i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 26 VEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred EEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 456666788999999999999999987764443
No 109
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=86.67 E-value=1.3 Score=46.69 Aligned_cols=39 Identities=36% Similarity=0.515 Sum_probs=35.6
Q ss_pred EEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCC
Q 009007 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179 (546)
Q Consensus 141 ~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~ 179 (546)
...+.||...++.+|||+|.+|++|+.+.|-+|.|...+
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 477889999999999999999999999999999997653
No 110
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=86.12 E-value=1.2 Score=43.64 Aligned_cols=51 Identities=16% Similarity=0.185 Sum_probs=44.8
Q ss_pred eEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 009007 152 GCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD 214 (546)
Q Consensus 152 g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~v~~A~~~I~~~l~~ 214 (546)
-+|||++|+|++.|+-.|.|-|-|.. .+|.+.|....+..+...+.+.+..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG------------~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG------------NTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC------------cEEEeecCcchHHHHHHHHHHHHhc
Confidence 57999999999999999999998854 3699999999999888888888765
No 111
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=85.96 E-value=2.8 Score=44.66 Aligned_cols=151 Identities=18% Similarity=0.229 Sum_probs=99.2
Q ss_pred eEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCc
Q 009007 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRS 219 (546)
Q Consensus 140 ~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~v~~A~~~I~~~l~~~~~~~ 219 (546)
-.+.+.+|...+..|||.+|..|+++..+.++.|.+.-.-+++. + .-+
T Consensus 449 ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~q---s-----------------------~~~------ 496 (657)
T COG5166 449 AEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQ---S-----------------------QWH------ 496 (657)
T ss_pred hheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcch---h-----------------------hhh------
Confidence 34789999999999999999999999999998887743222211 0 000
Q ss_pred cccccccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEEEeecCcccccc
Q 009007 220 QHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVI 299 (546)
Q Consensus 220 ~~~~~s~~~~~~~~~g~~~~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~~~~~p~~~~~~~~~~~~v~vp~~~~g~II 299 (546)
..+-+.+|.+..+.|+
T Consensus 497 ----------------------------------------------------------------dNV~I~~PrKn~~ni~ 512 (657)
T COG5166 497 ----------------------------------------------------------------DNVLIEAPRKNQDNIS 512 (657)
T ss_pred ----------------------------------------------------------------cceEEECCccCccchh
Confidence 1245778888899999
Q ss_pred cCCchhHHHHHhhh----CCeEEecCCCCCCCceEEEEecCcchhhhhhHHHHHHHHhcCccccccccccCCcceeEEEE
Q 009007 300 GKGGAIINQIRQES----GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLL 375 (546)
Q Consensus 300 Gk~G~~Ik~i~~~s----ga~I~i~~~~~~~~erii~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l~ 375 (546)
|++......+++.. ...|.+.+. ..++.++.+-.. .++.++.- +.+- ......+.+.
T Consensus 513 ~~KNd~~~~V~~~c~f~~Kgdirf~~~----~~sI~~v~~~~~-------~I~rv~kn-----e~v~---~~~p~~~~~y 573 (657)
T COG5166 513 GKKNDKLDKVKQQCRFNLKGDIRFCPQ----STSIFTVDIYSD-------EIERVIKN-----ETVL---LEFPAEMHFY 573 (657)
T ss_pred cccccHHHHHhhhcccccccceEEcCC----ceEEEEEccccc-------HHHHHhhc-----cceE---Eecccccccc
Confidence 99988888887655 234444432 345777776432 22322221 0000 0112456688
Q ss_pred EccCcceeEEc---CCChhHHHHHHhhCceEEE
Q 009007 376 VPTSRIGCLIG---KGGSIITEMRRLTKANIRI 405 (546)
Q Consensus 376 VP~~~vG~IIG---kgG~~Ik~I~~~Tga~I~i 405 (546)
+|+..++.-+| -.|++|..+...-.-.|..
T Consensus 574 ~~se~h~~g~gena~R~~ni~~~t~~y~~~ie~ 606 (657)
T COG5166 574 VPSEIHKKGIGENAFRGENIQRVTKLYNSYIEF 606 (657)
T ss_pred cchhhhhccCCcccccccchhhhhhhhhcccee
Confidence 99999999999 6788887777765555554
No 112
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=85.03 E-value=3.2 Score=38.72 Aligned_cols=57 Identities=28% Similarity=0.394 Sum_probs=49.8
Q ss_pred CCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCC
Q 009007 148 SDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNP 216 (546)
Q Consensus 148 ~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~v~~A~~~I~~~l~~~~ 216 (546)
+..+|+|+||+|.|--.|+..|.++|.+. +..|.|-|..+++.-|...|+.+|...+
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVla------------d~kIHiLG~~~niriAR~avcsLIlGsp 233 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA------------DSKIHILGAFQNIRIARDAVCSLILGSP 233 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEec------------CceEEEeecchhhHHHHHhhHhhhccCC
Confidence 34679999999999999999999999874 4469999999999999999999996643
No 113
>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=84.52 E-value=4 Score=36.43 Aligned_cols=93 Identities=25% Similarity=0.417 Sum_probs=58.8
Q ss_pred ecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEecCCccccccccCcccCCHHHHHHHHHHHHHHHh-hhcCCCCCCC
Q 009007 58 IGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAE-ELRGDEDSDG 136 (546)
Q Consensus 58 IGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~-~~~~~~~~~~ 136 (546)
+=.+|..|++|-++..-+|.|-.. +.. +.+-.+|...|.+.+-++ .+.+ -.
T Consensus 21 ~~~~~dli~~lAk~lrKRIvvR~d--------------ps~----------l~~~e~A~~~I~~ivP~ea~i~d----i~ 72 (145)
T cd02410 21 FAEDGDLVKDLAKDLRKRIVIRPD--------------PSV----------LKPPEEAIKIILEIVPEEAGITD----IY 72 (145)
T ss_pred HhcccHHHHHHHHHHhceEEEcCC--------------hhh----------cCCHHHHHHHHHHhCCCccCcee----eE
Confidence 335688999999999888876211 110 111235555554433222 1110 01
Q ss_pred CCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecC
Q 009007 137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (546)
Q Consensus 137 ~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~ 178 (546)
-+..+-++.|-...-|.+||++|.++++|..+||-.-.|...
T Consensus 73 Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 73 FDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred ecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 122235566777888999999999999999999999888765
No 114
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=84.18 E-value=0.63 Score=36.48 Aligned_cols=33 Identities=21% Similarity=0.267 Sum_probs=28.4
Q ss_pred cEEEEEEeecCcccccccCCchhHHHHHhhhCC
Q 009007 283 EFSLRLVCPVANIGGVIGKGGAIINQIRQESGA 315 (546)
Q Consensus 283 ~~~~~v~vp~~~~g~IIGk~G~~Ik~i~~~sga 315 (546)
...+.+.+..+..|.||||+|.+++.|+.-.+.
T Consensus 28 ~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 28 GDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred ceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 457888899999999999999999999876543
No 115
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=83.34 E-value=1.1 Score=35.96 Aligned_cols=35 Identities=9% Similarity=0.254 Sum_probs=30.3
Q ss_pred EEEEecCCccceEecCCcHHHHHHHHHhCCeEEEc
Q 009007 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIG 79 (546)
Q Consensus 45 ~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~ 79 (546)
.++.|....-|.|||++|++|++|+++-.-...+.
T Consensus 32 i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~ 66 (81)
T cd02413 32 TEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP 66 (81)
T ss_pred EEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence 67888899999999999999999999877666553
No 116
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=83.27 E-value=0.83 Score=48.11 Aligned_cols=41 Identities=32% Similarity=0.421 Sum_probs=36.6
Q ss_pred eeEEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCC
Q 009007 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKEN 410 (546)
Q Consensus 370 ~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~ 410 (546)
-...+.||..+++.||||+|.+|++|.++.|-+|.|...+.
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 34678999999999999999999999999999999976543
No 117
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=83.24 E-value=0.61 Score=37.06 Aligned_cols=33 Identities=18% Similarity=0.381 Sum_probs=28.5
Q ss_pred EEEEEecCCccceEecCCcHHHHHHHHHhCCeE
Q 009007 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKI 76 (546)
Q Consensus 44 ~~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I 76 (546)
...+.+.....+.|||++|++|++|.++..-.+
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 357788999999999999999999998876555
No 118
>KOG3875 consensus Peroxisomal biogenesis protein peroxin [Intracellular trafficking, secretion, and vesicular transport]
Probab=83.20 E-value=4.2 Score=40.62 Aligned_cols=22 Identities=41% Similarity=0.952 Sum_probs=9.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCC
Q 009007 504 GSYGSSQLGGTGSAYGSYGSYS 525 (546)
Q Consensus 504 g~~G~~~~~~~~~~yg~~g~~~ 525 (546)
|.||++.+|+-|++|..+++|+
T Consensus 79 g~YGgGygg~fGgGyN~~~~~g 100 (362)
T KOG3875|consen 79 GPYGGGYGGGFGGGYNRFGPYG 100 (362)
T ss_pred CCcCCCcCcccCcccccccccc
Confidence 3333333333344444444444
No 119
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=82.94 E-value=2.8 Score=40.55 Aligned_cols=47 Identities=21% Similarity=0.408 Sum_probs=39.3
Q ss_pred EEEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHH
Q 009007 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLD 429 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~ 429 (546)
+-+.||+..|-.+||++|+.++-|.+.|+|+|-|-.. -.|-|.+..+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N-----------G~IWV~~~~~ 194 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN-----------GRIWVDGENE 194 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC-----------CEEEecCCCc
Confidence 4588999999999999999999999999999999542 3566766544
No 120
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=82.73 E-value=0.52 Score=54.28 Aligned_cols=59 Identities=19% Similarity=0.205 Sum_probs=50.1
Q ss_pred CceEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcC-CCCCCCceEEEEecCCccc
Q 009007 41 EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE-TVPGSEERVVTVYSASDET 99 (546)
Q Consensus 41 ~~~~~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~-~~~~~~ervv~I~G~~~~~ 99 (546)
.....++-+|...+..|||++|.+|+.++.-||+-|.|.+ ...+..||.+++.|.++.+
T Consensus 1338 ~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~ 1397 (2131)
T KOG4369|consen 1338 PANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQ 1397 (2131)
T ss_pred cccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhh
Confidence 3445678899999999999999999999999999999987 3335679999999998764
No 121
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=81.66 E-value=3.3 Score=40.06 Aligned_cols=58 Identities=22% Similarity=0.406 Sum_probs=44.7
Q ss_pred EEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHH-HHHHHHHHHH
Q 009007 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASV-VKKALCQIAS 210 (546)
Q Consensus 142 ~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~-v~~A~~~I~~ 210 (546)
.-+.|++..+.++||++|+.++-|.++|+|+|-+-. ...|-|.+..+. ...|..+|..
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-----------NG~IWV~~~~~~~e~~~~~aI~~ 206 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-----------NGRIWVDGENESLEELAIEAIRK 206 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-----------CCEEEecCCCcchHHHHHHHHHH
Confidence 446789999999999999999999999999998854 345777777664 4444444444
No 122
>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=81.62 E-value=1.7 Score=34.47 Aligned_cols=34 Identities=26% Similarity=0.459 Sum_probs=28.0
Q ss_pred eEEEEEccCcceeEEcCCChhHHHHHHhhCceEE
Q 009007 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIR 404 (546)
Q Consensus 371 ~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~ 404 (546)
...+.|..+..|.+|||.|++++.||--+..-++
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 3557777888999999999999999987765544
No 123
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=81.23 E-value=1.4 Score=34.18 Aligned_cols=37 Identities=30% Similarity=0.500 Sum_probs=28.9
Q ss_pred EEEEEeecCc-----ccccccCCchhHHHHHhhh-CCeEEecC
Q 009007 285 SLRLVCPVAN-----IGGVIGKGGAIINQIRQES-GAAIKVDS 321 (546)
Q Consensus 285 ~~~v~vp~~~-----~g~IIGk~G~~Ik~i~~~s-ga~I~i~~ 321 (546)
...|.|.... +|..||++|.+|+.|.++. |-+|.+-.
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 3466777777 8999999999999999999 77777654
No 124
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=81.14 E-value=3.9 Score=43.72 Aligned_cols=129 Identities=24% Similarity=0.386 Sum_probs=77.0
Q ss_pred eEecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEecCCccccccccCcccCCHHHHHHHHHHHHHHHhhhcCCCCCC
Q 009007 56 SIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDSD 135 (546)
Q Consensus 56 ~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~ 135 (546)
.+|=+.|..|++|.++..-+|.|-.. +.. +.+..+|...|++.+-++.--.+ -
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~d--------------Psv----------l~~~e~A~~~I~eivP~ea~i~~---i 94 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPD--------------PSV----------LKPPEEARKIILEIVPEEAGITD---I 94 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccC--------------chh----------cCCHHHHHHHHHHhCccccCcee---E
Confidence 45667899999999999888877322 100 12235666666554433221100 1
Q ss_pred CCCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEE----EcCHHHHHHHHHHHHHH
Q 009007 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQI----SGEASVVKKALCQIASR 211 (546)
Q Consensus 136 ~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I----~G~~~~v~~A~~~I~~~ 211 (546)
.-+..+-.++|-.+.-|.||||+|++.++|..+||-.-.|.....++. .-+..| .-..+...+.++.|-..
T Consensus 95 ~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~PPi~S-----~ti~~ir~~l~~~~~eR~~iL~~vg~r 169 (637)
T COG1782 95 YFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTPPIQS-----RTIKSIREILRSERKERREILRNVGRR 169 (637)
T ss_pred EecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecCCCch-----hhHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 112234667788888999999999999999999998888876533221 111111 22334444555666666
Q ss_pred HhcCC
Q 009007 212 LHDNP 216 (546)
Q Consensus 212 l~~~~ 216 (546)
|+..+
T Consensus 170 Ihr~~ 174 (637)
T COG1782 170 IHREP 174 (637)
T ss_pred hcCCc
Confidence 65543
No 125
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=81.03 E-value=2.9 Score=40.97 Aligned_cols=51 Identities=24% Similarity=0.261 Sum_probs=42.5
Q ss_pred eeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHh
Q 009007 382 GCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRA 444 (546)
Q Consensus 382 G~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~ 444 (546)
-.+||.+|++++.|+-.|.|.|-|+. .+|.+.|....++.+...+.+.+..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG------------~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG------------NTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC------------cEEEeecCcchHHHHHHHHHHHHhc
Confidence 46899999999999999999999964 3899999988888777776666554
No 126
>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=80.73 E-value=0.7 Score=36.70 Aligned_cols=35 Identities=26% Similarity=0.406 Sum_probs=29.5
Q ss_pred eeEEEEEccCcceeEEcCCChhHHHHHHhhCceEE
Q 009007 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIR 404 (546)
Q Consensus 370 ~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~ 404 (546)
....+.+...+-|.|||++|++|++|++..+-.+.
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 45678899999999999999999999987765553
No 127
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=80.26 E-value=2.3 Score=39.10 Aligned_cols=34 Identities=32% Similarity=0.410 Sum_probs=28.5
Q ss_pred EEEecCCccceEecCCcHHHHHHHHHhCCeEEEcC
Q 009007 46 RYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE 80 (546)
Q Consensus 46 rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~ 80 (546)
-++|-... |.-|||+|++|++|++..|-+|.|-+
T Consensus 64 IfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 64 ILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 35555566 99999999999999999999998743
No 128
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=79.98 E-value=6.7 Score=35.02 Aligned_cols=91 Identities=18% Similarity=0.340 Sum_probs=59.1
Q ss_pred ccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhhhhHHHHHHHHhcCcccc--ccccccCCcceeEEEEE
Q 009007 299 IGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSE--KIERDSGLISFTTRLLV 376 (546)
Q Consensus 299 IGk~G~~Ik~i~~~sga~I~i~~~~~~~~erii~i~g~~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~~~~l~V 376 (546)
+=.++..|++|.++.--+|.|-.... +. ..-..+.+.+..+.|.-.. .+.- ...+-++.|
T Consensus 21 ~~~~~dli~~lAk~lrKRIvvR~dps------~l--------~~~e~A~~~I~~ivP~ea~i~di~F----d~~tGEV~I 82 (145)
T cd02410 21 FAEDGDLVKDLAKDLRKRIVIRPDPS------VL--------KPPEEAIKIILEIVPEEAGITDIYF----DDDTGEVII 82 (145)
T ss_pred HhcccHHHHHHHHHHhceEEEcCChh------hc--------CCHHHHHHHHHHhCCCccCceeeEe----cCCCcEEEE
Confidence 44567889999998888887753210 00 0002244455554442211 1111 123557888
Q ss_pred ccCcceeEEcCCChhHHHHHHhhCceEEEec
Q 009007 377 PTSRIGCLIGKGGSIITEMRRLTKANIRILP 407 (546)
Q Consensus 377 P~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~ 407 (546)
-...-|.|||++|.++++|..+||-.-.|.+
T Consensus 83 eaeKPG~ViGk~g~~~reI~~~tgW~p~vvR 113 (145)
T cd02410 83 EAEKPGLVIGKGGSTLREITRETGWAPKVVR 113 (145)
T ss_pred EEcCCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence 8899999999999999999999998888865
No 129
>PRK13764 ATPase; Provisional
Probab=79.89 E-value=4 Score=45.46 Aligned_cols=44 Identities=30% Similarity=0.453 Sum_probs=38.4
Q ss_pred CceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCC
Q 009007 138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHL 181 (546)
Q Consensus 138 ~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~ 181 (546)
..-...+.||...++.+|||+|.+|++|+++.|..|.|...++.
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~ 522 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEE 522 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcccc
Confidence 33457789999999999999999999999999999999876543
No 130
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=79.12 E-value=2.5 Score=34.01 Aligned_cols=35 Identities=20% Similarity=0.446 Sum_probs=28.6
Q ss_pred eEEEEEccCcceeEEcCCChhHHHHHHhhCceEEE
Q 009007 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405 (546)
Q Consensus 371 ~~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i 405 (546)
.+++.|....-|.|||++|+.|++|++.-.-...+
T Consensus 31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~ 65 (81)
T cd02413 31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF 65 (81)
T ss_pred eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence 46788888899999999999999999876544443
No 131
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=72.44 E-value=3.5 Score=35.16 Aligned_cols=30 Identities=23% Similarity=0.358 Sum_probs=26.0
Q ss_pred EEEEecCCccceEecCCcHHHHHHHHHhCC
Q 009007 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKS 74 (546)
Q Consensus 45 ~rilip~~~~g~IIGk~G~~Ik~i~~~tga 74 (546)
+++.|-...-|.|||++|++|++|++....
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence 567788888999999999999999987654
No 132
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=71.80 E-value=4.8 Score=36.97 Aligned_cols=36 Identities=33% Similarity=0.611 Sum_probs=31.3
Q ss_pred EEEEecCCceeEEeecCchHHHHHHhhcCceEEEecC
Q 009007 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (546)
Q Consensus 142 ~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~ 178 (546)
+-++|.... |..|||+|.+|+.+++..|-+|.+...
T Consensus 63 vIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 63 VILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred EEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence 556776666 999999999999999999999998754
No 133
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=70.98 E-value=7.7 Score=41.57 Aligned_cols=96 Identities=17% Similarity=0.290 Sum_probs=62.3
Q ss_pred ccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhhhhHHHHHHHHhcCccccccccccCCcceeEEEEE
Q 009007 297 GVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLV 376 (546)
Q Consensus 297 ~IIGk~G~~Ik~i~~~sga~I~i~~~~~~~~erii~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l~V 376 (546)
.++=+.|..|++|.++..-+|.|-.... +... . ..+...++.+.|.-..-.+-. -...+-++.|
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~dPs------vl~~-~-------e~A~~~I~eivP~ea~i~~i~--Fd~~tGEViI 105 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPDPS------VLKP-P-------EEARKIILEIVPEEAGITDIY--FDDDTGEVII 105 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccCch------hcCC-H-------HHHHHHHHHhCccccCceeEE--ecCCCceEEE
Confidence 4566788999999999988888864321 1111 1 224444444443321110000 0123456888
Q ss_pred ccCcceeEEcCCChhHHHHHHhhCceEEEecC
Q 009007 377 PTSRIGCLIGKGGSIITEMRRLTKANIRILPK 408 (546)
Q Consensus 377 P~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~ 408 (546)
-.+.-|.||||+|++.++|.++||-.-+|.+.
T Consensus 106 ea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 106 EAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred EecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 89999999999999999999999988777653
No 134
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=68.90 E-value=5.5 Score=32.22 Aligned_cols=28 Identities=25% Similarity=0.380 Sum_probs=23.4
Q ss_pred EEEEecCCccceEecCCcHHHHHHHHHh
Q 009007 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDT 72 (546)
Q Consensus 45 ~rilip~~~~g~IIGk~G~~Ik~i~~~t 72 (546)
.++.|....-|.+||++|.+|++|++.-
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 4555666889999999999999999775
No 135
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=66.79 E-value=10 Score=42.65 Aligned_cols=95 Identities=24% Similarity=0.439 Sum_probs=60.7
Q ss_pred EecCCcHHHHHHHHHhCCeEEEcCCCCCCCceEEEEecCCccccccccCcccCCHHHHHHHHHHHHHHHhh-hcCCCCCC
Q 009007 57 IIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEE-LRGDEDSD 135 (546)
Q Consensus 57 IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~~~v~~a~~a~~~i~~~i~~~~-~~~~~~~~ 135 (546)
.+=.++..|++|-++..-+|.|-.. +.- +.+-.+|...|.+.+-++. +. +-
T Consensus 37 ~~~~~~~~~~~~~~~~~~r~~~~~~--------------~~~----------~~~~~~~~~~i~~~~~~~~~~~----~~ 88 (630)
T TIGR03675 37 LFAKDDDLVKELAKKLRKRIVIRPD--------------PSV----------LLPPEEAIEKIKEIVPEEAGIT----DI 88 (630)
T ss_pred HhccchHHHHHHHHHhhceEEEecC--------------hhh----------cCCHHHHHHHHHHhCCCcCCce----eE
Confidence 4456789999999998888876211 110 1112345544444332221 10 01
Q ss_pred CCCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCC
Q 009007 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179 (546)
Q Consensus 136 ~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~ 179 (546)
.-+..+-+++|-...-|.||||+|.++++|..+||-.-.|.+..
T Consensus 89 ~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~ 132 (630)
T TIGR03675 89 YFDDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTP 132 (630)
T ss_pred EecCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecC
Confidence 11223456777788889999999999999999999999887753
No 136
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=66.30 E-value=6.8 Score=31.71 Aligned_cols=28 Identities=32% Similarity=0.615 Sum_probs=22.9
Q ss_pred EEEEEccCcceeEEcCCChhHHHHHHhh
Q 009007 372 TRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~T 399 (546)
..+.|....-|.+||++|+.|++|++.-
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 4566666788999999999999998753
No 137
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=65.91 E-value=5.4 Score=38.52 Aligned_cols=31 Identities=23% Similarity=0.351 Sum_probs=26.7
Q ss_pred eEEEEEecCCccceEecCCcHHHHHHHHHhC
Q 009007 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (546)
Q Consensus 43 ~~~rilip~~~~g~IIGk~G~~Ik~i~~~tg 73 (546)
...++.|....-|.||||+|++|++|+++..
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~ 81 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKELE 81 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHHHH
Confidence 3467888999999999999999999997654
No 138
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=65.66 E-value=5.5 Score=33.93 Aligned_cols=29 Identities=31% Similarity=0.524 Sum_probs=24.6
Q ss_pred EEEEEccCcceeEEcCCChhHHHHHHhhC
Q 009007 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTK 400 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tg 400 (546)
.++.|-...-|.|||++|+.|++|++...
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 56777788889999999999999987643
No 139
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=64.01 E-value=12 Score=40.08 Aligned_cols=128 Identities=15% Similarity=0.120 Sum_probs=79.9
Q ss_pred cccccCCchhHHHHHhhhCCeEE--ecCCCCCCCceEEEE-ecCcchhhhhhHHHHHHHHhcCccccccccccCCcceeE
Q 009007 296 GGVIGKGGAIINQIRQESGAAIK--VDSSSTEGDDCLITV-SSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTT 372 (546)
Q Consensus 296 g~IIGk~G~~Ik~i~~~sga~I~--i~~~~~~~~erii~i-~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~ 372 (546)
-++-||+..++.+|++..-|.+. +.... ..++.+. .|. .+.....+...+. .-....
T Consensus 392 dFl~gkkngK~TrIm~~v~c~~~~~i~~~~---gs~~~~~~~g~-------~~~F~k~~~~~~~----------EFpae~ 451 (657)
T COG5166 392 DFLRGKKNGKATRIMKGVSCSELSSIVSST---GSIVETNGIGE-------KMSFSKKLSIPPT----------EFPAEI 451 (657)
T ss_pred HHhccccCcchhhhhhhcccceeeEEEecC---CcEEEEeccCc-------chhhHHHhcCCcc----------cCchhe
Confidence 47788888889999998888744 33322 1233332 222 1122222222111 112456
Q ss_pred EEEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcC---HHHHHHHHHHHHHHHHhc
Q 009007 373 RLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD---LDLAKDALIQVMTRLRAN 445 (546)
Q Consensus 373 ~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~---~~~v~~A~~~I~~~i~~~ 445 (546)
.+.||...|..|||-||..|+++...-++.|+....-++|....-+ -|.|.-+ .+++--++.-+++++.+.
T Consensus 452 ~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~d--NV~I~~PrKn~~ni~~~KNd~~~~V~~~ 525 (657)
T COG5166 452 AFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHD--NVLIEAPRKNQDNISGKKNDKLDKVKQQ 525 (657)
T ss_pred EEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhc--ceEEECCccCccchhcccccHHHHHhhh
Confidence 7999999999999999999999999999999987665666532211 2556553 345555666666666654
No 140
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=63.98 E-value=22 Score=40.09 Aligned_cols=96 Identities=16% Similarity=0.280 Sum_probs=62.1
Q ss_pred ccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhhhhHHHHHHHHhcCccccccccccCCcceeEEEEE
Q 009007 297 GVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLV 376 (546)
Q Consensus 297 ~IIGk~G~~Ik~i~~~sga~I~i~~~~~~~~erii~i~g~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l~V 376 (546)
..+=.++..|++|.++..-+|.|-.... +. ..-..+.+.+.++.|.-..-.+- --...+-++.|
T Consensus 36 ~~~~~~~~~~~~~~~~~~~r~~~~~~~~------~~--------~~~~~~~~~i~~~~~~~~~~~~~--~f~~~~~~v~i 99 (630)
T TIGR03675 36 ELFAKDDDLVKELAKKLRKRIVIRPDPS------VL--------LPPEEAIEKIKEIVPEEAGITDI--YFDDVTGEVII 99 (630)
T ss_pred HHhccchHHHHHHHHHhhceEEEecChh------hc--------CCHHHHHHHHHHhCCCcCCceeE--EecCCCceEEE
Confidence 3455678999999999888887753211 00 00122455555555432110000 00124567888
Q ss_pred ccCcceeEEcCCChhHHHHHHhhCceEEEecC
Q 009007 377 PTSRIGCLIGKGGSIITEMRRLTKANIRILPK 408 (546)
Q Consensus 377 P~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~ 408 (546)
-.+.-|.||||+|.++++|.++||-.-+|.+.
T Consensus 100 ~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 100 EAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred EEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 89999999999999999999999998888653
No 141
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=63.54 E-value=6.8 Score=37.84 Aligned_cols=29 Identities=38% Similarity=0.543 Sum_probs=25.3
Q ss_pred eeEEEEEccCcceeEEcCCChhHHHHHHh
Q 009007 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRL 398 (546)
Q Consensus 370 ~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~ 398 (546)
..+++.|....-|.|||++|+.|++|++.
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 45778899999999999999999998754
No 142
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=58.96 E-value=12 Score=37.32 Aligned_cols=31 Identities=23% Similarity=0.318 Sum_probs=25.8
Q ss_pred ceeEEEEEccCcc-eeEEcCCChhHHHHHHhh
Q 009007 369 SFTTRLLVPTSRI-GCLIGKGGSIITEMRRLT 399 (546)
Q Consensus 369 ~~~~~l~VP~~~v-G~IIGkgG~~Ik~I~~~T 399 (546)
.+...+.|..+-+ +.||||+|+.||+|....
T Consensus 220 ~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 220 KIHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 4778888987666 999999999999987654
No 143
>COG1159 Era GTPase [General function prediction only]
Probab=54.01 E-value=9.3 Score=38.38 Aligned_cols=35 Identities=26% Similarity=0.544 Sum_probs=27.2
Q ss_pred cCCcceeEEEEEccCcc-eeEEcCCChhHHHHHHhh
Q 009007 365 SGLISFTTRLLVPTSRI-GCLIGKGGSIITEMRRLT 399 (546)
Q Consensus 365 ~~~~~~~~~l~VP~~~v-G~IIGkgG~~Ik~I~~~T 399 (546)
.....+...+.|+.+-. |-||||+|+.||+|-..+
T Consensus 224 ~~~~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~A 259 (298)
T COG1159 224 KGLLKIHATIYVERESQKGIIIGKNGAMIKKIGTAA 259 (298)
T ss_pred CCeEEEEEEEEEecCCccceEECCCcHHHHHHHHHH
Confidence 33445777888987655 999999999999986554
No 144
>PRK15494 era GTPase Era; Provisional
Probab=53.83 E-value=16 Score=37.89 Aligned_cols=30 Identities=23% Similarity=0.378 Sum_probs=25.1
Q ss_pred ceeEEEEEccCcc-eeEEcCCChhHHHHHHh
Q 009007 369 SFTTRLLVPTSRI-GCLIGKGGSIITEMRRL 398 (546)
Q Consensus 369 ~~~~~l~VP~~~v-G~IIGkgG~~Ik~I~~~ 398 (546)
.+...+.|..+-+ +.||||+|+.||+|..+
T Consensus 272 ~i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 272 KINQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 4678888987766 99999999999988654
No 145
>PRK00089 era GTPase Era; Reviewed
Probab=50.69 E-value=19 Score=36.20 Aligned_cols=31 Identities=23% Similarity=0.507 Sum_probs=24.9
Q ss_pred ceeEEEEEccCcc-eeEEcCCChhHHHHHHhh
Q 009007 369 SFTTRLLVPTSRI-GCLIGKGGSIITEMRRLT 399 (546)
Q Consensus 369 ~~~~~l~VP~~~v-G~IIGkgG~~Ik~I~~~T 399 (546)
.+...+.|..+-+ +.||||+|+.||+|....
T Consensus 225 ~i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~a 256 (292)
T PRK00089 225 RIEATIYVERDSQKGIIIGKGGAMLKKIGTEA 256 (292)
T ss_pred EEEEEEEEccCCceeEEEeCCcHHHHHHHHHH
Confidence 4777888886655 999999999999886543
No 146
>cd07055 BMC_like_2 Bacterial Micro-Compartment (BMC)-like domain 2. BMC like 2 domains exist in cyanobacteria, proteobacteria, and actinobacteria and are homologs of carboxysome shell proteins. They might be encoded from putative organelles involved in unknown metabolic process. Although it has been suggested that these carboxysome shell protein homologs form hexamers and further assemble into the flat facets of the polyhedral bacterial organelles shell at present no experimental evidence exists to directly support this view.
Probab=43.67 E-value=49 Score=24.99 Aligned_cols=40 Identities=10% Similarity=0.042 Sum_probs=26.5
Q ss_pred HhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHH
Q 009007 397 RLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTR 441 (546)
Q Consensus 397 ~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~ 441 (546)
+.+++.| +.....+|. .--.+.|.|+..+|+.|+..|.+.
T Consensus 21 Kaa~V~i-~d~f~gCPq----~~~~l~i~Gdvs~Ve~Al~~i~~~ 60 (61)
T cd07055 21 KASGVFV-SDIFGSCPQ----HMITLAIFGETSAVELAMREIEED 60 (61)
T ss_pred hccCeEE-EEecCCCCC----ceEEEEEEecHHHHHHHHHHHhhc
Confidence 4455555 444334453 334677999999999999888653
No 147
>TIGR03802 Asp_Ala_antiprt aspartate-alanine antiporter. All members of the seed alignment for this model are asparate-alanine anti-transporters (AspT) encoded next to the gene for aspartate 4-decarboxylase (AspD), which converts asparate to alanine, releasing CO2. The exchange of Asp for Ala is electrogenic, so the AspD/AspT system confers a proton-motive force. This transporter contains two copies of the AspT/YidE/YbjL antiporter duplication domain (TIGR01625).
Probab=42.51 E-value=5.2e+02 Score=28.78 Aligned_cols=62 Identities=24% Similarity=0.365 Sum_probs=36.1
Q ss_pred EEEEEecCCceeEEeecCchHHHHHH------hhcCceEEEecCC--CCCc---ccCCCCceEEEEcCHHHHHHHHHHH
Q 009007 141 TAKLLVPSDQIGCVIGKGGQIVQNIR------SETGAQIRILKDE--HLPS---CALRSDELVQISGEASVVKKALCQI 208 (546)
Q Consensus 141 ~~~l~Vp~~~vg~iIGk~G~~Ik~I~------~~tga~I~i~~~~--~~p~---~~~~~dr~v~I~G~~~~v~~A~~~I 208 (546)
..++.+|+ ..++|| +++++. +.+|+.|.-.... ++++ .....-..+.+.|++++++++.+.+
T Consensus 304 ~e~VV~~~---S~liGk---TL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~GD~LlV~G~~~~l~~~~~~l 376 (562)
T TIGR03802 304 TKDVVLTN---KEYNGK---TVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQRGDVVTLVGTPQDVDRAAKQL 376 (562)
T ss_pred EEEEEECC---cccCCc---cHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecCCCEEEEEeCHHHHHHHHHHc
Confidence 44455554 345555 778776 3678777644321 1221 1112234688999999999876653
No 148
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=39.73 E-value=35 Score=33.93 Aligned_cols=29 Identities=28% Similarity=0.432 Sum_probs=23.0
Q ss_pred eEEEEEecC-CceeEEeecCchHHHHHHhh
Q 009007 140 VTAKLLVPS-DQIGCVIGKGGQIVQNIRSE 168 (546)
Q Consensus 140 ~~~~l~Vp~-~~vg~iIGk~G~~Ik~I~~~ 168 (546)
+...++|.. ++-+.|||++|+.||+|..+
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 566777875 46799999999999987543
No 149
>CHL00048 rps3 ribosomal protein S3
Probab=39.57 E-value=31 Score=33.18 Aligned_cols=30 Identities=17% Similarity=0.217 Sum_probs=25.7
Q ss_pred EEEEEecCCccceEecCCcHHHHHHHHHhC
Q 009007 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (546)
Q Consensus 44 ~~rilip~~~~g~IIGk~G~~Ik~i~~~tg 73 (546)
..++.|-...-|.|||++|++|++|++.-.
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 466777788889999999999999998764
No 150
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=39.49 E-value=20 Score=34.01 Aligned_cols=35 Identities=14% Similarity=0.164 Sum_probs=28.3
Q ss_pred eEEEEEecCCccceEecCCcHHHHHHHHHhCCeEE
Q 009007 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIR 77 (546)
Q Consensus 43 ~~~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~ 77 (546)
-.+.+-+-.+..+.+||+.|+++..||--+++-++
T Consensus 91 ~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~ 125 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLN 125 (208)
T ss_pred cEEEEEecCCchhhhhccCCcchHHHHHHHHHHhh
Confidence 34556677777999999999999999988876554
No 151
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=39.34 E-value=32 Score=32.53 Aligned_cols=30 Identities=23% Similarity=0.454 Sum_probs=25.9
Q ss_pred EEEEecCCccceEecCCcHHHHHHHHHhCC
Q 009007 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKS 74 (546)
Q Consensus 45 ~rilip~~~~g~IIGk~G~~Ik~i~~~tga 74 (546)
.++.|....-|.|||++|..|++|+++-.-
T Consensus 40 ~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k 69 (195)
T TIGR01008 40 TKVIIFAERPGLVIGRGGRRIRELTEKLQK 69 (195)
T ss_pred EEEEEEECCCceEECCCchHHHHHHHHHHH
Confidence 677888888999999999999999987643
No 152
>PRK03818 putative transporter; Validated
Probab=39.06 E-value=3.6e+02 Score=30.00 Aligned_cols=133 Identities=14% Similarity=0.231 Sum_probs=69.3
Q ss_pred EEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCC---------CCC---CCceEEEEecCCccccccccCcccCCHH
Q 009007 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGET---------VPG---SEERVVTVYSASDETNAFEDGDKFVSPA 112 (546)
Q Consensus 45 ~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I~i~~~---------~~~---~~ervv~I~G~~~~~~~~~~~~~~v~~a 112 (546)
.++.|+++. ++ |+++++++......+.|..- .++ ....++.|.|..++
T Consensus 207 r~~~V~~s~---li---GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~-------------- 266 (552)
T PRK03818 207 INIRVENPN---LH---GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPED-------------- 266 (552)
T ss_pred EEEEEeCCC---CC---CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHH--------------
Confidence 556666443 34 56999999988776665311 111 12356777776443
Q ss_pred HHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEecCCceeEEeecCchHHHHH--HhhcCceEEEecC-C-CCCc---cc
Q 009007 113 QDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNI--RSETGAQIRILKD-E-HLPS---CA 185 (546)
Q Consensus 113 ~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I--~~~tga~I~i~~~-~-~~p~---~~ 185 (546)
+.++.+.+-.+.. .+.+..........+++|++ .++|| +++++ ++.+|+.|.=... + +++. ..
T Consensus 267 ---l~~l~~~~Gl~~~-~~~~~~~~~~~~E~Vvv~~S---~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~ 336 (552)
T PRK03818 267 ---LHKAQLVIGEEVD-TSLSTRGTDLRSERVVVTNE---KVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLS 336 (552)
T ss_pred ---HHHHHHhcCCccC-ccccccCcceEEEEEEEcCh---hccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCE
Confidence 3333332221100 00011112334445555553 55665 67776 5777877653322 1 2211 11
Q ss_pred CCCCceEEEEcCHHHHHHHHHH
Q 009007 186 LRSDELVQISGEASVVKKALCQ 207 (546)
Q Consensus 186 ~~~dr~v~I~G~~~~v~~A~~~ 207 (546)
...-..+.+.|+++++++..+.
T Consensus 337 Lq~GD~LlVvG~~~~i~~l~~~ 358 (552)
T PRK03818 337 LQFGDILNLVGRPEAIDAVANV 358 (552)
T ss_pred EecCCEEEEEECHHHHHHHHHH
Confidence 1223368899999999987664
No 153
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=38.94 E-value=32 Score=34.94 Aligned_cols=36 Identities=25% Similarity=0.511 Sum_probs=27.9
Q ss_pred cCCcceeEEEEEccCcc-eeEEcCCChhHHHHHHhhC
Q 009007 365 SGLISFTTRLLVPTSRI-GCLIGKGGSIITEMRRLTK 400 (546)
Q Consensus 365 ~~~~~~~~~l~VP~~~v-G~IIGkgG~~Ik~I~~~Tg 400 (546)
.+...+..++.+|.... -.||||+|..|++|-++-+
T Consensus 323 ~g~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 323 AGVLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred CcEEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 33456888899997655 7889999999999966543
No 154
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=38.69 E-value=32 Score=32.89 Aligned_cols=31 Identities=29% Similarity=0.426 Sum_probs=24.9
Q ss_pred EEEEecCCccceEecCCcHHHHHHHHHhCCe
Q 009007 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSK 75 (546)
Q Consensus 45 ~rilip~~~~g~IIGk~G~~Ik~i~~~tga~ 75 (546)
.++.|-...-|.+||++|++|++|++.-.-.
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 4555555889999999999999999886543
No 155
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=37.36 E-value=36 Score=32.22 Aligned_cols=29 Identities=31% Similarity=0.560 Sum_probs=24.6
Q ss_pred eEEEEEccCcceeEEcCCChhHHHHHHhh
Q 009007 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (546)
Q Consensus 371 ~~~l~VP~~~vG~IIGkgG~~Ik~I~~~T 399 (546)
.+++.|....-|.|||++|..|++|++.-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 46788888888999999999999997653
No 156
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=35.58 E-value=38 Score=32.73 Aligned_cols=32 Identities=9% Similarity=0.253 Sum_probs=26.6
Q ss_pred EEEEecCCccceEecCCcHHHHHHHHHhCCeE
Q 009007 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKI 76 (546)
Q Consensus 45 ~rilip~~~~g~IIGk~G~~Ik~i~~~tga~I 76 (546)
.++.|....-|.|||++|..|++|+++-.-.+
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 56777788889999999999999998865443
No 157
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=34.87 E-value=41 Score=32.23 Aligned_cols=29 Identities=34% Similarity=0.644 Sum_probs=23.5
Q ss_pred EEEEEccCcceeEEcCCChhHHHHHHhhC
Q 009007 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTK 400 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~Tg 400 (546)
..+.|....-|.+||++|++|+++++.-.
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lk 70 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILE 70 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHH
Confidence 45666668889999999999999987643
No 158
>CHL00048 rps3 ribosomal protein S3
Probab=34.55 E-value=42 Score=32.34 Aligned_cols=29 Identities=21% Similarity=0.169 Sum_probs=24.6
Q ss_pred eEEEEEccCcceeEEcCCChhHHHHHHhh
Q 009007 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (546)
Q Consensus 371 ~~~l~VP~~~vG~IIGkgG~~Ik~I~~~T 399 (546)
.+++.|-...-|.|||++|..|++|++.-
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 46677778888999999999999998764
No 159
>COG1159 Era GTPase [General function prediction only]
Probab=34.44 E-value=42 Score=33.81 Aligned_cols=37 Identities=27% Similarity=0.574 Sum_probs=27.0
Q ss_pred ceEEEEEecC-CceeEEeecCchHHHHH--------HhhcCceEEE
Q 009007 139 QVTAKLLVPS-DQIGCVIGKGGQIVQNI--------RSETGAQIRI 175 (546)
Q Consensus 139 ~~~~~l~Vp~-~~vg~iIGk~G~~Ik~I--------~~~tga~I~i 175 (546)
.+...+.|+. ++-+.||||+|+.||+| ++-.+++|.+
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L 273 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYL 273 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEE
Confidence 4455677775 57899999999999886 3445666655
No 160
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=34.25 E-value=40 Score=32.55 Aligned_cols=29 Identities=24% Similarity=0.458 Sum_probs=24.3
Q ss_pred eEEEEEccCcceeEEcCCChhHHHHHHhh
Q 009007 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (546)
Q Consensus 371 ~~~l~VP~~~vG~IIGkgG~~Ik~I~~~T 399 (546)
.+++.|....-|.|||++|..|++|++.-
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L 73 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLL 73 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHH
Confidence 36677878888999999999999997654
No 161
>PRK15494 era GTPase Era; Provisional
Probab=34.12 E-value=47 Score=34.31 Aligned_cols=36 Identities=17% Similarity=0.365 Sum_probs=27.0
Q ss_pred eEEEEEecC-CceeEEeecCchHHHHHHh--------hcCceEEE
Q 009007 140 VTAKLLVPS-DQIGCVIGKGGQIVQNIRS--------ETGAQIRI 175 (546)
Q Consensus 140 ~~~~l~Vp~-~~vg~iIGk~G~~Ik~I~~--------~tga~I~i 175 (546)
+...+.|.. ++-+.|||++|+.||+|.. -++++|.+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l 317 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHL 317 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEE
Confidence 556777875 4689999999999988744 45666654
No 162
>PRK00089 era GTPase Era; Reviewed
Probab=33.89 E-value=49 Score=33.12 Aligned_cols=36 Identities=31% Similarity=0.601 Sum_probs=26.4
Q ss_pred eEEEEEecC-CceeEEeecCchHHHHHHh--------hcCceEEE
Q 009007 140 VTAKLLVPS-DQIGCVIGKGGQIVQNIRS--------ETGAQIRI 175 (546)
Q Consensus 140 ~~~~l~Vp~-~~vg~iIGk~G~~Ik~I~~--------~tga~I~i 175 (546)
+...+.|.. ++.+.|||++|++||+|.. -++++|.+
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l 270 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL 270 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 556667764 4679999999999988754 45666655
No 163
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=33.51 E-value=97 Score=31.97 Aligned_cols=56 Identities=18% Similarity=0.157 Sum_probs=44.9
Q ss_pred ccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHH--HHHHh
Q 009007 377 PTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVM--TRLRA 444 (546)
Q Consensus 377 P~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~--~~i~~ 444 (546)
+.+..-.|.|..+.+++.|.+..|+.|... .+.++|+|+...|..|...+. +.+..
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~r------------G~~~~i~g~~~~v~~A~~~l~~l~~~~~ 79 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVAR------------GEAVRIIGARPLVDVATRVLLTLELLAE 79 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeC------------CceEEEEechHHHHHHHHHHhHHHHHHH
Confidence 356678899999999999999999998762 247999999878888877776 44443
No 164
>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=32.05 E-value=1.3e+02 Score=27.51 Aligned_cols=57 Identities=23% Similarity=0.234 Sum_probs=42.6
Q ss_pred CCceEEEEEecCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHH
Q 009007 137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASR 211 (546)
Q Consensus 137 ~~~~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~v~~A~~~I~~~ 211 (546)
...-++|+-+|...+- +.+++|.+-+|+-+.+ . .+..|.|.|..+.|.+|++.+..+
T Consensus 110 ~~~~~iRv~l~~~i~~-------erl~ei~E~~gvI~Ef-e----------e~~~V~I~Gdke~Ik~aLKe~s~~ 166 (169)
T PF09869_consen 110 PGFETIRVKLKKPIQE-------ERLQEISEWHGVIFEF-E----------EDDKVVIEGDKERIKKALKEFSSF 166 (169)
T ss_pred CCceeEEEecCccchH-------HHHHHHHHHhceeEEe-c----------CCcEEEEeccHHHHHHHHHHHHHH
Confidence 3344566666655432 5678999999999988 2 255799999999999999988765
No 165
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=30.79 E-value=1.2e+02 Score=30.95 Aligned_cols=12 Identities=33% Similarity=0.570 Sum_probs=7.2
Q ss_pred CCCCCCCCCCCC
Q 009007 474 NYESRDSKRHGR 485 (546)
Q Consensus 474 ~yg~~~~~~~g~ 485 (546)
+|++|+..|.|+
T Consensus 365 ~~gGrGgGRGgg 376 (465)
T KOG3973|consen 365 NWGGRGGGRGGG 376 (465)
T ss_pred CCCCCCCCCCCC
Confidence 677777655543
No 166
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=29.77 E-value=48 Score=31.53 Aligned_cols=36 Identities=14% Similarity=0.269 Sum_probs=29.6
Q ss_pred eEEEEEecCCceeEEeecCchHHHHHHhhcCceEEE
Q 009007 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRI 175 (546)
Q Consensus 140 ~~~~l~Vp~~~vg~iIGk~G~~Ik~I~~~tga~I~i 175 (546)
-.+.+.+..+..+.|||+.|.++..||--+++-++-
T Consensus 91 ~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 346667777779999999999999999988876654
No 167
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=27.43 E-value=1.8e+02 Score=29.83 Aligned_cols=12 Identities=33% Similarity=0.326 Sum_probs=6.1
Q ss_pred HHHhhCceEEEe
Q 009007 395 MRRLTKANIRIL 406 (546)
Q Consensus 395 I~~~Tga~I~i~ 406 (546)
+|+.|-++|+-.
T Consensus 286 ~Re~Taski~k~ 297 (465)
T KOG3973|consen 286 RRERTASKIHKL 297 (465)
T ss_pred hhhhhhhhhccc
Confidence 455555555433
No 168
>COG0490 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]
Probab=26.69 E-value=44 Score=30.52 Aligned_cols=62 Identities=23% Similarity=0.268 Sum_probs=38.7
Q ss_pred EEEEccCcceeEEcCCChhHHHHHHhhCceEE-EecCCCC-----CCCCCCCCceEEEEcCHHHHHHHHHHHH
Q 009007 373 RLLVPTSRIGCLIGKGGSIITEMRRLTKANIR-ILPKENL-----PKIASEDDEMVQISGDLDLAKDALIQVM 439 (546)
Q Consensus 373 ~l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~-i~~~~~~-----P~~~~~~~r~v~I~G~~~~v~~A~~~I~ 439 (546)
.+..-+.++|.=||- -+|+++|||.|. |.+.+++ |...-....++.+.|+...+..++.+..
T Consensus 91 ~i~~~s~~~GksiGd-----l~irq~TGaTIIAI~r~~e~I~SPgPy~vle~gDtlvviG~~~~~~r~~~f~~ 158 (162)
T COG0490 91 KIEAGSPFIGKTIGD-----LNIRQNTGATVIAIVRNEEKILSPGPYTVLEAGDTLVVIGEETGLKRAKRFLL 158 (162)
T ss_pred eeecCCcccCcchhh-----cccccccCcEEEEEEecCcEecCCCchhhhcCCCEEEEEecchHhHHHHHHhh
Confidence 333445566666665 567999999854 4443321 2211233568999999999988876653
No 169
>PTZ00473 Plasmodium Vir superfamily; Provisional
Probab=24.65 E-value=3e+02 Score=28.99 Aligned_cols=11 Identities=36% Similarity=0.462 Sum_probs=6.1
Q ss_pred HHHHHHHHHhC
Q 009007 63 EIVKQLRIDTK 73 (546)
Q Consensus 63 ~~Ik~i~~~tg 73 (546)
++||+|++|+.
T Consensus 9 ai~k~lk~ey~ 19 (420)
T PTZ00473 9 AIVKALKKEYP 19 (420)
T ss_pred HHHHHHHHhch
Confidence 34566666654
No 170
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=24.03 E-value=75 Score=30.50 Aligned_cols=29 Identities=28% Similarity=0.458 Sum_probs=24.7
Q ss_pred EEEEecCCccceEecCCcHHHHHHHHHhC
Q 009007 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (546)
Q Consensus 45 ~rilip~~~~g~IIGk~G~~Ik~i~~~tg 73 (546)
++|.|....-+.|||++|..|++|++.-.
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l~ 92 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDLQ 92 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHHH
Confidence 56777788889999999999999997654
No 171
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=22.74 E-value=85 Score=32.00 Aligned_cols=34 Identities=24% Similarity=0.454 Sum_probs=26.6
Q ss_pred CCceEEEEEecCC-ceeEEeecCchHHHHHHhhcC
Q 009007 137 GHQVTAKLLVPSD-QIGCVIGKGGQIVQNIRSETG 170 (546)
Q Consensus 137 ~~~~~~~l~Vp~~-~vg~iIGk~G~~Ik~I~~~tg 170 (546)
...+..++++|.. +...||||+|..|++|-.+.+
T Consensus 325 ~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 325 VLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 3456778888864 678899999999999876544
No 172
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=22.33 E-value=84 Score=30.19 Aligned_cols=28 Identities=39% Similarity=0.577 Sum_probs=23.4
Q ss_pred EEEEEccCcceeEEcCCChhHHHHHHhh
Q 009007 372 TRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~T 399 (546)
+++.|....-|.|||++|+.|++|++.-
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l 91 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDL 91 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHH
Confidence 5677777788999999999999998553
No 173
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=21.27 E-value=2.5e+02 Score=22.53 Aligned_cols=66 Identities=17% Similarity=0.110 Sum_probs=45.2
Q ss_pred EEEccCcceeEEcCCChhHHHHHHhhCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHH
Q 009007 374 LLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLR 443 (546)
Q Consensus 374 l~VP~~~vG~IIGkgG~~Ik~I~~~Tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~ 443 (546)
..+=.+.-|.|- |=..+.+|-+..++.++..-+|...- ...+.+++|.|+..++..|-+.++..|.
T Consensus 20 a~i~are~gV~a--G~~~~~~i~~~l~~~v~~~~~dG~~v--~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 20 ATIIAREDGVLA--GLEEAEEIFEKLGLEVEWLVKDGDRV--EPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp EEEEESSSEEE---SHHHHHHHHHHCTEEEEESS-TT-EE--ETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred EEEEeCCCEEEE--CHHHHHHHHhhccEEEEEEeCCCCCc--cCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 333333344453 45788888888899998875553221 2356899999999999999888887764
No 174
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=20.94 E-value=2.3e+02 Score=24.00 Aligned_cols=39 Identities=26% Similarity=0.264 Sum_probs=30.4
Q ss_pred hcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 009007 168 ETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN 215 (546)
Q Consensus 168 ~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~v~~A~~~I~~~l~~~ 215 (546)
..+++|-|... ....|.|+|+..+|+.|+..+.+.+++.
T Consensus 62 aa~V~igF~DR---------FsGslvitGdvs~Ve~Al~~V~~~l~~~ 100 (111)
T PRK15468 62 AADVHIGFLDR---------FSGALVIYGSVGAVEEALSQTVSGLGRL 100 (111)
T ss_pred ccCcEEeeeec---------cceeEEEEccHHHHHHHHHHHHHHHHhh
Confidence 34577766542 3446999999999999999999999773
No 175
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=20.80 E-value=1.9e+02 Score=29.96 Aligned_cols=51 Identities=18% Similarity=0.216 Sum_probs=42.6
Q ss_pred cCCceeEEeecCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHH
Q 009007 147 PSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIA 209 (546)
Q Consensus 147 p~~~vg~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~v~~A~~~I~ 209 (546)
+...+-.|.|..+.+++.|.+.+|+.|... .+.++|+|+...|..|...+.
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~r------------G~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVAR------------GEAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeC------------CceEEEEechHHHHHHHHHHh
Confidence 355677899999999999999999999653 346999999878888877777
No 176
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=20.44 E-value=1.5e+02 Score=25.13 Aligned_cols=26 Identities=27% Similarity=0.339 Sum_probs=23.6
Q ss_pred eEEEEcCHHHHHHHHHHHHHHHHhcc
Q 009007 421 MVQISGDLDLAKDALIQVMTRLRANL 446 (546)
Q Consensus 421 ~v~I~G~~~~v~~A~~~I~~~i~~~~ 446 (546)
.+.|+|+..+|+.|+..+++-+++..
T Consensus 76 slvitGdvs~Ve~Al~~V~~~l~~~L 101 (111)
T PRK15468 76 ALVIYGSVGAVEEALSQTVSGLGRLL 101 (111)
T ss_pred eEEEEccHHHHHHHHHHHHHHHHhhc
Confidence 68999999999999999999998743
Done!