Query 010373
Match_columns 512
No_of_seqs 333 out of 2043
Neff 8.3
Searched_HMMs 46136
Date Thu Mar 28 23:46:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010373.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010373hhsearch_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 2.4E-48 5.2E-53 403.7 35.0 399 8-428 8-416 (485)
2 KOG1676 K-homology type RNA bi 100.0 3.3E-44 7.2E-49 365.9 32.4 328 42-422 52-390 (600)
3 KOG2193 IGF-II mRNA-binding pr 100.0 8.7E-43 1.9E-47 339.1 20.9 353 39-424 194-567 (584)
4 KOG2192 PolyC-binding hnRNP-K 100.0 5E-34 1.1E-38 263.2 23.3 354 11-422 19-385 (390)
5 KOG1676 K-homology type RNA bi 100.0 1.9E-29 4.2E-34 258.1 21.1 229 41-315 136-373 (600)
6 KOG2191 RNA-binding protein NO 100.0 8.5E-27 1.8E-31 221.7 20.5 237 42-300 37-282 (402)
7 KOG2193 IGF-II mRNA-binding pr 99.9 3.5E-28 7.7E-33 237.3 9.4 242 139-424 197-484 (584)
8 KOG2191 RNA-binding protein NO 99.9 3.5E-23 7.6E-28 197.1 23.6 170 139-424 37-207 (402)
9 KOG2192 PolyC-binding hnRNP-K 99.9 1.3E-22 2.8E-27 187.9 15.1 174 259-456 45-218 (390)
10 KOG2190 PolyC-binding proteins 99.9 2E-20 4.3E-25 195.3 19.8 175 140-441 42-225 (485)
11 TIGR03665 arCOG04150 arCOG0415 99.6 2.1E-15 4.5E-20 138.3 9.4 137 48-216 2-152 (172)
12 TIGR03665 arCOG04150 arCOG0415 99.6 7E-15 1.5E-19 134.8 12.8 147 145-421 2-151 (172)
13 PRK13763 putative RNA-processi 99.6 1.2E-14 2.7E-19 134.0 10.8 141 44-216 3-158 (180)
14 PRK13763 putative RNA-processi 99.6 5E-14 1.1E-18 130.0 14.7 65 141-215 3-71 (180)
15 KOG2279 Kinase anchor protein 99.4 2.1E-12 4.4E-17 131.9 12.1 175 12-216 36-210 (608)
16 cd02396 PCBP_like_KH K homolog 99.4 1.1E-12 2.4E-17 100.4 7.5 63 349-415 2-64 (65)
17 cd02396 PCBP_like_KH K homolog 99.4 1.4E-12 3.1E-17 99.8 7.0 64 142-209 1-64 (65)
18 KOG2208 Vigilin [Lipid transpo 99.2 1.6E-11 3.5E-16 135.8 9.5 312 42-422 199-563 (753)
19 cd02394 vigilin_like_KH K homo 99.2 1.1E-11 2.4E-16 94.0 5.7 61 349-416 2-62 (62)
20 KOG2208 Vigilin [Lipid transpo 99.2 8.8E-11 1.9E-15 130.0 13.4 296 42-384 345-746 (753)
21 cd02393 PNPase_KH Polynucleoti 99.2 5.3E-11 1.2E-15 89.7 7.9 58 347-415 2-60 (61)
22 PF00013 KH_1: KH domain syndr 99.2 1.3E-11 2.9E-16 92.9 4.6 60 348-415 1-60 (60)
23 cd02394 vigilin_like_KH K homo 99.1 5.8E-11 1.3E-15 90.1 5.5 60 143-209 2-61 (62)
24 PF00013 KH_1: KH domain syndr 99.1 3E-11 6.4E-16 91.0 3.9 60 142-209 1-60 (60)
25 cd00105 KH-I K homology RNA-bi 99.1 1.7E-10 3.7E-15 87.9 8.1 62 349-415 2-63 (64)
26 cd02393 PNPase_KH Polynucleoti 99.1 4.4E-10 9.4E-15 84.7 7.8 58 141-209 2-60 (61)
27 cd00105 KH-I K homology RNA-bi 99.1 5.7E-10 1.2E-14 85.0 7.6 62 143-209 2-63 (64)
28 PF13014 KH_3: KH domain 99.0 1.1E-09 2.4E-14 76.4 5.1 42 54-95 1-43 (43)
29 PF13014 KH_3: KH domain 98.9 3.5E-09 7.5E-14 73.9 5.4 43 357-403 1-43 (43)
30 smart00322 KH K homology RNA-b 98.8 1.7E-08 3.7E-13 77.3 8.9 66 347-419 3-68 (69)
31 COG1094 Predicted RNA-binding 98.8 1.5E-07 3.2E-12 85.8 14.3 149 42-217 6-166 (194)
32 smart00322 KH K homology RNA-b 98.8 4.2E-08 9.2E-13 75.1 8.7 66 141-213 3-68 (69)
33 COG1094 Predicted RNA-binding 98.6 5.1E-07 1.1E-11 82.3 10.7 140 262-421 8-164 (194)
34 KOG2279 Kinase anchor protein 98.5 2E-07 4.4E-12 95.9 5.7 231 136-418 63-365 (608)
35 cd02395 SF1_like-KH Splicing f 98.4 1.5E-06 3.3E-11 74.5 8.1 67 355-421 14-95 (120)
36 cd02395 SF1_like-KH Splicing f 98.3 1.6E-06 3.4E-11 74.4 7.8 73 144-216 3-96 (120)
37 KOG2113 Predicted RNA binding 98.3 1.4E-06 3.1E-11 83.7 7.6 136 260-412 24-173 (394)
38 KOG2113 Predicted RNA binding 98.3 1.8E-06 3.9E-11 83.0 6.8 142 138-314 23-164 (394)
39 PRK08406 transcription elongat 98.1 3.9E-06 8.4E-11 74.1 6.0 104 44-177 32-135 (140)
40 TIGR02696 pppGpp_PNP guanosine 97.9 3E-05 6.4E-10 84.9 9.2 97 107-215 545-642 (719)
41 PRK08406 transcription elongat 97.8 6.2E-05 1.3E-09 66.5 6.7 104 262-383 32-135 (140)
42 TIGR01952 nusA_arch NusA famil 97.6 9.4E-05 2E-09 65.1 5.6 103 45-177 34-136 (141)
43 KOG0119 Splicing factor 1/bran 97.6 0.00051 1.1E-08 70.5 10.8 76 346-423 137-232 (554)
44 TIGR03591 polynuc_phos polyrib 97.6 0.00015 3.2E-09 80.7 7.4 97 108-215 518-615 (684)
45 KOG0119 Splicing factor 1/bran 97.6 0.00051 1.1E-08 70.5 10.5 79 137-215 134-230 (554)
46 TIGR02696 pppGpp_PNP guanosine 97.5 0.0002 4.2E-09 78.6 7.8 66 345-421 576-642 (719)
47 TIGR01952 nusA_arch NusA famil 97.5 0.00019 4.1E-09 63.2 5.7 103 263-383 34-136 (141)
48 KOG0336 ATP-dependent RNA heli 97.3 0.00027 5.8E-09 71.2 5.0 65 31-98 34-98 (629)
49 PLN00207 polyribonucleotide nu 97.2 0.00039 8.5E-09 78.0 5.6 98 107-215 651-750 (891)
50 COG0195 NusA Transcription elo 97.0 0.001 2.2E-08 61.6 5.6 104 45-179 77-180 (190)
51 TIGR03591 polynuc_phos polyrib 97.0 0.0009 2E-08 74.5 6.1 66 345-421 549-615 (684)
52 COG1185 Pnp Polyribonucleotide 97.0 0.0014 2.9E-08 70.7 6.5 97 108-215 519-616 (692)
53 KOG0336 ATP-dependent RNA heli 96.8 0.0016 3.5E-08 65.8 4.8 72 136-215 42-113 (629)
54 COG0195 NusA Transcription elo 96.8 0.003 6.5E-08 58.6 6.3 102 264-384 78-179 (190)
55 KOG1588 RNA-binding protein Sa 96.8 0.0015 3.2E-08 62.6 4.1 41 40-80 88-134 (259)
56 KOG2814 Transcription coactiva 96.7 0.0013 2.9E-08 64.6 3.6 69 43-125 56-124 (345)
57 KOG1588 RNA-binding protein Sa 96.7 0.0015 3.2E-08 62.6 3.9 44 136-179 87-136 (259)
58 KOG2814 Transcription coactiva 96.7 0.0018 3.9E-08 63.7 4.2 71 140-216 56-126 (345)
59 PRK11824 polynucleotide phosph 96.6 0.0019 4E-08 72.2 4.6 97 108-215 521-618 (693)
60 cd02134 NusA_KH NusA_K homolog 96.5 0.0037 8E-08 46.9 4.3 37 43-79 24-60 (61)
61 PLN00207 polyribonucleotide nu 96.4 0.0039 8.4E-08 70.2 5.1 67 344-421 682-750 (891)
62 COG1185 Pnp Polyribonucleotide 96.3 0.0053 1.1E-07 66.3 5.2 69 345-424 550-619 (692)
63 cd02134 NusA_KH NusA_K homolog 96.2 0.0076 1.7E-07 45.2 4.4 36 141-176 25-60 (61)
64 PRK12328 nusA transcription el 96.1 0.02 4.3E-07 58.4 8.3 96 53-180 251-347 (374)
65 TIGR01953 NusA transcription t 96.1 0.012 2.5E-07 60.0 6.6 95 271-385 243-339 (341)
66 TIGR01953 NusA transcription t 96.1 0.016 3.5E-07 58.9 7.5 96 53-179 243-339 (341)
67 PRK12328 nusA transcription el 96.1 0.014 3E-07 59.5 6.9 97 271-387 251-348 (374)
68 COG5176 MSL5 Splicing factor ( 96.0 0.017 3.6E-07 53.1 6.2 44 136-179 143-192 (269)
69 PRK12327 nusA transcription el 96.0 0.0092 2E-07 61.1 5.0 96 53-179 245-341 (362)
70 PRK04163 exosome complex RNA-b 95.9 0.016 3.5E-07 56.0 6.3 64 348-422 146-210 (235)
71 PRK00468 hypothetical protein; 95.8 0.0089 1.9E-07 46.7 3.2 34 40-73 26-59 (75)
72 PRK12329 nusA transcription el 95.7 0.021 4.6E-07 59.2 6.3 96 53-179 277-373 (449)
73 PRK12327 nusA transcription el 95.6 0.022 4.8E-07 58.4 6.1 96 271-385 245-341 (362)
74 TIGR03319 YmdA_YtgF conserved 95.5 0.032 7E-07 60.1 7.3 66 345-420 202-269 (514)
75 PRK00106 hypothetical protein; 95.5 0.033 7.1E-07 59.9 7.3 66 345-420 223-290 (535)
76 PRK02821 hypothetical protein; 95.5 0.013 2.9E-07 45.9 3.1 35 41-75 28-62 (77)
77 PRK12704 phosphodiesterase; Pr 95.4 0.038 8.1E-07 59.7 7.3 65 345-419 208-274 (520)
78 PF14611 SLS: Mitochondrial in 95.4 0.25 5.4E-06 46.9 12.2 132 46-218 28-168 (210)
79 PRK09202 nusA transcription el 95.4 0.039 8.5E-07 58.6 7.1 95 53-179 245-340 (470)
80 PRK12329 nusA transcription el 95.4 0.024 5.3E-07 58.7 5.4 94 271-384 277-372 (449)
81 PRK02821 hypothetical protein; 95.2 0.041 8.8E-07 43.2 4.9 35 137-171 27-61 (77)
82 KOG1067 Predicted RNA-binding 95.1 0.068 1.5E-06 56.3 7.6 114 91-216 543-661 (760)
83 PRK09202 nusA transcription el 95.1 0.037 8.1E-07 58.7 5.8 94 272-385 246-340 (470)
84 COG1837 Predicted RNA-binding 95.0 0.022 4.8E-07 44.3 3.1 33 41-73 27-59 (76)
85 PF14611 SLS: Mitochondrial in 95.0 0.47 1E-05 45.0 13.0 87 115-215 4-90 (210)
86 PRK00468 hypothetical protein; 94.9 0.028 6.2E-07 43.9 3.3 34 136-169 25-58 (75)
87 PRK01064 hypothetical protein; 94.8 0.032 6.9E-07 43.9 3.4 33 41-73 27-59 (78)
88 PRK04163 exosome complex RNA-b 94.8 0.047 1E-06 52.8 5.3 62 143-215 147-209 (235)
89 COG5176 MSL5 Splicing factor ( 94.7 0.063 1.4E-06 49.4 5.6 40 346-385 147-192 (269)
90 PRK11824 polynucleotide phosph 94.6 0.026 5.7E-07 63.1 3.6 65 346-421 553-618 (693)
91 TIGR03319 YmdA_YtgF conserved 94.6 0.075 1.6E-06 57.3 6.9 52 39-95 199-251 (514)
92 COG1837 Predicted RNA-binding 94.6 0.041 8.8E-07 42.9 3.5 34 136-169 25-58 (76)
93 PRK00106 hypothetical protein; 94.6 0.082 1.8E-06 56.9 6.9 52 39-95 220-272 (535)
94 PRK01064 hypothetical protein; 94.1 0.07 1.5E-06 42.0 3.9 34 136-169 25-58 (78)
95 PRK12704 phosphodiesterase; Pr 94.0 0.2 4.3E-06 54.2 8.4 64 142-215 211-276 (520)
96 PF13083 KH_4: KH domain; PDB: 92.8 0.061 1.3E-06 41.8 1.6 35 41-75 26-60 (73)
97 PRK12705 hypothetical protein; 92.1 0.17 3.7E-06 54.2 4.4 39 345-383 196-235 (508)
98 KOG3273 Predicted RNA-binding 92.0 0.34 7.4E-06 44.4 5.6 56 149-216 177-232 (252)
99 KOG0921 Dosage compensation co 91.3 0.78 1.7E-05 51.4 8.4 28 348-375 1085-1112(1282)
100 cd02410 archeal_CPSF_KH The ar 90.9 1.5 3.2E-05 38.6 8.2 93 61-180 23-115 (145)
101 COG5166 Uncharacterized conser 90.6 0.64 1.4E-05 48.7 6.6 204 57-382 393-606 (657)
102 KOG4369 RTK signaling protein 90.3 0.079 1.7E-06 60.0 -0.2 69 349-421 1342-1410(2131)
103 cd02409 KH-II KH-II (K homolo 90.2 0.41 8.8E-06 35.9 3.8 35 43-77 24-58 (68)
104 cd02409 KH-II KH-II (K homolo 88.6 0.72 1.6E-05 34.5 4.2 35 140-174 24-58 (68)
105 PF13083 KH_4: KH domain; PDB: 88.6 0.19 4.2E-06 39.0 0.9 33 139-171 27-59 (73)
106 COG1855 ATPase (PilT family) [ 88.5 0.81 1.8E-05 47.7 5.5 39 142-180 487-525 (604)
107 PRK12705 hypothetical protein; 88.2 0.37 7.9E-06 51.7 3.0 53 38-95 192-245 (508)
108 COG5166 Uncharacterized conser 88.1 1.2 2.6E-05 46.7 6.5 156 154-410 393-555 (657)
109 COG1782 Predicted metal-depend 87.9 1.8 4E-05 45.5 7.6 128 57-216 42-173 (637)
110 KOG3273 Predicted RNA-binding 87.8 0.26 5.7E-06 45.2 1.4 55 355-421 177-231 (252)
111 KOG2874 rRNA processing protei 86.5 1.2 2.6E-05 43.1 5.0 51 153-215 161-211 (356)
112 KOG4369 RTK signaling protein 86.4 0.3 6.6E-06 55.5 1.1 60 41-100 1337-1397(2131)
113 PF13184 KH_5: NusA-like KH do 86.2 0.45 9.8E-06 36.6 1.7 38 142-179 4-47 (69)
114 cd02414 jag_KH jag_K homology 85.9 0.87 1.9E-05 35.7 3.3 33 142-174 25-57 (77)
115 cd02414 jag_KH jag_K homology 85.7 0.72 1.6E-05 36.2 2.7 35 45-79 25-59 (77)
116 PF13184 KH_5: NusA-like KH do 85.4 0.7 1.5E-05 35.5 2.4 36 349-384 5-46 (69)
117 KOG1067 Predicted RNA-binding 85.3 1.2 2.5E-05 47.4 4.7 68 342-421 592-660 (760)
118 KOG3875 Peroxisomal biogenesis 84.2 1.7 3.7E-05 42.8 5.0 12 489-500 91-102 (362)
119 PRK13764 ATPase; Provisional 84.2 1.1 2.5E-05 49.1 4.2 43 347-389 481-523 (602)
120 COG1097 RRP4 RNA-binding prote 83.7 2.7 6E-05 40.2 6.1 55 144-209 149-204 (239)
121 PRK13764 ATPase; Provisional 83.7 2.6 5.6E-05 46.4 6.7 44 140-183 480-523 (602)
122 COG1855 ATPase (PilT family) [ 83.3 0.95 2.1E-05 47.2 3.0 41 347-387 486-526 (604)
123 cd02413 40S_S3_KH K homology R 82.9 0.67 1.5E-05 36.8 1.4 38 44-81 30-67 (81)
124 PF07650 KH_2: KH domain syndr 82.4 0.67 1.4E-05 36.4 1.2 35 44-78 25-59 (78)
125 PF07650 KH_2: KH domain syndr 80.3 0.78 1.7E-05 36.0 0.9 35 347-381 25-59 (78)
126 COG1097 RRP4 RNA-binding prote 80.0 3.8 8.2E-05 39.2 5.5 47 349-406 148-194 (239)
127 KOG2874 rRNA processing protei 79.7 3.7 8.1E-05 39.8 5.4 51 359-421 161-211 (356)
128 cd02410 archeal_CPSF_KH The ar 78.7 2.6 5.7E-05 37.1 3.7 39 46-84 78-116 (145)
129 PRK06418 transcription elongat 78.1 2.8 6E-05 38.1 3.9 35 46-81 63-97 (166)
130 TIGR03675 arCOG00543 arCOG0054 77.8 7.9 0.00017 43.1 8.1 96 58-180 37-132 (630)
131 PRK06418 transcription elongat 75.2 4.1 8.9E-05 37.0 4.1 37 142-179 62-98 (166)
132 cd02413 40S_S3_KH K homology R 74.4 3.9 8.4E-05 32.5 3.4 35 142-176 31-65 (81)
133 cd02412 30S_S3_KH K homology R 73.3 2.9 6.3E-05 35.2 2.6 32 45-76 62-93 (109)
134 COG1782 Predicted metal-depend 69.5 5.7 0.00012 42.0 4.1 96 153-299 41-136 (637)
135 cd02411 archeal_30S_S3_KH K ho 67.0 5.1 0.00011 32.0 2.6 28 46-73 40-67 (85)
136 COG0092 RpsC Ribosomal protein 64.5 5.1 0.00011 38.2 2.4 32 43-74 50-81 (233)
137 cd02412 30S_S3_KH K homology R 62.1 7 0.00015 32.9 2.7 30 142-171 62-91 (109)
138 cd02411 archeal_30S_S3_KH K ho 61.3 9.2 0.0002 30.6 3.1 28 143-170 40-67 (85)
139 PF09869 DUF2096: Uncharacteri 58.1 29 0.00062 31.3 5.8 57 140-214 112-168 (169)
140 COG0092 RpsC Ribosomal protein 57.3 9.1 0.0002 36.5 2.8 29 347-375 51-79 (233)
141 TIGR00436 era GTP-binding prot 54.5 15 0.00032 36.1 4.0 31 140-170 220-251 (270)
142 COG1159 Era GTPase [General fu 52.1 18 0.0004 35.9 4.0 34 136-169 224-258 (298)
143 cd07055 BMC_like_2 Bacterial M 52.0 33 0.00072 25.6 4.4 39 374-417 21-59 (61)
144 TIGR03675 arCOG00543 arCOG0054 49.7 16 0.00035 40.7 3.6 41 44-84 93-133 (630)
145 PRK15494 era GTPase Era; Provi 48.6 21 0.00046 36.5 4.1 30 140-169 272-302 (339)
146 COG4010 Uncharacterized protei 48.5 55 0.0012 28.8 5.9 44 161-215 126-169 (170)
147 TIGR00436 era GTP-binding prot 47.3 23 0.0005 34.8 4.0 31 346-376 220-251 (270)
148 PRK00089 era GTPase Era; Revie 46.7 23 0.00049 35.1 3.9 29 141-169 226-255 (292)
149 PRK03818 putative transporter; 46.5 2.6E+02 0.0057 30.7 12.3 135 45-209 206-359 (552)
150 KOG3973 Uncharacterized conser 45.2 78 0.0017 32.0 7.1 20 451-470 365-384 (465)
151 TIGR03802 Asp_Ala_antiprt aspa 44.3 2.8E+02 0.0061 30.5 12.2 63 142-210 304-377 (562)
152 PRK15494 era GTPase Era; Provi 41.0 32 0.0007 35.1 4.1 31 346-376 272-303 (339)
153 COG1847 Jag Predicted RNA-bind 40.1 38 0.00082 31.8 3.9 35 142-176 92-126 (208)
154 KOG1423 Ras-like GTPase ERA [C 38.1 31 0.00067 34.6 3.2 32 42-73 326-358 (379)
155 COG1847 Jag Predicted RNA-bind 38.1 22 0.00048 33.3 2.1 38 42-79 89-126 (208)
156 CHL00048 rps3 ribosomal protei 38.0 28 0.00062 33.1 2.9 32 43-74 65-96 (214)
157 PRK00089 era GTPase Era; Revie 37.6 40 0.00086 33.4 4.1 32 345-376 224-256 (292)
158 PRK04191 rps3p 30S ribosomal p 37.5 29 0.00062 32.9 2.8 31 46-76 42-72 (207)
159 TIGR01008 rpsC_E_A ribosomal p 37.5 30 0.00065 32.4 2.9 31 45-75 39-69 (195)
160 COG1159 Era GTPase [General fu 36.9 45 0.00098 33.2 4.1 34 343-376 225-259 (298)
161 KOG2044 5'-3' exonuclease HKE1 35.3 1.2E+02 0.0025 34.4 7.2 7 397-403 755-761 (931)
162 PTZ00084 40S ribosomal protein 34.4 34 0.00074 32.7 2.7 33 45-77 45-77 (220)
163 KOG1423 Ras-like GTPase ERA [C 33.0 45 0.00098 33.5 3.4 34 344-377 325-359 (379)
164 PRK15468 carboxysome structura 32.2 1.2E+02 0.0026 25.3 5.2 40 168-216 61-100 (111)
165 TIGR01008 rpsC_E_A ribosomal p 30.3 54 0.0012 30.7 3.3 29 142-170 39-67 (195)
166 COG1702 PhoH Phosphate starvat 30.0 1.4E+02 0.0029 30.6 6.3 51 354-416 22-72 (348)
167 PRK04191 rps3p 30S ribosomal p 28.8 57 0.0012 30.8 3.3 29 143-171 42-70 (207)
168 CHL00048 rps3 ribosomal protei 28.4 59 0.0013 30.9 3.3 29 142-170 67-95 (214)
169 PTZ00084 40S ribosomal protein 28.1 57 0.0012 31.1 3.1 30 142-171 45-74 (220)
170 COG1702 PhoH Phosphate starvat 25.9 1.4E+02 0.003 30.5 5.5 53 146-210 20-72 (348)
171 PF12235 FXR1P_C: Fragile X-re 25.8 23 0.00049 31.6 0.0 25 474-498 50-74 (155)
172 COG0490 Putative regulatory, l 24.3 1.4E+02 0.0031 27.0 4.7 61 351-416 92-158 (162)
173 PF10369 ALS_ss_C: Small subun 23.4 1.9E+02 0.004 22.4 4.8 41 366-415 16-56 (75)
174 TIGR01009 rpsC_bact ribosomal 22.9 71 0.0015 30.3 2.7 29 46-74 64-92 (211)
175 PF02080 TrkA_C: TrkA-C domain 22.7 1.5E+02 0.0032 22.0 4.1 49 160-208 14-69 (71)
176 PRK15468 carboxysome structura 22.3 1.3E+02 0.0028 25.2 3.7 25 398-422 76-100 (111)
177 COG4010 Uncharacterized protei 21.8 2.9E+02 0.0062 24.5 5.9 42 367-419 126-167 (170)
178 cd07049 BMC_EutL_repeat1 ethan 21.4 2.7E+02 0.0059 23.2 5.4 49 168-216 47-100 (103)
179 PF04202 Mfp-3: Foot protein 3 20.8 1.3E+02 0.0028 22.7 3.1 8 491-498 53-60 (71)
180 PF09869 DUF2096: Uncharacteri 20.6 2.8E+02 0.0062 25.1 5.8 54 346-417 112-165 (169)
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=2.4e-48 Score=403.71 Aligned_cols=399 Identities=42% Similarity=0.606 Sum_probs=319.0
Q ss_pred cCCCccCCCCCcCCCCCCCCCCCCCCCcccCCCCCCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCC
Q 010373 8 NYGKRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCD 87 (512)
Q Consensus 8 ~~~kr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ 87 (512)
...++........+++...++...+.... ...+...+|||||+.+.+|.||||+|.+|++||++|.++|+|.+..++|.
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~ 86 (485)
T KOG2190|consen 8 LPRPKNSTTSNVGDNGSIKRPSLGDPVIS-TGPDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCP 86 (485)
T ss_pred CccccCCCcccccCCCcccccCCCCCccc-CCCCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCC
Confidence 35566667777767777777777666443 34445555999999999999999999999999999999999999999999
Q ss_pred ccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccCC---cc---cCCCcceEEEEEeeCCceeEEecCCCh
Q 010373 88 ERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLAD---DE---FGELTLITVRMLVPADQIGCVIGKGGQ 161 (512)
Q Consensus 88 ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~~---~~---~~~~~~~~~~llVP~~~vg~IIGk~G~ 161 (512)
||+|+|+|...+ ..++++++|++++++++......++ ++ +.....+++|||||.+++|+||||+|+
T Consensus 87 eRIiti~g~~~~--------~~~~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~ 158 (485)
T KOG2190|consen 87 ERIITITGNRVE--------LNLSPATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGS 158 (485)
T ss_pred cceEEEeccccc--------ccCCchHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccCcH
Confidence 999999996222 2688899999999999987422111 11 122226899999999999999999999
Q ss_pred hHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCCccccccccCCCCccCC---CCcc
Q 010373 162 VIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQS---SGVY 238 (512)
Q Consensus 162 ~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~---gg~~ 238 (512)
.||+|+++|||+|+|.++ ++|. +++|.|+|.|++++|.+|+..|+.+|++++.+......+. ..|.+ -+..
T Consensus 159 ~Ik~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st--~~y~P~~~~~~~ 232 (485)
T KOG2190|consen 159 LIKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVST--IPYRPSASQGGP 232 (485)
T ss_pred HHHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCc--ccCCCcccccCc
Confidence 999999999999999999 8998 5789999999999999999999999999765522211111 11211 0001
Q ss_pred cCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEEecCCcccC
Q 010373 239 LSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFE 318 (512)
Q Consensus 239 ~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~i~g~~~~~ 318 (512)
..+.+......+........+.++.+++.+|...++.|+|+++..|+.|+.++++.|.+....++ |+++++..+.++
T Consensus 233 ~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~---~~i~~s~~e~~~ 309 (485)
T KOG2190|consen 233 VLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTD---RIVTISARENPE 309 (485)
T ss_pred cccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccCc---ceeeeccccCcc
Confidence 11111110101122233345677888999999999999999999999999999999999988754 999999999999
Q ss_pred CC-chhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCce
Q 010373 319 DP-SPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEE 397 (512)
Q Consensus 319 ~~-~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r 397 (512)
+. +++++|++..++.+.+....+. ...++.+|+||.+++||||||+|.+|.+||+.|||.|+|...++. ...+++
T Consensus 310 ~~~s~a~~a~~~~~~~~~~~~~~~~-~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~---~~~~e~ 385 (485)
T KOG2190|consen 310 DRYSMAQEALLLVQPRISENAGDDL-TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEV---SGVREA 385 (485)
T ss_pred cccccchhhhhhccccccccccccc-cceeeeeeccCccccceeecccccchHHHHHhcCCceEEcccccc---CCccee
Confidence 88 8999999999999988777655 778999999999999999999999999999999999999877653 146899
Q ss_pred EEEEEcCHHHHHHHHHHHHHHHhhchhcccC
Q 010373 398 MVQITGSLDVASSALSQVTLRLRANTFEREG 428 (512)
Q Consensus 398 ~V~I~G~~~~v~~A~~~I~~~l~~~~~~~~~ 428 (512)
+|+|+|+..+...|+.++..++........+
T Consensus 386 ~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~~ 416 (485)
T KOG2190|consen 386 LVQITGMLREDLLAQYLIRARLSAPKSSMGG 416 (485)
T ss_pred EEEecchhHHHHhhhhhcccccccCccCCCC
Confidence 9999999999999999998888776554444
No 2
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=3.3e-44 Score=365.93 Aligned_cols=328 Identities=23% Similarity=0.373 Sum_probs=256.5
Q ss_pred CCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHH
Q 010373 42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVH 121 (512)
Q Consensus 42 ~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~ 121 (512)
..++.+..||.+++++||||+|+.|..|..+++|+|.|.....+..+|.+.++|.++++ ++|..++-
T Consensus 52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v-------------~~aK~li~ 118 (600)
T KOG1676|consen 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENV-------------EVAKQLIG 118 (600)
T ss_pred cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccH-------------HHHHHhhh
Confidence 55668999999999999999999999999999999999888778899999999999994 34443333
Q ss_pred HHHhhhcccCC--cccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCH
Q 010373 122 DRIVAEDSLAD--DEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEP 199 (512)
Q Consensus 122 ~~i~~~~~~~~--~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~ 199 (512)
+.+ ....... .+......++.+|+||.+.+|.||||+|++||.|++++||++.+..+..... ..++.+.|+|++
T Consensus 119 evv-~r~~~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~---~~~KplritGdp 194 (600)
T KOG1676|consen 119 EVV-SRGRPPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIAT---GADKPLRITGDP 194 (600)
T ss_pred hhh-hccCCCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCC---CCCCceeecCCH
Confidence 322 2221000 1112256689999999999999999999999999999999999999865443 478899999999
Q ss_pred HHHHHHHHHHHHHHhcCCCccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccC
Q 010373 200 AVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGK 279 (512)
Q Consensus 200 ~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk 279 (512)
+.|+.|..+|.++|.+.... .+..++. ++ . ......+++|.||...||.||||
T Consensus 195 ~~ve~a~~lV~dil~e~~~~-----------~~g~~~~---------~g----~---~~g~~~~~~V~VPr~~VG~IIGk 247 (600)
T KOG1676|consen 195 DKVEQAKQLVADILREEDDE-----------VPGSGGH---------AG----V---RGGGSATREVKVPRSKVGIIIGK 247 (600)
T ss_pred HHHHHHHHHHHHHHHhcccC-----------CCccccc---------cC----c---CccccceeEEeccccceeeEEec
Confidence 99999999999999963211 0100000 00 0 01122378999999999999999
Q ss_pred CCccccchhhhcCCeEEecCCCC-CCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCC------CCcee--EEE
Q 010373 280 GGGIIKQIRQESGASIKVDSSGA-EGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERES------GDPVI--TTR 350 (512)
Q Consensus 280 ~G~~Ik~I~~~tga~I~v~~~~~-~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~------~~~~~--t~~ 350 (512)
+|++||+|+.+||++|+|.+++. ...+|++.|.|.. ..++.+.+++..+........ +.... ...
T Consensus 248 gGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~------d~ie~Aa~lI~eii~~~~~~~~~~~~~G~P~~~~~fy 321 (600)
T KOG1676|consen 248 GGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTV------DQIEHAAELINEIIAEAEAGAGGGMGGGAPGLVAQFY 321 (600)
T ss_pred CchHHHHHhhccCceeEeecCCCCCCccceeeeecCH------HHHHHHHHHHHHHHHHHhccCCCCcCCCCccceeeEE
Confidence 99999999999999999998776 6788988888864 355555555544432221110 12223 788
Q ss_pred EEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010373 351 ILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN 422 (512)
Q Consensus 351 l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~ 422 (512)
|.||.+.||.||||+|++||.|..+|||++.+.+. |+..+..+++|+|+|++.+|..|..||.+++...
T Consensus 322 ~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~---~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~~ 390 (600)
T KOG1676|consen 322 MKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ---PPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGDI 390 (600)
T ss_pred EeccccccccccCCCccchhhhcccCCccccccCC---CCCCCccceEEEEecCcccchHHHHHHHHHhccc
Confidence 99999999999999999999999999999999764 4455778999999999999999999999999774
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=8.7e-43 Score=339.07 Aligned_cols=353 Identities=25% Similarity=0.348 Sum_probs=276.8
Q ss_pred CCCCCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecC-CCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHH
Q 010373 39 IGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISE-TVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDAL 117 (512)
Q Consensus 39 ~~~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~-~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~ 117 (512)
....+..+|+|||..++|.||||.|+|||.|.+.|.|+|+|.. +..|..|+.|+|.+++|. +.+|+
T Consensus 194 ~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg-------------~s~Ac 260 (584)
T KOG2193|consen 194 QQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG-------------TSKAC 260 (584)
T ss_pred ccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc-------------hHHHH
Confidence 3467889999999999999999999999999999999999985 456899999999999998 67899
Q ss_pred HHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEec
Q 010373 118 FRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAG 197 (512)
Q Consensus 118 ~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G 197 (512)
.+|++.+..+... ++-...+.++++..+.+||+||||.|.+||+|+.+||++|.|++-.++..+ ..||.|++.|
T Consensus 261 ~~ILeimqkEA~~----~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~y--npERTItVkG 334 (584)
T KOG2193|consen 261 KMILEIMQKEAVD----DKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLY--NPERTITVKG 334 (584)
T ss_pred HHHHHHHHHhhhc----cchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhccc--CccceEEecc
Confidence 9999988765532 233466789999999999999999999999999999999999987665543 6799999999
Q ss_pred CHHHHHHHHHHHHHHHhcCCCccccccccCC---------CCccCCCCc--ccCCCCcCCCC-CCCccc--Cccccccce
Q 010373 198 EPAVVRKALVQIASRLHENPSRSQHLLLSSS---------SNIYQSSGV--YLSAPLVGSYG-NYSARR--DEASAREFS 263 (512)
Q Consensus 198 ~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~---------~~~~~~gg~--~~~~p~~~~~~-~~~~~~--~~~~~~~~~ 263 (512)
..|+|.+|..+|..+|++..+.+- ..-+. ...++.+.. .+++|+.-+.. -|..|. .....+.-.
T Consensus 335 siEac~~AE~eImkKlre~yEnDl--~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~ 412 (584)
T KOG2193|consen 335 SIEACVQAEAEIMKKLRECYENDL--AAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQ 412 (584)
T ss_pred cHHHHHHHHHHHHHHHHHHHhhhH--HHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhh
Confidence 999999999999999999765431 11110 011111111 11122111100 111111 112234457
Q ss_pred EEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCC-CCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCC-
Q 010373 264 LRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAE-GDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERE- 341 (512)
Q Consensus 264 ~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~-~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~- 341 (512)
+++.||...+|.|||++|.+||+|...+||.|++.++..+ ..+|+++|+|. -++.++.+.++..++..+
T Consensus 413 V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGp---------peaqfKAQgrifgKikEen 483 (584)
T KOG2193|consen 413 VRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGP---------PEAQFKAQGRIFGKIKEEN 483 (584)
T ss_pred eeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCC---------hHHHHhhhhhhhhhhhhhc
Confidence 8999999999999999999999999999999999986644 68999999995 356667776666554332
Q ss_pred ----CCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHH
Q 010373 342 ----SGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTL 417 (512)
Q Consensus 342 ----~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~ 417 (512)
......++.+.||...+|+||||||.+++||++.|+|.|.|+++ +.|- ..+..+|.|+|..-+.+.|...|.+
T Consensus 484 f~~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrd-qtpd--End~vivriiGhfyatq~aQrki~~ 560 (584)
T KOG2193|consen 484 FFLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRD-QTPD--ENDQVIVRIIGHFYATQNAQRKIAH 560 (584)
T ss_pred cCCchhhheeeeeeeccchhhhhhhccccccHHHHhccccceEEcccc-CCCC--ccceeeeeeechhhcchHHHHHHHH
Confidence 23456788999999999999999999999999999999999765 4553 3566789999999999999999999
Q ss_pred HHhhchh
Q 010373 418 RLRANTF 424 (512)
Q Consensus 418 ~l~~~~~ 424 (512)
+|.+...
T Consensus 561 iv~qvkq 567 (584)
T KOG2193|consen 561 IVNQVKQ 567 (584)
T ss_pred HHHHHHH
Confidence 9987544
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=5e-34 Score=263.22 Aligned_cols=354 Identities=20% Similarity=0.335 Sum_probs=227.8
Q ss_pred CccCCCCCcCCCCCCCCCCCCCCCcccCCCCCCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccE
Q 010373 11 KRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERI 90 (512)
Q Consensus 11 kr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~erv 90 (512)
|+-|+..+.+ .-.+|...|- +...+....+.+|||+.++.+|.||||+|++||+|+.+.+|.|.|++. ..+||+
T Consensus 19 ~~~~~~e~g~---~~gkrp~~d~-~~qa~k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri 92 (390)
T KOG2192|consen 19 ETFPNTETGG---EFGKRPAEDM-EEQAFKRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERI 92 (390)
T ss_pred hcCCCCcccc---cccCCcchhh-HHHHhhhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCcee
Confidence 3444444443 3334433333 344456778999999999999999999999999999999999999987 678999
Q ss_pred EEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhc
Q 010373 91 VTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTET 170 (512)
Q Consensus 91 v~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~t 170 (512)
++|+...+. +-+-|.+|+..+. +. ......+++||||+.+++|.|||++|+.||+||+++
T Consensus 93 ~tisad~~t-------------i~~ilk~iip~le-e~------f~~~~pce~rllihqs~ag~iigrngskikelrekc 152 (390)
T KOG2192|consen 93 LTISADIET-------------IGEILKKIIPTLE-EG------FQLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKC 152 (390)
T ss_pred EEEeccHHH-------------HHHHHHHHhhhhh-hC------CCCCCchhhhhhhhhhhccceecccchhHHHHHHhh
Confidence 999987443 3444444444442 22 234567899999999999999999999999999999
Q ss_pred CceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCCcccccccc--CCCCccCCCCcccCCCCcCCCC
Q 010373 171 RAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLS--SSSNIYQSSGVYLSAPLVGSYG 248 (512)
Q Consensus 171 ga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~--~~~~~~~~gg~~~~~p~~~~~~ 248 (512)
.|+++|... .|..++||+|.|.|.+.+|..+++.|.+.|.+.|-+.....+. .....|..||..|++......-
T Consensus 153 sarlkift~----c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~p 228 (390)
T KOG2192|consen 153 SARLKIFTE----CCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRP 228 (390)
T ss_pred hhhhhhhhc----cCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCC
Confidence 999999765 5668999999999999999999999999999987665432111 1122344455444321110000
Q ss_pred CCCcccC-ccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHH
Q 010373 249 NYSARRD-EASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAA 327 (512)
Q Consensus 249 ~~~~~~~-~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~ 327 (512)
+...++. +.. .-|.......+-++|.-= +.+--.+.|....+. ...++..++. +.+
T Consensus 229 gpapqrggqgp--------p~~~~sdlmay~r~GrpG----~rydg~vdFs~detw----------~saidtw~~S-ewq 285 (390)
T KOG2192|consen 229 GPAPQRGGQGP--------PPPRGSDLMAYDRRGRPG----DRYDGMVDFSADETW----------PSAIDTWSPS-EWQ 285 (390)
T ss_pred CCCCCCCCCCC--------CCCCccccceeccCCCCC----ccccccccccccccC----------CCcCCCcCcc-ccc
Confidence 0000000 000 000011111122222100 011111222221111 0000000111 001
Q ss_pred HhhCCcc--------cc--cccCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCce
Q 010373 328 LRLQPRC--------SE--KTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEE 397 (512)
Q Consensus 328 ~~~~~~~--------~~--~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r 397 (512)
+..-+.- .. ..-.+.+....|..+.||.++-|.||||+|++|++|+.++||.|+|.. | .+++.+|
T Consensus 286 maYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikide----p-leGsedr 360 (390)
T KOG2192|consen 286 MAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDE----P-LEGSEDR 360 (390)
T ss_pred cccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecC----c-CCCCCce
Confidence 1110000 00 001123456788999999999999999999999999999999999953 3 2478899
Q ss_pred EEEEEcCHHHHHHHHHHHHHHHhhc
Q 010373 398 MVQITGSLDVASSALSQVTLRLRAN 422 (512)
Q Consensus 398 ~V~I~G~~~~v~~A~~~I~~~l~~~ 422 (512)
+++|+||.++++.|++++...+++.
T Consensus 361 IitItGTqdQIqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 361 IITITGTQDQIQNAQYLLQNSVKQY 385 (390)
T ss_pred EEEEeccHHHHhhHHHHHHHHHHhh
Confidence 9999999999999999999999864
No 5
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.97 E-value=1.9e-29 Score=258.08 Aligned_cols=229 Identities=28% Similarity=0.378 Sum_probs=181.7
Q ss_pred CCCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCC--CCCCccEEEEEcCCCCcccccCCcccCcHHHHHHH
Q 010373 41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETV--PGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALF 118 (512)
Q Consensus 41 ~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~--~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~ 118 (512)
...++.+|+||..++|+||||+|++||+|++.+||++.+-.+. .....+-+.|+|+++. ++.|..
T Consensus 136 ~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~-------------ve~a~~ 202 (600)
T KOG1676|consen 136 SVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDK-------------VEQAKQ 202 (600)
T ss_pred ccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHH-------------HHHHHH
Confidence 5678999999999999999999999999999999999886542 2236788999999887 466777
Q ss_pred HHHHHHhhhcccCCc-----ccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceE
Q 010373 119 RVHDRIVAEDSLADD-----EFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELL 193 (512)
Q Consensus 119 ~i~~~i~~~~~~~~~-----~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v 193 (512)
++++.+.++.-.... ........+++|.||.+.||.||||+|++||+|+.+|||||+|.++ +.| .+.||.+
T Consensus 203 lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpD-d~p---~speR~~ 278 (600)
T KOG1676|consen 203 LVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPD-DDP---SSPERPA 278 (600)
T ss_pred HHHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecC-CCC---CCcccee
Confidence 777777643211110 1123344589999999999999999999999999999999999998 445 3889999
Q ss_pred EEecCHHHHHHHHHHHHHHHhcCCCccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCC
Q 010373 194 QVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNI 273 (512)
Q Consensus 194 ~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~v 273 (512)
.|.|+.++|..|.++|.++|.+..... ++++....| .....+.+.||.++|
T Consensus 279 ~IiG~~d~ie~Aa~lI~eii~~~~~~~-------------~~~~~~G~P----------------~~~~~fy~~VPa~Kc 329 (600)
T KOG1676|consen 279 QIIGTVDQIEHAAELINEIIAEAEAGA-------------GGGMGGGAP----------------GLVAQFYMKVPADKC 329 (600)
T ss_pred eeecCHHHHHHHHHHHHHHHHHHhccC-------------CCCcCCCCc----------------cceeeEEEecccccc
Confidence 999999999999999999998853211 011000000 011167899999999
Q ss_pred cccccCCCccccchhhhcCCeEEecCCC--CCCCCeEEEecCCc
Q 010373 274 GGVIGKGGGIIKQIRQESGASIKVDSSG--AEGDDCIIFISTKE 315 (512)
Q Consensus 274 g~IIGk~G~~Ik~I~~~tga~I~v~~~~--~~~~~~ii~i~g~~ 315 (512)
|+||||+|++||.|..++||++.+.+.. ....+++|+|.|.+
T Consensus 330 GLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG~~ 373 (600)
T KOG1676|consen 330 GLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGDK 373 (600)
T ss_pred ccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEecCc
Confidence 9999999999999999999999999872 22578999999976
No 6
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.95 E-value=8.5e-27 Score=221.71 Aligned_cols=237 Identities=28% Similarity=0.396 Sum_probs=174.5
Q ss_pred CCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEec---CCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHH
Q 010373 42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRIS---ETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALF 118 (512)
Q Consensus 42 ~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~---~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~ 118 (512)
..+.++||||+..+|.||||+|++|.+|+++|||+|+++ +..|++.||||.|.|+.|+ ....+.
T Consensus 37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~ea-------------i~av~e 103 (402)
T KOG2191|consen 37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEA-------------LNAVHE 103 (402)
T ss_pred CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHH-------------HHHHHH
Confidence 459999999999999999999999999999999999997 4689999999999998665 233445
Q ss_pred HHHHHHhhhcccCCc-cc-----CCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCce
Q 010373 119 RVHDRIVAEDSLADD-EF-----GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDEL 192 (512)
Q Consensus 119 ~i~~~i~~~~~~~~~-~~-----~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~ 192 (512)
.|.++|.+.....+. .+ ..+..-.++|+||++..|.||||+|.+||.|+|+++|.|+|++. .|.-....||+
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 556666543322211 11 11112358999999999999999999999999999999999953 23333467999
Q ss_pred EEEecCHHHHHHHHHHHHHHHhcCCCccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCC
Q 010373 193 LQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGN 272 (512)
Q Consensus 193 v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~ 272 (512)
|+++|++++.++|+.+|.++|.++|+....+..+.. +-.|.+-...|.-.+|+. ... ...........++...
T Consensus 182 vt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya---~vsGpvaNsnPtGspya~-~~~---~~~astas~~sva~~~ 254 (402)
T KOG2191|consen 182 VTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYA---NVSGPVANSNPTGSPYAY-QAH---VLPASTASTISVAAGL 254 (402)
T ss_pred EEecCCHHHHHHHHHHHHHHhhcCCcccceeccchh---cccCcccccCCCCCCCCC-CCc---cccccchhhccccccc
Confidence 999999999999999999999999887665542221 111222112222222221 111 1222334456788889
Q ss_pred CcccccCCCccccchhhhcCCeEEecCC
Q 010373 273 IGGVIGKGGGIIKQIRQESGASIKVDSS 300 (512)
Q Consensus 273 vg~IIGk~G~~Ik~I~~~tga~I~v~~~ 300 (512)
.|..-|.++.++-.|-.-+|+.+.++..
T Consensus 255 iG~a~gaG~~~~a~l~~~~G~l~~itq~ 282 (402)
T KOG2191|consen 255 IGGANGAGGAFGAALSGFTGALIAITQA 282 (402)
T ss_pred cccccccccccceeeecccccceeeccc
Confidence 9999999999999999999998887763
No 7
>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=3.5e-28 Score=237.29 Aligned_cols=242 Identities=25% Similarity=0.401 Sum_probs=189.5
Q ss_pred cceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCC
Q 010373 139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPS 218 (512)
Q Consensus 139 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~ 218 (512)
....+|+|||..+||.||||.|.+||+|.+.|.|+|.|...++ ++..|++|+|-+++|...+|+++|.+++..+..
T Consensus 197 ~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken----~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~ 272 (584)
T KOG2193|consen 197 KDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKEN----AGAAEKIITVHSTPEGTSKACKMILEIMQKEAV 272 (584)
T ss_pred cCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeeccc----CCcccCceEEecCccchHHHHHHHHHHHHHhhh
Confidence 3568999999999999999999999999999999999998743 357899999999999999999999999988533
Q ss_pred ccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEEec
Q 010373 219 RSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVD 298 (512)
Q Consensus 219 ~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~ 298 (512)
.. ....++.++++..+.+||++|||.|.+||+|+++||++|.|.
T Consensus 273 ~~------------------------------------k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis 316 (584)
T KOG2193|consen 273 DD------------------------------------KVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITIS 316 (584)
T ss_pred cc------------------------------------chhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeee
Confidence 22 234677889999999999999999999999999999999999
Q ss_pred CCCCC---CCCeEEEecCC-cccCCCchhHHH-----------HHhhCCccccc--------------c-cC---C----
Q 010373 299 SSGAE---GDDCIIFISTK-EFFEDPSPTITA-----------ALRLQPRCSEK--------------T-ER---E---- 341 (512)
Q Consensus 299 ~~~~~---~~~~ii~i~g~-~~~~~~~~~~~a-----------~~~~~~~~~~~--------------~-~~---~---- 341 (512)
+...- ..||+|++.|. |.+..+...+.+ +..++..+... + .+ .
T Consensus 317 ~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~ 396 (584)
T KOG2193|consen 317 KLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVT 396 (584)
T ss_pred ehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccc
Confidence 75432 47999999883 111111111111 11111111000 0 00 0
Q ss_pred ---------CCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHH
Q 010373 342 ---------SGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSAL 412 (512)
Q Consensus 342 ---------~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~ 412 (512)
.....-..+|.||...||.||||+|..||.|.+.+||.|+|...+ ..+..+|+|+|+|++++.-+|.
T Consensus 397 ~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE----~pdvseRMViItGppeaqfKAQ 472 (584)
T KOG2193|consen 397 FASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPE----IPDVSERMVIITGPPEAQFKAQ 472 (584)
T ss_pred cCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCC----CCCcceeEEEecCChHHHHhhh
Confidence 011334678999999999999999999999999999999997543 3367899999999999999999
Q ss_pred HHHHHHHhhchh
Q 010373 413 SQVTLRLRANTF 424 (512)
Q Consensus 413 ~~I~~~l~~~~~ 424 (512)
-.|..+|++..+
T Consensus 473 grifgKikEenf 484 (584)
T KOG2193|consen 473 GRIFGKIKEENF 484 (584)
T ss_pred hhhhhhhhhhcc
Confidence 999999998655
No 8
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.92 E-value=3.5e-23 Score=197.14 Aligned_cols=170 Identities=25% Similarity=0.450 Sum_probs=138.4
Q ss_pred cceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCC-CCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCC
Q 010373 139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEH-LPLCALSFDELLQVAGEPAVVRKALVQIASRLHENP 217 (512)
Q Consensus 139 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~-~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~ 217 (512)
..+.+++|||+..+|.||||+|++|.+|+.+|||+|++++..+ +| ..+||+|.|+|+.+++...+..|.++|++.+
T Consensus 37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyP---GTTeRvcli~Gt~eai~av~efI~dKire~p 113 (402)
T KOG2191|consen 37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYP---GTTERVCLIQGTVEALNAVHEFIADKIREKP 113 (402)
T ss_pred CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCC---CccceEEEEeccHHHHHHHHHHHHHHHHHhH
Confidence 3489999999999999999999999999999999999998744 45 4899999999999999999999999999853
Q ss_pred CccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEEe
Q 010373 218 SRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKV 297 (512)
Q Consensus 218 ~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v 297 (512)
..... ...++-|+
T Consensus 114 ~~~~k----------------------------------------~v~~~~pq--------------------------- 126 (402)
T KOG2191|consen 114 QAVAK----------------------------------------PVDILQPQ--------------------------- 126 (402)
T ss_pred HhhcC----------------------------------------CccccCCC---------------------------
Confidence 31100 00000000
Q ss_pred cCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHhC
Q 010373 298 DSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATR 377 (512)
Q Consensus 298 ~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TG 377 (512)
..+.....++.||..-+|.||||+|.+||.|++++|
T Consensus 127 --------------------------------------------t~~r~kqikivvPNstag~iigkggAtiK~~~Eqsg 162 (402)
T KOG2191|consen 127 --------------------------------------------TPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSG 162 (402)
T ss_pred --------------------------------------------CccccceeEEeccCCcccceecCCcchHHHHHHhhC
Confidence 000113468899999999999999999999999999
Q ss_pred CeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhchh
Q 010373 378 ASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTF 424 (512)
Q Consensus 378 a~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~~~ 424 (512)
|.|+|.+. .|..-.-.+|+|++.|++|+..+|..+|+++|.+++.
T Consensus 163 a~iqisPq--kpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpq 207 (402)
T KOG2191|consen 163 AWIQISPQ--KPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQ 207 (402)
T ss_pred cceEeccc--CCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCc
Confidence 99999853 3433356789999999999999999999999999865
No 9
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.89 E-value=1.3e-22 Score=187.91 Aligned_cols=174 Identities=26% Similarity=0.383 Sum_probs=142.7
Q ss_pred cccceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccc
Q 010373 259 AREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKT 338 (512)
Q Consensus 259 ~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~ 338 (512)
...+.+++++..+..|+||||+|.+||.|+.+++|+|.|+++.. .+++.+|++.. ....+-..++.+++.+.+
T Consensus 45 ~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~--peri~tisad~-----~ti~~ilk~iip~lee~f 117 (390)
T KOG2192|consen 45 RSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSG--PERILTISADI-----ETIGEILKKIIPTLEEGF 117 (390)
T ss_pred hcceeEEEEEecccccceeccccccHHHHhhhccceeeccCCCC--CceeEEEeccH-----HHHHHHHHHHhhhhhhCC
Confidence 34578999999999999999999999999999999999998774 68899998743 122333334455554443
Q ss_pred cCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHH
Q 010373 339 ERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLR 418 (512)
Q Consensus 339 ~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~ 418 (512)
.. ....+.+|+|+++++|.|||++|++|||||+++.|+++|... ++| .++||+|.|.|.+..|..++..|++.
T Consensus 118 ~~---~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~-c~p---~stdrv~l~~g~~k~v~~~i~~il~~ 190 (390)
T KOG2192|consen 118 QL---PSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE-CCP---HSTDRVVLIGGKPKRVVECIKIILDL 190 (390)
T ss_pred CC---CCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc-cCC---CCcceEEEecCCcchHHHHHHHHHHH
Confidence 22 245889999999999999999999999999999999999865 666 58999999999999999999999999
Q ss_pred HhhchhcccCcCCCCCCCCcCCCCCCCCCCCCCCCCCC
Q 010373 419 LRANTFEREGALAAHPPVLPYVPMSLDITDGSKYGNRD 456 (512)
Q Consensus 419 l~~~~~~~~~~~~~~~p~~~y~p~~~~~~~~~~yg~~~ 456 (512)
|.+.++ ++...||+|+.+++.+ .||++.
T Consensus 191 i~e~pi--------kgsa~py~p~fyd~t~--dyggf~ 218 (390)
T KOG2192|consen 191 ISESPI--------KGSAQPYDPNFYDETY--DYGGFT 218 (390)
T ss_pred hhcCCc--------CCcCCcCCccccCccc--ccCCce
Confidence 999766 6778899998888753 566543
No 10
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.85 E-value=2e-20 Score=195.27 Aligned_cols=175 Identities=33% Similarity=0.599 Sum_probs=139.3
Q ss_pred ceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEec---------CHHHHHHHHHHHH
Q 010373 140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAG---------EPAVVRKALVQIA 210 (512)
Q Consensus 140 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G---------~~~~V~~A~~~I~ 210 (512)
..++|||++.+.+|.||||+|.+|++|+.+|.++|+|... ++. ..+|+|+|+| ..+++.+|..+|.
T Consensus 42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~--~~~---c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv 116 (485)
T KOG2190|consen 42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNES--LPG---CPERIITITGNRVELNLSPATDALFKAFDMIV 116 (485)
T ss_pred cceEEEEeccccceeEEccCcHHHHHHhhcccccceeecC--CCC---CCcceEEEecccccccCCchHHHHHHHHHHHh
Confidence 3458999999999999999999999999999999999765 455 4799999999 9999999999998
Q ss_pred HHHhcCCCccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhh
Q 010373 211 SRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQE 290 (512)
Q Consensus 211 ~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~ 290 (512)
..++++..... +
T Consensus 117 ~~~~~d~~~~~-------------------------------------------------d------------------- 128 (485)
T KOG2190|consen 117 FKLEEDDEAAE-------------------------------------------------D------------------- 128 (485)
T ss_pred hcccccccccc-------------------------------------------------c-------------------
Confidence 87664211000 0
Q ss_pred cCCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeecCCchhHH
Q 010373 291 SGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIIS 370 (512)
Q Consensus 291 tga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik 370 (512)
.+.+.....++.+|+||.+++|+||||+|++||
T Consensus 129 -----------------------------------------------~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik 161 (485)
T KOG2190|consen 129 -----------------------------------------------NGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIK 161 (485)
T ss_pred -----------------------------------------------CCccccCCceEEEEEechhheeeeeccCcHHHH
Confidence 000001124789999999999999999999999
Q ss_pred HHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhchhcccCcCCCCCCCCcCCC
Q 010373 371 EMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTFEREGALAAHPPVLPYVP 441 (512)
Q Consensus 371 eI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~p~~~y~p 441 (512)
+|++.|||+|+|..+ .+|. .++|.|+|.|.+++|.+|+.+|..+|.++... ..+...-..+|.|
T Consensus 162 ~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av~~al~~Is~~L~~~~~~---~~~~~~st~~y~P 225 (485)
T KOG2190|consen 162 EIREETGAKIRVSSD-MLPN---STERAVTISGEPDAVKKALVQISSRLLENPPR---SPPPLVSTIPYRP 225 (485)
T ss_pred HHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHHHHHHHHHHHHHHhcCCc---CCCCCCCcccCCC
Confidence 999999999999776 7785 68889999999999999999999999996532 1122223356666
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=99.61 E-value=2.1e-15 Score=138.31 Aligned_cols=137 Identities=21% Similarity=0.220 Sum_probs=97.8
Q ss_pred EEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEE---cCCCCcccccCCcccCcHHHHHHHHHHHHH
Q 010373 48 YLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIY---SSSEGTNLFEDSGEFVSPAQDALFRVHDRI 124 (512)
Q Consensus 48 ilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~---G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i 124 (512)
+.||.+.+|.|||++|++|++|+++|+|+|++.+. +..|.|+ ++++. ++.|...|....
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~-------------i~kA~~~I~~i~ 63 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLA-------------VMKAREVVKAIG 63 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHH-------------HHHHHHHHHHHH
Confidence 56899999999999999999999999999999864 4568883 33322 344444443322
Q ss_pred hhhcccCCcc-cCCCcceEEE-EEeeC---------CceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceE
Q 010373 125 VAEDSLADDE-FGELTLITVR-MLVPA---------DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELL 193 (512)
Q Consensus 125 ~~~~~~~~~~-~~~~~~~~~~-llVP~---------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v 193 (512)
....+ ++. ......++.+ +-|+. ..+|+|||++|++++.|++.|||+|.|.. +.|
T Consensus 64 ~gf~~--e~A~~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------------~~v 129 (172)
T TIGR03665 64 RGFSP--EKALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------------KTV 129 (172)
T ss_pred cCCCH--HHHHHhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------------CEE
Confidence 21010 000 0001111222 33333 36899999999999999999999999853 469
Q ss_pred EEecCHHHHHHHHHHHHHHHhcC
Q 010373 194 QVAGEPAVVRKALVQIASRLHEN 216 (512)
Q Consensus 194 ~I~G~~~~V~~A~~~I~~~l~~~ 216 (512)
.|.|++++++.|..+|.+++...
T Consensus 130 ~i~G~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 130 GIIGDPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred EEECCHHHHHHHHHHHHHHHcCC
Confidence 99999999999999999999653
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=99.61 E-value=7e-15 Score=134.79 Aligned_cols=147 Identities=22% Similarity=0.342 Sum_probs=105.6
Q ss_pred EEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEE---ecCHHHHHHHHHHHHHHHhcCCCccc
Q 010373 145 MLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQV---AGEPAVVRKALVQIASRLHENPSRSQ 221 (512)
Q Consensus 145 llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I---~G~~~~V~~A~~~I~~~l~~~~~~~~ 221 (512)
|.||.+.+|.|||++|++|+.|+++|||+|.+..+ +..|.| +++++++.+|..+|..+.........
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~----------~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~A 71 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE----------TGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKA 71 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC----------CceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 57899999999999999999999999999999755 246888 89999999999999987654110000
Q ss_pred cccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCC
Q 010373 222 HLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSG 301 (512)
Q Consensus 222 ~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~ 301 (512)
.. ...+.+..++ +.+.+-
T Consensus 72 ~~---------------------------------l~gd~y~~~V----------------------------i~I~~~- 89 (172)
T TIGR03665 72 LK---------------------------------LLDDDYMLEV----------------------------IDLKEY- 89 (172)
T ss_pred HH---------------------------------hcCCcceEEE----------------------------EEhhhc-
Confidence 00 0000000000 011000
Q ss_pred CCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEE
Q 010373 302 AEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIR 381 (512)
Q Consensus 302 ~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~ 381 (512)
+. ++ ..+ ...+|.|||++|++++.|++.|||+|.
T Consensus 90 ----------~~-------~~----------------------~~~-------~~~~griIG~~G~t~~~ie~~t~~~i~ 123 (172)
T TIGR03665 90 ----------GK-------SP----------------------NAL-------RRIKGRIIGEGGKTRRIIEELTGVSIS 123 (172)
T ss_pred ----------cC-------CH----------------------HHH-------HHHHhhhcCCCcHHHHHHHHHHCCeEE
Confidence 00 00 000 236899999999999999999999999
Q ss_pred EecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010373 382 ILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA 421 (512)
Q Consensus 382 i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~ 421 (512)
|.. ..|.|.|++++++.|..+|.+++..
T Consensus 124 i~~------------~~v~i~G~~~~~~~A~~~i~~li~~ 151 (172)
T TIGR03665 124 VYG------------KTVGIIGDPEQVQIAREAIEMLIEG 151 (172)
T ss_pred EcC------------CEEEEECCHHHHHHHHHHHHHHHcC
Confidence 952 4799999999999999999998854
No 13
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.57 E-value=1.2e-14 Score=134.04 Aligned_cols=141 Identities=20% Similarity=0.155 Sum_probs=100.6
Q ss_pred eEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEE----cCCCCcccccCCcccCcHHHHHHHH
Q 010373 44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIY----SSSEGTNLFEDSGEFVSPAQDALFR 119 (512)
Q Consensus 44 ~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~----G~~e~~~~~~~~~~~~~~a~~a~~~ 119 (512)
+...+.||.+.++.|||++|++|+.|+++|+|+|++.+. +..|.|+ ++++. +..|...
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 567899999999999999999999999999999999865 4678886 33322 3444444
Q ss_pred HHHHHhhhcccCCcc-cCCCcceEEEE-E----ee-----CCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCC
Q 010373 120 VHDRIVAEDSLADDE-FGELTLITVRM-L----VP-----ADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALS 188 (512)
Q Consensus 120 i~~~i~~~~~~~~~~-~~~~~~~~~~l-l----VP-----~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~ 188 (512)
|.+.......+ +. ......+..++ - .+ ...+|+|||++|++++.|++.|||+|.|..+
T Consensus 65 I~ai~~gf~~e--~A~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~~--------- 133 (180)
T PRK13763 65 VKAIGRGFSPE--KALRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYGK--------- 133 (180)
T ss_pred HHHHhcCCCHH--HHHHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcCC---------
Confidence 44332210100 00 00011112221 1 11 1368999999999999999999999999633
Q ss_pred CCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010373 189 FDELLQVAGEPAVVRKALVQIASRLHEN 216 (512)
Q Consensus 189 ~dr~v~I~G~~~~V~~A~~~I~~~l~~~ 216 (512)
.|.|.|++++++.|...|..++...
T Consensus 134 ---~v~i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 134 ---TVAIIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred ---EEEEEeCHHHHHHHHHHHHHHHcCC
Confidence 4999999999999999999999654
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.57 E-value=5e-14 Score=130.04 Aligned_cols=65 Identities=23% Similarity=0.340 Sum_probs=57.6
Q ss_pred eEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEe----cCHHHHHHHHHHHHHHHhc
Q 010373 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVA----GEPAVVRKALVQIASRLHE 215 (512)
Q Consensus 141 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~----G~~~~V~~A~~~I~~~l~~ 215 (512)
+...+.||.+.++.|||++|++|+.|+++|||+|++..+ +..|.|. ++++++.+|..+|..++..
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~----------~g~V~I~~~~~~d~~~i~kA~~~I~ai~~g 71 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE----------TGEVIIEPTDGEDPLAVLKARDIVKAIGRG 71 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC----------CCeEEEEeCCCCCHHHHHHHHHHHHHHhcC
Confidence 367899999999999999999999999999999999755 2468884 8999999999999997764
No 15
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.39 E-value=2.1e-12 Score=131.86 Aligned_cols=175 Identities=24% Similarity=0.354 Sum_probs=129.4
Q ss_pred ccCCCCCcCCCCCCCCCCCCCCCcccCCCCCCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEE
Q 010373 12 RTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIV 91 (512)
Q Consensus 12 r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv 91 (512)
|.||....+++++..+.-.-.--..-....+++..++.+|...+..+|||.|++|+.|++.|++||.+.... -.++++.
T Consensus 36 k~RNdEee~~~~~~~~~~g~~~~~~e~e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~ 114 (608)
T KOG2279|consen 36 KYRNDEEERDSGGQLTFVGIRGQTEEQKPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVL 114 (608)
T ss_pred hhccccccccccccceeeeecccceecCchhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccch
Confidence 345555565666655544322111222356889999999999999999999999999999999999998652 2235666
Q ss_pred EEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcC
Q 010373 92 TIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETR 171 (512)
Q Consensus 92 ~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tg 171 (512)
++.|-+.. ++++..++ +..+. .+..+...+-+|...++.|+|++|+++++|+.-++
T Consensus 115 ~~~~~p~~----------v~~a~a~~---~~~~~-----------~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~ 170 (608)
T KOG2279|consen 115 LISGFPVQ----------VCKAKAAI---HQILT-----------ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSG 170 (608)
T ss_pred hhccCCCC----------CChHHHHH---HHHHh-----------cCCcccccccchhhhcccccccchhhhcchhcccc
Confidence 66554333 55555444 33332 23456778999999999999999999999999999
Q ss_pred ceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010373 172 AQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN 216 (512)
Q Consensus 172 a~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~ 216 (512)
|+|.+.... .| ..+++..|.+...-++.|..++.+.+.++
T Consensus 171 aki~~d~ng---r~--g~~~~~~i~~qqk~~~~a~~~~~~~~~ed 210 (608)
T KOG2279|consen 171 AKITCDKNG---RL--GLSRLIKISGQQKEVAAAKHLILEKVSED 210 (608)
T ss_pred ccccccccc---cc--ccccceecccccchHHHHHhhhhccccch
Confidence 999997662 22 56788899999988999999998888775
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=99.39 E-value=1.1e-12 Score=100.45 Aligned_cols=63 Identities=40% Similarity=0.621 Sum_probs=56.9
Q ss_pred EEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 010373 349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQV 415 (512)
Q Consensus 349 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I 415 (512)
.+|+||.+.+|+|||++|++|++|+++|||+|.+.+... + ..++|.|+|+|+++++..|+.+|
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~-~---~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-P---GSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-C---CCCceEEEEEeCHHHHHHHHHhh
Confidence 689999999999999999999999999999999976432 2 46789999999999999999987
No 17
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.37 E-value=1.4e-12 Score=99.83 Aligned_cols=64 Identities=47% Similarity=0.783 Sum_probs=58.0
Q ss_pred EEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHH
Q 010373 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQI 209 (512)
Q Consensus 142 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I 209 (512)
+++|+||.+.+|+||||+|.+|++|+++|||+|.+.+... + ...+|+|+|+|++++|.+|+.+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~-~---~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-P---GSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-C---CCCceEEEEEeCHHHHHHHHHhh
Confidence 3689999999999999999999999999999999987632 2 36799999999999999999887
No 18
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.24 E-value=1.6e-11 Score=135.77 Aligned_cols=312 Identities=21% Similarity=0.267 Sum_probs=197.3
Q ss_pred CCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCccc-----------ccC-----
Q 010373 42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNL-----------FED----- 105 (512)
Q Consensus 42 ~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~-----------~~~----- 105 (512)
.-+..++.+-...+.+|||++|.+++.++.++.+.|+|+.... ......|.+..+.+.. ++.
T Consensus 199 r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~--~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~ 276 (753)
T KOG2208|consen 199 RSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNK--SSPSNKIDGRLNSSSSINVEIQEALTRLESEFDYD 276 (753)
T ss_pred eeEEEEeeccccchhhhccccccccccccccceeEEEcccccc--cchhhhhccccccceehhhhhHHHHHHhcChhhhh
Confidence 3467889999999999999999999999999999999986522 2223344443332111 000
Q ss_pred --------------CcccCcHHHHHHHHHHHHHhhhcccCC--------cc--------------cCCCcceEEEEEeeC
Q 010373 106 --------------SGEFVSPAQDALFRVHDRIVAEDSLAD--------DE--------------FGELTLITVRMLVPA 149 (512)
Q Consensus 106 --------------~~~~~~~a~~a~~~i~~~i~~~~~~~~--------~~--------------~~~~~~~~~~llVP~ 149 (512)
..+.+....+....+.-.. ......+ +. .-....+.+.+-+-.
T Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~-~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~ 355 (753)
T KOG2208|consen 277 EIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIF-QNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFP 355 (753)
T ss_pred hhhhccccccccccccchhhHHHhhcchhhhhh-ccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecH
Confidence 0001111111100000000 0000000 00 011223677788889
Q ss_pred CceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCCccccccccCCC
Q 010373 150 DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSS 229 (512)
Q Consensus 150 ~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~ 229 (512)
..+..|+||+|.+|.+|++++.|.|.+... .+.+..+.++|...++.+|...|...+.+...
T Consensus 356 ~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~-------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n----------- 417 (753)
T KOG2208|consen 356 EELKFVIGKKGANIEKIREESQVKIDLPKQ-------GSNNKKVVITGVSANDEKAVEDVEKIIAEILN----------- 417 (753)
T ss_pred HhhhhhcCCCCccHHHHHHhhhhceecccc-------cCCCCCeEEeccccchhHHHHHHHHHHHhhhc-----------
Confidence 999999999999999999999999999774 25677899999999999999999998887421
Q ss_pred CccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcC-CeEEecCCCCCCCCeE
Q 010373 230 NIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESG-ASIKVDSSGAEGDDCI 308 (512)
Q Consensus 230 ~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tg-a~I~v~~~~~~~~~~i 308 (512)
......+.+|...+..+||.+|..|+.|..+++ ..|++.......+.-
T Consensus 418 ------------------------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~~~~~~~- 466 (753)
T KOG2208|consen 418 ------------------------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNNNSSDMV- 466 (753)
T ss_pred ------------------------------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCCcccccc-
Confidence 023456899999999999999999999999999 777777655432222
Q ss_pred EEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCC
Q 010373 309 IFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENV 388 (512)
Q Consensus 309 i~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~ 388 (512)
++.+.. .+......-.+.+.... .........+...+.|..+.+..+|+.|..+.. .+...-++..
T Consensus 467 -~~~~~~--~dv~~~~~~~~~~~~~a----~~~~~~~~~~~d~~~~~~~~~~~~g~~~~i~d~----~~~~~i~~~~--- 532 (753)
T KOG2208|consen 467 -TIRGIS--KDVEKSVSLLKALKADA----KNLKFRDVVTKDKLLPVKYIGKEIGKNGTIRDS----LGDKSIFPPN--- 532 (753)
T ss_pred -eEeccc--cccchhHHHHHhhhhhh----hcchhhhhhhccccchHHhhcccccCceeeecc----CCceeecccc---
Confidence 222211 00000111111111000 000111235566778888888888887776654 4444444322
Q ss_pred CCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010373 389 PKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN 422 (512)
Q Consensus 389 p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~ 422 (512)
...++..++|.|..+.|..|.+.+..++...
T Consensus 533 ---~~~~~~~i~i~gk~~~v~~a~~~L~~~~~~~ 563 (753)
T KOG2208|consen 533 ---EDEDHEKITIEGKLELVLEAPAELKALIEAL 563 (753)
T ss_pred ---cccccceeeecccccchhhhHHHHHhcchhh
Confidence 1345668999999999999988888776653
No 19
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.24 E-value=1.1e-11 Score=94.03 Aligned_cols=61 Identities=20% Similarity=0.335 Sum_probs=54.6
Q ss_pred EEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 010373 349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVT 416 (512)
Q Consensus 349 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~ 416 (512)
.+|.||.+++++|||++|++|++|+++|||+|.+++.. +.++.|+|+|++++|..|+.+|+
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 57899999999999999999999999999999996532 45679999999999999988763
No 20
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.21 E-value=8.8e-11 Score=130.01 Aligned_cols=296 Identities=17% Similarity=0.250 Sum_probs=187.1
Q ss_pred CCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHH
Q 010373 42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVH 121 (512)
Q Consensus 42 ~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~ 121 (512)
....+.+-+-...+..|+||+|.+|.+|++++.|+|.++.. +..+..+++++...++ .+|.+.+..+.
T Consensus 345 nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~~~----------~ka~~~v~~~~ 412 (753)
T KOG2208|consen 345 NNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSAND----------EKAVEDVEKII 412 (753)
T ss_pred cceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccccch----------hHHHHHHHHHH
Confidence 33566777788999999999999999999999999999984 5678889999998873 23444444444
Q ss_pred HHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcC-ceEEEeecCCCCcccCCCCceEEEecCHH
Q 010373 122 DRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETR-AQIRILKDEHLPLCALSFDELLQVAGEPA 200 (512)
Q Consensus 122 ~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tg-a~I~i~~~~~~p~~~~~~dr~v~I~G~~~ 200 (512)
..+.. ..+...+.+|...+.+|||.+|..|..|.++++ ..|++.... +....+++.|...
T Consensus 413 ~ei~n------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~-------~~~~~~~~~~~~~ 473 (753)
T KOG2208|consen 413 AEILN------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN-------NSSDMVTIRGISK 473 (753)
T ss_pred Hhhhc------------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC-------cccccceEecccc
Confidence 43321 134567999999999999999999999999999 666665442 2222355555544
Q ss_pred HHHHHHHHHHHHHh------------------------------------------------------------------
Q 010373 201 VVRKALVQIASRLH------------------------------------------------------------------ 214 (512)
Q Consensus 201 ~V~~A~~~I~~~l~------------------------------------------------------------------ 214 (512)
.|.++..+...+..
T Consensus 474 dv~~~~~~~~~~~~~a~~~~~~~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~~~i~~~~~~~~~~~i~i~gk~~~v~~a~ 553 (753)
T KOG2208|consen 474 DVEKSVSLLKALKADAKNLKFRDVVTKDKLLPVKYIGKEIGKNGTIRDSLGDKSIFPPNEDEDHEKITIEGKLELVLEAP 553 (753)
T ss_pred ccchhHHHHHhhhhhhhcchhhhhhhccccchHHhhcccccCceeeeccCCceeecccccccccceeeecccccchhhhH
Confidence 44444333322222
Q ss_pred --------cCCCccc---------c--ccccCC----CCccCCCCcccCCCCcCCCCC----------CCc---c---cC
Q 010373 215 --------ENPSRSQ---------H--LLLSSS----SNIYQSSGVYLSAPLVGSYGN----------YSA---R---RD 255 (512)
Q Consensus 215 --------~~~~~~~---------~--~~~~~~----~~~~~~gg~~~~~p~~~~~~~----------~~~---~---~~ 255 (512)
...+... + ++.... ....-.+|+.+.+|-...... +.+ . -.
T Consensus 554 ~~L~~~~~~~~~~~~~~v~~~~~~~~~~l~~~~~~~~~~~e~~~gv~~~fp~~~~~~~e~~i~g~~~~v~aa~~~~~~i~ 633 (753)
T KOG2208|consen 554 AELKALIEALIKATLLEVNNPPGQHRPFLIGKGIENRTYVEVFGGVVVPFPRSPTSSDEVSIKGAKDEVKAAKGRLEEIV 633 (753)
T ss_pred HHHHhcchhhhhhhhhhccCcchheeeeeeccccccccceeecCcccccCCCCCCchhhhccchhHHHHHHhhccchhhh
Confidence 1100000 0 000000 000011222222222111110 000 0 01
Q ss_pred ccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCccc
Q 010373 256 EASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCS 335 (512)
Q Consensus 256 ~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~ 335 (512)
+......+.++.+|...+..+.|.+|..+++++..+++.+.+++.........+.+.+.. +..+++.-+
T Consensus 634 ~~~~~~~~~~~~i~~~~~~~~~~~~g~~~~~~t~~~~~~~~~~~~~~~~s~~~~~~~~~~------~~~e~~~~~----- 702 (753)
T KOG2208|consen 634 EYLSAYATTNTKIPDKFHRSIVGYRGHIIEEITSKFGVGGYFGDAPTEGSVNTIHVSGEK------MQSEIAKIA----- 702 (753)
T ss_pred hhcccccceeeecccccceeeecCCCcccccceeecCccceeCCCCCccccCcchhhhhh------hhhhhcccc-----
Confidence 123344456699999999999999999999999999999999987644222112222211 111111000
Q ss_pred ccccCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEec
Q 010373 336 EKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILT 384 (512)
Q Consensus 336 ~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~ 384 (512)
......++..+.+|.+++..+||.+|++++.+..++++.+.++.
T Consensus 703 -----~~~~~~~~~~~~~p~~~~~~~ig~~g~~~r~~~~~~~~~~~~~~ 746 (753)
T KOG2208|consen 703 -----LEAKNLVTKEIEIPRSLHRYLIGPKGSNLRQLEKEFNVNIVVPN 746 (753)
T ss_pred -----cccccceeeEEeccHHHhhhccCCCCccHHHHHHHhccceecCC
Confidence 11224578999999999999999999999999999999998864
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=99.21 E-value=5.3e-11 Score=89.68 Aligned_cols=58 Identities=26% Similarity=0.354 Sum_probs=52.5
Q ss_pred eEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcC-HHHHHHHHHHH
Q 010373 347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGS-LDVASSALSQV 415 (512)
Q Consensus 347 ~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~-~~~v~~A~~~I 415 (512)
....|.||.+++|+|||++|++|++|+++|||+|.|.. ++.|.|+|+ +++++.|+.+|
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 45789999999999999999999999999999999952 357999998 99999998887
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=99.21 E-value=1.3e-11 Score=92.91 Aligned_cols=60 Identities=33% Similarity=0.530 Sum_probs=54.0
Q ss_pred EEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 010373 348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQV 415 (512)
Q Consensus 348 t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I 415 (512)
|.+|.||.+++|+|||++|++|++|+++|||+|++++. + +...|+|+|++++|+.|+.+|
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 67899999999999999999999999999999999643 2 345999999999999999876
No 23
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.15 E-value=5.8e-11 Score=90.05 Aligned_cols=60 Identities=28% Similarity=0.369 Sum_probs=54.9
Q ss_pred EEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHH
Q 010373 143 VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQI 209 (512)
Q Consensus 143 ~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I 209 (512)
.+|.||..++++|||++|++|++|+++|||+|.|++.. +.++.|+|+|+.++|.+|+.+|
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 57999999999999999999999999999999998762 4578899999999999999876
No 24
>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=99.15 E-value=3e-11 Score=91.03 Aligned_cols=60 Identities=37% Similarity=0.573 Sum_probs=54.2
Q ss_pred EEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHH
Q 010373 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQI 209 (512)
Q Consensus 142 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I 209 (512)
|.+|.||.+++++|||++|.+|++|+++|||+|.|+++ ..+..|+|+|++++|.+|+++|
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 67899999999999999999999999999999999765 1234899999999999999876
No 25
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.14 E-value=1.7e-10 Score=87.91 Aligned_cols=62 Identities=37% Similarity=0.627 Sum_probs=55.3
Q ss_pred EEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 010373 349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQV 415 (512)
Q Consensus 349 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I 415 (512)
.+|.||.+++++|||++|++|++|+++|||+|.|..... +..++.|+|.|+.+++..|+.+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~-----~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-----GSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC-----CCCceEEEEEcCHHHHHHHHHHh
Confidence 579999999999999999999999999999999975321 35688999999999999998876
No 26
>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=99.09 E-value=4.4e-10 Score=84.70 Aligned_cols=58 Identities=34% Similarity=0.437 Sum_probs=52.3
Q ss_pred eEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecC-HHHHHHHHHHH
Q 010373 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE-PAVVRKALVQI 209 (512)
Q Consensus 141 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~-~~~V~~A~~~I 209 (512)
....|.||.+++++||||+|++|++|+++|||+|.|.+ ++.|.|+|+ +++|++|+.+|
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 35679999999999999999999999999999999864 346999998 99999999876
No 27
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.06 E-value=5.7e-10 Score=85.03 Aligned_cols=62 Identities=40% Similarity=0.629 Sum_probs=55.9
Q ss_pred EEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHH
Q 010373 143 VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQI 209 (512)
Q Consensus 143 ~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I 209 (512)
.+|.||.+++++|||++|++|++|+++|+|+|.|..... ...++.|.|.|+.+++..|+.+|
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 579999999999999999999999999999999987632 25688999999999999998876
No 28
>PF13014 KH_3: KH domain
Probab=98.96 E-value=1.1e-09 Score=76.42 Aligned_cols=42 Identities=48% Similarity=0.823 Sum_probs=38.9
Q ss_pred ceeeeccCCchHHHHHHHhhCCeEEecC-CCCCCCccEEEEEc
Q 010373 54 KIGSIIGKGGEIVKQLRSETKSNIRISE-TVPGCDERIVTIYS 95 (512)
Q Consensus 54 ~~g~IIGk~G~~I~~I~~~tga~I~i~~-~~~~~~ervv~I~G 95 (512)
++|+||||+|++|++|+++|+|+|+|++ ..++..+|+|+|+|
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 4899999999999999999999999998 56788899999987
No 29
>PF13014 KH_3: KH domain
Probab=98.88 E-value=3.5e-09 Score=73.90 Aligned_cols=43 Identities=47% Similarity=0.734 Sum_probs=37.3
Q ss_pred ceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc
Q 010373 357 QIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG 403 (512)
Q Consensus 357 ~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G 403 (512)
+||+|||++|++|++|+++|||+|+|++ +..| .++++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~-~~~~---~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP-ENEP---GSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC-ccCC---CCCceEEEEEC
Confidence 5899999999999999999999999976 2233 47889999998
No 30
>smart00322 KH K homology RNA-binding domain.
Probab=98.85 E-value=1.7e-08 Score=77.34 Aligned_cols=66 Identities=29% Similarity=0.538 Sum_probs=58.6
Q ss_pred eEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 010373 347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRL 419 (512)
Q Consensus 347 ~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l 419 (512)
.+.++.||.++++++||++|++|++|++.||++|.+.... .....|+|.|+++++..|+.+|.+.+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------SEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 5788999999999999999999999999999999995321 24678999999999999999998876
No 31
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.79 E-value=1.5e-07 Score=85.80 Aligned_cols=149 Identities=21% Similarity=0.236 Sum_probs=102.3
Q ss_pred CCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHH
Q 010373 42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVH 121 (512)
Q Consensus 42 ~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~ 121 (512)
......+.||.+..+.+||+.|++.+.|.+.++++|.++.. +..|.|..+..... ++ ....|...|.
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~-----~~~V~i~~~~~t~D-------p~-~~~ka~d~Vk 72 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTED-------PL-ALLKARDVVK 72 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCC-------hH-HHHHHHHHHH
Confidence 44567799999999999999999999999999999999755 77899988732110 01 1122221111
Q ss_pred HHHhhhcccCCccc-CCCcceEEEE-----Eee--C----CceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCC
Q 010373 122 DRIVAEDSLADDEF-GELTLITVRM-----LVP--A----DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSF 189 (512)
Q Consensus 122 ~~i~~~~~~~~~~~-~~~~~~~~~l-----lVP--~----~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~ 189 (512)
.| ...+..+..- -....+.+.+ ++- . ...|+|||++|.+-+.|++-|+|.|.|...
T Consensus 73 -AI-grGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~---------- 140 (194)
T COG1094 73 -AI-GRGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGK---------- 140 (194)
T ss_pred -HH-hcCCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCc----------
Confidence 11 1222221110 0000112211 111 2 246999999999999999999999999755
Q ss_pred CceEEEecCHHHHHHHHHHHHHHHhcCC
Q 010373 190 DELLQVAGEPAVVRKALVQIASRLHENP 217 (512)
Q Consensus 190 dr~v~I~G~~~~V~~A~~~I~~~l~~~~ 217 (512)
.|.|.|.+++|+.|...|..++...+
T Consensus 141 --tVaiiG~~~~v~iAr~AVemli~G~~ 166 (194)
T COG1094 141 --TVAIIGGFEQVEIAREAVEMLINGAP 166 (194)
T ss_pred --EEEEecChhhhHHHHHHHHHHHcCCC
Confidence 69999999999999999999987643
No 32
>smart00322 KH K homology RNA-binding domain.
Probab=98.77 E-value=4.2e-08 Score=75.12 Aligned_cols=66 Identities=39% Similarity=0.664 Sum_probs=59.2
Q ss_pred eEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHH
Q 010373 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRL 213 (512)
Q Consensus 141 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l 213 (512)
.+.++.||...++.|||++|.+|++|++.|+++|.+.... .....|.|.|+.+++..|..+|.+.+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------SEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 5788999999999999999999999999999999997551 24678999999999999999998865
No 33
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.56 E-value=5.1e-07 Score=82.30 Aligned_cols=140 Identities=25% Similarity=0.318 Sum_probs=97.5
Q ss_pred ceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEEecCCcccCCCchhHHH--HHhhCCccccccc
Q 010373 262 FSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITA--ALRLQPRCSEKTE 339 (512)
Q Consensus 262 ~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a--~~~~~~~~~~~~~ 339 (512)
.+..+.+|.+-.+.+||+.|...+.|.+.++++|.++. .+..+.|...+...++.....| .+++..+. +.
T Consensus 8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~-----~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrG---F~ 79 (194)
T COG1094 8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS-----KTGSVTIRTTRKTEDPLALLKARDVVKAIGRG---FP 79 (194)
T ss_pred ceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC-----CCCeEEEEecCCCCChHHHHHHHHHHHHHhcC---CC
Confidence 35679999999999999999999999999999999998 4556677665444444211111 11111111 11
Q ss_pred CCC-----CCceeEEEEEe------c----CCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcC
Q 010373 340 RES-----GDPVITTRILV------P----SAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGS 404 (512)
Q Consensus 340 ~~~-----~~~~~t~~l~V------P----~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~ 404 (512)
++. .+...-..+.+ + ....|+|||++|.+-+-|++.|+|+|.|... +|.|.|.
T Consensus 80 pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~------------tVaiiG~ 147 (194)
T COG1094 80 PEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGK------------TVAIIGG 147 (194)
T ss_pred HHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCc------------EEEEecC
Confidence 000 00111111221 1 2356999999999999999999999999632 8999999
Q ss_pred HHHHHHHHHHHHHHHhh
Q 010373 405 LDVASSALSQVTLRLRA 421 (512)
Q Consensus 405 ~~~v~~A~~~I~~~l~~ 421 (512)
+++|+.|...|..++..
T Consensus 148 ~~~v~iAr~AVemli~G 164 (194)
T COG1094 148 FEQVEIAREAVEMLING 164 (194)
T ss_pred hhhhHHHHHHHHHHHcC
Confidence 99999999998888755
No 34
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=98.45 E-value=2e-07 Score=95.88 Aligned_cols=231 Identities=27% Similarity=0.385 Sum_probs=168.0
Q ss_pred CCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010373 136 GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE 215 (512)
Q Consensus 136 ~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~ 215 (512)
+...++.+++.||...|-+++|+.|.+|+.|+..++++|.+..++ . ..++...+.|.+.+|.+|...+..++.+
T Consensus 63 e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~-----g~e~~~~~~~~p~~v~~a~a~~~~~~~~ 136 (608)
T KOG2279|consen 63 KPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-V-----GDERVLLISGFPVQVCKAKAAIHQILTE 136 (608)
T ss_pred CchhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-C-----CcccchhhccCCCCCChHHHHHHHHHhc
Confidence 344677899999999999999999999999999999999998773 2 3456667777999999999999999987
Q ss_pred CCCccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCeE
Q 010373 216 NPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASI 295 (512)
Q Consensus 216 ~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I 295 (512)
++ .+...+.+|...++.|+|++|.+++.++..++++|
T Consensus 137 ~~-------------------------------------------pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki 173 (608)
T KOG2279|consen 137 NT-------------------------------------------PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKI 173 (608)
T ss_pred CC-------------------------------------------cccccccchhhhcccccccchhhhcchhccccccc
Confidence 42 34567789999999999999999999999999999
Q ss_pred EecCCCCCCCCeEEEecCCcccCCCc--------hhHHHHHhh-----CCcc---------cccc---------------
Q 010373 296 KVDSSGAEGDDCIIFISTKEFFEDPS--------PTITAALRL-----QPRC---------SEKT--------------- 338 (512)
Q Consensus 296 ~v~~~~~~~~~~ii~i~g~~~~~~~~--------~~~~a~~~~-----~~~~---------~~~~--------------- 338 (512)
.++........+++.|.+........ ..-+...+. +.+. .+.+
T Consensus 174 ~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t 253 (608)
T KOG2279|consen 174 TCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNT 253 (608)
T ss_pred ccccccccccccceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccc
Confidence 99998776677777777653211000 000000000 0000 0000
Q ss_pred ----cC-------CC-----------------------CCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEec
Q 010373 339 ----ER-------ES-----------------------GDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILT 384 (512)
Q Consensus 339 ----~~-------~~-----------------------~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~ 384 (512)
.+ +. .....--.|.||..++|.+||+.|+.|+.+...|++.+.|..
T Consensus 254 ~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t 333 (608)
T KOG2279|consen 254 SSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWT 333 (608)
T ss_pred hhccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEe
Confidence 00 00 011123478899999999999999999999999999988853
Q ss_pred CCCCCCCCCC-CceEEEEEcCHHHHHHHHHHHHHH
Q 010373 385 NENVPKVAYE-DEEMVQITGSLDVASSALSQVTLR 418 (512)
Q Consensus 385 ~~~~p~~~~~-~~r~V~I~G~~~~v~~A~~~I~~~ 418 (512)
.|-.... .--++.+.|+..-+..|+.|+..+
T Consensus 334 ---~pyt~~v~~~qic~~egkqh~~n~vl~ml~~~ 365 (608)
T KOG2279|consen 334 ---QPYTSRVLQLQICVNEGKQHYENSVLEMLTVH 365 (608)
T ss_pred ---ccccchhhhhhhheecchhHHHHHHHhhhhcc
Confidence 2321000 113678999999999999998833
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=98.36 E-value=1.5e-06 Score=74.47 Aligned_cols=67 Identities=21% Similarity=0.328 Sum_probs=51.9
Q ss_pred CCceeeeecCCchhHHHHHHHhCCeEEEecCCCC-----------CC-CCCCCceEEEEEcC---HHHHHHHHHHHHHHH
Q 010373 355 SAQIGCLIGRGGAIISEMRSATRASIRILTNENV-----------PK-VAYEDEEMVQITGS---LDVASSALSQVTLRL 419 (512)
Q Consensus 355 ~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~-----------p~-~~~~~~r~V~I~G~---~~~v~~A~~~I~~~l 419 (512)
.+++|.|||++|++||+|+++|||+|.|..+... |. ...++.-.|.|++. .++++.|+.+|..+|
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 4688999999999999999999999999765211 00 01123357899995 599999999999888
Q ss_pred hh
Q 010373 420 RA 421 (512)
Q Consensus 420 ~~ 421 (512)
..
T Consensus 94 ~~ 95 (120)
T cd02395 94 KP 95 (120)
T ss_pred cc
Confidence 74
No 36
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.35 E-value=1.6e-06 Score=74.39 Aligned_cols=73 Identities=23% Similarity=0.396 Sum_probs=55.1
Q ss_pred EEEee------CCceeEEecCCChhHHHHHhhcCceEEEeecCCC-----------Cccc-CCCCceEEEecCH---HHH
Q 010373 144 RMLVP------ADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHL-----------PLCA-LSFDELLQVAGEP---AVV 202 (512)
Q Consensus 144 ~llVP------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~-----------p~~~-~~~dr~v~I~G~~---~~V 202 (512)
+++|| .+.+|.|||++|.+||+|+++|||+|.|..+... |... ...+--|.|++.. +++
T Consensus 3 ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~ 82 (120)
T cd02395 3 KVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEAL 82 (120)
T ss_pred EEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHH
Confidence 45566 4678999999999999999999999999876211 0100 1122458898865 999
Q ss_pred HHHHHHHHHHHhcC
Q 010373 203 RKALVQIASRLHEN 216 (512)
Q Consensus 203 ~~A~~~I~~~l~~~ 216 (512)
.+|+.+|..++...
T Consensus 83 ~~A~~~I~~ll~~~ 96 (120)
T cd02395 83 AKAVEAIEELLKPA 96 (120)
T ss_pred HHHHHHHHHHhccC
Confidence 99999999998864
No 37
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.32 E-value=1.4e-06 Score=83.66 Aligned_cols=136 Identities=22% Similarity=0.334 Sum_probs=103.3
Q ss_pred ccceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccc-
Q 010373 260 REFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKT- 338 (512)
Q Consensus 260 ~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~- 338 (512)
..++..+.+|..+++.|+|++|..||.|+.+|.++|+-+... .+.++.++|.. +.++.+.+..+...+.+
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~---eePiF~vTg~~------edv~~aRrei~saaeH~~ 94 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG---EEPIFPVTGRH------EDVRRARREIPSAAEHFG 94 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC---CCCcceeccCc------hhHHHHhhcCccccceee
Confidence 567888999999999999999999999999999999998866 56888888864 23444444333222211
Q ss_pred ------------cCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHH
Q 010373 339 ------------ERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLD 406 (512)
Q Consensus 339 ------------~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~ 406 (512)
.........+..+.||...+|.|.|..|.+|+.|++.+...|.-+-++ .+-++.++|.+.
T Consensus 95 l~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~--------~~~Vf~Vtg~~~ 166 (394)
T KOG2113|consen 95 LIRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRC--------GEPVFCVTGAPK 166 (394)
T ss_pred eeeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeeccC--------CCceEEEecCCc
Confidence 111123456788999999999999999999999999999998876543 344899999888
Q ss_pred H-HHHHH
Q 010373 407 V-ASSAL 412 (512)
Q Consensus 407 ~-v~~A~ 412 (512)
. +++|.
T Consensus 167 nC~kra~ 173 (394)
T KOG2113|consen 167 NCVKRAR 173 (394)
T ss_pred chhhhcc
Confidence 7 55554
No 38
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.26 E-value=1.8e-06 Score=83.00 Aligned_cols=142 Identities=22% Similarity=0.333 Sum_probs=104.5
Q ss_pred CcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCC
Q 010373 138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENP 217 (512)
Q Consensus 138 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~ 217 (512)
...++..+.||..+++.|.|++|.+||.|+.+|.+.|+-+....+| ++.++|..+.|+.|.+.|...-+.
T Consensus 23 p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~eeP--------iF~vTg~~edv~~aRrei~saaeH-- 92 (394)
T KOG2113|consen 23 GQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEP--------IFPVTGRHEDVRRARREIPSAAEH-- 92 (394)
T ss_pred CCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCCCC--------cceeccCchhHHHHhhcCccccce--
Confidence 3678899999999999999999999999999999999988775444 688999999999999877552211
Q ss_pred CccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEEe
Q 010373 218 SRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKV 297 (512)
Q Consensus 218 ~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v 297 (512)
+-+.-....+. |+. -+|+ ...+....+.+|...++.+.|..|.+|+.+++.++..|.-
T Consensus 93 -----~~l~~~s~s~S-gg~----------~~~s------~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T 150 (394)
T KOG2113|consen 93 -----FGLIRASRSFS-GGT----------NGAS------ASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIAT 150 (394)
T ss_pred -----eeeeeeccccc-CCC----------cccc------ccCCCceeeeccceeeeeccccccCccchheecccceEee
Confidence 11100000000 000 0111 2334456778899999999999999999999999999988
Q ss_pred cCCCCCCCCeEEEecCC
Q 010373 298 DSSGAEGDDCIIFISTK 314 (512)
Q Consensus 298 ~~~~~~~~~~ii~i~g~ 314 (512)
+... .+.++.++|.
T Consensus 151 ~v~~---~~~Vf~Vtg~ 164 (394)
T KOG2113|consen 151 PVRC---GEPVFCVTGA 164 (394)
T ss_pred eccC---CCceEEEecC
Confidence 8766 5567777763
No 39
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.15 E-value=3.9e-06 Score=74.11 Aligned_cols=104 Identities=19% Similarity=0.262 Sum_probs=70.7
Q ss_pred eEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHH
Q 010373 44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDR 123 (512)
Q Consensus 44 ~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~ 123 (512)
-.+.++|+...+|..||++|++|+.|++..|-+|.|-+-. ++ +.+-+..++..
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s--------------~d-------------~~~fI~n~l~P 84 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYS--------------DD-------------PEEFIKNIFAP 84 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcC--------------CC-------------HHHHHHHHcCC
Confidence 4577888999999999999999999999998888874321 11 12222211111
Q ss_pred HhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEe
Q 010373 124 IVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRIL 177 (512)
Q Consensus 124 i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~ 177 (512)
..-....- ........+.+.|+....|.+|||+|++|+.++.-++-.+.|.
T Consensus 85 a~V~~v~I---~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 85 AAVRSVTI---KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred CEEEEEEE---EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 11010000 0112234667889999999999999999999999999887663
No 40
>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=97.94 E-value=3e-05 Score=84.89 Aligned_cols=97 Identities=25% Similarity=0.347 Sum_probs=77.2
Q ss_pred cccCcHHHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCccc
Q 010373 107 GEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCA 186 (512)
Q Consensus 107 ~~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~ 186 (512)
.+.+..|.++...|++.+....... .+-.........+.||.+.++.|||++|.+||.|+++|||+|.|..+
T Consensus 545 ~~aL~~A~~g~~~Il~~m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~------- 616 (719)
T TIGR02696 545 ASALKQARDARLAILDVMAEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDD------- 616 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecC-------
Confidence 4567778888899988776544333 22233445678899999999999999999999999999999999654
Q ss_pred CCCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010373 187 LSFDELLQVAG-EPAVVRKALVQIASRLHE 215 (512)
Q Consensus 187 ~~~dr~v~I~G-~~~~V~~A~~~I~~~l~~ 215 (512)
..|.|.+ +.+.+++|+.+|..++..
T Consensus 617 ----G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 617 ----GTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred ----cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 4688877 588899999999998874
No 41
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.77 E-value=6.2e-05 Score=66.51 Aligned_cols=104 Identities=19% Similarity=0.305 Sum_probs=71.0
Q ss_pred ceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCC
Q 010373 262 FSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERE 341 (512)
Q Consensus 262 ~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~ 341 (512)
-.+-+.++...+|..||++|++|+.|++..|-+|.+-.-+.+ +..-+..++.... + ....-.
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~d----------------~~~fI~n~l~Pa~-V-~~v~I~ 93 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDD----------------PEEFIKNIFAPAA-V-RSVTIK 93 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCCC----------------HHHHHHHHcCCCE-E-EEEEEE
Confidence 356788889999999999999999999999988887653311 1111222211110 0 000000
Q ss_pred CCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEe
Q 010373 342 SGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRIL 383 (512)
Q Consensus 342 ~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~ 383 (512)
.........+.|+.+..|..|||+|++|+.++..++-++.|.
T Consensus 94 ~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 94 KKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred ecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 011224566789999999999999999999999999888773
No 42
>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=97.62 E-value=9.4e-05 Score=65.14 Aligned_cols=103 Identities=22% Similarity=0.243 Sum_probs=68.9
Q ss_pred EEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHH
Q 010373 45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRI 124 (512)
Q Consensus 45 ~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i 124 (512)
.+-++|....+|..||++|++|+.|++..|-+|.|-+- +.++++ .+.+.+
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVey-----------s~D~~~-------------------fI~N~l 83 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEY-----------SENLEE-------------------FVANKL 83 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEc-----------CCCHHH-------------------HHHHcC
Confidence 67788899999999999999999999888888887432 111110 000101
Q ss_pred hhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEe
Q 010373 125 VAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRIL 177 (512)
Q Consensus 125 ~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~ 177 (512)
.......-.-........+.+.||.+..+..|||+|++++...+-++-++.|.
T Consensus 84 ~PA~V~~V~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 84 APAEVKNVTVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred CCceEEEEEEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 10000000000111234677899999999999999999999999998877664
No 43
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.58 E-value=0.00051 Score=70.50 Aligned_cols=76 Identities=17% Similarity=0.314 Sum_probs=58.9
Q ss_pred eeEEEEEec------CCceeeeecCCchhHHHHHHHhCCeEEEecCCC-------------CCCCCCCCceEEEEEc-CH
Q 010373 346 VITTRILVP------SAQIGCLIGRGGAIISEMRSATRASIRILTNEN-------------VPKVAYEDEEMVQITG-SL 405 (512)
Q Consensus 346 ~~t~~l~VP------~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~-------------~p~~~~~~~r~V~I~G-~~ 405 (512)
.++.+|.|| .++||.|||..|.+.|.|+++|||+|.|-.+.. .++ ..++--+.|+. |.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~--~~epLH~~Isadt~ 214 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPK--ENEPLHCLISADTQ 214 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccc--cccceeEEEecchH
Confidence 466778887 468999999999999999999999999976211 111 22334577888 78
Q ss_pred HHHHHHHHHHHHHHhhch
Q 010373 406 DVASSALSQVTLRLRANT 423 (512)
Q Consensus 406 ~~v~~A~~~I~~~l~~~~ 423 (512)
|.|++|+++|..+|.+..
T Consensus 215 eki~~Ai~vienli~~av 232 (554)
T KOG0119|consen 215 EKIKKAIAVIENLIQSAV 232 (554)
T ss_pred HHHHHHHHHHHHHHHhhc
Confidence 899999999999888643
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=97.56 E-value=0.00015 Score=80.70 Aligned_cols=97 Identities=24% Similarity=0.299 Sum_probs=71.7
Q ss_pred ccCcHHHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccC
Q 010373 108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL 187 (512)
Q Consensus 108 ~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 187 (512)
+.+..|.++...|++.+.........+...-......+.||.+.++.|||++|.+||.|+++|||+|.|..+
T Consensus 518 ~al~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd-------- 589 (684)
T TIGR03591 518 QALEQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD-------- 589 (684)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC--------
Confidence 455667777778877665433222222223345577899999999999999999999999999999999654
Q ss_pred CCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010373 188 SFDELLQVAG-EPAVVRKALVQIASRLHE 215 (512)
Q Consensus 188 ~~dr~v~I~G-~~~~V~~A~~~I~~~l~~ 215 (512)
-.|.|.+ ..+.+.+|..+|..+..+
T Consensus 590 ---G~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 590 ---GTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred ---eEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 3567665 577889999998887653
No 45
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.56 E-value=0.00051 Score=70.53 Aligned_cols=79 Identities=16% Similarity=0.230 Sum_probs=58.6
Q ss_pred CCcceEEEEEee------CCceeEEecCCChhHHHHHhhcCceEEEeecC---------CCCccc--CCCCceEEEecC-
Q 010373 137 ELTLITVRMLVP------ADQIGCVIGKGGQVIQNIRTETRAQIRILKDE---------HLPLCA--LSFDELLQVAGE- 198 (512)
Q Consensus 137 ~~~~~~~~llVP------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~---------~~p~~~--~~~dr~v~I~G~- 198 (512)
....++.+|.|| .++||+|||..|.|.|+|+++|||+|.|-... +.+... ...+--|.|+.+
T Consensus 134 ~p~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt 213 (554)
T KOG0119|consen 134 PPAKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADT 213 (554)
T ss_pred cccccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecch
Confidence 333778889998 46799999999999999999999999997621 001111 122233678776
Q ss_pred HHHHHHHHHHHHHHHhc
Q 010373 199 PAVVRKALVQIASRLHE 215 (512)
Q Consensus 199 ~~~V~~A~~~I~~~l~~ 215 (512)
-|.|++|++.|..+|.+
T Consensus 214 ~eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 214 QEKIKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 56689999999999986
No 46
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.54 E-value=0.0002 Score=78.61 Aligned_cols=66 Identities=23% Similarity=0.293 Sum_probs=58.5
Q ss_pred ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhh
Q 010373 345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA 421 (512)
Q Consensus 345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~ 421 (512)
......+.||.+.+|.|||+||.+||+|+++|||+|.|.. +..|.|.+ +.+++++|+.+|...+..
T Consensus 576 aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-----------~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 576 APRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED-----------DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred CCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec-----------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 4567889999999999999999999999999999999942 45888888 788999999999988874
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=97.49 E-value=0.00019 Score=63.21 Aligned_cols=103 Identities=21% Similarity=0.317 Sum_probs=70.7
Q ss_pred eEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCC
Q 010373 263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERES 342 (512)
Q Consensus 263 ~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~ 342 (512)
.+-+.+....+|..||++|++|+.|++..|-+|.+-.-+.+ +..-+.. .+.|.-...+....
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~D----------------~~~fI~N--~l~PA~V~~V~i~~ 95 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSEN----------------LEEFVAN--KLAPAEVKNVTVSE 95 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCC----------------HHHHHHH--cCCCceEEEEEEEc
Confidence 56678888999999999999999999888888877653311 1111111 11111111110000
Q ss_pred CCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEe
Q 010373 343 GDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRIL 383 (512)
Q Consensus 343 ~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~ 383 (512)
.+......+.||.+..+..|||+|++|+...+-++-++.|.
T Consensus 96 ~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 96 FNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred CCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 11235577889999999999999999999999999888773
No 48
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.31 E-value=0.00027 Score=71.22 Aligned_cols=65 Identities=23% Similarity=0.414 Sum_probs=55.4
Q ss_pred CCCCcccCCCCCCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCC
Q 010373 31 GDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSE 98 (512)
Q Consensus 31 ~~~~~~~~~~~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e 98 (512)
.++++......++.++.+.|-+.+||.|||++|+.|+.|+..|+++|+|.+. ..+-.|+|.|..+
T Consensus 34 ~~~~~~~aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~~ 98 (629)
T KOG0336|consen 34 RDSRDSAAAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGINH 98 (629)
T ss_pred CCCCcccccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechHH
Confidence 3455566678899999999999999999999999999999999999999764 3467799999644
No 49
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.22 E-value=0.00039 Score=77.96 Aligned_cols=98 Identities=16% Similarity=0.236 Sum_probs=75.7
Q ss_pred cccCcHHHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCce-EEEeecCCCCcc
Q 010373 107 GEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQ-IRILKDEHLPLC 185 (512)
Q Consensus 107 ~~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~-I~i~~~~~~p~~ 185 (512)
.+.+..|.++...|++.+.+.......+..........|.||.+.++.|||.+|.+||.|.++||++ |.+..+
T Consensus 651 ~eAL~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd------ 724 (891)
T PLN00207 651 ERALLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD------ 724 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC------
Confidence 3556778888888888776544333222233445678899999999999999999999999999999 887543
Q ss_pred cCCCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010373 186 ALSFDELLQVAG-EPAVVRKALVQIASRLHE 215 (512)
Q Consensus 186 ~~~~dr~v~I~G-~~~~V~~A~~~I~~~l~~ 215 (512)
-.|.|.+ +.+.+++|+.+|..++.+
T Consensus 725 -----g~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 725 -----GTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred -----eeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 3577777 688899999999988764
No 50
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=97.04 E-value=0.001 Score=61.62 Aligned_cols=104 Identities=26% Similarity=0.296 Sum_probs=68.1
Q ss_pred EEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHH
Q 010373 45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRI 124 (512)
Q Consensus 45 ~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i 124 (512)
.+-+.+-.+.+|..||++|++|+.|.++.|=+|+|-+-.+ ++++ -+.+|+.
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~-----------d~~~------------fI~nal~------ 127 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSE-----------DPAE------------FIKNALA------ 127 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCC-----------CHHH------------HHHHhcC------
Confidence 3444445577899999999999999999987776643210 0000 0112211
Q ss_pred hhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeec
Q 010373 125 VAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179 (512)
Q Consensus 125 ~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 179 (512)
......-.....+.. .+.+.||.++.+.+|||+|.+++.+.+-||-++.|...
T Consensus 128 -Pa~v~~V~~~~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~ 180 (190)
T COG0195 128 -PAEVLSVNIKEDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI 180 (190)
T ss_pred -cceEeEEEEEeCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence 100000000011111 77889999999999999999999999999999999754
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=97.03 E-value=0.0009 Score=74.49 Aligned_cols=66 Identities=24% Similarity=0.302 Sum_probs=55.8
Q ss_pred ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhh
Q 010373 345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA 421 (512)
Q Consensus 345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~ 421 (512)
.....++.||.+.++.|||++|++||+|+++|||+|.|.. +..|.|.+ ..+.+++|..+|......
T Consensus 549 ~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-----------dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 549 APRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-----------DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred CCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-----------CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 4567889999999999999999999999999999999952 34677776 678899998888877654
No 52
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.97 E-value=0.0014 Score=70.67 Aligned_cols=97 Identities=24% Similarity=0.270 Sum_probs=73.0
Q ss_pred ccCcHHHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccC
Q 010373 108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL 187 (512)
Q Consensus 108 ~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 187 (512)
+.+..|..|...|+..+.+.......+...-..-...+.|+.+.+.-+||++|.+|++|.++|||+|.+..+
T Consensus 519 ~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idiedd-------- 590 (692)
T COG1185 519 KALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD-------- 590 (692)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCC--------
Confidence 456667788888877765433222222222234467789999999999999999999999999999999733
Q ss_pred CCCceEEEecCH-HHHHHHHHHHHHHHhc
Q 010373 188 SFDELLQVAGEP-AVVRKALVQIASRLHE 215 (512)
Q Consensus 188 ~~dr~v~I~G~~-~~V~~A~~~I~~~l~~ 215 (512)
-.|.|.+.. +.+.+|+..|..+..+
T Consensus 591 ---Gtv~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 591 ---GTVKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred ---CcEEEEecchHHHHHHHHHHHHHHhh
Confidence 358888875 7789999999998866
No 53
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.78 E-value=0.0016 Score=65.81 Aligned_cols=72 Identities=22% Similarity=0.365 Sum_probs=59.5
Q ss_pred CCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010373 136 GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE 215 (512)
Q Consensus 136 ~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~ 215 (512)
.....+.+.+.|-+++||.|||++|++|+.|+..|+++|++.+. ..+-.|+|-|...--.+|...|...+..
T Consensus 42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~--------~~e~kv~ifg~~~m~~kaka~id~~~~k 113 (629)
T KOG0336|consen 42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC--------DLEVKVTIFGINHMRKKAKASIDRGQDK 113 (629)
T ss_pred cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc--------CceeEEEEechHHHHHHHHhhHhhhhhh
Confidence 34456788899999999999999999999999999999999876 3455799999888777887766655544
No 54
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.77 E-value=0.003 Score=58.57 Aligned_cols=102 Identities=25% Similarity=0.327 Sum_probs=68.0
Q ss_pred EEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCC
Q 010373 264 LRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESG 343 (512)
Q Consensus 264 ~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~ 343 (512)
+...+-.+.+|..||++|.+|+.|.++-|-+|.+-.-+.+ +.....-.+.+.-...+.-...
T Consensus 78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d------------------~~~fI~nal~Pa~v~~V~~~~~ 139 (190)
T COG0195 78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSED------------------PAEFIKNALAPAEVLSVNIKED 139 (190)
T ss_pred EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCC------------------HHHHHHHhcCcceEeEEEEEeC
Confidence 3445556778999999999999999999977766543211 1111111111111111100000
Q ss_pred CceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEec
Q 010373 344 DPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILT 384 (512)
Q Consensus 344 ~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~ 384 (512)
+.. ...+.||.+..+.+|||+|.+++-+.+-||-++.|..
T Consensus 140 d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 140 DGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred CCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 111 6788899999999999999999999999999999964
No 55
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.75 E-value=0.0015 Score=62.59 Aligned_cols=41 Identities=29% Similarity=0.476 Sum_probs=35.8
Q ss_pred CCCCeEEEEEecCC------ceeeeccCCchHHHHHHHhhCCeEEec
Q 010373 40 GSEDTVYRYLCPLR------KIGSIIGKGGEIVKQLRSETKSNIRIS 80 (512)
Q Consensus 40 ~~~~~~~rilvp~~------~~g~IIGk~G~~I~~I~~~tga~I~i~ 80 (512)
+.-.++.+|+||.+ +||.|+|.+|.++|+|+++|+|+|-|-
T Consensus 88 ~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 88 KPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred CceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 34556679999986 799999999999999999999998774
No 56
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.72 E-value=0.0013 Score=64.61 Aligned_cols=69 Identities=29% Similarity=0.328 Sum_probs=55.1
Q ss_pred CeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHH
Q 010373 43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHD 122 (512)
Q Consensus 43 ~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~ 122 (512)
+....+++++...+.|||++|.|.++|++||+++|.++.+ +.....|+|.|-..++ +..|+.+|..
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 4567799999999999999999999999999999999976 4445567777765543 6677777766
Q ss_pred HHh
Q 010373 123 RIV 125 (512)
Q Consensus 123 ~i~ 125 (512)
.|.
T Consensus 122 ~id 124 (345)
T KOG2814|consen 122 LID 124 (345)
T ss_pred HHH
Confidence 553
No 57
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.71 E-value=0.0015 Score=62.56 Aligned_cols=44 Identities=27% Similarity=0.516 Sum_probs=38.8
Q ss_pred CCCcceEEEEEeeC------CceeEEecCCChhHHHHHhhcCceEEEeec
Q 010373 136 GELTLITVRMLVPA------DQIGCVIGKGGQVIQNIRTETRAQIRILKD 179 (512)
Q Consensus 136 ~~~~~~~~~llVP~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 179 (512)
.....++.+|+||- +.||+|+|.+|.++|+|+++|+|+|.|-..
T Consensus 87 ~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGr 136 (259)
T KOG1588|consen 87 GKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGR 136 (259)
T ss_pred CCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecC
Confidence 45567788999994 489999999999999999999999999765
No 58
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.67 E-value=0.0018 Score=63.69 Aligned_cols=71 Identities=24% Similarity=0.342 Sum_probs=59.0
Q ss_pred ceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010373 140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN 216 (512)
Q Consensus 140 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~ 216 (512)
....-++|++...+.|||++|.+-++|+++|+++|.++.... ..+.++.+.+..++|.+|...|..+|.+.
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~------n~~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT------NKEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC------CcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 456679999999999999999999999999999999987621 33444555567888999999999988775
No 59
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.63 E-value=0.0019 Score=72.19 Aligned_cols=97 Identities=25% Similarity=0.330 Sum_probs=71.2
Q ss_pred ccCcHHHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccC
Q 010373 108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL 187 (512)
Q Consensus 108 ~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 187 (512)
+.+..|.++..+|++.+.........+-.........+.||.+.++.+||++|.+|+.|.++||++|.+..+
T Consensus 521 ~al~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~-------- 592 (693)
T PRK11824 521 EALEQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD-------- 592 (693)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC--------
Confidence 456678888888888776543222222122233455677799999999999999999999999998887433
Q ss_pred CCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010373 188 SFDELLQVAG-EPAVVRKALVQIASRLHE 215 (512)
Q Consensus 188 ~~dr~v~I~G-~~~~V~~A~~~I~~~l~~ 215 (512)
-.|.|.+ ..+.+.+|..+|..+..+
T Consensus 593 ---G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 593 ---GTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred ---ceEEEEcccHHHHHHHHHHHHHhccc
Confidence 3578877 578889999999887753
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=96.55 E-value=0.0037 Score=46.93 Aligned_cols=37 Identities=30% Similarity=0.433 Sum_probs=34.5
Q ss_pred CeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEe
Q 010373 43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRI 79 (512)
Q Consensus 43 ~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i 79 (512)
...+.+.||.+..|.+|||+|.+|+.+++.++-+|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 4688999999999999999999999999999988876
No 61
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.38 E-value=0.0039 Score=70.23 Aligned_cols=67 Identities=18% Similarity=0.252 Sum_probs=57.5
Q ss_pred CceeEEEEEecCCceeeeecCCchhHHHHHHHhCCe-EEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhh
Q 010373 344 DPVITTRILVPSAQIGCLIGRGGAIISEMRSATRAS-IRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA 421 (512)
Q Consensus 344 ~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~-I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~ 421 (512)
.......+.||.+.++.|||.||.+||+|.++||+. |.+. ++-.|.|.+ +.+.+++|+.+|...+.+
T Consensus 682 ~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~-----------ddg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 682 YAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ-----------DDGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred cCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-----------CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 345678899999999999999999999999999999 8873 245788888 788999999998888764
No 62
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.29 E-value=0.0053 Score=66.29 Aligned_cols=69 Identities=25% Similarity=0.286 Sum_probs=58.4
Q ss_pred ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCH-HHHHHHHHHHHHHHhhch
Q 010373 345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSL-DVASSALSQVTLRLRANT 423 (512)
Q Consensus 345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~-~~v~~A~~~I~~~l~~~~ 423 (512)
..-..++.|+.+.++.|||++|.+|++|.++|||+|.|. ++-.|.|.++. +.+..|+..|...+++..
T Consensus 550 aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-----------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~e 618 (692)
T COG1185 550 APRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-----------DDGTVKIAASDGESAKKAKERIEAITREVE 618 (692)
T ss_pred CCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-----------CCCcEEEEecchHHHHHHHHHHHHHHhhcc
Confidence 345678899999999999999999999999999999995 23378888855 789999999999987743
Q ss_pred h
Q 010373 424 F 424 (512)
Q Consensus 424 ~ 424 (512)
.
T Consensus 619 v 619 (692)
T COG1185 619 V 619 (692)
T ss_pred c
Confidence 3
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=96.21 E-value=0.0076 Score=45.21 Aligned_cols=36 Identities=39% Similarity=0.596 Sum_probs=33.6
Q ss_pred eEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEE
Q 010373 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRI 176 (512)
Q Consensus 141 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i 176 (512)
..+.+.||.+.+|.+|||+|.+|+.+++.++-+|.|
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 64
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.14 E-value=0.02 Score=58.38 Aligned_cols=96 Identities=20% Similarity=0.116 Sum_probs=64.0
Q ss_pred CceeeeccCCchHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccC
Q 010373 53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA 131 (512)
Q Consensus 53 ~~~g~IIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~ 131 (512)
+-+|..||++|++|+.|.++. |=+|+|-.-.++.. .+ +.+| +.......
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~---~f--------------------I~Na-------l~Pa~V~~ 300 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPE---IF--------------------IARA-------LAPAIISS 300 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHH---HH--------------------HHHh-------CCCceeeE
Confidence 458999999999999999998 77777743211000 00 0111 10000000
Q ss_pred CcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecC
Q 010373 132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE 180 (512)
Q Consensus 132 ~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~ 180 (512)
-. -....-.+.+.||..+.+..|||+|++++-..+-||.+|.|..-+
T Consensus 301 V~--i~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~ 347 (374)
T PRK12328 301 VK--IEEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG 347 (374)
T ss_pred EE--EcCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence 00 001123678999999999999999999999999999999998754
No 65
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=96.14 E-value=0.012 Score=59.99 Aligned_cols=95 Identities=24% Similarity=0.359 Sum_probs=64.4
Q ss_pred CCCcccccCCCccccchhhhc-CCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCccccccc-CCCCCceeE
Q 010373 271 GNIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTE-RESGDPVIT 348 (512)
Q Consensus 271 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~t 348 (512)
+-+|..||.+|++|+.|.++- |-+|.+-.-+.+ +...-.-.+.|.-...+. .+. ....
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d------------------~~~fi~nal~Pa~v~~v~i~~~--~~~~ 302 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDD------------------PAEFIANALSPAKVISVEVLDE--DKHS 302 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCC------------------HHHHHHHhcCCceEEEEEEEcC--CCcE
Confidence 357999999999999999888 677766543321 111111111111111110 011 1246
Q ss_pred EEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecC
Q 010373 349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTN 385 (512)
Q Consensus 349 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~ 385 (512)
..+.||.+..+..|||+|.+++-..+.||.+|.|.+.
T Consensus 303 ~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~ 339 (341)
T TIGR01953 303 AEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE 339 (341)
T ss_pred EEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence 7899999999999999999999999999999999653
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=96.10 E-value=0.016 Score=58.92 Aligned_cols=96 Identities=22% Similarity=0.304 Sum_probs=63.6
Q ss_pred CceeeeccCCchHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccC
Q 010373 53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA 131 (512)
Q Consensus 53 ~~~g~IIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~ 131 (512)
+-+|..||++|++|+.|.++. |=+|+|-.-..+.. .+ +.+|| .......
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~---~f--------------------i~nal-------~Pa~v~~ 292 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPA---EF--------------------IANAL-------SPAKVIS 292 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHH---HH--------------------HHHhc-------CCceEEE
Confidence 458999999999999999998 77777743210000 00 01111 0000000
Q ss_pred CcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeec
Q 010373 132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179 (512)
Q Consensus 132 ~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 179 (512)
-. -.....-.+.+.||.++.+..|||+|++++-...-||.+|.|...
T Consensus 293 v~-i~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~ 339 (341)
T TIGR01953 293 VE-VLDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE 339 (341)
T ss_pred EE-EEcCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence 00 000011378899999999999999999999999999999999764
No 67
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.10 E-value=0.014 Score=59.49 Aligned_cols=97 Identities=23% Similarity=0.221 Sum_probs=65.5
Q ss_pred CCCcccccCCCccccchhhhc-CCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEE
Q 010373 271 GNIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITT 349 (512)
Q Consensus 271 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~ 349 (512)
+-+|..||.+|.+|+.|.++- |-+|.+-.-+.+ +....+-.+.|.-...+... ......
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D------------------~~~fI~Nal~Pa~V~~V~i~--~~~~~~ 310 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNV------------------PEIFIARALAPAIISSVKIE--EEEKKA 310 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCC------------------HHHHHHHhCCCceeeEEEEc--CCCcEE
Confidence 457999999999999999888 677766543311 11111111111111111111 122467
Q ss_pred EEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCC
Q 010373 350 RILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNEN 387 (512)
Q Consensus 350 ~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~ 387 (512)
.+.||.+..+..|||+|.+++-..+.||.+|.|.+-+.
T Consensus 311 ~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 311 IVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS 348 (374)
T ss_pred EEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence 88999999999999999999999999999999987543
No 68
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.00 E-value=0.017 Score=53.09 Aligned_cols=44 Identities=20% Similarity=0.399 Sum_probs=38.0
Q ss_pred CCCcceEEEEEee------CCceeEEecCCChhHHHHHhhcCceEEEeec
Q 010373 136 GELTLITVRMLVP------ADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179 (512)
Q Consensus 136 ~~~~~~~~~llVP------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 179 (512)
.....++-++.|| .+.||.|||..|.++++|+..|+|+|-|-..
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 4455667788888 5689999999999999999999999999765
No 69
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.96 E-value=0.0092 Score=61.09 Aligned_cols=96 Identities=22% Similarity=0.260 Sum_probs=63.9
Q ss_pred CceeeeccCCchHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccC
Q 010373 53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA 131 (512)
Q Consensus 53 ~~~g~IIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~ 131 (512)
+-+|..||++|+.|+.|.++. |=+|+|-.-..+. .+ .|...+.......
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~---------------------------~~---fi~nal~Pa~v~~ 294 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDP---------------------------AE---FVANALSPAKVVS 294 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCCCH---------------------------HH---HHHHhCCCceEEE
Confidence 458999999999999999998 7788774321100 00 0001010000000
Q ss_pred CcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeec
Q 010373 132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179 (512)
Q Consensus 132 ~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 179 (512)
-. -.....-.+.+.||..+.+..|||+|++++--..-||.+|.|...
T Consensus 295 v~-i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 295 VE-VDDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred EE-EEcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 00 000112368899999999999999999999999999999999876
No 70
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.92 E-value=0.016 Score=56.02 Aligned_cols=64 Identities=17% Similarity=0.264 Sum_probs=52.2
Q ss_pred EEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhhc
Q 010373 348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGS-LDVASSALSQVTLRLRAN 422 (512)
Q Consensus 348 t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~-~~~v~~A~~~I~~~l~~~ 422 (512)
-..+.||.++++.+||++|.+|+.|.+.|++.|.|- .+-.|.|.++ .+++..|+.+|...-++.
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig-----------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG-----------QNGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc-----------CCcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 367889999999999999999999999999999993 2347888885 557888877777655543
No 71
>PRK00468 hypothetical protein; Provisional
Probab=95.82 E-value=0.0089 Score=46.71 Aligned_cols=34 Identities=26% Similarity=0.546 Sum_probs=30.0
Q ss_pred CCCCeEEEEEecCCceeeeccCCchHHHHHHHhh
Q 010373 40 GSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSET 73 (512)
Q Consensus 40 ~~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~t 73 (512)
.++.+.+++.|..+.+|.||||+|.+|+.||.-.
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 3456889999999999999999999999998754
No 72
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.68 E-value=0.021 Score=59.17 Aligned_cols=96 Identities=22% Similarity=0.236 Sum_probs=62.8
Q ss_pred CceeeeccCCchHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccC
Q 010373 53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA 131 (512)
Q Consensus 53 ~~~g~IIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~ 131 (512)
+-+|..||++|+.|+.|.++. |=+|.|-.-.++.. .+ +.+| +.......
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp~---~f--------------------I~Na-------LsPA~V~~ 326 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDPA---TY--------------------IANA-------LSPARVDE 326 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCHH---HH--------------------HHHh-------cCCceeeE
Confidence 458999999999999999998 77777743211000 00 0011 00000000
Q ss_pred CcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeec
Q 010373 132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179 (512)
Q Consensus 132 ~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 179 (512)
-.- .....-.+.+.||.++.+..|||+|++++--..-||.+|.|...
T Consensus 327 V~i-~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s~ 373 (449)
T PRK12329 327 VRL-VDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKDS 373 (449)
T ss_pred EEE-EcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccccH
Confidence 000 00111357899999999999999999999999999999998654
No 73
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.62 E-value=0.022 Score=58.37 Aligned_cols=96 Identities=23% Similarity=0.297 Sum_probs=64.6
Q ss_pred CCCcccccCCCccccchhhhc-CCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEE
Q 010373 271 GNIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITT 349 (512)
Q Consensus 271 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~ 349 (512)
+-+|..||.+|.+|+.|.++. |-+|.+-.-+.+ +...-.-.+.|.-...+... .......
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d------------------~~~fi~nal~Pa~v~~v~i~-~~~~~~~ 305 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSED------------------PAEFVANALSPAKVVSVEVD-DEEEKAA 305 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCCC------------------HHHHHHHhCCCceEEEEEEE-cCCCcEE
Confidence 357999999999999998888 677776543321 11111111111111111000 0122467
Q ss_pred EEEecCCceeeeecCCchhHHHHHHHhCCeEEEecC
Q 010373 350 RILVPSAQIGCLIGRGGAIISEMRSATRASIRILTN 385 (512)
Q Consensus 350 ~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~ 385 (512)
.+.||.+..+..|||+|.+++-..+.||.+|.|.+.
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 899999999999999999999999999999999754
No 74
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.54 E-value=0.032 Score=60.14 Aligned_cols=66 Identities=20% Similarity=0.248 Sum_probs=50.2
Q ss_pred ceeEEEEEecC-CceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHh
Q 010373 345 PVITTRILVPS-AQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLR 420 (512)
Q Consensus 345 ~~~t~~l~VP~-~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~ 420 (512)
...+..|.+|+ ++-|.||||.|.||+-+...||++|.|. + +...|+|++ +|---+.|..-|..++.
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid---d-------tp~~v~ls~fdp~rreia~~~l~~li~ 269 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---D-------TPEAVILSGFDPVRREIARMALEKLIQ 269 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc---C-------CCCeEEecCCchHHHHHHHHHHHHHHH
Confidence 34667788997 6779999999999999999999999994 2 334888999 67555556555444443
No 75
>PRK00106 hypothetical protein; Provisional
Probab=95.53 E-value=0.033 Score=59.91 Aligned_cols=66 Identities=23% Similarity=0.272 Sum_probs=50.7
Q ss_pred ceeEEEEEecC-CceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHh
Q 010373 345 PVITTRILVPS-AQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLR 420 (512)
Q Consensus 345 ~~~t~~l~VP~-~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~ 420 (512)
...+..+.+|+ ++-|.||||-|.+|+-+...||++|.|. ++...|+|++ +|---+.|..-+..++.
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid----------dtp~~v~lS~fdpvRReiAr~~le~Li~ 290 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID----------DTPEVVVLSGFDPIRREIARMTLESLIK 290 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc----------CCCCeEEEeCCChHHHHHHHHHHHHHHH
Confidence 44667788997 6779999999999999999999999994 2334888999 77666666555544443
No 76
>PRK02821 hypothetical protein; Provisional
Probab=95.49 E-value=0.013 Score=45.92 Aligned_cols=35 Identities=20% Similarity=0.400 Sum_probs=30.7
Q ss_pred CCCeEEEEEecCCceeeeccCCchHHHHHHHhhCC
Q 010373 41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKS 75 (512)
Q Consensus 41 ~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga 75 (512)
++.+.++|.|..+.+|.||||+|.+|+.||.--.+
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 45578999999999999999999999999987543
No 77
>PRK12704 phosphodiesterase; Provisional
Probab=95.42 E-value=0.038 Score=59.71 Aligned_cols=65 Identities=20% Similarity=0.231 Sum_probs=48.8
Q ss_pred ceeEEEEEecC-CceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHH
Q 010373 345 PVITTRILVPS-AQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRL 419 (512)
Q Consensus 345 ~~~t~~l~VP~-~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l 419 (512)
...+..+.+|+ ++-|.||||.|.||+-+...||++|.|. + +...|.|+| +|-.-+.|..-+...+
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid---d-------tp~~v~ls~~~~~rre~a~~~l~~l~ 274 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---D-------TPEAVILSGFDPIRREIARLALEKLV 274 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc---C-------CCCeEEEecCChhhHHHHHHHHHHHH
Confidence 34566788897 6779999999999999999999999994 2 334888999 6655445544444333
No 78
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=95.41 E-value=0.25 Score=46.90 Aligned_cols=132 Identities=14% Similarity=0.132 Sum_probs=88.0
Q ss_pred EEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHh
Q 010373 46 YRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIV 125 (512)
Q Consensus 46 ~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~ 125 (512)
+.+.++....-++...+|..++.|-...||+|.+... +..|.|+|+...++. +...+..++..+.
T Consensus 28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~-----~~~i~I~g~k~~~~~----------i~~~i~~~l~~i~ 92 (210)
T PF14611_consen 28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS-----ENRIRITGTKSTAEY----------IEASINEILSNIR 92 (210)
T ss_pred eEEEecchheeeeecCCchHHHHHHHhcCceEEEecC-----CcEEEEEccHHHHHH----------HHHHHHHHHhhcE
Confidence 3445558888999999999999998888999999766 678999998665322 3344444444433
Q ss_pred hhcccCCcccCCCcceEEEEEeeCCceeEEe----cCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEe-----
Q 010373 126 AEDSLADDEFGELTLITVRMLVPADQIGCVI----GKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVA----- 196 (512)
Q Consensus 126 ~~~~~~~~~~~~~~~~~~~llVP~~~vg~II----Gk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~----- 196 (512)
+..|-++.-.--.-. -.....++.|++.|++-|...+++ ..+.|+
T Consensus 93 ----------------~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~~----------~~~~i~~~~~~ 146 (210)
T PF14611_consen 93 ----------------TEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPDG----------NKLKISWLASP 146 (210)
T ss_pred ----------------EEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCCC----------CeEEEEEEeec
Confidence 333444422111111 124678999999999999987652 234444
Q ss_pred cCHHHHHHHHHHHHHHHhcCCC
Q 010373 197 GEPAVVRKALVQIASRLHENPS 218 (512)
Q Consensus 197 G~~~~V~~A~~~I~~~l~~~~~ 218 (512)
-....+..|..++...+..++.
T Consensus 147 ~~~~~~~~a~RlL~~a~~~~~~ 168 (210)
T PF14611_consen 147 ENEKRADRAKRLLLWALDYNPH 168 (210)
T ss_pred cccchHHHHHHHHHHhccCCcc
Confidence 3567788898888887754433
No 79
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.36 E-value=0.039 Score=58.60 Aligned_cols=95 Identities=20% Similarity=0.235 Sum_probs=63.4
Q ss_pred CceeeeccCCchHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccC
Q 010373 53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA 131 (512)
Q Consensus 53 ~~~g~IIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~ 131 (512)
+-+|..||++|++|+.|.++. |=+|.|-.-.++ ...+ +.+| +.......
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d---~~~f--------------------i~na-------l~pa~v~~ 294 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIILWSDD---PAQF--------------------IINA-------LSPAEVSS 294 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEEcCCC---HHHH--------------------HHHh-------CCCCEEEE
Confidence 358999999999999999998 777777432110 0000 0111 11000000
Q ss_pred CcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeec
Q 010373 132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179 (512)
Q Consensus 132 ~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 179 (512)
---+. ..-.+.+.||..+.+..|||+|++++...+-||.+|.|...
T Consensus 295 v~~~~--~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 295 VVVDE--DEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred EEEeC--CCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 00000 11278899999999999999999999999999999999875
No 80
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.35 E-value=0.024 Score=58.73 Aligned_cols=94 Identities=24% Similarity=0.327 Sum_probs=63.3
Q ss_pred CCCcccccCCCccccchhhhc-CCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCccccccc-CCCCCceeE
Q 010373 271 GNIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTE-RESGDPVIT 348 (512)
Q Consensus 271 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~t 348 (512)
+-+|..||.+|.+|+.|.++- |-+|.|-.-+.+ +...-.-.+.+.-...+. .+ .....
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~D------------------p~~fI~NaLsPA~V~~V~i~~--~~~k~ 336 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPD------------------PATYIANALSPARVDEVRLVD--PEGRH 336 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCC------------------HHHHHHHhcCCceeeEEEEEc--CCCcE
Confidence 457999999999999999888 666666543311 111111111111111110 01 11235
Q ss_pred EEEEecCCceeeeecCCchhHHHHHHHhCCeEEEec
Q 010373 349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILT 384 (512)
Q Consensus 349 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~ 384 (512)
..+.||.++.+..|||+|.+|+-..+.||.+|.|..
T Consensus 337 a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 337 AHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred EEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 689999999999999999999999999999999954
No 81
>PRK02821 hypothetical protein; Provisional
Probab=95.18 E-value=0.041 Score=43.20 Aligned_cols=35 Identities=31% Similarity=0.462 Sum_probs=29.6
Q ss_pred CCcceEEEEEeeCCceeEEecCCChhHHHHHhhcC
Q 010373 137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETR 171 (512)
Q Consensus 137 ~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tg 171 (512)
......++|.|..+-+|.||||+|.+|+.||.--.
T Consensus 27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 34457889999999999999999999999996533
No 82
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=95.09 E-value=0.068 Score=56.29 Aligned_cols=114 Identities=17% Similarity=0.211 Sum_probs=80.1
Q ss_pred EEEEcCCCCcccccCC----cccCcHHHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHH
Q 010373 91 VTIYSSSEGTNLFEDS----GEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNI 166 (512)
Q Consensus 91 v~I~G~~e~~~~~~~~----~~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I 166 (512)
..|.|+.+.+-++.-+ .+.+.+|.+|...|++.+..........+.....+...|.|+.+....+||.+|...|+|
T Consensus 543 FKiAGt~dGvTA~gi~l~Iv~eal~~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki 622 (760)
T KOG1067|consen 543 FKIAGTNDGVTALGIPLKIVMEALQKAREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKI 622 (760)
T ss_pred eeeccccCcceecCCcHHHHHHHHHhhhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeE
Confidence 3455555555443221 255667778888888877654433333345556778889999999999999999999999
Q ss_pred HhhcCceEEEeecCCCCcccCCCCceEEEec-CHHHHHHHHHHHHHHHhcC
Q 010373 167 RTETRAQIRILKDEHLPLCALSFDELLQVAG-EPAVVRKALVQIASRLHEN 216 (512)
Q Consensus 167 ~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G-~~~~V~~A~~~I~~~l~~~ 216 (512)
+.|||+.-.+. +..+.|-- ++.+.++|...|..++..+
T Consensus 623 ~~EtGai~~vD------------e~t~~i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 623 EVETGAISQVD------------EGTFSIFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred eeeccceeeec------------CceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence 99999655443 22455544 5677899999999988764
No 83
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.05 E-value=0.037 Score=58.74 Aligned_cols=94 Identities=22% Similarity=0.319 Sum_probs=63.9
Q ss_pred CCcccccCCCccccchhhhc-CCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEE
Q 010373 272 NIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTR 350 (512)
Q Consensus 272 ~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~ 350 (512)
-+|..||.+|++|+.|..+- |-+|.|-.-+.+ +...-.-.+.+.-...+..+. ..-...
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d------------------~~~fi~nal~pa~v~~v~~~~--~~~~~~ 305 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIILWSDD------------------PAQFIINALSPAEVSSVVVDE--DEHSAD 305 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEEcCCC------------------HHHHHHHhCCCCEEEEEEEeC--CCCEEE
Confidence 47999999999999999888 677766543311 111111111111111110011 123778
Q ss_pred EEecCCceeeeecCCchhHHHHHHHhCCeEEEecC
Q 010373 351 ILVPSAQIGCLIGRGGAIISEMRSATRASIRILTN 385 (512)
Q Consensus 351 l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~ 385 (512)
+.||.+..+..|||+|.+|+-..+.||.+|.|...
T Consensus 306 v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 306 VVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred EEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 99999999999999999999999999999999764
No 84
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.05 E-value=0.022 Score=44.35 Aligned_cols=33 Identities=18% Similarity=0.391 Sum_probs=29.9
Q ss_pred CCCeEEEEEecCCceeeeccCCchHHHHHHHhh
Q 010373 41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSET 73 (512)
Q Consensus 41 ~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~t 73 (512)
+..+.+++.+..+.+|.||||+|.+|+.||.--
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 567789999999999999999999999998754
No 85
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=95.04 E-value=0.47 Score=44.97 Aligned_cols=87 Identities=11% Similarity=0.210 Sum_probs=64.8
Q ss_pred HHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEE
Q 010373 115 DALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQ 194 (512)
Q Consensus 115 ~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~ 194 (512)
..+.+|+..+..-...+..+ ..-.+.+.++....-.|...+|..++.|-...||+|.+..+ +..|.
T Consensus 4 ~l~~~Il~d~W~l~v~e~v~----~~g~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~----------~~~i~ 69 (210)
T PF14611_consen 4 KLAERILRDCWNLEVSEEVD----ELGDLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS----------ENRIR 69 (210)
T ss_pred HHHHHHHHHhcCCcccceee----ccceeEEEecchheeeeecCCchHHHHHHHhcCceEEEecC----------CcEEE
Confidence 34556666666544332211 11134455568888999999999999999999999999765 45799
Q ss_pred EecCHHHHHHHHHHHHHHHhc
Q 010373 195 VAGEPAVVRKALVQIASRLHE 215 (512)
Q Consensus 195 I~G~~~~V~~A~~~I~~~l~~ 215 (512)
|+|+...++.+...|.+++..
T Consensus 70 I~g~k~~~~~i~~~i~~~l~~ 90 (210)
T PF14611_consen 70 ITGTKSTAEYIEASINEILSN 90 (210)
T ss_pred EEccHHHHHHHHHHHHHHHhh
Confidence 999999999999999998876
No 86
>PRK00468 hypothetical protein; Provisional
Probab=94.89 E-value=0.028 Score=43.89 Aligned_cols=34 Identities=29% Similarity=0.490 Sum_probs=29.6
Q ss_pred CCCcceEEEEEeeCCceeEEecCCChhHHHHHhh
Q 010373 136 GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTE 169 (512)
Q Consensus 136 ~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~ 169 (512)
.....+.++|.+..+-+|.||||+|.+|+.||.-
T Consensus 25 ~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 25 EGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred eCCCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence 3445578999999999999999999999999964
No 87
>PRK01064 hypothetical protein; Provisional
Probab=94.82 E-value=0.032 Score=43.93 Aligned_cols=33 Identities=30% Similarity=0.548 Sum_probs=29.8
Q ss_pred CCCeEEEEEecCCceeeeccCCchHHHHHHHhh
Q 010373 41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSET 73 (512)
Q Consensus 41 ~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~t 73 (512)
...+.+++.|.....|.+|||+|.+|+.||.-.
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 466889999999999999999999999998754
No 88
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=94.77 E-value=0.047 Score=52.80 Aligned_cols=62 Identities=21% Similarity=0.241 Sum_probs=51.0
Q ss_pred EEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHH-HHHHHHHHHHHHHhc
Q 010373 143 VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA-VVRKALVQIASRLHE 215 (512)
Q Consensus 143 ~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~-~V~~A~~~I~~~l~~ 215 (512)
+.+.||.+.++.|||++|.+|+.|.++|+++|.+-.+ -.|.|.+... ++.+|..+|..+-++
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N-----------G~VwI~~~~~~~~~~a~~~I~~~e~~ 209 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN-----------GRIWIKGPDEEDEEIAIEAIKKIERE 209 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC-----------cEEEEeeCCHHHHHHHHHHHHHHHhh
Confidence 4588999999999999999999999999999998543 3688888755 788888888765544
No 89
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=94.72 E-value=0.063 Score=49.36 Aligned_cols=40 Identities=30% Similarity=0.528 Sum_probs=34.3
Q ss_pred eeEEEEEec------CCceeeeecCCchhHHHHHHHhCCeEEEecC
Q 010373 346 VITTRILVP------SAQIGCLIGRGGAIISEMRSATRASIRILTN 385 (512)
Q Consensus 346 ~~t~~l~VP------~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~ 385 (512)
.++..+.|| .++||.|||..|.++++|++.|+|+|-|-.+
T Consensus 147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 455667776 5789999999999999999999999999654
No 90
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=94.63 E-value=0.026 Score=63.12 Aligned_cols=65 Identities=28% Similarity=0.341 Sum_probs=54.6
Q ss_pred eeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhh
Q 010373 346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA 421 (512)
Q Consensus 346 ~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~ 421 (512)
.....+.||.+.++.+||.||.+||+|.++||+.|.+. ++-.|.|.+ ..+.+++|+.+|......
T Consensus 553 p~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-----------d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 553 PRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-----------DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred chheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 44567888999999999999999999999999988772 234788888 788999999998887754
No 91
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=94.61 E-value=0.075 Score=57.33 Aligned_cols=52 Identities=27% Similarity=0.314 Sum_probs=43.9
Q ss_pred CCCCCeEEEEEecC-CceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEc
Q 010373 39 IGSEDTVYRYLCPL-RKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYS 95 (512)
Q Consensus 39 ~~~~~~~~rilvp~-~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G 95 (512)
...+.++-.+-+|+ ++-|.||||.|.||+.++.-||+.|-|+++ ..+|+|+|
T Consensus 199 ~~~e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt-----p~~v~ls~ 251 (514)
T TIGR03319 199 HVAETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT-----PEAVILSG 251 (514)
T ss_pred hhhhheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC-----CCeEEecC
Confidence 34567777888998 678999999999999999999999999876 34577877
No 92
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.59 E-value=0.041 Score=42.90 Aligned_cols=34 Identities=38% Similarity=0.561 Sum_probs=30.2
Q ss_pred CCCcceEEEEEeeCCceeEEecCCChhHHHHHhh
Q 010373 136 GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTE 169 (512)
Q Consensus 136 ~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~ 169 (512)
..+..++++|.+...-+|.||||+|.+|+.||.-
T Consensus 25 ~~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 25 EGEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred ecCCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 3466788999999999999999999999999954
No 93
>PRK00106 hypothetical protein; Provisional
Probab=94.56 E-value=0.082 Score=56.89 Aligned_cols=52 Identities=27% Similarity=0.373 Sum_probs=44.1
Q ss_pred CCCCCeEEEEEecC-CceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEc
Q 010373 39 IGSEDTVYRYLCPL-RKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYS 95 (512)
Q Consensus 39 ~~~~~~~~rilvp~-~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G 95 (512)
...+.++-.+.+|+ ++-|.||||-|.||+.++.-||+.|-|+++ ...|+|+|
T Consensus 220 ~~~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt-----p~~v~lS~ 272 (535)
T PRK00106 220 YVTEQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDT-----PEVVVLSG 272 (535)
T ss_pred hhhhheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCC-----CCeEEEeC
Confidence 34567778888998 688999999999999999999999999876 34577877
No 94
>PRK01064 hypothetical protein; Provisional
Probab=94.08 E-value=0.07 Score=41.99 Aligned_cols=34 Identities=35% Similarity=0.477 Sum_probs=29.8
Q ss_pred CCCcceEEEEEeeCCceeEEecCCChhHHHHHhh
Q 010373 136 GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTE 169 (512)
Q Consensus 136 ~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~ 169 (512)
.....+.+++.|...-.|.+|||+|.+|+.||.-
T Consensus 25 ~~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 25 QGTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred eCCCEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence 3456688999999999999999999999999964
No 95
>PRK12704 phosphodiesterase; Provisional
Probab=93.98 E-value=0.2 Score=54.23 Aligned_cols=64 Identities=22% Similarity=0.348 Sum_probs=47.3
Q ss_pred EEEEEeeC-CceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecC-HHHHHHHHHHHHHHHhc
Q 010373 142 TVRMLVPA-DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE-PAVVRKALVQIASRLHE 215 (512)
Q Consensus 142 ~~~llVP~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~-~~~V~~A~~~I~~~l~~ 215 (512)
.-.+.+|+ ++.|+|||+.|.+|+.++.-||+.|.|.+. | ..|.|+|. +-.-+.|...+..++.+
T Consensus 211 ~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt---p-------~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 211 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT---P-------EAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred eeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC---C-------CeEEEecCChhhHHHHHHHHHHHHhc
Confidence 33466776 689999999999999999999999999543 3 36889983 44434566566555544
No 96
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=92.77 E-value=0.061 Score=41.85 Aligned_cols=35 Identities=17% Similarity=0.230 Sum_probs=30.3
Q ss_pred CCCeEEEEEecCCceeeeccCCchHHHHHHHhhCC
Q 010373 41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKS 75 (512)
Q Consensus 41 ~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga 75 (512)
.+...+.+.|..+..|.||||.|.+++.||.-.+.
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 46678889999999999999999999999876543
No 97
>PRK12705 hypothetical protein; Provisional
Probab=92.06 E-value=0.17 Score=54.15 Aligned_cols=39 Identities=28% Similarity=0.379 Sum_probs=33.8
Q ss_pred ceeEEEEEecC-CceeeeecCCchhHHHHHHHhCCeEEEe
Q 010373 345 PVITTRILVPS-AQIGCLIGRGGAIISEMRSATRASIRIL 383 (512)
Q Consensus 345 ~~~t~~l~VP~-~~vG~IIGkgG~~IkeI~~~TGa~I~i~ 383 (512)
......+.+|. ++-|.||||-|.+|+-+...||+.|.|.
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid 235 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID 235 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEec
Confidence 34566788886 5669999999999999999999999995
No 98
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=92.02 E-value=0.34 Score=44.44 Aligned_cols=56 Identities=25% Similarity=0.354 Sum_probs=50.2
Q ss_pred CCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010373 149 ADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN 216 (512)
Q Consensus 149 ~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~ 216 (512)
+..+|+|+||+|.+=-.|++-|.++|.+... .|.|-|..+++.-|...|+.++.-.
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad~------------kIHiLG~~~niriAR~avcsLIlGs 232 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLADS------------KIHILGAFQNIRIARDAVCSLILGS 232 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecCc------------eEEEeecchhhHHHHHhhHhhhccC
Confidence 4568999999999999999999999998643 5999999999999999999999764
No 99
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=91.32 E-value=0.78 Score=51.40 Aligned_cols=28 Identities=11% Similarity=0.222 Sum_probs=14.9
Q ss_pred EEEEEecCCceeeeecCCchhHHHHHHH
Q 010373 348 TTRILVPSAQIGCLIGRGGAIISEMRSA 375 (512)
Q Consensus 348 t~~l~VP~~~vG~IIGkgG~~IkeI~~~ 375 (512)
...|.|..+.+.||+|-.-+.=.-+.+.
T Consensus 1085 WIklqIshEaAAcItgLr~AmEaLvvev 1112 (1282)
T KOG0921|consen 1085 WIKLQISHEAAACITGLRPAMEALVVEV 1112 (1282)
T ss_pred eeeEeccHHHHHHHhhhHHHHHHHHHHH
Confidence 3455566666666666555443333333
No 100
>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=90.85 E-value=1.5 Score=38.63 Aligned_cols=93 Identities=24% Similarity=0.373 Sum_probs=60.5
Q ss_pred CCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccCCcccCCCcc
Q 010373 61 KGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTL 140 (512)
Q Consensus 61 k~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~ 140 (512)
..+..|++|-++..-+|.|-.+ +.. +.+-.+|...|.+.+-++. .-.+-.. +.
T Consensus 23 ~~~dli~~lAk~lrKRIvvR~d--------------ps~----------l~~~e~A~~~I~~ivP~ea-~i~di~F--d~ 75 (145)
T cd02410 23 EDGDLVKDLAKDLRKRIVIRPD--------------PSV----------LKPPEEAIKIILEIVPEEA-GITDIYF--DD 75 (145)
T ss_pred cccHHHHHHHHHHhceEEEcCC--------------hhh----------cCCHHHHHHHHHHhCCCcc-CceeeEe--cC
Confidence 4678899999998777777432 111 1123456666665443221 1000000 11
Q ss_pred eEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecC
Q 010373 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE 180 (512)
Q Consensus 141 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~ 180 (512)
.+-++.|-...-|.+|||+|.++++|..+||-+-.|....
T Consensus 76 ~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtp 115 (145)
T cd02410 76 DTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTP 115 (145)
T ss_pred CCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecC
Confidence 1456778888889999999999999999999999998763
No 101
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=90.59 E-value=0.64 Score=48.70 Aligned_cols=204 Identities=14% Similarity=0.142 Sum_probs=125.4
Q ss_pred eeccCCchHHHHHHHhhCCeEEe--cCCCCCCCccEEEE-EcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccCCc
Q 010373 57 SIIGKGGEIVKQLRSETKSNIRI--SETVPGCDERIVTI-YSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADD 133 (512)
Q Consensus 57 ~IIGk~G~~I~~I~~~tga~I~i--~~~~~~~~ervv~I-~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~~~ 133 (512)
+|=||+--.+.+|++...|.+.+ .+.. | .++.++ .|..-. + ++++ ..+
T Consensus 393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~~-g--s~~~~~~~g~~~~----------F---~k~~----~~~--------- 443 (657)
T COG5166 393 FLRGKKNGKATRIMKGVSCSELSSIVSST-G--SIVETNGIGEKMS----------F---SKKL----SIP--------- 443 (657)
T ss_pred HhccccCcchhhhhhhcccceeeEEEecC-C--cEEEEeccCcchh----------h---HHHh----cCC---------
Confidence 67787766699999999888544 3321 1 233333 221100 1 1221 111
Q ss_pred ccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHH
Q 010373 134 EFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRL 213 (512)
Q Consensus 134 ~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l 213 (512)
..+..-++.+.||...|..|||.||..|++++...++.|++...-.+|. + ..
T Consensus 444 --~~EFpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~q----------------s----------~~ 495 (657)
T COG5166 444 --PTEFPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQ----------------S----------QW 495 (657)
T ss_pred --cccCchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcch----------------h----------hh
Confidence 1112235679999999999999999999999999999888865433332 0 12
Q ss_pred hcCCCccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhc--
Q 010373 214 HENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQES-- 291 (512)
Q Consensus 214 ~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~t-- 291 (512)
++ .+-+.+|.+..+.|+|++......+++..
T Consensus 496 ~d-----------------------------------------------NV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f 528 (657)
T COG5166 496 HD-----------------------------------------------NVLIEAPRKNQDNISGKKNDKLDKVKQQCRF 528 (657)
T ss_pred hc-----------------------------------------------ceEEECCccCccchhcccccHHHHHhhhccc
Confidence 22 14567899999999999888777777554
Q ss_pred --CCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeec---CCc
Q 010373 292 --GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIG---RGG 366 (512)
Q Consensus 292 --ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIG---kgG 366 (512)
...|.|.+. ..+++++-+-. ..++.+.+- ..+ .........+.+|.+.++.-+| -.|
T Consensus 529 ~~Kgdirf~~~----~~sI~~v~~~~------~~I~rv~kn-e~v-------~~~~p~~~~~y~~se~h~~g~gena~R~ 590 (657)
T COG5166 529 NLKGDIRFCPQ----STSIFTVDIYS------DEIERVIKN-ETV-------LLEFPAEMHFYVPSEIHKKGIGENAFRG 590 (657)
T ss_pred ccccceEEcCC----ceEEEEEcccc------cHHHHHhhc-cce-------EEecccccccccchhhhhccCCcccccc
Confidence 344555543 33466665532 234433331 111 0112355678899999999999 677
Q ss_pred hhHHHHHHHhCCeEEE
Q 010373 367 AIISEMRSATRASIRI 382 (512)
Q Consensus 367 ~~IkeI~~~TGa~I~i 382 (512)
++|..+.....-.|..
T Consensus 591 ~ni~~~t~~y~~~ie~ 606 (657)
T COG5166 591 ENIQRVTKLYNSYIEF 606 (657)
T ss_pred cchhhhhhhhhcccee
Confidence 8877777665555554
No 102
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=90.25 E-value=0.079 Score=59.96 Aligned_cols=69 Identities=22% Similarity=0.183 Sum_probs=57.2
Q ss_pred EEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010373 349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA 421 (512)
Q Consensus 349 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~ 421 (512)
-.+.+|.....+|||++|++|+-+|..|||.|.|..- -|. ...+|.+.+.|+++.++.|...|...+.+
T Consensus 1342 ~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekm--q~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1342 GKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKM--QPD--NQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred cccccchhhhhhhhccCcchhhhHhhccceEEehhhc--CCc--cchhhhcccCCCChhhhhhhccccceeec
Confidence 4577888889999999999999999999999999642 121 25689999999999999998877766654
No 103
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=90.18 E-value=0.41 Score=35.94 Aligned_cols=35 Identities=17% Similarity=0.245 Sum_probs=28.5
Q ss_pred CeEEEEEecCCceeeeccCCchHHHHHHHhhCCeE
Q 010373 43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNI 77 (512)
Q Consensus 43 ~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I 77 (512)
.....+.+.....|.+|||+|.+|++|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 45566666666789999999999999999997554
No 104
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=88.63 E-value=0.72 Score=34.54 Aligned_cols=35 Identities=31% Similarity=0.440 Sum_probs=28.5
Q ss_pred ceEEEEEeeCCceeEEecCCChhHHHHHhhcCceE
Q 010373 140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQI 174 (512)
Q Consensus 140 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I 174 (512)
...+.+.+.....|.+|||+|++|+.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 35666777766789999999999999999988544
No 105
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=88.56 E-value=0.19 Score=38.99 Aligned_cols=33 Identities=18% Similarity=0.300 Sum_probs=27.9
Q ss_pred cceEEEEEeeCCceeEEecCCChhHHHHHhhcC
Q 010373 139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETR 171 (512)
Q Consensus 139 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tg 171 (512)
....+.+-+..+..|.||||+|.+++.||--.+
T Consensus 27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred CceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence 344778888999999999999999999996544
No 106
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=88.49 E-value=0.81 Score=47.67 Aligned_cols=39 Identities=33% Similarity=0.436 Sum_probs=36.1
Q ss_pred EEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecC
Q 010373 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE 180 (512)
Q Consensus 142 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~ 180 (512)
.+.+.||...++.+|||+|.+|++|++..|-+|.|...+
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 577899999999999999999999999999999998763
No 107
>PRK12705 hypothetical protein; Provisional
Probab=88.24 E-value=0.37 Score=51.68 Aligned_cols=53 Identities=26% Similarity=0.317 Sum_probs=42.7
Q ss_pred CCCCCCeEEEEEecC-CceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEc
Q 010373 38 GIGSEDTVYRYLCPL-RKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYS 95 (512)
Q Consensus 38 ~~~~~~~~~rilvp~-~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G 95 (512)
....+.++-.+.+|+ ++-|.||||.|.+|+.++..||+.|-|++. .++|+|.+
T Consensus 192 ~~~~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt-----p~~V~ls~ 245 (508)
T PRK12705 192 ETASDLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT-----PEAVVISS 245 (508)
T ss_pred chhhhheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC-----ccchhhcc
Confidence 334566777788887 678999999999999999999999999876 33455655
No 108
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=88.10 E-value=1.2 Score=46.71 Aligned_cols=156 Identities=13% Similarity=0.096 Sum_probs=103.2
Q ss_pred EEecCCChhHHHHHhhcCceEEE--eecCCCCcccCCCCceE-EEecCHHHHHHHHHHHHHHHhcCCCccccccccCCCC
Q 010373 154 CVIGKGGQVIQNIRTETRAQIRI--LKDEHLPLCALSFDELL-QVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSN 230 (512)
Q Consensus 154 ~IIGk~G~~Ik~I~~~tga~I~i--~~~~~~p~~~~~~dr~v-~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~ 230 (512)
+|=||+--.+.+|++..-|-+.+ ..++ ..++. .+.|..-+-.+++..+.. +
T Consensus 393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~~--------gs~~~~~~~g~~~~F~k~~~~~~~---E--------------- 446 (657)
T COG5166 393 FLRGKKNGKATRIMKGVSCSELSSIVSST--------GSIVETNGIGEKMSFSKKLSIPPT---E--------------- 446 (657)
T ss_pred HhccccCcchhhhhhhcccceeeEEEecC--------CcEEEEeccCcchhhHHHhcCCcc---c---------------
Confidence 56677766688999888887443 3331 11222 256666666666543321 1
Q ss_pred ccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEE
Q 010373 231 IYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIF 310 (512)
Q Consensus 231 ~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~ 310 (512)
|+ -.+.+.||...|..|||.||..|++.+.+.++.|++...-.-
T Consensus 447 -Fp----------------------------ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~------- 490 (657)
T COG5166 447 -FP----------------------------AEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKF------- 490 (657)
T ss_pred -Cc----------------------------hheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhc-------
Confidence 11 145788999999999999999999999999998887652200
Q ss_pred ecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHh----CCeEEEecCC
Q 010373 311 ISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSAT----RASIRILTNE 386 (512)
Q Consensus 311 i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~T----Ga~I~i~~~~ 386 (512)
. + .+ .....-+..|..-.+.|+|++......+++.. ...|++.+
T Consensus 491 ---------~--q--s~-----------------~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~~Kgdirf~~-- 538 (657)
T COG5166 491 ---------G--Q--SQ-----------------WHDNVLIEAPRKNQDNISGKKNDKLDKVKQQCRFNLKGDIRFCP-- 538 (657)
T ss_pred ---------c--h--hh-----------------hhcceEEECCccCccchhcccccHHHHHhhhcccccccceEEcC--
Confidence 0 0 00 01224577899999999999999988888665 56677742
Q ss_pred CCCCCCCCCceEEEEEcCHHHHHH
Q 010373 387 NVPKVAYEDEEMVQITGSLDVASS 410 (512)
Q Consensus 387 ~~p~~~~~~~r~V~I~G~~~~v~~ 410 (512)
...+.+++-|-.+-+..
T Consensus 539 -------~~~sI~~v~~~~~~I~r 555 (657)
T COG5166 539 -------QSTSIFTVDIYSDEIER 555 (657)
T ss_pred -------CceEEEEEcccccHHHH
Confidence 23447887776655544
No 109
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=87.87 E-value=1.8 Score=45.54 Aligned_cols=128 Identities=22% Similarity=0.376 Sum_probs=79.2
Q ss_pred eeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccCCcccC
Q 010373 57 SIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFG 136 (512)
Q Consensus 57 ~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~~~~~~ 136 (512)
.++=+.|..|++|-++..-+|.|-.+. .+ +.+..+|...|++.+-++.--.+ .
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~dP--------sv----------------l~~~e~A~~~I~eivP~ea~i~~-i-- 94 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPDP--------SV----------------LKPPEEARKIILEIVPEEAGITD-I-- 94 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccCc--------hh----------------cCCHHHHHHHHHHhCccccCcee-E--
Confidence 345578899999999998888775431 11 22246677777765533321111 0
Q ss_pred CCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEE----EecCHHHHHHHHHHHHHH
Q 010373 137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQ----VAGEPAVVRKALVQIASR 212 (512)
Q Consensus 137 ~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~----I~G~~~~V~~A~~~I~~~ 212 (512)
.=...+-+++|-.+.-|.+|||+|++.+.|..+||-.-+|.....++. .-+-. +.-..+.-++.++.|..+
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 001125568888999999999999999999999998888887633321 11111 122233444556666666
Q ss_pred HhcC
Q 010373 213 LHEN 216 (512)
Q Consensus 213 l~~~ 216 (512)
|+..
T Consensus 170 Ihr~ 173 (637)
T COG1782 170 IHRE 173 (637)
T ss_pred hcCC
Confidence 6654
No 110
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=87.76 E-value=0.26 Score=45.17 Aligned_cols=55 Identities=24% Similarity=0.335 Sum_probs=48.7
Q ss_pred CCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010373 355 SAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA 421 (512)
Q Consensus 355 ~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~ 421 (512)
+..+|.|+||+|.+---|.+.|.++|.+.. ..|.|-|..++++.|...|+.+|-.
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad------------~kIHiLG~~~niriAR~avcsLIlG 231 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD------------SKIHILGAFQNIRIARDAVCSLILG 231 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecC------------ceEEEeecchhhHHHHHhhHhhhcc
Confidence 467899999999999999999999999852 2799999999999999999988843
No 111
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=86.48 E-value=1.2 Score=43.14 Aligned_cols=51 Identities=12% Similarity=0.193 Sum_probs=45.9
Q ss_pred eEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010373 153 GCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE 215 (512)
Q Consensus 153 g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~ 215 (512)
-+|||.+|.+++.|+--|.|-|-|... .|.+.|....+..+...|.+.+.+
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~------------TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN------------TVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc------------EEEeecCcchHHHHHHHHHHHHhc
Confidence 469999999999999999999998654 589999999999999999888876
No 112
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=86.37 E-value=0.3 Score=55.53 Aligned_cols=60 Identities=20% Similarity=0.155 Sum_probs=51.3
Q ss_pred CCCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecC-CCCCCCccEEEEEcCCCCc
Q 010373 41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISE-TVPGCDERIVTIYSSSEGT 100 (512)
Q Consensus 41 ~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~-~~~~~~ervv~I~G~~e~~ 100 (512)
......++-+|...+..|||++|++|+.++.-||+.|.|.+ ...+..||.+.+.|.++.+
T Consensus 1337 ~~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~ 1397 (2131)
T KOG4369|consen 1337 VPANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQ 1397 (2131)
T ss_pred CcccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhh
Confidence 34445678889999999999999999999999999999986 3445789999999998874
No 113
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=86.22 E-value=0.45 Score=36.55 Aligned_cols=38 Identities=26% Similarity=0.476 Sum_probs=30.4
Q ss_pred EEEEEeeCCc-----eeEEecCCChhHHHHHhhc-CceEEEeec
Q 010373 142 TVRMLVPADQ-----IGCVIGKGGQVIQNIRTET-RAQIRILKD 179 (512)
Q Consensus 142 ~~~llVP~~~-----vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~ 179 (512)
.+.+.|-+.. +|..||++|..|+.|+++. |-+|.|...
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~ 47 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY 47 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence 3566777777 8999999999999999999 999999865
No 114
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=85.95 E-value=0.87 Score=35.74 Aligned_cols=33 Identities=27% Similarity=0.509 Sum_probs=26.6
Q ss_pred EEEEEeeCCceeEEecCCChhHHHHHhhcCceE
Q 010373 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQI 174 (512)
Q Consensus 142 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I 174 (512)
.+.+-|..+..|.||||.|+++..||--++.-+
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~ 57 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVL 57 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHH
Confidence 456777788899999999999999996655433
No 115
>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=85.66 E-value=0.72 Score=36.20 Aligned_cols=35 Identities=20% Similarity=0.214 Sum_probs=27.7
Q ss_pred EEEEEecCCceeeeccCCchHHHHHHHhhCCeEEe
Q 010373 45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRI 79 (512)
Q Consensus 45 ~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i 79 (512)
.+.+.+..+..|.+|||.|++++.||--++.-+.-
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~ 59 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR 59 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence 45566677889999999999999999887654443
No 116
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=85.40 E-value=0.7 Score=35.51 Aligned_cols=36 Identities=25% Similarity=0.488 Sum_probs=28.1
Q ss_pred EEEEecCCc-----eeeeecCCchhHHHHHHHh-CCeEEEec
Q 010373 349 TRILVPSAQ-----IGCLIGRGGAIISEMRSAT-RASIRILT 384 (512)
Q Consensus 349 ~~l~VP~~~-----vG~IIGkgG~~IkeI~~~T-Ga~I~i~~ 384 (512)
..+.|-... +|..||++|++|+.|.++. |-+|.|-.
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 345555555 8999999999999999999 89999865
No 117
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=85.27 E-value=1.2 Score=47.40 Aligned_cols=68 Identities=18% Similarity=0.226 Sum_probs=56.9
Q ss_pred CCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHh
Q 010373 342 SGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLR 420 (512)
Q Consensus 342 ~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~ 420 (512)
.....+...+.|+.+....+||.+|...|.|..+||+.-.+ ++.+|.|.- ++.+.+.|+.+|...+.
T Consensus 592 ~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~t~~i~A~~~~am~~Ak~~I~~i~~ 659 (760)
T KOG1067|consen 592 KEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEGTFSIFAPTQAAMEEAKEFIDGIIK 659 (760)
T ss_pred cccCceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCceEEEEecCHHHHHHHHHHHHHHhc
Confidence 34466788999999999999999999999999999965554 234777777 78899999999998887
Q ss_pred h
Q 010373 421 A 421 (512)
Q Consensus 421 ~ 421 (512)
.
T Consensus 660 ~ 660 (760)
T KOG1067|consen 660 D 660 (760)
T ss_pred C
Confidence 6
No 118
>KOG3875 consensus Peroxisomal biogenesis protein peroxin [Intracellular trafficking, secretion, and vesicular transport]
Probab=84.24 E-value=1.7 Score=42.80 Aligned_cols=12 Identities=17% Similarity=0.545 Sum_probs=6.0
Q ss_pred CCCCCCCCCCCC
Q 010373 489 NAYGAYGDHSSG 500 (512)
Q Consensus 489 ~~yg~~~~~~~~ 500 (512)
+||+.++.|+..
T Consensus 91 gGyN~~~~~g~n 102 (362)
T KOG3875|consen 91 GGYNRFGPYGTN 102 (362)
T ss_pred cccccccccccC
Confidence 455555555533
No 119
>PRK13764 ATPase; Provisional
Probab=84.16 E-value=1.1 Score=49.11 Aligned_cols=43 Identities=23% Similarity=0.405 Sum_probs=38.7
Q ss_pred eEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCC
Q 010373 347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVP 389 (512)
Q Consensus 347 ~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p 389 (512)
.+..+.||...++.+|||+|.+|++|.+..|.+|.|...+..|
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 4678899999999999999999999999999999998776554
No 120
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=83.71 E-value=2.7 Score=40.16 Aligned_cols=55 Identities=24% Similarity=0.374 Sum_probs=43.2
Q ss_pred EEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHH-HHHHHHHH
Q 010373 144 RMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAV-VRKALVQI 209 (512)
Q Consensus 144 ~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~-V~~A~~~I 209 (512)
-+.||...|.++||++|..++-|.++|+|+|-|-... .|-|.++.+. ..-|...|
T Consensus 149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG-----------~IWV~~~~~~~e~~~~~aI 204 (239)
T COG1097 149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNG-----------RIWVDGENESLEELAIEAI 204 (239)
T ss_pred EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecCC-----------EEEecCCCcchHHHHHHHH
Confidence 4789999999999999999999999999999996552 4777777664 33343333
No 121
>PRK13764 ATPase; Provisional
Probab=83.69 E-value=2.6 Score=46.36 Aligned_cols=44 Identities=30% Similarity=0.400 Sum_probs=38.8
Q ss_pred ceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCC
Q 010373 140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLP 183 (512)
Q Consensus 140 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p 183 (512)
.-.+.+.||...++.+|||+|.+|++|.++.|..|.|...+..+
T Consensus 480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 33678999999999999999999999999999999998775443
No 122
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=83.27 E-value=0.95 Score=47.18 Aligned_cols=41 Identities=27% Similarity=0.349 Sum_probs=36.7
Q ss_pred eEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCC
Q 010373 347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNEN 387 (512)
Q Consensus 347 ~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~ 387 (512)
....+.||..+++.+|||+|.+|++|.+..|-+|.|...+.
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 34678899999999999999999999999999999976544
No 123
>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=82.94 E-value=0.67 Score=36.84 Aligned_cols=38 Identities=16% Similarity=0.316 Sum_probs=32.0
Q ss_pred eEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecC
Q 010373 44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISE 81 (512)
Q Consensus 44 ~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~ 81 (512)
..+++.|-...-|.|||++|+.|++|+++..-...+.+
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~ 67 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPE 67 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCC
Confidence 34788888899999999999999999998877666643
No 124
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=82.43 E-value=0.67 Score=36.37 Aligned_cols=35 Identities=23% Similarity=0.397 Sum_probs=29.3
Q ss_pred eEEEEEecCCceeeeccCCchHHHHHHHhhCCeEE
Q 010373 44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIR 78 (512)
Q Consensus 44 ~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~ 78 (512)
....+.+.....+.|||++|++|++|.++..-.+.
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 45678888999999999999999999887765553
No 125
>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=80.26 E-value=0.78 Score=35.97 Aligned_cols=35 Identities=26% Similarity=0.452 Sum_probs=29.2
Q ss_pred eEEEEEecCCceeeeecCCchhHHHHHHHhCCeEE
Q 010373 347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIR 381 (512)
Q Consensus 347 ~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~ 381 (512)
....+.+....-|.|||++|++|++|++..+-.+.
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 34677888999999999999999999988765553
No 126
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=79.96 E-value=3.8 Score=39.24 Aligned_cols=47 Identities=17% Similarity=0.403 Sum_probs=39.1
Q ss_pred EEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHH
Q 010373 349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLD 406 (512)
Q Consensus 349 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~ 406 (512)
.-+.||...|-.+||++|+.++.|.+.|+|+|-|-.. -.|-|.+..+
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 5678999999999999999999999999999998432 2566777555
No 127
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=79.74 E-value=3.7 Score=39.83 Aligned_cols=51 Identities=20% Similarity=0.221 Sum_probs=42.7
Q ss_pred eeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010373 359 GCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA 421 (512)
Q Consensus 359 G~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~ 421 (512)
-++||.+|++++-|+-.|.|.|-|+.. +|.+.|....++.+...+.+.+..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~------------TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN------------TVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc------------EEEeecCcchHHHHHHHHHHHHhc
Confidence 478999999999999999999999642 799999988888887776665543
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=78.67 E-value=2.6 Score=37.14 Aligned_cols=39 Identities=28% Similarity=0.440 Sum_probs=33.4
Q ss_pred EEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCC
Q 010373 46 YRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVP 84 (512)
Q Consensus 46 ~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~ 84 (512)
=++.|-.++-|.+|||+|.++++|..+||-+-.|-...|
T Consensus 78 GEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 78 GEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred cEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 356777889999999999999999999999888866544
No 129
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=78.14 E-value=2.8 Score=38.10 Aligned_cols=35 Identities=31% Similarity=0.416 Sum_probs=29.7
Q ss_pred EEEEecCCceeeeccCCchHHHHHHHhhCCeEEecC
Q 010373 46 YRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISE 81 (512)
Q Consensus 46 ~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~ 81 (512)
+-++|-... |.-|||+|+++++|++..|-+|.+-+
T Consensus 63 vIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 63 VILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 445666666 99999999999999999999998854
No 130
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=77.82 E-value=7.9 Score=43.10 Aligned_cols=96 Identities=23% Similarity=0.401 Sum_probs=62.6
Q ss_pred eccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccCCcccCC
Q 010373 58 IIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGE 137 (512)
Q Consensus 58 IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~ 137 (512)
.+=..+..|++|-++..-+|.|-.+ +.. +.+-.+|...|.+.+-++. .-.+- .
T Consensus 37 ~~~~~~~~~~~~~~~~~~r~~~~~~--------------~~~----------~~~~~~~~~~i~~~~~~~~-~~~~~--~ 89 (630)
T TIGR03675 37 LFAKDDDLVKELAKKLRKRIVIRPD--------------PSV----------LLPPEEAIEKIKEIVPEEA-GITDI--Y 89 (630)
T ss_pred HhccchHHHHHHHHHhhceEEEecC--------------hhh----------cCCHHHHHHHHHHhCCCcC-CceeE--E
Confidence 3446778999999988777776432 111 1123456666655443221 10000 0
Q ss_pred CcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecC
Q 010373 138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE 180 (512)
Q Consensus 138 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~ 180 (512)
=...+-+++|-...-|.||||+|.++++|..+||-+-+|.+..
T Consensus 90 f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~ 132 (630)
T TIGR03675 90 FDDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTP 132 (630)
T ss_pred ecCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecC
Confidence 0112456888888999999999999999999999999998773
No 131
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=75.20 E-value=4.1 Score=37.00 Aligned_cols=37 Identities=24% Similarity=0.504 Sum_probs=32.7
Q ss_pred EEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeec
Q 010373 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179 (512)
Q Consensus 142 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 179 (512)
.+-++|-... |..|||+|.+|+++++..|-+|.+...
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence 4567787777 999999999999999999999999765
No 132
>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=74.44 E-value=3.9 Score=32.49 Aligned_cols=35 Identities=14% Similarity=0.380 Sum_probs=29.4
Q ss_pred EEEEEeeCCceeEEecCCChhHHHHHhhcCceEEE
Q 010373 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRI 176 (512)
Q Consensus 142 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i 176 (512)
.+++.|....-|.|||++|+.|++|+++-.-...+
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 47788888899999999999999999886655544
No 133
>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=73.25 E-value=2.9 Score=35.21 Aligned_cols=32 Identities=28% Similarity=0.314 Sum_probs=26.6
Q ss_pred EEEEEecCCceeeeccCCchHHHHHHHhhCCe
Q 010373 45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSN 76 (512)
Q Consensus 45 ~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~ 76 (512)
.+++.+-....|.|||++|++|++|++.....
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~ 93 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQKL 93 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHHHH
Confidence 36777888889999999999999998876443
No 134
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=69.49 E-value=5.7 Score=42.04 Aligned_cols=96 Identities=24% Similarity=0.317 Sum_probs=67.3
Q ss_pred eEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCCccccccccCCCCcc
Q 010373 153 GCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIY 232 (512)
Q Consensus 153 g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~ 232 (512)
..++=+.|..|++|-++..-+|.|-++ |..- ..-+.|.+.|.+++-++..-.. +
T Consensus 41 P~~~~~~~dlik~lAk~lrKRI~iR~d---Psvl-------------~~~e~A~~~I~eivP~ea~i~~-i--------- 94 (637)
T COG1782 41 PELFAKDGDLIKDLAKDLRKRIIIRPD---PSVL-------------KPPEEARKIILEIVPEEAGITD-I--------- 94 (637)
T ss_pred HHHhccchhHHHHHHHHHhhceEeccC---chhc-------------CCHHHHHHHHHHhCccccCcee-E---------
Confidence 446778999999999999999998776 3210 1225688888887755321110 0
Q ss_pred CCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEEecC
Q 010373 233 QSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDS 299 (512)
Q Consensus 233 ~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~ 299 (512)
.-+..+-++.|-.+.-|.+|||+|++.++|.+++|-.-++-.
T Consensus 95 -------------------------~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR 136 (637)
T COG1782 95 -------------------------YFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVR 136 (637)
T ss_pred -------------------------EecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeee
Confidence 111224467888889999999999999999999996655544
No 135
>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=67.01 E-value=5.1 Score=32.02 Aligned_cols=28 Identities=21% Similarity=0.399 Sum_probs=23.2
Q ss_pred EEEEecCCceeeeccCCchHHHHHHHhh
Q 010373 46 YRYLCPLRKIGSIIGKGGEIVKQLRSET 73 (512)
Q Consensus 46 ~rilvp~~~~g~IIGk~G~~I~~I~~~t 73 (512)
+++.+-...-|.+||++|.+|++|++..
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 5555555888999999999999998775
No 136
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=64.48 E-value=5.1 Score=38.22 Aligned_cols=32 Identities=28% Similarity=0.366 Sum_probs=27.2
Q ss_pred CeEEEEEecCCceeeeccCCchHHHHHHHhhC
Q 010373 43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETK 74 (512)
Q Consensus 43 ~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tg 74 (512)
....++.|....-|.||||+|+.|++|+++..
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~ 81 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKELE 81 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHHH
Confidence 44577888899999999999999999987654
No 137
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=62.12 E-value=7 Score=32.91 Aligned_cols=30 Identities=30% Similarity=0.528 Sum_probs=25.0
Q ss_pred EEEEEeeCCceeEEecCCChhHHHHHhhcC
Q 010373 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETR 171 (512)
Q Consensus 142 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~tg 171 (512)
.+++.|-...-|.|||++|+.|++|++...
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~ 91 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQ 91 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence 366777788889999999999999987644
No 138
>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=61.30 E-value=9.2 Score=30.55 Aligned_cols=28 Identities=29% Similarity=0.554 Sum_probs=22.9
Q ss_pred EEEEeeCCceeEEecCCChhHHHHHhhc
Q 010373 143 VRMLVPADQIGCVIGKGGQVIQNIRTET 170 (512)
Q Consensus 143 ~~llVP~~~vg~IIGk~G~~Ik~I~~~t 170 (512)
+++.|....-|.+||++|+.|++|++.-
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 5566666888999999999999988653
No 139
>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=58.07 E-value=29 Score=31.33 Aligned_cols=57 Identities=18% Similarity=0.242 Sum_probs=43.7
Q ss_pred ceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHh
Q 010373 140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLH 214 (512)
Q Consensus 140 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~ 214 (512)
.-++|+-+|...+- +.++.|.+-+|+-+.+. + +..|.|.|+.+.|.+|++.++.+..
T Consensus 112 ~~~iRv~l~~~i~~-------erl~ei~E~~gvI~Efe-e----------~~~V~I~Gdke~Ik~aLKe~s~~wk 168 (169)
T PF09869_consen 112 FETIRVKLKKPIQE-------ERLQEISEWHGVIFEFE-E----------DDKVVIEGDKERIKKALKEFSSFWK 168 (169)
T ss_pred ceeEEEecCccchH-------HHHHHHHHHhceeEEec-C----------CcEEEEeccHHHHHHHHHHHHHHhc
Confidence 34666666665532 56789999999988882 2 3469999999999999999987654
No 140
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=57.27 E-value=9.1 Score=36.55 Aligned_cols=29 Identities=31% Similarity=0.543 Sum_probs=24.9
Q ss_pred eEEEEEecCCceeeeecCCchhHHHHHHH
Q 010373 347 ITTRILVPSAQIGCLIGRGGAIISEMRSA 375 (512)
Q Consensus 347 ~t~~l~VP~~~vG~IIGkgG~~IkeI~~~ 375 (512)
..+++.|....-|.|||++|+.|++|++.
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 46778888899999999999999988653
No 141
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=54.46 E-value=15 Score=36.15 Aligned_cols=31 Identities=29% Similarity=0.384 Sum_probs=24.7
Q ss_pred ceEEEEEee-CCceeEEecCCChhHHHHHhhc
Q 010373 140 LITVRMLVP-ADQIGCVIGKGGQVIQNIRTET 170 (512)
Q Consensus 140 ~~~~~llVP-~~~vg~IIGk~G~~Ik~I~~~t 170 (512)
.+.+.++|. .++.+.||||+|+.||+|..+.
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 366777887 5578999999999999887553
No 142
>COG1159 Era GTPase [General function prediction only]
Probab=52.12 E-value=18 Score=35.93 Aligned_cols=34 Identities=35% Similarity=0.505 Sum_probs=25.6
Q ss_pred CCCcceEEEEEee-CCceeEEecCCChhHHHHHhh
Q 010373 136 GELTLITVRMLVP-ADQIGCVIGKGGQVIQNIRTE 169 (512)
Q Consensus 136 ~~~~~~~~~llVP-~~~vg~IIGk~G~~Ik~I~~~ 169 (512)
.....+...|+|+ .++-+-||||+|++||+|-..
T Consensus 224 ~~~~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~ 258 (298)
T COG1159 224 KGLLKIHATIYVERESQKGIIIGKNGAMIKKIGTA 258 (298)
T ss_pred CCeEEEEEEEEEecCCccceEECCCcHHHHHHHHH
Confidence 3344556668888 557899999999999887644
No 143
>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=51.96 E-value=33 Score=25.57 Aligned_cols=39 Identities=13% Similarity=0.112 Sum_probs=26.9
Q ss_pred HHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHH
Q 010373 374 SATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTL 417 (512)
Q Consensus 374 ~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~ 417 (512)
+.+++.| +.....+|. ..-.+.|+|+..+|+.|+..+.+
T Consensus 21 Kaa~V~i-~d~f~gCPq----~~~~l~i~Gdvs~Ve~Al~~i~~ 59 (61)
T cd07055 21 KASGVFV-SDIFGSCPQ----HMITLAIFGETSAVELAMREIEE 59 (61)
T ss_pred hccCeEE-EEecCCCCC----ceEEEEEEecHHHHHHHHHHHhh
Confidence 4455555 444444553 44567899999999999988765
No 144
>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=49.67 E-value=16 Score=40.70 Aligned_cols=41 Identities=27% Similarity=0.436 Sum_probs=35.4
Q ss_pred eEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCC
Q 010373 44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVP 84 (512)
Q Consensus 44 ~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~ 84 (512)
.+=+++|-.++-|.||||+|+++++|.++||-+-+|-..+|
T Consensus 93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~~ 133 (630)
T TIGR03675 93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTPP 133 (630)
T ss_pred CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecCC
Confidence 34467888899999999999999999999999988876654
No 145
>PRK15494 era GTPase Era; Provisional
Probab=48.59 E-value=21 Score=36.45 Aligned_cols=30 Identities=23% Similarity=0.378 Sum_probs=23.8
Q ss_pred ceEEEEEee-CCceeEEecCCChhHHHHHhh
Q 010373 140 LITVRMLVP-ADQIGCVIGKGGQVIQNIRTE 169 (512)
Q Consensus 140 ~~~~~llVP-~~~vg~IIGk~G~~Ik~I~~~ 169 (512)
.+.+.|+|. .++.+.||||+|+.||+|..+
T Consensus 272 ~i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 272 KINQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 356778887 457899999999999987654
No 146
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=48.53 E-value=55 Score=28.77 Aligned_cols=44 Identities=27% Similarity=0.364 Sum_probs=35.9
Q ss_pred hhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010373 161 QVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE 215 (512)
Q Consensus 161 ~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~ 215 (512)
+.++.|-+..|+-|.+... .+|.|.|+.+.|.+|++.|....++
T Consensus 126 eRlqDi~E~hgvIiE~~E~-----------D~V~i~Gd~drVk~aLke~~~~wke 169 (170)
T COG4010 126 ERLQDIAETHGVIIEFEEY-----------DLVAIYGDSDRVKKALKEIGSFWKE 169 (170)
T ss_pred HHHHHHHHhhheeEEeeec-----------cEEEEeccHHHHHHHHHHHHHHHhc
Confidence 4567777889998888643 3699999999999999999887554
No 147
>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=47.27 E-value=23 Score=34.79 Aligned_cols=31 Identities=29% Similarity=0.398 Sum_probs=25.0
Q ss_pred eeEEEEEecCC-ceeeeecCCchhHHHHHHHh
Q 010373 346 VITTRILVPSA-QIGCLIGRGGAIISEMRSAT 376 (512)
Q Consensus 346 ~~t~~l~VP~~-~vG~IIGkgG~~IkeI~~~T 376 (512)
.+...+.|..+ +-+-|||++|+.||+|...+
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 46778888854 55899999999999887665
No 148
>PRK00089 era GTPase Era; Reviewed
Probab=46.68 E-value=23 Score=35.15 Aligned_cols=29 Identities=41% Similarity=0.704 Sum_probs=23.0
Q ss_pred eEEEEEee-CCceeEEecCCChhHHHHHhh
Q 010373 141 ITVRMLVP-ADQIGCVIGKGGQVIQNIRTE 169 (512)
Q Consensus 141 ~~~~llVP-~~~vg~IIGk~G~~Ik~I~~~ 169 (512)
+.+.|.|. .++.+.||||+|++|++|..+
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ 255 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTE 255 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHH
Confidence 55667777 557899999999999987654
No 149
>PRK03818 putative transporter; Validated
Probab=46.53 E-value=2.6e+02 Score=30.71 Aligned_cols=135 Identities=16% Similarity=0.169 Sum_probs=71.3
Q ss_pred EEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCC------------CCCCCccEEEEEcCCCCcccccCCcccCcH
Q 010373 45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISET------------VPGCDERIVTIYSSSEGTNLFEDSGEFVSP 112 (512)
Q Consensus 45 ~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~------------~~~~~ervv~I~G~~e~~~~~~~~~~~~~~ 112 (512)
..++.|+++. ++ |.+++++.......+.|..- ..=....++.|.|..++
T Consensus 206 ~r~~~V~~s~---li---GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~------------- 266 (552)
T PRK03818 206 TINIRVENPN---LH---GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPED------------- 266 (552)
T ss_pred eEEEEEeCCC---CC---CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHH-------------
Confidence 3666666443 34 67899999888766666311 11123466788886543
Q ss_pred HHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHH--HhhcCceEEEeecCC--CCc---c
Q 010373 113 AQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNI--RTETRAQIRILKDEH--LPL---C 185 (512)
Q Consensus 113 a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I--~~~tga~I~i~~~~~--~p~---~ 185 (512)
+.++.+..-.+. ..+.+.........++++|+ ..++|| +++++ ++++|+.|.-..+.. ++. -
T Consensus 267 ----l~~l~~~~Gl~~-~~~~~~~~~~~~~E~Vvv~~---S~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~ 335 (552)
T PRK03818 267 ----LHKAQLVIGEEV-DTSLSTRGTDLRSERVVVTN---EKVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDL 335 (552)
T ss_pred ----HHHHHHhcCCcc-CccccccCcceEEEEEEEcC---hhccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCC
Confidence 333332222111 00001111223344455555 467775 77777 477777755443321 211 1
Q ss_pred cCCCCceEEEecCHHHHHHHHHHH
Q 010373 186 ALSFDELLQVAGEPAVVRKALVQI 209 (512)
Q Consensus 186 ~~~~dr~v~I~G~~~~V~~A~~~I 209 (512)
....-..+.+.|++++++++.+.+
T Consensus 336 ~Lq~GD~LlVvG~~~~i~~l~~~L 359 (552)
T PRK03818 336 SLQFGDILNLVGRPEAIDAVANVL 359 (552)
T ss_pred EEecCCEEEEEECHHHHHHHHHHh
Confidence 111224588999999999977643
No 150
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=45.20 E-value=78 Score=32.01 Aligned_cols=20 Identities=25% Similarity=0.474 Sum_probs=9.3
Q ss_pred CCCCCCCCCCCCCCCCCCCC
Q 010373 451 KYGNRDNQSRGRGNSYATGN 470 (512)
Q Consensus 451 ~yg~~~~~~~g~g~~~~~g~ 470 (512)
+|++|++.+.|+|...++||
T Consensus 365 ~~gGrGgGRGggG~GGGggy 384 (465)
T KOG3973|consen 365 NWGGRGGGRGGGGRGGGGGY 384 (465)
T ss_pred CCCCCCCCCCCCCCCCCCCC
Confidence 44555444443444445555
No 151
>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=44.27 E-value=2.8e+02 Score=30.53 Aligned_cols=63 Identities=21% Similarity=0.348 Sum_probs=37.8
Q ss_pred EEEEEeeCCceeEEecCCChhHHHHH------hhcCceEEEeecCC--CCc---ccCCCCceEEEecCHHHHHHHHHHHH
Q 010373 142 TVRMLVPADQIGCVIGKGGQVIQNIR------TETRAQIRILKDEH--LPL---CALSFDELLQVAGEPAVVRKALVQIA 210 (512)
Q Consensus 142 ~~~llVP~~~vg~IIGk~G~~Ik~I~------~~tga~I~i~~~~~--~p~---~~~~~dr~v~I~G~~~~V~~A~~~I~ 210 (512)
..++++|+ ..++|| +|+++. +.+|+.|.-..+.. ++. -....-..+.+.|++++++++.+.+-
T Consensus 304 ~e~VV~~~---S~liGk---TL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~GD~LlV~G~~~~l~~~~~~lG 377 (562)
T TIGR03802 304 TKDVVLTN---KEYNGK---TVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQRGDVVTLVGTPQDVDRAAKQLG 377 (562)
T ss_pred EEEEEECC---cccCCc---cHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecCCCEEEEEeCHHHHHHHHHHcC
Confidence 34455554 456665 788876 36787766554422 221 11122345899999999999876644
No 152
>PRK15494 era GTPase Era; Provisional
Probab=41.04 E-value=32 Score=35.15 Aligned_cols=31 Identities=23% Similarity=0.394 Sum_probs=24.5
Q ss_pred eeEEEEEecCC-ceeeeecCCchhHHHHHHHh
Q 010373 346 VITTRILVPSA-QIGCLIGRGGAIISEMRSAT 376 (512)
Q Consensus 346 ~~t~~l~VP~~-~vG~IIGkgG~~IkeI~~~T 376 (512)
.+...+.|..+ +-+-|||++|+.||+|....
T Consensus 272 ~i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~a 303 (339)
T PRK15494 272 KINQVIVVSRESYKTIILGKNGSKIKEIGAKS 303 (339)
T ss_pred EEEEEEEECCCCceeEEEcCCcHHHHHHHHHH
Confidence 46678888855 55899999999999886554
No 153
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=40.13 E-value=38 Score=31.84 Aligned_cols=35 Identities=17% Similarity=0.338 Sum_probs=28.4
Q ss_pred EEEEEeeCCceeEEecCCChhHHHHHhhcCceEEE
Q 010373 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRI 176 (512)
Q Consensus 142 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i 176 (512)
.+.+-+-.+..+.|||+.|+++..||--+++-++-
T Consensus 92 ~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 92 RVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred EEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 55677777889999999999999999877765443
No 154
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=38.13 E-value=31 Score=34.62 Aligned_cols=32 Identities=25% Similarity=0.446 Sum_probs=26.0
Q ss_pred CCeEEEEEecC-CceeeeccCCchHHHHHHHhh
Q 010373 42 EDTVYRYLCPL-RKIGSIIGKGGEIVKQLRSET 73 (512)
Q Consensus 42 ~~~~~rilvp~-~~~g~IIGk~G~~I~~I~~~t 73 (512)
-.+..+++||. +....||||+|..|++|-.+-
T Consensus 326 l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a 358 (379)
T KOG1423|consen 326 LFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRA 358 (379)
T ss_pred EEEEEEEEcCCCcceeEEEcCCCccHHHHHHHH
Confidence 34667899996 567889999999999996654
No 155
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=38.07 E-value=22 Score=33.33 Aligned_cols=38 Identities=18% Similarity=0.177 Sum_probs=30.1
Q ss_pred CCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEe
Q 010373 42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRI 79 (512)
Q Consensus 42 ~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i 79 (512)
..-.+.+.+-.+..+.+||+.|.++..||--+++-+.-
T Consensus 89 ~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 89 EGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 34455666677779999999999999999988765554
No 156
>CHL00048 rps3 ribosomal protein S3
Probab=37.98 E-value=28 Score=33.06 Aligned_cols=32 Identities=9% Similarity=0.063 Sum_probs=26.5
Q ss_pred CeEEEEEecCCceeeeccCCchHHHHHHHhhC
Q 010373 43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETK 74 (512)
Q Consensus 43 ~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tg 74 (512)
...+++.|-....|.|||++|++|++|++...
T Consensus 65 ~~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 65 IDLIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred CCeEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 34467777788889999999999999988764
No 157
>PRK00089 era GTPase Era; Reviewed
Probab=37.57 E-value=40 Score=33.40 Aligned_cols=32 Identities=31% Similarity=0.587 Sum_probs=24.5
Q ss_pred ceeEEEEEecC-CceeeeecCCchhHHHHHHHh
Q 010373 345 PVITTRILVPS-AQIGCLIGRGGAIISEMRSAT 376 (512)
Q Consensus 345 ~~~t~~l~VP~-~~vG~IIGkgG~~IkeI~~~T 376 (512)
..+...+.|.. ++-+-|||++|++|++|...+
T Consensus 224 ~~i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~a 256 (292)
T PRK00089 224 VRIEATIYVERDSQKGIIIGKGGAMLKKIGTEA 256 (292)
T ss_pred EEEEEEEEEccCCceeEEEeCCcHHHHHHHHHH
Confidence 34667778874 456899999999999886654
No 158
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=37.53 E-value=29 Score=32.85 Aligned_cols=31 Identities=23% Similarity=0.417 Sum_probs=25.0
Q ss_pred EEEEecCCceeeeccCCchHHHHHHHhhCCe
Q 010373 46 YRYLCPLRKIGSIIGKGGEIVKQLRSETKSN 76 (512)
Q Consensus 46 ~rilvp~~~~g~IIGk~G~~I~~I~~~tga~ 76 (512)
.++.|-....|.+||++|++|++|++...-.
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 5555555889999999999999998887544
No 159
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=37.46 E-value=30 Score=32.39 Aligned_cols=31 Identities=19% Similarity=0.417 Sum_probs=26.2
Q ss_pred EEEEEecCCceeeeccCCchHHHHHHHhhCC
Q 010373 45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKS 75 (512)
Q Consensus 45 ~~rilvp~~~~g~IIGk~G~~I~~I~~~tga 75 (512)
..++.|-....|.|||++|+.|++|+++..-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k 69 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKLQK 69 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHHHH
Confidence 4777888888999999999999999887643
No 160
>COG1159 Era GTPase [General function prediction only]
Probab=36.91 E-value=45 Score=33.22 Aligned_cols=34 Identities=35% Similarity=0.549 Sum_probs=26.1
Q ss_pred CCceeEEEEEecC-CceeeeecCCchhHHHHHHHh
Q 010373 343 GDPVITTRILVPS-AQIGCLIGRGGAIISEMRSAT 376 (512)
Q Consensus 343 ~~~~~t~~l~VP~-~~vG~IIGkgG~~IkeI~~~T 376 (512)
....+...+.|+. ++=|-||||+|++||+|-..+
T Consensus 225 ~~~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~A 259 (298)
T COG1159 225 GLLKIHATIYVERESQKGIIIGKNGAMIKKIGTAA 259 (298)
T ss_pred CeEEEEEEEEEecCCccceEECCCcHHHHHHHHHH
Confidence 3445667788885 456999999999999886554
No 161
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=35.32 E-value=1.2e+02 Score=34.37 Aligned_cols=7 Identities=14% Similarity=0.610 Sum_probs=3.5
Q ss_pred eEEEEEc
Q 010373 397 EMVQITG 403 (512)
Q Consensus 397 r~V~I~G 403 (512)
+.+.+.|
T Consensus 755 ~a~~l~G 761 (931)
T KOG2044|consen 755 PAIRLDG 761 (931)
T ss_pred hhhhcCC
Confidence 3455555
No 162
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=34.35 E-value=34 Score=32.66 Aligned_cols=33 Identities=12% Similarity=0.257 Sum_probs=26.9
Q ss_pred EEEEEecCCceeeeccCCchHHHHHHHhhCCeE
Q 010373 45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNI 77 (512)
Q Consensus 45 ~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I 77 (512)
..++.|-....|.|||++|..|++|+++..-.+
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~ 77 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLLQKRF 77 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHHHHHh
Confidence 367777778889999999999999988875443
No 163
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=32.95 E-value=45 Score=33.50 Aligned_cols=34 Identities=29% Similarity=0.479 Sum_probs=26.8
Q ss_pred CceeEEEEEecCC-ceeeeecCCchhHHHHHHHhC
Q 010373 344 DPVITTRILVPSA-QIGCLIGRGGAIISEMRSATR 377 (512)
Q Consensus 344 ~~~~t~~l~VP~~-~vG~IIGkgG~~IkeI~~~TG 377 (512)
...+...+.+|.. +.-.||||+|..|++|-++-+
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 4567788899965 556889999999999976654
No 164
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=32.18 E-value=1.2e+02 Score=25.33 Aligned_cols=40 Identities=25% Similarity=0.278 Sum_probs=31.3
Q ss_pred hhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010373 168 TETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN 216 (512)
Q Consensus 168 ~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~ 216 (512)
+..++.|-+.++ + .-.|.|+|+..+|+.|+..|.+.+++.
T Consensus 61 Kaa~V~igF~DR--F-------sGslvitGdvs~Ve~Al~~V~~~l~~~ 100 (111)
T PRK15468 61 KAADVHIGFLDR--F-------SGALVIYGSVGAVEEALSQTVSGLGRL 100 (111)
T ss_pred hccCcEEeeeec--c-------ceeEEEEccHHHHHHHHHHHHHHHHhh
Confidence 345677777765 1 235999999999999999999999873
No 165
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=30.32 E-value=54 Score=30.69 Aligned_cols=29 Identities=28% Similarity=0.605 Sum_probs=24.4
Q ss_pred EEEEEeeCCceeEEecCCChhHHHHHhhc
Q 010373 142 TVRMLVPADQIGCVIGKGGQVIQNIRTET 170 (512)
Q Consensus 142 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~t 170 (512)
.+++.|....-|.|||++|+.|++|+++-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 46778888888999999999999888653
No 166
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=30.03 E-value=1.4e+02 Score=30.57 Aligned_cols=51 Identities=22% Similarity=0.199 Sum_probs=41.7
Q ss_pred cCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 010373 354 PSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVT 416 (512)
Q Consensus 354 P~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~ 416 (512)
+.+..-.+.|..+.+++.|.+..|+.|... .+.+.|+|+...|..|...+.
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 356677899999999999999999988763 237999999878888866665
No 167
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=28.82 E-value=57 Score=30.84 Aligned_cols=29 Identities=31% Similarity=0.576 Sum_probs=23.3
Q ss_pred EEEEeeCCceeEEecCCChhHHHHHhhcC
Q 010373 143 VRMLVPADQIGCVIGKGGQVIQNIRTETR 171 (512)
Q Consensus 143 ~~llVP~~~vg~IIGk~G~~Ik~I~~~tg 171 (512)
+++.|....-|.+||++|++|++|++.-.
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 55666667889999999999999887643
No 168
>CHL00048 rps3 ribosomal protein S3
Probab=28.38 E-value=59 Score=30.91 Aligned_cols=29 Identities=10% Similarity=0.253 Sum_probs=24.3
Q ss_pred EEEEEeeCCceeEEecCCChhHHHHHhhc
Q 010373 142 TVRMLVPADQIGCVIGKGGQVIQNIRTET 170 (512)
Q Consensus 142 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~t 170 (512)
.+++.|-....+.|||++|+.|++|++.-
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 46677777788999999999999998764
No 169
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=28.13 E-value=57 Score=31.14 Aligned_cols=30 Identities=17% Similarity=0.370 Sum_probs=24.4
Q ss_pred EEEEEeeCCceeEEecCCChhHHHHHhhcC
Q 010373 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETR 171 (512)
Q Consensus 142 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~tg 171 (512)
.+++.|....-|.|||++|..|++|+++..
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L~ 74 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLLQ 74 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHHH
Confidence 466777777789999999999999886643
No 170
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=25.90 E-value=1.4e+02 Score=30.53 Aligned_cols=53 Identities=13% Similarity=0.168 Sum_probs=43.5
Q ss_pred EeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHH
Q 010373 146 LVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIA 210 (512)
Q Consensus 146 lVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~ 210 (512)
+-+....-.|.|..+..++.|.+.+|+.|.... +.++|+|+...|..|...+.
T Consensus 20 ~~~~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG------------~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 20 LSDDNELVALFGPTDTNLSLLEIALGVSIVARG------------EAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred cCCchhhhhhcCCCCccHHHHHHHhCcEEEeCC------------ceEEEEechHHHHHHHHHHh
Confidence 344667888999999999999999998887643 36999999878888877776
No 171
>PF12235 FXR1P_C: Fragile X-related 1 protein C terminal; InterPro: IPR022034 Fragile X mental retardation 1 protein (FMR1P) , fragile X-related 1 protein (FXR1P) and fragile X-related 2 protein (FXR2P) are members of a small family of RNA-binding proteins that are thought to transport mRNA and to control their translation []. The proteins contain two KH domains and a RGG box that are characteristic motifs in RNA-binding proteins as well as nuclear localization and export signals. ; GO: 0003723 RNA binding; PDB: 2LA5_B.
Probab=25.81 E-value=23 Score=31.57 Aligned_cols=25 Identities=28% Similarity=0.419 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCC
Q 010373 474 RDSYGSYGGSLSGGGNAYGAYGDHS 498 (512)
Q Consensus 474 ~~~yg~yg~~~~~~~~~yg~~~~~~ 498 (512)
.++|++.|.+..|.+.+||+.+.-|
T Consensus 50 ~r~y~gRGRGRRG~~~~sGtNSe~S 74 (155)
T PF12235_consen 50 SRPYSGRGRGRRGPGYASGTNSEAS 74 (155)
T ss_dssp -------------------------
T ss_pred cCCCCCCCCCCCCCCcccccccccc
Confidence 4557777777767667777776654
No 172
>COG0490 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]
Probab=24.31 E-value=1.4e+02 Score=26.95 Aligned_cols=61 Identities=25% Similarity=0.199 Sum_probs=36.7
Q ss_pred EEecCCceeeeecCCchhHHHHHHHhCCeEE-EecCCCCCCCCC-----CCceEEEEEcCHHHHHHHHHHHH
Q 010373 351 ILVPSAQIGCLIGRGGAIISEMRSATRASIR-ILTNENVPKVAY-----EDEEMVQITGSLDVASSALSQVT 416 (512)
Q Consensus 351 l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~-i~~~~~~p~~~~-----~~~r~V~I~G~~~~v~~A~~~I~ 416 (512)
+..-+..+|.=||- -.|+++|||.|. |.+.+++=...+ ...-++.+.|+...+..++.++.
T Consensus 92 i~~~s~~~GksiGd-----l~irq~TGaTIIAI~r~~e~I~SPgPy~vle~gDtlvviG~~~~~~r~~~f~~ 158 (162)
T COG0490 92 IEAGSPFIGKTIGD-----LNIRQNTGATVIAIVRNEEKILSPGPYTVLEAGDTLVVIGEETGLKRAKRFLL 158 (162)
T ss_pred eecCCcccCcchhh-----cccccccCcEEEEEEecCcEecCCCchhhhcCCCEEEEEecchHhHHHHHHhh
Confidence 33334555655554 467999998854 444333211111 12337889999999998876543
No 173
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=23.36 E-value=1.9e+02 Score=22.41 Aligned_cols=41 Identities=17% Similarity=0.258 Sum_probs=28.9
Q ss_pred chhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 010373 366 GAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQV 415 (512)
Q Consensus 366 G~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I 415 (512)
-..|.+|-+..+|+|.-.. .+.-+|+++|+++.+...+.++
T Consensus 16 r~ei~~l~~~f~a~ivd~~---------~~~~iie~tG~~~kid~fi~~l 56 (75)
T PF10369_consen 16 RSEILQLAEIFRARIVDVS---------PDSIIIELTGTPEKIDAFIKLL 56 (75)
T ss_dssp HHHHHHHHHHTT-EEEEEE---------TTEEEEEEEE-HHHHHHHHHHS
T ss_pred HHHHHHHHHHhCCEEEEEC---------CCEEEEEEcCCHHHHHHHHHHh
Confidence 3567888899999865443 2456899999999999776554
No 174
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=22.90 E-value=71 Score=30.32 Aligned_cols=29 Identities=28% Similarity=0.459 Sum_probs=24.5
Q ss_pred EEEEecCCceeeeccCCchHHHHHHHhhC
Q 010373 46 YRYLCPLRKIGSIIGKGGEIVKQLRSETK 74 (512)
Q Consensus 46 ~rilvp~~~~g~IIGk~G~~I~~I~~~tg 74 (512)
++|.+-....+.|||++|..|++|++...
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 66777777889999999999999987653
No 175
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=22.67 E-value=1.5e+02 Score=21.99 Aligned_cols=49 Identities=18% Similarity=0.343 Sum_probs=32.1
Q ss_pred ChhHHH--HHhhcCceEEEeecCC---CC--cccCCCCceEEEecCHHHHHHHHHH
Q 010373 160 GQVIQN--IRTETRAQIRILKDEH---LP--LCALSFDELLQVAGEPAVVRKALVQ 208 (512)
Q Consensus 160 G~~Ik~--I~~~tga~I~i~~~~~---~p--~~~~~~dr~v~I~G~~~~V~~A~~~ 208 (512)
|.+|++ +++.+++.|.-..++. .| .........|.|.|..+.++++...
T Consensus 14 gk~l~el~l~~~~~~~i~~i~R~~~~~~p~~~~~l~~gD~l~v~g~~~~i~~~~~~ 69 (71)
T PF02080_consen 14 GKTLKELDLPERYGVRIVAIKRGGEIIIPDGDTVLQAGDILIVVGDPEDIERFREL 69 (71)
T ss_dssp TEBHHHCTHHCHHTEEEEEEEETEEEES--TT-BE-TTEEEEEEEEHHHHHHHHHH
T ss_pred CCCHHHCCCCccCCEEEEEEEECCEEECCCCCCEECCCCEEEEEECHHHHHHHHHh
Confidence 567888 7787898876655431 12 1222334568999999999988654
No 176
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=22.28 E-value=1.3e+02 Score=25.17 Aligned_cols=25 Identities=32% Similarity=0.276 Sum_probs=23.1
Q ss_pred EEEEEcCHHHHHHHHHHHHHHHhhc
Q 010373 398 MVQITGSLDVASSALSQVTLRLRAN 422 (512)
Q Consensus 398 ~V~I~G~~~~v~~A~~~I~~~l~~~ 422 (512)
.+.|+|+..+|+.|+..+.+-+++.
T Consensus 76 slvitGdvs~Ve~Al~~V~~~l~~~ 100 (111)
T PRK15468 76 ALVIYGSVGAVEEALSQTVSGLGRL 100 (111)
T ss_pred eEEEEccHHHHHHHHHHHHHHHHhh
Confidence 6899999999999999999999874
No 177
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.79 E-value=2.9e+02 Score=24.48 Aligned_cols=42 Identities=17% Similarity=0.207 Sum_probs=34.2
Q ss_pred hhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 010373 367 AIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRL 419 (512)
Q Consensus 367 ~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l 419 (512)
++++.|.+-.|+-|.+.. ..+|.|-|..+.|..|+..|...-
T Consensus 126 eRlqDi~E~hgvIiE~~E-----------~D~V~i~Gd~drVk~aLke~~~~w 167 (170)
T COG4010 126 ERLQDIAETHGVIIEFEE-----------YDLVAIYGDSDRVKKALKEIGSFW 167 (170)
T ss_pred HHHHHHHHhhheeEEeee-----------ccEEEEeccHHHHHHHHHHHHHHH
Confidence 567888888999888852 228999999999999999887653
No 178
>cd07049 BMC_EutL_repeat1 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1. EutL proteins are homologs of the carboxysome shell protein. They are encoded within the eut operon and might be required for the formation of the outer shell of the bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutL might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the eut organelles at present no experimental evidence directly supports this view. EutL proteins contain two tandem BMC domains. This CD includes domain 1 (the first BMC domain of EutL).
Probab=21.35 E-value=2.7e+02 Score=23.18 Aligned_cols=49 Identities=16% Similarity=0.112 Sum_probs=32.2
Q ss_pred hhcCceEEEeecCC-CCcccC---CCCceEEEec-CHHHHHHHHHHHHHHHhcC
Q 010373 168 TETRAQIRILKDEH-LPLCAL---SFDELLQVAG-EPAVVRKALVQIASRLHEN 216 (512)
Q Consensus 168 ~~tga~I~i~~~~~-~p~~~~---~~dr~v~I~G-~~~~V~~A~~~I~~~l~~~ 216 (512)
+.+++.|-+.++-- -..+.. +.+-++.|.| ++..|+.|+..+.+.+++.
T Consensus 47 Kaa~vev~~~~~f~gGa~h~~~~~sG~vi~ii~G~dvsdV~sal~~~l~~l~~~ 100 (103)
T cd07049 47 KAAEVEVVYARSFYAGAAHASTPLAGEVIGILAGPSPAEVRSGLNAAIDFIENE 100 (103)
T ss_pred hhcCeEEEEEeecccccccCccCCCccEEEEEeCCCHHHHHHHHHHHHHHHhcc
Confidence 55667776665510 011111 3444566999 9999999999999988763
No 179
>PF04202 Mfp-3: Foot protein 3; InterPro: IPR007328 Mytilus foot protein-3 (Mfp-3) is a highly polymorphic protein family located in the byssal adhesive plaques of blue mussels.
Probab=20.78 E-value=1.3e+02 Score=22.72 Aligned_cols=8 Identities=25% Similarity=0.526 Sum_probs=3.2
Q ss_pred CCCCCCCC
Q 010373 491 YGAYGDHS 498 (512)
Q Consensus 491 yg~~~~~~ 498 (512)
||.+-++.
T Consensus 53 YG~nkGwn 60 (71)
T PF04202_consen 53 YGGNKGWN 60 (71)
T ss_pred cCcccccc
Confidence 44444333
No 180
>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=20.57 E-value=2.8e+02 Score=25.14 Aligned_cols=54 Identities=15% Similarity=0.169 Sum_probs=40.8
Q ss_pred eeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHH
Q 010373 346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTL 417 (512)
Q Consensus 346 ~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~ 417 (512)
..+.++.+|...+ =+++.+|.+-.|+-+... ++.+|.|-|..+.|+.|+..+..
T Consensus 112 ~~~iRv~l~~~i~-------~erl~ei~E~~gvI~Efe-----------e~~~V~I~Gdke~Ik~aLKe~s~ 165 (169)
T PF09869_consen 112 FETIRVKLKKPIQ-------EERLQEISEWHGVIFEFE-----------EDDKVVIEGDKERIKKALKEFSS 165 (169)
T ss_pred ceeEEEecCccch-------HHHHHHHHHHhceeEEec-----------CCcEEEEeccHHHHHHHHHHHHH
Confidence 3456666666554 367889999999988872 23379999999999999987654
Done!