Query 014254
Match_columns 428
No_of_seqs 286 out of 1388
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 03:20:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014254.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014254hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2191 RNA-binding protein NO 100.0 4.4E-28 9.5E-33 238.3 20.2 186 185-381 38-238 (402)
2 KOG2190 PolyC-binding proteins 99.9 1.2E-25 2.5E-30 236.3 20.2 169 183-355 40-212 (485)
3 KOG1676 K-homology type RNA bi 99.9 7.3E-25 1.6E-29 229.4 16.1 252 91-352 27-301 (600)
4 KOG1676 K-homology type RNA bi 99.9 9.5E-23 2.1E-27 213.6 15.1 238 111-358 145-396 (600)
5 KOG2191 RNA-binding protein NO 99.9 2.4E-23 5.2E-28 205.1 8.0 221 119-351 53-315 (402)
6 KOG2190 PolyC-binding proteins 99.9 2.4E-21 5.1E-26 203.9 15.7 225 119-352 57-410 (485)
7 KOG2192 PolyC-binding hnRNP-K 99.8 1.9E-20 4E-25 180.5 11.8 221 115-352 58-385 (390)
8 KOG2192 PolyC-binding hnRNP-K 99.8 6.9E-20 1.5E-24 176.6 14.4 156 182-357 44-199 (390)
9 KOG2193 IGF-II mRNA-binding pr 99.8 3.1E-20 6.7E-25 187.8 10.7 160 184-356 409-569 (584)
10 KOG2193 IGF-II mRNA-binding pr 99.8 1.1E-18 2.3E-23 176.7 11.3 162 180-356 193-357 (584)
11 TIGR03665 arCOG04150 arCOG0415 99.6 7.8E-16 1.7E-20 142.5 10.7 142 190-356 2-156 (172)
12 PRK13763 putative RNA-processi 99.6 9.3E-15 2E-19 136.3 12.0 145 186-355 3-161 (180)
13 cd02396 PCBP_like_KH K homolog 99.4 4.6E-13 1E-17 104.6 7.3 65 279-346 1-65 (65)
14 cd02396 PCBP_like_KH K homolog 99.3 2.1E-12 4.6E-17 100.9 5.1 63 187-255 1-64 (65)
15 PF00013 KH_1: KH domain syndr 99.2 2.2E-11 4.7E-16 93.1 5.1 60 279-345 1-60 (60)
16 cd02394 vigilin_like_KH K homo 99.2 4.3E-11 9.3E-16 92.1 6.4 60 280-345 2-61 (62)
17 cd02393 PNPase_KH Polynucleoti 99.1 1.7E-10 3.8E-15 89.4 7.7 58 278-345 2-60 (61)
18 cd00105 KH-I K homology RNA-bi 99.1 3.4E-10 7.4E-15 86.7 7.7 62 280-345 2-63 (64)
19 PF00013 KH_1: KH domain syndr 99.0 3.3E-10 7.2E-15 86.6 3.2 52 187-241 1-52 (60)
20 cd00105 KH-I K homology RNA-bi 99.0 1.1E-09 2.4E-14 83.8 6.1 54 188-241 2-55 (64)
21 cd02394 vigilin_like_KH K homo 99.0 6E-10 1.3E-14 85.7 4.0 52 188-241 2-53 (62)
22 PF13014 KH_3: KH domain 98.9 1.5E-09 3.3E-14 78.0 5.2 42 196-237 1-43 (43)
23 PF13014 KH_3: KH domain 98.9 2.1E-09 4.5E-14 77.4 5.2 43 288-333 1-43 (43)
24 smart00322 KH K homology RNA-b 98.9 9.9E-09 2.1E-13 77.8 8.9 66 278-349 3-68 (69)
25 cd02393 PNPase_KH Polynucleoti 98.9 4.6E-09 9.9E-14 81.4 5.7 47 186-238 2-48 (61)
26 COG1094 Predicted RNA-binding 98.8 4.8E-08 1E-12 91.8 12.0 148 186-356 8-169 (194)
27 KOG2279 Kinase anchor protein 98.7 1.4E-08 3E-13 106.9 5.0 147 182-352 64-210 (608)
28 smart00322 KH K homology RNA-b 98.5 2.6E-07 5.6E-12 70.0 7.2 54 185-240 2-55 (69)
29 TIGR03665 arCOG04150 arCOG0415 98.2 1.2E-06 2.6E-11 81.3 5.1 61 282-351 2-65 (172)
30 PRK13763 putative RNA-processi 98.2 2.8E-06 6.1E-11 79.5 6.8 65 278-351 3-71 (180)
31 cd02395 SF1_like-KH Splicing f 98.1 6.3E-06 1.4E-10 72.5 7.2 67 287-353 15-97 (120)
32 PRK08406 transcription elongat 98.1 1E-05 2.3E-10 72.9 8.2 104 186-314 32-135 (140)
33 KOG2113 Predicted RNA binding 97.9 6.7E-06 1.5E-10 82.0 2.8 142 184-342 24-173 (394)
34 TIGR02696 pppGpp_PNP guanosine 97.9 6.3E-05 1.4E-09 83.3 10.1 92 247-351 550-642 (719)
35 cd02395 SF1_like-KH Splicing f 97.9 4E-05 8.8E-10 67.4 6.9 36 189-224 3-44 (120)
36 KOG2208 Vigilin [Lipid transpo 97.8 6.5E-05 1.4E-09 84.2 9.0 140 186-350 347-487 (753)
37 KOG2279 Kinase anchor protein 97.8 5.4E-05 1.2E-09 80.4 7.4 167 182-356 136-373 (608)
38 TIGR01952 nusA_arch NusA famil 97.7 8.3E-05 1.8E-09 67.2 6.3 103 187-314 34-136 (141)
39 TIGR03591 polynuc_phos polyrib 97.5 0.00033 7.1E-09 77.9 8.9 66 276-351 549-615 (684)
40 KOG0119 Splicing factor 1/bran 97.4 0.00074 1.6E-08 71.2 9.3 76 277-352 137-231 (554)
41 COG0195 NusA Transcription elo 97.4 0.00078 1.7E-08 63.8 8.5 101 188-314 78-178 (190)
42 KOG0336 ATP-dependent RNA heli 97.3 0.00057 1.2E-08 71.1 6.9 71 274-351 43-116 (629)
43 KOG2208 Vigilin [Lipid transpo 97.3 0.00067 1.4E-08 76.2 8.0 164 183-354 198-417 (753)
44 PLN00207 polyribonucleotide nu 97.0 0.0015 3.2E-08 74.2 7.4 67 275-351 682-750 (891)
45 TIGR02696 pppGpp_PNP guanosine 96.8 0.0019 4.1E-08 71.8 6.6 50 185-240 577-626 (719)
46 cd02134 NusA_KH NusA_K homolog 96.7 0.0027 5.8E-08 49.2 4.6 36 186-221 25-60 (61)
47 KOG0336 ATP-dependent RNA heli 96.6 0.0014 3E-08 68.4 2.9 57 181-240 42-98 (629)
48 TIGR03591 polynuc_phos polyrib 96.5 0.0032 6.9E-08 70.2 5.5 49 185-239 550-598 (684)
49 COG1185 Pnp Polyribonucleotide 96.5 0.0077 1.7E-07 66.2 8.1 73 277-359 551-624 (692)
50 cd02134 NusA_KH NusA_K homolog 96.5 0.004 8.7E-08 48.2 4.4 36 278-313 25-60 (61)
51 TIGR01953 NusA transcription t 96.4 0.0011 2.4E-08 68.0 1.2 94 195-314 243-337 (341)
52 PRK12328 nusA transcription el 96.4 0.0024 5.3E-08 66.1 3.5 93 195-314 251-344 (374)
53 KOG1588 RNA-binding protein Sa 96.4 0.0037 8E-08 61.6 4.2 39 184-222 90-134 (259)
54 PRK12327 nusA transcription el 96.4 0.0013 2.8E-08 68.0 1.1 94 195-314 245-339 (362)
55 PRK11824 polynucleotide phosph 96.3 0.0069 1.5E-07 67.7 6.6 65 277-351 553-618 (693)
56 KOG0119 Splicing factor 1/bran 96.3 0.0063 1.4E-07 64.4 5.9 39 185-223 137-181 (554)
57 PRK12329 nusA transcription el 96.2 0.011 2.4E-07 62.4 7.2 94 195-314 277-371 (449)
58 PRK04163 exosome complex RNA-b 96.2 0.011 2.4E-07 57.6 6.7 67 280-356 147-214 (235)
59 PRK09202 nusA transcription el 96.1 0.0025 5.3E-08 68.1 1.6 93 195-314 245-338 (470)
60 PRK00468 hypothetical protein; 95.9 0.0086 1.9E-07 48.6 3.6 35 182-216 26-60 (75)
61 KOG1588 RNA-binding protein Sa 95.8 0.046 1E-06 54.0 8.8 77 274-350 88-190 (259)
62 PRK02821 hypothetical protein; 95.7 0.011 2.4E-07 48.2 3.3 36 182-217 27-62 (77)
63 KOG2814 Transcription coactiva 95.6 0.016 3.4E-07 58.9 5.0 71 277-353 56-127 (345)
64 KOG2113 Predicted RNA binding 95.4 0.011 2.3E-07 59.7 3.0 65 275-347 23-88 (394)
65 PF14611 SLS: Mitochondrial in 95.4 0.66 1.4E-05 43.9 15.0 131 189-354 29-168 (210)
66 KOG2814 Transcription coactiva 95.4 0.019 4.1E-07 58.3 4.5 52 185-238 56-107 (345)
67 TIGR03319 YmdA_YtgF conserved 95.2 0.047 1E-06 59.1 7.4 64 279-351 205-270 (514)
68 COG1837 Predicted RNA-binding 95.2 0.022 4.8E-07 46.4 3.5 33 183-215 27-59 (76)
69 PRK00468 hypothetical protein; 95.1 0.024 5.1E-07 46.1 3.6 33 275-307 27-59 (75)
70 PRK12704 phosphodiesterase; Pr 95.1 0.056 1.2E-06 58.6 7.5 65 279-352 211-277 (520)
71 PRK00106 hypothetical protein; 94.9 0.071 1.5E-06 57.9 7.6 64 279-351 226-291 (535)
72 PLN00207 polyribonucleotide nu 94.9 0.027 5.9E-07 64.2 4.5 50 185-240 684-734 (891)
73 PRK01064 hypothetical protein; 94.8 0.029 6.3E-07 45.9 3.4 35 182-216 26-60 (78)
74 COG5176 MSL5 Splicing factor ( 94.8 0.074 1.6E-06 51.1 6.4 40 275-314 145-190 (269)
75 PRK02821 hypothetical protein; 94.7 0.032 6.9E-07 45.6 3.3 33 276-308 29-61 (77)
76 COG1837 Predicted RNA-binding 94.3 0.05 1.1E-06 44.3 3.6 32 275-306 27-58 (76)
77 PRK04163 exosome complex RNA-b 93.9 0.088 1.9E-06 51.3 5.2 47 188-240 147-193 (235)
78 KOG4369 RTK signaling protein 93.8 0.051 1.1E-06 62.7 3.6 70 279-351 1341-1410(2131)
79 PRK01064 hypothetical protein; 93.7 0.068 1.5E-06 43.8 3.4 33 275-307 27-59 (78)
80 COG1185 Pnp Polyribonucleotide 93.6 0.082 1.8E-06 58.4 4.7 48 187-240 553-600 (692)
81 COG5176 MSL5 Splicing factor ( 93.4 0.076 1.7E-06 51.0 3.5 39 185-223 147-191 (269)
82 PF13083 KH_4: KH domain; PDB: 92.8 0.069 1.5E-06 42.4 2.0 36 183-218 26-61 (73)
83 KOG3273 Predicted RNA-binding 92.7 0.068 1.5E-06 51.0 2.1 62 286-358 177-238 (252)
84 TIGR03319 YmdA_YtgF conserved 92.7 0.22 4.8E-06 54.0 6.3 48 186-238 204-252 (514)
85 PRK08406 transcription elongat 92.6 0.15 3.3E-06 46.1 4.2 37 278-314 32-68 (140)
86 PRK12704 phosphodiesterase; Pr 92.6 0.15 3.2E-06 55.4 4.8 48 186-238 210-258 (520)
87 PRK00106 hypothetical protein; 92.3 0.28 6E-06 53.5 6.4 48 186-238 225-273 (535)
88 PRK11824 polynucleotide phosph 92.1 0.13 2.8E-06 57.7 3.7 49 186-240 554-602 (693)
89 PRK06418 transcription elongat 91.7 0.83 1.8E-05 42.6 8.0 101 188-313 63-163 (166)
90 cd02409 KH-II KH-II (K homolo 91.7 0.27 5.8E-06 37.1 4.0 35 185-219 24-58 (68)
91 COG1094 Predicted RNA-binding 90.7 0.79 1.7E-05 43.7 6.9 68 278-354 8-80 (194)
92 PF13184 KH_5: NusA-like KH do 90.4 0.19 4.1E-06 40.1 2.1 35 188-222 5-45 (69)
93 cd02409 KH-II KH-II (K homolo 90.2 0.48 1E-05 35.7 4.2 35 277-311 24-58 (68)
94 PF13184 KH_5: NusA-like KH do 89.3 0.38 8.3E-06 38.4 3.1 36 279-314 4-45 (69)
95 PF07650 KH_2: KH domain syndr 89.1 0.22 4.9E-06 39.8 1.6 35 186-220 25-59 (78)
96 KOG1067 Predicted RNA-binding 88.1 1.2 2.7E-05 48.5 6.8 69 274-353 593-662 (760)
97 TIGR01952 nusA_arch NusA famil 88.0 0.68 1.5E-05 42.0 4.2 36 279-314 34-69 (141)
98 PF13083 KH_4: KH domain; PDB: 87.8 0.28 6E-06 38.9 1.4 33 276-308 27-59 (73)
99 PRK12705 hypothetical protein; 87.7 1.1 2.5E-05 48.5 6.4 63 280-351 200-264 (508)
100 PF07650 KH_2: KH domain syndr 87.1 0.3 6.5E-06 39.0 1.3 34 278-311 25-58 (78)
101 cd02414 jag_KH jag_K homology 86.9 0.63 1.4E-05 37.4 3.0 35 187-221 25-59 (77)
102 KOG4369 RTK signaling protein 85.8 0.33 7.2E-06 56.4 1.1 57 185-241 1339-1396(2131)
103 PRK12705 hypothetical protein; 83.8 0.8 1.7E-05 49.7 2.9 47 187-238 199-246 (508)
104 PF14611 SLS: Mitochondrial in 83.5 7.2 0.00016 36.9 9.0 63 280-351 28-90 (210)
105 COG0195 NusA Transcription elo 83.0 1.2 2.6E-05 42.4 3.3 37 187-223 143-179 (190)
106 COG1855 ATPase (PilT family) [ 82.7 0.9 1.9E-05 48.7 2.6 36 188-223 488-523 (604)
107 PRK13764 ATPase; Provisional 81.9 1.6 3.5E-05 48.3 4.4 37 278-314 481-517 (602)
108 cd02413 40S_S3_KH K homology R 81.9 1.6 3.4E-05 35.9 3.2 35 187-221 31-65 (81)
109 cd02414 jag_KH jag_K homology 81.8 1.6 3.4E-05 35.1 3.2 33 279-311 25-57 (77)
110 PRK12328 nusA transcription el 81.5 1.6 3.4E-05 45.7 3.8 39 185-223 307-345 (374)
111 COG1855 ATPase (PilT family) [ 81.4 1.1 2.3E-05 48.1 2.7 36 279-314 487-522 (604)
112 TIGR01953 NusA transcription t 80.9 1.7 3.6E-05 44.9 3.8 37 186-222 301-337 (341)
113 PRK13764 ATPase; Provisional 80.8 1.3 2.8E-05 49.1 3.1 38 186-223 481-518 (602)
114 KOG2874 rRNA processing protei 79.1 3.7 8E-05 41.3 5.4 51 290-351 161-211 (356)
115 COG1097 RRP4 RNA-binding prote 78.5 4 8.7E-05 40.1 5.4 59 280-348 148-207 (239)
116 cd02410 archeal_CPSF_KH The ar 78.0 6.3 0.00014 36.0 6.1 92 200-314 20-112 (145)
117 PRK12327 nusA transcription el 77.9 2.4 5.2E-05 44.2 3.9 39 185-223 302-340 (362)
118 PRK06418 transcription elongat 77.4 3.3 7.1E-05 38.7 4.2 35 279-314 62-96 (166)
119 PRK09202 nusA transcription el 76.7 2.1 4.6E-05 46.1 3.2 38 186-223 302-339 (470)
120 COG1097 RRP4 RNA-binding prote 76.4 4.6 0.0001 39.8 5.1 45 190-240 150-194 (239)
121 cd02412 30S_S3_KH K homology R 76.2 2.6 5.6E-05 36.3 3.0 31 187-217 62-92 (109)
122 PRK12329 nusA transcription el 74.3 2.8 6E-05 44.8 3.2 39 185-223 334-372 (449)
123 cd02411 archeal_30S_S3_KH K ho 73.9 3.5 7.7E-05 33.8 3.2 28 188-215 40-67 (85)
124 cd02413 40S_S3_KH K homology R 73.2 3.9 8.5E-05 33.5 3.2 35 279-313 31-65 (81)
125 cd02410 archeal_CPSF_KH The ar 73.2 4.6 0.0001 36.9 4.0 35 189-223 79-113 (145)
126 COG0092 RpsC Ribosomal protein 69.1 4.2 9.1E-05 39.9 2.9 31 185-215 50-80 (233)
127 COG1782 Predicted metal-depend 68.3 13 0.00028 40.6 6.5 93 199-314 42-135 (637)
128 TIGR00436 era GTP-binding prot 65.7 7.1 0.00015 38.3 3.9 30 186-215 221-251 (270)
129 cd02411 archeal_30S_S3_KH K ho 64.8 7.1 0.00015 32.0 3.1 28 280-307 40-67 (85)
130 cd02412 30S_S3_KH K homology R 64.5 6.3 0.00014 33.9 2.9 29 279-307 62-90 (109)
131 TIGR00436 era GTP-binding prot 61.5 8.8 0.00019 37.6 3.6 30 277-306 220-250 (270)
132 KOG3273 Predicted RNA-binding 57.3 4.8 0.00011 38.7 1.0 41 194-241 177-217 (252)
133 PRK00089 era GTPase Era; Revie 56.7 11 0.00025 37.0 3.5 38 277-314 225-271 (292)
134 PRK15494 era GTPase Era; Provi 56.5 12 0.00027 38.2 3.9 37 186-222 273-318 (339)
135 PRK15494 era GTPase Era; Provi 56.4 12 0.00025 38.4 3.6 37 278-314 273-318 (339)
136 PRK00089 era GTPase Era; Revie 55.9 13 0.00028 36.6 3.8 37 186-222 226-271 (292)
137 COG0092 RpsC Ribosomal protein 55.6 11 0.00023 37.1 3.0 38 277-314 50-92 (233)
138 TIGR03675 arCOG00543 arCOG0054 55.2 41 0.00089 37.7 7.9 93 200-315 37-130 (630)
139 COG5166 Uncharacterized conser 54.3 11 0.00023 41.1 3.0 127 199-351 393-524 (657)
140 KOG1423 Ras-like GTPase ERA [C 53.9 12 0.00025 38.7 3.0 32 185-216 327-359 (379)
141 COG1159 Era GTPase [General fu 50.5 18 0.00038 36.9 3.7 37 277-313 228-273 (298)
142 COG5166 Uncharacterized conser 49.0 17 0.00037 39.6 3.5 125 187-314 450-607 (657)
143 COG1159 Era GTPase [General fu 47.9 22 0.00047 36.2 3.9 38 185-222 228-274 (298)
144 KOG1067 Predicted RNA-binding 47.2 14 0.0003 40.7 2.5 49 184-239 595-643 (760)
145 CHL00048 rps3 ribosomal protei 43.8 23 0.00049 34.3 3.2 30 187-216 67-96 (214)
146 PRK04191 rps3p 30S ribosomal p 43.3 23 0.00051 34.0 3.2 31 188-218 42-72 (207)
147 TIGR01008 rpsC_E_A ribosomal p 43.1 24 0.00052 33.8 3.2 31 187-217 39-69 (195)
148 KOG1423 Ras-like GTPase ERA [C 41.3 25 0.00054 36.4 3.2 34 275-308 325-359 (379)
149 PTZ00084 40S ribosomal protein 41.3 26 0.00057 34.2 3.2 32 187-218 45-76 (220)
150 TIGR03675 arCOG00543 arCOG0054 39.3 32 0.00069 38.5 3.9 36 189-224 96-131 (630)
151 COG1847 Jag Predicted RNA-bind 38.6 23 0.0005 34.3 2.3 36 186-221 91-126 (208)
152 COG1782 Predicted metal-depend 37.1 36 0.00079 37.3 3.7 35 189-223 102-136 (637)
153 PRK13916 plasmid segregation p 34.7 24 0.00051 29.6 1.5 32 59-94 16-47 (97)
154 PRK04191 rps3p 30S ribosomal p 33.0 42 0.0009 32.3 3.2 28 280-307 42-69 (207)
155 KOG2874 rRNA processing protei 32.4 87 0.0019 31.9 5.3 37 197-240 160-196 (356)
156 TIGR01008 rpsC_E_A ribosomal p 31.1 48 0.001 31.8 3.2 28 279-306 39-66 (195)
157 COG1847 Jag Predicted RNA-bind 30.3 45 0.00098 32.3 2.9 35 279-313 92-126 (208)
158 CHL00048 rps3 ribosomal protei 30.0 49 0.0011 32.0 3.1 29 279-307 67-95 (214)
159 PTZ00084 40S ribosomal protein 29.4 51 0.0011 32.2 3.1 28 279-306 45-72 (220)
160 TIGR01009 rpsC_bact ribosomal 28.2 56 0.0012 31.6 3.2 29 188-216 64-92 (211)
161 COG1702 PhoH Phosphate starvat 27.7 1.4E+02 0.0031 31.1 6.1 52 284-346 21-72 (348)
162 PF02749 QRPTase_N: Quinolinat 23.6 4E+02 0.0087 21.6 7.7 70 275-350 15-85 (88)
163 PRK00310 rpsC 30S ribosomal pr 21.0 88 0.0019 30.7 3.0 30 187-216 63-92 (232)
164 TIGR01009 rpsC_bact ribosomal 20.8 92 0.002 30.1 3.1 27 280-306 64-90 (211)
No 1
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.96 E-value=4.4e-28 Score=238.32 Aligned_cols=186 Identities=26% Similarity=0.402 Sum_probs=148.0
Q ss_pred ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEcc---CCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhh
Q 014254 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA---TMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE 261 (428)
Q Consensus 185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~---~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e 261 (428)
.+++|||||+..+|.||||||++|.+||++|||+|++++ ++|+.+||+|.|+|+.+. .......|.++|.|
T Consensus 38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~ea------i~av~efI~dKire 111 (402)
T KOG2191|consen 38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEA------LNAVHEFIADKIRE 111 (402)
T ss_pred ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHH------HHHHHHHHHHHHHH
Confidence 499999999999999999999999999999999999986 489999999999998652 22233445566655
Q ss_pred ccccccc--C--CCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHH
Q 014254 262 GTSEKGL--D--FSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK 337 (428)
Q Consensus 262 ~~~~~g~--~--~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~a 337 (428)
....... + .....+....++|+||++.+|.||||||.+||.|++++||+|+|+. +.|...+..+|+||++|++++
T Consensus 112 ~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisP-qkpt~~sLqervvt~sge~e~ 190 (402)
T KOG2191|consen 112 KPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISP-QKPTGISLQERVVTVSGEPEQ 190 (402)
T ss_pred hHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecc-cCCCCccceeEEEEecCCHHH
Confidence 4322111 1 0111223356899999999999999999999999999999999983 345556789999999999999
Q ss_pred HHHHHHHHHHHhhhcCCCCc-cc-------CCCCCCCCCCCCCCCCCCCCCC
Q 014254 338 VKDAVYNVTGRLRDNHFSGT-LN-------TARTRSTSSVLTETSPYSRLKD 381 (428)
Q Consensus 338 V~~A~~lI~~~L~e~~~~~~-~~-------~p~~~~~~~~~~~~spy~~~~~ 381 (428)
..+|..+|.++|.++++.+. ++ .|.++++ +.+|||+...+
T Consensus 191 ~~~A~~~IL~Ki~eDpqs~scln~sya~vsGpvaNsn----PtGspya~~~~ 238 (402)
T KOG2191|consen 191 NMKAVSLILQKIQEDPQSGSCLNISYANVSGPVANSN----PTGSPYAYQAH 238 (402)
T ss_pred HHHHHHHHHHHhhcCCcccceeccchhcccCcccccC----CCCCCCCCCCc
Confidence 99999999999999998874 22 4555554 88889887633
No 2
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.94 E-value=1.2e-25 Score=236.29 Aligned_cols=169 Identities=37% Similarity=0.620 Sum_probs=144.6
Q ss_pred CCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhc
Q 014254 183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEG 262 (428)
Q Consensus 183 ~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~ 262 (428)
+...++||||+...+|.||||+|.+||+|+.+|+++|+|.+..+++.||+|+|+|..... ..+++++|+++++++++..
T Consensus 40 ~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~-~~~~~~~al~ka~~~iv~~ 118 (485)
T KOG2190|consen 40 DETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVEL-NLSPATDALFKAFDMIVFK 118 (485)
T ss_pred CCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccc-cCCchHHHHHHHHHHHhhc
Confidence 344559999999999999999999999999999999999999999999999999953222 6788999999999988764
Q ss_pred cc---ccccCCC-CCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHH
Q 014254 263 TS---EKGLDFS-SNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKV 338 (428)
Q Consensus 263 ~~---~~g~~~~-~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV 338 (428)
.. ....+.+ ......++++|+||.+++|+||||+|++||+|++.|||+|++.++++|. .++|.|+|.|++++|
T Consensus 119 ~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~---ster~V~IsG~~~av 195 (485)
T KOG2190|consen 119 LEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPN---STERAVTISGEPDAV 195 (485)
T ss_pred ccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCc---ccceeEEEcCchHHH
Confidence 21 1111222 1122368999999999999999999999999999999999999889998 588999999999999
Q ss_pred HHHHHHHHHHhhhcCCC
Q 014254 339 KDAVYNVTGRLRDNHFS 355 (428)
Q Consensus 339 ~~A~~lI~~~L~e~~~~ 355 (428)
.+|+..|..+|.+++..
T Consensus 196 ~~al~~Is~~L~~~~~~ 212 (485)
T KOG2190|consen 196 KKALVQISSRLLENPPR 212 (485)
T ss_pred HHHHHHHHHHHHhcCCc
Confidence 99999999999998743
No 3
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.92 E-value=7.3e-25 Score=229.38 Aligned_cols=252 Identities=22% Similarity=0.266 Sum_probs=187.8
Q ss_pred hhcCccccccCCcCcCCCCCCCCCc--------------cchhhhhcCccccccccccCCCCCcccCC-CCCceecccCC
Q 014254 91 LESGPQEILRRPLEVFAPESSHRSS--------------EALSIETQHRLFGAVSQEILPDLHVDILS-QRNSVLTTAPS 155 (428)
Q Consensus 91 ~~~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~~~~~~~~~~~v~~~~~~~~~~d~~P-gt~~rv~ti~G 155 (428)
||++++-. ++|.+.-+.+-.+.+| .+|-|+.||--|...+.++.=++...--| ++.+|.|.+.|
T Consensus 27 le~~~~p~-~~~~~~~~l~p~~~~s~~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G 105 (600)
T KOG1676|consen 27 LEDGPQPF-KGPSEDTDLDPDMDPSDTVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTG 105 (600)
T ss_pred ccccCccc-cCCCCccccCcccCCcccccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccC
Confidence 34444433 6666655555333333 34468888888888888886554433333 35889999999
Q ss_pred CcccccccccCCcccccccc--c-hhhhccCCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCC--CCCCc
Q 014254 156 SSISYVSAVRPLSLESDRVA--T-LDARTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATM--PECDE 230 (428)
Q Consensus 156 s~~~~~~a~~~~~~e~~~~~--~-~~~~~~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~--p~s~E 230 (428)
...++..+++.+.....+.. . ........+++.+|+||++++|+||||+|++||+|++.+||++.+-.+. .....
T Consensus 106 ~pe~v~~aK~li~evv~r~~~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~ 185 (600)
T KOG1676|consen 106 SPENVEVAKQLIGEVVSRGRPPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGAD 185 (600)
T ss_pred CcccHHHHHHhhhhhhhccCCCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCC
Confidence 99888888776655433321 1 1112234568999999999999999999999999999999999886542 23367
Q ss_pred eEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccc---cccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHh
Q 014254 231 RLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE---KGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVT 307 (428)
Q Consensus 231 RvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~---~g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~T 307 (428)
+.+.|+|.++. +..|..++++-+.+..-+ .....+.......+.++.||.+.||.||||+|++||+|+.+|
T Consensus 186 KplritGdp~~------ve~a~~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~et 259 (600)
T KOG1676|consen 186 KPLRITGDPDK------VEQAKQLVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNET 259 (600)
T ss_pred CceeecCCHHH------HHHHHHHHHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhcc
Confidence 88999999775 667777777766643221 112233334455689999999999999999999999999999
Q ss_pred CCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhc
Q 014254 308 GTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN 352 (428)
Q Consensus 308 GA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~ 352 (428)
|++|+|..|..|. +.+|.+.|.|+.+.|+.|.++|.++|.+.
T Consensus 260 G~KIQfkpDd~p~---speR~~~IiG~~d~ie~Aa~lI~eii~~~ 301 (600)
T KOG1676|consen 260 GAKIQFKPDDDPS---SPERPAQIIGTVDQIEHAAELINEIIAEA 301 (600)
T ss_pred CceeEeecCCCCC---CccceeeeecCHHHHHHHHHHHHHHHHHH
Confidence 9999999777764 89999999999999999999999999864
No 4
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.89 E-value=9.5e-23 Score=213.60 Aligned_cols=238 Identities=18% Similarity=0.238 Sum_probs=166.2
Q ss_pred CCCCccchhhhhcCccccccccccCCCC----CcccCCCCCceecccCCCcccccccc---cCCcccccc-ccchhh---
Q 014254 111 SHRSSEALSIETQHRLFGAVSQEILPDL----HVDILSQRNSVLTTAPSSSISYVSAV---RPLSLESDR-VATLDA--- 179 (428)
Q Consensus 111 ~~~~~~~~~~~~~~~~~~~v~~~~~~~~----~~d~~Pgt~~rv~ti~Gs~~~~~~a~---~~~~~e~~~-~~~~~~--- 179 (428)
-++...+|-|++||-.+-+||..+.-.. ..+.-++ +..-.-|.|....+..+. +.++.+... .+....
T Consensus 145 IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~-~~KplritGdp~~ve~a~~lV~dil~e~~~~~~g~~~~~g 223 (600)
T KOG1676|consen 145 IPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG-ADKPLRITGDPDKVEQAKQLVADILREEDDEVPGSGGHAG 223 (600)
T ss_pred cCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC-CCCceeecCCHHHHHHHHHHHHHHHHhcccCCCccccccC
Confidence 4677788999999999999999884211 1111121 334445556554444332 222222111 111101
Q ss_pred hccCCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC-CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHH
Q 014254 180 RTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT-MPECDERLITVTASEGPESRYSPAQKAVVLVFSR 258 (428)
Q Consensus 180 ~~~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~-~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~ 258 (428)
.......++++.||.+.||.||||+|++||+|+.+||++|+|-++ .+.+.||.+.|.|+.+. +..|..+|-+-
T Consensus 224 ~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~------ie~Aa~lI~ei 297 (600)
T KOG1676|consen 224 VRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQ------IEHAAELINEI 297 (600)
T ss_pred cCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHH------HHHHHHHHHHH
Confidence 112334599999999999999999999999999999999999754 56889999999999875 44454444333
Q ss_pred hhhccccc--ccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHH
Q 014254 259 LIEGTSEK--GLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFS 336 (428)
Q Consensus 259 i~e~~~~~--g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~ 336 (428)
+.+..... +...+. ........+.||.+.||.||||||++||.|..+|||++.++++ +...+.++++++|.|+..
T Consensus 298 i~~~~~~~~~~~~~G~-P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~--~p~~~~~ektf~IrG~~~ 374 (600)
T KOG1676|consen 298 IAEAEAGAGGGMGGGA-PGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ--PPNGNPKEKTFVIRGDKR 374 (600)
T ss_pred HHHHhccCCCCcCCCC-ccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC--CCCCCccceEEEEecCcc
Confidence 32221111 111111 1122278899999999999999999999999999999999966 444568899999999999
Q ss_pred HHHHHHHHHHHHhhhcCCCCcc
Q 014254 337 KVKDAVYNVTGRLRDNHFSGTL 358 (428)
Q Consensus 337 aV~~A~~lI~~~L~e~~~~~~~ 358 (428)
+|..|..||..++.+......+
T Consensus 375 QIdhAk~LIr~kvg~~~~n~~~ 396 (600)
T KOG1676|consen 375 QIDHAKQLIRDKVGDIAPNTPY 396 (600)
T ss_pred cchHHHHHHHHHhcccCCCCCC
Confidence 9999999999999986644333
No 5
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.88 E-value=2.4e-23 Score=205.08 Aligned_cols=221 Identities=20% Similarity=0.267 Sum_probs=175.9
Q ss_pred hhhhcCcccccccccc-----CCCCCcccCCCCCceecccCCCcccccccccCCccccccccch---------hhhccCC
Q 014254 119 SIETQHRLFGAVSQEI-----LPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATL---------DARTQQQ 184 (428)
Q Consensus 119 ~~~~~~~~~~~v~~~~-----~~~~~~d~~Pgt~~rv~ti~Gs~~~~~~a~~~~~~e~~~~~~~---------~~~~~~~ 184 (428)
-|++||+.|.++|.++ |+ ++.||||||++|||+|+|+. +...++|.|+.++.++.+. ++...++
T Consensus 53 IIGKGG~ti~~lqk~tgariklS-ks~dfyPGTTeRvcli~Gt~-eai~av~efI~dKire~p~~~~k~v~~~~pqt~~r 130 (402)
T KOG2191|consen 53 IIGKGGQTIVQLQKETGARIKLS-KSKDFYPGTTERVCLIQGTV-EALNAVHEFIADKIREKPQAVAKPVDILQPQTPDR 130 (402)
T ss_pred eeccchHHHHHHHhccCcEEEec-cccccCCCccceEEEEeccH-HHHHHHHHHHHHHHHHhHHhhcCCccccCCCCccc
Confidence 6899999999999998 78 99999999999999999999 5566788888887664332 2334556
Q ss_pred ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC---CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhh
Q 014254 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT---MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE 261 (428)
Q Consensus 185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~---~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e 261 (428)
..++||++|++.+|+||||+|.+||.|++++||.|+|++. .-+..||+|+++|++++ ..+|+-+|+.++.|
T Consensus 131 ~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~------~~~A~~~IL~Ki~e 204 (402)
T KOG2191|consen 131 IKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQ------NMKAVSLILQKIQE 204 (402)
T ss_pred cceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHH------HHHHHHHHHHHhhc
Confidence 6789999999999999999999999999999999999953 23678999999999875 78999999999987
Q ss_pred ccccc-----------c-----cCCC-------CCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc--cC
Q 014254 262 GTSEK-----------G-----LDFS-------SNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII--SD 316 (428)
Q Consensus 262 ~~~~~-----------g-----~~~~-------~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~--~d 316 (428)
..... + .+.+ ..........+-|+....|..-|.||.++-.+-..+|+.+.++ .+
T Consensus 205 Dpqs~scln~sya~vsGpvaNsnPtGspya~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l~ 284 (402)
T KOG2191|consen 205 DPQSGSCLNISYANVSGPVANSNPTGSPYAYQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQALN 284 (402)
T ss_pred CCcccceeccchhcccCcccccCCCCCCCCCCCccccccchhhccccccccccccccccccceeeecccccceeeccccc
Confidence 53210 0 0000 0112334556789999999999999999999999999999888 33
Q ss_pred CccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhh
Q 014254 317 QLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD 351 (428)
Q Consensus 317 ~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e 351 (428)
..- +..++ +-+.|-.-++..|-.+|..+...
T Consensus 285 ~m~---g~gy~-~n~~g~~ls~~aa~g~L~~~~~~ 315 (402)
T KOG2191|consen 285 TMA---GYGYN-TNILGLGLSILAAEGVLAAKVAS 315 (402)
T ss_pred ccc---ccccc-ccccchhhhhhhhhhHHHHhhcc
Confidence 222 24444 78889999999998888887754
No 6
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.86 E-value=2.4e-21 Score=203.89 Aligned_cols=225 Identities=28% Similarity=0.458 Sum_probs=168.4
Q ss_pred hhhhcCccccccccccCCCC-CcccCCCCCceecccCC---------CcccccccccCCccccccccc--hhh--hccCC
Q 014254 119 SIETQHRLFGAVSQEILPDL-HVDILSQRNSVLTTAPS---------SSISYVSAVRPLSLESDRVAT--LDA--RTQQQ 184 (428)
Q Consensus 119 ~~~~~~~~~~~v~~~~~~~~-~~d~~Pgt~~rv~ti~G---------s~~~~~~a~~~~~~e~~~~~~--~~~--~~~~~ 184 (428)
-|++.|..+...|+++-+.- -.+..|+..+|+.++.| ..+....+...+......+.. .+. .....
T Consensus 57 IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~ 136 (485)
T KOG2190|consen 57 IIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEEDDEAAEDNGEDASGP 136 (485)
T ss_pred EEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhcccccccccccCCccccCC
Confidence 57888999999998887633 45558999999999999 554444443333221111111 111 11122
Q ss_pred ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC-CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcc
Q 014254 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT-MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGT 263 (428)
Q Consensus 185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~-~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~ 263 (428)
++++|||||.+++|.||||+|+.||+|+++|||+|+|... .|.+++|.|+|.|.++. +.+|+..|...+.+..
T Consensus 137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~a------v~~al~~Is~~L~~~~ 210 (485)
T KOG2190|consen 137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDA------VKKALVQISSRLLENP 210 (485)
T ss_pred ceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHH------HHHHHHHHHHHHHhcC
Confidence 6899999999999999999999999999999999999876 79999999999999875 5666666666555410
Q ss_pred ----c---------c-----------cc----------------------------------------------------
Q 014254 264 ----S---------E-----------KG---------------------------------------------------- 267 (428)
Q Consensus 264 ----~---------~-----------~g---------------------------------------------------- 267 (428)
. . ..
T Consensus 211 ~~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~ 290 (485)
T KOG2190|consen 211 PRSPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASIS 290 (485)
T ss_pred CcCCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceE
Confidence 0 0 00
Q ss_pred -----cC-----C--CCCC-------------------------CceeEEEEEeccccccceeCCCCchHHHHHHHhCCe
Q 014254 268 -----LD-----F--SSNK-------------------------GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTS 310 (428)
Q Consensus 268 -----~~-----~--~~~~-------------------------~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~ 310 (428)
.+ . .... ...++.+|+||++++||||||+|++|.+||+.|||.
T Consensus 291 v~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~ 370 (485)
T KOG2190|consen 291 VGDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGAS 370 (485)
T ss_pred eccccCcceeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccchHHHHHhcCCc
Confidence 00 0 0000 234789999999999999999999999999999999
Q ss_pred EEEc-cCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhc
Q 014254 311 IRII-SDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDN 352 (428)
Q Consensus 311 IqI~-~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~ 352 (428)
|+|. +++.. ..+++.++|+|...+...|++++..++...
T Consensus 371 I~I~~~~~~~---~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~ 410 (485)
T KOG2190|consen 371 ISILNKEEVS---GVREALVQITGMLREDLLAQYLIRARLSAP 410 (485)
T ss_pred eEEccccccC---CcceeEEEecchhHHHHhhhhhcccccccC
Confidence 9999 55442 378999999999999999999998777643
No 7
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.83 E-value=1.9e-20 Score=180.52 Aligned_cols=221 Identities=19% Similarity=0.357 Sum_probs=161.0
Q ss_pred ccchhhhhcCccccccccccCCCCCcccCCCCCceecccCCCcccccccccCCccccccccchhh-hccCCceEEEEEec
Q 014254 115 SEALSIETQHRLFGAVSQEILPDLHVDILSQRNSVLTTAPSSSISYVSAVRPLSLESDRVATLDA-RTQQQEVSFRILCS 193 (428)
Q Consensus 115 ~~~~~~~~~~~~~~~v~~~~~~~~~~d~~Pgt~~rv~ti~Gs~~~~~~a~~~~~~e~~~~~~~~~-~~~~~evt~rIlVP 193 (428)
+.+--+++||+.|.+++-+...-..+ .-..+.+|+|+|+--...++.-...++ +.++. -.....+.+||||.
T Consensus 58 ~agavigkgg~nik~lr~d~na~v~v-pds~~peri~tisad~~ti~~ilk~ii------p~lee~f~~~~pce~rllih 130 (390)
T KOG2192|consen 58 NAGAVIGKGGKNIKALRTDYNASVSV-PDSSGPERILTISADIETIGEILKKII------PTLEEGFQLPSPCELRLLIH 130 (390)
T ss_pred cccceeccccccHHHHhhhccceeec-cCCCCCceeEEEeccHHHHHHHHHHHh------hhhhhCCCCCCchhhhhhhh
Confidence 34557899999999999886431111 123467899999865543332111111 11111 12334589999999
Q ss_pred cccccceeccCchHHHHHHHHhCCcEEEccC-CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccc-------
Q 014254 194 NDKVGAVIGKGGTIIRALQSEAGAFISVGAT-MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE------- 265 (428)
Q Consensus 194 ~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~-~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~------- 265 (428)
.+.+|.|||++|+.||.|++++.|+++|-.. .|++++|||.|.|.... ++..+..|++.+.|..+.
T Consensus 131 qs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~------v~~~i~~il~~i~e~pikgsa~py~ 204 (390)
T KOG2192|consen 131 QSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKR------VVECIKIILDLISESPIKGSAQPYD 204 (390)
T ss_pred hhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcch------HHHHHHHHHHHhhcCCcCCcCCcCC
Confidence 9999999999999999999999999998754 68999999999998776 556666666655441000
Q ss_pred ------------------------------------------------ccc---------C-------------------
Q 014254 266 ------------------------------------------------KGL---------D------------------- 269 (428)
Q Consensus 266 ------------------------------------------------~g~---------~------------------- 269 (428)
.+. +
T Consensus 205 p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~Sew 284 (390)
T KOG2192|consen 205 PNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEW 284 (390)
T ss_pred ccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCcCcccc
Confidence 000 0
Q ss_pred ----------------------CCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCc
Q 014254 270 ----------------------FSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDR 327 (428)
Q Consensus 270 ----------------------~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eR 327 (428)
.+.-.+...+.++.||.++-|.||||||..|++|++++||.|+|. +.+ .++.||
T Consensus 285 qmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikid-epl---eGsedr 360 (390)
T KOG2192|consen 285 QMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKID-EPL---EGSEDR 360 (390)
T ss_pred ccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEec-CcC---CCCCce
Confidence 000123456889999999999999999999999999999999996 212 247899
Q ss_pred EEEEEeCHHHHHHHHHHHHHHhhhc
Q 014254 328 VVQISGEFSKVKDAVYNVTGRLRDN 352 (428)
Q Consensus 328 vVtItGt~~aV~~A~~lI~~~L~e~ 352 (428)
+++|+|+.++++.|++++++.++.+
T Consensus 361 IitItGTqdQIqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 361 IITITGTQDQIQNAQYLLQNSVKQY 385 (390)
T ss_pred EEEEeccHHHHhhHHHHHHHHHHhh
Confidence 9999999999999999999999843
No 8
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.83 E-value=6.9e-20 Score=176.60 Aligned_cols=156 Identities=28% Similarity=0.490 Sum_probs=132.6
Q ss_pred cCCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhh
Q 014254 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE 261 (428)
Q Consensus 182 ~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e 261 (428)
....+.++||+.+..+|.||||||++||.|+.+.+|.|+|.+ .+..+|+++|+...+ .+..|+.+++.
T Consensus 44 k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpd--s~~peri~tisad~~----------ti~~ilk~iip 111 (390)
T KOG2192|consen 44 KRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPD--SSGPERILTISADIE----------TIGEILKKIIP 111 (390)
T ss_pred hhcceeEEEEEecccccceeccccccHHHHhhhccceeeccC--CCCCceeEEEeccHH----------HHHHHHHHHhh
Confidence 344589999999999999999999999999999999999987 567899999998654 55666665543
Q ss_pred cccccccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHH
Q 014254 262 GTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDA 341 (428)
Q Consensus 262 ~~~~~g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A 341 (428)
.. +.+ ......+.++|+|..+++|.|||++|++||++++++.|+.+|..+ .|..++||+|.|.|.+..|..+
T Consensus 112 ~l-ee~----f~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~---c~p~stdrv~l~~g~~k~v~~~ 183 (390)
T KOG2192|consen 112 TL-EEG----FQLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE---CCPHSTDRVVLIGGKPKRVVEC 183 (390)
T ss_pred hh-hhC----CCCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc---cCCCCcceEEEecCCcchHHHH
Confidence 21 111 123456889999999999999999999999999999999999754 4556999999999999999999
Q ss_pred HHHHHHHhhhcCCCCc
Q 014254 342 VYNVTGRLRDNHFSGT 357 (428)
Q Consensus 342 ~~lI~~~L~e~~~~~~ 357 (428)
++.|++.|.+.+.++.
T Consensus 184 i~~il~~i~e~pikgs 199 (390)
T KOG2192|consen 184 IKIILDLISESPIKGS 199 (390)
T ss_pred HHHHHHHhhcCCcCCc
Confidence 9999999999998763
No 9
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.82 E-value=3.1e-20 Score=187.76 Aligned_cols=160 Identities=26% Similarity=0.447 Sum_probs=138.1
Q ss_pred CceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC-CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhc
Q 014254 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT-MPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEG 262 (428)
Q Consensus 184 ~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~-~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~ 262 (428)
..-.+++.||...+|.||||+|.+||+|...+||.|+|..+ .++..+|.|+|+|.++. ..+|--.||.++.|.
T Consensus 409 e~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppea------qfKAQgrifgKikEe 482 (584)
T KOG2193|consen 409 EQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEA------QFKAQGRIFGKIKEE 482 (584)
T ss_pred chhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHH------HHhhhhhhhhhhhhh
Confidence 34578899999999999999999999999999999999875 57889999999998774 667888899998876
Q ss_pred ccccccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHH
Q 014254 263 TSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAV 342 (428)
Q Consensus 263 ~~~~g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~ 342 (428)
.+ +...+.-.....+-||++.+|+||||||++++|+++.|+|.+.|++|+.|+. .+.-+|.|+|...+.+.|+
T Consensus 483 nf-----~~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdE--nd~vivriiGhfyatq~aQ 555 (584)
T KOG2193|consen 483 NF-----FLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDE--NDQVIVRIIGHFYATQNAQ 555 (584)
T ss_pred cc-----CCchhhheeeeeeeccchhhhhhhccccccHHHHhccccceEEccccCCCCc--cceeeeeeechhhcchHHH
Confidence 54 2223456677889999999999999999999999999999999998888762 4445699999999999999
Q ss_pred HHHHHHhhhcCCCC
Q 014254 343 YNVTGRLRDNHFSG 356 (428)
Q Consensus 343 ~lI~~~L~e~~~~~ 356 (428)
+.|..++.+....+
T Consensus 556 rki~~iv~qvkq~~ 569 (584)
T KOG2193|consen 556 RKIAHIVNQVKQSG 569 (584)
T ss_pred HHHHHHHHHHHHhh
Confidence 99999999876543
No 10
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.77 E-value=1.1e-18 Score=176.73 Aligned_cols=162 Identities=23% Similarity=0.375 Sum_probs=132.7
Q ss_pred hccCCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC-CCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHH
Q 014254 180 RTQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT-MPECDERLITVTASEGPESRYSPAQKAVVLVFSR 258 (428)
Q Consensus 180 ~~~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~-~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~ 258 (428)
.....+..+|+|||..++|.||||.|++||.|-+.|.|+|.|... ..|..|+.|||.|+++. +-+|+.+|++-
T Consensus 193 ~~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg------~s~Ac~~ILei 266 (584)
T KOG2193|consen 193 KQQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG------TSKACKMILEI 266 (584)
T ss_pred cccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc------hHHHHHHHHHH
Confidence 344567899999999999999999999999999999999999764 46889999999999886 44566665554
Q ss_pred hhhcccccccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc--cCCccccCCCCCcEEEEEeCHH
Q 014254 259 LIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII--SDQLLKCISENDRVVQISGEFS 336 (428)
Q Consensus 259 i~e~~~~~g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~--~d~~P~~~~s~eRvVtItGt~~ 336 (428)
+-.+..+.. -...+.++++..+++||++|||.|.+||+|.++||++|.|. .| +.. .+.+|.+++.|+.+
T Consensus 267 mqkEA~~~k------~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqe-ls~--ynpERTItVkGsiE 337 (584)
T KOG2193|consen 267 MQKEAVDDK------VAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQE-LSL--YNPERTITVKGSIE 337 (584)
T ss_pred HHHhhhccc------hhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhh-hcc--cCccceEEecccHH
Confidence 433221111 12456778999999999999999999999999999999999 33 222 35799999999999
Q ss_pred HHHHHHHHHHHHhhhcCCCC
Q 014254 337 KVKDAVYNVTGRLRDNHFSG 356 (428)
Q Consensus 337 aV~~A~~lI~~~L~e~~~~~ 356 (428)
+|..|..+|+.+|+++.-.+
T Consensus 338 ac~~AE~eImkKlre~yEnD 357 (584)
T KOG2193|consen 338 ACVQAEAEIMKKLRECYEND 357 (584)
T ss_pred HHHHHHHHHHHHHHHHHhhh
Confidence 99999999999999887554
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=99.64 E-value=7.8e-16 Score=142.50 Aligned_cols=142 Identities=19% Similarity=0.257 Sum_probs=100.8
Q ss_pred EEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEee---CCCCCCcCccHHHHHHHHHHHHhhhccccc
Q 014254 190 ILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVT---ASEGPESRYSPAQKAVVLVFSRLIEGTSEK 266 (428)
Q Consensus 190 IlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtIt---Gs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~ 266 (428)
|.||.+.+|.|||+||++||.|+++|||+|++.+ ++..|.|. ++++ .+++|...+..-.....++.
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~-----~~g~V~I~~~t~d~~------~i~kA~~~I~~i~~gf~~e~ 70 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS-----ETGEVKIEEEDEDPL------AVMKAREVVKAIGRGFSPEK 70 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc-----CCceEEEecCCCCHH------HHHHHHHHHHHHHcCCCHHH
Confidence 5689999999999999999999999999999984 33568883 3322 25555544443222101110
Q ss_pred ccCCCCCCCceeEEE-EEecc---------ccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHH
Q 014254 267 GLDFSSNKGLLVNAR-LVVAS---------NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFS 336 (428)
Q Consensus 267 g~~~~~~~~~~vt~~-L~VP~---------s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~ 336 (428)
.. .. .+..+..+ +-|+. ..+|+|||++|++++.|++.|||+|.|. +..|.|+|+++
T Consensus 71 A~--~l-~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~-----------~~~v~i~G~~~ 136 (172)
T TIGR03665 71 AL--KL-LDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY-----------GKTVGIIGDPE 136 (172)
T ss_pred HH--Hh-cCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc-----------CCEEEEECCHH
Confidence 00 00 01112222 23333 3689999999999999999999999995 25699999999
Q ss_pred HHHHHHHHHHHHhhhcCCCC
Q 014254 337 KVKDAVYNVTGRLRDNHFSG 356 (428)
Q Consensus 337 aV~~A~~lI~~~L~e~~~~~ 356 (428)
+++.|..+|..+|.+.....
T Consensus 137 ~~~~A~~~i~~li~~~~~~~ 156 (172)
T TIGR03665 137 QVQIAREAIEMLIEGAPHGT 156 (172)
T ss_pred HHHHHHHHHHHHHcCCCChh
Confidence 99999999999997765443
No 12
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.59 E-value=9.3e-15 Score=136.27 Aligned_cols=145 Identities=17% Similarity=0.217 Sum_probs=101.4
Q ss_pred eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEee----CCCCCCcCccHHHHHHHHHHHHhhh
Q 014254 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVT----ASEGPESRYSPAQKAVVLVFSRLIE 261 (428)
Q Consensus 186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtIt----Gs~e~~~~~s~a~~Ai~~I~~~i~e 261 (428)
+...+.||.+.+|.|||++|++||.|+++|||+|++.+ ++..|.|. ++++ .+.+|...+..-...
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 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS-----ETGEVIIEPTDGEDPL------AVLKARDIVKAIGRG 71 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC-----CCCeEEEEeCCCCCHH------HHHHHHHHHHHHhcC
Confidence 45678999999999999999999999999999999984 34677785 3322 245555444432221
Q ss_pred cccccccCCCCCCCceeEEEE-Eec---------cccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEE
Q 014254 262 GTSEKGLDFSSNKGLLVNARL-VVA---------SNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQI 331 (428)
Q Consensus 262 ~~~~~g~~~~~~~~~~vt~~L-~VP---------~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtI 331 (428)
..++.... . .+..+..++ .|. ...+|+|||++|++++.|++.|||+|.|.. ..|.|
T Consensus 72 f~~e~A~~--l-~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~-----------~~v~i 137 (180)
T PRK13763 72 FSPEKALR--L-LDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG-----------KTVAI 137 (180)
T ss_pred CCHHHHHH--H-hCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC-----------CEEEE
Confidence 01110000 0 011112221 111 136899999999999999999999999952 34999
Q ss_pred EeCHHHHHHHHHHHHHHhhhcCCC
Q 014254 332 SGEFSKVKDAVYNVTGRLRDNHFS 355 (428)
Q Consensus 332 tGt~~aV~~A~~lI~~~L~e~~~~ 355 (428)
.|+++++..|...|..+++.....
T Consensus 138 ~G~~~~~~~A~~~I~~li~g~~~~ 161 (180)
T PRK13763 138 IGDPEQVEIAREAIEMLIEGAPHG 161 (180)
T ss_pred EeCHHHHHHHHHHHHHHHcCCCcH
Confidence 999999999999999999766543
No 13
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.42 E-value=4.6e-13 Score=104.61 Aligned_cols=65 Identities=42% Similarity=0.647 Sum_probs=58.1
Q ss_pred EEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHH
Q 014254 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVT 346 (428)
Q Consensus 279 t~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~ 346 (428)
+.+|+||.+.+|+||||+|++|++|++.|||+|++.++..+ ...+|+|+|+|++++++.|+.+|.
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLP---GSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCC---CCCceEEEEEeCHHHHHHHHHhhC
Confidence 36899999999999999999999999999999999844332 368999999999999999999873
No 14
>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=99.31 E-value=2.1e-12 Score=100.86 Aligned_cols=63 Identities=33% Similarity=0.665 Sum_probs=55.4
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCC-CCCceEEEeeCCCCCCcCccHHHHHHHHH
Q 014254 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMP-ECDERLITVTASEGPESRYSPAQKAVVLV 255 (428)
Q Consensus 187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p-~s~ERvVtItGs~e~~~~~s~a~~Ai~~I 255 (428)
++||+||.+.+|.||||+|++|++|+++|||+|++.+... +.++|+|+|+|+.++ +.+|+.+|
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 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSA------VQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHH------HHHHHHhh
Confidence 4799999999999999999999999999999999987643 788999999998765 66776654
No 15
>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=99.19 E-value=2.2e-11 Score=93.15 Aligned_cols=60 Identities=35% Similarity=0.528 Sum_probs=54.1
Q ss_pred EEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHH
Q 014254 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNV 345 (428)
Q Consensus 279 t~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI 345 (428)
|.+|.||.+++|+|||++|++|++|++.|||+|+|+++ ..+..|+|+|++++|+.|+.+|
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 57899999999999999999999999999999999743 1345899999999999999886
No 16
>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=99.18 E-value=4.3e-11 Score=92.09 Aligned_cols=60 Identities=20% Similarity=0.333 Sum_probs=54.5
Q ss_pred EEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHH
Q 014254 280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNV 345 (428)
Q Consensus 280 ~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI 345 (428)
.++.||.+++|+|||++|++|++|+++|||+|.|+... +.++.|+|+|+.++|..|..+|
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 57899999999999999999999999999999998432 4678999999999999999887
No 17
>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=99.13 E-value=1.7e-10 Score=89.39 Aligned_cols=58 Identities=21% Similarity=0.313 Sum_probs=52.6
Q ss_pred eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-HHHHHHHHHHH
Q 014254 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNV 345 (428)
Q Consensus 278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-~~aV~~A~~lI 345 (428)
....+.||.+++|+||||||++|++|+++|||+|.|.+ ++.|+|+|+ .++++.|..+|
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 35678999999999999999999999999999999962 457999999 99999999887
No 18
>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=99.09 E-value=3.4e-10 Score=86.68 Aligned_cols=62 Identities=35% Similarity=0.578 Sum_probs=55.3
Q ss_pred EEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHH
Q 014254 280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNV 345 (428)
Q Consensus 280 ~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI 345 (428)
.++.||.+++|+|||++|++|++|++.|||+|.|..... ...++.|+|.|+.+++..|+.+|
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 578999999999999999999999999999999983211 35789999999999999999886
No 19
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=98.97 E-value=3.3e-10 Score=86.56 Aligned_cols=52 Identities=27% Similarity=0.500 Sum_probs=46.0
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCC
Q 014254 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGP 241 (428)
Q Consensus 187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~ 241 (428)
|.+|.||.+.+|+||||+|++|++|+++|||+|+|++. + .+..|+|+|+.+.
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~--~-~~~~v~I~G~~~~ 52 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD--D-ERDIVTISGSPEQ 52 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--T-EEEEEEEEESHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--C-CcEEEEEEeCHHH
Confidence 57899999999999999999999999999999999865 3 4559999996553
No 20
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.97 E-value=1.1e-09 Score=83.80 Aligned_cols=54 Identities=33% Similarity=0.606 Sum_probs=48.6
Q ss_pred EEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCC
Q 014254 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGP 241 (428)
Q Consensus 188 ~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~ 241 (428)
.+|.||...+|.|||++|++|++|+++|||+|.|.+...+..++.|.|.|+.++
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~ 55 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEA 55 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHH
Confidence 579999999999999999999999999999999987555678999999998553
No 21
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.95 E-value=6e-10 Score=85.72 Aligned_cols=52 Identities=23% Similarity=0.254 Sum_probs=46.7
Q ss_pred EEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCC
Q 014254 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGP 241 (428)
Q Consensus 188 ~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~ 241 (428)
.+|.||.+.+|.|||++|++|++|+++|||+|.+++.. ..++.|+|+|+.++
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--~~~~~v~I~G~~~~ 53 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--SKSDTITITGPKEN 53 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--CCCCEEEEEcCHHH
Confidence 57899999999999999999999999999999998743 67899999998653
No 22
>PF13014 KH_3: KH domain
Probab=98.93 E-value=1.5e-09 Score=78.05 Aligned_cols=42 Identities=40% Similarity=0.743 Sum_probs=39.0
Q ss_pred cccceeccCchHHHHHHHHhCCcEEEcc-CCCCCCceEEEeeC
Q 014254 196 KVGAVIGKGGTIIRALQSEAGAFISVGA-TMPECDERLITVTA 237 (428)
Q Consensus 196 ~vG~IIGKgG~tIK~IqeeTGA~I~Is~-~~p~s~ERvVtItG 237 (428)
++|.||||+|++|++|+++|||+|+|++ ..++..+|+|+|+|
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 4799999999999999999999999998 56788999999998
No 23
>PF13014 KH_3: KH domain
Probab=98.91 E-value=2.1e-09 Score=77.39 Aligned_cols=43 Identities=44% Similarity=0.737 Sum_probs=38.0
Q ss_pred cccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEe
Q 014254 288 QVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG 333 (428)
Q Consensus 288 ~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItG 333 (428)
++|+||||+|++|++|+++|||+|+|+++..+ ..+++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~---~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEP---GSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCC---CCCceEEEEEC
Confidence 58999999999999999999999999963333 37899999998
No 24
>smart00322 KH K homology RNA-binding domain.
Probab=98.90 E-value=9.9e-09 Score=77.84 Aligned_cols=66 Identities=32% Similarity=0.553 Sum_probs=59.0
Q ss_pred eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHh
Q 014254 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRL 349 (428)
Q Consensus 278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L 349 (428)
.+.++.||...+|++||++|++|++|++.||++|.+.... .....|+|.|+.+++..|..+|.+.+
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 5678999999999999999999999999999999997321 25788999999999999999998876
No 25
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.85 E-value=4.6e-09 Score=81.43 Aligned_cols=47 Identities=28% Similarity=0.413 Sum_probs=42.5
Q ss_pred eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCC
Q 014254 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS 238 (428)
Q Consensus 186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs 238 (428)
....|.||.+.+|.||||||++||+|+++|||+|.|++ ++.|.|+|+
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~------~g~v~I~G~ 48 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED------DGTVYIAAS 48 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC------CCEEEEEeC
Confidence 35668999999999999999999999999999999974 467999996
No 26
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.81 E-value=4.8e-08 Score=91.76 Aligned_cols=148 Identities=20% Similarity=0.262 Sum_probs=102.0
Q ss_pred eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccc
Q 014254 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE 265 (428)
Q Consensus 186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~ 265 (428)
..+.+.||.+.+|.+||+.|++.+.|.+.+++++.+. +.+..|+|.......+ ....++|...+..- .
T Consensus 8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD-----~~~~~V~i~~~~~t~D-p~~~~ka~d~VkAI--g---- 75 (194)
T COG1094 8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID-----SKTGSVTIRTTRKTED-PLALLKARDVVKAI--G---- 75 (194)
T ss_pred ceeeeecCchhheeeecccccchHHHHhhcCeEEEEE-----CCCCeEEEEecCCCCC-hHHHHHHHHHHHHH--h----
Confidence 3566899999999999999999999999999999997 5678888987632111 11233333222111 0
Q ss_pred cccCCCCC---CCceeEEE------EEecc-----ccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEE
Q 014254 266 KGLDFSSN---KGLLVNAR------LVVAS-----NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQI 331 (428)
Q Consensus 266 ~g~~~~~~---~~~~vt~~------L~VP~-----s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtI 331 (428)
.|+++..+ -...+.+. +.-++ ...|+|||++|.+-+-|++.|||+|.|. +..|-|
T Consensus 76 rGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~-----------g~tVai 144 (194)
T COG1094 76 RGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY-----------GKTVAI 144 (194)
T ss_pred cCCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe-----------CcEEEE
Confidence 01110000 00011111 11111 2459999999999999999999999996 346999
Q ss_pred EeCHHHHHHHHHHHHHHhhhcCCCC
Q 014254 332 SGEFSKVKDAVYNVTGRLRDNHFSG 356 (428)
Q Consensus 332 tGt~~aV~~A~~lI~~~L~e~~~~~ 356 (428)
.|.+++|+.|...|..+|...+...
T Consensus 145 iG~~~~v~iAr~AVemli~G~~h~~ 169 (194)
T COG1094 145 IGGFEQVEIAREAVEMLINGAPHGK 169 (194)
T ss_pred ecChhhhHHHHHHHHHHHcCCCchh
Confidence 9999999999999999998776544
No 27
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=98.69 E-value=1.4e-08 Score=106.89 Aligned_cols=147 Identities=23% Similarity=0.387 Sum_probs=116.5
Q ss_pred cCCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhh
Q 014254 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE 261 (428)
Q Consensus 182 ~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e 261 (428)
..+++.++++|+...+-++|||+|++||.|++.++++|.+.+.. -.++++-++.|.+.+ ++++. ..++.++.+
T Consensus 64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p~~---v~~a~---a~~~~~~~~ 136 (608)
T KOG2279|consen 64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFPVQ---VCKAK---AAIHQILTE 136 (608)
T ss_pred chhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCCCC---CChHH---HHHHHHHhc
Confidence 34678899999999999999999999999999999999997532 245677777776554 33333 334444433
Q ss_pred cccccccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHH
Q 014254 262 GTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDA 341 (428)
Q Consensus 262 ~~~~~g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A 341 (428)
...+...+-+|...+++|+|++|.++.+|+..++|+|.+..+. .....+...|.|....+..|
T Consensus 137 -------------~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ng----r~g~~~~~~i~~qqk~~~~a 199 (608)
T KOG2279|consen 137 -------------NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNG----RLGLSRLIKISGQQKEVAAA 199 (608)
T ss_pred -------------CCcccccccchhhhcccccccchhhhcchhccccccccccccc----ccccccceecccccchHHHH
Confidence 3456778899999999999999999999999999999997331 12457788888888888899
Q ss_pred HHHHHHHhhhc
Q 014254 342 VYNVTGRLRDN 352 (428)
Q Consensus 342 ~~lI~~~L~e~ 352 (428)
..++.+++.++
T Consensus 200 ~~~~~~~~~ed 210 (608)
T KOG2279|consen 200 KHLILEKVSED 210 (608)
T ss_pred Hhhhhccccch
Confidence 99999988754
No 28
>smart00322 KH K homology RNA-binding domain.
Probab=98.55 E-value=2.6e-07 Score=69.95 Aligned_cols=54 Identities=33% Similarity=0.645 Sum_probs=46.9
Q ss_pred ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCC
Q 014254 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240 (428)
Q Consensus 185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e 240 (428)
.++.+|.||...+|.+||++|++|+.|++.||++|.+... .....+|.|.|..+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~--~~~~~~v~i~g~~~ 55 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPED--GSEERVVEITGPPE 55 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCC--CCCccEEEEEcCHH
Confidence 3578899999999999999999999999999999999752 22678899999854
No 29
>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=98.24 E-value=1.2e-06 Score=81.31 Aligned_cols=61 Identities=28% Similarity=0.367 Sum_probs=54.5
Q ss_pred EEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEE---EeCHHHHHHHHHHHHHHhhh
Q 014254 282 LVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQI---SGEFSKVKDAVYNVTGRLRD 351 (428)
Q Consensus 282 L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtI---tGt~~aV~~A~~lI~~~L~e 351 (428)
+.||.+.+|.|||+||++|++|++.|||+|++.. .+..|.| +++++++.+|..+|..+...
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~---------~~g~V~I~~~t~d~~~i~kA~~~I~~i~~g 65 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS---------ETGEVKIEEEDEDPLAVMKAREVVKAIGRG 65 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc---------CCceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence 5789999999999999999999999999999962 2356888 89999999999999997774
No 30
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.20 E-value=2.8e-06 Score=79.46 Aligned_cols=65 Identities=25% Similarity=0.270 Sum_probs=57.6
Q ss_pred eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEE----eCHHHHHHHHHHHHHHhhh
Q 014254 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQIS----GEFSKVKDAVYNVTGRLRD 351 (428)
Q Consensus 278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtIt----Gt~~aV~~A~~lI~~~L~e 351 (428)
....+.||.+.+|.|||++|++|+.|++.|||+|++.. .+..|.|. ++++++.+|+.+|..++..
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 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS---------ETGEVIIEPTDGEDPLAVLKARDIVKAIGRG 71 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC---------CCCeEEEEeCCCCCHHHHHHHHHHHHHHhcC
Confidence 35688999999999999999999999999999999962 23678885 8999999999999998874
No 31
>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=98.14 E-value=6.3e-06 Score=72.49 Aligned_cols=67 Identities=27% Similarity=0.318 Sum_probs=51.5
Q ss_pred ccccceeCCCCchHHHHHHHhCCeEEEccCCc------------cccCC-CCCcEEEEEeCH---HHHHHHHHHHHHHhh
Q 014254 287 NQVGCLLGKGGTIISEMRKVTGTSIRIISDQL------------LKCIS-ENDRVVQISGEF---SKVKDAVYNVTGRLR 350 (428)
Q Consensus 287 s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~------------P~~~~-s~eRvVtItGt~---~aV~~A~~lI~~~L~ 350 (428)
+++|.|||++|++||+|+++|||+|.|.++.. |.... ...-.|.|++.. +++++|..+|..++.
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~ 94 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK 94 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence 57899999999999999999999999984310 11011 122459999965 899999999999998
Q ss_pred hcC
Q 014254 351 DNH 353 (428)
Q Consensus 351 e~~ 353 (428)
+..
T Consensus 95 ~~~ 97 (120)
T cd02395 95 PAI 97 (120)
T ss_pred cCC
Confidence 443
No 32
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.11 E-value=1e-05 Score=72.89 Aligned_cols=104 Identities=20% Similarity=0.300 Sum_probs=70.8
Q ss_pred eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccc
Q 014254 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE 265 (428)
Q Consensus 186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~ 265 (428)
-.+.|+|+...+|..||++|++|+.|++..|-+|.|-. - +.+ ..+-+..++. .....
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve-----------~--s~d-------~~~fI~n~l~---Pa~V~ 88 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE-----------Y--SDD-------PEEFIKNIFA---PAAVR 88 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE-----------c--CCC-------HHHHHHHHcC---CCEEE
Confidence 35668999999999999999999999999998887743 1 112 1111111111 11000
Q ss_pred cccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254 266 KGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (428)
Q Consensus 266 ~g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~ 314 (428)
. ..- ........+.+.|+.+..|..|||+|++|+.++..+|-++.|.
T Consensus 89 ~-v~I-~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 89 S-VTI-KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred E-EEE-EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 0 000 0012234667889999999999999999999999999888773
No 33
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.88 E-value=6.7e-06 Score=81.99 Aligned_cols=142 Identities=21% Similarity=0.279 Sum_probs=99.0
Q ss_pred CceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHH-----
Q 014254 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSR----- 258 (428)
Q Consensus 184 ~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~----- 258 (428)
+.++..+-+|...++.|.|++|.+||.|+.+|...|+-+ ....+-++.++|..+. +..|-..+...
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tP---sr~eePiF~vTg~~ed------v~~aRrei~saaeH~~ 94 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTP---SRGEEPIFPVTGRHED------VRRARREIPSAAEHFG 94 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccC---CCCCCCcceeccCchh------HHHHhhcCccccceee
Confidence 568888899999999999999999999999999999865 2345578889998775 22222222110
Q ss_pred -hhhcccccccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc-cCCccccCCCCCcEEEEEeCHH
Q 014254 259 -LIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII-SDQLLKCISENDRVVQISGEFS 336 (428)
Q Consensus 259 -i~e~~~~~g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~-~d~~P~~~~s~eRvVtItGt~~ 336 (428)
+.......+.-.+.......+...-+|...+|.|.|..|.+|+.|++.+...|.-+ .+ .+-++.++|-+.
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 00000000001111123445667889999999999999999999999999999887 32 456677888777
Q ss_pred H-HHHHH
Q 014254 337 K-VKDAV 342 (428)
Q Consensus 337 a-V~~A~ 342 (428)
+ +++|.
T Consensus 167 nC~kra~ 173 (394)
T KOG2113|consen 167 NCVKRAR 173 (394)
T ss_pred chhhhcc
Confidence 7 44444
No 34
>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=97.86 E-value=6.3e-05 Score=83.27 Aligned_cols=92 Identities=16% Similarity=0.207 Sum_probs=69.4
Q ss_pred HHHHHHHHHHHHhhhcccccccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCC
Q 014254 247 PAQKAVVLVFSRLIEGTSEKGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISEND 326 (428)
Q Consensus 247 ~a~~Ai~~I~~~i~e~~~~~g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~e 326 (428)
.+.++...|++.+.+..... . ....-......+.||.+.+|.|||+||++|++|+++|||+|.|. .+
T Consensus 550 ~A~~g~~~Il~~m~~al~~p-~--~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~----------d~ 616 (719)
T TIGR02696 550 QARDARLAILDVMAEAIDTP-D--EMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE----------DD 616 (719)
T ss_pred HHHHHHHHHHHHHHHHHhCc-c--ccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe----------cC
Confidence 45556666665544322211 1 11233456778999999999999999999999999999999995 35
Q ss_pred cEEEEEeC-HHHHHHHHHHHHHHhhh
Q 014254 327 RVVQISGE-FSKVKDAVYNVTGRLRD 351 (428)
Q Consensus 327 RvVtItGt-~~aV~~A~~lI~~~L~e 351 (428)
..|.|.+. .+++++|+.+|..++..
T Consensus 617 G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 617 GTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 67999995 88999999999999884
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=97.85 E-value=4e-05 Score=67.40 Aligned_cols=36 Identities=28% Similarity=0.537 Sum_probs=31.1
Q ss_pred EEEecc------ccccceeccCchHHHHHHHHhCCcEEEccC
Q 014254 189 RILCSN------DKVGAVIGKGGTIIRALQSEAGAFISVGAT 224 (428)
Q Consensus 189 rIlVP~------~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~ 224 (428)
|+.||. +.+|.|||++|++||+|+++|||+|.|...
T Consensus 3 ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~ 44 (120)
T cd02395 3 KVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGK 44 (120)
T ss_pred EEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecC
Confidence 455665 478999999999999999999999999763
No 36
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=97.79 E-value=6.5e-05 Score=84.16 Aligned_cols=140 Identities=16% Similarity=0.258 Sum_probs=104.4
Q ss_pred eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccc
Q 014254 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE 265 (428)
Q Consensus 186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~ 265 (428)
+...+-+-......|+||+|.+|.+|+++++|.|.+.. .+.++..+.++|...+ +..+.+.+..++..+..
T Consensus 347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~--~~~~~~~v~~~~~~~~---~~ka~~~v~~~~~ei~n---- 417 (753)
T KOG2208|consen 347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK--QGSNNKKVVITGVSAN---DEKAVEDVEKIIAEILN---- 417 (753)
T ss_pred eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc--ccCCCCCeEEeccccc---hhHHHHHHHHHHHhhhc----
Confidence 56667778889999999999999999999999999986 5677888999997665 22333334333333321
Q ss_pred cccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhC-CeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHH
Q 014254 266 KGLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTG-TSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYN 344 (428)
Q Consensus 266 ~g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TG-A~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~l 344 (428)
......+.||...+..+||.+|..|++|...+| ..|+...+. .....+++.|....+..+..+
T Consensus 418 ----------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~------~~~~~~~~~~~~~dv~~~~~~ 481 (753)
T KOG2208|consen 418 ----------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN------NSSDMVTIRGISKDVEKSVSL 481 (753)
T ss_pred ----------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC------cccccceEeccccccchhHHH
Confidence 134557899999999999999999999999999 666665321 334557888887777766666
Q ss_pred HHHHhh
Q 014254 345 VTGRLR 350 (428)
Q Consensus 345 I~~~L~ 350 (428)
+..+..
T Consensus 482 ~~~~~~ 487 (753)
T KOG2208|consen 482 LKALKA 487 (753)
T ss_pred HHhhhh
Confidence 655554
No 37
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=97.77 E-value=5.4e-05 Score=80.41 Aligned_cols=167 Identities=19% Similarity=0.235 Sum_probs=113.0
Q ss_pred cCCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhh
Q 014254 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIE 261 (428)
Q Consensus 182 ~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e 261 (428)
.+..+...+-+|...++.|+|++|.+++.|+.-++|+|.+....-..-.+...|.|....+ ..|-.++.+++.+
T Consensus 136 ~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~------~~a~~~~~~~~~e 209 (608)
T KOG2279|consen 136 ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEV------AAAKHLILEKVSE 209 (608)
T ss_pred cCCcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchH------HHHHhhhhccccc
Confidence 3456777888999999999999999999999999999999876445567888888865431 1111112222111
Q ss_pred c----------------------cc-----------------------ccccCC-----C--------------------
Q 014254 262 G----------------------TS-----------------------EKGLDF-----S-------------------- 271 (428)
Q Consensus 262 ~----------------------~~-----------------------~~g~~~-----~-------------------- 271 (428)
. .+ ..+.+. +
T Consensus 210 deelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~ 289 (608)
T KOG2279|consen 210 DEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSF 289 (608)
T ss_pred hhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCcccccc
Confidence 0 00 000000 0
Q ss_pred CCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccC-CCCCcEEEEEeCHHHHHHHHHHHHHHhh
Q 014254 272 SNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCI-SENDRVVQISGEFSKVKDAVYNVTGRLR 350 (428)
Q Consensus 272 ~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~-~s~eRvVtItGt~~aV~~A~~lI~~~L~ 350 (428)
........-++.||..++|.+||+.|+.++.+...+++.+.|... |-.. ...-.++.+.|+..-+..|..|+..+.-
T Consensus 290 ~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~--pyt~~v~~~qic~~egkqh~~n~vl~ml~~~~p 367 (608)
T KOG2279|consen 290 QKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQ--PYTSRVLQLQICVNEGKQHYENSVLEMLTVHVP 367 (608)
T ss_pred ccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEec--cccchhhhhhhheecchhHHHHHHHhhhhccCC
Confidence 001122345789999999999999999999999999999999722 2200 0112457899999999999999996555
Q ss_pred hcCCCC
Q 014254 351 DNHFSG 356 (428)
Q Consensus 351 e~~~~~ 356 (428)
+..|..
T Consensus 368 ~~~f~e 373 (608)
T KOG2279|consen 368 DIVFAE 373 (608)
T ss_pred cccccc
Confidence 444443
No 38
>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=97.68 E-value=8.3e-05 Score=67.22 Aligned_cols=103 Identities=22% Similarity=0.284 Sum_probs=69.7
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhccccc
Q 014254 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEK 266 (428)
Q Consensus 187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~ 266 (428)
.+-|+|....+|..||++|++|+.|++..|-+|.|-. -+ .+. ...+.+.+......
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe-----------ys--~D~----------~~fI~N~l~PA~V~- 89 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE-----------YS--ENL----------EEFVANKLAPAEVK- 89 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE-----------cC--CCH----------HHHHHHcCCCceEE-
Confidence 5668999999999999999999999988888887743 11 111 00111111110000
Q ss_pred ccCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254 267 GLDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (428)
Q Consensus 267 g~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~ 314 (428)
.... ...+......+.||.+..|..|||+|++++...+.+|-++.|.
T Consensus 90 ~V~i-~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 90 NVTV-SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred EEEE-EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 0000 0012335678899999999999999999999999999888773
No 39
>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=97.49 E-value=0.00033 Score=77.94 Aligned_cols=66 Identities=21% Similarity=0.358 Sum_probs=56.5
Q ss_pred ceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-HHHHHHHHHHHHHHhhh
Q 014254 276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRLRD 351 (428)
Q Consensus 276 ~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-~~aV~~A~~lI~~~L~e 351 (428)
......+.||.+.+|.|||+||++||+|+++|||+|.|. .+-.|.|.+. ...+.+|..+|..+..+
T Consensus 549 ~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~----------ddG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 549 APRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE----------DDGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred CCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEe----------cCeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 355678899999999999999999999999999999995 2456888875 77889999999988764
No 40
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.38 E-value=0.00074 Score=71.22 Aligned_cols=76 Identities=21% Similarity=0.318 Sum_probs=57.9
Q ss_pred eeEEEEEecc------ccccceeCCCCchHHHHHHHhCCeEEEcc-----CCc------cccCCCCCc-EEEEEeC-HHH
Q 014254 277 LVNARLVVAS------NQVGCLLGKGGTIISEMRKVTGTSIRIIS-----DQL------LKCISENDR-VVQISGE-FSK 337 (428)
Q Consensus 277 ~vt~~L~VP~------s~VG~IIGKgG~~IkeIre~TGA~IqI~~-----d~~------P~~~~s~eR-vVtItGt-~~a 337 (428)
.++.+|.||- ++||.|||..|.+.|+|+++|||+|.|-+ |.. .......+. -+.|+++ .+.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek 216 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK 216 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence 5667788875 58999999999999999999999999983 111 111112233 3888886 778
Q ss_pred HHHHHHHHHHHhhhc
Q 014254 338 VKDAVYNVTGRLRDN 352 (428)
Q Consensus 338 V~~A~~lI~~~L~e~ 352 (428)
|++|+.+|..+|.+.
T Consensus 217 i~~Ai~vienli~~a 231 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSA 231 (554)
T ss_pred HHHHHHHHHHHHHhh
Confidence 999999999999963
No 41
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=97.36 E-value=0.00078 Score=63.78 Aligned_cols=101 Identities=28% Similarity=0.325 Sum_probs=67.4
Q ss_pred EEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccccc
Q 014254 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKG 267 (428)
Q Consensus 188 ~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~g 267 (428)
+-+.+-.+.+|..|||+|++|+.|+++.|-+|.|-. -++++ ..-+..++.-..-....
T Consensus 78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe-------------~s~d~-------~~fI~nal~Pa~v~~V~-- 135 (190)
T COG0195 78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVE-------------WSEDP-------AEFIKNALAPAEVLSVN-- 135 (190)
T ss_pred EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEE-------------eCCCH-------HHHHHHhcCcceEeEEE--
Confidence 334555678999999999999999999997676632 22332 11111111100000000
Q ss_pred cCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254 268 LDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (428)
Q Consensus 268 ~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~ 314 (428)
.. . .+.. ...+.||.++.+..|||+|.+++-+.+.||-++.|.
T Consensus 136 ~~--~-~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~ 178 (190)
T COG0195 136 IK--E-DDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIE 178 (190)
T ss_pred EE--e-CCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEE
Confidence 00 0 0111 678899999999999999999999999999999996
No 42
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.27 E-value=0.00057 Score=71.12 Aligned_cols=71 Identities=25% Similarity=0.289 Sum_probs=55.3
Q ss_pred CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHH---HHHhh
Q 014254 274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNV---TGRLR 350 (428)
Q Consensus 274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI---~~~L~ 350 (428)
........+.|.+++||.|||+||++|+.||..|+++|+|.+. ..+-.|+|-|...--.+|...| ..+..
T Consensus 43 g~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~-------~~e~kv~ifg~~~m~~kaka~id~~~~k~e 115 (629)
T KOG0336|consen 43 GGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC-------DLEVKVTIFGINHMRKKAKASIDRGQDKDE 115 (629)
T ss_pred CCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc-------CceeEEEEechHHHHHHHHhhHhhhhhhhh
Confidence 3455667788999999999999999999999999999999843 3467899999966555554444 44444
Q ss_pred h
Q 014254 351 D 351 (428)
Q Consensus 351 e 351 (428)
+
T Consensus 116 ~ 116 (629)
T KOG0336|consen 116 R 116 (629)
T ss_pred h
Confidence 4
No 43
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=97.27 E-value=0.00067 Score=76.18 Aligned_cols=164 Identities=18% Similarity=0.179 Sum_probs=108.1
Q ss_pred CCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCc-CccHHHHHHHHHHH----
Q 014254 183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPES-RYSPAQKAVVLVFS---- 257 (428)
Q Consensus 183 ~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~-~~s~a~~Ai~~I~~---- 257 (428)
..-+..++.+-...++.+||+||.+++.+++++.+.|+|.... .......|.|..+... ...-.+.++.++-.
T Consensus 198 ~r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn--~~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~ 275 (753)
T KOG2208|consen 198 ERSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSN--KSSPSNKIDGRLNSSSSINVEIQEALTRLESEFDY 275 (753)
T ss_pred ceeEEEEeeccccchhhhccccccccccccccceeEEEccccc--ccchhhhhccccccceehhhhhHHHHHHhcChhhh
Confidence 3447888999999999999999999999999999999998531 1111122222211100 00001111111100
Q ss_pred -----H----------------hhhc---------ccccccC----CC-----------------CCCCceeEEEEEecc
Q 014254 258 -----R----------------LIEG---------TSEKGLD----FS-----------------SNKGLLVNARLVVAS 286 (428)
Q Consensus 258 -----~----------------i~e~---------~~~~g~~----~~-----------------~~~~~~vt~~L~VP~ 286 (428)
+ +... .+....+ .+ .-....+.+.+.|-.
T Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~ 355 (753)
T KOG2208|consen 276 DEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFP 355 (753)
T ss_pred hhhhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecH
Confidence 0 0000 0000000 00 002344678889999
Q ss_pred ccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhcCC
Q 014254 287 NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHF 354 (428)
Q Consensus 287 s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~~~ 354 (428)
..+..++||+|.+|.+|++.+++.|.+... ++++..|.++|...++.+|...+...+.+-+.
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 999999999999999999999999999742 26788899999999999999999988887665
No 44
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.00 E-value=0.0015 Score=74.17 Aligned_cols=67 Identities=18% Similarity=0.260 Sum_probs=57.8
Q ss_pred CceeEEEEEeccccccceeCCCCchHHHHHHHhCCe-EEEccCCccccCCCCCcEEEEEeC-HHHHHHHHHHHHHHhhh
Q 014254 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTS-IRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRLRD 351 (428)
Q Consensus 275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~-IqI~~d~~P~~~~s~eRvVtItGt-~~aV~~A~~lI~~~L~e 351 (428)
-......+.||.+.+|.|||.||++|++|.++||++ |.+. .+-.|.|.+. .+++++|+.+|.++..+
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 345677899999999999999999999999999999 8884 2456889885 88999999999998764
No 45
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=96.85 E-value=0.0019 Score=71.82 Aligned_cols=50 Identities=32% Similarity=0.519 Sum_probs=43.8
Q ss_pred ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCC
Q 014254 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240 (428)
Q Consensus 185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e 240 (428)
.....+.||.+++|.|||+||.+||.|+++||++|.|.+ +..|.|.+...
T Consensus 577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------~G~V~I~a~d~ 626 (719)
T TIGR02696 577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADG 626 (719)
T ss_pred CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCH
Confidence 356778999999999999999999999999999999974 57799998643
No 46
>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=96.70 E-value=0.0027 Score=49.20 Aligned_cols=36 Identities=31% Similarity=0.541 Sum_probs=33.7
Q ss_pred eEEEEEeccccccceeccCchHHHHHHHHhCCcEEE
Q 014254 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV 221 (428)
Q Consensus 186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~I 221 (428)
..+.+.|+.+.+|.+|||+|.+|+.+++.+|-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 678899999999999999999999999999988876
No 47
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.59 E-value=0.0014 Score=68.40 Aligned_cols=57 Identities=23% Similarity=0.297 Sum_probs=49.1
Q ss_pred ccCCceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCC
Q 014254 181 TQQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240 (428)
Q Consensus 181 ~~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e 240 (428)
....++.+.|.|-+..||.|||+||++||.||..|+++|+|.+ ...+-.|+|-|...
T Consensus 42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~---~~~e~kv~ifg~~~ 98 (629)
T KOG0336|consen 42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIK---CDLEVKVTIFGINH 98 (629)
T ss_pred cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEec---cCceeEEEEechHH
Confidence 4567788899999999999999999999999999999999974 34567799999643
No 48
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=96.52 E-value=0.0032 Score=70.21 Aligned_cols=49 Identities=33% Similarity=0.508 Sum_probs=42.3
Q ss_pred ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCC
Q 014254 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239 (428)
Q Consensus 185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~ 239 (428)
.....+.||.+++|.|||+||++||.|+++|||+|.|.+ +-.|.|.+..
T Consensus 550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------dG~V~i~~~~ 598 (684)
T TIGR03591 550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------DGTVKIAASD 598 (684)
T ss_pred CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec------CeEEEEEECc
Confidence 456778999999999999999999999999999999974 4567787753
No 49
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.50 E-value=0.0077 Score=66.20 Aligned_cols=73 Identities=19% Similarity=0.291 Sum_probs=61.1
Q ss_pred eeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCH-HHHHHHHHHHHHHhhhcCCC
Q 014254 277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEF-SKVKDAVYNVTGRLRDNHFS 355 (428)
Q Consensus 277 ~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~-~aV~~A~~lI~~~L~e~~~~ 355 (428)
.....+.|+.+.++-+||+||++|++|.++|||+|.|. .+-.|.|.++. +.+.+|+..|.++.++.-..
T Consensus 551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie----------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg 620 (692)
T COG1185 551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE----------DDGTVKIAASDGESAKKAKERIEAITREVEVG 620 (692)
T ss_pred CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec----------CCCcEEEEecchHHHHHHHHHHHHHHhhcccc
Confidence 34567889999999999999999999999999999995 24469999985 78899999999999776554
Q ss_pred Cccc
Q 014254 356 GTLN 359 (428)
Q Consensus 356 ~~~~ 359 (428)
..|.
T Consensus 621 ~iy~ 624 (692)
T COG1185 621 EVYE 624 (692)
T ss_pred cEEE
Confidence 4443
No 50
>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=96.50 E-value=0.004 Score=48.21 Aligned_cols=36 Identities=39% Similarity=0.611 Sum_probs=33.9
Q ss_pred eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEE
Q 014254 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRI 313 (428)
Q Consensus 278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI 313 (428)
....+.|+.+.+|.+|||+|.+|+.+++.+|-+|.+
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 578899999999999999999999999999998876
No 51
>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=96.44 E-value=0.0011 Score=68.04 Aligned_cols=94 Identities=28% Similarity=0.393 Sum_probs=62.7
Q ss_pred ccccceeccCchHHHHHHHHh-CCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccccccCCCCC
Q 014254 195 DKVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN 273 (428)
Q Consensus 195 ~~vG~IIGKgG~tIK~IqeeT-GA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~g~~~~~~ 273 (428)
+-+|..||++|++|+.|.++. |=+|.|-. =+.++ ...+...+....... ..- .
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~-------------~s~d~----------~~fi~nal~Pa~v~~-v~i-~- 296 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIE-------------YSDDP----------AEFIANALSPAKVIS-VEV-L- 296 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEE-------------cCCCH----------HHHHHHhcCCceEEE-EEE-E-
Confidence 469999999999999999998 66666632 12221 001111111100000 000 0
Q ss_pred CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254 274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (428)
Q Consensus 274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~ 314 (428)
......+.+.||.++.+..|||+|.+++-..+.||.+|.|.
T Consensus 297 ~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~ 337 (341)
T TIGR01953 297 DEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVK 337 (341)
T ss_pred cCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEE
Confidence 01224688999999999999999999999999999999996
No 52
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.42 E-value=0.0024 Score=66.06 Aligned_cols=93 Identities=25% Similarity=0.293 Sum_probs=62.8
Q ss_pred ccccceeccCchHHHHHHHHh-CCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccccccCCCCC
Q 014254 195 DKVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN 273 (428)
Q Consensus 195 ~~vG~IIGKgG~tIK~IqeeT-GA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~g~~~~~~ 273 (428)
+-+|..||++|.+|+.|.++. |=+|.|-. =+.++ ...+...+....... ...
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~-------------~s~D~----------~~fI~Nal~Pa~V~~-V~i--- 303 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIE-------------YSNVP----------EIFIARALAPAIISS-VKI--- 303 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEE-------------cCCCH----------HHHHHHhCCCceeeE-EEE---
Confidence 469999999999999999998 66666632 12221 011111111100000 000
Q ss_pred CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254 274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (428)
Q Consensus 274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~ 314 (428)
......+.+.||.++.+..|||+|.+++-..+.||.+|.|.
T Consensus 304 ~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~ 344 (374)
T PRK12328 304 EEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELN 344 (374)
T ss_pred cCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEE
Confidence 01224678899999999999999999999999999999998
No 53
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.36 E-value=0.0037 Score=61.55 Aligned_cols=39 Identities=23% Similarity=0.457 Sum_probs=35.1
Q ss_pred CceEEEEEeccc------cccceeccCchHHHHHHHHhCCcEEEc
Q 014254 184 QEVSFRILCSND------KVGAVIGKGGTIIRALQSEAGAFISVG 222 (428)
Q Consensus 184 ~evt~rIlVP~~------~vG~IIGKgG~tIK~IqeeTGA~I~Is 222 (428)
-.++.||+||.. .||.|+|..|.++|+|+++|||+|.|-
T Consensus 90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 357888999975 799999999999999999999999885
No 54
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.36 E-value=0.0013 Score=68.04 Aligned_cols=94 Identities=28% Similarity=0.328 Sum_probs=63.1
Q ss_pred ccccceeccCchHHHHHHHHh-CCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccccccCCCCC
Q 014254 195 DKVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN 273 (428)
Q Consensus 195 ~~vG~IIGKgG~tIK~IqeeT-GA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~g~~~~~~ 273 (428)
+-+|..||++|.+|+.|.++. |-+|.|-.. +.++ ...+...+....... ..- .
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~-------------s~d~----------~~fi~nal~Pa~v~~-v~i-~- 298 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDW-------------SEDP----------AEFVANALSPAKVVS-VEV-D- 298 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEc-------------CCCH----------HHHHHHhCCCceEEE-EEE-E-
Confidence 469999999999999999998 777766421 2221 011111111100000 000 0
Q ss_pred CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254 274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (428)
Q Consensus 274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~ 314 (428)
......+.+.||.++.+..|||+|.+++--.+.||.+|.|.
T Consensus 299 ~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~ 339 (362)
T PRK12327 299 DEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIK 339 (362)
T ss_pred cCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEE
Confidence 01224678999999999999999999999999999999997
No 55
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.32 E-value=0.0069 Score=67.69 Aligned_cols=65 Identities=22% Similarity=0.337 Sum_probs=54.8
Q ss_pred eeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-HHHHHHHHHHHHHHhhh
Q 014254 277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRLRD 351 (428)
Q Consensus 277 ~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-~~aV~~A~~lI~~~L~e 351 (428)
.....+.||.+.++.+||.||.+|++|.++||++|.+. .+-.|.|.+. ..++.+|..+|..+..+
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 34456778999999999999999999999999988874 2456888884 88899999999988865
No 56
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.31 E-value=0.0063 Score=64.40 Aligned_cols=39 Identities=26% Similarity=0.435 Sum_probs=34.4
Q ss_pred ceEEEEEecc------ccccceeccCchHHHHHHHHhCCcEEEcc
Q 014254 185 EVSFRILCSN------DKVGAVIGKGGTIIRALQSEAGAFISVGA 223 (428)
Q Consensus 185 evt~rIlVP~------~~vG~IIGKgG~tIK~IqeeTGA~I~Is~ 223 (428)
.++-|+.||. +.||+|||..|.|.|+|+++|||+|.|-.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRG 181 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRG 181 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEec
Confidence 5677788886 47999999999999999999999999954
No 57
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.24 E-value=0.011 Score=62.41 Aligned_cols=94 Identities=28% Similarity=0.337 Sum_probs=62.3
Q ss_pred ccccceeccCchHHHHHHHHh-CCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccccccCCCCC
Q 014254 195 DKVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN 273 (428)
Q Consensus 195 ~~vG~IIGKgG~tIK~IqeeT-GA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~g~~~~~~ 273 (428)
+-+|..||++|.+|+.|.++. |=+|.|-. =+.++ ...+...+.......- .- .
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~-------------ys~Dp----------~~fI~NaLsPA~V~~V-~i-~- 330 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIR-------------WSPDP----------ATYIANALSPARVDEV-RL-V- 330 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEE-------------cCCCH----------HHHHHHhcCCceeeEE-EE-E-
Confidence 459999999999999999998 66666632 12221 0111111111000000 00 0
Q ss_pred CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254 274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (428)
Q Consensus 274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~ 314 (428)
......+.+.||.++.+..|||+|.+++--.+.||.+|.|.
T Consensus 331 ~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~ 371 (449)
T PRK12329 331 DPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIK 371 (449)
T ss_pred cCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccc
Confidence 01123578999999999999999999999999999999996
No 58
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.21 E-value=0.011 Score=57.57 Aligned_cols=67 Identities=22% Similarity=0.314 Sum_probs=57.5
Q ss_pred EEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-HHHHHHHHHHHHHHhhhcCCCC
Q 014254 280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRLRDNHFSG 356 (428)
Q Consensus 280 ~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-~~aV~~A~~lI~~~L~e~~~~~ 356 (428)
..+.||.++++.+||++|.+|+.|.+.++++|.+- .+-.|.|.|. .+++.+|..+|...-++++.++
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig----------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~~~ 214 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG----------QNGRIWIKGPDEEDEEIAIEAIKKIEREAHTSG 214 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc----------CCcEEEEeeCCHHHHHHHHHHHHHHHhhhhccC
Confidence 56889999999999999999999999999999983 3457999997 5588999999998887777654
No 59
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=96.09 E-value=0.0025 Score=68.12 Aligned_cols=93 Identities=28% Similarity=0.383 Sum_probs=62.8
Q ss_pred ccccceeccCchHHHHHHHHh-CCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccccccCCCCC
Q 014254 195 DKVGAVIGKGGTIIRALQSEA-GAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSN 273 (428)
Q Consensus 195 ~~vG~IIGKgG~tIK~IqeeT-GA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~g~~~~~~ 273 (428)
+-+|..||++|++|+.|.++. |=+|.|-. =+.++ ...+...+.......-. .
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~-------------~s~d~----------~~fi~nal~pa~v~~v~---~- 297 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIIL-------------WSDDP----------AQFIINALSPAEVSSVV---V- 297 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEE-------------cCCCH----------HHHHHHhCCCCEEEEEE---E-
Confidence 359999999999999999998 66666632 12221 11111111110000000 0
Q ss_pred CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254 274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (428)
Q Consensus 274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~ 314 (428)
......+.+.||.++.+..|||+|.+++-..+.||.+|.|.
T Consensus 298 ~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~ 338 (470)
T PRK09202 298 DEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIM 338 (470)
T ss_pred eCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEE
Confidence 01123778999999999999999999999999999999998
No 60
>PRK00468 hypothetical protein; Provisional
Probab=95.91 E-value=0.0086 Score=48.62 Aligned_cols=35 Identities=29% Similarity=0.508 Sum_probs=30.7
Q ss_pred cCCceEEEEEeccccccceeccCchHHHHHHHHhC
Q 014254 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAG 216 (428)
Q Consensus 182 ~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTG 216 (428)
.++.+.+++.|..+.+|.||||+|.+|+.|+.--.
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~ 60 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVK 60 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence 44568999999999999999999999999998643
No 61
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=95.80 E-value=0.046 Score=53.99 Aligned_cols=77 Identities=19% Similarity=0.245 Sum_probs=54.2
Q ss_pred CCceeEEEEEeccc------cccceeCCCCchHHHHHHHhCCeEEEcc-----C--------CccccCCCCCc---EEEE
Q 014254 274 KGLLVNARLVVASN------QVGCLLGKGGTIISEMRKVTGTSIRIIS-----D--------QLLKCISENDR---VVQI 331 (428)
Q Consensus 274 ~~~~vt~~L~VP~s------~VG~IIGKgG~~IkeIre~TGA~IqI~~-----d--------~~P~~~~s~eR---vVtI 331 (428)
...+.+.++.||-. +||+|||..|.++|+++++|||+|-|-+ | ..|+.+..++- .|+.
T Consensus 88 ~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~ 167 (259)
T KOG1588|consen 88 KPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIET 167 (259)
T ss_pred CceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEE
Confidence 34567788888865 8999999999999999999999999982 1 12222223332 3666
Q ss_pred EeCHHHH----HHHHHHHHHHhh
Q 014254 332 SGEFSKV----KDAVYNVTGRLR 350 (428)
Q Consensus 332 tGt~~aV----~~A~~lI~~~L~ 350 (428)
.+++.-+ ..|+..|...|.
T Consensus 168 ~~p~~ea~~rl~~AleeI~klL~ 190 (259)
T KOG1588|consen 168 EAPPAEAYARLAYALEEIKKLLV 190 (259)
T ss_pred eCCHHHHHHHHHHHHHHHHHhcC
Confidence 6665544 457777777776
No 62
>PRK02821 hypothetical protein; Provisional
Probab=95.65 E-value=0.011 Score=48.20 Aligned_cols=36 Identities=28% Similarity=0.523 Sum_probs=31.2
Q ss_pred cCCceEEEEEeccccccceeccCchHHHHHHHHhCC
Q 014254 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGA 217 (428)
Q Consensus 182 ~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA 217 (428)
.+..+.+.|.|..+.+|.||||+|.+|+.|+.--.+
T Consensus 27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 345578999999999999999999999999987554
No 63
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=95.65 E-value=0.016 Score=58.92 Aligned_cols=71 Identities=21% Similarity=0.298 Sum_probs=58.1
Q ss_pred eeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEe-CHHHHHHHHHHHHHHhhhcC
Q 014254 277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRDNH 353 (428)
Q Consensus 277 ~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItG-t~~aV~~A~~lI~~~L~e~~ 353 (428)
.....+.|+++..|.|||+.|.+-++|+++|+++|.+++ |+ ++...++|+| ..++|..|...|...|.+.-
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~---p~---~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPR---PN---TNKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccC---CC---CCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 345678999999999999999999999999999999983 22 3445566655 58889999999999887654
No 64
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=95.44 E-value=0.011 Score=59.69 Aligned_cols=65 Identities=23% Similarity=0.381 Sum_probs=57.5
Q ss_pred CceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc-cCCccccCCCCCcEEEEEeCHHHHHHHHHHHHH
Q 014254 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII-SDQLLKCISENDRVVQISGEFSKVKDAVYNVTG 347 (428)
Q Consensus 275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~-~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~ 347 (428)
...++..+.||..+++-|.|++|++||.++.+|..+|+-+ +.. +-++.++|..+.|..|...|..
T Consensus 23 p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~e--------ePiF~vTg~~edv~~aRrei~s 88 (394)
T KOG2113|consen 23 GQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGE--------EPIFPVTGRHEDVRRARREIPS 88 (394)
T ss_pred CCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCC--------CCcceeccCchhHHHHhhcCcc
Confidence 3678889999999999999999999999999999999998 432 3469999999999999988866
No 65
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=95.39 E-value=0.66 Score=43.94 Aligned_cols=131 Identities=16% Similarity=0.153 Sum_probs=85.6
Q ss_pred EEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhccccccc
Q 014254 189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKGL 268 (428)
Q Consensus 189 rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~g~ 268 (428)
.+.++....-++...+|..++.|-...||+|.+. ..+..|.|+|++. ..+.+...+..+..
T Consensus 29 ~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~-----~~~~~i~I~g~k~-------~~~~i~~~i~~~l~------- 89 (210)
T PF14611_consen 29 DVWLQPDEFFLLLTGNGRILENLAARNGAKIEVS-----RSENRIRITGTKS-------TAEYIEASINEILS------- 89 (210)
T ss_pred EEEecchheeeeecCCchHHHHHHHhcCceEEEe-----cCCcEEEEEccHH-------HHHHHHHHHHHHHh-------
Confidence 3444577788899999999999988899999997 3667899999865 33344443443332
Q ss_pred CCCCCCCceeEEEEEecccccccee----CCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEe-----CHHHHH
Q 014254 269 DFSSNKGLLVNARLVVASNQVGCLL----GKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-----EFSKVK 339 (428)
Q Consensus 269 ~~~~~~~~~vt~~L~VP~s~VG~II----GKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItG-----t~~aV~ 339 (428)
...+..+-++.-.--..- -.....+++|++.|++.|...++ +..+.|++ ....+.
T Consensus 90 -------~i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~---------~~~~~i~~~~~~~~~~~~~ 153 (210)
T PF14611_consen 90 -------NIRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD---------GNKLKISWLASPENEKRAD 153 (210)
T ss_pred -------hcEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC---------CCeEEEEEEeeccccchHH
Confidence 122333333322111111 11356799999999999999732 33355554 577888
Q ss_pred HHHHHHHHHhhhcCC
Q 014254 340 DAVYNVTGRLRDNHF 354 (428)
Q Consensus 340 ~A~~lI~~~L~e~~~ 354 (428)
.|..++.-.+..++.
T Consensus 154 ~a~RlL~~a~~~~~~ 168 (210)
T PF14611_consen 154 RAKRLLLWALDYNPH 168 (210)
T ss_pred HHHHHHHHhccCCcc
Confidence 999999888854443
No 66
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=95.36 E-value=0.019 Score=58.33 Aligned_cols=52 Identities=25% Similarity=0.362 Sum_probs=43.6
Q ss_pred ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCC
Q 014254 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS 238 (428)
Q Consensus 185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs 238 (428)
....-+++++..+|.|||+.|.+-|+|+++|+++|.++. |+.....|+|+|-
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~--p~~n~~~i~i~~~ 107 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPR--PNTNKEEIKIIGI 107 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccC--CCCCcceEEEeeh
Confidence 355668999999999999999999999999999999986 5555556667664
No 67
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.23 E-value=0.047 Score=59.12 Aligned_cols=64 Identities=19% Similarity=0.296 Sum_probs=50.2
Q ss_pred EEEEEecc-ccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEe-CHHHHHHHHHHHHHHhhh
Q 014254 279 NARLVVAS-NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD 351 (428)
Q Consensus 279 t~~L~VP~-s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItG-t~~aV~~A~~lI~~~L~e 351 (428)
...+.+|+ ++-|+||||.|.+|+-+...||+.|.|. . +...|+|+| +|---+.|...+..+|.|
T Consensus 205 ~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid--d-------tp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 205 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID--D-------TPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred eeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc--C-------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 34567887 5669999999999999999999999995 2 334688888 566666777777777764
No 68
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.18 E-value=0.022 Score=46.41 Aligned_cols=33 Identities=27% Similarity=0.535 Sum_probs=30.0
Q ss_pred CCceEEEEEeccccccceeccCchHHHHHHHHh
Q 014254 183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEA 215 (428)
Q Consensus 183 ~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeT 215 (428)
+..+.++|-+..+.+|.||||+|.+|+.|+.--
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 567889999999999999999999999999863
No 69
>PRK00468 hypothetical protein; Provisional
Probab=95.12 E-value=0.024 Score=46.06 Aligned_cols=33 Identities=33% Similarity=0.454 Sum_probs=29.0
Q ss_pred CceeEEEEEeccccccceeCCCCchHHHHHHHh
Q 014254 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVT 307 (428)
Q Consensus 275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~T 307 (428)
+..+..++.+..+.+|+||||+|.+|+.||..-
T Consensus 27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 455788999999999999999999999998643
No 70
>PRK12704 phosphodiesterase; Provisional
Probab=95.10 E-value=0.056 Score=58.61 Aligned_cols=65 Identities=18% Similarity=0.285 Sum_probs=49.8
Q ss_pred EEEEEecc-ccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEe-CHHHHHHHHHHHHHHhhhc
Q 014254 279 NARLVVAS-NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRDN 352 (428)
Q Consensus 279 t~~L~VP~-s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItG-t~~aV~~A~~lI~~~L~e~ 352 (428)
...+.+|+ ++-|+||||.|.+|+-+...||+.|.|. . +...|.|+| ++---+.|...+...+.+.
T Consensus 211 ~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid--d-------tp~~v~ls~~~~~rre~a~~~l~~l~~dg 277 (520)
T PRK12704 211 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID--D-------TPEAVILSGFDPIRREIARLALEKLVQDG 277 (520)
T ss_pred eeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc--C-------CCCeEEEecCChhhHHHHHHHHHHHHhcC
Confidence 33466787 5679999999999999999999999995 2 345688999 5655556777776666654
No 71
>PRK00106 hypothetical protein; Provisional
Probab=94.91 E-value=0.071 Score=57.94 Aligned_cols=64 Identities=22% Similarity=0.345 Sum_probs=50.6
Q ss_pred EEEEEecc-ccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEe-CHHHHHHHHHHHHHHhhh
Q 014254 279 NARLVVAS-NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISG-EFSKVKDAVYNVTGRLRD 351 (428)
Q Consensus 279 t~~L~VP~-s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItG-t~~aV~~A~~lI~~~L~e 351 (428)
...+.+|+ ++-|+||||.|.+|+-+...||+.+.|. . +...|+|+| +|---+.|...+..+|.|
T Consensus 226 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliid--d-------tp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 226 ITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID--D-------TPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred eeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc--C-------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 34567887 5679999999999999999999999995 2 345688998 576667777777777664
No 72
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=94.87 E-value=0.027 Score=64.20 Aligned_cols=50 Identities=22% Similarity=0.393 Sum_probs=43.4
Q ss_pred ceEEEEEeccccccceeccCchHHHHHHHHhCCc-EEEccCCCCCCceEEEeeCCCC
Q 014254 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAF-ISVGATMPECDERLITVTASEG 240 (428)
Q Consensus 185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~-I~Is~~~p~s~ERvVtItGs~e 240 (428)
.....|.||.+++|.|||.||.+||.|+++||++ |.+.+ +-.|.|.+...
T Consensus 684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d------dg~V~I~a~d~ 734 (891)
T PLN00207 684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD------DGTVKITAKDL 734 (891)
T ss_pred CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC------CeeEEEEeCCH
Confidence 4667789999999999999999999999999999 98863 56788888643
No 73
>PRK01064 hypothetical protein; Provisional
Probab=94.85 E-value=0.029 Score=45.92 Aligned_cols=35 Identities=20% Similarity=0.467 Sum_probs=30.9
Q ss_pred cCCceEEEEEeccccccceeccCchHHHHHHHHhC
Q 014254 182 QQQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAG 216 (428)
Q Consensus 182 ~~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTG 216 (428)
.+..+.+++.|.....|.+|||+|.+|+.|+.-.+
T Consensus 26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred CCCEEEEEEEECcccceEEECCCCccHHHHHHHHH
Confidence 35668999999999999999999999999998643
No 74
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=94.77 E-value=0.074 Score=51.06 Aligned_cols=40 Identities=23% Similarity=0.437 Sum_probs=34.4
Q ss_pred CceeEEEEEec------cccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254 275 GLLVNARLVVA------SNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (428)
Q Consensus 275 ~~~vt~~L~VP------~s~VG~IIGKgG~~IkeIre~TGA~IqI~ 314 (428)
...++-++.|| .++||.|||..|.++|++++.|+|+|.|-
T Consensus 145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIR 190 (269)
T COG5176 145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIR 190 (269)
T ss_pred cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEe
Confidence 44556667776 46899999999999999999999999997
No 75
>PRK02821 hypothetical protein; Provisional
Probab=94.73 E-value=0.032 Score=45.59 Aligned_cols=33 Identities=21% Similarity=0.416 Sum_probs=28.8
Q ss_pred ceeEEEEEeccccccceeCCCCchHHHHHHHhC
Q 014254 276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTG 308 (428)
Q Consensus 276 ~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TG 308 (428)
......|.+..+.+|+||||+|.+|+.||..-.
T Consensus 29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 446789999999999999999999999997543
No 76
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.31 E-value=0.05 Score=44.33 Aligned_cols=32 Identities=31% Similarity=0.493 Sum_probs=29.0
Q ss_pred CceeEEEEEeccccccceeCCCCchHHHHHHH
Q 014254 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKV 306 (428)
Q Consensus 275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~ 306 (428)
......+|.+..+.+|.||||+|.+|+.||-.
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 56778999999999999999999999999864
No 77
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=93.94 E-value=0.088 Score=51.34 Aligned_cols=47 Identities=32% Similarity=0.386 Sum_probs=40.1
Q ss_pred EEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCC
Q 014254 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240 (428)
Q Consensus 188 ~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e 240 (428)
+.+.||...++.+||++|.+|+.|.+++++.|.+.. +-.|.|.|...
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~------NG~VwI~~~~~ 193 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ------NGRIWIKGPDE 193 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC------CcEEEEeeCCH
Confidence 447889999999999999999999999999999963 35588888644
No 78
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=93.78 E-value=0.051 Score=62.68 Aligned_cols=70 Identities=17% Similarity=0.150 Sum_probs=58.2
Q ss_pred EEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhh
Q 014254 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD 351 (428)
Q Consensus 279 t~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e 351 (428)
.-++-+|-....+|||+||.+|+.++..|||.|.+.+-+ |. .-.||.+.+.|.++.++.|...|.-.|.|
T Consensus 1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq-~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ-PD--NQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred ccccccchhhhhhhhccCcchhhhHhhccceEEehhhcC-Cc--cchhhhcccCCCChhhhhhhccccceeec
Confidence 346778888899999999999999999999999997311 21 14689999999999999998888776654
No 79
>PRK01064 hypothetical protein; Provisional
Probab=93.74 E-value=0.068 Score=43.75 Aligned_cols=33 Identities=27% Similarity=0.438 Sum_probs=29.3
Q ss_pred CceeEEEEEeccccccceeCCCCchHHHHHHHh
Q 014254 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVT 307 (428)
Q Consensus 275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~T 307 (428)
...+..++.|..+..|.+|||+|++|+.||...
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 466788999999999999999999999999753
No 80
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=93.61 E-value=0.082 Score=58.43 Aligned_cols=48 Identities=35% Similarity=0.575 Sum_probs=41.6
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCC
Q 014254 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240 (428)
Q Consensus 187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e 240 (428)
...+.|+.++++-+||+||.+|+.|.++|||+|.|. ++-.|.|.++..
T Consensus 553 i~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie------ddGtv~i~~s~~ 600 (692)
T COG1185 553 IETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE------DDGTVKIAASDG 600 (692)
T ss_pred eEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec------CCCcEEEEecch
Confidence 456789999999999999999999999999999996 345588888754
No 81
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=93.37 E-value=0.076 Score=50.97 Aligned_cols=39 Identities=23% Similarity=0.360 Sum_probs=33.8
Q ss_pred ceEEEEEecc------ccccceeccCchHHHHHHHHhCCcEEEcc
Q 014254 185 EVSFRILCSN------DKVGAVIGKGGTIIRALQSEAGAFISVGA 223 (428)
Q Consensus 185 evt~rIlVP~------~~vG~IIGKgG~tIK~IqeeTGA~I~Is~ 223 (428)
.++-++.||. ..||+|||..|.|.|+|++.|+|+|-|-.
T Consensus 147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG 191 (269)
T COG5176 147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRG 191 (269)
T ss_pred cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEec
Confidence 4566778875 47999999999999999999999999964
No 82
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=92.76 E-value=0.069 Score=42.39 Aligned_cols=36 Identities=25% Similarity=0.344 Sum_probs=30.2
Q ss_pred CCceEEEEEeccccccceeccCchHHHHHHHHhCCc
Q 014254 183 QQEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAF 218 (428)
Q Consensus 183 ~~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~ 218 (428)
.....+.+-|..+..|.||||.|.+++.||.-.+.-
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~ 61 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAA 61 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHHHH
Confidence 345677788899999999999999999999876543
No 83
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=92.69 E-value=0.068 Score=51.04 Aligned_cols=62 Identities=26% Similarity=0.345 Sum_probs=53.5
Q ss_pred cccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhhcCCCCcc
Q 014254 286 SNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRDNHFSGTL 358 (428)
Q Consensus 286 ~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e~~~~~~~ 358 (428)
+..+|+|+||+|++--.|.+.|.++|.+. +..|.|-|..++++.|...|+..|-.++....|
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVla-----------d~kIHiLG~~~niriAR~avcsLIlGsppgkVy 238 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA-----------DSKIHILGAFQNIRIARDAVCSLILGSPPGKVY 238 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEec-----------CceEEEeecchhhHHHHHhhHhhhccCCchhHH
Confidence 45689999999999999999999999985 456999999999999999999999877654433
No 84
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=92.69 E-value=0.22 Score=54.02 Aligned_cols=48 Identities=21% Similarity=0.322 Sum_probs=39.0
Q ss_pred eEEEEEecc-ccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCC
Q 014254 186 VSFRILCSN-DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS 238 (428)
Q Consensus 186 vt~rIlVP~-~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs 238 (428)
++--+-+|+ +.-|.||||.|.|||.|+.-||+.|-|.+ +-..|+|+|.
T Consensus 204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd-----tp~~v~ls~f 252 (514)
T TIGR03319 204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-----TPEAVILSGF 252 (514)
T ss_pred eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC-----CCCeEEecCC
Confidence 344478887 57899999999999999999999999975 2334668873
No 85
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=92.60 E-value=0.15 Score=46.07 Aligned_cols=37 Identities=24% Similarity=0.496 Sum_probs=34.3
Q ss_pred eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (428)
Q Consensus 278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~ 314 (428)
-.+.++|+...+|..||++|++|+.|++..|-+|.+.
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVv 68 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELV 68 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEE
Confidence 3677899999999999999999999999999999997
No 86
>PRK12704 phosphodiesterase; Provisional
Probab=92.60 E-value=0.15 Score=55.40 Aligned_cols=48 Identities=21% Similarity=0.322 Sum_probs=39.3
Q ss_pred eEEEEEecc-ccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCC
Q 014254 186 VSFRILCSN-DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS 238 (428)
Q Consensus 186 vt~rIlVP~-~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs 238 (428)
++--+-+|+ +.-|.||||.|.|||.|+.-||+.|-|.+ +..+|+|+|.
T Consensus 210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd-----tp~~v~ls~~ 258 (520)
T PRK12704 210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-----TPEAVILSGF 258 (520)
T ss_pred ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC-----CCCeEEEecC
Confidence 334477887 57899999999999999999999999975 3345778885
No 87
>PRK00106 hypothetical protein; Provisional
Probab=92.28 E-value=0.28 Score=53.47 Aligned_cols=48 Identities=19% Similarity=0.340 Sum_probs=39.2
Q ss_pred eEEEEEecc-ccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCC
Q 014254 186 VSFRILCSN-DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS 238 (428)
Q Consensus 186 vt~rIlVP~-~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs 238 (428)
++--+-+|+ +.-|.||||.|.|||.|+.-||+.|-|.+ +...|+|+|.
T Consensus 225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd-----tp~~v~lS~f 273 (535)
T PRK00106 225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD-----TPEVVVLSGF 273 (535)
T ss_pred eeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC-----CCCeEEEeCC
Confidence 444488888 57899999999999999999999999975 2334668874
No 88
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=92.07 E-value=0.13 Score=57.73 Aligned_cols=49 Identities=33% Similarity=0.523 Sum_probs=39.9
Q ss_pred eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCC
Q 014254 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240 (428)
Q Consensus 186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e 240 (428)
....+.||.++++.+||+||.+||.|+++||++|.+.+ +-.|.|.+...
T Consensus 554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d------~G~v~i~~~~~ 602 (693)
T PRK11824 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED------DGTVKIAATDG 602 (693)
T ss_pred hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC------CceEEEEcccH
Confidence 34456779999999999999999999999999988853 45578887543
No 89
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=91.70 E-value=0.83 Score=42.60 Aligned_cols=101 Identities=23% Similarity=0.244 Sum_probs=60.0
Q ss_pred EEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccccc
Q 014254 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSEKG 267 (428)
Q Consensus 188 ~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~g 267 (428)
+-|+|-... |.-|||+|.+||++++..|-+|.+-. .+.+. ..++..++....-.+
T Consensus 63 vIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE-------------~s~d~-----------~~fl~Nl~~PA~V~g 117 (166)
T PRK06418 63 VILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE-------------KTNDI-----------KKLAVQLLSPARVLG 117 (166)
T ss_pred EEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE-------------cCCCH-----------HHHHHhcCCCcEEEE
Confidence 446777777 99999999999999999999998843 22221 111111111000000
Q ss_pred cCCCCCCCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEE
Q 014254 268 LDFSSNKGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRI 313 (428)
Q Consensus 268 ~~~~~~~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI 313 (428)
.......++....++.|+...-..+=.|-..-=.-+++.||..+.|
T Consensus 118 V~i~~~~dG~~~~kV~Vd~~Dk~~l~~k~e~~~~v~~kltgk~v~~ 163 (166)
T PRK06418 118 VNTVWLPDGTVQYVIRVSRRDRRRLPAKPELLESILSKITGTEVKI 163 (166)
T ss_pred EEEEEeCCCcEEEEEEECHHHhhcccccHHHHHHHHHHHHCCcEEE
Confidence 0000011234555677887777776666665555667788888776
No 90
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=91.66 E-value=0.27 Score=37.15 Aligned_cols=35 Identities=34% Similarity=0.495 Sum_probs=28.8
Q ss_pred ceEEEEEeccccccceeccCchHHHHHHHHhCCcE
Q 014254 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFI 219 (428)
Q Consensus 185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I 219 (428)
...+.+.+.....|.+|||+|.+++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 35566777766799999999999999999988554
No 91
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=90.71 E-value=0.79 Score=43.68 Aligned_cols=68 Identities=21% Similarity=0.218 Sum_probs=55.4
Q ss_pred eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-----HHHHHHHHHHHHHHhhhc
Q 014254 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-----FSKVKDAVYNVTGRLRDN 352 (428)
Q Consensus 278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-----~~aV~~A~~lI~~~L~e~ 352 (428)
....+.||...+|.+||+.|.+-+.|.+.+|+++.+. +.+..|+|..+ |.++.+|...|..+=+..
T Consensus 8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD---------~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF 78 (194)
T COG1094 8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID---------SKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGF 78 (194)
T ss_pred ceeeeecCchhheeeecccccchHHHHhhcCeEEEEE---------CCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCC
Confidence 3456899999999999999999999999999999996 34556777654 778899999888766554
Q ss_pred CC
Q 014254 353 HF 354 (428)
Q Consensus 353 ~~ 354 (428)
++
T Consensus 79 ~p 80 (194)
T COG1094 79 PP 80 (194)
T ss_pred CH
Confidence 43
No 92
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=90.37 E-value=0.19 Score=40.09 Aligned_cols=35 Identities=37% Similarity=0.547 Sum_probs=28.0
Q ss_pred EEEEecccc-----ccceeccCchHHHHHHHHh-CCcEEEc
Q 014254 188 FRILCSNDK-----VGAVIGKGGTIIRALQSEA-GAFISVG 222 (428)
Q Consensus 188 ~rIlVP~~~-----vG~IIGKgG~tIK~IqeeT-GA~I~Is 222 (428)
.++.|-... +|..||++|.+||.|.++. |-+|.|-
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence 456666666 9999999999999999999 8888874
No 93
>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=90.23 E-value=0.48 Score=35.72 Aligned_cols=35 Identities=29% Similarity=0.434 Sum_probs=28.2
Q ss_pred eeEEEEEeccccccceeCCCCchHHHHHHHhCCeE
Q 014254 277 LVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSI 311 (428)
Q Consensus 277 ~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~I 311 (428)
.....+.+.....|.+|||+|++|+.++..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 35556667666789999999999999999988544
No 94
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=89.34 E-value=0.38 Score=38.35 Aligned_cols=36 Identities=28% Similarity=0.548 Sum_probs=30.0
Q ss_pred EEEEEecccc-----ccceeCCCCchHHHHHHHh-CCeEEEc
Q 014254 279 NARLVVASNQ-----VGCLLGKGGTIISEMRKVT-GTSIRII 314 (428)
Q Consensus 279 t~~L~VP~s~-----VG~IIGKgG~~IkeIre~T-GA~IqI~ 314 (428)
.+.+.|-+.. +|..||++|.+|+.|.++. |-+|.+.
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence 3567777777 9999999999999999999 9999997
No 95
>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=89.07 E-value=0.22 Score=39.78 Aligned_cols=35 Identities=26% Similarity=0.370 Sum_probs=29.7
Q ss_pred eEEEEEeccccccceeccCchHHHHHHHHhCCcEE
Q 014254 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFIS 220 (428)
Q Consensus 186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~ 220 (428)
....+.+..+..|.|||++|++|+.|.+..+-.+.
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 35568889999999999999999999998766553
No 96
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=88.06 E-value=1.2 Score=48.48 Aligned_cols=69 Identities=19% Similarity=0.279 Sum_probs=57.0
Q ss_pred CCceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-HHHHHHHHHHHHHHhhhc
Q 014254 274 KGLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRLRDN 352 (428)
Q Consensus 274 ~~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-~~aV~~A~~lI~~~L~e~ 352 (428)
+...+...+.|+.+....+||.+|...|+|..+||+.-++. +..++|.-. +.+..+|+..|..++.+.
T Consensus 593 ~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD-----------e~t~~i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 593 EYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD-----------EGTFSIFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred ccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec-----------CceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence 34567788999999999999999999999999999655552 455777774 788899999999998864
Q ss_pred C
Q 014254 353 H 353 (428)
Q Consensus 353 ~ 353 (428)
-
T Consensus 662 ~ 662 (760)
T KOG1067|consen 662 Q 662 (760)
T ss_pred c
Confidence 3
No 97
>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=88.04 E-value=0.68 Score=42.00 Aligned_cols=36 Identities=31% Similarity=0.637 Sum_probs=33.7
Q ss_pred EEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (428)
Q Consensus 279 t~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~ 314 (428)
.+-++|....+|..||++|++|+.|++..|-+|.+.
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVV 69 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELI 69 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEE
Confidence 667899999999999999999999999999999997
No 98
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=87.77 E-value=0.28 Score=38.90 Aligned_cols=33 Identities=15% Similarity=0.253 Sum_probs=27.9
Q ss_pred ceeEEEEEeccccccceeCCCCchHHHHHHHhC
Q 014254 276 LLVNARLVVASNQVGCLLGKGGTIISEMRKVTG 308 (428)
Q Consensus 276 ~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TG 308 (428)
......+.+..+..|.||||.|++++.||-..+
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 344677888999999999999999999997654
No 99
>PRK12705 hypothetical protein; Provisional
Probab=87.71 E-value=1.1 Score=48.49 Aligned_cols=63 Identities=22% Similarity=0.228 Sum_probs=44.3
Q ss_pred EEEEecc-ccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeC-HHHHHHHHHHHHHHhhh
Q 014254 280 ARLVVAS-NQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGE-FSKVKDAVYNVTGRLRD 351 (428)
Q Consensus 280 ~~L~VP~-s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt-~~aV~~A~~lI~~~L~e 351 (428)
..+.+|+ ++-|+||||.|.+|+.+...||+.|.|. ..| +.|+|++- +.--+.|...+..+|.+
T Consensus 200 s~v~lp~demkGriIGreGrNir~~E~~tGvdliid--dtp-------~~V~ls~fdp~rreia~~~l~~Li~d 264 (508)
T PRK12705 200 SVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID--DTP-------EAVVISSFNPIRREIARLTLEKLLAD 264 (508)
T ss_pred eeeecCChHhhccccCccchhHHHHHHhhCCceEec--CCc-------cchhhcccCccchHHHHHHHHHHHhc
Confidence 3456776 4669999999999999999999999995 333 34666663 44445555555555544
No 100
>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=87.15 E-value=0.3 Score=39.03 Aligned_cols=34 Identities=24% Similarity=0.424 Sum_probs=28.8
Q ss_pred eEEEEEeccccccceeCCCCchHHHHHHHhCCeE
Q 014254 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSI 311 (428)
Q Consensus 278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~I 311 (428)
....+.+..++.|.|||++|++|++|+...+..+
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 3567889999999999999999999987765544
No 101
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=86.88 E-value=0.63 Score=37.43 Aligned_cols=35 Identities=31% Similarity=0.461 Sum_probs=27.9
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCCcEEE
Q 014254 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV 221 (428)
Q Consensus 187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~I 221 (428)
.+.+-+..+..|.+|||.|++++.||--++.-++-
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 34556667889999999999999999987765543
No 102
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=85.78 E-value=0.33 Score=56.44 Aligned_cols=57 Identities=19% Similarity=0.120 Sum_probs=49.3
Q ss_pred ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC-CCCCCceEEEeeCCCCC
Q 014254 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT-MPECDERLITVTASEGP 241 (428)
Q Consensus 185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~-~p~s~ERvVtItGs~e~ 241 (428)
...-++-+|...+.+|||+||.+|..++.-|||-|.|.+. ..+..||.+++.|.++.
T Consensus 1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~ 1396 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPS 1396 (2131)
T ss_pred ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChh
Confidence 3456788999999999999999999999999999999874 34568999999998763
No 103
>PRK12705 hypothetical protein; Provisional
Probab=83.79 E-value=0.8 Score=49.68 Aligned_cols=47 Identities=17% Similarity=0.291 Sum_probs=36.9
Q ss_pred EEEEEecc-ccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCC
Q 014254 187 SFRILCSN-DKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTAS 238 (428)
Q Consensus 187 t~rIlVP~-~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs 238 (428)
+--+-+|+ +.-|.||||.|.+||.++..||+.|-|.+ ....|+|++.
T Consensus 199 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd-----tp~~V~ls~f 246 (508)
T PRK12705 199 VSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD-----TPEAVVISSF 246 (508)
T ss_pred eeeeecCChHhhccccCccchhHHHHHHhhCCceEecC-----Cccchhhccc
Confidence 33367776 57899999999999999999999999975 2233566663
No 104
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=83.52 E-value=7.2 Score=36.88 Aligned_cols=63 Identities=16% Similarity=0.261 Sum_probs=52.5
Q ss_pred EEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhh
Q 014254 280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD 351 (428)
Q Consensus 280 ~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e 351 (428)
+.+.++....-.++..+|..+++|....||+|.+.. .+..+.|+|+...+..+...|.+.+..
T Consensus 28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~---------~~~~i~I~g~k~~~~~i~~~i~~~l~~ 90 (210)
T PF14611_consen 28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR---------SENRIRITGTKSTAEYIEASINEILSN 90 (210)
T ss_pred eEEEecchheeeeecCCchHHHHHHHhcCceEEEec---------CCcEEEEEccHHHHHHHHHHHHHHHhh
Confidence 345556778889999999999999888899999973 356799999999999988888888764
No 105
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=82.96 E-value=1.2 Score=42.42 Aligned_cols=37 Identities=24% Similarity=0.364 Sum_probs=34.7
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCCcEEEcc
Q 014254 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA 223 (428)
Q Consensus 187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~ 223 (428)
.+.+.||.+..+..|||+|.+++.+.+-||-++.|..
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 7778999999999999999999999999999999864
No 106
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=82.74 E-value=0.9 Score=48.70 Aligned_cols=36 Identities=28% Similarity=0.432 Sum_probs=33.3
Q ss_pred EEEEeccccccceeccCchHHHHHHHHhCCcEEEcc
Q 014254 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA 223 (428)
Q Consensus 188 ~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~ 223 (428)
..+.||...++.+|||+|.+|++|+++.|-+|.|-.
T Consensus 488 avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~ 523 (604)
T COG1855 488 AVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKP 523 (604)
T ss_pred EEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEE
Confidence 457899999999999999999999999999999965
No 107
>PRK13764 ATPase; Provisional
Probab=81.94 E-value=1.6 Score=48.34 Aligned_cols=37 Identities=27% Similarity=0.439 Sum_probs=34.8
Q ss_pred eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (428)
Q Consensus 278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~ 314 (428)
-.+.+.||...++.+|||||++|++|.+..|.+|.|-
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~ 517 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVR 517 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEE
Confidence 3567899999999999999999999999999999998
No 108
>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=81.89 E-value=1.6 Score=35.90 Aligned_cols=35 Identities=23% Similarity=0.298 Sum_probs=29.2
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCCcEEE
Q 014254 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV 221 (428)
Q Consensus 187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~I 221 (428)
.+++.|-...-|.|||++|+.|++|+++-.....+
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 46778888899999999999999999987655544
No 109
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=81.83 E-value=1.6 Score=35.14 Aligned_cols=33 Identities=15% Similarity=0.476 Sum_probs=26.2
Q ss_pred EEEEEeccccccceeCCCCchHHHHHHHhCCeE
Q 014254 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSI 311 (428)
Q Consensus 279 t~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~I 311 (428)
.+.+.|..+..|.+|||.|++++.||-.+..-+
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 355667778899999999999999997665433
No 110
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=81.49 E-value=1.6 Score=45.70 Aligned_cols=39 Identities=26% Similarity=0.243 Sum_probs=35.7
Q ss_pred ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEcc
Q 014254 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA 223 (428)
Q Consensus 185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~ 223 (428)
...+.+.||.+..+..|||+|.+++...+-||.+|.|-.
T Consensus 307 ~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s 345 (374)
T PRK12328 307 EKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNE 345 (374)
T ss_pred CcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEE
Confidence 356788999999999999999999999999999999953
No 111
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=81.41 E-value=1.1 Score=48.10 Aligned_cols=36 Identities=31% Similarity=0.458 Sum_probs=34.0
Q ss_pred EEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (428)
Q Consensus 279 t~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~ 314 (428)
...+.||...++.+|||+|.+|++|.+..|-+|.+.
T Consensus 487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~ 522 (604)
T COG1855 487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVK 522 (604)
T ss_pred eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEE
Confidence 467899999999999999999999999999999997
No 112
>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=80.87 E-value=1.7 Score=44.94 Aligned_cols=37 Identities=30% Similarity=0.429 Sum_probs=34.8
Q ss_pred eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEc
Q 014254 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVG 222 (428)
Q Consensus 186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is 222 (428)
..+.+.||.+..+..|||+|.+++....-||.+|.|-
T Consensus 301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~ 337 (341)
T TIGR01953 301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVK 337 (341)
T ss_pred cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEE
Confidence 5678999999999999999999999999999999985
No 113
>PRK13764 ATPase; Provisional
Probab=80.82 E-value=1.3 Score=49.11 Aligned_cols=38 Identities=26% Similarity=0.419 Sum_probs=34.6
Q ss_pred eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEcc
Q 014254 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA 223 (428)
Q Consensus 186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~ 223 (428)
-...+.||...++.+|||+|.+|++|+++.|..|.|-.
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~ 518 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP 518 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence 34558999999999999999999999999999999965
No 114
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=79.13 E-value=3.7 Score=41.33 Aligned_cols=51 Identities=20% Similarity=0.331 Sum_probs=45.9
Q ss_pred cceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhhh
Q 014254 290 GCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLRD 351 (428)
Q Consensus 290 G~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~e 351 (428)
-++||.+|.+++.|+-.|.|.|-+.+ ..|.+.|....++.+...+.+++..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG-----------~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG-----------NTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC-----------cEEEeecCcchHHHHHHHHHHHHhc
Confidence 57999999999999999999999963 3599999999999999999998875
No 115
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=78.47 E-value=4 Score=40.15 Aligned_cols=59 Identities=17% Similarity=0.292 Sum_probs=44.9
Q ss_pred EEEEeccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHH-HHHHHHHHHHH
Q 014254 280 ARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSK-VKDAVYNVTGR 348 (428)
Q Consensus 280 ~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~a-V~~A~~lI~~~ 348 (428)
.-+.|+...|-++||++|+.++-+.+.|+|+|-+- .+-.|=|.|..+. ...|...|..+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG----------~NG~IWV~~~~~~~e~~~~~aI~~i 207 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVG----------QNGRIWVDGENESLEELAIEAIRKI 207 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEe----------cCCEEEecCCCcchHHHHHHHHHHH
Confidence 45789999999999999999999999999999994 3445777777663 44444444443
No 116
>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=78.02 E-value=6.3 Score=36.03 Aligned_cols=92 Identities=15% Similarity=0.394 Sum_probs=58.0
Q ss_pred eeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccc-cccCCCCCCCcee
Q 014254 200 VIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE-KGLDFSSNKGLLV 278 (428)
Q Consensus 200 IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~-~g~~~~~~~~~~v 278 (428)
.+=..|..|++|-++..-+|.|-.+. . +--. -.+|...|.+ ++....+ .+..+ ...
T Consensus 20 ~~~~~~dli~~lAk~lrKRIvvR~dp-----s---~l~~---------~e~A~~~I~~-ivP~ea~i~di~F-----d~~ 76 (145)
T cd02410 20 LFAEDGDLVKDLAKDLRKRIVIRPDP-----S---VLKP---------PEEAIKIILE-IVPEEAGITDIYF-----DDD 76 (145)
T ss_pred HHhcccHHHHHHHHHHhceEEEcCCh-----h---hcCC---------HHHHHHHHHH-hCCCccCceeeEe-----cCC
Confidence 34466889999999888888774210 0 1111 1234444333 3321110 11111 122
Q ss_pred EEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (428)
Q Consensus 279 t~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~ 314 (428)
+.++.|-...-|.+|||+|.++++|...||=.-.+.
T Consensus 77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vv 112 (145)
T cd02410 77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVV 112 (145)
T ss_pred CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEE
Confidence 457788888889999999999999999999998887
No 117
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=77.94 E-value=2.4 Score=44.19 Aligned_cols=39 Identities=23% Similarity=0.307 Sum_probs=35.7
Q ss_pred ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEcc
Q 014254 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA 223 (428)
Q Consensus 185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~ 223 (428)
...+.+.||.+..+..|||+|.+++.-..-||.+|.|-.
T Consensus 302 ~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 302 EKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred CcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 356889999999999999999999999999999999863
No 118
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=77.39 E-value=3.3 Score=38.69 Aligned_cols=35 Identities=29% Similarity=0.523 Sum_probs=31.0
Q ss_pred EEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (428)
Q Consensus 279 t~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~ 314 (428)
.+-++|.... |.-|||+|.+|+.+++..|-+|.+.
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevV 96 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVV 96 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEE
Confidence 4556777777 9999999999999999999999997
No 119
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=76.67 E-value=2.1 Score=46.06 Aligned_cols=38 Identities=24% Similarity=0.337 Sum_probs=35.1
Q ss_pred eEEEEEeccccccceeccCchHHHHHHHHhCCcEEEcc
Q 014254 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA 223 (428)
Q Consensus 186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~ 223 (428)
-.+.+.||.+..+..|||+|.+||...+-||.+|.|-.
T Consensus 302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 47789999999999999999999999999999999853
No 120
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=76.45 E-value=4.6 Score=39.76 Aligned_cols=45 Identities=33% Similarity=0.496 Sum_probs=37.8
Q ss_pred EEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCC
Q 014254 190 ILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240 (428)
Q Consensus 190 IlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e 240 (428)
+.|+...+-.+|||+|+.++.|.++|+|.|-|.. +-| |=|.|..+
T Consensus 150 v~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-----NG~-IWV~~~~~ 194 (239)
T COG1097 150 VKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-----NGR-IWVDGENE 194 (239)
T ss_pred EEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-----CCE-EEecCCCc
Confidence 6788899999999999999999999999999963 334 55777655
No 121
>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=76.18 E-value=2.6 Score=36.32 Aligned_cols=31 Identities=26% Similarity=0.397 Sum_probs=26.0
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCC
Q 014254 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGA 217 (428)
Q Consensus 187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA 217 (428)
.+++.+-...-|.|||++|+.|++|++....
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence 3667777788999999999999999987544
No 122
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=74.31 E-value=2.8 Score=44.76 Aligned_cols=39 Identities=23% Similarity=0.298 Sum_probs=35.4
Q ss_pred ceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEcc
Q 014254 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA 223 (428)
Q Consensus 185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~ 223 (428)
...+.+.||.+..++.|||+|.+|+--..-||.+|.|..
T Consensus 334 ~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 334 GRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred CcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 345789999999999999999999999999999999863
No 123
>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=73.93 E-value=3.5 Score=33.78 Aligned_cols=28 Identities=36% Similarity=0.529 Sum_probs=22.9
Q ss_pred EEEEeccccccceeccCchHHHHHHHHh
Q 014254 188 FRILCSNDKVGAVIGKGGTIIRALQSEA 215 (428)
Q Consensus 188 ~rIlVP~~~vG~IIGKgG~tIK~IqeeT 215 (428)
+++.+-...-|.+||++|++|++|++.-
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 4455555788999999999999998874
No 124
>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=73.21 E-value=3.9 Score=33.54 Aligned_cols=35 Identities=14% Similarity=0.378 Sum_probs=27.9
Q ss_pred EEEEEeccccccceeCCCCchHHHHHHHhCCeEEE
Q 014254 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRI 313 (428)
Q Consensus 279 t~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI 313 (428)
.+++.|-...-|.|||++|+.|++|++.-.....+
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 47788888888999999999999998765444333
No 125
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=73.17 E-value=4.6 Score=36.89 Aligned_cols=35 Identities=34% Similarity=0.552 Sum_probs=30.0
Q ss_pred EEEeccccccceeccCchHHHHHHHHhCCcEEEcc
Q 014254 189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA 223 (428)
Q Consensus 189 rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~ 223 (428)
.+.|-..+-|++|||+|.+++.|..+||=+-.|-.
T Consensus 79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvR 113 (145)
T cd02410 79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVR 113 (145)
T ss_pred EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence 35666778899999999999999999999887754
No 126
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=69.06 E-value=4.2 Score=39.88 Aligned_cols=31 Identities=32% Similarity=0.434 Sum_probs=26.5
Q ss_pred ceEEEEEeccccccceeccCchHHHHHHHHh
Q 014254 185 EVSFRILCSNDKVGAVIGKGGTIIRALQSEA 215 (428)
Q Consensus 185 evt~rIlVP~~~vG~IIGKgG~tIK~IqeeT 215 (428)
....++.|-...-|.||||+|+.|++|++..
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l 80 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKEL 80 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHH
Confidence 3467788889999999999999999988763
No 127
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=68.33 E-value=13 Score=40.62 Aligned_cols=93 Identities=19% Similarity=0.349 Sum_probs=61.4
Q ss_pred ceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcc-cccccCCCCCCCce
Q 014254 199 AVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGT-SEKGLDFSSNKGLL 277 (428)
Q Consensus 199 ~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~-~~~g~~~~~~~~~~ 277 (428)
.+|-+.|..||+|-++..-+|.|-.+. . +--+ ..+|...|.+-+-++. +. ...+ ..
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~dP-s-------vl~~---------~e~A~~~I~eivP~ea~i~-~i~F-----d~ 98 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPDP-S-------VLKP---------PEEARKIILEIVPEEAGIT-DIYF-----DD 98 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccCc-h-------hcCC---------HHHHHHHHHHhCccccCce-eEEe-----cC
Confidence 366789999999999999998885321 0 1111 2234444443221111 00 0111 12
Q ss_pred eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc
Q 014254 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII 314 (428)
Q Consensus 278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~ 314 (428)
.+.+++|-...=|.+|||+|++.++|..+||-.-+|.
T Consensus 99 ~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~iv 135 (637)
T COG1782 99 DTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIV 135 (637)
T ss_pred CCceEEEEecCCceEEecCchHHHHHHHHhCCcceee
Confidence 3457888889999999999999999999999888887
No 128
>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=65.67 E-value=7.1 Score=38.27 Aligned_cols=30 Identities=27% Similarity=0.437 Sum_probs=24.4
Q ss_pred eEEEEEec-cccccceeccCchHHHHHHHHh
Q 014254 186 VSFRILCS-NDKVGAVIGKGGTIIRALQSEA 215 (428)
Q Consensus 186 vt~rIlVP-~~~vG~IIGKgG~tIK~IqeeT 215 (428)
+...|+|. .++-+.||||+|+.||+|..+.
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 66678888 4678999999999999886653
No 129
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=64.84 E-value=7.1 Score=31.97 Aligned_cols=28 Identities=21% Similarity=0.603 Sum_probs=22.3
Q ss_pred EEEEeccccccceeCCCCchHHHHHHHh
Q 014254 280 ARLVVASNQVGCLLGKGGTIISEMRKVT 307 (428)
Q Consensus 280 ~~L~VP~s~VG~IIGKgG~~IkeIre~T 307 (428)
+++.|-...-|.+||++|++|+++++.-
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 4555555788999999999999987653
No 130
>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=64.54 E-value=6.3 Score=33.91 Aligned_cols=29 Identities=24% Similarity=0.475 Sum_probs=24.0
Q ss_pred EEEEEeccccccceeCCCCchHHHHHHHh
Q 014254 279 NARLVVASNQVGCLLGKGGTIISEMRKVT 307 (428)
Q Consensus 279 t~~L~VP~s~VG~IIGKgG~~IkeIre~T 307 (428)
.+++.|-...-|.|||++|+.|++|++..
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l 90 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKEL 90 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHH
Confidence 35677777788999999999999998654
No 131
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=61.49 E-value=8.8 Score=37.63 Aligned_cols=30 Identities=23% Similarity=0.418 Sum_probs=24.2
Q ss_pred eeEEEEEec-cccccceeCCCCchHHHHHHH
Q 014254 277 LVNARLVVA-SNQVGCLLGKGGTIISEMRKV 306 (428)
Q Consensus 277 ~vt~~L~VP-~s~VG~IIGKgG~~IkeIre~ 306 (428)
.+.+.+.|. .++-|.||||+|+.||+|...
T Consensus 220 ~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ 250 (270)
T TIGR00436 220 KIHALISVERESQKKIIIGKNGSMIKAIGIA 250 (270)
T ss_pred EEEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence 466778887 557799999999999998653
No 132
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=57.34 E-value=4.8 Score=38.75 Aligned_cols=41 Identities=20% Similarity=0.292 Sum_probs=35.3
Q ss_pred cccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCC
Q 014254 194 NDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGP 241 (428)
Q Consensus 194 ~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~ 241 (428)
+..+|.|+||+|.+--.|++-|.++|.+.+ ..|.|-|...+
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad-------~kIHiLG~~~n 217 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD-------SKIHILGAFQN 217 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecC-------ceEEEeecchh
Confidence 467999999999999999999999999964 34888887665
No 133
>PRK00089 era GTPase Era; Reviewed
Probab=56.71 E-value=11 Score=37.00 Aligned_cols=38 Identities=24% Similarity=0.542 Sum_probs=28.9
Q ss_pred eeEEEEEec-cccccceeCCCCchHHHHHH--------HhCCeEEEc
Q 014254 277 LVNARLVVA-SNQVGCLLGKGGTIISEMRK--------VTGTSIRII 314 (428)
Q Consensus 277 ~vt~~L~VP-~s~VG~IIGKgG~~IkeIre--------~TGA~IqI~ 314 (428)
.+.+.|.|. .++-+.||||+|++||+|.. ..|++|.+.
T Consensus 225 ~i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 225 RIEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred EEEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 366677777 55779999999999998864 557776664
No 134
>PRK15494 era GTPase Era; Provisional
Probab=56.51 E-value=12 Score=38.19 Aligned_cols=37 Identities=19% Similarity=0.300 Sum_probs=28.0
Q ss_pred eEEEEEecc-ccccceeccCchHHHHHHHH--------hCCcEEEc
Q 014254 186 VSFRILCSN-DKVGAVIGKGGTIIRALQSE--------AGAFISVG 222 (428)
Q Consensus 186 vt~rIlVP~-~~vG~IIGKgG~tIK~Iqee--------TGA~I~Is 222 (428)
+...|+|.. ++-+.||||+|+.||+|..+ .|++|.+.
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 556688884 67899999999999987554 56666553
No 135
>PRK15494 era GTPase Era; Provisional
Probab=56.38 E-value=12 Score=38.41 Aligned_cols=37 Identities=27% Similarity=0.477 Sum_probs=28.4
Q ss_pred eEEEEEec-cccccceeCCCCchHHHHHH--------HhCCeEEEc
Q 014254 278 VNARLVVA-SNQVGCLLGKGGTIISEMRK--------VTGTSIRII 314 (428)
Q Consensus 278 vt~~L~VP-~s~VG~IIGKgG~~IkeIre--------~TGA~IqI~ 314 (428)
+.+.|.|. .++-+.||||+|+.||+|.. ..|++|.+.
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 56778887 45779999999999998864 557766654
No 136
>PRK00089 era GTPase Era; Reviewed
Probab=55.88 E-value=13 Score=36.58 Aligned_cols=37 Identities=24% Similarity=0.555 Sum_probs=27.5
Q ss_pred eEEEEEec-cccccceeccCchHHHHHHHH--------hCCcEEEc
Q 014254 186 VSFRILCS-NDKVGAVIGKGGTIIRALQSE--------AGAFISVG 222 (428)
Q Consensus 186 vt~rIlVP-~~~vG~IIGKgG~tIK~Iqee--------TGA~I~Is 222 (428)
+...|+|. .++-+.||||+|+.||+|... .|++|.+.
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 55567777 467899999999999987654 56666653
No 137
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=55.59 E-value=11 Score=37.08 Aligned_cols=38 Identities=26% Similarity=0.519 Sum_probs=29.9
Q ss_pred eeEEEEEeccccccceeCCCCchHHHHHH----HhCC-eEEEc
Q 014254 277 LVNARLVVASNQVGCLLGKGGTIISEMRK----VTGT-SIRII 314 (428)
Q Consensus 277 ~vt~~L~VP~s~VG~IIGKgG~~IkeIre----~TGA-~IqI~ 314 (428)
...+++.|-...=|.||||+|+.|++|++ .+|. +++|.
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~~v~I~ 92 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKENVQIN 92 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCCCceEE
Confidence 34677888888889999999999998864 6676 45554
No 138
>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=55.16 E-value=41 Score=37.65 Aligned_cols=93 Identities=16% Similarity=0.342 Sum_probs=60.2
Q ss_pred eeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCCCCcCccHHHHHHHHHHHHhhhcccc-cccCCCCCCCcee
Q 014254 200 VIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEGPESRYSPAQKAVVLVFSRLIEGTSE-KGLDFSSNKGLLV 278 (428)
Q Consensus 200 IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~-~g~~~~~~~~~~v 278 (428)
.+-+.|..||+|-++..-+|.|-.+. . +--+ -.+|...|.+ ++....+ ....+ ...
T Consensus 37 ~~~~~~~~~~~~~~~~~~r~~~~~~~-----~---~~~~---------~~~~~~~i~~-~~~~~~~~~~~~f-----~~~ 93 (630)
T TIGR03675 37 LFAKDDDLVKELAKKLRKRIVIRPDP-----S---VLLP---------PEEAIEKIKE-IVPEEAGITDIYF-----DDV 93 (630)
T ss_pred HhccchHHHHHHHHHhhceEEEecCh-----h---hcCC---------HHHHHHHHHH-hCCCcCCceeEEe-----cCC
Confidence 45678899999999998888875210 0 1111 1234433333 3321110 01111 223
Q ss_pred EEEEEeccccccceeCCCCchHHHHHHHhCCeEEEcc
Q 014254 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIIS 315 (428)
Q Consensus 279 t~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~ 315 (428)
+-++.|-...-|.||||+|.++++|.++||=.-+|.+
T Consensus 94 ~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~ 130 (630)
T TIGR03675 94 TGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVR 130 (630)
T ss_pred CceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEe
Confidence 4578888889999999999999999999999999973
No 139
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=54.28 E-value=11 Score=41.13 Aligned_cols=127 Identities=10% Similarity=0.060 Sum_probs=73.3
Q ss_pred ceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEe-eCCCCCCcCccHHHHHHHHHHHHhhhcccccccCCCCCCCce
Q 014254 199 AVIGKGGTIIRALQSEAGAFISVGATMPECDERLITV-TASEGPESRYSPAQKAVVLVFSRLIEGTSEKGLDFSSNKGLL 277 (428)
Q Consensus 199 ~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtI-tGs~e~~~~~s~a~~Ai~~I~~~i~e~~~~~g~~~~~~~~~~ 277 (428)
.|=||+--.+.+|++...|.++++=- ...+.++-+. .|..-. -+++ ++.+ .. +=.
T Consensus 393 Fl~gkkngK~TrIm~~v~c~~~~~i~-~~~gs~~~~~~~g~~~~------F~k~----~~~~-~~------------EFp 448 (657)
T COG5166 393 FLRGKKNGKATRIMKGVSCSELSSIV-SSTGSIVETNGIGEKMS------FSKK----LSIP-PT------------EFP 448 (657)
T ss_pred HhccccCcchhhhhhhcccceeeEEE-ecCCcEEEEeccCcchh------hHHH----hcCC-cc------------cCc
Confidence 56687777799999999998665421 1112243332 332211 1111 1111 10 111
Q ss_pred eEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEccC-CccccCCCCCcEEEEEeC---HHHHHHHHHHHHHHhhh
Q 014254 278 VNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRIISD-QLLKCISENDRVVQISGE---FSKVKDAVYNVTGRLRD 351 (428)
Q Consensus 278 vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d-~~P~~~~s~eRvVtItGt---~~aV~~A~~lI~~~L~e 351 (428)
....+.||...+-.|||-||..|++++..-++.|++... ..|.. --..-|.|.-. .+++.-|+.-+.+++++
T Consensus 449 ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs--~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~ 524 (657)
T COG5166 449 AEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQS--QWHDNVLIEAPRKNQDNISGKKNDKLDKVKQ 524 (657)
T ss_pred hheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchh--hhhcceEEECCccCccchhcccccHHHHHhh
Confidence 245689999999999999999999999999999999822 22221 11112555544 33344455555666653
No 140
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=53.85 E-value=12 Score=38.73 Aligned_cols=32 Identities=25% Similarity=0.546 Sum_probs=26.1
Q ss_pred ceEEEEEecc-ccccceeccCchHHHHHHHHhC
Q 014254 185 EVSFRILCSN-DKVGAVIGKGGTIIRALQSEAG 216 (428)
Q Consensus 185 evt~rIlVP~-~~vG~IIGKgG~tIK~IqeeTG 216 (428)
.++.+++||. +..-.||||||..|++|-++-+
T Consensus 327 ~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 327 FIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 4678899996 5577799999999999977654
No 141
>COG1159 Era GTPase [General function prediction only]
Probab=50.52 E-value=18 Score=36.87 Aligned_cols=37 Identities=24% Similarity=0.544 Sum_probs=27.5
Q ss_pred eeEEEEEec-cccccceeCCCCchHHHHHH--------HhCCeEEE
Q 014254 277 LVNARLVVA-SNQVGCLLGKGGTIISEMRK--------VTGTSIRI 313 (428)
Q Consensus 277 ~vt~~L~VP-~s~VG~IIGKgG~~IkeIre--------~TGA~IqI 313 (428)
.+...|.|+ .++=|-||||+|++||+|-. ..|++|.+
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L 273 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYL 273 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEE
Confidence 445567777 56779999999999998854 45666655
No 142
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=49.01 E-value=17 Score=39.57 Aligned_cols=125 Identities=15% Similarity=0.137 Sum_probs=78.6
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCCcEEEccC--CCCCCceE-EEeeCCCCCCcCccHHHHHHHHHHHHhhhcc
Q 014254 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT--MPECDERL-ITVTASEGPESRYSPAQKAVVLVFSRLIEGT 263 (428)
Q Consensus 187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~--~p~s~ERv-VtItGs~e~~~~~s~a~~Ai~~I~~~i~e~~ 263 (428)
.+-+.||...+-.|||-||..|.+...+.++.|++... .+.+..+- |.|..+..+.+..+-+.+.++.+.. +++
T Consensus 450 e~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~---~~c 526 (657)
T COG5166 450 EIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVK---QQC 526 (657)
T ss_pred heEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHh---hhc
Confidence 46679999999999999999999999999999999754 33333333 7788776665544444444443332 111
Q ss_pred -cc-ccc-------------C-CC------CC-----CCceeEEEEEeccccccceeC---CCCchHHHHHHHhCCeEEE
Q 014254 264 -SE-KGL-------------D-FS------SN-----KGLLVNARLVVASNQVGCLLG---KGGTIISEMRKVTGTSIRI 313 (428)
Q Consensus 264 -~~-~g~-------------~-~~------~~-----~~~~vt~~L~VP~s~VG~IIG---KgG~~IkeIre~TGA~IqI 313 (428)
+. ++. + .+ .. ..-.....+.+|+..++..+| -.|++|..+.....-.|..
T Consensus 527 ~f~~Kgdirf~~~~~sI~~v~~~~~~I~rv~kne~v~~~~p~~~~~y~~se~h~~g~gena~R~~ni~~~t~~y~~~ie~ 606 (657)
T COG5166 527 RFNLKGDIRFCPQSTSIFTVDIYSDEIERVIKNETVLLEFPAEMHFYVPSEIHKKGIGENAFRGENIQRVTKLYNSYIEF 606 (657)
T ss_pred ccccccceEEcCCceEEEEEcccccHHHHHhhccceEEecccccccccchhhhhccCCcccccccchhhhhhhhhcccee
Confidence 00 000 0 00 00 011233456677777888888 5677777777776666666
Q ss_pred c
Q 014254 314 I 314 (428)
Q Consensus 314 ~ 314 (428)
.
T Consensus 607 ~ 607 (657)
T COG5166 607 S 607 (657)
T ss_pred e
Confidence 5
No 143
>COG1159 Era GTPase [General function prediction only]
Probab=47.90 E-value=22 Score=36.24 Aligned_cols=38 Identities=21% Similarity=0.452 Sum_probs=27.7
Q ss_pred ceEEEEEec-cccccceeccCchHHHHHHH--------HhCCcEEEc
Q 014254 185 EVSFRILCS-NDKVGAVIGKGGTIIRALQS--------EAGAFISVG 222 (428)
Q Consensus 185 evt~rIlVP-~~~vG~IIGKgG~tIK~Iqe--------eTGA~I~Is 222 (428)
.+...|+|. .++=|.||||+|+.||+|-. -.+++|.+.
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L~ 274 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYLE 274 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEEE
Confidence 355557787 46789999999999998754 456666553
No 144
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=47.23 E-value=14 Score=40.73 Aligned_cols=49 Identities=29% Similarity=0.418 Sum_probs=39.7
Q ss_pred CceEEEEEeccccccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCC
Q 014254 184 QEVSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASE 239 (428)
Q Consensus 184 ~evt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~ 239 (428)
..+...+.++.++...+||.+|-..|+|+.+||+.-++ ++-.++|-...
T Consensus 595 ~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v-------De~t~~i~A~~ 643 (760)
T KOG1067|consen 595 SPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV-------DEGTFSIFAPT 643 (760)
T ss_pred CceeeEEeecchhhheeecCccceeeeEeeeccceeee-------cCceEEEEecC
Confidence 34677789999999999999999999999999954444 45567787753
No 145
>CHL00048 rps3 ribosomal protein S3
Probab=43.79 E-value=23 Score=34.34 Aligned_cols=30 Identities=17% Similarity=0.147 Sum_probs=25.2
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhC
Q 014254 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAG 216 (428)
Q Consensus 187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTG 216 (428)
.+++.|-...-|.|||++|++|++|++.-.
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 456677777889999999999999998764
No 146
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=43.29 E-value=23 Score=34.04 Aligned_cols=31 Identities=35% Similarity=0.464 Sum_probs=24.7
Q ss_pred EEEEeccccccceeccCchHHHHHHHHhCCc
Q 014254 188 FRILCSNDKVGAVIGKGGTIIRALQSEAGAF 218 (428)
Q Consensus 188 ~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~ 218 (428)
.++.|-...-|.+||++|++|++|++.-.-.
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 4455555788999999999999999886543
No 147
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=43.14 E-value=24 Score=33.76 Aligned_cols=31 Identities=29% Similarity=0.543 Sum_probs=26.0
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCC
Q 014254 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGA 217 (428)
Q Consensus 187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA 217 (428)
.+++.|-...-|.|||++|..|++|+++-.-
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 4667787888999999999999999987543
No 148
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=41.32 E-value=25 Score=36.37 Aligned_cols=34 Identities=32% Similarity=0.502 Sum_probs=26.3
Q ss_pred CceeEEEEEeccc-cccceeCCCCchHHHHHHHhC
Q 014254 275 GLLVNARLVVASN-QVGCLLGKGGTIISEMRKVTG 308 (428)
Q Consensus 275 ~~~vt~~L~VP~s-~VG~IIGKgG~~IkeIre~TG 308 (428)
...+..++.+|.. +.-.||||||+.|++|-++-+
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 3456788999955 556789999999999976543
No 149
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=41.29 E-value=26 Score=34.17 Aligned_cols=32 Identities=25% Similarity=0.287 Sum_probs=26.2
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhCCc
Q 014254 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAGAF 218 (428)
Q Consensus 187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~ 218 (428)
.+++.|-...-|.|||++|..|++|+++-.-.
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~ 76 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLLQKR 76 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHHHHH
Confidence 35667777788999999999999999886544
No 150
>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=39.34 E-value=32 Score=38.54 Aligned_cols=36 Identities=36% Similarity=0.573 Sum_probs=31.0
Q ss_pred EEEeccccccceeccCchHHHHHHHHhCCcEEEccC
Q 014254 189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGAT 224 (428)
Q Consensus 189 rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~~ 224 (428)
.++|-..+-|.||||+|.++++|-.+||-+-+|-..
T Consensus 96 ~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 96 EVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred eEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 356677888999999999999999999998888653
No 151
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=38.63 E-value=23 Score=34.27 Aligned_cols=36 Identities=25% Similarity=0.386 Sum_probs=28.5
Q ss_pred eEEEEEeccccccceeccCchHHHHHHHHhCCcEEE
Q 014254 186 VSFRILCSNDKVGAVIGKGGTIIRALQSEAGAFISV 221 (428)
Q Consensus 186 vt~rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~I 221 (428)
-.+.+-+-.+..|.+|||.|+++..||--+.+.++-
T Consensus 91 ~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 344455666669999999999999999988776654
No 152
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=37.08 E-value=36 Score=37.27 Aligned_cols=35 Identities=31% Similarity=0.541 Sum_probs=30.1
Q ss_pred EEEeccccccceeccCchHHHHHHHHhCCcEEEcc
Q 014254 189 RILCSNDKVGAVIGKGGTIIRALQSEAGAFISVGA 223 (428)
Q Consensus 189 rIlVP~~~vG~IIGKgG~tIK~IqeeTGA~I~Is~ 223 (428)
.++|-+.+-|++|||+|++.+.|..+||-.-+|-.
T Consensus 102 EViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR 136 (637)
T COG1782 102 EVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVR 136 (637)
T ss_pred eEEEEecCCceEEecCchHHHHHHHHhCCcceeee
Confidence 36777788899999999999999999998777643
No 153
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=34.69 E-value=24 Score=29.57 Aligned_cols=32 Identities=31% Similarity=0.298 Sum_probs=27.0
Q ss_pred chHHHhhhhcccCccccccccccchHHHHHHhhhcC
Q 014254 59 SHETIRRSLEAVPHDTIARPVEAVPQEILWRSLESG 94 (428)
Q Consensus 59 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (428)
.|-.|-.-|+|||.||.-.|| .|+|+|.+|+|
T Consensus 16 ~~~~iF~FL~~~P~GT~~~~i----R~~L~rYI~~~ 47 (97)
T PRK13916 16 DYPQIFDFLENVPRGTKTAHI----REALRRYIEEI 47 (97)
T ss_pred ccHHHHHHHHHCCCCCccHHH----HHHHHHHHHhc
Confidence 466777889999999988776 58999999887
No 154
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=33.04 E-value=42 Score=32.32 Aligned_cols=28 Identities=25% Similarity=0.641 Sum_probs=22.4
Q ss_pred EEEEeccccccceeCCCCchHHHHHHHh
Q 014254 280 ARLVVASNQVGCLLGKGGTIISEMRKVT 307 (428)
Q Consensus 280 ~~L~VP~s~VG~IIGKgG~~IkeIre~T 307 (428)
+.+.|-...-|.+||++|++|+++++.-
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~L 69 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEIL 69 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHH
Confidence 4555555788999999999999988654
No 155
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=32.44 E-value=87 Score=31.88 Aligned_cols=37 Identities=19% Similarity=0.319 Sum_probs=30.0
Q ss_pred ccceeccCchHHHHHHHHhCCcEEEccCCCCCCceEEEeeCCCC
Q 014254 197 VGAVIGKGGTIIRALQSEAGAFISVGATMPECDERLITVTASEG 240 (428)
Q Consensus 197 vG~IIGKgG~tIK~IqeeTGA~I~Is~~~p~s~ERvVtItGs~e 240 (428)
--.+||.+|+|+|.|+--|.|.|-|.. ..|.+.|...
T Consensus 160 RqRLiGpng~TLKAlelLT~CYilVqG-------~TVsaiGpfk 196 (356)
T KOG2874|consen 160 RQRLIGPNGSTLKALELLTNCYILVQG-------NTVSAIGPFK 196 (356)
T ss_pred HHHhcCCCchhHHHHHHHhhcEEEeeC-------cEEEeecCcc
Confidence 346999999999999999999999963 3467777644
No 156
>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=31.08 E-value=48 Score=31.76 Aligned_cols=28 Identities=21% Similarity=0.598 Sum_probs=23.6
Q ss_pred EEEEEeccccccceeCCCCchHHHHHHH
Q 014254 279 NARLVVASNQVGCLLGKGGTIISEMRKV 306 (428)
Q Consensus 279 t~~L~VP~s~VG~IIGKgG~~IkeIre~ 306 (428)
.+++.|-...-|.|||++|..|++|++.
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~ 66 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEK 66 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHH
Confidence 4677787888899999999999998754
No 157
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=30.32 E-value=45 Score=32.29 Aligned_cols=35 Identities=14% Similarity=0.348 Sum_probs=28.1
Q ss_pred EEEEEeccccccceeCCCCchHHHHHHHhCCeEEE
Q 014254 279 NARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRI 313 (428)
Q Consensus 279 t~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI 313 (428)
.+.+-|-.+..|.+||+.|++++.||-.+.+-+.-
T Consensus 92 ~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 92 RVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred EEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 55667777779999999999999999877654443
No 158
>CHL00048 rps3 ribosomal protein S3
Probab=29.96 E-value=49 Score=32.02 Aligned_cols=29 Identities=14% Similarity=0.167 Sum_probs=23.7
Q ss_pred EEEEEeccccccceeCCCCchHHHHHHHh
Q 014254 279 NARLVVASNQVGCLLGKGGTIISEMRKVT 307 (428)
Q Consensus 279 t~~L~VP~s~VG~IIGKgG~~IkeIre~T 307 (428)
.+++.|-...-|.|||++|..|++|++.-
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 46677777778999999999999987643
No 159
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=29.44 E-value=51 Score=32.17 Aligned_cols=28 Identities=18% Similarity=0.436 Sum_probs=23.0
Q ss_pred EEEEEeccccccceeCCCCchHHHHHHH
Q 014254 279 NARLVVASNQVGCLLGKGGTIISEMRKV 306 (428)
Q Consensus 279 t~~L~VP~s~VG~IIGKgG~~IkeIre~ 306 (428)
.+++.|-...-|.|||++|..|++|++.
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~ 72 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSL 72 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHH
Confidence 3667777777899999999999998754
No 160
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=28.21 E-value=56 Score=31.55 Aligned_cols=29 Identities=31% Similarity=0.515 Sum_probs=24.5
Q ss_pred EEEEeccccccceeccCchHHHHHHHHhC
Q 014254 188 FRILCSNDKVGAVIGKGGTIIRALQSEAG 216 (428)
Q Consensus 188 ~rIlVP~~~vG~IIGKgG~tIK~IqeeTG 216 (428)
++|.+-...-|.|||++|..|++|++.-.
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 56777777889999999999999997653
No 161
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=27.73 E-value=1.4e+02 Score=31.14 Aligned_cols=52 Identities=25% Similarity=0.216 Sum_probs=43.3
Q ss_pred eccccccceeCCCCchHHHHHHHhCCeEEEccCCccccCCCCCcEEEEEeCHHHHHHHHHHHH
Q 014254 284 VASNQVGCLLGKGGTIISEMRKVTGTSIRIISDQLLKCISENDRVVQISGEFSKVKDAVYNVT 346 (428)
Q Consensus 284 VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~ 346 (428)
-+.+..-.+.|..|.+++.|.+..|+.|... .+.++|+|+...|..|...+.
T Consensus 21 ~~~~~~~~l~G~~~~~l~l~e~~~gv~i~~r-----------G~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 21 SDDNELVALFGPTDTNLSLLEIALGVSIVAR-----------GEAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred CCchhhhhhcCCCCccHHHHHHHhCcEEEeC-----------CceEEEEechHHHHHHHHHHh
Confidence 3356778899999999999999999888774 346999999778888887776
No 162
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=23.59 E-value=4e+02 Score=21.62 Aligned_cols=70 Identities=17% Similarity=0.159 Sum_probs=49.1
Q ss_pred CceeEEEEEeccccccceeCCCCchHHHHHHHhCCeEEEc-cCCccccCCCCCcEEEEEeCHHHHHHHHHHHHHHhh
Q 014254 275 GLLVNARLVVASNQVGCLLGKGGTIISEMRKVTGTSIRII-SDQLLKCISENDRVVQISGEFSKVKDAVYNVTGRLR 350 (428)
Q Consensus 275 ~~~vt~~L~VP~s~VG~IIGKgG~~IkeIre~TGA~IqI~-~d~~P~~~~s~eRvVtItGt~~aV~~A~~lI~~~L~ 350 (428)
+...+..+..-.+.+ + -|-..+.++-+..|++++.. +|...- ...+.+++|.|+..++..|.+.++..|.
T Consensus 15 ~~~~~a~i~are~gV--~--aG~~~~~~i~~~l~~~v~~~~~dG~~v--~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 15 DKTGTATIIAREDGV--L--AGLEEAEEIFEKLGLEVEWLVKDGDRV--EPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp TSEEEEEEEESSSEE--E---SHHHHHHHHHHCTEEEEESS-TT-EE--ETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred CCEEEEEEEeCCCEE--E--ECHHHHHHHHhhccEEEEEEeCCCCCc--cCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 344555665555432 2 25567788888889999988 554321 2578999999999999999999888775
No 163
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=21.04 E-value=88 Score=30.69 Aligned_cols=30 Identities=33% Similarity=0.488 Sum_probs=23.9
Q ss_pred EEEEEeccccccceeccCchHHHHHHHHhC
Q 014254 187 SFRILCSNDKVGAVIGKGGTIIRALQSEAG 216 (428)
Q Consensus 187 t~rIlVP~~~vG~IIGKgG~tIK~IqeeTG 216 (428)
.+.|.|-...-|.|||++|..|++|++...
T Consensus 63 ~i~I~I~~~rP~~iiG~~g~~i~~l~~~L~ 92 (232)
T PRK00310 63 RVRVTIHTARPGIVIGKKGAEIEKLRKELE 92 (232)
T ss_pred eEEEEEEECCCccccCCCcHHHHHHHHHHH
Confidence 355566667789999999999999988753
No 164
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=20.81 E-value=92 Score=30.09 Aligned_cols=27 Identities=30% Similarity=0.572 Sum_probs=22.6
Q ss_pred EEEEeccccccceeCCCCchHHHHHHH
Q 014254 280 ARLVVASNQVGCLLGKGGTIISEMRKV 306 (428)
Q Consensus 280 ~~L~VP~s~VG~IIGKgG~~IkeIre~ 306 (428)
+++.|-...-|.|||++|+.|++|++.
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~ 90 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKD 90 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHH
Confidence 567777777899999999999999753
Done!