Query 019747
Match_columns 336
No_of_seqs 173 out of 1880
Neff 8.9
Searched_HMMs 46136
Date Fri Mar 29 04:13:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019747.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019747hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2192 PolyC-binding hnRNP-K 100.0 3.9E-40 8.6E-45 278.9 24.3 285 31-333 44-388 (390)
2 KOG1676 K-homology type RNA bi 100.0 1.5E-37 3.2E-42 290.6 23.7 260 21-330 126-390 (600)
3 KOG2191 RNA-binding protein NO 100.0 2.9E-35 6.3E-40 256.1 25.5 308 2-333 5-319 (402)
4 KOG2193 IGF-II mRNA-binding pr 100.0 8.3E-37 1.8E-41 273.2 15.5 281 30-331 194-483 (584)
5 KOG1676 K-homology type RNA bi 100.0 1E-33 2.2E-38 264.9 21.5 255 30-333 49-304 (600)
6 KOG2190 PolyC-binding proteins 100.0 1.5E-30 3.2E-35 247.3 27.6 291 34-331 42-411 (485)
7 KOG2193 IGF-II mRNA-binding pr 100.0 3.2E-31 6.9E-36 237.5 14.1 251 28-332 273-567 (584)
8 KOG2191 RNA-binding protein NO 99.9 6.5E-25 1.4E-29 191.6 18.3 170 121-332 38-207 (402)
9 KOG2190 PolyC-binding proteins 99.8 1.7E-18 3.6E-23 165.1 17.1 158 122-330 43-209 (485)
10 KOG2192 PolyC-binding hnRNP-K 99.8 1.9E-18 4.2E-23 147.2 12.3 159 31-194 119-384 (390)
11 TIGR03665 arCOG04150 arCOG0415 99.7 4.4E-17 9.4E-22 136.3 11.8 139 126-330 2-152 (172)
12 TIGR03665 arCOG04150 arCOG0415 99.7 9.4E-17 2E-21 134.3 10.8 138 39-195 2-152 (172)
13 PRK13763 putative RNA-processi 99.7 3.2E-16 6.8E-21 132.0 13.6 141 122-330 3-158 (180)
14 PRK13763 putative RNA-processi 99.7 6.3E-16 1.4E-20 130.2 12.6 143 34-195 2-158 (180)
15 cd02396 PCBP_like_KH K homolog 99.5 4.3E-14 9.4E-19 99.0 7.7 64 36-101 1-64 (65)
16 cd02396 PCBP_like_KH K homolog 99.5 3.9E-14 8.5E-19 99.2 7.1 63 259-323 2-64 (65)
17 KOG2279 Kinase anchor protein 99.5 7.6E-14 1.6E-18 130.4 10.7 278 28-325 61-364 (608)
18 cd02394 vigilin_like_KH K homo 99.4 5.7E-13 1.2E-17 92.5 5.8 61 259-324 2-62 (62)
19 PF00013 KH_1: KH domain syndr 99.4 4.5E-13 9.7E-18 92.4 5.2 60 258-323 1-60 (60)
20 cd02393 PNPase_KH Polynucleoti 99.4 2.6E-12 5.7E-17 88.4 6.9 59 257-324 2-61 (61)
21 PF00013 KH_1: KH domain syndr 99.3 1.4E-12 3.1E-17 89.8 5.0 60 36-101 1-60 (60)
22 cd00105 KH-I K homology RNA-bi 99.3 6E-12 1.3E-16 87.8 7.2 63 259-324 2-64 (64)
23 cd02394 vigilin_like_KH K homo 99.3 3.1E-12 6.8E-17 88.7 5.5 61 37-102 2-62 (62)
24 cd00105 KH-I K homology RNA-bi 99.3 2.8E-11 6.1E-16 84.4 8.1 62 37-101 2-63 (64)
25 cd02393 PNPase_KH Polynucleoti 99.2 3.9E-11 8.4E-16 82.6 7.9 58 35-101 2-60 (61)
26 KOG2208 Vigilin [Lipid transpo 99.2 2.2E-10 4.7E-15 115.8 12.1 226 34-326 200-485 (753)
27 PF13014 KH_3: KH domain 99.1 1.9E-10 4E-15 73.4 5.2 43 267-311 1-43 (43)
28 PF13014 KH_3: KH domain 99.1 3.2E-10 6.9E-15 72.4 5.8 43 45-89 1-43 (43)
29 COG1094 Predicted RNA-binding 99.1 1.1E-09 2.5E-14 90.9 9.6 144 122-331 8-166 (194)
30 smart00322 KH K homology RNA-b 99.1 1.2E-09 2.5E-14 76.8 8.4 66 257-327 3-68 (69)
31 KOG2208 Vigilin [Lipid transpo 99.0 4.3E-10 9.3E-15 113.7 7.8 217 35-331 347-564 (753)
32 smart00322 KH K homology RNA-b 99.0 3.7E-09 8.1E-14 74.2 9.3 67 34-105 2-68 (69)
33 COG1094 Predicted RNA-binding 99.0 1.5E-08 3.3E-13 84.2 12.8 144 34-196 7-166 (194)
34 KOG2279 Kinase anchor protein 98.7 9.2E-09 2E-13 96.8 4.3 145 120-330 66-210 (608)
35 cd02395 SF1_like-KH Splicing f 98.6 1.7E-07 3.8E-12 73.3 7.4 65 266-330 15-96 (120)
36 KOG2113 Predicted RNA binding 98.6 8.7E-08 1.9E-12 84.3 5.9 154 120-325 24-179 (394)
37 cd02395 SF1_like-KH Splicing f 98.6 3.5E-07 7.6E-12 71.6 8.4 69 38-106 3-94 (120)
38 PRK08406 transcription elongat 98.4 9.4E-07 2E-11 71.2 6.8 104 35-158 32-135 (140)
39 KOG2113 Predicted RNA binding 98.4 8.3E-07 1.8E-11 78.2 6.8 140 33-185 24-173 (394)
40 TIGR02696 pppGpp_PNP guanosine 98.1 1.3E-05 2.9E-10 80.0 9.8 64 257-329 578-642 (719)
41 PRK08406 transcription elongat 98.1 1.2E-05 2.6E-10 64.8 7.6 104 122-293 32-135 (140)
42 TIGR02696 pppGpp_PNP guanosine 98.1 2.3E-05 5.1E-10 78.4 11.1 91 94-194 551-642 (719)
43 TIGR01952 nusA_arch NusA famil 97.8 4.6E-05 1E-09 61.2 6.1 103 36-158 34-136 (141)
44 KOG0119 Splicing factor 1/bran 97.8 0.00014 3.1E-09 68.3 9.9 73 257-329 138-230 (554)
45 TIGR03591 polynuc_phos polyrib 97.7 0.00014 3.1E-09 73.7 9.6 90 95-193 524-614 (684)
46 TIGR03591 polynuc_phos polyrib 97.7 0.00011 2.3E-09 74.6 8.1 64 257-329 551-615 (684)
47 KOG0119 Splicing factor 1/bran 97.7 0.00038 8.3E-09 65.5 10.3 74 121-194 137-230 (554)
48 PF14611 SLS: Mitochondrial in 97.6 0.004 8.6E-08 54.0 15.8 129 123-328 27-164 (210)
49 TIGR01952 nusA_arch NusA famil 97.5 0.00042 9.1E-09 55.7 7.2 103 123-293 34-136 (141)
50 PLN00207 polyribonucleotide nu 97.5 0.00032 6.8E-09 72.0 7.5 91 95-194 658-750 (891)
51 PRK00106 hypothetical protein; 97.3 0.0014 3.1E-08 64.0 9.8 67 255-329 223-291 (535)
52 KOG2814 Transcription coactiva 97.3 0.00038 8.3E-09 62.5 5.2 70 257-331 57-127 (345)
53 COG1185 Pnp Polyribonucleotide 97.3 0.00099 2.1E-08 65.7 8.4 101 85-194 507-616 (692)
54 PLN00207 polyribonucleotide nu 97.3 0.00058 1.2E-08 70.1 7.0 64 257-329 685-750 (891)
55 TIGR03319 YmdA_YtgF conserved 97.3 0.0014 3.1E-08 64.2 9.6 67 255-329 202-270 (514)
56 KOG1588 RNA-binding protein Sa 97.2 0.00042 9.2E-09 60.5 4.8 44 29-72 86-135 (259)
57 PRK12704 phosphodiesterase; Pr 97.2 0.0016 3.5E-08 64.0 9.4 66 256-329 209-276 (520)
58 COG0195 NusA Transcription elo 97.2 0.00091 2E-08 56.5 6.5 102 36-159 77-179 (190)
59 cd02134 NusA_KH NusA_K homolog 97.2 0.00072 1.6E-08 46.3 4.7 37 34-70 24-60 (61)
60 KOG0336 ATP-dependent RNA heli 97.2 0.00071 1.5E-08 62.7 5.8 66 256-327 46-111 (629)
61 KOG0336 ATP-dependent RNA heli 97.2 0.00052 1.1E-08 63.6 4.8 66 31-102 43-108 (629)
62 COG1185 Pnp Polyribonucleotide 97.1 0.0016 3.5E-08 64.2 7.5 65 257-330 552-617 (692)
63 KOG2814 Transcription coactiva 97.0 0.00096 2.1E-08 60.0 5.2 71 34-108 56-126 (345)
64 PRK04163 exosome complex RNA-b 97.0 0.0018 3.8E-08 57.2 6.4 63 259-330 147-210 (235)
65 KOG1588 RNA-binding protein Sa 97.0 0.0045 9.8E-08 54.2 8.4 42 255-296 90-137 (259)
66 cd02134 NusA_KH NusA_K homolog 96.9 0.0014 3E-08 44.9 4.2 36 257-292 25-60 (61)
67 PRK11824 polynucleotide phosph 96.9 0.0018 3.8E-08 66.0 6.5 91 95-194 527-618 (693)
68 PRK00106 hypothetical protein; 96.9 0.0052 1.1E-07 60.2 9.3 68 119-194 222-291 (535)
69 PRK12704 phosphodiesterase; Pr 96.8 0.0053 1.2E-07 60.4 8.9 67 120-194 208-276 (520)
70 TIGR03319 YmdA_YtgF conserved 96.8 0.0072 1.6E-07 59.4 9.5 68 119-194 201-270 (514)
71 PRK00468 hypothetical protein; 96.6 0.0026 5.7E-08 45.3 3.7 36 30-65 25-60 (75)
72 PRK11824 polynucleotide phosph 96.6 0.0036 7.9E-08 63.8 6.1 64 257-329 554-618 (693)
73 PRK04163 exosome complex RNA-b 96.6 0.0044 9.6E-08 54.6 5.7 64 37-110 147-211 (235)
74 COG0195 NusA Transcription elo 96.6 0.0074 1.6E-07 51.1 6.7 37 258-294 143-179 (190)
75 COG5176 MSL5 Splicing factor ( 96.6 0.005 1.1E-07 51.7 5.4 41 33-73 146-192 (269)
76 PF14611 SLS: Mitochondrial in 96.5 0.11 2.3E-06 45.1 14.1 129 37-194 28-165 (210)
77 PRK12328 nusA transcription el 96.5 0.0054 1.2E-07 57.1 6.2 92 45-159 252-345 (374)
78 TIGR01953 NusA transcription t 96.5 0.0065 1.4E-07 56.4 6.5 93 45-159 244-338 (341)
79 PRK12327 nusA transcription el 96.5 0.0056 1.2E-07 57.2 6.1 94 45-160 246-341 (362)
80 PRK02821 hypothetical protein; 96.4 0.0031 6.8E-08 45.1 3.1 36 31-66 27-62 (77)
81 PRK12705 hypothetical protein; 96.4 0.01 2.2E-07 57.8 7.2 66 256-329 197-264 (508)
82 COG1837 Predicted RNA-binding 96.2 0.007 1.5E-07 43.0 3.8 34 31-64 26-59 (76)
83 PRK12328 nusA transcription el 96.2 0.017 3.6E-07 53.9 7.2 40 257-296 308-347 (374)
84 PRK12329 nusA transcription el 96.1 0.0078 1.7E-07 57.0 4.8 93 45-159 278-372 (449)
85 PRK01064 hypothetical protein; 96.1 0.0077 1.7E-07 43.2 3.6 34 31-64 26-59 (78)
86 TIGR01953 NusA transcription t 96.0 0.022 4.8E-07 52.9 7.3 38 257-294 301-338 (341)
87 COG5176 MSL5 Splicing factor ( 95.9 0.01 2.3E-07 49.8 4.2 31 266-296 163-193 (269)
88 KOG1067 Predicted RNA-binding 95.9 0.025 5.4E-07 54.6 7.0 93 93-195 568-661 (760)
89 PRK12327 nusA transcription el 95.8 0.03 6.5E-07 52.4 7.0 39 257-295 303-341 (362)
90 PRK09202 nusA transcription el 95.6 0.027 5.8E-07 54.6 6.4 39 257-295 302-340 (470)
91 PRK09202 nusA transcription el 95.6 0.028 6.1E-07 54.5 6.6 91 45-159 246-339 (470)
92 PRK00468 hypothetical protein; 95.5 0.016 3.4E-07 41.3 3.4 33 255-287 28-60 (75)
93 PRK12705 hypothetical protein; 95.5 0.033 7.2E-07 54.3 6.6 66 120-193 196-263 (508)
94 PRK02821 hypothetical protein; 95.4 0.019 4.1E-07 41.1 3.2 34 256-289 30-63 (77)
95 PRK12329 nusA transcription el 95.3 0.038 8.3E-07 52.4 6.1 38 257-294 335-372 (449)
96 KOG1067 Predicted RNA-binding 95.0 0.073 1.6E-06 51.5 6.9 64 257-330 597-661 (760)
97 COG1837 Predicted RNA-binding 94.7 0.042 9.2E-07 39.0 3.4 32 256-287 29-60 (76)
98 PRK01064 hypothetical protein; 94.4 0.041 9E-07 39.5 3.0 33 255-287 28-60 (78)
99 PF13083 KH_4: KH domain; PDB: 94.4 0.02 4.3E-07 40.7 1.3 35 32-66 26-60 (73)
100 KOG4369 RTK signaling protein 93.9 0.023 4.9E-07 59.1 1.0 70 256-327 1339-1408(2131)
101 KOG2874 rRNA processing protei 93.8 0.13 2.8E-06 45.4 5.3 51 269-329 161-211 (356)
102 cd02409 KH-II KH-II (K homolo 93.4 0.17 3.7E-06 34.7 4.5 35 34-68 24-58 (68)
103 KOG3273 Predicted RNA-binding 93.0 0.066 1.4E-06 44.9 2.2 55 265-329 177-231 (252)
104 KOG4369 RTK signaling protein 93.0 0.076 1.7E-06 55.4 3.0 73 28-102 1333-1405(2131)
105 PF13083 KH_4: KH domain; PDB: 93.0 0.056 1.2E-06 38.3 1.5 36 255-290 27-62 (73)
106 PF13184 KH_5: NusA-like KH do 92.9 0.12 2.7E-06 36.1 3.1 39 257-295 3-47 (69)
107 COG1097 RRP4 RNA-binding prote 92.8 0.26 5.7E-06 42.9 5.7 61 38-108 149-210 (239)
108 PF13184 KH_5: NusA-like KH do 92.6 0.1 2.3E-06 36.5 2.4 38 36-73 4-47 (69)
109 COG1097 RRP4 RNA-binding prote 92.5 0.36 7.8E-06 42.1 6.1 47 259-314 148-194 (239)
110 KOG3273 Predicted RNA-binding 92.3 0.096 2.1E-06 43.9 2.2 149 34-195 73-232 (252)
111 cd02410 archeal_CPSF_KH The ar 92.0 0.49 1.1E-05 38.0 5.9 39 257-295 76-114 (145)
112 cd02414 jag_KH jag_K homology 92.0 0.2 4.2E-06 35.9 3.3 34 36-69 25-58 (77)
113 cd02409 KH-II KH-II (K homolo 91.8 0.32 7E-06 33.2 4.2 34 257-290 25-58 (68)
114 PF07650 KH_2: KH domain syndr 91.5 0.1 2.2E-06 37.4 1.5 34 36-69 26-59 (78)
115 COG1855 ATPase (PilT family) [ 90.7 0.31 6.6E-06 46.5 4.0 66 94-160 459-524 (604)
116 KOG2874 rRNA processing protei 90.3 0.59 1.3E-05 41.4 5.2 51 134-194 161-211 (356)
117 COG5166 Uncharacterized conser 90.2 0.87 1.9E-05 43.9 6.6 152 36-294 450-608 (657)
118 cd02413 40S_S3_KH K homology R 90.2 0.44 9.5E-06 34.5 3.7 35 36-70 31-65 (81)
119 cd02414 jag_KH jag_K homology 89.8 0.39 8.5E-06 34.3 3.2 36 257-292 24-59 (77)
120 PRK06418 transcription elongat 89.1 0.67 1.5E-05 38.3 4.5 37 36-73 62-98 (166)
121 COG1855 ATPase (PilT family) [ 89.0 0.27 5.9E-06 46.9 2.3 39 36-74 487-525 (604)
122 PF07650 KH_2: KH domain syndr 88.4 0.31 6.7E-06 34.9 1.8 35 257-291 25-59 (78)
123 COG1782 Predicted metal-depend 87.9 2.1 4.5E-05 41.5 7.3 97 134-295 41-137 (637)
124 PRK13764 ATPase; Provisional 87.3 0.44 9.6E-06 47.7 2.7 40 35-74 481-520 (602)
125 PRK13764 ATPase; Provisional 87.1 0.87 1.9E-05 45.7 4.7 65 95-160 455-519 (602)
126 COG5166 Uncharacterized conser 86.6 0.59 1.3E-05 45.0 3.0 127 47-194 392-524 (657)
127 cd02412 30S_S3_KH K homology R 85.9 0.87 1.9E-05 35.0 3.2 29 37-65 63-91 (109)
128 cd02411 archeal_30S_S3_KH K ho 85.1 1.2 2.7E-05 32.4 3.5 28 37-64 40-67 (85)
129 cd02410 archeal_CPSF_KH The ar 82.6 2.1 4.6E-05 34.4 4.1 37 37-73 78-114 (145)
130 PRK06418 transcription elongat 82.4 2 4.3E-05 35.6 4.0 38 257-295 61-98 (166)
131 COG0092 RpsC Ribosomal protein 82.2 1.5 3.2E-05 38.2 3.3 31 34-64 50-80 (233)
132 cd02413 40S_S3_KH K homology R 81.4 2.1 4.6E-05 30.9 3.4 37 257-293 30-66 (81)
133 TIGR03675 arCOG00543 arCOG0054 78.7 3.9 8.4E-05 41.6 5.5 39 257-295 93-131 (630)
134 cd02412 30S_S3_KH K homology R 75.1 2.8 6.1E-05 32.2 2.7 30 259-288 63-92 (109)
135 COG1702 PhoH Phosphate starvat 74.0 9.9 0.00021 35.2 6.3 55 265-329 23-79 (348)
136 cd02411 archeal_30S_S3_KH K ho 73.7 3.9 8.4E-05 29.8 3.0 28 259-286 40-67 (85)
137 COG0092 RpsC Ribosomal protein 73.2 5.1 0.00011 34.9 4.0 30 257-286 51-80 (233)
138 TIGR03675 arCOG00543 arCOG0054 71.9 8.6 0.00019 39.1 5.9 73 37-112 95-167 (630)
139 COG1782 Predicted metal-depend 68.8 5.2 0.00011 38.9 3.4 37 36-72 100-136 (637)
140 TIGR00436 era GTP-binding prot 67.2 7.7 0.00017 34.8 4.1 29 35-63 221-250 (270)
141 TIGR01008 rpsC_E_A ribosomal p 64.2 9.1 0.0002 32.7 3.7 30 36-65 39-68 (195)
142 PRK04191 rps3p 30S ribosomal p 62.7 9.7 0.00021 32.9 3.6 30 37-66 42-71 (207)
143 KOG1423 Ras-like GTPase ERA [C 62.4 16 0.00035 33.5 5.0 31 120-150 326-357 (379)
144 CHL00048 rps3 ribosomal protei 62.0 10 0.00022 32.9 3.7 30 36-65 67-96 (214)
145 PTZ00084 40S ribosomal protein 61.3 10 0.00022 33.0 3.5 31 37-67 46-76 (220)
146 PRK00089 era GTPase Era; Revie 60.9 12 0.00027 33.8 4.3 36 257-292 226-270 (292)
147 PRK15494 era GTPase Era; Provi 60.7 12 0.00025 35.0 4.1 36 35-70 273-317 (339)
148 TIGR00436 era GTP-binding prot 59.7 22 0.00048 31.8 5.7 29 122-150 221-250 (270)
149 COG1159 Era GTPase [General fu 59.3 30 0.00065 31.5 6.2 38 121-158 228-274 (298)
150 PRK03818 putative transporter; 59.0 2E+02 0.0044 28.8 13.4 136 35-187 205-358 (552)
151 PRK00089 era GTPase Era; Revie 58.9 13 0.00029 33.6 4.1 36 35-70 226-270 (292)
152 COG1159 Era GTPase [General fu 58.1 16 0.00034 33.2 4.3 37 34-70 228-273 (298)
153 PRK15494 era GTPase Era; Provi 58.0 24 0.00051 32.9 5.7 37 122-158 273-318 (339)
154 COG1847 Jag Predicted RNA-bind 56.5 20 0.00044 30.7 4.4 38 33-70 89-126 (208)
155 PF09869 DUF2096: Uncharacteri 56.2 41 0.00089 27.7 5.9 58 119-192 110-167 (169)
156 COG1847 Jag Predicted RNA-bind 54.7 12 0.00026 32.1 2.8 36 257-292 91-126 (208)
157 COG1702 PhoH Phosphate starvat 54.5 30 0.00065 32.1 5.5 53 127-189 20-72 (348)
158 PRK03818 putative transporter; 54.0 97 0.0021 31.1 9.5 61 123-189 206-275 (552)
159 PRK04191 rps3p 30S ribosomal p 53.4 24 0.00052 30.4 4.5 31 259-289 42-72 (207)
160 TIGR03802 Asp_Ala_antiprt aspa 53.0 1.7E+02 0.0037 29.4 11.1 140 33-189 216-377 (562)
161 PTZ00084 40S ribosomal protein 52.2 22 0.00048 30.9 4.1 32 258-289 45-76 (220)
162 TIGR03802 Asp_Ala_antiprt aspa 50.7 1.7E+02 0.0037 29.4 10.7 62 258-325 304-378 (562)
163 CHL00048 rps3 ribosomal protei 49.8 27 0.00059 30.3 4.3 30 258-287 67-96 (214)
164 KOG1423 Ras-like GTPase ERA [C 48.1 19 0.0004 33.1 3.1 33 254-286 325-358 (379)
165 TIGR01009 rpsC_bact ribosomal 48.0 22 0.00047 30.8 3.4 28 37-64 64-91 (211)
166 PF02749 QRPTase_N: Quinolinat 47.0 52 0.0011 23.9 4.9 54 141-194 33-86 (88)
167 PF00472 RF-1: RF-1 domain; I 46.0 31 0.00068 26.5 3.7 48 50-109 22-74 (113)
168 TIGR01008 rpsC_E_A ribosomal p 45.8 38 0.00081 28.9 4.5 30 258-287 39-68 (195)
169 COG4010 Uncharacterized protei 43.8 87 0.0019 25.2 5.8 44 142-194 126-169 (170)
170 PF09869 DUF2096: Uncharacteri 41.2 92 0.002 25.7 5.8 54 33-102 111-164 (169)
171 PRK00310 rpsC 30S ribosomal pr 36.9 38 0.00082 29.8 3.3 28 37-64 64-91 (232)
172 PRK15405 ethanolamine utilizat 36.2 2.9E+02 0.0063 24.0 10.4 133 62-194 56-209 (217)
173 PRK15468 carboxysome structura 35.9 1.3E+02 0.0029 22.9 5.5 42 151-199 63-104 (111)
174 PF02749 QRPTase_N: Quinolinat 35.8 1.6E+02 0.0034 21.3 6.0 54 53-106 32-85 (88)
175 PF06183 DinI: DinI-like famil 30.4 1.8E+02 0.004 19.9 5.4 45 278-332 13-58 (65)
176 TIGR01009 rpsC_bact ribosomal 29.3 53 0.0012 28.4 2.9 28 259-286 64-91 (211)
177 PF10369 ALS_ss_C: Small subun 28.8 1.5E+02 0.0033 20.8 4.7 43 276-325 16-58 (75)
178 cd07055 BMC_like_2 Bacterial M 28.0 1.8E+02 0.0039 19.7 4.6 40 149-191 21-60 (61)
179 PRK04021 hypothetical protein; 28.0 1.3E+02 0.0027 22.3 4.3 40 277-320 50-90 (92)
180 COG4010 Uncharacterized protei 27.4 2.1E+02 0.0045 23.1 5.6 43 55-107 126-168 (170)
181 PF03958 Secretin_N: Bacterial 25.4 81 0.0018 22.1 2.9 24 303-326 53-76 (82)
182 PRK09256 hypothetical protein; 25.2 1.1E+02 0.0024 24.5 3.9 57 50-108 23-98 (138)
183 PRK15468 carboxysome structura 23.0 1.4E+02 0.003 22.8 3.7 27 83-109 75-101 (111)
184 KOG1960 Predicted RNA-binding 21.2 3.6E+02 0.0079 25.7 6.7 145 50-194 109-295 (531)
No 1
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=3.9e-40 Score=278.86 Aligned_cols=285 Identities=27% Similarity=0.439 Sum_probs=224.6
Q ss_pred CCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhcc
Q 019747 31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELH 110 (336)
Q Consensus 31 ~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~ 110 (336)
....+.++||+.+..+|+||||+|++||.|+.+++++|+|++++ .++|+|+|+.+.+.|...++.|+-.|.+.+
T Consensus 44 k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~-----~peri~tisad~~ti~~ilk~iip~lee~f- 117 (390)
T KOG2192|consen 44 KRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSS-----GPERILTISADIETIGEILKKIIPTLEEGF- 117 (390)
T ss_pred hhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCCC-----CCceeEEEeccHHHHHHHHHHHhhhhhhCC-
Confidence 44579999999999999999999999999999999999999876 579999999999999888887776655543
Q ss_pred ccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHH
Q 019747 111 AEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILL 190 (336)
Q Consensus 111 ~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~ 190 (336)
...+.+.++|+|..+.+|.|||++|++||+|++++.++++|.. +.|+++++|+|.+.|.+.+|..+++.|++
T Consensus 118 ------~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift--~c~p~stdrv~l~~g~~k~v~~~i~~il~ 189 (390)
T KOG2192|consen 118 ------QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFT--ECCPHSTDRVVLIGGKPKRVVECIKIILD 189 (390)
T ss_pred ------CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhh--ccCCCCcceEEEecCCcchHHHHHHHHHH
Confidence 2346799999999999999999999999999999999999987 78999999999999999999999999999
Q ss_pred HhhcCcC------CCCCc-CCCccCCCccccCC--CCCCCCCCCCC----CCCCCCCC----------------------
Q 019747 191 KLSEDTL------YSQTM-TVPYTYAGVFFSGF--HGMPYGAVPPP----VPAVPHNT---------------------- 235 (336)
Q Consensus 191 ~l~~~~~------~~~~~-~~~~~~~g~~~~~~--~~~p~~~~~~~----~~~~~~~~---------------------- 235 (336)
++.+.+. |.+.. ...+.|+|..+... .+.|. +.|++ +++++...
T Consensus 190 ~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pg-papqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~ 268 (390)
T KOG2192|consen 190 LISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPG-PAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSA 268 (390)
T ss_pred HhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCC-CCCCCCCCCCCCCCccccceeccCCCCCccccccccccc
Confidence 9988654 33332 23355666544322 11111 11111 11111101
Q ss_pred ----------------CCCCCCCCCCCCccCCC---------CCCceEEEEEeccCcccceeccCCchHHHHHhHhCCeE
Q 019747 236 ----------------AAHYGPNMGGRKFQNNK---------DDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARI 290 (336)
Q Consensus 236 ----------------~~~~~~~g~~~~~~~~~---------~~~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I 290 (336)
.|.|.+.++.....+++ ..+..+.+|.||+++-|.||||+|+.|++|++++||.|
T Consensus 269 detw~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~I 348 (390)
T KOG2192|consen 269 DETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASI 348 (390)
T ss_pred cccCCCcCCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceE
Confidence 12333332222111111 35678899999999999999999999999999999999
Q ss_pred EEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhhhc
Q 019747 291 KVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASDR 333 (336)
Q Consensus 291 ~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~ 333 (336)
+|.. |..++.+|+++|+||.+|++.|+.|++..++.+.+|
T Consensus 349 kide---pleGsedrIitItGTqdQIqnAQYLlQn~Vkq~rer 388 (390)
T KOG2192|consen 349 KIDE---PLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYRER 388 (390)
T ss_pred EecC---cCCCCCceEEEEeccHHHHhhHHHHHHHHHHhhhcc
Confidence 9987 577899999999999999999999999999987765
No 2
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=1.5e-37 Score=290.58 Aligned_cols=260 Identities=29% Similarity=0.388 Sum_probs=214.0
Q ss_pred CCCCCCCCCCCCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHH
Q 019747 21 APVKSLSSDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDL 100 (336)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~ 100 (336)
++..|+.+.+ ...++.+|+||++.+|+||||+|+|||+|++++||++.+..+..... ...+.+.|+|+++.|+.|..+
T Consensus 126 ~~~~~~~~q~-~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~-~~~KplritGdp~~ve~a~~l 203 (600)
T KOG1676|consen 126 PPGGFPDNQG-SVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIAT-GADKPLRITGDPDKVEQAKQL 203 (600)
T ss_pred CCCCccccCC-ccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCC-CCCCceeecCCHHHHHHHHHH
Confidence 4555555544 67899999999999999999999999999999999999988765433 378899999999999999999
Q ss_pred HHHHHHhhcccc-----ccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEE
Q 019747 101 VIDKLLTELHAE-----DQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT 175 (336)
Q Consensus 101 I~~~i~~~~~~~-----~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~ 175 (336)
+.|.|.++.... ..+.+.-...++++.||.+.+|.|||++|++||+|+.+||++|+|.++++ +.+.+|.+.|.
T Consensus 204 V~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~--p~speR~~~Ii 281 (600)
T KOG1676|consen 204 VADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD--PSSPERPAQII 281 (600)
T ss_pred HHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCC--CCCccceeeee
Confidence 999888652211 01122233458999999999999999999999999999999999999665 47789999999
Q ss_pred cCHHHHHHHHHHHHHHhhcCcCCCCCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCC
Q 019747 176 GTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDR 255 (336)
Q Consensus 176 G~~~~v~~A~~~i~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~ 255 (336)
|+.+.|+.|.++|.++|.+..... +.+..+.. ...
T Consensus 282 G~~d~ie~Aa~lI~eii~~~~~~~------------------~~~~~~G~---------------------------P~~ 316 (600)
T KOG1676|consen 282 GTVDQIEHAAELINEIIAEAEAGA------------------GGGMGGGA---------------------------PGL 316 (600)
T ss_pred cCHHHHHHHHHHHHHHHHHHhccC------------------CCCcCCCC---------------------------ccc
Confidence 999999999999999998743211 00000000 011
Q ss_pred ceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhh
Q 019747 256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYA 330 (336)
Q Consensus 256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~ 330 (336)
...+++.||.+++|+||||+|++||.|..+|||++.+++. .+..+..+++++|+|.+.+|+.|++||.+++...
T Consensus 317 ~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~-~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~~ 390 (600)
T KOG1676|consen 317 VAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ-PPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGDI 390 (600)
T ss_pred eeeEEEeccccccccccCCCccchhhhcccCCccccccCC-CCCCCccceEEEEecCcccchHHHHHHHHHhccc
Confidence 1278999999999999999999999999999999999997 4566678999999999999999999999998763
No 3
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=2.9e-35 Score=256.10 Aligned_cols=308 Identities=31% Similarity=0.449 Sum_probs=246.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCC
Q 019747 2 ETNESSYVPSPDVHGKRSTAPVKSLSSDPTEK-PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGT 80 (336)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~ 80 (336)
...|+-..-++.++..+++.|-.....+.-++ .+++|||||+..+|.||||+|++|.+|+++|||+|++++..+++||.
T Consensus 5 ~~~d~~~~~s~kr~~~a~pe~~~~k~~n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGT 84 (402)
T KOG2191|consen 5 VPIDSDAPDSRKRPLEAPPEPGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGT 84 (402)
T ss_pred CcccCCCCCCccccccCCCCccccccccCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCc
Confidence 34455566666777777776665444444444 49999999999999999999999999999999999999999999999
Q ss_pred CceEEEEEeeHHHHHHHHHHHHHHHHhhccccccCCC------CCCceeEEEEEecCccceeecCCChHHHHHHHhcCCE
Q 019747 81 TDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADD------VGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAV 154 (336)
Q Consensus 81 ~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~------~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~ 154 (336)
+||+|.|+|+.+++...++.|.|+|++..+......+ .+....+++++|++.+|.||||+|.+||.|++++||.
T Consensus 85 TeRvcli~Gt~eai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~ 164 (402)
T KOG2191|consen 85 TERVCLIQGTVEALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAW 164 (402)
T ss_pred cceEEEEeccHHHHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcc
Confidence 9999999999999999999999999998765422111 2333568999999999999999999999999999999
Q ss_pred EEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCCCCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCC
Q 019747 155 IKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHN 234 (336)
Q Consensus 155 I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~ 234 (336)
|+|.+..+..-+..+|+|++.|++++..+|+.+|+.++.+++++..+++.++.+..+...
T Consensus 165 iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya~vsGpva-------------------- 224 (402)
T KOG2191|consen 165 IQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYANVSGPVA-------------------- 224 (402)
T ss_pred eEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceeccchhcccCccc--------------------
Confidence 999976565556789999999999999999999999999999999888877665533111
Q ss_pred CCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChH
Q 019747 235 TAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQR 314 (336)
Q Consensus 235 ~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~ 314 (336)
.+++.|.......+...........++....|..-|.+|.++..|...+|+.+.+....+...+...+ .-+.|.+-
T Consensus 225 ---NsnPtGspya~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l~~m~g~gy~-~n~~g~~l 300 (402)
T KOG2191|consen 225 ---NSNPTGSPYAYQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQALNTMAGYGYN-TNILGLGL 300 (402)
T ss_pred ---ccCCCCCCCCCCCccccccchhhccccccccccccccccccceeeecccccceeeccccccccccccc-ccccchhh
Confidence 12222222222222233335566778899999999999999999999999999999876654455555 78889999
Q ss_pred hHHHHHHHHHHHHHhhhhc
Q 019747 315 SIRTAESMIMQKVAYASDR 333 (336)
Q Consensus 315 ~v~~A~~~I~~~i~~~~~~ 333 (336)
++..|-.+|...+....++
T Consensus 301 s~~aa~g~L~~~~~~a~t~ 319 (402)
T KOG2191|consen 301 SILAAEGVLAAKVASANTA 319 (402)
T ss_pred hhhhhhhHHHHhhcccCcc
Confidence 9999999998887765544
No 4
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=8.3e-37 Score=273.17 Aligned_cols=281 Identities=25% Similarity=0.430 Sum_probs=217.1
Q ss_pred CCCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhc
Q 019747 30 PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTEL 109 (336)
Q Consensus 30 ~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~ 109 (336)
.....+.+|++||..+||.||||.|+|||.|-++|.|+|.|.+.++ .|..|++++|.|+++...+|+++|++.|..+.
T Consensus 194 ~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken--~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA 271 (584)
T KOG2193|consen 194 QQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKEN--AGAAEKIITVHSTPEGTSKACKMILEIMQKEA 271 (584)
T ss_pred ccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeeccc--CCcccCceEEecCccchHHHHHHHHHHHHHhh
Confidence 3456678999999999999999999999999999999999998765 48899999999999999999999999998884
Q ss_pred cccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 019747 110 HAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELIL 189 (336)
Q Consensus 110 ~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~ 189 (336)
... .......++++..+.++|+||||.|.+||+|+.+||++|.|.+--+......+|.+++.|+-++|..|..+|+
T Consensus 272 ~~~----k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eIm 347 (584)
T KOG2193|consen 272 VDD----KVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIM 347 (584)
T ss_pred hcc----chhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHH
Confidence 332 2235688899999999999999999999999999999999998444444457999999999999999999999
Q ss_pred HHhhcCcCCCCC---cCCCccCCCcc------ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEE
Q 019747 190 LKLSEDTLYSQT---MTVPYTYAGVF------FSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLT 260 (336)
Q Consensus 190 ~~l~~~~~~~~~---~~~~~~~~g~~------~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~ 260 (336)
.+|++....+.. +-.++ ..|.. ++..++++++..||. +......|. .+.. ........
T Consensus 348 kKlre~yEnDl~a~s~q~~l-~P~l~~~~l~~f~ssS~~~~Ph~~Ps----~v~~a~p~~------~~hq--~pe~e~V~ 414 (584)
T KOG2193|consen 348 KKLRECYENDLAAMSLQCHL-PPGLNLPALGLFPSSSAVSPPHFPPS----PVTFASPYP------LFHQ--NPEQEQVR 414 (584)
T ss_pred HHHHHHHhhhHHHhhccCCC-CcccCccccCCCCcccccCCCCCCCC----ccccCCCch------hhhc--Ccchhhee
Confidence 999886332210 00000 00100 111111111111111 110000000 0000 12446788
Q ss_pred EEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747 261 IGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS 331 (336)
Q Consensus 261 v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~ 331 (336)
+.||...+|.|||++|.+||+|.+.+||.|+|.+++ .++..+|.|+|+|++++..+|+..|+.+|+++.
T Consensus 415 ~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE--~pdvseRMViItGppeaqfKAQgrifgKikEen 483 (584)
T KOG2193|consen 415 MFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPE--IPDVSERMVIITGPPEAQFKAQGRIFGKIKEEN 483 (584)
T ss_pred eeccHHHHHHHHhhcchhHHHHHHhccceeeecCCC--CCCcceeEEEecCChHHHHhhhhhhhhhhhhhc
Confidence 999999999999999999999999999999999875 566889999999999999999999999999875
No 5
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=1e-33 Score=264.92 Aligned_cols=255 Identities=25% Similarity=0.387 Sum_probs=207.9
Q ss_pred CCCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhc
Q 019747 30 PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTEL 109 (336)
Q Consensus 30 ~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~ 109 (336)
+....++-+..||...||+||||+|+.|..|+.++||+|++.... .+..+|.+.+.|.+++|+.|+.+|.+.+.+..
T Consensus 49 ~s~~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~---s~~~~r~~~~~G~pe~v~~aK~li~evv~r~~ 125 (600)
T KOG1676|consen 49 PSDTVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADP---SGIGYRSVDLTGSPENVEVAKQLIGEVVSRGR 125 (600)
T ss_pred CcccccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCC---CCcccccccccCCcccHHHHHHhhhhhhhccC
Confidence 334567889999999999999999999999999999999986544 34578999999999999999999997655543
Q ss_pred ccc-ccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 019747 110 HAE-DQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELI 188 (336)
Q Consensus 110 ~~~-~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i 188 (336)
... ...+......+..++||.+.+|.||||+|++||.|++.+||++.+..+.... ...++.+.|+|++++|+.|..+|
T Consensus 126 ~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~-~~~~KplritGdp~~ve~a~~lV 204 (600)
T KOG1676|consen 126 PPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIA-TGADKPLRITGDPDKVEQAKQLV 204 (600)
T ss_pred CCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcC-CCCCCceeecCCHHHHHHHHHHH
Confidence 111 1122234678999999999999999999999999999999999999854433 33678999999999999999999
Q ss_pred HHHhhcCcCCCCCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcc
Q 019747 189 LLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHI 268 (336)
Q Consensus 189 ~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~v 268 (336)
.++|.+........ ..++++. .....+.+|.||...|
T Consensus 205 ~dil~e~~~~~~g~---------------------------------~~~~g~~----------~g~~~~~~V~VPr~~V 241 (600)
T KOG1676|consen 205 ADILREEDDEVPGS---------------------------------GGHAGVR----------GGGSATREVKVPRSKV 241 (600)
T ss_pred HHHHHhcccCCCcc---------------------------------ccccCcC----------ccccceeEEeccccce
Confidence 99999642211000 0011111 1122589999999999
Q ss_pred cceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhhhc
Q 019747 269 GFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASDR 333 (336)
Q Consensus 269 g~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~ 333 (336)
|.||||+|++||+|+.+||++|.|.+++++ .+.+|.+.|.|+.++|+.|.+||.++|+.....
T Consensus 242 G~IIGkgGE~IKklq~etG~KIQfkpDd~p--~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~ 304 (600)
T KOG1676|consen 242 GIIIGKGGEMIKKLQNETGAKIQFKPDDDP--SSPERPAQIIGTVDQIEHAAELINEIIAEAEAG 304 (600)
T ss_pred eeEEecCchHHHHHhhccCceeEeecCCCC--CCccceeeeecCHHHHHHHHHHHHHHHHHHhcc
Confidence 999999999999999999999999998654 577999999999999999999999999987654
No 6
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=1.5e-30 Score=247.29 Aligned_cols=291 Identities=26% Similarity=0.400 Sum_probs=211.7
Q ss_pred cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEe---------eHHHHHHHHHHHHHH
Q 019747 34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG---------TIDEILRAVDLVIDK 104 (336)
Q Consensus 34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G---------~~~~v~~A~~~I~~~ 104 (336)
..++|+||+...+|.||||+|..||+|++++.++|+|.. ..++|.+|+++|+| ..+++.+|..+|...
T Consensus 42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~---~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~ 118 (485)
T KOG2190|consen 42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNE---SLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFK 118 (485)
T ss_pred cceEEEEeccccceeEEccCcHHHHHHhhcccccceeec---CCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhc
Confidence 344999999999999999999999999999999999975 36889999999999 999999999999977
Q ss_pred HHhhccccccCC-CCCC-ceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHH
Q 019747 105 LLTELHAEDQAD-DVGT-KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQM 182 (336)
Q Consensus 105 i~~~~~~~~~~~-~~~~-~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~ 182 (336)
+.++.....+.. ..+. ..+++|+||.+++|.||||+|+.||+|+++|||+|++.++ ..+.+++|.|+|.|.+++|.
T Consensus 119 ~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~--~lP~ster~V~IsG~~~av~ 196 (485)
T KOG2190|consen 119 LEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD--MLPNSTERAVTISGEPDAVK 196 (485)
T ss_pred ccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC--CCCcccceeEEEcCchHHHH
Confidence 664433332222 1222 4789999999999999999999999999999999999984 77889999999999999999
Q ss_pred HHHHHHHHHhhcCcCCCCC-cCC-----C-ccCCCccccCCCCCCCCCCCCCCCCC----------C-----------C-
Q 019747 183 RALELILLKLSEDTLYSQT-MTV-----P-YTYAGVFFSGFHGMPYGAVPPPVPAV----------P-----------H- 233 (336)
Q Consensus 183 ~A~~~i~~~l~~~~~~~~~-~~~-----~-~~~~g~~~~~~~~~p~~~~~~~~~~~----------~-----------~- 233 (336)
+|+..|...|.+.....+. ... | ..+.+............+++.....+ | +
T Consensus 197 ~al~~Is~~L~~~~~~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~ 276 (485)
T KOG2190|consen 197 KALVQISSRLLENPPRSPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGL 276 (485)
T ss_pred HHHHHHHHHHHhcCCcCCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCc
Confidence 9999999999986432111 111 1 11111111111110000000000000 0 0
Q ss_pred -------------C-C---------CCCCCCCCC----------------CCCccCCCCCCceEEEEEeccCcccceecc
Q 019747 234 -------------N-T---------AAHYGPNMG----------------GRKFQNNKDDRTNSLTIGVADEHIGFVVGR 274 (336)
Q Consensus 234 -------------~-~---------~~~~~~~g~----------------~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk 274 (336)
. + ......... ........ ...++.++.||++++|+||||
T Consensus 277 ~i~~l~~~~~~~i~v~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~-~~~v~~~l~vps~~igciiGk 355 (485)
T KOG2190|consen 277 VIRALRNETGASISVGDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDL-TQTVTQRLLVPSDLIGCIIGK 355 (485)
T ss_pred cchhhhhhcCCceEeccccCcceeeeccccCcccccccchhhhhhccccccccccccc-cceeeeeeccCccccceeecc
Confidence 0 0 000000000 00000011 445789999999999999999
Q ss_pred CCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747 275 GGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS 331 (336)
Q Consensus 275 ~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~ 331 (336)
+|.+|.+||+.|||.|.|....+ .....++.++|+|+..+...|+.++..++....
T Consensus 356 ~G~~iseir~~tgA~I~I~~~~~-~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~ 411 (485)
T KOG2190|consen 356 GGAKISEIRQRTGASISILNKEE-VSGVREALVQITGMLREDLLAQYLIRARLSAPK 411 (485)
T ss_pred cccchHHHHHhcCCceEEccccc-cCCcceeEEEecchhHHHHhhhhhcccccccCc
Confidence 99999999999999999998643 125679999999999999999999988776644
No 7
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.97 E-value=3.2e-31 Score=237.47 Aligned_cols=251 Identities=24% Similarity=0.385 Sum_probs=212.0
Q ss_pred CCCCCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747 28 SDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT 107 (336)
Q Consensus 28 ~~~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~ 107 (336)
.+....++.++++-++.++|.+|||.|.+||+|+.+||++|.|+.-.+..-=.+||.|++.|+.++|..|-.+|+.+|.+
T Consensus 273 ~~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre 352 (584)
T KOG2193|consen 273 DDKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRE 352 (584)
T ss_pred ccchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHH
Confidence 35556789999999999999999999999999999999999998766543335699999999999999999999998887
Q ss_pred hccccc-----------c-------------CC-------------C-------CCCceeEEEEEecCccceeecCCChH
Q 019747 108 ELHAED-----------Q-------------AD-------------D-------VGTKTKLRLIVPNSSCGSIIGKAGAT 143 (336)
Q Consensus 108 ~~~~~~-----------~-------------~~-------------~-------~~~~~~~~l~ip~~~~g~iIG~~G~~ 143 (336)
-+.++- . .. . .......+++||...+|.|||++|..
T Consensus 353 ~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~h 432 (584)
T KOG2193|consen 353 CYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQH 432 (584)
T ss_pred HHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchh
Confidence 654320 0 00 0 02446778999999999999999999
Q ss_pred HHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCCCCcCCCccCCCccccCCCCCCCCC
Q 019747 144 IKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGA 223 (336)
Q Consensus 144 Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~ 223 (336)
||.|.+.+|+.|+|.+ ...++..+|.|+|+|++++..+|.-.|..+|.+..++.+.
T Consensus 433 IKql~RfagASiKIap--pE~pdvseRMViItGppeaqfKAQgrifgKikEenf~~Pk---------------------- 488 (584)
T KOG2193|consen 433 IKQLSRFAGASIKIAP--PEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEENFFLPK---------------------- 488 (584)
T ss_pred HHHHHHhccceeeecC--CCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhccCCch----------------------
Confidence 9999999999999998 3456778999999999999999999999999887554322
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCc
Q 019747 224 VPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTS 303 (336)
Q Consensus 224 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~ 303 (336)
........+.||...+|+||||||.++++|+..|+|.|.|+++..+. ..+
T Consensus 489 -----------------------------eevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpd-End 538 (584)
T KOG2193|consen 489 -----------------------------EEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPD-END 538 (584)
T ss_pred -----------------------------hhheeeeeeeccchhhhhhhccccccHHHHhccccceEEccccCCCC-ccc
Confidence 23345678899999999999999999999999999999999987433 345
Q ss_pred ceEEEEEcChHhHHHHHHHHHHHHHhhhh
Q 019747 304 ERKVTISGPQRSIRTAESMIMQKVAYASD 332 (336)
Q Consensus 304 ~r~v~I~G~~~~v~~A~~~I~~~i~~~~~ 332 (336)
.-+|.|.|..-..+.|+..|.++|..++.
T Consensus 539 ~vivriiGhfyatq~aQrki~~iv~qvkq 567 (584)
T KOG2193|consen 539 QVIVRIIGHFYATQNAQRKIAHIVNQVKQ 567 (584)
T ss_pred eeeeeeechhhcchHHHHHHHHHHHHHHH
Confidence 67899999999999999999999988763
No 8
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.93 E-value=6.5e-25 Score=191.61 Aligned_cols=170 Identities=30% Similarity=0.431 Sum_probs=143.9
Q ss_pred ceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCCC
Q 019747 121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQ 200 (336)
Q Consensus 121 ~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~~ 200 (336)
.+.++++||+..+|.||||+|++|.+|++++||+|++.+..++.|+.+||+|.|.|+.+++....+.|.++|++.+....
T Consensus 38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~~~ 117 (402)
T KOG2191|consen 38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQAVA 117 (402)
T ss_pred ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHhhc
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999998755321
Q ss_pred CcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchHH
Q 019747 201 TMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIM 280 (336)
Q Consensus 201 ~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I~ 280 (336)
....-+. |. ...+....++.||+...|.||||+|.+||
T Consensus 118 k~v~~~~------------pq------------------------------t~~r~kqikivvPNstag~iigkggAtiK 155 (402)
T KOG2191|consen 118 KPVDILQ------------PQ------------------------------TPDRIKQIKIVVPNSTAGMIIGKGGATIK 155 (402)
T ss_pred CCccccC------------CC------------------------------CccccceeEEeccCCcccceecCCcchHH
Confidence 1100000 00 01233558999999999999999999999
Q ss_pred HHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhhh
Q 019747 281 EISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASD 332 (336)
Q Consensus 281 ~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~ 332 (336)
.|++++||+|+|++.....-.-.+|+|+++|++++..+|..+|.++|.++..
T Consensus 156 ~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpq 207 (402)
T KOG2191|consen 156 AIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQ 207 (402)
T ss_pred HHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCc
Confidence 9999999999999643223445689999999999999999999999988754
No 9
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.80 E-value=1.7e-18 Score=165.13 Aligned_cols=158 Identities=29% Similarity=0.491 Sum_probs=134.2
Q ss_pred eeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEc---------CHHHHHHHHHHHHHHh
Q 019747 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTG---------TLDEQMRALELILLKL 192 (336)
Q Consensus 122 ~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G---------~~~~v~~A~~~i~~~l 192 (336)
.++|++++...+|.+||++|..+++|+.++.++|++.. .+++..+|+++|+| ..+++.+|..+|...+
T Consensus 43 ~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~---~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~ 119 (485)
T KOG2190|consen 43 LTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNE---SLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKL 119 (485)
T ss_pred ceEEEEeccccceeEEccCcHHHHHHhhcccccceeec---CCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhcc
Confidence 44899999999999999999999999999999999986 35677899999999 8999999999999887
Q ss_pred hcCcCCCCCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCccccee
Q 019747 193 SEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVV 272 (336)
Q Consensus 193 ~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~II 272 (336)
.++.....+.... .....+++++.||..++|+||
T Consensus 120 ~~d~~~~~d~~~~----------------------------------------------~~~~~v~~RLlVp~sq~GslI 153 (485)
T KOG2190|consen 120 EEDDEAAEDNGED----------------------------------------------ASGPEVTCRLLVPSSQVGSLI 153 (485)
T ss_pred cccccccccCCcc----------------------------------------------ccCCceEEEEEechhheeeee
Confidence 6433222110000 011137899999999999999
Q ss_pred ccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhh
Q 019747 273 GRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYA 330 (336)
Q Consensus 273 Gk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~ 330 (336)
||+|+.||+|++.|||+|.+.++ ..|.+.+|.|+|+|.++.|.+|...|..+|.+.
T Consensus 154 GK~G~~Ik~Ire~TgA~I~v~~~--~lP~ster~V~IsG~~~av~~al~~Is~~L~~~ 209 (485)
T KOG2190|consen 154 GKGGSLIKEIREETGAKIRVSSD--MLPNSTERAVTISGEPDAVKKALVQISSRLLEN 209 (485)
T ss_pred ccCcHHHHHHHHhcCceEEecCC--CCCcccceeEEEcCchHHHHHHHHHHHHHHHhc
Confidence 99999999999999999999987 477889999999999999999999999998774
No 10
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.78 E-value=1.9e-18 Score=147.23 Aligned_cols=159 Identities=31% Similarity=0.536 Sum_probs=134.4
Q ss_pred CCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhcc
Q 019747 31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELH 110 (336)
Q Consensus 31 ~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~ 110 (336)
..+.+.+||||+.+++|.|||++|+.||+|++++.+++++-. +..|++++|++.+.|.+.+|..+++.|++.|.+.--
T Consensus 119 ~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift--~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pi 196 (390)
T KOG2192|consen 119 LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFT--ECCPHSTDRVVLIGGKPKRVVECIKIILDLISESPI 196 (390)
T ss_pred CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhh--ccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCc
Confidence 344578999999999999999999999999999999999964 567899999999999999999999999976654410
Q ss_pred cc--------------c-----cCC-C-----------------------------------------------------
Q 019747 111 AE--------------D-----QAD-D----------------------------------------------------- 117 (336)
Q Consensus 111 ~~--------------~-----~~~-~----------------------------------------------------- 117 (336)
+. + +.. +
T Consensus 197 kgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~sai 276 (390)
T KOG2192|consen 197 KGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAI 276 (390)
T ss_pred CCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcC
Confidence 00 0 000 0
Q ss_pred ----------------------------------CCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCC
Q 019747 118 ----------------------------------VGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHS 163 (336)
Q Consensus 118 ----------------------------------~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~ 163 (336)
.....+.++.||.++-|.|||++|..|++|+.++|+.|++.. +
T Consensus 277 dtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikide---p 353 (390)
T KOG2192|consen 277 DTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDE---P 353 (390)
T ss_pred CCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecC---c
Confidence 022367789999999999999999999999999999999985 5
Q ss_pred CCCCCceEEEEEcCHHHHHHHHHHHHHHhhc
Q 019747 164 YYGLNDRLVTLTGTLDEQMRALELILLKLSE 194 (336)
Q Consensus 164 ~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~ 194 (336)
..++.+|+++|+|+.++++.|..++...+..
T Consensus 354 leGsedrIitItGTqdQIqnAQYLlQn~Vkq 384 (390)
T KOG2192|consen 354 LEGSEDRIITITGTQDQIQNAQYLLQNSVKQ 384 (390)
T ss_pred CCCCCceEEEEeccHHHHhhHHHHHHHHHHh
Confidence 6678999999999999999999999988764
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=99.72 E-value=4.4e-17 Score=136.33 Aligned_cols=139 Identities=22% Similarity=0.284 Sum_probs=107.4
Q ss_pred EEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEE---EcCHHHHHHHHHHHHHHhhcCcCCCCCc
Q 019747 126 LIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTL---TGTLDEQMRALELILLKLSEDTLYSQTM 202 (336)
Q Consensus 126 l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I---~G~~~~v~~A~~~i~~~l~~~~~~~~~~ 202 (336)
+.||.+.++.|||++|++|+.|+++||++|.+.. .+..|.| +++++++.+|.++|..+........ ..
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~--------~~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~-A~ 72 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS--------ETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEK-AL 72 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc--------CCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHH-HH
Confidence 5689999999999999999999999999999996 2346777 7889999999999999776411000 00
Q ss_pred CCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEecc---------Ccccceec
Q 019747 203 TVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVAD---------EHIGFVVG 273 (336)
Q Consensus 203 ~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~---------~~vg~IIG 273 (336)
... ........+.|+. ...|+|||
T Consensus 73 ----~l~-------------------------------------------gd~y~~~Vi~I~~~~~~~~~~~~~~griIG 105 (172)
T TIGR03665 73 ----KLL-------------------------------------------DDDYMLEVIDLKEYGKSPNALRRIKGRIIG 105 (172)
T ss_pred ----Hhc-------------------------------------------CCcceEEEEEhhhccCCHHHHHHHHhhhcC
Confidence 000 0000111223332 37899999
Q ss_pred cCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhh
Q 019747 274 RGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYA 330 (336)
Q Consensus 274 k~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~ 330 (336)
++|++++.|+..|||+|.|+ +..|.|.|++++++.|+.+|.++++..
T Consensus 106 ~~G~t~~~ie~~t~~~i~i~----------~~~v~i~G~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 106 EGGKTRRIIEELTGVSISVY----------GKTVGIIGDPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred CCcHHHHHHHHHHCCeEEEc----------CCEEEEECCHHHHHHHHHHHHHHHcCC
Confidence 99999999999999999994 268999999999999999999988553
No 12
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=99.70 E-value=9.4e-17 Score=134.32 Aligned_cols=138 Identities=17% Similarity=0.216 Sum_probs=106.5
Q ss_pred EEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEE---EeeHHHHHHHHHHHHHHHHhhccccccC
Q 019747 39 FLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMI---SGTIDEILRAVDLVIDKLLTELHAEDQA 115 (336)
Q Consensus 39 i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I---~G~~~~v~~A~~~I~~~i~~~~~~~~~~ 115 (336)
|.||.+.+|.|||++|++|+.|+++|||+|++... +..|.| +++++++.+|..+|...... ...++..
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~--------~g~V~I~~~t~d~~~i~kA~~~I~~i~~g-f~~e~A~ 72 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE--------TGEVKIEEEDEDPLAVMKAREVVKAIGRG-FSPEKAL 72 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC--------CceEEEecCCCCHHHHHHHHHHHHHHHcC-CCHHHHH
Confidence 56899999999999999999999999999999642 245777 78899999999999864332 1111000
Q ss_pred -CCCCCceeEEEEEec---------CccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHH
Q 019747 116 -DDVGTKTKLRLIVPN---------SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRAL 185 (336)
Q Consensus 116 -~~~~~~~~~~l~ip~---------~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~ 185 (336)
.-.+......+.|+. ...|+|||++|.+++.|+..|||+|.|.. ..|.|.|++++++.|+
T Consensus 73 ~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~----------~~v~i~G~~~~~~~A~ 142 (172)
T TIGR03665 73 KLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG----------KTVGIIGDPEQVQIAR 142 (172)
T ss_pred HhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC----------CEEEEECCHHHHHHHH
Confidence 000111222234443 36899999999999999999999999974 5799999999999999
Q ss_pred HHHHHHhhcC
Q 019747 186 ELILLKLSED 195 (336)
Q Consensus 186 ~~i~~~l~~~ 195 (336)
++|.+++...
T Consensus 143 ~~i~~li~~~ 152 (172)
T TIGR03665 143 EAIEMLIEGA 152 (172)
T ss_pred HHHHHHHcCC
Confidence 9999999664
No 13
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.70 E-value=3.2e-16 Score=132.02 Aligned_cols=141 Identities=19% Similarity=0.246 Sum_probs=109.1
Q ss_pred eeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEE----cCHHHHHHHHHHHHHHhhcCcC
Q 019747 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT----GTLDEQMRALELILLKLSEDTL 197 (336)
Q Consensus 122 ~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~----G~~~~v~~A~~~i~~~l~~~~~ 197 (336)
....+.||.+.++.|||++|.+|+.|+++||++|++.. .+..|.|. ++++++.+|+++|..++.....
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~--------~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~~ 74 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS--------ETGEVIIEPTDGEDPLAVLKARDIVKAIGRGFSP 74 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC--------CCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCH
Confidence 46789999999999999999999999999999999996 23567785 8899999999999998764110
Q ss_pred CCC--CcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEe---------ccC
Q 019747 198 YSQ--TMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGV---------ADE 266 (336)
Q Consensus 198 ~~~--~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~v---------p~~ 266 (336)
... .... .| ....+.| ...
T Consensus 75 e~A~~l~gd--~y------------------------------------------------~~~Vi~i~~~~~~~~~~~r 104 (180)
T PRK13763 75 EKALRLLDD--DY------------------------------------------------VLEVIDLSDYGDSPNALRR 104 (180)
T ss_pred HHHHHHhCC--Cc------------------------------------------------eEEEEEhhhccCChhHHHH
Confidence 000 0000 00 0001111 113
Q ss_pred cccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhh
Q 019747 267 HIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYA 330 (336)
Q Consensus 267 ~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~ 330 (336)
.+|+|||++|++++.|++.|||+|.|.. ..|.|.|++++++.|+..|.++++..
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~----------~~v~i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYG----------KTVAIIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcC----------CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence 7899999999999999999999999953 34999999999999999999988553
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.67 E-value=6.3e-16 Score=130.22 Aligned_cols=143 Identities=18% Similarity=0.226 Sum_probs=108.8
Q ss_pred cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEE----eeHHHHHHHHHHHHHHHHhhc
Q 019747 34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMIS----GTIDEILRAVDLVIDKLLTEL 109 (336)
Q Consensus 34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~----G~~~~v~~A~~~I~~~i~~~~ 109 (336)
.+...+.||.+.+|.|||++|++|+.|+++|||+|++... +..|.|. ++++.+.+|+.+|.+.+...
T Consensus 2 ~~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~--------~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf- 72 (180)
T PRK13763 2 MMMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE--------TGEVIIEPTDGEDPLAVLKARDIVKAIGRGF- 72 (180)
T ss_pred CceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC--------CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCC-
Confidence 3578899999999999999999999999999999999642 2456774 88999999999999655421
Q ss_pred cccccCCCCCCceeEE-EEEec---------CccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHH
Q 019747 110 HAEDQADDVGTKTKLR-LIVPN---------SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLD 179 (336)
Q Consensus 110 ~~~~~~~~~~~~~~~~-l~ip~---------~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~ 179 (336)
..++...-..+.+... +.+.. ..+|+|||++|.+++.|+..|||+|.|.. +.|.|.|+++
T Consensus 73 ~~e~A~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~----------~~v~i~G~~~ 142 (180)
T PRK13763 73 SPEKALRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG----------KTVAIIGDPE 142 (180)
T ss_pred CHHHHHHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC----------CEEEEEeCHH
Confidence 1000000000111211 11111 36899999999999999999999999975 3489999999
Q ss_pred HHHHHHHHHHHHhhcC
Q 019747 180 EQMRALELILLKLSED 195 (336)
Q Consensus 180 ~v~~A~~~i~~~l~~~ 195 (336)
++..|.+.|.+++...
T Consensus 143 ~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 143 QVEIAREAIEMLIEGA 158 (180)
T ss_pred HHHHHHHHHHHHHcCC
Confidence 9999999999999654
No 15
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.52 E-value=4.3e-14 Score=98.96 Aligned_cols=64 Identities=42% Similarity=0.772 Sum_probs=59.1
Q ss_pred EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHH
Q 019747 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLV 101 (336)
Q Consensus 36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I 101 (336)
++||+||.+.+|.|||++|++|++|+++|||+|++.+... ++..+|++.|.|+++++.+|+.+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~--~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL--PGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC--CCCCceEEEEEeCHHHHHHHHHhh
Confidence 4799999999999999999999999999999999987543 567899999999999999999887
No 16
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.52 E-value=3.9e-14 Score=99.19 Aligned_cols=63 Identities=38% Similarity=0.592 Sum_probs=58.1
Q ss_pred EEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHH
Q 019747 259 LTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMI 323 (336)
Q Consensus 259 ~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I 323 (336)
.++.||..++|+|||++|++|++|+++|||+|.+.++.+ ++..+|+|+|+|++++++.|+.||
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~--~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL--PGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC--CCCCceEEEEEeCHHHHHHHHHhh
Confidence 689999999999999999999999999999999998643 356789999999999999999987
No 17
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.51 E-value=7.6e-14 Score=130.36 Aligned_cols=278 Identities=22% Similarity=0.272 Sum_probs=190.4
Q ss_pred CCCCCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747 28 SDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT 107 (336)
Q Consensus 28 ~~~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~ 107 (336)
.....+++.+++.||...+-+++||.|++|+.|++.++++|.+...+- ..++...+.|-+..+-.|...+++++..
T Consensus 61 e~e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~----g~e~~~~~~~~p~~v~~a~a~~~~~~~~ 136 (608)
T KOG2279|consen 61 EQKPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDV----GDERVLLISGFPVQVCKAKAAIHQILTE 136 (608)
T ss_pred ecCchhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccC----CcccchhhccCCCCCChHHHHHHHHHhc
Confidence 445558899999999999999999999999999999999999976441 3567777777888888888888877666
Q ss_pred hccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHH
Q 019747 108 ELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALEL 187 (336)
Q Consensus 108 ~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~ 187 (336)
. ..+...+.+|...+++++|++|.+++.|+..++++|.+..+ . -....+...|.|.......|..+
T Consensus 137 ~-----------~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n--g-r~g~~~~~~i~~qqk~~~~a~~~ 202 (608)
T KOG2279|consen 137 N-----------TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN--G-RLGLSRLIKISGQQKEVAAAKHL 202 (608)
T ss_pred C-----------Ccccccccchhhhcccccccchhhhcchhcccccccccccc--c-ccccccceecccccchHHHHHhh
Confidence 4 34677889999999999999999999999999999999873 1 12245788888888888899999
Q ss_pred HHHHhhcCcCCCCC----------cCCCccCCCccc--cCCCCCCCCCCCCCCCCCCCCCCCCCCC-CC--C---CCCc-
Q 019747 188 ILLKLSEDTLYSQT----------MTVPYTYAGVFF--SGFHGMPYGAVPPPVPAVPHNTAAHYGP-NM--G---GRKF- 248 (336)
Q Consensus 188 i~~~l~~~~~~~~~----------~~~~~~~~g~~~--~~~~~~p~~~~~~~~~~~~~~~~~~~~~-~g--~---~~~~- 248 (336)
+.+.+.++...... +..+....+..+ .+..+.+.-+.--.....++..+.+.++ .. + .+.|
T Consensus 203 ~~~~~~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~ 282 (608)
T KOG2279|consen 203 ILEKVSEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWE 282 (608)
T ss_pred hhccccchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccC
Confidence 98888765331110 111111111111 0001111100000000011100000000 00 0 0011
Q ss_pred ----cC-CCCCCceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCC--cceEEEEEcChHhHHHHHH
Q 019747 249 ----QN-NKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGT--SERKVTISGPQRSIRTAES 321 (336)
Q Consensus 249 ----~~-~~~~~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~--~~r~v~I~G~~~~v~~A~~ 321 (336)
+. .........+|.+|...+|.|||+.|++++.+...+++.+.|.-.. ..+. ...++.+.|+..-++.|..
T Consensus 283 ~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~p--yt~~v~~~qic~~egkqh~~n~vl~ 360 (608)
T KOG2279|consen 283 KPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQP--YTSRVLQLQICVNEGKQHYENSVLE 360 (608)
T ss_pred CccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEecc--ccchhhhhhhheecchhHHHHHHHh
Confidence 11 1234566789999999999999999999999999999998887642 1111 1267889999999999999
Q ss_pred HHHH
Q 019747 322 MIMQ 325 (336)
Q Consensus 322 ~I~~ 325 (336)
|+..
T Consensus 361 ml~~ 364 (608)
T KOG2279|consen 361 MLTV 364 (608)
T ss_pred hhhc
Confidence 9973
No 18
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.40 E-value=5.7e-13 Score=92.46 Aligned_cols=61 Identities=26% Similarity=0.583 Sum_probs=56.0
Q ss_pred EEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHH
Q 019747 259 LTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIM 324 (336)
Q Consensus 259 ~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~ 324 (336)
.++.||.+++++|||++|++|++|+++|||+|.+++.. +.++.|+|+|+++++..|+.+|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-----~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-----SKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-----CCCCEEEEEcCHHHHHHHHHHhC
Confidence 57899999999999999999999999999999998753 46899999999999999999873
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=99.39 E-value=4.5e-13 Score=92.35 Aligned_cols=60 Identities=33% Similarity=0.570 Sum_probs=55.1
Q ss_pred EEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHH
Q 019747 258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMI 323 (336)
Q Consensus 258 ~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I 323 (336)
|.+|.||.+++|+|||++|++|++|+++|||+|.++++ + ....|+|+|++++++.|+.+|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~-----~-~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD-----D-ERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST-----T-EEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC-----C-CcEEEEEEeCHHHHHHHHhhC
Confidence 57899999999999999999999999999999999764 2 456999999999999999986
No 20
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.35 E-value=2.6e-12 Score=88.43 Aligned_cols=59 Identities=27% Similarity=0.471 Sum_probs=53.9
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcC-hHhHHHHHHHHH
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGP-QRSIRTAESMIM 324 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~ 324 (336)
.+..+.||.+++|+|||++|++|++|+++|||+|.+++ ++.|.|+|+ +++++.|+.+|+
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~---------~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED---------DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC---------CCEEEEEeCCHHHHHHHHHHhC
Confidence 56789999999999999999999999999999999964 467999998 999999999873
No 21
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.34 E-value=1.4e-12 Score=89.84 Aligned_cols=60 Identities=30% Similarity=0.577 Sum_probs=54.6
Q ss_pred EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHH
Q 019747 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLV 101 (336)
Q Consensus 36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I 101 (336)
|.+|.||.+++|+|||++|++|++|+++|||+|+|++. + .+..+.|.|+.+++.+|+++|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~-----~-~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD-----D-ERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST-----T-EEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC-----C-CcEEEEEEeCHHHHHHHHhhC
Confidence 67999999999999999999999999999999999763 2 355999999999999999876
No 22
>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=99.32 E-value=6e-12 Score=87.82 Aligned_cols=63 Identities=37% Similarity=0.683 Sum_probs=56.9
Q ss_pred EEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHH
Q 019747 259 LTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIM 324 (336)
Q Consensus 259 ~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~ 324 (336)
.++.||.+++++|||++|++|++|++.|||+|.|++... +..++.|+|.|+.++++.|+.+|.
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~---~~~~~~v~i~G~~~~v~~a~~~i~ 64 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS---GSEERIVTITGTPEAVEKAKELIL 64 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC---CCCceEEEEEcCHHHHHHHHHHhC
Confidence 578999999999999999999999999999999988532 356899999999999999999873
No 23
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.31 E-value=3.1e-12 Score=88.72 Aligned_cols=61 Identities=21% Similarity=0.415 Sum_probs=55.8
Q ss_pred EEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHH
Q 019747 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVI 102 (336)
Q Consensus 37 ~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~ 102 (336)
.+|.||.++++.|||++|++|++|+++|||+|.|++.. ..++.|.|.|+.+++..|+.+|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-----~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-----SKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-----CCCCEEEEEcCHHHHHHHHHHhC
Confidence 67999999999999999999999999999999998643 56889999999999999998873
No 24
>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=99.26 E-value=2.8e-11 Score=84.41 Aligned_cols=62 Identities=40% Similarity=0.756 Sum_probs=56.2
Q ss_pred EEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHH
Q 019747 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLV 101 (336)
Q Consensus 37 ~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I 101 (336)
.+|.||.+++++|||++|++|++|+++|||.|.|+...+ ...++.+.|.|..+++..|..+|
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 689999999999999999999999999999999986542 35789999999999999998876
No 25
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.24 E-value=3.9e-11 Score=82.59 Aligned_cols=58 Identities=21% Similarity=0.388 Sum_probs=52.5
Q ss_pred EEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEee-HHHHHHHHHHH
Q 019747 35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT-IDEILRAVDLV 101 (336)
Q Consensus 35 ~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~-~~~v~~A~~~I 101 (336)
.+..|.||.+++|.|||++|++|++|+++|||+|.+++ ++.|.|.|. .++++.|..+|
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 46789999999999999999999999999999999964 357999998 89999998876
No 26
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.16 E-value=2.2e-10 Score=115.79 Aligned_cols=226 Identities=21% Similarity=0.271 Sum_probs=162.4
Q ss_pred cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCC--CCceEEEEEeeHHHHHHHHHHHHHHHHhh---
Q 019747 34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPG--TTDRIIMISGTIDEILRAVDLVIDKLLTE--- 108 (336)
Q Consensus 34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~--~~~r~i~I~G~~~~v~~A~~~I~~~i~~~--- 108 (336)
-+..++.+....+.++||++|.+++.++.++.+.++|+..+...+. ...+...+....-++..++.++...+...
T Consensus 200 ~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~~~ 279 (753)
T KOG2208|consen 200 SVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSSPSNKIDGRLNSSSSINVEIQEALTRLESEFDYDEII 279 (753)
T ss_pred eEEEEeeccccchhhhccccccccccccccceeEEEcccccccchhhhhccccccceehhhhhHHHHHHhcChhhhhhhh
Confidence 4889999999999999999999999999999999999876643221 11122233333344444444443211111
Q ss_pred ---cccc-----------------------cc---C-------------------------CCCCCceeEEEEEecCccc
Q 019747 109 ---LHAE-----------------------DQ---A-------------------------DDVGTKTKLRLIVPNSSCG 134 (336)
Q Consensus 109 ---~~~~-----------------------~~---~-------------------------~~~~~~~~~~l~ip~~~~g 134 (336)
++.. .. . ..........+.+-...+.
T Consensus 280 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~~~ 359 (753)
T KOG2208|consen 280 YRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPEELK 359 (753)
T ss_pred hccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHHhhh
Confidence 0000 00 0 0003446777888889999
Q ss_pred eeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCCCCcCCCccCCCcccc
Q 019747 135 SIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFS 214 (336)
Q Consensus 135 ~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~~~~~~~~~~~g~~~~ 214 (336)
.++|++|.++.+|++++.|.+.+.. .++.+..+.+.|...++.+|.+.+.....+....
T Consensus 360 ~v~GK~~~ni~ki~e~~~~~i~~~~-----~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~---------------- 418 (753)
T KOG2208|consen 360 FVIGKKGANIEKIREESQVKIDLPK-----QGSNNKKVVITGVSANDEKAVEDVEKIIAEILNS---------------- 418 (753)
T ss_pred hhcCCCCccHHHHHHhhhhceeccc-----ccCCCCCeEEeccccchhHHHHHHHHHHHhhhcc----------------
Confidence 9999999999999999999999987 3446788999999999999999999998774321
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchHHHHHhHhC-CeEEEc
Q 019747 215 GFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISG-ARIKVS 293 (336)
Q Consensus 215 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sg-a~I~i~ 293 (336)
.....+.+|...+.+|||.+|..|.+|...++ .+|+.+
T Consensus 419 -----------------------------------------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~ 457 (753)
T KOG2208|consen 419 -----------------------------------------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQ 457 (753)
T ss_pred -----------------------------------------cccceeecCccchhhhhccccccHHHHHhhcCcEEEecC
Confidence 14567899999999999999999999999999 566665
Q ss_pred cCCCCCCCCcceEEEEEcChHhHHHHHHHHHHH
Q 019747 294 DRGDFFSGTSERKVTISGPQRSIRTAESMIMQK 326 (336)
Q Consensus 294 ~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~ 326 (336)
+.. .....+++.|....+..++.++..+
T Consensus 458 ~~~-----~~~~~~~~~~~~~dv~~~~~~~~~~ 485 (753)
T KOG2208|consen 458 NNN-----NSSDMVTIRGISKDVEKSVSLLKAL 485 (753)
T ss_pred CCC-----cccccceEeccccccchhHHHHHhh
Confidence 542 4456677777766666655555444
No 27
>PF13014 KH_3: KH domain
Probab=99.09 E-value=1.9e-10 Score=73.43 Aligned_cols=43 Identities=40% Similarity=0.723 Sum_probs=38.7
Q ss_pred cccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc
Q 019747 267 HIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG 311 (336)
Q Consensus 267 ~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G 311 (336)
+||+|||++|++|++|+++|||+|.|++. ..++..++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~--~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPE--NEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCc--cCCCCCceEEEEEC
Confidence 58999999999999999999999999982 35567899999998
No 28
>PF13014 KH_3: KH domain
Probab=99.08 E-value=3.2e-10 Score=72.35 Aligned_cols=43 Identities=44% Similarity=0.890 Sum_probs=38.8
Q ss_pred ccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEe
Q 019747 45 LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG 89 (336)
Q Consensus 45 ~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G 89 (336)
++|+|||++|++|++|+++|+|+|+|++ +..+...++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~--~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP--ENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC--ccCCCCCceEEEEEC
Confidence 5899999999999999999999999988 345678899999987
No 29
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=99.05 E-value=1.1e-09 Score=90.86 Aligned_cols=144 Identities=18% Similarity=0.232 Sum_probs=107.1
Q ss_pred eeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEc-----CHHHHHHHHHHHHHHhhcCc
Q 019747 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTG-----TLDEQMRALELILLKLSEDT 196 (336)
Q Consensus 122 ~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G-----~~~~v~~A~~~i~~~l~~~~ 196 (336)
....+.||.+..+.++|+.|...+.|++.++++|.++.+ +..|.|.. ++-.+.+|.+.|..+-....
T Consensus 8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~--------~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~ 79 (194)
T COG1094 8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK--------TGSVTIRTTRKTEDPLALLKARDVVKAIGRGFP 79 (194)
T ss_pred ceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC--------CCeEEEEecCCCCChHHHHHHHHHHHHHhcCCC
Confidence 456789999999999999999999999999999999972 34455543 58899999999998865421
Q ss_pred CCCCCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEe------cc----C
Q 019747 197 LYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGV------AD----E 266 (336)
Q Consensus 197 ~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~v------p~----~ 266 (336)
... .-.+. ........+.+ +. .
T Consensus 80 pe~---A~~LL---------------------------------------------~d~~~levIdi~~~~~~~~~~l~R 111 (194)
T COG1094 80 PEK---ALKLL---------------------------------------------EDDYYLEVIDLKDVVTLSGDHLRR 111 (194)
T ss_pred HHH---HHHHh---------------------------------------------cCCcEEEEEEHHHhccCchhhhhH
Confidence 100 00000 00001111111 11 2
Q ss_pred cccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747 267 HIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS 331 (336)
Q Consensus 267 ~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~ 331 (336)
..|+|||++|.+.+.|++.|||+|.|. ..+|.|-|.+++++.|+..|..++....
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~----------g~tVaiiG~~~~v~iAr~AVemli~G~~ 166 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVY----------GKTVAIIGGFEQVEIAREAVEMLINGAP 166 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEe----------CcEEEEecChhhhHHHHHHHHHHHcCCC
Confidence 569999999999999999999999996 4789999999999999999999887643
No 30
>smart00322 KH K homology RNA-binding domain.
Probab=99.05 E-value=1.2e-09 Score=76.82 Aligned_cols=66 Identities=26% Similarity=0.668 Sum_probs=59.9
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHH
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKV 327 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i 327 (336)
.+..+.||..+++++||++|++|++|++.||++|.+.... .....+.|.|+++++..|+.+|.+.+
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 6788999999999999999999999999999999997642 25789999999999999999998876
No 31
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.04 E-value=4.3e-10 Score=113.72 Aligned_cols=217 Identities=19% Similarity=0.224 Sum_probs=160.8
Q ss_pred EEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhcccccc
Q 019747 35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQ 114 (336)
Q Consensus 35 ~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~~~ 114 (336)
..+.+.+-...+..++||+|.+|.+|+++++|.+.++... ..+..+.++|...++.+|...+...+.+....
T Consensus 347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~-----~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~--- 418 (753)
T KOG2208|consen 347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQG-----SNNKKVVITGVSANDEKAVEDVEKIIAEILNS--- 418 (753)
T ss_pred eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccccc-----CCCCCeEEeccccchhHHHHHHHHHHHhhhcc---
Confidence 6678888889999999999999999999999999998743 67888999999999999999999655554221
Q ss_pred CCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcC-CEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhh
Q 019747 115 ADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQ-AVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLS 193 (336)
Q Consensus 115 ~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tg-a~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~ 193 (336)
.....+.+|...+.+++|.+|..|..|..+++ ++|++... ......+++.|....+..+...+..+..
T Consensus 419 ------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~-----~~~~~~~~~~~~~~dv~~~~~~~~~~~~ 487 (753)
T KOG2208|consen 419 ------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN-----NNSSDMVTIRGISKDVEKSVSLLKALKA 487 (753)
T ss_pred ------cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC-----CcccccceEeccccccchhHHHHHhhhh
Confidence 24567999999999999999999999999999 77766652 2244557777877777776665555543
Q ss_pred cCcCCCCCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceec
Q 019747 194 EDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVG 273 (336)
Q Consensus 194 ~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIG 273 (336)
...... .....+.....|..+.+..+|
T Consensus 488 ~a~~~~-----------------------------------------------------~~~~~~~d~~~~~~~~~~~~g 514 (753)
T KOG2208|consen 488 DAKNLK-----------------------------------------------------FRDVVTKDKLLPVKYIGKEIG 514 (753)
T ss_pred hhhcch-----------------------------------------------------hhhhhhccccchHHhhccccc
Confidence 221100 011134455566677777777
Q ss_pred cCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhh
Q 019747 274 RGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYAS 331 (336)
Q Consensus 274 k~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~ 331 (336)
+.|..+...++.. .+.... +.++..++|.|..+.|..|+..+...+....
T Consensus 515 ~~~~i~d~~~~~~----i~~~~~----~~~~~~i~i~gk~~~v~~a~~~L~~~~~~~~ 564 (753)
T KOG2208|consen 515 KNGTIRDSLGDKS----IFPPNE----DEDHEKITIEGKLELVLEAPAELKALIEALI 564 (753)
T ss_pred CceeeeccCCcee----eccccc----ccccceeeecccccchhhhHHHHHhcchhhh
Confidence 7766555554444 444322 2468999999999999999999988876644
No 32
>smart00322 KH K homology RNA-binding domain.
Probab=99.00 E-value=3.7e-09 Score=74.18 Aligned_cols=67 Identities=30% Similarity=0.658 Sum_probs=59.5
Q ss_pred cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHH
Q 019747 34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKL 105 (336)
Q Consensus 34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i 105 (336)
.++.+|.||.+.++.+||++|++|++|+++++++|.+.... .....+.|.|..+++..|..+|.+.+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-----~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-----SEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-----CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 46789999999999999999999999999999999997533 25788999999999999999998654
No 33
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.96 E-value=1.5e-08 Score=84.22 Aligned_cols=144 Identities=17% Similarity=0.255 Sum_probs=105.6
Q ss_pred cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEe-----eHHHHHHHHHHHHHHHHhh
Q 019747 34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG-----TIDEILRAVDLVIDKLLTE 108 (336)
Q Consensus 34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G-----~~~~v~~A~~~I~~~i~~~ 108 (336)
..+..+.||.+..+.+||+.|++.+.|++.+++++.+.. .+..+.|.. ++-.+.+|...|. .+-..
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~--------~~~~V~i~~~~~t~Dp~~~~ka~d~Vk-AIgrG 77 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS--------KTGSVTIRTTRKTEDPLALLKARDVVK-AIGRG 77 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC--------CCCeEEEEecCCCCChHHHHHHHHHHH-HHhcC
Confidence 456779999999999999999999999999999999953 345566654 4567777877776 34333
Q ss_pred ccccccCCCCCCceeEE------EEE-ec----CccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcC
Q 019747 109 LHAEDQADDVGTKTKLR------LIV-PN----SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT 177 (336)
Q Consensus 109 ~~~~~~~~~~~~~~~~~------l~i-p~----~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~ 177 (336)
++.+....-.++...+. +.- +. ...|+|||++|.+.+.|++-|+|.|.+.. ..|.|-|.
T Consensus 78 F~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g----------~tVaiiG~ 147 (194)
T COG1094 78 FPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG----------KTVAIIGG 147 (194)
T ss_pred CCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC----------cEEEEecC
Confidence 32210000001111111 111 11 34689999999999999999999999986 57999999
Q ss_pred HHHHHHHHHHHHHHhhcCc
Q 019747 178 LDEQMRALELILLKLSEDT 196 (336)
Q Consensus 178 ~~~v~~A~~~i~~~l~~~~ 196 (336)
++++..|+++|..++....
T Consensus 148 ~~~v~iAr~AVemli~G~~ 166 (194)
T COG1094 148 FEQVEIAREAVEMLINGAP 166 (194)
T ss_pred hhhhHHHHHHHHHHHcCCC
Confidence 9999999999999997653
No 34
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=98.72 E-value=9.2e-09 Score=96.80 Aligned_cols=145 Identities=28% Similarity=0.465 Sum_probs=122.1
Q ss_pred CceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCC
Q 019747 120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYS 199 (336)
Q Consensus 120 ~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~ 199 (336)
......+.++...+.+++|+.|.+|+.|+..++++|.+..++- ..++.-.+.|-+.++..|..++..++.+..
T Consensus 66 k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~----g~e~~~~~~~~p~~v~~a~a~~~~~~~~~~--- 138 (608)
T KOG2279|consen 66 KDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDV----GDERVLLISGFPVQVCKAKAAIHQILTENT--- 138 (608)
T ss_pred hheeeeEeecccceeeeeccccCCcchhhcccccceecCcccC----CcccchhhccCCCCCChHHHHHHHHHhcCC---
Confidence 4577889999999999999999999999999999999987322 134555566688899999998888876532
Q ss_pred CCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchH
Q 019747 200 QTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNI 279 (336)
Q Consensus 200 ~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I 279 (336)
.+...+.+|...+++|+|++|.++
T Consensus 139 --------------------------------------------------------pvk~~lsvpqr~~~~i~grgget~ 162 (608)
T KOG2279|consen 139 --------------------------------------------------------PVSEQLSVPQRSVGRIIGRGGETI 162 (608)
T ss_pred --------------------------------------------------------cccccccchhhhcccccccchhhh
Confidence 256778899999999999999999
Q ss_pred HHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhh
Q 019747 280 MEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYA 330 (336)
Q Consensus 280 ~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~ 330 (336)
..|+..++|+|.+..++. ....+.+.|.|...-++.|+.++.+.+++.
T Consensus 163 ~si~~ss~aki~~d~ngr---~g~~~~~~i~~qqk~~~~a~~~~~~~~~ed 210 (608)
T KOG2279|consen 163 RSICKSSGAKITCDKNGR---LGLSRLIKISGQQKEVAAAKHLILEKVSED 210 (608)
T ss_pred cchhcccccccccccccc---cccccceecccccchHHHHHhhhhccccch
Confidence 999999999999998742 345788999999999999999999998764
No 35
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.59 E-value=1.7e-07 Score=73.26 Aligned_cols=65 Identities=18% Similarity=0.375 Sum_probs=52.8
Q ss_pred CcccceeccCCchHHHHHhHhCCeEEEccCCCCCC--------------CCcceEEEEEcC---hHhHHHHHHHHHHHHH
Q 019747 266 EHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFS--------------GTSERKVTISGP---QRSIRTAESMIMQKVA 328 (336)
Q Consensus 266 ~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~--------------~~~~r~v~I~G~---~~~v~~A~~~I~~~i~ 328 (336)
+++|.|||++|++||+|+++|||+|.|..++.... ..++-.|.|++. .++++.|..+|..++.
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 68899999999999999999999999988632111 123367889994 5999999999999887
Q ss_pred hh
Q 019747 329 YA 330 (336)
Q Consensus 329 ~~ 330 (336)
..
T Consensus 95 ~~ 96 (120)
T cd02395 95 PA 96 (120)
T ss_pred cC
Confidence 54
No 36
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.58 E-value=8.7e-08 Score=84.28 Aligned_cols=154 Identities=21% Similarity=0.269 Sum_probs=113.1
Q ss_pred CceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCC
Q 019747 120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYS 199 (336)
Q Consensus 120 ~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~ 199 (336)
+..+..+.+|...++.++|++|.+||.|+.+|.+.|+-+... .+-++.++|..+.|..|++.|...-+.- .
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~------eePiF~vTg~~edv~~aRrei~saaeH~---~ 94 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG------EEPIFPVTGRHEDVRRARREIPSAAEHF---G 94 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC------CCCcceeccCchhHHHHhhcCcccccee---e
Confidence 567888999999999999999999999999999999887632 3468999999999999998776633221 0
Q ss_pred CCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchH
Q 019747 200 QTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNI 279 (336)
Q Consensus 200 ~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I 279 (336)
.-. |-+. +.++.|. + ....+.+.++.+|...+|.|+|..|.+|
T Consensus 95 l~~-----~s~s---~Sgg~~~-~----------------------------s~s~qt~sy~svP~rvvglvv~~~~~ti 137 (394)
T KOG2113|consen 95 LIR-----ASRS---FSGGTNG-A----------------------------SASGQTTSYVSVPLRVVGLVVGPKGATI 137 (394)
T ss_pred eee-----eccc---ccCCCcc-c----------------------------cccCCCceeeeccceeeeeccccccCcc
Confidence 000 0000 0000000 0 0223467788899999999999999999
Q ss_pred HHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHh-HHHHH-HHHHH
Q 019747 280 MEISQISGARIKVSDRGDFFSGTSERKVTISGPQRS-IRTAE-SMIMQ 325 (336)
Q Consensus 280 ~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~-v~~A~-~~I~~ 325 (336)
+.|++.+...|.-.-+ ..+.++-++|.+++ +++|+ .-|++
T Consensus 138 ~~iqq~tnt~I~T~v~------~~~~Vf~Vtg~~~nC~kra~s~eie~ 179 (394)
T KOG2113|consen 138 KRIQQFTNTYIATPVR------CGEPVFCVTGAPKNCVKRARSCEIEQ 179 (394)
T ss_pred chheecccceEeeecc------CCCceEEEecCCcchhhhccccchhh
Confidence 9999999999887543 36899999998888 55566 34433
No 37
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.56 E-value=3.5e-07 Score=71.56 Aligned_cols=69 Identities=16% Similarity=0.360 Sum_probs=51.2
Q ss_pred EEEEecC------ccceeecCCChHHHHHHHHhCCeEEEcCCCCCC--------------CCCCceEEEEEee---HHHH
Q 019747 38 RFLVSNP------LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFF--------------PGTTDRIIMISGT---IDEI 94 (336)
Q Consensus 38 ~i~ip~~------~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~--------------~~~~~r~i~I~G~---~~~v 94 (336)
+|+||.+ ++|.|||++|++||+|+++|||+|.|....... .....--|.|.+. .+.+
T Consensus 3 ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~ 82 (120)
T cd02395 3 KVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEAL 82 (120)
T ss_pred EEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHH
Confidence 5666664 689999999999999999999999997642100 0112245777775 4889
Q ss_pred HHHHHHHHHHHH
Q 019747 95 LRAVDLVIDKLL 106 (336)
Q Consensus 95 ~~A~~~I~~~i~ 106 (336)
.+|+.+|...+.
T Consensus 83 ~~A~~~I~~ll~ 94 (120)
T cd02395 83 AKAVEAIEELLK 94 (120)
T ss_pred HHHHHHHHHHhc
Confidence 999999985554
No 38
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.38 E-value=9.4e-07 Score=71.20 Aligned_cols=104 Identities=20% Similarity=0.279 Sum_probs=72.4
Q ss_pred EEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhcccccc
Q 019747 35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQ 114 (336)
Q Consensus 35 ~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~~~ 114 (336)
=.+.++|+...+|..||++|++|+.|++..|-+|.+-..++ .+...|...+...-...-.
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~--------------------d~~~fI~n~l~Pa~V~~v~ 91 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSD--------------------DPEEFIKNIFAPAAVRSVT 91 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCC--------------------CHHHHHHHHcCCCEEEEEE
Confidence 46888999999999999999999999999999998854331 1222222222111000000
Q ss_pred CCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEe
Q 019747 115 ADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKIS 158 (336)
Q Consensus 115 ~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~ 158 (336)
-...+......+.|+.+..+.+||++|.+++.++.-++-.+.+.
T Consensus 92 I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 92 IKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred EEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 00112234566779999999999999999999999998877664
No 39
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.38 E-value=8.3e-07 Score=78.22 Aligned_cols=140 Identities=17% Similarity=0.252 Sum_probs=109.5
Q ss_pred CcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhcc--
Q 019747 33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELH-- 110 (336)
Q Consensus 33 ~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~-- 110 (336)
+.++..+.+|..+++.|+|++|.+||.|+.+|...|.-+-.. .+.+..++|..+.+..|++.|.. -.+.+.
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~------eePiF~vTg~~edv~~aRrei~s-aaeH~~l~ 96 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG------EEPIFPVTGRHEDVRRARREIPS-AAEHFGLI 96 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC------CCCcceeccCchhHHHHhhcCcc-ccceeeee
Confidence 789999999999999999999999999999999999886432 45788999999999999999873 111110
Q ss_pred -------ccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHH-HH
Q 019747 111 -------AEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDE-QM 182 (336)
Q Consensus 111 -------~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~-v~ 182 (336)
................-+|-..++.++|.+|.+|+.++..++..|...-. ..+.++-++|-+++ ++
T Consensus 97 ~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~------~~~~Vf~Vtg~~~nC~k 170 (394)
T KOG2113|consen 97 RASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR------CGEPVFCVTGAPKNCVK 170 (394)
T ss_pred eecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc------CCCceEEEecCCcchhh
Confidence 00011122445667788888899999999999999999999988887752 14578889998888 45
Q ss_pred HHH
Q 019747 183 RAL 185 (336)
Q Consensus 183 ~A~ 185 (336)
+|.
T Consensus 171 ra~ 173 (394)
T KOG2113|consen 171 RAR 173 (394)
T ss_pred hcc
Confidence 555
No 40
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.12 E-value=1.3e-05 Score=80.04 Aligned_cols=64 Identities=28% Similarity=0.396 Sum_probs=57.8
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHh
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAY 329 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~ 329 (336)
....+.||.+++|.|||+||++||.|.++||++|.|.+ +..|.|.+ ..+.+++|+.+|...+..
T Consensus 578 ~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---------~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 578 RIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---------DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred eeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 67789999999999999999999999999999999954 57888888 789999999999988773
No 41
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.11 E-value=1.2e-05 Score=64.77 Aligned_cols=104 Identities=20% Similarity=0.361 Sum_probs=74.9
Q ss_pred eeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCCCC
Q 019747 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQT 201 (336)
Q Consensus 122 ~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~~~ 201 (336)
....++|+...+|..||++|++|+.|++..|-+|.+-.- .- .+.+.|...+.......-.
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~--------------s~------d~~~fI~n~l~Pa~V~~v~ 91 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY--------------SD------DPEEFIKNIFAPAAVRSVT 91 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc--------------CC------CHHHHHHHHcCCCEEEEEE
Confidence 567789999999999999999999999999988888751 11 2344555554331110000
Q ss_pred cCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchHHH
Q 019747 202 MTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIME 281 (336)
Q Consensus 202 ~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I~~ 281 (336)
.. .........+.|+.+..|..|||+|++|+.
T Consensus 92 I~------------------------------------------------~~~~~~~~~V~V~~~d~g~aIGK~G~ni~l 123 (140)
T PRK08406 92 IK------------------------------------------------KKNGDKVAYVEVAPEDKGIAIGKNGKNIER 123 (140)
T ss_pred EE------------------------------------------------ecCCcEEEEEEECccccchhhCCCCHHHHH
Confidence 00 011124567889999999999999999999
Q ss_pred HHhHhCCeEEEc
Q 019747 282 ISQISGARIKVS 293 (336)
Q Consensus 282 I~~~sga~I~i~ 293 (336)
++..++-.+.|.
T Consensus 124 a~~L~~~~~di~ 135 (140)
T PRK08406 124 AKDLAKRHFDID 135 (140)
T ss_pred HHHHhCCccCCe
Confidence 999999988774
No 42
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.10 E-value=2.3e-05 Score=78.35 Aligned_cols=91 Identities=18% Similarity=0.191 Sum_probs=75.3
Q ss_pred HHHHHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEE
Q 019747 94 ILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVT 173 (336)
Q Consensus 94 v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~ 173 (336)
..+++..|++.+.+.+... ...+...+....+.||.+.++.|||++|.+||.|.++||++|.|.. +..|.
T Consensus 551 A~~g~~~Il~~m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---------~G~V~ 620 (719)
T TIGR02696 551 ARDARLAILDVMAEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---------DGTVY 620 (719)
T ss_pred HHHHHHHHHHHHHHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---------CcEEE
Confidence 3455666777777776655 4455566788899999999999999999999999999999999985 46788
Q ss_pred EEcC-HHHHHHHHHHHHHHhhc
Q 019747 174 LTGT-LDEQMRALELILLKLSE 194 (336)
Q Consensus 174 I~G~-~~~v~~A~~~i~~~l~~ 194 (336)
|.+. .+++++|+++|..+...
T Consensus 621 I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 621 IGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred EEeCCHHHHHHHHHHHHHhhCc
Confidence 8886 79999999999999874
No 43
>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=97.82 E-value=4.6e-05 Score=61.22 Aligned_cols=103 Identities=24% Similarity=0.329 Sum_probs=70.8
Q ss_pred EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhccccccC
Q 019747 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQA 115 (336)
Q Consensus 36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~ 115 (336)
.+-++|....+|..||++|++|+.|++..|-+|.+-..+ .++... |...+....-..-..
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys--------------~D~~~f------I~N~l~PA~V~~V~i 93 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYS--------------ENLEEF------VANKLAPAEVKNVTV 93 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcC--------------CCHHHH------HHHcCCCceEEEEEE
Confidence 788899999999999999999999999989888885432 112211 111111110000000
Q ss_pred CCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEe
Q 019747 116 DDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKIS 158 (336)
Q Consensus 116 ~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~ 158 (336)
...++.....+.||.+..+..||++|.+++...+-++-++.+.
T Consensus 94 ~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 94 SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 0112345677889999999999999999999999988777665
No 44
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.81 E-value=0.00014 Score=68.32 Aligned_cols=73 Identities=18% Similarity=0.299 Sum_probs=56.1
Q ss_pred eEEEEEecc------CcccceeccCCchHHHHHhHhCCeEEEccCCCCCC------------CC-cceEEEEEc-ChHhH
Q 019747 257 NSLTIGVAD------EHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFS------------GT-SERKVTISG-PQRSI 316 (336)
Q Consensus 257 ~~~~v~vp~------~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~------------~~-~~r~v~I~G-~~~~v 316 (336)
.+.+|.||- ++||+|||..|.++|+|+++|||+|.|-.++...+ +. ++=.+.|++ +.|.|
T Consensus 138 ~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki 217 (554)
T KOG0119|consen 138 LHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKI 217 (554)
T ss_pred cccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHH
Confidence 445666663 58999999999999999999999999987422111 11 223466777 89999
Q ss_pred HHHHHHHHHHHHh
Q 019747 317 RTAESMIMQKVAY 329 (336)
Q Consensus 317 ~~A~~~I~~~i~~ 329 (336)
++|..+|+.+|.+
T Consensus 218 ~~Ai~vienli~~ 230 (554)
T KOG0119|consen 218 KKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999999886
No 45
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.74 E-value=0.00014 Score=73.70 Aligned_cols=90 Identities=12% Similarity=0.138 Sum_probs=70.0
Q ss_pred HHHHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEE
Q 019747 95 LRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTL 174 (336)
Q Consensus 95 ~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I 174 (336)
.++...|++.+.+.+.......+...+....+.||.+.++.|||++|.+||.|+++|||+|.|.. +..|.|
T Consensus 524 ~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d---------dG~V~i 594 (684)
T TIGR03591 524 KEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED---------DGTVKI 594 (684)
T ss_pred HHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec---------CeEEEE
Confidence 34455566666666555434444556778889999999999999999999999999999999985 355667
Q ss_pred EcC-HHHHHHHHHHHHHHhh
Q 019747 175 TGT-LDEQMRALELILLKLS 193 (336)
Q Consensus 175 ~G~-~~~v~~A~~~i~~~l~ 193 (336)
.+. .+.+.+|.+.|..+..
T Consensus 595 ~~~~~~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 595 AASDGEAAEAAIKMIEGITA 614 (684)
T ss_pred EECcHHHHHHHHHHHHhhhc
Confidence 665 7888999999888865
No 46
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.70 E-value=0.00011 Score=74.65 Aligned_cols=64 Identities=31% Similarity=0.421 Sum_probs=55.4
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHh
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAY 329 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~ 329 (336)
....+.||.++++.|||++|++||+|.++|||+|.|.+ +..|.|.+ ..+.++.|+.+|..+...
T Consensus 551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d---------dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED---------DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec---------CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 67789999999999999999999999999999999954 35566665 788999999999887653
No 47
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.66 E-value=0.00038 Score=65.50 Aligned_cols=74 Identities=19% Similarity=0.193 Sum_probs=57.3
Q ss_pred ceeEEEEEec------CccceeecCCChHHHHHHHhcCCEEEEeccC------------CCCCCC-CceEEEEEcC-HHH
Q 019747 121 KTKLRLIVPN------SSCGSIIGKAGATIKSFMDDSQAVIKISRLD------------HSYYGL-NDRLVTLTGT-LDE 180 (336)
Q Consensus 121 ~~~~~l~ip~------~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~------------~~~~~~-~~r~v~I~G~-~~~ 180 (336)
.++-++.||. +++|.|||.+|.+.|+|+++|||+|.|-.+. ....+. .+=-|.|+++ .+.
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 5667787774 5689999999999999999999999998621 111122 2345778887 688
Q ss_pred HHHHHHHHHHHhhc
Q 019747 181 QMRALELILLKLSE 194 (336)
Q Consensus 181 v~~A~~~i~~~l~~ 194 (336)
|++|.+.|..+|.+
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999999986
No 48
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=97.63 E-value=0.004 Score=54.02 Aligned_cols=129 Identities=16% Similarity=0.150 Sum_probs=97.5
Q ss_pred eEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCCCCc
Q 019747 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTM 202 (336)
Q Consensus 123 ~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~~~~ 202 (336)
...+.++......|+..+|..+++|-...|++|.+.. ....+.|+|+...+..+...|.+.+..-
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~--------~~~~i~I~g~k~~~~~i~~~i~~~l~~i------- 91 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR--------SENRIRITGTKSTAEYIEASINEILSNI------- 91 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEec--------CCcEEEEEccHHHHHHHHHHHHHHHhhc-------
Confidence 4445556788889999999999999888899999987 5578999999999999999998888652
Q ss_pred CCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceec----cCCch
Q 019747 203 TVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVG----RGGRN 278 (336)
Q Consensus 203 ~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIG----k~G~~ 278 (336)
.+..+.++.-.--.-.+ .....
T Consensus 92 ------------------------------------------------------~~~~i~l~~~~~~~~~~~~~~~~~~~ 117 (210)
T PF14611_consen 92 ------------------------------------------------------RTEEIDLSPIISKHSEKKNSQFTPDL 117 (210)
T ss_pred ------------------------------------------------------EEEEEecchhhhhhcccccccccHHH
Confidence 45556555432211111 13667
Q ss_pred HHHHHhHhCCeEEEccCCCCCCCCcceEEEEE-----cChHhHHHHHHHHHHHHH
Q 019747 279 IMEISQISGARIKVSDRGDFFSGTSERKVTIS-----GPQRSIRTAESMIMQKVA 328 (336)
Q Consensus 279 I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~-----G~~~~v~~A~~~I~~~i~ 328 (336)
|+.|++.|++.|...+. ...+.|+ -.+..++.|+.++.-.+.
T Consensus 118 l~~i~~~t~~~ie~~~~--------~~~~~i~~~~~~~~~~~~~~a~RlL~~a~~ 164 (210)
T PF14611_consen 118 LEEIQKLTNVYIEKNPD--------GNKLKISWLASPENEKRADRAKRLLLWALD 164 (210)
T ss_pred HHHHHHHHcEEEEECCC--------CCeEEEEEEeeccccchHHHHHHHHHHhcc
Confidence 99999999999999764 2233333 578999999999988774
No 49
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=97.49 E-value=0.00042 Score=55.73 Aligned_cols=103 Identities=19% Similarity=0.375 Sum_probs=71.7
Q ss_pred eEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCCCCc
Q 019747 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTM 202 (336)
Q Consensus 123 ~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~~~~ 202 (336)
..-|+|....+|..+|++|.+|+.|++..|-+|.+-. ...+++ +.|...+....-..-..
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe--------------ys~D~~------~fI~N~l~PA~V~~V~i 93 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE--------------YSENLE------EFVANKLAPAEVKNVTV 93 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE--------------cCCCHH------HHHHHcCCCceEEEEEE
Confidence 6778999999999999999999999988888887764 222222 22333322110000000
Q ss_pred CCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchHHHH
Q 019747 203 TVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEI 282 (336)
Q Consensus 203 ~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I~~I 282 (336)
.+ ........+.||.+..+..|||+|++++..
T Consensus 94 -----------------------------------------------~~-~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la 125 (141)
T TIGR01952 94 -----------------------------------------------SE-FNGKKVAYVEVHPRDKGIAIGKGGKNIERA 125 (141)
T ss_pred -----------------------------------------------Ec-CCCCEEEEEEEChhhhhhhhCCCchhHHHH
Confidence 00 011255778899999999999999999999
Q ss_pred HhHhCCeEEEc
Q 019747 283 SQISGARIKVS 293 (336)
Q Consensus 283 ~~~sga~I~i~ 293 (336)
.+.+|-++.|.
T Consensus 126 ~~l~~~~~dI~ 136 (141)
T TIGR01952 126 KELAKRHHDID 136 (141)
T ss_pred HHHhcCccCCe
Confidence 99999988774
No 50
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.45 E-value=0.00032 Score=72.00 Aligned_cols=91 Identities=14% Similarity=0.127 Sum_probs=73.4
Q ss_pred HHHHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCE-EEEeccCCCCCCCCceEEE
Q 019747 95 LRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAV-IKISRLDHSYYGLNDRLVT 173 (336)
Q Consensus 95 ~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~-I~i~~~~~~~~~~~~r~v~ 173 (336)
.+|+..|++.|.+.+...+...+...+....+.||.+.++.|||.+|.+|+.|.++||+. |.+.. +-.|.
T Consensus 658 ~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d---------dg~V~ 728 (891)
T PLN00207 658 KDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD---------DGTVK 728 (891)
T ss_pred HHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC---------CeeEE
Confidence 445556676777776665555555667888999999999999999999999999999998 88864 45688
Q ss_pred EEcC-HHHHHHHHHHHHHHhhc
Q 019747 174 LTGT-LDEQMRALELILLKLSE 194 (336)
Q Consensus 174 I~G~-~~~v~~A~~~i~~~l~~ 194 (336)
|.+. .+.+++|+++|..++..
T Consensus 729 I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 729 ITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred EEeCCHHHHHHHHHHHHHHhcC
Confidence 8886 79999999999988763
No 51
>PRK00106 hypothetical protein; Provisional
Probab=97.31 E-value=0.0014 Score=64.05 Aligned_cols=67 Identities=22% Similarity=0.370 Sum_probs=57.3
Q ss_pred CceEEEEEecc-CcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHh
Q 019747 255 RTNSLTIGVAD-EHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAY 329 (336)
Q Consensus 255 ~~~~~~v~vp~-~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~ 329 (336)
...+..|.+|+ ++-|+|||+.|.||+.+...||+.|.|++ ++..|+|+| .|=--+.|+.-+..+|..
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--------tp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD--------TPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC--------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 34667889998 67799999999999999999999999976 467888999 888888898888877764
No 52
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=97.29 E-value=0.00038 Score=62.51 Aligned_cols=70 Identities=19% Similarity=0.306 Sum_probs=58.3
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHhhh
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAYAS 331 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~~~ 331 (336)
....+.+++.+.|.|||++|.+.+.|+++|++.|.++.+ +++...|+|+| ..++|..|...|...|.+.-
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p-----~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP-----NTNKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC-----CCCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 556788999999999999999999999999999999774 33445555555 89999999999988877654
No 53
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.29 E-value=0.00099 Score=65.68 Aligned_cols=101 Identities=18% Similarity=0.172 Sum_probs=80.1
Q ss_pred EEEEeeHH--------HHHHHHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEE
Q 019747 85 IMISGTID--------EILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIK 156 (336)
Q Consensus 85 i~I~G~~~--------~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~ 156 (336)
+.|.|-.. +...|+..|+..+.+.+...+...+...+....+.|+.+.++-+||++|.+|++|.++||++|.
T Consensus 507 iKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Id 586 (692)
T COG1185 507 IKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKID 586 (692)
T ss_pred eeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEE
Confidence 66667533 3355667788777777766544455556778889999999999999999999999999999999
Q ss_pred EeccCCCCCCCCceEEEEEcCH-HHHHHHHHHHHHHhhc
Q 019747 157 ISRLDHSYYGLNDRLVTLTGTL-DEQMRALELILLKLSE 194 (336)
Q Consensus 157 i~~~~~~~~~~~~r~v~I~G~~-~~v~~A~~~i~~~l~~ 194 (336)
+.. +..|.|.++. +.+.+|++.|..+..+
T Consensus 587 ied---------dGtv~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 587 IED---------DGTVKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred ecC---------CCcEEEEecchHHHHHHHHHHHHHHhh
Confidence 984 3568888884 8889999999999855
No 54
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.28 E-value=0.00058 Score=70.14 Aligned_cols=64 Identities=20% Similarity=0.393 Sum_probs=56.5
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCe-EEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHh
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGAR-IKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAY 329 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~-I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~ 329 (336)
....+.||.++++.|||.||.+||.|.++||+. |.+.+ +-.|.|.+ ..+.++.|+.+|.+++..
T Consensus 685 ~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d---------dg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 685 LIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD---------DGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred eeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC---------CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 677899999999999999999999999999999 99854 56777777 899999999999888653
No 55
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=97.28 E-value=0.0014 Score=64.23 Aligned_cols=67 Identities=22% Similarity=0.395 Sum_probs=56.9
Q ss_pred CceEEEEEecc-CcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHh
Q 019747 255 RTNSLTIGVAD-EHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAY 329 (336)
Q Consensus 255 ~~~~~~v~vp~-~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~ 329 (336)
...+..|.+|+ ++-|+|||+.|.||+.+...||+.|.|++ ++..|+|+| .|=--+.|+.-+..+|..
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd--------tp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--------TPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC--------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 34667889998 67799999999999999999999999975 467888999 888888888888877764
No 56
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.24 E-value=0.00042 Score=60.51 Aligned_cols=44 Identities=16% Similarity=0.387 Sum_probs=38.7
Q ss_pred CCCCCcEEEEEEEecC------ccceeecCCChHHHHHHHHhCCeEEEcC
Q 019747 29 DPTEKPTYIRFLVSNP------LAGAVIGKGGSTINDFQSQSGARIQLSR 72 (336)
Q Consensus 29 ~~~~~~~~~~i~ip~~------~vg~iIGk~G~~Ik~I~~~tg~~I~i~~ 72 (336)
+...-.++.+|+||.. +||.|+|++|.++|+|+++|||+|.|.-
T Consensus 86 ~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrG 135 (259)
T KOG1588|consen 86 SGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRG 135 (259)
T ss_pred cCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEec
Confidence 3455568899999988 7999999999999999999999999964
No 57
>PRK12704 phosphodiesterase; Provisional
Probab=97.23 E-value=0.0016 Score=63.97 Aligned_cols=66 Identities=24% Similarity=0.395 Sum_probs=55.2
Q ss_pred ceEEEEEecc-CcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHh
Q 019747 256 TNSLTIGVAD-EHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAY 329 (336)
Q Consensus 256 ~~~~~v~vp~-~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~ 329 (336)
..+..|.+|+ ++-|+|||+.|.||+.+...||+.|.|++ ++..|+|+| .|---+.|+..+...+..
T Consensus 209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd--------tp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--------TPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC--------CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 4567888998 67799999999999999999999999975 467888999 777777888877766653
No 58
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=97.22 E-value=0.00091 Score=56.54 Aligned_cols=102 Identities=22% Similarity=0.248 Sum_probs=69.3
Q ss_pred EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeH-HHHHHHHHHHHHHHHhhcccccc
Q 019747 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTI-DEILRAVDLVIDKLLTELHAEDQ 114 (336)
Q Consensus 36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~-~~v~~A~~~I~~~i~~~~~~~~~ 114 (336)
.+-+.+-.+.+|..||++|++|+.|.++.|=+|.+-...+ ++ +-+..|+.-. .+..-...
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~--------------d~~~fI~nal~Pa--~v~~V~~~--- 137 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSE--------------DPAEFIKNALAPA--EVLSVNIK--- 137 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCC--------------CHHHHHHHhcCcc--eEeEEEEE---
Confidence 3444555567899999999999999999998888754321 11 1122222100 00000000
Q ss_pred CCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEec
Q 019747 115 ADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR 159 (336)
Q Consensus 115 ~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~ 159 (336)
..+. ....+.||.+..+..||++|.+++-+.+-||-++.|..
T Consensus 138 --~~d~-~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 138 --EDDG-HVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred --eCCC-cEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 0012 26778899999999999999999999999999999976
No 59
>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=97.20 E-value=0.00072 Score=46.30 Aligned_cols=37 Identities=27% Similarity=0.451 Sum_probs=34.5
Q ss_pred cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEE
Q 019747 34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQL 70 (336)
Q Consensus 34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i 70 (336)
...+.+.|+.+..|..|||+|.+|+.+++.++-+|.+
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 4689999999999999999999999999999988876
No 60
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.18 E-value=0.00071 Score=62.74 Aligned_cols=66 Identities=30% Similarity=0.402 Sum_probs=55.3
Q ss_pred ceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHH
Q 019747 256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKV 327 (336)
Q Consensus 256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i 327 (336)
.....+.|-+.+||.|||++|++|+.||..|.++|+|.+- ..+..|+|-|.-+--.+|+..|...+
T Consensus 46 e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~------~~e~kv~ifg~~~m~~kaka~id~~~ 111 (629)
T KOG0336|consen 46 EFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC------DLEVKVTIFGINHMRKKAKASIDRGQ 111 (629)
T ss_pred CCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc------CceeEEEEechHHHHHHHHhhHhhhh
Confidence 3456777889999999999999999999999999999874 45788999998777777777765544
No 61
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.17 E-value=0.00052 Score=63.62 Aligned_cols=66 Identities=24% Similarity=0.343 Sum_probs=53.7
Q ss_pred CCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHH
Q 019747 31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVI 102 (336)
Q Consensus 31 ~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~ 102 (336)
-.+++.+.+.|-+++||.|||++|++||.|+..|+++|++.+. ..+-.++|.|...--.+|...|.
T Consensus 43 g~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~------~~e~kv~ifg~~~m~~kaka~id 108 (629)
T KOG0336|consen 43 GGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC------DLEVKVTIFGINHMRKKAKASID 108 (629)
T ss_pred CCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc------CceeEEEEechHHHHHHHHhhHh
Confidence 3456788899999999999999999999999999999999753 35677889998665555555554
No 62
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.08 E-value=0.0016 Score=64.19 Aligned_cols=65 Identities=26% Similarity=0.399 Sum_probs=56.9
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcC-hHhHHHHHHHHHHHHHhh
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGP-QRSIRTAESMIMQKVAYA 330 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~i~~~ 330 (336)
...++.|+.+.++.+||++|.+|++|.++||++|.|.+ +-+|.|.++ .+.+..|+..|.+++++.
T Consensus 552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied---------dGtv~i~~s~~~~~~~ak~~I~~i~~e~ 617 (692)
T COG1185 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED---------DGTVKIAASDGESAKKAKERIEAITREV 617 (692)
T ss_pred ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC---------CCcEEEEecchHHHHHHHHHHHHHHhhc
Confidence 56788899999999999999999999999999999953 567888885 589999999999888654
No 63
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=97.05 E-value=0.00096 Score=60.01 Aligned_cols=71 Identities=20% Similarity=0.333 Sum_probs=57.5
Q ss_pred cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhh
Q 019747 34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE 108 (336)
Q Consensus 34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~ 108 (336)
....-++++....+.|||++|.|-++|+++|+|+|.++++.+ ..+.++.+.+..++|.+|.++|...|...
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~----n~~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT----NKEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC----CcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 467788999999999999999999999999999999987652 33444555567888999999998444443
No 64
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.99 E-value=0.0018 Score=57.17 Aligned_cols=63 Identities=19% Similarity=0.241 Sum_probs=53.5
Q ss_pred EEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHhh
Q 019747 259 LTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAYA 330 (336)
Q Consensus 259 ~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~~ 330 (336)
..+.||.++++.+||++|.+|+.|.+.+++.|.+-. +-.|-|.+ +.+.++.|..+|+..-++.
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~---------NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ---------NGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC---------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 578899999999999999999999999999999943 56777888 5669999999997655443
No 65
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.96 E-value=0.0045 Score=54.22 Aligned_cols=42 Identities=19% Similarity=0.399 Sum_probs=36.3
Q ss_pred CceEEEEEecc------CcccceeccCCchHHHHHhHhCCeEEEccCC
Q 019747 255 RTNSLTIGVAD------EHIGFVVGRGGRNIMEISQISGARIKVSDRG 296 (336)
Q Consensus 255 ~~~~~~v~vp~------~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~ 296 (336)
...+.+|.||- ++||+|+|.+|.++|+|+++|||+|.|-.++
T Consensus 90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrg 137 (259)
T KOG1588|consen 90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRG 137 (259)
T ss_pred eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCC
Confidence 34667777775 4999999999999999999999999998764
No 66
>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=96.94 E-value=0.0014 Score=44.89 Aligned_cols=36 Identities=28% Similarity=0.674 Sum_probs=33.9
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEE
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKV 292 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i 292 (336)
....+.|+.+..|..|||+|.+|+.+++.+|-+|.+
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 678999999999999999999999999999988876
No 67
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.92 E-value=0.0018 Score=66.02 Aligned_cols=91 Identities=19% Similarity=0.180 Sum_probs=70.3
Q ss_pred HHHHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEE
Q 019747 95 LRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTL 174 (336)
Q Consensus 95 ~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I 174 (336)
.+++..|++.|.+.+...+.......+....+.||.+.++.+||.+|.+|++|.++||+.|.+.. +..|.|
T Consensus 527 ~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d---------~G~v~i 597 (693)
T PRK11824 527 KEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED---------DGTVKI 597 (693)
T ss_pred HHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC---------CceEEE
Confidence 45566677777777665544344445566778889999999999999999999999999877753 356788
Q ss_pred EcC-HHHHHHHHHHHHHHhhc
Q 019747 175 TGT-LDEQMRALELILLKLSE 194 (336)
Q Consensus 175 ~G~-~~~v~~A~~~i~~~l~~ 194 (336)
.+. .+.+.+|.+.|..+..+
T Consensus 598 ~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 598 AATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred EcccHHHHHHHHHHHHHhccc
Confidence 885 78899999999888753
No 68
>PRK00106 hypothetical protein; Provisional
Probab=96.91 E-value=0.0052 Score=60.24 Aligned_cols=68 Identities=19% Similarity=0.242 Sum_probs=56.0
Q ss_pred CCceeEEEEEec-CccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHhhc
Q 019747 119 GTKTKLRLIVPN-SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELILLKLSE 194 (336)
Q Consensus 119 ~~~~~~~l~ip~-~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~-~~~v~~A~~~i~~~l~~ 194 (336)
.......+.+|+ ++-|+|||+.|.+|+.++..||+.+.|+. +...|+++|. |---+-|+..+..++.+
T Consensus 222 ~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--------tp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 222 TEQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD--------TPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred hhheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC--------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 345666788998 67799999999999999999999999987 5567889984 77777788877777765
No 69
>PRK12704 phosphodiesterase; Provisional
Probab=96.84 E-value=0.0053 Score=60.38 Aligned_cols=67 Identities=21% Similarity=0.207 Sum_probs=53.3
Q ss_pred CceeEEEEEec-CccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHhhc
Q 019747 120 TKTKLRLIVPN-SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELILLKLSE 194 (336)
Q Consensus 120 ~~~~~~l~ip~-~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~-~~~v~~A~~~i~~~l~~ 194 (336)
......+.+|+ +.-|+|||+.|.+|+.++..||+.|.|+. +...|.++|. +-.-+.|+..+..++.+
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd--------tp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--------TPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC--------CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 44566788897 66799999999999999999999999987 5678889984 55555677766666654
No 70
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.80 E-value=0.0072 Score=59.37 Aligned_cols=68 Identities=21% Similarity=0.220 Sum_probs=55.2
Q ss_pred CCceeEEEEEec-CccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHhhc
Q 019747 119 GTKTKLRLIVPN-SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELILLKLSE 194 (336)
Q Consensus 119 ~~~~~~~l~ip~-~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~-~~~v~~A~~~i~~~l~~ 194 (336)
.......+.+|+ ++-|+|||+.|.+|+.++..||+.+.|+. +...|+|++- |---+-|+..+..++.+
T Consensus 201 ~e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd--------tp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 201 AETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--------TPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred hhheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC--------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 344666788897 66799999999999999999999999987 5567888884 66667777777777754
No 71
>PRK00468 hypothetical protein; Provisional
Probab=96.61 E-value=0.0026 Score=45.28 Aligned_cols=36 Identities=22% Similarity=0.307 Sum_probs=30.9
Q ss_pred CCCCcEEEEEEEecCccceeecCCChHHHHHHHHhC
Q 019747 30 PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSG 65 (336)
Q Consensus 30 ~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg 65 (336)
..++.+.+++.+..+.+|.||||+|.+|+.||.--.
T Consensus 25 ~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~ 60 (75)
T PRK00468 25 EGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVK 60 (75)
T ss_pred eCCCeEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence 345668999999999999999999999999996443
No 72
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.61 E-value=0.0036 Score=63.80 Aligned_cols=64 Identities=30% Similarity=0.428 Sum_probs=54.3
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHh
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAY 329 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~ 329 (336)
....+.||.+.++.+||.||.+||.|.++||+.|.+.+ +-.|.|.+ ..+.++.|+.+|......
T Consensus 554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d---------~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED---------DGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC---------CceEEEEcccHHHHHHHHHHHHHhccc
Confidence 45567779999999999999999999999999888843 46677777 789999999999887753
No 73
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.57 E-value=0.0044 Score=54.65 Aligned_cols=64 Identities=27% Similarity=0.345 Sum_probs=52.4
Q ss_pred EEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEee-HHHHHHHHHHHHHHHHhhcc
Q 019747 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT-IDEILRAVDLVIDKLLTELH 110 (336)
Q Consensus 37 ~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~-~~~v~~A~~~I~~~i~~~~~ 110 (336)
+.+.||.++++.+||++|.+|+.|.++|++.|.+-. +-.|-|.+. .+.+.+|..+|. .+.++.|
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~---------NG~VwI~~~~~~~~~~a~~~I~-~~e~~~~ 211 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ---------NGRIWIKGPDEEDEEIAIEAIK-KIEREAH 211 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC---------CcEEEEeeCCHHHHHHHHHHHH-HHHhhhh
Confidence 568899999999999999999999999999999943 345777765 567888888887 6666644
No 74
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.57 E-value=0.0074 Score=51.10 Aligned_cols=37 Identities=24% Similarity=0.526 Sum_probs=34.7
Q ss_pred EEEEEeccCcccceeccCCchHHHHHhHhCCeEEEcc
Q 019747 258 SLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSD 294 (336)
Q Consensus 258 ~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~ 294 (336)
...+.||.+..+..|||+|.+++.+.+.||-++.|..
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 6788899999999999999999999999999999965
No 75
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.55 E-value=0.005 Score=51.72 Aligned_cols=41 Identities=24% Similarity=0.387 Sum_probs=35.4
Q ss_pred CcEEEEEEEecC------ccceeecCCChHHHHHHHHhCCeEEEcCC
Q 019747 33 KPTYIRFLVSNP------LAGAVIGKGGSTINDFQSQSGARIQLSRS 73 (336)
Q Consensus 33 ~~~~~~i~ip~~------~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~ 73 (336)
..++-++.||.+ +||+|||+.|+|+|+|++.++|+|-|...
T Consensus 146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 346678888865 79999999999999999999999999643
No 76
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=96.54 E-value=0.11 Score=45.08 Aligned_cols=129 Identities=13% Similarity=0.113 Sum_probs=90.9
Q ss_pred EEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhccccccCC
Q 019747 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQAD 116 (336)
Q Consensus 37 ~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~ 116 (336)
+.+.++....-++...+|..++.|-...|++|.+.. .+..+.|+|+...+..+...|.+.+..-
T Consensus 28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~--------~~~~i~I~g~k~~~~~i~~~i~~~l~~i-------- 91 (210)
T PF14611_consen 28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR--------SENRIRITGTKSTAEYIEASINEILSNI-------- 91 (210)
T ss_pred eEEEecchheeeeecCCchHHHHHHHhcCceEEEec--------CCcEEEEEccHHHHHHHHHHHHHHHhhc--------
Confidence 344445788899999999999999888899999964 3467999999999988888888544443
Q ss_pred CCCCceeEEEEEecCccceee----cCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEE-----cCHHHHHHHHHH
Q 019747 117 DVGTKTKLRLIVPNSSCGSII----GKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT-----GTLDEQMRALEL 187 (336)
Q Consensus 117 ~~~~~~~~~l~ip~~~~g~iI----G~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~-----G~~~~v~~A~~~ 187 (336)
.+..+.++.-....-. -.....++.|++.|++.|...++ ...+.|. -....+..|..+
T Consensus 92 -----~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~--------~~~~~i~~~~~~~~~~~~~~a~Rl 158 (210)
T PF14611_consen 92 -----RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD--------GNKLKISWLASPENEKRADRAKRL 158 (210)
T ss_pred -----EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC--------CCeEEEEEEeeccccchHHHHHHH
Confidence 2334444422111111 12356789999999999998862 2233333 457788889988
Q ss_pred HHHHhhc
Q 019747 188 ILLKLSE 194 (336)
Q Consensus 188 i~~~l~~ 194 (336)
+...+..
T Consensus 159 L~~a~~~ 165 (210)
T PF14611_consen 159 LLWALDY 165 (210)
T ss_pred HHHhccC
Confidence 8888753
No 77
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.54 E-value=0.0054 Score=57.06 Aligned_cols=92 Identities=20% Similarity=0.199 Sum_probs=64.4
Q ss_pred ccceeecCCChHHHHHHHHh-CCeEEEcCCCCCCCCCCceEEEEEeeHH-HHHHHHHHHHHHHHhhccccccCCCCCCce
Q 019747 45 LAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTID-EILRAVDLVIDKLLTELHAEDQADDVGTKT 122 (336)
Q Consensus 45 ~vg~iIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~~~~~r~i~I~G~~~-~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~ 122 (336)
-+|..||++|++|+.|.++. |=+|.+-..++ ++. =+..|+.-. .+.. -..+ +...
T Consensus 252 PvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~--------------D~~~fI~Nal~Pa--~V~~------V~i~-~~~~ 308 (374)
T PRK12328 252 PIGATVGVKGVRINAVSKELNGENIDCIEYSN--------------VPEIFIARALAPA--IISS------VKIE-EEEK 308 (374)
T ss_pred hHHhhcCCCcchHHHHHHHhCCCeEEEEEcCC--------------CHHHHHHHhCCCc--eeeE------EEEc-CCCc
Confidence 58999999999999999998 88888854432 011 111111100 0000 0000 2235
Q ss_pred eEEEEEecCccceeecCCChHHHHHHHhcCCEEEEec
Q 019747 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR 159 (336)
Q Consensus 123 ~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~ 159 (336)
...+.||.++.+..||++|.+++-..+-||.+|.|..
T Consensus 309 ~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s 345 (374)
T PRK12328 309 KAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNE 345 (374)
T ss_pred EEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEE
Confidence 6788999999999999999999999999999999987
No 78
>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=96.49 E-value=0.0065 Score=56.40 Aligned_cols=93 Identities=20% Similarity=0.304 Sum_probs=64.7
Q ss_pred ccceeecCCChHHHHHHHHh-CCeEEEcCCCCCCCCCCceEEEEEeeHH-HHHHHHHHHHHHHHhhccccccCCCCCCce
Q 019747 45 LAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTID-EILRAVDLVIDKLLTELHAEDQADDVGTKT 122 (336)
Q Consensus 45 ~vg~iIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~~~~~r~i~I~G~~~-~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~ 122 (336)
-+|..||++|++|+.|.++. |=+|.+-..++ ++. -+..|+.-.. +..- .-.+ ....
T Consensus 244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~--------------d~~~fi~nal~Pa~--v~~v-----~i~~-~~~~ 301 (341)
T TIGR01953 244 PVGACVGPKGSRIQAISKELNGEKIDIIEYSD--------------DPAEFIANALSPAK--VISV-----EVLD-EDKH 301 (341)
T ss_pred cceeeECCCCchHHHHHHHhCCCeEEEEEcCC--------------CHHHHHHHhcCCce--EEEE-----EEEc-CCCc
Confidence 48999999999999999998 88888854432 111 1111111100 0000 0001 1225
Q ss_pred eEEEEEecCccceeecCCChHHHHHHHhcCCEEEEec
Q 019747 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR 159 (336)
Q Consensus 123 ~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~ 159 (336)
...+.||.++.+..||++|.+++-..+-||.+|.|..
T Consensus 302 ~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 302 SAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred EEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 7789999999999999999999999999999999976
No 79
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.49 E-value=0.0056 Score=57.18 Aligned_cols=94 Identities=21% Similarity=0.301 Sum_probs=65.3
Q ss_pred ccceeecCCChHHHHHHHHh-CCeEEEcCCCCCCCCCCceEEEEEeeHH-HHHHHHHHHHHHHHhhccccccCCCCCCce
Q 019747 45 LAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTID-EILRAVDLVIDKLLTELHAEDQADDVGTKT 122 (336)
Q Consensus 45 ~vg~iIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~~~~~r~i~I~G~~~-~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~ 122 (336)
-+|+.||++|.+|+.|.++. |=+|.+-..++ ++. -+..|+.-.. +..- .-.+ +...
T Consensus 246 pvGa~iG~~G~rI~~i~~el~gekIdiv~~s~--------------d~~~fi~nal~Pa~--v~~v-----~i~~-~~~~ 303 (362)
T PRK12327 246 AKGACVGPKGQRVQNIVSELKGEKIDIIDWSE--------------DPAEFVANALSPAK--VVSV-----EVDD-EEEK 303 (362)
T ss_pred chheeECCCChhHHHHHHHhCCCeEEEEEcCC--------------CHHHHHHHhCCCce--EEEE-----EEEc-CCCc
Confidence 58999999999999999998 88888854432 111 1111111100 0000 0001 2235
Q ss_pred eEEEEEecCccceeecCCChHHHHHHHhcCCEEEEecc
Q 019747 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRL 160 (336)
Q Consensus 123 ~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~ 160 (336)
...+.||.++.+..||++|.+++-..+-||.+|.|...
T Consensus 304 ~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 304 AARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred EEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 67899999999999999999999999999999999873
No 80
>PRK02821 hypothetical protein; Provisional
Probab=96.43 E-value=0.0031 Score=45.06 Aligned_cols=36 Identities=25% Similarity=0.377 Sum_probs=30.9
Q ss_pred CCCcEEEEEEEecCccceeecCCChHHHHHHHHhCC
Q 019747 31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGA 66 (336)
Q Consensus 31 ~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~ 66 (336)
.++.+.+++.+..+.+|.||||+|.+|+.||.--.+
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 445588999999999999999999999999966543
No 81
>PRK12705 hypothetical protein; Provisional
Probab=96.36 E-value=0.01 Score=57.80 Aligned_cols=66 Identities=21% Similarity=0.316 Sum_probs=52.1
Q ss_pred ceEEEEEecc-CcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHh
Q 019747 256 TNSLTIGVAD-EHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAY 329 (336)
Q Consensus 256 ~~~~~v~vp~-~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~ 329 (336)
.....|.+|+ ++-|+|||+.|.||+.+...||+.|.|++ ....|+|++ .|.--+.|+..+..+|..
T Consensus 197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--------tp~~V~ls~fdp~rreia~~~l~~Li~d 264 (508)
T PRK12705 197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD--------TPEAVVISSFNPIRREIARLTLEKLLAD 264 (508)
T ss_pred heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC--------CccchhhcccCccchHHHHHHHHHHHhc
Confidence 3567788897 56699999999999999999999999976 345677777 666666777776666543
No 82
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=96.21 E-value=0.007 Score=42.98 Aligned_cols=34 Identities=35% Similarity=0.418 Sum_probs=30.4
Q ss_pred CCCcEEEEEEEecCccceeecCCChHHHHHHHHh
Q 019747 31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQS 64 (336)
Q Consensus 31 ~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~t 64 (336)
.+..+.+++-+.....|.||||+|.+|+.||.--
T Consensus 26 ~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred cCCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 3677889999999999999999999999999543
No 83
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.16 E-value=0.017 Score=53.89 Aligned_cols=40 Identities=20% Similarity=0.383 Sum_probs=36.7
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCC
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRG 296 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~ 296 (336)
....+.||.+..+..|||+|.|++-..+.||.+|.|..-+
T Consensus 308 ~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~ 347 (374)
T PRK12328 308 KKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG 347 (374)
T ss_pred cEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence 4678899999999999999999999999999999998854
No 84
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.12 E-value=0.0078 Score=57.01 Aligned_cols=93 Identities=23% Similarity=0.262 Sum_probs=64.2
Q ss_pred ccceeecCCChHHHHHHHHh-CCeEEEcCCCCCCCCCCceEEEEEeeHH-HHHHHHHHHHHHHHhhccccccCCCCCCce
Q 019747 45 LAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTID-EILRAVDLVIDKLLTELHAEDQADDVGTKT 122 (336)
Q Consensus 45 ~vg~iIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~~~~~r~i~I~G~~~-~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~ 122 (336)
-+|..||++|++|+.|.++. |=+|.|-..++ ++. =|..|+.-. .+..- ...+ ....
T Consensus 278 PvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~--------------Dp~~fI~NaLsPA--~V~~V-----~i~~-~~~k 335 (449)
T PRK12329 278 PVGACIGARGSRIQAVVNELRGEKIDVIRWSP--------------DPATYIANALSPA--RVDEV-----RLVD-PEGR 335 (449)
T ss_pred hhhccCCCCcchHHHHHHHhCCCeEEEEEcCC--------------CHHHHHHHhcCCc--eeeEE-----EEEc-CCCc
Confidence 58999999999999999998 88888854431 111 111111110 00000 0001 1224
Q ss_pred eEEEEEecCccceeecCCChHHHHHHHhcCCEEEEec
Q 019747 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR 159 (336)
Q Consensus 123 ~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~ 159 (336)
...+.||.++.+..||++|.+++-..+-||.+|.|..
T Consensus 336 ~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 336 HAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred EEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 5789999999999999999999999999999999976
No 85
>PRK01064 hypothetical protein; Provisional
Probab=96.08 E-value=0.0077 Score=43.20 Aligned_cols=34 Identities=26% Similarity=0.420 Sum_probs=30.3
Q ss_pred CCCcEEEEEEEecCccceeecCCChHHHHHHHHh
Q 019747 31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQS 64 (336)
Q Consensus 31 ~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~t 64 (336)
.++.+.+++.|.....|.+|||+|.+|+.|+.-.
T Consensus 26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CCCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 3567899999999999999999999999999643
No 86
>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=96.02 E-value=0.022 Score=52.90 Aligned_cols=38 Identities=29% Similarity=0.593 Sum_probs=35.6
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEcc
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSD 294 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~ 294 (336)
....+.||.+..+..|||+|.|++-..+.||.+|.|..
T Consensus 301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 56789999999999999999999999999999999975
No 87
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.93 E-value=0.01 Score=49.84 Aligned_cols=31 Identities=26% Similarity=0.644 Sum_probs=28.9
Q ss_pred CcccceeccCCchHHHHHhHhCCeEEEccCC
Q 019747 266 EHIGFVVGRGGRNIMEISQISGARIKVSDRG 296 (336)
Q Consensus 266 ~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~ 296 (336)
++||.|||+.|.++|+|++.|+|+|-|-..+
T Consensus 163 NFVGLliGPRG~Tlk~le~~s~akIaIRG~g 193 (269)
T COG5176 163 NFVGLLIGPRGSTLKQLERISRAKIAIRGSG 193 (269)
T ss_pred ceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence 6999999999999999999999999997753
No 88
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=95.86 E-value=0.025 Score=54.57 Aligned_cols=93 Identities=16% Similarity=0.166 Sum_probs=75.0
Q ss_pred HHHHHHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEE
Q 019747 93 EILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLV 172 (336)
Q Consensus 93 ~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v 172 (336)
+...|...|++.+.+.++..+.......+....+.++.+....+||++|...|+|..+||+.-.++ +..+
T Consensus 568 ~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD----------e~t~ 637 (760)
T KOG1067|consen 568 KAREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD----------EGTF 637 (760)
T ss_pred hhhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec----------CceE
Confidence 445677788888888877776566666778889999999999999999999999999999655554 3567
Q ss_pred EEEcC-HHHHHHHHHHHHHHhhcC
Q 019747 173 TLTGT-LDEQMRALELILLKLSED 195 (336)
Q Consensus 173 ~I~G~-~~~v~~A~~~i~~~l~~~ 195 (336)
.|... ..+.++|++.|..++...
T Consensus 638 ~i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 638 SIFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred EEEecCHHHHHHHHHHHHHHhcCc
Confidence 77776 778899999999987653
No 89
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.76 E-value=0.03 Score=52.41 Aligned_cols=39 Identities=18% Similarity=0.438 Sum_probs=36.1
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccC
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDR 295 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~ 295 (336)
....+.||.+..+.-|||+|.|++--...||.+|.|...
T Consensus 303 ~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 303 KAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred cEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 567899999999999999999999999999999999764
No 90
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.64 E-value=0.027 Score=54.61 Aligned_cols=39 Identities=23% Similarity=0.534 Sum_probs=36.2
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccC
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDR 295 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~ 295 (336)
....+.||.+..+.-|||+|.|++...+.||.+|.|...
T Consensus 302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 467899999999999999999999999999999999764
No 91
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.63 E-value=0.028 Score=54.47 Aligned_cols=91 Identities=19% Similarity=0.275 Sum_probs=64.2
Q ss_pred ccceeecCCChHHHHHHHHh-CCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhccccc-cC-CCCCCc
Q 019747 45 LAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAED-QA-DDVGTK 121 (336)
Q Consensus 45 ~vg~iIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~~-~~-~~~~~~ 121 (336)
-+|..||++|++|+.|.++. |=+|.|-..++ ++.. .+...+.... .. .-....
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~--------------d~~~----------fi~nal~pa~v~~v~~~~~~ 301 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIILWSD--------------DPAQ----------FIINALSPAEVSSVVVDEDE 301 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEEcCC--------------CHHH----------HHHHhCCCCEEEEEEEeCCC
Confidence 48999999999999999998 78888854431 1111 1111111100 00 000112
Q ss_pred eeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEec
Q 019747 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR 159 (336)
Q Consensus 122 ~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~ 159 (336)
....+.||..+.+..||++|.+++-..+-||.+|.|..
T Consensus 302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 47789999999999999999999999999999999986
No 92
>PRK00468 hypothetical protein; Provisional
Probab=95.53 E-value=0.016 Score=41.30 Aligned_cols=33 Identities=30% Similarity=0.460 Sum_probs=28.5
Q ss_pred CceEEEEEeccCcccceeccCCchHHHHHhHhC
Q 019747 255 RTNSLTIGVADEHIGFVVGRGGRNIMEISQISG 287 (336)
Q Consensus 255 ~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sg 287 (336)
....+.+.+.++-+|+||||+|.+|+.||..-.
T Consensus 28 ~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~ 60 (75)
T PRK00468 28 QSVILELKVAPEDMGKVIGKQGRIAKAIRTVVK 60 (75)
T ss_pred CeEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence 346788999999999999999999999987654
No 93
>PRK12705 hypothetical protein; Provisional
Probab=95.52 E-value=0.033 Score=54.35 Aligned_cols=66 Identities=18% Similarity=0.185 Sum_probs=46.0
Q ss_pred CceeEEEEEec-CccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHhh
Q 019747 120 TKTKLRLIVPN-SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELILLKLS 193 (336)
Q Consensus 120 ~~~~~~l~ip~-~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~-~~~v~~A~~~i~~~l~ 193 (336)
......+.+|+ +.-|+|||+.|.+|+.++..||+.+.|+. +...|++.+. +..-+.|...+..++.
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--------tp~~V~ls~fdp~rreia~~~l~~Li~ 263 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD--------TPEAVVISSFNPIRREIARLTLEKLLA 263 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC--------CccchhhcccCccchHHHHHHHHHHHh
Confidence 44556678887 66799999999999999999999999986 3334555544 3333344444444443
No 94
>PRK02821 hypothetical protein; Provisional
Probab=95.35 E-value=0.019 Score=41.06 Aligned_cols=34 Identities=29% Similarity=0.567 Sum_probs=29.7
Q ss_pred ceEEEEEeccCcccceeccCCchHHHHHhHhCCe
Q 019747 256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGAR 289 (336)
Q Consensus 256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~ 289 (336)
...+.+.+.++-+|+||||+|.+|+.||..-.+-
T Consensus 30 ~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a~ 63 (77)
T PRK02821 30 GRTLEVRVHPDDLGKVIGRGGRTATALRTVVAAI 63 (77)
T ss_pred cEEEEEEEChhhCcceeCCCCchHHHHHHHHHHh
Confidence 3678899999999999999999999999876653
No 95
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.32 E-value=0.038 Score=52.44 Aligned_cols=38 Identities=18% Similarity=0.490 Sum_probs=35.3
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEcc
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSD 294 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~ 294 (336)
....+.||.+..+.-|||+|.|++--...||.+|.|..
T Consensus 335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 45689999999999999999999999999999999976
No 96
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=94.98 E-value=0.073 Score=51.51 Aligned_cols=64 Identities=22% Similarity=0.214 Sum_probs=54.1
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHHHHHHHHHHhh
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAESMIMQKVAYA 330 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~~ 330 (336)
....+.|+.+....+||.+|.+.|+|..+||+.-.+ ++.++.|-. +++..+.|+.+|...+...
T Consensus 597 ~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v----------De~t~~i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 597 VLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV----------DEGTFSIFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred eeeEEeecchhhheeecCccceeeeEeeeccceeee----------cCceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence 667888999999999999999999999999955554 356777776 8999999999999887653
No 97
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.65 E-value=0.042 Score=39.03 Aligned_cols=32 Identities=34% Similarity=0.581 Sum_probs=27.9
Q ss_pred ceEEEEEeccCcccceeccCCchHHHHHhHhC
Q 019747 256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISG 287 (336)
Q Consensus 256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sg 287 (336)
....++.+.+.-.|.||||+|.+|+.||-.-.
T Consensus 29 ~~~~~l~v~~~D~GkvIGk~GRti~AIRTll~ 60 (76)
T COG1837 29 TVTIELRVAPEDMGKVIGKQGRTIQAIRTLLS 60 (76)
T ss_pred eEEEEEEECcccccceecCCChhHHHHHHHHH
Confidence 46688899999999999999999999987654
No 98
>PRK01064 hypothetical protein; Provisional
Probab=94.42 E-value=0.041 Score=39.46 Aligned_cols=33 Identities=30% Similarity=0.444 Sum_probs=28.5
Q ss_pred CceEEEEEeccCcccceeccCCchHHHHHhHhC
Q 019747 255 RTNSLTIGVADEHIGFVVGRGGRNIMEISQISG 287 (336)
Q Consensus 255 ~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sg 287 (336)
....+.+.|.+.-.|.+|||+|.+|+.||....
T Consensus 28 ~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 28 HTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred CEEEEEEEECcccceEEECCCCccHHHHHHHHH
Confidence 346788999999999999999999999988644
No 99
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=94.41 E-value=0.02 Score=40.66 Aligned_cols=35 Identities=34% Similarity=0.385 Sum_probs=29.4
Q ss_pred CCcEEEEEEEecCccceeecCCChHHHHHHHHhCC
Q 019747 32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGA 66 (336)
Q Consensus 32 ~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~ 66 (336)
.+...+.+.+..+..|.+|||+|.+++.||.-.+.
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 45567888889999999999999999999965543
No 100
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=93.90 E-value=0.023 Score=59.08 Aligned_cols=70 Identities=24% Similarity=0.162 Sum_probs=58.5
Q ss_pred ceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHH
Q 019747 256 TNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKV 327 (336)
Q Consensus 256 ~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i 327 (336)
....++.+|-....+|||++|.+|+.++..|||.|+|.+-+ ..+..+|.+.+.|.++.+..|...|.-.+
T Consensus 1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq--~~Nqaers~~~kg~p~~~r~a~~~I~~~i 1408 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ--PDNQAERSKAPKGRPPSQRVATSPIGLPI 1408 (2131)
T ss_pred ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcC--CccchhhhcccCCCChhhhhhhcccccee
Confidence 34567788888899999999999999999999999998832 12356899999999999999988775544
No 101
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=93.79 E-value=0.13 Score=45.41 Aligned_cols=51 Identities=14% Similarity=0.325 Sum_probs=46.8
Q ss_pred cceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHh
Q 019747 269 GFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAY 329 (336)
Q Consensus 269 g~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~ 329 (336)
.++||.+|++++.|+-.|.|.|-++ ..+|.+.|+...+..++..+.+.+.+
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVq----------G~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQ----------GNTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEee----------CcEEEeecCcchHHHHHHHHHHHHhc
Confidence 6789999999999999999999995 36899999999999999999998865
No 102
>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=93.38 E-value=0.17 Score=34.69 Aligned_cols=35 Identities=29% Similarity=0.337 Sum_probs=28.5
Q ss_pred cEEEEEEEecCccceeecCCChHHHHHHHHhCCeE
Q 019747 34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARI 68 (336)
Q Consensus 34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I 68 (336)
.....+.+.....|.+||++|.+|+.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 45666667666789999999999999999988544
No 103
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=93.05 E-value=0.066 Score=44.88 Aligned_cols=55 Identities=25% Similarity=0.491 Sum_probs=49.2
Q ss_pred cCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHh
Q 019747 265 DEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAY 329 (336)
Q Consensus 265 ~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~ 329 (336)
+..+|+|+||+|.+--.|.+.|.++|.+. +..|.|-|+.+++..|+..|..+|..
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVla----------d~kIHiLG~~~niriAR~avcsLIlG 231 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA----------DSKIHILGAFQNIRIARDAVCSLILG 231 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEec----------CceEEEeecchhhHHHHHhhHhhhcc
Confidence 34789999999999999999999999994 47899999999999999999887654
No 104
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=92.98 E-value=0.076 Score=55.41 Aligned_cols=73 Identities=19% Similarity=0.130 Sum_probs=59.9
Q ss_pred CCCCCCcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHH
Q 019747 28 SDPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVI 102 (336)
Q Consensus 28 ~~~~~~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~ 102 (336)
+.+.......++.+|......|||++|.+|..++.-||+.|++.+-.. ....||.+.+.|.++....|...|.
T Consensus 1333 ~ss~~~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~--~Nqaers~~~kg~p~~~r~a~~~I~ 1405 (2131)
T KOG4369|consen 1333 DSSQVPANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQP--DNQAERSKAPKGRPPSQRVATSPIG 1405 (2131)
T ss_pred ccccCcccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCC--ccchhhhcccCCCChhhhhhhcccc
Confidence 344445566788999999999999999999999999999999975221 1146899999999999998887776
No 105
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=92.95 E-value=0.056 Score=38.29 Aligned_cols=36 Identities=14% Similarity=0.425 Sum_probs=30.3
Q ss_pred CceEEEEEeccCcccceeccCCchHHHHHhHhCCeE
Q 019747 255 RTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARI 290 (336)
Q Consensus 255 ~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I 290 (336)
......+.+..+..|.||||+|.+|+.||...+.-+
T Consensus 27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~ 62 (73)
T PF13083_consen 27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAA 62 (73)
T ss_dssp TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHH
T ss_pred CceEEEEEECCCccceEECCCCeeHHHHHHHHHHHH
Confidence 346788889999999999999999999988766443
No 106
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=92.86 E-value=0.12 Score=36.15 Aligned_cols=39 Identities=28% Similarity=0.491 Sum_probs=30.7
Q ss_pred eEEEEEeccCc-----ccceeccCCchHHHHHhHh-CCeEEEccC
Q 019747 257 NSLTIGVADEH-----IGFVVGRGGRNIMEISQIS-GARIKVSDR 295 (336)
Q Consensus 257 ~~~~v~vp~~~-----vg~IIGk~G~~I~~I~~~s-ga~I~i~~~ 295 (336)
....+.|-... +|..||++|.+|+.|.++. |-+|++-.-
T Consensus 3 ~r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~ 47 (69)
T PF13184_consen 3 NRTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY 47 (69)
T ss_dssp TEEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred ceEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence 34566677766 8999999999999999999 999998763
No 107
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=92.81 E-value=0.26 Score=42.89 Aligned_cols=61 Identities=23% Similarity=0.334 Sum_probs=45.8
Q ss_pred EEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHH-HHHHHHHHHHHHHhh
Q 019747 38 RFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDE-ILRAVDLVIDKLLTE 108 (336)
Q Consensus 38 ~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~-v~~A~~~I~~~i~~~ 108 (336)
-+.||...|..+||++|+.++.|.++++|.|-+-. +-.|-|.+..+. ...|.+.|. .+..+
T Consensus 149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~---------NG~IWV~~~~~~~e~~~~~aI~-~ie~e 210 (239)
T COG1097 149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ---------NGRIWVDGENESLEELAIEAIR-KIERE 210 (239)
T ss_pred EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec---------CCEEEecCCCcchHHHHHHHHH-HHhhh
Confidence 46889999999999999999999999999999953 334667776553 444555555 44444
No 108
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=92.57 E-value=0.1 Score=36.52 Aligned_cols=38 Identities=29% Similarity=0.417 Sum_probs=30.1
Q ss_pred EEEEEEecCc-----cceeecCCChHHHHHHHHh-CCeEEEcCC
Q 019747 36 YIRFLVSNPL-----AGAVIGKGGSTINDFQSQS-GARIQLSRS 73 (336)
Q Consensus 36 ~~~i~ip~~~-----vg~iIGk~G~~Ik~I~~~t-g~~I~i~~~ 73 (336)
..++.|-... +|..||++|.+|+.|.++. |-+|++-..
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~ 47 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY 47 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence 3567777777 9999999999999999999 899988544
No 109
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=92.52 E-value=0.36 Score=42.07 Aligned_cols=47 Identities=15% Similarity=0.357 Sum_probs=40.2
Q ss_pred EEEEeccCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChH
Q 019747 259 LTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQR 314 (336)
Q Consensus 259 ~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~ 314 (336)
.-+.|++..|-++||++|++++.|.+.++|+|.+-. +-.|=|.|..+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~---------NG~IWV~~~~~ 194 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ---------NGRIWVDGENE 194 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec---------CCEEEecCCCc
Confidence 567899999999999999999999999999999954 45666777655
No 110
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=92.30 E-value=0.096 Score=43.94 Aligned_cols=149 Identities=11% Similarity=0.067 Sum_probs=88.3
Q ss_pred cEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhh-cccc
Q 019747 34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE-LHAE 112 (336)
Q Consensus 34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~-~~~~ 112 (336)
.-+-++.||.+....+=--==..---|-+..+.+|.+.-... ...-|.+.-+-++.+++++...|...+... +...
T Consensus 73 ~e~Rkvpvpp~r~tplk~~W~kIytPive~lklqiRmNlK~r---~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~DA 149 (252)
T KOG3273|consen 73 IETRKVPVPPHRYTPLKDNWMKIYTPIVEHLKLQIRMNLKAR---SVELRTCKDTEDPSALQKGADFVRAFILGFDIDDA 149 (252)
T ss_pred cceeeccCCcccCChHHHhhHhhhhHHHHhhhheeEeecccc---eeEeecCCCCCChHHHHHHHHHHHHHHhCCcchhH
Confidence 456778888887643321111112234567777887742211 011233333345667777776666444332 0000
Q ss_pred ------cc--CCCC--CCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHH
Q 019747 113 ------DQ--ADDV--GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQM 182 (336)
Q Consensus 113 ------~~--~~~~--~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~ 182 (336)
++ .... .+..+++=.=-+..+|+|.|++|.+--.|+..|.++|.+.. ..+.|-|..+++.
T Consensus 150 iALlrlddlflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVlad----------~kIHiLG~~~nir 219 (252)
T KOG3273|consen 150 IALLRLDDLFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLAD----------SKIHILGAFQNIR 219 (252)
T ss_pred HHHHhhhhhhheeeeecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEecC----------ceEEEeecchhhH
Confidence 00 0000 01111111111356899999999999999999999999974 5799999999999
Q ss_pred HHHHHHHHHhhcC
Q 019747 183 RALELILLKLSED 195 (336)
Q Consensus 183 ~A~~~i~~~l~~~ 195 (336)
.|+..|..++-..
T Consensus 220 iAR~avcsLIlGs 232 (252)
T KOG3273|consen 220 IARDAVCSLILGS 232 (252)
T ss_pred HHHHhhHhhhccC
Confidence 9999999998654
No 111
>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=92.03 E-value=0.49 Score=37.99 Aligned_cols=39 Identities=28% Similarity=0.475 Sum_probs=34.2
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccC
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDR 295 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~ 295 (336)
.+.++.|-...-|.+||++|.++++|...||-.-.+-+.
T Consensus 76 ~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 76 DTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred CCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 456788888899999999999999999999988887664
No 112
>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=91.97 E-value=0.2 Score=35.92 Aligned_cols=34 Identities=24% Similarity=0.352 Sum_probs=27.2
Q ss_pred EEEEEEecCccceeecCCChHHHHHHHHhCCeEE
Q 019747 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQ 69 (336)
Q Consensus 36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~ 69 (336)
.+.+.|..+..|.+|||+|.++..||--.+.-++
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 4567777888999999999999999976664443
No 113
>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=91.79 E-value=0.32 Score=33.24 Aligned_cols=34 Identities=26% Similarity=0.447 Sum_probs=27.2
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeE
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARI 290 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I 290 (336)
....+.+.....|.+||++|++|+.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 4455566655679999999999999999998554
No 114
>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=91.52 E-value=0.1 Score=37.39 Aligned_cols=34 Identities=26% Similarity=0.462 Sum_probs=29.0
Q ss_pred EEEEEEecCccceeecCCChHHHHHHHHhCCeEE
Q 019747 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQ 69 (336)
Q Consensus 36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~ 69 (336)
.+.+.+...+-|.|||++|++|++|....+-.+.
T Consensus 26 ~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 26 QIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp EEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred eEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 4678899999999999999999999977765553
No 115
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=90.69 E-value=0.31 Score=46.54 Aligned_cols=66 Identities=20% Similarity=0.222 Sum_probs=48.1
Q ss_pred HHHHHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEecc
Q 019747 94 ILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRL 160 (336)
Q Consensus 94 v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~ 160 (336)
...|..+|...+...++.. ............+.+|..+++.+||++|.+|++|+++.|.+|.+...
T Consensus 459 ~~~a~~~i~~~i~r~~p~~-~eVe~~gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~ 524 (604)
T COG1855 459 LKLAEEEIEREIKRYLPGD-VEVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL 524 (604)
T ss_pred hHHHHHHHHHHHHHhCCCC-ceEEEecCCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence 4556666665566554421 11111223456789999999999999999999999999999999873
No 116
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=90.28 E-value=0.59 Score=41.39 Aligned_cols=51 Identities=16% Similarity=0.221 Sum_probs=46.2
Q ss_pred ceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhc
Q 019747 134 GSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE 194 (336)
Q Consensus 134 g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~ 194 (336)
.+|||++|.+++.|+--|.|.|-+.+ ..|.+.|....+..+.+.+.+.+..
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 47999999999999999999999976 5699999999999999999988865
No 117
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=90.21 E-value=0.87 Score=43.88 Aligned_cols=152 Identities=18% Similarity=0.223 Sum_probs=103.0
Q ss_pred EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhccccccC
Q 019747 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQA 115 (336)
Q Consensus 36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~ 115 (336)
.+-+.||...|..|||.||..|.+++.+.++-|.+...-+ .+.+ .+.
T Consensus 450 e~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~-~~qs------------------------~~~-------- 496 (657)
T COG5166 450 EIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYK-FGQS------------------------QWH-------- 496 (657)
T ss_pred heEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhh-cchh------------------------hhh--------
Confidence 4778999999999999999999999999999999964221 0100 111
Q ss_pred CCCCCceeEEEEEecCccceeecCCChHHHHHHHhc----CCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHH
Q 019747 116 DDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDS----QAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLK 191 (336)
Q Consensus 116 ~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~t----ga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~ 191 (336)
--+-+..|..-.+.|+|++......+++.. ...|.|. +++. +++++-|-...+.+..+. ...
T Consensus 497 ------dNV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~~Kgdirf~------~~~~-sI~~v~~~~~~I~rv~kn-e~v 562 (657)
T COG5166 497 ------DNVLIEAPRKNQDNISGKKNDKLDKVKQQCRFNLKGDIRFC------PQST-SIFTVDIYSDEIERVIKN-ETV 562 (657)
T ss_pred ------cceEEECCccCccchhcccccHHHHHhhhcccccccceEEc------CCce-EEEEEcccccHHHHHhhc-cce
Confidence 124567788888999999888877777543 3444444 3333 588888877665544330 111
Q ss_pred hhcCcCCCCCcCCCccCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccce
Q 019747 192 LSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFV 271 (336)
Q Consensus 192 l~~~~~~~~~~~~~~~~~g~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~I 271 (336)
+-. -....-+.+|++.++..
T Consensus 563 ~~~------------------------------------------------------------~p~~~~~y~~se~h~~g 582 (657)
T COG5166 563 LLE------------------------------------------------------------FPAEMHFYVPSEIHKKG 582 (657)
T ss_pred EEe------------------------------------------------------------cccccccccchhhhhcc
Confidence 100 11334566788899999
Q ss_pred ec---cCCchHHHHHhHhCCeEEEcc
Q 019747 272 VG---RGGRNIMEISQISGARIKVSD 294 (336)
Q Consensus 272 IG---k~G~~I~~I~~~sga~I~i~~ 294 (336)
+| -+|++|..+.....-.|...-
T Consensus 583 ~gena~R~~ni~~~t~~y~~~ie~~~ 608 (657)
T COG5166 583 IGENAFRGENIQRVTKLYNSYIEFST 608 (657)
T ss_pred CCcccccccchhhhhhhhhccceeec
Confidence 99 788888888888777776654
No 118
>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=90.20 E-value=0.44 Score=34.53 Aligned_cols=35 Identities=17% Similarity=0.347 Sum_probs=30.1
Q ss_pred EEEEEEecCccceeecCCChHHHHHHHHhCCeEEE
Q 019747 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQL 70 (336)
Q Consensus 36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i 70 (336)
.+++.|....-|.|||++|+.|++|+++-.-.+.+
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 48889999999999999999999999877665555
No 119
>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=89.81 E-value=0.39 Score=34.35 Aligned_cols=36 Identities=11% Similarity=0.517 Sum_probs=29.2
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEE
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKV 292 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i 292 (336)
....+.|..+..|.+|||+|++|..||-.....+.-
T Consensus 24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~ 59 (77)
T cd02414 24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR 59 (77)
T ss_pred CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence 446677778889999999999999999887755543
No 120
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=89.12 E-value=0.67 Score=38.34 Aligned_cols=37 Identities=22% Similarity=0.428 Sum_probs=31.8
Q ss_pred EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCC
Q 019747 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRS 73 (336)
Q Consensus 36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~ 73 (336)
.+-++|-... |.-|||+|.+|+++++..|-+|.+-..
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence 3567777777 999999999999999999999999653
No 121
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=88.95 E-value=0.27 Score=46.89 Aligned_cols=39 Identities=26% Similarity=0.406 Sum_probs=35.5
Q ss_pred EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCC
Q 019747 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSH 74 (336)
Q Consensus 36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~ 74 (336)
...+.||...++.+|||+|.+|++|++..|.+|.|...+
T Consensus 487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e 525 (604)
T COG1855 487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE 525 (604)
T ss_pred eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence 477899999999999999999999999999999996544
No 122
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=88.39 E-value=0.31 Score=34.88 Aligned_cols=35 Identities=23% Similarity=0.444 Sum_probs=28.6
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeEE
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIK 291 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~ 291 (336)
....+.+....-|.|||++|++|++|++..+-.+.
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 44677788899999999999999999877665553
No 123
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=87.85 E-value=2.1 Score=41.50 Aligned_cols=97 Identities=21% Similarity=0.252 Sum_probs=67.8
Q ss_pred ceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCCCCcCCCccCCCccc
Q 019747 134 GSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFF 213 (336)
Q Consensus 134 g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~~~~~~~~~~~g~~~ 213 (336)
..++-+.|..|++|-++..-+|.+-++... .- .-+.|.+.|.+++-+...-.. +
T Consensus 41 P~~~~~~~dlik~lAk~lrKRI~iR~dPsv-----------l~---~~e~A~~~I~eivP~ea~i~~-----i------- 94 (637)
T COG1782 41 PELFAKDGDLIKDLAKDLRKRIIIRPDPSV-----------LK---PPEEARKIILEIVPEEAGITD-----I------- 94 (637)
T ss_pred HHHhccchhHHHHHHHHHhhceEeccCchh-----------cC---CHHHHHHHHHHhCccccCcee-----E-------
Confidence 345567889999999999888888763111 11 224688888888754321100 0
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCceEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEc
Q 019747 214 SGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKDDRTNSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVS 293 (336)
Q Consensus 214 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~ 293 (336)
.-...+.++.|-.+.=|.+|||+|+++++|.+++|-.-.|-
T Consensus 95 ---------------------------------------~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~iv 135 (637)
T COG1782 95 ---------------------------------------YFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIV 135 (637)
T ss_pred ---------------------------------------EecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceee
Confidence 11225567888889999999999999999999999777766
Q ss_pred cC
Q 019747 294 DR 295 (336)
Q Consensus 294 ~~ 295 (336)
+.
T Consensus 136 R~ 137 (637)
T COG1782 136 RT 137 (637)
T ss_pred ec
Confidence 54
No 124
>PRK13764 ATPase; Provisional
Probab=87.31 E-value=0.44 Score=47.74 Aligned_cols=40 Identities=25% Similarity=0.336 Sum_probs=36.0
Q ss_pred EEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCC
Q 019747 35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSH 74 (336)
Q Consensus 35 ~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~ 74 (336)
-...+.||.+.++.+|||+|.+|++|+++.|.+|.|...+
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~ 520 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLD 520 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcc
Confidence 3567899999999999999999999999999999996544
No 125
>PRK13764 ATPase; Provisional
Probab=87.11 E-value=0.87 Score=45.69 Aligned_cols=65 Identities=22% Similarity=0.218 Sum_probs=47.0
Q ss_pred HHHHHHHHHHHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEecc
Q 019747 95 LRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRL 160 (336)
Q Consensus 95 ~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~ 160 (336)
..|..+|.+.+...+... ............+.||...++.+|||+|.+|++|+++.|..|.+...
T Consensus 455 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~ 519 (602)
T PRK13764 455 RLAEKEIEREIKRYLPGP-VEVEVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL 519 (602)
T ss_pred HHHHHHHHHHHHHhcCCc-eEEEEecCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence 445566665555543211 11111234567789999999999999999999999999999999874
No 126
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=86.64 E-value=0.59 Score=44.95 Aligned_cols=127 Identities=15% Similarity=0.074 Sum_probs=79.6
Q ss_pred ceeecCCChHHHHHHHHhCCeEE--EcCCCCCCCCCCceEEE-EEeeHHHHHHHHHHHHHHHHhhccccccCCCCCCcee
Q 019747 47 GAVIGKGGSTINDFQSQSGARIQ--LSRSHEFFPGTTDRIIM-ISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTK 123 (336)
Q Consensus 47 g~iIGk~G~~Ik~I~~~tg~~I~--i~~~~~~~~~~~~r~i~-I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~ 123 (336)
-.+=||+.-.+.+|++...|.+. +.... ..++.. +.|..-.-.+++..+. .+ -...
T Consensus 392 dFl~gkkngK~TrIm~~v~c~~~~~i~~~~------gs~~~~~~~g~~~~F~k~~~~~~----~E-----------Fpae 450 (657)
T COG5166 392 DFLRGKKNGKATRIMKGVSCSELSSIVSST------GSIVETNGIGEKMSFSKKLSIPP----TE-----------FPAE 450 (657)
T ss_pred HHhccccCcchhhhhhhcccceeeEEEecC------CcEEEEeccCcchhhHHHhcCCc----cc-----------Cchh
Confidence 37788888889999999999844 43322 234433 3455444455444333 22 2345
Q ss_pred EEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcC---HHHHHHHHHHHHHHhhc
Q 019747 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT---LDEQMRALELILLKLSE 194 (336)
Q Consensus 124 ~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~---~~~v~~A~~~i~~~l~~ 194 (336)
..+.||+..+..|||.+|..|++...++++.|.+...-+.....--.-|.|.-+ ..++.-++.-+.+++.+
T Consensus 451 ~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~ 524 (657)
T COG5166 451 IAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQ 524 (657)
T ss_pred eEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHhh
Confidence 789999999999999999999999999999999875211111111122555544 23444455555555554
No 127
>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=85.89 E-value=0.87 Score=34.98 Aligned_cols=29 Identities=21% Similarity=0.460 Sum_probs=25.5
Q ss_pred EEEEEecCccceeecCCChHHHHHHHHhC
Q 019747 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSG 65 (336)
Q Consensus 37 ~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg 65 (336)
+++.|....-|.|||++|++|++|+....
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~ 91 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQ 91 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence 77888888999999999999999986654
No 128
>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=85.13 E-value=1.2 Score=32.43 Aligned_cols=28 Identities=25% Similarity=0.485 Sum_probs=24.0
Q ss_pred EEEEEecCccceeecCCChHHHHHHHHh
Q 019747 37 IRFLVSNPLAGAVIGKGGSTINDFQSQS 64 (336)
Q Consensus 37 ~~i~ip~~~vg~iIGk~G~~Ik~I~~~t 64 (336)
+++.|....-|.+||++|.+|++|+..-
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 6677777899999999999999998654
No 129
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=82.57 E-value=2.1 Score=34.38 Aligned_cols=37 Identities=30% Similarity=0.524 Sum_probs=31.1
Q ss_pred EEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCC
Q 019747 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRS 73 (336)
Q Consensus 37 ~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~ 73 (336)
=++.|-...-|.+||++|.++++|..+||-.-.+.+.
T Consensus 78 GEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 78 GEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred cEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 3556666777999999999999999999988888653
No 130
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=82.39 E-value=2 Score=35.60 Aligned_cols=38 Identities=18% Similarity=0.427 Sum_probs=32.3
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccC
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDR 295 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~ 295 (336)
...-+.|.... |.-|||+|.+++.+++..|-+|.+-..
T Consensus 61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence 45566666666 999999999999999999999999774
No 131
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=82.16 E-value=1.5 Score=38.20 Aligned_cols=31 Identities=32% Similarity=0.506 Sum_probs=26.4
Q ss_pred cEEEEEEEecCccceeecCCChHHHHHHHHh
Q 019747 34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQS 64 (336)
Q Consensus 34 ~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~t 64 (336)
...+++.|....-|.|||++|+.|++|++..
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l 80 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKEL 80 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHH
Confidence 3457889999999999999999999987543
No 132
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=81.39 E-value=2.1 Score=30.94 Aligned_cols=37 Identities=22% Similarity=0.334 Sum_probs=29.8
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEc
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVS 293 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~ 293 (336)
...++.|-...-|.|||++|+.|++|++.-.....+.
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~ 66 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP 66 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence 3467777788889999999999999988876665553
No 133
>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=78.70 E-value=3.9 Score=41.57 Aligned_cols=39 Identities=28% Similarity=0.427 Sum_probs=34.6
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEEccC
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKVSDR 295 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~ 295 (336)
.+.+|.|-...-|.||||+|.++++|..+||-.-.+-+.
T Consensus 93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 556888888999999999999999999999988888764
No 134
>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=75.07 E-value=2.8 Score=32.15 Aligned_cols=30 Identities=13% Similarity=0.374 Sum_probs=24.6
Q ss_pred EEEEeccCcccceeccCCchHHHHHhHhCC
Q 019747 259 LTIGVADEHIGFVVGRGGRNIMEISQISGA 288 (336)
Q Consensus 259 ~~v~vp~~~vg~IIGk~G~~I~~I~~~sga 288 (336)
.+|.|-...-|.|||++|+.|++|++....
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence 566777777899999999999999876543
No 135
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=73.96 E-value=9.9 Score=35.24 Aligned_cols=55 Identities=18% Similarity=0.257 Sum_probs=46.9
Q ss_pred cCcccceeccCCchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHH--HHHHh
Q 019747 265 DEHIGFVVGRGGRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIM--QKVAY 329 (336)
Q Consensus 265 ~~~vg~IIGk~G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~--~~i~~ 329 (336)
.+..-.+.|..|.+++.|.+.+|++|.. ..+.++|+|+...++.|...+. +.+..
T Consensus 23 ~~~~~~l~G~~~~~l~l~e~~~gv~i~~----------rG~~~~i~g~~~~v~~A~~~l~~l~~~~~ 79 (348)
T COG1702 23 DNELVALFGPTDTNLSLLEIALGVSIVA----------RGEAVRIIGARPLVDVATRVLLTLELLAE 79 (348)
T ss_pred chhhhhhcCCCCccHHHHHHHhCcEEEe----------CCceEEEEechHHHHHHHHHHhHHHHHHH
Confidence 5677889999999999999999988887 3578999999889999999888 55444
No 136
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=73.71 E-value=3.9 Score=29.78 Aligned_cols=28 Identities=43% Similarity=0.754 Sum_probs=22.4
Q ss_pred EEEEeccCcccceeccCCchHHHHHhHh
Q 019747 259 LTIGVADEHIGFVVGRGGRNIMEISQIS 286 (336)
Q Consensus 259 ~~v~vp~~~vg~IIGk~G~~I~~I~~~s 286 (336)
..+.|-...-|.+||++|++|++|++.-
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 4555555777999999999999987764
No 137
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=73.16 E-value=5.1 Score=34.93 Aligned_cols=30 Identities=20% Similarity=0.420 Sum_probs=24.5
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHh
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQIS 286 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~s 286 (336)
....|.|....-|.|||++|+.|++|++..
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~l 80 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKEL 80 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHHH
Confidence 446777778888999999999999986543
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=71.87 E-value=8.6 Score=39.11 Aligned_cols=73 Identities=22% Similarity=0.314 Sum_probs=46.5
Q ss_pred EEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHhhcccc
Q 019747 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAE 112 (336)
Q Consensus 37 ~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~~~~~~ 112 (336)
=+++|-...-|+||||+|.++++|.++||-.-.+.+.. +.+ ...+-.|.....+..+-.+.++..+-+.++.+
T Consensus 95 ~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~-~~~--~~~~~~~~~~~~~~~~~r~~~l~~~~~~i~~~ 167 (630)
T TIGR03675 95 GEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTP-PIE--SKTIKNIREYLRSESEERKEFLRKLGRRIHRD 167 (630)
T ss_pred ceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecC-CCC--cHHHHHHHHHHHHhHHHHHHHHHHHHHhhcCC
Confidence 45666677779999999999999999999988886643 111 11111222222333444555666666666655
No 139
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=68.79 E-value=5.2 Score=38.85 Aligned_cols=37 Identities=30% Similarity=0.513 Sum_probs=31.4
Q ss_pred EEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcC
Q 019747 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSR 72 (336)
Q Consensus 36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~ 72 (336)
+=+++|-...-|++|||+|++.+.|..+||-.-.+-+
T Consensus 100 tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR 136 (637)
T COG1782 100 TGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVR 136 (637)
T ss_pred CceEEEEecCCceEEecCchHHHHHHHHhCCcceeee
Confidence 3456777788899999999999999999998777765
No 140
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=67.20 E-value=7.7 Score=34.79 Aligned_cols=29 Identities=24% Similarity=0.239 Sum_probs=23.3
Q ss_pred EEEEEEEecC-ccceeecCCChHHHHHHHH
Q 019747 35 TYIRFLVSNP-LAGAVIGKGGSTINDFQSQ 63 (336)
Q Consensus 35 ~~~~i~ip~~-~vg~iIGk~G~~Ik~I~~~ 63 (336)
+...|+|..+ +-+.|||++|+.||+|...
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ 250 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIA 250 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence 6677777755 7799999999999998643
No 141
>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=64.20 E-value=9.1 Score=32.67 Aligned_cols=30 Identities=23% Similarity=0.458 Sum_probs=25.9
Q ss_pred EEEEEEecCccceeecCCChHHHHHHHHhC
Q 019747 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSG 65 (336)
Q Consensus 36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg 65 (336)
.+++.|....-|.|||++|..|++|++.-.
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~ 68 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKLQ 68 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHHH
Confidence 478888899999999999999999986643
No 142
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=62.69 E-value=9.7 Score=32.87 Aligned_cols=30 Identities=27% Similarity=0.475 Sum_probs=25.1
Q ss_pred EEEEEecCccceeecCCChHHHHHHHHhCC
Q 019747 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGA 66 (336)
Q Consensus 37 ~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~ 66 (336)
+++.|....-|.+||++|++|++++..-.-
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk 71 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEK 71 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHH
Confidence 666777788999999999999999876544
No 143
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=62.39 E-value=16 Score=33.49 Aligned_cols=31 Identities=23% Similarity=0.357 Sum_probs=24.9
Q ss_pred CceeEEEEEec-CccceeecCCChHHHHHHHh
Q 019747 120 TKTKLRLIVPN-SSCGSIIGKAGATIKSFMDD 150 (336)
Q Consensus 120 ~~~~~~l~ip~-~~~g~iIG~~G~~Ik~I~~~ 150 (336)
.....++.+|. ++...|||++|..|++|-.+
T Consensus 326 l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~ 357 (379)
T KOG1423|consen 326 LFIQVEVVCPKNSQKKLLIGKGGKKISQIGTR 357 (379)
T ss_pred EEEEEEEEcCCCcceeEEEcCCCccHHHHHHH
Confidence 34667789996 66778999999999998665
No 144
>CHL00048 rps3 ribosomal protein S3
Probab=61.98 E-value=10 Score=32.92 Aligned_cols=30 Identities=17% Similarity=0.318 Sum_probs=25.7
Q ss_pred EEEEEEecCccceeecCCChHHHHHHHHhC
Q 019747 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSG 65 (336)
Q Consensus 36 ~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg 65 (336)
.+++.|-...-|.|||++|.+|++|++.-.
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 477788888889999999999999987653
No 145
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=61.35 E-value=10 Score=32.99 Aligned_cols=31 Identities=19% Similarity=0.355 Sum_probs=26.3
Q ss_pred EEEEEecCccceeecCCChHHHHHHHHhCCe
Q 019747 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGAR 67 (336)
Q Consensus 37 ~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~ 67 (336)
+++.|....-|.|||++|..|++|++.-.-.
T Consensus 46 i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~ 76 (220)
T PTZ00084 46 TEIIIRATRTREVLGDKGRRIRELTSLLQKR 76 (220)
T ss_pred EEEEEEECCCccEEcCCchHHHHHHHHHHHH
Confidence 7888888889999999999999998765443
No 146
>PRK00089 era GTPase Era; Reviewed
Probab=60.86 E-value=12 Score=33.76 Aligned_cols=36 Identities=25% Similarity=0.502 Sum_probs=27.0
Q ss_pred eEEEEEecc-CcccceeccCCchHHHH--------HhHhCCeEEE
Q 019747 257 NSLTIGVAD-EHIGFVVGRGGRNIMEI--------SQISGARIKV 292 (336)
Q Consensus 257 ~~~~v~vp~-~~vg~IIGk~G~~I~~I--------~~~sga~I~i 292 (336)
+...+.|.. .+-+-|||++|++|++| ++..+++|.+
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l 270 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL 270 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 456667775 45589999999999987 5566777766
No 147
>PRK15494 era GTPase Era; Provisional
Probab=60.72 E-value=12 Score=35.03 Aligned_cols=36 Identities=25% Similarity=0.371 Sum_probs=27.0
Q ss_pred EEEEEEEecC-ccceeecCCChHHHHHHH--------HhCCeEEE
Q 019747 35 TYIRFLVSNP-LAGAVIGKGGSTINDFQS--------QSGARIQL 70 (336)
Q Consensus 35 ~~~~i~ip~~-~vg~iIGk~G~~Ik~I~~--------~tg~~I~i 70 (336)
+...|+|..+ +-+.|||++|+.||+|.. -++++|..
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l 317 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHL 317 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEE
Confidence 5567777765 789999999999998863 34555555
No 148
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=59.66 E-value=22 Score=31.78 Aligned_cols=29 Identities=31% Similarity=0.275 Sum_probs=22.0
Q ss_pred eeEEEEEec-CccceeecCCChHHHHHHHh
Q 019747 122 TKLRLIVPN-SSCGSIIGKAGATIKSFMDD 150 (336)
Q Consensus 122 ~~~~l~ip~-~~~g~iIG~~G~~Ik~I~~~ 150 (336)
....+.|.. ++-+.|||++|+.||+|...
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ 250 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIA 250 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence 455677775 66789999999999886543
No 149
>COG1159 Era GTPase [General function prediction only]
Probab=59.31 E-value=30 Score=31.48 Aligned_cols=38 Identities=32% Similarity=0.351 Sum_probs=27.3
Q ss_pred ceeEEEEEec-CccceeecCCChHHHHH--------HHhcCCEEEEe
Q 019747 121 KTKLRLIVPN-SSCGSIIGKAGATIKSF--------MDDSQAVIKIS 158 (336)
Q Consensus 121 ~~~~~l~ip~-~~~g~iIG~~G~~Ik~I--------~~~tga~I~i~ 158 (336)
.....+.|+. ++-+-|||++|+.||+| ++-.+++|.+.
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 3444577775 77799999999999875 44456666654
No 150
>PRK03818 putative transporter; Validated
Probab=59.00 E-value=2e+02 Score=28.85 Aligned_cols=136 Identities=16% Similarity=0.252 Sum_probs=75.1
Q ss_pred EEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEc---CCCCC-CCC-----CCceEEEEEeeHHHHHHHHHHHHHHH
Q 019747 35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLS---RSHEF-FPG-----TTDRIIMISGTIDEILRAVDLVIDKL 105 (336)
Q Consensus 35 ~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~---~~~~~-~~~-----~~~r~i~I~G~~~~v~~A~~~I~~~i 105 (336)
...++.|+++. ++ |.+++++.......+.+. +.... .+. ....++.+.|+.+++.++...+-..+
T Consensus 205 ~~r~~~V~~s~---li---GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~l~~l~~~~Gl~~ 278 (552)
T PRK03818 205 QTINIRVENPN---LH---GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPEDLHKAQLVIGEEV 278 (552)
T ss_pred eeEEEEEeCCC---CC---CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHHHHHHHHhcCCcc
Confidence 34677777544 34 578999998877665552 11111 111 13356899999999877665543221
Q ss_pred HhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHH--HHhcCCEEEEecc-CCCC-CC-----CCceEEEEEc
Q 019747 106 LTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSF--MDDSQAVIKISRL-DHSY-YG-----LNDRLVTLTG 176 (336)
Q Consensus 106 ~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I--~~~tga~I~i~~~-~~~~-~~-----~~~r~v~I~G 176 (336)
. .+ .....+......+.+|+ ..++|+ +++++ ++++|+.|.--.+ +... +. ..-..+.+.|
T Consensus 279 ~----~~-~~~~~~~~~~E~Vvv~~---S~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq~GD~LlVvG 347 (552)
T PRK03818 279 D----TS-LSTRGTDLRSERVVVTN---EKVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLSLQFGDILNLVG 347 (552)
T ss_pred C----cc-ccccCcceEEEEEEEcC---hhccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCEEecCCEEEEEE
Confidence 1 00 01111223344455554 355554 67776 4667766554432 1111 11 1125789999
Q ss_pred CHHHHHHHHHH
Q 019747 177 TLDEQMRALEL 187 (336)
Q Consensus 177 ~~~~v~~A~~~ 187 (336)
+++++++..+.
T Consensus 348 ~~~~i~~l~~~ 358 (552)
T PRK03818 348 RPEAIDAVANV 358 (552)
T ss_pred CHHHHHHHHHH
Confidence 99999987764
No 151
>PRK00089 era GTPase Era; Reviewed
Probab=58.89 E-value=13 Score=33.59 Aligned_cols=36 Identities=25% Similarity=0.460 Sum_probs=25.6
Q ss_pred EEEEEEEecC-ccceeecCCChHHHHHHH--------HhCCeEEE
Q 019747 35 TYIRFLVSNP-LAGAVIGKGGSTINDFQS--------QSGARIQL 70 (336)
Q Consensus 35 ~~~~i~ip~~-~vg~iIGk~G~~Ik~I~~--------~tg~~I~i 70 (336)
+...|+|... +-+.|||++|++||+|.. -++++|+.
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l 270 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL 270 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 4555666644 679999999999998863 34555555
No 152
>COG1159 Era GTPase [General function prediction only]
Probab=58.09 E-value=16 Score=33.24 Aligned_cols=37 Identities=24% Similarity=0.407 Sum_probs=26.9
Q ss_pred cEEEEEEEecC-ccceeecCCChHHHHHH--------HHhCCeEEE
Q 019747 34 PTYIRFLVSNP-LAGAVIGKGGSTINDFQ--------SQSGARIQL 70 (336)
Q Consensus 34 ~~~~~i~ip~~-~vg~iIGk~G~~Ik~I~--------~~tg~~I~i 70 (336)
.+...|+|+.+ +-|.|||++|+.||+|- +-.+++|++
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 34455677654 78999999999999875 445666665
No 153
>PRK15494 era GTPase Era; Provisional
Probab=57.96 E-value=24 Score=32.93 Aligned_cols=37 Identities=22% Similarity=0.206 Sum_probs=26.6
Q ss_pred eeEEEEEec-CccceeecCCChHHHHH--------HHhcCCEEEEe
Q 019747 122 TKLRLIVPN-SSCGSIIGKAGATIKSF--------MDDSQAVIKIS 158 (336)
Q Consensus 122 ~~~~l~ip~-~~~g~iIG~~G~~Ik~I--------~~~tga~I~i~ 158 (336)
....+.|.. ++-+.|||++|+.||+| ++-++++|.+.
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 445677775 66788999999999875 44466666654
No 154
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=56.48 E-value=20 Score=30.71 Aligned_cols=38 Identities=21% Similarity=0.295 Sum_probs=30.4
Q ss_pred CcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEE
Q 019747 33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQL 70 (336)
Q Consensus 33 ~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i 70 (336)
..-++.+.|..+..+.+||+.|+++..||--++.-++-
T Consensus 89 ~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 89 EGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 34456777778889999999999999999877765544
No 155
>PF09869 DUF2096: Uncharacterized protein conserved in archaea (DUF2096); InterPro: IPR017098 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=56.24 E-value=41 Score=27.74 Aligned_cols=58 Identities=10% Similarity=0.113 Sum_probs=44.4
Q ss_pred CCceeEEEEEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHh
Q 019747 119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKL 192 (336)
Q Consensus 119 ~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l 192 (336)
.+..+.|+.++...+ =..+.+|.+-+|+-+.+. .+..|.|.|..+.|..|++.+..+.
T Consensus 110 ~~~~~iRv~l~~~i~-------~erl~ei~E~~gvI~Efe---------e~~~V~I~Gdke~Ik~aLKe~s~~w 167 (169)
T PF09869_consen 110 PGFETIRVKLKKPIQ-------EERLQEISEWHGVIFEFE---------EDDKVVIEGDKERIKKALKEFSSFW 167 (169)
T ss_pred CCceeEEEecCccch-------HHHHHHHHHHhceeEEec---------CCcEEEEeccHHHHHHHHHHHHHHh
Confidence 445666776665554 245789999999988883 3567999999999999999887664
No 156
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=54.72 E-value=12 Score=32.07 Aligned_cols=36 Identities=11% Similarity=0.391 Sum_probs=30.4
Q ss_pred eEEEEEeccCcccceeccCCchHHHHHhHhCCeEEE
Q 019747 257 NSLTIGVADEHIGFVVGRGGRNIMEISQISGARIKV 292 (336)
Q Consensus 257 ~~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~I~i 292 (336)
....+.+-.+..+.+||++|+++..||-.+.+.+.-
T Consensus 91 ~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 566777788889999999999999999988766655
No 157
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=54.55 E-value=30 Score=32.14 Aligned_cols=53 Identities=11% Similarity=0.097 Sum_probs=44.3
Q ss_pred EEecCccceeecCCChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 019747 127 IVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELIL 189 (336)
Q Consensus 127 ~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~ 189 (336)
+-+....-.|.|..+.+++.|++.+|+.|.... +.+.|.|....+..|...+.
T Consensus 20 ~~~~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG----------~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 20 LSDDNELVALFGPTDTNLSLLEIALGVSIVARG----------EAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred cCCchhhhhhcCCCCccHHHHHHHhCcEEEeCC----------ceEEEEechHHHHHHHHHHh
Confidence 333567788999999999999999999888765 56899999778888888777
No 158
>PRK03818 putative transporter; Validated
Probab=53.97 E-value=97 Score=31.08 Aligned_cols=61 Identities=21% Similarity=0.124 Sum_probs=36.5
Q ss_pred eEEEEEecCccceeecCCChHHHHHHHhcCCEEEEec---cCCC-C--C---CCCceEEEEEcCHHHHHHHHHHHH
Q 019747 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR---LDHS-Y--Y---GLNDRLVTLTGTLDEQMRALELIL 189 (336)
Q Consensus 123 ~~~l~ip~~~~g~iIG~~G~~Ik~I~~~tga~I~i~~---~~~~-~--~---~~~~r~v~I~G~~~~v~~A~~~i~ 189 (336)
..++.|+.+- ++ |.+++++.......+.+.+ +... . + -.....+.+.|+.+++.++...+-
T Consensus 206 ~r~~~V~~s~---li---GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~l~~l~~~~G 275 (552)
T PRK03818 206 TINIRVENPN---LH---GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPEDLHKAQLVIG 275 (552)
T ss_pred eEEEEEeCCC---CC---CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHHHHHHHHhcC
Confidence 4566676433 33 6689999887766665543 1110 0 1 123467899999998776665433
No 159
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=53.43 E-value=24 Score=30.43 Aligned_cols=31 Identities=39% Similarity=0.695 Sum_probs=24.0
Q ss_pred EEEEeccCcccceeccCCchHHHHHhHhCCe
Q 019747 259 LTIGVADEHIGFVVGRGGRNIMEISQISGAR 289 (336)
Q Consensus 259 ~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~ 289 (336)
..+.|-...-|.+||++|++|+++++.-.-.
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 4555555778999999999999998776543
No 160
>TIGR03802 Asp_Ala_antiprt aspartate-alanine antiporter. All members of the seed alignment for this model are asparate-alanine anti-transporters (AspT) encoded next to the gene for aspartate 4-decarboxylase (AspD), which converts asparate to alanine, releasing CO2. The exchange of Asp for Ala is electrogenic, so the AspD/AspT system confers a proton-motive force. This transporter contains two copies of the AspT/YidE/YbjL antiporter duplication domain (TIGR01625).
Probab=53.03 E-value=1.7e+02 Score=29.44 Aligned_cols=140 Identities=16% Similarity=0.234 Sum_probs=74.4
Q ss_pred CcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEc---CCCCC-CCC-----CCceEEEEEeeHHHHHHHHHHHHH
Q 019747 33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLS---RSHEF-FPG-----TTDRIIMISGTIDEILRAVDLVID 103 (336)
Q Consensus 33 ~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~---~~~~~-~~~-----~~~r~i~I~G~~~~v~~A~~~I~~ 103 (336)
.-....+.|++. ..++| .+|+++.......+.+. +.++. .|. .....+.+.|+.+++.+....+-.
T Consensus 216 ~~~~r~~~V~~~--s~liG---kTl~el~~~~~~~v~I~~I~R~g~~~~p~~dtvL~~GD~L~V~G~~e~L~~l~~~~G~ 290 (562)
T TIGR03802 216 ELVGRAYRVNRA--SSLIG---KTVGDLENLFAGRVTIERIRRDGKLLTVSPDLVLNAGDVVLVVGRRDAVVQFGAEIGE 290 (562)
T ss_pred ceeeEEEEECCC--cccCC---CcHHHHHhhhCCCeEEEEEEECCEEEcCCCCCeeCCCCEEEEEECHHHHHHHHHhcCC
Confidence 334555666654 33444 56999887765444432 21111 111 123568999999998877655432
Q ss_pred HHHhhccccccCCCCCCceeEEEEEecCccceeecCCChHHHHHH------HhcCCEEEEeccC-CCCCC------CCce
Q 019747 104 KLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFM------DDSQAVIKISRLD-HSYYG------LNDR 170 (336)
Q Consensus 104 ~i~~~~~~~~~~~~~~~~~~~~l~ip~~~~g~iIG~~G~~Ik~I~------~~tga~I~i~~~~-~~~~~------~~~r 170 (336)
.+.+. . . .+. +....++.+|+ ..++| ++++++. +.+|+.|.--.+. ..... ..-.
T Consensus 291 ~~~~~---~-~-~~~-~~~~e~VV~~~---S~liG---kTL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~GD 358 (562)
T TIGR03802 291 EVQEV---E-G-LDV-PMETKDVVLTN---KEYNG---KTVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQRGD 358 (562)
T ss_pred ccCCc---c-c-cCC-ceEEEEEEECC---cccCC---ccHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecCCC
Confidence 21110 0 0 111 12244455554 34444 4788876 2567766554422 11111 1225
Q ss_pred EEEEEcCHHHHHHHHHHHH
Q 019747 171 LVTLTGTLDEQMRALELIL 189 (336)
Q Consensus 171 ~v~I~G~~~~v~~A~~~i~ 189 (336)
.+.+.|++++++++.+.+-
T Consensus 359 ~LlV~G~~~~l~~~~~~lG 377 (562)
T TIGR03802 359 VVTLVGTPQDVDRAAKQLG 377 (562)
T ss_pred EEEEEeCHHHHHHHHHHcC
Confidence 7899999999988776543
No 161
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=52.25 E-value=22 Score=30.92 Aligned_cols=32 Identities=25% Similarity=0.330 Sum_probs=25.0
Q ss_pred EEEEEeccCcccceeccCCchHHHHHhHhCCe
Q 019747 258 SLTIGVADEHIGFVVGRGGRNIMEISQISGAR 289 (336)
Q Consensus 258 ~~~v~vp~~~vg~IIGk~G~~I~~I~~~sga~ 289 (336)
..+|.|-...-|.|||++|..|++|++...-.
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 35666667777999999999999997766443
No 162
>TIGR03802 Asp_Ala_antiprt aspartate-alanine antiporter. All members of the seed alignment for this model are asparate-alanine anti-transporters (AspT) encoded next to the gene for aspartate 4-decarboxylase (AspD), which converts asparate to alanine, releasing CO2. The exchange of Asp for Ala is electrogenic, so the AspD/AspT system confers a proton-motive force. This transporter contains two copies of the AspT/YidE/YbjL antiporter duplication domain (TIGR01625).
Probab=50.68 E-value=1.7e+02 Score=29.40 Aligned_cols=62 Identities=15% Similarity=0.166 Sum_probs=37.2
Q ss_pred EEEEEeccCcccceeccCCchHHHHH------hHhCCeEEEccCC-CCCCC------CcceEEEEEcChHhHHHHHHHHH
Q 019747 258 SLTIGVADEHIGFVVGRGGRNIMEIS------QISGARIKVSDRG-DFFSG------TSERKVTISGPQRSIRTAESMIM 324 (336)
Q Consensus 258 ~~~v~vp~~~vg~IIGk~G~~I~~I~------~~sga~I~i~~~~-~~~~~------~~~r~v~I~G~~~~v~~A~~~I~ 324 (336)
...+.+|+ ..++ |++|++++ +..|+.|.--.++ ...+. ....++.+.|++++++++.+.+-
T Consensus 304 ~e~VV~~~---S~li---GkTL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~GD~LlV~G~~~~l~~~~~~lG 377 (562)
T TIGR03802 304 TKDVVLTN---KEYN---GKTVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQRGDVVTLVGTPQDVDRAAKQLG 377 (562)
T ss_pred EEEEEECC---cccC---CccHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecCCCEEEEEeCHHHHHHHHHHcC
Confidence 34455554 3444 55888886 2677765544332 11111 12467999999999999887654
Q ss_pred H
Q 019747 325 Q 325 (336)
Q Consensus 325 ~ 325 (336)
.
T Consensus 378 ~ 378 (562)
T TIGR03802 378 Y 378 (562)
T ss_pred C
Confidence 3
No 163
>CHL00048 rps3 ribosomal protein S3
Probab=49.75 E-value=27 Score=30.29 Aligned_cols=30 Identities=17% Similarity=0.200 Sum_probs=24.3
Q ss_pred EEEEEeccCcccceeccCCchHHHHHhHhC
Q 019747 258 SLTIGVADEHIGFVVGRGGRNIMEISQISG 287 (336)
Q Consensus 258 ~~~v~vp~~~vg~IIGk~G~~I~~I~~~sg 287 (336)
..+|.|-...-|.|||++|..|++|++...
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 456666677779999999999999987764
No 164
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=48.13 E-value=19 Score=33.10 Aligned_cols=33 Identities=15% Similarity=0.314 Sum_probs=25.9
Q ss_pred CCceEEEEEecc-CcccceeccCCchHHHHHhHh
Q 019747 254 DRTNSLTIGVAD-EHIGFVVGRGGRNIMEISQIS 286 (336)
Q Consensus 254 ~~~~~~~v~vp~-~~vg~IIGk~G~~I~~I~~~s 286 (336)
......++.||. .+...||||+|..|++|-+..
T Consensus 325 ~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a 358 (379)
T KOG1423|consen 325 VLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRA 358 (379)
T ss_pred EEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHH
Confidence 345678889996 566888999999999985544
No 165
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=48.01 E-value=22 Score=30.79 Aligned_cols=28 Identities=36% Similarity=0.569 Sum_probs=24.5
Q ss_pred EEEEEecCccceeecCCChHHHHHHHHh
Q 019747 37 IRFLVSNPLAGAVIGKGGSTINDFQSQS 64 (336)
Q Consensus 37 ~~i~ip~~~vg~iIGk~G~~Ik~I~~~t 64 (336)
++|.|....-+.|||++|..|++|++.-
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l 91 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDL 91 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHH
Confidence 6788888888999999999999998554
No 166
>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=46.99 E-value=52 Score=23.88 Aligned_cols=54 Identities=11% Similarity=0.043 Sum_probs=41.4
Q ss_pred ChHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhc
Q 019747 141 GATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE 194 (336)
Q Consensus 141 G~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~ 194 (336)
-..+.++=+..++++.....+...-...+.++.+.|+..++..|-+.++.++..
T Consensus 33 ~~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~~ 86 (88)
T PF02749_consen 33 LEEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQR 86 (88)
T ss_dssp HHHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHHH
Confidence 355677888889988887544443445678999999999999999999988763
No 167
>PF00472 RF-1: RF-1 domain; InterPro: IPR000352 Peptide chain release factors (RFs) are required for the termination of protein biosynthesis []. At present two classes of RFs can be distinguished. Class I RFs bind to ribosomes that have encountered a stop codon at their decoding site and induce release of the nascent polypeptide. Class II RFs are GTP-binding proteins that interact with class I RFs and enhance class I RF activity. In prokaryotes there are two class I RFs that act in a codon specific manner []: RF-1 (gene prfA) mediates UAA and UAG-dependent termination while RF-2 (gene prfB) mediates UAA and UGA-dependent termination. RF-1 and RF-2 are structurally and evolutionary related proteins which have been shown to be part of a larger family [].; GO: 0003747 translation release factor activity, 0006415 translational termination; PDB: 2JY9_A 1ZBT_A 1GQE_A 3F1G_X 3F1E_X 1RQ0_C 4DH9_Y 2JVA_A 1J26_A 3D5A_X ....
Probab=45.95 E-value=31 Score=26.55 Aligned_cols=48 Identities=21% Similarity=0.294 Sum_probs=32.1
Q ss_pred ecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEee-----HHHHHHHHHHHHHHHHhhc
Q 019747 50 IGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT-----IDEILRAVDLVIDKLLTEL 109 (336)
Q Consensus 50 IGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~-----~~~v~~A~~~I~~~i~~~~ 109 (336)
=|+||.++++.. |.|.|.+... . ++|... ..|...|+..+.++|....
T Consensus 22 sGpGGQ~VNk~~--s~V~l~h~pt--------g--i~v~~~~~Rsq~~Nr~~A~~~L~~~l~~~~ 74 (113)
T PF00472_consen 22 SGPGGQNVNKTN--SKVRLRHIPT--------G--IVVKCQESRSQHQNREDALEKLREKLDEAY 74 (113)
T ss_dssp SSSSSCHHHSSS--EEEEEEETTT--------T--EEEEEESSSSHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCcccccC--CEEEEEEecc--------c--EEEEEcccCCHHHHHHHHHHHHHHHHHHHH
Confidence 399999999632 5566666421 1 555543 5688899998887776653
No 168
>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=45.78 E-value=38 Score=28.94 Aligned_cols=30 Identities=33% Similarity=0.570 Sum_probs=24.4
Q ss_pred EEEEEeccCcccceeccCCchHHHHHhHhC
Q 019747 258 SLTIGVADEHIGFVVGRGGRNIMEISQISG 287 (336)
Q Consensus 258 ~~~v~vp~~~vg~IIGk~G~~I~~I~~~sg 287 (336)
..++.|-...-|.|||++|..|++|++.-.
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~ 68 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKLQ 68 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHHH
Confidence 466777777789999999999999876654
No 169
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=43.77 E-value=87 Score=25.21 Aligned_cols=44 Identities=20% Similarity=0.256 Sum_probs=35.7
Q ss_pred hHHHHHHHhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhc
Q 019747 142 ATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE 194 (336)
Q Consensus 142 ~~Ik~I~~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~ 194 (336)
..++.|.+-.|+-|.+.. ...|.|.|+.+.|.+|++.+..+..+
T Consensus 126 eRlqDi~E~hgvIiE~~E---------~D~V~i~Gd~drVk~aLke~~~~wke 169 (170)
T COG4010 126 ERLQDIAETHGVIIEFEE---------YDLVAIYGDSDRVKKALKEIGSFWKE 169 (170)
T ss_pred HHHHHHHHhhheeEEeee---------ccEEEEeccHHHHHHHHHHHHHHHhc
Confidence 456778888898888763 35899999999999999999887543
No 170
>PF09869 DUF2096: Uncharacterized protein conserved in archaea (DUF2096); InterPro: IPR017098 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=41.19 E-value=92 Score=25.74 Aligned_cols=54 Identities=17% Similarity=0.306 Sum_probs=41.8
Q ss_pred CcEEEEEEEecCccceeecCCChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHH
Q 019747 33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVI 102 (336)
Q Consensus 33 ~~~~~~i~ip~~~vg~iIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~ 102 (336)
+--++|+-+|...+ =..+..|.+-.|+-+.+. .+..|.|.|..+.|.+|++.+.
T Consensus 111 ~~~~iRv~l~~~i~-------~erl~ei~E~~gvI~Efe---------e~~~V~I~Gdke~Ik~aLKe~s 164 (169)
T PF09869_consen 111 GFETIRVKLKKPIQ-------EERLQEISEWHGVIFEFE---------EDDKVVIEGDKERIKKALKEFS 164 (169)
T ss_pred CceeEEEecCccch-------HHHHHHHHHHhceeEEec---------CCcEEEEeccHHHHHHHHHHHH
Confidence 34456666666654 256788899999999992 2456999999999999999987
No 171
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=36.86 E-value=38 Score=29.79 Aligned_cols=28 Identities=29% Similarity=0.554 Sum_probs=23.7
Q ss_pred EEEEEecCccceeecCCChHHHHHHHHh
Q 019747 37 IRFLVSNPLAGAVIGKGGSTINDFQSQS 64 (336)
Q Consensus 37 ~~i~ip~~~vg~iIGk~G~~Ik~I~~~t 64 (336)
++|.|-...-+.|||++|..|++|++.-
T Consensus 64 i~I~I~~~rP~~iiG~~g~~i~~l~~~L 91 (232)
T PRK00310 64 VRVTIHTARPGIVIGKKGAEIEKLRKEL 91 (232)
T ss_pred EEEEEEECCCccccCCCcHHHHHHHHHH
Confidence 6677777888999999999999998665
No 172
>PRK15405 ethanolamine utilization protein EutL; Provisional
Probab=36.15 E-value=2.9e+02 Score=23.96 Aligned_cols=133 Identities=14% Similarity=0.068 Sum_probs=0.0
Q ss_pred HHhCCeEEEcCCC------CCCCCCCceEEEEEe-eHHHHHHHHHHHHHHHHhhccccccCCCCCCce------------
Q 019747 62 SQSGARIQLSRSH------EFFPGTTDRIIMISG-TIDEILRAVDLVIDKLLTELHAEDQADDVGTKT------------ 122 (336)
Q Consensus 62 ~~tg~~I~i~~~~------~~~~~~~~r~i~I~G-~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~------------ 122 (336)
+.+++.|-+.++. ...+-+.+-++.|.| +...|+.|++...+.+.+.+..-..+....-.+
T Consensus 56 KAAnVevv~a~~~~gGaghg~~~~~G~viiIi~G~dvsdVrsAveaa~~~i~~~~~f~~~n~~g~~~~~a~~~aRag~~l 135 (217)
T PRK15405 56 KQAMVEVVYARSFYAGAAHASTPLAGEVIGILAGPNPAEVRAGLDAMVAFIENGAAFQSANDDDSTAFFAHVVSRTGSYL 135 (217)
T ss_pred hhcceEEEEEEeeccccccCCCCCCccEEEEEeCCCHHHHHHHHHHHHHHHHhhhceEeeCCCCCEEEEEEEcccHHHHH
Q ss_pred eEEEEEec-CccceeecCCChHHHHHHHhcC-CEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhc
Q 019747 123 KLRLIVPN-SSCGSIIGKAGATIKSFMDDSQ-AVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE 194 (336)
Q Consensus 123 ~~~l~ip~-~~~g~iIG~~G~~Ik~I~~~tg-a~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~ 194 (336)
...+-+|. .-.+.|+|.=+.-+--+-...+ +.|++..--.+..+.+..-..++|+..+|++|+..-.+.+..
T Consensus 136 ~k~~g~~~G~a~~~li~~P~~~~~~~D~AlKaA~V~~~~~~~P~~~t~f~~~~ltG~~~A~r~A~~a~~e~v~~ 209 (217)
T PRK15405 136 SKTAGIAEGEPLAYLIAPPLEAMYGIDAALKAADVQLVTFVGPPSETNFGGALLTGSQSACKAACNAFTDAVLE 209 (217)
T ss_pred HHHcCCCCCceeEEEecCcHHHHHHHHHHHhhcCceEEEEeCCCCCceecCeeEEeCHHHHHHHHHHHHHHHHH
No 173
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=35.90 E-value=1.3e+02 Score=22.87 Aligned_cols=42 Identities=14% Similarity=0.105 Sum_probs=32.7
Q ss_pred cCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHhhcCcCCC
Q 019747 151 SQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYS 199 (336)
Q Consensus 151 tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~l~~~~~~~ 199 (336)
.+++|-|..+ -...+.|+|+-.+|+.|++.+.+.+.+...|.
T Consensus 63 a~V~igF~DR-------FsGslvitGdvs~Ve~Al~~V~~~l~~~L~F~ 104 (111)
T PRK15468 63 ADVHIGFLDR-------FSGALVIYGSVGAVEEALSQTVSGLGRLLNYT 104 (111)
T ss_pred cCcEEeeeec-------cceeEEEEccHHHHHHHHHHHHHHHHhhcCcc
Confidence 3567766642 23569999999999999999999998866554
No 174
>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=35.81 E-value=1.6e+02 Score=21.31 Aligned_cols=54 Identities=17% Similarity=0.152 Sum_probs=39.8
Q ss_pred CChHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHH
Q 019747 53 GGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLL 106 (336)
Q Consensus 53 ~G~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~ 106 (336)
|=.-+.++-+..++.++....+...-...+.++.+.|+..++..|-+.++..|.
T Consensus 32 G~~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 32 GLEEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp SHHHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 456778888888999988754433222457999999999999999888885544
No 175
>PF06183 DinI: DinI-like family; InterPro: IPR010391 This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity []. The structure of DinI is known [].; PDB: 1GHH_A.
Probab=30.38 E-value=1.8e+02 Score=19.91 Aligned_cols=45 Identities=13% Similarity=0.155 Sum_probs=25.2
Q ss_pred hHHHHHhHh-CCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHHHHHhhhh
Q 019747 278 NIMEISQIS-GARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQKVAYASD 332 (336)
Q Consensus 278 ~I~~I~~~s-ga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~ 332 (336)
-.|+|.+.+ .+.|.|.. ....-++|.|....= +..|.++|++.++
T Consensus 13 L~kRl~~~yPd~~v~Vr~-------~s~~~l~v~g~~~~~---k~~i~~iLqe~we 58 (65)
T PF06183_consen 13 LTKRLHRQYPDAEVRVRP-------GSANGLSVSGGKKDD---KERIEEILQEMWE 58 (65)
T ss_dssp HHHHHHHH-SS-EEEEEE-------ESS-EEEEES--HHH---HHHHHHHHHHHHH
T ss_pred HHHHHHHHCCCceEeeee-------cccCccccCCcCchH---HHHHHHHHHHHHh
Confidence 356777666 57888865 356789999987542 5555555555443
No 176
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=29.29 E-value=53 Score=28.41 Aligned_cols=28 Identities=18% Similarity=0.429 Sum_probs=23.0
Q ss_pred EEEEeccCcccceeccCCchHHHHHhHh
Q 019747 259 LTIGVADEHIGFVVGRGGRNIMEISQIS 286 (336)
Q Consensus 259 ~~v~vp~~~vg~IIGk~G~~I~~I~~~s 286 (336)
.+|.|-...-|.|||++|+.|++|++..
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l 91 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDL 91 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHH
Confidence 5566677777999999999999997655
No 177
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=28.85 E-value=1.5e+02 Score=20.81 Aligned_cols=43 Identities=16% Similarity=0.265 Sum_probs=31.8
Q ss_pred CchHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEcChHhHHHHHHHHHH
Q 019747 276 GRNIMEISQISGARIKVSDRGDFFSGTSERKVTISGPQRSIRTAESMIMQ 325 (336)
Q Consensus 276 G~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~ 325 (336)
-..|.+|-+.++|+|.=.. .+.-+|.++|+++.++....++..
T Consensus 16 r~ei~~l~~~f~a~ivd~~-------~~~~iie~tG~~~kid~fi~~l~~ 58 (75)
T PF10369_consen 16 RSEILQLAEIFRARIVDVS-------PDSIIIELTGTPEKIDAFIKLLKP 58 (75)
T ss_dssp HHHHHHHHHHTT-EEEEEE-------TTEEEEEEEE-HHHHHHHHHHSTG
T ss_pred HHHHHHHHHHhCCEEEEEC-------CCEEEEEEcCCHHHHHHHHHHhhh
Confidence 4567888899999865543 247899999999999998887654
No 178
>cd07055 BMC_like_2 Bacterial Micro-Compartment (BMC)-like domain 2. BMC like 2 domains exist in cyanobacteria, proteobacteria, and actinobacteria and are homologs of carboxysome shell proteins. They might be encoded from putative organelles involved in unknown metabolic process. Although it has been suggested that these carboxysome shell protein homologs form hexamers and further assemble into the flat facets of the polyhedral bacterial organelles shell at present no experimental evidence exists to directly support this view.
Probab=28.05 E-value=1.8e+02 Score=19.73 Aligned_cols=40 Identities=13% Similarity=-0.065 Sum_probs=25.7
Q ss_pred HhcCCEEEEeccCCCCCCCCceEEEEEcCHHHHHHHHHHHHHH
Q 019747 149 DDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLK 191 (336)
Q Consensus 149 ~~tga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~i~~~ 191 (336)
+..++.+ ++. -..||. .-..+.|.|+..+|+.|++.+.+.
T Consensus 21 Kaa~V~i-~d~-f~gCPq-~~~~l~i~Gdvs~Ve~Al~~i~~~ 60 (61)
T cd07055 21 KASGVFV-SDI-FGSCPQ-HMITLAIFGETSAVELAMREIEED 60 (61)
T ss_pred hccCeEE-EEe-cCCCCC-ceEEEEEEecHHHHHHHHHHHhhc
Confidence 3345555 332 234444 224677899999999999888753
No 179
>PRK04021 hypothetical protein; Reviewed
Probab=27.98 E-value=1.3e+02 Score=22.34 Aligned_cols=40 Identities=13% Similarity=0.285 Sum_probs=30.8
Q ss_pred chHHHHHhHhCCeEEEccCCCCCCCCcceEEEEEc-ChHhHHHHH
Q 019747 277 RNIMEISQISGARIKVSDRGDFFSGTSERKVTISG-PQRSIRTAE 320 (336)
Q Consensus 277 ~~I~~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~ 320 (336)
+-|+.|.+..|++|.|..-.. +...+|.|.| +++++....
T Consensus 50 ali~~LAk~l~~~I~I~~G~~----sr~K~v~i~g~~~e~l~~~L 90 (92)
T PRK04021 50 ELVKFFSKLLGAEVEIIRGET----SREKDLLVKGISLEEVKKKL 90 (92)
T ss_pred HHHHHHHHHhCCCEEEEecCC----cCceEEEEecCCHHHHHHHh
Confidence 457778999999999976432 5689999999 788776654
No 180
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.41 E-value=2.1e+02 Score=23.13 Aligned_cols=43 Identities=16% Similarity=0.322 Sum_probs=34.1
Q ss_pred hHHHHHHHHhCCeEEEcCCCCCCCCCCceEEEEEeeHHHHHHHHHHHHHHHHh
Q 019747 55 STINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT 107 (336)
Q Consensus 55 ~~Ik~I~~~tg~~I~i~~~~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~~ 107 (336)
..+..|.+-.|+-|.+.. ...+.|.|+.+.|.+|++.|- .+++
T Consensus 126 eRlqDi~E~hgvIiE~~E---------~D~V~i~Gd~drVk~aLke~~-~~wk 168 (170)
T COG4010 126 ERLQDIAETHGVIIEFEE---------YDLVAIYGDSDRVKKALKEIG-SFWK 168 (170)
T ss_pred HHHHHHHHhhheeEEeee---------ccEEEEeccHHHHHHHHHHHH-HHHh
Confidence 566777788889888853 456999999999999999998 4443
No 181
>PF03958 Secretin_N: Bacterial type II/III secretion system short domain; InterPro: IPR005644 This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (IPR004846 from INTERPRO).; PDB: 3EZJ_C 2Y3M_A 3OSS_D.
Probab=25.41 E-value=81 Score=22.08 Aligned_cols=24 Identities=13% Similarity=0.288 Sum_probs=20.3
Q ss_pred cceEEEEEcChHhHHHHHHHHHHH
Q 019747 303 SERKVTISGPQRSIRTAESMIMQK 326 (336)
Q Consensus 303 ~~r~v~I~G~~~~v~~A~~~I~~~ 326 (336)
....+.|+|+++.++..+.+|.++
T Consensus 53 ~tNsliv~g~~~~~~~i~~li~~L 76 (82)
T PF03958_consen 53 RTNSLIVRGTPEDLEQIRELIKQL 76 (82)
T ss_dssp TTTEEEEEEEHHHHHHHHHHHHHH
T ss_pred CCCEEEEEeCHHHHHHHHHHHHHH
Confidence 457788899999999999999654
No 182
>PRK09256 hypothetical protein; Provisional
Probab=25.17 E-value=1.1e+02 Score=24.47 Aligned_cols=57 Identities=18% Similarity=0.346 Sum_probs=32.2
Q ss_pred ecCCChHHHHHHHHhCCeEEEcCCCCCCCC--------------CCceEEEEEee-----HHHHHHHHHHHHHHHHhh
Q 019747 50 IGKGGSTINDFQSQSGARIQLSRSHEFFPG--------------TTDRIIMISGT-----IDEILRAVDLVIDKLLTE 108 (336)
Q Consensus 50 IGk~G~~Ik~I~~~tg~~I~i~~~~~~~~~--------------~~~r~i~I~G~-----~~~v~~A~~~I~~~i~~~ 108 (336)
=|+||.++++.. |.|.+.+.-....+|. ..+-.+.|... ..|...|++.+.+.|...
T Consensus 23 SGPGGQ~VNKt~--SkV~l~~~~~~~~lp~~~~~~l~~~~~~r~~~~g~l~i~~~~~RSQ~~Nr~~al~kL~~~i~~~ 98 (138)
T PRK09256 23 SGPGGQNVNKVS--TAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQEFRSQERNREDALERLVALIREA 98 (138)
T ss_pred CCCCcccccccc--eeeEEEechhhccCCHHHHHHHHHHhcCcccCCCcEEEEECCcCCHHHHHHHHHHHHHHHHHHH
Confidence 478888887644 5555554221101110 11223555543 468889999998777765
No 183
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=22.97 E-value=1.4e+02 Score=22.80 Aligned_cols=27 Identities=19% Similarity=0.284 Sum_probs=23.2
Q ss_pred eEEEEEeeHHHHHHHHHHHHHHHHhhc
Q 019747 83 RIIMISGTIDEILRAVDLVIDKLLTEL 109 (336)
Q Consensus 83 r~i~I~G~~~~v~~A~~~I~~~i~~~~ 109 (336)
-.+.|+|+...|+.|++.+.+.+.+.+
T Consensus 75 GslvitGdvs~Ve~Al~~V~~~l~~~L 101 (111)
T PRK15468 75 GALVIYGSVGAVEEALSQTVSGLGRLL 101 (111)
T ss_pred eeEEEEccHHHHHHHHHHHHHHHHhhc
Confidence 349999999999999999998877753
No 184
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=21.18 E-value=3.6e+02 Score=25.74 Aligned_cols=145 Identities=10% Similarity=0.037 Sum_probs=81.2
Q ss_pred ecCCChHHHHHHHHhCCeEEEcCCC----CCCCCCCce--EEEEEee-HHHHHHHHHHHHHHHHhhcccc----------
Q 019747 50 IGKGGSTINDFQSQSGARIQLSRSH----EFFPGTTDR--IIMISGT-IDEILRAVDLVIDKLLTELHAE---------- 112 (336)
Q Consensus 50 IGk~G~~Ik~I~~~tg~~I~i~~~~----~~~~~~~~r--~i~I~G~-~~~v~~A~~~I~~~i~~~~~~~---------- 112 (336)
+=..|.+.-.|+..+|+.|.....- ..--+..++ +..|.+. .+-+.+|+.+|.-.+.......
T Consensus 109 ~~TRg~~~d~Ie~~~G~~~~~RGs~~~~El~~vg~~~~pLv~hI~~~T~Ei~~~Ai~RIkgv~~~~~~~~n~~~V~i~~~ 188 (531)
T KOG1960|consen 109 TSTRGTSYDHIEGITGTTSASRGSAPAPELPPVGSSEGPLVDHIPPSTAEITSKAIERIKGVFMQDVEINNVRNVYILVR 188 (531)
T ss_pred eeccchhHHhhhhhccceeeccCCCCCccCCCCCCCCCcceeecCCccHHHHHHHHhhCccceeecccccccceEEEeec
Confidence 3467899999999999998874221 111233444 4556664 5667789888873332221100
Q ss_pred --------ccCC----CCCCceeEEEEE----ecCcc-ceeecCCChHHHHHHHhcCCEEEEecc----CCCCCC--C-C
Q 019747 113 --------DQAD----DVGTKTKLRLIV----PNSSC-GSIIGKAGATIKSFMDDSQAVIKISRL----DHSYYG--L-N 168 (336)
Q Consensus 113 --------~~~~----~~~~~~~~~l~i----p~~~~-g~iIG~~G~~Ik~I~~~tga~I~i~~~----~~~~~~--~-~ 168 (336)
.... .....+..++++ |...+ +..=+++-.++..++.++++.+-+..+ -+.+.+ + .
T Consensus 189 ~sP~~~i~~~V~~~~f~~G~~Y~~k~~v~~~~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~EsnE 268 (531)
T KOG1960|consen 189 ASPLSEIENKVGVQLFSKGRYYPNKALATDKDPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNEGNESNE 268 (531)
T ss_pred CCchhhhccccccccccccccchhheecccCCcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccCcccccccCC
Confidence 0000 001112223333 43343 334456677788899999888666431 122222 1 1
Q ss_pred c-eEEEEEcCHHHHHHHHHHHHHHhhc
Q 019747 169 D-RLVTLTGTLDEQMRALELILLKLSE 194 (336)
Q Consensus 169 ~-r~v~I~G~~~~v~~A~~~i~~~l~~ 194 (336)
. -+..+.+..+.+.+|.+++.++++.
T Consensus 269 PMYI~i~h~~~~g~~~A~r~~~nl~~~ 295 (531)
T KOG1960|consen 269 PMYIFSTHGNGNGENGAPRRKWNLEEK 295 (531)
T ss_pred ceeEEeecCCchhhccchhHHHhHHHH
Confidence 2 3455556689999999888877654
Done!