Query 012307
Match_columns 466
No_of_seqs 313 out of 1888
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 01:15:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012307.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012307hhsearch_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 1.3E-39 2.8E-44 301.2 26.6 312 76-415 46-387 (390)
2 KOG2190 PolyC-binding proteins 100.0 5.5E-35 1.2E-39 302.9 27.4 335 78-418 43-415 (485)
3 KOG1676 K-homology type RNA bi 100.0 4.4E-35 9.6E-40 299.1 25.6 252 75-415 136-392 (600)
4 KOG1676 K-homology type RNA bi 100.0 1.1E-33 2.4E-38 288.8 21.4 251 77-416 53-304 (600)
5 KOG2193 IGF-II mRNA-binding pr 100.0 2E-30 4.3E-35 253.3 16.2 287 76-416 197-485 (584)
6 KOG2193 IGF-II mRNA-binding pr 100.0 6.1E-29 1.3E-33 243.0 9.5 247 76-417 278-569 (584)
7 KOG2191 RNA-binding protein NO 100.0 1.1E-26 2.4E-31 221.3 22.9 271 76-415 37-318 (402)
8 KOG2191 RNA-binding protein NO 99.9 3E-24 6.5E-29 204.8 19.7 191 167-440 37-234 (402)
9 KOG2190 PolyC-binding proteins 99.8 1.4E-18 2.9E-23 181.0 16.3 160 167-414 41-210 (485)
10 KOG2192 PolyC-binding hnRNP-K 99.7 2.5E-16 5.4E-21 146.8 16.7 149 167-414 46-195 (390)
11 TIGR03665 arCOG04150 arCOG0415 99.7 2.3E-16 5E-21 144.2 10.9 139 173-413 2-152 (172)
12 PRK13763 putative RNA-processi 99.6 2.3E-15 4.9E-20 138.6 12.5 152 169-413 3-158 (180)
13 TIGR03665 arCOG04150 arCOG0415 99.6 9.6E-15 2.1E-19 133.5 10.3 139 82-244 2-152 (172)
14 PRK13763 putative RNA-processi 99.5 5.1E-14 1.1E-18 129.6 11.8 142 78-244 3-158 (180)
15 cd02396 PCBP_like_KH K homolog 99.5 7.3E-14 1.6E-18 107.0 6.6 63 345-407 2-65 (65)
16 KOG2279 Kinase anchor protein 99.4 1.8E-12 3.9E-17 132.2 12.1 292 75-411 65-367 (608)
17 PF00013 KH_1: KH domain syndr 99.3 1.7E-12 3.6E-17 97.7 5.2 60 344-406 1-60 (60)
18 cd02396 PCBP_like_KH K homolog 99.3 5.1E-12 1.1E-16 96.7 7.7 64 170-237 1-64 (65)
19 cd02394 vigilin_like_KH K homo 99.3 2.5E-12 5.5E-17 97.4 5.7 61 345-407 2-62 (62)
20 cd00105 KH-I K homology RNA-bi 99.3 1E-11 2.2E-16 94.5 7.3 63 345-407 2-64 (64)
21 cd02393 PNPase_KH Polynucleoti 99.3 1.3E-11 2.8E-16 93.1 6.8 58 344-407 3-61 (61)
22 cd02394 vigilin_like_KH K homo 99.1 1.4E-10 3.1E-15 87.8 5.6 61 171-238 2-62 (62)
23 PF00013 KH_1: KH domain syndr 99.1 1.6E-10 3.5E-15 86.9 5.1 60 170-237 1-60 (60)
24 cd00105 KH-I K homology RNA-bi 99.0 1.3E-09 2.8E-14 82.8 8.2 62 171-237 2-63 (64)
25 cd02393 PNPase_KH Polynucleoti 99.0 1.3E-09 2.9E-14 82.1 7.9 58 169-237 2-60 (61)
26 PF13014 KH_3: KH domain 99.0 7E-10 1.5E-14 77.6 5.2 42 88-129 1-43 (43)
27 smart00322 KH K homology RNA-b 99.0 3.2E-09 6.9E-14 80.9 8.6 67 343-411 3-69 (69)
28 PF13014 KH_3: KH domain 99.0 1E-09 2.2E-14 76.7 5.2 42 353-394 1-43 (43)
29 COG1094 Predicted RNA-binding 98.9 7.2E-09 1.6E-13 94.4 9.9 154 169-414 8-166 (194)
30 KOG2208 Vigilin [Lipid transpo 98.9 6.9E-09 1.5E-13 114.5 11.6 231 78-415 201-491 (753)
31 KOG2279 Kinase anchor protein 98.8 2.4E-09 5.1E-14 109.8 3.8 147 167-415 66-212 (608)
32 smart00322 KH K homology RNA-b 98.7 7.6E-08 1.6E-12 73.2 9.0 66 169-241 3-68 (69)
33 KOG2208 Vigilin [Lipid transpo 98.7 2.1E-08 4.4E-13 110.8 7.6 216 78-413 347-563 (753)
34 COG1094 Predicted RNA-binding 98.7 2E-07 4.3E-12 85.0 11.9 147 76-244 6-165 (194)
35 KOG2113 Predicted RNA binding 98.7 1.7E-08 3.7E-13 96.8 4.8 153 74-240 22-180 (394)
36 KOG2113 Predicted RNA binding 98.5 2.2E-07 4.7E-12 89.3 6.1 149 167-403 24-173 (394)
37 cd02395 SF1_like-KH Splicing f 98.5 5.1E-07 1.1E-11 77.4 7.5 64 351-414 14-97 (120)
38 cd02395 SF1_like-KH Splicing f 98.2 6.1E-06 1.3E-10 70.8 8.0 67 178-244 15-96 (120)
39 PRK08406 transcription elongat 98.1 1.3E-05 2.8E-10 70.8 7.4 103 78-204 32-134 (140)
40 PRK08406 transcription elongat 97.9 3.2E-05 6.8E-10 68.3 7.4 37 169-205 32-68 (140)
41 TIGR02696 pppGpp_PNP guanosine 97.8 7.1E-05 1.5E-09 81.7 10.1 63 344-412 579-642 (719)
42 TIGR01952 nusA_arch NusA famil 97.6 0.00028 6.1E-09 62.1 8.0 100 79-204 34-135 (141)
43 KOG0119 Splicing factor 1/bran 97.6 0.00045 9.8E-09 70.9 10.5 76 168-243 137-230 (554)
44 TIGR02696 pppGpp_PNP guanosine 97.5 0.00034 7.3E-09 76.5 8.5 66 167-243 576-642 (719)
45 TIGR03591 polynuc_phos polyrib 97.2 0.00048 1E-08 76.2 6.6 64 343-412 551-615 (684)
46 TIGR01952 nusA_arch NusA famil 97.2 0.00085 1.8E-08 59.1 6.8 36 170-205 34-69 (141)
47 KOG0119 Splicing factor 1/bran 97.2 0.00036 7.8E-09 71.6 4.6 73 76-150 136-230 (554)
48 KOG0336 ATP-dependent RNA heli 97.1 0.0017 3.7E-08 65.7 7.6 68 343-413 47-114 (629)
49 COG0195 NusA Transcription elo 97.0 0.0019 4.1E-08 59.8 7.3 100 79-205 77-178 (190)
50 KOG0336 ATP-dependent RNA heli 97.0 0.00032 6.9E-09 70.7 2.2 56 74-132 43-98 (629)
51 KOG1588 RNA-binding protein Sa 97.0 0.00081 1.7E-08 64.3 4.2 42 75-116 89-136 (259)
52 PLN00207 polyribonucleotide nu 96.9 0.002 4.3E-08 72.2 7.5 63 344-412 686-750 (891)
53 PF14611 SLS: Mitochondrial in 96.9 0.06 1.3E-06 50.8 16.5 88 142-244 4-91 (210)
54 cd02134 NusA_KH NusA_K homolog 96.9 0.0017 3.6E-08 48.8 4.4 37 77-113 24-60 (61)
55 PRK00106 hypothetical protein; 96.8 0.0072 1.6E-07 64.6 10.5 66 343-413 225-292 (535)
56 TIGR03591 polynuc_phos polyrib 96.8 0.0023 4.9E-08 70.9 6.6 66 167-243 549-615 (684)
57 COG1185 Pnp Polyribonucleotide 96.8 0.0019 4.1E-08 69.4 5.5 65 344-414 553-618 (692)
58 TIGR03319 YmdA_YtgF conserved 96.7 0.0042 9E-08 66.5 7.6 66 343-413 204-271 (514)
59 KOG4369 RTK signaling protein 96.6 0.0015 3.3E-08 72.8 3.8 102 24-132 731-835 (2131)
60 KOG1588 RNA-binding protein Sa 96.6 0.014 3.1E-07 55.9 9.9 42 166-207 89-136 (259)
61 PRK12704 phosphodiesterase; Pr 96.6 0.0053 1.1E-07 65.8 7.8 66 343-413 210-277 (520)
62 TIGR01953 NusA transcription t 96.6 0.0085 1.8E-07 60.7 8.4 93 88-206 244-338 (341)
63 PRK12328 nusA transcription el 96.5 0.0089 1.9E-07 60.7 8.4 97 87-209 251-348 (374)
64 COG0195 NusA Transcription elo 96.5 0.0081 1.8E-07 55.6 6.9 37 344-380 143-179 (190)
65 KOG2814 Transcription coactiva 96.4 0.0036 7.8E-08 61.6 4.6 73 342-415 56-128 (345)
66 cd02134 NusA_KH NusA_K homolog 96.4 0.0051 1.1E-07 46.2 4.1 36 343-378 25-60 (61)
67 PRK12327 nusA transcription el 96.3 0.012 2.7E-07 59.9 8.0 94 87-206 245-340 (362)
68 PRK12329 nusA transcription el 96.2 0.011 2.3E-07 61.2 6.8 93 87-205 277-371 (449)
69 PRK00468 hypothetical protein; 96.0 0.007 1.5E-07 47.4 3.5 32 75-106 27-58 (75)
70 PRK04163 exosome complex RNA-b 96.0 0.012 2.6E-07 56.7 5.8 63 345-413 147-210 (235)
71 KOG2814 Transcription coactiva 96.0 0.01 2.2E-07 58.5 5.0 72 168-245 56-127 (345)
72 PLN00207 polyribonucleotide nu 95.9 0.0086 1.9E-07 67.2 5.0 66 167-243 683-750 (891)
73 PRK09202 nusA transcription el 95.8 0.021 4.5E-07 60.4 7.0 93 88-206 246-339 (470)
74 PRK02821 hypothetical protein; 95.7 0.01 2.3E-07 46.6 3.3 33 76-108 29-61 (77)
75 COG5176 MSL5 Splicing factor ( 95.5 0.037 7.9E-07 51.0 6.5 41 167-207 146-192 (269)
76 COG5176 MSL5 Splicing factor ( 95.5 0.015 3.1E-07 53.6 3.7 42 75-116 145-192 (269)
77 TIGR01953 NusA transcription t 95.5 0.04 8.6E-07 55.9 7.3 37 344-380 302-338 (341)
78 PRK11824 polynucleotide phosph 95.3 0.015 3.2E-07 64.7 4.0 63 344-412 555-618 (693)
79 PRK12328 nusA transcription el 95.3 0.034 7.3E-07 56.6 6.1 37 344-380 309-345 (374)
80 COG1837 Predicted RNA-binding 95.3 0.022 4.8E-07 44.5 3.6 32 75-106 27-58 (76)
81 PRK01064 hypothetical protein; 95.2 0.023 5E-07 44.8 3.6 32 75-106 27-58 (78)
82 COG1185 Pnp Polyribonucleotide 95.2 0.026 5.7E-07 60.9 5.1 69 167-246 550-619 (692)
83 PRK00468 hypothetical protein; 95.1 0.049 1.1E-06 42.6 5.3 32 166-197 27-58 (75)
84 PRK09202 nusA transcription el 95.1 0.043 9.2E-07 58.1 6.3 37 344-380 303-339 (470)
85 PRK12327 nusA transcription el 95.0 0.062 1.3E-06 54.9 7.1 37 344-380 304-340 (362)
86 PRK02821 hypothetical protein; 94.9 0.058 1.3E-06 42.4 5.0 33 167-199 29-61 (77)
87 PRK04163 exosome complex RNA-b 94.8 0.064 1.4E-06 51.7 6.3 64 170-244 146-210 (235)
88 COG1837 Predicted RNA-binding 94.7 0.086 1.9E-06 41.2 5.6 32 166-197 27-58 (76)
89 PF14611 SLS: Mitochondrial in 94.7 0.53 1.1E-05 44.4 12.1 130 76-242 26-164 (210)
90 PRK12705 hypothetical protein; 94.6 0.044 9.6E-07 58.3 5.1 40 343-382 198-238 (508)
91 PRK12329 nusA transcription el 94.5 0.068 1.5E-06 55.4 5.9 37 344-380 336-372 (449)
92 PRK11824 polynucleotide phosph 94.4 0.038 8.2E-07 61.5 4.2 65 168-243 553-618 (693)
93 PRK12704 phosphodiesterase; Pr 94.3 0.17 3.7E-06 54.4 8.8 66 169-244 210-277 (520)
94 PRK00106 hypothetical protein; 94.3 0.2 4.3E-06 53.8 9.1 67 167-243 223-291 (535)
95 TIGR03319 YmdA_YtgF conserved 94.3 0.18 3.9E-06 54.1 8.8 66 168-243 203-270 (514)
96 PRK01064 hypothetical protein; 93.9 0.18 3.9E-06 39.8 5.8 32 166-197 27-58 (78)
97 PF13083 KH_4: KH domain; PDB: 92.8 0.054 1.2E-06 42.1 1.3 33 76-108 27-59 (73)
98 cd02409 KH-II KH-II (K homolo 92.4 0.22 4.8E-06 37.3 4.3 35 77-111 24-58 (68)
99 PF13184 KH_5: NusA-like KH do 91.5 0.14 3.1E-06 39.4 2.3 37 80-116 5-47 (69)
100 KOG4369 RTK signaling protein 89.6 0.4 8.6E-06 54.6 4.5 57 77-133 1339-1396(2131)
101 cd02410 archeal_CPSF_KH The ar 89.3 1.2 2.6E-05 39.2 6.5 93 93-206 21-113 (145)
102 PF07650 KH_2: KH domain syndr 88.9 0.21 4.7E-06 39.1 1.4 34 79-112 26-59 (78)
103 KOG1067 Predicted RNA-binding 88.7 0.53 1.1E-05 49.8 4.4 66 343-415 597-663 (760)
104 cd02414 jag_KH jag_K homology 87.9 0.53 1.1E-05 36.9 3.0 34 79-112 25-58 (77)
105 PRK12705 hypothetical protein; 87.6 1.1 2.3E-05 48.0 6.0 37 169-205 198-235 (508)
106 cd02409 KH-II KH-II (K homolo 87.5 0.9 2E-05 33.8 4.1 33 344-376 26-58 (68)
107 KOG3273 Predicted RNA-binding 87.3 0.43 9.2E-06 44.0 2.4 55 352-413 178-232 (252)
108 COG1855 ATPase (PilT family) [ 87.2 0.4 8.7E-06 49.8 2.5 38 79-116 487-524 (604)
109 PF13083 KH_4: KH domain; PDB: 87.2 0.32 7E-06 37.6 1.4 33 167-199 27-59 (73)
110 KOG3273 Predicted RNA-binding 86.7 0.29 6.3E-06 45.0 1.0 56 177-244 177-232 (252)
111 KOG1067 Predicted RNA-binding 86.5 1.5 3.3E-05 46.5 6.2 65 167-243 595-660 (760)
112 COG1097 RRP4 RNA-binding prote 86.5 0.86 1.9E-05 43.5 4.1 48 80-133 148-195 (239)
113 KOG2874 rRNA processing protei 86.3 1.3 2.9E-05 42.8 5.3 51 355-412 161-211 (356)
114 cd02413 40S_S3_KH K homology R 86.3 0.8 1.7E-05 36.4 3.2 36 79-114 31-66 (81)
115 PF13184 KH_5: NusA-like KH do 85.9 0.75 1.6E-05 35.4 2.8 35 346-380 6-46 (69)
116 COG1855 ATPase (PilT family) [ 85.4 1.8 3.8E-05 45.3 5.9 40 169-208 486-525 (604)
117 COG1782 Predicted metal-depend 85.0 2.3 4.9E-05 44.9 6.6 93 90-206 41-136 (637)
118 PRK13764 ATPase; Provisional 84.8 1.7 3.7E-05 47.5 6.0 45 167-211 479-523 (602)
119 PRK06418 transcription elongat 83.8 1.6 3.5E-05 39.6 4.4 37 79-116 62-98 (166)
120 KOG2874 rRNA processing protei 83.4 2 4.4E-05 41.6 5.0 51 181-243 161-211 (356)
121 PF07650 KH_2: KH domain syndr 83.0 0.62 1.3E-05 36.5 1.3 33 344-376 26-58 (78)
122 PRK13764 ATPase; Provisional 82.7 0.93 2E-05 49.5 2.8 39 78-116 481-519 (602)
123 cd02410 archeal_CPSF_KH The ar 82.3 2 4.3E-05 37.9 4.2 38 81-118 79-116 (145)
124 COG5166 Uncharacterized conser 81.7 3 6.5E-05 43.9 5.9 72 79-150 450-524 (657)
125 COG1097 RRP4 RNA-binding prote 81.6 4 8.7E-05 39.0 6.3 47 345-397 148-194 (239)
126 cd02414 jag_KH jag_K homology 81.0 1.8 4E-05 33.9 3.3 35 169-203 24-58 (77)
127 cd02412 30S_S3_KH K homology R 80.8 1.4 3.1E-05 37.0 2.8 31 79-109 62-92 (109)
128 cd02411 archeal_30S_S3_KH K ho 79.3 2.1 4.5E-05 34.3 3.1 28 80-107 40-67 (85)
129 TIGR03675 arCOG00543 arCOG0054 76.2 6.6 0.00014 43.4 6.9 95 91-206 36-130 (630)
130 COG0092 RpsC Ribosomal protein 76.2 2.3 5E-05 40.5 2.9 29 79-107 52-80 (233)
131 cd02413 40S_S3_KH K homology R 74.5 3.4 7.3E-05 32.8 3.0 35 344-378 31-65 (81)
132 PRK06418 transcription elongat 73.5 4.8 0.0001 36.5 4.1 36 169-205 61-96 (166)
133 cd02412 30S_S3_KH K homology R 65.8 5.4 0.00012 33.5 2.6 29 345-373 63-91 (109)
134 cd02411 archeal_30S_S3_KH K ho 65.4 6.5 0.00014 31.4 2.9 27 346-372 41-67 (85)
135 COG0092 RpsC Ribosomal protein 59.5 8.4 0.00018 36.7 2.9 37 344-380 52-95 (233)
136 COG5166 Uncharacterized conser 57.7 14 0.00031 39.0 4.5 126 90-243 392-524 (657)
137 PF02749 QRPTase_N: Quinolinat 54.1 40 0.00087 26.9 5.8 52 361-412 32-86 (88)
138 PRK04191 rps3p 30S ribosomal p 54.1 13 0.00027 35.1 3.2 31 80-110 42-72 (207)
139 TIGR01008 rpsC_E_A ribosomal p 53.7 13 0.00029 34.6 3.2 31 79-109 39-69 (195)
140 CHL00048 rps3 ribosomal protei 53.2 13 0.00029 35.2 3.2 30 79-108 67-96 (214)
141 PTZ00084 40S ribosomal protein 51.6 14 0.00031 35.1 3.1 32 79-110 45-76 (220)
142 TIGR00436 era GTP-binding prot 49.5 17 0.00037 35.5 3.5 30 343-372 221-251 (270)
143 COG1782 Predicted metal-depend 47.8 21 0.00046 37.9 3.9 39 80-118 101-139 (637)
144 TIGR00436 era GTP-binding prot 47.6 13 0.00028 36.3 2.3 30 78-107 221-251 (270)
145 TIGR03675 arCOG00543 arCOG0054 46.5 23 0.00049 39.3 4.2 39 80-118 95-133 (630)
146 PRK15494 era GTPase Era; Provi 45.0 21 0.00046 36.2 3.5 36 343-378 273-317 (339)
147 KOG1423 Ras-like GTPase ERA [C 44.9 21 0.00046 35.7 3.2 39 70-108 317-359 (379)
148 PRK00089 era GTPase Era; Revie 43.8 16 0.00035 35.9 2.4 36 78-113 226-270 (292)
149 PRK00089 era GTPase Era; Revie 43.6 23 0.00051 34.8 3.4 36 343-378 226-270 (292)
150 PF02749 QRPTase_N: Quinolinat 41.7 68 0.0015 25.6 5.3 55 187-243 32-86 (88)
151 COG1702 PhoH Phosphate starvat 41.5 61 0.0013 32.9 5.9 57 350-413 22-80 (348)
152 COG1847 Jag Predicted RNA-bind 41.4 19 0.00042 33.7 2.2 35 79-113 92-126 (208)
153 KOG1423 Ras-like GTPase ERA [C 40.6 28 0.00061 34.9 3.3 35 165-199 324-359 (379)
154 PRK15494 era GTPase Era; Provi 40.1 19 0.00042 36.5 2.3 36 78-113 273-317 (339)
155 COG1159 Era GTPase [General fu 39.9 21 0.00045 35.5 2.3 29 78-106 229-258 (298)
156 COG1159 Era GTPase [General fu 39.4 31 0.00066 34.3 3.4 29 343-371 229-258 (298)
157 TIGR01009 rpsC_bact ribosomal 38.7 29 0.00063 32.8 3.0 29 80-108 64-92 (211)
158 PRK04191 rps3p 30S ribosomal p 32.9 40 0.00087 31.8 3.0 28 346-373 43-70 (207)
159 TIGR01008 rpsC_E_A ribosomal p 31.6 44 0.00096 31.2 3.0 28 345-372 40-67 (195)
160 PTZ00084 40S ribosomal protein 31.1 44 0.00096 31.8 2.9 28 345-372 46-73 (220)
161 CHL00048 rps3 ribosomal protei 29.8 48 0.001 31.5 2.9 28 345-372 68-95 (214)
162 PF10369 ALS_ss_C: Small subun 28.8 99 0.0021 24.0 4.1 43 361-408 15-58 (75)
163 PRK00310 rpsC 30S ribosomal pr 28.3 50 0.0011 31.7 2.9 30 79-108 63-92 (232)
164 PRK03818 putative transporter; 28.3 7.7E+02 0.017 26.9 12.3 134 79-236 206-358 (552)
165 PF00936 BMC: BMC domain; Int 28.0 78 0.0017 24.5 3.4 36 216-251 37-72 (75)
166 PF03958 Secretin_N: Bacterial 27.3 1.6E+02 0.0035 22.5 5.2 33 372-409 44-76 (82)
167 COG1847 Jag Predicted RNA-bind 25.9 52 0.0011 30.9 2.4 35 344-378 92-126 (208)
168 KOG1960 Predicted RNA-binding 25.6 5.3E+02 0.011 26.9 9.5 65 349-413 220-296 (531)
169 PRK15468 carboxysome structura 24.6 1.8E+02 0.0039 24.4 5.0 44 193-245 57-101 (111)
170 COG1702 PhoH Phosphate starvat 23.9 1.7E+02 0.0038 29.7 5.8 52 175-238 21-72 (348)
171 cd07053 BMC_PduT_repeat1 1,2-p 22.2 1.2E+02 0.0026 23.7 3.4 36 216-251 36-71 (76)
172 PF10369 ALS_ss_C: Small subun 22.2 2.2E+02 0.0048 22.0 5.0 42 188-238 16-57 (75)
173 TIGR01009 rpsC_bact ribosomal 20.4 89 0.0019 29.5 2.8 28 345-372 64-91 (211)
174 TIGR01334 modD putative molybd 20.1 3.6E+02 0.0078 26.7 7.1 53 360-412 46-101 (277)
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=1.3e-39 Score=301.19 Aligned_cols=312 Identities=25% Similarity=0.402 Sum_probs=228.8
Q ss_pred CceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHh-cCC
Q 012307 76 GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRV-SGL 154 (466)
Q Consensus 76 ~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i-~~l 154 (466)
+.+.+|||+.++.+|.||||+|++||.|+.+++|.|+|++. +.++|+++|+... +.|..+++++ ..|
T Consensus 46 ~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri~tisad~----------~ti~~ilk~iip~l 113 (390)
T KOG2192|consen 46 SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILTISADI----------ETIGEILKKIIPTL 113 (390)
T ss_pred cceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCceeEEEeccH----------HHHHHHHHHHhhhh
Confidence 56899999999999999999999999999999999999988 6899999999876 4566666665 333
Q ss_pred CCCCcccccCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHH
Q 012307 155 PENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKAL 234 (466)
Q Consensus 155 ~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~ 234 (466)
.++... ...|.+||||..+.+|.|||++|++||+|++++.++++|.. +.+| .+++|+|.|.|.+..|..++
T Consensus 114 ee~f~~-----~~pce~rllihqs~ag~iigrngskikelrekcsarlkift-~c~p---~stdrv~l~~g~~k~v~~~i 184 (390)
T KOG2192|consen 114 EEGFQL-----PSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFT-ECCP---HSTDRVVLIGGKPKRVVECI 184 (390)
T ss_pred hhCCCC-----CCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhh-ccCC---CCcceEEEecCCcchHHHHH
Confidence 333221 35699999999999999999999999999999999999984 4445 89999999999999999999
Q ss_pred HHHHHHhhhccccCccccccccccCCcccccccccccccCCCcccC-CCCCCCCCCCCCccCCCc--ccCCCccc----c
Q 012307 235 EAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAA-TQSAISTEYTPSTRRESL--FLEREPQL----E 307 (466)
Q Consensus 235 ~~I~~~l~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~-~~~~~~~~y~~p~~~~~~--~~~~~~~~----~ 307 (466)
+.|++.|.+...+.+..||.+.-|.+.-.++...-++.+.|.-... ++.+ ...+|..+.++ .++|.... +
T Consensus 185 ~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrg---gqgpp~~~~sdlmay~r~GrpG~ryd 261 (390)
T KOG2192|consen 185 KIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRG---GQGPPPPRGSDLMAYDRRGRPGDRYD 261 (390)
T ss_pred HHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCC---CCCCCCCCccccceeccCCCCCcccc
Confidence 9999999999999999999887776654444333223332221110 1100 11112111111 12221110 0
Q ss_pred c------------cccCCCccc----CCC------CCCCcccccCCCCCCCCCcccceEEEEEeccCcccceeccccchH
Q 012307 308 S------------RYRLSGISI----YGQ------DPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSI 365 (466)
Q Consensus 308 ~------------~~~~~~~~~----yg~------~~~~~~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~I 365 (466)
. .++...++- |.+ +++..+.. ..|+..++|+ +|.++.||.++-|.||||+|.+|
T Consensus 262 g~vdFs~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~-GsYGdlGGPi---tTaQvtip~dlggsiigkggqri 337 (390)
T KOG2192|consen 262 GMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGY-GSYGDLGGPI---TTAQVTIPKDLGGSIIGKGGQRI 337 (390)
T ss_pred ccccccccccCCCcCCCcCccccccccCCCCCCCCCccccccc-cccCCCCCce---eeeeEecccccCcceecccchhh
Confidence 0 011111111 111 11111111 1234444554 46789999999999999999999
Q ss_pred HHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcC
Q 012307 366 ENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKE 415 (466)
Q Consensus 366 k~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~ 415 (466)
++||+++||.|+|+++.+++.+|+++|+||.+|++.||+|+|+.+...++
T Consensus 338 ~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vkq~re 387 (390)
T KOG2192|consen 338 KQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYRE 387 (390)
T ss_pred hhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHHhhhc
Confidence 99999999999999998889999999999999999999999999986443
No 2
>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=5.5e-35 Score=302.93 Aligned_cols=335 Identities=28% Similarity=0.373 Sum_probs=223.6
Q ss_pred eEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCC-
Q 012307 78 CVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPE- 156 (466)
Q Consensus 78 ~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~- 156 (466)
.++||||+...+|.||||+|..||+||.+|.++|+|.+..++++||+++|+|..... ....+.++++++++++-...+
T Consensus 43 ~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~-~~~~~~~al~ka~~~iv~~~~~ 121 (485)
T KOG2190|consen 43 LTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVEL-NLSPATDALFKAFDMIVFKLEE 121 (485)
T ss_pred ceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccc-cCCchHHHHHHHHHHHhhcccc
Confidence 348999999999999999999999999999999999999999999999999953332 677889999999998743211
Q ss_pred CC---cccc-cCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHH
Q 012307 157 ND---VDAK-ASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLK 232 (466)
Q Consensus 157 ~~---~~~~-~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~ 232 (466)
.. .+.. ......+++||+||..++|+||||+|+.||+|+++|||+|++.++ .+| ..++|.|+|.|.+++|.+
T Consensus 122 d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP---~ster~V~IsG~~~av~~ 197 (485)
T KOG2190|consen 122 DDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLP---NSTERAVTISGEPDAVKK 197 (485)
T ss_pred cccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCC---cccceeEEEcCchHHHHH
Confidence 11 1111 111225899999999999999999999999999999999999954 888 578999999999999999
Q ss_pred HHHHHHHHhhhc-----cccCccccccc--cccCCcccccccccc----ccc-----CCC---cccC-CCCCCCCCCCCC
Q 012307 233 ALEAVVGHLRKF-----LVDQGVLPLFE--KTYNASISQERQVET----WAD-----KSS---LHAA-TQSAISTEYTPS 292 (466)
Q Consensus 233 A~~~I~~~l~~~-----~~~~~~~p~~~--~~~~~~~~~~r~~~~----~~~-----~~~---~~~~-~~~~~~~~y~~p 292 (466)
|+..|..+|.++ ....+.++|++ ..+++.+...++.-. +.. ... +... ...+....++.+
T Consensus 198 al~~Is~~L~~~~~~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~ 277 (485)
T KOG2190|consen 198 ALVQISSRLLENPPRSPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLV 277 (485)
T ss_pred HHHHHHHHHHhcCCcCCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCcc
Confidence 999999999984 33566777777 222222211111000 000 000 0000 000000000000
Q ss_pred cc-----CCCcccCCCccccccccCCCcccCC------CCCCCcccccCCCCCCCCCcccceEEEEEeccCcccceeccc
Q 012307 293 TR-----RESLFLEREPQLESRYRLSGISIYG------QDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVG 361 (466)
Q Consensus 293 ~~-----~~~~~~~~~~~~~~~~~~~~~~~yg------~~~~~~~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkg 361 (466)
.. ....+.-.....+..+..+....+. ++..+.............. ...++.+|.||.+++|+||||+
T Consensus 278 i~~l~~~~~~~i~v~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~-~~~v~~~l~vps~~igciiGk~ 356 (485)
T KOG2190|consen 278 IRALRNETGASISVGDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDL-TQTVTQRLLVPSDLIGCIIGKG 356 (485)
T ss_pred chhhhhhcCCceEeccccCcceeeeccccCcccccccchhhhhhccccccccccccc-cceeeeeeccCccccceeeccc
Confidence 00 0000000000000000000000111 0000000000000000011 3457899999999999999999
Q ss_pred cchHHHHHhHhCCeEEEecCCC--CCCceEEEEEcCHHHHHHHHHHHHHHHhcCcCCCC
Q 012307 362 GTSIENIRRTSGAIITVQESRG--LPDEITVEIKGTSSQVQLAQQLIQEYMNNHKESIT 418 (466)
Q Consensus 362 G~~Ik~Ir~~SGA~I~I~~~~~--~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~~~~ 418 (466)
|.+|.+||+.|||.|+|.+... ..+++.++|+|+..+...|+++|..++...+....
T Consensus 357 G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~ 415 (485)
T KOG2190|consen 357 GAKISEIRQRTGASISILNKEEVSGVREALVQITGMLREDLLAQYLIRARLSAPKSSMG 415 (485)
T ss_pred ccchHHHHHhcCCceEEccccccCCcceeEEEecchhHHHHhhhhhcccccccCccCCC
Confidence 9999999999999999988665 67899999999999999999999999998776543
No 3
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=4.4e-35 Score=299.06 Aligned_cols=252 Identities=23% Similarity=0.369 Sum_probs=198.5
Q ss_pred CCceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC-C-CCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhc
Q 012307 75 PGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG-P-VSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVS 152 (466)
Q Consensus 75 ~~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~-~-~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~ 152 (466)
+.+++.+|+||.+++|+||||+|++||+|++.+||++.+..+ . .....+.+.|+|.++. +..|...+.+++..-.
T Consensus 136 ~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~---ve~a~~lV~dil~e~~ 212 (600)
T KOG1676|consen 136 SVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDK---VEQAKQLVADILREED 212 (600)
T ss_pred ccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHH---HHHHHHHHHHHHHhcc
Confidence 467899999999999999999999999999999999888755 2 2236788999999976 4556666666665421
Q ss_pred CCCCCCcccc-cCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHH
Q 012307 153 GLPENDVDAK-ASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVL 231 (466)
Q Consensus 153 ~l~~~~~~~~-~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~ 231 (466)
+-........ .......+.+|.||...||.||||+|++||+|+.+||++|+|.+++ .| .+.||++.|.|+.+.|.
T Consensus 213 ~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd-~p---~speR~~~IiG~~d~ie 288 (600)
T KOG1676|consen 213 DEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDD-DP---SSPERPAQIIGTVDQIE 288 (600)
T ss_pred cCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCC-CC---CCccceeeeecCHHHHH
Confidence 1111110000 1223455899999999999999999999999999999999999655 34 58899999999999999
Q ss_pred HHHHHHHHHhhhccccCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCcccccccc
Q 012307 232 KALEAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYR 311 (466)
Q Consensus 232 ~A~~~I~~~l~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~ 311 (466)
+|.++|.++|++...-. ...|
T Consensus 289 ~Aa~lI~eii~~~~~~~-------------------~~~~---------------------------------------- 309 (600)
T KOG1676|consen 289 HAAELINEIIAEAEAGA-------------------GGGM---------------------------------------- 309 (600)
T ss_pred HHHHHHHHHHHHHhccC-------------------CCCc----------------------------------------
Confidence 99999999998752110 0000
Q ss_pred CCCcccCCCCCCCcccccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecC--CCCCCceE
Q 012307 312 LSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQES--RGLPDEIT 389 (466)
Q Consensus 312 ~~~~~~yg~~~~~~~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~--~~~~~er~ 389 (466)
..+.|... ..++|.||.+++|.||||+|++||.|.++|||++.+.+. .++++|++
T Consensus 310 ----------------------~~G~P~~~-~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ekt 366 (600)
T KOG1676|consen 310 ----------------------GGGAPGLV-AQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKT 366 (600)
T ss_pred ----------------------CCCCccce-eeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceE
Confidence 00111111 267899999999999999999999999999999999875 34678999
Q ss_pred EEEEcCHHHHHHHHHHHHHHHhcCcC
Q 012307 390 VEIKGTSSQVQLAQQLIQEYMNNHKE 415 (466)
Q Consensus 390 V~I~Gt~~~V~~A~~lI~~~i~~~~~ 415 (466)
|+|+|+..||+.|++||+++|.....
T Consensus 367 f~IrG~~~QIdhAk~LIr~kvg~~~~ 392 (600)
T KOG1676|consen 367 FVIRGDKRQIDHAKQLIRDKVGDIAP 392 (600)
T ss_pred EEEecCcccchHHHHHHHHHhcccCC
Confidence 99999999999999999999998544
No 4
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=1.1e-33 Score=288.84 Aligned_cols=251 Identities=26% Similarity=0.321 Sum_probs=203.7
Q ss_pred ceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCC
Q 012307 77 HCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPE 156 (466)
Q Consensus 77 ~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~ 156 (466)
-.+.+..||.++||+||||+|+.|..|+.++||+|++.....+..+|.|.+.|.+++ ++.|...|..+..+.+ ...
T Consensus 53 ~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~---v~~aK~li~evv~r~~-~~~ 128 (600)
T KOG1676|consen 53 VQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPEN---VEVAKQLIGEVVSRGR-PPG 128 (600)
T ss_pred ccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCccc---HHHHHHhhhhhhhccC-CCC
Confidence 357788899999999999999999999999999999887777789999999999987 5566667777766654 111
Q ss_pred CCcccccCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHH
Q 012307 157 NDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEA 236 (466)
Q Consensus 157 ~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~ 236 (466)
...++ .....++.+++||...+|+||||+|++||+|++++||++.+..+.... ....+.+.|+|++++|+.|..|
T Consensus 129 ~~~~~--q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~---~~~~KplritGdp~~ve~a~~l 203 (600)
T KOG1676|consen 129 GFPDN--QGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIA---TGADKPLRITGDPDKVEQAKQL 203 (600)
T ss_pred Ccccc--CCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcC---CCCCCceeecCCHHHHHHHHHH
Confidence 11111 113668999999999999999999999999999999999999765543 4478899999999999999999
Q ss_pred HHHHhhhccccCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcc
Q 012307 237 VVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGIS 316 (466)
Q Consensus 237 I~~~l~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~ 316 (466)
|.++|++..... + + . ..
T Consensus 204 V~dil~e~~~~~----------------------~------------g----------------~-------------~~ 220 (600)
T KOG1676|consen 204 VADILREEDDEV----------------------P------------G----------------S-------------GG 220 (600)
T ss_pred HHHHHHhcccCC----------------------C------------c----------------c-------------cc
Confidence 999999742110 0 0 0 00
Q ss_pred cCCCCCCCcccccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCC-CCCceEEEEEcC
Q 012307 317 IYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRG-LPDEITVEIKGT 395 (466)
Q Consensus 317 ~yg~~~~~~~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~-~~~er~V~I~Gt 395 (466)
.+|.+ .....+.+|.||.+.||.||||+|++||+|+.+||++|+|..+.+ .+.||.+.|.|+
T Consensus 221 ~~g~~-----------------~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~ 283 (600)
T KOG1676|consen 221 HAGVR-----------------GGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGT 283 (600)
T ss_pred ccCcC-----------------ccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecC
Confidence 01111 012247899999999999999999999999999999999987665 577999999999
Q ss_pred HHHHHHHHHHHHHHHhcCcCC
Q 012307 396 SSQVQLAQQLIQEYMNNHKES 416 (466)
Q Consensus 396 ~~~V~~A~~lI~~~i~~~~~~ 416 (466)
.++|+.|.+||.++|++....
T Consensus 284 ~d~ie~Aa~lI~eii~~~~~~ 304 (600)
T KOG1676|consen 284 VDQIEHAAELINEIIAEAEAG 304 (600)
T ss_pred HHHHHHHHHHHHHHHHHHhcc
Confidence 999999999999999987654
No 5
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.97 E-value=2e-30 Score=253.34 Aligned_cols=287 Identities=21% Similarity=0.309 Sum_probs=203.2
Q ss_pred CceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC-CCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCC
Q 012307 76 GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG-PVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGL 154 (466)
Q Consensus 76 ~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~-~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l 154 (466)
.+..+|+|||..+||.||||.|.+||.|-..|.|||+|... ..+..||+++|-+.+|. ..+|...|++++.+-..
T Consensus 197 ~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg---~s~Ac~~ILeimqkEA~- 272 (584)
T KOG2193|consen 197 KDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG---TSKACKMILEIMQKEAV- 272 (584)
T ss_pred cCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc---hHHHHHHHHHHHHHhhh-
Confidence 44569999999999999999999999999999999999754 45789999999999986 56777777777654211
Q ss_pred CCCCcccccCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHH
Q 012307 155 PENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKAL 234 (466)
Q Consensus 155 ~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~ 234 (466)
+.+. .....++++-.+.+||+||||.|.+||+|+.+||++|.|.+--++.- -..||.+++.|..++|.+|.
T Consensus 273 -~~k~------~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~--ynpERTItVkGsiEac~~AE 343 (584)
T KOG2193|consen 273 -DDKV------AEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSL--YNPERTITVKGSIEACVQAE 343 (584)
T ss_pred -ccch------hhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcc--cCccceEEecccHHHHHHHH
Confidence 1011 14577899999999999999999999999999999999986444332 35699999999999999999
Q ss_pred HHHHHHhhhccccCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCC
Q 012307 235 EAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSG 314 (466)
Q Consensus 235 ~~I~~~l~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~ 314 (466)
.+|+.+|+++...+ +. .......+..+-....++.+++. +.++.|+.. +..-++. ..
T Consensus 344 ~eImkKlre~yEnD-l~---a~s~q~~l~P~l~~~~l~~f~ss---------S~~~~Ph~~-----Ps~v~~a-----~p 400 (584)
T KOG2193|consen 344 AEIMKKLRECYEND-LA---AMSLQCHLPPGLNLPALGLFPSS---------SAVSPPHFP-----PSPVTFA-----SP 400 (584)
T ss_pred HHHHHHHHHHHhhh-HH---HhhccCCCCcccCccccCCCCcc---------cccCCCCCC-----CCccccC-----CC
Confidence 99999999975432 00 00000000000000000000000 001111000 0000000 00
Q ss_pred cccCCCCCCCcccccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCC-CCCCceEEEEE
Q 012307 315 ISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESR-GLPDEITVEIK 393 (466)
Q Consensus 315 ~~~yg~~~~~~~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~-~~~~er~V~I~ 393 (466)
...+.+ . ..+....|.||...+|+||||+|.+||.|-+.+||.|+|..+. ++..+|.|+|+
T Consensus 401 ~~~~hq----------------~--pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViIt 462 (584)
T KOG2193|consen 401 YPLFHQ----------------N--PEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIIT 462 (584)
T ss_pred chhhhc----------------C--cchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEec
Confidence 000000 0 1334678999999999999999999999999999999997654 34679999999
Q ss_pred cCHHHHHHHHHHHHHHHhcCcCC
Q 012307 394 GTSSQVQLAQQLIQEYMNNHKES 416 (466)
Q Consensus 394 Gt~~~V~~A~~lI~~~i~~~~~~ 416 (466)
|.+++.-+|+-.|..+|.+....
T Consensus 463 GppeaqfKAQgrifgKikEenf~ 485 (584)
T KOG2193|consen 463 GPPEAQFKAQGRIFGKIKEENFF 485 (584)
T ss_pred CChHHHHhhhhhhhhhhhhhccC
Confidence 99999999999999999986543
No 6
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.95 E-value=6.1e-29 Score=242.96 Aligned_cols=247 Identities=23% Similarity=0.379 Sum_probs=196.8
Q ss_pred CceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC---CCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhc
Q 012307 76 GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG---PVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVS 152 (466)
Q Consensus 76 ~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~---~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~ 152 (466)
+++.+||+.++.++|++|||.|.+||+|+.+||++|.|++- ..-++||.|+|.|..|.| ..|-..|.+.++++-
T Consensus 278 ~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac---~~AE~eImkKlre~y 354 (584)
T KOG2193|consen 278 EEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEAC---VQAEAEIMKKLRECY 354 (584)
T ss_pred hhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHH---HHHHHHHHHHHHHHH
Confidence 77899999999999999999999999999999999999864 345789999999987764 345455554443320
Q ss_pred --C---------CCCCC-------cc-c-----------c----------cCCCcceEEEEEeccCcceeeecCCchhHH
Q 012307 153 --G---------LPEND-------VD-A-----------K----------ASGAAFCSVRLLVPSTQAINLIGKQGSLIK 192 (466)
Q Consensus 153 --~---------l~~~~-------~~-~-----------~----------~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik 192 (466)
+ +.++. +. . . ........++|.||...+|.||||+|..||
T Consensus 355 EnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIK 434 (584)
T KOG2193|consen 355 ENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIK 434 (584)
T ss_pred hhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHH
Confidence 0 11100 00 0 0 012355678999999999999999999999
Q ss_pred HHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhccccCccccccccccCCcccccccccccc
Q 012307 193 SIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWA 272 (466)
Q Consensus 193 ~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~ 272 (466)
.|.+.+||.|+|.+.+ .| +..+|.|+|+|.+++..+|...|..+|.+..+- .
T Consensus 435 ql~RfagASiKIappE-~p---dvseRMViItGppeaqfKAQgrifgKikEenf~---~--------------------- 486 (584)
T KOG2193|consen 435 QLSRFAGASIKIAPPE-IP---DVSERMVIITGPPEAQFKAQGRIFGKIKEENFF---L--------------------- 486 (584)
T ss_pred HHHHhccceeeecCCC-CC---CcceeEEEecCChHHHHhhhhhhhhhhhhhccC---C---------------------
Confidence 9999999999998643 34 788999999999999999999999999875321 0
Q ss_pred cCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCCcccccCCCCCCCCCcccceEEEEEeccC
Q 012307 273 DKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPIS 352 (466)
Q Consensus 273 ~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~~~~~s~~~~~~~~~~~~~t~~i~IP~~ 352 (466)
| + ....+..++.||..
T Consensus 487 -------------------P---------k------------------------------------eevklethirVPs~ 502 (584)
T KOG2193|consen 487 -------------------P---------K------------------------------------EEVKLETHIRVPSS 502 (584)
T ss_pred -------------------c---------h------------------------------------hhheeeeeeeccch
Confidence 0 0 01235678999999
Q ss_pred cccceeccccchHHHHHhHhCCeEEEecCC--CCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcCCC
Q 012307 353 YAEDIIGVGGTSIENIRRTSGAIITVQESR--GLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKESI 417 (466)
Q Consensus 353 ~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~--~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~~~ 417 (466)
.+|+||||||.++++|++.|+|.|.|+++. +..+.-+|.|.|..-+.+.|+..|.++|.+.+...
T Consensus 503 ~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhfyatq~aQrki~~iv~qvkq~~ 569 (584)
T KOG2193|consen 503 AAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHFYATQNAQRKIAHIVNQVKQSG 569 (584)
T ss_pred hhhhhhccccccHHHHhccccceEEccccCCCCccceeeeeeechhhcchHHHHHHHHHHHHHHHhh
Confidence 999999999999999999999999998754 23456788999999999999999999999987643
No 7
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.95 E-value=1.1e-26 Score=221.33 Aligned_cols=271 Identities=22% Similarity=0.332 Sum_probs=191.9
Q ss_pred CceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC---CCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhc
Q 012307 76 GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG---PVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVS 152 (466)
Q Consensus 76 ~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~---~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~ 152 (466)
+.+++|+|||+..+|.||||+|++|.+|+++|||||++++. .|++.||+|+|+|+.+. .+..+.-|.++|+
T Consensus 37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~ea------i~av~efI~dKir 110 (402)
T KOG2191|consen 37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEA------LNAVHEFIADKIR 110 (402)
T ss_pred CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHH------HHHHHHHHHHHHH
Confidence 34999999999999999999999999999999999999864 79999999999999753 1222233444554
Q ss_pred CCCCCCcc-----cccCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCH
Q 012307 153 GLPENDVD-----AKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEA 227 (466)
Q Consensus 153 ~l~~~~~~-----~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~ 227 (466)
+....... .+...+....++++||+..+|.||||+|.+||.|+++++|.|+|.+.+ |....-.+|+|++.|++
T Consensus 111 e~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqk--pt~~sLqervvt~sge~ 188 (402)
T KOG2191|consen 111 EKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQK--PTGISLQERVVTVSGEP 188 (402)
T ss_pred HhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccC--CCCccceeEEEEecCCH
Confidence 43322111 111122445699999999999999999999999999999999999633 44447789999999999
Q ss_pred HHHHHHHHHHHHHhhhccccCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCcccc
Q 012307 228 AKVLKALEAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLE 307 (466)
Q Consensus 228 ~~V~~A~~~I~~~l~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~ 307 (466)
++..+|+.+|+++|.+.....+.+. ++ |+.- .+...+|.
T Consensus 189 e~~~~A~~~IL~Ki~eDpqs~scln---------~s-------ya~v--------sGpvaNsn----------------- 227 (402)
T KOG2191|consen 189 EQNMKAVSLILQKIQEDPQSGSCLN---------IS-------YANV--------SGPVANSN----------------- 227 (402)
T ss_pred HHHHHHHHHHHHHhhcCCcccceec---------cc-------hhcc--------cCcccccC-----------------
Confidence 9999999999999987533221110 00 0000 00000000
Q ss_pred ccccCCCcccCCCCCCCcccccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCC---C
Q 012307 308 SRYRLSGISIYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRG---L 384 (466)
Q Consensus 308 ~~~~~~~~~~yg~~~~~~~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~---~ 384 (466)
+ ..+.|+. ...-+....+..+.++....|..-|.+|.++-.|-..+|+.+.|.+-.+ .
T Consensus 228 ----P-tGspya~--------------~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l~~m~g 288 (402)
T KOG2191|consen 228 ----P-TGSPYAY--------------QAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQALNTMAG 288 (402)
T ss_pred ----C-CCCCCCC--------------CCccccccchhhccccccccccccccccccceeeecccccceeeccccccccc
Confidence 0 0011110 0000112234456788999999999999999999999999999876433 3
Q ss_pred CCceEEEEEcCHHHHHHHHHHHHHHHhcCcC
Q 012307 385 PDEITVEIKGTSSQVQLAQQLIQEYMNNHKE 415 (466)
Q Consensus 385 ~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~ 415 (466)
+.++ +-+.|-.-.+..|.-+|...+.....
T Consensus 289 ~gy~-~n~~g~~ls~~aa~g~L~~~~~~a~t 318 (402)
T KOG2191|consen 289 YGYN-TNILGLGLSILAAEGVLAAKVASANT 318 (402)
T ss_pred cccc-ccccchhhhhhhhhhHHHHhhcccCc
Confidence 4455 77888899999999999888776543
No 8
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.92 E-value=3e-24 Score=204.80 Aligned_cols=191 Identities=25% Similarity=0.354 Sum_probs=149.9
Q ss_pred cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhccc
Q 012307 167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLV 246 (466)
Q Consensus 167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~ 246 (466)
....+++|||+..+|.||||+|++|.+||+++||+|+++... .++.+.+||+|.|+|+.+++....++|+++|++.+.
T Consensus 37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~--dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~ 114 (402)
T KOG2191|consen 37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSK--DFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQ 114 (402)
T ss_pred CceEEEEEeecccccceeccchHHHHHHHhccCcEEEecccc--ccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHH
Confidence 348899999999999999999999999999999999998533 345599999999999999999999999999998654
Q ss_pred cCcc-ccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCCc
Q 012307 247 DQGV-LPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALS 325 (466)
Q Consensus 247 ~~~~-~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~ 325 (466)
+... ...++ |+. .+|
T Consensus 115 ~~~k~v~~~~------------------------------------pqt-----~~r----------------------- 130 (402)
T KOG2191|consen 115 AVAKPVDILQ------------------------------------PQT-----PDR----------------------- 130 (402)
T ss_pred hhcCCccccC------------------------------------CCC-----ccc-----------------------
Confidence 3211 00000 000 000
Q ss_pred ccccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCC---CCCceEEEEEcCHHHHHHH
Q 012307 326 TIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRG---LPDEITVEIKGTSSQVQLA 402 (466)
Q Consensus 326 ~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~---~~~er~V~I~Gt~~~V~~A 402 (466)
.-..++.||+.-+|.||||+|.+||.|++++||.|+|.+..+ ...||+|+++|++++..+|
T Consensus 131 ----------------~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A 194 (402)
T KOG2191|consen 131 ----------------IKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKA 194 (402)
T ss_pred ----------------cceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHH
Confidence 013578999999999999999999999999999999985332 3458999999999999999
Q ss_pred HHHHHHHHhcCcCCCC---CCCCCCCCCCCCCCCCCCCCCC
Q 012307 403 QQLIQEYMNNHKESIT---SSYGQIDTGYRPSYPQLGNSSY 440 (466)
Q Consensus 403 ~~lI~~~i~~~~~~~~---~~~~~~~~g~~~~~~~~~~~~~ 440 (466)
..||.++|.++..... ..|+.+. |...+|.|.|+++.
T Consensus 195 ~~~IL~Ki~eDpqs~scln~sya~vs-GpvaNsnPtGspya 234 (402)
T KOG2191|consen 195 VSLILQKIQEDPQSGSCLNISYANVS-GPVANSNPTGSPYA 234 (402)
T ss_pred HHHHHHHhhcCCcccceeccchhccc-CcccccCCCCCCCC
Confidence 9999999999887654 3454443 23456666666653
No 9
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.79 E-value=1.4e-18 Score=180.96 Aligned_cols=160 Identities=28% Similarity=0.408 Sum_probs=131.8
Q ss_pred cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec---------CHHHHHHHHHHH
Q 012307 167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG---------EAAKVLKALEAV 237 (466)
Q Consensus 167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G---------~~~~V~~A~~~I 237 (466)
...+.|||++...+|.||||+|..||+|+.++.++|+|. +.++ +..+|+|+|+| ..+++.+|.++|
T Consensus 41 ~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~--~~~~---~c~eRIiti~g~~~~~~~~~~~~al~ka~~~i 115 (485)
T KOG2190|consen 41 ETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVN--ESLP---GCPERIITITGNRVELNLSPATDALFKAFDMI 115 (485)
T ss_pred CcceEEEEeccccceeEEccCcHHHHHHhhcccccceee--cCCC---CCCcceEEEecccccccCCchHHHHHHHHHHH
Confidence 334489999999999999999999999999999999996 3345 56799999999 999999999999
Q ss_pred HHHhhhccccCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCccc
Q 012307 238 VGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISI 317 (466)
Q Consensus 238 ~~~l~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~ 317 (466)
...+++..... +.
T Consensus 116 v~~~~~d~~~~------~d------------------------------------------------------------- 128 (485)
T KOG2190|consen 116 VFKLEEDDEAA------ED------------------------------------------------------------- 128 (485)
T ss_pred hhccccccccc------cc-------------------------------------------------------------
Confidence 88665221100 00
Q ss_pred CCCCCCCcccccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecC-CCCCCceEEEEEcCH
Q 012307 318 YGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQES-RGLPDEITVEIKGTS 396 (466)
Q Consensus 318 yg~~~~~~~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~-~~~~~er~V~I~Gt~ 396 (466)
.+.+ .. ...++.+|.||.+++|+||||+|++||+||++|||+|+|..+ ...+++|.|+|+|.+
T Consensus 129 ~~~~---------------~~-~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~ 192 (485)
T KOG2190|consen 129 NGED---------------AS-GPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEP 192 (485)
T ss_pred CCcc---------------cc-CCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCch
Confidence 0000 00 013789999999999999999999999999999999999876 456789999999999
Q ss_pred HHHHHHHHHHHHHHhcCc
Q 012307 397 SQVQLAQQLIQEYMNNHK 414 (466)
Q Consensus 397 ~~V~~A~~lI~~~i~~~~ 414 (466)
++|.+|...|..+|.+..
T Consensus 193 ~av~~al~~Is~~L~~~~ 210 (485)
T KOG2190|consen 193 DAVKKALVQISSRLLENP 210 (485)
T ss_pred HHHHHHHHHHHHHHHhcC
Confidence 999999999999999965
No 10
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.72 E-value=2.5e-16 Score=146.81 Aligned_cols=149 Identities=23% Similarity=0.322 Sum_probs=126.8
Q ss_pred cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhccc
Q 012307 167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLV 246 (466)
Q Consensus 167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~ 246 (466)
..+.+++|+-+..+|.||||+|++||.|+.++++.|.|+ +. ...+|+++|+...+.|..-++.|+-.|++...
T Consensus 46 ~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vp-ds------~~peri~tisad~~ti~~ilk~iip~lee~f~ 118 (390)
T KOG2192|consen 46 SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVP-DS------SGPERILTISADIETIGEILKKIIPTLEEGFQ 118 (390)
T ss_pred cceeEEEEEecccccceeccccccHHHHhhhccceeecc-CC------CCCceeEEEeccHHHHHHHHHHHhhhhhhCCC
Confidence 447899999999999999999999999999999999997 33 34599999999999988887777776665321
Q ss_pred cCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCCcc
Q 012307 247 DQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALST 326 (466)
Q Consensus 247 ~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~~ 326 (466)
..
T Consensus 119 ~~------------------------------------------------------------------------------ 120 (390)
T KOG2192|consen 119 LP------------------------------------------------------------------------------ 120 (390)
T ss_pred CC------------------------------------------------------------------------------
Confidence 10
Q ss_pred cccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEe-cCCCCCCceEEEEEcCHHHHHHHHHH
Q 012307 327 IRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQ-ESRGLPDEITVEIKGTSSQVQLAQQL 405 (466)
Q Consensus 327 ~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~-~~~~~~~er~V~I~Gt~~~V~~A~~l 405 (466)
..+..+|+|..+++|.|||++|++||++|+.+.|+++|- +....+++|+|.|.|.+..|..+.+.
T Consensus 121 --------------~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~ 186 (390)
T KOG2192|consen 121 --------------SPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKI 186 (390)
T ss_pred --------------CchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHH
Confidence 114667899999999999999999999999999999985 34567899999999999999999999
Q ss_pred HHHHHhcCc
Q 012307 406 IQEYMNNHK 414 (466)
Q Consensus 406 I~~~i~~~~ 414 (466)
|.+.|.+..
T Consensus 187 il~~i~e~p 195 (390)
T KOG2192|consen 187 ILDLISESP 195 (390)
T ss_pred HHHHhhcCC
Confidence 999998753
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=99.67 E-value=2.3e-16 Score=144.16 Aligned_cols=139 Identities=28% Similarity=0.400 Sum_probs=107.0
Q ss_pred EEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEE---ecCHHHHHHHHHHHHHHhhhccccCc
Q 012307 173 LLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEM---QGEAAKVLKALEAVVGHLRKFLVDQG 249 (466)
Q Consensus 173 llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I---~G~~~~V~~A~~~I~~~l~~~~~~~~ 249 (466)
|.||.+.+|.|||++|++|+.|+++||++|++.. ++..|.| +++++++.+|.++|..+.+.+..+..
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~----------~~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~A 71 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS----------ETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKA 71 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc----------CCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 5689999999999999999999999999999962 2356778 78999999999999987775422100
Q ss_pred cccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCCccccc
Q 012307 250 VLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALSTIRS 329 (466)
Q Consensus 250 ~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~~~~~ 329 (466)
.. ++...|.
T Consensus 72 ~~-l~gd~y~---------------------------------------------------------------------- 80 (172)
T TIGR03665 72 LK-LLDDDYM---------------------------------------------------------------------- 80 (172)
T ss_pred HH-hcCCcce----------------------------------------------------------------------
Confidence 00 0000000
Q ss_pred CCCCCCCCCcccceEEEEEec---------cCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHH
Q 012307 330 SALGRASGPIVTQITQTMQIP---------ISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQ 400 (466)
Q Consensus 330 s~~~~~~~~~~~~~t~~i~IP---------~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~ 400 (466)
-.-+.|+ ...+|+|||++|.+++.|++.|||+|.|++ ..|.|.|++++++
T Consensus 81 --------------~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~-------~~v~i~G~~~~~~ 139 (172)
T TIGR03665 81 --------------LEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG-------KTVGIIGDPEQVQ 139 (172)
T ss_pred --------------EEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC-------CEEEEECCHHHHH
Confidence 0001111 136899999999999999999999999953 6899999999999
Q ss_pred HHHHHHHHHHhcC
Q 012307 401 LAQQLIQEYMNNH 413 (466)
Q Consensus 401 ~A~~lI~~~i~~~ 413 (466)
.|+.+|+++|+..
T Consensus 140 ~A~~~i~~li~~~ 152 (172)
T TIGR03665 140 IAREAIEMLIEGA 152 (172)
T ss_pred HHHHHHHHHHcCC
Confidence 9999999999543
No 12
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.63 E-value=2.3e-15 Score=138.58 Aligned_cols=152 Identities=28% Similarity=0.383 Sum_probs=109.7
Q ss_pred eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEe----cCHHHHHHHHHHHHHHhhhc
Q 012307 169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQ----GEAAKVLKALEAVVGHLRKF 244 (466)
Q Consensus 169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~----G~~~~V~~A~~~I~~~l~~~ 244 (466)
....+.||.+.+|.|||++|++|+.|+++||++|++.. ++..|.|. ++++++.+|+++|..++..+
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~----------~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf 72 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS----------ETGEVIIEPTDGEDPLAVLKARDIVKAIGRGF 72 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC----------CCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCC
Confidence 45789999999999999999999999999999999962 23577785 89999999999999988754
Q ss_pred cccCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCC
Q 012307 245 LVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPAL 324 (466)
Q Consensus 245 ~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~ 324 (466)
..+.... ++...|...+ -. +..|+..
T Consensus 73 ~~e~A~~-l~gd~y~~~V-----------------------------------------i~---------i~~~~~~--- 98 (180)
T PRK13763 73 SPEKALR-LLDDDYVLEV-----------------------------------------ID---------LSDYGDS--- 98 (180)
T ss_pred CHHHHHH-HhCCCceEEE-----------------------------------------EE---------hhhccCC---
Confidence 2211000 0000000000 00 0000000
Q ss_pred cccccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHH
Q 012307 325 STIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQ 404 (466)
Q Consensus 325 ~~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~ 404 (466)
+ ......+|+|||++|.+++.|++.|||+|.|++ ..|.|.|++++++.|+.
T Consensus 99 -------------~---------~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~-------~~v~i~G~~~~~~~A~~ 149 (180)
T PRK13763 99 -------------P---------NALRRIKGRIIGEGGKTRRIIEELTGVDISVYG-------KTVAIIGDPEQVEIARE 149 (180)
T ss_pred -------------h---------hHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC-------CEEEEEeCHHHHHHHHH
Confidence 0 011236899999999999999999999999953 45999999999999999
Q ss_pred HHHHHHhcC
Q 012307 405 LIQEYMNNH 413 (466)
Q Consensus 405 lI~~~i~~~ 413 (466)
.|+++++..
T Consensus 150 ~I~~li~g~ 158 (180)
T PRK13763 150 AIEMLIEGA 158 (180)
T ss_pred HHHHHHcCC
Confidence 999999543
No 13
>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=99.57 E-value=9.6e-15 Score=133.51 Aligned_cols=139 Identities=19% Similarity=0.227 Sum_probs=97.7
Q ss_pred EEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEe---cCCCCCCCCCChhHHHHHHHHHHhcCCCCCC
Q 012307 82 MIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLI---SGKEEPEAPVSPAMDAAVRVFKRVSGLPEND 158 (466)
Q Consensus 82 llvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I---~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~ 158 (466)
|.||.+.+|.|||++|++||+|+++|||+|++.+. +..|.| +++++ .+.+|++.|..+... ....+
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~ 70 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPL---AVMKAREVVKAIGRG---FSPEK 70 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHH---HHHHHHHHHHHHHcC---CCHHH
Confidence 56899999999999999999999999999999864 356888 34332 244444444443221 00000
Q ss_pred cccccCCCcceEEEEEecc---------CcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHH
Q 012307 159 VDAKASGAAFCSVRLLVPS---------TQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229 (466)
Q Consensus 159 ~~~~~~~~~~~~~~llVP~---------~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~ 229 (466)
.-. ..+......-+.|+. ..+|+|||++|++++.|++.|||+|.|. ++.|.|.|.+++
T Consensus 71 A~~-l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~------------~~~v~i~G~~~~ 137 (172)
T TIGR03665 71 ALK-LLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY------------GKTVGIIGDPEQ 137 (172)
T ss_pred HHH-hcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc------------CCEEEEECCHHH
Confidence 000 000111112233333 3689999999999999999999999995 257999999999
Q ss_pred HHHHHHHHHHHhhhc
Q 012307 230 VLKALEAVVGHLRKF 244 (466)
Q Consensus 230 V~~A~~~I~~~l~~~ 244 (466)
++.|..+|.+++.+.
T Consensus 138 ~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 138 VQIAREAIEMLIEGA 152 (172)
T ss_pred HHHHHHHHHHHHcCC
Confidence 999999999988654
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.54 E-value=5.1e-14 Score=129.62 Aligned_cols=142 Identities=20% Similarity=0.243 Sum_probs=99.6
Q ss_pred eEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEec----CCCCCCCCCChhHHHHHHHHHHhcC
Q 012307 78 CVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLIS----GKEEPEAPVSPAMDAAVRVFKRVSG 153 (466)
Q Consensus 78 ~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~----G~~e~~~~v~~A~~ai~~i~~~i~~ 153 (466)
+...|.||.+.+|.|||++|++||.|+++|||+|++.+. +..|.|. ++++ .+.+|++.|..+..-
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~---~i~kA~~~I~ai~~g--- 71 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPL---AVLKARDIVKAIGRG--- 71 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHH---HHHHHHHHHHHHhcC---
Confidence 467899999999999999999999999999999999864 3567775 3332 244444444443321
Q ss_pred CCCCCcccccCCCcceEEE-EEec---------cCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEE
Q 012307 154 LPENDVDAKASGAAFCSVR-LLVP---------STQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEM 223 (466)
Q Consensus 154 l~~~~~~~~~~~~~~~~~~-llVP---------~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I 223 (466)
....+.- ...+.. +..+ +.+. ...+|+|||++|++++.|++.|||+|.|. ++.|.|
T Consensus 72 f~~e~A~-~l~gd~-y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~------------~~~v~i 137 (180)
T PRK13763 72 FSPEKAL-RLLDDD-YVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVY------------GKTVAI 137 (180)
T ss_pred CCHHHHH-HHhCCC-ceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEc------------CCEEEE
Confidence 0000000 000001 1111 1111 14789999999999999999999999995 234889
Q ss_pred ecCHHHHHHHHHHHHHHhhhc
Q 012307 224 QGEAAKVLKALEAVVGHLRKF 244 (466)
Q Consensus 224 ~G~~~~V~~A~~~I~~~l~~~ 244 (466)
.|.++++..|...|..+++.+
T Consensus 138 ~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 138 IGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred EeCHHHHHHHHHHHHHHHcCC
Confidence 999999999999999998765
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=99.48 E-value=7.3e-14 Score=106.99 Aligned_cols=63 Identities=41% Similarity=0.483 Sum_probs=58.6
Q ss_pred EEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCC-CCCceEEEEEcCHHHHHHHHHHHH
Q 012307 345 QTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRG-LPDEITVEIKGTSSQVQLAQQLIQ 407 (466)
Q Consensus 345 ~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~-~~~er~V~I~Gt~~~V~~A~~lI~ 407 (466)
.+|.||.+++|+|||++|.+|++|+++|||+|+|.+... ...+|+|+|+|++++|+.|+.||+
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhhC
Confidence 579999999999999999999999999999999987655 578999999999999999999984
No 16
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.40 E-value=1.8e-12 Score=132.22 Aligned_cols=292 Identities=18% Similarity=0.174 Sum_probs=182.5
Q ss_pred CCceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCC
Q 012307 75 PGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGL 154 (466)
Q Consensus 75 ~~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l 154 (466)
++++.++++|+...|-.||||.|.+||.|++.+++||.+.+.. -.+++...+.|.+.. +.+|..++.++...-
T Consensus 65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p~~---v~~a~a~~~~~~~~~--- 137 (608)
T KOG2279|consen 65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFPVQ---VCKAKAAIHQILTEN--- 137 (608)
T ss_pred hhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCCCC---CChHHHHHHHHHhcC---
Confidence 4789999999999999999999999999999999999997652 234566666666654 666777766654331
Q ss_pred CCCCcccccCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHH
Q 012307 155 PENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKAL 234 (466)
Q Consensus 155 ~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~ 234 (466)
..+...+-+|...+++|+|++|++++.|+..++++|.+... .- ..-.+...|.+..+.+..|.
T Consensus 138 ------------~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n--gr---~g~~~~~~i~~qqk~~~~a~ 200 (608)
T KOG2279|consen 138 ------------TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN--GR---LGLSRLIKISGQQKEVAAAK 200 (608)
T ss_pred ------------Ccccccccchhhhcccccccchhhhcchhcccccccccccc--cc---cccccceecccccchHHHHH
Confidence 45677888999999999999999999999999999998632 11 34578888999998999999
Q ss_pred HHHHHHhhhccccCccccccccccCCcccccccccccccCCCcccCCCCCCC-CCCCCCccCCCcccCC-CccccccccC
Q 012307 235 EAVVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAIS-TEYTPSTRRESLFLER-EPQLESRYRL 312 (466)
Q Consensus 235 ~~I~~~l~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~-~~y~~p~~~~~~~~~~-~~~~~~~~~~ 312 (466)
.++.+.+.+......-+|.-...- -.|.... ... ..++. +....++..+.....- .++.+
T Consensus 201 ~~~~~~~~edeelv~~~~e~~q~r-----vprk~p~-------n~~-~~~m~~~~~s~~~h~~~~t~~s~spg~~----- 262 (608)
T KOG2279|consen 201 HLILEKVSEDEELVKRIAESAQTR-----VPRKQPI-------NVR-REDMTEPGGAGEPHLWKNTSSSMSPGAP----- 262 (608)
T ss_pred hhhhccccchhHHhhhchhhcccC-----CCCCCCc-------ccc-chhhcccccCCccccCccchhccCCCCC-----
Confidence 999988876422111111111100 0000000 000 00000 0000000000000000 00000
Q ss_pred CCcccCCCCCCCcccccCC------CCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCC-
Q 012307 313 SGISIYGQDPALSTIRSSA------LGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLP- 385 (466)
Q Consensus 313 ~~~~~yg~~~~~~~~~~s~------~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~- 385 (466)
+...-|.+.+ ..++.. ..+.-...+...-.+|.||...+|.+||+.|..|+.+...|++.+.|--..-..
T Consensus 263 -~~~~eg~dm~--v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~ 339 (608)
T KOG2279|consen 263 -LVTKEGGDMA--VVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSR 339 (608)
T ss_pred -CcccCCCcce--eEEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEeccccch
Confidence 0000000000 000000 000001123345678999999999999999999999999999999885432211
Q ss_pred --CceEEEEEcCHHHHHHHHHHHHHHHh
Q 012307 386 --DEITVEIKGTSSQVQLAQQLIQEYMN 411 (466)
Q Consensus 386 --~er~V~I~Gt~~~V~~A~~lI~~~i~ 411 (466)
.-.++.+.|+...+..|..||...+-
T Consensus 340 v~~~qic~~egkqh~~n~vl~ml~~~~p 367 (608)
T KOG2279|consen 340 VLQLQICVNEGKQHYENSVLEMLTVHVP 367 (608)
T ss_pred hhhhhhheecchhHHHHHHHhhhhccCC
Confidence 12568899999999999999975543
No 17
>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=99.33 E-value=1.7e-12 Score=97.74 Aligned_cols=60 Identities=30% Similarity=0.527 Sum_probs=55.2
Q ss_pred EEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHH
Q 012307 344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLI 406 (466)
Q Consensus 344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI 406 (466)
|.+|.||.+++|+|||++|.+|++|+++|||+|.|++. + ++..|+|+|++++|+.|+.+|
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 57899999999999999999999999999999999765 2 456999999999999999987
No 18
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.32 E-value=5.1e-12 Score=96.74 Aligned_cols=64 Identities=47% Similarity=0.684 Sum_probs=57.9
Q ss_pred EEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHH
Q 012307 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAV 237 (466)
Q Consensus 170 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I 237 (466)
+++|+||...+|.|||++|++|++|+++|||+|.+.+... + ...+|+|+|.|++++|.+|+.+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~-~---~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-P---GSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-C---CCCceEEEEEeCHHHHHHHHHhh
Confidence 3689999999999999999999999999999999985432 2 57799999999999999999987
No 19
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.32 E-value=2.5e-12 Score=97.42 Aligned_cols=61 Identities=26% Similarity=0.400 Sum_probs=55.9
Q ss_pred EEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 012307 345 QTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQ 407 (466)
Q Consensus 345 ~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~ 407 (466)
.+|.||.+++++|||++|++|++|+++|||+|.|++.. ..++.|+|+|+.++|..|+.+|+
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 57899999999999999999999999999999997654 46789999999999999999874
No 20
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.28 E-value=1e-11 Score=94.46 Aligned_cols=63 Identities=37% Similarity=0.565 Sum_probs=57.9
Q ss_pred EEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 012307 345 QTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQ 407 (466)
Q Consensus 345 ~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~ 407 (466)
.+|.||.+++++|||++|++|++|++.|||+|.|.+......++.|+|.|+.++++.|+.+|+
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i~ 64 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELIL 64 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHhC
Confidence 478999999999999999999999999999999987655567899999999999999999874
No 21
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.26 E-value=1.3e-11 Score=93.13 Aligned_cols=58 Identities=31% Similarity=0.541 Sum_probs=53.2
Q ss_pred EEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcC-HHHHHHHHHHHH
Q 012307 344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGT-SSQVQLAQQLIQ 407 (466)
Q Consensus 344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt-~~~V~~A~~lI~ 407 (466)
+..|.||.+++|+|||++|++|++|+++|||+|.|++ ++.|.|+|+ +++++.|+.+|+
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~------~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED------DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC------CCEEEEEeCCHHHHHHHHHHhC
Confidence 5679999999999999999999999999999999965 357999999 899999999883
No 22
>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=99.10 E-value=1.4e-10 Score=87.80 Aligned_cols=61 Identities=26% Similarity=0.421 Sum_probs=55.0
Q ss_pred EEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHH
Q 012307 171 VRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVV 238 (466)
Q Consensus 171 ~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~ 238 (466)
.+|.||..+++.|||++|++|++|+++|||+|.+++. ...++.|+|+|+.++|.+|+.+|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~-------~~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDP-------GSKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCC-------CCCCCEEEEEcCHHHHHHHHHHhC
Confidence 5789999999999999999999999999999999743 245789999999999999998873
No 23
>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=99.07 E-value=1.6e-10 Score=86.89 Aligned_cols=60 Identities=33% Similarity=0.544 Sum_probs=54.1
Q ss_pred EEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHH
Q 012307 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAV 237 (466)
Q Consensus 170 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I 237 (466)
|.+|.||..++++|||++|.+|++|+++|||+|.+..+ + ....|+|.|+.++|.+|+++|
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 57899999999999999999999999999999999732 2 355999999999999999886
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=99.02 E-value=1.3e-09 Score=82.78 Aligned_cols=62 Identities=40% Similarity=0.609 Sum_probs=55.7
Q ss_pred EEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHH
Q 012307 171 VRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAV 237 (466)
Q Consensus 171 ~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I 237 (466)
.+|.||..+++.|||++|++|++|+++|||+|.|..... ...++.|.|.|..+++..|+.+|
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 689999999999999999999999999999999974321 36789999999999999999887
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=99.01 E-value=1.3e-09 Score=82.13 Aligned_cols=58 Identities=21% Similarity=0.327 Sum_probs=52.4
Q ss_pred eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecC-HHHHHHHHHHH
Q 012307 169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGE-AAKVLKALEAV 237 (466)
Q Consensus 169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~-~~~V~~A~~~I 237 (466)
....+.||..++|+|||++|++|++|+++|||+|.+.. ++.|.|.|+ .+++++|+++|
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 45678999999999999999999999999999999852 357999998 99999999887
No 26
>PF13014 KH_3: KH domain
Probab=98.99 E-value=7e-10 Score=77.57 Aligned_cols=42 Identities=40% Similarity=0.610 Sum_probs=38.6
Q ss_pred ccceeeecCChhHHHHHHHhCceEEEeC-CCCCCCCeEEEecC
Q 012307 88 KVGSIIGRKGELIKKTCEDTRARIKVLD-GPVSSPDRIVLISG 129 (466)
Q Consensus 88 ~vG~IIGk~G~~Ik~I~~etga~I~v~~-~~~~~~ervv~I~G 129 (466)
+||+||||+|++|++|+++|+|+|+|++ ..++..+|.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 5899999999999999999999999998 45678899999987
No 27
>smart00322 KH K homology RNA-binding domain.
Probab=98.97 E-value=3.2e-09 Score=80.92 Aligned_cols=67 Identities=34% Similarity=0.535 Sum_probs=60.0
Q ss_pred eEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 012307 343 ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMN 411 (466)
Q Consensus 343 ~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~ 411 (466)
.+.+|.||.++++.+||++|.+|++|++.+|++|.+..... ....|+|.|+.++++.|..+|.+.++
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--~~~~v~i~g~~~~v~~a~~~i~~~~~ 69 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--EERVVEITGPPENVEKAAELILEILE 69 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC--CccEEEEEcCHHHHHHHHHHHHHHhC
Confidence 46789999999999999999999999999999999965432 56899999999999999999988763
No 28
>PF13014 KH_3: KH domain
Probab=98.96 E-value=1e-09 Score=76.71 Aligned_cols=42 Identities=36% Similarity=0.605 Sum_probs=37.7
Q ss_pred cccceeccccchHHHHHhHhCCeEEEec-CCCCCCceEEEEEc
Q 012307 353 YAEDIIGVGGTSIENIRRTSGAIITVQE-SRGLPDEITVEIKG 394 (466)
Q Consensus 353 ~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~-~~~~~~er~V~I~G 394 (466)
++|+|||++|++|++|+++|||+|+|++ ......+++|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 5899999999999999999999999987 33456899999998
No 29
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.91 E-value=7.2e-09 Score=94.35 Aligned_cols=154 Identities=25% Similarity=0.286 Sum_probs=111.4
Q ss_pred eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec-----CHHHHHHHHHHHHHHhhh
Q 012307 169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG-----EAAKVLKALEAVVGHLRK 243 (466)
Q Consensus 169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G-----~~~~V~~A~~~I~~~l~~ 243 (466)
....+.||...++.|||+.|+.-+.|.+.++++|.+. ..+..|+|.. ++..+.+|.+.|..+-+.
T Consensus 8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD----------~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrG 77 (194)
T COG1094 8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID----------SKTGSVTIRTTRKTEDPLALLKARDVVKAIGRG 77 (194)
T ss_pred ceeeeecCchhheeeecccccchHHHHhhcCeEEEEE----------CCCCeEEEEecCCCCChHHHHHHHHHHHHHhcC
Confidence 4566899999999999999999999999999999995 4456676654 577899999999988887
Q ss_pred ccccCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCC
Q 012307 244 FLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPA 323 (466)
Q Consensus 244 ~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~ 323 (466)
|..+..+.-+....+-..+... -+-..
T Consensus 78 F~pe~A~~LL~d~~~levIdi~---------------------------------------------------~~~~~-- 104 (194)
T COG1094 78 FPPEKALKLLEDDYYLEVIDLK---------------------------------------------------DVVTL-- 104 (194)
T ss_pred CCHHHHHHHhcCCcEEEEEEHH---------------------------------------------------HhccC--
Confidence 7544322211110000000000 00000
Q ss_pred CcccccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHH
Q 012307 324 LSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQ 403 (466)
Q Consensus 324 ~~~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~ 403 (466)
. ... =....|+|||++|.+-+.|++.|||.|.|.. .+|-|.|.+++|+.|+
T Consensus 105 -----------~----~~~-------l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g-------~tVaiiG~~~~v~iAr 155 (194)
T COG1094 105 -----------S----GDH-------LRRIKGRIIGREGKTRRAIEELTGVYISVYG-------KTVAIIGGFEQVEIAR 155 (194)
T ss_pred -----------c----hhh-------hhHhhceeeCCCchHHHHHHHHhCCeEEEeC-------cEEEEecChhhhHHHH
Confidence 0 000 0234699999999999999999999999953 5899999999999999
Q ss_pred HHHHHHHhcCc
Q 012307 404 QLIQEYMNNHK 414 (466)
Q Consensus 404 ~lI~~~i~~~~ 414 (466)
..|..+|+..+
T Consensus 156 ~AVemli~G~~ 166 (194)
T COG1094 156 EAVEMLINGAP 166 (194)
T ss_pred HHHHHHHcCCC
Confidence 99999998754
No 30
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.90 E-value=6.9e-09 Score=114.51 Aligned_cols=231 Identities=22% Similarity=0.277 Sum_probs=161.6
Q ss_pred eEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhc-----
Q 012307 78 CVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVS----- 152 (466)
Q Consensus 78 ~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~----- 152 (466)
+..++.+....+.+|||++|.+|+.++.++.+.|+|++.. .......|.|..+.. ..+...+...+.++.
T Consensus 201 ~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn--~~~~~~~i~~~~~~~---~~~~~~i~~~~~~le~~~~~ 275 (753)
T KOG2208|consen 201 VFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSN--KSSPSNKIDGRLNSS---SSINVEIQEALTRLESEFDY 275 (753)
T ss_pred EEEEeeccccchhhhccccccccccccccceeEEEccccc--ccchhhhhccccccc---eehhhhhHHHHHHhcChhhh
Confidence 6789999999999999999999999999999999999662 222223344432221 111111111111110
Q ss_pred ---------CCCCCC-------------------------ccc----------------c-----cCCCcceEEEEEecc
Q 012307 153 ---------GLPEND-------------------------VDA----------------K-----ASGAAFCSVRLLVPS 177 (466)
Q Consensus 153 ---------~l~~~~-------------------------~~~----------------~-----~~~~~~~~~~llVP~ 177 (466)
.+.... .+. . ........+.+.+-.
T Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~ 355 (753)
T KOG2208|consen 276 DEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFP 355 (753)
T ss_pred hhhhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecH
Confidence 000000 000 0 112244677888889
Q ss_pred CcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhccccCccccccccc
Q 012307 178 TQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQGVLPLFEKT 257 (466)
Q Consensus 178 ~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~p~~~~~ 257 (466)
..+..++||+|.+|.+|++++.|.+.+... +++...+.++|...++.+|...+...+.+.+..
T Consensus 356 ~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~-------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~---------- 418 (753)
T KOG2208|consen 356 EELKFVIGKKGANIEKIREESQVKIDLPKQ-------GSNNKKVVITGVSANDEKAVEDVEKIIAEILNS---------- 418 (753)
T ss_pred HhhhhhcCCCCccHHHHHHhhhhceecccc-------cCCCCCeEEeccccchhHHHHHHHHHHHhhhcc----------
Confidence 999999999999999999999999999631 467888999999999999999999877765210
Q ss_pred cCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCCcccccCCCCCCCC
Q 012307 258 YNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALSTIRSSALGRASG 337 (466)
Q Consensus 258 ~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~~~~~s~~~~~~~ 337 (466)
T Consensus 419 -------------------------------------------------------------------------------- 418 (753)
T KOG2208|consen 419 -------------------------------------------------------------------------------- 418 (753)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcC
Q 012307 338 PIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKE 415 (466)
Q Consensus 338 ~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~ 415 (466)
.....+.||...+.+|||.+|..|++|...+|+ |+|...+.......+++.|....+..++.++..+....++
T Consensus 419 ----~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~-v~i~f~~~~~~~~~~~~~~~~~dv~~~~~~~~~~~~~a~~ 491 (753)
T KOG2208|consen 419 ----IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGG-VHIKFQNNNNSSDMVTIRGISKDVEKSVSLLKALKADAKN 491 (753)
T ss_pred ----cccceeecCccchhhhhccccccHHHHHhhcCc-EEEecCCCCcccccceEeccccccchhHHHHHhhhhhhhc
Confidence 124568899999999999999999999999995 5554444444556688888887777766666665554443
No 31
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=98.81 E-value=2.4e-09 Score=109.78 Aligned_cols=147 Identities=29% Similarity=0.448 Sum_probs=122.6
Q ss_pred cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhccc
Q 012307 167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLV 246 (466)
Q Consensus 167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~ 246 (466)
..+.+++.|+...+-+++||.|.+|+.|++.++++|.+.+++ -..+++-.+.|-+.++.+|..+++.++.+..
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 KDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED------VGDERVLLISGFPVQVCKAKAAIHQILTENT- 138 (608)
T ss_pred hheeeeEeecccceeeeeccccCCcchhhcccccceecCccc------CCcccchhhccCCCCCChHHHHHHHHHhcCC-
Confidence 557789999999999999999999999999999999997543 2346666777789999999999888765421
Q ss_pred cCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCCcc
Q 012307 247 DQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALST 326 (466)
Q Consensus 247 ~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~~ 326 (466)
T Consensus 139 -------------------------------------------------------------------------------- 138 (608)
T KOG2279|consen 139 -------------------------------------------------------------------------------- 138 (608)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred cccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHH
Q 012307 327 IRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLI 406 (466)
Q Consensus 327 ~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI 406 (466)
.+..++.+|...+++|+|++|.+|..|+..|+|+|.++...-.-..+.+.|.|..+-++.|+.++
T Consensus 139 ---------------pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~ 203 (608)
T KOG2279|consen 139 ---------------PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLI 203 (608)
T ss_pred ---------------cccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhh
Confidence 13456778999999999999999999999999999997763334578888999999999999999
Q ss_pred HHHHhcCcC
Q 012307 407 QEYMNNHKE 415 (466)
Q Consensus 407 ~~~i~~~~~ 415 (466)
.+.+++...
T Consensus 204 ~~~~~edee 212 (608)
T KOG2279|consen 204 LEKVSEDEE 212 (608)
T ss_pred hccccchhH
Confidence 999987543
No 32
>smart00322 KH K homology RNA-binding domain.
Probab=98.73 E-value=7.6e-08 Score=73.20 Aligned_cols=66 Identities=33% Similarity=0.568 Sum_probs=58.7
Q ss_pred eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHh
Q 012307 169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHL 241 (466)
Q Consensus 169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l 241 (466)
.+.++.||..+++.|||++|.+|++|++.++++|.+... ......|.|.|..+++..|..+|.+.+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~-------~~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPED-------GSEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCC-------CCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 578899999999999999999999999999999999632 125788999999999999999998765
No 33
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.72 E-value=2.1e-08 Score=110.83 Aligned_cols=216 Identities=18% Similarity=0.270 Sum_probs=160.0
Q ss_pred eEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCC
Q 012307 78 CVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPEN 157 (466)
Q Consensus 78 ~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~ 157 (466)
+...+-+-...+..|+||+|.+|.+|++++.|.|.+... +..+..+.++|...+ +..|++.+..++..+..
T Consensus 347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~~---~~ka~~~v~~~~~ei~n---- 417 (753)
T KOG2208|consen 347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSAN---DEKAVEDVEKIIAEILN---- 417 (753)
T ss_pred eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccccc---hhHHHHHHHHHHHhhhc----
Confidence 677788888999999999999999999999999999984 567778999998865 66788888887777643
Q ss_pred CcccccCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhC-CeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHH
Q 012307 158 DVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSG-ASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEA 236 (466)
Q Consensus 158 ~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sg-a~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~ 236 (466)
......+.+|...+..+||.+|..|..|..+++ ..|+.... ......+++.|....+.++..+
T Consensus 418 ---------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~-------~~~~~~~~~~~~~~dv~~~~~~ 481 (753)
T KOG2208|consen 418 ---------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN-------NNSSDMVTIRGISKDVEKSVSL 481 (753)
T ss_pred ---------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC-------CcccccceEeccccccchhHHH
Confidence 134567899999999999999999999999999 55555422 3445668888888888887766
Q ss_pred HHHHhhhccccCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcc
Q 012307 237 VVGHLRKFLVDQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGIS 316 (466)
Q Consensus 237 I~~~l~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~ 316 (466)
+..+........ |
T Consensus 482 ~~~~~~~a~~~~----------------------~--------------------------------------------- 494 (753)
T KOG2208|consen 482 LKALKADAKNLK----------------------F--------------------------------------------- 494 (753)
T ss_pred HHhhhhhhhcch----------------------h---------------------------------------------
Confidence 665443211000 0
Q ss_pred cCCCCCCCcccccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCH
Q 012307 317 IYGQDPALSTIRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTS 396 (466)
Q Consensus 317 ~yg~~~~~~~~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~ 396 (466)
...++.+...|..+.+..+|+.|..+...++..+..+..+ .++..++|.|..
T Consensus 495 -----------------------~~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~~~i~~~~~~-----~~~~~i~i~gk~ 546 (753)
T KOG2208|consen 495 -----------------------RDVVTKDKLLPVKYIGKEIGKNGTIRDSLGDKSIFPPNED-----EDHEKITIEGKL 546 (753)
T ss_pred -----------------------hhhhhccccchHHhhcccccCceeeeccCCceeecccccc-----cccceeeecccc
Confidence 0112334556677777777777766666555554444443 356689999999
Q ss_pred HHHHHHHHHHHHHHhcC
Q 012307 397 SQVQLAQQLIQEYMNNH 413 (466)
Q Consensus 397 ~~V~~A~~lI~~~i~~~ 413 (466)
+.|.+|+.+++..+...
T Consensus 547 ~~v~~a~~~L~~~~~~~ 563 (753)
T KOG2208|consen 547 ELVLEAPAELKALIEAL 563 (753)
T ss_pred cchhhhHHHHHhcchhh
Confidence 99999999998887764
No 34
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.69 E-value=2e-07 Score=85.02 Aligned_cols=147 Identities=21% Similarity=0.259 Sum_probs=99.5
Q ss_pred CceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCC---CCCCCCChhHHHHHHHHHHhc
Q 012307 76 GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKE---EPEAPVSPAMDAAVRVFKRVS 152 (466)
Q Consensus 76 ~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~---e~~~~v~~A~~ai~~i~~~i~ 152 (466)
....+.+.||...++.+||+.|+..+.|++.++++|.+. ..+..|.|.... ++ ..+.+|.+.|..+ . +
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD-----~~~~~V~i~~~~~t~Dp-~~~~ka~d~VkAI-g--r 76 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID-----SKTGSVTIRTTRKTEDP-LALLKARDVVKAI-G--R 76 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEE-----CCCCeEEEEecCCCCCh-HHHHHHHHHHHHH-h--c
Confidence 345677999999999999999999999999999999995 346778886653 32 1223333333222 0 1
Q ss_pred CCCCCCcccccCCCcceEEEEE-----e-----ccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEE
Q 012307 153 GLPENDVDAKASGAAFCSVRLL-----V-----PSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVE 222 (466)
Q Consensus 153 ~l~~~~~~~~~~~~~~~~~~ll-----V-----P~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~ 222 (466)
++.....-. .-........+. - -...-|+|||++|.+-+.|++-|+|.|.|. ...|.
T Consensus 77 GF~pe~A~~-LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~------------g~tVa 143 (194)
T COG1094 77 GFPPEKALK-LLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY------------GKTVA 143 (194)
T ss_pred CCCHHHHHH-HhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe------------CcEEE
Confidence 111000000 000000000010 0 123569999999999999999999999996 34799
Q ss_pred EecCHHHHHHHHHHHHHHhhhc
Q 012307 223 MQGEAAKVLKALEAVVGHLRKF 244 (466)
Q Consensus 223 I~G~~~~V~~A~~~I~~~l~~~ 244 (466)
|-|..++|..|.+.|..++...
T Consensus 144 iiG~~~~v~iAr~AVemli~G~ 165 (194)
T COG1094 144 IIGGFEQVEIAREAVEMLINGA 165 (194)
T ss_pred EecChhhhHHHHHHHHHHHcCC
Confidence 9999999999999999988764
No 35
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.68 E-value=1.7e-08 Score=96.82 Aligned_cols=153 Identities=20% Similarity=0.196 Sum_probs=112.1
Q ss_pred CCCceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHH---
Q 012307 74 WPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKR--- 150 (466)
Q Consensus 74 ~~~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~--- 150 (466)
.++.++..+-||..+|+.|.|++|.+||.|+.+|..+|+-+.. ..+-++.++|..+.+ .+|+..|...-+.
T Consensus 22 ~p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr---~eePiF~vTg~~edv---~~aRrei~saaeH~~l 95 (394)
T KOG2113|consen 22 IGQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---GEEPIFPVTGRHEDV---RRARREIPSAAEHFGL 95 (394)
T ss_pred CCCccceeeecCcccceeecccCccccchhhhhhcceeccCCC---CCCCcceeccCchhH---HHHhhcCccccceeee
Confidence 3578899999999999999999999999999999999988654 345788899999864 3444444442222
Q ss_pred hcCCCCCCcccc-cCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHH
Q 012307 151 VSGLPENDVDAK-ASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAK 229 (466)
Q Consensus 151 i~~l~~~~~~~~-~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~ 229 (466)
++.......+.. .......+...-+|...+|.|+|.+|.+|+.|++.++..|.-+-. ..+.++.++|.+++
T Consensus 96 ~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~--------~~~~Vf~Vtg~~~n 167 (394)
T KOG2113|consen 96 IRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR--------CGEPVFCVTGAPKN 167 (394)
T ss_pred eeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc--------CCCceEEEecCCcc
Confidence 222211111111 122355677788899999999999999999999999999987632 34678999999888
Q ss_pred -HHHHH-HHHHHH
Q 012307 230 -VLKAL-EAVVGH 240 (466)
Q Consensus 230 -V~~A~-~~I~~~ 240 (466)
+++|. ..|...
T Consensus 168 C~kra~s~eie~t 180 (394)
T KOG2113|consen 168 CVKRARSCEIEQT 180 (394)
T ss_pred hhhhccccchhhh
Confidence 56666 445443
No 36
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.47 E-value=2.2e-07 Score=89.34 Aligned_cols=149 Identities=21% Similarity=0.321 Sum_probs=108.2
Q ss_pred cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhccc
Q 012307 167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFLV 246 (466)
Q Consensus 167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~ 246 (466)
..++..+.||..+++.++|++|.+||.|+.+|.+.|+-+.... +-+|.++|..+.|..|+..|...-+.+-.
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~e--------ePiF~vTg~~edv~~aRrei~saaeH~~l 95 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGE--------EPIFPVTGRHEDVRRARREIPSAAEHFGL 95 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCCC--------CCcceeccCchhHHHHhhcCccccceeee
Confidence 6688899999999999999999999999999999999875433 45899999999999999888664433211
Q ss_pred cCccccccccccCCcccccccccccccCCCcccCCCCCCCCCCCCCccCCCcccCCCccccccccCCCcccCCCCCCCcc
Q 012307 247 DQGVLPLFEKTYNASISQERQVETWADKSSLHAATQSAISTEYTPSTRRESLFLEREPQLESRYRLSGISIYGQDPALST 326 (466)
Q Consensus 247 ~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~y~~p~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~~ 326 (466)
.. | .| ++ .+ +...|
T Consensus 96 ~~---------~------s~---s~-----------Sg-----------------------------g~~~~-------- 109 (394)
T KOG2113|consen 96 IR---------A------SR---SF-----------SG-----------------------------GTNGA-------- 109 (394)
T ss_pred ee---------e------cc---cc-----------cC-----------------------------CCccc--------
Confidence 00 0 00 00 00 00000
Q ss_pred cccCCCCCCCCCcccceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHH-HHHHH
Q 012307 327 IRSSALGRASGPIVTQITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQ-VQLAQ 403 (466)
Q Consensus 327 ~~~s~~~~~~~~~~~~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~-V~~A~ 403 (466)
....+.+.+..+|...+|.|.|..|.+|+.|++.+...|.-.-.. .+-++.++|-+.. +++|.
T Consensus 110 -----------s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~---~~~Vf~Vtg~~~nC~kra~ 173 (394)
T KOG2113|consen 110 -----------SASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRC---GEPVFCVTGAPKNCVKRAR 173 (394)
T ss_pred -----------cccCCCceeeeccceeeeeccccccCccchheecccceEeeeccC---CCceEEEecCCcchhhhcc
Confidence 011245677899999999999999999999999999888764332 3558888887776 44444
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=98.46 E-value=5.1e-07 Score=77.41 Aligned_cols=64 Identities=19% Similarity=0.376 Sum_probs=52.8
Q ss_pred cCcccceeccccchHHHHHhHhCCeEEEecCCC-----------------CCCceEEEEEcCH---HHHHHHHHHHHHHH
Q 012307 351 ISYAEDIIGVGGTSIENIRRTSGAIITVQESRG-----------------LPDEITVEIKGTS---SQVQLAQQLIQEYM 410 (466)
Q Consensus 351 ~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~-----------------~~~er~V~I~Gt~---~~V~~A~~lI~~~i 410 (466)
.+++|.|||.+|.+||+|+++|||+|.|..... ..+.-.|.|++.. +.++.|..+|++++
T Consensus 14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll 93 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL 93 (120)
T ss_pred CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence 368899999999999999999999999976410 1123689999965 89999999999999
Q ss_pred hcCc
Q 012307 411 NNHK 414 (466)
Q Consensus 411 ~~~~ 414 (466)
....
T Consensus 94 ~~~~ 97 (120)
T cd02395 94 KPAI 97 (120)
T ss_pred ccCC
Confidence 8543
No 38
>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=98.19 E-value=6.1e-06 Score=70.76 Aligned_cols=67 Identities=19% Similarity=0.305 Sum_probs=51.1
Q ss_pred CcceeeecCCchhHHHHHHHhCCeEEEecCCCCC-----------CCC-CCCceEEEEecC---HHHHHHHHHHHHHHhh
Q 012307 178 TQAINLIGKQGSLIKSIQENSGASVRVLSADEAP-----------FYV-TEDERIVEMQGE---AAKVLKALEAVVGHLR 242 (466)
Q Consensus 178 ~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p-----------~~~-~~~er~v~I~G~---~~~V~~A~~~I~~~l~ 242 (466)
.++|.|||++|.+||+|+++|||+|.|..+...- ... ..+.-.|.|.+. .+++.+|+.+|..++.
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 5789999999999999999999999997542111 000 122356888885 5899999999999887
Q ss_pred hc
Q 012307 243 KF 244 (466)
Q Consensus 243 ~~ 244 (466)
..
T Consensus 95 ~~ 96 (120)
T cd02395 95 PA 96 (120)
T ss_pred cC
Confidence 54
No 39
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.05 E-value=1.3e-05 Score=70.77 Aligned_cols=103 Identities=17% Similarity=0.176 Sum_probs=71.5
Q ss_pred eEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCC
Q 012307 78 CVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPEN 157 (466)
Q Consensus 78 ~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~ 157 (466)
-.+.++|+...+|..||++|++|+.|++..|-+|.|-.- +-. +.+-|..++.-.. +.+-
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~-----------s~d---------~~~fI~n~l~Pa~-V~~v 90 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY-----------SDD---------PEEFIKNIFAPAA-VRSV 90 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc-----------CCC---------HHHHHHHHcCCCE-EEEE
Confidence 467888999999999999999999999999988888543 111 1223333322110 0000
Q ss_pred CcccccCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEE
Q 012307 158 DVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRV 204 (466)
Q Consensus 158 ~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i 204 (466)
.. ..........+.|+....|.+|||+|.+|+.++.-++-.+.|
T Consensus 91 ~I---~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 91 TI---KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred EE---EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 00 001123566778999999999999999999999999887766
No 40
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.92 E-value=3.2e-05 Score=68.28 Aligned_cols=37 Identities=22% Similarity=0.342 Sum_probs=34.3
Q ss_pred eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEe
Q 012307 169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVL 205 (466)
Q Consensus 169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~ 205 (466)
..+.++|+...+|..||++|++|+.|++..|-+|.+.
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVv 68 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELV 68 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEE
Confidence 5688899999999999999999999999999999886
No 41
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.85 E-value=7.1e-05 Score=81.67 Aligned_cols=63 Identities=27% Similarity=0.446 Sum_probs=56.9
Q ss_pred EEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 012307 344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKG-TSSQVQLAQQLIQEYMNN 412 (466)
Q Consensus 344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~G-t~~~V~~A~~lI~~~i~~ 412 (466)
..+|.||.+++|.|||.||.+||.|.++|||+|.|.+ +..|.|.+ ..+.+++|+.+|+.++..
T Consensus 579 ~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 579 IITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred eEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 5679999999999999999999999999999999965 35799988 568999999999999985
No 42
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=97.58 E-value=0.00028 Score=62.15 Aligned_cols=100 Identities=19% Similarity=0.163 Sum_probs=69.6
Q ss_pred EEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCCC
Q 012307 79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPEND 158 (466)
Q Consensus 79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~ 158 (466)
.+-++|....+|..||++|++|+.|++..|=+|.|-.- +..++ +-|..++. +..
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVey-----------s~D~~---------~fI~N~l~------PA~ 87 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEY-----------SENLE---------EFVANKLA------PAE 87 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEc-----------CCCHH---------HHHHHcCC------Cce
Confidence 67788999999999999999999999999988888542 11110 11211111 000
Q ss_pred cccc--cCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEE
Q 012307 159 VDAK--ASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRV 204 (466)
Q Consensus 159 ~~~~--~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i 204 (466)
.... ...+......+.||.+..+..|||+|.+|+...+-++-++.|
T Consensus 88 V~~V~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI 135 (141)
T TIGR01952 88 VKNVTVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI 135 (141)
T ss_pred EEEEEEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence 0000 001134567788999999999999999999999998877766
No 43
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.58 E-value=0.00045 Score=70.88 Aligned_cols=76 Identities=14% Similarity=0.264 Sum_probs=57.5
Q ss_pred ceEEEEEecc------CcceeeecCCchhHHHHHHHhCCeEEEecCCCC---------CCCC--CCCceEEEEec-CHHH
Q 012307 168 FCSVRLLVPS------TQAINLIGKQGSLIKSIQENSGASVRVLSADEA---------PFYV--TEDERIVEMQG-EAAK 229 (466)
Q Consensus 168 ~~~~~llVP~------~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~---------p~~~--~~~er~v~I~G-~~~~ 229 (466)
..+.++.||. +++|+|||..|.|.|+|+++|||+|.|..+..+ +.+. ..++--+.|++ +.+.
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 5677888884 578999999999999999999999999862111 1111 12233467777 5778
Q ss_pred HHHHHHHHHHHhhh
Q 012307 230 VLKALEAVVGHLRK 243 (466)
Q Consensus 230 V~~A~~~I~~~l~~ 243 (466)
|++|+++|..+|.+
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999999886
No 44
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.47 E-value=0.00034 Score=76.54 Aligned_cols=66 Identities=18% Similarity=0.295 Sum_probs=57.8
Q ss_pred cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHhhh
Q 012307 167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG-EAAKVLKALEAVVGHLRK 243 (466)
Q Consensus 167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~ 243 (466)
......+.||.+.++.|||++|.+||.|+++||++|.|.. +..|.|.+ ..+.+++|+.+|..++..
T Consensus 576 aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-----------~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 576 APRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED-----------DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred CCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec-----------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 4567788999999999999999999999999999999951 45788887 688999999999988874
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=97.25 E-value=0.00048 Score=76.21 Aligned_cols=64 Identities=27% Similarity=0.425 Sum_probs=55.5
Q ss_pred eEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 012307 343 ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKG-TSSQVQLAQQLIQEYMNN 412 (466)
Q Consensus 343 ~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~G-t~~~V~~A~~lI~~~i~~ 412 (466)
...++.||.++++.|||+||.+||.|.++|||+|.|.+ +-.|.|.+ ..+.+++|+.+|..+...
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 35779999999999999999999999999999999965 34677776 567899999999988764
No 46
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=97.24 E-value=0.00085 Score=59.14 Aligned_cols=36 Identities=28% Similarity=0.412 Sum_probs=33.3
Q ss_pred EEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEe
Q 012307 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVL 205 (466)
Q Consensus 170 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~ 205 (466)
.+-++|....+|..||++|++|+.|++..|-+|.+.
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVV 69 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELI 69 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEE
Confidence 677889999999999999999999999999888886
No 47
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.20 E-value=0.00036 Score=71.59 Aligned_cols=73 Identities=22% Similarity=0.277 Sum_probs=51.8
Q ss_pred CceEEEEEeccc------ccceeeecCChhHHHHHHHhCceEEEeCC---------------CCCC-CCeEEEecCCCCC
Q 012307 76 GHCVFRMIVPVL------KVGSIIGRKGELIKKTCEDTRARIKVLDG---------------PVSS-PDRIVLISGKEEP 133 (466)
Q Consensus 76 ~~~~~rllvp~~------~vG~IIGk~G~~Ik~I~~etga~I~v~~~---------------~~~~-~ervv~I~G~~e~ 133 (466)
..++-||.||.+ +||+|||.+|.+.|+|++||||||.|.-. .++. ++=.|.|++..+
T Consensus 136 ~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~- 214 (554)
T KOG0119|consen 136 AKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQ- 214 (554)
T ss_pred cccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchH-
Confidence 367889999976 59999999999999999999999999741 1111 223467776554
Q ss_pred CCCCChhHHHHHHHHHH
Q 012307 134 EAPVSPAMDAAVRVFKR 150 (466)
Q Consensus 134 ~~~v~~A~~ai~~i~~~ 150 (466)
+.+.+|+..|..+++.
T Consensus 215 -eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 215 -EKIKKAIAVIENLIQS 230 (554)
T ss_pred -HHHHHHHHHHHHHHHh
Confidence 3455555555555544
No 48
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.06 E-value=0.0017 Score=65.68 Aligned_cols=68 Identities=21% Similarity=0.303 Sum_probs=56.9
Q ss_pred eEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 012307 343 ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNH 413 (466)
Q Consensus 343 ~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~ 413 (466)
...-+.|-.+++|.|||++|++|+.||..|.++|+|.+.. .+..|+|-|..+--.+|+..|...+...
T Consensus 47 ~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~---~e~kv~ifg~~~m~~kaka~id~~~~k~ 114 (629)
T KOG0336|consen 47 FPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD---LEVKVTIFGINHMRKKAKASIDRGQDKD 114 (629)
T ss_pred CchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC---ceeEEEEechHHHHHHHHhhHhhhhhhh
Confidence 4566789999999999999999999999999999997644 4678999999887777877776666543
No 49
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=97.04 E-value=0.0019 Score=59.80 Aligned_cols=100 Identities=22% Similarity=0.328 Sum_probs=70.1
Q ss_pred EEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCCC
Q 012307 79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPEND 158 (466)
Q Consensus 79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~ 158 (466)
.+-+++-.+.+|..||++|.+|+.|.++.|=+|.|-.-. ++. ..-|..++.-. .
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s-------------~d~-------~~fI~nal~Pa------~ 130 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS-------------EDP-------AEFIKNALAPA------E 130 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeC-------------CCH-------HHHHHHhcCcc------e
Confidence 455566677899999999999999999999778775431 111 12232222211 0
Q ss_pred cccc--cCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEe
Q 012307 159 VDAK--ASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVL 205 (466)
Q Consensus 159 ~~~~--~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~ 205 (466)
..+. ... ......+.||.++.+.+|||+|.+++-+.+-||-++.|.
T Consensus 131 v~~V~~~~~-d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~ 178 (190)
T COG0195 131 VLSVNIKED-DGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIE 178 (190)
T ss_pred EeEEEEEeC-CCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEE
Confidence 0000 000 112788899999999999999999999999999999996
No 50
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.02 E-value=0.00032 Score=70.74 Aligned_cols=56 Identities=29% Similarity=0.383 Sum_probs=48.9
Q ss_pred CCCceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCC
Q 012307 74 WPGHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132 (466)
Q Consensus 74 ~~~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e 132 (466)
+.+++.+.+-|-+++||.|||++|++||+||..|+++|++-+. ..+-.|+|.|..+
T Consensus 43 g~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~~ 98 (629)
T KOG0336|consen 43 GGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGINH 98 (629)
T ss_pred CCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechHH
Confidence 3567888999999999999999999999999999999999866 4566788888764
No 51
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.96 E-value=0.00081 Score=64.31 Aligned_cols=42 Identities=31% Similarity=0.509 Sum_probs=37.4
Q ss_pred CCceEEEEEeccc------ccceeeecCChhHHHHHHHhCceEEEeCC
Q 012307 75 PGHCVFRMIVPVL------KVGSIIGRKGELIKKTCEDTRARIKVLDG 116 (466)
Q Consensus 75 ~~~~~~rllvp~~------~vG~IIGk~G~~Ik~I~~etga~I~v~~~ 116 (466)
+-..+.||+||.+ .||.|+|.+|.++|+|+++|+|+|.|.-.
T Consensus 89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGr 136 (259)
T KOG1588|consen 89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGR 136 (259)
T ss_pred ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecC
Confidence 3457889999998 69999999999999999999999998744
No 52
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.92 E-value=0.002 Score=72.17 Aligned_cols=63 Identities=24% Similarity=0.356 Sum_probs=56.1
Q ss_pred EEEEEeccCcccceeccccchHHHHHhHhCCe-EEEecCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 012307 344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAI-ITVQESRGLPDEITVEIKG-TSSQVQLAQQLIQEYMNN 412 (466)
Q Consensus 344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~-I~I~~~~~~~~er~V~I~G-t~~~V~~A~~lI~~~i~~ 412 (466)
...|.||.++++.|||.||.+||.|.++||+. |.|.+ +-.|.|.+ ..+.++.|+.+|++++..
T Consensus 686 i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d------dg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 686 IHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD------DGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred eEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC------CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 56799999999999999999999999999999 99964 35788888 568999999999999874
No 53
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=96.89 E-value=0.06 Score=50.80 Aligned_cols=88 Identities=13% Similarity=0.232 Sum_probs=65.4
Q ss_pred HHHHHHHHHhcCCCCCCcccccCCCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEE
Q 012307 142 DAAVRVFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIV 221 (466)
Q Consensus 142 ~ai~~i~~~i~~l~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v 221 (466)
..+.+|+..+.++.-.+.. .....+.+.++....-.|...+|..++.|....|++|.+. ..+..+
T Consensus 4 ~l~~~Il~d~W~l~v~e~v-----~~~g~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~----------~~~~~i 68 (210)
T PF14611_consen 4 KLAERILRDCWNLEVSEEV-----DELGDLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVS----------RSENRI 68 (210)
T ss_pred HHHHHHHHHhcCCccccee-----eccceeEEEecchheeeeecCCchHHHHHHHhcCceEEEe----------cCCcEE
Confidence 4567777777665432211 0223445556688888999999999999988889999996 335689
Q ss_pred EEecCHHHHHHHHHHHHHHhhhc
Q 012307 222 EMQGEAAKVLKALEAVVGHLRKF 244 (466)
Q Consensus 222 ~I~G~~~~V~~A~~~I~~~l~~~ 244 (466)
.|+|+...+..+...|.+++...
T Consensus 69 ~I~g~k~~~~~i~~~i~~~l~~i 91 (210)
T PF14611_consen 69 RITGTKSTAEYIEASINEILSNI 91 (210)
T ss_pred EEEccHHHHHHHHHHHHHHHhhc
Confidence 99999999999998888877653
No 54
>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=96.86 E-value=0.0017 Score=48.84 Aligned_cols=37 Identities=22% Similarity=0.370 Sum_probs=34.4
Q ss_pred ceEEEEEecccccceeeecCChhHHHHHHHhCceEEE
Q 012307 77 HCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKV 113 (466)
Q Consensus 77 ~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v 113 (466)
...+.+.|+.+.+|.+|||+|.+|+.+++.++-+|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3688999999999999999999999999999988876
No 55
>PRK00106 hypothetical protein; Provisional
Probab=96.82 E-value=0.0072 Score=64.59 Aligned_cols=66 Identities=17% Similarity=0.363 Sum_probs=51.7
Q ss_pred eEEEEEeccC-cccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcC
Q 012307 343 ITQTMQIPIS-YAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKG-TSSQVQLAQQLIQEYMNNH 413 (466)
Q Consensus 343 ~t~~i~IP~~-~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~G-t~~~V~~A~~lI~~~i~~~ 413 (466)
.+..+.+|++ +-|+||||.|.||+.+...||+.|.|++..+ .|+|+| .|---+-|+.-|..+|.+.
T Consensus 225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp~-----~v~lS~fdpvRReiAr~~le~Li~dg 292 (535)
T PRK00106 225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTPE-----VVVLSGFDPIRREIARMTLESLIKDG 292 (535)
T ss_pred eeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCCC-----eEEEeCCChHHHHHHHHHHHHHHHcC
Confidence 3456889995 4599999999999999999999999987443 788998 6655566666666666543
No 56
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=96.78 E-value=0.0023 Score=70.94 Aligned_cols=66 Identities=18% Similarity=0.325 Sum_probs=55.2
Q ss_pred cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHhhh
Q 012307 167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG-EAAKVLKALEAVVGHLRK 243 (466)
Q Consensus 167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~ 243 (466)
......+.||.+.++.|||++|++||+|+++||++|.|.. +..|.|.+ ..+.+.+|..+|..+..+
T Consensus 549 ~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-----------dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 549 APRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-----------DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred CCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-----------CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 4567789999999999999999999999999999999951 34566665 678899999999877553
No 57
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.76 E-value=0.0019 Score=69.43 Aligned_cols=65 Identities=25% Similarity=0.431 Sum_probs=57.5
Q ss_pred EEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCH-HHHHHHHHHHHHHHhcCc
Q 012307 344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTS-SQVQLAQQLIQEYMNNHK 414 (466)
Q Consensus 344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~-~~V~~A~~lI~~~i~~~~ 414 (466)
..++.|+.+.++.|||++|.+|++|.++|||+|+|.+ +-+|.|.++. +.+..|+.+|.++.++..
T Consensus 553 i~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied------dGtv~i~~s~~~~~~~ak~~I~~i~~e~e 618 (692)
T COG1185 553 IETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED------DGTVKIAASDGESAKKAKERIEAITREVE 618 (692)
T ss_pred eEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC------CCcEEEEecchHHHHHHHHHHHHHHhhcc
Confidence 5679999999999999999999999999999999963 3379999976 789999999999997643
No 58
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.70 E-value=0.0042 Score=66.51 Aligned_cols=66 Identities=15% Similarity=0.352 Sum_probs=51.5
Q ss_pred eEEEEEeccCc-ccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcC
Q 012307 343 ITQTMQIPISY-AEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKG-TSSQVQLAQQLIQEYMNNH 413 (466)
Q Consensus 343 ~t~~i~IP~~~-~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~G-t~~~V~~A~~lI~~~i~~~ 413 (466)
.+..+.+|++- -|+||||.|.||+.+...||+.|.|++..+ .|+|+| .|---+.|+.-|..+|...
T Consensus 204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp~-----~v~ls~fdp~rreia~~~l~~li~dg 271 (514)
T TIGR03319 204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPE-----AVILSGFDPVRREIARMALEKLIQDG 271 (514)
T ss_pred eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCCC-----eEEecCCchHHHHHHHHHHHHHHHcC
Confidence 44568999965 599999999999999999999999987443 788888 5655566666666666543
No 59
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=96.64 E-value=0.0015 Score=72.83 Aligned_cols=102 Identities=10% Similarity=-0.067 Sum_probs=78.8
Q ss_pred ccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCceEEEEEecccccceeeecCChhH
Q 012307 24 ATTESPTTESEAPPTIGSENTEHTTESDSALPQSTGPDAAAVPEEKKWPGW---PGHCVFRMIVPVLKVGSIIGRKGELI 100 (466)
Q Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~rllvp~~~vG~IIGk~G~~I 100 (466)
-.-+++|+++.+...+....++++++.++.. |..-+..+|...| -..-.++.-.+..++.+||++.+.+|
T Consensus 731 r~~~e~t~~slskS~~~~id~~Te~n~~t~L-------T~acaggh~e~vellv~rganiehrdkkgf~plImaatagh~ 803 (2131)
T KOG4369|consen 731 RLEGEVTPNSLSKSYKTVIDPLTEPNIKTNL-------TSACAGGHREEVELLVVRGANIEHRDKKGFVPLIMAATAGHI 803 (2131)
T ss_pred hhhccccchhhccccceeeccccCccccccc-------cccccCccHHHHHHHHHhcccccccccccchhhhhhcccCch
Confidence 3456888999888888888888888888777 5555556665544 22235667788999999999999999
Q ss_pred HHHHHHhCceEEEeCCCCCCCCeEEEecCCCC
Q 012307 101 KKTCEDTRARIKVLDGPVSSPDRIVLISGKEE 132 (466)
Q Consensus 101 k~I~~etga~I~v~~~~~~~~ervv~I~G~~e 132 (466)
+-++.-+++.+.|......+.|+.+.|.+.-+
T Consensus 804 tvV~~llk~ha~veaQsdrtkdt~lSlacsgg 835 (2131)
T KOG4369|consen 804 TVVQDLLKAHADVEAQSDRTKDTMLSLACSGG 835 (2131)
T ss_pred HHHHHHHhhhhhhhhhcccccCceEEEecCCC
Confidence 99999999999998665567888888876543
No 60
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.63 E-value=0.014 Score=55.91 Aligned_cols=42 Identities=19% Similarity=0.408 Sum_probs=37.2
Q ss_pred CcceEEEEEeccC------cceeeecCCchhHHHHHHHhCCeEEEecC
Q 012307 166 AAFCSVRLLVPST------QAINLIGKQGSLIKSIQENSGASVRVLSA 207 (466)
Q Consensus 166 ~~~~~~~llVP~~------~vg~IIGk~G~~Ik~I~~~sga~I~i~~~ 207 (466)
....+.+|+||.. +||+|+|.+|.++|+|+++|||+|-|..+
T Consensus 89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGr 136 (259)
T KOG1588|consen 89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGR 136 (259)
T ss_pred ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecC
Confidence 3567788999965 79999999999999999999999999864
No 61
>PRK12704 phosphodiesterase; Provisional
Probab=96.62 E-value=0.0053 Score=65.84 Aligned_cols=66 Identities=15% Similarity=0.331 Sum_probs=51.4
Q ss_pred eEEEEEeccCc-ccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcC
Q 012307 343 ITQTMQIPISY-AEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKG-TSSQVQLAQQLIQEYMNNH 413 (466)
Q Consensus 343 ~t~~i~IP~~~-~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~G-t~~~V~~A~~lI~~~i~~~ 413 (466)
.+..+.+|++- -|+||||.|.||+.+...||+.|.|++.. ..|+|+| .+---+.|+..+...+...
T Consensus 210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp-----~~v~ls~~~~~rre~a~~~l~~l~~dg 277 (520)
T PRK12704 210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-----EAVILSGFDPIRREIARLALEKLVQDG 277 (520)
T ss_pred ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCC-----CeEEEecCChhhHHHHHHHHHHHHhcC
Confidence 44568899855 59999999999999999999999998744 3788999 5555556666666665543
No 62
>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=96.56 E-value=0.0085 Score=60.71 Aligned_cols=93 Identities=19% Similarity=0.278 Sum_probs=63.8
Q ss_pred ccceeeecCChhHHHHHHHh-CceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCCCcccc-cCC
Q 012307 88 KVGSIIGRKGELIKKTCEDT-RARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAK-ASG 165 (466)
Q Consensus 88 ~vG~IIGk~G~~Ik~I~~et-ga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~~~~~-~~~ 165 (466)
-+|..||++|.+|+.|.++. |=+|.|-.-..+ + ..-|..++. +...... ...
T Consensus 244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d-----------~---------~~fi~nal~------Pa~v~~v~i~~ 297 (341)
T TIGR01953 244 PVGACVGPKGSRIQAISKELNGEKIDIIEYSDD-----------P---------AEFIANALS------PAKVISVEVLD 297 (341)
T ss_pred cceeeECCCCchHHHHHHHhCCCeEEEEEcCCC-----------H---------HHHHHHhcC------CceEEEEEEEc
Confidence 49999999999999999998 778887543100 0 011111111 0000000 000
Q ss_pred CcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEec
Q 012307 166 AAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLS 206 (466)
Q Consensus 166 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~ 206 (466)
.......+.||..+.+..|||+|.+++-..+-||.+|.|.+
T Consensus 298 ~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 298 EDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred CCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 12357889999999999999999999999999999999974
No 63
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.55 E-value=0.0089 Score=60.73 Aligned_cols=97 Identities=16% Similarity=0.168 Sum_probs=65.8
Q ss_pred cccceeeecCChhHHHHHHHh-CceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCCCcccccCC
Q 012307 87 LKVGSIIGRKGELIKKTCEDT-RARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAKASG 165 (466)
Q Consensus 87 ~~vG~IIGk~G~~Ik~I~~et-ga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~~~~~~~~ 165 (466)
+-+|..||++|.+|+.|.++. |=+|.|-.-. .+. ..-|..++. +.........
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s-------------~D~-------~~fI~Nal~------Pa~V~~V~i~ 304 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYS-------------NVP-------EIFIARALA------PAIISSVKIE 304 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcC-------------CCH-------HHHHHHhCC------CceeeEEEEc
Confidence 359999999999999999998 7788875431 110 011111111 0000000000
Q ss_pred CcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCC
Q 012307 166 AAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADE 209 (466)
Q Consensus 166 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~ 209 (466)
.......+.||..+.+..|||+|.+++-..+-||.+|.|.+-.+
T Consensus 305 ~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 305 EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS 348 (374)
T ss_pred CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence 13357889999999999999999999999999999999986443
No 64
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.46 E-value=0.0081 Score=55.64 Aligned_cols=37 Identities=19% Similarity=0.304 Sum_probs=34.0
Q ss_pred EEEEEeccCcccceeccccchHHHHHhHhCCeEEEec
Q 012307 344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQE 380 (466)
Q Consensus 344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~ 380 (466)
...+.||.+..+.+|||+|.|++.+.+.||-++.|..
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 4567899999999999999999999999999999954
No 65
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.43 E-value=0.0036 Score=61.60 Aligned_cols=73 Identities=14% Similarity=0.172 Sum_probs=60.7
Q ss_pred ceEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcC
Q 012307 342 QITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNHKE 415 (466)
Q Consensus 342 ~~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~~~ 415 (466)
.....+.++..+.|.|||+.|.+-+.|+++|++.|.++.+... .+.++.+.+..++|..|...|.-+|.+..-
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n-~~~i~i~~~~~~~V~~a~~Ri~~~ids~r~ 128 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTN-KEEIKIIGISRNCVIQALERIAKLIDSDRK 128 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCC-cceEEEeehhHHHHHHHHHHHHHHHHhhhh
Confidence 4556789999999999999999999999999999999776642 344444555778999999999999998763
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=96.35 E-value=0.0051 Score=46.22 Aligned_cols=36 Identities=19% Similarity=0.277 Sum_probs=33.1
Q ss_pred eEEEEEeccCcccceeccccchHHHHHhHhCCeEEE
Q 012307 343 ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITV 378 (466)
Q Consensus 343 ~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I 378 (466)
....+.|+.+..|.+|||+|.+|+.+++.+|-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 356789999999999999999999999999988876
No 67
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.33 E-value=0.012 Score=59.94 Aligned_cols=94 Identities=18% Similarity=0.261 Sum_probs=64.6
Q ss_pred cccceeeecCChhHHHHHHHh-CceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCCCcccc-cC
Q 012307 87 LKVGSIIGRKGELIKKTCEDT-RARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAK-AS 164 (466)
Q Consensus 87 ~~vG~IIGk~G~~Ik~I~~et-ga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~~~~~-~~ 164 (466)
+-+|..||++|.+|+.|.++. |=+|.|-.-..+ + ...|..++. +...... ..
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d-----------~---------~~fi~nal~------Pa~v~~v~i~ 298 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSED-----------P---------AEFVANALS------PAKVVSVEVD 298 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCCC-----------H---------HHHHHHhCC------CceEEEEEEE
Confidence 359999999999999999998 778888543100 0 011111111 0000000 00
Q ss_pred CCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEec
Q 012307 165 GAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLS 206 (466)
Q Consensus 165 ~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~ 206 (466)
........+.||..+.+..|||+|.+++-..+-||.+|.|.+
T Consensus 299 ~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 299 DEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred cCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 013357889999999999999999999999999999999974
No 68
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.22 E-value=0.011 Score=61.25 Aligned_cols=93 Identities=22% Similarity=0.304 Sum_probs=63.2
Q ss_pred cccceeeecCChhHHHHHHHh-CceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCCCcccc-cC
Q 012307 87 LKVGSIIGRKGELIKKTCEDT-RARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAK-AS 164 (466)
Q Consensus 87 ~~vG~IIGk~G~~Ik~I~~et-ga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~~~~~-~~ 164 (466)
+-+|..||++|.+|+.|.++. |=+|.|-.-. .+. ..-|..++. +...... ..
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys-------------~Dp-------~~fI~NaLs------PA~V~~V~i~ 330 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWS-------------PDP-------ATYIANALS------PARVDEVRLV 330 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcC-------------CCH-------HHHHHHhcC------CceeeEEEEE
Confidence 359999999999999999998 7788775331 110 011111111 0000000 00
Q ss_pred CCcceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEe
Q 012307 165 GAAFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVL 205 (466)
Q Consensus 165 ~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~ 205 (466)
........+.||..+.+..|||+|.+++-..+-||.+|.|.
T Consensus 331 ~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~ 371 (449)
T PRK12329 331 DPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIK 371 (449)
T ss_pred cCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccc
Confidence 01235678999999999999999999999999999999985
No 69
>PRK00468 hypothetical protein; Provisional
Probab=96.03 E-value=0.007 Score=47.41 Aligned_cols=32 Identities=19% Similarity=0.379 Sum_probs=29.0
Q ss_pred CCceEEEEEecccccceeeecCChhHHHHHHH
Q 012307 75 PGHCVFRMIVPVLKVGSIIGRKGELIKKTCED 106 (466)
Q Consensus 75 ~~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~e 106 (466)
.+.+.++|.|..+.+|.||||+|.+|+.||.-
T Consensus 27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred CCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence 35588999999999999999999999999965
No 70
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.02 E-value=0.012 Score=56.70 Aligned_cols=63 Identities=21% Similarity=0.301 Sum_probs=53.6
Q ss_pred EEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCH-HHHHHHHHHHHHHHhcC
Q 012307 345 QTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTS-SQVQLAQQLIQEYMNNH 413 (466)
Q Consensus 345 ~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~-~~V~~A~~lI~~~i~~~ 413 (466)
..+.||.++++++||++|.+|+.|.+.+++.|.|.. +-.|-|.++. +.+++|+.+|+++-++.
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 458899999999999999999999999999999954 2478888865 58999999998766654
No 71
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=95.96 E-value=0.01 Score=58.55 Aligned_cols=72 Identities=26% Similarity=0.237 Sum_probs=58.3
Q ss_pred ceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhcc
Q 012307 168 FCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFL 245 (466)
Q Consensus 168 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~ 245 (466)
.....+.|+....+.|||++|.+-++|+++|+++|.++... +..+.++.+.+..++|.+|.+.|..+|.+.-
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~------~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN------TNKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC------CCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 35567889999999999999999999999999999997432 2334455555588999999999988887653
No 72
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=95.95 E-value=0.0086 Score=67.23 Aligned_cols=66 Identities=20% Similarity=0.232 Sum_probs=55.8
Q ss_pred cceEEEEEeccCcceeeecCCchhHHHHHHHhCCe-EEEecCCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHhhh
Q 012307 167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGAS-VRVLSADEAPFYVTEDERIVEMQG-EAAKVLKALEAVVGHLRK 243 (466)
Q Consensus 167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~-I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~ 243 (466)
......+.||.+.++.|||.+|.+||.|.++||++ |.+. + +-.|.|.+ ..+.+.+|+.+|..+..+
T Consensus 683 aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~--d---------dg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 683 APLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ--D---------DGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred CCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC--C---------CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 45678889999999999999999999999999999 8773 1 45677777 688999999999887653
No 73
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.82 E-value=0.021 Score=60.41 Aligned_cols=93 Identities=18% Similarity=0.310 Sum_probs=63.7
Q ss_pred ccceeeecCChhHHHHHHHh-CceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCCCcccccCCC
Q 012307 88 KVGSIIGRKGELIKKTCEDT-RARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAKASGA 166 (466)
Q Consensus 88 ~vG~IIGk~G~~Ik~I~~et-ga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~~~~~~~~~ 166 (466)
-+|..||++|.+|+.|.++. |=+|.|-.-.. + + ..-|...+. +..........
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~---d--------~---------~~fi~nal~------pa~v~~v~~~~ 299 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIILWSD---D--------P---------AQFIINALS------PAEVSSVVVDE 299 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEEcCC---C--------H---------HHHHHHhCC------CCEEEEEEEeC
Confidence 49999999999999999998 77888753310 0 0 011111111 00000000001
Q ss_pred cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEec
Q 012307 167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLS 206 (466)
Q Consensus 167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~ 206 (466)
......+.||..+.+..|||+|.+++...+-||.+|.|..
T Consensus 300 ~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 300 DEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred CCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 2247889999999999999999999999999999999975
No 74
>PRK02821 hypothetical protein; Provisional
Probab=95.74 E-value=0.01 Score=46.62 Aligned_cols=33 Identities=18% Similarity=0.177 Sum_probs=29.3
Q ss_pred CceEEEEEecccccceeeecCChhHHHHHHHhC
Q 012307 76 GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTR 108 (466)
Q Consensus 76 ~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etg 108 (466)
+.+.++|.|..+.+|.||||+|.+|+.||.--.
T Consensus 29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 457899999999999999999999999997643
No 75
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.52 E-value=0.037 Score=51.03 Aligned_cols=41 Identities=24% Similarity=0.360 Sum_probs=34.7
Q ss_pred cceEEEEEec------cCcceeeecCCchhHHHHHHHhCCeEEEecC
Q 012307 167 AFCSVRLLVP------STQAINLIGKQGSLIKSIQENSGASVRVLSA 207 (466)
Q Consensus 167 ~~~~~~llVP------~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~ 207 (466)
...+-++.|| ..+||+|||..|.+.|+|++.|+|+|-|-..
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 3455667777 4689999999999999999999999999753
No 76
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.48 E-value=0.015 Score=53.61 Aligned_cols=42 Identities=29% Similarity=0.492 Sum_probs=36.9
Q ss_pred CCceEEEEEeccc------ccceeeecCChhHHHHHHHhCceEEEeCC
Q 012307 75 PGHCVFRMIVPVL------KVGSIIGRKGELIKKTCEDTRARIKVLDG 116 (466)
Q Consensus 75 ~~~~~~rllvp~~------~vG~IIGk~G~~Ik~I~~etga~I~v~~~ 116 (466)
|..+.-++.||.. .||+|||..|.++|+|++.|+|+|-|...
T Consensus 145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 4567788899875 69999999999999999999999999754
No 77
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=95.46 E-value=0.04 Score=55.90 Aligned_cols=37 Identities=22% Similarity=0.322 Sum_probs=34.3
Q ss_pred EEEEEeccCcccceeccccchHHHHHhHhCCeEEEec
Q 012307 344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQE 380 (466)
Q Consensus 344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~ 380 (466)
...+.||.+..+..|||+|.|++-..+.||.+|.|..
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 5678999999999999999999999999999999954
No 78
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.33 E-value=0.015 Score=64.72 Aligned_cols=63 Identities=29% Similarity=0.495 Sum_probs=54.5
Q ss_pred EEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 012307 344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKG-TSSQVQLAQQLIQEYMNN 412 (466)
Q Consensus 344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~G-t~~~V~~A~~lI~~~i~~ 412 (466)
...+.||.+.++.+||.||.+||.|.++||+.|.|.+ +-.|.|.+ ..+.+++|+.+|+.+...
T Consensus 555 ~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d------~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 555 IETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED------DGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred heeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC------CceEEEEcccHHHHHHHHHHHHHhccc
Confidence 4568889999999999999999999999999988843 34688888 567899999999998865
No 79
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.30 E-value=0.034 Score=56.61 Aligned_cols=37 Identities=19% Similarity=0.224 Sum_probs=34.1
Q ss_pred EEEEEeccCcccceeccccchHHHHHhHhCCeEEEec
Q 012307 344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQE 380 (466)
Q Consensus 344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~ 380 (466)
...+.||.+..+..|||+|.|++-..+.||.+|.|..
T Consensus 309 ~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s 345 (374)
T PRK12328 309 KAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNE 345 (374)
T ss_pred EEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEE
Confidence 4568899999999999999999999999999999964
No 80
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.26 E-value=0.022 Score=44.50 Aligned_cols=32 Identities=19% Similarity=0.310 Sum_probs=29.0
Q ss_pred CCceEEEEEecccccceeeecCChhHHHHHHH
Q 012307 75 PGHCVFRMIVPVLKVGSIIGRKGELIKKTCED 106 (466)
Q Consensus 75 ~~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~e 106 (466)
+..+.++|-+..+.+|.||||+|.+|+.||.-
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 45678999999999999999999999999965
No 81
>PRK01064 hypothetical protein; Provisional
Probab=95.19 E-value=0.023 Score=44.81 Aligned_cols=32 Identities=25% Similarity=0.441 Sum_probs=29.0
Q ss_pred CCceEEEEEecccccceeeecCChhHHHHHHH
Q 012307 75 PGHCVFRMIVPVLKVGSIIGRKGELIKKTCED 106 (466)
Q Consensus 75 ~~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~e 106 (466)
.+.+.+++.|..+..|.+|||+|.+|+.||.-
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence 35688999999999999999999999999974
No 82
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=95.17 E-value=0.026 Score=60.91 Aligned_cols=69 Identities=23% Similarity=0.312 Sum_probs=58.5
Q ss_pred cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecC-HHHHHHHHHHHHHHhhhcc
Q 012307 167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGE-AAKVLKALEAVVGHLRKFL 245 (466)
Q Consensus 167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~-~~~V~~A~~~I~~~l~~~~ 245 (466)
......+.|+.+.+.-+||++|.+|++|.++||++|.+. ++-.|.|.+. .+.+.+|+..|..+.++..
T Consensus 550 aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-----------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~e 618 (692)
T COG1185 550 APRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-----------DDGTVKIAASDGESAKKAKERIEAITREVE 618 (692)
T ss_pred CCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-----------CCCcEEEEecchHHHHHHHHHHHHHHhhcc
Confidence 445677889999999999999999999999999999995 2446888875 5889999999999998764
Q ss_pred c
Q 012307 246 V 246 (466)
Q Consensus 246 ~ 246 (466)
+
T Consensus 619 v 619 (692)
T COG1185 619 V 619 (692)
T ss_pred c
Confidence 4
No 83
>PRK00468 hypothetical protein; Provisional
Probab=95.15 E-value=0.049 Score=42.64 Aligned_cols=32 Identities=28% Similarity=0.356 Sum_probs=28.6
Q ss_pred CcceEEEEEeccCcceeeecCCchhHHHHHHH
Q 012307 166 AAFCSVRLLVPSTQAINLIGKQGSLIKSIQEN 197 (466)
Q Consensus 166 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~ 197 (466)
.....+++.|...-+|+||||+|.+|+.|+.-
T Consensus 27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred CCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence 35678899999999999999999999999864
No 84
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.08 E-value=0.043 Score=58.05 Aligned_cols=37 Identities=16% Similarity=0.249 Sum_probs=34.4
Q ss_pred EEEEEeccCcccceeccccchHHHHHhHhCCeEEEec
Q 012307 344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQE 380 (466)
Q Consensus 344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~ 380 (466)
...+.||.+..+..|||+|.||+..++.||.+|.|..
T Consensus 303 ~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 303 SADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred EEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 5678999999999999999999999999999999965
No 85
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.01 E-value=0.062 Score=54.89 Aligned_cols=37 Identities=19% Similarity=0.211 Sum_probs=34.3
Q ss_pred EEEEEeccCcccceeccccchHHHHHhHhCCeEEEec
Q 012307 344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQE 380 (466)
Q Consensus 344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~ 380 (466)
...+.||.+..+..|||+|.|++-..+.||.+|.|..
T Consensus 304 ~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 304 AARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred EEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 4678999999999999999999999999999999964
No 86
>PRK02821 hypothetical protein; Provisional
Probab=94.87 E-value=0.058 Score=42.44 Aligned_cols=33 Identities=12% Similarity=0.155 Sum_probs=28.9
Q ss_pred cceEEEEEeccCcceeeecCCchhHHHHHHHhC
Q 012307 167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSG 199 (466)
Q Consensus 167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sg 199 (466)
....+++.|...-+|+||||+|.+|+.|+.--.
T Consensus 29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 557899999999999999999999999987543
No 87
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=94.80 E-value=0.064 Score=51.68 Aligned_cols=64 Identities=22% Similarity=0.318 Sum_probs=52.6
Q ss_pred EEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecC-HHHHHHHHHHHHHHhhhc
Q 012307 170 SVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGE-AAKVLKALEAVVGHLRKF 244 (466)
Q Consensus 170 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~-~~~V~~A~~~I~~~l~~~ 244 (466)
-..+.||...++.|||++|.+|+.|.+.++++|.+- . +-.|.|.+. .+++.+|..+|..+-++.
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig----------~-NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG----------Q-NGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc----------C-CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 366889999999999999999999999999999983 1 346778775 668888999887765553
No 88
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.72 E-value=0.086 Score=41.24 Aligned_cols=32 Identities=28% Similarity=0.388 Sum_probs=29.2
Q ss_pred CcceEEEEEeccCcceeeecCCchhHHHHHHH
Q 012307 166 AAFCSVRLLVPSTQAINLIGKQGSLIKSIQEN 197 (466)
Q Consensus 166 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~ 197 (466)
......++-|...-+|.||||+|.+|+.|+.-
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 46788999999999999999999999999975
No 89
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=94.67 E-value=0.53 Score=44.36 Aligned_cols=130 Identities=9% Similarity=0.108 Sum_probs=85.0
Q ss_pred CceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCC
Q 012307 76 GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLP 155 (466)
Q Consensus 76 ~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~ 155 (466)
+++.++ ++....-++...+|..++.|-...||+|.+... +..|.|+|++..+ ..+...|.++++.+
T Consensus 26 g~l~v~--l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~-----~~~i~I~g~k~~~---~~i~~~i~~~l~~i---- 91 (210)
T PF14611_consen 26 GDLDVW--LQPDEFFLLLTGNGRILENLAARNGAKIEVSRS-----ENRIRITGTKSTA---EYIEASINEILSNI---- 91 (210)
T ss_pred ceeEEE--ecchheeeeecCCchHHHHHHHhcCceEEEecC-----CcEEEEEccHHHH---HHHHHHHHHHHhhc----
Confidence 444444 457888999999999999998889999999754 5679999988542 22333334444333
Q ss_pred CCCcccccCCCcceEEEEEeccCcceeee----cCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEe-----cC
Q 012307 156 ENDVDAKASGAAFCSVRLLVPSTQAINLI----GKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQ-----GE 226 (466)
Q Consensus 156 ~~~~~~~~~~~~~~~~~llVP~~~vg~II----Gk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~-----G~ 226 (466)
.+..+-++.-.--.-. -.....++.|++.|++.|+..++ ...+.|. -.
T Consensus 92 -------------~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~----------~~~~~i~~~~~~~~ 148 (210)
T PF14611_consen 92 -------------RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD----------GNKLKISWLASPEN 148 (210)
T ss_pred -------------EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC----------CCeEEEEEEeeccc
Confidence 3344444422111111 12356789999999999998632 2223333 46
Q ss_pred HHHHHHHHHHHHHHhh
Q 012307 227 AAKVLKALEAVVGHLR 242 (466)
Q Consensus 227 ~~~V~~A~~~I~~~l~ 242 (466)
.+.+..|+.+++..+.
T Consensus 149 ~~~~~~a~RlL~~a~~ 164 (210)
T PF14611_consen 149 EKRADRAKRLLLWALD 164 (210)
T ss_pred cchHHHHHHHHHHhcc
Confidence 7788999999988774
No 90
>PRK12705 hypothetical protein; Provisional
Probab=94.62 E-value=0.044 Score=58.30 Aligned_cols=40 Identities=20% Similarity=0.354 Sum_probs=34.5
Q ss_pred eEEEEEeccCcc-cceeccccchHHHHHhHhCCeEEEecCC
Q 012307 343 ITQTMQIPISYA-EDIIGVGGTSIENIRRTSGAIITVQESR 382 (466)
Q Consensus 343 ~t~~i~IP~~~~-G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~ 382 (466)
.+..+.+|++-+ |+||||.|.||+.+...||+.|.|++..
T Consensus 198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp 238 (508)
T PRK12705 198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP 238 (508)
T ss_pred eeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc
Confidence 345678898655 9999999999999999999999998744
No 91
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=94.49 E-value=0.068 Score=55.38 Aligned_cols=37 Identities=19% Similarity=0.291 Sum_probs=34.0
Q ss_pred EEEEEeccCcccceeccccchHHHHHhHhCCeEEEec
Q 012307 344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQE 380 (466)
Q Consensus 344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~ 380 (466)
...+.||.+..+..|||+|.||+-..+.||.+|.|..
T Consensus 336 ~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 336 HAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred EEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 3568899999999999999999999999999999954
No 92
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=94.42 E-value=0.038 Score=61.52 Aligned_cols=65 Identities=22% Similarity=0.354 Sum_probs=53.1
Q ss_pred ceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHhhh
Q 012307 168 FCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG-EAAKVLKALEAVVGHLRK 243 (466)
Q Consensus 168 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~ 243 (466)
.....+.||.+.++.+||.+|.+||+|.++||++|.+. + +-.|.|.+ ..+.+.+|..+|..+..+
T Consensus 553 p~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~--d---------~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 553 PRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE--D---------DGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred chheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC--C---------CceEEEEcccHHHHHHHHHHHHHhccc
Confidence 34566777999999999999999999999999988773 2 34577777 678899999999887754
No 93
>PRK12704 phosphodiesterase; Provisional
Probab=94.34 E-value=0.17 Score=54.41 Aligned_cols=66 Identities=15% Similarity=0.213 Sum_probs=49.3
Q ss_pred eEEEEEecc-CcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHhhhc
Q 012307 169 CSVRLLVPS-TQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG-EAAKVLKALEAVVGHLRKF 244 (466)
Q Consensus 169 ~~~~llVP~-~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~~ 244 (466)
....+-+|+ ++-|+||||.|.+|+.++.-||+.|.|. .+...|.|+| .+-.-+.|...+..++.+.
T Consensus 210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid----------dtp~~v~ls~~~~~rre~a~~~l~~l~~dg 277 (520)
T PRK12704 210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID----------DTPEAVILSGFDPIRREIARLALEKLVQDG 277 (520)
T ss_pred ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc----------CCCCeEEEecCChhhHHHHHHHHHHHHhcC
Confidence 444566776 6889999999999999999999999994 3345677888 4555456666666655554
No 94
>PRK00106 hypothetical protein; Provisional
Probab=94.33 E-value=0.2 Score=53.81 Aligned_cols=67 Identities=15% Similarity=0.283 Sum_probs=50.2
Q ss_pred cceEEEEEecc-CcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHhhh
Q 012307 167 AFCSVRLLVPS-TQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG-EAAKVLKALEAVVGHLRK 243 (466)
Q Consensus 167 ~~~~~~llVP~-~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~ 243 (466)
......+-+|+ ++-|+||||.|.+|+.++.-||+.+.|. .+...|.|+| .|---+.|...+..++.+
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid----------dtp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID----------DTPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc----------CCCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 33455567787 6789999999999999999999999994 3345677888 565556666666665553
No 95
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=94.27 E-value=0.18 Score=54.14 Aligned_cols=66 Identities=15% Similarity=0.242 Sum_probs=49.4
Q ss_pred ceEEEEEecc-CcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHhhh
Q 012307 168 FCSVRLLVPS-TQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG-EAAKVLKALEAVVGHLRK 243 (466)
Q Consensus 168 ~~~~~llVP~-~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~ 243 (466)
.....+-+|+ ++-|+||||.|.+|+.++.-||+.|.|. .+...|.|++ .|---+.|...|..++.+
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid----------dtp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID----------DTPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc----------CCCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 3445566776 6789999999999999999999999994 2345677888 565555566666665553
No 96
>PRK01064 hypothetical protein; Provisional
Probab=93.87 E-value=0.18 Score=39.81 Aligned_cols=32 Identities=28% Similarity=0.325 Sum_probs=28.8
Q ss_pred CcceEEEEEeccCcceeeecCCchhHHHHHHH
Q 012307 166 AAFCSVRLLVPSTQAINLIGKQGSLIKSIQEN 197 (466)
Q Consensus 166 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~ 197 (466)
.....+++.|...-.|.+|||+|.+|+.|+.-
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence 46688999999999999999999999999874
No 97
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=92.75 E-value=0.054 Score=42.07 Aligned_cols=33 Identities=12% Similarity=0.132 Sum_probs=28.3
Q ss_pred CceEEEEEecccccceeeecCChhHHHHHHHhC
Q 012307 76 GHCVFRMIVPVLKVGSIIGRKGELIKKTCEDTR 108 (466)
Q Consensus 76 ~~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etg 108 (466)
+...+.+-|..+..|.||||+|.+++.||.-.+
T Consensus 27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred CceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence 456778888999999999999999999996544
No 98
>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=92.36 E-value=0.22 Score=37.27 Aligned_cols=35 Identities=20% Similarity=0.272 Sum_probs=28.1
Q ss_pred ceEEEEEecccccceeeecCChhHHHHHHHhCceE
Q 012307 77 HCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARI 111 (466)
Q Consensus 77 ~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I 111 (466)
...+.+.+.....|.+|||+|.+|+.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 34556666666789999999999999999988544
No 99
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=91.53 E-value=0.14 Score=39.42 Aligned_cols=37 Identities=32% Similarity=0.467 Sum_probs=29.0
Q ss_pred EEEEecccc-----cceeeecCChhHHHHHHHh-CceEEEeCC
Q 012307 80 FRMIVPVLK-----VGSIIGRKGELIKKTCEDT-RARIKVLDG 116 (466)
Q Consensus 80 ~rllvp~~~-----vG~IIGk~G~~Ik~I~~et-ga~I~v~~~ 116 (466)
.++.|-... +|..||++|.+||.|.++. |-+|+|-.-
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~ 47 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY 47 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence 456666666 9999999999999999999 888888543
No 100
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=89.65 E-value=0.4 Score=54.56 Aligned_cols=57 Identities=18% Similarity=0.144 Sum_probs=49.6
Q ss_pred ceEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC-CCCCCCeEEEecCCCCC
Q 012307 77 HCVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG-PVSSPDRIVLISGKEEP 133 (466)
Q Consensus 77 ~~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~-~~~~~ervv~I~G~~e~ 133 (466)
...-++.+|.....+|||++|.+|..++.-||+-|.|.+- ..+..||.+.+.|.++.
T Consensus 1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~ 1396 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPS 1396 (2131)
T ss_pred ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChh
Confidence 3455778899999999999999999999999999999873 44578999999999874
No 101
>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=89.32 E-value=1.2 Score=39.22 Aligned_cols=93 Identities=20% Similarity=0.356 Sum_probs=58.6
Q ss_pred eecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCCCcccccCCCcceEEE
Q 012307 93 IGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAKASGAAFCSVR 172 (466)
Q Consensus 93 IGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~~~~~~~~~~~~~~~ 172 (466)
+=.+|..|++|-.+-.-||.|..++. +.-.++ .|.+.|.++.-.-.++.+-.+ ...+-+
T Consensus 21 ~~~~~dli~~lAk~lrKRIvvR~dps--------~l~~~e------~A~~~I~~ivP~ea~i~di~F-------d~~tGE 79 (145)
T cd02410 21 FAEDGDLVKDLAKDLRKRIVIRPDPS--------VLKPPE------EAIKIILEIVPEEAGITDIYF-------DDDTGE 79 (145)
T ss_pred HhcccHHHHHHHHHHhceEEEcCChh--------hcCCHH------HHHHHHHHhCCCccCceeeEe-------cCCCcE
Confidence 34568899999999999998864420 111111 233333332210012222122 223456
Q ss_pred EEeccCcceeeecCCchhHHHHHHHhCCeEEEec
Q 012307 173 LLVPSTQAINLIGKQGSLIKSIQENSGASVRVLS 206 (466)
Q Consensus 173 llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~ 206 (466)
+.|-...-|.+||++|.++++|..+||-.-++..
T Consensus 80 V~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvR 113 (145)
T cd02410 80 VIIEAEKPGLVIGKGGSTLREITRETGWAPKVVR 113 (145)
T ss_pred EEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence 7777788899999999999999999998888864
No 102
>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=88.92 E-value=0.21 Score=39.13 Aligned_cols=34 Identities=29% Similarity=0.515 Sum_probs=29.0
Q ss_pred EEEEEecccccceeeecCChhHHHHHHHhCceEE
Q 012307 79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIK 112 (466)
Q Consensus 79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~ 112 (466)
...+.+.....|.|||++|++|++|.++.+-.+.
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 4678889999999999999999999988765553
No 103
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=88.67 E-value=0.53 Score=49.82 Aligned_cols=66 Identities=27% Similarity=0.406 Sum_probs=56.4
Q ss_pred eEEEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcCcC
Q 012307 343 ITQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKG-TSSQVQLAQQLIQEYMNNHKE 415 (466)
Q Consensus 343 ~t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~G-t~~~V~~A~~lI~~~i~~~~~ 415 (466)
+..+|.++.+..-.+||.+|.+.|.|..+||+.-.+ ++.++.|-- ++...++|+.+|..++.....
T Consensus 597 ~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v-------De~t~~i~A~~~~am~~Ak~~I~~i~~~~~~ 663 (760)
T KOG1067|consen 597 VLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV-------DEGTFSIFAPTQAAMEEAKEFIDGIIKDDQV 663 (760)
T ss_pred eeeEEeecchhhheeecCccceeeeEeeeccceeee-------cCceEEEEecCHHHHHHHHHHHHHHhcCccc
Confidence 467799999999999999999999999999977777 445788766 677889999999999887554
No 104
>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=87.91 E-value=0.53 Score=36.94 Aligned_cols=34 Identities=12% Similarity=0.224 Sum_probs=26.2
Q ss_pred EEEEEecccccceeeecCChhHHHHHHHhCceEE
Q 012307 79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIK 112 (466)
Q Consensus 79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~ 112 (466)
.+.+-|..+..|.+|||+|++++.||--.+.-++
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 3455566788999999999999999977664443
No 105
>PRK12705 hypothetical protein; Provisional
Probab=87.59 E-value=1.1 Score=47.98 Aligned_cols=37 Identities=19% Similarity=0.349 Sum_probs=31.3
Q ss_pred eEEEEEecc-CcceeeecCCchhHHHHHHHhCCeEEEe
Q 012307 169 CSVRLLVPS-TQAINLIGKQGSLIKSIQENSGASVRVL 205 (466)
Q Consensus 169 ~~~~llVP~-~~vg~IIGk~G~~Ik~I~~~sga~I~i~ 205 (466)
....+-+|+ ++-|+||||.|.+|+.++..||+.|.|.
T Consensus 198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid 235 (508)
T PRK12705 198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID 235 (508)
T ss_pred eeeeeecCChHhhccccCccchhHHHHHHhhCCceEec
Confidence 344455665 6789999999999999999999999994
No 106
>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=87.51 E-value=0.9 Score=33.83 Aligned_cols=33 Identities=12% Similarity=0.243 Sum_probs=26.2
Q ss_pred EEEEEeccCcccceeccccchHHHHHhHhCCeE
Q 012307 344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAII 376 (466)
Q Consensus 344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I 376 (466)
...+.+.....|.+||++|.+|+.|+..++-.+
T Consensus 26 ~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 26 EIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 444555555689999999999999999988554
No 107
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=87.34 E-value=0.43 Score=43.96 Aligned_cols=55 Identities=16% Similarity=0.272 Sum_probs=49.7
Q ss_pred CcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 012307 352 SYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNNH 413 (466)
Q Consensus 352 ~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~~ 413 (466)
..+|+|+||+|.+--.|.+.|..+|.+.+ ..|-|-|+.+++..|+..|+.+|...
T Consensus 178 RAIGRiaGk~GkTkfaIEn~trtrIVlad-------~kIHiLG~~~niriAR~avcsLIlGs 232 (252)
T KOG3273|consen 178 RAIGRIAGKGGKTKFAIENVTRTRIVLAD-------SKIHILGAFQNIRIARDAVCSLILGS 232 (252)
T ss_pred HHHHHhhcCCCcceeeeeccceeEEEecC-------ceEEEeecchhhHHHHHhhHhhhccC
Confidence 46799999999999999999999999953 47999999999999999999999863
No 108
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=87.22 E-value=0.4 Score=49.81 Aligned_cols=38 Identities=24% Similarity=0.242 Sum_probs=34.3
Q ss_pred EEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC
Q 012307 79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG 116 (466)
Q Consensus 79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~ 116 (466)
...+.||.++++.+|||+|.+|++|++..|.+|.|...
T Consensus 487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~ 524 (604)
T COG1855 487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL 524 (604)
T ss_pred eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence 35577899999999999999999999999999999754
No 109
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=87.17 E-value=0.32 Score=37.64 Aligned_cols=33 Identities=21% Similarity=0.232 Sum_probs=28.4
Q ss_pred cceEEEEEeccCcceeeecCCchhHHHHHHHhC
Q 012307 167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSG 199 (466)
Q Consensus 167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sg 199 (466)
....+.+-+.....|.||||+|.+++.||.-.+
T Consensus 27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred CceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence 456788889999999999999999999986544
No 110
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=86.72 E-value=0.29 Score=45.00 Aligned_cols=56 Identities=16% Similarity=0.169 Sum_probs=49.3
Q ss_pred cCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhc
Q 012307 177 STQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKF 244 (466)
Q Consensus 177 ~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~ 244 (466)
+..+|+|+||+|.+--.|+..|.++|.+. +..|.|-|..+++..|...|+.+|-..
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVla------------d~kIHiLG~~~niriAR~avcsLIlGs 232 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA------------DSKIHILGAFQNIRIARDAVCSLILGS 232 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEec------------CceEEEeecchhhHHHHHhhHhhhccC
Confidence 46789999999999999999999999985 346889999999999999999988654
No 111
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=86.52 E-value=1.5 Score=46.49 Aligned_cols=65 Identities=28% Similarity=0.328 Sum_probs=53.1
Q ss_pred cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHhhh
Q 012307 167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQG-EAAKVLKALEAVVGHLRK 243 (466)
Q Consensus 167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~ 243 (466)
......|.|+.+....+||.+|...|+|+.+||+.-.+ ++..|.|.. +....++|++.|..++.+
T Consensus 595 ~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 595 SPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEGTFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred CceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCceEEEEecCHHHHHHHHHHHHHHhcC
Confidence 45677889999999999999999999999999954444 245677766 677889999999887765
No 112
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=86.50 E-value=0.86 Score=43.48 Aligned_cols=48 Identities=27% Similarity=0.400 Sum_probs=39.9
Q ss_pred EEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCC
Q 012307 80 FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEP 133 (466)
Q Consensus 80 ~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~ 133 (466)
.-+.|+...|-++||++|..++.|.++|+|+|-|-.. -.|-|.+..+.
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N------G~IWV~~~~~~ 195 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN------GRIWVDGENES 195 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC------CEEEecCCCcc
Confidence 3466899999999999999999999999999999543 24778887763
No 113
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=86.32 E-value=1.3 Score=42.83 Aligned_cols=51 Identities=22% Similarity=0.405 Sum_probs=46.8
Q ss_pred cceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 012307 355 EDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEYMNN 412 (466)
Q Consensus 355 G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~i~~ 412 (466)
-++||.+|++++.|+-.|.|.|-|+. .+|.+.|....++.+...+.++|.+
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 57999999999999999999999964 4799999999999999999999886
No 114
>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=86.30 E-value=0.8 Score=36.42 Aligned_cols=36 Identities=17% Similarity=0.325 Sum_probs=30.4
Q ss_pred EEEEEecccccceeeecCChhHHHHHHHhCceEEEe
Q 012307 79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVL 114 (466)
Q Consensus 79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~ 114 (466)
.+++.|....-|.|||++|+.|++|+++-.-...+.
T Consensus 31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~ 66 (81)
T cd02413 31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP 66 (81)
T ss_pred eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence 478888999999999999999999998876666553
No 115
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=85.93 E-value=0.75 Score=35.40 Aligned_cols=35 Identities=26% Similarity=0.328 Sum_probs=27.2
Q ss_pred EEEeccCc-----ccceeccccchHHHHHhHh-CCeEEEec
Q 012307 346 TMQIPISY-----AEDIIGVGGTSIENIRRTS-GAIITVQE 380 (466)
Q Consensus 346 ~i~IP~~~-----~G~IIGkgG~~Ik~Ir~~S-GA~I~I~~ 380 (466)
.+.|-... +|..||++|.+|+.|.++. |-+|+|-+
T Consensus 6 kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 6 KVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred EEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 34455555 8999999999999999999 99999854
No 116
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=85.43 E-value=1.8 Score=45.27 Aligned_cols=40 Identities=28% Similarity=0.390 Sum_probs=36.4
Q ss_pred eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCC
Q 012307 169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSAD 208 (466)
Q Consensus 169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~ 208 (466)
....+.||...++.+|||+|.+|++|+++.|.+|.|.+.+
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e 525 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE 525 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence 4577899999999999999999999999999999998644
No 117
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=85.04 E-value=2.3 Score=44.85 Aligned_cols=93 Identities=23% Similarity=0.379 Sum_probs=63.3
Q ss_pred ceeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHh---cCCCCCCcccccCCC
Q 012307 90 GSIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRV---SGLPENDVDAKASGA 166 (466)
Q Consensus 90 G~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i---~~l~~~~~~~~~~~~ 166 (466)
..+|=+.|..||+|-++-.-||.|..++. +. -+ ..+|+..+++.+ .++.+-.+
T Consensus 41 P~~~~~~~dlik~lAk~lrKRI~iR~dPs------vl--~~---------~e~A~~~I~eivP~ea~i~~i~F------- 96 (637)
T COG1782 41 PELFAKDGDLIKDLAKDLRKRIIIRPDPS------VL--KP---------PEEARKIILEIVPEEAGITDIYF------- 96 (637)
T ss_pred HHHhccchhHHHHHHHHHhhceEeccCch------hc--CC---------HHHHHHHHHHhCccccCceeEEe-------
Confidence 44567889999999999999999965520 11 11 123444444433 22222222
Q ss_pred cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEec
Q 012307 167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLS 206 (466)
Q Consensus 167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~ 206 (466)
...+-+++|-...-|.+|||+|++.++|..++|-.-+|..
T Consensus 97 d~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR 136 (637)
T COG1782 97 DDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVR 136 (637)
T ss_pred cCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeee
Confidence 2245678888889999999999999999999998777764
No 118
>PRK13764 ATPase; Provisional
Probab=84.81 E-value=1.7 Score=47.49 Aligned_cols=45 Identities=31% Similarity=0.459 Sum_probs=39.3
Q ss_pred cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCC
Q 012307 167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAP 211 (466)
Q Consensus 167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p 211 (466)
......+.||...++.+|||+|.+|++|.++.|.+|.|-+.++.+
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 345678999999999999999999999999999999998765543
No 119
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=83.77 E-value=1.6 Score=39.56 Aligned_cols=37 Identities=16% Similarity=0.311 Sum_probs=31.1
Q ss_pred EEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC
Q 012307 79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG 116 (466)
Q Consensus 79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~ 116 (466)
.+-++|-... |.-|||+|.+|+++++..|-+|.+-+.
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 4556666666 999999999999999999999988653
No 120
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=83.37 E-value=2 Score=41.62 Aligned_cols=51 Identities=20% Similarity=0.247 Sum_probs=45.2
Q ss_pred eeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhh
Q 012307 181 INLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRK 243 (466)
Q Consensus 181 g~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~ 243 (466)
-+|||.+|.++|.|+--|.|.|-|. -..|.+.|....+..+...|.+++..
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 4699999999999999999999986 23688999999999999999988875
No 121
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=83.05 E-value=0.62 Score=36.46 Aligned_cols=33 Identities=24% Similarity=0.292 Sum_probs=27.7
Q ss_pred EEEEEeccCcccceeccccchHHHHHhHhCCeE
Q 012307 344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAII 376 (466)
Q Consensus 344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I 376 (466)
...+.+-....|.|||++|++|+.|+...+-.+
T Consensus 26 ~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 26 QIIIVIKASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp EEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred eEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 356788889999999999999999988776544
No 122
>PRK13764 ATPase; Provisional
Probab=82.70 E-value=0.93 Score=49.53 Aligned_cols=39 Identities=26% Similarity=0.248 Sum_probs=35.0
Q ss_pred eEEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC
Q 012307 78 CVFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG 116 (466)
Q Consensus 78 ~~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~ 116 (466)
....+.||.+.++.+|||+|.+|++|+++.|.+|.|...
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~ 519 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL 519 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence 355678999999999999999999999999999999754
No 123
>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=82.27 E-value=2 Score=37.89 Aligned_cols=38 Identities=26% Similarity=0.429 Sum_probs=32.5
Q ss_pred EEEecccccceeeecCChhHHHHHHHhCceEEEeCCCC
Q 012307 81 RMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPV 118 (466)
Q Consensus 81 rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~ 118 (466)
++.|-.+.-|.+|||+|.++++|..+||-+-.|...+|
T Consensus 79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 56666788999999999999999999999988876543
No 124
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=81.69 E-value=3 Score=43.89 Aligned_cols=72 Identities=18% Similarity=0.098 Sum_probs=55.7
Q ss_pred EEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC--CCCC-CCeEEEecCCCCCCCCCChhHHHHHHHHHH
Q 012307 79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG--PVSS-PDRIVLISGKEEPEAPVSPAMDAAVRVFKR 150 (466)
Q Consensus 79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~--~~~~-~ervv~I~G~~e~~~~v~~A~~ai~~i~~~ 150 (466)
.+-+.||...|-.|||.+|..|.+++...++.|++... .+.+ -..-|.|..+..+.+++.-+.+.++++.+.
T Consensus 450 e~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~ 524 (657)
T COG5166 450 EIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQ 524 (657)
T ss_pred heEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHhh
Confidence 45678999999999999999999999999999999854 1222 223378888877777777777777666653
No 125
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=81.64 E-value=4 Score=39.02 Aligned_cols=47 Identities=23% Similarity=0.439 Sum_probs=37.9
Q ss_pred EEEEeccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHH
Q 012307 345 QTMQIPISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSS 397 (466)
Q Consensus 345 ~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~ 397 (466)
+-+.|+..++-++||++|+.++.+.+.++|+|-|..+- .|=|.|..+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG------~IWV~~~~~ 194 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNG------RIWVDGENE 194 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecCC------EEEecCCCc
Confidence 34789999999999999999999999999999996422 455555444
No 126
>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=80.98 E-value=1.8 Score=33.85 Aligned_cols=35 Identities=20% Similarity=0.265 Sum_probs=27.5
Q ss_pred eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEE
Q 012307 169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVR 203 (466)
Q Consensus 169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~ 203 (466)
..+.+-|.....|.||||.|++++.||--.+.-++
T Consensus 24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 34667777889999999999999999876654443
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=80.84 E-value=1.4 Score=37.02 Aligned_cols=31 Identities=26% Similarity=0.402 Sum_probs=26.2
Q ss_pred EEEEEecccccceeeecCChhHHHHHHHhCc
Q 012307 79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRA 109 (466)
Q Consensus 79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga 109 (466)
.+++.|....-|.|||++|+.|++|++....
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence 3677788888999999999999999977543
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=79.30 E-value=2.1 Score=34.30 Aligned_cols=28 Identities=25% Similarity=0.374 Sum_probs=23.5
Q ss_pred EEEEecccccceeeecCChhHHHHHHHh
Q 012307 80 FRMIVPVLKVGSIIGRKGELIKKTCEDT 107 (466)
Q Consensus 80 ~rllvp~~~vG~IIGk~G~~Ik~I~~et 107 (466)
+++.|....-|.+||++|.+|++|++.-
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 5666666888999999999999998764
No 129
>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=76.20 E-value=6.6 Score=43.43 Aligned_cols=95 Identities=18% Similarity=0.329 Sum_probs=61.2
Q ss_pred eeeecCChhHHHHHHHhCceEEEeCCCCCCCCeEEEecCCCCCCCCCChhHHHHHHHHHHhcCCCCCCcccccCCCcceE
Q 012307 91 SIIGRKGELIKKTCEDTRARIKVLDGPVSSPDRIVLISGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAKASGAAFCS 170 (466)
Q Consensus 91 ~IIGk~G~~Ik~I~~etga~I~v~~~~~~~~ervv~I~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~~~~~~~~~~~~~ 170 (466)
..+=.+|+.||+|-.+-.-||.|..++. +.-.++ .|.+.|.++.-.-.++.+-.+ ...+
T Consensus 36 ~~~~~~~~~~~~~~~~~~~r~~~~~~~~--------~~~~~~------~~~~~i~~~~~~~~~~~~~~f-------~~~~ 94 (630)
T TIGR03675 36 ELFAKDDDLVKELAKKLRKRIVIRPDPS--------VLLPPE------EAIEKIKEIVPEEAGITDIYF-------DDVT 94 (630)
T ss_pred HHhccchHHHHHHHHHhhceEEEecChh--------hcCCHH------HHHHHHHHhCCCcCCceeEEe-------cCCC
Confidence 3455778999999999999999864420 111111 233333332211012211112 2345
Q ss_pred EEEEeccCcceeeecCCchhHHHHHHHhCCeEEEec
Q 012307 171 VRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLS 206 (466)
Q Consensus 171 ~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~ 206 (466)
-+++|-...-|.+|||+|.++++|.+++|-+-+|..
T Consensus 95 ~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~ 130 (630)
T TIGR03675 95 GEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVR 130 (630)
T ss_pred ceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEe
Confidence 677888888899999999999999999998888874
No 130
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=76.16 E-value=2.3 Score=40.48 Aligned_cols=29 Identities=28% Similarity=0.431 Sum_probs=25.6
Q ss_pred EEEEEecccccceeeecCChhHHHHHHHh
Q 012307 79 VFRMIVPVLKVGSIIGRKGELIKKTCEDT 107 (466)
Q Consensus 79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~et 107 (466)
..++.|....-|.||||+|++|++|+++.
T Consensus 52 ~~~V~I~aarPg~VIGk~G~~I~~L~~~l 80 (233)
T COG0092 52 GTRVTIHAARPGLVIGKKGSNIEKLRKEL 80 (233)
T ss_pred ceEEEEEeCCCcceEcCCCccHHHHHHHH
Confidence 57788899999999999999999988653
No 131
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=74.45 E-value=3.4 Score=32.85 Aligned_cols=35 Identities=11% Similarity=0.246 Sum_probs=28.1
Q ss_pred EEEEEeccCcccceeccccchHHHHHhHhCCeEEE
Q 012307 344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITV 378 (466)
Q Consensus 344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I 378 (466)
..++.|-...-|.|||++|.+|++|++.-.-...+
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 35677777888999999999999998876655555
No 132
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=73.52 E-value=4.8 Score=36.53 Aligned_cols=36 Identities=39% Similarity=0.446 Sum_probs=31.6
Q ss_pred eEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEe
Q 012307 169 CSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVL 205 (466)
Q Consensus 169 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~ 205 (466)
..+-++|-... |..|||+|.+|+.+++..|-+|.+.
T Consensus 61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevV 96 (166)
T PRK06418 61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVV 96 (166)
T ss_pred CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEE
Confidence 34667777777 9999999999999999999999997
No 133
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=65.77 E-value=5.4 Score=33.54 Aligned_cols=29 Identities=28% Similarity=0.370 Sum_probs=23.7
Q ss_pred EEEEeccCcccceeccccchHHHHHhHhC
Q 012307 345 QTMQIPISYAEDIIGVGGTSIENIRRTSG 373 (466)
Q Consensus 345 ~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SG 373 (466)
.++.|-...-|.|||+.|++|++|++...
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 45667777789999999999999987654
No 134
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=65.43 E-value=6.5 Score=31.37 Aligned_cols=27 Identities=22% Similarity=0.359 Sum_probs=21.3
Q ss_pred EEEeccCcccceeccccchHHHHHhHh
Q 012307 346 TMQIPISYAEDIIGVGGTSIENIRRTS 372 (466)
Q Consensus 346 ~i~IP~~~~G~IIGkgG~~Ik~Ir~~S 372 (466)
++.|-...-|.+||++|++|++|++.-
T Consensus 41 ~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 41 QITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred EEEEEECCCCceECCCchhHHHHHHHH
Confidence 444555777999999999999987754
No 135
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=59.47 E-value=8.4 Score=36.74 Aligned_cols=37 Identities=27% Similarity=0.441 Sum_probs=27.6
Q ss_pred EEEEEeccCcccceeccccchHHHHHh----HhCC---eEEEec
Q 012307 344 TQTMQIPISYAEDIIGVGGTSIENIRR----TSGA---IITVQE 380 (466)
Q Consensus 344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~----~SGA---~I~I~~ 380 (466)
...+.|-...-|.|||++|++|+.|++ .+|. +|.|.+
T Consensus 52 ~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~~v~I~i~E 95 (233)
T COG0092 52 GTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKENVQINIEE 95 (233)
T ss_pred ceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCCCceEEEEE
Confidence 356777788889999999999998865 4555 455544
No 136
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=57.72 E-value=14 Score=39.02 Aligned_cols=126 Identities=6% Similarity=0.030 Sum_probs=79.5
Q ss_pred ceeeecCChhHHHHHHHhCceEEEe--CCCCCCCCeEEEe-cCCCCCCCCCChhHHHHHHHHHHhcCCCCCCcccccCCC
Q 012307 90 GSIIGRKGELIKKTCEDTRARIKVL--DGPVSSPDRIVLI-SGKEEPEAPVSPAMDAAVRVFKRVSGLPENDVDAKASGA 166 (466)
Q Consensus 90 G~IIGk~G~~Ik~I~~etga~I~v~--~~~~~~~ervv~I-~G~~e~~~~v~~A~~ai~~i~~~i~~l~~~~~~~~~~~~ 166 (466)
-.|-||+--++.+|++...|.+.+. +. ...++.++ .|.. . +..+.++.+. . +
T Consensus 392 dFl~gkkngK~TrIm~~v~c~~~~~i~~~---~gs~~~~~~~g~~-------~---~F~k~~~~~~----~--------E 446 (657)
T COG5166 392 DFLRGKKNGKATRIMKGVSCSELSSIVSS---TGSIVETNGIGEK-------M---SFSKKLSIPP----T--------E 446 (657)
T ss_pred HHhccccCcchhhhhhhcccceeeEEEec---CCcEEEEeccCcc-------h---hhHHHhcCCc----c--------c
Confidence 3778888888999999999985443 32 12243332 3332 1 1222232221 1 1
Q ss_pred cceEEEEEeccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceE-EEEecCHHH---HHHHHHHHHHHhh
Q 012307 167 AFCSVRLLVPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERI-VEMQGEAAK---VLKALEAVVGHLR 242 (466)
Q Consensus 167 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~-v~I~G~~~~---V~~A~~~I~~~l~ 242 (466)
-.....+.||...+..|||-+|..|+++..+.++.|++...-..+ .+..+- |.|.-+.++ +--++.-+++++.
T Consensus 447 Fpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~---qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~ 523 (657)
T COG5166 447 FPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFG---QSQWHDNVLIEAPRKNQDNISGKKNDKLDKVK 523 (657)
T ss_pred CchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcc---hhhhhcceEEECCccCccchhcccccHHHHHh
Confidence 224577899999999999999999999999999999886433343 233333 667665544 4445555666665
Q ss_pred h
Q 012307 243 K 243 (466)
Q Consensus 243 ~ 243 (466)
+
T Consensus 524 ~ 524 (657)
T COG5166 524 Q 524 (657)
T ss_pred h
Confidence 4
No 137
>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=54.12 E-value=40 Score=26.91 Aligned_cols=52 Identities=19% Similarity=0.321 Sum_probs=42.3
Q ss_pred ccchHHHHHhHhCCeEEEecCCC---CCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 012307 361 GGTSIENIRRTSGAIITVQESRG---LPDEITVEIKGTSSQVQLAQQLIQEYMNN 412 (466)
Q Consensus 361 gG~~Ik~Ir~~SGA~I~I~~~~~---~~~er~V~I~Gt~~~V~~A~~lI~~~i~~ 412 (466)
|=.-+.+|=+..|++|+.....+ .+++.+++|+|....+..|...++++|..
T Consensus 32 G~~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~~ 86 (88)
T PF02749_consen 32 GLEEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQR 86 (88)
T ss_dssp SHHHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHHH
Confidence 44567788888899998865544 36789999999999999999999999863
No 138
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=54.07 E-value=13 Score=35.15 Aligned_cols=31 Identities=26% Similarity=0.401 Sum_probs=25.2
Q ss_pred EEEEecccccceeeecCChhHHHHHHHhCce
Q 012307 80 FRMIVPVLKVGSIIGRKGELIKKTCEDTRAR 110 (466)
Q Consensus 80 ~rllvp~~~vG~IIGk~G~~Ik~I~~etga~ 110 (466)
.++.|....-|.+||++|++|++|++.-.-.
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 5566666889999999999999999876543
No 139
>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=53.71 E-value=13 Score=34.64 Aligned_cols=31 Identities=26% Similarity=0.398 Sum_probs=26.2
Q ss_pred EEEEEecccccceeeecCChhHHHHHHHhCc
Q 012307 79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRA 109 (466)
Q Consensus 79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga 109 (466)
.+++.|....-|.|||++|..|++|+++-.-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k 69 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKLQK 69 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHHHH
Confidence 4678888888999999999999999877543
No 140
>CHL00048 rps3 ribosomal protein S3
Probab=53.16 E-value=13 Score=35.17 Aligned_cols=30 Identities=20% Similarity=0.181 Sum_probs=25.5
Q ss_pred EEEEEecccccceeeecCChhHHHHHHHhC
Q 012307 79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTR 108 (466)
Q Consensus 79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etg 108 (466)
..++.|....-|.|||++|.+|++|++.-.
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 467777788889999999999999998764
No 141
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=51.62 E-value=14 Score=35.10 Aligned_cols=32 Identities=19% Similarity=0.341 Sum_probs=26.6
Q ss_pred EEEEEecccccceeeecCChhHHHHHHHhCce
Q 012307 79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRAR 110 (466)
Q Consensus 79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~ 110 (466)
.+++.|....-|.|||++|..|++|+++-.-.
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 36777888889999999999999999876544
No 142
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=49.47 E-value=17 Score=35.45 Aligned_cols=30 Identities=23% Similarity=0.310 Sum_probs=23.3
Q ss_pred eEEEEEeccCcc-cceeccccchHHHHHhHh
Q 012307 343 ITQTMQIPISYA-EDIIGVGGTSIENIRRTS 372 (466)
Q Consensus 343 ~t~~i~IP~~~~-G~IIGkgG~~Ik~Ir~~S 372 (466)
+...+.|..+-. +-|||++|+.||+|....
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 566777876654 999999999999876543
No 143
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=47.79 E-value=21 Score=37.92 Aligned_cols=39 Identities=23% Similarity=0.374 Sum_probs=32.9
Q ss_pred EEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCC
Q 012307 80 FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPV 118 (466)
Q Consensus 80 ~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~ 118 (466)
=+++|-.++-|.||||+|++.+.|..+||-+-+|...+|
T Consensus 101 GEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~PP 139 (637)
T COG1782 101 GEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTPP 139 (637)
T ss_pred ceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecCC
Confidence 356677888999999999999999999998877765543
No 144
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=47.56 E-value=13 Score=36.27 Aligned_cols=30 Identities=23% Similarity=0.197 Sum_probs=22.6
Q ss_pred eEEEEEeccc-ccceeeecCChhHHHHHHHh
Q 012307 78 CVFRMIVPVL-KVGSIIGRKGELIKKTCEDT 107 (466)
Q Consensus 78 ~~~rllvp~~-~vG~IIGk~G~~Ik~I~~et 107 (466)
+...++|..+ +-+.|||++|+.||+|..+.
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 4556666644 57999999999999887543
No 145
>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=46.49 E-value=23 Score=39.27 Aligned_cols=39 Identities=26% Similarity=0.374 Sum_probs=33.4
Q ss_pred EEEEecccccceeeecCChhHHHHHHHhCceEEEeCCCC
Q 012307 80 FRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDGPV 118 (466)
Q Consensus 80 ~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~~~ 118 (466)
=+++|-.++-|.||||+|.++++|-.+||-+-+|...+|
T Consensus 95 ~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~~ 133 (630)
T TIGR03675 95 GEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTPP 133 (630)
T ss_pred ceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecCC
Confidence 356677788899999999999999999999988876654
No 146
>PRK15494 era GTPase Era; Provisional
Probab=45.05 E-value=21 Score=36.21 Aligned_cols=36 Identities=22% Similarity=0.294 Sum_probs=26.7
Q ss_pred eEEEEEeccCcc-cceeccccchHHHHHh--------HhCCeEEE
Q 012307 343 ITQTMQIPISYA-EDIIGVGGTSIENIRR--------TSGAIITV 378 (466)
Q Consensus 343 ~t~~i~IP~~~~-G~IIGkgG~~Ik~Ir~--------~SGA~I~I 378 (466)
+...|.|..+-. +-|||++|..||+|.. ..|++|.+
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 556778876655 8999999999997754 45666555
No 147
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=44.95 E-value=21 Score=35.70 Aligned_cols=39 Identities=18% Similarity=0.391 Sum_probs=29.4
Q ss_pred CCCCCCC---ceEEEEEeccc-ccceeeecCChhHHHHHHHhC
Q 012307 70 KWPGWPG---HCVFRMIVPVL-KVGSIIGRKGELIKKTCEDTR 108 (466)
Q Consensus 70 ~~~~~~~---~~~~rllvp~~-~vG~IIGk~G~~Ik~I~~etg 108 (466)
-|...++ .+..+++||.. ....||||+|..|++|-++-+
T Consensus 317 ~w~e~~~g~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 317 SWKERPAGVLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EeeecCCcEEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 3655455 36778999976 467889999999999976543
No 148
>PRK00089 era GTPase Era; Reviewed
Probab=43.80 E-value=16 Score=35.89 Aligned_cols=36 Identities=22% Similarity=0.336 Sum_probs=24.7
Q ss_pred eEEEEEecc-cccceeeecCChhHHHHHHH--------hCceEEE
Q 012307 78 CVFRMIVPV-LKVGSIIGRKGELIKKTCED--------TRARIKV 113 (466)
Q Consensus 78 ~~~rllvp~-~~vG~IIGk~G~~Ik~I~~e--------tga~I~v 113 (466)
+...|+|.. ++-+.|||++|++||+|..+ .+++|.+
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 334455553 35799999999999988643 5666555
No 149
>PRK00089 era GTPase Era; Reviewed
Probab=43.56 E-value=23 Score=34.77 Aligned_cols=36 Identities=25% Similarity=0.345 Sum_probs=26.2
Q ss_pred eEEEEEeccCc-ccceeccccchHHHHHh--------HhCCeEEE
Q 012307 343 ITQTMQIPISY-AEDIIGVGGTSIENIRR--------TSGAIITV 378 (466)
Q Consensus 343 ~t~~i~IP~~~-~G~IIGkgG~~Ik~Ir~--------~SGA~I~I 378 (466)
+...|.|..+- -+-|||++|.+|++|.. ..|++|.+
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 56667776554 48999999999997754 45666655
No 150
>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=41.69 E-value=68 Score=25.59 Aligned_cols=55 Identities=25% Similarity=0.305 Sum_probs=42.2
Q ss_pred CchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhh
Q 012307 187 QGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRK 243 (466)
Q Consensus 187 ~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~ 243 (466)
+=..+.+|-+..++++...-+|... ...++.++++.|...++..|-+.++..|..
T Consensus 32 G~~~~~~i~~~l~~~v~~~~~dG~~--v~~g~~i~~i~G~a~~ll~~ER~~LN~l~~ 86 (88)
T PF02749_consen 32 GLEEAEEIFEKLGLEVEWLVKDGDR--VEPGDVILEIEGPARALLTAERTALNFLQR 86 (88)
T ss_dssp SHHHHHHHHHHCTEEEEESS-TT-E--EETTCEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhhccEEEEEEeCCCCC--ccCCcEEEEEEeCHHHHHHHHHHHHHHHHH
Confidence 3446788888889999887544322 156789999999999999999999988763
No 151
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=41.48 E-value=61 Score=32.90 Aligned_cols=57 Identities=18% Similarity=0.212 Sum_probs=47.6
Q ss_pred ccCcccceeccccchHHHHHhHhCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHH--HHHhcC
Q 012307 350 PISYAEDIIGVGGTSIENIRRTSGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQ--EYMNNH 413 (466)
Q Consensus 350 P~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~--~~i~~~ 413 (466)
+.+.+-.+.|..|.+++.|.+..|+.|.. ..+.++|+|+...|+.|..+++ +.+...
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~-------rG~~~~i~g~~~~v~~A~~~l~~l~~~~~~ 80 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVA-------RGEAVRIIGARPLVDVATRVLLTLELLAEV 80 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEe-------CCceEEEEechHHHHHHHHHHhHHHHHHHH
Confidence 35567789999999999999999999887 3357999999889999999888 666654
No 152
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=41.44 E-value=19 Score=33.72 Aligned_cols=35 Identities=11% Similarity=0.144 Sum_probs=28.2
Q ss_pred EEEEEecccccceeeecCChhHHHHHHHhCceEEE
Q 012307 79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKV 113 (466)
Q Consensus 79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v 113 (466)
.+.+-+..+..+.|||+.|+++..||--+.+-++-
T Consensus 92 ~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 92 RVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred EEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 45566677779999999999999999877765544
No 153
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=40.57 E-value=28 Score=34.89 Aligned_cols=35 Identities=34% Similarity=0.532 Sum_probs=27.5
Q ss_pred CCcceEEEEEecc-CcceeeecCCchhHHHHHHHhC
Q 012307 165 GAAFCSVRLLVPS-TQAINLIGKQGSLIKSIQENSG 199 (466)
Q Consensus 165 ~~~~~~~~llVP~-~~vg~IIGk~G~~Ik~I~~~sg 199 (466)
+.-....++++|. ++...||||+|..|++|-++-+
T Consensus 324 g~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 324 GVLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred cEEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 3456788899995 5677889999999999876543
No 154
>PRK15494 era GTPase Era; Provisional
Probab=40.07 E-value=19 Score=36.52 Aligned_cols=36 Identities=17% Similarity=0.159 Sum_probs=25.6
Q ss_pred eEEEEEeccc-ccceeeecCChhHHHHHHH--------hCceEEE
Q 012307 78 CVFRMIVPVL-KVGSIIGRKGELIKKTCED--------TRARIKV 113 (466)
Q Consensus 78 ~~~rllvp~~-~vG~IIGk~G~~Ik~I~~e--------tga~I~v 113 (466)
+...|+|..+ +-+.|||++|+.||+|..+ .+++|.+
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 3455666654 6789999999999987643 5555555
No 155
>COG1159 Era GTPase [General function prediction only]
Probab=39.93 E-value=21 Score=35.47 Aligned_cols=29 Identities=31% Similarity=0.390 Sum_probs=21.1
Q ss_pred eEEEEEeccc-ccceeeecCChhHHHHHHH
Q 012307 78 CVFRMIVPVL-KVGSIIGRKGELIKKTCED 106 (466)
Q Consensus 78 ~~~rllvp~~-~vG~IIGk~G~~Ik~I~~e 106 (466)
+.-.|+|+.+ +-|.||||+|++||+|-..
T Consensus 229 I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~ 258 (298)
T COG1159 229 IHATIYVERESQKGIIIGKNGAMIKKIGTA 258 (298)
T ss_pred EEEEEEEecCCccceEECCCcHHHHHHHHH
Confidence 3444566544 6899999999999987543
No 156
>COG1159 Era GTPase [General function prediction only]
Probab=39.43 E-value=31 Score=34.31 Aligned_cols=29 Identities=28% Similarity=0.332 Sum_probs=21.8
Q ss_pred eEEEEEeccCc-ccceeccccchHHHHHhH
Q 012307 343 ITQTMQIPISY-AEDIIGVGGTSIENIRRT 371 (466)
Q Consensus 343 ~t~~i~IP~~~-~G~IIGkgG~~Ik~Ir~~ 371 (466)
+...+.|+.+- -|-||||+|++||+|-..
T Consensus 229 I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~ 258 (298)
T COG1159 229 IHATIYVERESQKGIIIGKNGAMIKKIGTA 258 (298)
T ss_pred EEEEEEEecCCccceEECCCcHHHHHHHHH
Confidence 45567777654 499999999999977443
No 157
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=38.70 E-value=29 Score=32.84 Aligned_cols=29 Identities=31% Similarity=0.550 Sum_probs=24.8
Q ss_pred EEEEecccccceeeecCChhHHHHHHHhC
Q 012307 80 FRMIVPVLKVGSIIGRKGELIKKTCEDTR 108 (466)
Q Consensus 80 ~rllvp~~~vG~IIGk~G~~Ik~I~~etg 108 (466)
+++.|....-|.|||++|..|++|++.-.
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l~ 92 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDLQ 92 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHHH
Confidence 66778888889999999999999986643
No 158
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=32.95 E-value=40 Score=31.78 Aligned_cols=28 Identities=21% Similarity=0.335 Sum_probs=22.1
Q ss_pred EEEeccCcccceeccccchHHHHHhHhC
Q 012307 346 TMQIPISYAEDIIGVGGTSIENIRRTSG 373 (466)
Q Consensus 346 ~i~IP~~~~G~IIGkgG~~Ik~Ir~~SG 373 (466)
++.|-...-|.+||++|.+|+++++.-.
T Consensus 43 ~I~I~ta~PGivIGk~G~~I~klk~~Lk 70 (207)
T PRK04191 43 RITIYAERPGMVIGRGGKNIRELTEILE 70 (207)
T ss_pred EEEEEECCCCeEECCCchhHHHHHHHHH
Confidence 4445557789999999999999877654
No 159
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=31.63 E-value=44 Score=31.20 Aligned_cols=28 Identities=21% Similarity=0.286 Sum_probs=22.9
Q ss_pred EEEEeccCcccceeccccchHHHHHhHh
Q 012307 345 QTMQIPISYAEDIIGVGGTSIENIRRTS 372 (466)
Q Consensus 345 ~~i~IP~~~~G~IIGkgG~~Ik~Ir~~S 372 (466)
.++.|-...-|.|||++|.+|++|++.-
T Consensus 40 ~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 40 TKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred EEEEEEECCCceEECCCchHHHHHHHHH
Confidence 4566777778999999999999887654
No 160
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=31.05 E-value=44 Score=31.80 Aligned_cols=28 Identities=14% Similarity=0.302 Sum_probs=22.6
Q ss_pred EEEEeccCcccceeccccchHHHHHhHh
Q 012307 345 QTMQIPISYAEDIIGVGGTSIENIRRTS 372 (466)
Q Consensus 345 ~~i~IP~~~~G~IIGkgG~~Ik~Ir~~S 372 (466)
.++.|-...-|.|||++|..|++|++.-
T Consensus 46 i~V~I~tarPg~vIG~~G~~i~~l~~~L 73 (220)
T PTZ00084 46 TEIIIRATRTREVLGDKGRRIRELTSLL 73 (220)
T ss_pred EEEEEEECCCccEEcCCchHHHHHHHHH
Confidence 4566667777999999999999887654
No 161
>CHL00048 rps3 ribosomal protein S3
Probab=29.82 E-value=48 Score=31.45 Aligned_cols=28 Identities=18% Similarity=0.235 Sum_probs=22.7
Q ss_pred EEEEeccCcccceeccccchHHHHHhHh
Q 012307 345 QTMQIPISYAEDIIGVGGTSIENIRRTS 372 (466)
Q Consensus 345 ~~i~IP~~~~G~IIGkgG~~Ik~Ir~~S 372 (466)
.++.|-...-|.|||++|.+|++|++.-
T Consensus 68 ~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 68 IQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred EEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 4566667777999999999999987765
No 162
>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=28.78 E-value=99 Score=23.95 Aligned_cols=43 Identities=23% Similarity=0.353 Sum_probs=31.1
Q ss_pred ccchHHHHHhHhCCeEE-EecCCCCCCceEEEEEcCHHHHHHHHHHHHH
Q 012307 361 GGTSIENIRRTSGAIIT-VQESRGLPDEITVEIKGTSSQVQLAQQLIQE 408 (466)
Q Consensus 361 gG~~Ik~Ir~~SGA~I~-I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~ 408 (466)
.-..|.+|-+..+|+|. +.+ +.-+|+++|+++.+.....++..
T Consensus 15 ~r~ei~~l~~~f~a~ivd~~~-----~~~iie~tG~~~kid~fi~~l~~ 58 (75)
T PF10369_consen 15 NRSEILQLAEIFRARIVDVSP-----DSIIIELTGTPEKIDAFIKLLKP 58 (75)
T ss_dssp HHHHHHHHHHHTT-EEEEEET-----TEEEEEEEE-HHHHHHHHHHSTG
T ss_pred CHHHHHHHHHHhCCEEEEECC-----CEEEEEEcCCHHHHHHHHHHhhh
Confidence 34567888888999854 433 56799999999999988777654
No 163
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=28.34 E-value=50 Score=31.70 Aligned_cols=30 Identities=27% Similarity=0.463 Sum_probs=24.5
Q ss_pred EEEEEecccccceeeecCChhHHHHHHHhC
Q 012307 79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTR 108 (466)
Q Consensus 79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etg 108 (466)
.++|.|....-|.|||++|..|++|++.-.
T Consensus 63 ~i~I~I~~~rP~~iiG~~g~~i~~l~~~L~ 92 (232)
T PRK00310 63 RVRVTIHTARPGIVIGKKGAEIEKLRKELE 92 (232)
T ss_pred eEEEEEEECCCccccCCCcHHHHHHHHHHH
Confidence 356666777789999999999999987754
No 164
>PRK03818 putative transporter; Validated
Probab=28.29 E-value=7.7e+02 Score=26.88 Aligned_cols=134 Identities=12% Similarity=0.180 Sum_probs=70.0
Q ss_pred EEEEEecccccceeeecCChhHHHHHHHhCceEEEeCC---------CCC---CCCeEEEecCCCCCCCCCChhHHHHHH
Q 012307 79 VFRMIVPVLKVGSIIGRKGELIKKTCEDTRARIKVLDG---------PVS---SPDRIVLISGKEEPEAPVSPAMDAAVR 146 (466)
Q Consensus 79 ~~rllvp~~~vG~IIGk~G~~Ik~I~~etga~I~v~~~---------~~~---~~ervv~I~G~~e~~~~v~~A~~ai~~ 146 (466)
..++.|+++. ++ |.+++++.......+.|..- .++ ....++.|.|..+ ++.+
T Consensus 206 ~r~~~V~~s~---li---GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e----------~l~~ 269 (552)
T PRK03818 206 TINIRVENPN---LH---GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPE----------DLHK 269 (552)
T ss_pred eEEEEEeCCC---CC---CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHH----------HHHH
Confidence 3566666443 34 67899999887766655311 111 1335677788764 4444
Q ss_pred HHHHhcCCCCCCcccccCCCcceEEEEEeccCcceeeecCCchhHHHH--HHHhCCeEEEecCCCCCCCCC-----CCce
Q 012307 147 VFKRVSGLPENDVDAKASGAAFCSVRLLVPSTQAINLIGKQGSLIKSI--QENSGASVRVLSADEAPFYVT-----EDER 219 (466)
Q Consensus 147 i~~~i~~l~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I--~~~sga~I~i~~~~~~p~~~~-----~~er 219 (466)
+.+....-.+.+.+ .........++++|+ ..++|| +++++ +++.|+.|.-..+........ ..-.
T Consensus 270 l~~~~Gl~~~~~~~--~~~~~~~~E~Vvv~~---S~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq~GD 341 (552)
T PRK03818 270 AQLVIGEEVDTSLS--TRGTDLRSERVVVTN---EKVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLSLQFGD 341 (552)
T ss_pred HHHhcCCccCcccc--ccCcceEEEEEEEcC---hhccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCEEecCC
Confidence 44333111000000 001123444555554 356665 67776 466777665443322111001 1224
Q ss_pred EEEEecCHHHHHHHHHH
Q 012307 220 IVEMQGEAAKVLKALEA 236 (466)
Q Consensus 220 ~v~I~G~~~~V~~A~~~ 236 (466)
++.+.|+.+++++..+.
T Consensus 342 ~LlVvG~~~~i~~l~~~ 358 (552)
T PRK03818 342 ILNLVGRPEAIDAVANV 358 (552)
T ss_pred EEEEEECHHHHHHHHHH
Confidence 58899999999997775
No 165
>PF00936 BMC: BMC domain; InterPro: IPR000249 This domain is found in a variety of polyhedral organelle shell proteins, including CsoS1A, CsoS1B and CsoS1C of Thiobacillus neapolitanus (Halothiobacillus neapolitanus) and their orthologs from other bacteria. Some autotrophic and non-autotrophic organisms form polyhedral organelles, carboxysomes/enterosomes []. The best studied is the carboxysome of Halothiobacillus neapolitanus, which is composed of at least 9 proteins: six shell proteins, CsoS1A, CsoS1B, CsoS1C, Cso2A, Cso2B and CsoS3 (carbonic anhydrase) [], one protein of unknown function and the large and small subunits of RuBisCo (CbbL and Cbbs). Carboxysomes appear to be approximately 120 nm in diameter, most often observed as regular hexagons, with a solid interior bounded by a unilamellar protein shell. The interior is filled with type I RuBisCo, which is composed of 8 large subunits and 8 small subunits; it accounts for 60% of the carboxysomal protein, which amounts to approximately 300 molecules of enzyme per carboxysome. Carboxysomes are required for autotrophic growth at low CO2 concentrations and are thought to function as part of a CO2-concentrating mechanism [, ]. Polyhedral organelles, enterosomes, from non-autotrophic organisms are involved in coenzyme B12-dependent 1,2-propanediol utilisation (e.g., in Salmonella enterica []) and ethanolamine utilisation (e.g., in Salmonella typhimurium []). Genes needed for enterosome formation are located in the 1,2-propanediol utilisation pdu [, ] or ethanolamine utilisation eut [, ] operons, respectively. Although enterosomes of non-autotrophic organisms are apparently related to carboxysomes structurally, a functional relationship is uncertain. A role in CO2 concentration, similar to that of the carboxysome, is unlikely since there is no known association between CO2 and coenzyme B12-dependent 1,2-propanediol or ethanolamine utilisation []. It seems probable that entrosomes help protect the cells from reactive aldehyde species in the degradation pathways of 1,2-propanediol and ethanolamine [].; PDB: 3F56_C 3FCH_A 3I87_A 3GFH_B 3I82_A 3MPV_A 3IO0_A 4AXJ_B 3N79_A 2G13_A ....
Probab=28.05 E-value=78 Score=24.53 Aligned_cols=36 Identities=25% Similarity=0.269 Sum_probs=28.3
Q ss_pred CCceEEEEecCHHHHHHHHHHHHHHhhhccccCccc
Q 012307 216 EDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQGVL 251 (466)
Q Consensus 216 ~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~ 251 (466)
...-.+.|+|+..+|+.|++...+.+.+.+....++
T Consensus 37 ~g~~~~~i~G~vs~V~~Av~a~~~~~~~~~v~~~vI 72 (75)
T PF00936_consen 37 GGKVTVIITGDVSAVKAAVDAAEEAAGKKLVSSTVI 72 (75)
T ss_dssp TTEEEEEEEESHHHHHHHHHHHHHHHHHTEEEEEEE
T ss_pred CCeEEEEEEECHHHHHHHHHHHHHHHhhceeeEEEe
Confidence 346678999999999999999999988865544333
No 166
>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=27.26 E-value=1.6e+02 Score=22.52 Aligned_cols=33 Identities=21% Similarity=0.391 Sum_probs=25.1
Q ss_pred hCCeEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHH
Q 012307 372 SGAIITVQESRGLPDEITVEIKGTSSQVQLAQQLIQEY 409 (466)
Q Consensus 372 SGA~I~I~~~~~~~~er~V~I~Gt~~~V~~A~~lI~~~ 409 (466)
.+.+|..++.. ..+.|+|+++.++..+.||.++
T Consensus 44 ~~~~i~~d~~t-----Nsliv~g~~~~~~~i~~li~~L 76 (82)
T PF03958_consen 44 SSGRIVADERT-----NSLIVRGTPEDLEQIRELIKQL 76 (82)
T ss_dssp TTTEEEEECTT-----TEEEEEEEHHHHHHHHHHHHHH
T ss_pred CCeEEEEECCC-----CEEEEEeCHHHHHHHHHHHHHH
Confidence 44577776533 3788999999999999999654
No 167
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=25.89 E-value=52 Score=30.92 Aligned_cols=35 Identities=14% Similarity=0.229 Sum_probs=29.0
Q ss_pred EEEEEeccCcccceeccccchHHHHHhHhCCeEEE
Q 012307 344 TQTMQIPISYAEDIIGVGGTSIENIRRTSGAIITV 378 (466)
Q Consensus 344 t~~i~IP~~~~G~IIGkgG~~Ik~Ir~~SGA~I~I 378 (466)
+..+.|-.+..+.+||+.|.+++.||-.+.+.+.-
T Consensus 92 ~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 92 RVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred EEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 55677878889999999999999999887766554
No 168
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=25.64 E-value=5.3e+02 Score=26.87 Aligned_cols=65 Identities=12% Similarity=-0.012 Sum_probs=44.8
Q ss_pred eccCcc-cceeccccchHHHHHhHhCCeEEEecCC--------C-CCCc-e-EEEEEcCHHHHHHHHHHHHHHHhcC
Q 012307 349 IPISYA-EDIIGVGGTSIENIRRTSGAIITVQESR--------G-LPDE-I-TVEIKGTSSQVQLAQQLIQEYMNNH 413 (466)
Q Consensus 349 IP~~~~-G~IIGkgG~~Ik~Ir~~SGA~I~I~~~~--------~-~~~e-r-~V~I~Gt~~~V~~A~~lI~~~i~~~ 413 (466)
+|..++ +.+=|++-..+..++.++++.+-+.... + .+.| . +..+-+..+.+..|.+++.++++..
T Consensus 220 ~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMYI~i~h~~~~g~~~A~r~~~nl~~~v 296 (531)
T KOG1960|consen 220 DPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNEGNESNEPMYIFSTHGNGNGENGAPRRKWNLEEKV 296 (531)
T ss_pred CcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccCcccccccCCceeEEeecCCchhhccchhHHHhHHHHH
Confidence 555555 5666788888999999999997773211 1 1222 3 4445568899999999998887753
No 169
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=24.60 E-value=1.8e+02 Score=24.40 Aligned_cols=44 Identities=18% Similarity=0.249 Sum_probs=33.1
Q ss_pred HHHHH-hCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHhhhcc
Q 012307 193 SIQEN-SGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVVGHLRKFL 245 (466)
Q Consensus 193 ~I~~~-sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~ 245 (466)
.|..+ .++.|-+. +.-...+.|+|.-.+|+.|+..|.+.+++.+
T Consensus 57 DIA~Kaa~V~igF~---------DRFsGslvitGdvs~Ve~Al~~V~~~l~~~L 101 (111)
T PRK15468 57 DLALKAADVHIGFL---------DRFSGALVIYGSVGAVEEALSQTVSGLGRLL 101 (111)
T ss_pred HhhhhccCcEEeee---------eccceeEEEEccHHHHHHHHHHHHHHHHhhc
Confidence 34444 34666665 3445679999999999999999999988753
No 170
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=23.90 E-value=1.7e+02 Score=29.75 Aligned_cols=52 Identities=15% Similarity=0.198 Sum_probs=42.8
Q ss_pred eccCcceeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHH
Q 012307 175 VPSTQAINLIGKQGSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVV 238 (466)
Q Consensus 175 VP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~ 238 (466)
-+...+-.|.|..+.+++.|++.+|+.|... .+.++|.|+...|..|...+.
T Consensus 21 ~~~~~~~~l~G~~~~~l~l~e~~~gv~i~~r------------G~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 21 SDDNELVALFGPTDTNLSLLEIALGVSIVAR------------GEAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred CCchhhhhhcCCCCccHHHHHHHhCcEEEeC------------CceEEEEechHHHHHHHHHHh
Confidence 3456677899999999999999999988764 346889999778888887776
No 171
>cd07053 BMC_PduT_repeat1 1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 1. PduT proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduT might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view. PduT proteins contain two tandem BMC domains repeats. This CD contains repeat 1 (the first BMC domain of PduT) as well as carboxysome shell protein sequence homolog, EutM protein, are also included in this CD. They too might exist as hexamers and might play similar functional roles in the construction of the eut organelle outer shell which still remains poorly understood.
Probab=22.25 E-value=1.2e+02 Score=23.70 Aligned_cols=36 Identities=28% Similarity=0.303 Sum_probs=28.4
Q ss_pred CCceEEEEecCHHHHHHHHHHHHHHhhhccccCccc
Q 012307 216 EDERIVEMQGEAAKVLKALEAVVGHLRKFLVDQGVL 251 (466)
Q Consensus 216 ~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~ 251 (466)
...-.+.|+|...+|+.|++...+...+.+++..++
T Consensus 36 ~Gk~~vii~GdvsaV~~Av~a~~~~~~~~~v~~~vI 71 (76)
T cd07053 36 PGKYIIIVSGDVGAVQAAVDAGKEIGGKYVVDSFVL 71 (76)
T ss_pred CCEEEEEEEEcHHHHHHHHHHHHHHhCCcEEEEEEe
Confidence 345578899999999999999998887766655444
No 172
>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=22.24 E-value=2.2e+02 Score=21.95 Aligned_cols=42 Identities=24% Similarity=0.234 Sum_probs=30.7
Q ss_pred chhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEecCHHHHHHHHHHHH
Q 012307 188 GSLIKSIQENSGASVRVLSADEAPFYVTEDERIVEMQGEAAKVLKALEAVV 238 (466)
Q Consensus 188 G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~ 238 (466)
-..|.+|.+.++++|.-.. .+.-++.++|+++.+..-++++.
T Consensus 16 r~ei~~l~~~f~a~ivd~~---------~~~~iie~tG~~~kid~fi~~l~ 57 (75)
T PF10369_consen 16 RSEILQLAEIFRARIVDVS---------PDSIIIELTGTPEKIDAFIKLLK 57 (75)
T ss_dssp HHHHHHHHHHTT-EEEEEE---------TTEEEEEEEE-HHHHHHHHHHST
T ss_pred HHHHHHHHHHhCCEEEEEC---------CCEEEEEEcCCHHHHHHHHHHhh
Confidence 3467889999999887663 44668999999999987776664
No 173
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=20.40 E-value=89 Score=29.53 Aligned_cols=28 Identities=25% Similarity=0.388 Sum_probs=22.4
Q ss_pred EEEEeccCcccceeccccchHHHHHhHh
Q 012307 345 QTMQIPISYAEDIIGVGGTSIENIRRTS 372 (466)
Q Consensus 345 ~~i~IP~~~~G~IIGkgG~~Ik~Ir~~S 372 (466)
.++.|-...-|.|||++|.+|++|++.-
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 4566667777999999999999987544
No 174
>TIGR01334 modD putative molybdenum utilization protein ModD. The gene modD for a member of this family is found with molybdenum transport genes modABC in Rhodobacter capsulatus. However, disruption of modD causes only a 4-fold (rather than 500-fold for modA, modB, modC) change in the external molybdenum concentration required to suppress an alternative nitrogenase. ModD proteins are highly similar to nicotinate-nucleotide pyrophosphorylase (also called quinolinate phosphoribosyltransferase). The function unknown.
Probab=20.06 E-value=3.6e+02 Score=26.65 Aligned_cols=53 Identities=21% Similarity=0.288 Sum_probs=43.7
Q ss_pred cccchHHHHHhHhCCeEEEecCCC---CCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 012307 360 VGGTSIENIRRTSGAIITVQESRG---LPDEITVEIKGTSSQVQLAQQLIQEYMNN 412 (466)
Q Consensus 360 kgG~~Ik~Ir~~SGA~I~I~~~~~---~~~er~V~I~Gt~~~V~~A~~lI~~~i~~ 412 (466)
-|-.-..+|-+..|+++++....+ .+++.+++++|....+..|.+.++++|+.
T Consensus 46 ~G~~~~~~i~~~l~~~~~~~~~dG~~v~~g~~i~~~~G~a~~ll~~eR~alN~l~~ 101 (277)
T TIGR01334 46 SGVSEAAKLLKQLGASIDYAVPSGSRALAGTLLLEAKGSAGQLHQGWKSAQSVLEW 101 (277)
T ss_pred ECHHHHHHHHHHcCCEEEEEeCCCCEeCCCCEEEEEEecHHHHHHHHHHHHHHHHH
Confidence 445667788888899999876554 37899999999999999999999888875
Done!