Query 045766
Match_columns 663
No_of_seqs 272 out of 2472
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 05:19:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045766.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045766hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2193 IGF-II mRNA-binding pr 100.0 4.5E-42 9.7E-47 346.5 20.8 354 42-479 195-567 (584)
2 KOG1676 K-homology type RNA bi 100.0 4E-39 8.7E-44 341.7 30.7 324 44-478 52-391 (600)
3 KOG2190 PolyC-binding proteins 100.0 4.5E-38 9.7E-43 340.7 34.7 358 40-476 37-409 (485)
4 KOG1676 K-homology type RNA bi 100.0 5.9E-38 1.3E-42 332.9 24.5 317 185-658 52-389 (600)
5 KOG2192 PolyC-binding hnRNP-K 100.0 1.2E-35 2.6E-40 284.0 27.5 322 314-662 45-388 (390)
6 KOG2193 IGF-II mRNA-binding pr 100.0 1.7E-34 3.7E-39 291.7 15.9 308 185-658 197-564 (584)
7 KOG2192 PolyC-binding hnRNP-K 100.0 2.4E-29 5.2E-34 240.9 21.2 301 7-384 17-379 (390)
8 KOG2190 PolyC-binding proteins 100.0 3.2E-28 6.8E-33 264.1 28.2 331 315-661 41-412 (485)
9 KOG2191 RNA-binding protein NO 99.9 7.9E-25 1.7E-29 216.2 20.0 266 314-661 36-318 (402)
10 KOG2191 RNA-binding protein NO 99.9 1.3E-24 2.7E-29 214.8 16.7 252 5-355 12-282 (402)
11 TIGR03665 arCOG04150 arCOG0415 99.6 4.7E-15 1E-19 141.7 11.0 137 406-657 2-150 (172)
12 PRK13763 putative RNA-processi 99.5 6.2E-14 1.3E-18 134.9 13.4 150 402-657 3-156 (180)
13 TIGR03665 arCOG04150 arCOG0415 99.5 1.6E-14 3.6E-19 138.0 8.3 137 321-477 2-152 (172)
14 PRK13763 putative RNA-processi 99.5 1E-13 2.3E-18 133.3 10.3 140 317-477 3-158 (180)
15 KOG2208 Vigilin [Lipid transpo 99.4 8.8E-13 1.9E-17 152.0 11.0 280 45-476 200-488 (753)
16 cd02396 PCBP_like_KH K homolog 99.3 2.5E-12 5.5E-17 102.6 7.6 63 591-653 2-65 (65)
17 KOG2208 Vigilin [Lipid transpo 99.3 2.3E-11 5.1E-16 140.3 16.1 287 185-655 128-485 (753)
18 cd02394 vigilin_like_KH K homo 99.3 5.6E-12 1.2E-16 99.7 5.8 61 591-653 2-62 (62)
19 cd02396 PCBP_like_KH K homolog 99.2 3.4E-11 7.3E-16 96.1 7.9 64 403-470 1-64 (65)
20 PF00013 KH_1: KH domain syndr 99.2 1E-11 2.2E-16 97.6 4.1 60 590-652 1-60 (60)
21 cd00105 KH-I K homology RNA-bi 99.2 5.7E-11 1.2E-15 94.5 7.9 63 591-653 2-64 (64)
22 cd02393 PNPase_KH Polynucleoti 99.2 4.4E-11 9.5E-16 93.9 7.1 58 590-653 3-61 (61)
23 KOG2279 Kinase anchor protein 99.1 4.6E-10 9.9E-15 119.4 13.6 295 313-656 64-366 (608)
24 cd02393 PNPase_KH Polynucleoti 99.1 5.7E-10 1.2E-14 87.6 8.4 58 402-470 2-60 (61)
25 KOG2279 Kinase anchor protein 99.1 1.5E-09 3.3E-14 115.5 13.6 254 41-370 63-352 (608)
26 cd02394 vigilin_like_KH K homo 99.1 2.6E-10 5.6E-15 90.1 5.8 60 404-470 2-61 (62)
27 PF00013 KH_1: KH domain syndr 99.0 3.3E-10 7.2E-15 88.9 4.3 60 403-470 1-60 (60)
28 cd00105 KH-I K homology RNA-bi 98.9 3.6E-09 7.9E-14 84.0 8.1 62 404-470 2-63 (64)
29 PF13014 KH_3: KH domain 98.9 4E-09 8.7E-14 76.7 5.7 42 599-640 1-43 (43)
30 PF13014 KH_3: KH domain 98.9 1.9E-09 4.2E-14 78.3 3.6 42 56-97 1-43 (43)
31 smart00322 KH K homology RNA-b 98.8 2.4E-08 5.3E-13 79.8 8.9 66 589-656 3-68 (69)
32 COG1094 Predicted RNA-binding 98.6 4.9E-07 1.1E-11 85.8 13.4 143 315-477 6-165 (194)
33 smart00322 KH K homology RNA-b 98.6 2.3E-07 5E-12 74.1 9.2 66 402-474 3-68 (69)
34 COG1094 Predicted RNA-binding 98.5 1.3E-06 2.8E-11 83.0 11.8 152 402-658 8-164 (194)
35 cd02395 SF1_like-KH Splicing f 98.1 6.5E-06 1.4E-10 73.6 7.0 62 598-659 15-96 (120)
36 cd02395 SF1_like-KH Splicing f 98.1 1.3E-05 2.8E-10 71.6 8.4 66 411-476 15-95 (120)
37 KOG2113 Predicted RNA binding 98.1 7.1E-06 1.5E-10 82.0 6.5 149 400-649 24-173 (394)
38 KOG2113 Predicted RNA binding 97.8 3.1E-05 6.8E-10 77.5 5.4 146 315-474 24-181 (394)
39 TIGR02696 pppGpp_PNP guanosine 97.7 9.7E-05 2.1E-09 84.3 8.9 90 376-476 548-642 (719)
40 PRK08406 transcription elongat 97.7 0.00016 3.5E-09 66.6 8.0 101 317-437 32-134 (140)
41 TIGR03591 polynuc_phos polyrib 97.4 0.00031 6.8E-09 81.5 7.6 89 377-476 521-615 (684)
42 PRK08406 transcription elongat 97.4 0.00019 4.1E-09 66.2 4.6 39 46-84 32-70 (140)
43 TIGR02696 pppGpp_PNP guanosine 97.4 0.00043 9.3E-09 79.2 8.0 64 589-658 578-642 (719)
44 KOG0336 ATP-dependent RNA heli 97.2 0.00043 9.4E-09 72.4 4.8 66 42-110 43-108 (629)
45 TIGR01952 nusA_arch NusA famil 97.1 0.0019 4E-08 59.4 8.0 100 318-437 34-135 (141)
46 PLN00207 polyribonucleotide nu 97.1 0.00057 1.2E-08 79.9 5.3 90 376-476 654-750 (891)
47 COG1185 Pnp Polyribonucleotide 97.1 0.0011 2.4E-08 74.3 7.0 91 376-477 521-617 (692)
48 KOG0119 Splicing factor 1/bran 96.9 0.0071 1.5E-07 64.8 11.3 76 401-476 137-230 (554)
49 TIGR03591 polynuc_phos polyrib 96.7 0.0023 4.9E-08 74.5 6.5 63 589-657 551-614 (684)
50 TIGR01952 nusA_arch NusA famil 96.7 0.0039 8.4E-08 57.4 6.4 38 47-84 34-71 (141)
51 KOG0336 ATP-dependent RNA heli 96.5 0.0048 1E-07 64.8 6.1 64 590-656 48-111 (629)
52 KOG1588 RNA-binding protein Sa 96.4 0.0022 4.8E-08 63.9 3.2 44 40-83 86-135 (259)
53 PRK11824 polynucleotide phosph 96.4 0.0039 8.5E-08 72.7 5.2 90 376-476 523-618 (693)
54 COG0195 NusA Transcription elo 96.4 0.014 3E-07 56.5 8.1 99 319-438 78-178 (190)
55 cd02134 NusA_KH NusA_K homolog 96.3 0.003 6.6E-08 49.4 2.5 37 45-81 24-60 (61)
56 KOG0119 Splicing factor 1/bran 96.0 0.015 3.2E-07 62.5 7.1 61 598-658 153-230 (554)
57 cd02134 NusA_KH NusA_K homolog 96.0 0.011 2.4E-07 46.3 4.5 36 589-624 25-60 (61)
58 COG1185 Pnp Polyribonucleotide 95.8 0.011 2.4E-07 66.4 5.1 63 589-657 552-615 (692)
59 KOG2814 Transcription coactiva 95.7 0.015 3.2E-07 59.8 5.2 71 402-478 57-127 (345)
60 PLN00207 polyribonucleotide nu 95.6 0.0096 2.1E-07 69.9 3.7 63 589-657 685-749 (891)
61 PRK04163 exosome complex RNA-b 95.5 0.025 5.4E-07 57.2 5.9 64 404-478 147-211 (235)
62 PF14611 SLS: Mitochondrial in 95.4 0.76 1.7E-05 45.5 16.4 66 402-477 26-91 (210)
63 PRK00468 hypothetical protein; 95.4 0.033 7.3E-07 45.4 5.3 49 382-430 4-58 (75)
64 KOG1588 RNA-binding protein Sa 95.4 0.02 4.4E-07 57.2 4.8 41 313-353 88-134 (259)
65 PF14611 SLS: Mitochondrial in 95.4 0.23 4.9E-06 49.3 12.4 129 318-475 27-164 (210)
66 PRK04163 exosome complex RNA-b 95.3 0.029 6.3E-07 56.7 5.8 60 590-655 146-206 (235)
67 PRK12328 nusA transcription el 95.2 0.066 1.4E-06 57.0 8.3 95 326-442 251-348 (374)
68 TIGR03319 YmdA_YtgF conserved 95.1 0.051 1.1E-06 61.2 7.6 65 590-659 205-271 (514)
69 PRK00106 hypothetical protein; 95.1 0.096 2.1E-06 58.8 9.5 67 400-476 223-291 (535)
70 TIGR01953 NusA transcription t 95.1 0.089 1.9E-06 55.9 8.9 92 326-439 243-338 (341)
71 PRK02821 hypothetical protein; 95.1 0.044 9.5E-07 44.8 5.1 51 381-431 4-60 (77)
72 PRK00106 hypothetical protein; 95.1 0.062 1.3E-06 60.3 7.9 65 590-659 226-292 (535)
73 KOG2814 Transcription coactiva 95.0 0.031 6.8E-07 57.4 5.0 69 590-659 58-126 (345)
74 PRK12704 phosphodiesterase; Pr 95.0 0.057 1.2E-06 60.9 7.5 63 591-658 212-276 (520)
75 COG1837 Predicted RNA-binding 95.0 0.058 1.3E-06 43.8 5.5 50 381-430 3-58 (76)
76 TIGR03319 YmdA_YtgF conserved 95.0 0.097 2.1E-06 58.9 9.2 85 379-476 184-270 (514)
77 PRK12704 phosphodiesterase; Pr 94.9 0.1 2.2E-06 58.8 9.2 85 379-476 190-276 (520)
78 PRK01064 hypothetical protein; 94.6 0.09 2E-06 43.2 5.7 50 382-431 4-59 (78)
79 PRK12327 nusA transcription el 94.5 0.14 2.9E-06 54.9 8.4 92 326-439 245-340 (362)
80 COG0195 NusA Transcription elo 94.5 0.06 1.3E-06 52.1 5.2 37 590-626 143-179 (190)
81 COG5176 MSL5 Splicing factor ( 94.5 0.045 9.7E-07 52.3 4.1 30 597-626 162-191 (269)
82 COG5176 MSL5 Splicing factor ( 94.3 0.031 6.6E-07 53.4 2.7 43 42-84 144-192 (269)
83 KOG4369 RTK signaling protein 94.2 0.013 2.9E-07 68.2 0.1 66 591-656 1342-1408(2131)
84 PRK00468 hypothetical protein; 94.2 0.053 1.2E-06 44.2 3.5 33 314-346 27-59 (75)
85 PRK12329 nusA transcription el 94.1 0.12 2.6E-06 56.0 7.0 90 326-437 277-370 (449)
86 PRK09202 nusA transcription el 94.0 0.11 2.5E-06 57.5 6.8 92 326-440 245-340 (470)
87 PRK12328 nusA transcription el 93.8 0.53 1.2E-05 50.3 10.9 38 589-626 308-345 (374)
88 PRK02821 hypothetical protein; 93.5 0.075 1.6E-06 43.5 3.3 33 315-347 29-61 (77)
89 TIGR01953 NusA transcription t 93.4 0.16 3.4E-06 54.1 6.4 38 589-626 301-338 (341)
90 PRK11824 polynucleotide phosph 93.3 0.058 1.3E-06 63.1 3.2 63 589-657 554-617 (693)
91 PRK01064 hypothetical protein; 93.3 0.07 1.5E-06 43.8 2.7 32 43-74 27-58 (78)
92 COG1837 Predicted RNA-binding 93.2 0.097 2.1E-06 42.6 3.4 33 314-346 27-59 (76)
93 PRK12329 nusA transcription el 92.7 0.12 2.6E-06 56.0 4.2 30 55-84 277-307 (449)
94 KOG1067 Predicted RNA-binding 92.4 0.21 4.5E-06 54.8 5.6 88 378-477 568-661 (760)
95 PRK09202 nusA transcription el 92.4 0.84 1.8E-05 50.8 10.4 38 589-626 302-339 (470)
96 PRK12327 nusA transcription el 92.1 0.18 3.9E-06 54.0 4.7 31 187-217 303-333 (362)
97 PRK12705 hypothetical protein; 88.8 0.89 1.9E-05 50.9 6.6 56 379-437 178-234 (508)
98 PF13083 KH_4: KH domain; PDB: 88.4 0.15 3.3E-06 41.3 0.2 33 44-76 27-59 (73)
99 PRK12705 hypothetical protein; 88.3 0.49 1.1E-05 52.9 4.2 64 591-659 200-265 (508)
100 cd02409 KH-II KH-II (K homolo 87.3 0.49 1.1E-05 37.1 2.6 35 45-79 24-58 (68)
101 PF13184 KH_5: NusA-like KH do 86.3 0.4 8.6E-06 38.5 1.5 38 47-84 4-47 (69)
102 COG5166 Uncharacterized conser 84.9 1.2 2.7E-05 48.5 4.8 129 329-476 392-524 (657)
103 PF13083 KH_4: KH domain; PDB: 84.8 0.45 9.7E-06 38.6 1.1 34 315-348 27-60 (73)
104 KOG2874 rRNA processing protei 84.7 1.5 3.4E-05 44.0 5.0 51 414-476 161-211 (356)
105 KOG3273 Predicted RNA-binding 83.4 0.7 1.5E-05 44.2 1.9 56 597-659 177-232 (252)
106 KOG3273 Predicted RNA-binding 83.4 0.65 1.4E-05 44.4 1.7 56 410-477 177-232 (252)
107 COG1097 RRP4 RNA-binding prote 82.3 2.7 5.9E-05 41.9 5.7 60 320-387 149-208 (239)
108 cd02409 KH-II KH-II (K homolo 82.1 2.4 5.2E-05 33.1 4.4 34 402-435 25-58 (68)
109 COG1097 RRP4 RNA-binding prote 82.1 3 6.5E-05 41.6 5.9 60 404-474 148-208 (239)
110 PF13184 KH_5: NusA-like KH do 81.8 1 2.3E-05 36.1 2.1 38 590-627 4-47 (69)
111 KOG4369 RTK signaling protein 81.7 0.43 9.2E-06 56.4 -0.2 71 402-476 1340-1410(2131)
112 PRK13764 ATPase; Provisional 81.3 2.2 4.7E-05 49.0 5.2 67 378-444 456-523 (602)
113 COG5166 Uncharacterized conser 81.2 2.4 5.3E-05 46.3 5.2 121 318-438 450-607 (657)
114 COG1855 ATPase (PilT family) [ 80.5 1.7 3.7E-05 47.2 3.8 40 402-441 486-525 (604)
115 cd02414 jag_KH jag_K homology 79.3 1.4 3E-05 36.1 2.1 34 47-80 25-58 (77)
116 cd02410 archeal_CPSF_KH The ar 78.8 7.3 0.00016 35.9 6.8 92 332-440 21-114 (145)
117 KOG1067 Predicted RNA-binding 78.7 7.9 0.00017 43.1 8.1 92 156-250 569-662 (760)
118 COG1855 ATPase (PilT family) [ 78.0 0.97 2.1E-05 49.0 1.1 38 47-84 487-524 (604)
119 PF07650 KH_2: KH domain syndr 77.7 0.59 1.3E-05 38.4 -0.5 34 47-80 26-59 (78)
120 cd02413 40S_S3_KH K homology R 77.4 1.4 3.1E-05 36.5 1.7 38 47-84 31-68 (81)
121 cd02414 jag_KH jag_K homology 75.5 3.1 6.8E-05 34.0 3.2 36 402-437 24-59 (77)
122 PRK13764 ATPase; Provisional 75.2 2.4 5.2E-05 48.6 3.3 40 588-627 480-519 (602)
123 PF07650 KH_2: KH domain syndr 73.4 1.5 3.2E-05 35.9 0.8 34 589-622 25-58 (78)
124 PRK06418 transcription elongat 72.4 2.5 5.3E-05 40.1 2.1 37 47-84 62-98 (166)
125 cd02410 archeal_CPSF_KH The ar 69.1 4 8.7E-05 37.5 2.6 37 48-84 78-114 (145)
126 cd02413 40S_S3_KH K homology R 68.9 6.8 0.00015 32.5 3.8 37 589-625 30-66 (81)
127 cd02412 30S_S3_KH K homology R 66.2 2.9 6.3E-05 36.8 1.1 31 47-77 62-92 (109)
128 COG0092 RpsC Ribosomal protein 65.1 3.5 7.7E-05 40.9 1.6 32 45-76 50-81 (233)
129 COG1782 Predicted metal-depend 64.9 24 0.00052 39.1 7.8 94 330-440 42-137 (637)
130 PRK06418 transcription elongat 63.5 11 0.00025 35.6 4.6 36 318-354 62-97 (166)
131 KOG2874 rRNA processing protei 63.2 14 0.00031 37.4 5.4 50 601-657 161-210 (356)
132 cd02411 archeal_30S_S3_KH K ho 63.1 4.2 9.2E-05 34.0 1.5 28 48-75 40-67 (85)
133 cd02411 archeal_30S_S3_KH K ho 56.3 13 0.00029 31.0 3.4 29 590-618 39-67 (85)
134 cd02412 30S_S3_KH K homology R 51.6 14 0.0003 32.5 2.8 30 590-619 62-91 (109)
135 TIGR03675 arCOG00543 arCOG0054 50.4 47 0.001 38.7 7.7 93 331-440 37-131 (630)
136 PF09869 DUF2096: Uncharacteri 50.1 44 0.00095 31.5 5.9 56 401-474 112-167 (169)
137 COG0092 RpsC Ribosomal protein 49.1 17 0.00037 36.3 3.3 38 589-626 51-95 (233)
138 COG1702 PhoH Phosphate starvat 43.7 50 0.0011 35.1 5.9 54 597-657 23-78 (348)
139 COG1159 Era GTPase [General fu 38.9 24 0.00052 36.6 2.7 56 185-240 227-291 (298)
140 COG4010 Uncharacterized protei 37.1 89 0.0019 28.7 5.6 43 422-475 126-168 (170)
141 TIGR00436 era GTP-binding prot 36.9 21 0.00046 36.7 2.0 30 46-75 221-251 (270)
142 COG1702 PhoH Phosphate starvat 33.9 86 0.0019 33.3 5.8 56 409-476 22-79 (348)
143 TIGR01008 rpsC_E_A ribosomal p 32.2 25 0.00055 34.3 1.6 32 47-78 39-70 (195)
144 PRK04191 rps3p 30S ribosomal p 31.8 26 0.00056 34.6 1.6 32 48-79 42-73 (207)
145 CHL00048 rps3 ribosomal protei 31.6 26 0.00057 34.8 1.6 30 47-76 67-96 (214)
146 KOG1423 Ras-like GTPase ERA [C 31.4 31 0.00067 36.0 2.1 31 45-75 327-358 (379)
147 COG1782 Predicted metal-depend 31.1 30 0.00065 38.4 2.0 37 48-84 101-137 (637)
148 TIGR00436 era GTP-binding prot 30.8 61 0.0013 33.3 4.2 30 402-431 221-251 (270)
149 PRK15494 era GTPase Era; Provi 29.5 34 0.00074 36.5 2.2 29 46-74 273-302 (339)
150 PTZ00084 40S ribosomal protein 29.0 29 0.00064 34.5 1.4 33 47-79 45-77 (220)
151 COG1159 Era GTPase [General fu 28.9 61 0.0013 33.7 3.7 35 590-624 230-273 (298)
152 TIGR03675 arCOG00543 arCOG0054 28.9 39 0.00085 39.4 2.6 37 48-84 95-131 (630)
153 COG1847 Jag Predicted RNA-bind 27.7 57 0.0012 32.0 3.1 38 400-437 89-126 (208)
154 PF02749 QRPTase_N: Quinolinat 27.3 2.2E+02 0.0047 23.7 6.3 64 592-657 19-85 (88)
155 PRK15494 era GTPase Era; Provi 26.9 77 0.0017 33.9 4.3 29 402-430 273-302 (339)
156 COG1847 Jag Predicted RNA-bind 26.5 37 0.00081 33.3 1.6 37 45-81 90-126 (208)
157 PRK00089 era GTPase Era; Revie 26.3 33 0.00071 35.6 1.3 26 187-212 226-252 (292)
158 PRK03818 putative transporter; 26.2 6.8E+02 0.015 28.8 12.0 130 318-469 206-358 (552)
159 PRK00089 era GTPase Era; Revie 25.0 86 0.0019 32.4 4.2 29 402-430 226-255 (292)
160 PRK04191 rps3p 30S ribosomal p 24.0 80 0.0017 31.2 3.5 28 591-618 42-69 (207)
161 KOG1423 Ras-like GTPase ERA [C 23.4 77 0.0017 33.3 3.2 34 314-347 325-359 (379)
162 TIGR01008 rpsC_E_A ribosomal p 23.2 90 0.002 30.5 3.6 30 589-618 38-67 (195)
163 CHL00048 rps3 ribosomal protei 21.5 99 0.0021 30.7 3.5 29 590-618 67-95 (214)
164 PTZ00084 40S ribosomal protein 20.5 1E+02 0.0022 30.8 3.4 29 590-618 45-73 (220)
165 PF10369 ALS_ss_C: Small subun 20.1 2.7E+02 0.0059 22.5 5.3 41 609-654 17-58 (75)
No 1
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=4.5e-42 Score=346.46 Aligned_cols=354 Identities=23% Similarity=0.381 Sum_probs=261.2
Q ss_pred CCCceEEEEEeeccceeeeecCCCccccchhhccCCeEEEcC-CCCCCCceEEEEEeCCCcccchhhhhhhhhhhccCcc
Q 045766 42 FPGGIMFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEE-TVSGSDERLVVIEASDNKKETSENLEASIERSENNGR 120 (663)
Q Consensus 42 ~~~~~~~rilvp~~~vg~IIGk~G~~I~~i~~etga~I~v~~-~~~g~~ervi~I~G~~e~~~~a~~~~~~~~~~~~~~~ 120 (663)
...++++|+|||..++|.||||.|.|||.|...|.|||+|.+ ...|..||+|+|.|++|.+
T Consensus 195 q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~------------------ 256 (584)
T KOG2193|consen 195 QLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGT------------------ 256 (584)
T ss_pred cccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccch------------------
Confidence 367899999999999999999999999999999999999986 4679999999999999988
Q ss_pred ccccccccccccccCCccccchhccccCccccchHHHHHHHHHHhhhhccCCCcccccccCCCCCceEEEEEEcCCceeE
Q 045766 121 EEASVADESDNKKEDSVNEGSVLMDGLNSEKETSKVQKALLLVFERMVEVEPETEVADQENTKSSKFVLRLLVLSTQVGC 200 (663)
Q Consensus 121 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~llVP~~~vG~ 200 (663)
-+|..+++|-|.....+++ ....+.++++.++++||+
T Consensus 257 ------------------------------------s~Ac~~ILeimqkEA~~~k-------~~~e~pLk~lAHN~lvGR 293 (584)
T KOG2193|consen 257 ------------------------------------SKACKMILEIMQKEAVDDK-------VAEEIPLKILAHNNLVGR 293 (584)
T ss_pred ------------------------------------HHHHHHHHHHHHHhhhccc-------hhhhcchhhhhhcchhhh
Confidence 2455556666653222111 125688999999999999
Q ss_pred EecCcchhhhcccCCC-----------CCCCCCccEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCC
Q 045766 201 LLGKGGCVIKQIDKLP-----------TCALASDEVVQITGEVDTVRKALKLISHQLLDNSPRDHESIPGNPTGPSHPLP 269 (663)
Q Consensus 201 IIGkgG~~Ik~I~~~p-----------~~~~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~p 269 (663)
||||.|.+||+|+.-. ......||+++++|+.|+|.+|..+|..+|++++++|.....-. ..+|
T Consensus 294 LIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q-----~~l~ 368 (584)
T KOG2193|consen 294 LIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQ-----CHLP 368 (584)
T ss_pred hhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhcc-----CCCC
Confidence 9999999999994311 12346799999999999999999999999999998884311110 1111
Q ss_pred CCCCCCCCCCCCC----CCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEEeeccccceeeccCchhHHhHHhH
Q 045766 270 DHSVSSQGAPYAT----GHRDVADIHLPMPPSIPKFHESGVLDRPKPSPEILTFRLLCHDERVGGVIGKGGAIIRSLKQE 345 (663)
Q Consensus 270 ~~~~~~~g~~y~~----~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~Ik~I~~~ 345 (663)
|..+.+.-++|.. .++.++..+....+++|.|+.+ ++...++++||...+|.|||++|.+||+|.+.
T Consensus 369 P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~---------pe~e~V~~fiP~~~vGAiIGkkG~hIKql~Rf 439 (584)
T KOG2193|consen 369 PGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQN---------PEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRF 439 (584)
T ss_pred cccCccccCCCCcccccCCCCCCCCccccCCCchhhhcC---------cchhheeeeccHHHHHHHHhhcchhHHHHHHh
Confidence 1111111000110 0000000011111233444332 25668899999999999999999999999999
Q ss_pred hCCeEEEecc-CCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHHHhhcCCC--CCCcceEEEEEecccceeEEEcCCch
Q 045766 346 TGCDIKVMEA-VSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTRIARAIPD--NREQTVMTRLLVASNQIGCLLGKGGS 422 (663)
Q Consensus 346 tga~I~i~~~-~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~i~~~~~~--~~~~~~~~~l~Vp~~~vg~IIGk~G~ 422 (663)
+|++|+|..+ .++..+|.|+|+|++ + +..+|--.++.+|.+..-. ..+-....++.||...+|+||||||.
T Consensus 440 agASiKIappE~pdvseRMViItGpp---e---aqfKAQgrifgKikEenf~~PkeevklethirVPs~~aGRvIGKGGk 513 (584)
T KOG2193|consen 440 AGASIKIAPPEIPDVSERMVIITGPP---E---AQFKAQGRIFGKIKEENFFLPKEEVKLETHIRVPSSAAGRVIGKGGK 513 (584)
T ss_pred ccceeeecCCCCCCcceeEEEecCCh---H---HHHhhhhhhhhhhhhhccCCchhhheeeeeeeccchhhhhhhccccc
Confidence 9999999853 477889999999998 1 1123333344444433211 12345678899999999999999999
Q ss_pred HHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHHHHHHhhccc
Q 045766 423 IIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQEALFQITTRLRHHFF 479 (663)
Q Consensus 423 ~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~~ 479 (663)
++++|+..|+|.|.| ++++.|+. .+..+|.|.|...+.+.|.+.|.+++.+...
T Consensus 514 tVnELQnlt~AeV~v-PrdqtpdE--nd~vivriiGhfyatq~aQrki~~iv~qvkq 567 (584)
T KOG2193|consen 514 TVNELQNLTSAEVVV-PRDQTPDE--NDQVIVRIIGHFYATQNAQRKIAHIVNQVKQ 567 (584)
T ss_pred cHHHHhccccceEEc-cccCCCCc--cceeeeeeechhhcchHHHHHHHHHHHHHHH
Confidence 999999999999999 77776652 3455689999999999999999999998543
No 2
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=4e-39 Score=341.74 Aligned_cols=324 Identities=22% Similarity=0.339 Sum_probs=255.6
Q ss_pred CceEEEEEeeccceeeeecCCCccccchhhccCCeEEEcCCCCCCCceEEEEEeCCCcccchhhhhhhhhhhccCccccc
Q 045766 44 GGIMFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEETVSGSDERLVVIEASDNKKETSENLEASIERSENNGREEA 123 (663)
Q Consensus 44 ~~~~~rilvp~~~vg~IIGk~G~~I~~i~~etga~I~v~~~~~g~~ervi~I~G~~e~~~~a~~~~~~~~~~~~~~~~~~ 123 (663)
.-++.+.-||++++|+||||+|+.|+.|.++|||+|.+.....+..+|-+.++|.+++++.||.|+..+.....
T Consensus 52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~aK~li~evv~r~~------ 125 (600)
T KOG1676|consen 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEVAKQLIGEVVSRGR------ 125 (600)
T ss_pred cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHHHHHHhhhhhhhccC------
Confidence 67788899999999999999999999999999999999888788899999999999999989888651111000
Q ss_pred cccccccccccCCccccchhccccCccccchHHHHHHHHHHhhhhccCCCcccccccCCCCCceEEEEEEcCCceeEEec
Q 045766 124 SVADESDNKKEDSVNEGSVLMDGLNSEKETSKVQKALLLVFERMVEVEPETEVADQENTKSSKFVLRLLVLSTQVGCLLG 203 (663)
Q Consensus 124 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~llVP~~~vG~IIG 203 (663)
+. ..-..+-....++..|+||.+.+|+|||
T Consensus 126 ------------------------------------------------~~--~~~~~~q~~~~ttqeI~IPa~k~GlIIG 155 (600)
T KOG1676|consen 126 ------------------------------------------------PP--GGFPDNQGSVETTQEILIPANKCGLIIG 155 (600)
T ss_pred ------------------------------------------------CC--CCccccCCccceeeeeccCccceeeEec
Confidence 00 0000011146789999999999999999
Q ss_pred CcchhhhcccCCCCCC----------CCCccEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCC
Q 045766 204 KGGCVIKQIDKLPTCA----------LASDEVVQITGEVDTVRKALKLISHQLLDNSPRDHESIPGNPTGPSHPLPDHSV 273 (663)
Q Consensus 204 kgG~~Ik~I~~~p~~~----------~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~ 273 (663)
|+|+|||.|.+...|. ...++.+.|+|++++|+.|..+|.++|++...... .
T Consensus 156 KgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e~~~~~~---g--------------- 217 (600)
T KOG1676|consen 156 KGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILREEDDEVP---G--------------- 217 (600)
T ss_pred cCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHhcccCCC---c---------------
Confidence 9999999995544331 22678999999999999999999999997321110 0
Q ss_pred CCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEEeeccccceeeccCchhHHhHHhHhCCeEEEe
Q 045766 274 SSQGAPYATGHRDVADIHLPMPPSIPKFHESGVLDRPKPSPEILTFRLLCHDERVGGVIGKGGAIIRSLKQETGCDIKVM 353 (663)
Q Consensus 274 ~~~g~~y~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~ 353 (663)
.+..|+.. .....+++|.||...||.||||+|++||+|+.+||++|+|.
T Consensus 218 --~~~~~g~~-----------------------------~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfk 266 (600)
T KOG1676|consen 218 --SGGHAGVR-----------------------------GGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFK 266 (600)
T ss_pred --cccccCcC-----------------------------ccccceeEEeccccceeeEEecCchHHHHHhhccCceeEee
Confidence 00001100 11233899999999999999999999999999999999998
Q ss_pred cc-CCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHHHhhcCCC-----CCCcceEEEEEecccceeEEEcCCchHHHHH
Q 045766 354 EA-VSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTRIARAIPD-----NREQTVMTRLLVASNQIGCLLGKGGSIIAEM 427 (663)
Q Consensus 354 ~~-~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~i~~~~~~-----~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I 427 (663)
.+ .+.+.||.+.|.|+. +.|..|.+.|.+|+......... .......+.|.||.+.||.||||+|++||.|
T Consensus 267 pDd~p~speR~~~IiG~~---d~ie~Aa~lI~eii~~~~~~~~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~i 343 (600)
T KOG1676|consen 267 PDDDPSSPERPAQIIGTV---DQIEHAAELINEIIAEAEAGAGGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQI 343 (600)
T ss_pred cCCCCCCccceeeeecCH---HHHHHHHHHHHHHHHHHhccCCCCcCCCCccceeeEEEeccccccccccCCCccchhhh
Confidence 54 458899999999999 77888888888887776553211 1111227899999999999999999999999
Q ss_pred HHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHHHHHHhhcc
Q 045766 428 RKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQEALFQITTRLRHHF 478 (663)
Q Consensus 428 ~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~ 478 (663)
..+|||++.++ ++ +...+..+++|+|+|++.+|+.|+.+|..++.+..
T Consensus 344 n~qSGA~~el~-r~--~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~~~ 391 (600)
T KOG1676|consen 344 NQQSGARCELS-RQ--PPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGDIA 391 (600)
T ss_pred cccCCcccccc-CC--CCCCCccceEEEEecCcccchHHHHHHHHHhcccC
Confidence 99999999994 43 33345789999999999999999999999998743
No 3
>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=4.5e-38 Score=340.72 Aligned_cols=358 Identities=38% Similarity=0.617 Sum_probs=262.5
Q ss_pred CCCCCceEEEEEeeccceeeeecCCCccccchhhccCCeEEEcCCCCCCCceEEEEEeCCCcccchhhhhhhhhhhccCc
Q 045766 40 KSFPGGIMFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEETVSGSDERLVVIEASDNKKETSENLEASIERSENNG 119 (663)
Q Consensus 40 ~~~~~~~~~rilvp~~~vg~IIGk~G~~I~~i~~etga~I~v~~~~~g~~ervi~I~G~~e~~~~a~~~~~~~~~~~~~~ 119 (663)
...+....||+||+.+.+|.||||+|++|++||.+|.++|+|.+..++|+||+++|+|+....
T Consensus 37 ~~p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~----------------- 99 (485)
T KOG2190|consen 37 TGPDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVEL----------------- 99 (485)
T ss_pred CCCCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccc-----------------
Confidence 333444459999999999999999999999999999999999999999999999999972111
Q ss_pred cccccccccccccccCCccccchhccccCccccchHHHHHHHHHHhhhhccCC---CcccccccCCCCCceEEEEEEcCC
Q 045766 120 REEASVADESDNKKEDSVNEGSVLMDGLNSEKETSKVQKALLLVFERMVEVEP---ETEVADQENTKSSKFVLRLLVLST 196 (663)
Q Consensus 120 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~llVP~~ 196 (663)
+.|-+ +.|+.++++.+..... +...+.........+++|||||.+
T Consensus 100 ----------------~~~~~----------------~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~s 147 (485)
T KOG2190|consen 100 ----------------NLSPA----------------TDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSS 147 (485)
T ss_pred ----------------cCCch----------------HHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechh
Confidence 12333 4444445554443211 101011101112268999999999
Q ss_pred ceeEEecCcchhhhcc------------cCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCC
Q 045766 197 QVGCLLGKGGCVIKQI------------DKLPTCALASDEVVQITGEVDTVRKALKLISHQLLDNSPRDHESIPGNPTGP 264 (663)
Q Consensus 197 ~vG~IIGkgG~~Ik~I------------~~~p~~~~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~ 264 (663)
++|+||||+|+.||+| +++|. +++|.|+|.|.+++|.+|+..|+.+|+++.++... +...
T Consensus 148 q~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~---ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~-----~~~s 219 (485)
T KOG2190|consen 148 QVGSLIGKGGSLIKEIREETGAKIRVSSDMLPN---STERAVTISGEPDAVKKALVQISSRLLENPPRSPP-----PLVS 219 (485)
T ss_pred heeeeeccCcHHHHHHHHhcCceEEecCCCCCc---ccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCC-----CCCC
Confidence 9999999999999999 34565 67899999999999999999999999996544111 1111
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEEeeccccceeeccCchhHHhHHh
Q 045766 265 SHPLPDHSVSSQGAPYATGHRDVADIHLPMPPSIPKFHESGVLDRPKPSPEILTFRLLCHDERVGGVIGKGGAIIRSLKQ 344 (663)
Q Consensus 265 ~~~~p~~~~~~~g~~y~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~Ik~I~~ 344 (663)
..+|.| ...++.++. ..+..+ .+.++ .........++.+++.+|.+.++.|||++|..|+.|+.
T Consensus 220 t~~y~P--~~~~~~~~~------~s~~~~----~~~~~----~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~ 283 (485)
T KOG2190|consen 220 TIPYRP--SASQGGPVL------PSTAQT----SPDAH----PFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRN 283 (485)
T ss_pred cccCCC--cccccCccc------cccccC----Ccccc----cccccccchhhhhhhcCchhhceeeecCCCccchhhhh
Confidence 111111 000110000 000000 00000 00112245677889999999999999999999999999
Q ss_pred HhCCeEEEeccCCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHHHhhcCCCCCCcceEEEEEecccceeEEEcCCchHH
Q 045766 345 ETGCDIKVMEAVSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTRIARAIPDNREQTVMTRLLVASNQIGCLLGKGGSII 424 (663)
Q Consensus 345 ~tga~I~i~~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~i~~~~~~~~~~~~~~~l~Vp~~~vg~IIGk~G~~I 424 (663)
++++.|.+.+...+ +.++++....+.+..+.|++++..++.++.+...+.....++.+|+||++++|+||||+|.+|
T Consensus 284 ~~~~~i~v~~~~~~---~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~i 360 (485)
T KOG2190|consen 284 ETGASISVGDSRTD---RIVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKI 360 (485)
T ss_pred hcCCceEeccccCc---ceeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccch
Confidence 99999999876433 899999998887888899999999998887765432266789999999999999999999999
Q ss_pred HHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHHHHHHhh
Q 045766 425 AEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQEALFQITTRLRH 476 (663)
Q Consensus 425 k~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~ 476 (663)
.+|++.|||.|.|..+++.. ...++.++|+|...+...|+.++...+..
T Consensus 361 seir~~tgA~I~I~~~~~~~---~~~e~~~~I~~~~~~~~~~~~~~~~~~~~ 409 (485)
T KOG2190|consen 361 SEIRQRTGASISILNKEEVS---GVREALVQITGMLREDLLAQYLIRARLSA 409 (485)
T ss_pred HHHHHhcCCceEEccccccC---CcceeEEEecchhHHHHhhhhhccccccc
Confidence 99999999999997665431 35789999999999999999888666654
No 4
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=5.9e-38 Score=332.87 Aligned_cols=317 Identities=23% Similarity=0.366 Sum_probs=253.1
Q ss_pred CceEEEEEEcCCceeEEecCcchhhhcccCCCCCC--------CCCccEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCC
Q 045766 185 SKFVLRLLVLSTQVGCLLGKGGCVIKQIDKLPTCA--------LASDEVVQITGEVDTVRKALKLISHQLLDNSPRDHES 256 (663)
Q Consensus 185 ~~~~~~llVP~~~vG~IIGkgG~~Ik~I~~~p~~~--------~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~ 256 (663)
...+.+.-||..++|+||||+|+-|..|.....|. ...+|.|.++|.+++|+.|+.||.+++.... .
T Consensus 52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~aK~li~evv~r~~--~--- 126 (600)
T KOG1676|consen 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEVAKQLIGEVVSRGR--P--- 126 (600)
T ss_pred cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHHHHHHhhhhhhhccC--C---
Confidence 56789999999999999999999999997666654 2378999999999999999999988875421 0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEEeeccccceeeccCc
Q 045766 257 IPGNPTGPSHPLPDHSVSSQGAPYATGHRDVADIHLPMPPSIPKFHESGVLDRPKPSPEILTFRLLCHDERVGGVIGKGG 336 (663)
Q Consensus 257 ~~~~~~~~~~~~p~~~~~~~g~~y~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G 336 (663)
+..++.+. ....++.++.||..++|+||||+|
T Consensus 127 --------------------------------------~~~~~~~q----------~~~~ttqeI~IPa~k~GlIIGKgG 158 (600)
T KOG1676|consen 127 --------------------------------------PGGFPDNQ----------GSVETTQEILIPANKCGLIIGKGG 158 (600)
T ss_pred --------------------------------------CCCccccC----------CccceeeeeccCccceeeEeccCc
Confidence 00001110 146779999999999999999999
Q ss_pred hhHHhHHhHhCCeEEEeccC--CCCCceEEEEeCCCCCCCCCChHHHHHHHHHHHHhhcCCC-------CCCcceEEEEE
Q 045766 337 AIIRSLKQETGCDIKVMEAV--SGTEDRLIVISGPAHPDDRISAPQDAVLRVQTRIARAIPD-------NREQTVMTRLL 407 (663)
Q Consensus 337 ~~Ik~I~~~tga~I~i~~~~--~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~i~~~~~~-------~~~~~~~~~l~ 407 (663)
++||+|++++||++.+-.+. .....+.+.|+|.+ +.++.|+..+.+++..-.+.... ......+.+|.
T Consensus 159 ETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp---~~ve~a~~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~ 235 (600)
T KOG1676|consen 159 ETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDP---DKVEQAKQLVADILREEDDEVPGSGGHAGVRGGGSATREVK 235 (600)
T ss_pred cHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCH---HHHHHHHHHHHHHHHhcccCCCccccccCcCccccceeEEe
Confidence 99999999999998887432 22367889999999 77888888888777753322111 12234589999
Q ss_pred ecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHHHHHHhhccccCCCCCCC
Q 045766 408 VASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQEALFQITTRLRHHFFRDAFPSIN 487 (663)
Q Consensus 408 Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~ 487 (663)
||+..||.||||+|++||+|+.+|||+|+|.++ +.|. +.+|.+.|.|+.++|+.|.++|.++|++.....-
T Consensus 236 VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpD-d~p~---speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~~~----- 306 (600)
T KOG1676|consen 236 VPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPD-DDPS---SPERPAQIIGTVDQIEHAAELINEIIAEAEAGAG----- 306 (600)
T ss_pred ccccceeeEEecCchHHHHHhhccCceeEeecC-CCCC---CccceeeeecCHHHHHHHHHHHHHHHHHHhccCC-----
Confidence 999999999999999999999999999999554 4453 7899999999999999999999999998421100
Q ss_pred CCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCCCCCCCCCCC
Q 045766 488 RPLNPTFLDQVSPFPSFIGRRELSPPGMYSNFGPSFHKFDAVGGPPPPGSFHPHDDHSAFMHHIHRPGMPPHMPDMKPWG 567 (663)
Q Consensus 488 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~ 567 (663)
+ +|+
T Consensus 307 ------~----------------------------------------------------------------------~~~ 310 (600)
T KOG1676|consen 307 ------G----------------------------------------------------------------------GMG 310 (600)
T ss_pred ------C----------------------------------------------------------------------CcC
Confidence 0 000
Q ss_pred CCCccccCCCCCCCCCCCCCc--ceEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeCC--CCCCcceEEEEEcCHH
Q 045766 568 PQGLMEVGGPMGFPDFVGPPH--RRVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITDP--KPGATETVIIISGTPE 643 (663)
Q Consensus 568 ~~g~~~~~~~~~~~~~~~~~~--~~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~--~~~~~~r~v~IsGt~e 643 (663)
.+.+. ..+.+.||...+|.||||||++||+|.++|||++.+.+. .....+++|+|+|++.
T Consensus 311 ----------------~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG~~~ 374 (600)
T KOG1676|consen 311 ----------------GGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGDKR 374 (600)
T ss_pred ----------------CCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEecCcc
Confidence 00111 267899999999999999999999999999999999975 3345789999999999
Q ss_pred HHHHHHHHHHHHHhc
Q 045766 644 QTHAAQSLIQAFVMS 658 (663)
Q Consensus 644 ~v~~A~~lI~~~v~~ 658 (663)
||+.|++||..+|..
T Consensus 375 QIdhAk~LIr~kvg~ 389 (600)
T KOG1676|consen 375 QIDHAKQLIRDKVGD 389 (600)
T ss_pred cchHHHHHHHHHhcc
Confidence 999999999998864
No 5
>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=1.2e-35 Score=284.01 Aligned_cols=322 Identities=27% Similarity=0.453 Sum_probs=229.9
Q ss_pred CcceEEEEEeeccccceeeccCchhHHhHHhHhCCeEEEeccCCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHHHhhc
Q 045766 314 PEILTFRLLCHDERVGGVIGKGGAIIRSLKQETGCDIKVMEAVSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTRIARA 393 (663)
Q Consensus 314 ~~~~~~~v~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~i~~~ 393 (663)
...+.+++++.++.+|+||||+|++||.|+.+++++|+|++. +..+|+++|+... +.|.++++++...
T Consensus 45 ~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri~tisad~----------~ti~~ilk~iip~ 112 (390)
T KOG2192|consen 45 RSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILTISADI----------ETIGEILKKIIPT 112 (390)
T ss_pred hcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCceeEEEeccH----------HHHHHHHHHHhhh
Confidence 356899999999999999999999999999999999999876 5789999998865 6777777776544
Q ss_pred CCC--CCCcceEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHHH
Q 045766 394 IPD--NREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQEALFQIT 471 (663)
Q Consensus 394 ~~~--~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~ 471 (663)
..+ ....++.++|+|..+++|.|||++|++||++++++.|+++|.. ..|..+++|+|.|.|.+..|..+++.|+
T Consensus 113 lee~f~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift----~c~p~stdrv~l~~g~~k~v~~~i~~il 188 (390)
T KOG2192|consen 113 LEEGFQLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFT----ECCPHSTDRVVLIGGKPKRVVECIKIIL 188 (390)
T ss_pred hhhCCCCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhh----ccCCCCcceEEEecCCcchHHHHHHHHH
Confidence 332 2345689999999999999999999999999999999999953 3566689999999999999999999999
Q ss_pred HHHhhccccCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCc-----
Q 045766 472 TRLRHHFFRDAFPSINRPLNPTFLDQVSPFPSFIGRRELSPPGMYSNFGPSFHKFDAVGGPPPPGSFHPHDDHSA----- 546 (663)
Q Consensus 472 ~~l~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----- 546 (663)
++|.+.....+ ..+|.|.|+.+.++|..|.= ....+|+.. + ........++|+|..++.......+
T Consensus 189 ~~i~e~pikgs----a~py~p~fyd~t~dyggf~M-~f~d~pg~p---g-papqrggqgpp~~~~sdlmay~r~GrpG~r 259 (390)
T KOG2192|consen 189 DLISESPIKGS----AQPYDPNFYDETYDYGGFTM-MFDDRPGRP---G-PAPQRGGQGPPPPRGSDLMAYDRRGRPGDR 259 (390)
T ss_pred HHhhcCCcCCc----CCcCCccccCcccccCCcee-ecCCCCCCC---C-CCCCCCCCCCCCCCccccceeccCCCCCcc
Confidence 99999877664 36789999999988876540 000001000 0 0000011122222222211100000
Q ss_pred c--ccCC-CCCCCCC-CCC-CCCCCCCCCccccC---------CCCC-CCCCCCCCcceEEEEecCCCcCeeecCCChhH
Q 045766 547 F--MHHI-HRPGMPP-HMP-DMKPWGPQGLMEVG---------GPMG-FPDFVGPPHRRVPVVVPRSLVPIIQGEDGACL 611 (663)
Q Consensus 547 ~--~~~~-~~~g~~~-~~~-~~~~~~~~g~~~~~---------~~~~-~~~~~~~~~~~~~v~IP~~~vg~IIGkgG~~I 611 (663)
+ +..| +..+-|+ ++. ..+.|.+ ++-+.+ +-++ +.+. +++..+.+|+||.++-|.||||||++|
T Consensus 260 ydg~vdFs~detw~saidtw~~Sewqm-aYePQgGs~ydysyAG~~GsYGdl-GGPitTaQvtip~dlggsiigkggqri 337 (390)
T KOG2192|consen 260 YDGMVDFSADETWPSAIDTWSPSEWQM-AYEPQGGSGYDYSYAGGYGSYGDL-GGPITTAQVTIPKDLGGSIIGKGGQRI 337 (390)
T ss_pred ccccccccccccCCCcCCCcCcccccc-ccCCCCCCCCCccccccccccCCC-CCceeeeeEecccccCcceecccchhh
Confidence 0 0000 0000000 000 0111211 111111 1011 2222 357788999999999999999999999
Q ss_pred HHHHHHcCCEEEEeCCCCCCcceEEEEEcCHHHHHHHHHHHHHHHhccccC
Q 045766 612 KQIRQISDAKITITDPKPGATETVIIISGTPEQTHAAQSLIQAFVMSETET 662 (663)
Q Consensus 612 ~~I~~~sGa~I~i~~~~~~~~~r~v~IsGt~e~v~~A~~lI~~~v~~~~~~ 662 (663)
++|++++||+|+|.++.+++.+|+++|+||.+|++.||+|+++.|....||
T Consensus 338 ~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vkq~rer 388 (390)
T KOG2192|consen 338 KQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYRER 388 (390)
T ss_pred hhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHHhhhcc
Confidence 999999999999999999999999999999999999999999999877665
No 6
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=1.7e-34 Score=291.68 Aligned_cols=308 Identities=24% Similarity=0.412 Sum_probs=244.1
Q ss_pred CceEEEEEEcCCceeEEecCcchhhhcccCCCCC---------CCCCccEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCC
Q 045766 185 SKFVLRLLVLSTQVGCLLGKGGCVIKQIDKLPTC---------ALASDEVVQITGEVDTVRKALKLISHQLLDNSPRDHE 255 (663)
Q Consensus 185 ~~~~~~llVP~~~vG~IIGkgG~~Ik~I~~~p~~---------~~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~ 255 (663)
....+|++||..+||.||||.|+|||.|.....| ....|+.++|.|++|...+|.++|++++...-..+.
T Consensus 197 ~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~~~k- 275 (584)
T KOG2193|consen 197 KDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGTSKACKMILEIMQKEAVDDK- 275 (584)
T ss_pred cCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccchHHHHHHHHHHHHHhhhccc-
Confidence 3478999999999999999999999999443322 356889999999999999999999999987432221
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEEeeccccceeeccC
Q 045766 256 SIPGNPTGPSHPLPDHSVSSQGAPYATGHRDVADIHLPMPPSIPKFHESGVLDRPKPSPEILTFRLLCHDERVGGVIGKG 335 (663)
Q Consensus 256 ~~~~~~~~~~~~~p~~~~~~~g~~y~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~ 335 (663)
..+.+.++++..+.++|++|||.
T Consensus 276 ---------------------------------------------------------~~~e~pLk~lAHN~lvGRLIGKe 298 (584)
T KOG2193|consen 276 ---------------------------------------------------------VAEEIPLKILAHNNLVGRLIGKE 298 (584)
T ss_pred ---------------------------------------------------------hhhhcchhhhhhcchhhhhhhhc
Confidence 23667899999999999999999
Q ss_pred chhHHhHHhHhCCeEEEecc---CCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHHHhhc-------------------
Q 045766 336 GAIIRSLKQETGCDIKVMEA---VSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTRIARA------------------- 393 (663)
Q Consensus 336 G~~Ik~I~~~tga~I~i~~~---~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~i~~~------------------- 393 (663)
|.+||+|+++||++|.|+.- ..-+.||.|+|+|+- ++|..|...|.+-+.+..+.
T Consensus 299 GrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsi---Eac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~ 375 (584)
T KOG2193|consen 299 GRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSI---EACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPA 375 (584)
T ss_pred cccHHHHHhhcCCceeeeehhhhcccCccceEEecccH---HHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccc
Confidence 99999999999999999842 234569999999976 56665655554433332110
Q ss_pred ---CCC------------------------CCCcceEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCC
Q 045766 394 ---IPD------------------------NREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKC 446 (663)
Q Consensus 394 ---~~~------------------------~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~ 446 (663)
.+. .......++|.||...+|.|||++|..||.|.+.+||.|+|.+. +.|+
T Consensus 376 l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIapp-E~pd- 453 (584)
T KOG2193|consen 376 LGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPP-EIPD- 453 (584)
T ss_pred cCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCC-CCCC-
Confidence 000 11133568999999999999999999999999999999999443 3444
Q ss_pred CCCCCcEEEEEecHHHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCcC
Q 045766 447 ASENEEVVLINGEFEAVQEALFQITTRLRHHFFRDAFPSINRPLNPTFLDQVSPFPSFIGRRELSPPGMYSNFGPSFHKF 526 (663)
Q Consensus 447 ~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 526 (663)
..+|.|+|+|++++..+|.-.|..+|.|..+.. |.
T Consensus 454 --vseRMViItGppeaqfKAQgrifgKikEenf~~----------Pk--------------------------------- 488 (584)
T KOG2193|consen 454 --VSERMVIITGPPEAQFKAQGRIFGKIKEENFFL----------PK--------------------------------- 488 (584)
T ss_pred --cceeEEEecCChHHHHhhhhhhhhhhhhhccCC----------ch---------------------------------
Confidence 689999999999999999999999998843211 00
Q ss_pred CCCCCCCCCCCCCCCCCCCccccCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCCCCCCcceEEEEecCCCcCeeecC
Q 045766 527 DAVGGPPPPGSFHPHDDHSAFMHHIHRPGMPPHMPDMKPWGPQGLMEVGGPMGFPDFVGPPHRRVPVVVPRSLVPIIQGE 606 (663)
Q Consensus 527 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk 606 (663)
........+.||....|+||||
T Consensus 489 ----------------------------------------------------------eevklethirVPs~~aGRvIGK 510 (584)
T KOG2193|consen 489 ----------------------------------------------------------EEVKLETHIRVPSSAAGRVIGK 510 (584)
T ss_pred ----------------------------------------------------------hhheeeeeeeccchhhhhhhcc
Confidence 0001345699999999999999
Q ss_pred CChhHHHHHHHcCCEEEEeCCCC--CCcceEEEEEcCHHHHHHHHHHHHHHHhc
Q 045766 607 DGACLKQIRQISDAKITITDPKP--GATETVIIISGTPEQTHAAQSLIQAFVMS 658 (663)
Q Consensus 607 gG~~I~~I~~~sGa~I~i~~~~~--~~~~r~v~IsGt~e~v~~A~~lI~~~v~~ 658 (663)
||.++++|++.|+|-|.||+... +.+.-+|.|.|..-+++.|+..|.++|..
T Consensus 511 GGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhfyatq~aQrki~~iv~q 564 (584)
T KOG2193|consen 511 GGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHFYATQNAQRKIAHIVNQ 564 (584)
T ss_pred ccccHHHHhccccceEEccccCCCCccceeeeeeechhhcchHHHHHHHHHHHH
Confidence 99999999999999999997532 23446889999999999999999998864
No 7
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.97 E-value=2.4e-29 Score=240.85 Aligned_cols=301 Identities=23% Similarity=0.362 Sum_probs=202.9
Q ss_pred CCCCCCCCCCCCCCCCCccccccCCCCCCCCCCCCCCCceEEEEEeeccceeeeecCCCccccchhhccCCeEEEcCCCC
Q 045766 7 PSKRPHDDDNHTEPNGKEKSQKLAGDYSENQPSKSFPGGIMFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEETVS 86 (663)
Q Consensus 7 ~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rilvp~~~vg~IIGk~G~~I~~i~~etga~I~v~~~~~ 86 (663)
+-||.|+-. ++++-.||.+.+. +.++++ -..+.+|||+.++.+|.||||+|+|||+|+.+.+|.|.|++.
T Consensus 17 ~~~~~~~~e---~g~~~gkrp~~d~---~~qa~k--~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds-- 86 (390)
T KOG2192|consen 17 PEETFPNTE---TGGEFGKRPAEDM---EEQAFK--RSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS-- 86 (390)
T ss_pred hhhcCCCCc---ccccccCCcchhh---HHHHhh--hcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--
Confidence 457777743 3344456665552 233333 245899999999999999999999999999999999999997
Q ss_pred CCCceEEEEEeCCCcccchhhhhhhhhhhccCccccccccccccccccCCccccchhccccCccccchHHHHHHHHHHhh
Q 045766 87 GSDERLVVIEASDNKKETSENLEASIERSENNGREEASVADESDNKKEDSVNEGSVLMDGLNSEKETSKVQKALLLVFER 166 (663)
Q Consensus 87 g~~ervi~I~G~~e~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~a~~~~~~~ 166 (663)
..+||+++|+...+.+ ..+++.
T Consensus 87 ~~peri~tisad~~ti----------------------------------------------------------~~ilk~ 108 (390)
T KOG2192|consen 87 SGPERILTISADIETI----------------------------------------------------------GEILKK 108 (390)
T ss_pred CCCceeEEEeccHHHH----------------------------------------------------------HHHHHH
Confidence 6799999998875544 122222
Q ss_pred hhccCCCcccccccCCCCCceEEEEEEcCCceeEEecCcchhhhcccC---------CCCCCCCCccEEEEEcCHHHHHH
Q 045766 167 MVEVEPETEVADQENTKSSKFVLRLLVLSTQVGCLLGKGGCVIKQIDK---------LPTCALASDEVVQITGEVDTVRK 237 (663)
Q Consensus 167 ~~~~~~~~~~~~~~~~~~~~~~~~llVP~~~vG~IIGkgG~~Ik~I~~---------~p~~~~~~dr~V~I~G~~~~V~~ 237 (663)
++... + +.....+++.+||||+.+++|.|||++|++||+|.+ ..+|+.++||+|.|.|.+..|..
T Consensus 109 iip~l-e-----e~f~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~ 182 (390)
T KOG2192|consen 109 IIPTL-E-----EGFQLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVE 182 (390)
T ss_pred Hhhhh-h-----hCCCCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHH
Confidence 22100 0 111234679999999999999999999999999943 24678899999999999999999
Q ss_pred HHHHHHHHHhcCCCCCCC-CCCCCC-------------CCCCC----CCC-------C-------CCCCCCC---CCCCC
Q 045766 238 ALKLISHQLLDNSPRDHE-SIPGNP-------------TGPSH----PLP-------D-------HSVSSQG---APYAT 282 (663)
Q Consensus 238 A~~~I~~~l~~~~~~~~~-~~~~~~-------------~~~~~----~~p-------~-------~~~~~~g---~~y~~ 282 (663)
+++.|.++|.+.+-+.+. +|.++- ++.++ +.| | +.+...| ..|..
T Consensus 183 ~i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg 262 (390)
T KOG2192|consen 183 CIKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDG 262 (390)
T ss_pred HHHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccc
Confidence 999999999998766653 222210 11100 000 0 1112211 11110
Q ss_pred ---------CCCCCcCC-----CCCCCCCC-CCCC--CCCCCC-CCCCCCcceEEEEEeeccccceeeccCchhHHhHHh
Q 045766 283 ---------GHRDVADI-----HLPMPPSI-PKFH--ESGVLD-RPKPSPEILTFRLLCHDERVGGVIGKGGAIIRSLKQ 344 (663)
Q Consensus 283 ---------~~~~~~~~-----~~~~~~~~-p~~~--~~~~~~-~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~Ik~I~~ 344 (663)
.++..+.| .++++|.. ..|. ..+.-. ...-.....+..|.||.++-|.||||+|+.|++|++
T Consensus 263 ~vdFs~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~ 342 (390)
T KOG2192|consen 263 MVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRH 342 (390)
T ss_pred cccccccccCCCcCCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhh
Confidence 01111111 11222211 1111 112111 222223556889999999999999999999999999
Q ss_pred HhCCeEEEeccCCCCCceEEEEeCCCCCCCCCChHHHHHH
Q 045766 345 ETGCDIKVMEAVSGTEDRLIVISGPAHPDDRISAPQDAVL 384 (663)
Q Consensus 345 ~tga~I~i~~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~ 384 (663)
++|+.|++.++..++.+|+++|+|++ +.+..|+..+.
T Consensus 343 esGA~IkidepleGsedrIitItGTq---dQIqnAQYLlQ 379 (390)
T KOG2192|consen 343 ESGASIKIDEPLEGSEDRIITITGTQ---DQIQNAQYLLQ 379 (390)
T ss_pred ccCceEEecCcCCCCCceEEEEeccH---HHHhhHHHHHH
Confidence 99999999998999999999999998 55555544433
No 8
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.96 E-value=3.2e-28 Score=264.14 Aligned_cols=331 Identities=30% Similarity=0.420 Sum_probs=213.5
Q ss_pred cceEEEEEeeccccceeeccCchhHHhHHhHhCCeEEEeccCCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHHHhhcC
Q 045766 315 EILTFRLLCHDERVGGVIGKGGAIIRSLKQETGCDIKVMEAVSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTRIARAI 394 (663)
Q Consensus 315 ~~~~~~v~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~i~~~~ 394 (663)
...++|++|+...+|.||||+|..|++|+.++.++|+|.+..+++.+|+++|+|+... .....+.+|++++++++....
T Consensus 41 ~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~-~~~~~~~~al~ka~~~iv~~~ 119 (485)
T KOG2190|consen 41 ETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVE-LNLSPATDALFKAFDMIVFKL 119 (485)
T ss_pred CcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEeccccc-ccCCchHHHHHHHHHHHhhcc
Confidence 4445999999999999999999999999999999999999899999999999995332 256677889998888876531
Q ss_pred C-----------CCCCcceEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHH
Q 045766 395 P-----------DNREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAV 463 (663)
Q Consensus 395 ~-----------~~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v 463 (663)
. +.....++++|+||..++|+||||+|+.||+|+++|||+|.+.+ +.+|. ..++.|+|.|.+++|
T Consensus 120 ~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~-~~lP~---ster~V~IsG~~~av 195 (485)
T KOG2190|consen 120 EEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSS-DMLPN---STERAVTISGEPDAV 195 (485)
T ss_pred cccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecC-CCCCc---ccceeEEEcCchHHH
Confidence 1 11222589999999999999999999999999999999999954 48888 578889999999999
Q ss_pred HHHHHHHHHHHhhccccCCCC-CCCCCCCC-CCCCCCCCCCccCCCCC-CCCCCCCCCCCCCC---------CcCCCCCC
Q 045766 464 QEALFQITTRLRHHFFRDAFP-SINRPLNP-TFLDQVSPFPSFIGRRE-LSPPGMYSNFGPSF---------HKFDAVGG 531 (663)
Q Consensus 464 ~~A~~~I~~~l~~~~~~~~~~-~~~~~~~p-~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~---------~~~~~~~~ 531 (663)
.+|+..|..+|.++..+.-.+ .....|.| .+... +..+....... ..+.+.... ...+ ..+...+.
T Consensus 196 ~~al~~Is~~L~~~~~~~~~~~~st~~y~P~~~~~~-~~~~s~~~~~~~~~~~~~~~~-~~e~~~~~~~p~~~~~~v~g~ 273 (485)
T KOG2190|consen 196 KKALVQISSRLLENPPRSPPPLVSTIPYRPSASQGG-PVLPSTAQTSPDAHPFGGIVP-EEELVFKLICPSDKVGSVIGK 273 (485)
T ss_pred HHHHHHHHHHHHhcCCcCCCCCCCcccCCCcccccC-ccccccccCCccccccccccc-chhhhhhhcCchhhceeeecC
Confidence 999999999999964321110 01122333 10000 00000000000 000000000 0000 00000000
Q ss_pred CC-CCCC--------CCCCCCCCc--cccCCCCCCCCC----CCCCCCCCCCCCccccCCCCCCCCCCC-CCcceEEEEe
Q 045766 532 PP-PPGS--------FHPHDDHSA--FMHHIHRPGMPP----HMPDMKPWGPQGLMEVGGPMGFPDFVG-PPHRRVPVVV 595 (663)
Q Consensus 532 ~~-~~~~--------~~~~~~~~~--~~~~~~~~g~~~----~~~~~~~~~~~g~~~~~~~~~~~~~~~-~~~~~~~v~I 595 (663)
.. +... ....+.... +..+ ....|. ..+....|. ........... ....+.++.|
T Consensus 274 ~~~~i~~l~~~~~~~i~v~~~~~~~~i~~s--~~e~~~~~~s~a~~a~~~~-------~~~~~~~~~~~~~~~v~~~l~v 344 (485)
T KOG2190|consen 274 GGLVIRALRNETGASISVGDSRTDRIVTIS--ARENPEDRYSMAQEALLLV-------QPRISENAGDDLTQTVTQRLLV 344 (485)
T ss_pred CCccchhhhhhcCCceEeccccCcceeeec--cccCcccccccchhhhhhc-------cccccccccccccceeeeeecc
Confidence 00 0000 000000000 0000 000000 000000000 00000000001 2335678999
Q ss_pred cCCCcCeeecCCChhHHHHHHHcCCEEEEeCCCC--CCcceEEEEEcCHHHHHHHHHHHHHHHhcccc
Q 045766 596 PRSLVPIIQGEDGACLKQIRQISDAKITITDPKP--GATETVIIISGTPEQTHAAQSLIQAFVMSETE 661 (663)
Q Consensus 596 P~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~--~~~~r~v~IsGt~e~v~~A~~lI~~~v~~~~~ 661 (663)
|.+++|+||||+|++|.+||+.|||.|.|.+... ...++.++|+|+..+...|+++|..++.....
T Consensus 345 ps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~~ 412 (485)
T KOG2190|consen 345 PSDLIGCIIGKGGAKISEIRQRTGASISILNKEEVSGVREALVQITGMLREDLLAQYLIRARLSAPKS 412 (485)
T ss_pred CccccceeecccccchHHHHHhcCCceEEccccccCCcceeEEEecchhHHHHhhhhhcccccccCcc
Confidence 9999999999999999999999999999998776 77899999999999999999999988887665
No 9
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.93 E-value=7.9e-25 Score=216.21 Aligned_cols=266 Identities=26% Similarity=0.382 Sum_probs=197.4
Q ss_pred CcceEEEEEeeccccceeeccCchhHHhHHhHhCCeEEEe---ccCCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHHH
Q 045766 314 PEILTFRLLCHDERVGGVIGKGGAIIRSLKQETGCDIKVM---EAVSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTRI 390 (663)
Q Consensus 314 ~~~~~~~v~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~---~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~i 390 (663)
...++++|+||+..+|.||||+|++|.+|+.++||+|+++ +..|+++||+|.|+|+. +++.+ .+..|+++|
T Consensus 36 ~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~---eai~a---v~efI~dKi 109 (402)
T KOG2191|consen 36 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTV---EALNA---VHEFIADKI 109 (402)
T ss_pred CCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccH---HHHHH---HHHHHHHHH
Confidence 3559999999999999999999999999999999999998 45689999999999997 22222 222334444
Q ss_pred hhcCC------C-----CCCcceEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEec
Q 045766 391 ARAIP------D-----NREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGE 459 (663)
Q Consensus 391 ~~~~~------~-----~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~ 459 (663)
.+... + ..+....+++.||++-+|.||||+|.+||.|++++||.|+|++- .|....-.+|+|++.|+
T Consensus 110 re~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPq--kpt~~sLqervvt~sge 187 (402)
T KOG2191|consen 110 REKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQ--KPTGISLQERVVTVSGE 187 (402)
T ss_pred HHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEeccc--CCCCccceeEEEEecCC
Confidence 33211 1 22333569999999999999999999999999999999999642 24445567899999999
Q ss_pred HHHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCC
Q 045766 460 FEAVQEALFQITTRLRHHFFRDAFPSINRPLNPTFLDQVSPFPSFIGRRELSPPGMYSNFGPSFHKFDAVGGPPPPGSFH 539 (663)
Q Consensus 460 ~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 539 (663)
+++..+|..+|+++|.+++..... .|.+|. +.++ |..
T Consensus 188 ~e~~~~A~~~IL~Ki~eDpqs~sc------ln~sya--------------------------------~vsG--pva--- 224 (402)
T KOG2191|consen 188 PEQNMKAVSLILQKIQEDPQSGSC------LNISYA--------------------------------NVSG--PVA--- 224 (402)
T ss_pred HHHHHHHHHHHHHHhhcCCcccce------eccchh--------------------------------cccC--ccc---
Confidence 999999999999999997654321 121111 1110 000
Q ss_pred CCCCCCccccCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCCCCCCcceEEEEecCCCcCeeecCCChhHHHHHHHcC
Q 045766 540 PHDDHSAFMHHIHRPGMPPHMPDMKPWGPQGLMEVGGPMGFPDFVGPPHRRVPVVVPRSLVPIIQGEDGACLKQIRQISD 619 (663)
Q Consensus 540 ~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGkgG~~I~~I~~~sG 619 (663)
.+.++|.++.+..............|+....|-.-|.||.++-.|...+|
T Consensus 225 ------------------------------NsnPtGspya~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G 274 (402)
T KOG2191|consen 225 ------------------------------NSNPTGSPYAYQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTG 274 (402)
T ss_pred ------------------------------ccCCCCCCCCCCCccccccchhhccccccccccccccccccceeeecccc
Confidence 01112333333333333345556888999999999999999999999999
Q ss_pred CEEEEeCCC---CCCcceEEEEEcCHHHHHHHHHHHHHHHhcccc
Q 045766 620 AKITITDPK---PGATETVIIISGTPEQTHAAQSLIQAFVMSETE 661 (663)
Q Consensus 620 a~I~i~~~~---~~~~~r~v~IsGt~e~v~~A~~lI~~~v~~~~~ 661 (663)
+.+.++... .+..++ .-+.|.+-++..|-.+|-..+.+-.+
T Consensus 275 ~l~~itq~l~~m~g~gy~-~n~~g~~ls~~aa~g~L~~~~~~a~t 318 (402)
T KOG2191|consen 275 ALIAITQALNTMAGYGYN-TNILGLGLSILAAEGVLAAKVASANT 318 (402)
T ss_pred cceeeccccccccccccc-ccccchhhhhhhhhhHHHHhhcccCc
Confidence 999998643 344555 88999999999999999888766444
No 10
>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=1.3e-24 Score=214.78 Aligned_cols=252 Identities=25% Similarity=0.401 Sum_probs=174.2
Q ss_pred CCCCCCCCCCCCCCCCCCCccccccCCCCCCCCCCCCCCCceEEEEEeeccceeeeecCCCccccchhhccCCeEEEcC-
Q 045766 5 LTPSKRPHDDDNHTEPNGKEKSQKLAGDYSENQPSKSFPGGIMFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEE- 83 (663)
Q Consensus 5 ~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rilvp~~~vg~IIGk~G~~I~~i~~etga~I~v~~- 83 (663)
-.++||+.+ .++| -..+||.++++. ..+.+|||||+..+|.||||+|++|.+|+++|||+|++++
T Consensus 12 ~~s~kr~~~--a~pe-~~~~k~~n~ge~-----------~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks 77 (402)
T KOG2191|consen 12 PDSRKRPLE--APPE-PGSTKRTNTGED-----------GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKS 77 (402)
T ss_pred CCCcccccc--CCCC-ccccccccCCCC-----------CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccc
Confidence 356777777 3322 345566666642 4499999999999999999999999999999999999985
Q ss_pred --CCCCCCceEEEEEeCCCcccchhhhhhhhhhhccCccccccccccccccccCCccccchhccccCccccchHHHHHHH
Q 045766 84 --TVSGSDERLVVIEASDNKKETSENLEASIERSENNGREEASVADESDNKKEDSVNEGSVLMDGLNSEKETSKVQKALL 161 (663)
Q Consensus 84 --~~~g~~ervi~I~G~~e~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~a~~ 161 (663)
.+||..||||.|+|+.+++-.. +.
T Consensus 78 ~dfyPGTTeRvcli~Gt~eai~av------------------------------------------------------~e 103 (402)
T KOG2191|consen 78 KDFYPGTTERVCLIQGTVEALNAV------------------------------------------------------HE 103 (402)
T ss_pred cccCCCccceEEEEeccHHHHHHH------------------------------------------------------HH
Confidence 4899999999999998876111 11
Q ss_pred HHHhhhhccCCCccc---ccccCCCCCceEEEEEEcCCceeEEecCcchhhhcccC-----------CCCCCCCCccEEE
Q 045766 162 LVFERMVEVEPETEV---ADQENTKSSKFVLRLLVLSTQVGCLLGKGGCVIKQIDK-----------LPTCALASDEVVQ 227 (663)
Q Consensus 162 ~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~llVP~~~vG~IIGkgG~~Ik~I~~-----------~p~~~~~~dr~V~ 227 (663)
.++|++.+...+.+. ..++...+..-.++|+||++.+|.||||+|.+||.|.+ .|......||+|+
T Consensus 104 fI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt 183 (402)
T KOG2191|consen 104 FIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVT 183 (402)
T ss_pred HHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEE
Confidence 222333221111010 00112233445699999999999999999999999933 2333456899999
Q ss_pred EEcCHHHHHHHHHHHHHHHhcCCCCCCCC-CCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCC
Q 045766 228 ITGEVDTVRKALKLISHQLLDNSPRDHES-IPGN-PTGPSHPLPDHSVSSQGAPYATGHRDVADIHLPMPPSIPKFHESG 305 (663)
Q Consensus 228 I~G~~~~V~~A~~~I~~~l~~~~~~~~~~-~~~~-~~~~~~~~p~~~~~~~g~~y~~~~~~~~~~~~~~~~~~p~~~~~~ 305 (663)
+.|++++..+|..+|.++|.++++..... .++. ..|+. ..+.+-|.+|+...+.
T Consensus 184 ~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya~vsGpv-----aNsnPtGspya~~~~~------------------- 239 (402)
T KOG2191|consen 184 VSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYANVSGPV-----ANSNPTGSPYAYQAHV------------------- 239 (402)
T ss_pred ecCCHHHHHHHHHHHHHHhhcCCcccceeccchhcccCcc-----cccCCCCCCCCCCCcc-------------------
Confidence 99999999999999999999987666541 1111 11111 1122233334432221
Q ss_pred CCCCCCCCCcceEEEEEeeccccceeeccCchhHHhHHhHhCCeEEEecc
Q 045766 306 VLDRPKPSPEILTFRLLCHDERVGGVIGKGGAIIRSLKQETGCDIKVMEA 355 (663)
Q Consensus 306 ~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 355 (663)
.+........++....|..-|.+|.++-.|-.-+|..+.+++.
T Consensus 240 -------~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~ 282 (402)
T KOG2191|consen 240 -------LPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQA 282 (402)
T ss_pred -------ccccchhhccccccccccccccccccceeeecccccceeeccc
Confidence 1223344566788888999999999999999999998888754
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=99.60 E-value=4.7e-15 Score=141.73 Aligned_cols=137 Identities=25% Similarity=0.354 Sum_probs=105.4
Q ss_pred EEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEE---EecHHHHHHHHHHHHHHHhhccccCC
Q 045766 406 LLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLI---NGEFEAVQEALFQITTRLRHHFFRDA 482 (663)
Q Consensus 406 l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I---~G~~~~v~~A~~~I~~~l~~~~~~~~ 482 (663)
|.||.+.+|.|||++|++|+.|+++|||+|++.+ .+..|.| +++++++.+|+.+|..+.+.......
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 6789999999999999999999999999999921 2356888 89999999999999998765221110
Q ss_pred CCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCCCCCC
Q 045766 483 FPSINRPLNPTFLDQVSPFPSFIGRRELSPPGMYSNFGPSFHKFDAVGGPPPPGSFHPHDDHSAFMHHIHRPGMPPHMPD 562 (663)
Q Consensus 483 ~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~ 562 (663)
+.... +. |..
T Consensus 72 ~~l~g------------------------------------------------------d~---y~~------------- 81 (172)
T TIGR03665 72 LKLLD------------------------------------------------------DD---YML------------- 81 (172)
T ss_pred HHhcC------------------------------------------------------Cc---ceE-------------
Confidence 00000 00 000
Q ss_pred CCCCCCCCccccCCCCCCCCCCCCCcceEEEEec---------CCCcCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcc
Q 045766 563 MKPWGPQGLMEVGGPMGFPDFVGPPHRRVPVVVP---------RSLVPIIQGEDGACLKQIRQISDAKITITDPKPGATE 633 (663)
Q Consensus 563 ~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~v~IP---------~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~ 633 (663)
.-+.|+ ....|+|||++|++++.|++.|||+|.|++
T Consensus 82 ----------------------------~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------- 126 (172)
T TIGR03665 82 ----------------------------EVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------- 126 (172)
T ss_pred ----------------------------EEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC-------
Confidence 001111 246899999999999999999999999963
Q ss_pred eEEEEEcCHHHHHHHHHHHHHHHh
Q 045766 634 TVIIISGTPEQTHAAQSLIQAFVM 657 (663)
Q Consensus 634 r~v~IsGt~e~v~~A~~lI~~~v~ 657 (663)
+.|.|.|++++++.|+.+|+.++.
T Consensus 127 ~~v~i~G~~~~~~~A~~~i~~li~ 150 (172)
T TIGR03665 127 KTVGIIGDPEQVQIAREAIEMLIE 150 (172)
T ss_pred CEEEEECCHHHHHHHHHHHHHHHc
Confidence 589999999999999999999884
No 12
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.54 E-value=6.2e-14 Score=134.92 Aligned_cols=150 Identities=23% Similarity=0.368 Sum_probs=108.3
Q ss_pred eEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEE----ecHHHHHHHHHHHHHHHhhc
Q 045766 402 VMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLIN----GEFEAVQEALFQITTRLRHH 477 (663)
Q Consensus 402 ~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~----G~~~~v~~A~~~I~~~l~~~ 477 (663)
....+.||.+.+|.|||++|++|+.|+++|||+|++. ..+..|.|. ++++++++|+.+|..++...
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 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEID----------SETGEVIIEPTDGEDPLAVLKARDIVKAIGRGF 72 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEE----------CCCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCC
Confidence 4678999999999999999999999999999999992 123678885 89999999999999988742
Q ss_pred cccCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCccccCCCCCCCC
Q 045766 478 FFRDAFPSINRPLNPTFLDQVSPFPSFIGRRELSPPGMYSNFGPSFHKFDAVGGPPPPGSFHPHDDHSAFMHHIHRPGMP 557 (663)
Q Consensus 478 ~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~ 557 (663)
.....+.... +. |....
T Consensus 73 ~~e~A~~l~g------------------------------------------------------d~---y~~~V------ 89 (180)
T PRK13763 73 SPEKALRLLD------------------------------------------------------DD---YVLEV------ 89 (180)
T ss_pred CHHHHHHHhC------------------------------------------------------CC---ceEEE------
Confidence 1111000000 00 00000
Q ss_pred CCCCCCCCCCCCCccccCCCCCCCCCCCCCcceEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEEE
Q 045766 558 PHMPDMKPWGPQGLMEVGGPMGFPDFVGPPHRRVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITDPKPGATETVII 637 (663)
Q Consensus 558 ~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~ 637 (663)
..+..+...+ - .....+|+|||++|++++.|++.|||+|.|.+ +.|.
T Consensus 90 --------------------i~i~~~~~~~-----~-~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~-------~~v~ 136 (180)
T PRK13763 90 --------------------IDLSDYGDSP-----N-ALRRIKGRIIGEGGKTRRIIEELTGVDISVYG-------KTVA 136 (180)
T ss_pred --------------------EEhhhccCCh-----h-HHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC-------CEEE
Confidence 0000000000 0 01247899999999999999999999999963 3599
Q ss_pred EEcCHHHHHHHHHHHHHHHh
Q 045766 638 ISGTPEQTHAAQSLIQAFVM 657 (663)
Q Consensus 638 IsGt~e~v~~A~~lI~~~v~ 657 (663)
|.|++++++.|+..|++++.
T Consensus 137 i~G~~~~~~~A~~~I~~li~ 156 (180)
T PRK13763 137 IIGDPEQVEIAREAIEMLIE 156 (180)
T ss_pred EEeCHHHHHHHHHHHHHHHc
Confidence 99999999999999999884
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=99.53 E-value=1.6e-14 Score=137.97 Aligned_cols=137 Identities=20% Similarity=0.291 Sum_probs=97.1
Q ss_pred EEeeccccceeeccCchhHHhHHhHhCCeEEEeccCCCCCceEEEEe---CCCCCCCCCChHHHHHHHHHHH--HhhcCC
Q 045766 321 LLCHDERVGGVIGKGGAIIRSLKQETGCDIKVMEAVSGTEDRLIVIS---GPAHPDDRISAPQDAVLRVQTR--IARAIP 395 (663)
Q Consensus 321 v~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~v~I~---G~~~~~~~v~~a~~ai~~i~~~--i~~~~~ 395 (663)
+.||.+.+|.|||++|++|+.|+++|||+|++.+. +..|.|+ +.+ +.+..|++.|..+..- ..+...
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~~ 73 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDP---LAVMKAREVVKAIGRGFSPEKALK 73 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCH---HHHHHHHHHHHHHHcCCCHHHHHH
Confidence 56899999999999999999999999999999642 2468883 333 3334444444333221 000000
Q ss_pred CCCCcceEEEEEecc---------cceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHHHHH
Q 045766 396 DNREQTVMTRLLVAS---------NQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQEA 466 (663)
Q Consensus 396 ~~~~~~~~~~l~Vp~---------~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A 466 (663)
-..+.-...-+.|+. ..+|+|||++|++++.|+..|||+|.|. +..|.|.|++++++.|
T Consensus 74 l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~------------~~~v~i~G~~~~~~~A 141 (172)
T TIGR03665 74 LLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY------------GKTVGIIGDPEQVQIA 141 (172)
T ss_pred hcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc------------CCEEEEECCHHHHHHH
Confidence 001111112233443 3689999999999999999999999991 2679999999999999
Q ss_pred HHHHHHHHhhc
Q 045766 467 LFQITTRLRHH 477 (663)
Q Consensus 467 ~~~I~~~l~~~ 477 (663)
+++|.+++...
T Consensus 142 ~~~i~~li~~~ 152 (172)
T TIGR03665 142 REAIEMLIEGA 152 (172)
T ss_pred HHHHHHHHcCC
Confidence 99999999653
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.49 E-value=1e-13 Score=133.35 Aligned_cols=140 Identities=19% Similarity=0.278 Sum_probs=99.6
Q ss_pred eEEEEEeeccccceeeccCchhHHhHHhHhCCeEEEeccCCCCCceEEEEe----CCCCCCCCCChHHHHHHHHHHH--H
Q 045766 317 LTFRLLCHDERVGGVIGKGGAIIRSLKQETGCDIKVMEAVSGTEDRLIVIS----GPAHPDDRISAPQDAVLRVQTR--I 390 (663)
Q Consensus 317 ~~~~v~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~v~I~----G~~~~~~~v~~a~~ai~~i~~~--i 390 (663)
+...+.||.+.++.|||++|++|+.|+++|||+|++.+. +..|.|. +++ +.+..|++.|..+..- .
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~---~~i~kA~~~I~ai~~gf~~ 74 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDP---LAVLKARDIVKAIGRGFSP 74 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCH---HHHHHHHHHHHHHhcCCCH
Confidence 467899999999999999999999999999999999743 2467786 333 3444444444433321 0
Q ss_pred hhcCCCCCCcceEEE-EEec---------ccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecH
Q 045766 391 ARAIPDNREQTVMTR-LLVA---------SNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEF 460 (663)
Q Consensus 391 ~~~~~~~~~~~~~~~-l~Vp---------~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~ 460 (663)
.+.... ....+..+ +.|. ...+|+|||++|++++.|++.|||+|.|. +..|.|.|++
T Consensus 75 e~A~~l-~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~------------~~~v~i~G~~ 141 (180)
T PRK13763 75 EKALRL-LDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVY------------GKTVAIIGDP 141 (180)
T ss_pred HHHHHH-hCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEc------------CCEEEEEeCH
Confidence 000000 01111212 1111 13689999999999999999999999992 2349999999
Q ss_pred HHHHHHHHHHHHHHhhc
Q 045766 461 EAVQEALFQITTRLRHH 477 (663)
Q Consensus 461 ~~v~~A~~~I~~~l~~~ 477 (663)
++++.|...|..+++..
T Consensus 142 ~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 142 EQVEIAREAIEMLIEGA 158 (180)
T ss_pred HHHHHHHHHHHHHHcCC
Confidence 99999999999999663
No 15
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.40 E-value=8.8e-13 Score=152.00 Aligned_cols=280 Identities=18% Similarity=0.248 Sum_probs=206.3
Q ss_pred ceEEEEEeeccceeeeecCCCccccchhhccCCeEEEcCCCCCCCceEEEEEeCCCcccchhhhhhhhhhhccCcccccc
Q 045766 45 GIMFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEETVSGSDERLVVIEASDNKKETSENLEASIERSENNGREEAS 124 (663)
Q Consensus 45 ~~~~rilvp~~~vg~IIGk~G~~I~~i~~etga~I~v~~~~~g~~ervi~I~G~~e~~~~a~~~~~~~~~~~~~~~~~~~ 124 (663)
.+..++.+-...+.++||++|.+++.++.++.+.|.|+.... ..-.+.|.|....+..+
T Consensus 200 ~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~--~~~~~~i~~~~~~~~~~------------------- 258 (753)
T KOG2208|consen 200 SVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNK--SSPSNKIDGRLNSSSSI------------------- 258 (753)
T ss_pred eEEEEeeccccchhhhccccccccccccccceeEEEcccccc--cchhhhhccccccceeh-------------------
Confidence 367788888999999999999999999999999999997622 22334455544443100
Q ss_pred ccccccccccCCccccchhccccCccccchHHHHHHHHHHhhhhccCCCcccccccCCCCCceEEEEEEcCCceeEEecC
Q 045766 125 VADESDNKKEDSVNEGSVLMDGLNSEKETSKVQKALLLVFERMVEVEPETEVADQENTKSSKFVLRLLVLSTQVGCLLGK 204 (663)
Q Consensus 125 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~llVP~~~vG~IIGk 204 (663)
..-.+.++.++ +....+.+.++....-+++|.
T Consensus 259 ----------------------------~~~i~~~~~~l--------------------e~~~~~~~~~~~~~~~~~~~~ 290 (753)
T KOG2208|consen 259 ----------------------------NVEIQEALTRL--------------------ESEFDYDEIIYRRLPRFIRGI 290 (753)
T ss_pred ----------------------------hhhhHHHHHHh--------------------cChhhhhhhhhcccccccccc
Confidence 00012222211 133456677888888999999
Q ss_pred cchhhhccc-C-------CCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 045766 205 GGCVIKQID-K-------LPTCALASDEVVQITGEVDTVRKALKLISHQLLDNSPRDHESIPGNPTGPSHPLPDHSVSSQ 276 (663)
Q Consensus 205 gG~~Ik~I~-~-------~p~~~~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~ 276 (663)
.|..++.|. . .+. ..+.+..+.++|....+..+......++...
T Consensus 291 ~~~~~~~~~~~~~~~~~i~~~-~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------------------- 342 (753)
T KOG2208|consen 291 PGEEINQLRDYMPEVDSIFQN-YPSKDDSIVLSGFEVGAVLAKRDKTLLLKNS--------------------------- 342 (753)
T ss_pred ccchhhHHHhhcchhhhhhcc-ccccceeEeecccccchhhhhhHHHHHHHHh---------------------------
Confidence 999999992 1 122 1244558899998877777776665555442
Q ss_pred CCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEEeeccccceeeccCchhHHhHHhHhCCeEEEeccC
Q 045766 277 GAPYATGHRDVADIHLPMPPSIPKFHESGVLDRPKPSPEILTFRLLCHDERVGGVIGKGGAIIRSLKQETGCDIKVMEAV 356 (663)
Q Consensus 277 g~~y~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~ 356 (663)
..+.+...+.+-...+..|+||+|.+|.+|++++.|.+.++..
T Consensus 343 ------------------------------------~~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~- 385 (753)
T KOG2208|consen 343 ------------------------------------EENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ- 385 (753)
T ss_pred ------------------------------------hccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc-
Confidence 1123567788889999999999999999999999999999873
Q ss_pred CCCCceEEEEeCCCCCCCCCChHHHHHHHHHHHHhhcCCCCCCcceEEEEEecccceeEEEcCCchHHHHHHHHhC-ceE
Q 045766 357 SGTEDRLIVISGPAHPDDRISAPQDAVLRVQTRIARAIPDNREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSG-AYI 435 (663)
Q Consensus 357 ~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~i~~~~~~~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tG-a~I 435 (663)
+.....+++.|.. +++..|.+.+..++..+.+. .....+.+|...+.+|||.+|..|+.|..++| .+|
T Consensus 386 -~~~~~~v~~~~~~---~~~~ka~~~v~~~~~ei~n~-------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i 454 (753)
T KOG2208|consen 386 -GSNNKKVVITGVS---ANDEKAVEDVEKIIAEILNS-------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHI 454 (753)
T ss_pred -cCCCCCeEEeccc---cchhHHHHHHHHHHHhhhcc-------cccceeecCccchhhhhccccccHHHHHhhcCcEEE
Confidence 4566679999998 78888888888888776541 45678999999999999999999999999999 777
Q ss_pred EEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHHHHHHhh
Q 045766 436 RILGKDQIPKCASENEEVVLINGEFEAVQEALFQITTRLRH 476 (663)
Q Consensus 436 ~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~ 476 (663)
++. .. ......+++.|....+..++.++..+...
T Consensus 455 ~f~-~~------~~~~~~~~~~~~~~dv~~~~~~~~~~~~~ 488 (753)
T KOG2208|consen 455 KFQ-NN------NNSSDMVTIRGISKDVEKSVSLLKALKAD 488 (753)
T ss_pred ecC-CC------CcccccceEeccccccchhHHHHHhhhhh
Confidence 772 21 13445688899888888877666665543
No 16
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.35 E-value=2.5e-12 Score=102.62 Aligned_cols=63 Identities=37% Similarity=0.549 Sum_probs=58.4
Q ss_pred EEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeCCCC-CCcceEEEEEcCHHHHHHHHHHHH
Q 045766 591 VPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITDPKP-GATETVIIISGTPEQTHAAQSLIQ 653 (663)
Q Consensus 591 ~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~-~~~~r~v~IsGt~e~v~~A~~lI~ 653 (663)
+.+.||...+|+|||++|++|++|+++|||+|.+.+... +..+|.|+|+|++++|+.|..||.
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 568999999999999999999999999999999998654 677899999999999999999983
No 17
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.31 E-value=2.3e-11 Score=140.30 Aligned_cols=287 Identities=18% Similarity=0.242 Sum_probs=203.1
Q ss_pred CceEEEEEEcCCceeEEecCcchhhhcccC---CC-CCCCCCccEEEEEcCHHHHHHHHHHHHHHHhcCCCCCCCCCCCC
Q 045766 185 SKFVLRLLVLSTQVGCLLGKGGCVIKQIDK---LP-TCALASDEVVQITGEVDTVRKALKLISHQLLDNSPRDHESIPGN 260 (663)
Q Consensus 185 ~~~~~~llVP~~~vG~IIGkgG~~Ik~I~~---~p-~~~~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~ 260 (663)
.......+++...+-.++|+.|.+-..+.. +. ......+..+.+.|..++|..|...+...+...
T Consensus 128 ~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~G~~e~V~~a~~~~~~~~~~~----------- 196 (753)
T KOG2208|consen 128 SSISQLVLAEGFLHRVMIGSKGANLTNVIWPSRLKIGEKAKKDPQIKLQGVVESVERAREPILNLIDRK----------- 196 (753)
T ss_pred cchhhhccchhhhhHhhccCccchhcccccccchhhhhhcccCCeeeeecchhhhhhhhhhhhhhhhcc-----------
Confidence 345566777888899999999998887722 11 112234679999999999999999998887551
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCcceEEEEEeeccccceeeccCchhHH
Q 045766 261 PTGPSHPLPDHSVSSQGAPYATGHRDVADIHLPMPPSIPKFHESGVLDRPKPSPEILTFRLLCHDERVGGVIGKGGAIIR 340 (663)
Q Consensus 261 ~~~~~~~~p~~~~~~~g~~y~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~v~vp~~~vg~IIGk~G~~Ik 340 (663)
....+..++.+....+..+||++|.+++
T Consensus 197 ----------------------------------------------------~~r~~~~k~~v~~~~~~~~~g~g~~~~~ 224 (753)
T KOG2208|consen 197 ----------------------------------------------------NERSVFEKMNVGITLHSHIIGRGGSNIS 224 (753)
T ss_pred ----------------------------------------------------cceeEEEEeeccccchhhhccccccccc
Confidence 1234678888999999999999999999
Q ss_pred hHHhHhCCeEEEeccCCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHHHhh----------------------------
Q 045766 341 SLKQETGCDIKVMEAVSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTRIAR---------------------------- 392 (663)
Q Consensus 341 ~I~~~tga~I~i~~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~i~~---------------------------- 392 (663)
.++.++.++++|+....... ...+.|.. ..+..+.-.+..++.++..
T Consensus 225 ~~~d~~~~~i~ip~sn~~~~--~~~i~~~~---~~~~~~~~~i~~~~~~le~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 299 (753)
T KOG2208|consen 225 IIMDETKVHIHIPDSNKSSP--SNKIDGRL---NSSSSINVEIQEALTRLESEFDYDEIIYRRLPRFIRGIPGEEINQLR 299 (753)
T ss_pred cccccceeEEEcccccccch--hhhhcccc---ccceehhhhhHHHHHHhcChhhhhhhhhccccccccccccchhhHHH
Confidence 99999999999985432111 22233322 1111111111111111100
Q ss_pred -cC----------C---------------------------CCCCcceEEEEEecccceeEEEcCCchHHHHHHHHhCce
Q 045766 393 -AI----------P---------------------------DNREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAY 434 (663)
Q Consensus 393 -~~----------~---------------------------~~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~ 434 (663)
.. + ........+.+.|-+..+..|+|++|.+|.+|++.+.+.
T Consensus 300 ~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~ 379 (753)
T KOG2208|consen 300 DYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPEELKFVIGKKGANIEKIREESQVK 379 (753)
T ss_pred hhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhc
Confidence 00 0 012234667888889999999999999999999999999
Q ss_pred EEEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCC
Q 045766 435 IRILGKDQIPKCASENEEVVLINGEFEAVQEALFQITTRLRHHFFRDAFPSINRPLNPTFLDQVSPFPSFIGRRELSPPG 514 (663)
Q Consensus 435 I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~ 514 (663)
+.+ . . ..+++..+.++|....+++|...++..+.+....
T Consensus 380 i~~-~-----~-~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~---------------------------------- 418 (753)
T KOG2208|consen 380 IDL-P-----K-QGSNNKKVVITGVSANDEKAVEDVEKIIAEILNS---------------------------------- 418 (753)
T ss_pred eec-c-----c-ccCCCCCeEEeccccchhHHHHHHHHHHHhhhcc----------------------------------
Confidence 999 2 2 2356778999999999999999999998874211
Q ss_pred CCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCCCCCCcceEEEE
Q 045766 515 MYSNFGPSFHKFDAVGGPPPPGSFHPHDDHSAFMHHIHRPGMPPHMPDMKPWGPQGLMEVGGPMGFPDFVGPPHRRVPVV 594 (663)
Q Consensus 515 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~v~ 594 (663)
.....+.
T Consensus 419 -------------------------------------------------------------------------~~~~~~~ 425 (753)
T KOG2208|consen 419 -------------------------------------------------------------------------IVKEEVQ 425 (753)
T ss_pred -------------------------------------------------------------------------cccceee
Confidence 0234588
Q ss_pred ecCCCcCeeecCCChhHHHHHHHcC-CEEEEeCCCCCCcceEEEEEcCHHHHHHHHHHHHHH
Q 045766 595 VPRSLVPIIQGEDGACLKQIRQISD-AKITITDPKPGATETVIIISGTPEQTHAAQSLIQAF 655 (663)
Q Consensus 595 IP~~~vg~IIGkgG~~I~~I~~~sG-a~I~i~~~~~~~~~r~v~IsGt~e~v~~A~~lI~~~ 655 (663)
||+.++.++||.+|+.|+.|...+| ..|++++. ....+.+++.|....+..++.++..+
T Consensus 426 iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~--~~~~~~~~~~~~~~dv~~~~~~~~~~ 485 (753)
T KOG2208|consen 426 IPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN--NNSSDMVTIRGISKDVEKSVSLLKAL 485 (753)
T ss_pred cCccchhhhhccccccHHHHHhhcCcEEEecCCC--CcccccceEeccccccchhHHHHHhh
Confidence 9999999999999999999999999 55555544 44456788888877776655554443
No 18
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.28 E-value=5.6e-12 Score=99.74 Aligned_cols=61 Identities=28% Similarity=0.464 Sum_probs=56.3
Q ss_pred EEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEEEEEcCHHHHHHHHHHHH
Q 045766 591 VPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITDPKPGATETVIIISGTPEQTHAAQSLIQ 653 (663)
Q Consensus 591 ~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~IsGt~e~v~~A~~lI~ 653 (663)
.++.||..++|+|||++|++|++|++.|||+|.|++.. ..++.|+|+|++++|..|+.+|+
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 56899999999999999999999999999999999764 46789999999999999999874
No 19
>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=99.23 E-value=3.4e-11 Score=96.12 Aligned_cols=64 Identities=47% Similarity=0.637 Sum_probs=56.5
Q ss_pred EEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHH
Q 045766 403 MTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQEALFQI 470 (663)
Q Consensus 403 ~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I 470 (663)
+++|.||.+.+|+|||++|++|++|+++|||+|.+.+... ....+++|+|+|+++++.+|+.+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~----~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL----PGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC----CCCCceEEEEEeCHHHHHHHHHhh
Confidence 3689999999999999999999999999999999944322 236789999999999999999887
No 20
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.21 E-value=1e-11 Score=97.55 Aligned_cols=60 Identities=37% Similarity=0.578 Sum_probs=55.3
Q ss_pred eEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEEEEEcCHHHHHHHHHHH
Q 045766 590 RVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITDPKPGATETVIIISGTPEQTHAAQSLI 652 (663)
Q Consensus 590 ~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~IsGt~e~v~~A~~lI 652 (663)
+.+|.||.+++|+|||++|++|++|++.|||+|.|++. + ....|+|+|++++|+.|+.+|
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 46799999999999999999999999999999999877 3 456999999999999999987
No 21
>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=99.20 E-value=5.7e-11 Score=94.49 Aligned_cols=63 Identities=43% Similarity=0.656 Sum_probs=58.3
Q ss_pred EEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEEEEEcCHHHHHHHHHHHH
Q 045766 591 VPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITDPKPGATETVIIISGTPEQTHAAQSLIQ 653 (663)
Q Consensus 591 ~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~IsGt~e~v~~A~~lI~ 653 (663)
.++.||.+++++|||++|++|++|++.|||+|.|++...+..++.|+|+|+.++++.|+.+|+
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 468999999999999999999999999999999998766667899999999999999999874
No 22
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.20 E-value=4.4e-11 Score=93.90 Aligned_cols=58 Identities=22% Similarity=0.392 Sum_probs=53.5
Q ss_pred eEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEEEEEcC-HHHHHHHHHHHH
Q 045766 590 RVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITDPKPGATETVIIISGT-PEQTHAAQSLIQ 653 (663)
Q Consensus 590 ~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~IsGt-~e~v~~A~~lI~ 653 (663)
...+.||.+++|+|||+||++|++|++.|||+|.|++ ++.|+|+|+ +++++.|+++|+
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 4679999999999999999999999999999999976 357999999 999999999984
No 23
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.14 E-value=4.6e-10 Score=119.42 Aligned_cols=295 Identities=17% Similarity=0.201 Sum_probs=182.3
Q ss_pred CCcceEEEEEeeccccceeeccCchhHHhHHhHhCCeEEEeccCCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHHHhh
Q 045766 313 SPEILTFRLLCHDERVGGVIGKGGAIIRSLKQETGCDIKVMEAVSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTRIAR 392 (663)
Q Consensus 313 ~~~~~~~~v~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~i~~ 392 (663)
....+.+++.|+++.+-+++|+.|++|+.|+..++++|.+.+.. -..++.-.+.|-+ ..+..++.++.+...
T Consensus 64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p---~~v~~a~a~~~~~~~---- 135 (608)
T KOG2279|consen 64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFP---VQVCKAKAAIHQILT---- 135 (608)
T ss_pred chhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCC---CCCChHHHHHHHHHh----
Confidence 35788999999999999999999999999999999999997543 2345555555555 566666666554432
Q ss_pred cCCCCCCcceEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHHHH
Q 045766 393 AIPDNREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQEALFQITT 472 (663)
Q Consensus 393 ~~~~~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~ 472 (663)
....+...+.+|...+++|+|++|++++.|+.-++|+|.+ ... -. ..-.+...|.|...-+..|+.++.+
T Consensus 136 -----~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~-d~n--gr--~g~~~~~~i~~qqk~~~~a~~~~~~ 205 (608)
T KOG2279|consen 136 -----ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITC-DKN--GR--LGLSRLIKISGQQKEVAAAKHLILE 205 (608)
T ss_pred -----cCCcccccccchhhhcccccccchhhhcchhccccccccc-ccc--cc--cccccceecccccchHHHHHhhhhc
Confidence 3455788899999999999999999999999999999999 332 12 2456778888888888899999998
Q ss_pred HHhhcc-ccCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCccccCC
Q 045766 473 RLRHHF-FRDAFPSINRPLNPTFLDQVSPFPSFIGRRELSPPGMYSNFGPSFHKFDAVGGPPPPGSFHPHDDHSAFMHHI 551 (663)
Q Consensus 473 ~l~~~~-~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 551 (663)
.+.+.. ...++|...+.- ++......+ +. ..|+...+...+ +... .+. ..
T Consensus 206 ~~~edeelv~~~~e~~q~r-vprk~p~n~---~~-------~~m~~~~~s~~~--------h~~~---------~t~-~s 256 (608)
T KOG2279|consen 206 KVSEDEELVKRIAESAQTR-VPRKQPINV---RR-------EDMTEPGGAGEP--------HLWK---------NTS-SS 256 (608)
T ss_pred cccchhHHhhhchhhcccC-CCCCCCccc---cc-------hhhcccccCCcc--------ccCc---------cch-hc
Confidence 888732 222332222111 111110100 00 011111100000 0000 000 00
Q ss_pred CCCCCCCCCCCCCCCCCCCccccCCCCCCCCCCC----CCcceEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeCC
Q 045766 552 HRPGMPPHMPDMKPWGPQGLMEVGGPMGFPDFVG----PPHRRVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITDP 627 (663)
Q Consensus 552 ~~~g~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~----~~~~~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~ 627 (663)
..+|.+.......+... + ..-+++...+.-+. ......++.+|...+|.+||+.|..+..+...|++.+.|--.
T Consensus 257 ~spg~~~~~~eg~dm~v-~-vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~ 334 (608)
T KOG2279|consen 257 MSPGAPLVTKEGGDMAV-V-VSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQ 334 (608)
T ss_pred cCCCCCCcccCCCccee-E-EecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEec
Confidence 01111111100000000 0 00000000000000 112334699999999999999999999999999999888753
Q ss_pred CCCCc---ceEEEEEcCHHHHHHHHHHHHHHH
Q 045766 628 KPGAT---ETVIIISGTPEQTHAAQSLIQAFV 656 (663)
Q Consensus 628 ~~~~~---~r~v~IsGt~e~v~~A~~lI~~~v 656 (663)
..... ..++.+.|+..-++.+-.||...+
T Consensus 335 pyt~~v~~~qic~~egkqh~~n~vl~ml~~~~ 366 (608)
T KOG2279|consen 335 PYTSRVLQLQICVNEGKQHYENSVLEMLTVHV 366 (608)
T ss_pred cccchhhhhhhheecchhHHHHHHHhhhhccC
Confidence 22221 257899999999999999997544
No 24
>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=99.07 E-value=5.7e-10 Score=87.59 Aligned_cols=58 Identities=24% Similarity=0.366 Sum_probs=52.6
Q ss_pred eEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEec-HHHHHHHHHHH
Q 045766 402 VMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGE-FEAVQEALFQI 470 (663)
Q Consensus 402 ~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~-~~~v~~A~~~I 470 (663)
....|.||.+++|+|||++|++|++|+++|||+|.+. .++.|.|.|+ +++++.|+.+|
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~-----------~~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIE-----------DDGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeC-----------CCCEEEEEeCCHHHHHHHHHHh
Confidence 5678999999999999999999999999999999992 2467999998 99999999876
No 25
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.06 E-value=1.5e-09 Score=115.51 Aligned_cols=254 Identities=20% Similarity=0.303 Sum_probs=158.4
Q ss_pred CCCCceEEEEEeeccceeeeecCCCccccchhhccCCeEEEcCCCCCCCceEEEEEeCCCcccchhhhhhhhhhhccCcc
Q 045766 41 SFPGGIMFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEETVSGSDERLVVIEASDNKKETSENLEASIERSENNGR 120 (663)
Q Consensus 41 ~~~~~~~~rilvp~~~vg~IIGk~G~~I~~i~~etga~I~v~~~~~g~~ervi~I~G~~e~~~~a~~~~~~~~~~~~~~~ 120 (663)
....++.+.+.||...+-.+|||.|++|+.|+..+++||.+.+..-+ ++++.++.|-+..+
T Consensus 63 e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g-~e~~~~~~~~p~~v------------------ 123 (608)
T KOG2279|consen 63 KPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG-DERVLLISGFPVQV------------------ 123 (608)
T ss_pred CchhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCC-cccchhhccCCCCC------------------
Confidence 34578899999999999999999999999999999999999976333 67777777766555
Q ss_pred ccccccccccccccCCccccchhccccCccccchHHHHHHHHHHhhhhccCCCcccccccCCCCCceEEEEEEcCCceeE
Q 045766 121 EEASVADESDNKKEDSVNEGSVLMDGLNSEKETSKVQKALLLVFERMVEVEPETEVADQENTKSSKFVLRLLVLSTQVGC 200 (663)
Q Consensus 121 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~llVP~~~vG~ 200 (663)
|++ +|. +.+.+. ....+...+-+|...++.
T Consensus 124 -----------------~~a-----------------~a~--~~~~~~--------------~~~pvk~~lsvpqr~~~~ 153 (608)
T KOG2279|consen 124 -----------------CKA-----------------KAA--IHQILT--------------ENTPVSEQLSVPQRSVGR 153 (608)
T ss_pred -----------------ChH-----------------HHH--HHHHHh--------------cCCcccccccchhhhccc
Confidence 322 111 122222 124677889999999999
Q ss_pred EecCcchhhhcccCCC----CC----CCCCccEEEEEcCHHHHHHHHHHHHHHHhcCC------CCCCCCCCCCC-----
Q 045766 201 LLGKGGCVIKQIDKLP----TC----ALASDEVVQITGEVDTVRKALKLISHQLLDNS------PRDHESIPGNP----- 261 (663)
Q Consensus 201 IIGkgG~~Ik~I~~~p----~~----~~~~dr~V~I~G~~~~V~~A~~~I~~~l~~~~------~~~~~~~~~~~----- 261 (663)
|+|++|.++++|.... .| ..-.++...|.|....++.|..++.+.+.++- +.......+..
T Consensus 154 i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~ 233 (608)
T KOG2279|consen 154 IIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINV 233 (608)
T ss_pred ccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCccc
Confidence 9999999999993211 11 12355788999999999999999988877632 11111111110
Q ss_pred ----------CCCCCCCCC-CCCCCCCCCCCCCCCCCcCCCCCCCCCC---CCCCCCCCCCCCCCCCcceEEEEEeeccc
Q 045766 262 ----------TGPSHPLPD-HSVSSQGAPYATGHRDVADIHLPMPPSI---PKFHESGVLDRPKPSPEILTFRLLCHDER 327 (663)
Q Consensus 262 ----------~~~~~~~p~-~~~~~~g~~y~~~~~~~~~~~~~~~~~~---p~~~~~~~~~~~~~~~~~~~~~v~vp~~~ 327 (663)
.+++|-.+- ..+...|.+.. ..-...|...+ +.+. ..-.+............|.+|...
T Consensus 234 ~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~------~~eg~dm~v~vsk~~s~~-~~~d~s~~k~~~l~i~e~e~p~~l 306 (608)
T KOG2279|consen 234 RREDMTEPGGAGEPHLWKNTSSSMSPGAPLV------TKEGGDMAVVVSKEGSWE-KPSDDSFQKSEALAIPEMEMPEIL 306 (608)
T ss_pred cchhhcccccCCccccCccchhccCCCCCCc------ccCCCcceeEEecccccC-CccccccccccccccceeecCccc
Confidence 011111110 00000000000 00000111000 0010 000111111234557789999999
Q ss_pred cceeeccCchhHHhHHhHhCCeEEEeccCCCCC---ceEEEEeCCC
Q 045766 328 VGGVIGKGGAIIRSLKQETGCDIKVMEAVSGTE---DRLIVISGPA 370 (663)
Q Consensus 328 vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~---er~v~I~G~~ 370 (663)
+|.|||+.|+.++.+...+++.++|........ ..+|.+.|+.
T Consensus 307 sg~lig~~gey~s~yssasn~~~hi~t~pyt~~v~~~qic~~egkq 352 (608)
T KOG2279|consen 307 SGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSRVLQLQICVNEGKQ 352 (608)
T ss_pred ccchhhhhhhhhhhhhhccCccceEEeccccchhhhhhhheecchh
Confidence 999999999999999999999999985432222 2578899987
No 26
>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=99.06 E-value=2.6e-10 Score=90.13 Aligned_cols=60 Identities=23% Similarity=0.334 Sum_probs=53.7
Q ss_pred EEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHH
Q 045766 404 TRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQEALFQI 470 (663)
Q Consensus 404 ~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I 470 (663)
.+|.||..++++|||++|++|++|+++|||+|.|++.. ..++.|+|+|+.++|..|+.+|
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-------~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-------SKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-------CCCCEEEEEcCHHHHHHHHHHh
Confidence 57999999999999999999999999999999993221 4578899999999999999876
No 27
>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=99.00 E-value=3.3e-10 Score=88.88 Aligned_cols=60 Identities=33% Similarity=0.495 Sum_probs=53.3
Q ss_pred EEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHH
Q 045766 403 MTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQEALFQI 470 (663)
Q Consensus 403 ~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I 470 (663)
|.+|.||.+++++|||++|++|++|+++|||+|.|+.. ..+..|+|+|++++|++|+++|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~--------~~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD--------DERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--------TEEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--------CCcEEEEEEeCHHHHHHHHhhC
Confidence 57899999999999999999999999999999999322 1345899999999999999876
No 28
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.94 E-value=3.6e-09 Score=84.01 Aligned_cols=62 Identities=42% Similarity=0.605 Sum_probs=54.5
Q ss_pred EEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHH
Q 045766 404 TRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQEALFQI 470 (663)
Q Consensus 404 ~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I 470 (663)
.+|.||.+++++|||++|++|++|+++|||+|.|..... ...++.|.|.|+.+++..|+.+|
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 589999999999999999999999999999999943221 25688999999999999999876
No 29
>PF13014 KH_3: KH domain
Probab=98.87 E-value=4e-09 Score=76.66 Aligned_cols=42 Identities=40% Similarity=0.684 Sum_probs=38.3
Q ss_pred CcCeeecCCChhHHHHHHHcCCEEEEeC-CCCCCcceEEEEEc
Q 045766 599 LVPIIQGEDGACLKQIRQISDAKITITD-PKPGATETVIIISG 640 (663)
Q Consensus 599 ~vg~IIGkgG~~I~~I~~~sGa~I~i~~-~~~~~~~r~v~IsG 640 (663)
+||+|||++|++|++|+++|||+|+|++ ..++..++.|+|+|
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 44567789999998
No 30
>PF13014 KH_3: KH domain
Probab=98.86 E-value=1.9e-09 Score=78.32 Aligned_cols=42 Identities=33% Similarity=0.631 Sum_probs=39.0
Q ss_pred ceeeeecCCCccccchhhccCCeEEEcC-CCCCCCceEEEEEe
Q 045766 56 KIDGVIGKDGEMMSQISQDTGVTIRVEE-TVSGSDERLVVIEA 97 (663)
Q Consensus 56 ~vg~IIGk~G~~I~~i~~etga~I~v~~-~~~g~~ervi~I~G 97 (663)
++|+||||+|++|++|+++|||+|+|++ ..++..+|+|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 4899999999999999999999999998 56788999999987
No 31
>smart00322 KH K homology RNA-binding domain.
Probab=98.81 E-value=2.4e-08 Score=79.83 Aligned_cols=66 Identities=30% Similarity=0.526 Sum_probs=59.6
Q ss_pred ceEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEEEEEcCHHHHHHHHHHHHHHH
Q 045766 589 RRVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITDPKPGATETVIIISGTPEQTHAAQSLIQAFV 656 (663)
Q Consensus 589 ~~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~IsGt~e~v~~A~~lI~~~v 656 (663)
.+..+.||.++++.+||++|++|++|++.||++|.++.... ....|+|.|+.++++.|..+|...+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--EERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC--CccEEEEEcCHHHHHHHHHHHHHHh
Confidence 46789999999999999999999999999999999976532 4689999999999999999998876
No 32
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.64 E-value=4.9e-07 Score=85.79 Aligned_cols=143 Identities=22% Similarity=0.345 Sum_probs=99.8
Q ss_pred cceEEEEEeeccccceeeccCchhHHhHHhHhCCeEEEeccCCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHHHhhcC
Q 045766 315 EILTFRLLCHDERVGGVIGKGGAIIRSLKQETGCDIKVMEAVSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTRIARAI 394 (663)
Q Consensus 315 ~~~~~~v~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~i~~~~ 394 (663)
......+.||.+..+.+||+.|+..+.|.+.+++++.+. +.+..|.|..+....+. .....|.. +++.+....
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD-----~~~~~V~i~~~~~t~Dp-~~~~ka~d-~VkAIgrGF 78 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID-----SKTGSVTIRTTRKTEDP-LALLKARD-VVKAIGRGF 78 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEE-----CCCCeEEEEecCCCCCh-HHHHHHHH-HHHHHhcCC
Confidence 344677999999999999999999999999999999994 55567888877321111 11112211 111111100
Q ss_pred C-C-----CCCcceEEE-EEe------c----ccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEE
Q 045766 395 P-D-----NREQTVMTR-LLV------A----SNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLIN 457 (663)
Q Consensus 395 ~-~-----~~~~~~~~~-l~V------p----~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~ 457 (663)
+ + ..+ ...+. +.+ + ....|+|||++|.+.+-|++.|||.|.| ...+|.|.
T Consensus 79 ~pe~A~~LL~d-~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V------------~g~tVaii 145 (194)
T COG1094 79 PPEKALKLLED-DYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISV------------YGKTVAII 145 (194)
T ss_pred CHHHHHHHhcC-CcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEE------------eCcEEEEe
Confidence 0 0 011 12211 111 1 1246999999999999999999999999 35679999
Q ss_pred ecHHHHHHHHHHHHHHHhhc
Q 045766 458 GEFEAVQEALFQITTRLRHH 477 (663)
Q Consensus 458 G~~~~v~~A~~~I~~~l~~~ 477 (663)
|.+++|+.|++.|+.++...
T Consensus 146 G~~~~v~iAr~AVemli~G~ 165 (194)
T COG1094 146 GGFEQVEIAREAVEMLINGA 165 (194)
T ss_pred cChhhhHHHHHHHHHHHcCC
Confidence 99999999999999999873
No 33
>smart00322 KH K homology RNA-binding domain.
Probab=98.62 E-value=2.3e-07 Score=74.10 Aligned_cols=66 Identities=33% Similarity=0.495 Sum_probs=58.3
Q ss_pred eEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHHHHHH
Q 045766 402 VMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQEALFQITTRL 474 (663)
Q Consensus 402 ~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l 474 (663)
.+.++.||..+++.+||++|++|++|++.||++|.+.... .....|+|.|+.+++..|..+|.+.+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------SEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 6789999999999999999999999999999999993211 24688999999999999999998876
No 34
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.50 E-value=1.3e-06 Score=83.01 Aligned_cols=152 Identities=20% Similarity=0.262 Sum_probs=106.3
Q ss_pred eEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEe-----cHHHHHHHHHHHHHHHhh
Q 045766 402 VMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLING-----EFEAVQEALFQITTRLRH 476 (663)
Q Consensus 402 ~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G-----~~~~v~~A~~~I~~~l~~ 476 (663)
....+.||....+.+||+.|++-+.|.+.++++|.+- +.+..|+|.. +|-.+.+|...|..+-+.
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 4556899999999999999999999999999999992 3445666655 477899999888887665
Q ss_pred ccccCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCccccCCCCCCC
Q 045766 477 HFFRDAFPSINRPLNPTFLDQVSPFPSFIGRRELSPPGMYSNFGPSFHKFDAVGGPPPPGSFHPHDDHSAFMHHIHRPGM 556 (663)
Q Consensus 477 ~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~ 556 (663)
.....++...+ + .-++--+
T Consensus 78 F~pe~A~~LL~------------------------------------------------------d--~~~levI----- 96 (194)
T COG1094 78 FPPEKALKLLE------------------------------------------------------D--DYYLEVI----- 96 (194)
T ss_pred CCHHHHHHHhc------------------------------------------------------C--CcEEEEE-----
Confidence 43322210000 0 0000000
Q ss_pred CCCCCCCCCCCCCCccccCCCCCCCCCCCCCcceEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEE
Q 045766 557 PPHMPDMKPWGPQGLMEVGGPMGFPDFVGPPHRRVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITDPKPGATETVI 636 (663)
Q Consensus 557 ~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v 636 (663)
.+.++.+.+.. . =....|+|||++|.+.+.|.+.|||+|-|.. .+|
T Consensus 97 ----------------------di~~~~~~~~~----~-l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g-------~tV 142 (194)
T COG1094 97 ----------------------DLKDVVTLSGD----H-LRRIKGRIIGREGKTRRAIEELTGVYISVYG-------KTV 142 (194)
T ss_pred ----------------------EHHHhccCchh----h-hhHhhceeeCCCchHHHHHHHHhCCeEEEeC-------cEE
Confidence 00000000000 0 0245699999999999999999999999963 489
Q ss_pred EEEcCHHHHHHHHHHHHHHHhc
Q 045766 637 IISGTPEQTHAAQSLIQAFVMS 658 (663)
Q Consensus 637 ~IsGt~e~v~~A~~lI~~~v~~ 658 (663)
-|-|.+++++.|+..|+.++..
T Consensus 143 aiiG~~~~v~iAr~AVemli~G 164 (194)
T COG1094 143 AIIGGFEQVEIAREAVEMLING 164 (194)
T ss_pred EEecChhhhHHHHHHHHHHHcC
Confidence 9999999999999999988764
No 35
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.12 E-value=6.5e-06 Score=73.58 Aligned_cols=62 Identities=26% Similarity=0.390 Sum_probs=51.2
Q ss_pred CCcCeeecCCChhHHHHHHHcCCEEEEeCCCC---C--------------CcceEEEEEcCH---HHHHHHHHHHHHHHh
Q 045766 598 SLVPIIQGEDGACLKQIRQISDAKITITDPKP---G--------------ATETVIIISGTP---EQTHAAQSLIQAFVM 657 (663)
Q Consensus 598 ~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~---~--------------~~~r~v~IsGt~---e~v~~A~~lI~~~v~ 657 (663)
+++|.|||++|++|++|+++|||+|.|..... + ...-.|.|++.. +++++|+.+|+.++.
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 78999999999999999999999999986411 0 112578999964 999999999999887
Q ss_pred cc
Q 045766 658 SE 659 (663)
Q Consensus 658 ~~ 659 (663)
..
T Consensus 95 ~~ 96 (120)
T cd02395 95 PA 96 (120)
T ss_pred cC
Confidence 44
No 36
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.09 E-value=1.3e-05 Score=71.65 Aligned_cols=66 Identities=36% Similarity=0.503 Sum_probs=50.8
Q ss_pred cceeEEEcCCchHHHHHHHHhCceEEEecCCCC-----------CCCC-CCCCcEEEEEecH---HHHHHHHHHHHHHHh
Q 045766 411 NQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQI-----------PKCA-SENEEVVLINGEF---EAVQEALFQITTRLR 475 (663)
Q Consensus 411 ~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~-----------p~~~-~~~~~~v~I~G~~---~~v~~A~~~I~~~l~ 475 (663)
+++|.|||++|++||+|+++|||+|.|..+... |... ....-.|.|++.. +++.+|+.+|..++.
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 578999999999999999999999999544211 1111 1122468999965 899999999999988
Q ss_pred h
Q 045766 476 H 476 (663)
Q Consensus 476 ~ 476 (663)
.
T Consensus 95 ~ 95 (120)
T cd02395 95 P 95 (120)
T ss_pred c
Confidence 5
No 37
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.06 E-value=7.1e-06 Score=82.04 Aligned_cols=149 Identities=26% Similarity=0.395 Sum_probs=109.9
Q ss_pred cceEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHHHHHHhhccc
Q 045766 400 QTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQEALFQITTRLRHHFF 479 (663)
Q Consensus 400 ~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~~ 479 (663)
..++..+.||..+++.|.|++|++|+.|+.+|..+|.-+.+. .+-++.++|.++.|..|++.|...-+..-.
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~--------eePiF~vTg~~edv~~aRrei~saaeH~~l 95 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG--------EEPIFPVTGRHEDVRRARREIPSAAEHFGL 95 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC--------CCCcceeccCchhHHHHhhcCccccceeee
Confidence 568899999999999999999999999999999999995553 345799999999999999877654433211
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCCC
Q 045766 480 RDAFPSINRPLNPTFLDQVSPFPSFIGRRELSPPGMYSNFGPSFHKFDAVGGPPPPGSFHPHDDHSAFMHHIHRPGMPPH 559 (663)
Q Consensus 480 ~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~ 559 (663)
.... ++| ++ |.+
T Consensus 96 ~~~s--------~s~----------------------Sg------------------------------------g~~-- 107 (394)
T KOG2113|consen 96 IRAS--------RSF----------------------SG------------------------------------GTN-- 107 (394)
T ss_pred eeec--------ccc----------------------cC------------------------------------CCc--
Confidence 1100 000 00 000
Q ss_pred CCCCCCCCCCCccccCCCCCCCCCCCCCcceEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEEEEE
Q 045766 560 MPDMKPWGPQGLMEVGGPMGFPDFVGPPHRRVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITDPKPGATETVIIIS 639 (663)
Q Consensus 560 ~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~Is 639 (663)
|+ ....+.+.++.+|...+|.|.|..|++|+.|++.+...|.-+-+. .+.++.++
T Consensus 108 ----------~~------------s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~---~~~Vf~Vt 162 (394)
T KOG2113|consen 108 ----------GA------------SASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRC---GEPVFCVT 162 (394)
T ss_pred ----------cc------------cccCCCceeeeccceeeeeccccccCccchheecccceEeeeccC---CCceEEEe
Confidence 00 001235667899999999999999999999999999998876542 45699999
Q ss_pred cCHHHHH-HHH
Q 045766 640 GTPEQTH-AAQ 649 (663)
Q Consensus 640 Gt~e~v~-~A~ 649 (663)
|-+.+|. +|.
T Consensus 163 g~~~nC~kra~ 173 (394)
T KOG2113|consen 163 GAPKNCVKRAR 173 (394)
T ss_pred cCCcchhhhcc
Confidence 9999844 444
No 38
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.77 E-value=3.1e-05 Score=77.52 Aligned_cols=146 Identities=17% Similarity=0.284 Sum_probs=109.7
Q ss_pred cceEEEEEeeccccceeeccCchhHHhHHhHhCCeEEEeccCCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHHHhhcC
Q 045766 315 EILTFRLLCHDERVGGVIGKGGAIIRSLKQETGCDIKVMEAVSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTRIARAI 394 (663)
Q Consensus 315 ~~~~~~v~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~i~~~~ 394 (663)
..++..+.+|...++.|.|++|.+||.|+.+|...|+-+.. ..+-++.++|.. +.|..|+..|....+.+.-..
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr---~eePiF~vTg~~---edv~~aRrei~saaeH~~l~~ 97 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---GEEPIFPVTGRH---EDVRRARREIPSAAEHFGLIR 97 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCC---CCCCcceeccCc---hhHHHHhhcCccccceeeeee
Confidence 67888999999999999999999999999999999998743 223578889988 666666665554333221110
Q ss_pred ---------CC-CCCcceEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHH-H
Q 045766 395 ---------PD-NREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEA-V 463 (663)
Q Consensus 395 ---------~~-~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~-v 463 (663)
.. ......+....+|...+|.|.|..|.+|+.|++.+...|.-+-+ ..+.++.++|.+.+ +
T Consensus 98 ~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~--------~~~~Vf~Vtg~~~nC~ 169 (394)
T KOG2113|consen 98 ASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR--------CGEPVFCVTGAPKNCV 169 (394)
T ss_pred ecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc--------CCCceEEEecCCcchh
Confidence 00 12455678889999999999999999999999999998887322 35678999998888 5
Q ss_pred HHHH-HHHHHHH
Q 045766 464 QEAL-FQITTRL 474 (663)
Q Consensus 464 ~~A~-~~I~~~l 474 (663)
++|. ..|+.-+
T Consensus 170 kra~s~eie~ta 181 (394)
T KOG2113|consen 170 KRARSCEIEQTA 181 (394)
T ss_pred hhccccchhhhh
Confidence 6665 4554433
No 39
>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=97.71 E-value=9.7e-05 Score=84.33 Aligned_cols=90 Identities=22% Similarity=0.330 Sum_probs=71.4
Q ss_pred CChHHHHHHHHHHHHhhcCCC----CCCcceEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCC
Q 045766 376 ISAPQDAVLRVQTRIARAIPD----NREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENE 451 (663)
Q Consensus 376 v~~a~~ai~~i~~~i~~~~~~----~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~ 451 (663)
+..|+++...+++.+...+.. ....+....+.||.+.++.|||+||++||+|+++|||+|.+ ..+
T Consensus 548 L~~A~~g~~~Il~~m~~al~~p~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi-----------~d~ 616 (719)
T TIGR02696 548 LKQARDARLAILDVMAEAIDTPDEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISI-----------EDD 616 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHhCccccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEE-----------ecC
Confidence 445666666666655543222 23356788999999999999999999999999999999999 346
Q ss_pred cEEEEEe-cHHHHHHHHHHHHHHHhh
Q 045766 452 EVVLING-EFEAVQEALFQITTRLRH 476 (663)
Q Consensus 452 ~~v~I~G-~~~~v~~A~~~I~~~l~~ 476 (663)
..|.|.+ +.+.+++|+.+|..++..
T Consensus 617 G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 617 GTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 7899888 478999999999999874
No 40
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.66 E-value=0.00016 Score=66.59 Aligned_cols=101 Identities=22% Similarity=0.368 Sum_probs=71.7
Q ss_pred eEEEEEeeccccceeeccCchhHHhHHhHhCCeEEEeccCCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHHHhhc-C-
Q 045766 317 LTFRLLCHDERVGGVIGKGGAIIRSLKQETGCDIKVMEAVSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTRIARA-I- 394 (663)
Q Consensus 317 ~~~~v~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~i~~~-~- 394 (663)
-.+.+.|+...+|..||++|++|+.|++..|-+|.+-+-..+ +++-+..++....-. .
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~d--------------------~~~fI~n~l~Pa~V~~v~ 91 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDD--------------------PEEFIKNIFAPAAVRSVT 91 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCCC--------------------HHHHHHHHcCCCEEEEEE
Confidence 467788899999999999999999999999988887532110 112222221111000 0
Q ss_pred CCCCCcceEEEEEecccceeEEEcCCchHHHHHHHHhCceEEE
Q 045766 395 PDNREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRI 437 (663)
Q Consensus 395 ~~~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i 437 (663)
-...+......+.|+.+..|.+|||+|.+++.++..+|-++.+
T Consensus 92 I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 92 IKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred EEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 0012233567788999999999999999999999999988877
No 41
>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=97.39 E-value=0.00031 Score=81.52 Aligned_cols=89 Identities=21% Similarity=0.355 Sum_probs=68.3
Q ss_pred ChHHHHHHHHHHHHhhcCCC-----CCCcceEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCC
Q 045766 377 SAPQDAVLRVQTRIARAIPD-----NREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENE 451 (663)
Q Consensus 377 ~~a~~ai~~i~~~i~~~~~~-----~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~ 451 (663)
..|.++...+++.+...+.. ....+....+.||.+.++.|||+||++||+|+++|||+|.| ..+
T Consensus 521 ~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i-----------~dd 589 (684)
T TIGR03591 521 EQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDI-----------EDD 589 (684)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEE-----------ecC
Confidence 34556666666655543322 23456788999999999999999999999999999999999 235
Q ss_pred cEEEEEe-cHHHHHHHHHHHHHHHhh
Q 045766 452 EVVLING-EFEAVQEALFQITTRLRH 476 (663)
Q Consensus 452 ~~v~I~G-~~~~v~~A~~~I~~~l~~ 476 (663)
..|.|.+ ..+.+++|+.+|..+...
T Consensus 590 G~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 590 GTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred eEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 6677777 477889999999888654
No 42
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.39 E-value=0.00019 Score=66.18 Aligned_cols=39 Identities=21% Similarity=0.272 Sum_probs=35.1
Q ss_pred eEEEEEeeccceeeeecCCCccccchhhccCCeEEEcCC
Q 045766 46 IMFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEET 84 (663)
Q Consensus 46 ~~~rilvp~~~vg~IIGk~G~~I~~i~~etga~I~v~~~ 84 (663)
-.+.++|+...+|..||++|++|+.|++..|-+|+|-+-
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~ 70 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY 70 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc
Confidence 367788999999999999999999999999999988773
No 43
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.36 E-value=0.00043 Score=79.20 Aligned_cols=64 Identities=25% Similarity=0.421 Sum_probs=57.4
Q ss_pred ceEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEEEEEcC-HHHHHHHHHHHHHHHhc
Q 045766 589 RRVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITDPKPGATETVIIISGT-PEQTHAAQSLIQAFVMS 658 (663)
Q Consensus 589 ~~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~IsGt-~e~v~~A~~lI~~~v~~ 658 (663)
...++.||.+.+|.|||+||.+|+.|.+.|||+|.|.+ +..|.|.+. .++.++|+.+|+.++..
T Consensus 578 ~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 578 RIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred eeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 45789999999999999999999999999999999975 257888885 88999999999988873
No 44
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.16 E-value=0.00043 Score=72.40 Aligned_cols=66 Identities=18% Similarity=0.196 Sum_probs=56.5
Q ss_pred CCCceEEEEEeeccceeeeecCCCccccchhhccCCeEEEcCCCCCCCceEEEEEeCCCcccchhhhhh
Q 045766 42 FPGGIMFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEETVSGSDERLVVIEASDNKKETSENLEA 110 (663)
Q Consensus 42 ~~~~~~~rilvp~~~vg~IIGk~G~~I~~i~~etga~I~v~~~~~g~~ervi~I~G~~e~~~~a~~~~~ 110 (663)
..++.++.+-+-+++||.|||++|++|++|+..|+++|++.. ...|-.|+|.|...-...|++-++
T Consensus 43 g~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~---~~~e~kv~ifg~~~m~~kaka~id 108 (629)
T KOG0336|consen 43 GGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIK---CDLEVKVTIFGINHMRKKAKASID 108 (629)
T ss_pred CCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEec---cCceeEEEEechHHHHHHHHhhHh
Confidence 357888999999999999999999999999999999999987 446778999998776666666555
No 45
>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=97.12 E-value=0.0019 Score=59.45 Aligned_cols=100 Identities=21% Similarity=0.333 Sum_probs=69.9
Q ss_pred EEEEEeeccccceeeccCchhHHhHHhHhCCeEEEeccCCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHH--HhhcCC
Q 045766 318 TFRLLCHDERVGGVIGKGGAIIRSLKQETGCDIKVMEAVSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTR--IARAIP 395 (663)
Q Consensus 318 ~~~v~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~--i~~~~~ 395 (663)
.+-+.|....+|..||++|++|+.|++..|-+|.+-+-..+.. +-+..++.- +..-.-
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~D~~--------------------~fI~N~l~PA~V~~V~i 93 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSENLE--------------------EFVANKLAPAEVKNVTV 93 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCCHH--------------------HHHHHcCCCceEEEEEE
Confidence 6778889999999999999999999988898888754211100 111111000 000000
Q ss_pred CCCCcceEEEEEecccceeEEEcCCchHHHHHHHHhCceEEE
Q 045766 396 DNREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRI 437 (663)
Q Consensus 396 ~~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i 437 (663)
...++.....+.||.+..+..|||+|.+++...+.+|-++.+
T Consensus 94 ~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI 135 (141)
T TIGR01952 94 SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI 135 (141)
T ss_pred EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence 011234667888999999999999999999999999988877
No 46
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.08 E-value=0.00057 Score=79.88 Aligned_cols=90 Identities=12% Similarity=0.301 Sum_probs=72.2
Q ss_pred CChHHHHHHHHHHHHhhcCCC-----CCCcceEEEEEecccceeEEEcCCchHHHHHHHHhCce-EEEecCCCCCCCCCC
Q 045766 376 ISAPQDAVLRVQTRIARAIPD-----NREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAY-IRILGKDQIPKCASE 449 (663)
Q Consensus 376 v~~a~~ai~~i~~~i~~~~~~-----~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~-I~i~~~~~~p~~~~~ 449 (663)
+..|+++...+++.+...++. ....+....|.||.+.++.|||.||.+||+|.++||+. |.+ .
T Consensus 654 L~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi-----------~ 722 (891)
T PLN00207 654 LLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDT-----------Q 722 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCc-----------C
Confidence 345667777777766654432 24456789999999999999999999999999999999 998 3
Q ss_pred CCcEEEEEe-cHHHHHHHHHHHHHHHhh
Q 045766 450 NEEVVLING-EFEAVQEALFQITTRLRH 476 (663)
Q Consensus 450 ~~~~v~I~G-~~~~v~~A~~~I~~~l~~ 476 (663)
.+..|.|.+ +.+.+++|+.+|..++.+
T Consensus 723 ddg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 723 DDGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 356788888 577999999999988764
No 47
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.06 E-value=0.0011 Score=74.28 Aligned_cols=91 Identities=21% Similarity=0.313 Sum_probs=74.3
Q ss_pred CChHHHHHHHHHHHHhhcCCC-----CCCcceEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCC
Q 045766 376 ISAPQDAVLRVQTRIARAIPD-----NREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASEN 450 (663)
Q Consensus 376 v~~a~~ai~~i~~~i~~~~~~-----~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~ 450 (663)
+.+|+.+-+.++..+.+.+.. ....+....+.|+.+.++.+||++|.+|++|.++|||+|++ ..
T Consensus 521 L~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idi-----------ed 589 (692)
T COG1185 521 LEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDI-----------ED 589 (692)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEe-----------cC
Confidence 356777777777777665443 23345678899999999999999999999999999999999 34
Q ss_pred CcEEEEEecH-HHHHHHHHHHHHHHhhc
Q 045766 451 EEVVLINGEF-EAVQEALFQITTRLRHH 477 (663)
Q Consensus 451 ~~~v~I~G~~-~~v~~A~~~I~~~l~~~ 477 (663)
+..|.|.++. +.+.+|+..|..++++.
T Consensus 590 dGtv~i~~s~~~~~~~ak~~I~~i~~e~ 617 (692)
T COG1185 590 DGTVKIAASDGESAKKAKERIEAITREV 617 (692)
T ss_pred CCcEEEEecchHHHHHHHHHHHHHHhhc
Confidence 6679999986 78899999999999773
No 48
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.92 E-value=0.0071 Score=64.84 Aligned_cols=76 Identities=24% Similarity=0.432 Sum_probs=57.0
Q ss_pred ceEEEEEecc------cceeEEEcCCchHHHHHHHHhCceEEEecCCC----------CCCCCCCCCcE-EEEEec-HHH
Q 045766 401 TVMTRLLVAS------NQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQ----------IPKCASENEEV-VLINGE-FEA 462 (663)
Q Consensus 401 ~~~~~l~Vp~------~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~----------~p~~~~~~~~~-v~I~G~-~~~ 462 (663)
..+.+|.||- +++|.|||..|.|.|+|+++|||+|.|.-+.. +.......+.+ +.|+.+ .|.
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 5667788874 57999999999999999999999999954211 11111123333 778875 668
Q ss_pred HHHHHHHHHHHHhh
Q 045766 463 VQEALFQITTRLRH 476 (663)
Q Consensus 463 v~~A~~~I~~~l~~ 476 (663)
|++|+++|..+|.+
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 89999999999986
No 49
>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=96.74 E-value=0.0023 Score=74.50 Aligned_cols=63 Identities=22% Similarity=0.336 Sum_probs=54.8
Q ss_pred ceEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEEEEEc-CHHHHHHHHHHHHHHHh
Q 045766 589 RRVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITDPKPGATETVIIISG-TPEQTHAAQSLIQAFVM 657 (663)
Q Consensus 589 ~~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~IsG-t~e~v~~A~~lI~~~v~ 657 (663)
...++.||.+.+|.|||+||.+|+.|.++|||+|.|.+. ..|.|.+ ..+.+++|+.+|..+..
T Consensus 551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd------G~V~i~~~~~~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD------GTVKIAASDGEAAEAAIKMIEGITA 614 (684)
T ss_pred eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC------eEEEEEECcHHHHHHHHHHHHhhhc
Confidence 557899999999999999999999999999999999752 4566666 58899999999988765
No 50
>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=96.70 E-value=0.0039 Score=57.37 Aligned_cols=38 Identities=21% Similarity=0.330 Sum_probs=33.2
Q ss_pred EEEEEeeccceeeeecCCCccccchhhccCCeEEEcCC
Q 045766 47 MFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEET 84 (663)
Q Consensus 47 ~~rilvp~~~vg~IIGk~G~~I~~i~~etga~I~v~~~ 84 (663)
.+=++|....+|..||++|++|+.|++..|-+|+|-+-
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVey 71 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEY 71 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEc
Confidence 45567888999999999999999999889999988763
No 51
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.48 E-value=0.0048 Score=64.84 Aligned_cols=64 Identities=19% Similarity=0.240 Sum_probs=54.0
Q ss_pred eEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEEEEEcCHHHHHHHHHHHHHHH
Q 045766 590 RVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITDPKPGATETVIIISGTPEQTHAAQSLIQAFV 656 (663)
Q Consensus 590 ~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~IsGt~e~v~~A~~lI~~~v 656 (663)
..-+.|-.++||.|||+||++|+.|+..|.++|+|.+- ..+-.|+|-|..+--.+|+..|...+
T Consensus 48 plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~~m~~kaka~id~~~ 111 (629)
T KOG0336|consen 48 PLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGINHMRKKAKASIDRGQ 111 (629)
T ss_pred chhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechHHHHHHHHhhHhhhh
Confidence 34478889999999999999999999999999999864 34578999999887778887776554
No 52
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.44 E-value=0.0022 Score=63.92 Aligned_cols=44 Identities=23% Similarity=0.474 Sum_probs=38.8
Q ss_pred CCCCCceEEEEEeecc------ceeeeecCCCccccchhhccCCeEEEcC
Q 045766 40 KSFPGGIMFRVLCPVS------KIDGVIGKDGEMMSQISQDTGVTIRVEE 83 (663)
Q Consensus 40 ~~~~~~~~~rilvp~~------~vg~IIGk~G~~I~~i~~etga~I~v~~ 83 (663)
....-.+..||+||.+ +||.|+|.+|.++|+|+++|||||-|.-
T Consensus 86 ~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrG 135 (259)
T KOG1588|consen 86 SGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRG 135 (259)
T ss_pred cCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEec
Confidence 3445788999999985 6999999999999999999999998864
No 53
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.35 E-value=0.0039 Score=72.72 Aligned_cols=90 Identities=22% Similarity=0.347 Sum_probs=69.7
Q ss_pred CChHHHHHHHHHHHHhhcCCC-----CCCcceEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCC
Q 045766 376 ISAPQDAVLRVQTRIARAIPD-----NREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASEN 450 (663)
Q Consensus 376 v~~a~~ai~~i~~~i~~~~~~-----~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~ 450 (663)
+..|+++...+++.+...+.. ....+....+.||.+.++.+||.||.+||+|.++||+.|.+ ..
T Consensus 523 l~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi-----------~d 591 (693)
T PRK11824 523 LEQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDI-----------ED 591 (693)
T ss_pred HHHHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCcccc-----------CC
Confidence 345667777777777655432 22345567788899999999999999999999999998888 23
Q ss_pred CcEEEEEe-cHHHHHHHHHHHHHHHhh
Q 045766 451 EEVVLING-EFEAVQEALFQITTRLRH 476 (663)
Q Consensus 451 ~~~v~I~G-~~~~v~~A~~~I~~~l~~ 476 (663)
+..|.|.+ ..+.+++|+.+|..+..+
T Consensus 592 ~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 592 DGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred CceEEEEcccHHHHHHHHHHHHHhccc
Confidence 56788888 577899999999888764
No 54
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.35 E-value=0.014 Score=56.53 Aligned_cols=99 Identities=22% Similarity=0.342 Sum_probs=67.1
Q ss_pred EEEEeeccccceeeccCchhHHhHHhHhCCeEEEeccCCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHHHh--hcCCC
Q 045766 319 FRLLCHDERVGGVIGKGGAIIRSLKQETGCDIKVMEAVSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTRIA--RAIPD 396 (663)
Q Consensus 319 ~~v~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~i~--~~~~~ 396 (663)
+.+.+-.+.+|..||++|++|+.|.++.|-+|.|-+-. .. ..+-+..++.... .-.-.
T Consensus 78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s------------~d--------~~~fI~nal~Pa~v~~V~~~ 137 (190)
T COG0195 78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS------------ED--------PAEFIKNALAPAEVLSVNIK 137 (190)
T ss_pred EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeC------------CC--------HHHHHHHhcCcceEeEEEEE
Confidence 33444567789999999999999999999777764321 11 0122222221100 00000
Q ss_pred CCCcceEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEe
Q 045766 397 NREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRIL 438 (663)
Q Consensus 397 ~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~ 438 (663)
..+.. ...+.||.+..+..|||+|.+++.+.+.||-++.|.
T Consensus 138 ~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~ 178 (190)
T COG0195 138 EDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIE 178 (190)
T ss_pred eCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEE
Confidence 11222 778889999999999999999999999999999993
No 55
>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=96.27 E-value=0.003 Score=49.44 Aligned_cols=37 Identities=27% Similarity=0.337 Sum_probs=34.6
Q ss_pred ceEEEEEeeccceeeeecCCCccccchhhccCCeEEE
Q 045766 45 GIMFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRV 81 (663)
Q Consensus 45 ~~~~rilvp~~~vg~IIGk~G~~I~~i~~etga~I~v 81 (663)
...+.+.|+.+..|..|||+|.+|+.+++.+|-+|+|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3688999999999999999999999999999999886
No 56
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.05 E-value=0.015 Score=62.47 Aligned_cols=61 Identities=26% Similarity=0.358 Sum_probs=48.0
Q ss_pred CCcCeeecCCChhHHHHHHHcCCEEEEeCCC---C------------CC-cceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 045766 598 SLVPIIQGEDGACLKQIRQISDAKITITDPK---P------------GA-TETVIIISG-TPEQTHAAQSLIQAFVMS 658 (663)
Q Consensus 598 ~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~---~------------~~-~~r~v~IsG-t~e~v~~A~~lI~~~v~~ 658 (663)
+|||.|||..|.+.|+|.++|||+|.|--.. + .. .+=-+.|++ |.|.|++|..+|+.+|.+
T Consensus 153 NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 153 NFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQS 230 (554)
T ss_pred ceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHh
Confidence 7899999999999999999999999997411 0 00 112355665 478999999999999885
No 57
>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=96.00 E-value=0.011 Score=46.26 Aligned_cols=36 Identities=28% Similarity=0.475 Sum_probs=33.7
Q ss_pred ceEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEE
Q 045766 589 RRVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITI 624 (663)
Q Consensus 589 ~~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i 624 (663)
....+.||.+..|.+|||+|.||+.+++.+|-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 578899999999999999999999999999988876
No 58
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=95.78 E-value=0.011 Score=66.43 Aligned_cols=63 Identities=22% Similarity=0.331 Sum_probs=55.9
Q ss_pred ceEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEEEEEcCH-HHHHHHHHHHHHHHh
Q 045766 589 RRVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITDPKPGATETVIIISGTP-EQTHAAQSLIQAFVM 657 (663)
Q Consensus 589 ~~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~IsGt~-e~v~~A~~lI~~~v~ 657 (663)
.-.++.|+.+.++-|||+||.+|++|.+.|||+|+|.+ +..|.|.++. +.+++|+.+|.+++.
T Consensus 552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied------dGtv~i~~s~~~~~~~ak~~I~~i~~ 615 (692)
T COG1185 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED------DGTVKIAASDGESAKKAKERIEAITR 615 (692)
T ss_pred ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC------CCcEEEEecchHHHHHHHHHHHHHHh
Confidence 45679999999999999999999999999999999963 2469999986 899999999998874
No 59
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=95.72 E-value=0.015 Score=59.79 Aligned_cols=71 Identities=25% Similarity=0.347 Sum_probs=57.2
Q ss_pred eEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHHHHHHhhcc
Q 045766 402 VMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQEALFQITTRLRHHF 478 (663)
Q Consensus 402 ~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~ 478 (663)
....+.|++...+.|||++|.+.++|+++|+++|.+ |......+.++.+.+.-++|.+|.+.|..++.+..
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~l------p~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFL------PRPNTNKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEc------cCCCCCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 556788999999999999999999999999999999 33222334444455578899999999999998743
No 60
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=95.57 E-value=0.0096 Score=69.95 Aligned_cols=63 Identities=19% Similarity=0.258 Sum_probs=55.6
Q ss_pred ceEEEEecCCCcCeeecCCChhHHHHHHHcCCE-EEEeCCCCCCcceEEEEEc-CHHHHHHHHHHHHHHHh
Q 045766 589 RRVPVVVPRSLVPIIQGEDGACLKQIRQISDAK-ITITDPKPGATETVIIISG-TPEQTHAAQSLIQAFVM 657 (663)
Q Consensus 589 ~~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~-I~i~~~~~~~~~r~v~IsG-t~e~v~~A~~lI~~~v~ 657 (663)
...++.||.+.+|.|||.||.+|+.|.++||++ |.+.+ +-.|.|.+ +.+.+++|+.+|..++.
T Consensus 685 ~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d------dg~V~I~a~d~~~i~~A~~~I~~l~~ 749 (891)
T PLN00207 685 LIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD------DGTVKITAKDLSSLEKSKAIISSLTM 749 (891)
T ss_pred eeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC------CeeEEEEeCCHHHHHHHHHHHHHHhc
Confidence 456799999999999999999999999999999 99965 25677877 58999999999998875
No 61
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.47 E-value=0.025 Score=57.16 Aligned_cols=64 Identities=22% Similarity=0.278 Sum_probs=54.5
Q ss_pred EEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHH-HHHHHHHHHHHHHhhcc
Q 045766 404 TRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFE-AVQEALFQITTRLRHHF 478 (663)
Q Consensus 404 ~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~-~v~~A~~~I~~~l~~~~ 478 (663)
..+.||..+++.+||++|.+|+.|.+.+++.|.+ ..+..|.|.+... .+.+|+.+|..+-++..
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~i-----------g~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~ 211 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIV-----------GQNGRIWIKGPDEEDEEIAIEAIKKIEREAH 211 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEE-----------cCCcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence 5688999999999999999999999999999999 3457788888754 88888888888776644
No 62
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=95.44 E-value=0.76 Score=45.53 Aligned_cols=66 Identities=18% Similarity=0.193 Sum_probs=55.7
Q ss_pred eEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHHHHHHhhc
Q 045766 402 VMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQEALFQITTRLRHH 477 (663)
Q Consensus 402 ~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~ 477 (663)
..+.+.++....-.+...+|..++.|....||+|.+. ..+..|.|+|+...++.+...|.+++...
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 GDLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVS----------RSENRIRITGTKSTAEYIEASINEILSNI 91 (210)
T ss_pred ceeEEEecchheeeeecCCchHHHHHHHhcCceEEEe----------cCCcEEEEEccHHHHHHHHHHHHHHHhhc
Confidence 4455666788889999999999999988889999993 23568999999999999999999988763
No 63
>PRK00468 hypothetical protein; Provisional
Probab=95.43 E-value=0.033 Score=45.37 Aligned_cols=49 Identities=27% Similarity=0.415 Sum_probs=35.8
Q ss_pred HHHHHHHHHhhcCCC------CCCcceEEEEEecccceeEEEcCCchHHHHHHHH
Q 045766 382 AVLRVQTRIARAIPD------NREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKL 430 (663)
Q Consensus 382 ai~~i~~~i~~~~~~------~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~ 430 (663)
.+..+.+.+.+...+ ..+....+++.+..+.+|+||||+|.+|+.|+.-
T Consensus 4 Lv~~iv~~LVd~Pe~v~V~~~~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 4 LVETIAKALVDNPDAVQVNEIEGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred HHHHHHHHhcCCCCeEEEEEEeCCCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence 344445555443332 2345578899999999999999999999999865
No 64
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=95.40 E-value=0.02 Score=57.17 Aligned_cols=41 Identities=34% Similarity=0.603 Sum_probs=36.1
Q ss_pred CCcceEEEEEeecc------ccceeeccCchhHHhHHhHhCCeEEEe
Q 045766 313 SPEILTFRLLCHDE------RVGGVIGKGGAIIRSLKQETGCDIKVM 353 (663)
Q Consensus 313 ~~~~~~~~v~vp~~------~vg~IIGk~G~~Ik~I~~~tga~I~i~ 353 (663)
..-.++.+|+||.+ +||+|+|.+|.++|+|+++|||+|.|-
T Consensus 88 ~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 88 KPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred CceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 34567889999964 799999999999999999999999985
No 65
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=95.37 E-value=0.23 Score=49.31 Aligned_cols=129 Identities=13% Similarity=0.133 Sum_probs=86.9
Q ss_pred EEEEEeeccccceeeccCchhHHhHHhHhCCeEEEeccCCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHHHhhcCCCC
Q 045766 318 TFRLLCHDERVGGVIGKGGAIIRSLKQETGCDIKVMEAVSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTRIARAIPDN 397 (663)
Q Consensus 318 ~~~v~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~i~~~~~~~ 397 (663)
.+.+.++....-.+...+|..++.|....||+|.+. ..+..+.|+|++ ..+..+...|..+++.
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~-----~~~~~i~I~g~k---~~~~~i~~~i~~~l~~-------- 90 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVS-----RSENRIRITGTK---STAEYIEASINEILSN-------- 90 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEe-----cCCcEEEEEccH---HHHHHHHHHHHHHHhh--------
Confidence 344555677889999999999999988889999995 334579999998 3333333333333333
Q ss_pred CCcceEEEEEecccceeEEEc----CCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEe-----cHHHHHHHHH
Q 045766 398 REQTVMTRLLVASNQIGCLLG----KGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLING-----EFEAVQEALF 468 (663)
Q Consensus 398 ~~~~~~~~l~Vp~~~vg~IIG----k~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G-----~~~~v~~A~~ 468 (663)
..+.+|.++.-..-.--+ .....++.|++.|++.|...+ ....+.|.. ....++.|++
T Consensus 91 ---i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~----------~~~~~~i~~~~~~~~~~~~~~a~R 157 (210)
T PF14611_consen 91 ---IRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNP----------DGNKLKISWLASPENEKRADRAKR 157 (210)
T ss_pred ---cEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECC----------CCCeEEEEEEeeccccchHHHHHH
Confidence 355566665432211111 246788999999999999932 233455554 5678899999
Q ss_pred HHHHHHh
Q 045766 469 QITTRLR 475 (663)
Q Consensus 469 ~I~~~l~ 475 (663)
++.-.+.
T Consensus 158 lL~~a~~ 164 (210)
T PF14611_consen 158 LLLWALD 164 (210)
T ss_pred HHHHhcc
Confidence 8888875
No 66
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.32 E-value=0.029 Score=56.69 Aligned_cols=60 Identities=20% Similarity=0.319 Sum_probs=52.0
Q ss_pred eEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEEEEEcC-HHHHHHHHHHHHHH
Q 045766 590 RVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITDPKPGATETVIIISGT-PEQTHAAQSLIQAF 655 (663)
Q Consensus 590 ~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~IsGt-~e~v~~A~~lI~~~ 655 (663)
-+.+.||.++++.+||++|.+|+.|.+.+++.|.|-. +..|-|+++ .+++++|+.+|+..
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~------NG~VwI~~~~~~~~~~a~~~I~~~ 206 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ------NGRIWIKGPDEEDEEIAIEAIKKI 206 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC------CcEEEEeeCCHHHHHHHHHHHHHH
Confidence 3669999999999999999999999999999999953 357888887 55999999998764
No 67
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.23 E-value=0.066 Score=57.01 Aligned_cols=95 Identities=22% Similarity=0.257 Sum_probs=65.0
Q ss_pred cccceeeccCchhHHhHHhHh-CCeEEEeccCCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHH--HhhcCCCCCCcce
Q 045766 326 ERVGGVIGKGGAIIRSLKQET-GCDIKVMEAVSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTR--IARAIPDNREQTV 402 (663)
Q Consensus 326 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~--i~~~~~~~~~~~~ 402 (663)
+-+|..||++|++|+.|.++. |-+|.|-.-..+.. +-|..++.- +..-. ..+...
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~--------------------~fI~Nal~Pa~V~~V~--i~~~~~ 308 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPE--------------------IFIARALAPAIISSVK--IEEEEK 308 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHH--------------------HHHHHhCCCceeeEEE--EcCCCc
Confidence 458999999999999999998 78888753221111 111100000 00000 011235
Q ss_pred EEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCC
Q 045766 403 MTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQ 442 (663)
Q Consensus 403 ~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~ 442 (663)
...+.||.++.+..|||+|.+++...+.||.+|.|.+-+.
T Consensus 309 ~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 309 KAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS 348 (374)
T ss_pred EEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence 6788999999999999999999999999999999965543
No 68
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.14 E-value=0.051 Score=61.15 Aligned_cols=65 Identities=18% Similarity=0.374 Sum_probs=54.4
Q ss_pred eEEEEecCCC-cCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEEEEEc-CHHHHHHHHHHHHHHHhcc
Q 045766 590 RVPVVVPRSL-VPIIQGEDGACLKQIRQISDAKITITDPKPGATETVIIISG-TPEQTHAAQSLIQAFVMSE 659 (663)
Q Consensus 590 ~~~v~IP~~~-vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~IsG-t~e~v~~A~~lI~~~v~~~ 659 (663)
.-.|.+|++- -|+||||.|.||+.+...||+.|.|++. ...|+||| .|---+-|+.-|+.+|..+
T Consensus 205 ~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt-----p~~v~ls~fdp~rreia~~~l~~li~dg 271 (514)
T TIGR03319 205 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT-----PEAVILSGFDPVRREIARMALEKLIQDG 271 (514)
T ss_pred eeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC-----CCeEEecCCchHHHHHHHHHHHHHHHcC
Confidence 3458999955 6999999999999999999999999764 35788999 6877888888888887654
No 69
>PRK00106 hypothetical protein; Provisional
Probab=95.11 E-value=0.096 Score=58.79 Aligned_cols=67 Identities=24% Similarity=0.444 Sum_probs=52.6
Q ss_pred cceEEEEEecc-cceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEe-cHHHHHHHHHHHHHHHhh
Q 045766 400 QTVMTRLLVAS-NQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLING-EFEAVQEALFQITTRLRH 476 (663)
Q Consensus 400 ~~~~~~l~Vp~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l~~ 476 (663)
...+..+.+|+ ++-|+|||+.|.+|+-+...||+.+.| |+.| ..|+|+| +|---+-|+..+..++.+
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdlii---ddtp-------~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVII---DDTP-------EVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEE---cCCC-------CeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 34566788888 566999999999999999999999999 3323 4588888 677777777777777665
No 70
>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=95.10 E-value=0.089 Score=55.92 Aligned_cols=92 Identities=22% Similarity=0.412 Sum_probs=63.4
Q ss_pred cccceeeccCchhHHhHHhHh-CCeEEEeccCCCCCceEEEEeCCCCCCCCCChHHHHHHHHHH--HHhhc-CCCCCCcc
Q 045766 326 ERVGGVIGKGGAIIRSLKQET-GCDIKVMEAVSGTEDRLIVISGPAHPDDRISAPQDAVLRVQT--RIARA-IPDNREQT 401 (663)
Q Consensus 326 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~--~i~~~-~~~~~~~~ 401 (663)
+-+|..||++|++|+.|.++. |-+|.+-.-..+.. +-|..++. ++..- .. .+..
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~--------------------~fi~nal~Pa~v~~v~i~--~~~~ 300 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPA--------------------EFIANALSPAKVISVEVL--DEDK 300 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHH--------------------HHHHHhcCCceEEEEEEE--cCCC
Confidence 458999999999999999998 78888753221111 00100000 00000 00 1122
Q ss_pred eEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEec
Q 045766 402 VMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILG 439 (663)
Q Consensus 402 ~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~ 439 (663)
....+.||.++.+..|||+|.+++...+.||.+|.|.+
T Consensus 301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 57889999999999999999999999999999999943
No 71
>PRK02821 hypothetical protein; Provisional
Probab=95.09 E-value=0.044 Score=44.84 Aligned_cols=51 Identities=22% Similarity=0.375 Sum_probs=36.9
Q ss_pred HHHHHHHHHHhhcCCC------CCCcceEEEEEecccceeEEEcCCchHHHHHHHHh
Q 045766 381 DAVLRVQTRIARAIPD------NREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLS 431 (663)
Q Consensus 381 ~ai~~i~~~i~~~~~~------~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~t 431 (663)
+.+..+.+.+.+...+ ..+....+++.+.++.+|+||||+|.+|+.|+.--
T Consensus 4 ~lv~~ivk~LVd~Pe~V~V~~~~~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv 60 (77)
T PRK02821 4 DAVEHLVRGIVDNPDDVRVDSHTNRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVV 60 (77)
T ss_pred HHHHHHHHHhCCCCCeEEEEEEECCCcEEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence 4444555555543332 23445789999999999999999999999999763
No 72
>PRK00106 hypothetical protein; Provisional
Probab=95.07 E-value=0.062 Score=60.27 Aligned_cols=65 Identities=18% Similarity=0.396 Sum_probs=54.6
Q ss_pred eEEEEecCCC-cCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEEEEEc-CHHHHHHHHHHHHHHHhcc
Q 045766 590 RVPVVVPRSL-VPIIQGEDGACLKQIRQISDAKITITDPKPGATETVIIISG-TPEQTHAAQSLIQAFVMSE 659 (663)
Q Consensus 590 ~~~v~IP~~~-vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~IsG-t~e~v~~A~~lI~~~v~~~ 659 (663)
.-.|.+|++- -|+||||-|.||+.+...||+.|.|++. ...|+||| .|---+-|+..|+.+|..+
T Consensus 226 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt-----p~~v~lS~fdpvRReiAr~~le~Li~dg 292 (535)
T PRK00106 226 ITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDT-----PEVVVLSGFDPIRREIARMTLESLIKDG 292 (535)
T ss_pred eeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCC-----CCeEEEeCCChHHHHHHHHHHHHHHHcC
Confidence 3458999954 6999999999999999999999999764 35788999 7888888888888877654
No 73
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=95.04 E-value=0.031 Score=57.41 Aligned_cols=69 Identities=19% Similarity=0.300 Sum_probs=56.6
Q ss_pred eEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEEEEEcCHHHHHHHHHHHHHHHhcc
Q 045766 590 RVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITDPKPGATETVIIISGTPEQTHAAQSLIQAFVMSE 659 (663)
Q Consensus 590 ~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~IsGt~e~v~~A~~lI~~~v~~~ 659 (663)
...+.|+..+.|.|||+.|.+.+.|+++|+++|.+|.|... .+.++.+-+..++|.+|...|.-+|.+.
T Consensus 58 ~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n-~~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 58 SSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTN-KEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred hhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCC-cceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 34589999999999999999999999999999999987532 2334444556889999999998887654
No 74
>PRK12704 phosphodiesterase; Provisional
Probab=95.01 E-value=0.057 Score=60.88 Aligned_cols=63 Identities=21% Similarity=0.394 Sum_probs=51.9
Q ss_pred EEEEecCCC-cCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 045766 591 VPVVVPRSL-VPIIQGEDGACLKQIRQISDAKITITDPKPGATETVIIISG-TPEQTHAAQSLIQAFVMS 658 (663)
Q Consensus 591 ~~v~IP~~~-vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~IsG-t~e~v~~A~~lI~~~v~~ 658 (663)
-.|.+|++- -|+||||.|.||+.+...||+.|.|++. ...|+||| .|---+.|+..|+.++..
T Consensus 212 ~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt-----p~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 212 SVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT-----PEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred eeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC-----CCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 358899855 6999999999999999999999999764 45899999 677767888887776653
No 75
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.00 E-value=0.058 Score=43.82 Aligned_cols=50 Identities=30% Similarity=0.427 Sum_probs=37.3
Q ss_pred HHHHHHHHHHhhcCCC------CCCcceEEEEEecccceeEEEcCCchHHHHHHHH
Q 045766 381 DAVLRVQTRIARAIPD------NREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKL 430 (663)
Q Consensus 381 ~ai~~i~~~i~~~~~~------~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~ 430 (663)
+.+..+.+.+.+...+ ..+....++|.+.+...|+||||+|.+|+.|+.-
T Consensus 3 ~lv~~ivk~lVd~Pd~v~V~~~~~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 3 ELVEFIVKPLVDNPDDVRVDEEEGEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred hHHHHHHHHhcCCccceEEEEEecCCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 3445555555544332 2356788999999999999999999999999965
No 76
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=94.97 E-value=0.097 Score=58.95 Aligned_cols=85 Identities=19% Similarity=0.343 Sum_probs=59.0
Q ss_pred HHHHHHHHHHHHhhcCCCCCCcceEEEEEecc-cceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEE
Q 045766 379 PQDAVLRVQTRIARAIPDNREQTVMTRLLVAS-NQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLIN 457 (663)
Q Consensus 379 a~~ai~~i~~~i~~~~~~~~~~~~~~~l~Vp~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~ 457 (663)
|+.-|...++++... ......+..+.+|+ ++-|+|||+.|.+|+-+...||+.|.| |+.| ..|+|+
T Consensus 184 a~~i~~~aiqr~a~~---~~~e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~ii---ddtp-------~~v~ls 250 (514)
T TIGR03319 184 AKEILATAIQRYAGD---HVAETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLII---DDTP-------EAVILS 250 (514)
T ss_pred HHHHHHHHHHhccch---hhhhheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEE---cCCC-------CeEEec
Confidence 334444444444322 22234566778888 566999999999999999999999999 3323 457788
Q ss_pred e-cHHHHHHHHHHHHHHHhh
Q 045766 458 G-EFEAVQEALFQITTRLRH 476 (663)
Q Consensus 458 G-~~~~v~~A~~~I~~~l~~ 476 (663)
| +|---+-|+..+..++.+
T Consensus 251 ~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 251 GFDPVRREIARMALEKLIQD 270 (514)
T ss_pred CCchHHHHHHHHHHHHHHHc
Confidence 8 666667777777777654
No 77
>PRK12704 phosphodiesterase; Provisional
Probab=94.89 E-value=0.1 Score=58.84 Aligned_cols=85 Identities=19% Similarity=0.345 Sum_probs=58.3
Q ss_pred HHHHHHHHHHHHhhcCCCCCCcceEEEEEecc-cceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEE
Q 045766 379 PQDAVLRVQTRIARAIPDNREQTVMTRLLVAS-NQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLIN 457 (663)
Q Consensus 379 a~~ai~~i~~~i~~~~~~~~~~~~~~~l~Vp~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~ 457 (663)
|+.-|...++++... ......+..+.+|+ ++-|+|||+.|.+|+-+...||+.|.| |+.| ..|.|+
T Consensus 190 a~~i~~~a~qr~a~~---~~~e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~ii---ddtp-------~~v~ls 256 (520)
T PRK12704 190 AKEILAQAIQRCAAD---HVAETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLII---DDTP-------EAVILS 256 (520)
T ss_pred HHHHHHHHHHhhcch---hhhhhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEE---cCCC-------CeEEEe
Confidence 444444445554322 12234556677887 566999999999999999999999999 3223 468888
Q ss_pred e-cHHHHHHHHHHHHHHHhh
Q 045766 458 G-EFEAVQEALFQITTRLRH 476 (663)
Q Consensus 458 G-~~~~v~~A~~~I~~~l~~ 476 (663)
| ++-.-+.|+..+..++.+
T Consensus 257 ~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 257 GFDPIRREIARLALEKLVQD 276 (520)
T ss_pred cCChhhHHHHHHHHHHHHhc
Confidence 8 565656677766666654
No 78
>PRK01064 hypothetical protein; Provisional
Probab=94.61 E-value=0.09 Score=43.17 Aligned_cols=50 Identities=24% Similarity=0.382 Sum_probs=36.5
Q ss_pred HHHHHHHHHhhcCCC------CCCcceEEEEEecccceeEEEcCCchHHHHHHHHh
Q 045766 382 AVLRVQTRIARAIPD------NREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLS 431 (663)
Q Consensus 382 ai~~i~~~i~~~~~~------~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~t 431 (663)
.+..+.+.+.+...+ ..+....+++.|..+..|.+|||+|.+|+.|+.-.
T Consensus 4 Lv~~iv~~LVd~Pe~V~V~~~~~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 4 FLAYIVKNLVDRPEEVHIKEVQGTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred HHHHHHHHhcCCCCeEEEEEEeCCCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 444455555543332 23556788999999999999999999999998753
No 79
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=94.50 E-value=0.14 Score=54.93 Aligned_cols=92 Identities=20% Similarity=0.333 Sum_probs=63.5
Q ss_pred cccceeeccCchhHHhHHhHh-CCeEEEeccCCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHH--Hhh-cCCCCCCcc
Q 045766 326 ERVGGVIGKGGAIIRSLKQET-GCDIKVMEAVSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTR--IAR-AIPDNREQT 401 (663)
Q Consensus 326 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~--i~~-~~~~~~~~~ 401 (663)
+-+|..||++|.+|+.|.++. |-+|.+-.-..+.. +-+..++.- +.. ... .+..
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~--------------------~fi~nal~Pa~v~~v~i~--~~~~ 302 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPA--------------------EFVANALSPAKVVSVEVD--DEEE 302 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCCCHH--------------------HHHHHhCCCceEEEEEEE--cCCC
Confidence 458999999999999999998 88888753221110 111110000 000 000 1123
Q ss_pred eEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEec
Q 045766 402 VMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILG 439 (663)
Q Consensus 402 ~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~ 439 (663)
....+.||.++.+..|||+|.+++.-.+.||.+|.|.+
T Consensus 303 ~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 303 KAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred cEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 56789999999999999999999999999999999944
No 80
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=94.48 E-value=0.06 Score=52.15 Aligned_cols=37 Identities=24% Similarity=0.367 Sum_probs=34.4
Q ss_pred eEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeC
Q 045766 590 RVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITD 626 (663)
Q Consensus 590 ~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~ 626 (663)
...+.||.+..+.+|||+|.|++-+++.||-+|.|..
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 5678999999999999999999999999999999964
No 81
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=94.47 E-value=0.045 Score=52.31 Aligned_cols=30 Identities=40% Similarity=0.620 Sum_probs=27.9
Q ss_pred CCCcCeeecCCChhHHHHHHHcCCEEEEeC
Q 045766 597 RSLVPIIQGEDGACLKQIRQISDAKITITD 626 (663)
Q Consensus 597 ~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~ 626 (663)
.+|||.|||..|.++++|++.|+|+|.|-.
T Consensus 162 ~NFVGLliGPRG~Tlk~le~~s~akIaIRG 191 (269)
T COG5176 162 SNFVGLLIGPRGSTLKQLERISRAKIAIRG 191 (269)
T ss_pred cceeEEEecCCcchHHHHHHHhCCeEEEec
Confidence 378999999999999999999999999964
No 82
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=94.32 E-value=0.031 Score=53.39 Aligned_cols=43 Identities=19% Similarity=0.337 Sum_probs=37.3
Q ss_pred CCCceEEEEEeec------cceeeeecCCCccccchhhccCCeEEEcCC
Q 045766 42 FPGGIMFRVLCPV------SKIDGVIGKDGEMMSQISQDTGVTIRVEET 84 (663)
Q Consensus 42 ~~~~~~~rilvp~------~~vg~IIGk~G~~I~~i~~etga~I~v~~~ 84 (663)
.+..+.-++.||. ++||+|||..|.|+++|++.|+|+|-|.-.
T Consensus 144 rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 144 RPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred CcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 3567778888885 679999999999999999999999999763
No 83
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=94.21 E-value=0.013 Score=68.24 Aligned_cols=66 Identities=18% Similarity=0.132 Sum_probs=58.4
Q ss_pred EEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeC-CCCCCcceEEEEEcCHHHHHHHHHHHHHHH
Q 045766 591 VPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITD-PKPGATETVIIISGTPEQTHAAQSLIQAFV 656 (663)
Q Consensus 591 ~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~-~~~~~~~r~v~IsGt~e~v~~A~~lI~~~v 656 (663)
-++.+|.....+|||+||+||+.+|..|||-|+|.+ ......+|.+++.|+++.+.-|..+|...+
T Consensus 1342 ~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i 1408 (2131)
T KOG4369|consen 1342 GKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPI 1408 (2131)
T ss_pred cccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhcccccee
Confidence 348999999999999999999999999999999998 444467899999999999999998886544
No 84
>PRK00468 hypothetical protein; Provisional
Probab=94.17 E-value=0.053 Score=44.20 Aligned_cols=33 Identities=27% Similarity=0.472 Sum_probs=29.4
Q ss_pred CcceEEEEEeeccccceeeccCchhHHhHHhHh
Q 045766 314 PEILTFRLLCHDERVGGVIGKGGAIIRSLKQET 346 (663)
Q Consensus 314 ~~~~~~~v~vp~~~vg~IIGk~G~~Ik~I~~~t 346 (663)
...+.+++.+..+.+|.||||+|.+|+.||.--
T Consensus 27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 356789999999999999999999999999764
No 85
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=94.11 E-value=0.12 Score=56.01 Aligned_cols=90 Identities=22% Similarity=0.352 Sum_probs=62.0
Q ss_pred cccceeeccCchhHHhHHhHh-CCeEEEeccCCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHH--Hhhc-CCCCCCcc
Q 045766 326 ERVGGVIGKGGAIIRSLKQET-GCDIKVMEAVSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTR--IARA-IPDNREQT 401 (663)
Q Consensus 326 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~--i~~~-~~~~~~~~ 401 (663)
+-+|..||++|++|+.|.++. |-+|.|-.-..+.. .-|..++.- +..- .. .+..
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp~--------------------~fI~NaLsPA~V~~V~i~--~~~~ 334 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDPA--------------------TYIANALSPARVDEVRLV--DPEG 334 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCHH--------------------HHHHHhcCCceeeEEEEE--cCCC
Confidence 458999999999999999998 77888753221110 111110000 0000 00 1112
Q ss_pred eEEEEEecccceeEEEcCCchHHHHHHHHhCceEEE
Q 045766 402 VMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRI 437 (663)
Q Consensus 402 ~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i 437 (663)
....+.||.++.+..|||+|.+++.-...||-+|.|
T Consensus 335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI 370 (449)
T PRK12329 335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDI 370 (449)
T ss_pred cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecc
Confidence 456899999999999999999999999999999999
No 86
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=93.98 E-value=0.11 Score=57.49 Aligned_cols=92 Identities=22% Similarity=0.350 Sum_probs=63.7
Q ss_pred cccceeeccCchhHHhHHhHh-CCeEEEeccCCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHHHhhcC-CC--CCCcc
Q 045766 326 ERVGGVIGKGGAIIRSLKQET-GCDIKVMEAVSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTRIARAI-PD--NREQT 401 (663)
Q Consensus 326 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~i~~~~-~~--~~~~~ 401 (663)
+-+|..||++|++|+.|.++. |-+|.|-.-.++.. .- +...+.... .+ ..+..
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~--------------------~f---i~nal~pa~v~~v~~~~~~ 301 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPA--------------------QF---IINALSPAEVSSVVVDEDE 301 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEEcCCCHH--------------------HH---HHHhCCCCEEEEEEEeCCC
Confidence 348999999999999999998 78888753211110 01 111111000 00 01112
Q ss_pred eEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecC
Q 045766 402 VMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGK 440 (663)
Q Consensus 402 ~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~ 440 (663)
....+.||..+.+..|||+|.+++...+.||.+|.|...
T Consensus 302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 478899999999999999999999999999999999653
No 87
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=93.75 E-value=0.53 Score=50.26 Aligned_cols=38 Identities=11% Similarity=0.244 Sum_probs=35.4
Q ss_pred ceEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeC
Q 045766 589 RRVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITD 626 (663)
Q Consensus 589 ~~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~ 626 (663)
....+.||.+..+..|||+|+|++-.++.||.+|.|-.
T Consensus 308 ~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s 345 (374)
T PRK12328 308 KKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNE 345 (374)
T ss_pred cEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEE
Confidence 45779999999999999999999999999999999974
No 88
>PRK02821 hypothetical protein; Provisional
Probab=93.55 E-value=0.075 Score=43.49 Aligned_cols=33 Identities=27% Similarity=0.479 Sum_probs=29.2
Q ss_pred cceEEEEEeeccccceeeccCchhHHhHHhHhC
Q 045766 315 EILTFRLLCHDERVGGVIGKGGAIIRSLKQETG 347 (663)
Q Consensus 315 ~~~~~~v~vp~~~vg~IIGk~G~~Ik~I~~~tg 347 (663)
....+.+.|..+.+|.||||+|.+|+.|+.--.
T Consensus 29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 457889999999999999999999999998754
No 89
>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=93.40 E-value=0.16 Score=54.07 Aligned_cols=38 Identities=18% Similarity=0.382 Sum_probs=35.2
Q ss_pred ceEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeC
Q 045766 589 RRVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITD 626 (663)
Q Consensus 589 ~~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~ 626 (663)
....+.||.+..+..|||+|+|++-.++.||.+|.|-.
T Consensus 301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 45789999999999999999999999999999999963
No 90
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=93.29 E-value=0.058 Score=63.11 Aligned_cols=63 Identities=24% Similarity=0.389 Sum_probs=54.0
Q ss_pred ceEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEEEEEc-CHHHHHHHHHHHHHHHh
Q 045766 589 RRVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITDPKPGATETVIIISG-TPEQTHAAQSLIQAFVM 657 (663)
Q Consensus 589 ~~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~IsG-t~e~v~~A~~lI~~~v~ 657 (663)
....+.||.+.++.+||.||.+|+.|.++||++|.+.+ +-.|.|.+ ..+.+++|+.+|+.++.
T Consensus 554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d------~G~v~i~~~~~~~~~~a~~~I~~~~~ 617 (693)
T PRK11824 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED------DGTVKIAATDGEAAEAAKERIEGITA 617 (693)
T ss_pred hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC------CceEEEEcccHHHHHHHHHHHHHhcc
Confidence 34568889999999999999999999999999988843 24688888 48899999999998775
No 91
>PRK01064 hypothetical protein; Provisional
Probab=93.25 E-value=0.07 Score=43.80 Aligned_cols=32 Identities=22% Similarity=0.426 Sum_probs=29.1
Q ss_pred CCceEEEEEeeccceeeeecCCCccccchhhc
Q 045766 43 PGGIMFRVLCPVSKIDGVIGKDGEMMSQISQD 74 (663)
Q Consensus 43 ~~~~~~rilvp~~~vg~IIGk~G~~I~~i~~e 74 (663)
...+.+++-|...-.|.+|||+|.+|+.||.-
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 35689999999999999999999999999985
No 92
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=93.22 E-value=0.097 Score=42.56 Aligned_cols=33 Identities=30% Similarity=0.467 Sum_probs=29.5
Q ss_pred CcceEEEEEeeccccceeeccCchhHHhHHhHh
Q 045766 314 PEILTFRLLCHDERVGGVIGKGGAIIRSLKQET 346 (663)
Q Consensus 314 ~~~~~~~v~vp~~~vg~IIGk~G~~Ik~I~~~t 346 (663)
.....+++.+..+..|.||||+|.+|+.|+.--
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 467789999999999999999999999999753
No 93
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=92.68 E-value=0.12 Score=55.96 Aligned_cols=30 Identities=20% Similarity=0.350 Sum_probs=26.7
Q ss_pred cceeeeecCCCccccchhhcc-CCeEEEcCC
Q 045766 55 SKIDGVIGKDGEMMSQISQDT-GVTIRVEET 84 (663)
Q Consensus 55 ~~vg~IIGk~G~~I~~i~~et-ga~I~v~~~ 84 (663)
+-+|..||++|+.|+.|.++. |=+|+|-.-
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~y 307 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRW 307 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEc
Confidence 569999999999999999998 888888764
No 94
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=92.40 E-value=0.21 Score=54.80 Aligned_cols=88 Identities=20% Similarity=0.298 Sum_probs=66.5
Q ss_pred hHHHHHHHHHHHHhhcCCC-----CCCcceEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCc
Q 045766 378 APQDAVLRVQTRIARAIPD-----NREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEE 452 (663)
Q Consensus 378 ~a~~ai~~i~~~i~~~~~~-----~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~ 452 (663)
+|.++-..|++.+...++. ....++...+.|+.+....+||.+|...|+|..+||+.-.+ ++.
T Consensus 568 ~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~ 635 (760)
T KOG1067|consen 568 KAREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEG 635 (760)
T ss_pred hhhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCc
Confidence 3445555555555544432 34567889999999999999999999999999999966666 345
Q ss_pred EEEEEe-cHHHHHHHHHHHHHHHhhc
Q 045766 453 VVLING-EFEAVQEALFQITTRLRHH 477 (663)
Q Consensus 453 ~v~I~G-~~~~v~~A~~~I~~~l~~~ 477 (663)
.++|-- ++.+.++|+..|..++...
T Consensus 636 t~~i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 636 TFSIFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred eEEEEecCHHHHHHHHHHHHHHhcCc
Confidence 677665 5778899999999988763
No 95
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=92.37 E-value=0.84 Score=50.76 Aligned_cols=38 Identities=24% Similarity=0.421 Sum_probs=35.5
Q ss_pred ceEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeC
Q 045766 589 RRVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITD 626 (663)
Q Consensus 589 ~~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~ 626 (663)
..+.+.||....+..|||+|+|++-.++.||.+|.|-.
T Consensus 302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 46789999999999999999999999999999999975
No 96
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=92.14 E-value=0.18 Score=54.05 Aligned_cols=31 Identities=23% Similarity=0.265 Sum_probs=27.2
Q ss_pred eEEEEEEcCCceeEEecCcchhhhcccCCCC
Q 045766 187 FVLRLLVLSTQVGCLLGKGGCVIKQIDKLPT 217 (663)
Q Consensus 187 ~~~~llVP~~~vG~IIGkgG~~Ik~I~~~p~ 217 (663)
..+.+.||..+.+.-|||+|.+++--..+..
T Consensus 303 ~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~ 333 (362)
T PRK12327 303 KAARVVVPDYQLSLAIGKEGQNARLAARLTG 333 (362)
T ss_pred cEEEEEEChhhcchhhcCCChhHHHHHHHHC
Confidence 4688999999999999999999998866655
No 97
>PRK12705 hypothetical protein; Provisional
Probab=88.80 E-value=0.89 Score=50.90 Aligned_cols=56 Identities=21% Similarity=0.356 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHHhhcCCCCCCcceEEEEEeccc-ceeEEEcCCchHHHHHHHHhCceEEE
Q 045766 379 PQDAVLRVQTRIARAIPDNREQTVMTRLLVASN-QIGCLLGKGGSIIAEMRKLSGAYIRI 437 (663)
Q Consensus 379 a~~ai~~i~~~i~~~~~~~~~~~~~~~l~Vp~~-~vg~IIGk~G~~Ik~I~~~tGa~I~i 437 (663)
|+.-|...++++.... .....+..+.+|++ +-|+|||+.|.+||.+...||+.+.|
T Consensus 178 A~~ii~~aiqr~a~~~---~~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdlii 234 (508)
T PRK12705 178 AQNILAQAMQRIASET---ASDLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLII 234 (508)
T ss_pred HHHHHHHHHHHhccch---hhhheeeeeecCChHhhccccCccchhHHHHHHhhCCceEe
Confidence 4455555555544321 22335556777874 56999999999999999999999999
No 98
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=88.35 E-value=0.15 Score=41.34 Aligned_cols=33 Identities=18% Similarity=0.204 Sum_probs=28.0
Q ss_pred CceEEEEEeeccceeeeecCCCccccchhhccC
Q 045766 44 GGIMFRVLCPVSKIDGVIGKDGEMMSQISQDTG 76 (663)
Q Consensus 44 ~~~~~rilvp~~~vg~IIGk~G~~I~~i~~etg 76 (663)
+...+.+-|..+..|.||||+|.|++.||.-.+
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 455778888999999999999999999986543
No 99
>PRK12705 hypothetical protein; Provisional
Probab=88.35 E-value=0.49 Score=52.88 Aligned_cols=64 Identities=17% Similarity=0.334 Sum_probs=47.3
Q ss_pred EEEEecCCC-cCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEEEEEcC-HHHHHHHHHHHHHHHhcc
Q 045766 591 VPVVVPRSL-VPIIQGEDGACLKQIRQISDAKITITDPKPGATETVIIISGT-PEQTHAAQSLIQAFVMSE 659 (663)
Q Consensus 591 ~~v~IP~~~-vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~IsGt-~e~v~~A~~lI~~~v~~~ 659 (663)
-.|.+|++- -|+||||-|.||+.+...||+.|.|++. ...|+|++- |.--+.|...+..+|..+
T Consensus 200 s~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt-----p~~V~ls~fdp~rreia~~~l~~Li~dg 265 (508)
T PRK12705 200 SVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT-----PEAVVISSFNPIRREIARLTLEKLLADG 265 (508)
T ss_pred eeeecCChHhhccccCccchhHHHHHHhhCCceEecCC-----ccchhhcccCccchHHHHHHHHHHHhcC
Confidence 347888855 5999999999999999999999999764 234666664 555555666666655443
No 100
>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=87.32 E-value=0.49 Score=37.14 Aligned_cols=35 Identities=17% Similarity=0.209 Sum_probs=27.8
Q ss_pred ceEEEEEeeccceeeeecCCCccccchhhccCCeE
Q 045766 45 GIMFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTI 79 (663)
Q Consensus 45 ~~~~rilvp~~~vg~IIGk~G~~I~~i~~etga~I 79 (663)
.....+.+.....|.+|||+|.+++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 34555666666789999999999999999988544
No 101
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=86.28 E-value=0.4 Score=38.50 Aligned_cols=38 Identities=29% Similarity=0.412 Sum_probs=29.7
Q ss_pred EEEEEeeccc-----eeeeecCCCccccchhhcc-CCeEEEcCC
Q 045766 47 MFRVLCPVSK-----IDGVIGKDGEMMSQISQDT-GVTIRVEET 84 (663)
Q Consensus 47 ~~rilvp~~~-----vg~IIGk~G~~I~~i~~et-ga~I~v~~~ 84 (663)
...+.|-+.. +|..||++|..|+.|.++. |-+|+|-+-
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~ 47 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY 47 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence 3456666666 9999999999999999999 999988764
No 102
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=84.86 E-value=1.2 Score=48.48 Aligned_cols=129 Identities=12% Similarity=0.079 Sum_probs=84.4
Q ss_pred ceeeccCchhHHhHHhHhCCeEEEeccCCCCCceEEE-EeCCCCCCCCCChHHHHHHHHHHHHhhcCCCCCCcceEEEEE
Q 045766 329 GGVIGKGGAIIRSLKQETGCDIKVMEAVSGTEDRLIV-ISGPAHPDDRISAPQDAVLRVQTRIARAIPDNREQTVMTRLL 407 (663)
Q Consensus 329 g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~v~-I~G~~~~~~~v~~a~~ai~~i~~~i~~~~~~~~~~~~~~~l~ 407 (663)
-.|-||+.-.+.+|++...|.+.+.=... ...++.+ +.|.. -+..+.++.+. .+-+....+.
T Consensus 392 dFl~gkkngK~TrIm~~v~c~~~~~i~~~-~gs~~~~~~~g~~----------~~F~k~~~~~~------~EFpae~~f~ 454 (657)
T COG5166 392 DFLRGKKNGKATRIMKGVSCSELSSIVSS-TGSIVETNGIGEK----------MSFSKKLSIPP------TEFPAEIAFI 454 (657)
T ss_pred HHhccccCcchhhhhhhcccceeeEEEec-CCcEEEEeccCcc----------hhhHHHhcCCc------ccCchheEEE
Confidence 37888887779999999999865541111 1123322 34433 22222222222 3445678899
Q ss_pred ecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEec---HHHHHHHHHHHHHHHhh
Q 045766 408 VASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGE---FEAVQEALFQITTRLRH 476 (663)
Q Consensus 408 Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~---~~~v~~A~~~I~~~l~~ 476 (663)
||...|..|||-||..|++++.+.++.|++...-.+|.. .....|.|.-+ ..++.-++--+.+++.+
T Consensus 455 i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs--~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~ 524 (657)
T COG5166 455 IMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQS--QWHDNVLIEAPRKNQDNISGKKNDKLDKVKQ 524 (657)
T ss_pred eecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchh--hhhcceEEECCccCccchhcccccHHHHHhh
Confidence 999999999999999999999999999999655555542 22233666654 34566677777777775
No 103
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=84.76 E-value=0.45 Score=38.57 Aligned_cols=34 Identities=24% Similarity=0.284 Sum_probs=28.8
Q ss_pred cceEEEEEeeccccceeeccCchhHHhHHhHhCC
Q 045766 315 EILTFRLLCHDERVGGVIGKGGAIIRSLKQETGC 348 (663)
Q Consensus 315 ~~~~~~v~vp~~~vg~IIGk~G~~Ik~I~~~tga 348 (663)
+...+.+.+..+..|.||||+|.+++.|+.-.+.
T Consensus 27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred CceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 4557888899999999999999999999876543
No 104
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=84.70 E-value=1.5 Score=44.04 Aligned_cols=51 Identities=22% Similarity=0.401 Sum_probs=45.6
Q ss_pred eEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHHHHHHhh
Q 045766 414 GCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQEALFQITTRLRH 476 (663)
Q Consensus 414 g~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~ 476 (663)
.++||.+|.+++.|+-.|.|.|-| .-.+|.+.|....+..+.+.|.+.+.+
T Consensus 161 qRLiGpng~TLKAlelLT~CYilV------------qG~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILV------------QGNTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEe------------eCcEEEeecCcchHHHHHHHHHHHHhc
Confidence 479999999999999999999999 134699999999999999999988876
No 105
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=83.37 E-value=0.7 Score=44.17 Aligned_cols=56 Identities=18% Similarity=0.329 Sum_probs=50.3
Q ss_pred CCCcCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEEEEEcCHHHHHHHHHHHHHHHhcc
Q 045766 597 RSLVPIIQGEDGACLKQIRQISDAKITITDPKPGATETVIIISGTPEQTHAAQSLIQAFVMSE 659 (663)
Q Consensus 597 ~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~IsGt~e~v~~A~~lI~~~v~~~ 659 (663)
...+|+|+||+|.+--.|...|.++|.+.+. .|-|-|+.+++..|+..|..+|...
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad~-------kIHiLG~~~niriAR~avcsLIlGs 232 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLADS-------KIHILGAFQNIRIARDAVCSLILGS 232 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecCc-------eEEEeecchhhHHHHHhhHhhhccC
Confidence 4678999999999999999999999999754 7999999999999999999888643
No 106
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=83.36 E-value=0.65 Score=44.39 Aligned_cols=56 Identities=21% Similarity=0.337 Sum_probs=49.5
Q ss_pred ccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHHHHHHhhc
Q 045766 410 SNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQEALFQITTRLRHH 477 (663)
Q Consensus 410 ~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~ 477 (663)
+..+|+|+|++|.+--.|...|-++|.+ .+..|.|-|..+++.-|...|+.++...
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVl------------ad~kIHiLG~~~niriAR~avcsLIlGs 232 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVL------------ADSKIHILGAFQNIRIARDAVCSLILGS 232 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEe------------cCceEEEeecchhhHHHHHhhHhhhccC
Confidence 3468999999999999999999999999 2456999999999999999999998663
No 107
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=82.33 E-value=2.7 Score=41.88 Aligned_cols=60 Identities=27% Similarity=0.430 Sum_probs=45.4
Q ss_pred EEEeeccccceeeccCchhHHhHHhHhCCeEEEeccCCCCCceEEEEeCCCCCCCCCChHHHHHHHHH
Q 045766 320 RLLCHDERVGGVIGKGGAIIRSLKQETGCDIKVMEAVSGTEDRLIVISGPAHPDDRISAPQDAVLRVQ 387 (663)
Q Consensus 320 ~v~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~ 387 (663)
-+.|+...+.++||++|+.++.|.+.++|+|-+-.+ -.|-|.|..+ .....|..||..+-
T Consensus 149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N------G~IWV~~~~~--~~e~~~~~aI~~ie 208 (239)
T COG1097 149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN------GRIWVDGENE--SLEELAIEAIRKIE 208 (239)
T ss_pred EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC------CEEEecCCCc--chHHHHHHHHHHHh
Confidence 377899999999999999999999999999999432 2588888762 12334555555543
No 108
>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=82.13 E-value=2.4 Score=33.07 Aligned_cols=34 Identities=29% Similarity=0.446 Sum_probs=27.3
Q ss_pred eEEEEEecccceeEEEcCCchHHHHHHHHhCceE
Q 045766 402 VMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYI 435 (663)
Q Consensus 402 ~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I 435 (663)
....+.+.....|.+||++|.+++.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 5556666666789999999999999999988443
No 109
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=82.12 E-value=3 Score=41.60 Aligned_cols=60 Identities=18% Similarity=0.320 Sum_probs=46.6
Q ss_pred EEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHH-HHHHHHHHHHHH
Q 045766 404 TRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEA-VQEALFQITTRL 474 (663)
Q Consensus 404 ~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~-v~~A~~~I~~~l 474 (663)
.-+.|++..+.++||++|+.++-+.+.++|.|.+ ..+..|=|.|..+. ...|...|..+=
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~V-----------G~NG~IWV~~~~~~~e~~~~~aI~~ie 208 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIV-----------GQNGRIWVDGENESLEELAIEAIRKIE 208 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEE-----------ecCCEEEecCCCcchHHHHHHHHHHHh
Confidence 3477889999999999999999999999999999 34567788887773 444554444443
No 110
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=81.83 E-value=1 Score=36.09 Aligned_cols=38 Identities=26% Similarity=0.308 Sum_probs=29.2
Q ss_pred eEEEEecCCC-----cCeeecCCChhHHHHHHHc-CCEEEEeCC
Q 045766 590 RVPVVVPRSL-----VPIIQGEDGACLKQIRQIS-DAKITITDP 627 (663)
Q Consensus 590 ~~~v~IP~~~-----vg~IIGkgG~~I~~I~~~s-Ga~I~i~~~ 627 (663)
+..+.|-... +|..||++|++|+.|+++. |-+|+|=.-
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~ 47 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY 47 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence 4556666666 8999999999999999999 899888643
No 111
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=81.68 E-value=0.43 Score=56.43 Aligned_cols=71 Identities=21% Similarity=0.163 Sum_probs=57.9
Q ss_pred eEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHHHHHHhh
Q 045766 402 VMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQEALFQITTRLRH 476 (663)
Q Consensus 402 ~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~ 476 (663)
...++.+|-....+|||++|.+|+.++..|||.|.+ .+-+ |+ +..+|.+.+.|.++.+.-|.-.|...+.+
T Consensus 1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~iel-ekmq-~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIEL-EKMQ-PD--NQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred cccccccchhhhhhhhccCcchhhhHhhccceEEeh-hhcC-Cc--cchhhhcccCCCChhhhhhhccccceeec
Confidence 345678888889999999999999999999999999 3211 22 25689999999999999998877766655
No 112
>PRK13764 ATPase; Provisional
Probab=81.27 E-value=2.2 Score=48.99 Aligned_cols=67 Identities=21% Similarity=0.249 Sum_probs=47.5
Q ss_pred hHHHHHHHHHHHHhhcCCC-CCCcceEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCC
Q 045766 378 APQDAVLRVQTRIARAIPD-NREQTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIP 444 (663)
Q Consensus 378 ~a~~ai~~i~~~i~~~~~~-~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p 444 (663)
.|.+.|...+.++.....+ .........+.||..+++.+|||+|.+|++|.++.|.+|.|.+.++.+
T Consensus 456 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 456 LAEKEIEREIKRYLPGPVEVEVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred HHHHHHHHHHHHhcCCceEEEEecCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 3445555555554421111 112345677889999999999999999999999999999997666544
No 113
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=81.20 E-value=2.4 Score=46.32 Aligned_cols=121 Identities=21% Similarity=0.224 Sum_probs=84.4
Q ss_pred EEEEEeeccccceeeccCchhHHhHHhHhCCeEEEecc--CCCCCce-EEEEeCCCCCCCCCChHHHHHHHHHHHHhhc-
Q 045766 318 TFRLLCHDERVGGVIGKGGAIIRSLKQETGCDIKVMEA--VSGTEDR-LIVISGPAHPDDRISAPQDAVLRVQTRIARA- 393 (663)
Q Consensus 318 ~~~v~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~--~~~~~er-~v~I~G~~~~~~~v~~a~~ai~~i~~~i~~~- 393 (663)
.+.+.||...|..|||.||..|++++...++.|++... .+.+..+ -|.|..+....+++..++.-++.+++.-...
T Consensus 450 e~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~ 529 (657)
T COG5166 450 EIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQQCRFN 529 (657)
T ss_pred heEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHhhhcccc
Confidence 46688999999999999999999999999999999732 1223333 3888888755566666666666555432110
Q ss_pred -CCC-----------------------------CCCcceEEEEEecccceeEEEc---CCchHHHHHHHHhCceEEEe
Q 045766 394 -IPD-----------------------------NREQTVMTRLLVASNQIGCLLG---KGGSIIAEMRKLSGAYIRIL 438 (663)
Q Consensus 394 -~~~-----------------------------~~~~~~~~~l~Vp~~~vg~IIG---k~G~~Ik~I~~~tGa~I~i~ 438 (663)
-.+ -..-+....+.+|++.++.-+| -.|++|..+.....-.|...
T Consensus 530 ~Kgdirf~~~~~sI~~v~~~~~~I~rv~kne~v~~~~p~~~~~y~~se~h~~g~gena~R~~ni~~~t~~y~~~ie~~ 607 (657)
T COG5166 530 LKGDIRFCPQSTSIFTVDIYSDEIERVIKNETVLLEFPAEMHFYVPSEIHKKGIGENAFRGENIQRVTKLYNSYIEFS 607 (657)
T ss_pred cccceEEcCCceEEEEEcccccHHHHHhhccceEEecccccccccchhhhhccCCcccccccchhhhhhhhhccceee
Confidence 000 0112334556788888999999 67888888888877777773
No 114
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=80.51 E-value=1.7 Score=47.20 Aligned_cols=40 Identities=28% Similarity=0.316 Sum_probs=35.6
Q ss_pred eEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCC
Q 045766 402 VMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKD 441 (663)
Q Consensus 402 ~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~ 441 (663)
....+.||..+++.+|||+|.+|++|.++.|-+|.+.+.+
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 4567889999999999999999999999999999995543
No 115
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=79.25 E-value=1.4 Score=36.15 Aligned_cols=34 Identities=18% Similarity=0.255 Sum_probs=26.2
Q ss_pred EEEEEeeccceeeeecCCCccccchhhccCCeEE
Q 045766 47 MFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIR 80 (663)
Q Consensus 47 ~~rilvp~~~vg~IIGk~G~~I~~i~~etga~I~ 80 (663)
.+.+-+..+..|.||||+|+++..|+--++.-++
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 3445556788899999999999999877664444
No 116
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=78.76 E-value=7.3 Score=35.86 Aligned_cols=92 Identities=16% Similarity=0.348 Sum_probs=58.3
Q ss_pred eccCchhHHhHHhHhCCeEEEeccCCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHHHhhc--CCCCCCcceEEEEEec
Q 045766 332 IGKGGAIIRSLKQETGCDIKVMEAVSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTRIARA--IPDNREQTVMTRLLVA 409 (663)
Q Consensus 332 IGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~i~~~--~~~~~~~~~~~~l~Vp 409 (663)
+-.+|..|++|-++..-+|.|-.+ + +....-.+|...+.+.+-+. +.+-.=...+-++.|-
T Consensus 21 ~~~~~dli~~lAk~lrKRIvvR~d--------------p---s~l~~~e~A~~~I~~ivP~ea~i~di~Fd~~tGEV~Ie 83 (145)
T cd02410 21 FAEDGDLVKDLAKDLRKRIVIRPD--------------P---SVLKPPEEAIKIILEIVPEEAGITDIYFDDDTGEVIIE 83 (145)
T ss_pred HhcccHHHHHHHHHHhceEEEcCC--------------h---hhcCCHHHHHHHHHHhCCCccCceeeEecCCCcEEEEE
Confidence 345688999999988888887422 1 11111224444444333221 1111112234567777
Q ss_pred ccceeEEEcCCchHHHHHHHHhCceEEEecC
Q 045766 410 SNQIGCLLGKGGSIIAEMRKLSGAYIRILGK 440 (663)
Q Consensus 410 ~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~ 440 (663)
.+.-|.+||++|.++++|..+||-.-.+...
T Consensus 84 aeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 84 AEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred EcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 7889999999999999999999988888443
No 117
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=78.69 E-value=7.9 Score=43.06 Aligned_cols=92 Identities=17% Similarity=0.234 Sum_probs=66.5
Q ss_pred HHHHHHHHHhhhhccCCCcccccccCCCCCceEEEEEEcCCceeEEecCcchhhhcccCCCCC-CCCCccEEEEEc-CHH
Q 045766 156 VQKALLLVFERMVEVEPETEVADQENTKSSKFVLRLLVLSTQVGCLLGKGGCVIKQIDKLPTC-ALASDEVVQITG-EVD 233 (663)
Q Consensus 156 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~llVP~~~vG~IIGkgG~~Ik~I~~~p~~-~~~~dr~V~I~G-~~~ 233 (663)
|..|...+++.|.+.-...-. ......++...|.|+.+....+||.+|...|+|+.-... ..-+|.++.|.- ++.
T Consensus 569 a~~ar~~Il~~m~k~i~~Pr~---~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vDe~t~~i~A~~~~ 645 (760)
T KOG1067|consen 569 AREARLQILDIMEKNINSPRG---SDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVDEGTFSIFAPTQA 645 (760)
T ss_pred hhHHHHHHHHHHHhhcCCccc---CccccCceeeEEeecchhhheeecCccceeeeEeeeccceeeecCceEEEEecCHH
Confidence 345667788887753332111 112346788999999999999999999999999654432 234667888887 588
Q ss_pred HHHHHHHHHHHHHhcCC
Q 045766 234 TVRKALKLISHQLLDNS 250 (663)
Q Consensus 234 ~V~~A~~~I~~~l~~~~ 250 (663)
+.++|...|..++....
T Consensus 646 am~~Ak~~I~~i~~~~~ 662 (760)
T KOG1067|consen 646 AMEEAKEFIDGIIKDDQ 662 (760)
T ss_pred HHHHHHHHHHHHhcCcc
Confidence 99999999988887643
No 118
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=78.02 E-value=0.97 Score=48.98 Aligned_cols=38 Identities=32% Similarity=0.441 Sum_probs=34.7
Q ss_pred EEEEEeeccceeeeecCCCccccchhhccCCeEEEcCC
Q 045766 47 MFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEET 84 (663)
Q Consensus 47 ~~rilvp~~~vg~IIGk~G~~I~~i~~etga~I~v~~~ 84 (663)
...+.||.+.++.+|||+|.+|++|++..|.+|+|.+.
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 45678999999999999999999999999999999763
No 119
>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=77.67 E-value=0.59 Score=38.36 Aligned_cols=34 Identities=21% Similarity=0.308 Sum_probs=29.1
Q ss_pred EEEEEeeccceeeeecCCCccccchhhccCCeEE
Q 045766 47 MFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIR 80 (663)
Q Consensus 47 ~~rilvp~~~vg~IIGk~G~~I~~i~~etga~I~ 80 (663)
...+.+.....|.|||++|++|++|+++.+-.+.
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 4667888999999999999999999988766554
No 120
>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=77.38 E-value=1.4 Score=36.52 Aligned_cols=38 Identities=11% Similarity=0.267 Sum_probs=32.4
Q ss_pred EEEEEeeccceeeeecCCCccccchhhccCCeEEEcCC
Q 045766 47 MFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEET 84 (663)
Q Consensus 47 ~~rilvp~~~vg~IIGk~G~~I~~i~~etga~I~v~~~ 84 (663)
.+++.+....-|.|||++|++|++|+++-.-...+.++
T Consensus 31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~~ 68 (81)
T cd02413 31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPEG 68 (81)
T ss_pred eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCCC
Confidence 47888999999999999999999999987766666543
No 121
>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=75.47 E-value=3.1 Score=34.03 Aligned_cols=36 Identities=19% Similarity=0.397 Sum_probs=28.8
Q ss_pred eEEEEEecccceeEEEcCCchHHHHHHHHhCceEEE
Q 045766 402 VMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRI 437 (663)
Q Consensus 402 ~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i 437 (663)
..+.+.|..+..|.+|||+|++++.||--...-++-
T Consensus 24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~ 59 (77)
T cd02414 24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR 59 (77)
T ss_pred CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence 346677778889999999999999999776655443
No 122
>PRK13764 ATPase; Provisional
Probab=75.23 E-value=2.4 Score=48.64 Aligned_cols=40 Identities=23% Similarity=0.385 Sum_probs=36.3
Q ss_pred cceEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeCC
Q 045766 588 HRRVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITITDP 627 (663)
Q Consensus 588 ~~~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~ 627 (663)
..+..+.||..+++.+|||+|.+|++|.+..|..|.|...
T Consensus 480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~ 519 (602)
T PRK13764 480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL 519 (602)
T ss_pred CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence 3556799999999999999999999999999999999754
No 123
>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=73.39 E-value=1.5 Score=35.93 Aligned_cols=34 Identities=24% Similarity=0.424 Sum_probs=28.4
Q ss_pred ceEEEEecCCCcCeeecCCChhHHHHHHHcCCEE
Q 045766 589 RRVPVVVPRSLVPIIQGEDGACLKQIRQISDAKI 622 (663)
Q Consensus 589 ~~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I 622 (663)
....+.+-...-|.|||++|++|+.|++..+-.+
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 4567889999999999999999999997765443
No 124
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=72.40 E-value=2.5 Score=40.09 Aligned_cols=37 Identities=27% Similarity=0.413 Sum_probs=31.1
Q ss_pred EEEEEeeccceeeeecCCCccccchhhccCCeEEEcCC
Q 045766 47 MFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEET 84 (663)
Q Consensus 47 ~~rilvp~~~vg~IIGk~G~~I~~i~~etga~I~v~~~ 84 (663)
.+=++|-... |.-|||+|++|++|++..|-+|.|-+.
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 3445666666 999999999999999999999999764
No 125
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=69.07 E-value=4 Score=37.53 Aligned_cols=37 Identities=32% Similarity=0.411 Sum_probs=32.3
Q ss_pred EEEEeeccceeeeecCCCccccchhhccCCeEEEcCC
Q 045766 48 FRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEET 84 (663)
Q Consensus 48 ~rilvp~~~vg~IIGk~G~~I~~i~~etga~I~v~~~ 84 (663)
=.+.|-.++-|.+|||+|.+++.|..+||-+-.|.+.
T Consensus 78 GEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 78 GEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred cEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 3456667889999999999999999999999988765
No 126
>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=68.88 E-value=6.8 Score=32.49 Aligned_cols=37 Identities=11% Similarity=0.377 Sum_probs=29.8
Q ss_pred ceEEEEecCCCcCeeecCCChhHHHHHHHcCCEEEEe
Q 045766 589 RRVPVVVPRSLVPIIQGEDGACLKQIRQISDAKITIT 625 (663)
Q Consensus 589 ~~~~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~ 625 (663)
..+++.|-...-|.|||++|++|++|++.-.-...++
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~ 66 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP 66 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence 4577888889999999999999999998765444443
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=66.23 E-value=2.9 Score=36.82 Aligned_cols=31 Identities=16% Similarity=0.249 Sum_probs=26.7
Q ss_pred EEEEEeeccceeeeecCCCccccchhhccCC
Q 045766 47 MFRVLCPVSKIDGVIGKDGEMMSQISQDTGV 77 (663)
Q Consensus 47 ~~rilvp~~~vg~IIGk~G~~I~~i~~etga 77 (663)
.+++.+....-|.|||++|++|++|+++...
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 4678888899999999999999999987543
No 128
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=65.09 E-value=3.5 Score=40.94 Aligned_cols=32 Identities=22% Similarity=0.246 Sum_probs=27.6
Q ss_pred ceEEEEEeeccceeeeecCCCccccchhhccC
Q 045766 45 GIMFRVLCPVSKIDGVIGKDGEMMSQISQDTG 76 (663)
Q Consensus 45 ~~~~rilvp~~~vg~IIGk~G~~I~~i~~etg 76 (663)
....++.|....-|.||||+|++|++|+++..
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~ 81 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKELE 81 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHHH
Confidence 34678889999999999999999999988754
No 129
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=64.85 E-value=24 Score=39.09 Aligned_cols=94 Identities=18% Similarity=0.296 Sum_probs=63.0
Q ss_pred eeeccCchhHHhHHhHhCCeEEEeccCCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHHHhhcCC--CCCCcceEEEEE
Q 045766 330 GVIGKGGAIIRSLKQETGCDIKVMEAVSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTRIARAIP--DNREQTVMTRLL 407 (663)
Q Consensus 330 ~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~i~~~~~--~~~~~~~~~~l~ 407 (663)
.++-+.|..|++|.++..-+|.+..+. ......++|+..+.+-+-.+.. +-.-...+-++.
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~dP-----------------svl~~~e~A~~~I~eivP~ea~i~~i~Fd~~tGEVi 104 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPDP-----------------SVLKPPEEARKIILEIVPEEAGITDIYFDDDTGEVI 104 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccCc-----------------hhcCCHHHHHHHHHHhCccccCceeEEecCCCceEE
Confidence 345678999999999999888885321 1222334565555544422111 101122445777
Q ss_pred ecccceeEEEcCCchHHHHHHHHhCceEEEecC
Q 045766 408 VASNQIGCLLGKGGSIIAEMRKLSGAYIRILGK 440 (663)
Q Consensus 408 Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~ 440 (663)
|-.+.-|.+|||+|++.++|..+||-.-.+...
T Consensus 105 Iea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 105 IEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred EEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 888889999999999999999999988777443
No 130
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=63.51 E-value=11 Score=35.63 Aligned_cols=36 Identities=33% Similarity=0.495 Sum_probs=30.9
Q ss_pred EEEEEeeccccceeeccCchhHHhHHhHhCCeEEEec
Q 045766 318 TFRLLCHDERVGGVIGKGGAIIRSLKQETGCDIKVME 354 (663)
Q Consensus 318 ~~~v~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~ 354 (663)
.+-+.|.... |..||++|++|+++++..|-+|.+-+
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 4556676666 99999999999999999999999854
No 131
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=63.23 E-value=14 Score=37.38 Aligned_cols=50 Identities=12% Similarity=0.290 Sum_probs=44.6
Q ss_pred CeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEEEEEcCHHHHHHHHHHHHHHHh
Q 045766 601 PIIQGEDGACLKQIRQISDAKITITDPKPGATETVIIISGTPEQTHAAQSLIQAFVM 657 (663)
Q Consensus 601 g~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~IsGt~e~v~~A~~lI~~~v~ 657 (663)
-++||.+|++++.|.-.|.|.|-+.. .+|.+-|....++.+...+.+.+.
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG-------~TVsaiGpfkGlkevr~IV~DcM~ 210 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG-------NTVSAIGPFKGLKEVRKIVEDCMK 210 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC-------cEEEeecCcchHHHHHHHHHHHHh
Confidence 47999999999999999999999953 479999999999999998888764
No 132
>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=63.14 E-value=4.2 Score=33.99 Aligned_cols=28 Identities=14% Similarity=0.254 Sum_probs=24.1
Q ss_pred EEEEeeccceeeeecCCCccccchhhcc
Q 045766 48 FRVLCPVSKIDGVIGKDGEMMSQISQDT 75 (663)
Q Consensus 48 ~rilvp~~~vg~IIGk~G~~I~~i~~et 75 (663)
+++.+....-|.+||++|.+|++|++.-
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 6666777899999999999999998874
No 133
>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=56.27 E-value=13 Score=30.96 Aligned_cols=29 Identities=10% Similarity=0.283 Sum_probs=23.5
Q ss_pred eEEEEecCCCcCeeecCCChhHHHHHHHc
Q 045766 590 RVPVVVPRSLVPIIQGEDGACLKQIRQIS 618 (663)
Q Consensus 590 ~~~v~IP~~~vg~IIGkgG~~I~~I~~~s 618 (663)
.+.+.|-...-|.+||++|++|++|++.-
T Consensus 39 ~i~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 39 GTQITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred cEEEEEEECCCCceECCCchhHHHHHHHH
Confidence 35566666888999999999999998654
No 134
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=51.56 E-value=14 Score=32.53 Aligned_cols=30 Identities=30% Similarity=0.449 Sum_probs=25.4
Q ss_pred eEEEEecCCCcCeeecCCChhHHHHHHHcC
Q 045766 590 RVPVVVPRSLVPIIQGEDGACLKQIRQISD 619 (663)
Q Consensus 590 ~~~v~IP~~~vg~IIGkgG~~I~~I~~~sG 619 (663)
.+.+.|-...-|.|||+.|++|++|++...
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~ 91 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQ 91 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence 466888888899999999999999987643
No 135
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=50.42 E-value=47 Score=38.70 Aligned_cols=93 Identities=17% Similarity=0.359 Sum_probs=60.1
Q ss_pred eeccCchhHHhHHhHhCCeEEEeccCCCCCceEEEEeCCCCCCCCCChHHHHHHHHHHHHhhc--CCCCCCcceEEEEEe
Q 045766 331 VIGKGGAIIRSLKQETGCDIKVMEAVSGTEDRLIVISGPAHPDDRISAPQDAVLRVQTRIARA--IPDNREQTVMTRLLV 408 (663)
Q Consensus 331 IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~v~I~G~~~~~~~v~~a~~ai~~i~~~i~~~--~~~~~~~~~~~~l~V 408 (663)
.+-.+|..|++|-++..-+|.|-.. + +......+|...+.+.+-++ +.+-.=...+-++.|
T Consensus 37 ~~~~~~~~~~~~~~~~~~r~~~~~~--------------~---~~~~~~~~~~~~i~~~~~~~~~~~~~~f~~~~~~v~i 99 (630)
T TIGR03675 37 LFAKDDDLVKELAKKLRKRIVIRPD--------------P---SVLLPPEEAIEKIKEIVPEEAGITDIYFDDVTGEVII 99 (630)
T ss_pred HhccchHHHHHHHHHhhceEEEecC--------------h---hhcCCHHHHHHHHHHhCCCcCCceeEEecCCCceEEE
Confidence 4456789999999998888887422 1 11111224444443333221 111111234567778
Q ss_pred cccceeEEEcCCchHHHHHHHHhCceEEEecC
Q 045766 409 ASNQIGCLLGKGGSIIAEMRKLSGAYIRILGK 440 (663)
Q Consensus 409 p~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~ 440 (663)
-.+.-|.|||++|.++++|.++||-.-.+...
T Consensus 100 ~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 100 EAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred EEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 88889999999999999999999999888543
No 136
>PF09869 DUF2096: Uncharacterized protein conserved in archaea (DUF2096); InterPro: IPR017098 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=50.11 E-value=44 Score=31.50 Aligned_cols=56 Identities=18% Similarity=0.288 Sum_probs=43.1
Q ss_pred ceEEEEEecccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHHHHHH
Q 045766 401 TVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQEALFQITTRL 474 (663)
Q Consensus 401 ~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l 474 (663)
..++++.+|...+ =+.+++|.+-+|+-+.+ ..+..|.|-|..+.|.+|++.+....
T Consensus 112 ~~~iRv~l~~~i~-------~erl~ei~E~~gvI~Ef-----------ee~~~V~I~Gdke~Ik~aLKe~s~~w 167 (169)
T PF09869_consen 112 FETIRVKLKKPIQ-------EERLQEISEWHGVIFEF-----------EEDDKVVIEGDKERIKKALKEFSSFW 167 (169)
T ss_pred ceeEEEecCccch-------HHHHHHHHHHhceeEEe-----------cCCcEEEEeccHHHHHHHHHHHHHHh
Confidence 3455565555543 35788999999999999 34667999999999999999887653
No 137
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=49.11 E-value=17 Score=36.27 Aligned_cols=38 Identities=16% Similarity=0.406 Sum_probs=29.2
Q ss_pred ceEEEEecCCCcCeeecCCChhHHHHHH----HcCC---EEEEeC
Q 045766 589 RRVPVVVPRSLVPIIQGEDGACLKQIRQ----ISDA---KITITD 626 (663)
Q Consensus 589 ~~~~v~IP~~~vg~IIGkgG~~I~~I~~----~sGa---~I~i~~ 626 (663)
..+.|.|-...-|.|||++|++|++|++ .+|. +|.|.+
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~~v~I~i~E 95 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKENVQINIEE 95 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCCCceEEEEE
Confidence 4567888888999999999999999874 5565 344443
No 138
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=43.73 E-value=50 Score=35.07 Aligned_cols=54 Identities=11% Similarity=0.135 Sum_probs=45.8
Q ss_pred CCCcCeeecCCChhHHHHHHHcCCEEEEeCCCCCCcceEEEEEcCHHHHHHHHHHHH--HHHh
Q 045766 597 RSLVPIIQGEDGACLKQIRQISDAKITITDPKPGATETVIIISGTPEQTHAAQSLIQ--AFVM 657 (663)
Q Consensus 597 ~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~IsGt~e~v~~A~~lI~--~~v~ 657 (663)
.+..-.+.|..|.+++.|.+..|+.|... .+.++|+|+.+.|+.|...++ +.+.
T Consensus 23 ~~~~~~l~G~~~~~l~l~e~~~gv~i~~r-------G~~~~i~g~~~~v~~A~~~l~~l~~~~ 78 (348)
T COG1702 23 DNELVALFGPTDTNLSLLEIALGVSIVAR-------GEAVRIIGARPLVDVATRVLLTLELLA 78 (348)
T ss_pred chhhhhhcCCCCccHHHHHHHhCcEEEeC-------CceEEEEechHHHHHHHHHHhHHHHHH
Confidence 55678999999999999999999998873 357999999889999999888 5443
No 139
>COG1159 Era GTPase [General function prediction only]
Probab=38.94 E-value=24 Score=36.60 Aligned_cols=56 Identities=29% Similarity=0.431 Sum_probs=35.3
Q ss_pred CceEEEEEEcC-CceeEEecCcchhhhcc--------cCCCCCCCCCccEEEEEcCHHHHHHHHH
Q 045766 185 SKFVLRLLVLS-TQVGCLLGKGGCVIKQI--------DKLPTCALASDEVVQITGEVDTVRKALK 240 (663)
Q Consensus 185 ~~~~~~llVP~-~~vG~IIGkgG~~Ik~I--------~~~p~~~~~~dr~V~I~G~~~~V~~A~~ 240 (663)
..+...++|+. +|-|-||||+|++||+| +.+-.|...-+=.|.+.-.+..=..++.
T Consensus 227 ~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L~L~VKVk~~W~~~~~~l~ 291 (298)
T COG1159 227 LKIHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYLELWVKVKKNWRDDEEALR 291 (298)
T ss_pred EEEEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEEEEEEEEccccccCHHHHH
Confidence 34556677875 68899999999999999 2233333333445666655544444433
No 140
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=37.09 E-value=89 Score=28.70 Aligned_cols=43 Identities=23% Similarity=0.388 Sum_probs=35.9
Q ss_pred hHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHHHHHHh
Q 045766 422 SIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQEALFQITTRLR 475 (663)
Q Consensus 422 ~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~ 475 (663)
+.++.|.+-.|+-|.+ +.-..|.|-|+.+.|.+|++.|....+
T Consensus 126 eRlqDi~E~hgvIiE~-----------~E~D~V~i~Gd~drVk~aLke~~~~wk 168 (170)
T COG4010 126 ERLQDIAETHGVIIEF-----------EEYDLVAIYGDSDRVKKALKEIGSFWK 168 (170)
T ss_pred HHHHHHHHhhheeEEe-----------eeccEEEEeccHHHHHHHHHHHHHHHh
Confidence 5678888999999999 234579999999999999999887654
No 141
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=36.88 E-value=21 Score=36.69 Aligned_cols=30 Identities=27% Similarity=0.332 Sum_probs=24.1
Q ss_pred eEEEEEee-ccceeeeecCCCccccchhhcc
Q 045766 46 IMFRVLCP-VSKIDGVIGKDGEMMSQISQDT 75 (663)
Q Consensus 46 ~~~rilvp-~~~vg~IIGk~G~~I~~i~~et 75 (663)
+...|+|. .+.-+-||||+|+.||+|..+.
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 56667777 5778999999999999886553
No 142
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=33.88 E-value=86 Score=33.33 Aligned_cols=56 Identities=21% Similarity=0.177 Sum_probs=45.5
Q ss_pred cccceeEEEcCCchHHHHHHHHhCceEEEecCCCCCCCCCCCCcEEEEEecHHHHHHHHHHHH--HHHhh
Q 045766 409 ASNQIGCLLGKGGSIIAEMRKLSGAYIRILGKDQIPKCASENEEVVLINGEFEAVQEALFQIT--TRLRH 476 (663)
Q Consensus 409 p~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~--~~l~~ 476 (663)
+....-.|.|..+.+++.|.+..|+.|.. ..+.++|+|+...|..|...+. +++..
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~------------rG~~~~i~g~~~~v~~A~~~l~~l~~~~~ 79 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVA------------RGEAVRIIGARPLVDVATRVLLTLELLAE 79 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEe------------CCceEEEEechHHHHHHHHHHhHHHHHHH
Confidence 35566789999999999999999998888 2356999999878888888877 44443
No 143
>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=32.21 E-value=25 Score=34.31 Aligned_cols=32 Identities=16% Similarity=0.242 Sum_probs=27.2
Q ss_pred EEEEEeeccceeeeecCCCccccchhhccCCe
Q 045766 47 MFRVLCPVSKIDGVIGKDGEMMSQISQDTGVT 78 (663)
Q Consensus 47 ~~rilvp~~~vg~IIGk~G~~I~~i~~etga~ 78 (663)
..++.+....-|.|||++|.+|++|+++-.-+
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k~ 70 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKLQKK 70 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHHHHH
Confidence 47888888999999999999999999875443
No 144
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=31.82 E-value=26 Score=34.64 Aligned_cols=32 Identities=16% Similarity=0.241 Sum_probs=26.5
Q ss_pred EEEEeeccceeeeecCCCccccchhhccCCeE
Q 045766 48 FRVLCPVSKIDGVIGKDGEMMSQISQDTGVTI 79 (663)
Q Consensus 48 ~rilvp~~~vg~IIGk~G~~I~~i~~etga~I 79 (663)
.++.+....-|.+||++|.+|++|++.-.-..
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk~~ 73 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEKKF 73 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHHHh
Confidence 66666678899999999999999999865543
No 145
>CHL00048 rps3 ribosomal protein S3
Probab=31.56 E-value=26 Score=34.81 Aligned_cols=30 Identities=10% Similarity=0.169 Sum_probs=26.0
Q ss_pred EEEEEeeccceeeeecCCCccccchhhccC
Q 045766 47 MFRVLCPVSKIDGVIGKDGEMMSQISQDTG 76 (663)
Q Consensus 47 ~~rilvp~~~vg~IIGk~G~~I~~i~~etg 76 (663)
..+|.|-...-|.|||++|.+|++|++.-.
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 477777788899999999999999998764
No 146
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=31.44 E-value=31 Score=36.03 Aligned_cols=31 Identities=39% Similarity=0.568 Sum_probs=25.7
Q ss_pred ceEEEEEeec-cceeeeecCCCccccchhhcc
Q 045766 45 GIMFRVLCPV-SKIDGVIGKDGEMMSQISQDT 75 (663)
Q Consensus 45 ~~~~rilvp~-~~vg~IIGk~G~~I~~i~~et 75 (663)
-+...++||. +..-.||||||..|++|-++-
T Consensus 327 ~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a 358 (379)
T KOG1423|consen 327 FIQVEVVCPKNSQKKLLIGKGGKKISQIGTRA 358 (379)
T ss_pred EEEEEEEcCCCcceeEEEcCCCccHHHHHHHH
Confidence 5677889995 667789999999999997654
No 147
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=31.13 E-value=30 Score=38.38 Aligned_cols=37 Identities=30% Similarity=0.392 Sum_probs=32.3
Q ss_pred EEEEeeccceeeeecCCCccccchhhccCCeEEEcCC
Q 045766 48 FRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEET 84 (663)
Q Consensus 48 ~rilvp~~~vg~IIGk~G~~I~~i~~etga~I~v~~~ 84 (663)
=.++|-.++-|.||||+|++.+.|.++||-.-.|-+.
T Consensus 101 GEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 101 GEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred ceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 3567778999999999999999999999988888764
No 148
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=30.83 E-value=61 Score=33.26 Aligned_cols=30 Identities=23% Similarity=0.372 Sum_probs=22.3
Q ss_pred eEEEEEeccc-ceeEEEcCCchHHHHHHHHh
Q 045766 402 VMTRLLVASN-QIGCLLGKGGSIIAEMRKLS 431 (663)
Q Consensus 402 ~~~~l~Vp~~-~vg~IIGk~G~~Ik~I~~~t 431 (663)
+...+.|..+ +-+-|||++|+.||+|...+
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 4556667654 55899999999999886543
No 149
>PRK15494 era GTPase Era; Provisional
Probab=29.49 E-value=34 Score=36.54 Aligned_cols=29 Identities=21% Similarity=0.305 Sum_probs=23.5
Q ss_pred eEEEEEee-ccceeeeecCCCccccchhhc
Q 045766 46 IMFRVLCP-VSKIDGVIGKDGEMMSQISQD 74 (663)
Q Consensus 46 ~~~rilvp-~~~vg~IIGk~G~~I~~i~~e 74 (663)
+.-.|+|. .+.-+-||||+|+.||+|..+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 55667787 577899999999999987654
No 150
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=28.97 E-value=29 Score=34.54 Aligned_cols=33 Identities=9% Similarity=0.238 Sum_probs=27.7
Q ss_pred EEEEEeeccceeeeecCCCccccchhhccCCeE
Q 045766 47 MFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTI 79 (663)
Q Consensus 47 ~~rilvp~~~vg~IIGk~G~~I~~i~~etga~I 79 (663)
.+++.+....-|.|||++|..|++|+++-.-.+
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~ 77 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLLQKRF 77 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHHHHHh
Confidence 477888888899999999999999998865543
No 151
>COG1159 Era GTPase [General function prediction only]
Probab=28.91 E-value=61 Score=33.72 Aligned_cols=35 Identities=29% Similarity=0.478 Sum_probs=26.6
Q ss_pred eEEEEecCCCc-CeeecCCChhHHHHH--------HHcCCEEEE
Q 045766 590 RVPVVVPRSLV-PIIQGEDGACLKQIR--------QISDAKITI 624 (663)
Q Consensus 590 ~~~v~IP~~~v-g~IIGkgG~~I~~I~--------~~sGa~I~i 624 (663)
...+.|+.+.. |-||||+|+.|++|- +..+++|.+
T Consensus 230 ~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L 273 (298)
T COG1159 230 HATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYL 273 (298)
T ss_pred EEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEE
Confidence 34578887765 999999999999875 455666655
No 152
>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=28.89 E-value=39 Score=39.38 Aligned_cols=37 Identities=35% Similarity=0.413 Sum_probs=32.9
Q ss_pred EEEEeeccceeeeecCCCccccchhhccCCeEEEcCC
Q 045766 48 FRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRVEET 84 (663)
Q Consensus 48 ~rilvp~~~vg~IIGk~G~~I~~i~~etga~I~v~~~ 84 (663)
=.++|-.++-|.||||+|.+++.|.++||-+-.|-+.
T Consensus 95 ~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 95 GEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred ceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 3567778899999999999999999999999998775
No 153
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=27.66 E-value=57 Score=32.00 Aligned_cols=38 Identities=18% Similarity=0.375 Sum_probs=30.6
Q ss_pred cceEEEEEecccceeEEEcCCchHHHHHHHHhCceEEE
Q 045766 400 QTVMTRLLVASNQIGCLLGKGGSIIAEMRKLSGAYIRI 437 (663)
Q Consensus 400 ~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I~~~tGa~I~i 437 (663)
...++.+.|-.+..+.|||+.|.+++.||-.+.+.++-
T Consensus 89 ~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 89 EGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 34566777778889999999999999999887765554
No 154
>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=27.30 E-value=2.2e+02 Score=23.72 Aligned_cols=64 Identities=8% Similarity=0.045 Sum_probs=46.2
Q ss_pred EEEecCCCcCeeecCCChhHHHHHHHcCCEEEEeCCCCC---CcceEEEEEcCHHHHHHHHHHHHHHHh
Q 045766 592 PVVVPRSLVPIIQGEDGACLKQIRQISDAKITITDPKPG---ATETVIIISGTPEQTHAAQSLIQAFVM 657 (663)
Q Consensus 592 ~v~IP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~---~~~r~v~IsGt~e~v~~A~~lI~~~v~ 657 (663)
+..+=...-|.+- |=.-+.++-+..|++++...++.. ..+.+++|+|+..++..|...++++|.
T Consensus 19 ~a~i~are~gV~a--G~~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 19 TATIIAREDGVLA--GLEEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp EEEEEESSSEEE---SHHHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred EEEEEeCCCEEEE--CHHHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 3333333334444 556888888888999988755432 367899999999999999999999875
No 155
>PRK15494 era GTPase Era; Provisional
Probab=26.87 E-value=77 Score=33.87 Aligned_cols=29 Identities=28% Similarity=0.376 Sum_probs=21.5
Q ss_pred eEEEEEeccc-ceeEEEcCCchHHHHHHHH
Q 045766 402 VMTRLLVASN-QIGCLLGKGGSIIAEMRKL 430 (663)
Q Consensus 402 ~~~~l~Vp~~-~vg~IIGk~G~~Ik~I~~~ 430 (663)
+...+.|..+ +-+-|||++|+.||+|...
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 4456667654 5589999999999887643
No 156
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=26.51 E-value=37 Score=33.26 Aligned_cols=37 Identities=16% Similarity=0.199 Sum_probs=28.7
Q ss_pred ceEEEEEeeccceeeeecCCCccccchhhccCCeEEE
Q 045766 45 GIMFRVLCPVSKIDGVIGKDGEMMSQISQDTGVTIRV 81 (663)
Q Consensus 45 ~~~~rilvp~~~vg~IIGk~G~~I~~i~~etga~I~v 81 (663)
+-.+.+-+-.+..+.||||.|.++..||--+++-++-
T Consensus 90 ~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 90 GRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred CcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 3455555666669999999999999999887766555
No 157
>PRK00089 era GTPase Era; Reviewed
Probab=26.35 E-value=33 Score=35.60 Aligned_cols=26 Identities=35% Similarity=0.664 Sum_probs=21.8
Q ss_pred eEEEEEEc-CCceeEEecCcchhhhcc
Q 045766 187 FVLRLLVL-STQVGCLLGKGGCVIKQI 212 (663)
Q Consensus 187 ~~~~llVP-~~~vG~IIGkgG~~Ik~I 212 (663)
+...++|. .+|-+.||||+|++||+|
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i 252 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKI 252 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHH
Confidence 55667776 467899999999999999
No 158
>PRK03818 putative transporter; Validated
Probab=26.19 E-value=6.8e+02 Score=28.76 Aligned_cols=130 Identities=15% Similarity=0.240 Sum_probs=70.5
Q ss_pred EEEEEeeccccceeeccCchhHHhHHhHhCCeEEEecc---------CCC---CCceEEEEeCCCCCCCCCChHHHHHHH
Q 045766 318 TFRLLCHDERVGGVIGKGGAIIRSLKQETGCDIKVMEA---------VSG---TEDRLIVISGPAHPDDRISAPQDAVLR 385 (663)
Q Consensus 318 ~~~v~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~---------~~~---~~er~v~I~G~~~~~~~v~~a~~ai~~ 385 (663)
..++.|+++. ++ |.+++++.......+.+..- .++ .....+.|.|+. +++.+
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---GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQP----------EDLHK 269 (552)
T ss_pred eEEEEEeCCC---CC---CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECH----------HHHHH
Confidence 3556666433 33 67899999888766655411 011 112467788876 44444
Q ss_pred HHHHHhhcCC---C-CCCcceEEEEEecccceeEEEcCCchHHHHH--HHHhCceEEEecCCCCC--CCCC---CCCcEE
Q 045766 386 VQTRIARAIP---D-NREQTVMTRLLVASNQIGCLLGKGGSIIAEM--RKLSGAYIRILGKDQIP--KCAS---ENEEVV 454 (663)
Q Consensus 386 i~~~i~~~~~---~-~~~~~~~~~l~Vp~~~vg~IIGk~G~~Ik~I--~~~tGa~I~i~~~~~~p--~~~~---~~~~~v 454 (663)
+.+....... + ..+......+.+|++ .++|+ +++++ +++.|+.|.-..+.+.. ...+ ..-..+
T Consensus 270 l~~~~Gl~~~~~~~~~~~~~~~E~Vvv~~S---~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq~GD~L 343 (552)
T PRK03818 270 AQLVIGEEVDTSLSTRGTDLRSERVVVTNE---KVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLSLQFGDIL 343 (552)
T ss_pred HHHhcCCccCccccccCcceEEEEEEEcCh---hccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCEEecCCEE
Confidence 4444322211 1 112233444445543 45554 78877 46678776655443211 1110 123568
Q ss_pred EEEecHHHHHHHHHH
Q 045766 455 LINGEFEAVQEALFQ 469 (663)
Q Consensus 455 ~I~G~~~~v~~A~~~ 469 (663)
.+.|++++++++.+.
T Consensus 344 lVvG~~~~i~~l~~~ 358 (552)
T PRK03818 344 NLVGRPEAIDAVANV 358 (552)
T ss_pred EEEECHHHHHHHHHH
Confidence 999999999987764
No 159
>PRK00089 era GTPase Era; Reviewed
Probab=25.03 E-value=86 Score=32.43 Aligned_cols=29 Identities=24% Similarity=0.565 Sum_probs=21.0
Q ss_pred eEEEEEecc-cceeEEEcCCchHHHHHHHH
Q 045766 402 VMTRLLVAS-NQIGCLLGKGGSIIAEMRKL 430 (663)
Q Consensus 402 ~~~~l~Vp~-~~vg~IIGk~G~~Ik~I~~~ 430 (663)
+...+.|.. ++-+-|||++|++|++|...
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ 255 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTE 255 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHH
Confidence 344566654 45589999999999887644
No 160
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=24.01 E-value=80 Score=31.21 Aligned_cols=28 Identities=11% Similarity=0.297 Sum_probs=22.9
Q ss_pred EEEEecCCCcCeeecCCChhHHHHHHHc
Q 045766 591 VPVVVPRSLVPIIQGEDGACLKQIRQIS 618 (663)
Q Consensus 591 ~~v~IP~~~vg~IIGkgG~~I~~I~~~s 618 (663)
+.+.|-...-|.+||++|++|+++++.-
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~L 69 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEIL 69 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHH
Confidence 5566666888999999999999998654
No 161
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=23.35 E-value=77 Score=33.26 Aligned_cols=34 Identities=21% Similarity=0.421 Sum_probs=26.6
Q ss_pred CcceEEEEEeecc-ccceeeccCchhHHhHHhHhC
Q 045766 314 PEILTFRLLCHDE-RVGGVIGKGGAIIRSLKQETG 347 (663)
Q Consensus 314 ~~~~~~~v~vp~~-~vg~IIGk~G~~Ik~I~~~tg 347 (663)
.-.+..++.||.. ....|||++|..|++|-++-+
T Consensus 325 ~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 325 VLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 3567788899964 467799999999999876644
No 162
>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=23.24 E-value=90 Score=30.53 Aligned_cols=30 Identities=10% Similarity=0.204 Sum_probs=24.7
Q ss_pred ceEEEEecCCCcCeeecCCChhHHHHHHHc
Q 045766 589 RRVPVVVPRSLVPIIQGEDGACLKQIRQIS 618 (663)
Q Consensus 589 ~~~~v~IP~~~vg~IIGkgG~~I~~I~~~s 618 (663)
..+++.|-...-|.|||++|++|++|++.-
T Consensus 38 ~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 38 LGTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred CcEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 346788878888999999999999987553
No 163
>CHL00048 rps3 ribosomal protein S3
Probab=21.54 E-value=99 Score=30.75 Aligned_cols=29 Identities=7% Similarity=0.209 Sum_probs=24.2
Q ss_pred eEEEEecCCCcCeeecCCChhHHHHHHHc
Q 045766 590 RVPVVVPRSLVPIIQGEDGACLKQIRQIS 618 (663)
Q Consensus 590 ~~~v~IP~~~vg~IIGkgG~~I~~I~~~s 618 (663)
.+.+.|-...-|.|||++|++|++|++.-
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 45677777888999999999999998665
No 164
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=20.51 E-value=1e+02 Score=30.75 Aligned_cols=29 Identities=10% Similarity=0.386 Sum_probs=24.1
Q ss_pred eEEEEecCCCcCeeecCCChhHHHHHHHc
Q 045766 590 RVPVVVPRSLVPIIQGEDGACLKQIRQIS 618 (663)
Q Consensus 590 ~~~v~IP~~~vg~IIGkgG~~I~~I~~~s 618 (663)
.+++.|-...-|.|||++|+.|++|++.-
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L 73 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLL 73 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHH
Confidence 46677877888999999999999987554
No 165
>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=20.11 E-value=2.7e+02 Score=22.52 Aligned_cols=41 Identities=24% Similarity=0.450 Sum_probs=30.7
Q ss_pred hhHHHHHHHcCCE-EEEeCCCCCCcceEEEEEcCHHHHHHHHHHHHH
Q 045766 609 ACLKQIRQISDAK-ITITDPKPGATETVIIISGTPEQTHAAQSLIQA 654 (663)
Q Consensus 609 ~~I~~I~~~sGa~-I~i~~~~~~~~~r~v~IsGt~e~v~~A~~lI~~ 654 (663)
..|.+|-+.++|+ |.+.+ ..-+|.++|+++.++....++..
T Consensus 17 ~ei~~l~~~f~a~ivd~~~-----~~~iie~tG~~~kid~fi~~l~~ 58 (75)
T PF10369_consen 17 SEILQLAEIFRARIVDVSP-----DSIIIELTGTPEKIDAFIKLLKP 58 (75)
T ss_dssp HHHHHHHHHTT-EEEEEET-----TEEEEEEEE-HHHHHHHHHHSTG
T ss_pred HHHHHHHHHhCCEEEEECC-----CEEEEEEcCCHHHHHHHHHHhhh
Confidence 4678888999999 55543 34799999999999998888754
Done!