Query 009695
Match_columns 528
No_of_seqs 250 out of 1968
Neff 7.9
Searched_HMMs 46136
Date Thu Mar 28 16:14:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009695.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009695hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2190 PolyC-binding proteins 100.0 3.6E-48 7.8E-53 407.0 32.9 430 17-511 35-473 (485)
2 KOG1676 K-homology type RNA bi 100.0 1.8E-43 3.9E-48 364.9 30.0 341 23-447 52-396 (600)
3 KOG2193 IGF-II mRNA-binding pr 100.0 2.2E-44 4.7E-49 354.6 20.6 373 18-445 192-569 (584)
4 KOG2192 PolyC-binding hnRNP-K 100.0 1.8E-34 3.9E-39 269.8 20.9 292 18-348 41-383 (390)
5 KOG1676 K-homology type RNA bi 100.0 6E-30 1.3E-34 265.0 20.9 246 126-441 51-301 (600)
6 KOG2192 PolyC-binding hnRNP-K 100.0 1.9E-28 4.1E-33 229.4 19.8 233 128-441 47-385 (390)
7 KOG2193 IGF-II mRNA-binding pr 100.0 8.2E-29 1.8E-33 244.7 11.5 240 128-441 198-482 (584)
8 KOG2191 RNA-binding protein NO 100.0 2.7E-27 6E-32 228.0 20.1 239 18-311 32-281 (402)
9 KOG2191 RNA-binding protein NO 99.9 8.2E-25 1.8E-29 211.0 16.3 166 272-449 37-213 (402)
10 KOG2190 PolyC-binding proteins 99.9 4E-21 8.6E-26 202.8 20.6 168 272-444 41-212 (485)
11 TIGR03665 arCOG04150 arCOG0415 99.6 9.9E-15 2.1E-19 135.4 10.6 138 29-201 2-152 (172)
12 PRK13763 putative RNA-processi 99.5 6.7E-14 1.4E-18 130.8 13.4 142 25-201 3-158 (180)
13 TIGR03665 arCOG04150 arCOG0415 99.5 2.6E-14 5.6E-19 132.6 10.0 136 278-440 2-151 (172)
14 PRK13763 putative RNA-processi 99.5 2.8E-13 6.1E-18 126.6 11.3 141 275-440 4-157 (180)
15 cd02396 PCBP_like_KH K homolog 99.4 1.7E-12 3.7E-17 100.7 7.4 64 130-194 1-64 (65)
16 cd02396 PCBP_like_KH K homolog 99.3 2.1E-12 4.6E-17 100.2 7.0 64 367-434 1-64 (65)
17 KOG2279 Kinase anchor protein 99.3 1.6E-11 3.4E-16 127.1 11.2 257 18-310 61-332 (608)
18 KOG2279 Kinase anchor protein 99.2 2.9E-11 6.3E-16 125.1 10.1 232 127-440 66-368 (608)
19 cd02394 vigilin_like_KH K homo 99.2 1.7E-11 3.7E-16 94.2 6.0 61 368-435 2-62 (62)
20 PF00013 KH_1: KH domain syndr 99.2 1.2E-11 2.6E-16 94.4 3.3 60 367-434 1-60 (60)
21 cd02393 PNPase_KH Polynucleoti 99.2 8E-11 1.7E-15 89.9 7.7 59 366-435 2-61 (61)
22 cd00105 KH-I K homology RNA-bi 99.1 1.4E-10 3.1E-15 89.4 7.5 62 368-434 2-63 (64)
23 KOG2208 Vigilin [Lipid transpo 99.1 9.2E-10 2E-14 123.3 14.4 214 128-440 346-562 (753)
24 cd02394 vigilin_like_KH K homo 99.1 1.8E-10 3.9E-15 88.5 5.9 60 131-194 2-61 (62)
25 PF00013 KH_1: KH domain syndr 99.1 7.7E-11 1.7E-15 89.9 3.7 60 130-194 1-60 (60)
26 cd02393 PNPase_KH Polynucleoti 99.1 7.9E-10 1.7E-14 84.5 8.1 58 129-194 2-60 (61)
27 cd00105 KH-I K homology RNA-bi 99.0 1.2E-09 2.5E-14 84.3 7.9 62 131-194 2-63 (64)
28 KOG2208 Vigilin [Lipid transpo 98.9 2.1E-09 4.6E-14 120.4 9.5 288 25-441 347-636 (753)
29 PF13014 KH_3: KH domain 98.9 1.3E-09 2.9E-14 77.1 5.1 42 35-76 1-43 (43)
30 PF13014 KH_3: KH domain 98.9 3E-09 6.5E-14 75.3 4.6 42 284-325 1-43 (43)
31 smart00322 KH K homology RNA-b 98.9 1.4E-08 3.1E-13 78.6 8.8 67 365-438 2-68 (69)
32 smart00322 KH K homology RNA-b 98.7 7.8E-08 1.7E-12 74.4 9.2 67 128-198 2-68 (69)
33 COG1094 Predicted RNA-binding 98.6 2.8E-07 6.1E-12 85.1 10.6 143 273-440 7-164 (194)
34 COG1094 Predicted RNA-binding 98.6 9.5E-07 2.1E-11 81.7 12.8 146 23-201 6-165 (194)
35 cd02395 SF1_like-KH Splicing f 98.3 2.6E-06 5.6E-11 74.1 7.6 68 374-441 14-96 (120)
36 cd02395 SF1_like-KH Splicing f 98.2 7.9E-06 1.7E-10 71.0 8.5 64 138-201 15-96 (120)
37 PRK08406 transcription elongat 98.0 1.2E-05 2.6E-10 71.9 6.0 103 26-165 33-135 (140)
38 TIGR02696 pppGpp_PNP guanosine 97.8 7.3E-05 1.6E-09 82.8 9.8 92 335-440 550-642 (719)
39 KOG2113 Predicted RNA binding 97.8 1.8E-05 3.9E-10 77.3 4.3 143 272-431 24-173 (394)
40 PRK08406 transcription elongat 97.8 6.1E-05 1.3E-09 67.4 7.0 100 275-401 33-134 (140)
41 TIGR02696 pppGpp_PNP guanosine 97.8 0.00011 2.5E-09 81.3 10.3 94 98-200 548-642 (719)
42 TIGR01952 nusA_arch NusA famil 97.5 0.00026 5.6E-09 63.2 7.2 102 26-165 34-136 (141)
43 KOG2113 Predicted RNA binding 97.5 0.00026 5.6E-09 69.4 6.7 141 127-326 24-164 (394)
44 TIGR03591 polynuc_phos polyrib 97.4 0.00036 7.7E-09 78.5 8.5 94 98-199 520-614 (684)
45 TIGR01952 nusA_arch NusA famil 97.4 0.00033 7.3E-09 62.5 5.8 101 275-402 34-136 (141)
46 KOG0119 Splicing factor 1/bran 97.4 0.00094 2E-08 69.5 9.8 74 128-201 137-231 (554)
47 KOG0119 Splicing factor 1/bran 97.4 0.0017 3.7E-08 67.6 11.6 81 365-445 137-235 (554)
48 TIGR03591 polynuc_phos polyrib 97.2 0.0008 1.7E-08 75.7 8.0 92 336-440 523-615 (684)
49 COG0195 NusA Transcription elo 97.1 0.0018 4E-08 60.7 7.9 102 27-166 78-179 (190)
50 PLN00207 polyribonucleotide nu 97.0 0.0011 2.3E-08 75.4 6.6 95 98-200 654-750 (891)
51 KOG1588 RNA-binding protein Sa 96.9 0.0011 2.3E-08 64.3 4.2 38 24-61 91-134 (259)
52 PLN00207 polyribonucleotide nu 96.8 0.002 4.4E-08 73.2 6.5 92 336-440 657-750 (891)
53 COG1185 Pnp Polyribonucleotide 96.8 0.003 6.6E-08 68.9 7.1 97 336-445 524-621 (692)
54 COG1185 Pnp Polyribonucleotide 96.8 0.0043 9.2E-08 67.7 8.2 95 98-200 521-616 (692)
55 KOG0336 ATP-dependent RNA heli 96.7 0.0024 5.2E-08 65.3 5.8 67 364-438 45-111 (629)
56 KOG0336 ATP-dependent RNA heli 96.7 0.0015 3.2E-08 66.9 4.2 61 17-80 39-99 (629)
57 cd02134 NusA_KH NusA_K homolog 96.6 0.0025 5.5E-08 48.5 3.9 37 24-60 24-60 (61)
58 KOG2814 Transcription coactiva 96.6 0.0024 5.1E-08 63.7 4.7 69 129-201 57-126 (345)
59 COG0195 NusA Transcription elo 96.6 0.0044 9.6E-08 58.2 6.1 99 278-404 80-180 (190)
60 TIGR01953 NusA transcription t 96.4 0.009 1.9E-07 61.5 7.8 95 34-166 243-338 (341)
61 PRK12329 nusA transcription el 96.4 0.0082 1.8E-07 62.9 7.1 95 34-166 277-372 (449)
62 PRK12327 nusA transcription el 96.4 0.01 2.3E-07 61.4 7.8 96 34-167 245-341 (362)
63 PRK11824 polynucleotide phosph 96.3 0.0046 9.9E-08 69.8 5.5 95 98-200 523-618 (693)
64 cd02134 NusA_KH NusA_K homolog 96.3 0.0069 1.5E-07 46.1 4.5 36 129-164 25-60 (61)
65 PRK12328 nusA transcription el 96.3 0.011 2.4E-07 60.9 7.4 95 34-167 251-346 (374)
66 KOG1588 RNA-binding protein Sa 96.1 0.032 7E-07 54.3 9.0 77 363-439 89-190 (259)
67 PRK11824 polynucleotide phosph 96.0 0.008 1.7E-07 67.9 5.4 92 336-440 526-618 (693)
68 TIGR01953 NusA transcription t 96.0 0.016 3.5E-07 59.7 7.0 95 283-403 243-338 (341)
69 PRK12328 nusA transcription el 95.8 0.032 6.9E-07 57.6 8.0 99 283-408 251-350 (374)
70 PRK04163 exosome complex RNA-b 95.8 0.017 3.6E-07 56.6 5.7 66 368-444 147-213 (235)
71 PRK09202 nusA transcription el 95.6 0.025 5.3E-07 60.8 6.9 95 34-167 245-340 (470)
72 PRK00468 hypothetical protein; 95.6 0.012 2.5E-07 46.7 3.3 35 21-55 26-60 (75)
73 KOG2814 Transcription coactiva 95.6 0.015 3.3E-07 58.0 4.8 71 365-441 56-126 (345)
74 PRK12327 nusA transcription el 95.6 0.025 5.5E-07 58.6 6.5 96 283-404 245-341 (362)
75 COG5176 MSL5 Splicing factor ( 95.4 0.073 1.6E-06 49.7 8.1 44 363-406 145-194 (269)
76 PRK02821 hypothetical protein; 95.3 0.017 3.7E-07 46.0 3.0 35 22-56 28-62 (77)
77 PRK00468 hypothetical protein; 95.2 0.019 4.1E-07 45.5 3.3 32 125-156 26-57 (75)
78 PRK12704 phosphodiesterase; Pr 95.2 0.05 1.1E-06 59.4 7.5 68 364-441 208-277 (520)
79 PRK12329 nusA transcription el 95.2 0.045 9.7E-07 57.5 6.8 93 283-403 277-372 (449)
80 PF14611 SLS: Mitochondrial in 95.2 0.28 6.1E-06 47.0 11.9 126 278-439 30-164 (210)
81 TIGR03319 YmdA_YtgF conserved 95.1 0.053 1.2E-06 59.1 7.4 67 364-440 202-270 (514)
82 PRK02821 hypothetical protein; 95.0 0.038 8.2E-07 44.0 4.4 32 126-157 28-59 (77)
83 PF14611 SLS: Mitochondrial in 95.0 0.94 2E-05 43.4 14.9 87 103-200 4-90 (210)
84 PRK00106 hypothetical protein; 94.9 0.068 1.5E-06 58.2 7.5 67 364-440 223-291 (535)
85 PRK09202 nusA transcription el 94.9 0.059 1.3E-06 57.9 6.8 95 283-404 245-340 (470)
86 COG1837 Predicted RNA-binding 94.9 0.03 6.6E-07 44.3 3.4 33 125-157 26-58 (76)
87 COG5176 MSL5 Splicing factor ( 94.8 0.046 9.9E-07 51.0 4.9 42 22-63 145-192 (269)
88 PRK04163 exosome complex RNA-b 94.7 0.06 1.3E-06 52.7 5.9 63 131-201 147-210 (235)
89 COG1837 Predicted RNA-binding 94.6 0.037 8E-07 43.8 3.2 33 22-54 27-59 (76)
90 PRK01064 hypothetical protein; 94.5 0.048 1E-06 43.5 3.9 32 125-156 26-57 (78)
91 TIGR03319 YmdA_YtgF conserved 94.5 0.15 3.3E-06 55.6 9.1 64 130-200 205-270 (514)
92 PRK01064 hypothetical protein; 94.5 0.037 8.1E-07 44.2 3.1 34 22-55 27-60 (78)
93 PRK00106 hypothetical protein; 94.3 0.2 4.3E-06 54.6 9.3 64 130-200 226-291 (535)
94 PRK12704 phosphodiesterase; Pr 94.3 0.18 3.8E-06 55.2 9.0 62 132-200 213-276 (520)
95 KOG1067 Predicted RNA-binding 93.4 0.2 4.4E-06 53.5 7.1 94 99-201 567-661 (760)
96 KOG4369 RTK signaling protein 93.2 0.051 1.1E-06 62.1 2.3 69 368-440 1342-1410(2131)
97 PF13083 KH_4: KH domain; PDB: 92.2 0.088 1.9E-06 41.5 1.9 35 22-56 26-60 (73)
98 cd02409 KH-II KH-II (K homolo 90.4 0.38 8.1E-06 36.6 3.8 35 24-58 24-58 (68)
99 KOG4369 RTK signaling protein 90.3 0.22 4.8E-06 57.2 3.3 62 26-87 1341-1403(2131)
100 KOG1067 Predicted RNA-binding 90.3 0.88 1.9E-05 48.9 7.5 89 338-440 571-660 (760)
101 PF13083 KH_4: KH domain; PDB: 89.8 0.16 3.5E-06 40.0 1.3 34 272-305 27-60 (73)
102 PRK12705 hypothetical protein; 89.2 0.75 1.6E-05 49.9 6.2 61 132-199 201-263 (508)
103 PF13184 KH_5: NusA-like KH do 88.9 0.39 8.4E-06 37.5 2.8 36 27-62 5-46 (69)
104 KOG3273 Predicted RNA-binding 88.5 0.23 5E-06 46.2 1.5 54 374-439 177-230 (252)
105 PF13184 KH_5: NusA-like KH do 87.4 0.37 8E-06 37.6 1.9 38 367-404 4-47 (69)
106 COG1855 ATPase (PilT family) [ 87.0 0.91 2E-05 47.9 4.9 38 130-167 487-524 (604)
107 KOG3273 Predicted RNA-binding 86.9 0.37 8.1E-06 44.8 1.8 57 137-202 177-233 (252)
108 cd02409 KH-II KH-II (K homolo 86.9 1.1 2.3E-05 34.0 4.2 35 365-399 24-58 (68)
109 PF07650 KH_2: KH domain syndr 86.5 0.38 8.3E-06 38.3 1.5 33 27-59 27-59 (78)
110 PRK12705 hypothetical protein; 86.1 1.1 2.3E-05 48.8 5.1 40 364-403 196-236 (508)
111 PRK13764 ATPase; Provisional 86.1 1.1 2.4E-05 49.7 5.3 65 99-167 455-519 (602)
112 cd02410 archeal_CPSF_KH The ar 84.1 5.7 0.00012 35.5 7.8 37 131-167 78-114 (145)
113 cd02413 40S_S3_KH K homology R 83.9 0.58 1.3E-05 37.7 1.4 36 27-62 32-67 (81)
114 KOG2874 rRNA processing protei 83.5 1.9 4.2E-05 42.3 5.0 51 141-200 161-211 (356)
115 COG1855 ATPase (PilT family) [ 83.3 0.83 1.8E-05 48.2 2.6 38 26-63 487-524 (604)
116 cd02414 jag_KH jag_K homology 83.3 1.1 2.3E-05 35.7 2.7 34 27-60 26-59 (77)
117 cd02414 jag_KH jag_K homology 83.1 1.3 2.7E-05 35.3 3.1 33 276-308 26-58 (77)
118 PRK06418 transcription elongat 83.0 1.2 2.7E-05 40.9 3.4 33 29-62 65-97 (166)
119 COG1097 RRP4 RNA-binding prote 82.6 2.7 5.9E-05 40.7 5.7 57 368-435 148-205 (239)
120 PF07650 KH_2: KH domain syndr 82.3 0.52 1.1E-05 37.5 0.6 35 129-163 25-59 (78)
121 KOG2874 rRNA processing protei 82.0 2.3 4.9E-05 41.8 4.9 51 378-440 161-211 (356)
122 PRK13764 ATPase; Provisional 80.3 1.6 3.4E-05 48.6 3.6 45 364-408 479-523 (602)
123 COG1097 RRP4 RNA-binding prote 80.2 3.9 8.5E-05 39.6 5.8 57 132-196 149-206 (239)
124 PRK06418 transcription elongat 79.7 2.2 4.8E-05 39.2 3.8 35 131-166 63-97 (166)
125 COG1782 Predicted metal-depend 79.6 3.7 7.9E-05 43.9 5.8 97 37-167 41-137 (637)
126 cd02412 30S_S3_KH K homology R 79.0 1.8 3.9E-05 37.0 2.8 31 27-57 63-93 (109)
127 cd02410 archeal_CPSF_KH The ar 76.3 3.1 6.6E-05 37.2 3.5 37 29-65 80-116 (145)
128 cd02411 archeal_30S_S3_KH K ho 75.0 2.8 6E-05 34.0 2.8 28 27-54 40-67 (85)
129 cd02413 40S_S3_KH K homology R 74.8 3.6 7.7E-05 33.2 3.3 35 130-164 31-65 (81)
130 COG0092 RpsC Ribosomal protein 71.9 3 6.5E-05 40.3 2.6 34 25-58 51-84 (233)
131 COG1782 Predicted metal-depend 70.5 12 0.00025 40.3 6.7 95 288-404 43-137 (637)
132 COG5166 Uncharacterized conser 68.8 5.5 0.00012 42.5 3.9 132 283-440 389-524 (657)
133 cd02411 archeal_30S_S3_KH K ho 63.3 7.6 0.00017 31.4 3.0 27 131-157 40-66 (85)
134 cd02412 30S_S3_KH K homology R 62.8 6.3 0.00014 33.6 2.5 28 276-303 63-90 (109)
135 TIGR00436 era GTP-binding prot 61.8 9.9 0.00022 37.8 4.2 28 129-156 221-249 (270)
136 TIGR03675 arCOG00543 arCOG0054 61.5 20 0.00044 40.3 6.9 38 130-167 94-131 (630)
137 COG0092 RpsC Ribosomal protein 58.8 8.5 0.00018 37.2 2.9 37 128-164 50-91 (233)
138 PRK15494 era GTPase Era; Provi 57.8 13 0.00027 38.5 4.2 27 129-155 273-300 (339)
139 PRK00089 era GTPase Era; Revie 56.5 14 0.0003 37.1 4.2 27 129-155 226-253 (292)
140 COG5166 Uncharacterized conser 54.8 20 0.00043 38.6 4.9 91 38-166 393-486 (657)
141 COG1159 Era GTPase [General fu 53.9 16 0.00034 36.8 4.0 28 128-155 228-256 (298)
142 TIGR00436 era GTP-binding prot 51.1 18 0.00038 36.0 3.9 31 365-395 220-251 (270)
143 COG1159 Era GTPase [General fu 46.1 21 0.00045 36.0 3.4 32 364-395 227-259 (298)
144 PRK15494 era GTPase Era; Provi 45.8 23 0.00051 36.5 4.0 30 365-394 272-302 (339)
145 TIGR01008 rpsC_E_A ribosomal p 45.4 18 0.0004 34.2 2.8 32 26-57 39-70 (195)
146 PRK04191 rps3p 30S ribosomal p 44.9 18 0.0004 34.6 2.8 31 27-57 42-72 (207)
147 PRK00089 era GTPase Era; Revie 44.6 25 0.00054 35.2 3.9 37 365-401 225-270 (292)
148 CHL00048 rps3 ribosomal protei 43.6 20 0.00043 34.6 2.8 30 26-55 67-96 (214)
149 KOG1423 Ras-like GTPase ERA [C 42.9 26 0.00056 35.6 3.5 34 126-159 325-359 (379)
150 TIGR03675 arCOG00543 arCOG0054 42.8 24 0.00052 39.8 3.7 95 288-404 37-131 (630)
151 PTZ00084 40S ribosomal protein 41.8 22 0.00048 34.3 2.8 32 27-58 46-77 (220)
152 COG1847 Jag Predicted RNA-bind 33.8 30 0.00065 32.9 2.2 35 275-309 92-126 (208)
153 COG1847 Jag Predicted RNA-bind 31.7 37 0.0008 32.3 2.5 34 27-60 93-126 (208)
154 KOG1423 Ras-like GTPase ERA [C 31.5 52 0.0011 33.5 3.5 35 363-397 325-360 (379)
155 TIGR01008 rpsC_E_A ribosomal p 30.8 50 0.0011 31.3 3.2 28 130-157 39-66 (195)
156 PRK04191 rps3p 30S ribosomal p 30.3 50 0.0011 31.6 3.2 29 131-159 42-70 (207)
157 TIGR01009 rpsC_bact ribosomal 29.9 45 0.00098 32.0 2.8 29 27-55 64-92 (211)
158 CHL00048 rps3 ribosomal protei 29.5 53 0.0012 31.6 3.3 29 130-158 67-95 (214)
159 PRK03818 putative transporter; 29.3 3.5E+02 0.0075 30.1 10.0 60 128-193 289-358 (552)
160 COG1702 PhoH Phosphate starvat 29.2 87 0.0019 32.3 4.8 55 374-440 23-79 (348)
161 PTZ00084 40S ribosomal protein 28.2 55 0.0012 31.7 3.1 28 131-158 46-73 (220)
162 COG1702 PhoH Phosphate starvat 24.8 1.3E+02 0.0029 31.0 5.2 54 133-195 19-72 (348)
163 TIGR03802 Asp_Ala_antiprt aspa 24.4 5.1E+02 0.011 28.8 10.2 59 130-194 304-376 (562)
164 PF09869 DUF2096: Uncharacteri 23.6 2.4E+02 0.0051 26.0 6.0 57 127-198 111-167 (169)
165 PRK00310 rpsC 30S ribosomal pr 22.6 73 0.0016 31.1 2.8 30 27-56 64-93 (232)
166 PRK15468 carboxysome structura 22.6 2E+02 0.0043 24.5 4.9 41 392-441 60-100 (111)
167 PF00936 BMC: BMC domain; Int 20.7 1E+02 0.0022 24.3 2.8 51 389-445 19-69 (75)
168 cd07053 BMC_PduT_repeat1 1,2-p 20.5 1.2E+02 0.0026 24.0 3.2 36 414-449 37-72 (76)
No 1
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=3.6e-48 Score=407.02 Aligned_cols=430 Identities=27% Similarity=0.400 Sum_probs=318.4
Q ss_pred CCCCCCCceEEEEEecccccccccccCchHHHHHHhhhCceEEecCCCCCCCceEEEEEcCCcchhhhhcccccccccCC
Q 009695 17 PLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGG 96 (528)
Q Consensus 17 ~~~~~~~~~~~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i~~~~~~~~eRvi~I~G~~~~~~~~~~~~~~~~~~~~ 96 (528)
+...++...+||||||.+.+|.||||+|.+|++||++|.++|+|.+..++|+|||++|+|...+ .
T Consensus 35 ~~~~p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~---------------~ 99 (485)
T KOG2190|consen 35 ISTGPDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVE---------------L 99 (485)
T ss_pred ccCCCCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEeccccc---------------c
Confidence 3344455556999999999999999999999999999999999999999999999999997322 2
Q ss_pred CcchHHHHHHHHHHHHhhhhhccC-----CCCC-CCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCC
Q 009695 97 EVSSTQEAVIRVFERMWEVEAEVE-----GDGD-GDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPAC 170 (528)
Q Consensus 97 ~~s~A~~al~~v~~~i~~~~~~~~-----~~~~-~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~ 170 (528)
..++|++|++++|+++.....+++ .... ...++++|||||++++|+||||+|+.||+|+++|||+|+|.++ ..
T Consensus 100 ~~~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~l 178 (485)
T KOG2190|consen 100 NLSPATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-ML 178 (485)
T ss_pred cCCchHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CC
Confidence 478899999999999987533221 1111 2226999999999999999999999999999999999999996 66
Q ss_pred CCCCCceEEEeccHHHHHHHHHHHHHHHccCCCCCCC---CcccCCCccccccCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009695 171 AAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKS---PICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDN 247 (528)
Q Consensus 171 ~~~~er~V~I~G~~~~V~kA~~~I~~~l~~~~~~~~~---~~~~~~p~~~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~y 247 (528)
+..++|.|+|.|.+++|.+|+..|..+|++++..... ...+|.|.. ..+. ..+|........+
T Consensus 179 P~ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~y~P~~--------~~~~------~~~~s~~~~~~~~ 244 (485)
T KOG2190|consen 179 PNSTERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIPYRPSA--------SQGG------PVLPSTAQTSPDA 244 (485)
T ss_pred CcccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCcccCCCcc--------cccC------ccccccccCCccc
Confidence 6779999999999999999999999999997543221 122333300 0000 1111111100000
Q ss_pred CCCCCCCCCCCCCCCCCCCcCCCCcceEEEEEeeccccceeeccCCchhHhhHhhcCeeEEEeCCCCCCCccEEEEeccc
Q 009695 248 ASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALE 327 (528)
Q Consensus 248 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~l~vP~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~~~~~~eR~V~I~G~e 327 (528)
+++ .......++.+++.+|.+.++.|||++|..|+.|+.++|+.|.+.++..+ |.|+++..+
T Consensus 245 ----~~~-----------~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~---~~i~~s~~e 306 (485)
T KOG2190|consen 245 ----HPF-----------GGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTD---RIVTISARE 306 (485)
T ss_pred ----ccc-----------cccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccCc---ceeeecccc
Confidence 000 00123467778899999999999999999999999999999999877655 999999999
Q ss_pred ccCCCCChHHHHHHHHHhhhhhcccCCCCCCCCCCCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCc
Q 009695 328 YLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQV 407 (528)
Q Consensus 328 ~p~~~~~~a~~A~~~i~~~i~e~~~~~~~~~~~~~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~ 407 (528)
.+++.++++++|+++++.++.+.... +....++.+++||++++||||||+|.+|.+|++.|||.|+|...++.
T Consensus 307 ~~~~~~s~a~~a~~~~~~~~~~~~~~-------~~~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~ 379 (485)
T KOG2190|consen 307 NPEDRYSMAQEALLLVQPRISENAGD-------DLTQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEV 379 (485)
T ss_pred Ccccccccchhhhhhccccccccccc-------cccceeeeeeccCccccceeecccccchHHHHHhcCCceEEcccccc
Confidence 99999999999999999988765321 11467899999999999999999999999999999999999988763
Q ss_pred cccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhhcCCCcccCCCCCCCCCCCCCCCCCcccccccCCCCccccccccccc
Q 009695 408 LGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNEARPRSPSGRVGGPALHKLHQSVALSPEFEQETIAVQG 487 (528)
Q Consensus 408 p~~~~~~~~~V~ItG~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~~~p~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~ 487 (528)
. ...++.++|+|...+...|++++..++.......+...... ..+.+.. |.+..+-.......+.+....-+..
T Consensus 380 ~---~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~ 453 (485)
T KOG2190|consen 380 S---GVREALVQITGMLREDLLAQYLIRARLSAPKSSMGGSSESY-SPTSGGR--PSPPSQSRMGGTPYSVNHSDRLGGS 453 (485)
T ss_pred C---CcceeEEEecchhHHHHhhhhhcccccccCccCCCCCcccC-CcccCCC--cCCccccccCccccccchhhhcccc
Confidence 2 46789999999999999999999888875443332222111 1111111 1111110011122222222211111
Q ss_pred ceeeeeeccccceeEEEEcccchh
Q 009695 488 VDQFVLPLNRSQTLQVKVCASCAF 511 (528)
Q Consensus 488 ~~~~~~~~~~~~~~~~~~~~~~~~ 511 (528)
.+|+-++++|+|+++++-.+
T Consensus 454 ----~~~~~~~~~~~~~~~~~~~~ 473 (485)
T KOG2190|consen 454 ----PGPLPPSPSLEVVIPAASYG 473 (485)
T ss_pred ----cCCCCCCCCccccchhhhcc
Confidence 18899999999999987643
No 2
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=1.8e-43 Score=364.94 Aligned_cols=341 Identities=23% Similarity=0.308 Sum_probs=259.4
Q ss_pred CceEEEEEecccccccccccCchHHHHHHhhhCceEEecCCCCCCCceEEEEEcCCcchhhhhcccccccccCCCcchHH
Q 009695 23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ 102 (528)
Q Consensus 23 ~~~~~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i~~~~~~~~eRvi~I~G~~~~~~~~~~~~~~~~~~~~~~s~A~ 102 (528)
..++-+.-||..+||.||||+|+-|..|++++||+|.+.....+.++|-+.++|..++++. |.
T Consensus 52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~-----------------aK 114 (600)
T KOG1676|consen 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEV-----------------AK 114 (600)
T ss_pred cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHHH-----------------HH
Confidence 3456788999999999999999999999999999999887777789999999999998543 33
Q ss_pred HHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEec
Q 009695 103 EAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG 182 (528)
Q Consensus 103 ~al~~v~~~i~~~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G 182 (528)
..+-.|..+..... .. ........++..++||++.+|+||||+|++||.+++++||++.+..+...+...++.+.|+|
T Consensus 115 ~li~evv~r~~~~~-~~-~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritG 192 (600)
T KOG1676|consen 115 QLIGEVVSRGRPPG-GF-PDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITG 192 (600)
T ss_pred HhhhhhhhccCCCC-Cc-cccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecC
Confidence 33334444433110 00 01122457899999999999999999999999999999999999997333445889999999
Q ss_pred cHHHHHHHHHHHHHHHccCCCCCCCCcccCCCccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009695 183 ATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDH 262 (528)
Q Consensus 183 ~~~~V~kA~~~I~~~l~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~y~~~~~p~~~~~~~~~ 262 (528)
++++|+.|+.+|.++|++...-.- +..+.++ .+
T Consensus 193 dp~~ve~a~~lV~dil~e~~~~~~-----------------------------------g~~~~~g----------~~-- 225 (600)
T KOG1676|consen 193 DPDKVEQAKQLVADILREEDDEVP-----------------------------------GSGGHAG----------VR-- 225 (600)
T ss_pred CHHHHHHHHHHHHHHHHhcccCCC-----------------------------------ccccccC----------cC--
Confidence 999999999999999986310000 0000000 00
Q ss_pred CCCCcCCCCcceEEEEEeeccccceeeccCCchhHhhHhhcCeeEEEeCC-CCCCCccEEEEecccccCCCCChHHHHHH
Q 009695 263 PGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP-LTKSGERVVTISALEYLDTRHSPVQNAAV 341 (528)
Q Consensus 263 ~~~~~~~~~~~~~~~l~vP~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~-~~~~~eR~V~I~G~e~p~~~~~~a~~A~~ 341 (528)
.....+++|.||+..||.||||+|++||+|+.+||++|+|.++ .+.+.||.+.|.|+. .....|..
T Consensus 226 -------~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~------d~ie~Aa~ 292 (600)
T KOG1676|consen 226 -------GGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTV------DQIEHAAE 292 (600)
T ss_pred -------ccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCH------HHHHHHHH
Confidence 0123378899999999999999999999999999999999854 558999999999994 23334444
Q ss_pred HHHhhhhhcccCCCCCCCCCCC---CceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEE
Q 009695 342 LVFARSVEVEGQQGFSSGENKG---DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVI 418 (528)
Q Consensus 342 ~i~~~i~e~~~~~~~~~~~~~~---~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V 418 (528)
+|.+-|.+.....+. +...+ .....+|.||++.||.||||||++||.|.++|||++++.+. .| ..+..+++|
T Consensus 293 lI~eii~~~~~~~~~--~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~--~p-~~~~~ektf 367 (600)
T KOG1676|consen 293 LINEIIAEAEAGAGG--GMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ--PP-NGNPKEKTF 367 (600)
T ss_pred HHHHHHHHHhccCCC--CcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC--CC-CCCccceEE
Confidence 443333322211111 11111 11278999999999999999999999999999999999886 23 356789999
Q ss_pred EEcCCHHHHHHHHHHHHHHHhhhcCCCcc
Q 009695 419 QISGEYKNVQNALSEVVGRLRHNLKSGEI 447 (528)
Q Consensus 419 ~ItG~~~~v~~A~~~I~~~l~~~~~~~~~ 447 (528)
+|.|++.+|+.|+.||.+++.+.......
T Consensus 368 ~IrG~~~QIdhAk~LIr~kvg~~~~n~~~ 396 (600)
T KOG1676|consen 368 VIRGDKRQIDHAKQLIRDKVGDIAPNTPY 396 (600)
T ss_pred EEecCcccchHHHHHHHHHhcccCCCCCC
Confidence 99999999999999999999886555543
No 3
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=2.2e-44 Score=354.62 Aligned_cols=373 Identities=21% Similarity=0.332 Sum_probs=273.3
Q ss_pred CCCCCCceEEEEEecccccccccccCchHHHHHHhhhCceEEecCC-CCCCCceEEEEEcCCcchhhhhcccccccccCC
Q 009695 18 LNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGG-FPGSDHRVILVVGSGSIDRRIMFCENDVVVEGG 96 (528)
Q Consensus 18 ~~~~~~~~~~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i~~~-~~~~~eRvi~I~G~~~~~~~~~~~~~~~~~~~~ 96 (528)
..-...++.+|+|||..++|+||||.|++||.|..+|.|+|+|... ..|..||+|+|-|.+|.
T Consensus 192 ~~~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg---------------- 255 (584)
T KOG2193|consen 192 HKQQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG---------------- 255 (584)
T ss_pred ccccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc----------------
Confidence 3344668999999999999999999999999999999999999764 56889999999999987
Q ss_pred CcchHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCC-CCCCCCCC
Q 009695 97 EVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PACAAIDD 175 (528)
Q Consensus 97 ~~s~A~~al~~v~~~i~~~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~-p~~~~~~e 175 (528)
.+.|...++.|. ..++.+++ ...++.++++.++..||+||||.|.++|+|+.+||++|.|++- .......|
T Consensus 256 -~s~Ac~~ILeim---qkEA~~~k----~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpE 327 (584)
T KOG2193|consen 256 -TSKACKMILEIM---QKEAVDDK----VAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPE 327 (584)
T ss_pred -hHHHHHHHHHHH---HHhhhccc----hhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCcc
Confidence 444544444443 33322221 2247889999999999999999999999999999999999985 33344569
Q ss_pred ceEEEeccHHHHHHHHHHHHHHHccCCCCCCCCcccCCCccccccCCCCCCCCCCCCCCC-CCCC-CCCCCCCCCCCCCC
Q 009695 176 QLIQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLS-LVPP-LTGNPSDNASEFHS 253 (528)
Q Consensus 176 r~V~I~G~~~~V~kA~~~I~~~l~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~p~~~-~~p~-~~~~~~~y~~~~~p 253 (528)
|.|++.|+.|+|.+|..+|..+|+++...+-.......+++.+ ...+.-.+||..+ +.|+ .......+++.++-
T Consensus 328 RTItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~----l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~ 403 (584)
T KOG2193|consen 328 RTITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPG----LNLPALGLFPSSSAVSPPHFPPSPVTFASPYPL 403 (584)
T ss_pred ceEEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcc----cCccccCCCCcccccCCCCCCCCccccCCCchh
Confidence 9999999999999999999999998743331111111111100 0000011122111 1111 00111111111000
Q ss_pred CCCCCCCCCCCCCcCCCCcceEEEEEeeccccceeeccCCchhHhhHhhcCeeEEEeCC-CCCCCccEEEEecccccCCC
Q 009695 254 SSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP-LTKSGERVVTISALEYLDTR 332 (528)
Q Consensus 254 ~~~~~~~~~~~~~~~~~~~~~~~~l~vP~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~-~~~~~eR~V~I~G~e~p~~~ 332 (528)
+ ......-.++|+||..++|.||||+|.+||.|.+.+||+|+|..+ .++..+|+|+|+|. |+
T Consensus 404 ~-------------hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGp--pe-- 466 (584)
T KOG2193|consen 404 F-------------HQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGP--PE-- 466 (584)
T ss_pred h-------------hcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCC--hH--
Confidence 0 011133467899999999999999999999999999999999865 67889999999998 32
Q ss_pred CChHHHHHHHHHhhhhhcccCCCCCCCCCCCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCC
Q 009695 333 HSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAA 412 (528)
Q Consensus 333 ~~~a~~A~~~i~~~i~e~~~~~~~~~~~~~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~ 412 (528)
+.-.|.-.+|.++.|..+- .+.......+.+.||+..+|+||||||.+++|+++.|+|.+.|++. +.|. .
T Consensus 467 --aqfKAQgrifgKikEenf~-----~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrd-qtpd--E 536 (584)
T KOG2193|consen 467 --AQFKAQGRIFGKIKEENFF-----LPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRD-QTPD--E 536 (584)
T ss_pred --HHHhhhhhhhhhhhhhccC-----CchhhheeeeeeeccchhhhhhhccccccHHHHhccccceEEcccc-CCCC--c
Confidence 2235666677777664321 2234567889999999999999999999999999999999988665 4554 4
Q ss_pred CCCcEEEEcCCHHHHHHHHHHHHHHHhhhcCCC
Q 009695 413 QNDVVIQISGEYKNVQNALSEVVGRLRHNLKSG 445 (528)
Q Consensus 413 ~~~~~V~ItG~~~~v~~A~~~I~~~l~~~~~~~ 445 (528)
.+..+|.|+|.+.+.+.|++.|.+++.++-...
T Consensus 537 nd~vivriiGhfyatq~aQrki~~iv~qvkq~~ 569 (584)
T KOG2193|consen 537 NDQVIVRIIGHFYATQNAQRKIAHIVNQVKQSG 569 (584)
T ss_pred cceeeeeeechhhcchHHHHHHHHHHHHHHHhh
Confidence 566789999999999999999999998775554
No 4
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=1.8e-34 Score=269.77 Aligned_cols=292 Identities=17% Similarity=0.256 Sum_probs=207.1
Q ss_pred CCCCCCceEEEEEecccccccccccCchHHHHHHhhhCceEEecCCCCCCCceEEEEEcCCcchhhhhcccccccccCCC
Q 009695 18 LNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGE 97 (528)
Q Consensus 18 ~~~~~~~~~~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i~~~~~~~~eRvi~I~G~~~~~~~~~~~~~~~~~~~~~ 97 (528)
-....+.+.+|||+.++.+|+||||+|+|||.|+.+++|.|.|.|+ ..+|||++|++..+.+
T Consensus 41 qa~k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri~tisad~~ti---------------- 102 (390)
T KOG2192|consen 41 QAFKRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILTISADIETI---------------- 102 (390)
T ss_pred HHhhhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCceeEEEeccHHHH----------------
Confidence 3445567999999999999999999999999999999999999987 6789999999866432
Q ss_pred cchHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCce
Q 009695 98 VSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQL 177 (528)
Q Consensus 98 ~s~A~~al~~v~~~i~~~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~ 177 (528)
-+.|.+|+.++.+.- ...++..+||||+.+++|.|||++|++||++++++.|+++|..+ -|+.++||+
T Consensus 103 ----~~ilk~iip~lee~f-------~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~-c~p~stdrv 170 (390)
T KOG2192|consen 103 ----GEILKKIIPTLEEGF-------QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE-CCPHSTDRV 170 (390)
T ss_pred ----HHHHHHHhhhhhhCC-------CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc-cCCCCcceE
Confidence 233334444433221 12347889999999999999999999999999999999999994 889999999
Q ss_pred EEEeccHHHHHHHHHHHHHHHccCCCCCCC-Cc--ccCCCccccccCCCCC------CCCCCCCCC--CCCCCCCCC---
Q 009695 178 IQITGATLAVKKALVAVTTCLQHLSTMEKS-PI--CFNRPIEKVFYSNSSD------PHREFFPHL--SLVPPLTGN--- 243 (528)
Q Consensus 178 V~I~G~~~~V~kA~~~I~~~l~~~~~~~~~-~~--~~~~p~~~~~~~~~~~------~~~~~~p~~--~~~p~~~~~--- 243 (528)
|.|.|.+.+|..++..|.+.|.+.+.+... +. .||.+. ..+..++. ......|++ ...|+-.+.
T Consensus 171 ~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t--~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlm 248 (390)
T KOG2192|consen 171 VLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNFYDET--YDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLM 248 (390)
T ss_pred EEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccccCcc--cccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccc
Confidence 999999999999999999999998776653 21 222222 22222211 011112222 111110000
Q ss_pred --------CCCC-------------------CCCCCCCCCC----------CCCCCCCCCcCCCCcceEEEEEeeccccc
Q 009695 244 --------PSDN-------------------ASEFHSSSAD----------ADRDHPGLDKKGRKQEVALRMLFSGWTAS 286 (528)
Q Consensus 244 --------~~~y-------------------~~~~~p~~~~----------~~~~~~~~~~~~~~~~~~~~l~vP~~~vG 286 (528)
...| +++-|.+... +.+...+... ....-++..+.||.++-|
T Consensus 249 ay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGd-lGGPitTaQvtip~dlgg 327 (390)
T KOG2192|consen 249 AYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGD-LGGPITTAQVTIPKDLGG 327 (390)
T ss_pred eeccCCCCCccccccccccccccCCCcCCCcCccccccccCCCCCCCCCccccccccccCC-CCCceeeeeEecccccCc
Confidence 0011 1111111000 0000000111 113456777899999999
Q ss_pred eeeccCCchhHhhHhhcCeeEEEeCCCCCCCccEEEEecccccCCCCChHHHHHHHHHhhhh
Q 009695 287 GIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSV 348 (528)
Q Consensus 287 ~IIGkgG~~Ik~I~~~tGa~I~i~~~~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i~~~i~ 348 (528)
.||||||.+|++|++++||+|+++++..++.+|+++|+|++ ...+.|..++++.+.
T Consensus 328 siigkggqri~~ir~esGA~IkidepleGsedrIitItGTq------dQIqnAQYLlQn~Vk 383 (390)
T KOG2192|consen 328 SIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ------DQIQNAQYLLQNSVK 383 (390)
T ss_pred ceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccH------HHHhhHHHHHHHHHH
Confidence 99999999999999999999999999999999999999995 456777777776553
No 5
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.97 E-value=6e-30 Score=264.96 Aligned_cols=246 Identities=20% Similarity=0.307 Sum_probs=195.9
Q ss_pred CCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHccCCCCC
Q 009695 126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTME 205 (528)
Q Consensus 126 ~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G~~~~V~kA~~~I~~~l~~~~~~~ 205 (528)
+..++.+.-||...+|+||||+|+.|..|+.+|||+|++..+ .....+|.+.++|.+++|+.|+.+|.+++....
T Consensus 51 ~~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~--~s~~~~r~~~~~G~pe~v~~aK~li~evv~r~~--- 125 (600)
T KOG1676|consen 51 DTVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAAD--PSGIGYRSVDLTGSPENVEVAKQLIGEVVSRGR--- 125 (600)
T ss_pred ccccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCC--CCCcccccccccCCcccHHHHHHhhhhhhhccC---
Confidence 357788999999999999999999999999999999998764 234589999999999999999999998885431
Q ss_pred CCCcccCCCccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCcceEEEEEeecccc
Q 009695 206 KSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTA 285 (528)
Q Consensus 206 ~~~~~~~~p~~~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~y~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~l~vP~~~v 285 (528)
.. ..|++ .....+++.+|+||++++
T Consensus 126 -~~--------------------~~~~~----------------------------------~q~~~~ttqeI~IPa~k~ 150 (600)
T KOG1676|consen 126 -PP--------------------GGFPD----------------------------------NQGSVETTQEILIPANKC 150 (600)
T ss_pred -CC--------------------CCccc----------------------------------cCCccceeeeeccCccce
Confidence 00 00111 011356789999999999
Q ss_pred ceeeccCCchhHhhHhhcCeeEEEeCC--CCCCCccEEEEecccccCCCCChHHHHHHHHHhhhhhcccCCC---CCCCC
Q 009695 286 SGIIGKRGAIVRSLQNASGALISFAAP--LTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQG---FSSGE 360 (528)
Q Consensus 286 G~IIGkgG~~Ik~I~~~tGa~I~i~~~--~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i~~~i~e~~~~~~---~~~~~ 360 (528)
|.||||+|++||.|++.+||.+.+... ......+.+.|+|.. ...+.|..++.+.+.|..-+.. ...+.
T Consensus 151 GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp------~~ve~a~~lV~dil~e~~~~~~g~~~~~g~ 224 (600)
T KOG1676|consen 151 GLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDP------DKVEQAKQLVADILREEDDEVPGSGGHAGV 224 (600)
T ss_pred eeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCH------HHHHHHHHHHHHHHHhcccCCCccccccCc
Confidence 999999999999999999999887642 333478899999982 3455666677666654221111 11122
Q ss_pred CCCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 009695 361 NKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH 440 (528)
Q Consensus 361 ~~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~~~~v~~A~~~I~~~l~~ 440 (528)
......+.+|.||.+.||.||||+|++||+|+.+|||+|+|.+.++ | .+.+|.++|.|++++|++|.++|.++|++
T Consensus 225 ~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~-p---~speR~~~IiG~~d~ie~Aa~lI~eii~~ 300 (600)
T KOG1676|consen 225 RGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD-P---SSPERPAQIIGTVDQIEHAAELINEIIAE 300 (600)
T ss_pred CccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCC-C---CCccceeeeecCHHHHHHHHHHHHHHHHH
Confidence 2344569999999999999999999999999999999999988765 3 47899999999999999999999999986
Q ss_pred h
Q 009695 441 N 441 (528)
Q Consensus 441 ~ 441 (528)
.
T Consensus 301 ~ 301 (600)
T KOG1676|consen 301 A 301 (600)
T ss_pred H
Confidence 4
No 6
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.96 E-value=1.9e-28 Score=229.41 Aligned_cols=233 Identities=21% Similarity=0.344 Sum_probs=188.8
Q ss_pred ceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHccCCCCCCC
Q 009695 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKS 207 (528)
Q Consensus 128 ~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G~~~~V~kA~~~I~~~l~~~~~~~~~ 207 (528)
.+.++||+.++.+|.||||||++||+++.+++|+|+|.. ....+|+++|+.+.+-|-+-++.|.-.|++...
T Consensus 47 r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpd----s~~peri~tisad~~ti~~ilk~iip~lee~f~---- 118 (390)
T KOG2192|consen 47 RVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPD----SSGPERILTISADIETIGEILKKIIPTLEEGFQ---- 118 (390)
T ss_pred ceeEEEEEecccccceeccccccHHHHhhhccceeeccC----CCCCceeEEEeccHHHHHHHHHHHhhhhhhCCC----
Confidence 689999999999999999999999999999999999977 356899999999999999999999888877420
Q ss_pred CcccCCCccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCcceEEEEEeeccccce
Q 009695 208 PICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASG 287 (528)
Q Consensus 208 ~~~~~~p~~~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~y~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~l~vP~~~vG~ 287 (528)
....+.++|+|..+++|.
T Consensus 119 --------------------------------------------------------------~~~pce~rllihqs~ag~ 136 (390)
T KOG2192|consen 119 --------------------------------------------------------------LPSPCELRLLIHQSLAGG 136 (390)
T ss_pred --------------------------------------------------------------CCCchhhhhhhhhhhccc
Confidence 123467889999999999
Q ss_pred eeccCCchhHhhHhhcCeeEEEe-CCCCCCCccEEEEecccccCCCCChHHHHHHHHHhhhhhccc--------------
Q 009695 288 IIGKRGAIVRSLQNASGALISFA-APLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG-------------- 352 (528)
Q Consensus 288 IIGkgG~~Ik~I~~~tGa~I~i~-~~~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i~~~i~e~~~-------------- 352 (528)
|||++|++||+|++++.|+.+|- .-.+++++|++.|.|.. ....+-+..+.+.+.|..+
T Consensus 137 iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~------k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~ 210 (390)
T KOG2192|consen 137 IIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKP------KRVVECIKIILDLISESPIKGSAQPYDPNFYDE 210 (390)
T ss_pred eecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCc------chHHHHHHHHHHHhhcCCcCCcCCcCCccccCc
Confidence 99999999999999999999886 45889999999999972 2233333334433333200
Q ss_pred --------------------------------------------------------------------------CCCCCC
Q 009695 353 --------------------------------------------------------------------------QQGFSS 358 (528)
Q Consensus 353 --------------------------------------------------------------------------~~~~~~ 358 (528)
+.++++
T Consensus 211 t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYeP 290 (390)
T KOG2192|consen 211 TYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEP 290 (390)
T ss_pred ccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCcCccccccccCC
Confidence 000000
Q ss_pred -----------C------CCCCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEc
Q 009695 359 -----------G------ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQIS 421 (528)
Q Consensus 359 -----------~------~~~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~It 421 (528)
+ .-.+...|+.+.||++.-|.||||||+.|++|++++||.|+|....+ .+.+++++|+
T Consensus 291 QgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikideple-----GsedrIitIt 365 (390)
T KOG2192|consen 291 QGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLE-----GSEDRIITIT 365 (390)
T ss_pred CCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCC-----CCCceEEEEe
Confidence 0 00123578999999999999999999999999999999999976433 6789999999
Q ss_pred CCHHHHHHHHHHHHHHHhhh
Q 009695 422 GEYKNVQNALSEVVGRLRHN 441 (528)
Q Consensus 422 G~~~~v~~A~~~I~~~l~~~ 441 (528)
|+.+|++.|++++...++.+
T Consensus 366 GTqdQIqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 366 GTQDQIQNAQYLLQNSVKQY 385 (390)
T ss_pred ccHHHHhhHHHHHHHHHHhh
Confidence 99999999999999999854
No 7
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.96 E-value=8.2e-29 Score=244.75 Aligned_cols=240 Identities=18% Similarity=0.296 Sum_probs=191.1
Q ss_pred ceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHccCCCCCCC
Q 009695 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKS 207 (528)
Q Consensus 128 ~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G~~~~V~kA~~~I~~~l~~~~~~~~~ 207 (528)
+..+|+|||..++|.||||.|.+||.|-..|-|+|.|... ..++..|+.++|-|.+|...+|+.+|.++++.....++
T Consensus 198 D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrk-en~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~~~k- 275 (584)
T KOG2193|consen 198 DWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRK-ENAGAAEKIITVHSTPEGTSKACKMILEIMQKEAVDDK- 275 (584)
T ss_pred CcceeeeeccceeEEEecCCCccccCcchhhhheeeeeec-ccCCcccCceEEecCccchHHHHHHHHHHHHHhhhccc-
Confidence 4568999999999999999999999999999999999986 45688999999999999999999999999976421111
Q ss_pred CcccCCCccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCcceEEEEEeeccccce
Q 009695 208 PICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASG 287 (528)
Q Consensus 208 ~~~~~~p~~~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~y~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~l~vP~~~vG~ 287 (528)
...++.++++-.+.++|+
T Consensus 276 --------------------------------------------------------------~~~e~pLk~lAHN~lvGR 293 (584)
T KOG2193|consen 276 --------------------------------------------------------------VAEEIPLKILAHNNLVGR 293 (584)
T ss_pred --------------------------------------------------------------hhhhcchhhhhhcchhhh
Confidence 135778889999999999
Q ss_pred eeccCCchhHhhHhhcCeeEEEeCC---CCCCCccEEEEecccccCCCCChHHHHHHHHHhhhhh---ccc---------
Q 009695 288 IIGKRGAIVRSLQNASGALISFAAP---LTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVE---VEG--------- 352 (528)
Q Consensus 288 IIGkgG~~Ik~I~~~tGa~I~i~~~---~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i~~~i~e---~~~--------- 352 (528)
+|||.|.+||+|+++||+.|.|..- .--..||+|++.|+- + +...|-.+|..++.+ +++
T Consensus 294 LIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsi--E----ac~~AE~eImkKlre~yEnDl~a~s~q~~l 367 (584)
T KOG2193|consen 294 LIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSI--E----ACVQAEAEIMKKLRECYENDLAAMSLQCHL 367 (584)
T ss_pred hhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccH--H----HHHHHHHHHHHHHHHHHhhhHHHhhccCCC
Confidence 9999999999999999999999752 234569999999972 2 222233333333322 111
Q ss_pred CCCC--------C-----------CCC-----------CCCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEe
Q 009695 353 QQGF--------S-----------SGE-----------NKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLV 402 (528)
Q Consensus 353 ~~~~--------~-----------~~~-----------~~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~ 402 (528)
..++ + +.. .......++|.||...+|.|||++|++||.|.+.+||.|+|.
T Consensus 368 ~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIa 447 (584)
T KOG2193|consen 368 PPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIA 447 (584)
T ss_pred CcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeec
Confidence 0000 0 000 011346689999999999999999999999999999999998
Q ss_pred CCCCccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhh
Q 009695 403 GGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN 441 (528)
Q Consensus 403 ~~~~~p~~~~~~~~~V~ItG~~~~v~~A~~~I~~~l~~~ 441 (528)
+.+- | +..+|+|+|+|++++..+|+..|..+|++.
T Consensus 448 ppE~-p---dvseRMViItGppeaqfKAQgrifgKikEe 482 (584)
T KOG2193|consen 448 PPEI-P---DVSERMVIITGPPEAQFKAQGRIFGKIKEE 482 (584)
T ss_pred CCCC-C---CcceeEEEecCChHHHHhhhhhhhhhhhhh
Confidence 8653 3 578999999999999999999999999863
No 8
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.95 E-value=2.7e-27 Score=227.98 Aligned_cols=239 Identities=22% Similarity=0.307 Sum_probs=170.9
Q ss_pred CCCCCCceEEEEEecccccccccccCchHHHHHHhhhCceEEecC---CCCCCCceEEEEEcCCcchhhhhccccccccc
Q 009695 18 LNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEG---GFPGSDHRVILVVGSGSIDRRIMFCENDVVVE 94 (528)
Q Consensus 18 ~~~~~~~~~~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i~~---~~~~~~eRvi~I~G~~~~~~~~~~~~~~~~~~ 94 (528)
+....+.+++|+|||+..+|.||||+|++|.+||++|||+|++++ .+|++.||||.|.|+.+++
T Consensus 32 n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai------------- 98 (402)
T KOG2191|consen 32 NTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEAL------------- 98 (402)
T ss_pred cCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHH-------------
Confidence 334455699999999999999999999999999999999999975 4899999999999987542
Q ss_pred CCCcchHHHHHH-HHHHHHhhhhhccCC------CCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcC-
Q 009695 95 GGEVSSTQEAVI-RVFERMWEVEAEVEG------DGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP- 166 (528)
Q Consensus 95 ~~~~s~A~~al~-~v~~~i~~~~~~~~~------~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~- 166 (528)
.|+. .+.++|.+.....++ ....++.-.++++||++.+|.||||+|.+||.|++++||.|+|++
T Consensus 99 --------~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPq 170 (402)
T KOG2191|consen 99 --------NAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQ 170 (402)
T ss_pred --------HHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEeccc
Confidence 2222 233344443222222 012334456899999999999999999999999999999999994
Q ss_pred CCCCCCCCCceEEEeccHHHHHHHHHHHHHHHccCCCCCCCCcccCCCccccccCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009695 167 PPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSD 246 (528)
Q Consensus 167 ~p~~~~~~er~V~I~G~~~~V~kA~~~I~~~l~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~ 246 (528)
+|.--...||+|++.|++++..+|+.+|.++|.++++........| ..-. +...+++.+..+
T Consensus 171 kpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sy--------a~vs----------GpvaNsnPtGsp 232 (402)
T KOG2191|consen 171 KPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISY--------ANVS----------GPVANSNPTGSP 232 (402)
T ss_pred CCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceeccch--------hccc----------CcccccCCCCCC
Confidence 3666678999999999999999999999999999876554322111 0000 000011111112
Q ss_pred CCCCCCCCCCCCCCCCCCCCcCCCCcceEEEEEeeccccceeeccCCchhHhhHhhcCeeEEEeC
Q 009695 247 NASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAA 311 (528)
Q Consensus 247 y~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~l~vP~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~ 311 (528)
|+.. ... .....+...-++....|..-|.+|.++-.|-.-+|+.+.+.+
T Consensus 233 ya~~-------~~~---------~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq 281 (402)
T KOG2191|consen 233 YAYQ-------AHV---------LPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQ 281 (402)
T ss_pred CCCC-------Ccc---------ccccchhhccccccccccccccccccceeeecccccceeecc
Confidence 2111 100 011112224578889999999999999999999999888865
No 9
>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=8.2e-25 Score=210.97 Aligned_cols=166 Identities=22% Similarity=0.315 Sum_probs=137.1
Q ss_pred cceEEEEEeeccccceeeccCCchhHhhHhhcCeeEEEeC---CCCCCCccEEEEecccccCCCCChHHHHHHHHHhhhh
Q 009695 272 QEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAA---PLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSV 348 (528)
Q Consensus 272 ~~~~~~l~vP~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~---~~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i~~~i~ 348 (528)
..+.++++||+..+|.||||||++|.+||.+|||+|++.+ .-|+++||++.|+|+- ++++.+++.|.
T Consensus 37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~----------eai~av~efI~ 106 (402)
T KOG2191|consen 37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTV----------EALNAVHEFIA 106 (402)
T ss_pred CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccH----------HHHHHHHHHHH
Confidence 4489999999999999999999999999999999999985 3789999999999992 45555555554
Q ss_pred hcccCCCCCC--------CCCCCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEE
Q 009695 349 EVEGQQGFSS--------GENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQI 420 (528)
Q Consensus 349 e~~~~~~~~~--------~~~~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~I 420 (528)
++..+.+... ....+....+++.||+..+|.||||+|.+||.|++++||+|+|.+. .|...+..+|+||+
T Consensus 107 dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPq--kpt~~sLqervvt~ 184 (402)
T KOG2191|consen 107 DKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQ--KPTGISLQERVVTV 184 (402)
T ss_pred HHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEeccc--CCCCccceeEEEEe
Confidence 4322211110 0112334568999999999999999999999999999999999973 34444678999999
Q ss_pred cCCHHHHHHHHHHHHHHHhhhcCCCcccC
Q 009695 421 SGEYKNVQNALSEVVGRLRHNLKSGEILN 449 (528)
Q Consensus 421 tG~~~~v~~A~~~I~~~l~~~~~~~~~~~ 449 (528)
+|++|+..+|..+|.++|.+++...+|++
T Consensus 185 sge~e~~~~A~~~IL~Ki~eDpqs~scln 213 (402)
T KOG2191|consen 185 SGEPEQNMKAVSLILQKIQEDPQSGSCLN 213 (402)
T ss_pred cCCHHHHHHHHHHHHHHhhcCCcccceec
Confidence 99999999999999999999999999987
No 10
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.87 E-value=4e-21 Score=202.81 Aligned_cols=168 Identities=27% Similarity=0.401 Sum_probs=140.9
Q ss_pred cceEEEEEeeccccceeeccCCchhHhhHhhcCeeEEEeCCCCCCCccEEEEecccccCCCCChHHHHHHHHHhhhhhcc
Q 009695 272 QEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVE 351 (528)
Q Consensus 272 ~~~~~~l~vP~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i~~~i~e~~ 351 (528)
...++||+|+...+|.||||+|.+|++|+.+|.++|+|.+..+++.||+++|+|+.... ..+++++|+..+++++....
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 ETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVEL-NLSPATDALFKAFDMIVFKL 119 (485)
T ss_pred CcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccc-cCCchHHHHHHHHHHHhhcc
Confidence 34459999999999999999999999999999999999999999999999999953332 55788999999999987642
Q ss_pred c---CCCCCCCCC-CCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcCCHHHH
Q 009695 352 G---QQGFSSGEN-KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNV 427 (528)
Q Consensus 352 ~---~~~~~~~~~-~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~~~~v 427 (528)
. ....+.+.. ....++.+|+||.+++|+||||+|+.||+|++.|||+|++.+. .+|. .+++.|+|.|++++|
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 EEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAV 195 (485)
T ss_pred cccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHH
Confidence 1 111111111 2225899999999999999999999999999999999999887 6675 677889999999999
Q ss_pred HHHHHHHHHHHhhhcCC
Q 009695 428 QNALSEVVGRLRHNLKS 444 (528)
Q Consensus 428 ~~A~~~I~~~l~~~~~~ 444 (528)
.+|+..|..+|.+++.+
T Consensus 196 ~~al~~Is~~L~~~~~~ 212 (485)
T KOG2190|consen 196 KKALVQISSRLLENPPR 212 (485)
T ss_pred HHHHHHHHHHHHhcCCc
Confidence 99999999999986544
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=99.57 E-value=9.9e-15 Score=135.42 Aligned_cols=138 Identities=18% Similarity=0.208 Sum_probs=95.8
Q ss_pred EEecccccccccccCchHHHHHHhhhCceEEecCCCCCCCceEEEEE---cCCcchhhhhcccccccccCCCcchHHHHH
Q 009695 29 LVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVV---GSGSIDRRIMFCENDVVVEGGEVSSTQEAV 105 (528)
Q Consensus 29 ilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i~~~~~~~~eRvi~I~---G~~~~~~~~~~~~~~~~~~~~~~s~A~~al 105 (528)
+.||.+++|.|||++|++|++|+++|||+|++++. +..|.|. +.++. +..|.+.+
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~-----------------i~kA~~~I 59 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLA-----------------VMKAREVV 59 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHH-----------------HHHHHHHH
Confidence 45799999999999999999999999999999864 3457773 32222 22333333
Q ss_pred HHHHHHHhhhhhccCCCCCCCCceEEEE-Eeec---------ceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCC
Q 009695 106 IRVFERMWEVEAEVEGDGDGDDVAYCGL-LANT---------TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDD 175 (528)
Q Consensus 106 ~~v~~~i~~~~~~~~~~~~~~~~v~~rl-lVp~---------~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~e 175 (528)
..+.. ...++..- ...+..+++++ -+.. ..+|+|||++|++++.|++.|||+|.|. +
T Consensus 60 ~~i~~---gf~~e~A~-~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~---------~ 126 (172)
T TIGR03665 60 KAIGR---GFSPEKAL-KLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY---------G 126 (172)
T ss_pred HHHHc---CCCHHHHH-HhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc---------C
Confidence 32211 00111000 00011223222 2222 3789999999999999999999999994 3
Q ss_pred ceEEEeccHHHHHHHHHHHHHHHccC
Q 009695 176 QLIQITGATLAVKKALVAVTTCLQHL 201 (528)
Q Consensus 176 r~V~I~G~~~~V~kA~~~I~~~l~~~ 201 (528)
+.|.|.|++++++.|..+|.+++.+.
T Consensus 127 ~~v~i~G~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 127 KTVGIIGDPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred CEEEEECCHHHHHHHHHHHHHHHcCC
Confidence 77999999999999999999999654
No 12
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.54 E-value=6.7e-14 Score=130.75 Aligned_cols=142 Identities=17% Similarity=0.213 Sum_probs=98.1
Q ss_pred eEEEEEecccccccccccCchHHHHHHhhhCceEEecCCCCCCCceEEEEE----cCCcchhhhhcccccccccCCCcch
Q 009695 25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVV----GSGSIDRRIMFCENDVVVEGGEVSS 100 (528)
Q Consensus 25 ~~~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i~~~~~~~~eRvi~I~----G~~~~~~~~~~~~~~~~~~~~~~s~ 100 (528)
+...+.||.+++|.|||++|++|+.|+++|||+|++.+. +..|.|. ++++. +..
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~-----------------i~k 60 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLA-----------------VLK 60 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHH-----------------HHH
Confidence 567889999999999999999999999999999999864 3556775 22222 222
Q ss_pred HHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEE-----ee-----cceeeEEecCCChHHHHHHhhhCCeEEEcCCCCC
Q 009695 101 TQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLL-----AN-----TTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPAC 170 (528)
Q Consensus 101 A~~al~~v~~~i~~~~~~~~~~~~~~~~v~~rll-----Vp-----~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~ 170 (528)
|++.+..+.. ...++... ...+..+..++. .+ ...+|+|||++|++++.|++.|||+|.|..
T Consensus 61 A~~~I~ai~~---gf~~e~A~-~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~---- 132 (180)
T PRK13763 61 ARDIVKAIGR---GFSPEKAL-RLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG---- 132 (180)
T ss_pred HHHHHHHHhc---CCCHHHHH-HHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC----
Confidence 3333332221 00011000 000012222211 11 136899999999999999999999999954
Q ss_pred CCCCCceEEEeccHHHHHHHHHHHHHHHccC
Q 009695 171 AAIDDQLIQITGATLAVKKALVAVTTCLQHL 201 (528)
Q Consensus 171 ~~~~er~V~I~G~~~~V~kA~~~I~~~l~~~ 201 (528)
+.|.|.|++++++.|...|..+++..
T Consensus 133 -----~~v~i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 133 -----KTVAIIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred -----CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence 44899999999999999999999654
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=99.54 E-value=2.6e-14 Score=132.65 Aligned_cols=136 Identities=22% Similarity=0.245 Sum_probs=96.1
Q ss_pred EEeeccccceeeccCCchhHhhHhhcCeeEEEeCCCCCCCccEEEEe-cccccCCCCChHHHHHHHHHhhhhhcccCCCC
Q 009695 278 MLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTIS-ALEYLDTRHSPVQNAAVLVFARSVEVEGQQGF 356 (528)
Q Consensus 278 l~vP~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~~~~~~eR~V~I~-G~e~p~~~~~~a~~A~~~i~~~i~e~~~~~~~ 356 (528)
+.||.+++|.|||+||++|+.|+++||++|++.+. +..|.|. .+.+| ...+.|...+..... ++
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~----~~i~kA~~~I~~i~~------gf 66 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDP----LAVMKAREVVKAIGR------GF 66 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCH----HHHHHHHHHHHHHHc------CC
Confidence 56899999999999999999999999999999742 3568883 11112 233444444433221 11
Q ss_pred CCC----CCCCCceEEEEEeCC---------cceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcCC
Q 009695 357 SSG----ENKGDAVAVSILVGA---------DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGE 423 (528)
Q Consensus 357 ~~~----~~~~~~~t~~v~VP~---------~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~ 423 (528)
++. .-.+.-.-.-+.|+. ..+|+|||++|++++.|+..|||+|.|.+ ..|.|+|+
T Consensus 67 ~~e~A~~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------------~~v~i~G~ 134 (172)
T TIGR03665 67 SPEKALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------------KTVGIIGD 134 (172)
T ss_pred CHHHHHHhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------------CEEEEECC
Confidence 110 000111122233433 47999999999999999999999998842 57999999
Q ss_pred HHHHHHHHHHHHHHHhh
Q 009695 424 YKNVQNALSEVVGRLRH 440 (528)
Q Consensus 424 ~~~v~~A~~~I~~~l~~ 440 (528)
+++++.|..+|...|..
T Consensus 135 ~~~~~~A~~~i~~li~~ 151 (172)
T TIGR03665 135 PEQVQIAREAIEMLIEG 151 (172)
T ss_pred HHHHHHHHHHHHHHHcC
Confidence 99999999999998853
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.47 E-value=2.8e-13 Score=126.58 Aligned_cols=141 Identities=18% Similarity=0.221 Sum_probs=96.5
Q ss_pred EEEEEeeccccceeeccCCchhHhhHhhcCeeEEEeCCCCCCCccEEEEe---cccccCCCCChHHHHHHHHHhhhhhcc
Q 009695 275 ALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTIS---ALEYLDTRHSPVQNAAVLVFARSVEVE 351 (528)
Q Consensus 275 ~~~l~vP~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~~~~~~eR~V~I~---G~e~p~~~~~~a~~A~~~i~~~i~e~~ 351 (528)
...+.||.+.+|.|||++|++|+.|+++||++|++.+. +..|.|. +. ++ ...+.|...+..-.....
T Consensus 4 ~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~-d~----~~i~kA~~~I~ai~~gf~ 73 (180)
T PRK13763 4 MEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGE-DP----LAVLKARDIVKAIGRGFS 73 (180)
T ss_pred eEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCC-CH----HHHHHHHHHHHHHhcCCC
Confidence 45688999999999999999999999999999999743 3677776 22 12 233344444433221100
Q ss_pred cCCCCCCCCCCCCceEEE-EEeC---------CcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEc
Q 009695 352 GQQGFSSGENKGDAVAVS-ILVG---------ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQIS 421 (528)
Q Consensus 352 ~~~~~~~~~~~~~~~t~~-v~VP---------~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~It 421 (528)
.+..+- . .+.....+ +.+. ...+|+|||++|++++.|+..|||+|+|.. ..|.|.
T Consensus 74 ~e~A~~--l-~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~------------~~v~i~ 138 (180)
T PRK13763 74 PEKALR--L-LDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG------------KTVAII 138 (180)
T ss_pred HHHHHH--H-hCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC------------CEEEEE
Confidence 000000 0 01111111 1111 137999999999999999999999999852 349999
Q ss_pred CCHHHHHHHHHHHHHHHhh
Q 009695 422 GEYKNVQNALSEVVGRLRH 440 (528)
Q Consensus 422 G~~~~v~~A~~~I~~~l~~ 440 (528)
|++++++.|...|...++.
T Consensus 139 G~~~~~~~A~~~I~~li~g 157 (180)
T PRK13763 139 GDPEQVEIAREAIEMLIEG 157 (180)
T ss_pred eCHHHHHHHHHHHHHHHcC
Confidence 9999999999999998864
No 15
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.36 E-value=1.7e-12 Score=100.74 Aligned_cols=64 Identities=31% Similarity=0.549 Sum_probs=59.0
Q ss_pred EEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEeccHHHHHHHHHHH
Q 009695 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV 194 (528)
Q Consensus 130 ~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G~~~~V~kA~~~I 194 (528)
+++|+||.+.+|+||||+|++|++|+++|||+|++.+. ......+|+|+|+|+++++.+|+.+|
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 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKS-VLPGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCC-CCCCCCceEEEEEeCHHHHHHHHHhh
Confidence 36899999999999999999999999999999999984 33478899999999999999999987
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=2.1e-12 Score=100.21 Aligned_cols=64 Identities=28% Similarity=0.471 Sum_probs=58.0
Q ss_pred EEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcCCHHHHHHHHHHH
Q 009695 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEV 434 (528)
Q Consensus 367 t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~~~~v~~A~~~I 434 (528)
+.+|.||.+.+|+|||++|.+|++|+++|||+|++.+... ...++++|+|+|++++++.|+.+|
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 3689999999999999999999999999999999987543 246789999999999999999987
No 17
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.29 E-value=1.6e-11 Score=127.06 Aligned_cols=257 Identities=20% Similarity=0.229 Sum_probs=164.9
Q ss_pred CCCCCCceEEEEEecccccccccccCchHHHHHHhhhCceEEecCCCCCCCceEEEEEcCCcchhhhhcccccccccCCC
Q 009695 18 LNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGE 97 (528)
Q Consensus 18 ~~~~~~~~~~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i~~~~~~~~eRvi~I~G~~~~~~~~~~~~~~~~~~~~~ 97 (528)
..-+++++.+.+.|++..+-.+|||.|++|+.|+..|++||.+.+...+ ++++.++.|.+.+
T Consensus 61 e~e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g-~e~~~~~~~~p~~----------------- 122 (608)
T KOG2279|consen 61 EQKPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG-DERVLLISGFPVQ----------------- 122 (608)
T ss_pred ecCchhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCC-cccchhhccCCCC-----------------
Confidence 4456789999999999999999999999999999999999999776433 5788888876655
Q ss_pred cchHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCce
Q 009695 98 VSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQL 177 (528)
Q Consensus 98 ~s~A~~al~~v~~~i~~~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~ 177 (528)
+++|..++.. .+.+. ..+...+-+|...++.|+|++|+++++|+.-++|+|.+... .-...++.
T Consensus 123 v~~a~a~~~~---~~~~~-----------~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n--gr~g~~~~ 186 (608)
T KOG2279|consen 123 VCKAKAAIHQ---ILTEN-----------TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN--GRLGLSRL 186 (608)
T ss_pred CChHHHHHHH---HHhcC-----------Ccccccccchhhhcccccccchhhhcchhcccccccccccc--cccccccc
Confidence 4555544433 22221 26777889999999999999999999999999999999884 23456788
Q ss_pred EEEeccHHHHHHHHHHHHHHHccCCC-------CCCCCcccCCCccccccCCCCCCCCCCCCCC------CCCCCCCCCC
Q 009695 178 IQITGATLAVKKALVAVTTCLQHLST-------MEKSPICFNRPIEKVFYSNSSDPHREFFPHL------SLVPPLTGNP 244 (528)
Q Consensus 178 V~I~G~~~~V~kA~~~I~~~l~~~~~-------~~~~~~~~~~p~~~~~~~~~~~~~~~~~p~~------~~~p~~~~~~ 244 (528)
..|.|...-+..|..++.+.+.++-. ..........|......... .+.....+|. ++.|..++..
T Consensus 187 ~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~~~~~m~-~~~~s~~~h~~~~t~~s~spg~~~~~ 265 (608)
T KOG2279|consen 187 IKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINVRREDMT-EPGGAGEPHLWKNTSSSMSPGAPLVT 265 (608)
T ss_pred eecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCccccchhhc-ccccCCccccCccchhccCCCCCCcc
Confidence 88988888888899999888865311 11111111112111111000 0001111110 1112211111
Q ss_pred CCCCCCCCCC--CCCCCCCCCCCCcCCCCcceEEEEEeeccccceeeccCCchhHhhHhhcCeeEEEe
Q 009695 245 SDNASEFHSS--SADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFA 310 (528)
Q Consensus 245 ~~y~~~~~p~--~~~~~~~~~~~~~~~~~~~~~~~l~vP~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~ 310 (528)
..+..+... ..+....+.-...........++|.+|+..+|.+||+.|+.++.+...+++.++|-
T Consensus 266 -~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~ 332 (608)
T KOG2279|consen 266 -KEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIW 332 (608)
T ss_pred -cCCCcceeEEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEE
Confidence 000000000 00000000000011223455678999999999999999999999999999999885
No 18
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.24 E-value=2.9e-11 Score=125.05 Aligned_cols=232 Identities=18% Similarity=0.204 Sum_probs=168.5
Q ss_pred CceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHccCCCCCC
Q 009695 127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEK 206 (528)
Q Consensus 127 ~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G~~~~V~kA~~~I~~~l~~~~~~~~ 206 (528)
..+.++++|+...+.+++||+|++|+.|+..++++|.+..+ ....++...+.|-+.++.+|...+..++.+..
T Consensus 66 k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~e---d~g~e~~~~~~~~p~~v~~a~a~~~~~~~~~~---- 138 (608)
T KOG2279|consen 66 KDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTE---DVGDERVLLISGFPVQVCKAKAAIHQILTENT---- 138 (608)
T ss_pred hheeeeEeecccceeeeeccccCCcchhhcccccceecCcc---cCCcccchhhccCCCCCChHHHHHHHHHhcCC----
Confidence 46788999999999999999999999999999999999875 23355556666689999999999998886531
Q ss_pred CCcccCCCccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCcceEEEEEeeccccc
Q 009695 207 SPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTAS 286 (528)
Q Consensus 207 ~~~~~~~p~~~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~y~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~l~vP~~~vG 286 (528)
.+...+.+|...++
T Consensus 139 ------------------------------------------------------------------pvk~~lsvpqr~~~ 152 (608)
T KOG2279|consen 139 ------------------------------------------------------------------PVSEQLSVPQRSVG 152 (608)
T ss_pred ------------------------------------------------------------------cccccccchhhhcc
Confidence 22334568899999
Q ss_pred eeeccCCchhHhhHhhcCeeEEEeCCCCCCCccEEEEecccccCCCCChHHHHHHHHHhhhhhc----------------
Q 009695 287 GIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEV---------------- 350 (528)
Q Consensus 287 ~IIGkgG~~Ik~I~~~tGa~I~i~~~~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i~~~i~e~---------------- 350 (528)
+|+|++|.+++.|+.-++|+|.++...-..-.|...|.+...+ ...|-.++.+++.++
T Consensus 153 ~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~------~~~a~~~~~~~~~edeelv~~~~e~~q~rvp 226 (608)
T KOG2279|consen 153 RIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKE------VAAAKHLILEKVSEDEELVKRIAESAQTRVP 226 (608)
T ss_pred cccccchhhhcchhcccccccccccccccccccceecccccch------HHHHHhhhhccccchhHHhhhchhhcccCCC
Confidence 9999999999999999999999986644455677777776321 112222333322211
Q ss_pred ------cc-----------------------CCCCCC-----------------------CC--CCCCceEEEEEeCCcc
Q 009695 351 ------EG-----------------------QQGFSS-----------------------GE--NKGDAVAVSILVGADF 376 (528)
Q Consensus 351 ------~~-----------------------~~~~~~-----------------------~~--~~~~~~t~~v~VP~~~ 376 (528)
.+ ..+.+. +. ......-.+|.+|...
T Consensus 227 rk~p~n~~~~~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 227 RKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEIL 306 (608)
T ss_pred CCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCccc
Confidence 00 000000 00 0112344689999999
Q ss_pred eeeeecCCCchhHHHHHhhCCeEEEeCCCCccccC-CCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 009695 377 VGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCA-AQNDVVIQISGEYKNVQNALSEVVGRLRH 440 (528)
Q Consensus 377 ~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~-~~~~~~V~ItG~~~~v~~A~~~I~~~l~~ 440 (528)
+|.|||+.|.+++.+...|++.+.|... |-.. -..-.++++.|...-+..+..|+..+.-+
T Consensus 307 sg~lig~~gey~s~yssasn~~~hi~t~---pyt~~v~~~qic~~egkqh~~n~vl~ml~~~~p~ 368 (608)
T KOG2279|consen 307 SGDLIGHAGEYLSVYSSASNHPNHIWTQ---PYTSRVLQLQICVNEGKQHYENSVLEMLTVHVPD 368 (608)
T ss_pred ccchhhhhhhhhhhhhhccCccceEEec---cccchhhhhhhheecchhHHHHHHHhhhhccCCc
Confidence 9999999999999999999999988653 2210 11226788999999999999999866543
No 19
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.23 E-value=1.7e-11 Score=94.19 Aligned_cols=61 Identities=20% Similarity=0.330 Sum_probs=55.4
Q ss_pred EEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcCCHHHHHHHHHHHH
Q 009695 368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVV 435 (528)
Q Consensus 368 ~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~~~~v~~A~~~I~ 435 (528)
.++.||.+++|+|||++|++|++|+++|||+|++++.. +.++.|+|+|+.++|..|+.+|.
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 58999999999999999999999999999999997642 45788999999999999998873
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=99.19 E-value=1.2e-11 Score=94.39 Aligned_cols=60 Identities=27% Similarity=0.422 Sum_probs=54.7
Q ss_pred EEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcCCHHHHHHHHHHH
Q 009695 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEV 434 (528)
Q Consensus 367 t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~~~~v~~A~~~I 434 (528)
|.+|.||.+++|+|||++|++|++|+++|||+|++++. + ++..|+|+|++++|+.|+.+|
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 67999999999999999999999999999999999753 2 355999999999999999986
No 21
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.18 E-value=8e-11 Score=89.94 Aligned_cols=59 Identities=15% Similarity=0.255 Sum_probs=53.5
Q ss_pred eEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcCC-HHHHHHHHHHHH
Q 009695 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGE-YKNVQNALSEVV 435 (528)
Q Consensus 366 ~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~-~~~v~~A~~~I~ 435 (528)
.+..+.||.+++|+|||+||++|++|+++|||+|.+.. +..|+|+|+ +++++.|+.+|.
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----------~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-----------DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-----------CCEEEEEeCCHHHHHHHHHHhC
Confidence 46789999999999999999999999999999999853 357999999 999999999873
No 22
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.14 E-value=1.4e-10 Score=89.42 Aligned_cols=62 Identities=26% Similarity=0.489 Sum_probs=56.4
Q ss_pred EEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcCCHHHHHHHHHHH
Q 009695 368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEV 434 (528)
Q Consensus 368 ~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~~~~v~~A~~~I 434 (528)
.++.||.+++++|||++|++|++|+++|||+|.|++... +..++.|+|.|+.+++..|+.+|
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 589999999999999999999999999999999987533 35688999999999999999887
No 23
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.09 E-value=9.2e-10 Score=123.32 Aligned_cols=214 Identities=20% Similarity=0.257 Sum_probs=153.9
Q ss_pred ceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHccCCCCCCC
Q 009695 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKS 207 (528)
Q Consensus 128 ~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G~~~~V~kA~~~I~~~l~~~~~~~~~ 207 (528)
.+...+-+....+..++||+|.+|.+|++++.+.+.+.. .+.++..+.++|...++.+|...|.....+-...
T Consensus 346 n~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~----~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~--- 418 (753)
T KOG2208|consen 346 NENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK----QGSNNKKVVITGVSANDEKAVEDVEKIIAEILNS--- 418 (753)
T ss_pred ceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc----ccCCCCCeEEeccccchhHHHHHHHHHHHhhhcc---
Confidence 466677888889999999999999999999999999966 4678899999999999999999999988763210
Q ss_pred CcccCCCccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCcceEEEEEeeccccce
Q 009695 208 PICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASG 287 (528)
Q Consensus 208 ~~~~~~p~~~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~y~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~l~vP~~~vG~ 287 (528)
.....+.+|...+.+
T Consensus 419 -----------------------------------------------------------------~~~~~~~iP~k~~~~ 433 (753)
T KOG2208|consen 419 -----------------------------------------------------------------IVKEEVQIPTKSHKR 433 (753)
T ss_pred -----------------------------------------------------------------cccceeecCccchhh
Confidence 112336689999999
Q ss_pred eeccCCchhHhhHhhcC-eeEEEeCCCCCCCccEEEEecccccCCCCChHHHHHHHHHh--hhhhcccCCCCCCCCCCCC
Q 009695 288 IIGKRGAIVRSLQNASG-ALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFA--RSVEVEGQQGFSSGENKGD 364 (528)
Q Consensus 288 IIGkgG~~Ik~I~~~tG-a~I~i~~~~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i~~--~i~e~~~~~~~~~~~~~~~ 364 (528)
+||.+|..|+.|..++| ..|++.. .......+++.|... .... +..+... ..... ...-.
T Consensus 434 iig~~g~~i~~I~~k~~~v~i~f~~--~~~~~~~~~~~~~~~---dv~~---~~~~~~~~~~~a~~---------~~~~~ 496 (753)
T KOG2208|consen 434 IIGTKGALINYIMGKHGGVHIKFQN--NNNSSDMVTIRGISK---DVEK---SVSLLKALKADAKN---------LKFRD 496 (753)
T ss_pred hhccccccHHHHHhhcCcEEEecCC--CCcccccceEecccc---ccch---hHHHHHhhhhhhhc---------chhhh
Confidence 99999999999999999 5566543 344445566666521 1111 1111111 11110 01123
Q ss_pred ceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 009695 365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH 440 (528)
Q Consensus 365 ~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~~~~v~~A~~~I~~~l~~ 440 (528)
..+.+.+.|..+.+..+|+.|..+.. .+...-++... ..++..++|.|..+.|..|+..+...+..
T Consensus 497 ~~~~d~~~~~~~~~~~~g~~~~i~d~----~~~~~i~~~~~------~~~~~~i~i~gk~~~v~~a~~~L~~~~~~ 562 (753)
T KOG2208|consen 497 VVTKDKLLPVKYIGKEIGKNGTIRDS----LGDKSIFPPNE------DEDHEKITIEGKLELVLEAPAELKALIEA 562 (753)
T ss_pred hhhccccchHHhhcccccCceeeecc----CCceeeccccc------ccccceeeecccccchhhhHHHHHhcchh
Confidence 45667788888888888888875554 45555444332 35678899999999999999999888763
No 24
>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=99.09 E-value=1.8e-10 Score=88.47 Aligned_cols=60 Identities=27% Similarity=0.354 Sum_probs=55.3
Q ss_pred EEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEeccHHHHHHHHHHH
Q 009695 131 CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV 194 (528)
Q Consensus 131 ~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G~~~~V~kA~~~I 194 (528)
.++.||..++++|||++|++|++|+++|||+|.+... ...++.|+|+|+.++|.+|+.+|
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~----~~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDP----GSKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCC----CCCCCEEEEEcCHHHHHHHHHHh
Confidence 4789999999999999999999999999999999873 26789999999999999999886
No 25
>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=99.08 E-value=7.7e-11 Score=89.87 Aligned_cols=60 Identities=23% Similarity=0.418 Sum_probs=54.7
Q ss_pred EEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEeccHHHHHHHHHHH
Q 009695 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV 194 (528)
Q Consensus 130 ~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G~~~~V~kA~~~I 194 (528)
|.+|.||.+++|+|||++|++|++|+++|||+|.+..+ + .+..|+|+|+.++|.+|+.+|
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 67899999999999999999999999999999999772 2 455999999999999999886
No 26
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.05 E-value=7.9e-10 Score=84.45 Aligned_cols=58 Identities=26% Similarity=0.343 Sum_probs=52.9
Q ss_pred eEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEecc-HHHHHHHHHHH
Q 009695 129 AYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAV 194 (528)
Q Consensus 129 v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G~-~~~V~kA~~~I 194 (528)
++..+-||.+.+|+||||+|++|++|+++|||+|.+.. ++.|.|.|+ .+++++|+.+|
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~--------~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED--------DGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC--------CCEEEEEeCCHHHHHHHHHHh
Confidence 45678999999999999999999999999999999965 367999999 99999999887
No 27
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.02 E-value=1.2e-09 Score=84.27 Aligned_cols=62 Identities=31% Similarity=0.532 Sum_probs=56.2
Q ss_pred EEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEeccHHHHHHHHHHH
Q 009695 131 CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV 194 (528)
Q Consensus 131 ~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G~~~~V~kA~~~I 194 (528)
.++.||.++++.|||++|++|++|+++|||+|.|... .....++.|.|.|..+++.+|+.+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~--~~~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDS--GSGSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCC--CCCCCceEEEEEcCHHHHHHHHHHh
Confidence 5899999999999999999999999999999999874 1246789999999999999999876
No 28
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.94 E-value=2.1e-09 Score=120.44 Aligned_cols=288 Identities=16% Similarity=0.153 Sum_probs=193.5
Q ss_pred eEEEEEecccccccccccCchHHHHHHhhhCceEEecCCCCCCCceEEEEEcCCcchhhhhcccccccccCCCcchHHHH
Q 009695 25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEA 104 (528)
Q Consensus 25 ~~~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i~~~~~~~~eRvi~I~G~~~~~~~~~~~~~~~~~~~~~~s~A~~a 104 (528)
....+-+-......|+||+|.+|.+|+++++|.|.+... +..+..+.++|...+ +..|.+.
T Consensus 347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~~-----------------~~ka~~~ 407 (753)
T KOG2208|consen 347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSAN-----------------DEKAVED 407 (753)
T ss_pred eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccccc-----------------hhHHHHH
Confidence 445556677889999999999999999999999999884 556778999988765 5556677
Q ss_pred HHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhC-CeEEEcCCCCCCCCCCceEEEecc
Q 009695 105 VIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESG-AKIVMLPPPACAAIDDQLIQITGA 183 (528)
Q Consensus 105 l~~v~~~i~~~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tG-a~I~i~~~p~~~~~~er~V~I~G~ 183 (528)
+..++..+... .+...+.+|...+..|||.+|..|..|++++| ..|+.... ......+++.|.
T Consensus 408 v~~~~~ei~n~------------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~----~~~~~~~~~~~~ 471 (753)
T KOG2208|consen 408 VEKIIAEILNS------------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN----NNSSDMVTIRGI 471 (753)
T ss_pred HHHHHHhhhcc------------cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC----CcccccceEecc
Confidence 66666555431 34456899999999999999999999999999 55555442 345556788888
Q ss_pred HHHHHHHHHHHHHHHccCCCCCCCCcccCCCccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009695 184 TLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHP 263 (528)
Q Consensus 184 ~~~V~kA~~~I~~~l~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~y~~~~~p~~~~~~~~~~ 263 (528)
...+..+......+..+.....
T Consensus 472 ~~dv~~~~~~~~~~~~~a~~~~---------------------------------------------------------- 493 (753)
T KOG2208|consen 472 SKDVEKSVSLLKALKADAKNLK---------------------------------------------------------- 493 (753)
T ss_pred ccccchhHHHHHhhhhhhhcch----------------------------------------------------------
Confidence 7777776666555443311000
Q ss_pred CCCcCCCCcceEEEEEeeccccceeeccCCchhHhhHhhcCeeEEEeCCCCCCCccEEEEecccccCCCCChHHHHHHHH
Q 009695 264 GLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLV 343 (528)
Q Consensus 264 ~~~~~~~~~~~~~~l~vP~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i 343 (528)
.....+-+...|..+.+..+|+.|..++.++++.+..+.. ..++-.++|.|..... .+|...+
T Consensus 494 ------~~~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~~~i~~~~~-----~~~~~~i~i~gk~~~v------~~a~~~L 556 (753)
T KOG2208|consen 494 ------FRDVVTKDKLLPVKYIGKEIGKNGTIRDSLGDKSIFPPNE-----DEDHEKITIEGKLELV------LEAPAEL 556 (753)
T ss_pred ------hhhhhhccccchHHhhcccccCceeeeccCCceeeccccc-----ccccceeeecccccch------hhhHHHH
Confidence 0011122344567777777888777777666655543332 3456778888885221 1222222
Q ss_pred HhhhhhcccCCCCCCCCCCCCceEEEEEeCCcc-eeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcC
Q 009695 344 FARSVEVEGQQGFSSGENKGDAVAVSILVGADF-VGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG 422 (528)
Q Consensus 344 ~~~i~e~~~~~~~~~~~~~~~~~t~~v~VP~~~-~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG 422 (528)
...+... .......+.+|..+ .-++++++....+..+...|+.+.+++. ..+.+.++|.|
T Consensus 557 ~~~~~~~------------~~~~~~~v~~~~~~~~~~l~~~~~~~~~~~e~~~gv~~~fp~~-------~~~~~e~~i~g 617 (753)
T KOG2208|consen 557 KALIEAL------------IKATLLEVNNPPGQHRPFLIGKGIENRTYVEVFGGVVVPFPRS-------PTSSDEVSIKG 617 (753)
T ss_pred Hhcchhh------------hhhhhhhccCcchheeeeeeccccccccceeecCcccccCCCC-------CCchhhhccch
Confidence 2222110 01122345555544 4677777777777777777889977664 23445799999
Q ss_pred CHHHHHHHHHHHHHHHhhh
Q 009695 423 EYKNVQNALSEVVGRLRHN 441 (528)
Q Consensus 423 ~~~~v~~A~~~I~~~l~~~ 441 (528)
....++.|...+......+
T Consensus 618 ~~~~v~aa~~~~~~i~~~~ 636 (753)
T KOG2208|consen 618 AKDEVKAAKGRLEEIVEYL 636 (753)
T ss_pred hHHHHHHhhccchhhhhhc
Confidence 9999999999988887643
No 29
>PF13014 KH_3: KH domain
Probab=98.94 E-value=1.3e-09 Score=77.09 Aligned_cols=42 Identities=40% Similarity=0.727 Sum_probs=38.7
Q ss_pred ccccccccCchHHHHHHhhhCceEEecC-CCCCCCceEEEEEc
Q 009695 35 VVGGLIGRSGSIISSIRRDTKCRIHCEG-GFPGSDHRVILVVG 76 (528)
Q Consensus 35 ~vG~VIGk~G~~Ik~I~~eTga~I~i~~-~~~~~~eRvi~I~G 76 (528)
++|+||||+|++|++|+++|||+|+|++ ..++..+|+|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 4799999999999999999999999998 56678899999987
No 30
>PF13014 KH_3: KH domain
Probab=98.86 E-value=3e-09 Score=75.29 Aligned_cols=42 Identities=36% Similarity=0.541 Sum_probs=38.9
Q ss_pred ccceeeccCCchhHhhHhhcCeeEEEeC-CCCCCCccEEEEec
Q 009695 284 TASGIIGKRGAIVRSLQNASGALISFAA-PLTKSGERVVTISA 325 (528)
Q Consensus 284 ~vG~IIGkgG~~Ik~I~~~tGa~I~i~~-~~~~~~eR~V~I~G 325 (528)
++|+|||++|++|++|+++|||+|+|++ ..++..+|.|+|+|
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 5799999999999999999999999987 56788999999987
No 31
>smart00322 KH K homology RNA-binding domain.
Probab=98.86 E-value=1.4e-08 Score=78.56 Aligned_cols=67 Identities=30% Similarity=0.527 Sum_probs=59.8
Q ss_pred ceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcCCHHHHHHHHHHHHHHH
Q 009695 365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRL 438 (528)
Q Consensus 365 ~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~~~~v~~A~~~I~~~l 438 (528)
..+.++.||.+++|++||++|++|++|++.||++|.+.... .....|+|.|+.++++.|..+|.+.+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------SEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 35789999999999999999999999999999999986531 25788999999999999999998876
No 32
>smart00322 KH K homology RNA-binding domain.
Probab=98.73 E-value=7.8e-08 Score=74.36 Aligned_cols=67 Identities=27% Similarity=0.487 Sum_probs=60.3
Q ss_pred ceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHH
Q 009695 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL 198 (528)
Q Consensus 128 ~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G~~~~V~kA~~~I~~~l 198 (528)
.++.++.||...+|.+||++|++|++|++++|++|.+... ......+.|.|..+++..|..+|.+.+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~----~~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPED----GSEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCC----CCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 4678999999999999999999999999999999999773 226789999999999999999998876
No 33
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.61 E-value=2.8e-07 Score=85.12 Aligned_cols=143 Identities=18% Similarity=0.234 Sum_probs=97.4
Q ss_pred ceEEEEEeeccccceeeccCCchhHhhHhhcCeeEEEeCCCCCCCccEEEEecccccCCCCChHHHHHHHHHhhhhhccc
Q 009695 273 EVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG 352 (528)
Q Consensus 273 ~~~~~l~vP~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i~~~i~e~~~ 352 (528)
.....+.||.+.++.+||+.|+..+.|.+.+|+++.++ +.+..|+|..++...+.. ..+.|...+.. +
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD-----~~~~~V~i~~~~~t~Dp~-~~~ka~d~VkA------I 74 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID-----SKTGSVTIRTTRKTEDPL-ALLKARDVVKA------I 74 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEE-----CCCCeEEEEecCCCCChH-HHHHHHHHHHH------H
Confidence 33556889999999999999999999999999999994 456778887763111111 12222222211 1
Q ss_pred CCCCCCCC----CCCCceEE-EE-----Ee-C----CcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcE
Q 009695 353 QQGFSSGE----NKGDAVAV-SI-----LV-G----ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVV 417 (528)
Q Consensus 353 ~~~~~~~~----~~~~~~t~-~v-----~V-P----~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~ 417 (528)
..|+++.- -.+ .... .+ .= + ...-|+|||++|.+-+-|+..|||+|.|. ...
T Consensus 75 grGF~pe~A~~LL~d-~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~------------g~t 141 (194)
T COG1094 75 GRGFPPEKALKLLED-DYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY------------GKT 141 (194)
T ss_pred hcCCCHHHHHHHhcC-CcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe------------CcE
Confidence 12222110 000 1111 01 11 1 23569999999999999999999999884 357
Q ss_pred EEEcCCHHHHHHHHHHHHHHHhh
Q 009695 418 IQISGEYKNVQNALSEVVGRLRH 440 (528)
Q Consensus 418 V~ItG~~~~v~~A~~~I~~~l~~ 440 (528)
|.|.|.+++|+.|...|...|..
T Consensus 142 VaiiG~~~~v~iAr~AVemli~G 164 (194)
T COG1094 142 VAIIGGFEQVEIAREAVEMLING 164 (194)
T ss_pred EEEecChhhhHHHHHHHHHHHcC
Confidence 99999999999999999998863
No 34
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.57 E-value=9.5e-07 Score=81.66 Aligned_cols=146 Identities=16% Similarity=0.221 Sum_probs=98.4
Q ss_pred CceEEEEEecccccccccccCchHHHHHHhhhCceEEecCCCCCCCceEEEEEcCCcchhhhhcccccccccCCCcchHH
Q 009695 23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ 102 (528)
Q Consensus 23 ~~~~~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i~~~~~~~~eRvi~I~G~~~~~~~~~~~~~~~~~~~~~~s~A~ 102 (528)
....+.+.+|.+..+.+||+.|++.+.|++.++++|.++. .+..|.|........- ..+-.|.
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~-----~~~~V~i~~~~~t~Dp------------~~~~ka~ 68 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS-----KTGSVTIRTTRKTEDP------------LALLKAR 68 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC-----CCCeEEEEecCCCCCh------------HHHHHHH
Confidence 3456779999999999999999999999999999999965 3667888765321000 0011121
Q ss_pred HHHHHHHHHHhhhhhccCCC---CCCCCceEEEE-----Eee------cceeeEEecCCChHHHHHHhhhCCeEEEcCCC
Q 009695 103 EAVIRVFERMWEVEAEVEGD---GDGDDVAYCGL-----LAN------TTKIGVVVGKGGRNVTRMRIESGAKIVMLPPP 168 (528)
Q Consensus 103 ~al~~v~~~i~~~~~~~~~~---~~~~~~v~~rl-----lVp------~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p 168 (528)
+-+.. .....+.+ .-.+..+.+.+ ++. ....|+|||++|.+-+.|++-|||+|.|.
T Consensus 69 d~VkA-------IgrGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~--- 138 (194)
T COG1094 69 DVVKA-------IGRGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY--- 138 (194)
T ss_pred HHHHH-------HhcCCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe---
Confidence 11111 00000000 00000111111 111 12569999999999999999999999994
Q ss_pred CCCCCCCceEEEeccHHHHHHHHHHHHHHHccC
Q 009695 169 ACAAIDDQLIQITGATLAVKKALVAVTTCLQHL 201 (528)
Q Consensus 169 ~~~~~~er~V~I~G~~~~V~kA~~~I~~~l~~~ 201 (528)
+..|.|-|.+++|.-|..+|..++...
T Consensus 139 ------g~tVaiiG~~~~v~iAr~AVemli~G~ 165 (194)
T COG1094 139 ------GKTVAIIGGFEQVEIAREAVEMLINGA 165 (194)
T ss_pred ------CcEEEEecChhhhHHHHHHHHHHHcCC
Confidence 478999999999999999999999764
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=98.28 E-value=2.6e-06 Score=74.05 Aligned_cols=68 Identities=19% Similarity=0.346 Sum_probs=53.7
Q ss_pred CcceeeeecCCCchhHHHHHhhCCeEEEeCCCCcccc------------CCCCCcEEEEcCCH---HHHHHHHHHHHHHH
Q 009695 374 ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGC------------AAQNDVVIQISGEY---KNVQNALSEVVGRL 438 (528)
Q Consensus 374 ~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~------------~~~~~~~V~ItG~~---~~v~~A~~~I~~~l 438 (528)
.+++|.|||++|.+||+|+++|||+|.|..+...-.. ..++.-.|.|++.- +++++|..+|...|
T Consensus 14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll 93 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL 93 (120)
T ss_pred CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence 3789999999999999999999999999876321100 01233678999965 89999999999999
Q ss_pred hhh
Q 009695 439 RHN 441 (528)
Q Consensus 439 ~~~ 441 (528)
...
T Consensus 94 ~~~ 96 (120)
T cd02395 94 KPA 96 (120)
T ss_pred ccC
Confidence 843
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=98.18 E-value=7.9e-06 Score=71.01 Aligned_cols=64 Identities=25% Similarity=0.335 Sum_probs=51.9
Q ss_pred ceeeEEecCCChHHHHHHhhhCCeEEEcCC-CCC--------------CCCCCceEEEeccH---HHHHHHHHHHHHHHc
Q 009695 138 TKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PAC--------------AAIDDQLIQITGAT---LAVKKALVAVTTCLQ 199 (528)
Q Consensus 138 ~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~-p~~--------------~~~~er~V~I~G~~---~~V~kA~~~I~~~l~ 199 (528)
+.+|.|||++|++||+|+++|||+|.|..+ ... ....+-.|.|++.. +++.+|+.+|..++.
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 678999999999999999999999999875 100 01223578899865 999999999999997
Q ss_pred cC
Q 009695 200 HL 201 (528)
Q Consensus 200 ~~ 201 (528)
..
T Consensus 95 ~~ 96 (120)
T cd02395 95 PA 96 (120)
T ss_pred cC
Confidence 54
No 37
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.98 E-value=1.2e-05 Score=71.89 Aligned_cols=103 Identities=14% Similarity=0.158 Sum_probs=69.0
Q ss_pred EEEEEecccccccccccCchHHHHHHhhhCceEEecCCCCCCCceEEEEEcCCcchhhhhcccccccccCCCcchHHHHH
Q 009695 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAV 105 (528)
Q Consensus 26 ~~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i~~~~~~~~eRvi~I~G~~~~~~~~~~~~~~~~~~~~~~s~A~~al 105 (528)
.+.++|+...+|..||++|++|+.|++..|-+|+|=+... . +.+-+
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~-----------d-----------------------~~~fI 78 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSD-----------D-----------------------PEEFI 78 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCC-----------C-----------------------HHHHH
Confidence 4568889999999999999999999999998888743211 0 11111
Q ss_pred HHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEc
Q 009695 106 IRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVML 165 (528)
Q Consensus 106 ~~v~~~i~~~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~ 165 (528)
..++....-....- ...+....+.+.|+..+.|..|||+|++|+.++.-+|-++.|.
T Consensus 79 ~n~l~Pa~V~~v~I---~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 79 KNIFAPAAVRSVTI---KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred HHHcCCCEEEEEEE---EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 11111000000000 0011235667789999999999999999999999999888763
No 38
>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=97.82 E-value=7.3e-05 Score=82.82 Aligned_cols=92 Identities=13% Similarity=0.202 Sum_probs=71.9
Q ss_pred hHHHHHHHHHhhhhhcccCCCCCCCCCCCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCC
Q 009695 335 PVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQN 414 (528)
Q Consensus 335 ~a~~A~~~i~~~i~e~~~~~~~~~~~~~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~ 414 (528)
.+.++...+++.+.+.... + ...+...+....+.||.+.+|.|||+||.+||+|+++|||+|.|.+
T Consensus 550 ~A~~g~~~Il~~m~~al~~-p--~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d----------- 615 (719)
T TIGR02696 550 QARDARLAILDVMAEAIDT-P--DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED----------- 615 (719)
T ss_pred HHHHHHHHHHHHHHHHHhC-c--cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec-----------
Confidence 3456666676665443322 2 2234456788999999999999999999999999999999999843
Q ss_pred CcEEEEcC-CHHHHHHHHHHHHHHHhh
Q 009695 415 DVVIQISG-EYKNVQNALSEVVGRLRH 440 (528)
Q Consensus 415 ~~~V~ItG-~~~~v~~A~~~I~~~l~~ 440 (528)
+..|.|.+ +.+++++|+.+|...+..
T Consensus 616 ~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 616 DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 56788887 577999999999999984
No 39
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.81 E-value=1.8e-05 Score=77.31 Aligned_cols=143 Identities=18% Similarity=0.268 Sum_probs=99.3
Q ss_pred cceEEEEEeeccccceeeccCCchhHhhHhhcCeeEEEeCCCCCCCccEEEEecccccCCCCChHHHHHHHHHh---hhh
Q 009695 272 QEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFA---RSV 348 (528)
Q Consensus 272 ~~~~~~l~vP~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i~~---~i~ 348 (528)
+.++..+.+|...++.|.|++|.+||.|+.+|...|+-+.. ..|-++.++|.. ++ +..|...+-. ++.
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr---~eePiF~vTg~~--ed----v~~aRrei~saaeH~~ 94 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---GEEPIFPVTGRH--ED----VRRARREIPSAAEHFG 94 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCC---CCCCcceeccCc--hh----HHHHhhcCccccceee
Confidence 56677788999999999999999999999999999886422 234677888872 11 1112111111 100
Q ss_pred hcccCCCCC---CCCCCCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcCCHH
Q 009695 349 EVEGQQGFS---SGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYK 425 (528)
Q Consensus 349 e~~~~~~~~---~~~~~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~~~ 425 (528)
-....+.+. .+.....+.+..+.+|...+|.+.|..|.+|+.|++.+...|.-+-+ ..+.++-++|.+.
T Consensus 95 l~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~--------~~~~Vf~Vtg~~~ 166 (394)
T KOG2113|consen 95 LIRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR--------CGEPVFCVTGAPK 166 (394)
T ss_pred eeeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc--------CCCceEEEecCCc
Confidence 000001111 12223567888999999999999999999999999999999977654 3467888899888
Q ss_pred H-HHHHH
Q 009695 426 N-VQNAL 431 (528)
Q Consensus 426 ~-v~~A~ 431 (528)
+ +++|.
T Consensus 167 nC~kra~ 173 (394)
T KOG2113|consen 167 NCVKRAR 173 (394)
T ss_pred chhhhcc
Confidence 7 55555
No 40
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.79 E-value=6.1e-05 Score=67.39 Aligned_cols=100 Identities=16% Similarity=0.185 Sum_probs=69.8
Q ss_pred EEEEEeeccccceeeccCCchhHhhHhhcCeeEEEeCCCCCCCccEEEEecccccCCCCChHHHHHHHHHhhh--hhccc
Q 009695 275 ALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARS--VEVEG 352 (528)
Q Consensus 275 ~~~l~vP~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i~~~i--~e~~~ 352 (528)
.+-+.|+...+|..||++|++|+.|++..|-+|.+-.-.++ .++-+..++.-. .+..+
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~d--------------------~~~fI~n~l~Pa~V~~v~I 92 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDD--------------------PEEFIKNIFAPAAVRSVTI 92 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCCC--------------------HHHHHHHHcCCCEEEEEEE
Confidence 45577899999999999999999999999988877431100 111121111110 00000
Q ss_pred CCCCCCCCCCCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEE
Q 009695 353 QQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKL 401 (528)
Q Consensus 353 ~~~~~~~~~~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i 401 (528)
...+......+.|+.+..|..|||+|++|+.+++-+|-++.|
T Consensus 93 -------~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 93 -------KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred -------EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 011234677889999999999999999999999999999876
No 41
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.77 E-value=0.00011 Score=81.34 Aligned_cols=94 Identities=18% Similarity=0.232 Sum_probs=73.8
Q ss_pred cchHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCce
Q 009695 98 VSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQL 177 (528)
Q Consensus 98 ~s~A~~al~~v~~~i~~~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~ 177 (528)
+..|.++..++++.+.+..... .......+....+.||.+.+|.|||+||++||.|.++||++|.|.. +..
T Consensus 548 L~~A~~g~~~Il~~m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d--------~G~ 618 (719)
T TIGR02696 548 LKQARDARLAILDVMAEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED--------DGT 618 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec--------CcE
Confidence 4556777777776665543333 2222333667788999999999999999999999999999999955 477
Q ss_pred EEEecc-HHHHHHHHHHHHHHHcc
Q 009695 178 IQITGA-TLAVKKALVAVTTCLQH 200 (528)
Q Consensus 178 V~I~G~-~~~V~kA~~~I~~~l~~ 200 (528)
|.|.+. .+++++|+.+|..++..
T Consensus 619 V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 619 VYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred EEEEeCCHHHHHHHHHHHHHhhCc
Confidence 888886 89999999999998864
No 42
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=97.54 E-value=0.00026 Score=63.24 Aligned_cols=102 Identities=14% Similarity=0.135 Sum_probs=68.4
Q ss_pred EEEEEecccccccccccCchHHHHHHhhhCceEEecCCCCCCCceEEEEEcCCcch-hhhhcccccccccCCCcchHHHH
Q 009695 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSID-RRIMFCENDVVVEGGEVSSTQEA 104 (528)
Q Consensus 26 ~~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i~~~~~~~~eRvi~I~G~~~~~-~~~~~~~~~~~~~~~~~s~A~~a 104 (528)
-+=++|....+|..||++|++|+.|++..|=+|+|-+.. ...+.- .. .++||.
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys-----------~D~~~fI~N-------------~l~PA~-- 87 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYS-----------ENLEEFVAN-------------KLAPAE-- 87 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcC-----------CCHHHHHHH-------------cCCCce--
Confidence 455778888999999999999999998889888874321 111000 00 011110
Q ss_pred HHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEc
Q 009695 105 VIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVML 165 (528)
Q Consensus 105 l~~v~~~i~~~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~ 165 (528)
+...... . .++.....+.|+..+.+..|||+|++|+...+-+|-++.|.
T Consensus 88 -------V~~V~i~----~-~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 88 -------VKNVTVS----E-FNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred -------EEEEEEE----c-CCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 0000000 0 11245677889999999999999999999999999887764
No 43
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.46 E-value=0.00026 Score=69.40 Aligned_cols=141 Identities=13% Similarity=0.256 Sum_probs=98.4
Q ss_pred CceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHccCCCCCC
Q 009695 127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEK 206 (528)
Q Consensus 127 ~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G~~~~V~kA~~~I~~~l~~~~~~~~ 206 (528)
..++..+-||..+++.|.|++|.+||.|+.+|.+.|.-... ..|-+..++|..+.|+.|+..|...-+..-
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr-----~eePiF~vTg~~edv~~aRrei~saaeH~~---- 94 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR-----GEEPIFPVTGRHEDVRRARREIPSAAEHFG---- 94 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCC-----CCCCcceeccCchhHHHHhhcCccccceee----
Confidence 57888899999999999999999999999999999988653 245778899999999999988744221100
Q ss_pred CCcccCCCccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCcceEEEEEeeccccc
Q 009695 207 SPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTAS 286 (528)
Q Consensus 207 ~~~~~~~p~~~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~y~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~l~vP~~~vG 286 (528)
.+ -+.+...+..+.|. .....+..+.+|...+|
T Consensus 95 ------l~--------------------~~s~s~Sgg~~~~s---------------------~s~qt~sy~svP~rvvg 127 (394)
T KOG2113|consen 95 ------LI--------------------RASRSFSGGTNGAS---------------------ASGQTTSYVSVPLRVVG 127 (394)
T ss_pred ------ee--------------------eecccccCCCcccc---------------------ccCCCceeeeccceeee
Confidence 00 00000111111110 01122333567888999
Q ss_pred eeeccCCchhHhhHhhcCeeEEEeCCCCCCCccEEEEecc
Q 009695 287 GIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISAL 326 (528)
Q Consensus 287 ~IIGkgG~~Ik~I~~~tGa~I~i~~~~~~~~eR~V~I~G~ 326 (528)
.|.|..|.+|+.||+.+...|.-.- ...+-++.++|.
T Consensus 128 lvv~~~~~ti~~iqq~tnt~I~T~v---~~~~~Vf~Vtg~ 164 (394)
T KOG2113|consen 128 LVVGPKGATIKRIQQFTNTYIATPV---RCGEPVFCVTGA 164 (394)
T ss_pred eccccccCccchheecccceEeeec---cCCCceEEEecC
Confidence 9999999999999999998887532 334567777775
No 44
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.44 E-value=0.00036 Score=78.49 Aligned_cols=94 Identities=21% Similarity=0.272 Sum_probs=69.7
Q ss_pred cchHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCce
Q 009695 98 VSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQL 177 (528)
Q Consensus 98 ~s~A~~al~~v~~~i~~~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~ 177 (528)
+..|.++..++++.+.+...+.......-.+....+-||.+.++.|||+||++||+|+++|||+|.|.. +..
T Consensus 520 l~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d--------dG~ 591 (684)
T TIGR03591 520 LEQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED--------DGT 591 (684)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec--------CeE
Confidence 334566666666655554333222222233667789999999999999999999999999999999955 466
Q ss_pred EEEecc-HHHHHHHHHHHHHHHc
Q 009695 178 IQITGA-TLAVKKALVAVTTCLQ 199 (528)
Q Consensus 178 V~I~G~-~~~V~kA~~~I~~~l~ 199 (528)
|.|.+. .+.+.+|..+|..+..
T Consensus 592 V~i~~~~~~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 592 VKIAASDGEAAEAAIKMIEGITA 614 (684)
T ss_pred EEEEECcHHHHHHHHHHHHhhhc
Confidence 777664 8889999999988764
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=97.37 E-value=0.00033 Score=62.51 Aligned_cols=101 Identities=14% Similarity=0.120 Sum_probs=68.9
Q ss_pred EEEEEeeccccceeeccCCchhHhhHhhcCeeEEEeCCCCCCCccEEEEecccccCCCCChHHHHHHHHH--hhhhhccc
Q 009695 275 ALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVF--ARSVEVEG 352 (528)
Q Consensus 275 ~~~l~vP~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i~--~~i~e~~~ 352 (528)
.+-+.|....+|..||++|++|+.|++..|=+|.+-.-.++ +. +-+..++ .++.+...
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 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSEN-------------------LE-EFVANKLAPAEVKNVTV 93 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCC-------------------HH-HHHHHcCCCceEEEEEE
Confidence 34467888999999999999999999988888877431111 00 0010000 00000000
Q ss_pred CCCCCCCCCCCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEe
Q 009695 353 QQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLV 402 (528)
Q Consensus 353 ~~~~~~~~~~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~ 402 (528)
...++...+.+.||.+..+..|||+|++++-..+-+|-++.|.
T Consensus 94 -------~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 94 -------SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred -------EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 0112346788999999999999999999999999999998663
No 46
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.37 E-value=0.00094 Score=69.47 Aligned_cols=74 Identities=19% Similarity=0.250 Sum_probs=57.8
Q ss_pred ceEEEEEeec------ceeeEEecCCChHHHHHHhhhCCeEEEcCC-------------CCCCCC-CCceEEEecc-HHH
Q 009695 128 VAYCGLLANT------TKIGVVVGKGGRNVTRMRIESGAKIVMLPP-------------PACAAI-DDQLIQITGA-TLA 186 (528)
Q Consensus 128 ~v~~rllVp~------~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~-------------p~~~~~-~er~V~I~G~-~~~ 186 (528)
.++.++.||- +.+|+|||..|.|.|+|+++|||||.|..+ ...... .+=-+.|+++ -|.
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 5666788875 479999999999999999999999999873 011111 2335677777 899
Q ss_pred HHHHHHHHHHHHccC
Q 009695 187 VKKALVAVTTCLQHL 201 (528)
Q Consensus 187 V~kA~~~I~~~l~~~ 201 (528)
|++|+..|..+|++.
T Consensus 217 i~~Ai~vienli~~a 231 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSA 231 (554)
T ss_pred HHHHHHHHHHHHHhh
Confidence 999999999999763
No 47
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.36 E-value=0.0017 Score=67.63 Aligned_cols=81 Identities=17% Similarity=0.315 Sum_probs=60.5
Q ss_pred ceEEEEEeC------CcceeeeecCCCchhHHHHHhhCCeEEEeCCCCc---------cc--cCCCCCcEEEEcCCH-HH
Q 009695 365 AVAVSILVG------ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQV---------LG--CAAQNDVVIQISGEY-KN 426 (528)
Q Consensus 365 ~~t~~v~VP------~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~---------p~--~~~~~~~~V~ItG~~-~~ 426 (528)
..+.+|.|| .+++|.|||..|.|.|+|+++|||+|.|-.+... +. ...+++--+.|+++. |.
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 566778777 4789999999999999999999999999873221 00 113344567777765 58
Q ss_pred HHHHHHHHHHHHhhhcCCC
Q 009695 427 VQNALSEVVGRLRHNLKSG 445 (528)
Q Consensus 427 v~~A~~~I~~~l~~~~~~~ 445 (528)
|++|..+|..+|.+.....
T Consensus 217 i~~Ai~vienli~~av~~~ 235 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSAVSVP 235 (554)
T ss_pred HHHHHHHHHHHHHhhccCc
Confidence 9999999999998643333
No 48
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.21 E-value=0.0008 Score=75.72 Aligned_cols=92 Identities=14% Similarity=0.224 Sum_probs=66.4
Q ss_pred HHHHHHHHHhhhhhcccCCCCCCCCCCCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCC
Q 009695 336 VQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQND 415 (528)
Q Consensus 336 a~~A~~~i~~~i~e~~~~~~~~~~~~~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~ 415 (528)
+.++...+++.+.+....... ..+...+...++.||.+.+|.|||+||.+||+|+++|||+|.|.. +
T Consensus 523 a~~~~~~I~~~m~~~l~~~~~--~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-----------d 589 (684)
T TIGR03591 523 AKEGRLHILGEMNKVISEPRA--ELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-----------D 589 (684)
T ss_pred HHHHHHHHHHHHHHHHhhhhc--cccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-----------C
Confidence 334455555554433221111 122345778899999999999999999999999999999999943 3
Q ss_pred cEEEEcC-CHHHHHHHHHHHHHHHhh
Q 009695 416 VVIQISG-EYKNVQNALSEVVGRLRH 440 (528)
Q Consensus 416 ~~V~ItG-~~~~v~~A~~~I~~~l~~ 440 (528)
..|.|.+ +.+.+++|..+|.....+
T Consensus 590 G~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 590 GTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred eEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 4566665 667899999999988764
No 49
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=97.10 E-value=0.0018 Score=60.74 Aligned_cols=102 Identities=19% Similarity=0.232 Sum_probs=67.0
Q ss_pred EEEEecccccccccccCchHHHHHHhhhCceEEecCCCCCCCceEEEEEcCCcchhhhhcccccccccCCCcchHHHHHH
Q 009695 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVI 106 (528)
Q Consensus 27 ~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i~~~~~~~~eRvi~I~G~~~~~~~~~~~~~~~~~~~~~~s~A~~al~ 106 (528)
+-..+-.+.+|..||++|++|+.|.++.|=+|+|-...++ ... -..+|+.
T Consensus 78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d-----------~~~-------------------fI~nal~ 127 (190)
T COG0195 78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSED-----------PAE-------------------FIKNALA 127 (190)
T ss_pred EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCC-----------HHH-------------------HHHHhcC
Confidence 3344455778999999999999999999987777432110 000 0001110
Q ss_pred HHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcC
Q 009695 107 RVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP 166 (528)
Q Consensus 107 ~v~~~i~~~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~ 166 (528)
- .++....... .++. ...+.||..+.+..|||+|.+++.+.+-||-++.|..
T Consensus 128 P--a~v~~V~~~~-----~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 128 P--AEVLSVNIKE-----DDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred c--ceEeEEEEEe-----CCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 0 0000000000 0112 7788999999999999999999999999999999976
No 50
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.03 E-value=0.0011 Score=75.43 Aligned_cols=95 Identities=14% Similarity=0.199 Sum_probs=73.0
Q ss_pred cchHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCe-EEEcCCCCCCCCCCc
Q 009695 98 VSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAK-IVMLPPPACAAIDDQ 176 (528)
Q Consensus 98 ~s~A~~al~~v~~~i~~~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~-I~i~~~p~~~~~~er 176 (528)
+..|.++...+++.+.+.............+....+-||.+.++.|||.||.+||.|.++||++ |.+.. +-
T Consensus 654 L~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d--------dg 725 (891)
T PLN00207 654 LLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD--------DG 725 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC--------Ce
Confidence 4456777777777666553332211122336778899999999999999999999999999999 88854 46
Q ss_pred eEEEecc-HHHHHHHHHHHHHHHcc
Q 009695 177 LIQITGA-TLAVKKALVAVTTCLQH 200 (528)
Q Consensus 177 ~V~I~G~-~~~V~kA~~~I~~~l~~ 200 (528)
.|.|.+. .+++++|+.+|..+..+
T Consensus 726 ~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 726 TVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred eEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 7888885 99999999999998863
No 51
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.85 E-value=0.0011 Score=64.29 Aligned_cols=38 Identities=21% Similarity=0.558 Sum_probs=35.0
Q ss_pred ceEEEEEeccc------ccccccccCchHHHHHHhhhCceEEec
Q 009695 24 VVSFRLVCPTP------VVGGLIGRSGSIISSIRRDTKCRIHCE 61 (528)
Q Consensus 24 ~~~~rilvp~~------~vG~VIGk~G~~Ik~I~~eTga~I~i~ 61 (528)
....|++||.+ +||.|+|.+|.++|+|+++|||+|.|-
T Consensus 91 k~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 91 KLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred eEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 56788999997 799999999999999999999999884
No 52
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.81 E-value=0.002 Score=73.23 Aligned_cols=92 Identities=14% Similarity=0.189 Sum_probs=68.1
Q ss_pred HHHHHHHHHhhhhhcccCCCCCCCCCCCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCe-EEEeCCCCccccCCCC
Q 009695 336 VQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTD-IKLVGGEQVLGCAAQN 414 (528)
Q Consensus 336 a~~A~~~i~~~i~e~~~~~~~~~~~~~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~-I~i~~~~~~p~~~~~~ 414 (528)
+.++...+++.|.+.. ..+. ...+...+....+.||.+.+|.|||.||.+||+|.++||+. |.+. +
T Consensus 657 A~~g~~~Il~~M~~~i-~~pr-~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~-----------d 723 (891)
T PLN00207 657 AKDGRKHILAEMSKCS-PPPS-KRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ-----------D 723 (891)
T ss_pred HHHHHHHHHHHHHHHH-hhhh-hhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-----------C
Confidence 4455556665554432 1110 11234567889999999999999999999999999999999 8663 2
Q ss_pred CcEEEEcC-CHHHHHHHHHHHHHHHhh
Q 009695 415 DVVIQISG-EYKNVQNALSEVVGRLRH 440 (528)
Q Consensus 415 ~~~V~ItG-~~~~v~~A~~~I~~~l~~ 440 (528)
+-.|.|.+ +.+.++.|+.+|.+...+
T Consensus 724 dg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 724 DGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 45677777 677999999999998864
No 53
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.76 E-value=0.003 Score=68.87 Aligned_cols=97 Identities=13% Similarity=0.165 Sum_probs=72.1
Q ss_pred HHHHHHHHHhhhhhcccCCCCCCCCCCCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCC
Q 009695 336 VQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQND 415 (528)
Q Consensus 336 a~~A~~~i~~~i~e~~~~~~~~~~~~~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~ 415 (528)
|..|.++++..+.+..-.. . .......+...++.|+.+.++-+||+||.+|++|..+|||+|+|. ++
T Consensus 524 Ak~aRlhIL~~M~~ai~~p-r-~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-----------dd 590 (692)
T COG1185 524 AKGARLHILIVMNEAISEP-R-KELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-----------DD 590 (692)
T ss_pred HHHHHHHHHHHHHHHHhhh-h-hhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-----------CC
Confidence 4456666666654432110 0 111234567889999999999999999999999999999999994 24
Q ss_pred cEEEEcCCH-HHHHHHHHHHHHHHhhhcCCC
Q 009695 416 VVIQISGEY-KNVQNALSEVVGRLRHNLKSG 445 (528)
Q Consensus 416 ~~V~ItG~~-~~v~~A~~~I~~~l~~~~~~~ 445 (528)
..|.|.++. +.++.|+..|.++.++...-.
T Consensus 591 Gtv~i~~s~~~~~~~ak~~I~~i~~e~evg~ 621 (692)
T COG1185 591 GTVKIAASDGESAKKAKERIEAITREVEVGE 621 (692)
T ss_pred CcEEEEecchHHHHHHHHHHHHHHhhccccc
Confidence 568888887 689999999999998754444
No 54
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.75 E-value=0.0043 Score=67.74 Aligned_cols=95 Identities=20% Similarity=0.240 Sum_probs=71.9
Q ss_pred cchHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCce
Q 009695 98 VSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQL 177 (528)
Q Consensus 98 ~s~A~~al~~v~~~i~~~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~ 177 (528)
+..|.+|.++++..+.+.-.+.......-.+-...+-++...++.+||+||++|++|.++||++|.+.. +..
T Consensus 521 L~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied--------dGt 592 (692)
T COG1185 521 LEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED--------DGT 592 (692)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC--------CCc
Confidence 555777777777766654332221111222455677889999999999999999999999999999954 567
Q ss_pred EEEecc-HHHHHHHHHHHHHHHcc
Q 009695 178 IQITGA-TLAVKKALVAVTTCLQH 200 (528)
Q Consensus 178 V~I~G~-~~~V~kA~~~I~~~l~~ 200 (528)
|.|.+. .+.+.+|+..|..+.++
T Consensus 593 v~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 593 VKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred EEEEecchHHHHHHHHHHHHHHhh
Confidence 888888 58999999999999966
No 55
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.74 E-value=0.0024 Score=65.35 Aligned_cols=67 Identities=18% Similarity=0.294 Sum_probs=54.6
Q ss_pred CceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcCCHHHHHHHHHHHHHHH
Q 009695 364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRL 438 (528)
Q Consensus 364 ~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~~~~v~~A~~~I~~~l 438 (528)
.....-+.+-++++|.+||+||+.|+.|+..|.++|+|... +.+..|+|-|..+--.+|...|..-+
T Consensus 45 ~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~--------~~e~kv~ifg~~~m~~kaka~id~~~ 111 (629)
T KOG0336|consen 45 GEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC--------DLEVKVTIFGINHMRKKAKASIDRGQ 111 (629)
T ss_pred CCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc--------CceeEEEEechHHHHHHHHhhHhhhh
Confidence 34556677888999999999999999999999999999874 44788999999886666666654433
No 56
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.73 E-value=0.0015 Score=66.90 Aligned_cols=61 Identities=23% Similarity=0.305 Sum_probs=51.6
Q ss_pred CCCCCCCceEEEEEecccccccccccCchHHHHHHhhhCceEEecCCCCCCCceEEEEEcCCcc
Q 009695 17 PLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSI 80 (528)
Q Consensus 17 ~~~~~~~~~~~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i~~~~~~~~eRvi~I~G~~~~ 80 (528)
+.....+++.+++-+-+.+||.|||++|++|+.||..|+++|+|... ..+-.|+|.|...-
T Consensus 39 ~~aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~~m 99 (629)
T KOG0336|consen 39 SAAAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGINHM 99 (629)
T ss_pred ccccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechHHH
Confidence 45556678899999999999999999999999999999999999753 35677888887643
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=96.62 E-value=0.0025 Score=48.50 Aligned_cols=37 Identities=22% Similarity=0.261 Sum_probs=34.4
Q ss_pred ceEEEEEecccccccccccCchHHHHHHhhhCceEEe
Q 009695 24 VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC 60 (528)
Q Consensus 24 ~~~~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i 60 (528)
.-.+.+.|+.+..|.+|||+|.+|+.+++.+|-+|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3688999999999999999999999999999988876
No 58
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.62 E-value=0.0024 Score=63.68 Aligned_cols=69 Identities=19% Similarity=0.277 Sum_probs=57.1
Q ss_pred eEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEE-eccHHHHHHHHHHHHHHHccC
Q 009695 129 AYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQI-TGATLAVKKALVAVTTCLQHL 201 (528)
Q Consensus 129 v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I-~G~~~~V~kA~~~I~~~l~~~ 201 (528)
...-++|+++..|+|||++|.+-++|+++|+++|.++. +..+...+.| .+..++|.+|...|...+.+.
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~----p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPR----PNTNKEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccC----CCCCcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 44568999999999999999999999999999999977 2334444444 556999999999999998764
No 59
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.59 E-value=0.0044 Score=58.17 Aligned_cols=99 Identities=21% Similarity=0.228 Sum_probs=67.3
Q ss_pred EEeeccccceeeccCCchhHhhHhhcCeeEEEeCCCCCCCccEEEEecccccCCCCChHHHHHHHHHh--hhhhcccCCC
Q 009695 278 MLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFA--RSVEVEGQQG 355 (528)
Q Consensus 278 l~vP~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i~~--~i~e~~~~~~ 355 (528)
..+-.+.+|..||++|++|+.|+++.|=+|.|-.- +++ ++ +-+..++. ++....+
T Consensus 80 ~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~-------------s~d------~~-~fI~nal~Pa~v~~V~~--- 136 (190)
T COG0195 80 NVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW-------------SED------PA-EFIKNALAPAEVLSVNI--- 136 (190)
T ss_pred eecCcCchhhhccCCChHHHHHHHHhCCceEEEEe-------------CCC------HH-HHHHHhcCcceEeEEEE---
Confidence 34557788999999999999999999966666322 111 11 11111111 1100000
Q ss_pred CCCCCCCCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCC
Q 009695 356 FSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGG 404 (528)
Q Consensus 356 ~~~~~~~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~ 404 (528)
.......+.+.||.+..+..|||+|++++-..+-||-++.|...
T Consensus 137 -----~~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~ 180 (190)
T COG0195 137 -----KEDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI 180 (190)
T ss_pred -----EeCCCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence 01112278999999999999999999999999999999999653
No 60
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=96.43 E-value=0.009 Score=61.48 Aligned_cols=95 Identities=21% Similarity=0.280 Sum_probs=63.5
Q ss_pred cccccccccCchHHHHHHhhh-CceEEecCCCCCCCceEEEEEcCCcchhhhhcccccccccCCCcchHHHHHHHHHHHH
Q 009695 34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM 112 (528)
Q Consensus 34 ~~vG~VIGk~G~~Ik~I~~eT-ga~I~i~~~~~~~~eRvi~I~G~~~~~~~~~~~~~~~~~~~~~~s~A~~al~~v~~~i 112 (528)
+-+|+.||++|+.|+.|.++. |=+|+|-....+-.+- |. + .++||. +
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~f---i~-------n-------------al~Pa~---------v 290 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEF---IA-------N-------------ALSPAK---------V 290 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHHHH---HH-------H-------------hcCCce---------E
Confidence 458999999999999999999 7788874321110000 00 0 011110 0
Q ss_pred hhhhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcC
Q 009695 113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP 166 (528)
Q Consensus 113 ~~~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~ 166 (528)
....... +....+.+.||..+.+..|||+|.+++-...-||.+|.|..
T Consensus 291 ~~v~i~~------~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 291 ISVEVLD------EDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred EEEEEEc------CCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 0000000 01346789999999999999999999999999999999965
No 61
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.38 E-value=0.0082 Score=62.89 Aligned_cols=95 Identities=23% Similarity=0.262 Sum_probs=63.1
Q ss_pred cccccccccCchHHHHHHhhh-CceEEecCCCCCCCceEEEEEcCCcchhhhhcccccccccCCCcchHHHHHHHHHHHH
Q 009695 34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM 112 (528)
Q Consensus 34 ~~vG~VIGk~G~~Ik~I~~eT-ga~I~i~~~~~~~~eRvi~I~G~~~~~~~~~~~~~~~~~~~~~~s~A~~al~~v~~~i 112 (528)
+-+|+.||++|+.|+.|.++. |=+|+|=....+-.+ .|. + .++||. |
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp~~---fI~-------N-------------aLsPA~-----V---- 324 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDPAT---YIA-------N-------------ALSPAR-----V---- 324 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCHHH---HHH-------H-------------hcCCce-----e----
Confidence 568999999999999999999 778877332111000 000 0 011110 0
Q ss_pred hhhhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcC
Q 009695 113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP 166 (528)
Q Consensus 113 ~~~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~ 166 (528)
....... .....+.+.||..+.+..|||+|.+++--..-||.+|.|..
T Consensus 325 ~~V~i~~------~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 325 DEVRLVD------PEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred eEEEEEc------CCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 0000000 11235689999999999999999999999999999999966
No 62
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.37 E-value=0.01 Score=61.40 Aligned_cols=96 Identities=18% Similarity=0.241 Sum_probs=64.1
Q ss_pred cccccccccCchHHHHHHhhh-CceEEecCCCCCCCceEEEEEcCCcchhhhhcccccccccCCCcchHHHHHHHHHHHH
Q 009695 34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM 112 (528)
Q Consensus 34 ~~vG~VIGk~G~~Ik~I~~eT-ga~I~i~~~~~~~~eRvi~I~G~~~~~~~~~~~~~~~~~~~~~~s~A~~al~~v~~~i 112 (528)
+-+|+.||++|+.|+.|.++. |=+|+|=....+-.+ .|. + .++||. +
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~~---fi~-------n-------------al~Pa~-----v---- 292 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPAE---FVA-------N-------------ALSPAK-----V---- 292 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCCCHHH---HHH-------H-------------hCCCce-----E----
Confidence 458999999999999999999 788887432111000 000 0 011110 0
Q ss_pred hhhhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCC
Q 009695 113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (528)
Q Consensus 113 ~~~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~ 167 (528)
....... +....+.+.||..+.+..|||+|.+++--..-||.+|.|...
T Consensus 293 ~~v~i~~------~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 293 VSVEVDD------EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred EEEEEEc------CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 0000000 113467899999999999999999999999999999999774
No 63
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.34 E-value=0.0046 Score=69.85 Aligned_cols=95 Identities=20% Similarity=0.249 Sum_probs=69.2
Q ss_pred cchHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCce
Q 009695 98 VSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQL 177 (528)
Q Consensus 98 ~s~A~~al~~v~~~i~~~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~ 177 (528)
+..|.++..++++.+.+...+.........+....+.|+.+.++.+||.||.+||+|.++||++|.+.. +..
T Consensus 523 l~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d--------~G~ 594 (693)
T PRK11824 523 LEQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED--------DGT 594 (693)
T ss_pred HHHHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC--------Cce
Confidence 445667777777776655333221111223445566779999999999999999999999999888743 567
Q ss_pred EEEecc-HHHHHHHHHHHHHHHcc
Q 009695 178 IQITGA-TLAVKKALVAVTTCLQH 200 (528)
Q Consensus 178 V~I~G~-~~~V~kA~~~I~~~l~~ 200 (528)
|.|.+. .+++.+|+.+|..+..+
T Consensus 595 v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 595 VKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred EEEEcccHHHHHHHHHHHHHhccc
Confidence 888885 89999999999887753
No 64
>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=96.29 E-value=0.0069 Score=46.09 Aligned_cols=36 Identities=28% Similarity=0.471 Sum_probs=33.7
Q ss_pred eEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEE
Q 009695 129 AYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVM 164 (528)
Q Consensus 129 v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i 164 (528)
....+.|+....|..|||+|.+|+.+++.+|-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 577899999999999999999999999999998876
No 65
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.29 E-value=0.011 Score=60.93 Aligned_cols=95 Identities=16% Similarity=0.244 Sum_probs=63.8
Q ss_pred cccccccccCchHHHHHHhhh-CceEEecCCCCCCCceEEEEEcCCcchhhhhcccccccccCCCcchHHHHHHHHHHHH
Q 009695 34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM 112 (528)
Q Consensus 34 ~~vG~VIGk~G~~Ik~I~~eT-ga~I~i~~~~~~~~eRvi~I~G~~~~~~~~~~~~~~~~~~~~~~s~A~~al~~v~~~i 112 (528)
+-+|+.||++|+.|+.|.++. |=+|+|-....+-.+ .|. + .++||. +..|
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~~---fI~-------N-------------al~Pa~--V~~V---- 301 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPEI---FIA-------R-------------ALAPAI--ISSV---- 301 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHHH---HHH-------H-------------hCCCce--eeEE----
Confidence 458999999999999999998 778877332111000 000 0 011110 0000
Q ss_pred hhhhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCC
Q 009695 113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (528)
Q Consensus 113 ~~~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~ 167 (528)
... +..-.+.+.||..+.+..|||+|.+++-...-||.+|.|..-
T Consensus 302 ---~i~-------~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~ 346 (374)
T PRK12328 302 ---KIE-------EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI 346 (374)
T ss_pred ---EEc-------CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence 000 113467889999999999999999999999999999999874
No 66
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.08 E-value=0.032 Score=54.26 Aligned_cols=77 Identities=23% Similarity=0.337 Sum_probs=55.6
Q ss_pred CCceEEEEEeCC------cceeeeecCCCchhHHHHHhhCCeEEEeCCCCc------------cccC---CCCCcEEEEc
Q 009695 363 GDAVAVSILVGA------DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQV------------LGCA---AQNDVVIQIS 421 (528)
Q Consensus 363 ~~~~t~~v~VP~------~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~------------p~~~---~~~~~~V~It 421 (528)
....+.+|.||- ++||.|+|..|.++|+++++|||+|-|-.+... |+.+ .+-...|+..
T Consensus 89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~ 168 (259)
T KOG1588|consen 89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETE 168 (259)
T ss_pred ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEe
Confidence 456778888884 699999999999999999999999999877442 1111 1223678888
Q ss_pred CCHHHHHH----HHHHHHHHHh
Q 009695 422 GEYKNVQN----ALSEVVGRLR 439 (528)
Q Consensus 422 G~~~~v~~----A~~~I~~~l~ 439 (528)
++++-+.. |+..|...|.
T Consensus 169 ~p~~ea~~rl~~AleeI~klL~ 190 (259)
T KOG1588|consen 169 APPAEAYARLAYALEEIKKLLV 190 (259)
T ss_pred CCHHHHHHHHHHHHHHHHHhcC
Confidence 88876654 5555555443
No 67
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.03 E-value=0.008 Score=67.93 Aligned_cols=92 Identities=14% Similarity=0.227 Sum_probs=66.6
Q ss_pred HHHHHHHHHhhhhhcccCCCCCCCCCCCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCC
Q 009695 336 VQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQND 415 (528)
Q Consensus 336 a~~A~~~i~~~i~e~~~~~~~~~~~~~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~ 415 (528)
+.++..++++.+.+..-.. . .......+....+.||.+.++.+||.||.+||+|.++||+.|.+. ++
T Consensus 526 a~~g~~~I~~~M~~aI~~~-r-~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-----------d~ 592 (693)
T PRK11824 526 AKEGRLHILGKMNEAISEP-R-AELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-----------DD 592 (693)
T ss_pred HHHHHHHHHHHHHHHhcCC-h-hhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------CC
Confidence 4455566666665432111 0 011223556778888999999999999999999999999988662 24
Q ss_pred cEEEEcC-CHHHHHHHHHHHHHHHhh
Q 009695 416 VVIQISG-EYKNVQNALSEVVGRLRH 440 (528)
Q Consensus 416 ~~V~ItG-~~~~v~~A~~~I~~~l~~ 440 (528)
..|.|.+ ..+.+++|+.+|.....+
T Consensus 593 G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 593 GTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred ceEEEEcccHHHHHHHHHHHHHhccc
Confidence 5677877 677999999999988864
No 68
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=96.01 E-value=0.016 Score=59.67 Aligned_cols=95 Identities=19% Similarity=0.287 Sum_probs=63.3
Q ss_pred cccceeeccCCchhHhhHhhc-CeeEEEeCCCCCCCccEEEEecccccCCCCChHHHHHHHHHhhhhhcccCCCCCCCCC
Q 009695 283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN 361 (528)
Q Consensus 283 ~~vG~IIGkgG~~Ik~I~~~t-Ga~I~i~~~~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i~~~i~e~~~~~~~~~~~~ 361 (528)
+-+|..||++|++|+.|.++. |=+|.|-.-.++..+-+ .. ..+|| ++....+ .+
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~fi--~n-------al~Pa---------~v~~v~i-------~~ 297 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEFI--AN-------ALSPA---------KVISVEV-------LD 297 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHHHHH--HH-------hcCCc---------eEEEEEE-------Ec
Confidence 567999999999999999888 77777642211110000 00 00010 0000000 00
Q ss_pred CCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeC
Q 009695 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVG 403 (528)
Q Consensus 362 ~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~ 403 (528)
.......+.||.++.+..|||+|++++-..+-||.+|.|..
T Consensus 298 -~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 298 -EDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred -CCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 12357899999999999999999999999999999999965
No 69
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.77 E-value=0.032 Score=57.61 Aligned_cols=99 Identities=12% Similarity=0.073 Sum_probs=66.4
Q ss_pred cccceeeccCCchhHhhHhhc-CeeEEEeCCCCCCCccEEEEecccccCCCCChHHHHHHHHHhhhhhcccCCCCCCCCC
Q 009695 283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN 361 (528)
Q Consensus 283 ~~vG~IIGkgG~~Ik~I~~~t-Ga~I~i~~~~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i~~~i~e~~~~~~~~~~~~ 361 (528)
+-+|..||++|.+|+.|.++. |=+|.|-.-.++..+-+ .- ..+|| ++.... .+
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~~fI---~N------al~Pa---------~V~~V~--------i~ 304 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPEIFI---AR------ALAPA---------IISSVK--------IE 304 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHHHHH---HH------hCCCc---------eeeEEE--------Ec
Confidence 567999999999999999888 77777642211110000 00 00010 000000 01
Q ss_pred CCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCcc
Q 009695 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVL 408 (528)
Q Consensus 362 ~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p 408 (528)
+......+.||.++.+..|||+|++++-..+-||.+|.|..-++.-
T Consensus 305 -~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~~~ 350 (374)
T PRK12328 305 -EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGSKE 350 (374)
T ss_pred -CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCCCc
Confidence 2335789999999999999999999999999999999998866533
No 70
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.76 E-value=0.017 Score=56.59 Aligned_cols=66 Identities=20% Similarity=0.174 Sum_probs=55.7
Q ss_pred EEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcCCHH-HHHHHHHHHHHHHhhhcCC
Q 009695 368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYK-NVQNALSEVVGRLRHNLKS 444 (528)
Q Consensus 368 ~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~~~-~v~~A~~~I~~~l~~~~~~ 444 (528)
..+.||.+.++.+||++|.+|+.|.+.+++.|.+-. +-.|.|+++.. ++..|..+|...-++....
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-----------NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~~ 213 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-----------NGRIWIKGPDEEDEEIAIEAIKKIEREAHTS 213 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-----------CcEEEEeeCCHHHHHHHHHHHHHHHhhhhcc
Confidence 578999999999999999999999999999998732 45688888876 8889999998877665443
No 71
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.64 E-value=0.025 Score=60.76 Aligned_cols=95 Identities=21% Similarity=0.294 Sum_probs=63.2
Q ss_pred cccccccccCchHHHHHHhhh-CceEEecCCCCCCCceEEEEEcCCcchhhhhcccccccccCCCcchHHHHHHHHHHHH
Q 009695 34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM 112 (528)
Q Consensus 34 ~~vG~VIGk~G~~Ik~I~~eT-ga~I~i~~~~~~~~eRvi~I~G~~~~~~~~~~~~~~~~~~~~~~s~A~~al~~v~~~i 112 (528)
+-+|+.||++|+.|+.|.++. |=+|+|-....+- . ..|.- .++||. |
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~-~--~fi~n--------------------al~pa~-----v---- 292 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIILWSDDP-A--QFIIN--------------------ALSPAE-----V---- 292 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEEcCCCH-H--HHHHH--------------------hCCCCE-----E----
Confidence 348999999999999999998 7788773321110 0 00000 011110 0
Q ss_pred hhhhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCC
Q 009695 113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (528)
Q Consensus 113 ~~~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~ 167 (528)
...... +..-.+.+.||..+.+.-|||+|.+|+...+-||.+|.|...
T Consensus 293 ~~v~~~-------~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 293 SSVVVD-------EDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred EEEEEe-------CCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 000000 012367899999999999999999999999999999999763
No 72
>PRK00468 hypothetical protein; Provisional
Probab=95.64 E-value=0.012 Score=46.71 Aligned_cols=35 Identities=29% Similarity=0.442 Sum_probs=30.3
Q ss_pred CCCceEEEEEecccccccccccCchHHHHHHhhhC
Q 009695 21 PDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTK 55 (528)
Q Consensus 21 ~~~~~~~rilvp~~~vG~VIGk~G~~Ik~I~~eTg 55 (528)
.++.+.+++-|..+.+|.||||+|.+|+.||.--.
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~ 60 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVK 60 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence 34567899999999999999999999999987644
No 73
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=95.62 E-value=0.015 Score=58.03 Aligned_cols=71 Identities=24% Similarity=0.315 Sum_probs=58.0
Q ss_pred ceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhh
Q 009695 365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN 441 (528)
Q Consensus 365 ~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~~~~v~~A~~~I~~~l~~~ 441 (528)
.....+.|++...|.|||++|.+-+.|+++|+++|.++.+. +..+.++.+-+..++|..|...|...|-+.
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~------~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN------TNKEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC------CCcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 45668899999999999999999999999999999887642 233445555567779999999999888754
No 74
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.59 E-value=0.025 Score=58.58 Aligned_cols=96 Identities=19% Similarity=0.214 Sum_probs=64.1
Q ss_pred cccceeeccCCchhHhhHhhc-CeeEEEeCCCCCCCccEEEEecccccCCCCChHHHHHHHHHhhhhhcccCCCCCCCCC
Q 009695 283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN 361 (528)
Q Consensus 283 ~~vG~IIGkgG~~Ik~I~~~t-Ga~I~i~~~~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i~~~i~e~~~~~~~~~~~~ 361 (528)
+-+|..||++|.+|+.|.++. |=+|.|-.-.++..+-+ .- ..+|| ++..... .
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~~fi---~n------al~Pa---------~v~~v~i--------~ 298 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPAEFV---AN------ALSPA---------KVVSVEV--------D 298 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCCCHHHHH---HH------hCCCc---------eEEEEEE--------E
Confidence 567999999999999998888 77777642211110000 00 00010 0000000 0
Q ss_pred CCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCC
Q 009695 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGG 404 (528)
Q Consensus 362 ~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~ 404 (528)
.+......+.||.++.+.-|||+|++++--.+-||.+|.|...
T Consensus 299 ~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 299 DEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred cCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 1233578999999999999999999999999999999999764
No 75
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.43 E-value=0.073 Score=49.67 Aligned_cols=44 Identities=23% Similarity=0.434 Sum_probs=36.8
Q ss_pred CCceEEEEEeC------CcceeeeecCCCchhHHHHHhhCCeEEEeCCCC
Q 009695 363 GDAVAVSILVG------ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ 406 (528)
Q Consensus 363 ~~~~t~~v~VP------~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~ 406 (528)
....+-++.|| .+++|.|||..|.+.++|++.|+|+|-|-....
T Consensus 145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gs 194 (269)
T COG5176 145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGS 194 (269)
T ss_pred cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccc
Confidence 34566677776 589999999999999999999999999976544
No 76
>PRK02821 hypothetical protein; Provisional
Probab=95.26 E-value=0.017 Score=46.00 Aligned_cols=35 Identities=17% Similarity=0.288 Sum_probs=30.7
Q ss_pred CCceEEEEEecccccccccccCchHHHHHHhhhCc
Q 009695 22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKC 56 (528)
Q Consensus 22 ~~~~~~rilvp~~~vG~VIGk~G~~Ik~I~~eTga 56 (528)
++.+.++|-|..+.+|.||||+|.+|+.||.--.+
T Consensus 28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 34578999999999999999999999999987654
No 77
>PRK00468 hypothetical protein; Provisional
Probab=95.24 E-value=0.019 Score=45.52 Aligned_cols=32 Identities=28% Similarity=0.479 Sum_probs=28.6
Q ss_pred CCCceEEEEEeecceeeEEecCCChHHHHHHh
Q 009695 125 GDDVAYCGLLANTTKIGVVVGKGGRNVTRMRI 156 (528)
Q Consensus 125 ~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~ 156 (528)
.+..+.++|.+....+|.||||+|.+|+.||.
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRt 57 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRT 57 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHH
Confidence 34568899999999999999999999999984
No 78
>PRK12704 phosphodiesterase; Provisional
Probab=95.19 E-value=0.05 Score=59.41 Aligned_cols=68 Identities=13% Similarity=0.231 Sum_probs=53.1
Q ss_pred CceEEEEEeCC-cceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcC-CHHHHHHHHHHHHHHHhhh
Q 009695 364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEVVGRLRHN 441 (528)
Q Consensus 364 ~~~t~~v~VP~-~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG-~~~~v~~A~~~I~~~l~~~ 441 (528)
...+..|.+|+ ++-|+||||.|.+|+-+...||++|-|. ++...|.||| +|---+.|...+...+.+.
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid----------dtp~~v~ls~~~~~rre~a~~~l~~l~~dg 277 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID----------DTPEAVILSGFDPIRREIARLALEKLVQDG 277 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc----------CCCCeEEEecCChhhHHHHHHHHHHHHhcC
Confidence 34566888998 6779999999999999999999999773 3345788999 6666567777766666554
No 79
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.19 E-value=0.045 Score=57.52 Aligned_cols=93 Identities=20% Similarity=0.194 Sum_probs=62.5
Q ss_pred cccceeeccCCchhHhhHhhc-CeeEEEeCCCCCCCccEEEEecccccCCCCChHHHHHHHHH--hhhhhcccCCCCCCC
Q 009695 283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVF--ARSVEVEGQQGFSSG 359 (528)
Q Consensus 283 ~~vG~IIGkgG~~Ik~I~~~t-Ga~I~i~~~~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i~--~~i~e~~~~~~~~~~ 359 (528)
+-+|..||++|.+|+.|.++. |=+|.|-.-.++. . .-+...+ .++....+
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp-------------------~-~fI~NaLsPA~V~~V~i------- 329 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDP-------------------A-TYIANALSPARVDEVRL------- 329 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCH-------------------H-HHHHHhcCCceeeEEEE-------
Confidence 568999999999999999888 7677664221111 0 0000000 00100000
Q ss_pred CCCCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeC
Q 009695 360 ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVG 403 (528)
Q Consensus 360 ~~~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~ 403 (528)
.........+.||.++.+.-|||+|++++--.+-||-+|.|..
T Consensus 330 -~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 330 -VDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred -EcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 0012346799999999999999999999999999999998854
No 80
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=95.16 E-value=0.28 Score=47.03 Aligned_cols=126 Identities=13% Similarity=0.097 Sum_probs=86.3
Q ss_pred EEeeccccceeeccCCchhHhhHhhcCeeEEEeCCCCCCCccEEEEecccccCCCCChHHHHHHHHHhhhhhcccCCCCC
Q 009695 278 MLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFS 357 (528)
Q Consensus 278 l~vP~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i~~~i~e~~~~~~~~ 357 (528)
+..+....-.+...+|..++.|....||+|.+.. ++..|.|+|++ .+.+.+......+..
T Consensus 30 v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-----~~~~i~I~g~k-------~~~~~i~~~i~~~l~-------- 89 (210)
T PF14611_consen 30 VWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR-----SENRIRITGTK-------STAEYIEASINEILS-------- 89 (210)
T ss_pred EEecchheeeeecCCchHHHHHHHhcCceEEEec-----CCcEEEEEccH-------HHHHHHHHHHHHHHh--------
Confidence 4455777788999999999999888899999953 35689999994 233333333333322
Q ss_pred CCCCCCCceEEEEEeCCcceeeeecC----CCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEc-----CCHHHHH
Q 009695 358 SGENKGDAVAVSILVGADFVGCLTGS----GSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQIS-----GEYKNVQ 428 (528)
Q Consensus 358 ~~~~~~~~~t~~v~VP~~~~g~IIGk----gG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~It-----G~~~~v~ 428 (528)
...+.++.++.-.--.--++ ....+++|++.|++.|+..+. +..+.|+ -....++
T Consensus 90 ------~i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~----------~~~~~i~~~~~~~~~~~~~ 153 (210)
T PF14611_consen 90 ------NIRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD----------GNKLKISWLASPENEKRAD 153 (210)
T ss_pred ------hcEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC----------CCeEEEEEEeeccccchHH
Confidence 33456666664322111112 366899999999999988653 2234444 4667999
Q ss_pred HHHHHHHHHHh
Q 009695 429 NALSEVVGRLR 439 (528)
Q Consensus 429 ~A~~~I~~~l~ 439 (528)
.|++++..-+.
T Consensus 154 ~a~RlL~~a~~ 164 (210)
T PF14611_consen 154 RAKRLLLWALD 164 (210)
T ss_pred HHHHHHHHhcc
Confidence 99999999885
No 81
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.09 E-value=0.053 Score=59.11 Aligned_cols=67 Identities=13% Similarity=0.243 Sum_probs=54.0
Q ss_pred CceEEEEEeCC-cceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcC-CHHHHHHHHHHHHHHHhh
Q 009695 364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEVVGRLRH 440 (528)
Q Consensus 364 ~~~t~~v~VP~-~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG-~~~~v~~A~~~I~~~l~~ 440 (528)
......|.+|+ ++-|.||||.|.+|+-+...||+++-|. ++...|+|+| +|---+.|..-+...|.+
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid----------dtp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID----------DTPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc----------CCCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 45667889998 6779999999999999999999999773 3345788988 777777777777777664
No 82
>PRK02821 hypothetical protein; Provisional
Probab=95.01 E-value=0.038 Score=44.01 Aligned_cols=32 Identities=25% Similarity=0.435 Sum_probs=28.3
Q ss_pred CCceEEEEEeecceeeEEecCCChHHHHHHhh
Q 009695 126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIE 157 (528)
Q Consensus 126 ~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~ 157 (528)
+..+.+.|.|....+|.||||+|.+|+.||.-
T Consensus 28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtl 59 (77)
T PRK02821 28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTV 59 (77)
T ss_pred CCcEEEEEEEChhhCcceeCCCCchHHHHHHH
Confidence 34578899999999999999999999999854
No 83
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=94.97 E-value=0.94 Score=43.41 Aligned_cols=87 Identities=18% Similarity=0.318 Sum_probs=65.2
Q ss_pred HHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEec
Q 009695 103 EAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG 182 (528)
Q Consensus 103 ~al~~v~~~i~~~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G 182 (528)
..+.++++.++.......-+ ..-.+.+.++....-.|+..+|..++.|....||+|.+.. .+..|.|+|
T Consensus 4 ~l~~~Il~d~W~l~v~e~v~----~~g~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-------~~~~i~I~g 72 (210)
T PF14611_consen 4 KLAERILRDCWNLEVSEEVD----ELGDLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR-------SENRIRITG 72 (210)
T ss_pred HHHHHHHHHhcCCcccceee----ccceeEEEecchheeeeecCCchHHHHHHHhcCceEEEec-------CCcEEEEEc
Confidence 34556777777664332211 1123334445778899999999999999888999999977 567899999
Q ss_pred cHHHHHHHHHHHHHHHcc
Q 009695 183 ATLAVKKALVAVTTCLQH 200 (528)
Q Consensus 183 ~~~~V~kA~~~I~~~l~~ 200 (528)
+...+..+...|.+.+..
T Consensus 73 ~k~~~~~i~~~i~~~l~~ 90 (210)
T PF14611_consen 73 TKSTAEYIEASINEILSN 90 (210)
T ss_pred cHHHHHHHHHHHHHHHhh
Confidence 999999999999888854
No 84
>PRK00106 hypothetical protein; Provisional
Probab=94.93 E-value=0.068 Score=58.17 Aligned_cols=67 Identities=15% Similarity=0.285 Sum_probs=53.9
Q ss_pred CceEEEEEeCC-cceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcC-CHHHHHHHHHHHHHHHhh
Q 009695 364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEVVGRLRH 440 (528)
Q Consensus 364 ~~~t~~v~VP~-~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG-~~~~v~~A~~~I~~~l~~ 440 (528)
......|.+|+ ++-|+||||.|.+|+-+...||+++-|. ++...|+|+| +|---+.|...+...+.+
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid----------dtp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID----------DTPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc----------CCCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 45667888998 6779999999999999999999999773 3345688999 777777777777766664
No 85
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=94.87 E-value=0.059 Score=57.91 Aligned_cols=95 Identities=17% Similarity=0.216 Sum_probs=63.7
Q ss_pred cccceeeccCCchhHhhHhhc-CeeEEEeCCCCCCCccEEEEecccccCCCCChHHHHHHHHHhhhhhcccCCCCCCCCC
Q 009695 283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN 361 (528)
Q Consensus 283 ~~vG~IIGkgG~~Ik~I~~~t-Ga~I~i~~~~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i~~~i~e~~~~~~~~~~~~ 361 (528)
+-+|..||++|++|+.|.++. |=+|.|-.-.++ ++ ..+.+-+.......- -.+
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d-------------------~~----~fi~nal~pa~v~~v---~~~ 298 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIILWSDD-------------------PA----QFIINALSPAEVSSV---VVD 298 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEEcCCC-------------------HH----HHHHHhCCCCEEEEE---EEe
Confidence 457999999999999999888 777776422111 11 111111100000000 000
Q ss_pred CCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCC
Q 009695 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGG 404 (528)
Q Consensus 362 ~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~ 404 (528)
.......+.||.++.+.-|||+|++++-..+.||.+|.|...
T Consensus 299 -~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 299 -EDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred -CCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 123488999999999999999999999999999999999764
No 86
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.86 E-value=0.03 Score=44.26 Aligned_cols=33 Identities=27% Similarity=0.496 Sum_probs=29.5
Q ss_pred CCCceEEEEEeecceeeEEecCCChHHHHHHhh
Q 009695 125 GDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIE 157 (528)
Q Consensus 125 ~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~ 157 (528)
.+..++++|-+.....|.||||+|.+|+.|+.-
T Consensus 26 ~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred cCCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 356889999999999999999999999999853
No 87
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=94.81 E-value=0.046 Score=50.98 Aligned_cols=42 Identities=26% Similarity=0.442 Sum_probs=35.1
Q ss_pred CCceEEEEEecc------cccccccccCchHHHHHHhhhCceEEecCC
Q 009695 22 DDVVSFRLVCPT------PVVGGLIGRSGSIISSIRRDTKCRIHCEGG 63 (528)
Q Consensus 22 ~~~~~~rilvp~------~~vG~VIGk~G~~Ik~I~~eTga~I~i~~~ 63 (528)
+..+.-++++|. ++||.|||..|+|.|+|++.|+|+|-|--.
T Consensus 145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 334556788885 579999999999999999999999999543
No 88
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=94.72 E-value=0.06 Score=52.69 Aligned_cols=63 Identities=21% Similarity=0.260 Sum_probs=53.8
Q ss_pred EEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEecc-HHHHHHHHHHHHHHHccC
Q 009695 131 CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQHL 201 (528)
Q Consensus 131 ~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G~-~~~V~kA~~~I~~~l~~~ 201 (528)
+.+-||...++.+||++|.+|+.|.++++++|.+-. +..|.|.+. .+++.+|+.+|..+-++.
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~--------NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ--------NGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC--------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 357889999999999999999999999999999944 367888888 668899999998877664
No 89
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.57 E-value=0.037 Score=43.78 Aligned_cols=33 Identities=27% Similarity=0.458 Sum_probs=29.6
Q ss_pred CCceEEEEEecccccccccccCchHHHHHHhhh
Q 009695 22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDT 54 (528)
Q Consensus 22 ~~~~~~rilvp~~~vG~VIGk~G~~Ik~I~~eT 54 (528)
+..+.++|-+.....|.||||+|.+|+.||.--
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 567789999999999999999999999998653
No 90
>PRK01064 hypothetical protein; Provisional
Probab=94.54 E-value=0.048 Score=43.55 Aligned_cols=32 Identities=28% Similarity=0.548 Sum_probs=28.8
Q ss_pred CCCceEEEEEeecceeeEEecCCChHHHHHHh
Q 009695 125 GDDVAYCGLLANTTKIGVVVGKGGRNVTRMRI 156 (528)
Q Consensus 125 ~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~ 156 (528)
.+..+.+++.|.....|.+|||+|.+|+.|+.
T Consensus 26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~ 57 (78)
T PRK01064 26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRT 57 (78)
T ss_pred CCCEEEEEEEECcccceEEECCCCccHHHHHH
Confidence 35578999999999999999999999999985
No 91
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=94.52 E-value=0.15 Score=55.60 Aligned_cols=64 Identities=16% Similarity=0.296 Sum_probs=48.1
Q ss_pred EEEEEeec-ceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEecc-HHHHHHHHHHHHHHHcc
Q 009695 130 YCGLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQH 200 (528)
Q Consensus 130 ~~rllVp~-~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G~-~~~V~kA~~~I~~~l~~ 200 (528)
+..+-+|+ ..-|+||||.|.+|+.++.-||+++-|.. +...|.|+|- |--=+-|...+..++.+
T Consensus 205 ~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd-------tp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 205 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-------TPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred eeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC-------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 33455665 78999999999999999999999999977 5577888873 44444555555555544
No 92
>PRK01064 hypothetical protein; Provisional
Probab=94.47 E-value=0.037 Score=44.18 Aligned_cols=34 Identities=26% Similarity=0.527 Sum_probs=30.2
Q ss_pred CCceEEEEEecccccccccccCchHHHHHHhhhC
Q 009695 22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTK 55 (528)
Q Consensus 22 ~~~~~~rilvp~~~vG~VIGk~G~~Ik~I~~eTg 55 (528)
.+.+.+++-|.....|.+|||+|.+|+.||.-.+
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHHHH
Confidence 4567899999999999999999999999998644
No 93
>PRK00106 hypothetical protein; Provisional
Probab=94.32 E-value=0.2 Score=54.61 Aligned_cols=64 Identities=13% Similarity=0.331 Sum_probs=48.8
Q ss_pred EEEEEeec-ceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEec-cHHHHHHHHHHHHHHHcc
Q 009695 130 YCGLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG-ATLAVKKALVAVTTCLQH 200 (528)
Q Consensus 130 ~~rllVp~-~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G-~~~~V~kA~~~I~~~l~~ 200 (528)
+..+-+|+ ..-|+||||.|.+|+.++.-||+++-|.. +...|.|+| +|---+-|...+..++.+
T Consensus 226 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd-------tp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 226 ITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD-------TPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred eeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC-------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 33555665 78999999999999999999999999977 557788988 354445555555555544
No 94
>PRK12704 phosphodiesterase; Provisional
Probab=94.32 E-value=0.18 Score=55.22 Aligned_cols=62 Identities=16% Similarity=0.312 Sum_probs=47.6
Q ss_pred EEEeec-ceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEecc-HHHHHHHHHHHHHHHcc
Q 009695 132 GLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQH 200 (528)
Q Consensus 132 rllVp~-~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G~-~~~V~kA~~~I~~~l~~ 200 (528)
.+-+|+ ..-|+||||.|.+|+.++.-||++|-|.. +...|.|+|- +--=+.|...+...+.+
T Consensus 213 ~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd-------tp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 213 VVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-------TPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred eeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC-------CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 445555 78999999999999999999999999977 5677889983 44434566666555554
No 95
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=93.44 E-value=0.2 Score=53.47 Aligned_cols=94 Identities=17% Similarity=0.228 Sum_probs=68.5
Q ss_pred chHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceE
Q 009695 99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLI 178 (528)
Q Consensus 99 s~A~~al~~v~~~i~~~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V 178 (528)
..|.+|-..+++.+...............++...|-|+.+....+||.+|...|+|..+||+.-++ +|..+
T Consensus 567 ~~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v---------De~t~ 637 (760)
T KOG1067|consen 567 QKAREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV---------DEGTF 637 (760)
T ss_pred HhhhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeee---------cCceE
Confidence 345555555655544433222222223457888999999999999999999999999999966665 55677
Q ss_pred EEecc-HHHHHHHHHHHHHHHccC
Q 009695 179 QITGA-TLAVKKALVAVTTCLQHL 201 (528)
Q Consensus 179 ~I~G~-~~~V~kA~~~I~~~l~~~ 201 (528)
.|-.. ..+..+|+..|..++.+.
T Consensus 638 ~i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 638 SIFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred EEEecCHHHHHHHHHHHHHHhcCc
Confidence 77766 788899999999988654
No 96
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=93.17 E-value=0.051 Score=62.07 Aligned_cols=69 Identities=17% Similarity=-0.030 Sum_probs=59.2
Q ss_pred EEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 009695 368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH 440 (528)
Q Consensus 368 ~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~~~~v~~A~~~I~~~l~~ 440 (528)
-++.+|-....+|||+||.+|+.++..|||.|++..-. |+ +..+|.+.+.|.++.++.|...|.-.|.|
T Consensus 1342 ~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq--~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1342 GKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ--PD--NQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred cccccchhhhhhhhccCcchhhhHhhccceEEehhhcC--Cc--cchhhhcccCCCChhhhhhhccccceeec
Confidence 47888888899999999999999999999999997621 11 45789999999999999999998877764
No 97
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=92.23 E-value=0.088 Score=41.45 Aligned_cols=35 Identities=17% Similarity=0.273 Sum_probs=29.7
Q ss_pred CCceEEEEEecccccccccccCchHHHHHHhhhCc
Q 009695 22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKC 56 (528)
Q Consensus 22 ~~~~~~rilvp~~~vG~VIGk~G~~Ik~I~~eTga 56 (528)
.+...+.+-|..+..|.||||+|.+++.||.-.+.
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 44567778889999999999999999999987654
No 98
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=90.42 E-value=0.38 Score=36.58 Aligned_cols=35 Identities=17% Similarity=0.274 Sum_probs=27.8
Q ss_pred ceEEEEEecccccccccccCchHHHHHHhhhCceE
Q 009695 24 VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRI 58 (528)
Q Consensus 24 ~~~~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I 58 (528)
.....+.+.....|.+|||+|.+++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 34555666665789999999999999999998554
No 99
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=90.33 E-value=0.22 Score=57.18 Aligned_cols=62 Identities=19% Similarity=0.069 Sum_probs=51.3
Q ss_pred EEEEEecccccccccccCchHHHHHHhhhCceEEecC-CCCCCCceEEEEEcCCcchhhhhcc
Q 009695 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEG-GFPGSDHRVILVVGSGSIDRRIMFC 87 (528)
Q Consensus 26 ~~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i~~-~~~~~~eRvi~I~G~~~~~~~~~~~ 87 (528)
.-++-+|.....+|||++|+||+.++.-||+.|+++. ...+..||-+++.|.++..+-+...
T Consensus 1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~ 1403 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSP 1403 (2131)
T ss_pred ccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhcc
Confidence 3456678899999999999999999999999999987 3445679999999999876554443
No 100
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=90.32 E-value=0.88 Score=48.87 Aligned_cols=89 Identities=13% Similarity=0.125 Sum_probs=64.3
Q ss_pred HHHHHHHhhhhhcccCCCCCCCCCCCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcE
Q 009695 338 NAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVV 417 (528)
Q Consensus 338 ~A~~~i~~~i~e~~~~~~~~~~~~~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~ 417 (528)
+|...|.+.+.+.....-. ...+..++..+|.|+.+....+||.+|...|.|..+||+--++ ++..
T Consensus 571 ~ar~~Il~~m~k~i~~Pr~--~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~t 636 (760)
T KOG1067|consen 571 EARLQILDIMEKNINSPRG--SDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEGT 636 (760)
T ss_pred HHHHHHHHHHHhhcCCccc--CccccCceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCce
Confidence 4455566655443211111 1234678999999999999999999999999999999955544 2345
Q ss_pred EEEcC-CHHHHHHHHHHHHHHHhh
Q 009695 418 IQISG-EYKNVQNALSEVVGRLRH 440 (528)
Q Consensus 418 V~ItG-~~~~v~~A~~~I~~~l~~ 440 (528)
++|.- ++.+.++|+.+|...+.+
T Consensus 637 ~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 637 FSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred EEEEecCHHHHHHHHHHHHHHhcC
Confidence 66554 566889999999999976
No 101
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=89.79 E-value=0.16 Score=39.97 Aligned_cols=34 Identities=26% Similarity=0.342 Sum_probs=28.2
Q ss_pred cceEEEEEeeccccceeeccCCchhHhhHhhcCe
Q 009695 272 QEVALRMLFSGWTASGIIGKRGAIVRSLQNASGA 305 (528)
Q Consensus 272 ~~~~~~l~vP~~~vG~IIGkgG~~Ik~I~~~tGa 305 (528)
....+.+.+..+..|.+|||+|.+++.||.-.++
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 3446677889999999999999999999876654
No 102
>PRK12705 hypothetical protein; Provisional
Probab=89.18 E-value=0.75 Score=49.93 Aligned_cols=61 Identities=15% Similarity=0.256 Sum_probs=42.2
Q ss_pred EEEee-cceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEecc-HHHHHHHHHHHHHHHc
Q 009695 132 GLLAN-TTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQ 199 (528)
Q Consensus 132 rllVp-~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G~-~~~V~kA~~~I~~~l~ 199 (528)
.+-+| +..-|+||||.|.+|+.++..||+.+.|.. ..+.|.|.+- +..=+.|...+..++.
T Consensus 201 ~v~lp~demkGriIGreGrNir~~E~~tGvdliidd-------tp~~V~ls~fdp~rreia~~~l~~Li~ 263 (508)
T PRK12705 201 VVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD-------TPEAVVISSFNPIRREIARLTLEKLLA 263 (508)
T ss_pred eeecCChHhhccccCccchhHHHHHHhhCCceEecC-------CccchhhcccCccchHHHHHHHHHHHh
Confidence 34445 478999999999999999999999999977 3344556554 3333344444444443
No 103
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=88.95 E-value=0.39 Score=37.47 Aligned_cols=36 Identities=25% Similarity=0.360 Sum_probs=27.8
Q ss_pred EEEEecccc-----cccccccCchHHHHHHhhh-CceEEecC
Q 009695 27 FRLVCPTPV-----VGGLIGRSGSIISSIRRDT-KCRIHCEG 62 (528)
Q Consensus 27 ~rilvp~~~-----vG~VIGk~G~~Ik~I~~eT-ga~I~i~~ 62 (528)
..+.|-+.. +|..||++|+.|+.|.++. |-+|+|=.
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 345566666 9999999999999999999 88888743
No 104
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=88.54 E-value=0.23 Score=46.15 Aligned_cols=54 Identities=30% Similarity=0.445 Sum_probs=48.1
Q ss_pred CcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHh
Q 009695 374 ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLR 439 (528)
Q Consensus 374 ~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~~~~v~~A~~~I~~~l~ 439 (528)
+..+|+|+||+|.+---|...|.++|.+. +..|.|-|..++++.|...|...|-
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVla------------d~kIHiLG~~~niriAR~avcsLIl 230 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA------------DSKIHILGAFQNIRIARDAVCSLIL 230 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEec------------CceEEEeecchhhHHHHHhhHhhhc
Confidence 45789999999999999999999999773 4579999999999999999988774
No 105
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=87.45 E-value=0.37 Score=37.58 Aligned_cols=38 Identities=21% Similarity=0.297 Sum_probs=30.8
Q ss_pred EEEEEeCCcc-----eeeeecCCCchhHHHHHhh-CCeEEEeCC
Q 009695 367 AVSILVGADF-----VGCLTGSGSSAVSEMEDVT-GTDIKLVGG 404 (528)
Q Consensus 367 t~~v~VP~~~-----~g~IIGkgG~~Ik~I~~~t-ga~I~i~~~ 404 (528)
.+.+.|-+.. +|..||++|++|+.|+++. |-+|++..-
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 4567777777 9999999999999999999 999999764
No 106
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=86.96 E-value=0.91 Score=47.89 Aligned_cols=38 Identities=26% Similarity=0.385 Sum_probs=35.1
Q ss_pred EEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCC
Q 009695 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (528)
Q Consensus 130 ~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~ 167 (528)
...+.||..+++.+|||+|.+|++|+++.|-+|.|...
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 46788999999999999999999999999999999773
No 107
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=86.93 E-value=0.37 Score=44.84 Aligned_cols=57 Identities=26% Similarity=0.352 Sum_probs=50.2
Q ss_pred cceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHccCC
Q 009695 137 TTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLS 202 (528)
Q Consensus 137 ~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G~~~~V~kA~~~I~~~l~~~~ 202 (528)
+-.+|+|+||+|.+--.|++-|-++|.+.. ..|-|-|..++++-|...|+.++...+
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad---------~kIHiLG~~~niriAR~avcsLIlGsp 233 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD---------SKIHILGAFQNIRIARDAVCSLILGSP 233 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecC---------ceEEEeecchhhHHHHHhhHhhhccCC
Confidence 346899999999999999999999999944 568899999999999999999997654
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=86.88 E-value=1.1 Score=33.99 Aligned_cols=35 Identities=11% Similarity=0.260 Sum_probs=29.3
Q ss_pred ceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeE
Q 009695 365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDI 399 (528)
Q Consensus 365 ~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I 399 (528)
.....+.+.....|.+||++|++++.++..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 45667777776789999999999999999998655
No 109
>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=86.50 E-value=0.38 Score=38.27 Aligned_cols=33 Identities=27% Similarity=0.428 Sum_probs=28.7
Q ss_pred EEEEecccccccccccCchHHHHHHhhhCceEE
Q 009695 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIH 59 (528)
Q Consensus 27 ~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~ 59 (528)
..+.+.....|.|||++|++|++|.++.+-.+.
T Consensus 27 ~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 27 IIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp EEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred EEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 567889999999999999999999998776654
No 110
>PRK12705 hypothetical protein; Provisional
Probab=86.11 E-value=1.1 Score=48.79 Aligned_cols=40 Identities=18% Similarity=0.336 Sum_probs=34.1
Q ss_pred CceEEEEEeCC-cceeeeecCCCchhHHHHHhhCCeEEEeC
Q 009695 364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVG 403 (528)
Q Consensus 364 ~~~t~~v~VP~-~~~g~IIGkgG~~Ik~I~~~tga~I~i~~ 403 (528)
......+.+|+ ++-|+||||.|.+|+-+...||+.+-|.+
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd 236 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD 236 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC
Confidence 34566788888 66699999999999999999999997743
No 111
>PRK13764 ATPase; Provisional
Probab=86.07 E-value=1.1 Score=49.71 Aligned_cols=65 Identities=22% Similarity=0.287 Sum_probs=46.1
Q ss_pred chHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCC
Q 009695 99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (528)
Q Consensus 99 s~A~~al~~v~~~i~~~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~ 167 (528)
.-|.+.+.+.+.++.....+.+ -.+.-...+.||...++.+|||+|.+|++|.++.|.+|.|...
T Consensus 455 ~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~ 519 (602)
T PRK13764 455 RLAEKEIEREIKRYLPGPVEVE----VVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL 519 (602)
T ss_pred HHHHHHHHHHHHHhcCCceEEE----EecCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence 3455566666666552211111 0123356788999999999999999999999999999999774
No 112
>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=84.11 E-value=5.7 Score=35.54 Aligned_cols=37 Identities=24% Similarity=0.443 Sum_probs=32.2
Q ss_pred EEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCC
Q 009695 131 CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (528)
Q Consensus 131 ~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~ 167 (528)
-.+.+-...-|.+|||+|.++++|..+||-.-.|...
T Consensus 78 GEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 78 GEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred cEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 3566667788999999999999999999999998775
No 113
>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=83.90 E-value=0.58 Score=37.72 Aligned_cols=36 Identities=11% Similarity=0.204 Sum_probs=31.0
Q ss_pred EEEEecccccccccccCchHHHHHHhhhCceEEecC
Q 009695 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEG 62 (528)
Q Consensus 27 ~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i~~ 62 (528)
.++.+....-|.|||++|++|++|+++-.-...+++
T Consensus 32 i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~ 67 (81)
T cd02413 32 TEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPE 67 (81)
T ss_pred EEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCC
Confidence 778889999999999999999999999776666643
No 114
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=83.50 E-value=1.9 Score=42.29 Aligned_cols=51 Identities=14% Similarity=0.331 Sum_probs=46.2
Q ss_pred eEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHcc
Q 009695 141 GVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH 200 (528)
Q Consensus 141 G~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G~~~~V~kA~~~I~~~l~~ 200 (528)
-++||.+|+++|.|+--|.|.|-|.. ..|.+.|....+..+...|.+++..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG---------~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG---------NTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC---------cEEEeecCcchHHHHHHHHHHHHhc
Confidence 36999999999999999999999966 5789999999999999999999865
No 115
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=83.29 E-value=0.83 Score=48.18 Aligned_cols=38 Identities=18% Similarity=0.285 Sum_probs=34.4
Q ss_pred EEEEEecccccccccccCchHHHHHHhhhCceEEecCC
Q 009695 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGG 63 (528)
Q Consensus 26 ~~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i~~~ 63 (528)
...+.+|.+..+.+|||+|.+|++|++..|-+|+|.+.
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 35578899999999999999999999999999999654
No 116
>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=83.26 E-value=1.1 Score=35.74 Aligned_cols=34 Identities=15% Similarity=0.255 Sum_probs=26.8
Q ss_pred EEEEecccccccccccCchHHHHHHhhhCceEEe
Q 009695 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC 60 (528)
Q Consensus 27 ~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i 60 (528)
+.+-+..+..|.+|||+|+++..||--++.-+.-
T Consensus 26 i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~ 59 (77)
T cd02414 26 VEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR 59 (77)
T ss_pred EEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence 3455567888999999999999999987755443
No 117
>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=83.06 E-value=1.3 Score=35.28 Aligned_cols=33 Identities=27% Similarity=0.405 Sum_probs=26.5
Q ss_pred EEEEeeccccceeeccCCchhHhhHhhcCeeEE
Q 009695 276 LRMLFSGWTASGIIGKRGAIVRSLQNASGALIS 308 (528)
Q Consensus 276 ~~l~vP~~~vG~IIGkgG~~Ik~I~~~tGa~I~ 308 (528)
+.+.+..+..|.+|||.|.+++.||--+...++
T Consensus 26 i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 26 VEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred EEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 445566788899999999999999987765444
No 118
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=83.01 E-value=1.2 Score=40.86 Aligned_cols=33 Identities=18% Similarity=0.277 Sum_probs=28.3
Q ss_pred EEecccccccccccCchHHHHHHhhhCceEEecC
Q 009695 29 LVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEG 62 (528)
Q Consensus 29 ilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i~~ 62 (528)
++|-... |.-|||+|++|++|++..|-+|.+=+
T Consensus 65 fvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 65 LLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 4555566 99999999999999999999999843
No 119
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=82.61 E-value=2.7 Score=40.68 Aligned_cols=57 Identities=18% Similarity=0.221 Sum_probs=44.8
Q ss_pred EEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcCCHHH-HHHHHHHHH
Q 009695 368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKN-VQNALSEVV 435 (528)
Q Consensus 368 ~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~~~~-v~~A~~~I~ 435 (528)
.-+.|++..+.++||++|+.++-+.+.|+|.|-+-. +-.|.|.|+.+. ...|...|.
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-----------NG~IWV~~~~~~~e~~~~~aI~ 205 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-----------NGRIWVDGENESLEELAIEAIR 205 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-----------CCEEEecCCCcchHHHHHHHHH
Confidence 578899999999999999999999999999997743 445888888773 444443333
No 120
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=82.33 E-value=0.52 Score=37.47 Aligned_cols=35 Identities=23% Similarity=0.436 Sum_probs=28.8
Q ss_pred eEEEEEeecceeeEEecCCChHHHHHHhhhCCeEE
Q 009695 129 AYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIV 163 (528)
Q Consensus 129 v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~ 163 (528)
-...+.+..++.|.+||++|++|++|....+-.+.
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 34578889999999999999999999877655543
No 121
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=82.05 E-value=2.3 Score=41.78 Aligned_cols=51 Identities=20% Similarity=0.290 Sum_probs=44.7
Q ss_pred eeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 009695 378 GCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH 440 (528)
Q Consensus 378 g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~~~~v~~A~~~I~~~l~~ 440 (528)
.++||.+|++++.|+--|.|.|-+.. .+|.+.|.+..++.+...+.+.+.+
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG------------~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG------------NTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC------------cEEEeecCcchHHHHHHHHHHHHhc
Confidence 47999999999999999999997743 4689999999999999998888764
No 122
>PRK13764 ATPase; Provisional
Probab=80.28 E-value=1.6 Score=48.57 Aligned_cols=45 Identities=16% Similarity=0.209 Sum_probs=40.6
Q ss_pred CceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCcc
Q 009695 364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVL 408 (528)
Q Consensus 364 ~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p 408 (528)
....+.+.||.+.++.+|||+|.+|++|.+..|.+|.|-+.++.+
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 456788999999999999999999999999999999998876644
No 123
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=80.18 E-value=3.9 Score=39.64 Aligned_cols=57 Identities=19% Similarity=0.278 Sum_probs=43.3
Q ss_pred EEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEeccHHH-HHHHHHHHHH
Q 009695 132 GLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLA-VKKALVAVTT 196 (528)
Q Consensus 132 rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G~~~~-V~kA~~~I~~ 196 (528)
-+.|+...+.++||++|+.++-+.++++|+|-|-.+ ..|=|.|..+. ..-|...|..
T Consensus 149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N--------G~IWV~~~~~~~e~~~~~aI~~ 206 (239)
T COG1097 149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN--------GRIWVDGENESLEELAIEAIRK 206 (239)
T ss_pred EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC--------CEEEecCCCcchHHHHHHHHHH
Confidence 367889999999999999999999999999999663 34667776553 4444444443
No 124
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=79.71 E-value=2.2 Score=39.22 Aligned_cols=35 Identities=23% Similarity=0.406 Sum_probs=30.2
Q ss_pred EEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcC
Q 009695 131 CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP 166 (528)
Q Consensus 131 ~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~ 166 (528)
+-++|-... |.-|||+|++|+++++..|-+|.+..
T Consensus 63 vIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 63 VILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 345666666 99999999999999999999999965
No 125
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=79.58 E-value=3.7 Score=43.94 Aligned_cols=97 Identities=22% Similarity=0.272 Sum_probs=62.5
Q ss_pred ccccccCchHHHHHHhhhCceEEecCCCCCCCceEEEEEcCCcchhhhhcccccccccCCCcchHHHHHHHHHHHHhhhh
Q 009695 37 GGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVE 116 (528)
Q Consensus 37 G~VIGk~G~~Ik~I~~eTga~I~i~~~~~~~~eRvi~I~G~~~~~~~~~~~~~~~~~~~~~~s~A~~al~~v~~~i~~~~ 116 (528)
...+-+.|..|++|.++-.-+|.|-..+.. +.+..+|...+.+-+-+.
T Consensus 41 P~~~~~~~dlik~lAk~lrKRI~iR~dPsv-------------------------------l~~~e~A~~~I~eivP~e- 88 (637)
T COG1782 41 PELFAKDGDLIKDLAKDLRKRIIIRPDPSV-------------------------------LKPPEEARKIILEIVPEE- 88 (637)
T ss_pred HHHhccchhHHHHHHHHHhhceEeccCchh-------------------------------cCCHHHHHHHHHHhCccc-
Confidence 456677888899998888888877543210 223344544444333221
Q ss_pred hccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCC
Q 009695 117 AEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (528)
Q Consensus 117 ~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~ 167 (528)
++-..... ...+-.++|-...-|.+|||+|++.++|..++|-.-+|...
T Consensus 89 a~i~~i~F--d~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 89 AGITDIYF--DDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred cCceeEEe--cCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 11100000 12344677888899999999999999999999998888775
No 126
>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=79.00 E-value=1.8 Score=37.00 Aligned_cols=31 Identities=23% Similarity=0.356 Sum_probs=26.7
Q ss_pred EEEEecccccccccccCchHHHHHHhhhCce
Q 009695 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCR 57 (528)
Q Consensus 27 ~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~ 57 (528)
+++.+....-|.|||++|++|++|+++....
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~ 93 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQKL 93 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHHHH
Confidence 6778888899999999999999999886543
No 127
>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=76.26 E-value=3.1 Score=37.22 Aligned_cols=37 Identities=24% Similarity=0.338 Sum_probs=31.8
Q ss_pred EEecccccccccccCchHHHHHHhhhCceEEecCCCC
Q 009695 29 LVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFP 65 (528)
Q Consensus 29 ilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i~~~~~ 65 (528)
+++-..+-|.||||+|.+++.|..+||-+-.|-..+|
T Consensus 80 V~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 80 VIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred EEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 6667788999999999999999999999888865543
No 128
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=75.01 E-value=2.8 Score=34.02 Aligned_cols=28 Identities=21% Similarity=0.247 Sum_probs=24.0
Q ss_pred EEEEecccccccccccCchHHHHHHhhh
Q 009695 27 FRLVCPTPVVGGLIGRSGSIISSIRRDT 54 (528)
Q Consensus 27 ~rilvp~~~vG~VIGk~G~~Ik~I~~eT 54 (528)
.++.+....-|.+||++|.+|++|++.-
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 5666677899999999999999998875
No 129
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=74.75 E-value=3.6 Score=33.17 Aligned_cols=35 Identities=14% Similarity=0.283 Sum_probs=27.8
Q ss_pred EEEEEeecceeeEEecCCChHHHHHHhhhCCeEEE
Q 009695 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVM 164 (528)
Q Consensus 130 ~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i 164 (528)
.+++.+....-|.|||++|+.|++|+++-.-...+
T Consensus 31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~ 65 (81)
T cd02413 31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF 65 (81)
T ss_pred eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence 36788888899999999999999998765444333
No 130
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=71.92 E-value=3 Score=40.25 Aligned_cols=34 Identities=24% Similarity=0.339 Sum_probs=28.0
Q ss_pred eEEEEEecccccccccccCchHHHHHHhhhCceE
Q 009695 25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRI 58 (528)
Q Consensus 25 ~~~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I 58 (528)
...++.+....-|.||||+|++|++|+++..-..
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~ 84 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLF 84 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHHHHHHh
Confidence 3467888999999999999999999988754433
No 131
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=70.55 E-value=12 Score=40.33 Aligned_cols=95 Identities=20% Similarity=0.259 Sum_probs=63.6
Q ss_pred eeccCCchhHhhHhhcCeeEEEeCCCCCCCccEEEEecccccCCCCChHHHHHHHHHhhhhhcccCCCCCCCCCCCCceE
Q 009695 288 IIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVA 367 (528)
Q Consensus 288 IIGkgG~~Ik~I~~~tGa~I~i~~~~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i~~~i~e~~~~~~~~~~~~~~~~~t 367 (528)
.|-+.|+.|++|.++..-+|.|-... . ..++..+|...|.+-+-+.. +... -.-...+
T Consensus 43 ~~~~~~dlik~lAk~lrKRI~iR~dP---s--------------vl~~~e~A~~~I~eivP~ea---~i~~--i~Fd~~t 100 (637)
T COG1782 43 LFAKDGDLIKDLAKDLRKRIIIRPDP---S--------------VLKPPEEARKIILEIVPEEA---GITD--IYFDDDT 100 (637)
T ss_pred HhccchhHHHHHHHHHhhceEeccCc---h--------------hcCCHHHHHHHHHHhCcccc---Ccee--EEecCCC
Confidence 45588999999999998888874221 0 01233456655554442210 0000 0112345
Q ss_pred EEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCC
Q 009695 368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGG 404 (528)
Q Consensus 368 ~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~ 404 (528)
-++.|-.+.=|.+|||+|++.++|.++||-.-+|.+.
T Consensus 101 GEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 101 GEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred ceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 5888999999999999999999999999998888764
No 132
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=68.80 E-value=5.5 Score=42.52 Aligned_cols=132 Identities=9% Similarity=0.051 Sum_probs=79.5
Q ss_pred cccceeeccCCchhHhhHhhcCeeEEEeCCCCCCCccEEEE-ecccccCCCCChHHHHHHHHHhhhhhcccCCCCCCCCC
Q 009695 283 WTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTI-SALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN 361 (528)
Q Consensus 283 ~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~~~~~~eR~V~I-~G~e~p~~~~~~a~~A~~~i~~~i~e~~~~~~~~~~~~ 361 (528)
+.-..+=||+..++.+|.+...|.+++.= ...++.+..+. .|.. + .-+++.. +...
T Consensus 389 d~EdFl~gkkngK~TrIm~~v~c~~~~~i-~~~~gs~~~~~~~g~~-~-----~F~k~~~-----~~~~----------- 445 (657)
T COG5166 389 DNEDFLRGKKNGKATRIMKGVSCSELSSI-VSSTGSIVETNGIGEK-M-----SFSKKLS-----IPPT----------- 445 (657)
T ss_pred chHHHhccccCcchhhhhhhcccceeeEE-EecCCcEEEEeccCcc-h-----hhHHHhc-----CCcc-----------
Confidence 44456778888889999999988865431 11222233322 2321 1 1122221 1111
Q ss_pred CCCceEEEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcCCH---HHHHHHHHHHHHHH
Q 009695 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEY---KNVQNALSEVVGRL 438 (528)
Q Consensus 362 ~~~~~t~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~~---~~v~~A~~~I~~~l 438 (528)
+=+....+.+|...|..|||.||..|+++++.-++.|++...-..|.... ...|.|.-+. .++..|+.-+.+++
T Consensus 446 -EFpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~--~dNV~I~~PrKn~~ni~~~KNd~~~~V 522 (657)
T COG5166 446 -EFPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQW--HDNVLIEAPRKNQDNISGKKNDKLDKV 522 (657)
T ss_pred -cCchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhh--hcceEEECCccCccchhcccccHHHHH
Confidence 11234688999999999999999999999999999999977655554211 1224454433 34555565666666
Q ss_pred hh
Q 009695 439 RH 440 (528)
Q Consensus 439 ~~ 440 (528)
.+
T Consensus 523 ~~ 524 (657)
T COG5166 523 KQ 524 (657)
T ss_pred hh
Confidence 53
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=63.29 E-value=7.6 Score=31.45 Aligned_cols=27 Identities=22% Similarity=0.527 Sum_probs=22.2
Q ss_pred EEEEeecceeeEEecCCChHHHHHHhh
Q 009695 131 CGLLANTTKIGVVVGKGGRNVTRMRIE 157 (528)
Q Consensus 131 ~rllVp~~~vG~IIGkgG~~Ik~I~~~ 157 (528)
.++.+....-|.+||++|+.|++|++.
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~ 66 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEI 66 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHH
Confidence 456666688899999999999998754
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=62.76 E-value=6.3 Score=33.63 Aligned_cols=28 Identities=25% Similarity=0.328 Sum_probs=23.1
Q ss_pred EEEEeeccccceeeccCCchhHhhHhhc
Q 009695 276 LRMLFSGWTASGIIGKRGAIVRSLQNAS 303 (528)
Q Consensus 276 ~~l~vP~~~vG~IIGkgG~~Ik~I~~~t 303 (528)
+++.+-...-|.|||++|++|++|++..
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l 90 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKEL 90 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHH
Confidence 4566777788999999999999988664
No 135
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=61.79 E-value=9.9 Score=37.79 Aligned_cols=28 Identities=14% Similarity=0.315 Sum_probs=23.2
Q ss_pred eEEEEEee-cceeeEEecCCChHHHHHHh
Q 009695 129 AYCGLLAN-TTKIGVVVGKGGRNVTRMRI 156 (528)
Q Consensus 129 v~~rllVp-~~~vG~IIGkgG~~Ik~I~~ 156 (528)
+.+.++|. .+|-+.||||+|++||+|..
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~ 249 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGI 249 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHH
Confidence 56677777 57889999999999998753
No 136
>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=61.54 E-value=20 Score=40.35 Aligned_cols=38 Identities=24% Similarity=0.434 Sum_probs=33.5
Q ss_pred EEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCC
Q 009695 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (528)
Q Consensus 130 ~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~ 167 (528)
+-.+++-...-|.+|||+|.+.++|..+||-.-.|...
T Consensus 94 ~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 94 TGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred CceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 34667777888999999999999999999999999875
No 137
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=58.75 E-value=8.5 Score=37.23 Aligned_cols=37 Identities=22% Similarity=0.406 Sum_probs=29.1
Q ss_pred ceEEEEEeecceeeEEecCCChHHHHHHh----hhCC-eEEE
Q 009695 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRI----ESGA-KIVM 164 (528)
Q Consensus 128 ~v~~rllVp~~~vG~IIGkgG~~Ik~I~~----~tGa-~I~i 164 (528)
+..+++.|....-|.||||+|+.|++|++ .+|. +++|
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~~v~I 91 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKENVQI 91 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCCCceE
Confidence 44578888999999999999999998764 4666 3444
No 138
>PRK15494 era GTPase Era; Provisional
Probab=57.79 E-value=13 Score=38.54 Aligned_cols=27 Identities=11% Similarity=0.302 Sum_probs=22.5
Q ss_pred eEEEEEee-cceeeEEecCCChHHHHHH
Q 009695 129 AYCGLLAN-TTKIGVVVGKGGRNVTRMR 155 (528)
Q Consensus 129 v~~rllVp-~~~vG~IIGkgG~~Ik~I~ 155 (528)
+...++|. .+|-+.||||+|++||+|.
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~ 300 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIG 300 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHH
Confidence 55677777 4789999999999999875
No 139
>PRK00089 era GTPase Era; Reviewed
Probab=56.50 E-value=14 Score=37.10 Aligned_cols=27 Identities=19% Similarity=0.529 Sum_probs=22.1
Q ss_pred eEEEEEee-cceeeEEecCCChHHHHHH
Q 009695 129 AYCGLLAN-TTKIGVVVGKGGRNVTRMR 155 (528)
Q Consensus 129 v~~rllVp-~~~vG~IIGkgG~~Ik~I~ 155 (528)
+.+.+.|. .+|-+.||||+|++||+|.
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~ 253 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIG 253 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHH
Confidence 55667776 5788999999999999875
No 140
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=54.79 E-value=20 Score=38.56 Aligned_cols=91 Identities=13% Similarity=0.148 Sum_probs=59.5
Q ss_pred cccccCchHHHHHHhhhCceEE--ecCCCCCCCceEEEEE-cCCcchhhhhcccccccccCCCcchHHHHHHHHHHHHhh
Q 009695 38 GLIGRSGSIISSIRRDTKCRIH--CEGGFPGSDHRVILVV-GSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWE 114 (528)
Q Consensus 38 ~VIGk~G~~Ik~I~~eTga~I~--i~~~~~~~~eRvi~I~-G~~~~~~~~~~~~~~~~~~~~~~s~A~~al~~v~~~i~~ 114 (528)
.+=||+.-.+.+|.+...|.+. +... ++.++.+.. |..- .++ ++ ++.
T Consensus 393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~---~gs~~~~~~~g~~~-----------------~F~---k~----~~~--- 442 (657)
T COG5166 393 FLRGKKNGKATRIMKGVSCSELSSIVSS---TGSIVETNGIGEKM-----------------SFS---KK----LSI--- 442 (657)
T ss_pred HhccccCcchhhhhhhcccceeeEEEec---CCcEEEEeccCcch-----------------hhH---HH----hcC---
Confidence 5668887779999999999844 4333 123544443 2211 111 11 111
Q ss_pred hhhccCCCCCCCCceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcC
Q 009695 115 VEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP 166 (528)
Q Consensus 115 ~~~~~~~~~~~~~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~ 166 (528)
.. .+-+-...+.++.+.+..|||-||..|++++.+.++.|++..
T Consensus 443 ~~--------~EFpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n 486 (657)
T COG5166 443 PP--------TEFPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKN 486 (657)
T ss_pred Cc--------ccCchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhh
Confidence 11 111345578999999999999999999999999998888855
No 141
>COG1159 Era GTPase [General function prediction only]
Probab=53.93 E-value=16 Score=36.82 Aligned_cols=28 Identities=14% Similarity=0.437 Sum_probs=22.6
Q ss_pred ceEEEEEee-cceeeEEecCCChHHHHHH
Q 009695 128 VAYCGLLAN-TTKIGVVVGKGGRNVTRMR 155 (528)
Q Consensus 128 ~v~~rllVp-~~~vG~IIGkgG~~Ik~I~ 155 (528)
.+...++|+ .+|-|.||||+|++||+|-
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG 256 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKIG 256 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHHH
Confidence 445567777 5799999999999999874
No 142
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=51.08 E-value=18 Score=36.02 Aligned_cols=31 Identities=13% Similarity=0.118 Sum_probs=25.1
Q ss_pred ceEEEEEeCC-cceeeeecCCCchhHHHHHhh
Q 009695 365 AVAVSILVGA-DFVGCLTGSGSSAVSEMEDVT 395 (528)
Q Consensus 365 ~~t~~v~VP~-~~~g~IIGkgG~~Ik~I~~~t 395 (528)
.+.+.+.|.. ++-+.|||++|+.||+|...+
T Consensus 220 ~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 220 KIHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 4778888887 455999999999999887554
No 143
>COG1159 Era GTPase [General function prediction only]
Probab=46.15 E-value=21 Score=35.97 Aligned_cols=32 Identities=13% Similarity=0.253 Sum_probs=25.1
Q ss_pred CceEEEEEeCC-cceeeeecCCCchhHHHHHhh
Q 009695 364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVT 395 (528)
Q Consensus 364 ~~~t~~v~VP~-~~~g~IIGkgG~~Ik~I~~~t 395 (528)
-.+...+.|+. ++=|-||||+|++||+|-..+
T Consensus 227 ~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~A 259 (298)
T COG1159 227 LKIHATIYVERESQKGIIIGKNGAMIKKIGTAA 259 (298)
T ss_pred EEEEEEEEEecCCccceEECCCcHHHHHHHHHH
Confidence 35667788887 566999999999999885443
No 144
>PRK15494 era GTPase Era; Provisional
Probab=45.83 E-value=23 Score=36.54 Aligned_cols=30 Identities=17% Similarity=0.312 Sum_probs=24.0
Q ss_pred ceEEEEEeCC-cceeeeecCCCchhHHHHHh
Q 009695 365 AVAVSILVGA-DFVGCLTGSGSSAVSEMEDV 394 (528)
Q Consensus 365 ~~t~~v~VP~-~~~g~IIGkgG~~Ik~I~~~ 394 (528)
.+...+.|.. ++-+.|||++|+.||+|...
T Consensus 272 ~i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 272 KINQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 3667888887 45599999999999987643
No 145
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=45.37 E-value=18 Score=34.21 Aligned_cols=32 Identities=19% Similarity=0.298 Sum_probs=27.1
Q ss_pred EEEEEecccccccccccCchHHHHHHhhhCce
Q 009695 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCR 57 (528)
Q Consensus 26 ~~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~ 57 (528)
..+|.+....-|.|||++|..|++|+++-.-.
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 36788888899999999999999999886543
No 146
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=44.91 E-value=18 Score=34.58 Aligned_cols=31 Identities=23% Similarity=0.269 Sum_probs=26.0
Q ss_pred EEEEecccccccccccCchHHHHHHhhhCce
Q 009695 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCR 57 (528)
Q Consensus 27 ~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~ 57 (528)
.++.+....-|.+||++|.+|++|++.-.-.
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk~ 72 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEKK 72 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHHH
Confidence 5666666889999999999999999987554
No 147
>PRK00089 era GTPase Era; Reviewed
Probab=44.63 E-value=25 Score=35.23 Aligned_cols=37 Identities=19% Similarity=0.401 Sum_probs=27.7
Q ss_pred ceEEEEEeCC-cceeeeecCCCchhHHHHH--------hhCCeEEE
Q 009695 365 AVAVSILVGA-DFVGCLTGSGSSAVSEMED--------VTGTDIKL 401 (528)
Q Consensus 365 ~~t~~v~VP~-~~~g~IIGkgG~~Ik~I~~--------~tga~I~i 401 (528)
.+.+.+.|.. ++-+.|||++|++|++|.. ..|++|.+
T Consensus 225 ~i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l 270 (292)
T PRK00089 225 RIEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL 270 (292)
T ss_pred EEEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 3677888887 5559999999999998764 45666544
No 148
>CHL00048 rps3 ribosomal protein S3
Probab=43.62 E-value=20 Score=34.57 Aligned_cols=30 Identities=20% Similarity=0.195 Sum_probs=25.8
Q ss_pred EEEEEecccccccccccCchHHHHHHhhhC
Q 009695 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTK 55 (528)
Q Consensus 26 ~~rilvp~~~vG~VIGk~G~~Ik~I~~eTg 55 (528)
..+|.+....-|.|||++|.+|++|++.-.
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 366777888899999999999999998764
No 149
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=42.87 E-value=26 Score=35.60 Aligned_cols=34 Identities=12% Similarity=0.345 Sum_probs=26.8
Q ss_pred CCceEEEEEeec-ceeeEEecCCChHHHHHHhhhC
Q 009695 126 DDVAYCGLLANT-TKIGVVVGKGGRNVTRMRIESG 159 (528)
Q Consensus 126 ~~~v~~rllVp~-~~vG~IIGkgG~~Ik~I~~~tG 159 (528)
.-.+..++++|. ++...||||||..|++|-.+.+
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 345667888985 6788899999999999876544
No 150
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=42.82 E-value=24 Score=39.75 Aligned_cols=95 Identities=21% Similarity=0.236 Sum_probs=62.0
Q ss_pred eeccCCchhHhhHhhcCeeEEEeCCCCCCCccEEEEecccccCCCCChHHHHHHHHHhhhhhcccCCCCCCCCCCCCceE
Q 009695 288 IIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVA 367 (528)
Q Consensus 288 IIGkgG~~Ik~I~~~tGa~I~i~~~~~~~~eR~V~I~G~e~p~~~~~~a~~A~~~i~~~i~e~~~~~~~~~~~~~~~~~t 367 (528)
.+=.+|..|++|.++-.-+|.|-.+. . . ..+..+|...|.+-+-+.. +.. .-.-...+
T Consensus 37 ~~~~~~~~~~~~~~~~~~r~~~~~~~---~-------------~-~~~~~~~~~~i~~~~~~~~---~~~--~~~f~~~~ 94 (630)
T TIGR03675 37 LFAKDDDLVKELAKKLRKRIVIRPDP---S-------------V-LLPPEEAIEKIKEIVPEEA---GIT--DIYFDDVT 94 (630)
T ss_pred HhccchHHHHHHHHHhhceEEEecCh---h-------------h-cCCHHHHHHHHHHhCCCcC---Cce--eEEecCCC
Confidence 34467899999999888887774211 0 0 1122345544443332210 000 00123445
Q ss_pred EEEEeCCcceeeeecCCCchhHHHHHhhCCeEEEeCC
Q 009695 368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGG 404 (528)
Q Consensus 368 ~~v~VP~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~ 404 (528)
-++.|-.+.-|.+|||+|.++++|.++||-.-++.+.
T Consensus 95 ~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 95 GEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred ceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 6899999999999999999999999999999999875
No 151
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=41.83 E-value=22 Score=34.33 Aligned_cols=32 Identities=13% Similarity=0.205 Sum_probs=27.1
Q ss_pred EEEEecccccccccccCchHHHHHHhhhCceE
Q 009695 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRI 58 (528)
Q Consensus 27 ~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I 58 (528)
.++.+....-|.|||++|..|++|+++-.-..
T Consensus 46 i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~ 77 (220)
T PTZ00084 46 TEIIIRATRTREVLGDKGRRIRELTSLLQKRF 77 (220)
T ss_pred EEEEEEECCCccEEcCCchHHHHHHHHHHHHh
Confidence 66777888899999999999999998865544
No 152
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=33.78 E-value=30 Score=32.93 Aligned_cols=35 Identities=23% Similarity=0.327 Sum_probs=28.0
Q ss_pred EEEEEeeccccceeeccCCchhHhhHhhcCeeEEE
Q 009695 275 ALRMLFSGWTASGIIGKRGAIVRSLQNASGALISF 309 (528)
Q Consensus 275 ~~~l~vP~~~vG~IIGkgG~~Ik~I~~~tGa~I~i 309 (528)
.+.+.+..+..|.+||+.|.+++.||--+.+.++-
T Consensus 92 ~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 92 RVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred EEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 34466777779999999999999999888765543
No 153
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=31.65 E-value=37 Score=32.34 Aligned_cols=34 Identities=15% Similarity=0.236 Sum_probs=27.1
Q ss_pred EEEEecccccccccccCchHHHHHHhhhCceEEe
Q 009695 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC 60 (528)
Q Consensus 27 ~rilvp~~~vG~VIGk~G~~Ik~I~~eTga~I~i 60 (528)
+.+-+.++..+.+||+.|++...||--++.-+.-
T Consensus 93 v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 93 VVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred EEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 3344466669999999999999999998876654
No 154
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=31.50 E-value=52 Score=33.53 Aligned_cols=35 Identities=14% Similarity=0.172 Sum_probs=27.6
Q ss_pred CCceEEEEEeCC-cceeeeecCCCchhHHHHHhhCC
Q 009695 363 GDAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGT 397 (528)
Q Consensus 363 ~~~~t~~v~VP~-~~~g~IIGkgG~~Ik~I~~~tga 397 (528)
...+..++.+|. .+.-.||||||..|++|-++.+-
T Consensus 325 ~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~~ 360 (379)
T KOG1423|consen 325 VLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRANE 360 (379)
T ss_pred EEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHHH
Confidence 346788999998 55578899999999999766543
No 155
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=30.83 E-value=50 Score=31.29 Aligned_cols=28 Identities=21% Similarity=0.507 Sum_probs=23.7
Q ss_pred EEEEEeecceeeEEecCCChHHHHHHhh
Q 009695 130 YCGLLANTTKIGVVVGKGGRNVTRMRIE 157 (528)
Q Consensus 130 ~~rllVp~~~vG~IIGkgG~~Ik~I~~~ 157 (528)
..++.+....-|.|||++|..|++|+++
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~ 66 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEK 66 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHH
Confidence 3677888888899999999999998754
No 156
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=30.30 E-value=50 Score=31.62 Aligned_cols=29 Identities=21% Similarity=0.457 Sum_probs=23.1
Q ss_pred EEEEeecceeeEEecCCChHHHHHHhhhC
Q 009695 131 CGLLANTTKIGVVVGKGGRNVTRMRIESG 159 (528)
Q Consensus 131 ~rllVp~~~vG~IIGkgG~~Ik~I~~~tG 159 (528)
.++.+....-|.+||++|++|+++++.-.
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lk 70 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILE 70 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHH
Confidence 45666667889999999999999876543
No 157
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=29.90 E-value=45 Score=32.03 Aligned_cols=29 Identities=34% Similarity=0.542 Sum_probs=25.3
Q ss_pred EEEEecccccccccccCchHHHHHHhhhC
Q 009695 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTK 55 (528)
Q Consensus 27 ~rilvp~~~vG~VIGk~G~~Ik~I~~eTg 55 (528)
++|.+....-|.|||++|..+++|++.-.
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l~ 92 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDLQ 92 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHHH
Confidence 66888888899999999999999997754
No 158
>CHL00048 rps3 ribosomal protein S3
Probab=29.54 E-value=53 Score=31.61 Aligned_cols=29 Identities=14% Similarity=0.282 Sum_probs=24.0
Q ss_pred EEEEEeecceeeEEecCCChHHHHHHhhh
Q 009695 130 YCGLLANTTKIGVVVGKGGRNVTRMRIES 158 (528)
Q Consensus 130 ~~rllVp~~~vG~IIGkgG~~Ik~I~~~t 158 (528)
..++.+....-|.|||++|+.|++|++.-
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 45777777888999999999999987654
No 159
>PRK03818 putative transporter; Validated
Probab=29.27 E-value=3.5e+02 Score=30.08 Aligned_cols=60 Identities=15% Similarity=0.182 Sum_probs=36.3
Q ss_pred ceEEEEEeecceeeEEecCCChHHHHH--HhhhCCeEEEcCC--CCC-C-----CCCCceEEEeccHHHHHHHHHH
Q 009695 128 VAYCGLLANTTKIGVVVGKGGRNVTRM--RIESGAKIVMLPP--PAC-A-----AIDDQLIQITGATLAVKKALVA 193 (528)
Q Consensus 128 ~v~~rllVp~~~vG~IIGkgG~~Ik~I--~~~tGa~I~i~~~--p~~-~-----~~~er~V~I~G~~~~V~kA~~~ 193 (528)
....++++|+ ..++|| +++++ ++++|+.|.-..+ ... + -..-..+.+.|+++++++..+.
T Consensus 289 ~~~E~Vvv~~---S~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq~GD~LlVvG~~~~i~~l~~~ 358 (552)
T PRK03818 289 LRSERVVVTN---EKVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLSLQFGDILNLVGRPEAIDAVANV 358 (552)
T ss_pred eEEEEEEEcC---hhccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCEEecCCEEEEEECHHHHHHHHHH
Confidence 3444566665 356666 78887 5778877554443 011 0 1112357789999999987664
No 160
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=29.23 E-value=87 Score=32.32 Aligned_cols=55 Identities=20% Similarity=0.166 Sum_probs=45.3
Q ss_pred CcceeeeecCCCchhHHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcCCHHHHHHHHHHHH--HHHhh
Q 009695 374 ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVV--GRLRH 440 (528)
Q Consensus 374 ~~~~g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~~~~v~~A~~~I~--~~l~~ 440 (528)
.+..-.+.|..|.+++.|.+..|+.|... .+.++|+|+.+.+..|...+. ..+..
T Consensus 23 ~~~~~~l~G~~~~~l~l~e~~~gv~i~~r------------G~~~~i~g~~~~v~~A~~~l~~l~~~~~ 79 (348)
T COG1702 23 DNELVALFGPTDTNLSLLEIALGVSIVAR------------GEAVRIIGARPLVDVATRVLLTLELLAE 79 (348)
T ss_pred chhhhhhcCCCCccHHHHHHHhCcEEEeC------------CceEEEEechHHHHHHHHHHhHHHHHHH
Confidence 56778899999999999999999999442 356999999889998888887 55543
No 161
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=28.24 E-value=55 Score=31.66 Aligned_cols=28 Identities=18% Similarity=0.336 Sum_probs=23.2
Q ss_pred EEEEeecceeeEEecCCChHHHHHHhhh
Q 009695 131 CGLLANTTKIGVVVGKGGRNVTRMRIES 158 (528)
Q Consensus 131 ~rllVp~~~vG~IIGkgG~~Ik~I~~~t 158 (528)
.++.+....-|.|||++|..|++|+++-
T Consensus 46 i~V~I~tarPg~vIG~~G~~i~~l~~~L 73 (220)
T PTZ00084 46 TEIIIRATRTREVLGDKGRRIRELTSLL 73 (220)
T ss_pred EEEEEEECCCccEEcCCchHHHHHHHHH
Confidence 5677777788999999999999987553
No 162
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=24.81 E-value=1.3e+02 Score=31.04 Aligned_cols=54 Identities=24% Similarity=0.339 Sum_probs=45.6
Q ss_pred EEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEeccHHHHHHHHHHHH
Q 009695 133 LLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVT 195 (528)
Q Consensus 133 llVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G~~~~V~kA~~~I~ 195 (528)
++-++..+-.|.|..|.+++.|++.+|+.|.... +.++|.|....|..|...+.
T Consensus 19 ~~~~~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG---------~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 19 LLSDDNELVALFGPTDTNLSLLEIALGVSIVARG---------EAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred ccCCchhhhhhcCCCCccHHHHHHHhCcEEEeCC---------ceEEEEechHHHHHHHHHHh
Confidence 3445677888999999999999999999998855 67899999778888887776
No 163
>TIGR03802 Asp_Ala_antiprt aspartate-alanine antiporter. All members of the seed alignment for this model are asparate-alanine anti-transporters (AspT) encoded next to the gene for aspartate 4-decarboxylase (AspD), which converts asparate to alanine, releasing CO2. The exchange of Asp for Ala is electrogenic, so the AspD/AspT system confers a proton-motive force. This transporter contains two copies of the AspT/YidE/YbjL antiporter duplication domain (TIGR01625).
Probab=24.41 E-value=5.1e+02 Score=28.82 Aligned_cols=59 Identities=14% Similarity=0.236 Sum_probs=36.1
Q ss_pred EEEEEeecceeeEEecCCChHHHHHH------hhhCCeEEEcCC--------CCCCCCCCceEEEeccHHHHHHHHHHH
Q 009695 130 YCGLLANTTKIGVVVGKGGRNVTRMR------IESGAKIVMLPP--------PACAAIDDQLIQITGATLAVKKALVAV 194 (528)
Q Consensus 130 ~~rllVp~~~vG~IIGkgG~~Ik~I~------~~tGa~I~i~~~--------p~~~~~~er~V~I~G~~~~V~kA~~~I 194 (528)
..++++|+ ..++|| +++++. +++|+.|.-..+ +...-..--.+.+.|++++++++...+
T Consensus 304 ~e~VV~~~---S~liGk---TL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~GD~LlV~G~~~~l~~~~~~l 376 (562)
T TIGR03802 304 TKDVVLTN---KEYNGK---TVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQRGDVVTLVGTPQDVDRAAKQL 376 (562)
T ss_pred EEEEEECC---cccCCc---cHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecCCCEEEEEeCHHHHHHHHHHc
Confidence 44566665 445555 788886 267887655543 111111224577899999999876653
No 164
>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=23.65 E-value=2.4e+02 Score=25.99 Aligned_cols=57 Identities=14% Similarity=0.144 Sum_probs=42.0
Q ss_pred CceEEEEEeecceeeEEecCCChHHHHHHhhhCCeEEEcCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHH
Q 009695 127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL 198 (528)
Q Consensus 127 ~~v~~rllVp~~~vG~IIGkgG~~Ik~I~~~tGa~I~i~~~p~~~~~~er~V~I~G~~~~V~kA~~~I~~~l 198 (528)
+.-+.|+-++.... =..+++|.+-.|+=+.+ . .+..|.|.|+.+.|.+|++.++...
T Consensus 111 ~~~~iRv~l~~~i~-------~erl~ei~E~~gvI~Ef-e-------e~~~V~I~Gdke~Ik~aLKe~s~~w 167 (169)
T PF09869_consen 111 GFETIRVKLKKPIQ-------EERLQEISEWHGVIFEF-E-------EDDKVVIEGDKERIKKALKEFSSFW 167 (169)
T ss_pred CceeEEEecCccch-------HHHHHHHHHHhceeEEe-c-------CCcEEEEeccHHHHHHHHHHHHHHh
Confidence 34455655554432 25678888889988888 3 4567999999999999999987654
No 165
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=22.62 E-value=73 Score=31.07 Aligned_cols=30 Identities=27% Similarity=0.446 Sum_probs=24.9
Q ss_pred EEEEecccccccccccCchHHHHHHhhhCc
Q 009695 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKC 56 (528)
Q Consensus 27 ~rilvp~~~vG~VIGk~G~~Ik~I~~eTga 56 (528)
++|.+....-|.|||++|..|++|++.-.-
T Consensus 64 i~I~I~~~rP~~iiG~~g~~i~~l~~~L~~ 93 (232)
T PRK00310 64 VRVTIHTARPGIVIGKKGAEIEKLRKELEK 93 (232)
T ss_pred EEEEEEECCCccccCCCcHHHHHHHHHHHH
Confidence 556667788899999999999999887643
No 166
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=22.60 E-value=2e+02 Score=24.45 Aligned_cols=41 Identities=22% Similarity=0.216 Sum_probs=32.2
Q ss_pred HHhhCCeEEEeCCCCccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhh
Q 009695 392 EDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN 441 (528)
Q Consensus 392 ~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~~~~v~~A~~~I~~~l~~~ 441 (528)
.+..++.|-+.++ -...+.|+|+..+|+.|+..+.+.+++.
T Consensus 60 ~Kaa~V~igF~DR---------FsGslvitGdvs~Ve~Al~~V~~~l~~~ 100 (111)
T PRK15468 60 LKAADVHIGFLDR---------FSGALVIYGSVGAVEEALSQTVSGLGRL 100 (111)
T ss_pred hhccCcEEeeeec---------cceeEEEEccHHHHHHHHHHHHHHHHhh
Confidence 3456777777543 3456889999999999999999999873
No 167
>PF00936 BMC: BMC domain; InterPro: IPR000249 This domain is found in a variety of polyhedral organelle shell proteins, including CsoS1A, CsoS1B and CsoS1C of Thiobacillus neapolitanus (Halothiobacillus neapolitanus) and their orthologs from other bacteria. Some autotrophic and non-autotrophic organisms form polyhedral organelles, carboxysomes/enterosomes []. The best studied is the carboxysome of Halothiobacillus neapolitanus, which is composed of at least 9 proteins: six shell proteins, CsoS1A, CsoS1B, CsoS1C, Cso2A, Cso2B and CsoS3 (carbonic anhydrase) [], one protein of unknown function and the large and small subunits of RuBisCo (CbbL and Cbbs). Carboxysomes appear to be approximately 120 nm in diameter, most often observed as regular hexagons, with a solid interior bounded by a unilamellar protein shell. The interior is filled with type I RuBisCo, which is composed of 8 large subunits and 8 small subunits; it accounts for 60% of the carboxysomal protein, which amounts to approximately 300 molecules of enzyme per carboxysome. Carboxysomes are required for autotrophic growth at low CO2 concentrations and are thought to function as part of a CO2-concentrating mechanism [, ]. Polyhedral organelles, enterosomes, from non-autotrophic organisms are involved in coenzyme B12-dependent 1,2-propanediol utilisation (e.g., in Salmonella enterica []) and ethanolamine utilisation (e.g., in Salmonella typhimurium []). Genes needed for enterosome formation are located in the 1,2-propanediol utilisation pdu [, ] or ethanolamine utilisation eut [, ] operons, respectively. Although enterosomes of non-autotrophic organisms are apparently related to carboxysomes structurally, a functional relationship is uncertain. A role in CO2 concentration, similar to that of the carboxysome, is unlikely since there is no known association between CO2 and coenzyme B12-dependent 1,2-propanediol or ethanolamine utilisation []. It seems probable that entrosomes help protect the cells from reactive aldehyde species in the degradation pathways of 1,2-propanediol and ethanolamine [].; PDB: 3F56_C 3FCH_A 3I87_A 3GFH_B 3I82_A 3MPV_A 3IO0_A 4AXJ_B 3N79_A 2G13_A ....
Probab=20.69 E-value=1e+02 Score=24.25 Aligned_cols=51 Identities=14% Similarity=0.144 Sum_probs=35.5
Q ss_pred HHHHHhhCCeEEEeCCCCccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhhcCCC
Q 009695 389 SEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSG 445 (528)
Q Consensus 389 k~I~~~tga~I~i~~~~~~p~~~~~~~~~V~ItG~~~~v~~A~~~I~~~l~~~~~~~ 445 (528)
..+-+.+.+.+.-... . ....-.+.|+|+..+|+.|.....+.+.+.+...
T Consensus 19 D~alKaa~V~l~~~~~----~--~~g~~~~~i~G~vs~V~~Av~a~~~~~~~~~v~~ 69 (75)
T PF00936_consen 19 DAALKAANVELVEIEL----I--CGGKVTVIITGDVSAVKAAVDAAEEAAGKKLVSS 69 (75)
T ss_dssp HHHHHHSSEEEEEEEE----E--STTEEEEEEEESHHHHHHHHHHHHHHHHHTEEEE
T ss_pred HHHhhcCCEEEEEEEe----c--CCCeEEEEEEECHHHHHHHHHHHHHHHhhceeeE
Confidence 4455566665533321 1 1346689999999999999999999998864443
No 168
>cd07053 BMC_PduT_repeat1 1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 1. PduT proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduT might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view. PduT proteins contain two tandem BMC domains repeats. This CD contains repeat 1 (the first BMC domain of PduT) as well as carboxysome shell protein sequence homolog, EutM protein, are also included in this CD. They too might exist as hexamers and might play similar functional roles in the construction of the eut organelle outer shell which still remains poorly understood.
Probab=20.54 E-value=1.2e+02 Score=23.99 Aligned_cols=36 Identities=19% Similarity=0.155 Sum_probs=28.5
Q ss_pred CCcEEEEcCCHHHHHHHHHHHHHHHhhhcCCCcccC
Q 009695 414 NDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILN 449 (528)
Q Consensus 414 ~~~~V~ItG~~~~v~~A~~~I~~~l~~~~~~~~~~~ 449 (528)
..-.+.|+|+-.+|+.|.....+...+.+....+++
T Consensus 37 Gk~~vii~GdvsaV~~Av~a~~~~~~~~~v~~~vI~ 72 (76)
T cd07053 37 GKYIIIVSGDVGAVQAAVDAGKEIGGKYVVDSFVLP 72 (76)
T ss_pred CEEEEEEEEcHHHHHHHHHHHHHHhCCcEEEEEEeC
Confidence 456899999999999999999998876655554443
Done!