Query 005922
Match_columns 669
No_of_seqs 353 out of 2149
Neff 5.4
Searched_HMMs 46136
Date Thu Mar 28 15:44:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005922.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005922hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1676 K-homology type RNA bi 100.0 2.5E-36 5.4E-41 331.8 33.4 395 44-470 54-461 (600)
2 KOG1676 K-homology type RNA bi 100.0 7.1E-34 1.5E-38 312.5 24.2 227 61-295 159-390 (600)
3 KOG2191 RNA-binding protein NO 100.0 5.8E-30 1.3E-34 264.6 21.8 194 128-327 38-234 (402)
4 KOG2192 PolyC-binding hnRNP-K 99.9 2.2E-26 4.7E-31 232.5 11.2 230 46-297 56-387 (390)
5 KOG2190 PolyC-binding proteins 99.9 4.9E-24 1.1E-28 236.9 15.9 229 61-295 63-410 (485)
6 KOG2190 PolyC-binding proteins 99.9 4.8E-23 1E-27 229.1 15.1 161 129-298 43-212 (485)
7 KOG2193 IGF-II mRNA-binding pr 99.9 4E-24 8.7E-29 226.6 5.3 223 61-296 219-483 (584)
8 KOG2192 PolyC-binding hnRNP-K 99.9 5.4E-21 1.2E-25 193.6 18.0 152 129-300 48-199 (390)
9 KOG2191 RNA-binding protein NO 99.9 1.1E-21 2.4E-26 203.5 10.5 277 10-295 11-316 (402)
10 KOG2193 IGF-II mRNA-binding pr 99.8 7.6E-22 1.6E-26 209.5 7.3 223 61-297 300-567 (584)
11 TIGR03665 arCOG04150 arCOG0415 99.7 6.6E-18 1.4E-22 165.6 11.5 138 133-294 2-151 (172)
12 PRK13763 putative RNA-processi 99.7 3.4E-17 7.3E-22 161.7 13.0 143 129-294 3-157 (180)
13 cd02396 PCBP_like_KH K homolog 99.3 3.2E-12 7E-17 105.9 7.7 64 223-289 2-65 (65)
14 cd02396 PCBP_like_KH K homolog 99.3 1.9E-12 4E-17 107.3 5.7 65 130-196 1-65 (65)
15 cd02393 PNPase_KH Polynucleoti 99.2 9.8E-11 2.1E-15 96.3 7.7 59 221-289 2-61 (61)
16 cd02394 vigilin_like_KH K homo 99.1 5.9E-11 1.3E-15 96.9 5.9 61 223-289 2-62 (62)
17 COG1094 Predicted RNA-binding 99.1 8.9E-11 1.9E-15 116.3 8.1 145 129-296 8-166 (194)
18 PF00013 KH_1: KH domain syndr 99.1 3.7E-11 8E-16 97.5 3.8 60 222-288 1-60 (60)
19 cd02394 vigilin_like_KH K homo 99.1 6.4E-11 1.4E-15 96.7 4.9 62 130-196 1-62 (62)
20 cd00105 KH-I K homology RNA-bi 99.1 2.1E-10 4.5E-15 93.3 7.9 63 223-289 2-64 (64)
21 PF00013 KH_1: KH domain syndr 99.1 3.7E-11 7.9E-16 97.5 2.6 60 130-195 1-60 (60)
22 cd02393 PNPase_KH Polynucleoti 99.1 1.9E-10 4.2E-15 94.5 5.2 59 129-196 2-61 (61)
23 cd00105 KH-I K homology RNA-bi 99.0 2.7E-10 5.8E-15 92.7 5.7 63 131-196 2-64 (64)
24 KOG2279 Kinase anchor protein 99.0 2.6E-10 5.5E-15 126.1 3.9 211 61-292 88-366 (608)
25 KOG2279 Kinase anchor protein 98.9 5.5E-10 1.2E-14 123.6 4.4 143 128-294 67-209 (608)
26 smart00322 KH K homology RNA-b 98.9 6.8E-09 1.5E-13 83.7 9.2 67 221-293 3-69 (69)
27 smart00322 KH K homology RNA-b 98.8 9.1E-09 2E-13 82.9 7.0 66 129-199 3-68 (69)
28 TIGR03665 arCOG04150 arCOG0415 98.8 2.7E-09 5.9E-14 104.9 3.0 123 61-202 18-152 (172)
29 PF13014 KH_3: KH domain 98.8 1.1E-08 2.4E-13 78.1 5.7 43 231-276 1-43 (43)
30 KOG2113 Predicted RNA binding 98.8 7.5E-09 1.6E-13 108.1 5.5 150 128-291 25-180 (394)
31 PRK13763 putative RNA-processi 98.7 4E-09 8.7E-14 104.5 2.4 123 61-202 23-158 (180)
32 PF13014 KH_3: KH domain 98.7 8.3E-09 1.8E-13 78.8 3.6 43 139-183 1-43 (43)
33 cd02395 SF1_like-KH Splicing f 98.6 9E-08 2E-12 89.2 8.5 67 229-295 14-96 (120)
34 COG1185 Pnp Polyribonucleotide 98.6 3.8E-08 8.3E-13 112.4 5.7 150 128-295 452-617 (692)
35 cd02395 SF1_like-KH Splicing f 98.6 1E-07 2.2E-12 88.9 6.4 73 131-203 2-97 (120)
36 TIGR02696 pppGpp_PNP guanosine 98.4 1.7E-06 3.7E-11 100.9 10.9 89 190-294 553-642 (719)
37 KOG2208 Vigilin [Lipid transpo 98.3 9.7E-07 2.1E-11 104.4 8.3 140 129-293 347-487 (753)
38 KOG2208 Vigilin [Lipid transpo 98.3 7.5E-07 1.6E-11 105.3 7.0 189 81-295 168-415 (753)
39 KOG0119 Splicing factor 1/bran 98.3 5E-06 1.1E-10 91.8 12.7 65 230-294 153-230 (554)
40 PRK08406 transcription elongat 98.3 1.1E-06 2.4E-11 84.1 5.8 104 129-257 32-135 (140)
41 KOG0119 Splicing factor 1/bran 98.2 2.3E-06 5.1E-11 94.4 6.1 76 128-203 137-232 (554)
42 TIGR03591 polynuc_phos polyrib 98.1 5.6E-06 1.2E-10 97.3 9.1 89 191-294 526-615 (684)
43 PLN00207 polyribonucleotide nu 97.9 1.6E-05 3.4E-10 94.9 7.5 88 192-294 661-750 (891)
44 TIGR01952 nusA_arch NusA famil 97.9 2.8E-05 6E-10 74.6 6.6 103 130-257 34-136 (141)
45 KOG1588 RNA-binding protein Sa 97.7 0.00014 3E-09 75.6 9.0 75 220-294 91-191 (259)
46 TIGR03591 polynuc_phos polyrib 97.6 6.8E-05 1.5E-09 88.3 5.8 65 129-201 551-615 (684)
47 PRK11824 polynucleotide phosph 97.6 0.00011 2.3E-09 86.9 6.5 90 190-294 528-618 (693)
48 TIGR02696 pppGpp_PNP guanosine 97.5 0.0001 2.3E-09 86.3 6.1 64 129-201 578-642 (719)
49 PF14611 SLS: Mitochondrial in 97.5 0.0013 2.9E-08 66.3 12.8 129 131-294 28-165 (210)
50 COG0195 NusA Transcription elo 97.5 0.00028 6.2E-09 70.8 7.1 102 130-257 77-178 (190)
51 KOG1960 Predicted RNA-binding 97.4 0.00045 9.8E-09 75.0 8.4 158 140-298 106-299 (531)
52 KOG1067 Predicted RNA-binding 97.4 0.00018 3.8E-09 81.0 5.3 93 190-298 571-664 (760)
53 KOG0336 ATP-dependent RNA heli 97.4 0.00015 3.1E-09 79.4 4.3 69 221-296 47-115 (629)
54 PLN00207 polyribonucleotide nu 97.2 0.0001 2.3E-09 88.1 0.5 66 129-203 685-752 (891)
55 KOG0336 ATP-dependent RNA heli 97.2 0.00028 6E-09 77.3 3.5 71 127-203 45-115 (629)
56 KOG1588 RNA-binding protein Sa 97.1 0.00045 9.8E-09 71.8 4.7 37 129-165 92-134 (259)
57 PRK00106 hypothetical protein; 97.1 0.0026 5.6E-08 73.0 10.4 65 222-295 226-292 (535)
58 TIGR03319 YmdA_YtgF conserved 97.1 0.0024 5.3E-08 73.1 10.1 65 222-295 205-271 (514)
59 COG1185 Pnp Polyribonucleotide 96.9 0.00088 1.9E-08 77.5 5.0 67 129-204 552-619 (692)
60 PRK12704 phosphodiesterase; Pr 96.9 0.0041 8.8E-08 71.4 10.2 64 222-294 211-276 (520)
61 TIGR01953 NusA transcription t 96.9 0.0017 3.7E-08 70.7 6.4 94 139-258 244-338 (341)
62 PRK12328 nusA transcription el 96.8 0.0015 3.2E-08 71.7 5.4 95 138-259 251-346 (374)
63 KOG2814 Transcription coactiva 96.8 0.0015 3.3E-08 69.9 5.3 68 223-296 59-127 (345)
64 KOG2814 Transcription coactiva 96.8 0.001 2.2E-08 71.2 3.6 70 129-203 57-127 (345)
65 PRK04163 exosome complex RNA-b 96.8 0.0023 4.9E-08 66.3 6.1 62 223-294 147-209 (235)
66 PRK12327 nusA transcription el 96.8 0.0023 5.1E-08 70.2 6.3 94 139-258 246-340 (362)
67 PRK12329 nusA transcription el 96.6 0.0026 5.7E-08 70.9 5.5 92 140-257 279-371 (449)
68 PRK09202 nusA transcription el 96.5 0.0045 9.7E-08 70.2 6.3 92 140-258 247-339 (470)
69 COG1094 Predicted RNA-binding 96.4 0.0035 7.6E-08 62.9 4.6 55 139-203 112-166 (194)
70 KOG2113 Predicted RNA binding 96.4 0.0027 5.8E-08 67.4 3.6 128 61-199 46-181 (394)
71 COG5176 MSL5 Splicing factor ( 96.4 0.0049 1.1E-07 62.2 5.2 38 128-165 147-190 (269)
72 PRK04163 exosome complex RNA-b 96.3 0.006 1.3E-07 63.2 5.6 66 131-204 147-212 (235)
73 cd02134 NusA_KH NusA_K homolog 96.3 0.0071 1.5E-07 49.8 4.8 36 221-256 25-60 (61)
74 PRK11824 polynucleotide phosph 96.3 0.0019 4.1E-08 76.5 1.9 64 129-201 554-618 (693)
75 cd02134 NusA_KH NusA_K homolog 96.1 0.0059 1.3E-07 50.3 3.5 36 129-164 25-60 (61)
76 KOG3273 Predicted RNA-binding 96.0 0.0065 1.4E-07 61.1 4.0 151 128-295 73-232 (252)
77 PRK12705 hypothetical protein; 96.0 0.017 3.7E-07 66.1 7.6 64 222-294 199-264 (508)
78 TIGR03319 YmdA_YtgF conserved 95.9 0.013 2.8E-07 67.3 6.5 64 129-200 204-269 (514)
79 COG5176 MSL5 Splicing factor ( 95.9 0.0099 2.1E-07 60.1 4.8 66 230-295 163-241 (269)
80 PRK00106 hypothetical protein; 95.8 0.015 3.3E-07 66.8 6.5 64 129-200 225-290 (535)
81 PRK02821 hypothetical protein; 95.7 0.018 3.8E-07 50.1 5.0 32 220-251 30-61 (77)
82 PRK12704 phosphodiesterase; Pr 95.7 0.017 3.8E-07 66.4 6.2 65 129-201 210-276 (520)
83 PRK00468 hypothetical protein; 95.6 0.017 3.6E-07 49.9 4.6 32 220-251 29-60 (75)
84 COG1837 Predicted RNA-binding 95.3 0.034 7.4E-07 48.2 5.2 32 219-250 28-59 (76)
85 COG1782 Predicted metal-depend 95.1 0.025 5.5E-07 63.8 5.0 96 140-257 40-135 (637)
86 cd02410 archeal_CPSF_KH The ar 94.9 0.07 1.5E-06 51.5 6.7 94 142-257 19-112 (145)
87 PRK01064 hypothetical protein; 94.8 0.041 8.9E-07 47.9 4.5 32 219-250 28-59 (78)
88 KOG1067 Predicted RNA-binding 94.6 0.02 4.4E-07 65.0 2.6 66 128-203 596-662 (760)
89 PRK00468 hypothetical protein; 94.5 0.031 6.6E-07 48.3 2.9 29 129-157 30-58 (75)
90 KOG4369 RTK signaling protein 94.4 0.016 3.5E-07 70.0 1.2 72 129-202 1340-1411(2131)
91 PRK02821 hypothetical protein; 94.2 0.04 8.6E-07 47.9 3.0 31 129-159 31-61 (77)
92 KOG1960 Predicted RNA-binding 94.2 0.022 4.8E-07 62.3 1.7 148 132-299 213-380 (531)
93 KOG4369 RTK signaling protein 93.7 0.018 3.9E-07 69.6 -0.0 70 222-294 1341-1410(2131)
94 COG1837 Predicted RNA-binding 93.4 0.069 1.5E-06 46.3 3.0 29 129-157 30-58 (76)
95 PRK01064 hypothetical protein; 93.3 0.073 1.6E-06 46.3 3.0 30 128-157 29-58 (78)
96 KOG3273 Predicted RNA-binding 92.9 0.057 1.2E-06 54.5 2.0 57 138-204 178-234 (252)
97 COG5166 Uncharacterized conser 92.8 0.09 2E-06 59.4 3.6 128 129-257 449-607 (657)
98 TIGR03675 arCOG00543 arCOG0054 92.7 0.15 3.2E-06 60.1 5.4 96 141-258 35-130 (630)
99 PF14611 SLS: Mitochondrial in 92.4 1 2.2E-05 45.5 10.4 66 222-296 27-92 (210)
100 COG1855 ATPase (PilT family) [ 92.4 0.23 5E-06 56.0 6.0 67 187-259 458-524 (604)
101 PRK12705 hypothetical protein; 92.2 0.15 3.2E-06 58.6 4.4 38 130-167 199-237 (508)
102 PRK06418 transcription elongat 91.9 0.56 1.2E-05 46.5 7.5 103 129-256 61-163 (166)
103 COG5166 Uncharacterized conser 90.9 0.17 3.7E-06 57.3 3.1 128 140-294 391-524 (657)
104 COG1097 RRP4 RNA-binding prote 90.9 0.52 1.1E-05 49.1 6.4 47 223-279 148-194 (239)
105 PRK08406 transcription elongat 90.8 0.28 6.1E-06 47.2 4.1 38 221-258 32-69 (140)
106 cd02409 KH-II KH-II (K homolo 90.8 0.32 6.9E-06 39.2 3.9 34 129-162 25-58 (68)
107 PF13083 KH_4: KH domain; PDB: 90.3 0.14 2.9E-06 43.4 1.3 35 220-254 28-62 (73)
108 PRK13764 ATPase; Provisional 90.3 0.49 1.1E-05 55.5 6.3 67 187-259 453-519 (602)
109 PF13083 KH_4: KH domain; PDB: 90.1 0.14 3E-06 43.3 1.2 32 129-160 29-60 (73)
110 PF13184 KH_5: NusA-like KH do 89.8 0.29 6.4E-06 41.6 2.9 38 129-166 3-46 (69)
111 TIGR03802 Asp_Ala_antiprt aspa 89.6 1.7 3.6E-05 50.9 9.9 144 129-294 218-382 (562)
112 PRK12328 nusA transcription el 88.8 0.35 7.6E-06 53.5 3.4 37 129-165 308-344 (374)
113 PRK03818 putative transporter; 88.6 1.9 4.2E-05 50.2 9.5 139 129-289 205-360 (552)
114 cd02409 KH-II KH-II (K homolo 88.6 0.64 1.4E-05 37.4 4.0 34 221-254 25-58 (68)
115 KOG2874 rRNA processing protei 88.0 0.8 1.7E-05 48.6 5.2 52 232-294 160-211 (356)
116 COG1097 RRP4 RNA-binding prote 87.8 0.86 1.9E-05 47.5 5.3 35 131-165 148-182 (239)
117 KOG1924 RhoA GTPase effector D 86.3 4.4 9.6E-05 48.4 10.4 22 273-294 376-397 (1102)
118 COG1782 Predicted metal-depend 86.2 0.78 1.7E-05 52.3 4.2 39 129-167 99-137 (637)
119 cd02414 jag_KH jag_K homology 85.5 0.77 1.7E-05 39.4 3.0 33 130-162 25-57 (77)
120 PF13184 KH_5: NusA-like KH do 84.2 0.56 1.2E-05 39.9 1.6 36 223-258 5-46 (69)
121 TIGR01953 NusA transcription t 84.0 0.85 1.9E-05 50.1 3.2 38 129-166 301-338 (341)
122 TIGR01952 nusA_arch NusA famil 83.9 1.3 2.7E-05 42.9 4.0 37 222-258 34-70 (141)
123 PF07054 Pericardin_rpt: Peric 83.6 1 2.2E-05 33.0 2.4 22 609-630 1-23 (34)
124 cd02414 jag_KH jag_K homology 83.2 1.1 2.4E-05 38.4 3.0 35 221-255 24-58 (77)
125 COG1855 ATPase (PilT family) [ 82.8 0.84 1.8E-05 51.7 2.6 37 130-166 487-523 (604)
126 PF07650 KH_2: KH domain syndr 82.2 0.56 1.2E-05 40.0 0.8 34 129-162 25-58 (78)
127 PF07650 KH_2: KH domain syndr 82.2 0.63 1.4E-05 39.7 1.1 35 221-255 25-59 (78)
128 TIGR03675 arCOG00543 arCOG0054 81.5 1.6 3.5E-05 51.6 4.5 39 129-167 93-131 (630)
129 PRK09202 nusA transcription el 81.1 1.1 2.4E-05 51.2 2.8 39 129-167 302-340 (470)
130 KOG1423 Ras-like GTPase ERA [C 80.2 5.7 0.00012 43.3 7.6 31 220-250 327-358 (379)
131 PRK15405 ethanolamine utilizat 80.0 33 0.00072 35.5 12.6 136 151-294 51-209 (217)
132 KOG2874 rRNA processing protei 79.2 2.1 4.6E-05 45.5 3.9 52 140-201 160-211 (356)
133 PRK00089 era GTPase Era; Revie 79.2 4.5 9.9E-05 42.5 6.5 36 221-256 226-270 (292)
134 cd02410 archeal_CPSF_KH The ar 78.8 3.4 7.3E-05 40.2 4.9 38 130-167 77-114 (145)
135 KOG1924 RhoA GTPase effector D 78.1 8.6 0.00019 46.2 8.7 14 13-26 15-28 (1102)
136 COG0092 RpsC Ribosomal protein 77.9 4.5 9.8E-05 42.2 5.8 30 220-249 50-79 (233)
137 PRK06418 transcription elongat 77.4 2.9 6.3E-05 41.5 4.1 38 221-259 61-98 (166)
138 PRK13764 ATPase; Provisional 77.2 2.3 5E-05 50.1 3.9 39 129-167 481-519 (602)
139 PRK12329 nusA transcription el 76.7 1.6 3.5E-05 49.3 2.4 38 129-166 335-372 (449)
140 COG0195 NusA Transcription elo 76.3 2.2 4.8E-05 43.2 3.0 37 130-166 143-179 (190)
141 cd02413 40S_S3_KH K homology R 75.7 2.4 5.2E-05 37.1 2.7 36 129-164 30-65 (81)
142 PRK15494 era GTPase Era; Provi 75.0 3.9 8.4E-05 44.6 4.7 35 222-256 274-317 (339)
143 cd02413 40S_S3_KH K homology R 71.2 5 0.00011 35.1 3.6 36 221-256 30-65 (81)
144 cd02412 30S_S3_KH K homology R 70.1 3.2 6.8E-05 38.2 2.2 30 130-159 62-91 (109)
145 TIGR00436 era GTP-binding prot 68.7 6.2 0.00013 41.3 4.4 29 221-249 221-250 (270)
146 COG1847 Jag Predicted RNA-bind 67.9 25 0.00053 36.3 8.2 36 221-256 91-126 (208)
147 COG0490 Putative regulatory, l 67.0 10 0.00022 37.6 5.1 57 228-289 95-158 (162)
148 PRK12327 nusA transcription el 66.7 5.5 0.00012 44.2 3.6 38 129-166 303-340 (362)
149 TIGR01334 modD putative molybd 65.2 37 0.00081 36.4 9.4 66 226-294 36-101 (277)
150 COG1159 Era GTPase [General fu 64.6 9.1 0.0002 41.4 4.6 34 223-256 231-273 (298)
151 cd02411 archeal_30S_S3_KH K ho 63.3 6.2 0.00013 34.6 2.6 28 131-158 40-67 (85)
152 cd02412 30S_S3_KH K homology R 60.4 6.9 0.00015 35.9 2.5 31 221-251 61-91 (109)
153 CHL00100 ilvH acetohydroxyacid 60.0 54 0.0012 32.9 8.9 45 239-291 97-141 (174)
154 COG0092 RpsC Ribosomal protein 59.8 7.1 0.00015 40.8 2.7 29 129-157 51-79 (233)
155 cd02411 archeal_30S_S3_KH K ho 57.6 11 0.00023 33.0 3.1 29 222-250 39-67 (85)
156 PF02749 QRPTase_N: Quinolinat 57.3 22 0.00047 31.2 5.0 69 131-201 18-86 (88)
157 cd01572 QPRTase Quinolinate ph 57.1 55 0.0012 34.8 9.0 96 193-294 2-99 (268)
158 PRK06559 nicotinate-nucleotide 56.9 69 0.0015 34.7 9.6 97 191-294 13-114 (290)
159 cd01573 modD_like ModD; Quinol 56.5 63 0.0014 34.5 9.2 55 239-294 43-97 (272)
160 PRK04191 rps3p 30S ribosomal p 55.8 13 0.00028 38.1 3.9 30 223-252 42-71 (207)
161 PRK04972 putative transporter; 55.3 49 0.0011 38.9 8.9 148 129-294 214-377 (558)
162 TIGR01008 rpsC_E_A ribosomal p 55.2 23 0.0005 36.1 5.4 30 221-250 38-67 (195)
163 PRK08385 nicotinate-nucleotide 54.1 78 0.0017 34.1 9.5 55 239-294 45-99 (278)
164 cd00652 TBP_TLF TATA box bindi 52.7 72 0.0016 31.8 8.4 35 159-202 47-83 (174)
165 cd01568 QPRTase_NadC Quinolina 52.0 71 0.0015 33.9 8.8 96 193-294 2-98 (269)
166 PRK07428 nicotinate-nucleotide 51.7 77 0.0017 34.2 9.0 97 192-294 14-113 (288)
167 PRK06096 molybdenum transport 50.3 91 0.002 33.7 9.3 55 239-294 48-102 (284)
168 COG4010 Uncharacterized protei 50.1 21 0.00046 34.8 4.0 44 149-201 126-169 (170)
169 TIGR00078 nadC nicotinate-nucl 49.5 70 0.0015 34.0 8.2 68 224-294 28-95 (265)
170 PF02749 QRPTase_N: Quinolinat 49.0 37 0.00081 29.8 5.2 58 233-293 28-85 (88)
171 PTZ00084 40S ribosomal protein 48.8 16 0.00035 37.9 3.2 31 221-251 44-74 (220)
172 PRK11895 ilvH acetolactate syn 47.9 86 0.0019 31.1 8.0 94 178-291 47-141 (161)
173 CHL00048 rps3 ribosomal protei 47.7 54 0.0012 33.9 6.9 30 221-250 66-95 (214)
174 PRK08072 nicotinate-nucleotide 45.7 70 0.0015 34.3 7.6 54 240-294 50-105 (277)
175 cd04517 TLF TBP-like factors ( 45.2 1.6E+02 0.0034 29.5 9.5 25 270-294 148-174 (174)
176 PRK06543 nicotinate-nucleotide 45.0 1.3E+02 0.0029 32.4 9.5 55 239-294 50-106 (281)
177 PRK06106 nicotinate-nucleotide 44.8 1.1E+02 0.0024 32.9 8.9 55 239-294 55-111 (281)
178 COG2101 SPT15 TATA-box binding 44.4 2.4E+02 0.0051 28.7 10.3 25 271-295 156-182 (185)
179 COG1702 PhoH Phosphate starvat 43.5 52 0.0011 36.4 6.2 56 228-294 22-79 (348)
180 cd02191 FtsZ FtsZ is a GTPase 43.4 22 0.00049 38.4 3.5 129 149-293 138-276 (303)
181 TIGR00119 acolac_sm acetolacta 42.9 1.5E+02 0.0033 29.1 8.9 45 239-291 96-140 (157)
182 PLN02716 nicotinate-nucleotide 41.7 1.6E+02 0.0035 32.2 9.6 99 191-294 19-119 (308)
183 PF09869 DUF2096: Uncharacteri 41.1 34 0.00074 34.1 3.9 57 129-201 113-169 (169)
184 PRK05848 nicotinate-nucleotide 40.7 2.2E+02 0.0048 30.6 10.3 97 191-294 3-99 (273)
185 COG1702 PhoH Phosphate starvat 40.3 44 0.00096 37.0 5.1 58 134-201 20-79 (348)
186 COG1847 Jag Predicted RNA-bind 40.3 28 0.00061 35.9 3.4 36 129-164 91-126 (208)
187 PF03958 Secretin_N: Bacterial 38.5 84 0.0018 26.4 5.6 24 268-291 53-76 (82)
188 TIGR00065 ftsZ cell division p 37.7 35 0.00075 37.8 3.9 130 149-294 155-297 (349)
189 TIGR01009 rpsC_bact ribosomal 37.2 70 0.0015 33.0 5.7 29 222-250 63-91 (211)
190 KOG3294 WW domain binding prot 36.7 1.4E+02 0.003 31.7 7.7 27 176-202 56-82 (261)
191 cd04518 TBP_archaea archaeal T 36.6 1.1E+02 0.0023 30.7 6.8 25 270-294 147-173 (174)
192 PRK04191 rps3p 30S ribosomal p 36.5 27 0.00058 35.9 2.6 29 131-159 42-70 (207)
193 PLN00062 TATA-box-binding prot 36.4 2.2E+02 0.0047 28.7 9.0 27 270-296 147-175 (179)
194 CHL00048 rps3 ribosomal protei 35.7 28 0.0006 36.0 2.6 30 129-158 66-95 (214)
195 COG0331 FabD (acyl-carrier-pro 35.6 1.4E+02 0.003 32.6 8.0 56 231-293 132-189 (310)
196 TIGR01008 rpsC_E_A ribosomal p 35.2 29 0.00063 35.4 2.6 29 130-158 39-67 (195)
197 PTZ00084 40S ribosomal protein 33.3 32 0.00068 35.8 2.5 30 130-159 45-74 (220)
198 cd02201 FtsZ_type1 FtsZ is a G 32.6 52 0.0011 35.4 4.1 131 149-294 138-278 (304)
199 PRK07896 nicotinate-nucleotide 32.4 3.2E+02 0.007 29.6 10.0 99 191-294 15-117 (289)
200 PRK00310 rpsC 30S ribosomal pr 32.4 93 0.002 32.6 5.8 30 221-250 62-91 (232)
201 cd04516 TBP_eukaryotes eukaryo 32.3 3.5E+02 0.0076 27.1 9.7 25 270-294 147-173 (174)
202 TIGR00436 era GTP-binding prot 32.2 36 0.00078 35.6 2.8 29 129-157 221-250 (270)
203 cd07055 BMC_like_2 Bacterial M 30.9 57 0.0012 27.4 3.2 38 156-198 21-60 (61)
204 PRK06978 nicotinate-nucleotide 30.6 5.2E+02 0.011 28.2 11.2 68 224-294 54-123 (294)
205 PRK09016 quinolinate phosphori 30.1 5E+02 0.011 28.4 11.0 68 224-294 57-126 (296)
206 COG0014 ProA Gamma-glutamyl ph 30.0 28 0.00061 39.2 1.6 112 126-255 104-221 (417)
207 cd01573 modD_like ModD; Quinol 29.9 1E+02 0.0022 33.0 5.7 68 132-201 30-97 (272)
208 PRK09616 pheT phenylalanyl-tRN 29.6 74 0.0016 37.2 5.1 112 173-294 221-339 (552)
209 PF10369 ALS_ss_C: Small subun 29.5 79 0.0017 27.1 4.0 43 240-290 16-58 (75)
210 PRK00089 era GTPase Era; Revie 29.4 42 0.00091 35.3 2.8 25 132-156 229-254 (292)
211 COG0331 FabD (acyl-carrier-pro 29.4 54 0.0012 35.8 3.6 58 138-201 131-190 (310)
212 PF02080 TrkA_C: TrkA-C domain 29.4 51 0.0011 26.8 2.7 49 240-288 14-70 (71)
213 PF08920 SF3b1: Splicing facto 28.7 20 0.00042 35.0 0.1 12 13-24 5-16 (144)
214 COG0072 PheT Phenylalanyl-tRNA 28.5 86 0.0019 37.6 5.4 110 176-294 217-329 (650)
215 PRK09330 cell division protein 27.4 56 0.0012 36.7 3.4 128 148-294 150-291 (384)
216 PRK00394 transcription factor; 27.3 6.4E+02 0.014 25.3 10.5 25 270-294 148-174 (179)
217 PRK05412 putative nucleotide-b 26.6 4.1E+02 0.0088 26.6 8.7 42 241-291 106-148 (161)
218 KOG1423 Ras-like GTPase ERA [C 26.0 53 0.0011 36.2 2.7 29 129-157 328-357 (379)
219 COG2090 Uncharacterized protei 25.7 3.6E+02 0.0079 26.3 7.9 65 220-293 63-127 (141)
220 PRK04021 hypothetical protein; 25.2 1.3E+02 0.0027 27.2 4.6 40 241-285 50-90 (92)
221 COG3874 Uncharacterized conser 25.1 1.1E+02 0.0023 29.5 4.2 74 222-295 34-113 (138)
222 PRK13018 cell division protein 24.9 96 0.0021 34.8 4.6 129 149-294 166-304 (378)
223 COG0206 FtsZ Cell division GTP 24.6 94 0.002 34.4 4.4 39 129-167 128-167 (338)
224 TIGR02516 type_III_yscC type I 24.2 9.8E+02 0.021 27.3 12.7 25 268-292 206-230 (462)
225 TIGR01334 modD putative molybd 24.1 2E+02 0.0044 30.9 6.7 68 132-201 34-101 (277)
226 PRK15494 era GTPase Era; Provi 24.0 60 0.0013 35.5 2.8 26 131-156 275-301 (339)
227 TIGR01009 rpsC_bact ribosomal 23.1 60 0.0013 33.5 2.5 28 131-158 64-91 (211)
228 COG1839 Uncharacterized conser 23.1 1E+02 0.0022 30.3 3.7 65 221-292 6-79 (162)
229 TIGR00471 pheT_arch phenylalan 22.8 1.7E+02 0.0036 34.4 6.3 113 173-294 223-342 (551)
230 PRK05742 nicotinate-nucleotide 22.6 8.1E+02 0.018 26.4 10.9 96 192-294 10-107 (277)
231 COG4598 HisP ABC-type histidin 22.6 32 0.0007 35.3 0.4 79 223-301 68-151 (256)
232 TIGR00078 nadC nicotinate-nucl 22.4 2.1E+02 0.0046 30.4 6.4 68 132-201 28-95 (265)
233 PF04461 DUF520: Protein of un 22.2 3.9E+02 0.0085 26.6 7.7 41 242-291 107-148 (160)
234 PF06183 DinI: DinI-like famil 22.0 2.2E+02 0.0048 24.0 5.2 44 242-293 13-58 (65)
235 cd01572 QPRTase Quinolinate ph 21.9 2.2E+02 0.0047 30.4 6.4 68 132-201 30-99 (268)
236 PF03958 Secretin_N: Bacterial 21.3 1.2E+02 0.0026 25.4 3.6 33 158-198 44-76 (82)
237 cd01568 QPRTase_NadC Quinolina 21.0 2.2E+02 0.0048 30.2 6.3 68 132-201 30-98 (269)
238 PRK08072 nicotinate-nucleotide 20.5 1.7E+02 0.0038 31.3 5.4 52 150-201 52-105 (277)
No 1
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=2.5e-36 Score=331.79 Aligned_cols=395 Identities=28% Similarity=0.342 Sum_probs=260.7
Q ss_pred CCCCCCCCCCCCcc---chHHHHHHHHHHHccccccCCC--CCCCCceecCCCCCCCCccccccCCcccccCCCCCCCCC
Q 005922 44 PTSYNSVPPPADEF---QDFQAAKRRAEQIAARLCNSVS--AEAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIP 118 (669)
Q Consensus 44 p~s~~~v~pp~~~~---~~~e~IkkIaeEtaARI~I~~~--~~~ERiisisg~~~~eav~kA~~~i~~~l~~i~~~~~~~ 118 (669)
...+.+|+.+..++ ---+.|.+|-.+++|||.|... ...+|.+++.|. .+.+..+..+|.+++.+.....
T Consensus 54 ~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~--pe~v~~aK~li~evv~r~~~~~--- 128 (600)
T KOG1676|consen 54 QTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGS--PENVEVAKQLIGEVVSRGRPPG--- 128 (600)
T ss_pred cccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCC--cccHHHHHHhhhhhhhccCCCC---
Confidence 34677888887662 1124699999999999997632 358999999998 4557777777777766442111
Q ss_pred CCCCCCC-CCCceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHH
Q 005922 119 VSYGGYQ-SMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLIND 197 (669)
Q Consensus 119 ~s~g~~~-~~~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~e 197 (669)
.+...+ ..+++.+|+||..++|+||||+|+|||.|++++||+|.+..|+....+ .++.|.|+|+++.|++|+.||.|
T Consensus 129 -~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~-~~KplritGdp~~ve~a~~lV~d 206 (600)
T KOG1676|consen 129 -GFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG-ADKPLRITGDPDKVEQAKQLVAD 206 (600)
T ss_pred -CccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC-CCCceeecCCHHHHHHHHHHHHH
Confidence 111112 245899999999999999999999999999999999999988764444 78999999999999999999999
Q ss_pred HHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC
Q 005922 198 VLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT 277 (669)
Q Consensus 198 lI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~ 277 (669)
+|+|+.....+.............+++|.||.++||+||||+|++||+|+.+||+||+|++++.+ .+.||+++|.|+
T Consensus 207 il~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p---~speR~~~IiG~ 283 (600)
T KOG1676|consen 207 ILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDP---SSPERPAQIIGT 283 (600)
T ss_pred HHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCC---CCccceeeeecC
Confidence 99985543322211000111223488999999999999999999999999999999999988766 678999999999
Q ss_pred HHHHHHHHHHHHHHHhhcccCCC-CCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCC
Q 005922 278 SEQIESAKQLVNEVISENRIRNP-AMAGGYSQQ---GYQARPPTSWGTPGAPSMQQPGYG-YVQPGAYPGQTPQYNMSQP 352 (669)
Q Consensus 278 peqVq~Ak~LI~dlL~e~~~r~~-~~~GG~~~~---gY~p~Pp~~~Gppg~~~~~q~gYg-y~~~g~Y~~~~~qy~~~q~ 352 (669)
+++|+.|.+||.+||+++...++ ++.+|.+.. .|.-.|..-||..-+. ++...+. ....|+|-....+ .
T Consensus 284 ~d~ie~Aa~lI~eii~~~~~~~~~~~~~G~P~~~~~fy~~VPa~KcGLvIGr-GGEtIK~in~qSGA~~el~r~-----~ 357 (600)
T KOG1676|consen 284 VDQIEHAAELINEIIAEAEAGAGGGMGGGAPGLVAQFYMKVPADKCGLVIGR-GGETIKQINQQSGARCELSRQ-----P 357 (600)
T ss_pred HHHHHHHHHHHHHHHHHHhccCCCCcCCCCccceeeEEEeccccccccccCC-CccchhhhcccCCccccccCC-----C
Confidence 99999999999999999765543 344444433 4556788888765433 1122222 2333554432221 2
Q ss_pred CCCCCCCCCCCCCCCCCCCCCC-CCCCC-CCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCccCCCCCCC
Q 005922 353 PYGGYPSQPTPGGYPGNWDQTP-TQQTS-QGSGYDYYSQQPSSQQPQAPGGSAAPADSTGYSYSQPPASGYNQQGQGYAQ 430 (669)
Q Consensus 353 pyggy~~~~~~~~y~~gwdq~~-~~~~~-~~~gy~yY~qq~~~~~~~~~~~~~~p~~~~~~~~~q~~~~~y~~~~~~~~~ 430 (669)
|++++..- .-.-+ -|.++ .|-.+ --.-++++...... . ..++..|. ...++|++...-.|++..+++.+
T Consensus 358 p~~~~~ek-tf~Ir---G~~~QIdhAk~LIr~kvg~~~~n~~~-~---~~~a~gp~-~q~~~~~p~~~g~~~~~~~~~~~ 428 (600)
T KOG1676|consen 358 PNGNPKEK-TFVIR---GDKRQIDHAKQLIRDKVGDIAPNTPY-P---NPGAGGPQ-TQFGNYGPHAPGPFGQQQQGAPQ 428 (600)
T ss_pred CCCCccce-EEEEe---cCcccchHHHHHHHHHhcccCCCCCC-C---CCCcCCCC-CCCCCCCCCCCCCCCCCCCCCCC
Confidence 33322221 11111 11222 11000 00112333333221 1 11122222 34455555422236777888999
Q ss_pred CCCCCcCCCCCcCCCCCCccccCCCCCCCCCCCccCCCCC
Q 005922 431 DSYGGYHAPQSGYGQAAPYDQQQGYNSAAGYGNVNNTSQE 470 (669)
Q Consensus 431 ~~y~~y~~~q~~y~q~~~~~~q~~~~~~~~~~~~~~~~~~ 470 (669)
+.+++|.+.|..|++. .++.+- -+.++.||+.+
T Consensus 429 p~~g~p~~s~~~~g~g-~~~p~~------q~~~~~~P~~~ 461 (600)
T KOG1676|consen 429 PANGGPPASQQPYGQG-GQQPQV------QPQQTMAPSAA 461 (600)
T ss_pred CCCCCCCcccCCCCcc-ccCCcc------cCCCCCCcccC
Confidence 9999998888888876 333221 15566677666
No 2
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=7.1e-34 Score=312.47 Aligned_cols=227 Identities=34% Similarity=0.523 Sum_probs=185.2
Q ss_pred HHHHHHHHHHccccccCCCC----CCCCceecCCCCCCCCccccccCCcccccCCCCCC-CCCCCCCCCCCCCceEEEEe
Q 005922 61 QAAKRRAEQIAARLCNSVSA----EAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPS-AIPVSYGGYQSMGTSKKIEI 135 (669)
Q Consensus 61 e~IkkIaeEtaARI~I~~~~----~~ERiisisg~~~~eav~kA~~~i~~~l~~i~~~~-~~~~s~g~~~~~~vt~rIlV 135 (669)
|+||+++++++|++.+.... ...+.+.|+|+ .+.+..+..++.++|.+..... ......+.+.....+++|.|
T Consensus 159 ETikqlqe~sg~k~i~iqd~~~~~~~~KplritGd--p~~ve~a~~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~V 236 (600)
T KOG1676|consen 159 ETIKQLQEQSGVKMILVQDGSIATGADKPLRITGD--PDKVEQAKQLVADILREEDDEVPGSGGHAGVRGGGSATREVKV 236 (600)
T ss_pred cHHHHHHhhcCCceEEEecCCcCCCCCCceeecCC--HHHHHHHHHHHHHHHHhcccCCCccccccCcCccccceeEEec
Confidence 89999999999998776433 25678888886 5668888888888876322111 11133444455567999999
Q ss_pred ccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhccc
Q 005922 136 PNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLT 215 (669)
Q Consensus 136 P~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~ 215 (669)
|...||.||||+|++||+|+.+||+||+|..|+ ++.+.||++.|.|++|.|++|.++|.+||++......+......
T Consensus 237 Pr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd--~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~~~~~~~~G~- 313 (600)
T KOG1676|consen 237 PRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDD--DPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAGAGGGMGGGA- 313 (600)
T ss_pred cccceeeEEecCchHHHHHhhccCceeEeecCC--CCCCccceeeeecCHHHHHHHHHHHHHHHHHHhccCCCCcCCCC-
Confidence 999999999999999999999999999999886 46899999999999999999999999999997765322111000
Q ss_pred CCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922 216 GQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN 295 (669)
Q Consensus 216 ~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~ 295 (669)
.....++.|.||.++||+||||+|+|||.|..+|||+|.+..+ ++..+..||+|+|.|++.+|+.|+.||+++|...
T Consensus 314 -P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~--~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~~ 390 (600)
T KOG1676|consen 314 -PGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ--PPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGDI 390 (600)
T ss_pred -ccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC--CCCCCccceEEEEecCcccchHHHHHHHHHhccc
Confidence 1112278999999999999999999999999999999999876 5667889999999999999999999999999874
No 3
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.97 E-value=5.8e-30 Score=264.56 Aligned_cols=194 Identities=30% Similarity=0.459 Sum_probs=163.0
Q ss_pred CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCC
Q 005922 128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGS 207 (669)
Q Consensus 128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~ 207 (669)
.+.+|||||+..+|.||||+|+||.+|+++|||+|+++|+.|++|+.+||||.|+|+.|+|...+++|.|+|+|......
T Consensus 38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~~~ 117 (402)
T KOG2191|consen 38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQAVA 117 (402)
T ss_pred ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHhhc
Confidence 38999999999999999999999999999999999999999999999999999999999999999999999999764322
Q ss_pred Ccc-hhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHH
Q 005922 208 GIV-ARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQ 286 (669)
Q Consensus 208 ~~~-~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~ 286 (669)
+.. ........+..+++|+||++.+|.||||+|.+||.|+|+++|.|+|.+.. +..-+..||+|+|.|+++++.+|..
T Consensus 118 k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqk-pt~~sLqervvt~sge~e~~~~A~~ 196 (402)
T KOG2191|consen 118 KPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQK-PTGISLQERVVTVSGEPEQNMKAVS 196 (402)
T ss_pred CCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccC-CCCccceeEEEEecCCHHHHHHHHH
Confidence 211 00001123345689999999999999999999999999999999999643 3344677999999999999999999
Q ss_pred HHHHHHhhcccCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCC
Q 005922 287 LVNEVISENRIRNPAMAGGYSQQGYQ--ARPPTSWGTPGAPSM 327 (669)
Q Consensus 287 LI~dlL~e~~~r~~~~~GG~~~~gY~--p~Pp~~~Gppg~~~~ 327 (669)
||+++|.|++ +++.|.+..|. ..|..|++|.+.++.
T Consensus 197 ~IL~Ki~eDp-----qs~scln~sya~vsGpvaNsnPtGspya 234 (402)
T KOG2191|consen 197 LILQKIQEDP-----QSGSCLNISYANVSGPVANSNPTGSPYA 234 (402)
T ss_pred HHHHHhhcCC-----cccceeccchhcccCcccccCCCCCCCC
Confidence 9999999986 44556667664 557788888776543
No 4
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.93 E-value=2.2e-26 Score=232.50 Aligned_cols=230 Identities=23% Similarity=0.318 Sum_probs=184.7
Q ss_pred CCCCCCCCCCccchHHHHHHHHHHHccccccCCCCCCCCceecCCCCCCCCccccccCCcccccCCCCCCCCCCCCCCCC
Q 005922 46 SYNSVPPPADEFQDFQAAKRRAEQIAARLCNSVSAEAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPVSYGGYQ 125 (669)
Q Consensus 46 s~~~v~pp~~~~~~~e~IkkIaeEtaARI~I~~~~~~ERiisisg~~~~eav~kA~~~i~~~l~~i~~~~~~~~s~g~~~ 125 (669)
|.|+........ ++||+++.+.+|.|.|.+.+.+||+++|+.+ .+.+...+..|+..|++-. ..
T Consensus 56 sk~agavigkgg---~nik~lr~d~na~v~vpds~~peri~tisad--~~ti~~ilk~iip~lee~f-----------~~ 119 (390)
T KOG2192|consen 56 SKNAGAVIGKGG---KNIKALRTDYNASVSVPDSSGPERILTISAD--IETIGEILKKIIPTLEEGF-----------QL 119 (390)
T ss_pred cccccceecccc---ccHHHHhhhccceeeccCCCCCceeEEEecc--HHHHHHHHHHHhhhhhhCC-----------CC
Confidence 566666666666 7999999999999999999999999999986 4445555555555555221 12
Q ss_pred CCCceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcC
Q 005922 126 SMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESG 205 (669)
Q Consensus 126 ~~~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~ 205 (669)
...|++||||..+++|.||||+|++||+|+|++.|+++|... .++++++|||.|.|...+|..|++.|+++|+|....
T Consensus 120 ~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~--c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pik 197 (390)
T KOG2192|consen 120 PSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE--CCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIK 197 (390)
T ss_pred CCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc--cCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcC
Confidence 234899999999999999999999999999999999999754 589999999999999999999999999999985321
Q ss_pred CC-----------------------------C----------------c---chh------------------cccC---
Q 005922 206 GS-----------------------------G----------------I---VAR------------------RLTG--- 216 (669)
Q Consensus 206 ~~-----------------------------~----------------~---~~r------------------r~~~--- 216 (669)
++ + . ..+ .|..
T Consensus 198 gsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~said 277 (390)
T KOG2192|consen 198 GSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAID 277 (390)
T ss_pred CcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcCC
Confidence 00 0 0 000 0000
Q ss_pred --------------------------------CCC-CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCC
Q 005922 217 --------------------------------QAG-SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPP 263 (669)
Q Consensus 217 --------------------------------~~~-~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~pp 263 (669)
..+ .++..+.||.++-|.||||+|..||+|++++||.|+|.. +
T Consensus 278 tw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikide----p 353 (390)
T KOG2192|consen 278 TWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDE----P 353 (390)
T ss_pred CcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecC----c
Confidence 001 246789999999999999999999999999999999963 4
Q ss_pred CCCCCccEEEEEcCHHHHHHHHHHHHHHHhhccc
Q 005922 264 GDTSTERTVQIDGTSEQIESAKQLVNEVISENRI 297 (669)
Q Consensus 264 ge~s~er~VtItG~peqVq~Ak~LI~dlL~e~~~ 297 (669)
.+.++||+|+|+|+.++|+.|+.|+...++.-++
T Consensus 354 leGsedrIitItGTqdQIqnAQYLlQn~Vkq~re 387 (390)
T KOG2192|consen 354 LEGSEDRIITITGTQDQIQNAQYLLQNSVKQYRE 387 (390)
T ss_pred CCCCCceEEEEeccHHHHhhHHHHHHHHHHhhhc
Confidence 5578899999999999999999999998886443
No 5
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.91 E-value=4.9e-24 Score=236.93 Aligned_cols=229 Identities=25% Similarity=0.314 Sum_probs=177.6
Q ss_pred HHHHHHHHHHccccccCC--CCCCCCceecCC-------CCCCCCccccccCCcccccCCCCCCCCCCCCCCCCCCCceE
Q 005922 61 QAAKRRAEQIAARLCNSV--SAEAKRPRVENG-------SGGFDSADKGFSSPPSDLKSIPAPSAIPVSYGGYQSMGTSK 131 (669)
Q Consensus 61 e~IkkIaeEtaARI~I~~--~~~~ERiisisg-------~~~~eav~kA~~~i~~~l~~i~~~~~~~~s~g~~~~~~vt~ 131 (669)
+.||+||+++.+||+|.+ .+|.|||++|.+ ....+++++++.+|..+++............. ...++++
T Consensus 63 ~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~--~~~~v~~ 140 (485)
T KOG2190|consen 63 DIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEEDDEAAEDNGEDA--SGPEVTC 140 (485)
T ss_pred HHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhcccccccccccCCccc--cCCceEE
Confidence 689999988888888885 459999999999 22267789999999988662111111111111 1124899
Q ss_pred EEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh----cCC-
Q 005922 132 KIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE----SGG- 206 (669)
Q Consensus 132 rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~----~~~- 206 (669)
|||||..++|+||||+|++||+|+++|||+|+|.+++ ++++++|.|+|.|+.+.|.+|+..|..+|.+.. ...
T Consensus 141 RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~--lP~ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~ 218 (485)
T KOG2190|consen 141 RLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDM--LPNSTERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLV 218 (485)
T ss_pred EEEechhheeeeeccCcHHHHHHHHhcCceEEecCCC--CCcccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCC
Confidence 9999999999999999999999999999999999885 899999999999999999999999999998842 100
Q ss_pred -------------------CC-c-----------------------------------chh---------------cc--
Q 005922 207 -------------------SG-I-----------------------------------VAR---------------RL-- 214 (669)
Q Consensus 207 -------------------~~-~-----------------------------------~~r---------------r~-- 214 (669)
.. . ..+ +.
T Consensus 219 st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~~ 298 (485)
T KOG2190|consen 219 STIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTDR 298 (485)
T ss_pred CcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccCcc
Confidence 00 0 000 00
Q ss_pred ---------cC--------------------C----CCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCC
Q 005922 215 ---------TG--------------------Q----AGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHL 261 (669)
Q Consensus 215 ---------~~--------------------~----~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ 261 (669)
.. . ...++.+|+||++++++||||+|++|.+||+.|||.|+|.....
T Consensus 299 ~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~ 378 (485)
T KOG2190|consen 299 IVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEE 378 (485)
T ss_pred eeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccchHHHHHhcCCceEEccccc
Confidence 00 0 11156799999999999999999999999999999999985422
Q ss_pred CCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922 262 PPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN 295 (669)
Q Consensus 262 ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~ 295 (669)
. ....|+.|+|++...+...++.+|...|...
T Consensus 379 ~--~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~ 410 (485)
T KOG2190|consen 379 V--SGVREALVQITGMLREDLLAQYLIRARLSAP 410 (485)
T ss_pred c--CCcceeEEEecchhHHHHhhhhhcccccccC
Confidence 1 1467999999999999999999997777653
No 6
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.89 E-value=4.8e-23 Score=229.06 Aligned_cols=161 Identities=29% Similarity=0.437 Sum_probs=138.6
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC---------CHHHHHHHHHHHHHHH
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG---------TPEQIAKAEQLINDVL 199 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG---------t~E~V~kA~~lI~elI 199 (669)
.++|||++.+++|.||||+|++||+|+++|.++|+|... +++|.+|+|+|+| ..++|.+|+++|..++
T Consensus 43 ~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~---~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~ 119 (485)
T KOG2190|consen 43 LTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNES---LPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKL 119 (485)
T ss_pred ceEEEEeccccceeEEccCcHHHHHHhhcccccceeecC---CCCCCcceEEEecccccccCCchHHHHHHHHHHHhhcc
Confidence 458999999999999999999999999999999999754 6899999999999 9999999999999987
Q ss_pred HhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHH
Q 005922 200 AEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSE 279 (669)
Q Consensus 200 ~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~pe 279 (669)
+++......... ......++++|+||.++||.||||+|++||+|+++|||+|+|.++++| .+++|.|+|.|.++
T Consensus 120 ~~d~~~~~d~~~---~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP---~ster~V~IsG~~~ 193 (485)
T KOG2190|consen 120 EEDDEAAEDNGE---DASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLP---NSTERAVTISGEPD 193 (485)
T ss_pred cccccccccCCc---cccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCC---cccceeEEEcCchH
Confidence 754432211110 001114789999999999999999999999999999999999998887 67799999999999
Q ss_pred HHHHHHHHHHHHHhhcccC
Q 005922 280 QIESAKQLVNEVISENRIR 298 (669)
Q Consensus 280 qVq~Ak~LI~dlL~e~~~r 298 (669)
.|.+|...|..+|.++..+
T Consensus 194 av~~al~~Is~~L~~~~~~ 212 (485)
T KOG2190|consen 194 AVKKALVQISSRLLENPPR 212 (485)
T ss_pred HHHHHHHHHHHHHHhcCCc
Confidence 9999999999999986433
No 7
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.89 E-value=4e-24 Score=226.62 Aligned_cols=223 Identities=24% Similarity=0.315 Sum_probs=179.7
Q ss_pred HHHHHHHHHHccccccCCCC---CCCCceecCCCCCCCCccccccCCcccccCCCCCCCCCCCCCCCCCCCceEEEEecc
Q 005922 61 QAAKRRAEQIAARLCNSVSA---EAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPVSYGGYQSMGTSKKIEIPN 137 (669)
Q Consensus 61 e~IkkIaeEtaARI~I~~~~---~~ERiisisg~~~~eav~kA~~~i~~~l~~i~~~~~~~~s~g~~~~~~vt~rIlVP~ 137 (669)
++||.|...+.+||+|-... ..||++++.+. .+...+|..+|++++..-.. .+. ...++.+||+..+
T Consensus 219 ~TIknItkqTqsriD~hrken~Gaaek~itvh~t--pEg~s~Ac~~ILeimqkEA~------~~k--~~~e~pLk~lAHN 288 (584)
T KOG2193|consen 219 ATIKNITKQTQSRIDVHRKENAGAAEKIITVHST--PEGTSKACKMILEIMQKEAV------DDK--VAEEIPLKILAHN 288 (584)
T ss_pred ccccCcchhhhheeeeeecccCCcccCceEEecC--ccchHHHHHHHHHHHHHhhh------ccc--hhhhcchhhhhhc
Confidence 48999999999999987432 57999999998 55577888888888752110 000 1134889999999
Q ss_pred ccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCC----------
Q 005922 138 IRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGS---------- 207 (669)
Q Consensus 138 ~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~---------- 207 (669)
.+||+||||.|.+||+|+.+||++|+|++-.|...-++||.|+|.|+.|+|.+|..+|..+|+|+-..+.
T Consensus 289 ~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~ 368 (584)
T KOG2193|consen 289 NLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLP 368 (584)
T ss_pred chhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCC
Confidence 9999999999999999999999999999877766678899999999999999999999999998633210
Q ss_pred --------Ccchh--------------cc------cC-CCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 005922 208 --------GIVAR--------------RL------TG-QAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIP 258 (669)
Q Consensus 208 --------~~~~r--------------r~------~~-~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~ 258 (669)
+.... .+ .. ......++|.||...||.||||+|.+||.|.+.+||.|+|.+
T Consensus 369 P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIap 448 (584)
T KOG2193|consen 369 PGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAP 448 (584)
T ss_pred cccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecC
Confidence 00000 00 00 123456799999999999999999999999999999999986
Q ss_pred CCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhcc
Q 005922 259 LHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENR 296 (669)
Q Consensus 259 ~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~~ 296 (669)
-+. .+..+|+|+|+|++++.-+|.-.|-.+|+|..
T Consensus 449 pE~---pdvseRMViItGppeaqfKAQgrifgKikEen 483 (584)
T KOG2193|consen 449 PEI---PDVSERMVIITGPPEAQFKAQGRIFGKIKEEN 483 (584)
T ss_pred CCC---CCcceeEEEecCChHHHHhhhhhhhhhhhhhc
Confidence 543 46789999999999999999999999998853
No 8
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.86 E-value=5.4e-21 Score=193.58 Aligned_cols=152 Identities=26% Similarity=0.417 Sum_probs=137.0
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCC
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSG 208 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~ 208 (669)
|+++|||-++.+|.||||+|++||.|+.+.+|.|.|. +.+.++|||+|+-+.+.|...++.|.-.|++....
T Consensus 48 ~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vp-----ds~~peri~tisad~~ti~~ilk~iip~lee~f~~--- 119 (390)
T KOG2192|consen 48 VELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVP-----DSSGPERILTISADIETIGEILKKIIPTLEEGFQL--- 119 (390)
T ss_pred eeEEEEEecccccceeccccccHHHHhhhccceeecc-----CCCCCceeEEEeccHHHHHHHHHHHhhhhhhCCCC---
Confidence 8999999999999999999999999999999999997 45789999999999999988888888777764321
Q ss_pred cchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHH
Q 005922 209 IVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLV 288 (669)
Q Consensus 209 ~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI 288 (669)
....+++|+|..++.|.|||++|++||+||++..||++|.-.+.+ .+++|+|.|.|.++.|..+.+.|
T Consensus 120 ---------~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p---~stdrv~l~~g~~k~v~~~i~~i 187 (390)
T KOG2192|consen 120 ---------PSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCP---HSTDRVVLIGGKPKRVVECIKII 187 (390)
T ss_pred ---------CCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCC---CCcceEEEecCCcchHHHHHHHH
Confidence 225789999999999999999999999999999999999877776 78899999999999999999999
Q ss_pred HHHHhhcccCCC
Q 005922 289 NEVISENRIRNP 300 (669)
Q Consensus 289 ~dlL~e~~~r~~ 300 (669)
+++|+|.+.+..
T Consensus 188 l~~i~e~pikgs 199 (390)
T KOG2192|consen 188 LDLISESPIKGS 199 (390)
T ss_pred HHHhhcCCcCCc
Confidence 999999877654
No 9
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.86 E-value=1.1e-21 Score=203.49 Aligned_cols=277 Identities=24% Similarity=0.244 Sum_probs=211.3
Q ss_pred CCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCC--CCCCCCCCCCCCCCccchHHHHHHHHHHHccccccCCCC-----CC
Q 005922 10 DGTPSKRKYEDQTTPPSAAARRPTGFSAPDPA--VAPTSYNSVPPPADEFQDFQAAKRRAEQIAARLCNSVSA-----EA 82 (669)
Q Consensus 10 ~~~~~Kr~~~d~~~p~~~~~~r~~~~s~~p~~--~~p~s~~~v~pp~~~~~~~e~IkkIaeEtaARI~I~~~~-----~~ 82 (669)
..+++||..+...||+ .++|.+..+..... +..+++.+-+...+.. ++|..+.+|++|||+++... ..
T Consensus 11 ~~~s~kr~~~a~pe~~--~~k~~n~ge~~~y~ikvLips~AaGsIIGKGG---~ti~~lqk~tgariklSks~dfyPGTT 85 (402)
T KOG2191|consen 11 APDSRKRPLEAPPEPG--STKRTNTGEDGQYFLKVLIPSYAAGSIIGKGG---QTIVQLQKETGARIKLSKSKDFYPGTT 85 (402)
T ss_pred CCCCccccccCCCCcc--ccccccCCCCCceEEEEEeecccccceeccch---HHHHHHHhccCcEEEeccccccCCCcc
Confidence 4568899998887766 67899988888776 5677999989888888 89999999999999999654 58
Q ss_pred CCceecCCCCCCCCccccccCCcccccCCCCCCCCCCCC-C-CCCCCCceEEEEeccccccceeccCCcchhHHHhhcCc
Q 005922 83 KRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPVSY-G-GYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGA 160 (669)
Q Consensus 83 ERiisisg~~~~eav~kA~~~i~~~l~~i~~~~~~~~s~-g-~~~~~~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGA 160 (669)
||+|.|.|. .+++...+..|.+++.+.+....-.+.. . -..+..-.+||+||+.-+|.||||+|.|||.|+|+++|
T Consensus 86 eRvcli~Gt--~eai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga 163 (402)
T KOG2191|consen 86 ERVCLIQGT--VEALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGA 163 (402)
T ss_pred ceEEEEecc--HHHHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCc
Confidence 999999998 6667777888888876444322211111 0 01223356899999999999999999999999999999
Q ss_pred EEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcc----------hhccc----------CCCCC
Q 005922 161 KIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIV----------ARRLT----------GQAGS 220 (669)
Q Consensus 161 kI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~----------~rr~~----------~~~~~ 220 (669)
.|+|+...++.-+..||+|+|+|++|++.+|+++|+++|.|+........ .+..+ .....
T Consensus 164 ~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya~vsGpvaNsnPtGspya~~~~~~~as 243 (402)
T KOG2191|consen 164 WIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYANVSGPVANSNPTGSPYAYQAHVLPAS 243 (402)
T ss_pred ceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceeccchhcccCcccccCCCCCCCCCCCcccccc
Confidence 99998555556788899999999999999999999999999864322110 01000 01112
Q ss_pred cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922 221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN 295 (669)
Q Consensus 221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~ 295 (669)
....+-|+..++|..-|.++.++-.|...+|+.|.|... +........+ +.+.|....+..|..||..++...
T Consensus 244 tas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~-l~~m~g~gy~-~n~~g~~ls~~aa~g~L~~~~~~a 316 (402)
T KOG2191|consen 244 TASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQA-LNTMAGYGYN-TNILGLGLSILAAEGVLAAKVASA 316 (402)
T ss_pred chhhccccccccccccccccccceeeecccccceeeccc-cccccccccc-ccccchhhhhhhhhhHHHHhhccc
Confidence 334567899999999999999999999999999988643 1112233344 788888999999999998887653
No 10
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.85 E-value=7.6e-22 Score=209.46 Aligned_cols=223 Identities=24% Similarity=0.329 Sum_probs=171.3
Q ss_pred HHHHHHHHHHccccccCCCC-----CCCCceecCCCCCCCCccccccCCccccc-----CC---------C---------
Q 005922 61 QAAKRRAEQIAARLCNSVSA-----EAKRPRVENGSGGFDSADKGFSSPPSDLK-----SI---------P--------- 112 (669)
Q Consensus 61 e~IkkIaeEtaARI~I~~~~-----~~ERiisisg~~~~eav~kA~~~i~~~l~-----~i---------~--------- 112 (669)
.++|+|.++++++|.|+.-- .+||-|++.|. .+++.+|-..|..+|. ++ +
T Consensus 300 rnlKkIeq~TgTkITis~lqels~ynpERTItVkGs--iEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~ 377 (584)
T KOG2193|consen 300 RNLKKIEQDTGTKITISKLQELSLYNPERTITVKGS--IEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPALG 377 (584)
T ss_pred ccHHHHHhhcCCceeeeehhhhcccCccceEEeccc--HHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccccC
Confidence 47999999999999998432 68999999996 5666665444444432 10 0
Q ss_pred ---CC--C------CCCCCCCC-----CC-CCCceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCC
Q 005922 113 ---AP--S------AIPVSYGG-----YQ-SMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSP 175 (669)
Q Consensus 113 ---~~--~------~~~~s~g~-----~~-~~~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~ 175 (669)
+. . ..++.+.. .+ .....++|+||...||.||||+|.+||+|.+.+||.|+|.... .++..
T Consensus 378 ~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE--~pdvs 455 (584)
T KOG2193|consen 378 LFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPE--IPDVS 455 (584)
T ss_pred CCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCC--CCCcc
Confidence 00 0 00000000 01 1235689999999999999999999999999999999997543 56788
Q ss_pred CccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEE
Q 005922 176 TRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQ 255 (669)
Q Consensus 176 eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIq 255 (669)
+|.|+|+|.+|...||-..|..+|+|+...+... ....+.+|.||...+|+||||||.++++|++.|+|.|.
T Consensus 456 eRMViItGppeaqfKAQgrifgKikEenf~~Pke--------evklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~ 527 (584)
T KOG2193|consen 456 ERMVIITGPPEAQFKAQGRIFGKIKEENFFLPKE--------EVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVV 527 (584)
T ss_pred eeEEEecCChHHHHhhhhhhhhhhhhhccCCchh--------hheeeeeeeccchhhhhhhccccccHHHHhccccceEE
Confidence 9999999999999999999999999976433211 12345688999999999999999999999999999999
Q ss_pred eccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhccc
Q 005922 256 VIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENRI 297 (669)
Q Consensus 256 I~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~~~ 297 (669)
|..+. .+ ++.+.-+|.|.|..-+.+.|...|.++|.+++.
T Consensus 528 vPrdq-tp-dEnd~vivriiGhfyatq~aQrki~~iv~qvkq 567 (584)
T KOG2193|consen 528 VPRDQ-TP-DENDQVIVRIIGHFYATQNAQRKIAHIVNQVKQ 567 (584)
T ss_pred ccccC-CC-CccceeeeeeechhhcchHHHHHHHHHHHHHHH
Confidence 97665 33 344566799999999999999999999998653
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=99.74 E-value=6.6e-18 Score=165.60 Aligned_cols=138 Identities=28% Similarity=0.454 Sum_probs=107.7
Q ss_pred EEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccc---cCCHHHHHHHHHHHHHHHHhhhcCCCCc
Q 005922 133 IEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVEL---MGTPEQIAKAEQLINDVLAEAESGGSGI 209 (669)
Q Consensus 133 IlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtI---tGt~E~V~kA~~lI~elI~e~~~~~~~~ 209 (669)
|.||.+++|.|||++|++||.|+++|||+|+|+.+ +..|.| +++++++.+|+.+|..++......
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~--------~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e---- 69 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE--------TGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPE---- 69 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC--------CceEEEecCCCCHHHHHHHHHHHHHHHcCCCHH----
Confidence 57899999999999999999999999999999743 234666 889999999999999987742211
Q ss_pred chhcccCCCCCcEEEEeeCC---------CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHH
Q 005922 210 VARRLTGQAGSDHFAMKIPN---------NKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQ 280 (669)
Q Consensus 210 ~~rr~~~~~~~~t~~I~VP~---------~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peq 280 (669)
...++... ...-..+.|.. ..+|+|||++|++|+.|++.|||+|.|. ++.|+|.|++++
T Consensus 70 ~A~~l~gd-~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~-----------~~~v~i~G~~~~ 137 (172)
T TIGR03665 70 KALKLLDD-DYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY-----------GKTVGIIGDPEQ 137 (172)
T ss_pred HHHHhcCC-cceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc-----------CCEEEEECCHHH
Confidence 00000000 00111223333 3689999999999999999999999995 368999999999
Q ss_pred HHHHHHHHHHHHhh
Q 005922 281 IESAKQLVNEVISE 294 (669)
Q Consensus 281 Vq~Ak~LI~dlL~e 294 (669)
|+.|+++|++||+.
T Consensus 138 ~~~A~~~i~~li~~ 151 (172)
T TIGR03665 138 VQIAREAIEMLIEG 151 (172)
T ss_pred HHHHHHHHHHHHcC
Confidence 99999999999955
No 12
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.72 E-value=3.4e-17 Score=161.69 Aligned_cols=143 Identities=29% Similarity=0.428 Sum_probs=109.5
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccc----cCCHHHHHHHHHHHHHHHHhhhc
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVEL----MGTPEQIAKAEQLINDVLAEAES 204 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtI----tGt~E~V~kA~~lI~elI~e~~~ 204 (669)
+...|.||.+++|.|||++|++||.|+++|||+|+|+.+ +..|.| +++++.+++|+++|.+++.....
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~--------~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~~ 74 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE--------TGEVIIEPTDGEDPLAVLKARDIVKAIGRGFSP 74 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC--------CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCH
Confidence 678999999999999999999999999999999999743 245556 58999999999999999884211
Q ss_pred CCCCcchhcccCCC-CCcEEEEe--eC-----CCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEc
Q 005922 205 GGSGIVARRLTGQA-GSDHFAMK--IP-----NNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDG 276 (669)
Q Consensus 205 ~~~~~~~rr~~~~~-~~~t~~I~--VP-----~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG 276 (669)
. ...++.+.. ..+.++|. .. ...+|+|||++|++||.|++.|||+|.|. ++.|+|.|
T Consensus 75 e----~A~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~-----------~~~v~i~G 139 (180)
T PRK13763 75 E----KALRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVY-----------GKTVAIIG 139 (180)
T ss_pred H----HHHHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEc-----------CCEEEEEe
Confidence 0 000000000 00011110 11 13689999999999999999999999995 34699999
Q ss_pred CHHHHHHHHHHHHHHHhh
Q 005922 277 TSEQIESAKQLVNEVISE 294 (669)
Q Consensus 277 ~peqVq~Ak~LI~dlL~e 294 (669)
++++|+.|+++|++||+.
T Consensus 140 ~~~~~~~A~~~I~~li~g 157 (180)
T PRK13763 140 DPEQVEIAREAIEMLIEG 157 (180)
T ss_pred CHHHHHHHHHHHHHHHcC
Confidence 999999999999999955
No 13
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.33 E-value=3.2e-12 Score=105.89 Aligned_cols=64 Identities=39% Similarity=0.628 Sum_probs=57.7
Q ss_pred EEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHH
Q 005922 223 FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVN 289 (669)
Q Consensus 223 ~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~ 289 (669)
++|+||.+++++||||+|++||+|+++|||+|.|.+... ....+|+|+|+|+.++|++|+.||.
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL---PGSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC---CCCCceEEEEEeCHHHHHHHHHhhC
Confidence 689999999999999999999999999999999975432 2567899999999999999999983
No 14
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.32 E-value=1.9e-12 Score=107.32 Aligned_cols=65 Identities=37% Similarity=0.563 Sum_probs=59.4
Q ss_pred eEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHH
Q 005922 130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLIN 196 (669)
Q Consensus 130 t~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~ 196 (669)
+++|+||...+|+||||+|++||+|+++|||+|+|.++. +.+..+|+|+|+|+.|+|.+|+.+|.
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~--~~~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSV--LPGSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCC--CCCCCceEEEEEeCHHHHHHHHHhhC
Confidence 379999999999999999999999999999999998654 34678999999999999999999883
No 15
>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=99.16 E-value=9.8e-11 Score=96.27 Aligned_cols=59 Identities=39% Similarity=0.586 Sum_probs=53.4
Q ss_pred cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHH
Q 005922 221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVN 289 (669)
Q Consensus 221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~ 289 (669)
+...|.||.+++++||||+|++||+|+++|||+|.|.. ++.|+|+|+ .+.|+.|+++|+
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 35678999999999999999999999999999999851 468999999 999999999984
No 16
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.15 E-value=5.9e-11 Score=96.91 Aligned_cols=61 Identities=30% Similarity=0.474 Sum_probs=55.1
Q ss_pred EEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHH
Q 005922 223 FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVN 289 (669)
Q Consensus 223 ~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~ 289 (669)
.+|.||.+++++|||++|++|++|+++|||+|.|... ++.++.|+|+|+.++|..|+.+|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~------~~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDP------GSKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCC------CCCCCEEEEEcCHHHHHHHHHHhC
Confidence 5789999999999999999999999999999999642 256889999999999999999874
No 17
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=99.14 E-value=8.9e-11 Score=116.26 Aligned_cols=145 Identities=28% Similarity=0.401 Sum_probs=106.6
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC-----CHHHHHHHHHHHHHHHHhhh
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG-----TPEQIAKAEQLINDVLAEAE 203 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG-----t~E~V~kA~~lI~elI~e~~ 203 (669)
.++.+.||..+++.|||+.|++.|.|++.++++|.|+.. +..|+|.. ++..+.+|...|..+-.-..
T Consensus 8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~--------~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~ 79 (194)
T COG1094 8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK--------TGSVTIRTTRKTEDPLALLKARDVVKAIGRGFP 79 (194)
T ss_pred ceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC--------CCeEEEEecCCCCChHHHHHHHHHHHHHhcCCC
Confidence 567899999999999999999999999999999999643 33444433 57788999988877644321
Q ss_pred cCCCCcchhcccCC-CCCcEEE---Eee-CC----CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEE
Q 005922 204 SGGSGIVARRLTGQ-AGSDHFA---MKI-PN----NKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQI 274 (669)
Q Consensus 204 ~~~~~~~~rr~~~~-~~~~t~~---I~V-P~----~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtI 274 (669)
.. ..-++... .-.+.++ +.- +. ...|+|||++|.+.+-|++.|+|.|.|. +.+|.|
T Consensus 80 pe----~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~-----------g~tVai 144 (194)
T COG1094 80 PE----KALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY-----------GKTVAI 144 (194)
T ss_pred HH----HHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe-----------CcEEEE
Confidence 10 00001000 0001111 111 11 2468999999999999999999999996 569999
Q ss_pred EcCHHHHHHHHHHHHHHHhhcc
Q 005922 275 DGTSEQIESAKQLVNEVISENR 296 (669)
Q Consensus 275 tG~peqVq~Ak~LI~dlL~e~~ 296 (669)
.|..++|+.|++.|+++|+...
T Consensus 145 iG~~~~v~iAr~AVemli~G~~ 166 (194)
T COG1094 145 IGGFEQVEIAREAVEMLINGAP 166 (194)
T ss_pred ecChhhhHHHHHHHHHHHcCCC
Confidence 9999999999999999998743
No 18
>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=99.13 E-value=3.7e-11 Score=97.48 Aligned_cols=60 Identities=35% Similarity=0.607 Sum_probs=54.3
Q ss_pred EEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHH
Q 005922 222 HFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLV 288 (669)
Q Consensus 222 t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI 288 (669)
|++|.||.+++++|||++|++||+|+++|||+|.|..+ + ++..|+|+|+.++|++|++||
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 57899999999999999999999999999999999632 2 456999999999999999987
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=99.12 E-value=6.4e-11 Score=96.69 Aligned_cols=62 Identities=29% Similarity=0.498 Sum_probs=56.3
Q ss_pred eEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHH
Q 005922 130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLIN 196 (669)
Q Consensus 130 t~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~ 196 (669)
+++|.||..++++|||++|++||+|+++|||+|.|.+. +..++.|+|+|+.++|.+|+.+|+
T Consensus 1 ~~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~-----~~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDP-----GSKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred CeEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCC-----CCCCCEEEEEcCHHHHHHHHHHhC
Confidence 36899999999999999999999999999999999854 257899999999999999999873
No 20
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.12 E-value=2.1e-10 Score=93.35 Aligned_cols=63 Identities=43% Similarity=0.647 Sum_probs=56.2
Q ss_pred EEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHH
Q 005922 223 FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVN 289 (669)
Q Consensus 223 ~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~ 289 (669)
++|.||.+++++|||++|++|++|+++|+|+|.|.... ++..++.|+|.|+.++|+.|+.+|+
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~----~~~~~~~v~i~G~~~~v~~a~~~i~ 64 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSG----SGSEERIVTITGTPEAVEKAKELIL 64 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCC----CCCCceEEEEEcCHHHHHHHHHHhC
Confidence 57999999999999999999999999999999997432 1456899999999999999999874
No 21
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.10 E-value=3.7e-11 Score=97.51 Aligned_cols=60 Identities=42% Similarity=0.732 Sum_probs=54.6
Q ss_pred eEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHH
Q 005922 130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLI 195 (669)
Q Consensus 130 t~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI 195 (669)
|++|+||...+++||||+|++||+|+++|+|+|.|+++ + .+..|+|+|+.++|++|+++|
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 57899999999999999999999999999999999754 2 345999999999999999987
No 22
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.06 E-value=1.9e-10 Score=94.54 Aligned_cols=59 Identities=27% Similarity=0.469 Sum_probs=53.8
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCC-HHHHHHHHHHHH
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGT-PEQIAKAEQLIN 196 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt-~E~V~kA~~lI~ 196 (669)
.+..|.||..++|+||||+|++||+|+++|||+|.|++ ++.|.|+|+ .++|++|+++|+
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 46889999999999999999999999999999999974 357999998 999999999884
No 23
>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=99.05 E-value=2.7e-10 Score=92.67 Aligned_cols=63 Identities=41% Similarity=0.655 Sum_probs=56.9
Q ss_pred EEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHH
Q 005922 131 KKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLIN 196 (669)
Q Consensus 131 ~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~ 196 (669)
.+|.||..++++|||++|++|++|+++|+|+|.|....+ ...+++|+|.|+.++|.+|+.+|.
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~---~~~~~~v~i~G~~~~v~~a~~~i~ 64 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS---GSEERIVTITGTPEAVEKAKELIL 64 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC---CCCceEEEEEcCHHHHHHHHHHhC
Confidence 689999999999999999999999999999999986432 467899999999999999998873
No 24
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=98.98 E-value=2.6e-10 Score=126.14 Aligned_cols=211 Identities=19% Similarity=0.217 Sum_probs=155.5
Q ss_pred HHHHHHHHHHccccccCC-CCCCCCceecCCCCCCCCccccccCCcccccCCCCCCCCCCCCCCCCCCCceEEEEecccc
Q 005922 61 QAAKRRAEQIAARLCNSV-SAEAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPVSYGGYQSMGTSKKIEIPNIR 139 (669)
Q Consensus 61 e~IkkIaeEtaARI~I~~-~~~~ERiisisg~~~~eav~kA~~~i~~~l~~i~~~~~~~~s~g~~~~~~vt~rIlVP~~~ 139 (669)
.+||.|++.+.+||.+.. .+..||...+.+- ...+.++...+..++.... .|.+.+-||...
T Consensus 88 snik~l~~~t~aKi~L~~ed~g~e~~~~~~~~--p~~v~~a~a~~~~~~~~~~---------------pvk~~lsvpqr~ 150 (608)
T KOG2279|consen 88 SNIKQLRKQTGAKIDLDTEDVGDERVLLISGF--PVQVCKAKAAIHQILTENT---------------PVSEQLSVPQRS 150 (608)
T ss_pred CCcchhhcccccceecCcccCCcccchhhccC--CCCCChHHHHHHHHHhcCC---------------cccccccchhhh
Confidence 379999999999999995 3477887777764 4456666666666655322 267888899999
Q ss_pred ccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCC------------
Q 005922 140 VGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGS------------ 207 (669)
Q Consensus 140 vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~------------ 207 (669)
+++|||++|++|+.|++-++|+|.+++. -.+...+++.|.+...-++.|..+|.+.+.+++....
T Consensus 151 ~~~i~grgget~~si~~ss~aki~~d~n---gr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvpr 227 (608)
T KOG2279|consen 151 VGRIIGRGGETIRSICKSSGAKITCDKN---GRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPR 227 (608)
T ss_pred cccccccchhhhcchhcccccccccccc---cccccccceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCC
Confidence 9999999999999999999999999865 2456678999999888888899999888776532100
Q ss_pred --Cc------------------chhc--cc---------------------------------CCCCCcEEEEeeCCCce
Q 005922 208 --GI------------------VARR--LT---------------------------------GQAGSDHFAMKIPNNKV 232 (669)
Q Consensus 208 --~~------------------~~rr--~~---------------------------------~~~~~~t~~I~VP~~~v 232 (669)
.. ..+. +. ........+|.||+.++
T Consensus 228 k~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~ls 307 (608)
T KOG2279|consen 228 KQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILS 307 (608)
T ss_pred CCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCcccc
Confidence 00 0000 00 00012345899999999
Q ss_pred eeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHH
Q 005922 233 GLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVI 292 (669)
Q Consensus 233 G~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL 292 (669)
|.|||+.|++|+.+...+++++.|.-.... ..-....+++|.|....++.|.+||...+
T Consensus 308 g~lig~~gey~s~yssasn~~~hi~t~pyt-~~v~~~qic~~egkqh~~n~vl~ml~~~~ 366 (608)
T KOG2279|consen 308 GDLIGHAGEYLSVYSSASNHPNHIWTQPYT-SRVLQLQICVNEGKQHYENSVLEMLTVHV 366 (608)
T ss_pred cchhhhhhhhhhhhhhccCccceEEecccc-chhhhhhhheecchhHHHHHHHhhhhccC
Confidence 999999999999999999999998643211 00111256889999999999999988443
No 25
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=98.94 E-value=5.5e-10 Score=123.57 Aligned_cols=143 Identities=32% Similarity=0.541 Sum_probs=122.5
Q ss_pred CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCC
Q 005922 128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGS 207 (669)
Q Consensus 128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~ 207 (669)
.+.+++.|+...|-+||||.|.+||.|++.+++||.+..+. -..+++.++.|-+..+.+|+.+|++++.+..
T Consensus 67 ~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed----~g~e~~~~~~~~p~~v~~a~a~~~~~~~~~~---- 138 (608)
T KOG2279|consen 67 DIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED----VGDERVLLISGFPVQVCKAKAAIHQILTENT---- 138 (608)
T ss_pred heeeeEeecccceeeeeccccCCcchhhcccccceecCccc----CCcccchhhccCCCCCChHHHHHHHHHhcCC----
Confidence 37899999999999999999999999999999999997543 3457778888899999999999999888743
Q ss_pred CcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHH
Q 005922 208 GIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQL 287 (669)
Q Consensus 208 ~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~L 287 (669)
.+.+.+.||...+++|||++|.+|++|+..++++|.+... +.+-..+.+.|.+....++.|+.|
T Consensus 139 ------------pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n----gr~g~~~~~~i~~qqk~~~~a~~~ 202 (608)
T KOG2279|consen 139 ------------PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN----GRLGLSRLIKISGQQKEVAAAKHL 202 (608)
T ss_pred ------------cccccccchhhhcccccccchhhhcchhcccccccccccc----cccccccceecccccchHHHHHhh
Confidence 3456778999999999999999999999999999998632 334557788888888889999999
Q ss_pred HHHHHhh
Q 005922 288 VNEVISE 294 (669)
Q Consensus 288 I~dlL~e 294 (669)
+.+.|++
T Consensus 203 ~~~~~~e 209 (608)
T KOG2279|consen 203 ILEKVSE 209 (608)
T ss_pred hhccccc
Confidence 9888866
No 26
>smart00322 KH K homology RNA-binding domain.
Probab=98.92 E-value=6.8e-09 Score=83.67 Aligned_cols=67 Identities=42% Similarity=0.698 Sum_probs=59.7
Q ss_pred cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHh
Q 005922 221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVIS 293 (669)
Q Consensus 221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~ 293 (669)
.+.+|.||.+++++|||++|++|++|++.|+|+|.+... ......|+|.|+.+.|+.|+.+|.++|+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~------~~~~~~v~i~g~~~~v~~a~~~i~~~~~ 69 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPED------GSEERVVEITGPPENVEKAAELILEILE 69 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCC------CCCccEEEEEcCHHHHHHHHHHHHHHhC
Confidence 467899999999999999999999999999999999632 1257899999999999999999999873
No 27
>smart00322 KH K homology RNA-binding domain.
Probab=98.83 E-value=9.1e-09 Score=82.92 Aligned_cols=66 Identities=42% Similarity=0.711 Sum_probs=59.9
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHH
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVL 199 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI 199 (669)
++.+|.||...+++|||++|.+|++|+++|+++|.+.... ....+|+|.|+.+++..|+.+|.+++
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-----~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-----SEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-----CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 6789999999999999999999999999999999997442 25688999999999999999999876
No 28
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=98.78 E-value=2.7e-09 Score=104.94 Aligned_cols=123 Identities=18% Similarity=0.182 Sum_probs=83.3
Q ss_pred HHHHHHHHHHccccccCCCCCCCCceec--CCCCCCCCccccccCCcccccCCC-CCCCCCCCCCCCCCCCceEEEEecc
Q 005922 61 QAAKRRAEQIAARLCNSVSAEAKRPRVE--NGSGGFDSADKGFSSPPSDLKSIP-APSAIPVSYGGYQSMGTSKKIEIPN 137 (669)
Q Consensus 61 e~IkkIaeEtaARI~I~~~~~~ERiisi--sg~~~~eav~kA~~~i~~~l~~i~-~~~~~~~s~g~~~~~~vt~rIlVP~ 137 (669)
++|++|.++++++|.+.+. +..+.| ... +.+++.+|...|........ ..+....... -+..-+.|..
T Consensus 18 ~~Ik~I~~~tgv~I~Id~~---~g~V~I~~~t~-d~~~i~kA~~~I~~i~~gf~~e~A~~l~gd~-----y~~~Vi~I~~ 88 (172)
T TIGR03665 18 ETKKEIEERTGVKLDIDSE---TGEVKIEEEDE-DPLAVMKAREVVKAIGRGFSPEKALKLLDDD-----YMLEVIDLKE 88 (172)
T ss_pred hHHHHHHHHhCcEEEEEcC---CceEEEecCCC-CHHHHHHHHHHHHHHHcCCCHHHHHHhcCCc-----ceEEEEEhhh
Confidence 7999999999999999863 234555 221 34556666665544322100 0000000001 0112233333
Q ss_pred ---------ccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh
Q 005922 138 ---------IRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA 202 (669)
Q Consensus 138 ---------~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~ 202 (669)
..+|+|||++|+|+|.|++.|+|+|.|.. +.|.|.|+.++|+.|+++|++||+..
T Consensus 89 ~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~----------~~v~i~G~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 89 YGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG----------KTVGIIGDPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred ccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC----------CEEEEECCHHHHHHHHHHHHHHHcCC
Confidence 36999999999999999999999999962 56999999999999999999999654
No 29
>PF13014 KH_3: KH domain
Probab=98.78 E-value=1.1e-08 Score=78.07 Aligned_cols=43 Identities=51% Similarity=0.772 Sum_probs=37.4
Q ss_pred ceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEc
Q 005922 231 KVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDG 276 (669)
Q Consensus 231 ~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG 276 (669)
+|++||||+|++||+|+++|+|+|+|..+. ..++++++|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~---~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPEN---EPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCcc---CCCCCceEEEEEC
Confidence 589999999999999999999999997622 2367799999997
No 30
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.76 E-value=7.5e-09 Score=108.09 Aligned_cols=150 Identities=21% Similarity=0.317 Sum_probs=112.8
Q ss_pred CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh---hc
Q 005922 128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA---ES 204 (669)
Q Consensus 128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~---~~ 204 (669)
.+++.+.||...|+.|+|++|.+||.|+.+|...|+.... ..|-++.++|..|.|+.|++.|...-+.. .-
T Consensus 25 nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr------~eePiF~vTg~~edv~~aRrei~saaeH~~l~~~ 98 (394)
T KOG2113|consen 25 NVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR------GEEPIFPVTGRHEDVRRARREIPSAAEHFGLIRA 98 (394)
T ss_pred ccceeeecCcccceeecccCccccchhhhhhcceeccCCC------CCCCcceeccCchhHHHHhhcCccccceeeeeee
Confidence 4899999999999999999999999999999999998532 34589999999999999999987632221 00
Q ss_pred CCCCc-chhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHH-HH
Q 005922 205 GGSGI-VARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQ-IE 282 (669)
Q Consensus 205 ~~~~~-~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peq-Vq 282 (669)
..... .... .......+..+.||...+++|+|..|++||.|++.+..-|.-.- ...+.++.|+|-++. ++
T Consensus 99 s~s~Sgg~~~-~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v-------~~~~~Vf~Vtg~~~nC~k 170 (394)
T KOG2113|consen 99 SRSFSGGTNG-ASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPV-------RCGEPVFCVTGAPKNCVK 170 (394)
T ss_pred cccccCCCcc-ccccCCCceeeeccceeeeeccccccCccchheecccceEeeec-------cCCCceEEEecCCcchhh
Confidence 00000 0000 01234456778899999999999999999999999999887642 234778999998666 77
Q ss_pred HHH-HHHHHH
Q 005922 283 SAK-QLVNEV 291 (669)
Q Consensus 283 ~Ak-~LI~dl 291 (669)
+|+ ..|+..
T Consensus 171 ra~s~eie~t 180 (394)
T KOG2113|consen 171 RARSCEIEQT 180 (394)
T ss_pred hccccchhhh
Confidence 776 445443
No 31
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.73 E-value=4e-09 Score=104.52 Aligned_cols=123 Identities=17% Similarity=0.198 Sum_probs=81.1
Q ss_pred HHHHHHHHHHccccccCCCCCCCCceecC-C-CCCCCCccccccCCcccccCCC-CCCCCCCCCCCCCCCCceEEE-Eec
Q 005922 61 QAAKRRAEQIAARLCNSVSAEAKRPRVEN-G-SGGFDSADKGFSSPPSDLKSIP-APSAIPVSYGGYQSMGTSKKI-EIP 136 (669)
Q Consensus 61 e~IkkIaeEtaARI~I~~~~~~ERiisis-g-~~~~eav~kA~~~i~~~l~~i~-~~~~~~~s~g~~~~~~vt~rI-lVP 136 (669)
++|+.|.++++++|++.+.. ..+.|. . ..+.+++.+|...|...+.... ..+..... ..+..++ .|.
T Consensus 23 k~Ik~I~e~tg~~I~i~~~~---g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~~e~A~~l~g------d~y~~~Vi~i~ 93 (180)
T PRK13763 23 ETKKEIEERTGVKLEIDSET---GEVIIEPTDGEDPLAVLKARDIVKAIGRGFSPEKALRLLD------DDYVLEVIDLS 93 (180)
T ss_pred hHHHHHHHHHCcEEEEECCC---CeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCHHHHHHHhC------CCceEEEEEhh
Confidence 79999999999999999632 334443 1 1134556666655544332100 00000001 1122221 111
Q ss_pred ---------cccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh
Q 005922 137 ---------NIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA 202 (669)
Q Consensus 137 ---------~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~ 202 (669)
...+|+||||+|+|+|.|++.|||+|.|.. +.|.|.|+.++++.|.+.|++|++..
T Consensus 94 ~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~----------~~v~i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 94 DYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG----------KTVAIIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred hccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC----------CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence 136999999999999999999999999963 33888999999999999999999654
No 32
>PF13014 KH_3: KH domain
Probab=98.73 E-value=8.3e-09 Score=78.80 Aligned_cols=43 Identities=44% Similarity=0.643 Sum_probs=38.8
Q ss_pred cccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC
Q 005922 139 RVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG 183 (669)
Q Consensus 139 ~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG 183 (669)
+||+||||+|++||+|+++|+|+|+|.++ ..++..+|+|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~--~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPE--NEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCc--cCCCCCceEEEEEC
Confidence 47999999999999999999999999873 36788899999987
No 33
>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=98.65 E-value=9e-08 Score=89.17 Aligned_cols=67 Identities=25% Similarity=0.390 Sum_probs=53.9
Q ss_pred CCceeeeecCCchHHHHHHHHhCCeEEeccCCCCC-------------CCCCCccEEEEEcCH---HHHHHHHHHHHHHH
Q 005922 229 NNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPP-------------GDTSTERTVQIDGTS---EQIESAKQLVNEVI 292 (669)
Q Consensus 229 ~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~pp-------------ge~s~er~VtItG~p---eqVq~Ak~LI~dlL 292 (669)
.+++|+|||++|++||+|+++|||+|.|.++.... .+.+++-.|.|++.. +.+++|+++|+++|
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 37899999999999999999999999998652111 112234679999975 89999999999999
Q ss_pred hhc
Q 005922 293 SEN 295 (669)
Q Consensus 293 ~e~ 295 (669)
...
T Consensus 94 ~~~ 96 (120)
T cd02395 94 KPA 96 (120)
T ss_pred ccC
Confidence 864
No 34
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.60 E-value=3.8e-08 Score=112.39 Aligned_cols=150 Identities=25% Similarity=0.328 Sum_probs=102.4
Q ss_pred CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCC-CCC------ccccccCC-HHHH-------HHHH
Q 005922 128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLN-SPT------RSVELMGT-PEQI-------AKAE 192 (669)
Q Consensus 128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~-~~e------RvVtItGt-~E~V-------~kA~ 192 (669)
.+.++-.|..-.+|+|.- |++.+-|.+..|-. .-..||++.-. +.+ .-+.|.|- .+-+ ..|.
T Consensus 452 GVPIk~pVAGIAMGLI~e--g~~~~vLsDI~G~E-DhlGDMDFKVAGT~~GiTAlQMDiKi~Git~eim~~AL~QAk~aR 528 (692)
T COG1185 452 GVPIKAPVAGIAMGLIKE--GDKYAVLSDILGDE-DHLGDMDFKVAGTDDGITALQMDIKIKGITKEIMKKALEQAKGAR 528 (692)
T ss_pred CCcccccccchhccceec--CCceEeeccccccc-cccCCceeEEecCCCcceeeeeeeeecCCCHHHHHHHHHHHHHHH
Confidence 377888899899999955 55444444444433 11233332211 111 33567774 3322 3445
Q ss_pred HHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEE
Q 005922 193 QLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTV 272 (669)
Q Consensus 193 ~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~V 272 (669)
..|+++|.+........ ....-+..+.+.|+.+++..|||++|++||+|.++|||+|.|. ++.+|
T Consensus 529 lhIL~~M~~ai~~pr~e-----ls~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie----------ddGtv 593 (692)
T COG1185 529 LHILIVMNEAISEPRKE-----LSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE----------DDGTV 593 (692)
T ss_pred HHHHHHHHHHHhhhhhh-----hhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec----------CCCcE
Confidence 57777887765433211 1112245678999999999999999999999999999999994 36789
Q ss_pred EEEcC-HHHHHHHHHHHHHHHhhc
Q 005922 273 QIDGT-SEQIESAKQLVNEVISEN 295 (669)
Q Consensus 273 tItG~-peqVq~Ak~LI~dlL~e~ 295 (669)
.|.+. .+.+++|+++|++++++.
T Consensus 594 ~i~~s~~~~~~~ak~~I~~i~~e~ 617 (692)
T COG1185 594 KIAASDGESAKKAKERIEAITREV 617 (692)
T ss_pred EEEecchHHHHHHHHHHHHHHhhc
Confidence 99999 689999999999999874
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=98.57 E-value=1e-07 Score=88.85 Aligned_cols=73 Identities=36% Similarity=0.496 Sum_probs=53.1
Q ss_pred EEEEecc------ccccceeccCCcchhHHHhhcCcEEEEccCCcc---------------CCCCCCccccccCC--HHH
Q 005922 131 KKIEIPN------IRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEA---------------DLNSPTRSVELMGT--PEQ 187 (669)
Q Consensus 131 ~rIlVP~------~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~---------------~p~~~eRvVtItGt--~E~ 187 (669)
.||+||. .++|+|||.+|.|||+|+++|||+|.|..+... ..+.+..|++..-+ .+.
T Consensus 2 ~ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~ 81 (120)
T cd02395 2 EKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEA 81 (120)
T ss_pred CEEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHH
Confidence 4566665 458999999999999999999999999754100 01122333333445 699
Q ss_pred HHHHHHHHHHHHHhhh
Q 005922 188 IAKAEQLINDVLAEAE 203 (669)
Q Consensus 188 V~kA~~lI~elI~e~~ 203 (669)
+++|+.+|++||....
T Consensus 82 ~~~A~~~I~~ll~~~~ 97 (120)
T cd02395 82 LAKAVEAIEELLKPAI 97 (120)
T ss_pred HHHHHHHHHHHhccCC
Confidence 9999999999998644
No 36
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.36 E-value=1.7e-06 Score=100.93 Aligned_cols=89 Identities=31% Similarity=0.445 Sum_probs=70.7
Q ss_pred HHHHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCc
Q 005922 190 KAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTE 269 (669)
Q Consensus 190 kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~e 269 (669)
++...|.++|++..... ... ...-+....|.||.++++.|||.||++||.|+++|||+|.|. ++
T Consensus 553 ~g~~~Il~~m~~al~~p-~~~-----s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~----------d~ 616 (719)
T TIGR02696 553 DARLAILDVMAEAIDTP-DEM-----SPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE----------DD 616 (719)
T ss_pred HHHHHHHHHHHHHHhCc-ccc-----ccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe----------cC
Confidence 34456777777765433 111 111245678999999999999999999999999999999995 26
Q ss_pred cEEEEEcC-HHHHHHHHHHHHHHHhh
Q 005922 270 RTVQIDGT-SEQIESAKQLVNEVISE 294 (669)
Q Consensus 270 r~VtItG~-peqVq~Ak~LI~dlL~e 294 (669)
..|.|.+. .+.+++|+++|+.++..
T Consensus 617 G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 617 GTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 78999998 89999999999999984
No 37
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.33 E-value=9.7e-07 Score=104.38 Aligned_cols=140 Identities=23% Similarity=0.356 Sum_probs=111.6
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCC
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSG 208 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~ 208 (669)
+...+.|-...+..||||+|.+|.+|++++.|+|.+.+. +..+..|++++...++.+|++.|++++.+....
T Consensus 347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~-----~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~--- 418 (753)
T KOG2208|consen 347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ-----GSNNKKVVITGVSANDEKAVEDVEKIIAEILNS--- 418 (753)
T ss_pred eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc-----cCCCCCeEEeccccchhHHHHHHHHHHHhhhcc---
Confidence 567788888999999999999999999999999999752 456788999999999999999999999885431
Q ss_pred cchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCC-eEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHH
Q 005922 209 IVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGA-RIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQL 287 (669)
Q Consensus 209 ~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGA-rIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~L 287 (669)
..+..+.||...+.+|||.+|..|..|++++++ .|++.. +......++|.|....|..++.+
T Consensus 419 -----------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~------~~~~~~~~~~~~~~~dv~~~~~~ 481 (753)
T KOG2208|consen 419 -----------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQN------NNNSSDMVTIRGISKDVEKSVSL 481 (753)
T ss_pred -----------cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCC------CCcccccceEeccccccchhHHH
Confidence 234678999999999999999999999999995 444421 23334557777776666666555
Q ss_pred HHHHHh
Q 005922 288 VNEVIS 293 (669)
Q Consensus 288 I~dlL~ 293 (669)
+..+..
T Consensus 482 ~~~~~~ 487 (753)
T KOG2208|consen 482 LKALKA 487 (753)
T ss_pred HHhhhh
Confidence 554443
No 38
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.32 E-value=7.5e-07 Score=105.30 Aligned_cols=189 Identities=17% Similarity=0.225 Sum_probs=119.6
Q ss_pred CCCCceecCCCCCCCCccccccCCcccccCCCCCCCCCCCCCCCCCCCceEEEEeccccccceeccCCcchhHHHhhcCc
Q 005922 81 EAKRPRVENGSGGFDSADKGFSSPPSDLKSIPAPSAIPVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGA 160 (669)
Q Consensus 81 ~~ERiisisg~~~~eav~kA~~~i~~~l~~i~~~~~~~~s~g~~~~~~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGA 160 (669)
..++.+.+.|. .+++..|...+...+... ....+..++.|....+.+|||++|.+|+.+++++.+
T Consensus 168 ~~~~~i~~~G~--~e~V~~a~~~~~~~~~~~-------------~~r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~ 232 (753)
T KOG2208|consen 168 KKDPQIKLQGV--VESVERAREPILNLIDRK-------------NERSVFEKMNVGITLHSHIIGRGGSNISIIMDETKV 232 (753)
T ss_pred ccCCeeeeecc--hhhhhhhhhhhhhhhhcc-------------cceeEEEEeeccccchhhhcccccccccccccccee
Confidence 44566666665 444444444444433322 112277899999999999999999999999999999
Q ss_pred EEEEccCCccCCCCCCccccccC-------CHHHHHHHHHHHHH-HHHh-hhcCC--------CC---------------
Q 005922 161 KIQVTRDTEADLNSPTRSVELMG-------TPEQIAKAEQLIND-VLAE-AESGG--------SG--------------- 208 (669)
Q Consensus 161 kI~Iskd~e~~p~~~eRvVtItG-------t~E~V~kA~~lI~e-lI~e-~~~~~--------~~--------------- 208 (669)
.|+|..+. .......|.+ ..-.+..++.+++. ++.. ..... .+
T Consensus 233 ~i~ip~sn-----~~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 307 (753)
T KOG2208|consen 233 HIHIPDSN-----KSSPSNKIDGRLNSSSSINVEIQEALTRLESEFDYDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDS 307 (753)
T ss_pred EEEccccc-----ccchhhhhccccccceehhhhhHHHHHHhcChhhhhhhhhccccccccccccchhhHHHhhcchhhh
Confidence 99996332 2222233333 23333333333322 1111 00000 00
Q ss_pred --------cchhcc-------------------cCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCC
Q 005922 209 --------IVARRL-------------------TGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHL 261 (669)
Q Consensus 209 --------~~~rr~-------------------~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ 261 (669)
.....+ ..........+.|-...+..||||+|.+|.+|++++.|.|.+..
T Consensus 308 i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~--- 384 (753)
T KOG2208|consen 308 IFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK--- 384 (753)
T ss_pred hhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc---
Confidence 000000 00011245567788889999999999999999999999999852
Q ss_pred CCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922 262 PPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN 295 (669)
Q Consensus 262 ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~ 295 (669)
..++++.|+|+|....+++|+++|++.+.+.
T Consensus 385 ---~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei 415 (753)
T KOG2208|consen 385 ---QGSNNKKVVITGVSANDEKAVEDVEKIIAEI 415 (753)
T ss_pred ---ccCCCCCeEEeccccchhHHHHHHHHHHHhh
Confidence 2466889999999999999999988877663
No 39
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=98.32 E-value=5e-06 Score=91.83 Aligned_cols=65 Identities=29% Similarity=0.396 Sum_probs=51.4
Q ss_pred CceeeeecCCchHHHHHHHHhCCeEEeccCC-----------CCCCC-CCCccEEEEEcC-HHHHHHHHHHHHHHHhh
Q 005922 230 NKVGLVIGKGGETIKNMQARTGARIQVIPLH-----------LPPGD-TSTERTVQIDGT-SEQIESAKQLVNEVISE 294 (669)
Q Consensus 230 ~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~-----------~ppge-~s~er~VtItG~-peqVq~Ak~LI~dlL~e 294 (669)
++||+|||..|.|.|+|+++|||||.|.++. +.... ..++-.+.|+.+ .|.|++|.++|+.||.+
T Consensus 153 NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 153 NFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQS 230 (554)
T ss_pred ceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHh
Confidence 7999999999999999999999999998630 11111 222334778877 88899999999999986
No 40
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.28 E-value=1.1e-06 Score=84.06 Aligned_cols=104 Identities=20% Similarity=0.365 Sum_probs=76.1
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCC
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSG 208 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~ 208 (669)
-...|+|....+|..||++|++||.|++..|-+|.|-.-. +.+..+|.++|.-.......
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s--------------------~d~~~fI~n~l~Pa~V~~v~ 91 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYS--------------------DDPEEFIKNIFAPAAVRSVT 91 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcC--------------------CCHHHHHHHHcCCCEEEEEE
Confidence 3578888999999999999999999999999999885321 12445565555442211100
Q ss_pred cchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEec
Q 005922 209 IVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVI 257 (669)
Q Consensus 209 ~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~ 257 (669)
.........+.+.|+.+..+++|||+|.+|+.++..++-++.|.
T Consensus 92 -----I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 92 -----IKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred -----EEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 00111134567889999999999999999999999999888774
No 41
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=98.17 E-value=2.3e-06 Score=94.38 Aligned_cols=76 Identities=32% Similarity=0.371 Sum_probs=58.0
Q ss_pred CceEEEEeccc------cccceeccCCcchhHHHhhcCcEEEEcc-----------C-CccCCCCC--CccccccCCHHH
Q 005922 128 GTSKKIEIPNI------RVGVIIGKSGETIKYLQLQSGAKIQVTR-----------D-TEADLNSP--TRSVELMGTPEQ 187 (669)
Q Consensus 128 ~vt~rIlVP~~------~vG~IIGKgGetIK~IqeeTGAkI~Isk-----------d-~e~~p~~~--eRvVtItGt~E~ 187 (669)
.++.||.||.+ +||+|||..|.|+|+|++||||||.|.. + .....+.. +..+++.-+.|.
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 37788888864 4999999999999999999999999943 1 11122222 344455557899
Q ss_pred HHHHHHHHHHHHHhhh
Q 005922 188 IAKAEQLINDVLAEAE 203 (669)
Q Consensus 188 V~kA~~lI~elI~e~~ 203 (669)
|++|+++|+.||.+..
T Consensus 217 i~~Ai~vienli~~av 232 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSAV 232 (554)
T ss_pred HHHHHHHHHHHHHhhc
Confidence 9999999999999743
No 42
>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=98.14 E-value=5.6e-06 Score=97.30 Aligned_cols=89 Identities=25% Similarity=0.352 Sum_probs=67.2
Q ss_pred HHHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCcc
Q 005922 191 AEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTER 270 (669)
Q Consensus 191 A~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er 270 (669)
+...|.++|++....... .....-+....+.||.++++.|||+||++||+|+++|||+|.|. ++.
T Consensus 526 ~~~~I~~~m~~~l~~~~~-----~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~----------ddG 590 (684)
T TIGR03591 526 GRLHILGEMNKVISEPRA-----ELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE----------DDG 590 (684)
T ss_pred HHHHHHHHHHHHHhhhhc-----cccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEe----------cCe
Confidence 334566666665432211 11112245678999999999999999999999999999999995 256
Q ss_pred EEEEEcC-HHHHHHHHHHHHHHHhh
Q 005922 271 TVQIDGT-SEQIESAKQLVNEVISE 294 (669)
Q Consensus 271 ~VtItG~-peqVq~Ak~LI~dlL~e 294 (669)
.|.|.+. .+.+++|+++|+.++.+
T Consensus 591 ~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 591 TVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred EEEEEECcHHHHHHHHHHHHhhhcc
Confidence 8888876 88999999999998765
No 43
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.93 E-value=1.6e-05 Score=94.92 Aligned_cols=88 Identities=22% Similarity=0.339 Sum_probs=68.2
Q ss_pred HHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCe-EEeccCCCCCCCCCCcc
Q 005922 192 EQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGAR-IQVIPLHLPPGDTSTER 270 (669)
Q Consensus 192 ~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGAr-IqI~~~~~ppge~s~er 270 (669)
...|.++|++........ ....-.....|.|+.++++.|||.||.+||.|+++||++ |.|. ++-
T Consensus 661 ~~~Il~~M~~~i~~pr~~-----~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~----------ddg 725 (891)
T PLN00207 661 RKHILAEMSKCSPPPSKR-----LSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ----------DDG 725 (891)
T ss_pred HHHHHHHHHHHHhhhhhh-----hcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC----------CCe
Confidence 345666666655432211 111224567899999999999999999999999999999 8874 257
Q ss_pred EEEEEcC-HHHHHHHHHHHHHHHhh
Q 005922 271 TVQIDGT-SEQIESAKQLVNEVISE 294 (669)
Q Consensus 271 ~VtItG~-peqVq~Ak~LI~dlL~e 294 (669)
.|.|.+. .+.+++|+++|++++.+
T Consensus 726 ~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 726 TVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred eEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 8999987 89999999999999875
No 44
>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=97.87 E-value=2.8e-05 Score=74.56 Aligned_cols=103 Identities=22% Similarity=0.336 Sum_probs=72.7
Q ss_pred eEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCc
Q 005922 130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGI 209 (669)
Q Consensus 130 t~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~ 209 (669)
..-|+|....+|..||++|++||.|++..|-+|.|-. .+.+++ .+|..+|.-......
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe--------------ys~D~~------~fI~N~l~PA~V~~V-- 91 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE--------------YSENLE------EFVANKLAPAEVKNV-- 91 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE--------------cCCCHH------HHHHHcCCCceEEEE--
Confidence 5778899999999999999999999999999998842 222222 233333322111000
Q ss_pred chhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEec
Q 005922 210 VARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVI 257 (669)
Q Consensus 210 ~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~ 257 (669)
......+.....+.|+.+..++.|||+|.||+...+.++-++.|.
T Consensus 92 ---~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 92 ---TVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred ---EEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 000011234567889999999999999999999999999888774
No 45
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.70 E-value=0.00014 Score=75.60 Aligned_cols=75 Identities=15% Similarity=0.271 Sum_probs=51.0
Q ss_pred CcEEEEeeCC------CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCC---------------CCC-ccEEEEEcC
Q 005922 220 SDHFAMKIPN------NKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGD---------------TST-ERTVQIDGT 277 (669)
Q Consensus 220 ~~t~~I~VP~------~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge---------------~s~-er~VtItG~ 277 (669)
..+.+|.||. ++||+|||..|.++|+|+++|+|+|.|-++...... +.. .-.|++..+
T Consensus 91 k~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p 170 (259)
T KOG1588|consen 91 KLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEAP 170 (259)
T ss_pred eEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeCC
Confidence 3456777765 699999999999999999999999999865221110 011 112555566
Q ss_pred HHH----HHHHHHHHHHHHhh
Q 005922 278 SEQ----IESAKQLVNEVISE 294 (669)
Q Consensus 278 peq----Vq~Ak~LI~dlL~e 294 (669)
+.. |..|.+.|+.+|.-
T Consensus 171 ~~ea~~rl~~AleeI~klL~P 191 (259)
T KOG1588|consen 171 PAEAYARLAYALEEIKKLLVP 191 (259)
T ss_pred HHHHHHHHHHHHHHHHHhcCC
Confidence 544 44688888887743
No 46
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.60 E-value=6.8e-05 Score=88.33 Aligned_cols=65 Identities=25% Similarity=0.345 Sum_probs=56.3
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHh
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAE 201 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e 201 (669)
....|.||.++++.|||++|++||+|+++|||+|.|..+ -.+.+...+.+.+++|+++|..++.+
T Consensus 551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd--------G~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD--------GTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC--------eEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 678899999999999999999999999999999999743 24445555789999999999999775
No 47
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.55 E-value=0.00011 Score=86.86 Aligned_cols=90 Identities=31% Similarity=0.428 Sum_probs=67.7
Q ss_pred HHHHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCc
Q 005922 190 KAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTE 269 (669)
Q Consensus 190 kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~e 269 (669)
++...|.++|.+......... .........+.|+.++++.|||.||.+||.|+++||++|.|. ++
T Consensus 528 ~g~~~I~~~M~~aI~~~r~~~-----~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~----------d~ 592 (693)
T PRK11824 528 EGRLHILGKMNEAISEPRAEL-----SPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE----------DD 592 (693)
T ss_pred HHHHHHHHHHHHHhcCChhhh-----cccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC----------CC
Confidence 344566777777654322111 111234567788999999999999999999999999988873 25
Q ss_pred cEEEEEcC-HHHHHHHHHHHHHHHhh
Q 005922 270 RTVQIDGT-SEQIESAKQLVNEVISE 294 (669)
Q Consensus 270 r~VtItG~-peqVq~Ak~LI~dlL~e 294 (669)
..|.|.+. .+.+++|+++|+.++.+
T Consensus 593 G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 593 GTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred ceEEEEcccHHHHHHHHHHHHHhccc
Confidence 78999997 89999999999999865
No 48
>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=97.54 E-value=0.0001 Score=86.33 Aligned_cols=64 Identities=25% Similarity=0.409 Sum_probs=57.1
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC-CHHHHHHHHHHHHHHHHh
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG-TPEQIAKAEQLINDVLAE 201 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG-t~E~V~kA~~lI~elI~e 201 (669)
....|.|+.++++.|||.||.+||.|+++|||+|.|..+ -.|.|.+ +.+.+++|+.+|+.++..
T Consensus 578 ~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~---------G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 578 RIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDD---------GTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred eeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecC---------cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 678999999999999999999999999999999999743 3466655 789999999999999985
No 49
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=97.50 E-value=0.0013 Score=66.32 Aligned_cols=129 Identities=17% Similarity=0.221 Sum_probs=95.1
Q ss_pred EEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcc
Q 005922 131 KKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIV 210 (669)
Q Consensus 131 ~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~ 210 (669)
+.|.+.....-+|+..+|..++.|-...||+|.+..+ +..|.|+|++..++.+...|.+++....
T Consensus 28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~--------~~~i~I~g~k~~~~~i~~~i~~~l~~i~------- 92 (210)
T PF14611_consen 28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS--------ENRIRITGTKSTAEYIEASINEILSNIR------- 92 (210)
T ss_pred eEEEecchheeeeecCCchHHHHHHHhcCceEEEecC--------CcEEEEEccHHHHHHHHHHHHHHHhhcE-------
Confidence 4555567888899999999999998889999999754 4679999999999999999999988732
Q ss_pred hhcccCCCCCcEEEEeeCCCceeeee----cCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEc-----CHHHH
Q 005922 211 ARRLTGQAGSDHFAMKIPNNKVGLVI----GKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDG-----TSEQI 281 (669)
Q Consensus 211 ~rr~~~~~~~~t~~I~VP~~~vG~II----GKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG-----~peqV 281 (669)
+.+|.++.-.--... -.....|+.|++.|++.|...+ ++..+.|+. ..+.+
T Consensus 93 -----------~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~---------~~~~~~i~~~~~~~~~~~~ 152 (210)
T PF14611_consen 93 -----------TEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNP---------DGNKLKISWLASPENEKRA 152 (210)
T ss_pred -----------EEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECC---------CCCeEEEEEEeeccccchH
Confidence 233333321111111 1236679999999999999853 233455554 47889
Q ss_pred HHHHHHHHHHHhh
Q 005922 282 ESAKQLVNEVISE 294 (669)
Q Consensus 282 q~Ak~LI~dlL~e 294 (669)
+.|++|+.-.+..
T Consensus 153 ~~a~RlL~~a~~~ 165 (210)
T PF14611_consen 153 DRAKRLLLWALDY 165 (210)
T ss_pred HHHHHHHHHhccC
Confidence 9999999998864
No 50
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=97.45 E-value=0.00028 Score=70.81 Aligned_cols=102 Identities=26% Similarity=0.359 Sum_probs=71.6
Q ss_pred eEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCc
Q 005922 130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGI 209 (669)
Q Consensus 130 t~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~ 209 (669)
..-+++-.+.+|..||++|++||.|.++.|-+|.|-.-. +.-..+|.++|.-.....
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s--------------------~d~~~fI~nal~Pa~v~~--- 133 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS--------------------EDPAEFIKNALAPAEVLS--- 133 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeC--------------------CCHHHHHHHhcCcceEeE---
Confidence 345556667799999999999999999999888874321 112334444444211100
Q ss_pred chhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEec
Q 005922 210 VARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVI 257 (669)
Q Consensus 210 ~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~ 257 (669)
....+. ......+.|+.+..+++|||+|.+|+.+.+.||-+|.|.
T Consensus 134 V~~~~~---d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~ 178 (190)
T COG0195 134 VNIKED---DGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIE 178 (190)
T ss_pred EEEEeC---CCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEE
Confidence 000000 112678889999999999999999999999999999996
No 51
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=97.41 E-value=0.00045 Score=75.01 Aligned_cols=158 Identities=14% Similarity=0.027 Sum_probs=96.1
Q ss_pred ccceeccCCcchhHHHhhcCcEEEEccCC---ccCC-CCCC--ccccccC-CHHHHHHHHHHHHHHHHhhhcCCCCc-c-
Q 005922 140 VGVIIGKSGETIKYLQLQSGAKIQVTRDT---EADL-NSPT--RSVELMG-TPEQIAKAEQLINDVLAEAESGGSGI-V- 210 (669)
Q Consensus 140 vG~IIGKgGetIK~IqeeTGAkI~Iskd~---e~~p-~~~e--RvVtItG-t~E~V~kA~~lI~elI~e~~~~~~~~-~- 210 (669)
+..++.| |.+..+|++++|+.|.+.... |..+ +..+ -+..|.+ +.|-+++|+..|.-+++.+....... +
T Consensus 106 ~~~~~TR-g~~~d~Ie~~~G~~~~~RGs~~~~El~~vg~~~~pLv~hI~~~T~Ei~~~Ai~RIkgv~~~~~~~~n~~~V~ 184 (531)
T KOG1960|consen 106 TKATSTR-GTSYDHIEGITGTTSASRGSAPAPELPPVGSSEGPLVDHIPPSTAEITSKAIERIKGVFMQDVEINNVRNVY 184 (531)
T ss_pred ccceecc-chhHHhhhhhccceeeccCCCCCccCCCCCCCCCcceeecCCccHHHHHHHHhhCccceeecccccccceEE
Confidence 5566666 999999999999999885321 1111 1222 3445666 78999999999997766543211100 0
Q ss_pred -hhcc---------cC----CCCC--cE---EEEeeCCCc-eeeeecCCchHHHHHHHHhCCeEEeccC---CCCC--CC
Q 005922 211 -ARRL---------TG----QAGS--DH---FAMKIPNNK-VGLVIGKGGETIKNMQARTGARIQVIPL---HLPP--GD 265 (669)
Q Consensus 211 -~rr~---------~~----~~~~--~t---~~I~VP~~~-vG~IIGKGGstIK~Iqe~TGArIqI~~~---~~pp--ge 265 (669)
..++ .. ..+. .. +-+.+|... -+.+=+++-.++.+|+.++++++.|.++ +..+ ++
T Consensus 185 i~~~~sP~~~i~~~V~~~~f~~G~~Y~~k~~v~~~~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~ 264 (531)
T KOG1960|consen 185 ILVRASPLSEIENKVGVQLFSKGRYYPNKALATDKDPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNEGN 264 (531)
T ss_pred EeecCCchhhhccccccccccccccchhheecccCCcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccCccccc
Confidence 0000 00 0010 01 112234333 3445567778899999999999887554 2222 22
Q ss_pred CCC-ccEEEEEcC-HHHHHHHHHHHHHHHhhcccC
Q 005922 266 TST-ERTVQIDGT-SEQIESAKQLVNEVISENRIR 298 (669)
Q Consensus 266 ~s~-er~VtItG~-peqVq~Ak~LI~dlL~e~~~r 298 (669)
++. -+.|-|++. ++.+..|+++|.+|++.+...
T Consensus 265 EsnEPMYI~i~h~~~~g~~~A~r~~~nl~~~v~~~ 299 (531)
T KOG1960|consen 265 ESNEPMYIFSTHGNGNGENGAPRRKWNLEEKVYIN 299 (531)
T ss_pred ccCCceeEEeecCCchhhccchhHHHhHHHHHHHH
Confidence 333 345777766 999999999999999886443
No 52
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=97.40 E-value=0.00018 Score=81.02 Aligned_cols=93 Identities=25% Similarity=0.341 Sum_probs=71.6
Q ss_pred HHHHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCc
Q 005922 190 KAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTE 269 (669)
Q Consensus 190 kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~e 269 (669)
.|+..|.++|.+.+....... .....+...|.|+.+++..+||.+|.++|+|..+||+.-+|. |
T Consensus 571 ~ar~~Il~~m~k~i~~Pr~~~-----~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD-----------e 634 (760)
T KOG1067|consen 571 EARLQILDIMEKNINSPRGSD-----KEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD-----------E 634 (760)
T ss_pred HHHHHHHHHHHhhcCCcccCc-----cccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec-----------C
Confidence 345677777777654332211 122356678999999999999999999999999999777763 5
Q ss_pred cEEEEEcC-HHHHHHHHHHHHHHHhhcccC
Q 005922 270 RTVQIDGT-SEQIESAKQLVNEVISENRIR 298 (669)
Q Consensus 270 r~VtItG~-peqVq~Ak~LI~dlL~e~~~r 298 (669)
.+|+|.-. ...+++|+++|..++..++..
T Consensus 635 ~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~ 664 (760)
T KOG1067|consen 635 GTFSIFAPTQAAMEEAKEFIDGIIKDDQVQ 664 (760)
T ss_pred ceEEEEecCHHHHHHHHHHHHHHhcCcccc
Confidence 68888887 888999999999999875443
No 53
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.38 E-value=0.00015 Score=79.42 Aligned_cols=69 Identities=32% Similarity=0.439 Sum_probs=59.8
Q ss_pred cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhcc
Q 005922 221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENR 296 (669)
Q Consensus 221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~~ 296 (669)
..+.+.|-.++||.|||++|++||+|+..|.++|+|+. ...+-.|+|.|..+.-.+|+..|..+++.+.
T Consensus 47 ~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~-------~~~e~kv~ifg~~~m~~kaka~id~~~~k~e 115 (629)
T KOG0336|consen 47 FPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIK-------CDLEVKVTIFGINHMRKKAKASIDRGQDKDE 115 (629)
T ss_pred CchhhhhhhhhhheeeccCcchhhhhhcccceeEEEec-------cCceeEEEEechHHHHHHHHhhHhhhhhhhh
Confidence 34567889999999999999999999999999999984 2346789999999999999999988887643
No 54
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.17 E-value=0.0001 Score=88.07 Aligned_cols=66 Identities=18% Similarity=0.366 Sum_probs=56.9
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcE-EEEccCCccCCCCCCccccccC-CHHHHHHHHHHHHHHHHhhh
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAK-IQVTRDTEADLNSPTRSVELMG-TPEQIAKAEQLINDVLAEAE 203 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAk-I~Iskd~e~~p~~~eRvVtItG-t~E~V~kA~~lI~elI~e~~ 203 (669)
....|.|+.++++.|||.||.|||.|.++||++ |.|..+ -.|.|.+ +.+.+++|+++|++++.+..
T Consensus 685 ~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd---------g~V~I~a~d~~~i~~A~~~I~~l~~~~~ 752 (891)
T PLN00207 685 LIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD---------GTVKITAKDLSSLEKSKAIISSLTMVPT 752 (891)
T ss_pred eeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC---------eeEEEEeCCHHHHHHHHHHHHHHhcCcC
Confidence 688999999999999999999999999999999 999643 2355544 88999999999999988643
No 55
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.16 E-value=0.00028 Score=77.32 Aligned_cols=71 Identities=24% Similarity=0.284 Sum_probs=62.5
Q ss_pred CCceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922 127 MGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE 203 (669)
Q Consensus 127 ~~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~ 203 (669)
.++.++|-|-+.+||.|||++|++||+|+..|+++|+|.+. ..+-.|+|.|..+--.+|+..|...+++.+
T Consensus 45 ~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~------~~e~kv~ifg~~~m~~kaka~id~~~~k~e 115 (629)
T KOG0336|consen 45 GEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC------DLEVKVTIFGINHMRKKAKASIDRGQDKDE 115 (629)
T ss_pred CCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc------CceeEEEEechHHHHHHHHhhHhhhhhhhh
Confidence 45889999999999999999999999999999999999753 456789999999988899999988887654
No 56
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.14 E-value=0.00045 Score=71.85 Aligned_cols=37 Identities=32% Similarity=0.579 Sum_probs=34.3
Q ss_pred ceEEEEeccc------cccceeccCCcchhHHHhhcCcEEEEc
Q 005922 129 TSKKIEIPNI------RVGVIIGKSGETIKYLQLQSGAKIQVT 165 (669)
Q Consensus 129 vt~rIlVP~~------~vG~IIGKgGetIK~IqeeTGAkI~Is 165 (669)
++.||+||.+ +||+|||.+|.|+|+|+++|+|+|.|.
T Consensus 92 ~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 92 LTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred EEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 7889999976 599999999999999999999999993
No 57
>PRK00106 hypothetical protein; Provisional
Probab=97.07 E-value=0.0026 Score=72.98 Aligned_cols=65 Identities=23% Similarity=0.432 Sum_probs=55.3
Q ss_pred EEEEeeCC-CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhhc
Q 005922 222 HFAMKIPN-NKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEVISEN 295 (669)
Q Consensus 222 t~~I~VP~-~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dlL~e~ 295 (669)
...|.+|+ ++.|+||||.|.|||.|...|||.|.|. ++...|+|++. +---+.|+.-++.||.+.
T Consensus 226 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliid---------dtp~~v~lS~fdpvRReiAr~~le~Li~dg 292 (535)
T PRK00106 226 ITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID---------DTPEVVVLSGFDPIRREIARMTLESLIKDG 292 (535)
T ss_pred eeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc---------CCCCeEEEeCCChHHHHHHHHHHHHHHHcC
Confidence 44677887 7899999999999999999999999994 45678999996 888888888888888664
No 58
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=97.06 E-value=0.0024 Score=73.11 Aligned_cols=65 Identities=23% Similarity=0.430 Sum_probs=54.8
Q ss_pred EEEEeeCC-CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhhc
Q 005922 222 HFAMKIPN-NKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEVISEN 295 (669)
Q Consensus 222 t~~I~VP~-~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dlL~e~ 295 (669)
...|.+|+ ++.|+||||.|.|||.|...||+.|.|. ++...|+|++. +---+.|+.-|+.||.+.
T Consensus 205 ~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid---------dtp~~v~ls~fdp~rreia~~~l~~li~dg 271 (514)
T TIGR03319 205 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---------DTPEAVILSGFDPVRREIARMALEKLIQDG 271 (514)
T ss_pred eeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc---------CCCCeEEecCCchHHHHHHHHHHHHHHHcC
Confidence 34677887 7899999999999999999999999994 45678999996 777788888888888654
No 59
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.93 E-value=0.00088 Score=77.53 Aligned_cols=67 Identities=28% Similarity=0.431 Sum_probs=57.2
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC-CHHHHHHHHHHHHHHHHhhhc
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG-TPEQIAKAEQLINDVLAEAES 204 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG-t~E~V~kA~~lI~elI~e~~~ 204 (669)
-.+.|.|+.+.+..|||++|++||+|.++|||+|.|..+ -.|.|.+ +.+.+.+|++.|.+++++...
T Consensus 552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idiedd---------Gtv~i~~s~~~~~~~ak~~I~~i~~e~ev 619 (692)
T COG1185 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD---------GTVKIAASDGESAKKAKERIEAITREVEV 619 (692)
T ss_pred ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCC---------CcEEEEecchHHHHHHHHHHHHHHhhccc
Confidence 567888999999999999999999999999999999732 3466666 458999999999999987554
No 60
>PRK12704 phosphodiesterase; Provisional
Probab=96.92 E-value=0.0041 Score=71.44 Aligned_cols=64 Identities=22% Similarity=0.422 Sum_probs=52.4
Q ss_pred EEEEeeCC-CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhh
Q 005922 222 HFAMKIPN-NKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEVISE 294 (669)
Q Consensus 222 t~~I~VP~-~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dlL~e 294 (669)
...|.+|+ ++.|+||||.|.|||.|...||+.|.|. ++...|+|++. +-.-+.|+..++.+|..
T Consensus 211 ~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid---------dtp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 211 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---------DTPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred eeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc---------CCCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 34667887 7899999999999999999999999994 45678999996 66666777777777654
No 61
>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=96.87 E-value=0.0017 Score=70.72 Aligned_cols=94 Identities=23% Similarity=0.433 Sum_probs=65.2
Q ss_pred cccceeccCCcchhHHHhhc-CcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCC
Q 005922 139 RVGVIIGKSGETIKYLQLQS-GAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQ 217 (669)
Q Consensus 139 ~vG~IIGKgGetIK~IqeeT-GAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~ 217 (669)
-+|..||++|.+|+.|.++. |-+|.|-.-.+ + -..+|...|.-...... ....
T Consensus 244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~--------------d------~~~fi~nal~Pa~v~~v-----~i~~- 297 (341)
T TIGR01953 244 PVGACVGPKGSRIQAISKELNGEKIDIIEYSD--------------D------PAEFIANALSPAKVISV-----EVLD- 297 (341)
T ss_pred cceeeECCCCchHHHHHHHhCCCeEEEEEcCC--------------C------HHHHHHHhcCCceEEEE-----EEEc-
Confidence 39999999999999999998 88888853221 1 11123332221111000 0000
Q ss_pred CCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 005922 218 AGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIP 258 (669)
Q Consensus 218 ~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~ 258 (669)
.......+.|+.+..++.|||+|.|||...+.||++|.|..
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 11246789999999999999999999999999999999973
No 62
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.83 E-value=0.0015 Score=71.72 Aligned_cols=95 Identities=20% Similarity=0.256 Sum_probs=66.4
Q ss_pred ccccceeccCCcchhHHHhhc-CcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccC
Q 005922 138 IRVGVIIGKSGETIKYLQLQS-GAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTG 216 (669)
Q Consensus 138 ~~vG~IIGKgGetIK~IqeeT-GAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~ 216 (669)
+-+|..||++|.+|+.|.++. |-+|.|-.-.+ + -..+|...|.-...... ...
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~--------------D------~~~fI~Nal~Pa~V~~V------~i~ 304 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSN--------------V------PEIFIARALAPAIISSV------KIE 304 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCC--------------C------HHHHHHHhCCCceeeEE------EEc
Confidence 349999999999999999998 88888853221 1 11233333322111000 000
Q ss_pred CCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccC
Q 005922 217 QAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPL 259 (669)
Q Consensus 217 ~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~ 259 (669)
.......+.|+.+..++.|||+|.|||...+.||.+|.|..-
T Consensus 305 -~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~ 346 (374)
T PRK12328 305 -EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI 346 (374)
T ss_pred -CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence 112467889999999999999999999999999999999854
No 63
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.82 E-value=0.0015 Score=69.87 Aligned_cols=68 Identities=22% Similarity=0.395 Sum_probs=57.0
Q ss_pred EEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhhcc
Q 005922 223 FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEVISENR 296 (669)
Q Consensus 223 ~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dlL~e~~ 296 (669)
..++|+..+++.|||+.|.|.|+|+++|+|+|.+.. + +.....|+|+|- .++|.+|.+.|..+|.+++
T Consensus 59 ~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~----p--~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 59 SSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPR----P--NTNKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred hhhhhhHHHhhhhhcccchHHHHHHHhhccceEccC----C--CCCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 467899999999999999999999999999999853 1 223445666655 9999999999999999876
No 64
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.78 E-value=0.001 Score=71.19 Aligned_cols=70 Identities=21% Similarity=0.240 Sum_probs=59.9
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCC-CCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLN-SPTRSVELMGTPEQIAKAEQLINDVLAEAE 203 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~-~~eRvVtItGt~E~V~kA~~lI~elI~e~~ 203 (669)
+...|+|....++.|||++|.|.|+|++||+++|.+++. + ..+.++.+....+.|.+|.+.|.-+|.+..
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p-----~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP-----NTNKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC-----CCCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 677889999999999999999999999999999999853 4 334455555689999999999999998865
No 65
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.77 E-value=0.0023 Score=66.31 Aligned_cols=62 Identities=31% Similarity=0.365 Sum_probs=54.7
Q ss_pred EEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhh
Q 005922 223 FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEVISE 294 (669)
Q Consensus 223 ~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dlL~e 294 (669)
+.+.||.+++++|||++|.+|+.|.++|+|+|.|- .+-.|.|++. .+.+++|+++|+++-++
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig----------~NG~VwI~~~~~~~~~~a~~~I~~~e~~ 209 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG----------QNGRIWIKGPDEEDEEIAIEAIKKIERE 209 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc----------CCcEEEEeeCCHHHHHHHHHHHHHHHhh
Confidence 56889999999999999999999999999999983 1468999998 77899999999876655
No 66
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.75 E-value=0.0023 Score=70.19 Aligned_cols=94 Identities=19% Similarity=0.345 Sum_probs=65.8
Q ss_pred cccceeccCCcchhHHHhhc-CcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCC
Q 005922 139 RVGVIIGKSGETIKYLQLQS-GAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQ 217 (669)
Q Consensus 139 ~vG~IIGKgGetIK~IqeeT-GAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~ 217 (669)
-+|..||++|.+|+.|.++. |-+|.|-.-.+ + ...+|...|.-...... ....
T Consensus 246 pvGa~iG~~G~rI~~i~~el~gekIdiv~~s~--------------d------~~~fi~nal~Pa~v~~v------~i~~ 299 (362)
T PRK12327 246 AKGACVGPKGQRVQNIVSELKGEKIDIIDWSE--------------D------PAEFVANALSPAKVVSV------EVDD 299 (362)
T ss_pred chheeECCCChhHHHHHHHhCCCeEEEEEcCC--------------C------HHHHHHHhCCCceEEEE------EEEc
Confidence 39999999999999999998 88888853221 1 12233333322111000 0000
Q ss_pred CCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 005922 218 AGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIP 258 (669)
Q Consensus 218 ~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~ 258 (669)
.......+.|+.+..++.|||+|.|||...+.||++|.|..
T Consensus 300 ~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 300 EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 12346789999999999999999999999999999999974
No 67
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.61 E-value=0.0026 Score=70.93 Aligned_cols=92 Identities=28% Similarity=0.437 Sum_probs=64.1
Q ss_pred ccceeccCCcchhHHHhhc-CcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCCC
Q 005922 140 VGVIIGKSGETIKYLQLQS-GAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQA 218 (669)
Q Consensus 140 vG~IIGKgGetIK~IqeeT-GAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~ 218 (669)
||..||++|.+|+.|.++. |=+|.|..-.+ + -..+|...|.-...... .... .
T Consensus 279 vGacVG~kG~RI~~I~~eL~gEkIDVI~ys~--------------D------p~~fI~NaLsPA~V~~V-----~i~~-~ 332 (449)
T PRK12329 279 VGACIGARGSRIQAVVNELRGEKIDVIRWSP--------------D------PATYIANALSPARVDEV-----RLVD-P 332 (449)
T ss_pred hhccCCCCcchHHHHHHHhCCCeEEEEEcCC--------------C------HHHHHHHhcCCceeeEE-----EEEc-C
Confidence 9999999999999999998 88888853211 1 11233332222111000 0000 1
Q ss_pred CCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEec
Q 005922 219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVI 257 (669)
Q Consensus 219 ~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~ 257 (669)
......+.|+.+..++.|||+|.|||...+.||.+|.|.
T Consensus 333 ~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~ 371 (449)
T PRK12329 333 EGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIK 371 (449)
T ss_pred CCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccc
Confidence 124578999999999999999999999999999999996
No 68
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=96.46 E-value=0.0045 Score=70.18 Aligned_cols=92 Identities=24% Similarity=0.445 Sum_probs=64.8
Q ss_pred ccceeccCCcchhHHHhhc-CcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCCC
Q 005922 140 VGVIIGKSGETIKYLQLQS-GAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQA 218 (669)
Q Consensus 140 vG~IIGKgGetIK~IqeeT-GAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~ 218 (669)
||..||++|.+|+.|.++. |-+|.|..-.+ + -..+|...|.-...... ... .
T Consensus 247 vga~vG~~G~ri~~i~~el~ge~Idiv~~s~--------------d------~~~fi~nal~pa~v~~v------~~~-~ 299 (470)
T PRK09202 247 VGACVGMRGSRIQAISNELGGEKIDIILWSD--------------D------PAQFIINALSPAEVSSV------VVD-E 299 (470)
T ss_pred hHccCCCCCchHHHHHHHhCCCeEEEEEcCC--------------C------HHHHHHHhCCCCEEEEE------EEe-C
Confidence 9999999999999999998 88888853211 1 11133332222111000 000 0
Q ss_pred CCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 005922 219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIP 258 (669)
Q Consensus 219 ~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~ 258 (669)
....+.+.|+.+..++.|||+|.|||...+.||.+|.|..
T Consensus 300 ~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 300 DEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred CCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 1246789999999999999999999999999999999975
No 69
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=96.43 E-value=0.0035 Score=62.93 Aligned_cols=55 Identities=27% Similarity=0.419 Sum_probs=49.6
Q ss_pred cccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhh
Q 005922 139 RVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAE 203 (669)
Q Consensus 139 ~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~ 203 (669)
..|+|||++|.|.+.|++-|+|.|.|-. ..|.|.|..++|..|++.|+.||....
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g----------~tVaiiG~~~~v~iAr~AVemli~G~~ 166 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYG----------KTVAIIGGFEQVEIAREAVEMLINGAP 166 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeC----------cEEEEecChhhhHHHHHHHHHHHcCCC
Confidence 4799999999999999999999999963 359999999999999999999988643
No 70
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=96.38 E-value=0.0027 Score=67.40 Aligned_cols=128 Identities=17% Similarity=0.194 Sum_probs=87.3
Q ss_pred HHHHHHHHHHccccccCCCCCCCCceecCCCCCCCCccccccCCccccc------CCCCCCCCCCCCCCCCCCCceEEEE
Q 005922 61 QAAKRRAEQIAARLCNSVSAEAKRPRVENGSGGFDSADKGFSSPPSDLK------SIPAPSAIPVSYGGYQSMGTSKKIE 134 (669)
Q Consensus 61 e~IkkIaeEtaARI~I~~~~~~ERiisisg~~~~eav~kA~~~i~~~l~------~i~~~~~~~~s~g~~~~~~vt~rIl 134 (669)
..||.|+.++..+|+-+- -..|.+..+++. .+.+..|.+.|....+ .+..... ..-+.......+..+-
T Consensus 46 ~kikalr~KTqtyi~tPs-r~eePiF~vTg~--~edv~~aRrei~saaeH~~l~~~s~s~Sg--g~~~~s~s~qt~sy~s 120 (394)
T KOG2113|consen 46 CKIKALRAKTQTYIKTPS-RGEEPIFPVTGR--HEDVRRARREIPSAAEHFGLIRASRSFSG--GTNGASASGQTTSYVS 120 (394)
T ss_pred cccchhhhhhcceeccCC-CCCCCcceeccC--chhHHHHhhcCccccceeeeeeecccccC--CCccccccCCCceeee
Confidence 689999999999998763 234577777776 4556667666665332 1111111 1011111233678888
Q ss_pred eccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHH-HHHHH-HHHHHHH
Q 005922 135 IPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQ-IAKAE-QLINDVL 199 (669)
Q Consensus 135 VP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~-V~kA~-~lI~elI 199 (669)
||-..+|+|+|.+|.+||+|++.+..-|... -.+.+.|+.++|-.++ ++++. +.|+..+
T Consensus 121 vP~rvvglvv~~~~~ti~~iqq~tnt~I~T~------v~~~~~Vf~Vtg~~~nC~kra~s~eie~ta 181 (394)
T KOG2113|consen 121 VPLRVVGLVVGPKGATIKRIQQFTNTYIATP------VRCGEPVFCVTGAPKNCVKRARSCEIEQTA 181 (394)
T ss_pred ccceeeeeccccccCccchheecccceEeee------ccCCCceEEEecCCcchhhhccccchhhhh
Confidence 9999999999999999999999999887763 3556788999997776 66666 4555433
No 71
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.36 E-value=0.0049 Score=62.20 Aligned_cols=38 Identities=42% Similarity=0.518 Sum_probs=33.8
Q ss_pred CceEEEEecc------ccccceeccCCcchhHHHhhcCcEEEEc
Q 005922 128 GTSKKIEIPN------IRVGVIIGKSGETIKYLQLQSGAKIQVT 165 (669)
Q Consensus 128 ~vt~rIlVP~------~~vG~IIGKgGetIK~IqeeTGAkI~Is 165 (669)
.++.+|.||- .+||+|||..|.|+|+|++.|+|+|-|.
T Consensus 147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIR 190 (269)
T COG5176 147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIR 190 (269)
T ss_pred cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEe
Confidence 3778888885 4599999999999999999999999995
No 72
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.29 E-value=0.006 Score=63.20 Aligned_cols=66 Identities=27% Similarity=0.324 Sum_probs=54.5
Q ss_pred EEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhc
Q 005922 131 KKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAES 204 (669)
Q Consensus 131 ~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~ 204 (669)
+.|.||..++++|||++|.+|+.|.++++++|.|-.+ -++.+..-+.+.+++|+.+|+++-++...
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N--------G~VwI~~~~~~~~~~a~~~I~~~e~~~~~ 212 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN--------GRIWIKGPDEEDEEIAIEAIKKIEREAHT 212 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC--------cEEEEeeCCHHHHHHHHHHHHHHHhhhhc
Confidence 6688999999999999999999999999999999532 34444555778999999999988777543
No 73
>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=96.25 E-value=0.0071 Score=49.83 Aligned_cols=36 Identities=28% Similarity=0.668 Sum_probs=33.8
Q ss_pred cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEe
Q 005922 221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQV 256 (669)
Q Consensus 221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI 256 (669)
....+.|+.+.++.+|||+|.+|+.+++.++.+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 567899999999999999999999999999999886
No 74
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.25 E-value=0.0019 Score=76.48 Aligned_cols=64 Identities=30% Similarity=0.485 Sum_probs=54.1
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC-CHHHHHHHHHHHHHHHHh
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG-TPEQIAKAEQLINDVLAE 201 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG-t~E~V~kA~~lI~elI~e 201 (669)
....+.|+.++++.|||.||.|||+|.++||++|.|..+ -.|.|++ +.+.+++|+++|+.++.+
T Consensus 554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~---------G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD---------GTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC---------ceEEEEcccHHHHHHHHHHHHHhccc
Confidence 456777899999999999999999999999999988543 2355555 789999999999998865
No 75
>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=96.09 E-value=0.0059 Score=50.31 Aligned_cols=36 Identities=25% Similarity=0.586 Sum_probs=33.8
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEE
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQV 164 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~I 164 (669)
...+|.|+.+.+|.+|||+|.+|+.+++.++-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 578999999999999999999999999999988876
No 76
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=96.02 E-value=0.0065 Score=61.06 Aligned_cols=151 Identities=17% Similarity=0.235 Sum_probs=98.0
Q ss_pred CceEEEEeccccccceeccCCcch-hHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCC
Q 005922 128 GTSKKIEIPNIRVGVIIGKSGETI-KYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGG 206 (669)
Q Consensus 128 ~vt~rIlVP~~~vG~IIGKgGetI-K~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~ 206 (669)
.-+.+|.||..++--|--. ..+| .-|-+..+..|.++-. .-....|.+.-+-+..++.++...|..++.-.....
T Consensus 73 ~e~Rkvpvpp~r~tplk~~-W~kIytPive~lklqiRmNlK---~r~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~D 148 (252)
T KOG3273|consen 73 IETRKVPVPPHRYTPLKDN-WMKIYTPIVEHLKLQIRMNLK---ARSVELRTCKDTEDPSALQKGADFVRAFILGFDIDD 148 (252)
T ss_pred cceeeccCCcccCChHHHh-hHhhhhHHHHhhhheeEeecc---cceeEeecCCCCCChHHHHHHHHHHHHHHhCCcchh
Confidence 3577888888776554211 1122 3466777777766411 012234666667778899999999988876543221
Q ss_pred CCcchhcccCCCCCcEEEE--------eeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCH
Q 005922 207 SGIVARRLTGQAGSDHFAM--------KIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTS 278 (669)
Q Consensus 207 ~~~~~rr~~~~~~~~t~~I--------~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~p 278 (669)
.-..- |+.. .-.++++| .-=...+|+|+||+|.+--.|.+.|..||.+. +..|+|-|.-
T Consensus 149 AiALl-rldd-lflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVla-----------d~kIHiLG~~ 215 (252)
T KOG3273|consen 149 AIALL-RLDD-LFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLA-----------DSKIHILGAF 215 (252)
T ss_pred HHHHH-hhhh-hhheeeeecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEec-----------CceEEEeecc
Confidence 10000 0000 00111221 11224579999999999999999999999986 5689999999
Q ss_pred HHHHHHHHHHHHHHhhc
Q 005922 279 EQIESAKQLVNEVISEN 295 (669)
Q Consensus 279 eqVq~Ak~LI~dlL~e~ 295 (669)
++|..|+..|+.||..+
T Consensus 216 ~niriAR~avcsLIlGs 232 (252)
T KOG3273|consen 216 QNIRIARDAVCSLILGS 232 (252)
T ss_pred hhhHHHHHhhHhhhccC
Confidence 99999999999999764
No 77
>PRK12705 hypothetical protein; Provisional
Probab=95.96 E-value=0.017 Score=66.07 Aligned_cols=64 Identities=22% Similarity=0.372 Sum_probs=47.9
Q ss_pred EEEEeeCC-CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHHhh
Q 005922 222 HFAMKIPN-NKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEVISE 294 (669)
Q Consensus 222 t~~I~VP~-~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dlL~e 294 (669)
...+.+|+ ++.|+||||.|.|||.+...||+.|.|. ++.+.|+|.+. +.--+.|+..++.+|..
T Consensus 199 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliid---------dtp~~V~ls~fdp~rreia~~~l~~Li~d 264 (508)
T PRK12705 199 VSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID---------DTPEAVVISSFNPIRREIARLTLEKLLAD 264 (508)
T ss_pred eeeeecCChHhhccccCccchhHHHHHHhhCCceEec---------CCccchhhcccCccchHHHHHHHHHHHhc
Confidence 34566776 6899999999999999999999999994 33455667766 55556666666655544
No 78
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.92 E-value=0.013 Score=67.30 Aligned_cols=64 Identities=27% Similarity=0.459 Sum_probs=44.6
Q ss_pred ceEEEEecc-ccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC-CHHHHHHHHHHHHHHHH
Q 005922 129 TSKKIEIPN-IRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG-TPEQIAKAEQLINDVLA 200 (669)
Q Consensus 129 vt~rIlVP~-~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG-t~E~V~kA~~lI~elI~ 200 (669)
++-.|.+|+ ++-|+||||.|.|||.|+..|||+|.|+...+ +|+|++ ++-.-+.|+..|+.||.
T Consensus 204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp~--------~v~ls~fdp~rreia~~~l~~li~ 269 (514)
T TIGR03319 204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPE--------AVILSGFDPVRREIARMALEKLIQ 269 (514)
T ss_pred eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCCC--------eEEecCCchHHHHHHHHHHHHHHH
Confidence 445566776 67899999999999999999999999975432 355666 44333444444444443
No 79
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.92 E-value=0.0099 Score=60.07 Aligned_cols=66 Identities=26% Similarity=0.308 Sum_probs=44.7
Q ss_pred CceeeeecCCchHHHHHHHHhCCeEEeccCCC-CCCCCCC---------cc---EEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922 230 NKVGLVIGKGGETIKNMQARTGARIQVIPLHL-PPGDTST---------ER---TVQIDGTSEQIESAKQLVNEVISEN 295 (669)
Q Consensus 230 ~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~-ppge~s~---------er---~VtItG~peqVq~Ak~LI~dlL~e~ 295 (669)
++||+|||..|.|+|+|++.|+|+|-|-+... ..+..+. +. .+.+.-..+.|.+++.++..+|.+.
T Consensus 163 NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adsedki~~~ik~~~n~I~~a 241 (269)
T COG5176 163 NFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSEDKICRLIKSQLNAIREA 241 (269)
T ss_pred ceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchhhhHHHHHHHHHHHHHHH
Confidence 79999999999999999999999999976411 0111111 11 1223333666777777777777764
No 80
>PRK00106 hypothetical protein; Provisional
Probab=95.82 E-value=0.015 Score=66.85 Aligned_cols=64 Identities=25% Similarity=0.434 Sum_probs=45.0
Q ss_pred ceEEEEecc-ccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC-CHHHHHHHHHHHHHHHH
Q 005922 129 TSKKIEIPN-IRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG-TPEQIAKAEQLINDVLA 200 (669)
Q Consensus 129 vt~rIlVP~-~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG-t~E~V~kA~~lI~elI~ 200 (669)
++-.|.+|+ ++-|+||||.|.|||.|+..|||+|.|+...+ .|+|++ ++-.-+.|+..|+.||.
T Consensus 225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp~--------~v~lS~fdpvRReiAr~~le~Li~ 290 (535)
T PRK00106 225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTPE--------VVVLSGFDPIRREIARMTLESLIK 290 (535)
T ss_pred eeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCCC--------eEEEeCCChHHHHHHHHHHHHHHH
Confidence 445566776 67899999999999999999999999975432 355666 44444444444444443
No 81
>PRK02821 hypothetical protein; Provisional
Probab=95.72 E-value=0.018 Score=50.07 Aligned_cols=32 Identities=22% Similarity=0.536 Sum_probs=28.4
Q ss_pred CcEEEEeeCCCceeeeecCCchHHHHHHHHhC
Q 005922 220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTG 251 (669)
Q Consensus 220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TG 251 (669)
...++|.|..+.+|+||||+|.+|+.||..-.
T Consensus 30 ~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 30 GRTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred cEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 36789999999999999999999999997654
No 82
>PRK12704 phosphodiesterase; Provisional
Probab=95.67 E-value=0.017 Score=66.36 Aligned_cols=65 Identities=25% Similarity=0.437 Sum_probs=46.3
Q ss_pred ceEEEEecc-ccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccC-CHHHHHHHHHHHHHHHHh
Q 005922 129 TSKKIEIPN-IRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMG-TPEQIAKAEQLINDVLAE 201 (669)
Q Consensus 129 vt~rIlVP~-~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItG-t~E~V~kA~~lI~elI~e 201 (669)
++-.|.+|+ ++-|+||||.|.|||.|+.-||++|.|+... .+|+|++ ++-.-+.|+..|+.++.+
T Consensus 210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp--------~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP--------EAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCC--------CeEEEecCChhhHHHHHHHHHHHHhc
Confidence 344555666 6789999999999999999999999997443 3466776 444434555555555543
No 83
>PRK00468 hypothetical protein; Provisional
Probab=95.65 E-value=0.017 Score=49.92 Aligned_cols=32 Identities=28% Similarity=0.431 Sum_probs=28.2
Q ss_pred CcEEEEeeCCCceeeeecCCchHHHHHHHHhC
Q 005922 220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTG 251 (669)
Q Consensus 220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TG 251 (669)
...++|.|..+.+|+||||+|.+|+.||..-.
T Consensus 29 ~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~ 60 (75)
T PRK00468 29 SVILELKVAPEDMGKVIGKQGRIAKAIRTVVK 60 (75)
T ss_pred eEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence 46789999999999999999999999997643
No 84
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.28 E-value=0.034 Score=48.16 Aligned_cols=32 Identities=25% Similarity=0.477 Sum_probs=28.2
Q ss_pred CCcEEEEeeCCCceeeeecCCchHHHHHHHHh
Q 005922 219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQART 250 (669)
Q Consensus 219 ~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~T 250 (669)
...+++|.|..+.+|+||||+|.+|+.||..-
T Consensus 28 ~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 28 KTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 35678999999999999999999999999753
No 85
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=95.13 E-value=0.025 Score=63.83 Aligned_cols=96 Identities=27% Similarity=0.390 Sum_probs=71.0
Q ss_pred ccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCCCC
Q 005922 140 VGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAG 219 (669)
Q Consensus 140 vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~~ 219 (669)
.-.+|-+.|+.||+|-++..-+|.|..|... + ..-++|++.|.+++-++..-.. -.+ .
T Consensus 40 ~P~~~~~~~dlik~lAk~lrKRI~iR~dPsv----------l----~~~e~A~~~I~eivP~ea~i~~----i~F----d 97 (637)
T COG1782 40 NPELFAKDGDLIKDLAKDLRKRIIIRPDPSV----------L----KPPEEARKIILEIVPEEAGITD----IYF----D 97 (637)
T ss_pred CHHHhccchhHHHHHHHHHhhceEeccCchh----------c----CCHHHHHHHHHHhCccccCcee----EEe----c
Confidence 3556778899999999999999999755321 1 1236788899999866432110 001 1
Q ss_pred CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEec
Q 005922 220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVI 257 (669)
Q Consensus 220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~ 257 (669)
.++-+++|-.++-|+||||+|+++++|..+||-.-.|.
T Consensus 98 ~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~iv 135 (637)
T COG1782 98 DDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIV 135 (637)
T ss_pred CCCceEEEEecCCceEEecCchHHHHHHHHhCCcceee
Confidence 34557888999999999999999999999999887775
No 86
>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=94.93 E-value=0.07 Score=51.53 Aligned_cols=94 Identities=26% Similarity=0.391 Sum_probs=66.9
Q ss_pred ceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCCCCCc
Q 005922 142 VIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSD 221 (669)
Q Consensus 142 ~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~~ 221 (669)
.++=..++.||+|-++..-+|.|..|... ...=++|.++|.+++-++.. -.+. .+ ..+
T Consensus 19 ~~~~~~~dli~~lAk~lrKRIvvR~dps~--------------l~~~e~A~~~I~~ivP~ea~-i~di---~F----d~~ 76 (145)
T cd02410 19 ELFAEDGDLVKDLAKDLRKRIVIRPDPSV--------------LKPPEEAIKIILEIVPEEAG-ITDI---YF----DDD 76 (145)
T ss_pred HHHhcccHHHHHHHHHHhceEEEcCChhh--------------cCCHHHHHHHHHHhCCCccC-ceee---Ee----cCC
Confidence 44556689999999999999999644210 01125688899998865421 0000 01 123
Q ss_pred EEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEec
Q 005922 222 HFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVI 257 (669)
Q Consensus 222 t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~ 257 (669)
+-++.|-.++-|+||||+|.++++|..+||-+-.|.
T Consensus 77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vv 112 (145)
T cd02410 77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVV 112 (145)
T ss_pred CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEE
Confidence 457888889999999999999999999999988885
No 87
>PRK01064 hypothetical protein; Provisional
Probab=94.82 E-value=0.041 Score=47.91 Aligned_cols=32 Identities=25% Similarity=0.492 Sum_probs=28.1
Q ss_pred CCcEEEEeeCCCceeeeecCCchHHHHHHHHh
Q 005922 219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQART 250 (669)
Q Consensus 219 ~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~T 250 (669)
..+.+++.|..+.+|+||||+|.+|+.||...
T Consensus 28 ~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 28 HTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 34678999999999999999999999999754
No 88
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=94.60 E-value=0.02 Score=65.04 Aligned_cols=66 Identities=17% Similarity=0.358 Sum_probs=55.4
Q ss_pred CceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccc-cCCHHHHHHHHHHHHHHHHhhh
Q 005922 128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVEL-MGTPEQIAKAEQLINDVLAEAE 203 (669)
Q Consensus 128 ~vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtI-tGt~E~V~kA~~lI~elI~e~~ 203 (669)
.+.+.|.|+.+.+..|||.+|.+.|+|+.|||+...|+. ..+.| .-+...+++|+++|..++..+.
T Consensus 596 P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vDe----------~t~~i~A~~~~am~~Ak~~I~~i~~~~~ 662 (760)
T KOG1067|consen 596 PVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVDE----------GTFSIFAPTQAAMEEAKEFIDGIIKDDQ 662 (760)
T ss_pred ceeeEEeecchhhheeecCccceeeeEeeeccceeeecC----------ceEEEEecCHHHHHHHHHHHHHHhcCcc
Confidence 378999999999999999999999999999997777752 22444 3478999999999999998754
No 89
>PRK00468 hypothetical protein; Provisional
Probab=94.51 E-value=0.031 Score=48.32 Aligned_cols=29 Identities=21% Similarity=0.375 Sum_probs=26.9
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhh
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQ 157 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~Iqee 157 (669)
+.++|.|....+|+||||+|.+|+.||.-
T Consensus 30 ~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 30 VILELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred EEEEEEEChhhCcceecCCChhHHHHHHH
Confidence 78899999999999999999999999864
No 90
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=94.37 E-value=0.016 Score=69.96 Aligned_cols=72 Identities=22% Similarity=0.251 Sum_probs=63.1
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA 202 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~ 202 (669)
...++.||...+.+|||++|.||+.|++-|||.|.|.+-. ..|-.||.+.+.|.++.++.|...|.-+|.+.
T Consensus 1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq--~~Nqaers~~~kg~p~~~r~a~~~I~~~i~Dp 1411 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ--PDNQAERSKAPKGRPPSQRVATSPIGLPIIDP 1411 (2131)
T ss_pred cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcC--CccchhhhcccCCCChhhhhhhccccceeecC
Confidence 5568889999999999999999999999999999998632 23577999999999999999999998877663
No 91
>PRK02821 hypothetical protein; Provisional
Probab=94.21 E-value=0.04 Score=47.88 Aligned_cols=31 Identities=19% Similarity=0.358 Sum_probs=27.7
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcC
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSG 159 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTG 159 (669)
+.++|.|....+|+||||+|.+|+.||.-..
T Consensus 31 ~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 31 RTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred EEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 7899999999999999999999999986533
No 92
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=94.17 E-value=0.022 Score=62.31 Aligned_cols=148 Identities=15% Similarity=0.086 Sum_probs=100.6
Q ss_pred EEEeccc-----cccceeccCCcchhHHHhhcCcEEEEccC--------CccCCCCCCccccccCCHHHHHHHHHHHHHH
Q 005922 132 KIEIPNI-----RVGVIIGKSGETIKYLQLQSGAKIQVTRD--------TEADLNSPTRSVELMGTPEQIAKAEQLINDV 198 (669)
Q Consensus 132 rIlVP~~-----~vG~IIGKgGetIK~IqeeTGAkI~Iskd--------~e~~p~~~eRvVtItGt~E~V~kA~~lI~el 198 (669)
|++|+.+ +-+..-+++-.++..|+.++++++-++.. .....+.+.+|.++.+.++.+.+|.++|.+|
T Consensus 213 k~~v~~~~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMYI~i~h~~~~g~~~A~r~~~nl 292 (531)
T KOG1960|consen 213 KALATDKDPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNEGNESNEPMYIFSTHGNGNGENGAPRRKWNL 292 (531)
T ss_pred heecccCCcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccCcccccccCCceeEEeecCCchhhccchhHHHhH
Confidence 4555544 23445567777888899999998777321 1123456668999999999999999999999
Q ss_pred HHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCC-----CCCCC--ccE
Q 005922 199 LAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPP-----GDTST--ERT 271 (669)
Q Consensus 199 I~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~pp-----ge~s~--er~ 271 (669)
++..-...+.++ ..-.|+|.-|.++|+|+.++-.+++|++..... ..... -.+
T Consensus 293 ~~~v~~~~sr~~--------------------~~~~~~~p~~~y~~~~~~~~~~~~~~~g~~s~~i~p~~~~~~~~p~~~ 352 (531)
T KOG1960|consen 293 EEKVYINLSRGF--------------------HRQAIVGPQGAYVKHIQQETRTRVQIKGQGSAFIEPSTNRESDEPIHL 352 (531)
T ss_pred HHHHHHHhhhhh--------------------hhcccccCCcccccccCCCCCcceeccCccceeecCCCCCCCCCCccc
Confidence 887433221111 011366778889999999999999998652211 11111 234
Q ss_pred EEEEcCHHHHHHHHHHHHHHHhhcccCC
Q 005922 272 VQIDGTSEQIESAKQLVNEVISENRIRN 299 (669)
Q Consensus 272 VtItG~peqVq~Ak~LI~dlL~e~~~r~ 299 (669)
..|.-++..|+.|+-||.++|..+....
T Consensus 353 ~~~~~~~~~~~~~~~~~~~~i~~v~~qy 380 (531)
T KOG1960|consen 353 CIMSHDPNAIQRAKVLCEDLIASVHQQY 380 (531)
T ss_pred ccccCChhhhhhhhhcccccCCcccccC
Confidence 5677779999999999999998765443
No 93
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=93.73 E-value=0.018 Score=69.59 Aligned_cols=70 Identities=23% Similarity=0.262 Sum_probs=59.8
Q ss_pred EEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 222 HFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 222 t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
..++.||...+.+|||++|.+|+.||..||+.|.|.+-+ .++-.||.+.+.|.++.+..|..+|.-+|.+
T Consensus 1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq---~~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ---PDNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred ccccccchhhhhhhhccCcchhhhHhhccceEEehhhcC---CccchhhhcccCCCChhhhhhhccccceeec
Confidence 346778988999999999999999999999999996422 2356699999999999999999999877755
No 94
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=93.38 E-value=0.069 Score=46.31 Aligned_cols=29 Identities=24% Similarity=0.473 Sum_probs=27.0
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhh
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQ 157 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~Iqee 157 (669)
+.++|.|....+|.||||+|.+|+.||.-
T Consensus 30 ~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 30 VTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred EEEEEEECcccccceecCCChhHHHHHHH
Confidence 78999999999999999999999999864
No 95
>PRK01064 hypothetical protein; Provisional
Probab=93.31 E-value=0.073 Score=46.35 Aligned_cols=30 Identities=30% Similarity=0.462 Sum_probs=27.4
Q ss_pred CceEEEEeccccccceeccCCcchhHHHhh
Q 005922 128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQ 157 (669)
Q Consensus 128 ~vt~rIlVP~~~vG~IIGKgGetIK~Iqee 157 (669)
.+.++|.|....+|+||||+|.||+.|+.-
T Consensus 29 ~~~~~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 29 TIIYELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred EEEEEEEECcccceEEECCCCccHHHHHHH
Confidence 378999999999999999999999999874
No 96
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=92.90 E-value=0.057 Score=54.48 Aligned_cols=57 Identities=18% Similarity=0.313 Sum_probs=50.2
Q ss_pred ccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhc
Q 005922 138 IRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAES 204 (669)
Q Consensus 138 ~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~ 204 (669)
..+|+|+||+|.|--.|++-|..+|.+.. ..|.|-|..++|.-|...|+.||.-...
T Consensus 178 RAIGRiaGk~GkTkfaIEn~trtrIVlad----------~kIHiLG~~~niriAR~avcsLIlGspp 234 (252)
T KOG3273|consen 178 RAIGRIAGKGGKTKFAIENVTRTRIVLAD----------SKIHILGAFQNIRIARDAVCSLILGSPP 234 (252)
T ss_pred HHHHHhhcCCCcceeeeeccceeEEEecC----------ceEEEeecchhhHHHHHhhHhhhccCCc
Confidence 45999999999999999999999999963 3488889999999999999999987544
No 97
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=92.80 E-value=0.09 Score=59.43 Aligned_cols=128 Identities=16% Similarity=0.115 Sum_probs=81.6
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCcc-ccccC---CHHHHHHHHHHHHHHHHhhhc
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRS-VELMG---TPEQIAKAEQLINDVLAEAES 204 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRv-VtItG---t~E~V~kA~~lI~elI~e~~~ 204 (669)
..+.|.|+...+..|||.||..|.+++.+.++.|++...-+.. -+--+- |+|.. +.++|.-++.-+.+++++-..
T Consensus 449 ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~-qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~~c~ 527 (657)
T COG5166 449 AEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFG-QSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQQCR 527 (657)
T ss_pred hheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcc-hhhhhcceEEECCccCccchhcccccHHHHHhhhcc
Confidence 5688999999999999999999999999999999996544321 111121 44433 456777777777888876431
Q ss_pred C-CCCcch-------------------hcccCC----CCCcEEEEeeCCCceeeeec---CCchHHHHHHHHhCCeEEec
Q 005922 205 G-GSGIVA-------------------RRLTGQ----AGSDHFAMKIPNNKVGLVIG---KGGETIKNMQARTGARIQVI 257 (669)
Q Consensus 205 ~-~~~~~~-------------------rr~~~~----~~~~t~~I~VP~~~vG~IIG---KGGstIK~Iqe~TGArIqI~ 257 (669)
- ..+..+ |-.-+. .-..++.+-++.+.++..|| -.|++|-.+...-.-.|...
T Consensus 528 f~~Kgdirf~~~~~sI~~v~~~~~~I~rv~kne~v~~~~p~~~~~y~~se~h~~g~gena~R~~ni~~~t~~y~~~ie~~ 607 (657)
T COG5166 528 FNLKGDIRFCPQSTSIFTVDIYSDEIERVIKNETVLLEFPAEMHFYVPSEIHKKGIGENAFRGENIQRVTKLYNSYIEFS 607 (657)
T ss_pred cccccceEEcCCceEEEEEcccccHHHHHhhccceEEecccccccccchhhhhccCCcccccccchhhhhhhhhccceee
Confidence 1 111000 000000 01223445567788888999 67888887776656666554
No 98
>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=92.68 E-value=0.15 Score=60.15 Aligned_cols=96 Identities=26% Similarity=0.352 Sum_probs=69.1
Q ss_pred cceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCCCCC
Q 005922 141 GVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGS 220 (669)
Q Consensus 141 G~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~ 220 (669)
-.++-+.++.||+|-++..-+|.|..|... + ..-++|+++|.+++-++..- .+. .+ ..
T Consensus 35 ~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~----------~----~~~~~~~~~i~~~~~~~~~~-~~~---~f----~~ 92 (630)
T TIGR03675 35 PELFAKDDDLVKELAKKLRKRIVIRPDPSV----------L----LPPEEAIEKIKEIVPEEAGI-TDI---YF----DD 92 (630)
T ss_pred HHHhccchHHHHHHHHHhhceEEEecChhh----------c----CCHHHHHHHHHHhCCCcCCc-eeE---Ee----cC
Confidence 345567789999999999999999644310 0 11255888898888664210 000 01 13
Q ss_pred cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 005922 221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIP 258 (669)
Q Consensus 221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~ 258 (669)
++-++.|-.++-|+||||+|.++++|.++||-+..|..
T Consensus 93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~ 130 (630)
T TIGR03675 93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVR 130 (630)
T ss_pred CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEe
Confidence 45578889999999999999999999999999988863
No 99
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=92.39 E-value=1 Score=45.46 Aligned_cols=66 Identities=27% Similarity=0.475 Sum_probs=57.4
Q ss_pred EEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhcc
Q 005922 222 HFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENR 296 (669)
Q Consensus 222 t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~~ 296 (669)
.+.+.+.....-+|+..+|..+++|....||+|.|. ..+..|.|+|+...|+.+...|.+++...+
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~---------~~~~~i~I~g~k~~~~~i~~~i~~~l~~i~ 92 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVS---------RSENRIRITGTKSTAEYIEASINEILSNIR 92 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEe---------cCCcEEEEEccHHHHHHHHHHHHHHHhhcE
Confidence 456666788899999999999999988889999995 346799999999999999999999997743
No 100
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=92.38 E-value=0.23 Score=55.96 Aligned_cols=67 Identities=30% Similarity=0.535 Sum_probs=49.8
Q ss_pred HHHHHHHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccC
Q 005922 187 QIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPL 259 (669)
Q Consensus 187 ~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~ 259 (669)
....|.++|++.|+....+.... .+ .+.....+.||+.+++.||||+|.+|++|.++.|-+|.|...
T Consensus 458 ~~~~a~~~i~~~i~r~~p~~~eV---e~---~gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~ 524 (604)
T COG1855 458 ALKLAEEEIEREIKRYLPGDVEV---EV---VGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL 524 (604)
T ss_pred hhHHHHHHHHHHHHHhCCCCceE---EE---ecCCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence 45667777777777755431110 01 123456789999999999999999999999999999999854
No 101
>PRK12705 hypothetical protein; Provisional
Probab=92.20 E-value=0.15 Score=58.60 Aligned_cols=38 Identities=24% Similarity=0.462 Sum_probs=31.5
Q ss_pred eEEEEecc-ccccceeccCCcchhHHHhhcCcEEEEccC
Q 005922 130 SKKIEIPN-IRVGVIIGKSGETIKYLQLQSGAKIQVTRD 167 (669)
Q Consensus 130 t~rIlVP~-~~vG~IIGKgGetIK~IqeeTGAkI~Iskd 167 (669)
+-.|.+|+ ++-|+||||.|.|||.|+..||+.|.|+..
T Consensus 199 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt 237 (508)
T PRK12705 199 VSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT 237 (508)
T ss_pred eeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC
Confidence 33444554 678999999999999999999999999754
No 102
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=91.90 E-value=0.56 Score=46.46 Aligned_cols=103 Identities=17% Similarity=0.223 Sum_probs=63.8
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCC
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSG 208 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~ 208 (669)
-.+-|+|-... |..|||+|++||+|++..|-+|.|-... .+ ...+|.+++.-....+.
T Consensus 61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~s--------------~d------~~~fl~Nl~~PA~V~gV- 118 (166)
T PRK06418 61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEKT--------------ND------IKKLAVQLLSPARVLGV- 118 (166)
T ss_pred CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEcC--------------CC------HHHHHHhcCCCcEEEEE-
Confidence 35667777777 9999999999999999999999995332 11 33455555443221110
Q ss_pred cchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEe
Q 005922 209 IVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQV 256 (669)
Q Consensus 209 ~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI 256 (669)
+-++.. .+...+.+.|.......|-.|--..-+-+++.||..|.|
T Consensus 119 --~i~~~~-dG~~~~kV~Vd~~Dk~~l~~k~e~~~~v~~kltgk~v~~ 163 (166)
T PRK06418 119 --NTVWLP-DGTVQYVIRVSRRDRRRLPAKPELLESILSKITGTEVKI 163 (166)
T ss_pred --EEEEeC-CCcEEEEEEECHHHhhcccccHHHHHHHHHHHHCCcEEE
Confidence 001111 123444577777666665555554444567778888776
No 103
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=90.94 E-value=0.17 Score=57.27 Aligned_cols=128 Identities=14% Similarity=0.157 Sum_probs=85.1
Q ss_pred ccceeccCCcchhHHHhhcCcEEEEc--cCCccCCCCCCccc-cccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccC
Q 005922 140 VGVIIGKSGETIKYLQLQSGAKIQVT--RDTEADLNSPTRSV-ELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTG 216 (669)
Q Consensus 140 vG~IIGKgGetIK~IqeeTGAkI~Is--kd~e~~p~~~eRvV-tItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~ 216 (669)
--+|-||+--++.+|++...|-+.+. ++. + .+++ .+.|..-...+++.+|..-+
T Consensus 391 EdFl~gkkngK~TrIm~~v~c~~~~~i~~~~----g--s~~~~~~~g~~~~F~k~~~~~~~EF----------------- 447 (657)
T COG5166 391 EDFLRGKKNGKATRIMKGVSCSELSSIVSST----G--SIVETNGIGEKMSFSKKLSIPPTEF----------------- 447 (657)
T ss_pred HHHhccccCcchhhhhhhcccceeeEEEecC----C--cEEEEeccCcchhhHHHhcCCcccC-----------------
Confidence 34788888888999999988885543 221 1 2333 34566666665555443211
Q ss_pred CCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCH---HHHHHHHHHHHHHHh
Q 005922 217 QAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTS---EQIESAKQLVNEVIS 293 (669)
Q Consensus 217 ~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~p---eqVq~Ak~LI~dlL~ 293 (669)
..++.+.|++..+..|||-||..|.+++.+.++.|+++.... .+.+-....|.|.-+. +.|-.+|.=++++|.
T Consensus 448 ---pae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~-~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~ 523 (657)
T COG5166 448 ---PAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYK-FGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVK 523 (657)
T ss_pred ---chheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhh-cchhhhhcceEEECCccCccchhcccccHHHHHh
Confidence 235678999999999999999999999999999999875411 1112223337777663 345566766777776
Q ss_pred h
Q 005922 294 E 294 (669)
Q Consensus 294 e 294 (669)
+
T Consensus 524 ~ 524 (657)
T COG5166 524 Q 524 (657)
T ss_pred h
Confidence 5
No 104
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=90.87 E-value=0.52 Score=49.07 Aligned_cols=47 Identities=36% Similarity=0.541 Sum_probs=38.8
Q ss_pred EEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHH
Q 005922 223 FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSE 279 (669)
Q Consensus 223 ~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~pe 279 (669)
.-+.|+..+|.+||||+|+.|+.|.++|+|+|.|-- .-.|.|.+..+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~----------NG~IWV~~~~~ 194 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ----------NGRIWVDGENE 194 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec----------CCEEEecCCCc
Confidence 457899999999999999999999999999999841 34666666644
No 105
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=90.79 E-value=0.28 Score=47.17 Aligned_cols=38 Identities=32% Similarity=0.716 Sum_probs=34.8
Q ss_pred cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 005922 221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIP 258 (669)
Q Consensus 221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~ 258 (669)
..+.+.|+...+|..||++|++||.|++..|-+|.|..
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE
Confidence 46778899999999999999999999999999999875
No 106
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=90.78 E-value=0.32 Score=39.22 Aligned_cols=34 Identities=26% Similarity=0.347 Sum_probs=27.4
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEE
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKI 162 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI 162 (669)
....+.+.....|.+|||+|++|+.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 4556666666789999999999999999988443
No 107
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=90.33 E-value=0.14 Score=43.40 Aligned_cols=35 Identities=29% Similarity=0.460 Sum_probs=29.7
Q ss_pred CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeE
Q 005922 220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARI 254 (669)
Q Consensus 220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArI 254 (669)
...+.+.|..+..|+||||+|.+|+.||.....-+
T Consensus 28 ~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~ 62 (73)
T PF13083_consen 28 GDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAA 62 (73)
T ss_dssp TTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHH
T ss_pred ceEEEEEECCCccceEECCCCeeHHHHHHHHHHHH
Confidence 45788899999999999999999999997765433
No 108
>PRK13764 ATPase; Provisional
Probab=90.31 E-value=0.49 Score=55.53 Aligned_cols=67 Identities=27% Similarity=0.433 Sum_probs=49.4
Q ss_pred HHHHHHHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccC
Q 005922 187 QIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPL 259 (669)
Q Consensus 187 ~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~ 259 (669)
....|.++|++.|+....+..... + .......+.||...++.||||+|.+|++|.++.|.+|.|...
T Consensus 453 ~~~~~~~~~~~~~~~~~~~~~~~~---~---~~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~ 519 (602)
T PRK13764 453 VWRLAEKEIEREIKRYLPGPVEVE---V---VSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL 519 (602)
T ss_pred HHHHHHHHHHHHHHHhcCCceEEE---E---ecCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence 445567777777776552221110 0 123467889999999999999999999999999999999865
No 109
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=90.09 E-value=0.14 Score=43.31 Aligned_cols=32 Identities=31% Similarity=0.440 Sum_probs=28.0
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCc
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGA 160 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGA 160 (669)
..+.+.|..+..|+||||.|.|++.||.-...
T Consensus 29 ~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 29 DTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred eEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 67888899999999999999999999876543
No 110
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=89.76 E-value=0.29 Score=41.56 Aligned_cols=38 Identities=34% Similarity=0.510 Sum_probs=31.0
Q ss_pred ceEEEEecccc-----ccceeccCCcchhHHHhhc-CcEEEEcc
Q 005922 129 TSKKIEIPNIR-----VGVIIGKSGETIKYLQLQS-GAKIQVTR 166 (669)
Q Consensus 129 vt~rIlVP~~~-----vG~IIGKgGetIK~IqeeT-GAkI~Isk 166 (669)
...+|.|-... +|.+||++|.+||.|.++. |-+|.|-.
T Consensus 3 ~r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 3 NRTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp TEEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred ceEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 35677777777 9999999999999999999 99999853
No 111
>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=89.63 E-value=1.7 Score=50.85 Aligned_cols=144 Identities=18% Similarity=0.268 Sum_probs=80.8
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEE---ccCCccC-CCC-----CCccccccCCHHHHHHHHHHHHHHH
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQV---TRDTEAD-LNS-----PTRSVELMGTPEQIAKAEQLINDVL 199 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~I---skd~e~~-p~~-----~eRvVtItGt~E~V~kA~~lI~elI 199 (669)
+...+.|++. ..+||| ||++|+.....+|.| .++.+.. +.. ...++.|.|+.|++++..+.+-..+
T Consensus 218 ~~r~~~V~~~--s~liGk---Tl~el~~~~~~~v~I~~I~R~g~~~~p~~dtvL~~GD~L~V~G~~e~L~~l~~~~G~~~ 292 (562)
T TIGR03802 218 VGRAYRVNRA--SSLIGK---TVGDLENLFAGRVTIERIRRDGKLLTVSPDLVLNAGDVVLVVGRRDAVVQFGAEIGEEV 292 (562)
T ss_pred eeEEEEECCC--cccCCC---cHHHHHhhhCCCeEEEEEEECCEEEcCCCCCeeCCCCEEEEEECHHHHHHHHHhcCCcc
Confidence 4566777665 346666 899998776544444 2222111 111 1256788999999987776654332
Q ss_pred HhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHH------HHhCCeEEeccCC---CCCCC---CC
Q 005922 200 AEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQ------ARTGARIQVIPLH---LPPGD---TS 267 (669)
Q Consensus 200 ~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iq------e~TGArIqI~~~~---~ppge---~s 267 (669)
.+... .. ......++.+++ ..+||| +|++|+ ++.|+.|.-..+. ..... -.
T Consensus 293 ~~~~~-----~~------~~~~~e~VV~~~---S~liGk---TL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~ 355 (562)
T TIGR03802 293 QEVEG-----LD------VPMETKDVVLTN---KEYNGK---TVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQ 355 (562)
T ss_pred CCccc-----cC------CceEEEEEEECC---cccCCc---cHHHHhccccccccCCeEEEEEeeCCccccCCCCCEec
Confidence 21100 00 011233444553 456766 788886 2667777655441 11100 11
Q ss_pred CccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 268 TERTVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 268 ~er~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
.-.+|+|.|+++.++++++.+-+...+
T Consensus 356 ~GD~LlV~G~~~~l~~~~~~lG~~~~~ 382 (562)
T TIGR03802 356 RGDVVTLVGTPQDVDRAAKQLGYAIAP 382 (562)
T ss_pred CCCEEEEEeCHHHHHHHHHHcCCchhh
Confidence 235699999999999988876554443
No 112
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=88.78 E-value=0.35 Score=53.51 Aligned_cols=37 Identities=19% Similarity=0.336 Sum_probs=34.8
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEc
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVT 165 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Is 165 (669)
-...+.|+....++.|||+|.|||-..+-||.+|.|.
T Consensus 308 ~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~ 344 (374)
T PRK12328 308 KKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELN 344 (374)
T ss_pred cEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEE
Confidence 4678899999999999999999999999999999995
No 113
>PRK03818 putative transporter; Validated
Probab=88.62 E-value=1.9 Score=50.19 Aligned_cols=139 Identities=19% Similarity=0.298 Sum_probs=77.8
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEc---cCCcc-CC-----CCCCccccccCCHHHHHHHHHHHHHHH
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVT---RDTEA-DL-----NSPTRSVELMGTPEQIAKAEQLINDVL 199 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Is---kd~e~-~p-----~~~eRvVtItGt~E~V~kA~~lI~elI 199 (669)
...++.|+++. +|| +||+++++....++.|. ++... .+ -....++.|.|+.|.++++.+.+-..+
T Consensus 205 ~~r~~~V~~s~---liG---kTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~l~~l~~~~Gl~~ 278 (552)
T PRK03818 205 QTINIRVENPN---LHG---KAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPEDLHKAQLVIGEEV 278 (552)
T ss_pred eeEEEEEeCCC---CCC---CcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHHHHHHHHhcCCcc
Confidence 44667777443 454 59999998877666652 22111 11 112356788999998887776654322
Q ss_pred HhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHH--HHHhCCeEEeccC---CCCCCCC---CCccE
Q 005922 200 AEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNM--QARTGARIQVIPL---HLPPGDT---STERT 271 (669)
Q Consensus 200 ~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~I--qe~TGArIqI~~~---~~ppge~---s~er~ 271 (669)
.++. .......+..++.++++ .++|| +|++| +++.|+.|.-..+ ......+ ..-.+
T Consensus 279 ~~~~----------~~~~~~~~~E~Vvv~~S---~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq~GD~ 342 (552)
T PRK03818 279 DTSL----------STRGTDLRSERVVVTNE---KVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLSLQFGDI 342 (552)
T ss_pred Cccc----------cccCcceEEEEEEEcCh---hccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCEEecCCE
Confidence 1100 00001122334445543 67776 67777 5667777654433 1111110 12356
Q ss_pred EEEEcCHHHHHHHHHHHH
Q 005922 272 VQIDGTSEQIESAKQLVN 289 (669)
Q Consensus 272 VtItG~peqVq~Ak~LI~ 289 (669)
|.|.|+++.+++..+.+.
T Consensus 343 LlVvG~~~~i~~l~~~Lg 360 (552)
T PRK03818 343 LNLVGRPEAIDAVANVLG 360 (552)
T ss_pred EEEEECHHHHHHHHHHhC
Confidence 999999999999877644
No 114
>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=88.57 E-value=0.64 Score=37.44 Aligned_cols=34 Identities=26% Similarity=0.433 Sum_probs=27.4
Q ss_pred cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeE
Q 005922 221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARI 254 (669)
Q Consensus 221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArI 254 (669)
.+..+.+.....++||||+|++|+.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 4455666666789999999999999999988554
No 115
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=88.04 E-value=0.8 Score=48.58 Aligned_cols=52 Identities=23% Similarity=0.357 Sum_probs=45.9
Q ss_pred eeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 232 VGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 232 vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
.-+|||.+|+++|.|+-.|.|-|-|. ..+|.+.|.-..++.++.+|+|.|.+
T Consensus 160 RqRLiGpng~TLKAlelLT~CYilVq-----------G~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 160 RQRLIGPNGSTLKALELLTNCYILVQ-----------GNTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHHhcCCCchhHHHHHHHhhcEEEee-----------CcEEEeecCcchHHHHHHHHHHHHhc
Confidence 35699999999999999999999996 35899999999999999998887765
No 116
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=87.79 E-value=0.86 Score=47.51 Aligned_cols=35 Identities=31% Similarity=0.573 Sum_probs=32.4
Q ss_pred EEEEeccccccceeccCCcchhHHHhhcCcEEEEc
Q 005922 131 KKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVT 165 (669)
Q Consensus 131 ~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Is 165 (669)
.-|.|+..+|-++|||+|+.|++|.++|+|+|-|-
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG 182 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVG 182 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEe
Confidence 56778999999999999999999999999999994
No 117
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=86.34 E-value=4.4 Score=48.45 Aligned_cols=22 Identities=9% Similarity=0.279 Sum_probs=11.7
Q ss_pred EEEcCHHHHHHHHHHHHHHHhh
Q 005922 273 QIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 273 tItG~peqVq~Ak~LI~dlL~e 294 (669)
.|++.-+....+-+|+...+++
T Consensus 376 dir~emDd~~~~f~lL~n~vkd 397 (1102)
T KOG1924|consen 376 DIRAEMDDANEVFELLANTVKD 397 (1102)
T ss_pred hhhhhhccHHHHHHHHHHhhhh
Confidence 3455545555555555555544
No 118
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=86.20 E-value=0.78 Score=52.32 Aligned_cols=39 Identities=23% Similarity=0.479 Sum_probs=33.4
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccC
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRD 167 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd 167 (669)
.+-+++|-.++=|+||||+|+++++|..+||-.-.|.+.
T Consensus 99 ~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 99 DTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred CCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 456777888899999999999999999999988777653
No 119
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=85.48 E-value=0.77 Score=39.40 Aligned_cols=33 Identities=27% Similarity=0.521 Sum_probs=26.5
Q ss_pred eEEEEeccccccceeccCCcchhHHHhhcCcEE
Q 005922 130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKI 162 (669)
Q Consensus 130 t~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI 162 (669)
.++|.|.....|+||||.|+|++.|+--+..-+
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~ 57 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVL 57 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHH
Confidence 466777788899999999999999887655433
No 120
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=84.25 E-value=0.56 Score=39.86 Aligned_cols=36 Identities=31% Similarity=0.555 Sum_probs=28.4
Q ss_pred EEEeeCCCc-----eeeeecCCchHHHHHHHHh-CCeEEecc
Q 005922 223 FAMKIPNNK-----VGLVIGKGGETIKNMQART-GARIQVIP 258 (669)
Q Consensus 223 ~~I~VP~~~-----vG~IIGKGGstIK~Iqe~T-GArIqI~~ 258 (669)
..+.|-... +|.+||++|.+||.|.++. |-+|.|..
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 345555555 8999999999999999999 99999874
No 121
>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=83.97 E-value=0.85 Score=50.05 Aligned_cols=38 Identities=24% Similarity=0.486 Sum_probs=35.5
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEcc
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTR 166 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Isk 166 (669)
-...+.|+....++.|||+|.|||-..+-||.+|.|..
T Consensus 301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 46889999999999999999999999999999999964
No 122
>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=83.86 E-value=1.3 Score=42.89 Aligned_cols=37 Identities=30% Similarity=0.624 Sum_probs=33.7
Q ss_pred EEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 005922 222 HFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIP 258 (669)
Q Consensus 222 t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~ 258 (669)
.+-+.|....+|..||++|++||.|++..|-+|.|..
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 5677899999999999999999999999999998874
No 123
>PF07054 Pericardin_rpt: Pericardin like repeat; InterPro: IPR009765 This entry represents a repeated sequence of around 34 residues in length, which is found in multiple copies in Drosophila pericardin and other extracellular matrix proteins [, ].
Probab=83.60 E-value=1 Score=33.03 Aligned_cols=22 Identities=50% Similarity=1.055 Sum_probs=12.0
Q ss_pred CCCCC-CCCCCCCCCCCCCCCCC
Q 005922 609 QPGYG-SAAYGAPPGGSQAGYGQ 630 (669)
Q Consensus 609 ~~~~~-~~~~~~~~~~~~~~~~~ 630 (669)
||||| .|..|.-++++|++||-
T Consensus 1 QpgyG~QpGvggQ~g~gQpGYg~ 23 (34)
T PF07054_consen 1 QPGYGSQPGVGGQTGAGQPGYGT 23 (34)
T ss_pred CCccccCCccccccCCCCCcccc
Confidence 45555 44554444556666664
No 124
>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=83.24 E-value=1.1 Score=38.37 Aligned_cols=35 Identities=29% Similarity=0.557 Sum_probs=28.7
Q ss_pred cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEE
Q 005922 221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQ 255 (669)
Q Consensus 221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIq 255 (669)
..+.+.|..+..|+||||.|++|+.||-.+..-+.
T Consensus 24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 35677788889999999999999999987765444
No 125
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=82.80 E-value=0.84 Score=51.70 Aligned_cols=37 Identities=30% Similarity=0.516 Sum_probs=34.1
Q ss_pred eEEEEeccccccceeccCCcchhHHHhhcCcEEEEcc
Q 005922 130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTR 166 (669)
Q Consensus 130 t~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Isk 166 (669)
...+.||...++.||||+|.+|++|+++.|.+|.|..
T Consensus 487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~ 523 (604)
T COG1855 487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKP 523 (604)
T ss_pred eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEE
Confidence 4678899999999999999999999999999999963
No 126
>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=82.18 E-value=0.56 Score=39.99 Aligned_cols=34 Identities=26% Similarity=0.412 Sum_probs=28.5
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEE
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKI 162 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI 162 (669)
....|.|...+.+.||||+|++|++|.++..-++
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 3577888999999999999999999988765544
No 127
>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=82.17 E-value=0.63 Score=39.69 Aligned_cols=35 Identities=29% Similarity=0.553 Sum_probs=29.7
Q ss_pred cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEE
Q 005922 221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQ 255 (669)
Q Consensus 221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIq 255 (669)
....+.|...+.+.|||++|++|++|.+...-++.
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 45778899999999999999999999887765553
No 128
>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=81.47 E-value=1.6 Score=51.64 Aligned_cols=39 Identities=26% Similarity=0.480 Sum_probs=33.9
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccC
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRD 167 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd 167 (669)
.+-+++|-.++-|+||||+|.|+++|.++||-+..|.+.
T Consensus 93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 456777778889999999999999999999999888654
No 129
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=81.11 E-value=1.1 Score=51.21 Aligned_cols=39 Identities=23% Similarity=0.507 Sum_probs=35.9
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccC
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRD 167 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd 167 (669)
-...+.|+....++.|||+|.|||...+-||.+|.|...
T Consensus 302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 478899999999999999999999999999999999653
No 130
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=80.24 E-value=5.7 Score=43.32 Aligned_cols=31 Identities=32% Similarity=0.546 Sum_probs=24.8
Q ss_pred CcEEEEeeCCC-ceeeeecCCchHHHHHHHHh
Q 005922 220 SDHFAMKIPNN-KVGLVIGKGGETIKNMQART 250 (669)
Q Consensus 220 ~~t~~I~VP~~-~vG~IIGKGGstIK~Iqe~T 250 (669)
.++.++++|.+ ...+||||||..|++|-++.
T Consensus 327 ~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a 358 (379)
T KOG1423|consen 327 FIQVEVVCPKNSQKKLLIGKGGKKISQIGTRA 358 (379)
T ss_pred EEEEEEEcCCCcceeEEEcCCCccHHHHHHHH
Confidence 35668889975 57789999999999986654
No 131
>PRK15405 ethanolamine utilization protein EutL; Provisional
Probab=80.03 E-value=33 Score=35.54 Aligned_cols=136 Identities=14% Similarity=0.155 Sum_probs=77.4
Q ss_pred hhHHHhhcCcEEEEccCCc------cCCCCCCccccccC-CHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCCCCCcE-
Q 005922 151 IKYLQLQSGAKIQVTRDTE------ADLNSPTRSVELMG-TPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDH- 222 (669)
Q Consensus 151 IK~IqeeTGAkI~Iskd~e------~~p~~~eRvVtItG-t~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t- 222 (669)
+.++.|.++++|-+.++.. .-+.+.+.+++|.| +...|+.|++...+.|++....-. .+..+..+
T Consensus 51 aDeA~KAAnVevv~a~~~~gGaghg~~~~~G~viiIi~G~dvsdVrsAveaa~~~i~~~~~f~~-------~n~~g~~~~ 123 (217)
T PRK15405 51 LDEATKQAMVEVVYARSFYAGAAHASTPLAGEVIGILAGPNPAEVRAGLDAMVAFIENGAAFQS-------ANDDDSTAF 123 (217)
T ss_pred HHHHHhhcceEEEEEEeeccccccCCCCCCccEEEEEeCCCHHHHHHHHHHHHHHHHhhhceEe-------eCCCCCEEE
Confidence 3556677888888876641 11234456789999 999999999999988887532100 00001111
Q ss_pred -------------EEEeeCC-CceeeeecCCchHHHHHHHHhC-CeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHH
Q 005922 223 -------------FAMKIPN-NKVGLVIGKGGETIKNMQARTG-ARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQL 287 (669)
Q Consensus 223 -------------~~I~VP~-~~vG~IIGKGGstIK~Iqe~TG-ArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~L 287 (669)
..+-+|. +-.+.|||.=+.-+--+=.... +.|+|..-..|+.+.+ -.-++|+|+...|..|.+.
T Consensus 124 ~a~~~aRag~~l~k~~g~~~G~a~~~li~~P~~~~~~~D~AlKaA~V~~~~~~~P~~~t~-f~~~~ltG~~~A~r~A~~a 202 (217)
T PRK15405 124 FAHVVSRTGSYLSKTAGIAEGEPLAYLIAPPLEAMYGIDAALKAADVQLVTFVGPPSETN-FGGALLTGSQSACKAACNA 202 (217)
T ss_pred EEEEcccHHHHHHHHcCCCCCceeEEEecCcHHHHHHHHHHHhhcCceEEEEeCCCCCce-ecCeeEEeCHHHHHHHHHH
Confidence 1223444 3467788766554433322221 3444432222333322 2239999998888887777
Q ss_pred HHHHHhh
Q 005922 288 VNEVISE 294 (669)
Q Consensus 288 I~dlL~e 294 (669)
-.+.++.
T Consensus 203 ~~e~v~~ 209 (217)
T PRK15405 203 FTDAVLE 209 (217)
T ss_pred HHHHHHH
Confidence 6666655
No 132
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=79.21 E-value=2.1 Score=45.48 Aligned_cols=52 Identities=23% Similarity=0.431 Sum_probs=43.4
Q ss_pred ccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHh
Q 005922 140 VGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAE 201 (669)
Q Consensus 140 vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e 201 (669)
.-+|||.+|.|+|.|+--|.|-|-|... .|.+.|...+|..+.+.|.+.|..
T Consensus 160 RqRLiGpng~TLKAlelLT~CYilVqG~----------TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 160 RQRLIGPNGSTLKALELLTNCYILVQGN----------TVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHHhcCCCchhHHHHHHHhhcEEEeeCc----------EEEeecCcchHHHHHHHHHHHHhc
Confidence 5689999999999999999999999632 477778888888888777777765
No 133
>PRK00089 era GTPase Era; Reviewed
Probab=79.19 E-value=4.5 Score=42.53 Aligned_cols=36 Identities=22% Similarity=0.505 Sum_probs=27.0
Q ss_pred cEEEEeeCC-CceeeeecCCchHHHHHHH--------HhCCeEEe
Q 005922 221 DHFAMKIPN-NKVGLVIGKGGETIKNMQA--------RTGARIQV 256 (669)
Q Consensus 221 ~t~~I~VP~-~~vG~IIGKGGstIK~Iqe--------~TGArIqI 256 (669)
+...|.|.. ++.+.||||+|++||+|.. .++|+|.+
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l 270 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL 270 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 344666664 6789999999999999754 46777766
No 134
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=78.83 E-value=3.4 Score=40.18 Aligned_cols=38 Identities=26% Similarity=0.480 Sum_probs=32.9
Q ss_pred eEEEEeccccccceeccCCcchhHHHhhcCcEEEEccC
Q 005922 130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRD 167 (669)
Q Consensus 130 t~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd 167 (669)
+-++.|-...-|++|||+|.++++|..+||-+-.|.+.
T Consensus 77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 45677777888999999999999999999999888653
No 135
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=78.11 E-value=8.6 Score=46.18 Aligned_cols=14 Identities=14% Similarity=-0.033 Sum_probs=7.1
Q ss_pred CCCCCCCCCCCCCC
Q 005922 13 PSKRKYEDQTTPPS 26 (669)
Q Consensus 13 ~~Kr~~~d~~~p~~ 26 (669)
+.||+--|..|++.
T Consensus 15 ~~k~~~r~~de~~t 28 (1102)
T KOG1924|consen 15 FLKPNSRDIDEERT 28 (1102)
T ss_pred ccCCCccCcccchh
Confidence 44555555555443
No 136
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=77.89 E-value=4.5 Score=42.15 Aligned_cols=30 Identities=30% Similarity=0.511 Sum_probs=25.5
Q ss_pred CcEEEEeeCCCceeeeecCCchHHHHHHHH
Q 005922 220 SDHFAMKIPNNKVGLVIGKGGETIKNMQAR 249 (669)
Q Consensus 220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~ 249 (669)
...++|.|....=|.||||+|++|++|++.
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 345688888999999999999999998754
No 137
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=77.43 E-value=2.9 Score=41.53 Aligned_cols=38 Identities=24% Similarity=0.506 Sum_probs=32.7
Q ss_pred cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccC
Q 005922 221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPL 259 (669)
Q Consensus 221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~ 259 (669)
..+.++|-... |.-|||+|.+||.|++..|-+|.|.+.
T Consensus 61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence 34567777777 999999999999999999999999853
No 138
>PRK13764 ATPase; Provisional
Probab=77.21 E-value=2.3 Score=50.11 Aligned_cols=39 Identities=26% Similarity=0.422 Sum_probs=34.8
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccC
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRD 167 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd 167 (669)
....|.|+.+.++.+|||+|.+|++|+++.|.+|.|...
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~ 519 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL 519 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence 346778999999999999999999999999999999643
No 139
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=76.74 E-value=1.6 Score=49.28 Aligned_cols=38 Identities=21% Similarity=0.437 Sum_probs=35.1
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEcc
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTR 166 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Isk 166 (669)
-...+.|+....++.|||+|.|||-..+-||.+|.|..
T Consensus 335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 45789999999999999999999999999999999963
No 140
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=76.33 E-value=2.2 Score=43.19 Aligned_cols=37 Identities=19% Similarity=0.419 Sum_probs=34.8
Q ss_pred eEEEEeccccccceeccCCcchhHHHhhcCcEEEEcc
Q 005922 130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTR 166 (669)
Q Consensus 130 t~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Isk 166 (669)
...+.|+.+..+++|||+|.+|+.+.+-||-+|.|..
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 6888899999999999999999999999999999964
No 141
>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=75.65 E-value=2.4 Score=37.09 Aligned_cols=36 Identities=22% Similarity=0.331 Sum_probs=29.7
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEE
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQV 164 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~I 164 (669)
...+|.|-..+-|.|||++|++|++|+++..-.+.+
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~ 65 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF 65 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence 347888889999999999999999999876555544
No 142
>PRK15494 era GTPase Era; Provisional
Probab=75.00 E-value=3.9 Score=44.65 Aligned_cols=35 Identities=20% Similarity=0.394 Sum_probs=26.4
Q ss_pred EEEEeeCC-CceeeeecCCchHHHHHHH--------HhCCeEEe
Q 005922 222 HFAMKIPN-NKVGLVIGKGGETIKNMQA--------RTGARIQV 256 (669)
Q Consensus 222 t~~I~VP~-~~vG~IIGKGGstIK~Iqe--------~TGArIqI 256 (669)
...|.|.. ++.++||||+|++||+|.. .++|+|.+
T Consensus 274 ~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l 317 (339)
T PRK15494 274 NQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHL 317 (339)
T ss_pred EEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEE
Confidence 34666765 6789999999999999754 46777665
No 143
>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=71.20 E-value=5 Score=35.11 Aligned_cols=36 Identities=17% Similarity=0.325 Sum_probs=29.9
Q ss_pred cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEe
Q 005922 221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQV 256 (669)
Q Consensus 221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI 256 (669)
..+++.|-...-|.|||++|++|++|++...-...+
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~ 65 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF 65 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence 457888999999999999999999999886555444
No 144
>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=70.06 E-value=3.2 Score=38.17 Aligned_cols=30 Identities=33% Similarity=0.512 Sum_probs=25.4
Q ss_pred eEEEEeccccccceeccCCcchhHHHhhcC
Q 005922 130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSG 159 (669)
Q Consensus 130 t~rIlVP~~~vG~IIGKgGetIK~IqeeTG 159 (669)
.++|.|-..+-|+|||++|++|++|+++..
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~ 91 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQ 91 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence 367788888899999999999999887644
No 145
>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=68.68 E-value=6.2 Score=41.30 Aligned_cols=29 Identities=24% Similarity=0.428 Sum_probs=22.5
Q ss_pred cEEEEeeCC-CceeeeecCCchHHHHHHHH
Q 005922 221 DHFAMKIPN-NKVGLVIGKGGETIKNMQAR 249 (669)
Q Consensus 221 ~t~~I~VP~-~~vG~IIGKGGstIK~Iqe~ 249 (669)
+...|.|.. ++.++||||+|++||+|..+
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ 250 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIA 250 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence 345666764 67899999999999998654
No 146
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=67.95 E-value=25 Score=36.26 Aligned_cols=36 Identities=22% Similarity=0.375 Sum_probs=30.2
Q ss_pred cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEe
Q 005922 221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQV 256 (669)
Q Consensus 221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI 256 (669)
..+.+.|-.+..++|||+.|.+++.||-.+.+-+..
T Consensus 91 ~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 456777888889999999999999999888766554
No 147
>COG0490 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]
Probab=66.98 E-value=10 Score=37.60 Aligned_cols=57 Identities=26% Similarity=0.405 Sum_probs=36.1
Q ss_pred CCCceeeeecCCchHHHHHHHHhCCeEEeccCC----CCCCC---CCCccEEEEEcCHHHHHHHHHHHH
Q 005922 228 PNNKVGLVIGKGGETIKNMQARTGARIQVIPLH----LPPGD---TSTERTVQIDGTSEQIESAKQLVN 289 (669)
Q Consensus 228 P~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~----~ppge---~s~er~VtItG~peqVq~Ak~LI~ 289 (669)
-..++|+-||. -+|+++|||.|.-+-++ +.|+- -....+|.+.|+...+.+++.++.
T Consensus 95 ~s~~~GksiGd-----l~irq~TGaTIIAI~r~~e~I~SPgPy~vle~gDtlvviG~~~~~~r~~~f~~ 158 (162)
T COG0490 95 GSPFIGKTIGD-----LNIRQNTGATVIAIVRNEEKILSPGPYTVLEAGDTLVVIGEETGLKRAKRFLL 158 (162)
T ss_pred CCcccCcchhh-----cccccccCcEEEEEEecCcEecCCCchhhhcCCCEEEEEecchHhHHHHHHhh
Confidence 33445555542 46899999998655331 11111 122457999999999999888764
No 148
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=66.69 E-value=5.5 Score=44.20 Aligned_cols=38 Identities=21% Similarity=0.498 Sum_probs=35.4
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEcc
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTR 166 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Isk 166 (669)
....+.|+....++.|||+|.|||-..+-||.+|.|..
T Consensus 303 ~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 303 KAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred cEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 56889999999999999999999999999999999964
No 149
>TIGR01334 modD putative molybdenum utilization protein ModD. The gene modD for a member of this family is found with molybdenum transport genes modABC in Rhodobacter capsulatus. However, disruption of modD causes only a 4-fold (rather than 500-fold for modA, modB, modC) change in the external molybdenum concentration required to suppress an alternative nitrogenase. ModD proteins are highly similar to nicotinate-nucleotide pyrophosphorylase (also called quinolinate phosphoribosyltransferase). The function unknown.
Probab=65.21 E-value=37 Score=36.42 Aligned_cols=66 Identities=14% Similarity=0.160 Sum_probs=46.6
Q ss_pred eeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 226 KIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 226 ~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
.|-...-+.| -|-..+++|-+..+|+|++.-.+-.. -...+.+++|.|+...+..+.+.++.+|+-
T Consensus 36 ~~~are~gv~--~G~~~~~~i~~~l~~~~~~~~~dG~~-v~~g~~i~~~~G~a~~ll~~eR~alN~l~~ 101 (277)
T TIGR01334 36 TFTARDEGIV--SGVSEAAKLLKQLGASIDYAVPSGSR-ALAGTLLLEAKGSAGQLHQGWKSAQSVLEW 101 (277)
T ss_pred EEEEcCCEEE--ECHHHHHHHHHHcCCEEEEEeCCCCE-eCCCCEEEEEEecHHHHHHHHHHHHHHHHH
Confidence 3333333444 34567889999999999886432111 145678899999999999999998888753
No 150
>COG1159 Era GTPase [General function prediction only]
Probab=64.58 E-value=9.1 Score=41.36 Aligned_cols=34 Identities=24% Similarity=0.536 Sum_probs=25.4
Q ss_pred EEEeeCC-CceeeeecCCchHHHHHHH--------HhCCeEEe
Q 005922 223 FAMKIPN-NKVGLVIGKGGETIKNMQA--------RTGARIQV 256 (669)
Q Consensus 223 ~~I~VP~-~~vG~IIGKGGstIK~Iqe--------~TGArIqI 256 (669)
..|.|.. ++-+.||||+|++||+|-. ..+|+|.+
T Consensus 231 a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L 273 (298)
T COG1159 231 ATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYL 273 (298)
T ss_pred EEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEE
Confidence 4566764 6789999999999999744 45666655
No 151
>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=63.26 E-value=6.2 Score=34.55 Aligned_cols=28 Identities=32% Similarity=0.487 Sum_probs=23.1
Q ss_pred EEEEeccccccceeccCCcchhHHHhhc
Q 005922 131 KKIEIPNIRVGVIIGKSGETIKYLQLQS 158 (669)
Q Consensus 131 ~rIlVP~~~vG~IIGKgGetIK~IqeeT 158 (669)
.++.|....-|.|||++|.+|++|++..
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 5566666888999999999999988764
No 152
>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=60.44 E-value=6.9 Score=35.95 Aligned_cols=31 Identities=26% Similarity=0.536 Sum_probs=26.1
Q ss_pred cEEEEeeCCCceeeeecCCchHHHHHHHHhC
Q 005922 221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTG 251 (669)
Q Consensus 221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TG 251 (669)
..++|.|-...-|+|||++|++|++|++...
T Consensus 61 ~~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~ 91 (109)
T cd02412 61 DRVEVTIHTARPGIIIGKKGAGIEKLRKELQ 91 (109)
T ss_pred CCEEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence 3467888888899999999999999987653
No 153
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=60.02 E-value=54 Score=32.86 Aligned_cols=45 Identities=13% Similarity=0.230 Sum_probs=36.1
Q ss_pred CchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHH
Q 005922 239 GGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEV 291 (669)
Q Consensus 239 GGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dl 291 (669)
.-..|.+|.+.++++|.=. ..+.-+|.|+|+++.|..-.++++..
T Consensus 97 ~r~ei~~~~~~f~a~ivdv--------~~~~~~ie~tG~~~ki~a~~~~l~~~ 141 (174)
T CHL00100 97 TRPEILEIAQIFRAKVVDL--------SEESLILEVTGDPGKIVAIEQLLEKF 141 (174)
T ss_pred CHHHHHHHHHHhCCEEEEe--------cCCEEEEEEcCCHHHHHHHHHHhhhc
Confidence 3456889999999998754 23456899999999999999988764
No 154
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=59.82 E-value=7.1 Score=40.76 Aligned_cols=29 Identities=31% Similarity=0.597 Sum_probs=25.2
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhh
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQ 157 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~Iqee 157 (669)
...+|.|...+=|.||||+|++|++|+++
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 45788888999999999999999887754
No 155
>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=57.57 E-value=11 Score=33.05 Aligned_cols=29 Identities=28% Similarity=0.563 Sum_probs=23.9
Q ss_pred EEEEeeCCCceeeeecCCchHHHHHHHHh
Q 005922 222 HFAMKIPNNKVGLVIGKGGETIKNMQART 250 (669)
Q Consensus 222 t~~I~VP~~~vG~IIGKGGstIK~Iqe~T 250 (669)
.+++.|-...-|.|||++|++|++|++..
T Consensus 39 ~i~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 39 GTQITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred cEEEEEEECCCCceECCCchhHHHHHHHH
Confidence 35666666889999999999999988764
No 156
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=57.28 E-value=22 Score=31.24 Aligned_cols=69 Identities=16% Similarity=0.172 Sum_probs=50.2
Q ss_pred EEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHh
Q 005922 131 KKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAE 201 (669)
Q Consensus 131 ~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e 201 (669)
.++.|-.+.-|.|=|. +-+++|-++.+++|++...+...-...+.+++|.|+...|..|.+.+..+|..
T Consensus 18 ~~a~i~are~gV~aG~--~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~~ 86 (88)
T PF02749_consen 18 GTATIIAREDGVLAGL--EEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQR 86 (88)
T ss_dssp EEEEEEESSSEEE-SH--HHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred EEEEEEeCCCEEEECH--HHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHHH
Confidence 3444444555666543 67888999999999987544334455679999999999999999999998864
No 157
>cd01572 QPRTase Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide. QPRTase functions as a homodimer with two active sites, each formed by the C-terminal region of one subunit and the N-terminal region of the other.
Probab=57.14 E-value=55 Score=34.81 Aligned_cols=96 Identities=10% Similarity=0.166 Sum_probs=57.3
Q ss_pred HHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHh--CCeEEeccCCCCCCCCCCcc
Q 005922 193 QLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQART--GARIQVIPLHLPPGDTSTER 270 (669)
Q Consensus 193 ~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~T--GArIqI~~~~~ppge~s~er 270 (669)
++|.++|+|+..... ....-+. ......++.|-...-+.|- |-..+++|-+.. +++|.+.-.+-.. -...+.
T Consensus 2 ~~i~~~l~ED~~~~D-~tt~~~~--~~~~~~~~~~~ar~~~v~~--G~~~~~~i~~~~~~~l~v~~~~~dG~~-v~~g~~ 75 (268)
T cd01572 2 AIVRLALAEDLGRGD-ITSEAII--PPDARAEARLIAKEEGVLA--GLPVAEEVFELLDPGIEVEWLVKDGDR-VEPGQV 75 (268)
T ss_pred HHHHHHHHhcCCCCC-CCccccc--CCCCeEEEEEEEcCCEEEE--CHHHHHHHHHHcCCCeEEEEEeCCCCE-ecCCCE
Confidence 467888888764211 0000010 0112233333333334444 456788899988 8888654221111 135688
Q ss_pred EEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 271 TVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 271 ~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
+++|.|....+..+.+.++.+|+-
T Consensus 76 i~~i~G~~~~ll~~Er~~ln~L~~ 99 (268)
T cd01572 76 LATVEGPARSLLTAERTALNFLQR 99 (268)
T ss_pred EEEEEECHHHHHHHHHHHHHHHHH
Confidence 999999999999999999888854
No 158
>PRK06559 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=56.89 E-value=69 Score=34.70 Aligned_cols=97 Identities=9% Similarity=0.106 Sum_probs=57.1
Q ss_pred HHHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEec-----cCCCCCCC
Q 005922 191 AEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVI-----PLHLPPGD 265 (669)
Q Consensus 191 A~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~-----~~~~ppge 265 (669)
...+|..+|+|+..... .....+. ......++.+-...-+.|- |-..+++|-+..++.|.+. .+.. .-
T Consensus 13 ~~~~i~~~l~ED~~~gD-lTt~~l~--~~~~~~~~~~~are~gvla--G~~~a~~if~~l~~~~~~~~~~~~~dG~--~v 85 (290)
T PRK06559 13 IDDTLKAALREDVHSED-YSTNAIF--DHHGQAKVSLFAKEAGVLA--GLTVFQRVFTLFDAEVTFQNPHQFKDGD--RL 85 (290)
T ss_pred HHHHHHHHHHhcCCCCC-CCccccC--CCCCeEEEEEEecCCeEEE--CHHHHHHHHHHhCCcEEEEEeecCCCCC--Ee
Confidence 45677778888754211 0000000 0011223333333334443 4467788999999988885 2211 11
Q ss_pred CCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 266 TSTERTVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 266 ~s~er~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
...+.+++|.|+...|..+.+.++.+|+-
T Consensus 86 ~~G~~i~~v~G~a~~ll~~ER~alN~l~~ 114 (290)
T PRK06559 86 TSGDLVLEIIGSVRSLLTCERVALNFLQH 114 (290)
T ss_pred cCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 44588999999999999999998888753
No 159
>cd01573 modD_like ModD; Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase) present in some modABC operons in bacteria, which are involved in molybdate transport. In general, QPRTases are part of the de novo synthesis pathway of NAD in both prokaryotes and eukaryotes. They catalyse the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide.
Probab=56.51 E-value=63 Score=34.48 Aligned_cols=55 Identities=7% Similarity=0.125 Sum_probs=40.4
Q ss_pred CchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 239 GGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 239 GGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
|-..+++|-+..+++|.+.-.+-.. -...+.+++|.|+...+..+.+.++.+|.-
T Consensus 43 G~~~~~~~~~~~~~~v~~~~~dG~~-v~~g~~i~~i~G~~~~ll~~Er~~ln~l~~ 97 (272)
T cd01573 43 GTEEAARILELLGLEVDLAAASGSR-VAAGAVLLEAEGPAAALHLGWKVAQTLLEW 97 (272)
T ss_pred CHHHHHHHHHHcCcEEEEEcCCCCE-ecCCCEEEEEEEcHHHHHHHHHHHHHHHHH
Confidence 3457788989999998754221111 134588999999999999999999888743
No 160
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=55.84 E-value=13 Score=38.12 Aligned_cols=30 Identities=27% Similarity=0.542 Sum_probs=24.6
Q ss_pred EEEeeCCCceeeeecCCchHHHHHHHHhCC
Q 005922 223 FAMKIPNNKVGLVIGKGGETIKNMQARTGA 252 (669)
Q Consensus 223 ~~I~VP~~~vG~IIGKGGstIK~Iqe~TGA 252 (669)
.++.|-...-|+|||++|++|++|++...-
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk 71 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEK 71 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHH
Confidence 566666688999999999999999877543
No 161
>PRK04972 putative transporter; Provisional
Probab=55.31 E-value=49 Score=38.88 Aligned_cols=148 Identities=11% Similarity=0.151 Sum_probs=76.1
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEE---ccCCcc-CCCC-----CCccccccCCHHHHHHHHHHHHHHH
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQV---TRDTEA-DLNS-----PTRSVELMGTPEQIAKAEQLINDVL 199 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~I---skd~e~-~p~~-----~eRvVtItGt~E~V~kA~~lI~elI 199 (669)
+...+.|.+..+-.++ |++|++|......+|.| .++... .+.. ...++.|.|+.|.++++.+.+. +
T Consensus 214 ~~r~~~V~~~~~~~~~---Gktl~el~~~~~~~v~I~~I~R~g~~~~p~~dt~L~~GDiL~V~G~~e~l~~l~~~~~--l 288 (558)
T PRK04972 214 VIRAYRVGPELVAWTD---GKNLRELGIYRQTGCYIERIRRNGILANPDGDAVLQMGDEIALVGYPDAHARLDPSFR--N 288 (558)
T ss_pred eeeEEEECCccccCcC---CCCHHHHHhhcCCCEEEEEEEECCEEecCCCCCEeCCCCEEEEEECHHHHHHHHHhhc--C
Confidence 3566667665333334 55999998877555444 232211 1111 1246778899998766654430 1
Q ss_pred HhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHH-HhCCeEEeccC---CCCCCC---CCCccEE
Q 005922 200 AEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQA-RTGARIQVIPL---HLPPGD---TSTERTV 272 (669)
Q Consensus 200 ~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe-~TGArIqI~~~---~~ppge---~s~er~V 272 (669)
.++... + .. .......|..|..+ ..+||| +|++|+- +.|+.|.-..+ ...... -....+|
T Consensus 289 g~e~~~------~-~~-~~~~~~~E~vVv~~--s~liGk---TL~eL~~r~~gv~Vl~I~R~g~~~~~~~~~~L~~GD~L 355 (558)
T PRK04972 289 GKEVFD------R-DL-LDMRIVTEEIVVKN--HNAVGK---RLSQLKLTDHGCFLNRVIRSQIEMPIDDNVVLNKGDVL 355 (558)
T ss_pred CCcccC------c-cc-cCcceEEEEEEEcC--cccCCC---CHHHhCCccCCeEEEEEecCCcccCCCCCCEecCCCEE
Confidence 111000 0 00 01111233444332 356766 6777742 36777655443 111111 1223569
Q ss_pred EEEcCHHHHHHHHHHHHHHHhh
Q 005922 273 QIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 273 tItG~peqVq~Ak~LI~dlL~e 294 (669)
.|.|+++.+++..+.+-.++.+
T Consensus 356 lVvG~~~~i~~l~~~lG~~~~~ 377 (558)
T PRK04972 356 QVSGDARRVKTIADRIGFISIH 377 (558)
T ss_pred EEEECHHHHHHHHHHhCCcccc
Confidence 9999999999987766554433
No 162
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=55.16 E-value=23 Score=36.13 Aligned_cols=30 Identities=30% Similarity=0.509 Sum_probs=25.7
Q ss_pred cEEEEeeCCCceeeeecCCchHHHHHHHHh
Q 005922 221 DHFAMKIPNNKVGLVIGKGGETIKNMQART 250 (669)
Q Consensus 221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~T 250 (669)
..++|.|-...-+.|||++|.+|++|+++.
T Consensus 38 ~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 38 LGTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred CcEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 457888888899999999999999987664
No 163
>PRK08385 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=54.07 E-value=78 Score=34.05 Aligned_cols=55 Identities=16% Similarity=0.206 Sum_probs=40.9
Q ss_pred CchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 239 GGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 239 GGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
|-..+.+|-+..+++|.+.-.+-.. -...+.+++|.|+...+..+.+.++.+|+-
T Consensus 45 G~~~a~~i~~~l~~~v~~~~~dG~~-v~~g~~i~~i~G~~~~ll~~Er~~ln~l~~ 99 (278)
T PRK08385 45 GLEEAKALFEHFGVKVEVRKRDGEE-VKAGEVILELKGNARAILLVERTALNIIGR 99 (278)
T ss_pred CHHHHHHHHHHcCCEEEEEcCCCCE-ecCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 3456788888899999884321111 135588999999999999999999888853
No 164
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=52.74 E-value=72 Score=31.81 Aligned_cols=35 Identities=11% Similarity=0.150 Sum_probs=26.2
Q ss_pred CcEEEEccCCccCCCCCCccccccC--CHHHHHHHHHHHHHHHHhh
Q 005922 159 GAKIQVTRDTEADLNSPTRSVELMG--TPEQIAKAEQLINDVLAEA 202 (669)
Q Consensus 159 GAkI~Iskd~e~~p~~~eRvVtItG--t~E~V~kA~~lI~elI~e~ 202 (669)
.+.+.|-.+. -++++| +.|.+.+|+++|.++|++.
T Consensus 47 ~~t~lIf~sG---------KivitGaks~~~~~~a~~~~~~~L~~~ 83 (174)
T cd00652 47 KTTALIFSSG---------KMVITGAKSEEDAKLAARKYARILQKL 83 (174)
T ss_pred cEEEEEECCC---------EEEEEecCCHHHHHHHHHHHHHHHHHc
Confidence 4666665432 377777 6899999999999999874
No 165
>cd01568 QPRTase_NadC Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide. QPRTase functions as a homodimer with two active sites, each formed by the C-terminal region of one subunit and the N-terminal region of the other.
Probab=51.98 E-value=71 Score=33.93 Aligned_cols=96 Identities=14% Similarity=0.237 Sum_probs=57.3
Q ss_pred HHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHh-CCeEEeccCCCCCCCCCCccE
Q 005922 193 QLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQART-GARIQVIPLHLPPGDTSTERT 271 (669)
Q Consensus 193 ~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~T-GArIqI~~~~~ppge~s~er~ 271 (669)
.+|..+|+|+..... .....+. ......++.|-...-+.|-| =..+++|-+.. +++|...-.+-.. -...+.+
T Consensus 2 ~~i~~~l~ED~~~gD-~tt~~~~--~~~~~~~~~i~~r~~~v~~G--~~~~~~i~~~~~~~~v~~~~~dG~~-v~~g~~i 75 (269)
T cd01568 2 ALLDRALAEDLGYGD-LTTEALI--PGDAPATATLIAKEEGVLAG--LEVAEEVFELLDGIEVEWLVKDGDR-VEAGQVL 75 (269)
T ss_pred HHHHHHHHhcCCCCC-CCccccc--CCCceEEEEEEecCCEEEEC--HHHHHHHHHHhCCeEEEEEeCCCCE-ecCCCEE
Confidence 467788888754211 1011010 01222344443444455554 46778888888 8888554221111 1355889
Q ss_pred EEEEcCHHHHHHHHHHHHHHHhh
Q 005922 272 VQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 272 VtItG~peqVq~Ak~LI~dlL~e 294 (669)
++|+|+...+..+.+.++.+|.-
T Consensus 76 ~~i~G~~~~l~~~Er~~ln~L~~ 98 (269)
T cd01568 76 LEVEGPARSLLTAERVALNLLQR 98 (269)
T ss_pred EEEEEcHHHHHHHHHHHHHHHHH
Confidence 99999999999999999888854
No 166
>PRK07428 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=51.72 E-value=77 Score=34.24 Aligned_cols=97 Identities=14% Similarity=0.208 Sum_probs=56.9
Q ss_pred HHHHHHHHHhhhcCCCCcchhcccCCCCC-cEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCC--CCC
Q 005922 192 EQLINDVLAEAESGGSGIVARRLTGQAGS-DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGD--TST 268 (669)
Q Consensus 192 ~~lI~elI~e~~~~~~~~~~rr~~~~~~~-~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge--~s~ 268 (669)
..+|.++|+|+..... ...+-+. ... ...++.|-...-+.|- |-..+.+|-+..+++|+|.-. ...++ ...
T Consensus 14 ~~~i~~~l~ED~~~~D-lTt~~~~--~~~~~~~~~~i~ar~~gv~~--G~~~a~~i~~~~~~~~~~~~~-~~dG~~v~~g 87 (288)
T PRK07428 14 DPLLQQWLREDIGRGD-RTTQGLL--LEDATTGQAKWIAKESGVIA--GLPIAARVFQLLDPQVSFTPL-VAEGAACESG 87 (288)
T ss_pred HHHHHHHHHhcCCCCC-CCccccc--CCCCcEEEEEEEecCCeEEE--CHHHHHHHHHHcCCcEEEEEE-cCCCCEecCC
Confidence 4567778888754211 1010010 001 2233333333444453 446778999999988874311 01111 345
Q ss_pred ccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 269 ERTVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 269 er~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
+.+++|.|+...+..+.+.++.+|+-
T Consensus 88 ~~i~~~~G~a~~ll~~eR~~lN~l~~ 113 (288)
T PRK07428 88 QVVAEIEGPLDALLMGERVALNLAMR 113 (288)
T ss_pred CEEEEEEEcHHHHHHHHHHHHHHHHH
Confidence 78999999999999999999888853
No 167
>PRK06096 molybdenum transport protein ModD; Provisional
Probab=50.27 E-value=91 Score=33.66 Aligned_cols=55 Identities=15% Similarity=0.151 Sum_probs=41.3
Q ss_pred CchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 239 GGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 239 GGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
|-..+++|-+..+++|.+.-.+-.. -...+.+++|.|+...+..+.+.++.+|+-
T Consensus 48 G~~~a~~if~~l~~~v~~~~~dG~~-v~~G~~i~~~~G~a~~ll~~eR~alN~l~~ 102 (284)
T PRK06096 48 GISVACKMLTTLGLTIDDAVSDGSQ-ANAGQRLISAQGNAAALHQGWKAVQNVLEW 102 (284)
T ss_pred CHHHHHHHHHHcCCEEEEEeCCCCE-eCCCCEEEEEEeCHHHHHHHHHHHHHHHHH
Confidence 4467888999999998886332111 134578999999999999999998888743
No 168
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=50.11 E-value=21 Score=34.81 Aligned_cols=44 Identities=20% Similarity=0.303 Sum_probs=37.8
Q ss_pred cchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHh
Q 005922 149 ETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAE 201 (669)
Q Consensus 149 etIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e 201 (669)
+.+.+|.+-.|+.|.+.. -.+|.|.|+.|.|.+|++.|.++.++
T Consensus 126 eRlqDi~E~hgvIiE~~E---------~D~V~i~Gd~drVk~aLke~~~~wke 169 (170)
T COG4010 126 ERLQDIAETHGVIIEFEE---------YDLVAIYGDSDRVKKALKEIGSFWKE 169 (170)
T ss_pred HHHHHHHHhhheeEEeee---------ccEEEEeccHHHHHHHHHHHHHHHhc
Confidence 567889999999999862 24799999999999999999998775
No 169
>TIGR00078 nadC nicotinate-nucleotide pyrophosphorylase. Synonym: quinolinate phosphoribosyltransferase (decarboxylating)
Probab=49.50 E-value=70 Score=34.01 Aligned_cols=68 Identities=9% Similarity=0.183 Sum_probs=45.2
Q ss_pred EEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 224 AMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 224 ~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
++.|-...-+.|- |-..+.+|-+..+++|++.-.+-.. -...+.+++|.|....+..+.+.++.+|+-
T Consensus 28 ~~~~~ar~~~v~~--G~~~~~~i~~~~~~~v~~~~~dG~~-v~~g~~i~~i~G~~~~il~~Er~~ln~l~~ 95 (265)
T TIGR00078 28 TASLVAKEDGVLA--GLPVARRVFEQLGVQVEWLVKDGDR-VEPGEVVAEVEGPARSLLTAERTALNFLGR 95 (265)
T ss_pred EEEEEecCCEEEE--CHHHHHHHHHHcCeEEEEEeCCCCE-ecCCCEEEEEEEcHHHHHHHHHHHHHHHHH
Confidence 3333333334443 3456788888889887554221111 135588999999999999999999888854
No 170
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=48.99 E-value=37 Score=29.76 Aligned_cols=58 Identities=12% Similarity=0.232 Sum_probs=43.0
Q ss_pred eeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHh
Q 005922 233 GLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVIS 293 (669)
Q Consensus 233 G~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~ 293 (669)
+.|- |=..+++|-++.+++|++.-.+-.. -...+.+++|.|+...|..|.+.++.+|.
T Consensus 28 gV~a--G~~~~~~i~~~l~~~v~~~~~dG~~-v~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 28 GVLA--GLEEAEEIFEKLGLEVEWLVKDGDR-VEPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp EEE---SHHHHHHHHHHCTEEEEESS-TT-E-EETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred EEEE--CHHHHHHHHhhccEEEEEEeCCCCC-ccCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 4443 5577889999999999876321111 13457899999999999999999999885
No 171
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=48.82 E-value=16 Score=37.93 Aligned_cols=31 Identities=16% Similarity=0.251 Sum_probs=26.0
Q ss_pred cEEEEeeCCCceeeeecCCchHHHHHHHHhC
Q 005922 221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTG 251 (669)
Q Consensus 221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TG 251 (669)
..++|.|-...-|.|||++|..|++|+++..
T Consensus 44 ~~i~V~I~tarPg~vIG~~G~~i~~l~~~L~ 74 (220)
T PTZ00084 44 IRTEIIIRATRTREVLGDKGRRIRELTSLLQ 74 (220)
T ss_pred CcEEEEEEECCCccEEcCCchHHHHHHHHHH
Confidence 3467888888899999999999999987653
No 172
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=47.87 E-value=86 Score=31.07 Aligned_cols=94 Identities=14% Similarity=0.170 Sum_probs=56.7
Q ss_pred cccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCCCCCcE-EEEeeCCCceeeeecCCchHHHHHHHHhCCeEEe
Q 005922 178 SVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDH-FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQV 256 (669)
Q Consensus 178 vVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t-~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI 256 (669)
.+++.++.+.|++.++.|+.++.=......... ..-..+ +-++|..+. ..-..|.+|.+.++|+|.=
T Consensus 47 ti~V~~~~~~i~qi~kQl~KLidV~~V~~~~~~------~~v~rEl~LiKv~~~~------~~r~~i~~i~~~f~a~ivd 114 (161)
T PRK11895 47 TIVTSGDEQVIEQITKQLNKLIDVLKVVDLTEE------AHVERELALVKVRASG------ENRAEILRLADIFRAKIVD 114 (161)
T ss_pred EEEEECCHHHHHHHHHHHhccccEEEEEecCCc------chhheEEEEEEEECCc------ccHHHHHHHHHHhCCEEEE
Confidence 456678888888888777776653221100000 000011 112222211 1235788999999999874
Q ss_pred ccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHH
Q 005922 257 IPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEV 291 (669)
Q Consensus 257 ~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dl 291 (669)
. +.+.-+|.++|.++.|+.-.++++.+
T Consensus 115 v--------~~~~~~iE~tG~~~ki~~~~~~l~~~ 141 (161)
T PRK11895 115 V--------TPESLTIEVTGDSDKIDAFIDLLRPY 141 (161)
T ss_pred e--------cCCEEEEEEeCCHHHHHHHHHHhhhc
Confidence 3 33467899999999999988888764
No 173
>CHL00048 rps3 ribosomal protein S3
Probab=47.72 E-value=54 Score=33.87 Aligned_cols=30 Identities=23% Similarity=0.279 Sum_probs=25.7
Q ss_pred cEEEEeeCCCceeeeecCCchHHHHHHHHh
Q 005922 221 DHFAMKIPNNKVGLVIGKGGETIKNMQART 250 (669)
Q Consensus 221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~T 250 (669)
..++|.|-...-+.|||++|.+|++|++..
T Consensus 66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 66 DLIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred CeEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 456778888889999999999999998765
No 174
>PRK08072 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=45.70 E-value=70 Score=34.32 Aligned_cols=54 Identities=9% Similarity=0.072 Sum_probs=37.0
Q ss_pred chHHHHHHHHhCCe--EEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 240 GETIKNMQARTGAR--IQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 240 GstIK~Iqe~TGAr--IqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
-..+++|-+..+.+ |.+.-.+-. .-...+.+++|.|....+..+.+.++.+|+-
T Consensus 50 ~~~a~~i~~~~~~~~~v~~~~~dG~-~v~~g~~i~~~~G~~~~ll~~er~~ln~l~~ 105 (277)
T PRK08072 50 RLVIEEGYKLLDERIEVELHKKDGD-LVKKGEIIATVQGPVASLLTGERVILNLIQR 105 (277)
T ss_pred HHHHHHHHHHcCCceEEEEEeCCCC-EEcCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 34567888877755 444321111 1134578999999999999999999888853
No 175
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=45.21 E-value=1.6e+02 Score=29.49 Aligned_cols=25 Identities=20% Similarity=0.395 Sum_probs=20.1
Q ss_pred cEEEEEcC--HHHHHHHHHHHHHHHhh
Q 005922 270 RTVQIDGT--SEQIESAKQLVNEVISE 294 (669)
Q Consensus 270 r~VtItG~--peqVq~Ak~LI~dlL~e 294 (669)
..|+|+|. .+.+++|.+.|..+|.+
T Consensus 148 GkivitGaks~~~~~~a~~~i~pil~~ 174 (174)
T cd04517 148 GSVTVTGARSMEDVREAVEKIYPIVFE 174 (174)
T ss_pred CEEEEEecCCHHHHHHHHHHHHHHHhC
Confidence 35888987 68899999999888753
No 176
>PRK06543 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=44.99 E-value=1.3e+02 Score=32.40 Aligned_cols=55 Identities=7% Similarity=0.058 Sum_probs=39.2
Q ss_pred CchHHHHHHHHhCCeEE--eccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 239 GGETIKNMQARTGARIQ--VIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 239 GGstIK~Iqe~TGArIq--I~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
|-..+.+|-+..++.++ +.-.+-. .-...+.+++|.|+...+..+.+.++.+|+-
T Consensus 50 G~~~a~~if~~~~~~~~v~~~~~dG~-~v~~G~~i~~~~G~a~~ll~~eR~alN~l~~ 106 (281)
T PRK06543 50 GIDVFAAAFRLVDPAITVTLAVADGE-RFEAGDILATVTGPARSVLTAERIALNFTQR 106 (281)
T ss_pred CHHHHHHHHHHhCCCeEEEEEeCCCC-EecCCCEEEEEEecHHHHHHHHHHHHHHHHH
Confidence 45678899899987444 3322111 1135688999999999999999999888853
No 177
>PRK06106 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=44.81 E-value=1.1e+02 Score=32.93 Aligned_cols=55 Identities=15% Similarity=0.214 Sum_probs=39.1
Q ss_pred CchHHHHHHHHhCCeEEeccCCCCCCC--CCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 239 GGETIKNMQARTGARIQVIPLHLPPGD--TSTERTVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 239 GGstIK~Iqe~TGArIqI~~~~~ppge--~s~er~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
|-..+++|-+..++.|++.-. ...++ ...+.+++|+|....+..+.+.++.+|.-
T Consensus 55 G~~~a~~vf~~~~~~~~~~~~-~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~L~~ 111 (281)
T PRK06106 55 GLDLARLAFRLVDPEIEMRRH-LPDGAAVAPGDVIATISGPARGLLTAERTALNFLCH 111 (281)
T ss_pred CHHHHHHHHHHhCCceEEEEE-eCCCCEEcCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 345678899999866444321 11111 34578999999999999999999888854
No 178
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=44.41 E-value=2.4e+02 Score=28.66 Aligned_cols=25 Identities=24% Similarity=0.338 Sum_probs=21.3
Q ss_pred EEEEEcC--HHHHHHHHHHHHHHHhhc
Q 005922 271 TVQIDGT--SEQIESAKQLVNEVISEN 295 (669)
Q Consensus 271 ~VtItG~--peqVq~Ak~LI~dlL~e~ 295 (669)
.+.|||- ++.++.|.+.|.+.|++-
T Consensus 156 K~ViTGaK~~ed~~~Av~~i~~~L~el 182 (185)
T COG2101 156 KLVITGAKSEEDAEQAVEKIQSRLEEL 182 (185)
T ss_pred cEEEecCCCHHHHHHHHHHHHHHHHHh
Confidence 4678887 788999999999999873
No 179
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=43.47 E-value=52 Score=36.43 Aligned_cols=56 Identities=18% Similarity=0.316 Sum_probs=46.9
Q ss_pred CCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHH--HHHhh
Q 005922 228 PNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVN--EVISE 294 (669)
Q Consensus 228 P~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~--dlL~e 294 (669)
+++.+-.|.|..+.+++.|.+..|+.|... .+.++|+|+...|+.|..++. +++..
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~r-----------G~~~~i~g~~~~v~~A~~~l~~l~~~~~ 79 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVAR-----------GEAVRIIGARPLVDVATRVLLTLELLAE 79 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeC-----------CceEEEEechHHHHHHHHHHhHHHHHHH
Confidence 356777899999999999999999998863 468999999779999988888 55544
No 180
>cd02191 FtsZ FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells.
Probab=43.39 E-value=22 Score=38.36 Aligned_cols=129 Identities=12% Similarity=0.132 Sum_probs=63.4
Q ss_pred cchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCCC--CCcEEEEe
Q 005922 149 ETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQA--GSDHFAMK 226 (669)
Q Consensus 149 etIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~--~~~t~~I~ 226 (669)
..|++|++.+.+-|.|+.+ ++..+... ..++.|++.+.++|.+.........+ ..+.. ....++..
T Consensus 138 ~~l~~L~~~~D~~iv~dN~---------~L~~~~~~-~~~~~af~~~N~~ia~~i~~it~~i~--~~g~invD~~dv~~~ 205 (303)
T cd02191 138 EGFQTLVREVDNLMVIPNE---------KLRQIGEK-ASLEGAFDHADEVLVRAVGGLFGAIE--IEGEINVDFADVKNV 205 (303)
T ss_pred HHHHHHHHhCCEEEEEehH---------HHHHHhhc-CChHHHHHHHHHHHHHHHHHHHHhhc--cCCcccCCHHHHHHH
Confidence 4789999999999998743 23333222 23456777777777765432211110 00000 00001111
Q ss_pred eCCC---ceeeeecCCchHHHHHHHHh-CCeEEeccCCCCCCCCCCccEEEEEcCH----HHHHHHHHHHHHHHh
Q 005922 227 IPNN---KVGLVIGKGGETIKNMQART-GARIQVIPLHLPPGDTSTERTVQIDGTS----EQIESAKQLVNEVIS 293 (669)
Q Consensus 227 VP~~---~vG~IIGKGGstIK~Iqe~T-GArIqI~~~~~ppge~s~er~VtItG~p----eqVq~Ak~LI~dlL~ 293 (669)
+-.. .+|.=.+++-.++++.-++. ...+--. ......+.-.|.|+|.+ +.|..+.++|.+.+.
T Consensus 206 l~~~G~a~ig~g~~~g~~~~~~a~~~Al~~pll~~----~~~~~A~~~Lv~i~g~~~l~~~e~~~~~~~i~~~~~ 276 (303)
T cd02191 206 MDGGGVAMVGYGSEDVTNRATEAVRKAALGPLLLP----CEIEGAEGALLVMAGPPDLNLKEIERVRKWLEEQTG 276 (303)
T ss_pred hccCCeEEEEEEEecCchHHHHHHHHHHhCCCCCC----CCcccCCEEEEEEECCCCCCHHHHHHHHHHHHHHcC
Confidence 1111 22222344555565544443 2221110 01123345679999964 477778888877765
No 181
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=42.87 E-value=1.5e+02 Score=29.15 Aligned_cols=45 Identities=22% Similarity=0.372 Sum_probs=35.7
Q ss_pred CchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHH
Q 005922 239 GGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEV 291 (669)
Q Consensus 239 GGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dl 291 (669)
.-..|.+|.+.++|+|.=. ..+.-+|.++|+++.|..-.+++...
T Consensus 96 ~r~~i~~i~~~f~a~ivdv--------~~~~~~ie~tG~~~ki~~~~~~l~~~ 140 (157)
T TIGR00119 96 GRDEIIRLTNIFRGRIVDV--------SPDSYTVEVTGDSDKIDAFLELLRPF 140 (157)
T ss_pred CHHHHHHHHHHhCCEEEEe--------cCCEEEEEEcCCHHHHHHHHHHhhhc
Confidence 3457889999999998743 23456899999999999988888764
No 182
>PLN02716 nicotinate-nucleotide diphosphorylase (carboxylating)
Probab=41.74 E-value=1.6e+02 Score=32.19 Aligned_cols=99 Identities=12% Similarity=0.107 Sum_probs=56.5
Q ss_pred HHHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhC--CeEEeccCCCCCCCCCC
Q 005922 191 AEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTG--ARIQVIPLHLPPGDTST 268 (669)
Q Consensus 191 A~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TG--ArIqI~~~~~ppge~s~ 268 (669)
...+|...|+|+.....+.....+. ....+.++.|-...-+.|-| -..+++|-+..+ ++|.+.-.+-.. -...
T Consensus 19 ~~~~i~~~L~ED~~~~gDlTt~~~~--~~~~~~~a~i~ake~gvlaG--~~~a~~vf~~l~~~~~v~~~~~dG~~-v~~G 93 (308)
T PLN02716 19 IEAVIKLALAEDAGDRGDVTCLATI--PGDMEAEATFLAKADGVLAG--IALADMVFEEVDPSLKVEWAAIDGDF-VHKG 93 (308)
T ss_pred HHHHHHHHHHHhCCCCCCCCccccc--CCCCeEEEEEEeCCCEEEEC--HHHHHHHHHHcCCCeEEEEEeCCCCE-ecCC
Confidence 4557777888876411111000000 01112233333333444443 456788888888 666654221111 1345
Q ss_pred ccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 269 ERTVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 269 er~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
+.+++|+|+...|..+.+.++.+|.-
T Consensus 94 ~~i~~v~G~a~~il~~ER~aLN~L~~ 119 (308)
T PLN02716 94 LKFGKVTGPAHSILVAERVVLNFMQR 119 (308)
T ss_pred CEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 78999999999999999999888853
No 183
>PF09869 DUF2096: Uncharacterized protein conserved in archaea (DUF2096); InterPro: IPR017098 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=41.07 E-value=34 Score=34.12 Aligned_cols=57 Identities=16% Similarity=0.208 Sum_probs=43.4
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHh
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAE 201 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e 201 (669)
.+.||.++.... =+++.+|.+-.|+.|.+.. +.+|.|.|+.|.|.+|++.|..+.+|
T Consensus 113 ~~iRv~l~~~i~-------~erl~ei~E~~gvI~Efee---------~~~V~I~Gdke~Ik~aLKe~s~~wke 169 (169)
T PF09869_consen 113 ETIRVKLKKPIQ-------EERLQEISEWHGVIFEFEE---------DDKVVIEGDKERIKKALKEFSSFWKE 169 (169)
T ss_pred eeEEEecCccch-------HHHHHHHHHHhceeEEecC---------CcEEEEeccHHHHHHHHHHHHHHhcC
Confidence 455666555432 3567889999999999932 35699999999999999999887654
No 184
>PRK05848 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=40.74 E-value=2.2e+02 Score=30.56 Aligned_cols=97 Identities=13% Similarity=0.153 Sum_probs=58.6
Q ss_pred HHHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCcc
Q 005922 191 AEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTER 270 (669)
Q Consensus 191 A~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er 270 (669)
...+|..+|+|+..... ... ..... ....++.|-...-+.|- |-..+++|-+..+|+|.+.-.+-.. -...+.
T Consensus 3 ~~~~i~~~l~ED~~~~D-lTt-~~~~~--~~~~~a~i~ar~~~v~~--G~~~a~~i~~~l~~~~~~~~~dG~~-v~~g~~ 75 (273)
T PRK05848 3 IKDFLEAALKEDLGRGD-LFE-RLLEK--DFKATAKIIAKSEGVFS--GEKYALELLEMTGIECVFTIKDGER-FKKGDI 75 (273)
T ss_pred HHHHHHHHHHhcCCCCC-ccc-cccCC--CCeEEEEEEEcCCEEEE--CHHHHHHHHHHcCCEEEEEcCCCCE-ecCCCE
Confidence 34577778888754211 101 11100 12233333333344443 3467888999999988865332111 135678
Q ss_pred EEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 271 TVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 271 ~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
+++|.|....+..+.+.++.+|+-
T Consensus 76 i~~i~G~a~~ll~~Er~~ln~l~~ 99 (273)
T PRK05848 76 LMEIEGDFSMLLKVERTLLNLLQH 99 (273)
T ss_pred EEEEEECHHHHHHHHHHHHHHHHH
Confidence 999999999999999999888854
No 185
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=40.35 E-value=44 Score=36.97 Aligned_cols=58 Identities=17% Similarity=0.335 Sum_probs=47.7
Q ss_pred EeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHH--HHHHh
Q 005922 134 EIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLIN--DVLAE 201 (669)
Q Consensus 134 lVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~--elI~e 201 (669)
+-++..+-.|.|..+++++.|++..|++|.... +-++|+|+.+.|+.|.+.|. +++..
T Consensus 20 ~~~~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG----------~~~~i~g~~~~v~~A~~~l~~l~~~~~ 79 (348)
T COG1702 20 LSDDNELVALFGPTDTNLSLLEIALGVSIVARG----------EAVRIIGARPLVDVATRVLLTLELLAE 79 (348)
T ss_pred cCCchhhhhhcCCCCccHHHHHHHhCcEEEeCC----------ceEEEEechHHHHHHHHHHhHHHHHHH
Confidence 334677888999999999999999999999863 34899999888888888888 55554
No 186
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=40.26 E-value=28 Score=35.87 Aligned_cols=36 Identities=25% Similarity=0.353 Sum_probs=28.4
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhcCcEEEE
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQV 164 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~I 164 (669)
-.+.+.|-....++||||.|++++.||.-+.+-++-
T Consensus 91 ~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 345666677779999999999999999877665544
No 187
>PF03958 Secretin_N: Bacterial type II/III secretion system short domain; InterPro: IPR005644 This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (IPR004846 from INTERPRO).; PDB: 3EZJ_C 2Y3M_A 3OSS_D.
Probab=38.53 E-value=84 Score=26.39 Aligned_cols=24 Identities=21% Similarity=0.553 Sum_probs=20.9
Q ss_pred CccEEEEEcCHHHHHHHHHHHHHH
Q 005922 268 TERTVQIDGTSEQIESAKQLVNEV 291 (669)
Q Consensus 268 ~er~VtItG~peqVq~Ak~LI~dl 291 (669)
....|.|+|+++.++..++||.+|
T Consensus 53 ~tNsliv~g~~~~~~~i~~li~~L 76 (82)
T PF03958_consen 53 RTNSLIVRGTPEDLEQIRELIKQL 76 (82)
T ss_dssp TTTEEEEEEEHHHHHHHHHHHHHH
T ss_pred CCCEEEEEeCHHHHHHHHHHHHHH
Confidence 356899999999999999999875
No 188
>TIGR00065 ftsZ cell division protein FtsZ. This family consists of cell division protein FtsZ, a GTPase found in bacteria, the chloroplast of plants, and in archaebacteria. Structurally similar to tubulin, FtsZ undergoes GTP-dependent polymerization into filaments that form a cytoskeleton involved in septum synthesis.
Probab=37.65 E-value=35 Score=37.76 Aligned_cols=130 Identities=15% Similarity=0.220 Sum_probs=65.2
Q ss_pred cchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCCC--CCcEEEEe
Q 005922 149 ETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQA--GSDHFAMK 226 (669)
Q Consensus 149 etIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~--~~~t~~I~ 226 (669)
..|++|++.+.+-|.|+.+ +++.+... ..+..|++.+.++|.+....-....+ ..+.. ....++-.
T Consensus 155 ~~l~~L~~~~D~vividNd---------~L~~~~~~-~~i~~af~~~N~iia~~i~~it~~ir--~~g~iNvDf~dv~~v 222 (349)
T TIGR00065 155 EGLERLKQAVDTLIVIPND---------KLLEVVPN-LPLNDAFKVADDVLVRAVKGISELIT--KPGLINIDFADVRAV 222 (349)
T ss_pred HHHHHHHHhCCEEEEEeCH---------HHHHhhcC-CCHHHHHHHHHHHHHHHHHhHHHhhc--cCCcCcCCHHHHHHH
Confidence 3789999999999999743 44545444 44566888877777775432211100 00000 00001111
Q ss_pred eCC---CceeeeecCCch----HHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC----HHHHHHHHHHHHHHHhh
Q 005922 227 IPN---NKVGLVIGKGGE----TIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT----SEQIESAKQLVNEVISE 294 (669)
Q Consensus 227 VP~---~~vG~IIGKGGs----tIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~----peqVq~Ak~LI~dlL~e 294 (669)
+-. .++|.=.+++-. ..+-+++...+..--. ......+.-.|.|+|. .+.|..+.++|.+.+..
T Consensus 223 l~~~G~a~iG~g~~~g~~~~~r~~~A~~~al~~pLl~~----~~i~~A~~~Lv~i~~~~~l~l~ev~~~~~~i~~~~~~ 297 (349)
T TIGR00065 223 MSGGGVAMMGIGEALGEDTANRAFEAVRKALSSPLLDV----DKISGAKGALVHITGGADLTLLEAEEIQEIITSELDQ 297 (349)
T ss_pred HhcCCeEEEEEEEecCCcchHHHHHHHHHHHhCCCcCC----cccccccEEEEEEEcCCCCCHHHHHHHHHHHHHhcCC
Confidence 111 123333344444 2333444333332110 0012334456899985 56788888888887753
No 189
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=37.23 E-value=70 Score=33.00 Aligned_cols=29 Identities=28% Similarity=0.543 Sum_probs=24.6
Q ss_pred EEEEeeCCCceeeeecCCchHHHHHHHHh
Q 005922 222 HFAMKIPNNKVGLVIGKGGETIKNMQART 250 (669)
Q Consensus 222 t~~I~VP~~~vG~IIGKGGstIK~Iqe~T 250 (669)
.++|.|-...-+.|||++|.+|++|++..
T Consensus 63 ~i~I~I~~~~pg~vIG~~g~~i~~l~~~l 91 (211)
T TIGR01009 63 KIRVTIHTARPGIVIGKKGSEIEKLRKDL 91 (211)
T ss_pred ceEEEEEeCCCcceeCCCchHHHHHHHHH
Confidence 46788888888999999999999998654
No 190
>KOG3294 consensus WW domain binding protein WBP-2, contains GRAM domain [Signal transduction mechanisms]
Probab=36.72 E-value=1.4e+02 Score=31.71 Aligned_cols=27 Identities=11% Similarity=0.199 Sum_probs=14.6
Q ss_pred CccccccCCHHHHHHHHHHHHHHHHhh
Q 005922 176 TRSVELMGTPEQIAKAEQLINDVLAEA 202 (669)
Q Consensus 176 eRvVtItGt~E~V~kA~~lI~elI~e~ 202 (669)
-|||-|+-.+..-.+.+.|=..+|++.
T Consensus 56 ~RiIFis~~~~D~fksF~MPf~~mkd~ 82 (261)
T KOG3294|consen 56 HRIIFISSKPKDAFKSFMMPFNLMKDV 82 (261)
T ss_pred ceEEEecCCCCcchhhhcchhhhhhhc
Confidence 356666555444455555555555553
No 191
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=36.57 E-value=1.1e+02 Score=30.68 Aligned_cols=25 Identities=20% Similarity=0.256 Sum_probs=20.3
Q ss_pred cEEEEEcC--HHHHHHHHHHHHHHHhh
Q 005922 270 RTVQIDGT--SEQIESAKQLVNEVISE 294 (669)
Q Consensus 270 r~VtItG~--peqVq~Ak~LI~dlL~e 294 (669)
..|+|+|. .+.+++|.+.|..+|++
T Consensus 147 GKvvitGaks~~~~~~a~~~i~~~l~~ 173 (174)
T cd04518 147 GKMVITGAKSEEDAKRAVEKLLSRLKE 173 (174)
T ss_pred CEEEEEecCCHHHHHHHHHHHHHHHhh
Confidence 36889987 77899999999888864
No 192
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=36.48 E-value=27 Score=35.85 Aligned_cols=29 Identities=31% Similarity=0.475 Sum_probs=23.4
Q ss_pred EEEEeccccccceeccCCcchhHHHhhcC
Q 005922 131 KKIEIPNIRVGVIIGKSGETIKYLQLQSG 159 (669)
Q Consensus 131 ~rIlVP~~~vG~IIGKgGetIK~IqeeTG 159 (669)
.++.|-...-|.||||+|++|++|++...
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 55556668889999999999999887653
No 193
>PLN00062 TATA-box-binding protein; Provisional
Probab=36.42 E-value=2.2e+02 Score=28.71 Aligned_cols=27 Identities=30% Similarity=0.393 Sum_probs=22.6
Q ss_pred cEEEEEcC--HHHHHHHHHHHHHHHhhcc
Q 005922 270 RTVQIDGT--SEQIESAKQLVNEVISENR 296 (669)
Q Consensus 270 r~VtItG~--peqVq~Ak~LI~dlL~e~~ 296 (669)
..|+|+|. .+.++.|.+.|..+|.+-+
T Consensus 147 GkvvitGaks~~~~~~ai~~i~p~L~~~~ 175 (179)
T PLN00062 147 GKIVITGAKVREEIYTAFENIYPVLTEFR 175 (179)
T ss_pred CEEEEEecCCHHHHHHHHHHHHHHHHHhc
Confidence 36888888 6789999999999998754
No 194
>CHL00048 rps3 ribosomal protein S3
Probab=35.69 E-value=28 Score=36.01 Aligned_cols=30 Identities=20% Similarity=0.175 Sum_probs=25.1
Q ss_pred ceEEEEeccccccceeccCCcchhHHHhhc
Q 005922 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQS 158 (669)
Q Consensus 129 vt~rIlVP~~~vG~IIGKgGetIK~IqeeT 158 (669)
...+|.|-...-|.|||++|++|++|+++.
T Consensus 66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 66 DLIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred CeEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 346777778888999999999999988765
No 195
>COG0331 FabD (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]
Probab=35.58 E-value=1.4e+02 Score=32.65 Aligned_cols=56 Identities=20% Similarity=0.350 Sum_probs=42.7
Q ss_pred ceeeeecCCchHHHHHHHHhCCe--EEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHh
Q 005922 231 KVGLVIGKGGETIKNMQARTGAR--IQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVIS 293 (669)
Q Consensus 231 ~vG~IIGKGGstIK~Iqe~TGAr--IqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~ 293 (669)
-...|+|--=+.|+++.++..-. |.|... |. ++.|.|+|.++.|++|...++++=.
T Consensus 132 ~Maav~gl~~e~v~~~~~~~~~~~~v~iaN~------N~-~~QiVIsG~~~ale~a~~~~~~~g~ 189 (310)
T COG0331 132 GMAAVLGLDDEQVEKACEEAAQGTVVEIANY------NS-PGQIVISGTKEALEKAAEILKEAGA 189 (310)
T ss_pred cHHHHcCCCHHHHHHHHHHhccCCeEEEeee------CC-CCcEEEECCHHHHHHHHHHHHHhhh
Confidence 34456777778899999888753 666532 23 4899999999999999999988663
No 196
>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=35.18 E-value=29 Score=35.40 Aligned_cols=29 Identities=31% Similarity=0.470 Sum_probs=24.8
Q ss_pred eEEEEeccccccceeccCCcchhHHHhhc
Q 005922 130 SKKIEIPNIRVGVIIGKSGETIKYLQLQS 158 (669)
Q Consensus 130 t~rIlVP~~~vG~IIGKgGetIK~IqeeT 158 (669)
..+|.|....-|.|||++|.+|++|+++.
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 47788888889999999999999887654
No 197
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=33.31 E-value=32 Score=35.82 Aligned_cols=30 Identities=23% Similarity=0.307 Sum_probs=25.1
Q ss_pred eEEEEeccccccceeccCCcchhHHHhhcC
Q 005922 130 SKKIEIPNIRVGVIIGKSGETIKYLQLQSG 159 (669)
Q Consensus 130 t~rIlVP~~~vG~IIGKgGetIK~IqeeTG 159 (669)
..+|.|-...-|.|||++|.+|++|+++..
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L~ 74 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLLQ 74 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHHH
Confidence 467778888899999999999999887643
No 198
>cd02201 FtsZ_type1 FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells.
Probab=32.58 E-value=52 Score=35.43 Aligned_cols=131 Identities=18% Similarity=0.239 Sum_probs=64.2
Q ss_pred cchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCCC--CCcEEEEe
Q 005922 149 ETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQA--GSDHFAMK 226 (669)
Q Consensus 149 etIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~--~~~t~~I~ 226 (669)
..|++|++.+.+-|.|+.+ ++..+......+.+|++.+.++|.+....-....+ ..+.. ....++..
T Consensus 138 ~~l~~L~~~~d~~ividN~---------~L~~~~~~~~~i~~af~~~n~~ia~~i~~it~~~~--~~g~invD~~dv~~v 206 (304)
T cd02201 138 EGLEELRKHVDTLIVIPND---------KLLEVVDKNLPLLEAFKLADDVLAQAVKGISDLIT--KPGLINLDFADVKTV 206 (304)
T ss_pred HHHHHHHHhCCEEEEEecH---------HHHHhhccCCCHHHHHHHHHHHHHHHHHHHHHHhc--cCccccCCHHHHHHH
Confidence 4688999999999998743 34444443334556777777666664332110000 00000 00000001
Q ss_pred eCC---CceeeeecCCchHHHH-HHHHhCCeEEeccCCCCCCCCCCccEEEEEcC----HHHHHHHHHHHHHHHhh
Q 005922 227 IPN---NKVGLVIGKGGETIKN-MQARTGARIQVIPLHLPPGDTSTERTVQIDGT----SEQIESAKQLVNEVISE 294 (669)
Q Consensus 227 VP~---~~vG~IIGKGGstIK~-Iqe~TGArIqI~~~~~ppge~s~er~VtItG~----peqVq~Ak~LI~dlL~e 294 (669)
+-. ..+|.-.+++-.++++ |++...+.+.-. . ..++.+.-.|.|+|. .+.|+.+.++|.+.+.+
T Consensus 207 l~~~G~a~ig~g~~~g~~r~~~Av~~Al~~pLl~~--~--~i~~A~~~Lv~I~~~~~l~l~e~~~~~~~i~~~~~~ 278 (304)
T cd02201 207 MKNKGVALMGIGEASGENRAIEAAEKAISSPLLED--D--SISGAKGVLVNITGGSDLTLEEVNEAAEIIKEKVDP 278 (304)
T ss_pred hccCCeEEEEEEEecCchHHHHHHHHHHhCcCcCC--C--ChhcccEEEEEEEcCCCCCHHHHHHHHHHHHHHhCC
Confidence 111 1233333444334433 444443332211 0 012334456899995 55788888888888765
No 199
>PRK07896 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=32.40 E-value=3.2e+02 Score=29.62 Aligned_cols=99 Identities=10% Similarity=0.101 Sum_probs=54.0
Q ss_pred HHHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHH-HhCC---eEEeccCCCCCCCC
Q 005922 191 AEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQA-RTGA---RIQVIPLHLPPGDT 266 (669)
Q Consensus 191 A~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe-~TGA---rIqI~~~~~ppge~ 266 (669)
...+|..+|+|+.....+...+-+. ......++.|-...-+.|- |-..+.+|-+ ..++ +|.+.-.+-. .-.
T Consensus 15 ~~~~i~~~l~ED~~~~~DlTt~~l~--~~~~~~~a~i~are~gila--G~~~a~~if~~~~~~~~~~v~~~~~dG~-~v~ 89 (289)
T PRK07896 15 ARAVIRRALDEDLRYGPDVTTVATV--PADAVATASVVSREAGVVA--GLDVALLVLDEVLGTDGYEVLDRVEDGA-RVP 89 (289)
T ss_pred HHHHHHHHHHHhCCCCCCCCcCccC--CCCCeEEEEEEecCCEEEE--CHHHHHHHHHHhcCCCceEEEEEcCCCC-Eec
Confidence 4567777888876421011010000 0111223333333334443 3456777774 5566 5544322111 113
Q ss_pred CCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 267 STERTVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 267 s~er~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
..+.+++|.|....+..+.+.++.+|.-
T Consensus 90 ~g~~i~~i~G~a~~ll~~ER~aLN~L~~ 117 (289)
T PRK07896 90 PGQALLTVTAPTRGLLTAERTMLNLLCH 117 (289)
T ss_pred CCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 4578999999999999999999888854
No 200
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=32.37 E-value=93 Score=32.58 Aligned_cols=30 Identities=27% Similarity=0.526 Sum_probs=24.5
Q ss_pred cEEEEeeCCCceeeeecCCchHHHHHHHHh
Q 005922 221 DHFAMKIPNNKVGLVIGKGGETIKNMQART 250 (669)
Q Consensus 221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~T 250 (669)
..++|.|-...-+.|||++|..|++|++..
T Consensus 62 ~~i~I~I~~~rP~~iiG~~g~~i~~l~~~L 91 (232)
T PRK00310 62 KRVRVTIHTARPGIVIGKKGAEIEKLRKEL 91 (232)
T ss_pred CeEEEEEEECCCccccCCCcHHHHHHHHHH
Confidence 346677777888999999999999987664
No 201
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=32.35 E-value=3.5e+02 Score=27.07 Aligned_cols=25 Identities=16% Similarity=0.292 Sum_probs=20.5
Q ss_pred cEEEEEcC--HHHHHHHHHHHHHHHhh
Q 005922 270 RTVQIDGT--SEQIESAKQLVNEVISE 294 (669)
Q Consensus 270 r~VtItG~--peqVq~Ak~LI~dlL~e 294 (669)
..|+|+|. .+.++.|.+.|..+|.+
T Consensus 147 GkvvitGaks~~~~~~a~~~i~p~L~~ 173 (174)
T cd04516 147 GKIVLTGAKSREEIYQAFENIYPILLQ 173 (174)
T ss_pred CEEEEEecCCHHHHHHHHHHHHHHHhh
Confidence 36888887 77899999999988864
No 202
>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=32.18 E-value=36 Score=35.60 Aligned_cols=29 Identities=28% Similarity=0.446 Sum_probs=20.4
Q ss_pred ceEEEEec-cccccceeccCCcchhHHHhh
Q 005922 129 TSKKIEIP-NIRVGVIIGKSGETIKYLQLQ 157 (669)
Q Consensus 129 vt~rIlVP-~~~vG~IIGKgGetIK~Iqee 157 (669)
+...|+|. +++-+.||||+|++||+|..+
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ 250 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIA 250 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence 33445555 345789999999999987543
No 203
>cd07055 BMC_like_2 Bacterial Micro-Compartment (BMC)-like domain 2. BMC like 2 domains exist in cyanobacteria, proteobacteria, and actinobacteria and are homologs of carboxysome shell proteins. They might be encoded from putative organelles involved in unknown metabolic process. Although it has been suggested that these carboxysome shell protein homologs form hexamers and further assemble into the flat facets of the polyhedral bacterial organelles shell at present no experimental evidence exists to directly support this view.
Probab=30.88 E-value=57 Score=27.42 Aligned_cols=38 Identities=16% Similarity=0.173 Sum_probs=26.1
Q ss_pred hhcCcEEEEccCCccCCCCCCcc--ccccCCHHHHHHHHHHHHHH
Q 005922 156 LQSGAKIQVTRDTEADLNSPTRS--VELMGTPEQIAKAEQLINDV 198 (669)
Q Consensus 156 eeTGAkI~Iskd~e~~p~~~eRv--VtItGt~E~V~kA~~lI~el 198 (669)
|..++.| +++ ..+|+-++ +.|+|+..+|+.|++.|++.
T Consensus 21 Kaa~V~i-~d~----f~gCPq~~~~l~i~Gdvs~Ve~Al~~i~~~ 60 (61)
T cd07055 21 KASGVFV-SDI----FGSCPQHMITLAIFGETSAVELAMREIEED 60 (61)
T ss_pred hccCeEE-EEe----cCCCCCceEEEEEEecHHHHHHHHHHHhhc
Confidence 4455666 432 45666543 44799999999999998764
No 204
>PRK06978 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=30.65 E-value=5.2e+02 Score=28.17 Aligned_cols=68 Identities=12% Similarity=0.170 Sum_probs=44.3
Q ss_pred EEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCC--CCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 224 AMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGD--TSTERTVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 224 ~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge--~s~er~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
++.|-...-+.|- |-..+++|-+..+++|++.-. ...++ ...+.+++|+|....+..+.+.++.+|+-
T Consensus 54 ~a~i~are~gvla--G~~~a~~if~~l~~~~~v~~~-~~dG~~v~~G~~i~~~~G~a~~lL~~ER~aLN~l~~ 123 (294)
T PRK06978 54 RARVIVREEAVLC--GVPWFDAVMRAVDPSIEVTWR-YREGDRMTADSTVCELEGPARALLTAERNALNFLQL 123 (294)
T ss_pred EEEEEEcCCEEEE--CHHHHHHHHHHhCCCeEEEEE-cCCCCEeCCCCEEEEEEeCHHHHHHHHHHHHHHHHH
Confidence 3334334444443 346788899988874444321 11111 34578899999999999999999888853
No 205
>PRK09016 quinolinate phosphoribosyltransferase; Validated
Probab=30.05 E-value=5e+02 Score=28.35 Aligned_cols=68 Identities=10% Similarity=0.118 Sum_probs=43.5
Q ss_pred EEeeCCCceeeeecCCchHHHHHHHHhCCe--EEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 224 AMKIPNNKVGLVIGKGGETIKNMQARTGAR--IQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 224 ~I~VP~~~vG~IIGKGGstIK~Iqe~TGAr--IqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
++.|-...-+.|-| -..+++|-+..+++ |++.-.+-.. -...+.+++|.|....|..+.+.++.+|.-
T Consensus 57 ~~~i~ake~gi~aG--~~~a~~vf~~l~~~~~v~~~~~dG~~-v~~G~~i~~i~G~a~~ll~~ER~~LN~L~~ 126 (296)
T PRK09016 57 HATIITREDGVFCG--KRWVEEVFIQLGDDVTIEWHVDDGDV-ITANQTLFELTGPARVLLTGERTALNFVQT 126 (296)
T ss_pred EEEEEEcCCEEEEC--HHHHHHHHHHcCCCeEEEEEcCCCCE-ecCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 33333333344433 35678888999866 4333221111 134578999999999999999999888853
No 206
>COG0014 ProA Gamma-glutamyl phosphate reductase [Amino acid transport and metabolism]
Probab=29.98 E-value=28 Score=39.17 Aligned_cols=112 Identities=22% Similarity=0.263 Sum_probs=55.5
Q ss_pred CCCceEEEEeccccccceeccCCcc---hhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhh
Q 005922 126 SMGTSKKIEIPNIRVGVIIGKSGET---IKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEA 202 (669)
Q Consensus 126 ~~~vt~rIlVP~~~vG~IIGKgGet---IK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~ 202 (669)
++....++.||-..+|.|-=-.=+. +-.|+-+|| .-|++.|..|.+.-.. .|.++|++.
T Consensus 104 nGL~i~~~rvPLGVigvIYEsRPnVtvdaaaLclKsG-----------------NAvILRGGsea~~Sn~-ai~~~i~~a 165 (417)
T COG0014 104 NGLQIYRVRVPLGVIGVIYESRPNVTVDAAALCLKSG-----------------NAVILRGGSEAIHSNA-AIVEVIQEA 165 (417)
T ss_pred CCCEEEEEEccceEEEEEEecCCccHHHHHHHHHhcC-----------------CEEEEeCcHHHhhhHH-HHHHHHHHH
Confidence 3457889999999998875322111 122333333 3466677777765433 233333332
Q ss_pred hcC-CCCcchhcccC-CCCCcEEEEeeCCCceeeeecCCchHH-HHHHHHhCCeEE
Q 005922 203 ESG-GSGIVARRLTG-QAGSDHFAMKIPNNKVGLVIGKGGETI-KNMQARTGARIQ 255 (669)
Q Consensus 203 ~~~-~~~~~~rr~~~-~~~~~t~~I~VP~~~vG~IIGKGGstI-K~Iqe~TGArIq 255 (669)
... ......-.+.. ..+....+|+--..++..||=+||+.+ +.|++.+.+=|.
T Consensus 166 L~~~~lP~~aVqli~~~~R~~v~~ll~l~~yiD~iIPRGg~~Li~~v~~~a~vPVi 221 (417)
T COG0014 166 LEKAGLPADAVQLIEDTDREEVLELLRLDGYIDLVIPRGGAGLIRRVVENATVPVI 221 (417)
T ss_pred HHHcCCCHHHhhhccCCCHHHHHHHHhhcCceeEEEcCCcHHHHHHHHhCCcCCEE
Confidence 211 11110000000 001111233445678889999999864 556666544443
No 207
>cd01573 modD_like ModD; Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase) present in some modABC operons in bacteria, which are involved in molybdate transport. In general, QPRTases are part of the de novo synthesis pathway of NAD in both prokaryotes and eukaryotes. They catalyse the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide.
Probab=29.93 E-value=1e+02 Score=32.97 Aligned_cols=68 Identities=15% Similarity=0.183 Sum_probs=48.2
Q ss_pred EEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHh
Q 005922 132 KIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAE 201 (669)
Q Consensus 132 rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e 201 (669)
++.|-.+.-|.|=|. +.+++|-+..+++|.+.......-...+.+++|.|....+..+.+.+..+|..
T Consensus 30 ~~~~~ak~~gv~aG~--~~~~~~~~~~~~~v~~~~~dG~~v~~g~~i~~i~G~~~~ll~~Er~~ln~l~~ 97 (272)
T cd01573 30 KITFRARDPGVLCGT--EEAARILELLGLEVDLAAASGSRVAAGAVLLEAEGPAAALHLGWKVAQTLLEW 97 (272)
T ss_pred EEEEEECCCEEEECH--HHHHHHHHHcCcEEEEEcCCCCEecCCCEEEEEEEcHHHHHHHHHHHHHHHHH
Confidence 333444445555443 46788888899988865433334456689999999999999999988888764
No 208
>PRK09616 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed
Probab=29.55 E-value=74 Score=37.22 Aligned_cols=112 Identities=14% Similarity=0.150 Sum_probs=72.6
Q ss_pred CCCCccccccC-CHHHHHHHHHHHHHHHHhhhcCCCCcchhcccC----CCCCcEEEEeeCCCceeeeecCC--chHHHH
Q 005922 173 NSPTRSVELMG-TPEQIAKAEQLINDVLAEAESGGSGIVARRLTG----QAGSDHFAMKIPNNKVGLVIGKG--GETIKN 245 (669)
Q Consensus 173 ~~~eRvVtItG-t~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~----~~~~~t~~I~VP~~~vG~IIGKG--GstIK~ 245 (669)
++.+-+++++| +++.+.+|++.+..+|.+.. +........... ........|.+..+.+-.|+|.. -+.|++
T Consensus 221 ~Tkni~lE~ag~d~~~~~~al~~~~~ll~~~~-g~v~~~~~~~~~~~~~~~~~~~~~i~l~~~~i~~~lG~~i~~~~i~~ 299 (552)
T PRK09616 221 GTRNLFIDVTGTDLEAVLLALNIIATALAERG-GTIESVKVIYPDGELTTPDLTPRTREVSVEYINKLLGIDLSAEEIIE 299 (552)
T ss_pred CCcEEEEEeccCCHHHHHHHHHHHHHHHHHhC-CEEEEEEEEeCCCCEeCCCCCceEEEecHHHHHHHhCCCCCHHHHHH
Confidence 34455667777 56788889998888887752 211000000000 00123346788888889999965 357999
Q ss_pred HHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 246 MQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 246 Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
|-++.|+.|... .+.-.|+|---...|.....||+|+++-
T Consensus 300 iL~~Lgf~~~~~---------~~~~~v~vP~~R~DI~~~~DliEEiaR~ 339 (552)
T PRK09616 300 LLERMRYDAEIG---------DDKVKVTVPPYRVDILHEVDVIEDVAIA 339 (552)
T ss_pred HHHHcCCCcEec---------CCeEEEEeCCCcccccccchHHHHHHHH
Confidence 999999998642 1234466665577788889999999875
No 209
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=29.50 E-value=79 Score=27.12 Aligned_cols=43 Identities=21% Similarity=0.318 Sum_probs=32.6
Q ss_pred chHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHH
Q 005922 240 GETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNE 290 (669)
Q Consensus 240 GstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~d 290 (669)
-..|.+|-+.++|+|.-. +.+.-+|.++|+++.|....+++..
T Consensus 16 r~ei~~l~~~f~a~ivd~--------~~~~~iie~tG~~~kid~fi~~l~~ 58 (75)
T PF10369_consen 16 RSEILQLAEIFRARIVDV--------SPDSIIIELTGTPEKIDAFIKLLKP 58 (75)
T ss_dssp HHHHHHHHHHTT-EEEEE--------ETTEEEEEEEE-HHHHHHHHHHSTG
T ss_pred HHHHHHHHHHhCCEEEEE--------CCCEEEEEEcCCHHHHHHHHHHhhh
Confidence 356888999999998755 3446789999999999988888765
No 210
>PRK00089 era GTPase Era; Reviewed
Probab=29.42 E-value=42 Score=35.28 Aligned_cols=25 Identities=32% Similarity=0.567 Sum_probs=18.1
Q ss_pred EEEec-cccccceeccCCcchhHHHh
Q 005922 132 KIEIP-NIRVGVIIGKSGETIKYLQL 156 (669)
Q Consensus 132 rIlVP-~~~vG~IIGKgGetIK~Iqe 156 (669)
.|+|. .++.+.||||+|++||+|..
T Consensus 229 ~i~v~~~~~k~i~ig~~g~~i~~i~~ 254 (292)
T PRK00089 229 TIYVERDSQKGIIIGKGGAMLKKIGT 254 (292)
T ss_pred EEEEccCCceeEEEeCCcHHHHHHHH
Confidence 44444 34578999999999987654
No 211
>COG0331 FabD (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]
Probab=29.41 E-value=54 Score=35.76 Aligned_cols=58 Identities=19% Similarity=0.351 Sum_probs=45.7
Q ss_pred ccccceeccCCcchhHHHhhcCcE--EEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHh
Q 005922 138 IRVGVIIGKSGETIKYLQLQSGAK--IQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAE 201 (669)
Q Consensus 138 ~~vG~IIGKgGetIK~IqeeTGAk--I~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e 201 (669)
.-+..|+|-.-+.|+++.++..-. |.|... |++ +.|+|+|.++.|+++...+.++-.+
T Consensus 131 g~Maav~gl~~e~v~~~~~~~~~~~~v~iaN~-----N~~-~QiVIsG~~~ale~a~~~~~~~g~k 190 (310)
T COG0331 131 GGMAAVLGLDDEQVEKACEEAAQGTVVEIANY-----NSP-GQIVISGTKEALEKAAEILKEAGAK 190 (310)
T ss_pred ccHHHHcCCCHHHHHHHHHHhccCCeEEEeee-----CCC-CcEEEECCHHHHHHHHHHHHHhhhh
Confidence 557788888899999999988753 666432 344 8899999999999999888777633
No 212
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=29.36 E-value=51 Score=26.79 Aligned_cols=49 Identities=33% Similarity=0.548 Sum_probs=32.0
Q ss_pred chHHHH--HHHHhCCeEEeccCC----CCCCC--CCCccEEEEEcCHHHHHHHHHHH
Q 005922 240 GETIKN--MQARTGARIQVIPLH----LPPGD--TSTERTVQIDGTSEQIESAKQLV 288 (669)
Q Consensus 240 GstIK~--Iqe~TGArIqI~~~~----~ppge--~s~er~VtItG~peqVq~Ak~LI 288 (669)
|.+|++ +++.++|.|.-..+. .+..+ -.....|.|.|..+.|++..+++
T Consensus 14 gk~l~el~l~~~~~~~i~~i~R~~~~~~p~~~~~l~~gD~l~v~g~~~~i~~~~~~~ 70 (71)
T PF02080_consen 14 GKTLKELDLPERYGVRIVAIKRGGEIIIPDGDTVLQAGDILIVVGDPEDIERFRELF 70 (71)
T ss_dssp TEBHHHCTHHCHHTEEEEEEEETEEEES--TT-BE-TTEEEEEEEEHHHHHHHHHHT
T ss_pred CCCHHHCCCCccCCEEEEEEEECCEEECCCCCCEECCCCEEEEEECHHHHHHHHHhh
Confidence 346888 788889888665432 11111 12245799999999999888764
No 213
>PF08920 SF3b1: Splicing factor 3B subunit 1; InterPro: IPR015016 This group of proteins consists of several eukaryotic splicing factor 3B subunit 1 proteins, which associate with p14 through a C terminus beta-strand that interacts with beta-3 of the p14 RNA recognition motif (RRM) beta-sheet, which is in turn connected to an alpha-helix by a loop that makes extensive contacts with both the shorter C-terminal helix and RRM of p14. This subunit is required for 'A' splicing complex assembly (formed by the stable binding of U2 snRNP to the branchpoint sequence in pre-mRNA) and 'E' splicing complex assembly []. ; PDB: 2FHO_A 3LQV_P 2PEH_D 2F9J_P 2F9D_Q.
Probab=28.66 E-value=20 Score=34.98 Aligned_cols=12 Identities=33% Similarity=0.299 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCC
Q 005922 13 PSKRKYEDQTTP 24 (669)
Q Consensus 13 ~~Kr~~~d~~~p 24 (669)
++||||+|+|..
T Consensus 5 ~kkrsRWDetP~ 16 (144)
T PF08920_consen 5 KKKRSRWDETPA 16 (144)
T ss_dssp ------------
T ss_pred ccccccccCCcc
Confidence 459999998864
No 214
>COG0072 PheT Phenylalanyl-tRNA synthetase beta subunit [Translation, ribosomal structure and biogenesis]
Probab=28.52 E-value=86 Score=37.60 Aligned_cols=110 Identities=20% Similarity=0.178 Sum_probs=71.7
Q ss_pred CccccccC-CHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeec--CCchHHHHHHHHhCC
Q 005922 176 TRSVELMG-TPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIG--KGGETIKNMQARTGA 252 (669)
Q Consensus 176 eRvVtItG-t~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIG--KGGstIK~Iqe~TGA 252 (669)
...+-++| +.+.++.|+..+..+|.+...+...................|.+..+.+..|+| -.-+.|++|-++.|+
T Consensus 217 ~~~r~~rGvD~~~v~~al~~~~~ll~e~~gg~v~~~~~~~~~~~~~~~~~i~~~~~~i~~llG~~ls~eei~~iL~rLg~ 296 (650)
T COG0072 217 ASFRFERGVDPELVEKALNRATTLLAEICGGEVSSVVIVGGDEKLTPPRKIELRLERINRLLGLELSAEEIEKILKRLGF 296 (650)
T ss_pred eeEEeecCCCHHHHHHHHHHHHHHHHHhcCCeeeeEEEecCCcCCCCCceEEecHHHHHHHhCCCCCHHHHHHHHHHcCC
Confidence 34455566 578999999999999988653211111000000000002466777888888999 457789999999999
Q ss_pred eEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 253 RIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 253 rIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
.+....+ .-.|+|---...|.....||+|+++-
T Consensus 297 ~~~~~~~---------~~~V~vPs~R~DI~~e~DliEEv~r~ 329 (650)
T COG0072 297 KVEVKGD---------GLTVTVPSYRVDILIEADLIEEVARI 329 (650)
T ss_pred eeEecCC---------cEEEeCCCCcccccchhHHHHHHHHH
Confidence 9987521 23455555577788889999998865
No 215
>PRK09330 cell division protein FtsZ; Validated
Probab=27.43 E-value=56 Score=36.71 Aligned_cols=128 Identities=16% Similarity=0.236 Sum_probs=64.8
Q ss_pred CcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCC------CcchhcccCCCCCc
Q 005922 148 GETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGS------GIVARRLTGQAGSD 221 (669)
Q Consensus 148 GetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~------~~~~rr~~~~~~~~ 221 (669)
-+.|++|++.+.+-|.|+.+ +++.+......+..|++++.++|.+....-. +.....+.
T Consensus 150 ~~gL~~L~~~~D~vIvi~Nd---------~L~~~~~~~~~l~~Af~~ad~vL~~~v~~It~~i~~pG~iNvDfa------ 214 (384)
T PRK09330 150 EEGIEELRKHVDTLIVIPND---------KLLEVVDKKTPLLDAFKAADDVLRQAVQGITDLITKPGLINLDFA------ 214 (384)
T ss_pred HHHHHHHHHHCCEEEEEecH---------HHHhhccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCCcccCCHH------
Confidence 34789999999999999743 5555555444556677666666665432111 00000000
Q ss_pred EEEEeeC---CCceeeeecCCchHHHHHHHHh-CCeEEeccCCCCCCCCCCccEEEEEcC----HHHHHHHHHHHHHHHh
Q 005922 222 HFAMKIP---NNKVGLVIGKGGETIKNMQART-GARIQVIPLHLPPGDTSTERTVQIDGT----SEQIESAKQLVNEVIS 293 (669)
Q Consensus 222 t~~I~VP---~~~vG~IIGKGGstIK~Iqe~T-GArIqI~~~~~ppge~s~er~VtItG~----peqVq~Ak~LI~dlL~ 293 (669)
.++-.+- ..++|.=.+.+-.++++.-++. ....- .. ...+..+.-+|.|+|. .+.|..+.++|.+.+.
T Consensus 215 Dvk~vm~~~G~a~~G~G~a~g~~ra~~A~~~Ai~spLl-~~---~~i~~A~~vLv~I~g~~~l~l~e~~~~~~~i~~~~~ 290 (384)
T PRK09330 215 DVKTVMSEMGLAMMGIGEASGEDRAREAAEKAISSPLL-ED---VDISGAKGVLVNITGGPDLTLFEVEEAAEIIREAAD 290 (384)
T ss_pred HHHHHHhcCCeEEEEEEEecCccHHHHHHHHHHhCcCc-CC---CChhhcceEEEEEECCCCCCHHHHHHHHHHHHHHhC
Confidence 0000011 1123333444444454433332 21110 00 0012334456899985 4678888888888876
Q ss_pred h
Q 005922 294 E 294 (669)
Q Consensus 294 e 294 (669)
+
T Consensus 291 ~ 291 (384)
T PRK09330 291 P 291 (384)
T ss_pred C
Confidence 4
No 216
>PRK00394 transcription factor; Reviewed
Probab=27.27 E-value=6.4e+02 Score=25.34 Aligned_cols=25 Identities=28% Similarity=0.363 Sum_probs=20.9
Q ss_pred cEEEEEcC--HHHHHHHHHHHHHHHhh
Q 005922 270 RTVQIDGT--SEQIESAKQLVNEVISE 294 (669)
Q Consensus 270 r~VtItG~--peqVq~Ak~LI~dlL~e 294 (669)
..|+|+|. .+.+++|.+.|..+|++
T Consensus 148 GKvvitGaks~~~~~~a~~~i~~~l~~ 174 (179)
T PRK00394 148 GKLVITGAKSEEDAEKAVEKILEKLEE 174 (179)
T ss_pred CEEEEEecCCHHHHHHHHHHHHHHHHH
Confidence 35889988 67899999999998876
No 217
>PRK05412 putative nucleotide-binding protein; Reviewed
Probab=26.59 E-value=4.1e+02 Score=26.58 Aligned_cols=42 Identities=12% Similarity=0.291 Sum_probs=29.6
Q ss_pred hHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHH
Q 005922 241 ETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEV 291 (669)
Q Consensus 241 stIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dl 291 (669)
..|..+...+..+|+.. -....|.|+|- .+.++.+..||.+.
T Consensus 106 KkIvK~IKd~klKVqa~---------IQGd~vRVtgKkrDDLQ~viallk~~ 148 (161)
T PRK05412 106 KKIVKLIKDSKLKVQAQ---------IQGDQVRVTGKKRDDLQAVIALLRKA 148 (161)
T ss_pred HHHHHHHHhcCCceeEE---------ecCcEEEEecCCHhHHHHHHHHHHhc
Confidence 34555566677666653 22458999997 78899988888764
No 218
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=26.03 E-value=53 Score=36.18 Aligned_cols=29 Identities=21% Similarity=0.379 Sum_probs=22.9
Q ss_pred ceEEEEecccc-ccceeccCCcchhHHHhh
Q 005922 129 TSKKIEIPNIR-VGVIIGKSGETIKYLQLQ 157 (669)
Q Consensus 129 vt~rIlVP~~~-vG~IIGKgGetIK~Iqee 157 (669)
+..+|+||... ..+||||+|..|++|-++
T Consensus 328 I~~~v~~pK~s~~klliGkgG~ki~qI~~~ 357 (379)
T KOG1423|consen 328 IQVEVVCPKNSQKKLLIGKGGKKISQIGTR 357 (379)
T ss_pred EEEEEEcCCCcceeEEEcCCCccHHHHHHH
Confidence 55678888655 678999999999988654
No 219
>COG2090 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.70 E-value=3.6e+02 Score=26.25 Aligned_cols=65 Identities=15% Similarity=0.232 Sum_probs=45.8
Q ss_pred CcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHh
Q 005922 220 SDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVIS 293 (669)
Q Consensus 220 ~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~ 293 (669)
.+.+.|.++ ..+..|||.|-.. +.-+...+|.|-... --.+|+|.|.-++.+-..-++||+.|=+
T Consensus 63 ~i~vvi~~~-~~~D~viG~Ghp~---ltl~~~~~mV~RkS~-----yv~~rTl~I~adKAA~DldR~lV~~Lk~ 127 (141)
T COG2090 63 RIRVVIRVG-GLVDEVIGRGHPR---LTLEHPTSMVFRKSD-----YVDDRTLMIRADKAAADLDRELVEALKD 127 (141)
T ss_pred eEEEEEEcC-CcEEEEEeecCCC---cccCCCceEEEEecC-----cccCceEEEecchhhhhhhHHHHHHHhC
Confidence 355667777 8899999998654 334566777775432 2347899999988777777777776543
No 220
>PRK04021 hypothetical protein; Reviewed
Probab=25.17 E-value=1.3e+02 Score=27.23 Aligned_cols=40 Identities=28% Similarity=0.491 Sum_probs=30.6
Q ss_pred hHHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHH
Q 005922 241 ETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAK 285 (669)
Q Consensus 241 stIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak 285 (669)
+-|+-|.+.++++|.|. .+..+..++|.|.|. .+.+....
T Consensus 50 ali~~LAk~l~~~I~I~-----~G~~sr~K~v~i~g~~~e~l~~~L 90 (92)
T PRK04021 50 ELVKFFSKLLGAEVEII-----RGETSREKDLLVKGISLEEVKKKL 90 (92)
T ss_pred HHHHHHHHHhCCCEEEE-----ecCCcCceEEEEecCCHHHHHHHh
Confidence 34677888899999986 455778999999995 77766543
No 221
>COG3874 Uncharacterized conserved protein [Function unknown]
Probab=25.15 E-value=1.1e+02 Score=29.53 Aligned_cols=74 Identities=23% Similarity=0.336 Sum_probs=45.1
Q ss_pred EEEEeeCCCceeeeecCCchHHHHHHHH------hCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhhc
Q 005922 222 HFAMKIPNNKVGLVIGKGGETIKNMQAR------TGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN 295 (669)
Q Consensus 222 t~~I~VP~~~vG~IIGKGGstIK~Iqe~------TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e~ 295 (669)
.-.++||-+++++=.|-||..-|.=..+ +|+-+.|.+..+--..+...|+|.|.+.-.-+++-.++|-++|++.
T Consensus 34 dgs~iiPvsKv~fGFgaGGgEgk~~t~~~g~GGG~GaGa~I~PiAflvl~~d~vrml~l~~~g~~~~kl~d~vPqiiekI 113 (138)
T COG3874 34 DGSTIIPVSKVGFGFGAGGGEGKKSTGEKGFGGGAGAGASIEPIAFLVLKSDGVRMLPLDEKGHLLEKLVDMVPQIIEKI 113 (138)
T ss_pred CCcEEEEEEEEeeeeccCCcccccccCcCCCCCCCCCccccceeEEEEEecCCEEEEEecccccHHHHHHHHHHHHHHHH
Confidence 3467899999999999888766433122 1222222221100111456899999987667777777777777663
No 222
>PRK13018 cell division protein FtsZ; Provisional
Probab=24.93 E-value=96 Score=34.82 Aligned_cols=129 Identities=16% Similarity=0.204 Sum_probs=67.6
Q ss_pred cchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHhhhcCCCCcchhcccCCCCC--cEEEEe
Q 005922 149 ETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGS--DHFAMK 226 (669)
Q Consensus 149 etIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e~~~~~~~~~~rr~~~~~~~--~t~~I~ 226 (669)
..|++|++.+.+-|.|+.+ +++.+. ....+..|++.+.++|.+....-....+ +.+.... ..++-.
T Consensus 166 ~gL~~L~e~~D~vividNd---------~L~~i~-~~~~i~~af~~~N~iIa~~I~~It~~i~--~~G~iN~Df~dv~~v 233 (378)
T PRK13018 166 EGIERLREAADTVIVIDNN---------RLLDIV-PNLPIADAFSVADEVIAETVKGITETIT--KPSLINLDFADVKSV 233 (378)
T ss_pred HHHHHHHHhCCEEEEEecH---------HHHHHH-hcCCHHHHHHHHHHHHHHHHHhhhhhcc--cCCceecCHHHHHHH
Confidence 5789999999999999743 444444 3334667888888888776543221110 0000000 000001
Q ss_pred eCC---CceeeeecCCchHHHH-HHHHhCCeEEeccCCCCCCCCCCccEEEEEcC----HHHHHHHHHHHHHHHhh
Q 005922 227 IPN---NKVGLVIGKGGETIKN-MQARTGARIQVIPLHLPPGDTSTERTVQIDGT----SEQIESAKQLVNEVISE 294 (669)
Q Consensus 227 VP~---~~vG~IIGKGGstIK~-Iqe~TGArIqI~~~~~ppge~s~er~VtItG~----peqVq~Ak~LI~dlL~e 294 (669)
+-+ ..+|.=.+++..++++ |++...+.+ +. . ..+..+.-.|.|+|. .+.|..+.++|.+.+..
T Consensus 234 l~~~G~a~iG~G~a~g~~r~~~Av~~Al~spL-L~-~---di~~A~~~Lv~I~g~~~l~l~ev~~~~~~i~~~~~~ 304 (378)
T PRK13018 234 MKGGGVAMMGVGEAKGQNRAMEAVRAALANPL-LD-V---DYRGAKGALVHITGGPDLTLKEANEAASRITEELDP 304 (378)
T ss_pred hccCCEEEEEEEEecCCcHHHHHHHHHHhCCC-cC-C---ChhhhceEEEEEECCCCCCHHHHHHHHHHHHHHcCC
Confidence 111 1233333455555554 444444332 21 0 111334467999995 56788888888887754
No 223
>COG0206 FtsZ Cell division GTPase [Cell division and chromosome partitioning]
Probab=24.61 E-value=94 Score=34.41 Aligned_cols=39 Identities=21% Similarity=0.194 Sum_probs=26.8
Q ss_pred ceEEEEecccccc-ceeccCCcchhHHHhhcCcEEEEccC
Q 005922 129 TSKKIEIPNIRVG-VIIGKSGETIKYLQLQSGAKIQVTRD 167 (669)
Q Consensus 129 vt~rIlVP~~~vG-~IIGKgGetIK~IqeeTGAkI~Iskd 167 (669)
+.--+.+|...-| .-+-+--+-|++|++.+..-|.|+.+
T Consensus 128 tvavvt~Pf~~EG~~r~~~A~~gi~~L~~~~DtlIvi~Nd 167 (338)
T COG0206 128 TVAVVTLPFSFEGSPRMENAEEGIEELREVVDTLIVIPND 167 (338)
T ss_pred EEEEEEecchhcCchHHHHHHHHHHHHHHhCCcEEEEecH
Confidence 3445556766665 33444456789999999999999743
No 224
>TIGR02516 type_III_yscC type III secretion outer membrane pore, YscC/HrcC family. A number of proteins homologous to the type IV pilus secretin PilQ (TIGR02515) are involved in type IV pilus formation, competence for transformation, type III secretion, and type II secretion (also called the main terminal branch of the general secretion pathway). The clade described by this model contains the outer membrane pore proteins of bacterial type III secretion systems, typified by YscC for animal pathogens and HrcC for plant pathogens.
Probab=24.16 E-value=9.8e+02 Score=27.26 Aligned_cols=25 Identities=20% Similarity=0.287 Sum_probs=20.8
Q ss_pred CccEEEEEcCHHHHHHHHHHHHHHH
Q 005922 268 TERTVQIDGTSEQIESAKQLVNEVI 292 (669)
Q Consensus 268 ~er~VtItG~peqVq~Ak~LI~dlL 292 (669)
....|.|+|+++.+++.++||.++=
T Consensus 206 ~tNsliv~~~~~~~~~i~~lI~~LD 230 (462)
T TIGR02516 206 RTNAVLIRDRPERMAIYEQLIQQLD 230 (462)
T ss_pred CCCEEEEEeCHHHHHHHHHHHHHhC
Confidence 3567999999999999999888643
No 225
>TIGR01334 modD putative molybdenum utilization protein ModD. The gene modD for a member of this family is found with molybdenum transport genes modABC in Rhodobacter capsulatus. However, disruption of modD causes only a 4-fold (rather than 500-fold for modA, modB, modC) change in the external molybdenum concentration required to suppress an alternative nitrogenase. ModD proteins are highly similar to nicotinate-nucleotide pyrophosphorylase (also called quinolinate phosphoribosyltransferase). The function unknown.
Probab=24.15 E-value=2e+02 Score=30.94 Aligned_cols=68 Identities=21% Similarity=0.170 Sum_probs=50.0
Q ss_pred EEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHh
Q 005922 132 KIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAE 201 (669)
Q Consensus 132 rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e 201 (669)
++.|-.+.-|.|=| -+.+++|-+..+++|++.......-...+.++++.|+...|..+.+.+..+|..
T Consensus 34 ~~~~~are~gv~~G--~~~~~~i~~~l~~~~~~~~~dG~~v~~g~~i~~~~G~a~~ll~~eR~alN~l~~ 101 (277)
T TIGR01334 34 HITFTARDEGIVSG--VSEAAKLLKQLGASIDYAVPSGSRALAGTLLLEAKGSAGQLHQGWKSAQSVLEW 101 (277)
T ss_pred EEEEEEcCCEEEEC--HHHHHHHHHHcCCEEEEEeCCCCEeCCCCEEEEEEecHHHHHHHHHHHHHHHHH
Confidence 33344445555544 357788999999999886554434456688999999999999999988888765
No 226
>PRK15494 era GTPase Era; Provisional
Probab=23.99 E-value=60 Score=35.45 Aligned_cols=26 Identities=27% Similarity=0.418 Sum_probs=19.0
Q ss_pred EEEEec-cccccceeccCCcchhHHHh
Q 005922 131 KKIEIP-NIRVGVIIGKSGETIKYLQL 156 (669)
Q Consensus 131 ~rIlVP-~~~vG~IIGKgGetIK~Iqe 156 (669)
..|+|. .++-+.||||+|++||+|..
T Consensus 275 ~~i~v~~~sqk~iiiG~~g~~ik~i~~ 301 (339)
T PRK15494 275 QVIVVSRESYKTIILGKNGSKIKEIGA 301 (339)
T ss_pred EEEEECCCCceeEEEcCCcHHHHHHHH
Confidence 445555 34578999999999987643
No 227
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=23.08 E-value=60 Score=33.45 Aligned_cols=28 Identities=32% Similarity=0.570 Sum_probs=23.7
Q ss_pred EEEEeccccccceeccCCcchhHHHhhc
Q 005922 131 KKIEIPNIRVGVIIGKSGETIKYLQLQS 158 (669)
Q Consensus 131 ~rIlVP~~~vG~IIGKgGetIK~IqeeT 158 (669)
++|.|-...-+.|||++|.+|++|++..
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l 91 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDL 91 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHH
Confidence 6677778888999999999999988654
No 228
>COG1839 Uncharacterized conserved protein [Function unknown]
Probab=23.06 E-value=1e+02 Score=30.26 Aligned_cols=65 Identities=22% Similarity=0.337 Sum_probs=44.9
Q ss_pred cEEEEeeCCCceeeeecCCchHHHHHHHHh--------CCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHH
Q 005922 221 DHFAMKIPNNKVGLVIGKGGETIKNMQART--------GARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEV 291 (669)
Q Consensus 221 ~t~~I~VP~~~vG~IIGKGGstIK~Iqe~T--------GArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dl 291 (669)
+.+.|.+|+. +-.|||..-- ||.+.+.. +++.-|. .++-+.+|.|..+|+ .+-++.|.+.++.+
T Consensus 6 e~vdi~~Pe~-~nvIiGqshF-IkTVeDL~ealvt~vP~~kfgiA-----f~EAsg~rLvR~~GND~eL~~lA~ena~~I 78 (162)
T COG1839 6 EVVDIEIPEG-VNVIIGQSHF-IKTVEDLYEALVTAVPGLKFGIA-----FNEASGPRLVRYTGNDEELVKLAIENALKI 78 (162)
T ss_pred EEEEecCcCC-ceEEEeechh-heeHHHHHHHHHhcCCCceEEEE-----eecccCCeeEEecCCcHHHHHHHHHHHHHh
Confidence 3567888887 8899998753 77665442 4444443 456778999999999 55566777776655
Q ss_pred H
Q 005922 292 I 292 (669)
Q Consensus 292 L 292 (669)
-
T Consensus 79 ~ 79 (162)
T COG1839 79 G 79 (162)
T ss_pred c
Confidence 3
No 229
>TIGR00471 pheT_arch phenylalanyl-tRNA synthetase, beta subunit. Every known example of the phenylalanyl-tRNA synthetase, except the monomeric form of mitochondrial, is an alpha 2 beta 2 heterotetramer. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps. This model represents the subfamily that includes the beta subunit from eukaryotic cytosol, the Archaea, and spirochetes.
Probab=22.83 E-value=1.7e+02 Score=34.42 Aligned_cols=113 Identities=13% Similarity=0.175 Sum_probs=72.1
Q ss_pred CCCCccccccC-CHHHHHHHHHHHHHHHHhhhcCCCCcc-hhc---ccCCCCCcEEEEeeCCCceeeeecCC--chHHHH
Q 005922 173 NSPTRSVELMG-TPEQIAKAEQLINDVLAEAESGGSGIV-ARR---LTGQAGSDHFAMKIPNNKVGLVIGKG--GETIKN 245 (669)
Q Consensus 173 ~~~eRvVtItG-t~E~V~kA~~lI~elI~e~~~~~~~~~-~rr---~~~~~~~~t~~I~VP~~~vG~IIGKG--GstIK~ 245 (669)
++++-+|+.+| +++.+..|+..+..+|.+...+..... ... ...........|.+..+++..|+|.. -+.|++
T Consensus 223 ~T~nIllE~Ag~D~~~~~~al~~a~~li~~~~~g~~~~~~v~~~~~~~~~p~~~~~~i~~~~~~i~~~lG~~l~~~ei~~ 302 (551)
T TIGR00471 223 NTRNLLIDVTGTDKTAVEITLNIACTMFADRGDGRITVVEVERPDEHLGQPNLAPRFMEVSVEYINSLLGLNLSADEIAH 302 (551)
T ss_pred CCceEEEEEecCCHHHHHHHHHHHHHHHHHhCCCceeEEEEEECCCcccCCCCccceEEecHHHHHHHhCCCCCHHHHHH
Confidence 44556677778 567888888888888887532211110 000 00000123346788888999999964 367889
Q ss_pred HHHHhCCeEEeccCCCCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 246 MQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 246 Iqe~TGArIqI~~~~~ppge~s~er~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
|-++.|++|.... +.-.|+|=--...|..-..+|+|+++-
T Consensus 303 iL~~Lg~~v~~~~---------~~~~v~vP~~R~DI~~~~DliEEIaR~ 342 (551)
T TIGR00471 303 SLKKMRLDAVQSD---------EKLKVVIPAYRVDILHEVDIIEDVAIG 342 (551)
T ss_pred HHHHhCCCeEecC---------CcEEEEcCCCccccCchhHHHHHHHHH
Confidence 9999999985431 123455554477888899999998865
No 230
>PRK05742 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=22.57 E-value=8.1e+02 Score=26.37 Aligned_cols=96 Identities=11% Similarity=0.156 Sum_probs=54.4
Q ss_pred HHHHHHHHHhhhcCCCCcchhcccCCCCCcEEEEeeCCCceeeeecCCchHHHHHHHHhCCeEE--eccCCCCCCCCCCc
Q 005922 192 EQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQ--VIPLHLPPGDTSTE 269 (669)
Q Consensus 192 ~~lI~elI~e~~~~~~~~~~rr~~~~~~~~t~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIq--I~~~~~ppge~s~e 269 (669)
.++|..+|+|+..... ... .... .....++.|-...-+.|- |-..+.+|-+..+++|+ +.-.+-. .-...+
T Consensus 10 ~~~i~~~l~ED~~~gD-lTt-~~~~--~~~~~~~~i~ar~~gi~~--G~~~~~~i~~~~~~~~~~~~~~~dG~-~v~~g~ 82 (277)
T PRK05742 10 EANVRRALAEDIGSGD-ITA-QLIP--AERLAKATVITREAAVIA--GTAWVDAVFRQLDPRVAVHWQVADGE-RVSANQ 82 (277)
T ss_pred HHHHHHHHHhcCCCCC-CCc-cccC--CCcEEEEEEEECCCEEEE--CHHHHHHHHHHcCCceEEEEEeCCCC-EEcCCC
Confidence 4567777777654211 111 0111 112223333333334443 34677888888986643 3321111 113457
Q ss_pred cEEEEEcCHHHHHHHHHHHHHHHhh
Q 005922 270 RTVQIDGTSEQIESAKQLVNEVISE 294 (669)
Q Consensus 270 r~VtItG~peqVq~Ak~LI~dlL~e 294 (669)
.+++|.|+...+..+.+.++.+|+-
T Consensus 83 ~i~~i~G~~~~ll~~ER~~ln~l~~ 107 (277)
T PRK05742 83 VLFHLEGPARSLLTGERSALNFLQL 107 (277)
T ss_pred EEEEEEEcHHHHHHHHHHHHHHHHH
Confidence 8999999999999999999888854
No 231
>COG4598 HisP ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]
Probab=22.56 E-value=32 Score=35.28 Aligned_cols=79 Identities=24% Similarity=0.360 Sum_probs=52.5
Q ss_pred EEEeeCCCceeeeecCCchHHHHHHHHhCCeEEeccC--CCCCCCCCCccEEEEEcC--HHHHHHHHHHHHHH-Hhhccc
Q 005922 223 FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPL--HLPPGDTSTERTVQIDGT--SEQIESAKQLVNEV-ISENRI 297 (669)
Q Consensus 223 ~~I~VP~~~vG~IIGKGGstIK~Iqe~TGArIqI~~~--~~ppge~s~er~VtItG~--peqVq~Ak~LI~dl-L~e~~~ 297 (669)
.+|.+-.+..|.++...-..|.+||.+.+--.+-... +...-+|-.|..|+|-|- .+.|++|..++..+ |.+.+.
T Consensus 68 eei~~k~~~~G~l~~ad~~q~~r~Rs~L~mVFQ~FNLWsHmtvLeNViEaPvhVLg~~k~ea~e~Ae~~L~kVGi~ek~~ 147 (256)
T COG4598 68 EEIRLKRDKDGQLKPADKRQLQRLRTRLGMVFQHFNLWSHMTVLENVIEAPVHVLGVSKAEAIERAEKYLAKVGIAEKAD 147 (256)
T ss_pred eEEEeeeCCCCCeeeCCHHHHHHHHHHhhHhhhhcchhHHHHHHHHHHhcchHhhcCCHHHHHHHHHHHHHHhCchhhhh
Confidence 3566667888999999999999999888754433221 222223455777888888 57788888887664 444444
Q ss_pred CCCC
Q 005922 298 RNPA 301 (669)
Q Consensus 298 r~~~ 301 (669)
.++.
T Consensus 148 ~YP~ 151 (256)
T COG4598 148 AYPA 151 (256)
T ss_pred cCcc
Confidence 4443
No 232
>TIGR00078 nadC nicotinate-nucleotide pyrophosphorylase. Synonym: quinolinate phosphoribosyltransferase (decarboxylating)
Probab=22.37 E-value=2.1e+02 Score=30.45 Aligned_cols=68 Identities=15% Similarity=0.177 Sum_probs=48.1
Q ss_pred EEEeccccccceeccCCcchhHHHhhcCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHh
Q 005922 132 KIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAE 201 (669)
Q Consensus 132 rIlVP~~~vG~IIGKgGetIK~IqeeTGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e 201 (669)
++.|-.+.-+.|-|. +.+.+|-+..+++|++.......-...+.+++|.|....|..+.+.+..+|..
T Consensus 28 ~~~~~ar~~~v~~G~--~~~~~i~~~~~~~v~~~~~dG~~v~~g~~i~~i~G~~~~il~~Er~~ln~l~~ 95 (265)
T TIGR00078 28 TASLVAKEDGVLAGL--PVARRVFEQLGVQVEWLVKDGDRVEPGEVVAEVEGPARSLLTAERTALNFLGR 95 (265)
T ss_pred EEEEEecCCEEEECH--HHHHHHHHHcCeEEEEEeCCCCEecCCCEEEEEEEcHHHHHHHHHHHHHHHHH
Confidence 334444455555443 46678888889887665433333456689999999999999999999888865
No 233
>PF04461 DUF520: Protein of unknown function (DUF520); InterPro: IPR007551 This entry represents the UPF0234 family of uncharacterised proteins.; PDB: 1IN0_A.
Probab=22.17 E-value=3.9e+02 Score=26.65 Aligned_cols=41 Identities=15% Similarity=0.292 Sum_probs=27.3
Q ss_pred HHHHHHHHhCCeEEeccCCCCCCCCCCccEEEEEcC-HHHHHHHHHHHHHH
Q 005922 242 TIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGT-SEQIESAKQLVNEV 291 (669)
Q Consensus 242 tIK~Iqe~TGArIqI~~~~~ppge~s~er~VtItG~-peqVq~Ak~LI~dl 291 (669)
.|..+...++.+|+.. -....|.|+|- .+.++.+..||.+.
T Consensus 107 kIvK~IKd~klKVqa~---------IQgd~vRVtgKkrDDLQ~viallk~~ 148 (160)
T PF04461_consen 107 KIVKLIKDSKLKVQAQ---------IQGDQVRVTGKKRDDLQEVIALLKEQ 148 (160)
T ss_dssp HHHHHHHHH--SEEEE---------EETTEEEEEES-HHHHHHHHHHHHHS
T ss_pred HHHHHHHhcCCceeEE---------ecCcEEEEecCCHHHHHHHHHHHHcc
Confidence 3444556676666653 12458999999 88899998888764
No 234
>PF06183 DinI: DinI-like family; InterPro: IPR010391 This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity []. The structure of DinI is known [].; PDB: 1GHH_A.
Probab=22.02 E-value=2.2e+02 Score=24.03 Aligned_cols=44 Identities=16% Similarity=0.360 Sum_probs=22.2
Q ss_pred HHHHHHHHh-CCeEEeccCCCCCCCCCCccEEEEEcCHH-HHHHHHHHHHHHHh
Q 005922 242 TIKNMQART-GARIQVIPLHLPPGDTSTERTVQIDGTSE-QIESAKQLVNEVIS 293 (669)
Q Consensus 242 tIK~Iqe~T-GArIqI~~~~~ppge~s~er~VtItG~pe-qVq~Ak~LI~dlL~ 293 (669)
-.|+|.+.. .|.|.|.. .....|+|.|..+ .-+...++|+++.+
T Consensus 13 L~kRl~~~yPd~~v~Vr~--------~s~~~l~v~g~~~~~k~~i~~iLqe~we 58 (65)
T PF06183_consen 13 LTKRLHRQYPDAEVRVRP--------GSANGLSVSGGKKDDKERIEEILQEMWE 58 (65)
T ss_dssp HHHHHHHH-SS-EEEEEE--------ESS-EEEEES--HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHCCCceEeeee--------cccCccccCCcCchHHHHHHHHHHHHHh
Confidence 356666665 47777762 2346899999954 33344444444443
No 235
>cd01572 QPRTase Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide. QPRTase functions as a homodimer with two active sites, each formed by the C-terminal region of one subunit and the N-terminal region of the other.
Probab=21.86 E-value=2.2e+02 Score=30.35 Aligned_cols=68 Identities=12% Similarity=0.108 Sum_probs=48.5
Q ss_pred EEEeccccccceeccCCcchhHHHhhc--CcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHh
Q 005922 132 KIEIPNIRVGVIIGKSGETIKYLQLQS--GAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAE 201 (669)
Q Consensus 132 rIlVP~~~vG~IIGKgGetIK~IqeeT--GAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e 201 (669)
++.|-.+.-+.|-| -+.+.+|-+.. +++|++.......-...+.+++|.|....|..+.+.+..+|..
T Consensus 30 ~~~~~ar~~~v~~G--~~~~~~i~~~~~~~l~v~~~~~dG~~v~~g~~i~~i~G~~~~ll~~Er~~ln~L~~ 99 (268)
T cd01572 30 EARLIAKEEGVLAG--LPVAEEVFELLDPGIEVEWLVKDGDRVEPGQVLATVEGPARSLLTAERTALNFLQR 99 (268)
T ss_pred EEEEEEcCCEEEEC--HHHHHHHHHHcCCCeEEEEEeCCCCEecCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 33333444455544 35778888888 8888665433334456789999999999999999999888865
No 236
>PF03958 Secretin_N: Bacterial type II/III secretion system short domain; InterPro: IPR005644 This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (IPR004846 from INTERPRO).; PDB: 3EZJ_C 2Y3M_A 3OSS_D.
Probab=21.29 E-value=1.2e+02 Score=25.42 Aligned_cols=33 Identities=30% Similarity=0.516 Sum_probs=23.7
Q ss_pred cCcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHH
Q 005922 158 SGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDV 198 (669)
Q Consensus 158 TGAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~el 198 (669)
...+|..+.. ...|+|+|+.+.+++..++|.+|
T Consensus 44 ~~~~i~~d~~--------tNsliv~g~~~~~~~i~~li~~L 76 (82)
T PF03958_consen 44 SSGRIVADER--------TNSLIVRGTPEDLEQIRELIKQL 76 (82)
T ss_dssp TTTEEEEECT--------TTEEEEEEEHHHHHHHHHHHHHH
T ss_pred CCeEEEEECC--------CCEEEEEeCHHHHHHHHHHHHHH
Confidence 3456766543 35688889999999888777665
No 237
>cd01568 QPRTase_NadC Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide. QPRTase functions as a homodimer with two active sites, each formed by the C-terminal region of one subunit and the N-terminal region of the other.
Probab=21.01 E-value=2.2e+02 Score=30.22 Aligned_cols=68 Identities=15% Similarity=0.185 Sum_probs=48.2
Q ss_pred EEEeccccccceeccCCcchhHHHhhc-CcEEEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHh
Q 005922 132 KIEIPNIRVGVIIGKSGETIKYLQLQS-GAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAE 201 (669)
Q Consensus 132 rIlVP~~~vG~IIGKgGetIK~IqeeT-GAkI~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e 201 (669)
++.|-.+.-+.|-|. +.+++|-+.. +++|++.......-...+.+++|.|+...+..+.+.+..+|..
T Consensus 30 ~~~i~~r~~~v~~G~--~~~~~i~~~~~~~~v~~~~~dG~~v~~g~~i~~i~G~~~~l~~~Er~~ln~L~~ 98 (269)
T cd01568 30 TATLIAKEEGVLAGL--EVAEEVFELLDGIEVEWLVKDGDRVEAGQVLLEVEGPARSLLTAERVALNLLQR 98 (269)
T ss_pred EEEEEecCCEEEECH--HHHHHHHHHhCCeEEEEEeCCCCEecCCCEEEEEEEcHHHHHHHHHHHHHHHHH
Confidence 333334455666553 5677888888 8888664333334456789999999999999999999888865
No 238
>PRK08072 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=20.54 E-value=1.7e+02 Score=31.35 Aligned_cols=52 Identities=8% Similarity=0.115 Sum_probs=37.0
Q ss_pred chhHHHhhcCcE--EEEccCCccCCCCCCccccccCCHHHHHHHHHHHHHHHHh
Q 005922 150 TIKYLQLQSGAK--IQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAE 201 (669)
Q Consensus 150 tIK~IqeeTGAk--I~Iskd~e~~p~~~eRvVtItGt~E~V~kA~~lI~elI~e 201 (669)
..++|-+..+.+ |.+.......-...+.+++|.|....|..+.+.+..+|..
T Consensus 52 ~a~~i~~~~~~~~~v~~~~~dG~~v~~g~~i~~~~G~~~~ll~~er~~ln~l~~ 105 (277)
T PRK08072 52 VIEEGYKLLDERIEVELHKKDGDLVKKGEIIATVQGPVASLLTGERVILNLIQR 105 (277)
T ss_pred HHHHHHHHcCCceEEEEEeCCCCEEcCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 447777777755 5444222223345578999999999999999999888765
Done!