Query 003942
Match_columns 784
No_of_seqs 415 out of 1888
Neff 6.3
Searched_HMMs 46136
Date Thu Mar 28 14:43:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003942.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003942hhsearch_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 4.7E-47 1E-51 421.1 33.1 249 116-374 138-394 (600)
2 KOG1676 K-homology type RNA bi 100.0 5.6E-37 1.2E-41 341.0 37.1 248 118-373 55-304 (600)
3 KOG2192 PolyC-binding hnRNP-K 100.0 3.7E-30 7.9E-35 260.8 17.4 240 116-369 47-384 (390)
4 KOG2193 IGF-II mRNA-binding pr 100.0 1.1E-28 2.4E-33 262.9 11.2 246 118-369 200-481 (584)
5 KOG2190 PolyC-binding proteins 100.0 4.1E-27 8.9E-32 266.2 23.0 252 119-374 45-414 (485)
6 KOG2191 RNA-binding protein NO 99.9 3.1E-26 6.8E-31 238.7 20.5 170 197-371 36-206 (402)
7 KOG2191 RNA-binding protein NO 99.9 2.4E-25 5.3E-30 232.1 14.8 251 117-369 39-315 (402)
8 KOG2193 IGF-II mRNA-binding pr 99.9 7.8E-26 1.7E-30 241.3 11.4 242 116-373 279-568 (584)
9 KOG2192 PolyC-binding hnRNP-K 99.9 1.1E-20 2.4E-25 192.2 18.5 147 199-369 47-193 (390)
10 KOG2190 PolyC-binding proteins 99.8 1.4E-20 3.1E-25 213.2 15.6 159 199-370 42-209 (485)
11 TIGR03665 arCOG04150 arCOG0415 99.7 1.1E-17 2.4E-22 167.1 11.8 139 204-370 2-152 (172)
12 PRK13763 putative RNA-processi 99.7 5.5E-17 1.2E-21 163.2 14.0 143 200-370 3-158 (180)
13 TIGR03665 arCOG04150 arCOG0415 99.5 5.6E-15 1.2E-19 147.7 7.1 141 121-273 2-152 (172)
14 KOG2279 Kinase anchor protein 99.5 9E-15 1.9E-19 162.3 9.0 235 116-366 67-365 (608)
15 PRK13763 putative RNA-processi 99.5 9.5E-15 2E-19 147.1 6.8 144 118-272 4-157 (180)
16 cd02396 PCBP_like_KH K homolog 99.3 2.7E-12 5.8E-17 108.0 7.7 65 297-364 1-65 (65)
17 cd02396 PCBP_like_KH K homolog 99.3 6.5E-12 1.4E-16 105.7 6.5 65 201-267 1-65 (65)
18 COG1094 Predicted RNA-binding 99.3 6.2E-11 1.3E-15 118.5 13.7 140 199-370 7-165 (194)
19 cd02393 PNPase_KH Polynucleoti 99.1 9.8E-11 2.1E-15 97.4 7.4 58 297-364 3-61 (61)
20 PF00013 KH_1: KH domain syndr 99.1 3.9E-11 8.4E-16 99.1 4.8 60 297-363 1-60 (60)
21 cd02394 vigilin_like_KH K homo 99.1 6E-11 1.3E-15 98.6 5.9 61 298-364 2-62 (62)
22 cd00105 KH-I K homology RNA-bi 99.1 1.4E-10 3E-15 96.4 7.8 63 298-364 2-64 (64)
23 KOG2279 Kinase anchor protein 99.1 1.6E-10 3.5E-15 129.0 6.3 144 198-369 66-209 (608)
24 cd02394 vigilin_like_KH K homo 99.1 1.9E-10 4.1E-15 95.6 5.0 62 201-267 1-62 (62)
25 PF00013 KH_1: KH domain syndr 99.0 1.1E-10 2.5E-15 96.2 3.2 60 201-266 1-60 (60)
26 cd00105 KH-I K homology RNA-bi 99.0 5.6E-10 1.2E-14 92.7 6.4 64 201-267 1-64 (64)
27 cd02393 PNPase_KH Polynucleoti 99.0 5.2E-10 1.1E-14 93.1 6.2 59 200-267 2-61 (61)
28 smart00322 KH K homology RNA-b 98.9 7.6E-09 1.7E-13 85.7 9.2 67 296-368 3-69 (69)
29 COG1094 Predicted RNA-binding 98.8 8.2E-09 1.8E-13 103.4 7.8 146 118-273 9-165 (194)
30 KOG2208 Vigilin [Lipid transpo 98.8 2.2E-08 4.7E-13 120.5 11.6 213 117-367 273-486 (753)
31 PF13014 KH_3: KH domain 98.8 1E-08 2.2E-13 79.2 5.6 43 306-351 1-43 (43)
32 smart00322 KH K homology RNA-b 98.8 2.6E-08 5.7E-13 82.4 8.0 67 199-270 2-68 (69)
33 KOG2208 Vigilin [Lipid transpo 98.8 8.9E-09 1.9E-13 123.8 6.9 218 114-369 344-562 (753)
34 KOG2113 Predicted RNA binding 98.7 1.3E-08 2.9E-13 106.9 5.3 153 198-365 24-179 (394)
35 PF13014 KH_3: KH domain 98.7 3.1E-08 6.8E-13 76.5 4.7 43 210-254 1-43 (43)
36 cd02395 SF1_like-KH Splicing f 98.6 1.2E-07 2.5E-12 89.6 8.7 67 305-371 15-97 (120)
37 cd02395 SF1_like-KH Splicing f 98.6 1.2E-07 2.7E-12 89.4 7.2 71 203-273 3-96 (120)
38 KOG0119 Splicing factor 1/bran 98.5 4.1E-07 9E-12 101.1 9.4 75 199-273 137-231 (554)
39 PRK08406 transcription elongat 98.3 1.8E-06 3.9E-11 83.7 7.0 104 200-332 32-135 (140)
40 TIGR02696 pppGpp_PNP guanosine 98.2 5.6E-06 1.2E-10 98.3 10.8 89 261-369 553-642 (719)
41 KOG0119 Splicing factor 1/bran 98.2 6.2E-06 1.4E-10 92.0 10.3 75 295-369 137-230 (554)
42 KOG2113 Predicted RNA binding 98.2 3E-06 6.4E-11 89.6 6.9 146 116-270 25-181 (394)
43 TIGR01952 nusA_arch NusA famil 97.9 3.3E-05 7.1E-10 75.0 8.2 103 201-332 34-136 (141)
44 TIGR03591 polynuc_phos polyrib 97.9 2.7E-05 5.8E-10 93.7 9.3 65 295-369 550-615 (684)
45 TIGR02696 pppGpp_PNP guanosine 97.8 3.1E-05 6.6E-10 92.2 7.7 67 197-272 575-642 (719)
46 PRK08406 transcription elongat 97.8 1.7E-05 3.7E-10 77.0 4.2 102 118-236 33-135 (140)
47 PLN00207 polyribonucleotide nu 97.8 1.1E-05 2.5E-10 97.6 2.7 68 197-273 682-751 (891)
48 KOG1588 RNA-binding protein Sa 97.8 0.0001 2.3E-09 77.3 9.3 75 294-368 90-190 (259)
49 TIGR03591 polynuc_phos polyrib 97.7 5.1E-05 1.1E-09 91.3 7.7 67 197-272 548-615 (684)
50 KOG1588 RNA-binding protein Sa 97.6 0.00019 4.2E-09 75.3 9.1 44 196-239 88-137 (259)
51 PF14611 SLS: Mitochondrial in 97.6 0.00095 2.1E-08 69.0 14.1 129 201-368 27-164 (210)
52 PLN00207 polyribonucleotide nu 97.6 9.5E-05 2.1E-09 89.9 7.7 67 295-371 684-752 (891)
53 COG0195 NusA Transcription elo 97.6 0.00017 3.7E-09 73.3 8.0 103 201-333 77-179 (190)
54 COG1185 Pnp Polyribonucleotide 97.6 0.00012 2.7E-09 85.5 7.6 94 261-373 526-620 (692)
55 COG5176 MSL5 Splicing factor ( 97.5 0.00016 3.4E-09 72.9 5.9 70 197-272 145-221 (269)
56 KOG0336 ATP-dependent RNA heli 97.5 0.00014 3.1E-09 80.0 5.6 75 195-275 42-116 (629)
57 KOG0336 ATP-dependent RNA heli 97.5 9.5E-05 2.1E-09 81.4 4.2 72 294-372 45-116 (629)
58 KOG3273 Predicted RNA-binding 97.4 0.00012 2.5E-09 73.5 4.0 149 198-369 72-231 (252)
59 KOG3273 Predicted RNA-binding 97.4 0.00025 5.4E-09 71.1 5.2 106 158-273 115-232 (252)
60 COG1185 Pnp Polyribonucleotide 97.3 0.00037 8E-09 81.6 6.1 68 198-274 550-618 (692)
61 PRK11824 polynucleotide phosph 97.2 0.00036 7.9E-09 84.3 5.9 64 296-369 554-618 (693)
62 TIGR01952 nusA_arch NusA famil 97.2 0.00023 4.9E-09 69.2 3.4 102 118-236 34-136 (141)
63 PRK12328 nusA transcription el 97.2 0.00098 2.1E-08 74.1 8.4 95 209-334 251-346 (374)
64 PRK00106 hypothetical protein; 97.0 0.0027 5.9E-08 74.0 10.0 66 295-369 224-291 (535)
65 TIGR03319 YmdA_YtgF conserved 97.0 0.0025 5.5E-08 74.5 9.7 66 295-369 203-270 (514)
66 TIGR01953 NusA transcription t 97.0 0.0019 4.1E-08 71.7 8.2 94 210-333 244-338 (341)
67 KOG2814 Transcription coactiva 96.9 0.00088 1.9E-08 72.3 4.6 71 199-274 56-127 (345)
68 PRK12704 phosphodiesterase; Pr 96.9 0.0035 7.5E-08 73.4 9.8 65 296-369 210-276 (520)
69 PRK12329 nusA transcription el 96.9 0.0018 4E-08 73.1 7.0 94 210-333 278-372 (449)
70 PRK11824 polynucleotide phosph 96.9 0.00073 1.6E-08 81.7 3.9 67 198-273 552-619 (693)
71 PRK12327 nusA transcription el 96.9 0.0026 5.6E-08 71.1 7.9 94 210-333 246-340 (362)
72 COG5176 MSL5 Splicing factor ( 96.8 0.0042 9.2E-08 62.9 8.1 69 305-373 163-244 (269)
73 TIGR03319 YmdA_YtgF conserved 96.7 0.0035 7.6E-08 73.3 7.7 90 171-272 179-270 (514)
74 COG0195 NusA Transcription elo 96.7 0.0014 3.1E-08 66.7 3.9 101 120-238 79-180 (190)
75 PRK00106 hypothetical protein; 96.7 0.0039 8.4E-08 72.8 7.8 90 171-272 200-291 (535)
76 PRK09202 nusA transcription el 96.7 0.0029 6.3E-08 73.0 6.6 103 200-333 231-339 (470)
77 PRK04163 exosome complex RNA-b 96.6 0.0031 6.7E-08 66.6 6.2 65 297-371 146-211 (235)
78 KOG2814 Transcription coactiva 96.6 0.0024 5.2E-08 69.0 4.9 71 296-372 57-128 (345)
79 PRK04163 exosome complex RNA-b 96.5 0.0038 8.2E-08 65.9 5.8 65 201-274 146-211 (235)
80 cd02134 NusA_KH NusA_K homolog 96.5 0.003 6.5E-08 52.6 4.0 37 199-235 24-60 (61)
81 PRK12704 phosphodiesterase; Pr 96.5 0.0053 1.2E-07 71.9 7.4 90 171-272 185-276 (520)
82 cd02134 NusA_KH NusA_K homolog 96.4 0.0052 1.1E-07 51.2 4.6 37 295-331 24-60 (61)
83 KOG1960 Predicted RNA-binding 96.3 0.016 3.4E-07 63.9 9.3 163 218-382 112-306 (531)
84 PRK12705 hypothetical protein; 96.2 0.0088 1.9E-07 69.5 6.9 64 296-368 198-263 (508)
85 PRK12328 nusA transcription el 96.2 0.0048 1.1E-07 68.7 4.5 95 126-238 251-346 (374)
86 KOG1067 Predicted RNA-binding 96.2 0.0089 1.9E-07 68.4 6.5 66 295-371 596-662 (760)
87 TIGR01953 NusA transcription t 96.0 0.0065 1.4E-07 67.5 4.3 95 127-238 244-339 (341)
88 PRK12329 nusA transcription el 95.8 0.0061 1.3E-07 69.0 3.3 94 127-237 278-372 (449)
89 PRK12327 nusA transcription el 95.7 0.0086 1.9E-07 67.0 3.9 95 127-238 246-341 (362)
90 KOG1960 Predicted RNA-binding 95.7 0.011 2.5E-07 64.9 4.7 215 131-370 108-376 (531)
91 PRK12705 hypothetical protein; 95.7 0.014 3.1E-07 67.8 5.8 89 171-271 173-263 (508)
92 PRK00468 hypothetical protein; 95.6 0.0077 1.7E-07 52.4 2.5 33 196-228 26-58 (75)
93 COG1782 Predicted metal-depend 95.6 0.023 5E-07 64.7 6.7 96 212-333 41-136 (637)
94 COG1837 Predicted RNA-binding 95.6 0.011 2.3E-07 51.5 3.0 33 196-228 26-58 (76)
95 PRK02821 hypothetical protein; 95.4 0.0089 1.9E-07 52.2 2.2 35 196-230 27-61 (77)
96 KOG1067 Predicted RNA-binding 95.3 0.028 6.2E-07 64.5 6.2 69 195-273 592-661 (760)
97 cd02410 archeal_CPSF_KH The ar 95.2 0.052 1.1E-06 52.8 6.7 94 214-333 20-113 (145)
98 COG5166 Uncharacterized conser 95.2 0.032 7E-07 63.4 6.0 192 127-333 390-608 (657)
99 PRK09202 nusA transcription el 95.1 0.015 3.3E-07 67.1 3.6 94 127-238 246-340 (470)
100 cd02410 archeal_CPSF_KH The ar 95.1 0.035 7.6E-07 53.9 5.4 95 130-238 19-114 (145)
101 PRK01064 hypothetical protein; 94.8 0.021 4.6E-07 50.0 2.7 33 196-228 26-58 (78)
102 PRK00468 hypothetical protein; 94.6 0.034 7.3E-07 48.4 3.3 32 294-325 28-59 (75)
103 PRK02821 hypothetical protein; 94.4 0.036 7.8E-07 48.5 3.2 33 294-326 29-61 (77)
104 COG1782 Predicted metal-depend 94.3 0.055 1.2E-06 61.8 5.2 97 128-238 40-137 (637)
105 KOG4369 RTK signaling protein 94.0 0.016 3.4E-07 70.7 0.2 72 295-369 1339-1410(2131)
106 COG1837 Predicted RNA-binding 93.9 0.058 1.3E-06 47.0 3.4 33 293-325 27-59 (76)
107 KOG4369 RTK signaling protein 93.7 0.019 4.2E-07 70.0 0.2 74 199-274 1339-1412(2131)
108 PF14611 SLS: Mitochondrial in 93.7 0.48 1E-05 49.0 10.5 66 296-370 26-91 (210)
109 PF13083 KH_4: KH domain; PDB: 93.5 0.021 4.6E-07 49.1 -0.1 34 197-230 26-59 (73)
110 COG1097 RRP4 RNA-binding prote 93.4 0.14 3.1E-06 53.7 5.9 59 202-269 148-207 (239)
111 PRK01064 hypothetical protein; 93.4 0.09 2E-06 46.1 3.7 33 293-325 27-59 (78)
112 TIGR03675 arCOG00543 arCOG0054 92.5 0.2 4.3E-06 60.3 6.3 96 213-334 36-131 (630)
113 PRK06418 transcription elongat 92.2 0.54 1.2E-05 47.1 7.9 103 200-331 61-163 (166)
114 KOG2874 rRNA processing protei 92.1 0.22 4.8E-06 52.9 5.1 51 308-369 161-211 (356)
115 KOG2874 rRNA processing protei 91.8 0.2 4.3E-06 53.2 4.5 93 165-273 120-212 (356)
116 COG5166 Uncharacterized conser 91.8 0.37 8E-06 55.2 6.8 127 210-368 390-523 (657)
117 cd02414 jag_KH jag_K homology 91.6 0.15 3.2E-06 44.4 2.8 32 200-231 24-55 (77)
118 TIGR03675 arCOG00543 arCOG0054 91.5 0.21 4.5E-06 60.2 4.9 96 129-238 35-131 (630)
119 COG1097 RRP4 RNA-binding prote 90.5 0.53 1.1E-05 49.5 6.1 48 297-354 147-194 (239)
120 COG1855 ATPase (PilT family) [ 90.2 0.49 1.1E-05 53.9 5.8 66 259-334 459-524 (604)
121 cd02409 KH-II KH-II (K homolo 89.5 0.47 1E-05 39.0 4.0 34 200-233 25-58 (68)
122 PF13083 KH_4: KH domain; PDB: 89.5 0.19 4.1E-06 43.2 1.5 37 293-329 26-62 (73)
123 PF13184 KH_5: NusA-like KH do 89.4 0.26 5.6E-06 42.3 2.3 39 201-239 4-48 (69)
124 cd02409 KH-II KH-II (K homolo 88.9 0.58 1.3E-05 38.5 4.1 34 296-329 25-58 (68)
125 PF13184 KH_5: NusA-like KH do 87.9 0.34 7.3E-06 41.5 2.0 37 297-333 4-46 (69)
126 cd02413 40S_S3_KH K homology R 87.3 0.99 2.1E-05 39.9 4.7 37 295-331 29-65 (81)
127 COG1855 ATPase (PilT family) [ 87.3 0.39 8.4E-06 54.7 2.6 39 200-238 486-524 (604)
128 TIGR03802 Asp_Ala_antiprt aspa 86.9 6.9 0.00015 46.8 12.9 143 199-367 217-380 (562)
129 PRK03818 putative transporter; 86.3 6.2 0.00013 47.0 12.1 140 200-365 205-361 (552)
130 COG0092 RpsC Ribosomal protein 85.6 3.4 7.5E-05 43.4 8.3 37 295-331 50-91 (233)
131 PRK13764 ATPase; Provisional 85.2 0.72 1.6E-05 55.1 3.6 66 174-239 455-520 (602)
132 PRK13764 ATPase; Provisional 85.1 1.1 2.3E-05 53.8 4.9 66 259-334 454-519 (602)
133 PF10446 DUF2457: Protein of u 84.7 0.64 1.4E-05 52.6 2.7 21 151-171 181-201 (458)
134 cd02414 jag_KH jag_K homology 84.5 0.97 2.1E-05 39.3 3.2 36 295-330 23-58 (77)
135 PF07650 KH_2: KH domain syndr 83.7 0.56 1.2E-05 40.7 1.4 35 296-330 25-59 (78)
136 KOG0299 U3 snoRNP-associated p 83.3 3 6.4E-05 47.5 7.1 40 33-72 44-83 (479)
137 COG0092 RpsC Ribosomal protein 81.0 1.2 2.6E-05 46.7 2.9 51 177-228 29-79 (233)
138 PF07650 KH_2: KH domain syndr 80.9 0.81 1.7E-05 39.6 1.3 35 200-234 25-59 (78)
139 PRK03818 putative transporter; 80.4 5.9 0.00013 47.2 8.7 96 162-267 256-360 (552)
140 PRK06418 transcription elongat 80.0 2.2 4.8E-05 42.8 4.2 39 294-333 59-97 (166)
141 PRK15494 era GTPase Era; Provi 79.9 4.8 0.0001 44.9 7.4 35 298-332 275-318 (339)
142 cd02413 40S_S3_KH K homology R 79.3 1.7 3.6E-05 38.5 2.8 36 200-235 30-65 (81)
143 cd02412 30S_S3_KH K homology R 78.9 2.6 5.7E-05 39.2 4.1 32 296-327 61-92 (109)
144 KOG1924 RhoA GTPase effector D 78.8 11 0.00024 45.6 10.0 21 348-368 376-396 (1102)
145 COG2985 Predicted permease [Ge 78.3 5.9 0.00013 45.8 7.3 126 131-268 214-357 (544)
146 COG1159 Era GTPase [General fu 78.3 5 0.00011 43.8 6.5 34 298-331 231-273 (298)
147 COG1847 Jag Predicted RNA-bind 77.8 2 4.3E-05 44.4 3.2 63 173-235 64-126 (208)
148 cd02412 30S_S3_KH K homology R 77.6 1.6 3.4E-05 40.8 2.2 30 201-230 62-91 (109)
149 TIGR03802 Asp_Ala_antiprt aspa 76.1 13 0.00027 44.6 9.8 101 161-272 269-382 (562)
150 TIGR00436 era GTP-binding prot 75.3 8.7 0.00019 41.2 7.5 36 296-331 221-265 (270)
151 cd02411 archeal_30S_S3_KH K ho 74.3 4.8 0.0001 35.7 4.3 30 296-325 38-67 (85)
152 KOG1999 RNA polymerase II tran 74.1 3.6 7.9E-05 50.7 4.5 34 201-235 236-269 (1024)
153 PRK00089 era GTPase Era; Revie 73.7 8.8 0.00019 41.4 7.1 37 296-332 226-271 (292)
154 PRK04191 rps3p 30S ribosomal p 71.3 7.6 0.00016 40.4 5.6 32 296-327 40-71 (207)
155 COG1847 Jag Predicted RNA-bind 70.4 17 0.00037 37.7 7.8 38 294-331 89-126 (208)
156 COG0490 Putative regulatory, l 70.3 6.5 0.00014 39.2 4.6 56 304-364 96-158 (162)
157 PTZ00084 40S ribosomal protein 67.9 8.3 0.00018 40.5 5.0 32 295-326 43-74 (220)
158 PRK15405 ethanolamine utilizat 67.6 67 0.0014 33.7 11.3 144 222-371 51-211 (217)
159 TIGR01008 rpsC_E_A ribosomal p 65.8 12 0.00025 38.7 5.5 31 295-325 37-67 (195)
160 PRK04972 putative transporter; 63.4 98 0.0021 37.1 13.5 144 200-366 214-374 (558)
161 COG0490 Putative regulatory, l 62.1 11 0.00024 37.6 4.4 65 198-267 86-158 (162)
162 cd02411 archeal_30S_S3_KH K ho 61.9 6.7 0.00014 34.8 2.6 28 202-229 40-67 (85)
163 KOG0943 Predicted ubiquitin-pr 59.9 9 0.0002 48.2 3.9 6 120-125 1799-1804(3015)
164 PRK04972 putative transporter; 59.0 70 0.0015 38.3 11.2 102 162-272 268-377 (558)
165 KOG1999 RNA polymerase II tran 58.9 22 0.00048 44.3 7.0 90 176-267 129-231 (1024)
166 COG1702 PhoH Phosphate starvat 58.3 24 0.00051 39.5 6.6 57 207-273 22-80 (348)
167 KOG1423 Ras-like GTPase ERA [C 58.1 14 0.00031 40.7 4.7 32 295-326 327-359 (379)
168 PF02749 QRPTase_N: Quinolinat 56.7 34 0.00074 30.4 6.3 60 211-272 27-86 (88)
169 PTZ00084 40S ribosomal protein 56.4 22 0.00047 37.4 5.7 31 200-230 44-74 (220)
170 COG0331 FabD (acyl-carrier-pro 55.9 48 0.001 36.7 8.5 56 306-368 132-189 (310)
171 KOG2038 CAATT-binding transcri 54.6 12 0.00027 45.3 3.9 12 18-29 825-836 (988)
172 CHL00048 rps3 ribosomal protei 53.5 18 0.00039 37.9 4.6 31 295-325 65-95 (214)
173 TIGR01008 rpsC_E_A ribosomal p 52.7 23 0.00049 36.6 5.0 30 200-229 38-67 (195)
174 COG1159 Era GTPase [General fu 52.1 27 0.00059 38.2 5.7 37 200-236 229-274 (298)
175 COG2101 SPT15 TATA-box binding 50.9 30 0.00065 35.0 5.3 112 249-369 63-181 (185)
176 TIGR00436 era GTP-binding prot 50.8 18 0.00039 38.7 4.2 30 200-229 221-251 (270)
177 COG1702 PhoH Phosphate starvat 48.9 33 0.00071 38.4 5.8 56 303-369 22-79 (348)
178 PRK00089 era GTPase Era; Revie 48.6 25 0.00054 37.9 4.9 37 200-236 226-271 (292)
179 cd00652 TBP_TLF TATA box bindi 48.3 1.9E+02 0.0042 29.2 10.9 36 230-274 47-84 (174)
180 TIGR00119 acolac_sm acetolacta 47.6 35 0.00076 34.0 5.3 90 164-268 47-139 (157)
181 PRK11895 ilvH acetolactate syn 47.4 38 0.00082 34.0 5.5 91 163-268 47-140 (161)
182 PRK15494 era GTPase Era; Provi 45.3 24 0.00052 39.4 4.2 37 200-236 273-318 (339)
183 TIGR01009 rpsC_bact ribosomal 45.1 26 0.00056 36.7 4.1 30 296-325 62-91 (211)
184 CHL00048 rps3 ribosomal protei 44.3 52 0.0011 34.5 6.2 30 200-229 66-95 (214)
185 COG4010 Uncharacterized protei 43.5 42 0.0009 32.9 4.8 44 220-272 126-169 (170)
186 cd04517 TLF TBP-like factors ( 43.1 2.8E+02 0.0061 28.1 11.1 36 229-273 46-83 (174)
187 PRK04191 rps3p 30S ribosomal p 42.3 17 0.00038 37.8 2.3 29 202-230 42-70 (207)
188 KOG0699 Serine/threonine prote 41.1 24 0.00052 39.4 3.2 18 211-229 459-476 (542)
189 KOG0262 RNA polymerase I, larg 39.9 36 0.00077 43.6 4.7 16 257-272 1529-1544(1640)
190 KOG2236 Uncharacterized conser 38.5 7.1E+02 0.015 29.2 16.6 22 120-141 199-220 (483)
191 PRK05848 nicotinate-nucleotide 38.4 1.7E+02 0.0038 31.8 9.3 159 203-364 32-224 (273)
192 TIGR01009 rpsC_bact ribosomal 38.3 66 0.0014 33.6 5.9 29 201-229 63-91 (211)
193 cd00652 TBP_TLF TATA box bindi 38.0 1.2E+02 0.0026 30.7 7.6 101 162-272 56-174 (174)
194 KOG0262 RNA polymerase I, larg 37.9 16 0.00034 46.6 1.3 10 200-209 1443-1452(1640)
195 PRK05848 nicotinate-nucleotide 37.6 2.8E+02 0.006 30.3 10.7 68 298-368 31-98 (273)
196 PRK06559 nicotinate-nucleotide 36.5 3.1E+02 0.0068 30.2 10.9 66 299-368 43-113 (290)
197 PRK08385 nicotinate-nucleotide 35.9 2E+02 0.0043 31.5 9.3 53 220-272 47-99 (278)
198 cd01568 QPRTase_NadC Quinolina 35.9 1.8E+02 0.0038 31.5 8.9 69 203-273 30-99 (269)
199 cd01568 QPRTase_NadC Quinolina 35.8 3.1E+02 0.0068 29.6 10.8 68 298-369 29-98 (269)
200 PF09869 DUF2096: Uncharacteri 35.3 63 0.0014 32.5 4.8 57 199-271 112-168 (169)
201 PLN00062 TATA-box-binding prot 35.1 3.4E+02 0.0075 27.7 10.3 27 345-371 147-175 (179)
202 TIGR01334 modD putative molybd 34.9 2.3E+02 0.0049 31.0 9.5 146 219-364 48-230 (277)
203 cd01572 QPRTase Quinolinate ph 34.8 3.5E+02 0.0076 29.3 11.0 67 299-369 30-99 (268)
204 cd01572 QPRTase Quinolinate ph 34.7 2E+02 0.0044 31.1 9.1 62 210-273 37-100 (268)
205 COG2090 Uncharacterized protei 34.5 3E+02 0.0066 26.9 9.0 61 199-267 63-123 (141)
206 COG5014 Predicted Fe-S oxidore 34.5 81 0.0018 32.1 5.4 102 220-372 81-187 (228)
207 PRK00310 rpsC 30S ribosomal pr 34.4 45 0.00097 35.4 3.9 30 296-325 62-91 (232)
208 cd04516 TBP_eukaryotes eukaryo 34.1 4.4E+02 0.0095 26.7 10.8 36 229-273 46-83 (174)
209 PLN00062 TATA-box-binding prot 33.9 1.8E+02 0.0038 29.7 8.0 26 248-273 147-174 (179)
210 cd01573 modD_like ModD; Quinol 33.5 2.3E+02 0.005 30.8 9.3 53 220-272 45-97 (272)
211 COG2985 Predicted permease [Ge 32.8 90 0.0019 36.6 6.2 97 248-365 254-357 (544)
212 TIGR00078 nadC nicotinate-nucl 32.8 2.1E+02 0.0044 31.0 8.8 69 203-273 28-96 (265)
213 KOG4264 Nucleo-cytoplasmic pro 32.4 50 0.0011 38.6 4.1 11 130-140 136-146 (694)
214 KOG2133 Transcriptional corepr 31.8 35 0.00075 42.5 2.9 20 124-143 107-126 (1229)
215 COG0014 ProA Gamma-glutamyl ph 31.8 24 0.00051 40.2 1.4 114 196-329 103-220 (417)
216 PRK07428 nicotinate-nucleotide 31.7 3.8E+02 0.0083 29.4 10.7 68 297-368 42-112 (288)
217 PRK07428 nicotinate-nucleotide 31.5 2.5E+02 0.0055 30.8 9.3 160 203-365 44-239 (288)
218 PF03958 Secretin_N: Bacterial 31.1 1.3E+02 0.0028 25.7 5.7 33 229-269 44-76 (82)
219 CHL00100 ilvH acetohydroxyacid 31.0 1.7E+02 0.0037 29.7 7.3 93 164-268 48-140 (174)
220 PF02749 QRPTase_N: Quinolinat 31.0 2.2E+02 0.0047 25.3 7.2 69 297-368 17-85 (88)
221 PF02080 TrkA_C: TrkA-C domain 30.8 49 0.0011 27.4 2.9 49 315-363 14-70 (71)
222 TIGR01334 modD putative molybd 30.6 4.6E+02 0.01 28.7 11.0 67 299-368 34-100 (277)
223 COG2061 ACT-domain-containing 30.3 5.7E+02 0.012 25.6 11.7 64 306-369 92-157 (170)
224 PRK00310 rpsC 30S ribosomal pr 29.7 94 0.002 33.0 5.4 29 201-229 63-91 (232)
225 PRK11895 ilvH acetolactate syn 29.7 3.4E+02 0.0073 27.3 9.0 99 249-372 47-148 (161)
226 KOG3181 40S ribosomal protein 29.5 67 0.0015 33.0 4.0 37 200-236 44-80 (244)
227 cd04517 TLF TBP-like factors ( 28.5 1.5E+02 0.0032 30.1 6.4 103 162-272 56-174 (174)
228 cd01573 modD_like ModD; Quinol 28.2 5.1E+02 0.011 28.1 10.9 66 299-368 30-96 (272)
229 PF03958 Secretin_N: Bacterial 27.6 1.7E+02 0.0037 24.9 5.8 24 343-366 53-76 (82)
230 PRK08385 nicotinate-nucleotide 27.6 5.1E+02 0.011 28.3 10.7 53 314-368 45-98 (278)
231 PRK06096 molybdenum transport 26.8 3.6E+02 0.0079 29.6 9.4 54 219-272 49-102 (284)
232 COG4598 HisP ABC-type histidin 26.6 45 0.00098 34.4 2.2 68 299-366 69-140 (256)
233 cd04516 TBP_eukaryotes eukaryo 25.9 2.9E+02 0.0062 28.1 7.9 25 248-272 147-173 (174)
234 KOG1423 Ras-like GTPase ERA [C 25.9 55 0.0012 36.3 2.8 31 199-229 327-358 (379)
235 TIGR00237 xseA exodeoxyribonuc 25.8 1E+02 0.0022 35.7 5.3 53 170-228 97-149 (432)
236 cd04518 TBP_archaea archaeal T 25.8 6E+02 0.013 25.8 10.2 26 249-274 57-84 (174)
237 PF04461 DUF520: Protein of un 25.6 6.3E+02 0.014 25.4 9.9 40 318-366 108-148 (160)
238 PRK06978 nicotinate-nucleotide 25.6 5.5E+02 0.012 28.4 10.5 94 263-368 26-122 (294)
239 CHL00100 ilvH acetohydroxyacid 25.0 6.4E+02 0.014 25.6 10.2 51 314-372 97-148 (174)
240 PF03460 NIR_SIR_ferr: Nitrite 24.9 2.4E+02 0.0052 23.4 6.1 57 200-268 10-68 (69)
241 TIGR00119 acolac_sm acetolacta 24.4 6.4E+02 0.014 25.1 9.9 45 314-366 96-140 (157)
242 KOG1548 Transcription elongati 24.3 1.1E+03 0.023 26.8 13.2 54 130-184 153-207 (382)
243 KOG2147 Nucleolar protein invo 24.0 43 0.00093 40.8 1.8 18 168-185 431-448 (823)
244 PTZ00415 transmission-blocking 23.8 4E+02 0.0087 36.2 9.9 9 296-304 360-368 (2849)
245 PRK08072 nicotinate-nucleotide 23.6 2.9E+02 0.0063 30.2 7.9 51 316-368 51-104 (277)
246 PLN02716 nicotinate-nucleotide 23.5 4.6E+02 0.0099 29.2 9.4 69 203-273 50-120 (308)
247 PF06183 DinI: DinI-like famil 23.4 1.9E+02 0.0041 24.6 5.1 44 316-367 12-57 (65)
248 PF10446 DUF2457: Protein of u 23.3 69 0.0015 36.9 3.1 12 247-258 191-202 (458)
249 PRK05412 putative nucleotide-b 23.1 7.9E+02 0.017 24.8 10.4 41 317-366 107-148 (161)
250 COG0331 FabD (acyl-carrier-pro 23.0 1.1E+02 0.0024 34.0 4.6 57 209-271 131-189 (310)
251 COG1570 XseA Exonuclease VII, 23.0 4.4E+02 0.0096 30.7 9.5 54 300-366 129-191 (440)
252 PRK00286 xseA exodeoxyribonucl 23.0 4.4E+02 0.0095 30.4 9.8 78 257-365 104-190 (438)
253 COG5271 MDN1 AAA ATPase contai 22.9 98 0.0021 41.9 4.5 15 167-181 4156-4170(4600)
254 PRK00394 transcription factor; 22.8 8.2E+02 0.018 24.9 10.9 35 230-273 46-82 (179)
255 PRK15468 carboxysome structura 22.2 1.7E+02 0.0038 27.4 4.9 43 320-370 57-100 (111)
256 TIGR00078 nadC nicotinate-nucl 22.1 5.8E+02 0.013 27.6 9.9 67 299-369 28-95 (265)
257 PRK08072 nicotinate-nucleotide 22.0 2.2E+02 0.0048 31.0 6.7 54 220-273 51-106 (277)
258 COG2101 SPT15 TATA-box binding 21.9 1.8E+02 0.0039 29.7 5.3 95 170-273 72-182 (185)
259 KOG2076 RNA polymerase III tra 21.7 58 0.0013 40.5 2.3 14 172-185 154-167 (895)
260 PRK10811 rne ribonuclease E; R 21.7 2.1E+02 0.0046 36.4 7.0 40 295-334 436-476 (1068)
261 PRK04021 hypothetical protein; 21.4 1.6E+02 0.0035 26.8 4.6 40 316-360 50-90 (92)
262 PRK05742 nicotinate-nucleotide 21.3 8.5E+02 0.019 26.6 11.0 97 260-368 7-106 (277)
263 TIGR02931 anfK_nitrog Fe-only 21.0 6.5E+02 0.014 29.4 10.7 52 164-229 71-123 (461)
264 PRK14476 nitrogenase molybdenu 20.8 3.8E+02 0.0082 31.3 8.7 57 165-236 72-133 (455)
265 TIGR00237 xseA exodeoxyribonuc 20.5 7.6E+02 0.016 28.6 11.0 77 258-365 99-184 (432)
266 TIGR00065 ftsZ cell division p 20.5 89 0.0019 35.2 3.4 149 203-369 137-297 (349)
267 PRK06559 nicotinate-nucleotide 20.2 5E+02 0.011 28.6 8.9 145 219-365 57-240 (290)
268 PF00352 TBP: Transcription fa 20.1 1.9E+02 0.0041 25.5 4.7 36 229-273 48-85 (86)
No 1
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=4.7e-47 Score=421.12 Aligned_cols=249 Identities=33% Similarity=0.521 Sum_probs=209.5
Q ss_pred ccceeeeccccccccccCCCchhhhhhhcccCceeeeccccc-c-cccceeeecCchhchhhhhhhhhHhhhcCCCCCCC
Q 003942 116 EQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETK-E-VTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPS 193 (784)
Q Consensus 116 ~~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~-~-~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~ 193 (784)
+++.+|.||.+++|+||||+||+||.|++.+++++.+..+.. . ...|.|.|+|+.+.|++|+.|++++|+++..+...
T Consensus 138 ~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e~~~~~~g 217 (600)
T KOG1676|consen 138 ETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILREEDDEVPG 217 (600)
T ss_pred ceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHhcccCCCc
Confidence 467899999999999999999999999987777765554443 3 37899999999999999999999999854332221
Q ss_pred ------CCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHH
Q 003942 194 ------STDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLIN 267 (784)
Q Consensus 194 ------~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~ 267 (784)
.......+++|.||+++||.||||+|+|||+|+.+||+||+|..|+ ++.+.+|.+.|+|+++.|.+|.+||.
T Consensus 218 ~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd--~p~speR~~~IiG~~d~ie~Aa~lI~ 295 (600)
T KOG1676|consen 218 SGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDD--DPSSPERPAQIIGTVDQIEHAAELIN 295 (600)
T ss_pred cccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCC--CCCCccceeeeecCHHHHHHHHHHHH
Confidence 2223456999999999999999999999999999999999999875 45788999999999999999999999
Q ss_pred HHHHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEE
Q 003942 268 AVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIV 347 (784)
Q Consensus 268 elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V 347 (784)
+||++...+... -+.+|.. .....+.|.||.++||+||||+|+|||.|.++|||+|.+.++ ++..+..+|+|
T Consensus 296 eii~~~~~~~~~-~~~~G~P-----~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~--~p~~~~~ektf 367 (600)
T KOG1676|consen 296 EIIAEAEAGAGG-GMGGGAP-----GLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ--PPNGNPKEKTF 367 (600)
T ss_pred HHHHHHhccCCC-CcCCCCc-----cceeeEEEeccccccccccCCCccchhhhcccCCccccccCC--CCCCCccceEE
Confidence 999998653110 0111211 123389999999999999999999999999999999999987 46778899999
Q ss_pred EEEcCHHHHHHHHHHHHHHHhcccCCC
Q 003942 348 RVTGDMRQIEIAQEMIKEVLSQTVRPS 374 (784)
Q Consensus 348 ~I~Gt~~qV~~Ak~lI~~~L~~~~r~~ 374 (784)
+|+|++.+|++|+.||+++|....++.
T Consensus 368 ~IrG~~~QIdhAk~LIr~kvg~~~~n~ 394 (600)
T KOG1676|consen 368 VIRGDKRQIDHAKQLIRDKVGDIAPNT 394 (600)
T ss_pred EEecCcccchHHHHHHHHHhcccCCCC
Confidence 999999999999999999998766654
No 2
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=5.6e-37 Score=340.99 Aligned_cols=248 Identities=27% Similarity=0.446 Sum_probs=212.3
Q ss_pred ceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCC--C
Q 003942 118 HSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSS--T 195 (784)
Q Consensus 118 ~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~--~ 195 (784)
+.+..||..+|+.||||+|+-|..|..+++|++.|..+......|.|.++|..++|+.|+.||.+++++......+. .
T Consensus 55 ~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~aK~li~evv~r~~~~~~~~~~q 134 (600)
T KOG1676|consen 55 TERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEVAKQLIGEVVSRGRPPGGFPDNQ 134 (600)
T ss_pred ccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHHHHHHhhhhhhhccCCCCCccccC
Confidence 34678999999999999999999999999999999999988899999999999999999999999998664322221 1
Q ss_pred CCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhc
Q 003942 196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADA 275 (784)
Q Consensus 196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~ 275 (784)
....++.+|+||.+++|+||||+|+|||.|++.+||+|.+..++....+ .++.|.|+|+.+.|+.|+.||.++|+|++.
T Consensus 135 ~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~-~~KplritGdp~~ve~a~~lV~dil~e~~~ 213 (600)
T KOG1676|consen 135 GSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG-ADKPLRITGDPDKVEQAKQLVADILREEDD 213 (600)
T ss_pred CccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC-CCCceeecCCHHHHHHHHHHHHHHHHhccc
Confidence 2456899999999999999999999999999999999999998765433 789999999999999999999999998643
Q ss_pred CCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHH
Q 003942 276 GGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQ 355 (784)
Q Consensus 276 ~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~q 355 (784)
.........+. ......+++|.||+++||.||||+|+|||+|+.+||+||+|++++.+ .+.||.+.|+|+.++
T Consensus 214 ~~~g~~~~~g~----~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p---~speR~~~IiG~~d~ 286 (600)
T KOG1676|consen 214 EVPGSGGHAGV----RGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDP---SSPERPAQIIGTVDQ 286 (600)
T ss_pred CCCccccccCc----CccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCC---CCccceeeeecCHHH
Confidence 32222111111 11234589999999999999999999999999999999999988754 688999999999999
Q ss_pred HHHHHHHHHHHHhcccCC
Q 003942 356 IEIAQEMIKEVLSQTVRP 373 (784)
Q Consensus 356 V~~Ak~lI~~~L~~~~r~ 373 (784)
|++|.+||.+||++..+.
T Consensus 287 ie~Aa~lI~eii~~~~~~ 304 (600)
T KOG1676|consen 287 IEHAAELINEIIAEAEAG 304 (600)
T ss_pred HHHHHHHHHHHHHHHhcc
Confidence 999999999999876554
No 3
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.97 E-value=3.7e-30 Score=260.83 Aligned_cols=240 Identities=23% Similarity=0.336 Sum_probs=191.7
Q ss_pred ccceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCC
Q 003942 116 EQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSST 195 (784)
Q Consensus 116 ~~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~ 195 (784)
.++.+|++.++.++.||||+|+|||.|+.+.++.+.|.+... .+|+|.|+.+.+.|-...+.|.-.|+ +.+.
T Consensus 47 r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~--peri~tisad~~ti~~ilk~iip~le-e~f~----- 118 (390)
T KOG2192|consen 47 RVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSG--PERILTISADIETIGEILKKIIPTLE-EGFQ----- 118 (390)
T ss_pred ceeEEEEEecccccceeccccccHHHHhhhccceeeccCCCC--CceeEEEeccHHHHHHHHHHHhhhhh-hCCC-----
Confidence 577899999999999999999999999999999999887654 46888887776665544333333332 1121
Q ss_pred CCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhc
Q 003942 196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADA 275 (784)
Q Consensus 196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~ 275 (784)
....+.+||||.++++|.||||+|+.||+||+++.|+++|.. ++++++++|+|.|.|..++|..|++.|+++|+|...
T Consensus 119 ~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift--~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pi 196 (390)
T KOG2192|consen 119 LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFT--ECCPHSTDRVVLIGGKPKRVVECIKIILDLISESPI 196 (390)
T ss_pred CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhh--ccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCc
Confidence 233589999999999999999999999999999999999985 589999999999999999999999999999998641
Q ss_pred CCC------------------C-------c--------------------cc---ccc-----------cchh-------
Q 003942 276 GGS------------------P-------S--------------------LV---ARG-----------LATA------- 289 (784)
Q Consensus 276 ~g~------------------p-------~--------------------~~---~~g-----------~~~~------- 289 (784)
.++ + . ++ .+| |...
T Consensus 197 kgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~sai 276 (390)
T KOG2192|consen 197 KGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAI 276 (390)
T ss_pred CCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcC
Confidence 100 0 0 00 000 0000
Q ss_pred --------------------------------hccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCC
Q 003942 290 --------------------------------QASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLP 337 (784)
Q Consensus 290 --------------------------------~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p 337 (784)
.......+.++.||.++-|.||||+|+.||+|++++||.|.|..
T Consensus 277 dtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikide---- 352 (390)
T KOG2192|consen 277 DTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDE---- 352 (390)
T ss_pred CCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecC----
Confidence 01123567899999999999999999999999999999999964
Q ss_pred CCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942 338 EGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 369 (784)
Q Consensus 338 ~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~ 369 (784)
+-+.+.+|+|+|+|+.++|+.|+.|+...+++
T Consensus 353 pleGsedrIitItGTqdQIqnAQYLlQn~Vkq 384 (390)
T KOG2192|consen 353 PLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ 384 (390)
T ss_pred cCCCCCceEEEEeccHHHHhhHHHHHHHHHHh
Confidence 34678899999999999999999999998863
No 4
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.95 E-value=1.1e-28 Score=262.88 Aligned_cols=246 Identities=25% Similarity=0.302 Sum_probs=207.3
Q ss_pred ceeeeccccccccccCCCchhhhhhhcccCceeeeccccc-ccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCC
Q 003942 118 HSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETK-EVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTD 196 (784)
Q Consensus 118 ~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~-~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~ 196 (784)
..+++||...++.||||+|.+||+|.+.+.++|++.+... ...+|.+.|.++.|...+|.++|.+++..+..+....
T Consensus 200 PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~~~k~~-- 277 (584)
T KOG2193|consen 200 PLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGTSKACKMILEIMQKEAVDDKVA-- 277 (584)
T ss_pred ceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccchHHHHHHHHHHHHHhhhccchh--
Confidence 4589999999999999999999999999999998887654 6778999999999999999999999997665544433
Q ss_pred CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcC
Q 003942 197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAG 276 (784)
Q Consensus 197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~ 276 (784)
.++.++|+..+++||+||||.|.+||+|+.+||++|+|++--+..--+.+|.|+|.|+.|+|.+|..+|+.+|+++-+.
T Consensus 278 -~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEn 356 (584)
T KOG2193|consen 278 -EEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYEN 356 (584)
T ss_pred -hhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhh
Confidence 5688999999999999999999999999999999999998666555567999999999999999999999999987532
Q ss_pred CC----------Cccc--ccccch-----------------------hhccCCccEEEEEecCCceeeeecCCchHHHHH
Q 003942 277 GS----------PSLV--ARGLAT-----------------------AQASGAAEQVEIKVPNEKVGLIIGRGGETIKGL 321 (784)
Q Consensus 277 g~----------p~~~--~~g~~~-----------------------~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~I 321 (784)
.. +.++ .-+.++ .......+.++|.||...||.||||+|.+||.|
T Consensus 357 Dl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql 436 (584)
T KOG2193|consen 357 DLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQL 436 (584)
T ss_pred hHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHH
Confidence 11 1111 001000 011235678999999999999999999999999
Q ss_pred HHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942 322 QTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 369 (784)
Q Consensus 322 q~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~ 369 (784)
.+.+||.|+|... +.++..+|.|+|+|.+++.-+|.-.|..+|.+
T Consensus 437 ~RfagASiKIapp---E~pdvseRMViItGppeaqfKAQgrifgKikE 481 (584)
T KOG2193|consen 437 SRFAGASIKIAPP---EIPDVSERMVIITGPPEAQFKAQGRIFGKIKE 481 (584)
T ss_pred HHhccceeeecCC---CCCCcceeEEEecCChHHHHhhhhhhhhhhhh
Confidence 9999999999764 45678999999999999999999999988876
No 5
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.95 E-value=4.1e-27 Score=266.23 Aligned_cols=252 Identities=24% Similarity=0.349 Sum_probs=206.3
Q ss_pred eeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecC---------chhchhhhhhhhhHhhhcCCC
Q 003942 119 SSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVK---------EEESVEPSNVVPQQVVDNSKS 189 (784)
Q Consensus 119 ~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G---------~~e~Ve~A~~lI~~ii~~~~~ 189 (784)
++++|+.+++|.||||+|++|++||.++.++|+|.+....+.+|++.|.| ..+++.+|..+|...++++..
T Consensus 45 ~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~d~~ 124 (485)
T KOG2190|consen 45 YRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEEDDE 124 (485)
T ss_pred EEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhccccccc
Confidence 89999999999999999999999999999999999999999999999999 999999999999887763332
Q ss_pred CCCCC---CCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHH
Q 003942 190 DDPSS---TDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLI 266 (784)
Q Consensus 190 ~~~~~---~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I 266 (784)
..... .....+++||+||.+.+|.||||+|++||+||++|||+|+|..+ .+|.+++|.|+|.|..+.|.+|+..|
T Consensus 125 ~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~--~lP~ster~V~IsG~~~av~~al~~I 202 (485)
T KOG2190|consen 125 AAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD--MLPNSTERAVTISGEPDAVKKALVQI 202 (485)
T ss_pred ccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC--CCCcccceeEEEcCchHHHHHHHHHH
Confidence 22111 12225899999999999999999999999999999999999986 68999999999999999999999999
Q ss_pred HHHHHhhh----c-CCC-----C----------ccc---------------------------------ccc--------
Q 003942 267 NAVIAEAD----A-GGS-----P----------SLV---------------------------------ARG-------- 285 (784)
Q Consensus 267 ~elI~e~~----~-~g~-----p----------~~~---------------------------------~~g-------- 285 (784)
..+|.+.. . ..+ + .+. ..+
T Consensus 203 s~~L~~~~~~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~ 282 (485)
T KOG2190|consen 203 SSRLLENPPRSPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALR 282 (485)
T ss_pred HHHHHhcCCcCCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhh
Confidence 99998842 0 000 0 000 000
Q ss_pred ------------cc------hh----h--------c-----------c----CCccEEEEEecCCceeeeecCCchHHHH
Q 003942 286 ------------LA------TA----Q--------A-----------S----GAAEQVEIKVPNEKVGLIIGRGGETIKG 320 (784)
Q Consensus 286 ------------~~------~~----~--------~-----------~----~~~~~~~i~VP~~~vG~VIGkgG~~IK~ 320 (784)
+. .. . + . ....+.+|+||++++|+||||+|++|.+
T Consensus 283 ~~~~~~i~v~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~ise 362 (485)
T KOG2190|consen 283 NETGASISVGDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKISE 362 (485)
T ss_pred hhcCCceEeccccCcceeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccchHH
Confidence 00 00 0 0 0 2236789999999999999999999999
Q ss_pred HHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcccCCC
Q 003942 321 LQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRPS 374 (784)
Q Consensus 321 Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~~r~~ 374 (784)
||+.|||.|.|.... ......++.|+|+|...+...+..+|...|+...+..
T Consensus 363 ir~~tgA~I~I~~~~--~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~~~~ 414 (485)
T KOG2190|consen 363 IRQRTGASISILNKE--EVSGVREALVQITGMLREDLLAQYLIRARLSAPKSSM 414 (485)
T ss_pred HHHhcCCceEEcccc--ccCCcceeEEEecchhHHHHhhhhhcccccccCccCC
Confidence 999999999998643 1126789999999999999999999988887666554
No 6
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.94 E-value=3.1e-26 Score=238.69 Aligned_cols=170 Identities=34% Similarity=0.532 Sum_probs=145.9
Q ss_pred CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcC
Q 003942 197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAG 276 (784)
Q Consensus 197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~ 276 (784)
+..+.+|||||+..+|.||||+|++|.+|+++|||+|++++..|..|+.++|+|.|.|+.++|...+++|.++|+|....
T Consensus 36 ~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~ 115 (402)
T KOG2191|consen 36 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQA 115 (402)
T ss_pred CCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHh
Confidence 44589999999999999999999999999999999999999999999999999999999999999999999999997531
Q ss_pred CC-CcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHH
Q 003942 277 GS-PSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQ 355 (784)
Q Consensus 277 g~-p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~q 355 (784)
.. +..+ +..+..++..+++|.||+..+|.||||+|++||.|++++||.|+|.+.. +..-...+|+|+|+|++++
T Consensus 116 ~~k~v~~----~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqk-pt~~sLqervvt~sge~e~ 190 (402)
T KOG2191|consen 116 VAKPVDI----LQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQK-PTGISLQERVVTVSGEPEQ 190 (402)
T ss_pred hcCCccc----cCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccC-CCCccceeEEEEecCCHHH
Confidence 11 1111 0111134556799999999999999999999999999999999999643 3556788999999999999
Q ss_pred HHHHHHHHHHHHhccc
Q 003942 356 IEIAQEMIKEVLSQTV 371 (784)
Q Consensus 356 V~~Ak~lI~~~L~~~~ 371 (784)
+.+|..||.++|.++-
T Consensus 191 ~~~A~~~IL~Ki~eDp 206 (402)
T KOG2191|consen 191 NMKAVSLILQKIQEDP 206 (402)
T ss_pred HHHHHHHHHHHhhcCC
Confidence 9999999999887653
No 7
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.93 E-value=2.4e-25 Score=232.09 Aligned_cols=251 Identities=23% Similarity=0.184 Sum_probs=200.4
Q ss_pred cceeeeccccccccccCCCchhhhhhhcccCceeeeccccc---ccccceeeecCchhchhhhhhhhhHhhhcCCCCCCC
Q 003942 117 QHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETK---EVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPS 193 (784)
Q Consensus 117 ~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~---~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~ 193 (784)
.++||+||+..+|.||||+|++|..|+.+++++|+++++.+ ..++|+|.|.|+.++|....++|.++|++.......
T Consensus 39 y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~~~k 118 (402)
T KOG2191|consen 39 YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQAVAK 118 (402)
T ss_pred eEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHhhcC
Confidence 78999999999999999999999999999999999998876 688999999999999999999999999844432211
Q ss_pred -------CCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHH
Q 003942 194 -------STDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLI 266 (784)
Q Consensus 194 -------~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I 266 (784)
...++...++|+||++.+|.||||+|.|||.|+++++|-|+|.......-+..+|+|+|+|++|++.+|+++|
T Consensus 119 ~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~I 198 (402)
T KOG2191|consen 119 PVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLI 198 (402)
T ss_pred CccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHH
Confidence 1123345689999999999999999999999999999999999544455577899999999999999999999
Q ss_pred HHHHHhhhcCCCCccccc-------------c---cchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEE
Q 003942 267 NAVIAEADAGGSPSLVAR-------------G---LATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQ 330 (784)
Q Consensus 267 ~elI~e~~~~g~p~~~~~-------------g---~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIq 330 (784)
+++|.|+...++..-... | ..............+.|+..++|.+-|++|.++-.|-..+|+.|.
T Consensus 199 L~Ki~eDpqs~scln~sya~vsGpvaNsnPtGspya~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~ 278 (402)
T KOG2191|consen 199 LQKIQEDPQSGSCLNISYANVSGPVANSNPTGSPYAYQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIA 278 (402)
T ss_pred HHHhhcCCcccceeccchhcccCcccccCCCCCCCCCCCccccccchhhccccccccccccccccccceeeeccccccee
Confidence 999999864322111000 0 001122334455667899999999999999999999999999988
Q ss_pred eccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942 331 LIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 369 (784)
Q Consensus 331 I~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~ 369 (784)
|.... ..-.....+ +.+.|...++..|..||..++..
T Consensus 279 itq~l-~~m~g~gy~-~n~~g~~ls~~aa~g~L~~~~~~ 315 (402)
T KOG2191|consen 279 ITQAL-NTMAGYGYN-TNILGLGLSILAAEGVLAAKVAS 315 (402)
T ss_pred ecccc-ccccccccc-ccccchhhhhhhhhhHHHHhhcc
Confidence 87532 112233444 77888889999999999887754
No 8
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.93 E-value=7.8e-26 Score=241.26 Aligned_cols=242 Identities=21% Similarity=0.246 Sum_probs=201.0
Q ss_pred ccceeeeccccccccccCCCchhhhhhhcccCceeeeccccc---ccccceeeecCchhchhhhhhhhhHhhhcC---CC
Q 003942 116 EQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETK---EVTVKEEETVKEEESVEPSNVVPQQVVDNS---KS 189 (784)
Q Consensus 116 ~~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~---~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~---~~ 189 (784)
+...||+.-+..+|+||||.|.+||+|..+++++|.|+.-.+ ...+|.+.++|+.|+|..|..+|.++|+++ ++
T Consensus 279 e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl 358 (584)
T KOG2193|consen 279 EIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDL 358 (584)
T ss_pred hcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhH
Confidence 445588999999999999999999999999999999987654 566899999999999999999998887611 00
Q ss_pred ------C--------------CCCC----------------------CCCCCeEEEEEecCCccceeeccCcchHhhHHh
Q 003942 190 ------D--------------DPSS----------------------TDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQY 227 (784)
Q Consensus 190 ------~--------------~~~~----------------------~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~ 227 (784)
+ ...+ -..+...++|.||...||.||||+|.+||.|.+
T Consensus 359 ~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~R 438 (584)
T KOG2193|consen 359 AAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSR 438 (584)
T ss_pred HHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHH
Confidence 0 0000 002345679999999999999999999999999
Q ss_pred hcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccchhhccCCccEEEEEecCCce
Q 003942 228 NSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKV 307 (784)
Q Consensus 228 ~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~v 307 (784)
.+||.|+|... ..+...+|.|+|+|..+...||.-.|.-+|+|+..+.. ..+...+.+|.||...+
T Consensus 439 fagASiKIapp--E~pdvseRMViItGppeaqfKAQgrifgKikEenf~~P------------keevklethirVPs~~a 504 (584)
T KOG2193|consen 439 FAGASIKIAPP--EIPDVSERMVIITGPPEAQFKAQGRIFGKIKEENFFLP------------KEEVKLETHIRVPSSAA 504 (584)
T ss_pred hccceeeecCC--CCCCcceeEEEecCChHHHHhhhhhhhhhhhhhccCCc------------hhhheeeeeeeccchhh
Confidence 99999999864 35668899999999999999999999999999753211 11345567899999999
Q ss_pred eeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcccCC
Q 003942 308 GLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVRP 373 (784)
Q Consensus 308 G~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~~r~ 373 (784)
|+||||||.|+++|++.|+|.|.|.++.. .+..+..+|.|+|..-+++.|.+.|.++|.+.++.
T Consensus 505 GRvIGKGGktVnELQnlt~AeV~vPrdqt--pdEnd~vivriiGhfyatq~aQrki~~iv~qvkq~ 568 (584)
T KOG2193|consen 505 GRVIGKGGKTVNELQNLTSAEVVVPRDQT--PDENDQVIVRIIGHFYATQNAQRKIAHIVNQVKQS 568 (584)
T ss_pred hhhhccccccHHHHhccccceEEccccCC--CCccceeeeeeechhhcchHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999988763 33455667899999999999999999999987664
No 9
>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=1.1e-20 Score=192.23 Aligned_cols=147 Identities=22% Similarity=0.401 Sum_probs=130.7
Q ss_pred CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCC
Q 003942 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGS 278 (784)
Q Consensus 199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~ 278 (784)
.+.++|||-+..+|.||||+|++||+|+.+++|+|+|.+. +..+|+|+|+.+.+.|...++.|.-.|++...
T Consensus 47 r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds-----~~peri~tisad~~ti~~ilk~iip~lee~f~--- 118 (390)
T KOG2192|consen 47 RVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS-----SGPERILTISADIETIGEILKKIIPTLEEGFQ--- 118 (390)
T ss_pred ceeEEEEEecccccceeccccccHHHHhhhccceeeccCC-----CCCceeEEEeccHHHHHHHHHHHhhhhhhCCC---
Confidence 4799999999999999999999999999999999999864 46799999999999988888777777766411
Q ss_pred CcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHH
Q 003942 279 PSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEI 358 (784)
Q Consensus 279 p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~ 358 (784)
.....+++|+|..+++|.||||+|++||+||++..||++|..++.| .+++|+|.|.|.++.|-.
T Consensus 119 -------------~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p---~stdrv~l~~g~~k~v~~ 182 (390)
T KOG2192|consen 119 -------------LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCP---HSTDRVVLIGGKPKRVVE 182 (390)
T ss_pred -------------CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCC---CCcceEEEecCCcchHHH
Confidence 1245788999999999999999999999999999999999987655 789999999999999999
Q ss_pred HHHHHHHHHhc
Q 003942 359 AQEMIKEVLSQ 369 (784)
Q Consensus 359 Ak~lI~~~L~~ 369 (784)
++++|+++|++
T Consensus 183 ~i~~il~~i~e 193 (390)
T KOG2192|consen 183 CIKIILDLISE 193 (390)
T ss_pred HHHHHHHHhhc
Confidence 99999999987
No 10
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.84 E-value=1.4e-20 Score=213.24 Aligned_cols=159 Identities=29% Similarity=0.484 Sum_probs=134.9
Q ss_pred CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec---------chhhHHHHHHHHHHH
Q 003942 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG---------TLSNIDKAEKLINAV 269 (784)
Q Consensus 199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G---------~~e~V~kA~~~I~el 269 (784)
..++||+++-..||.||||+|++||+||++|.++|+|.. .++++.+|+|+|+| ..++|.+|.++|...
T Consensus 42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~---~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~ 118 (485)
T KOG2190|consen 42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNE---SLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFK 118 (485)
T ss_pred cceEEEEeccccceeEEccCcHHHHHHhhcccccceeec---CCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhc
Confidence 345899999999999999999999999999999999985 36788999999999 999999999999988
Q ss_pred HHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEE
Q 003942 270 IAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRV 349 (784)
Q Consensus 270 I~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I 349 (784)
+.+++... .+.+. ......++++|+||.++||.||||+|++||+|+++|||+|+|..+.+| .+++|.|+|
T Consensus 119 ~~~d~~~~----~d~~~---~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP---~ster~V~I 188 (485)
T KOG2190|consen 119 LEEDDEAA----EDNGE---DASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLP---NSTERAVTI 188 (485)
T ss_pred cccccccc----ccCCc---cccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCC---cccceeEEE
Confidence 77442210 00010 001114789999999999999999999999999999999999998777 678999999
Q ss_pred EcCHHHHHHHHHHHHHHHhcc
Q 003942 350 TGDMRQIEIAQEMIKEVLSQT 370 (784)
Q Consensus 350 ~Gt~~qV~~Ak~lI~~~L~~~ 370 (784)
.|..+.|.+|...|..+|.+.
T Consensus 189 sG~~~av~~al~~Is~~L~~~ 209 (485)
T KOG2190|consen 189 SGEPDAVKKALVQISSRLLEN 209 (485)
T ss_pred cCchHHHHHHHHHHHHHHHhc
Confidence 999999999999999988764
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=1.1e-17 Score=167.12 Aligned_cols=139 Identities=27% Similarity=0.444 Sum_probs=109.0
Q ss_pred EEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEE---ecchhhHHHHHHHHHHHHHhhhcCCCCc
Q 003942 204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEI---IGTLSNIDKAEKLINAVIAEADAGGSPS 280 (784)
Q Consensus 204 I~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I---~G~~e~V~kA~~~I~elI~e~~~~g~p~ 280 (784)
|.||.+++|.|||++|++||.|+++|+|+|.|..+ +..|.| +++.+.+.+|+++|..+..... +.
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--------TGEVKIEEEDEDPLAVMKAREVVKAIGRGFS----PE 69 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC--------CceEEEecCCCCHHHHHHHHHHHHHHHcCCC----HH
Confidence 67899999999999999999999999999999854 356788 6799999999999999876421 10
Q ss_pred ccccccchhhccCCccEEEEEecC---------CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEc
Q 003942 281 LVARGLATAQASGAAEQVEIKVPN---------EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG 351 (784)
Q Consensus 281 ~~~~g~~~~~~~~~~~~~~i~VP~---------~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~G 351 (784)
.. ..+ .........+.|.. +.+|+|||++|++|+.|++.|||+|.|. +++|+|.|
T Consensus 70 ~A-~~l----~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~-----------~~~v~i~G 133 (172)
T TIGR03665 70 KA-LKL----LDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY-----------GKTVGIIG 133 (172)
T ss_pred HH-HHh----cCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc-----------CCEEEEEC
Confidence 00 000 00111222233433 3799999999999999999999999994 36899999
Q ss_pred CHHHHHHHHHHHHHHHhcc
Q 003942 352 DMRQIEIAQEMIKEVLSQT 370 (784)
Q Consensus 352 t~~qV~~Ak~lI~~~L~~~ 370 (784)
+.++|+.|+++|+++|+..
T Consensus 134 ~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 134 DPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred CHHHHHHHHHHHHHHHcCC
Confidence 9999999999999999643
No 12
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.72 E-value=5.5e-17 Score=163.23 Aligned_cols=143 Identities=27% Similarity=0.426 Sum_probs=110.8
Q ss_pred eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEe----cchhhHHHHHHHHHHHHHhhhc
Q 003942 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEII----GTLSNIDKAEKLINAVIAEADA 275 (784)
Q Consensus 200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~----G~~e~V~kA~~~I~elI~e~~~ 275 (784)
+...|.||.+++|.|||++|++||.|+++|||+|+|..+ +..|.|. ++.+.+.+|+++|++++...+.
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 578999999999999999999999999999999999854 3577885 6999999999999998873210
Q ss_pred CCCCcccccccchhhccCCccEEEEEec----C-----CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceE
Q 003942 276 GGSPSLVARGLATAQASGAAEQVEIKVP----N-----EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERI 346 (784)
Q Consensus 276 ~g~p~~~~~g~~~~~~~~~~~~~~i~VP----~-----~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~ 346 (784)
...-.++. .......+.|. + ..+|+|||++|++||.|++.|||+|.|. ++.
T Consensus 75 e~A~~l~g---------d~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~-----------~~~ 134 (180)
T PRK13763 75 EKALRLLD---------DDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVY-----------GKT 134 (180)
T ss_pred HHHHHHhC---------CCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEc-----------CCE
Confidence 00000000 01111111111 1 3789999999999999999999999995 345
Q ss_pred EEEEcCHHHHHHHHHHHHHHHhcc
Q 003942 347 VRVTGDMRQIEIAQEMIKEVLSQT 370 (784)
Q Consensus 347 V~I~Gt~~qV~~Ak~lI~~~L~~~ 370 (784)
|+|.|+.++|+.|+++|+.+++..
T Consensus 135 v~i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 135 VAIIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred EEEEeCHHHHHHHHHHHHHHHcCC
Confidence 999999999999999999999643
No 13
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=99.55 E-value=5.6e-15 Score=147.71 Aligned_cols=141 Identities=23% Similarity=0.285 Sum_probs=110.5
Q ss_pred eeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCC-CCCCC
Q 003942 121 VEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSS-TDDST 199 (784)
Q Consensus 121 i~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~-~~~~~ 199 (784)
+.||.++++.|||++|++|+.|++.++++|+|.+++.....+ ..+++.+++.+|+.+|..+...+....... ..+..
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~g~V~I~--~~t~d~~~i~kA~~~I~~i~~gf~~e~A~~l~gd~y 79 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIE--EEDEDPLAVMKAREVVKAIGRGFSPEKALKLLDDDY 79 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcCCceEEEe--cCCCCHHHHHHHHHHHHHHHcCCCHHHHHHhcCCcc
Confidence 568999999999999999999999999999999764322111 248999999999999999887544321110 11222
Q ss_pred eEEEEEecC---------CccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHH
Q 003942 200 MSRKIEVPN---------NKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVI 270 (784)
Q Consensus 200 ~t~rI~VP~---------~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI 270 (784)
+..-|.|.. ..+|+|||++|+|||.|++.|+|+|.|.. +.|+|+|+.++|+.|+++|++||
T Consensus 80 ~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~----------~~v~i~G~~~~~~~A~~~i~~li 149 (172)
T TIGR03665 80 MLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG----------KTVGIIGDPEQVQIAREAIEMLI 149 (172)
T ss_pred eEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC----------CEEEEECCHHHHHHHHHHHHHHH
Confidence 233344444 36999999999999999999999999973 57999999999999999999999
Q ss_pred Hhh
Q 003942 271 AEA 273 (784)
Q Consensus 271 ~e~ 273 (784)
...
T Consensus 150 ~~~ 152 (172)
T TIGR03665 150 EGA 152 (172)
T ss_pred cCC
Confidence 543
No 14
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.55 E-value=9e-15 Score=162.34 Aligned_cols=235 Identities=22% Similarity=0.247 Sum_probs=179.3
Q ss_pred ccceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCC
Q 003942 116 EQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSST 195 (784)
Q Consensus 116 ~~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~ 195 (784)
....+++++...+-++|||.|.+|+.|+..+.++|.+.+++..+ .+...+.+-...+.+|+.+|..++.++
T Consensus 67 ~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g~-e~~~~~~~~p~~v~~a~a~~~~~~~~~-------- 137 (608)
T KOG2279|consen 67 DIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVGD-ERVLLISGFPVQVCKAKAAIHQILTEN-------- 137 (608)
T ss_pred heeeeEeecccceeeeeccccCCcchhhcccccceecCcccCCc-ccchhhccCCCCCChHHHHHHHHHhcC--------
Confidence 34568999999999999999999999999999999888777654 444555568889999999988888533
Q ss_pred CCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhc
Q 003942 196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADA 275 (784)
Q Consensus 196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~ 275 (784)
..+.+.+-||...+++||||+|++|+.|++.++++|.+..... ....+...|.+...-++.|..+|.+.+.+...
T Consensus 138 --~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr---~g~~~~~~i~~qqk~~~~a~~~~~~~~~edee 212 (608)
T KOG2279|consen 138 --TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGR---LGLSRLIKISGQQKEVAAAKHLILEKVSEDEE 212 (608)
T ss_pred --Ccccccccchhhhcccccccchhhhcchhcccccccccccccc---cccccceecccccchHHHHHhhhhccccchhH
Confidence 3477889999999999999999999999999999999987632 34578888888888888999999888776541
Q ss_pred C-------------------------------CCCccc-------ccc--------------c-----c-h-----hhcc
Q 003942 276 G-------------------------------GSPSLV-------ARG--------------L-----A-T-----AQAS 292 (784)
Q Consensus 276 ~-------------------------------g~p~~~-------~~g--------------~-----~-~-----~~~~ 292 (784)
. +.+.+- ..+ + + . ....
T Consensus 213 lv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~ 292 (608)
T KOG2279|consen 213 LVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKS 292 (608)
T ss_pred HhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccc
Confidence 0 000000 000 0 0 0 0011
Q ss_pred CCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCC-CceEEEEEcCHHHHHHHHHHHHHH
Q 003942 293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGS-KERIVRVTGDMRQIEIAQEMIKEV 366 (784)
Q Consensus 293 ~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~-~er~V~I~Gt~~qV~~Ak~lI~~~ 366 (784)
......+|.||+.++|+|||+.|++|+.+...|++++.|.-.. ..... .-.+|+|.|+...++++..||..+
T Consensus 293 ~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~p--yt~~v~~~qic~~egkqh~~n~vl~ml~~~ 365 (608)
T KOG2279|consen 293 EALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQP--YTSRVLQLQICVNEGKQHYENSVLEMLTVH 365 (608)
T ss_pred cccccceeecCcccccchhhhhhhhhhhhhhccCccceEEecc--ccchhhhhhhheecchhHHHHHHHhhhhcc
Confidence 2234578899999999999999999999999999999886543 11111 124688999999999999999844
No 15
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.53 E-value=9.5e-15 Score=147.07 Aligned_cols=144 Identities=20% Similarity=0.267 Sum_probs=110.8
Q ss_pred ceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCC-CC
Q 003942 118 HSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSS-TD 196 (784)
Q Consensus 118 ~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~-~~ 196 (784)
...+.||.++++.|||++|++|+.|++.++++|+|.+++.....+.+. +++.+++++|+.+|..++..+....... ..
T Consensus 4 ~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g~V~I~~~~-~~d~~~i~kA~~~I~ai~~gf~~e~A~~l~g 82 (180)
T PRK13763 4 MEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPTD-GEDPLAVLKARDIVKAIGRGFSPEKALRLLD 82 (180)
T ss_pred eEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECCCCeEEEEeCC-CCCHHHHHHHHHHHHHHhcCCCHHHHHHHhC
Confidence 457899999999999999999999999999999999865333222223 6899999999999999987543221100 01
Q ss_pred CCCeEEEEEecC---------CccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHH
Q 003942 197 DSTMSRKIEVPN---------NKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLIN 267 (784)
Q Consensus 197 ~~~~t~rI~VP~---------~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~ 267 (784)
+.....-+.|.. ..+|+|||++|+|+|.|++.|+|+|.|.. +.|+|+|+.++++.|+++|+
T Consensus 83 d~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~----------~~v~i~G~~~~~~~A~~~I~ 152 (180)
T PRK13763 83 DDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG----------KTVAIIGDPEQVEIAREAIE 152 (180)
T ss_pred CCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC----------CEEEEEeCHHHHHHHHHHHH
Confidence 111112222221 36999999999999999999999999973 34899999999999999999
Q ss_pred HHHHh
Q 003942 268 AVIAE 272 (784)
Q Consensus 268 elI~e 272 (784)
+||..
T Consensus 153 ~li~g 157 (180)
T PRK13763 153 MLIEG 157 (180)
T ss_pred HHHcC
Confidence 99954
No 16
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.34 E-value=2.7e-12 Score=108.04 Aligned_cols=65 Identities=35% Similarity=0.630 Sum_probs=58.5
Q ss_pred EEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 003942 297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIK 364 (784)
Q Consensus 297 ~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~ 364 (784)
+++|+||.+++|+||||+|++||+|+++|||+|.|.+... ....+|+|+|.|+.++|.+|+.||.
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 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL---PGSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC---CCCCceEEEEEeCHHHHHHHHHhhC
Confidence 3689999999999999999999999999999999986432 3578999999999999999999983
No 17
>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=99.27 E-value=6.5e-12 Score=105.68 Aligned_cols=65 Identities=35% Similarity=0.567 Sum_probs=59.1
Q ss_pred EEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHH
Q 003942 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLIN 267 (784)
Q Consensus 201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~ 267 (784)
+++|+||.+++|+||||+|++||+|+++|||+|.|..+.+ ....+|+|+|+|+.++|.+|+.+|.
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 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL--PGSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC--CCCCceEEEEEeCHHHHHHHHHhhC
Confidence 4799999999999999999999999999999999987542 4577899999999999999999983
No 18
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=99.26 E-value=6.2e-11 Score=118.45 Aligned_cols=140 Identities=28% Similarity=0.463 Sum_probs=109.2
Q ss_pred CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecc-----hhhHHHHHHHHHHHHHhh
Q 003942 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGT-----LSNIDKAEKLINAVIAEA 273 (784)
Q Consensus 199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~-----~e~V~kA~~~I~elI~e~ 273 (784)
...+.+.||...++.|||++|++.|.|.+.++++|.|+.+ +..|+|..+ +-.+.+|+++|..+=
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~--------~~~V~i~~~~~t~Dp~~~~ka~d~VkAIg--- 75 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK--------TGSVTIRTTRKTEDPLALLKARDVVKAIG--- 75 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC--------CCeEEEEecCCCCChHHHHHHHHHHHHHh---
Confidence 3567899999999999999999999999999999999854 467777654 457888888887753
Q ss_pred hcCCCCcccccccchhhcc----CCccEEEEEe------cC----CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCC
Q 003942 274 DAGGSPSLVARGLATAQAS----GAAEQVEIKV------PN----EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEG 339 (784)
Q Consensus 274 ~~~g~p~~~~~g~~~~~~~----~~~~~~~i~V------P~----~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~ 339 (784)
+||.+..+. .......|.| .. ...|+|||++|.|-+.|.+.|+|.|.|-
T Consensus 76 ----------rGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~------- 138 (194)
T COG1094 76 ----------RGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY------- 138 (194)
T ss_pred ----------cCCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe-------
Confidence 344433221 1222222222 11 3569999999999999999999999994
Q ss_pred CCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Q 003942 340 DGSKERIVRVTGDMRQIEIAQEMIKEVLSQT 370 (784)
Q Consensus 340 ~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~ 370 (784)
..+|.|.|..++|+.|++.|+.+|+..
T Consensus 139 ----g~tVaiiG~~~~v~iAr~AVemli~G~ 165 (194)
T COG1094 139 ----GKTVAIIGGFEQVEIAREAVEMLINGA 165 (194)
T ss_pred ----CcEEEEecChhhhHHHHHHHHHHHcCC
Confidence 568999999999999999999999754
No 19
>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=99.15 E-value=9.8e-11 Score=97.43 Aligned_cols=58 Identities=29% Similarity=0.514 Sum_probs=53.1
Q ss_pred EEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHH
Q 003942 297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIK 364 (784)
Q Consensus 297 ~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~ 364 (784)
...|.||.+++|+||||+|++||+|+++|||+|.|.. ++.|+|+|+ .+.|+.|+++|+
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~----------~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED----------DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC----------CCEEEEEeCCHHHHHHHHHHhC
Confidence 5679999999999999999999999999999999953 468999999 999999999984
No 20
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.15 E-value=3.9e-11 Score=99.07 Aligned_cols=60 Identities=37% Similarity=0.629 Sum_probs=54.5
Q ss_pred EEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 003942 297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMI 363 (784)
Q Consensus 297 ~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI 363 (784)
+.+|.||.+++++|||++|++||+|+++|||+|.|.++ + ....|+|+|+.++|+.|++||
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 57899999999999999999999999999999999642 2 456999999999999999987
No 21
>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=99.14 E-value=6e-11 Score=98.59 Aligned_cols=61 Identities=28% Similarity=0.499 Sum_probs=55.5
Q ss_pred EEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 003942 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIK 364 (784)
Q Consensus 298 ~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~ 364 (784)
.+|.||.+++++|||++|++|++|+++|||+|.|.+.. ..++.|+|+|+.++|+.|+.+|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~------~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG------SKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC------CCCCEEEEEcCHHHHHHHHHHhC
Confidence 57999999999999999999999999999999996532 56899999999999999999873
No 22
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.14 E-value=1.4e-10 Score=96.41 Aligned_cols=63 Identities=43% Similarity=0.695 Sum_probs=56.8
Q ss_pred EEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 003942 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIK 364 (784)
Q Consensus 298 ~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~ 364 (784)
.+|.||.+++++|||++|++|++|+++|||+|.|.... +...++.|+|.|+.++|+.|+.+|+
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 57999999999999999999999999999999997632 2467899999999999999999873
No 23
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.06 E-value=1.6e-10 Score=129.00 Aligned_cols=144 Identities=30% Similarity=0.527 Sum_probs=123.3
Q ss_pred CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCC
Q 003942 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGG 277 (784)
Q Consensus 198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g 277 (784)
..+.++++|+...|-+||||.|.+||.|++.+++||.+..+. ...+++..+.|....|.+|..+|+.++.+.
T Consensus 66 k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed----~g~e~~~~~~~~p~~v~~a~a~~~~~~~~~---- 137 (608)
T KOG2279|consen 66 KDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED----VGDERVLLISGFPVQVCKAKAAIHQILTEN---- 137 (608)
T ss_pred hheeeeEeecccceeeeeccccCCcchhhcccccceecCccc----CCcccchhhccCCCCCChHHHHHHHHHhcC----
Confidence 457889999999999999999999999999999999998653 233566666779999999999999988775
Q ss_pred CCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHH
Q 003942 278 SPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIE 357 (784)
Q Consensus 278 ~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~ 357 (784)
..++..+.||.+.+++||||+|++|+.|+..|+++|.+... +-....+.+.|.+...-++
T Consensus 138 ----------------~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n----gr~g~~~~~~i~~qqk~~~ 197 (608)
T KOG2279|consen 138 ----------------TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN----GRLGLSRLIKISGQQKEVA 197 (608)
T ss_pred ----------------Ccccccccchhhhcccccccchhhhcchhcccccccccccc----cccccccceecccccchHH
Confidence 33567788999999999999999999999999999998753 3445678888889888999
Q ss_pred HHHHHHHHHHhc
Q 003942 358 IAQEMIKEVLSQ 369 (784)
Q Consensus 358 ~Ak~lI~~~L~~ 369 (784)
.|+.||.+.|++
T Consensus 198 ~a~~~~~~~~~e 209 (608)
T KOG2279|consen 198 AAKHLILEKVSE 209 (608)
T ss_pred HHHhhhhccccc
Confidence 999999988765
No 24
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.05 E-value=1.9e-10 Score=95.58 Aligned_cols=62 Identities=27% Similarity=0.506 Sum_probs=56.4
Q ss_pred EEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHH
Q 003942 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLIN 267 (784)
Q Consensus 201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~ 267 (784)
+++|.||..++++|||++|++|++|+++|||+|.|.... ..++.|+|+|+.++|.+|+.+|+
T Consensus 1 ~~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-----~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-----SKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred CeEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-----CCCCEEEEEcCHHHHHHHHHHhC
Confidence 368999999999999999999999999999999999652 55789999999999999999874
No 25
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.04 E-value=1.1e-10 Score=96.25 Aligned_cols=60 Identities=40% Similarity=0.668 Sum_probs=54.8
Q ss_pred EEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHH
Q 003942 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLI 266 (784)
Q Consensus 201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I 266 (784)
|.+|+||..++|+|||++|++||+|+++|+|+|+|.++ . .+..|+|+|+.++|++|+++|
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 67999999999999999999999999999999999854 2 345999999999999999987
No 26
>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=99.01 E-value=5.6e-10 Score=92.73 Aligned_cols=64 Identities=38% Similarity=0.601 Sum_probs=57.3
Q ss_pred EEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHH
Q 003942 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLIN 267 (784)
Q Consensus 201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~ 267 (784)
+.+|.||.+++++|||++|++|++|+++|+|+|.|....+ ...++.|+|.|+.++|.+|+.+|.
T Consensus 1 ~~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~---~~~~~~v~i~G~~~~v~~a~~~i~ 64 (64)
T cd00105 1 TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS---GSEERIVTITGTPEAVEKAKELIL 64 (64)
T ss_pred CEEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC---CCCceEEEEEcCHHHHHHHHHHhC
Confidence 3689999999999999999999999999999999997532 456889999999999999999873
No 27
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.01 E-value=5.2e-10 Score=93.09 Aligned_cols=59 Identities=29% Similarity=0.470 Sum_probs=53.8
Q ss_pred eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecc-hhhHHHHHHHHH
Q 003942 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGT-LSNIDKAEKLIN 267 (784)
Q Consensus 200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~-~e~V~kA~~~I~ 267 (784)
.+..|.||.+++|+||||+|++||+|+++|||+|.|.+ ++.|+|+|+ .++|++|+++|+
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 46789999999999999999999999999999999985 357999997 999999999884
No 28
>smart00322 KH K homology RNA-binding domain.
Probab=98.90 E-value=7.6e-09 Score=85.68 Aligned_cols=67 Identities=42% Similarity=0.746 Sum_probs=60.0
Q ss_pred cEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 003942 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS 368 (784)
Q Consensus 296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~ 368 (784)
.+.+|.|+.+++++|||++|++|++|++.|+|+|.+.... ...++|+|.|+.++|+.|+.+|.++|+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~------~~~~~v~i~g~~~~v~~a~~~i~~~~~ 69 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG------SEERVVEITGPPENVEKAAELILEILE 69 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC------CCccEEEEEcCHHHHHHHHHHHHHHhC
Confidence 5688999999999999999999999999999999996432 257899999999999999999998873
No 29
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.82 E-value=8.2e-09 Score=103.41 Aligned_cols=146 Identities=17% Similarity=0.224 Sum_probs=116.5
Q ss_pred ceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCC-
Q 003942 118 HSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTD- 196 (784)
Q Consensus 118 ~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~- 196 (784)
...+.||...++.|||+.|++.+.|...+++++.|...+.....+...-+.+.-++.+|+.+|..+-..++........
T Consensus 9 ~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~A~~LL~ 88 (194)
T COG1094 9 SEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEKALKLLE 88 (194)
T ss_pred eeeeecCchhheeeecccccchHHHHhhcCeEEEEECCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHHHHHHhc
Confidence 4468999999999999999999999988888888887776665555555678889999999999988766654443211
Q ss_pred CCCeEEEEEecC----------CccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHH
Q 003942 197 DSTMSRKIEVPN----------NKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLI 266 (784)
Q Consensus 197 ~~~~t~rI~VP~----------~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I 266 (784)
+..+...|.|-. ...|+|||++|.|.+.|++-|+|.|.|-. ..|.|.|..++|..|++.|
T Consensus 89 d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g----------~tVaiiG~~~~v~iAr~AV 158 (194)
T COG1094 89 DDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG----------KTVAIIGGFEQVEIAREAV 158 (194)
T ss_pred CCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC----------cEEEEecChhhhHHHHHHH
Confidence 233333343321 24799999999999999999999999984 4899999999999999999
Q ss_pred HHHHHhh
Q 003942 267 NAVIAEA 273 (784)
Q Consensus 267 ~elI~e~ 273 (784)
+.+|.-.
T Consensus 159 emli~G~ 165 (194)
T COG1094 159 EMLINGA 165 (194)
T ss_pred HHHHcCC
Confidence 9998754
No 30
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.79 E-value=2.2e-08 Score=120.51 Aligned_cols=213 Identities=18% Similarity=0.193 Sum_probs=149.7
Q ss_pred cceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCC
Q 003942 117 QHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTD 196 (784)
Q Consensus 117 ~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~ 196 (784)
......+.....-.+++..|+.|..|..... ++.+...+.......+++.+....+..+.+....++.+. .
T Consensus 273 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~ 343 (753)
T KOG2208|consen 273 FDYDEIIYRRLPRFIRGIPGEEINQLRDYMP-EVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNS--------E 343 (753)
T ss_pred hhhhhhhhccccccccccccchhhHHHhhcc-hhhhhhccccccceeEeecccccchhhhhhHHHHHHHHh--------h
Confidence 3445666677777899999999999973221 222222222233344566666666555554333333211 1
Q ss_pred CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcC
Q 003942 197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAG 276 (784)
Q Consensus 197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~ 276 (784)
...+...+.|-...+..||||+|.+|.+|++++.|+|.+... .+.+..|.|++...++.+|.+.|+.++.+...
T Consensus 344 ~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~-----~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n- 417 (753)
T KOG2208|consen 344 ENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ-----GSNNKKVVITGVSANDEKAVEDVEKIIAEILN- 417 (753)
T ss_pred ccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc-----cCCCCCeEEeccccchhHHHHHHHHHHHhhhc-
Confidence 223677888888999999999999999999999999999874 34578999999999999999999999998632
Q ss_pred CCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCC-eEEeccCCCCCCCCCCceEEEEEcCHHH
Q 003942 277 GSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGA-RIQLIPQHLPEGDGSKERIVRVTGDMRQ 355 (784)
Q Consensus 277 g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGa-rIqI~~~~~p~~~~~~er~V~I~Gt~~q 355 (784)
...+..+.||...+.+|||.+|..|..|..++++ .|++.+.. +....++|.|....
T Consensus 418 -----------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~------~~~~~~~~~~~~~d 474 (753)
T KOG2208|consen 418 -----------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN------NSSDMVTIRGISKD 474 (753)
T ss_pred -----------------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC------cccccceEeccccc
Confidence 1346679999999999999999999999999995 45554322 33445666666555
Q ss_pred HHHHHHHHHHHH
Q 003942 356 IEIAQEMIKEVL 367 (784)
Q Consensus 356 V~~Ak~lI~~~L 367 (784)
|..++.++..+.
T Consensus 475 v~~~~~~~~~~~ 486 (753)
T KOG2208|consen 475 VEKSVSLLKALK 486 (753)
T ss_pred cchhHHHHHhhh
Confidence 555555544433
No 31
>PF13014 KH_3: KH domain
Probab=98.78 E-value=1e-08 Score=79.21 Aligned_cols=43 Identities=51% Similarity=0.883 Sum_probs=38.1
Q ss_pred ceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEc
Q 003942 306 KVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG 351 (784)
Q Consensus 306 ~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~G 351 (784)
+||+||||+|++||+|+++|||+|+|.++ ......+|+|+|+|
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 58999999999999999999999999873 33467899999997
No 32
>smart00322 KH K homology RNA-binding domain.
Probab=98.77 E-value=2.6e-08 Score=82.43 Aligned_cols=67 Identities=37% Similarity=0.677 Sum_probs=60.2
Q ss_pred CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHH
Q 003942 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVI 270 (784)
Q Consensus 199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI 270 (784)
.++.+|.|+.+++++|||++|++|+.|++.|+++|.+.... .....|+|.|..+++..|+.+|.+++
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-----~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-----SEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-----CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 36789999999999999999999999999999999998542 14678999999999999999999876
No 33
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.76 E-value=8.9e-09 Score=123.78 Aligned_cols=218 Identities=16% Similarity=0.243 Sum_probs=160.6
Q ss_pred ccccceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCC
Q 003942 114 KTEQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPS 193 (784)
Q Consensus 114 ~~~~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~ 193 (784)
+.+..+++.|....+.-++||+|.+|.+|++++++.|.+..... ..+.+.+++...++++|.+.|.+++.+....
T Consensus 344 ~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~--~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~--- 418 (753)
T KOG2208|consen 344 ENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQGS--NNKKVVITGVSANDEKAVEDVEKIIAEILNS--- 418 (753)
T ss_pred ccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccccC--CCCCeEEeccccchhHHHHHHHHHHHhhhcc---
Confidence 34566788888889999999999999999999999999988443 3467888999999999999998888533221
Q ss_pred CCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcC-CEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHh
Q 003942 194 STDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSG-AKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAE 272 (784)
Q Consensus 194 ~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TG-akI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e 272 (784)
.+...+.||...+.+|||.+|..|..|.++++ +.|.+... .+....+++.+....|.+++.++..+...
T Consensus 419 -----~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~-----~~~~~~~~~~~~~~dv~~~~~~~~~~~~~ 488 (753)
T KOG2208|consen 419 -----IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN-----NNSSDMVTIRGISKDVEKSVSLLKALKAD 488 (753)
T ss_pred -----cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC-----CcccccceEeccccccchhHHHHHhhhhh
Confidence 45778999999999999999999999999999 66666543 33445678888777777777776665554
Q ss_pred hhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC
Q 003942 273 ADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD 352 (784)
Q Consensus 273 ~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt 352 (784)
.... ......+.+.+.+..+++.++|+.|. |++..+.+..|.. .+...+..++|.|.
T Consensus 489 a~~~--------------~~~~~~~~d~~~~~~~~~~~~g~~~~----i~d~~~~~~i~~~-----~~~~~~~~i~i~gk 545 (753)
T KOG2208|consen 489 AKNL--------------KFRDVVTKDKLLPVKYIGKEIGKNGT----IRDSLGDKSIFPP-----NEDEDHEKITIEGK 545 (753)
T ss_pred hhcc--------------hhhhhhhccccchHHhhcccccCcee----eeccCCceeeccc-----ccccccceeeeccc
Confidence 3210 00122344556666777777776665 4555555544432 22345678999999
Q ss_pred HHHHHHHHHHHHHHHhc
Q 003942 353 MRQIEIAQEMIKEVLSQ 369 (784)
Q Consensus 353 ~~qV~~Ak~lI~~~L~~ 369 (784)
.+.|..|.++|..+++.
T Consensus 546 ~~~v~~a~~~L~~~~~~ 562 (753)
T KOG2208|consen 546 LELVLEAPAELKALIEA 562 (753)
T ss_pred ccchhhhHHHHHhcchh
Confidence 99999999999877764
No 34
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.70 E-value=1.3e-08 Score=106.88 Aligned_cols=153 Identities=22% Similarity=0.333 Sum_probs=113.6
Q ss_pred CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhc-C
Q 003942 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADA-G 276 (784)
Q Consensus 198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~-~ 276 (784)
..+++.+.||..+|+.|+|++|.+||.|+.+|.+.|...... .+-+|.++|..+.|+.|++.|...-+..-. .
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~------eePiF~vTg~~edv~~aRrei~saaeH~~l~~ 97 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG------EEPIFPVTGRHEDVRRARREIPSAAEHFGLIR 97 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC------CCCcceeccCchhHHHHhhcCccccceeeeee
Confidence 568899999999999999999999999999999999988653 256899999999999999999763222100 0
Q ss_pred CCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHH-H
Q 003942 277 GSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMR-Q 355 (784)
Q Consensus 277 g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~-q 355 (784)
.++... .+.. ........+....||-+.||+|+|..|++||.|++.+...|...-. ..+.++.|+|-.. +
T Consensus 98 ~s~s~S-gg~~-~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~-------~~~~Vf~Vtg~~~nC 168 (394)
T KOG2113|consen 98 ASRSFS-GGTN-GASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR-------CGEPVFCVTGAPKNC 168 (394)
T ss_pred eccccc-CCCc-cccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc-------CCCceEEEecCCcch
Confidence 000000 0000 0112345677889999999999999999999999999998876432 3578899999755 4
Q ss_pred HHHHH-HHHHH
Q 003942 356 IEIAQ-EMIKE 365 (784)
Q Consensus 356 V~~Ak-~lI~~ 365 (784)
|++|+ ..|+.
T Consensus 169 ~kra~s~eie~ 179 (394)
T KOG2113|consen 169 VKRARSCEIEQ 179 (394)
T ss_pred hhhccccchhh
Confidence 77777 44554
No 35
>PF13014 KH_3: KH domain
Probab=98.65 E-value=3.1e-08 Score=76.46 Aligned_cols=43 Identities=44% Similarity=0.696 Sum_probs=38.5
Q ss_pred ccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec
Q 003942 210 KVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG 254 (784)
Q Consensus 210 ~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G 254 (784)
+||+||||+|++||+|+++|+|+|+|.+ +..+...+|.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~--~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP--ENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC--ccCCCCCceEEEEEC
Confidence 4899999999999999999999999998 345577899999987
No 36
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.63 E-value=1.2e-07 Score=89.61 Aligned_cols=67 Identities=28% Similarity=0.416 Sum_probs=53.7
Q ss_pred CceeeeecCCchHHHHHHHHhCCeEEeccCCCCC-------------CCCCCceEEEEEcCH---HHHHHHHHHHHHHHh
Q 003942 305 EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPE-------------GDGSKERIVRVTGDM---RQIEIAQEMIKEVLS 368 (784)
Q Consensus 305 ~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~-------------~~~~~er~V~I~Gt~---~qV~~Ak~lI~~~L~ 368 (784)
|++|+|||.+|.+||+|+++|||+|.|..+..-. .+....-.|.|++.. +++++|+++|+.+|.
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~ 94 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK 94 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence 8999999999999999999999999998653111 112334678899964 899999999999997
Q ss_pred ccc
Q 003942 369 QTV 371 (784)
Q Consensus 369 ~~~ 371 (784)
...
T Consensus 95 ~~~ 97 (120)
T cd02395 95 PAI 97 (120)
T ss_pred cCC
Confidence 543
No 37
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.57 E-value=1.2e-07 Score=89.43 Aligned_cols=71 Identities=30% Similarity=0.434 Sum_probs=56.1
Q ss_pred EEEecC------CccceeeccCcchHhhHHhhcCCEEEEccCCCCCC--------------CCCCCcEEEec-c--hhhH
Q 003942 203 KIEVPN------NKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADP--------------HAATRPVEIIG-T--LSNI 259 (784)
Q Consensus 203 rI~VP~------~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p--------------~s~eR~V~I~G-~--~e~V 259 (784)
+|.||. +++|+|||.+|+|||+|+++|||+|.|..+..... ......|.|++ + .+.+
T Consensus 3 ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~ 82 (120)
T cd02395 3 KVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEAL 82 (120)
T ss_pred EEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHH
Confidence 555554 68999999999999999999999999997631110 11235788888 5 6999
Q ss_pred HHHHHHHHHHHHhh
Q 003942 260 DKAEKLINAVIAEA 273 (784)
Q Consensus 260 ~kA~~~I~elI~e~ 273 (784)
++|+.+|+.+|...
T Consensus 83 ~~A~~~I~~ll~~~ 96 (120)
T cd02395 83 AKAVEAIEELLKPA 96 (120)
T ss_pred HHHHHHHHHHhccC
Confidence 99999999999865
No 38
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=98.48 E-value=4.1e-07 Score=101.12 Aligned_cols=75 Identities=31% Similarity=0.419 Sum_probs=60.6
Q ss_pred CeEEEEEecC------CccceeeccCcchHhhHHhhcCCEEEEccCCC-------------CCCCCCCCcEEEec-chhh
Q 003942 199 TMSRKIEVPN------NKVGVLIGKAGDTIRYLQYNSGAKIQITRDAD-------------ADPHAATRPVEIIG-TLSN 258 (784)
Q Consensus 199 ~~t~rI~VP~------~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~-------------~~p~s~eR~V~I~G-~~e~ 258 (784)
.++.||.||. ++||+|||.+|.|+|+|+++|||||.|..+.. ......+..|.|++ +.|.
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 5777888875 68999999999999999999999999987321 11112345678888 8899
Q ss_pred HHHHHHHHHHHHHhh
Q 003942 259 IDKAEKLINAVIAEA 273 (784)
Q Consensus 259 V~kA~~~I~elI~e~ 273 (784)
|++|+++|+.||.+.
T Consensus 217 i~~Ai~vienli~~a 231 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSA 231 (554)
T ss_pred HHHHHHHHHHHHHhh
Confidence 999999999999974
No 39
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.26 E-value=1.8e-06 Score=83.74 Aligned_cols=104 Identities=21% Similarity=0.363 Sum_probs=76.2
Q ss_pred eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCC
Q 003942 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSP 279 (784)
Q Consensus 200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p 279 (784)
-.+.|+|....+|..||++|++||.|++..|-+|.|...++ .+.++|..+|.-..
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~--------------------d~~~fI~n~l~Pa~----- 86 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSD--------------------DPEEFIKNIFAPAA----- 86 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCC--------------------CHHHHHHHHcCCCE-----
Confidence 46788999999999999999999999999999998885432 23444555443221
Q ss_pred cccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEec
Q 003942 280 SLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLI 332 (784)
Q Consensus 280 ~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~ 332 (784)
+..-.. ........+.+.|+.+..|++|||+|.||+.++..++-++.|.
T Consensus 87 --V~~v~I--~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 87 --VRSVTI--KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred --EEEEEE--EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 000000 0012234567789999999999999999999999999998774
No 40
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.20 E-value=5.6e-06 Score=98.31 Aligned_cols=89 Identities=27% Similarity=0.380 Sum_probs=69.6
Q ss_pred HHHHHHHHHHHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCC
Q 003942 261 KAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGD 340 (784)
Q Consensus 261 kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~ 340 (784)
+|+..|.++|++....- ..+ .........|.|+.+++|.|||.||.+||.|+++|||+|.|.+
T Consensus 553 ~g~~~Il~~m~~al~~p-~~~---------s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------- 615 (719)
T TIGR02696 553 DARLAILDVMAEAIDTP-DEM---------SPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------- 615 (719)
T ss_pred HHHHHHHHHHHHHHhCc-ccc---------ccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec-------
Confidence 44455677777764321 111 1123467889999999999999999999999999999999953
Q ss_pred CCCceEEEEEcC-HHHHHHHHHHHHHHHhc
Q 003942 341 GSKERIVRVTGD-MRQIEIAQEMIKEVLSQ 369 (784)
Q Consensus 341 ~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~ 369 (784)
+.+|.|.+. .+.+++|+++|+.++..
T Consensus 616 ---~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 616 ---DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred ---CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 578999997 89999999999999983
No 41
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=98.20 E-value=6.2e-06 Score=91.98 Aligned_cols=75 Identities=24% Similarity=0.329 Sum_probs=55.7
Q ss_pred ccEEEEEecC------CceeeeecCCchHHHHHHHHhCCeEEeccCCC-----------CCCC-CCCceEEEEEcC-HHH
Q 003942 295 AEQVEIKVPN------EKVGLIIGRGGETIKGLQTRSGARIQLIPQHL-----------PEGD-GSKERIVRVTGD-MRQ 355 (784)
Q Consensus 295 ~~~~~i~VP~------~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~-----------p~~~-~~~er~V~I~Gt-~~q 355 (784)
..+.+|.||- ||||+|||-+|.|.|+|+++|||||.|..... .... ..++--|.|+.+ .+.
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 3445555554 79999999999999999999999999985221 0011 112223677776 789
Q ss_pred HHHHHHHHHHHHhc
Q 003942 356 IEIAQEMIKEVLSQ 369 (784)
Q Consensus 356 V~~Ak~lI~~~L~~ 369 (784)
|++|+++|+.||.+
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999999986
No 42
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.18 E-value=3e-06 Score=89.60 Aligned_cols=146 Identities=15% Similarity=0.171 Sum_probs=111.7
Q ss_pred ccceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCC-------
Q 003942 116 EQHSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSK------- 188 (784)
Q Consensus 116 ~~~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~------- 188 (784)
++...+.+|..+++.|.|++|..||.|+.++.+.|+-..+.+. -++.++|..++|+.||+.|....+...
T Consensus 25 nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~ee---PiF~vTg~~edv~~aRrei~saaeH~~l~~~s~s 101 (394)
T KOG2113|consen 25 NVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEE---PIFPVTGRHEDVRRARREIPSAAEHFGLIRASRS 101 (394)
T ss_pred ccceeeecCcccceeecccCccccchhhhhhcceeccCCCCCC---CcceeccCchhHHHHhhcCccccceeeeeeeccc
Confidence 4555677889999999999999999999888888876655544 578899999999999999987333111
Q ss_pred C--CCCCCCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhh-HHHHH-H
Q 003942 189 S--DDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSN-IDKAE-K 264 (784)
Q Consensus 189 ~--~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~-V~kA~-~ 264 (784)
+ .....-.....+..+.||...||+|+|.+|.+||+|++.+..-|.... .+.+.++.++|-.++ +++|+ .
T Consensus 102 ~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v------~~~~~Vf~Vtg~~~nC~kra~s~ 175 (394)
T KOG2113|consen 102 FSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPV------RCGEPVFCVTGAPKNCVKRARSC 175 (394)
T ss_pred ccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeec------cCCCceEEEecCCcchhhhcccc
Confidence 1 111112345678889999999999999999999999999998887664 344679999997777 66676 5
Q ss_pred HHHHHH
Q 003942 265 LINAVI 270 (784)
Q Consensus 265 ~I~elI 270 (784)
.|+..+
T Consensus 176 eie~ta 181 (394)
T KOG2113|consen 176 EIEQTA 181 (394)
T ss_pred chhhhh
Confidence 555443
No 43
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=97.92 E-value=3.3e-05 Score=74.98 Aligned_cols=103 Identities=18% Similarity=0.319 Sum_probs=74.4
Q ss_pred EEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCc
Q 003942 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPS 280 (784)
Q Consensus 201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~ 280 (784)
..-|+|....+|..||++|++||.|++..|-+|.|..-++ + +.++|++.. +|.
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~------D------------------~~~fI~N~l---~PA 86 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSE------N------------------LEEFVANKL---APA 86 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCC------C------------------HHHHHHHcC---CCc
Confidence 7788999999999999999999999999999998875432 1 333333321 121
Q ss_pred ccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEec
Q 003942 281 LVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLI 332 (784)
Q Consensus 281 ~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~ 332 (784)
.+..-.. ....+.....+.|+.+..+++|||+|.||+...+.++-++.|.
T Consensus 87 ~V~~V~i--~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 87 EVKNVTV--SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred eEEEEEE--EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 1110000 0012345677889999999999999999999999999998774
No 44
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.92 E-value=2.7e-05 Score=93.71 Aligned_cols=65 Identities=25% Similarity=0.455 Sum_probs=57.4
Q ss_pred ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhc
Q 003942 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQ 369 (784)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~ 369 (784)
.....|.|+.++++.|||+||++||.|+++|||+|.|.+ +..|.|.+. .+.+++|+++|+.++..
T Consensus 550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d----------dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED----------DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec----------CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 456789999999999999999999999999999999953 467888776 78999999999998764
No 45
>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=97.84 E-value=3.1e-05 Score=92.18 Aligned_cols=67 Identities=28% Similarity=0.409 Sum_probs=60.7
Q ss_pred CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHHh
Q 003942 197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAE 272 (784)
Q Consensus 197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e 272 (784)
.......|.|+.+++|.|||.+|++||.|.++|||+|.|.++ ..|.|.+ +.+.+++|+++|+.++..
T Consensus 575 ~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~---------G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 575 YAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDD---------GTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred CCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecC---------cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 446788999999999999999999999999999999999853 5888888 889999999999999884
No 46
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.81 E-value=1.7e-05 Score=77.00 Aligned_cols=102 Identities=14% Similarity=0.103 Sum_probs=71.7
Q ss_pred ceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCC-CCCC
Q 003942 118 HSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDP-SSTD 196 (784)
Q Consensus 118 ~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~-~~~~ 196 (784)
...+++....+|..||++|++|+.|++..+.+|.+-.-+ +.++.+|..++.......- ....
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s-----------------~d~~~fI~n~l~Pa~V~~v~I~~~ 95 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYS-----------------DDPEEFIKNIFAPAAVRSVTIKKK 95 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcC-----------------CCHHHHHHHHcCCCEEEEEEEEec
Confidence 446777888999999999999999986666565554422 1234455555543322111 1112
Q ss_pred CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEc
Q 003942 197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQIT 236 (784)
Q Consensus 197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~ 236 (784)
.......|.|+...+|++|||+|.||+.++.-++-++.|.
T Consensus 96 ~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 96 NGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred CCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 2345677889999999999999999999999999888764
No 47
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.77 E-value=1.1e-05 Score=97.65 Aligned_cols=68 Identities=22% Similarity=0.434 Sum_probs=60.3
Q ss_pred CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCE-EEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHHhh
Q 003942 197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAK-IQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAEA 273 (784)
Q Consensus 197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGak-I~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e~ 273 (784)
.......|.|+.++++.|||.+|.|||.|.++||++ |.|.++ -.|.|.+ +.+.+++|+++|+.++.+.
T Consensus 682 ~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd---------g~V~I~a~d~~~i~~A~~~I~~l~~~~ 751 (891)
T PLN00207 682 YAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD---------GTVKITAKDLSSLEKSKAIISSLTMVP 751 (891)
T ss_pred cCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC---------eeEEEEeCCHHHHHHHHHHHHHHhcCc
Confidence 446788999999999999999999999999999999 888753 4788888 8899999999999998753
No 48
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.76 E-value=0.0001 Score=77.28 Aligned_cols=75 Identities=23% Similarity=0.324 Sum_probs=51.3
Q ss_pred CccEEEEEecC------CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCC-------------CCCCc---eEEEEEc
Q 003942 294 AAEQVEIKVPN------EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEG-------------DGSKE---RIVRVTG 351 (784)
Q Consensus 294 ~~~~~~i~VP~------~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~-------------~~~~e---r~V~I~G 351 (784)
...+.+|.||- |+||+|||.+|.++|+|+++|||||.|....+-.. +...+ -.|++..
T Consensus 90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~ 169 (259)
T KOG1588|consen 90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEA 169 (259)
T ss_pred eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeC
Confidence 34566677765 79999999999999999999999999985432111 01111 2355666
Q ss_pred CHHHH----HHHHHHHHHHHh
Q 003942 352 DMRQI----EIAQEMIKEVLS 368 (784)
Q Consensus 352 t~~qV----~~Ak~lI~~~L~ 368 (784)
+.+.+ ..|++.|+.+|-
T Consensus 170 p~~ea~~rl~~AleeI~klL~ 190 (259)
T KOG1588|consen 170 PPAEAYARLAYALEEIKKLLV 190 (259)
T ss_pred CHHHHHHHHHHHHHHHHHhcC
Confidence 65433 457888888774
No 49
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.74 E-value=5.1e-05 Score=91.35 Aligned_cols=67 Identities=30% Similarity=0.418 Sum_probs=59.0
Q ss_pred CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHHh
Q 003942 197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAE 272 (784)
Q Consensus 197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e 272 (784)
.......|.|+.++++.|||++|++||.|+++|||+|.|..+ ..|.|.+ +.+.+++|+++|..++.+
T Consensus 548 ~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd---------G~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 548 YAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD---------GTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred cCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC---------eEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 346788999999999999999999999999999999999853 4677776 889999999999998765
No 50
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.64 E-value=0.00019 Score=75.33 Aligned_cols=44 Identities=30% Similarity=0.539 Sum_probs=38.8
Q ss_pred CCCCeEEEEEecC------CccceeeccCcchHhhHHhhcCCEEEEccCC
Q 003942 196 DDSTMSRKIEVPN------NKVGVLIGKAGDTIRYLQYNSGAKIQITRDA 239 (784)
Q Consensus 196 ~~~~~t~rI~VP~------~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~ 239 (784)
....++.+|+||- ++||+|||.+|.++|+|+++|+|+|.|....
T Consensus 88 ~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrg 137 (259)
T KOG1588|consen 88 KPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRG 137 (259)
T ss_pred CceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCC
Confidence 4456788999987 5899999999999999999999999998754
No 51
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=97.63 E-value=0.00095 Score=68.99 Aligned_cols=129 Identities=17% Similarity=0.238 Sum_probs=95.7
Q ss_pred EEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCc
Q 003942 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPS 280 (784)
Q Consensus 201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~ 280 (784)
.+.|.+.....-+|+..+|..++.|-...||+|.|..+ +..|.|+|++..|+.++..|.+++...
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~--------~~~i~I~g~k~~~~~i~~~i~~~l~~i------- 91 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS--------ENRIRITGTKSTAEYIEASINEILSNI------- 91 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEecC--------CcEEEEEccHHHHHHHHHHHHHHHhhc-------
Confidence 34455557788899999999999998889999999864 468999999999999999999988764
Q ss_pred ccccccchhhccCCccEEEEEecCCceeeee----cCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEc-----
Q 003942 281 LVARGLATAQASGAAEQVEIKVPNEKVGLII----GRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG----- 351 (784)
Q Consensus 281 ~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VI----GkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~G----- 351 (784)
.+.+|.++.-..-... -.....|+.|++.|++.|+...+ ...+.|..
T Consensus 92 ---------------~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~---------~~~~~i~~~~~~~ 147 (210)
T PF14611_consen 92 ---------------RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD---------GNKLKISWLASPE 147 (210)
T ss_pred ---------------EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC---------CCeEEEEEEeecc
Confidence 2344444432111111 11367899999999999998643 23344443
Q ss_pred CHHHHHHHHHHHHHHHh
Q 003942 352 DMRQIEIAQEMIKEVLS 368 (784)
Q Consensus 352 t~~qV~~Ak~lI~~~L~ 368 (784)
..+.++.|++||.-.+.
T Consensus 148 ~~~~~~~a~RlL~~a~~ 164 (210)
T PF14611_consen 148 NEKRADRAKRLLLWALD 164 (210)
T ss_pred ccchHHHHHHHHHHhcc
Confidence 47899999999998886
No 52
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.63 E-value=9.5e-05 Score=89.86 Aligned_cols=67 Identities=25% Similarity=0.430 Sum_probs=58.8
Q ss_pred ccEEEEEecCCceeeeecCCchHHHHHHHHhCCe-EEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhccc
Q 003942 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGAR-IQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQTV 371 (784)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGar-IqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~~~ 371 (784)
.....|.|+.++++.|||.||.+||.|.++||++ |.|.+ +..|.|.+. .+.+++|+++|++++.+..
T Consensus 684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d----------dg~V~I~a~d~~~i~~A~~~I~~l~~~~~ 752 (891)
T PLN00207 684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD----------DGTVKITAKDLSSLEKSKAIISSLTMVPT 752 (891)
T ss_pred CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC----------CeeEEEEeCCHHHHHHHHHHHHHHhcCcC
Confidence 4678899999999999999999999999999999 88743 567888886 8999999999999986543
No 53
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=97.61 E-value=0.00017 Score=73.33 Aligned_cols=103 Identities=22% Similarity=0.354 Sum_probs=72.1
Q ss_pred EEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCc
Q 003942 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPS 280 (784)
Q Consensus 201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~ 280 (784)
.+-+++-.+.||..||++|.+||.|.++.|-+|.|...++ .-.++|..+|. |.
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~--------------------d~~~fI~nal~-------Pa 129 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSE--------------------DPAEFIKNALA-------PA 129 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCC--------------------CHHHHHHHhcC-------cc
Confidence 4555556678999999999999999999998888875431 11223333332 11
Q ss_pred ccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 003942 281 LVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIP 333 (784)
Q Consensus 281 ~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~ 333 (784)
.+..-. ..........+.|+.+..+++|||+|.+|+-+.+.||-+|.|..
T Consensus 130 ~v~~V~---~~~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 130 EVLSVN---IKEDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred eEeEEE---EEeCCCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 000000 00011227788899999999999999999999999999999964
No 54
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.60 E-value=0.00012 Score=85.49 Aligned_cols=94 Identities=23% Similarity=0.302 Sum_probs=71.5
Q ss_pred HHHHHHHHHHHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCC
Q 003942 261 KAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGD 340 (784)
Q Consensus 261 kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~ 340 (784)
.|+..|+.+|.+....-... ...-......+.|+.++++.|||++|++||.|.++|||+|.|.
T Consensus 526 ~aRlhIL~~M~~ai~~pr~e---------ls~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-------- 588 (692)
T COG1185 526 GARLHILIVMNEAISEPRKE---------LSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-------- 588 (692)
T ss_pred HHHHHHHHHHHHHHhhhhhh---------hhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec--------
Confidence 44556777776653211001 1112345678999999999999999999999999999999995
Q ss_pred CCCceEEEEEcC-HHHHHHHHHHHHHHHhcccCC
Q 003942 341 GSKERIVRVTGD-MRQIEIAQEMIKEVLSQTVRP 373 (784)
Q Consensus 341 ~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~~~r~ 373 (784)
++.+|.|.++ .+.+++|+++|.+++++....
T Consensus 589 --ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg 620 (692)
T COG1185 589 --DDGTVKIAASDGESAKKAKERIEAITREVEVG 620 (692)
T ss_pred --CCCcEEEEecchHHHHHHHHHHHHHHhhcccc
Confidence 3567999998 589999999999999876443
No 55
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=97.50 E-value=0.00016 Score=72.87 Aligned_cols=70 Identities=33% Similarity=0.457 Sum_probs=50.3
Q ss_pred CCCeEEEEEecC------CccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHH
Q 003942 197 DSTMSRKIEVPN------NKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAV 269 (784)
Q Consensus 197 ~~~~t~rI~VP~------~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~el 269 (784)
...++.+|.||- ++||+|||..|.|+|+|++.|+|+|-|..... ...+.|+. +.+.+..|.+.|+.+
T Consensus 145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gs------vKegk~ssd~p~~~~N~e~~lhcL 218 (269)
T COG5176 145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGS------VKEGKISSDTPESLKNAEAVLHCL 218 (269)
T ss_pred cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccc------cccCcccccCchhhhhhHHhHHHH
Confidence 345777888874 68999999999999999999999999987532 23444544 355555555555555
Q ss_pred HHh
Q 003942 270 IAE 272 (784)
Q Consensus 270 I~e 272 (784)
|..
T Consensus 219 I~a 221 (269)
T COG5176 219 IEA 221 (269)
T ss_pred hhc
Confidence 544
No 56
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.47 E-value=0.00014 Score=80.03 Aligned_cols=75 Identities=21% Similarity=0.310 Sum_probs=64.1
Q ss_pred CCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhh
Q 003942 195 TDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD 274 (784)
Q Consensus 195 ~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~ 274 (784)
.....+.+.|.|-++.||.|||++|++||+|+..|+++|+|.+- ..+-.|+|.|..+--.+|...|...++..+
T Consensus 42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~------~~e~kv~ifg~~~m~~kaka~id~~~~k~e 115 (629)
T KOG0336|consen 42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC------DLEVKVTIFGINHMRKKAKASIDRGQDKDE 115 (629)
T ss_pred cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc------CceeEEEEechHHHHHHHHhhHhhhhhhhh
Confidence 34567888999999999999999999999999999999999863 236688999998888888888888887665
Q ss_pred c
Q 003942 275 A 275 (784)
Q Consensus 275 ~ 275 (784)
.
T Consensus 116 ~ 116 (629)
T KOG0336|consen 116 R 116 (629)
T ss_pred h
Confidence 4
No 57
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.47 E-value=9.5e-05 Score=81.36 Aligned_cols=72 Identities=29% Similarity=0.360 Sum_probs=60.7
Q ss_pred CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcccC
Q 003942 294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQTVR 372 (784)
Q Consensus 294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~~r 372 (784)
..-.+.|.|-+++||.|||++|++||.||..|.++|+|++.. .+..|+|.|....-.+|+..|...++...+
T Consensus 45 ~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~-------~e~kv~ifg~~~m~~kaka~id~~~~k~e~ 116 (629)
T KOG0336|consen 45 GEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD-------LEVKVTIFGINHMRKKAKASIDRGQDKDER 116 (629)
T ss_pred CCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC-------ceeEEEEechHHHHHHHHhhHhhhhhhhhh
Confidence 344567889999999999999999999999999999998643 478899999988888899888877765443
No 58
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=97.44 E-value=0.00012 Score=73.45 Aligned_cols=149 Identities=19% Similarity=0.283 Sum_probs=102.7
Q ss_pred CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEe-----cchhhHHHHHHHHHHHHHh
Q 003942 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEII-----GTLSNIDKAEKLINAVIAE 272 (784)
Q Consensus 198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~-----G~~e~V~kA~~~I~elI~e 272 (784)
...+.+|.||.+++--+--.+-....-|-+..+..|.+.-+ .|.|.|. -+..++.++..+|..++.-
T Consensus 72 k~e~Rkvpvpp~r~tplk~~W~kIytPive~lklqiRmNlK--------~r~VelRt~~~t~D~s~Lqk~adfv~Af~lG 143 (252)
T KOG3273|consen 72 KIETRKVPVPPHRYTPLKDNWMKIYTPIVEHLKLQIRMNLK--------ARSVELRTCKDTEDPSALQKGADFVRAFILG 143 (252)
T ss_pred ccceeeccCCcccCChHHHhhHhhhhHHHHhhhheeEeecc--------cceeEeecCCCCCChHHHHHHHHHHHHHHhC
Confidence 34578899999998887666666677788888888877532 3555554 3556899999999888765
Q ss_pred hhcCCCCccc------ccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceE
Q 003942 273 ADAGGSPSLV------ARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERI 346 (784)
Q Consensus 273 ~~~~g~p~~~------~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~ 346 (784)
.+....-.|. -..|. .....+++=.--...+|+|+||+|.|--.|.+.|.+||.+. +..
T Consensus 144 F~i~DAiALlrlddlflesFE----i~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVla-----------d~k 208 (252)
T KOG3273|consen 144 FDIDDAIALLRLDDLFLESFE----IKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLA-----------DSK 208 (252)
T ss_pred CcchhHHHHHhhhhhhheeee----ecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEec-----------Cce
Confidence 4321111110 00000 00111111111235789999999999999999999999984 557
Q ss_pred EEEEcCHHHHHHHHHHHHHHHhc
Q 003942 347 VRVTGDMRQIEIAQEMIKEVLSQ 369 (784)
Q Consensus 347 V~I~Gt~~qV~~Ak~lI~~~L~~ 369 (784)
|+|.|....+..|+..|+.+|-.
T Consensus 209 IHiLG~~~niriAR~avcsLIlG 231 (252)
T KOG3273|consen 209 IHILGAFQNIRIARDAVCSLILG 231 (252)
T ss_pred EEEeecchhhHHHHHhhHhhhcc
Confidence 99999999999999999998853
No 59
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=97.35 E-value=0.00025 Score=71.13 Aligned_cols=106 Identities=16% Similarity=0.285 Sum_probs=80.7
Q ss_pred ccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCC--CCCCCeEEEEEecC----------CccceeeccCcchHhhH
Q 003942 158 EVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSS--TDDSTMSRKIEVPN----------NKVGVLIGKAGDTIRYL 225 (784)
Q Consensus 158 ~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~--~~~~~~t~rI~VP~----------~~vG~IIGkgG~tIK~I 225 (784)
....|.+.-+-+..++.++...|..++-.++++.... ..+..+..+|.|-. ..+|+|+||+|.|--.|
T Consensus 115 ~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~DAiALlrlddlflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaI 194 (252)
T KOG3273|consen 115 SVELRTCKDTEDPSALQKGADFVRAFILGFDIDDAIALLRLDDLFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAI 194 (252)
T ss_pred eeEeecCCCCCChHHHHHHHHHHHHHHhCCcchhHHHHHhhhhhhheeeeecccccccchhHHHHHHHhhcCCCcceeee
Confidence 4445667777788888898888888887666544331 11233444454433 45899999999999999
Q ss_pred HhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942 226 QYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA 273 (784)
Q Consensus 226 q~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~ 273 (784)
++.|.++|.|.. ..|+|.|..++|..|+..|+.+|--.
T Consensus 195 En~trtrIVlad----------~kIHiLG~~~niriAR~avcsLIlGs 232 (252)
T KOG3273|consen 195 ENVTRTRIVLAD----------SKIHILGAFQNIRIARDAVCSLILGS 232 (252)
T ss_pred eccceeEEEecC----------ceEEEeecchhhHHHHHhhHhhhccC
Confidence 999999999973 47999999999999999999998743
No 60
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.26 E-value=0.00037 Score=81.64 Aligned_cols=68 Identities=28% Similarity=0.426 Sum_probs=59.6
Q ss_pred CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHHhhh
Q 003942 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAEAD 274 (784)
Q Consensus 198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e~~ 274 (784)
....+.+.|+..+...|||++|++||.|.++|||+|.|..+ ..|.|.+ +.+.+.+|+++|..++++..
T Consensus 550 aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idiedd---------Gtv~i~~s~~~~~~~ak~~I~~i~~e~e 618 (692)
T COG1185 550 APRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD---------GTVKIAASDGESAKKAKERIEAITREVE 618 (692)
T ss_pred CCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCC---------CcEEEEecchHHHHHHHHHHHHHHhhcc
Confidence 34577889999999999999999999999999999999843 4788888 56899999999999998763
No 61
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.23 E-value=0.00036 Score=84.26 Aligned_cols=64 Identities=28% Similarity=0.514 Sum_probs=55.9
Q ss_pred cEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhc
Q 003942 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQ 369 (784)
Q Consensus 296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~ 369 (784)
....+.|+.++++.|||.||.+||.|.++||++|.|.. +..|.|.+. .+.+++|+++|+.++.+
T Consensus 554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d----------~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED----------DGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC----------CceEEEEcccHHHHHHHHHHHHHhccc
Confidence 45677889999999999999999999999999988742 567888886 88999999999998865
No 62
>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=97.23 E-value=0.00023 Score=69.20 Aligned_cols=102 Identities=15% Similarity=0.087 Sum_probs=68.8
Q ss_pred ceeeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCC-CCCC
Q 003942 118 HSSVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDP-SSTD 196 (784)
Q Consensus 118 ~~ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~-~~~~ 196 (784)
-.-+++-...+|..||++|.+|+.|++..+.+|.|-+-+.. -+.+|...+.-.....- ....
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~D-----------------~~~fI~N~l~PA~V~~V~i~~~ 96 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSEN-----------------LEEFVANKLAPAEVKNVTVSEF 96 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCC-----------------HHHHHHHcCCCceEEEEEEEcC
Confidence 34567777899999999999999998766666665542221 11223332221111110 0111
Q ss_pred CCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEc
Q 003942 197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQIT 236 (784)
Q Consensus 197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~ 236 (784)
+......+.|+.+..+++|||+|.|||..++-++-++.|.
T Consensus 97 ~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 97 NGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred CCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 2345678999999999999999999999999998888765
No 63
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=97.20 E-value=0.00098 Score=74.07 Aligned_cols=95 Identities=18% Similarity=0.273 Sum_probs=68.1
Q ss_pred CccceeeccCcchHhhHHhhc-CCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccc
Q 003942 209 NKVGVLIGKAGDTIRYLQYNS-GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLA 287 (784)
Q Consensus 209 ~~vG~IIGkgG~tIK~Iq~~T-GakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~ 287 (784)
+-||..||++|.+|+.|.++. |-+|.|..-++. +.++|++.. +|.-+.+-.
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D------------------------~~~fI~Nal---~Pa~V~~V~- 302 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNV------------------------PEIFIARAL---APAIISSVK- 302 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCC------------------------HHHHHHHhC---CCceeeEEE-
Confidence 359999999999999999998 888888764321 222333321 111111000
Q ss_pred hhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccC
Q 003942 288 TAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQ 334 (784)
Q Consensus 288 ~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~ 334 (784)
.........+.|+.+..++.|||+|.|||-..+.||.+|.|..-
T Consensus 303 ---i~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~ 346 (374)
T PRK12328 303 ---IEEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI 346 (374)
T ss_pred ---EcCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence 01233577899999999999999999999999999999999853
No 64
>PRK00106 hypothetical protein; Provisional
Probab=97.01 E-value=0.0027 Score=74.04 Aligned_cols=66 Identities=23% Similarity=0.411 Sum_probs=55.5
Q ss_pred ccEEEEEecC-CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhc
Q 003942 295 AEQVEIKVPN-EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQ 369 (784)
Q Consensus 295 ~~~~~i~VP~-~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~ 369 (784)
.....+.+|+ ++.|+||||.|.|||.|...|||.|.|++ +...|+|++. +-.-+.|+.-|+.+|.+
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd---------tp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD---------TPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC---------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 3456778899 78999999999999999999999999953 4567889995 77778888888888764
No 65
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=97.00 E-value=0.0025 Score=74.47 Aligned_cols=66 Identities=27% Similarity=0.427 Sum_probs=55.0
Q ss_pred ccEEEEEecC-CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhc
Q 003942 295 AEQVEIKVPN-EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQ 369 (784)
Q Consensus 295 ~~~~~i~VP~-~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~ 369 (784)
.....+.+|+ ++.|+||||.|.|||.+...|||.|.|++ +...|+|++. +-.-+.|+.-|+.+|.+
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd---------tp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD---------TPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC---------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 3455678888 78999999999999999999999999953 4567889985 66778888888888764
No 66
>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=97.00 E-value=0.0019 Score=71.66 Aligned_cols=94 Identities=28% Similarity=0.422 Sum_probs=67.1
Q ss_pred ccceeeccCcchHhhHHhhc-CCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccch
Q 003942 210 KVGVLIGKAGDTIRYLQYNS-GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLAT 288 (784)
Q Consensus 210 ~vG~IIGkgG~tIK~Iq~~T-GakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~ 288 (784)
-||..||++|.+|+.|.++. |-+|.|..-++. +.++|.+.. +|..+.+-.-
T Consensus 244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d------------------------~~~fi~nal---~Pa~v~~v~i- 295 (341)
T TIGR01953 244 PVGACVGPKGSRIQAISKELNGEKIDIIEYSDD------------------------PAEFIANAL---SPAKVISVEV- 295 (341)
T ss_pred cceeeECCCCchHHHHHHHhCCCeEEEEEcCCC------------------------HHHHHHHhc---CCceEEEEEE-
Confidence 59999999999999999998 888888764321 222333321 1111111000
Q ss_pred hhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 003942 289 AQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIP 333 (784)
Q Consensus 289 ~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~ 333 (784)
.........+.|+.+..++.|||+|.|||-..+.||++|.|..
T Consensus 296 --~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 296 --LDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred --EcCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 0112357889999999999999999999999999999999974
No 67
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.92 E-value=0.00088 Score=72.28 Aligned_cols=71 Identities=27% Similarity=0.373 Sum_probs=60.6
Q ss_pred CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHHhhh
Q 003942 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAEAD 274 (784)
Q Consensus 199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e~~ 274 (784)
.....|+|...+.+.|||++|.|.|+|+++|+++|.+++. +.....|+|+| ..+.|.+|++.|..+|.+..
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p-----~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP-----NTNKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC-----CCCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 3566789999999999999999999999999999999965 33345666666 89999999999999998864
No 68
>PRK12704 phosphodiesterase; Provisional
Probab=96.91 E-value=0.0035 Score=73.44 Aligned_cols=65 Identities=28% Similarity=0.420 Sum_probs=53.0
Q ss_pred cEEEEEecC-CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhc
Q 003942 296 EQVEIKVPN-EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQ 369 (784)
Q Consensus 296 ~~~~i~VP~-~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~ 369 (784)
....+.+|+ ++.|+||||.|.|||.+...|||.|.|++ +..+|.|+|. +-.-+.|+..|+.+|.+
T Consensus 210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd---------tp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD---------TPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC---------CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 445677888 78999999999999999999999999953 4667889995 55656788887777654
No 69
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.89 E-value=0.0018 Score=73.06 Aligned_cols=94 Identities=26% Similarity=0.369 Sum_probs=66.7
Q ss_pred ccceeeccCcchHhhHHhhc-CCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccch
Q 003942 210 KVGVLIGKAGDTIRYLQYNS-GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLAT 288 (784)
Q Consensus 210 ~vG~IIGkgG~tIK~Iq~~T-GakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~ 288 (784)
-||..||++|.+|+.|.++. |-+|.|..-++ + +..+|++.. +|..+..-..
T Consensus 278 PvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~------D------------------p~~fI~NaL---sPA~V~~V~i- 329 (449)
T PRK12329 278 PVGACIGARGSRIQAVVNELRGEKIDVIRWSP------D------------------PATYIANAL---SPARVDEVRL- 329 (449)
T ss_pred hhhccCCCCcchHHHHHHHhCCCeEEEEEcCC------C------------------HHHHHHHhc---CCceeeEEEE-
Confidence 59999999999999999998 88888875432 1 222233221 1211111000
Q ss_pred hhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 003942 289 AQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIP 333 (784)
Q Consensus 289 ~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~ 333 (784)
.........+.|+.+..++.|||+|.|||-....||.+|.|..
T Consensus 330 --~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 330 --VDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred --EcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 0112356789999999999999999999999999999999964
No 70
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.87 E-value=0.00073 Score=81.68 Aligned_cols=67 Identities=31% Similarity=0.473 Sum_probs=57.4
Q ss_pred CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHHhh
Q 003942 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAEA 273 (784)
Q Consensus 198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e~ 273 (784)
......+.|+.++++.|||.+|.|||.|.++||++|.+..+ -.|.|.+ +.+.+++|+++|..++.+.
T Consensus 552 ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~---------G~v~i~~~~~~~~~~a~~~I~~~~~~~ 619 (693)
T PRK11824 552 APRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD---------GTVKIAATDGEAAEAAKERIEGITAEP 619 (693)
T ss_pred CchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC---------ceEEEEcccHHHHHHHHHHHHHhcccC
Confidence 34566777899999999999999999999999999998643 4778887 8899999999999988653
No 71
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.86 E-value=0.0026 Score=71.07 Aligned_cols=94 Identities=21% Similarity=0.330 Sum_probs=67.5
Q ss_pred ccceeeccCcchHhhHHhhc-CCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccch
Q 003942 210 KVGVLIGKAGDTIRYLQYNS-GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLAT 288 (784)
Q Consensus 210 ~vG~IIGkgG~tIK~Iq~~T-GakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~ 288 (784)
-||..||++|.+|+.|.++. |-+|.|..-++. +.++|++.. +|..+.+-.-
T Consensus 246 pvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d------------------------~~~fi~nal---~Pa~v~~v~i- 297 (362)
T PRK12327 246 AKGACVGPKGQRVQNIVSELKGEKIDIIDWSED------------------------PAEFVANAL---SPAKVVSVEV- 297 (362)
T ss_pred chheeECCCChhHHHHHHHhCCCeEEEEEcCCC------------------------HHHHHHHhC---CCceEEEEEE-
Confidence 59999999999999999988 888888764321 222333321 1211111000
Q ss_pred hhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 003942 289 AQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIP 333 (784)
Q Consensus 289 ~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~ 333 (784)
.........+.|+.+..++.|||+|.||+-....||++|.|..
T Consensus 298 --~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 298 --DDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred --EcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 0123357889999999999999999999999999999999975
No 72
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.82 E-value=0.0042 Score=62.86 Aligned_cols=69 Identities=25% Similarity=0.273 Sum_probs=47.4
Q ss_pred CceeeeecCCchHHHHHHHHhCCeEEeccCCC----------CCCCCCCceE---EEEEcCHHHHHHHHHHHHHHHhccc
Q 003942 305 EKVGLIIGRGGETIKGLQTRSGARIQLIPQHL----------PEGDGSKERI---VRVTGDMRQIEIAQEMIKEVLSQTV 371 (784)
Q Consensus 305 ~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~----------p~~~~~~er~---V~I~Gt~~qV~~Ak~lI~~~L~~~~ 371 (784)
|+||+|||..|.|+|.|++.|+|+|-|..... ++.-...+.+ +++.-+.+.+++++.+|..+|.+.+
T Consensus 163 NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adsedki~~~ik~~~n~I~~a~ 242 (269)
T COG5176 163 NFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSEDKICRLIKSQLNAIREAR 242 (269)
T ss_pred ceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchhhhHHHHHHHHHHHHHHHh
Confidence 89999999999999999999999999974321 1110111111 2333446778888888888877665
Q ss_pred CC
Q 003942 372 RP 373 (784)
Q Consensus 372 r~ 373 (784)
+.
T Consensus 243 ~~ 244 (269)
T COG5176 243 RN 244 (269)
T ss_pred cC
Confidence 54
No 73
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.70 E-value=0.0035 Score=73.32 Aligned_cols=90 Identities=20% Similarity=0.321 Sum_probs=61.2
Q ss_pred hchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCC-ccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCc
Q 003942 171 ESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNN-KVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRP 249 (784)
Q Consensus 171 e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~-~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~ 249 (784)
++-.+|+.+|..-+...... .....++..|.+|++ .-|+||||.|.|||.|..-|||+|.|++. ...
T Consensus 179 ~a~~~a~~i~~~aiqr~a~~----~~~e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt--------p~~ 246 (514)
T TIGR03319 179 EADKKAKEILATAIQRYAGD----HVAETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT--------PEA 246 (514)
T ss_pred HHHHHHHHHHHHHHHhccch----hhhhheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC--------CCe
Confidence 34455666666655433221 123356677888884 78999999999999999999999999853 246
Q ss_pred EEEec-chhhHHHHHHHHHHHHHh
Q 003942 250 VEIIG-TLSNIDKAEKLINAVIAE 272 (784)
Q Consensus 250 V~I~G-~~e~V~kA~~~I~elI~e 272 (784)
|+|++ ++-.-+.|+..|..||.+
T Consensus 247 v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 247 VILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred EEecCCchHHHHHHHHHHHHHHHc
Confidence 77887 555445555555555543
No 74
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.70 E-value=0.0014 Score=66.72 Aligned_cols=101 Identities=18% Similarity=0.178 Sum_probs=67.7
Q ss_pred eeeccccccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCC-CCCCCC
Q 003942 120 SVEEQASVDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDP-SSTDDS 198 (784)
Q Consensus 120 ki~iP~~~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~-~~~~~~ 198 (784)
...+-...+|..||++|.+|+.|.++.+.+|+|-.-... -..+|...|.-.....- ....+.
T Consensus 79 ~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d-----------------~~~fI~nal~Pa~v~~V~~~~~d~ 141 (190)
T COG0195 79 SNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSED-----------------PAEFIKNALAPAEVLSVNIKEDDG 141 (190)
T ss_pred EeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCC-----------------HHHHHHHhcCcceEeEEEEEeCCC
Confidence 445555677899999999999999777655555443321 12223333321111000 011112
Q ss_pred CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccC
Q 003942 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (784)
Q Consensus 199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~ 238 (784)
. ...+.|+.+..+++|||+|.+++.+.+-||.+|.|...
T Consensus 142 ~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~ 180 (190)
T COG0195 142 H-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI 180 (190)
T ss_pred c-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence 2 78899999999999999999999999999999999753
No 75
>PRK00106 hypothetical protein; Provisional
Probab=96.67 E-value=0.0039 Score=72.81 Aligned_cols=90 Identities=18% Similarity=0.269 Sum_probs=62.4
Q ss_pred hchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCC-ccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCc
Q 003942 171 ESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNN-KVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRP 249 (784)
Q Consensus 171 e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~-~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~ 249 (784)
++-.+|+.+|..-+.....+. ....++..|.+|++ .-|+||||.|.|||.|..-|||+|.|++. ...
T Consensus 200 ~a~~~a~~ii~~aiqr~a~~~----~~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt--------p~~ 267 (535)
T PRK00106 200 RSDKMAKDLLAQAMQRLAGEY----VTEQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDT--------PEV 267 (535)
T ss_pred HHHHHHHHHHHHHHHHhcchh----hhhheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCC--------CCe
Confidence 344556666666554332211 23356777888984 78999999999999999999999999853 346
Q ss_pred EEEec-chhhHHHHHHHHHHHHHh
Q 003942 250 VEIIG-TLSNIDKAEKLINAVIAE 272 (784)
Q Consensus 250 V~I~G-~~e~V~kA~~~I~elI~e 272 (784)
|+|++ ++-.-+.|+..|+.||.+
T Consensus 268 v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 268 VVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred EEEeCCChHHHHHHHHHHHHHHHc
Confidence 77888 555555566666655554
No 76
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=96.66 E-value=0.0029 Score=72.98 Aligned_cols=103 Identities=26% Similarity=0.425 Sum_probs=71.6
Q ss_pred eEEEEEecCC-----ccceeeccCcchHhhHHhhc-CCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942 200 MSRKIEVPNN-----KVGVLIGKAGDTIRYLQYNS-GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA 273 (784)
Q Consensus 200 ~t~rI~VP~~-----~vG~IIGkgG~tIK~Iq~~T-GakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~ 273 (784)
...+|-|-++ -||..||++|++|+.|.++. |-+|.|..-++ + +..+|.+.
T Consensus 231 ~RaKvAV~s~d~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~------d------------------~~~fi~na 286 (470)
T PRK09202 231 SRAKIAVKSNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILWSD------D------------------PAQFIINA 286 (470)
T ss_pred ceeEEEEEcCCCCCChhHccCCCCCchHHHHHHHhCCCeEEEEEcCC------C------------------HHHHHHHh
Confidence 3445555443 49999999999999999998 78888875432 1 22233332
Q ss_pred hcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 003942 274 DAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIP 333 (784)
Q Consensus 274 ~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~ 333 (784)
. +|..+.+-. .......+.+.|+.+..++.|||+|.|||-..+.||.+|.|..
T Consensus 287 l---~pa~v~~v~----~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 287 L---SPAEVSSVV----VDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred C---CCCEEEEEE----EeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 1 111111100 0112357889999999999999999999999999999999975
No 77
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.65 E-value=0.0031 Score=66.61 Aligned_cols=65 Identities=25% Similarity=0.328 Sum_probs=56.4
Q ss_pred EEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhccc
Q 003942 297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQTV 371 (784)
Q Consensus 297 ~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~~~ 371 (784)
-+.|.||.+++++|||++|.+|+.|.++++|+|.|-. +..|.|.+. .+.+.+|+.+|+.+-++..
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~----------NG~VwI~~~~~~~~~~a~~~I~~~e~~~~ 211 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ----------NGRIWIKGPDEEDEEIAIEAIKKIEREAH 211 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC----------CcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence 4678999999999999999999999999999999843 467888888 6799999999998776543
No 78
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.59 E-value=0.0024 Score=69.03 Aligned_cols=71 Identities=21% Similarity=0.316 Sum_probs=57.5
Q ss_pred cEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcccC
Q 003942 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG-DMRQIEIAQEMIKEVLSQTVR 372 (784)
Q Consensus 296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~G-t~~qV~~Ak~lI~~~L~~~~r 372 (784)
....+.|...+++.|||++|.|-|+|+++|+|+|.+.+.. .....|+|+| ..++|..|.+.|..+|.+.++
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~------~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r~ 128 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN------TNKEEIKIIGISRNCVIQALERIAKLIDSDRK 128 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC------CCcceEEEeehhHHHHHHHHHHHHHHHHhhhh
Confidence 4556889999999999999999999999999999996532 2333455554 589999999999999987653
No 79
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.51 E-value=0.0038 Score=65.94 Aligned_cols=65 Identities=26% Similarity=0.335 Sum_probs=56.5
Q ss_pred EEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHHhhh
Q 003942 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAEAD 274 (784)
Q Consensus 201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e~~ 274 (784)
-+.|.|+.+++++|||++|.+|+.|.++|+++|.|-. +-.|.|.+ +.+.+.+|+.+|+.+-++..
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~---------NG~VwI~~~~~~~~~~a~~~I~~~e~~~~ 211 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ---------NGRIWIKGPDEEDEEIAIEAIKKIEREAH 211 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC---------CcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence 3578899999999999999999999999999999974 35789998 67799999999998777654
No 80
>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=96.50 E-value=0.003 Score=52.61 Aligned_cols=37 Identities=32% Similarity=0.614 Sum_probs=34.4
Q ss_pred CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEE
Q 003942 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQI 235 (784)
Q Consensus 199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V 235 (784)
....+|.|+.+.+|.+|||+|.+|+.+++.++.+|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3688999999999999999999999999999988876
No 81
>PRK12704 phosphodiesterase; Provisional
Probab=96.50 E-value=0.0053 Score=71.91 Aligned_cols=90 Identities=20% Similarity=0.335 Sum_probs=62.1
Q ss_pred hchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCC-ccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCc
Q 003942 171 ESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNN-KVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRP 249 (784)
Q Consensus 171 e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~-~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~ 249 (784)
++-.+|+.+|..-+....... ....++..|.+|++ .-|+||||.|.|||.|+.-|||+|.|++. ..+
T Consensus 185 ~a~~~a~~i~~~a~qr~a~~~----~~e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt--------p~~ 252 (520)
T PRK12704 185 EADKKAKEILAQAIQRCAADH----VAETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT--------PEA 252 (520)
T ss_pred HHHHHHHHHHHHHHHhhcchh----hhhhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC--------CCe
Confidence 344556666666554332211 23345667888884 88999999999999999999999999853 347
Q ss_pred EEEec-chhhHHHHHHHHHHHHHh
Q 003942 250 VEIIG-TLSNIDKAEKLINAVIAE 272 (784)
Q Consensus 250 V~I~G-~~e~V~kA~~~I~elI~e 272 (784)
|.|++ ++-.-+.|+..|+.+|.+
T Consensus 253 v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 253 VILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred EEEecCChhhHHHHHHHHHHHHhc
Confidence 77888 454445666666666654
No 82
>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=96.38 E-value=0.0052 Score=51.21 Aligned_cols=37 Identities=27% Similarity=0.680 Sum_probs=34.6
Q ss_pred ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEe
Q 003942 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQL 331 (784)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI 331 (784)
.....+.|+.+.+|.+|||+|.+|+.|++.++.+|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3688999999999999999999999999999999887
No 83
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=96.35 E-value=0.016 Score=63.88 Aligned_cols=163 Identities=15% Similarity=0.010 Sum_probs=99.9
Q ss_pred CcchHhhHHhhcCCEEEEccCCCC------CCCCCCCcEEEec-chhhHHHHHHHHHHHHHhhhcCCCCccc---cc---
Q 003942 218 AGDTIRYLQYNSGAKIQITRDADA------DPHAATRPVEIIG-TLSNIDKAEKLINAVIAEADAGGSPSLV---AR--- 284 (784)
Q Consensus 218 gG~tIK~Iq~~TGakI~V~~~~~~------~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e~~~~g~p~~~---~~--- 284 (784)
+|.+..+|.+.+|+.|.+...-.. .+++.-.+.+|.+ +.|-+++|+..|.-++..+....+...+ .+
T Consensus 112 Rg~~~d~Ie~~~G~~~~~RGs~~~~El~~vg~~~~pLv~hI~~~T~Ei~~~Ai~RIkgv~~~~~~~~n~~~V~i~~~~sP 191 (531)
T KOG1960|consen 112 RGTSYDHIEGITGTTSASRGSAPAPELPPVGSSEGPLVDHIPPSTAEITSKAIERIKGVFMQDVEINNVRNVYILVRASP 191 (531)
T ss_pred cchhHHhhhhhccceeeccCCCCCccCCCCCCCCCcceeecCCccHHHHHHHHhhCccceeecccccccceEEEeecCCc
Confidence 588899999999999988764221 1222334678888 8899999999998666544221111000 00
Q ss_pred ------c-----cchhhccCCccEEEEEecC-CceeeeecCCchHHHHHHHHhCCeEEeccCC----CC--CCCCCCceE
Q 003942 285 ------G-----LATAQASGAAEQVEIKVPN-EKVGLIIGRGGETIKGLQTRSGARIQLIPQH----LP--EGDGSKERI 346 (784)
Q Consensus 285 ------g-----~~~~~~~~~~~~~~i~VP~-~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~----~p--~~~~~~er~ 346 (784)
- |.....-.....+.+.+|. ++.+++=+++-.++.+|+.+|++++.|..+. .| ..+..+-+.
T Consensus 192 ~~~i~~~V~~~~f~~G~~Y~~k~~v~~~~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMY 271 (531)
T KOG1960|consen 192 LSEIENKVGVQLFSKGRYYPNKALATDKDPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNEGNESNEPMY 271 (531)
T ss_pred hhhhccccccccccccccchhheecccCCcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccCcccccccCCcee
Confidence 0 0000000011122223444 4567777888889999999999998774322 11 123444567
Q ss_pred EEEEcC-HHHHHHHHHHHHHHHhcccCCCCCCCCCCC
Q 003942 347 VRVTGD-MRQIEIAQEMIKEVLSQTVRPSTLSGGFNQ 382 (784)
Q Consensus 347 V~I~Gt-~~qV~~Ak~lI~~~L~~~~r~~~~~gg~~~ 382 (784)
|.|++. .+.+.+|+++|.++++.+... ++.+|++
T Consensus 272 I~i~h~~~~g~~~A~r~~~nl~~~v~~~--~sr~~~~ 306 (531)
T KOG1960|consen 272 IFSTHGNGNGENGAPRRKWNLEEKVYIN--LSRGFHR 306 (531)
T ss_pred EEeecCCchhhccchhHHHhHHHHHHHH--hhhhhhh
Confidence 777765 899999999999999765443 2344443
No 84
>PRK12705 hypothetical protein; Provisional
Probab=96.19 E-value=0.0088 Score=69.49 Aligned_cols=64 Identities=22% Similarity=0.353 Sum_probs=47.7
Q ss_pred cEEEEEecC-CceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHh
Q 003942 296 EQVEIKVPN-EKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLS 368 (784)
Q Consensus 296 ~~~~i~VP~-~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~ 368 (784)
....+.+|+ ++.|+||||.|.|||.+...||+.|.|++ +.+.|+|++. +..-+.|+..+..+|.
T Consensus 198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd---------tp~~V~ls~fdp~rreia~~~l~~Li~ 263 (508)
T PRK12705 198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD---------TPEAVVISSFNPIRREIARLTLEKLLA 263 (508)
T ss_pred eeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC---------CccchhhcccCccchHHHHHHHHHHHh
Confidence 445677888 78999999999999999999999999954 3445666665 4455556665555554
No 85
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.18 E-value=0.0048 Score=68.68 Aligned_cols=95 Identities=14% Similarity=0.129 Sum_probs=62.6
Q ss_pred cccccccCCCchhhhhhhccc-CceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEE
Q 003942 126 SVDNQQISVKEETKEVLFSTE-EAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKI 204 (784)
Q Consensus 126 ~~vg~iIGk~Ge~Ik~iq~~s-~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI 204 (784)
+-+|..||++|.+|+.|..+- +.+|+|-.-.... ..+|...|.-.....-.. ........+
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~-----------------~~fI~Nal~Pa~V~~V~i-~~~~~~~~V 312 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVP-----------------EIFIARALAPAIISSVKI-EEEEKKAIV 312 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCH-----------------HHHHHHhCCCceeeEEEE-cCCCcEEEE
Confidence 345699999999999997443 5555554433321 112222221111100000 122357899
Q ss_pred EecCCccceeeccCcchHhhHHhhcCCEEEEccC
Q 003942 205 EVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (784)
Q Consensus 205 ~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~ 238 (784)
.|+....++.|||+|.|||...+-||.+|.|..-
T Consensus 313 ~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~ 346 (374)
T PRK12328 313 TLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI 346 (374)
T ss_pred EEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence 9999999999999999999999999999999864
No 86
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=96.17 E-value=0.0089 Score=68.41 Aligned_cols=66 Identities=24% Similarity=0.310 Sum_probs=56.4
Q ss_pred ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhccc
Q 003942 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQTV 371 (784)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~~~ 371 (784)
.....|.|+.+++..+||.+|.++|+|..+||+.-.++ +.+|+|.-. ...+++|+++|..++....
T Consensus 596 P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD-----------e~t~~i~A~~~~am~~Ak~~I~~i~~~~~ 662 (760)
T KOG1067|consen 596 PVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD-----------EGTFSIFAPTQAAMEEAKEFIDGIIKDDQ 662 (760)
T ss_pred ceeeEEeecchhhheeecCccceeeeEeeeccceeeec-----------CceEEEEecCHHHHHHHHHHHHHHhcCcc
Confidence 45678899999999999999999999999999777663 556887776 7899999999999886543
No 87
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=95.97 E-value=0.0065 Score=67.46 Aligned_cols=95 Identities=17% Similarity=0.238 Sum_probs=61.9
Q ss_pred ccccccCCCchhhhhhhccc-CceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEE
Q 003942 127 VDNQQISVKEETKEVLFSTE-EAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIE 205 (784)
Q Consensus 127 ~vg~iIGk~Ge~Ik~iq~~s-~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~ 205 (784)
-+|..||++|.+|+.|..+- +.+|+|-.-.... ..+|...|.-.....-...........+.
T Consensus 244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~-----------------~~fi~nal~Pa~v~~v~i~~~~~~~~~v~ 306 (341)
T TIGR01953 244 PVGACVGPKGSRIQAISKELNGEKIDIIEYSDDP-----------------AEFIANALSPAKVISVEVLDEDKHSAEVV 306 (341)
T ss_pred cceeeECCCCchHHHHHHHhCCCeEEEEEcCCCH-----------------HHHHHHhcCCceEEEEEEEcCCCcEEEEE
Confidence 46699999999999997443 5555554433221 11122212111100000001123578999
Q ss_pred ecCCccceeeccCcchHhhHHhhcCCEEEEccC
Q 003942 206 VPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (784)
Q Consensus 206 VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~ 238 (784)
|+.+..++.|||+|.|||...+-||.+|.|...
T Consensus 307 V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~ 339 (341)
T TIGR01953 307 VPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE 339 (341)
T ss_pred EChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence 999999999999999999999999999999753
No 88
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.84 E-value=0.0061 Score=69.00 Aligned_cols=94 Identities=18% Similarity=0.232 Sum_probs=61.4
Q ss_pred ccccccCCCchhhhhhhccc-CceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEE
Q 003942 127 VDNQQISVKEETKEVLFSTE-EAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIE 205 (784)
Q Consensus 127 ~vg~iIGk~Ge~Ik~iq~~s-~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~ 205 (784)
-+|..||++|.+|+.|..+. +.+|+|-.-.... ..+|...|.-.....-...........|.
T Consensus 278 PvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp-----------------~~fI~NaLsPA~V~~V~i~~~~~k~a~V~ 340 (449)
T PRK12329 278 PVGACIGARGSRIQAVVNELRGEKIDVIRWSPDP-----------------ATYIANALSPARVDEVRLVDPEGRHAHVL 340 (449)
T ss_pred hhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCH-----------------HHHHHHhcCCceeeEEEEEcCCCcEEEEE
Confidence 45699999999999997443 5555554433221 11222222111110000001223467899
Q ss_pred ecCCccceeeccCcchHhhHHhhcCCEEEEcc
Q 003942 206 VPNNKVGVLIGKAGDTIRYLQYNSGAKIQITR 237 (784)
Q Consensus 206 VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~ 237 (784)
|+.+..++.|||+|.|||...+-||.+|.|..
T Consensus 341 V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 341 VPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred EChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 99999999999999999999999999999974
No 89
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.71 E-value=0.0086 Score=66.95 Aligned_cols=95 Identities=18% Similarity=0.259 Sum_probs=62.6
Q ss_pred ccccccCCCchhhhhhhccc-CceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEE
Q 003942 127 VDNQQISVKEETKEVLFSTE-EAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIE 205 (784)
Q Consensus 127 ~vg~iIGk~Ge~Ik~iq~~s-~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~ 205 (784)
-+|..||++|.+|+.|..+. +.+|+|-.-.... ..+|...|.-.....-...........+.
T Consensus 246 pvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~-----------------~~fi~nal~Pa~v~~v~i~~~~~~~~~v~ 308 (362)
T PRK12327 246 AKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDP-----------------AEFVANALSPAKVVSVEVDDEEEKAARVV 308 (362)
T ss_pred chheeECCCChhHHHHHHHhCCCeEEEEEcCCCH-----------------HHHHHHhCCCceEEEEEEEcCCCcEEEEE
Confidence 46799999999999997444 5555554433221 11222222111110000001223578999
Q ss_pred ecCCccceeeccCcchHhhHHhhcCCEEEEccC
Q 003942 206 VPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (784)
Q Consensus 206 VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~ 238 (784)
|+.+..++.|||+|.|||...+-||.+|.|...
T Consensus 309 V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 309 VPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred EChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 999999999999999999999999999999854
No 90
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=95.71 E-value=0.011 Score=64.92 Aligned_cols=215 Identities=12% Similarity=0.051 Sum_probs=127.1
Q ss_pred ccCCCchhhhhhhcccCceeeeccccc-------cccc--ceeeec-CchhchhhhhhhhhHhhhcCCCC----------
Q 003942 131 QISVKEETKEVLFSTEEAFIDVKEETK-------EVTV--KEEETV-KEEESVEPSNVVPQQVVDNSKSD---------- 190 (784)
Q Consensus 131 iIGk~Ge~Ik~iq~~s~a~I~I~~~~~-------~~s~--r~~~i~-G~~e~Ve~A~~lI~~ii~~~~~~---------- 190 (784)
-.-..|.+...|...+++.+.+..... .+.+ ..++|. -+.|-+.+|...|.-++..+...
T Consensus 108 ~~~TRg~~~d~Ie~~~G~~~~~RGs~~~~El~~vg~~~~pLv~hI~~~T~Ei~~~Ai~RIkgv~~~~~~~~n~~~V~i~~ 187 (531)
T KOG1960|consen 108 ATSTRGTSYDHIEGITGTTSASRGSAPAPELPPVGSSEGPLVDHIPPSTAEITSKAIERIKGVFMQDVEINNVRNVYILV 187 (531)
T ss_pred ceeccchhHHhhhhhccceeeccCCCCCccCCCCCCCCCcceeecCCccHHHHHHHHhhCccceeecccccccceEEEee
Confidence 334567888888888888877665532 2233 334444 35677778888887544311100
Q ss_pred --------------CCCCCCCCCeEEEEEecCC-----ccceeeccCcchHhhHHhhcCCEEEEccCCC--CCCCC----
Q 003942 191 --------------DPSSTDDSTMSRKIEVPNN-----KVGVLIGKAGDTIRYLQYNSGAKIQITRDAD--ADPHA---- 245 (784)
Q Consensus 191 --------------~~~~~~~~~~t~rI~VP~~-----~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~--~~p~s---- 245 (784)
..+. ......-+++|+.+ +-+++=+++-.+|..|+.++++++.++.+.. ..+++
T Consensus 188 ~~sP~~~i~~~V~~~~f~-~G~~Y~~k~~v~~~~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~Es 266 (531)
T KOG1960|consen 188 RASPLSEIENKVGVQLFS-KGRYYPNKALATDKDPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNEGNES 266 (531)
T ss_pred cCCchhhhcccccccccc-ccccchhheecccCCcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccCccccccc
Confidence 0000 00111112333322 3344556677788999999999987754321 11111
Q ss_pred --CCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHH
Q 003942 246 --ATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQT 323 (784)
Q Consensus 246 --~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~ 323 (784)
...++.+-++.+.+.+|+++|.+|++.....- .|+|.. =.|+|.-|..+|+|+.
T Consensus 267 nEPMYI~i~h~~~~g~~~A~r~~~nl~~~v~~~~-----sr~~~~-------------------~~~~~p~~~y~~~~~~ 322 (531)
T KOG1960|consen 267 NEPMYIFSTHGNGNGENGAPRRKWNLEEKVYINL-----SRGFHR-------------------QAIVGPQGAYVKHIQQ 322 (531)
T ss_pred CCceeEEeecCCchhhccchhHHHhHHHHHHHHh-----hhhhhh-------------------cccccCCcccccccCC
Confidence 22244444599999999999998877643211 111111 1356777889999999
Q ss_pred HhCCeEEeccCCCCCCC-------CCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Q 003942 324 RSGARIQLIPQHLPEGD-------GSKERIVRVTGDMRQIEIAQEMIKEVLSQT 370 (784)
Q Consensus 324 ~SGarIqI~~~~~p~~~-------~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~ 370 (784)
.+-.++.|+....-..+ +.--.++.|.-.+.+|+.|+-||.++|..+
T Consensus 323 ~~~~~~~~~g~~s~~i~p~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~~v 376 (531)
T KOG1960|consen 323 ETRTRVQIKGQGSAFIEPSTNRESDEPIHLCIMSHDPNAIQRAKVLCEDLIASV 376 (531)
T ss_pred CCCcceeccCccceeecCCCCCCCCCCcccccccCChhhhhhhhhcccccCCcc
Confidence 99999998754311111 122345778888999999999998888654
No 91
>PRK12705 hypothetical protein; Provisional
Probab=95.69 E-value=0.014 Score=67.75 Aligned_cols=89 Identities=18% Similarity=0.276 Sum_probs=56.7
Q ss_pred hchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCC-ccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCc
Q 003942 171 ESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNN-KVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRP 249 (784)
Q Consensus 171 e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~-~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~ 249 (784)
++-.+|+.+|..-+.....+. ....++..|.+|++ .-|+||||.|.|||.|+..||+.|.|++.. +.
T Consensus 173 ~a~~~A~~ii~~aiqr~a~~~----~~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp--------~~ 240 (508)
T PRK12705 173 EAERKAQNILAQAMQRIASET----ASDLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP--------EA 240 (508)
T ss_pred HHHHHHHHHHHHHHHHhccch----hhhheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc--------cc
Confidence 344456666666664333221 22345667778875 789999999999999999999999998542 34
Q ss_pred EEEec-chhhHHHHHHHHHHHHH
Q 003942 250 VEIIG-TLSNIDKAEKLINAVIA 271 (784)
Q Consensus 250 V~I~G-~~e~V~kA~~~I~elI~ 271 (784)
|.|++ ++..-+.|+..+..+|.
T Consensus 241 V~ls~fdp~rreia~~~l~~Li~ 263 (508)
T PRK12705 241 VVISSFNPIRREIARLTLEKLLA 263 (508)
T ss_pred hhhcccCccchHHHHHHHHHHHh
Confidence 55555 33333344444444433
No 92
>PRK00468 hypothetical protein; Provisional
Probab=95.64 E-value=0.0077 Score=52.38 Aligned_cols=33 Identities=18% Similarity=0.395 Sum_probs=29.3
Q ss_pred CCCCeEEEEEecCCccceeeccCcchHhhHHhh
Q 003942 196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYN 228 (784)
Q Consensus 196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~ 228 (784)
.+..+.++|.|..+.+|+||||+|.+|+.||.-
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence 345588999999999999999999999999874
No 93
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=95.61 E-value=0.023 Score=64.72 Aligned_cols=96 Identities=25% Similarity=0.442 Sum_probs=71.6
Q ss_pred ceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccchhhc
Q 003942 212 GVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQA 291 (784)
Q Consensus 212 G~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~ 291 (784)
-.+|-+.|+.||+|-++...+|.|..+... ...-++|++.|+++|-++-. ...+. |
T Consensus 41 P~~~~~~~dlik~lAk~lrKRI~iR~dPsv--------------l~~~e~A~~~I~eivP~ea~--i~~i~---F----- 96 (637)
T COG1782 41 PELFAKDGDLIKDLAKDLRKRIIIRPDPSV--------------LKPPEEARKIILEIVPEEAG--ITDIY---F----- 96 (637)
T ss_pred HHHhccchhHHHHHHHHHhhceEeccCchh--------------cCCHHHHHHHHHHhCccccC--ceeEE---e-----
Confidence 446778899999999999999999865211 13356899999999966421 11111 1
Q ss_pred cCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 003942 292 SGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIP 333 (784)
Q Consensus 292 ~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~ 333 (784)
...+-++.|-.++=|+||||+|+++++|..+||-+-+|.+
T Consensus 97 --d~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR 136 (637)
T COG1782 97 --DDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVR 136 (637)
T ss_pred --cCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeee
Confidence 2245678888999999999999999999999998877765
No 94
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.56 E-value=0.011 Score=51.52 Aligned_cols=33 Identities=27% Similarity=0.487 Sum_probs=29.6
Q ss_pred CCCCeEEEEEecCCccceeeccCcchHhhHHhh
Q 003942 196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYN 228 (784)
Q Consensus 196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~ 228 (784)
.+..+.++|.|....+|+||||+|.+|+.||.-
T Consensus 26 ~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred cCCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 356678999999999999999999999999974
No 95
>PRK02821 hypothetical protein; Provisional
Probab=95.45 E-value=0.0089 Score=52.23 Aligned_cols=35 Identities=20% Similarity=0.342 Sum_probs=30.1
Q ss_pred CCCCeEEEEEecCCccceeeccCcchHhhHHhhcC
Q 003942 196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSG 230 (784)
Q Consensus 196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TG 230 (784)
....+.++|.|..+.+|+||||+|.+|+.||.-..
T Consensus 27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 34457899999999999999999999999997544
No 96
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=95.32 E-value=0.028 Score=64.45 Aligned_cols=69 Identities=22% Similarity=0.385 Sum_probs=59.5
Q ss_pred CCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHHHHHhh
Q 003942 195 TDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINAVIAEA 273 (784)
Q Consensus 195 ~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e~ 273 (784)
.....+.+.+.|+.+++..+||.+|.++|+|..+||+.-.|+ +..|+|.. +...+++|+++|..++...
T Consensus 592 ~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD----------e~t~~i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 592 KEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD----------EGTFSIFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred cccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec----------CceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence 345678899999999999999999999999999999666665 35788887 8889999999999999875
No 97
>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=95.20 E-value=0.052 Score=52.82 Aligned_cols=94 Identities=26% Similarity=0.479 Sum_probs=67.8
Q ss_pred eeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccchhhccC
Q 003942 214 LIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASG 293 (784)
Q Consensus 214 IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~ 293 (784)
++=.+++.||+|-++..-+|.|..|.+ + ...=+.|.++|.++|-++- +...+. |
T Consensus 20 ~~~~~~dli~~lAk~lrKRIvvR~dps-----------~---l~~~e~A~~~I~~ivP~ea--~i~di~---F------- 73 (145)
T cd02410 20 LFAEDGDLVKDLAKDLRKRIVIRPDPS-----------V---LKPPEEAIKIILEIVPEEA--GITDIY---F------- 73 (145)
T ss_pred HHhcccHHHHHHHHHHhceEEEcCChh-----------h---cCCHHHHHHHHHHhCCCcc--CceeeE---e-------
Confidence 344568899999999988898875421 0 0123569999999886541 111111 1
Q ss_pred CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 003942 294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIP 333 (784)
Q Consensus 294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~ 333 (784)
...+-++.|-.++-|+||||+|.++++|..+||-+-.|.+
T Consensus 74 d~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvR 113 (145)
T cd02410 74 DDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVR 113 (145)
T ss_pred cCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence 2245578888899999999999999999999999988864
No 98
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=95.16 E-value=0.032 Score=63.35 Aligned_cols=192 Identities=12% Similarity=0.033 Sum_probs=122.3
Q ss_pred ccccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEe
Q 003942 127 VDNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEV 206 (784)
Q Consensus 127 ~vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~V 206 (784)
..+-|-||+--.+.+|....++.+.+.-....++.-.-.+.|..-++.++.+++...+ ...+.|.|
T Consensus 390 ~EdFl~gkkngK~TrIm~~v~c~~~~~i~~~~gs~~~~~~~g~~~~F~k~~~~~~~EF--------------pae~~f~i 455 (657)
T COG5166 390 NEDFLRGKKNGKATRIMKGVSCSELSSIVSSTGSIVETNGIGEKMSFSKKLSIPPTEF--------------PAEIAFII 455 (657)
T ss_pred hHHHhccccCcchhhhhhhcccceeeEEEecCCcEEEEeccCcchhhHHHhcCCcccC--------------chheEEEe
Confidence 4446666666567888777888866665555555333444566666666655554433 23678999
Q ss_pred cCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCC-cEEEecc---hhhHHHHHHHHHHHHHhhhcCCCCcc-
Q 003942 207 PNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATR-PVEIIGT---LSNIDKAEKLINAVIAEADAGGSPSL- 281 (784)
Q Consensus 207 P~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR-~V~I~G~---~e~V~kA~~~I~elI~e~~~~g~p~~- 281 (784)
+...+-.|||-+|..|.++..+.++.|.+...-+ .+.+.-+ -|.|... .++|.-++.-++++|.+.....+..+
T Consensus 456 ~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~-~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~~Kgdi 534 (657)
T COG5166 456 MESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYK-FGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQQCRFNLKGDI 534 (657)
T ss_pred ecccceeeeccCchhhHHhhhhhhhhhhhhhhhh-cchhhhhcceEEECCccCccchhcccccHHHHHhhhcccccccce
Confidence 9999999999999999999999999998875321 2222222 3677764 44666677778888887653211111
Q ss_pred -cccc---------cch--hhc-------cCCccEEEEEecCCceeeeec---CCchHHHHHHHHhCCeEEecc
Q 003942 282 -VARG---------LAT--AQA-------SGAAEQVEIKVPNEKVGLIIG---RGGETIKGLQTRSGARIQLIP 333 (784)
Q Consensus 282 -~~~g---------~~~--~~~-------~~~~~~~~i~VP~~~vG~VIG---kgG~~IK~Iq~~SGarIqI~~ 333 (784)
...+ ... .+. .+-.....+.++.+.++..|| -+|++|..+.....-.|....
T Consensus 535 rf~~~~~sI~~v~~~~~~I~rv~kne~v~~~~p~~~~~y~~se~h~~g~gena~R~~ni~~~t~~y~~~ie~~~ 608 (657)
T COG5166 535 RFCPQSTSIFTVDIYSDEIERVIKNETVLLEFPAEMHFYVPSEIHKKGIGENAFRGENIQRVTKLYNSYIEFST 608 (657)
T ss_pred EEcCCceEEEEEcccccHHHHHhhccceEEecccccccccchhhhhccCCcccccccchhhhhhhhhccceeec
Confidence 0000 000 000 111233455677788899999 788998888887777777653
No 99
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.15 E-value=0.015 Score=67.14 Aligned_cols=94 Identities=16% Similarity=0.232 Sum_probs=61.7
Q ss_pred ccccccCCCchhhhhhhccc-CceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEE
Q 003942 127 VDNQQISVKEETKEVLFSTE-EAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIE 205 (784)
Q Consensus 127 ~vg~iIGk~Ge~Ik~iq~~s-~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~ 205 (784)
-+|..||++|.+|+.|..+- +.+|.|-.-+... ..+|...|.-.....-.. +.......|.
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~-----------------~~fi~nal~pa~v~~v~~-~~~~~~~~v~ 307 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIILWSDDP-----------------AQFIINALSPAEVSSVVV-DEDEHSADVV 307 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEEcCCCH-----------------HHHHHHhCCCCEEEEEEE-eCCCCEEEEE
Confidence 45699999999999997443 5556554433321 111222121111000000 1112488999
Q ss_pred ecCCccceeeccCcchHhhHHhhcCCEEEEccC
Q 003942 206 VPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (784)
Q Consensus 206 VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~ 238 (784)
|+....++.|||+|.|||..++-||.+|.|...
T Consensus 308 V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 308 VPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred ECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 999999999999999999999999999999864
No 100
>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=95.14 E-value=0.035 Score=53.95 Aligned_cols=95 Identities=16% Similarity=0.197 Sum_probs=64.6
Q ss_pred cccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcC-CCCCCCCCCCCCeEEEEEecC
Q 003942 130 QQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNS-KSDDPSSTDDSTMSRKIEVPN 208 (784)
Q Consensus 130 ~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~-~~~~~~~~~~~~~t~rI~VP~ 208 (784)
..+-.+++.|++|-.+-.-+|.|..+... ...-+.|+++|.+++-.+ .++.-.. ...+-+|.|-.
T Consensus 19 ~~~~~~~dli~~lAk~lrKRIvvR~dps~-----------l~~~e~A~~~I~~ivP~ea~i~di~F---d~~tGEV~Iea 84 (145)
T cd02410 19 ELFAEDGDLVKDLAKDLRKRIVIRPDPSV-----------LKPPEEAIKIILEIVPEEAGITDIYF---DDDTGEVIIEA 84 (145)
T ss_pred HHHhcccHHHHHHHHHHhceEEEcCChhh-----------cCCHHHHHHHHHHhCCCccCceeeEe---cCCCcEEEEEE
Confidence 55566788888886555545554433321 112367899999988432 2211111 12356788888
Q ss_pred CccceeeccCcchHhhHHhhcCCEEEEccC
Q 003942 209 NKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (784)
Q Consensus 209 ~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~ 238 (784)
.+-|+||||+|.++++|..+||-+-.|.+.
T Consensus 85 eKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 85 EKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred cCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 899999999999999999999998888753
No 101
>PRK01064 hypothetical protein; Provisional
Probab=94.83 E-value=0.021 Score=50.03 Aligned_cols=33 Identities=27% Similarity=0.472 Sum_probs=29.5
Q ss_pred CCCCeEEEEEecCCccceeeccCcchHhhHHhh
Q 003942 196 DDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYN 228 (784)
Q Consensus 196 ~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~ 228 (784)
....+.++|.|..+.+|+||||+|.||+.||.-
T Consensus 26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred CCCEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence 356688999999999999999999999999874
No 102
>PRK00468 hypothetical protein; Provisional
Probab=94.56 E-value=0.034 Score=48.43 Aligned_cols=32 Identities=31% Similarity=0.522 Sum_probs=28.1
Q ss_pred CccEEEEEecCCceeeeecCCchHHHHHHHHh
Q 003942 294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRS 325 (784)
Q Consensus 294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~S 325 (784)
....++|.|..+-+|+||||+|.+|+.||..-
T Consensus 28 ~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 28 QSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 44678889999999999999999999999754
No 103
>PRK02821 hypothetical protein; Provisional
Probab=94.42 E-value=0.036 Score=48.48 Aligned_cols=33 Identities=33% Similarity=0.629 Sum_probs=28.8
Q ss_pred CccEEEEEecCCceeeeecCCchHHHHHHHHhC
Q 003942 294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSG 326 (784)
Q Consensus 294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SG 326 (784)
....++|.|..+-+|+||||+|.+|+.||..-.
T Consensus 29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 446789999999999999999999999997643
No 104
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=94.34 E-value=0.055 Score=61.77 Aligned_cols=97 Identities=16% Similarity=0.203 Sum_probs=71.1
Q ss_pred cccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcCC-CCCCCCCCCCCeEEEEEe
Q 003942 128 DNQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNSK-SDDPSSTDDSTMSRKIEV 206 (784)
Q Consensus 128 vg~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~-~~~~~~~~~~~~t~rI~V 206 (784)
...+|-++|+.|++|-.+-..+|.|..+-.. ...-+.|+++|.+++-.+. +..-. -...+.+|+|
T Consensus 40 ~P~~~~~~~dlik~lAk~lrKRI~iR~dPsv-----------l~~~e~A~~~I~eivP~ea~i~~i~---Fd~~tGEViI 105 (637)
T COG1782 40 NPELFAKDGDLIKDLAKDLRKRIIIRPDPSV-----------LKPPEEARKIILEIVPEEAGITDIY---FDDDTGEVII 105 (637)
T ss_pred CHHHhccchhHHHHHHHHHhhceEeccCchh-----------cCCHHHHHHHHHHhCccccCceeEE---ecCCCceEEE
Confidence 3477888899999998777777777655432 2356788999999884322 21111 1224567888
Q ss_pred cCCccceeeccCcchHhhHHhhcCCEEEEccC
Q 003942 207 PNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (784)
Q Consensus 207 P~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~ 238 (784)
-..+-|+||||+|+++++|..+||-.-.|.+.
T Consensus 106 ea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 106 EAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred EecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 88999999999999999999999987777753
No 105
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=94.02 E-value=0.016 Score=70.65 Aligned_cols=72 Identities=24% Similarity=0.237 Sum_probs=61.7
Q ss_pred ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 369 (784)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~ 369 (784)
..+-++.||.+.+.+|||++|.+|+.|+.-||+.|.|.+-+ .+...||.+.+.|.++.+..|..+|.-+|.+
T Consensus 1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq---~~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ---PDNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcC---CccchhhhcccCCCChhhhhhhccccceeec
Confidence 44567789999999999999999999999999999997633 2346799999999999999999999876654
No 106
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=93.91 E-value=0.058 Score=46.97 Aligned_cols=33 Identities=30% Similarity=0.567 Sum_probs=28.7
Q ss_pred CCccEEEEEecCCceeeeecCCchHHHHHHHHh
Q 003942 293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRS 325 (784)
Q Consensus 293 ~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~S 325 (784)
+....++|.|...-+|+||||+|.+|+.||..-
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 345678899999999999999999999999753
No 107
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=93.73 E-value=0.019 Score=69.98 Aligned_cols=74 Identities=20% Similarity=0.225 Sum_probs=63.9
Q ss_pred CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhh
Q 003942 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD 274 (784)
Q Consensus 199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~ 274 (784)
....++.||-....+|||++|.||+.||.-|||.|.|.+- ...+-.+|.+.+.|..+.+..|..+|..+|.+-+
T Consensus 1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekm--q~~Nqaers~~~kg~p~~~r~a~~~I~~~i~Dpd 1412 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKM--QPDNQAERSKAPKGRPPSQRVATSPIGLPIIDPD 1412 (2131)
T ss_pred ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhc--CCccchhhhcccCCCChhhhhhhccccceeecCC
Confidence 4566889999999999999999999999999999999862 1224568999999999999999999998887754
No 108
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=93.70 E-value=0.48 Score=48.96 Aligned_cols=66 Identities=24% Similarity=0.447 Sum_probs=57.3
Q ss_pred cEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Q 003942 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQT 370 (784)
Q Consensus 296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~ 370 (784)
..+.+.+.....-+|...+|..++.|....||+|.+.. .+..|.|+|+...|+.+...|.++|...
T Consensus 26 g~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~---------~~~~i~I~g~k~~~~~i~~~i~~~l~~i 91 (210)
T PF14611_consen 26 GDLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR---------SENRIRITGTKSTAEYIEASINEILSNI 91 (210)
T ss_pred ceeEEEecchheeeeecCCchHHHHHHHhcCceEEEec---------CCcEEEEEccHHHHHHHHHHHHHHHhhc
Confidence 45566667888999999999999999888899999975 3678999999999999999999998753
No 109
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=93.45 E-value=0.021 Score=49.07 Aligned_cols=34 Identities=29% Similarity=0.470 Sum_probs=29.1
Q ss_pred CCCeEEEEEecCCccceeeccCcchHhhHHhhcC
Q 003942 197 DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSG 230 (784)
Q Consensus 197 ~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TG 230 (784)
.....+.|.|..+..|+||||+|.||+.||.-..
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence 4456888999999999999999999999987544
No 110
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=93.41 E-value=0.14 Score=53.65 Aligned_cols=59 Identities=22% Similarity=0.389 Sum_probs=47.2
Q ss_pred EEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhh-HHHHHHHHHHH
Q 003942 202 RKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSN-IDKAEKLINAV 269 (784)
Q Consensus 202 ~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~-V~kA~~~I~el 269 (784)
.-|.|+..+|-++|||+|++|+.|+++|+|+|.|-.+ -.|.|.+..+. ...|.+.|..+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N---------G~IWV~~~~~~~e~~~~~aI~~i 207 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN---------GRIWVDGENESLEELAIEAIRKI 207 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC---------CEEEecCCCcchHHHHHHHHHHH
Confidence 4688999999999999999999999999999999753 47888886663 44455555443
No 111
>PRK01064 hypothetical protein; Provisional
Probab=93.39 E-value=0.09 Score=46.14 Aligned_cols=33 Identities=33% Similarity=0.484 Sum_probs=28.5
Q ss_pred CCccEEEEEecCCceeeeecCCchHHHHHHHHh
Q 003942 293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRS 325 (784)
Q Consensus 293 ~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~S 325 (784)
.....++|.|..+-+|+||||+|++|+.||...
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 345678889999999999999999999999753
No 112
>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=92.53 E-value=0.2 Score=60.31 Aligned_cols=96 Identities=24% Similarity=0.412 Sum_probs=70.3
Q ss_pred eeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccchhhcc
Q 003942 213 VLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQAS 292 (784)
Q Consensus 213 ~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~ 292 (784)
.++=..++.||+|-++..-+|.|..+.. + ...=++|+++|.++|-++- +...+. |
T Consensus 36 ~~~~~~~~~~~~~~~~~~~r~~~~~~~~-----------~---~~~~~~~~~~i~~~~~~~~--~~~~~~---f------ 90 (630)
T TIGR03675 36 ELFAKDDDLVKELAKKLRKRIVIRPDPS-----------V---LLPPEEAIEKIKEIVPEEA--GITDIY---F------ 90 (630)
T ss_pred HHhccchHHHHHHHHHhhceEEEecChh-----------h---cCCHHHHHHHHHHhCCCcC--CceeEE---e------
Confidence 4556778999999999999999975421 1 1223568999999887641 111111 1
Q ss_pred CCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccC
Q 003942 293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQ 334 (784)
Q Consensus 293 ~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~ 334 (784)
...+-++.|-.++-|+||||+|.++++|..+||-+.+|.+.
T Consensus 91 -~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 91 -DDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred -cCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 23456788889999999999999999999999999888653
No 113
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=92.20 E-value=0.54 Score=47.08 Aligned_cols=103 Identities=17% Similarity=0.226 Sum_probs=61.7
Q ss_pred eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCC
Q 003942 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSP 279 (784)
Q Consensus 200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p 279 (784)
-.+-|+|-... |..|||+|.+||+|++..|-+|.|...++ + ..++|.+++. |
T Consensus 61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~s~------d--------------~~~fl~Nl~~-------P 112 (166)
T PRK06418 61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEKTN------D--------------IKKLAVQLLS-------P 112 (166)
T ss_pred CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEcCC------C--------------HHHHHHhcCC-------C
Confidence 45677787777 99999999999999999999999986532 1 2233333332 1
Q ss_pred cccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEe
Q 003942 280 SLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQL 331 (784)
Q Consensus 280 ~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI 331 (784)
..+.. ........+...+.+.|..+....|-.|--..-+-+++.||..+.|
T Consensus 113 A~V~g-V~i~~~~dG~~~~kV~Vd~~Dk~~l~~k~e~~~~v~~kltgk~v~~ 163 (166)
T PRK06418 113 ARVLG-VNTVWLPDGTVQYVIRVSRRDRRRLPAKPELLESILSKITGTEVKI 163 (166)
T ss_pred cEEEE-EEEEEeCCCcEEEEEEECHHHhhcccccHHHHHHHHHHHHCCcEEE
Confidence 11100 0000001223344477777666665555544444557778877766
No 114
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=92.06 E-value=0.22 Score=52.89 Aligned_cols=51 Identities=18% Similarity=0.384 Sum_probs=46.8
Q ss_pred eeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942 308 GLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 369 (784)
Q Consensus 308 G~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~ 369 (784)
-+|||.+|.|+|.|+-.|.|-|-|. ..+|.+.|....++.++.+|.++|.+
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVq-----------G~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQ-----------GNTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEee-----------CcEEEeecCcchHHHHHHHHHHHHhc
Confidence 5799999999999999999999984 45799999999999999999999976
No 115
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=91.83 E-value=0.2 Score=53.20 Aligned_cols=93 Identities=15% Similarity=0.235 Sum_probs=63.1
Q ss_pred eecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCC
Q 003942 165 ETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPH 244 (784)
Q Consensus 165 ~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~ 244 (784)
.+.+...-++.|.+++.+.+.++-+........ ..+| -.+--+|||.+|.|+|.|+--|.|-|-|..
T Consensus 120 KLlaRsVp~eqAvkiLqDev~CdiIkIgn~V~n---kerF---vKRRqRLiGpng~TLKAlelLT~CYilVqG------- 186 (356)
T KOG2874|consen 120 KLLARSVPFEQAVKILQDEVACDIIKIGNLVRN---KERF---VKRRQRLIGPNGSTLKALELLTNCYILVQG------- 186 (356)
T ss_pred HHHHcCCCHHHHHHHHhhccceeeeehhhhhcc---HHHH---HHHHHHhcCCCchhHHHHHHHhhcEEEeeC-------
Confidence 344555666777777766664443322221000 0000 012357999999999999999999999985
Q ss_pred CCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942 245 AATRPVEIIGTLSNIDKAEKLINAVIAEA 273 (784)
Q Consensus 245 s~eR~V~I~G~~e~V~kA~~~I~elI~e~ 273 (784)
..|.+.|....|..++++|.+.|...
T Consensus 187 ---~TVsaiGpfkGlkevr~IV~DcM~Ni 212 (356)
T KOG2874|consen 187 ---NTVSAIGPFKGLKEVRKIVEDCMKNI 212 (356)
T ss_pred ---cEEEeecCcchHHHHHHHHHHHHhcc
Confidence 37899999999999999888887764
No 116
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=91.81 E-value=0.37 Score=55.15 Aligned_cols=127 Identities=13% Similarity=0.066 Sum_probs=81.4
Q ss_pred ccceeeccCcchHhhHHhhcCCEEEE--ccCCCCCCCCCCCcE-EEecchhhHHHHHHHHHHHHHhhhcCCCCccccccc
Q 003942 210 KVGVLIGKAGDTIRYLQYNSGAKIQI--TRDADADPHAATRPV-EIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGL 286 (784)
Q Consensus 210 ~vG~IIGkgG~tIK~Iq~~TGakI~V--~~~~~~~p~s~eR~V-~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~ 286 (784)
.--.|-||+--.+.+|++...|.+.+ .... + .++. .+.|..-...++++++..-+
T Consensus 390 ~EdFl~gkkngK~TrIm~~v~c~~~~~i~~~~----g--s~~~~~~~g~~~~F~k~~~~~~~EF---------------- 447 (657)
T COG5166 390 NEDFLRGKKNGKATRIMKGVSCSELSSIVSST----G--SIVETNGIGEKMSFSKKLSIPPTEF---------------- 447 (657)
T ss_pred hHHHhccccCcchhhhhhhcccceeeEEEecC----C--cEEEEeccCcchhhHHHhcCCcccC----------------
Confidence 34477888877799999999988544 3321 1 2333 33455555555555543321
Q ss_pred chhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceE-EEEEcCH---HHHHHHHHH
Q 003942 287 ATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERI-VRVTGDM---RQIEIAQEM 362 (784)
Q Consensus 287 ~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~-V~I~Gt~---~qV~~Ak~l 362 (784)
..++.|.|+...+..|||-||..|.+++.+.++.|++...- ....+..+- |.|.-+. +.+..+|.=
T Consensus 448 --------pae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~--~~~qs~~~dNV~I~~PrKn~~ni~~~KNd 517 (657)
T COG5166 448 --------PAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFY--KFGQSQWHDNVLIEAPRKNQDNISGKKND 517 (657)
T ss_pred --------chheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhh--hcchhhhhcceEEECCccCccchhccccc
Confidence 23567999999999999999999999999999999987532 111222222 5565542 345555555
Q ss_pred HHHHHh
Q 003942 363 IKEVLS 368 (784)
Q Consensus 363 I~~~L~ 368 (784)
+++++.
T Consensus 518 ~~~~V~ 523 (657)
T COG5166 518 KLDKVK 523 (657)
T ss_pred HHHHHh
Confidence 555554
No 117
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=91.58 E-value=0.15 Score=44.40 Aligned_cols=32 Identities=31% Similarity=0.612 Sum_probs=26.1
Q ss_pred eEEEEEecCCccceeeccCcchHhhHHhhcCC
Q 003942 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGA 231 (784)
Q Consensus 200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGa 231 (784)
..+.|.|.....|+||||+|+||+.|+.-+..
T Consensus 24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~ 55 (77)
T cd02414 24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANL 55 (77)
T ss_pred CEEEEEEecCCCCeEECCCCccHHHHHHHHHH
Confidence 35667777889999999999999999875543
No 118
>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=91.52 E-value=0.21 Score=60.16 Aligned_cols=96 Identities=16% Similarity=0.199 Sum_probs=67.7
Q ss_pred ccccCCCchhhhhhhcccCceeeecccccccccceeeecCchhchhhhhhhhhHhhhcC-CCCCCCCCCCCCeEEEEEec
Q 003942 129 NQQISVKEETKEVLFSTEEAFIDVKEETKEVTVKEEETVKEEESVEPSNVVPQQVVDNS-KSDDPSSTDDSTMSRKIEVP 207 (784)
Q Consensus 129 g~iIGk~Ge~Ik~iq~~s~a~I~I~~~~~~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~-~~~~~~~~~~~~~t~rI~VP 207 (784)
.+++-++++.|++|-.+-.-+|.|+.+... ...-+.|+++|.+++-.+ .++.-. -...+-+|+|-
T Consensus 35 ~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~-----------~~~~~~~~~~i~~~~~~~~~~~~~~---f~~~~~~v~i~ 100 (630)
T TIGR03675 35 PELFAKDDDLVKELAKKLRKRIVIRPDPSV-----------LLPPEEAIEKIKEIVPEEAGITDIY---FDDVTGEVIIE 100 (630)
T ss_pred HHHhccchHHHHHHHHHhhceEEEecChhh-----------cCCHHHHHHHHHHhCCCcCCceeEE---ecCCCceEEEE
Confidence 366777889999997666555555544321 123367889999988533 221111 12345688888
Q ss_pred CCccceeeccCcchHhhHHhhcCCEEEEccC
Q 003942 208 NNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (784)
Q Consensus 208 ~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~ 238 (784)
..+-|+||||+|.++++|.++||-+..|.+.
T Consensus 101 ~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 101 AEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred EcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 8999999999999999999999998888764
No 119
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=90.51 E-value=0.53 Score=49.52 Aligned_cols=48 Identities=25% Similarity=0.430 Sum_probs=40.2
Q ss_pred EEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHH
Q 003942 297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMR 354 (784)
Q Consensus 297 ~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~ 354 (784)
-.-+.|+..+|-+||||+|.+|+.|.++|+|+|.|-. ...|-|.+..+
T Consensus 147 G~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~----------NG~IWV~~~~~ 194 (239)
T COG1097 147 GQIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ----------NGRIWVDGENE 194 (239)
T ss_pred CEEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec----------CCEEEecCCCc
Confidence 3567899999999999999999999999999999853 44677777644
No 120
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=90.21 E-value=0.49 Score=53.95 Aligned_cols=66 Identities=26% Similarity=0.403 Sum_probs=49.0
Q ss_pred HHHHHHHHHHHHHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccC
Q 003942 259 IDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQ 334 (784)
Q Consensus 259 V~kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~ 334 (784)
...|.+.|++.|+....+ +.. -...+.....+.||...++.||||+|.+|++|.++.|.+|.|...
T Consensus 459 ~~~a~~~i~~~i~r~~p~--~~e--------Ve~~gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~ 524 (604)
T COG1855 459 LKLAEEEIEREIKRYLPG--DVE--------VEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL 524 (604)
T ss_pred hHHHHHHHHHHHHHhCCC--Cce--------EEEecCCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence 555777777777765321 110 011234567899999999999999999999999999999999853
No 121
>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=89.50 E-value=0.47 Score=39.03 Aligned_cols=34 Identities=32% Similarity=0.406 Sum_probs=27.8
Q ss_pred eEEEEEecCCccceeeccCcchHhhHHhhcCCEE
Q 003942 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKI 233 (784)
Q Consensus 200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI 233 (784)
....+.+.....|.+|||+|.+|+.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 5556666666799999999999999999887554
No 122
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=89.45 E-value=0.19 Score=43.17 Aligned_cols=37 Identities=24% Similarity=0.458 Sum_probs=31.1
Q ss_pred CCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeE
Q 003942 293 GAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARI 329 (784)
Q Consensus 293 ~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarI 329 (784)
.....+.+.|..+..|+||||+|+||+.||.....-+
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~ 62 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAA 62 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHHHHH
Confidence 3567888999999999999999999999997765443
No 123
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=89.43 E-value=0.26 Score=42.27 Aligned_cols=39 Identities=31% Similarity=0.509 Sum_probs=30.9
Q ss_pred EEEEEecCCc-----cceeeccCcchHhhHHhhc-CCEEEEccCC
Q 003942 201 SRKIEVPNNK-----VGVLIGKAGDTIRYLQYNS-GAKIQITRDA 239 (784)
Q Consensus 201 t~rI~VP~~~-----vG~IIGkgG~tIK~Iq~~T-GakI~V~~~~ 239 (784)
..+|.|-... +|.+||++|.+||.|.++. |-+|.|...+
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~s 48 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEYS 48 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE--
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEcC
Confidence 4567777777 9999999999999999999 9999998653
No 124
>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=88.89 E-value=0.58 Score=38.50 Aligned_cols=34 Identities=29% Similarity=0.473 Sum_probs=27.0
Q ss_pred cEEEEEecCCceeeeecCCchHHHHHHHHhCCeE
Q 003942 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARI 329 (784)
Q Consensus 296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarI 329 (784)
..+.+.+.....|.+|||+|++|+.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 4445555555689999999999999999988554
No 125
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=87.86 E-value=0.34 Score=41.54 Aligned_cols=37 Identities=27% Similarity=0.566 Sum_probs=29.3
Q ss_pred EEEEEecCCc-----eeeeecCCchHHHHHHHHh-CCeEEecc
Q 003942 297 QVEIKVPNEK-----VGLIIGRGGETIKGLQTRS-GARIQLIP 333 (784)
Q Consensus 297 ~~~i~VP~~~-----vG~VIGkgG~~IK~Iq~~S-GarIqI~~ 333 (784)
++.+.|-.+. +|..||++|.+||.|.++. |-+|.|..
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 4556666655 9999999999999999999 99999864
No 126
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=87.34 E-value=0.99 Score=39.92 Aligned_cols=37 Identities=19% Similarity=0.375 Sum_probs=31.0
Q ss_pred ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEe
Q 003942 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQL 331 (784)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI 331 (784)
...+++.|-...-|.|||++|++|++|++...-+..+
T Consensus 29 ~~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~ 65 (81)
T cd02413 29 PTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF 65 (81)
T ss_pred CCeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence 4568899999999999999999999999876555544
No 127
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=87.28 E-value=0.39 Score=54.73 Aligned_cols=39 Identities=26% Similarity=0.420 Sum_probs=35.8
Q ss_pred eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccC
Q 003942 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238 (784)
Q Consensus 200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~ 238 (784)
....|.||...++.||||+|.+|++|+++.|.+|.|...
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~ 524 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL 524 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence 456788999999999999999999999999999999864
No 128
>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=86.93 E-value=6.9 Score=46.77 Aligned_cols=143 Identities=20% Similarity=0.290 Sum_probs=76.6
Q ss_pred CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEc---cCCCC-CC-----CCCCCcEEEecchhhHHHHHHHHHHH
Q 003942 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQIT---RDADA-DP-----HAATRPVEIIGTLSNIDKAEKLINAV 269 (784)
Q Consensus 199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~---~~~~~-~p-----~s~eR~V~I~G~~e~V~kA~~~I~el 269 (784)
.+...+.|+.. ..+| |.+|++|......+|.|. ++.+. .+ -....++.|.|+.++|+++++.+...
T Consensus 217 ~~~r~~~V~~~--s~li---GkTl~el~~~~~~~v~I~~I~R~g~~~~p~~dtvL~~GD~L~V~G~~e~L~~l~~~~G~~ 291 (562)
T TIGR03802 217 LVGRAYRVNRA--SSLI---GKTVGDLENLFAGRVTIERIRRDGKLLTVSPDLVLNAGDVVLVVGRRDAVVQFGAEIGEE 291 (562)
T ss_pred eeeEEEEECCC--cccC---CCcHHHHHhhhCCCeEEEEEEECCEEEcCCCCCeeCCCCEEEEEECHHHHHHHHHhcCCc
Confidence 34556667654 2244 457888876654333332 21110 01 11235779999999998877665443
Q ss_pred HHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHH-H-----HhCCeEEeccCC---CCC--
Q 003942 270 IAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQ-T-----RSGARIQLIPQH---LPE-- 338 (784)
Q Consensus 270 I~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq-~-----~SGarIqI~~~~---~p~-- 338 (784)
+.+.. .. . ......++.+++ ..+||| +|++|+ + +.|+.|.-..+. ++.
T Consensus 292 ~~~~~----------~~----~-~~~~~e~VV~~~---S~liGk---TL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~ 350 (562)
T TIGR03802 292 VQEVE----------GL----D-VPMETKDVVLTN---KEYNGK---TVAEILKNAQQFMRHGVYVEKIKRDDQPLPILP 350 (562)
T ss_pred cCCcc----------cc----C-CceEEEEEEECC---cccCCc---cHHHHhccccccccCCeEEEEEeeCCccccCCC
Confidence 32210 00 0 011233445554 345654 888887 2 568775444321 110
Q ss_pred -CCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 003942 339 -GDGSKERIVRVTGDMRQIEIAQEMIKEVL 367 (784)
Q Consensus 339 -~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L 367 (784)
..-..-.++.|.|+.+.++++++.+-+..
T Consensus 351 d~~L~~GD~LlV~G~~~~l~~~~~~lG~~~ 380 (562)
T TIGR03802 351 ETVLQRGDVVTLVGTPQDVDRAAKQLGYAI 380 (562)
T ss_pred CCEecCCCEEEEEeCHHHHHHHHHHcCCch
Confidence 01122356899999999999877755433
No 129
>PRK03818 putative transporter; Validated
Probab=86.29 E-value=6.2 Score=47.04 Aligned_cols=140 Identities=18% Similarity=0.288 Sum_probs=77.3
Q ss_pred eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEcc---CCCC------CCCCCCCcEEEecchhhHHHHHHHHHHHH
Q 003942 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITR---DADA------DPHAATRPVEIIGTLSNIDKAEKLINAVI 270 (784)
Q Consensus 200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~---~~~~------~p~s~eR~V~I~G~~e~V~kA~~~I~elI 270 (784)
..+++.|+++. +| |++|++++.....++.|.+ +.+. ..-....++.|.|+.++++++++.+...+
T Consensus 205 ~~r~~~V~~s~---li---GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~l~~l~~~~Gl~~ 278 (552)
T PRK03818 205 QTINIRVENPN---LH---GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPEDLHKAQLVIGEEV 278 (552)
T ss_pred eeEEEEEeCCC---CC---CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHHHHHHHHhcCCcc
Confidence 34677777443 34 5689999887766554432 2110 11122357889999999887776655332
Q ss_pred HhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHH--HHHhCCeEEeccC-C--CCCCC---CC
Q 003942 271 AEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGL--QTRSGARIQLIPQ-H--LPEGD---GS 342 (784)
Q Consensus 271 ~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~I--q~~SGarIqI~~~-~--~p~~~---~~ 342 (784)
.+. . ..........++.++++ .++|| +|++| +++.|+.|.-.++ . ++... -.
T Consensus 279 ~~~------------~--~~~~~~~~~E~Vvv~~S---~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq 338 (552)
T PRK03818 279 DTS------------L--STRGTDLRSERVVVTNE---KVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLSLQ 338 (552)
T ss_pred Ccc------------c--cccCcceEEEEEEEcCh---hccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCEEe
Confidence 110 0 00011223344445543 56655 78888 4667776443322 1 11111 12
Q ss_pred CceEEEEEcCHHHHHHHHHHHHH
Q 003942 343 KERIVRVTGDMRQIEIAQEMIKE 365 (784)
Q Consensus 343 ~er~V~I~Gt~~qV~~Ak~lI~~ 365 (784)
.-.++.|.|+.+++++..+.+.+
T Consensus 339 ~GD~LlVvG~~~~i~~l~~~Lg~ 361 (552)
T PRK03818 339 FGDILNLVGRPEAIDAVANVLGN 361 (552)
T ss_pred cCCEEEEEECHHHHHHHHHHhCC
Confidence 23468999999999998776543
No 130
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=85.65 E-value=3.4 Score=43.44 Aligned_cols=37 Identities=24% Similarity=0.539 Sum_probs=29.1
Q ss_pred ccEEEEEecCCceeeeecCCchHHHHHHH----HhCC-eEEe
Q 003942 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQT----RSGA-RIQL 331 (784)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~----~SGa-rIqI 331 (784)
...+++.|....=|.||||+|++|+.|++ .+|. .|+|
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~~v~I 91 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKENVQI 91 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCCCceE
Confidence 45678888899999999999999998864 4565 3444
No 131
>PRK13764 ATPase; Provisional
Probab=85.21 E-value=0.72 Score=55.12 Aligned_cols=66 Identities=15% Similarity=0.180 Sum_probs=47.1
Q ss_pred hhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCC
Q 003942 174 EPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDA 239 (784)
Q Consensus 174 e~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~ 239 (784)
..|.+.|.+.|...-...-...........|.|+...++.+|||+|.+|++|+++.|.+|.|....
T Consensus 455 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~ 520 (602)
T PRK13764 455 RLAEKEIEREIKRYLPGPVEVEVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLD 520 (602)
T ss_pred HHHHHHHHHHHHHhcCCceEEEEecCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcc
Confidence 445566666664333111111112445778999999999999999999999999999999998654
No 132
>PRK13764 ATPase; Provisional
Probab=85.14 E-value=1.1 Score=53.77 Aligned_cols=66 Identities=26% Similarity=0.373 Sum_probs=48.8
Q ss_pred HHHHHHHHHHHHHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccC
Q 003942 259 IDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQ 334 (784)
Q Consensus 259 V~kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~ 334 (784)
...|.+.|++.|+....+... -......+..+.|+...++.||||+|.+|++|.++.|.+|.|...
T Consensus 454 ~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~ 519 (602)
T PRK13764 454 WRLAEKEIEREIKRYLPGPVE----------VEVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL 519 (602)
T ss_pred HHHHHHHHHHHHHHhcCCceE----------EEEecCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence 345677777777765311000 011245678899999999999999999999999999999999753
No 133
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=84.74 E-value=0.64 Score=52.64 Aligned_cols=21 Identities=10% Similarity=0.113 Sum_probs=11.2
Q ss_pred eecccccccccceeeecCchh
Q 003942 151 DVKEETKEVTVKEEETVKEEE 171 (784)
Q Consensus 151 ~I~~~~~~~s~r~~~i~G~~e 171 (784)
+|...+.........|.|+.+
T Consensus 181 ~~Rp~tP~LPDSTDFVCGTLD 201 (458)
T PF10446_consen 181 KIRPGTPELPDSTDFVCGTLD 201 (458)
T ss_pred CCCCCCCCCCCcccccCCCcC
Confidence 444444455555566666643
No 134
>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=84.46 E-value=0.97 Score=39.31 Aligned_cols=36 Identities=28% Similarity=0.635 Sum_probs=29.4
Q ss_pred ccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEE
Q 003942 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQ 330 (784)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIq 330 (784)
...+.+.|-.+..|+||||+|++|+.||--+...+.
T Consensus 23 ~~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 23 GDTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred CCEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 346778888899999999999999999977665444
No 135
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=83.73 E-value=0.56 Score=40.67 Aligned_cols=35 Identities=23% Similarity=0.518 Sum_probs=30.2
Q ss_pred cEEEEEecCCceeeeecCCchHHHHHHHHhCCeEE
Q 003942 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQ 330 (784)
Q Consensus 296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIq 330 (784)
..+.+.|-....|.|||++|++|++|.+.+.-++.
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 56788899999999999999999999887766654
No 136
>KOG0299 consensus U3 snoRNP-associated protein (contains WD40 repeats) [RNA processing and modification]
Probab=83.26 E-value=3 Score=47.48 Aligned_cols=40 Identities=30% Similarity=0.289 Sum_probs=21.6
Q ss_pred hcCCccccccCchhhccccccccccCCCccCCccccCCCC
Q 003942 33 AEGMRDDEAKNSDEVEKNVDGFAEAHGSEVKRPRLDDDKT 72 (784)
Q Consensus 33 ~~~~~~~e~~~~~e~~~~~~~~~~~d~~e~Krpr~ddd~~ 72 (784)
+++|.-||++|+.+.++-..++.+..+..+||.||-++.+
T Consensus 44 ~eei~Sd~Een~~~g~~e~e~e~~~Eta~ekr~RlA~e~L 83 (479)
T KOG0299|consen 44 AEEIESDEEENSLAGEEEEEDEFEEETAGEKRLRLAEEYL 83 (479)
T ss_pred hhhhccccccccccchhhhcccchhcchhHHHHHHHHHHH
Confidence 4455544555555553333333344445558888777765
No 137
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=81.03 E-value=1.2 Score=46.73 Aligned_cols=51 Identities=16% Similarity=0.294 Sum_probs=34.9
Q ss_pred hhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCCccceeeccCcchHhhHHhh
Q 003942 177 NVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYN 228 (784)
Q Consensus 177 ~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~ 228 (784)
++.|.+.+.+..+..-.... ....++|.|-..+-|.||||+|++|++|++.
T Consensus 29 re~l~k~l~~Ag~s~veIeR-~~~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 29 REFLEKELSNAGISGVEIER-TPKGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred HHHHHHHHHhCCcceEEEEe-cCCceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 34555555555443322211 2457789999999999999999999988764
No 138
>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=80.89 E-value=0.81 Score=39.65 Aligned_cols=35 Identities=20% Similarity=0.376 Sum_probs=29.6
Q ss_pred eEEEEEecCCccceeeccCcchHhhHHhhcCCEEE
Q 003942 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQ 234 (784)
Q Consensus 200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~ 234 (784)
....|.|-....|.|||++|++|++|+....-.+.
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 46788889999999999999999999887665554
No 139
>PRK03818 putative transporter; Validated
Probab=80.41 E-value=5.9 Score=47.21 Aligned_cols=96 Identities=20% Similarity=0.275 Sum_probs=56.8
Q ss_pred ceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCCccceeeccCcchHhhH--HhhcCCEEEEccCC
Q 003942 162 KEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYL--QYNSGAKIQITRDA 239 (784)
Q Consensus 162 r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~I--q~~TGakI~V~~~~ 239 (784)
..+.+.|+.++++++...+...+.. .....+.....++|+++++ .++|| +|++| +++.|+.|.-.++.
T Consensus 256 DiLlV~G~~e~l~~l~~~~Gl~~~~----~~~~~~~~~~~E~Vvv~~S---~liGk---TL~eL~~r~~~Gv~VlaI~R~ 325 (552)
T PRK03818 256 DLLHLVGQPEDLHKAQLVIGEEVDT----SLSTRGTDLRSERVVVTNE---KVLGK---KLRDLHLKNKYGVVISRLNRA 325 (552)
T ss_pred CEEEEEECHHHHHHHHHhcCCccCc----cccccCcceEEEEEEEcCh---hccCC---cHHHhcccccCCeEEEEEeEC
Confidence 5677888999888877665544321 0111122345666777764 55655 78777 46677766443332
Q ss_pred CCCC-CC------CCCcEEEecchhhHHHHHHHHH
Q 003942 240 DADP-HA------ATRPVEIIGTLSNIDKAEKLIN 267 (784)
Q Consensus 240 ~~~p-~s------~eR~V~I~G~~e~V~kA~~~I~ 267 (784)
+..- .. .-.++.+.|+++++++..+.+.
T Consensus 326 g~~l~~~~d~~Lq~GD~LlVvG~~~~i~~l~~~Lg 360 (552)
T PRK03818 326 GVELVASPDLSLQFGDILNLVGRPEAIDAVANVLG 360 (552)
T ss_pred CeecCCCCCCEEecCCEEEEEECHHHHHHHHHHhC
Confidence 2111 11 1236789999999999877644
No 140
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=80.01 E-value=2.2 Score=42.81 Aligned_cols=39 Identities=23% Similarity=0.488 Sum_probs=34.2
Q ss_pred CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEecc
Q 003942 294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIP 333 (784)
Q Consensus 294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~ 333 (784)
....+-|.|-... |..|||+|.+||.+++..|-+|.|..
T Consensus 59 ~ddrvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 59 VDDLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred eCCEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 3467788887777 99999999999999999999999974
No 141
>PRK15494 era GTPase Era; Provisional
Probab=79.92 E-value=4.8 Score=44.87 Aligned_cols=35 Identities=26% Similarity=0.375 Sum_probs=26.6
Q ss_pred EEEEecC-CceeeeecCCchHHHHHH--------HHhCCeEEec
Q 003942 298 VEIKVPN-EKVGLIIGRGGETIKGLQ--------TRSGARIQLI 332 (784)
Q Consensus 298 ~~i~VP~-~~vG~VIGkgG~~IK~Iq--------~~SGarIqI~ 332 (784)
..|.|.. +..+.||||+|++||+|. +..+|+|.+.
T Consensus 275 ~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 275 QVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred EEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 4566766 678999999999999775 4457776663
No 142
>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=79.34 E-value=1.7 Score=38.51 Aligned_cols=36 Identities=17% Similarity=0.276 Sum_probs=29.5
Q ss_pred eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEE
Q 003942 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQI 235 (784)
Q Consensus 200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V 235 (784)
...+|.|-..+-|.|||++|++|++|+++....+.+
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 457888888999999999999999999876544433
No 143
>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=78.88 E-value=2.6 Score=39.24 Aligned_cols=32 Identities=28% Similarity=0.579 Sum_probs=26.9
Q ss_pred cEEEEEecCCceeeeecCCchHHHHHHHHhCC
Q 003942 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGA 327 (784)
Q Consensus 296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGa 327 (784)
..++|.|-...-|+|||++|++|++|++....
T Consensus 61 ~~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 61 DRVEVTIHTARPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred CCEEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence 45788888889999999999999999876443
No 144
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=78.82 E-value=11 Score=45.63 Aligned_cols=21 Identities=10% Similarity=0.275 Sum_probs=10.2
Q ss_pred EEEcCHHHHHHHHHHHHHHHh
Q 003942 348 RVTGDMRQIEIAQEMIKEVLS 368 (784)
Q Consensus 348 ~I~Gt~~qV~~Ak~lI~~~L~ 368 (784)
.|++.-+....+.+|+...+.
T Consensus 376 dir~emDd~~~~f~lL~n~vk 396 (1102)
T KOG1924|consen 376 DIRAEMDDANEVFELLANTVK 396 (1102)
T ss_pred hhhhhhccHHHHHHHHHHhhh
Confidence 345554444455555554443
No 145
>COG2985 Predicted permease [General function prediction only]
Probab=78.31 E-value=5.9 Score=45.82 Aligned_cols=126 Identities=13% Similarity=0.159 Sum_probs=78.3
Q ss_pred ccCCCchhhhhhhcccCceeeeccccc---------ccccceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeE
Q 003942 131 QISVKEETKEVLFSTEEAFIDVKEETK---------EVTVKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMS 201 (784)
Q Consensus 131 iIGk~Ge~Ik~iq~~s~a~I~I~~~~~---------~~s~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t 201 (784)
+-|+.=+++-.++.+.|...+++++.. ...-..+.+.|..+++++++..|-+.++... ..+.+-.+
T Consensus 214 ~~g~~l~d~p~l~~~~v~~sRikrd~~~~~p~~~~~i~~Gd~l~lVG~~~~l~r~~~~~G~evd~~~-----~~~~~l~~ 288 (544)
T COG2985 214 LDGLNLRDLPILRQEGVYCSRIKRDGILAVPDPDTIIQVGDELHLVGYPDALARLDLRIGKEVDDRL-----LLDTRLRT 288 (544)
T ss_pred ccccchhhcccccCCceEEEEEecCCeeecCCCCcccccCcEEEecCChHHHHHHHHhccccccccc-----ccccceee
Confidence 455555556666677777777777733 1112567888999999999977766664322 22445678
Q ss_pred EEEEecCCccceeeccCcchHhhHH-hhcCCEE--------EEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHH
Q 003942 202 RKIEVPNNKVGVLIGKAGDTIRYLQ-YNSGAKI--------QITRDADADPHAATRPVEIIGTLSNIDKAEKLINA 268 (784)
Q Consensus 202 ~rI~VP~~~vG~IIGkgG~tIK~Iq-~~TGakI--------~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~e 268 (784)
+||.|-++.| .| ++|++|. .+.||-| .+..+.+.. -..-.+++++|.++.|+.+.+.|-+
T Consensus 289 ~rivVtn~~v---lG---k~l~~L~~~~~g~~I~Ri~Ra~iElv~~~d~~-lq~gDvl~vvg~~~~v~~~~~~lG~ 357 (544)
T COG2985 289 ERVVVTNENV---LG---KRLRDLNLTEYGVFINRINRADIELVASDDVV-LQKGDVLQVVGRARRVKAVADVLGN 357 (544)
T ss_pred EEEEeechhh---hc---cchhhcCccccceeeeehhhcCccccCCcchh-hhhcceeeeccchHHHHHHHHHhcc
Confidence 8999998865 33 3455544 2244433 332222111 1223477999999999988887755
No 146
>COG1159 Era GTPase [General function prediction only]
Probab=78.26 E-value=5 Score=43.78 Aligned_cols=34 Identities=32% Similarity=0.560 Sum_probs=25.7
Q ss_pred EEEEecC-CceeeeecCCchHHHHHH--------HHhCCeEEe
Q 003942 298 VEIKVPN-EKVGLIIGRGGETIKGLQ--------TRSGARIQL 331 (784)
Q Consensus 298 ~~i~VP~-~~vG~VIGkgG~~IK~Iq--------~~SGarIqI 331 (784)
..|.|.+ +.-+.||||+|++||+|- +..+|+|.+
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 4466776 688999999999999775 445666665
No 147
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=77.75 E-value=2 Score=44.40 Aligned_cols=63 Identities=16% Similarity=0.248 Sum_probs=43.4
Q ss_pred hhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEE
Q 003942 173 VEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQI 235 (784)
Q Consensus 173 Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V 235 (784)
...++..+.+++..-++...........++.+.|-.+..++|||++|.+++.|+.-+.+-+.-
T Consensus 64 ~~~~~~~L~ell~~m~~~~~i~v~~~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 64 AQEAKDYLEELLELMDFEVTITVSEEGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred HHHHHHHHHHHHHHhCCceEEEEeecCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 355667777777644443333323345567778888889999999999999999876654443
No 148
>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=77.64 E-value=1.6 Score=40.76 Aligned_cols=30 Identities=23% Similarity=0.442 Sum_probs=25.6
Q ss_pred EEEEEecCCccceeeccCcchHhhHHhhcC
Q 003942 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSG 230 (784)
Q Consensus 201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TG 230 (784)
.++|.|-..+.|.|||++|++|++|++...
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 467888888999999999999999987643
No 149
>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=76.10 E-value=13 Score=44.56 Aligned_cols=101 Identities=18% Similarity=0.206 Sum_probs=60.2
Q ss_pred cceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCCccceeeccCcchHhhHH------hhcCCEEE
Q 003942 161 VKEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQ------YNSGAKIQ 234 (784)
Q Consensus 161 ~r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq------~~TGakI~ 234 (784)
...+.+.|+.+++++..+.+...+..... . +.....++|.++++ .+|| ++|++|+ ++.|+.|.
T Consensus 269 GD~L~V~G~~e~L~~l~~~~G~~~~~~~~----~-~~~~~~e~VV~~~S---~liG---kTL~eL~~r~~~~~~~Gv~Vl 337 (562)
T TIGR03802 269 GDVVLVVGRRDAVVQFGAEIGEEVQEVEG----L-DVPMETKDVVLTNK---EYNG---KTVAEILKNAQQFMRHGVYVE 337 (562)
T ss_pred CCEEEEEECHHHHHHHHHhcCCccCCccc----c-CCceEEEEEEECCc---ccCC---ccHHHHhccccccccCCeEEE
Confidence 35677889999988887665544322111 1 11123666666654 4455 4888886 26777775
Q ss_pred EccCCCC-CCCC------CCCcEEEecchhhHHHHHHHHHHHHHh
Q 003942 235 ITRDADA-DPHA------ATRPVEIIGTLSNIDKAEKLINAVIAE 272 (784)
Q Consensus 235 V~~~~~~-~p~s------~eR~V~I~G~~e~V~kA~~~I~elI~e 272 (784)
-..+.+. .... .-.+++|.|+.++++++.+.+.+..++
T Consensus 338 ~I~R~g~~i~~~~d~~L~~GD~LlV~G~~~~l~~~~~~lG~~~~~ 382 (562)
T TIGR03802 338 KIKRDDQPLPILPETVLQRGDVVTLVGTPQDVDRAAKQLGYAIAP 382 (562)
T ss_pred EEeeCCccccCCCCCEecCCCEEEEEeCHHHHHHHHHHcCCchhh
Confidence 4433221 1111 123778999999999988876655443
No 150
>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=75.31 E-value=8.7 Score=41.17 Aligned_cols=36 Identities=25% Similarity=0.348 Sum_probs=26.3
Q ss_pred cEEEEEecC-CceeeeecCCchHHHHHHH--------HhCCeEEe
Q 003942 296 EQVEIKVPN-EKVGLIIGRGGETIKGLQT--------RSGARIQL 331 (784)
Q Consensus 296 ~~~~i~VP~-~~vG~VIGkgG~~IK~Iq~--------~SGarIqI 331 (784)
....|.|.. +..+.||||+|++||+|.. ..||+|.+
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ar~~l~~~~~~~v~l 265 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIAARKDILELFDCDVFL 265 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 344566766 6789999999999997754 44666655
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=74.29 E-value=4.8 Score=35.70 Aligned_cols=30 Identities=33% Similarity=0.603 Sum_probs=24.8
Q ss_pred cEEEEEecCCceeeeecCCchHHHHHHHHh
Q 003942 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRS 325 (784)
Q Consensus 296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~S 325 (784)
..+++.|-...-|.|||++|++|++|++.-
T Consensus 38 ~~i~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 38 LGTQITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred CcEEEEEEECCCCceECCCchhHHHHHHHH
Confidence 346777777899999999999999988654
No 152
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=74.07 E-value=3.6 Score=50.71 Aligned_cols=34 Identities=18% Similarity=0.170 Sum_probs=18.7
Q ss_pred EEEEEecCCccceeeccCcchHhhHHhhcCCEEEE
Q 003942 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQI 235 (784)
Q Consensus 201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V 235 (784)
...++||...+-.|+-..= .+..|...+-++|+.
T Consensus 236 ~~~~lVPikEM~dvLkV~K-~~v~L~~gswVRiKr 269 (1024)
T KOG1999|consen 236 NRILLVPIKEMPDVLKVVK-KVVQLSEGSWVRIKR 269 (1024)
T ss_pred ccEEEEehhHhhhhhhhhh-hhhccCccceEEEec
Confidence 3567777766666554332 333555556566543
No 153
>PRK00089 era GTPase Era; Reviewed
Probab=73.74 E-value=8.8 Score=41.40 Aligned_cols=37 Identities=30% Similarity=0.511 Sum_probs=27.4
Q ss_pred cEEEEEecC-CceeeeecCCchHHHHHH--------HHhCCeEEec
Q 003942 296 EQVEIKVPN-EKVGLIIGRGGETIKGLQ--------TRSGARIQLI 332 (784)
Q Consensus 296 ~~~~i~VP~-~~vG~VIGkgG~~IK~Iq--------~~SGarIqI~ 332 (784)
....|.|.. +..+.||||+|++||+|. +..+|+|.+.
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 344556666 678999999999999765 4567777764
No 154
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=71.34 E-value=7.6 Score=40.44 Aligned_cols=32 Identities=31% Similarity=0.539 Sum_probs=25.9
Q ss_pred cEEEEEecCCceeeeecCCchHHHHHHHHhCC
Q 003942 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGA 327 (784)
Q Consensus 296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGa 327 (784)
..+++.|-...-|.|||++|++|++|++...-
T Consensus 40 ~~i~I~I~ta~PGivIGk~G~~I~klk~~Lkk 71 (207)
T PRK04191 40 LGTRITIYAERPGMVIGRGGKNIRELTEILEK 71 (207)
T ss_pred CcEEEEEEECCCCeEECCCchhHHHHHHHHHH
Confidence 34667777788999999999999999876543
No 155
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=70.44 E-value=17 Score=37.73 Aligned_cols=38 Identities=24% Similarity=0.440 Sum_probs=31.3
Q ss_pred CccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEe
Q 003942 294 AAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQL 331 (784)
Q Consensus 294 ~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI 331 (784)
....+.+.|-.+..++||||.|.+++.||-.+.+.+..
T Consensus 89 ~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 89 EGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 44567788888889999999999999999887765543
No 156
>COG0490 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]
Probab=70.28 E-value=6.5 Score=39.20 Aligned_cols=56 Identities=20% Similarity=0.283 Sum_probs=36.7
Q ss_pred CCceeeeecCCchHHHHHHHHhCCeEEeccCC----CCCC---CCCCceEEEEEcCHHHHHHHHHHHH
Q 003942 304 NEKVGLIIGRGGETIKGLQTRSGARIQLIPQH----LPEG---DGSKERIVRVTGDMRQIEIAQEMIK 364 (784)
Q Consensus 304 ~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~----~p~~---~~~~er~V~I~Gt~~qV~~Ak~lI~ 364 (784)
..++|+=|| --+|+++|||.|.-..+. +.++ .-....+|.|.|+...+.+++.++.
T Consensus 96 s~~~GksiG-----dl~irq~TGaTIIAI~r~~e~I~SPgPy~vle~gDtlvviG~~~~~~r~~~f~~ 158 (162)
T COG0490 96 SPFIGKTIG-----DLNIRQNTGATVIAIVRNEEKILSPGPYTVLEAGDTLVVIGEETGLKRAKRFLL 158 (162)
T ss_pred CcccCcchh-----hcccccccCcEEEEEEecCcEecCCCchhhhcCCCEEEEEecchHhHHHHHHhh
Confidence 356666665 247899999986544221 1111 1234468999999999999888764
No 157
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=67.93 E-value=8.3 Score=40.53 Aligned_cols=32 Identities=19% Similarity=0.307 Sum_probs=26.8
Q ss_pred ccEEEEEecCCceeeeecCCchHHHHHHHHhC
Q 003942 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSG 326 (784)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SG 326 (784)
...+++.|-...-|.|||++|..|++|++...
T Consensus 43 ~~~i~V~I~tarPg~vIG~~G~~i~~l~~~L~ 74 (220)
T PTZ00084 43 PIRTEIIIRATRTREVLGDKGRRIRELTSLLQ 74 (220)
T ss_pred CCcEEEEEEECCCccEEcCCchHHHHHHHHHH
Confidence 34578888888899999999999999886653
No 158
>PRK15405 ethanolamine utilization protein EutL; Provisional
Probab=67.59 E-value=67 Score=33.67 Aligned_cols=144 Identities=13% Similarity=0.132 Sum_probs=78.1
Q ss_pred HhhHHhhcCCEEEEccCCC------CCCCCCCCcEEEec-chhhHHHHHHHHHHHHHhhhcC------CCCcccccccch
Q 003942 222 IRYLQYNSGAKIQITRDAD------ADPHAATRPVEIIG-TLSNIDKAEKLINAVIAEADAG------GSPSLVARGLAT 288 (784)
Q Consensus 222 IK~Iq~~TGakI~V~~~~~------~~p~s~eR~V~I~G-~~e~V~kA~~~I~elI~e~~~~------g~p~~~~~g~~~ 288 (784)
+...-+.++++|.+.++.. ..+.+.+-++.|.| +...|+.|++...+.|++...+ +...+...-..+
T Consensus 51 aDeA~KAAnVevv~a~~~~gGaghg~~~~~G~viiIi~G~dvsdVrsAveaa~~~i~~~~~f~~~n~~g~~~~~a~~~aR 130 (217)
T PRK15405 51 LDEATKQAMVEVVYARSFYAGAAHASTPLAGEVIGILAGPNPAEVRAGLDAMVAFIENGAAFQSANDDDSTAFFAHVVSR 130 (217)
T ss_pred HHHHHhhcceEEEEEEeeccccccCCCCCCccEEEEEeCCCHHHHHHHHHHHHHHHHhhhceEeeCCCCCEEEEEEEccc
Confidence 3445567778887766531 11123344668888 8999999999999988875321 000000000000
Q ss_pred hhccCCccEEEEEecC-CceeeeecCCchHHHHHH---HHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 003942 289 AQASGAAEQVEIKVPN-EKVGLIIGRGGETIKGLQ---TRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIK 364 (784)
Q Consensus 289 ~~~~~~~~~~~i~VP~-~~vG~VIGkgG~~IK~Iq---~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~ 364 (784)
. .......+-+|. +..|.|||-=++-+--+= +...++| ..-..|+.+.+- .-+.|+|+...|+.|.+.-.
T Consensus 131 a---g~~l~k~~g~~~G~a~~~li~~P~~~~~~~D~AlKaA~V~~--~~~~~P~~~t~f-~~~~ltG~~~A~r~A~~a~~ 204 (217)
T PRK15405 131 T---GSYLSKTAGIAEGEPLAYLIAPPLEAMYGIDAALKAADVQL--VTFVGPPSETNF-GGALLTGSQSACKAACNAFT 204 (217)
T ss_pred H---HHHHHHHcCCCCCceeEEEecCcHHHHHHHHHHHhhcCceE--EEEeCCCCCcee-cCeeEEeCHHHHHHHHHHHH
Confidence 0 000112234455 567889988765554443 2334444 321122223222 22899999888888877777
Q ss_pred HHHhccc
Q 003942 365 EVLSQTV 371 (784)
Q Consensus 365 ~~L~~~~ 371 (784)
+.++...
T Consensus 205 e~v~~~a 211 (217)
T PRK15405 205 DAVLEVA 211 (217)
T ss_pred HHHHHHH
Confidence 6665543
No 159
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=65.79 E-value=12 Score=38.72 Aligned_cols=31 Identities=32% Similarity=0.592 Sum_probs=26.5
Q ss_pred ccEEEEEecCCceeeeecCCchHHHHHHHHh
Q 003942 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRS 325 (784)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~S 325 (784)
...+++.|-...-|.|||++|.+|++|++.-
T Consensus 37 ~~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 37 PLGTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred CCcEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 4568888988999999999999999987654
No 160
>PRK04972 putative transporter; Provisional
Probab=63.45 E-value=98 Score=37.12 Aligned_cols=144 Identities=18% Similarity=0.241 Sum_probs=72.5
Q ss_pred eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEc---cCCCC-CC-----CCCCCcEEEecchhhHHHHHHHHHHHH
Q 003942 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQIT---RDADA-DP-----HAATRPVEIIGTLSNIDKAEKLINAVI 270 (784)
Q Consensus 200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~---~~~~~-~p-----~s~eR~V~I~G~~e~V~kA~~~I~elI 270 (784)
+...+.|.+..+-.++ |++|++|.......|.|. ++.+. .+ -....++.|.|+.+.+.++++.+. +
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 3666777665332223 668888877664444332 22110 01 112347789999988766654431 0
Q ss_pred HhhhcCCCCcccccccchhhccCC-ccEEEEEecCCceeeeecCCchHHHHHHH-HhCCeEEeccC-C--CCCCC---CC
Q 003942 271 AEADAGGSPSLVARGLATAQASGA-AEQVEIKVPNEKVGLIIGRGGETIKGLQT-RSGARIQLIPQ-H--LPEGD---GS 342 (784)
Q Consensus 271 ~e~~~~g~p~~~~~g~~~~~~~~~-~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~-~SGarIqI~~~-~--~p~~~---~~ 342 (784)
.++. .++ ...+. ....++.+++ ..+||| +|++|+- +.|+.|.-..+ . ..... -.
T Consensus 289 g~e~-------~~~-----~~~~~~~~~E~vVv~~---s~liGk---TL~eL~~r~~gv~Vl~I~R~g~~~~~~~~~~L~ 350 (558)
T PRK04972 289 GKEV-------FDR-----DLLDMRIVTEEIVVKN---HNAVGK---RLSQLKLTDHGCFLNRVIRSQIEMPIDDNVVLN 350 (558)
T ss_pred CCcc-------cCc-----cccCcceEEEEEEEcC---cccCCC---CHHHhCCccCCeEEEEEecCCcccCCCCCCEec
Confidence 1100 000 00011 1233444443 345654 7887742 36777544333 1 11111 12
Q ss_pred CceEEEEEcCHHHHHHHHHHHHHH
Q 003942 343 KERIVRVTGDMRQIEIAQEMIKEV 366 (784)
Q Consensus 343 ~er~V~I~Gt~~qV~~Ak~lI~~~ 366 (784)
...++.|.|+.+.+++..+.+-.+
T Consensus 351 ~GD~LlVvG~~~~i~~l~~~lG~~ 374 (558)
T PRK04972 351 KGDVLQVSGDARRVKTIADRIGFI 374 (558)
T ss_pred CCCEEEEEECHHHHHHHHHHhCCc
Confidence 235789999999999977765543
No 161
>COG0490 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]
Probab=62.09 E-value=11 Score=37.57 Aligned_cols=65 Identities=23% Similarity=0.337 Sum_probs=40.9
Q ss_pred CCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEc-cCCCCC--CC-----CCCCcEEEecchhhHHHHHHHHH
Q 003942 198 STMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQIT-RDADAD--PH-----AATRPVEIIGTLSNIDKAEKLIN 267 (784)
Q Consensus 198 ~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~-~~~~~~--p~-----s~eR~V~I~G~~e~V~kA~~~I~ 267 (784)
....+++..-+.++|+-||- -+|+.+|||.|.-. ++.+.. |+ .....|.++|+...+.++..++.
T Consensus 86 ~~~~~~i~~~s~~~GksiGd-----l~irq~TGaTIIAI~r~~e~I~SPgPy~vle~gDtlvviG~~~~~~r~~~f~~ 158 (162)
T COG0490 86 IIEWFKIEAGSPFIGKTIGD-----LNIRQNTGATVIAIVRNEEKILSPGPYTVLEAGDTLVVIGEETGLKRAKRFLL 158 (162)
T ss_pred hheeeeeecCCcccCcchhh-----cccccccCcEEEEEEecCcEecCCCchhhhcCCCEEEEEecchHhHHHHHHhh
Confidence 34455666666677776664 47889999887543 332211 11 23357888999998888776653
No 162
>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=61.90 E-value=6.7 Score=34.80 Aligned_cols=28 Identities=29% Similarity=0.483 Sum_probs=23.0
Q ss_pred EEEEecCCccceeeccCcchHhhHHhhc
Q 003942 202 RKIEVPNNKVGVLIGKAGDTIRYLQYNS 229 (784)
Q Consensus 202 ~rI~VP~~~vG~IIGkgG~tIK~Iq~~T 229 (784)
.++.|-..+-|.|||++|.+|++|++..
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 5566666899999999999999988753
No 163
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=59.86 E-value=9 Score=48.22 Aligned_cols=6 Identities=50% Similarity=0.540 Sum_probs=2.6
Q ss_pred eeeccc
Q 003942 120 SVEEQA 125 (784)
Q Consensus 120 ki~iP~ 125 (784)
+|+|-.
T Consensus 1799 RieVq~ 1804 (3015)
T KOG0943|consen 1799 RIEVQA 1804 (3015)
T ss_pred eeEEee
Confidence 444433
No 164
>PRK04972 putative transporter; Provisional
Probab=58.95 E-value=70 Score=38.33 Aligned_cols=102 Identities=13% Similarity=0.119 Sum_probs=55.1
Q ss_pred ceeeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCCccceeeccCcchHhhHHh-hcCCEEEEccCC-
Q 003942 162 KEEETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQY-NSGAKIQITRDA- 239 (784)
Q Consensus 162 r~~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~-~TGakI~V~~~~- 239 (784)
..+.+.|+.++++++.+.+. +..+ .......+.....++++++++ .+||| +|++|+- +.|+.|.-.++.
T Consensus 268 DiL~V~G~~e~l~~l~~~~~--lg~e-~~~~~~~~~~~~~E~vVv~~s---~liGk---TL~eL~~r~~gv~Vl~I~R~g 338 (558)
T PRK04972 268 DEIALVGYPDAHARLDPSFR--NGKE-VFDRDLLDMRIVTEEIVVKNH---NAVGK---RLSQLKLTDHGCFLNRVIRSQ 338 (558)
T ss_pred CEEEEEECHHHHHHHHHhhc--CCCc-ccCccccCcceEEEEEEEcCc---ccCCC---CHHHhCCccCCeEEEEEecCC
Confidence 45667788888766654421 1111 111110111124666666654 44554 7777742 367766544332
Q ss_pred -CCCCC-----CCCCcEEEecchhhHHHHHHHHHHHHHh
Q 003942 240 -DADPH-----AATRPVEIIGTLSNIDKAEKLINAVIAE 272 (784)
Q Consensus 240 -~~~p~-----s~eR~V~I~G~~e~V~kA~~~I~elI~e 272 (784)
+..+. ..-.++.|.|+++++++..+.+..++.+
T Consensus 339 ~~~~~~~~~~L~~GD~LlVvG~~~~i~~l~~~lG~~~~~ 377 (558)
T PRK04972 339 IEMPIDDNVVLNKGDVLQVSGDARRVKTIADRIGFISIH 377 (558)
T ss_pred cccCCCCCCEecCCCEEEEEECHHHHHHHHHHhCCcccc
Confidence 11111 1123778999999999988877665544
No 165
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=58.89 E-value=22 Score=44.26 Aligned_cols=90 Identities=13% Similarity=0.174 Sum_probs=49.1
Q ss_pred hhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCCc------cceeeccCcchHhhHHhh------cCCEEEEccCCCCCC
Q 003942 176 SNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNK------VGVLIGKAGDTIRYLQYN------SGAKIQITRDADADP 243 (784)
Q Consensus 176 A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~~------vG~IIGkgG~tIK~Iq~~------TGakI~V~~~~~~~p 243 (784)
++++..+.+....+.+........++.+.|+|..+ |-+-||+.-+++..|+++ |++.++|..- ...
T Consensus 129 ~~r~aee~~~~~~~~~~~~~~~d~I~Q~~LLPsvkDP~LW~VKC~iG~Er~~a~~LMrK~i~~~~t~~plqI~Sv--~a~ 206 (1024)
T KOG1999|consen 129 AKRYAEEYIEKYGFEDGDDEDSDDIPQQALLPSVKDPNLWIVKCKIGREREVAFCLMRKFIELDKTDTPLQIKSV--FAK 206 (1024)
T ss_pred HHHHHHhhcccccccccchhcccchhHHhhCCCCCCCCeeEEEeccccHHHHHHHHHHHHHhhcccCCCceEEEE--Eec
Confidence 33444444433333333333456778889998864 888999998877776653 4444444321 011
Q ss_pred CCCCCcEEEecchh-hHHHHHHHHH
Q 003942 244 HAATRPVEIIGTLS-NIDKAEKLIN 267 (784)
Q Consensus 244 ~s~eR~V~I~G~~e-~V~kA~~~I~ 267 (784)
..-.-.|-|...++ .|..|++=+.
T Consensus 207 D~lkGyIYIEA~KqshV~~Ai~gv~ 231 (1024)
T KOG1999|consen 207 DHLKGYIYIEADKQSHVKEAIEGVR 231 (1024)
T ss_pred cccceeEEEEechhHHHHHHHhhhh
Confidence 11234566666443 4666665543
No 166
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=58.31 E-value=24 Score=39.46 Aligned_cols=57 Identities=25% Similarity=0.399 Sum_probs=48.3
Q ss_pred cCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHH--HHHHhh
Q 003942 207 PNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLIN--AVIAEA 273 (784)
Q Consensus 207 P~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~--elI~e~ 273 (784)
+.+.+-.|.|..+.+++.|++.+|+.|.... +.++|+|+...|+.|.+.|. +++...
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG----------~~~~i~g~~~~v~~A~~~l~~l~~~~~~ 80 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVARG----------EAVRIIGARPLVDVATRVLLTLELLAEV 80 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeCC----------ceEEEEechHHHHHHHHHHhHHHHHHHH
Confidence 3567788999999999999999999998874 57899999889999999988 655554
No 167
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=58.11 E-value=14 Score=40.67 Aligned_cols=32 Identities=38% Similarity=0.642 Sum_probs=25.3
Q ss_pred ccEEEEEecC-CceeeeecCCchHHHHHHHHhC
Q 003942 295 AEQVEIKVPN-EKVGLIIGRGGETIKGLQTRSG 326 (784)
Q Consensus 295 ~~~~~i~VP~-~~vG~VIGkgG~~IK~Iq~~SG 326 (784)
....++.+|. +..-+||||||..|++|-++.+
T Consensus 327 ~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 327 FIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 4456778888 5778899999999998866544
No 168
>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=56.71 E-value=34 Score=30.43 Aligned_cols=60 Identities=17% Similarity=0.147 Sum_probs=44.5
Q ss_pred cceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHh
Q 003942 211 VGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAE 272 (784)
Q Consensus 211 vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e 272 (784)
-|.|-| =..+++|-+..+++|.+...+...-...+.+++|.|+...|..|.+.+..+|..
T Consensus 27 ~gV~aG--~~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~~ 86 (88)
T PF02749_consen 27 DGVLAG--LEEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQR 86 (88)
T ss_dssp SEEE-S--HHHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred CEEEEC--HHHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHHH
Confidence 344543 477888999999999887543333334578999999999999999999988864
No 169
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=56.36 E-value=22 Score=37.45 Aligned_cols=31 Identities=19% Similarity=0.283 Sum_probs=25.8
Q ss_pred eEEEEEecCCccceeeccCcchHhhHHhhcC
Q 003942 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSG 230 (784)
Q Consensus 200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TG 230 (784)
...+|.|-..+-|.|||++|..|++|+++..
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 3467888888899999999999999987643
No 170
>COG0331 FabD (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]
Probab=55.85 E-value=48 Score=36.72 Aligned_cols=56 Identities=14% Similarity=0.272 Sum_probs=44.7
Q ss_pred ceeeeecCCchHHHHHHHHhCC--eEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 003942 306 KVGLIIGRGGETIKGLQTRSGA--RIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS 368 (784)
Q Consensus 306 ~vG~VIGkgG~~IK~Iq~~SGa--rIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~ 368 (784)
-+..|+|-.-+.|+++.++..- .|.|.+.+ .++.|.|+|.++.|++|..+++++=.
T Consensus 132 ~Maav~gl~~e~v~~~~~~~~~~~~v~iaN~N-------~~~QiVIsG~~~ale~a~~~~~~~g~ 189 (310)
T COG0331 132 GMAAVLGLDDEQVEKACEEAAQGTVVEIANYN-------SPGQIVISGTKEALEKAAEILKEAGA 189 (310)
T ss_pred cHHHHcCCCHHHHHHHHHHhccCCeEEEeeeC-------CCCcEEEECCHHHHHHHHHHHHHhhh
Confidence 4556777788899999988875 47776543 35889999999999999999987653
No 171
>KOG2038 consensus CAATT-binding transcription factor/60S ribosomal subunit biogenesis protein [Translation, ribosomal structure and biogenesis; Transcription]
Probab=54.63 E-value=12 Score=45.29 Aligned_cols=12 Identities=25% Similarity=0.493 Sum_probs=6.3
Q ss_pred hhhcCCCCchhh
Q 003942 18 KRKLDDLEPDEA 29 (784)
Q Consensus 18 krk~ed~~~~~~ 29 (784)
|.+.+|++.|+.
T Consensus 825 k~~~ed~~~Ee~ 836 (988)
T KOG2038|consen 825 KESAEDVDDEEF 836 (988)
T ss_pred hhhhccCchHHH
Confidence 333666665543
No 172
>CHL00048 rps3 ribosomal protein S3
Probab=53.54 E-value=18 Score=37.86 Aligned_cols=31 Identities=23% Similarity=0.300 Sum_probs=26.5
Q ss_pred ccEEEEEecCCceeeeecCCchHHHHHHHHh
Q 003942 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRS 325 (784)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~S 325 (784)
...+++.|-...-|.|||++|++|++|++..
T Consensus 65 ~~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 65 IDLIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred CCeEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 4567888888889999999999999998765
No 173
>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=52.69 E-value=23 Score=36.63 Aligned_cols=30 Identities=27% Similarity=0.484 Sum_probs=25.5
Q ss_pred eEEEEEecCCccceeeccCcchHhhHHhhc
Q 003942 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNS 229 (784)
Q Consensus 200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~T 229 (784)
...+|.|-..+-|.|||++|.+|++|+++.
T Consensus 38 ~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 38 LGTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred CcEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 457888888889999999999999988754
No 174
>COG1159 Era GTPase [General function prediction only]
Probab=52.06 E-value=27 Score=38.24 Aligned_cols=37 Identities=27% Similarity=0.474 Sum_probs=26.4
Q ss_pred eEEEEEecCC-ccceeeccCcchHhhHHh--------hcCCEEEEc
Q 003942 200 MSRKIEVPNN-KVGVLIGKAGDTIRYLQY--------NSGAKIQIT 236 (784)
Q Consensus 200 ~t~rI~VP~~-~vG~IIGkgG~tIK~Iq~--------~TGakI~V~ 236 (784)
+...|.|..+ .-+-||||+|++||+|-. -.+++|.+.
T Consensus 229 I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L~ 274 (298)
T COG1159 229 IHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYLE 274 (298)
T ss_pred EEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEEE
Confidence 4445677665 788999999999998744 455666553
No 175
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=50.95 E-value=30 Score=35.01 Aligned_cols=112 Identities=17% Similarity=0.144 Sum_probs=57.7
Q ss_pred cEEEec--chhhHHHHHHHHHHHHHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHH-h
Q 003942 249 PVEIIG--TLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTR-S 325 (784)
Q Consensus 249 ~V~I~G--~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~-S 325 (784)
.+.++| +.+++.+|++.+.++|++... ...... .....+...+..|.++-++-+..||-+.+++..==+. -
T Consensus 63 K~VcTGaKs~ed~~~av~~~~~~L~~~g~---~~~~~p---~i~iQNIVaSadL~~~lnL~~iA~~lg~e~~eYEPEqFP 136 (185)
T COG2101 63 KVVCTGAKSVEDVHRAVKKLAKKLKDGGI---DIDFEP---EIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFP 136 (185)
T ss_pred cEEEeccCcHHHHHHHHHHHHHHHHhcCc---CcCCCC---ceEEEEEEEEeccCccccHHHHHHhccccccccccccCC
Confidence 456666 778999999999999987321 100000 0001112223344445555555666655543211111 1
Q ss_pred CCeEEeccCCCCCCC--CCCceEEEEEcC--HHHHHHHHHHHHHHHhc
Q 003942 326 GARIQLIPQHLPEGD--GSKERIVRVTGD--MRQIEIAQEMIKEVLSQ 369 (784)
Q Consensus 326 GarIqI~~~~~p~~~--~~~er~V~I~Gt--~~qV~~Ak~lI~~~L~~ 369 (784)
|.--++..-. .- -=....+.|+|- .+.++.|.+.|.+.|++
T Consensus 137 GLVYRl~~P~---VV~LiF~SGK~ViTGaK~~ed~~~Av~~i~~~L~e 181 (185)
T COG2101 137 GLVYRLDEPR---VVLLLFGSGKLVITGAKSEEDAEQAVEKIQSRLEE 181 (185)
T ss_pred eeEEEcCCCC---EEEEEecCCcEEEecCCCHHHHHHHHHHHHHHHHH
Confidence 2211211100 00 001234678886 78999999999998875
No 176
>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=50.83 E-value=18 Score=38.72 Aligned_cols=30 Identities=23% Similarity=0.433 Sum_probs=23.3
Q ss_pred eEEEEEecCC-ccceeeccCcchHhhHHhhc
Q 003942 200 MSRKIEVPNN-KVGVLIGKAGDTIRYLQYNS 229 (784)
Q Consensus 200 ~t~rI~VP~~-~vG~IIGkgG~tIK~Iq~~T 229 (784)
+...|.|..+ .-+.||||+|++||+|..+.
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 5667777765 67889999999999886543
No 177
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=48.92 E-value=33 Score=38.39 Aligned_cols=56 Identities=18% Similarity=0.322 Sum_probs=46.8
Q ss_pred cCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHH--HHHhc
Q 003942 303 PNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIK--EVLSQ 369 (784)
Q Consensus 303 P~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~--~~L~~ 369 (784)
+++.+-.|.|..+.+++.|.+..|+.|... .+.++|+|+...|+.|..++. .++..
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 357778899999999999999999999863 457999999779999988888 55544
No 178
>PRK00089 era GTPase Era; Reviewed
Probab=48.58 E-value=25 Score=37.93 Aligned_cols=37 Identities=24% Similarity=0.469 Sum_probs=26.5
Q ss_pred eEEEEEecCC-ccceeeccCcchHhhHHh--------hcCCEEEEc
Q 003942 200 MSRKIEVPNN-KVGVLIGKAGDTIRYLQY--------NSGAKIQIT 236 (784)
Q Consensus 200 ~t~rI~VP~~-~vG~IIGkgG~tIK~Iq~--------~TGakI~V~ 236 (784)
+...|.|..+ ..+.||||+|++||+|.. -++++|.+.
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 4556666654 678899999999998854 456666553
No 179
>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=48.26 E-value=1.9e+02 Score=29.18 Aligned_cols=36 Identities=11% Similarity=0.125 Sum_probs=27.3
Q ss_pred CCEEEEccCCCCCCCCCCCcEEEec--chhhHHHHHHHHHHHHHhhh
Q 003942 230 GAKIQITRDADADPHAATRPVEIIG--TLSNIDKAEKLINAVIAEAD 274 (784)
Q Consensus 230 GakI~V~~~~~~~p~s~eR~V~I~G--~~e~V~kA~~~I~elI~e~~ 274 (784)
.+.+.|... ..|.|+| +.+.+.+|++.|.++|++..
T Consensus 47 ~~t~lIf~s---------GKivitGaks~~~~~~a~~~~~~~L~~~g 84 (174)
T cd00652 47 KTTALIFSS---------GKMVITGAKSEEDAKLAARKYARILQKLG 84 (174)
T ss_pred cEEEEEECC---------CEEEEEecCCHHHHHHHHHHHHHHHHHcC
Confidence 455666643 3678888 68899999999999998753
No 180
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=47.58 E-value=35 Score=34.03 Aligned_cols=90 Identities=19% Similarity=0.203 Sum_probs=53.1
Q ss_pred eeecCchhchhhhhhhhhHhhhc---CCCCCCCCCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCC
Q 003942 164 EETVKEEESVEPSNVVPQQVVDN---SKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDAD 240 (784)
Q Consensus 164 ~~i~G~~e~Ve~A~~lI~~ii~~---~~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~ 240 (784)
+.+.++...+++..+.|.++++- .+++....-......++|.++. ..-..|.+|.+.++++|.=...
T Consensus 47 i~V~~d~~~i~qi~kQl~Kli~V~~V~~~~~~~~v~rEl~LiKv~~~~--------~~r~~i~~i~~~f~a~ivdv~~-- 116 (157)
T TIGR00119 47 IVVVGDDKVLEQITKQLNKLVDVIKVSDLTESAIVERELCLVKVSAPG--------EGRDEIIRLTNIFRGRIVDVSP-- 116 (157)
T ss_pred EEEECCHHHHHHHHHHHhcCccEEEEEecCCCcceeeEEEEEEEECCc--------cCHHHHHHHHHHhCCEEEEecC--
Confidence 34456777777777777777751 1111111101111222222222 2345688999999999864422
Q ss_pred CCCCCCCCcEEEecchhhHHHHHHHHHH
Q 003942 241 ADPHAATRPVEIIGTLSNIDKAEKLINA 268 (784)
Q Consensus 241 ~~p~s~eR~V~I~G~~e~V~kA~~~I~e 268 (784)
..-+|.++|+.+.|+.-++++..
T Consensus 117 -----~~~~ie~tG~~~ki~~~~~~l~~ 139 (157)
T TIGR00119 117 -----DSYTVEVTGDSDKIDAFLELLRP 139 (157)
T ss_pred -----CEEEEEEcCCHHHHHHHHHHhhh
Confidence 24589999999998877776655
No 181
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=47.45 E-value=38 Score=33.97 Aligned_cols=91 Identities=16% Similarity=0.142 Sum_probs=56.0
Q ss_pred eeeecCchhchhhhhhhhhHhhhcC---CCCCCCCCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCC
Q 003942 163 EEETVKEEESVEPSNVVPQQVVDNS---KSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDA 239 (784)
Q Consensus 163 ~~~i~G~~e~Ve~A~~lI~~ii~~~---~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~ 239 (784)
.+.+.++.+.+++..+.|.++++-. +++....-......++|.+... .-..|.+|.+.++++|.=...
T Consensus 47 ti~V~~~~~~i~qi~kQl~KLidV~~V~~~~~~~~v~rEl~LiKv~~~~~--------~r~~i~~i~~~f~a~ivdv~~- 117 (161)
T PRK11895 47 TIVTSGDEQVIEQITKQLNKLIDVLKVVDLTEEAHVERELALVKVRASGE--------NRAEILRLADIFRAKIVDVTP- 117 (161)
T ss_pred EEEEECCHHHHHHHHHHHhccccEEEEEecCCcchhheEEEEEEEECCcc--------cHHHHHHHHHHhCCEEEEecC-
Confidence 3555678888998888888877521 1111111111122333333222 235688999999999864422
Q ss_pred CCCCCCCCCcEEEecchhhHHHHHHHHHH
Q 003942 240 DADPHAATRPVEIIGTLSNIDKAEKLINA 268 (784)
Q Consensus 240 ~~~p~s~eR~V~I~G~~e~V~kA~~~I~e 268 (784)
..-+|.++|+.+.|+.-++++..
T Consensus 118 ------~~~~iE~tG~~~ki~~~~~~l~~ 140 (161)
T PRK11895 118 ------ESLTIEVTGDSDKIDAFIDLLRP 140 (161)
T ss_pred ------CEEEEEEeCCHHHHHHHHHHhhh
Confidence 24689999999998877776654
No 182
>PRK15494 era GTPase Era; Provisional
Probab=45.29 E-value=24 Score=39.38 Aligned_cols=37 Identities=19% Similarity=0.336 Sum_probs=27.0
Q ss_pred eEEEEEecCC-ccceeeccCcchHhhHHh--------hcCCEEEEc
Q 003942 200 MSRKIEVPNN-KVGVLIGKAGDTIRYLQY--------NSGAKIQIT 236 (784)
Q Consensus 200 ~t~rI~VP~~-~vG~IIGkgG~tIK~Iq~--------~TGakI~V~ 236 (784)
+...|.|... .-+.||||+|++||+|.. -++++|.+.
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 4566777765 678899999999998854 456666553
No 183
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=45.11 E-value=26 Score=36.66 Aligned_cols=30 Identities=20% Similarity=0.589 Sum_probs=25.3
Q ss_pred cEEEEEecCCceeeeecCCchHHHHHHHHh
Q 003942 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRS 325 (784)
Q Consensus 296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~S 325 (784)
..++|.|-..+-|.|||++|++|++|++..
T Consensus 62 ~~i~I~I~~~~pg~vIG~~g~~i~~l~~~l 91 (211)
T TIGR01009 62 DKIRVTIHTARPGIVIGKKGSEIEKLRKDL 91 (211)
T ss_pred CceEEEEEeCCCcceeCCCchHHHHHHHHH
Confidence 347788888888999999999999998554
No 184
>CHL00048 rps3 ribosomal protein S3
Probab=44.34 E-value=52 Score=34.47 Aligned_cols=30 Identities=23% Similarity=0.169 Sum_probs=25.6
Q ss_pred eEEEEEecCCccceeeccCcchHhhHHhhc
Q 003942 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNS 229 (784)
Q Consensus 200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~T 229 (784)
...+|.|-..+-|.|||++|.+|++|++..
T Consensus 66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 66 DLIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred CeEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 456777888889999999999999998765
No 185
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=43.47 E-value=42 Score=32.93 Aligned_cols=44 Identities=23% Similarity=0.276 Sum_probs=36.4
Q ss_pred chHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHh
Q 003942 220 DTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAE 272 (784)
Q Consensus 220 ~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e 272 (784)
+.+..|.+-.|+.|.+... .+|.|.|+.+.|.+|++.|..+.++
T Consensus 126 eRlqDi~E~hgvIiE~~E~---------D~V~i~Gd~drVk~aLke~~~~wke 169 (170)
T COG4010 126 ERLQDIAETHGVIIEFEEY---------DLVAIYGDSDRVKKALKEIGSFWKE 169 (170)
T ss_pred HHHHHHHHhhheeEEeeec---------cEEEEeccHHHHHHHHHHHHHHHhc
Confidence 5677788888888888732 4899999999999999999988654
No 186
>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=43.06 E-value=2.8e+02 Score=28.09 Aligned_cols=36 Identities=11% Similarity=0.180 Sum_probs=26.9
Q ss_pred cCCEEEEccCCCCCCCCCCCcEEEec--chhhHHHHHHHHHHHHHhh
Q 003942 229 SGAKIQITRDADADPHAATRPVEIIG--TLSNIDKAEKLINAVIAEA 273 (784)
Q Consensus 229 TGakI~V~~~~~~~p~s~eR~V~I~G--~~e~V~kA~~~I~elI~e~ 273 (784)
..|.+.|... ..|.|+| +.+.+.+|++.|.++|++.
T Consensus 46 Pk~t~lIF~s---------GKiviTGaks~~~~~~a~~~~~~~l~~~ 83 (174)
T cd04517 46 PRATASVWSS---------GKITITGATSEEEAKQAARRAARLLQKL 83 (174)
T ss_pred CcEEEEEECC---------CeEEEEccCCHHHHHHHHHHHHHHHHHc
Confidence 3455666643 3678888 5789999999999998875
No 187
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=42.26 E-value=17 Score=37.80 Aligned_cols=29 Identities=28% Similarity=0.471 Sum_probs=23.6
Q ss_pred EEEEecCCccceeeccCcchHhhHHhhcC
Q 003942 202 RKIEVPNNKVGVLIGKAGDTIRYLQYNSG 230 (784)
Q Consensus 202 ~rI~VP~~~vG~IIGkgG~tIK~Iq~~TG 230 (784)
.+|.|-..+-|.|||++|++|++|++...
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 55566668899999999999999987654
No 188
>KOG0699 consensus Serine/threonine protein phosphatase [Signal transduction mechanisms]
Probab=41.08 E-value=24 Score=39.43 Aligned_cols=18 Identities=11% Similarity=0.099 Sum_probs=8.7
Q ss_pred cceeeccCcchHhhHHhhc
Q 003942 211 VGVLIGKAGDTIRYLQYNS 229 (784)
Q Consensus 211 vG~IIGkgG~tIK~Iq~~T 229 (784)
|..+|- +++.+..|+++.
T Consensus 459 vr~~l~-~n~~ls~iceeL 476 (542)
T KOG0699|consen 459 VRDLLA-KNSSLSEICEEL 476 (542)
T ss_pred HHHHHh-cCchHHHHHHHH
Confidence 333444 335555665553
No 189
>KOG0262 consensus RNA polymerase I, large subunit [Transcription]
Probab=39.92 E-value=36 Score=43.60 Aligned_cols=16 Identities=13% Similarity=0.202 Sum_probs=10.5
Q ss_pred hhHHHHHHHHHHHHHh
Q 003942 257 SNIDKAEKLINAVIAE 272 (784)
Q Consensus 257 e~V~kA~~~I~elI~e 272 (784)
-.|+.|++.|..-|..
T Consensus 1529 yGVEAar~~Iv~Ev~~ 1544 (1640)
T KOG0262|consen 1529 YGVEAARNAIVNEVNN 1544 (1640)
T ss_pred hhHHHHHHHHHHHHHH
Confidence 4578887777665554
No 190
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.55 E-value=7.1e+02 Score=29.17 Aligned_cols=22 Identities=0% Similarity=-0.050 Sum_probs=10.0
Q ss_pred eeeccccccccccCCCchhhhh
Q 003942 120 SVEEQASVDNQQISVKEETKEV 141 (784)
Q Consensus 120 ki~iP~~~vg~iIGk~Ge~Ik~ 141 (784)
.|.|+.+..-+-+|+--..++.
T Consensus 199 ~i~l~e~~~~~plG~V~svv~~ 220 (483)
T KOG2236|consen 199 EITLEEKGELLPLGKVSSVVDQ 220 (483)
T ss_pred ceeecCCcceechhHHHHHhhh
Confidence 3444444444555554333333
No 191
>PRK05848 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=38.42 E-value=1.7e+02 Score=31.79 Aligned_cols=159 Identities=16% Similarity=0.134 Sum_probs=87.1
Q ss_pred EEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhc-------
Q 003942 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADA------- 275 (784)
Q Consensus 203 rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~------- 275 (784)
++.|-...-|.|-| -..+++|-+..+++|.+...+...-...+.+++|.|....|..+.+.+..+|.....
T Consensus 32 ~a~i~ar~~~v~~G--~~~a~~i~~~l~~~~~~~~~dG~~v~~g~~i~~i~G~a~~ll~~Er~~ln~l~~~SGIAT~t~~ 109 (273)
T PRK05848 32 TAKIIAKSEGVFSG--EKYALELLEMTGIECVFTIKDGERFKKGDILMEIEGDFSMLLKVERTLLNLLQHSSGIATLTSR 109 (273)
T ss_pred EEEEEEcCCEEEEC--HHHHHHHHHHcCCEEEEEcCCCCEecCCCEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333334444433 366788888889888766543333345678999999999999999988887765320
Q ss_pred -----CCCCc-cc-ccccchh------hc--cCC------ccEEEEEecCCceeeeecCCchHHHHHHHHhC--CeEEec
Q 003942 276 -----GGSPS-LV-ARGLATA------QA--SGA------AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSG--ARIQLI 332 (784)
Q Consensus 276 -----~g~p~-~~-~~g~~~~------~~--~~~------~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SG--arIqI~ 332 (784)
.+... +. .|-..+. .+ ..+ .-...++|-.|++.+. |.=-+.|++|+++.. .+|.+.
T Consensus 110 ~v~~~~~~~~~i~~TRKt~Pg~r~~~k~Av~~GGg~~HR~gL~d~vlikdnHi~~~-g~i~~~v~~~k~~~p~~~~I~VE 188 (273)
T PRK05848 110 YVEALESHKVKLLDTRKTRPLLRIFEKYSVRNGGASNHRLGLDDCLMLKDTHLKHI-KDLKEFIQHARKNIPFTAKIEIE 188 (273)
T ss_pred HHHHhcCCCeEEEecCCCCcchhHHHHHHHHhCCCccccCCchhhhCcCHHHHHHH-CcHHHHHHHHHHhCCCCceEEEE
Confidence 11111 11 1111110 00 011 1223456666665443 433477899998876 567765
Q ss_pred cCCCCCC---CCCCceEEEEEcC-HHHHHHHHHHHH
Q 003942 333 PQHLPEG---DGSKERIVRVTGD-MRQIEIAQEMIK 364 (784)
Q Consensus 333 ~~~~p~~---~~~~er~V~I~Gt-~~qV~~Ak~lI~ 364 (784)
-+.+-.. ....-.+|.+... .+.+.++.+++.
T Consensus 189 v~tleea~~A~~~GaDiI~LDn~~~e~l~~~v~~~~ 224 (273)
T PRK05848 189 CESLEEAKNAMNAGADIVMCDNMSVEEIKEVVAYRN 224 (273)
T ss_pred eCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHhh
Confidence 4331100 0111235556554 777777777653
No 192
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=38.29 E-value=66 Score=33.64 Aligned_cols=29 Identities=24% Similarity=0.509 Sum_probs=24.4
Q ss_pred EEEEEecCCccceeeccCcchHhhHHhhc
Q 003942 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNS 229 (784)
Q Consensus 201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~T 229 (784)
.++|.|-..+-+.|||++|.+|++|++..
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 36788888888999999999999998654
No 193
>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=38.05 E-value=1.2e+02 Score=30.68 Aligned_cols=101 Identities=12% Similarity=0.084 Sum_probs=53.7
Q ss_pred ceeeecC--chhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCC
Q 003942 162 KEEETVK--EEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDA 239 (784)
Q Consensus 162 r~~~i~G--~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~ 239 (784)
-.+.++| +.+.+..|.+.|.++|........ ....++++-.|-...++.= -.++.|-...+..+....+
T Consensus 56 GKivitGaks~~~~~~a~~~~~~~L~~~g~~~~---~~~~~~v~NIvas~~l~~~-----i~L~~la~~~~~~~~YePe- 126 (174)
T cd00652 56 GKMVITGAKSEEDAKLAARKYARILQKLGFPVE---KFPEFKVQNIVASCDLGFP-----IRLEELALKHPENASYEPE- 126 (174)
T ss_pred CEEEEEecCCHHHHHHHHHHHHHHHHHcCCCcc---ccCceEEEEEEEEEECCCc-----ccHHHHHhhhhcccEECCc-
Confidence 3456666 467777788888888865544331 1123344444433333332 2355555444322222211
Q ss_pred CCCC---------CC-----CCCcEEEec--chhhHHHHHHHHHHHHHh
Q 003942 240 DADP---------HA-----ATRPVEIIG--TLSNIDKAEKLINAVIAE 272 (784)
Q Consensus 240 ~~~p---------~s-----~eR~V~I~G--~~e~V~kA~~~I~elI~e 272 (784)
..| .. ....|.|+| +.+.+.+|++.|..+|.+
T Consensus 127 -~fpgli~r~~~pk~t~lIF~sGkvvitGaks~~~~~~a~~~i~~~L~~ 174 (174)
T cd00652 127 -LFPGLIYRMDEPKVVLLIFVSGKIVITGAKSREDIYEAVEKIYPILKE 174 (174)
T ss_pred -cCceEEEEecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHHHHHhC
Confidence 111 11 134668888 567899999999988753
No 194
>KOG0262 consensus RNA polymerase I, large subunit [Transcription]
Probab=37.89 E-value=16 Score=46.58 Aligned_cols=10 Identities=10% Similarity=0.371 Sum_probs=5.6
Q ss_pred eEEEEEecCC
Q 003942 200 MSRKIEVPNN 209 (784)
Q Consensus 200 ~t~rI~VP~~ 209 (784)
++++|.+|..
T Consensus 1443 cev~~~lp~~ 1452 (1640)
T KOG0262|consen 1443 CEVELKLPLD 1452 (1640)
T ss_pred EEEEEEecCC
Confidence 5555555554
No 195
>PRK05848 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=37.60 E-value=2.8e+02 Score=30.25 Aligned_cols=68 Identities=13% Similarity=0.178 Sum_probs=46.9
Q ss_pred EEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 003942 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS 368 (784)
Q Consensus 298 ~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~ 368 (784)
.++.|-.+.-|.|- |-..+++|-+..+|+|.+....- ..-...+.+++|.|....+..+.+.+..+|.
T Consensus 31 ~~a~i~ar~~~v~~--G~~~a~~i~~~l~~~~~~~~~dG-~~v~~g~~i~~i~G~a~~ll~~Er~~ln~l~ 98 (273)
T PRK05848 31 ATAKIIAKSEGVFS--GEKYALELLEMTGIECVFTIKDG-ERFKKGDILMEIEGDFSMLLKVERTLLNLLQ 98 (273)
T ss_pred EEEEEEEcCCEEEE--CHHHHHHHHHHcCCEEEEEcCCC-CEecCCCEEEEEEECHHHHHHHHHHHHHHHH
Confidence 34444444445453 45678899899999887653210 1123467899999999999999998887775
No 196
>PRK06559 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=36.45 E-value=3.1e+02 Score=30.17 Aligned_cols=66 Identities=12% Similarity=0.233 Sum_probs=45.7
Q ss_pred EEEecCCceeeeecCCchHHHHHHHHhCCeEEec-----cCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 003942 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLI-----PQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS 368 (784)
Q Consensus 299 ~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~-----~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~ 368 (784)
++.|-.+.-|.|= |-+.+++|-+..++.+.+. ++. ..-...+.+++|.|+...+..+.+.+..+|+
T Consensus 43 ~~~~~are~gvla--G~~~a~~if~~l~~~~~~~~~~~~~dG--~~v~~G~~i~~v~G~a~~ll~~ER~alN~l~ 113 (290)
T PRK06559 43 KVSLFAKEAGVLA--GLTVFQRVFTLFDAEVTFQNPHQFKDG--DRLTSGDLVLEIIGSVRSLLTCERVALNFLQ 113 (290)
T ss_pred EEEEEecCCeEEE--CHHHHHHHHHHhCCcEEEEEeecCCCC--CEecCCCEEEEEEECHHHHHHHHHHHHHHHH
Confidence 3333333334443 4567888999999988875 332 2223467899999999999999888887765
No 197
>PRK08385 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=35.94 E-value=2e+02 Score=31.46 Aligned_cols=53 Identities=17% Similarity=0.236 Sum_probs=40.4
Q ss_pred chHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHh
Q 003942 220 DTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAE 272 (784)
Q Consensus 220 ~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e 272 (784)
..+.+|-+..+++|.+...+...-...+.+++|.|....|..+.+.++.+|..
T Consensus 47 ~~a~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~~~~ll~~Er~~ln~l~~ 99 (278)
T PRK08385 47 EEAKALFEHFGVKVEVRKRDGEEVKAGEVILELKGNARAILLVERTALNIIGR 99 (278)
T ss_pred HHHHHHHHHcCCEEEEEcCCCCEecCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 56678888889999885433223345678999999999999999888877754
No 198
>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=35.94 E-value=1.8e+02 Score=31.51 Aligned_cols=69 Identities=14% Similarity=0.143 Sum_probs=46.3
Q ss_pred EEEecCCccceeeccCcchHhhHHhhc-CCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942 203 KIEVPNNKVGVLIGKAGDTIRYLQYNS-GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA 273 (784)
Q Consensus 203 rI~VP~~~vG~IIGkgG~tIK~Iq~~T-GakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~ 273 (784)
++.|-...-+.|-| =+.+++|-+.. +++|.+...+...-...+.+++|.|....+..+.+.++.+|...
T Consensus 30 ~~~i~~r~~~v~~G--~~~~~~i~~~~~~~~v~~~~~dG~~v~~g~~i~~i~G~~~~l~~~Er~~ln~L~~~ 99 (269)
T cd01568 30 TATLIAKEEGVLAG--LEVAEEVFELLDGIEVEWLVKDGDRVEAGQVLLEVEGPARSLLTAERVALNLLQRL 99 (269)
T ss_pred EEEEEecCCEEEEC--HHHHHHHHHHhCCeEEEEEeCCCCEecCCCEEEEEEEcHHHHHHHHHHHHHHHHHH
Confidence 33333334455544 36677888887 88885443322233456889999999999999999988887653
No 199
>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=35.84 E-value=3.1e+02 Score=29.62 Aligned_cols=68 Identities=13% Similarity=0.239 Sum_probs=46.2
Q ss_pred EEEEecCCceeeeecCCchHHHHHHHHh-CCeEEec-cCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942 298 VEIKVPNEKVGLIIGRGGETIKGLQTRS-GARIQLI-PQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 369 (784)
Q Consensus 298 ~~i~VP~~~vG~VIGkgG~~IK~Iq~~S-GarIqI~-~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~ 369 (784)
.++.|-.+.-+.|-| =+.+++|-+.. +++|.+. ++. ..-...+.+++|+|+...+..+.+.+..+|..
T Consensus 29 ~~~~i~~r~~~v~~G--~~~~~~i~~~~~~~~v~~~~~dG--~~v~~g~~i~~i~G~~~~l~~~Er~~ln~L~~ 98 (269)
T cd01568 29 ATATLIAKEEGVLAG--LEVAEEVFELLDGIEVEWLVKDG--DRVEAGQVLLEVEGPARSLLTAERVALNLLQR 98 (269)
T ss_pred EEEEEEecCCEEEEC--HHHHHHHHHHhCCeEEEEEeCCC--CEecCCCEEEEEEEcHHHHHHHHHHHHHHHHH
Confidence 344444444455544 56778888888 8888544 332 11235688999999999999999988887753
No 200
>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=35.30 E-value=63 Score=32.50 Aligned_cols=57 Identities=14% Similarity=0.138 Sum_probs=43.1
Q ss_pred CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHH
Q 003942 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIA 271 (784)
Q Consensus 199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~ 271 (784)
..+.||.++.... =+.+..|.+-.|+-|.+.. +..|.|.|..+.|.+|++.+..+.+
T Consensus 112 ~~~iRv~l~~~i~-------~erl~ei~E~~gvI~Efee---------~~~V~I~Gdke~Ik~aLKe~s~~wk 168 (169)
T PF09869_consen 112 FETIRVKLKKPIQ-------EERLQEISEWHGVIFEFEE---------DDKVVIEGDKERIKKALKEFSSFWK 168 (169)
T ss_pred ceeEEEecCccch-------HHHHHHHHHHhceeEEecC---------CcEEEEeccHHHHHHHHHHHHHHhc
Confidence 3455666655443 3567889999999999832 3479999999999999999887654
No 201
>PLN00062 TATA-box-binding protein; Provisional
Probab=35.14 E-value=3.4e+02 Score=27.66 Aligned_cols=27 Identities=30% Similarity=0.249 Sum_probs=22.0
Q ss_pred eEEEEEcC--HHHHHHHHHHHHHHHhccc
Q 003942 345 RIVRVTGD--MRQIEIAQEMIKEVLSQTV 371 (784)
Q Consensus 345 r~V~I~Gt--~~qV~~Ak~lI~~~L~~~~ 371 (784)
..|+|+|. .+.++.|.+.|..+|.+.+
T Consensus 147 GkvvitGaks~~~~~~ai~~i~p~L~~~~ 175 (179)
T PLN00062 147 GKIVITGAKVREEIYTAFENIYPVLTEFR 175 (179)
T ss_pred CEEEEEecCCHHHHHHHHHHHHHHHHHhc
Confidence 46888887 6789999999999987654
No 202
>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=34.94 E-value=2.3e+02 Score=31.01 Aligned_cols=146 Identities=16% Similarity=0.122 Sum_probs=82.0
Q ss_pred cchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhh-------------cCCCC--ccc-
Q 003942 219 GDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD-------------AGGSP--SLV- 282 (784)
Q Consensus 219 G~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~-------------~~g~p--~~~- 282 (784)
-..+++|.+..+++|.+...+...-...+.++++.|....|..+.+.+..+|.... ....+ .+.
T Consensus 48 ~~~~~~i~~~l~~~~~~~~~dG~~v~~g~~i~~~~G~a~~ll~~eR~alN~l~~~SGIAT~T~~~V~~~~~~~~~~~I~~ 127 (277)
T TIGR01334 48 VSEAAKLLKQLGASIDYAVPSGSRALAGTLLLEAKGSAGQLHQGWKSAQSVLEWSCGVATYTHKMVTLAKKISPMAVVAC 127 (277)
T ss_pred HHHHHHHHHHcCCEEEEEeCCCCEeCCCCEEEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCEEEe
Confidence 36788999999999988765443444567899999999999999988887775432 00001 011
Q ss_pred ccccchh------hc--cCCc------cEEEEEecCCceeeeec--CCchHHHHHHHHh-CCeEEeccCCCCC---CCCC
Q 003942 283 ARGLATA------QA--SGAA------EQVEIKVPNEKVGLIIG--RGGETIKGLQTRS-GARIQLIPQHLPE---GDGS 342 (784)
Q Consensus 283 ~~g~~~~------~~--~~~~------~~~~i~VP~~~vG~VIG--kgG~~IK~Iq~~S-GarIqI~~~~~p~---~~~~ 342 (784)
.|-..+. .+ ..+. -...++|-.|++.++=+ .=.+.|+.+++.. ..+|.|.-+.+.. .-..
T Consensus 128 TRKT~Pg~R~l~k~Av~~GGg~~HR~gLsd~ilikdnHi~~~g~~~~i~~av~~~r~~~~~~kIeVEv~tleea~ea~~~ 207 (277)
T TIGR01334 128 TRKAIPLTRPLAVKAVLAAGGVIHRIGLSETLLVFANHRTFLNDNFDWGGAIGRLKQTAPERKITVEADTIEQALTVLQA 207 (277)
T ss_pred cCCCCCChhHHHHHHHHhCCCcCeecCCchhheehHHHHHHhCCcccHHHHHHHHHHhCCCCCEEEECCCHHHHHHHHHc
Confidence 1110000 00 0111 12345666676665421 2235677888764 3567765332100 0012
Q ss_pred CceEEEEEcC-HHHHHHHHHHHH
Q 003942 343 KERIVRVTGD-MRQIEIAQEMIK 364 (784)
Q Consensus 343 ~er~V~I~Gt-~~qV~~Ak~lI~ 364 (784)
.-.+|.+..- ++.+..+.++|.
T Consensus 208 GaDiI~lDn~~~e~l~~~v~~l~ 230 (277)
T TIGR01334 208 SPDILQLDKFTPQQLHHLHERLK 230 (277)
T ss_pred CcCEEEECCCCHHHHHHHHHHHh
Confidence 2334555553 788888877764
No 203
>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=34.77 E-value=3.5e+02 Score=29.27 Aligned_cols=67 Identities=13% Similarity=0.219 Sum_probs=45.6
Q ss_pred EEEecCCceeeeecCCchHHHHHHHHh--CCeEEec-cCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942 299 EIKVPNEKVGLIIGRGGETIKGLQTRS--GARIQLI-PQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 369 (784)
Q Consensus 299 ~i~VP~~~vG~VIGkgG~~IK~Iq~~S--GarIqI~-~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~ 369 (784)
++.|-.+.-+.|- |-+.+++|-+.. +++|.+. ++. ..-...+.+++|.|....+..+.+.+..+|+-
T Consensus 30 ~~~~~ar~~~v~~--G~~~~~~i~~~~~~~l~v~~~~~dG--~~v~~g~~i~~i~G~~~~ll~~Er~~ln~L~~ 99 (268)
T cd01572 30 EARLIAKEEGVLA--GLPVAEEVFELLDPGIEVEWLVKDG--DRVEPGQVLATVEGPARSLLTAERTALNFLQR 99 (268)
T ss_pred EEEEEEcCCEEEE--CHHHHHHHHHHcCCCeEEEEEeCCC--CEecCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 3333333334444 456788888888 8888554 322 11235688999999999999999998887753
No 204
>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=34.67 E-value=2e+02 Score=31.14 Aligned_cols=62 Identities=13% Similarity=0.080 Sum_probs=43.8
Q ss_pred ccceeeccCcchHhhHHhhc--CCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942 210 KVGVLIGKAGDTIRYLQYNS--GAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA 273 (784)
Q Consensus 210 ~vG~IIGkgG~tIK~Iq~~T--GakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~ 273 (784)
.-+.|-| -+.+++|-+.. +++|.+...+...-...+.+++|.|....+..+.+.+..+|...
T Consensus 37 ~~~v~~G--~~~~~~i~~~~~~~l~v~~~~~dG~~v~~g~~i~~i~G~~~~ll~~Er~~ln~L~~~ 100 (268)
T cd01572 37 EEGVLAG--LPVAEEVFELLDPGIEVEWLVKDGDRVEPGQVLATVEGPARSLLTAERTALNFLQRL 100 (268)
T ss_pred CCEEEEC--HHHHHHHHHHcCCCeEEEEEeCCCCEecCCCEEEEEEECHHHHHHHHHHHHHHHHHH
Confidence 3344443 36778888888 88885553322233456889999999999999999988887653
No 205
>COG2090 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.55 E-value=3e+02 Score=26.89 Aligned_cols=61 Identities=16% Similarity=0.223 Sum_probs=40.2
Q ss_pred CeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHH
Q 003942 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLIN 267 (784)
Q Consensus 199 ~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~ 267 (784)
.+.+.|.++ ..+-.|||++=.. |.-++..+|.+.+.+ -...|.|.|..++..-+.-+++|+
T Consensus 63 ~i~vvi~~~-~~~D~viG~Ghp~---ltl~~~~~mV~RkS~----yv~~rTl~I~adKAA~DldR~lV~ 123 (141)
T COG2090 63 RIRVVIRVG-GLVDEVIGRGHPR---LTLEHPTSMVFRKSD----YVDDRTLMIRADKAAADLDRELVE 123 (141)
T ss_pred eEEEEEEcC-CcEEEEEeecCCC---cccCCCceEEEEecC----cccCceEEEecchhhhhhhHHHHH
Confidence 366677777 7888899987443 445677888888754 234688999877654443334333
No 206
>COG5014 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=34.52 E-value=81 Score=32.11 Aligned_cols=102 Identities=18% Similarity=0.260 Sum_probs=0.0
Q ss_pred chHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccchhhccCCccEEE
Q 003942 220 DTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVE 299 (784)
Q Consensus 220 ~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~ 299 (784)
+.+.+|.++-|+ ..|.|+|..--+.+ +.|+++|+
T Consensus 81 eRL~ei~K~~g~----------------d~vRiSG~EP~l~~--EHvlevIe---------------------------- 114 (228)
T COG5014 81 ERLLEISKKRGC----------------DLVRISGAEPILGR--EHVLEVIE---------------------------- 114 (228)
T ss_pred HHHHHHHHhcCC----------------cEEEeeCCCccccH--HHHHHHHH----------------------------
Q ss_pred EEecCCce----eeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhcccC
Q 003942 300 IKVPNEKV----GLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEVLSQTVR 372 (784)
Q Consensus 300 i~VP~~~v----G~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~L~~~~r 372 (784)
+.+-+.+| |.|||-+-+.++++-+.-++.|.|+-.... .+..+.|+|- ++-...-.+.+.-++.+..+
T Consensus 115 Ll~~~tFvlETNG~~~g~drslv~el~nr~nv~vRVsvKG~d-----pesF~kIT~asp~~F~~QL~aLr~L~~~g~r 187 (228)
T COG5014 115 LLVNNTFVLETNGLMFGFDRSLVDELVNRLNVLVRVSVKGWD-----PESFEKITGASPEYFRYQLKALRHLHGKGHR 187 (228)
T ss_pred hccCceEEEEeCCeEEecCHHHHHHHhcCCceEEEEEecCCC-----HHHHHHHhcCChHHHHHHHHHHHHHHhcCce
No 207
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=34.37 E-value=45 Score=35.42 Aligned_cols=30 Identities=23% Similarity=0.582 Sum_probs=25.1
Q ss_pred cEEEEEecCCceeeeecCCchHHHHHHHHh
Q 003942 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRS 325 (784)
Q Consensus 296 ~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~S 325 (784)
..++|.|-...-+.|||++|..|++|++..
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 457777777888999999999999887664
No 208
>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=34.07 E-value=4.4e+02 Score=26.73 Aligned_cols=36 Identities=11% Similarity=0.086 Sum_probs=26.4
Q ss_pred cCCEEEEccCCCCCCCCCCCcEEEec--chhhHHHHHHHHHHHHHhh
Q 003942 229 SGAKIQITRDADADPHAATRPVEIIG--TLSNIDKAEKLINAVIAEA 273 (784)
Q Consensus 229 TGakI~V~~~~~~~p~s~eR~V~I~G--~~e~V~kA~~~I~elI~e~ 273 (784)
-.+.+.|... ..+.|+| +.+.+.+|++.|.++|++.
T Consensus 46 Pk~t~lIF~S---------GKiviTGaks~e~a~~a~~~i~~~L~~~ 83 (174)
T cd04516 46 PKTTALIFSS---------GKMVCTGAKSEDDSKLAARKYARIIQKL 83 (174)
T ss_pred CcEEEEEECC---------CeEEEEecCCHHHHHHHHHHHHHHHHHc
Confidence 3455666543 3678887 6778999999999988875
No 209
>PLN00062 TATA-box-binding protein; Provisional
Probab=33.91 E-value=1.8e+02 Score=29.74 Aligned_cols=26 Identities=27% Similarity=0.226 Sum_probs=21.5
Q ss_pred CcEEEec--chhhHHHHHHHHHHHHHhh
Q 003942 248 RPVEIIG--TLSNIDKAEKLINAVIAEA 273 (784)
Q Consensus 248 R~V~I~G--~~e~V~kA~~~I~elI~e~ 273 (784)
..|.|+| +.+.+.+|++.|..+|.+.
T Consensus 147 GkvvitGaks~~~~~~ai~~i~p~L~~~ 174 (179)
T PLN00062 147 GKIVITGAKVREEIYTAFENIYPVLTEF 174 (179)
T ss_pred CEEEEEecCCHHHHHHHHHHHHHHHHHh
Confidence 3667887 5688999999999999875
No 210
>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=33.47 E-value=2.3e+02 Score=30.76 Aligned_cols=53 Identities=9% Similarity=0.102 Sum_probs=39.9
Q ss_pred chHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHh
Q 003942 220 DTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAE 272 (784)
Q Consensus 220 ~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e 272 (784)
+.+++|-+..+++|.+...+...-...+.+++|.|....+..+.+.++.+|..
T Consensus 45 ~~~~~~~~~~~~~v~~~~~dG~~v~~g~~i~~i~G~~~~ll~~Er~~ln~l~~ 97 (272)
T cd01573 45 EEAARILELLGLEVDLAAASGSRVAAGAVLLEAEGPAAALHLGWKVAQTLLEW 97 (272)
T ss_pred HHHHHHHHHcCcEEEEEcCCCCEecCCCEEEEEEEcHHHHHHHHHHHHHHHHH
Confidence 56788888889888754332222345578999999999999999888877754
No 211
>COG2985 Predicted permease [General function prediction only]
Probab=32.83 E-value=90 Score=36.58 Aligned_cols=97 Identities=18% Similarity=0.287 Sum_probs=60.2
Q ss_pred CcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHH-HHhC
Q 003942 248 RPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQ-TRSG 326 (784)
Q Consensus 248 R~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq-~~SG 326 (784)
..+++.|.++.++++...|-+.+..... ......+.|+.|-++.| . |++|++|. .+.|
T Consensus 254 d~l~lVG~~~~l~r~~~~~G~evd~~~~---------------~~~~l~~~rivVtn~~v---l---Gk~l~~L~~~~~g 312 (544)
T COG2985 254 DELHLVGYPDALARLDLRIGKEVDDRLL---------------LDTRLRTERVVVTNENV---L---GKRLRDLNLTEYG 312 (544)
T ss_pred cEEEecCChHHHHHHHHhcccccccccc---------------cccceeeEEEEeechhh---h---ccchhhcCccccc
Confidence 4779999999999999777665554321 11244567888888763 3 34566664 3366
Q ss_pred CeEEeccCC---CCC---CCCCCceEEEEEcCHHHHHHHHHHHHH
Q 003942 327 ARIQLIPQH---LPE---GDGSKERIVRVTGDMRQIEIAQEMIKE 365 (784)
Q Consensus 327 arIqI~~~~---~p~---~~~~~er~V~I~Gt~~qV~~Ak~lI~~ 365 (784)
|.|.-.++. +.. .....-.++++.|.++.|+.+...+-+
T Consensus 313 ~~I~Ri~Ra~iElv~~~d~~lq~gDvl~vvg~~~~v~~~~~~lG~ 357 (544)
T COG2985 313 VFINRINRADIELVASDDVVLQKGDVLQVVGRARRVKAVADVLGN 357 (544)
T ss_pred eeeeehhhcCccccCCcchhhhhcceeeeccchHHHHHHHHHhcc
Confidence 665443321 111 112233578999999999887777654
No 212
>TIGR00078 nadC nicotinate-nucleotide pyrophosphorylase. Synonym: quinolinate phosphoribosyltransferase (decarboxylating)
Probab=32.80 E-value=2.1e+02 Score=31.03 Aligned_cols=69 Identities=14% Similarity=0.139 Sum_probs=46.3
Q ss_pred EEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA 273 (784)
Q Consensus 203 rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~ 273 (784)
++.|-...-+.|-| -..+.+|-+..+++|.+...+...-...+.+++|.|....+..+.+.+..+|...
T Consensus 28 ~~~~~ar~~~v~~G--~~~~~~i~~~~~~~v~~~~~dG~~v~~g~~i~~i~G~~~~il~~Er~~ln~l~~~ 96 (265)
T TIGR00078 28 TASLVAKEDGVLAG--LPVARRVFEQLGVQVEWLVKDGDRVEPGEVVAEVEGPARSLLTAERTALNFLGRL 96 (265)
T ss_pred EEEEEecCCEEEEC--HHHHHHHHHHcCeEEEEEeCCCCEecCCCEEEEEEEcHHHHHHHHHHHHHHHHHH
Confidence 33333334444543 3567788888888875443322223456789999999999999999998887653
No 213
>KOG4264 consensus Nucleo-cytoplasmic protein MLN51 [General function prediction only]
Probab=32.39 E-value=50 Score=38.58 Aligned_cols=11 Identities=9% Similarity=-0.173 Sum_probs=4.9
Q ss_pred cccCCCchhhh
Q 003942 130 QQISVKEETKE 140 (784)
Q Consensus 130 ~iIGk~Ge~Ik 140 (784)
..|-|.|..-.
T Consensus 136 ~yIpk~g~fy~ 146 (694)
T KOG4264|consen 136 AYIPKTGRFYM 146 (694)
T ss_pred ccccccccccc
Confidence 44445444433
No 214
>KOG2133 consensus Transcriptional corepressor Atrophin-1/DRPLA [General function prediction only]
Probab=31.80 E-value=35 Score=42.52 Aligned_cols=20 Identities=0% Similarity=-0.145 Sum_probs=11.7
Q ss_pred cccccccccCCCchhhhhhh
Q 003942 124 QASVDNQQISVKEETKEVLF 143 (784)
Q Consensus 124 P~~~vg~iIGk~Ge~Ik~iq 143 (784)
...+...+-+++|.|-+.+-
T Consensus 107 Ds~~~~Sl~~dg~sn~~g~v 126 (1229)
T KOG2133|consen 107 DSLYSRSLTGDGGSNCRGIV 126 (1229)
T ss_pred cchhcccccCCCCCCCccch
Confidence 33334567777777755553
No 215
>COG0014 ProA Gamma-glutamyl phosphate reductase [Amino acid transport and metabolism]
Probab=31.78 E-value=24 Score=40.16 Aligned_cols=114 Identities=18% Similarity=0.290 Sum_probs=57.7
Q ss_pred CCCCeEEEEEecCCccceeeccCcch---HhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHh
Q 003942 196 DDSTMSRKIEVPNNKVGVLIGKAGDT---IRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAE 272 (784)
Q Consensus 196 ~~~~~t~rI~VP~~~vG~IIGkgG~t---IK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e 272 (784)
.+.....++.||-..+|.|-=.+=+. +-.|+-+|| .-|.+.|.+|.+.....++.-+-+-
T Consensus 103 ~nGL~i~~~rvPLGVigvIYEsRPnVtvdaaaLclKsG-----------------NAvILRGGsea~~Sn~ai~~~i~~a 165 (417)
T COG0014 103 PNGLQIYRVRVPLGVIGVIYESRPNVTVDAAALCLKSG-----------------NAVILRGGSEAIHSNAAIVEVIQEA 165 (417)
T ss_pred CCCCEEEEEEccceEEEEEEecCCccHHHHHHHHHhcC-----------------CEEEEeCcHHHhhhHHHHHHHHHHH
Confidence 45567889999999888886433221 223333333 3556667666665544333322222
Q ss_pred hhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchH-HHHHHHHhCCeE
Q 003942 273 ADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGET-IKGLQTRSGARI 329 (784)
Q Consensus 273 ~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~-IK~Iq~~SGarI 329 (784)
....++|.....- .....+....+|+=-++++-+||=|||+. |+.|++++.+=|
T Consensus 166 L~~~~lP~~aVql---i~~~~R~~v~~ll~l~~yiD~iIPRGg~~Li~~v~~~a~vPV 220 (417)
T COG0014 166 LEKAGLPADAVQL---IEDTDREEVLELLRLDGYIDLVIPRGGAGLIRRVVENATVPV 220 (417)
T ss_pred HHHcCCCHHHhhh---ccCCCHHHHHHHHhhcCceeEEEcCCcHHHHHHHHhCCcCCE
Confidence 2122233210000 00001111222333457888899999965 677787765444
No 216
>PRK07428 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=31.65 E-value=3.8e+02 Score=29.41 Aligned_cols=68 Identities=9% Similarity=0.126 Sum_probs=46.7
Q ss_pred EEEEEecCCceeeeecCCchHHHHHHHHhCCeEEec---cCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 003942 297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLI---PQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS 368 (784)
Q Consensus 297 ~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~---~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~ 368 (784)
..++.|-.+.-|.|= |-+.+.+|-+..+++|+|. .+. ..-...+.+++|.|....+..+.+.+..+|+
T Consensus 42 ~~~~~i~ar~~gv~~--G~~~a~~i~~~~~~~~~~~~~~~dG--~~v~~g~~i~~~~G~a~~ll~~eR~~lN~l~ 112 (288)
T PRK07428 42 TGQAKWIAKESGVIA--GLPIAARVFQLLDPQVSFTPLVAEG--AACESGQVVAEIEGPLDALLMGERVALNLAM 112 (288)
T ss_pred EEEEEEEecCCeEEE--CHHHHHHHHHHcCCcEEEEEEcCCC--CEecCCCEEEEEEEcHHHHHHHHHHHHHHHH
Confidence 344444444445553 4577889999999887743 222 1123467899999999999999998887775
No 217
>PRK07428 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=31.55 E-value=2.5e+02 Score=30.79 Aligned_cols=160 Identities=15% Similarity=0.169 Sum_probs=84.8
Q ss_pred EEEecCCccceeeccCcchHhhHHhhcCCEEEEc--cCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhh------
Q 003942 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQIT--RDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEAD------ 274 (784)
Q Consensus 203 rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~--~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~------ 274 (784)
++.|-...-|.|-| -+.+.+|.+..+++|.|. ..+...-...+.+++|.|....|..+.+.+..+|....
T Consensus 44 ~~~i~ar~~gv~~G--~~~a~~i~~~~~~~~~~~~~~~dG~~v~~g~~i~~~~G~a~~ll~~eR~~lN~l~~~SGIAT~T 121 (288)
T PRK07428 44 QAKWIAKESGVIAG--LPIAARVFQLLDPQVSFTPLVAEGAACESGQVVAEIEGPLDALLMGERVALNLAMRLSGIATLT 121 (288)
T ss_pred EEEEEecCCeEEEC--HHHHHHHHHHcCCcEEEEEEcCCCCEecCCCEEEEEEEcHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333344444533 367789999999777633 32222223467899999999999999998887775532
Q ss_pred ------cCCCCc-ccc-cccchh--------------hccCCccEEEEEecCCceeeeecCCchHHHHHHHHhC--CeEE
Q 003942 275 ------AGGSPS-LVA-RGLATA--------------QASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSG--ARIQ 330 (784)
Q Consensus 275 ------~~g~p~-~~~-~g~~~~--------------~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SG--arIq 330 (784)
..+... +.+ |-..+. ..-.-.-...++|-.|++.++ |-=-+.|+.+++..+ .+|.
T Consensus 122 ~~~v~~~~~~~~~i~~TRKt~Pg~R~l~k~AV~~GGg~~HR~gL~d~ilikdNHi~~~-g~i~~av~~~r~~~~~~~~I~ 200 (288)
T PRK07428 122 RQYVEKIADLPTQLVDTRKTTPGLRLLEKYATQVGGAINHRMGLDDAVMIKDNHIQAA-GGIGEAITRIRQRIPYPLTIE 200 (288)
T ss_pred HHHHHHhcCCCeEEEecCCCCCcchHHHHHHHHhcCcccccCCchheeeecHHHHHHh-CCHHHHHHHHHHhCCCCCEEE
Confidence 011100 111 111110 000112234567777665443 322367788888876 4577
Q ss_pred eccCCCCCC---CCCCceEEEEEc-CHHHHHHHHHHHHH
Q 003942 331 LIPQHLPEG---DGSKERIVRVTG-DMRQIEIAQEMIKE 365 (784)
Q Consensus 331 I~~~~~p~~---~~~~er~V~I~G-t~~qV~~Ak~lI~~ 365 (784)
|.-+++... -...-..|.+.- +.+.+++|.++|..
T Consensus 201 VEv~tleea~eA~~~GaD~I~LDn~~~e~l~~av~~~~~ 239 (288)
T PRK07428 201 VETETLEQVQEALEYGADIIMLDNMPVDLMQQAVQLIRQ 239 (288)
T ss_pred EECCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHh
Confidence 754321100 011112333332 27888888877654
No 218
>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=31.09 E-value=1.3e+02 Score=25.67 Aligned_cols=33 Identities=21% Similarity=0.385 Sum_probs=24.3
Q ss_pred cCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHH
Q 003942 229 SGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAV 269 (784)
Q Consensus 229 TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~el 269 (784)
...+|..... ...|.|+|+.+.+++.+++|..|
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 3446776643 35788999999998888888764
No 219
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=30.98 E-value=1.7e+02 Score=29.73 Aligned_cols=93 Identities=15% Similarity=0.141 Sum_probs=51.7
Q ss_pred eeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCCCCCC
Q 003942 164 EETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADP 243 (784)
Q Consensus 164 ~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~~~~p 243 (784)
+.+.++...++...+.+.++++......-. ....+..+|.+=.-.+. ...-.-|.+|.+.++++|.-...
T Consensus 48 Ivv~~~~~~ieqL~kQL~KLidVl~V~~~~--~~~~v~rEl~LiKv~~~---~~~r~ei~~~~~~f~a~ivdv~~----- 117 (174)
T CHL00100 48 MVVPGDDRTIEQLTKQLYKLVNILKVQDIT--NIPCVERELMLIKINVN---SQTRPEILEIAQIFRAKVVDLSE----- 117 (174)
T ss_pred EEEECCHHHHHHHHHHHHHHhHhhEEEecC--CccceeeEEEEEEEecC---CcCHHHHHHHHHHhCCEEEEecC-----
Confidence 445555444666666666666422211111 11122222222111110 12345688899999999865532
Q ss_pred CCCCCcEEEecchhhHHHHHHHHHH
Q 003942 244 HAATRPVEIIGTLSNIDKAEKLINA 268 (784)
Q Consensus 244 ~s~eR~V~I~G~~e~V~kA~~~I~e 268 (784)
..-+|.++|+.+.|+..++++..
T Consensus 118 --~~~~ie~tG~~~ki~a~~~~l~~ 140 (174)
T CHL00100 118 --ESLILEVTGDPGKIVAIEQLLEK 140 (174)
T ss_pred --CEEEEEEcCCHHHHHHHHHHhhh
Confidence 24689999999999887777764
No 220
>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=30.97 E-value=2.2e+02 Score=25.27 Aligned_cols=69 Identities=13% Similarity=0.205 Sum_probs=47.1
Q ss_pred EEEEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 003942 297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS 368 (784)
Q Consensus 297 ~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~ 368 (784)
..++.|=.+.-|.|= |=..+++|-+..+++|++....- ..-...+.+++|.|+...+..|.+.+..+|.
T Consensus 17 ~~~a~i~are~gV~a--G~~~~~~i~~~l~~~v~~~~~dG-~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 17 TGTATIIAREDGVLA--GLEEAEEIFEKLGLEVEWLVKDG-DRVEPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp EEEEEEEESSSEEE---SHHHHHHHHHHCTEEEEESS-TT--EEETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred EEEEEEEeCCCEEEE--CHHHHHHHHhhccEEEEEEeCCC-CCccCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 334444443344443 55788899999999998763210 1112457889999999999999999998875
No 221
>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=30.82 E-value=49 Score=27.40 Aligned_cols=49 Identities=37% Similarity=0.532 Sum_probs=31.8
Q ss_pred chHHHH--HHHHhCCeEEeccCC----CCCC--CCCCceEEEEEcCHHHHHHHHHHH
Q 003942 315 GETIKG--LQTRSGARIQLIPQH----LPEG--DGSKERIVRVTGDMRQIEIAQEMI 363 (784)
Q Consensus 315 G~~IK~--Iq~~SGarIqI~~~~----~p~~--~~~~er~V~I~Gt~~qV~~Ak~lI 363 (784)
|.+|++ +++.++|+|.-..+. .|.. .-.....|.|.|..+.+++.++++
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 457888 778789886554322 1111 123446799999999999888764
No 222
>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=30.57 E-value=4.6e+02 Score=28.66 Aligned_cols=67 Identities=16% Similarity=0.191 Sum_probs=47.0
Q ss_pred EEEecCCceeeeecCCchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 003942 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS 368 (784)
Q Consensus 299 ~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~ 368 (784)
++.|-.+.-|.| .|-..+++|-+..+|+|++....- ..-...+.+++|.|+...+..|.+.+..+|+
T Consensus 34 ~~~~~are~gv~--~G~~~~~~i~~~l~~~~~~~~~dG-~~v~~g~~i~~~~G~a~~ll~~eR~alN~l~ 100 (277)
T TIGR01334 34 HITFTARDEGIV--SGVSEAAKLLKQLGASIDYAVPSG-SRALAGTLLLEAKGSAGQLHQGWKSAQSVLE 100 (277)
T ss_pred EEEEEEcCCEEE--ECHHHHHHHHHHcCCEEEEEeCCC-CEeCCCCEEEEEEecHHHHHHHHHHHHHHHH
Confidence 444444444444 345778899999999988874321 1123567889999999999999888887765
No 223
>COG2061 ACT-domain-containing protein, predicted allosteric regulator of homoserine dehydrogenase [Amino acid transport and metabolism]
Probab=30.30 E-value=5.7e+02 Score=25.64 Aligned_cols=64 Identities=19% Similarity=0.331 Sum_probs=41.6
Q ss_pred ceeeeecCC-chHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 003942 306 KVGLIIGRG-GETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG-DMRQIEIAQEMIKEVLSQ 369 (784)
Q Consensus 306 ~vG~VIGkg-G~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~G-t~~qV~~Ak~lI~~~L~~ 369 (784)
++|.|+-.+ -.||.+|...-||.|.=-....|.-+....-.|+|.- ..+.++.|.++|+++-.+
T Consensus 92 LIGhiv~tdiqDTId~In~ig~A~vvDl~L~Mp~~e~~SsA~iti~a~~~e~l~ea~~~l~ev~~e 157 (170)
T COG2061 92 LIGHIVHTDIQDTIDRINSIGGAEVVDLSLSMPGIEGESSARITIIAVGKEKLDEALRRLKEVAME 157 (170)
T ss_pred EEEeeecCcHHHHHHHhhccCCEEEEEEEeecCCCCCCcceeEEEEEcChhHHHHHHHHHHHHHhh
Confidence 345555332 3678888888888754222233434444556677777 588999999999987654
No 224
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=29.73 E-value=94 Score=33.01 Aligned_cols=29 Identities=24% Similarity=0.486 Sum_probs=23.7
Q ss_pred EEEEEecCCccceeeccCcchHhhHHhhc
Q 003942 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNS 229 (784)
Q Consensus 201 t~rI~VP~~~vG~IIGkgG~tIK~Iq~~T 229 (784)
.++|.|-...-+.|||++|.+|++|++..
T Consensus 63 ~i~I~I~~~rP~~iiG~~g~~i~~l~~~L 91 (232)
T PRK00310 63 RVRVTIHTARPGIVIGKKGAEIEKLRKEL 91 (232)
T ss_pred eEEEEEEECCCccccCCCcHHHHHHHHHH
Confidence 45666666788999999999999988764
No 225
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=29.69 E-value=3.4e+02 Score=27.26 Aligned_cols=99 Identities=20% Similarity=0.270 Sum_probs=58.6
Q ss_pred cEEEecchhhHHHHHHHHHHHHHhhhcCCC--CcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhC
Q 003942 249 PVEIIGTLSNIDKAEKLINAVIAEADAGGS--PSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSG 326 (784)
Q Consensus 249 ~V~I~G~~e~V~kA~~~I~elI~e~~~~g~--p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SG 326 (784)
.+++.|+.+.|++.++.|+.++.=..-... ...+.| ...-+++.+..+ .-..|.+|.+..+
T Consensus 47 ti~V~~~~~~i~qi~kQl~KLidV~~V~~~~~~~~v~r---------El~LiKv~~~~~--------~r~~i~~i~~~f~ 109 (161)
T PRK11895 47 TIVTSGDEQVIEQITKQLNKLIDVLKVVDLTEEAHVER---------ELALVKVRASGE--------NRAEILRLADIFR 109 (161)
T ss_pred EEEEECCHHHHHHHHHHHhccccEEEEEecCCcchhhe---------EEEEEEEECCcc--------cHHHHHHHHHHhC
Confidence 456668888888888888877653211000 000000 011122222221 2357889999999
Q ss_pred CeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHH-HhcccC
Q 003942 327 ARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEV-LSQTVR 372 (784)
Q Consensus 327 arIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~-L~~~~r 372 (784)
|+|.=.. .+.-+|.++|+.+.|+.-.++++.. |.+..|
T Consensus 110 a~ivdv~--------~~~~~iE~tG~~~ki~~~~~~l~~~gi~e~~R 148 (161)
T PRK11895 110 AKIVDVT--------PESLTIEVTGDSDKIDAFIDLLRPYGIKEIVR 148 (161)
T ss_pred CEEEEec--------CCEEEEEEeCCHHHHHHHHHHhhhcCCEEEEc
Confidence 9965322 2467899999999999988888764 333344
No 226
>KOG3181 consensus 40S ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=29.52 E-value=67 Score=32.97 Aligned_cols=37 Identities=16% Similarity=0.276 Sum_probs=26.5
Q ss_pred eEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEc
Q 003942 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQIT 236 (784)
Q Consensus 200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~ 236 (784)
+..+|.|-..+.-.+||.+|..|++|..-.--+..+.
T Consensus 44 tr~eiIi~atrtq~vlGEkgrRirelt~lvqkRf~f~ 80 (244)
T KOG3181|consen 44 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFKFP 80 (244)
T ss_pred cceeEEEEecchhhhhhhcchhHHHHHHHHHHhcCCC
Confidence 4456677777777899999999999976544444443
No 227
>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=28.53 E-value=1.5e+02 Score=30.11 Aligned_cols=103 Identities=13% Similarity=0.136 Sum_probs=50.8
Q ss_pred ceeeecCc--hhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCCccceeeccCcchHhhHHhhcCCEEEEccCC
Q 003942 162 KEEETVKE--EESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDA 239 (784)
Q Consensus 162 r~~~i~G~--~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TGakI~V~~~~ 239 (784)
-.+.++|. .+.+++|.+.|.++|........ ....+++.-.|-...++.=| .|+.|-....-.+....+.
T Consensus 56 GKiviTGaks~~~~~~a~~~~~~~l~~~g~~~~---~~~~f~v~nIvat~~~~~~i-----~L~~la~~~~~~~~YePE~ 127 (174)
T cd04517 56 GKITITGATSEEEAKQAARRAARLLQKLGFKVV---RFSNFRVVNVLATCSMPFPI-----RLDELAAKNRSSASYEPEL 127 (174)
T ss_pred CeEEEEccCCHHHHHHHHHHHHHHHHHcCCCcc---cCCceEEEEEEEEEeCCCcc-----cHHHHHHhchhhcEeCCcc
Confidence 34555554 56677777777777765443220 11234444444333333322 2444433222111111100
Q ss_pred C-------CCCCC-----CCCcEEEec--chhhHHHHHHHHHHHHHh
Q 003942 240 D-------ADPHA-----ATRPVEIIG--TLSNIDKAEKLINAVIAE 272 (784)
Q Consensus 240 ~-------~~p~s-----~eR~V~I~G--~~e~V~kA~~~I~elI~e 272 (784)
- ..+.. ....|.|+| +.+.+.+|++.|..++.+
T Consensus 128 fPgliyr~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i~pil~~ 174 (174)
T cd04517 128 HPGVVYRITGPRATLSIFSTGSVTVTGARSMEDVREAVEKIYPIVFE 174 (174)
T ss_pred CCEEEEEECCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHHHHHhC
Confidence 0 00011 134668888 568999999999887753
No 228
>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=28.23 E-value=5.1e+02 Score=28.11 Aligned_cols=66 Identities=12% Similarity=0.237 Sum_probs=44.7
Q ss_pred EEEecCCceeeeecCCchHHHHHHHHhCCeEEec-cCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 003942 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLI-PQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS 368 (784)
Q Consensus 299 ~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~-~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~ 368 (784)
++.|-.+.-|.|= |-..+++|-+..+++|.+. ++. ..-...+.+++|.|+...+..+.+.+..+|.
T Consensus 30 ~~~~~ak~~gv~a--G~~~~~~~~~~~~~~v~~~~~dG--~~v~~g~~i~~i~G~~~~ll~~Er~~ln~l~ 96 (272)
T cd01573 30 KITFRARDPGVLC--GTEEAARILELLGLEVDLAAASG--SRVAAGAVLLEAEGPAAALHLGWKVAQTLLE 96 (272)
T ss_pred EEEEEECCCEEEE--CHHHHHHHHHHcCcEEEEEcCCC--CEecCCCEEEEEEEcHHHHHHHHHHHHHHHH
Confidence 3333333344443 3457788888889998754 332 1123467899999999999999988887775
No 229
>PF03958 Secretin_N: Bacterial type II/III secretion system short domain; InterPro: IPR005644 This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (IPR004846 from INTERPRO).; PDB: 3EZJ_C 2Y3M_A 3OSS_D.
Probab=27.62 E-value=1.7e+02 Score=24.95 Aligned_cols=24 Identities=25% Similarity=0.439 Sum_probs=20.8
Q ss_pred CceEEEEEcCHHHHHHHHHHHHHH
Q 003942 343 KERIVRVTGDMRQIEIAQEMIKEV 366 (784)
Q Consensus 343 ~er~V~I~Gt~~qV~~Ak~lI~~~ 366 (784)
....|.|+|+++.++..+.||..+
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 356789999999999999999875
No 230
>PRK08385 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=27.56 E-value=5.1e+02 Score=28.33 Aligned_cols=53 Identities=21% Similarity=0.324 Sum_probs=39.9
Q ss_pred CchHHHHHHHHhCCeEEecc-CCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 003942 314 GGETIKGLQTRSGARIQLIP-QHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS 368 (784)
Q Consensus 314 gG~~IK~Iq~~SGarIqI~~-~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~ 368 (784)
|-..+.+|-+..+|+|.+.. +. ..-...+.+++|.|....+..+.+.+..+|+
T Consensus 45 G~~~a~~i~~~l~~~v~~~~~dG--~~v~~g~~i~~i~G~~~~ll~~Er~~ln~l~ 98 (278)
T PRK08385 45 GLEEAKALFEHFGVKVEVRKRDG--EEVKAGEVILELKGNARAILLVERTALNIIG 98 (278)
T ss_pred CHHHHHHHHHHcCCEEEEEcCCC--CEecCCCEEEEEEECHHHHHHHHHHHHHHHH
Confidence 34567788888899988843 22 1123567899999999999999988887775
No 231
>PRK06096 molybdenum transport protein ModD; Provisional
Probab=26.82 E-value=3.6e+02 Score=29.57 Aligned_cols=54 Identities=13% Similarity=0.117 Sum_probs=41.8
Q ss_pred cchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHh
Q 003942 219 GDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAE 272 (784)
Q Consensus 219 G~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e 272 (784)
-+.+++|-+..+++|.+...+...-...+.++++.|....|..+.+.+..+|..
T Consensus 49 ~~~a~~if~~l~~~v~~~~~dG~~v~~G~~i~~~~G~a~~ll~~eR~alN~l~~ 102 (284)
T PRK06096 49 ISVACKMLTTLGLTIDDAVSDGSQANAGQRLISAQGNAAALHQGWKAVQNVLEW 102 (284)
T ss_pred HHHHHHHHHHcCCEEEEEeCCCCEeCCCCEEEEEEeCHHHHHHHHHHHHHHHHH
Confidence 367788888889998887554333345678999999999999998888777654
No 232
>COG4598 HisP ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]
Probab=26.56 E-value=45 Score=34.39 Aligned_cols=68 Identities=26% Similarity=0.322 Sum_probs=46.1
Q ss_pred EEEecCCceeeeecCCchHHHHHHHHhCCeEEeccC--CCCCCCCCCceEEEEEcC--HHHHHHHHHHHHHH
Q 003942 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIPQ--HLPEGDGSKERIVRVTGD--MRQIEIAQEMIKEV 366 (784)
Q Consensus 299 ~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~~--~~p~~~~~~er~V~I~Gt--~~qV~~Ak~lI~~~ 366 (784)
+|.+-.+..|.++...-..|.+||.+.|-..+-.+. |...-++..|.-|+|.|. .+.|++|..++..+
T Consensus 69 ei~~k~~~~G~l~~ad~~q~~r~Rs~L~mVFQ~FNLWsHmtvLeNViEaPvhVLg~~k~ea~e~Ae~~L~kV 140 (256)
T COG4598 69 EIRLKRDKDGQLKPADKRQLQRLRTRLGMVFQHFNLWSHMTVLENVIEAPVHVLGVSKAEAIERAEKYLAKV 140 (256)
T ss_pred EEEeeeCCCCCeeeCCHHHHHHHHHHhhHhhhhcchhHHHHHHHHHHhcchHhhcCCHHHHHHHHHHHHHHh
Confidence 455566777888888888999999988865554431 111112334556888887 57888898887764
No 233
>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=25.92 E-value=2.9e+02 Score=28.07 Aligned_cols=25 Identities=16% Similarity=0.235 Sum_probs=19.8
Q ss_pred CcEEEec--chhhHHHHHHHHHHHHHh
Q 003942 248 RPVEIIG--TLSNIDKAEKLINAVIAE 272 (784)
Q Consensus 248 R~V~I~G--~~e~V~kA~~~I~elI~e 272 (784)
..|.|+| +.+.+.+|++.|..+|.+
T Consensus 147 GkvvitGaks~~~~~~a~~~i~p~L~~ 173 (174)
T cd04516 147 GKIVLTGAKSREEIYQAFENIYPILLQ 173 (174)
T ss_pred CEEEEEecCCHHHHHHHHHHHHHHHhh
Confidence 3567777 567899999999988865
No 234
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=25.90 E-value=55 Score=36.33 Aligned_cols=31 Identities=26% Similarity=0.458 Sum_probs=24.9
Q ss_pred CeEEEEEecCC-ccceeeccCcchHhhHHhhc
Q 003942 199 TMSRKIEVPNN-KVGVLIGKAGDTIRYLQYNS 229 (784)
Q Consensus 199 ~~t~rI~VP~~-~vG~IIGkgG~tIK~Iq~~T 229 (784)
.+..+|+||.. ...+||||+|..|++|-.+.
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 46778889987 56679999999999986653
No 235
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit. This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.
Probab=25.80 E-value=1e+02 Score=35.66 Aligned_cols=53 Identities=11% Similarity=0.102 Sum_probs=33.4
Q ss_pred hhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCCccceeeccCcchHhhHHhh
Q 003942 170 EESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKAGDTIRYLQYN 228 (784)
Q Consensus 170 ~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~ 228 (784)
.-++..+++.+.+.+..+..-.... ...|-.-..++|.|-.+.|+-|+.|.+.
T Consensus 97 ~G~l~~~~~~lk~~L~~eGlfd~~~------k~~lP~~p~~i~vits~~~aa~~D~~~~ 149 (432)
T TIGR00237 97 EGLLQLAYEQLKEKLAAEGLFDQEY------KKPLPHFPKRVGVITSQTGAALADILHI 149 (432)
T ss_pred hHHHHHHHHHHHHHHHHCCCCCchh------cCCCCCCCCEEEEEeCCccHHHHHHHHH
Confidence 4566777777777776555432222 2233333468888999998887777654
No 236
>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=25.79 E-value=6e+02 Score=25.76 Aligned_cols=26 Identities=15% Similarity=0.240 Sum_probs=21.3
Q ss_pred cEEEec--chhhHHHHHHHHHHHHHhhh
Q 003942 249 PVEIIG--TLSNIDKAEKLINAVIAEAD 274 (784)
Q Consensus 249 ~V~I~G--~~e~V~kA~~~I~elI~e~~ 274 (784)
.+.|+| +.+.+..|++.|.++|++..
T Consensus 57 Kiv~tGaks~~~a~~a~~~~~~~L~~~g 84 (174)
T cd04518 57 KMVCTGAKSVEDLHRAVKEIIKKLKDYG 84 (174)
T ss_pred eEEEEccCCHHHHHHHHHHHHHHHHhcC
Confidence 678887 67889999999999888753
No 237
>PF04461 DUF520: Protein of unknown function (DUF520); InterPro: IPR007551 This entry represents the UPF0234 family of uncharacterised proteins.; PDB: 1IN0_A.
Probab=25.62 E-value=6.3e+02 Score=25.42 Aligned_cols=40 Identities=28% Similarity=0.295 Sum_probs=26.7
Q ss_pred HHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHH
Q 003942 318 IKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEV 366 (784)
Q Consensus 318 IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~ 366 (784)
|..+...++.+|+..- ....|.|+|. .+.++.++.||.+.
T Consensus 108 IvK~IKd~klKVqa~I---------Qgd~vRVtgKkrDDLQ~viallk~~ 148 (160)
T PF04461_consen 108 IVKLIKDSKLKVQAQI---------QGDQVRVTGKKRDDLQEVIALLKEQ 148 (160)
T ss_dssp HHHHHHHH--SEEEEE---------ETTEEEEEES-HHHHHHHHHHHHHS
T ss_pred HHHHHHhcCCceeEEe---------cCcEEEEecCCHHHHHHHHHHHHcc
Confidence 4444566776666542 3457999998 78999999998853
No 238
>PRK06978 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=25.61 E-value=5.5e+02 Score=28.37 Aligned_cols=94 Identities=16% Similarity=0.185 Sum_probs=0.0
Q ss_pred HHHHHHHHHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeEEec---cCCCCCC
Q 003942 263 EKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLI---PQHLPEG 339 (784)
Q Consensus 263 ~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~---~~~~p~~ 339 (784)
.++|...|+|+ +..+--+..........++.|-.+.-|.| .|-..+++|-+..+++|++. ++. ..
T Consensus 26 ~~~i~~~L~ED--------~~~gDlTt~~~~~~~~~~a~i~are~gvl--aG~~~a~~if~~l~~~~~v~~~~~dG--~~ 93 (294)
T PRK06978 26 ARNVADAIAED--------VGSGDQTGRLVPAGEPRRARVIVREEAVL--CGVPWFDAVMRAVDPSIEVTWRYREG--DR 93 (294)
T ss_pred HHHHHHHHHhc--------CCCCCCCccccCCCceEEEEEEEcCCEEE--ECHHHHHHHHHHhCCCeEEEEEcCCC--CE
Q ss_pred CCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 003942 340 DGSKERIVRVTGDMRQIEIAQEMIKEVLS 368 (784)
Q Consensus 340 ~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~ 368 (784)
-...+.+++|+|....+..+.+.+..+|.
T Consensus 94 v~~G~~i~~~~G~a~~lL~~ER~aLN~l~ 122 (294)
T PRK06978 94 MTADSTVCELEGPARALLTAERNALNFLQ 122 (294)
T ss_pred eCCCCEEEEEEeCHHHHHHHHHHHHHHHH
No 239
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=24.98 E-value=6.4e+02 Score=25.63 Aligned_cols=51 Identities=18% Similarity=0.266 Sum_probs=37.9
Q ss_pred CchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHH-HhcccC
Q 003942 314 GGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEV-LSQTVR 372 (784)
Q Consensus 314 gG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~-L~~~~r 372 (784)
.-.-|.+|.+..+|+|.-.. .+.-+|.|+|+.+.+..-.++++.. |.+..|
T Consensus 97 ~r~ei~~~~~~f~a~ivdv~--------~~~~~ie~tG~~~ki~a~~~~l~~~gi~e~~R 148 (174)
T CHL00100 97 TRPEILEIAQIFRAKVVDLS--------EESLILEVTGDPGKIVAIEQLLEKFGIIEIAR 148 (174)
T ss_pred CHHHHHHHHHHhCCEEEEec--------CCEEEEEEcCCHHHHHHHHHHhhhcCCEEEEc
Confidence 44678899999999975432 2457899999999999999998864 334444
No 240
>PF03460 NIR_SIR_ferr: Nitrite/Sulfite reductase ferredoxin-like half domain; InterPro: IPR005117 Sulphite reductases (SiRs) and related nitrite reductases (NiRs) catalyse the six-electron reduction reactions of sulphite to sulphide, and nitrite to ammonia, respectively. The Escherichia coli SiR enzyme is a complex composed of two proteins, a flavoprotein alpha-component (SiR-FP) and a hemoprotein beta-component (SiR-HP), and has an alpha(8)beta(4) quaternary structure []. SiR-FP contains both FAD and FMN, while SiR-HP contains a Fe(4)S(4) cluster coupled to a sirohaem through a cysteine bridge. Electrons are transferred from NADPH to FAD, and on to FMN in SiR-FP, from which they are transferred to the metal centre of SiR-HP, where they reduce the siroheme-bound sulphite. SiR-HP has a two-fold symmetry, which generates a distinctive three-domain alpha/beta fold that controls assembly and reactivity []. This entry describes the ferrodoxin-like (alpha/beta sandwich) domain, which consists of a duplication containing two subdomains of this fold.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3B0H_A 4GEP_A 2GEP_A 2AOP_A 5AOP_A 6GEP_A 4AOP_A 1AOP_A 3AOP_A 8GEP_A ....
Probab=24.93 E-value=2.4e+02 Score=23.39 Aligned_cols=57 Identities=14% Similarity=0.271 Sum_probs=42.3
Q ss_pred eEEEEEecCCccceeeccCcchHhhHHhhcC-CEEEEccCCCCCCCCCCCcEEEec-chhhHHHHHHHHHH
Q 003942 200 MSRKIEVPNNKVGVLIGKAGDTIRYLQYNSG-AKIQITRDADADPHAATRPVEIIG-TLSNIDKAEKLINA 268 (784)
Q Consensus 200 ~t~rI~VP~~~vG~IIGkgG~tIK~Iq~~TG-akI~V~~~~~~~p~s~eR~V~I~G-~~e~V~kA~~~I~e 268 (784)
+.++|.++. |.|-...=..|.+|-++.| ..|.+.. ...|.|.+ ..++|....+.|.+
T Consensus 10 ~~v~~~~~~---G~i~~~~l~~la~ia~~yg~~~irlT~---------~Q~l~l~~v~~~~~~~i~~~L~~ 68 (69)
T PF03460_consen 10 YMVRIRIPG---GRISAEQLRALAEIAEKYGDGEIRLTT---------RQNLQLRGVPEENLPAIFEELKE 68 (69)
T ss_dssp EEEEEB-GG---GEEEHHHHHHHHHHHHHHSTSEEEEET---------TSCEEEEEEEGGGHHHHHHHHHH
T ss_pred EEEEEeCCC---EEECHHHHHHHHHHHHHhCCCeEEECC---------CCeEEEeCCCHHHHHHHHHHHHc
Confidence 588888885 7776666777888888888 7888874 34678888 77888877777654
No 241
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=24.37 E-value=6.4e+02 Score=25.13 Aligned_cols=45 Identities=27% Similarity=0.354 Sum_probs=35.0
Q ss_pred CchHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHH
Q 003942 314 GGETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEV 366 (784)
Q Consensus 314 gG~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~ 366 (784)
.-..|.+|.+..+|+|.=.. .+.-+|.++|+.+.+..-.+++...
T Consensus 96 ~r~~i~~i~~~f~a~ivdv~--------~~~~~ie~tG~~~ki~~~~~~l~~~ 140 (157)
T TIGR00119 96 GRDEIIRLTNIFRGRIVDVS--------PDSYTVEVTGDSDKIDAFLELLRPF 140 (157)
T ss_pred CHHHHHHHHHHhCCEEEEec--------CCEEEEEEcCCHHHHHHHHHHhhhc
Confidence 44678899999999975321 2466899999999999988888763
No 242
>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]
Probab=24.26 E-value=1.1e+03 Score=26.79 Aligned_cols=54 Identities=11% Similarity=-0.042 Sum_probs=31.2
Q ss_pred cccCCCchhhhhhhcccCceeeecccc-cccccceeeecCchhchhhhhhhhhHhh
Q 003942 130 QQISVKEETKEVLFSTEEAFIDVKEET-KEVTVKEEETVKEEESVEPSNVVPQQVV 184 (784)
Q Consensus 130 ~iIGk~Ge~Ik~iq~~s~a~I~I~~~~-~~~s~r~~~i~G~~e~Ve~A~~lI~~ii 184 (784)
.+.+|-|=+++.++. ..-+|++=.++ .......+++--..++|+.|..++.+-.
T Consensus 153 ~~~sKcGiI~~d~~t-~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~ 207 (382)
T KOG1548|consen 153 EVMSKCGIIMRDPQT-GEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDE 207 (382)
T ss_pred HHHHhcceEeccCCC-CCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCccc
Confidence 566777777777762 22334333333 2233344455567888888888775543
No 243
>KOG2147 consensus Nucleolar protein involved in 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]
Probab=23.95 E-value=43 Score=40.76 Aligned_cols=18 Identities=22% Similarity=0.104 Sum_probs=10.9
Q ss_pred CchhchhhhhhhhhHhhh
Q 003942 168 KEEESVEPSNVVPQQVVD 185 (784)
Q Consensus 168 G~~e~Ve~A~~lI~~ii~ 185 (784)
|+++.+++-..++...|.
T Consensus 431 gNk~kl~kf~~~LLqy~~ 448 (823)
T KOG2147|consen 431 GNKKKLEKFYGVLLQYFD 448 (823)
T ss_pred chHHHHHHHHHHHHHHHH
Confidence 566666666665555543
No 244
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=23.77 E-value=4e+02 Score=36.18 Aligned_cols=9 Identities=22% Similarity=0.519 Sum_probs=4.8
Q ss_pred cEEEEEecC
Q 003942 296 EQVEIKVPN 304 (784)
Q Consensus 296 ~~~~i~VP~ 304 (784)
..++|.+|.
T Consensus 360 g~i~f~lpp 368 (2849)
T PTZ00415 360 GVIEFTLPP 368 (2849)
T ss_pred eeEEEecCC
Confidence 345565554
No 245
>PRK08072 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=23.59 E-value=2.9e+02 Score=30.16 Aligned_cols=51 Identities=16% Similarity=0.144 Sum_probs=35.5
Q ss_pred hHHHHHHHHhCCe--EEecc-CCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 003942 316 ETIKGLQTRSGAR--IQLIP-QHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS 368 (784)
Q Consensus 316 ~~IK~Iq~~SGar--IqI~~-~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~ 368 (784)
+.+++|-+..+++ |.+.. +. ..-...+.+++|.|....+..+.+.+..+|+
T Consensus 51 ~~a~~i~~~~~~~~~v~~~~~dG--~~v~~g~~i~~~~G~~~~ll~~er~~ln~l~ 104 (277)
T PRK08072 51 LVIEEGYKLLDERIEVELHKKDG--DLVKKGEIIATVQGPVASLLTGERVILNLIQ 104 (277)
T ss_pred HHHHHHHHHcCCceEEEEEeCCC--CEEcCCCEEEEEEECHHHHHHHHHHHHHHHH
Confidence 4557787777755 44432 21 1123467899999999999999998887775
No 246
>PLN02716 nicotinate-nucleotide diphosphorylase (carboxylating)
Probab=23.50 E-value=4.6e+02 Score=29.19 Aligned_cols=69 Identities=14% Similarity=0.108 Sum_probs=46.0
Q ss_pred EEEecCCccceeeccCcchHhhHHhhcC--CEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSG--AKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA 273 (784)
Q Consensus 203 rI~VP~~~vG~IIGkgG~tIK~Iq~~TG--akI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~ 273 (784)
++.|-...-|.|-|. ..+++|-+..+ ++|.+...+...-...+.+++|.|....|..+.+.++.+|...
T Consensus 50 ~a~i~ake~gvlaG~--~~a~~vf~~l~~~~~v~~~~~dG~~v~~G~~i~~v~G~a~~il~~ER~aLN~L~~~ 120 (308)
T PLN02716 50 EATFLAKADGVLAGI--ALADMVFEEVDPSLKVEWAAIDGDFVHKGLKFGKVTGPAHSILVAERVVLNFMQRM 120 (308)
T ss_pred EEEEEeCCCEEEECH--HHHHHHHHHcCCCeEEEEEeCCCCEecCCCEEEEEEECHHHHHHHHHHHHHHHHHH
Confidence 333333344445443 56788888888 7776654332223446789999999999999999988877653
No 247
>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=23.35 E-value=1.9e+02 Score=24.62 Aligned_cols=44 Identities=23% Similarity=0.366 Sum_probs=23.5
Q ss_pred hHHHHHHHHh-CCeEEeccCCCCCCCCCCceEEEEEcCHHH-HHHHHHHHHHHH
Q 003942 316 ETIKGLQTRS-GARIQLIPQHLPEGDGSKERIVRVTGDMRQ-IEIAQEMIKEVL 367 (784)
Q Consensus 316 ~~IK~Iq~~S-GarIqI~~~~~p~~~~~~er~V~I~Gt~~q-V~~Ak~lI~~~L 367 (784)
+..|+|.+.. .|.|+|..- ....|+|.|..+. -+...++|+++.
T Consensus 12 EL~kRl~~~yPd~~v~Vr~~--------s~~~l~v~g~~~~~k~~i~~iLqe~w 57 (65)
T PF06183_consen 12 ELTKRLHRQYPDAEVRVRPG--------SANGLSVSGGKKDDKERIEEILQEMW 57 (65)
T ss_dssp HHHHHHHHH-SS-EEEEEEE--------SS-EEEEES--HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHCCCceEeeeec--------ccCccccCCcCchHHHHHHHHHHHHH
Confidence 4567887775 677887642 3567999998643 333344444443
No 248
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=23.31 E-value=69 Score=36.90 Aligned_cols=12 Identities=25% Similarity=0.268 Sum_probs=5.7
Q ss_pred CCcEEEecchhh
Q 003942 247 TRPVEIIGTLSN 258 (784)
Q Consensus 247 eR~V~I~G~~e~ 258 (784)
+-.=.|.||.+.
T Consensus 191 DSTDFVCGTLDE 202 (458)
T PF10446_consen 191 DSTDFVCGTLDE 202 (458)
T ss_pred CcccccCCCcCC
Confidence 333355565543
No 249
>PRK05412 putative nucleotide-binding protein; Reviewed
Probab=23.10 E-value=7.9e+02 Score=24.80 Aligned_cols=41 Identities=22% Similarity=0.293 Sum_probs=28.7
Q ss_pred HHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHH
Q 003942 317 TIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-MRQIEIAQEMIKEV 366 (784)
Q Consensus 317 ~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-~~qV~~Ak~lI~~~ 366 (784)
.|..+...++.+|+..- ....|.|+|. .+.++.++.||.+.
T Consensus 107 kIvK~IKd~klKVqa~I---------QGd~vRVtgKkrDDLQ~viallk~~ 148 (161)
T PRK05412 107 KIVKLIKDSKLKVQAQI---------QGDQVRVTGKKRDDLQAVIALLRKA 148 (161)
T ss_pred HHHHHHHhcCCceeEEe---------cCcEEEEecCCHhHHHHHHHHHHhc
Confidence 34455566776666542 3457999996 68999999988753
No 250
>COG0331 FabD (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]
Probab=23.00 E-value=1.1e+02 Score=33.96 Aligned_cols=57 Identities=14% Similarity=0.262 Sum_probs=45.2
Q ss_pred CccceeeccCcchHhhHHhhcCCE--EEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHH
Q 003942 209 NKVGVLIGKAGDTIRYLQYNSGAK--IQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIA 271 (784)
Q Consensus 209 ~~vG~IIGkgG~tIK~Iq~~TGak--I~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~ 271 (784)
.-+..|+|---+.|+++.++..-. |.+... ++ .+-|.|+|.++.|++|...++++-.
T Consensus 131 g~Maav~gl~~e~v~~~~~~~~~~~~v~iaN~-----N~-~~QiVIsG~~~ale~a~~~~~~~g~ 189 (310)
T COG0331 131 GGMAAVLGLDDEQVEKACEEAAQGTVVEIANY-----NS-PGQIVISGTKEALEKAAEILKEAGA 189 (310)
T ss_pred ccHHHHcCCCHHHHHHHHHHhccCCeEEEeee-----CC-CCcEEEECCHHHHHHHHHHHHHhhh
Confidence 456778888889999999988754 666543 22 4899999999999999998887663
No 251
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=22.98 E-value=4.4e+02 Score=30.71 Aligned_cols=54 Identities=20% Similarity=0.353 Sum_probs=37.2
Q ss_pred EEecC--CceeeeecCCchHHHHHHHHh-----CCeEEeccCCCCCCCCCCceEEEEEcC--HHHHHHHHHHHHHH
Q 003942 300 IKVPN--EKVGLIIGRGGETIKGLQTRS-----GARIQLIPQHLPEGDGSKERIVRVTGD--MRQIEIAQEMIKEV 366 (784)
Q Consensus 300 i~VP~--~~vG~VIGkgG~~IK~Iq~~S-----GarIqI~~~~~p~~~~~~er~V~I~Gt--~~qV~~Ak~lI~~~ 366 (784)
..+|. ++||.|..+-|+-|+.|.... .|+|.|.+ +.|.|. ..+|-.|++..+++
T Consensus 129 kpLP~~p~~IGVITS~tgAairDIl~~~~rR~P~~~viv~p-------------t~VQG~~A~~eIv~aI~~an~~ 191 (440)
T COG1570 129 KPLPFFPKKIGVITSPTGAALRDILHTLSRRFPSVEVIVYP-------------TLVQGEGAAEEIVEAIERANQR 191 (440)
T ss_pred CCCCCCCCeEEEEcCCchHHHHHHHHHHHhhCCCCeEEEEe-------------ccccCCCcHHHHHHHHHHhhcc
Confidence 34454 899999999999999887543 35555542 456676 56677777666543
No 252
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=22.96 E-value=4.4e+02 Score=30.39 Aligned_cols=78 Identities=21% Similarity=0.303 Sum_probs=49.3
Q ss_pred hhHHHHHHHHHHHHHhhhcCCCCcccccccchhhccCCccEEEEEecC--CceeeeecCCchHHHHHHHHh-----CCeE
Q 003942 257 SNIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPN--EKVGLIIGRGGETIKGLQTRS-----GARI 329 (784)
Q Consensus 257 e~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~--~~vG~VIGkgG~~IK~Iq~~S-----GarI 329 (784)
-.+..+++.+.++++++ |++. ...+..||. ..||.|-.+.|+-|+.|.+.. .|+|
T Consensus 104 G~l~~~~~~lk~~L~~e-----------Glfd-------~~~k~~lP~~p~~I~viTs~~gAa~~D~~~~~~~r~p~~~~ 165 (438)
T PRK00286 104 GALAAAFEQLKEKLAAE-----------GLFD-------PERKKPLPFFPKRIGVITSPTGAAIRDILTVLRRRFPLVEV 165 (438)
T ss_pred cHHHHHHHHHHHHHHHC-----------CCCC-------hhhcCCCCCCCCEEEEEeCCccHHHHHHHHHHHhcCCCCeE
Confidence 45666777777776654 2221 112345665 899999999999988887554 3555
Q ss_pred EeccCCCCCCCCCCceEEEEEcC--HHHHHHHHHHHHH
Q 003942 330 QLIPQHLPEGDGSKERIVRVTGD--MRQIEIAQEMIKE 365 (784)
Q Consensus 330 qI~~~~~p~~~~~~er~V~I~Gt--~~qV~~Ak~lI~~ 365 (784)
.+.. +.|.|. ..+|..|++.+..
T Consensus 166 ~~~~-------------~~vQG~~A~~~i~~al~~~~~ 190 (438)
T PRK00286 166 IIYP-------------TLVQGEGAAASIVAAIERANA 190 (438)
T ss_pred EEec-------------CcCcCccHHHHHHHHHHHhcC
Confidence 5542 456666 5566666666544
No 253
>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=22.87 E-value=98 Score=41.88 Aligned_cols=15 Identities=13% Similarity=0.118 Sum_probs=8.3
Q ss_pred cCchhchhhhhhhhh
Q 003942 167 VKEEESVEPSNVVPQ 181 (784)
Q Consensus 167 ~G~~e~Ve~A~~lI~ 181 (784)
+...++.+.|.+..+
T Consensus 4156 s~~~ea~~ea~~~~q 4170 (4600)
T COG5271 4156 STPKEAMSEADRQYQ 4170 (4600)
T ss_pred CCcHHHHHHHHHHHH
Confidence 355666666654443
No 254
>PRK00394 transcription factor; Reviewed
Probab=22.83 E-value=8.2e+02 Score=24.89 Aligned_cols=35 Identities=23% Similarity=0.265 Sum_probs=26.5
Q ss_pred CCEEEEccCCCCCCCCCCCcEEEec--chhhHHHHHHHHHHHHHhh
Q 003942 230 GAKIQITRDADADPHAATRPVEIIG--TLSNIDKAEKLINAVIAEA 273 (784)
Q Consensus 230 GakI~V~~~~~~~p~s~eR~V~I~G--~~e~V~kA~~~I~elI~e~ 273 (784)
.+.+.|... -.+.|+| +.+.+.+|++.|.++|++.
T Consensus 46 k~t~lIf~s---------GKiv~tGa~S~~~a~~a~~~~~~~l~~~ 82 (179)
T PRK00394 46 KIAALIFRS---------GKVVCTGAKSVEDLHEAVKIIIKKLKEL 82 (179)
T ss_pred ceEEEEEcC---------CcEEEEccCCHHHHHHHHHHHHHHHHHc
Confidence 366666643 3678888 7789999999999988775
No 255
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=22.23 E-value=1.7e+02 Score=27.39 Aligned_cols=43 Identities=14% Similarity=0.202 Sum_probs=32.5
Q ss_pred HHHHHh-CCeEEeccCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Q 003942 320 GLQTRS-GARIQLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQT 370 (784)
Q Consensus 320 ~Iq~~S-GarIqI~~~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~~ 370 (784)
.|-.++ ++.|-|.++- ...|.|+|+-.+|+.|.+.|.+.|++.
T Consensus 57 DIA~Kaa~V~igF~DRF--------sGslvitGdvs~Ve~Al~~V~~~l~~~ 100 (111)
T PRK15468 57 DLALKAADVHIGFLDRF--------SGALVIYGSVGAVEEALSQTVSGLGRL 100 (111)
T ss_pred HhhhhccCcEEeeeecc--------ceeEEEEccHHHHHHHHHHHHHHHHhh
Confidence 444443 5677776543 456999999999999999999998764
No 256
>TIGR00078 nadC nicotinate-nucleotide pyrophosphorylase. Synonym: quinolinate phosphoribosyltransferase (decarboxylating)
Probab=22.13 E-value=5.8e+02 Score=27.58 Aligned_cols=67 Identities=13% Similarity=0.230 Sum_probs=45.0
Q ss_pred EEEecCCceeeeecCCchHHHHHHHHhCCeEEecc-CCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 003942 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQLIP-QHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQ 369 (784)
Q Consensus 299 ~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarIqI~~-~~~p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~~ 369 (784)
++.|-.+.-+.|- |-..+.+|-+..+++|++.. +. ..-...+.+++|.|....+..+.+.+..+|+.
T Consensus 28 ~~~~~ar~~~v~~--G~~~~~~i~~~~~~~v~~~~~dG--~~v~~g~~i~~i~G~~~~il~~Er~~ln~l~~ 95 (265)
T TIGR00078 28 TASLVAKEDGVLA--GLPVARRVFEQLGVQVEWLVKDG--DRVEPGEVVAEVEGPARSLLTAERTALNFLGR 95 (265)
T ss_pred EEEEEecCCEEEE--CHHHHHHHHHHcCeEEEEEeCCC--CEecCCCEEEEEEEcHHHHHHHHHHHHHHHHH
Confidence 3444333334443 34677888888898875442 22 11234678999999999999999998887753
No 257
>PRK08072 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=22.05 E-value=2.2e+02 Score=31.05 Aligned_cols=54 Identities=9% Similarity=0.078 Sum_probs=37.1
Q ss_pred chHhhHHhhcCCE--EEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhh
Q 003942 220 DTIRYLQYNSGAK--IQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEA 273 (784)
Q Consensus 220 ~tIK~Iq~~TGak--I~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~ 273 (784)
+.+++|-+..+.+ |.+...+...-...+.+++|.|....|..+.+.+..+|...
T Consensus 51 ~~a~~i~~~~~~~~~v~~~~~dG~~v~~g~~i~~~~G~~~~ll~~er~~ln~l~~~ 106 (277)
T PRK08072 51 LVIEEGYKLLDERIEVELHKKDGDLVKKGEIIATVQGPVASLLTGERVILNLIQRM 106 (277)
T ss_pred HHHHHHHHHcCCceEEEEEeCCCCEEcCCCEEEEEEECHHHHHHHHHHHHHHHHHH
Confidence 3457777777644 55543322222345789999999999999999988877653
No 258
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=21.92 E-value=1.8e+02 Score=29.67 Aligned_cols=95 Identities=16% Similarity=0.152 Sum_probs=50.0
Q ss_pred hhchhhhhhhhhHhhhcCCCCCCCCCC----CCCeEEEEEecCCccceeeccCcchHhhHHh----------hcCCEEEE
Q 003942 170 EESVEPSNVVPQQVVDNSKSDDPSSTD----DSTMSRKIEVPNNKVGVLIGKAGDTIRYLQY----------NSGAKIQI 235 (784)
Q Consensus 170 ~e~Ve~A~~lI~~ii~~~~~~~~~~~~----~~~~t~rI~VP~~~vG~IIGkgG~tIK~Iq~----------~TGakI~V 235 (784)
.+++..|.+.+.++|.....+...... +-..+..|.++-++-...||-+.+++..==+ +-++-+-|
T Consensus 72 ~ed~~~av~~~~~~L~~~g~~~~~~p~i~iQNIVaSadL~~~lnL~~iA~~lg~e~~eYEPEqFPGLVYRl~~P~VV~Li 151 (185)
T COG2101 72 VEDVHRAVKKLAKKLKDGGIDIDFEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDEPRVVLLL 151 (185)
T ss_pred HHHHHHHHHHHHHHHHhcCcCcCCCCceEEEEEEEEeccCccccHHHHHHhccccccccccccCCeeEEEcCCCCEEEEE
Confidence 556666666666776543332222100 1112233344445555566666654322111 12222222
Q ss_pred ccCCCCCCCCCCCcEEEec--chhhHHHHHHHHHHHHHhh
Q 003942 236 TRDADADPHAATRPVEIIG--TLSNIDKAEKLINAVIAEA 273 (784)
Q Consensus 236 ~~~~~~~p~s~eR~V~I~G--~~e~V~kA~~~I~elI~e~ 273 (784)
.. ...+.|+| ..+.+.+|++.|.+.|.+.
T Consensus 152 F~---------SGK~ViTGaK~~ed~~~Av~~i~~~L~el 182 (185)
T COG2101 152 FG---------SGKLVITGAKSEEDAEQAVEKIQSRLEEL 182 (185)
T ss_pred ec---------CCcEEEecCCCHHHHHHHHHHHHHHHHHh
Confidence 21 23557777 6789999999999999875
No 259
>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]
Probab=21.75 E-value=58 Score=40.48 Aligned_cols=14 Identities=14% Similarity=0.335 Sum_probs=7.4
Q ss_pred chhhhhhhhhHhhh
Q 003942 172 SVEPSNVVPQQVVD 185 (784)
Q Consensus 172 ~Ve~A~~lI~~ii~ 185 (784)
+++.|.+++.++|.
T Consensus 154 ~~eeA~~i~~EvIk 167 (895)
T KOG2076|consen 154 DLEEAEEILMEVIK 167 (895)
T ss_pred CHHHHHHHHHHHHH
Confidence 34445555555553
No 260
>PRK10811 rne ribonuclease E; Reviewed
Probab=21.69 E-value=2.1e+02 Score=36.40 Aligned_cols=40 Identities=15% Similarity=0.420 Sum_probs=34.6
Q ss_pred ccEEEEEecCCceeeeecCCchHHHHHH-HHhCCeEEeccC
Q 003942 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQ-TRSGARIQLIPQ 334 (784)
Q Consensus 295 ~~~~~i~VP~~~vG~VIGkgG~~IK~Iq-~~SGarIqI~~~ 334 (784)
...+.+.+....+..|.......|+.|. +..|++|.|..+
T Consensus 436 ~~~~~i~~~~~va~~l~~~~~~~~~~ie~e~~g~~i~I~~n 476 (1068)
T PRK10811 436 TQEVHAIVPVPIASYLLNEKRSAVNAIETRQGGVRCVIVPN 476 (1068)
T ss_pred cccEEEEECHHHHHHHhhhhhhHHHHHhhhhcCceEEEEec
Confidence 4568888999999999998889999999 999999998754
No 261
>PRK04021 hypothetical protein; Reviewed
Probab=21.44 E-value=1.6e+02 Score=26.75 Aligned_cols=40 Identities=25% Similarity=0.438 Sum_probs=30.3
Q ss_pred hHHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEc-CHHHHHHHH
Q 003942 316 ETIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTG-DMRQIEIAQ 360 (784)
Q Consensus 316 ~~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~G-t~~qV~~Ak 360 (784)
+-|+-|.+..|+.|.|.. +..+..++|.|.| +.+.+....
T Consensus 50 ali~~LAk~l~~~I~I~~-----G~~sr~K~v~i~g~~~e~l~~~L 90 (92)
T PRK04021 50 ELVKFFSKLLGAEVEIIR-----GETSREKDLLVKGISLEEVKKKL 90 (92)
T ss_pred HHHHHHHHHhCCCEEEEe-----cCCcCceEEEEecCCHHHHHHHh
Confidence 457778888899999873 4567899999999 467665543
No 262
>PRK05742 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=21.31 E-value=8.5e+02 Score=26.57 Aligned_cols=97 Identities=16% Similarity=0.214 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHhhhcCCCCcccccccchhhccCCccEEEEEecCCceeeeecCCchHHHHHHHHhCCeE---EeccCCC
Q 003942 260 DKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARI---QLIPQHL 336 (784)
Q Consensus 260 ~kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SGarI---qI~~~~~ 336 (784)
....++|...|+|+ +..+--+..........++.|-.+.-|.| .|-+.+.+|-+..+++| ...++.
T Consensus 7 ~~~~~~i~~~l~ED--------~~~gDlTt~~~~~~~~~~~~i~ar~~gi~--~G~~~~~~i~~~~~~~~~~~~~~~dG- 75 (277)
T PRK05742 7 AEIEANVRRALAED--------IGSGDITAQLIPAERLAKATVITREAAVI--AGTAWVDAVFRQLDPRVAVHWQVADG- 75 (277)
T ss_pred HHHHHHHHHHHHhc--------CCCCCCCccccCCCcEEEEEEEECCCEEE--ECHHHHHHHHHHcCCceEEEEEeCCC-
Q ss_pred CCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 003942 337 PEGDGSKERIVRVTGDMRQIEIAQEMIKEVLS 368 (784)
Q Consensus 337 p~~~~~~er~V~I~Gt~~qV~~Ak~lI~~~L~ 368 (784)
..-...+.+++|.|....+..+.+.+..+|+
T Consensus 76 -~~v~~g~~i~~i~G~~~~ll~~ER~~ln~l~ 106 (277)
T PRK05742 76 -ERVSANQVLFHLEGPARSLLTGERSALNFLQ 106 (277)
T ss_pred -CEEcCCCEEEEEEEcHHHHHHHHHHHHHHHH
No 263
>TIGR02931 anfK_nitrog Fe-only nitrogenase, beta subunit. Nitrogenase is the enzyme of biological nitrogen fixation. The most wide-spread and most efficient nitrogenase contains a molybdenum cofactor. This protein family, AnfK, represents the beta subunit of the iron-only alternative nitrogenase. It is homologous to NifK and VnfK, of the molybdenum-containing and the vanadium (V)-containing types, respectively.
Probab=20.98 E-value=6.5e+02 Score=29.40 Aligned_cols=52 Identities=13% Similarity=0.070 Sum_probs=30.1
Q ss_pred eeecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCCccceeeccC-cchHhhHHhhc
Q 003942 164 EETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKA-GDTIRYLQYNS 229 (784)
Q Consensus 164 ~~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkg-G~tIK~Iq~~T 229 (784)
..|.|..+++++|.+-+.+.... -.-|.|=..++..|||-. ...|++++++.
T Consensus 71 d~VfGg~~~L~~ai~~~~~~~~~--------------p~~i~v~ttc~~eiiGDDi~~v~~~~~~~~ 123 (461)
T TIGR02931 71 GAVFGALDRVEEAVDVLLTRYPD--------------VKVVPIITTCSTEIIGDDVDGLISKLNEEL 123 (461)
T ss_pred ceEECcHHHHHHHHHHHHHhcCC--------------CCEEEEECCchHHhhhcCHHHHHHHHHhhh
Confidence 34557777776666555444410 123556667778888765 33446666554
No 264
>PRK14476 nitrogenase molybdenum-cofactor biosynthesis protein NifN; Provisional
Probab=20.77 E-value=3.8e+02 Score=31.28 Aligned_cols=57 Identities=11% Similarity=0.113 Sum_probs=32.9
Q ss_pred eecCchhchhhhhhhhhHhhhcCCCCCCCCCCCCCeEEEEEecCCccceeeccC-cchHhhHHhhc----CCEEEEc
Q 003942 165 ETVKEEESVEPSNVVPQQVVDNSKSDDPSSTDDSTMSRKIEVPNNKVGVLIGKA-GDTIRYLQYNS----GAKIQIT 236 (784)
Q Consensus 165 ~i~G~~e~Ve~A~~lI~~ii~~~~~~~~~~~~~~~~t~rI~VP~~~vG~IIGkg-G~tIK~Iq~~T----GakI~V~ 236 (784)
.|.|..+++.++.+-|.+... -.-|.|=..++..|||-. -..+++++++. ++.|...
T Consensus 72 ~VfGg~~~L~~aI~~~~~~~~---------------P~~I~V~ttC~~eiIGDDi~~v~~~~~~~~p~~~~~pvi~v 133 (455)
T PRK14476 72 TILGGDENVEEAILNICKKAK---------------PKIIGLCTTGLTETRGDDVAGALKEIRARHPELADTPIVYV 133 (455)
T ss_pred eEeCCHHHHHHHHHHHHHhhC---------------CCEEEEeCcchHhhhhccHHHHHHHHHhhccccCCCeEEEe
Confidence 355877777776665555441 013444477888888876 34456666653 4544443
No 265
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit. This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.
Probab=20.48 E-value=7.6e+02 Score=28.63 Aligned_cols=77 Identities=18% Similarity=0.359 Sum_probs=49.2
Q ss_pred hHHHHHHHHHHHHHhhhcCCCCcccccccchhhccCCccEEEEEecC--CceeeeecCCchHHHHHHHHh-----CCeEE
Q 003942 258 NIDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPN--EKVGLIIGRGGETIKGLQTRS-----GARIQ 330 (784)
Q Consensus 258 ~V~kA~~~I~elI~e~~~~g~p~~~~~g~~~~~~~~~~~~~~i~VP~--~~vG~VIGkgG~~IK~Iq~~S-----GarIq 330 (784)
.+..+++.|.++|+.+ |+|. ...+..||. ..||.|-.+.|+-|+.|.+.. .|+|.
T Consensus 99 ~l~~~~~~lk~~L~~e-----------Glfd-------~~~k~~lP~~p~~i~vits~~~aa~~D~~~~~~~r~p~~~~~ 160 (432)
T TIGR00237 99 LLQLAYEQLKEKLAAE-----------GLFD-------QEYKKPLPHFPKRVGVITSQTGAALADILHILKRRDPSLKVV 160 (432)
T ss_pred HHHHHHHHHHHHHHHC-----------CCCC-------chhcCCCCCCCCEEEEEeCCccHHHHHHHHHHHhhCCCceEE
Confidence 5666666676666654 2221 112345554 899999999999998887653 35555
Q ss_pred eccCCCCCCCCCCceEEEEEcC--HHHHHHHHHHHHH
Q 003942 331 LIPQHLPEGDGSKERIVRVTGD--MRQIEIAQEMIKE 365 (784)
Q Consensus 331 I~~~~~p~~~~~~er~V~I~Gt--~~qV~~Ak~lI~~ 365 (784)
|.. +.|.|. ..+|..|++.+..
T Consensus 161 ~~~-------------~~vQG~~a~~~i~~al~~~~~ 184 (432)
T TIGR00237 161 IYP-------------TLVQGEGAVQSIVESIELANT 184 (432)
T ss_pred Eec-------------ccccCccHHHHHHHHHHHhhc
Confidence 542 567776 5667777766654
No 266
>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=20.46 E-value=89 Score=35.18 Aligned_cols=149 Identities=21% Similarity=0.272 Sum_probs=72.3
Q ss_pred EEEecCCccceee-ccCcchHhhHHhhcCCEEEEccCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhcCCCCcc
Q 003942 203 KIEVPNNKVGVLI-GKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADAGGSPSL 281 (784)
Q Consensus 203 rI~VP~~~vG~II-GkgG~tIK~Iq~~TGakI~V~~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~~g~p~~ 281 (784)
-+..|...-|.+- =.--..|++|++.+.+-|.|+.+ +.+.+... ..+..|.+.++++|.+...+-...+
T Consensus 137 ivt~Pf~~Eg~~r~~nA~~~l~~L~~~~D~vividNd---------~L~~~~~~-~~i~~af~~~N~iia~~i~~it~~i 206 (349)
T TIGR00065 137 VVTKPFKFEGLKRRKKAEEGLERLKQAVDTLIVIPND---------KLLEVVPN-LPLNDAFKVADDVLVRAVKGISELI 206 (349)
T ss_pred EEeCCccccchhhHHHHHHHHHHHHHhCCEEEEEeCH---------HHHHhhcC-CCHHHHHHHHHHHHHHHHHhHHHhh
Confidence 3344665554211 11234689999999988888743 34444443 4466677777777776532111001
Q ss_pred cccccchhhccCCccEEEEEecC---CceeeeecCCch----HHHHHHHHhCCeEEeccCCCCCCCCCCceEEEEEcC--
Q 003942 282 VARGLATAQASGAAEQVEIKVPN---EKVGLIIGRGGE----TIKGLQTRSGARIQLIPQHLPEGDGSKERIVRVTGD-- 352 (784)
Q Consensus 282 ~~~g~~~~~~~~~~~~~~i~VP~---~~vG~VIGkgG~----~IK~Iq~~SGarIqI~~~~~p~~~~~~er~V~I~Gt-- 352 (784)
...++-.. +...++-.+-+ .++|.=.+++-. .++.+++...+..--.. .-...+.-+|.|+|.
T Consensus 207 r~~g~iNv----Df~dv~~vl~~~G~a~iG~g~~~g~~~~~r~~~A~~~al~~pLl~~~----~i~~A~~~Lv~i~~~~~ 278 (349)
T TIGR00065 207 TKPGLINI----DFADVRAVMSGGGVAMMGIGEALGEDTANRAFEAVRKALSSPLLDVD----KISGAKGALVHITGGAD 278 (349)
T ss_pred ccCCcCcC----CHHHHHHHHhcCCeEEEEEEEecCCcchHHHHHHHHHHHhCCCcCCc----ccccccEEEEEEEcCCC
Confidence 01110000 00000000000 123333444444 34445554444421110 011234457889984
Q ss_pred --HHHHHHHHHHHHHHHhc
Q 003942 353 --MRQIEIAQEMIKEVLSQ 369 (784)
Q Consensus 353 --~~qV~~Ak~lI~~~L~~ 369 (784)
.+.|..+.++|.+.+..
T Consensus 279 l~l~ev~~~~~~i~~~~~~ 297 (349)
T TIGR00065 279 LTLLEAEEIQEIITSELDQ 297 (349)
T ss_pred CCHHHHHHHHHHHHHhcCC
Confidence 57888888888888764
No 267
>PRK06559 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=20.24 E-value=5e+02 Score=28.60 Aligned_cols=145 Identities=14% Similarity=0.185 Sum_probs=82.3
Q ss_pred cchHhhHHhhcCCEEEEc-----cCCCCCCCCCCCcEEEecchhhHHHHHHHHHHHHHhhhc------------CCCC-c
Q 003942 219 GDTIRYLQYNSGAKIQIT-----RDADADPHAATRPVEIIGTLSNIDKAEKLINAVIAEADA------------GGSP-S 280 (784)
Q Consensus 219 G~tIK~Iq~~TGakI~V~-----~~~~~~p~s~eR~V~I~G~~e~V~kA~~~I~elI~e~~~------------~g~p-~ 280 (784)
-+.+++|.+..++++.+. ++.+ .-...+.+++|.|....|..+.+.+..+|....- .+.. .
T Consensus 57 ~~~a~~if~~l~~~~~~~~~~~~~dG~-~v~~G~~i~~v~G~a~~ll~~ER~alN~l~~~SGIAT~T~~~V~~~~~~~~~ 135 (290)
T PRK06559 57 LTVFQRVFTLFDAEVTFQNPHQFKDGD-RLTSGDLVLEIIGSVRSLLTCERVALNFLQHLSGIASMTAAYVEALGDDRIK 135 (290)
T ss_pred HHHHHHHHHHhCCcEEEEEeecCCCCC-EecCCCEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeE
Confidence 366788888999888775 4433 2234578999999999999999888877755320 0010 0
Q ss_pred cc-ccccchh--------------hccCCccEEEEEecCCceeeeecCCchHHHHHHHHhC--CeEEeccCCCCCC---C
Q 003942 281 LV-ARGLATA--------------QASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSG--ARIQLIPQHLPEG---D 340 (784)
Q Consensus 281 ~~-~~g~~~~--------------~~~~~~~~~~i~VP~~~vG~VIGkgG~~IK~Iq~~SG--arIqI~~~~~p~~---~ 340 (784)
+. .|-..+. ..-.-.-...++|-.|++.++ |.=.+.|+.+++... .+|.|.-+.+... -
T Consensus 136 i~~TRKT~PG~R~l~k~AV~~GGG~~HR~gLsD~iLIkdNHi~~~-g~i~~av~~~r~~~~~~~kIeVEv~tleea~~a~ 214 (290)
T PRK06559 136 VFDTRKTTPNLRLFEKYAVRVGGGYNHRFNLSDAIMLKDNHIAAV-GSVQKAIAQARAYAPFVKMVEVEVESLAAAEEAA 214 (290)
T ss_pred EEeecCCCCcchHHHHHHHHhcCCcccCCCCcceEEEcHHHHHhh-ccHHHHHHHHHHhCCCCCeEEEECCCHHHHHHHH
Confidence 10 0100000 000112234667777776553 433467888888875 5677754331100 0
Q ss_pred CCCceEEEEE-cCHHHHHHHHHHHHH
Q 003942 341 GSKERIVRVT-GDMRQIEIAQEMIKE 365 (784)
Q Consensus 341 ~~~er~V~I~-Gt~~qV~~Ak~lI~~ 365 (784)
...-.+|.+. -+++.++.|.++|..
T Consensus 215 ~agaDiImLDnmspe~l~~av~~~~~ 240 (290)
T PRK06559 215 AAGADIIMLDNMSLEQIEQAITLIAG 240 (290)
T ss_pred HcCCCEEEECCCCHHHHHHHHHHhcC
Confidence 1112234443 458888888887763
No 268
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=20.14 E-value=1.9e+02 Score=25.54 Aligned_cols=36 Identities=19% Similarity=0.219 Sum_probs=28.0
Q ss_pred cCCEEEEccCCCCCCCCCCCcEEEec--chhhHHHHHHHHHHHHHhh
Q 003942 229 SGAKIQITRDADADPHAATRPVEIIG--TLSNIDKAEKLINAVIAEA 273 (784)
Q Consensus 229 TGakI~V~~~~~~~p~s~eR~V~I~G--~~e~V~kA~~~I~elI~e~ 273 (784)
..|.+.|... ..|.|+| +.+.+.+|++.|..+|++.
T Consensus 48 p~~t~~IF~s---------Gki~itGaks~~~~~~a~~~i~~~L~~~ 85 (86)
T PF00352_consen 48 PKATVLIFSS---------GKIVITGAKSEEEAKKAIEKILPILQKL 85 (86)
T ss_dssp TTEEEEEETT---------SEEEEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred CcEEEEEEcC---------CEEEEEecCCHHHHHHHHHHHHHHHHHc
Confidence 4567777753 3778888 6889999999999998863
Done!